examples.py

from wsi_tile_cleanup import filters, utils

# pen marks and black artifacts

tile_path = "data/images/tiles/3.jpeg"
print(tile_path)
vi_tile = utils.read_image(tile_path)

bands = utils.split_rgb(vi_tile)

colors = ["red", "green", "blue"]

for color in colors:
    perc = filters.pen_percent(bands, color)
    print(f"{color}: {perc*100:.3f}%")

perc = filters.blackish_percent(bands)
print(f"blackish: {perc*100:.3f}%")


# background (via otsu)

wsi_path = "data/images/wsi/TCGA-A1-A0SB-01Z-00-DX1.B34C267B-CAAA-4AB6-AD5C-276C26F997A1.svs-level=2.jpg"
print(wsi_path)
vi_wsi = utils.read_image(wsi_path, access="sequential")

otsu = filters.otsu_threshold(vi_wsi)
print(f"otsu_threshold: {otsu}")

tile_bg = "data/images/tiles/20_15.png"
print(tile_bg)
vi_bg = utils.read_image(tile_bg)

perc = filters.background_percent(vi_bg, otsu)
print(f"background: {perc*100:.3f}%")