Mercurial > repos > imgteam > binary2labelimage
annotate binary2label.py @ 4:8f0dd9a58ec3 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
| author | imgteam |
|---|---|
| date | Sat, 03 Jan 2026 14:14:05 +0000 |
| parents | a041e4e9d449 |
| children |
| rev | line source |
|---|---|
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4
8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
3
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1 import giatools |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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2 import numpy as np |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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3 import scipy.ndimage as ndi |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
3
diff
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4 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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5 # Fail early if an optional backend is not available |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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6 giatools.require_backend('omezarr') |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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7 |
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0
1cde6ba34356
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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8 |
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4
8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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9 def label_watershed(arr: np.ndarray, **kwargs) -> np.ndarray: |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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10 import skimage.util |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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11 from skimage.feature import peak_local_max |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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12 from skimage.segmentation import watershed |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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13 distance = ndi.distance_transform_edt(arr) |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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14 local_max_indices = peak_local_max( |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
3
diff
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15 distance, |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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16 labels=arr, |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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17 **kwargs, |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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18 ) |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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19 local_max_mask = np.zeros(arr.shape, dtype=bool) |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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20 local_max_mask[tuple(local_max_indices.T)] = True |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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21 markers = ndi.label(local_max_mask)[0] |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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22 res = watershed(-distance, markers, mask=arr) |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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23 return skimage.util.img_as_uint(res) # converts to uint16 |
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3
a041e4e9d449
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents:
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24 |
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a041e4e9d449
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
imgteam
parents:
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diff
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25 |
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4
8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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26 if __name__ == '__main__': |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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27 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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28 tool = giatools.ToolBaseplate() |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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29 tool.add_input_image('input') |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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30 tool.add_output_image('output') |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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31 tool.parse_args() |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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32 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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33 # Validate the input image and the selected method |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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34 try: |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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35 input_image = tool.args.input_images['input'] |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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36 if (method := tool.args.params.pop('method')) == 'watershed' and input_image.shape[input_image.axes.index('Z')] > 1: |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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37 raise ValueError(f'Method "{method}" is not applicable to 3-D images.') |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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38 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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39 elif input_image.shape[input_image.axes.index('C')] > 1: |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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40 raise ValueError('Multi-channel images are forbidden to avoid confusion with multi-channel labels (e.g., RGB labels).') |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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41 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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42 else: |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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43 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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44 # Choose the requested labeling method |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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45 match method: |
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a041e4e9d449
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
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46 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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47 case 'cca': |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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48 joint_axes = 'ZYX' |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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49 label = lambda input_section_bin: ( # noqa: E731 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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50 ndi.label(input_section_bin, **tool.args.params)[0].astype(np.uint16) |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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51 ) |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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52 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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53 case 'watershed': |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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54 joint_axes = 'YX' |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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55 label = lambda input_section_bin: ( # noqa: E731 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
parents:
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56 label_watershed(input_section_bin, **tool.args.params) # already uint16 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
imgteam
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57 ) |
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1cde6ba34356
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binary2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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58 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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59 case _: |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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60 raise ValueError(f'Unknown method: "{method}"') |
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a041e4e9d449
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
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61 |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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62 # Perform the labeling |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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63 for section in tool.run(joint_axes): |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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64 section['output'] = label( |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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65 section['input'].data > 0, # ensure that the input data is truly binary |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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66 ) |
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a041e4e9d449
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit 48df7d9c58fb88e472caeb4d4a1e14170d79b643
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67 |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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68 # Exit and print error to stderr |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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69 except ValueError as err: |
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8f0dd9a58ec3
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ commit f5a4de7535e433e3b0e96e0694e481b6643a54f8
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70 exit(err.args[0]) |