diff concat_channels.py @ 3:4c43875c790c draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit c045f067a57e8308308cf6329060c7ccd3fc372f

--- a/concat_channels.py	Mon Nov 13 22:10:47 2023 +0000
+++ b/concat_channels.py	Thu Apr 04 15:25:29 2024 +0000
@@ -1,33 +1,42 @@
 import argparse
-import warnings
 
 import numpy as np
 import skimage.io
 import skimage.util
 
 
-def concat_channels(input_image_paths, output_image_path, axis):
+def concat_channels(input_image_paths, output_image_path, axis, preserve_values):
     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)
+
+        # Preserve values: Convert to `float` dtype without changing the values
+        if preserve_values:
+            raw_image = raw_image.astype(float)
+
+        # Preserve brightness: Scale values to 0..1
+        else:
+            raw_image = skimage.util.img_as_float(raw_image)
+
         images.append(raw_image)
+
+    # Do the concatenation and save
     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')
+    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('input_files', type=argparse.FileType('r'), nargs='+')
+    parser.add_argument('-o', dest='out_file', type=argparse.FileType('w'))
+    parser.add_argument('--axis', dest='axis', type=int, default=0, choices=[0, 2])
+    parser.add_argument('--preserve_values', default=False, action='store_true')
     args = parser.parse_args()
 
-    concat_channels([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, args.preserve_values)