Fix several issues concerning the transformation and image info loggi…

…ng of AnnotationLabelImages

src/main/java/org/embl/mobie/command/context/SourcesInfoCommand.java

@@ -35,6 +35,7 @@
 import net.imglib2.realtransform.AffineTransform3D;
 import org.embl.mobie.DataStore;
 import org.embl.mobie.command.CommandConstants;
+import org.embl.mobie.lib.image.RegionAnnotationImage;
 import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.image.Image;
 import org.embl.mobie.lib.io.ImageDataInfo;
@@ -69,11 +70,14 @@ public void run()
         visibleSacs.forEach( sac ->
         {
             Image< ? > image = DataStore.sourceToImage().get( sac );
+            if ( image instanceof RegionAnnotationImage )
+                return;
+
             ImageDataInfo imageDataInfo = MoBIEHelper.fetchImageDataInfo( image );
 
             Source< ? > source = sac.getSpimSource();
-            AffineTransform3D transform3D = new AffineTransform3D();
-            sac.getSpimSource().getSourceTransform( t, 0, transform3D );
+            AffineTransform3D sourceTransform = new AffineTransform3D();
+            sac.getSpimSource().getSourceTransform( t, 0, sourceTransform );
 
             IJ.log( "" );
             IJ.log( "# " + source.getName() );
@@ -88,11 +92,11 @@ public void run()
             Transformation imageTransformation = transformations.get( 0 );
             if ( imageTransformation instanceof AffineTransformation )
             {
-                AffineTransform3D imageTransform = ( ( AffineTransformation ) imageTransformation ).getAffineTransform3D();
-                IJ.log( "Original image transformation: " + MoBIEHelper.print( imageTransform.getRowPackedCopy(), 3 ) );
-                AffineTransform3D additionalTransform = transform3D.copy().concatenate( imageTransform.inverse() );
-                IJ.log( "Additional MoBIE transformation: " + MoBIEHelper.print( additionalTransform.getRowPackedCopy(), 3 ) );
-                IJ.log( "Total transformation: " +  MoBIEHelper.print( transform3D.getRowPackedCopy(), 3 )  );
+                AffineTransform3D initialTransform = ( ( AffineTransformation ) imageTransformation ).getAffineTransform3D();
+                IJ.log( "Original image transformation: " + MoBIEHelper.print( initialTransform.getRowPackedCopy(), 3 ) );
+                AffineTransform3D additionalTransform = sourceTransform.copy().concatenate( initialTransform.inverse() );
+                IJ.log( "Combined additional transformation: " + MoBIEHelper.print( additionalTransform.getRowPackedCopy(), 3 ) );
+                IJ.log( "Total transformation: " +  MoBIEHelper.print( sourceTransform.getRowPackedCopy(), 3 )  );
             }
 
             if ( showTransformationHistory )

src/main/java/org/embl/mobie/command/open/project/OpenPlatyBrowserCommand.java

@@ -37,7 +37,7 @@
 import java.io.IOException;
 
 
-@Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN_PROJECT + "Open PlatyBrowser")
+@Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN + "Open PlatyBrowser")
 public class OpenPlatyBrowserCommand implements Command
 {
 	static { net.imagej.patcher.LegacyInjector.preinit(); }

src/main/java/org/embl/mobie/command/open/special/OpenOpenOrganelleDataCommand.java

@@ -0,0 +1,94 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2024 EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.embl.mobie.command.open.special;
+
+import loci.common.DebugTools;
+import net.imagej.ImageJ;
+import org.embl.mobie.MoBIE;
+import org.embl.mobie.MoBIESettings;
+import org.embl.mobie.command.CommandConstants;
+import org.embl.mobie.command.SpatialCalibration;
+import org.embl.mobie.command.open.OpenCollectionTableCommand;
+import org.embl.mobie.lib.transform.GridType;
+import org.embl.mobie.ui.UserInterfaceHelper;
+import org.jboss.netty.channel.UpstreamMessageEvent;
+import org.scijava.ItemVisibility;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+@Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN + "Open OpenOrganelle" )
+public class OpenOpenOrganelleDataCommand implements Command {
+
+	static { net.imagej.patcher.LegacyInjector.preinit(); }
+
+	@Override
+	public void run()
+	{
+		final URL resource = OpenOpenOrganelleDataCommand.class.getResource( "/open-organelle.txt" );
+		String file = resource.getFile();
+		OpenCollectionTableCommand command = new OpenCollectionTableCommand();
+		command.table = new File( file );
+		command.run();
+	}
+
+	public static void main( String[] args )
+	{
+		// to update the table use org.embl.mobie.lib.util.OpenOrganelleCollectionTableCreator
+
+		new ImageJ().ui().showUI();
+		new OpenOpenOrganelleDataCommand().run();
+
+		// TODO
+		// - [X] The grid overlay boundaries are too thick for some reason
+		// - [X] Auto-contrast in a Transformed Grid View should be determined from an image that is currently visible!
+		// - [ ] Auto-contrast in the beginning of a grid view display would be nice
+		// - [X] For each RegionDisplay automatically overlay the region_id as an annotation
+		// - [X] The grids should not be exclusive in this case
+		// - [X] The EM should show first
+		// - [ ] How to implement one Grid and RegionDisplay for many sources?
+		//     - how to deal with the fact that then there are multiple table rows for each region?
+		// - [ ] It would be cleaner if all the layers would be part of the same grid
+		//     - this could be achieved by adding a "grid_position" column
+		//     - but then we would also need a "display" column to sort the entries into the respective displays
+		//     - an issue with this would be how to implement the region display, because s.a.
+		// - [X] Zoom to region when clicking on a RegionTable row
+		// - [ ] Yannick: exclusive column
+		// - [ ] John: Membrane segmentation pixel shit in jrc_jurkat-1/labels/pm_seg
+
+	}
+}

src/main/java/org/embl/mobie/lib/annotation/AnnotationUI.java

@@ -29,7 +29,6 @@
 package org.embl.mobie.lib.annotation;
 
 import de.embl.cba.tables.Logger;
-import de.embl.cba.tables.SwingUtils;
 import ij.IJ;
 import net.imglib2.type.numeric.ARGBType;
 import org.embl.mobie.lib.color.CategoricalAnnotationColoringModel;
@@ -40,16 +39,13 @@
 import org.embl.mobie.lib.table.AnnotationTableModel;
 import org.embl.mobie.lib.table.DefaultValues;
 import org.embl.mobie.ui.MoBIELaf;
+import org.embl.mobie.ui.SwingHelper;
 
 import javax.swing.*;
 import javax.swing.table.TableModel;
 import java.awt.*;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 import java.util.stream.Collectors;
 
 import static org.embl.mobie.lib.color.lut.LUTs.DARK_GREY;
@@ -166,7 +162,7 @@ private void showFrame()
 
 	private void addCreateCategoryButton()
 	{
-		final JPanel panel = SwingUtils.horizontalLayoutPanel();
+		final JPanel panel = SwingHelper.horizontalBoxLayoutPanel();
 		final JButton button = new JButton( "Create new category" );
 		final JTextField textField = new JTextField( "nice_cell" );
 		panel.add( button );
@@ -190,7 +186,7 @@ private void addAnnotationButtons()
 		annotationButtonsPanel.setBorder( BorderFactory.createEmptyBorder(0,10,10,10) );
 		panel.add( annotationButtonsPanel );
 
-		final JPanel panel = SwingUtils.horizontalLayoutPanel();
+		final JPanel panel = SwingHelper.horizontalBoxLayoutPanel();
 		panel.add( new JLabel( "Annotate selected " + objectName + "(s) as:" ) );
 		panel.add( new JLabel( "      " ) );
 		annotationButtonsPanel.add( panel );
@@ -219,7 +215,7 @@ private void addAnnotationButtonPanel( String annotationName, A annotation )
 
 		annotationNames.add( annotationName );
 
-		final JPanel panel = SwingUtils.horizontalLayoutPanel();
+		final JPanel panel = SwingHelper.horizontalBoxLayoutPanel();
 		final JButton annotateButton = new JButton( String.format("%1$15s", annotationName) );
 		annotateButton.setFont( new Font("monospaced", Font.PLAIN, 12) );
 		annotateButton.setOpaque( true );
@@ -271,7 +267,7 @@ private void addAnnotationButtonPanel( String annotationName, A annotation )
 
 	private void addSelectPreviousAndNextPanel( )
 	{
-		final JPanel panel = SwingUtils.horizontalLayoutPanel();
+		final JPanel panel = SwingHelper.horizontalBoxLayoutPanel();
 		final JButton clear = createClearSelectionButton();
 		final JButton previous = createSelectPreviousButton();
 		final JButton next = createSelectNextButton();
@@ -283,7 +279,7 @@ private void addSelectPreviousAndNextPanel( )
 
 	private void addSelectIDPanel( )
 	{
-		final JPanel panel = SwingUtils.horizontalLayoutPanel();
+		final JPanel panel = SwingHelper.horizontalBoxLayoutPanel();
 		final JButton button = createSelectButton();
 		selectAnnotationTextField = new JTextField( "" );
 		selectAnnotationTextField.setText( "1" );
@@ -463,7 +459,7 @@ private void selectRow( A row )
 
 	private void addSkipNonePanel( )
 	{
-		final JPanel panel = SwingUtils.horizontalLayoutPanel();
+		final JPanel panel = SwingHelper.horizontalBoxLayoutPanel();
 
 		final JCheckBox checkBox = new JCheckBox( "Skip \"None\" & \"NaN\"" );
 		checkBox.setSelected( false );
@@ -479,7 +475,7 @@ private void addSkipNonePanel( )
 
 	private void addKeepSelectedPanel( )
 	{
-		final JPanel panel = SwingUtils.horizontalLayoutPanel();
+		final JPanel panel = SwingHelper.horizontalBoxLayoutPanel();
 
 		final JCheckBox checkBox = new JCheckBox( "Keep "+ objectName +"(s) selected after assignment" );
 		checkBox.setSelected( false );

src/main/java/org/embl/mobie/lib/bdv/AutoContrastAdjuster.java

@@ -25,12 +25,15 @@ public double[] computeMinMax()
     {
         double viewerVoxelSpacing = BdvHandleHelper.getViewerVoxelSpacing( bdvHandle );
         ScreenShotMaker screenShotMaker = new ScreenShotMaker( bdvHandle, "" );
-        screenShotMaker.run( Collections.singletonList( sourceAndConverter ), 4 * viewerVoxelSpacing );
+        screenShotMaker.run(
+                Collections.singletonList( sourceAndConverter ),
+                16 * viewerVoxelSpacing // times 16 to make it faster
+        );
         ImagePlus imagePlus = screenShotMaker.getCompositeImagePlus();
         Roi[] rois = screenShotMaker.getMasks();
         if ( rois != null && rois.length > 0 )
             imagePlus.setRoi( rois[ 0 ] );
-        IJ.run( imagePlus, "Enhance Contrast", "saturated=0.35" );
+        IJ.run( imagePlus, "Enhance Contrast", "saturated=0.03" );
         // imagePlus.show();
         double[] minMax = { imagePlus.getDisplayRangeMin(), imagePlus.getDisplayRangeMax() };
         return minMax;

src/main/java/org/embl/mobie/lib/bdv/overlay/AnnotatedRegionsOverlay.java

@@ -85,6 +85,12 @@ public void close()
 		sliceViewer.getBdvHandle().getViewerPanel().requestRepaint();
 	}
 
+	@Override
+	public void setVisible( boolean visible )
+	{
+		overlaySource.setActive( visible );
+	}
+
 	@Override
 	protected synchronized void draw( Graphics2D g )
 	{

src/main/java/org/embl/mobie/lib/bdv/overlay/AnnotatedSegmentsOrSpotsOverlay.java

@@ -82,6 +82,12 @@ public void close()
 		sliceViewer.getBdvHandle().getViewerPanel().requestRepaint();
 	}
 
+	@Override
+	public void setVisible( boolean visible )
+	{
+		overlaySource.setActive( visible );
+	}
+
 	@Override
 	protected synchronized void draw( Graphics2D g )
 	{

src/main/java/org/embl/mobie/lib/bdv/overlay/AnnotationOverlay.java

@@ -3,4 +3,6 @@
 public interface AnnotationOverlay
 {
     void close();
+
+    void setVisible( boolean visible );
 }

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

@@ -33,12 +33,16 @@
 import bdv.viewer.Source;
 import bdv.viewer.SourceAndConverter;
 import bdv.viewer.SynchronizedViewerState;
+import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.Volatile;
 import net.imglib2.converter.Converter;
+import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.roi.RealMaskRealInterval;
 import net.imglib2.type.numeric.ARGBType;
+import net.imglib2.util.LinAlgHelpers;
 import org.embl.mobie.DataStore;
 import org.embl.mobie.MoBIE;
+import org.embl.mobie.lib.annotation.AnnotatedRegion;
 import org.embl.mobie.lib.annotation.Annotation;
 import org.embl.mobie.lib.annotation.SliceViewAnnotationSelector;
 import org.embl.mobie.lib.color.AnnotationARGBConverter;
@@ -56,6 +60,8 @@
 import org.embl.mobie.lib.source.BoundarySource;
 import org.embl.mobie.lib.source.SourceHelper;
 import org.embl.mobie.lib.source.VolatileBoundarySource;
+import org.embl.mobie.lib.table.saw.TableSawAnnotatedImages;
+import org.embl.mobie.lib.transform.viewer.MoBIEViewerTransformAdjuster;
 import org.embl.mobie.lib.transform.viewer.ViewerTransformChanger;
 import org.embl.mobie.lib.volume.SegmentVolumeViewer;
 import sc.fiji.bdvpg.services.SourceAndConverterServices;
@@ -142,10 +148,17 @@ private void configureRendering( SourceAndConverter< ? > sourceAndConverter )
 				{
 					final String someRegion = display.sources.keySet().iterator().next();
 					final String someSource = display.sources.get( someRegion ).get( 0 );
-					final RealMaskRealInterval mask = DataStore.getImage( someSource ).getMask();
-					double width = mask.realMax( 0 ) - mask.realMin( 0 );
-					width = Math.min( width, mask.realMax( 1 ) - mask.realMin( 1 ) );
-					boundaryThickness = width * boundaryThickness;
+					Image< ? > image = DataStore.getImage( someSource );
+					final RealMaskRealInterval mask = image.getMask();
+					RandomAccessibleInterval< ? extends Volatile< ? > > source = image.getSourcePair().getVolatileSource().getSource( 0, 0 );
+					long[] dimensions = source.dimensionsAsLongArray();
+					double[] realDimensions = new double[3];
+					LinAlgHelpers.subtract( mask.maxAsDoubleArray(), mask.minAsDoubleArray(), realDimensions );
+					double minimalExtent = Double.MAX_VALUE;
+					for ( int d = 0; d < 3; d++ )
+						if ( dimensions[d] > 1 )
+							minimalExtent = Math.min( minimalExtent, realDimensions[d ] );
+					boundaryThickness = minimalExtent * boundaryThickness;
 				}
 			}
 		}
@@ -175,7 +188,7 @@ public void coloringChanged()
 	public synchronized void focusEvent( A selection, Object initiator )
 	{
 		if ( initiator instanceof SliceViewAnnotationSelector )
-			return;
+			return; // such that it is not focussed twice
 
 		final BdvHandle bdvHandle = getSliceViewer().getBdvHandle();
 		final SynchronizedViewerState state = bdvHandle.getViewerPanel().state();
@@ -184,11 +197,23 @@ public synchronized void focusEvent( A selection, Object initiator )
 		if ( timepoint != null )
 			state.setCurrentTimepoint( timepoint );
 
-		final double[] position = selection.positionAsDoubleArray();
-		if ( position != null )
-			new sc.fiji.bdvpg.bdv.navigate.ViewerTransformChanger(
+		AffineTransform3D viewerTransform;
+		if ( selection instanceof AnnotatedRegion )
+		{
+			RealMaskRealInterval mask = ( ( AnnotatedRegion ) selection ).getMask();
+			viewerTransform = MoBIEViewerTransformAdjuster.getViewerTransform( bdvHandle, mask );
+		}
+		else
+		{
+			final double[] position = selection.positionAsDoubleArray();
+			if ( position == null ) return;
+			viewerTransform = BdvPlaygroundHelper.getViewerTransformWithNewCenter( bdvHandle, position );
+
+		}
+
+		new sc.fiji.bdvpg.bdv.navigate.ViewerTransformChanger(
 				bdvHandle,
-				BdvPlaygroundHelper.getViewerTransformWithNewCenter( bdvHandle, position ),
+				viewerTransform,
 				false,
 				ViewerTransformChanger.animationDurationMillis ).run();
 	}

src/main/java/org/embl/mobie/lib/create/ui/ProjectsCreatorUI.java

@@ -28,7 +28,6 @@
  */
 package org.embl.mobie.lib.create.ui;
 
-import de.embl.cba.tables.SwingUtils;
 import ij.IJ;
 import ij.ImagePlus;
 import ij.gui.GenericDialog;
@@ -327,7 +326,7 @@ private void addSeparatorToGrid( int rowIndex ) {
     }
 
     private void addButtonsPanel() {
-        final JPanel buttonsPanel = SwingUtils.horizontalLayoutPanel();
+        final JPanel buttonsPanel = SwingHelper.horizontalBoxLayoutPanel();
 
         JButton remoteButton = new JButton("Add/update remote");
         JButton openMoBIEButton = new JButton("Open in MoBIE");