view permutate_axis.py @ 3:7e7215e721af draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:11:38 +0000
parents 91e255c78eb5
children
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import argparse
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)