Mercurial > repos > thomaswollmann > permutate_axis
changeset 0:8fb82d514666 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
| author | thomaswollmann |
|---|---|
| date | Wed, 12 Dec 2018 04:50:51 -0500 |
| parents | |
| children | |
| files | permutate_axis.py permutate_axis.xml test-data/galaxyIcon_noText.png test-data/galaxyIcon_noText.tif test-data/res.tif |
| diffstat | 5 files changed, 72 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/permutate_axis.py Wed Dec 12 04:50:51 2018 -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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/permutate_axis.xml Wed Dec 12 04:50:51 2018 -0500 @@ -0,0 +1,32 @@ +<tool id="permutate_axis" name="Permutate Axis" version="0.1"> + <description> Permutates axes </description> + <requirements> + <requirement type="package" version="0.14.0">scikit-image</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/permutate_axis.py' '$input' '$output' $permutate --axis $axis + ]]> + </command> + <inputs> + <param name="input" type="data" format="tiff" label="Binary Image File"/> + <param name="permutate" type="text" value="0,1,2" label="new channel order"> + <validator type="regex" message="Input has to be a sequence of axis, separated by commas">([0-4],)+[0-4]</validator> + </param> + <param name="axis" type="integer" value="0" label="concatenation axis" help="Concatenation axis (0-4)" /><!-- why not have a selection from 0 to 4?--> + </inputs> + <outputs> + <data format="tiff" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="galaxyIcon_noText.tif"/> + <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/> + </test> + </tests> + <help>Permutates the image along a specified axis.</help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool> \ No newline at end of file