Mercurial > repos > imgteam > wsi_extract_top_view

annotate 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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a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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2 import openslide
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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3 import os
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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4 import fnmatch
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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5 import skimage.io
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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6 import numpy as np
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cfe88c6041e9 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 0
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a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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8 def wsi_extract_top_view(input_path, out_path):
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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9 img_raw = openslide.OpenSlide(input_path)
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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10 top_size = img_raw.level_dimensions[len(img_raw.level_dimensions)-1]
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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11 img_area = img_raw.read_region((0,0), len(img_raw.level_dimensions)-1, top_size)
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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12 img_area = np.asarray(img_area, dtype=np.uint8)
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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13 skimage.io.imsave(out_path, img_area, plugin="tifffile")
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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16 if __name__ == "__main__":
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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17 parser = argparse.ArgumentParser()
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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18 parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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19 parser.add_argument('out_file', help='out file')
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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20 args = parser.parse_args()
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cfe88c6041e9 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 0
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a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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22 wsi_extract_top_view(args.input_file.name, args.out_file)