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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
author imgteam
date Fri, 06 Jun 2025 12:46:50 +0000
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f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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diff changeset
1 import argparse
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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2 import os
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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3
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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4 import numpy as np
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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5 from giatools.image import Image
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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6
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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7
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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8 def crop_image(
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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9 image_filepath: str,
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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10 labelmap_filepath: str,
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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11 output_ext: str,
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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12 output_dir: str,
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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13 skip_labels: frozenset[int],
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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14 ):
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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15 image = Image.read(image_filepath)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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16 labelmap = Image.read(labelmap_filepath)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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18 if image.axes != labelmap.axes:
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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19 raise ValueError(f'Axes mismatch between image ({image.axes}) and label map ({labelmap.axes}).')
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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21 if image.data.shape != labelmap.data.shape:
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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22 raise ValueError(f'Shape mismatch between image ({image.data.shape}) and label map ({labelmap.data.shape}).')
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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24 for label in np.unique(labelmap.data):
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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25 if label in skip_labels:
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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26 continue
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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27 roi_mask = (labelmap.data == label)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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28 roi = crop_image_to_mask(image.data, roi_mask)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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29 roi_image = Image(roi, image.axes).normalize_axes_like(image.original_axes)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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30 roi_image.write(os.path.join(output_dir, f'{label}.{output_ext}'))
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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33 def crop_image_to_mask(data: np.ndarray, mask: np.ndarray) -> np.ndarray:
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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34 """
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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35 Crop the `data` array to the minimal bounding box in `mask`.
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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36
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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37 The arguments are not modified.
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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38 """
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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39 assert data.shape == mask.shape
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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40
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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41 # Crop `data` to the convex hull of the mask in each dimension
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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42 for dim in range(data.ndim):
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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43 mask1d = mask.any(axis=tuple(i for i in range(mask.ndim) if i != dim))
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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44 mask1d_indices = np.where(mask1d)[0]
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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45 mask1d_indices_cvxhull = np.arange(min(mask1d_indices), max(mask1d_indices) + 1)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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46 data = data.take(axis=dim, indices=mask1d_indices_cvxhull)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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47
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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48 return data
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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49
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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50
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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51 if __name__ == "__main__":
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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52 parser = argparse.ArgumentParser()
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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53 parser.add_argument('image', type=str)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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54 parser.add_argument('labelmap', type=str)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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55 parser.add_argument('skip_labels', type=str)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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56 parser.add_argument('output_ext', type=str)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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57 parser.add_argument('output_dir', type=str)
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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58 args = parser.parse_args()
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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59
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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60 crop_image(
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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61 image_filepath=args.image,
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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62 labelmap_filepath=args.labelmap,
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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63 output_ext=args.output_ext,
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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64 output_dir=args.output_dir,
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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65 skip_labels=frozenset(
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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66 int(label.strip()) for label in args.skip_labels.split(',') if label.strip()
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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67 ) if args.skip_labels.strip() else frozenset(),
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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68 )