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The issue above is entirely in the python <-> c++ cv::Rect conversion. In python, the list[4] is x, y, height, width, not x1, y1, x2, y2 (as I was led to believed by a bug in the code I was porting).
The code above works correctly if I change the following lines.
While printing:
out << '[' << rectangles[i].tl().x << ',' << rectangles[i].tl().y << ',' << rectangles[i].width << ',' << rectangles[i].height << ']';
While constructing the cv::Rect:
return cv::Rect((int)coord[0], (int)coord[1], (int)coord[2], (int)coord[3]);