From 033b9530a0f12fe0ba95195530b4e01090bcc445 Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Thu, 5 Feb 2026 11:50:00 -0600 Subject: [PATCH 1/2] Update the installed NXDL files from the NeXus definitions repository --- .../definitions/applications/NXapm.nxdl.xml | 37 +- .../applications/NXarchive.nxdl.xml | 4 +- .../applications/NXazint1d.nxdl.xml | 304 +++ .../applications/NXazint2d.nxdl.xml | 345 +++ .../applications/NXcanSAS.nxdl.xml | 6 +- .../applications/NXdirecttof.nxdl.xml | 4 +- .../applications/NXellipsometry.nxdl.xml | 2 +- .../definitions/applications/NXem.nxdl.xml | 1770 ++++++++++++++ .../applications/NXlauetof.nxdl.xml | 4 +- .../definitions/applications/NXmx.nxdl.xml | 8 +- .../applications/NXstress.nxdl.xml | 1149 ++++++++++ .../applications/NXtomoproc.nxdl.xml | 4 +- .../definitions/applications/NXxps.nxdl.xml | 21 +- .../stress/Beam_profile_sketch3.jpg | Bin 0 -> 127844 bytes .../applications/stress/gauge_volume.png | Bin 0 -> 37887 bytes .../applications/stress/gauge_volume.py | 83 + .../base_classes/NXaberration.nxdl.xml | 78 + .../base_classes/NXactuator.nxdl.xml | 19 +- ...apm.nxdl.xml => NXapm_event_data.nxdl.xml} | 6 +- ...apm.nxdl.xml => NXapm_instrument.nxdl.xml} | 20 +- .../base_classes/NXapm_measurement.nxdl.xml | 4 +- .../NXapm_reconstruction.nxdl.xml | 16 +- .../definitions/base_classes/NXatom.nxdl.xml | 25 +- .../base_classes/NXattenuator.nxdl.xml | 6 +- .../definitions/base_classes/NXbeam.nxdl.xml | 2 +- .../base_classes/NXcalibration.nxdl.xml | 22 +- .../base_classes/NXcg_alpha_complex.nxdl.xml | 101 + .../base_classes/NXcg_cylinder.nxdl.xml | 133 ++ .../base_classes/NXcg_ellipsoid.nxdl.xml | 81 + .../NXcg_face_list_data_structure.nxdl.xml | 227 ++ .../NXcg_grid.nxdl.xml | 116 +- .../NXcg_half_edge_data_structure.nxdl.xml | 195 ++ .../base_classes/NXcg_hexahedron.nxdl.xml | 191 ++ .../base_classes/NXcg_parallelogram.nxdl.xml | 101 + .../base_classes/NXcg_point.nxdl.xml | 87 + .../base_classes/NXcg_polygon.nxdl.xml | 126 + .../base_classes/NXcg_polyhedron.nxdl.xml | 104 + .../base_classes/NXcg_polyline.nxdl.xml | 140 ++ .../base_classes/NXcg_primitive.nxdl.xml | 247 ++ .../NXcg_roi.nxdl.xml} | 34 +- .../base_classes/NXcg_tetrahedron.nxdl.xml | 76 + .../base_classes/NXcg_triangle.nxdl.xml | 92 + .../NXcg_unit_normal.nxdl.xml} | 31 +- .../base_classes/NXcollectioncolumn.nxdl.xml | 2 +- .../base_classes/NXcomponent.nxdl.xml | 15 +- .../base_classes/NXcorrector_cs.nxdl.xml | 178 ++ .../base_classes/NXcs_profiling.nxdl.xml | 9 +- .../definitions/base_classes/NXdata.nxdl.xml | 6 +- .../base_classes/NXdetector.nxdl.xml | 4 +- .../base_classes/NXdetector_channel.nxdl.xml | 2 - .../base_classes/NXebeam_column.nxdl.xml | 239 ++ ...dl.xml => NXelectromagnetic_lens.nxdl.xml} | 4 +- .../base_classes/NXelectron_detector.nxdl.xml | 2 - .../base_classes/NXelectronanalyzer.nxdl.xml | 2 +- .../base_classes/NXem_ebsd.nxdl.xml | 685 ++++++ .../base_classes/NXem_eds.nxdl.xml | 200 ++ .../NXem_eels.nxdl.xml} | 52 +- .../base_classes/NXem_event_data.nxdl.xml | 157 ++ .../base_classes/NXem_img.nxdl.xml | 62 + .../base_classes/NXem_instrument.nxdl.xml | 232 ++ .../NXem_interaction_volume.nxdl.xml | 56 + .../NXem_measurement.nxdl.xml} | 18 +- .../base_classes/NXem_optical_system.nxdl.xml | 164 ++ .../NXem_simulation.nxdl.xml} | 18 +- .../base_classes/NXenergydispersion.nxdl.xml | 2 +- .../definitions/base_classes/NXentry.nxdl.xml | 4 +- .../base_classes/NXfabrication.nxdl.xml | 3 +- .../definitions/base_classes/NXfit.nxdl.xml | 8 +- .../base_classes/NXhistory.nxdl.xml | 2 +- .../base_classes/NXibeam_column.nxdl.xml | 155 ++ .../definitions/base_classes/NXimage.nxdl.xml | 239 +- .../base_classes/NXinsertion_device.nxdl.xml | 6 +- .../base_classes/NXinstrument.nxdl.xml | 3 +- .../definitions/base_classes/NXlog.nxdl.xml | 2 +- .../base_classes/NXparameters.nxdl.xml | 70 +- .../definitions/base_classes/NXpdb.nxdl.xml | 6 +- .../definitions/base_classes/NXphase.nxdl.xml | 55 + .../base_classes/NXpid_controller.nxdl.xml | 6 +- .../base_classes/NXprocess.nxdl.xml | 17 +- .../base_classes/NXresolution.nxdl.xml | 15 +- .../base_classes/NXrotations.nxdl.xml | 244 ++ .../base_classes/NXsample.nxdl.xml | 2 +- .../base_classes/NXscan_controller.nxdl.xml | 81 + .../base_classes/NXsensor.nxdl.xml | 14 - .../base_classes/NXsource.nxdl.xml | 4 +- .../base_classes/NXspindispersion.nxdl.xml | 2 +- .../base_classes/NXsubentry.nxdl.xml | 1 - .../base_classes/NXtransformations.nxdl.xml | 4 +- .../NXaberration.nxdl.xml | 55 - .../NXaberration_model.nxdl.xml | 105 - .../NXaberration_model_ceos.nxdl.xml | 91 - .../NXaberration_model_nion.nxdl.xml | 63 - .../NXaperture_em.nxdl.xml | 58 - .../contributed_definitions/NXapm.nxdl.xml | 1696 -------------- .../NXapm_composition_space_results.nxdl.xml | 488 ---- .../NXapm_compositionspace_config.nxdl.xml | 208 ++ .../NXapm_compositionspace_results.nxdl.xml | 420 ++++ .../NXapm_input_ranging.nxdl.xml | 63 - .../NXapm_input_reconstruction.nxdl.xml | 58 - .../NXapm_paraprobe_clusterer_config.nxdl.xml | 295 +++ ...NXapm_paraprobe_clusterer_results.nxdl.xml | 229 ++ .../NXapm_paraprobe_config_clusterer.nxdl.xml | 477 ---- .../NXapm_paraprobe_config_distancer.nxdl.xml | 257 --- ...Xapm_paraprobe_config_intersector.nxdl.xml | 348 --- .../NXapm_paraprobe_config_nanochem.nxdl.xml | 1114 --------- .../NXapm_paraprobe_config_ranger.nxdl.xml | 297 --- .../NXapm_paraprobe_config_selector.nxdl.xml | 142 -- .../NXapm_paraprobe_config_spatstat.nxdl.xml | 374 --- .../NXapm_paraprobe_config_surfacer.nxdl.xml | 289 --- ...Xapm_paraprobe_config_tessellator.nxdl.xml | 253 -- ...NXapm_paraprobe_config_transcoder.nxdl.xml | 119 - .../NXapm_paraprobe_distancer_config.nxdl.xml | 119 + ...NXapm_paraprobe_distancer_results.nxdl.xml | 139 ++ ...Xapm_paraprobe_intersector_config.nxdl.xml | 253 ++ ...apm_paraprobe_intersector_results.nxdl.xml | 219 ++ .../NXapm_paraprobe_nanochem_config.nxdl.xml | 864 +++++++ .../NXapm_paraprobe_nanochem_results.nxdl.xml | 1177 ++++++++++ .../NXapm_paraprobe_ranger_config.nxdl.xml | 55 + .../NXapm_paraprobe_ranger_results.nxdl.xml | 66 + ...NXapm_paraprobe_results_clusterer.nxdl.xml | 503 ---- ...NXapm_paraprobe_results_distancer.nxdl.xml | 388 ---- ...apm_paraprobe_results_intersector.nxdl.xml | 395 ---- .../NXapm_paraprobe_results_nanochem.nxdl.xml | 1965 ---------------- .../NXapm_paraprobe_results_ranger.nxdl.xml | 425 ---- .../NXapm_paraprobe_results_selector.nxdl.xml | 274 --- .../NXapm_paraprobe_results_spatstat.nxdl.xml | 364 --- .../NXapm_paraprobe_results_surfacer.nxdl.xml | 503 ---- ...apm_paraprobe_results_tessellator.nxdl.xml | 677 ------ ...Xapm_paraprobe_results_transcoder.nxdl.xml | 568 ----- ... NXapm_paraprobe_selector_config.nxdl.xml} | 28 +- ...NXapm_paraprobe_selector_results.nxdl.xml} | 32 +- .../NXapm_paraprobe_spatstat_config.nxdl.xml | 259 +++ .../NXapm_paraprobe_spatstat_results.nxdl.xml | 141 ++ .../NXapm_paraprobe_surfacer_config.nxdl.xml | 151 ++ .../NXapm_paraprobe_surfacer_results.nxdl.xml | 222 ++ ...Xapm_paraprobe_tessellator_config.nxdl.xml | 93 + ...apm_paraprobe_tessellator_results.nxdl.xml | 277 +++ .../NXapm_paraprobe_tool_common.nxdl.xml | 102 + .../NXapm_paraprobe_tool_config.nxdl.xml | 125 + .../NXapm_paraprobe_tool_parameters.nxdl.xml | 114 + ... => NXapm_paraprobe_tool_process.nxdl.xml} | 53 +- .../NXapm_paraprobe_tool_results.nxdl.xml | 106 + .../NXbeam_path.nxdl.xml | 452 ---- .../NXbeam_splitter.nxdl.xml | 264 +-- .../NXcg_alpha_complex.nxdl.xml | 151 -- .../NXcg_cylinder_set.nxdl.xml | 165 -- .../NXcg_ellipsoid_set.nxdl.xml | 135 -- .../NXcg_face_list_data_structure.nxdl.xml | 243 -- .../NXcg_geodesic_mesh.nxdl.xml | 57 - .../NXcg_half_edge_data_structure.nxdl.xml | 174 -- .../NXcg_hexahedron_set.nxdl.xml | 239 -- .../NXcg_marching_cubes.nxdl.xml | 74 - .../NXcg_parallelogram_set.nxdl.xml | 183 -- .../NXcg_point_set.nxdl.xml | 98 - .../NXcg_polygon_set.nxdl.xml | 225 -- .../NXcg_polyhedron_set.nxdl.xml | 194 -- .../NXcg_polyline_set.nxdl.xml | 183 -- .../NXcg_sphere_set.nxdl.xml | 121 - .../NXcg_tetrahedron_set.nxdl.xml | 175 -- .../NXcg_triangle_set.nxdl.xml | 132 -- .../NXcg_triangulated_surface_mesh.nxdl.xml | 56 - .../NXchamber.nxdl.xml | 39 - .../NXcircuit_board.nxdl.xml | 45 - .../NXclustering.nxdl.xml | 124 - .../NXcollectioncolumn.nxdl.xml | 86 - .../NXcoordinate_system_set.nxdl.xml | 137 -- .../NXcorrector_cs.nxdl.xml | 76 - .../NXcs_computer.nxdl.xml | 80 - .../NXcs_filter_boolean_mask.nxdl.xml | 104 - .../NXcs_io_obj.nxdl.xml | 56 - .../NXcs_mm_sys.nxdl.xml | 39 - .../NXcs_prng.nxdl.xml | 85 - .../NXcs_profiling.nxdl.xml | 149 -- .../NXcs_profiling_event.nxdl.xml | 95 - .../contributed_definitions/NXcsg.nxdl.xml | 32 +- .../contributed_definitions/NXdac.nxdl.xml | 38 - .../NXdeflector.nxdl.xml | 57 - .../NXdelocalization.nxdl.xml | 162 +- .../NXdispersion.nxdl.xml | 8 +- .../NXdispersion_function.nxdl.xml | 6 +- .../NXdispersion_repeated_parameter.nxdl.xml | 20 +- .../NXdispersion_single_parameter.nxdl.xml | 8 +- .../NXdispersion_table.nxdl.xml | 26 +- .../NXdispersive_material.nxdl.xml | 87 +- .../NXebeam_column.nxdl.xml | 103 - .../NXelectronanalyser.nxdl.xml | 139 -- .../NXelectrostatic_kicker.nxdl.xml | 16 +- .../NXellipsometry.nxdl.xml | 357 --- .../contributed_definitions/NXem.nxdl.xml | 2034 ----------------- .../NXem_calorimetry.nxdl.xml | 297 +++ .../NXem_ebsd.nxdl.xml | 1926 ---------------- .../NXem_ebsd_conventions.nxdl.xml | 610 ----- ...NXem_ebsd_crystal_structure_model.nxdl.xml | 224 -- .../NXenergydispersion.nxdl.xml | 90 - .../NXevent_data_em.nxdl.xml | 226 -- .../NXgraph_edge_set.nxdl.xml | 113 - .../NXgraph_node_set.nxdl.xml | 89 - .../NXgraph_root.nxdl.xml | 36 - .../NXibeam_column.nxdl.xml | 137 -- .../NXimage_set.nxdl.xml | 128 -- .../NXimage_set_em_adf.nxdl.xml | 156 -- .../NXimage_set_em_kikuchi.nxdl.xml | 205 -- .../NXinteraction_vol_em.nxdl.xml | 37 - .../contributed_definitions/NXion.nxdl.xml | 168 -- .../NXisocontour.nxdl.xml | 45 +- .../NXiv_temp.nxdl.xml | 19 + ...ctro_chemo_mechanical_preparation.nxdl.xml | 188 -- .../NXlab_sample_mounting.nxdl.xml | 93 - .../NXlens_opt.nxdl.xml | 185 -- .../NXmagnetic_kicker.nxdl.xml | 16 +- .../NXmanipulator.nxdl.xml | 82 - .../NXmatch_filter.nxdl.xml | 35 +- .../NXmicrostructure.nxdl.xml | 886 +++++++ ....xml => NXmicrostructure_feature.nxdl.xml} | 26 +- .../NXmicrostructure_ipf.nxdl.xml | 245 ++ .../NXmicrostructure_kanapy_results.nxdl.xml | 193 ++ .../NXmicrostructure_mtex_config.nxdl.xml | 325 +++ .../NXmicrostructure_odf.nxdl.xml | 230 ++ .../NXmicrostructure_pf.nxdl.xml | 113 + .../NXmicrostructure_score_config.nxdl.xml | 724 ++++++ .../NXmicrostructure_score_results.nxdl.xml | 567 +++++ ... => NXmicrostructure_slip_system.nxdl.xml} | 44 +- .../contributed_definitions/NXmpes.nxdl.xml | 371 --- .../contributed_definitions/NXms.nxdl.xml | 529 ----- .../NXms_feature_set.nxdl.xml | 300 --- .../NXms_score_config.nxdl.xml | 452 ---- .../NXms_score_results.nxdl.xml | 720 ------ .../NXms_snapshot.nxdl.xml | 54 - .../NXms_snapshot_set.nxdl.xml | 62 - .../contributed_definitions/NXopt.nxdl.xml | 868 ------- ...iber.nxdl.xml => NXoptical_fiber.nxdl.xml} | 119 +- ....nxdl.xml => NXoptical_polarizer.nxdl.xml} | 148 +- .../NXoptical_system_em.nxdl.xml | 83 - .../NXorientation_set.nxdl.xml | 133 -- .../contributed_definitions/NXpeak.nxdl.xml | 87 - .../NXpulser_apm.nxdl.xml | 165 -- .../contributed_definitions/NXpump.nxdl.xml | 42 - .../NXquadric.nxdl.xml | 4 +- .../NXquadrupole_magnet.nxdl.xml | 12 +- .../NXreflectron.nxdl.xml | 44 - .../NXscanbox_em.nxdl.xml | 46 - .../NXsensor_scan.nxdl.xml | 176 +- .../NXseparator.nxdl.xml | 18 +- .../NXsimilarity_grouping.nxdl.xml | 103 +- .../NXsolid_geometry.nxdl.xml | 14 +- .../NXspatial_filter.nxdl.xml | 80 +- .../NXspectrum_set.nxdl.xml | 162 -- .../NXspectrum_set_em_eels.nxdl.xml | 188 -- .../NXspectrum_set_em_xray.nxdl.xml | 311 --- .../NXspin_rotator.nxdl.xml | 18 +- .../NXspindispersion.nxdl.xml | 79 - .../NXstage_lab.nxdl.xml | 154 -- .../NXsubsampling_filter.nxdl.xml | 48 +- .../NXsubstance.nxdl.xml | 10 +- .../NXtransmission.nxdl.xml | 211 +- .../NXwaveplate.nxdl.xml | 173 -- .../contributed_definitions/NXxpcs.nxdl.xml | 8 +- .../contributed_definitions/NXxrd.nxdl.xml | 99 + .../NXxrd_pan.nxdl.xml | 335 +++ src/nexusformat/definitions/nxdl.xsd | 2 +- 260 files changed, 19273 insertions(+), 30371 deletions(-) create mode 100644 src/nexusformat/definitions/applications/NXazint1d.nxdl.xml create mode 100644 src/nexusformat/definitions/applications/NXazint2d.nxdl.xml create mode 100644 src/nexusformat/definitions/applications/NXem.nxdl.xml create mode 100644 src/nexusformat/definitions/applications/NXstress.nxdl.xml create mode 100644 src/nexusformat/definitions/applications/stress/Beam_profile_sketch3.jpg create mode 100644 src/nexusformat/definitions/applications/stress/gauge_volume.png create mode 100644 src/nexusformat/definitions/applications/stress/gauge_volume.py create mode 100644 src/nexusformat/definitions/base_classes/NXaberration.nxdl.xml rename src/nexusformat/definitions/base_classes/{NXevent_data_apm.nxdl.xml => NXapm_event_data.nxdl.xml} (96%) rename src/nexusformat/definitions/base_classes/{NXinstrument_apm.nxdl.xml => NXapm_instrument.nxdl.xml} (96%) create mode 100644 src/nexusformat/definitions/base_classes/NXcg_alpha_complex.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_cylinder.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_ellipsoid.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_face_list_data_structure.nxdl.xml rename src/nexusformat/definitions/{contributed_definitions => base_classes}/NXcg_grid.nxdl.xml (59%) create mode 100644 src/nexusformat/definitions/base_classes/NXcg_half_edge_data_structure.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_hexahedron.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_parallelogram.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_point.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_polygon.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_polyhedron.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_polyline.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_primitive.nxdl.xml rename src/nexusformat/definitions/{contributed_definitions/NXcs_cpu.nxdl.xml => base_classes/NXcg_roi.nxdl.xml} (53%) create mode 100644 src/nexusformat/definitions/base_classes/NXcg_tetrahedron.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXcg_triangle.nxdl.xml rename src/nexusformat/definitions/{contributed_definitions/NXcg_unit_normal_set.nxdl.xml => base_classes/NXcg_unit_normal.nxdl.xml} (68%) create mode 100644 src/nexusformat/definitions/base_classes/NXcorrector_cs.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXebeam_column.nxdl.xml rename src/nexusformat/definitions/base_classes/{NXlens_em.nxdl.xml => NXelectromagnetic_lens.nxdl.xml} (95%) create mode 100644 src/nexusformat/definitions/base_classes/NXem_ebsd.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXem_eds.nxdl.xml rename src/nexusformat/definitions/{contributed_definitions/NXprogram.nxdl.xml => base_classes/NXem_eels.nxdl.xml} (52%) create mode 100644 src/nexusformat/definitions/base_classes/NXem_event_data.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXem_img.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXem_instrument.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXem_interaction_volume.nxdl.xml rename src/nexusformat/definitions/{contributed_definitions/NXcs_io_sys.nxdl.xml => base_classes/NXem_measurement.nxdl.xml} (71%) create mode 100644 src/nexusformat/definitions/base_classes/NXem_optical_system.nxdl.xml rename src/nexusformat/definitions/{contributed_definitions/NXevent_data_em_set.nxdl.xml => base_classes/NXem_simulation.nxdl.xml} (69%) mode change 100755 => 100644 src/nexusformat/definitions/base_classes/NXentry.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXibeam_column.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXphase.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXrotations.nxdl.xml create mode 100644 src/nexusformat/definitions/base_classes/NXscan_controller.nxdl.xml delete mode 100644 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src/nexusformat/definitions/contributed_definitions/NXspindispersion.nxdl.xml delete mode 100644 src/nexusformat/definitions/contributed_definitions/NXstage_lab.nxdl.xml delete mode 100644 src/nexusformat/definitions/contributed_definitions/NXwaveplate.nxdl.xml create mode 100644 src/nexusformat/definitions/contributed_definitions/NXxrd.nxdl.xml create mode 100644 src/nexusformat/definitions/contributed_definitions/NXxrd_pan.nxdl.xml mode change 100644 => 100755 src/nexusformat/definitions/nxdl.xsd diff --git a/src/nexusformat/definitions/applications/NXapm.nxdl.xml b/src/nexusformat/definitions/applications/NXapm.nxdl.xml index 1a65930..75cd9d3 100644 --- a/src/nexusformat/definitions/applications/NXapm.nxdl.xml +++ b/src/nexusformat/definitions/applications/NXapm.nxdl.xml @@ -44,7 +44,7 @@ Number of pulses collected in between start_time and end_time resolved by an - instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of + instance of :ref:`NXapm_event_data`. If this is not defined, p is the number of ions included in the reconstructed volume if the application definition is used to store results of an already reconstructed dataset. @@ -84,7 +84,7 @@ is considered as a narrow synonym for crystal defects. The aim of the NXapm application definition is to provide a general yet specific enough - solution to serialize artifacts for virtually all atom probe and field-ion microcopy experiments. + solution to serialize artifacts for virtually all atom probe and field-ion microscopy experiments. Before summarizing the design of the base classes and the parts of the NXapm application definition, it is worthwhile to recall and distinguish concepts that are related to atom extraction @@ -149,7 +149,7 @@ or a new file. Removing the specimen from the instrument is an interruption. Changing evaporation conditions while the specimen is remains in the analysis_chamber and resuming thereafter the measurement is not considered as an interruption. It is a common strategy to probe the evaporation process for different - instrument parameters. Each individual collection should then though be stored in an own NXevent_data_apm + instrument parameters. Each individual collection should then though be stored in an own NXapm_event_data group. Parking the specimen to the buffer_chamber and resuming the measurement at a later stage is an interruption. During a run, the microscope is used for a certain amount of time to characterize a single specimen. - The groups ``sample`` and ``specimen`` provide concepts for storing metadata about the sample and the specimen, @@ -187,7 +187,7 @@ NXapm defines constraints on the existence and cardinality of concepts and its concept branches but seeks to offer a compromise. The key design pattern followed is that most branches are made optional or at most recommended but their child concepts are conditionally required. Thereby, NXapm can cover a variety of simple but also complex - use cases. An example of this parent-optional-but-childs-stronger-restricted design is the combination of the + use cases. An example of this parent-optional-but-children-stronger-restricted design is the combination of the optional group ``measurement`` with its required child ``measurement/instrument``: Users which report simulations are not forced to document the instrument but users which have characterized a specimen are motivated to report about the instrument. They are though not necessarily required to report all @@ -203,7 +203,7 @@ events that can be time-stamped individually. Each instance of a group ``measurement/eventID`` contains ``measurement/instrument`` whose purpose is to store those specific state and settings of the instrument that was present during the collection of the event. - Thereby, changing conditions such as compaigns with different target detection rate can be stored. + Thereby, changing conditions such as campaigns with different target detection rate can be stored. Noteworthy, such an approach of the atom probe detecting groups of events and storing these as groups has also been in use in the proprietary software via CamecaRoot, a set of customized data structures and file formats that use @@ -215,7 +215,7 @@ considered best practice by AMETEK/Cameca, ``raw_data`` for delay-line timing data, ``hit_finding`` for details of the hit finding algorithm, ``hit_spatial_filtering`` a process that filters hits of too low quality and those laying outside the about to be computed reconstruction volume. Furthermore, group ``voltage_and_bowl`` offers a place for documenting calibrations - and processing non-linearities. Group ``mass_to_charge_conversion`` is used to document the mass calibration and the + and processing nonlinearities. Group ``mass_to_charge_conversion`` is used to document the mass calibration and the conversion from time-of-flight to mass-to-charge-state-ratio values. Finally, the groups ``reconstruction`` and ``ranging`` were designed to match and document the classical approaches how @@ -340,7 +340,7 @@ More detailed timing data over the course of the experiment have to be collected to compute this event chain during the experiment. For this - purpose the :ref:`NXevent_data_apm` instance should be used. + purpose the :ref:`NXapm_event_data` instance should be used. @@ -361,6 +361,11 @@ + + + The author(s) of that reference. + + @@ -673,7 +678,7 @@ - + A coordinate system. Multiple instances require unique names. @@ -740,7 +745,7 @@ - + @@ -752,7 +757,7 @@ - + @@ -832,14 +837,14 @@ - + - + - + @@ -979,7 +984,7 @@ In the case of an open-source instrument, like P. Felfer's Oxcart or G. Schmitz's M-TAP instruments, also use program1, program2, ... with program1 representing - the control software e.g. `M. Monajem and P. Felfer pyCCAPT <https://pyccapt.readthedocs.io/en/latest/>`_. + the control software e.g. `M. Monajem and P. Felfer PYCCAPT <https://pyccapt.readthedocs.io/en/latest/>`_. Further instances (program2, ...) can be used to list the dependencies, the python virtual environment. @@ -1260,7 +1265,7 @@ - + Mass calibration with unit peaks/interp. as mentioned by `T. Blum et al. @@ -1308,7 +1313,7 @@ - + diff --git a/src/nexusformat/definitions/applications/NXarchive.nxdl.xml b/src/nexusformat/definitions/applications/NXarchive.nxdl.xml index 650847b..fecdc99 100644 --- a/src/nexusformat/definitions/applications/NXarchive.nxdl.xml +++ b/src/nexusformat/definitions/applications/NXarchive.nxdl.xml @@ -3,7 +3,7 @@ + + + + The symbol(s) listed here will be used below to coordinate datasets with the same shape. + + + Number of integrated images + + + Number of radial bins + + + Number of radial bin edges (nRad+1) + + + + + Application definition for data from two-dimensional area detectors that has been integrated azimuthally, + with a certain radial binning in units of q or 2theta. + + An example application that creates these files is documented here: https://maxiv-science.github.io/azint_writer/ + + + + + + + .. index:: plotting + + Declares which :ref:`NXdata` group + contains the data to be shown by default. + It is needed to resolve ambiguity when more than one :ref:`NXdata` group exists. + The value is the name of the default :ref:`NXdata` group. + + + + + .. index:: NXazint1d (applications) + + The ``NXsubentry`` or Multi-Method Data convention described here: + https://manual.nexusformat.org/rules.html#table-nxsubentry + should be used when different method (e.g. ``NXcanSAS`` or ``NXmonopd``), ``NXazint2d`` + or other ``NXazint1d`` data, integrated with different options, should + be stored under the same ``NXentry``. + + In case of a single ``NXazint1d`` data processing the standard convention with + the application definition directly under ``NXentry`` should be used. + + + + Official NeXus NXDL schema to which this file conforms. + + + + + + + is solid angle correction applied or not. + + + + is polarization correction applied or not. + + + + + is a normalization correction applied or not. + + It indicates that integrated intensities and their errors were already divided by the appropriate normalization factors accounting + for the effective number or weighted contribution of detector pixels to each integration bin. + + + + + + is a monitor correction applied or not. + + The monitor correction accounts for external factors that are independent of the azimuthal integration process. + Most commonly, this involves normalizing for fluctuations in the incident beam intensity or, where applicable, variations in exposure time. + + + + + + + Name of instrument (beamline) where data was collected. + + + + + Wavelength in angstrom. + + + Energy in keV. + + + + + + Name of laboratory where data was collected. + + + Type of laboratory where data was collected. + + + Type of probe. + + + + + + + + + Name of the program that made this file. + + + Version of the progam that made this file. + + + Date the file was created + + + Citation or other references for the algorithm used in the processing. + + + Notes required to help interpret the data, e.g. on coordinate systems. + + + + + Parameters should exactly match those required by the algorithm used in the processing. + For example, `azint` requires `error_model`, `mask`, `n_splitting`, `poni`, etc. + + + + + + + Monitor data for example `I_zero`. + + + + + + + + + + + Azimuthally integrated data with radial binning in q or 2theta. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Values of the normalization correction. + + The normalization correction accounts for the effective number or weighted contribution of detector pixels to each integration bin. + + Note: An important aspect of the normalization strategy is how polarization and solid angle corrections are incorporated, which can vary + depending on the specific application, software, and its configuration options (see, for example, PyFAI documentation). + Additionally, the normalization strategy may include a relative or absolute calibration factor. Two common normalization approaches are: + "Relative normalization" to the PONI (Point Of Normal Incidence) pixel, and "Absolute calibration", which yields the number of photons + scattered by the sample in a given direction per unit solid angle. The type of the normalization strategy is not indicated on this level. + It must be concluded from the software used or its parameters. + + The monitor correction is not included in the normalization correction and it is specified separately. + + + + + + + + + + + + + + + + + + diff --git a/src/nexusformat/definitions/applications/NXazint2d.nxdl.xml b/src/nexusformat/definitions/applications/NXazint2d.nxdl.xml new file mode 100644 index 0000000..ae12e37 --- /dev/null +++ b/src/nexusformat/definitions/applications/NXazint2d.nxdl.xml @@ -0,0 +1,345 @@ + + + + + + + The symbol(s) listed here will be used below to coordinate datasets with the same shape. + + + Number of integrated images + + + Number of radial bins + + + Number of radial bin edges (nRad+1) + + + Number of azimuthal bins + + + Number of azimuthal bin edges (nEta+1) + + + + + Application definition for data from two-dimensional area detectors that has been integrated azimuthally, + with a certain radial binning in units of q or 2theta and with a binning around the azimuthal angle eta. + + An example application that creates these files is documented here: https://maxiv-science.github.io/azint_writer/ + + + + + + + .. index:: plotting + + Declares which :ref:`NXdata` group + contains the data to be shown by default. + It is needed to resolve ambiguity when more than one :ref:`NXdata` group exists. + The value is the name of the default :ref:`NXdata` group. + + + + + .. index:: NXazint2d (applications) + + The ``NXsubentry`` or Multi-Method Data convention described here: + https://manual.nexusformat.org/rules.html#table-nxsubentry + should be used when different method (e.g. ``NXcanSAS`` or ``NXmonopd``), ``NXazint1d`` + or other ``NXazint2d`` data, integrated with different options, should + be stored under the same ``NXentry``. + + In case of a single ``NXazint2d`` data processing the standard convention with + the application definition directly under ``NXentry`` should be used. + + + + Official NeXus NXDL schema to which this file conforms. + + + + + + + is solid angle correction applied or not. + + + + is polarization correction applied or not. + + + + + is a normalization correction applied or not. + + It indicates that integrated intensities and their errors were already divided by the appropriate normalization factors accounting + for the effective number or weighted contribution of detector pixels to each integration bin. + + + + + + is a monitor correction applied or not. + + The monitor correction accounts for external factors that are independent of the azimuthal integration process. + Most commonly, this involves normalizing for fluctuations in the incident beam intensity or, where applicable, variations in exposure time. + + + + + + + Name of instrument (beamline) where data was collected. + + + + + Wavelength in angstrom. + + + Energy in keV. + + + + + + Name of laboratory where data was collected. + + + Type of laboratory where data was collected. + + + Type of probe. + + + + + + + + Name of the program that made this file. + + + Version of the progam that made this file. + + + Date the file was created. + + + Citation or other references for the algorithm used in the processing. + + + Notes required to help interpret the data, e.g. on coordinate systems. + + + + + Parameters should exactly match those required by the algorithm used in the processing. + For example, `azint` requires `error_model`, `mask`, `n_splitting`, `poni`, etc. + + + + + + + Monitor data for example `I_zero`. + + + + + + + + + + Azimuthally integrated data with radial binning in q or 2theta and with azimuthal binning. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Values of the normalization correction. + + The normalization correction accounts for the effective number or weighted contribution of detector pixels to each integration bin. + + Note: An important aspect of the normalization strategy is how polarization and solid angle corrections are incorporated, which can vary + depending on the specific application, software, and its configuration options (see, for example, PyFAI documentation). + Additionally, the normalization strategy may include a relative or absolute calibration factor. Two common normalization approaches are: + "Relative normalization" to the PONI (Point Of Normal Incidence) pixel, and "Absolute calibration", which yields the number of photons + scattered by the sample in a given direction per unit solid angle. The type of the normalization strategy is not indicated on this level. + It must be concluded from the software used or its parameters. + + The monitor correction is not included in the normalization correction and it is specified separately. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/nexusformat/definitions/applications/NXcanSAS.nxdl.xml b/src/nexusformat/definitions/applications/NXcanSAS.nxdl.xml index 6c255e8..4297aeb 100644 --- a/src/nexusformat/definitions/applications/NXcanSAS.nxdl.xml +++ b/src/nexusformat/definitions/applications/NXcanSAS.nxdl.xml @@ -3,7 +3,7 @@ + + + Application definition for normalized representation of electron microscopy research. + + This application definition is a comprehensive, general description for the + standardization of data and metadata collected using electron microscopy. + + NXem is designed to be used for documenting experiments or computer simulations in which + controlled electron beams are used to study electron-beam matter interactions, to simulate this, + to explore physical mechanisms and phenomena, or to characterize materials. + + *The NeXus application definition NXem defines a hierarchical data model with ten building blocks:* + + The data model represents a tree of concepts. The tree is constructed from groups of concepts + representing the branches surplus fields and attributes representing leafs. + + *NXem an introduction for typical use cases in material characterization and simulation:* + + Transmission electron microscopy (TEM) and Scanning Transmission Electron Microscopy (STEM) + Scanning Electron Microscopy (SEM) + Scanning Electron Microscopy combined a Focused-Ion Beam (SEM/FIB) + + *A deeper dive into the branches of NXem:* + + NXem is constructed from composing and specializing base classes into the following ten categories: + + - The field ``definition`` specifies that the data schema is NXem. In combination with + administrative metadata such as the ``NeXus_version`` provided by :ref:`NXroot` this + specifies which version of NXem the instance data in a NeXus/HDF5 file are compliant with. + - The fields ``identifier_experiment``, ``experiment_alias``, ``experiment_description`` and + the group ``userID`` provide concepts for storing organizational metadata that + contextualize the work within the research workflow and humans involved in this. + - The fields ``start_time``, ``end_time`` provide concepts for framing a temporal context for the research. + - The groups ``citeID``, ``noteID`` provide concepts for adding contextual details such as citations + that are associated with or notes, i.e. other artifacts that are deemed relevant when reporting about a measurement + or simulation. These groups are useful when NXem is used as a serialization format for technology-partner-agnostic + archival of data and metadata that have been collected during a session with an electron microscope or when a + simulation was performed. + - The group ``sampleID`` provides concepts for storing metadata about the sample that was + characterized or simulated during the session. + - The group ``measurement`` provides concepts that are useful for describing a measurement + during a session with an electron microscope. This includes the chain of events of data and metadata that + were collected during such a session. + - The group``simulation`` provides concepts that are useful for describing a simulation of an + electron beam that interacts with matter. Combined with ``measurement`` this provides a data schema + for defining a digital twin of the microscope and its optical setup. + - The groups ``consistent_rotations``, ``NAMED_reference_frame`` provide concepts for + reporting coordinate systems (frames of reference) and rotation conventions that clarify how data + should be interpreted specifying the rotation of orientable objects in the microscope, its components, + or of crystals and crystal defects in the material analyzed. These metadata support interpretation for + downstream or on-the-fly data analyses which electron microscopes typically nowadays perform + during a session. Examples are the indexing of diffraction patterns, image analysis in general, or + analyses of the chemical composition. + - The group ``roiID`` provides concepts for reporting several domain- and technique-specific + configuration parameter and results of data processing steps that were applied. + - The group ``profiling`` provides concepts for reporting computational details such as + programs and libraries used, for documenting the libraries of virtual environments such as those used + by conda or python virtual environment, including details about the computing hardware used, and + documenting capabilities for performance analyses and benchmarking of the software or its parts. + + *Design choices:* + + Specific details about how an electron microscope was used and eventually its configuration modified differ + between user groups. This holds also true for computer simulations of electron-beam matter interaction. + Different peer groups in different sub-domains in electron microscopy consider different data and metadata + relevant. NXem defines constraints on the existence and cardinality of concepts and its concept branches + but seeks to offer a compromise. The key design pattern followed is that most branches are made optional + or at most recommended but their child concepts conditional required. Thereby, NXem can cover a variety + of simple but also complex use cases. An example of this parent-optional-but-children-stronger-restricted design + is the combination of the optional group ``measurement`` with its required child + ``measurement/instrument``: Users which report simulations are not forced to document the instrument + but users which have characterized a sample are motivated to report about the instrument. They are though not + necessarily required to report all the details of the instruments' components because the design pattern is-used + applied recursively. + + *Inclusive design, one schema for scanning, focused-ion beam, and transmission electron microscopes:* + + Contrary to many other proposals of a data schema for electron microscopy, NXem seeks to highlight the similarity + of the three fundamental types of electron microscopes that are nowadays used most routinely in academia and + industry: An electron microscope is a beamline that provides a controlled beam of electrons combined with eventually + beams of other particles (ions) to investigate electron/ion(-beam) matter interaction. + This design of per-particle-type concept branches is realized in the base classes ``NXebeam_column`` and ``NXibeam_column``. + These provide concepts for reporting the technical components that are typically used for generating a controllable + (and typically scanning) beam of particles such as electrons or ions. + + Focused-ion beam capabilities are modelled by adding an optional group ``measurement/instrument/ibeam_column``. + We foresee that this design is beneficial also in the future when research should be documented where photon-electron + interactions via an electron microscope are combined. The current proposal though does not include such a + ``NXpbeam_column`` base class that could be used for photon-/light-beam, i.e. laser plus optical + beam path descriptions and components. + + We acknowledge that scanning and transmission electron microscopes are different types of instruments that have distinct differences + in the electron-optical setup and the components used. What remains the same from the perspective of an observer who monitors the + experiment inside the electron-matter interaction volume, i.e. in, on, or close to the surface of the specimen is the imaginary split + into an upper and a lower half-space. In the upper half-space a specific but eventually differently shaped electron beam illuminates + the specimen when comparing a scanning with a transmission electron microscope. In the lower half-space the beam or particles exit + the specimen or end up thermalized in thick specimens. + + *NXem distinguishes and stores instance data based on how long they remain unchanged:* + + ``measurement`` provides two groups ``measurement/instrument`` and ``measurement/eventID``. + The first group is designed for storing metadata about the instrument which do not change over the course of the session. Examples are + the name of the technology partner who built the microscope, the microscope's serial number, or the type of lenses mounted, etc. + The second group is designed for metadata and data that are collected during the microscope session. For these, specializations of + ``NXdata`` specifically ``NXimage`` and ``NXspectrum`` are provided. Each ``measurement/eventID`` event can be time-stamped + individually. Each instance of a group ``measurement/eventID`` contains ``measurement/instrument`` whose purpose + is to store those specific state and settings of the microscope that was present during the collection of the event. + This includes lens settings, apertures used, aberrations, and other components, etc. + By virtue of design this reduces unnecessary repetition of metadata stored in the first group like is often observed + in image-based archival formats like TIFF, PNG, etc. + + *NXem offers domain-specific classes for standardized reporting of method-specific configurations, data processing, and results:* + + These include ``NXem_img`` for generic and specific imaging including diffraction, ``NXem_eds`` for energy-dispersive X-ray spectroscopy, + ``NXem_ebsd`` for electron backscatter diffraction, as well as ``NXem_eels`` for electron energy loss spectroscopy. These branches provide + examples that proof how NeXus can be used for combining session-centric data storage with data processing. These examples are naturally + incomplete but show at different levels of technical depth and breath how standardization can be useful even to report specifically formatted + data representations like multi-dimensional plotting. Thereby, downstream processing using software for data analyses or research data + management can take advantage of a standardized reporting rather than demanding for a zoo of parsers that interconvert + between many representations. + + *NXem within the ecosystem of data schemata for electron microscopy:** + + We support the statement that substantially fewer standardized rather than many ad hoc schemata are required to facilitate the + documentation and exchange of knowledge within electron microscopy. We tailored NXem to serve the materials science and + materials engineering usage of electron microscopy to provide a complementary coverage to what OMERO has established for + the bio- and life science usage of electron microscopy. + + + + + + + + + + The configuration of the software that was used to generate this NeXus file. + + + + A collection of all programs and libraries used to generate this NeXus file. + Ideally, this would enable a binary recreation from the input data. + + Examples include the name and version of the libraries used to write the + instance. Ideally, the software which writes these NXprogram instances + also includes the version of the set of NeXus classes i.e. the specific set + of base classes, application definitions, and contributed definitions + with which the here described concepts can be resolved. + + For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ + which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ + research data management system, it makes sense to store e.g. the GitHub + repository commit and respective submodule references used. + + Instances can also be used to document the modules and libraries that + are offered by the computational environment such as those parsed + from conda or python virtualenv environments. + + + + + + + + + A (globally) unique persistent identifier for referring to this experiment. + + + + + Alias (short name) which scientists can use to refer to this experiment. + + + + + Free-text description about the experiment. + + Users are strongly advised to parameterize the description of their experiment + by using respective groups and fields and base classes instead of writing prose + into the field. + + + + + ISO 8601 time code with local time zone offset to UTC information included + when the microscope session started. If the application demands that time + codes in this section of the application definition should only be used + for specifying when the experiment was performed - and the exact + duration is not relevant - use this start_time field. + + Often though it is useful to specify a time interval via setting both a start_time + and an end_time because this enables software tools and users to collect a + more detailed bookkeeping of the experiment. + + Users should be aware though that even using only start_time and end_time + may not be sufficient to infer how long the experiment took or for how long + data were acquired. To bookkeep more fine-grained timestamps over the + course of the experiment is possible with start_time and end_time fields + of respective :ref:`NXem_event_data` instances. + + + + + ISO 8601 time code with local time zone offset to UTC included when + the microscope session ended. + + See docstring of the start_time field to see how to use the + start_time and end_time together. + + + + + + The author(s) of that reference. + + + + + + + Collection of serialized resources associated with the experiment. + Examples of such resources are files which are formatted using proprietary + data models of technology partners as those generated by the control software + of the microscope during the instrument session. + + + + + + + + + Information about persons who performed or were involved in the microscope + session or simulation run. + + + + + + + Given (first) name and surname. + + + + + Name of the affiliation at the point in time when the experiment was performed. + + + + + Postal address of the affiliation. + + + + + Email address at the point in time when the experiment was performed. + + Writing the most permanently used email is recommended. + + + + + Telephone number at the point in time when the experiment was performed. + + + + + User role at the point in time when the experiment was performed. + + Examples are technician operating the microscope, student, postdoc, + principle investigator, or guest. + + + + + + A physical entity which contains material intended to be investigated. + Sample and specimen are treated as de facto synonyms. + Samples can be real or virtual ones as annotated via is_simulation. + + The suggested best practice is to call this group sample. In those cases when + multiple samples need to be grouped inside one entry, these SAMPLE groups + should be named using the prefix sample followed an index starting from 1, i.e. + (sample1, sample2). + + There are at least two strategies how to store (meta)data when one analyzes multiple + samples - not different ROIs on a single sample though - in one session. + + One strategy is to store each sample and its results under an own NXem/ENTRY. + This is one of the most frequent use cases as during most sessions typically only a + single sample is investigated. In this case the name of this group should be sample. + + If multiple samples are investigated storing each of them in their own ENTRY group eventually will + demand unnecessary duplication of instrument details. + + This can be avoided by using another strategy for storing samples and their results. + Namely, by using only one instance of NXem/ENTRY. That NXem/ENTRY should then be named, + like in the previous case, NXem/entry1 and the samples should be named sample1, sample2, etc., + i.e. instances should use sample as a name prefix. + + In this case the collection of events should use identifier_sample to state clearly for which + of the samples loaded the (characterization) event was detected. + + This concept is related to term `Specimen`_ of the EMglossary standard. + + .. _Specimen: https://purls.helmholtz-metadaten.de/emg/EMG_00000046 + + + + Qualifier whether the sample is a real (in which case is_simulation should be set to false) + or a virtual one (in which case is_simulation should be set to true). + + + + + + + + + + + + + Ideally, (globally) unique persistent identifier which distinguishes this sample from all others + and especially the predecessor/origin from where that sample was cut off. An example of cutting off + is a steel sheet that is the parent sample from which a small portion was wire-eroded that + represents the sample that was then prepared for characterization with an electron microscope. + + The terms sample and specimen are here considered as exact synonyms. + + This field must not be used for an alias for the sample name. Instead, use name. + + In cases where multiple specimens were loaded into the microscope, the identifier has to resolve + the specific sample, whose results are stored by this :ref:`NXentry` instance, because a single + NXentry should be used for the characterization of a single specimen. + + Details about the specimen preparation should be stored in resources referring to identifier_parent. + + + + + + Identifier of the sample from which the sample was cut off or the string *None*. + I.e. the parent to this sample. + + The purpose of this field is to support functionalities for tracking + sample provenance in a research data management system. + + + + + + ISO 8601 time code with local time zone offset to UTC information + when the specimen was prepared. + + Ideally, report the end of the preparation, i.e. the last known timestamp when + the measured specimen surface was actively prepared. Ideally, this matches + the last timestamp that is mentioned in the digital resource pointed to by + identifier_parent. + + Knowing when the specimen was exposed to e.g. specific atmosphere is especially + required for material that is sensitive to the environment such as specimens that were + charged with fast diffusing elements or short-lived radioactive tracers. + + Additional time stamps prior to preparation_date are better placed in resources which + describe but do not pollute the description here with prose. Resolving these + connected metadata is considered the responsibility of the research data management + system and not the a NeXus file. + + + + + Specimen name + + + + + List of comma-separated elements from the periodic table that are contained in the sample. + If the sample substance has multiple components, all elements from each component + must be included in atom_types. + + The purpose of the field is to offer research data management systems an opportunity + to parse the relevant elements without having to interpret these from the resources + pointed to by identifier_parent or walk through eventually deeply nested groups in + individual data instances. + + + + + (Measured) sample thickness. + + The information is recorded to qualify if the beam used was likely + able to shine through the specimen. For scanning electron microscopy, + in many cases the specimen is typically thicker than what is illuminable + by the electron beam. + + In this case the value should be set to the actual thickness of the specimen + viewed for an illumination situation where the nominal surface normal of the + specimen is parallel to the optical axis. + + + + + (Measured) density of the specimen. + + For multi-layered specimens this field should only be used to describe + the density of the excited volume. For scanning electron microscopy + the usage of this field is discouraged and instead an instance of a + region-of-interest connected to individual :ref:`NXem_event_data` + instances can provide a cleaner description of the relevant details. + + + + + Discouraged free-text field to provide further detail. + + + + + + The conventions used when reporting crystal orientations. + We follow the best practices of the Material Science community + that are defined in reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + Convention how a positive rotation angle is defined when viewing + from the end of the rotation unit vector towards its origin. + This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + Counter_clockwise is equivalent to a right-handed choice. + Clockwise is equivalent to a left-handed choice. + + + + + + + + + How are rotations interpreted into an orientation according to convention 3 + of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + + + + + + How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) + according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + The most frequently used convention in Materials Science is zxz, which is based on the work + of H.-J. Bunge but using other conventions is possible. Proper Euler angles are distinguished + from (improper) Tait-Bryan angles. + + + + + + + + + + + + + + + + + + + To which angular range is the rotation angle argument of an + axis-angle pair parameterization constrained according to + convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + + + + + Which sign convention is followed when converting orientations + between different parametrizations/representations according + to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + + + + + + + + + + + + + + + + + + + + + + + + Location of the origin of the processing_reference_frame. + + It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. + Edges are interpreted by inspecting the direction of their outer unit normals + (which point either parallel or antiparallel) along respective base vector direction + of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. + + + + + + + + + + + + + + + + Direction of the positively pointing x-axis base vector of the + processing_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing y-axis base vector of the + processing_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing z-axis base vector of the + processing_reference_frame. + + + + + + + + + + + + + + + Reference to the specifically named :ref:`NXsample` instance(s) for + which these conventions apply (e.g. /entry1/sample1). + + + + + + + Location of the origin of the sample_reference_frame. + + It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. + Edges are interpreted by inspecting the direction of their outer unit normals + (which point either parallel or antiparallel) along respective base vector direction + of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. + + + + + + + + + + + + + + + + Direction of the positively pointing x-axis base vector of the + sample_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing y-axis base vector of the + sample_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing z-axis base vector of the + sample_reference_frame. + + + + + + + + + + + + + + The reference frame that is defined by a specific detector. + + + + Reference to the specifically named :ref:`NXdetector` instance for + which these conventions apply (e.g. /entry1/instrument/detector1). + + + + + + + Location of the origin of the detector_reference_frame. + + If the regions-of-interest forms a rectangle or cuboid, it is assumed that edges are interpreted + by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) + along respective base vector direction of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. + + + + + + + + + + + + + + + + Direction of the positively pointing x-axis base vector of the + detector_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing y-axis base vector of the + detector_reference_frame. + + + + + + + + + + + + + + Direction of the positively pointing z-axis base vector of the + detector_reference_frame. + + + + + + + + + + + + + + + + + + + + + + + + + Details about the control program used for operating the microscope. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A spherical aberration corrector is a typical component in a transmission electron microscope. + Many instruments have only one, in this case the variadic suffix should be dropped. + If there are multiple instances these should be numbered starting from 1, i.e. corrector_cs1, + corrector_cs2. + + + + Use specifically when there are multiple instances. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Descriptor for the aperture setting when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Descriptor for the aperture setting when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. + + + + + + + + + + + + + + + + + + + + + Operation mode of the detector as displayed by the control software. + + + + + + + + + + + + + + Nominal current of the heater. + + + + + Nominal voltage of the heater. + + + + + + + + + + + + + + + + Documentation for a simulation of electron beam-matter interaction. + + + + The program with which the simulation was performed. + + + + + + + + Programs and libraries representing the computational environment + + + + + + + + + + Configuration of the simulation + + + + + Results of the simulation + + + + + + + + + + + + + This concept is related to term `Region Of Interest`_ of the EMglossary standard. + + .. _Region Of Interest: https://purls.helmholtz-metadaten.de/emg/EMG_00000042 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/nexusformat/definitions/applications/NXlauetof.nxdl.xml b/src/nexusformat/definitions/applications/NXlauetof.nxdl.xml index 060efbc..f59743a 100644 --- a/src/nexusformat/definitions/applications/NXlauetof.nxdl.xml +++ b/src/nexusformat/definitions/applications/NXlauetof.nxdl.xml @@ -3,7 +3,7 @@ + + + + Number of diffractogram channels. + + + Number of diffractograms. For example the number of energy-dispersive detectors or the number of azimuthal sections in an area detector. + + + Number of reflections. + + + Diffractogram X units. + + + Diffractogram Y units. + + + Converted diffractogram X units (could be the same as *x_Unit*). + + + number of temperatures + + + number of values in applied stress field + + + number of scan points (only present in scanning measurements) + + + number of detector pixels in the first (slowest) direction + + + number of detector pixels in the second (faster) direction + + + + Application definition for stress and strain analysis of crystalline material defined by the `EASI-STRESS consortium <https://easi-stress.eu>`_. + + When a crystal is loaded (applied or residual stress) its crystallographic parameters change. + + Stress and strain analysis calculates deformation (strain) and the associated force (stress) + from diffraction data. + + This application definition essentially standardizes the result of diffraction pattern analysis + from different types of diffraction experiments for the purpose of stress and strain analysis. + The analysis is typically some form of diffraction peak indexing and fitting. + The experiments are for example + + - energy-dispersive X-ray powder diffraction + - angular-dispersive X-ray powder diffraction + - angular-dispersive neutron powder diffraction + - time-of-flight (TOF) neutron powder diffraction. + + In addition, the application definition guarantees that the information about instrumental setups, measurement conditions, and data analysis workflows are described. + This ensures not only the reproducability and tracability of the measured data, but also the metadata. Since not all participating beamlines or instruments can provide an input to all the NeXus fields listed in this application definition, not all of them are "required". + + However, when possible and technically feasible, the instrument using the NXstress application definition is expected to provide the type of information outlined below. + + Sample and detector positions can be defined with :ref:`NXtransformations`. If you don't specify the direction of gravity + and the direction of the beam then the standard NeXus Coordinate System is used. + + It is highly recommended that when certain parameters or values are the same for all the measurements (acquistions) in the same + file, they are stored only in one location and then linked in the other instances. For example, if during an acquisition all + + instrumental parameters but one stay the same and only the sample table moves in one direction (e.g. Xtranslation), then all the + static instrumental parameters should be saved just once (e.g. in just one NXentry or in a *Shared_Information group*) and their + values linked to every *instrument group* under all the other acquisitions. The value for the variable that changes, Xtranslation + in this example, is suggested to be saved only at every instrument group under each acquistion but not in the *Shared_Information group*. + + It is not always necessary to link each field. In case all the fields with an entire group are the same, the entire group can be linked. + + + + + The name of the *NXentry group(s)* can be freely chosen by the facility. The *NXentry group* can contain any form of data acquisition (e.g. a measurement point, multiple measurement points, a line scan, a mesh, all data points from one sample …). + + + Official NeXus NXDL schema to which this file conforms + + + + + + Extended title for the entry. + + + + Unique identifier for the experiment as defined by the facility (e.g. DOI, proposal id, ...). At ILL, this could be, for example, ``exp_1-02-286``, ``exp_INDU-229``, or ``exp_INTER-569``. + + + + + Brief summary of the experiment, including key objectives. At least one of the following information should be provided: + * ``energy-dispersive X-ray powder diffraction`` + * ``angular-dispersive X-ray powder diffraction`` + * ``angular-dispersive neutron powder diffraction`` + * ``time-of-flight (TOF) neutron powder diffraction`` + + + + + + The starting time(s) of measurement(s) which can be provided in form of a list if multiple measurements are included in the same NXentry. + + + + + The end time(s) of measurement(s) which can be provided in form of a list if multiple measurements are included in the same NXentry. + + + + + + User or Data Acquisition defined identifier from which + the content of this application definition is derived. This can be freely chosen by the user or the instrument scientist and could be, for example, ``05_DA_650_AX_B3P5``, ``SENB-14``, ``Quartz``,.... + + + + + Brief summary of the collection, including grouping criteria. The information provided in this field can highlight, for example, the measurement setup or information about experimental conditions. + + + + + Describes the way strain :math:`\varepsilon` can be calculated from the :ref:`center </NXstress/ENTRY/peaks/center-field>` + peak parameter. + + + + + :math:`\varepsilon = \large \frac{sin(\mathrm{\theta}_{0})}{sin(\mathrm{\theta})}-1` + + + + + :math:`\varepsilon = \large \frac{\mathrm{E}_{0}}{\mathrm{E}}-1` + + + + + :math:`\varepsilon = \large \frac{\mathrm{d}}{\mathrm{d}_{0}}-1` + + + + + :math:`\varepsilon = \large \frac{\mathrm{TOF}}{\mathrm{TOF}_{0}}-1` + + + + + A description of the :math:`\mathrm{\sin}^{2}\psi` method can be found in the literature. Two examples are + `Fitzpatrick et al. 2005 <http://eprintspublications.npl.co.uk/id/eprint/2391>`_ + and + `DIN ISO 15305:2009-01 <https://www.en-standard.eu/din-en-15305-non-destructive-testing-test-method-for-residual-stress-analysis-by-x-ray-diffraction/>`_. + + + + + + + Describes the specific measurement direction covered by the data in this file. + + + + + + + + + + + Information about the person who performed the experiment. + + + + Role of user responsible for this entry. Suggested roes are, for example, ``local contact``, ``beamline_scientist``, ``post_doc``,… + + + + + Name of the diffractometer, instrument, or beamline used for the experiment. This could be, for example, *Strain Analyser for Large and Small scale engineering Applications*. + + Short name for the instrument, perhaps the acronym, which would be for the the example above ``SALSA``. + + + + This group contains information about the geometry and/or efficiency measurement(s). + + Describe the type of calibration. + + + File name(s) and/or path(s) (within file(s)) containing data from the last calibration(s). This can be an array. + + + + Calibration file content. + + + Mime content type of calibration *data* field e.g. text/plain, application/json,... + + + Author or creator of the calibration. + + + Date calibration was created/added + + + + + + Type of radiation source + + + + + + + + + + + + + + Type of radiation probe + + + + + + + + + Zero or more of these groups describe the detectors used in the experiment. + + name/manufacturer/model/etc. information + + + + Description of type such as \ :sup:`3`\ He gas cylinder, \ :sup:`3`\ He PSD, scintillator, fission chamber, proportion counter, ion chamber, CCD, pixel, image plate, CMOS, … + + + + + This is the distance to the previous component in the + instrument; most often the sample. The usage depends on the + nature of the detector: Most often it is the distance of the + detector assembly. But there are irregular detectors. In this + case the distance must be specified for each detector pixel. + + Note, it is recommended to use NXtransformations instead. + + + + + + + + + + efficiency of the detector + + + + + + + + This field can be two things: + + 1. For a pixel detector it provides the nominal wavelength + for which the detector has been calibrated. + + 2. For other detectors this field has to be seen together with + the efficiency field above. + For some detectors, the efficiency is wavelength dependent. + Thus this field provides the wavelength axis for the efficiency field. + In this use case, the efficiency and wavelength arrays must + have the same dimensionality. + + + + + + + + Detector dead time + + + + + + + + Elapsed actual counting time + + + + + + + The axis on which the detector position depends may be stored + anywhere, but is normally stored in the *NXtransformations + group* within the *NXdetector group*. + + + + + This is the recommended location for detector goniometer + and other related axes. + + + + + + Defines the dimensions of the beam profile used for probing the sample which corresponds to or can be used to determine the instrumental gauge volume. + A description of the subsequent fields can be found in the folowing figure. The term "primary" in the subsequent fields refers to the beam path between the sample and the source. The term "secondary" refers to the beam path between the sample and the detector(s). + + .. figure:: stress/Beam_profile_sketch3.jpg + :width: 70% + :alt: Examples for the beam intensity profile. + + Some examples for the beam intensity profile. The 1D description of the beam profile on the right can equally be applied for the horizontal and vertical direction for the primary and the secondary side. + + + + If the beam profile was measured, the filename(s) of the measurement can be specified here. + + + + Defines the last device right in front of the sample used to shape the beam. This could be, for example, a :ref:`(radial) collimator <NXcollimator>` or a :ref:`slit <NXslit>`. + + + + Defines the primary beam size intensity profile on the side closer to the source in the vertical direction. + + + + + Defines the primary beam size intensity profile on the side closer to the sample in the vertical direction. + + + + + Defines the distance between the center of the gauge volume and the beam shaping device. + + + + + Describes how the beam intensity profile in the primary vertical direction was determined. Examples of valid entries are: ``measured``, ``theoretical``, ``estimated``, ... + + + + + Defines the last device right in front of the sample used to shape the beam. This could be, for example, a :ref:`(radial) collimator <NXcollimator>` or a :ref:`slit <NXslit>`. + + + + Defines the primary beam size intensity profile on the side closer to the source in the horizontal direction. + + + + + Defines the primary beam size intensity profile on the side closer to the sample in the horizontal direction. + + + + + Defines the distance between the center of the gauge volume and the beam shaping device. + + + + + Describes how the beam intensity profile in the primary horizontal direction was determined. Examples of valid entries are: ``measured``, ``theoretical``, ``estimated``, ... + + + + + Defines the last device right in front of the sample used to shape the beam. This could be, for example, a :ref:`(radial) collimator <NXcollimator>` or a :ref:`slit <NXslit>`. + + + + Defines the secondary beam size intensity profile on the side closer to the detector in the horizontal direction. + + + + + Defines the secondary beam size intensity profile on the side closer to the sample in the horizontal direction. + + + + + Defines the distance between the center of the gauge volume and the beam shaping device. + + + + + Describes how the beam intensity profile in the secondary horizontal direction was determined. Examples of valid entries are: ``measured``, ``theoretical``, ``estimated``, ... + + + + Incident energy mostly useful for monochromatic beams. + + + Incident wavelength mostly useful for monochromatic beams. + + + + + + + This is the recommended location for describing parameters associated with the sample. + + + + Descriptive name of sample + + + + + The chemical formula specified using CIF conventions. + Abbreviated version of CIF standard: + + * Only recognized element symbols may be used. + * Each element symbol is followed by a 'count' number. A count of '1' may be omitted. + * A space or parenthesis must separate each cluster of (element symbol + count). + * Where a group of elements is enclosed in parentheses, the multiplier for the + group must follow the closing parentheses. That is, all element and group + multipliers are assumed to be printed as subscripted numbers. + * Unless the elements are ordered in a manner that corresponds to their chemical + structure, the order of the elements within any group or moiety depends on + whether or not carbon is present. + * If carbon is present, the order should be: + + - C, then H, then the other elements in alphabetical order of their symbol. + - If carbon is not present, the elements are listed purely in alphabetic order of their symbol. + + * This is the *Hill* system used by Chemical Abstracts. + + + + Sample temperature. This could be a scanned variable + + + + + + Applied external stress field + + + + + + + + + + + + + The gauge volume can be described with the following parameters: + .. figure:: stress/gauge_volume.png + :width: 70% + :alt: Gauge volume parameters and coordinate system. + + Gauge volume parameters and coordinate system. + + + + Length of the first diagonal. + + + + + Length of the second diagonal normal to :ref:`x </NXstress/ENTRY/sample_description/gauge_volume/a-field>`. + + + + + Height of the gauge volume. + + + + + In the local coordinate system, the beam is aligned along the X-axis, + and the Z-axis is oriented in the opposite direction of gravity. The origin + is the center to the gauge volume. + + + + + The last field typically depends on the first + field of the :ref:`sample transformations </NXstress/ENTRY/SAMPLE_DESCRIPTION/TRANSFORMATIONS-group>`. + + + + + + The axis on which the sample position depends may be stored + anywhere, but is normally stored in the NXtransformations + group within the NXsample group. + + + + + This is the recommended location for sample goniometer + and other related axes. + + + + + + + Zero or more groups to describe the data processing steps + to obtain the content of this application definition. + + + + The raw data file name(s) used during the data reduction process. This can be a list. + + + + + Date when the raw data was reduced and the data in the *NXstress* file format generated. + + + + + Software package used to perform data reduction including the version number or release date. + + + + + Describes how the data was integrated. + + + + + Describes the type of binning used during data reduction. + + + + + Describes how the fitting of the peaks was done. For example, single peak fit, multiple peak fit, Pawley refinement, Rietveld refinement, … + + + + + Describes the data range used for peak fitting. + + + + + Type and value describing the goodness of fit. For example, Rw 0.23. + + + + + Describes whether the data was normalized and if so , how. Examples of valid entries are: ``None``, ``time``, ``primary monitor``, ``detector``, … + + + + Information about the person who performed the data reduction. + + + + Role of user responsible for this entry. Suggested roles are, for example, ``local contact``, ``beamline_scientist``, ``post_doc``,… + + + + + The note will contain information about how the data was processed + or anything about the data provenance. + The contents of the note can be anything that the processing code + can understand, or a simple text. + + The name will be numbered to allow for ordering of steps. + + + + + This group contains all diffraction peak fit parameters. + This information is not required for stress and strain calculations. + + + Diffraction peak profile. + + + + + + + + + + + + Diffraction peak area (not including the background) in *y_Unit* units. + + + + + Specify the *y_Unit* units + + + + + Error value(s) asscociated with :ref:`area </NXstress/ENTRY/fit/peak_parameters/area-field>` + + + + + + + + Diffraction peak position in *x_Unit* units. + + + + + Specify the *x_Unit* units + + + + + Error value(s) asscociated with :ref:`center </NXstress/ENTRY/fit/peak_parameters/center-field>` + + + + + + + + Diffraction peak height (not including the background) in *y_Unit* units. + + + + + Specify the *y_Unit* units + + + + + Error value(s) asscociated with :ref:`height </NXstress/ENTRY/fit/peak_parameters/height-field>` + + + + + + + + Diffraction peak full width at half maximum in *x_Unit* units. + + + + + Specify the *x_Unit* units + + + + + Error value(s) asscociated with :ref:`fwhm </NXstress/ENTRY/fit/peak_parameters/fwhm-field>` + + + + + + + + Left-side FWHM for split profiles in *x_Unit* units. + + + + + Specify the *x_Unit* units + + + + + Error value(s) asscociated with :ref:`fwhm_left </NXstress/ENTRY/fit/peak_parameters/fwhm_left-field>` + + + + + + + + Right-side FWHM for split profiles in *x_Unit* units. + + + + + Specify the *x_Unit* units + + + + + Error value(s) asscociated with :ref:`fwhm_right </NXstress/ENTRY/fit/peak_parameters/fwhm_right-field>` + + + + + + + + + - Voigt or Pseudo-Voigt: Lorentzian fraction + - Pearson VII: decay parameter + - Other profiles: not applicable + + + + + + + + Error value(s) asscociated with :ref:`form_factor </NXstress/ENTRY/fit/peak_parameters/form_factor-field>` + + + + + + + + + Angle that defines the position of the integrated sector in the diffraction cone + for angular-dispersive diffraction or the position of the detector for energy-dispersive + diffraction. + + + + + + + + + This group contains all background fit parameters. + This information is not required for stress and strain calculations. + + + + Diffraction background profile. Required when background parameter fields are present. + Some example values with equations are shown below: + + - ``manual`` : No equations nor variables needed to describe this background. + - ``linear`` : \ :math:`\small background= A0 + A1 \cdot x` + - ``5-degree polynomial`` : \ :math:`\small background= A0 + A1 \cdot x + A2 \cdot \mathrm{x}^{2} + A3 \cdot \mathrm{x}^{3} + A4 \cdot \mathrm{x}^{4} + A5 \cdot \mathrm{x}^{5}` + - ``shape function plus polynomial`` : A shape function is not a mathematical function, it contains a manual background obtained from a fit and a polynomial part. This allows to adapt and modify the fit for subsequent measurements in the same measurement campaign. The function describing it is the following: \ :math:`\small background= as + b \cdot SHAPE(x-o)` Where SHAPE is the name of the variable used to describe the background value at the position x. x can be e.g. the scattering angle \ :math:`2\theta` in degrees. + + + + Background parameter(s). For example a second-degree polynomial will have fields ``A0``, ``A1`` and ``A2``. + + + + + + Background parameter *constant* for SHAPE function. + + + + + + Error associated with background parameter *constant* for SHAPE function. + + + + + + Background parameter *amplitude* for SHAPE function. + + + + + + Error associated with background parameter *amplitude* for SHAPE function. + + + + + + Background parameter *offset* for SHAPE function. + + + + + + Error associated with background parameter *offset* for SHAPE function. + + + + + + The background area in *y_Unit* units, integrated over a confidence interval around the center (*0.95* by default). + + + + + Specify the *y_Unit* units + + + + + Confidence interval from which the background counts are integrated. + For example *0.95* means that the background is integrated over the range in + which the integrated peak area is 95% of the total peak area. + + + + + + + Diffractogram with fit results in :ref:`peak_parameters </NXstress/ENTRY/fit/peak_parameters-group>` + and :ref:`background_parameters </NXstress/ENTRY/fit/background_parameters-group>`. + This information is not required for stress and strain calculations. + + + List of the one to two axes field name(s) to be used by default. The axes are further described in the fields DAXIS and XAXIS. + + + + + One or more fields that contain the values for the **n_D** dimension. + For example the azimuthal positions of different energy-dispersive detectors + or the average azimuth of different azimuthal sections on an area detector. + + + + + + + + + One or more fields that contain the values for the **n_X** dimension in *x_Unit* units. + For example: MCA channels, scattering angle \ :math:`2\theta` in degrees, + scattering vector length q in \ :math:`\mathrm{nm}^{-1}`, ... + + + + + + Specify the *x_Unit* units + + + + + Default field name to be plotted. + + + + + + + List of additional field names to be plotted. This could be e.g. fit, background, residuals, … + + + + Diffractogram counts in *y_Unit* units (default signal) + + + + + + + + + + + Specify the *y_Unit* units + + + + + Diffractogram counts error in *y_Unit* units (default signal) + + + + + + + + + + + Specify the *y_Unit* units + + + + + Diffractogram fit counts (auxiliary signal). + + + + + + + + + + + + + Diffractogram fit counts error (auxiliary signal). + + + + + + + + In case the diffraction background was manually determined. Diffractogram background counts (auxiliary signal). + + + + + + + + + + + + Difference between diffractogram and fit (auxiliary signal). + + + + + + + + + + + + + + + + User description of the data acquisitions. + A description of data analysis goes in the + :ref:`fit descriptions </NXstress/ENTRY/FIT/DESCRIPTION-group>`. + + + + + + This group contains all diffraction peak parameters that could be needed for stress and strain calculations. + These parameters are derived from :ref:`peak_parameters </NXstress/ENTRY/fit/peak_parameters-group>` and additional metadata. + + + First Miller index. + + + + + + Second Miller index. + + + + + + Third Miller index. + + + + + + Crystal lattice systems (*cubic*, *hexagonal*, ...) + + + + + + Crystallographic space group :math:`(Fm\bar{3}m, Im\bar{3}m, ...)` + + + + + + Name of the crystallographic phase (hematite, goethite, \ :math:`\alpha`-Al\ :sub:`2`\ O\ :sub:`3`\ , ...). + + + + + + + First component of the *normalized* scattering vector *Q* in the sample reference frame. + The sample reference frame is defined by the :ref:`sample transformations </NXstress/ENTRY/sample_description/TRANSFORMATIONS-group>`. + + + + + + + + Second component of the *normalized* scattering vector *Q* in the sample reference frame. + The sample reference frame is defined by the :ref:`sample transformations </NXstress/ENTRY/sample_description/TRANSFORMATIONS-group>`. + + + + + + + + Third component of the *normalized* scattering vector *Q* in the sample reference frame. + The sample reference frame is defined by the :ref:`sample transformations </NXstress/ENTRY/sample_description/TRANSFORMATIONS-group>`. + + + + + + + Diffraction peak position in *c_Unit* units. + + + + + Specify the *c_Unit* units (see :ref:`center_type </NXstress/ENTRY/peaks/center_type-field>`) + + + two-theta + + + energy + + + momentum-transfer + + + d-spacing + + + time-of-flight + + + channel (dimensionless) + + + + + + Uncentrainties on :ref:`center </NXstress/ENTRY/peaks/center-field>` in *c_Unit* units. + + + + + Specify the *c_Unit* units (see :ref:`center_type </NXstress/ENTRY/peaks/center_type-field>`) + + + two-theta + + + energy + + + momentum-transfer + + + d-spacing + + + time-of-flight + + + channel (dimensionless) + + + + + + + The space in which :ref:`center </NXstress/ENTRY/peaks/center-field>` is defined. + It defines the *c_Unit* as follows + + - if *center_type="two-theta"* then *c_Unit* must have the angle unit *degrees* + - if *center_type="energy"* then *c_Unit* must have the unit *keV* + - if *center_type="momentum-transfer"* then *c_Unit* must have the unit \ :math:`Å^{-1}` + - if *center_type="d-spacing"* then *c_Unit* must have the unit \ :math:`Å` + - if *center_type="channel"* then *c_Unit* must be *dimensioness* + - if *center_type="time-of-flight"* then *c_Unit* must have the unit \ :math:`\mu\mathrm{s}` + + + + + + + + + + + + + First component of the sample position in the sample reference frame. + The sample reference frame is defined by the :ref:`sample transformations </NXstress/ENTRY/sample_description/TRANSFORMATIONS-group>`. + + + + + + + + + First component of the sample position in the sample reference frame. + The sample reference frame is defined by the :ref:`sample transformations </NXstress/ENTRY/sample_description/TRANSFORMATIONS-group>`. + + + + + + + + First component of the sample position in the sample reference frame. + The sample reference frame is defined by the :ref:`sample transformations </NXstress/ENTRY/sample_description/TRANSFORMATIONS-group>`. + + + + + + + + + diff --git a/src/nexusformat/definitions/applications/NXtomoproc.nxdl.xml b/src/nexusformat/definitions/applications/NXtomoproc.nxdl.xml index 78c19b9..21838c6 100644 --- a/src/nexusformat/definitions/applications/NXtomoproc.nxdl.xml +++ b/src/nexusformat/definitions/applications/NXtomoproc.nxdl.xml @@ -83,7 +83,7 @@ - + This is the reconstructed volume. This can be different things. Please indicate in the unit attribute what physical @@ -91,7 +91,7 @@ - + diff --git a/src/nexusformat/definitions/applications/NXxps.nxdl.xml b/src/nexusformat/definitions/applications/NXxps.nxdl.xml index e38757f..3f48322 100644 --- a/src/nexusformat/definitions/applications/NXxps.nxdl.xml +++ b/src/nexusformat/definitions/applications/NXxps.nxdl.xml @@ -142,7 +142,7 @@ Reference to the transformation describing the direction of the beam relative to a defined coordinate system. - + Should point to /entry/instrument/beam_probe/transformations/beam_direction. @@ -199,7 +199,8 @@ - This should point to the coordinate system defined in /entry/xps_coordinate_system. + This should point to the coordinate system defined in + /entry/xps_coordinate_system. @@ -251,7 +252,8 @@ - Azimuthal rotation of the analyzer from the y-direction defined by the sample stage. + Azimuthal rotation of the analyzer from the y-direction defined by the sample + stage. @@ -265,7 +267,8 @@ - This should point to the coordinate system defined in /entry/xps_coordinate_system. + This should point to the coordinate system defined in + /entry/xps_coordinate_system. @@ -481,7 +484,7 @@ Area of the peak. - + Width of a peak at a defined fraction of the peak height. @@ -578,7 +581,7 @@ modeling the XPS background in situations where the background is integrated from the peak intensities at each binding energy to higher kinetic energies. It is useful when fitting the background in spectra that display significant low-energy tailing or when the background - exhibits a non-linear rise with binding energy. + exhibits a nonlinear rise with binding energy. The model incorporates the notion of electron energy loss and the behavior of the photoelectrons as they travel through the material and lose energy. 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zd`FtfqS(&aF(3U$9xlcX+NoXk?XxeH1Y?EgdvJ{&XR5OHJ#GGX1`kJD-i_zCLfh5V z?40aJm$!e{dpE|ajrX9#kM|%ljtV{cfSjR%spAS$^vt%criSVyNWW6!vZ%D|PcWAJ z_M|UpG=rxM?R3vcsu8 zce341!R2p4mYmO%HLS=!Z9lJekMHiL7p_m|h2Ud9(An6`r!@I)Koe!uaxY>wud-X*^r9a7z_Xr23s1$dULe9@O{hFAptfW+IH^gcP2O=bP^4AZ)_kvpr7e{au z47!-c?BKq-J*w}_d|Lv9_sZijfBw!iHPGp3{d8mRv*_6W&ilf~@2ZFNBV?|&9ZfV$ zA87kAT+n>5sAR#~{a8PSSHA*%d50$5TZDFSYjT&_4XjzZnp35cKBTl`={AprZnunTwO!GPiLkf}@i1}ES>~9(7UmuX#FPyI?BRRpw^2?4DI7 z3+}7AkzQU`epaVG1?^h_Rtlb>rM#vq4_uE1uJr#`dD8hzWu0I9si(hp8wkJ`*vRcSo@Fs1Ux-sewrU!Od*XP$la zD*gH4r5pC^dlv1!>!mhXN>=vjfddX#SqvIhJFj76Te)^^sE$~$j@a%GhB~K%)FuaN zO$Cyc8<$kq915@W+HUkv`(2Lq{;idr4~kE{EIRczZ-e|TiUGB+#JtHw*K-@p6+`EI855)m#|+j+H1!u8``9pAqGo7`c$ z`Tl$N?v;|45BK*!KXtBs!z-6HjOISIwR<0Z-0|q+kJkP`&V8ric1`7se=4`H#;*QX zOMZ3q&$FM|=O2D(v8#Q3oL+e9p>pqe!Ux3z6hwl4WO$lO^=eg#)I7ggl)0kVWA#n{ zs9*bP9(~@r*3>h|YU;H&huNdzs@7il<^MbGh=eEs+=lac$xCA^D{?yZ=C0jhc0akYKIfWUT6XqoHg8zZ);*E}uydFWtxaPZ=9-^zIT`LlC! zeCqc9-=)vUAdtRekHF<@u}l$E&S-X6>_HJ8`0*nJ0UK zOcJj{XoTn571axG*WG`V8@R}Fp-ZvT$!$x1z55dTU6bj+$_`V8(8TMvuKqb*sk(@> z)OD9g76(v<@xV-=Ees57kMBz}GBEJCtpSn}JrT?d3 + + + + + Quantified aberration coefficient in an aberration_model. + + For an introduction in the details about aberrations with relevance for electron microscopy + see `R. Dunin-Borkowski et al. <https://doi.org/10.1017/9781316337455.022>`_ and + `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) + for different definitions available and further details. + Table 7-2 of Ibid. publication (page 305ff) documents how to convert from the Nion to the CEOS definitions. + Conversion tables are also summarized by `Y. Liao <https://www.globalsino.com/EM/page3740.html>`_ an introduction. + + The use of the base class is not restricted to electron microscopy but can also be useful for classical optics. + + + + Magnitude of the aberration + + + + + Uncertainty of the magnitude of the aberration + + + + + Free-text description how magnitude_errors was quantified + e.g. via the 95% confidence interval, variance, standard deviation, + using which algorithm or statistical model. + + + + + Time elapsed since the last measurement. + + + + + For the CEOS definitions the C aberrations are radial-symmetric and have + no angle entry, while the A, B, D, S, or R aberrations are n-fold + symmetric and have an angle entry. + For the NION definitions the coordinate system differs to the one + used in CEOS and instead two aberration coefficients a and b are used. + + + + + Given name to this aberration. + + + + + Alias to name or refer to this specific type of aberration. + + + diff --git a/src/nexusformat/definitions/base_classes/NXactuator.nxdl.xml b/src/nexusformat/definitions/base_classes/NXactuator.nxdl.xml index 626cc5f..74ac967 100644 --- a/src/nexusformat/definitions/base_classes/NXactuator.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXactuator.nxdl.xml @@ -3,7 +3,7 @@ - + An actuator used to control an external condition. @@ -76,19 +76,4 @@ stored here. - - - Refers to the last transformation specifying the position of the actuator - in the NXtransformations chain. - - - - - This is the group recommended for holding the chain of translation - and rotation operations necessary to position the actuator within - the instrument. The dependency chain may however traverse similar groups in - other component groups. - - - diff --git a/src/nexusformat/definitions/base_classes/NXevent_data_apm.nxdl.xml b/src/nexusformat/definitions/base_classes/NXapm_event_data.nxdl.xml similarity index 96% rename from src/nexusformat/definitions/base_classes/NXevent_data_apm.nxdl.xml rename to src/nexusformat/definitions/base_classes/NXapm_event_data.nxdl.xml index 820f061..162cd3e 100644 --- a/src/nexusformat/definitions/base_classes/NXevent_data_apm.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXapm_event_data.nxdl.xml @@ -21,7 +21,7 @@ # # For further information, see http://www.nexusformat.org --> - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -37,7 +37,7 @@ Having at least one instance for an instance of NXapm is recommended. - This base class applies the concept of the :ref:`NXevent_data_em` base class to the specific needs + This base class applies the concept of the :ref:`NXem_event_data` base class to the specific needs of atom probe research. Again static and dynamic quantities are split to avoid a duplication of information. Specifically, the time interval considered is the entire time starting at start_time until end_time during which we assume the pulser triggered pulses. @@ -110,7 +110,7 @@ - + Place to store dynamic metadata of the instrument to document as close as possible the state of the instrument during the event, i.e. in between start_time and end_time. diff --git a/src/nexusformat/definitions/base_classes/NXinstrument_apm.nxdl.xml b/src/nexusformat/definitions/base_classes/NXapm_instrument.nxdl.xml similarity index 96% rename from src/nexusformat/definitions/base_classes/NXinstrument_apm.nxdl.xml rename to src/nexusformat/definitions/base_classes/NXapm_instrument.nxdl.xml index cd4bd92..0d859aa 100644 --- a/src/nexusformat/definitions/base_classes/NXinstrument_apm.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXapm_instrument.nxdl.xml @@ -24,9 +24,9 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -34,7 +34,7 @@ or volatile (meta)data.--> Number of pulses collected in between start_time and end_time - inside a parent instance of :ref:`NXevent_data_apm`. + inside a parent instance of :ref:`NXapm_event_data`. @@ -44,7 +44,7 @@ or volatile (meta)data.--> For collecting data and experiments which are simulations of an atom probe microscope or a session with such instrument use the :ref:`NXapm` application definition - and the :ref:`NXevent_data_apm` groups it provides. + and the :ref:`NXapm_event_data` groups it provides. This base class implements the concept of :ref:`NXapm` whereby (meta)data are distinguished whether these typically change during a session, so-called dynamic, or not, so-called static metadata. @@ -121,13 +121,13 @@ or volatile (meta)data.--> - + A counter electrode of the LEAP 6000 series atom probes. - + A local electrode guiding the ion flight path. Also called counter or extraction electrode. @@ -142,8 +142,8 @@ or volatile (meta)data.--> The type of aperture used when the local_electrode has an aperture or acts as an aperture in addition to acting as an extraction electrode. - The local electrode is a component which combines functionalities of :ref:`NXlens_em`, - :ref:`NXaperture`, if not even :ref:`NXdeflector`: + The local electrode is a component which combines functionalities + of :ref:`NXelectromagnetic_lens`, :ref:`NXaperture`, if not even :ref:`NXdeflector`: * "n/a", use when no aperture is present in the experiment * "conical", conical aperture with a circular hole @@ -194,7 +194,7 @@ or volatile (meta)data.--> Laser- and/or voltage-pulsing device to trigger ion removal. - When the base class NXinstrument_apm is used in the NXapm + When the base class NXapm_instrument is used in the NXapm application definition, the values for the following fields: * pulse_frequency @@ -208,7 +208,7 @@ or volatile (meta)data.--> * spot_position should be recorded in the order of, and assumed associated, - with the pulse_id in an instance of :ref:`NXevent_data_apm`. + with the pulse_id in an instance of :ref:`NXapm_event_data`. diff --git a/src/nexusformat/definitions/base_classes/NXapm_measurement.nxdl.xml b/src/nexusformat/definitions/base_classes/NXapm_measurement.nxdl.xml index c536a2d..d4f1f07 100644 --- a/src/nexusformat/definitions/base_classes/NXapm_measurement.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXapm_measurement.nxdl.xml @@ -65,6 +65,6 @@ field of a CamecaRoot ROOT file. - - + + diff --git a/src/nexusformat/definitions/base_classes/NXapm_reconstruction.nxdl.xml b/src/nexusformat/definitions/base_classes/NXapm_reconstruction.nxdl.xml index 43068bd..b1680ce 100644 --- a/src/nexusformat/definitions/base_classes/NXapm_reconstruction.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXapm_reconstruction.nxdl.xml @@ -130,9 +130,10 @@ field of a CamecaRoot ROOT file. - + - Sum of ion volumes + The factor :math:`k` in :math:`R_0 = \frac{V}{kF}` with :math:`R_0` tip_radius_zero + :math:`V` the voltage and :math:`F` the evaporation field. The value can be extracted from the CAnalysis.CSpatial.fKfactor field of a CamecaRoot ROOT file. @@ -186,6 +187,9 @@ performed with APSuite / IVAS see also `B. Gault et al. <https://doi.org/10.1093/mam/ozae081>_` and `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). for best practices on the reporting of metadata in atom probe tomography. + + The value can be extracted from the CAnalysis.CResults.fComments + field of a CamecaRoot ROOT file. @@ -204,6 +208,14 @@ + + + Qualitative statement about the reconstruction. + + The value can be extracted from the CAnalysis.CResults.fQuality + field of a CamecaRoot ROOT file. + + diff --git a/src/nexusformat/definitions/base_classes/NXatom.nxdl.xml b/src/nexusformat/definitions/base_classes/NXatom.nxdl.xml index e8f2a55..3df36e8 100644 --- a/src/nexusformat/definitions/base_classes/NXatom.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXatom.nxdl.xml @@ -138,10 +138,12 @@ - + - Path to a reference frame in which positions are defined - to resolve ambiguity when the reference frame is different + Path to an instance of :ref:`NXcoordinate_system` to document + the reference frame in which the positions are defined. + + This resolves ambiguity when the reference frame is different to the NeXus default reference frame (McStas). @@ -163,16 +165,19 @@ Individual hash values :math:`H` `encode <https://doi.org/10.1017/S1431927621012241>`_ for each nuclide or element the number of protons :math:`Z` and a constant :math:`c` - via the following hashing rule :math:`H = Z + c \cdot 256` . :math:`Z and c` must be 8-bit unsigned integers. + via the following hashing rule :math:`H = Z + c \cdot 256`. :math:`Z` and :math:`c` must be 8-bit unsigned integers. The constant :math:`c` is either set to number of neutrons :math:`N` or to the special value 255. The special value 255 is used to refer to all isotopes of an element from the IUPAC periodic table. - Exemplified for hydrogen (meaning irrespective which isotope), its hash value is :math:`H = 1 + 255 \cdot 256 = 65281`. - Exemplified for the :math:`^{1}H` hydrogen isotope (:math:`Z = 1, N = 0`), its hash value is :math:`H = 1 + 0 \cdot 256 = 1`. - Exemplified for the :math:`^{2}H` deuterium isotope (:math:`Z = 1, N = 1`), its hash value is :math:`H = 1 + 1 \cdot 256 = 257`. - Exemplified for the :math:`^{3}H` tritium isotope (:math:`Z = 1, N = 2`), its hash value is :math:`H = 1 + 2 \cdot 256 = 513`. - Exemplified for the :math:`^{99}Tc` technetium isotope (:math:`Z = 43, N = 56`), its hash value is :math:`H = 43 + 56 \cdot 256 = 14379`. + Some examples: + + * The element hydrogen (meaning irrespective which isotope), its hash value is :math:`H = 1 + 255 \cdot 256 = 65281`. + * The :math:`^{1}H` hydrogen isotope (:math:`Z = 1, N = 0`), its hash value is :math:`H = 1 + 0 \cdot 256 = 1`. + * The :math:`^{2}H` deuterium isotope (:math:`Z = 1, N = 1`), its hash value is :math:`H = 1 + 1 \cdot 256 = 257`. + * The :math:`^{3}H` tritium isotope (:math:`Z = 1, N = 2`), its hash value is :math:`H = 1 + 2 \cdot 256 = 513`. + * The :math:`^{99}Tc` technetium isotope (:math:`Z = 43, N = 56`), its hash value is :math:`H = 43 + 56 \cdot 256 = 14379`. + The special hash value :math:`0` is a placeholder. This hashing rule implements a bitshift operation. The benefit is that this enables encoding of all @@ -186,7 +191,7 @@ Table which decodes the entries in nuclide_hash into a human-readable matrix - instances for either nuclids or elements. Specifically, the first row specifies the + instances for either nuclides or elements. Specifically, the first row specifies the nuclide mass number. When the nuclide_hash values are used this means the row should report the sum :math:`Z + N` or 0. The value 0 documents that an element from the IUPAC periodic table is meant. diff --git a/src/nexusformat/definitions/base_classes/NXattenuator.nxdl.xml b/src/nexusformat/definitions/base_classes/NXattenuator.nxdl.xml index 52ff615..af33018 100644 --- a/src/nexusformat/definitions/base_classes/NXattenuator.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXattenuator.nxdl.xml @@ -3,7 +3,7 @@ + + + + Computational geometry of alpha complexes (alpha shapes or alpha wrappings) about primitives. + + For details see: + + * https://dx.doi.org/10.1109/TIT.1983.1056714 for 2D, + * https://dx.doi.org/10.1145/174462.156635 for 3D, + * https://dl.acm.org/doi/10.5555/871114 for weighted, and + * https://doc.cgal.org/latest/Alpha_shapes_3 for 3D implementation of alpha shapes, and + * https://doc.cgal.org/latest/Manual/packages.html#PkgAlphaWrap3 for 3D alpha wrappings + + in CGAL, the Computational Geometry Algorithms Library respectively. + As a starting point, we follow the conventions of the CGAL library. + + In general, an alpha complex is a not necessarily connected or not necessarily pure complex, + i.e. singular faces may exist. The number of cells, faces, and edges depends on how a specific + alpha complex is filtered for lower-dimensional simplices. The fields is_regularized and + regularization can be used to provide details about regularization procedures. + + + + Type of alpha complex following the terminology used by CGAL for now. + + Alpha_shape means meshes created using one of the alpha_shape algorithm. + Alpha_wrapping means meshes created using the alpha_wrapping algorithm. + + + + + + + + + + Human-readable description about regularization procedures. + + + + + Was the alpha complex regularized, i.e. have singular faces been removed, or not. + + + + + The alpha parameter, i.e. the squared radius of the alpha-sphere + that is used when computing the alpha complex. + + + + + The offset distance parameter used when computing alpha_wrappings. + + + + + + Point cloud serving as input for the computation of the alpha complex. + + + + + Triangle soup serving as input for the computation of the alpha complex. + + + + + Triangle mesh representing the output of the computation, i.e. the alpha complex. + + + + + Tetrahedra representing an interior volume of the alpha complex (if such exists). + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_cylinder.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_cylinder.nxdl.xml new file mode 100644 index 0000000..2459121 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_cylinder.nxdl.xml @@ -0,0 +1,133 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality of the space in which the members are assumed embedded. + + + + + The cardinality of the set, i.e. the number of members. + + + + + Computational geometry description of a set of cylinders or (truncated) cones. + + The radius can either be defined in the radii field or by filling the upper_cap_radii + and lower_cap_radii fields respectively. The latter field case can + thus be used to represent (truncated) cones. + + It is possible to define only one of the cap_radii fields + to represent half-open cylinder. + + + + A direction vector which is parallel to the cylinder/cone axis + and whose magnitude is the height of the cylinder/cone. + + The upper_cap is assumed to represent the end while the + lower_cap is assumed to represent the start of the + respective cylinder instances when inspecting along the + direction vector. + + + + + + + + + Radius of the cylinder if all have the same radius. + + + + + Radii of the cylinder. + + + + + + + + Radii of the upper circular cap. + + This field, combined with lower_cap_radius can be used to describe + (eventually truncated) circular cones. + + + + + + + + Radii of the upper circular cap. + + This field, combined with upper_cap_radius can be used to describe + (eventually truncated) circular cones. + + + + + + + + + Lateral surface area of each cylinder. + + + + + + + + Area of the upper cap of each cylinder. + + + + + + + + Area of the lower cap of each cylinder. + + + + + + + + Sum of upper and lower cap area and lateral surface area of each cylinder. + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_ellipsoid.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_ellipsoid.nxdl.xml new file mode 100644 index 0000000..c34a489 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_ellipsoid.nxdl.xml @@ -0,0 +1,81 @@ + + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality of the space in which the members are assumed embedded. + + + + + The cardinality of the set, i.e. the number of members. + + + + + Computational geometry description of a set of ellipsoids. + + + + Length of the semi-axes (e.g. semi-major and semi-minor + respectively for an ellipse). + + Use if all ellipsoids in the set have the same half-axes. + + + + + + + + Length of the semi-axes if ellipsoids have individually different lengths. + + + + + + + + + + In the case that all ellipsoids are spheres. + + + + + In the case that all ellipsoids are spheres whose radii differ. + For a mixture of spheres use semi_axes_values. + + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_face_list_data_structure.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_face_list_data_structure.nxdl.xml new file mode 100644 index 0000000..5fcfde6 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_face_list_data_structure.nxdl.xml @@ -0,0 +1,227 @@ + + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality, which has to be at least 2. + + + + + The number of vertices. + + + + + The number of edges. + + + + + The number of faces. + + + + + The total number of vertices of all faces. Faces are polygons. + + + + + Computational geometry of primitives via a face-and-edge-list data structure. + + Primitives must neither be degenerated nor self-intersect but can have different + properties. A face-and-edge-list-based description of primitives is + frequently used for triangles and polyhedra to store them on disk for + visualization purposes (see OFF, PLY, VTK, or STL file formats). + + Although this description is storage efficient, it is not well-suited for + topological analyses. In this case using a half-edge data structure is + an alternative. + + Having an own base class for the data structure how primitives are stored is + useful to embrace both users with small or detailed specification demands. + + Indices can be used as identifier and thus names for individual instances. + + + + + Number of vertices for each face. + + Each entry represents the total number of vertices for that face, + irrespectively whether vertices are shared among faces or not. + + + + + + + + Number of edges for each face. + + Each entry represents the total number of edges for that face, + irrespectively whether edges are shared across faces or not. + + + + + + + + Number of faces of the primitives. + + + + + Integer offset whereby the identifier of the first member + of the vertices differs from zero. + + Identifier can be defined explicitly or implicitly. + Inspect the definition of NXcg_primitive for further details. + + + + + Integer offset whereby the identifier of the first member + of the edges differs from zero. + + Identifier can be defined explicitly or implicitly. + Inspect the definition of NXcg_primitive for further details. + + + + + Integer offset whereby the identifier of the first member + of the faces differs from zero. + + Identifier can be defined explicitly or implicitly. + Inspect the definition of NXcg_primitive for further details. + + + + + Integer identifier to distinguish all vertices explicitly. + + + + + + + + Integer used to distinguish all edges explicitly. + + + + + + + + Integer used to distinguish all faces explicitly. + + + + + + + + Positions of the vertices. + + Users are encouraged to reduce the vertices to a unique set as this may + result in more efficient storage. Alternatively, storing vertex positions naively + should be indicated with setting vertices_are_unique to False. + Naively means that each vertex is stored even though many vertices may + share the same positions. + + + + + + + + + The edges are stored as pairs of vertex identifier. + + + + + + + + + The faces are stored as a concatenated array of vertex identifier tuples. + + The first entry is the identifier of the start vertex of the first face, + followed by the second vertex of the first face, until the last vertex + of the first face. Thereafter, the start vertex of the second face, the + second vertex of the second face, and so on and so forth. + + Therefore, summating over the number_of_vertices, allows to extract + the vertex identifiers for the i-th face on the following index interval + of the faces array: :math:`[\sum_{i = 0}^{i = n-1}, \sum_{i=0}^{i = n}]`. + + + + + + + + + If true, indicates that the vertices are all placed at different positions + and have different identifiers, i.e. no points overlap or are counted more + than once. + + + + + If true, indicates that no edge is stored more than once. + + Users are encouraged to consider using a half_edge_data_structure instead. + + + + + If true, indicates that no face is stored more than once. + + + + + Specifies for each face which winding order was used if any: + + * 0 - undefined + * 1 - counter-clockwise (CCW) + * 2 - clock-wise (CW) + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_grid.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_grid.nxdl.xml similarity index 59% rename from src/nexusformat/definitions/contributed_definitions/NXcg_grid.nxdl.xml rename to src/nexusformat/definitions/base_classes/NXcg_grid.nxdl.xml index f3cbc28..07abb10 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_grid.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXcg_grid.nxdl.xml @@ -2,9 +2,9 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -33,36 +33,36 @@ - The cardinality or total number of cells/grid points. + The cardinality or total number of cells aka grid points. - Number of boundaries of the bounding box or primitive to the grid. + Number of boundaries of the bounding box or primitive housing the grid. - Computational geometry description of a Wigner-Seitz cell grid in Euclidean space. + Computational geometry description of a grid of Wigner-Seitz cells in Euclidean space. - Frequently convenient three-dimensional grids with cubic cells are used. - Exemplar applications are spectral-solver based crystal plasticity - and stencil methods like phase-field or cellular automata. + Three-dimensional grids with cubic cells are if not the most frequently used + example of such grids. Numerical methods and models that use grids are used + in many cases in the natural sciences and engineering disciplines. Examples are + discretizations in space and time used for phase-field, cellular automata, or Monte Carlo + modeling. - - - - - - - - - + + + Location of the origin of the grid. + + Use the depends_on field that is inherited from the :ref:`NXcg_primitive` + class to specify the coordinate system in which the origin location is defined. + - + The symmetry of the lattice defining the shape of the unit cell. @@ -78,49 +78,23 @@ - + Number of unit cells along each of the d unit vectors. - The total number of cells, or grid points has to be the cardinality. + + The total number of cells or grid points has to be the cardinality. If the grid has an irregular number of grid positions in each direction, as it could be for instance the case of a grid where all grid points outside some masking primitive are removed, this extent field should - not be used. Instead use the coordinate field. + not be used. Instead, use the coordinate field. - - - Reference to or definition of a coordinate system with - which the positions and directions are interpretable. - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for cells. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish cells for explicit indexing. - - - - - - + Position of each cell in Euclidean space. @@ -139,26 +113,27 @@ should constraints on the grid be place here or not--> - + - A tight bounding box or sphere or bounding primitive about the grid. + A tight bounding box about the grid. - - + - How many distinct boundaries are distinguished? + Number of boundaries distinguished + Most grids discretize a cubic or cuboidal region. In this case six sides can be distinguished, each making an own boundary. - + - Name of domain boundaries of the simulation box/ROI e.g. left, right, - front, back, bottom, top. + Name of domain boundaries of the simulation box/ROI + e.g. left, right, front, back, bottom, top. - @@ -178,4 +153,25 @@ https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallele + + + Details about the computational geometry method and implementation + used for discretizing internal surfaces as e.g. obtained with marching methods, + like marching squares or marching cubes. + + Documenting which specific version was used helps with understanding how + robust the results are with respect to the topology of the triangulation. + Reference to the specific implementation of marching cubes used. + + See for example the following papers for details about how to identify a + DOI which specifies the implementation used: + + * `W. E. Lorensen <https://doi.org/10.1109/MCG.2020.2971284>`_ + * `T. S. Newman and H. Yi <https://doi.org/10.1016/j.cag.2006.07.021>`_ + + The value placed here should ideally be an identifier of a program. + If not possible, an identifier for a paper, technical report, or free-text + description can be used instead. + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_half_edge_data_structure.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_half_edge_data_structure.nxdl.xml new file mode 100644 index 0000000..91eb74b --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_half_edge_data_structure.nxdl.xml @@ -0,0 +1,195 @@ + + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality, which has to be at least 2. + + + + + The number of vertices. + + + + + The number of faces. + + + + + The number of half-edges. + + + + + Computational geometry description of a half-edge data structure. + + Such a data structure can be used to efficiently circulate around faces + and iterate over vertices of a planar graph. The data structure is also + known as a doubly connected edge list. + + Indices can be used as identifier and thus names for individual instances. + + + + Dimensionality of the primitives described. + + + + + + Number of vertices for each face. + + Each entry represents the total number of vertices for that face, + irrespectively whether vertices are shared among faces or not. + + + + + + + + Number of edges for each face. + + Each entry represents the total number of edges for that face, + irrespectively whether edges are shared across faces or not. + + + + + + + + Integer offset whereby the identifier of the first member + of the vertices differs from zero. + + Identifier can be defined explicitly or implicitly. + Inspect the definition of :ref:`NXcg_primitive` for further details. + + + + + Integer offset whereby the identifier of the first member + of the edges differs from zero. + + Identifier can be defined explicitly or implicitly. + Inspect the definition of :ref:`NXcg_primitive` for further details. + + + + + Integer offset whereby the identifier of the first member + of the faces differs from zero. + + Identifier can be defined explicitly or implicitly. + Inspect the definition of :ref:`NXcg_primitive` for further details. + + + + + + The position of the vertices. + + + + + + + + + Identifier of the incident half-edge. + + + + + + + + Identifier of the (starting)/associated half-edge of the face. + + + + + + + + The identifier of the vertex from which this half-edge is outwards pointing. + + + + + + + + Identifier of the associated oppositely pointing half-edge. + + + + + + + + If the half-edge is a boundary half-edge the + incident face identifier is NULL, i.e. 0. + + + + + + + + Identifier of the next half-edge. + + + + + + + + Identifier of the previous half-edge. + + + + + + + + Users are referred to the literature for the background of L. Weinberg's + work about topological characterization of planar graphs: + + * `L. Weinberg 1966a, <https://dx.doi.org/10.1109/TCT.1964.1082216>`_ + * `L. Weinberg, 1966b, <https://dx.doi.org/10.1137/0114062>`_ + * `E. A. Lazar et al. <https://doi.org/10.1103/PhysRevLett.109.095505>`_ + + and how this work can e.g. be applied in space-filling tessellations + of microstructural objects like crystals/grains. + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_hexahedron.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_hexahedron.nxdl.xml new file mode 100644 index 0000000..2684550 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_hexahedron.nxdl.xml @@ -0,0 +1,191 @@ + + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The cardinality of the set, i.e. the number of hexahedra. + + + + + Computational geometry description of a set of hexahedra in Euclidean space. + + This class can also be used to describe cuboids or cubes, axis-aligned or not. + The class represents different access and description levels to offer both + applied scientists and computational geometry experts an approach whereby + different specific views can be implemented using the same base class: + + * In the simplest case experimentalists may use this base class to describe + the dimensions or size of a specimen. In this case the alignment with axes + is not relevant as eventually only the volume of the specimen is of interest. + * In many cases, take for example an experiment where a specimen was cut out + from a specifically deformed piece of material, the orientation of the + specimen's edges with the experiment coordinate system is of high relevance. + Examples include knowledge about the specimen edge, whether it is + parallel to the rolling, the transverse, or the normal direction. + * While the above-mentioned use cases are sufficient to pinpoint the sample + within a known laboratory/experiment coordinate system, these descriptions + are not detailed enough to specify e.g. a CAD model of the specimen. + * Therefore, groups and fields for an additional, computational-geometry- + based view of hexahedra is offered to serve additional computational + tasks: storage-oriented simple views or detailed topological/graph-based + descriptions. + + Hexahedra are important geometrical primitives, which are among the most + frequently used elements in finite element meshing/modeling. + + As a specialization of the :ref:`NXcg_primitive` base class hexahedra + are assumed non-degenerated, closed, and built of polygons that are + not self-intersecting. + + The term hexahedra will be used throughout this base class but includes + the special cases cuboid, cube, box, axis-aligned bounding box (AABB), + and optimal bounding box (OBB). + + An axis-aligned bounding box is a common data object in computational science + and simulation codes to represent a cuboid whose edges are aligned with the + base vectors of a coordinate system. As a part of binary trees, these data + objects are important for making time- as well as space-efficient queries + of geometric primitives in techniques like kd-trees. + + An optimal bounding box is a common data object which provides the best + tightly fitting box about an arbitrary object. In general, such boxes are + rotated. Exact and substantially faster in practice approximate algorithms + exist to compute optimal or near optimal bounding boxes for sets of points. + + + + + Qualifier for the shape of each hexahedron. + + + + + + + + + Qualifier that is useful in cases when one edge is longer than all other + edges of the hexahedra. Often the term length is associated with the + assumption that one edge is parallel to an axis of the coordinate system. + + + + + + + + Qualifier often used to describe the extent of an object in the horizontal + direction assuming a specific coordinate system. + + For the sake of explicitness quantities like length, width, and height + should not be reported without specifying also the assumed reference frame. + + + + + + + + Qualifier often used to describe the extent of an object in the vertical + direction assuming a specific coordinate system. + + + + + + + + Volume of each hexahedron. + + + + + + + + Total (surface) area (of all six faces) of each hexahedron. + + + + + + + + Area of each of the six faces of each hexahedron. + + + + + + + + + Specifies if the hexahedra represent cuboids or cubes eventually rotated + ones but at least not too exotic six-faced polyhedra. + + + + + + + + Only to be used if is_box is present. In this case, this field describes + whether hexahedra are boxes whose primary edges are parallel to the + axes of the coordinate system. + + + + + + + + + + + + Combined storage of all primitives of all hexahedra. + + + + + Individual storage of each hexahedron. + + + + + Individual storage of each hexahedron as a graph. + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_parallelogram.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_parallelogram.nxdl.xml new file mode 100644 index 0000000..3a18f45 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_parallelogram.nxdl.xml @@ -0,0 +1,101 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The cardinality of the set, i.e. the number of parallelograms. + + + + + Computational geometry description of a set of parallelograms. + + This class can also be used to describe rectangles or squares, irrespective + whether these are axis-aligned or not. The class represents different + access and description levels to embrace applied scientists and computational + geometry experts with their different views: + + * The simplest case is the communication of dimensions aka the size of a + region of interest in the 2D plane. In this case, communicating the + alignment with axes is maybe not as relevant as it is to report the area + of the ROI. + * In other cases the extent of the parallelogram is relevant though. + * Finally, in CAD models it should be possible to specify the polygons + which the parallelograms represent with exact numerical details. + + Parallelograms are important geometrical primitives as their usage for + describing many scanning experiments shows where typically parallelogram-shaped + ROIs are scanned across the surface of a sample. + + The term parallelogram will be used throughout this base class thus including + the important special cases rectangle, square, 2D box, axis-aligned bounding box + (AABB), or optimal bounding box (OBB) as analogous 2D variants to their 3D + counterparts. See :ref:`NXcg_hexahedron` for the generalization in 3D. + + An axis-aligned bounding box is a common data object in computational science + and simulation codes to represent a rectangle whose edges are aligned with the + axes of a coordinate system. As a part of binary trees AABBs are important data + objects for executing time- as well as space-efficient queries + of geometric primitives in techniques like kd-trees. + + An optimal bounding box is a common data object which provides the best, i.e. + most tightly fitting box about an arbitrary object. In general such boxes are + rotated. Other than in 3D dimensions, the rotation caliper method offers + a rigorous approach to compute an optimal bounding box to a point set in 2D. + + + + + To specify which parallelogram is a rectangle. + + + + + + + + Only to be used if is_rectangle is present. In this case, this field + describes whether parallelograms are rectangles whose primary edges + are parallel to the axes of the coordinate system. + + + + + + + + + Combined storage of all parallelograms. + + + + + Individual storage of each parallelogram. + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_point.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_point.nxdl.xml new file mode 100644 index 0000000..169abbe --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_point.nxdl.xml @@ -0,0 +1,87 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality. + + + + + The cardinality of the set, i.e. the number of points. + + + + + Computational geometry description of a set of points. + + Points may have an associated time value. Users are advised though to store + time data of point sets rather as instances of time events, where for each + point in time there is an :ref:`NXcg_point` instance which specifies the + points' locations. + + This is a frequent situation in experiments and computer simulations, where + positions of points are taken at the same point in time (real time or + simulated physical time). Thereby, the storage of redundant timestamp + information per point is considered as obsolete. + + + + Coordinates of the points. + + + + + + + + + (Elapsed) time for each point. + + If the field time is needed contextualize the time_offset relative to which + time values are defined. Alternative store timestamp. + + + + + + + + ISO8601 with local time zone offset for each point. + + + + + + + + ISO8601 with local time zone offset that serves as the reference + for values in the field time. + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_polygon.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_polygon.nxdl.xml new file mode 100644 index 0000000..d20f4ae --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_polygon.nxdl.xml @@ -0,0 +1,126 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality, which has to be either 2 or 3. + + + + + The cardinality of the set, i.e. the number of polygons. + + + + + + The total number of vertices when visiting every polygon. + + + + + + Computational geometry description of a set of polygons in Euclidean space. + + Polygons are specialized polylines: + + * A polygon is a geometric primitive that is bounded by a closed polyline + * All vertices of this polyline lay in the d-1 dimensional plane. + whereas vertices of a polyline do not necessarily lay on a plane. + * A polygon has at least three vertices. + + Each polygon is built from a sequence of vertices (points with identifiers). + The members of a set of polygons may have a different number of vertices. + Sometimes a collection/set of polygons is referred to as a soup of polygons. + + As three-dimensional objects, a set of polygons can be used to define the + hull of what is effectively a polyhedron; however users are advised to use + the specific :ref:`NXcg_polyhedron` base class if they wish to describe closed + polyhedra. Even more general complexes can be thought of. An example are the + so-called piecewise-linear complexes used in the TetGen library. + + As these complexes can have holes though, polyhedra without holes are one + subclass of such complexes, users should rather design their own base class + e.g. NXcg_polytope to describe such even more complex primitives instead + of abusing this base class for such purposes. + + + + The total number of vertices in the set. + + + + + + Combined storage of all primitives of all polygons. + + + + + Individual storage of the mesh of each polygon. + + + + + Individual storage of each polygon as a graph. + + + + + + For each polygon its accumulated length along its edges. + + + + + + + + Interior angles for each polygon. There are as many values per polygon + as there are number_of_vertices. + The angle is the angle at the specific vertex, i.e. between the adjoining + edges of the vertex according to the sequence in the polygons array. + Usually, the winding_order field is required to interpret the value. + + + + + + + + Curvature type: + + * 0 - unspecified, + * 1 - convex, + * 2 - concave + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_polyhedron.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_polyhedron.nxdl.xml new file mode 100644 index 0000000..5e72d60 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_polyhedron.nxdl.xml @@ -0,0 +1,104 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The cardinality of the set, i.e. the number of polyhedra. + + + + + The total number of edges for all polyhedra. + + + + + The total number of faces for all polyhedra. + + + + + Computational geometry description of a set of polyhedra in Euclidean space. + + Polyhedra or so-called cells (especially in the convex of tessellations) are + constructed from polygon meshes. Polyhedra may make contact to allow a usage + of this base class for a description of tessellations. + + For the description of more complicated manifolds and especially for polyhedra + with holes, users are advised to check if their particular needs are described + by creating customized instances of an :ref:`NXcg_polygon`. + + + + + The number of faces for each polyhedron. Faces of adjoining polyhedra + are counted for each polyhedron. + + + + + + + + Area of each of faces. + + + + + + + + The number of edges for each polyhedron. Edges of adjoining polyhedra + are counted for each polyhedron. + + + + + Length of each edge. + + + + + + + + + Combined storage of all primitives of all polyhedra. + + + + + Individual storage of each polyhedron. + + + + + Individual storage of each polygon as a graph. + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_polyline.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_polyline.nxdl.xml new file mode 100644 index 0000000..f5e247c --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_polyline.nxdl.xml @@ -0,0 +1,140 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality, which has to be at least 1. + + + + + The cardinality of the set, i.e. the number of polylines. + + + + + + The number of vertices, supporting the polylines. + + + + + The total number of vertices traversed when visiting every polyline. + + + + + Computational geometry description of a set of polylines. + + Each polyline is built from a sequence of vertices (points with identifiers). + Each polyline must have a start and an end point. + The sequence describes the traversal along the polyline when + walking from the first to the last vertex. + + + + Reference to an instance of :ref:`NXcg_point` which defines the + location of the vertices that are referred to in this + NXcg_polyline instance. + + + + + The total number of vertices that have different positions. + + + + + The total number of vertices, irrespective of their eventual uniqueness. + + + + + The total number of vertices of each polyline, irrespectively + whether vertices are shared by vertices or not. + + + + + + + + + Positions of the vertices which support the members of the polyline set. + + Users are encouraged to reduce the vertices to unique positions and vertices + as this often supports with storing geometry data more efficiently. + It is also possible though to store the vertex positions naively + in which case vertices_are_unique is likely False. + Naively, here means that one stores each vertex of a triangle mesh + even though many vertices are shared between triangles and thus + storing multiple copies of their positions is redundant. + + + + + + + + + If true indicates that the vertices are all placed at different + positions and have different identifiers, i.e. no points overlap + or are counted several times. + + + + + Sequence of identifier for vertices how they build each polyline. + + A trivial example is a set with two polylines with three vertices each. + If the polylines meet at a vertex (assume for example that the second vertex + is shared and marking the junction between the two polylines), it is possible + that there are only five unique positions. This suggests to store five + unique vertices. + + A non-trivial example is a set with several polylines. Assume that each + has a different number of vertices. The array stores the identifier of + the vertices in the sequence how the polylines are visited: + + The first entry is the identifier of the first vertex of the first polyline, + followed by the second vertex of the first polyline, until the last vertex + of the first polyline. + Thereafter, the first vertex of the second polyline, and so on and so forth. + Using the (cumulated) counts in number_of_vertices (:math:`n^v_i`), + the vertices of the N-th polyline can be accessed on the array + index interval :math:`[\sum_{i=0}^{i=N-1} n^v_i, \sum_{i=0}^{i=N} n^v_i]`. + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_primitive.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_primitive.nxdl.xml new file mode 100644 index 0000000..eb5b01f --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_primitive.nxdl.xml @@ -0,0 +1,247 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality of the embedding space. + + + + + The cardinality of the set, i.e. the number of members. + + + + + Computational geometry description of a set of primitives in Euclidean space. + + Primitives must neither be degenerated nor self-intersect. + Individual primitives can differ in their properties (e.g. size, shape, rotation). + + + + Reference to an instance of :ref:`NXcoordinate_system` in which these primitives + are defined. + + + + + The dimensionality of the primitive set with value up to d. + + + + + + + + + + + The cardinality of the primitive set. Value should be equal to c. + + + + + Integer offset whereby the identifier of the first member + of the set differs from zero. + + Indices can be used as identifiers and thus names of instances. + + Identifiers can be defined either implicitly or explicitly. + For implicit indexing identifiers are defined on the interval + :math:`[index\_offset, index\_offset + c - 1]`. + + Therefore, implicit identifier are completely defined by the value of + index_offset and cardinality. For example if identifier run from + -2 to 3 the value for index_offset is -2. + + For explicit indexing the field identifier has to be used. + Fortran-/Matlab- and C-/Python-style indexing have specific implicit + identifier conventions where index_offset is 1 and 0 respectively. + + + + + Identifier of each member for explicit indexing. + + + + + + + + The center of each primitive + + + + + + + + + True if the center is a center of mass. + + + + + + + + Shape of each primitive + + + + + + + + + Length of each primitive + + Often the term is associated with the assumption that one + edge is parallel to an axis of the coordinate system. + + + + + + + + Width of each primitive + + Often the term is associated with the assumption that one + edge is parallel to an axis of the coordinate system. + + + + + + + + Height of each primitive + + Often the term is associated with the assumption that one + edge is parallel to an axis of the coordinate system. + + + + + + + + True if primitive is closed such that it has properties like area or volume. + + + + + + + + Volume of each primitive. + + Set to NaN if does not apply for primitives for which is_closed is False. + Volume is an N-D concept for values of dimensionality larger than 1, + Area is an alias for the two-dimensional case. + + + + + + + + Alias for surface_area of each primitive. + + Set to NaN if does not apply for primitives for which is_closed is False. + + + + + + + + Direction unit vector which points along the + longest principal axis of each primitive. + + Use the depends_on attribute to specify in which coordinate system + these direction unit vectors are defined. + + + + + + + + + Do the primitives define a mesh. + + + + + Do the primitives define a triangle mesh or not. + + + + + Do the primitives discretize the surface of an object or not. + + + + + Do the primitives define a geodesic mesh or not. + + A geodesic surface mesh is a triangulated surface mesh with metadata which + can be used as an approximation to describe the surface of a sphere. + Triangulation of spheres are commonly used in Materials Science + for quantifying texture of materials, i.e. the relative rotation of + crystals to sample directions. + + For additional details or an introduction into the topic of geodesic meshes + see (from which specifically the section on subdivision schemes is relevant). + + * `E. S. Popko and C. J. Kitrick <https://doi.org/10.1201/9781003134114>`_ + + Earth scientists have specific demands and different views about what should + be included in such a base class, given that nested geodesic meshes are a key + component of climate modelling software. For now we propose to use this + base class as a container for organizing data related to geodesic meshes. + + Specifically an instance of this base class should detail the rule set how + e.g. a geodesic (surface) mesh was instantiated as there are many + possibilities to do so. + + + + + Possibility to store details such as when primitives form a (specific) type + of mesh such as geodesic meshes. + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXcs_cpu.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_roi.nxdl.xml similarity index 53% rename from src/nexusformat/definitions/contributed_definitions/NXcs_cpu.nxdl.xml rename to src/nexusformat/definitions/base_classes/NXcg_roi.nxdl.xml index b27b874..329c767 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXcs_cpu.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXcg_roi.nxdl.xml @@ -2,9 +2,9 @@ - + + - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays. + Use :ref:`NXcg_primitive` and :ref:`NXcoordinate_system` classes to + define explicitly the reference frame in which the primitives are + defined. - Computer science description of a central processing unit (CPU) of a computer. + Base class for a region-of-interest (ROI) bound by geometric primitives. + + So-called region-of-interest(s) (ROIs) are typically used to describe a + region in space (and time) where an observation is made or for which + a computer simulation is performed with given boundary conditions. - - - Given name of the CPU. Users should be as specific as possible. - - - + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_tetrahedron.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_tetrahedron.nxdl.xml new file mode 100644 index 0000000..95bf4e0 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_tetrahedron.nxdl.xml @@ -0,0 +1,76 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The cardinality of the set, i.e. the number of tetrahedra. + + + + + Computational geometry description of a set of tetrahedra. + + Among hexahedral elements, tetrahedral elements are one of the most + frequently used geometric primitive for meshing and describing volumetric + objects in continuum-field simulations. + + + + + Area of each of the four triangular faces of each tetrahedron. + + + + + + + + + Length of each edge of each tetrahedron. + + + + + + + + + Combined storage of all primitives of all tetrahedra. + + + + + Individual storage of each tetrahedron. + + + + + Individual storage of each tetrahedron as a graph. + + + diff --git a/src/nexusformat/definitions/base_classes/NXcg_triangle.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_triangle.nxdl.xml new file mode 100644 index 0000000..d6c9145 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXcg_triangle.nxdl.xml @@ -0,0 +1,92 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality, which has to be at least 2. + + + + + The cardinality of the set, i.e. the number of triangles. + + + + + The number of unique vertices supporting the triangles. + + + + + Computational geometry description of a set of triangles. + + + + Number of unique vertices in the triangle set. + + + + + Combined storage of all primitives of all triangles. + + This description resembles the typical representation of primitives + in file formats such as OFF, PLY, VTK, or STL. + + + + + Individual storage of each triangle. + Users are advised that using such individual storage of primitives + may be less storage efficient than creating a combined storage. + + + + + Length of the edges of each triangle. + + For each triangle values are reported via traversing + the vertices in the sequence as these are defined. + + + + + + + + + Interior angles of each triangle. + + For each triangle values are reported for the angle opposite + to the respective edges in the sequence how vertices are defined. + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_unit_normal_set.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcg_unit_normal.nxdl.xml similarity index 68% rename from src/nexusformat/definitions/contributed_definitions/NXcg_unit_normal_set.nxdl.xml rename to src/nexusformat/definitions/base_classes/NXcg_unit_normal.nxdl.xml index 68f9c84..5eaacd9 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_unit_normal_set.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXcg_unit_normal.nxdl.xml @@ -2,9 +2,9 @@ - - + + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -42,12 +44,14 @@ rather make this a set of vectors, irrespective whether these are unit or not--> Computational geometry description of a set of (oriented) unit normal vectors. + + Store normal vector information as properties of primitives. + Use only only as a child of an instance of :ref:`NXcg_primitive` + so that this instance acts as the parent to define a context. - - - + - Direction of each normal + Direction of each normal - a unit normal. @@ -56,12 +60,13 @@ rather make this a set of vectors, irrespective whether these are unit or not--> - Qualifier how which specifically oriented normal to its primitive each - normal represents. + An indicator which details the orientation of each normal vector + in relation to its primitive, assuming the object is viewed + from a position outside the object. * 0 - undefined - * 1 - outer - * 2 - inner + * 1 - outer unit normal vector + * 2 - inner unit normal vector diff --git a/src/nexusformat/definitions/base_classes/NXcollectioncolumn.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcollectioncolumn.nxdl.xml index 97d2aef..02fb82a 100644 --- a/src/nexusformat/definitions/base_classes/NXcollectioncolumn.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXcollectioncolumn.nxdl.xml @@ -91,7 +91,7 @@ Deflectors in the collection column section - + Individual lenses in the collection column section diff --git a/src/nexusformat/definitions/base_classes/NXcomponent.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcomponent.nxdl.xml index 2c36f9a..c01336f 100644 --- a/src/nexusformat/definitions/base_classes/NXcomponent.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXcomponent.nxdl.xml @@ -3,7 +3,7 @@ + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of images taken, at least one. + + + + + Base class for a corrector reducing (spherical) aberrations of an electron optical setup. + + Different technology partners use different conventions and + models for quantifying the aberration coefficients. + + Aberration correction components are especially important for (scanning) + transmission electron microscopy. Composed of multiple lenses and multipole stigmators, + their technical details are specific for the technology partner as well as + the microscope and instrument. Most technical details are proprietary knowledge. + + If one component corrects for multiple types of aberrations (like it is the case + reported here `CEOS <https://www.ceos-gmbh.de/en/research/electrostat>`_) follow this + design when using corrector and monochromator in an application definition: + + * Use :ref:`NXcorrector_cs` for spherical aberration + * Use :ref:`NXmonochromator` for energy filtering or chromatic aberration + * Use the group corrector_ax in :ref:`NXem` for axial astigmatism aberration + + Although this base class currently provides concepts that are foremost used in + the field of electron microscopy using this base class is not restricted to this + research field. NXcorrector_cs can also serve as a container to detail, in + combination with :ref:`NXaberration`, about measured aberrations in classical optics. + In optics, though, the difference is that the design of the :ref:NXoptical_lens` + itself (e.g., using aspheric lenses or combinations of lenses) enables to + reduce spherical aberrations. + + + + + Was the corrector used? + + + + + Specific information about the alignment procedure. This is a process during which + the corrector is configured to enable calibrated usage of the instrument. + + This :ref:`NXprocess` group should also be used when one describes in a computer + simulation the specific details about the modeled or assumed aberrations. + + + + Discouraged free-text field to add further details about the alignment + procedure. + + + + + The outer tilt angle of the beam in tableau acquisition. + + TODO: The relevant axes which span the tilt_angle need a + cleaner description. Suggestions from the community are + welcome here for guiding an improvement of this base class. + + + + + + + + The exposure time of single tilt images. + + + + + + + + The factor of enlargement of the apparent size, + not the physical size, of an object. + + + + + + + + Image(s) taken during the alignment procedure + + + + + Convention used for storing measured or estimated aberrations (for each or the final image) + via fields c_1, a_1, c_1_0, c_1_2_a, and so on and so forth. + + See `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) + for different definitions available and further details. Table 7-2 of Ibid. publication (page 305ff) documents how + to convert from the Nion to the CEOS definitions. Conversion tables are also summarized by `Y. Liao <https://www.globalsino.com/EM/page3740.html>`_. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXcs_profiling.nxdl.xml b/src/nexusformat/definitions/base_classes/NXcs_profiling.nxdl.xml index 7905c13..2d56301 100644 --- a/src/nexusformat/definitions/base_classes/NXcs_profiling.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXcs_profiling.nxdl.xml @@ -41,7 +41,8 @@ information across a network and these are used usually by multiple users. At the most basic level users may wish to document how long e.g. a data - analysis with a scientific software i.e. an app took. + analysis with a scientific software, i.e. an app took. + A frequent idea is here to answer practical questions like how critical is the effect on the workflow of the scientists, i.e. is the analysis possible in a few seconds or would it take days if I were to run this analysis on a @@ -127,10 +128,6 @@ The number of nominal GPUs that the app invoked at runtime. - A collection with one or more computing nodes each with own resources. @@ -145,6 +142,4 @@ complicated models should be captured.--> ID is an increasing unsigned integer starting at 1. - diff --git a/src/nexusformat/definitions/base_classes/NXdata.nxdl.xml b/src/nexusformat/definitions/base_classes/NXdata.nxdl.xml index 991adf0..56d6206 100644 --- a/src/nexusformat/definitions/base_classes/NXdata.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXdata.nxdl.xml @@ -494,7 +494,7 @@ data. The units must be appropriate for the measurement. This is a special case of a :ref:`AXISNAME field </NXdata/AXISNAME-field>` - kept for backward compatiblity. + kept for backward compatibility. @@ -506,7 +506,7 @@ data. The units must be appropriate for the measurement. This is a special case of a :ref:`AXISNAME field </NXdata/AXISNAME-field>` - kept for backward compatiblity. + kept for backward compatibility. @@ -518,7 +518,7 @@ data. The units must be appropriate for the measurement. This is a special case of a :ref:`AXISNAME field </NXdata/AXISNAME-field>` - kept for backward compatiblity. + kept for backward compatibility. diff --git a/src/nexusformat/definitions/base_classes/NXdetector.nxdl.xml b/src/nexusformat/definitions/base_classes/NXdetector.nxdl.xml index f55c702..d00b3d3 100644 --- a/src/nexusformat/definitions/base_classes/NXdetector.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXdetector.nxdl.xml @@ -26,8 +26,6 @@ xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd" xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xmlns:xs="http://www.w3.org/2001/XMLSchema" - xmlns:ns="http://definition.nexusformat.org/nxdl/@NXDL_RELEASE@" > @@ -715,7 +713,7 @@ This field allow to distinguish different types of exposure to the same detector "data" field. - Some techniques require frequent (re-)calibration inbetween measuremnts and this way of + Some techniques require frequent (re-)calibration inbetween measurements and this way of recording the different measurements preserves the chronological order with is important for correct processing. diff --git a/src/nexusformat/definitions/base_classes/NXdetector_channel.nxdl.xml b/src/nexusformat/definitions/base_classes/NXdetector_channel.nxdl.xml index 2ca7c68..d4ecd18 100644 --- a/src/nexusformat/definitions/base_classes/NXdetector_channel.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXdetector_channel.nxdl.xml @@ -26,8 +26,6 @@ xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd" xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xmlns:xs="http://www.w3.org/2001/XMLSchema" - xmlns:ns="http://definition.nexusformat.org/nxdl/@NXDL_RELEASE@" > diff --git a/src/nexusformat/definitions/base_classes/NXebeam_column.nxdl.xml b/src/nexusformat/definitions/base_classes/NXebeam_column.nxdl.xml new file mode 100644 index 0000000..36612f8 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXebeam_column.nxdl.xml @@ -0,0 +1,239 @@ + + + + + + Base class for a set of components providing a controllable electron beam. + + The idea behind defining :ref:`NXebeam_column` as an own base class vs. adding these + concepts in :ref:`NXem_instrument` is that the electron beam generating component + might be worthwhile to use also in other types of experiments. + + + + Tech-partner, microscope-, and control-software-specific name of the + specific operation mode how the ebeam_column and its components are + controlled to achieve specific illumination conditions. + + In many cases the users of an instrument do not or can not be expected to know + all intricate spatiotemporal dynamics of their hardware. Instead, they rely on + assumptions that the instrument, its control software, and components work as + expected to focus on their research questions. + + For these cases, having a place for documenting the operation_mode is useful + in as much as at least some constraints on how the illumination conditions were + is documented. + + + + + A physical part of an electron or ion microscope from which + the particles that form the beam are emitted. + + The hardware for an electron source in an electron microscope + may contain several components which affect the beam path. + + This concept is related to term `Source`_ of the EMglossary standard. + + .. _Source: https://purls.helmholtz-metadaten.de/emg/EMG_00000045 + + + + The potential difference between anode and cathode. + + This concept is related to term `Acceleration Voltage`_ of the EMglossary standard. + + .. _Acceleration Voltage: https://purls.helmholtz-metadaten.de/emg/EMG_00000004 + + + + + Voltage which is used to create an electric field that draws particles from + the source. + + This concept is related to term `Extraction Voltage`_ of the EMglossary standard. + + .. _Extraction Voltage: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 + + + + + Electrical current which is released from the source. + + This concept is related to term `Emission Current`_ of the EMglossary standard. + + .. _Emission Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 + + + + + Electrical current which flows through the source. + + This concept is related to term `Filament Current`_ of the EMglossary standard. + + .. _Filament Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000027 + + + + + Type of radiation. + + + + + + + + Emitter type used to create the beam. + + If the emitter type is other, give further details + in the description field. + + + + + + Material of which the emitter is build, e.g. the filament material. + + + + + + How long has the source been in operation. + + + + + + + + + A component for blanking the beam or generating pulsed electron beams. + See e.g . `I. G. C. Weppelman et al. <https://doi.org/10.1016/j.ultramic.2017.10.002>`_ + or `Y. Liao <https://www.globalsino.com/EM/page2464.html>`_ for details. + + + + + Device to improve energy resolution or chromatic aberration. + + Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector + like <https://www.ceos-gmbh.de/en/basics/cc-corrector>`_ + + + + + Qualitative type of the component. + + + + + + + + + + + + + + Was the corrector used? + + + + + + Energy dispersion in e.g. µm/eV. + + + + + Corresponding voltage for that energy dispersion. + + + + + + + Component that reshapes an ellipse-shaped electron beam into a circular one. + + * `L. Reimer 1998, Springer, 1998 <https://dx.doi.org/10.1007/978-3-540-3896>`_ + * `M. Tanaka et al., Electron Microscopy Glossary, 2024 <https://www.jeol.com/words/semterms/20201020.111014.php#gsc.tab=0>`_ + + Stigmator is an exact synonym. + + + + Descriptor for the correction strength along the first direction when exact technical details + are unknown or not directly controllable as the control software of the microscope does not + enable or was not configured to display these values for users. + + + + + Descriptor for the correction strength along the second direction when exact technical details + are unknown or not directly controllable as the control software of the microscope does not + enable or was not configured to display these values for users. + + + + + + Electron biprism as it is used e.g. for electron holography. + + + + + Device that causes a change in the phase of an electron wave. + + * `M. Malac et al. <https://doi.org/10.1093/jmicro/dfaa070>`_ + * `R. R. Schröder et al. <https://www.lem.kit.edu/152.php>`_ + + + + Qualitative type + + + + + + + + + + + + Individual characterization results for the position, shape, + and characteristics of the electron beam at a given location. + + :ref:`NXtransformations` should be used to specify the location + or the position at which details about the beam were probed. + + This concept is related to term `Electron Beam`_ of the EMglossary standard. + + .. _Electron Beam: https://purls.helmholtz-metadaten.de/emg/EMG_00000021 + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXlens_em.nxdl.xml b/src/nexusformat/definitions/base_classes/NXelectromagnetic_lens.nxdl.xml similarity index 95% rename from src/nexusformat/definitions/base_classes/NXlens_em.nxdl.xml rename to src/nexusformat/definitions/base_classes/NXelectromagnetic_lens.nxdl.xml index 340b92c..a13375c 100644 --- a/src/nexusformat/definitions/base_classes/NXlens_em.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXelectromagnetic_lens.nxdl.xml @@ -21,12 +21,12 @@ # # For further information, see http://www.nexusformat.org --> - + Base class for an electro-magnetic lens or a compound lens. For :ref:`NXtransformations` the origin of the coordinate system is placed - in the center of the lens its polepiece, pinhole, or another point of reference. + in the center of the lens its pole piece, pinhole, or another point of reference. The origin should be specified in the :ref:`NXtransformations`. For details of electro-magnetic lenses in the literature see e.g. diff --git a/src/nexusformat/definitions/base_classes/NXelectron_detector.nxdl.xml b/src/nexusformat/definitions/base_classes/NXelectron_detector.nxdl.xml index 2f8f629..a82603c 100644 --- a/src/nexusformat/definitions/base_classes/NXelectron_detector.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXelectron_detector.nxdl.xml @@ -26,8 +26,6 @@ xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd" xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xmlns:xs="http://www.w3.org/2001/XMLSchema" - xmlns:ns="http://definition.nexusformat.org/nxdl/@NXDL_RELEASE@" > A subclass of NXdetector for detectors that detect electrons. diff --git a/src/nexusformat/definitions/base_classes/NXelectronanalyzer.nxdl.xml b/src/nexusformat/definitions/base_classes/NXelectronanalyzer.nxdl.xml index 6d0d4b6..1d990fe 100644 --- a/src/nexusformat/definitions/base_classes/NXelectronanalyzer.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXelectronanalyzer.nxdl.xml @@ -272,7 +272,7 @@ Deflectors outside the main optics ensembles described by the subclasses - + Individual lenses outside the main optics ensembles described by the subclasses diff --git a/src/nexusformat/definitions/base_classes/NXem_ebsd.nxdl.xml b/src/nexusformat/definitions/base_classes/NXem_ebsd.nxdl.xml new file mode 100644 index 0000000..7b01786 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXem_ebsd.nxdl.xml @@ -0,0 +1,685 @@ + + + + + + + + Number of arguments per orientation for given parameterization. + + + + + Number of scan points. + + + + + Number of pixel along the slowest changing dimension for a rediscretized, + i.e. standardized default plot orientation mapping. + + + + + Number of pixel along slow changing dimension for a rediscretized i.e. + standardized default plot orientation mapping. + + + + + Number of pixel along fast changing dimension for a rediscretized i.e. + standardized default plot orientation mapping. + + + + + Number of phase solutions + + + + + Number of reflectors (Miller crystallographic plane triplets). + + + + + Base class method-specific for Electron Backscatter Diffraction (EBSD). + + The general procedure of an EBSD experiment is as follows: + Users load the specimen, collect first a coarse image of the surface. + Next, they set an approximate value for the calibrated working distance + and tilt the stage into diffraction conditions. + + Users then typically configure the microscope for collecting quality data. + The EBSD detector is pushed in (if retractable). Subsequently, they fine tune + the illumination and aberration corrector settings and select one or multiple ROIs + for the microscope to machine off automatically. They configure on-the-fly + indexing parameter and then typically start the measurement queue. + From this point onwards typically the microscope runs automatically. + + Diffraction pattern get collected until the queue finishes or gets interrupted by + either errors or arrival at the end of the users' allocated time slot at the instrument. + + Kikuchi pattern (EBSP) are usually indexed on-the-fly. These patterns are the raw data. + Once indexed, these patterns are often not stored. + + Results are stored in files, which afterwards are typically copied + automatically or manually for archival purposes to certain storage + locations for further consumption. The result of such an EBSD + measurement/experiment is a set of usually proprietary or open files + from technology partners. + + This :ref:`NXem_ebsd` base class is a proposal how to represent method-specific + data, metadata, and connections between these for the research field of + electron microscopy exemplified here for electron backscatter diffraction (EBSD). + The base class solves two key documentation issues within the EBSD community: + + Firstly, an instance of NXem_ebsd (such as a NeXus/HDF5 file that is formatted + according to NXem_ebsd) stores the connection between the microscope session and + the key datasets which are considered typically results of the afore-mentioned + steps involved in an EBSD experiment. + + Different groups in NXem_ebsd make connections to data artifacts which were collected + when working with electron microscopes via the NXem application definition. + Using a file which stores information according to the NXem application definition + has the benefit that it connects the sample, references to the sample processing, + the user operating the microscope, details about the microscope session, + and details about the acquisition and eventual indexing of Kikuchi patterns, + associated overview images, like secondary electron or backscattered electron + images of the region-of-interest probed, and many more (meta)data. + + Secondly, NXem_ebsd connects and stores the conventions and reference frames + which were used and which are the key to a correct mathematical interpretation + of every experiment or simulation using EBSD. + + Otherwise, results would be ripped out of their context like it is the current situation + with many traditional studies where EBSD data were indexed on-the-fly and shared + with the community only via sharing the strongly processed files with results in some + formatting but without communicating all conventions used or just relying on the assumptions + that colleagues likely know these conventions even though + multiple definitions are possible. + + NXem_ebsd covers experiments with one-, two-dimensional, and so-called three- + dimensional EBSD datasets. The third dimension is either time (in the case of + quasi in-situ experiments) or space (in the case of serial-sectioning) experiments + where a combination of repetitive removal of material from the surface layer to measure + otherwise the same region-of-interest at different depth increments. Material removal + can be achieved with mechanical, electron, or ion polishing, using manual steps or + automated equipment like a robot system `S. Tsai et al. <https://doi.org/10.1063/5.0087945>`_. + + Three-dimensional experiments require to follow a sequence of specimen, surface + preparation, and data collection steps. By virtue of design, these methods are destructive + either because of the necessary material removal or surface degradation due to e.g. + contamination or other electron-matter interaction. + + For three-dimensional EBSD, multiple two-dimensional EBSD orientation mappings + are combined into one reconstructed stack via a computational workflow. Users collect + data for each serial sectioning step via an experiment. This assures that data for associated + microscope sessions and steps of data processing stay contextualized and connected. + + Eventual tomography methods also use such a workflow because first diffraction + images are collected (e.g. with X-ray) and then these images are indexed to process + a 3D orientation mapping. Therefore, the here proposed base class can be a blueprint + also for future classes to embrace our colleagues from X-ray-based techniques be it 3DXRD or HEDM. + + This concept is related to term `Electron Backscatter Diffraction`_ of the EMglossary standard. + + .. _Electron Backscatter Diffraction: https://purls.helmholtz-metadaten.de/emg/EMG_00000019 + + + + Details about the gnomonic (projection) reference frame. + + It is assumed that the configuration is inspected by looking towards the sample surface. + If a detector is involved, it is assumed that the configuration is inspected from a position + that is located behind this detector. + + If any of these assumptions are not met, the user is required to explicitly state this. + + Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the + base vectors of this coordinate system as :math:`X_g, Y_g, Z_g`. + + + + Origin of the gnomonic_reference_frame. + + Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to + assume that this is coordinate :math:`Xg = 0, Yg = 0, Zg = 0`. + + + + + + + + Direction of the positively pointing x-axis base vector of the + gnomonic_reference_frame. + + + + + + + + + + + + + Direction of the positively pointing y-axis base vector of the + gnomonic_reference_frame. + + + + + + + + + + + + + Direction of the positively pointing z-axis base vector of the + gnomonic_reference_frame. + + + + + + + + + + + + + + Details about the definition of the pattern center as a special point in the + gnomonic_reference_frame. + + Typically the gnomonic space is embedded in the detector space. + Specifically, the XgYg plane is defined such that it is laying inside the + XdYd plane (of the detector reference frame). + + When the normalization direction is the same as e.g. the detector x-axis direction + one effectively normalizes in fractions of the width of the detector. + + The issue with terms like width and height, though, is that these become degenerated + if the detector region-of-interest is square-shaped. This is why instead of referring to + width and height it is better to state explicitly which direction is considered positive + when measuring distances. + + For the concepts used to specify the boundary_convention it is assumed that the + region-of-interest is defined by a rectangle, referring to the direction of outer-unit + normals to the respective edges of this rectangle. + + + + From which border of the EBSP (in the detector reference frame) is the pattern + center's x-position (PCx) measured. + + + + + + + + + + + In which direction are positive values for the x-axis coordinate value measured + from the specified boundary. + + + + + + + + + + + From which border of the EBSP (in the detector reference frame) is the pattern + center's y-position (PCy) measured. + + + + + + + + + + + In which direction are positive values for the y-axis coordinate value measured + from the specified boundary. + + + + + + + + + + + + This group documents relevant details about the conditions and the + tools for measuring diffraction patterns with an electron microscope. + + The most frequently collected EBSD data are captured for rectangular + regions-of-interest using a discretization into square or hexagon tiles. + + + + Physical time since the beginning of a timestamp that is required to be + the same for all experiments in the set. The purpose of this marker is + to identify how all experiments in the set need to be arranged + sequentially based on the time elapsed. + The time is relevant to sort e.g. experiments of consecutive quasi + in-situ experiments where a measurement was e.g. taken after 0 minutes, + 30 minutes, 6 hours, or 24 hours of annealing. + + + + Timestamp relative to which time was counted to aid + converting between time and timestamp. + + + + + + Path to an instance of :ref:`NXdata` where the measured patterns are stored. + + + + + Reference (e.g. path and filename) to an existent data artifact which + stores either the measured patterns or input (already processed EBSD data). + + + + + + This group documents relevant details about the conditions and the tools + used for simulating diffraction patterns with some physical model. + + This group should be used if (e.g. instead of a measurement) the patterns + were simulated (possibly awaiting indexing). + + In many practical cases where patterns are analyzed on-the-fly and dictionary + indexing strategies used, so-called master pattern(s) are used to compare + measured or simulated patterns with the master patterns. + + + + Path to an instance of :ref:`NXimage` where the simulated patterns are stored. + + + + + Reference (e.g. path and filename) to an existent digital resource which + stores either the patterns or input (already processed EBSD data) that are + about to become processed further as described by this NXem_ebsd instance. + + + + + + The EBSD system, including components like the electron gun, pole-piece, + stage tilt, EBSD detector, and the gnomonic projection have to be + calibrated to achieve reliable, precise, and accurate scientific results. + + Specifically, the gnomonic projection has to be calibrated. + Typically, standard specimens made from silicon or quartz crystals + in specific orientations are used for this purpose. + + Considering that a system used is already calibrated well-enough is much + more frequently the case in practice than that users perform the calibration + themselves (with above-mentioned standard specimens). + + In the first case, the user assumes that the principle geometry of the + hardware components and the settings in the control and EBSD pattern + acquisition software has been calibrated already. Consequently, users pick from + an existent library of phase candidates, i.e. :ref:`NXunit_cell` instances. + Examples are reflector models as stored in CRY files (HKL/Channel 5/Flamenco). + + In the second case, users calibrate the system during the session + using standards (silicon, quartz, or other common specimens). + There is usually one person in each lab responsible for doing such + calibrations. Often this person or technician is also in charge of + configuring the graphical user interface and software with which most + users control and perform their analyses. + + For EBSD this has key implications: Taking TSL OIM/EDAX as an example, + the conventions how orientations are stored is affected by how the + reference frames are configured and how this setup in the GUI. + + Unfortunately, these pieces of information are not necessarily stored + in the results files. In effect, key conventions become disconnected + from the data so it remains the users' obligation to remember these + settings or write these down in a lab notebook. Otherwise, these metadata + get lost. All these issues are a motivation and problem which :ref:`NXem_ebsd` + solves in that all conventions can be specified explicitly. + + + + Path to an instance of :ref:`NXem` where calibration data are stored. + + + + + Reference to a digital resource where the calibration is stored. + + + + + + Indexing is a data processing step performed either after or while (aka on-the-fly) + the beam scans the specimen. The resulting method is also + known as orientation imaging microscopy (OIM). + + Different algorithms can be used to index EBSP. Common to them is the + computational step where simulated or theoretically assumed patterns + are compared with the measured ones. These latter patterns are referred + to via the measurement or simulation groups of this base class respectively. + + Quality descriptors are defined based on which an indexing algorithm + yields a quantitative measure of how similar measured and reference + patterns are, and thus if no, one, or multiple so-called solutions were found. + + Assumed or simulated patterns are simulated using kinematical or dynamical + theory of electron diffraction delivering master patterns. + + The Hough transform, one of the most frequently used traditional method for indexing + EBSP is essentially a discretized Radon transform (for details see `M. van Ginkel et al. <https://www.semanticscholar.org/paper/A-short-introduction-to-the-Radon-and-Hough-and-how-Ginkel/fb6226f606cad489a15e38ed961c419037ccc858>`_). Recently, dictionary-based and artificial intelligence-based methods + find more widespread usage for indexing. + + + + This group enables to establish a logical connection between previous + processing steps or on-the-fly-performed indexing of the EBSD map. + Typically these processing steps are performed with commercial software. + Therefore, in many cases a results file from this indexing is often + all that is communicated and saved. These are typically files in a format + specific to the instrument and its configuration. + + Typical file formats are CPR/CRC, ANG, OSC, HDF5, H5EBSD, EDAXH5. + + + + + Principal algorithm used for indexing. + + + + + + + + + + Details about the background correction applied to each Kikuchi pattern. + + + + + Binning i.e. downsampling to each pattern. + + + + + Specific parameter relevant only for certain algorithms used. + + + + + Details for each phase used as a model with which the patterns were + indexed. Instances of :ref:`NXunit_cell` in this group must + have the group name prefixed with phase. The identifier in the name is an + integer. Start counting from 1 because the value 0 is reserved for + the special phase that is the null-model, the null phase also known + as notIndexed. + + + + Spacing between the crystallographic planes that are defined via ``miller``. + + + + + + + + Relative intensity for the computed diffraction intensity (signal) for the + plane. + + + + + + + + In case the :ref:`NXunit_cell` base class is used with analyzed orientation maps + this field stores how many scan points of the map were identified as matching best + with this phase. + + + + + How many reflectors for crystallographic planes are distinguished. + + + + + Miller indices :math:`(hkl)[uvw]` of the planes. + + The first triplet specifies :math:`(hkl)`. The second triplet specifies :math:`[uvw]`. + Miller indices refer to the Cartesian right-handed coordinate system of the unit cell. + + + + + + + + + + Which return value did the indexing algorithm yield for each scan point. + + * 0 - Not analyzed + * 1 - Too high angular deviation + * 2 - No solution + * 100 - Success + * 255 - Unexpected errors + + + + + + + + How many phases i.e. crystal structure models were used to index each + scan point if any? Let's assume an example to explain how this field + should be used: In the simplest case users collected one pattern for + each scan point and have indexed using one phase, i.e. one instance + of an :ref:`NXunit_cell`. + + In another example users may have skipped some scan points (not indexed + them at all) or used differing numbers of phases for indexing different scan points. + + The cumulated of this array decodes how phase_id and matching_phase + arrays have to be interpreted. In the simplest case (one pattern per scan + point, and all scan points indexed using that same single phase model), + phase_id has as many entries as scan points + and matching_phase has also as many entries as scan points. + + + + + + + + The array phases_per_scan_point details how the phase_id + and the matching_phase arrays have to be interpreted. + + For the example of a single-phase material phase_id has trivial + values either 0 (no solution) or 1 (solution matching + sufficiently significant with the model for phase1, an instance of :ref:`NXphase`). + + For the example of multi-phase material, it is possible (although not frequently + required) that a pattern agrees significantly with multiple patterns. Examples are + cases of pseudosymmetry, insufficiently precise and accurate calibrated systems, + or usage of inaccurate phase models. Having such field is especially relevant + for recent dictionary- or artificial intelligence-based indexing methods to communicate + the results in a model-agnostic way in combination with matching_phase. + + Depending on the phases_per_scan_point value, phase_id and + matching_phase arrays represent a collection of concatenated tuples. + These are organized in sequence: The solutions for the 0-th scan point, + the 1-th scan point, the n_sc - 1 th scan point and omitting tuples + for those scan points with no phases according to phases_per_scan_point. + + + + + + + + One-dimensional array, pattern-by-pattern labelling the solutions found. + The array phases_per_scan_point has to be specified because it details + how the phase_id and the matching_phase arrays are interpreted. + See documentation of phase_id for further details. + + + + + + + + Phase_matching is a descriptor for how well the solution matches or not. + Examples can be confidence_index, mean_angular_deviation, or other. + + + + + + + + + + + Calibrated center positions of each scan point + in the sample surface reference system. + + + + + + + + + Fraction of successfully indexed patterns with a phase + not the null-phase vs the number_of_scan_points. + + + + + Number of scan points in the original mapping. + + + + + The shape of the polygon or polyhedron that was used for the tiling + respectively tessellation of the region-of-interest into scan points. + + + + + + + + + + + An overview of the entire ROI. + + + + Descriptor representing the image contrast. + + + + + + + + + + Title of the default plot. + + + + + Descriptor values displaying the ROI. + + + + + + + + Descriptor values + + + + + + Calibrated coordinate along the y-axis. + + + + + + + Label for the y axis + + + + + + Calibrated coordinate along the x-axis. + + + + + + + Label for the x axis + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXem_eds.nxdl.xml b/src/nexusformat/definitions/base_classes/NXem_eds.nxdl.xml new file mode 100644 index 0000000..31d4beb --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXem_eds.nxdl.xml @@ -0,0 +1,200 @@ + + + + + + + + Number of X-ray photon energy (bins) + + + + + Number of identified elements + + + + + Number of peaks detected + + + + + Number of IUPAC line names + + + + + Base class method-specific for energy-dispersive X-ray spectroscopy (EDS/EDXS). + + `IUPAC instead of Siegbahn notation <https://doi.org/10.1002/xrs.1300200308>`_ should be used. + + X-ray spectroscopy is a surface-sensitive technique. Therefore, three-dimensional elemental + characterization requires typically a sequence of characterization and preparation of the + surface to expose new surface layer that can be characterized in the next acquisition. + In effect, the resulting three-dimensional elemental information mappings are truly the + result of a correlation and post-processing of several measurements which is the field + of correlative tomographic usage of electron microscopy. + + + + Details about computational steps how peaks were indexed as elements. + + + + The program with which the indexing was performed. + + + + + Accumulated intensity over all pixels of the region-of-interest. + + + + Accumulated counts + + + + + + + Counts + + + + + + Energy axis + + + + + + + Energy + + + + + + + Comma-separated list of symbols for elements from the periodic table that have + been confirmed present by the here reported EDS analysis. + + This field can be used when creating instances of :ref:`NXpeak` is not desired. + However, a collection of instances of NXpeak with individual NXatom + can be used to add isotopic information and other relevant context. + + + + + Details about individual indexed peaks. + + + + + Associated lower :math:`[e_{min}, e_{max}]` bounds of the + energy which is assumed associated with this peak. + + + + + + + + Theoretical energy of the line according to IUPAC. + + + + + IUPAC notation identifier of the line which the peak represents. + + This can be a list of IUPAC notations for (the seldom) case that + multiple lines are grouped with the same peak. + + + + + + + + + + Individual element-specific EDS/EDX/EDXS/SXES mapping + + A composition map is an image whose intensities for each pixel are the + accumulated X-ray quanta *under the curve(s)* of a set of peaks. + + These element-specific EDS maps are instances of :ref:`NXimage` + that should be named by the element from the atom_types field. + + When signal contributions from several peaks were decomposed + users should ideally use a respective number of NXpeak instances + to give further context about the individual signal contributions + are summarized and shown together, e.g. the combined signal + under the curve of carbon and oxygen. + + In this case specify the processing details use peak and weight. + + + + Discouraged free-text field to add additional information. + + + + + Comma-separated list of chemical_symbol-IUPAC X-ray (emission) line name that + documents which elements and their specific lines are theoretically located within + the energy_range of the spectrum from which the EDS (element) map was computed. + + + + + Associated :math:`[e_{min}, e_{max}]` bounds of the energy + range for which spectrum counts were accumulated. + + + + + + + + + A list of :ref:`NXpeak` instance names whose X-ray quanta were + accumulated for each pixel to obtain an element-specific + EDS map. + + + + + + + + A list of weights by how much the intensity of each peak + contributes to the intensity of the EDS map. + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXprogram.nxdl.xml b/src/nexusformat/definitions/base_classes/NXem_eels.nxdl.xml similarity index 52% rename from src/nexusformat/definitions/contributed_definitions/NXprogram.nxdl.xml rename to src/nexusformat/definitions/base_classes/NXem_eels.nxdl.xml index e92363e..f76b090 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXprogram.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXem_eels.nxdl.xml @@ -2,9 +2,9 @@ - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - + - Base class to describe a software tool or library. + Base class method-specific for Electron Energy Loss Spectroscopy (EELS). - + + + Details about computational steps how the zero-loss peak was threaded. + + + + The program with which the zero-loss peak correction was performed. + + + + - Given name of the program. Program can be a commercial one a script, - or a library or a library component. + Details about computational steps how peaks were indexed as elements. - + + + The program with which the indexing was performed. + + + - Program version plus build number, or commit hash. + Name and location of each peak in the spectrum considered to be of relevance. - - + + - Description of an ideally ever persistent resource where the source code - of the program or this specific compiled version of the program can be - found so that the program yields repeatably exactly the same numerical - and categorical results. + NXspectrum specialized for EELS. - - + + diff --git a/src/nexusformat/definitions/base_classes/NXem_event_data.nxdl.xml b/src/nexusformat/definitions/base_classes/NXem_event_data.nxdl.xml new file mode 100644 index 0000000..beb08d4 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXem_event_data.nxdl.xml @@ -0,0 +1,157 @@ + + + + + + Base class to store state and (meta)data of events for electron microscopy. + + Event-related (meta)data, typically measured datasets like images and spectra. + To avoid repetitively storing static instrument-related metadata, + the dynamic (meta)data that typically changes for each image and spectrum + is split from the static (meta)data. + + Which temporal granularity is adequate to log events depends on the situation and + research question. Using a model which enables a collection of events offers + the most flexible way to cater for both experiments with controlled electron + beams in a real microscope or the simulation of such experiments or + individual aspects of such experiments. + + Electron microscopes are dynamic. Scientists often report that microscopes + *perform differently* across sessions. That *they* perform differently from + one day or another. In some cases, root causes for performance differences + are unclear. Users of the instrument may consider such conditions impractical, + or *too poor*, and thus abort their session. Alternatively, users may try to + bring the microscope into a state where conditions are considered better + or of whatever high enough quality for starting or continuing the measurement. + + In all these use cases it is useful to have a mechanism whereby time-dependent + data of the instrument state can be stored and documented in an representation + that facilitates interoperability. This is the idea behind this base class. + + :ref:`NXem_event_data` represents an instance to describe and serialize flexibly + whatever is considered a time interval during which the instrument is + considered stable enough for allowing any working on tasks with it. + Examples of such tasks are the collecting of data (images and spectra) or + the calibrating the instrument or individual of its components. Users may wish to take + only a single scan or image and complete their session thereafter. + Alternatively, users are working for much longer time at the instrument, + perform recalibrations in between and take several scans (of different + ROIs on the specimen), or they explore the state of the microscope for + service or maintenance tasks. + + :ref:`NXem_event_data` serves the harmonization and documentation of these cases: + + * Firstly, via a header section whose purpose is to contextualize + and identify the event instance in time. + * Secondly, via a data and metadata section where individual data + collections can be stored in a standardized representation. + + We are aware of the fact that given the variety how an electron microscope + is used, there is a need for a flexible and adaptive documentation system. + At the same time we are also convinced though that just because one has + different requirements for some specific aspect under the umbrella of settings + to an electron microscope, this does not necessarily warrant that one has to + cook up an own data schema. + + Instead, the electron microscopy community should work towards reusing schema + components as frequently as possible. This will enable that there is at all + not only a value of harmonizing electron microscopy research content but also + there is a technical possibility to build services around such harmonized data. + + Arguably it is oftentimes tricky to specify a clear time interval when the + microscope is *stable enough*. Take for instance the acquisition of an image + or a stack of spectra. Having to deal with instabilities is a common theme in + electron microscopy practice. Numerical protocols can be used during data + post-processing to correct for some of the instabilities. + A few exemplar references provide an overview on the subject: + + * `C. Ophus et al. <https://dx.doi.org/10.1016/j.ultramic.2015.12.002>`_ + * `B. Berkels et al. <https://doi.org/10.1016/j.ultramic.2018.12.016>`_ + * `L. Jones et al. <https://link.springer.com/article/10.1186/s40679-015-0008-4>`_ + + For specific simulation purposes, mainly in an effort to digitally repeat or simulate + the experiment (digital twin), it is tempting to consider dynamics of the instrument, + implemented as time-dependent functional descriptions of e.g. lens excitations, + beam shape functions, trajectories of groups of electrons and ions, or detector noise models. + This also warrants to document the time-dependent details of individual components + of the microscope via the here implemented class :ref:`NXem_event_data`. + + + + ISO 8601 time code with local time zone offset to UTC information included + when the snapshot time interval started. + + If users wish to specify an interval of time that the snapshot should represent + during which the instrument was stable and configured using specific settings and + calibrations, the start_time is the start (left bound of the time interval) while + the end_time specifies the end (right bound) of the time interval. + + + + + ISO 8601 time code with local time zone offset to UTC information included + when the snapshot time interval ended. + + + + + Identifier of a specific state and setting of the microscope. + + + + + The name of the sample to resolve ambiguities. + + + + + Which specific event/measurement type. Examples are: + + * In-lens/backscattered electron, usually has quadrants + * Secondary_electron, image, topography, fractography, overview images + * Backscattered_electron, image, Z or channeling contrast (ECCI) + * Bright_field, image, TEM + * Dark_field, image, crystal defects + * Annular dark field, image (medium- or high-angle), TEM + * Diffraction, image, TEM, or a comparable technique in the SEM + * Kikuchi, image, SEM EBSD and TEM diffraction + * X-ray spectra (point, line, surface, volume), composition EDS/EDX(S) + * Electron energy loss spectra for points, lines, surfaces, TEM + * Auger, spectrum, (low Z contrast element composition) + * Cathodoluminescence (optical spectra) + * Ronchigram, image, alignment utility specifically in TEM + * Chamber, e.g. TV camera inside the chamber, education purposes. + + This field may also be used for storing additional information + about the event for which there is at the moment no other place. + + In the long run such free-text field description should be avoided as + it is difficult to machine-interpret. Instead, an enumeration should + be used. + + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXem_img.nxdl.xml b/src/nexusformat/definitions/base_classes/NXem_img.nxdl.xml new file mode 100644 index 0000000..10c580b --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXem_img.nxdl.xml @@ -0,0 +1,62 @@ + + + + + + Base class for method-specific generic imaging with electron microscopes. + + In the majority of cases simple d-dimensional regular scan patterns are used + to probe regions-of-interest (ROIs). Examples can be single point aka spot + measurements, line profiles, or (rectangular) surface mappings. + The latter pattern is the most frequently used. + + For now the base class provides for scans for which the settings, + binning, and energy resolution is the same for each scan point. + + + + + Which imaging mode was used? + + + + + + + + + + + Annulus inner (first value) and outer (second value) half angle. + + + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXem_instrument.nxdl.xml b/src/nexusformat/definitions/base_classes/NXem_instrument.nxdl.xml new file mode 100644 index 0000000..8034040 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXem_instrument.nxdl.xml @@ -0,0 +1,232 @@ + + + + + + Base class for instrument-related details of a real or simulated electron microscope. + + For collecting data and experiments which are simulations of an electron + microscope (or such session) use the :ref:`NXem` application definition and + the :ref:`NXem_event_data` groups it provides. + + This base class implements the concept of :ref:`NXem` whereby (meta)data are distinguished + whether these typically change during a session (dynamic) or not (static metadata). + This design allows to store e.g. hardware related concepts only once instead of demanding + that each image or spectrum from the session needs to be stored also with the static metadata. + + + + Given name of the microscope at the hosting institution. + This is an alias. Examples could be NionHermes, Titan, JEOL, + Gemini, etc. + + + + + Location of the lab or place where the instrument is installed. + Using GEOREF is preferred. + + + + + Different types of electron microscopes exist: + + * sem, a scanning electron microscope without focused-ion beam capabilities + * fib, a scanning electron microscope with focused-ion beam capabilities + irrespective whether these were used or not + * tem, a transmission electron microscope + + NXem is one joint data model that can be used to document research that is performed + with several of these types of microscopes (SEM, TEM, or FIB). The NXem data model + stresses that these types of instruments despite having several differences are still all + electron beamlines with which to probe electron and/or ion matter interaction and in fact + in practice have many similarities in how they are used, the components, they contain, etc. + + This field can be used in research data management systems for enabling a categorization + or tagging of experiments without having to analyze if groups like NXibeam_column are present + (which would indicate type is fib) or if certain lens configurations or instrument models are used + which suggests the microscope is a scanning (sem) or transmission electron microscope (tem): + + + + + + + + + + + + + + + Description of the type of the detector. + + Electron microscopes have typically multiple detectors. + Different technologies are in use like CCD, scintillator, + direct electron, CMOS, or image plate to name but a few. + + + + + Stages in an electron microscope are multi-functional devices. + + Stages enable experimentalists the application of controlled external stimuli + on the specimen. Modern stages realize a hierarchy of components. + A multi-axial tilt rotation holder is a good example where the control of + each degree of freedom is technically implemented via providing instances + of e.g. :ref:`NXpositioner` or :ref:`NXactuator` that achieve the rotating + and positioning of the specimen. + + The physical process of mounting a specimen on a stage in practice often + comes with an own hierarchy of fixtures to bridge e.g. length scales technically. + An example from atom probe microscopy is that researchers may work + with wire samples which are clipped into a larger fixing unit to enable + careful specimen handling. Alternatively, a microtip is a silicon post + upon which e.g. an atom probe specimen is mounted. Multiple of such microtips + are then grouped into a microtip array to conveniently enable loading of multiple + specimens into the instrument with fewer operations. There are further scenarios + typically encountered related to mounting and locating specimens inside an + electron microscope, a few examples follow: + + * A nanoparticle on a copper grid. The copper grid is the holder. + This grid itself is fixed to a stage. + * An atom probe specimen fixed in a stub. In this case the stub can be + considered the holder, while the cryostat temperature control unit is + a component of the stage. + * For in-situ experiments with e.g. chips with read-out electronics + as actuators, the chips are again placed in a larger unit. A typical + example are in-situ experiments using e.g. the tools of `Protochips <https://www.protochips.com>`_. + * Other examples are (quasi) in-situ experiments where experimentalists + anneal or deform the specimen via e.g. in-situ tensile testing machines + which are mounted on the specimen holder. + + For specific details and inspiration about stages in electron microscopes: + + * `Holders with multiple axes <https://www.nanotechnik.com/e5as.html>`_ + * `Chip-based designs <https://www.protochips.com/products/fusion/fusion-select-components/>`_ + * `Further chip-based designs <https://www.nanoprobetech.com/about>`_ + * `Stages in transmission electron microscopy <https://doi.org/10.1007/978-3-662-14824-2>`_ (page 103, table 4.2) + * `Further stages in transmission electron microscopy <https://doi.org/10.1007/978-1-4757-2519-3>`_ (page 124ff) + * `Specimens in atom probe <https://doi.org/10.1007/978-1-4614-8721-0>`_ (page 47ff) + * `Exemplar micro-manipulators <https://nano.oxinst.com/products/omniprobe/omniprobe-200>`_ + + + + + Principal design of the stage. + + Exemplar terms could be side_entry, top_entry, + single_tilt, quick_change, multiple_specimen, + bulk_specimen, double_tilt, tilt_rotate, + heating_chip, atmosphere_chip, + electrical_biasing_chip, liquid_cell_chip + + + + + Free-text field to give a term how that a stage_lab at this level of the + stage_lab hierarchy is commonly referred to. Examples could be stub, + puck, carousel, microtip, clip, holder, etc. + + + + + + The interpretation of this tilt1 value can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + tilt is defined explicitly using instances of :ref:`NXtransformations` and + respective instances of :ref:`NXcoordinate_system`. Especially when this + NXem_instrument base class is used in an application definition like NXem. + + + + Discouraged free-text field to provide details about how to interpret tilt1. + + + + + + The interpretation of this tilt2 value can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + tilt is defined explicitly using instances of :ref:`NXtransformations` and + respective instances of :ref:`NXcoordinate_system`. Especially when this + NXem_instrument base class is used in an application definition like NXem. + + + + Discouraged free-text field to provide details about how to interpret tilt2. + + + + + + The interpretation of this rotation value can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + rotation is defined explicitly using instances of :ref:`NXtransformations` and + respective instances of :ref:`NXcoordinate_system`. Especially when this + NXem_instrument base class is used in an application definition like NXem. + + + + Discouraged free-text field to provide details about how to interpret rotation. + + + + + + The interpretation of these position values can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + position values are defined explicitly using instances of :ref:`NXtransformations` + and respective instances of :ref:`NXcoordinate_system`. Especially when this + NXem_instrument base class is used in an application definition like NXem. + + + + + + + + + In contrast to the stage, the nanoprobe is an additional manipulator that is a specifically + frequently found component of FIB/SEM instruments. A nanoprobe is used to pick up and + relocated portions of the specimen that have been cut off during site-specific lift-outs + and specimen preparation. + + + + + Gas injection systems (GIS) are components of microscopes that are equipped with focused-ion beam + capabilities. The component is used to introduce reactive neutral gases to the sample surface for + enhanced etching, preferential etching, or material deposition. + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXem_interaction_volume.nxdl.xml b/src/nexusformat/definitions/base_classes/NXem_interaction_volume.nxdl.xml new file mode 100644 index 0000000..c7f6fe2 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXem_interaction_volume.nxdl.xml @@ -0,0 +1,56 @@ + + + + + + Base class to describe the volume of interaction for particle-matter interaction. + + Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam + interaction simulations can be used to qualify and (or) quantify the shape of + the interaction volume. Results of such simulations can be summary statistics + or single-particle-resolved sets of trajectories. + + Explicit or implicit descriptions of the geometry of this + interaction volume are possible: + + * An implicit description is via a set of electron/specimen interactions + represented ideally as trajectory data from the computer simulation. + * An explicit description is via iso-contour surface using either + a simulation grid or a triangulated surface mesh of the approximated + iso-contour surface evaluated at specific threshold values. + Iso-contours could be computed from electron or particle flux through + an imaginary control surface (the iso-surface) or energy-levels + (e.g. the case of X-rays). Details depend on the model. + * Another explicit description is via theoretical models which may + be relevant e.g. for X-ray spectroscopy + + Further details on how the interaction volume can be quantified + is available in the literature for example: + + * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ + * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ + * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXcs_io_sys.nxdl.xml b/src/nexusformat/definitions/base_classes/NXem_measurement.nxdl.xml similarity index 71% rename from src/nexusformat/definitions/contributed_definitions/NXcs_io_sys.nxdl.xml rename to src/nexusformat/definitions/base_classes/NXem_measurement.nxdl.xml index 5608c9f..8dda84b 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXcs_io_sys.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXem_measurement.nxdl.xml @@ -2,9 +2,9 @@ - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - + - Computer science description of system of a computer. + Base class for documenting a measurement with an electron microscope. - + + diff --git a/src/nexusformat/definitions/base_classes/NXem_optical_system.nxdl.xml b/src/nexusformat/definitions/base_classes/NXem_optical_system.nxdl.xml new file mode 100644 index 0000000..73c90f0 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXem_optical_system.nxdl.xml @@ -0,0 +1,164 @@ + + + + + + Base class for qualifying an electron optical system. + + + + Distance which is present between the specimen surface and the detector plane. + + This concept is related to term `Camera Length`_ of the EMglossary standard. + + .. _Camera Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000008 + + + + + The factor of enlargement of the apparent size, + not the physical size, of an object. + + + + + The defocus aberration constant (oftentimes referred to as c_1_0). + See respective details in :ref:`NXaberration` class instances. + + + + + The angle which is given by the semi-opening angle of the cone in a convergent + beam. + + This concept is related to term `Convergence Angle`_ of the EMglossary standard. + + .. _Convergence Angle: https://purls.helmholtz-metadaten.de/emg/EMG_00000010 + + + + + The extent of the observable parts of the specimen given the current + magnification and other settings of the instrument. + + + + + Distance which is determined along the optical axis within the column from (1) the + lower end of the final optical element between the source and the specimen stage; + to (2) the point where the beam is focused. + + This concept is related to term `Working Distance`_ of the EMglossary standard. + + .. _Working Distance: https://purls.helmholtz-metadaten.de/emg/EMG_00000050 + + + + + + Geometry of the cross-section formed when the primary beam shines onto the + specimen surface. Reported as length of the semiaxes of the ellipsoidal + cross-section with semiaxes values sorted by decreasing length. + + + + + + + + + Electrical current which arrives at the specimen. + + This concept is related to term `Probe Current`_ of the EMglossary standard. + + .. _Probe Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000041 + + + + + Specify further details how incipient electron or ion dose was quantified + (using beam_current, probe_current). + + `Reference <https://doi.org/10.1017/S1551929522000840>`_ discusses + an approach for (electron) dose monitoring in an electron microscope. + + The unit of the nominal dose rate is e-/(angstrom^2*s). + + + + + Nominal dose rate. + + + + + In the process of passing through an :ref:`NXelectromagnetic_lens` electrons are typically accelerated + on a helical path about the optical axis. This causes an image rotation whose strength + is affected by the magnification. + + Microscopes may be equipped with compensation methods (implemented in hardware + or software) that reduce but not necessarily eliminate this rotation. + + See `L. Reimer <https://doi.org/10.1007/978-3-540-38967-5>`_ for details. + + + + + Distance which lies between the principal plane of the lens and the focal point + along the optical axis. + + This concept is related to term `Focal Length`_ of the EMglossary standard. + + .. _Focal Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000029 + + + + + Details about an imaging setting used during acquisition to correct perspective + distortion when imaging a tilted surface or cross section. + + This concept is related to term `Tilt Correction`_ of the EMglossary standard. + + .. _Tilt Correction: https://purls.helmholtz-metadaten.de/emg/EMG_00000047 + + + + + Details about a dynamic focus correction used. + + This concept is related to term `Dynamic Focus Correction`_ of the EMglossary standard. + + .. _Dynamic Focus Correction: https://purls.helmholtz-metadaten.de/emg/EMG_00000016 + + + + + Details about a workflow used to keep the specimen in focus by automatic means. + + This concept is related to term `Dynamic Refocusing`_ of the EMglossary standard. + + .. _Dynamic Refocusing: https://purls.helmholtz-metadaten.de/emg/EMG_00000017 + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXevent_data_em_set.nxdl.xml b/src/nexusformat/definitions/base_classes/NXem_simulation.nxdl.xml similarity index 69% rename from src/nexusformat/definitions/contributed_definitions/NXevent_data_em_set.nxdl.xml rename to src/nexusformat/definitions/base_classes/NXem_simulation.nxdl.xml index 7ec2667..6ec01a7 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXevent_data_em_set.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXem_simulation.nxdl.xml @@ -2,9 +2,9 @@ - + - Container to hold NXevent_data_em instances of an electron microscope session. - - An event is a time interval during which the microscope was configured, - considered stable, and used for characterization. + Base class for documenting a simulation of electron beam-matter interaction. - + + + + diff --git a/src/nexusformat/definitions/base_classes/NXenergydispersion.nxdl.xml b/src/nexusformat/definitions/base_classes/NXenergydispersion.nxdl.xml index 1381cb6..0e42021 100644 --- a/src/nexusformat/definitions/base_classes/NXenergydispersion.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXenergydispersion.nxdl.xml @@ -168,7 +168,7 @@ Deflectors in the energy dispersive section - + Individual lenses in the energy dispersive section diff --git a/src/nexusformat/definitions/base_classes/NXentry.nxdl.xml b/src/nexusformat/definitions/base_classes/NXentry.nxdl.xml old mode 100755 new mode 100644 index 7c29503..6641a1a --- a/src/nexusformat/definitions/base_classes/NXentry.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXentry.nxdl.xml @@ -70,7 +70,7 @@ do not use an application definition. It is recommended strongly that all NeXus data files provide a NXdata group. - It is permissable to omit the NXdata group only when + It is permissible to omit the NXdata group only when defining the default plot is not practical or possible from the available data. @@ -118,7 +118,7 @@ Brief summary of the collection, including grouping criteria. - unique identifier for the measurement, defined by the facility. + Unique identifier for the measurement, defined by the facility. UUID identifier for the measurement. diff --git a/src/nexusformat/definitions/base_classes/NXfabrication.nxdl.xml b/src/nexusformat/definitions/base_classes/NXfabrication.nxdl.xml index 8895d64..a9b7367 100644 --- a/src/nexusformat/definitions/base_classes/NXfabrication.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXfabrication.nxdl.xml @@ -51,7 +51,8 @@ Datetime of component's initial construction. This refers to the date of first measurement after new construction or to the relocation date, if it describes a multicomponent/custom-build setup. - Just the year is often sufficient, but if a full date/time is used, it is recommended to add an explicit time zone. + Just the year is often sufficient, but if a full date/time is used, + it is recommended to add an explicit time zone. diff --git a/src/nexusformat/definitions/base_classes/NXfit.nxdl.xml b/src/nexusformat/definitions/base_classes/NXfit.nxdl.xml index fce5993..0d0bcf1 100644 --- a/src/nexusformat/definitions/base_classes/NXfit.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXfit.nxdl.xml @@ -164,9 +164,9 @@ Description of the method used to optimize the parameters during peak fitting. Examples: - + - least squares - - non-linear least squares + - nonlinear least squares - Levenberg-Marquardt algorithm (damped least-squares) - linear regression - Bayesian linear regression @@ -181,7 +181,7 @@ :math:`min(\chi^2)`, where :math:`\chi^2` is the sum of squared residuals between the model and the observed data: :math:`min(\chi^2) = \sum_{i=1}^{N} \left( y_i - \left( \text{peak}_1(p_1, x_i) + \text{peak}_2(p_2, x_i) + \text{backgr}(p_3, x_i) \right) \right)^2` - + It is however also possible to supply more involved formulas (e.g., in the case of constrained fits). @@ -197,7 +197,7 @@ Metric used to determine the goodness of fit. Examples include: - + - :math:`\chi^2`, the squared sum of the sigma-weighted residuals - reduced :math:`\chi^2`:, :math:`\chi^2`: per degree of freedom - :math:`R^2`, the coefficient of determination diff --git a/src/nexusformat/definitions/base_classes/NXhistory.nxdl.xml b/src/nexusformat/definitions/base_classes/NXhistory.nxdl.xml index 96baa7d..3ce1747 100644 --- a/src/nexusformat/definitions/base_classes/NXhistory.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXhistory.nxdl.xml @@ -3,7 +3,7 @@ + + + Base class for a set of components equipping an instrument with FIB capabilities. + + Focused-ion-beam (FIB) capabilities turn especially scanning electron microscopes + into specimen preparation labs. FIB is a material preparation technique whereby + portions of the sample are illuminated with a focused ion beam with controlled + intensity. The beam is controlled such that it is intense, focused, and equipped + with sufficient ion having sufficient momentum to remove material in a controlled + manner. + + The fact that an electron microscope with FIB capabilities achieves these functionalities + via a second component (aka the ion gun) that has its own relevant control circuits, + focusing lenses, and other components, warrants the definition of an own base class + to group these components and distinguish them from the lenses and components for creating + and shaping the electron beam. + + For more details about the relevant physics and application examples + consult the literature, for example: + + * `L. A. Giannuzzi et al. <https://doi.org/10.1007/b101190>`_ + * `E. I. Preiß et al. <https://link.springer.com/content/pdf/10.1557/s43578-020-00045-w.pdf>`_ + * `J. F. Ziegler et al. <https://www.sciencedirect.com/science/article/pii/S0168583X10001862>`_ + * `J. Lili <https://www.osti.gov/servlets/purl/924801>`_ + * `N. Yao <https://doi.org/10.1017/CBO9780511600302>`_ + + + + Tech-partner, microscope-, and control-software-specific name of the + specific operation mode how the ibeam_column and its components are + controlled to achieve specific illumination conditions. + + In many cases the users of an instrument do not or can not be expected to know + all intricate spatiotemporal dynamics of their hardware. Instead, they rely on + assumptions that the instrument, its control software, and components work as + expected to focus on their research questions. + + For these cases, having a place for documenting the operation_mode is useful + in as much as at least some constraints on how the illumination conditions were + is documented. + + + + + The source which creates the ion beam. + + + + Given name/alias for the ion gun. + + + + + Emitter type used to create the ion beam. + + If the emitter type is other, give further + details in the description field. + + + + + + + + + + + Ideally, a (globally) unique persistent identifier, link, + or text to a resource which gives further details. + + + + + Which elements, ions, or molecular ions form the beam. + Examples are gallium, helium, neon, argon, krypton, + or xenon, O2+. + + + + + Average/nominal flux + + + + + Average/nominal brightness + + + + + + Charge current + + + + + Ion acceleration voltage upon source exit and + entering the vacuum flight path. + + + + + To be defined more specifically. Community suggestions are welcome. + + + + + + + + + A component for blanking the ion beam or generating pulsed ion beams. + + + + + + + + Individual characterization results for the position, shape, + and characteristics of the ion beam. + + :ref:`NXtransformations` should be used to specify the location or position + at which details about the ion beam are probed. + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXimage.nxdl.xml b/src/nexusformat/definitions/base_classes/NXimage.nxdl.xml index 8859586..1bbf7b2 100644 --- a/src/nexusformat/definitions/base_classes/NXimage.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXimage.nxdl.xml @@ -29,6 +29,11 @@ Number of images in the stack, for stacks the slowest dimension. + + + Number of image points along the slowest dimension. + + Number of image points along the slow dimension (k equivalent to z). @@ -85,6 +90,17 @@ That is indices_image are always counting from offset in increments of one as each image is its own entity. By contrast, a group may contain no, or several images. Consequently, indices_group are not required to be contiguous. + + Classically, images depict objects in real space. Such usage of NXimage essentially is equivalent to + storing pictures. For this purpose the image_1d, image_2d, or image_3d NXdata instances respectively + should be used such that all their axes axis_i, axis_j, axis_k are constrained to NeXus Unit Category NX_LENGTH. + + Imaging modes in electron microscopy are typically more versatile, specifically for use cases + in scanning transmission electron microscopy, so-called 4DSTEM. In this case, one two-dimensional + diffraction image is taken for each point that gets scanned in real space. Consequently, + image_3d and image_4d NXdata instances should be used for these cases with axis_k and axis_m + respectively of NeXus Unit Category NX_LENGTH and axis_i and axis_j respectively of + NeXus Unit Category NX_WAVENUMBER or NX_UNITLESS. @@ -159,9 +175,15 @@ - + Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -215,9 +237,15 @@ - + Point coordinate along the fast dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -228,9 +256,15 @@ - + Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -288,9 +322,15 @@ - + Point coordinate along the slow dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -301,9 +341,15 @@ - + Point coordinate along the fast dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -314,9 +360,142 @@ - + Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. + + + + + + + Point coordinate along the fastest dimension. + + + + + + + Four-dimensional image. + + + + Intensity for real-valued images as an alternative for real. + Magnitude of the image intensity for complex-valued data. + + + + + + + + + + + Real part of the image intensity per point. + + + + + + + + + + + Imaginary part of the image intensity per point. + + + + + + + + + + + Image intensity as a complex number as an alternative to real and + imag fields if values are stored as interleaved complex numbers. + + + + + + + + + + + Point coordinate along the slowest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. + + + + + + + Point coordinate along the slowest dimension. + + + + + + Point coordinate along the slow dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. + + + + + + + Point coordinate along the slow dimension. + + + + + + Point coordinate along the fast dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. + + + + + + + Point coordinate along the fast dimension. + + + + + + Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -396,9 +575,15 @@ - + Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -482,9 +667,15 @@ - + Point coordinate along the fast dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -495,9 +686,15 @@ - + Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -585,9 +782,15 @@ - + Point coordinate along the slow dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -598,9 +801,15 @@ - + Point coordinate along the fast dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. @@ -611,9 +820,15 @@ - + Point coordinate along the fastest dimension. + + Different NeXus Unit Category are allowed: + + * NX_LENGTH for images slicing real space. + * NX_WAVENUMBER or NX_UNITLESS respectively + for images slicing reciprocal space. diff --git a/src/nexusformat/definitions/base_classes/NXinsertion_device.nxdl.xml b/src/nexusformat/definitions/base_classes/NXinsertion_device.nxdl.xml index 4c3eace..c086878 100644 --- a/src/nexusformat/definitions/base_classes/NXinsertion_device.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXinsertion_device.nxdl.xml @@ -28,9 +28,11 @@ type="group" extends="NXcomponent"> An insertion device, as used in a synchrotron light source. + It is recommended (effective from 2025) to use the "wavelength_shifter" choice for 3-pole wigglers, while reserving the generic "wiggler" designation for extended multipole wigglers. - - + + + diff --git a/src/nexusformat/definitions/base_classes/NXinstrument.nxdl.xml b/src/nexusformat/definitions/base_classes/NXinstrument.nxdl.xml index 9eae025..523761f 100644 --- a/src/nexusformat/definitions/base_classes/NXinstrument.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXinstrument.nxdl.xml @@ -3,7 +3,7 @@ + A parameter (also known as a term) that is used in or results from processing. + + diff --git a/src/nexusformat/definitions/base_classes/NXpdb.nxdl.xml b/src/nexusformat/definitions/base_classes/NXpdb.nxdl.xml index 5f3317f..c30450d 100644 --- a/src/nexusformat/definitions/base_classes/NXpdb.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXpdb.nxdl.xml @@ -63,9 +63,9 @@ should always be presented as a 1-dimensional array. The columns in an unlooped PDB category should be presented as scalar values. If a PDB category specifies particular units for columns, the same - units should beused for the corresponding fields. + units should be used for the corresponding fields. - A PDB entry is unambigous when all information is carried as text. + A PDB entry is unambiguous when all information is carried as text. All text data should be presented as quoted strings, with the quote marks except for the null values "." or "?" @@ -81,7 +81,7 @@ but may be used to provide internal documentation. The nesting of NXpdb groups and datasets that correspond to a CIF with - two categories and one saveframe, including the NXpdb_class attribues is:: + two categories and one saveframe, including the NXpdb_class attributes is:: (datablock1):NXpdb @NXpdb_class:CBF_cbfdb diff --git a/src/nexusformat/definitions/base_classes/NXphase.nxdl.xml b/src/nexusformat/definitions/base_classes/NXphase.nxdl.xml new file mode 100644 index 0000000..f38da4b --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXphase.nxdl.xml @@ -0,0 +1,55 @@ + + + + + + Base class to describe a (thermodynamic) phase as a component of a material. + + Instances of phases can be crystalline. + + + + Identifier for each phase. + + The value 0 is reserved for the unknown phase that represents the + null-model (no sufficiently significant information available). + In other words, the phase_name is n/a aka notIndexed. + + The phase_id value should match with the integer suffix of the + group name which represents that instance in a NeXus/HDF5 file, i.e. + if three phases were used e.g. 0, 1, and 2, three instances of + :ref:`NXphase` named phase0, phase1, and phase2 should be stored + in that HDF5 file. + + + + + Given name as an alias for identifying this phase. + + If the phase_id is 0 and one would like to use + the field name, the value should be n/a or notIndexed. + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXpid_controller.nxdl.xml b/src/nexusformat/definitions/base_classes/NXpid_controller.nxdl.xml index 4f22762..6a19442 100644 --- a/src/nexusformat/definitions/base_classes/NXpid_controller.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXpid_controller.nxdl.xml @@ -44,8 +44,8 @@ * K_ff A classic PID controller only implements the P, I and D terms and the values of the K_p, K_i and K_d constants are sufficient to fully - describe the behaviour of the feedback system implemented by such a PID controller. The inclusion of a Feed Forward term in a feedback system - is a modern adaptation that aids optimisation of the automated control. It is not present in all PID controllers, but it is also not uncommon. + describe the behavior of the feedback system implemented by such a PID controller. The inclusion of a Feed Forward term in a feedback system + is a modern adaptation that aids optimization of the automated control. It is not present in all PID controllers, but it is also not uncommon. Note that the ``NXpid_controller`` is designed to be a child object of the actuator that its output is connected to. The parent object representing the actuator is likely to be represented by an ``NXactuator`` or ``NXpositioner`` base class, but there is a wide variety @@ -130,7 +130,7 @@ the Process Variable that is lower than the Setpoint results in a positive Error Value and a generally positive control output that tells the actuator to push the value of the Process Variable upwards. In some implementations, the actuator will respond to a more positive control output by pushing the Process Variable towards lower values (e.g. - a Peltier cooler) and so the output of the feedback system must be reversed to match the behaviour of the physical system. + a Peltier cooler) and so the output of the feedback system must be reversed to match the behavior of the physical system. A feedback system may also be implemented with reverse action in order to ensure that failures (e.g. disconnected sensor output or actuator input) result in a safe state (e.g. a valve should be left open to release pressure). diff --git a/src/nexusformat/definitions/base_classes/NXprocess.nxdl.xml b/src/nexusformat/definitions/base_classes/NXprocess.nxdl.xml index bc8e69e..8686b88 100644 --- a/src/nexusformat/definitions/base_classes/NXprocess.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXprocess.nxdl.xml @@ -1,5 +1,5 @@ - + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The cardinality of the set, i.e. the number of value tuples. + + + + + How many phases with usually different crystal and symmetry are distinguished. + + + + + + Base class to detail a set of rotations, orientations, and disorientations. + + For getting a more detailed insight into the discussion of the + parameterized description of orientations in materials science see: + + * `H.-J. Bunge <https://doi.org/10.1016/C2013-0-11769-2>`_ + * `T. B. Britton et al. <https://doi.org/10.1016/j.matchar.2016.04.008>`_ + * `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_ + * `A. Morawiec <https://doi.org/10.1007/978-3-662-09156-2>`_ + + Once orientations are defined, one can continue to characterize the + misorientation and specifically the disorientation. The misorientation describes + the rotation that is required to register the lattices of two oriented objects + (like crystal lattice) into a crystallographic equivalent orientation: + + * `R. Bonnet <https://doi.org/10.1107/S0567739480000186>`_ + + The concepts of mis- and disorientation are relevant when analyzing the + crystallography of interfaces. + + + + Reference to an instance of :ref:`NXcoordinate_system` which contextualizes + how the here reported parameterized quantities can be interpreted. + + + + + Point group which defines the symmetry of the crystal. + + This has to be at least a single string. If crystal_symmetry is not + provided, point group 1 is assumed. + + In the case that misorientation or disorientation fields are used + and the two crystal sets resolve for phases with a different + crystal symmetry, this field needs to encode two strings: + The first string is for phase A. The second string is for phase B. + An example of this most complex case is the description of the + disorientation between crystals adjoining a hetero-phase boundary. + + + + + + + + Point group which defines an assumed symmetry imprinted upon processing + the material/sample which could give rise to or may justify to use a + simplified description of rotations, orientations, misorientations, + and disorientations via numerical procedures that are known as + symmetrization. + + If sample_symmetry is not provided, point group 1 is assumed. + + The traditionally used symmetrization operations within the texture + community in Materials Science, though, have become obsolete thanks + to improvements in methods, software, and available computing power. + + Therefore, users are encouraged to set the sample_symmetry to 1 (triclinic). + + In practice one often faces situations where indeed these assumed + symmetries are anyway not fully observed, and thus an accepting of + eventual inaccuracies just for the sake of reporting a simplified + symmetrized description should be avoided. + + + + + + + + The set of rotations expressed in quaternion parameterization considering + crystal_symmetry and sample_symmetry. Rotations which should be + interpreted as antipodal are not marked as such. + + + + + + + + + The set of rotations expressed in Euler angle parameterization considering + the same applied symmetries as detailed for the field rotation_quaternion. + To interpret Euler angles correctly, it is necessary to inspect the rotation + conventions behind reference_frame to resolve which of the many possible + Euler-angle conventions (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. + + + + + + + + + + + True for all those value tuples which have assumed antipodal symmetry. + False for all others. + + + + + + + + The set of orientations expressed in quaternion parameterization and + obeying symmetry for equivalent cases as detailed in crystal_symmetry + and sample_symmetry. The supplementary field is_antipodal can be used + to mark orientations with the antipodal property. + + + + + + + + + The set of orientations expressed in Euler angle parameterization following + the same assumptions like for orientation_quaternion. + To interpret Euler angles correctly, it is necessary to inspect the rotation + conventions behind reference_frame to resolve which of the many Euler-angle + conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. + + + + + + + + + + The set of misorientations expressed in quaternion parameterization + obeying symmetry operations for equivalent misorientations + as defined by crystal_symmetry and sample_symmetry. + + The misorientation should not be confused with the disorientation, + as for the latter the angular argument is expected to be the minimal + obeying symmetries. + + + + + + + + + Misorientation angular argument (eventually signed) following the same + symmetry assumptions as expressed for the field misorientation_quaternion. + + + + + + + + Misorientation axis (normalized) and signed following the same + symmetry assumptions as expressed for the field misorientation_angle. + + + + + + + + + + The set of disorientations expressed in quaternion parameterization + obeying symmetry operations for equivalent disorientations + as defined by crystal_symmetry and sample_symmetry. + + + + + + + + + Disorientations angular argument (should not be signed, see + `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_) + following the same symmetry assumptions as expressed for the field + disorientation_quaternion. + + + + + + + + Disorientations axis (normalized) following the same symmetry assumptions + as expressed for the field disorientation_angle. + + + + + + + diff --git a/src/nexusformat/definitions/base_classes/NXsample.nxdl.xml b/src/nexusformat/definitions/base_classes/NXsample.nxdl.xml index 10717cb..09f8249 100644 --- a/src/nexusformat/definitions/base_classes/NXsample.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXsample.nxdl.xml @@ -248,7 +248,7 @@ One group per sample component - This is the perferred way of recording per component information over the n_comp arrays + This is the preferred way of recording per component information over the n_comp arrays diff --git a/src/nexusformat/definitions/base_classes/NXscan_controller.nxdl.xml b/src/nexusformat/definitions/base_classes/NXscan_controller.nxdl.xml new file mode 100644 index 0000000..b839a85 --- /dev/null +++ b/src/nexusformat/definitions/base_classes/NXscan_controller.nxdl.xml @@ -0,0 +1,81 @@ + + + + + + The scan box or scan controller is a component that is used to deflect a + beam of charged particles in a controlled manner. + + The scan box is instructed by (an) instance(s) of :ref:`NXprogram`, some control software, + which is not necessarily the same program as the one controlling other parts of the instrument. + + The scan box directs the probe of charged particles (electrons, ions) + to controlled locations according to a scan scheme and plan. + + + + + Name of the typically tech-partner-specific term that specifies an + automated protocol which details how the components of the scan_box + and the instrument work together to achieve a controlled + scanning of the beam (over the sample surface). + + Oftentimes users do not need to or are not able to disentangle the intricate + details of the spatiotemporal dynamics of their instrument. Instead, often + they rely on the assumption that the instrument and its controlling programs + work as expected. The field scan_schema can be used to add some constraints + on how the beam was scanned over the surface. + + + + + + Time period during which the beam remains at one position. + + This concept is related to term `Dwell Time`_ of the EMglossary standard. + + .. _Dwell Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000015 + + + + + Time period during which the beam moves from the final position of one scan + line to the starting position of the subsequent scan line. + + This concept is related to term `Flyback Time`_ of the EMglossary standard. + + .. _Flyback Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000028 + + + + + + Details about components which realize the deflection technically. + + This concept should be used for all those components that implement + the scanning of the beam, while components like beam blankers etc. should + use rather the NXdeflector concept of the NXebeam_column base class. + + + + diff --git a/src/nexusformat/definitions/base_classes/NXsensor.nxdl.xml b/src/nexusformat/definitions/base_classes/NXsensor.nxdl.xml index d46d176..a2f24d0 100644 --- a/src/nexusformat/definitions/base_classes/NXsensor.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXsensor.nxdl.xml @@ -155,20 +155,6 @@ This group describes the shape of the sensor when necessary. - - - - .. index:: plotting - - Declares which child group contains a path leading - to a :ref:`NXdata` group. - - It is recommended (as of NIAC2014) to use this attribute - to help define the path to the default dataset to be plotted. - See https://www.nexusformat.org/2014_How_to_find_default_data.html - for a summary of the discussion. - - .. todo:: diff --git a/src/nexusformat/definitions/base_classes/NXsource.nxdl.xml b/src/nexusformat/definitions/base_classes/NXsource.nxdl.xml index 211f900..3f8d880 100644 --- a/src/nexusformat/definitions/base_classes/NXsource.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXsource.nxdl.xml @@ -234,7 +234,7 @@ The size and position of an aperture inside the source. - + Individual electromagnetic lenses inside the source. @@ -263,4 +263,4 @@ - \ No newline at end of file + diff --git a/src/nexusformat/definitions/base_classes/NXspindispersion.nxdl.xml b/src/nexusformat/definitions/base_classes/NXspindispersion.nxdl.xml index f1ac6bc..1de107b 100644 --- a/src/nexusformat/definitions/base_classes/NXspindispersion.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXspindispersion.nxdl.xml @@ -72,7 +72,7 @@ Deflectors in the spin dispersive section - + Individual lenses in the spin dispersive section diff --git a/src/nexusformat/definitions/base_classes/NXsubentry.nxdl.xml b/src/nexusformat/definitions/base_classes/NXsubentry.nxdl.xml index 2a95f45..377369b 100644 --- a/src/nexusformat/definitions/base_classes/NXsubentry.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXsubentry.nxdl.xml @@ -186,4 +186,3 @@ - diff --git a/src/nexusformat/definitions/base_classes/NXtransformations.nxdl.xml b/src/nexusformat/definitions/base_classes/NXtransformations.nxdl.xml index 9000491..01702ea 100644 --- a/src/nexusformat/definitions/base_classes/NXtransformations.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXtransformations.nxdl.xml @@ -99,7 +99,7 @@ documents the fields commonly used within NeXus for positioning purposes and their meaning. Whenever there is a need for positioning a beam line component please use the existing names. Use as many fields as needed in order to position the component. Feel free to add more axis if required. In the description - given below, only those atttributes which are defined through the name are specified. Add the other attributes + given below, only those attributes which are defined through the name are specified. Add the other attributes of the full set: * vector @@ -127,7 +127,7 @@ by HDF5. The values given should be the start points of exposures for the corresponding - frames. The end points should be given in ``AXISNAME_end``. + frames. The end points should be given in ``AXISNAME_end``. diff --git a/src/nexusformat/definitions/contributed_definitions/NXaberration.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXaberration.nxdl.xml deleted file mode 100644 index 3c784de..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXaberration.nxdl.xml +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - Quantified aberration coefficient in an aberration_model. - - - - - Confidence - - - - - How was the uncertainty quantified e.g. via the 95% confidence interval. - - - - - Time elapsed since the last measurement. - - - - - For the CEOS definitions the C aberrations are radial-symmetric and have no - angle entry, while the A, B, D, S, or R aberrations are n-fold - symmetric and have an angle entry. - For the NION definitions the coordinate system differs to the one - used in CEOS and instead two aberration coefficients a and b are used. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXaberration_model.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXaberration_model.nxdl.xml deleted file mode 100644 index c340fc2..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXaberration_model.nxdl.xml +++ /dev/null @@ -1,105 +0,0 @@ - - - - - - Models for aberrations of electro-magnetic lenses in electron microscopy. - - See `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) - for different definitions available and further details. Table 7-2 of Ibid. - publication (page 305ff) documents how to convert from the NION to the - CEOS definitions. - - - - - - - - - - - Defocus - - - - - Two-fold astigmatism - - - - - Two-fold astigmatism - - - - - Second-order axial coma - - - - - Second-order axial coma - - - - - Threefold astigmatism - - - - - Threefold astigmatism - - - - - Spherical aberration - - - - - Star aberration - - - - - Star aberration - - - - - Fourfold astigmatism - - - - - Fourfold astigmatism - - - - - Fifth-order spherical aberration - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXaberration_model_ceos.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXaberration_model_ceos.nxdl.xml deleted file mode 100644 index 584ef6c..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXaberration_model_ceos.nxdl.xml +++ /dev/null @@ -1,91 +0,0 @@ - - - - - - CEOS definitions/model for aberrations of electro-magnetic lenses. - - See `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) - for different definitions available and further details. Table 7-2 of Ibid. - publication (page 305ff) documents how to convert from the NION to the - CEOS definitions. - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXaberration_model_nion.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXaberration_model_nion.nxdl.xml deleted file mode 100644 index cb74995..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXaberration_model_nion.nxdl.xml +++ /dev/null @@ -1,63 +0,0 @@ - - - - - - NION definitions/model for aberrations of electro-magnetic lenses. - - See `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) - for different definitions available and further details. Table 7-2 of Ibid. - publication (page 305ff) documents how to convert from the NION to the - CEOS definitions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXaperture_em.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXaperture_em.nxdl.xml deleted file mode 100644 index ae5bf24..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXaperture_em.nxdl.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - Details of an individual aperture for beams in electron microscopy. - - - - Given name/alias of the aperture. - - - - - Relevant value from the control software. - - This is not always just the diameter of (not even in the case) - of a circular aperture. Usually it is a mode setting value which - is selected in the control software. - Which settings are behind the value should be defined - for now in the description field, if these are known - in more detail. - - - - - Ideally, a (globally) unique persistent identifier, link, or text to a - resource which gives further details. Alternatively a free-text field. - - - - - Affine transformation which detail the arrangement in the - microscope relative to the optical axis and beam path. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm.nxdl.xml deleted file mode 100644 index 6f02ae1..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm.nxdl.xml +++ /dev/null @@ -1,1696 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Total number of ions collected. - - - - - Total number of independent wires in the delay-line detector. - - - - - Number of support points for e.g. modeling peaks. - - - - - Maximum number of allowed atoms per (molecular) ion (fragment). - Needs to match maximum_number_of_atoms_per_molecular_ion. - - - - - Number of mass-to-charge-state-ratio intervals of this ion type. - - - - - Number of bins in the x direction. - - - - - Number of bins in the y direction. - - - - - Number of bins in the z direction. - - - - - Number of bins. - - - - - Total number of integers in the supplementary XDMF topology array. - - - - - Application definition for atom probe and field ion microscopy experiments. - - This application definition provides a place to document data and metadata to - an atom probe experiment. Primarily the measurement itself is documented. - However, as most atom probe experiments are controlled with commercial software - which does not allow to access the raw detector hits, this application definition - also includes two key groups of processing steps (reconstruction and ranging). - - During tomographic reconstruction measured data are processed into a point cloud - of reconstructed positions of certain ions. During ranging time-of-flight data - are identified as representing specific ions to annotate each ion with a label. - - Commercial software used in atom probe research is designed as an integrated - acquisition and instrument control software. For AMETEK/Cameca local electrode - atom probe (LEAP) instruments the least processed (rawest) numerical results - and metadata are stored in so-called STR, RRAW, RHIT, and HITS files, which - are proprietary and their file format specifications not publicly documented. - - Supplementary metadata are kept in a database (formerly known as the ISDb) - which is connected to the instrument control software and synced with the - experiment while ions are detected. In effect, RHIT and HITS files - store the (rawest) experiment data in a closed manner that is - practically useless for users unless they have access to the - commercial software. - - To arrive at a state that atom probe microscopy (APM) with LEAP instruments - delivers a dataset with which users can study reconstructed atomic - position and do e.g. composition analyses or other post-processing - analysis tasks, these raw data have to be processed. Therefore, it is - necessary that for an application definition to be useful, details about - the physical acquisition of the raw data and all its - processing steps have to be stored. - - With this a user can create derived quantities like ion hit positions - (on the detector) and calibrated time-of-flight data. These derived - quantities are also needed to obtain calibrated mass-to-charge-state - ratios, and finally the tomographic reconstruction of the ion positions. - - In most cases, an APM dataset is useful only if it gets post-processed - via so-called ranging. Ranging defines rules for mapping time-of-flight - and mass-to-charge-state ratio values on ion species. This is post-processing - even though in practice it is performed sometimes already (as preview) - already while data are still being collected. - - The ion types decode molecular identities which can very often be - mapped to elemental identities, and also be used to distinguish isotopes. - All these steps are in most cases performed using commercial software. - - Frequently, though, ranging and post-processing is also performed with - (open-source) research software. Therefore, there is strictly speaking - not a single program used throughout an atom probe analysis not even - for the early stage of data acquisition and processing stages to obtain - a useful reconstructed and ranged dataset. - - This application definition documents not only the measurement but also the - key post-processing steps which transform the proprietary data into a - tomographic reconstruction with ranging definitions. - - Future guidance by the technology partners like AMETEK/Cameca could improve - this description to cover a substantial larger number of eventually metadata - that so far are neither publicly documented nor accessible. - - - - - An at least as strong as SHA256 hashvalue of the file - that specifies the application definition. - - - - - - NeXus NXDL schema to which this file conforms. - - - - - - - - Ideally, a (globally) unique persistent identifier - for referring to this experiment. - - The identifier is usually defined/issued by the facility, laboratory, - or the principle investigator. The identifier enables to link - experiments to e.g. proposals. - - - - - Free-text description about the experiment. - - Users are strongly advised to detail the sample history in the - respective field and fill rather as completely as possible the fields - of the application definition behind instead of filling in these - details into the experiment_description free-text description field. - - Users are encouraged to add in this field eventual DOIs to papers - which yield further details to the experiment. - - - - - ISO 8601 time code with local time zone offset to UTC information - included when the microscope session started. - If the application demands that time codes in this section of the - application definition should only be used for specifying when the - experiment was performed - and the exact duration is not relevant - - this start_time field should be used. - - Often though it is useful to specify a time interval with specifying - both start_time and end_time to allow for more detailed bookkeeping - and interpretation of the experiment. The user should be aware that - even with having both dates specified, it may not be possible - to infer how long the experiment took or for how long data - were collected. - - More detailed timing data over the course of the experiment have to be - collected to compute this event chain during the experiment. - - - - - - ISO 8601 time code with local time zone offset to UTC included - when the microscope session ended. - - - - - - - - - - - Neither the specimen_name nor the experiment_identifier but the identifier - through which the experiment is referred to in the control software. - For LEAP instruments it is recommended to use the IVAS/APSuite - run_number. For other instruments, such as the one from Stuttgart or - Oxcart from Erlangen, or the instruments at GPM in Rouen, use the - identifier which is closest in meaning to the LEAP run number. - The field does not have to be required if the information is recoverable - in the dataset which for LEAP instruments is the case when RHIT or HITS - files are also stored alongside a data artifact instance which is - generated according to this NXapm application definition. - - As a destructive microscopy technique, a run can be performed only once. - It is possible, however, to interrupt a run and restart data acquisition - while still using the same specimen. In this case, each evaporation run - needs to be distinguished with different run numbers. - We follow this habit of most atom probe groups. - - This application definition does currently not allow storing the - entire set of such interrupted runs. Not because of a technical limitation - within NeXus but because we have not seen a covering use case based - on which we could have designed and implemented this case. - Atom probers are invited to contact the respective people in the - FAIRmat team to fix this. - - - - - Binary container for a file or a compressed collection of files which - can be used to add further descriptions and details to the experiment. - The container can hold a compressed archive. - - Required for operation_mode apt_fim or other to give further details. - Users should not abuse this field to provide free-text information. - Instead, these pieces of information should be mapped to - respective groups and sections. - - - - - A small image that is representative of the entry; this can be an - image taken from the dataset like a thumbnail of a spectrum. - A 640 x 480 pixel jpeg image is recommended. - Adding a scale bar to that image is recommended but not required - as the main purpose of the thumbnail is to provide e.g. thumbnail - images for displaying them in data repositories. - - - - - - What type of atom probe microscopy experiment is performed. - This field is primarily meant to inform materials database systems - to qualitatively filter experiments: - - * apt are experiments where the analysis_chamber has no imaging gas. - experiment with LEAP instruments are typically performed as apt. - * fim are experiments where the analysis_chamber has an imaging gas, - which should be specified with the atmosphere in the analysis_chamber group. - * apt_fim should be used for combinations of the two imaging modes. - * other should be used in combination with the user specifying details in the - experiment_documentation field. - - - - - - - - - - - - Contact information and eventually details person(s) involved in the - microscope session. This can be the principle investigator who performed - this experiment. Adding multiple users if relevant is recommended. - - - - Given (first) name and surname of the user. - - - - - Name of the affiliation of the user at the point in time - when the experiment was performed. - - - - - Postal address of the affiliation. - - - - - Email address of the user at the point in time when the experiment - was performed. Writing the most permanently used email is recommended. - - - - - Globally unique identifier of the user as offered by services - like ORCID or ResearcherID. If this field is field the specific - service should also be written in orcid_platform - - - - - Name of the OrcID or ResearcherID where the account - under orcid is registered. - - - - - (Business) (tele)phone number of the user at the point - in time when the experiment was performed. - - - - - Which role does the user have in the place and at the point - in time when the experiment was performed? Technician operating - the microscope. Student, postdoc, principle investigator, guest - are common examples. - - - - - Account name that is associated with the user - in social media platforms. - - - - - Name of the social media platform where the account - under social_media_name is registered. - - - - - - Description of the sample from which the specimen was prepared or - site-specifically cut out using e.g. a focused-ion beam instrument. - - The sample group is currently a place for storing suggestions from - atom probers about other knowledge they have gained about the sample - from which they cut the specimen which is field-evaporated during the - experiment. Typically this is possible because the atom probe specimen - is usually not heat treated as is but one assumes that one has the sample - prepared as needed (i.e. with a specific grain diameter) and can thus - just cut out the specimen from that material. - - There are cases though where the specimen is processed further, i.e. the - specimen is machined further or exposed to external stimuli during the - experiment. In this case, these details should not be stored in the - sample group but atom probers should make suggestions how this application - definition can be improved to find a better place and compromise - how to improve this application definition. - - In the future also details like how the grain_diameter was characterized, - how the sample was prepared, how the material was heat-treated etc., - should be stored as using specific application definitions/schemas - which are then arranged and documented with a description of the workflow - so that actionable graphs become instantiatable. - - - - Qualitative information about the grain size, here specifically - described as the equivalent spherical diameter of an assumed - average grain size for the crystal ensemble. - Users of this information should be aware that although the grain - diameter or radius is often referred to as grain size and used in - e.g. Hall-Petch-type materials models this is if at all an ensemble - average whose reporting may be very informative or not if the specimen - contains a few grains only. In atom probe the latter is often the case - because grains are measured partially as their diameter can be in the - order of magnitude of the physical diameter of the specimen. - - Reporting a grain size is useful though as it allows judging if - specific features are expected to be found in the detector hit map. - - - - - Magnitude of the standard deviation of the grain_diameter. - - - - - The temperature of the last heat treatment step before quenching. - Knowledge about this value can give an idea how the sample - was heat treated, however if available a documentation of the - annealing treatment should be delivered by adding additional files - which are uploaded alongside an NXapm instance. - In the future there should better be an own schema used for the - heat treatment. - - - - - Magnitude of the standard deviation of the heat_treatment_temperature. - - - - - Rate of the last quenching step. - Knowledge about this value can give an idea how the specimen - was heat treated, however there are many situations where one - can imagine that the scalar value for just the quenching rate, - i.e. the first derivative of the measured time-temperature profile - is itself time-dependant. An example is when the specimen was - left in the furnace after the furnace was switched off. In this case - the specimen cools down with a specific rate of how this furnace - cools down in the lab. Processes which in practice are often not - documented with measuring the time-temperature profile. - - This can be problematic because when the furnace door was left open - or the ambient temperature in the lab changes, i.e. for a series of - experiments where one is conducted on a hot summer - day and the next during winter as might have an effect on the - evolution of the microstructure. There are many cases where this - has been reported to be an issue in industry, e.g. think about aging - aluminium samples left on the factory parking lot on a hot summer - day. - - - - - Magnitude of the standard deviation of the heat_treatment_quenching_rate. - - - - - - The chemical composition of the sample. Typically it is assumed that - this more macroscopic composition is representative for the material - so that the composition of the typically substantially less voluminous - specimen probes from the more voluminous sample. - - - - Reporting compositions as atom and weight percent yields both - dimensionless quantities but their conceptual interpretation - differs. A normalization based on atom_percent counts relative to the - total number of atoms are of a particular type. By contrast, weight_percent - normalization factorizes in the respective mass of the elements. - Python libraries like pint are challenged by these differences as - at.-% and wt.-% both yield fractional quantities. - - - - - - - - - - Human-readable name of the element/ion (e.g. Fe). - Name has to be a symbol of an element from the periodic table. - All symbols in the set of NXion instances inside the group - chemical_composition need to be disjoint. - - - - - Composition value for the element/ion referred to under name. - The value is normalized based on normalization, i.e. composition - is either an atom or weight percent quantity. - - - - - Magnitude of the standard deviation of the composition (value). - - - - - - - - - - Descriptive name or ideally (globally) unique persistent identifier. - The name distinguishes the specimen from all others and especially the - predecessor/origin (see the sample group) from where this specimen was cut. - In cases where the specimen was e.g. site-specifically cut from the - sample referred to in the sample group or in cases of an instrument session - during which multiple specimens are loaded, the name has to be descriptive - enough to resolve which specimen on e.g. the microtip array was taken. - - The user is advised to store the details how a specimen was cut/prepared - from a specific sample in the sample_history. The sample_history field - must not be used for writing an alias of the specimen. Instead, - use the field alias for this. As an example there may be a specimen/sample - monitoring system in a lab with bar codes. The bar code is a good - specimen/sample name. A shorter and more human readable alias like - A0 can be an example for something to write in the alias field. - - In cases where multiple specimens have been loaded into the microscope - the name has to be the specific one, whose results are stored - by this NXentry, because a single NXentry is to be used for the - characterization of a single specimen in a single continuous run. - - Details about the specimen preparation should be stored in the - sample_history or if this is not possible in the sample group. - - - - - Ideally, a reference to the location of or a (globally) unique - persistent identifier of e.g. another file which should document - ideally as many details as possible of the material, its - microstructure, and its thermo-chemo-mechanical processing/ - preparation history. - - In the case that such a detailed history of the sample/specimen is not - available, use this field as a free-text description to specify a - sub-set of the entire sample history, i.e. what you would consider - as being the key steps and relevant information about the specimen, - its material, microstructure, thermo-chemo-mechanical processing - state and details of the preparation. - - - - - ISO 8601 time code with local time zone offset to UTC information - when the specimen was prepared. - - Ideally, report the end of the preparation, i.e. the last known time - the measured specimen surface was actively prepared. Usually this - should be a part of the sample history, i.e. the sample is imagined - handed over for the analysis. At the point it enters the microscope - the session starts. - - Knowing when the specimen was exposed to e.g. specific atmosphere is - especially required for environmentally sensitive material such as - hydrogen charged specimens or experiments including tracers with a - short half time. Further time stamps prior to preparation_date should - better be placed in resources which describe the sample_history. - - - - - Short_name or abbreviation of the specimen name field. - - - - - List of comma-separated elements from the periodic table - that are contained in the sample. - If the sample substance has multiple components, all - elements from each component must be included in `atom_types`. - - The purpose of the field is to offer materials database systems an - opportunity to parse the relevant elements without having to interpret - these from the sample history or from other data sources. - - - - - Discouraged free-text field in case properly designed records - for the sample_history or sample section are not available. - - - - - Report if the specimen is polycrystalline, in which case it - contains a grain or phase boundary, or if the specimen is a - single crystal. - - - - - - - Hard link to a location in the hierarchy of the NeXus file - where the data for default plotting are stored. - - - - - Container to hold different coordinate systems conventions. - - For the specific idea and conventions to use with the - NXcoordinate_system_set inspect the description of the - NXcoordinate_system_set base class. Specific details for application - in atom probe microscopy follow. - - In this research field scientists distinguish usually several - Euclidean coordinate systems (CS): - - * World space; - a CS specifying a local coordinate system of the planet earth which - identifies into which direction gravity is pointing such that - the laboratory space CS can be rotated into this world CS. - * The laboratory space; - a CS specifying the room where the instrument is located in or - a physical landmark on the instrument, e.g. the direction of the - transfer rod where positive is the direction how the rod - has to be pushed during loading a specimen into the instrument. - In summary, this CS is defined by the chassis of the instrument. - * The specimen space; - a CS affixed to either the base or the initial apex of the specimen, - whose z axis points towards the detector. - * The detector space; - a CS affixed to the detector plane whose xy plane is usually in the - detector and whose z axis points towards the specimen. - This is a distorted space with respect to the reconstructed ion - positions. - * The reconstruction space; - a CS in which the reconstructed ion positions are defined. - The orientation depends on the analysis software used. - * Eventually further coordinate systems attached to the - flight path of individual ions might be defined. - - Coordinate systems should be right-handed ones. - Clockwise rotations should be considered positive rotations. - - In atom probe microscopy a frequently used choice for the detector - space (CS) is discussed with the so-called detector space image - (stack). This is a stack of two-dimensional histograms of detected ions - within a predefined evaporation ID interval. Typically, the set of - ion evaporation sequence IDs is grouped into chunks. - - For each chunk a histogram of the ion hit positions on the detector - is computed. This leaves the possibility for inconsistency between - the so-called detector space and the e.g. specimen space. - - The transformation here resolves this ambiguity by specifying how - the positive z-axes of either coordinate systems is oriented. - Consult the work of A. J. Breen and B. Gault and team - for further details. - - - - - - - - - - Metadata and numerical data of the atom probe and the lab in which it - stands. - - An atom probe microscope (experiment) is different compared to a large- - scale facility or electron accelerator experiments in at least two ways: - - * First, ionized atoms and molecular ion(s fragments) - (in the case of atom probe tomography) - and (primarily) imaging gas ions (in the case of field ion - microscopy) are accelerated towards a position-sensitive - and time-of-flight taking detector system. - Hence, there is no real probe/beam. - * Second, the specimen is the lens of the microscope. - - - - - Given name of the atom probe at the hosting institution. This is an - alias. Examples could be LEAP5000, Raptor, Oxcart, one atom at a time, - etc. - - - - - Location of the lab or place where the instrument is installed. - Using GEOREF is preferred. - - - - - - - - - - - The space inside the atom probe along which ions pass nominally - when they leave the specimen and travel to the detector. - - THIS DOCSTRING NEEDS CLARIFICATION. - - - - - - The nominal diameter of the specimen ROI which is measured in the - experiment. It is important to mention that the physical specimen - cannot be measured completely because ions may launch but not be - detected or hit elsewhere in the analysis_chamber. - - - - - - - Is a reflectron installed and was it used? - - - - - - - - - - - - - - - - A local electrode guiding the ion flight path. Also called - counter or extraction electrode. - - - - Identifier of the local_electrode in an e.g. database. - - - - - - - - - - - - - - - - Detector for taking raw time-of-flight and - ion/hit impact positions data. - - - - Description of the detector type. Specify if the detector is - not the usual type, i.e. not a delay-line detector. - In the case the detector is a multi-channel plate/ - delay line detector, use mcp_dld. In the case the detector is - a phosphor CCD use phosphor_ccd. In other case specify - the detector type via free-text. - - - - - - Given name/alias. - - - - - - Given brand or model name by the manufacturer. - - - - - Given hardware name/serial number or hash identifier - issued by the manufacturer. - - - - - Given name of the manufacturer. - - - - - Amplitude of the signal detected on the multi-channel plate (MCP). - - This field should be used for storing the signal amplitude quantity - within ATO files. The ATO file format is used primarily by the - atom probe groups of the GPM in Rouen, France. - - - - - - - - - - - - - - - - - - - Atom probe microscopes use controlled laser, voltage, or a - combination of pulsing strategies to trigger the excitation - and eventual field evaporation/emission of an ion during - an experiment. - If pulse_mode is set to laser or laser_and_voltage (e.g. for - LEAP6000-type instruments) having the group/section laser_gun - is required and the following of its fields have to be filled: - - * name - * wavelength - * energy - - - - - - - - - - - - - - - - - - - - - - Average temperature at the specimen base, i.e. - base_temperature during the measurement. - - - - - The best estimate, at experiment time, for the temperature at the - sample base (furthest point along sample apex and holding assembly - that is removable from the sample stage). - - - - - - - - - - - - - - - - - - - - Average pressure in the analysis chamber. - - - - - - - - - - - - - - - - Average pressure in the buffer chamber. - - - - - - - - - - - - - - - - Average pressure in the load_lock_chamber. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A possible place, which has to be discussed with the atom probe - community more though, where quantitative details about the calibration - of the counter electrode could be stored. Work in this direction was - e.g. reported by the `Erlangen group <https://www.youtube.com/watch?v=99hNEkqdj78t=1876s>`_ - (see `P. Felfer et al. <http://dx.doi.org/10.1016/j.ultramic.2016.07.008>`_ ) - - - - - - - A place where details about the initial shape of the specimen - can be stored. Ideally, here also data about the shape evolution - of the specimen can be stored. There are currently very few - techniques which can measure the shape evolution: - - * Correlative electron microscopy coupled with modeling - but this usually takes an interrupted experiment - in which the specimen is transferred, an image taken, - and a new evaporation sequence initiated. - Examples are `I. Mouton et al. <https://doi.org/10.1017/S1431927618016161>`_ - and `C. Fletcher <https://doi.org/10.1088/1361-6463/abaaa6>`_. - * Another method, which is less accurate though, is to monitor - the specimen evolution via the in-built camera system - (if available) in the instrument. - * Another method is to use correlated scanning force microscopy - methods like reported in `C. Fleischmann <https://doi.org/10.1016/j.ultramic.2018.08.010>`_. - * A continuous monitoring of the specimen in a - correlative electron microscopy/atom probe experiment - is planned to be developed by `T. Kelly et al. <https://doi.org/10.1017/S1431927620022205>`_ - Nothing can be said about the outcome of this research yet but - here is where such spatio-temporally data could be stored. - - - - - Ideally measured or best elaborated guess of the - initial radius of the specimen. - - - - - Ideally measured or best elaborated guess of the shank angle. - This is a measure of the specimen taper. Define it in such a way - that the base of the specimen is modelled as a conical frustrum so - that the shank angle is the (shortest) angle between the specimen - space z-axis and a vector on the lateral surface of the cone. - - - - - Average detection rate over the course of the experiment. - - - - - - Estimated field at the apex along the evaporation sequence. - - - - - - - - - The majority of atom probe microscopes come from a - single commercial manufacturer `AMETEK (formerly Cameca) <https://www.atomprobe.com>`_. - Their instruments are controlled via an(/a set) of integrated - instrument control system(s) (APSuite/IVAS/DAVis). - - By contrast, instruments which were built by individual - research groups such as of the French (GPM, Rouen, France), - the Schmitz (Inspico, Stuttgart, Germany), - the Felfer (Oxcart, Erlangen, Germany), - the Northwestern (D. Isheim, Seidman group et al.), - or the PNNL group (Pacific Northwest National Laborary, - Portland, Oregon, U.S.) have other solutions - to control the instrument. - - Some of which are modularized and open, - some of which realize also integrated control units with - portions of eventually undisclosed source code and - (so far) lacking (support of)/open APIs. - - Currently, there is no accepted/implemented - community-specific API for getting finely granularized - access to such control settings. - - These considerations motivated the design of the NXapm - application definition in that it stores quantities in NXcollection. - groups to begin with. Holding heterogeneous, not yet standardized - but relevant pieces of information is the purpose of this collection. - - - - - - - - - - Track time-dependent details over the course of the measurement about the - buffer_chamber. - - - - - Track time-dependent details over the course of the measurement about the - load_lock_chamber. - - - - - Track time-dependent details over the course of the measurement about the - analysis_chamber. - - - - - - - - A statement whether the measurement was successful or failed prematurely. - - - - - - - - - - - - - Details about where ions hit the ion_detector and data processing - steps related to analog-to-digital conversion of detector signals - into ion hit positions. For AMETEK LEAP instruments this processing - takes place partly in the control unit of the detector partly - in the software. The process is controlled by the acquisition/ - instrument control software (IVAS/APSuite/DAVis). - The exact details are not documented by AMETEK in an open manner. - For instruments built by individual research groups, - like the Oxcart instrument, individual timing data from the - delay-line detector are openly accessible. - - - - - - - - - - - Raw readings from the analog-to-digital-converter - timing circuits of the detector wires. - - - - - - - - - - Evaluated ion impact coordinates at the detector - (either as computed from the arrival time data - or as reported by the control software). - If the acquisition software enables it one can also store in this - field the hit_positions, as measured by the detector, without any - corrections. - - - - - - - - - - - This could be a place where currently the publicly undocumented - algorithmic steps are stored how detected hits are judged for their - quality. In CamecaRoot this there is something mentioned like - golden and partial hits, here is where this could be documented. - - - - - - - Data post-processing step which is, like the impact position analyses, - usually executed in the integrated control software. This processing - yields how many ions were detected with each pulse. - - It is possible that multiple ions evaporate and hit the same or - different pixels of the detector on the same pulse. - These data form the basis to analyses of the so-called - (hit) multiplicity of an ion. - - Multiplicity must not be confused with how many atoms - f the same element or isotope, respectively, a molecular - ion contains (which is instead encoded with the - isotope_vector field of each NXion instance). - - - - - - - - - - Number of pulses since the last detected ion pulse. - For multi-hit records, after the first record, this is zero. - - - - - - - - - Number of pulses since the start of the atom probe - run/evaporation sequence. - - - - - - - - - Hit multiplicity. - - - - - - - - - Like impact position and hit multiplicity computations, - ion filtering is a data post-processing step with which users - identify which of the detected ions should be included - in the voltage-and-bowl correction. - This post-processing is usually performed via GUI interaction - in the reconstruction pipeline of IVAS/APSuite. - - - - - - - - - - Bitmask which is set to true if the ion - is considered and false otherwise. - - - - - - - - - - Data post-processing step to correct for ion impact - position flight path differences, detector biases, - and nonlinearities. This step is usually performed - with commercial software. - - - - - - - - - - - Raw time-of-flight data as read out from the acquisition software - if these data are available and accessible. - - - - - - - - - Calibrated time-of-flight. - - - - - - - - The key idea and algorithm of the voltage-and-bowl correction is - qualitatively similar for instruments of different manufacturers - or research groups. - - Specific differences exists though in the form of different - calibration models. For now we do not wish to resolve or - generalize these differences. Rather the purpose of this collection - is to provide a container where model-specific parameters - and calibration models can be stored if users know these - for sure. - - For AMETEK LEAP instruments this should be the place for - storing initial calibration values. These values are - accessible normally only by AMETEK service engineers. - They use these for calibrating the detector and instrument. - - Users can also use this NXcollection for storing the - iteratively identified calibrations which scientists - will see displayed in e.g. APSuite while they execute - the voltage-and-bowl correction as a part of the - reconstruction pipeline in APSuite. - - - - - - - Data post-processing step in which calibrated time-of-flight data - (ToF) are interpreted into mass-to-charge-state ratios. - - - - - - - - - - Store vendor-specific calibration models here (if available). - - - - - Mass-to-charge-state ratio values. - - - - - - - - - - - Data post-processing step to create a tomographic reconstruction - of the specimen based on selected calibrated ion hit positions, - the evaporation sequence, and voltage curve data. - Very often scientists use own software scripts according to - published procedures, so-called reconstruction protocols, - i.e. numerical recipes how to compute x, y, z atomic positions - from the input data. - - - - - - - - - - Qualitative statement about which reconstruction protocol was used. - - - - - - - - - - - - - Different reconstruction protocols exist. Although these approaches - are qualitatively similar, each protocol uses different parameters - (and interprets these differently). The source code to IVAS/APSuite - is not open. For now users should store reconstruction parameter - in a collection. - - - - - - Different strategies for crystallographic calibration of the - reconstruction are possible. The field is required and details - should be specified in free-text at least. If the not crystallographic - calibration was performed the field should be filled with the n/a, - meaning not applied. - - - - - Three-dimensional reconstructed positions of the ions. - Interleaved array of x, y, z positions in the specimen space. - - - - - - - - - - An array of triplets of integers which can serve as a supplementary - array for Paraview to display the reconstructed dataset. - The XDMF primitive type is here 1, the number of primitives 1 per - triplet, the last integer in each triplet is the identifier of - each point starting from zero. - - - - - - - - - - Six equally formatted sextets chained together. For each - sextett the first entry is an XDMF primitive topology - key (here 5 for polygon), the second entry the XDMF primitive - count value (here 4 because each face is a quad). - The remaining four values are the vertex indices. - - - - - - - - To get a first overview of the reconstructed dataset, - the format conversion computes a simple 3d histogram - of the ion density using one nanometer cubic bins without - applying smoothening algorithms on this histogram. - - - - - - - - - A default three-dimensional histogram of the total - number of ions in each bin obtained via using a rectangular - transfer function. - - - - - - - - - Array of counts for each bin. - - - - - - - - - - Bin center of mass position along the z axis. - - - - - - - - - Bin center of mass position along the y axis. - - - - - - - - - Bin center of mass position along the x axis. - - - - - - - - - - - - - Data post-processing step in which elemental, isotopic, - and/or molecular identities are assigned to the ions. - The documentation of these steps is based on ideas - described in the literature: - - * `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ - * `D. Haley et al. <https://doi.org/10.1017/S1431927620024290>`_ - * `M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_ - - - - - - - - - - How many ion types are distinguished. - If no ranging was performed each ion is of the special unknown type. - The iontype ID of this unknown type is 0 which is a reserve value. - Consequently, iontypes start counting from 1. - - - - - Assumed maximum value that suffices to store all relevant - molecular ions, even the most complicated ones. - Currently a value of 32 is used. - - - - - Specifies the computation of the mass-to-charge histogram. - Usually mass-to-charge values are studied as an ensemble quantity, - specifically these values are binned. - This (NXprocess) stores the settings of this binning. - - - - - - - - - Smallest and largest mass-to-charge-state ratio value. - - - - - - - - - Binning width of the mass-to-charge-state ratio values. - - - - - - A default histogram aka mass spectrum of - the mass-to-charge-state ratio values. - - - - - - - - - Array of counts for each bin. - - - - - - - - - Right boundary of each mass-to-charge-state ratio value bin. - - - - - - - - - - - - Details of the background model which was used to - correct the total counts per bin into counts. - - - - - - - - - - - How where peaks in the background-corrected in the histogram - of mass-to-charge-state ratio values identified? - - - - - - - - - - - THIS DOCSTRING NEEDS CLARIFICATION. - - - - - - - Details about how peaks, with taking into account - error models, were interpreted as ion types or not. - - - - - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_composition_space_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_composition_space_results.nxdl.xml deleted file mode 100644 index 15c107d..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_composition_space_results.nxdl.xml +++ /dev/null @@ -1,488 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of voxel of discretized domain for analyzed part of the dataset. - - - - - The dimensionality of the grid. - - - - - The cardinality or total number of cells/grid points. - - - - - Number of terms in the composition clustering dictionary - - - - - Number of terms in the position clustering dictionary - - - - - Results of a run with Alaukik Saxena's composition space tool. - - This is an initial draft application definition for the common NFDI-MatWerk, - FAIRmat infrastructure use case IUC09 how to improve the organization and - results storage of the composition space tool and make these data at the same - time directly understandable for NOMAD. - - This draft does no contain yet the annotations for how to also store - in the HDF5 file a default visualization whereby the composition grid - could directly be explored using H5Web. I am happy to add this ones the - data have been mapped on this schema, i.e. more discussion needed. - - Also iso-surfaces can be described, for paraprobe, this is a solved problem, - check the respective group in the NXapm_paraprobe_results_nanochem data - schema/application definition. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - - - - - - TBD, maybe how to link between pyiron state tracking and app state tracking - - - - - Disencouraged place for free-text for e.g. comments. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. when composition space tool was started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and composition space tool exited as a process. - - - - - The path and name of the config file for this analysis. - TBD, this can be e.g. Alaukik's YAML file for composition space. - - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - - The path and name of the file (technology partner or community format) - from which reconstructed ion positions were loaded. - - - - - - - - The path and name of the file (technology partner or community format - from which ranging definitions, i.e. how to map mass-to- - charge-state ratios on iontypes were loaded. - - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - A statement whether the executable managed to process the analysis - or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must not compute any analysis. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - - - - The individual coordinate systems which should be used. - Some suggestions follow, e.g. that field names should be prefixed - with the following controlled terms indicating which individual - coordinate system is described: - - * world - * composition_space - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Reference to or definition of a coordinate system with - which the positions and directions are interpretable. - - - - - - - - - - Position of each cell in Euclidean space. - - - - - - - - - - - - - - - - For each ion, the identifier of the voxel in which the ion is located. - - - - - - - - - - - - - - - - - - In Alaukik's tool the GMM step. - - - - - - - - - The keywords of the dictionary of distinguished compositionally- - defined cluster, e.g. the phases. Examples for keywords could be - phase1, phase2, and so one and so forth. - - - - - - - - Resolves for each keyword in cluster_dict which integer is used to - label something that it belongs or is assumed to represent this - cluster. - - - - - - - - - For example if the voxel grid is used to report that there - are voxels which are assumed to represent volume of either phase1 - or phase2, the cluster_dict_keyword would be a list with two names - phase1 and phase2, respectively. The cluster_dict_value would be a - list of e.g. integers 1 and 2. These could be used to build an - array with as many entries as there are voxel and store in this array - the respective value to encode which phase is assumed for each voxel. - - - - - - - - - - In Alaukik's tool the DBScan step after the GMM step. - - - - - - - - - The keywords of the dictionary of distinguished spatially-contiguous - clusters. Examples for keywords could be precipitate1, precipitate2, - and so one and so forth. - - - - - - - - Resolves for each keyword in cluster_dict which integer is used to - label something that it belongs or is assumed to represent this - cluster. - - - - - - - - - For example if the voxel grid is used to report that there - are voxels which are assumed to represent volume of certain precipitates, - say we found ten precipitates and consider the rest as matrix. - We could make a list of say matrix, precipitate1, precipitate2, ..., - precipitate10. With cluster_dict_value then running from 0 to 10, - i.e. matrix is flagged special as 0 and the remaining particles - are indexed conveniently as 1, 2, ..., 10 like end users expect. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_compositionspace_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_compositionspace_config.nxdl.xml new file mode 100644 index 0000000..157a362 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_compositionspace_config.nxdl.xml @@ -0,0 +1,208 @@ + + + + + + Application definition for a configuration of the CompositionSpace tool used in atom probe. + + * `A. Saxena et al. <https://www.github.com/eisenforschung/CompositionSpace.git>`_ + + This is an application definition for the common NFDI-MatWerk/FAIRmat infrastructure + use case IUC09 that explores how to improve the organization and results storage of the + CompositionSpace tool by using the NeXus data model and semantics. + + + + + + + + + + + + Specification of the tomographic reconstruction used for this analysis. + + Reconstructions in the field of atom probe tomography are communicated via + a file which stores the reconstructed position and mass-to-charge-state-ratio + value for each ion. + + Container file formats like HDF5, such as NeXus/HDF5 files using :ref:`NXapm`, + can store multiple reconstructions. In this case, the position and mass_to_charge + concepts point to specific instances in the file referred to by file_name for the + analysis with CompositionSpace. + + + + + + + Name of the node which resolves the reconstructed + ion position values to use for this analysis. + + + + + Name of the node which resolves the mass-to-charge-state-ratio + values for each reconstructed ion to use for this analysis. + + + + + + Specification of the ranging definitions used for this analysis. + + Ranging definitions in the field of atom probe tomography are communicated via + a file which stores the mass-to-charge-state-ratio interval and the number of elements + of which each (molecular) ion is composed. These values are stored for each ion. + + Container file formats like HDF5, such as NeXus/HDF5 files using :ref:`NXapm`, + can store multiple ranging definitions. + + Indices of ions start from 1. The value 0 is reserved for the null model of unranged positions + whose iontype is referred to as the unknown_type. The value 0 is also reserved for voxels + that lie outside the dataset. + + + + + + + Name of that (parent) node whose child stores the ranging definitions that + are applied in this analysis with CompositionSpace. + + + + + + Step during which the point cloud is discretized to compute element-specific composition fields. + Iontypes are atomically decomposed to correctly account for the multiplicity of each element that + was ranged for each ion. + + + + Edge length of cubic voxels building the 3D grid that is used for discretizing + the point cloud. + + + + + Optional step during which the subsequent segmentation step is prepared with the aim to eventually + reduce the dimensionality of the chemical space in which the machine learning model works. + + In this step a supervised reduction of the dimensionality of the chemical space is quantified using + the (Gini) feature importance of each element to suggest which columns of the composition matrix + should be taken for the subsequent segmentation step. + + + + Was the automated phase assignment used? + + + + + Estimated guess for which a Gaussian mixture model is evaluated to preprocess a result that + is subsequently post-processed with a random_forest_classifier to lower the number of + dimensions in the chemical space to the subset of trunc_species many elements with the + highest feature importance. + + + + + The number of elements to use for reducing the dimensionality. + + + + + Configuration for the random forest classification model. + + + + + + + Step during which the voxel set is segmented into voxel sets + with different chemical composition. + + + + A principal component analysis of the chemical space to guide a decision into how many sets of voxels + with different chemical composition the machine learning algorithm suggests to split the voxel set. + + + + + The decision is guided through the evaluation of the information criterion + minimization. + + + + The maximum number of chemical classes to probe with the Gaussian mixture model + with which the voxel set is segmented into a mixture of voxels with that many different + chemical compositions. + + + + + Configuration for the Gaussian mixture model that is used in the segmentation + step. + + + + + + + Step during which the chemically segmented voxel sets are analyzed for their + spatial organization. + + + + Configuration for the DBScan algorithm that is used in the clustering step. + + + + The maximum distance between voxel pairs in a neighborhood to be considered + connected. + + + + + The number of voxels in a neighborhood for a voxel to be considered as a core + point. + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_compositionspace_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_compositionspace_results.nxdl.xml new file mode 100644 index 0000000..92a2f35 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_compositionspace_results.nxdl.xml @@ -0,0 +1,420 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The dimensionality of the grid. + + + + + Total number of voxels. + + + + + Total number of ions in the reconstructed dataset. + + + + + Application definition for results of the CompositionSpace tool used in atom probe. + + * `A. Saxena et al. <https://www.github.com/eisenforschung/CompositionSpace.git>`_ + + This is an application definition for the common NFDI-MatWerk/FAIRmat infrastructure + use case IUC09 that explores how to improve the organization and results storage of the + CompositionSpace software using NeXus. + + + + + + + + + + + + + + + + + + + + + + + Programs and libraries representing the computational environment + + + + + + + + + + + Configuration file that was used in this analysis. + + + + + + + + + + Contextualize back to the specimen from which the + dataset was collected that was here analyzed with + CompositionSpace tool. + + + + True, if the specimen that the reconstructed dataset + describes is a simulated one. + False, if the specimen that the reconstructed dataset + describes is a real one. + + + + + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by identifier_parent or walk through + eventually deeply nested groups in data instances. + + + + + + Step during which the point cloud is discretized to compute element-specific composition fields. + Iontypes are atomically decomposed to correctly account for the multiplicity of each element that + was ranged for each ion. + + Using a discretization grid that is larger than the average distance between reconstructed ion positions + reduces computational costs. This is the key idea of the CompositionSpace tool compared to other methods + used in atom probe for characterizing microstructural features that use the ion position data directly. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Position of each cell in Euclidean space. + + + + + + + + + Discrete coordinate of each voxel. + + + + + + + + + + For each ion, the identifier of the voxel into which the ion binned. + + + + + + + + + Total number of weight (counts for discretization with a rectangular transfer function) + for the occupancy of each voxel with atoms. + + + + + + + + + Chemical symbol of the element from the periodic table. + + + + + Element-specific weight (counts for discretization with a rectangular transfer function) + for the occupancy of each voxel with atoms of this element. + + + + + + + + + + Optional step during which the subsequent segmentation step is prepared to + improve the segmentation. + + + + + + + + + + + + + + Element identifier stored sorted in descending order of feature importance. + + + + + + + Axis caption + + + + + + Element relative feature importance stored sorted in descending order of feature + importance. + + + + + + + Axis caption + + + + + + + + Step during which the voxel set is segmented into voxel sets with different + chemical composition. + + + + PCA in the chemical space (essentially composition correlation analyses). + + + + + + + + + + + + + + + Explained variance values + + + + + + + + Elements identifier matching those from ENTRY/voxelization/ionID + used during the principal component analysis. + + + + + + + + + + Information criterion minimization. + + + + + + + + + + Results of the Gaussian mixture analysis for n_components equal to n_ic_cluster. + + + + n_components argument of the Gaussian mixture model. + + + + + y_pred return values of the computation. + + + + + + + + + Information criterion as a function of number of n_ic_cluster aka dimensions. + + + + + + + + Akaike information criterion values + + + + + + + + Bayes information criterion values + + + + + + + + Actual n_ic_cluster values used + + + + + + + + + + + Step during which the chemically segmented voxel sets are analyzed for their spatial organization + into different spatial clusters of voxels in the same chemical set but representing individual objects. + The objects are constructed from blobs of neighboring voxels. + The objects are not necessarily watertight or topologically closed. + + + + + + + + + + Respective DBScan clustering result for each segmentation/ic_opt case. + + + + + + The maximum distance between voxel pairs in a neighborhood + to be considered connected. + + + + + The number of voxels in a neighborhood for a voxel to be considered as a core + point. + + + + + Raw label return values + + + + + + + + Voxel identifier + + Using these identifiers correlated element-wise with the values in the label array + specifies for which voxel in the grid clusters from this process were found. + + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_input_ranging.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_input_ranging.nxdl.xml deleted file mode 100644 index b82a78e..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_input_ranging.nxdl.xml +++ /dev/null @@ -1,63 +0,0 @@ - - - - - - - Metadata to ranging definitions made for a dataset in atom probe microscopy. - - Ranging is the process of labeling time-of-flight data with so-called iontypes - which ideally specify the most likely ion/molecular ion evaporated within a - given mass-to-charge-state-ratio value interval. - - The paraprobe-toolbox uses the convention that the so-called UNKNOWNTYPE - iontype (or unranged ions) represents the default iontype. - The ID of this special iontype is always reserved as 0. Each ion - is assigned to the UNKNOWNTYPE by default. Iontypes are assigned - by checking if the mass-to-charge-state-ratio values of an ion matches - to any of the defined mass-to-charge-state-ratio intervals. - - - - Path and name of the NeXus/HDF5 file which stores ranging definitions. - - - - Version identifier of the file (representing an at least SHA256 strong) - hash. Such hashes serve reproducibility as they can be used for tracking - provenance metadata in a workflow. - - - - - - Name of the group (prefix to the individual ranging definitions) inside - the file referred to by filename which points to the specific ranging - definition to use. - An HDF5 file can store multiple ranging definitions. Using an ID is - the mechanism to distinguish which specific ranging (version) will - be processed. Reconstruction and ranging IDs can differ. - They specify different IDs. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_input_reconstruction.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_input_reconstruction.nxdl.xml deleted file mode 100644 index 8ed7b90..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_input_reconstruction.nxdl.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - Metadata of a dataset (tomographic reconstruction) in atom probe microscopy. - - - - Name of the (NeXus)/HDF5 file which stores reconstructed ion position - and mass-to-charge-state ratios. Such an HDF5 file can store multiple - reconstructions. Using the information within the dataset_name fields - is the mechanism whereby paraprobe decides which reconstruction to - process. With this design it is possible that the same HDF5 - file can store multiple versions of a reconstruction. - - - - Version identifier of the file (representing an at least SHA256 strong) - hash. Such hashes serve reproducibility as they can be used for tracking - provenance metadata in a workflow. - - - - - - Name of the dataset inside the HDF5 file which refers to the - specific reconstructed ion positions to use for this analysis. - - - - - Name of the dataset inside the HDF5 file which refers to the - specific mass-to-charge-state-ratio values to use for this analysis. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml new file mode 100644 index 0000000..e0fe10b --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml @@ -0,0 +1,295 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + + Maximum number of atoms per molecular ion. Should be 32 for paraprobe. + + + + + Number of clustering algorithms used. + + + + + Number of different iontypes to distinguish during clustering. + + + + + Application definition for a configuration file of the paraprobe-clusterer tool. + + The tool paraprobe-clusterer evaluates how points cluster in space. + + + + + + + + + + This process maps results from a cluster analysis made with IVAS / AP Suite + into an interoperable representation. IVAS / AP Suite usually exports such results + as a list of reconstructed ion positions with one cluster label per position. + These labels are reported via the mass-to-charge-state-ratio column of what is effectively + a binary file that is formatted like a POS file but cluster labels written out using floating + point numbers. + + + + + + + + + + + File with the results of the cluster analyses that was computed with IVAS / AP suite + (e.g. maximum-separation method clustering algorithm `J. Hyde et al. <https://doi.org/10.1557/PROC-650-R6.6>`_). + The information is stored in an improper (.indexed.) POS file as a matrix of floating + point quadruplets, one quadruplet for each ion. The first three values of each + quadruplet encode the position of the ion. The fourth value is the integer identifier + of the cluster encoded as a floating point number. + + + + + + + + Specifies if paraprobe-clusterer should use the evaporation_ids from reconstruction + for recovering for each position in the :ref:`NXnote` results the closest matching position + (within floating point accuracy). This can be useful when users wish to recover the + original evaporation_id, which IVAS /AP Suite drops when writing their *.indexed.* cluster + results POS files that is referred to results. + + + + + + + This process performs a cluster analysis on a + reconstructed dataset or a ROI within it. + + + + Distance between each ion and triangulated surface mesh. + + + + + + + + + How should iontypes be considered during the cluster analysis. + + The value resolve_all will set an ion active + in the analysis regardless of which iontype it is. + + The value resolve_unknown will set an ion active + when it is of the UNKNOWNTYPE. + + The value resolve_ion will set an ion active + if it is of the specific iontype, irregardless of its nuclide structure. + + The value resolve_element will set an ion active and account as many times + for it, as the (molecular) ion contains atoms of elements in the whitelist + ion_query_nuclide_vector. + + The value resolve_isotope will set an ion active and account as many times + for it, as the (molecular) ion contains nuclides in the whitelist + ion_query_nuclide_vector. + + In effect, ion_query_nuclide_vector acts as a whitelist to filter which ions are + considered as source ions of the correlation statistics and how the multiplicity + of each ion will be factorized. + + This is relevant as in atom probe we have the situation that an ion of a molecular + ion with more than one nuclide, say Ti O for example is counted potentially several + times because at that position (reconstructed) position it has been assumed that + there was a Ti and an O atom. This multiplicity affects the size of the feature and its + chemical composition. + + + + + + + + + Matrix of nuclide vectors, as many as rows as different candidates + for iontypes should be distinguished as possible source iontypes. + In the simplest case, the matrix contains only the proton number + of the element in the row, all other values set to zero. + + + + + + + + + + Settings for DBScan clustering algorithm. For original details about the + algorithm and (performance-relevant) details consider: + + * `M. Ester et al. <https://dx.doi.org/10.5555/3001460.3001507>`_ + * `M. Götz et al. <https://dx.doi.org/10.1145/2834892.2834894>`_ + + For details about how the DBScan algorithms is the key behind the + specific modification known as the maximum-separation method in the + atom probe community consider `E. Jägle et al. <https://dx.doi.org/10.1017/S1431927614013294>`_ + + + + Strategy how a set of cluster analyses with different parameter is executed: + + * For tuple as many runs are performed as parameter values have been defined. + * For combinatorics individual parameter arrays are looped over. + + As an example we may provide ten entries for eps and three entries for min_pts. + If high_throughput_method is set to tuple, the analysis is invalid because we have + an insufficient number of min_pts values to pair them with our ten eps values. + By contrast, if high_throughput_method is set to combinatorics, the tool will run three + individual min_pts runs for each eps value, resulting in a total of 30 analyses. + + A typical example from the literature `M. Kühbach et al. <https://dx.doi.org/10.1038/s41524-020-00486-1>`_ + can be instructed via setting eps to an array of values np.linspace(0.2, 5.0, nums=241, endpoint=True), + one min_pts value that is equal to 1, and high_throughput_method set to combinatorics. + + + + + + + + + Array of epsilon (eps) parameter values. + + + + + + + + Array of minimum points (min_pts) parameter values. + + + + + + + + + + Settings for the HPDBScan clustering algorithm. + + * L. McInnes et al. <https://dx.doi.org/10.21105/joss.00205>`_ + * scikit-learn hdbscan library `<https://hdbscan.readthedocs.io/en/latest/how_hdbscan_works.html>`_ + + See also this documentation for details about the parameter. + Here we use the terminology of the hdbscan documentation. + + + + Strategy how runs with different parameter values are composed, + following the explanation for high_throughput_method of dbscan. + + + + + + + + + Array of min_cluster_size parameter values. + + + + + + + + Array of min_samples parameter values. + + + + + + + + Array of cluster_selection parameter values. + + + + + + + + Array of alpha parameter values. + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml new file mode 100644 index 0000000..031010b --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml @@ -0,0 +1,229 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The total number of ions in the reconstruction. + + + + + Number of clusters found. + + + + + Application definition for a results file of the paraprobe-clusterer tool. + + The tool paraprobe-clusterer evaluates how points cluster in space. + + + + + + + + + + + + Results of a DBScan clustering analysis. + + + + The epsilon (eps) parameter used. + + + + + The minimum points (min_pts) parameter used. + + + + + Number of members in the set which is partitioned into features. + Specifically, this is the total number of targets filtered from the + dataset, i.e. typically the number of clusters which is usually not and + for sure not necessarily the total number of ions in the dataset. + + + + + Which identifier is the first to be used to label a cluster. + + The value should be chosen in such a way that special values can be resolved: + * index_offset - 1 indicates an object belongs to no cluster. + * index_offset - 2 indicates an object belongs to the noise category. + + Setting for instance index_offset to 1 recovers the commonly used + case that objects of the noise category get the value of -1 and points of the + unassigned category get the value 0. + + + + + The evaporation (sequence) id (aka evaporation_id) to figure out + which ions from the reconstruction were considered targets. The length + of this array is not necessarily n_ions. + Instead, it is the value of cardinality. + + + + + + + + + The number of solutions found for each target. Typically, + this value is 1 in which case the field can be omitted. + Otherwise, this array is the concatenated set of values of solution + tuples for each target that can be used to decode model_labels, + core_sample_indices, and weight. + + + + + + + + The raw labels from the DBScan clustering backend process. + The length of this array is not necessarily n_ions. + Instead, it is typically the value of cardinality provided that each + target has only one associated cluster. If targets are assigned to + multiple cluster this array is as long as the total number of solutions + found and + + + + + + + + The raw array of core sample indices which specify which of the + targets are core points. + + + + + + + + Numerical label for each target (member in the set) aka cluster identifier. + + + + + + + + Categorical label(s) for each target (member in the set) aka cluster name(s). + + + + + + + + Weights for each target that specifies how probable the target is assigned to + a specific cluster. + + For the DBScan algorithm and atom probe tomography this value is the + multiplicity of each ion with respect to the cluster. That is how many times + should the position of the ion be accounted for because the ion is e.g. a + molecular ion with several elements or nuclides of requested type. + + + + + + + + Are targets assigned to the noise category or not. + + + + + + + + Are targets assumed a core point. + + + + + + + + In addition to the detailed storage which members were grouped to which + feature here summary statistics are stored that communicate e.g. how many + cluster were found. + + + + + Total number of targets in the set, i.e. ions that were filtered + and considered in this cluster analysis. + + + + + Total number of members in the set which are categorized as noise. + + + + + Total number of members in the set which are categorized as a core point. + + + + + Total number of clusters (excluding noise and unassigned). + + + + + + Numerical identifier of each feature aka cluster_id. + + + + + + + + Number of members for each feature. + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_clusterer.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_clusterer.nxdl.xml deleted file mode 100644 index 4f13739..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_clusterer.nxdl.xml +++ /dev/null @@ -1,477 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - - Maximum number of atoms per molecular ion. Should be 32 for paraprobe. - - - - - Number of clustering algorithms used. - - - - - Number of different iontypes to distinguish during clustering. - - - - - Configuration of a paraprobe-clusterer tool run in atom probe microscopy. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when this configuration file was created. - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - How many tasks to perform? - - - - - This process maps results from cluster analyses performed with IVAS/APSuite - into an interoperable representation. Specifically in this process - paraprobe-clusterer takes results from clustering methods from other tools - of the APM community, like IVAS/APSuite. These results are usually reported - in two ways. Either as an explicit list of reconstructed ion positions. - In the case of IVAS these positions are reported through a text file - with a cluster label for each position. - - Alternatively, the list of positions is reported, as it is the case for - AMETEK (IVAS/AP Suite) but the cluster labels are specified implicitly - only in the following way: The mass-to-charge-state ratio column of a - what is effectively a file formatted like POS is used to assign a hypothetical - mass-to-charge value which resolves a floating point representation - of the cluster ID. - - Another case can occur where all disjoint floating point values, - i.e. here cluster labels, are reported and then a dictionary is created - how each value matches to a cluster ID. - - In general the cluster ID zero is reserved for marking the dataset - as to not be assigned to any cluster. Therefore, indices of disjoint - clusters start at 1. - - - - - - - - - AMETEK/Cameca results of cluster analyses, like with the maximum- - separation (MS) method clustering algorithm `J. Hyde et al. <https://doi.org/10.1557/PROC-650-R6.6>`_ - are stored as an improper POS file: This is a matrix of floating - point quadruplets, one for each ion and as many quadruplets as - ions were investigated. The first three values encode the position - of the ion. The fourth value is an improper mass-to-charge-state-ratio - value which encodes the integer identifier of the cluster as a floating - point number. - - - - - - - Specifies if the tool should try to recover for each position the closest - matching position from dataset/dataset_name_reconstruction (within - floating point accuracy). This can be useful for instance when users - wish to recover the original evaporation ID, which IVAS/AP Suite drops - for instance when writing their *.indexed.* cluster results POS files. - - - - - - - This process performs a cluster analysis on a reconstructed dataset - or a portion of the reconstruction. - - - - - - - - - - - - - - - - - The tool enables to inject precomputed distance information for each - point/ion which can be used for further post-processing and analysis. - - - - Name of an HDF5 file which contains the ion distances. - - - - Version identifier of the file such as a secure hash which documents - the binary state of the file to add an additional layer of - reproducibility from which file specifically contains these data. - - - - - - Absolute HDF5 path to the dataset with distance values for each ion. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - How should iontypes be interpreted/considered during the cluster analysis. - Different options exist how iontypes are interpreted (if considered at all) - given an iontype represents in general a (molecular) ion with different isotopes - that have individually different multiplicity. - - The value resolve_all will set an ion active in the analysis - regardless of which iontype it is. - The value resolve_unknown will set an ion active when it is of the - UNKNOWNTYPE. - The value resolve_ion will set an ion active if it is of the - specific iontype, irregardless of its elemental or isotopic details. - The value resolve_element will set an ion active, and most importantly, - account as many times for it, as the (molecular) ion contains - atoms of elements in the whitelist ion_query_isotope_vector. - The value resolve_isotope will set an ion active, and most importantly, - account as many times for it, as the (molecular) ion contains isotopes - in the whitelist ion_query_isotope_vector. - - In effect, ion_query_isotope_vector acts as a whitelist to filter - which ions are considered as source ions of the correlation statistics - and how the multiplicity of each ion will be factorized. - - This is relevant as in atom probe we have the situation that a ion - of a molecular ion with more than one nuclid, say Ti O for example - is counted such that although there is a single TiO molecular ion - at a position that the cluster has two members. This multiplicity - affects the size of the feature and chemical composition. - - - - - - - - - Matrix of isotope vectors, as many as rows as different candidates - for iontypes should be distinguished as possible source iontypes. - In the simplest case, the matrix contains only the proton number - of the element in the row, all other values set to zero. - Combined with ion_query_type_source set to resolve_element this will - recover usual spatial correlation statistics like the 1NN C-C - spatial statistics. - - - - - - - - - Settings for DBScan clustering algorithm. For original details about the - algorithms and (performance-relevant) details consider: - - * `M. Ester et al. <https://dx.doi.org/10.5555/3001460.3001507>`_ - * `M. Götz et al. <https://dx.doi.org/10.1145/2834892.2834894>`_ - - For details about how the DBScan algorithms is the key behind the - specific modification known as the maximum-separation method in the - atom probe community consider `E. Jägle et al. <https://dx.doi.org/10.1017/S1431927614013294>`_ - - - - Strategy how runs are performed with different parameter: - - * For tuple as many runs are performed as parameter values. - * For combinatorics individual parameter arrays are looped over. - - As an example we may define eps with ten entries and min_pts with - three entries. If high_throughput_method is tuple the analysis is - invalid as we have an insufficient number of min_pts for the ten - eps values. - By contrast, for combinatorics paraprobe-clusterer will run three - individual min_pts runs for each eps value, resulting in a total - of 30 analyses. - As an example the DBScan analysis reported in `M. Kühbach et al. <https://dx.doi.org/10.1038/s41524-020-00486-1>`_ - would have defined an array of values np.linspace(0.2, 5.0, nums=241, endpoint=True) - eps values, min_pts one, and high_throughput_method set to combinatorics. - - - - - - - - - Array of epsilon (eps) parameter values. - - - - - - - - Array of minimum points (min_pts) parameter values. - - - - - - - - - - Settings for the OPTICS clustering algorithm. - - * `M. Ankerest et al. <https://dx.doi.org/10.1145/304181.304187>`_ - - - - Strategy how runs are performed with different parameter: - - * For tuple as many runs are performed as parameter values. - * For combinatorics individual parameter arrays are looped over. - - See the explanation for the corresponding parameter for dbscan - processes above-mentioned for further details. - - - - - - - - - Array of minimum points (min_pts) parameter values. - - - - - - - - Array of maximum epsilon (eps) parameter values. - - - - - - - - - Settings for the HPDBScan clustering algorithm. - - * L. McInnes et al. <https://dx.doi.org/10.21105/joss.00205>`_ - * scikit-learn hdbscan library `<https://hdbscan.readthedocs.io/en/latest/how_hdbscan_works.html>`_ - - See also this documentation for details about the parameter. - Here we use the terminology of the hdbscan documentation. - - - - Strategy how runs are performed with different parameter: - - * For tuple as many runs are performed as parameter values. - * For combinatorics individual parameter arrays are looped over. - - See the explanation for the corresponding parameter for dbscan - processes above-mentioned for further details. - - - - - - - - - Array of min_cluster_size parameter values. - - - - - - - - Array of min_samples parameter values. - - - - - - - - Array of cluster_selection parameter values. - - - - - - - - Array of alpha parameter values. - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_distancer.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_distancer.nxdl.xml deleted file mode 100644 index 4a24598..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_distancer.nxdl.xml +++ /dev/null @@ -1,257 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Configuration/settings of a paraprobe-distancer software tool run. - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when this configuration file was created. - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - How many individual analyses should the tool execute. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Compute for all filtered points, e.g. ions of the point set - the shortest Euclidean distance to the closest triangle of the - set of triangles. The triangles can formed a closed surface mesh. - Distances are not simple distances based on normal projections but - giving an exact solution. - - - - - Paraprobe-distancer enables the computation of the Euclidean shortest - distance for each member of a set of points against a set of triangles. - In contrast to comparable methods used in atom probe the here computed - distance is not simply the projected distance to one of the triangles - but the more costly but robust computation of the distance between - a point and a triangle. - - The triangles can represent for instance the facets of a triangulated - surface mesh of a model for the edge of the dataset. Such a model can - be computed with paraprobe-surfacer. Alternatively, the triangles can - be those from the set of all facets for a set of convex hulls, alpha-shapes, - or alpha wrappings about three-dimensional objects like precipitates - (computed with e.g. paraprobe-nanochem). - - Currently, the tool does not check if the respectively specified - triangle sets are consistent, what their topology is, or whether or - not they are consistently oriented. - Each dataset that is referred to in the list_of _dataset_names_vertices - should be an (Nvertices, 3) array of NX_FLOAT. Each dataset referred - to in the list_of_dataset_names_facet_indices should be an - (Nfacets, 3) array of NX_UINT. - Facet indices refer to vertex indices. These need to start at zero - and must not exceed Nvertices - 1, i.e. the identifier_offset is 0 - and vertices are indexed thus implicitly. - Facet normal vectors have to be also an array - of shape (Nfacets, 3) of NX_FLOAT. - - - - How many triangle sets to consider. - - - - - List of triangle sets. This design allows users to combine - multiple triangle sets. - - - - Name of the HDF5 file(s) which contain(s) vertex coordinates - and facet indices to describe the desired set of triangles. - - - - Version identifier of the file such as a secure hash which - documents the binary state of the file to add an additional - layer of reproducibility. - - - - - - Absolute HDF5 path to the dataset which - specifies the array of vertex positions. - - - - - Absolute HDF5 path to the dataset which - specifies the array of facet indices. - - - - - Absolute HDF5 path to the dataset which - specifies the array of facet normal vectors. - - - - - - - Specifies for which ions/points the tool will compute distances. - The purpose of this setting is to avoid unnecessary computations - when the user requests to only compute distances of ions within a - threshold distance to the triangle soup. - - By default the distances are computed for all ions; however - the setting skin enables to compute distances only for those - ions which are not farther away located to a triangle - than threshold_distance. - - - - - - - - - - Maximum distance for which distances are computed when method is skin. - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_intersector.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_intersector.nxdl.xml deleted file mode 100644 index 615b3b7..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_intersector.nxdl.xml +++ /dev/null @@ -1,348 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Configuration of a paraprobe-intersector tool run in atom probe microscopy. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - ISO 8601 formatted time code with local time zone offset to - UTC information included when this configuration file was created. - - - - - For now a support field for the tool to identify how many individual - analyses the tool should execute as part of the analysis. - - - - - Tracking volume_volume_spatial_correlation is the process of building logical - relations between volumetric features based on meshes, their proximity and - eventual intersections. Volumetric overlap and proximity of volumetric - features is identified for members of sets of features to members of - other sets of volumetric features. - Specifically, for each time step k pairs of sets are compared: - Members of a so-called current_set to members of a so-called next_set. - Members can be different types of volumetric features. - In the analysis of M. Kuehbach et al. specifically features can be - so-called objects (closed non-degnerated polyhedra representing watertight - parts of an e.g. iso-surface) and/or proxies. Proxies are computed - doppelganger/replacement meshes for parts of an iso-surface which initially - were not resulting in watertight meshes because objects at the edge - of the dataset or incompletely measured or truncated objects. - - - - Specifies the method whereby to decide if two objects intersect volumetrically. - For reasons which are detailed in the supplementary material of - `M. Kühbach et al. <https://arxiv.org/abs/2205.13510>`_, the tool by - default assumes that two objects intersect if they share at least one - ion with the same evaporation ID (shared_ion). - Alternatively, with specifying tetrahedra_intersections, - the tool can perform an intersection analysis which attempts to - tetrahedralize first each polyhedron. If successful, the tool then checks - for at least one pair of intersecting tetrahedra to identify if two objects - intersect or not. - - However, we found that these geometrical analyses can result in corner - cases which the currently used library (TetGen) was not unable to - tetrahedralize successfully. These cases were virtually always - associated with complicated non-convex polyhedra which had portions - of the mesh that were connected by almost point like tubes of triangles. - Finding more robust methods for computing intersections between - not necessarily convex polyhedra might improve the situation in the future. - - - - - - - - Specifies if the tool evaluates if for each pair the two objects - (and proxies if used) intersect volumetrically. - - - - - Specifies if the tool evaluates if for each pair the two objects - (and proxies if used) lie closer to one another than the - threshold_proximity. - - - - - Specifies if the tool evaluates, ones all tracking tasks were - successfully completed, how intersecting or proximity related - objects build sub-graphs. This is the feature which enabled - M. Kühbach et al. 2022 the high-throughput analyses of how many - objects are coprecipitates in the sense that they are single, - duplet, triplet, or high-order. For these analyses to work - has_object_volume needs to be activated. - - - - - The maximum Euclidean distance between two objects below which - both objects are still considered within proximity. - - - - - - Specifies if the tool stores the so-called forward relations between - nodes representing members of the current_set to nodes representing - members of the next_set. - - - - - Specifies if the tool stores the so-called backward relations between - nodes representing members of the next_set to nodes representing - members of the current_set. - - - - - Current set stores a set of members, meshes of volumetric features, - which will be checked for proximity and/or volumetric intersection, - to members of the current_set. - The meshes were generated as a result of some other meshing process. - - - - This identifier can be used to label the current set. The label - effectively represents (can be interpreted as) the time/iteration - step when the current set was taken. As it is detailed in `M. Kühbach - et al. 2022 <https://arxiv.org/abs/2205.13510>`_, this identifier - takes the role of the time variable :math:`k`. - - - - - - The total number of distinguished feature sets FEATURE. - It is assumed that the members within all these FEATURE sets - are representing a set together. As an example this set might represent - all volumetric_features. However, users might have formed - a subset of this set where individuals were regrouped. - For paraprobe-nanochem this is the case for objects and proxies. - Specifically, objects are distinguished further into those far - from and those close to the edge of the dataset. - Similarly, proxies are distinguished further into those far - from and those close to the edge of the dataset. - So while these four sub-sets contain different so-called types of - features key is that they were all generated for one set, here the - current_set. - - - - - - Descriptive category explaining what these features are. - - - - - - - - - - - Name of the (NeXus)/HDF5 file which contains triangulated - surface meshes of the members of the set as instances of - NXcg_polyhedron_set. - - - - - Version identifier of the file such as a secure hash which documents - the binary state of the file to add an additional layer of - reproducibility from which file specifically contains these data. - - - - - - String whereby the path to the geometry data can be interferred automatically. - Currently groupname_geometry_prefix/object<ID>/polyhedron. - - - - - Array of identifier whereby the path to the geometry data - can be interferred automatically. - - - - - - - - - - Next set stores a set of members, meshes of volumetric features, - which will be checked for proximity and/or volumetric intersection, - to members of the next_set. - The meshes were generated as a result of some other meshing process. - - - - This identifier can be used to label the next_set. The label - effectively represents (can be interpreted as) the time/iteration - step when the current set was taken. As it is detailed in `M. Kühbach - et al. 2022 <https://arxiv.org/abs/2205.13510>`_, this identifier - takes the role of the time variable :math:`k + 1`. - - - - - - The total number of distinguished feature sets FEATURE. - It is assumed that the members within all these FEATURE sets - are representing a set together. As an example this set might represent - all volumetric_features. However, users might have formed - a subset of this set where individuals were regrouped. - For paraprobe-nanochem this is the case for objects and proxies. - Specifically, objects are distinguished further into those far - from and those close to the edge of the dataset. - Similarly, proxies are distinguished further into those far - from and those close to the edge of the dataset. - So while these four sub-sets contain different so-called types of - features key is that they were all generated for one set, here the - next_set. - - - - - - Descriptive category explaining what these features are. - - - - - - - - - - - Name of the (NeXus)/HDF5 file which contains triangulated - surface meshes of the members of the set as instances of - NXcg_polyhedron_set. - - - - - Version identifier of the file such as a secure hash which documents - the binary state of the file to add an additional layer of - reproducibility from which file specifically contains these data. - - - - - - String whereby the path to the geometry data can be interferred automatically. - Currently groupname_geometry_prefix/object<ID>/polyhedron. - - - - - Array of identifier whereby the path to the geometry data - can be interferred automatically. - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_nanochem.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_nanochem.nxdl.xml deleted file mode 100644 index ab98e2e..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_nanochem.nxdl.xml +++ /dev/null @@ -1,1114 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - How many iontypes does the delocalization filter specify. - - - - - How many disjoint control points are defined. - - - - - How many iontypes does the interface meshing iontype filter specify. - - - - - How many DCOM iterations. - - - - - Maximum number of atoms per molecular ion. - - - - - Configuration of a paraprobe-nanochem tool run in atom probe microscopy. - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - ISO 8601 formatted time code with local time zone offset to - UTC information included when this configuration file was created. - - - - - How many individual analyses should the tool execute as part of the analysis. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The tool enables to inject a previously computed triangle soup or - triangulated surface mesh representing a model (of the surface) of - the edge of the dataset. This model can be used to detect and control - various sources of bias in the analyses. - - - - - Name of the HDF5 file which contains vertex coordinates and facet - indices to describe the desired set of triangles which represents - the edge of the dataset. - - - - Version identifier of the file such as a secure hash which documents - the binary state of the file to add an additional layer of - reproducibility from which file specifically contains these data. - - - - - - Absolute path to the HDF5 dataset in the respectively specified HDF5 - file under filename which details the array of vertex positions. - - - - - Absolute path to the HDF5 dataset in the respective specified HDF5 - file under filename which details the array of facet indices. - - - - - - The tool enables to inject precomputed distance information for each - point/ion which can be used for further post-processing and analysis. - - - - - Name of an HDF5 file which contains the ion distances. - - - - Version identifier of the file such as a secure hash which documents - the binary state of the file to add an additional layer of - reproducibility from which file specifically contains these data. - - - - - - Absolute HDF5 path to the dataset with distance values for each ion. - - - - - - - - Discretization of the ion point cloud on a three-dimensional grid. - - - - Delocalization in the field of atom probe microscopy is the process - of discretizing a point cloud. By default the tool computes a full - kernel density estimation of decomposed ions to create one discretized - field for each element. - - Although, this uses an efficient multithreaded algorithm, - the computation is costly. Therefore, it can be advantageous for users - to load an already computed delocalization. This can be achieved with - the load_existent option. - When using this option the user is responsible to assure that the - settings which were used for computing this already existent delocalization - are specified in the same manner as they were. - - - - - - - - - - - Matrix of isotope vectors representing iontypes. - The filter specifies a matrix of isotope_vectors which is the most - general approach to define if and how many times an ion is counted. - Currently, paraprobe_nanochem performs a so-called atomic decomposition - of all iontypes. Specifically, the tool interprets of how many - elements/atoms a molecular ion is composed; and thus determines the - atoms multiplicity with respect to the iontype. - - Let's take the hydroxonium H3O+ molecular ion as an example: - It contains hydrogen and oxygen as atoms. The multiplicity of hydrogen - is three whereas that of oxygen is one. Therefore in an atomic - decomposition computation of the iso-surface each H3O+ ion adds - three hydrogen counts. This is a practical solution which accepts - the situation that during an atom probe experiment not each bond - of each ion/a group of neighboring atoms is broken but molecular - ions get detected. The exact ab-initio details depend on the local - field conditions and thus also the detailed spatial arrangement - of the atoms and their own electronic state and that of the neighbors - before and upon launch. - Being able to measure the information for such sites only as - molecular ions causes an inherent information loss with respect to the - detailed spatial arrangement. This information loss is more relevant - for local electrode atom probe than for field ion microscopy setting - how precisely the atomic positions can be reconstructed. - Accounting for multiplicities assures that at least the - compositional information is analyzed. - - - - - - - - - List of individual grid resolutions to analyse. - Paraprobe discretizes on a cuboidal 3D grid with cubic cells, with - an edge length of values in gridresolutions. - - - - - - Half the width of a :math:`{(2 \cdot n + 1)}^3` cubic kernel of voxel - beyond which the Gaussian Ansatz function will be truncated. - Intensity beyond the kernel is refactored into the kernel via - a normalization procedure. - - - - - Variance of the Gaussian Ansatz kernel :math:`\sigma_x = \sigma_y = 2 \cdot - \sigma_z`. - - - - - - How should the results of the kernel-density estimation be computed - into quantities. By default the tool computes the total number - (intensity) of ions or elements. Alternatively the tool can compute - the total intensity, the composition, or the concentration of the - ions/elements specified by the white list of elements in each voxel. - - - - - - - - - - - Specifies if the tool should report the delocalization 3D field values. - - - - - - - Optional computation of iso-surfaces after each computed delocalization - to identify for instance objects in the microstructure - (line features, interfaces, precipitates). - - - - As it is detailed in M. Kühbach et al. 2022 npj Comp. Mat., - the handling of triangles at the edge of the dataset requires - special attention. Especially for composition-normalized - delocalization it is possible that the composition increases - towards the edge of the dataset because the quotient of two numbers - which are both smaller than one is larger instead of smaller than - the counter. By default, the tool uses a modified marching cubes - algorithm of Lewiner et al. which detects if voxels face such a - situation. In this case, no triangles are generated for such voxels. - Alternatively, (via setting keep_edge_triangles) the user can - instruct the tool to not remove these triangles at the cost of bias. - - Specifically, in this case the user should understand that all - objects/microstructural features in contact with the edge of the - dataset get usually artificial enlarged and their surface mesh - often closed during the marching. This closure however is artificial! - It can result in biased shape analyses for those objects. - The reason why this should in general be avoided is a similar - argument as when one analyzes grain shapes in orientation microscopy - via e.g. SEM/EBSD. Namely, these grains, here the objects at the - edge of the dataset, were not fully captured during e.g. limited - field of view. - Therefore, it is questionable if one would like to make - substantiated quantitative statements about them. - - Thanks to collaboration with the V. V. Rielli and S. Primig, though, - paraprobe-nanochem implements a complete pipeline to - process even these objects at the edge of the dataset. Specifically, - the objects are replaced by so-called proxies, i.e. replacement - objects whose holes on the surface mesh have been closed if possible - via iterative mesh and hole-filling procedures with fairing operations. - In the results of each paraprobe-nanochem run, these proxy objects - are listed separately to allow users to quantify and analyze in - detail the differences when accounting for these objects or not. - Especially this is relevant in atom probe microscopy as objects - can contain a few dozen atoms only. - Users should be aware that results from fairing operations should - be compared to results from analyses where all objects at the edge - of the dataset have been removed. - - Also users should be careful with overestimating the statistical - significance of their dataset especially when using atom probe - to compare multiple descriptors: Even though a dataset may give - statistically significant results for compositions, this does not - necessarily mean it will yield also statistically significant - and unbiased results for three-dimensional object analyses. - Being able to quantify these effects and making atom probers - aware of these subtleties was one of the main reasons why the - paraprobe-nanochem tool was implemented. - - - - - - - - - The ion-to-edge-distance that is used in the analyses of objects - (and proxies) to identify whether these are inside the dataset or - close to the edge of the dataset. If an object has at least one ion - with an ion-to-edge-distance below this threshold, the object is - considered as one which lies close to the edge of the dataset. - This implements essentially a distance-based approach to solve - the in general complicated and involved treatment of computing - volumetric intersections between not-necessarily convex - closed 2-manifolds. In fact, such computational geometry analyses - can face numerical robustness issues as a consequence of which a - mesh can be detected as lying completely inside a dataset although - in reality it is epsilon-close only, i.e. almost touching only - the edge (e.g. from inside). - Practically, humans would state in such case that the object is - close to the edge of the dataset; however mathematically the object - is indeed completely inside. - In short, a distance-based approach is rigorous and more flexible. - - - - - - Array of iso-contour values. For each value the tool computes - an iso-surface and performs subsequent analyses. - The unit depends on the choice for the normalization of the - accumulated ion intensity values per voxel: - - * total, total number of ions, irrespective their iontype - * candidates, total number of ions with type in the isotope_whitelist. - * composition, candidates but normalized by composition, i.e. at.-% - * concentration, candidates but normalized by voxel volume, i.e. ions/nm^3 - - - - - - Specifies if the tool should report the triangle soup which represents - each triangle of the iso-surface complex. - Each triangle is reported with an ID specifying to which triangle - cluster (with IDs starting at zero) the triangle belongs. - The clustering is performed with a modified DBScan algorithm. - - - - - Specifies if the tool should analyze for each cluster of triangles - how they can be combinatorially processed to describe a closed - polyhedron. Such a closed polyhedron (not-necessarily convex!) - can be used to describe objects with relevance in the microstructure. - Users should be aware that the resulting mesh does not necessarily - represent the original precipitate. In fact, inaccuracies in the - reconstructed positions cause inaccuracies in all downstream - processing operations. Especially the effect on one-dimensional - spatial statistics like nearest neighbor correlation functions these - effects were discussed in the literature - `B. Gault et al. <https://doi.org/10.1017/S1431927621012952>`_ - In continuation of these thoughts this applies also to reconstructed - objects. A well-known example is the discussion of shape deviations - of Al3Sc precipitates in aluminium alloys which in reconstructions - can appear as ellipsoids although they should be almost spherical, - depending on their size. - - - - - Specifies if the tool should report a triangulated surface mesh - for each identified closed polyhedron. It is common that a - marching cubes algorithm creates iso-surfaces with a fraction of very - small sub-complexes (e.g. small isolated tetrahedra). - - These can be for instance be small tetrahedra/polyhedra about the - center of a voxel of the support grid on which marching cubes operates. - When these objects are small, it is possible that they contain no ion; - especially when considering that delocalization procedures smoothen - the positions of the ions. Although these small objects are interesting - from a numerical point of view, scientists may argue they are not worth - to be reported: - Physically a microstructural feature should contain at least a few - atoms to become relevant. Therefore, paraprobe-nanochem by default - does not report closed objects which bound not at least one ion. - - - - - Specifies if the tool should report properties of each closed - polyhedron, such as volume and other details. - - - - - Specifies if the tool should report for each closed polyhedron an - approximately optimal bounding box fitted to all triangles of the - surface mesh of the object and ion positions inside or on the - surface of the mesh. - This bounding box informs about the closed object's shape - (aspect ratios). - - - - - - Specifies if the tool should report for each closed polyhedron - all evaporation IDs of those ions which lie inside or on the - boundary of the polyhedron. This information can be used e.g. - in the paraprobe-intersector tool to infer if two objects share - common ions, which can be interpreted as an argument to assume - that the two objects intersect. - - Users should be aware that two arbitrarily closed polyhedra - in three-dimensional space can intersect but not share a common ion. - In fact, the volume bounded by the polyhedron has sharp edges. - When taking two objects, an edge of one object may for instance - pierce into the surface of another object. In this case the - objects partially overlap / intersect volumetrically; - however this piercing might be so small or happening in the volume - between two ion positions and thus sharing ions is a sufficient - but not a necessary condition for object intersections. - - Paraprobe-intersector implements a rigorous alternative to handle - such intersections using a tetrahedralization of closed objects. - However, in many practical cases, we found through examples that there - are polyhedra (especially when they are non-convex and have almost - point-like) connected channels, where tetrahedralization libraries - have challenges dealing with. In this case checking intersections - via shared_ions is a more practical alternative. - - - - - Specifies if the tool should report if a (closed) object has - contact with the edge of the dataset. For this the tool currently - inspects if the shortest distance between the set of triangles of the - surface mesh and the triangles of the edge model is larger than the - edge_threshold. If this is the case, the object is assumed to be - deeply embedded in the interior of the dataset. Otherwise, the object - is considered to have an edge contact, i.e. it is likely affected - by the fact that the dataset is finite. - - - - - - Specifies if the tool should analyze a doppelganger/proxy mesh for - each cluster of triangles whose combinatorial analysis according - to has_object showed that the object is not a closed polyhedron. - Such proxies are closed via iterative hole-filling, mesh refinement, - and fairing operations. - Users should be aware that the resulting mesh does not necessarily - represent the original precipitate. In most cases objects, - like precipitates in atom probe end up as open objects because - they have been clipped by the edge of the dataset. Using a proxy is - then a strategy to still be able to account for these objects. - Nevertheless users should make themselves familiar with the - potential consequences and biases which this can introduce - into the analysis. - - - - - Like has_object_geometry but for the proxies. - - - - - Like has_object_properties but for the proxies. - - - - - Like has_object_obb but for the proxies. - - - - - Like has_object_ions but for the proxies. - - - - - Like has_object_edge_contact but for the proxies. - - - - - Specifies if the tool should report for each closed object a - (cylindrical) region of interest placed, centered, and align - with the local normal for each triangle of the object. - - - - - Specifies if the tool should report for each ROI that was placed - at a triangle of each object if this ROI intersects the edge of - the dataset. Currently paraprobe-nanochem supports cylindrical - ROIs. A possible intersection of these with the edge of the - dataset, i.e. the triangulated surface mesh model for the edge - is performed. This test checks if the cylinder intersects with - a triangle of the surface mesh. If this is the case, the ROI is - assumed to make edge contact, else, the ROI is assumed to have - no edge contact. - - This approach does not work if the ROI would be completely - outside the dataset. Also in this case there would be - no intersection. For atom probe this case is practically - irrelevant because for such a ROI there would also be no ion - laying inside the ROI. Clearly it has thus to be assumed that - the edge model culls the entire dataset. Instead, if one would - cut a portion of the dataset, compute an edge model for this - point cloud, it might make sense to place a ROI but in this - case the edge contact detection is not expected to work properly. - - - - - - - Analyses of interfacial excess. - - - - Interfacial excess computations are performed for local regions-of-interests - (ROIs) at selected facets or interface patch. - For instance many scientist compute the interfacial excess for - selected triangle facets of a created iso-surface. In this case, - computed iso-surfaces of paraprobe could be used. An example are triangle - facet sets about closed polyhedra, for instance to compute interfacial - excess related to phase boundaries of second-phase precipitates. - - Another example are free-standing triangle patches of the iso- - surfaces which paraprobe creates. These could be characterized - for interfacial excess. The sub-routines during iso-surface - computations already include a procedure to automatically align - local triangle normals based on the gradients of e.g. composition - fields. In this case, these triangulated surface patches - could also be used as a source for computing interfacial - excess. - - Often scientists face situations, though, in which there is no - immediately evident composition gradient across the interface - (grain or phase boundary) and orientation information about the - adjoining crystal is neither available nor reliable enough. - - In this case `P. Felfer et al. <https://doi.org/10.1016/j.ultramic.2015.06.002>`_ proposed a method - to manually place control points and run an automated tessellation-based - algorithm to create a triangulated surface patch, i.e. a model of the - location of the interface. In a post-processing step this triangle - set can then be used to compute again interfacial excess in an - automated manner by placing ROIs and aligning them with - consistently precomputed triangle normals. - - A similar use case is conceptually the one proposed by `X. Zhou et al. <https://doi.org/10.1016/j.actamat.2022.117633>`_ - They used first a deep-learning method to locate planar triangulated - grain boundary patches. These are eventually processed further - with manual editing of the mesh via tools like Blender. - Once the user is satisfied with the mesh, the computations of interfacial - excess reduce again to an automated placing of ROIs, computations - of the distributing of ions to respective ROIs and - reporting the findings via plotting. - - Yet another approach for constructing an triangulated surface patch - of an interface is to use point cloud processing methods which have - been proposed in the laser-scanning, geoinformatics, and CAD community. - Different computational geometry methods are available for fitting - a parameterized surface to a set of points, using e.g. non-uniform - rational B-splines (NURBS) and triangulating these according - to prescribed mesh quality demands. - - The advantage of these methods is that they can be automated and - pick up curved interface segments. The disadvantage is their often - strong sensitivity to parameterization. As a result also such methods - can be post-processed to yield a triangulated surface patch, - and thus enable to run again automated ROI placement methods. - For example like these which were explored for the use case of - iso-surfaces with closed objects and free-standing - surface patches that delineate regions of the dataset with a - pronounced composition gradient normal to the interface. - - This summary of the situations which atom probers can face when - requesting for interfacial excess computations, substantiates there - exists a common set of settings which can describe all of these methods - and, specifically, as here exemplified, the automated placing - and alignment functionalities for ROIs that is an important - step all these workflows. - - Specifically, paraprobe-nanochem operates on an already existent - triangle set. - - - - - - - - - - The interface model is the result of a previous (set of) processing - steps as a result of which the user has created a triangulated - surface mesh (or a set of, eventually connected such meshes). - These interface models are useful, if not required, in cases when - there is no other independent approach to locate an interface. - - These are cases when insufficient crystallographic latent - information is available and also no consistent concentration - gradient detectable across the interface. It is then the users' - responsibility to deliver a triangle mesh of the interface model. - - - - Filename to HDF5 file which contain vertex coordinates, facet indices, - facet unit normals. The user is responsible for the triangle - and winding order to be consistent. - Input is expected as a matrix of the coordinates for all disjoint - vertices, a (Nvertices, 3)-shaped array of NX_FLOAT. - Input is expected to include also a matrix of facet indices - referring to these disjoint vertices. This matrix should be a - (Nfacets, 3)-shaped array of NX_UINT. Further required input - is a (Nfacets, 3)-shaped array of NX_FLOAT signed facet unit - normals and a (Nvertices, 3)-shaped array of NX_FLOAT signed - vertex unit normals. Vertex indices need to start at zero and - must not exceed Nvertices - 1, i.e. the identifier_offset is 0 - and facet indices are indexed implicitly, i.e. [0, Nvertices-1]. - - - - Version identifier of the file such as a secure hash which - documents the binary state of the file to add an additional - layer of reproducibility from which file specifically - contains these data. - - - - - - Absolute HDF5 path to the dataset which specifies the - array of vertex positions. - - - - - Absolute HDF5 path to the dataset which specifies the - array of facet indices. - - - - - Absolute HDF5 path to the dataset which specifies the - array of facet signed unit normals. - - - - - Absolute HDF5 path to the dataset which specifies the - array of vertex signed unit normals. - - Users should be aware that triangulated surface meshes are - only approximations to a given complex, eventually curved shape. - Consequently, computations of normals show differences between - the vertex and facet normals. Vertex normals have to be - interpolated from normals of neighboring facets. Consequently, - these normals are affected by the underlying parameterization - and curvature estimation algorithms, irrespective of how - contributions from neighboring facets are weighted. By contrast, - facet normals are clearly defined by the associated triangle. - Their disadvantage is that they the normal field has discontinuities - at the edges. In general the coarser an object is triangulated - the more significant the difference becomes between computations - based on facet or vertex normals. - Paraprobe-nanochem works with facet normals as it can use - parts of the numerical performance gained by using cutting - edge libraries to work rather with finer meshes. - - - - - - - - Create a simple principle component analysis (PCA) to mesh a - free-standing interface patch through a point cloud of decorating solutes. - These models can be useful for quantification of Gibbsian - interfacial excess for interfaces where iso-surface based methods - may fail or closed objects from iso-surfaces are not desired or - when e.g. there are no substantial or consistently oriented - concentration gradients across the interface patch. - - The interface_meshing functionality of paraprobe-nanochem can be useful - when there is also insufficient latent crystallographic information - available that could otherwise support modelling the interface, - via e.g. ion density traces in field-desorption maps, as were used and - discussed by `Y. Wei et al. <https://doi.org/10.1371/journal.pone.0225041>`_ - or are discussed by `A. Breen et al. <https://github.com/breen-aj/detector>`_ - - It is noteworthy that the method here used is conceptually very similar - in implementation to the work by `Z. Peng et al. <https://doi.org/10.1017/S1431927618016112>`_ - Noteworthy, her team uses the DCOM approach originally proposed by P. Felfer et al. - However, both of these previous works neither discuss in detail - nor implement inspection functionalities which enable a detection of - potential geometric inconsistencies or self-interactions of the - resulting DCOM mesh. This is what paraprobe-nanochem implements - via the Computational Geometry Algorithms Library. - - - - Method how to initialize the PCA: - - * default, means based on segregated solutes in the ROI - * control_point_file, means based on reading an external list of - control points, currently coming from the Leoben APT_Analyzer. - - The control_point_file is currently expected with a specific format. - The Leoben group lead by L. Romaner has developed a GUI tool `A. Reichmann et al. <https://github.com/areichm/APT_analyzer>`_ - to create a control_point_file which can be parsed by paraprobe-parmsetup - to match the here required formatting in control_points. - - - - - - - - - The name of the control point file to use. - - - - Version identifier of the file such as a secure hash which - documents the binary state of the file to add an additional - layer of reproducibility from which file specifically - contains these data. - - - - - - X, Y, Z coordinates of disjoint control point read from - an HDF5 file named according to control_point_file. - - - - - - - - - - Method used for identifying and refining the location of the - interface. Currently, paraprobe-nanochem implements a PCA followed - by an iterative loop of isotropic mesh refinement and DCOM step(s), - paired with self-intersection detection in a more robust - implementation. - - - - - - - - Specify the types of those ions which decorate the interface and - can thus be assumed as markers for locating the interface and - refining its local curvature. - - - - Array of iontypes to filter. The list is interpreted as a whitelist, - i.e. ions of these types are considered the decorating species (solutes). - - - - - - - - - How many times should the DCOM and mesh refinement be applied? - - - - - Array of decreasing positive not smaller than one nanometer real values - which specify how the initial triangles of the mesh should be iteratively - refined by edge splitting and related mesh refinement operations. - - - - - - - - - Array of decreasing positive not smaller than one nanometer real values - which specify the radius of the spherical region of interest within - which the DCOM algorithm decides for each vertex how the vertex will - be eventually relocated. The larger the DCOM radius is relative to - the target_edge_length the more likely it is that vertices will be - relocated so substantially that eventually triangle self-intersections - can occur. If the code detects these it warns and stops in a - controlled manner so that the user can repeat the analyses - with a smaller value. - - - - - - - - - Array of integers which specify for each DCOM step how many times - the mesh should be iteratively smoothened. - - Users should be aware the three array target_edge_length, - target_dcom_radius, and target_smoothing_step are interpreted in the - same sequence, i.e. the zeroth entry of each array specifies the - values to be used in the first DCOM iteration. The first entry of - each array those for the second DCOM iteration and so on and so forth. - - - - - - - - - Functionalities for placing regions-of-interest (ROIs) in the dataset - or at specific microstructural features to characterize composition - profiles and cumulated profiles for quantification of interfacial excess. - Paraprobe-nanochem currently places cylindrical ROIs. ROIs are probed - across the triangulated surface of a user-defined mesh. - ROIs are placed at the barycenter of the triangular facet. - - The tool can be instructed to orient the profile for each ROIs with - the positive normal of the triangle facet normals. Profiles are - computed for each ROI and facet triangle. The code will test which - ROIs are completely embedded in the dataset. - Specifically, in this test the tool evaluates if the ROI cuts at least - one triangle of the triangulated surface mesh of the edge of the dataset. - If this is the case the ROI will be considered close to the edge - (of the dataset) and not analyzed further; else the ROI will be - processed further. - Users should be aware that the latter intersection analysis is strictly - speaking not a volumetric intersection analysis as such one is much - more involved because the edge model can be a closed non-convex polyhedron - in which case one would have to test robustly if the cylinder pierces - or is laying completely inside the polyhedron. For this the polyhedron has - to be tessellated into convex polyhedra as otherwise tests like the - Gilbert-Johnson-Keerthi algorithm would not be applicable. - - Specifically, the tool computes atomically decomposed profiles. - This means molecular ions are split into atoms/isotopes with respective - multiplicity. As an example an H3O+ molecular ion contains three - hydrogen and one oxygen atom respectively. The tool then evaluates - how many ions are located inside the ROI or on the surface of the - ROI respectively. All atom types and the unranged ions are distinguished. - As a result, the analyses yield for each ROI a set of sorted lists of - signed distance values. Currently, the distance is the projected - distance of the ion position to the barycenter of the triangle - and triangle plane. - - This will return a one-dimensional profile. Post-processing the set - of atom-type-specific profiles into cumulated profiles enable the - classical Krakauer/Seidman-style interfacial excess analyses. - Furthermore, the tool can be instructed to compute for each - (or a selected sub-set of facet) a set of differently oriented profiles. - - - - - The feature mesh enables the injection of previously computed triangle - soup or mesh data. Such a mesh can be the model for a grain- or phase - boundary patch (from e.g. interface_meshing) jobs. - - - - Name of the HDF5 file which contains vertex coordinates and facet - indices to describe the desired set of triangles which represents - the feature. - - - - Version identifier of the file such as a secure hash which documents - the binary state of the file to add an additional layer of - reproducibility from which file specifically contains these data. - - - - - - Absolute path to the HDF5 dataset in the respectively specified HDF5 - file under filename which details the array of vertex positions. - - - - - Absolute path to the HDF5 dataset in the respective specified HDF5 - file under filename which details the array of facet indices. - - - - - Absolute path to the HDF5 dataset in the respective specified HDF5 - file under filename which details consistently oriented facet - normals of the facets. - - - - - - - - - - - The tool enables to inject precomputed distance information for each - point which can be used for further post-processing and analysis. - - - - - Name of an HDF5 file which contains ion distances. - - - - Version identifier of the file such as a secure hash which - documents the binary state of the file to add an additional - layer of reproducibility from which file specifically contains - these data. - - - - - - Absolute HDF5 path to the dataset with distance values for each ion. - - - - - - Which type of distance should be reported for the profile. - - - - - - - - - In which directions should the tool probe for each ROI. - - - - - - - - - For each ROI, how high (projected on the cylinder axis) - should the cylindrical ROI be. - - - - - - For each ROI, how wide (radius) should the cylindrical ROI be. - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_ranger.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_ranger.nxdl.xml deleted file mode 100644 index f832bf0..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_ranger.nxdl.xml +++ /dev/null @@ -1,297 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The number of isotopes to consider as building blocks for searching molecular - ions. - - - - - The number of compositions to consider for molecular ion search tasks. - - - - - Configuration of a paraprobe-ranger tool run in atom probe microscopy. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when this configuration file was created. - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - How many task to perform? - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A list of pairs of number of protons and either the value 0 (per row) - or the mass number for all those isotopes which are assumed present - in a virtual specimen. - The purpose of this field is to compute also composition-weighted - products to yield a simple estimation which could potentially help - scientists to judge if certain molecular ions are to be expected. - The corresponding setting store_composition_weighted_product should be - activated. - - - - - - - - - - A list of pairs of number of protons and mass number for all isotopes - to consider that can be composed into (molecular) ions, during the - recursive molecular_ion_search. - - - - - - - - - The mass-to-charge-state ratio interval in which - all molecular ions are searched. - - - - - - - - The maximum charge that a molecular ion should have. - - - - - The maximum number of isotopes of which the molecular ion - should be composed. Currently this must not be larger than 32. - - Users should be warned that the larger the maximum_charge and - especially the larger the maximum_number_of_isotopes is chosen, - the eventually orders of magnitude more costly the search becomes. - - This is because paraprobe-ranger computes really all (at least) - theoretically possible combinations that would have likely a - mass-to-charge-state ratio in the specified mass_to_charge_interval. - It is the challenge in atom probe to judge which of these (molecular) - ions are feasible and also practically possible. This tool does not - answer this question. - - Namely, which specific molecular ion will evaporate, remain stable - during flight and becomes detected is a complicated and in many cases - not yet in detail understood phenomenon. The ab-initio conditions - before and during launch, the local environment, arrangement and field - as well as the flight phase in an evacuated but not analysis chamber - with a complex electrical field, eventual laser pulsing in place, - temperature and remaining atoms or molecules all can have an effect - which iontypes are really physically evaporating and detected. - - - - - Report the accumulated atomic mass from each isotope building the ion. - Accounts for each identified ion. - Relatistic effects are not accounted for. - - - - - Report the product of the natural abundances from each isotope building - the ion. Accounts for each identified ion. - - The value zero indicates it is not possible to build such molecular ion - from nuclids which are all observationally stable. - Very small values can give an idea/about how likely such a molecular ion - is expected to form assuming equal probabilities. - - However in atom probe experiments this product has to be modified - by the (spatially-correlated) local composition in the region from - which the ions launch because the formation of a molecular ion depends - as summarized under maximum_number_of_isotopes on the specific - quantum-mechanical configuration and field state upon launch - or/and (early state) of flight respectively. - We are aware that this modified product can have a substantially - different value than the natural_abundance_product. - - Natural abundancies folded with the estimated compositions of the - specimen can differ by orders of magnitude. - - - - - - Report the charge state of the ions. - - - - - Report if identified ions should be characterized - wrt to their number of disjoint isotopes. - - - - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_selector.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_selector.nxdl.xml deleted file mode 100644 index 1293fb9..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_selector.nxdl.xml +++ /dev/null @@ -1,142 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Configuration of a paraprobe-selector tool run in atom probe microscopy. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when this configuration file was created. - - - - - How many roi_selection processes should the tool execute. - - - - - This process identifies which of the points/ions in the datasets are - inside or on the surface of geometric primitives and meet optionally - specific other filtering constraints. - A typical use case of a roi_selection is to restrict analyses to - specific regions of the dataset, eventually regions with a complicated - shape. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_spatstat.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_spatstat.nxdl.xml deleted file mode 100644 index d886dc0..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_spatstat.nxdl.xml +++ /dev/null @@ -1,374 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Maximum number of atoms per molecular ion. Should be 32 for paraprobe. - - - - - Number of different sources iontypes to distinguish. - - - - - Number of different target iontypes to distinguish. - - - - - Configuration of a paraprobe-spatstat tool run in atom probe microscopy. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when this configuration file was created. - - - - - How many range_with_existent_iontypes processes should - the tool execute as part of the analysis. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The tool enables to inject precomputed distances of each ion to a - representation of the edge of the dataset which can be used to - control and substantially reduce edge effects when computing - spatial statistics. - - - - Name of an HDF5 file which contains ion-to-edge distances. - - - - - Absolute HDF5 path to the dataset with the - ion-to-edge distance values for each ion. - The shape of the distance values has to match the length - of the ion positions array in dataset/dataset_name_reconstruction - and dataset_name_mass_to_charge respectively. - - - - - Threshold to define how large an ion has to lay at least far away - from the edge of the dataset so that the ion can act as a source, - i.e. that an ROI is placed at the location of the ion and its - neighbors are analyzed how they contribute to the computed statistics. - - The ion_to_edge_distances threshold can be combined with a threshold - for the ion_to_feature_distances. - Specifically, if ion_to_feature_distances are loaded an ion only - acts as a source if both threshold criteria are met. - - The threshold is useful to process the dataset such that ROIs do - not protrude out of the dataset as this would add bias. - - - - - - In addition to spatial filtering, and considering how far ions lie - to the edge of the dataset, it is possible to restrict the analyses - to a sub-set of ions within a distance not farther away to a feature than - a threshold value. - - - - Name of an HDF5 file which contains ion-to-feature distances. - - - - - Absolute HDF5 path to the dataset with the - ion-to-feature distance values for each ion. - - - - - Threshold to define how close an ion has to lay to a feature so that - the ion can at all qualify as a source, i.e. that an ROI is placed - at the location of the ion and its neighbors are then analyzed - how they contribute to the computed statistics. - - Recall that the ion_to_feature_distances threshold is combined - with the ion_to_edge_distances threshold. - - - - - - - Specifies if the iontypes are randomized for the point cloud or not. - Internally paraprobe uses a sequentially executed deterministic MT19987 - (MersenneTwister) pseudo-random number generator to shuffle the - iontype labels randomly across the entire set of ions. - - - - - - - - - - How should the iontype be interpreted on the source-side, i.e. - all these ion positions where a regions-of-interest (ROI) around - so-called source ions will be placed. Different options exist - how iontypes are interpreted given an iontype represents - in general a (molecular) ion with different isotopes that have - individually different multiplicity. - - The value resolve_all will set an ion active in the analysis regardless - of which iontype it is. Each active ion is accounted for once. - - The value resolve_unknown will set an ion active when the ion is - of the UNKNOWNTYPE type. Each active ion is accounted for once. - - The value resolve_ion will set an ion active if it is of the specific - iontype, irregardless of its elemental or isotopic details. - Each active ion is counted once. - - The value resolve_element will set an ion active, and most importantly, - account for each as many times as the (molecular) ion contains - atoms of elements in the whitelist ion_query_isotope_vector. - - The value resolve_isotope will set an ion active, and most importantly, - account for each as many times as the (molecular) ion contains - isotopes in the whitelist ion_query_isotope_vector. - - In effect, ion_query_isotope_vector acts as a whitelist to filter - which ions are considered as source ions of the correlation statistics - and how the multiplicity of each ion will be factorized, i.e. how - often it is accounted for. - - - - - - - - - - - - Matrix of isotope vectors, as many as rows as different candidates - for iontypes should be distinguished as possible source iontypes. - In the simplest case, the matrix contains only the proton number - of the element in the row, all other values set to zero. - Combined with ion_query_type_source set to resolve_element this will - recover usual spatial correlation statistics like the 1NN C-C - spatial statistics. - - - - - - - - - Similarly as ion_query_type_source how should iontypes be interpreted - on the target-side, i.e. how many counts will be bookkept for ions - which are neighbors of source ions within or on the surface of each - inspection/ROI about each source ion. - Source ion in the center of the ROI are not accounted for during - counting the summary statistics. - For details about the resolve values consider the explanations in - ion_query_type_source. These account for ion_query_type_target as well. - - - - - - - - - - - - - Matrix of isotope vectors, as many as rows as different candidates for - iontypes to distinguish as possible targets. See additional comments - under ion_query_isotope_vector_source. - - - - - - - - - Specifies which spatial statistics to compute. - - - - Compute k-th nearest neighbour statistics. - - - - Order k. - - - - - Minimum value, increment, and maximum value of the histogram binning. - - - - - - - - - - Compute radial distribution function. - - - - Minimum value, increment, and maximum value of the histogram binning. - - - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_surfacer.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_surfacer.nxdl.xml deleted file mode 100644 index 5f30cc0..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_surfacer.nxdl.xml +++ /dev/null @@ -1,289 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of alpha values (and offset values) to probe. - - - - - How many different match values does the filter specify. - - - - - Configuration of a paraprobe-surfacer tool run in atom probe microscopy. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when this configuration file was created. - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - For now a support field for the tool to identify how many individual - analyses the tool should executed as part of the analysis. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specifies the method that is used to preprocess the point cloud. - The main purpose of this setting is to specify whether the point - cloud should be segmented or not during the preprocessing - to identify which points are more likely lying close to the edge - of the point cloud. These points could be more relevant than the - interior points for certain alpha-shape constructions. - - By default no such filtering is used during pre-processing. - By contrast, the option kuehbach activates a preprocessing - during which a Hoshen-Kopelman percolation analysis is used - to identify which points are closer to the edge of the dataset. - This can reduce the number of points in the alpha-shape - computation and thus improve performance substantially. - Details about the methods are reported in - `M. Kühbach et al. <https://doi.org/10.1038/s41524-020-00486-1>`_. - - - - - - - - - - When using the kuehbach preprocessing, this is the width of the - kernel for identifying which ions are in voxels close to the - edge of the point cloud. - - - - - Specifies which method to use to define the alpha value. - The value convex_hull_naive is the default. This instructs the tool - to use a fast specialized algorithm for computing only the convex - hull. The resulting triangles can be skinny. - - The value convex_hull_refine computes first also a convex_hull_naive - but refines the mesh by triangle flipping and splitting to improve - the quality of the mesh. - - The value smallest_solid instructs the CGAL library to choose a - value which realizes an alpha-shape that is the smallest solid. - - The value cgal_optimal instructs the library to choose a value - which the library considers as an optimal value. Details are - define in the respective section of the CGAL library on 3D alpha - shapes. - - The value set_of_values instructs to compute a list of - alpha-shapes for the specified alpha-values. - - The value set_of_alpha_wrappings instructs the library to generate - a set of so-called alpha wrappings. These are a method - which is similar to alpha shapes but provide additional guarantees - though such as watertightness and proximity constraints on the - resulting wrapping. - - - - - - - - - - - - - - Array of alpha values to use when alpha_value_choice is set_of_values - or when alpha_value_choice is set_of_alpha_wrappings. - - - - - - - - - Array of offset values to use when alpha_value_choice is - set_of_alpha_wrappings. The array of alpha_values and offset_values - define a sequence of (alpha and offset value). - - - - - - - - - Specifies if the tool should compute the set of exterior triangle - facets for each alpha complex (for convex hull, alpha shapes, and wrappings) - - - - - Specifies if the tool should check if the alpha complex of exterior - triangular facets is a closed polyhedron. - - - - - Specifies if the tool should compute all interior tetrahedra - of the alpha complex (currently only for alpha shapes). - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_tessellator.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_tessellator.nxdl.xml deleted file mode 100644 index ca0798c..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_tessellator.nxdl.xml +++ /dev/null @@ -1,253 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Configuration of a paraprobe-tessellator tool run in atom probe microscopy. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when this configuration file was created. - - - - - How many individual analyses should the tool execute. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The tool enables to inject precomputed distance information for - each point which can be used for further post-processing and analysis. - - - - Name of an HDF5 file which contains the ion distances. - Users are responsible this file and referred to dataset under - dataset_name have an ion_distance value for each ion. - - - - Version identifier of the file such as a secure hash which - documents the binary state of the file to add an additional layer of - reproducibility. - - - - - - Absolute HDF5 path to the dataset with distance values for each ion. - - - - - - - Specifies for which points the tool will compute the tessellation. - By default, a Voronoi tessellation is computed for all ions in the - filtered point cloud. - - - - - - - - - - Specifies if the tool should report the volume of each cell. - - - - - Specifies if the tool should report the first-order neighbors of each cell. - - - - - Specifies if the tool should report the facets and vertices of each cell. - - - - - Specifies if the tool should report if the cell makes contact with - the tight axis-aligned bounding box about the point cloud. - This can be used to identify if the shape of the cell is affected - by the edge of the dataset or if cells are deeply enough embedded - into the point cloud so that the shape of their cells are not affected - by the presence of the boundary. - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_transcoder.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_transcoder.nxdl.xml deleted file mode 100644 index 4d548e5..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_config_transcoder.nxdl.xml +++ /dev/null @@ -1,119 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Configurations of a paraprobe-transcoder tool run in atom probe microscopy. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ideally an ever persistent resource where the source code of the - program and build instructions can be found so that the program can be - configured ideally in such a manner that the result of this computational - process is recreatable deterministically. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when this configuration file was created. - - - - - - - - The path and name of the file (technology partner or community format) - from which to read the reconstructed ion positions. Currently, POS, - ePOS, APT files from APSuite, and NXS, i.e. NeXus/HDF5 files - are supported. - - - - - - - - The path and name of the file (technology partner or community format - from which to read the ranging definitions, i.e. how to map mass-to- - charge-state ratios on iontypes. Currently, RRNG, RNG, and NXS, i.e. - NeXus/HDF5 files are supported. - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml new file mode 100644 index 0000000..d7d0f13 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml @@ -0,0 +1,119 @@ + + + + + + Application definition for a configuration file of the paraprobe-distancer tool. + + The tool paraprobe-distancer tool evaluates exactly the shortest Euclidean distance for each + member of a set of points against a set of triangles. + + Triangles can represent for instance the facets of a triangulated surface mesh like those returned by + paraprobe-surfacer or any other set of triangles. Triangles do not have to be connected. + + Currently, paraprobe-distancer does not check if the respectively specified triangle sets are consistent, + what their topology is, or whether or not these triangles are consistently oriented. + + + + + + + + + + + Specifies for which point the tool will compute distances. + + The value *default* configures that distances are computed for all points. + The value *skin* configures that distances are computed only for those + points which are not farther away located to a triangle than + threshold_distance. + + + + + + + + + Maximum distance for which distances are + computed when *method* is *skin*. + + + + + How many triangle sets to consider. + Multiple triangle sets can be defined which are + composed into one joint triangle set for the analysis. + + + + + Each triangle_set that is referred to here should be a face_list_data_structure, + i.e. an array of (n_vertices, 3) of NX_FLOAT for vertex coordinates, an (n_facets, 3) + array of NX_UINT incident vertices of each facet. Vertex indices are assumed to + start at zero and must not exceed n_vertices - 1, i.e. the index_offset is 0. + Facet normal have to be provided as an array of (n_facets, 3) of NX_FLOAT. + + + + + + + Absolute path in the (HDF5) file that points to the array + of vertex positions for the triangles in that triangle_set. + + + + + Absolute path in the (HDF5) file that points to the array + of vertex indices for the triangles in that triangle_set. + + + + + Absolute path in the (HDF5) file that points to the array + of vertex normal vectors for the triangles in that triangle_set. + + + + + Absolute path in the (HDF5) file that points to the array + of facet normal vectors for the triangles in that triangle_set. + + + + + Absolute path in the (HDF5) file that points to the array + of identifier for the triangles in that triangle_set. + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml new file mode 100644 index 0000000..1cffc8e --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml @@ -0,0 +1,139 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The total number of points, i.e. ions in the reconstruction. + + + + + The total number of triangles in the set. + + + + + Application definition for a results file of the paraprobe-distancer tool. + + The tool paraprobe-distancer tool evaluates exactly the shortest Euclidean distance for each + member of a set of points against a set of triangles. + + Triangles can represent for instance the facets of a triangulated surface mesh like those returned by + paraprobe-surfacer or any other set of triangles. Triangles do not have to be connected. + + Currently, paraprobe-distancer does not check if the respectively specified triangle sets are consistent, + what their topology is, or whether or not these triangles are consistently oriented. + + + + + + + + + + + The shortest analytical distance of each point to their + respectively closest triangle from the joint triangle set. + + + + + + + + For each point the identifier of the triangle for which the + shortest distance was found. + + + + + + + + A support field to enable the visualization of each point + by an explicit identifier on the interval [0, n_ions - 1]. + The field can be used to visualize the points as a function + of their distance to the triangle set (e.g. via XDMF/Paraview). + + + + + + + + A bitmask that identifies which of the distance values is + assumed to have a consistent sign because the closest + triangle had a consistent outer unit normal defined. + + For points whose bit is set to 0 the distance is correct + but the sign is not reliable. + + + + Number of triangles covered by the mask. + + + + + Bitdepth of the elementary datatype that is used to store + the information content of the mask (typically 8 bit, uint8). + + + + + The content of the mask. Like for all masks used in the tools + of the paraprobe-toolbox, padding is used when number_of_objects + is not an integer multiple of bitdepth. If padding is used, + padded bits are set to 0. + + + + + + + + + A bitmask that identifies which of the triangles in the set were + considered when certain triangles have been filtered out. + + + + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml new file mode 100644 index 0000000..76a3c27 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml @@ -0,0 +1,253 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of entries + + + + + Application definition for a configuration file of the paraprobe-intersector + tool. + + + + + + + + + + Tracking volume_volume_spatial_correlations (v_v) is the process of building logical + relations between objects, their proximity and eventual volumetric intersections. + Here, objects are assumed to be represented as a set of triangulated surface meshes. + + Volumetric overlap and proximity of volumetric features is identified for members of + sets of features to members of other sets of volumetric features. Specifically, for each time + step :math:`k` pairs of sets are compared: + Members of a so-called current_set to members of a so-called next_set. + Members can be different types of volumetric features. + + + + Specifies the method whereby to decide if two objects intersect volumetrically. + For reasons which are detailed in the supplementary material of `M. Kühbach et al. <https://arxiv.org/abs/2205.13510>`_, + it is assumed by default that two objects intersect if they share at least one ion with the same evaporation ID (shared_ion). + + Alternatively, with specifying tetrahedra_intersections, the tool can perform an intersection analysis which attempts to + tetrahedralize first each polyhedron. If successful, the tool then checks for at least one pair of intersecting tetrahedra + to identify if two objects intersect or not. However, we found that these geometrical analyses can result in corner + cases which the tetrahedralization library used in the tests (TetGen) was not unable to tetrahedralize successfully. + These cases were virtually always associated with complicated non-convex polyhedra which had portions + of the mesh that were connected by almost point like tubes of triangles. + + Finding more robust methods for computing intersections between not necessarily convex polyhedra might improve + the situation in the future. For practical reasons we have thus deactivated the functionality of tetrahedra-tetrahedron + intersections in paraprobe-intersector. + + + + + + + + Specifies if the tool evaluates if objects intersect volumetrically. + + + + + Specifies if the tool evaluates if objects lay closer to one another than + threshold_proximity. + + + + + Specifies if the tool evaluates, provided that all (preprocessing tasks were successful), how intersecting + or proximity related objects build sub-graphs. This is the feature that was used in `M. Kühbach et al. <https://arxiv.org/abs/2205.13510>`_ + for the high-throughput analyses of how many objects are coprecipitates in the sense that they are single, + duplet, triplet, or high-order local groups. + + + + + + The maximum Euclidean distance between two objects below which they are + considered within proximity. + + + + + Specifies if the tool stores the so-called forward relations between nodes representing members of the + current_set to nodes representing members of the next_set. + + + + + Specifies if the tool stores the so-called backward relations between nodes representing members of the + next_set to nodes representing members of the current_set. + + + + + Current set stores a set of members, meshes of volumetric features, + which will be checked for proximity and/or volumetric intersection, + to members of the current_set. + The meshes were generated as a result of some other meshing process. + + + + This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k`) + step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). + + + + + + The total number of distinguished feature sets featureID. + It is assumed that the members within all these featureID sets + are representing a set together. As an example this set might represent + all volumetric_features. However, users might have formed + a subset of this set where individuals were regrouped. + For paraprobe-nanochem this is the case for objects and proxies. + Specifically, objects are distinguished further into those far + from and those close to the edge of the dataset. + Similarly, proxies are distinguished further into those far + from and those close to the edge of the dataset. + So while these four sub-sets contain different so-called types of + features, key is that they were all generated for one set, here the + current_set. + + + + + Name of the (NeXus)/HDF5 file which contains triangulated surface meshes of the + members of the set as instances of NXcg_polyhedron. + + + + Descriptive category explaining what these features are. + + + + + + + + + + + + + + + Absolute path to the group with geometry data in the HDF5 file referred to by + path. + + + + + + Array of identifier whereby the path to the geometry data can be inferred + automatically. + + + + + + + + + + Next set stores a set of members, meshes of volumetric features, + which will be checked for proximity and/or volumetric intersection, + to members of the next_set. + The meshes were generated as a result of some other meshing process. + + + + This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k + 1`) + step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). + + + + + + The total number of distinguished feature sets featureID. + It is assumed that the members within all these featureID sets + are representing a set together. As an example this set might represent + all volumetric_features. However, users might have formed + a subset of this set where individuals were regrouped. + For paraprobe-nanochem this is the case for objects and proxies. + Specifically, objects are distinguished further into those far + from and those close to the edge of the dataset. + Similarly, proxies are distinguished further into those far + from and those close to the edge of the dataset. + So while these four sub-sets contain different so-called types of + features key is that they were all generated for one set, here the + next_set. + + + + + + Descriptive category explaining what these features are. + + + + + + + + + + + + + + Absolute path to the group with geometry data in the HDF5 file referred to by + path. + + + + + + Array of identifier whereby the path to the geometry data can be inferred + automatically. + + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml new file mode 100644 index 0000000..dff4a65 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml @@ -0,0 +1,219 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The total number of links pointing from current to next. + + + + + The total number of links pointing from next to current. + + + + + The total number of members in the current_set. + + + + + The total number of members in the next_set. + + + + + The total number of cluster found for coprecipitation analysis. + + + + + The number of rows in the table/matrix for coprecipitation statistics. + + + + + Application definition for results files of the paraprobe-intersector tool. + + + + + + + + + + The results of an overlap/intersection analysis. + + + + + A matrix of indices_feature that specifies which named features + from the current_set have directed link(s) pointing to which named + feature(s) from the next_set. + + + + + + + + + For each link/pair in current_to_next a characterization whether the + link is due to volumetric overlap (0x00 == 0), proximity (0x01 == 1), + or something else unknown (0xFF == 255). + + + + + + + + A matrix of indices_feature which specifies which named feature(s) + from the next_set have directed link(s) pointing to which named + feature(s) from the current_set. Only if the mapping whereby the + links are defined is symmetric it holds that next_to_current maps + the links for current_to_next in just the opposite direction. + + + + + + + + + For each link/pair in next_to_current a characterization whether the + link is due to a volumetric overlap (0x00 == 0), proximity (0x01 == 1), + or something else unknown (0xFF == 255). + + + + + + + + For each pair of links in current_to_next the volume of the + intersection, i.e. how much volume do the two features share. + If features do not intersect the volume is zero. + + + + + + + + During coprecipitation analysis the current and next set are analyzed + for links in a special way. Three set comparisons are made. Members + of the set in each comparison are analyzed for overlap and proximity: + + The first comparison is the current_set against the current_set. + The second comparison is the next_set against the next_set. + The third comparison is the current_set against the next_set. + + Once the (forward) links for these comparisons are ready, pair relations + are analyzed with respect to which objects with indices_feature + cluster in identifier space. Thereby, a logical connection (link) is + established between the features in the current_set and the next_set. + Recall that these two sets typically represent different features + within an observed system for otherwise the same parameterization. + + Examples include two sets of e.g. precipitates with differing + chemical composition that were characterized in the same material + volume representing a snapshot of an e.g. microstructure at the same + point in time. Researchers may have performed two analyses, one to + characterize precipitates A and another one for precipitates B. + + Coprecipitation analysis now logically connects these independent + characterization results to establish spatial correlations of e.g. + the precipitates' spatial arrangement. + + + + Matrix of indices_feature and cluster_id pairs which + encodes the cluster to which each indices_feature was assigned. + Here for features of the current_set. + + + + + + + + + Matrix of indices_feature and cluster_id pairs which + encodes the cluster to which each indices_feature was assigned. + Here for features of the next_set. + + + + + + + + + The identifier (names) of the cluster. + + + + + + + + Pivot table as a matrix. + The first column encodes how many members from the current_set + are in each cluster, one row per cluster. + + The second column encodes how many members from the next_set + are in each cluster, in the same row per cluster respectively. + + The third column encodes the total number of members in the cluster. + + + + + + + + + Pivot table as a matrix. + + The first column encodes the different types of + clusters based on their number of members in the sub-graph. + + The second column encodes how many clusters with + as many members exist. + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml new file mode 100644 index 0000000..98b61e3 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml @@ -0,0 +1,864 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + How many iontypes does the delocalization filter specify. + + + + + How many grid_resolutions values. + + + + + How many kernel_variance values. + + + + + How many disjoint control points are defined. + + + + + How many iontypes does the interface meshing iontype filter specify. + + + + + How many DCOM iterations. + + + + + Maximum number of atoms per molecular ion. + + + + + Number of cylinder ROIs to place for oned_profile if no feature mesh is used. + + + + + Application definition for a configuration file of the paraprobe-nanochem tool. + + + + + + + + + + Discretization and distributing of the ion point cloud on a 3D grid + to enable analyses at the continuum scale. + + By default, the tool computes a full kernel density estimation of decomposed + ions to create one discretized field for each element. + + One delocalization task configures a parameter sweep with at least one + delocalization. The total number of runs depends on the number of + grid_resolution and kernel_variance values. For example, setting two grid_resolutions + and three kernel_variance will compute six runs. Two sets of three with the first set using + the first grid_resolutions and in sequence the kernel_variance respectively. + + + + + A precomputed triangulated surface mesh representing a model (of the surface) + of the edge of the dataset. This model can be used to detect and control + various sources of bias in the analyses. + + + + + + + Absolute path in the (HDF5) file that points to the array + of vertex positions for the triangles in that triangle_set. + + + + + Absolute path in the (HDF5) file that points to the array + of vertex indices for the triangles in that triangle_set. + + + + + + Distance between each ion and triangulated surface mesh. + + + + + + + + + Configuration for the algorithm that defines the multiplicity of + each reconstructed position during the delocalization. + + + + The multiplicity of an ion at a reconstructed position is defined as follows: + + * resolve_unknown, multiplicity equals 1 for all ions of the unknown_type + This mode is useful for segmenting regions with poor ranging. + * resolve_point, multiplicity equals 1 for all ions + This mode is useful for segmenting point density. + * resolve_atom, multiplicity equals the number of atoms per ion + This mode is useful for segmenting atomic density. + * resolve_element, multiplicity equals the number of elements in the whitelist per ion + This mode is useful for segmenting regions of specific elemental composition (ignoring nuclids) + * resolve_element_charge, ???multiplicity like resolve_element when charge is met + * resolve_isotope, multiplicity equals the number of nuclides in the whitelist per ion + This mode is useful for segmenting regions of specific isotopic composition + * resolve_isotope_charge, ??? + + Other multiplicities are 0. + + + + + + + + + + + + + + TODO + + + + + TODO + + + + + + + Compute delocalization or load an existent one from input. + + + + + + + + + Serialized result of an already computed delocalization which is for performance + reasons here just loaded and not computed again. + + + + + + + Absolute path in the (HDF5) file that points to the group within which + individual delocalization results are stored. + + + + + + + Matrix of nuclides representing how iontypes should be accounted for during + the delocalization. This is the most general approach to define if and how many + times an ion is to be counted. The tool performs a so-called atomic decomposition + of all iontypes, i.e. the tool analyses from how many atoms of each nuclide + or element respectively an (molecular) ion is built from. + + Taking the hydroxonium H3O+ molecular ion as an example: + It contains hydrogen and oxygen atoms. The multiplicity of hydrogen + is three whereas that of oxygen is one. Therefore, the respective atomic decomposition + analysis prior to the iso-surface computation adds three hydrogen counts for each + H3O+ ion. + + This is a practical solution which accepts that on the one hand not every bond is + broken during an atom probe experiment but also that ions may react further during + their flight to the detector. The exact details depend on the local field conditions, + quantum mechanics of possible electron transfer and thus the detailed trajectory + of the system and its electronic state. + + The detection of molecular ions instead of always single atom ions only is the + reason that an atom probe experiment tells much about field evaporation physics + but also faces an inherent loss of information with respect to the detailed spatial + arrangement that is independent of other imprecisions such as effect of limited + accuracy of reconstruction protocols and their parameterization. + + Unused values in each row of the matrix are nullified. + Nuclides are identified as hashed nuclide (see :ref:`NXatom`) for further details. + + + + + + + + + Array of edge lengths of the cubic cells used for discretizing the reconstructed dataset + on a cuboidal 3D grid (:ref:`NXcg_grid`). The tool performs as many delocalization + computations as values are specified in grid_resolution. + + + + + + + + Half the width of a :math:`{(2 \cdot n + 1)}^3` cubic kernel of cubic voxel + beyond which the Gaussian Ansatz function will be truncated. Intensity outside + the kernel is factorized into the kernel via a normalization procedure. + + + + + Array of variance values :math:`\sigma` of the Gaussian Ansatz kernel + (:math:`\sigma_x := \sigma`, :math:`\sigma_x = \sigma_y = 2 \cdot \sigma_z`). + The tool performs as many delocalization computations as values are specified + in kernel_variance. + + + + + + + + How should the results of the kernel-density estimation be normalized into quantities. + By default, the tool computes the total number (intensity) of ions or elements. + Alternatively, the tool can compute the total intensity, the composition, + or the concentration of the ions/elements specified by the nuclide_whitelist. + + + + + + + + + + Specifies if the tool should report the delocalization 3D field values. + + + + + Configuration of the set of iso-surfaces to compute using that delocalization. + Such iso-surfaces are the starting point for a reconstruction of so-called objects or + (microstructural) features. Examples of scientific relevant are (line features e.g. dislocations + poles, surface features such as interfaces, i.e. phase and grain boundaries, or volumetric + features such as precipitates. + Users should be aware that reconstructed datasets in atom probe are a model and may face + inaccuracies and artifacts that can be mistaken incorrectly as microstructural features. + + + + As it is detailed in `M. Kühbach et al. <https://arxiv.org/abs/2205.13510>`_, the handling of + triangles at the surface (edge) of the dataset requires special attention especially for + composition-normalized delocalization. Here, it is possible that the composition + increases towards the edge of the dataset because the quotient of two numbers + that are both smaller than one is larger instead of smaller than the counter. + + By default, the tool uses a modified marching cubes algorithm of Lewiner et al. + which detects if voxels face such a situation. In this case, no triangles are generated + for such voxels. + + Alternatively, keep_edge_triangles instructs the tool to not remove triangles at the + edge of the dataset at the cost of bias. When using this keep_edge_triangles users + should understand that all features in contact with the edge of the dataset get usually + artificial enlarged. Consequently, triangulated surface meshes of these objects are + closed during the marching. However, this closure is artificial and can bias shape + analyses for those objects. This also holds for such practices that are offered in + proprietary software like IVAS / AP Suite. The situation is comparable to analyses + of grain shapes via orientation microscopy from electron microscopy or X-ray + diffraction tomography. Features at the edge of the dataset may have not been + captured fully. + + Thanks to collaboration with V. V. Rielli and S. Primig from the Sydney atom probe group, + paraprobe-nanochem implements a complete pipeline to process features at the edge of the + dataset. Specifically, these are modelled and replaced with closed polyhedral objects using + an iterative mesh and hole-filling procedures with fairing operations. + + The tool bookkeeps such objects separately to lead the decision whether or not to + consider these objects to the user. Users should be aware that results from fairing operations + should be compared to results from analyses where all objects at the edge + of the dataset have been removed. Furthermore, users should be careful with overestimating + the statistical significance of their dataset especially when using atom probe when they + use their atom probe result to compare different descriptors. Even though a dataset may + deliver statistically significant results for compositions, this does not necessarily mean that + same dataset will also yield statistically significant and insignificantly biased results for + 3D object analyses! + + Being able to quantify these effects and making atom probers aware of these subtleties + was one of the main reasons why the paraprobe-nanochem tool was implemented. + + + + + + + + + The ion-to-surface distance that is used in the analyses of features to identify whether + these are laying inside the dataset or close to the surface (edge) of the dataset. + + If an object has at least one ion with an ion-to-surface-distance below this threshold, + the object is considered close to the edge of the dataset. The tool uses a distance-based + approach to solve the in general complicated and involved treatment of computing + volumetric intersections between closed 2-manifolds that are not necessarily convex. + The main practical reason is that such computational geometry analyses face numerical + robustness issues as a consequence of which a mesh can be detected as being completely + inside another mesh although in reality it is only :math:`\epsilon`-close only, i.e. almost + touching only the edge (e.g. from inside). + + Practically, humans would likely still state in such case that the object is close to the + edge of the dataset; however mathematically the object is indeed completely inside. + In short, a distance-based approach is rigorous and flexible. + + + + + Iso-contour values. For each value, the tool computes an iso-surface and performs + subsequent analyses for each iso-surface. The unit depends on the choice for the + normalization of the accumulated ion intensity values per voxel: + + * total, total number of ions, irrespective their iontype + * candidates, total number of ions with type in the isotope_whitelist. + * composition, candidates but normalized by composition, i.e. at.-% + * concentration, candidates but normalized by voxel volume, i.e. ions/nm^3 + + + + + Specifies if the tool should report the triangle soup which represents each triangle of the + iso-surface complex. The resulting set of triangles is colloquially referred to as a soup + because different sub-set may not be connected. + + Each triangle is reported with an ID specifying to which triangle cluster (with IDs starting at zero) + the triangle belongs. The clustering of triangles within the soup is performed with a + modified DBScan algorithm. + + + + + Specifies if the tool should analyze for each cluster of triangles how they can be combinatorially + processed to describe a closed polyhedron. Such a closed polyhedron (not-necessarily convex!) + can be used to describe objects with relevance in the microstructure. + + Users should be aware that the resulting mesh does not necessarily represent the original precipitate. + In fact, inaccuracies in the reconstructed positions cause inaccuracies in all downstream processing + operations. Especially the effect on one-dimensional spatial statistics like nearest neighbor correlation + functions were discussed in the literature `B. Gault et al. <https://doi.org/10.1017/S1431927621012952>`_. + + In continuation of these thoughts, this applies also to reconstructed objects. + A well-known example is the discussion of shape deviations of scandium-rich precipitates in aluminum alloys + which in reconstructions may appear as ellipsoids although they should be indeed almost spherical + provided their size is larger than the atomic length scale. + + + + + Specifies if the tool should report a triangulated surface mesh for each identified closed polyhedron. + It is common that a marching cubes algorithm creates iso-surfaces with a fraction of tiny sub-complexes + (e.g. small isolated tetrahedra). + + These can be small tetrahedra/polyhedra about the center of a voxel of the support grid + on which marching cubes operates. Such objects may not contain an ion; especially when considering + that delocalization procedures smoothen the positions of the ions. Although these small objects are + interesting from a numerical point of view, scientists may argue they are not worth to be reported because + a microstructural feature should contain at least a few atoms to become relevant. + Therefore, paraprobe-nanochem by default does not report closed objects which bound a volume + that contains no ion. + + + + + Specifies if the tool should report properties of each closed polyhedron, such + as volume and other details. + + + + + Specifies if the tool should report for each closed polyhedron an approximately optimal bounding box + fitted to all triangles of the surface mesh of the object and ion positions inside or on the surface of the mesh. + This bounding box informs about the closed object's shape (aspect ratios). + + Users should be aware that the choice of the algorithm to compute the bounding box can have an + effect on aspect ratio statistics. It is known that computing the true optimal bounding box of in 3D + is an :math:`\mathcal{O}^3`-time-complex task. The tool uses well-established approximate algorithms + of the Computational Geometry Algorithms Library (CGAL). + + + + + Specifies if the tool should report for each closed polyhedron all evaporation IDs of those ions which + lay inside or on the boundary of the polyhedron. This information is used by the paraprobe-intersector + tool to infer if two objects share common ions, which is then understood as that the two objects intersect. + + Users should be aware that two arbitrarily closed polyhedra in three-dimensional space can intersect + but not share a common ion. In fact, the volume bounded by the polyhedron has sharp edges and flat + face(t)s. When taking two objects, an edge of one object may for instance pierce into the surface of + another object. In this case the objects partially overlap / intersect volumetrically; however this piercing + might be so small or happening in the volume between two reconstructed ion positions. Consequently, + sharing ions is a sufficient but not a necessary condition for interpreting (volumetric) intersections + between objects. + + Paraprobe-intersector implements a rigorous alternative to handle such intersections using a tetrahedralization + of closed objects. However, in many practical cases, we found through examples that there are polyhedra (especially when they are non-convex and have almost point-like) connected channels, where + tetrahedralization libraries have challenges dealing with. In this case, checking intersections + via shared_ions is a more practical alternative. + + + + + Specifies if the tool should report if a (closed) object has contact with the surface aka edge of the dataset. + For this the tool currently inspects if the shortest distance between the set of triangles of the triangulated + surface mesh and the triangles of the edge model is larger than edge_threshold. + If this is the case, the object is assumed to be deeply embedded in the interior of the dataset. + Otherwise, the object is considered to have an edge contact, i.e. it shape is likely affected by the edge. + + + + + Specifies if the tool should analyze a closed polyhedron (aka proxy) for each cluster of triangles whose + combinatorial analysis according to has_object returned that the object is not a closed polyhedron. + Such proxies are closed via iterative hole-filling, mesh refinement, and fairing operations. + + Users should be aware that the resulting mesh does not necessarily represent the original feature. + In most cases objects, precipitates in atom probe end up as open objects because they have been + clipped by the edge of the dataset. Using a proxy is in this case a strategy to still be able to account + for these objects. However, users should make themselves familiar with the consequences and + potential bias which this can introduce into the analysis. + + + + + Like has_object_geometry but for the proxies. + + + + + Like has_object_properties but for the proxies. + + + + + Like has_object_obb but for the proxies. + + + + + Like has_object_ions but for the proxies. + + + + + Like has_object_edge_contact but for the proxies. + + + + + Specifies if the tool should report for each closed object a (cylindrical) region-of-interest (ROI) that gets + placed, centered, and aligned with the local normal for each triangle of the object. + + + + + Specifies if the tool should report for each ROI that was placed at a triangle of each object if this ROI intersects + with the edge the dataset. Currently, the tool supports cylindrical ROIs. A computational geometry test is + performed to check for a possible intersection of each ROI with the triangulated surface mesh that is defined + via surface. Results of this cylinder-set-of-triangles intersection are interpreted as follows: + If the cylinder intersects with at least one triangle of the surface (mesh) the ROI is assumed to make edge contact. + Otherwise, the ROI is assumed to make no edge contact. + + Users should note that this approach does not work if the ROI is laying completely outside the dataset as also + in this case the cylinder intersects with any triangle. However, for atom probe this case is practically irrelevant + provided constructions such as alpha shapes or alpha wrappings (such as paraprobe-surfacer does) about the + ions of the entire reconstructed volume are used. + + + + + + + + Use a principle component analysis (PCA) to mesh a single free-standing interface patch within + the reconstructed volume that is decorated by ions of specific iontypes (e.g. solute atoms). + + Interface_meshing is a typical starting point for the quantification of Gibbsian interfacial excess + in cases when closed objects constructed from patches e.g. iso-surfaces are not available or + when there is no substantial or consistently oriented concentration gradients across an interface + patch. The functionality can also be useful when the amount of latent crystallographic information + within the point cloud is insufficient or when combined with interface_meshing based on ion density + traces in field-desorption maps (see `Y. Wei et al. <https://doi.org/10.1371/journal.pone.0225041>`_ + and `A. Breen et al. <https://github.com/breen-aj/detector>`_ for details). + + Noteworthy to mention is that the method used is conceptually similar to the work of `Z. Peng et al. <https://doi.org/10.1017/S1431927618016112>`_ and related work (DCOM algorithm) by `P. Felfer et al. <https://doi.org/10.1016/j.ultramic.2015.06.002>`_. Compared to these implementations + paraprobe-nanochem uses inspection functionalities which detect potential geometric + inconsistencies or self-interactions of the evolved DCOM mesh. + + + + A precomputed triangulated surface mesh representing a model (of the surface) + of the edge of the dataset. This model can be used to detect and control + various sources of bias in the analyses. + + + + + + + Absolute path in the (HDF5) file that points to the array + of vertex positions for the triangles in that triangle_set. + + + + + Absolute path in the (HDF5) file that points to the array + of vertex indices for the triangles in that triangle_set. + + + + + + + How is the PCA initialized: + + * default, means based on segregated solutes in the ROI + * control_point_file, means based on reading an external list of + control points, currently coming from the Leoben APT_Analyzer. + + The control_point_file is currently expected with a specific format. + The Leoben group lead by L. Romaner has developed a GUI tool `A. Reichmann et al. <https://github.com/areichm/APT_analyzer>`_ creates a control_point_file that + can be parsed by paraprobe-parmsetup-nanochem to match the here required + formatting in control_points. + + + + + + + + + Details about the control point file used. + + + + + + + X, Y, Z position matrix of disjoint control points. + + + + + + Method used for identifying and refining the location of the interface. Currently, + paraprobe-nanochem implements a PCA followed by an iterative loop of isotropic + mesh refinement and DCOM step(s), paired with self-intersection detection. + + + + + + + + Specify those nuclides which the tool should inspect iontypes for if they contain such nuclides. + If this is the case ions of such type are taken with the number of nuclides of this multiplicity found. + The atoms of these ions are assumed to serve as useful markers for locating the interface and + refining the interface mesh. + + + + + + + + + Array of nuclide iontypes to filter. + + + + + + + + + + How many times should the DCOM and mesh refinement be applied? + + + + + Array of decreasing positive not smaller than one nanometer real values + which specify how the initial triangles of the mesh should be iteratively + refined by edge splitting and related mesh refinement operations. + + + + + + + + Array of decreasing positive not smaller than one nanometer real values + which specify the radius of the spherical region of interest within which the + DCOM algorithm decides for each vertex how the vertex might be relocated. + + The larger it is the DCOM radius in relation to the target_edge_length the more + likely it becomes that vertices will be relocated so substantially that triangle + self-intersections may occur. The tool detects these and stops in a controlled + manner so that the user can repeat the analyses with using a different parameterization. + + + + + + + + Array of integers which specify for each DCOM step how many times the mesh + should be iteratively smoothened. Users should be aware that all three arrays + target_edge_length, target_dcom_radius, and target_smoothing_step are interpreted + in the same sequence, i.e. the zeroth entry of each array specifies the respective + parameter values to be used in the first DCOM iteration. The first entry of each array + those for the second DCOM iteration and so on and so forth. + + + + + + + + + Analysis of one-dimensional profiles in ROIs placed in the dataset. + Such analyses are useful for quantifying interfacial excess or for + performing classical composition analyses. + + The tool will test for each ROIs if it is completely embedded in the dataset. + Specifically, each such test evaluates if the ROI cuts at least one triangle + of the triangulated surface mesh that is referred to by surface. + If this is the case the ROI is marked as one close to the surface + and not analyzed further. Otherwise, the ROI is marked as one far + from the surface and processed further. + + For each ROI the tool computes atomically decomposed profiles. + This means, molecular ions are split into nuclides as many times as + their respective multiplicity. For each processed ROI the tool stores + a sorted list of signed distance values to enable post-processing with + other software like e.g. reporter to perform classical + Krakauer/Seidman-style interfacial excess analyses. + + Users should be aware that the latter intersection analysis is not + a volumetric intersection analysis. Given that the triangulated mesh + referred to in surface is not required to mesh neither a watertight + nor convex polyhedron a rigorous testing of volumetric intersection + is much more involved. If the mesh is watertight one could use split + the task in first tessellating the mesh into convex polyhedra (e.g. + tetrahedra and apply a volumetric intersection method like the + Gilbert-Johnson-Keerthi algorithm (GJK). In cases when the mesh is not + even watertight distance-based segmentation in combination with again + intersection of triangles and convex polyhedra is a robust but currently + not implemented method to quantify intersections. + + + + A precomputed triangulated surface mesh representing a model (of the surface) + of the edge of the dataset. This model can be used to detect and control + various sources of bias in the analyses. + + + + + + + Absolute path in the (HDF5) file that points to the array + of vertex positions for the triangles in that triangle_set. + + + + + Absolute path in the (HDF5) file that points to the array + of vertex indices for the triangles in that triangle_set. + + + + + + Distance between each ion and triangulated surface mesh. + + + + + + + Absolute path in the (HDF5) file that points to the distance values. + The tool assumes that the values are stored in the same order as + points (ions). + + + + + + A precomputed triangulated mesh of the feature representing a model of the + interface at which to place ROIs to profile. This can be the mesh of an + interface as returned e.g. by a previous interface_meshing task or the + mesh of an iso-surface from a previous delocalization task. + + + + + + + Absolute HDF5 path to the dataset that specifies the array of vertex positions. + + + + + Absolute HDF5 path to the dataset that specifies the array of facet indices + which refer to vertices. + + + + + Absolute HDF5 path to the dataset that specifies the array of facet signed unit + normals. + + + + + Absolute HDF5 path to the dataset that specifies the array of vertex signed unit + normals. + + + + + + If interface_model is isosurface this filter can be used to restrict the analysis to specific + patches of an iso-surface. + + + + + + + + To enable an additional filtration of specific parts of the feature + mesh it is recommended to feed precomputed distances of each ion to + the triangles of the feature mesh. + + + + + + + Absolute path in the (HDF5) file that points to the distance values. + The tool assumes that the values are stored in the same order as + points (ions). + + + + + + + As an alternative mode the tool can be instructed to place ROIs + at specific locations into the dataset. This is the programmatic + equivalent to the classical approach in atom probe to place ROIs + for composition analyses via positioning and rotating them via + a graphical user interface (such as in IVAS / AP Suite). + + + + + + + + + + + + + + + + + + + + + + + + + + + Which type of distance should be reported for the profile. + + + + + + + + For each ROI, along which direction should the cylindrical ROI + be oriented if ROIs are placed at triangles of the feature mesh. + + + + + + + + For each ROI, how high (projected onto the cylinder axis) should + the cylindrical ROI be if ROIs are placed at triangles + of the feature mesh. + + + + + For each ROI, how wide (in radius) should the cylindrical ROI + be if ROIs are placed at triangles of the feature mesh. + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml new file mode 100644 index 0000000..431f236 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml @@ -0,0 +1,1177 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The total number of ions in the reconstruction. + + + + + The total number of atoms in the atomic_decomposition match filter. + + + + + The total number of isotopes in the isotopic_decomposition match filter. + + + + + The dimensionality of the delocalization grid. + + + + + The cardinality/total number of cells/grid points in the delocalization grid. + + + + + + The total number of faces of triangles. + + + + + The total number of XDMF values to represent all faces of triangles via XDMF. + + + + + The total number of entries in a feature dictionary. + + + + + The total number of volumetric features. + + + + + The total number of member distinguished when reporting composition. + + + + + The total number of ROIs placed in a oned_profile task. + + + + + Application definition for a results file of the paraprobe-nanochem tool. + + + + + + + + + + + + + + + + + + The discretized domain/grid on which the delocalization is applied. + + + + + + + + + + + The total number of cells/voxels of the grid. + + + + + + + + + + The symmetry of the lattice defining the shape of the unit cell. + + + + + + + + The unit cell dimensions according to the coordinate system defined under + coordinate_system. + + + + + + + + Number of unit cells along each of the d-dimensional base vectors. + The total number of cells, or grid points has to be the cardinality. + If the grid has an irregular number of grid positions in each direction, + as it could be for instance the case of a grid where all grid points + outside some masking primitive are removed, this extent field should + not be used. Instead use the coordinate field. + + + + + + + + + Integer which specifies the first index to be used for distinguishing identifiers for cells. + Identifiers are defined either implicitly or explicitly. For implicit indexing the identifiers are + defined on the interval :math:`[identifier\_offset, identifier\_offset + c - 1]`. + For explicit indexing the identifier array has to be defined. + + + + + Halfwidth of the kernel about the central voxel. + The shape of the kernel is that of a cuboid + of extent 2*kernel_extent[i] + 1 in each dimension i. + + + + + + + + Functional form of the kernel (Ansatz function). + + + + + + + + Standard deviation :math:`\sigma_i` of the kernel in each dimension + in the paraprobe coordinate_system with i = 0 is x, i = 1 is y, i = 2 is z. + + + + + + + + Expectation value :math:`\mu_i` of the kernel in each dimension + in the paraprobe coordinate_system with i = 0 is x, i = 1 is y, i = 2 is z. + + + + + + + + How were results of the kernel-density estimation normalized: + + * total, the total number (intensity) of ions or elements. + * candidates, the total number (intensity) of ions matching weighting_model + * composition, the value for candidates divided by the value for total, + * concentration, the value for candidates divided by the volume of the cell. + + + + + + + + + + + A tight axis-aligned bounding box about the grid. + + + + For atom probe should be set to true. + + + + + Integer which specifies the first index to be used for distinguishing + hexahedra. Identifiers are defined either implicitly or explicitly. + For implicit indexing the identifiers are defined on the interval + :math:`[identifier\_offset, identifier\_offset + c - 1]`. + For explicit indexing the identifier array has to be defined. + + + + + + Integer which specifies the first index to be used for distinguishing + identifiers for vertices. Identifiers are defined either implicitly or explicitly. + For implicit indexing the identifiers are defined on the interval + :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing the identifier array + has to be defined. + + + + + Integer which specifies the first index to be used for distinguishing + identifiers for faces. Identifiers are defined either implicitly or explicitly. + For implicit indexing the identifiers are defined on the interval + :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing the identifier array + has to be defined. + + + + + Positions of the vertices. + Users are encouraged to reduce the vertices to unique set of positions + and vertices as this supports a more efficient storage of the geometry data. + It is also possible though to store the vertex positions naively in which + case vertices_are_unique is likely False. + Naively here means that one for example stores each vertex of a triangle + mesh even though many vertices are shared between triangles and thus + the positions of these vertices do not have to be duplicated. + + + + + + + + + Array of identifiers from vertices which describe each face. + + The first entry is the identifier of the start vertex of the first face, + followed by the second vertex of the first face, until the last vertex + of the first face. Thereafter, the start vertex of the second face, the + second vertex of the second face, and so on and so forth. + + Therefore, summating over the number_of_vertices, allows to extract + the vertex identifiers for the i-th face on the following index interval + of the faces array: :math:`[\sum_{i = 0}^{i = n-1}, \sum_{i=0}^{i = n}]`. + + + + + + + + + Six equally formatted sextets chained together. For each sextett the first entry is an + XDMF primitive topology key (here 5 for polygon), the second entry the XDMF + primitive count value (here 4 because each face is a quad). + The remaining four values are the vertex indices. + + + + + + + + How many distinct boundaries are distinguished? + Most grids discretize a cubic or cuboidal region. In this case + six sides can be distinguished, each making an own boundary. + + + + + Name of the boundaries. E.g. left, right, front, back, bottom, top, + The field must have as many entries as there are number_of_boundaries. + + + + + + + + The boundary conditions for each boundary: + + 0 - undefined + 1 - open + 2 - periodic + 3 - mirror + 4 - von Neumann + 5 - Dirichlet + + + + + + + + + + + The result of the delocalization :math:`\Phi = f(x, y, z)` based on which subsequent iso-surfaces + will be computed. In commercial software so far there is no possibility to export this information. + + If the intensity for all matches of the weighting_model are summarized, name this NXdata instance + scalar_field_magn_total. + + If the intensity is reported for each iontype, one can avoid many subsequent + computations as individual intensities can be reinterpreted using a different weighting_model in + down-stream usage of the here reported values (e.g. with Python scripting). + In this case name the individual NXdata instances scalar_field_magn_ionID using the ID of the ion as + per the configuration of the ranging definitions used. + + + + + Intensity of the field at given point + + + + + + + + Center of mass positions of each voxel for rendering the scalar field + via XDMF in e.g. Paraview. + + + + + + + + + XDMF topology for rendering in combination with xdmf_xyz the scalar field + via XDMF in e.g. Paraview. + + + + + + + + + The three-dimensional gradient :math:`\nabla \Phi`. + Follow the naming convention of scalar_field_magn_SUFFIX to report parallel structures. + + + + + The gradient vector formatted for direct visualization via XDMF in e.g. + Paraview. + + + + + + + + + Center of mass positions of each voxel for rendering the scalar field gradient + via XDMF in e.g. Paraview. + + + + + + + + + XDMF topology for rendering in combination with xdmf_xyz the scalar field + via XDMF in e.g. Paraview. + + + + + + + + + + An iso-surface is the boundary between two regions across which the magnitude of a + scalar field falls below/exceeds a threshold magnitude :math:`\varphi`. + + For applications in atom probe microscopy, the location and shape of such a boundary (set) + is typically approximated by discretization - triangulation to be specific. + + This yields a complex of not necessarily connected geometric primitives. + Paraprobe-nanochem approximates this complex with a soup of triangles. + + + + + The threshold or iso-contour value :math:`\varphi`. + + + + + Reference to the specific implementation of marching cubes used. + The value placed here should be a DOI. If there are no specific + DOI or details write not_further_specified, or give at least a + free-text description. The program and version used is the + specific paraprobe-nanochem. + + + + + The resulting triangle soup computed via marching cubes. + + + + + + + + + + + + Positions of the vertices. + + Users are encouraged to reduce the vertices to a unique set as this may + result in a more efficient storage of the geometry data. + It is also possible though to store the vertex positions naively in which + case vertices_are_unique is likely False. Naively here means that each + vertex is stored even though many share the same positions. + + + + + + + + + Array of identifiers from vertices which describe each face. + + The first entry is the identifier of the start vertex of the first face, + followed by the second vertex of the first face, until the last vertex + of the first face. Thereafter, the start vertex of the second face, the + second vertex of the second face, and so on and so forth. + + Therefore, summating over the number_of_vertices, allows to extract + the vertex identifiers for the i-th face on the following index interval + of the faces array: :math:`[\sum_{i = 0}^{i = n-1}, \sum_{i=0}^{i = n}]`. + + + + + + + + A list of as many tuples of XDMF topology key, XDMF number + of vertices and a triple of vertex indices specifying each + triangle. The total number of entries is n_f_tri * (1+1+3). + + + + + + + + + Direction of each normal. + + + + + + + + + Qualifier how which specifically oriented normal to its + primitive each normal represents. + + * 0 - undefined + * 1 - outer + * 2 - inner + + + + + + + + + + + Direction of each normal. + + + + + + + + + Qualifier how which specifically oriented normal to its + primitive each normal represents. + + * 0 - undefined + * 1 - outer + * 2 - inner + + + + + + + + Triangle normals are oriented in the direction of the + gradient vector of the local delocalized scalar field. + :math:`\sum_{x, y, z} {\nabla{c}_i}^2`. + + + + + + + + + Triangle normals are oriented in the direction of the + gradient vector of the local delocalized scalar field. + The projection variable here describes the cosine of the + angle between the gradient direction and the normal + direction vector. + This is a descriptor of how parallel the projection is + that is especially useful to document those triangles + for whose the projection is almost perpendicular. + + + + + + + + + + + + + + Array of edge length values. For each triangle the edge length + is reported for the edges traversed according to the sequence + in which vertices are indexed in triangles. + + + + + + + + + Array of interior angle values. For each triangle the angle + is reported for the angle opposite to the edges which are + traversed according to the sequence in which vertices + are indexed in triangles. + + + + + + + + + The center of mass of each triangle. + + + + + + + + + Iso-surfaces of arbitrary scalar three-dimensional fields can show a complicated topology. + Paraprobe-nanochem can run a DBScan-like clustering algorithm which performs a + connectivity analysis on the triangle soup representation of such iso-surface. + This may yield a set of connected features whose individual surfaces are discretized + by a triangulated mesh each. Such volumetric features can be processed further using + paraprobe-nanochem using a workflow with at most two steps. + + In the first step, the tool distinguishes three types of (v) i.e. volumetric features: + + 1. So-called objects, i.e. necessarily watertight features represented by polyhedra. + These objects were already watertight within the triangulated iso-surface. + 2. So-called proxies, i.e. features that were not necessarily watertight within the triangulated + iso-surface but were subsequently replaced by a watertight mesh using polyhedral mesh + processing operations (hole filling, refinement, fairing operations). + 3. Remaining triangle surface meshes or parts of these of arbitrary shape and cardinality + that are not transformable into proxies or for which no transformation into proxies was + instructed. + + These features can be interpreted as microstructural features. Some of them may be precipitates, + some of them may be poles, some of them may be segments of dislocation lines or other + crystal defects which are decorated (or not) with solutes. + + In the second step, the tool can be used to analyze the proximity of these objects to a + model of the surface (edge) of the dataset. + + + + The identifier which the triangle_soup connectivity analysis + returned, which constitutes the first step of the + volumetric_feature identification process. + + + + + + + + The array of keywords of feature_type dictionary. + + + + + + + + The array of values for each keyword of the + feature_type dictionary. + + + + + + + + The array of controlled keywords, need to be from + feature_type_dict_keyword, which specify which type + each feature triangle cluster belongs to. + Keep in mind that not each feature is an object or proxy. + + + + + + + + The explicit identifier of features. + + + + + + + + In all situations instances of the parent NXprocess group are returned with a very similar + information structuring and thus we here replace the template name FEATURE + with one of the following types feature-specific group names: + + * objects, objects, irrespective their distance to the surface + * objects_close_to_edge, sub-set of v_feature_object close surface + * objects_far_from_edge, sub-set of v_feature_object not close to the surface + * proxies, proxies, irrespective their distance to the surface + * proxies_close_to_edge, sub-set of v_feature_proxies, close to surface + * proxies_far_from_edge, sub-set of v_feature_proxies, not close to surface + + + + Explicit identifier of the feature a sub-set of the indices_feature in the + parent group. + + + + + + + + Volume of the feature. NaN for non-watertight objects. + + + + + + + + An oriented bounding box (OBB) to each object. + + + + Edge length of the oriented bounding box from largest to smallest value. + + + + + + + + + Oriented bounding box aspect ratio. + YX versus ZY or second-largest over largest and smallest over second largest. + + + + + + + + + Position of the geometric center, which often is but + not necessarily has to be the center_of_mass of the + hexahedrally-shaped sample/sample part. + + + + + + + + + A simple approach to describe the entire set of hexahedra when the main intention + is to store the shape of the hexahedra for visualization. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Array of evaporation_id / identifier_ion which details which ions + lie inside or on the surface of the feature. + + + + + + + + + + + Total (count) of ions inside or on the surface of the feature relevant for normalization. + NaN for non watertight objects. + + + + + + + + + + + + + Count or weight which, when divided by total, yields the composition of this element, + nuclide, or (molecular) ion within the volume of the feature/object. + + + + + + + + + + + + + + + + + + + The multiplicity whereby the ion position is accounted for + irrespective whether the ion is considered as a decorator + of the interface or not. + As an example, with atom probe it is typically not possible + to resolve the positions of the atoms which arrive at the detector + as molecular ions. Therefore, an exemplar molecular ion of two carbon + atoms can be considered to have a multiplicity of two to account that + this molecular ion contributes two carbon atoms at the reconstructed + location considering that the spatial resolution of atom probe + experiments is limited. + + + + + + + + The multiplicity whereby the ion position is accounted for when + the ion is considered one which is a decorator of the interface. + + + + + + + + The equation of the plane that is fitted initially. + + + + The four parameter :math:`ax + by + cz + d = 0` which define the plane. + + + + + + + + + The triangle surface mesh representing the interface model. + Exported at state before or after the next DCOM step. + + + + Was this state exported before or after the next DCOM step. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Direction of each vertex normal. + + + + + + + + + Qualifier which details how specifically oriented the + face normal is with respect to its primitive (triangle): + + * 0 - undefined + * 1 - outer + * 2 - inner + + + + + + + + + + + + + + Direction of each face normal. + + + + + + + + + Qualifier which details how specifically oriented the + face normal is with respect to its primitive (triangle): + + * 0 - undefined + * 1 - outer + * 2 - inner + + + + + + + + + + + + + + + + + + + Array of edge length values. For each triangle the edge length is + reported for the edges traversed according to the sequence + in which vertices are indexed in triangles. + + + + + + + + + Array of interior angle values. For each triangle the angle is + reported for the angle opposite to the edges which are traversed + according to the sequence in which vertices are indexed in triangles. + + + + + + + + + + + + + The ROIs are defined as cylinders for the computations. To visualize these we discretize + them into regular n-gons. Using for instance 360-gons, i.e. a regular n-gon with 360 edges, + resolves the lateral surface of each cylinder such that their renditions are smooth in + visualization software like Paraview. + + + + + + Position of the geometric center, which often is but not + necessarily has to be the center_of_mass of the polyhedra. + + + + + + + + + The orientation of the ROI defined via a vector which points along + the cylinder axis and whose length is the height of the cylinder. + + + + + + + + + + XDMF support to enable coloring each ROI by its identifier. + + + + + + + + XDMF support to enable coloring each ROI whether it has edge contact or not. + + + + + + + + XDMF support to enable coloring each ROI by its number of atoms. + + + + + + + + XDMF support to enable coloring each ROI by its number of ions. + + + + + + + + Distance and iontype-specific processed data for each ROI. + Arrays signed_distance and nuclide_hash are sorted by increasing + distance. + Array nuclide_hash reports one hash for each atom of each isotope. + Effectively, this can yield to groups of values on signed_distance + with the same distance value as molecular ions are reported decomposed + into their atoms. + Therefore, the XDMF support fields number_of_atoms and number_of_ions + are only expected to display pairwise the same values respectively, + if all ions are built from a single atom only. + + + + + Sorted in increasing order projected along the positive direction + of the ROI as defined by orientation in the parent group. + + + + + + + + Hashvalue as defined in :ref:`NXatom`. + + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml new file mode 100644 index 0000000..2852414 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml @@ -0,0 +1,55 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The number of isotopes to consider as building blocks for searching molecular + ions. + + + + + The number of compositions to consider for molecular ion search tasks. + + + + + Application definition for a configuration file of the paraprobe-ranger tool. + + The tool paraprobe-ranger evaluates how mass-to-charge-state-ratio + values map on (molecular) ion types. + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml new file mode 100644 index 0000000..2d42fa8 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml @@ -0,0 +1,66 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The total number of ions in the reconstructed volume. + + + + + Application definition for results files of the paraprobe-ranger tool. + + The tool paraprobe-ranger evaluates how mass-to-charge-state-ratio + values map on (molecular) ion types. + + + + + + + + + + The tool loads ranging definitions from the configuration file and + evaluates for each ion to which iontype it matches. + If an ion matches on no type, the ion is assume of the default + *unknown_type*. In this case, the value *iontypes* is 0. + In other cases the value is larger than 0. + + + + The iontype (identifier) for each ion that was best matching, + stored in the order of the evaporation sequence ID. + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_clusterer.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_clusterer.nxdl.xml deleted file mode 100644 index eb89794..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_clusterer.nxdl.xml +++ /dev/null @@ -1,503 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of ions in the reconstruction. - - - - - The total number of entries in the restricted_identifier dictionary. - - - - - Results of a paraprobe-clusterer tool run. - - - - - - Version specifier of this application definition. - - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. the paraprobe-tool executable started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and the paraprobe-tool executable exited as a process. - - - - - The absolute path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - A statement whether the paraprobe-tool executable managed to - process the analysis or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must no longer compute analyses. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases, it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - If nothing else is specified we assume that there - has to be at least one set of NXtransformations named - paraprobe defined, which specifies the coordinate system. - In which all positions are defined. - - - - - The individual coordinate systems which should be used. - Field names should be prefixed with the following controlled terms - indicating which individual coordinate system is described: - - * paraprobe - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - A bitmask which identifies which of the ions in the dataset were - analyzed during this process. - - - - Number of ions covered by the mask. - The mask value for most may be 0. - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used, padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe-toolbox executable. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth (padding). - - - - - - - - - The result of a cluster analyses. These include typically the label for - each ion/point documenting to which feature (if any) an ion is assigned. - Typically, each analysis/run yields only a single cluster. - In cases of fuzzy clustering it can be possible that an ion is assigned - to multiple cluster (eventually with different) weight/probability. - - - - Results of a DBScan clustering analysis. - - - - The epsilon (eps) parameter. - - - - - The minimum points (min_pts) parameter. - - - - - Number of members in the set which is partitioned into features. - Specifically, this is the total number of targets filtered from the - dataset. Cardinality here is not the total number of ions in the - dataset. - - - - - - Which identifier is the first to be used to label a cluster. - - The value should be chosen in such a way that special values can be resolved: - * identifier_offset-1 indicates an object belongs to no cluster. - * identifier_offset-2 indicates an object belongs to the noise category. - Setting for instance identifier_offset to 1 recovers the commonly used - case that objects of the noise category get values to -1 and unassigned points to 0. - Numerical identifier have to be strictly increasing. - - - - - - The evaporation sequence identifier to figure out which ions - from the reconstruction were considered targets. - - - - - - - - - The raw labels from the DBScan clustering backend process. - - - - - - - - The raw array of core sample indices which specify which of the - targets are core points. - - - - - - - - - Matrix of numerical label for each member in the set. - For classical clustering algorithms this can for instance - encode the cluster_identifier. - - - - - - - - - The array of weight which specifies how surely/likely the - cluster is associated/assigned to a specific identifier as - is specified in the cluster_identifier array. - For the DBScan and atom probe tomography the multiplicity - of each ion with respect to the cluster. That is how many times - should the position of the ion be accounted for because the ion - is e.g. a molecular ion with several elements or isotope of - requested type. - - - - - - - - Optional bitmask encoding if members of the set are assigned to as noise or not. - - - - - - - - Optional bitmask encoding if member of the set are a core point. - For details to which feature/cluster an ion/point is a core point - consider numerical_label. - - - - - - - - In addition to the detailed storage which members was grouped to - which feature/group summary statistics are stored under this group. - - - - - Total number of members in the set which are categorized as noise. - - - - - - Total number of members in the set which are categorized as a core point. - - - - - - Total number of clusters (excluding noise and unassigned). - - - - - Array of numerical identifier of each feature (cluster). - - - - - - - - Array of number of members for each feature. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_distancer.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_distancer.nxdl.xml deleted file mode 100644 index 54ad4dc..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_distancer.nxdl.xml +++ /dev/null @@ -1,388 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of ions in the reconstruction. - - - - - The total number of triangles in the set. - - - - - Results of a paraprobe-distancer tool run. - - - - - - Version specifier of this application definition. - - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. the paraprobe-tool executable started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and the paraprobe-tool executable exited as a process. - - - - - The absolute path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - A statement whether the paraprobe-tool executable managed to - process the analysis or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must not compute any analysis. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - - - - The individual coordinate systems which should be used. - Field names should be prefixed with the following controlled terms - indicating which individual coordinate system is described: - - * paraprobe - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - The tool can be used to compute the analytical distance of each ion - to a set of triangles. - - - - A bitmask which identifies which of the ions in the dataset were - analyzed. - - - - Number of ions covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - A bitmask which identifies which of the triangles in the set - were considered. Usually these are all but sometimes users may - wish to filter certain portions of the triangles out. - If window_triangles is not provided it means that - all triangles were taken. - - - - Number of triangles covered by the mask. - The mask value for most may be 0. - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - The closest analytical distance of the ions to their respectively - closest triangle from the triangle set. - - - - - - - - A bitmask which identifies which of the distance values - can be assumed to have a consistent sign because the closest - triangle had a consistent outer unit normal defined. - For points whose bit is set 0 the distance is correct but the - sign is not reliable. - - - - Number of triangles covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. - - - - - - - - - The identifier of the triangle that is closest for each ion. - - - - - - - - A support field to visualize each ion and with this the distance - informations using XDMF and e.g. Paraview. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_intersector.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_intersector.nxdl.xml deleted file mode 100644 index 1c60505..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_intersector.nxdl.xml +++ /dev/null @@ -1,395 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of links pointing from current to next. - - - - - The total number of links pointing from next to current. - - - - - The total number of members in the current_set. - - - - - The total number of members in the next_set. - - - - - The total number of cluster found for coprecipitation analysis. - - - - - The number of rows in the table/matrix for coprecipitation stats. - - - - - Results of a paraprobe-intersector tool run. - - - - - - Version specifier of this application definition. - - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. the paraprobe-tool executable started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and the paraprobe-tool executable exited as a process. - - - - - The absolute path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - - - - The individual coordinate systems which should be used. - Field names should be prefixed with the following controlled terms - indicating which individual coordinate system is described: - - * paraprobe - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - The results of an overlap/intersection analysis. - - - - A matrix of feature_identifier which specifies which named features - from the current set have directed link(s) pointing to which named - feature(s) from the next set. - - - - - - - - - For each link/pair in current_to_next a characterization - whether the link is due to a volumetric overlap (0x00 == 0), - proximity (0x01 == 1), or something else unknown (0xFF == 255). - - - - - - - - A matrix of feature_identifier which specifies which named feature(s) - from the next set have directed link(s) pointing to which named - feature(s) from the current set. Only if the mapping whereby the - links is symmetric next_to_current maps the links in current_to_next - in the opposite direction. - - - - - - - - - For each link/pair in next_to_current a characterization - whether the link is due to a volumetric overlap (0x00 == 0), - proximity (0x01 == 1), or something else unknown (0xFF == 255). - - - - - - - - For each pair of links in current_to_next the volume of the - intersection, i.e. how much volume do the two features share. - If features do not intersect the volume is zero. - - - - - - - - During coprecipitation analysis the current and next set are analyzed - for links in a special way. Three set comparisons are made. Members - of the set in each comparison are analyzed for overlap and proximity: - - The first comparison is the current_set against the current_set. - The second comparison is the next_set against the next_set. - The third comparison is the current_set against the next_set. - - Once the (forward) links for these comparisons are ready the - pair relations are analyzed with respect to which feature identifier - cluster in identifier space. Thereby a logical connection (link) is - established between the features in the current_set and next_set. - Recall that these two set typically represent different features - within an observed system for otherwise the same parameterization. - Examples include two sets of e.g. precipitates with differing - chemical composition that were characterized in the same material - volume representing a snapshot of an e.g. microstructure at the same - point in time. Researchers may have performed two analyses, one to - characterize precipitates A and another one to characterize percipitates - B. Coprecipitation analysis now logically connects these independent - characterization results to establish spatial correlations of e.g. - precipitates spatial arrangement. - - - - Matrix of feature_identifier and cluster_identifier pairs which - encodes the cluster to which each feature_identifier was assigned. - Here for features of the current_set. - - - - - - - - - Matrix of feature_identifier and cluster_identifier pairs which - encodes the cluster to which each feature_identifier was assigned. - Here for features of the next_set. - - - - - - - - - The identifier (names) of the cluster. - - - - - - - - Pivot table as a matrix. The first column encodes how many - members from the current_set are in each cluster, one row per cluster. - The second column encodes how many members from the next_set are - in each cluster, in the same row per cluster respectively. - The last column encodes the total number of members in the cluster. - - - - - - - - - Pivot table as a matrix. The first column encodes the different - types of clusters based on their number of members in the sub-graph. - The second column encodes how many clusters with as many members - exist. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_nanochem.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_nanochem.nxdl.xml deleted file mode 100644 index aae1654..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_nanochem.nxdl.xml +++ /dev/null @@ -1,1965 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of ions in the reconstruction. - - - - - The total number of atoms in the atomic_decomposition match filter. - - - - - The total number of isotopes in the isotopic_decomposition match filter. - - - - - The dimensionality of the delocalization grid. - - - - - The cardinality/total number of cells/grid points in the delocalization grid. - - - - - - The total number of XDMF values to represent all faces of triangles via XDMF. - - - - - The total number of entries in a feature dictionary. - - - - - The total number of member distinguished when reporting composition. - - - - - Results of a paraprobe-nanochem tool run. - - - - - - Version specifier of this application definition. - - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. the paraprobe-tool executable started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and the paraprobe-tool executable exited as a process. - - - - - The absolute path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - A statement whether the paraprobe-tool executable managed to - process the analysis or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must no longer compute analyses. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases, it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - If nothing else is specified we assume that there - has to be at least one set of NXtransformations named - paraprobe defined, which specifies the coordinate system. - In which all positions are defined. - - - - - The individual coordinate systems which should be used. - Field names should be prefixed with the following controlled terms - indicating which individual coordinate system is described: - - * paraprobe - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - A bitmask which identifies which of the ions in the dataset were - analyzed during this process. - - - - Number of ions covered by the mask. - The mask value for most may be 0. - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used, padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe-toolbox executable. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth (padding). - - - - - - - - - - - The weighting model specifies how mark data are mapped to a weight - per point/ion. For atom probe microscopy (APM) mark data are e.g. - which iontype an ion has. As an example, different models are used - which account differently for the multiplicity of a point/ion - during delocalization: - - * unity, all points/ions get the same weight 1. - * atomic_decomposition, points get as much weight as they - have atoms of a type in atomic_decomposition_rule, - * isotope_decomposition, points get as much weight as they have - isotopes of a type in isotopic_decomposition_rule. - - - - - - - - - - - A list of elements (via proton number) to consider for the - atomic_decomposition weighting model. - Elements must exist in the periodic table of elements and be - specified by their number of protons. - Values in match are isotope hash values using the following - hashing rule $H = Z + 256*N$ with $Z$ the number of protons - and $N$ the number of neutrons of the isotope. - In the case of elements this hashing rule has the advantage - that for elements the proton number is their hash value because - N is zero. - - - - Meaning of the filter: - Whitelist specifies which entries with said value to include. - Entries with all other values will be filtered out. - - Blacklist specifies which entries with said value to exclude. - Entries with all other values will be included. - - - - - - - - - Array of values to filter according to method. For example, - if the filter specifies [1, 5, 6] and method is whitelist, - only entries with values matching 1, 5 or 6 will be processed. - All other entries will be filtered out/not considered. - - - - - - - - - A list of isotopes (via proton and neutron number) to consider - for the isotopic_decomposition weighting model. - Isotopes must exist in the nuclid table. - Values in match are isotope hash values using the following - hashing rule $H = Z + 256*N$ with $Z$ the number of protons - and $N$ the number of neutrons of the isotope. - - - - Meaning of the filter: - Whitelist specifies which entries with said value to include. - Entries with all other values will be filtered out. - - Blacklist specifies which entries with said value to exclude. - Entries with all other values will be included. - - - - - - - - - Array of values to filter according to method. For example, - if the filter specifies [1, 5, 6] and method is whitelist, - only entries with values matching 1, 5 or 6 will be processed. - All other entries will be filtered out/not considered. - - - - - - - - - How results of the kernel-density estimation were computed - into quantities. By default the tool computes the total number - (intensity) of ions or elements. Alternatively the tool can compute - the total intensity, the composition, or the concentration of the - ions/elements specified by the white list of elements in each voxel. - - - - - - - - - - - Weighting factor, in atom probe, often termed multiplicity. - The weighting factor is the multiplier with which the integrated - intensity contribution from the point/ion gets multiplied. - The delocalization computes the integrated intensity for each - grid cell. Effectively, this is an explicitly evaluated kernel - method where each specific position of an ion is replaced by a - smoothing kernel. For atom probe weights are positive and integer - specifically the multiplicity of the ion, in accordance with the - respective rulesets as defined by weighting_model. - - - - - - - - The discretized domain/grid on which the delocalization is applied. - - - - - - - - - - - The total number of cells/voxels of the grid. - - - - - - - - - - The symmetry of the lattice defining the shape of the unit cell. - - - - - - - - The unit cell dimensions according to the coordinate system - defined under coordinate_system. - - - - - - - - Number of unit cells along each of the d unit vectors. - The total number of cells, or grid points has to be the cardinality. - If the grid has an irregular number of grid positions in each direction, - as it could be for instance the case of a grid where all grid points - outside some masking primitive are removed, this extent field should - not be used. Instead use the coordinate field. - - - - - - - - - Reference to or definition of a coordinate system with - which the positions and directions are interpretable. - If the coordinate system is not specified the paraprobe - coordinate system is used. - - - - - - Integer which specifies the first index to be used for - distinguishing identifiers for cells. Identifiers are defined - either implicitly or explicitly. For implicit indexing the - identifiers are defined on the interval - [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - - - - A tight axis-aligned bounding box about the grid. - - - - For atom probe should be set to true. - - - - - Integer which specifies the first index to be used for distinguishing - hexahedra. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for vertices. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for faces. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - - - - Positions of the vertices. - - Users are encouraged to reduce the vertices to unique set of positions - and vertices as this supports a more efficient storage of the geometry data. - It is also possible though to store the vertex positions naively in which - case vertices_are_unique is likely False. - Naively here means that one for example stores each vertex of a triangle - mesh even though many vertices are shared between triangles and thus - the positions of these vertices do not have to be duplicated. - - - - - - - - - Array of identifiers from vertices which describe each face. - - The first entry is the identifier of the start vertex of the first face, - followed by the second vertex of the first face, until the last vertex - of the first face. Thereafter, the start vertex of the second face, the - second vertex of the second face, and so on and so forth. - - Therefore, summating over the number_of_vertices, allows to extract - the vertex identifiers for the i-th face on the following index interval - of the faces array: [$\sum_i = 0}^{i = n-1}$, $\sum_{i=0}^{i = n}$]. - - - - - - - - - Six equally formatted sextets chained together. For each - sextett the first entry is an XDMF primitive topology - key (here 5 for polygon), the second entry the XDMF primitive - count value (here 4 because each face is a quad). - The remaining four values are the vertex indices. - - - - - - - - How many distinct boundaries are distinguished? - Most grids discretize a cubic or cuboidal region. In this case - six sides can be distinguished, each making an own boundary. - - - - - - Name of the boundaries. E.g. left, right, front, back, bottom, top, - The field must have as many entries as there are number_of_boundaries. - - - - - - - - The boundary conditions for each boundary: - - 0 - undefined - 1 - open - 2 - periodic - 3 - mirror - 4 - von Neumann - 5 - Dirichlet - - - - - - - - - - The result of the delocalization based on which subsequent - iso-surfaces will be computed. In commercial software so far - there is not a possibility to export such grid. - - - - - - - - - - - - - - - - - - Cell center of mass positions along x. - - - - - - - - - Cell center of mass positions along y. - - - - - - - - Cell center of mass positions along z. - - - - - - - - Intensity of the field at given point - - - - - - - - Center of mass positions of each voxel for - rendering the scalar field via XDMF in e.g. - Paraview. - - - - - - - - - XDMF topology for rendering in combination with - xdmf_xyz the scalar field via XDFM in e.g. Paraview. - - - - - - - - - The three-dimensional gradient nabla operator applied to - scalar_field_magnitude. - - - - - - - - - - - - - - - - - - - - Cell center of mass positions along x. - - - - - - - - - Cell center of mass positions along y. - - - - - - - - Cell center of mass positions along z. - - - - - - - - The gradient vector. - - - - - - - - - Center of mass positions of each voxel for - rendering the scalar field via XDMF in e.g. - Paraview. - - - - - - - - - XDMF topology for rendering in combination with - xdmf_xyz the scalar field via XDFM in e.g. Paraview. - - - - - - - - - Halfwidth of the kernel about the central voxel. - The shape of the kernel is that of a cuboid - of extent 2*kernel_extent[i] + 1 in each dimension i. - - - - - - - - - - Sigma of the kernel in each dimension in the paraprobe - coordinate_system with i = 0 is x, i = 1 is y, i = 2 is z. - - - - - - - - Expectation value of the kernel in each dimension in the paraprobe - coordinate_system with i = 0 is x, i = 1 is y, i = 2 is z. - - - - - - - - - - An iso-surface is the boundary between two regions across which - the magnitude of a scalar field falls below/exceeds a threshold - magnitude phi. - For applications in atom probe microscopy the location and shape - of such a boundary (set) is typically approximated by - discretization. - This yields a complex of not necessarily connected geometric - primitives. Paraprobe-nanochem approximates this complex with - a soup of triangles. - - - - - The threshold or iso-contour value. - - - - - Details about the specific marching cubes algorithm - which was taken to compute the iso-surface. - The grid is the delocalization grid. - - - - Reference to the specific implementation of marching cubes used. - The value placed here should be a DOI. If there are no specific - DOI or details write not_further_specified, or give at least a - free-text description. The program and version used is the - specific paraprobe-nanochem. - - - - - - The resulting triangle soup computed via marching cubes. - - - - - - Integer which specifies the first index to be used for - distinguishing triangles. Identifiers are defined either - implicitly or explicitly. For implicit indexing the - identifiers are defined on the interval - [identifier_offset, identifier_offset+c-1]. - - - - - - Number of vertices. - - - - - Number of faces. - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for vertices. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for faces. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - - - - - Positions of the vertices. - - Users are encouraged to reduce the vertices to unique set of positions - and vertices as this supports a more efficient storage of the geometry data. - It is also possible though to store the vertex positions naively in which - case vertices_are_unique is likely False. - Naively here means that one for example stores each vertex of a triangle - mesh even though many vertices are shared between triangles and thus - the positions of these vertices do not have to be duplicated. - - - - - - - - - Array of identifiers from vertices which describe each face. - - The first entry is the identifier of the start vertex of the first face, - followed by the second vertex of the first face, until the last vertex - of the first face. Thereafter, the start vertex of the second face, the - second vertex of the second face, and so on and so forth. - - Therefore, summating over the number_of_vertices, allows to extract - the vertex identifiers for the i-th face on the following index interval - of the faces array: [$\sum_i = 0}^{i = n-1}$, $\sum_{i=0}^{i = n}$]. - - - - - - - - A list of as many tuples of XDMF topology key, XDMF number - of vertices and a triple of vertex indices specifying each - triangle. The total number of entries is n_f_tri * (1+1+3). - - - - - - - - - Direction of each normal. - - - - - - - - - Qualifier how which specifically oriented normal to its - primitive each normal represents. - - * 0 - undefined - * 1 - outer - * 2 - inner - - - - - - - - - - - Direction of each normal. - - - - - - - - - Qualifier how which specifically oriented normal to its - primitive each normal represents. - - * 0 - undefined - * 1 - outer - * 2 - inner - - - - - - - - Triangle normals are oriented in the direction of the - gradient vector of the local delocalized scalar field. - :math:`\sum_{x, y, z} {\nabla{c}_i}^2`. - - - - - - - - - Triangle normals are oriented in the direction of the - gradient vector of the local delocalized scalar field. - The projection variable here describes the cosine of the - angle between the gradient direction and the normal - direction vector. - This is a descriptor of how parallel the projection is - that is especially useful to document those triangles - for whose projection is almost perpendicular. - - - - - - - - - - - - - - Array of edge length values. For each triangle the edge length - is reported for the edges traversed according to the sequence - in which vertices are indexed in triangles. - - - - - - - - - Array of interior angle values. For each triangle the angle - is reported for the angle opposite to the edges which are - traversed according to the sequence in which vertices - are indexed in triangles. - - - - - - - - - The center of mass of each triangle. - - - - - - - - - - Iso-surfaces of arbitrary scalar three-dimensional fields - can show a complicated topology. Paraprobe-nanochem can run - a DBScan-like clustering algorithm which performs a - connectivity analysis on the triangle soup. This yields a - set of connected features with their surfaces discretized - by triangles. Currently, the tool distinguishes at most - three types of features: - - 1. So-called objects, i.e. necessarily watertight features - represented polyhedra. - 2. So-called proxies, i.e. features that were replaced by a - proxy mesh and made watertight. - 3. Remaining triangle surface meshes of arbitrary shape and - cardinality. - - These features can be interpreted as microstructural features. - Some of them may be precipitates, some of them may be poles, - some of them may be segments of dislocation lines or other - crystal defects which are decorated (or not) with solutes. - - - - - The identifier which the triangle_soup connectivity analysis - returned, which constitutes the first step of the - volumetric_feature identification process. - - - - - - - - The array of keywords of feature_type dictionary. - - - - - - - - The array of values for each keyword of the - feature_type dictionary. - - - - - - - - The array of controlled keywords, need to be from - feature_type_dict_keyword, which specify which type - each feature triangle cluster belongs to. - Keep in mind that not each feature is an object or proxy. - - - - - - - - The explicit identifier of features. - - - - - - - - - Details for features which are (closed) objects. - Identifier have to exist in feature_identifier. - - - - - - - - - - - - - - - An oriented bounding box (OBB) to each object. - - - - Edge length of the oriented bounding box from largest - to smallest value. - - - - - - - - - - Oriented bounding box aspect ratio. YX versus ZY. - - - - - - - - - Position of the geometric center, which often is but - not necessarily has to be the center_of_mass of the - hexahedrally-shaped sample/sample part. - - - - - - - - - - A simple approach to describe the entire set of hexahedra - when the main intention is to store the shape of the - hexahedra for visualization. - - - - - - - - - - - - - - - - - - - - - - - - Details for all those objects close to edge, i.e. those which - have at least one ion which lays closer to a modelled edge - of the dataset than threshold. - - - - - - - - - - - - - - - Total (count) relevant for normalization. - - - - - - - - - - - - Count or weight which, when divided by total, - yields the composition of this element, isotope, - molecule or ion. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Array of evaporation_identifier / ion_identifier which - specify ions laying inside or on the surface of the feature. - - - - - - - - - - - Details for all those objects far from edge, i.e. those - whose ions lay all at least threshold distant from a - modelled edge of the dataset. - - - - - - - - - - - - - - - Total (count) relevant for normalization. - - - - - - - - - - - - Count or weight which, when divided by total - yields the composition of this element, isotope, - molecule or ion. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Array of evaporation_identifier / ion_identifier which - specify ions laying inside or on the surface of the feature. - - - - - - - - - - - - - Details for features which are so-called proxies, i.e. objects - which have been reconstructed and combinatorially closed with - processing their partial triangulated_surface_mesh - (hole filling, refinement). - Identifier have to exist in feature_identifier. - - - - - - - - - - - - - - - - Details for those proxies close to edge, i.e. those which - have at least one ion which lays closer to a modelled edge - of the dataset than threshold. - Identifier have to exist in feature_identifier. - - - - - - - - - - - - - - - - Total (count) relevant for normalization. - - - - - - - - - - Count or weight which, when divided by total - yields the composition of this element, isotope, - molecule or ion. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Array of evaporation_identifier / ion_identifier which - specify ions laying inside or on the surface of the feature. - - - - - - - - - - - Details for those proxies far from edge, i.e. those whose - ions lay all at least threshold distant from a - modelled edge of the dataset. - - - - - - - - - - - - - - - Total (count) relevant for normalization. - - - - - - - - - - Count or weight which, when divided by total - yields the composition of this element, isotope, - molecule or ion. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Array of evaporation_identifier / ion_identifier which - specify ions laying inside or on the surface of the feature. - - - - - - - - - - - - - - - - - - The multiplicity whereby the ion position is accounted for - irrespective whether the ion is considered as a decorator - of the interface or not. - As an example, with atom probe it is typically not possible - to resolve the positions of the atoms which arrive at the detector - as molecular ions. Therefore, an exemplar molecular ion of two carbon - atoms can be considered to have a multiplicity of two to account that - this molecular ion contributes two carbon atoms at the reconstructed - location considering that the spatial resolution of atom probe - experiments is limited. - - - - - - - - The multiplicity whereby the ion position is accounted for when - the ion is considered one which is a decorator of the interface. - - - - - - - - The equation of the plane that is fitted initially. - - - - The four parameter :math:`ax + by + cz + d = 0` which define the plane. - - - - - - - - - The triangle surface mesh representing the interface model. - Exported at some iteration before the next DCOM step. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Direction of each normal - - - - - - - - - Qualifier how which specifically oriented normal to its primitive each - normal represents. - - * 0 - undefined - * 1 - outer - * 2 - inner - - - - - - - - - - - - Direction of each normal - - - - - - - - - Qualifier how which specifically oriented normal to its primitive each - normal represents. - - * 0 - undefined - * 1 - outer - * 2 - inner - - - - - - - - - - - - - - Array of edge length values. For each triangle the edge length is - reported for the edges traversed according to the sequence - in which vertices are indexed in triangles. - - - - - - - - - Array of interior angle values. For each triangle the angle is - reported for the angle opposite to the edges which are traversed - according to the sequence in which vertices are indexed in triangles. - - - - - - - - - - The triangle surface mesh representing the interface model. - Exported at some iteration after the next DCOM step. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Direction of each normal - - - - - - - - - Qualifier how which specifically oriented normal to its primitive each - normal represents. - - * 0 - undefined - * 1 - outer - * 2 - inner - - - - - - - - - - - - Direction of each normal - - - - - - - - - Qualifier how which specifically oriented normal to its primitive each - normal represents. - - * 0 - undefined - * 1 - outer - * 2 - inner - - - - - - - - - - - - - - Array of edge length values. For each triangle the edge length is - reported for the edges traversed according to the sequence - in which vertices are indexed in triangles. - - - - - - - - - Array of interior angle values. For each triangle the angle is - reported for the angle opposite to the edges which are traversed - according to the sequence in which vertices are indexed in triangles. - - - - - - - - - - - - The ROIs are defined as cylinders for the computations. - To visualize these though we discretize them into regular n-gons. - Using for instance a 360-gon, i.e. a regular n-gon with 360 - edges resolves the lateral surface of each cylinder very finely - so that they are rendered smoothly in visualization software. - - - - - - Position of the geometric center, which often is but not - necessarily has to be the center_of_mass of the polyhedra. - - - - - - - - - Integer which specifies the first index to be used for distinguishing - ROI cylinder. Identifiers are defined explicitly. - - - - - - - - - - - - - - - The number of atoms in each ROI. - - - - - - - - The number of ions in each ROI. - - - - - - - - The orientation of the ROI defined via a vector which points along - the cylinder axis and whose length is the height of the cylinder. - - - - - - - - - - In the direction of the ROI. - - - - - Hashvalue - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_ranger.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_ranger.nxdl.xml deleted file mode 100644 index 52e41fc..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_ranger.nxdl.xml +++ /dev/null @@ -1,425 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of ions in the reconstruction. - - - - - Maximum number of allowed atoms per (molecular) ion (fragment). - Needs to match maximum_number_of_atoms_per_molecular_ion. - - - - - Results of a paraprobe-ranger tool run. - - - - - - Version specifier of this application definition. - - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. the paraprobe-tool executable started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and the paraprobe-tool executable exited as a process. - - - - - The path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - A statement whether the paraprobe-tool executable managed to - process the analysis or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must not compute any analysis. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - - - - The individual coordinate systems which should be used. - Field names should be prefixed with the following controlled terms - indicating which individual coordinate system is described: - - * paraprobe - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - Paraprobe-ranger loads the iontypes and evaluates for each - ion on which iontype it matches. If it matches on none, the - ion is considered of the default unknown type with a 0 as its - respective value in the iontypes array. - - - - - The length of the isotope_vector used to describe molecular ions. - - - - - - - - - - - The iontype ID for each ion that was best matching, stored in the - order of the evaporation sequence ID. The here computed iontypes - do not take into account the charge state of the ion which is - equivalent to interpreting a RNG and RRNG range files for each - ion in such a way that only the elements of which a (molecular) ion - is build are considered. By contrast, charged_iontypes takes - into account also the charge state. - - - - - - - - A bitmask which identifies exactly all those ions ranged irrespective - the type they ended up with. - - - - Number of ions covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - - Paraprobe-ranger performs a combinatorial search over - all possible or a reduced set of nuclids to identify - into which ions these can be composed. - - - - The main result is the list of molecular ions, here formatted - according to the definitions of a set of isotope_vectors - as detailed in :ref:`NXion`. - - - - - - - - - The mass-to-charge-state ratio of each molecular ion - without considering relativistic or quantum effects. - - - - - - - - The mass of each molecular ion without - considering relativistic or quantum effects. - - - - - - - - - The charge_state of each molecular ion. - - - - - - - - The product of the natural abundance of the isotopes building - each molecular ion. Further details are available in - :ref:`NXapm_paraprobe_config_ranger`. - - - - - - - - The product of the natural abundance of the isotopes building - each molecular ion. Further details are available in - :ref:`NXapm_paraprobe_config_ranger`. - - - - - - - - The number of disjoint nuclids for each molecular ion. - - - - - - - - The number of nuclids for each molecular ion. - - - - - - - - - Paraprobe-ranger loads iontypes and evaluates for each ion on which - iontype it matches. If it matches on none, the ion is considered of - the default unknown type with a 0 as its respective value in the - iontypes array. In contrast to use_existent_ranging this process - does neither needs measured ion position nor mass-to-charge-state - ratio values. - - - - - The length of the isotope_vector used to describe molecular ions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_selector.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_selector.nxdl.xml deleted file mode 100644 index 38fac70..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_selector.nxdl.xml +++ /dev/null @@ -1,274 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of ions in the reconstruction. - - - - - Results of a paraprobe-selector tool run. - - - - - - Version specifier of this application definition. - - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. the paraprobe-tool executable started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and the paraprobe-tool executable exited as a process. - - - - - The absolute path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - A statement whether the paraprobe-tool executable managed to - process the analysis or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must not compute any analysis. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - - - - The individual coordinate systems which should be used. - Field names should be prefixed with the following controlled terms - indicating which individual coordinate system is described: - - * paraprobe - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - A bitmask which identifies which of the ions in the dataset - were selected to become included in the region-of-interest (ROI). - - - - Number of ions covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_spatstat.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_spatstat.nxdl.xml deleted file mode 100644 index d87d2f5..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_spatstat.nxdl.xml +++ /dev/null @@ -1,364 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of ions in the reconstruction. - - - - - Results of a paraprobe-spatstat tool run. - - - - - - Version specifier of this application definition. - - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. the paraprobe-tool executable started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and the paraprobe-tool executable exited as a process. - - - - - The absolute path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - A statement whether the paraprobe-tool executable managed to - process the analysis or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must not compute any analysis. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - - - - The individual coordinate systems which should be used. - Field names should be prefixed with the following controlled terms - indicating which individual coordinate system is described: - - * paraprobe - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - A bitmask which identifies which of the ions in the dataset were - analyzed. - - - - Number of ions covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - The iontype ID for each ion that was assigned to each ion during - the randomization of the ionlabels. Iontype labels are just permuted - but the total number of values for each iontype stay the same. - - The order matches the iontypes array from a given ranging results - as is specified in the configuration settings inside the specific - config_filename that was used for this spatstat analysis. - - - - - - - - K-nearest neighbor statistics. - - - - Right boundary of the binning. - - - - - - - - - - - - - Cumulated - - - - - - - - Cumulated and normalized by total counts - - - - - - - - - Radial distribution statistics. - - - - Right boundary of the binning. - - - - - - - - - - - - - Cumulated - - - - - - - - Cumulated and normalized by total counts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_surfacer.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_surfacer.nxdl.xml deleted file mode 100644 index dbb0bb4..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_surfacer.nxdl.xml +++ /dev/null @@ -1,503 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of ions in the reconstruction. - - - - - The number of vertices of the alpha complex. - - - - - The number of faces of the alpha complex. - - - - - The total number of XDMF values to represent all faces of triangles via XDMF. - - - - - The total number of XDMF values to represent all faces of tetrahedra via XDMF. - - - - - Results of a paraprobe-surfacer tool run. - - - - - - Version specifier of this application definition. - - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. the paraprobe-tool executable started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and the paraprobe-tool executable exited as a process. - - - - - The absolute path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - A statement whether the paraprobe-tool executable managed to - process the analysis or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must not compute any analysis. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - - - - The individual coordinate systems which should be used. - Field names should be prefixed with the following controlled terms - indicating which individual coordinate system is described: - - * paraprobe - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - A bitmask which identifies which of the ions in the dataset were - analyzed. Computations of alpha complexes may have filtered this - ion set further but this process is deterministic. - - - - Number of ions covered by the mask. The mask may be 0 for most. - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - Paraprobe-surfacer can be used to load a ROI that is the entire or a - sub-set of the ion point cloud. In the point_cloud_wrapping process - the tool computes a triangulated surface mesh which encloses the - ROI/point cloud. This mesh can be seen as a model for the edge of - the dataset. - Different algorithms can be used with paraprobe-surfacer to create - this mesh such as convex hulls, alpha-shapes as their generalization, - or alpha wrappings. - Ideally, the resulting mesh should be a watertight polyhedron. - This polyhedron is not necessarily convex. For some algorithms there - is no guarantee that the resulting mesh yields a watertight mesh. - - - - - - A bitmask which identifies exactly all those ions whose positions - were considered when defining the filtered point set from which - the alpha complex was then in fact computed. This window - can be different to the entire window as irrelevant ions might - have been filtered out to reduce the computational costs of the - alpha complex analysis. - - - - - Number of ions covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The set of triangles in the coordinate system paraprobe - which discretizes the exterior surface of the alpha complex. - - - - Integer which specifies the first index to be used for distinguishing - triangles. Identifiers are defined either implicitly or explicitly. - For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - - - - - - - Number of vertices. - - - - - Number of faces. - - - - - - - - - - - - - - - - - - - A list of as many tuples of XDMF topology key, XDMF number - of vertices and a triple of vertex indices specifying each - triangle. The total number of entries is n_f_tri * (1+1+3). - - - - - - - - - Do the triangles define a triangulated surface mesh which - is watertight? - - - - - The volume which the triangulated surface mesh encloses - provided that the mesh is watertight. - - - - - - The set of tetrahedra which represent the interior volume of the - complex if that is a closed 2-manifold. - - - - Integer which specifies the first index to be used for distin- - guishing tetrahedra. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined - on the interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - - - - The accumulated volume of all interior tetrahedra. - - - - - - Number of vertices. - - - - - Number of faces. - - - - - - - - - - - - - A list of as many tuples of XDMF topology key, XDMF number - of vertices and a triple of vertex indices specifying each - triangle. The total number of entries is n_f_tet * (1+1+4). - - - - - - - - - - - - In the future we may want to wrap other primitives - like triangles or polylines. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_tessellator.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_tessellator.nxdl.xml deleted file mode 100644 index 4d8eb24..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_tessellator.nxdl.xml +++ /dev/null @@ -1,677 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of ions in the reconstruction. - - - - - The total number of facets/polygons defining the tessellation. - - - - - Results of a paraprobe-tessellator tool run. - - - - - - Version specifier of this application definition. - - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. the paraprobe-tool executable started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and the paraprobe-tool executable exited as a process. - - - - - The absolute path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - A statement whether the paraprobe-tool executable managed to - process the analysis or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must not compute any analysis. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - - - - The individual coordinate systems which should be used. - Field names should be prefixed with the following controlled terms - indicating which individual coordinate system is described: - - * paraprobe - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - The tool can be used to compute a Voronoi tessellation the entire - or a sub-set of the reconstruction. The point cloud in the ROI is - wrapped into a tight axis-aligned bounding box. The tool detects if - Voronoi cells make contact with the walls of this bounding box. - The tessellation is computed without periodic boundary conditions. - - - - A bitmask which identifies which of the ions in the dataset were - analyzed. - - - - Number of ions covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - A bitmask which identifies which of points have Voronoi cells that - are truncated by the global axis-aligned bounding box, i.e. boundaries - of the threads are ignored. - - - - Number of points covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - - A bitmask which identifies which of points have Voronoi cells that - are truncated by a specific wall of the axis-aligned bounding box. - The left wall has the negative x axis of the paraprobe coordinate - system as the outer unit normal. - - - - Number of points covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - A bitmask which identifies which of points have Voronoi cells that - are truncated by a specific wall of the axis-aligned bounding box. - The right wall has the positive x axis of the paraprobe coordinate - system as the outer unit normal. - - - - Number of points covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - A bitmask which identifies which of points have Voronoi cells that - are truncated by a specific wall of the axis-aligned bounding box. - The front wall has the negative y axis of the paraprobe coordinate - system as the outer unit normal. - - - - Number of points covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - A bitmask which identifies which of points have Voronoi cells that - are truncated by a specific wall of the axis-aligned bounding box. - The rear wall has the positive y axis of the paraprobe coordinate - system as the outer unit normal. - - - - Number of points covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - A bitmask which identifies which of points have Voronoi cells that - are truncated by a specific wall of the axis-aligned bounding box. - The left wall has the negative z axis of the paraprobe coordinate - system as the outer unit normal. - - - - Number of points covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - A bitmask which identifies which of points have Voronoi cells that - are truncated by a specific wall of the axis-aligned bounding box. - The left wall has the positive z axis of the paraprobe coordinate - system as the outer unit normal. - - - - Number of points covered by the mask. - The mask value for most may be 0. - - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits are set to 0. The mask is for - convenience always as large as the entire dataset as it will - be stored compressed anyway. The convenience feature with this - is that then the mask can be decoded with numpy and mirrored - against the evaporation_id array and one immediately can filter - out all points that were used by the paraprobe. - The length of the array adds to the next unsigned integer - if the number of ions in the dataset is not an integer - multiple of the bitdepth. - - - - - - - - - - - - - - - - Interior volume - - - - - - - - By which MPI process was the Voronoi cell computed. - - - - - - - - By which OpenMP thread was the Voronoi cell computed. - - - - - - - - The number of faces for each polyhedron. Faces of adjoining polyhedra - are counted for each polyhedron. This field can be used to interpret - the array/field with the individual area values for each face. - - - - - - - - - Integer which specifies the first index to be used for distinguishing - polyhedra. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - - - - Integer used to distinguish polyhedra for explicit indexing. - - - - - - - - A simple approach to describe the entire set of polyhedra when - the main intention is to store the shape of the polyhedra for - visualization. - - - - - Number of vertices. - - - - - Number of faces. - - - - - - - - - - - - - A sequence of always first an XDMF topology type key, followed - by the XDMF number of vertices of the polygon, followed by - the vertex identifier which define the facet polygon. First - we store the polygon of the first facet of the first cell, then - the second facet of the first cell, until the last facet of the - first cell, followed by the first facet of the second cell, - and so on and so forth. - - - - - - - - A sequence of cell identifier so that each facet is associated - with its cell because of which it is then possible to segment - out cells three-dimensionally based on cell i.e. evaporation_id. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_transcoder.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_transcoder.nxdl.xml deleted file mode 100644 index f7e0f34..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_results_transcoder.nxdl.xml +++ /dev/null @@ -1,568 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The total number of ions in the reconstruction. - - - - - Maximum number of allowed atoms per (molecular) ion (fragment). - Needs to match maximum_number_of_atoms_per_molecular_ion. - - - - - Number of mass-to-charge-state-ratio intervals mapped on this ion type. - - - - - Total number of integers in the supplementary XDMF topology array. - - - - - Number of ions probed in the combinatorial analysis of the charge states - - - - - Results of a paraprobe-transcoder tool run. - - - - - - Version specifier of this application definition. - - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - Given name of the program/software/tool with which this NeXus - (configuration) file was generated. - - - - Ideally program version plus build number, or commit hash or description - of ever persistent resources where the source code of the program and - build instructions can be found so that the program can be configured - ideally in such a manner that the result of this computational process - is recreatable in the same deterministic manner. - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - was started, i.e. the paraprobe-tool executable started as a process. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when the analysis behind this results file - were completed and the paraprobe-tool executable exited as a process. - - - - - The absolute path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - A statement whether the paraprobe-tool executable managed to - process the analysis or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must not compute any analysis. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - If used, contact information and eventually details - of at least the person who performed this analysis. - - - - - - - - - - - - - - - Details about the coordinate system conventions used. - - - - The individual coordinate systems which should be used. - Field names should be prefixed with the following controlled terms - indicating which individual coordinate system is described: - - * paraprobe - * lab - * specimen - * laser - * leap - * detector - * recon - - - - - - - - An array of triplets of integers which can serve as a supplementary - array for Paraview to display the reconstruction. The XDMF datatype - is here 1, the number of primitives 1 per triplet, the last integer - in each triplet is the identifier of each point starting from zero. - - - - - - - - - - On a mid term perspective we would like to evolve the paraprobe-toolbox - to an implementation stage where it works exclusively with completely - provenance-tracked formats for both the configuration of the workflow step - and/or analysis with each tool and also for the output of these analyses - in the form of so-called tool-specific results files. - Currently the Hierarchical Data Format 5 (HDF5) is used to store such data. - - Different file formats can be used to inject reconstructed datasets and - ranging definitions into the toolbox. Traditionally, these are the POS, - ePOS, and APT files with the tomographic reconstruction and other metadata - and RNG and RRNG file formats for the ranging definitions how mass-to-charge - state-ratio values map on (molecular) ion types. Such input should be - injected via specific NeXus/HDF5 files which are documented - in compliance with the NXapm application definition. - - So far the paraprobe-toolbox was used as a standalone tool. Therefore, it - was not relevant during the development to focus on interoperability. - Essentially paraprobe-transcoder was used as a parser to transcode data - in the above-mentioned file formats into a paraprobe-specific - representation. This transcoding should become deprecated. - Here we describe steps we have taken into this direction. - - With the work in the FAIRmat project and the desire to make the paraprobe- - toolbox also accessible as a cloud-computing capable service in the Nomad - Remote Tools Hub (NORTH) the topic of interoperability became more important - and eventually the NXapm application definition was proposed. - NORTH is a GUI and related service in a NOMAD OASIS instance which allows - to spawn preconfigured docker containers via JupyterHub. - Currently, NORTH includes the so-called apm container. A container with - tools specific for analyzing data from atom probe microscopy as well as - processing of point cloud and mesh data. - - The NXapm application definition and related implementation work within - NOMAD OASIS enabled users to parse content of POS, ePOS, APT, RNG, and - RRNG files, surplus key metadata from vendor-agnostic electronic lab notebook - solutions directly into NOMAD OASIS via the uploads section. - The process is automated and yields an NXapm-compliant NeXus/HDF5 file - inside the uploads section in return. - - With these improvements made there is no longer a need for - at least the - users of a NOMAD OASIS and NORTH instance to use the deprecated - PARAPROBE.Transcoder.Results.*.h5 files. Ideally, paraprobe should - automatically detect that the input can now be an NXapm-compliant NeXus/HDF5 - file and in response work with this file directly. - To remain compliant with users however who do not have or do not wish - to use a NOMAD OASIS or NXapm or NeXus at all right now, the solution is - as follows: - - Calling the configuration stage of paraprobe-transcoder is always mandatory. - It is always the first step of working with the toolbox. In this process - the user defines the input files. These can either be nxs i.e. the NXapm/NeXus/ - HDF5 file from e.g. the upload section, or such a file that was obtained from - a colleague with a NOMAD OASIS instance. - In all other cases, users can pass the reconstruction and ranging definitions - using the traditional POS, ePOS, or APT and RNG or RRNG file formats respectively. - - Based on which input the user delivers, the parmsetup-transcoder tool then - creates a configuration file PARAPROBE.Transcoder.Config.SimID.*.nxs and - informs the user whether the input was NeXus (and thus if all relevant - input is already available) or whether the paraprobe-transcoder tool needs - to be executed to convert the content of the vendor files first into a - format which paraprobe can provenance track and understand. - In the latter case, the PARAPROBE.Transcoder.Config.SimID.*.nxs file is - used to communicate to all subsequently used tools from which files - the tools can expect to find the reconstruction and ranging definitions. - - All subsequent analysis steps start also with a tool-specific configuration. - This configuration step reads in (among others) the - PARAPROBE.Transcoder.Config.SimID.*.nxs file from which the configuration - tool identifies automatically whether to read the reconstruction and ranging data - from PARAPROBE.Transcoder.Results.SimID.*.h5 or directly the NXapm-compliant - NeXus/HDF5 file that was created upon preparing the upload or the file shared - from a colleague. This design removes the need for unnecessary copies of the data. - Currently still though users should execute the transcoder step as it will - generate a supplementary XDMF topology field with which the data in either - the NeXus/HDF5 or the transcoded vendor files can be displayed using e.g. - Paraview. For this purpose XDMF is used. - - Of course ideally the APT community would at some point converge to use - a common data exchange file format. To this end, AMETEK/Cameca's APT file format - could be a good starting point but so far it is lacking a consistent way of - how to store generalized ranging definitions and post-processing results. - POS, ePOS, Rouen's ATO, as well as other so far used representations of data - like CSV or text files have, to the best of our current knowledge, no - concept of how to marry reconstruction and (optional) ranging data into - one self-descriptive format. - - This summarizes the rationale behind the current choices of the I/O for - paraprobe. Furthermore, this summarizes also why the fundamental design - of splitting an analysis always into steps of configuration (with parmsetup), - task execution (with the respective C/C++ or Python tool of the toolbox), - and post-processing (e.g. with autoreporter) is useful because it offers - a clear description of provenance tracking. This is a necessary step to make - atom probe microscopy data at all better aligned with the aims of the - FAIR principles. - - The internal organization of the data entries in the atom_probe group - in this application definition for paraprobe-transcoder results files - mirror the definitions of the NXapm for consistency reasons. - - - - - - Mass-to-charge-state ratio values. - - - - - - - - - - - - Three-dimensional reconstructed positions of the ions. - Interleaved array of x, y, z positions in the specimen space. - - - - - - - - - - - Details about how peaks, with taking into account - error models, were interpreted as ion types or not. - - - - - - - - - Details and results of the combinatorial analyses of this - range definition to identify the charge_state for an ion. - - - - Currently charge_state not charge! - - - - - - - - Specific isotopes building each candidate matching the range. - - - - - - - - - Accumulated mass of the isotopes in each candidate. - Not corrected for quantum effects. - - - - - - - - - Product of natural abundance of the isotopes per candidate. - - - - - - - - Filter criterion on the product of the natural abundances - computed from each isotope building the (molecular) ion. - Such a filter can be used to reduce the number of possible - molecular ions considered when trying to find a unique solution - to the question which charge_state does a molecular ion - within a given range and given combination of elements have. - - - - - Filter criterion on the minimum half life which all isotopes - building the (molecular) ion need to have to consider the - candidate. - Such a filter can be used to reduce the number of possible - molecular ions considered when trying to find a unique solution - to the question which charge_state does a molecular ion - within a given range and given combination of elements have. - - - - - - If the value is zero/false it means that non-unique solutions - are accepted. These are solutions where multiple candidates - differ in their isotopes but have the same charge. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXadc.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml similarity index 57% rename from src/nexusformat/definitions/contributed_definitions/NXadc.nxdl.xml rename to src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml index b3edd70..d57fa80 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXadc.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml @@ -2,9 +2,9 @@ - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - + - Analog-to-digital converter component/integrated circuit. + Application definition for a configuration file of the paraprobe-selector tool. - - - TBD. - - + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_roi_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml similarity index 52% rename from src/nexusformat/definitions/contributed_definitions/NXcg_roi_set.nxdl.xml rename to src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml index ab2b677..760d26b 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_roi_set.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml @@ -2,9 +2,9 @@ - - + - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays. + + + The total number of ions in the reconstruction. + + - Base class to hold geometric primitives. + Application definition for a results file of the paraprobe-selector tool. - - - - - + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml new file mode 100644 index 0000000..34d3efc --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml @@ -0,0 +1,259 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Maximum number of atoms per molecular ion. Should be 32 for paraprobe. + + + + + Number of different source iontypes to distinguish. + + + + + Number of different target iontypes to distinguish. + + + + + Application definition for a configuration file of the paraprobe-spatstat tool. + + The tool paraprobe-spatstat evaluates spatial distribution functions. + + + + + + + + + + + + + + + + Threshold to define how far an ion has to lay at least from the edge + of the dataset so that the ion can act as a source. This means that + an ROI is placed at the location of the ion and its neighbors are + analyzed how they contribute to the computed statistics. + + The edge_distance threshold can be combined with the feature_distance threshold. This threshold defines defines up to which distance to a + microstructural feature an ROI is placed. + + The threshold is useful to process the dataset such that ROIs do + not protrude out of the dataset as this would add bias. + + + + + + Distance between each ion and triangulated mesh of microstructural features. + In addition to spatial filtering and considering how far ions lie to the + edge of the dataset, it is possible to restrict the analyses to a sub-set of + ions within a distance not farther away to a feature than the feature_distance + threshold value. + + + + + + + Absolute path in the (HDF5) file which points to the distance of each + ion to the closest feature. + + + + + Threshold to define how close an ion has to lay to a feature so that + the ion can at all qualify as a source, i.e. that an ROI is placed + at the location of the ion and its neighbors are then analyzed + how they contribute to the computed statistics. + + Recall that this feature_distance threshold is used in combination + with the edge_distance threshold when placing ROI about source ions. + + + + + + Specifies, if the iontypes are randomized for the point cloud or not. + Internally, paraprobe uses a sequentially executed deterministic MT19987 + (MersenneTwister) pseudo-random number generator to shuffle the + iontypes randomly across the entire set of ions. That is the total + number of ions of either type remain the same but the information about + their location is randomized. + + + + + + + + + + How should the iontype be interpreted on the source-side, i.e. + all these ion positions where a regions-of-interest (ROI) around + so-called source ions will be placed. Different options exist + how iontypes are interpreted given an iontype represents + in general a (molecular) ion with different isotopes that have + individually different multiplicity. + + The value resolve_all will set an ion active in the analysis regardless + of which iontype it is. Each active ion is accounted for once. + + The value resolve_unknown will set an ion active when the ion is + of the UNKNOWNTYPE type. Each active ion is accounted for once. + + The value resolve_ion will set an ion active if it is of the specific + iontype, irregardless of its elemental or isotopic details. + Each active ion is counted once. + + The value resolve_element will set an ion active, and most importantly, + account for each as many times as the (molecular) ion contains + atoms of elements in the whitelist ion_query_isotope_vector. + + The value resolve_isotope will set an ion active, and most importantly, + account for each as many times as the (molecular) ion contains + isotopes in the whitelist ion_query_isotope_vector. + + In effect, ion_query_isotope_vector acts as a whitelist to filter + which ions are considered as source ions of the correlation statistics + and how the multiplicity of each ion will be factorized, i.e. how + often it is accounted for. + + + + + + + + + + + + Matrix of isotope vectors, as many as rows as different candidates + for iontypes should be distinguished as possible source iontypes. + In the simplest case, the matrix contains only the proton number + of the element in the row, all other values set to zero. + Combined with ion_query_type_source set to resolve_element this will + recover usual spatial correlation statistics like the 1NN C-C + spatial statistics. + + + + + + + + + Similarly as ion_query_type_source how should iontypes be interpreted + on the target-side, i.e. how many counts will be bookkept for ions + which are neighbors of source ions within or on the surface of each + inspection/ROI about each source ion. + Source ion in the center of the ROI are not accounted for during + counting the summary statistics. + For details about the resolve values consider the explanations in + ion_query_type_source. These account for ion_query_type_target as well. + + + + + + + + + + + + + Matrix of isotope vectors, as many as rows as different candidates for + iontypes to distinguish as possible targets. See additional comments + under ion_query_isotope_vector_source. + + + + + + + + + Specifies which spatial statistics to compute. + + + + Compute k-th nearest neighbour statistics. + + + + Order k. + + + + + Minimum value of the histogram binning. + + + + + Increment of the histogram binning. + + + + + Maximum value of the histogram binning. + + + + + + Compute radial distribution function. + + + + Minimum value of the histogram binning. + + + + + Increment value of the histogram binning. + + + + + Maximum value of the histogram binning. + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml new file mode 100644 index 0000000..094a3f9 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml @@ -0,0 +1,141 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The total number of ions in the reconstruction. + + + + + The total number of bins in the histogram for the k-th nearest neighbor. + + + + + The total number of bins in the histogram for the radial distribution function. + + + + + Application definition for a results file of the paraprobe-spatstat tool. + + The tool paraprobe-spatstat evaluates spatial distribution functions. + + + + + + + + + + + The iontype ID for each ion that was assigned to each ion during + the randomization of the ionlabels. Iontype labels are just permuted + but the total number of values for each iontype remain the same. + + The order matches the iontypes array from a given ranging results + as it is specified in the configuration settings inside the specific + config_filename that was used for this paraprobe-spatstat analysis. + + + + + + + + K-nearest neighbor statistics. + + + + Right boundary of the binning. + + + + + + + + + + + + + Cumulated not normalized by total counts. + + + + + + + + Cumulated and normalized by total counts. + + + + + + + + + Radial distribution statistics. + + + + Right boundary of the binning. + + + + + + + + + + + + + Cumulated not normalized by total counts. + + + + + + + + Cumulated and normalized by total counts. + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml new file mode 100644 index 0000000..cf9b4f6 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml @@ -0,0 +1,151 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of alpha values (and offset values) to probe. + + + + + How many different match values does the filter specify. + + + + + Application definition for a configuration file of the paraprobe-surfacer tool. + + + + + + + + + + + + Specifies the method that is used to preprocess the point cloud + prior to the alpha-shape computation. + + The option *default* specifies that no such filtering is applied. + The option *percolation* specifies that a Hoshen-Kopelman + percolation analysis is used to identify points that lie closer + to the edge of the dataset. Details about the methods are reported + in `M. Kühbach et al. <https://doi.org/10.1038/s41524-020-00486-1>`_. + + + + + + + + + When using the *percolation* preprocessing, this is the width of the + kernel for identifying which ions are in voxels close to the + edge of the point cloud. + + + + + + Specifies which method to use to define the alpha value. + + The value *convex_hull_naive* is the default. The setting instructs + the tool to use a fast specialized algorithm for computing only + the convex hull. The resulting triangles can be skinny. + + The value *convex_hull_refine* instructs to tool to refine the + quality of the mesh resulting from *convex_hull_naive* + via triangle flipping and splitting. + + The value *smallest_solid* instructs the CGAL library to choose a + value which realizes an alpha-shape that is the smallest solid. + + The value *cgal_optimal* instructs the CGAL library to choose a + value which the library considers as to be an optimal value. + Details are defined in the respective section of the CGAL library + on 3D alpha shapes. + + The value *set_of_values* instructs the tool to compute a list + collection of alpha-shapes for the specified alpha-values. + + The value *set_of_alpha_wrappings* instructs the tool to generate + a set of so-called alpha wrappings. These are similar to alpha-shapes + but provide additional guarantees (such as watertightness and + proximity constraints) on the resulting wrapping. + + + + + + + + + + + + + Array of alpha values to use when alpha_value_choice is + set_of_values or when alpha_value_choice is set_of_alpha_wrappings. + + + + + + + + Array of offset values to use when alpha_value_choice is set_of_alpha_wrappings. + The array of alpha_values and offset_values define a sequence of (alpha and offset value). + + + + + + + + Specifies if the tool should compute the set of exterior triangle facets + for each alpha complex (for convex hull, alpha shapes, and wrappings). + + + + + Specifies if the tool should check if the alpha complex of + exterior triangular facets is a closed polyhedron. + + + + + Specifies if the tool should compute all interior tetrahedra + of the alpha complex (currently only for alpha shapes). + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml new file mode 100644 index 0000000..42c1143 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml @@ -0,0 +1,222 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The total number of ions in the reconstruction. + + + + + The number of vertices of the alpha complex. + + + + + The number of faces of the alpha complex. + + + + + The total number of XDMF values to represent all faces of triangles via XDMF. + + + + + The total number of XDMF values to represent all faces of tetrahedra via XDMF. + + + + + Application definition for a results file of the paraprobe-surfacer tool. + + + + + + + + + + Paraprobe-surfacer can be used to load a ROI that is the entire or a + sub-set of the ion point cloud. In the point_cloud_wrapping process + the tool computes a triangulated surface mesh which encloses the + ROI/point cloud. This mesh can be seen as a model for the edge of + the dataset. + + Different algorithms can be used with paraprobe-surfacer to create + this mesh such as convex hulls, alpha-shapes as their generalization, + or alpha wrappings. + + Ideally, the resulting mesh should be a watertight polyhedron. + This polyhedron is not necessarily convex. For some algorithms there + is no guarantee that the resulting mesh yields a watertight mesh. + + + + + + A bitmask which identifies exactly all those ions whose positions + were considered when defining the filtered point set from which + that alpha_complex instance was computed. + + This window can be different to the window of the *point_set_wrapping* + parent group because irrelevant ions might have been filtered out in addition + to the window defined in *point_set_wrapping* to reduce e.g. computational + costs of the alpha complex computation. + + + + + Number of ions covered by the mask. + + + + + Number of bits assumed matching on a default datatype. + + + + + The bitfield of the mask. See :ref:`NXcs_filter_boolean_mask` for + how this bitfield is to be interpreted. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The set of triangles in the coordinate system paraprobe + which discretizes the exterior surface of the alpha complex. + + + + + + + + + + + + + + + + + + + + + + + A list of as many tuples of XDMF topology key, XDMF number + of vertices and a triple of vertex indices specifying each + triangle. The total number of entries is n_f_tri * (1+1+3). + + + + + + + + Do the triangles define a triangulated surface mesh that is watertight? + + + + + The volume which the triangulated surface mesh + encloses if that mesh is watertight. + + + + + + + The set of tetrahedra which represent the interior volume + of the complex if that is a closed two-manifold. + + + + + The accumulated volume of all interior tetrahedra. + + + + + + + + + + + + + + + + A list of as many tuples of XDMF topology key, XDMF number + of vertices and a triple of vertex indices specifying each + triangle. The total number of entries is n_f_tet * (1+1+4). + + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml new file mode 100644 index 0000000..c6aa0c5 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml @@ -0,0 +1,93 @@ + + + + + + + Application definition for a configuration file of the paraprobe-tessellator tool. + + The tool paraprobe-tessellator computes a tessellation of the reconstructed positions. + + + + + + + + + + + + + + + + + The method used to compute the tessellation. + The value *default* configures the computation of the Voronoi tessellation. + + + + + + + + + Specifies if the tool should report the volume of each cell. + + + + + Specifies if the tool should report the first-order neighbors of each cell. + + + + + Specifies if the tool should report the facets and vertices of each cell. + + + + + Specifies if the tool should report for each cell if it makes contact with + the tight axis-aligned bounding box about the point cloud. + This can be used to identify if the shape of the cell is likely affected + by the edge of the dataset or if cells are deeply enough embedded + into the point cloud so that the shape of their cells are not affected + anymore by the boundary. This is valuable information to judge + about the significance of finite size effects. + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml new file mode 100644 index 0000000..04604c0 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml @@ -0,0 +1,277 @@ + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The total number of ions in the reconstruction. + + + + + The total number of values required to represent all faces of each cell. + + + + + The total number of values required to represent all faces of each cell + (polyhedron) using XDMF. + + + + + Application definition for a results file of the paraprobe-tessellator tool. + + The tool paraprobe-tessellator computes a tessellation of the reconstructed positions. + + + + + + + + + + The tool can be used to compute a Voronoi tessellation the entire + or of a sub-set of the reconstructed volume. Each point (ion) is wrapped + in one (Voronoi) cell. The point cloud in the ROI is wrapped into an + axis-aligned bounding box (AABB) that is tight. This means points at + the edge of the point cloud can lay on the surface of the bounding box. + The tool detects if cells make contact with the walls of this bounding box. + The tessellation is computed without periodic boundary conditions. + + + + The (tight) axis-aligned bounding box about the point cloud. + + + + Coordinate triplet of the corner that lays closest + to the origin of the *paraprobe* coordinate system. + + + + + + + + Coordinate triplet of the corner that lays farthest away + from the origin of the *paraprobe* coordinate system. + + + + + + + + + + + + + + + The number of points (and thus cells). + + + + + Volume of each Voronoi cell. + + + + + + + + Which MPI process computed which Voronoi cell. + + + + + + + + Which OpenMP thread computed which Voronoi cell. + + + + + + + + The number of faces for each cell. Faces of adjoining polyhedra are counted + for each polyhedron. This field can be used to interpret the concatenated vector + with the individual values for the area of each face. + + + + + + + + + A simple approach to describe the entire set of polyhedra when the main + intention is to store the shape of the polyhedra for visualization purposes. + + + + + + + + + + Sequence of tuples, concatenated in the order of the Voronoi cells. + Each tuple contains encodes information to visualize using XDMF: + Firstly, an XDMF geometric primitive type key. + Secondly, the number of vertices of the polygon. + Third, the sequence of indices_vertex which define the facet. + Tuples encode faces faster than cells. + + + + + + + + Sequence of cell identifier, concatenated such that each face is + associated with its cell. Given that paraprobe-tessellator assigns + each cell the evaporation_id of the ion that the cell wraps this + information enables the segmentation of the tessellation and + thus correlate per-ion properties with the volume that each cell + represents. + + + + + + + + + A bitmask that documents which of the cells are likely truncated because they + share at least one face with the *aabb* of the point cloud. This field encodes the + result of the boolean or operator applied to the value of all six wall_contact groups + that document contact in specific outer unit normal directions of the *aabb*. + + + + + + + + + + + + + In the spirit of wall_contact_global, the left face of *aabb*. + Its outer unit normal points in the opposite direction of the + x-axis of the *paraprobe* coordinate system. + + + + + + + + + + + + In the spirit of wall_contact_global, the right face of *aabb*. + Its outer unit normal points in the direction of the x-axis + of the *paraprobe* coordinate system. + + + + + + + + + + + + In the spirit of wall_contact_global, the front face of *aabb*. + Its outer unit normal points in the opposite direction of the + y-axis of the *paraprobe* coordinate system. + + + + + + + + + + + + In the spirit of wall_contact_global, the rear face of *aabb*. + Its outer unit normal points in the direction of the y-axis + of the *paraprobe* coordinate system. + + + + + + + + + + + + In the spirit of wall_contact_global, the front face of *aabb*. + Its outer unit normal points in the opposite direction of the + z-axis of the *paraprobe* coordinate system. + + + + + + + + + + + + In the spirit of wall_contact_global, the front face of *aabb*. + Its outer unit normal points in the direction of the z-axis of the + *paraprobe* coordinate system. + + + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_common.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_common.nxdl.xml new file mode 100644 index 0000000..eead897 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_common.nxdl.xml @@ -0,0 +1,102 @@ + + + + + + Base class documenting organizational metadata used by all tools of the + paraprobe-toolbox. + + + + A statement whether the tool executable managed to process the analysis + or whether this failed. Status is written to the results file after the + end_time beyond which point in time the tool must no longer compute + any further analysis results but exit. + + Only when this status message is present and its value is `success`, + one should consider the results of the tool. In all other cases it might + be that the tool has terminated prematurely or another error occurred. + + + + + + + + + Internal identifier used by the tool to refer to an analysis. + Simulation ID is an alias. + + + + + The configuration file that was used to parameterize + the algorithms that this tool has executed. + + + + + + + ISO 8601 formatted time code with local time zone offset to UTC + information included when the analysis in this results file was started, + i.e. when the respective executable/tool was started as a process. + + + + + ISO 8601 formatted time code with local time zone offset to UTC + information included when the analysis in this results file were + completed and the respective process of the tool exited. + + + + + Wall-clock time. + + + + + + + Details about coordinate systems (reference frames) used. In atom probe several coordinate + systems have to be distinguished. Names of instances of such :ref:`NXcoordinate_system` + should be documented explicitly and doing so by picking from the + following controlled set of names: + + * paraprobe_reference_frame + * lab_reference_frame + * specimen_reference_frame + * laser_reference_frame + * instrument_reference_frame + * detector_reference_frame + * reconstruction_reference_frame + + The aim of this convention is to support users with contextualizing which reference frame + each instance (coordinate system) is. If needed, instances of :ref:`NXtransformations` + are used to detail the explicit affine transformations whereby one can convert + representations between different reference frames. + Inspect :ref:`NXtransformations` for further details. + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml new file mode 100644 index 0000000..edd9849 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml @@ -0,0 +1,125 @@ + + + + + + Application definition for a (configuration) file of a tool from the paraprobe-toolbox. + + The paraprobe-toolbox is a collection of open-source tools for performing + efficient analyses of point cloud data where each point can represent atoms or + (molecular) ions. A key application of the toolbox has been for research in the + field of Atom Probe Tomography (APT) and related Field Ion Microscopy (FIM): + + * `paraprobe-toolbox <https://www.gitlab.com/paraprobe/paraprobe-toolbox>`_ + * `M. Kühbach et al. <https://paraprobe-toolbox.readthedocs.io/en/main/>`_ + + The toolbox does not replace but complements existent software tools in this + research field. Given its capabilities of handling points as objects with + properties and enabling analyses of the spatial arrangement of and inter- + sections between geometric primitives, the software can equally be used + for analyzing data in Materials Science and Materials Engineering. + + + + + + + + A specific configuration to achieve a processing result + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_parameters.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_parameters.nxdl.xml new file mode 100644 index 0000000..7305242 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_parameters.nxdl.xml @@ -0,0 +1,114 @@ + + + + + + Base class documenting parameters for processing used by all tools of the + paraprobe-toolbox. + + + + Internal identifier used by the tool to refer to an analysis. + Simulation ID an alias. + + + + + Possibility for leaving a free-text description about this analysis. + + Although offered here for convenience, we strongly encourage to + parameterize such descriptions as much as possible to support + reusage and clearer communication. + + + + + + Specification of the tomographic reconstruction to use for this analysis. + + Typically, reconstructions in the field of atom probe tomography are communicated + via files which store at least reconstructed ion positions and mass-to-charge-state-ratio + values. Container files like HDF5 though can store multiple reconstructions. + Therefore, the position and mass_to_charge concepts point to specific instances + to use for this analysis. + + + + Name of the node which resolves the reconstructed ion position + values to use for this analysis. + + + + + Name of the node which resolves the mass-to-charge-state-ratio + values to use for this analysis. + + + + + + Specification of the ranging definitions to use for this analysis. + + Ranging is the process of labeling time-of-flight data with so-called iontypes + (aka ion species). Ideally, iontypes specify the most likely (molecular) ion + that is assumed to have been evaporated given that its mass-to-charge-state ratio + lies within the specific mass-to-charge-state-ratio value interval of the iontype. + + The so-called unknown_type iontype represents the null model of an ion + that has not been ranged (for whatever reasons) or is not rangeable. + The identifier of this special iontype is always the reserved value 0. + + + + Name of the (parent) node directly below which (in the hierarchy) + the ranging definition for (molecular) ions are stored. + + + + + + Specification of the triangulated surface mesh to use for this analysis. + + Such a surface mesh can be used to define the edge of the reconstructed + volume to account for finite size effects. + + + + + Specification of the point-to-triangulated-surface-mesh distances to + use for this analysis. + + + + Absolute path in the (HDF5) file that points to the distance values. + The tool assumes that the values are stored in the same order as + points (ions). + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXchemical_composition.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_process.nxdl.xml similarity index 50% rename from src/nexusformat/definitions/contributed_definitions/NXchemical_composition.nxdl.xml rename to src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_process.nxdl.xml index 0625ccf..a42c6f3 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXchemical_composition.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_process.nxdl.xml @@ -2,9 +2,9 @@ - + - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays. - + - The number of samples or things. + The number of entries in the mask. - (Chemical) composition of a sample or a set of things. + Base class documenting a processing step within a tool of the paraprobe-toolbox. - - + - Total based on which composition information is normalized. + Possibility for leaving a free-text description about this analysis. - - - - - + + + A bitmask which identifies all ions considered in the analysis. + + - Count or weight which, when divided by total yields the composition - of this element, isotope, molecule or ion. + Number of ions covered by the mask. + By default, the total number of ions in the dataset. + + + + + Number of bits assumed matching on a default datatype. - - - - + - Count divided by total in atom percent. + The mask. The length of the mask is an integer multiple of bitdepth. + In such case, padded bits are set to 0. - + diff --git a/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_results.nxdl.xml new file mode 100644 index 0000000..485397e --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXapm_paraprobe_tool_results.nxdl.xml @@ -0,0 +1,106 @@ + + + + + + Application definition for storing processing results of a tool from the paraprobe-toolbox. + + The paraprobe-toolbox is a collection of open-source tools for performing + efficient analyses of point cloud data where each point can represent atoms or + (molecular) ions. A key application of the toolbox has been for research in the + field of Atom Probe Tomography (APT) and related Field Ion Microscopy (FIM): + + * `paraprobe-toolbox <https://www.gitlab.com/paraprobe/paraprobe-toolbox>`_ + * `M. Kühbach et al. <https://paraprobe-toolbox.readthedocs.io/en/main/>`_ + + The toolbox does not replace but complements existent software tools in this + research field. Given its capabilities of handling points as objects with + properties and enabling analyses of the spatial arrangement of and inter- + sections between geometric primitives, the software can equally be used + for analyzing data in Materials Science and Materials Engineering. + + + + + + + + A specific processing result + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If used, metadata of at least the person who performed this analysis. + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXbeam_path.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXbeam_path.nxdl.xml deleted file mode 100644 index 670fcd7..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXbeam_path.nxdl.xml +++ /dev/null @@ -1,452 +0,0 @@ - - - - - - - - A beam path consisting of one or more optical elements. - - NXbeam_path is used in NXopt to describe the beam path, i.e. the arrangement - of optical elements between the excitation source and the sample, or between - the sample and the detector unit. - - To describe the order of the elements, use 'order(NXtransformations)', where - each element's position points to the preceding element via '@depends_on'. - Special case beam splitter: A beam splitter is a device which separates the - beam into two or more beams. If such a device is part of the beam path use - two or more NXbeam_paths to describe the beam paths after the beam splitter. - In this case, in the dependency chain of the new beam paths, the first - elements each point to the beam splitter, as this is the previous element. - - Describe the relevant optical elements in the beam path by using the - appropriate base classes. You may use as many elements as needed, also - several elements of the same type as long as each element has its own name. - - - - Entry point of the dependency chain defined by the NXtransformations - field, i.e. a link to the last element in the beam path. - Example: /entry/instrument/beam_path/detector. - - - - - - Specify the order of the optical elements by defining a dependency chain. - For each element, a '@depends_on' attribute should be used to state the - position of the element in the beam path by pointing to the previous - element. For the very first element, use the string "." instead. - - - - For each element in the beam path, one such field must exist with a - '@depends_on' attribute defined to specify its position in the beam - path. Note that also 'NXopt/ENTRY/INSTRUMENT/sample_stage' and windows - ('NXopt/ENTRY/INSTRUMENT/sample_stage/entry_window' and - 'NXopt/ENTRY/INSTRUMENT/sample_stage/exit_window') may be added to the - dependency chain, i.e. may have an entry in this class even if they are - not described in the beam path. - ELEMENT is a place holder for the name of an optical beam path element. - Note that the name of this field must be exactly the same as the - element's field name. - - - - Add a link to the previous beam path element. - - - - - - - Excitation source. One or more may be needed (e.g. two for a pump-probe - setup with one pump and one probe beam). - Depending on the source type, different properties are relevant, which - are provided through the respective base class (e.g. use NXopt_source for - lamps or lasers, NXchem_source for chemical reaction etc.). - Some base classes are incomplete (NXchem_source, NXbio_source); the - expertise of the respective communities is needed. - - - - Use this field to point to the previous optical element. - - - - - Type of excitation source. - - - - - - - - - - - - - - - - - - - - - - - Lifespan of the excitation (typically provided in hours). - - - - - How many hours has the lamp been used? - - - - - Wavelengths or energy vector of the excitation source. This can be a - single value or a spectrum, depending on the type of experiment. - - - - Unit of wavelength or energy. - - - - - - - Two- or three-dimensional beam profile. - - - - - - - - - Power of one light pulse if the source is a pulsed source. - - - - - Is the excitation source continuous wave (CW)? - - - - - Power of CW beam. - - - - - FWHM bandwidth of the excitation source. - - - - - Coherence length. - - - - - Divergence of the excitation beam. - - - - - - Use this field to describe a simple pinhole (round geometry). Define its - dimension using 'diameter'. For more complex geometries, 'NXaperture' - should be used. - - - - - Use this field to describe a simple slit (rectangular geometry). Define - its dimensions using 'x_gap' and 'y_gap'. For more complex geometries, - 'NXaperture' should be used. - - - - - Use this field to describe an aperture. To specify a window, use the - field 'window_NUMBER(NXaperture)'. - - - - - A window, e.g. an entry or exit window of a cryostat. - - - - Use this field to point to the previous optical element. - - - - - The material of the window. - - - - - - - - - - - - - - - If you specified 'other' as material, decsribe here what it is. - - - - - Thickness of the window - - - - - Angle of the window normal (outer) vs. the substrate normal - (similar to the angle of incidence). - - - - - If reference data were measured add a link to the NeXus file where they - are described. - - - - - - - - A device that reduces the intensity of a beam by attenuation. - - - - The transmitted intensity divided by the incident intensity. - - - - - Attenuation of the attenuator in dB. - - - - Unit of the measured data is not covered by NXDL units state - here which unit was used. - - - - - - Input and output aperture of the attenuator. - - - - - Geometry (shape, size etc.) of the attenuator. - - - - - - A diffraction grating. Define relevant parameters in the corresponding - fields, e.g. order of diffration (diffraction_order) or angular - dispersion (angular_dispersion). - - - - Define the type of the grating. - - - - - Dispersion of the grating in nm/mm (or e.g. nm/mrad). - - - - - Number of grooves per mm. - - - - - Blaze wavelength of the grating. - - - - - Efficiency curve versus wavelength or energy. - - - - - - - - Spectral values, e.g. wavelength or energy. Vector of length - N_spectrum. - - - - Unit of wavelength array (e.g. nanometer or Angstrom) - - - - - - - A device blocking the beam in a temporal periodic pattern, e.g. a optical - chopper wheel. Specify the frequency range using 'min_frequency' and - 'max_frequency'. - - - - Minimum frequency in Hertz. - - - - - Maximum frequency in Hertz. - - - - - Frequency resolution in Hertz. - - - - - - A monochromator or spectrometer. - - - - Spectral values of the monochromator, e.g. wavelength or energy values - used for the measurement. - - - - Unit of wavelength array (e.g. nanometer or Angstrom) - - - - - - Diffraction grating. If two or more gratings were used, define the - angular dispersion and the wavelength range (min/max wavelength) for - each grating and make sure that the wavelength ranges do not overlap. - The dispersion should be defined for the entire wavelength range of the - experiment. - - - - Dispersion of the grating in nm/mm. - - - - - Minimum wavelength of the grating. - - - - - Maximum wavelength of the grating. - - - - - - Spectral resolution of the instrument. - - - - - Define the width of the monochromator slit in the subfield x_gap. - - - - Was the slit width fixed? - - - - - If slit width was not fixed, define the maximum slit width. - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXbeam_splitter.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXbeam_splitter.nxdl.xml index e4b2d38..636a33d 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXbeam_splitter.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXbeam_splitter.nxdl.xml @@ -3,7 +3,7 @@ - - + + - Length of the spectrum vector (e.g. wavelength or energy) for which the - refractive index of the beam splitter material and/or coating is defined. + Length of the spectrum vector (e.g. wavelength or energy) for which the + refractive index of the beam splitter material and/or coating is defined. - Length of the spectrum vector (e.g. wavelength or energy) for which the - reflectance or transmission of the beam splitter is given. + Length of the spectrum vector (e.g. wavelength or energy) for which the + reflectance or transmission of the beam splitter is given. - Number of parameters needed do descripe the shape of the beam splitter. + Number of parameters needed do describe the shape of the beam splitter. - Number of objects the beam splitter is made up of. + Number of objects the beam splitter is made up of. - Number of outputs, i.e. number of paths the beam takes after being split by - the beam splitter. + Number of outputs, i.e. number of paths the beam takes after being split by + the beam splitter. - A beam splitter, i.e. a device splitting the light into two or more beams. - - Information about types and properties of beam splitters is provided e.g. - [here](https://www.rp-photonics.com/beam_splitters.html). - - Use two or more NXbeam_paths to describe the beam paths after the beam - splitter. In the dependency chain of the new beam paths, the first elements - each point to this beam splitter, as this is the previous element. + A beam splitter, i.e. a device splitting the light into two or more beams. + + Information about types and properties of beam splitters is provided e.g. + [here](https://www.rp-photonics.com/beam_splitters.html). + + Use two or more instances of NXbeam to describe the beam paths after the beam + splitter. In the dependency chain of the new beam paths, the first elements + each point to this beam splitter, as this is the previous element. - Specify the beam splitter type (e.g. dielectric mirror, pellicle, - dichroic mirror etc.). Shape (e.g. prism, plate, cube) and dimension - should be described in 'geometry'. Define if the beam splitter is - polarizing or not in the field 'polarizing(NX_BOOLEAN)'. + Specify the beam splitter type (e.g. dielectric mirror, pellicle, + dichroic mirror etc.). Shape (e.g. prism, plate, cube) and dimension + should be described in 'geometry'. Define if the beam splitter is + polarizing or not in the field 'polarizing(NX_BOOLEAN)'. @@ -79,45 +80,37 @@ - - - - - If you selected 'other' in 'type' use this field to specify which type of - beam splitter was used. - - - Is the beam splitter polarizing? + Is the beam splitter polarizing? - Does the beam splitter have multiple outputs (diffractive optical - element), i.e. more than two outputs? + Does the beam splitter have multiple outputs (diffractive optical + element), i.e. more than two outputs? - Describe the geometry (shape, dimension etc.) of the beam splitter. - Specify the dimensions in 'SHAPE/size'. A sketch of the device should be - provided in the 'sketch(NXdata)' field to clarify (i) the shape and - dimensions of the device, and (ii) the input and outputs (i.e. the - direction of the incoming and outcoming (split) beams). + Describe the geometry (shape, dimension etc.) of the beam splitter. + Specify the dimensions in 'SHAPE/size'. A sketch of the device should be + provided in the 'sketch(NXdata)' field to clarify (i) the shape and + dimensions of the device, and (ii) the input and outputs (i.e. the + direction of the incoming and outcoming (split) beams). - Describe the shape (plate, cube, wedged, prism etc.). + Describe the shape (plate, cube, wedged, prism etc.). @@ -128,34 +121,29 @@ in 'substrate/substrate_thickness' and 'coating/coating_thickness'.--> - - - If you chose 'other' in 'shape' describe what it is. - - - Sketch of the beam splitter showing its geometry. The paths of the - incoming and split beam should be illustrated and labelled (0 for the - incoming beam, and 1, 2,..., N_outputs for the outputs (i.e. the split - beam paths)). + Sketch of the beam splitter showing its geometry. The paths of the + incoming and split beam should be illustrated and labelled (0 for the + incoming beam, and 1, 2,..., N_outputs for the outputs (i.e. the split + beam paths)). - Physical extent of the beam splitter device. The beam splitter might be - made up of one or more objects (NX_objects). The meaning and location - of the axes used will vary according to the value of the 'shape' - variable. 'N_shapepar' defines how many parameters: - - * For 'cube' the parameters are (width, length). - * For 'cylinder' the parameters are (diameter, length). - * For 'plate' the parameters are (width, height, length). - * For 'prism' the parameters are (width, height, length). - * For 'wedged' the parameters are (width, height, shortest length). - The wedge angle should be provided in 'SHAPE/wedge_angle'. - * For 'other' the parameters may be (A, B, C, ...) with the labels - defined in the sketch plotted in 'SHAPE/sketch'. + Physical extent of the beam splitter device. The beam splitter might be + made up of one or more objects (NX_objects). The meaning and location + of the axes used will vary according to the value of the 'shape' + variable. 'N_shapepar' defines how many parameters: + + * For 'cube' the parameters are (width, length). + * For 'cylinder' the parameters are (diameter, length). + * For 'plate' the parameters are (width, height, length). + * For 'prism' the parameters are (width, height, length). + * For 'wedged' the parameters are (width, height, shortest length). + The wedge angle should be provided in 'SHAPE/wedge_angle'. + * For 'other' the parameters may be (A, B, C, ...) with the labels + defined in the sketch plotted in 'SHAPE/sketch'. @@ -164,41 +152,41 @@ in 'substrate/substrate_thickness' and 'coating/coating_thickness'.--> - Wedge angle if 'shape' is 'wedged'. + Wedge angle if 'shape' is 'wedged'. +doc: | +Specify the length of the beam splitter. If the device has a wedged +shape provide the minimum and maximum length of the device. +Otherwise, if the beam splitter has a homogeneous thickness, the two +values are equal. +dimensions: +rank: 1 +dim: [[1,2]]--> - Beam splitting ratio(s) for the various outputs (i.e. the - paths of the beam after being split by the beam splitter). - The order of the ratios must be consistent with the labels - 1, 2, ... N_outputs defined by the sketch in 'SHAPE/sketch', starting with 1. + Beam splitting ratio(s) for the various outputs (i.e. the + paths of the beam after being split by the beam splitter). + The order of the ratios must be consistent with the labels + 1, 2, ... N_outputs defined by the sketch in 'SHAPE/sketch', starting with 1. @@ -206,39 +194,39 @@ length(NX_FLOAT): - Clear aperture of the device (e.g. 90% of diameter for a disc, or 90% of - length and height for square geometry). + Clear aperture of the device (e.g. 90% of diameter for a disc, or 90% of + length and height for square geometry). - Substrate of the beam splitter. Describe the material of the substrate in - substrate/substrate_material and provide its index of refraction in - substrate/index_of_refraction_substrate, if known. + Substrate of the beam splitter. Describe the material of the substrate in + substrate/substrate_material and provide its index of refraction in + substrate/index_of_refraction_substrate, if known. - Specify the material of the beam splitter. If the device has a coating - it should be described in coating/coating_material. Is the material - birefringent? + Specify the material of the beam splitter. If the device has a coating + it should be described in coating/coating_material. Is the material + birefringent? - Thickness of the beam splitter substrate. Define the minimum and - maximum thickness (for a wedged geomtry). For a homogeneous thickness - (e.g. as in plate beam splitters) the minimum and maximum values are - equal. + Thickness of the beam splitter substrate. Define the minimum and + maximum thickness (for a wedged geometry). For a homogeneous thickness + (e.g. as in plate beam splitters) the minimum and maximum values are + equal. - + - Complex index of refraction of the beam splitter substrate. Specify at - given spectral values (e.g. wavelength, energy, wavenumber etc.). + Complex index of refraction of the beam splitter substrate. Specify at + given spectral values (e.g. wavelength, energy, wavenumber etc.). @@ -248,32 +236,32 @@ length(NX_FLOAT): - Is the beam splitter coated? If yes, specify the type and material of the - coating and the spectral range for which it is designed. If known, you - may also provide its index of refraction. For a beam splitter cube - consisting of two prisms which are glued together, you may want to - specify the the glue and the coatings of each prism. + Is the beam splitter coated? If yes, specify the type and material of the + coating and the spectral range for which it is designed. If known, you + may also provide its index of refraction. For a beam splitter cube + consisting of two prisms which are glued together, you may want to + specify the the glue and the coatings of each prism. - Specify the coating type (e.g. dielectric, anti-reflection (AR), - multilayer coating etc.). + Specify the coating type (e.g. dielectric, anti-reflection (AR), + multilayer coating etc.). - Specify the coating material. + Specify the coating material. - Thickness of the coating. + Thickness of the coating. - Wavelength range for which the coating is designed. Enter the minimum - and maximum values of the wavelength range. + Wavelength range for which the coating is designed. Enter the minimum + and maximum values of the wavelength range. @@ -281,8 +269,8 @@ length(NX_FLOAT): - Complex index of refraction of the coating. Specify at given spectral - values (e.g. wavelength, energy, wavenumber etc.). + Complex index of refraction of the coating. Specify at given spectral + values (e.g. wavelength, energy, wavenumber etc.). @@ -292,10 +280,10 @@ length(NX_FLOAT): - Wavelength range for which the beam splitter is designed. Enter the - minimum and maximum values of the wavelength range. Alternatively, or - additionally, you may define the wavelength range for the coating in - coating/wavelength_range_coating. + Wavelength range for which the beam splitter is designed. Enter the + minimum and maximum values of the wavelength range. Alternatively, or + additionally, you may define the wavelength range for the coating in + coating/wavelength_range_coating. @@ -303,11 +291,11 @@ length(NX_FLOAT): - Optical loss of the beam splitter for the various outputs (i.e. the paths - of the beam after being split by the beam splitter). - The order of the ratios must be consistent with the labels - 1, 2, ... N_outputs defined by the sketch in 'SHAPE/sketch', starting - with 1. + Optical loss of the beam splitter for the various outputs (i.e. the paths + of the beam after being split by the beam splitter). + The order of the ratios must be consistent with the labels + 1, 2, ... N_outputs defined by the sketch in 'SHAPE/sketch', starting + with 1. @@ -315,20 +303,20 @@ length(NX_FLOAT): - Optimized angle of incidence for the desired splitting ratio. + Optimized angle of incidence for the desired splitting ratio. - Angle of deflection corresponding to the optimized angle of incidence - defined in incident_angle. + Angle of deflection corresponding to the optimized angle of incidence + defined in incident_angle. - + - Range of the angles of incidence (AOI) for which the beam splitter can be - operated. Specify the minimum and maximum angles of the range. + Range of the angles of incidence (AOI) for which the beam splitter can be + operated. Specify the minimum and maximum angles of the range. @@ -338,10 +326,10 @@ length(NX_FLOAT): use dim: [[1,N_angles]], N_angles being the number of angles for which the beam splitter can be operated? If this is the case for some devices, we might also have to define a field -for the corresponding defelction angles...--> +for the corresponding deflection angles...--> - Reflectance of the beam splitter at given spectral values. + Reflectance of the beam splitter at given spectral values. @@ -349,11 +337,11 @@ for the corresponding defelction angles...--> - Transmission at given spectral values for the various outputs (i.e. the - paths of the beam after being split by the beam splitter). - The order of the ratios must be consistent with the labels - 1, 2, ... N_outputs defined by the sketch in 'SHAPE/sketch', starting - with 1. + Transmission at given spectral values for the various outputs (i.e. the + paths of the beam after being split by the beam splitter). + The order of the ratios must be consistent with the labels + 1, 2, ... N_outputs defined by the sketch in 'SHAPE/sketch', starting + with 1. diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_alpha_complex.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_alpha_complex.nxdl.xml deleted file mode 100644 index 1b3e344..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_alpha_complex.nxdl.xml +++ /dev/null @@ -1,151 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality of the alpha shape, for now 2 or 3. - - - - - - The number of edges. - - - - - The number of faces. - - - - - The number of cells. - - - - - Computational geometry description of alpha shapes or wrappings to primitives. - - For details see: - - * https://dx.doi.org/10.1109/TIT.1983.1056714 for 2D, - * https://dx.doi.org/10.1145/174462.156635 for 3D, - * https://dl.acm.org/doi/10.5555/871114 for weighted, and - * https://doc.cgal.org/latest/Alpha_shapes_3 for 3D implementation - * https://doc.cgal.org/latest/Manual/packages.html#PkgAlphaWrap3 for 3D wrap - - in CGAL, the Computational Geometry Algorithms Library. - As a starting point, we follow the conventions of the CGAL library. - - - - - - - - - - Specify which general type of alpha shape is computed. - Using for now the CGAL terminology. Basic means (unweighted) alpha shapes. - Alpha_wrapping means meshes created using alpha wrapping procedures. - - - - - - - - - - Specifically when computed with the CGAL, the mode specifies if singular - faces are removed (regularized) of the alpha complex. - - - - - - - - - - The alpha, (radius of the alpha-sphere) parameter to be used for alpha - shapes and alpha wrappings. - - - - - The offset distance parameter to be used in addition to alpha - in the case of alpha_wrapping. - - - - - - Point cloud for which the alpha shape or wrapping should be computed. - - - - - - Triangle soup for which the alpha wrapping should be computed. - - - - - A meshed representation of the resulting shape. - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_cylinder_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_cylinder_set.nxdl.xml deleted file mode 100644 index e5e5e88..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_cylinder_set.nxdl.xml +++ /dev/null @@ -1,165 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The cardinality of the set, i.e. the number of cylinders or cones. - - - - - Computational geometry description of a set of cylinders in Euclidean space. - - The members of the set can have different size. For each member the position - of the center and the height is mandatory. The radius can either be defined - in the radius field or by filling both the upper and the lower radius field. - The latter case can be used to represent truncated cones. - - - - - - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for cylinders. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish members for explicit indexing. - - - - - - - - The geometric center of each member. - - - - - - - - - A direction vector which is parallel to the cylinder/cone axis and - whose magnitude is the height of the cylinder/cone. - - - - - - - - - - - - - - - The radius of the upper circular cap. - This field, combined with lower_cap_radius can be used to - describe (eventually truncated) circular cones. - - - - - - - - The radius of the upper circular cap. - This field, combined with lower_cap_radius can be used to - describe (eventually truncated) circular cones. - - - - - - - - Reference to or definition of a coordinate system with - which the positions and directions are interpretable. - - - - - - Interior volume of each cylinder - - - - - - - - Lateral surface area - - - - - - - - Area of the upper and the lower cap of each cylinder respectively. - - - - - - - - - Cap and lateral surface area for each cylinder. - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_ellipsoid_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_ellipsoid_set.nxdl.xml deleted file mode 100644 index 38a448a..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_ellipsoid_set.nxdl.xml +++ /dev/null @@ -1,135 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality, which has to be at least 2. - - - - - The cardinality of the set, i.e. the number of ellipses, or ellipsoids. - - - - - Computational geometry description of a set of ellipsoids in Euclidean space. - - Individual ellipsoids can have different half axes. - - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for ellipsoids. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish ellipsoids for explicit indexing. - - - - - - - - Geometric center of the ellipsoids. This can be the center of mass. - Dimensionality and cardinality of the point and ellipsoid set have to match. - The identifier_offset and identifier field of NXcg_point_set do not need - to be used as they should be same as the identifier_offset and the - identifier for the ellipsoids. - - - - - - - - - If all ellipsoids in the set have the same half-axes. - - - - - - - - In the case that ellipsoids have different radii use this field - instead of half_axes_radius. - - - - - - - - - Reference to or definition of a coordinate system with - which the positions and directions are interpretable. - - - - - - Are the ellipsoids closed or hollow? - - - - - - - - - - - - - - - - - - - Direction unit vector which points along the largest half-axes. - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_face_list_data_structure.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_face_list_data_structure.nxdl.xml deleted file mode 100644 index ea8faee..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_face_list_data_structure.nxdl.xml +++ /dev/null @@ -1,243 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality, which has to be at least 2. - - - - - The number of vertices. - - - - - The number of edges. - - - - - The number of faces. - - - - - The total number of vertices of all faces. Faces are polygons. - - - - - The total number of Weinberg vector values of all faces. - - - - - Computational geometry description of geometric primitives via a face and edge list. - - Primitives must not be degenerated or self-intersect. - Such descriptions of primitives are frequently used for triangles and polyhedra - to store them on disk for visualization purposes. Although storage efficient, - such a description is not well suited for topological and neighborhood queries - of especially meshes that are built from primitives. - - In this case, scientists may need a different view on the primitives which - is better represented for instance with a half_edge_data_structure instance. - The reason to split thus the geometric description of primitives, sets, and - specifically meshes of primitives is to keep the structure simple enough for - users without these computational geometry demands but also enable those more - computational geometry savy users the storing of the additionally relevant - data structure. - - This is beneficial and superior over NXoff_geometry because for instance a - half_edge_data_structure instance can be immediately use to reinstantiate - the set without having to recompute the half_edge_structure from the vertex - and face-list based representation and thus offer a more efficient route - to serve applications where topological and graph-based operations are key. - - - - Dimensionality. - - - - - - Array which specifies of how many vertices each face is built. - Each entry represent the total number of vertices for face, irrespectively - whether vertices are shared among faces/are unique or not. - - - - - - - - Number of edges. - - - - - Number of faces. - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for vertices. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for edges. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for faces. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish vertices explicitly. - - - - - - - - Integer used to distinguish edges explicitly. - - - - - - - - Integer used to distinguish faces explicitly. - - - - - - - - Positions of the vertices. - - Users are encouraged to reduce the vertices to unique set of positions - and vertices as this supports a more efficient storage of the geometry data. - It is also possible though to store the vertex positions naively in which - case vertices_are_unique is likely False. - Naively here means that one for example stores each vertex of a triangle - mesh even though many vertices are shared between triangles and thus - the positions of these vertices do not have to be duplicated. - - - - - - - - - The edges are stored as a pairs of vertex identifier values. - - - - - - - - - Array of identifiers from vertices which describe each face. - - The first entry is the identifier of the start vertex of the first face, - followed by the second vertex of the first face, until the last vertex - of the first face. Thereafter, the start vertex of the second face, the - second vertex of the second face, and so on and so forth. - - Therefore, summating over the number_of_vertices, allows to extract - the vertex identifiers for the i-th face on the following index interval - of the faces array: [$\sum_i = 0}^{i = n-1}$, $\sum_{i=0}^{i = n}$]. - - - - - - - - - If true indicates that the vertices are all placed at different positions - and have different identifiers, i.e. no points overlap or are counted twice. - - - - - If true indicates that no edge is stored twice. Users are encouraged to - consider and use the half_edge_data_structure instead as this will work - towards achieving a cleaner graph-based description if relevant and possible. - - - - - - Specifies for each face which winding order was used if any: - - * 0 - undefined - * 1 - counter-clockwise (CCW) - * 2 - clock-wise (CW) - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_geodesic_mesh.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_geodesic_mesh.nxdl.xml deleted file mode 100644 index 1b69e9b..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_geodesic_mesh.nxdl.xml +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computational geometry description of a geodesic mesh. - - People from geodesic/surveyors will likely have specific demands and - different views about what should be included in such a base class, given - that nested geodesic meshes are a key component of climate modelling tools. - For now we propose to use this base class as a container to organize metadata - and data related to geodesic meshes. - - Specifically an instance of this base class should detail the rule set how - how the geodesic (surface) mesh was instantiated as there are many - possibilities. A geodesic surface mesh is in this sense a triangulated - surface mesh with metadata. For additional details as an introduction - into the topic see e.g.: - - * `E. S. Popko and C. J. Kitrick <https://doi.org/10.1201/9781003134114>`_ - - Here, especially the section on subdivision schemes is relevant. - - - - Reference to or definition of a coordinate system with - which the positions and directions are interpretable. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_half_edge_data_structure.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_half_edge_data_structure.nxdl.xml deleted file mode 100644 index 81c66fb..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_half_edge_data_structure.nxdl.xml +++ /dev/null @@ -1,174 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality, which has to be at least 2. - - - - - The number of vertices. - - - - - The number of faces. - - - - - The number of half-edges. - - - - - Computational geeometry description of a half-edge data structure. - - Such a data structure can be used to efficiently circulate around faces - and iterate over vertices of a planar graph. - - - - - - - - In this half-edge data structure vertex identifiers start at 1. - Vertices are identified with consecutive integers up to number_of_vertices. - This field can be used to document which constant integer has to be - added to another set of vertex_identifier to assure that these other - identifiers also start at 1. - - - - - In this half-edge data structure face identifiers start at 1. - Faces are identified with consecutive integers up to number_of_faces. - This field can be used to document which constant integer has to be - added to another set of face_identifier to assure that these other - identifiers also start at 1. - - The face identifier zero is reserved for the NULL face ! - - - - - In this half-edge data structure half-edge identifiers start at 1. - Half-edges are identified with consecutive integers up to number_of_half_edges. - This field can be used to document which constant integer has to be - added to another set of half_edge_identifier to assure that these other - identifiers also start at 1. - - - - - - The position of the vertices. - - - - - - - - - Identifier of the incident half-edge. - - - - - - - - Identifier of the (starting)/associated half-edge of the face. - - - - - - - - The identifier of the vertex from which this half-edge is outwards pointing. - - - - - - - - Identifier of the associated oppositely pointing half-edge. - - - - - - - - If the half-edge is a boundary half-edge the - incident face identifier is NULL, i.e. 0. - - - - - - - - Identifier of the next half-edge. - - - - - - - - Identifier of the previous half-edge. - - - - - - - - Users are referred to the literature for the background of L. Weinberg's - work about topological characterization of planar graphs: - - * `L. Weinberg 1966a, <https://dx.doi.org/10.1109/TCT.1964.1082216>`_ - * `L. Weinberg, 1966b, <https://dx.doi.org/10.1137/0114062>`_ - * `E. A. Lazar et al. <https://doi.org/10.1103/PhysRevLett.109.095505>`_ - - and how this work can e.g. be applied in space-filling tessellations - of microstructural objects like crystals/grains. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_hexahedron_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_hexahedron_set.nxdl.xml deleted file mode 100644 index 96c2d71..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_hexahedron_set.nxdl.xml +++ /dev/null @@ -1,239 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The cardinality of the set, i.e. the number of hexahedra. - - - - - Computational geometry description of a set of hexahedra in Euclidean space. - - The hexahedra do not have to be connected, can have different size, - can intersect, and be rotated. - This class can also be used to describe cuboids or cubes, axis-aligned or not. - The class represents different access and description levels to offer both - applied scientists and computational geometry experts to use the same - base class but rather their specific view on the data: - - * Most simple many experimentalists wish to communicate dimensions/the size - of specimens. In this case the alignment with axes is not relevant as - eventually the only relevant information to convey is the volume of the - specimen. - * In many cases, take for instance an experiment where a specimen was taken - from a specifically deformed piece of material, e.g. cold-rolled, - channel-die deformed, the orientation of the specimen edges with the - experiment coordinate system can be of very high relevance. - Examples include to know which specimen edge is parallel to the rolling, - the transverse, or the normal direction. - * Sufficient to pinpoint the sample and laboratory/experiment coordinate - system, the above-mentioned descriptions are not detailed enough though - to create a CAD model of the specimen. - * Therefore, groups and fields for an additional, computational-geometry- - based view of the hexahedra is offered which serve different computational - tasks: storage-oriented simple views or detailed topological/graph-based - descriptions. - - Hexahedra are important geometrical primitives, which are among the most - frequently used elements in finite element meshing/modeling. - - Hexahedra have to be non-degenerated, closed, and built of polygons - which are not self-intersecting. - - The term hexahedra will be used throughout this base class but includes - the especially in engineering and more commonly used special cases, - cuboid, cube, box, axis-aligned bounding box (AABB), optimal bounding - box (OBB). - - An axis-aligned bounding box is a common data object in - computational science and codes to represent a cuboid whose edges - are aligned with a coordinate system. As a part of binary trees these - are important data objects for time as well as space efficient queries - of geometric primitives in techniques like kd-trees. - - An optimal bounding box is a common data object which provides the best - tight fitting box about an arbitrary object. In general such boxes are - rotated. Exact and substantially faster in practice approximate algorithms - exist for computing optimal or near optimal bounding boxes for point sets. - - - - - - - - - - - A qualitative description of each hexahedron/cuboid/cube/box. - - - - - - - - - Qualifier how one edge is longer than all other edges of the hexahedra. - Often the term length is associated with one edge being parallel to - an axis of the coordinate system. - - - - - - - - Qualifier often used to describe the length of an edge within - a specific coordinate system. - - - - - - - - Qualifier often used to describe the length of an edge within - a specific coordinate system. - - - - - - - - Position of the geometric center, which often is but not necessarily - has to be the center_of_mass of the hexahedrally-shaped sample/sample part. - - - - - - - - - - - - - - Total area (of all six faces) of each hexahedron. - - - - - - - - Area of each of the six faces of each hexahedron. - - - - - - - - - Specifies if the hexahedra represent cuboids or cubes eventually rotated - ones but at least not too exotic six-faced polyhedra. - - - - - - - - Only to be used if is_box is present. In this case, this field describes - whether hexahedra are boxes whose primary edges are parallel to the - axes of the Cartesian coordinate system. - - - - - - - - Reference to or definition of a coordinate system with - which the qualifiers and mesh data are interpretable. - - - - - Integer which specifies the first index to be used for distinguishing - hexahedra. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish hexahedra for explicit indexing. - - - - - - - - - - - - - - - A simple approach to describe the entire set of hexahedra when the - main intention is to store the shape of the hexahedra for visualization. - - - - - - Disentangled representations of the mesh of specific hexahedra. - - - - - - Disentangled representation of the planar graph that each hexahedron - represents. Such a description simplifies topological processing - or analyses of mesh primitive operations and neighborhood queries. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_marching_cubes.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_marching_cubes.nxdl.xml deleted file mode 100644 index b1f8e92..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_marching_cubes.nxdl.xml +++ /dev/null @@ -1,74 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computational geometry description of the marching cubes algorithm. - - Documenting which specific version was used can help to understand how robust - the results are with respect to the topology of the triangulation. - - - - Reference/link to and/or details of the grid on which a specific - marching cubes algorithm implementation is operating. - - - - - Reference to the specific implementation of marching cubes used. - - See for example the following papers for details about how to identify a - DOI which specifies the implementation used: - - * `W. E. Lorensen <https://doi.org/10.1109/MCG.2020.2971284>`_ - * `T. S. Newman and H. Yi <https://doi.org/10.1016/j.cag.2006.07.021>`_ - - The value placed here should be a DOI. If there are no specific DOI or - details write not_further_specified, or give at least a free-text - description. - - - - - Commercial or otherwise given name to the program which was used. - - - - Program version plus build number, commit hash, or description of - an ever persistent resource where the source code of the program - and build instructions can be found so that the program can be - configured in such a manner that the result file is ideally - recreatable yielding the same results. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_parallelogram_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_parallelogram_set.nxdl.xml deleted file mode 100644 index ca4a569..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_parallelogram_set.nxdl.xml +++ /dev/null @@ -1,183 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The cardinality of the set, i.e. the number of parallelograms. - - - - - Computational geometry description of a set of parallelograms in Euclidean space. - - The parallelograms do not have to be connected, can have different size, - can intersect, and be rotated. - This class can also be used to describe rectangles or squares, axis-aligned or not. - The class represents different access and description levels to offer both - applied scientists and computational geometry experts to use the same - base class but rather their specific view on the data: - - * Most simple many experimentalists wish to communicate dimensions/the size - of e.g. a region of interest in the 2D plane. In this case the alignment - with axes is not relevant as eventually relevant is only the area of the ROI. - * In other cases the extent of the parallelogram is relevant though. - * Finally in CAD models we would like to specify the polygon - which is parallelogram represents. - - Parallelograms are important geometrical primitives. Not so much because of their - uses in nowadays, thanks to improvements in computing power, not so frequently - any longer performed 2D simulation. Many scanning experiments probe though - parallelogram-shaped ROIs on the surface of samples. - - Parallelograms have to be non-degenerated, closed, and built of polygons - which are not self-intersecting. - - The term parallelogram will be used throughout this base class but includes - the especially in engineering and more commonly used special cases, - rectangle, square, 2D box, axis-aligned bounding box (AABB), or - optimal bounding box (OBB) but here the analogous 2D cases. - - An axis-aligned bounding box is a common data object in computational science - and codes to represent a rectangle whose edges are aligned with the axes - of a coordinate system. As a part of binary trees these are important data - objects for time- as well as space-efficient queries - of geometric primitives in techniques like kd-trees. - - An optimal bounding box is a common data object which provides the best - tight fitting box about an arbitrary object. In general such boxes are - rotated. Other than in 3D dimensions the rotation calipher method offers - a rigorous approach to compute optimal bounding boxes in 2D. - - - - - - - - - - - A qualitative description of each parallelogram/rectangle/square/box. - - - - - - - - - Qualifier how one edge is longer than all the other edge of the parallelogam. - Often the term length is associated with one edge being parallel to - an axis of the coordinate system. - - - - - - - - Qualifier often used to describe the length of an edge within - a specific coordinate system. - - - - - - - - Position of the geometric center, which often is but not necessarily - has to be the center_of_mass of the parallelogram. - - - - - - - - - - - - - - Only to be used if is_box is present. In this case, this field describes - whether parallelograms are rectangles/squares whose primary edges - are parallel to the axes of the Cartesian coordinate system. - - - - - - - - Reference to or definition of a coordinate system with - which the qualifiers and mesh data are interpretable. - - - - - Integer which specifies the first index to be used for distinguishing - parallelograms. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish parallelograms for explicit indexing. - - - - - - - - - - - - - - - A simple approach to describe the entire set of parallelograms when the - main intention is to store the shape of the parallelograms for visualization. - - - - - - Disentangled representations of the mesh of specific parallelograms. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_point_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_point_set.nxdl.xml deleted file mode 100644 index e5c3518..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_point_set.nxdl.xml +++ /dev/null @@ -1,98 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality, which has to be at least 1. - - - - - The cardinality of the set, i.e. the number of points. - - - - - Computational geometry description of a set of points in Euclidean space. - - The relevant coordinate system should be referred to in the NXtransformations - instance. Points may have an associated time value; however users are advised - to store time data of point sets rather as instances of time events, where - for each point in time there is an NXcg_point_set instance which specifies the - points locations. This is a frequent situation in experiments and computer - simulations, where positions of points are taken at the same point in time; - and therefore an additional time array would demand to store redundant pieces - of information for each point. - - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for points. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish points for explicit indexing. - - - - - - - - The array of point coordinates. - - - - - - - - - The optional array of time for each vertex. - - - - - - - - Reference to or definition of a coordinate system with - which the positions and directions are interpretable. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_polygon_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_polygon_set.nxdl.xml deleted file mode 100644 index e90dd65..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_polygon_set.nxdl.xml +++ /dev/null @@ -1,225 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality, which has to be either 2 or 3. - - - - - The cardinality of the set, i.e. the number of polygons. - - - - - - The total number of vertices when visiting every polygon. - - - - - - Computational geometry description of a set of polygons in Euclidean space. - - Polygons are related are specialized polylines: - - * A polygon is a geometric primitive that is bounded by a closed polyline - * All vertices of this polyline lay in the d-1 dimensional plane. - whereas vertices of a polyline do not necessarily lay on a plane. - * A polygon has at least three vertices. - - Each polygon is built from a sequence of vertices (points with identifiers). - The members of a set of polygons may have a different number of vertices. - Sometimes a collection/set of polygons is referred to as a soup of polygons. - - As three-dimensional objects, a set of polygons can be used to define the - hull of what is effectively a polyhedron; however users are advised to use - the specific NXcg_polyhedron_set base class if they wish to describe closed - polyhedra. Even more general complexes can be thought, for instance - piecewise-linear complexes, as these can have holes though, polyhedra without - holes are one subclass of such complexes, users should rather design an own - base class e.g. NXcg_polytope_set to describe such even more - complex primitives. - - - - - - - - - - - - Integer which specifies the first index to be used for distinguishing - polygons. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish polygons for explicit indexing. - - - - - - - - - A simple approach to describe the entire set of polygons when the - main intention is to store the shape of the polygons for visualization. - - - - - - - - - - - - - - - The accumulated length of the polygon edge. - - - - - - - - Array of interior angles. There are many values per polygon as number_of_vertices. - The angle is the angle at the specific vertex, i.e. between the adjoining - edges of the vertex according to the sequence in the polygons array. - Usually, the winding_order field is required to interpret the value. - - - - - - - - Curvature type: - - * 0 - unspecified, - * 1 - convex, - * 2 - concave - - - - - - - - The center of mass of each polygon. - - - - - - - - - Axis-aligned or (approximate) (optimal) bounding boxes to each polygon. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_polyhedron_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_polyhedron_set.nxdl.xml deleted file mode 100644 index e3a6e99..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_polyhedron_set.nxdl.xml +++ /dev/null @@ -1,194 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The cardinality of the set, i.e. the number of polyhedra. - - - - - The total number of edges for all polyhedra. - - - - - The total number of faces for all polyhedra. - - - - - Computational geometry description of a polyhedra in Euclidean space. - - Polyhedra, also so-called cells (especially in the convex of tessellations), - here described have to be all non-degenerated, closed, built of and thus - built out of not-self-intersecting polygon meshes. Polyhedra may make contact, - so that this base class can be used for a future description of tessellations. - - For more complicated manifolds and especially for polyhedra with holes, users - are advised to check if their particular needs are described by creating - (eventually customized) instances of an NXcg_polygon_set, which can be - extended for the description of piecewise-linear complexes. - - - - - - - - - - - Interior volume - - - - - - - - Position of the geometric center, which often is but not necessarily - has to be the center_of_mass of the polyhedra. - - - - - - - - - Total surface area as the sum of all faces. - - - - - - - - The number of faces for each polyhedron. Faces of adjoining polyhedra - are counted for each polyhedron. This field can be used to interpret - the array/field with the individual area values for each face. - - - - - - - - Area of each of the four triangular faces of each tetrahedron. - - - - - - - - The number of edges for each polyhedron. Edges of adjoining polyhedra - are counterd for each polyhedron. This field can be used to interpret - the array/field with the individual length for each edge. - - - - - Length of each edge of each tetrahedron. - - - - - - - - Reference to or definition of a coordinate system with - which the qualifiers and mesh data are interpretable. - - - - - - Integer which specifies the first index to be used for distinguishing - polyhedra. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish polyhedra for explicit indexing. - - - - - - - - - - - - - A simple approach to describe the entire set of polyhedra when the - main intention is to store the shape of the polyhedra for visualization. - - - - - - Disentangled representations of the mesh of specific polyhedron. - - - - - - Disentangled representation of the planar graph that each polyhedron - represents. Such a description simplifies topological processing - or analyses of mesh primitive operations and neighborhood queries. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_polyline_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_polyline_set.nxdl.xml deleted file mode 100644 index b64c346..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_polyline_set.nxdl.xml +++ /dev/null @@ -1,183 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality, which has to be at least 1. - - - - - The cardinality of the set, i.e. the number of polylines. - - - - - - The number of vertices, supporting the polylines. - - - - - The total number of vertices traversed when visiting every polyline. - - - - - Computational geometry description of a set of polylines in Euclidean space. - - Each polyline is built from a sequence of vertices (points with identifiers). - Each polyline must have a start and an end point. - The sequence describes the positive traversal along the polyline when walking - from the start vertex to the end/last vertex. - - - - - - - The total number of vertices, irrespective of their eventual uniqueness, - i.e. the total number of vertices that have to be visited when walking - along each polyline. - - - - - Array which specifies of how many vertices each polyline is built. - The number of vertices represent the total number of vertices for - each polyline, irrespectively whether vertices are shared or not. - See the docstring for polylines for further details about how - a set with different polyline members should be stored. - - - - - - - - Reference to or definition of a coordinate system with - which the qualifiers and polyline data are interpretable. - - - - - Integer which specifies the first index to be used for distinguishing - polylines. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish polylines for explicit indexing. - - - - - - - - - Positions of the vertices which support the members of the polyline set. - - Users are encouraged to reduce the vertices to unique set of positions - and vertices as this supports a more efficient storage of the geometry data. - It is also possible though to store the vertex positions naively in which - case vertices_are_unique is likely False. - Naively here means that one for example stores each vertex of a triangle - mesh even though many vertices are shared between triangles and thus - the positions of these vertices do not have to be duplicated. - - - - - - - - - If true indicates that the vertices are all placed at different - positions and have different identifiers, i.e. no points overlap - or are counted twice. - - - - - Sequence of vertex identifiers which describe each polyline. - - A trivial example is a set with two polylines with three vertices each. - If the polylines meet in a junction, say the second vertex is shared - and marking the junction between the two polylines, it is possible that - there are only five unique positions suggesting five unique vertices. - - A non-trivial example is a set with several polylines, each of which with - eventually different number of vertices. The array stores the vertex - identifiers in the order how the polylines are visited: - - The first entry is the identifier of the start vertex of the first polyline, - followed by the second vertex of the first polyline, until the last vertex - of the polyline. Thereafter, the start vertex of the second polyline, and - so on and so forth. Using the (cumulated) counts in number_of_vertices, - the vertices of the n-th polyline can be accessed on the following - array index interval: - :math:`[\sum_{i=0}^{i=N-1}, \sum_{i=0}^{i=N}]`. - - - - - - - - - The length of each polyline. - - - - - - - - If true specifies that a polyline is closed, i.e. - its end point is connected to the start point. - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_sphere_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_sphere_set.nxdl.xml deleted file mode 100644 index e50192c..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_sphere_set.nxdl.xml +++ /dev/null @@ -1,121 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality, which has to be at least 2. - - - - - The cardinality of the set, i.e. the number of circles or spheres. - - - - - Computational geometry description of a set of spheres in Euclidean space. - - Each sphere can have a different radius. - - - - - - Integer which specifies the first index to be used for distinguishing - identifiers for spheres. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish spheres for explicit indexing. - - - - - - - - Geometric center of the spheres. This can be the center of mass. - Dimensionality and cardinality of the point and sphere set have to match. - The identifier_offset and identifier field of NXcg_point_set do not need - to be used as they should be same as the identifier_offset and the - identifier for the spheres. - - - - - - - - - In the case that all spheres have the same radius. - - - - - In the case that spheres have different radius use this - instead of the radius field. - - - - - - - - Reference to or definition of a coordinate system with - which the positions and directions are interpretable. - - - - - - Are the spheres closed or hollow? - - - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_tetrahedron_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_tetrahedron_set.nxdl.xml deleted file mode 100644 index b3e27b0..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_tetrahedron_set.nxdl.xml +++ /dev/null @@ -1,175 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The cardinality of the set, i.e. the number of tetrahedra. - - - - - Computational geometry description of a set of tetrahedra in Euclidean space. - - The tetrahedra do not have to be connected. - As tetrahedral elements they are among hexahedral elements one of the most - frequently used geometric primitive for meshing and describing volumetric - and surface descriptions of objects at the continuum scale. - - A set of tetrahedra in 3D Euclidean space. - - The tetrahedra do not have to be connected, can have different size, - can intersect, and be rotated. - - Tetrahedra are the simplest and thus important geometrical primitive. - They are frequently used as elements in finite element meshing/modeling. - - Tetrahedra have to be non-degenerated, closed, and built of triangles - which are not self-intersecting. - - - - - - - - - - - Interior volume - - - - - - - - Position of the geometric center, which often is but not necessarily - has to be the center_of_mass of the tetrahedra. - - - - - - - - - Total surface area as the sum of all four triangular faces. - - - - - - - - Area of each of the four triangular faces of each tetrahedron. - - - - - - - - - Length of each edge of each tetrahedron. - - - - - - - - - Reference to or definition of a coordinate system with - which the qualifiers and mesh data are interpretable. - - - - - - Integer which specifies the first index to be used for distinguishing - tetrahedra. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish tetrahedra for explicit indexing. - - - - - - - - - - - - - A simple approach to describe the entire set of tetrahedra when the - main intention is to store the shape of the tetrahedra for visualization. - should take the possibility to describe - - - - - - Disentangled representations of the mesh of specific tetrahedra. - - - - - - Disentangled representation of the planar graph that each tetrahedron - represents. Such a description simplifies topological processing - or analyses of mesh primitive operations and neighborhood queries. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_triangle_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_triangle_set.nxdl.xml deleted file mode 100644 index 3640f8f..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_triangle_set.nxdl.xml +++ /dev/null @@ -1,132 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality, which has to be at least 2. - - - - - The cardinality of the set, i.e. the number of triangles. - - - - - The number of unique vertices supporting the triangles. - - - - - Computational geometry description of a set of triangles in Euclidean space. - - - - - - - Reference to or definition of a coordinate system with - which the qualifiers and primitive data are interpretable. - - - - - Integer which specifies the first index to be used for distinguishing - triangles. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish triangles for explicit indexing. - - - - - - - - - A simple approach to describe the entire set of triangles when the - main intention is to store the shape of the triangles for visualization. - - - - - - - - - - - - - - - Array of edge length values. For each triangle the edge length is - reported for the edges traversed according to the sequence - in which vertices are indexed in triangles. - - - - - - - - - Array of interior angle values. For each triangle the angle is - reported for the angle opposite to the edges which are traversed - according to the sequence in which vertices are indexed in triangles. - - - - - - - - - The center of mass of each polygon. - - - - - - - - - Axis-aligned or (approximate) (optimal) bounding boxes to each polygon. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcg_triangulated_surface_mesh.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcg_triangulated_surface_mesh.nxdl.xml deleted file mode 100644 index 51ec02b..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcg_triangulated_surface_mesh.nxdl.xml +++ /dev/null @@ -1,56 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computational geometry description of a mesh of triangles. - - The mesh may be self-intersecting and have holes but the - triangles must not be degenerated. - - - - - - A graph-based approach to describe the mesh when it is also desired - to perform topological processing or analyses on the mesh. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXchamber.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXchamber.nxdl.xml deleted file mode 100644 index 30da2e9..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXchamber.nxdl.xml +++ /dev/null @@ -1,39 +0,0 @@ - - - - - - Component of an instrument to store or place objects and specimens. - - - - Given name/alias. - - - - - Free-text field for describing details about the chamber. - For example out of which material was the chamber built. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcircuit_board.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcircuit_board.nxdl.xml deleted file mode 100644 index 4e64e65..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcircuit_board.nxdl.xml +++ /dev/null @@ -1,45 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Circuit board with e.g. ADC and/or DAC electronic components. - - Currently used to store the settings of the so-called magboards used in - Nion electron microscopes but likely this could be a useful base class for - substantially more use cases where details at a deep technical instrument design - level are relevant or important. - - - - TBD by Nion Co. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXclustering.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXclustering.nxdl.xml deleted file mode 100644 index 7635175..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXclustering.nxdl.xml +++ /dev/null @@ -1,124 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of numeral labels per object. - - - - - Number of categorical labels per object. - - - - - Total number of clusters detected. - - - - - Metadata to the results of a clustering analysis. - - Clustering algorithms are routine tools to segment a set of objects/primitives - into groups, objects of different type. A plethora of algorithms have been - proposed for geometric primitives as objects, such as points, triangles, - or (abstract) objects. - - This base class considers metadata and results of one clustering - applied to a set in which objects are either categorized as noise - or belonging to a cluster, specifically here only one cluster. - - - - How many numeric labels does each object have. - - - - - How many categorical labels does each object have. - - - - - Reference to a set of objects investigated in a cluster analysis. - Objects must have clear integer identifier. - - - - - Reference to numeric attribute data for each object. - - - - - Reference to categorical attribute data for each object. - - - - - - Which identifier is the first to be used to label a cluster. - - The value should be chosen in such a way that special values can be resolved: - * identifier_offset-1 indicates an object belongs to no cluster. - * identifier_offset-2 indicates an object belongs to the noise category. - Setting for instance identifier_offset to 1 recovers the commonly used - case that objects of the noise category get values to -1 and unassigned points to 0. - - - - - Total number of objects categorized as unassigned. - - - - - Total number of objects categorized as noise. - - - - - Total number of clusters (excluding noise and unassigned). - - - - - Number of objects associated to each cluster. The labels are implicit, - meaning the zeroth/first entry in the array belongs to the first cluster, - the second entry to the second cluster and so on and so forth. - The first cluster has the value of identifier_offset as its identifier. - The second cluster has identifier_offset + 1, and so on and so forth. - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcollectioncolumn.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcollectioncolumn.nxdl.xml deleted file mode 100644 index 2720309..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcollectioncolumn.nxdl.xml +++ /dev/null @@ -1,86 +0,0 @@ - - - - - - Subclass of NXelectronanalyser to describe the electron collection column of a - photoelectron analyser. - - - - Scheme of the electron collection lens, i.e. standard, deflector, PEEM, momentum - microscope, etc. - - - - - Voltage applied to the extractor lens - - - - - Current necessary to keep the extractor lens at a set voltage. Variations - indicate leakage, field emission or arc currents to the extractor lens. - - - - - Distance between sample and detector entrance - - - - - Labelling of the lens setting in use. - - - - - The space projected in the angularly dispersive directions, real or reciprocal - - - - - - - - - The magnification of the electron lens assembly. - - - - - The size and position of an aperture inserted in the column, e.g. field aperture - or contrast aperture - - - - - Deflectors in the collection column section - - - - - Individual lenses in the collection column section - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcoordinate_system_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcoordinate_system_set.nxdl.xml deleted file mode 100644 index c2276f3..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcoordinate_system_set.nxdl.xml +++ /dev/null @@ -1,137 +0,0 @@ - - - - - - Container to hold different coordinate systems conventions. - - It is the purpose of this base class to define these conventions and - offer a place to store mappings between different coordinate systems - which are relevant for the interpretation of the data described - by the application definition and base class instances. - - For each Cartesian coordinate system users should use a set of - NXtransformations: - - * These should define the three base vectors. - * The location of the origin. - * The affine transformations which bring each axis of this coordinate system - into registration with the McStas coordinate system. - * Equally, affine transformations should be given for the inverse mapping. - - As an example one may take an experiment or computer simulation where - there is a laboratory (lab) coordinate system, a sample/specimen coordinate - system, a crystal coordinate system, and additional coordinate systems, - which are eventually attached to components of the instrument. - - If no additional transformation is specified in this group or if an - instance of an NXcoordinate_system_set is absent it should be assumed - the so-called McStas coordinate system is used. - - Many application definitions in NeXus refer to this `McStas <https://mailman2.mcstas.org/pipermail/mcstas-users/2021q2/001431.html>`_ coordinate system. - This is a Cartesian coordinate system whose z axis points along the neutron - propagation axis. The systems y axis is vertical up, while the x axis points - left when looking along the z-axis. Thus, McStas is a right-handed coordinate system. - - Within each NXtransformations a depends_on section is required. The depends_on - field specifies if the coordinate system is the root/reference - (which is indicated by writing "." in the depends_on section.) - - - - - A group of transformations which specify: - - * Three base vectors of the coordinate system. - * Origin of the coordinate system. - * A depends_on keyword. Its value can be "." or the name of an - NXtransformations instance which needs to exist in the - NXcoordinate_system_set instance. - * If the coordinate system is the reference one it has to be named - reference. - - In case of having more than one NXtransformations there has to be for - each additional coordinate system, i.e. the one not the reference: - - * A set of translations and rotations which map each base vector to the reference. - * A set of translations and rotations which map each reference base vector - to the coordinate system. - - The NXtransformations for these mappings need to be formatted - according to the descriptions in NXtransformations. - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcorrector_cs.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcorrector_cs.nxdl.xml deleted file mode 100644 index a4c834a..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcorrector_cs.nxdl.xml +++ /dev/null @@ -1,76 +0,0 @@ - - - - - - Corrector for aberrations in an electron microscope. - - Different technology partners use different naming schemes and models - for quantifying the aberration coefficients. - - The corrector in an electron microscope is composed of multiple lenses and - multipole stigmators with vendor-specific details which are often undisclosed. - - - - - Specific information about the concrete alignment procedure which is a - process during which the corrector is configured to enable a calibrated - usage of the microscope. - - - - Discouraged free-text field to add further details about the alignment - procedure. - - - - - The outer tilt angle of the beam in tableau aquisition. - - - - - The exposure time of the single tilt images. - - - - - The factor of enlargement of the apparent size, - not physical size, of an object. - - - - - Place for storing measured or estimated aberrations (for each image or final). - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcs_computer.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcs_computer.nxdl.xml deleted file mode 100644 index b6cd467..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcs_computer.nxdl.xml +++ /dev/null @@ -1,80 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computer science description of a set of computing nodes. - - - - Given name/alias to the computing system, e.g. MyDesktop. - - - - - Name of the operating system, e.g. Windows, Linux, Mac, Android. - - - - Version plus build number, commit hash, or description of an ever - persistent resource where the source code of the program and build - instructions can be found so that the program can be configured in - such a manner that the result file is ideally recreatable yielding - the same results. - - - - - - - Ideally a (globally) unique persistent identifier of the computer, i.e. - the Universally Unique Identifier (UUID) of the computing node. - - - - - - A list of physical processing units (can be multi-core chips). - - - - - A list of physical coprocessor/graphic cards/accelerator units. - - - - - Details about the memory sub-system. - - - - - Details about the I/O sub-system. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml deleted file mode 100644 index fe1707a..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml +++ /dev/null @@ -1,104 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of entries (e.g. number of points or objects). - - - - - Number of bits assumed for the container datatype used. - - - - - Length of mask considering the eventual need for padding. - - - - - Computer science base class for packing and unpacking booleans. - - One use case is processing of object sets (like point cloud data). - When one applies e.g. a spatial filter to a set of points to define which - points are analyzed and which not, it is useful to document which points were - taken. One can store this information in a compact manner with an array of - boolean values. If the value is True the point is taken, else it is not. - - If the points are identified by an array of integer identifiers and an - arbitrary spatial filtering, the boolean array will be filled with True and False - values in an arbitrary manner. Especially when the number of points is large, - for instance several thousands and more, some situations can be more efficiently - stored if one would not store the boolean array but just list the identifiers - of the points taken. For instance if within a set of 1000 points only one point is - taken, it would take (naively) 4000 bits to store the array but only 32 bits - to store e.g. the ID of that taken point. Of course the 4000 bit field is so - sparse that it could be compressed resulting also in a substantial reduction - of the storage demands. Therefore boolean masks are useful compact descriptions - to store information about set memberships in a compact manner. - In general it is true, though, that which representation is best, i.e. - most compact (especially when compressed) depends strongly on occupation of - the array. - - This base class just bookkeeps metadata to inform software about necessary - modulo operations to decode the set membership of each object. This is useful - because the number of objects not necessarily is an integer multiple of the bit depth. - - - - Number of objects represented by the mask. - - - - - Number of bits assumed matching on a default datatype. - (e.g. 8 bits for a C-style uint8). - - - - - The unsigned integer array representing the content of the mask. - If padding is used the padded bits have to be set to 0. - - - - - - - - Link to/or array of identifiers for the objects. The decoded mask is - interpreted consecutively, i.e. the first bit in the mask matches - to the first identifier, the second bit in the mask to the second - identifier and so on and so forth. - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcs_io_obj.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcs_io_obj.nxdl.xml deleted file mode 100644 index eb1e7e1..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcs_io_obj.nxdl.xml +++ /dev/null @@ -1,56 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computer science description of a storage object in an input/output system. - - - - Qualifier for the type of storage medium used. - - - - - - - - - - - Total amount of data which the medium can hold. - - - - - - Given name to the I/O unit. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcs_mm_sys.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcs_mm_sys.nxdl.xml deleted file mode 100644 index d9c6779..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcs_mm_sys.nxdl.xml +++ /dev/null @@ -1,39 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computer science description of a main memory system of a computer. - - - - How much physical memory does the system provide. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcs_prng.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcs_prng.nxdl.xml deleted file mode 100644 index 16d192c..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcs_prng.nxdl.xml +++ /dev/null @@ -1,85 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computer science description of pseudo-random number generator. - - The purpose of such metadata is to identify if exactly the same sequence - can be reproduced, like for a PRNG or not (for a true physically random source). - - - - Different approaches for generating random numbers with a computer exists. - Some use a dedicated physical device where the state is unpredictable (physically). - Some use a mangling of the system clock (system_clock), where also without - additional pieces of information the sequence is not reproducible. - Some use so-called pseudo-random number generator (PRNG) are used. - These are algorithms which yield a deterministic sequence of practically - randomly appearing numbers. These algorithms different in their quality in - how close the resulting sequences are random. - Nowadays one of the most commonly used algorithm is - the MersenneTwister (mt19937). - - - - - - - - - - - Name of the PRNG implementation and version. If such information is not - available or if the PRNG type was set to other the DOI to the publication - or the source code should be given. - - - - Version and build number, or commit hash. - - - - - - Parameter of the PRNG controlling its initialization and thus the specific - sequence of numbers it generates. - - - - - - Number of initial draws from the PRNG which are discarded in an effort - to equilibrate the sequence and make it thus to statistically more random. - If no warmup was performed or if warmup procedures are unclear, - users should set the value to zero. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcs_profiling.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcs_profiling.nxdl.xml deleted file mode 100644 index 97105a1..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcs_profiling.nxdl.xml +++ /dev/null @@ -1,149 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computer science description for summary performance/profiling data of an application. - - Performance monitoring and benchmarking of software is a task where questions - can be asked at various levels of detail. In general, there are three main - contributions to performance: - - * Hardware capabilities and configuration - * Software configuration and capabilities - * Dynamic effects of the system in operation and the system working together - with eventually multiple computers, especially when these have to exchange - information across a network. - - At the most basic level users may wish to document how long e.g. a data - analysis with a scientific software (app). - A frequent idea is here to judge how critical the effect is on the workflow - of the scientists, i.e. is the analysis possible in a few seconds or would it - take days if I were to run this analysis on a comparable machine. In this case, - mainly the order of magnitude is relevant, as well as how this can be achieved - with using parallelization (i.e. reporting the number of CPU and GPU resources - used, the number of processes and/or threads, and basic details about the - computing node/computer. - - At more advanced levels benchmarks may go as deep as detailed temporal tracking - of individual processor instructions, their relation to other instructions, the - state of call stacks, in short eventually the entire app execution history - and hardware state history. Such analyses are mainly used for performance - optimization as well as for tracking bugs and other development purposes. - Specialized software exists which documents such performance data in - specifically-formatted event log files or databases. - - This base class cannot and should not replace these specific solutions. - Instead, the intention of the base class is to serve scientists at the - basic level to enable simple monitoring of performance data and log profiling - data of key algorithmic steps or parts of computational workflows, so that - these pieces of information can guide users which order of magnitude differences - should be expected or not. - - Developers of application definitions should add additional fields and - references to e.g. more detailed performance data to which they wish to link - the metadata in this base class. - - - - - Path to the directory from which the tool was called. - - - - - Command line call with arguments if applicable. - - - - - ISO 8601 time code with local time zone offset to UTC information - included when the app was started. - - - - - ISO 8601 time code with local time zone offset to UTC information - included when the app terminated or crashed. - - - - - Wall-clock time how long the app execution took. This may be in principle - end_time minus start_time; however usage of eventually more precise timers - may warrant to use a finer temporal discretization, - and thus demand a more precise record of the wall-clock time. - - - - - Qualifier which specifies with how many nominal processes the app was - invoked. The main idea behind this field, for instance for app using a - Message Passing Interface parallelization is to communicate how many - processes were used. - - For sequentially running apps number_of_processes and number_of_threads - is 1. If the app uses exclusively GPU parallelization number_of_gpus - can be larger than 1. If no GPU is used number_of_gpus is 0 even though - the hardware may have GPUs installed, thus indicating these were not - used though. - - - - - Qualifier with how many nominal threads were accessible to the app at - runtime. Specifically here the maximum number of threads used for the - high-level threading library used (e.g. OMP_NUM_THREADS), posix. - - - - - Qualifier with how many nominal GPUs the app was invoked at runtime. - - - - - - A collection with one or more computing nodes each with own resources. - This can be as simple as a laptop or the nodes of a cluster computer. - - - - - A collection of individual profiling event data which detail e.g. how - much time the app took for certain computational steps and/or how much - memory was consumed during these operations. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcs_profiling_event.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcs_profiling_event.nxdl.xml deleted file mode 100644 index 195dee8..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXcs_profiling_event.nxdl.xml +++ /dev/null @@ -1,95 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of processes. - - - - - Computer science description of a profiling event. - - - - ISO 8601 time code with local time zone offset to UTC information - included when the event tracking started. - - - - - ISO 8601 time code with local time zone offset to UTC information - included when the event tracking ended. - - - - - Free-text description what was monitored/executed during the event. - - - - - Wall-clock time how long the event took. This may be in principle - end_time minus start_time; however usage of eventually more precise timers - may warrant to use a finer temporal discretization, - and thus demand a more precise record of the wall-clock time. - Elapsed time may contain time portions where resources were idling. - - - - - Number of processes used (max) during the execution of this event. - - - - - Number of threads used (max) during the execution of this event. - - - - - Number of GPUs used (max) during the execution of this event. - - - - - Maximum amount of virtual memory allocated per process during the event. - - - - - - - - Maximum amount of resident memory allocated per process during the event. - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXcsg.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXcsg.nxdl.xml index 9416202..6dd48ec 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXcsg.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXcsg.nxdl.xml @@ -3,7 +3,7 @@ - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Digital-to-analog converter component/integrated circuit. - - - - TBD. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXdeflector.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXdeflector.nxdl.xml deleted file mode 100644 index 34a5af5..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXdeflector.nxdl.xml +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - Deflectors as they are used e.g. in an electron analyser. - - - - Qualitative type of deflector with respect to the number of pole pieces - - - - - - - - - - - Colloquial or short name for the deflector. For manufacturer names and - identifiers use ``NXfabrication`` and ``identifierNAME``. - - - - - Excitation voltage of the deflector. For dipoles it is a single number. For - higher orders, it is an array. - - - - - Excitation current of the deflector. For dipoles it is a single number. For - higher orders, it is an array. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXdelocalization.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXdelocalization.nxdl.xml index f061f7f..a555db2 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXdelocalization.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXdelocalization.nxdl.xml @@ -2,9 +2,9 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -41,30 +41,30 @@ Number of atoms in the whitelist. - + Number of isotopes in the whitelist. - Base class to describe the delocalization of point-like objects on a grid. + Base class of the configuration and results of a delocalization algorithm. - Such a procedure is for instance used in image processing and e.g. atom probe - microscopy (APM) to discretize a point cloud onto a grid to enable e.g. - computing of point density, composition, or concentration values, obtain - scalar fields, and compute gradients of these fields. + Delocalization is used to distribute point-like objects on a grid to obtain + e.g. smoother count, composition, or concentration values of scalar fields + and compute gradients of these fields. - + - Reference or link to the grid on which the delocalization is applied. + Details about the grid on which the delocalization is applied. - - - - Reference or link to the points which are delocalized on the grid. - - + + - - - The weighting model specifies how mark data are mapped to a weight per point. - For atom probe microscopy (APM) as an example, different models are used which - account differently for the multiplicity of an ion/atom: - - * default, points all get the same weight 1.; - for APM this is equivalent to ion species - * atomic_decomposition, points get as much weight as they have atoms - of a type in element_whitelist, - * isotope_decomposition, points get as much weight as they have - isotopes of a type in isotope_whitelist. - - This description shows an example that could be reinterpreted for - similar such data processing steps in other fields of science. - - - - - - - - - - - A list of elements (via proton number) to consider for the atomic_decomposition - weighting model. Elements must exist in the periodic table of elements. - - - - - - - - A list of isotopes to consider for the isotope_decomposition weighting model. - Isotopes must exist in the nuclid table. Entries in the fastest changing - dimension should be the pair of proton (first entry) and neutron number - (second entry). - - - - - - - + - Attribute data for each member of the point cloud. For APM these are the - ion species labels generated via ranging. The number of mark data per - point is 1 in the case for atom probe. + The weighting model specifies how mark data are mapped to a weight per + point/object. - - - - - - - - Weighting factor with which the integrated intensity per grid cell is - multiplied specifically for each point. For APM the weight are positive - integer values, specifically the multiplicity of the ion, - according to the details of the weighting_model. - - + + + As an example from the research field of atom probe points/objects are (molecular) ions. + Different methods are used for weighting ions: + + * default, points get all the same weight 1., which for atom probe is equivalent + to (molecular) iontype-based delocalization. + * element, points get as much weight as they have atoms representing a nuclide + with a proton number that is matching to a respective entry in whitelist. + In atom probe jargon, this means atomic_decomposition. + * isotope, points get as much weight as they have atoms representing a nuclides + from a respective entry in whitelist. + In atom probe jargon, this means isotope_decomposition. + + + + + + + + + + + + + + + + A list of nuclides based on which to evaluate the weight. Nuclides need to exist in the nuclide table. + Values are nuclide (isotope) hash values using the hashing rule defined in :ref:`NXatom`. + + + + + + + + Attribute data for each member of the point cloud. For APM these are the + iontypes generated via ranging. The number of mark data per point is 1 + in the case for atom probe. + + + + + + + + + Weighting factor with which the integrated intensity per grid cell is + multiplied specifically for each point/object. For APM the weight are + positive integer values, specifically the multiplicity of the ion, + according to the details of the weighting_method. + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXdispersion.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXdispersion.nxdl.xml index b581fb8..06d8152 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXdispersion.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXdispersion.nxdl.xml @@ -23,13 +23,13 @@ --> - A dispersion denoting a sum of different dispersions. - All NXdispersion_table and NXdispersion_function groups will be added together - to form a single dispersion. + A dispersion denoting a sum of different dispersions. + All NXdispersion_table and NXdispersion_function groups will be added together + to form a single dispersion. - The name of the composite model. + The name of the composite model. diff --git a/src/nexusformat/definitions/contributed_definitions/NXdispersion_function.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXdispersion_function.nxdl.xml index 4aac709..9fd6025 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXdispersion_function.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXdispersion_function.nxdl.xml @@ -73,13 +73,13 @@ The energy unit used in the formula. The field value is a scaling factor for the units attribute. - It is recommeded to set the field value to 1 and carry all the unit + It is recommended to set the field value to 1 and carry all the unit scaling information in the units attribute. - The identifier useed to represent wavelength + The identifier used to represent wavelength in the formula. It is recommended to use `lambda`. @@ -87,7 +87,7 @@ The wavelength unit used in the formula. The field value is a scaling factor for the units attribute. - It is recommeded to set the field value to 1 and carry all the unit + It is recommended to set the field value to 1 and carry all the unit scaling information in the units attribute. diff --git a/src/nexusformat/definitions/contributed_definitions/NXdispersion_repeated_parameter.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXdispersion_repeated_parameter.nxdl.xml index 871ff09..f4913ca 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXdispersion_repeated_parameter.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXdispersion_repeated_parameter.nxdl.xml @@ -25,30 +25,30 @@ - The number of parameter repetitions + The number of parameter repetitions - A repeated parameter for a dispersion function + A repeated parameter for a dispersion function - The name of the parameter + The name of the parameter - A description of what this parameter represents + A description of what this parameter represents - A unit array associating a unit with each parameter. - The first element should be equal to values/@unit. - The values should be SI interpretable standard units - with common prefixes (e.g. mikro, nano etc.) or their - short-hand notation (e.g. nm, mm, kHz etc.). + A unit array associating a unit with each parameter. + The first element should be equal to values/@unit. + The values should be SI interpretable standard units + with common prefixes (e.g. mikro, nano etc.) or their + short-hand notation (e.g. nm, mm, kHz etc.). @@ -56,7 +56,7 @@ - The value of the parameter + The value of the parameter diff --git a/src/nexusformat/definitions/contributed_definitions/NXdispersion_single_parameter.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXdispersion_single_parameter.nxdl.xml index 59b3878..d5d6b4c 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXdispersion_single_parameter.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXdispersion_single_parameter.nxdl.xml @@ -23,21 +23,21 @@ --> - A single parameter for a dispersion function + A single parameter for a dispersion function - The name of the parameter + The name of the parameter - A description of what this parameter represents + A description of what this parameter represents - The value of the parameter + The value of the parameter diff --git a/src/nexusformat/definitions/contributed_definitions/NXdispersion_table.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXdispersion_table.nxdl.xml index f0a0851..48897dc 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXdispersion_table.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXdispersion_table.nxdl.xml @@ -24,25 +24,25 @@ - The symbols in this schema to denote the dimensions + The symbols in this schema to denote the dimensions - The number of energy and dielectric function points + The number of energy and dielectric function points - A dispersion table denoting energy, dielectric function tabulated values. + A dispersion table denoting energy, dielectric function tabulated values. - The name of this dispersion model. + The name of this dispersion model. - The sign convention being used (n + or - ik) + The sign convention being used (n + or - ik) @@ -51,9 +51,9 @@ - The wavelength array of the tabulated dataset. - This is essentially a duplicate of the energy field. - There should be one or both of them present. + The wavelength array of the tabulated dataset. + This is essentially a duplicate of the energy field. + There should be one or both of them present. @@ -61,9 +61,9 @@ - The energy array of the tabulated dataset. - This is essentially a duplicate of the wavelength field. - There should be one or both of them present. + The energy array of the tabulated dataset. + This is essentially a duplicate of the wavelength field. + There should be one or both of them present. @@ -71,7 +71,7 @@ - The refractive index array of the tabulated dataset. + The refractive index array of the tabulated dataset. @@ -79,7 +79,7 @@ - The dielectric function of the tabulated dataset. + The dielectric function of the tabulated dataset. diff --git a/src/nexusformat/definitions/contributed_definitions/NXdispersive_material.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXdispersive_material.nxdl.xml index e4e4118..1726fc1 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXdispersive_material.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXdispersive_material.nxdl.xml @@ -23,103 +23,90 @@ --> - NXdispersion + An application definition for describing a dispersive material. - - An application definition for a dispersive material. - - Version number to identify which definition of this application definition was - used for this entry/data. + Version number to identify which definition of this application definition was + used for this entry/data. - + - URL where to find further material (documentation, examples) relevant to the - application definition + URL where to find further material (documentation, examples) relevant to the + application definition - - Name of the program used for creating this dispersion - - - Version of the program used - - - Date and time of creating this dispersion. - - List of comma-separated elements from the periodic table - that are contained in the sample. - If the sample substance has multiple components, all - elements from each component must be included in `atom_types`. + List of comma-separated elements from the periodic table + that are contained in the sample. + If the sample substance has multiple components, all + elements from each component must be included in `atom_types`. - The colloquial name of the material, e.g. graphite or diamond for carbon. + The colloquial name of the material, e.g. graphite or diamond for carbon. - The phase of the material + The phase of the material - + - - Additional information about the phase if the - material phase is other. + Additional information about the phase if the + material phase is not from the enumerated list. - This field may be used to denote additional phase information, - such as crystalin phase of a crystal (e.g. 4H or 6H for SiC) or - if a measurement was done on a thin film or bulk material. + This field may be used to denote additional phase information, + such as crystalline phase of a crystal (e.g. 4H or 6H for SiC) or + if a measurement was done on a thin film or bulk material. - Denotes whether the dispersion is calculated or derived from an experiment + Denotes whether the dispersion is calculated or derived from an experiment - + - A text description of this reference, e.g. - `E. Example et al, The mighty example, An example journal 50 (2023), 100` + A text description of this reference, e.g. + `E. Example et al, The mighty example, An example journal 50 (2023), 100` - The dispersion along the optical axis of the material. - This should be the only dispersion available for isotropic materials. - For uniaxial materials this denotes the ordinary axis. - For biaxial materials this denotes the x axis or epsilon 11 tensor element - of the diagionalized permittivity tensor. + The dispersion along the optical axis of the material. + This should be the only dispersion available for isotropic materials. + For uniaxial materials this denotes the ordinary axis. + For biaxial materials this denotes the x axis or epsilon 11 tensor element + of the diagonalized permittivity tensor. @@ -155,13 +142,13 @@ - This should only be filled for biaxial materials. - It denotes the epsilon 22 direction of the diagionalized - permittivity tensor. + This should only be filled for biaxial materials. + It denotes the epsilon 22 direction of the diagonalized + permittivity tensor. - The name of this dispersion model. + The name of this dispersion model. @@ -193,14 +180,14 @@ - This should only be filled for uniaxial or biaxial materials. - For uniaxial materials this denotes the extraordinary axis. - For biaxial materials this denotes the epsilon 33 tensor element - of the diagionalized perimittivty tensor. + This should only be filled for uniaxial or biaxial materials. + For uniaxial materials this denotes the extraordinary axis. + For biaxial materials this denotes the epsilon 33 tensor element + of the diagonalized permittivity tensor. - The name of this dispersion model. + The name of this dispersion model. @@ -231,4 +218,4 @@ - + \ No newline at end of file diff --git a/src/nexusformat/definitions/contributed_definitions/NXebeam_column.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXebeam_column.nxdl.xml deleted file mode 100644 index 3edca25..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXebeam_column.nxdl.xml +++ /dev/null @@ -1,103 +0,0 @@ - - - - - - - Container for components to form a controlled beam in electron microscopy. - - - - - The source which creates the electron beam. - - - - Voltage relevant to compute the energy of the electrons - immediately after they left the gun. - - - - - Type of radiation. - - - - - - - - Emitter type used to create the beam. - - If the emitter type is other, give further details - in the description field. - - - - - - - - - - - Material of which the emitter is build, e.g. the filament material. - - - - - - Ideally, a (globally) unique persistent identifier, link, - or text to a resource which gives further details. - - - - - - Affine transformation which detail the arrangement in the - microscope relative to the optical axis and beam path. - - - - - - - - - - - A sensor used to monitor an external or internal condition. - - - - - Individual ocharacterization results for the position, shape, - and characteristics of the electron beam. - - NXtransformations should be used to specify the location - of the position at which the beam was probed. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXelectronanalyser.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXelectronanalyser.nxdl.xml deleted file mode 100644 index 8b2bc82..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXelectronanalyser.nxdl.xml +++ /dev/null @@ -1,139 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays - - - - Number of fast axes (axes acquired symultaneously, without scanning a pysical - quantity) - - - - - Number of slow axes (axes acquired scanning a pysical quantity) - - - - - Subclass of NXinstrument to describe a photoelectron analyser. - - - - Free text description of the type of the detector - - - - - Name or model of the equipment - - - - Acronym or other shorthand name - - - - - - Energy resolution of the electron analyser (FWHM of gaussian broadening) - - - - - Momentum resolution of the electron analyser (FWHM) - - - - - Angular resolution of the electron analyser (FWHM) - - - - - Spatial resolution of the electron analyser (Airy disk radius) - - - - - List of the axes that are acquired simultaneously by the detector. - These refer only to the experimental variables recorded by the electron analyser. - Other variables such as temperature, manipulator angles etc. are labeled as fast or slow in the data. - - .. csv-table:: Examples - :header: "Mode", "fast_axes", "slow_axes" - - Hemispherical in ARPES mode, "['energy', 'kx']","" - "Hemispherical with channeltron, sweeping energy mode", "", [\"energy\"] - "Tof", "['energy', 'kx', 'ky']","" - "Momentum microscope, spin-resolved", "['energy', 'kx', 'ky']", "['spin up-down', 'spin left-right']" - - Axes may be less abstract than this, i.e. ['detector_x', 'detector_y']. - If energy_scan_mode=sweep, fast_axes: ['energy', 'kx']; slow_axes: ['energy'] is allowed. - - - - - - - - List of the axes that are acquired by scanning a physical parameter, listed in - order of decreasing speed. See fast_axes for examples. - - - - - - - - Describes the electron collection (spatial and momentum imaging) column - - - - - Describes the energy dispersion section - - - - - Describes the spin dispersion section - - - - - Describes the electron detector - - - - - Deflectors outside the main optics ensambles described by the subclasses - - - - - Individual lenses outside the main optics ensambles described by the subclasses - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXelectrostatic_kicker.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXelectrostatic_kicker.nxdl.xml index 16d9bfe..c36c4a2 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXelectrostatic_kicker.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXelectrostatic_kicker.nxdl.xml @@ -26,35 +26,35 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd" > -definition for a electrostatic kicker. +Base class for an electrostatic kicker. -extended description of the kicker. +Extended description of the kicker. -define position of beamline element relative to production target +Define position of beamline element relative to production target -kicker timing as defined by ``description`` attribute +Kicker timing as defined by ``description`` attribute -current set on supply. +Current set on supply. -current read from supply. +Current read from supply. -volage set on supply. +Voltage set on supply. -voltage read from supply. +Voltage read from supply. diff --git a/src/nexusformat/definitions/contributed_definitions/NXellipsometry.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXellipsometry.nxdl.xml deleted file mode 100644 index b082b31..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXellipsometry.nxdl.xml +++ /dev/null @@ -1,357 +0,0 @@ - - - - - - - - - - - Variables used throughout the document, e.g. dimensions or parameters. - - - - Length of the spectrum array (e.g. wavelength or energy) of the measured - data. - - - - - Number of sensors used to measure parameters that influence the sample, - such as temperature or pressure. - - - - - Number of measurements (1st dimension of measured_data array). This is - equal to the number of parameters scanned. For example, if the experiment - was performed at three different temperatures and two different pressures - N_measurements = 2*3 = 6. - - - - - Number of detection angles of the beam reflected or scattered off the - sample. - - - - - Number of angles of incidence of the incident beam. - - - - - Number of observables that are saved in a measurement. e.g. one for - intensity, reflectivity or transmittance, two for Psi and Delta etc. This - is equal to the second dimension of the data array 'measured_data' and the - number of column names. - - - - - Number of time points measured, the length of NXsample/time_points - - - - - Ellipsometry, complex systems, up to variable angle spectroscopy. - - Information on ellipsometry is provided, e.g. in: - - * H. Fujiwara, Spectroscopic ellipsometry: principles and applications, - John Wiley & Sons, 2007. - * R. M. A. Azzam and N. M. Bashara, Ellipsometry and Polarized Light, - North-Holland Publishing Company, 1977. - * H. G. Tompkins and E. A. Irene, Handbook of Ellipsometry, - William Andrew, 2005. - - Open access sources: - - * https://www.angstromadvanced.com/resource.asp - * https://pypolar.readthedocs.io/en/latest/ - - Review articles: - - * T. E. Jenkins, "Multiple-angle-of-incidence ellipsometry", - J. Phys. D: Appl. Phys. 32, R45 (1999), - https://doi.org/10.1088/0022-3727/32/9/201 - * D. E. Aspnes, "Spectroscopic ellipsometry - Past, present, and future", - Thin Solid Films 571, 334-344 (2014), - https://doi.org/10.1016/j.tsf.2014.03.056 - * R. M. A. Azzam, "Mueller-matrix ellipsometry: a review", - Proc. SPIE 3121, Polarization: Measurement, Analysis, and Remote Sensing, - (3 October 1997), - https://doi.org/10.1117/12.283870 - * E. A. Irene, "Applications of spectroscopic ellipsometry to microelectronics", - Thin Solid Films 233, 96-111 (1993), - https://doi.org/10.1016/0040-6090(93)90069-2 - * S. Zollner et al., "Spectroscopic ellipsometry from 10 to 700 K", - Adv. Opt. Techn., (2022), - https://doi.org/10.1515/aot-2022-0016 - - - - This is the application definition describing ellipsometry experiments. - - Such experiments may be as simple as identifying how a reflected - beam of light with a single wavelength changes its polarization state, - to a variable angle spectroscopic ellipsometry experiment. - - The application definition defines: - - * elements of the experimental instrument - * calibration information if available - * parameters used to tune the state of the sample - * sample description - - - - An application definition for ellipsometry. - - - - Version number to identify which definition of this application - definition was used for this entry/data. - - - - - URL where to find further material (documentation, examples) relevant - to the application definition. - - - - - - - - - An optional free-text description of the experiment. - - However, details of the experiment should be defined in the specific - fields of this application definition rather than in this experiment - description. - - - - - Specify the type of ellipsometry. - - - - - - - - - - - - - - Properties of the ellipsometry equipment. - - - - Name of the company which build the instrument. - - - - - ISO8601 date when the instrument was constructed. - UTC offset should be specified. - - - - - - Commercial or otherwise defined given name of the program that was - used to generate the result file(s) with measured data and metadata. - This program converts the measured signals to ellipsometry data. If - home written, one can provide the actual steps in the NOTE subfield - here. - - - - - - What type of ellipsometry was used? See Fujiwara Table 4.2. - - - - - - - - - - - - - - - - - - - Define which element rotates, e.g. polarizer or analyzer. - - - - - - - - - - - - Specify the used light source. Multiple selection possible. - - - - - - - - - - - - - If focussing probes (lenses) were used, please state if the data - were corrected for the window effects. - - - - Were the recorded data corrected by the window effects of the - focussing probes (lenses)? - - - - - Specify the angular spread caused by the focussing probes. - - - - - - Properties of the detector used. Integration time is the count time - field, or the real time field. See their definition. - - - - - Properties of the rotating element defined in - 'instrument/rotating_element_type'. - - - - Define how many revolutions of the rotating element were averaged - for each measurement. If the number of revolutions was fixed to a - certain value use the field 'fixed_revolutions' instead. - - - - - Define how many revolutions of the rotating element were taken - into account for each measurement (if number of revolutions was - fixed to a certain value, i.e. not averaged). - - - - - Specify the maximum value of revolutions of the rotating element - for each measurement. - - - - - - The spectroscope element of the ellipsometer before the detector, - but often integrated to form one closed unit. Information on the - dispersive element can be specified in the subfield GRATING. Note - that different gratings might be used for different wavelength - ranges. The dispersion of the grating for each wavelength range can - be stored in grating_dispersion. - - - - - - - - Was the backside of the sample roughened? Relevant for infrared - ellipsometry. - - - - - - - Select which type of data was recorded, for example Psi and Delta - (see: https://en.wikipedia.org/wiki/Ellipsometry#Data_acquisition). - It is possible to have multiple selections. Data types may also be - converted to each other, e.g. a Mueller matrix contains N,C,S data - as well. This selection defines how many columns (N_observables) are - stored in the data array. - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXem.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXem.nxdl.xml deleted file mode 100644 index ad33f94..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXem.nxdl.xml +++ /dev/null @@ -1,2034 +0,0 @@ - - - - - - - Characterization of a sample during a session on an electron microscope. - - **The idea and aim of NXem**: - Electron microscopy (EM) research, whether it be performed with scanning electron - microscope (SEM) or transmission electron microscope (TEM) instruments, uses - versatile tools for preparing and characterizing samples and specimens. - The term specimen is considered a synonym for sample in this application definition. - A specimen is a physical portion of material that is studied/characterized during - the microscope session, eventually in different places on the specimen surface, - illuminating the surface layers or shining through thin specimens. - These places are named regions of interest (ROIs). - - Fundamentally, an electron microscope is an electron accelerator. - Experimentalists use it in sessions during which they characterize as well as - prepare specimens. This application definition describes data and metadata about - processes and characterization tasks applied to one specimen. - The application definition focuses on the usage of EM in materials research. - The application definition design makes it in principle applicable also in - cryo-EM on biomaterials. - - Multiple specimens have to be described with multiple :ref:`NXentry` instances. - - **Electron microscopes motivate the development of a comprehensive data schema:** - There are research groups who use an EM in a manner where it is exclusively - operated by a single, instrument-responsible scientists or a team of scientists. - These users may perform analyses for other users as a service task, especially - in large research facility settings. Oftentimes, though, and especially for - cutting-edge instruments, the scientists guide the process and maybe even control - the microscope. Instruments are usually controlled on-premises but also more - and more functionalities for remote control have become available. - Scientists oftentimes can ask technicians for support. In all cases, - these people are considered users. Users might have different - roles though. - - The rational behind a common EM schema rather than making separate schemas - for SEM or TEM are primarily the key similarities of SEM and TEM - instruments: - - Both type of instruments have electro-magnetic lenses. These may differ in - design, alignment, number, and level of corrected for aberrations. - As an obvious difference, a TEM is mainly used for measuring the transmitted - electron beam. This calls for using a different lens setup and relative - placement of the specimen in the lens setup. Also TEM specimens are - substantially thinner than specimens characterized with SEM to enable an - illumination through the specimen. This offers capabilities for probing of - additional physical mechanisms of electron-matter interaction which are - unavailable in SEMs. - - Nevertheless, both types of electron microscopes use detector systems which - measure different types of signals that originate from the same set of - radiation/specimen interactions. Often these detectors have a similar design - and technology or are even used both in SEMs and TEMs. - - **A comprehensive schema instead of specific SEM or TEM schemas**: - Given these physical and technical differences, different instruments have - been developed. This led to a coexistence of two broad interacting - communities: SEM and TEM users. From a data science perspective, we - acknowledge that the more specific a research question is and the narrower it - is the addressed circle of users which develops or uses schemas for research - data management (RDM) with EM, the more understandable it is that scientists - of either community (or sub-community) ask for designing method-specific schemas. - - Researchers who have a single (main) microscope of some vendor in their lab, - may argue they need an NXem_vendor_name schema or an NXem_microscope_name or - an NXem_sem or a NXem_tem schema. - Scientists exclusively working with one technique or type of signal probed - (X-rays, electrons) may argue they wish to be pragmatic and store only - what is immediately relevant for their particular technique and - research questions. In effect, they may advocate for method-specific - schemas such as NXem_ebsd, NXem_eels, NXem_edx, or NXem_imaging. - - However, the history of electron microscopy has shown that these activities led - to a zoo of schemas and vocabulary, with implementation in many data and file formats, - difficult to make interoperable. Instead of trying to maintain this, we would like - to advocate that the `FAIR principles <https://doi.org/10.1038/sdata.2016.18>`_ - should guide all decisions how data and metadata should be stored. - - EM instruments, software, and research are moving targets. Consequently, - there is a key challenge and inconvenience with having many different schemas - with associated representations of data and metadata: Each combination of - schemas or an interoperable-made handshake between two file formats or software - packages has to be maintained by software developers. This counts especially - when data should be processed interoperably between software packages. - - This brings two problems: Many software tools and parsers for the handshaking - between tools have to be maintained. This can result in usage of different - terminology, which in turn results in representations and connections made - between different data representations and workflows that are not - machine-actionable. - `There are community efforts to harmonize the terminology. <https://gitlab.hzdr.de/em_glossary/em_glossary>`_ - - **The advantage of working towards a common vocabulary and representation**: - A common vocabulary can serve interoperability as developers of schemas and - scientists can reuse for instance these terms, thus supporting interoperability. - Ideally, scientists specialize an application definition only for the few very - specific additional quantities of their instruments and techniques. This is - better than reimplementing the wheel for descriptions of EM instruments. - This route of more standardization can support the EM community in that it - removes the necessity for having to maintain a very large number of schemas. - - Aiming for more standardization, i.e. a lower number of schemas rather than - a single standard for electron microscopy is a compromise that can serve - academia and industry as it enables a focusing of software development - efforts on those schemas, on fixing and discussing them, and on harmonizing - their common vocabulary. These activities can be specifically relevant also - for technology partners building EM hard- and software as it improves the - longevity of certain schemas; and thus can help with incentivizing them to support - the community with implementing support for such schemas into their applications. - - In effect, everybody can gain from this as it will likely reduce the cases - in which scientists have to fix bugs in making their own tools compliant and - interoperable with tools of their colleagues and the wider community. - - The here proposed NXem application definition offers modular components - (EM-research specific base classes) for defining schemas for EM research. - Thereby, NXem can be useful to extends top-level ontologies towards a domain- - and method-specific ontology for electron microscopy as it is used for - materials research. - - Working towards a common vocabulary is a community activity that profits from - everybody reflecting in detail whether certain terms they have used in the past - are not eventually conceptually similar if not the same as what this application - definition and its base classes provide. We are happy for receiving your feedback. - - **Addressing the generality versus specificity challenge**: - It is noteworthy to understand that (not only for NeXus), schemas differ - already if at least one field is required in one version of the schema, - but it is set optional in another schema. If group(s), field(s), or - attributes are removed or added, or even a docstring is changed, schemas can - become inconsistent. It is noteworthy to mention that the idea of a NeXus application - definition serves as a contract between a data provider and a data consumer. - Providers can be the software of a specific microscopes or users with specific - analysis needs. Consumers can be again specific software tools, like vendor - software for controlling the instrument or a scientific software for doing - artificial intelligence analyses on EM data). Such changes of a schema lead - to new versions. - - **Verification of constraints and conditions**: - Tools like NeXus do not avoid or protect against all such possible inconsistencies; - however NeXus offers a mechanism and toolset, through which schemas can be - documented and defined. In effect, having an openly documented - (at a case-specific level of technical detail) schema is a necessary but alone - not a sufficient step to take EM research on a route of machine-actionable - and interoperable FAIR data. - - This stresses again the fundamental and necessary role of working towards - a common vocabulary and, with a longer perspective in mind, a machine-actionable - knowledge representation and verification engine. So far many conditions and - requirements are formulated in the docstrings of the respective entries of - the application definition. - - **NXem takes a key step towards standardization of EM data schemas**. - It offers a controlled vocabulary and set of relations between concepts and - enables the description of the data which are collected for research with - electron microscopes. To be most efficient and offering reusability, the NXem - application definition should be understood as a template that one should - ideally use as is. NXem can be considered a base for designing more specialized - definitions. These should ideally be prefixed with NXem_method (e.g. NXem_ebsd). - - **The use of NXem should be as follows:** - Offspring application definitions should not remove groups but leave these - optional or, even better, propose changes to NXem. - - A particular challenge with electron microscopes as physical instruments are - their dynamics. To make EM data understandable, repeatable, and eventually - corresponding experiments reproducible in general requires a documentation - of the spatio-temporal dynamics of the instrument in its environment. - It is questionable to which level such a reproducibility is possible with EM - at all considering beam damage, effects of the environment, and other not - exactly quantifiable influences. - While this points to the physical limitations there are also practical and - economical constraints on how completely EM research can be documented: - For most commercial systems there is a specific accessibility beyond which - detailed settings like lens excitations and low-level hardware settings - may not be retrievable as technology partners have a substantiated interest in - finding a compromise between being open to their users and securing their - business models. - - By design, EM experiments illuminate the specimen with electrons as a - consequence of which the specimen changes if not may get destroyed. - As such, repeatability of numerical processing and clear descriptions of - procedures and system setups should be addressed first. - - If especially a certain simulation package needs a detailed view of the - geometry of the lens system and its excitations during the course of the - experiment, it is difficult to fully abstract the technical details of the - hardware into a set of names for fields and groups that make for a compromise - between clarity but being system-agnostic at the same time. - Settings of apertures are an example where aperture modes are in most cases - aliases behind which there is a set of very detailed settings specific to the - software and control units used. These settings are difficult to retrieve, - are not fully documented by technology partners. This simplification for - users of microscopes makes experiments easier understandable. - On the flipside these subtilities limit the opportunities of especially open- - source developments to make data schemas covering enough for general usage and - specific enough and sufficiently detailed to remain useful for - research by electron microscopy domain experts. - - Instead, currently it is for the docstring to specify what is conceptually - eventually behind such aliases. The design rule we followed while drafting - this NXem application definition and base classes is that there are numerous - (technical) details about an EM which may warrant a very detailed technical - disentangling of settings and reflection of numerous settings as deeply - nested groups, fields and attributes. An application definition can offer a - place to hold these nested representations; however as discussed - at the cost of generality. - - Which specific details matter for answering scientific research questions is - a difficult question to answer by a single team of scientists, especially - if the application definition is to speak for a number of vendors. What makes - it especially challenging is when the application definition is expected to - hold all data that might be of relevance for future questions. - - We are skeptical if there is one such representation that can fulfill all these - aims and interest, while remaining at the same time approachable and executable - by a large number of scientists in a community. However, we are also convinced - that this is not a reason to accept the status quo of having a very large set - of oftentimes strongly overlapping and redundant schemas. - - NXem is our proposal to motivate the EM community to work towards more - standardization and discussion of what constitutes data, i.e. metadata, - numerical and categorical data in research with electron microscopes. We found - that existent terminology can be encoded into a more controlled vocabulary. - - We have concluded that despite all these details of current EM research with - SEM, TEM, and focused-ion beam instruments, there a clearly identifiable - common components and generalizable settings of EM research use cases. - Therefore, - - **This application definition has the following components at the top-level:** - - * Each signal, such as a spectrum or image taken at the microscope, should - have an associated time-zone-aware time stamp and report of the specific - settings of the microscope at that point in time when the image was taken. - This is why instances of :ref:`NXevent_data_em` have their own em_lab section. - The reason is that EMs can be highly dynamic, used to illuminate the specimen - differently or show drift during signal acquisition, to name but a few effects. - What constitutes a single EM experiment/measurement? - This can be the collecting of a single diffraction pattern with a scanning TEM (STEM), - taking of a secondary electron image for fracture analysis, taking a set of - EBSD line scans and/or surface mappings in an SEM, or the ion-beam-milling of a - specimen in preparation for e.g. an atom probe experiment. - * :ref:`NXmonitor`; - instances to keep track of time-dependent quantities - pertaining to specific components of the instrument. - Alternatively, NXevent_data_em instances can be used to store - time-zone-aware dates of the components, which is - relevant for documenting as exactly as practically possible settings - when images and spectra were taken. - * :ref:`NXinstrument`; - conceptually this is a container to store an arbitrary level of detail of the - technical components of the microscope as a device and the lab in which - the microscope is operated. - * :ref:`NXuser`; - conceptually, this is a set with at least one NXuser instance which details - who operated or performed the measurement. Additional NXusers can be - referred to in an NXevent_data_em instance to store - individualized details of who executed an event of data acquisition or processing. - * :ref:`NXevent_data_em` instances as an NXevent_data_em_set; - each NXevent_data_em instance is a container to group specific details - about the state of the microscope when a measurement was taken and - relevant data and eventual processing steps were taken (on-the-fly). - * :ref:`NXdata`; at the top-level, this is a place for documenting available - default plottable data. A default plottable can be useful for research data - management systems to show a visual representation of some - aspect of the content of the EM session. - Default plottables are not intended to serve every possible analysis and - visualization demand but are instead a preview. We made this choice - because what constitutes a useful default plot is often a matter of interpretation, - somewhat of personal taste, and community standards. In effect, default - plottables are case- and method-specific. - - Usually a session at a microscope is used to collect multiple signals. - Examples for possible default plottables could be arbitrarily taken secondary, - back-scattered, electron image, diffraction pattern, EELS spectra, composition, - or orientation mappings to name but a few. - - **There are a few design choices to consider with sub-ordinate groups:** - - * Images and spectra should be stored as :ref:`NXimage_set` and :ref:`NXspectrum_set` - instances to hold data at the earliest possible step in the computational - processing (which is usually performed with the microscope control and or - integrated analysis software). The formatting of the NXdata groups enables the - display of image and spectra with web technology visualization software. - * When two- and three-dimensional geometric primitive data are stored, it is useful - to write additional optional `XDMF <https://www.xdmf.org/index.php/XDMF_Model_and_Format>`_ - fields which support additional plotting of the data with visualization software. - * Consumable results of EM characterization tasks are usually a sub-set of - data artifacts, as there is not an infinite amount of possible - electron/ion beam-specimen interactions. - * Images based on electron counts are typically detected with specific operation modes - such as bright field or dark field imaging in TEM or secondary/back-scattered electron - imaging in SEM. - * Also spectra (X-ray quanta or Auger electron counts) typically are referred to - under the assumption of a specific operation mode of the microscope. - * These data are in virtually all cases a result of some numerical processing. - These data and processing steps are modelled as instances of :ref:`NXprocess` - which use terms from a controlled vocabulary e.g. SE (secondary electron), - BSE (back-scattered electron), Kikuchi, X-ray, Auger, Cathodolum(inescence). - - **A key question often asked with EM experiments is how the actual (meta)data - should be stored (in memory or on disk)**. - - The application definition NXem is a graph which describes how numerical data - and (meta)data for EM research are related to one another. - - Electron microscopy experiments are usually controlled/performed via - commercial integrated acquisition and instrument control software. - In many cases, an EM dataset is useful only if it gets post-processed - already during the acquisition, i.e. while the scientist is sitting - at the microscope. - Many of these processes are automated, while some demand GUI - interactions with the control software. Examples include collecting - of diffraction pattern and on-the-fly indexing of these. - - It is possible that different types of programs might be used to - perform these processing steps whether on-the-fly or not. If this is - the case the processing should be structured with individual :ref:`NXprocess` - instances. If the program and/or version used for processing referred - to in an NXprocess group is different to the program and version - mentioned in this field, the NXprocess needs - to hold an own program and version. - - - - - - An at least as strong as SHA256 hashvalue of the file - that specifies the application definition. - - - - - - NeXus NXDL schema to which this file conforms. - - - - - - - - Ideally, a (globally) unique persistent identifier - for referring to this experiment. - - The identifier is usually defined/issued by the facility, - laboratory, or the principle investigator. - The identifier enables to link experiments to e.g. proposals. - - - - - Free-text description about the experiment. - - Users are strongly advised to detail the sample history in the respective - field and fill rather as completely as possible the fields of this - application definition rather than write details about the experiment - into this free-text description field. - - - - - ISO 8601 time code with local time zone offset to UTC information included - when the microscope session started. If the application demands that time - codes in this section of the application definition should only be used - for specifying when the experiment was performed - and the exact - duration is not relevant - this start_time field should be used. - - Often though it is useful to specify a time interval by specifying both - a start_time and an end_time to allow for more detailed bookkeeping and - interpretation of the experiment. The user should be aware that even - with having both time instances specified, it may not be possible - to infer how long the experiment took or for how long data were acquired. - - More detailed timing data over the course of the experiment have - to be collected to compute this. These computations can take - advantage of individual time stamps in NXevent_data_em instances to - provide additional pieces of information. - - - - - ISO 8601 time code with local time zone offset to UTC included when - the microscope session ended. - - - - - - - - - - Binary container for a file or a compressed collection of files which - can be used to add further descriptions and details to the experiment. - The container can hold a compressed archive. - - - - - A small image that is representative of the entry; this can be an - image taken from the dataset like a thumbnail of a spectrum. - A 640 x 480 pixel jpeg image is recommended. - Adding a scale bar to that image is recommended but not required - as the main purpose of the thumbnail is to provide e.g. thumbnail - images for displaying them in data repositories. - - - - - - Contact information and eventually details of at least one person - involved in the taking of the microscope session. This can be the - principle investigator who performed this experiment. - Adding multiple users if relevant is recommended. - - - - Given (first) name and surname of the user. - - - - - Name of the affiliation of the user at the point in time - when the experiment was performed. - - - - - Postal address of the affiliation. - - - - - Email address of the user at the point in time when the experiment - was performed. Writing the most permanently used email is recommended. - - - - - Globally unique identifier of the user as offered by services - like ORCID or ResearcherID. If this field is field the specific service - should also be written in orcid_platform - - - - - Name of the OrcID or ResearcherID where the account - under orcid is registered. - - - - - (Business) (tele)phone number of the user at the point - in time when the experiment was performed. - - - - - Which role does the user have in the place and at the point - in time when the experiment was performed? Technician operating - the microscope. Student, postdoc, principle investigator, guest - are common examples. - - - - - Account name that is associated with the user in social media platforms. - - - - - Name of the social media platform where the account - under social_media_name is registered. - - - - - - - A description of the material characterized in the experiment. - Sample and specimen are threaded as de facto synonyms. - - - - A qualifier whether the sample is a real one or a - virtual one (in a computer simulation) - - - - - - - - - - Ideally (globally) unique persistent identifier. The name distinguishes - the specimen from all others and especially the predecessor/origin - from where the specimen was cut. - - This field must not be used for an alias of the sample. - Instead, use short_title for this, more convenient alias name. - - In cases where multiple specimens have been loaded into the microscope - the name has to identify the specific one, whose results are stored - by this NXentry, because a single NXentry should be used only for - the characterization of a single specimen. - - Details about the specimen preparation should be stored in the - sample history. - - - - - Ideally, a reference to a (globally) unique persistent identifier, - representing a data artifact which documents ideally as many details - of the material, its microstructure, and its thermo-chemo-mechanical - processing/preparation history as possible. - - The sample_history is the record what happened before the specimen - was placed into the microscope at the beginning of the session. - - In the case that such a detailed history of the sample/specimen is not - available, use this field as a free-text description to specify a - sub-set of the entire sample history, i.e. what you would consider are - the key steps and relevant information about the specimen, - its material, microstructure, thermo-chemo-mechanical processing state, - and the details of the preparation. - - Specific details about eventual physically-connected material like - embedding resin should be documented ideally also in the sample_history. - If all fails, the description field can be used but it is strongly - discouraged because it leads to eventually non-machine-actionable - data. - - - - - ISO 8601 time code with local time zone offset to UTC information - when the specimen was prepared. - - Ideally report the end of the preparation, i.e. the last known time - the measured specimen surface was actively prepared. Usually this should - be a part of the sample history, i.e. the sample is imagined handed over - for analysis. - - Knowing when the specimen was exposed to e.g. specific atmosphere is - especially required for environmentally sensitive material such as - hydrogen charged specimens or experiments - including tracers with a short half time. Further time stamps prior - to preparation_date should better be placed in resources which - describe the sample_history. - - - - - Possibility to give an abbreviation or alias of the specimen name field. - - - - - List of comma-separated elements from the periodic table that are - contained in the sample. If the sample substance has multiple - components, all elements from each component must be included in - `atom_types`. - - The purpose of the field is to offer materials database systems an - opportunity to parse the relevant elements without having to interpret - these from the sample history. - - - - - - (Measured) sample thickness. The information is recorded to qualify - if the beam used was likely able to shine through the specimen. - For scanning electron microscopy, in many cases the specimen is much - thicker than what is illuminatable by the electron beam. - In this case the value should be set to the actual thickness of - the specimen viewed for an illumination situation where the nominal - surface normal of the specimen is parallel to the optical axis. - - - - - - (Measured) density of the specimen. For multi-layered specimens this - field should only be used to describe the density of the excited - volume. For scanning electron microscopy the usage of this field is - discouraged and instead an instance of an :ref:`NXinteraction_vol_em` - within individual :ref:`NXevent_data_em` instances can provide a much - better description of the relevant details why one may wish to store - the density of the specimen. - - - - - - Discouraged free-text field in case properly designed records - for the sample_history are not available. - - - - - - Hard link to a location in the hierarchy of the NeXus file - where the data for default plotting are stored. - - - - - - - - - - - - Metadata and numerical data of the microscope and the lab in which it stands. - - The em_lab section contains a description of the instrument and its components. - The component descriptions in this section differ from those inside individual - NXevent_data_em sections. These event instances take the role of time snapshot. - For an NXevent_data_em instance users should store only those settings for a - component which are relevant to understand the current state of the component. - Here, current means at the point in time, i.e. the time interval, - which the event represents. - - For example it is not relevant to store in each event's electron_source - group again the details of the gun type and manufacturer but only the - high-voltage if for that event the high-voltage was different. If for all - events the high-voltage was the same it is not even necessary to include - an electron_source section in the event. - - Individual sections of specific type should have the following names: - - * NXaperture: the name should match with the name of the lens - * NXlens_em: condenser_lens, objective_lens are commonly used names - * NXcorrector_cs: device for correcting spherical aberrations - * NXstage_lab: a collection of component for holding the specimen and - eventual additional component for applying external stimuli on the sample - * NXdetector: several possible names like secondary_electron, - backscattered_electron, direct_electron, ebsd, edx, wds, auger, - cathodoluminescence, camera, ronchigram - - - - Given name of the microscope at the hosting institution. This is an alias. - Examples could be NionHermes, Titan, JEOL, Gemini, etc. - - - - - Location of the lab or place where the instrument is installed. - Using GEOREF is preferred. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If the lens is described at least one of the fields - voltage, current, or value should be defined. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If the lens is described at least one of the fields - voltage, current, or value should be defined. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Description of the type of the detector. - - Electron microscopes have typically multiple detectors. - Different technologies are in use like CCD, scintillator, - direct electron, CMOS, or image plate to name but a few. - - - - Instrument-specific alias/name - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A container for storing a set of NXevent_data_em instances. - - An event is a time interval during which the microscope was configured - in a specific way. The microscope is considered as stable enough during - this interval that a measurement with one or multiple detectors is - possible. What constitutes such time interval depends on how the - microscope is used and which measurements the user would like to perform. - - Each NXevent_data_em instance holds one acquisition task with detectors. - Each NXevent_data_em section contains an em_lab group in which specific - settings and states of the microscope during the time interval - can be stored to document the history of states of the microscope over - the course of the session. - - The NXem application definition offers maximal flexibility. - One extreme could be that the only one NXevent_data_em instance is used - and this covers the time interval of the entire session at the microscope. - The other extreme case is that each collection of an image or even - single spot measurement is defined as an NXevent_data_em instance. - In this case the em_lab group inside the NXevent_data_em also holds - the specific time-dependent state of the microscope with which in theory - all dynamics of the system (if measured) can be captured and documented. - - Nowadays microscopes exists for which hard- and software solutions - enable a tracking of the dynamics of the microscope and the actions - of the user (such as with solution like AXONSynchronicity from Protochips). - The NXem application definition can however also be used for less - complex interaction and lower demands wrt to time tracking activities. - - An NXevent_data_em instance holds specific details about how raw data from - a detector were processed. Raw data may already be post-processed as - they are accessible only by the control software with after some internal - processing happened. Nevertheless, these data have to be distinguished from - post-processed data where e.g. raw data are converted to interpreted - spectra, or orientation mappings. - - This post-processing tasks can be performed (on-the-fly, i.e. during - acquisition for sure during the microscope session) or afterwards. - Post-processing is performed with commercial software or various - types and scripts. - - Currently, several specializations of NXimage_set and Nspectrum_set - are used which store some details of this processing. However, as post- - processing tasks can be substantially more advanced and involved it - is clear that data artifacts from the measurement and data artifacts - generated during post-processing are weakly connected only, maybe - exclusively by the fact that a complex numerical post-processing workflow - just takes one raw dataset from an NXevent_data_em instance but generates - multiple derived data artifacts from this. All these should be described - as own application definitions and only weak connections should be made - to an instance of NXem. Instances of NXsubentry is one mechanism in - NeXus how this can be achieved in the future. - - - - A container holding a specific result of the measurement and - eventually metadata how that result was obtained numerically. - - NXevent_data_em instances can hold several specific NXimage_em or - NXspectrum_em instances taken and considered as one event, i.e. - a point in time when the microscope had the settings specified - either in NXinstrument or in this NXevent_data_em instance. - - The application definition is designed without an explicit need for - having an NXevent_data_em instance that contains an NXimage_em or - NXspectra_em instance. Thereby, an NXevent_data_em can also be used - for just documentation about the specific state of the microscope - irrespective whether data have been collected during this time interval. - - In other words the NXinstrument group details primarily the more - static settings and components of the microscope as they are found - by the operator during the session. The NXevent_data_em samples - the dynamics. - - It is not necessary to store data in NXebeam, NXibeam instances - of NXevent_data_em but in this case it is assumed that the settings - were constant over the entire course of the microscope session - and thus all relevant metadata inside the NXinstrument groups - are sufficient to understand the session. - - So far there exists no standard which a majority of the technology - partners and the materials science electron microscopy community - have accepted which could be used for a very generic documentation, - storage and exchange of electron microscope data. Therefore, it is - still a frequent case that specific files have many fields which cannot - safely be mapped or interpreted. - **Therefore, users are always given the advice to keep the vendor files.** - Working however with these vendor files inside specific software, - like materials databases, demands for parsers which extract pieces of - information from the vendor representation (numerical data and metadata) - and map them on a schema with which the database and its associated - software tools can work with. - - Currently, one would loose immediately track of e.g. provenance and - the origin of certain data in NXevent_data_em instances unless really - all data are safely and reliably copied over into an instance of the - schema. Currently, though, this is sadly effectively prevented in many - cases as vendors indeed implemented often sophisticated provenance - and commercial software state tracking tools but these are not yet - documented covering enough in our opinion so that it is safe to assume - all vendor field names are known, logically understood, interpretable, - and thus mappable on a common schema using a controlled common - vocabulary. - - Therefore we encourage user for now to store for each NXimage_set - or NXspectra_set instance to supply the so-called source of the data. - This can for instance be the name and hashvalue of the original - file which was acquired during the microscope session and from which then - certain details like numerical data and metadata were copied into an - instance of this schema for the purpose of working with the data in - e.g. tools offered by research data management (RDM) systems or - materials database. - - During our work on implementing file format/metadata parsers and - developing this application definition, we realized that **several - software tools currently do not consistently format critical metadata - like time-zone-aware timestamps** when events of data collection or - processing happened. - - We would like to encourage the community and especially the vendors - to work towards a standardization, or at least an open documentation - of the way how time-zone-aware time data are collected and stored how - and where during a microscope session and how they end up in files - and databases with which users interact. - This would enable to supplement instances of this schema with specific - time data and assure that these time data can be used to reliably - contextualize individual datasets and processing steps in materials - information systems. - - For the reason that these measures have not yet been fully taken, - the start_time and end_time is a recommended option. - The idea behind these time-zone-aware dates is to identify when - the data were collected at the microscope but NOT when they were - transcoded by some software tool(s) while storing the data in an - instance of this schema. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Annulus inner half angle - - - - - Annulus outer half angle - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXem_calorimetry.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXem_calorimetry.nxdl.xml new file mode 100644 index 0000000..ad838cb --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXem_calorimetry.nxdl.xml @@ -0,0 +1,297 @@ + + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + Number of diffraction pattern. + + + + + Number of radial integration bins. + + + + + Number of coordinates along i axis. + + + + + Number of coordinates along j axis. + + + + + Application definition for minimal example in-situ calorimetry. + + TODO: + + * What is the technique about. + * General context. + * Literature references. + + + + + + + + + + + Details about performance, profiling, etc. + + + + + + + + Name of the program whereby this config file was created. + + + + + + + + Programs and libraries representing the computational environment + + + + + + + + + + + + Qualifier whether the sample is a real (in which case is_simulation should be set to false) + or a virtual one (in which case is_simulation should be set to true). + + + + + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources. + + + + + + + + + Reference to the resource which stores acquired pattern from the + experiment or simulation that are analyzed in this workflow. + + Can refer to the original EMD or MRC files or the parsed NXem + in RDM e.g. NOMAD OASIS. + + + + + + + + Reference to the resource which stores actuator log file from the experiment. + + + + + + + + Configuration file that was used for parametrizing this analysis workflow. + + + + + + + + Assumptions and computations whereby timestamping data from + the detector and actuator (e.g. heating chip) were synchronized. + + + + + ISO8601 with local time zone reference timestamp that tells + with which delta_time can be converted in timestamp. + The reference timestamp is defined as the time when the + actuator started acting on the sample. + + Time differences to this timestamp when correlated signals such + as diffraction pattern matching with a specific state of the sample + (e.g. obtained temperature via the actuator) are reported through + delta_time. + + + + + + + + + + Time difference to start_time. + + Collecting diffraction pattern also takes some time. + It is assumed that the acquisition time for each pattern is + substantial shorter than the time it takes the actuator to + cause a change in stimulus (e.g. temperature). + + + + + + + + + + Computation of the center for each pattern using e.g. a Circular Hough + Transformation. + + + + + + Computed center for each pattern. + + + + + + + + + + + Elliptical distortion correction as a step when computing the center for + patterns. + + + + + + Computed center for each pattern. + + + + + + + + + + + Integrated diffraction pattern intensity as a function of radial distance from the center + azimuthally integrated as a function of time. + + + + + + The integrated intensities: + + * result_with_background + * result_without_background + + + + + + + + Integrated intensity as a function of time and the radial distance from the + pattern center. + + + + + + + + + + Identifier for each pattern. + + + + + + + + + Positions in reciprocal space. + + + + + + + + + + Time since start of the in-situ experiment + + + + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXem_ebsd.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXem_ebsd.nxdl.xml deleted file mode 100644 index aa3dd46..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXem_ebsd.nxdl.xml +++ /dev/null @@ -1,1926 +0,0 @@ - - - - - - - - - - Number of arguments per orientation for given parameterization. - - - - - Number of scan points. - - - - - Number of pixel along the slowest changing dimension for a rediscretized, i.e. - standardized default orientation mapping. - - - - - Number of pixel along slow changing dimension for a rediscretized i.e. - standardized default orientation mapping. - - - - - Number of pixel along fast changing dimension for a rediscretized i.e. - standardized default orientation mapping. - - - - - - Application definition for collecting and indexing Kikuchi pattern into orientation maps. - - This NXem_ebsd application is a proposal how to represent data, metadata, and - connections between these for the research field of electron microscopy. - More specifically, exemplified here for electron backscatter diffraction (EBSD). - The application definition solves two key documentation issues which are missing - so far to document provenance of data and metadata in the field of EBSD. - The application definition can be an example that is relevant for related - workflows in orientation microscopy. - - Firstly, an instance of NXem_ebsd (such as a NeXus/HDF5 file which is formatted - according to the NXem_ebsd application definition) stores the connection between - the microscope session and the key datasets which are considered typically results - of the various processing steps involved when working with EBSD data. - - Different groups in this application definition make connections to data artifacts - which were collected when working with electron microscopes via the NXem partner - application definition. Using a file which stores information according to the - NXem application definition has the benefit that it connects the sample, references - to the sample processing, the user operating the microscope, details about the - microscope session, and details about the acquistion and eventual indexing of - Kikuchi pattern, associated overview images, like secondary electron or - backscattered electron images of the region-of-interest probed and many - more pieces of information. - - Secondly, this NXem_ebsd application definition connects and stores the conventions - and reference frames which were used and are the key to mathematically correctly - interpret every EBSD result. Otherwise, results would be ripped out of their - context, as it is the situation with many traditional studies where EBSD data were - indexed on-the-fly and shared with the community only via sharing the results file - with some technology-partner-specific file but leaving important conventions out - or relying on the assumptions that colleagues know these even though multiple - definitions are possible. - - This application definition covers experiments with one-, two-dimensional, and - so-called three-dimensional EBSD datasets. The third dimension is either time - (in the case of quasi in-situ experiments) or space (in the case of serial- - sectioning) methods where a combination of mechanical or ion milling is used - repetitively to measure the same region-of-interest at different depth increments. - Material removal can be achieved with electron or ion polishing, using manual - steps or using automated equipment like a robot system. - - Three-dimensional experiments require to follow a sequence of specimen, surface - preparation, and data collection steps. By nature these methods are destructive - in that they either require the removal of the previously measured material region - or that the sample surface can degrade due to e.g. contamination or other - electron-matter interaction. - - For three-dimensional EBSD, multiple two-dimensional EBSD orientation mappings are - combined into one reconstructed stack. That is serial-sectioning is mainly a - computational workflow. Users collect data for each serial sectioning step - via an experiment. This assures that data for associated microscope sessions - and steps of data processing stay connected and contextualized. - - Eventual tomography methods also use such a workflow because first diffraction - images are collected (e.g. with X-ray) and then these imagres are indexed and - computed into a 3D orientation mapping. The here proposed NXem_ebsd application - definition contains conceptual ideas how this splitting between measurement and - post-processing can be granularized also for such X-ray-based techniques, whether - it be 3DXRD or HEDM. - - - - - An at least as strong as SHA256 hashvalue of the file - that specifies the application definition. - - - - - - NeXus NXDL schema to which this file conforms. - - - - - - - - Ideally, a (globally) unique persistent identifier - for referring to this workflow. - - The identifier is usually defined/issued by the facility, laboratory, - or the principle investigator. The identifier enables to link - workflows/experiments to e.g. proposals. - - - - - Free-text description about the workflow. - - Users are strongly advised to detail the sample history in the respective - field and fill rather as completely as possible the fields of the application - definition behind instead of filling in these details into the experiment_description - free-text description field. - - - - - ISO 8601 time code with local time zone offset to UTC information - included when the processing of the workflow started. - If the application demands that time codes in this section of the - application definition should only be used for specifying when the - workflow was executed - and the exact duration is not relevant - - this start_time field should be used. - - Often though it is useful to specify a time interval with specifying - both start_time and end_time to allow for more detailed bookkeeping - and interpretation of the workflow. - - - - - ISO 8601 time code with local time zone offset to UTC included - when the processing of the workflow ended. - - - - - Program which was used for creating the file instance which is - formatted according to the NXem_ebsd application definition. - - - - - - - - Contact information and eventually details of at least one person - involved in performing the workflow. This can be the principle investigator - who performed this experiment. Adding multiple users if relevant is - recommended. - - - - Given (first) name and surname of the user. - - - - - Name of the affiliation of the user at the point in time - when the experiment was performed. - - - - - Postal address of the affiliation. - - - - - Email address of the user at the point in time when the experiment - was performed. Writing the most permanently used email is recommended. - - - - - Globally unique identifier of the user as offered by services - like ORCID or ResearcherID. If this field is field the specific - service should also be written in orcid_platform - - - - - Name of the OrcID or ResearcherID where the account - under orcid is registered. - - - - - (Business) (tele)phone number of the user at the point - in time when the experiment was performed. - - - - - Which role does the user have in the place and at the point - in time when the experiment was performed? Technician operating - the microscope. Student, postdoc, principle investigator, guest - are common examples. - - - - - Account name that is associated with the user - in social media platforms. - - - - - Name of the social media platform where the account - under social_media_name is registered. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Details about simulations for Kikuchi pattern using kinematic or dynamic - diffraction theory. Usually, the output of such computer simulations are - spherical Kikuchi images which only when projected or observed in some - region-of-interest will represent a set of rectangular Kikuchi pattern - with the same rectangular shape and image size. - - Therefore, these pattern should be stored. The spherical diffraction - pattern can be stored as a set of triangulated geodesic meshes. - The rectangular patterns should be stored as NXimage_set_em_kikuchi stack. - - Do not store pattern in the simulation group if they - have been measured are not simulated. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The experiment group captures relevant details about the conditions of - and the tools used for collecting the Kikuchi diffraction pattern. - - The most frequently collected EBSD data are captured as rectangular ROIs - composed from square or hexagonally-shaped pixels. Substantially less - frequently, because such experiments are more costly and technically - demanding, correlated experiments are performed. - - One important class of such correlated experiments are the so-called - (quasi) in-situ experiments. Here the same or nearly the same ROI is - analyzed via a cycles of thermomechanical treatment, sample preparation, - measurement, on-the-fly-indexing. Phenomena investigated like this are - recrystallization, strain accumulation, material damage. - Post-processing is required to correlate and reidentify eventual - features or local ROIs across several orientation maps. - - Another important class of correlated experiments are the so-called - serial-sectioning experiments. Here the same sample is repetitively measured - and polished to create a stack of orientation data which can be reconstructed - to a three-dimensional volume ROI. - - - - Physical time since the beginning of a timestamp that is required to be - same for all experiments in the set. The purpose of this marker is - to identify how all experiments in the set have have to be arranged - sequentially based on the time elapsed. - The time is relevant to sort e.g. experiments of consecutive quasi - in-situ experiments where a measurement was e.g. taken after 0 minutes - of annealing, 30 minutes, 6 hours, or 24 hours of annealing. - - - - - Transformation which details where the region-of-interest described under - indexing is located in absolute coordinates and rotation with respect - to which coordinate system. - - - - - - The EBSD system, including components like the electron gun, pole-piece, - stage tilting, EBSD detector, and the gnomonic projection have to be - calibrated to achieve reliable results. Specifically, the gnomonic projection - has to be calibrated. - - In most practical cases, especially in engineering, there is a substantially - larger number of sessions where such a calibrated system is used assuming - that somebody has properly calibrated the system rather than that the user - actively recalibrates it or is even allowed to do so. - Especially the projection geometry has to calibrated which is usually - achieved with measuring silicon, quartz or standards, and comparing - against simulated diffraction pattern. - - In the first case, the user assumes that the principle geometry of the - hardware components and the settings in the control and EBSD pattern - acquisition software are calibrated. Consequently, users pick from an - existent library of phase candidates. One example are the CRY or CIF - files of the classical HKL/Channel 5/Flamenco software products. - Each entry of the library of such phase candidates in this NeXus proposal - is represented by one NXem_ebsd_crystal_structure_model base class. - For each phase an instance of this base class is to be used to store - crystallographic and simulation-relevant data. - - Indexing is a data processing step performed after/during the beam scans - the specimen (depends on configuration). Users load the specimen, and first - collect a coarse image of the surface. Next, an approximate value for the - calibrated working distance is chosen and the stage tilted. - Users then may configure the microscope for collecting higher quality data - and push in the EBSD detector. Subsequently, they fine tune the illumination - and aberration settings and select one or multiple ROIs to machine off. - The on-the-fly indexing parameter are defined and usually the automated - measurement queue started. - - Nowadays, this is usually an automated/unsupervised process. The pattern - collection runs during the allocated session time slot which the user has - booked ends or when the queue finishes prematurely. Kikuchi pattern surplus - eventually multi-modal detector signals are collected and usually indexed - on-the-fly. The Kikuchi patterns may or not be deleted directly after a - solution was found (on-the-fly) so Kikuchi pattern are not always stored. - - Results files are in many labs afterwards copied automatically - for archival purposes to certain storage locations. The result of such an - EBSD measurement/experiment is a set of usually proprietary or open files - from technology partners (microscope and EBSD detector manufacturers). - - In the second case, the system is being calibrated during the session - using standards (silicon, quartz, or other common specimens). - There is usually one person in each lab responsible for doing such - calibrations. Important is that often this person or technician(s) are also - in charge of configuring the graphical user interface and software - with which most users control and perform their analyses. - For EBSD this has key implications because, taking TSL OIM/EDAX as an example, - the conventions how orientations are stored is affected by how reference frames - are set up and this setup is made at the level of the GUI software. - Unfortunately, these pieces of information are not necessarily stored - in the results files. In effect, key conventions become disconnected - from the data so it remains the users personal obligation to remember these - settings, write them down in the lab notebook, or these metadata get lost. - All these issues are a motivation and problem which NXem_ebsd solves. - - - - - A link/cross reference to an existent instance of NXem_ebsd with ideally - an associated instance of NXem detailed under measurement which informs - about the calibration procedures. - - - - Commit identifying this resource. - - - - - - Path which resolves which specific NXimage_set_em_kikuchi instance - was used as the raw data to the EBSD data (post)-processing workflow - when performing the calibration. - - - - - - - Relevant result of the session at the microscope for this experiment - which enables to connect the measurement of the Kikuchi pattern and - their processing into orientation microscopy maps. - - - - - Name or link to an existent instance of an EBSD raw dataset ideally - as an instance of an NXem application definition which has at least - one NXimage_set_em_kikuchi instance i.e. one stack of Kikuchi pattern. - The path to this instance in the origin has to be specified under path. - - When NXem is not used or the aim is to rather explore first how - community-specific files with EBSD data, such as ANG, CPR, or HDF5- - based formats can be parsed from, inject here the name of that file. - - The em_om parser will currently not interpret the majority of the - many system- and technique-specific metadata which come with the - files from e.g. technology partners. This is because the current - culture in the EBSD community is that many of the metadata fields - are neither in all cases fully documented nor use a standardized - vocabulary although many people understand terms from different - implementations and how these metadata can likely be compared to - one another. - - In addition, it is common practice in the research field of EBSD that - users transcode their raw data into other (often text-based or HDF5) - files with custom formatting to realize an information transfer - between specific software tools including commercial software from - technology partner, custom scripts in Matlab using tools like MTex, - or Python scripting with tools like hyperspy, pyxem, orix, diffsims, - kikuchipy, or EBSD data stack alignment tools like DREAM.3D. - We have opted that in the first iteration this implementation of a - RDMS-agnostic FAIR data schema for EBSD that we discard these metadata - because these ad hoc file formats are not designed to communicate - also specifically and most importantly the eventually different context - of the metadata. - Another reason for this choice was also to emphasize that in fact such - challenges do exist in the community and thus pointing them out may - support the discussion to arrive at eventually more complete solutions. - As developing these solutions should not be our authority and necessarily - demands feedback from the technology partners, we have opted for this - intermediate approach to stimulate discussion. - - - - Commit or e.g. at least SHA256 checksum identifying this resource. - - - - - - Path which resolves which specific NXimage_set_em_kikuchi instance - was used as the raw data to this EBSD data (post)-processing workflow. - - - - - - - - OIM, orientation imaging microscopy. Post-processing of the Kikuchi - patterns to obtain orientation per phase model and scan point. - Fundamentally different algorithms can be used to index EBSD/EBSP pattern. - - Common is that pattern indexing is a computational step of comparing - simulated with measured diffraction pattern. Quality descriptors are defined - based on which an indexing algorithm yields a quantitative measure of - how similar measured and assumed/simulated pattern are, and thus if - no, one, or multiple so-called solutions were found. - - Assumed or simulated pattern use kinematical or dynamical electron - diffraction theory. Hough transform (which is essentially a discretized - Radon transform, for details see e.g A short introduction to the Radon - and Hough transforms and how they relate by M. van Ginkel et al.). - Recently, dictionary-based indexing methods are increasingly becoming used - partly driven by the move to use artificial intelligence algorithms. - - An inspection of publicly available EBSD datasets with an open-source - license which are available on Zenodo was performed prior to implementing - of the associated em_om parser for NXem_ebsd. This analysis revealed that - EBSD data are in most cases stored in two ways: Case one was via a file in - formats from technology partners. Examples are binary formats like OSC, - H5OINA, OIP, EBSP, and many derived text-based formats like CPR, CRC, ANG, - CTF, HKL and more. Recently, there is trend towards using HDF5-based formats. - - These files contain some result and metadata to the numerical steps and the - computational workflow which was performed to index Kikuchi pattern - on-the-fly. Examples of metadata include scan point positions, indexing - solutions per scan point, some quality descriptors for the solutions, - as well as crystal structure and phase metadata. - - Case two were raw pattern in some custom format, often text-based with - some but in general no conclusive and interoperable representation of all - relevant metadata. - Often it remains unclear what individual fields and data arrays of these - fields resolve and/or mean conceptually. For some fields, publications were - referred to. However, software tools change over time and thus which specific - data end in a file and which specific conceptual information is behind - these data can change with software versions. - - Other cases were storing results of custom post-processing steps and - associated Kikuchi pattern. Testing of advanced indexing, pseudo-symmetry - resolving methods, i.e. any sort of prototyping or alternative indexing - strategies so far seem to require some flexibility for implementing - rapid prototypic capabilities. The drawback of this is that such results - come formatted on a case-by-case basis and are thus not interoperable. - - Therefore, we first need to collect how these files have been generated - and which metadata in these files (or database entries) represent - which pieces of information conceptually. Ideally, one would do so by - creating a complete set of information in e.g. an NXem application definition, - such as a log of timestamped events and processing steps, metadata and data. - Eventually even interactions with the graphical user interface of commercial - software during the microscope session should be stored and become a - part of the application definition. - - Such a set of pieces of information could then be used via reading directly - for the NXem application definition. However, in most cases such a data - representation is not available yet. - - - - - Therefore, the on_the_fly_indexing group stores which source_file contains - the results of the on-the-fly indexing. For commercial systems these files - can be e.g. ANG, CPR/CRC, H5OINA, OSC. It is possible that the file or - database entry which is referred to under origin is the same as the one - under a given acquisition/origin in one of the experiment groups. - This is because some commercial file formats make no clear distinction - between which metadata are acquisition and/or indexing metadata. - - - - Commercial program which was used to index the EBSD data - incrementally after they have been captured and while the - microscope was capturing (on-the-fly). This is the usual - production workflow how EBSD data are collected in - materials engineering, in industry, and academia. - - - - - - - - Name of the file from which data relevant for creating default plots - were taken in the case that the data in the experiment group were - indexed on-the-fly. - - - - Hash of that file. - - - - - - TBD, path which resolves which specific NXimage_set_em_kikuchi instance - was used as the raw data to this EBSD data (post)-processing workflow - when performing the calibration. - - - - - - Principal algorithm used for indexing. - - - - - - - - - - - - Details about the background correction applied to each Kikuchi pattern. - - - - - - - Binning i.e. downsampling of the pattern. - - - - - - - Specific parameter relevant only for certain algorithms used - - - - - - - - - - - - - - - - - - - - - - - - - - - Which return value did the indexing algorithm yield for each scan point. - Practically useful is to use an uint8 mask. - - * 0 - Not analyzed - * 1 - Too high angular deviation - * 2 - No solution - * 100 - Success - * 255 - Unexpected errors - - - - - - - - - How many phases i.e. crystal structure models were used to index each - scan point if any? Let's assume an example to explain how this field - should be used: In the simplest case users collected one pattern for - each scan point and have indexed using one phase, i.e. one instance - of an NXem_ebsd_crystal_structure_model. - - In another example users may have skipped some scan points (not indexed) - them at all) and/or used differing numbers of phases for different scan - points. - - The cumulated of this array decodes how phase_identifier and phase_matching - arrays have to be interpreted. In the simplest case (one pattern per scan - point, and all scan points indexed using that same single phase model), - phase_identifier has as many entries as scan points - and phase_matching has also as many entries as scan points. - - - - - - - - The array n_phases_per_scan_point details how the phase_identifier - and the phase_matching arrays have to be interpreted. - - For the example with a single phase phase_identifier has trivial - values either 0 (no solution) or 1 (solution matching - sufficiently significant with the model for phase 1). - - When there are multiple phases, it is possible (although not frequently - needed) that a pattern matches eventually (not equally well) sufficiently - significant with multiple pattern. This can especially happen in cases of - pseudosymmetry and more frequently with an improperly calibrated system - or false or inaccurate phase models e.g. (ferrite, austenite). - Having such field is especially relevant for recent machine learning - or dictionary based indexing schemes because in combination with - phase_matching these fields communicate the results in a model-agnostic - way. - - Depending on the n_phases_per_scan_point value phase_identifier and - phase_matching arrays represent a collection of concatenated tuples, - which are organized in sequence: The solutions for the 0-th scan point, - the 1-th scan point, the n_sc - 1 th scan point and omitting tuples - for those scan points with no phases according to n_phases_per_scan_point - - - - - - - - One-dimensional array, pattern by pattern labelling the solutions found. - The array n_phases_per_scan_point has to be specified because it details - how the phase_identifier and the phase_matching arrays have to be interpreted. - See documentation of phase_identifier for further details. - - - - - - - - Phase_matching is a descriptor for how well the solution matches or not. - Examples can be confidence index (ci), mean angular deviation (mad), - some AI-based matching probability (other), i.e. the details are implementation-specific. - - - - - - - - - - - How are orientations parameterized? Inspect euler_angle_convention - in case of using euler to clarify the sequence of rotations assumed. - - - - - - - - - - - - Matrix of parameterized orientations identified. The slow dimension - iterates of the individual solutions as defined by n_phases_per_scan_point. - Values for phases without a solution should be correctly identified as - IEEE NaN. - - - - - - - - em_lab/ebeam_deflector to retrieve the actual scan positions -although this would be much cleaner--> - - Matrix of calibrated centre positions of each scan point - in the sample surface reference system. - - - - - - - - - - - Fraction of successfully indexed pattern - of the set averaged over entire set. - - - - - - An overview of the entire area which was scanned. - For details about what defines the image contrast - inspect descriptor. - - - - Descriptor representing the image contrast. - - - - - - - - - - Container holding a default plot of the region on the sample - investigated with EBSD. - - - - - - - - - - Descriptor values displaying the ROI. - - - - - - - - - Signal - - - - - - Calibrated center of mass of the pixel along the slow axis. - - - - - - - Label for the y axis - - - - - - Calibrated center of mass of the pixel along the fast axis. - - - - - - - Label for the x axis - - - - - - - - Default inverse pole figure (IPF) plot of the data specific for each - phase. No ipf_mapID instances for non-indexed scan points as these are - by definition assigned the null phase with phase_identifier 0. - - The IPF mapping is interpolated from the scan point data mapping - onto a rectangular domain with square pixels and the - orientations colored according to the coloring scheme used in the - respective ipf_color_modelID/program. - - The main purpose of the ipf_mapID group is not to keep raw data or - scan point related data but offer a default way how a research data - management system can display a preview of the dataset so that users - working with the RDMS can get an overview of the dataset. - - This matches the first aim of NXem_ebsd which is foremost to bring - colleagues and users of EBSD together to discuss which pieces of information - need to be stored together. We are convinced a step-by-step design and - community-driven discussion about which pieces of information should - and/or need to be included is a practical strategy to work towards an - interoperable description and data model for exchanging - data from EBSD between different tools and research data management - systems (RDMS). - - With this design the individual RDMS solutions and tools can still continue - to support specific custom data analyses workflow and routes but at least - there is then one common notation of understanding whereby also users - not necessarily expert in all the details of the EBSD story can understand - better these data and thus eventually this can motivate data reuse and - repurposing. - - It is important to mention that we cannot assume, at least for now, - that the parser which writes to an NXem_ebsd-compliant file is also - responsible or capable at all of computing the inverse pole figure - color keys and maps itself. This cannot be assumed working because - this mapping of orientation data uses involved mathematical algorithms - and functions which not every tools used in the EBSD community is capable - of using or is for sure not using in exactly the same way. - - Currently, we assume it is the responsibilty of the tool used which - generated the data under on_the_fly_indexing to compute these - plots and deliver these to the parser. - - Specific case studies have been explored by the experiment team of - Area B of the FAIRmat project to realize and implement such mapping. - - The first case study uses the H5OINA format and the pyxem/orix library. - As orix is a Python library, the coloring is performed by the em_om parser. - - The second case study uses MTex and its EBSD color coding model. - As MTex is a Matlab tool, an intermediate format is written from MTex - first which stores these pieces of information. The parser then pulls - these data from the intermediate Matlab-agnostic representation and - supplements the file with missing pieces of information as it is - required by NXem_ebsd. - - The third case study shows how a generic set of Kikuchi pattern - can be loaded with the em_om parser. The pattern are loaded directly - from a ZIP file and mapped to an simulation image section for now. - - The fourth case study uses the DREAM.3D package which provides an own - set of EBSD data post-processing procedures. DREAM.3D documents the - processing steps with a pipeline file which is stored inside DREAM.3D - output files. In this case study, the parser reads the DREAM.3D file - and maps data relevant from the perspective of NXem_ebsd plus adds - relevant IPF color maps as they were computed by DREAM.3D. - Given that in this case the origin of the data is the DREAM.3D file - again provenance is kept and more details can be followed upon when - resolving origin. - - These examples offer a first set of suggestions on how to make EBSD - data injectable into research data management system using schemes - which themselves are agnostic to the specific RDMS and interoperable. - Steps of collecting the raw data and post-processing these with custom - scripts like MTex or commercial tools so far are mainly undocumented. - The limitation is that a program which consumes results or dump files - from these tools may not have necessarily all the sufficient information - available to check if the injected orientation data and color models - are matching the conventions which a user or automated system has - injected into an electronic lab notebook from which currently the em_om - parser collects the conventions and stores them into this NXem_ebsd instance. - The immediate benefit of the here presented NXem_ebsd concept though - is that the conventions and reference frame definitions are expected - in an ELN-agnostic representation to make NXem_ebsd a generally useful - data scheme for EBSD. - - Ideally, the em_om parser would load convention-compliant EBSD data - and use subsequently a community library to transcode/convert orientation - conventions and parameterized orientation values. Thereafter, convention- - compliant default plot(s) could be created that would be truely interoperable. - - However, given the variety of post-processing tools available surplus - the fact that these are not usually executed along standardized - post-processing workflows which perform exactly the same algorithmic steps, - this is currently not a practically implementable option. Indeed, first - developers who wish to implement this would first have to create a library - for performing such tasks, mapping generally between conventions, - i.e. map and rotate coordinate systems at the parser level. - - The unfortunate situation in EBSD is that due to historical reasons - and competitive strategies, different players in the field have - implemented (slightly) different approaches each of which misses - some part of a complete workflow description which is behind EBSD analyses: - Sample preparation, measurement, indexing, post-processing, paper... - - The here exemplified default plot do not so far apply relevant rotations - but takes the orientation values as they come from the origin and using - coloring them as they come. It is thus the scientists responsibility to - enter and check if the respective dataset is rotation-conventions-wise - consistent and fit for a particular task. - - Ideally, with all conventions defined it can be possible to develop - a converter which rotates the input data. This application definition - does not assume this and users should be aware of this limitation. - - The key point is that the conventions however are captured and this is - the most important step to the development of such a generic transcoder - for creating interoperable EBSD datasets. - - Currently the conventions remain in the mind or manual lab book of the - respective scientists or technicians instead of getting stored and - communicated with research papers that are written based on - specific dataset, i.e. database entries. - - The default gridded representation of the data should not be - misinterpreted as the only possible way how EBSD data and OIM - maps can be created! - - Indeed, the most general case is that patterns are collected for - scan points. The scan generator of an electron microscope is instructed - to steer the beam in such a way across the specimen surface that the - beam illuminates certain positions for a certain amount time (usually - equally-spaced and spending about the same amount of time at each - position). - - Therefore, scan positions can be due to such regular flight plans and - represent sampling on lines, line stacks, rectangular regions-of- - interests, but also could instruct spiral, random, or adaptive scans - instead of tessellations with square or hexagonal pixels. - - The majority of EBSD maps is though is reporting results for a regular - grid (square, hexagon). What matters though in terms of damage induced - by the electron beam and signal quality is the real electron dose - history, i.e. for how long the beam exposed which location of the - specimen. Especially when electron charging occurs (i.e. an excess - amount of charge accumulates due to e.g. poor conducting away of this - charge or an improper mounting, too high dose, etc. such details are - relevant. - - Specifically, the default visualization is an inverse pole-figure (IPF) - map with the usual RGB color coding. Different strategies and - normalization schemes are in use to define such color coding. - - Finally, we should mention that each ipf_map represents data for - scan points indexed as one phase. The alias/name of this phase should - be stored in phase_name, the phase_identifier give an ID which must - not be zero as this value is reserved for non-indexed / null model scan - points. - - - - Specifying which phase this IPF mapping visualizes. - - - - - Alias/name for the phase whose indexed scan points are displayed. - - - - - Which IPF definition computation according to backend. - - - - - - - Along which axis to project? Typically [0, 0, 1] is chosen. - - - - - - - - Bitdepth used for the RGB color model. Usually 8 bit. - - - - - - The tool/implementation used for creating the IPF color map from - the orientation data. Effectively, this program is the backend - which performs the computation of the inverse pole figure mappings - which can be for some use cases the parser. - Consider the explanations in the docstring of the ipf_mapID group. - - - - - - - - - The RGB image which represents the IPF map. - - - - - - - - - - RGB array, with resolution per fastest changing value - defined by bitdepth. - - - - - - - - - - IPF color-coded orientation mapping - - - - - - Calibrated center of mass of the pixel along the slow axis. - - - - - - - Label for the y axis - - - - - - - Calibrated center of mass of the pixel along the fast axis. - - - - - - - Label for the x axis - - - - - - - For each stereographic standard triangle (SST), i.e. a rendering of - the fundamental zone of the crystal-symmetry-reduced orientation space SO3, - it is possible to define a color model which assigns each point in - the fundamental zone a color. - Different mapping models are in use and implement (slightly) different - scaling relations. Differences are which base colors of the RGB - color model are placed in which extremal position of the SST - and where the white point is located. For further details see: - - * [G. Nolze et al.](https://doi.org/10.1107/S1600576716012942) - * Srikanth Patala and coworkers"'" work and of others. - - Details are implementation-specific and not standardized yet. - Given that the SST has a complicated geometry, it cannot yet be - visualized using tools like H5Web, which is why for now the em_om - parsers takes a rasterized image which is rendered by the backend - tool. - - - - - - - - - - RGB array, with resolution per fastest changing value defined by bitdepth. - - - - - - - - - - IPF color key in stereographic standard triangle (SST) - - - - - - Pixel coordinate along the slow axis. - - - - - - - Label for the y axis - - - - - - Pixel coordinate along the fast axis. - - - - - - - Label for the x axis - - - - - - - - - - This application definition also enables to describe a workflow where several - EBSD datasets are not only documented but also correlated based on time, - position (spatial), or both (spatiotemporal). - - Spatial correlations between repetitively characterized regions-of-interests - are typically correlated using image registration and alignment algorithms. - For this typically so-called landmarks are used. These can be grains with - a very large size or specific shape, i.e. grains which are qualitatively - different enough to be used as a guide how images are shifted relative to - one another. Other commonly used landmarks are fiducial marks which are - milled into the specimen surface using focus-ion beam milling and/or various - types of indentation methods. - - As far as the same physical region-of-interest is just measured several times, - the additional issue of the depth increment is not a concern. However, correct - assumptions for the depth increment, amount of material removed along the milling - direction is relevant for accurate and precise three-dimensional (serial-sectioning) - correlations. For these studies it can be tricky though to assume or estimate - useful depth increments. Different strategies have been proposed like - calibrations, wedged-shaped landmarks and computer simulation assisted - assumption making. - - Despite the use of landmarks, there are many practical issues which make the - processing of correlations imprecise and inaccurate. Among these are drift - and shift of the specimen, instabilities of the holder, the beam, irrespective - of the source of the drift, charging effects, here specifically causing local - image distortions and rotations which may require special processing algorithms - to reduce such imprecisions. - - Time correlations face all of the above-mentioned issues surplus the challenge - that specific experimental protocols have to be used to ensure the material state - is observed at specific physical time. The example of quasi in-situ characterization - of crystal growth phenomena, a common topic in engineering or modern catalysis research - makes it necessary to consider that e.g. the target value for the desired annealing - temperature is not just gauged based on macroscopic arguments but considers - that transient effects take place. Heating or quenching a sample might thus might - not have been executed under conditions in the interaction volume as they are - documented and/or assumed. - - These issue cause that correlations have an error margin as to how accurately - respective datasets were not only just synced based on the geometry of the - region-of-interests and the time markers but also to asssure which physical - conditions the specimen experienced over the course of the measurements. - - The fourth example of the em_om reference implementation explores the use of the - correlation group with a serial-sectioning datasets that was collected by the - classical Inconel 100 dataset collected by M. D. Uchic and colleagues - (M. Groeber M, Haley BK, Uchic MD, Dimiduk DM, Ghosh S 3d reconstruction and - characterization of polycrystalline microstructures using a fib-sem system data set. - Mater Charac 2006, 57 259–273. 10.1016/j.matchar.2006.01.019M). - - This dataset was specifically relevant in driving forward the implementation - of the DREAM.3D software. DREAM.3D is an open-source software project for - post-processing and reconstructing, i.e. correlating sets of orientation - microscopy data foremost spatially. One focus of the software is the - (post-)processing of EBSD datasets. Another cutting edge tool with similar - scope but a commercial solution by Bruker is QUBE which was developed by - P. Konijnenberg and coworkers. - - Conceptually, software like DREAM.3D supports users with creating linear - workflows of post-processing tasks. Workflows can be instructed via the - graphical user interface or via so-called pipeline processing via command line - calls. DREAM.3D is especially useful because its internal system documents all - input, output, and parameter of the processing steps. This makes DREAM.3D a - good candidate to interface with tools like em_om parser. Specifically, DREAM.3D - documents numerical results via a customized HDF5 file format called DREAM3D. - Workflow steps and settings are stored as nested dictionaries in JSON syntax - inside a supplementary JSON file or alongside the data in the DREAM3D file. - DREAM.3D has a few hundred algorithms implemented. These are called filters - in DREAM.3D terminology. - - Users configure a workflow which instructs DREAM.3D to send the data through - a chain of predefined and configured filters. Given that for each analysis - the filter is documented via its version tags surplus its parameter and setting - via a controlled vocabulary, interpreting the content of a DREAM3D HDF5 file - is possible in an automated manner using a parser. This makes DREAM.3D analyses - repeatable and self-descriptive. A key limitation though is that most frequently - the initial set of input data come from commercial files like ANG. - This missing link between the provenance of these input files, their associated - creation as electron microscope session, is also what NXem_ebsd solves. - - Nevertheless, as this can be solved with e.g. NXem_ebsd we are convinced that - the DREAM.3D and the em_om parser can work productively together to realize - RDMS-agnostic parsing of serial-section analyses. - - The internal documentation of the DREAM.3D workflow also simplifies the - provenance tracking represented by an instance of NXem_ebsd as not every - intermediate results has to be stored. Therefore, the fourth example - focuses on the key result obtained from DREAM.3D - the reconstructed - and aligned three-dimensional orientation map. - - Usually, this result is the starting point for further post-processing - and characterization of structural features. As here orientation microscopy - is insofar scale invariant using DREAM.3D, NXem_ebsd, and em_om should - be useful for different characterization methods, such as EBSD, Transmission - Kikuchi Diffraction (TKD), Automated Crystal Orientation Mapping (ACOM), - Nanobeam Electron Diffraction (using commercial systems like NanoMegas ASTAR) - or open-source implementations of these techniques (such as via pyxem/orix). - - The result of orientation microscopy methods are maps of local orientation - and thermodynamic phase (crystal structure) pieces of information. Virtually - all post-processing of such results for structural features includes again - a workflow of steps which are covered though by the NXms partner application - definition. The respective source of the data in an instance of NXms can - again be a link or reference to an instance of NXem_ebsd to complete the - chain of provenance. - - - - - - - - - - - - - - - - An overview of the entire reconstructed volume. For details about - what defines the image contrast inspect descriptor. - - - - Descriptor representing the image contrast. - - - - - - Container holding a default plot of the reconstructed volume. - - - - - - - - - - Descriptor values displaying the ROI. - - - - - - - - - - Signal - - - - - - Calibrated center of mass of the pixel along the slow axis. - - - - - - - Label for the z axis - - - - - - Calibrated center of mass of the pixel along the fast axis. - - - - - - - Label for the y axis - - - - - - Calibrated center of mass of the pixel along the fastest axis. - - - - - - - Label for the x axis - - - - - - - - Default inverse pole figure (IPF) plot of the data specific for each - phase. No ipf_mapID instances for non-indexed scan points as these are - by definition assigned the null phase with phase_identifier 0. - The same comments apply as to the two-dimensional representation. - - - - Specifying which phase this IPF mapping visualizes. - - - - - Alias/name for the phase whose indexed scan points are displayed. - - - - - Which IPF definition computation according to backend. - - - - - - Along which axis to project? Typically [0, 0, 1] is chosen. - - - - - - - - Bitdepth used for the RGB color model. Usually 8 bit. - - - - - The tool/implementation used for creating the IPF color map from - the orientation data. Effectively, this program is the backend - which performs the computation of the inverse pole figure mappings - which can be for some use cases the parser. - Consider the explanations in the docstring of the ipf_mapID group. - - - - - - - - - The RGB image which represents the IPF map. - - - - - - - - - - RGB array, with resolution per fastest changing value - defined by bitdepth. - - - - - - - - - - - IPF color-coded orientation mapping - - - - - - Calibrated center of mass of the pixel along the slow axis. - - - - - - - Label for the z axis - - - - - - - Calibrated center of mass of the pixel along the faster axis. - - - - - - - Label for the y axis - - - - - - - Calibrated center of mass of the pixel along the fastest axis. - - - - - - - Label for the x axis - - - - - - - Same comments as for the two-dimensional case apply. - - - - - - - - - - RGB array, with resolution per fastest changing value defined by bitdepth. - - - - - - - - - - IPF color key in stereographic standard triangle (SST) - - - - - - Pixel coordinate along the slow axis. - - - - - - - Label for the y axis - - - - - - Pixel coordinate along the fast axis. - - - - - - - Label for the x axis - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXem_ebsd_conventions.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXem_ebsd_conventions.nxdl.xml deleted file mode 100644 index 7ef85f8..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXem_ebsd_conventions.nxdl.xml +++ /dev/null @@ -1,610 +0,0 @@ - - - - - - - Conventions for rotations and coordinate systems to interpret EBSD data. - - This is the main issue which currently is not in all cases documented - and thus limits the interoperability and value of collected EBSD data. - Not communicating EBSD data with such contextual pieces of information - and the use of file formats which do not store this information is the - key unsolved problem. - - - - - Mathematical conventions and materials-science-specific conventions - required for interpreting every collection of orientation data. - - - - Convention how a positive rotation angle is defined when viewing - from the end of the rotation unit vector towards its origin, - i.e. in accordance with convention 2 of - DOI: 10.1088/0965-0393/23/8/083501. - Counter_clockwise is equivalent to a right-handed choice. - Clockwise is equivalent to a left-handed choice. - - - - - - - - - - How are rotations interpreted into an orientation - according to convention 3 of - DOI: 10.1088/0965-0393/23/8/083501. - - - - - - - - - - How are Euler angles interpreted given that there are several - choices (e.g. ZXZ, XYZ, etc.) according to convention 4 of - DOI: 10.1088/0965-0393/23/8/083501. - The most frequently used convention is ZXZ which is based on - the work of H.-J. Bunge but other conventions are possible. - - - - - - - - - To which angular range is the rotation angle argument of an - axis-angle pair parameterization constrained according to - convention 5 of DOI: 10.1088/0965-0393/23/8/083501. - - - - - - - - - Which sign convention is followed when converting orientations - between different parameterizations/representations according - to convention 6 of DOI: 10.1088/0965-0393/23/8/083501. - - - - - - - - - - - Details about eventually relevant named directions that may - give reasons for anisotropies. The classical example is cold-rolling - where one has to specify which directions (rolling, transverse, and normal) - align how with the direction of the base vectors of the sample_reference_frame. - - - - Type of coordinate system and reference frame according to - convention 1 of DOI: 10.1088/0965-0393/23/8/083501. - - - - - - - - - - Direction of the positively pointing x-axis base vector of - the processing_reference_frame. We assume the configuration - is inspected by looking towards the sample surface from a position - that is located behind the detector. - - - - - - - - - - - - - - Name or alias assigned to the x-axis base vector, e.g. rolling direction. - - - - - Direction of the positively pointing y-axis base vector of - the processing_reference_frame. We assume the configuration - is inspected by looking towards the sample surface from a position - that is located behind the detector. For further information consult - also the help info for the xaxis_direction field. - - - - - - - - - - - - - - Name or alias assigned to the y-axis base vector, e.g. transverse direction. - - - - - Direction of the positively pointing z-axis base vector of - the processing_reference frame. We assume the configuration - is inspected by looking towards the sample surface from a position - that is located behind the detector. For further information consult - also the help info for the xaxis_direction field. - - - - - - - - - - - - - - Name or alias assigned to the z-axis base vector, e.g. normal direction. - - - - - Location of the origin of the processing_reference_frame. - This specifies the location Xp = 0, Yp = 0, Zp = 0. - Assume regions-of-interest in this reference frame form a - rectangle or cuboid. - Edges are interpreted by inspecting the direction of their - outer unit normals (which point either parallel or antiparallel) - along respective base vector direction of the reference frame. - - - - - - - - - - - - - - - - - Details about the sample/specimen reference frame. - - - - Type of coordinate system and reference frame according to - convention 1 of DOI: 10.1088/0965-0393/23/8/083501. - The reference frame for the sample surface reference is used for - identifying positions on a (virtual) image which is formed by - information collected from an electron beam scanning the - sample surface. We assume the configuration is inspected by - looking towards the sample surface from a position that is - located behind the detector. - Reference DOI: 10.1016/j.matchar.2016.04.008 - The sample surface reference frame has coordinates Xs, Ys, Zs. - In three dimensions these coordinates are not necessarily - located on the surface of the sample as there are multiple - faces/sides of the sample. Most frequently though the coordinate - system here is used to define the surface which the electron - beam scans. - - - - - - - - - - Direction of the positively pointing x-axis base vector of - the sample surface reference frame. We assume the configuration - is inspected by looking towards the sample surface from a position - that is located behind the detector. - Different tools assume that different strategies can be used - and are perceived as differently convenient to enter - details about coordinate system definitions. In this ELN users - have to possibility to fill in what they assume is sufficient to - define the coordinate system directions unambiguously. - Software which works with this user input needs to offer parsing - capabilities which detect conflicting input and warn accordingly. - - - - - - - - - - - - - - Direction of the positively pointing y-axis base vector of - the sample surface reference frame. We assume the configuration - is inspected by looking towards the sample surface from a position - that is located behind the detector. For further information consult - also the help info for the xaxis_direction field. - - - - - - - - - - - - - - Direction of the positively pointing z-axis base vector of - the sample surface reference frame. We assume the configuration - is inspected by looking towards the sample surface from a position - that is located behind the detector. For further information consult - also the help info for the xaxis_direction field. - - - - - - - - - - - - - - Location of the origin of the sample surface reference frame. - This specifies the location Xs = 0, Ys = 0, Zs = 0. - Assume regions-of-interest in this reference frame form a - rectangle or cuboid. - Edges are interpreted by inspecting the direction of their - outer unit normals (which point either parallel or antiparallel) - along respective base vector direction of the reference frame. - - - - - - - - - - - - - - - - - Details about the detector reference frame. - - - - Type of coordinate system/reference frame used for - identifying positions in detector space Xd, Yd, Zd, - according to DOI: 10.1016/j.matchar.2016.04.008. - - - - - - - - - - Direction of the positively pointing x-axis base vector of - the detector space reference frame. We assume the configuration - is inspected by looking towards the sample surface from a - position that is located behind the detector. - Different tools assume that different strategies can be used - and are perceived as differently convenient to enter - details about coordinate system definitions. In this ELN users - have to possibility to fill in what they assume is sufficient to - define the coordinate system directions unambiguously. - Software which works with this user input needs to offer parsing - capabilities which detect conflicting input and warn accordingly. - - - - - - - - - - - - - - Direction of the positively pointing y-axis base vector of - the detector space reference frame. We assume the configuration - is inspected by looking towards the sample surface from a - position that is located behind the detector. - For further information consult also the help info for the - xaxis_direction field. - - - - - - - - - - - - - - Direction of the positively pointing z-axis base vector of - the detector space reference frame. We assume the configuration - is inspected by looking towards the sample surface from a - position that is located behind the detector. - For further information consult also the help info for the - xaxis_direction field. - - - - - - - - - - - - - - Where is the origin of the detector space reference - frame located. This is the location of Xd = 0, Yd = 0, Zd = 0. - Assume regions-of-interest in this reference frame form a - rectangle or cuboid. - Edges are interpreted by inspecting the direction of their - outer unit normals (which point either parallel or antiparallel) - along respective base vector direction of the reference frame. - - - - - - - - - - - - - - - - - Details about the gnomonic projection reference frame. - - - - Type of coordinate system/reference frame used for identifying - positions in the gnomonic projection space Xg, Yg, Zg - according to DOI: 10.1016/j.matchar.2016.04.008. - - - - - - - - - - Direction of the positively pointing "gnomomic" x-axis base - vector when viewing how the diffraction pattern looks on the - detector screen. We assume the configuration is inspected by - looking towards the sample surface from a position - that is located behind the detector. - Different tools assume that different strategies can be used - and are perceived as differently convenient to enter - details about coordinate system definitions. In this ELN users - have to possibility to fill in what they assume is sufficient to - define the coordinate system directions unambiguously. - Software which works with this user input needs to offer parsing - capabilities which detect conflicting input and warn accordingly. - - - - - - - - - - - - - - Direction of the positively pointing "gnomomic" y-axis base - vector when viewing how the diffraction pattern looks on the - detector screen. We assume the configuration is inspected by - looking towards the sample surface from a position - that is located behind the detector. - For further information consult also the help info for the - xaxis_direction field. - - - - - - - - - - - - - - Direction of the positively pointing "gnomomic" z-axis base - vector when viewing how the diffraction pattern looks on the - detector screen. We assume the configuration is inspected by - looking towards the sample surface from a position - that is located behind the detector. - For further information consult also the help info for the - xaxis_direction field. - - - - - - - - - - - - - - Is the origin of the gnomonic coordinate system located - where we assume the location of the pattern centre. - This is the location Xg = 0, Yg = 0, Zg = 0 according to - reference DOI: 10.1016/j.matchar.2016.04.008. - - - - - - - - - - Details about the definition of the pattern centre - as a special point in the gnomonic projection reference frame. - - - - From which border of the EBSP (in the detector reference frame) - is the pattern centre's x-position (PCx) measured? - Keywords assume the region-of-interest is defined by - a rectangle. We observe this rectangle and inspect the - direction of the outer-unit normals to the edges of - this rectangle. - - - - - - - - - - - - In which direction are positive values for PCx measured from - the specified boundary. Keep in mind that the gnomonic space - is in virtually all cases embedded in the detector space. - Specifically, the XgYg plane is defined such that it is - embedded/laying inside the XdYd plane (of the detector - reference frame). - When the normalization direction is the same as e.g. the - detector x-axis direction, we state that we effectively - normalize in fractions of the width of the detector. - - The issue with terms like width and height is that these - degenerate if the detector region-of-interest is square-shaped. - This is why we should better avoid talking about width and height but - state how we would measure distances practically with a ruler and - how we then measure positive distances. - - - - - - - - - - - - From which border of the EBSP (in the detector reference - frame) is the pattern centre's y-position (PCy) measured? - For further details inspect the help button of - xaxis_boundary_convention. - - - - - - - - - - - - In which direction are positive values for PCy measured from - the specified boundary. - For further details inspect the help button of - xaxis_normalization_direction. - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXem_ebsd_crystal_structure_model.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXem_ebsd_crystal_structure_model.nxdl.xml deleted file mode 100644 index 5b0b1ff..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXem_ebsd_crystal_structure_model.nxdl.xml +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - - - Number of reflectors (Miller crystallographic plane triplets). - - - - - Number of atom positions. - - - - - Crystal structure phase models used for indexing Kikuchi pattern. - - This base class contains key metadata relevant to every physical - kinematic or dynamic diffraction model to be used for simulating - Kikuchi diffraction pattern. - The actual indexing of Kikuchi pattern however maybe use different - algorithms which build on these simulation results but evaluate different - workflows of comparing simulated and measured Kikuchi pattern to make - suggestions which orientation is the most likely (if any) for each - scan point investigated. - - Traditionally Hough transform based indexing has been the most frequently - used algorithm. More and more dictionary based alternatives are used. - Either way both algorithm need a crystal structure model. - - - - - Identifier of an entry from crystallographic_database which was used - for creating this structure model. - - - - - Name of the crystallographic database to resolve - crystallographic_database_identifier e.g. COD or others. - - - - - - Crystallography unit cell parameters a, b, and c. - - - - - - - - - Crystallography unit cell parameters alpha, beta, and gamma. - - - - - - - - Volume of the unit cell - - - - - Crystallographic space group - - - - - - True if space group is considered a centrosymmetric one. - False if space group is considered a non-centrosymmetric one. - Centrosymmetric has all types and combinations of symmetry elements - (translation, rotational axis, mirror planes, center of inversion) - Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). - Chiral compared to non-centrosymmetric is constrained (no mirror planes). - - - - - True if space group is considered a chiral one. - False if space group is consider a non-chiral one. - - - - - Laue group - - - - - - Point group using International Notation. - - - - - - Crystal system - - - - - - - - - - - - - - Numeric identifier for each phase. - The value 0 is reserved for the unknown phase essentially representing the - null-model that no phase model was sufficiently significantly confirmed. - Consequently, the value 0 must not be used as a phase_identifier. - - - - - Name of the phase/alias. - - - - - Labels for each atom position - - - - - - - - The hash value :math:`H` is :math:`H = Z + N*256` with :math:`Z` - the number of protons and :math:`N` the number of neutrons - of each isotope respectively. Z and N have to be 8-bit unsigned integers. - For the rationale behind this `M. Kühbach et al. (2021) <https://doi.org/10.1017/S1431927621012241>`_ - - - - - - - - Atom positions x, y, z. - - - - - - - - - - Relative occupancy of the atom position. - - - - - - - - How many reflectors are distinguished. Value has to be n_hkl. - - - - - - Miller indices :math:`(hkl)`. - - - - - - - - - D-spacing. - - - - - - - - Relative intensity of the signal for the plane. - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXenergydispersion.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXenergydispersion.nxdl.xml deleted file mode 100644 index c2f63d7..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXenergydispersion.nxdl.xml +++ /dev/null @@ -1,90 +0,0 @@ - - - - - - Subclass of NXelectronanalyser to describe the energy dispersion section of a - photoelectron analyser. - - - - Energy dispersion scheme employed, for example: tof, hemispherical, cylindrical, - mirror, retarding grid, etc. - - - - - Energy of the electrons on the mean path of the analyser. Pass energy for - hemispherics, drift energy for tofs. - - - - - Center of the energy window - - - - - The interval of transmitted energies. It can be two different things depending - on whether the scan is fixed or swept. With a fixed scan it is a 2 vector - containing the extrema of the transmitted energy window (smaller number first). - With a swept scan of m steps it is a 2xm array of windows one for each - measurement point. - - - - - Size, position and shape of a slit in dispersive analyzer, e.g. entrance and - exit slits. - - - - - Diameter of the dispersive orbit - - - - - Way of scanning the energy axis (fixed or sweep). - - - - - - - - - Length of the tof drift electrode - - - - - Deflectors in the energy dispersive section - - - - - Individual lenses in the energy dispersive section - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXevent_data_em.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXevent_data_em.nxdl.xml deleted file mode 100644 index 4192c48..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXevent_data_em.nxdl.xml +++ /dev/null @@ -1,226 +0,0 @@ - - - - - - Metadata and settings of an electron microscope for scans and images. - - The need for such a structuring of data is evident from the fact that - electron microscopes are dynamic. Oftentimes it suffices to calibrate the - instrument at the start of the session. Subsequently, data (images, spectra, etc.) - can be collected. Users may wish to take only a single scan or image and - complete their microscope session; however - - frequently users are working much longer at the microscope, recalibrate and take - multiple data items (scans, images, spectra). Each item comes with own detector - and eventually on-the-fly processing settings and calibrations. - - For the single data item use case one may argue that the need for an additional - grouping is redundant. Instead, the metadata could equally be stored inside - the respective groups of the top-level mandatory NXinstrument group. - On the flip side, even for a session with a single image, it would also not - harm to nest the data. - - In fact, oftentimes scientists feel that there is a need to store details - about eventual drift of the specimen in its holder (if such data is available) - or record changes to the lens excitations or apertures used and/or changed. - Although current microscopes are usually equipped with stabilization - systems for many of the individual components, it can still be useful - to store time-dependent data in detail. - - Another reason if not a need for having more finely granularizable options for - storing time-dependent data, is that over the course of a session one may - reconfigure the microscope. What is a reconfiguration? This could be the - change of an aperture mode because a scientist may first collect an image - with some aperture and then pick a different value and continue. - As the aperture affects the electron beam, it will affect the system. - - Let aside for a moment the technology and business models, an EM could be - monitored (and will likely become so more in the future) for streaming out - spatio-temporal details about its components, locations of (hardware components) and objects within the region-of-interest. Eventually external stimuli are applied - and the specimen repositioned. - - Some snapshot or integrated data from this stream are relevant for understanding - signal genesis and electron/ion-beam-sample interaction (paths). In such a generic - case it might be necessary to sync these streaming data with those intervals - in time when specific measurements are taken (spectra collected, - images taken, diffraction images indexed on-the-fly). - - Therefore, both the instrument and specimen should always be considered as dynamic. - Scientists often report or feel (difficult to quantify) observations that - microscopes *perform differently* across sessions, without sometimes being - able to identify clear root causes. Users of the instrument may consider - such conditions impractical, or *too poor* and thus either abort their session - or try to bring the microscope first into a state where conditions are considered - more stable, better, or of some whatever high enough quality to reuse - data collection. - - In all these cases it is practical to have a mechanism how time-dependent data - of the instrument state can be stored and documented in a interoperable way. - Where should these data be stored? With NeXus these data should not only be - stored in the respective instrument component groups of the top-level NXinstrument. - The reason is that this group should be reserved for as stable as possible - quantities which do not change over the session. Thereby we can avoid to store - repetitively that there is a certain gun or detector available but just store - the changes. This is exactly what the em_lab group is for inside NXevent_data_em. - - Ideally, NXevent_data_em are equipped with a start_time and end_time - to represent a time interval (remind the idea of the instrument state stream) - during which the scientist considered (or practically has to consider) - the microscope (especially ebeam and specimen) as stable enough. - - Arguably it is oftentimes tricky to specify a clear time interval when the - microscope is stable enough. Take for instance the acquisition of an image - or spectra stack. It is not fully possible (technically) to avoid that even - within a single image instabilities of the beam are faced and drift occurs. - Maybe in many cases this these instabilities are irrelevant but does this - warrant to create a data schema where either the microscope state can only - be stored very coarsely or one is forced to store it very finely? - - This is a question of how one wishes to granularize pieces of information. - A possible solution is to consider each probed position, i.e. point in time - when the beam was not blanked and thus when the beam illuminates a portion of - the material, i.e. the interaction volume, whose signal contributions are then - counted by the one or multiple detector(s) as per pixel- or per voxel signal - in the region-of-interest. - NXevent_data_em in combination with the NXem application definition - allows researchers to document this. Noteworty to mention is that we understand - that in many cases realizing such a fine temporal and logical granularization - and data collection is hard to achieve in practice. - - A frequently made choice, mainly for convenience, is that drift and scan distortions - are considered a feature or inaccuracy of the image and/or spectrum and thus - one de facto accepts that the microscope was not as stable as expected during - the acquisition of the image. We learn that the idea of a time interval - during the microscope session may be interpreted differently by different - users. Here we consider the choice to focus on images and spectra, and eventually - single position measurements as the smallest granularization level. - Which eventually may require to add optional NXprocess instances for respectively - collected data to describe the relevant distortions. Nevertheless, the distortions - are typically corrected for by numerical protocols. This fact warrants to - consider the distortion correction a computational workflow which can be - modelled as a chain of NXprocess instances each with own parameters. an own - A more detailed overview of such computational steps to cope with scan distortions - is available in the literature: - - * `C. Ophus et al. <https://dx.doi.org/10.1016/j.ultramic.2015.12.002>`_ - * `B. Berkels et al. <https://doi.org/10.1016/j.ultramic.2018.12.016>`_ - * `L. Jones et al. <https://link.springer.com/article/10.1186/s40679-015-0008-4>`_ - - For specific simulation purposes, mainly in an effort to digitally repeat - or simulate the experiment, it is tempting to consider dynamics of the - instrument, implemented as time-dependent functional descriptions of - e.g. lens excitations, beam shape functions, trajectories of groups of - electrons, or detector noise models. - - For now the preferred strategy to handle these cases is through - customizations of the specific fields within NXevent_data_em instances. - - Another alternative could be to sample finer, eventually dissimilarly along - the time axi; however this may cause situations where an NXevent_data_em - instance does not contain specific measurements (i.e. images, spectra of - scientific relevance). - - In this case one should better go for a customized application definition - with a functional property description inside members (fields or groups) - in NXevent_data_em instances; or resort to a specific offspring application - definition of NXem which documents metadata for tracking explicitly electrons - (with ray-tracing based descriptors/computational geometry descriptors) - or tracking of wave bundles. - - This perspective on much more subtle time-dependent considerations of electron - microscopy can be advantageous also for storing details of time-dependent - additional components that are coupled to and/or synced with a microscope. - - Examples include cutting-edge experiments where the electron beam gets - coupled/excited by e.g. lasers. In this case, the laser unit should be - registered under the top-level NXinstrument section. Its spatio-temporal - details could be stored inside respective additional groups of the NXinstrument - though inside instances of here detailed NXevent_data_em. - - - - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval started. If the user wishes to specify an - interval of time that the snapshot should represent during which the instrument - was stable and configured using specific settings and calibrations, - the start_time is the start (left bound of the time interval) while - the end_time specifies the end (right bound) of the time interval. - - - - - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval ended. - - - - - Reference to a specific state and setting of the microscope. - - - - - Which specific event/measurement type. Examples are: - - * In-lens/backscattered electron, usually has quadrants - * Secondary_electron, image, topography, fractography, overview images - * Backscattered_electron, image, Z or channeling contrast (ECCI) - * Bright_field, image, TEM - * Dark_field, image, crystal defects - * Annular dark field, image (medium- or high-angle), TEM - * Diffraction, image, TEM, or a comparable technique in the SEM - * Kikuchi, image, SEM EBSD and TEM diffraction - * X-ray spectra (point, line, surface, volume), composition EDS/EDX(S) - * Electron energy loss spectra for points, lines, surfaces, TEM - * Auger, spectrum, (low Z contrast element composition) - * Cathodoluminescence (optical spectra) - * Ronchigram, image, alignment utility specifically in TEM - * Chamber, e.g. TV camera inside the chamber, education purposes. - - This field may also be used for storing additional information about the event. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXgraph_edge_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXgraph_edge_set.nxdl.xml deleted file mode 100644 index 69440ae..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXgraph_edge_set.nxdl.xml +++ /dev/null @@ -1,113 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The number of edges. - - - - - A set of (eventually directed) edges which connect nodes/vertices of a graph. - - - - Total number of edges, counting eventual bidirectional edges only once. - - - - - Integer which specifies the first index to be used for distinguishing - edges. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish edges for explicit indexing. - - - - - - - - Specifier whether each edge is non-directional, one-directional, - or bidirectional. Use the smallest available binary representation - which can store three different states: - - * 0 / state 0x00 is non-directional - * 1 / state 0x01 is one-directional - * 2 / state 0x02 is bi-directional - - - - - - - - Pairs of node/vertex identifier. Each pair represents the connection - between two nodes. - - In the case that the edge is non- or bi-directional - node identifier should be stored in ascending order is preferred. - - In the case of one-directional, for each pair the identifier of the source - node is the first entry in the pair. The identifier of the target is the - second entry in the pair, i.e. the pair encodes the information as - if one traverses the edge from the source node walking to the target node. - - - - - - - - - A human-readable qualifier which type or e.g. class instance the - edge is an instance of. - - - - - - - - A human-readable label/caption/tag for the edge. - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXgraph_node_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXgraph_node_set.nxdl.xml deleted file mode 100644 index 9b98765..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXgraph_node_set.nxdl.xml +++ /dev/null @@ -1,89 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality of the graph. Eventually use one for categorical. - - - - - The cardinality of the set, i.e. the number of nodes/vertices of the graph. - - - - - A set of nodes/vertices in space representing members of a graph. - - - - - - Integer which specifies the first index to be used for distinguishing - nodes. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish nodes for explicit indexing. - - - - - - - - A human-readable qualifier which type or e.g. class instance the - node is an instance of. As e.g. a NeXus application definition is a - graph, more specifically a hierarchical directed labelled property graph, - instances which are groups like NXgraph_node_set could have an is_a - qualifier reading NXgraph_node_set. - - - - - - - - A human-readable label/caption/tag of the graph. - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXgraph_root.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXgraph_root.nxdl.xml deleted file mode 100644 index 0e41c38..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXgraph_root.nxdl.xml +++ /dev/null @@ -1,36 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - An instance of a graph. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXibeam_column.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXibeam_column.nxdl.xml deleted file mode 100644 index e08b7e8..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXibeam_column.nxdl.xml +++ /dev/null @@ -1,137 +0,0 @@ - - - - - - - Container for components of a focused-ion-beam (FIB) system. - - FIB capabilities turn especially scanning electron microscopes - into specimen preparation labs. FIB is a material preparation - technique whereby portions of the sample are illuminated with a - focused ion beam with controlled intensity intense enough and with - sufficient ion momentum to remove material in a controllable manner. - - The fact that an electron microscope with FIB capabilities has needs a - second gun with own relevant control circuits, focusing lenses, and - other components, warrants an own base class to group these components - and distinguish them from the lenses and components for creating and - shaping the electron beam. - - For more details about the relevant physics and application examples - consult the literature, for example: - - * `L. A. Giannuzzi et al. <https://doi.org/10.1007/b101190>`_ - * `E. I. Preiß et al. <https://link.springer.com/content/pdf/10.1557/s43578-020-00045-w.pdf>`_ - * `J. F. Ziegler et al. <https://www.sciencedirect.com/science/article/pii/S0168583X10001862>`_ - * `J. Lili <https://www.osti.gov/servlets/purl/924801>`_ - - - - The source which creates the ion beam. - - - - Given name/alias for the ion gun. - - - - - Emitter type used to create the ion beam. - - If the emitter type is other, give further - details in the description field. - - - - - - - - - - - Which ionized elements or molecular ions form the beam. - Examples are gallium, helium, neon, argon, krypton, - or xenon, O2+. - - - - - - Average/nominal brightness - - - - - - Charge current - - - - - Ion acceleration voltage upon source exit and entering the vacuum flight path. - - - - - - Affine transformation which detail the arrangement in the microscope relative to - the optical axis and beam path. - - - - - - - - - - - Individual characterization results for the position, shape, - and characteristics of the ion beam. - - NXtransformations should be used to specify the location or position - at which details about the ion beam are probed. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXimage_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXimage_set.nxdl.xml deleted file mode 100644 index a482480..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXimage_set.nxdl.xml +++ /dev/null @@ -1,128 +0,0 @@ - - - - - - - - Number of images in the stack. - - - - - Number of pixel per image in the slow direction. - - - - - Number of pixel per image in the fast direction. - - - - - Container for reporting a set of images taken. - - - - Details how images were processed from the detector readings. - - - - Resolvable data artifact (e.g. filename) from which the all values in - the NXdata instances in this NXimage_set were loaded during parsing. - - - - An at least as strong as SHA256 hashvalue of the data artifact which - source represents digitally to support provenance tracking. - - - - - - Imaging (data collection) mode of the instrument during acquisition - of the data in this NXimage_set instance. - - - - - Link or name of an NXdetector instance with which the data were collected. - - - - - - - Image (stack). - - - - Image intensity values. - - - - - - - - - - Image identifier - - - - - - - Image identifier. - - - - - - Pixel coordinate center of mass along y direction. - - - - - - - Coordinate along y direction. - - - - - - Pixel coordinate center of mass along x direction. - - - - - - - Coordinate along x direction. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXimage_set_em_adf.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXimage_set_em_adf.nxdl.xml deleted file mode 100644 index 21616ca..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXimage_set_em_adf.nxdl.xml +++ /dev/null @@ -1,156 +0,0 @@ - - - - - - - - Number of images in the stack. - - - - - Number of pixel per image in the slow direction. - - - - - Number of pixel per image in the fast direction. - - - - - Container for reporting a set of annular dark field images. - - Virtually the most important case is that spectra are collected in - a scanning microscope (SEM or STEM) for a collection of points. - The majority of cases use simple d-dimensional regular scan pattern, - such as single point, line profiles, or (rectangular) surface mappings. - The latter pattern is the most frequently used. - - For now the base class provides for scans for which the settings, - binning, and energy resolution is the same for each scan point. - - - - Details how (HA)ADF images were processed from the detector readings. - - - - Typically the name of the input, (vendor) file from which all - the NXdata instances in this NXimage_set_em_adf were loaded during - parsing to represent them in e.g. databases. - - - - An at least as strong as SHA256 hashvalue of the dataset/file - which represents the source digitally to support provenance tracking. - - - - - - Commercial or otherwise given name to the program which was used - to process detector data into the adf image(s). - - - - Program version plus build number, commit hash, or description - of an ever persistent resource where the source code of the program - and build instructions can be found so that the program - can be configured in such a manner that the result file - is ideally recreatable yielding the same results. - - - - - - Annulus inner half angle - - - - - Annulus outer half angle - - - - - - Annular dark field image stack. - - - - - Image intensity values. - - - - - - - - - - Image identifier - - - - - - - Image ID. - - - - - - Pixel center of mass along y direction. - - - - - - - Coordinate along y direction. - - - - - - Pixel center of mass along x direction. - - - - - - - Coordinate along x direction. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXimage_set_em_kikuchi.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXimage_set_em_kikuchi.nxdl.xml deleted file mode 100644 index 776b539..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXimage_set_em_kikuchi.nxdl.xml +++ /dev/null @@ -1,205 +0,0 @@ - - - - - - - - Number of scanned points. Scan point may have none, one, or more pattern. - - - - - Number of diffraction pattern. - - - - - Number of pixel per Kikuchi pattern in the slow direction. - - - - - Number of pixel per Kikuchi pattern in the fast direction. - - - - - Measured set of electron backscatter diffraction data, aka Kikuchi pattern. - Kikuchi pattern are the raw data for computational workflows in the field - of orientation (imaging) microscopy. The technique is especially used in - materials science and materials engineering. - - Based on a fuse of the `M. A. Jackson et al. <https://doi.org/10.1186/2193-9772-3-4>`_ - of the DREAM.3D community and the open H5OINA format of Oxford Instruments - `P. Pinard et al. <https://doi.org/10.1017/S1431927621006103>`_ - - EBSD can be used, usually with FIB/SEM microscopes, for three-dimensional - orientation microscopy. So-called serial section analyses. For a detailed - overview of these techniques see e.g. - - * `M. A. Groeber et al. <https://doi.org/10.1186/2193-9772-3-5>`_ - * `A. J. Schwartz et al. <https://doi.org/10.1007/978-1-4757-3205-4>`_ - * `P. A. Rottman et al. <https://doi.org/10.1016/j.mattod.2021.05.003>`_ - - With serial-sectioning this involves however always a sequence of measuring, - milling. In this regard, each serial section (measuring) and milling - is an own NXevent_data_em instance and thus there such a three-dimensional - characterization should be stored as a set of two-dimensional data, - with as many NXevent_data_em instances as sections were measured. - - These measured serial sectioning images need virtually always post-processing - to arrive at the aligned and cleaned image stack before a respective digital - model of the inspected microstructure can be analyzed. The resulting volume - is often termed a so-called (representative) volume element (RVE). - Several software packages are available for performing this post-processing. - For now we do not consider metadata of these post-processing steps - as a part of this base class because the connection between the large variety - of such post-processing steps and the measured electron microscopy data - is usually very small. - - If we envision a (knowledge) graph for EBSD it consists of individual - sub-graphs which convey information about the specimen preparation, - the measurement of the specimen in the electron microscope, - the indexing of the collected Kikuchi pattern stack, - eventual post-processing of the indexed orientation image - via similarity grouping algorithms to yield (grains, texture). - Conceptually these post-processing steps are most frequently - serving the idea to reconstruct quantitatively so-called - microstructural features (grains, phases, interfaces). Materials scientists - use these features according to the multi-scale materials modeling paradigm - to infer material properties. They do so by quantifying correlations between - the spatial arrangement of the features, their individual properties, - and (macroscopic) properties of materials. - - - - - Details how Kikuchi pattern were processed from the detector readings. - Scientists interested in EBSD should inspect the respective NXem_ebsd - application definition which can be used as a partner application definition - to detail substantially more details to this processing. - - - - - Collected Kikuchi pattern as an image stack. As raw and closest to the - first retrievable measured data as possible, i.e. do not use this - container to store already averaged, filtered or whatever post-processed - pattern unless these are generated unmodifiably by the instrument - given the way how the instrument and control software was configured - for your microscope session. - - - - Array which resolves the scan point to which each pattern belongs. - Scan points are evaluated in sequence starting from scan point zero - until scan point n_sc - 1. Evaluating the cumulated of this array - decodes which pattern in intensity belong to which scan point. - In an example we may assume we collected three scan points. For the first - we measure one pattern, for the second we measure three pattern, - for the last we measure no pattern. - The values of scan_point_identifier will be 0, 1, 1, 1, as we have - measured four pattern in total. - - In most cases usually one pattern is averaged by the detector for - some amount of time and then reported as one pattern. Use compressed - arrays allows to store the scan_point_identifier efficiently. - - - - - - - - Signal intensity. For so-called three-dimensional or serial sectioning - EBSD it is necessary to follow a sequence of specimen surface preparation - and data collection. In this case users should collect the data for each - serial sectioning step in an own instance of NXimage_set_em_kikuchi. - All eventual post-processing of these measured data should be documented - via NXebsd, resulting microstructure representations should be stored - as NXms. - - - - - - - - - - Kikuchi pattern intensity - - - - - - - Pattern are enumerated starting from 0 to n_p - 1. - - - - - - - Kikuchi pattern identifier - - - - - - Pixel coordinate along the y direction. - - - - - - - Label for the y axis - - - - - - Pixel coordinate along the x direction. - - - - - - - Label for the x axis - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXinteraction_vol_em.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXinteraction_vol_em.nxdl.xml deleted file mode 100644 index a6beeb6..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXinteraction_vol_em.nxdl.xml +++ /dev/null @@ -1,37 +0,0 @@ - - - - - Base class for storing details about a modelled shape of interaction volume. - - The interaction volume is mainly relevant in scanning electron microscopy - when the sample is thick enough so that the beam is unable to illuminate - through the specimen. - Computer models like Monte Carlo or molecular dynamics / electron beam - interaction simulations can be used to qualify and/or quantify the shape of - the interaction volume. - - Explicit or implicit descriptions are possible. - - * An implicit description is via a set of electron/specimen interactions - represented ideally as trajectory data from the computer simulation. - * An explicit description is via an iso-contour surface using either - a simulation grid or a triangulated surface mesh of the approximated - iso-contour surface evaluated at specific threshold values. - Iso-contours could be computed from electron or particle fluxes through - an imaginary control surface (the iso-surface). - Threshold values can be defined by particles passing through a unit control - volume (electrons) or energy-levels (e.g. the case of X-rays). - Details depend on the model. - * Another explicit description is via theoretical models which may - be relevant e.g. for X-ray spectroscopy - - Further details on how the interaction volume can be quantified - is available in the literature for example: - - * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ - * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXion.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXion.nxdl.xml deleted file mode 100644 index 99a19f2..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXion.nxdl.xml +++ /dev/null @@ -1,168 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Maximum number of atoms/isotopes allowed per (molecular) ion (fragment). - - - - - Number of mass-to-charge-state-ratio range intervals for ion type. - - - - - Set of atoms of a molecular ion or fragment in e.g. ToF mass spectrometry. - - - - A unique identifier whereby such an ion can be referred to - via the service offered as described in identifier_type. - - - - - How can the identifier be resolved? - - - - - - - - Ion type (ion species) identifier. The identifier zero - is reserved for the special unknown ion type. - - - - - A vector of isotope hash values. - These values have to be stored in an array, sorted in decreasing order. - The array is filled with zero hash values indicating unused places. - The individual hash values are built with the following hash function: - - The hash value :math:`H` is :math:`H = Z + N*256` with :math:`Z` - the number of protons and :math:`N` the number of neutrons - of each isotope respectively. - - Z and N have to be 8-bit unsigned integers. - For the rationale behind this `M. Kühbach et al. (2021) <https://doi.org/10.1017/S1431927621012241>`_ - - - - - - - - - A supplementary row vector which decodes the isotope_vector into - a human-readable matrix of nuclids with the following formatting: - - The first row specifies the isotope mass number, i.e. using the hashvalues - from the isotope_vector this is :math:`Z + N`. As an example for a - carbon-14 isotope the number is 14. - The second row specifies the number of protons :math:`Z`, e.g. 6 for the - carbon-14 example. This row matrix is thus a mapping the notation of - using superscribed isotope mass and subscripted number of protons to - identify isotopes. - Unused places filling up to n_ivecmax need to be filled with zero. - - - - - - - - - Color code used for visualizing such ions. - - - - - Assumed volume of the ion. - - In atom probe microscopy this field can be used to store the reconstructed - volume per ion (average) which is typically stored in range files and will - be used when building a tomographic reconstruction of an atom probe - dataset. - - - - - Charge of the ion. - - - - - Signed charge state of the ion in multiples of electron charge. - - Only positive values will be measured in atom probe microscopy as the - ions are accelerated by a negatively signed bias electric field. - In the case that the charge state is not explicitly recoverable, - the value should be set to zero. - - In atom probe microscopy this is for example the case when using - classical range file formats like RNG, RRNG for atom probe data. - These file formats do not document the charge state explicitly. - They report the number of atoms of each element per molecular ion - surplus the mass-to-charge-state-ratio interval. - With this it is possible to recover the charge state only for - specific molecular ions as the accumulated mass of the molecular ion - is defined by the isotopes, which without knowing the charge leads - to an underconstrained problem. - Details on ranging can be found in the literature: `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ - - - - - Human-readable ion type name (e.g. Al +++) - The string should consists of ASCII UTF-8 characters, - ideally using LaTeX notation to specify the isotopes, ions, and charge - state. Examples are 12C + or Al +++. - Although this name may be human-readable and intuitive, parsing such - names becomes impractical for more complicated cases. Therefore, for the - field of atom probe microscopy the isotope_vector should be the - preferred machine-readable format to use. - - - - - Associated lower (mqmin) and upper (mqmax) bounds of - mass-to-charge-state ratio interval(s) [mqmin, mqmax] - (boundaries included) for which the respective ion is one to be labelled - with ion_identifier. The field is primarily of interest to document the - result of indexing a ToF/mass spectrum. - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXisocontour.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXisocontour.nxdl.xml index 8c4361d..eace731 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXisocontour.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXisocontour.nxdl.xml @@ -2,9 +2,9 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -33,24 +33,35 @@ - Computational geometry description of isocontouring/phase-fields in Euclidean space. + Base class for describing isocontouring/phase-fields in Euclidean space. + + Iso-contouring algorithms such as Marching Cubes and others are frequently + used to segment d-dimensional regions at crossings of a threshold value, + the so-called isovalue. - Iso-contouring algorithms such as MarchingCubes and others are frequently - used to segment d-dimensional regions into regions where intensities are - lower or higher than a threshold value, the so-called isovalue. + In Computational Materials Science phase-field methods are frequently used. + Phase-field variables are discretized frequently using regular grids. - Frequently in computational materials science phase-field methods are - used which generate data on discretized grids. Isocontour algorithms - are often used in such context to pinpoint the locations of microstructural - features from this implicit phase-field-variable-based description. + Isocontour algorithms are often used in such context to pinpoint the + locations of microstructural features from this implicit phase-field- + variable-value-based description. One of the key intentions of this base class is to provide a starting point - for scientists from the phase-field community (condensed matter physicists, - and materials engineers) to incentivize that also phase-field simulation - data could be described with NeXus, provided base classes such as the this one - get further extend according to the liking of the phase-field community. + for scientists from the phase-field community (condensed-matter physicists, + and materials engineers) to incentivize that also phase-field (and other) + simulation data can take advantage of NeXus base class to improve + interoperability. - + + + The dimensionality of the space in which the isocontour is embedded. + + + + + + + The discretized grid on which the iso-contour algorithm operates. diff --git a/src/nexusformat/definitions/contributed_definitions/NXiv_temp.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXiv_temp.nxdl.xml index 927c7bb..6d88101 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXiv_temp.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXiv_temp.nxdl.xml @@ -51,6 +51,25 @@ + + + + Descriptive name or ideally (globally) unique persistent identifier. + + + + + List of comma-separated elements from the periodic table + that are contained in the sample. + If the sample substance has multiple components, all + elements from each component must be included in `atom_types`. + + The purpose of the field is to offer materials database systems an + opportunity to parse the relevant elements without having to interpret + these from the sample history or from other data sources. + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXlab_electro_chemo_mechanical_preparation.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXlab_electro_chemo_mechanical_preparation.nxdl.xml deleted file mode 100644 index 8bb1e4f..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXlab_electro_chemo_mechanical_preparation.nxdl.xml +++ /dev/null @@ -1,188 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Grinding and polishing of a sample using abrasives in a wet lab. - Manual procedures, electro-chemical, vibropolishing. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - - - - - - - - - - A preparation step performed by a human or a robot/automated system. - - - - - - - - Carrier/plate used on which the abrasive/(lubricant) mixture was applied. - - - - - - Medium on the abrasive_medium_carrier (cloth or grinding plate) - whereby material is abrasively weared. - - - - - - Lubricant - - - - - - Qualitative statement how the revelation of the machine was configured. - If the rotation was controlled manually, e.g. by turning knobs - choose manual and estimate the nominal average rotation. - If the rotation was controlled via choosing from a fixed set - of options offered by the machine choose fixed and - specify the nominal rotation. - If programmed use rotation_history (e.g. for automated/robot systems). - - - - - - - - - - - Qualitative statement how the (piston) force with which the sample - was pressed into/against the abrasive medium was controlled if at all. - If the force was controlled manually e.g. by turning knobs - choose manual and estimate nominal average force. - If the force was controlled via choosing from a fixed set - of options offered by the machine choose fixed and - specify the nominal force. - If programmed use force_history (e.g. for automated/robot systems). - - - - - - - - - - - Qualitative statement for how long (assuming regular uninterrupted) - preparation at the specified conditions the preparation step was - applied. - - - - - - - - - - - Turns per unit time. - - - - - - Force exerted on the sample to press it into the abrasive. - - - - - - Seconds - - - - - Qualitative statement how the material removal was characterized. - - - - - - - - - - How thick a layer was removed. - - - - - - - A preparation step performed by a human or a robot/automated system - with the aim to remove residual abrasive medium from the specimen surface. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXlab_sample_mounting.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXlab_sample_mounting.nxdl.xml deleted file mode 100644 index 9127e40..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXlab_sample_mounting.nxdl.xml +++ /dev/null @@ -1,93 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Embedding of a sample in a medium for easing processability. - - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - - - - - - - - - - Qualitative statement how the sample was mounted. - - - - - - - - - Type of material. - - - - - - - - - Electrical conductivity of the embedding medium. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXlens_opt.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXlens_opt.nxdl.xml deleted file mode 100644 index 4738a7b..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXlens_opt.nxdl.xml +++ /dev/null @@ -1,185 +0,0 @@ - - - - - - - - - Size of the wavelength array for which the refractive index of the material - is given. - - - - - Size of the wavelength array for which the refractive index of the coating - is given. - - - - - Size of the wavelength array for which the reflectance or transmission of - the lens is given. - - - - - Description of an optical lens. - - - - Type of the lens (e.g. concave, convex etc.). - - - - - - - - - - - - - - - If you chose 'other' as type specify what it is. - - - - - Is it a chromatic lens? - - - - - Diameter of the lens. - - - - - Properties of the substrate material of the lens. If the lens has a - coating specify the coating material and its properties in 'coating'. - - - - Specify the substrate material of the lens. - - - - - Thickness of the lens substrate at the optical axis. - - - - - Complex index of refraction of the lens material. Specify at given - wavelength (or energy, wavenumber etc.) values. - - - - - - - - - - - If the lens has a coating describe the material and its properties. - Some basic information can be found e.g. [here] - (https://www.opto-e.com/basics/reflection-transmission-and-coatings). - If the back and front side of the lens are coated with different - materials, use separate COATING(NXsample) fields to describe the coatings - on the front and back side, respectively. For example: - coating_front(NXsample) and coating_back(NXsample). - - - - Specify the coating type (e.g. dielectric, anti-reflection (AR), - multilayer coating etc.). - - - - - Describe the coating material (e.g. MgF2). - - - - - Thickness of the coating. - - - - - Complex index of refraction of the coating. Specify at given spectral - values (wavelength, energy, wavenumber etc.). - - - - - - - - - - Reflectance of the lens at given spectral values. - - - - - - - - Transmission of the lens at given spectral values. - - - - - - - - Focal length of the lens on the front side (first value), i.e. where the - beam is incident, and on the back side (second value). - - - - - - - - Curvature radius of the lens. - Instead of 'FACE' in the name of this field, the user is advised to - specify for which surface (e.g. front or back) the curvature is provided: - e.g. curvature_front or curvature_back. The front face is the surface on - which the light beam is incident, while the back face is the one from - which the light beam exits the lens. - - - - - Abbe number (or V-number) of the lens. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXmagnetic_kicker.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmagnetic_kicker.nxdl.xml index 1ce3aec..89a610d 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXmagnetic_kicker.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXmagnetic_kicker.nxdl.xml @@ -26,32 +26,32 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd" > - definition for a magnetic kicker. + Base class for a magnetic kicker. - extended description of the kicker. + Extended description of the kicker. - define position of beamline element relative to production target + Define position of beamline element relative to production target - kicker timing as defined by ``description`` attribute + Kicker timing as defined by ``description`` attribute - current set on supply. + Current set on supply. - current read from supply. + Current read from supply. - voltage set on supply. + Voltage set on supply. - voltage read from supply. + Voltage read from supply. diff --git a/src/nexusformat/definitions/contributed_definitions/NXmanipulator.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmanipulator.nxdl.xml deleted file mode 100644 index 68b656b..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXmanipulator.nxdl.xml +++ /dev/null @@ -1,82 +0,0 @@ - - - - - - Extension of NXpositioner to include fields to describe the use of manipulators - in photoemission experiments. - - - - Name of the manipulator. - - - - - A description of the manipulator. - - - - - Type of manipulator, Hexapod, Rod, etc. - - - - - Is cryocoolant flowing through the manipulator? - - - - - Temperature of the cryostat (coldest point) - - - - - Power in the heater for temperature control. - - - - - Temperature at the closest point to the sample. This field may also be found in - NXsample if present. - - - - - Current to neutralize the photoemission current. This field may also be found in - NXsample if present. - - - - - Possible bias of the sample with trespect to analyser ground. This field may - also be found in NXsample if present. - - - - - Class to describe the motors that are used in the manipulator - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXmatch_filter.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmatch_filter.nxdl.xml index 482b028..757e61c 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXmatch_filter.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXmatch_filter.nxdl.xml @@ -2,9 +2,9 @@ - + - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays. - How many different match values does the filter specify. + How many different match values does the filter specify. - Settings of a filter to select or remove entries based on their value. + Base class of a filter to select members of a set based on their identifier. - + - Meaning of the filter: - Whitelist specifies which entries with said value to include. - Entries with all other values will be filtered out. - - Blacklist specifies which entries with said value to exclude. - Entries with all other values will be included. + Definition of the logic what the filter yields: + + * Whitelist specifies which entries with said value to include. + Entries with all other values will be excluded. + * Blacklist specifies which entries with said value to exclude. + Entries with all other values will be included. @@ -51,10 +51,9 @@ - Array of values to filter according to method. For example if the filter - specifies [1, 5, 6] and method is whitelist, only entries with values - matching 1, 5 or 6 will be processed. All other entries will be filtered - out. + Array of values to filter according to method. If the match e.g. specifies + [1, 5, 6] and method is set to whitelist, only entries with values matching + 1, 5 or 6 will be processed. All other entries will be excluded. diff --git a/src/nexusformat/definitions/contributed_definitions/NXmicrostructure.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure.nxdl.xml new file mode 100644 index 0000000..e5059f1 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure.nxdl.xml @@ -0,0 +1,886 @@ + + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays. + + + + The number of crystals or their projections + + + + + The number of interfaces or their projections + + + + + The number of triple junctions or their projections + + + + + The number of quadruple junctions or their projections + + + + + + The number of one-dimensional crystal projections + + + + + The number of one-dimensional interface projections + + + + + + The number of two-dimensional crystal projections + + + + + The number of two-dimensional interface projections + + + + + The number of two-dimensional triple line projections + + + + + The number of two-dimensional line defect projections + + + + + + The number of crystals (grain and sub-grain are exact synonyms for crystal). + + + + + The number of interfaces (grain boundary and phase boundary are subclasses of + interfaces). + + + + + The number of triple junctions (triple line is a exact synonym for triple + junction, triple point is projection of a triple junction). + + + + + The number of quadruple junctions. + + + + + + The dimensionality of the representation that needs to match the value for + configuration/dimensionality + + + + + Base class to describe a microstructure, its structural aspects, associated descriptors, properties. + + Whether one uses a continuum or atomic scale description of materials, these are always a model only of + the true internal structure of a material. Such models are useful as they enable a coarse-graining and + categorizing of properties and representational aspects from which measured or simulated descriptions + can be correlated with properties, i.e. descriptor values. The base class here can be used to describe + the structural aspect of a region-of-interest for a specimen that was investigated or a computer + simulation that was performed for a virtual specimen. + + Specimens experience thermo-chemo-mechanical processing (steps) before characterization. Therefore, + the characterized microstructure may not turn out to be the same structure as of the untreated + sample from which the region-of-interests on the specimen were sampled. + + Fields such as time and increment enable a quantification of the spatiotemporal evolution of a materials' + structure by using multiple instances of NXmicrostructure. Both measurements and simulation virtually + always sample this evolution. Most microscopy techniques characterize only a two-dimensional representation + (projection) of the characterized material volume. Often materials are characterized only for specific states + or via sampling coarsely in time relative to the timescale at which the physical phenomena take place. + This is typically a compromise between the research questions and technical surplus practical limitations. + + The term microstructural feature covers here crystals and all sorts of crystal defects within the material + (interfaces, triple junctions, dislocations, pores, etc.). + A key challenge with the description of representations and properties of such microstructural features is that + they can be represented and view as features with different dimensionality. Furthermore, combinations of features of + different dimensionality are frequently expected to be documented with intuitive naming conventions when + flat property lists are used. For these key-value dictionaries often folksonomies are used. These can be based + on ad hoc documentation of such dictionaries in the literature and the metadata section of public data repositories. + + NXmicrostructure is an attempt to standardize these descriptions stronger. + + For crystals the number of typically used technical terms are smaller than for interfaces or line like defects and + junctions of different types of crystal defects. The term grain describes a contiguous region of material that is + delineated by interfaces (phase or grain boundaries). With its origin motivated by light optical microscopy though + a grain is not necessarily a single crystal but can have an internal structure of defect such as dislocations. + In this base class we use the term and respective group crystals though for single crystals and grains. + The reason why this is possible is that when e.g. materials engineers talk about grains they inherently assume + that the internal structure of these grains can be described with homogenized effective properties. + If alternatively the individual structural crystalline or features of this grain should be distinguished + it is useful to instantiate these as individual instances of crystals. + + Grain boundaries and phase boundaries are two main categories of interfaces. + A grain boundary delineates two regions with similar crystal structure and phase but different orientation. + A grain boundary is thus a homophase interface. By contrast, a heterophase boundary delineates two regions with typically + but not necessarily dissimilar crystal structure but a different atomic occupation that justifies to distinguish two + phases. There is a substantial variety of interfaces whose distinction was classically based on geometrical arguments + but considers that atomic segregation is an equally important structural aspect to consider when classifying grain + boundaries. A concise overview on theoretical aspect of and the semantics for characterizing interfaces and their properties + is provided in e.g. `W. Bollmann <https://doi.org/10.1007/978-3-642-49173-3>`_ and A. Sutton and R. W. Baluffi, + Interfaces in Crystalline Materials, Clarendon Press, ISBN 9780198500612. + + Also for junctions between crystal defects there is a considerable variety of terms. Junctions are features in + three-dimensional Euclidean space even if they are formed maybe only through a monolayer or a pearl chain of atoms. + Either way their local atomic and electronic environment is different compared to the situation of an ideal crystal, + or the adjoining defects, which gives typically rise to a plethora of configurations of which some yield useful material + properties or affect material properties. + + Like crystals and interfaces, junctions are assumed to represent groups of atoms that have specific descriptor values + which are different to other features. Taking an example, a triple junction is practically a three-dimensional defect as its atoms + are arranged in three-dimensional space but the characteristics of that defect can often be reduced to a lower-dimensional + description such as a triple line or a triple point as the projection of a line. Therefore, different representations can + be used to describe the location, shape, and structure of such defect. + + This base class provides definitions for crystals, grains, interfaces, triple junctions, and quadruple junctions thus covering, + volumetric, patch, line, and point like features that can serve as examples for future extension. + + As different types of crystal defects can interact, there is a substantial number of in principle characterizable and representable + objects. Take again a triple line as an example. It is a tubular feature built from three adjoining interfaces. However, dislocations + as line defects can interact with triple lines. Therefore, one can also argue that along a triple line there exist dislocation-line- + triple-line junctions, likewise dislocations form own junctions. + + The description took inspiration from `E. E. Underwood <https://doi.org/10.1111/j.1365-2818.1972.tb03709.x>`_ + and E. E. Underwood's book on Quantitative Stereology published in 1970 to categorize features based on their dimensionality. + + Indices can be defined either implicitly or explicitly. Indices for implicit indexing are defined + on the interval :math:`[index\_offset, index\_offset + cardinality - 1]`. Indices can be used as identifiers + for distinguishing instances, i.e. indices are equivalent to instance names of individual crystals. + + + + + Discouraged free-text field for leaving comments + + + + + ISO8601 with offset to local time zone included when a timestamp is required. + + + + + Measured or simulated physical time stamp for this microstructure snapshot. + Not to be confused with wall-clock timing or profiling data. + + + + + Iteration or increment counter. + + + + + Group where to store details about the configuration and parameterization of algorithms + used whereby microstructural features were identified. + + + + Dimensionality of Euclidean space in which the analysis is performed. + + This field can be used e.g. by a research data management system to identify + if the description specifies one-, two-, or three-dimensional microstructural representations. + + + + + + + + + + Algorithm whereby interfaces between crystals were reconstructed. + + * Disorientation clustering groups nearby material points based on their crystallographic disorientation + * Fast multiscale clustering based on `D. Kushnir et al. <https://doi.org/10.1016/j.patcog.2006.04.007>`_ + * Markov chain clustering `F. Niessen et al. <https://doi.org/10.1107/S1600576721011560>`_ + + + + + + + + + + + + Threshold to define at which disorientation angle to assume two crystalline regions have a significant + orientation difference that warrants to assume that there exists an interface between the two regions. + + + + + The program with which the microstructure was reconstructed. + + + + + + + + + + + + + + + The chemical composition of this microstructure (region). + + + + + Different (thermodynamic) phases can be distinguished for the region-of- + interest. + + + + First identifier whereby to identify phases implicitly. + + + + + + + One- or two-dimensional projections, or three-dimensional representations of crystals. + + An example for a volume bounded by other crystal defects. Crystals can be grains of + different phases, precipitates, dispersoids; there are many terms used specifically in + the materials engineering community. + + Typically, crystals are measured on the surface of a sample via optical or electron microscopy. + Using X-ray diffraction methods crystals can be observed in bulk specimens. + + Crystals are represented by a set of pixel, voxel, or polygons and their polyline boundaries. + In rare cases the volume bounded gets represented using constructive solid geometry approaches. + + + + + Reference to an instance of: + + * :ref:`NXcg_polyline` for a one- or two-dimensional representation as only a projection is available (like in linear intercept analysis) + * :ref:`NXcg_polygon`, :ref:`NXcg_triangle`, or :ref:`NXcg_polyhedron` for a two- or three-dimensional representation as only a projection is available (like in most experiments) + * :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D) + + which represent the geometrical entities of the discretization. + + + + + How many crystals are distinguished. + + Crystals are listed irrespective of the phase to which these are assigned. + + + + + How many phases are distinguished. + + Phases are typically distinguished based on statistical thermodynamics argument and crystal structure. + + + + + First identifier whereby to identify crystals implicitly. + + + + + Identifier whereby to identify each crystal explicitly. + + + + + + + + Identifier whereby to identify phase for each crystal explicitly. + + + + + + + + + True, if the feature makes contact with the edge of the ROI. + False, if the feature does not make contact with the edge of the ROI. + + + + + + + + Average disorientation angle for each crystal between individual orientations + of that crystal evaluated as a summary statistic for all probed positions vs the + average disorientation of that crystal. + + + + + + + + Length of each crystal + + + + + + + + Area of each crystal. + + + + + + + + Volume of each crystal + + + + + + + + Possibility to store the mean orientation of the grain. + + + + + + One- or two-dimensional projections or three-dimensional representation of interfaces + between crystals as topological entities equivalent to dual_junctions. + + An example for a surface defect. Most important are interfaces such as grain and phase boundaries + but factually interfaces also exist between the environment and crystals exposed at the + surface of the specimen or internal surfaces like between crystals, cracks, or pores. + + Interfaces are typically reported as discretized features. For interface projections on the 2D plane + these are most frequently polyline segments. For interface patches in 3D these are most frequently + triangulations. Descriptions with continuous functions are seldom used unless simplified configurations + are studied in modeling and theoretical studies. + + When using discretizations the individual interface segments need to be distinguished from the interfaces + themselves. Consequently, there are two sets of indices. + + + + Reference to an instance of: + + * :ref:`NXcg_point` for a one-dimensional representation as only a projection is available (as in linear intercept analyses) + * :ref:`NXcg_polyline` or :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) + * :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D) using (boolean) masks + (like in computer simulations or 3D experiments) + + which represent the geometrical entities of the discretization. + + + + + How many interfaces are distinguished. + + + + + First identifier whereby to identify interfaces implicitly. + + + + + Identifier whereby to identify each interface explicitly. + + An array with as many entries as interfaces or their projections. + + + + + + + + + Set of pairs of indices_crystal values, for each interface one value pair. + + An array with as many pairs as interfaces or their projections. + + + + + + + + The specific identifiers whereby to resolve ambiguities. + + + + + + Set of pairs of indices_phase values, for each interface one value pair. + + An array with as many pairs as interfaces or their projections. + + + + + + + + The specific identifiers whereby to resolve ambiguities. + + + + + + + Interfaces can be the physical three-dimensional surfaces or two- or one-dimensional + projections. The latter situation applies typically for characterization with electron + microscopy. + + In the case of a two-dimensional projection interfaces are interface traces. These have + two terminating junctions. In three dimensions though the interface is a surface patch + that is bounded by multiple triple lines. + + Number of triple_junctions adjoining each interface. This array resolves the number of + values along the second dimension for the field indices_triple_junctions. + + + + + + + + Set of pairs of indices_triple_junction for each interface. + + An array with as many tuples of pairs to describe + all junctions about all interfaces. + + + + + + + The specific identifiers whereby to resolve ambiguities. + + + + + + + True, if the interface makes contact with the edge of the ROI. + False, if the interface does not make contact with the edge of the ROI. + + + + + + + + Gibbs free surface energy for each interface. + + + + + + + + Non-intrinsic mobility of each interface. + + + + + + + + The length of each interface if only projections are available. + + This is not necessarily the same as the length of the individual + polyline segments whereby the interface is discretized. + + + + + + + + The surface area of all interfaces. + + + + + + + + + Projections or representations of junctions at which three interfaces meet. + + An example for a line defect. Triple junctions are characterized as triple lines or triple points as their projections, + or junctions observed between crystals (at the specimen surface exposed to an environment) + (including wetting phenomena) or inside the specimen (crack, pores). + + + + Reference to an instance of: + + * :ref:`NXcg_point` for a one-dimensional representation as only a projection is available (like in most experiments) + * :ref:`NXcg_polyline` for a two-dimensional representation as only a projection is available + * :ref:`NXcg_polygon` for a two-dimensional representation in the (seldom) case of sufficient spatial resolution + and the line in the projection plane or cases where triple junction locations are approximated e.g. using a set of triangles + * :ref:`NXcg_polyhedron` for a three-dimensional representation via e.g. a representation of Voronoi cells about atoms + * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks + + which represent the geometrical entities of the discretization. + + + + + Number of triple junctions. + + + + + First identifier to identify triple junctions implicitly. + + + + + Identifier to identify each triple junction explicitly. + + + + + + + + + Set of identifier for positions whereby to identify the location of each + junction. + + + + + + + The specific identifiers whereby to resolve ambiguities. + + + + + + Explicit positions. + + + + + + + + + Set of tuples of identifier of crystals connected to the junction for each + triple junction. + + + + + + + + + + Set of tuples of identifier of interfaces connected to the junction for each + triple junction. + + + + + + + + The specific interface identifiers whereby to resolve ambiguities. + + + + + + + Set of tuples of identifier for polyline segments connected to the junction for + each triple junction. + + + + + + + + The specific indices_polyline whereby to resolve ambiguities. + + + + + + + True, if the triple line makes contact with the edge of the ROI. + False, if the triple line does not make contact with the edge of the ROI. + + + + + + + + Specific line energy of each triple junction + + + + + + + + Non-intrinsic mobility of each triple junction. + + + + + + + + The length of each triple junction. + + This is not necessarily the same as the length of the individual + polyline segments whereby the junction is discretized. + + + + + + + + The volume about each triple junction. + + Respective cut-off criteria need to be specified. + + + + + + + + + Quadruple junctions as a region where four crystals meet. + + An example for a point (like) defect. + + Thermodynamically such junctions can be unstable. + Specifically when discretizations are used in simulations + that do not address the thermodynamics of and splitting characteristics + of junctions in cases when more than four crystals meet, it is possible + that so-called higher-order junctions are observed. + + + + Reference to an instance of: + + * :ref:`NXcg_point` + * :ref:`NXcg_grid` for regularly pixelated (in 1D, 2D) or voxelated representations (in 3D) using (boolean) masks + + which represent the geometrical entities of the discretization. + + + + + Number of quadruple junctions. + + + + + First identifier to identify quadruple junctions implicitly. + + + + + Identifier to identify each quadruple junction explicitly. + + + + + + + + + Set of identifier for positions whereby to identify the location of each + junction. + + + + + + + The specific point identifier whereby to resolve ambiguities. + + + + + + Explicit positions. + + + + + + + + + + Set of tuples of identifier of crystals connected to the junction for each + junction. + + + + + + + + The specific identifier to instances of crystal identifiers whereby to resolve + ambiguities. + + + + + + Set of tuples of identifier of interfaces connected to the junction for each + junction. + + + + + + + + The specific identifier to instances of interface identifiers whereby to resolve + ambiguities. + + + + + + + Set of tuples of identifier for triple junctions connected to the junction for + each quadruple junction. + + + + + + + + The specific identifier to instances of triple junction identifiers whereby to + resolve ambiguities. + + + + + + + Set of tuples of identifier for phases of crystals connected to the junction for + each quadruple junction. + + + + + + + + The specific identifier to instances of phase identifier whereby to resolve + ambiguities. + + + + + + + True, if the junction makes contact with the edge of the ROI. + True, if the junction does not make contact with the edge of the ROI. + + + + + + + + Energy of the quadruple_junction as a defect. + + + + + + + + Non-intrinsic mobility of each quadruple_junction. + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXcs_gpu.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_feature.nxdl.xml similarity index 63% rename from src/nexusformat/definitions/contributed_definitions/NXcs_gpu.nxdl.xml rename to src/nexusformat/definitions/contributed_definitions/NXmicrostructure_feature.nxdl.xml index 3392e41..0a34117 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXcs_gpu.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_feature.nxdl.xml @@ -2,9 +2,9 @@ - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - + - Computer science description of a graphic processing unit (GPU) of a computer. + Base class for documenting structuring features of a microstructure. + + Instances of the class enable sub-grouping of microstructural features + as the abstract base class NXobject should not be used for this purpose. - + - Given name of the GPU. Users should be as specific as possible. + The chemical composition of this microstructural feature + or set of such features. - - + diff --git a/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_ipf.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_ipf.nxdl.xml new file mode 100644 index 0000000..59ae193 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_ipf.nxdl.xml @@ -0,0 +1,245 @@ + + + + + + + + Number of pixel along the slow direction used for the IPF color key. + + + + + Number of pixel along the fast direction used for the IPF color key. + + + + + Number of pixel along the slowest direction, typically labeled z or k. + + + + + Number of pixel along the slow direction, typically labeled y or j. + + + + + Number of pixel along the fast direction, typically labeled x or i. + + + + + Number of RGB values along the fastest direction, always three. + + + + + Base class to store an inverse pole figure (IPF) mapping (IPF map). + + + + Reference to an instance of :ref:`NXcoordinate_system` in which the axes axis_z, + axis_y, and axis_x are defined. + + + + + The algorithm whereby orientations are colored. + + + + + + + + + The direction normal vector along which orientations are projected. + + + + + + + Reference to an instance of :ref:`NXcoordinate_system` in which the projection_direction is defined. + + If the field depends_on is not provided but parents of the instance of this base class or its + specializations define an instance of :ref:`NXcoordinate_system`, projection_direction + is defined in this coordinate system. + + If nothing is provided, it is assumed that projection_direction is defined in the McStas coordinate system. + + + + + + Details about the original grid, i.e. the grid for which the IPF map was computed + when that IPF map was exported from the tech partner's file format representation. + + + + + Details about the grid onto which the IPF is recomputed. + + Rescaling the visualization of the IPF map may be needed to enable + visualization in specific software tools like H5Web. + + + + + How where orientation values at positions of input_grid computed to values on output_grid. + + Nearest neighbour means the orientation of the closed (Euclidean distance) grid point of the input_grid was taken. + + + + + + + + Inverse pole figure mapping. + + Instances named phase0 should by definition refer to the null phase notIndexed. + Inspect the definition of :ref:`NXphase` and its field phase_id + for further details. + + Details about possible regridding and associated interpolation + during the computation of the IPF map visualization can be stored + using the input_grid, output_grid, and interpolation fields. + + The main purpose of this map is to offer a normalized default representation + of the IPF map for consumption by a research data management system (RDMS). + + + + Inverse pole figure color code for each map coordinate. + + Different types of AXISNAME dimensional scale axes are found in practice. A few examples: + + * No scaling, e.g. pixel position values like 0, 1, 2, 3 pixel. + Pixels on the map can be distinguished but that map is disconnected from + any sample surface context and eventually physical scaling + * Scaling but no offset, e.g. calibrated pixel position 0., 0.5, 1.0, 1.5 micron. + Pixels on the map can be compared for their distance to obtain e.g. size of features + but the position of the map relative to the e.g. the sample surface is unclear. + For IPF maps this is the most frequently reported situation. + * Scaling and offset, which resolves also the absolute position of the map in + relation to the sample surface. This is useful information for stitching multiple + mappings together and other processing where precise and accurate + position data are relevant e.g. for correlative materials characterization. + + Three types of dimensional constraints for maps are possible: + + * (n_x, 3), a one-dimensional map, + typically used for coarse sampling and crystal size statistics. + * (n_y, n_x, 3), a two-dimensional map, + the most frequently found reported + * (n_z, n_y, n_x, 3), a three-dimensional map, + these are commonly generated using computational methods, + or in cases multiple EBSD maps have been stitched/reconstructed + into a three-dimensional map. + + + + + + Pixel center coordinate calibrated for step size along the z axis of the map. + + + + + + + + Pixel center coordinate calibrated for step size along the y axis of the map. + + + + + + + + Pixel center coordinate calibrated for step size along the x axis of the map. + + + + + + + + + The color code which maps color to orientation in the fundamental zone. + + For each stereographic standard triangle (SST), i.e. a rendering of the + fundamental zone of the crystal-symmetry-reduced orientation space + SO3, it is possible to define a color model which assigns a color to each + point in the fundamental zone. + + Different mapping models are used. These implement (slightly) different + scaling relations. Differences exist across representations of tech partners. + + Differences are which base colors of the RGB color model are placed in + which extremal position of the SST and where the white point is located. + + For further details see: + + * [G. Nolze et al.](https://doi.org/10.1107/S1600576716012942) + * [S. Patala et al.](https://doi.org/10.1016/j.pmatsci.2012.04.002). + + Details are implementation-specific and not standardized yet. + + + + + + Inverse pole figure color code for each map coordinate. + + + + + + + + + + Pixel along the y-axis. + + + + + + + + Pixel along the x-axis. + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml new file mode 100644 index 0000000..40dc06c --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml @@ -0,0 +1,193 @@ + + + + + + + + Number of material points along the z axis of the domain. + + + + + Number of material points along the y axis of the domain. + + + + + Number of material points along the x axis of the domain. + + + + + Number of crystals. + + + + + Application definition for the microstructure generator kanapy from ICAMS Bochum. + + * `A. Hartmeier et al. <https://joss.theoj.org/papers/10.21105/joss.01732>`_ + + A draft application definition to support discussion within the infrastructure use case IUC07 of the + NFDI-MatWerk consortium of the German NFDI working on a data model for documenting simulations + of spatiotemporal microstructure evolution with scientific software from this community. + + + + + + + + + + Discouraged free-text field to add further details to the computation. + + + + + + + + + + + + + + + + + + + + + + Programs and libraries representing the computational environment + + + + + + + + + + + + + + + + + Default plot showing the grid. + + + + + + + + Crystal identifier that was assigned to each material point. + + + + + + Material point barycenter coordinate along z direction. + + + + + + + Coordinate along z direction. + + + + + + Material point barycenter coordinate along y direction. + + + + + + + Coordinate along y direction. + + + + + + Material point barycenter coordinate along x direction. + + + + + + + Coordinate along x direction. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Bunge-Euler angle orientation of each crystal. + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_mtex_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_mtex_config.nxdl.xml new file mode 100644 index 0000000..a9c13a1 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_mtex_config.nxdl.xml @@ -0,0 +1,325 @@ + + + + + + + + Number of entries in the default color map + + + + + Number of entries in color map + + + + + Base class to store the configuration when using the MTex/Matlab software. + + MTex is a Matlab package for texture analysis used in the Materials and Earth Sciences. + See `R. Hielscher et al. <https://mtex-toolbox.github.io/publications>`_ and + the `MTex source code <https://github.com/mtex-toolbox>`_ for details. + + + + MTex reference frame and orientation conventions. + Consult the `MTex docs <https://mtex-toolbox.github.io/EBSDReferenceFrame.html>`_ for details. + + + + TODO with MTex developers + + + + + + TODO with MTex developers + + + + + + TODO with MTex developers + + + + + + TODO with MTex developers + + + + + + TODO with MTex developers + + + + + + + + + + + Settings relevant for generating plots. + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + True, if MTex renders a scale bar with figures. + + + + + True, if MTex renders a grid with figures. + + + + + Code for the function handle used for annotating pole figure plots. + + + + + TODO with MTex developers + + + + + + + + + TODO with MTex developers + + + + + + + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + + Miscellaneous other settings of MTex. + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + + Miscellaneous settings relevant for numerics. + + + + Return value of the Matlab eps command. + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + + Miscellaneous settings relevant of the system where MTex runs. + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + TODO with MTex developers + + + + + + Collection of paths from where MTex reads information and code. + + + + Absolute path to specific component of MTex source code. + + + + + Absolute path to specific component of MTex source code. + + + + + Absolute path to specific component of MTex source code. + + + + + Absolute path to specific component of MTex source code. + + + + + Absolute path to specific component of MTex source code. + + + + + Absolute path to specific component of MTex source code. + + + + + Absolute path to specific component of MTex source code. + + + + + Absolute path to specific component of MTex source code. + + + + + Absolute path to specific component of MTex source code. + + + + + List of file type suffixes for which MTex assumes + texture/pole figure information. + + + + + List of file type suffixes for which MTex assumes EBSD content. + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_odf.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_odf.nxdl.xml new file mode 100644 index 0000000..0d79585 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_odf.nxdl.xml @@ -0,0 +1,230 @@ + + + + + + + + Number of pixel per varphi section plot along the :math:`\varphi_2` slow + direction. + + + + + Number of pixel per varphi section plot along the :math:`\Phi` fast direction. + + + + + Number of pixel per varphi section plot along the :math:`\varphi_1` fastest + direction. + + + + + Number of local maxima evaluated in the component analysis. + + + + + Number of sampled positions in orientation space. + + + + + Base class to store an orientation distribution function (ODF). + + An orientation distribution function is a probability distribution that details how + much volume of material has a specific orientation. An ODF is computed from + pole figure data in a computational process called `pole figure inversion <https://doi.org/10.1107/S0021889808030112>`_. + + + + Details about the algorithm used for computing the ODF. + + + + Point group of the crystal structure of the phase for which the here documented + phase-dependent ODF was computed following the notation of the + International Table of Crystallography. + + + + + Point group assumed for additionally considered sample symmetries + following the notation of the International Table of Crystallography. + + + + + Halfwidth of the kernel. + + + + + Name of the kernel. + + + + + Resolution of the kernel. + + + + + + Group to store descriptors for a rough classification of an ODF. + + + + The texture index :math:`t = \int_{\mathcal{SO(3)}} f(R)^{2}dR` with :math:`f(R)`, denoting the ODF + is evaluated in orientation space :math:`\mathcal{SO(3)}`. + + The higher it is the texture index the sharper it is the ODF. + + + + + + + Group to store descriptors and summary statistics for extrema of the ODF. + + + + Minima or maxima, if extrema is set to minima values for location and volume_fraction + are sorted in increasing order. If extrema is set to maxima values for location and + volume_fraction are sorted in decreasing order. Therefore, the global extremum is + always the first entry in location and volume_fraction. + + + + + + + + + Number of local extrema evaluated + + + + + + Disorientation threshold within which intensity of the ODF + is integrated for the component analysis. + + + + + Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the + kth-most maxima in decreasing order of the intensity maximum. + + + + + + + + + Integrated ODF intensity within a theta angular region of the orientation space :math:`SO3` + about each location (obeying symmetries) as specified for each location. + + + + + + + + + The ODF intensity values (weights) as sampled with a software. + + + + Sampling resolution + + + + + Bunge-Euler (i.e. ZXZ convention) locations of each position + in orientation space for which a weight was sampled. + + + + + + + + + Weight at each sampled position following the order in euler. + + + + + + + + + Visualization of the ODF intensity as discretized orthogonal sections through + orientation space parameterized using Bunge-Euler angles. + + This is one example of typical default plots used in the texture community in materials engineering. + + Mind that the orientation space is a distorted space when it using an Euler angle parameterization. + Therefore, equivalent orientations show intensity contributions in eventually multiple locations. + + + + ODF intensity at probed locations relative to the intensity of the null model of + a random texture. + + + + + + + + + + Pixel center angular position along the :math:`\varphi_1` direction. + + + + + + + + Pixel center angular position along the :math:`\Phi` direction. + + + + + + + + Pixel center angular position along the :math:`\varphi_2` direction. + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_pf.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_pf.nxdl.xml new file mode 100644 index 0000000..3c82854 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_pf.nxdl.xml @@ -0,0 +1,113 @@ + + + + + + + + Number of pixel per pole figure in the slow direction. + + + + + Number of pixel per pole figure in the fast direction. + + + + + Base class to store a pole figure (PF) computation. + + A pole figure is the X-ray diffraction intensity for specific integrated + peaks for a hemispherical illumination of a real or virtual specimen. + + + + Details about the algorithm that was used to compute the pole figure. + + + + Point group of the crystal structure of the phase for which the pole figure was + computed following the notation of the International Table of Crystallography. + + + + + Point group of assumed sample symmetries following the + notation of the International Table of Crystallography. + + + + + + Halfwidth of the kernel. + + + + + Miller (:math:`(hkl)[uvw]`) or Miller-Bravais indices used to specify the pole + figure. + + + + + Resolution of the kernel. + + + + + + Pole figure. + + + + + Pole figure intensity. + + + + + + + + + Pixel center along y direction in the equatorial plane of + a stereographic projection of the unit sphere. + + + + + + + + Pixel center along x direction in the equatorial plane of + a stereographic projection of the unit sphere. + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_score_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_score_config.nxdl.xml new file mode 100644 index 0000000..32a66a1 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_score_config.nxdl.xml @@ -0,0 +1,724 @@ + + + + + + + + Number of Bunge-Euler angle triplets for deformed grains. + + + + + Number of Bunge-Euler angle triplets for recrystallization nuclei. + + + + + Number of texture components to analyze. + + + + + Number of support points for the linearized drag profile. + + + + + Number of support points for the desired time-temperature profile. + + + + + Number of entries when to defragment i.e. garbage collect the memory holding + state information for recrystallized cells. + + + + + Number of entries when to collect snapshots of the evolving microstructure. + + + + + Number of solitary unit domains to export. + + + + + Dimensionality of the simulation. + + + + + Application definition to configure a simulation with the SCORE model. + + * `M. Kühbach et al. <https://doi.org/10.1016/j.actamat.2016.01.068>`_ + * `M. Diehl et al. <https://doi.org/10.1088/1361-651X/ab51bd>`_ + + + + + + + + + + An alias to refer to this simulation. + + + + + Discouraged free-text field to add further details to the computation. + + + + + ISO 8601 time code with local time zone offset to UTC information + included when the configuration file was created. + + + + + + + + + Dimensionality of the simulation. + + + + + + + + + + A qualifier whether the sample is a real one or a virtual one. + + + + + + + + + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from other sources. + + + + + + Name of the program whereby this config file was created. + + + + + + + + Programs and libraries representing the computational environment + + + + + + + + + + (Mechanical) properties of the material which scale the + amount of stored (elastic) energy in the system and + thus mainly affect recrystallization kinetics. + + + + Reference shear modulus at zero Kelvin. + + + + + Magnitude of the Burgers vector at zero Kelvin. + + + + + + Melting temperature + + + + + + Details about the geometry and properties of the polycrystal that represents the + starting configuration (typically a deformed microstructure) for the simulation. + + + + Which model should be used to generate a starting microstructure. + + * cuboidal, a regular array of equally-shaped cuboidal grains + * poisson_voronoi, a discretized Poisson Voronoi tessellation + * ebsd, a microstructure synthesized based on a simulated or a measured EBSD orientation map + * damask, the result of a simulation from `DAMASK <https://damask-multiphysics.org>`_. + + + + + + + + + + + + Extent of each deformed grain in voxel along the + x, y, and z direction when model is cuboidal. + + + + + + + + Average spherical diameter when model is poisson_voronoi. + + + + + Settings for instantiating properties of deformed grains when model is cuboidal + or poisson. + + + + Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) + out of which the orientations of deformed grains are sampled. + + + + + + + + + Set of stored elastic energy quantified as a dislocation density which is assigned + to deformed grains with orientations from bunge_euler with index queries matching + for the bunge_euler and stored_energy fields. + + + + + + + + + Settings for instantiating properties of deformed grains from an + EBSD orientation map when model is cuboidal or poisson. + + + + + + + Extent of the pixel of the EBSD orientation mapping assuming square-shaped pixels + or cube-shaped voxels respectively. + + + + + + + + + Settings for instantiating properties of deformed grains and nuclei when model + is damask. + + + + Name of the DREAM.3D HDF5 file that was instantiated from the + a previously performed DAMASK simulation. + + + + + + + + + Phenomenological model according to which recrystallization nuclei + are placed into the domain. Studying the growth of these nuclei + is the main purpose of a SCORE simulation. + + + + According to which model will the nuclei become distributed spatially: + + * csr, complete spatial randomness + * custom, implementation-specific + * gb, nuclei placed at grain boundaries + + + + + + + + + According to which model will the nuclei start to grow: + + * site_saturation, instantaneously + + + + + + + + According to which model will the nuclei get their orientation assigned: + + * ensemble, picking randomly one from ensemble/bunge_euler + * random, picking randomly on the SO3 + * damask, picking based on information provided in deformation/damask + + + + + + + + + + + Settings for instantiating properties of nuclei for recrystallizing grains. + + + + Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) + out of which the orientations of nuclei/recrystallized grains are sampled. + + + + + + + + + Incubation time which is assigned to deformed grains with orientations from bunge_euler + with index queries matching for the bunge_euler and stored_energy fields. + + + + + + + + + + Model for the assumed mobility of grain boundaries with different disorientation + implemented as a parameterized Turnbull's model for thermally-activated + grain boundary migration. + + + + Which type of fundamental model for the grain boundary mobility. + + Grain boundaries with disorientation angle smaller than 15 degree are considered + as low-angle grain boundaries. Other grain boundaries are high-angle boundaries. + + + + + + + + + + Parameter of the Sebald-Gottstein migration model. + + + + + Pre-exponential factor for low-angle grain boundaries. + + + + + Migration activation enthalpy for low-angle grain boundaries. + + + + + Pre-exponential factor for high-angle grain boundaries. + + + + + Migration activation enthalpy for high-angle grain boundaries. + + + + + Pre-exponential factor for high-angle grain boundaries which in + bicrystal or other tailored experiments showed a particular high + mobility. + + + + + Migration activation enthalpy for high-angle grain boundaries which in + bicrystal or other tailored experiments showed a particular high + mobility. + + + + + + Parameter of the Rollett-Holm migration model. + + + + + Pre-exponential factor for the fastest grain boundary in the system. + + + + + Migration activation enthalpy for the fastest grain boundary in the system. + + + + + Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not 1. + + + + + Mobility scaling factor :math:`c_2`. Typically 5. + + + + + Mobility scaling factor :math:`c_3`. Typically 9. + + + + + + + Time-dependent reduction of the stored energy to account for recovery effects. + + + + Which type of recovery model. + + + + + + + + + Reduction of the grain boundary migration speed due to the presence of dispersoids + through which the total grain boundary area of the recrystallization front can be reduced + while the boundary is arrested at the dispersoids. + + + + Which type of drag model. + + + + + + + + + + Parameter of the Zener-Smith drag model when model is zener_smith. + + + + Configuration-dependent constant which factorizes the drag pressure. + + + + + Average surface energy of the grain-boundary-dispersoid-surface configuration + which factorizes the drag pressure. + + + + + + Assumed dispersoid mean radius-time profile + + + + + + + + + Support point of the linearized curve of simulated time matching + a specific support point of the average dispersoid radius. + + + + + + + + + Support point of the linearized curve of the average dispersoid radius. + + + + + + + + + + + + + Given name of a texture component. + + + + + + + + Bunge-Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the + of texture components in sequence of the name field. + + + + + + + + + Integration radius that constraints the theta angular region of the orientation space (SO3) + about each central location (obeying symmetries) as specified by bunge_euler indexed in + the same sequence as the bunge_euler and name fields. + + + + + + + + + Desired simulated time-temperature profile + + + + + + + + + Support point of the linearized curve of simulated time matching + a specific support point of the temperature. + + + + + + + + + Support point of the linearized curve of the temperature. + + + + + + + + + + Relevant data to instantiate a starting configuration that is typically + a microstructure in deformed conditions where (elastic) energy is stored + in the form of crystal defects (mostly dislocations). The SCORE model + does not resolve individual dislocations but works with one + homogenized mean-field density per grain. For simulations that are + instantiated from EBSD datasets or crystal plasticity simulations + individual values are available for each voxel that may be used as is + for each voxel or may need a pre-processing of the data to coarse-grain + material point-specific values to values averaged per deformed grain. + + + + + Extend of each CA domain in voxel along the x, y, and z direction. + Deformation of sheet material is assumed. + The x axis is assumed pointing along the rolling direction. + The y axis is assumed pointing along the transverse direction. + The z axis is assumed pointing along the normal direction. + + + + + + + + Edge length of the material point that in SCORE + is discretized via equisized cubic voxels. + + + + + + + + Criteria which enable to stop the simulation in a controlled manner + and assure a stable numerical integration. + Whichever criterion is fulfilled first stops the simulation. + + + + Maximum recrystallized volume fraction. + + + + + Maximum simulated physical time. + + + + + Maximum number of iteration steps. + + + + + Maximum fraction equivalent to the migration of the + fastest grain boundary in the system how much a cell + may be consumed in a single iteration. + + + + + List of target values at which recrystallized volume fractions the state + of the CA is evaluated and stored. The code documents summary statistics + like recrystallized volume fraction for each iteration and the volume of each + grain. Furthermore, snapshots of the microstructure are stored. + These can take much disk space though because SCORE is able to evolve CA + with up to :math:`1600^3` cells. Snapshot data document the current microstructure + including the assignment of grains and cells surplus the state of the + recrystallization front. + + Despite these, data about the cells that define the recrystallization front make up + for approximately one order of magnitude less cells than present in the domain. + For the cells in this front, though, more data have to be collected + than just a grain identifier. + + + + + + + + Parameter which control the memory management + of cells in the recrystallization front. + + + + Fraction of the total number of cells in the CA which + should initially be allocated for offering storage for + cells making up the recrystallization front. + + + + + By how much more times should the already allocated memory + be increased to offer space for storing states of cells + in the recrystallization front. + + + + + Should the cache for cells in the recrystallization front + be defragmented on-the-fly or not. + + + + + Target values at which recrystallized volume fraction the cache + for cells in the recrystallization front will be defragmented + on-the-fly. Defragmentation packs active cells closer into + main memory to reduce cache misses in subsequent evaluations + of the recrystallization front. + + + + + + + + + + + Perform a statistical analyses of the results as it was proposed + by M. Kühbach (solitary unit model ensemble approach). + + + + + How many independent cellular automaton domains + should be instantiated. + + + + + Into how many time steps should the real time interval be discretized upon + during post-processing the results with the solitary unit modeling approach. + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_score_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_score_results.nxdl.xml new file mode 100644 index 0000000..f9f6c8b --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_score_results.nxdl.xml @@ -0,0 +1,567 @@ + + + + + + + + The symbols used in the schema to specify e.g. dimensions of arrays + + + + The total number of summary statistic log entries + + + + + Number of boundaries of the bounding box or primitive about the computational + domain + + + + + Number of parameter required for chosen orientation parameterization + + + + + Number of texture components identified + + + + + Dimensionality + + + + + Cardinality + + + + + Number of active cells in the (recrystallization) front + + + + + Number of grains in the computer simulation + + + + + Application definition for storing results of the SCORE cellular automata model. + + The SCORE cellular automata model for primary recrystallization is an example + of a typical materials engineering application used within the field of so-called + Integral Computational Materials Engineering (ICME) whereby one can simulate + the evolution of microstructures. + + Specifically the SCORE model can be used to simulate the growth of nuclei during + static recrystallization. The model is described in the literature: + + * `M. Kühbach et al. <https://doi.org/10.1016/j.actamat.2016.01.068>`_ + * `C. Haase et al. <https://doi.org/10.1016/j.actamat.2015.08.057>`_ + * `M. Diehl et al. <https://doi.org/10.1088/1361-651X/ab51bd>`_ + + + + + + + + + + Simulation ID as an alias to refer to this simulation. + + + + + Configuration file with the parameterization of the + SCORE model that was used for this simulation. + + + + + + + + Discouraged free-text field to add further details to the computation. + + + + + ISO 8601 time code with local time zone offset to UTC information + included when the simulation was started. + + + + + ISO 8601 time code with local time zone offset to UTC information + included when the simulation ended. + + + + + + + Name of the program with which the simulation was performed. + + + + + + + + Programs and libraries representing the computational environment + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A tight bounding box or sphere or bounding primitive about the grid. + + + + + How many distinct boundaries are distinguished? + Most grids discretize a cubic or cuboidal region. In this case + six sides can be distinguished, each making an own boundary. + + + + + The boundary conditions for each boundary: + + * 0 - undefined + * 1 - open + * 2 - periodic + * 3 - mirror + * 4 - von Neumann + * 5 - Dirichlet + + + + + + + + Name of the boundaries. Left, right, front, back, bottom, top, + The field must have as many entries as there are number_of_boundaries. + + + + + + + + + + Documentation of the spatiotemporal evolution for each CA domain. + + SCORE is a hybrid parallelized code that can evolve multiple replicas + in parallel. The set of replicas is distributed across MPI processes. + Each such replica is then evolved via OpenMP multi-threading. + + + + + Summary quantities which are the result of some post-processing of the snapshot data + (averaging, integrating, interpolating) happening for practical and performance reasons + during the simulation. Place used for storing descriptors from continuum mechanics + and thermodynamics at the scale of the entire ROI. + + + + Evolution of the recrystallized volume fraction over time. + + + + + + + + + + + Evolution of the physical time not to be confused with wall-clock time or + profiling data. + + + + + + + + Iteration or increment counter. + + + + + + + + Evolution of the simulated temperature over time. + + + + + + + + Recrystallized volume fraction. + + + + + + + + + + Which type of stress. + + + + + + + + Applied external stress tensor on the ROI. + + + + + + + + + + + + Which type of strain. + + + + + Applied external strain tensor on the ROI. + + + + + + + + + + + + Which type of deformation gradient. + + + + + + + + Applied deformation gradient tensor on the ROI. + + + + + + + + + + + + + + Simulated physical time for this snapshot. + + + + + Iteration or increment counter of this snapshot. + + + + + Simulated temperature for this snapshot. + + + + + Current recrystallized volume fraction (taking fractional infections into + account). + + + + + Target value for which a snapshot was requested for the recrystallized volume + fraction. + + + + + + + Index for each crystal whereby its metadata can be retrieved. + + + + + + + + + + Identifier of the OpenMP thread that processed this part of the grid. + + + + + + + + + + + + + + + + + + + + + + + + + + + Volume of each grain (partially transformed cells are accounted for). + + + + + + + + + Bunge-Euler angle triplets for each grain. + + + + + + + + + Current value for the dislocation density as a measure of the remaining + stored energy in assumed crystal defects inside each grain. + + + + + + + + Is the grain deformed. + + + + + + + + Is the grain recrystallized. + + + + + + + + + Details about those cells which in this time step + represent the discrete recrystallization front. + + Each CA is processed by a team of OpenMP threads. + + + + Which cells are currently in a halo region of threads. + + The halo region is a layer of cells about the sub-domain + of the simulation grid evolved by a thread. + + + + + + + + So-called mobility weight which is a scaling factor to control the + mobility of the grain boundary that is modelled sweeping cells that + make the discrete recrystallization front. + + + + + + + + The x, y, z grid coordinates of each cell in the recrystallization front. + + + + + + + + + Grain identifier assigned to each cell in the recrystallization front. + + + + + + + + Grain identifier assigned to each nucleus which affected that cell in the + recrystallization front. + + + + + + + + Identifier of the OpenMP thread processing each cell in the recrystallization + front. + + + + + + + + Hint about the direction from which the cell was infected. + + + + + + + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXslip_system_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_slip_system.nxdl.xml similarity index 65% rename from src/nexusformat/definitions/contributed_definitions/NXslip_system_set.nxdl.xml rename to src/nexusformat/definitions/contributed_definitions/NXmicrostructure_slip_system.nxdl.xml index 8fafee2..f938709 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXslip_system_set.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXmicrostructure_slip_system.nxdl.xml @@ -2,9 +2,9 @@ - + - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays. - Number of slip systems. + Number of slip systems. + + + + + Number of indices used for reporting Miller (3) or Miller-Bravais indices (4). - Base class for describing a set of crystallographic slip systems. + Base class for describing a set of crystallographic slip systems. - - - + + + Bravais lattice type + @@ -50,33 +54,29 @@ identifier(NX_UINT):--> - - Array of Miller indices which describe the crystallographic plane. + Array of Miller indices which describe the crystallographic planes. - - Array of Miller indices which describe the crystallographic direction. + Array of Miller or Miller-Bravais indices that describe the crystallographic + direction. - + - For each slip system a marker whether the specified Miller indices - refer to the specific slip system or the set of crystallographic equivalent - slip systems of the respective family of slip systems. + For each slip system a marker whether the Miller indices refer to a specific slip system + or to a set of equivalent crystallographic slip systems. diff --git a/src/nexusformat/definitions/contributed_definitions/NXmpes.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXmpes.nxdl.xml deleted file mode 100644 index c2bfe95..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXmpes.nxdl.xml +++ /dev/null @@ -1,371 +0,0 @@ - - - - - - - This is the most general application definition for multidimensional - photoelectron spectroscopy. - - - - - - Datetime of the start of the measurement. - - - - - - - - - - - Contact information of at least the user of the instrument or the investigator - who performed this experiment. Adding multiple users if relevant is recommended. - - - - Name of the user. - - - - - Name of the affiliation of the user at the point in time when the experiment was - performed. - - - - - Full address (street, street number, ZIP, city, country) of the user's - affiliation. - - - - - Email address of the user. - - - - - Author ID defined by https://orcid.org/. - - - - - - - - The source used to generate the primary photons. Properties refer strictly to - parameters of the source, not of the output beam. For example, the energy of the - source is not the optical power of the beam, but the energy of the electron beam - in a synchrotron and so on. - - - - - - - - - - - - - - - - - - Type of probe. In photoemission it's always photons, so the full NIAC list is - restricted. - - - - - - - - - - - - Distance of the point of evaluation of the beam from the sample surface. - - - - - - - - - - - Energy resolution of the analyser with the current setting. May be linked from a - NXcalibration. - - - - - - - - Scheme of the electron collection column. - - - - - - - - - - - - - - - The size and position of the field aperture inserted in the column. To add - additional or other apertures use the APERTURE group of NXcollectioncolumn. - - - - - The size and position of the contrast aperture inserted in the column. To add - additional or other apertures use the APERTURE group of NXcollectioncolumn. - - - - - - - - - - - - - - - - - - - Size, position and shape of the entrance slit in dispersive analyzers. To add - additional or other slits use the APERTURE group of NXenergydispersion. - - - - - Size, position and shape of the exit slit in dispersive analyzers. To add - additional or other slits use the APERTURE group of NXenergydispersion. - - - - - - - Type of electron amplifier in the first amplification step. - - - - - - - - - - Description of the detector type. - - - - - - - - - - - - - - - - - - - Raw data before calibration. - - - - - - - - Manipulator for positioning of the sample. - - - - - - - - - Document an event of data processing, reconstruction, or analysis for this data. - Describe the appropriate axis calibrations for your experiment using one or more - of the following NXcalibrations - - - - - Has an energy calibration been applied? - - - - - This is the calibrated energy axis to be used for data plotting. - - - - - - - Has an angular calibration been applied? - - - - - This is the calibrated angular axis to be used for data plotting. - - - - - - - Has an spatial calibration been applied? - - - - - This is the calibrated spatial axis to be used for data plotting. - - - - - - - Has an momentum calibration been applied? - - - - - This is the momentum axis to be used for data plotting. - - - - - - - - - The chemical formula of the sample. For mixtures use the NXsample_component - group in NXsample instead. - - - - - A descriptor to keep track of the treatment of the sample before entering the - photoemission experiment. Ideally, a full report of the previous operations, in - any format (NXnote allows to add pictures, audio, movies). Alternatively, a - reference to the location or a unique identifier or other metadata file. In the - case these are not available, free-text description. - - - - - List of comma-separated elements from the periodic table - that are contained in the sample. - If the sample substance has multiple components, all - elements from each component must be included in `atom_types`. - - - - - Date of preparation of the sample for the XPS experiment (i.e. cleaving, last - annealing). - - - - - Description of the surface preparation technique for the XPS experiment, i.e. - UHV cleaving, in-situ growth, sputtering/annealing etc. Ideally, a full report - of the previous operations, in any format(NXnote allows to add pictures, audio, - movies). Alternatively, a reference to the location or a unique identifier or - other metadata file. In the case these are not available, free-text description. - - - - - - In the case of a fixed temperature measurement this is the scalar temperature of - the sample. In the case of an experiment in which the temperature is changed and - recoded, this is an array of length m of temperatures. This should be a link to - /entry/instrument/manipulator/sample_temperature. - - - - - - - - - - - - - - - - - - - - - - Represents a measure of one- or more-dimensional photoemission counts, where the - varied axis may be for example energy, momentum, spatial coordinate, pump-probe - delay, spin index, temperature, etc. The axes traces should be linked to the - actual encoder position in NXinstrument or calibrated axes in NXprocess. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXms.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXms.nxdl.xml deleted file mode 100644 index 75a010f..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXms.nxdl.xml +++ /dev/null @@ -1,529 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of boundaries of the bounding box or primitive to domain. - - - - - Number of parameter required for the chosen orientation parameterization. - - - - - Number of texture components identified. - - - - - Application definition, spatiotemporal characterization of a microstructure. - - - - - An at least as strong as SHA256 hashvalue of the file - that specifies the application definition. - - - - - - NeXus NXDL schema to which this file conforms. - - - - - - - - Ideally, a (globally) unique persistent identifier - for referring to this experiment or computer simulation. - - The identifier is usually defined/issued by the facility, laboratory, - or the principle investigator. The identifier enables to link - experiments to e.g. proposals. - - - - - Free-text description about the workflow (experiment/analysis/simulation). - - Users are strongly advised to detail the sample history in the - respective field and fill rather as completely as possible the fields - of this application definition rather than write details about the - experiment into this free-text description field. - - - - - ISO 8601 time code with local time zone offset to UTC information - included when the characterization started. - - - - - ISO 8601 time code with local time zone offset to UTC included - when the characterization ended. - - - - - - - - - - Specify if the (characterization) results/data of this instance of an - application definition are based on the results of a simulation or the - results of a post-processing of measured data to describe - a microstructure. - - The term microstructure is used to describe the spatial arrangement of - crystal defects inside a sample/specimen without demanding necessarily - that this structure is mainly at the micron length scale. - Nanostructure and macrostructure are close synonyms. - Material architecture is a narrow synonym. - - Given that microstructure simulations nowadays more and more consider - the atomic arrangement, this application definition can also be used - to describe features at the scale of atoms. - - - - - - - - - Contact information and eventually details of at least one person - involved in creating this result. This can be the principle investigator - who performed this experiment. Adding multiple users if relevant is recommended. - - - - Given (first) name and surname of the user. - - - - - Name of the affiliation of the user at the point in time - when the experiment was performed. - - - - - Postal address of the affiliation. - - - - - Email address of the user at the point in time when the experiment - was performed. Writing the most permanently used email is recommended. - - - - - Globally unique identifier of the user as offered by services - like ORCID or ResearcherID. If this field is field the specific service - should also be written in orcid_platform - - - - - Name of the OrcID or ResearcherID where the account - under orcid is registered. - - - - - (Business) (tele)phone number of the user at the point - in time when the experiment was performed. - - - - - Which role does the user have in the place and at the point - in time when the experiment was performed? Technician operating - the microscope. Student, postdoc, principle investigator, guest - are common examples. - - - - - Account name that is associated with the user in social media platforms. - - - - - Name of the social media platform where the account - under social_media_name is registered. - - - - - - - - Descriptive name or ideally (globally) unique persistent identifier. - - - - - - - Hard link to a location in the hierarchy of the NeXus file - where the data for default plotting are stored. - - - - - Container to hold different coordinate systems conventions. - A least a right-handed Cartesian coordinate system with base vectors - named x, y, and z has to be specified. Each base vector of the - coordinate system should be described with an NXtransformations instance. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The simulated or characterized material volume element aka domain. - At least one instance of geometry required either NXcg_grid, - NXcg_polyhedron_set, or NXcg_point_set. This geometry group needs - to contain details about the boundary conditions. - - - - - - - - A boundary to the volume element. - Either an instance of NXcg_hexahedron_set or of NXcg_ellipsoid_set. - - - - - How many distinct boundaries are distinguished. Value required equal to n_b. - - - - - Name of the boundaries. E.g. left, right, front, back, bottom, top, - - - - - - - - The boundary conditions for each boundary: - - 0 - undefined - 1 - open - 2 - periodic - 3 - mirror - 4 - von Neumann - 5 - Dirichlet - - - - - - - - - Collection of microstructural data observed/simulated. - - - - Integer which specifies the first index to be used for distinguishing - snapshots. Identifiers are defined either implicitly or explicitly. - For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate - if the identifiers are expected to start from 1 (referred to as - Fortran-/Matlab-) or from 0 (referred to as C-, Python-style index - notation) respectively. - - - - - - Summary quantities which are the result of some post-processing of - the snapshot data (averaging, integrating, interpolating). - Frequently used descriptors from continuum mechanics and thermodynamics - can be used here. A few examples are given. Each descriptor is currently - modelled as an instance of an NXprocess because it is relevant to - understand how the descriptors are computed. - - - - - - - - - - - - - - Measured or simulated physical time stamp for this snapshot. - Not to be confused with wall-clock timing or profiling data. - - - - - Iteration or increment counter. - - - - - - - - - - Conceptually distinguished object/feature in the ROI/ - system with some relevance. Instances of NXms_feature_set can - be nested to build a hierarchy of logically-related objects. - - A typical example for MD simulations is to have one - ms_feature_set for the atoms which is the parent to another - ms_feature_set for monomers/molecules/proteins which is then the - parent to another ms_feature_set for the secondary, another feature_set - for the tertiary, and the parent for another feature_set for the - quaternary structure. - - Another typical example from materials engineering is to have - one ms_feature_set for crystals (grains/phases) which serves as - the parent to another ms_feature_set for interfaces between these - crystals which then is the parent for another ms_feature_set to - describe the triple junctions which is then the parent for the - quadruple/higher-order junctions between which connect the - triple lines. - - Another example from discrete dislocation dynamics could be to - have one ms_feature_set for the dislocations (maybe separate - sets for each dislocation type or family) which are then - parents to other ms_feature_set which describe junctions between - dislocations or features along the dislocation line network. - - - - - - Details about the orientation distribution function - within the entire domain. - - - - With which method was the ODF approximated? - - - - - - TO BE DEFINED - - - - - TO BE DEFINED - - - - - Collection of texture components commonly referred to. - - - - Reference to or definition of a coordinate system with - which the definitions are interpretable. - - - - - - - - - - - Parameterized orientations. - - - - - - - - - Name of each texture component, e.g. Cube, Dillamore, Y. - - - - - - - - The portion of orientation space integrated over - to compute the volume fraction. - - - - - - - - The volume fraction of each texture component. - - - - - - - - - - - Details about the disorientation distribution function - within the entire domain. - - - - - Details about the grain boundary character distribution - within the entire domain. - - - - - - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXms_feature_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXms_feature_set.nxdl.xml deleted file mode 100644 index 326d8cc..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXms_feature_set.nxdl.xml +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Dimensionality - - - - - Cardinality/number of members/features in the feature set. - - - - - Number of types in the dictionary of human-readable types of features. - - - - - Total number of parent identifier. - - - - - Set of topological/spatial features in materials build from other features. - - - - - - Name (or link?) to another NXms_feature_set which defines features what are - assumed as the parents/super_features of all members in this feature set. - If depends_on is set to "." or this attribute is not defined in an instance - of this application definition, assume that this feature_set instance - represents the root feature_set of the feature tree/graph. - - - - - - - What is the best matching description how dimensional the feature is. - - - - - - - - - - - - How many features/members are in this set? - - - - - - The keywords of the dictionary of human-readable types of features. - Using terms from a community-agreed upon controlled vocabulary, e.g. - atom, solute, vacancy, monomer, molecule, anti-site, crowd_ion, - quadruple junction, triple line, disconnection, dislocation, - kink, jog, stacking_fault, homo_phase_boundary, hetero_phase_boundary, - surface, thermal_groove_root, precipitate, dispersoid, pore, crack - is recommended. - - - - - - - - - The integer identifier used to resolve of which type each feature is, - i.e. the values of the dictionary of human-readable types of features. - - - - - - - - For each feature in the set specify the associated number of identifier - to parent features as are resolvable via depends_on. - This array enables to compute the array interval from which details for - specific features can be extracted as if they would be stored in an own - group. - - - - - - - - Concatenated array of parent identifier for each feature (in the sequence) - according to identifier and how the identifier of features in the here - described feature set are defined (implicitly from 0, to c-1 or via explicit - identifier. - - - - - - - - - Integer which specifies the first index to be used for distinguishing - features. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish features for explicit indexing. - - - - - - - - - Assumptions and parameter to arrive at geometric primitives - to locate zero-dimensional/point-(like) features which are - discretized/represented by points. - - - - - Assumptions, parameters, and details how positional uncertainty - of the geometry is quantified. - - - - - - - Assumptions and parameters to arrive at geometric primitives - to locate one-dimensional/line-like features which are - discretized by polylines. - - - - - - Assumptions, parameters, and details how positional uncertainty - of the geometry is quantified. - - - - - - Assumptions and parameters to arrive at geometric primitives - to locate two-dimensional/interface features which are - discretized by triangulated surface meshes. - - - - - - Assumptions, parameters, and details how positional uncertainty - of the geometry is quantified. - - - - - - Assumptions and parameters to arrive at geometric primitives - to locate three-dimensional/volumetric features which are - discretized by triangulated surface meshes of polyhedra. - - - - - - Assumptions, parameters, and details how positional uncertainty - of the geometry is quantified. - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXms_score_config.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXms_score_config.nxdl.xml deleted file mode 100644 index 7aab836..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXms_score_config.nxdl.xml +++ /dev/null @@ -1,452 +0,0 @@ - - - - - - - - Number of Bunge-Euler angle triplets for deformed grains. - - - - - Number of Bunge-Euler angle triplets for recrystallization nuclei. - - - - - Number of solitary unit domains to export. - - - - - Application definition to control a simulation with the SCORE model. - - - - - Version specifier of this application definition. - - - - - Official NeXus NXDL schema with which this file was written. - - - - - - - - - - - - - Ideally, a (globally persistent) unique identifier for referring - to this analysis. - - - - - Possibility for leaving a free-text description about this analysis. - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - ISO 8601 formatted time code with local time zone offset to UTC - information included when this configuration file was created. - - - - - Relevant data to instantiate a starting configuration that is typically - a microstructure in deformed conditions where stored (elastic) energy - is stored in the form of crystal defects, which in the SCORE model are - is considered as mean-field dislocation content. - - - - Which model should be used to generate a starting microstructure. - - - - - - - - - - - Edge length of the cubic cells of each CA domain. - - - - - Extend of each CA domain in voxel along the x, y, and z direction. - Deformation of sheet material is assumed. - The x axis is assumed pointing along the rolling direction. - The y axis is assumed pointing along the transverse direction. - The z axis is assumed pointing along the normal direction. - - - - - - - - Extent of each deformed grain along the x, y, and z direction when type is - cuboidal. - - - - - - - - Average spherical diameter when type is poisson_voronoi. - - - - - Set of Bunge-Euler angles to sample orientations randomly from. - - - - - - - - - The EBSD dataset from which the initial microstructure is instantiated - if initial_microstructure/type has value ebsd. - - - - Path and name of the EBSD dataset from which to generate the starting - microstructure. - - - - SHA256 checksum of the file which contains the EBSD dataset. - - - - - - Size of the EBSD. The EBSD orientation mapping has to be on a - regular grid of square-shaped pixels. - - - - - - - - - - Phenomenological model according to which it nuclei are placed - into the domain and assumed growing. - - - - According to which model will the nuclei become distributed spatially. - CSR means complete spatial randomness. - Custom is implementation specific. - GB places nuclei at grain boundaries. - - - - - - - - - - According to which model will the nuclei start to grow. - - - - - - - - According to which model will the nuclei get their orientation assigned. - - - - - - - - Set of Bunge-Euler angles to sample orientations of nuclei randomly from. - - - - - - - - - - (Mechanical) properties of the material which scale the amount - of stored (elastic) energy in the ROI/system. - - - - Shear modulus at zero Kelvin. - - - - - Magnitude at the Burgers vector at zero Kelvin. - - - - - - Melting temperature in degrees Celsius. - - - - - - Model for the assumed mobility of grain boundaries with different - disorientation. - - - - Which type of fundamental model for the grain boundary mobility: - For the Sebald-Gottstein model the following equation is used. - For the Rollett-Holm model the following equation is used. - - - - - - - - - - - - - - - - - - - - - - - - - Simulated evolution of the dislocation density as the stored - (elastic) energy assumed stored in each grain. - - - - Which type of recovery model. - - - - - - - - - Simulated reduction of the grain boundary speed due to - the presence of dispersoids through which the total grain boundary - area of the recrystallization front can be reduced. - - - - Which type of drag model. - - - - - - - - - - - - Support point of the linearized curve of simulated time matching - a specific support point of the average dispersoid radius. - - - - - - - - Support point of the linearized curve of the average dispersoid radius. - - - - - - - - - - Simulated time temperature profile - - - - Support point of the linearized curve of simulated time matching - a specific support point of the temperature. - - - - - - - - Support point of the linearized curve of the temperature. - - - - - - - - - Criteria which enable to stop the simulation in a controlled manner. - Whichever criterion is fulfilled first stops the simulation. - - - - Maximum recrystallized volume fraction. - - - - - Maximum simulated physical time. - - - - - Maximum number of iteration steps. - - - - - - Settings relevant for stable numerical integration. - - - - Maximum fraction equivalent to the migration of the - fastest grain boundary in the system how much a cell - may be consumed in a single iteration. - - - - - Fraction of the total number of cells in the CA which - should initially be allocated for offering cells in the - recrystallization front. - - - - - By how much more times should the already allocated memory - be is increased to offer space for storing states of cells - in the recrystallization front. - - - - - Should the cache for cells in the recrystallization front - be defragmented on-the-fly. - - - - - Heuristic recrystallized volume target values at which - the cache for cells in the recrystallization front - will be defragmented on-the-fly. - - - - - - - - List of recrystallized volume target values at which a - snapshot of the CA state should be exported for. - - - - - - - - - - Perform a statistical analyses of the results as it was - proposed by M. Kühbach (solitary unit model ensemble approach). - - - - - How many independent cellular automaton domains - should be instantiated. - - - - - Into how many time steps should the real time interval be discretized upon - during post-processing the results with the solitary unit modeling approach. - - - - - List of identifier for those domain which should be rendered. - Identifier start from 0. - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXms_score_results.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXms_score_results.nxdl.xml deleted file mode 100644 index 0e95761..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXms_score_results.nxdl.xml +++ /dev/null @@ -1,720 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of boundaries of the bounding box or primitive to domain. - - - - - Number of parameter required for chosen orientation parameterization. - - - - - Number of texture components identified. - - - - - Dimensionality. - - - - - Cardinality. - - - - - Number of active cells in the (recrystallization) front. - - - - - Number of grains in the computer simulation. - - - - - Application definition for storing results of the SCORE cellular automaton. - - The SCORE cellular automaton model for primary recrystallization is an - example of typical materials engineering applications used within the field - of so-called Integral Computational Materials Engineering (ICME) whereby - one can simulate the evolution of microstructures. - - Specifically the SCORE model can be used to simulate the growth of static - recrystallization nuclei. The model is described in the literature: - - * `M. Kühbach et al. <https://doi.org/10.1016/j.actamat.2016.01.068>`_ - * `C. Haase et al. <https://doi.org/10.1016/j.actamat.2015.08.057>`_ - * `M. Diehl et al. <https://doi.org/10.1088/1361-651X/ab51bd>`_ - - - - - An at least as strong as SHA256 hashvalue of the file - that specifies the application definition. - - - - - - NeXus NXDL schema to which this file conforms. - - - - - - - - Ideally, a (globally) unique persistent identifier - for referring to this computer simulation. - - The identifier is usually defined/issued by the facility, laboratory, - or the principle investigator. The identifier enables to link - experiments to e.g. proposals. - - - - - Free-text description about the workflow (analysis/simulation). - - Users are strongly advised to detail the sample history in the - respective field and fill rather as completely as possible the fields - of this application definition rather than write details about the - experiment into this free-text description field. - - - - - ISO 8601 time code with local time zone offset to UTC information - included when the characterization started. - - - - - ISO 8601 time code with local time zone offset to UTC included - when the characterization ended. - - - - - - - - - - Specify if the (characterization) results/data of this instance of an - application definition are based on the results of a simulation or the - results of a post-processing of measured data to describe a microstructure. - The term microstructure is used to describe the spatial arrangement of - crystal defects inside a sample/specimen without demanding necessarily - that this structure is mainly at the micron length scale. - Nanostructure and macrostructure are close synonyms. - Material architecture is a narrow synonym. - - - - - - - - - - The path and name of the config file for this analysis. - - - - At least SHA256 strong hash of the specific config_file for - tracking provenance. - - - - - - Path to the directory where the tool should store NeXus/HDF5 results - of this analysis. If not specified results will be stored in the - current working directory. - - - - - A statement whether the SCORE executable managed to - process the analysis or failed prematurely. - - This status is written to the results file after the end_time - at which point the executable must not compute any analysis. - Only when this status message is present and shows `success`, the - user should consider the results. In all other cases it might be - that the executable has terminated prematurely or another error - occurred. - - - - - - - - - Contact information and eventually details of at least one person - involved in creating this result. This can be the principle investigator - who performed this experiment. Adding multiple users if relevant is recommended. - - - - Given (first) name and surname of the user. - - - - - Name of the affiliation of the user at the point in time - when the experiment was performed. - - - - - Postal address of the affiliation. - - - - - Email address of the user at the point in time when the experiment - was performed. Writing the most permanently used email is recommended. - - - - - Globally unique identifier of the user as offered by services - like ORCID or ResearcherID. If this field is field the specific service - should also be written in orcid_platform - - - - - Name of the OrcID or ResearcherID where the account - under orcid is registered. - - - - - (Business) (tele)phone number of the user at the point - in time when the experiment was performed. - - - - - Which role does the user have in the place and at the point - in time when the experiment was performed? Technician operating - the microscope. Student, postdoc, principle investigator, guest - are common examples. - - - - - Account name that is associated with the user in social media platforms. - - - - - Name of the social media platform where the account - under social_media_name is registered. - - - - - - - - Descriptive name or ideally (globally) unique persistent identifier. - - - - - - - Hard link to a location in the hierarchy of the NeXus file - where the data for default plotting are stored. - - - - - Container to hold different coordinate systems conventions. - A least a right-handed Cartesian coordinate system with base vectors - named x, y, and z has to be specified. Each base vector of the - coordinate system should be described with an NXtransformations instance. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The simulated or characterized material volume element aka domain. - At least one instance of geometry required either NXcg_grid, - NXcg_polyhedron_set, or NXcg_point_set. This geometry group needs - to contain details about the boundary conditions. - - - - - - - - - - - - - A tight bounding box or sphere or bounding primitive about the grid. - - - - - How many distinct boundaries are distinguished? - Most grids discretize a cubic or cuboidal region. In this case - six sides can be distinguished, each making an own boundary. - - - - - Name of the boundaries. E.g. left, right, front, back, bottom, top, - The field must have as many entries as there are number_of_boundaries. - - - - - The boundary conditions for each boundary: - - 0 - undefined - 1 - open - 2 - periodic - 3 - mirror - 4 - von Neumann - 5 - Dirichlet - - - - - - - - - Collection of microstructural data observed/simulated. - - - - Integer which specifies the first index to be used for distinguishing - snapshots. Identifiers are defined either implicitly or explicitly. - For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate - if the identifiers are expected to start from 1 (referred to as - Fortran-/Matlab-) or from 0 (referred to as C-, Python-style index - notation) respectively. - - - - - - Summary quantities which are the result of some post-processing of - the snapshot data (averaging, integrating, interpolating). - Frequently used descriptors from continuum mechanics and thermodynamics - can be used here. A few examples are given. Each descriptor is currently - modelled as an instance of an NXprocess because it is relevant to - understand how the descriptors are computed. - - - - Evolution of the physical time. - - - - - Evolution of the simulated temperature over time. - - - - - - Evolution of the recrystallized volume fraction over time. - - - - - - - - Measured or simulated physical time stamp for this snapshot. - Not to be confused with wall-clock timing or profiling data. - - - - - Simulated temperature. - - - - - Iteration or increment counter. - - - - - - - Grain identifier for each cell. - - - - - - - - - - Identifier of the OpenMP thread which processed this part of the grid. - - - - - - - - - - - - Details about those cells which in this time step represent - the discretized recrystallization front. - - - - Which cells are currently in a halo region of threads. - - - - - - - - So-called mobility weight which is a scaling factor to - control the mobility of the grain boundary which is assumed - to sweep currently this volume. - - - - - - - - Grid coordinates of each cell in the recrystallization front. - - - - - - - - - Grain identifier assigned to each cell in the recrystallization front. - - - - - - - - Grain identifier assigned to each nucleus which affected that cell in the - recrystallization front. - - - - - - - - Relative volume transformed as a measure of infection progress. - - - - - - - - Identifier of the OpenMP thread processing each cell in the recrystallization - front. - - - - - - - - Hint about the direction from which the cell was infected. - - - - - - - - - Current grain-related quantities. - - - - Bunge-Euler angle triplets for each grain. - - - - - - - - - Discrete volume of each grain accounting also for partially - transformed cells. - - - - - - - - Current value for the dislocation density as a measure of - the remaining stored energy in assumed crystal defects inside - each grain. The difference between these values scales the - driving force of grain boundary migration. - - - - - - - - Is the grain deformed. - - - - - - - - Is the grain recrystallized. - - - - - - - - - Current recrystallized volume fraction. - - - - Currently evaluated actual recrystallized volume fraction. - This takes into account partially recrystallized cells. - - - - - Currently desired target recrystallized volume fraction at - which the user requested to log a snapshot. - - - - - - - - Currently assumed globally applied Cauchy stress tensor on the ROI. - - - - - - - - - - - Currently assumed globally applied Cauchy strain tensor on the ROI. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Specify if it was different from the number_of_processes - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - Specify if it was different from the number_of_threads - in the NXcs_profiling super class. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXms_snapshot.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXms_snapshot.nxdl.xml deleted file mode 100644 index 1f922e2..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXms_snapshot.nxdl.xml +++ /dev/null @@ -1,54 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Base class for data on the state of the microstructure at a given - time/iteration. - - - - Is this time for a measurement or a simulation. - - - - - - - - - Measured or simulated physical time stamp for this snapshot. - Not to be confused with wall-clock timing or profiling data. - - - - - Iteration or increment counter. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXms_snapshot_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXms_snapshot_set.nxdl.xml deleted file mode 100644 index 6cff36c..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXms_snapshot_set.nxdl.xml +++ /dev/null @@ -1,62 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - A collection of spatiotemporal microstructure data. - - - - Is this set describing a measurement or a simulation? - - - - - - - - - Integer which specifies the first index to be used for distinguishing - snapshots. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXopt.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXopt.nxdl.xml deleted file mode 100644 index be63659..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXopt.nxdl.xml +++ /dev/null @@ -1,868 +0,0 @@ - - - - - - - - - Variables used throughout the document, e.g. dimensions or parameters. - - - - Length of the spectrum array (e.g. wavelength or energy) of the measured - data. - - - - - Number of sensors used to measure parameters that influence the sample, - such as temperature or pressure. - - - - - Number of measurements (1st dimension of measured_data array). This is - equal to the number of parameters scanned. For example, if the experiment - was performed at three different temperatures and two different pressures - N_measurements = 2*3 = 6. - - - - - Number of detection angles of the beam reflected or scattered off the - sample. - - - - - Number of angles of incidence of the incident beam. - - - - - Number of observables that are saved in a measurement. e.g. one for - intensity, reflectivity or transmittance, two for Psi and Delta etc. This - is equal to the second dimension of the data array 'measured_data' and the - number of column names. - - - - - An application definition for optical spectroscopy experiments. - - - - An application definition template for optical spectroscopy experiments. - - A general optical experiment consists of a light or excitation source, a - beam path, a sample + its stage + its environment, and a detection unit. - Examples are reflection or transmission measurements, photoluminescence, - Raman spectroscopy, ellipsometry etc. - - - - An application definition describing a general optical experiment. - - - - Version number to identify which definition of this application - definition was used for this entry/data. - - - - - URL where to find further material (documentation, examples) relevant - to the application definition. - - - - - - - - - A (globally persistent) unique identifier of the experiment. - (i) The identifier is usually defined by the facility or principle - investigator. - (ii) The identifier enables to link experiments to e.g. proposals. - - - - - An optional free-text description of the experiment. - - However, details of the experiment should be defined in the specific - fields of this application definition rather than in this experiment - description. - - - - - Specify the type of the optical experiment. - - - - - Start time of the experiment. UTC offset should be specified. - - - - - Contact information of at least the user of the instrument or the - investigator who performed this experiment. - Adding multiple users, if relevant, is recommended. - - - - Name of the user. - - - - - Name of the affiliation of the user at the point in time when the - experiment was performed. - - - - - Street address of the user's affiliation. - - - - - Email address of the user. - - - - - Author ID defined by https://orcid.org/. - - - - - Telephone number of the user. - - - - - - Properties of the experimental setup. This includes general information - about the instrument (such as model, company etc.), information about - the calibration of the instrument, elements of the beam path including - the excitation or light source and the detector unit, the sample stage - (plus the sample environment, which also includes sensors used to - monitor external conditions) and elements of the beam path. - - Meta data describing the sample should be specified in ENTRY/SAMPLE - outside of ENTRY/INSTRUMENT. - - - - The name of the instrument. - - - - The used version of the hardware if available. If not a commercial - instrument use date of completion of the hardware. - - - - - - Name of the company which build the instrument. - - - - - ISO8601 date when the instrument was constructed. - UTC offset should be specified. - - - - - - Commercial or otherwise defined given name of the program that was - used to measure the data, i.e. the software used to start and - record the measured data and/or metadata. - If home written, one can provide the actual steps in the NOTE - subfield here. - - - - - Either version with build number, commit hash, or description of a - (online) repository where the source code of the program and build - instructions can be found so that the program can be configured in - such a way that result files can be created ideally in a - deterministic manner. - - - - - Website of the software. - - - - - - Commercial or otherwise defined name of the firmware that was used - for the measurement - if available. - - - - Version and build number or commit hash of the software source code. - - - - - Website of the software. - - - - - - Was a calibration performed? If yes, when was it done? If the - calibration time is provided, it should be specified in - ENTRY/INSTRUMENT/calibration/calibration_time. - - - - - - - - - - - - The calibration data and metadata should be described in a separate NeXus file - with the link provided in 'calibration_link'. - - - - If calibtration status is 'calibration time provided', specify the - ISO8601 date when calibration was last performed before this - measurement. UTC offset should be specified. - - - - - Link to the NeXus file containing the calibration data and metadata. - - - - - - Describes an arrangement of optical or other elements, e.g. the beam - path between the light source and the sample, or between the sample - and the detector unit (including the sources and detectors - themselves). - - If a beam splitter (i.e. a device that splits the incoming beam into - two or more beams) is part of the beam path, two or more NXbeam_path - fields may be needed to fully describe the beam paths and the correct - sequence of the beam path elements. - Use as many beam paths as needed to describe the setup. - - - - - Angle(s) of the incident beam vs. the normal of the bottom reflective - (substrate) surface in the sample. - - - - - - - - - Detection angle(s) of the beam reflected or scattered off the sample - vs. the normal of the bottom reflective (substrate) surface in the - sample if not equal to the angle(s) of incidence. - - - - - - - - Sample stage, holding the sample at a specific position in X,Y,Z - (Cartesian) coordinate system and at an orientation defined - by three Euler angles (alpha, beta, gamma). - - - - Specify the type of the sample stage. - - - - - - - - - - - - If there is no motorized stage, we should at least qualify where - the beam hits the sample and in what direction the sample stands - in a free-text description, e.g. 'center of sample, long edge - parallel to the plane of incidence'. - - - - - Specify external parameters that have influenced the sample, such - as the surrounding medium, and varied parameters e.g. temperature, - pressure, pH value, optical excitation etc. - - - - Describe what was the medium above or around the sample. The - common model is built up from the substrate to the medium on the - other side. Both boundaries are assumed infinite in the model. - Here, define the name of the medium (e.g. water, air, UHV, etc.). - - - - - Array of pairs of complex refractive indices n + ik of the medium - for every measured spectral point/wavelength/energy. - Only necessary if the measurement was performed not in air, or - something very well known, e.g. high purity water. - - - - - - - - - A sensor used to monitor an external condition influencing the - sample, such as temperature or pressure. It is suggested to - replace 'PARAMETER' by the type of the varied parameter defined - in 'parameter_type'. - The measured parameter values should be provided in 'values'. - For each parameter, a 'PARAMETER(NXsensor)' field needs to exist. - In other words, there are N_sensors 'PARAMETER(NXsensor)' fields. - - - - Indicates which parameter was changed. Its definition must exist - below. The specified variable has to be N_measurements long, - providing the parameters for each data set. If you vary more than - one parameter simultaneously. - If the measured parameter is not contained in the list `other` - should be specified and the `parameter_type_name` should be provided. - - - - - - - - - - - - - - - - - - - - - - - - - If the parameter_type is `other` a name should be specified here. - - - - - Number of different parameter values at which the measurement - was performed. For example, if the measurement was performed at - temperatures of 4, 77 and 300 K, then number_of_parameters = 3. - - - - - Vector containing the values of the varied parameter. Its - length is equal to N_measurements. The order of the values - should be as follows: - - * Order the sensors according to number_of_parameters starting - with the lowest number. If number_of_parameters is equal for - two sensors order them alphabetically (sensor/parameter name). - * The first sensor's j parameters should be ordered in the - following way. The first N_measurements/number_of_parameters - entries of the vector contain the first parameter (a1), the - second N_measurements/number_of_parameters contain the second - parameter (a2) etc., so the vector looks like: - [ - a1,a1,...,a1, - a2,a2,...,a2, - ... - aj,aj,...aj - ] - * The kth sensor's m parameters should be ordered in the - following way: - [ - p1,...p1,p2,...,p2,...pm,...,pm, - p1,...p1,p2,...,p2,...pm,...,pm, - ... - p1,...p1,p2,...,p2,...pm,...,pm - ] - * The last sensor's n parameters should be ordered in the - following way: - [ - z1,z2,...,zn, - z1,z2,...,zn, - ... - z1,z2,...,zn] - - For example, if the experiment was performed at three different - temperatures (T1, T2, T3), two different pressures (p1, p2) and - two different angles of incidence (a1, a2), then - N_measurements = 12 and the order of the values for the various - parameter vectors is: - - * angle_of_incidence: [a1,a1,a1,a1,a1,a1,a2,a2,a2,a2,a2,a2] - * pressure: [p1,p1,p1,p2,p2,p2,p1,p1,p1,p2,p2,p2] - * temperature: [T1,T2,T3,T1,T2,T3,T1,T2,T3,T1,T2,T3] - - - - - - - - - - For environmental measurements, the environment (liquid, vapor - etc.) is enclosed in a cell, which has windows both in the - direction of the source (entry window) and the detector (exit - window) (looking from the sample). In case that the entry and exit - windows are not the same type and do not have the same properties, - use a second 'WINDOW(MXaperture)' field. - - The windows also add a phase shift to the light altering the - measured signal. This shift has to be corrected based on measuring - a known sample (reference sample) or the actual sample of interest - in the environmental cell. State if a window correction has been - performed in 'window_effects_corrected'. Reference data should be - considered as a separate experiment, and a link to the NeXus file - should be added in reference_data_link in measured_data. - - The window is considered to be a part of the sample stage but also - beam path. Hence, its position within the beam path should be - defined by the 'depends_on' field. - - - - Specify the position of the window in the beam path by pointing - to the preceding element in the sequence of beam path elements. - - - - - Was a window correction performed? If 'True' describe the window - correction procedure in 'window_correction/procedure'. - - - - - Was a window correction performed? If 'True' describe the - window correction procedure in '' - - - - Describe when (before or after the main measurement + time - stamp in 'date') and how the window effects have been - corrected, i.e. either mathematically or by performing a - reference measurement. In the latter case, provide the link to - to the reference data in 'reference_data_link'. - - - - - Link to the NeXus file which describes the reference data if a - reference measurement for window correction was performed. - Ideally, the reference measurement was performed on a reference - sample and on the same sample, and using the same conditions as - for the actual measurement with and without windows. It should - have been conducted as close in time to the actual measurement - as possible. - - - - - - The material of the window. - - - - - - - - - - - - - - - If you specified 'other' as material, decsribe here what it is. - - - - - Thickness of the window. - - - - - Angle of the window normal (outer) vs. the substrate normal - (similar to the angle of incidence). - - - - - - - - Properties of the sample, such as sample type, layer structure, - chemical formula, atom types, its history etc. - Information about the sample stage and sample environment should be - described in ENTRY/INSTRUMENT/sample_stage. - - - - Descriptive name of the sample - - - - - Specify the type of sample, e.g. thin film, single crystal etc. - - - - - - - - - - - - Qualitative description of the layer structure for the sample, - starting with the top layer (i.e. the one on the front surface, on - which the light incident), e.g. native oxide/bulk substrate, or - Si/native oxide/thermal oxide/polymer/peptide. - - - - - Chemical formula of the sample. Use the Hill system (explained here: - https://en.wikipedia.org/wiki/Chemical_formula#Hill_system) to write - the chemical formula. In case the sample consists of several layers, - this should be a list of the chemical formulas of the individual - layers, where the first entry is the chemical formula of the top - layer (the one on the front surface, on which the light incident). - The order must be consistent with layer_structure - - - - - List of comma-separated elements from the periodic table that are - contained in the sample. If the sample substance has multiple - components, all elements from each component must be included in - 'atom_types'. - - - - - Ideally, a reference to the location or a unique (globally - persistent) identifier (e.g.) of e.g. another file which gives - as many as possible details of the material, its microstructure, - and its thermo-chemo-mechanical processing/preparation history. - In the case that such a detailed history of the sample is not - available, use this field as a free-text description to specify - details of the sample and its preparation. - - - - - ISO8601 date with time zone (UTC offset) specified. - - - - - Description of the substrate. - - - - - Specify the sample orientation. - - - - - - Measured data, data errors, and varied parameters. If reference data - were measured they should be considered a separate experiment and a - link to its NeXus file should be added in reference_data_link. - - - - An identifier to correlate data to the experimental conditions, - if several were used in this measurement; typically an index of 0-N. - - - - - Select which type of data was recorded, for example intensity, - reflectivity, transmittance, Psi and Delta etc. - It is possible to have multiple selections. The enumeration list - depends on the type of experiment and may differ for different - application definitions. - - - - - - - - - - - - - - - - - Spectral values (e.g. wavelength or energy) used for the measurement. - An array of 1 or more elements. Length defines N_spectrum. Replace - 'SPECTRUM' by the physical quantity that is used, e.g. wavelength. - - - - - - - If applicable, change 'unit: NX_ANY' to the appropriate NXDL unit. - If the unit of the measured data is not covered by NXDL units state - here which unit was used. - - - - - - Resulting data from the measurement, described by 'data_type'. - - The first dimension is defined by the number of measurements taken, - (N_measurements). The instructions on how to order the values - contained in the parameter vectors given in the doc string of - INSTRUMENT/sample_stage/environment_conditions/PARAMETER/values, - define the N_measurements parameter sets. For example, if the - experiment was performed at three different temperatures - (T1, T2, T3), two different pressures (p1, p2) and two different - angles of incidence (a1, a2), the first measurement was taken at the - parameters {a1,p1,T1}, the second measurement at {a1,p1,T2} etc. - - - - - - - - - If applicable, change 'unit: NX_ANY' to the appropriate NXDL unit. - If the unit of the measured data is not covered by NXDL units state - here which unit was used. - - - - - - Specified uncertainties (errors) of the data described by 'data_type' - and provided in 'measured_data'. - - - - - - - - - If applicable, change 'unit: NX_ANY' to the appropriate NXDL unit. - If the unit of the measured data is not covered by NXDL units state - here which unit was used. - - - - - - List of links to the values of the sensors. Add a link for each - varied parameter (i.e. for each sensor). - - - - - - - - Link to the NeXus file which describes the reference data if a - reference measurement was performed. Ideally, the reference - measurement was performed using the same conditions as the actual - measurement and should be as close in time to the actual measurement - as possible. - - - - - - Commercial or otherwise defined given name of the program that was - used to generate the result file(s) with measured data and/or - metadata (in most cases, this is the same as INSTRUMENT/software). - If home written, one can provide the actual steps in the NOTE - subfield here. - - - - - Either version with build number, commit hash, or description of a - (online) repository where the source code of the program and build - instructions can be found so that the program can be configured in - such a way that result files can be created ideally in a - deterministic manner. - - - - - Website of the software. - - - - - - A plot of the multi-dimensional data array provided in - ENTRY/data/measured_data. - - - - Spectrum, i.e. x-axis of the data (e.g. wavelength, energy etc.) - - - - - - - Parameters that are derived from the measured data. - - - - Light loss due to depolarization as a value in [0-1]. - - - - - - - - - - Jones quality factor. - - - - - - - - - - Reflectivity. - - - - - - - - - - Transmittance. - - - - - - - - - - - Commercial or otherwise defined given name of the program that was - used to generate or calculate the derived parameters. - If home written, one can provide the actual steps in the NOTE - subfield here. - - - - - Either version with build number, commit hash, or description of a - (online) repository where the source code of the program and build - instructions can be found so that the program can be configured in - such a way that result files can be created ideally in a - deterministic manner. - - - - - - - A default view of the data provided in ENTRY/data_collection/measured_data. This - should be the part of the data set which provides the most suitable - representation of the data. - - - - Spectrum, i.e. x-axis of the data (e.g. wavelength, energy etc.) - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXfiber.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXoptical_fiber.nxdl.xml similarity index 53% rename from src/nexusformat/definitions/contributed_definitions/NXfiber.nxdl.xml rename to src/nexusformat/definitions/contributed_definitions/NXoptical_fiber.nxdl.xml index f4a32db..15358ba 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXfiber.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXoptical_fiber.nxdl.xml @@ -3,7 +3,7 @@ - + - Length of the spectrum vector (e.g. wavelength or energy) for which the - refractive index of the core material is given. + Length of the spectrum vector (e.g. wavelength or energy) for which the + refractive index of the core material is given. - Length of the spectrum vector (e.g. wavelength or energy) for which the - refractive index of the cladding material is given. + Length of the spectrum vector (e.g. wavelength or energy) for which the + refractive index of the cladding material is given. - Length of the spectrum vector (e.g. wavelength or energy) for which the - attenuation curve is given. + Length of the spectrum vector (e.g. wavelength or energy) for which the + attenuation curve is given. - An optical fiber, e.g. glass fiber. - - Specify the quantities that define the fiber. Fiber optics are described in - detail [here](https://www.photonics.com/Article.aspx?AID=25151&PID=4), for - example. + An optical fiber, e.g. glass fiber. + + Specify the quantities that define the fiber. Fiber optics are described in + detail [here](https://www.photonics.com/Article.aspx?AID=25151&PID=4), for + example. - Descriptive name or brief description of the fiber, e.g. by stating its - dimension. The dimension of a fiber can be given as 60/100/200 which - refers to a core diameter of 60 micron, a clad diameter of 100 micron, - and a coating diameter of 200 micron. + Descriptive name or brief description of the fiber, e.g. by stating its + dimension. The dimension of a fiber can be given as 60/100/200 which + refers to a core diameter of 60 micron, a clad diameter of 100 micron, + and a coating diameter of 200 micron. - Type/mode of the fiber. Modes of fiber transmission are shown in - Fig. 5 [here](https://www.photonics.com/Article.aspx?AID=25151&PID=4). + Type/mode of the fiber. Modes of fiber transmission are shown in + Fig. 5 [here](https://www.photonics.com/Article.aspx?AID=25151&PID=4). @@ -71,9 +71,9 @@ - Type of dispersion. + Type of dispersion. - + @@ -81,8 +81,8 @@ - Spectrum-dependent (or refractive index-dependent) dispersion of the - fiber. Specify in ps/nm*km. + Spectrum-dependent (or refractive index-dependent) dispersion of the + fiber. Specify in ps/nm*km. @@ -90,22 +90,22 @@ - Core of the fiber, i.e. the part of the fiber which transmits the light. + Core of the fiber, i.e. the part of the fiber which transmits the light. - + - Specify the material of the core of the fiber. + Specify the material of the core of the fiber. - + - Core diameter of the fiber (e.g. given in micrometer). + Core diameter of the fiber (e.g. given in micrometer). - + - Complex index of refraction of the fiber. Specify at given wavelength - (or energy, wavenumber etc.) values. + Complex index of refraction of the fiber. Specify at given wavelength + (or energy, wavenumber etc.) values. @@ -115,22 +115,22 @@ - Core of the fiber, i.e. the part of the fiber which transmits the light. + Core of the fiber, i.e. the part of the fiber which transmits the light. - + - Specify the material of the core of the fiber. + Specify the material of the core of the fiber. - + - Clad diameter of the fiber (e.g. given in micrometer). + Clad diameter of the fiber (e.g. given in micrometer). - + - Complex index of refraction of the fiber. Specify at given wavelength - (or energy, wavenumber etc.) values. + Complex index of refraction of the fiber. Specify at given wavelength + (or energy, wavenumber etc.) values. @@ -140,64 +140,59 @@ - Coating of the fiber. + Coating of the fiber. - + - Specify the material of the coating of the fiber. + Specify the material of the coating of the fiber. - + - Outer diameter of the fiber (e.g. given in micrometer). + Outer diameter of the fiber (e.g. given in micrometer). - Length of the fiber. + Length of the fiber. - Spectral range for which the fiber is designed. Enter the minimum and - maximum values (lower and upper limit) of the wavelength range. + Spectral range for which the fiber is designed. Enter the minimum and + maximum values (lower and upper limit) of the wavelength range. - Unit of spectral array (e.g. nanometer or angstrom for wavelength, or - electronvolt for energy etc.). + Unit of spectral array (e.g. nanometer or angstrom for wavelength, or + electronvolt for energy etc.). - + - Transfer rate of the fiber (in GB per second). + Transfer rate of the fiber (in GB per second). - - - GB/s - - - Numerical aperture (NA) of the fiber. + Numerical aperture (NA) of the fiber. - + - Wavelength-dependent attenuation of the fiber (specify in dB/km). + Wavelength-dependent attenuation of the fiber (specify in dB/km). - Use dB/km. + Use dB/km. @@ -206,12 +201,12 @@ - Power loss of the fiber in percentage. + Power loss of the fiber in percentage. - Acceptance angle of the fiber. + Acceptance angle of the fiber. diff --git a/src/nexusformat/definitions/contributed_definitions/NXpolarizer_opt.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXoptical_polarizer.nxdl.xml similarity index 51% rename from src/nexusformat/definitions/contributed_definitions/NXpolarizer_opt.nxdl.xml rename to src/nexusformat/definitions/contributed_definitions/NXoptical_polarizer.nxdl.xml index 9142ae4..9536b38 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXpolarizer_opt.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXoptical_polarizer.nxdl.xml @@ -3,7 +3,7 @@ - - + - Size of the wavelength array for which the refractive index of the material - and/or coating is given. + Size of the wavelength array for which the refractive index of the material + and/or coating is given. - Size of the wavelength array for which the reflectance or transmission of - the polarizer is given. + Size of the wavelength array for which the reflectance or transmission of + the polarizer is given. - An optical polarizer. - - Information on the properties of polarizer is provided e.g. - [here](https://www.rp-photonics.com/polarizers.html). + An optical polarizer. + + Information on the properties of polarizer is provided e.g. + [here](https://www.rp-photonics.com/polarizers.html). - Type of the polarizer (e.g. dichroic, linear, circular etc.) + Type of the polarizer - + @@ -61,23 +62,16 @@ - - - - - If you selected 'other' in type specify what it is. - - - Angle of the polarizer. + Angle of the polarizer. - Acceptance angle of the polarizer (range). + Acceptance angle of the polarizer (range). @@ -85,18 +79,17 @@ - Describe the geometry (shape, dimension etc.) of the device. - Specify the dimensions in 'SHAPE/size'. A sketch of the device should be - provided in the 'sketch(NXdata)' field to clarify (i) the shape and - dimensions of the device, and (ii) the input and outputs (i.e. the - direction of the incoming and outcoming (split) beams). + Describe the geometry (shape, dimension etc.) of the device. + Specify the dimensions in 'SHAPE/size'. A sketch of the device should be + provided in the 'sketch(NXdata)' field to clarify (i) the shape and + dimensions of the device, and (ii) the input and outputs (i.e. the + direction of the incoming and outcoming (split) beams). - - Describe the shape (plate, cube, wedged, prism etc.). + Describe the shape (plate, cube, wedged, prism etc.). - + @@ -105,33 +98,28 @@ - - - If you chose 'other' in 'shape' describe what it is. - - - Sketch of thedevice showing its geometry. The paths of the - incoming and outgoing beam should be illustrated and labelled (0 for - the incoming beam, and 1, 2,..., N_outputs for the outputs). + Sketch of the device showing its geometry. The paths of the + incoming and outgoing beam should be illustrated and labelled (0 for + the incoming beam, and 1, 2,..., N_outputs for the outputs). - Physical extent of the device. The device might be made up of one or - more objects (NX_objects). The meaning and location of the axes used - will vary according to the value of the 'shape' variable. 'N_shapepar' - defines how many parameters: - - * For 'cube' the parameters are (width, length). - * For 'cylinder' the parameters are (diameter, length). - * For 'plate' the parameters are (width, height, length). - * For 'prism' the parameters are (width, height, length). - * For 'wedged' the parameters are (width, height, shortest length). - The wedge angle should be provided in 'SHAPE/wedge_angle'. - * For 'other' the parameters may be (A, B, C, ...) with the labels - defined in the sketch plotted in 'SHAPE/sketch'. + Physical extent of the device. The device might be made up of one or + more objects (NX_objects). The meaning and location of the axes used + will vary according to the value of the 'shape' variable. 'N_shapepar' + defines how many parameters: + + * For 'cube' the parameters are (width, length). + * For 'cylinder' the parameters are (diameter, length). + * For 'plate' the parameters are (width, height, length). + * For 'prism' the parameters are (width, height, length). + * For 'wedged' the parameters are (width, height, shortest length). + The wedge angle should be provided in 'SHAPE/wedge_angle'. + * For 'other' the parameters may be (A, B, C, ...) with the labels + defined in the sketch plotted in 'SHAPE/sketch'. @@ -140,14 +128,14 @@ - Wedge angle if 'shape' is 'wedged'. + Wedge angle if 'shape' is 'wedged'. - Wavelength range for which the polarizer is designed. Enter the minimum - and maximum wavelength (lower and upper limit) of the range. + Wavelength range for which the polarizer is designed. Enter the minimum + and maximum wavelength (lower and upper limit) of the range. @@ -155,23 +143,23 @@ - Properties of the substrate material of the polarizer. If the device has - a coating specify the coating material and its properties in 'coating'. + Properties of the substrate material of the polarizer. If the device has + a coating specify the coating material and its properties in ``COATING``. - Specify the substrate material of the polarizer. + Specify the substrate material of the polarizer. - Thickness of the polarizer substrate. + Thickness of the polarizer substrate. - Complex index of refraction of the polarizer material. Specify at given - spectral values (wavelength, energy, wavenumber etc.). + Complex index of refraction of the polarizer material. Specify at given + spectral values (wavelength, energy, wavenumber etc.). @@ -179,36 +167,37 @@ - - - If the device has a coating describe the material and its properties. - Some basic information can be found e.g. [here] - (https://www.opto-e.com/basics/reflection-transmission-and-coatings). - If the back and front side of the polarizer are coated with different - materials, you may define two coatings (e.g. COATING1 and COATING2). + If the device has a coating describe the material and its properties. + Some basic information can be found e.g. [here] + (https://www.opto-e.com/basics/reflection-transmission-and-coatings). + If the back and front side of the polarizer are coated with different + materials, you may define two coatings (e.g. coating_front and + coating_back). - + - Specify the coating type (e.g. dielectric, anti-reflection (AR), - multilayer coating etc.). + Specify the coating type (e.g. dielectric, anti-reflection (AR), + multilayer coating etc.). - + - Describe the coating material (e.g. MgF2). + Describe the coating material (e.g. MgF2). - + - Thickness of the coating. + Thickness of the coating. - Complex index of refraction of the coating. Specify at given spectral - values (wavelength, energy, wavenumber etc.). + Complex index of refraction of the coating. Specify at given spectral + values (wavelength, energy, wavenumber etc.). @@ -218,7 +207,7 @@ the device has different coatings on the front and back side.--> - Extinction ratio (maximum to minimum transmission). + Extinction ratio (maximum to minimum transmission). @@ -226,7 +215,7 @@ the device has different coatings on the front and back side.--> - Reflection of the polarizer at given wavelength values. + Reflection of the polarizer at given wavelength values. @@ -234,11 +223,10 @@ the device has different coatings on the front and back side.--> - Transmission of the polarizer at given wavelength values. + Transmission of the polarizer at given wavelength values. - diff --git a/src/nexusformat/definitions/contributed_definitions/NXoptical_system_em.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXoptical_system_em.nxdl.xml deleted file mode 100644 index 0f75300..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXoptical_system_em.nxdl.xml +++ /dev/null @@ -1,83 +0,0 @@ - - - - - - A container for qualifying an electron optical system. - - - - - Citing the JEOL TEM glossary this is *an effective distance from a specimen - to a plane where an observed diffraction pattern is formed*. - - - - - The factor of enlargement of the apparent size, not physical size, of an object. - - - - - The defocus aberration constant oftentimes taken as the C_1_0 which - is described in more details in NXaberration. - - - - - Citing the JEOL TEM glosssary this is the value *when a cone shaped, - convergent electron beam illuminates a specimen, the semi-angle of the cone - is termed convergence angle.* - - - - - The extent of the observable parts of the specimen given the current - magnification and other settings of the instrument. - - - - - Citing `Globalsino <https://www.globalsino.com/EM/page4586.html>`_ this is - *a distance between the specimen and the lower pole piece in SEM system*. - - - - - Beam current as measured relevant for the illumination of the specimen. - Users should specify further details like how the beam current was measured - using the beam_current_description field. - - - - - Specify further details how the beam current was measured or estimated. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXorientation_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXorientation_set.nxdl.xml deleted file mode 100644 index 73f5e3c..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXorientation_set.nxdl.xml +++ /dev/null @@ -1,133 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality of the reference space/coordinate system. - - - - - The cardinality of the set, i.e. the number of orientations. - - - - - Number of parameters for the chosen parameterization. - - - - - Details about individual orientations of a set of objects. - - For a more detailed insight into the discussion of parameterizing - orientations in materials science see: - - * https://doi.org/10.1016/j.matchar.2016.04.008 - * https://doi.org/10.1088/0965-0393/23/8/083501 - * https://doi.org/10.1007/978-3-662-09156-2 group-theory of rotations - * https://doi.org/10.1016/C2013-0-11769-2 the classical book of H.-J. Bunge - - - - - Reference to or definition of a coordinate system with - which the definitions are interpretable. - - - - - - - - - - - - A link or reference to the objects whose identifier are referred to in - identifier to resolve which row tuple is the orientation of each object - by reading orientations. - - - - - Integer which specifies which orientation (row of array orientation) matches - to which object.e first index to be used for distinguishing - hexahedra. Identifiers are defined either implicitly - or explicitly. For implicit indexing the identifiers are defined on the - interval [identifier_offset, identifier_offset+c-1]. - For explicit indexing the identifier array has to be defined. - - The identifier_offset field can for example be used to communicate if the - identifiers are expected to start from 1 (referred to as Fortran-/Matlab-) - or from 0 (referred to as C-, Python-style index notation) respectively. - - - - - Integer used to distinguish how a row in orientation describes a specific - object with an explicit identifier that can be queried via inspecting the - list of available objects in objects. - - The rational behind having such a more complicated pattern is that not - all objects referred when following the link in objects may still exists - or are still tracked when the orientation set was characterized. - - This design enables to also use NXorientation_set in situations where - the orientation of objects change as a function in time. - - - - - - - - Parameterized orientations. - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXpeak.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXpeak.nxdl.xml deleted file mode 100644 index 4a030c6..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXpeak.nxdl.xml +++ /dev/null @@ -1,87 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of support points - - - - - Description of peaks, their functional form or measured support. - - - - Human-readable identifier to specify which concept/entity - the peak represents/identifies. - - - - - Is the peak described analytically via a functional form - or is it empirically defined via measured/reported - intensity/counts as a function of an independent variable. - - If the functional form is not empirical or gaussian, users - should enter other for the peak_model and add relevant details - in the NXcollection. - - - - - - - - - - - In the case of an empirical description of the peak and its shoulders, - this array holds the position values for the independent variable. - - - - - - - - In the case of an empirical description of the peak and its shoulders, - this array holds the intensity/count values at each position. - - - - - - - - In the case of an analytical description (or if peak_model is other) this - collection holds parameter of (and eventually) the functional form. - For example in the case of Gaussians mu, sigma, cut-off values, - and background intensity are relevant parameter. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXpulser_apm.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXpulser_apm.nxdl.xml deleted file mode 100644 index f2a6eda..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXpulser_apm.nxdl.xml +++ /dev/null @@ -1,165 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Total number of ions collected. - - - - - Metadata for laser- and/or voltage-pulsing in atom probe microscopy. - - - - How is field evaporation physically triggered. - - - - - - - - - - Frequency with which the high voltage or laser pulser fires. - - - - - - - - - Fraction of the pulse_voltage that is applied in addition - to the standing_voltage at peak voltage of a pulse. - - If a standing voltage is applied, this gives nominal pulse fraction - (as a function of standing voltage). Otherwise this field should not be - present. - - - - - - - - In laser pulsing mode the values will be zero so the this field is recommended. - However, for voltage pulsing mode it is highly recommended that users report the pulsed_voltage. - - - - - - - - Absolute number of pulses starting from the beginning of the experiment. - - - - - - - - Direct current voltage between the specimen and the (local electrode) in - the case of local electrode atom probe (LEAP) instrument. - The standing voltage applied to the sample, relative to system ground. - - - - - - - - Atom probe microscopes use controlled laser, voltage, - or a combination of pulsing strategies to trigger the - excitation and eventual field evaporation/emission of - an ion during an experiment. - - - - Given name/alias. - - - - - - Nominal wavelength of the laser radiation. - - - - - Nominal power of the laser source while illuminating the specimen. - - - - - - Average energy of the laser at peak of each pulse. - - - - - Details about specific positions along the focused laser beam - which illuminates the (atom probe) specimen. - - - - Track time-dependent settings over the course of the - measurement how the laser beam in tip space/reconstruction space - laser impinges on the sample, i.e. the mean vector is parallel to - the laser propagation direction. - - - - - Track time-dependent settings over the course of the - measurement where the laser beam exits the - focusing optics. - - - - - Track time-dependent settings over the course of the - measurement where the laser hits the specimen. - - - - - - Affine transformations which describe the geometry how the - laser focusing optics/pinhole-attached coordinate system is - defined, how it has to be transformed so that it aligns with - the specimen coordinate system. - A right-handed Cartesian coordinate system, the so-called laser space, - should be assumed, whose positive z-axis points - into the direction of the propagating laser beam. - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXpump.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXpump.nxdl.xml deleted file mode 100644 index bf50623..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXpump.nxdl.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - - - - Device to reduce an atmosphere to a controlled remaining pressure level. - - - - Principle type of the pump. - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXquadric.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXquadric.nxdl.xml index b7a0761..a0a6e44 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXquadric.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXquadric.nxdl.xml @@ -3,7 +3,7 @@ - - - Device for reducing flight time differences of ions in ToF experiments. - For atom probe the reflectron can be considered an energy_compensation - device, which can e.g. be realized technically as via a Poschenrieder lens - (see US patent 3863068 or US patents for the reflectron 6740872, or the curved reflectron 8134119 design). - - - - - Affine transformation(s) which detail where the reflectron - is located relative to e.g. the origin of the specimen space - reference coordinate system. - This group can also be used for specifying how the reflectron - is rotated relative to the specimen axis. - The purpose of these more detailed instrument descriptions - is to support the creation of a digital twin of the instrument - for computational science. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXscanbox_em.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXscanbox_em.nxdl.xml deleted file mode 100644 index 086ec56..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXscanbox_em.nxdl.xml +++ /dev/null @@ -1,46 +0,0 @@ - - - - - - Scan box and coils which deflect an electron beam in a controlled manner. - - In electron microscopy, the scan box is instructed by the microscope - control software. This component directs the probe to controlled - locations according to a scan scheme and plan. - - - - - - - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXsensor_scan.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXsensor_scan.nxdl.xml index afa6a1f..0a03843 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXsensor_scan.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXsensor_scan.nxdl.xml @@ -2,9 +2,9 @@ - + - Variables used to set a common size for collected sensor data. + Variables used to set a common size for collected sensor data. - The number of scan points measured in this scan. + The number of scan points measured in this scan. - Application definition for a generic scan using sensors. - - In this application definition, times should be specified always together - with an UTC offset. + Application definition for a generic scan using sensors. + + In this application definition, times should be specified always together + with an UTC offset. + + + .. index:: plotting + + Declares which child group contains a path leading + to a :ref:`NXdata` group. + + It is recommended (as of NIAC2014) to use this attribute + to help define the path to the default dataset to be visualized upon entry. + See https://www.nexusformat.org/2014_How_to_find_default_data.html + for a summary of the discussion. + + - - - - + + + The unique identifier for the entry. The identifier is mainly lab-defined and + can be a combination of the sample name, date and time, experiment condition + (such as temperature) or instrument-generated unique identifier. + + + + + The unique identifier for the collection. The identifier is used to group a + number of the experiments run upon the same setup and/or same sample. + + + + + - Define the program that was used to generate the results file(s) - with measured data and metadata. + Define the program that was used to generate the results file(s) + with measured data and metadata. - Commercial or otherwise defined given name of the program - (or a link to the instrument software). + Commercial or otherwise defined given name of the program + (or a link to the instrument software). - Either version with build number, commit hash, or description of an - (online) repository where the source code of the program and build - instructions can be found so that the program can be configured in - such a way that result files can be created ideally in a - deterministic manner. + Either version with build number, commit hash, or description of an + (online) repository where the source code of the program and build + instructions can be found so that the program can be configured in + such a way that result files can be created ideally in a + deterministic manner. - Website of the software. + Website of the software. - Contact information of at least the user of the instrument or the - investigator who performed this experiment. Adding multiple users if - relevant is recommended. + Contact information of at least the user of the instrument or the + investigator who performed this experiment. Adding multiple users if + relevant is recommended. - Name of the user. + Name of the user. - Name of the affiliation of the user at the point in time when - the experiment was performed. + Name of the affiliation of the user at the point in time when + the experiment was performed. - Full address (street, street number, ZIP, city, country) - of the user's affiliation. + Full address (street, street number, ZIP, city, country) + of the user's affiliation. - Email address of the user. + Email address of the user. - Author ID defined by https://orcid.org/. + Author ID defined by https://orcid.org/. - Official telephone number of the user. + Official telephone number of the user. + + + Any additional information or notes (e.g. purpose of the experiment) that might + be useful to understand the experiment. + + - Describes an environment setup for the experiment. - - All the setting values of the independently scanned controllers are listed under corresponding - NXsensor groups. Similarly, seperate NXsensor groups are used to store the readings from each - measurement sensor. - - For example, in a temperature-dependent IV measurement, the temperature and voltage must be - present as independently scanned controllers and the current sensor must also be present with - its readings. + Describes an environment setup for the experiment. + + All the setting values of the independently scanned controllers are listed under corresponding + NXsensor groups. Similarly, separate NXsensor groups are used to store the readings from each + measurement sensor. + + For example, in a temperature-dependent IV measurement, the temperature and voltage must be + present as independently scanned controllers and the current sensor must also be present with + its readings. - + - Plot of measured signal as a function of the timestamp of when they have been - acquired is also possible. + Plot of measured signal as a function of the timestamp of when they have been + acquired is also possible. - For each point in the scan space, either the nominal setpoint of an independently scanned controller - or a representative average value of a measurement sensor is registered. - - The length of each sensor's data value array stored in this group should be equal to the number of scan points - probed in this scan. For every scan point [N], the corresponding sensor value can be picked from index [N]. - This allows the scan to be made in any order as the user describes above in the experiment. We get matching - values simply using the index of the scan point. + For each point in the scan space, either the nominal setpoint of an independently scanned controller + or a representative average value of a measurement sensor is registered. + + The length of each sensor's data value array stored in this group should be equal to the number of scan points + probed in this scan. For every scan point [N], the corresponding sensor value can be picked from index [N]. + This allows the scan to be made in any order as the user describes above in the experiment. We get matching + values simply using the index of the scan point. @@ -150,48 +181,49 @@ - Timestamp for when the values provided in the value field were registered. - - Individual readings can be stored with their timestamps under value_log. This is to timestamp - the nominal setpoint or average reading values listed above in the value field. + Timestamp for when the values provided in the value field were registered. + + Individual readings can be stored with their timestamps under value_log. This is to timestamp + the nominal setpoint or average reading values listed above in the value field. - Free-text describing the data acquisition control: an internal - sweep using the built-in functionality of the controller device, - or a set/wait/read/repeat mechanism. + Free-text describing the data acquisition control: an internal + sweep using the built-in functionality of the controller device, + or a set/wait/read/repeat mechanism. - + - ISO8601 datum when calibration was last performed - before this measurement. UTC offset should be specified. + ISO8601 datum when calibration was last performed + before this measurement. UTC offset should be specified. - - + + - A list of names of NXsensor groups used as independently scanned controllers. + A list of names of NXsensor groups used as independently scanned controllers. - + - A list of names of NXsensor groups used as measurement sensors. + A list of names of NXsensor groups used as measurement sensors. - + + - A scan specific representation of the measured signals as a function of the independently controlled environment settings. - Plot of every measured signal as a function of the timestamp of when they have been acquired is also possible. + A scan specific representation of the measured signals as a function of the independently controlled environment settings. + Plot of every measured signal as a function of the timestamp of when they have been acquired is also possible. diff --git a/src/nexusformat/definitions/contributed_definitions/NXseparator.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXseparator.nxdl.xml index 81ba465..1b90017 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXseparator.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXseparator.nxdl.xml @@ -26,32 +26,32 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd" > - definition for an electrostatic separator. + Base class for an electrostatic separator. - extended description of the separator. + Extended description of the separator. - define position of beamline element relative to production target + Define position of beamline element relative to production target - current set on magnet supply. + Current set on magnet supply. - + current read from magnet supply. - + voltage read from magnet supply. - + current set on HT supply. - + current read from HT supply. - + voltage read from HT supply. diff --git a/src/nexusformat/definitions/contributed_definitions/NXsimilarity_grouping.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXsimilarity_grouping.nxdl.xml index 2973b9d..0a0878f 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXsimilarity_grouping.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXsimilarity_grouping.nxdl.xml @@ -2,9 +2,9 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -43,29 +43,26 @@ - Total number of similarity groups aka features, objects, clusters. + Total number of similarity groups aka features/clusters. - Metadata to the results of a similarity grouping analysis. + Base class to store results obtained from applying a similarity grouping (clustering) algorithm. - Similarity grouping analyses can be supervised segmentation or machine learning - clustering algorithms. These are routine methods which partition the member of - a set of objects/geometric primitives into (sub-)groups, features of - different type. A plethora of algorithms have been proposed which can be applied - also on geometric primitives like points, triangles, or (abstract) features aka - objects (including categorical sub-groups). + Similarity grouping algorithms are segmentation or machine learning algorithms for + partitioning the members of a set of objects (e.g. geometric primitives) into + (sub-)groups aka features of different kind/type. A plethora of algorithms exists. - This base class considers metadata and results of one similarity grouping - analysis applied to a set in which objects are either categorized as noise - or belonging to a cluster. - As the results of the analysis each similarity group, here called feature - aka object can get a number of numerical and/or categorical labels. + This base class considers metadata and results of having a similarity grouping + algorithm applied to a set in which objects are either categorized as noise + or belonging to a cluster, i.e. members of a cluster. + The algorithm assigns each similarity group (feature/cluster) at least one + identifier (numerical or categorical labels) to distinguish different cluster. - + - Number of members in the set which is partitioned into features. + Number of members in the set which gets partitioned into features. @@ -78,30 +75,29 @@ How many categorical labels does each feature have. - - + + - Which identifier is the first to be used to label a cluster. + Which numerical index is the first to be used to label a feature. The value should be chosen in such a way that special values can be resolved: - * identifier_offset-1 indicates an object belongs to no cluster. - * identifier_offset-2 indicates an object belongs to the noise category. - Setting for instance identifier_offset to 1 recovers the commonly used - case that objects of the noise category get values to -1 and unassigned points to 0. - Numerical identifier have to be strictly increasing. + * index_offset - 1 indicates that an object belongs to no cluster. + * index_offset - 2 indicates that an object belongs to the noise category. + Setting for instance index_offset to 1 recovers the commonly used + case that objects of the noise category get values to -1 and unassigned + points to 0. Numerical identifier have to be strictly increasing. - - - - + Matrix of numerical label for each member in the set. For classical clustering algorithms this can for instance - encode the cluster_identifier. + encode the indices_cluster. @@ -112,8 +108,6 @@ Matrix of categorical attribute data for each member in the set. - @@ -121,44 +115,39 @@ e.g. (NXclustering_hdbscan):--> - In addition to the detailed storage which members was grouped to which + In addition to the detailed storage which objects were grouped to which feature/group summary statistics are stored under this group. - - + + - Total number of members in the set which are categorized as unassigned. + Total number of features categorized as unassigned. - - - - Total number of members in the set which are categorized as noise. + Total number of features categorized as noise. - - - - - + - Total number of clusters (excluding noise and unassigned). + Total number of features. - + + - Array of numerical identifier of each feature (cluster). + Array of numerical identifier of each feature. - + - - + - Array of number of members for each feature. + Array of number of objects for each feature. diff --git a/src/nexusformat/definitions/contributed_definitions/NXsolid_geometry.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXsolid_geometry.nxdl.xml index fb5751f..12fc198 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXsolid_geometry.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXsolid_geometry.nxdl.xml @@ -3,7 +3,7 @@ - The geometries defined, made up of instances of :ref:`NXquadric` and :ref:`NXoff_geometry`. + The geometries defined, made up of e.g. instances of :ref:`NXquadric`, :ref:`NXoff_geometry`, + or instances of other base classes that define geometries. diff --git a/src/nexusformat/definitions/contributed_definitions/NXspatial_filter.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXspatial_filter.nxdl.xml index 25e5ae8..6836706 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXspatial_filter.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXspatial_filter.nxdl.xml @@ -2,9 +2,9 @@ - - + + - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays. - + - Number of ellipsoids. + Number of hexahedra. - + - Number of hexahedra. + Number of cylinders. - + + + Number of ellipsoids. + + + - Number of cylinders. + Number of polyhedra. - Spatial filter to filter entries within a region-of-interest based on their - position. + Base class for a spatial filter for objects within a region-of-interest (ROI). + + Objects can be points, objects composed from other geometric primitives, + or objects. - + - Qualitative statement which specifies which spatial filtering with respective - geometric primitives or bitmask is used. These settings are possible: - - * entire_dataset, no filter is applied, the entire dataset is used. - * union_of_primitives, a filter with (rotated) geometric primitives. - All ions in or on the surface of the primitives are considered - while all other ions are ignored. - * bitmasked_points, a boolean array whose bits encode with 1 - which ions should be included. Those ions whose bit is set to 0 - will be excluded. Users of python can use the bitfield operations - of the numpy package to define such bitfields. - - Conditions: - In the case that windowing_method is entire_dataset all entries are processed. - In the case that windowing_method is union_of_primitives, - it is possible to specify none or all types of primitives - (ellipsoids, cylinder, hexahedra). If no primitives are specified - the filter falls back to entire_dataset. - In the case that windowing_method is bitmask, the bitmask has to be defined; - otherwise the filter falls back to entire dataset. + Qualitative statement which describes the logical operations + that define which objects will be included and which excluded: + + * entire_dataset, no filter is applied, all objects are included. + * union_of_primitives, a filter with (possibly non-axis-aligned) geometric + primitives. Objects in or on the surface of the primitives are included. + All other objects are excluded. + * bitmask, a boolean array whose bits encode with 1 which objects + are included. Bits set to zero encode which objects are excluded. + + Users of python can use the bitfield operations of the numpy package to work with bitfields. + Multiple instances of NXcg base classes are used to compose a union_of_primitives. @@ -78,8 +77,9 @@ - - - + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXspectrum_set.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXspectrum_set.nxdl.xml deleted file mode 100644 index 9ca3aab..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXspectrum_set.nxdl.xml +++ /dev/null @@ -1,162 +0,0 @@ - - - - - - - - - Number of pixel in the slow direction. - - - - - Number of pixel in the fast direction. - - - - - Number of energy bins. - - - - - Container for reporting a set of spectra. - - - - Details how spectra were processed from the detector readings. - - - - Resolvable data artifact (e.g. filename) from which the all values in - the NXdata instances in this NXspectrum_set were loaded during parsing. - - - - An at least as strong as SHA256 hashvalue of the data artifact which - source represents digitally to support provenance tracking. - - - - - - Imaging (data collection) mode of the instrument during acquisition - of the data in this NXspectrum_set instance. - - - - - Link or name of an NXdetector instance with which the data were collected. - - - - - - - - Collected spectra for all pixels of a rectangular region-of-interest. - This representation supports rectangular scan pattern. - - - - - - - - - - Counts - - - - - - - - - - - Coordinate along y direction - - - - - - - - - - Coordinate along x direction - - - - - - - - - - Energy - - - - - - - - Accumulated counts over all pixels of the region-of-interest. - This representation supports rectangular scan pattern. - - - - - - - - Counts - - - - - - - - - - - Energy - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXspectrum_set_em_eels.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXspectrum_set_em_eels.nxdl.xml deleted file mode 100644 index 4e58d92..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXspectrum_set_em_eels.nxdl.xml +++ /dev/null @@ -1,188 +0,0 @@ - - - - - - - - - Number of pixel per EELS mapping in the slow direction. - - - - - Number of pixel per EELS mapping in the fast direction. - - - - - Number of electron energy loss bins. - - - - - Container for reporting a set of electron energy loss (EELS) spectra. - - Virtually the most important case is that spectra are collected in - a scanning microscope (SEM or STEM) for a collection of points. - The majority of cases use simple d-dimensional regular scan pattern, - such as single point, line profiles, or (rectangular) surface mappings. - - The latter pattern is the most frequently used. - For now the base class provides for scans for which the settings, - binning, and energy resolution is the same for each scan point. - - - - Details how EELS spectra were processed from the detector readings. - - - - Typically the name of the input, (vendor) file from which all - the NXdata instances in this NXspectrum_set_em_eels were loaded during - parsing to represent them in e.g. databases. - - - - An at least as strong as SHA256 hashvalue of the dataset/file - which represents the source digitally to support provenance tracking. - - - - - - Commercial or otherwise given name to the program which was used - to process detector data into the EELS spectra stack and summary. - - - - Program version plus build number, commit hash, or description - of an ever persistent resource where the source code of the program - and build instructions can be found so that the program - can be configured in such a manner that the result file - is ideally recreatable yielding the same results. - - - - - - - Collected EELS spectra for all pixels of a rectangular region-of-interest. - This representation supports rectangular scan pattern. - - - - Counts for one spectrum per each pixel. - - - - - - - - - EELS counts - - - - - - - Pixel center of mass position y-coordinates. - - - - - - - Coordinate along y direction. - - - - - - Pixel center of mass position x-coordinates. - - - - - - - Coordinate along x direction. - - - - - - Pixel center of mass energy loss bins. - - - - - - - Coordinate along energy loss axis. - - - - - - - Accumulated EELS spectrum over all pixels of a rectangular - region-of-interest. This representation supports rectangular scan pattern. - - - - Counts for specific energy losses. - - - - - - - Counts electrons with an energy loss within binned range. - - - - - - - Pixel center of mass energy loss bins. - - - - - - - Coordinate along energy loss axis. - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXspectrum_set_em_xray.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXspectrum_set_em_xray.nxdl.xml deleted file mode 100644 index 53916bb..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXspectrum_set_em_xray.nxdl.xml +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - - - - - Number of pixel per X-ray mapping in the slow direction - - - - - Number of pixel per X-ray mapping in the fast direction - - - - - Number of X-ray photon energy (bins) - - - - - Number of identified elements - - - - - Number of peaks - - - - - Container for reporting a set of energy-dispersive X-ray spectra. - - Virtually the most important case is that spectra are collected in - a scanning microscope (SEM or STEM) for a collection of points. - The majority of cases use simple d-dimensional regular scan pattern, - such as single point, line profiles, or (rectangular) surface mappings. - The latter pattern is the most frequently used. - - For now the base class provides for scans for which the settings, - binning, and energy resolution is the same for each scan point. - - `IUPAC instead of Siegbahn notation <https://doi.org/10.1002/xrs.1300200308>`_ - should be used. - - - - Details how X-ray spectra were processed from the detector readings. - - - - Typically the name of the input, (vendor) file from which all - the NXdata instances in this NXspectrum_set_em_xray were loaded during - parsing to represent them in e.g. databases. - - - - An at least as strong as SHA256 hashvalue of the dataset/file - which represents the source digitally to support provenance tracking. - - - - - - Commercial or otherwise given name to the program which was used - to process detector data into the X-ray spectra stack and summary. - - - - Program version plus build number, commit hash, or description - of an ever persistent resource where the source code of the program - and build instructions can be found so that the program - can be configured in such a manner that the result file - is ideally recreatable yielding the same results. - - - - - - - - Collected X-ray spectra for all pixels of a rectangular region-of-interest. - This representation supports rectangular scan pattern. - - - - - - - - - - X-ray photon counts - - - - - - - - - - - Coordinate along y direction. - - - - - - - - - - Coordinate along x direction. - - - - - - - - - - Photon energy. - - - - - - - Accumulated X-ray spectrum over all pixels of a rectangular - region-of-interest. This representation supports rectangular scan pattern. - - - - - - - - X-ray photon counts - - - - - - - - - - - Photon energy - - - - - - - - Details about computational steps how peaks were indexed as elements. - - - - Given name of the program that was used to perform this computation. - - - - Program version plus build number, commit hash, or description of an - ever persistent resource where the source code of the program and - build instructions can be found so that the program can be configured - in such a manner that the result file is ideally recreatable yielding - the same results. - - - - - - Name and location of each X-ray line which was indexed as a known ion. - For each ion an NXion instance should be created which specifies - the origin of the signal. For each ion also the relevant IUPAC notation - X-ray lines should be specified. - - - - - IUPAC notation identifier of the line which the peak represents. - - This can be a list of IUPAC notations for (the seldom) case that - multiple lines are group with the same peak. - - - - - - - List of the names of identified elements. - - - - - - - - Individual element-specific EDX/EDS/EDXS/SXES mapping - - A composition map is an image whose intensities for each pixel are the - accumulated X-ray quanta *under the curve(s)* of a set of peaks. - - - - Given name of the program that was used to perform this computation. - - - - Program version plus build number, commit hash, or description of an - ever persistent resource where the source code of the program and - build instructions can be found so that the program can be configured - in such a manner that the result file is ideally recreatable yielding - the same results. - - - - - - A list of strings of named instances of NXpeak from indexing - whose X-ray quanta where accumulated for each pixel. - - - - - - - - Human-readable, given name to the image. - - - - - - Individual element-specific maps. Individual maps should - each be a group and be named according to element_names. - - - - - - - - - Accumulated photon counts for observed element. - - - - - - - - - - - Coordinate along y direction. - - - - - - - - - - Coordinate along x direction. - - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXspin_rotator.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXspin_rotator.nxdl.xml index 8c0b93a..e0e4046 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXspin_rotator.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXspin_rotator.nxdl.xml @@ -26,32 +26,32 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd" > - definition for a spin rotator. + Base class for a spin rotator. - extended description of the spin rotator. + Extended description of the spin rotator. - define position of beamline element relative to production target + Define position of beamline element relative to production target - + current set on magnet supply. - + current read from magnet supply. - + voltage read from magnet supply. - + current set on HT supply. - + current read from HT supply. - + voltage read from HT supply. diff --git a/src/nexusformat/definitions/contributed_definitions/NXspindispersion.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXspindispersion.nxdl.xml deleted file mode 100644 index 619794d..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXspindispersion.nxdl.xml +++ /dev/null @@ -1,79 +0,0 @@ - - - - - - Subclass of NXelectronanalyser to describe the spin filters in photoemission - experiments. - - - - Type of spin detector, VLEED, SPLEED, Mott, etc. - - - - - Figure of merit of the spin detector - - - - - Effective Shermann function, calibrated spin selectivity factor - - - - - Energy of the spin-selective scattering - - - - - Angle of the spin-selective scattering - - - - - Name of the target - - - - - Preparation procedure of the spin target - - - - - Date of last preparation of the spin target - - - - - Deflectors in the spin dispersive section - - - - - Individual lenses in the spin dispersive section - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXstage_lab.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXstage_lab.nxdl.xml deleted file mode 100644 index dca422c..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXstage_lab.nxdl.xml +++ /dev/null @@ -1,154 +0,0 @@ - - - - - - A stage lab can be used to hold, align, orient, and prepare a specimen. - - Modern stages are multi-functional devices. Many of which offer a controlled - environment around (a part) of the specimen. Stages enable experimentalists - to apply stimuli. A stage_lab is a multi-purpose/-functional tools which - can have multiple actuators, sensors, and other components. - - With such stages comes the need for storing various (meta)data - that are generated while manipulating the sample. - - Modern stages realize a hierarchy of components: For example the specimen - might be mounted on a multi-axial tilt rotation holder. This holder is - fixed in the support unit which connects the holder to the rest of the - microscope. - - In other examples, taken from atom probe microscopy, researchers may work - with wire samples which are clipped into a larger fixing unit for - convenience and enable for a more careful specimen handling. - This fixture unit is known in atom probe jargon as a stub. - Stubs in turn are positioned onto pucks. - Pucks are then loaded onto carousels. - A carousel is a carrier unit with which eventually entire sets of specimens - can be moved in between parts of the microscope. - - An NXstage_lab instance reflects this hierarchical design. The stage is the - root of the hierarchy. A stage carries the holder. - In the case that it is not practical to distinguish these two layers, - the holder should be given preference. - - Some examples for stage_labs in applications: - - * A nanoparticle on a copper grid. The copper grid is the holder. - The grid itself is fixed to the stage. - * An atom probe specimen fixed in a stub. In this case the stub can be - considered the holder, while the cryostat temperature control unit is - a component of the stage. - * Samples with arrays of specimens, like a microtip on a microtip array - is an example of a three-layer hierarchy commonly employed for - efficient sequential processing of atom probe experiments. - * With one entry of an application definition only one microtip should be - described. Therefore, the microtip is the specimen, - the array is the holder and the remaining mounting unit - that is attached to the cryo-controller is the stage. - * For in-situ experiments with e.g. chips with read-out electronics - as actuators, the chips are again placed in a larger unit. - * Other examples are (quasi) in-situ experiments where experimentalists - anneal or deform the specimen via e.g. in-situ tensile testing machines - which are mounted on the specimen holder. - - To cover for an as flexible design of complex stages, users should nest - multiple instances of NXstage_lab objects according to their needs to reflect - the differences between what they consider as the holder and what - they consider is the stage. - - Instances should be named with integers starting from 1 as the top level unit. - In the microtip example stage_lab_1 for the stage, stage_lab_2 for the holder - (microtip array), stage_lab_3 for the microtip specimen, respectively. - The depends_on keyword should be used with relative or absolute naming inside - the file to specify how different stage_lab instances build a hierarchy - if this is not obvious from numbered identifiers like the stage_lab_1 to - stage_lab 3 example. The lower it is the number the higher it is the - rank in the hierarchy. - - For specific details and inspiration about stages in electron microscopes: - - * `Holders with multiple axes <https://www.nanotechnik.com/e5as.html>`_ - * `Chip-based designs <https://www.protochips.com/products/fusion/fusion-select-components/>`_ - * `Further chip-based designs <https://www.nanoprobetech.com/about>`_ - * `Stages in transmission electron microscopy <https://doi.org/10.1007/978-3-662-14824-2>`_ (page 103, table 4.2) - * `Further stages in transmission electron microscopy <https://doi.org/10.1007/978-1-4757-2519-3>`_ (page 124ff) - * `Specimens in atom probe <https://doi.org/10.1007/978-1-4614-8721-0>`_ (page 47ff) - * `Exemplar micro-manipulators <https://nano.oxinst.com/products/omniprobe/omniprobe-200>`_ - - - - Principal design of the stage. - - Exemplar terms could be side_entry, top_entry, - single_tilt, quick_change, multiple_specimen, - bulk_specimen, double_tilt, tilt_rotate, - heating_chip, atmosphere_chip, - electrical_biasing_chip, liquid_cell_chip - - - - - Should be defined by the application definition. - - - - - Should be defined by the application definition. - - - - - Should be defined by the application definition. - - - - - Should be defined by the application definition. - - - - - - - - Voltage applied to the stage to decelerate electrons. - - - - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXsubsampling_filter.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXsubsampling_filter.nxdl.xml index ea378ea..29d2399 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXsubsampling_filter.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXsubsampling_filter.nxdl.xml @@ -2,9 +2,9 @@ - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - + - Settings of a filter to sample entries based on their value. + Base class of a filter to sample members in a set based on their indices. + + The filter defines three parameters: The minimum, the increment, and the maximum + index of values to include of a sequence :math:`[i_0, i_0 + 1, i_0 + 2, \ldots, i_0 + \mathcal{N}] with i_0 \in \mathcal{Z}` + of indices. The increment controls which n-th index (value) to take. + + Take as an example a dataset with 100 indices (aka entries). Assume that the indices start at zero, + i.e., index_offset is 0. Assume further that min, increment, max are set to 0, 1, and 99, respectively. + In this case the filter will yield all indices. Setting min, increment, max to 0, 2, and 99, respectively + will yield each second index value. Setting min, increment, max to 90, 3, and 99 respectively will yield + each third index value beginning from index values 90 up to 99. - + + + Minimum index. + + + + + Increment. + + + - Triplet of the minimum, increment, and maximum value which will - be included in the analysis. The increment controls which n-th entry to take. - - Take as an example a dataset with 100 entries (their indices start at zero) - and the filter set to 0, 1, 99. This will process each entry. - 0, 2, 99 will take each second entry. 90, 3, 99 will take only each third - entry beginning from entry 90 up to 99. + Maximum index. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXsubstance.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXsubstance.nxdl.xml index 8ac1084..7e4b19f 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXsubstance.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXsubstance.nxdl.xml @@ -1,9 +1,9 @@ - + - - + - Variables used throughout the experiment + Variables used throughout the experiment - Number of wavelength points + Number of wavelength points - Number of scans + Number of scans - Application definition for transmission experiments + Application definition for transmission experiments - - This application definition - - - An application definition for transmission. - - Version number to identify which definition of this application definition was - used for this entry/data. + Version number to identify which definition of this application definition was + used for this entry/data. - + - URL where to find further material (documentation, examples) relevant to the - application definition. + URL where to find further material (documentation, examples) relevant to the + application definition. @@ -68,170 +63,148 @@ Draft NeXus application definition for transmission experiments--> - Start time of the experiment. + Start time of the experiment. - + - Unique identifier of the experiment, such as a (globally persistent) - unique identifier. - - * The identifier is usually defined by the facility or principle - investigator. - * The identifier enables to link experiments to e.g. proposals. + Unique identifier of the experiment, such as a (globally persistent) + unique identifier. + + * The identifier is usually defined by the facility or principle + investigator. + * The identifier enables to link experiments to e.g. proposals. - An optional free-text description of the experiment. However, details of the - experiment should be defined in the specific fields of this application - definition rather than in this experiment description. + An optional free-text description of the experiment. However, details of the + experiment should be defined in the specific fields of this application + definition rather than in this experiment description. - - Commercial or otherwise defined given name to the program that was - used to generate the result file(s) with measured data and metadata. + Commercial or otherwise defined given name to the program that was + used to generate the result file(s) with measured data and metadata. - + - Version number of the program that was used to generate the result - file(s) with measured data and metadata. + Version number of the program that was used to generate the result + file(s) with measured data and metadata. - Website of the software + Website of the software - + - Contact information of at least the user of the instrument or the investigator - who performed this experiment. Adding multiple users if relevant is recommended. + Contact information of at least the user of the instrument or the investigator + who performed this experiment. Adding multiple users if relevant is recommended. - Name of the user. - - - - - Name of the affiliation of the user at the point in time when the experiment was - performed. + Name of the user. - + - Street address of the user's affiliation. - - - - - Email address of the user. - - - - - Author ID defined by reasearch id services, e.g. orcid (https://orcid.org/). - - - - - Telephone number of the user. + Name of the affiliation of the user at the point in time when the experiment was + performed. - Manufacturer of the instrument. + Manufacturer of the instrument. - Common beam mask to shape the incident beam + Common beam mask to shape the incident beam - The height of the common beam in percentage of the beam + The height of the common beam in percentage of the beam - If true, the incident beam is depolarized. + If true, the incident beam is depolarized. - Polarizer value inside the beam path + Polarizer value inside the beam path - Attenuator in the reference beam + Attenuator in the reference beam - Attenuator in the sample beam + Attenuator in the sample beam - Wavelength value(s) used for the measurement. - An array of 1 or more elements. Length defines N_wavelenghts + Wavelength value(s) used for the measurement. + An array of 1 or more elements. Length defines N_wavelenghts - + - Overall spectral resolution of this spectrometer. - If several gratings are employed the spectral resoultion - should rather be specified for each grating inside the - NXgrating group of this spectrometer. + Overall spectral resolution of this spectrometer. + If several gratings are employed the spectral resolution + should rather be specified for each grating inside the + NXgrating group of this spectrometer. - + + - Diffraction grating, as could be used in a monochromator. - If two or more gratings were used, define the angular - dispersion and the wavelength range (min/max wavelength) - for each grating and make sure that the wavelength ranges - do not overlap. The dispersion should be defined for the - entire wavelength range of the experiment. + Diffraction grating, as could be used in a monochromator. + If two or more gratings were used, define the angular + dispersion and the wavelength range (min/max wavelength) + for each grating and make sure that the wavelength ranges + do not overlap. The dispersion should be defined for the + entire wavelength range of the experiment. - + - Dispersion of the grating in nm/mm used. + Dispersion of the grating in nm/mm used. - The blaze wavelength of the grating used. + The blaze wavelength of the grating used. - + - Overall spectral resolution of the instrument - when this grating is used. + Overall spectral resolution of the instrument + when this grating is used. - + + - Wavelength range in which this grating was used + Wavelength range in which this grating was used @@ -242,7 +215,7 @@ of instrument.--> - Wavelength range in which this detector was used + Wavelength range in which this detector was used @@ -250,7 +223,7 @@ of instrument.--> - Detector type + Detector type @@ -260,17 +233,17 @@ of instrument.--> - Response time of the detector + Response time of the detector - Detector gain + Detector gain - Slit setting used for measurement with this detector + Slit setting used for measurement with this detector @@ -282,7 +255,7 @@ of instrument.--> - An array of relative scan start time points. + An array of relative scan start time points. @@ -290,11 +263,11 @@ of instrument.--> - Resulting data from the measurement. - The length of the 2nd dimension is - the number of time points. - If it has length one the time_points - may be empty. + Resulting data from the measurement. + The length of the 2nd dimension is + the number of time points. + If it has length one the time_points + may be empty. @@ -303,20 +276,20 @@ of instrument.--> - The lamp used for illumination + The lamp used for illumination - The type of lamp, e.g. halogen, D2 etc. + The type of lamp, e.g. halogen, D2 etc. - + - The spectrum of the lamp used + The spectrum of the lamp used @@ -324,7 +297,7 @@ of instrument.--> - Wavelength range in which the lamp was used + Wavelength range in which the lamp was used @@ -333,22 +306,20 @@ of instrument.--> - - Properties of the sample measured + Properties of the sample measured - A default view of the data emitted intensity vs. wavelength. - From measured_data plot intensity and wavelength. + A default view of the data emitted intensity vs. wavelength. + From measured_data plot intensity and wavelength. - We recommend to use wavelength as a default attribute, but it can be - replaced by any suitable parameter along the X-axis. + We recommend to use wavelength as a default attribute, but it can be + replaced by any suitable parameter along the X-axis. diff --git a/src/nexusformat/definitions/contributed_definitions/NXwaveplate.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXwaveplate.nxdl.xml deleted file mode 100644 index b4fd298..0000000 --- a/src/nexusformat/definitions/contributed_definitions/NXwaveplate.nxdl.xml +++ /dev/null @@ -1,173 +0,0 @@ - - - - - - - - - Size of the wavelength array for which the refractive index of the material - and/or coating is given. - - - - - Number of discrete wavelengths for which the waveplate is designed. If it - operates for a range of wavelengths then N_wavelengths = 2 and the minimum - and maximum values of the range should be provided. - - - - - A waveplate or retarder. - - - - Type of waveplate (e.g. achromatic waveplate or zero-order waveplate). - - - - - - - - - - - - - - If you selected 'other' in type describe what it is. - - - - - Specify the retardance of the waveplate (e.g. full-wave, half-wave - (lambda/2), quarter-wave (lambda/4) plate). - - - - - - - - - - Discrete wavelengths for which the waveplate is designed. If the - waveplate operates over an entire range of wavelengths, enter the minimum - and maximum values of the wavelength range (in this case - N_wavelengths = 2). - - - - - - - - Diameter of the waveplate. - - - - - Clear aperture of the device (e.g. 90% of diameter for a disc or 90% of - length/height for square geometry). - - - - - - Describe the material of the substrate of the wave plate in - substrate/substrate_material and provide its index of refraction in - substrate/index_of_refraction_substrate, if known. - - - - Specify the material of the wave plate. If the device has a - coating it should be described in coating/coating_material. - - - - - Thickness of the wave plate substrate. - - - - - Complex index of refraction of the wave plate substrate. Specify at - given wavelength (or energy, wavenumber etc.) values. - - - - - - - - - - Is the wave plate coated? If yes, specify the type and material of the - coating and the wavelength range for which it is designed. If known, you - may also provide its index of refraction. - - - - Specify the coating type (e.g. dielectric, anti-reflection (AR), - multilayer coating etc.). - - - - - Specify the coating material. - - - - - Thickness of the coating. - - - - - Wavelength range for which the coating is designed. Enter the minimum - and maximum values of the wavelength range. - - - - - - - - Complex index of refraction of the coating. Specify at given spectral - values (wavelength, energy, wavenumber etc.). - - - - - - - - - - Average reflectance of the waveplate in percentage. - - - diff --git a/src/nexusformat/definitions/contributed_definitions/NXxpcs.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXxpcs.nxdl.xml index 6d3c14d..f7e112b 100644 --- a/src/nexusformat/definitions/contributed_definitions/NXxpcs.nxdl.xml +++ b/src/nexusformat/definitions/contributed_definitions/NXxpcs.nxdl.xml @@ -253,7 +253,7 @@ storage_mode describes the format of the data to be loaded - We encourage the documention of other formats represented here. + We encourage the documentation of other formats represented here. @@ -419,7 +419,7 @@ Size (2-D) of the beam at this position. - @@ -523,7 +523,7 @@ The only requirement for the list is that it may be iterable. Some expected formats are: * iterable list of floats (i.e., :math:`Q(r)`) - * iterable list of tuples (i.e., :math:`Q(r)`, :math:`\varphi`), but preferable use the seperate :math:`\varphi` field below + * iterable list of tuples (i.e., :math:`Q(r)`, :math:`\varphi`), but preferable use the separate :math:`\varphi` field below * iterable list of tuples (e.g., (H, K, L); (qx, qy, qz); (horizontal_pixel, vertical_pixel)) * iterable list of integers (for Nth roi_map value) or strings @@ -565,7 +565,7 @@ dynamics from XPCS analysis). For non-equilibrium sample conditions (i.e., changing sample or process conditions - during the XPCS measurement) will require either a new entry or an additional atttribute. + during the XPCS measurement) will require either a new entry or an additional attribute. --> diff --git a/src/nexusformat/definitions/contributed_definitions/NXxrd.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXxrd.nxdl.xml new file mode 100644 index 0000000..626a138 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXxrd.nxdl.xml @@ -0,0 +1,99 @@ + + + + + + + NXxrd on top of NXmonopd + + + + + Official NeXus NXDL schema to which this file conforms + + + + + + + + + + + + + raw detector signal (usually counts) as collected + it can be a multi-dimensional dataset depending on + the detector type (faster axes) and + the scanning method (slower axes) + + + + + The 2-theta range of the diffractogram + + + + + + + + + + + + + + + + link (suggested target:/NXentry/NXinstrument/NXdetector/polar_angle) + Link to polar ale in /NXentry/NXinstrument/NXdetector + + + + + + + + link (suggested target:/NXentry/NXinstrument/NXdetector/data) + Link to data in /Nxentry/Nxinstrument/Nxdetector + + + + + + + + + Description of a processing or analysis step, such as the + baseline extraction or azimuth integration. + Add additional fields as needed to describe value(s) of + any variable, parameter, or term related to + the NXprocess step. Be sure to include units attributes + for all numerical fields. + + + + diff --git a/src/nexusformat/definitions/contributed_definitions/NXxrd_pan.nxdl.xml b/src/nexusformat/definitions/contributed_definitions/NXxrd_pan.nxdl.xml new file mode 100644 index 0000000..a406ba6 --- /dev/null +++ b/src/nexusformat/definitions/contributed_definitions/NXxrd_pan.nxdl.xml @@ -0,0 +1,335 @@ + + + + + + NXxrd_pan is a specialization of NXxrd with extra properties + for the PANalytical XRD data format. + + + + + Name of the data file. + + + + + Type of measurement. + + + + + Official NeXus NXDL schema to which this file conforms. + + + + + + + + Method used to collect the data + default='X-Ray Diffraction (XRD)' + + + + + + + + + + + Type of the X-ray tube. + + + + + + + + + + + + + + Current of the X-ray tube. + + + + + Voltage of the X-ray tube. + + + + + + Wavelength of the K\u03b1 1 line. + + + + + + + + + + Wavelength of the K\u03b1 2 line. + + + + + + + + + + K\u03b1 2/K\u03b1 1 intensity ratio. + + + + + Wavelength of the K\u00df line. + + + + + + + + + + Wavelength of the X-ray source. Used to convert from 2-theta to Q. + + + + + + + Axis scanned. + + + + + Mode of scan. + + + + + Integration time per channel. + + + + + + + + Collect user inputs e.g. name or path of the input file. + + + + + Starting value of the diffraction angle. + + + + + Ending value of the diffraction angle. + + + + + Minimum step size in-between two diffraction angles. + + + + + + + Starting value of the incident angle. + + + + + Ending value of the incident angle. + + + + + Minimum step size in the between two incident angles. + + + + + + Beam attenuation factors over the path. + + + + + Goniometer position X. + + + + + Goniometer position Y. + + + + + Goniometer position Z + + + + + Total time of count. + + + + + + All experiment results data such as scattering angle (2theta), + intensity, incident angle, scattering vector, etc will be stored here. + + + + Number of scattered electrons per unit time. + + + + + + + + Two-theta (scattering angle) of the diffractogram. + + + + + + + + Incident angle of the diffractogram. + + + + + + + + The phi range of the diffractogram. + + + + + + + + The chi range of the diffractogram + + + + + + + + The scattering vector component, which is parallel to the sample surface. + + + + + The scattering vector component, which is perpendicular to the sample surface. + + + + + The norm value of the scattering vector, q. The scattering vector is defined as a + difference between the incident and scattered wave vectors. + For details: https://en.wikipedia.org/wiki/Powder_diffraction + and https://theory.labster.com/scattering-vector/ + + + + + + The desired view for scattering vectors. + + + + This concept corresponds to the norm value of the scattering vector(q). + The concept is the same as 'q_norm' of 'experiment_result' + and should be linked to /entry[ENTRY]/experiment_result/q_norm. + + + + + Number of scattered electrons per unit time at each scattering vector (q) value. + The concept is the same as the 'intensity' of experiment_result + and should be linked to /entry[ENTRY]/experiment_result/intensity. + + + + + The scattering vector (q) component, which is parallel to the sample surface. + This component is used in the Reciprocal Space Mapping (RSM) technique of + X-ray diffraction method. + + The concept is the same as 'q_parallel' of experiment_result, + and should be linked to /entry[ENTRY]/experiment_result/q_parallel. + + + + + The scattering vector component, which is perpendicular to the sample surface. + + The concept is the same as 'q_perpendicular' of experiment_result, + and should be linked to /entry[ENTRY]/experiment_result/q_perpendicular. + + + + + + Description on sample. + + + + Mode of sample. + + + + + Id of sample. + + + + + Usually in xrd sample are being analyzed, but sample might be identified by + assumed name or given name. + + + + + diff --git a/src/nexusformat/definitions/nxdl.xsd b/src/nexusformat/definitions/nxdl.xsd old mode 100644 new mode 100755 index ac0a411..0a9a27b --- a/src/nexusformat/definitions/nxdl.xsd +++ b/src/nexusformat/definitions/nxdl.xsd @@ -1120,7 +1120,7 @@ https://stackoverflow.com/a/48980995/1046449 --> Group attribute that provides a URL to a group in another file. More information is described in the *NeXus Programmers Reference*. - http://manual.nexusformat.org/_static/NeXusIntern.pdf + https://github.com/nexusformat/code/blob/master/doc/api/NeXusIntern.pdf From b6166196973c90d43ac3bd1717be231bf9868d42 Mon Sep 17 00:00:00 2001 From: Ray Osborn Date: Thu, 5 Feb 2026 11:53:42 -0600 Subject: [PATCH 2/2] Include updates to the NXparameter base class --- .../base_classes/NXparameters.nxdl.xml | 80 +++++++++++++++++-- 1 file changed, 72 insertions(+), 8 deletions(-) diff --git a/src/nexusformat/definitions/base_classes/NXparameters.nxdl.xml b/src/nexusformat/definitions/base_classes/NXparameters.nxdl.xml index 43445c1..6550ff4 100644 --- a/src/nexusformat/definitions/base_classes/NXparameters.nxdl.xml +++ b/src/nexusformat/definitions/base_classes/NXparameters.nxdl.xml @@ -24,13 +24,77 @@ - Container for parameters, usually used in processing or analysis. - - - A parameter (also known as a term) that is used in or results from processing. - + name="NXparameters" type="group" extends="NXobject"> + + + Container for parameters used in processing or analysing data. + + Typically, this group is stored in a :ref:`NXprocess` group in + order to contain parameters that are either inputs to or + resulting from the process defined by the parent group. However, + this base class can also be added to other groups for use in + other contexts. + + Although this base class can be used to store any kind of + parameter, one possible use case is to store parameters that are + refined by a fitting function or model. A number of attributes + have been defined to store metadata associated with such a + refinement. + + + + The name of the model used in optimizing the parameter + values. Fitting packages such as LMFIT + (https://lmfit.github.io/lmfit-py/) provide models, which + instantiate functions to be fitted to the data. If this + attribute is provided, it is assumed that all the parameters + in this group are associated with this model. + + + + + A parameter that is used in or results from processing. + + + + + The standard deviation of the parameter after optimizing + its value. + + + + + A description of what this parameter represents. + + + + + A string representing an expression that can be used to + relate the parameter to another parameter's value. The + format of this string is dependent on the program used + to optimize the parameters and is not specified by + NeXus. + + + + + The initial value of the parameter used in optimization. + + + + + The upper bound of the parameter used in optimization. + + + + + The lower bound of the parameter used in optimization. + + + + + True if the parameter was varied during optimization. + + -