Implement reading pixel calibration from OME-XML

src/main/java/org/embl/mobie/MoBIE.java

@@ -36,6 +36,7 @@
 import loci.common.DebugTools;
 import mpicbg.spim.data.generic.AbstractSpimData;
 import mpicbg.spim.data.sequence.ImgLoader;
+import mpicbg.spim.data.sequence.VoxelDimensions;
 import net.imagej.ImageJ;
 import org.embl.mobie.io.ImageDataFormat;
 import org.embl.mobie.io.ome.zarr.loaders.N5OMEZarrImageLoader;
@@ -118,11 +119,6 @@ public class MoBIE
 	private HashMap< String, ImgLoader > sourceNameToImgLoader;
 	private final ArrayList< String > projectCommands = new ArrayList<>();
 
-	public MoBIE( String projectLocation ) throws IOException
-	{
-		this( projectLocation, new MoBIESettings() );
-	}
-
 	public MoBIE( String projectLocation, MoBIESettings settings ) throws IOException
 	{
 		this.settings = settings;
@@ -144,7 +140,7 @@ public static MoBIE getInstance()
 		return moBIE;
 	}
 
-	public MoBIE( String hcsDataLocation, MoBIESettings settings, double relativeWellMargin, double relativeSiteMargin ) throws IOException
+	public MoBIE( String hcsDataLocation, MoBIESettings settings, double relativeWellMargin, double relativeSiteMargin, @Nullable VoxelDimensions voxelDimensions ) throws IOException
 	{
 		this.settings = settings;
 		this.projectLocation = hcsDataLocation;
@@ -154,7 +150,7 @@ public MoBIE( String hcsDataLocation, MoBIESettings settings, double relativeWel
 		IJ.log("\n# MoBIE" );
 		IJ.log("Opening: " + hcsDataLocation );
 
-		openHCSDataset( relativeWellMargin, relativeSiteMargin );
+		openHCSDataset( relativeWellMargin, relativeSiteMargin, voxelDimensions );
 	}
 
 	public MoBIE( List< String > imagePaths, List< String > labelPaths, List< String > labelTablePaths, String root, GridType grid, MoBIESettings settings ) throws IOException
@@ -261,10 +257,10 @@ private void initImageJAndMoBIE()
 		moBIE = this;
 	}
 
-	private void openHCSDataset( double wellMargin, double siteMargin ) throws IOException
+	private void openHCSDataset( double wellMargin, double siteMargin, @Nullable VoxelDimensions voxelDimensions ) throws IOException
 	{
 		initProject( "HCS" );
-		final Plate plate = new Plate( projectLocation );
+		final Plate plate = new Plate( projectLocation, voxelDimensions );
 		new HCSDataAdder( plate, wellMargin, siteMargin ).addData( dataset );
 		initUIandShowView( dataset.views().keySet().iterator().next() );
 	}

src/main/java/org/embl/mobie/cmd/HCSCmd.java

@@ -60,7 +60,7 @@ public Void call() throws Exception {
 				.openedFromCLI( true )
 				.removeSpatialCalibration( removeSpatialCalibration );
 
-		new MoBIE( hcs, settings, wellMargin, siteMargin );
+		new MoBIE( hcs, settings, wellMargin, siteMargin, null );
 
 		return null;
 	}

src/main/java/org/embl/mobie/command/open/OpenHCSDatasetCommand.java

@@ -28,15 +28,18 @@
  */
 package org.embl.mobie.command.open;
 
+import mpicbg.spim.data.sequence.VoxelDimensions;
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.io.util.IOHelper;
+import org.embl.mobie.lib.hcs.OMEXMLParser;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.scijava.widget.Button;
 
+import java.io.File;
 import java.io.IOException;
 
 
@@ -57,16 +60,42 @@ public class OpenHCSDatasetCommand implements Command
 	@Parameter ( label = "Help", callback = "help")
 	public Button help;
 
+	public enum VoxelDimensionFetching
+	{
+		FromImageFiles,
+		FromOMEXML
+	}
+
+	@Parameter ( label = "Voxel Dimensions" )
+	public VoxelDimensionFetching voxelDimensionFetching = VoxelDimensionFetching.FromImageFiles;
+
+	@Parameter ( label = "OME-XML (optional)", required = false )
+	public File omeXML;
+
 	@Override
 	public void run()
 	{
+		VoxelDimensions voxelDimensions = initVoxelDimensions();
+
 		try
 		{
-			new MoBIE( hcsDirectory, new MoBIESettings(), wellMargin, siteMargin );
+			new MoBIE( hcsDirectory, new MoBIESettings(), wellMargin, siteMargin, voxelDimensions );
 		}
 		catch ( IOException e )
 		{
-			e.printStackTrace();
+			throw new RuntimeException( e );
+		}
+	}
+
+	private VoxelDimensions initVoxelDimensions()
+	{
+		if ( voxelDimensionFetching.equals( VoxelDimensionFetching.FromOMEXML ) )
+		{
+			return OMEXMLParser.readVoxelDimensions( omeXML );
+		}
+		else
+		{
+			return null;
 		}
 	}
 

src/main/java/org/embl/mobie/lib/ThreadHelper.java

@@ -51,7 +51,9 @@ public class ThreadHelper
 
 	public static ExecutorService ioExecutorService = Executors.newFixedThreadPool( N_IO_THREADS );
 
-	public static final SharedQueue sharedQueue = new SharedQueue( N_IO_THREADS );
+	public static final int NUM_PRIORITIES = 6; // https://imagesc.zulipchat.com/#narrow/stream/327326-BigDataViewer/topic/SharedQueue
+
+	public static final SharedQueue sharedQueue = new SharedQueue( N_IO_THREADS, NUM_PRIORITIES );
 
 	public static ExecutorService executorService = Executors.newFixedThreadPool( N_THREADS );
 

src/main/java/org/embl/mobie/lib/hcs/OMEXMLParser.java

@@ -14,13 +14,12 @@
 
 public class OMEXMLParser
 {
-    public static VoxelDimensions readVoxelDimensions( String filePath )
+    public static VoxelDimensions readVoxelDimensions( File omeXml )
     {
         try {
-            File inputFile = new File(filePath);
             DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
             DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
-            Document doc = dBuilder.parse(inputFile);
+            Document doc = dBuilder.parse(omeXml);
             doc.getDocumentElement().normalize();
 
             // Assuming VoxelDimensions is a class you have that can store these values

src/main/java/org/embl/mobie/lib/hcs/Plate.java

@@ -51,6 +51,7 @@
 import ch.epfl.biop.bdv.img.bioformats.entity.SeriesIndex;
 import org.embl.mobie.lib.hcs.omezarr.OMEZarrHCSHelper;
 
+import javax.annotation.Nullable;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
@@ -82,14 +83,16 @@ public class Plate
 	private boolean siteIDsAreOneBased = true;
 	private boolean is2d = true;
 	private int numSlices;
+	private boolean fetchSpatialMetadata = true;
 
 
-	public Plate( String hcsDirectory ) throws IOException
+	public Plate( String hcsDirectory, @Nullable VoxelDimensions voxelDimensions ) throws IOException
 	{
 		this.hcsDirectory = hcsDirectory;
+		this.voxelDimensions = voxelDimensions;
 
-		// FIXME: fetch operetta paths from XML?!
-		// FIXME: fetch OME-Zarr paths entry point JSON?!
+		// TODO: fetch operetta paths from XML?!
+		// TODO: fetch OME-Zarr paths entry point JSON?!
 
 		IJ.log( "Looking for image files..." );
 		long start = System.currentTimeMillis();
@@ -217,10 +220,10 @@ private void buildPlateMap( List< String > imagePaths )
 						channel.setContrastLimits( contrastLimits );
 					}
 
-					// determine spatial metadata (for all channels the same)
-					//
-					if ( voxelDimensions == null )
+					if ( fetchSpatialMetadata )
 					{
+						fetchSpatialMetadata= false; // should be the same for all files and channels
+
 						if ( operettaMetadata != null )
 						{
 							voxelDimensions = operettaMetadata.getVoxelDimensions( imagePath );
@@ -230,27 +233,30 @@ private void buildPlateMap( List< String > imagePaths )
 						{
 							final Calibration calibration = singleChannelImagePlus.getCalibration();
 
-							if ( hcsPattern.hasZ() )
-							{
-								/*
-								If the z-positions are distributed over multiple files
-								typically the z-calibration metadata in the individual files is wrong.
-								We thus just put something sensible here such that browsing in BDV along the
-								z-axis is convenient
-								 */
-								voxelDimensions = new FinalVoxelDimensions(
-										calibration.getUnit(),
-										calibration.pixelWidth,
-										calibration.pixelHeight,
-										10 * calibration.pixelHeight );
-							}
-							else
+							if ( voxelDimensions == null )
 							{
-								voxelDimensions = new FinalVoxelDimensions(
-										calibration.getUnit(),
-										calibration.pixelWidth,
-										calibration.pixelHeight,
-										calibration.pixelDepth );
+								if ( hcsPattern.hasZ() )
+								{
+									/*
+									If the z-positions are distributed over multiple files
+									typically the z-calibration metadata in the individual files is wrong.
+									We thus just put something sensible here such that browsing in BDV along the
+									z-axis is convenient
+									 */
+									voxelDimensions = new FinalVoxelDimensions(
+											calibration.getUnit(),
+											calibration.pixelWidth,
+											calibration.pixelHeight,
+											10 * calibration.pixelHeight );
+								}
+								else
+								{
+									voxelDimensions = new FinalVoxelDimensions(
+											calibration.getUnit(),
+											calibration.pixelWidth,
+											calibration.pixelHeight,
+											calibration.pixelDepth );
+								}
 							}
 
 							siteDimensions = new int[]{ singleChannelImagePlus.getWidth(), singleChannelImagePlus.getHeight() };

src/test/java/develop/MergedGrid3D.java

@@ -30,6 +30,7 @@
 
 import net.imagej.ImageJ;
 import org.embl.mobie.MoBIE;
+import org.embl.mobie.MoBIESettings;
 
 import java.io.IOException;
 
@@ -41,7 +42,7 @@ public static void main( String[] args )
 		imageJ.ui().showUI();
 
 		try {
-			new MoBIE("/Users/tischer/Downloads/example/mobie-example-project" );//.getViewManager().show( "cell-segmentation" );
+			new MoBIE("/Users/tischer/Downloads/example/mobie-example-project", new MoBIESettings() );//.getViewManager().show( "cell-segmentation" );
 		} catch ( IOException e) {
 			e.printStackTrace();
 		}

src/test/java/develop/hcs/HCS.java

@@ -41,16 +41,16 @@ public static void main( String[] args ) throws SpimDataException, IOException
 	{
 		new ImageJ().ui().showUI();
 
-		//new MoBIE( "/Users/tischer/Downloads/Operetta", new MoBIESettings(), 0.1, 0.0  );
+		//new MoBIE( "/Users/tischer/Downloads/Operetta", new MoBIESettings(), 0.1, 0.0, null  );
 
-		//new MoBIE( "/Users/tischer/Downloads/IncuCyte", new MoBIESettings(), 0.1, 0.0 );
+		//new MoBIE( "/Users/tischer/Downloads/IncuCyte", new MoBIESettings(), 0.1, 0.0, null );
 
-		//new MoBIE( "/Users/tischer/Downloads/incu2/", new MoBIESettings(), 0.1, 0.0  );
+		//new MoBIE( "/Users/tischer/Downloads/incu2/", new MoBIESettings(), 0.1, 0.0, null  );
 
-		//new MoBIE( "/g/cba/exchange/mobie-data/incucyte-drug-screen/images", new MoBIESettings(), 0.1, 0.0  );
+		//new MoBIE( "/g/cba/exchange/mobie-data/incucyte-drug-screen/images", new MoBIESettings(), 0.1, 0.0, null  );
 
-		//new MoBIE( "/Users/tischer/Documents/faim-hcs/resources/MIP-2P-2sub/2022-07-05/1075", new MoBIESettings(), 0.1, 0.0  );
+		//new MoBIE( "/Users/tischer/Documents/faim-hcs/resources/MIP-2P-2sub/2022-07-05/1075", new MoBIESettings(), 0.1, 0.0, null  );
 
-		new MoBIE( "/Volumes/cba/exchange/hcs-test/Samples", new MoBIESettings(), 0.1, 0.0  );
+		new MoBIE( "/Volumes/cba/exchange/hcs-test/Samples", new MoBIESettings(), 0.1, 0.0, null );
 	}
 }

src/test/java/develop/hcs/HCSInCellAnalyzer6000.java

@@ -42,6 +42,6 @@ public static void main( String[] args ) throws SpimDataException, IOException
 	{
 		new ImageJ().ui().showUI();
 
-		new MoBIE( "/Users/tischer/Downloads/incell", new MoBIESettings(), 0.1, 0.0  );
+		new MoBIE( "/Users/tischer/Downloads/incell", new MoBIESettings(), 0.1, 0.0, null  );
 	}
 }

src/test/java/develop/hcs/HCSIncuyte.java

@@ -41,16 +41,16 @@ public static void main( String[] args ) throws SpimDataException, IOException
 	{
 		new ImageJ().ui().showUI();
 
-		//new MoBIE( "/Users/tischer/Downloads/Operetta", new MoBIESettings(), 0.1, 0.0  );
+		//new MoBIE( "/Users/tischer/Downloads/Operetta", new MoBIESettings(), 0.1, 0.0, null  );
 
-		//new MoBIE( "/Users/tischer/Downloads/IncuCyte", new MoBIESettings(), 0.1, 0.0 );
+		//new MoBIE( "/Users/tischer/Downloads/IncuCyte", new MoBIESettings(), 0.1, 0.0, null );
 
-		//new MoBIE( "/Users/tischer/Downloads/incu2/", new MoBIESettings(), 0.1, 0.0  );
+		//new MoBIE( "/Users/tischer/Downloads/incu2/", new MoBIESettings(), 0.1, 0.0, null  );
 
-		//new MoBIE( "/g/cba/exchange/mobie-data/incucyte-drug-screen/images", new MoBIESettings(), 0.1, 0.0  );
+		//new MoBIE( "/g/cba/exchange/mobie-data/incucyte-drug-screen/images", new MoBIESettings(), 0.1, 0.0, null  );
 
-		//new MoBIE( "/Users/tischer/Documents/faim-hcs/resources/MIP-2P-2sub/2022-07-05/1075", new MoBIESettings(), 0.1, 0.0  );
+		//new MoBIE( "/Users/tischer/Documents/faim-hcs/resources/MIP-2P-2sub/2022-07-05/1075", new MoBIESettings(), 0.1, 0.0, null  );
 
-		new MoBIE( "/Volumes/cba/exchange/hcs-test/Samples", new MoBIESettings(), 0.1, 0.0  );
+		new MoBIE( "/Volumes/cba/exchange/hcs-test/Samples", new MoBIESettings(), 0.1, 0.0, null  );
 	}
 }

src/test/java/develop/hcs/HCSIncuyteRaw.java

@@ -41,7 +41,7 @@ class HCSIncuyteRaw
 	public static void main( String[] args ) throws SpimDataException, IOException
 	{
 		new ImageJ().ui().showUI();
-		//new MoBIE( "/Users/tischer/Downloads/incu-test-data/2207/19", new MoBIESettings(), 0.1, 0.0  );
-		new MoBIE( "https://s3.embl.de/i2k-2020/incu-test-data/2207/19", new MoBIESettings(), 0.1, 0.0  );
+		//new MoBIE( "/Users/tischer/Downloads/incu-test-data/2207/19", new MoBIESettings(), 0.1, 0.0, null  );
+		new MoBIE( "https://s3.embl.de/i2k-2020/incu-test-data/2207/19", new MoBIESettings(), 0.1, 0.0, null  );
 	}
 }

src/test/java/develop/hcs/HCSOMEZarr.java

@@ -41,8 +41,8 @@ public static void main( String[] args ) throws SpimDataException, IOException
 	{
 		new ImageJ().ui().showUI();
 
-		//new MoBIE( "/Volumes/cba/exchange/ome-zarr/bugra/HCS/testdata.zarr", new MoBIESettings(), 0.1, 0.0  );
-		//new MoBIE( "/Users/tischer/Downloads/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr", new MoBIESettings(), 0.1, 0.0  );
-		new MoBIE( "/Users/tischer/Downloads/test-plate.zarr", new MoBIESettings(), 0.1, 0.0  );
+		//new MoBIE( "/Volumes/cba/exchange/ome-zarr/bugra/HCS/testdata.zarr", new MoBIESettings(), 0.1, 0.0, null  );
+		//new MoBIE( "/Users/tischer/Downloads/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr", new MoBIESettings(), 0.1, 0.0, null  );
+		new MoBIE( "/Users/tischer/Downloads/test-plate.zarr", new MoBIESettings(), 0.1, 0.0, null  );
 	}
 }

src/test/java/develop/hcs/HCSOMEZarrS3.java

@@ -41,8 +41,8 @@ public static void main( String[] args ) throws SpimDataException, IOException
 	{
 		new ImageJ().ui().showUI();
 
-		//new MoBIE( "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/plates/5966.zarr", new MoBIESettings(), 0.1, 0.0  );
-		//new MoBIE( "https://radosgw.public.os2.wwu.de/ngff/test.zarr", new MoBIESettings(), 0.1, 0.0  );
-		new MoBIE( "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/plates/2551.zarr", new MoBIESettings(), 0.1, 0.0 );
+		//new MoBIE( "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/plates/5966.zarr", new MoBIESettings(), 0.1, 0.0, null  );
+		//new MoBIE( "https://radosgw.public.os2.wwu.de/ngff/test.zarr", new MoBIESettings(), 0.1, 0.0, null  );
+		new MoBIE( "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/plates/2551.zarr", new MoBIESettings(), 0.1, 0.0, null );
 	}
 }

src/test/java/develop/hcs/HCSOperetta4.java

@@ -40,6 +40,6 @@ class HCSOperetta4
 	public static void main( String[] args ) throws SpimDataException, IOException
 	{
 		new ImageJ().ui().showUI();
-		new MoBIE( "/Volumes/cba/exchange/hcs-test/operetta4/Samples", new MoBIESettings(), 0.1, 0.0  );
+		new MoBIE( "/Volumes/cba/exchange/hcs-test/operetta4/Samples", new MoBIESettings(), 0.1, 0.0, null  );
 	}
 }

src/test/java/develop/hcs/HCSOperetta5.java

@@ -40,6 +40,6 @@ class HCSOperetta5
 	public static void main( String[] args ) throws SpimDataException, IOException
 	{
 		new ImageJ().ui().showUI();
-		new MoBIE( "/Volumes/cba/exchange/hcs-test/operetta5/CLSsamples", new MoBIESettings(), 0.1, 0.0  );
+		new MoBIE( "/Volumes/cba/exchange/hcs-test/operetta5/CLSsamples", new MoBIESettings(), 0.1, 0.0, null  );
 	}
 }

src/test/java/develop/hcs/HCSYokogawaCQ1.java

@@ -23,6 +23,6 @@ public static void main( String[] args ) throws SpimDataException, IOException
         new MoBIE( "/Users/tischer/Desktop/moritz/CQ1_testfiles",
                 new MoBIESettings().removeSpatialCalibration( true ), // TODO: what is the z-spacing, how to add this?
                 0.1,
-                0.0  );
+                0.0, null  );
     }
 }

src/test/java/projects/OpenLocalJulianNoTables.java

@@ -30,6 +30,7 @@
 
 import net.imagej.ImageJ;
 import org.embl.mobie.MoBIE;
+import org.embl.mobie.MoBIESettings;
 
 import java.io.IOException;
 
@@ -39,7 +40,7 @@ public static void main( String[] args ) throws IOException
 	{
 		final ImageJ imageJ = new ImageJ();
 		imageJ.ui().showUI();
-		final MoBIE moBIE = new MoBIE("/Volumes/emcf/hennies/for_constantin/mobie_no_table_test/" );
+		final MoBIE moBIE = new MoBIE("/Volumes/emcf/hennies/for_constantin/mobie_no_table_test/", new MoBIESettings() );
 		moBIE.getViewManager().show( "seg-test" );
 	}
 }