This release Fixes #1208

mobie · Jan 10, 2025 · c1da1d9 · c1da1d9
1 parent 781a924
commit c1da1d9
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Showing 18 changed files with 18 additions and 342 deletions.
diff --git a/.gitignore b/.gitignore
@@ -18,7 +18,7 @@ hs_err_*.log
 pom.xml.releaseBackup
 
 src/test/java/projects/
-
+src/test/java/debug/DebugS3.java
 
 mobie-files
 mobie-hcs

diff --git a/pom.xml b/pom.xml
@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.5.9</version>
+    <version>5.6.4-SNAPSHOT</version>
 
     <!-- mvn clean install -Dmaven.test.skip=true -Dscijava.app.directory=/Users/tischer/Desktop/Fiji/Fiji-MoBIE.app -->
     <!--  ../scijava-scripts/release-version.sh - -skip-version-check - -skip-license-update -->

diff --git a/src/main/java/org/embl/mobie/lib/bdv/overlay/AnnotatedRegionsOverlay.java b/src/main/java/org/embl/mobie/lib/bdv/overlay/AnnotatedRegionsOverlay.java
@@ -28,6 +28,7 @@
  */
 package org.embl.mobie.lib.bdv.overlay;
 
+import IceInternal.Ex;
 import bdv.util.*;
 import bdv.viewer.TransformListener;
 import net.imglib2.FinalRealInterval;
@@ -82,8 +83,15 @@ public AnnotatedRegionsOverlay(
 	public void close()
 	{
 		overlaySource.removeFromBdv();
-		sliceViewer.updateTimepointSlider();
-		sliceViewer.getBdvHandle().getViewerPanel().requestRepaint();
+		try
+		{
+			sliceViewer.updateTimepointSlider();
+			sliceViewer.getBdvHandle().getViewerPanel().requestRepaint();
+		}
+		catch ( Exception e )
+		{
+			// do nothing
+		}
 	}
 
 	@Override

diff --git a/src/main/java/org/embl/mobie/lib/view/ViewManager.java b/src/main/java/org/embl/mobie/lib/view/ViewManager.java
@@ -735,12 +735,14 @@ private void initSegmentVolumeViewer( SegmentationDisplay< ? extends AnnotatedSe
 	@SuppressWarnings( { "rawtypes", "unchecked" } )
 	public synchronized void removeDisplay( Display display, boolean closeImgLoader )
 	{
-		//remove sources from BVV
 		if ( display instanceof AbstractDisplay )
 		{
-			if(((AbstractDisplay)display).bigVolumeViewer.getBVV() != null)
+			if ( ( ( AbstractDisplay ) display).bigVolumeViewer != null )
 			{
-				((AbstractDisplay)display).bigVolumeViewer.removeSources( display.sourceAndConverters() );
+				if ( ( ( AbstractDisplay ) display ).bigVolumeViewer.getBVV() != null )
+				{
+					( ( AbstractDisplay ) display ).bigVolumeViewer.removeSources( display.sourceAndConverters() );
+				}
 			}
 		}
 
@@ -768,7 +770,6 @@ else if ( display instanceof ImageDisplay )
 			final ImageDisplay imageDisplay = ( ImageDisplay ) display;
 			imageDisplay.imageSliceView.close( false );
 			imageDisplay.imageVolumeViewer.close();
-
 		}
 
 		userInterface.removeDisplaySettingsPanel( display );

diff --git a/src/main/java/org/embl/mobie/ui/UserInterfaceHelper.java b/src/main/java/org/embl/mobie/ui/UserInterfaceHelper.java
@@ -598,6 +598,7 @@ public JPanel createSpotDisplaySettingsPanel( SpotDisplay display )
 		panel.add( space() );
 		panel.add( createSliceViewerVisibilityCheckbox( display.isVisible(), sourceAndConverters ) );
 		panel.add( createCheckboxPlaceholder() );
+		panel.add( createCheckboxPlaceholder() );
 		panel.add( createTableVisibilityCheckbox( display.tableView, display.showTable() ) );
 		panel.add( createScatterPlotViewerVisibilityCheckbox( display.scatterPlotView, display.showScatterPlot() ) );
 		return panel;

diff --git a/src/test/java/debug/DebugAngelikaOMEZarrIssue.java b/src/test/java/debug/DebugAngelikaOMEZarrIssue.java
diff --git a/src/test/java/debug/DebugFileLocationEnumIssue.java b/src/test/java/debug/DebugFileLocationEnumIssue.java
diff --git a/src/test/java/debug/DebugFloatSourceBVV.java b/src/test/java/debug/DebugFloatSourceBVV.java
diff --git a/src/test/java/debug/DebugIssue1096.java b/src/test/java/debug/DebugIssue1096.java
diff --git a/src/test/java/debug/DebugIssue1101.java b/src/test/java/debug/DebugIssue1101.java
diff --git a/src/test/java/debug/DebugIssue1167.java b/src/test/java/debug/DebugIssue1167.java
diff --git a/src/test/java/debug/DebugIssue1199.java b/src/test/java/debug/DebugIssue1199.java
diff --git a/src/test/java/debug/DebugOpen3DIlastikImage.java b/src/test/java/debug/DebugOpen3DIlastikImage.java
diff --git a/src/test/java/debug/DebugOpenCollectionTableWithCredentials.java b/src/test/java/debug/DebugOpenCollectionTableWithCredentials.java
diff --git a/src/test/java/debug/DebugOpenMicrogliaTable.java b/src/test/java/debug/DebugOpenMicrogliaTable.java
diff --git a/src/test/java/debug/DebugOpenOMEZarrWithCredentials.java b/src/test/java/debug/DebugOpenOMEZarrWithCredentials.java