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annotate split.py @ 2:227e8928af6e draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
author imgteam
date Fri, 12 Dec 2025 21:02:25 +0000
parents 4b7940d0c051
children
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5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
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diff changeset
1 import argparse
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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2 import math
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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3 import os
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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4 import pathlib
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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5 import shutil
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5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
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6
5deaa390ca62 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 giatools
5deaa390ca62 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 import numpy as np
5deaa390ca62 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 import tifffile
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
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5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
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227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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12 class OutputWriter:
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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14 def __init__(self, dir_path: pathlib.Path, num_images: int, squeeze: bool, verbose: bool):
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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15 print(f'Writing {num_images} image(s)')
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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16 decimals = math.ceil(math.log10(1 + num_images))
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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17 self.output_filepath_pattern = str(dir_path / f'%0{decimals}d.tiff')
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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18 self.last_idx = 0
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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19 self.squeeze = squeeze
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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20 self.verbose = verbose
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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22 def write(self, img: giatools.Image):
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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23 self.last_idx += 1
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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24 if self.squeeze:
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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25 img = img.squeeze()
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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26 if self.last_idx == 1 or self.verbose:
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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27 prefix = f'Output {self.last_idx}' if self.verbose else 'Output'
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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28 print(f'{prefix} axes:', img.axes)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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29 print(f'{prefix} shape:', img.data.shape)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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30 img.write(self.output_filepath_pattern % self.last_idx)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
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32
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227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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33 if __name__ == '__main__':
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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35 parser = argparse.ArgumentParser()
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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36 parser.add_argument('input', type=pathlib.Path)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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37 parser.add_argument('axis', type=str, choices=list(giatools.default_normalized_axes) + ['S', ''])
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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38 parser.add_argument('output', type=pathlib.Path)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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39 parser.add_argument('--squeeze', action='store_true', default=False)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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40 args = parser.parse_args()
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5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
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41
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227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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42 # If splitting a file that contains multiple images...
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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43 if args.axis == '':
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5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
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44
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227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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45 # Peek the number of series in the input file (if it is a TIFF)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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46 try:
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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47 with tifffile.TiffFile(args.input) as tiff:
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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48 num_tiff_series = len(tiff.series)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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49 print(f'Found TIFF with {num_tiff_series} series')
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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50 except tifffile.TiffFileError:
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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51 num_tiff_series = 0 # not a TIFF file
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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52 print('Not a TIFF file')
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5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
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53
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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54 # If the file is a multi-series TIFF, extract the individual series
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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55 # (for consistency, also accept only a single series if squeezing is requested)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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56 if num_tiff_series >= 2 or (num_tiff_series == 1 and args.squeeze):
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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57 output = OutputWriter(
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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58 dir_path=args.output,
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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59 num_images=num_tiff_series,
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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60 squeeze=args.squeeze,
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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61 verbose=True,
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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62 )
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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63 for series in range(num_tiff_series):
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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64 img = giatools.Image.read(args.input, series=series)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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65 output.write(
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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66 img.squeeze_like(img.original_axes),
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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67 )
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
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68
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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69 # Otherwise, there is nothing to be split (or squeeze)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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70 # (the input is either a single-series TIFF or not a TIFF at all)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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71 elif num_tiff_series == 1: # input is a single-series TIFF (output = input)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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72 try:
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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73 os.symlink(args.input, args.output / '1.tiff')
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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74 except OSError:
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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75 shutil.copyfile(args.input, args.output / '1.tiff')
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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76 else: # input is not a TIFF, conversion needed
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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77 img = giatools.Image.read(args.input)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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78 OutputWriter(
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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79 dir_path=args.output,
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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80 num_images=1,
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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81 squeeze=args.squeeze,
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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82 verbose=False,
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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83 ).write(
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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84 img.squeeze_like(img.original_axes),
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
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85 )
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
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86
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87 # If splitting along an image axes...
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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88 else:
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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89
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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90 # Validate and normalize input parameters
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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91 axis = args.axis.replace('S', 'C')
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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92
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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93 # Read input image with normalized axes
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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94 img_in = giatools.Image.read(args.input)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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95 print('Input image axes:', img_in.original_axes)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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96 print('Input image shape:', img_in.squeeze_like(img_in.original_axes).data.shape)
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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97
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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98 # Determine the axis to split along
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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99 axis_pos = img_in.axes.index(axis)
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100
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101 # Perform the splitting
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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102 arr = np.moveaxis(img_in.data, axis_pos, 0)
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103 output = OutputWriter(
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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104 dir_path=args.output,
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105 num_images=arr.shape[0],
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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106 squeeze=args.squeeze,
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107 verbose=False,
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108 )
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109 for img_idx, img in enumerate(arr):
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110 img = np.moveaxis(img[None], 0, axis_pos)
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111
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112 # Construct the output image, remove axes added by normalization
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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113 img_out = giatools.Image(
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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114 data=img,
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115 axes=img_in.axes,
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116 metadata=img_in.metadata,
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117 ).squeeze_like(
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118 img_in.original_axes,
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119 )
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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120
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
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121 # Save the result (write stdout during first iteration)
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122 output.write(img_out)