Mercurial > repos > thomaswollmann > wsi_extract_top_view

annotate wsi_extract_top_view.py @ 0:9f01fd145af4 draft

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