diff scale_image.py @ 0:c4c76f1ebad2 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scale_image.py	Sat Feb 09 14:46:03 2019 -0500
@@ -0,0 +1,44 @@
+import argparse
+import sys
+import skimage.io
+import skimage.transform
+import scipy.misc
+import warnings
+import os
+from PIL import Image
+
+
+def scale_image(input_file, output_file, scale, order=1):
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        Image.MAX_IMAGE_PIXELS = 50000*50000
+        img_in = skimage.io.imread(input_file)
+        if order == 0:
+            interp = 'nearest'
+        elif order == 1:
+            interp = 'bilinear'
+        elif order == 2:
+            interp = 'bicubic'
+
+        if ',' in scale:
+            scale = scale[1:-1].split(',')
+            scale.reverse()
+            scale = [int(i) for i in scale]
+        elif '.' in scale:
+            scale = float(scale)
+        else:
+            scale = int(scale)
+
+        res = scipy.misc.imresize(img_in, scale, interp=interp)
+        skimage.io.imsave(output_file, res)
+
+
+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 (PNG)') 
+    parser.add_argument('scale', type=str, help='fraction scaling factor(float), percentage scaling factor(int), output size(tuple(height,width))') # integer option not implemented in galaxy wrapper
+    parser.add_argument('order', type=int, default=1, help='interpolation method')
+    args = parser.parse_args()
+
+    scale_image(args.input_file.name, args.out_file.name, args.scale, args.order)
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