diff filter_image.py @ 0:f264ae82f735 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581

--- /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')