Mercurial > repos > imgteam > wsi_extract_top_view

annotate wsi_extract_top_view.py @ 2:3bd767eee603 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:12:44 +0000
parents cfe88c6041e9
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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
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3bd767eee603 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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3bd767eee603 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
3 import numpy as np
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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
4 import openslide
a1d02d2e814a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
5 import skimage.io
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3bd767eee603 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
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3bd767eee603 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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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
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
parents:
diff changeset
9 img_raw = openslide.OpenSlide(input_path)
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3bd767eee603 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
10 top_size = img_raw.level_dimensions[len(img_raw.level_dimensions) - 1]
3bd767eee603 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
11 img_area = img_raw.read_region((0, 0), len(img_raw.level_dimensions) - 1, top_size)
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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
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:
diff changeset
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:
diff changeset
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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
parents:
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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:
diff changeset
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:
diff changeset
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:
diff changeset
20 args = parser.parse_args()
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3bd767eee603 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
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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
22 wsi_extract_top_view(args.input_file.name, args.out_file)