diff concat_channels.py @ 5:8d50a0a9e4af draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7

--- a/concat_channels.py	Wed Apr 24 08:12:22 2024 +0000
+++ b/concat_channels.py	Sun Dec 07 16:16:03 2025 +0000
@@ -1,43 +1,59 @@
 import argparse
 
-import giatools.io
+import giatools
 import numpy as np
 import skimage.io
 import skimage.util
 
 
-def concat_channels(input_image_paths, output_image_path, axis, preserve_values):
+normalized_axes = 'QTZYXC'
+
+
+def concat_channels(
+    input_image_paths: list[str],
+    output_image_path: str,
+    axis: str,
+    preserve_values: bool,
+):
+    # Create list of arrays to be concatenated
     images = []
     for image_path in input_image_paths:
 
-        raw_image = giatools.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)
+        img = giatools.Image.read(image_path, normalize_axes=normalized_axes)
+        arr = img.data
 
         # Preserve values: Convert to `float` dtype without changing the values
         if preserve_values:
-            raw_image = raw_image.astype(float)
+            arr = arr.astype(float)
 
         # Preserve brightness: Scale values to 0..1
         else:
-            raw_image = skimage.util.img_as_float(raw_image)
+            arr = skimage.util.img_as_float(arr)
 
-        images.append(raw_image)
+        images.append(arr)
 
-    # Do the concatenation and save
-    res = np.concatenate(images, axis)
-    skimage.io.imsave(output_image_path, res, plugin='tifffile')
+    # Do the concatenation
+    axis_pos = normalized_axes.index(axis)
+    arr = np.concatenate(images, axis_pos)
+    res = giatools.Image(arr, normalized_axes)
+
+    # Squeeze singleton axes and save
+    squeezed_axes = ''.join(np.array(list(res.axes))[np.array(arr.shape) > 1])
+    res = res.squeeze_like(squeezed_axes)
+    res.write(output_image_path, backend='tifffile')
 
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    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('input_files', type=str, nargs='+')
+    parser.add_argument('out_file', type=str)
+    parser.add_argument('axis', type=str)
     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, args.preserve_values)
+    concat_channels(
+        args.input_files,
+        args.out_file,
+        args.axis,
+        args.preserve_values,
+    )