Function tile_is_not_empty

extract_features.py:424–440

(tile, threshold_white=20)

    return filtered_tiles

def tile_is_not_empty(tile, threshold_white=20):
    histogram = tile.histogram()

    # Take the median of each RGB channel. Alpha channel is not of interest.
    # If roughly each chanel median is below a threshold, i.e close to 0 till color value around 250 (white reference) then tile mostly white.
    whiteness_check = [0, 0, 0]
    for channel_id in (0, 1, 2):
        whiteness_check[channel_id] = np.median(
            histogram[256 * channel_id : 256 * (channel_id + 1)][100:200]
        )

    if all(c <= threshold_white for c in whiteness_check):
        # exclude tile
        return False

    # keep tile
    return True

def crop_rect_from_slide(slide, rect):
    minx, miny, maxx, maxy = rect.bounds