Mercurial > repos > imgteam > wsi_extract_top_view

comparison wsi_extract_top_view.py @ 1:cfe88c6041e9 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:03:44 -0500
parents a1d02d2e814a
children 3bd767eee603
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0:a1d02d2e814a 1:cfe88c6041e9
2 import openslide 2 import openslide
3 import os 3 import os
4 import fnmatch 4 import fnmatch
5 import skimage.io 5 import skimage.io
6 import numpy as np 6 import numpy as np
7 7
8 def wsi_extract_top_view(input_path, out_path): 8 def wsi_extract_top_view(input_path, out_path):
9 img_raw = openslide.OpenSlide(input_path) 9 img_raw = openslide.OpenSlide(input_path)
10 top_size = img_raw.level_dimensions[len(img_raw.level_dimensions)-1] 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) 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) 12 img_area = np.asarray(img_area, dtype=np.uint8)
16 if __name__ == "__main__": 16 if __name__ == "__main__":
17 parser = argparse.ArgumentParser() 17 parser = argparse.ArgumentParser()
18 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file') 18 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
19 parser.add_argument('out_file', help='out file') 19 parser.add_argument('out_file', help='out file')
20 args = parser.parse_args() 20 args = parser.parse_args()
21 21
22 wsi_extract_top_view(args.input_file.name, args.out_file) 22 wsi_extract_top_view(args.input_file.name, args.out_file)