comparison wsi_extract_top_view.py @ 0:9f01fd145af4 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
author thomaswollmann
date Mon, 07 Jan 2019 08:38:08 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9f01fd145af4
1 import argparse
2 import openslide
3 import os
4 import fnmatch
5 import skimage.io
6 import numpy as np
7
8 def wsi_extract_top_view(input_path, out_path):
9 img_raw = openslide.OpenSlide(input_path)
10 top_size = img_raw.level_dimensions[len(img_raw.level_dimensions)-1]
11 img_area = img_raw.read_region((0,0), len(img_raw.level_dimensions)-1, top_size)
12 img_area = np.asarray(img_area, dtype=np.uint8)
13 skimage.io.imsave(out_path, img_area, plugin="tifffile")
14
15
16 if __name__ == "__main__":
17 parser = argparse.ArgumentParser()
18 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
19 parser.add_argument('out_file', help='out file')
20 args = parser.parse_args()
21
22 wsi_extract_top_view(args.input_file.name, args.out_file)