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comparison 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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-1:000000000000 0:6b42bec75e69
1 import argparse
2 import math
3
4 import giatools
5 import giatools.util
6 import numpy as np
7 import tifffile
8
9
10 parser = argparse.ArgumentParser()
11 parser.add_argument('input', type=str)
12 parser.add_argument('axis', type=str)
13 parser.add_argument('output', type=str)
14 parser.add_argument('--squeeze', action='store_true', default=False)
15 args = parser.parse_args()
16
17 # Validate and normalize input parameters
18 assert len(args.axis) == 1, 'Axis input must be a single character.'
19 axis = args.axis.replace('S', 'C')
20
21 # Read input image as TZYXC
22 img_in = giatools.Image.read(args.input)
23
24 # Determine the axis to split along
25 axis_pos = img_in.axes.index(axis)
26
27 # Perform the splitting
28 arr = np.moveaxis(img_in.data, axis_pos, 0)
29 decimals = math.ceil(math.log10(1 + arr.shape[0]))
30 output_filename_pattern = f'{args.output}/%0{decimals}d.tiff'
31 for img_idx, img in enumerate(arr):
32 img = np.moveaxis(img[None], 0, axis_pos)
33
34 # Optionally, squeeze the image
35 if args.squeeze:
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']
37 img = np.squeeze(img, axis=tuple(s))
38 img_axes = giatools.util.str_without_positions(img_in.axes, s)
39 else:
40 img_axes = img_in.axes
41
42 # Save the result
43 filename = output_filename_pattern % (img_idx + 1)
44 tifffile.imwrite(filename, img, metadata=dict(axes=img_axes))