How to crop away convexity defects?

I'm trying to detect and fine-locate some objects in images from contours. The contours that I get often include some noise (maybe form the background, I don't know). The objects should look similar to rectangles or squares like:

I get very good results with shape matching (cv::matchShapes) to detect contours with those objects in them, with and without noise, but I have problems with the fine-location in case of noise.

Noise looks like:

or for example.

My idea was to find convexity defects and if they become too strong, somehow crop away the part that leads to concavity. Detecting the defects is ok, typically I get two defects per "unwanted structure", but I'm stuck on how to decide what and where I should remove points from the contours.

Here are some contours, their masks (so you can extract the contours easily) and the convex hull including thresholded convexity defects:

Could I just walk through the contour and locally decide whether a "left turn" is performed by the contour (if walking clockwise) and if so, remove contour points until the next left turn is taken? Maybe starting at a convexity defect?

I'm looking for algorithms or code, programming language should not be important, algorithm is more important.

This approach works only on points. You don't need to create masks for this.

The main idea is:

1. Find defects on contour
2. If I find at least two defects, find the two closest defects
3. Remove from the contour the points between the two closest defects
4. Restart from 1 on the new contour

I get the following results. As you can see, it has some drawbacks for smooth defects (e.g. 7th image), but works pretty good for clearly visible defects. I don't know if this will solve your problem, but can be a starting point. In practice should be quite fast (you can surely optimize the code below, specially the removeFromContour function). Also, the only parameter of this approach is the amount of the convexity defect, so it works well with both small and big defecting blobs.

#include <opencv2/opencv.hpp>
using namespace cv;
using namespace std;

int ed2(const Point& lhs, const Point& rhs)
{
    return (lhs.x - rhs.x)*(lhs.x - rhs.x) + (lhs.y - rhs.y)*(lhs.y - rhs.y);
}

vector<Point> removeFromContour(const vector<Point>& contour, const vector<int>& defectsIdx)
{
    int minDist = INT_MAX;
    int startIdx;
    int endIdx;

    // Find nearest defects
    for (int i = 0; i < defectsIdx.size(); ++i)
    {
        for (int j = i + 1; j < defectsIdx.size(); ++j)
        {
            float dist = ed2(contour[defectsIdx[i]], contour[defectsIdx[j]]);
            if (minDist > dist)
            {
                minDist = dist;
                startIdx = defectsIdx[i];
                endIdx = defectsIdx[j];
            }
        }
    }

    // Check if intervals are swapped
    if (startIdx <= endIdx)
    {
        int len1 = endIdx - startIdx;
        int len2 = contour.size() - endIdx + startIdx;
        if (len2 < len1)
        {
            swap(startIdx, endIdx);
        }
    }
    else
    {
        int len1 = startIdx - endIdx;
        int len2 = contour.size() - startIdx + endIdx;
        if (len1 < len2)
        {
            swap(startIdx, endIdx);
        }
    }

    // Remove unwanted points
    vector<Point> out;
    if (startIdx <= endIdx)
    {
        out.insert(out.end(), contour.begin(), contour.begin() + startIdx);
        out.insert(out.end(), contour.begin() + endIdx, contour.end());
    } 
    else
    {
        out.insert(out.end(), contour.begin() + endIdx, contour.begin() + startIdx);
    }

    return out;
}

int main()
{
    Mat1b img = imread("path_to_mask", IMREAD_GRAYSCALE);

    Mat3b out;
    cvtColor(img, out, COLOR_GRAY2BGR);

    vector<vector<Point>> contours;
    findContours(img.clone(), contours, RETR_EXTERNAL, CHAIN_APPROX_NONE);

    vector<Point> pts = contours[0];

    vector<int> hullIdx;
    convexHull(pts, hullIdx, false);

    vector<Vec4i> defects;
    convexityDefects(pts, hullIdx, defects);

    while (true)
    {
        // For debug
        Mat3b dbg;
        cvtColor(img, dbg, COLOR_GRAY2BGR);

        vector<vector<Point>> tmp = {pts};
        drawContours(dbg, tmp, 0, Scalar(255, 127, 0));

        vector<int> defectsIdx;
        for (const Vec4i& v : defects)
        {
            float depth = float(v[3]) / 256.f;
            if (depth > 2) //  filter defects by depth
            {
                // Defect found
                defectsIdx.push_back(v[2]);

                int startidx = v[0]; Point ptStart(pts[startidx]);
                int endidx = v[1]; Point ptEnd(pts[endidx]);
                int faridx = v[2]; Point ptFar(pts[faridx]);

                line(dbg, ptStart, ptEnd, Scalar(255, 0, 0), 1);
                line(dbg, ptStart, ptFar, Scalar(0, 255, 0), 1);
                line(dbg, ptEnd, ptFar, Scalar(0, 0, 255), 1);
                circle(dbg, ptFar, 4, Scalar(127, 127, 255), 2);
            }
        }

        if (defectsIdx.size() < 2)
        {
            break;
        }

        // If I have more than two defects, remove the points between the two nearest defects
        pts = removeFromContour(pts, defectsIdx);
        convexHull(pts, hullIdx, false);
        convexityDefects(pts, hullIdx, defects);
    }


    // Draw result contour
    vector<vector<Point>> tmp = { pts };
    drawContours(out, tmp, 0, Scalar(0, 0, 255), 1);

    imshow("Result", out);
    waitKey();

    return 0;
}

---

UPDATE

Working on an approximated contour (e.g. using CHAIN_APPROX_SIMPLE in findContours) may be faster, but the length of contours must be computed using arcLength().

This is the snippet to replace in the swapping part of removeFromContour:

// Check if intervals are swapped
if (startIdx <= endIdx)
{
    //int len11 = endIdx - startIdx;
    vector<Point> inside(contour.begin() + startIdx, contour.begin() + endIdx);
    int len1 = (inside.empty()) ? 0 : arcLength(inside, false);

    //int len22 = contour.size() - endIdx + startIdx;
    vector<Point> outside1(contour.begin(), contour.begin() + startIdx);
    vector<Point> outside2(contour.begin() + endIdx, contour.end());
    int len2 = (outside1.empty() ? 0 : arcLength(outside1, false)) + (outside2.empty() ? 0 : arcLength(outside2, false));

    if (len2 < len1)
    {
        swap(startIdx, endIdx);
    }
}
else
{
    //int len1 = startIdx - endIdx;
    vector<Point> inside(contour.begin() + endIdx, contour.begin() + startIdx);
    int len1 = (inside.empty()) ? 0 : arcLength(inside, false);


    //int len2 = contour.size() - startIdx + endIdx;
    vector<Point> outside1(contour.begin(), contour.begin() + endIdx);
    vector<Point> outside2(contour.begin() + startIdx, contour.end());
    int len2 = (outside1.empty() ? 0 : arcLength(outside1, false)) + (outside2.empty() ? 0 : arcLength(outside2, false));

    if (len1 < len2)
    {
        swap(startIdx, endIdx);
    }
}