Mercurial > repos > imgteam > wsi_extract_top_view
comparison wsi_extract_top_view.py @ 0:a1d02d2e814a draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
| author | imgteam |
|---|---|
| date | Sat, 09 Feb 2019 14:49:03 -0500 |
| parents | |
| children | cfe88c6041e9 |
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| -1:000000000000 | 0:a1d02d2e814a |
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| 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) |