add label/filter/ChamferLabelErosion2DShort.java

src/main/java/inra/ijpb/label/filter/ChamferLabelDilation3DShort.java

@@ -214,7 +214,7 @@ private void backwardIteration(ImageStack res, ImageStack distMap, double distMa
 		Collection<ShortOffset> offsets = mask.getBackwardOffsets();
 
 		// Iterate over voxels
-		for (int z = 0; z < sizeZ; z++) 
+		for (int z = sizeZ-1; z >= 0; z--) 
 		{
 			this.fireProgressChanged(this, z, sizeZ);
 			for (int y = sizeY-1; y >= 0; y--)

src/main/java/inra/ijpb/label/filter/ChamferLabelErosion2DShort.java

@@ -0,0 +1,99 @@
+/**
+ * 
+ */
+package inra.ijpb.label.filter;
+
+import ij.process.ImageProcessor;
+import inra.ijpb.algo.AlgoStub;
+import inra.ijpb.binary.distmap.ChamferMask2D;
+import inra.ijpb.morphology.Strel;
+import inra.ijpb.morphology.strel.ChamferStrel;
+
+/**
+ * Implementation of morphological erosion for 2D label images / label maps.
+ * 
+ * Can be applied to label maps encoded with 8 or 16 bits integers, or 32 bit
+ * floats.
+ * 
+ * 
+ * @author dlegland
+ *
+ */
+public class ChamferLabelErosion2DShort extends AlgoStub
+{
+    /**
+     * The chamfer mask used to propagate distances.
+     */
+    ChamferMask2D mask;
+
+    /**
+     * The radius of dilation of labels. In practice, the distance is propagated
+     * up to radius + 0.5.
+     */
+    double radius;
+
+    /**
+     * For erosion, we can work only with the structuring element.
+     */
+    Strel strel;
+
+    public ChamferLabelErosion2DShort(ChamferMask2D mask, double radius)
+    {
+        this.mask = mask;
+        this.radius = radius;
+
+        this.strel = new ChamferStrel(mask, radius);
+    }
+
+    public ImageProcessor process(ImageProcessor image)
+    {
+        // retrieve image size
+        int sizeX = image.getWidth();
+        int sizeY = image.getHeight();
+
+        // allocate memory for output
+        ImageProcessor res = image.createProcessor(sizeX, sizeY);
+
+        // pre-compute strel shifts
+        int[][] shifts = strel.getShifts();
+
+        // iterate over pixels within output image
+        for (int y = 0; y < sizeY; y++)
+        {
+            for (int x = 0; x < sizeX; x++)
+            {
+                int label = (int) image.getf(x, y);
+
+                // no need to process background pixels
+                if (label == 0)
+                {
+                    continue;
+                }
+
+                // iterate over neighbors defined by strel
+                for (int[] shift : shifts)
+                {
+                    // position of neighbor
+                    int x2 = x + shift[0];
+                    int y2 = y + shift[1];
+
+                    // do not process pixels outside of image bounds
+                    if (x2 < 0 || x2 >= sizeX) continue;
+                    if (y2 < 0 || y2 >= sizeY) continue;
+
+                    // check if neighbor is background
+                    int label2 = (int) image.getf(x2, y2);
+                    if (label2 == 0)
+                    {
+                        label = 0;
+                        break;
+                    }
+                }
+
+                res.setf(x, y, label);
+            }
+        }
+
+        return res;
+    }
+}

src/main/java/inra/ijpb/label/filter/ChamferLabelErosion3DShort.java

@@ -0,0 +1,104 @@
+/**
+ * 
+ */
+package inra.ijpb.label.filter;
+
+import ij.ImageStack;
+import inra.ijpb.algo.AlgoStub;
+import inra.ijpb.binary.distmap.ChamferMask3D;
+import inra.ijpb.morphology.Strel3D;
+import inra.ijpb.morphology.strel.ChamferStrel3D;
+
+/**
+ * Implementation of morphological erosion for 3D label images / label maps.
+ * 
+ * Can be applied to label maps encoded with 8 or 16 bits integers, or 32 bit
+ * floats.
+ * 
+ * 
+ * @author dlegland
+ *
+ */
+public class ChamferLabelErosion3DShort extends AlgoStub
+{
+    /**
+     * The chamfer mask used to propagate distances.
+     */
+    ChamferMask3D mask;
+
+    /**
+     * The radius of dilation of labels. In practice, the distance is propagated
+     * up to radius + 0.5.
+     */
+    double radius;
+
+    /**
+     * For erosion, we can work only with the structuring element.
+     */
+    Strel3D strel;
+
+    public ChamferLabelErosion3DShort(ChamferMask3D mask, double radius)
+    {
+        this.mask = mask;
+        this.radius = radius;
+
+        this.strel = new ChamferStrel3D(mask, radius);
+    }
+
+    public ImageStack process(ImageStack image)
+    {
+        // retrieve image size
+        int sizeX = image.getWidth();
+        int sizeY = image.getHeight();
+        int sizeZ = image.getSize();
+
+        // allocate memory for output
+        ImageStack res = ImageStack.create(sizeX, sizeY, sizeZ, image.getBitDepth());
+
+        // pre-compute strel shifts
+        int[][] shifts = strel.getShifts3D();
+
+        // iterate over pixels within output image
+        for (int z = 0; z < sizeZ; z++)
+        {
+            for (int y = 0; y < sizeY; y++)
+            {
+                for (int x = 0; x < sizeX; x++)
+                {
+                    int label = (int) image.getVoxel(x, y, z);
+
+                    // no need to process background pixels
+                    if (label == 0)
+                    {
+                        continue;
+                    }
+
+                    // iterate over neighbors defined by strel
+                    for (int[] shift : shifts)
+                    {
+                        // position of neighbor
+                        int x2 = x + shift[0];
+                        int y2 = y + shift[1];
+                        int z2 = z + shift[2];
+
+                        // do not process pixels outside of image bounds
+                        if (x2 < 0 || x2 >= sizeX) continue;
+                        if (y2 < 0 || y2 >= sizeY) continue;
+                        if (z2 < 0 || z2 >= sizeZ) continue;
+
+                        // check if neighbor is background
+                        int label2 = (int) image.getVoxel(x2, y2, z2);
+                        if (label2 == 0)
+                        {
+                            label = 0;
+                            break;
+                        }
+                    }
+
+                    res.setVoxel(x, y, z, label);
+                }
+            }
+        }
+        return res;
+    }
+}

src/main/java/inra/ijpb/morphology/strel/AbstractStrel3D.java

@@ -147,7 +147,7 @@ public ImageStack dilation(ImageStack image)
 	    int sizeZ = image.getSize();
 
 	    // allocate result
-	    ImageStack res = ImageStack.create(sizeX, sizeX, sizeZ, image.getBitDepth());
+	    ImageStack res = ImageStack.create(sizeX, sizeY, sizeZ, image.getBitDepth());
 
 	    // iterate over pixels
 	    int[][] shifts = getShifts3D();
@@ -201,7 +201,7 @@ public ImageStack erosion(ImageStack image)
 	    int sizeZ = image.getSize();
 
 	    // allocate result
-	    ImageStack res = ImageStack.create(sizeX, sizeX, sizeZ, image.getBitDepth());
+	    ImageStack res = ImageStack.create(sizeX, sizeY, sizeZ, image.getBitDepth());
 
 	    // iterate over pixels
 	    int[][] shifts = getShifts3D();