Fix bug in CollectionTable where different channels would wrongly yie…

…ld the same image name
mobie · Feb 9, 2025 · 53e588d · 53e588d
1 parent 4a0e08a
commit 53e588d
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Showing 4 changed files with 29 additions and 17 deletions.
diff --git a/pom.xml b/pom.xml
@@ -9,10 +9,9 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>6.0.2-SNAPSHOT</version>
+    <version>6.0.3-SNAPSHOT</version>
 
     <!-- mvn clean install -Dmaven.test.skip=true -Dscijava.app.directory=/Users/tischer/Desktop/Fiji/Fiji-MoBIE.app -->
-    <!-- mvn clean install -Dmaven.test.skip=true -Dscijava.app.directory=/Users/tischer/Desktop/Fiji/Fiji-40.0.0.app -->
 
     <!--  ../scijava-scripts/release-version.sh - -skip-version-check - -skip-license-update -->
     <!-- ../scijava-scripts/release-version.sh - -skip-version-check  - -skip-license-update -->

diff --git a/src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java b/src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java
@@ -1,5 +1,6 @@
 package org.embl.mobie.lib.data;
 
+import IceInternal.Ex;
 import ij.IJ;
 import net.imglib2.type.numeric.ARGBType;
 import org.embl.mobie.DataStore;
@@ -235,7 +236,7 @@ else if ( existingDisplay instanceof ImageDisplay )
                 gridRegionDisplay.sources.put( source, Collections.singletonList( source ) );
 
             // TODO: in some cases only do this once for several grids
-            dataset.views().get( viewName ).displays().add( gridRegionDisplay );
+             dataset.views().get( viewName ).displays().add( gridRegionDisplay );
         }
 
     }
@@ -313,7 +314,17 @@ private static String getName( Row row )
     private static String getNameFromURI( Row row )
     {
         String uri = getUri( row );
-        return MoBIEHelper.removeExtension( IOHelper.getFileName( uri ) );
+        String name = MoBIEHelper.removeExtension( IOHelper.getFileName( uri ) );
+        try
+        {
+            int channelIndex = row.getInt( CollectionTableConstants.CHANNEL );
+            name = name + "_c" + channelIndex;
+        }
+        catch ( Exception e )
+        {
+            // do nothing
+        }
+        return name;
     }
 
     private static String getDataType( Row row )
@@ -351,7 +362,10 @@ private static String getGridId( Row row )
     private static int getChannel( Row row )
     {
         try {
-            return row.getInt( CollectionTableConstants.CHANNEL );
+            int channelIndex = row.getInt( CollectionTableConstants.CHANNEL );
+            if ( channelIndex < 0 )
+                return 0; // Sometimes an empty string yields a negative number
+            return channelIndex;
         }
         catch ( Exception e )
         {
@@ -482,7 +496,7 @@ private static double[] getContrastLimits( Row row )
 
             if ( doubles.length != 2 )
                 throw new UnsupportedOperationException("Contrast limits must have exactly two values: (min, max).\n" +
-                        "This table cell entry does not adhere to this specification: " + string );
+                        string + "does not adhere to this specification." );
 
             return doubles;
         }

diff --git a/src/main/java/org/embl/mobie/lib/image/ImageDataImage.java b/src/main/java/org/embl/mobie/lib/image/ImageDataImage.java
@@ -52,7 +52,7 @@ public class ImageDataImage< T extends NumericType< T > & NativeType< T > > impl
 {
 	private ImageDataFormat imageDataFormat;
 	private String uri;
-	private int setupId;
+	private int setupId = 0;
 	private SourcePair< T > sourcePair;
 	private String name;
 	private Site site;
@@ -68,7 +68,7 @@ public ImageDataImage( ImageData< ? > imageData, Integer setupId, String name, V
 		this.imageDataFormat = null;
 		this.uri = null;
 		this.sharedQueue = null;
-		this.setupId = setupId == null ? 0 : setupId;
+		if ( setupId != null ) this.setupId = setupId;
 		this.name = name; // FIXME: add the datasetname to the name ?!
 		System.out.println("Name: " + name );
 		System.out.println("SetupID: " + setupId );
@@ -80,14 +80,14 @@ public ImageDataImage( ImageData< ? > imageData, Integer setupId, String name, V
 	public ImageDataImage(
 			ImageDataFormat imageDataFormat,
 			String uri,
-			int setupId,
+			Integer setupId,
 			String name,
 			@Nullable SharedQueue sharedQueue,
 			VoxelDimensions voxelDimensions )
 	{
 		this.imageDataFormat = imageDataFormat;
 		this.uri = uri;
-		this.setupId = setupId;
+		if ( setupId != null ) this.setupId = setupId;
 		this.name = name;
 		this.sharedQueue = sharedQueue;
 		this.voxelDimensions = voxelDimensions;

diff --git a/src/main/java/org/embl/mobie/lib/io/FileImageSource.java b/src/main/java/org/embl/mobie/lib/io/FileImageSource.java
@@ -28,7 +28,6 @@
  */
 package org.embl.mobie.lib.io;
 
-import org.apache.commons.io.FilenameUtils;
 import org.embl.mobie.lib.util.MoBIEHelper;
 
 import java.io.File;
@@ -44,15 +43,15 @@ public class FileImageSource
 	 * "path=name;channelIndex"
 	 * where everything after path is optional
 	 *
-	 * @param string
-	 * 				the string to be parsed
+	 * @param uri
+	 * 				the uri to be parsed
 	 */
-	public FileImageSource( String string )
+	public FileImageSource( String uri )
 	{
-		String[] split = new String[]{ string };
-		if ( string.contains( ";" ) )
+		String[] split = new String[]{ uri };
+		if ( uri.contains( ";" ) )
 		{
-			split = string.split( ";" );
+			split = uri.split( ";" );
 			channelIndex = Integer.parseInt( split[ 1 ] );
 		}