Fixes #1101

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

@@ -168,11 +168,11 @@ public MoBIE( List< String > imagePaths, List< String > labelPaths, List< String
 
 		final SourcesFromPathsCreator sourcesCreator = new SourcesFromPathsCreator( imagePaths, labelPaths, labelTablePaths, root, grid );
 
-		final List< ImageFileSources > imageFileSources = sourcesCreator.getImageSources();
+		final List< ImageFileSources > imageSources = sourcesCreator.getImageSources();
 		final List< LabelFileSources > labelSources = sourcesCreator.getLabelSources();
 		Table regionTable = sourcesCreator.getRegionTable();
 
-		openImagesAndLabels( imageFileSources, labelSources, regionTable );
+		openImagesAndLabels( imageSources, labelSources, regionTable );
 	}
 
 	// open an image or object table

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

@@ -129,12 +129,12 @@ private void addGridView( Dataset dataset, ArrayList< ImageFileSources > allSour
 			if ( regionDisplay == null )
 			{
 				// init RegionDisplay
-				regionDisplay = new RegionDisplay<>( this.regionTable.name() );
+				regionDisplay = new RegionDisplay<>( regionTable.name() );
 
 				// add table
 				final StorageLocation storageLocation = new StorageLocation();
-				storageLocation.data = this.regionTable;
-				final RegionTableSource regionTableSource = new RegionTableSource( this.regionTable.name() );
+				storageLocation.data = regionTable;
+				final RegionTableSource regionTableSource = new RegionTableSource( regionTable.name() );
 				regionTableSource.addTable( TableDataFormat.Table, storageLocation );
 				DataStore.addRawData( regionTableSource );
 
@@ -155,7 +155,7 @@ private void addGridView( Dataset dataset, ArrayList< ImageFileSources > allSour
 
 				for ( int regionIndex = 0; regionIndex < numRegions; regionIndex++ )
 				{
-					String regionName = this.regionTable.getString( regionIndex, ColumnNames.REGION_ID );
+					String regionName = regionTable.getString( regionIndex, ColumnNames.REGION_ID );
 					regionDisplay.sources.put( regionName, new ArrayList<>() );
 				}
 			}
@@ -165,7 +165,7 @@ private void addGridView( Dataset dataset, ArrayList< ImageFileSources > allSour
 			{
 				// TODO: This is brittle as it requires that the sourceNames have the same
 				//   order as the regions in the regionTable
-				String regionName = this.regionTable.getString( regionIndex, ColumnNames.REGION_ID );
+				String regionName = regionTable.getString( regionIndex, ColumnNames.REGION_ID );
 				regionDisplay.sources.get( regionName ).add( sourceNames.get( regionIndex ) );
 				//System.out.println("Region: " +  regionName + "; source: " + sourceNames.get( regionIndex ) );
 			}

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

@@ -83,7 +83,7 @@ public ImageFileSources( String name, String pathRegex, Integer channelIndex, St
 		this.metadata = MoBIEHelper.getMetadataFromImageFile( nameToFullPath.get( metadataSource ), channelIndex );
 
 		// FIXME: move this out to a separate function
-		regionTable = Table.create( this.name );
+		regionTable = Table.create( name + " table" );
 		regionTable.addColumns( StringColumn.create( ColumnNames.REGION_ID, new ArrayList<>( nameToFullPath.keySet() ) ) );
 		regionTable.addColumns( StringColumn.create( "source_path", new ArrayList<>( nameToFullPath.values() ) ) );
 	}

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

@@ -28,33 +28,28 @@
  */
 package org.embl.mobie.lib.files;
 
-import org.apache.commons.compress.utils.FileNameUtils;
 import org.embl.mobie.lib.io.FileImageSource;
-import org.embl.mobie.lib.table.ColumnNames;
 import org.embl.mobie.lib.transform.GridType;
-import tech.tablesaw.api.StringColumn;
 import tech.tablesaw.api.Table;
 
-import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.stream.Collectors;
 
 public class SourcesFromPathsCreator
 {
-	private List< ImageFileSources > imageFileSources;
+	private List< ImageFileSources > imageSources;
 	private List< LabelFileSources > labelSources;
 	private Table regionTable;
 
 	public SourcesFromPathsCreator( List < String > imagePaths, List < String > labelPaths, List < String > labelTablePaths, String root, GridType grid )
 	{
 		// images
 		//
-		imageFileSources = new ArrayList<>();
+		imageSources = new ArrayList<>();
 		for ( String imagePath : imagePaths )
 		{
 			final FileImageSource fileImageSource = new FileImageSource( imagePath );
-			imageFileSources.add( new ImageFileSources( fileImageSource.name, fileImageSource.path, fileImageSource.channelIndex, root, grid ) );
+			imageSources.add( new ImageFileSources( fileImageSource.name, fileImageSource.path, fileImageSource.channelIndex, root, grid ) );
 		}
 
 		// segmentation images
@@ -74,47 +69,11 @@ public SourcesFromPathsCreator( List < String > imagePaths, List < String > labe
 				labelSources.add( new LabelFileSources( fileImageSource.name, fileImageSource.path, fileImageSource.channelIndex, root, grid ) );
 			}
 		}
-
-		// region table
-		//
-		regionTable = Table.create( "image table" );
-		final List< String > regions = imagePaths.stream().map( path -> FileNameUtils.getBaseName(  path  ) ).collect( Collectors.toList() );
-		regionTable.addColumns( StringColumn.create( ColumnNames.REGION_ID, regions ) );
 	}
 
-	// TODO consider adding back the functionality of groups for sorting the grid
-	//			final List< String > groups = MoBIEHelper.getGroupNames( regex );
-	//			if ( groups.size() > 0 )
-	//			{
-	//				final Pattern pattern = Pattern.compile( regex );
-	//				final Set< String > set = new LinkedHashSet<>();
-	//				for ( String path : paths )
-	//				{
-	//					final Matcher matcher = pattern.matcher( path );
-	//					matcher.matches();
-	//					set.add( matcher.group( 1 ) );
-	//				}
-	//
-	//				final ArrayList< String > categories = new ArrayList<>( set );
-	//				final int[] numSources = new int[ categories.size() ];
-	//				grid.positions = new ArrayList<>();
-	//				for ( String source : sources )
-	//				{
-	//					final Matcher matcher = pattern.matcher( source );
-	//					matcher.matches();
-	//					final int row = categories.indexOf( matcher.group( rowGroup ) );
-	//					final int column = numSources[ row ];
-	//					numSources[ row ]++;
-	//					grid.positions.add( new int[]{ column, row } );
-	//				}
-	//			}
-	//			}
-	//			else
-	//			{
-
 	public List< ImageFileSources > getImageSources()
 	{
-		return imageFileSources;
+		return imageSources;
 	}
 
 	public List< LabelFileSources > getLabelSources()
@@ -124,6 +83,11 @@ public List< LabelFileSources > getLabelSources()
 
 	public Table getRegionTable()
 	{
-		return regionTable;
+		// all images should be shown on the same grid,
+		// thus we just return one of the region tables
+		if ( ! imageSources.isEmpty() )
+			return imageSources.get( 0 ).getRegionTable();
+		else
+			return labelSources.get( 0 ).getRegionTable();
 	}
 }

src/test/java/debug/DebugIssue1101.java

@@ -0,0 +1,17 @@
+package debug;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.command.open.OpenMultipleImagesAndLabelsCommand;
+
+import java.io.File;
+
+public class DebugIssue1101
+{
+    public static void main( String[] args )
+    {
+        new ImageJ().ui().showUI();
+        final OpenMultipleImagesAndLabelsCommand command = new OpenMultipleImagesAndLabelsCommand();
+        command.image0 = new File( "/Users/tischer/Downloads/example-png-no-open/iso.*.png" );
+        command.run();
+    }
+}

src/test/java/org/embl/mobie/command/OpenIlastikImagesAndSegmentationsCommandTest.java

@@ -0,0 +1,52 @@
+/*-
+ * #%L
+ * Fiji viewer for MoBIE projects
+ * %%
+ * Copyright (C) 2018 - 2023 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;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.command.open.OpenImageAndLabelsCommand;
+import org.embl.mobie.command.open.OpenMultipleImagesAndLabelsCommand;
+
+import java.io.File;
+
+public class OpenIlastikImagesAndSegmentationsCommandTest
+{
+	static { net.imagej.patcher.LegacyInjector.preinit(); }
+
+	public static void main( String[] args )
+	{
+		new ImageJ().ui().showUI(); // initialise SciJava Services
+
+		final OpenMultipleImagesAndLabelsCommand command = new OpenMultipleImagesAndLabelsCommand();
+		command.image0 = new File( "src/test/resources/ilastik-multiple/raw/iso.*.png" );
+		command.image1 = new File( "src/test/resources/ilastik-multiple/pc/iso..*_Probabilities.h5" );
+		command.labels0 = new File( "src/test/resources/ilastik-multiple/oc/iso..*_Object Identities.h5" );
+		command.table0 = new File( "src/test/resources/ilastik-multiple/oc/iso..*_table.csv" );
+		command.run();
+	}
+}

src/test/java/projects/colony_detection_anavo/OpenColonyObjectsTable.java

@@ -0,0 +1,21 @@
+package projects.colony_detection_anavo;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.command.open.OpenTableCommand;
+
+import java.io.File;
+
+public class OpenColonyObjectsTable
+{
+    public static void main( String[] args )
+    {
+        new ImageJ().ui().showUI();
+        final OpenTableCommand command = new OpenTableCommand();
+        command.root = new File( "/Users/tischer/Desktop/moritz/HCT116_dataset-wells" );
+        command.table = new File( "/Users/tischer/Desktop/moritz/HCT116_dataset-wells/colony_table.csv" );
+        command.images = "file_name";
+        command.labels = "labels_file_name";
+        command.removeSpatialCalibration = true;
+        command.run();
+    }
+}

src/test/resources/ilastik-multiple/README.txt

@@ -0,0 +1,3 @@
+This data is courtesy of the FlyEM project, HHMI Janelia Research Campus
+
+Derived data created using ilastik 1.4.1b13 by Dominik Kutra