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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
author imgteam
date Fri, 09 Jan 2026 14:55:04 +0000
parents d52317f0ac21
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d52317f0ac21 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
d52317f0ac21 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
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
imgteam
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4 import dask.array as da
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
imgteam
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5 import giatools
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
imgteam
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6 import giatools.image
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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7 import numpy as np
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2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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9 # Fail early if an optional backend is not available
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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10 giatools.require_backend('omezarr')
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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13 def crop_image(
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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14 image_filepath: str,
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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15 labelmap_filepath: str,
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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16 output_ext: str,
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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17 output_dir: str,
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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18 skip_labels: frozenset[int],
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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19 ):
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2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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20 axes = giatools.default_normalized_axes
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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21 image = giatools.Image.read(image_filepath, normalize_axes=axes)
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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22 labelmap = giatools.Image.read(labelmap_filepath, normalize_axes=axes)
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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24 # Establish compatibility of multi-channel/frame/etc. images with single-channel/frame/etc. label maps
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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25 original_labelmap_shape = labelmap.shape
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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26 for image_s, labelmap_s, (axis_idx, axis) in zip(image.shape, labelmap.shape, enumerate(axes)):
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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27 if image_s > 1 and labelmap_s == 1 and axis not in 'YX':
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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28 target_shape = list(labelmap.shape)
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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29 target_shape[axis_idx] = image_s
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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31 # Broadcast the labelmap data to the target shape without copying
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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32 if hasattr(labelmap.data, 'compute'):
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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33 labelmap.data = da.broadcast_to(labelmap.data, target_shape) # `data` is Dask array
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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34 else:
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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35 labelmap.data = np.broadcast_to(labelmap.data, target_shape, subok=True) # `data` is NumPy array
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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37 # Validate that the shapes of the images are compatible
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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38 if image.shape != labelmap.shape:
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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39 labelmap_shape_str = str(original_labelmap_shape)
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
imgteam
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40 if labelmap.shape != original_labelmap_shape:
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
imgteam
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41 labelmap_shape_str = f'{labelmap_shape_str}, broadcasted to {labelmap.shape}'
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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42 raise ValueError(
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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43 f'Shape mismatch between image {image.shape} and label map {labelmap_shape_str}, with {axes} axes.',
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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44 )
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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45
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46 # Extract the image crops
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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47 for label in giatools.image._unique(labelmap.data):
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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48 if label in skip_labels:
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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49 continue
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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50 roi_mask = (labelmap.data == label)
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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51 roi = crop_image_to_mask(image.data, roi_mask)
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52 roi_image = giatools.Image(roi, image.axes).normalize_axes_like(image.original_axes)
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53 roi_image.write(os.path.join(output_dir, f'{label}.{output_ext}'))
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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56 def crop_image_to_mask(data: np.ndarray, mask: np.ndarray) -> np.ndarray:
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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57 """
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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58 Crop the `data` array to the minimal bounding box in `mask`.
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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59
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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60 The arguments are not modified.
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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61 """
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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62 assert data.shape == mask.shape
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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63
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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64 # Crop `data` to the convex hull of the mask in each dimension
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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65 for dim in range(data.ndim):
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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66 mask1d = mask.any(axis=tuple(i for i in range(mask.ndim) if i != dim))
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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67 mask1d_indices = np.where(mask1d)[0]
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68
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69 # Convert `mask1d_indices` to a NumPy array if it is a Dask array
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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70 if hasattr(mask1d_indices, 'compute'):
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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71 mask1d_indices = mask1d_indices.compute()
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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72
0
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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73 mask1d_indices_cvxhull = np.arange(min(mask1d_indices), max(mask1d_indices) + 1)
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75 # Crop the `data` to the minimal bounding box
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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76 if hasattr(data, 'compute'):
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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77 data = da.take(data, axis=dim, indices=mask1d_indices_cvxhull) # `data` is a Dask array
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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78 else:
2852af87036d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 52a95105291e38f3410e347ed3b60d6acd6d5daa
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79 data = data.take(axis=dim, indices=mask1d_indices_cvxhull) # `data` is a NumPy array
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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81 return data
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d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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84 if __name__ == "__main__":
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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85 parser = argparse.ArgumentParser()
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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86 parser.add_argument('image', type=str)
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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87 parser.add_argument('labelmap', type=str)
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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88 parser.add_argument('skip_labels', type=str)
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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89 parser.add_argument('output_ext', type=str)
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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90 parser.add_argument('output_dir', type=str)
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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91 args = parser.parse_args()
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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92
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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93 crop_image(
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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94 image_filepath=args.image,
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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95 labelmap_filepath=args.labelmap,
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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96 output_ext=args.output_ext,
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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97 output_dir=args.output_dir,
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98 skip_labels=frozenset(
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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99 int(label.strip()) for label in args.skip_labels.split(',') if label.strip()
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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100 ) if args.skip_labels.strip() else frozenset(),
d52317f0ac21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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101 )