Mercurial > repos > imgteam > 2d_simple_filter
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_image.py Sat Feb 09 14:29:13 2019 -0500 @@ -0,0 +1,34 @@ +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')