Mercurial > repos > imgteam > 2d_simple_filter

annotate filter.py @ 2:b2d9c92bc431 draft

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author imgteam
date Fri, 12 Dec 2025 21:18:04 +0000
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2
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
imgteam
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diff changeset
1 import argparse
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
imgteam
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2 import json
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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3 from typing import (
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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4 Any,
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5 Callable,
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6 )
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7
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8 import giatools
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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9 import numpy as np
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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10 import scipy.ndimage as ndi
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11 from skimage.morphology import disk
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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12
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13
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14 def image_astype(img: giatools.Image, dtype: np.dtype) -> giatools.Image:
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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15 return giatools.Image(
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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16 data=img.data.astype(dtype),
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17 axes=img.axes,
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18 original_axes=img.original_axes,
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19 metadata=img.metadata,
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20 )
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21
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22
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23 filters = {
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24 'gaussian': lambda img, sigma, order=0, axis=None: (
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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25 apply_2d_filter(
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26 ndi.gaussian_filter,
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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27 img if order == 0 else image_astype(img, float),
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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28 sigma=sigma,
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29 order=order,
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30 axes=axis,
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31 )
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32 ),
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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33 'uniform': lambda img, size: (
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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34 apply_2d_filter(ndi.uniform_filter, img, size=size)
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35 ),
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36 'median': lambda img, radius: (
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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37 apply_2d_filter(ndi.median_filter, img, footprint=disk(radius))
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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38 ),
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39 'prewitt': lambda img, axis: (
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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40 apply_2d_filter(ndi.prewitt, img, axis=axis)
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41 ),
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42 'sobel': lambda img, axis: (
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43 apply_2d_filter(ndi.sobel, img, axis=axis)
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44 ),
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45 }
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46
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47
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48 def apply_2d_filter(
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49 filter_impl: Callable[[np.ndarray, Any, ...], np.ndarray],
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50 img: giatools.Image,
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51 **kwargs: Any,
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52 ) -> giatools.Image:
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53 """
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54 Apply the 2-D filter to the 2-D/3-D, potentially multi-frame and multi-channel image.
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55 """
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56 result_data = None
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57 for qtzc in np.ndindex(
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58 img.data.shape[ 0], # Q axis
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59 img.data.shape[ 1], # T axis
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60 img.data.shape[ 2], # Z axis
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61 img.data.shape[-1], # C axis
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62 ):
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63 sl = np.s_[*qtzc[:3], ..., qtzc[3]] # noqa: E999
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64 arr = img.data[sl]
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65 assert arr.ndim == 2 # sanity check, should always be True
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66
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67 # Perform 2-D filtering
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68 res = filter_impl(arr, **kwargs)
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69 if result_data is None:
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70 result_data = np.empty(img.data.shape, res.dtype)
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71 result_data[sl] = res
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72
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73 # Return results
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74 return giatools.Image(result_data, img.axes)
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75
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76
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77 def apply_filter(
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78 input_filepath: str,
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79 output_filepath: str,
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80 filter_type: str,
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81 **kwargs: Any,
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82 ):
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83 # Read the input image
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84 img = giatools.Image.read(input_filepath)
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85
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86 # Perform filtering
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87 filter_impl = filters[filter_type]
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88 res = filter_impl(img, **kwargs).normalize_axes_like(img.original_axes)
b2d9c92bc431 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8
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89
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90 # Adopt metadata and write the result
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91 res.metadata = img.metadata
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92 res.write(output_filepath, backend='tifffile')
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93
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94
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95 if __name__ == "__main__":
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96 parser = argparse.ArgumentParser()
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97 parser.add_argument('input', type=str, help='Input image filepath')
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98 parser.add_argument('output', type=str, help='Output image filepath (TIFF)')
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99 parser.add_argument('params', type=str)
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100 args = parser.parse_args()
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101
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102 # Read the config file
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103 with open(args.params) as cfgf:
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104 cfg = json.load(cfgf)
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105
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106 apply_filter(
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107 args.input,
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108 args.output,
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109 **cfg,
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110 )