npy2dzi.py

import fire

import numpy as np
import PIL
from PIL import Image

import os
import sys
import deepzoom
import time
import shutil

def main(wsi_name, web_dir, shrink_factor=1):
    # disable safety checks for large images
    PIL.Image.MAX_IMAGE_PIXELS = None

    assert(wsi_name[-4:] == ".npy")

    wsi_prefix = wsi_name[:-4]

    prefix_path = os.path.join(web_dir, "images", wsi_prefix)
    npy_path = prefix_path + ".npy"
    png_path = prefix_path + ".png"
    dzi_path = prefix_path + ".dzi"
    base_html_path = "npy2dzi.html"
    new_html_path = os.path.join(web_dir, "index.html")
    openseadragon_src = "openseadragon/"
    openseadragon_dst = os.path.join(web_dir, "openseadragon/")

    iter_name = web_dir[web_dir.rindex("/") + 1:]
    title = iter_name + " " + wsi_name

    START_TIME = time.time()
    print("Loading .npy file")
    img = np.load(npy_path)
    print("Execution time (s):", time.time() - START_TIME)
    print("Done.\n")

    START_TIME = time.time()
    print("Reducing .npy file")
    if shrink_factor == 1:
        comp_img = img
    else:
        comp_img = np.zeros((img.shape[0] // shrink_factor, img.shape[1] // shrink_factor, img.shape[2]), dtype=np.uint32)
        print(comp_img.shape)
        for i in range(shrink_factor):
            j1 = img.shape[0] - img.shape[0] % shrink_factor
            j2 = img.shape[1] - img.shape[1] % shrink_factor
            comp_img += img[i:j1:shrink_factor, i:j2:shrink_factor]
        comp_img //= shrink_factor
    print("Execution time (s):", time.time() - START_TIME)
    print("Done.\n")

    # create png files
    START_TIME = time.time()
    print("Creating .png file")
    Image.fromarray(comp_img.astype(np.uint8)).save(png_path, compress_level=1)
    print("Execution time (s):", time.time() - START_TIME)
    print("Done.\n")

    # create dzi files
    START_TIME = time.time()
    print("Creating .dzi file")
    creator = deepzoom.ImageCreator(
        tile_size=256,
        tile_overlap=0,
        tile_format="png",
        image_quality=1.0,
    )
    creator.create(png_path, dzi_path)
    print("Execution time (s):", time.time() - START_TIME)
    print("Done.\n")

    START_TIME = time.time()
    print("Creating HTML files")
    # create html files
    with open(base_html_path, "r") as f:
        HTML_STR = "".join(f.readlines())
    HTML_STR = HTML_STR.replace("{REPLACE_wsi_prefix}", os.path.join("images", wsi_prefix))
    HTML_STR = HTML_STR.replace("{REPLACE_title}", title)
    with open(new_html_path, "w") as f:
        f.write(HTML_STR)
    # copy openseadragon
    if not os.path.isdir(openseadragon_dst):
        shutil.copytree(openseadragon_src, openseadragon_dst)
    print("Execution time (s):", time.time() - START_TIME)
    print("Done.\n")

if __name__=="__main__":
    fire.Fire(main)