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annotate run-segmetrics.py @ 0:0729657d9e4e draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
author imgteam
date Fri, 07 Oct 2022 22:05:59 +0000
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children c90b52773d2e
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0
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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1 """
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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2 Copyright 2022 Leonid Kostrykin, Biomedical Computer Vision Group, Heidelberg University.
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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3
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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4 Distributed under the MIT license.
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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5 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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6
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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7 """
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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8
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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9 import argparse
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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10 import csv
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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11 import itertools
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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12 import pathlib
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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13 import tempfile
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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14 import zipfile
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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15
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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16 import numpy as np
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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17 import segmetrics as sm
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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18 import skimage.io
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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19
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0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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21 measures = [
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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22 ('dice', 'Dice', sm.regional.Dice()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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23 ('seg', 'SEG', sm.regional.ISBIScore()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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24 ('jc', 'Jaccard coefficient', sm.regional.JaccardSimilarityIndex()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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25 ('ji', 'Jaccard index', sm.regional.JaccardIndex()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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26 ('ri', 'Rand index', sm.regional.RandIndex()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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27 ('ari', 'Adjusted Rand index', sm.regional.AdjustedRandIndex()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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28 ('hsd_sym', 'HSD (sym)', sm.boundary.Hausdorff('sym')),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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29 ('hsd_e2a', 'HSD (e2a)', sm.boundary.Hausdorff('e2a')),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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30 ('hsd_a2e', 'HSD (a2e)', sm.boundary.Hausdorff('a2e')),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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31 ('nsd', 'NSD', sm.boundary.NSD()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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32 ('o_hsd_sym', 'Ob. HSD (sym)', sm.boundary.ObjectBasedDistance(sm.boundary.Hausdorff('sym'))),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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33 ('o_hsd_e2a', 'Ob. HSD (e2a)', sm.boundary.ObjectBasedDistance(sm.boundary.Hausdorff('e2a'))),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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34 ('o_hsd_a2e', 'Ob. HSD (a2e)', sm.boundary.ObjectBasedDistance(sm.boundary.Hausdorff('a2e'))),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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35 ('o_nsd', 'Ob. NSD', sm.boundary.ObjectBasedDistance(sm.boundary.NSD())),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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36 ('fs', 'Split', sm.detection.FalseSplit()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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37 ('fm', 'Merge', sm.detection.FalseMerge()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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38 ('fp', 'Spurious', sm.detection.FalsePositive()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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39 ('fn', 'Missing', sm.detection.FalseNegative()),
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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40 ]
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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41
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42
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43 def process_batch(study, gt_filelist, seg_filelist, namelist, gt_is_unique, seg_is_unique):
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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44 for gt_filename, seg_filename, name in zip(gt_filelist, seg_filelist, namelist):
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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45 img_ref = skimage.io.imread(gt_filename)
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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46 img_seg = skimage.io.imread(seg_filename)
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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47 study.set_expected(img_ref, unique=gt_is_unique)
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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48 study.process(img_seg, unique=seg_is_unique, chunk_id=name)
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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49
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50
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51 def aggregate(measure, values):
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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52 fnc = np.sum if measure.ACCUMULATIVE else np.mean
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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53 return fnc(values)
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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54
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55
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56 def is_zip_filepath(filepath):
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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57 return filepath.lower().endswith('.zip')
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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58
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59
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60 def is_image_filepath(filepath):
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61 suffixes = ['png', 'tif', 'tiff']
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62 return any((filepath.lower().endswith(f'.{suffix}') for suffix in suffixes))
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63
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64
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65 if __name__ == "__main__":
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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66 parser = argparse.ArgumentParser(description='Image segmentation and object detection performance measures for 2-D image data')
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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67 parser.add_argument('input_seg', help='Path to the segmented image or image archive (ZIP)')
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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68 parser.add_argument('input_gt', help='Path to the ground truth image or image archive (ZIP)')
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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69 parser.add_argument('results', help='Path to the results file (CSV)')
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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70 parser.add_argument('-unzip', action='store_true')
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71 parser.add_argument('-seg_unique', action='store_true')
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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72 parser.add_argument('-gt_unique', action='store_true')
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73 for measure in measures:
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74 parser.add_argument(f'-measure-{measure[0]}', action='store_true', help=f'Include {measure[1]}')
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75
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76 args = parser.parse_args()
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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77 study = sm.study.Study()
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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78
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79 used_measures = []
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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80 for measure in measures:
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81 if getattr(args, f'measure_{measure[0]}'):
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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82 used_measures.append(measure)
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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83 study.add_measure(measure[2], measure[1])
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84
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85 if args.unzip:
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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86 zipfile_seg = zipfile.ZipFile(args.input_seg)
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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87 zipfile_gt = zipfile.ZipFile(args.input_gt)
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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88 namelist = [filepath for filepath in zipfile_seg.namelist() if is_image_filepath(filepath) and filepath in zipfile_gt.namelist()]
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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89 print('namelist:', namelist)
0729657d9e4e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
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90 with tempfile.TemporaryDirectory() as tmpdir:
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91 basepath = pathlib.Path(tmpdir)
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92 gt_path, seg_path = basepath / 'gt', basepath / 'seg'
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93 zipfile_seg.extractall(str(seg_path))
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94 zipfile_gt.extractall(str(gt_path))
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95 gt_filelist, seg_filelist = list(), list()
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96 for filepath in namelist:
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97 seg_filelist.append(str(seg_path / filepath))
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98 gt_filelist.append(str(gt_path / filepath))
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99 process_batch(study, gt_filelist, seg_filelist, namelist, args.gt_unique, args.seg_unique)
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100
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101 else:
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102 namelist = ['']
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103 process_batch(study, [args.input_gt], [args.input_seg], namelist, args.gt_unique, args.seg_unique)
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104
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105 # define header
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106 rows = [[''] + [measure[1] for measure in used_measures]]
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107
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108 # define rows
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109 if len(namelist) > 1:
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110 for chunk_id in namelist:
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111 row = [chunk_id]
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112 for measure in used_measures:
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113 measure_name = measure[1]
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114 measure = study.measures[measure_name]
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115 chunks = study.results[measure_name]
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116 row += [aggregate(measure, chunks[chunk_id])]
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117 rows.append(row)
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118
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119 # define footer
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120 rows.append([''])
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121 for measure in used_measures:
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122 measure_name = measure[1]
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123 measure = study.measures[measure_name]
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124 chunks = study.results[measure_name]
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125 values = list(itertools.chain(*[chunks[chunk_id] for chunk_id in chunks]))
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126 val = aggregate(measure, values)
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127 rows[-1].append(val)
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128
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129 # write results
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130 with open(args.results, 'w', newline='') as fout:
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131 csv_writer = csv.writer(fout, delimiter=';', quotechar='|', quoting=csv.QUOTE_MINIMAL)
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132 for row in rows:
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133 csv_writer.writerow(row)