Mercurial > repos > imgteam > concat_channels

changeset 2:212627bfb759 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:47 +0000
parents d42501109c05
children 4c43875c790c
files concat_channels.py concat_channels.xml
diffstat 2 files changed, 13 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/concat_channels.py	Mon Jul 22 05:02:26 2019 -0400
+++ b/concat_channels.py	Mon Nov 13 22:10:47 2023 +0000
@@ -1,33 +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] 
+                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
+        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')
+    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)
--- a/concat_channels.xml	Mon Jul 22 05:02:26 2019 -0400
+++ b/concat_channels.xml	Mon Nov 13 22:10:47 2023 +0000
@@ -1,5 +1,11 @@
-<tool id="ip_concat_channels" name="Concatenate images" version="0.2"> 
+<tool id="ip_concat_channels" name="Concatenate images or channels" version="0.2-2">
     <description></description>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="0.14.2">scikit-image</requirement>
         <requirement type="package" version="1.15.4">numpy</requirement>