Function create_tissue_tiles

extract_features.py:369–422

(wsi, tissue_mask_scaled, tile_size_microns, offsets_micron=None)

    return tissue_mask_scaled

def create_tissue_tiles(wsi, tissue_mask_scaled, tile_size_microns, offsets_micron=None):

    print(f"tile size is {tile_size_microns} um")

    # Compute the tile size in pixels from the desired tile size in microns and the image resolution
    assert (
        openslide.PROPERTY_NAME_MPP_X in wsi.properties
    ), "microns per pixel along X-dimension not available"
    assert (
        openslide.PROPERTY_NAME_MPP_Y in wsi.properties
    ), "microns per pixel along Y-dimension not available"

    mpp_x = float(wsi.properties[openslide.PROPERTY_NAME_MPP_X])
    mpp_y = float(wsi.properties[openslide.PROPERTY_NAME_MPP_Y])

    # For larger tiles in micron, NKI scanner outputs mppx slight different than mppy.
    # Force tiles to be squared.
    mpp_scale_factor = min(mpp_x, mpp_y)
    if mpp_x != mpp_y:
        print(
            f"mpp_x of {mpp_x} and mpp_y of {mpp_y} are not the same. Using smallest value: {mpp_scale_factor}"
        )

    tile_size_pix = round(tile_size_microns / mpp_scale_factor)

    # Use the tissue mask bounds as base offsets (+ a margin of a few tiles) to avoid wasting CPU power creating tiles that are never going
    # to be inside the tissue mask.
    tissue_margin_pix = tile_size_pix * 2
    minx, miny, maxx, maxy = tissue_mask_scaled.bounds
    min_offset_x = minx - tissue_margin_pix
    min_offset_y = miny - tissue_margin_pix
    offsets = [(min_offset_x, min_offset_y)]

    if offsets_micron is not None:
        assert (
            len(offsets_micron) > 0
        ), "offsets_micron needs to contain at least one value"
        # Compute the offsets in micron scale
        offset_pix = [round(o / mpp_scale_factor) for o in offsets_micron]
        offsets = [(o + min_offset_x, o + min_offset_y) for o in offset_pix]

    # Generate tiles covering the entire WSI
    all_tiles = generate_tiles(
        tile_size_pix,
        tile_size_pix,
        maxx + tissue_margin_pix,
        maxy + tissue_margin_pix,
        offsets=offsets,
    )

    # Retain only the tiles that sit within the tissue mask polygon
    filtered_tiles = [rect for rect in all_tiles if tissue_mask_scaled.intersects(rect)]

    return filtered_tiles

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