Mercurial > repos > imgteam > 2d_simple_filter
view filter_image.py @ 0:f264ae82f735 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author | imgteam |
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date | Sat, 09 Feb 2019 14:29:13 -0500 |
parents | |
children | dba87c4b32d3 |
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import argparse import sys import warnings import numpy as np import skimage.io import skimage.filters import skimage.util from skimage.morphology import disk filterOptions = { 'median' : lambda img_raw, radius: skimage.filters.median(img_raw, disk(radius)), 'gaussian' : lambda img_raw, radius: skimage.filters.gaussian(img_raw, sigma=radius), 'prewitt' : lambda img_raw, radius: skimage.filters.prewitt(img_raw), 'sobel' : lambda img_raw, radius: skimage.filters.sobel(img_raw), 'scharr' : lambda img_raw, radius: skimage.filters.scharr(img_raw), } if __name__ == "__main__": parser = argparse.ArgumentParser() 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('filter_type', choices=filterOptions.keys(), help='conversion type') parser.add_argument('radius', default=3.0, type=float, help='Radius/Sigma') args = parser.parse_args() img_in = skimage.io.imread(args.input_file.name) res = filterOptions[args.filter_type](img_in, args.radius) res[res<-1]=-1 res[res>1]=1 with warnings.catch_warnings(): warnings.simplefilter("ignore") res = skimage.util.img_as_uint(res) #Attention: precision loss skimage.io.imsave(args.out_file.name, res, plugin='tifffile')