diff concat_channels.py @ 0:30517f733f7b draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/concat_channels.py	Sat Feb 09 14:33:14 2019 -0500
@@ -0,0 +1,33 @@
+import argparse
+import sys
+import warnings
+import numpy as np
+import skimage.io
+import skimage.util
+
+def concat_channels(input_image_paths, output_image_path, axis):
+    images = []
+    for image_path in input_image_paths:
+        raw_image = skimage.io.imread(image_path)
+        if len(raw_image.shape) == 2:
+            if axis == 0:
+                raw_image = [raw_image]
+            else:
+                raw_image = np.expand_dims(raw_image, 2)
+        images.append(raw_image)
+    res = np.concatenate(images, axis)
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        res = skimage.util.img_as_uint(res) #Attention: precision loss
+        skimage.io.imsave(output_image_path, res, plugin='tifffile')
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('input_files', type=argparse.FileType('r'), nargs='+', help='input file')
+    parser.add_argument('-o', dest='out_file', type=argparse.FileType('w'), help='out file (TIFF)')
+    parser.add_argument('--axis', dest='axis', type=int, default=0, choices=[0,2], help='concatenation axis')
+    args = parser.parse_args()
+
+    # print([x.name for x in args.input_files], args.out_file.name, args.axis)
+    concat_channels([x.name for x in args.input_files], args.out_file.name, args.axis)
+    # concat_channels(args.input_files, args.out_file, args.axis)