--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/permutate_axis.py	Sat Feb 09 14:42:29 2019 -0500
@@ -0,0 +1,40 @@
+import argparse
+import sys
+import warnings
+import numpy as np
+import skimage.io
+import skimage.util
+
+def permutate_axis(input_image_path, output_image_path, axis, permutate):
+    images = []
+    raw_image = skimage.io.imread(input_image_path, plugin='tifffile')
+    for i in permutate:
+        # TODO generalise
+        if axis == 0:
+            a_slice = raw_image[i]
+        elif axis == 1:
+            a_slice = raw_image[:,i]
+        elif axis == 2:
+            a_slice = raw_image[:,:,i]
+        elif axis == 3:
+            a_slice = raw_image[:,:,:,i]
+        elif axis == 4:
+            a_slice = raw_image[:,:,:,:,i]
+        images.append(np.expand_dims(a_slice, axis))
+
+    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_file', type=argparse.FileType('r'), help='input file')
+    parser.add_argument('out_file', type=argparse.FileType('w'), help='out file (TIFF)')
+    parser.add_argument('permutate', help='new channel order', default='0,1,2', type=str)
+    parser.add_argument('--axis', dest='axis', type=int, default=0, help='concatenation axis')
+    args = parser.parse_args()
+
+    permutate = [int(item) for item in args.permutate.split(',')]
+    permutate_axis(args.input_file.name, args.out_file.name, args.axis, permutate)