diff --git a/pom.xml b/pom.xml
index 7c1ba005..3df94d1b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -9,10 +9,9 @@
org.embl.mobie
mobie-viewer-fiji
- 6.0.2-SNAPSHOT
+ 6.0.3-SNAPSHOT
-
diff --git a/src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java b/src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java
index 43ca04ec..fc3cb0fa 100644
--- 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
index 22922dbd..685bddc4 100644
--- 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
index 56356c96..ee22d722 100644
--- 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 ] );
}