Update segmentation logic with dropped singleton dimensions.

Author: Stefan Hahmann

src/main/java/org/mastodon/mamut/detection/DeepLearningDetector.java

@@ -204,7 +204,8 @@ private void detectAndAddSpots( final List< SourceAndConverter< ? > > sources, f
 		}
 
 		System.err.println(); // show the FIJI console
-		final Img< ? > segmentation = performSegmentation( image, source.getVoxelDimensions().dimensionsAsDoubleArray() );
+		final Img< ? > segmentation =
+				performSegmentation( Views.dropSingletonDimensions( image ), source.getVoxelDimensions().dimensionsAsDoubleArray() );
 
 		if ( segmentation != null )
 		{
@@ -234,8 +235,11 @@ private boolean validateAndInitializeSettings()
 		return true;
 	}
 
-	protected double getAnisotropy( double[] voxelSizes )
+	protected double getAnisotropy( double[] voxelSizes, boolean is3D )
 	{
+		if ( !is3D )
+			return 1.0;
+
 		if ( voxelSizes == null || voxelSizes.length == 0 )
 		{
 			throw new IllegalArgumentException( "Array must not be empty" );

src/main/java/org/mastodon/mamut/detection/cellpose/Cellpose3Detector.java

@@ -51,6 +51,7 @@
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.Img;
 import net.imglib2.util.Cast;
+import net.imglib2.view.Views;
 
 import org.mastodon.mamut.detection.DeepLearningDetector;
 import org.mastodon.tracking.mamut.detection.SpotDetectorOp;
@@ -102,14 +103,15 @@ && checkParameter( settings, KEY_GPU_ID, Integer.class, errorHolder )
 	{
 		try (Cellpose3 cellpose = new Cellpose3( ( Cellpose3.ModelType ) settings.get( KEY_MODEL_TYPE ) ))
 		{
-			cellpose.set3D( is3D( image ) );
+			boolean is3D = is3D( image );
+			cellpose.set3D( is3D );
 			cellpose.setCellProbThreshold( ( double ) settings.get( KEY_CELL_PROBABILITY_THRESHOLD ) );
 			cellpose.setFlowThreshold( ( double ) settings.get( KEY_FLOW_THRESHOLD ) );
 			cellpose.setDiameter( ( double ) settings.get( KEY_DIAMETER ) );
 			cellpose.setGpuID( ( int ) settings.get( KEY_GPU_ID ) );
 			cellpose.setGpuMemoryFraction( ( double ) settings.get( KEY_GPU_MEMORY_FRACTION ) );
 			final boolean respectAnisotropy = ( boolean ) settings.get( KEY_RESPECT_ANISOTROPY );
-			double anisotropy = respectAnisotropy ? getAnisotropy( voxelDimensions ) : 1.0;
+			double anisotropy = respectAnisotropy ? getAnisotropy( voxelDimensions, is3D ) : 1.0;
 			cellpose.setAnisotropy( ( float ) anisotropy );
 			return cellpose.segmentImage( Cast.unchecked( image ) );
 		}