view histogram_equalization.py @ 0:70316d792fc9 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c

import argparse
import os
import sys
import skimage.io
import skimage.exposure
import skimage.util

hOptions = {
    'default' : lambda img_raw: skimage.exposure.equalize_hist(img_raw),
    'clahe' : lambda img_raw: skimage.exposure.equalize_adapthist(img_raw)
}

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description='Histogram equalization')
    parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
    parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
    parser.add_argument('h_type', choices=hOptions.keys(), help='histogram equalization method')
    args = parser.parse_args()

    img_in = skimage.io.imread(args.input_file.name)
    res = hOptions[args.h_type](img_in)
    res = skimage.util.img_as_uint(res)
    skimage.io.imsave(args.out_file.name, res, plugin="tifffile")