Improve opening OME-Zarr files as a grid view

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

@@ -89,7 +89,7 @@ public class MoBIE
 		new Thread(() -> {
 			long start = System.currentTimeMillis();
 			AmazonS3ClientBuilder.standard();
-			IJ.log( "Initialised AmazonS3ClientBuilder in " + ( System.currentTimeMillis() -start ) + " ms." );
+			IJ.log( "( Initialised AmazonS3ClientBuilder in " + ( System.currentTimeMillis() -start ) + " ms. )" );
 		}).start();
 	}
 

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

@@ -46,10 +46,11 @@ public class OpenImageAndLabelsFilesCommand implements Command {
 
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 
-	@Parameter( label = "Image Path", required = false )
+	// FIXME: https://forum.image.sc/t/scijava-ui-open-both-file-and-directory/97389
+	@Parameter( label = "Image Path", style = "both", required = false )
 	public File image;
 
-	@Parameter( label = "Label Mask Path", required = false )
+	@Parameter( label = "Label Mask Path", style = "both", required = false )
 	public File labels;
 
 	@Parameter( label = "Label Mask Table Path", required = false )
@@ -58,13 +59,14 @@ public class OpenImageAndLabelsFilesCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
+	@Parameter( label = "Grid type", description = "If the images are different and not too many, use Transformed; otherwise use Stitched for better performance.")
+	public GridType gridType = GridType.Transformed;
+
 	@Override
 	public void run()
 	{
 		final MoBIESettings settings = new MoBIESettings();
 
-		final GridType gridType = GridType.Stitched; // TODO: fetch from UI
-
 		final ArrayList< String > imageList = new ArrayList<>();
 		if ( image != null ) imageList.add( image.getAbsolutePath() );
 
@@ -85,7 +87,7 @@ public void run()
 		}
 		catch ( IOException e )
 		{
-			e.printStackTrace();
+			throw new RuntimeException( e );
 		}
 	}
 

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

@@ -57,13 +57,14 @@ public class OpenImageAndLabelsURIsCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
+	@Parameter( label = "Grid type", description = "If the images are different and not too many, use Transformed; otherwise use Stitched for better performance.")
+	public GridType gridType = GridType.Transformed;
+
 	@Override
 	public void run()
 	{
 		final MoBIESettings settings = new MoBIESettings();
 
-		final GridType gridType = GridType.Stitched; // TODO: maybe fetch from UI
-
 		final ArrayList< String > imageList = new ArrayList<>();
 		if ( image != null ) imageList.add( image );
 

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

@@ -73,13 +73,14 @@ public class OpenMultipleImagesAndLabelsFilesCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
+	@Parameter( label = "Grid type", description = "If the images are different and not too many, use Transformed; otherwise use Stitched for better performance.")
+	public GridType gridType = GridType.Transformed;
+
 	@Override
 	public void run()
 	{
 		final MoBIESettings settings = new MoBIESettings();
 
-		final GridType gridType = GridType.Stitched; // TODO: fetch from UI
-
 		final ArrayList< String > imageList = new ArrayList<>();
 		if ( image0 != null ) imageList.add( image0.getAbsolutePath() );
 		if ( image1 != null ) imageList.add( image1.getAbsolutePath() );

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

@@ -72,13 +72,14 @@ public class OpenMultipleImagesAndLabelsURIsCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
+	@Parameter( label = "Grid type", description = "If the images are different and not too many, use Transformed; otherwise use Stitched for better performance.")
+	public GridType gridType = GridType.Transformed;
+
 	@Override
 	public void run()
 	{
 		final MoBIESettings settings = new MoBIESettings();
 
-		final GridType gridType = GridType.Stitched; // TODO: fetch from UI
-
 		final ArrayList< String > imageList = new ArrayList<>();
 		if ( image0 != null ) imageList.add( image0 );
 		if ( image1 != null ) imageList.add( image1 );

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

@@ -74,10 +74,13 @@ public class OpenTableCommand implements Command {
 	@Parameter( label = "Spatial Calibration" )
 	public SpatialCalibration spatialCalibration = SpatialCalibration.FromImage;
 
+	@Parameter( label = "Grid type", description = "If the images are different and not too many, use \"Transformed\"; otherwise use \"Stitched\" for better performance.")
+	public GridType gridType = GridType.Transformed;
+
 	@Override
 	public void run()
 	{
-		run( GridType.Stitched );
+		run( gridType );
 	}
 
 	public void run( GridType gridType )

src/main/java/org/embl/mobie/lib/bdv/view/SliceViewer.java

@@ -205,6 +205,7 @@ public static BdvHandle createBdv( boolean is2D, String frameTitle )
 		final MobieSerializableBdvOptions sOptions = new MobieSerializableBdvOptions();
 		sOptions.is2D = is2D;
 		sOptions.frameTitle = frameTitle;
+		sOptions.interpolate = !is2D;
 		IBdvSupplier bdvSupplier = new MobieBdvSupplier( sOptions );
 		//SourceAndConverterServices.getBdvDisplayService().setDefaultBdvSupplier( bdvSupplier );
 		//BdvHandle bdvHandle = SourceAndConverterServices.getBdvDisplayService().getNewBdv();

src/main/java/org/embl/mobie/lib/files/ImageFileSources.java

@@ -31,9 +31,11 @@
 import bdv.viewer.Source;
 import ij.IJ;
 import loci.formats.in.CellSensReader;
+import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.Volatile;
 import net.imglib2.realtransform.AffineTransform3D;
 import org.apache.commons.io.FilenameUtils;
+import org.embl.mobie.MoBIE;
 import org.embl.mobie.io.ImageDataOpener;
 import org.embl.mobie.io.imagedata.ImageData;
 import org.embl.mobie.io.util.IOHelper;
@@ -169,12 +171,17 @@ protected static boolean isCellProfilerColumn( String column, Table table )
 	private void setMetadata( Integer channelIndex )
 	{
 		metadataSource = nameToFullPath.keySet().iterator().next();
+		IJ.log( "Fetching metadata from " + nameToFullPath.get( metadataSource ) );
 		ImageData< ? > imageData = ImageDataOpener.open( nameToFullPath.get( metadataSource ) );
 		CanonicalDatasetMetadata canonicalDatasetMetadata = imageData.getMetadata( channelIndex );
 		metadata = new Metadata( canonicalDatasetMetadata );
-		Source< ? extends Volatile< ? > > source = imageData.getSourcePair( channelIndex ).getB();
+		Source< ? > source = imageData.getSourcePair( channelIndex ).getA();
 		metadata.numZSlices = (int) source.getSource( 0, 0  ).dimension( 2 );
 		metadata.numTimePoints = SourceHelper.getNumTimePoints( source );
+		metadata.contrastLimits = MoBIEHelper.computeMinMax( ( RandomAccessibleInterval ) source.getSource( 0, source.getNumMipmapLevels() -1 ) );
+		IJ.log( "Slices: " + metadata.numZSlices );
+		IJ.log( "Frames: " + metadata.numTimePoints );
+		IJ.log( "Min, max: " + Arrays.toString( metadata.contrastLimits ) );
 	}
 
 	private static String applyPathMapping( String pathMapping, String path )

src/main/java/org/embl/mobie/lib/source/SourceHelper.java

@@ -105,6 +105,7 @@ public static int getNumTimePoints( Source< ? > source )
         if ( numSourceTimepoints == maxNumTimePoints )
 		{
 			System.err.println( source.getName() + " has more than " + maxNumTimePoints + " time-points. Is this an error?!" );
+			return 1;
 		}
 
 		return numSourceTimepoints;

src/test/java/develop/OpenAutoMicTable.java

@@ -29,7 +29,6 @@
 package develop;
 
 import net.imagej.ImageJ;
-import org.embl.mobie.command.open.OpenTableAdvancedCommand;
 import org.embl.mobie.lib.transform.GridType;
 
 import java.io.File;

src/main/java/org/embl/mobie/command/open/OpenTableAdvancedCommand.java → src/test/java/projects/OpenLocalYannickZarrs.java

@@ -26,25 +26,33 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.embl.mobie.command.open;
+package projects;
 
-import org.embl.mobie.command.CommandConstants;
+import net.imagej.ImageJ;
+import org.embl.mobie.MoBIE;
+import org.embl.mobie.MoBIESettings;
+import org.embl.mobie.command.open.OpenImageAndLabelsFilesCommand;
 import org.embl.mobie.lib.transform.GridType;
-import org.scijava.command.Command;
-import org.scijava.plugin.Parameter;
-import org.scijava.plugin.Plugin;
 
-@Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN + "Open Table (Advanced)..." )
-public class OpenTableAdvancedCommand extends OpenTableCommand {
+import java.io.File;
+import java.io.IOException;
 
-	static { net.imagej.patcher.LegacyInjector.preinit(); }
+public class OpenLocalYannickZarrs
+{
+	public static void main( String[] args ) throws IOException
+	{
+		final ImageJ imageJ = new ImageJ();
+		imageJ.ui().showUI();
 
-	@Parameter( label = "Grid type" )
-	public GridType gridType = GridType.Transformed;
+		OpenImageAndLabelsFilesCommand command = new OpenImageAndLabelsFilesCommand();
+		command.gridType = GridType.Transformed;
+		command.image = new File("/Volumes/schwab/schwab/MoBIE-GRIDtestJUNE2024/JEOL1400_20240426/.*.ome.zarr");
+		//command.image = new File("/Volumes/schwab/schwab/MoBIE-GRIDtestJUNE2024/JEOL1400_20240426/Alex_ASH_BlockA1_Grid11_PS_ser1_cell4_8k_blend.ome.zarr");
 
-	@Override
-	public void run()
-	{
-		super.run( gridType );
+		// FIXME
+		// - why does the software complain that there are more than 1000 time-points?
+		// - add the relative paths to the table
+		// - add the full paths to the table
+		command.run();
 	}
 }

src/test/java/projects/muscle_patterning_drosophila/OpenTeresaData.java

@@ -29,7 +29,6 @@
 package projects.muscle_patterning_drosophila;
 
 import net.imagej.ImageJ;
-import org.embl.mobie.command.open.OpenTableAdvancedCommand;
 import org.embl.mobie.lib.transform.GridType;
 
 import java.io.File;