Function construct_polygon

extract_features.py:253–296

(foreground_contours, hole_contours, min_area)

    return foreground_contours, hole_contours

def construct_polygon(foreground_contours, hole_contours, min_area):
    polys = []
    for foreground, holes in zip(foreground_contours, hole_contours):
        # We remove all contours that consist of fewer than 3 points, as these won't work with the Polygon constructor.
        if len(foreground) < 3:
            continue

        # remove redundant dimensions from the contour and convert to Shapely Polygon
        poly = Polygon(np.squeeze(foreground))

        # discard all polygons that are considered too small
        if poly.area < min_area:
            continue

        if not poly.is_valid:
            # This is likely becausee the polygon is self-touching or self-crossing.
            # Try and 'correct' the polygon using the zero-length buffer() trick.
            # See https://shapely.readthedocs.io/en/stable/manual.html#object.buffer
            poly = poly.buffer(0)

        # Punch the holes in the polygon
        for hole_contour in holes:
            if len(hole_contour) < 3:
                continue

            hole = Polygon(np.squeeze(hole_contour))

            if not hole.is_valid:
                continue

            # ignore all very small holes
            if hole.area < min_area:
                continue

            poly = poly.difference(hole)

        polys.append(poly)

    if len(polys) == 0:
        raise Exception("Raw tissue mask consists of 0 polygons")

    # If we have multiple polygons, we merge any overlap between them using unary_union().
    # This will result in a Polygon or MultiPolygon with most tissue masks.
    return unary_union(polys)

def generate_tiles(tile_width_pix, tile_height_pix, img_width, img_height, offsets=[(0, 0)]):
    # Generate tiles covering the entire image.