Mercurial > repos > imgteam > 2d_histogram_equalization
comparison histogram_equalization.py @ 0:70316d792fc9 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
| author | imgteam |
|---|---|
| date | Tue, 23 Jul 2019 14:07:07 -0400 |
| parents | |
| children | 77f7159d775a |
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| -1:000000000000 | 0:70316d792fc9 |
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| 1 import argparse | |
| 2 import os | |
| 3 import sys | |
| 4 import skimage.io | |
| 5 import skimage.exposure | |
| 6 import skimage.util | |
| 7 | |
| 8 hOptions = { | |
| 9 'default' : lambda img_raw: skimage.exposure.equalize_hist(img_raw), | |
| 10 'clahe' : lambda img_raw: skimage.exposure.equalize_adapthist(img_raw) | |
| 11 } | |
| 12 | |
| 13 if __name__ == "__main__": | |
| 14 parser = argparse.ArgumentParser(description='Histogram equalization') | |
| 15 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') | |
| 16 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)') | |
| 17 parser.add_argument('h_type', choices=hOptions.keys(), help='histogram equalization method') | |
| 18 args = parser.parse_args() | |
| 19 | |
| 20 img_in = skimage.io.imread(args.input_file.name) | |
| 21 res = hOptions[args.h_type](img_in) | |
| 22 res = skimage.util.img_as_uint(res) | |
| 23 skimage.io.imsave(args.out_file.name, res, plugin="tifffile") |