diff --git a/schema/1_tables.sql b/schema/1_tables.sql index 1c388a2..e7e27cc 100644 --- a/schema/1_tables.sql +++ b/schema/1_tables.sql @@ -936,6 +936,7 @@ CREATE TABLE `BeamLineSetup` ( `minTransmission` double DEFAULT NULL, `CS` float DEFAULT NULL, `recordTimeStamp` timestamp NOT NULL DEFAULT current_timestamp() COMMENT 'Creation or last update date/time', + `amplitudeContrast` float DEFAULT NULL COMMENT 'Needed for cryo-ET', PRIMARY KEY (`beamLineSetupId`) ) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; @@ -2889,6 +2890,9 @@ CREATE TABLE `Movie` ( `xmlMetaDataFullPath` varchar(255) DEFAULT NULL, `dosePerImage` varchar(45) DEFAULT NULL, `createdTimeStamp` timestamp NOT NULL DEFAULT current_timestamp(), + `angle` float DEFAULT NULL COMMENT 'unit: degrees relative to perpendicular to beam', + `fluence` float DEFAULT NULL COMMENT 'accumulated electron fluence from start to end of acquisition of this movie (commonly, but incorrectly, referred to as ‘dose’)', + `numberOfFrames` int(11) unsigned DEFAULT NULL COMMENT 'number of frames per movie. This should be equivalent to the number of MotionCorrectionDrift entries, but the latter is a property of data analysis, whereas the number of frames is an intrinsic property of acquisition.', PRIMARY KEY (`movieId`), KEY `dataCollectionToMovie_idx` (`dataCollectionId`), KEY `movieFullPath_idx` (`movieFullPath`(191)), @@ -4652,6 +4656,69 @@ CREATE TABLE `Superposition` ( ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; +-- +-- Table structure for table `TiltImageAlignment` +-- + +DROP TABLE IF EXISTS `TiltImageAlignment`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `TiltImageAlignment` ( + `movieId` int(11) NOT NULL COMMENT 'FK to Movie table', + `tomogramId` int(11) unsigned NOT NULL COMMENT 'FK to Tomogram table; tuple (movieID, tomogramID) is unique', + `defocusU` float DEFAULT NULL COMMENT 'unit: Angstroms', + `defocusV` float DEFAULT NULL COMMENT 'unit: Angstroms', + `psdFile` varchar(255) DEFAULT NULL, + `resolution` float DEFAULT NULL COMMENT 'unit: Angstroms', + `fitQuality` float DEFAULT NULL, + `refinedMagnification` float DEFAULT NULL COMMENT 'unitless', + `refinedTiltAngle` float DEFAULT NULL COMMENT 'units: degrees', + `refinedTiltAxis` float DEFAULT NULL COMMENT 'units: degrees', + `residualError` float DEFAULT NULL COMMENT 'Residual error, unit: nm', + PRIMARY KEY (`movieId`,`tomogramId`), + KEY `TiltImageAlignment_fk_tomogramId` (`tomogramId`), + CONSTRAINT `TiltImageAlignment_fk_movieId` FOREIGN KEY (`movieId`) REFERENCES `Movie` (`movieId`) ON DELETE CASCADE ON UPDATE CASCADE, + CONSTRAINT `TiltImageAlignment_fk_tomogramId` FOREIGN KEY (`tomogramId`) REFERENCES `Tomogram` (`tomogramId`) ON DELETE CASCADE ON UPDATE CASCADE +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='For storing per-movie analysis results (reconstruction)'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Tomogram` +-- + +DROP TABLE IF EXISTS `Tomogram`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `Tomogram` ( + `tomogramId` int(11) unsigned NOT NULL AUTO_INCREMENT, + `dataCollectionId` int(10) unsigned DEFAULT NULL COMMENT 'FK to DataCollection table', + `autoProcProgramId` int(10) unsigned DEFAULT NULL COMMENT 'FK, gives processing times/status and software information', + `volumeFile` varchar(255) DEFAULT NULL COMMENT '.mrc file representing the reconstructed tomogram volume', + `stackFile` varchar(255) DEFAULT NULL COMMENT '.mrc file containing the motion corrected images ordered by angle used as input for the reconstruction', + `sizeX` int(11) unsigned DEFAULT NULL COMMENT 'unit: pixels', + `sizeY` int(11) unsigned DEFAULT NULL COMMENT 'unit: pixels', + `sizeZ` int(11) unsigned DEFAULT NULL COMMENT 'unit: pixels', + `pixelSpacing` float DEFAULT NULL COMMENT 'Angstrom/pixel conversion factor', + `residualErrorMean` float DEFAULT NULL COMMENT 'Alignment error, unit: nm', + `residualErrorSD` float DEFAULT NULL COMMENT 'Standard deviation of the alignment error, unit: nm', + `xAxisCorrection` float DEFAULT NULL COMMENT 'X axis angle (etomo), unit: degrees', + `tiltAngleOffset` float DEFAULT NULL COMMENT 'tilt Axis offset (etomo), unit: degrees', + `zShift` float DEFAULT NULL COMMENT 'shift to center volumen in Z (etomo)', + `fileDirectory` varchar(255) DEFAULT NULL COMMENT 'Directory path for files referenced by this table', + `centralSliceImage` varchar(255) DEFAULT NULL COMMENT 'Tomogram central slice file', + `tomogramMovie` varchar(255) DEFAULT NULL COMMENT 'Movie traversing the tomogram across an axis', + `xyShiftPlot` varchar(255) DEFAULT NULL COMMENT 'XY shift plot file', + `projXY` varchar(255) DEFAULT NULL COMMENT 'XY projection file', + `projXZ` varchar(255) DEFAULT NULL COMMENT 'XZ projection file', + `recordTimeStamp` datetime DEFAULT current_timestamp() COMMENT 'Creation or last update date/time', + PRIMARY KEY (`tomogramId`), + KEY `Tomogram_fk_dataCollectionId` (`dataCollectionId`), + KEY `Tomogram_fk_autoProcProgramId` (`autoProcProgramId`), + CONSTRAINT `Tomogram_fk_autoProcProgramId` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE SET NULL ON UPDATE CASCADE, + CONSTRAINT `Tomogram_fk_dataCollectionId` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='For storing per-sample, per-position data analysis results (reconstruction)'; +/*!40101 SET character_set_client = @saved_cs_client */; + -- -- Table structure for table `UntrustedRegion` -- diff --git a/schema/2_lookups.sql b/schema/2_lookups.sql index a3a3fea..ce2ec34 100644 --- a/schema/2_lookups.sql +++ b/schema/2_lookups.sql @@ -114,7 +114,9 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (107,'2021_08_25_New_column_for_Structure.sql','DONE','2021-08-25 10:44:17'), (108,'2022_08_17_AdminVar_bump_version.sql','DONE','2022-08-17 08:47:30'), (109,'2022_08_17_User_Portal_Sync_permission.sql','DONE','2022-08-17 13:13:52'), -(110,'2022_11_21_SSX_experiment.sql','DONE','2023-01-04 12:40:19'); +(110,'2022_11_21_SSX_experiment.sql','DONE','2023-01-04 12:40:19'), +(111,'2022_06_22_cryo-ET_tables.sql','DONE','2023-02-01 12:29:40'), +(112,'2023_01_16_Tomogram_new_cols.sql','DONE','2023-02-01 12:29:40'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; -- diff --git a/schema/3_data.sql b/schema/3_data.sql index 44aa922..8fc7e98 100644 --- a/schema/3_data.sql +++ b/schema/3_data.sql @@ -1310,6 +1310,20 @@ INSERT INTO `Shipping` (`shippingId`, `proposalId`, `shippingName`, `deliveryAge /*!40000 ALTER TABLE `Superposition` DISABLE KEYS */; /*!40000 ALTER TABLE `Superposition` ENABLE KEYS */; +-- +-- Dumping data for table `TiltImageAlignment` +-- + +/*!40000 ALTER TABLE `TiltImageAlignment` DISABLE KEYS */; +/*!40000 ALTER TABLE `TiltImageAlignment` ENABLE KEYS */; + +-- +-- Dumping data for table `Tomogram` +-- + +/*!40000 ALTER TABLE `Tomogram` DISABLE KEYS */; +/*!40000 ALTER TABLE `Tomogram` ENABLE KEYS */; + -- -- Dumping data for table `UntrustedRegion` --