Default Unit Values

virtualcell · Aug 23, 2024 · 8c33b44 · 8c33b44
1 parent 2faada1
commit 8c33b44
Show file tree

Hide file tree

Showing 2 changed files with 20 additions and 6 deletions.
diff --git a/vcell-core/src/main/java/cbit/vcell/export/server/N5Exporter.java b/vcell-core/src/main/java/cbit/vcell/export/server/N5Exporter.java
@@ -69,7 +69,6 @@ public N5Exporter(ExportServiceImpl exportServiceImpl) {
 }
 
 	private ExportOutput exportToN5(OutputContext outputContext, long jobID, N5Specs n5Specs, ExportSpecs exportSpecs, FileDataContainerManager fileDataContainerManager) throws Exception {
-		VCUnitDefinition lengthUnit = ModelUnitSystem.createDefaultVCModelUnitSystem().getLengthUnit();
 		double[] allTimes = dataServer.getDataSetTimes(user, vcDataID);
 		TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
 		String[] variableNames = exportSpecs.getVariableSpecs().getVariableNames();
@@ -135,7 +134,7 @@ private ExportOutput exportToN5(OutputContext outputContext, long jobID, N5Specs
 		N5Specs.writeImageJMetaData(jobID, dimensions, blockSize, n5Specs.getCompression(), n5FSWriter,
 				n5Specs.dataSetName, numVariables, sizeZ, allTimes.length,
 				exportSpecs.getHumanReadableExportData().subVolume,
-				lengthPerPixelY, lengthPerPixelX, lengthPerPixelZ, lengthUnit.getSymbol(), channelInfo);
+				lengthPerPixelY, lengthPerPixelX, lengthPerPixelZ, getLengthUnit(), getTimeUnit(),channelInfo);
 
 		int timeLoops = 1;
 		double progress = 0;
@@ -192,6 +191,21 @@ private boolean containsPostProcessedVariable(String[] variableNames, OutputCont
 		return false;
 	}
 
+	private String getTimeUnit(){
+		VCUnitDefinition timeUnit = ModelUnitSystem.createDefaultVCModelUnitSystem().getTimeUnit();
+		return timeUnit.getSymbol();
+	}
+
+	private String getSpeciesUnit(){
+		VCUnitDefinition speciesUnit = ModelUnitSystem.createDefaultVCModelUnitSystem().getVolumeConcentrationUnit();
+		return speciesUnit.getSymbol();
+	}
+
+	private String getLengthUnit(){
+		VCUnitDefinition lengthUnit = ModelUnitSystem.createDefaultVCModelUnitSystem().getLengthUnit();
+		return lengthUnit.getSymbol();
+	}
+
 	public void initalizeDataControllers(User user, DataServerImpl dataServer, VCSimulationDataIdentifier vcSimulationDataIdentifier) throws IOException, DataAccessException {
 		this.user = user;
 		this.vcDataID = vcSimulationDataIdentifier;

diff --git a/vcell-core/src/main/java/cbit/vcell/export/server/N5Specs.java b/vcell-core/src/main/java/cbit/vcell/export/server/N5Specs.java
@@ -95,11 +95,11 @@ public String toString() {
 
 	public static void writeImageJMetaData(long jobID,long[] dimensions, int[] blockSize, Compression compression, N5FSWriter n5FSWriter, String datasetName, int numChannels, int zSlices,
 										   int timeLength, HashMap<Integer, String> maskMapping, double pixelHeight,
-										   double pixelWidth, double pixelDepth, String unit, HashMap<Integer, Object> channelInfo) throws MathException, DataAccessException {
+										   double pixelWidth, double pixelDepth, String unit, String timeUnit, HashMap<Integer, Object> channelInfo) throws MathException, DataAccessException {
 		try {
 			HashMap<String, String> compresssionMap = new HashMap<>(){{put("type", compression.getType().toLowerCase());}};
 			ImageJMetaData imageJMetaData = ImageJMetaData.generateDefaultRecord(dimensions, blockSize, compresssionMap, datasetName, numChannels, zSlices, timeLength,
-					maskMapping, pixelHeight, pixelWidth, pixelDepth, unit, channelInfo);
+					maskMapping, pixelHeight, pixelWidth, pixelDepth, unit, timeUnit , channelInfo);
 			Path path = Path.of(n5FSWriter.getURI().getPath(), String.valueOf(jobID), "attributes.json");
 			Gson gson = n5FSWriter.getGson();
 			String jsonRepresentation = gson.toJson(imageJMetaData, ImageJMetaData.class);
@@ -112,7 +112,7 @@ public static void writeImageJMetaData(long jobID,long[] dimensions, int[] block
 
     }
 
-	record ImageJMetaData(long[] dimensions ,int[] blockSize, HashMap<String, String> compression, String dataType, String name, double fps, double frameInterval, double pixelWidth,
+	private record ImageJMetaData(long[] dimensions ,int[] blockSize, HashMap<String, String> compression, String dataType, String name, double fps, double frameInterval, double pixelWidth,
 						  double pixelHeight, double pixelDepth, double xOrigin, double yOrigin, double zOrigin, int numChannels, int numSlices, int numFrames,
 						  int type, String unit, HashMap<Integer, String> maskMapping, HashMap<Integer, Object> channelInfo){
 
@@ -122,7 +122,7 @@ record ImageJMetaData(long[] dimensions ,int[] blockSize, HashMap<String, String
 
 		public static ImageJMetaData generateDefaultRecord(long[] dimensions ,int[] blockSize, HashMap<String, String> compression, String dataSetName, int numChannels,
 														   int numSlices, int numFrames, HashMap<Integer, String> maskMapping, double pixelHeight, double pixelWidth,
-														   double pixelDepth, String unit, HashMap<Integer, Object> channelInfo){
+														   double pixelDepth, String unit, String timeUnit , HashMap<Integer, Object> channelInfo){
 			return  new ImageJMetaData(dimensions, blockSize, compression, DataType.FLOAT64.name().toLowerCase() ,dataSetName, 0.0, 0.0,
 					pixelWidth, pixelHeight, pixelDepth, 0.0, 0.0, 0.0, numChannels, numSlices, numFrames, 2, unit, maskMapping, channelInfo);
 		}