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annotate scale_image.py @ 4:5122286b700e draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
author imgteam
date Sat, 13 Dec 2025 22:11:13 +0000
parents ba2b1a6f1b84
children
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8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
4
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
parents: 3
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2 import json
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8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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3 import sys
4
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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4 from typing import (
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
parents: 3
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5 Any,
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
parents: 3
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6 Literal,
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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7 )
3
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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8
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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9 import giatools.io
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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10 import numpy as np
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8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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11 import skimage.io
8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 import skimage.transform
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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13 import skimage.util
4
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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14
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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16 def get_uniform_scale(
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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17 img: giatools.Image,
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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18 axes: Literal['all', 'spatial'],
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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19 factor: float,
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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20 ) -> tuple[float, ...]:
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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21 """
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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22 Determine a tuple of `scale` factors for uniform or spatially uniform scaling.
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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23
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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24 Axes, that are not present in the original image data, are ignored.
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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25 """
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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26 ignored_axes = [
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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27 axis for axis_idx, axis in enumerate(img.axes)
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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28 if axis not in img.original_axes or (
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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29 factor < 1 and img.data.shape[axis_idx] == 1
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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30 )
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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31 ]
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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32 match axes:
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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33
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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34 case 'all':
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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35 return tuple(
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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36 [
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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37 (factor if axis not in ignored_axes else 1)
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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38 for axis in img.axes if axis != 'C'
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39 ]
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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40 )
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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41
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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42 case 'spatial':
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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43 return tuple(
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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44 [
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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45 (factor if axis in 'YXZ' and axis not in ignored_axes else 1)
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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46 for axis in img.axes if axis != 'C'
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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47 ]
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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48 )
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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49
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50 case _:
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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51 raise ValueError(f'Unknown axes for uniform scaling: "{axes}"')
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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52
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53
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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54 def get_scale_for_isotropy(
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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55 img: giatools.Image,
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56 sample: Literal['up', 'down'],
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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57 ) -> tuple[float, ...]:
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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58 """
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imgteam
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59 Determine a tuple of `scale` factors to establish spatial isotropy.
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60
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61 The `sample` parameter governs whether to up-sample or down-sample the image data.
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imgteam
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62 """
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imgteam
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63 scale = [1] * (len(img.axes) - 1) # omit the channel axis
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64 z_axis, y_axis, x_axis = [
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65 img.axes.index(axis) for axis in 'ZYX'
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66 ]
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67
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68 # Determine the pixel size of the image
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69 if 'resolution' in img.metadata:
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70 pixel_size = np.divide(1, img.metadata['resolution'])
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imgteam
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71 else:
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72 sys.exit('Resolution information missing in image metadata')
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73
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74 # Define unified transformation of pixel/voxel sizes to scale factors
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75 def voxel_size_to_scale(voxel_size: np.ndarray) -> list:
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76 match sample:
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77 case 'up':
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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78 return (voxel_size / voxel_size.min()).tolist()
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79 case 'down':
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80 return (voxel_size / voxel_size.max()).tolist()
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81 case _:
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82 raise ValueError(f'Unknown value for sample: "{sample}"')
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83
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84 # Handle the 3-D case
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85 if img.data.shape[z_axis] > 1:
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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86
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87 # Determine the voxel depth of the image
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88 if (voxel_depth := img.metadata.get('z_spacing', None)) is None:
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89 sys.exit('Voxel depth information missing in image metadata')
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90
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91 # Determine the XYZ scale factors
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92 scale[x_axis], scale[y_axis], scale[z_axis] = (
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93 voxel_size_to_scale(
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94 np.array([*pixel_size, voxel_depth]),
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95 )
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96 )
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97
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98 # Handle the 2-D case
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99 else:
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100
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101 # Determine the XY scale factors
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102 scale[x_axis], scale[y_axis] = (
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103 voxel_size_to_scale(
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104 np.array(pixel_size),
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105 )
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106 )
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107
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108 return tuple(scale)
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109
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110
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111 def get_aa_sigma_by_scale(scale: float) -> float:
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112 """
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113 Determine the optimal size of the Gaussian filter for anti-aliasing.
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114
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115 See for details: https://scikit-image.org/docs/0.25.x/api/skimage.transform.html#skimage.transform.rescale
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116 """
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117 return (1 / scale - 1) / 2 if scale < 1 else 0
0
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118
3
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119
4
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120 def get_new_metadata(
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121 old: giatools.Image,
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122 scale: float | tuple[float, ...],
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123 arr: np.ndarray,
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124 ) -> dict[str, Any]:
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125 """
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126 Determine the result metadata (copy and adapt).
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127 """
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128 metadata = dict(old.metadata)
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129 scales = (
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130 [scale] * (len(old.axes) - 1) # omit the channel axis
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131 if isinstance(scale, float) else scale
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132 )
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133
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134 # Determine the original pixel size
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135 old_pixel_size = (
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136 np.divide(1, old.metadata['resolution'])
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137 if 'resolution' in old.metadata else (1, 1)
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138 )
3
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139
4
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140 # Determine the new pixel size and update metadata
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141 new_pixel_size = np.divide(
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142 old_pixel_size,
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143 (
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144 scales[old.axes.index('X')],
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145 scales[old.axes.index('Y')],
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146 ),
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147 )
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148 metadata['resolution'] = tuple(1 / new_pixel_size)
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149
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150 # Update the metadata for the new voxel depth
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151 old_voxel_depth = old.metadata.get('z_spacing', 1)
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152 metadata['z_spacing'] = old_voxel_depth / scales[old.axes.index('Z')]
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153
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154 return metadata
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155
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156
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157 def metadata_to_str(metadata: dict) -> str:
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158 tokens = list()
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159 for key in sorted(metadata.keys()):
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160 value = metadata[key]
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161 if isinstance(value, tuple):
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162 value = '(' + ', '.join([f'{val}' for val in value]) + ')'
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163 tokens.append(f'{key}: {value}')
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164 if len(metadata_str := ', '.join(tokens)) > 0:
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165 return metadata_str
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166 else:
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167 return 'has no metadata'
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168
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169
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170 def write_output(filepath: str, img: giatools.Image):
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171 """
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172 Validate that the output file format is suitable for the image data, then write it.
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173 """
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174 print('Output shape:', img.data.shape)
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175 print('Output axes:', img.axes)
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176 print('Output', metadata_to_str(img.metadata))
3
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177
4
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178 # Validate that the output file format is suitable for the image data
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179 if filepath.lower().endswith('.png'):
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180 if not frozenset(img.axes) <= frozenset('YXC'):
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181 sys.exit(f'Cannot write PNG file with axes "{img.axes}"')
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182
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183 # Write image data to the output file
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184 img.write(filepath)
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185
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186
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187 def scale_image(
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188 input_filepath: str,
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189 output_filepath: str,
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190 mode: Literal['uniform', 'explicit', 'isotropy'],
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191 order: int,
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192 anti_alias: bool,
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193 **cfg,
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194 ):
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195 img = giatools.Image.read(input_filepath)
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196 print('Input axes:', img.original_axes)
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197 print('Input', metadata_to_str(img.metadata))
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198
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199 # Determine `scale` for scaling
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200 match mode:
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201
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202 case 'uniform':
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203 scale = get_uniform_scale(img, cfg['axes'], cfg['factor'])
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204
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205 case 'explicit':
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206 scale = tuple(
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207 [cfg.get(f'factor_{axis.lower()}', 1) for axis in img.axes if axis != 'C']
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208 )
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209
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210 case 'isotropy':
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211 scale = get_scale_for_isotropy(img, cfg['sample'])
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212
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213 case _:
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214 raise ValueError(f'Unknown mode: "{mode}"')
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215
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216 # Assemble remaining `rescale` parameters
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217 rescale_kwargs = dict(
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218 scale=scale,
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219 order=order,
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220 preserve_range=True,
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221 channel_axis=img.axes.index('C'),
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222 )
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223 if (anti_alias := anti_alias and (np.array(scale) < 1).any()):
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224 rescale_kwargs['anti_aliasing'] = anti_alias
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225 rescale_kwargs['anti_aliasing_sigma'] = tuple(
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226 [
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227 get_aa_sigma_by_scale(s) for s in scale
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228 ] + [0] # `skimage.transform.rescale` also expects a value for the channel axis
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229 )
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230 else:
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231 rescale_kwargs['anti_aliasing'] = False
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232
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233 # Re-sample the image data to perform the scaling
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234 for key, value in rescale_kwargs.items():
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235 print(f'{key}: {value}')
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236 arr = skimage.transform.rescale(img.data, **rescale_kwargs)
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237
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238 # Preserve the `dtype` so that both brightness and range of values is preserved
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239 if arr.dtype != img.data.dtype:
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240 if np.issubdtype(img.data.dtype, np.integer):
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241 arr = arr.round()
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242 arr = arr.astype(img.data.dtype)
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243
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244 # Determine the result metadata and save result
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245 metadata = get_new_metadata(img, scale, arr)
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246 write_output(
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247 output_filepath,
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248 giatools.Image(
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249 data=arr,
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250 axes=img.axes,
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251 metadata=metadata,
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252 ).squeeze()
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253 )
0
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254
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255
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256 if __name__ == "__main__":
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257 parser = argparse.ArgumentParser()
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258 parser.add_argument('input', type=str)
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259 parser.add_argument('output', type=str)
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260 parser.add_argument('params', type=str)
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261 args = parser.parse_args()
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262
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263 # Read the config file
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264 with open(args.params) as cfgf:
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265 cfg = json.load(cfgf)
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266
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267 # Perform scaling
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268 scale_image(
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269 args.input,
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270 args.output,
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271 **cfg,
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272 )