New tables and columns for Cryo-ET

schema/updates/2022_06_22_cryo-ET_tables.sql

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+INSERT INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2022_06_22_cryo-ET_tables.sql', 'ONGOING');
+
+ALTER TABLE Movie
+  ADD COLUMN IF NOT EXISTS angle float COMMENT 'unit: degrees relative to perpendicular to beam',
+  ADD COLUMN IF NOT EXISTS fluence float COMMENT 'accumulated electron fluence from start to end of acquisition of this movie (commonly, but incorrectly, referred to as ‘dose’)',
+  ADD COLUMN IF NOT EXISTS numberOfFrames int(11) unsigned 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.';
+
+CREATE TABLE Tomogram (
+  tomogramId int(11) unsigned NOT NULL AUTO_INCREMENT PRIMARY KEY,
+  dataCollectionId int(10) unsigned COMMENT 'FK to DataCollection table',
+  autoProcProgramId int(10) unsigned COMMENT 'FK, gives processing times/status and software information',
+  volumeFile varchar(255) COMMENT '.mrc file representing the reconstructed tomogram volume',
+  stackFile varchar(255) NULL DEFAULT NULL COMMENT '.mrc file containing the motion corrected images ordered by angle used as input for the reconstruction',
+  sizeX int(11) unsigned COMMENT 'unit: pixels',
+  sizeY int(11) unsigned COMMENT 'unit: pixels',
+  sizeZ int(11) unsigned COMMENT 'unit: pixels',
+  pixelSpacing float COMMENT 'Angstrom/pixel conversion factor',
+  residualErrorMean float COMMENT 'Alignment error, unit: nm',
+  residualErrorSD float COMMENT 'Standard deviation of the alignment error, unit: nm',
+  xAxisCorrection float COMMENT 'X axis angle (etomo), unit: degrees',
+  tiltAngleOffset float COMMENT 'tilt Axis offset (etomo), unit: degrees',
+  zShift float COMMENT 'shift to center volumen in Z (etomo)',
+  CONSTRAINT FOREIGN KEY Tomogram_fk_dataCollectionId (dataCollectionId) REFERENCES DataCollection (dataCollectionId) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT FOREIGN KEY Tomogram_fk_autoProcProgramId (autoProcProgramId) REFERENCES AutoProcProgram (autoProcProgramId) ON DELETE SET NULL ON UPDATE CASCADE
+)
+COMMENT 'For storing per-sample, per-position data analysis results (reconstruction)';
+
+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 COMMENT 'unit: Angstroms',
+  defocusV float COMMENT 'unit: Angstroms',
+  psdFile varchar(255),
+  resolution float COMMENT 'unit: Angstroms',
+  fitQuality float,
+  refinedMagnification float NULL DEFAULT NULL COMMENT 'unitless',
+  refinedTiltAngle float COMMENT 'units: degrees',
+  refinedTiltAxis float COMMENT 'units: degrees',
+  residualError float COMMENT 'Residual error, unit: nm',
+  PRIMARY KEY (movieId, tomogramId),
+  CONSTRAINT FOREIGN KEY TiltImageAlignment_fk_movieId (movieId) REFERENCES Movie (movieId) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT FOREIGN KEY TiltImageAlignment_fk_tomogramId (tomogramId) REFERENCES Tomogram (tomogramId) ON DELETE CASCADE ON UPDATE CASCADE
+)
+COMMENT 'For storing per-movie analysis results (reconstruction)';
+
+ALTER TABLE BeamLineSetup
+  ADD amplitudeContrast float COMMENT 'Needed for cryo-ET';
+
+UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2022_06_22_cryo-ET_tables.sql';

schema/updates/2023_01_16_Tomogram_new_cols.sql

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+INSERT INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2023_01_16_Tomogram_new_cols.sql', 'ONGOING');
+
+ALTER TABLE Tomogram
+  ADD fileDirectory varchar(255) DEFAULT NULL COMMENT 'Directory path for files referenced by this table',
+  ADD centralSliceImage varchar(255) DEFAULT NULL COMMENT 'Tomogram central slice file',
+  ADD tomogramMovie varchar(255) DEFAULT NULL COMMENT 'Movie traversing the tomogram across an axis',
+  ADD xyShiftPlot varchar(255) DEFAULT NULL COMMENT 'XY shift plot file',
+  ADD projXY varchar(255) DEFAULT NULL COMMENT 'XY projection file',
+  ADD projXZ varchar(255) DEFAULT NULL COMMENT 'XZ projection file',
+  ADD recordTimeStamp datetime DEFAULT current_timestamp() COMMENT 'Creation or last update date/time';
+
+/*
+-- Undo changes
+ALTER TABLE Tomogram
+  DROP IF EXISTS fileDirectory,
+  DROP IF EXISTS centralSliceImage,
+  DROP IF EXISTS tomogramMovie,
+  DROP IF EXISTS xyShiftPlot,
+  DROP IF EXISTS projXY,
+  DROP IF EXISTS projXZ,
+  DROP IF EXISTS recordTimeStamp;
+*/
+
+UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2023_01_16_Tomogram_new_cols.sql';