Mercurial > repos > imgteam > 2d_histogram_equalization

annotate histogram_equalization.py @ 1:77f7159d775a draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:25 +0000
parents 70316d792fc9
children b1c2c210813c
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70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
1 import argparse
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
2 import sys
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77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
4 import skimage.exposure
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70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
5 import skimage.io
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
6 import skimage.util
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
8 hOptions = {
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77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
9 'default': lambda img_raw: skimage.exposure.equalize_hist(img_raw),
77f7159d775a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
10 'clahe': lambda img_raw: skimage.exposure.equalize_adapthist(img_raw)
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70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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11 }
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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13 if __name__ == "__main__":
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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14 parser = argparse.ArgumentParser(description='Histogram equalization')
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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15 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
16 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
17 parser.add_argument('h_type', choices=hOptions.keys(), help='histogram equalization method')
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
18 args = parser.parse_args()
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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20 img_in = skimage.io.imread(args.input_file.name)
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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21 res = hOptions[args.h_type](img_in)
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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22 res = skimage.util.img_as_uint(res)
70316d792fc9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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23 skimage.io.imsave(args.out_file.name, res, plugin="tifffile")