ImageJ distance map using OpenCV java bindings

src/ImageJ/Dist_OpenCV.java

+import ij.*;
+import ij.plugin.filter.PlugInFilter;
+import ij.process.*;
+import java.awt.*;
+import java.awt.image.*;
+
+import org.opencv.core.Core;
+import org.opencv.core.Mat;
+import org.opencv.core.CvType;
+import org.opencv.imgproc.Imgproc;
+
+public class Dist_OpenCV implements PlugInFilter {
+
+    static{ System.loadLibrary(Core.NATIVE_LIBRARY_NAME); }
+
+    public int setup(String arg, ImagePlus imp) {
+        if (IJ.versionLessThan("1.37j"))
+            return DONE;
+        else    
+            return DOES_ALL+DOES_STACKS+SUPPORTS_MASKING;
+    }
+
+    public void run(ImageProcessor ip) {
+        ImageProcessor ipOut = ip.duplicate();
+        Mat ipMat = ip2mat(ip);
+        Mat ipDist = DistTransform(ipMat);
+        
+        Rectangle r = ip.getRoi();
+        // int pad = r.height % 2;
+        int pad = 0;
+
+        for (int y=r.y; y<(r.y+r.height); y++) {
+            for (int x=r.x; x<(r.x+r.width); x++) {
+                try {
+                    double[] val = ipDist.get(y, x);
+                    ipOut.set(x, y, (int) Math.round(val[0]));
+
+                } catch (IndexOutOfBoundsException e) {
+                    IJ.log(String.format("exception! idx = %d, x = %d, y = %d, pad = %d", x + y*r.width + y * pad, x, y, pad));
+                    throw e;
+                }
+            }
+        }
+        new ImagePlus("Distance Transform", ipOut).show();
+    }
+
+    private Mat ip2mat(ImageProcessor src) {
+        BufferedImage bi = src.getBufferedImage();
+        return bufferedImageToMat(bi);
+    }
+
+    public Mat bufferedImageToMat(BufferedImage bi) {
+        Mat mat = new Mat(bi.getHeight(), bi.getWidth(), CvType.CV_8U);
+        byte[] data = ((DataBufferByte) bi.getRaster().getDataBuffer()).getData();
+        mat.put(0, 0, data);
+        return mat;
+    }
+
+    private Mat DistTransform(Mat matIn) {
+        Mat matOut = new Mat(matIn.size(), CvType.CV_32F);
+        Imgproc.distanceTransform(matIn, matOut, Imgproc.CV_DIST_L2, 3);
+        return matOut;
+    }
+
+    public BufferedImage matToBufferedImage(Mat matrix) {
+        int cols = matrix.cols();
+        int rows = matrix.rows();
+        int elemSize = (int)matrix.elemSize();
+        byte[] data = new byte[cols * rows * elemSize];
+        int type;
+
+        matrix.get(0, 0, data);
+
+        switch (matrix.channels()) {
+            case 1:
+                type = BufferedImage.TYPE_BYTE_GRAY;
+                break;
+
+            case 3: 
+                type = BufferedImage.TYPE_3BYTE_BGR;
+
+                // bgr to rgb
+                byte b;
+                for(int i=0; i<data.length; i=i+3) {
+                    b = data[i];
+                    data[i] = data[i+2];
+                    data[i+2] = b;
+                }
+                break;
+
+            default:
+                return null;
+        }
+
+        BufferedImage image = new BufferedImage(cols, rows, type);
+        image.getRaster().setDataElements(0, 0, cols, rows, data);
+
+        return image;
+    }
+}