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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
author imgteam
date Wed, 26 Jun 2024 08:03:08 +0000
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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diff changeset
1 import argparse
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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2 import json
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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4 import yaml
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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7 # This script genereates the config file required by PlantSeg.
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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8 # For an overview of the config fields, see:
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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9 # https://github.com/kreshuklab/plant-seg/blob/master/examples/config.yaml
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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12 def listify(d, k, sep=',', dtype=float):
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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13 if k not in d:
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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14 return
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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15 d[k] = [dtype(token.strip()) for token in str(d[k]).split(sep)]
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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18 if __name__ == '__main__':
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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20 parser = argparse.ArgumentParser()
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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21 parser.add_argument('--inputs', type=str, help='Path to the inputs file', required=True)
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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22 parser.add_argument('--config', type=str, help='Path to the config file', required=True)
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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23 parser.add_argument('--img_in', type=str, help='Path to the input image', required=True)
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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24 parser.add_argument('--workers', type=int, default=1)
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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25 args = parser.parse_args()
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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27 with open(args.inputs, 'r') as fp:
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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28 inputs = json.load(fp)
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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30 # Set configuration options from the tool wrapper
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
imgteam
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31 cfg = dict(path=args.img_in)
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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32 for section_name in (
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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33 'preprocessing',
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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34 'cnn_prediction',
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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35 'cnn_postprocessing',
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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36 'segmentation',
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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37 'segmentation_postprocessing',
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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38 ):
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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39 cfg[section_name] = inputs[section_name]
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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41 # Set additional required configuration options
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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42 cfg['preprocessing']['save_directory'] = 'PreProcessing'
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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43 cfg['preprocessing']['crop_volume'] = '[:,:,:]'
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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44 cfg['preprocessing']['filter'] = dict(state=False, type='gaussian', filter_param=1.0)
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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46 cfg['cnn_prediction']['device'] = 'cuda'
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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47 cfg['cnn_prediction']['num_workers'] = args.workers
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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48 cfg['cnn_prediction']['model_update'] = False
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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50 cfg['segmentation']['name'] = 'MultiCut'
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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51 cfg['segmentation']['save_directory'] = 'MultiCut'
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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53 # Parse lists of values encoded as strings as actual lists of values
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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54 listify(cfg['preprocessing'], 'factor')
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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55 listify(cfg['cnn_prediction'], 'patch')
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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57 with open(args.config, 'w') as fp:
e59c0e930b1f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ commit 842fb4a9435114d06329e2cdfaeb8ed8d8479681
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58 fp.write(yaml.dump(cfg))