Mercurial > repos > imgteam > 2d_simple_filter
view filter_image.py @ 1:dba87c4b32d3 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit 8e0d09b4c4eadfaaf125f4a0ae7dcbd1bee5ee51
author | imgteam |
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date | Thu, 18 Jul 2019 08:51:58 -0400 |
parents | f264ae82f735 |
children | f70b215d155c |
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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 from skimage import img_as_uint 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 = img_as_uint(filterOptions[args.filter_type](img_in, args.radius)) skimage.io.imsave(args.out_file.name, res, plugin='tifffile')