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This issue was being caused by a bug in OpenCV 3.1.0 - https://github.com/Itseez/opencv/issu....

By reverting my OpenCV version back to 2.4.9, the program works properly again.

yes. Right now im on Windows, and I have some system limitations, so I'll just have to revert back to 2.4.9 for now

Thank you. About when will a version with this fixed be released?

First off, I am using the OpenCV 3.1.0 Java wrapper (NOT JavaCV).

I am trying to find the convexity defects on a hand, but it is not giving the expected results. For examples, here is a binary image of a hand:

(The white lines show the convex hull, and the blue lines show the contour that I am working with).

Here is the same image showing the attempted convexity defect detection:

(blue dots show defects, and pink lines show the resulting shape)

As you can see, the defect between the index and thumb is not being detected.

Here is my code:

    ...
    hull = new MatOfInt();

    Imgproc.convexHull(approxContour, hull, false);

    MatOfInt4 defects = new MatOfInt4();
    Imgproc.convexityDefects(approxContour, hull, defects);

    numPoints = defects.total();
    if (numPoints > max_points) {
        System.out.println("Processing " + max_points + " defect pts");
        numPoints = max_points;
    }

    for (int i = 0; i < numPoints; i++) {
        double[] dat = defects.get(i, 0);

        double[] startdat = approxContour.get((int) dat[0], 0);

        Point startPt = new Point(startdat[0], startdat[1]);

        tipPts[i] = startPt;

        double[] enddat = approxContour.get((int) dat[1], 0);
        endPts[i] = new Point(enddat[0], enddat[1]);

        double[] depthdat = approxContour.get((int) dat[2], 0);
        Point depthPt = new Point(depthdat[0], depthdat[1]);
        foldPts[i] = depthPt;

        depths[i] = dat[3];
    }
    ...
    for (int i = 0; i < numPoints; i++) {
        Imgproc.circle(im, tipPts[i], 2, new Scalar(0, 0, 255));
        Imgproc.circle(im, foldPts[i], 2, new Scalar(255, 0, 0));
        Imgproc.circle(im, endPts[i], 2, new Scalar(0, 255, 0));
        Imgproc.line(im, tipPts[i], foldPts[i], new Scalar(255, 0, 255));
        Imgproc.line(im, tipPts[i], endPts[i], new Scalar(255, 255, 255));
        Imgproc.line(im, endPts[i], foldPts[i], new Scalar(255, 0, 255));
    }