Change way to determine whether an image is 3d or not for Cellpose3 and Cellpose4 Detectors

Author: Stefan Hahmann

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

@@ -163,8 +163,7 @@ public void compute( final List< SourceAndConverter< ? > > sources, final ModelG
 				 * will have a size of 1.
 				 */
 				double[] voxelDimensions = source.getVoxelDimensions().dimensionsAsDoubleArray();
-				boolean is3D = voxelDimensions.length == 3;
-				cellpose.set3D( is3D );
+				cellpose.set3D( is3D( image ) );
 				double anisotropy = respectAnisotropy ? getAnisotropy( voxelDimensions ) : 1.0;
 				cellpose.setAnisotropy( ( float ) anisotropy );
 				cellpose.setCellprobThreshold( cellProbabilityThreshold );
@@ -232,4 +231,21 @@ private double getAnisotropy( double[] voxelSizes )
 		return highestValue / lowestValue;
 	}
 
+	private boolean is3D( final RandomAccessibleInterval< ? > image )
+	{
+		long[] dimensions = image.dimensionsAsLongArray();
+		if ( dimensions.length <= 2 )
+			return false;
+		else
+		{
+			int nonPlaneDimensionCount = 0;
+			for ( final long dimension : dimensions )
+			{
+				if ( dimension > 1 )
+					nonPlaneDimensionCount++;
+			}
+			return nonPlaneDimensionCount > 2;
+		}
+	}
+
 }

src/main/java/org/mastodon/mamut/detection/Cellpose4Detector.java

@@ -155,9 +155,7 @@ public void compute( final List< SourceAndConverter< ? > > sources, final ModelG
 				 * channel. It is always 3D. If the source is 2D, the 3rd dimension
 				 * will have a size of 1.
 				 */
-				double[] voxelDimensions = source.getVoxelDimensions().dimensionsAsDoubleArray();
-				boolean is3D = voxelDimensions.length == 3;
-				cellpose.set3D( is3D );
+				cellpose.set3D( is3D( image ) );
 				cellpose.setCellprobThreshold( cellProbabilityThreshold );
 				cellpose.setFlowThreshold( flowThreshold );
 				Img< ? > segmentation = cellpose.segmentImage( Cast.unchecked( image ) );
@@ -196,4 +194,21 @@ public Map< String, Object > getDefaultSettings()
 		defaultSettings.put( KEY_FLOW_THRESHOLD, Cellpose4.DEFAULT_FLOW_THRESHOLD );
 		return defaultSettings;
 	}
+
+	private boolean is3D( final RandomAccessibleInterval< ? > image )
+	{
+		long[] dimensions = image.dimensionsAsLongArray();
+		if ( dimensions.length <= 2 )
+			return false;
+		else
+		{
+			int nonPlaneDimensionCount = 0;
+			for ( final long dimension : dimensions )
+			{
+				if ( dimension > 1 )
+					nonPlaneDimensionCount++;
+			}
+			return nonPlaneDimensionCount > 2;
+		}
+	}
 }