Improve opening of OpenOrganelle data and default collection table vi…

…ews to exclusive=false and add another column column to modify this behaviour
mobie · Nov 2, 2024 · a0f972b · a0f972b
1 parent 1832be3
commit a0f972b
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Showing 63 changed files with 575 additions and 123 deletions.
diff --git a/pom.xml b/pom.xml
@@ -9,9 +9,9 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.5.5</version>
-    <!-- mvn clean install -Dmaven.test.skip=true -Dscijava.app.directory=/Users/tischer/Desktop/Fiji/Fiji-MoBIE.app -->
+    <version>5.5.6-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 -->
     <!-- ../scijava-scripts/release-version.sh - -skip-version-check  - -skip-license-update -->
 
@@ -83,7 +83,7 @@
         <license.copyrightOwners>EMBL</license.copyrightOwners>
         <enforcer.skip>true</enforcer.skip>
 
-        <mobie-io.version>3.0.4</mobie-io.version>
+        <mobie-io.version>3.1.0-SNAPSHOT</mobie-io.version>
         <imagej-utils.version>0.7.0</imagej-utils.version>
 
         <bigdataviewer-playground.version>0.9.0</bigdataviewer-playground.version>

diff --git a/src/main/java/org/embl/mobie/MoBIE.java b/src/main/java/org/embl/mobie/MoBIE.java
@@ -56,6 +56,8 @@
 import org.embl.mobie.lib.table.columns.CollectionTableConstants;
 import org.embl.mobie.lib.table.saw.TableOpener;
 import org.embl.mobie.lib.transform.GridType;
+import org.embl.mobie.lib.util.MoBIEHelper;
+import org.embl.mobie.lib.util.ThreadHelper;
 import org.embl.mobie.lib.view.ViewManager;
 import org.embl.mobie.plugins.platybrowser.GeneSearchCommand;
 import org.embl.mobie.ui.UserInterface;
@@ -137,7 +139,7 @@ public MoBIE( String uri, MoBIESettings settings ) throws IOException
 
 			CollectionTableDataSetter dataSetter = new CollectionTableDataSetter( table, settings.values.getDataRoot() );
 			dataSetter.addToDataset( dataset );
-			dataset.is2D( false ); // TODO: determine from data?!
+			dataset.is2D( settings.values.getBdvViewingMode().equals( BdvViewingMode.TwoDimensional ) );
 
 			initUiAndShowView( dataset.views().values().iterator().next().getName() );
 		}

diff --git a/src/main/java/org/embl/mobie/cmd/HCSCmd.java b/src/main/java/org/embl/mobie/cmd/HCSCmd.java
@@ -30,7 +30,6 @@
 
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.MoBIESettings;
-import org.embl.mobie.lib.MoBIEHelper;
 import picocli.CommandLine;
 import picocli.CommandLine.Option;
 

diff --git a/src/main/java/org/embl/mobie/command/context/AbstractTransformationCommand.java b/src/main/java/org/embl/mobie/command/context/AbstractTransformationCommand.java
@@ -37,7 +37,7 @@
 import org.embl.mobie.ProjectType;
 import org.embl.mobie.command.widget.SelectableImages;
 import org.embl.mobie.command.widget.SwingSelectableImagesWidget;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.image.Image;
 import org.embl.mobie.lib.image.RegionAnnotationImage;
 import org.embl.mobie.lib.serialize.View;

diff --git a/src/main/java/org/embl/mobie/command/context/AutomaticRegistrationCommand.txt b/src/main/java/org/embl/mobie/command/context/AutomaticRegistrationCommand.txt
@@ -40,7 +40,7 @@ import ij.process.ImageConverter;
 import net.imglib2.display.ColorConverter;
 import net.imglib2.realtransform.AffineTransform3D;
 import org.embl.mobie.command.CommandConstants;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.align.TurboReg2DAligner;
 import org.embl.mobie.lib.bdv.ScreenShotMaker;
 import org.embl.mobie.lib.align.SIFT2DAligner;

diff --git a/src/main/java/org/embl/mobie/command/context/SourcesInfoCommand.java b/src/main/java/org/embl/mobie/command/context/SourcesInfoCommand.java
@@ -35,7 +35,7 @@
 import net.imglib2.realtransform.AffineTransform3D;
 import org.embl.mobie.DataStore;
 import org.embl.mobie.command.CommandConstants;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.image.Image;
 import org.embl.mobie.lib.io.ImageDataInfo;
 import org.embl.mobie.lib.serialize.transformation.AffineTransformation;

diff --git a/src/main/java/org/embl/mobie/command/open/OpenCollectionTableCommand.java b/src/main/java/org/embl/mobie/command/open/OpenCollectionTableCommand.java
@@ -33,7 +33,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.ProjectType;
 import org.embl.mobie.command.CommandConstants;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.bdv.BdvViewingMode;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;

diff --git a/src/main/java/org/embl/mobie/command/open/OpenHCSDatasetCommand.java b/src/main/java/org/embl/mobie/command/open/OpenHCSDatasetCommand.java
@@ -33,7 +33,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.io.util.IOHelper;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.hcs.OMEXMLParser;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;

diff --git a/src/main/java/org/embl/mobie/command/open/OpenImageAndLabelsCommand.java b/src/main/java/org/embl/mobie/command/open/OpenImageAndLabelsCommand.java
@@ -32,13 +32,12 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.command.SpatialCalibration;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.transform.GridType;
 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.util.ArrayList;
 

diff --git a/src/main/java/org/embl/mobie/command/open/OpenMultipleImagesAndLabelsCommand.java b/src/main/java/org/embl/mobie/command/open/OpenMultipleImagesAndLabelsCommand.java
@@ -32,7 +32,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.command.SpatialCalibration;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.transform.GridType;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;

diff --git a/src/main/java/org/embl/mobie/command/open/OpenOMEZARRCommand.java b/src/main/java/org/embl/mobie/command/open/OpenOMEZARRCommand.java
@@ -31,7 +31,7 @@
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.transform.GridType;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;

diff --git a/src/main/java/org/embl/mobie/command/open/OpenTableCommand.java b/src/main/java/org/embl/mobie/command/open/OpenTableCommand.java
@@ -33,7 +33,7 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.command.SpatialCalibration;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.transform.GridType;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;

diff --git a/src/main/java/org/embl/mobie/command/open/project/OpenMoBIEProjectExpertCommand.java b/src/main/java/org/embl/mobie/command/open/project/OpenMoBIEProjectExpertCommand.java
@@ -29,8 +29,8 @@
 package org.embl.mobie.command.open.project;
 
 import org.embl.mobie.command.CommandConstants;
-import org.embl.mobie.lib.MoBIEHelper;
-import org.embl.mobie.lib.ThreadHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
+import org.embl.mobie.lib.util.ThreadHelper;
 import org.embl.mobie.lib.bdv.view.SliceViewer;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;

diff --git a/src/main/java/org/embl/mobie/command/open/special/OpenMicrogliaTableCommand.java b/src/main/java/org/embl/mobie/command/open/special/OpenMicrogliaTableCommand.java
@@ -33,7 +33,6 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.command.SpatialCalibration;
-import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.transform.GridType;
 import org.scijava.ItemVisibility;
 import org.scijava.command.Command;

diff --git a/src/main/java/org/embl/mobie/command/view/ViewCurrentImageCommand.java b/src/main/java/org/embl/mobie/command/view/ViewCurrentImageCommand.java
@@ -33,7 +33,7 @@
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.io.imagedata.ImageData;
 import org.embl.mobie.io.imagedata.ImagePlusImageData;
-import org.embl.mobie.lib.ThreadHelper;
+import org.embl.mobie.lib.util.ThreadHelper;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;

diff --git a/src/main/java/org/embl/mobie/command/view/ViewImageAndLabelsAndTableCommand.java b/src/main/java/org/embl/mobie/command/view/ViewImageAndLabelsAndTableCommand.java
@@ -35,7 +35,7 @@
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.io.imagedata.ImageData;
 import org.embl.mobie.io.imagedata.ImagePlusImageData;
-import org.embl.mobie.lib.ThreadHelper;
+import org.embl.mobie.lib.util.ThreadHelper;
 import org.embl.mobie.lib.io.StorageLocation;
 import org.embl.mobie.lib.table.TableDataFormat;
 import org.scijava.Initializable;

diff --git a/src/main/java/org/embl/mobie/command/widget/SwingSelectableImagesWidget.java b/src/main/java/org/embl/mobie/command/widget/SwingSelectableImagesWidget.java
@@ -31,7 +31,7 @@
 import bdv.util.BdvHandle;
 import bdv.viewer.SourceAndConverter;
 import org.embl.mobie.MoBIE;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.jetbrains.annotations.NotNull;
 import org.scijava.Priority;
 import org.scijava.plugin.Plugin;

diff --git a/src/main/java/org/embl/mobie/lib/ImageDataAdder.java b/src/main/java/org/embl/mobie/lib/ImageDataAdder.java
@@ -42,6 +42,7 @@
 import org.embl.mobie.lib.serialize.display.ImageDisplay;
 import org.embl.mobie.lib.serialize.display.SegmentationDisplay;
 import org.embl.mobie.lib.table.TableDataFormat;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata;
 
 import java.io.File;

diff --git a/src/main/java/org/embl/mobie/lib/SourcesFromTableCreator.java b/src/main/java/org/embl/mobie/lib/SourcesFromTableCreator.java
@@ -33,10 +33,12 @@
 import org.embl.mobie.lib.data.ImageGridSources;
 import org.embl.mobie.lib.data.LabelGridSources;
 import org.embl.mobie.lib.io.TableImageSource;
-import org.embl.mobie.lib.table.ColumnNames;
+import org.embl.mobie.lib.table.columns.ColumnNames;
 import org.embl.mobie.lib.table.saw.Aggregators;
 import org.embl.mobie.lib.table.saw.TableOpener;
 import org.embl.mobie.lib.transform.GridType;
+import org.embl.mobie.lib.util.MoBIEHelper;
+import org.embl.mobie.lib.util.ThreadHelper;
 import tech.tablesaw.api.NumberColumn;
 import tech.tablesaw.api.StringColumn;
 import tech.tablesaw.api.Table;

diff --git a/src/main/java/org/embl/mobie/lib/bdv/MobieSerializableBdvOptions.java b/src/main/java/org/embl/mobie/lib/bdv/MobieSerializableBdvOptions.java
@@ -31,7 +31,7 @@
 import bdv.util.AxisOrder;
 import bdv.util.BdvOptions;
 import bdv.viewer.render.AccumulateProjectorFactory;
-import org.embl.mobie.lib.ThreadHelper;
+import org.embl.mobie.lib.util.ThreadHelper;
 import org.embl.mobie.lib.bdv.blend.AccumulateAlphaBlendingProjectorARGBFactory;
 import net.imglib2.type.numeric.ARGBType;
 

diff --git a/src/main/java/org/embl/mobie/lib/bdv/ScreenShotMaker.java b/src/main/java/org/embl/mobie/lib/bdv/ScreenShotMaker.java
@@ -47,8 +47,8 @@
 import net.imglib2.type.Type;
 import net.imglib2.type.logic.BitType;
 import net.imglib2.type.numeric.real.FloatType;
-import org.embl.mobie.lib.MoBIEHelper;
-import org.embl.mobie.lib.ThreadHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
+import org.embl.mobie.lib.util.ThreadHelper;
 import org.embl.mobie.lib.annotation.Annotation;
 import org.embl.mobie.lib.bdv.blend.AccumulateAlphaBlendingProjectorARGB;
 import net.imglib2.algorithm.util.Grids;

diff --git a/src/main/java/org/embl/mobie/lib/bdv/overlay/ImageNameOverlay.java b/src/main/java/org/embl/mobie/lib/bdv/overlay/ImageNameOverlay.java
@@ -122,6 +122,7 @@ private void updateOverlayItems( Graphics2D g )
 
 		FinalRealInterval viewerInterval = BdvHandleHelper.getViewerGlobalBoundingInterval( bdvHandle );
 
+
 		final Set< SourceAndConverter< ? > > sourceAndConverters = viewerState.getVisibleAndPresentSources();
 
 		for ( final SourceAndConverter< ? > sourceAndConverter : sourceAndConverters )

diff --git a/src/main/java/org/embl/mobie/lib/bdv/view/AnnotationSliceView.java b/src/main/java/org/embl/mobie/lib/bdv/view/AnnotationSliceView.java
@@ -143,7 +143,8 @@ 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();
-					final double width = mask.realMax( 0 ) - mask.realMin( 0 );
+					double width = mask.realMax( 0 ) - mask.realMin( 0 );
+					width = Math.min( width, mask.realMax( 1 ) - mask.realMin( 1 ) );
 					boundaryThickness = width * boundaryThickness;
 				}
 			}

diff --git a/src/main/java/org/embl/mobie/lib/create/DatasetSerializer.java b/src/main/java/org/embl/mobie/lib/create/DatasetSerializer.java
@@ -29,7 +29,7 @@
 package org.embl.mobie.lib.create;
 
 import de.embl.cba.tables.color.ColoringLuts;
-import org.embl.mobie.lib.table.ColumnNames;
+import org.embl.mobie.lib.table.columns.ColumnNames;
 import org.embl.mobie.lib.serialize.display.ImageDisplay;
 import org.embl.mobie.lib.serialize.display.SegmentationDisplay;
 import org.embl.mobie.lib.serialize.display.Display;
@@ -48,7 +48,6 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.net.URI;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;

diff --git a/src/main/java/org/embl/mobie/lib/create/ProjectCreator.java b/src/main/java/org/embl/mobie/lib/create/ProjectCreator.java
@@ -29,10 +29,9 @@
 package org.embl.mobie.lib.create;
 
 import mpicbg.spim.data.SpimDataException;
-import net.imagej.patcher.LegacyInjector;
 import org.embl.mobie.io.ImageDataFormat;
 import org.embl.mobie.io.util.IOHelper;
-import org.embl.mobie.lib.MoBIEHelper;
+import org.embl.mobie.lib.util.MoBIEHelper;
 import org.embl.mobie.lib.serialize.*;
 
 import java.io.File;
Original file line number	Diff line number	Diff line change
Expand Up		@@ -122,6 +122,7 @@ private void updateOverlayItems( Graphics2D g )

		FinalRealInterval viewerInterval = BdvHandleHelper.getViewerGlobalBoundingInterval( bdvHandle );


		final Set< SourceAndConverter< ? > > sourceAndConverters = viewerState.getVisibleAndPresentSources();

		for ( final SourceAndConverter< ? > sourceAndConverter : sourceAndConverters )
Expand Down