Mercurial > repos > imgteam > concat_channels
changeset 5:8d50a0a9e4af draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit 4573c7c050968a40f6377a95727694105fbd69c7
| author | imgteam |
|---|---|
| date | Sun, 07 Dec 2025 16:16:03 +0000 |
| parents | 2592a29a785e |
| children | |
| files | concat_channels.py concat_channels.xml creators.xml |
| diffstat | 3 files changed, 104 insertions(+), 32 deletions(-) [+] |
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--- 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, + )
--- a/concat_channels.xml Wed Apr 24 08:12:22 2024 +0000 +++ b/concat_channels.xml Sun Dec 07 16:16:03 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="ip_concat_channels" name="Concatenate images or channels" version="0.3-1" profile="20.05"> +<tool id="ip_concat_channels" name="Concatenate images or channels" version="0.4" profile="20.05"> <description></description> <macros> <import>creators.xml</import> @@ -14,10 +14,10 @@ <xref type="bio.tools">galaxy_image_analysis</xref> </xrefs> <requirements> - <requirement type="package" version="0.18.3">scikit-image</requirement> - <requirement type="package" version="1.24.1">numpy</requirement> - <requirement type="package" version="2021.7.2">tifffile</requirement> - <requirement type="package" version="0.1">giatools</requirement> + <requirement type="package" version="0.25.2">scikit-image</requirement> + <requirement type="package" version="2.3.5">numpy</requirement> + <requirement type="package" version="2025.10.16">tifffile</requirement> + <requirement type="package" version="0.4.1">giatools</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ @@ -27,15 +27,23 @@ '$input' #end for - $mode + '$output' + '$axis' - -o '$output' --axis '$axis' + $mode ]]></command> <inputs> <param name="inputs" type="data" multiple="true" format="tiff,png" label="Images to concatenate"/> - <param name="axis" type="integer" min="0" value="0" label="Concatenation axis" help="The images will be concatenated along this axis. For a 2-D image, a value of 0 corresponds to horizontal concatenation, and a value of 1 to vertical concatenation. For an RGB image, a value of 2 corresponds to concatenation of the channels of the images."/> - <param name="mode" type="select" label="Scaling of values" help="If the brightness is to be preserved (default), then the values will be scaled between 0 and 1, and the pixel type will be float."> + <param name="axis" type="select" label="Concatenation axis" help="The images will be concatenated along this axis."> + <option value="X">X-axis (concatenate images or image sequences horizontally)</option> + <option value="Y">Y-axis (concatenate images or image sequences vertically)</option> + <option value="T">T-axis (concatenate images as frames of a temporal image sequence)</option> + <option value="Z">Z-axis (concatenate images as slices of a 3-D image or image sequence)</option> + <option value="C" selected="true">C-axis (concatenate the channels/samples of images or image sequences)</option> + <option value="Q">Q-axis (concatenate along other or unknown axis)</option> + </param> + <param name="mode" type="select" label="Scaling of values" help="If the brightness is to be preserved (default), then the values will be scaled between 0 and 1, and a floating point pixel data type will be used."> <option value="" selected="true">Preserve brightness</option> <option value="--preserve_values">Preserve range of values</option> </param> @@ -44,17 +52,17 @@ <data format="tiff" name="output"/> </outputs> <tests> - <!-- Test with "preserve brightness" --> + <!-- Test with "preserve brightness", vertical concatenation --> <test> <param name="inputs" value="input1_uint8.png,input2_float.tiff"/> - <param name="axis" value="0"/> + <param name="axis" value="Y"/> <param name="mode" value=""/> <expand macro="tests/intensity_image_diff" name="output" value="res_preserve_brightness.tiff" ftype="tiff"/> </test> - <!-- Test with "preserve range of values" --> + <!-- Test with "preserve range of values", vertical concatenation --> <test> <param name="inputs" value="input1_uint8.png,input2_float.tiff"/> - <param name="axis" value="0"/> + <param name="axis" value="Y"/> <param name="mode" value="--preserve_values"/> <expand macro="tests/intensity_image_diff" name="output" value="res_preserve_values.tiff" ftype="tiff"> <!-- @@ -70,6 +78,34 @@ <has_image_mean_intensity min="0" max="255"/> </expand> </test> + <!-- Test concatenation of channels (axis *exists* in both images) --> + <test> + <param name="inputs" value="input1_uint8.png,input2_float.tiff"/> + <param name="axis" value="C"/> + <output name="output" ftype="tiff"> + <assert_contents> + <has_image_width width="119"/> + <has_image_height height="119"/> + <has_image_depth depth="1"/> + <has_image_channels channels="8"/> + <has_image_frames frames="1"/> + </assert_contents> + </output> + </test> + <!-- Test concatenation of frames (axis *does not* exist in both images) --> + <test> + <param name="inputs" value="input1_uint8.png,input2_float.tiff"/> + <param name="axis" value="T"/> + <output name="output" ftype="tiff"> + <assert_contents> + <has_image_width width="119"/> + <has_image_height height="119"/> + <has_image_depth depth="1"/> + <has_image_channels channels="4"/> + <has_image_frames frames="2"/> + </assert_contents> + </output> + </test> </tests> <help>
--- a/creators.xml Wed Apr 24 08:12:22 2024 +0000 +++ b/creators.xml Sun Dec 07 16:16:03 2025 +0000 @@ -5,6 +5,16 @@ <yield /> </xml> + <xml name="creators/kostrykin"> + <person givenName="Leonid" familyName="Kostrykin"/> + <yield/> + </xml> + + <xml name="creators/rmassei"> + <person givenName="Riccardo" familyName="Massei"/> + <yield/> + </xml> + <xml name="creators/alliecreason"> <person givenName="Allison" familyName="Creason"/> <yield/> @@ -19,5 +29,15 @@ <person givenName="Till" familyName="Korten"/> <yield/> </xml> - + + <xml name="creators/pavanvidem"> + <person givenName="Pavan" familyName="Videm"/> + <yield/> + </xml> + + <xml name="creators/tuncK"> + <person givenName="Tunc" familyName="Kayikcioglu"/> + <yield/> + </xml> + </macros>