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annotate auto_threshold.py @ 5:1ae14e703e5b draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
author imgteam
date Sat, 03 Jan 2026 14:42:51 +0000
parents 7d80eb2411fb
children
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1 """
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2 Copyright 2017-2025 Biomedical Computer Vision Group, Heidelberg University.
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4 Distributed under the MIT license.
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
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6 """
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8 import giatools
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9 import numpy as np
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10 import skimage.filters
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11 import skimage.util
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1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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13 # Fail early if an optional backend is not available
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14 giatools.require_backend('omezarr')
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17 class DefaultThresholdingMethod:
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19 def __init__(self, thres, **kwargs):
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20 self.thres = thres
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21 self.kwargs = kwargs
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23 def __call__(self, image, *args, offset=0, **kwargs):
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24 thres = self.thres(image, *args, **(self.kwargs | kwargs))
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25 return image > thres + offset
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27 def __str__(self):
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28 return self.thres.__name__
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31 class ManualThresholding:
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33 def __call__(self, image, threshold1: float, threshold2: float | None, **kwargs):
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34 if threshold2 is None:
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35 return image > threshold1
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36 else:
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37 threshold1, threshold2 = sorted((threshold1, threshold2))
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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38 return skimage.filters.apply_hysteresis_threshold(image, threshold1, threshold2)
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
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40 def __str__(self):
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41 return 'Manual'
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44 methods = {
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45 'manual': ManualThresholding(),
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47 'otsu': DefaultThresholdingMethod(skimage.filters.threshold_otsu),
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48 'li': DefaultThresholdingMethod(skimage.filters.threshold_li),
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49 'yen': DefaultThresholdingMethod(skimage.filters.threshold_yen),
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50 'isodata': DefaultThresholdingMethod(skimage.filters.threshold_isodata),
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52 'loc_gaussian': DefaultThresholdingMethod(skimage.filters.threshold_local, method='gaussian'),
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53 'loc_median': DefaultThresholdingMethod(skimage.filters.threshold_local, method='median'),
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54 'loc_mean': DefaultThresholdingMethod(skimage.filters.threshold_local, method='mean'),
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55 }
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58 if __name__ == "__main__":
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59 tool = giatools.ToolBaseplate()
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60 tool.add_input_image('input')
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61 tool.add_output_image('output')
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62 tool.parse_args()
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64 # Retrieve general parameters
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65 method = tool.args.params.pop('method')
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66 invert = tool.args.params.pop('invert')
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68 # Perform thresholding
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69 method_impl = methods[method]
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70 print(
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71 'Thresholding:',
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72 str(method_impl),
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73 'with',
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74 ', '.join(
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75 f'{key}={repr(value)}' for key, value in (tool.args.params | dict(invert=invert)).items()
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76 ),
4
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77 )
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78 for section in tool.run('ZYX', output_dtype_hint='binary'):
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79 section_output = method_impl(
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80 image=np.asarray(section['input'].data), # some implementations have issues with Dask arrays
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81 **tool.args.params,
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82 )
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83 if invert:
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84 section_output = np.logical_not(section_output)
1ae14e703e5b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 71f7ecabba78de48147d4a5e6ea380b6b70b16e8
imgteam
parents: 4
diff changeset
85 section['output'] = section_output