Fix bug reported on issue #87 of watershed-labeled voxels out of the

valid mask.

The problem was in the creation of markers, where neighbors of the
original markers were also added to the list without checking the valid
mask.

Author: iarganda

src/main/java/inra/ijpb/watershed/MarkerControlledWatershedTransform3D.java

@@ -555,7 +555,7 @@ public ImagePlus applyWithPriorityQueue()
 												+ cDist2cur ) );
       						}
 						}
-						else if ( tabLabels[u][v][w] > 0 &&
+						else if ( tabLabels[u][v][w] > 0 && maskStack.getVoxel( u, v, w ) > 0 &&
 								! neighborLabels.contains(
 										tabLabels[ u ][ v ][ w ] ) )
 						{
@@ -572,8 +572,14 @@ else if ( tabLabels[u][v][w] > 0 &&
 					// now that we know the voxel is labeled, add neighbors to list
 					for( VoxelRecord v : neighborVoxels )
 					{
-						tabLabels[ v.getCursor().getX() ][ v.getCursor().getY() ][ v.getCursor().getZ() ] = INQUEUE;
-						voxelList.add( v );
+						final int x = v.getCursor().getX();
+						final int y = v.getCursor().getY();
+						final int z = v.getCursor().getZ();
+						if ( maskStack.getVoxel( x, y, z ) > 0 )
+						{
+							tabLabels[ x ][ y ][ z ] = INQUEUE;
+							voxelList.add( v );
+						}
 					}
 				}
 			}
@@ -1050,6 +1056,7 @@ public PriorityQueue<VoxelRecord> extractVoxelValuesPriorityQueue(
 									if ( u >= 0 && u < size1 && 
 											v >= 0 && v < size2 && 
 											w >= 0 && w < size3 &&
+											ipMask.getf( u, v ) > 0 &&
 											(int) seedStack.getVoxel( u, v, w ) == 0 &&
 											tabLabels[ u ][ v ][ w ] != INQUEUE )															 
 									{

src/test/java/inra/ijpb/plugins/Watershed3DMaskTest.java

@@ -0,0 +1,71 @@
+/*-
+ * #%L
+ * Mathematical morphology library and plugins for ImageJ/Fiji.
+ * %%
+ * Copyright (C) 2014 - 2026 INRA.
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ * #L%
+ */
+package inra.ijpb.plugins;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.Test;
+
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.process.FloatProcessor;
+import ij.process.ImageProcessor;
+import ij.process.ByteProcessor;
+import inra.ijpb.watershed.Watershed;
+
+public class Watershed3DMaskTest {
+
+    @Test
+    public void testWatershedRespectsMask3D() {
+        final int w = 5, h = 5, d = 3;
+
+        ImageStack inputStack = new ImageStack(w, h);
+        ImageStack maskStack = new ImageStack(w, h);
+
+        for (int z = 0; z < d; z++) {
+            FloatProcessor fp = new FloatProcessor(w, h);
+            ByteProcessor mp = new ByteProcessor(w, h);
+            for (int y = 0; y < h; y++) {
+                for (int x = 0; x < w; x++) {
+                    // simple gradient
+                    fp.setf(x, y, (float) (z * 10 + x + y));
+                    // mask center 3x3 is 1, border is 0
+                    if (x >= 1 && x <= 3 && y >= 1 && y <= 3)
+                        mp.setf(x, y, 1);
+                    else
+                        mp.setf(x, y, 0);
+                }
+            }
+            inputStack.addSlice(fp);
+            maskStack.addSlice(mp);
+        }
+
+        ImagePlus input = new ImagePlus("input", inputStack);
+        ImagePlus mask = new ImagePlus("mask", maskStack);
+
+        ImagePlus ws = Watershed.computeWatershed(input, mask, 6);
+        // verify no labels outside mask
+        ImageStack out = ws.getImageStack();
+        for (int z = 0; z < d; z++) {
+            ImageProcessor outIp = out.getProcessor(z+1);
+            ImageProcessor maskIp = maskStack.getProcessor(z+1);
+            for (int y = 0; y < h; y++) {
+                for (int x = 0; x < w; x++) {
+                    if (maskIp.getf(x, y) == 0) {
+                        assertEquals("Label outside mask at ("+x+","+y+","+z+")", 0f, outIp.getf(x, y), 0f);
+                    }
+                }
+            }
+        }
+    }
+}