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annotate split.py @ 0:6b42bec75e69 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
author imgteam
date Fri, 07 Mar 2025 08:08:05 +0000
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children 73d7a4ffc03d
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6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
1 import argparse
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
2 import math
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
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3
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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4 import giatools
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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5 import giatools.util
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
6 import numpy as np
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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7 import tifffile
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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8
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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9
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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10 parser = argparse.ArgumentParser()
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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11 parser.add_argument('input', type=str)
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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12 parser.add_argument('axis', type=str)
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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13 parser.add_argument('output', type=str)
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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14 parser.add_argument('--squeeze', action='store_true', default=False)
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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15 args = parser.parse_args()
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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17 # Validate and normalize input parameters
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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18 assert len(args.axis) == 1, 'Axis input must be a single character.'
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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19 axis = args.axis.replace('S', 'C')
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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21 # Read input image as TZYXC
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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22 img_in = giatools.Image.read(args.input)
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
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6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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24 # Determine the axis to split along
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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25 axis_pos = img_in.axes.index(axis)
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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27 # Perform the splitting
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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28 arr = np.moveaxis(img_in.data, axis_pos, 0)
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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29 decimals = math.ceil(math.log10(1 + arr.shape[0]))
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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30 output_filename_pattern = f'{args.output}/%0{decimals}d.tiff'
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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31 for img_idx, img in enumerate(arr):
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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32 img = np.moveaxis(img[None], 0, axis_pos)
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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34 # Optionally, squeeze the image
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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35 if args.squeeze:
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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36 s = [axis_pos for axis_pos in range(len(img_in.axes)) if img.shape[axis_pos] == 1 and img_in.axes[axis_pos] not in 'YX']
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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37 img = np.squeeze(img, axis=tuple(s))
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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38 img_axes = giatools.util.str_without_positions(img_in.axes, s)
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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39 else:
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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40 img_axes = img_in.axes
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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42 # Save the result
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
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43 filename = output_filename_pattern % (img_idx + 1)
6b42bec75e69 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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44 tifffile.imwrite(filename, img, metadata=dict(axes=img_axes))