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annotate 2d_feature_extraction.py @ 0:96909b9d1df1 draft

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author imgteam
date Sat, 09 Feb 2019 14:28:26 -0500
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96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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diff changeset
1 import argparse
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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2 import numpy as np
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 import pandas as pd
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4 import tifffile
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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5 import skimage.io
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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6 import skimage.measure
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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7 import skimage.feature
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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8 import skimage.segmentation
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9 import skimage.morphology
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11 #TODO make importable by python script
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 parser = argparse.ArgumentParser(description='Extract Features 2D')
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 #TODO create factory for boilerplate code
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 features = parser.add_argument_group('compute features')
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17 features.add_argument('--all', dest='all_features', action='store_true')
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18 features.add_argument('--label', dest='add_label', action='store_true')
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19 features.add_argument('--patches', dest='add_roi_patches', action='store_true')
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20 features.add_argument('--max_intensity', dest='max_intensity', action='store_true')
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21 features.add_argument('--mean_intensity', dest='mean_intensity', action='store_true')
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22 features.add_argument('--min_intensity', dest='min_intensity', action='store_true')
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23 features.add_argument('--moments_hu', dest='moments_hu', action='store_true')
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24 features.add_argument('--centroid', dest='centroid', action='store_true')
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25 features.add_argument('--bbox', dest='bbox', action='store_true')
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26 features.add_argument('--area', dest='area', action='store_true')
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27 features.add_argument('--filled_area', dest='filled_area', action='store_true')
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 features.add_argument('--convex_area', dest='convex_area', action='store_true')
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29 features.add_argument('--perimeter', dest='perimeter', action='store_true')
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30 features.add_argument('--extent', dest='extent', action='store_true')
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31 features.add_argument('--eccentricity', dest='eccentricity', action='store_true')
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32 features.add_argument('--equivalent_diameter', dest='equivalent_diameter', action='store_true')
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33 features.add_argument('--euler_number', dest='euler_number', action='store_true')
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34 features.add_argument('--inertia_tensor_eigvals', dest='inertia_tensor_eigvals', action='store_true')
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 features.add_argument('--major_axis_length', dest='major_axis_length', action='store_true')
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36 features.add_argument('--minor_axis_length', dest='minor_axis_length', action='store_true')
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37 features.add_argument('--orientation', dest='orientation', action='store_true')
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38 features.add_argument('--solidity', dest='solidity', action='store_true')
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39 features.add_argument('--moments', dest='moments', action='store_true')
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40 features.add_argument('--convexity', dest='convexity', action='store_true')
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41
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42 parser.add_argument('--label_file_binary', dest='label_file_binary', action='store_true')
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43
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44 parser.add_argument('--raw', dest='raw_file', type=argparse.FileType('r'),
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45 help='Original input file', required=False)
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46 parser.add_argument('label_file', type=argparse.FileType('r'),
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47 help='Label input file')
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48 parser.add_argument('output_file', type=argparse.FileType('w'),
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49 help='Tabular output file')
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50 args = parser.parse_args()
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51
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52 label_file_binary = args.label_file_binary
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53 label_file = args.label_file.name
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54 out_file = args.output_file.name
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55 add_patch = args.add_roi_patches
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56
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57 raw_image = None
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58 if args.raw_file is not None:
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59 raw_image = skimage.io.imread(args.raw_file.name)
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60
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61 raw_label_image = skimage.io.imread(label_file)
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62
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63 df = pd.DataFrame()
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64 if label_file_binary:
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65 raw_label_image = skimage.measure.label(raw_label_image)
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66 regions = skimage.measure.regionprops(raw_label_image, intensity_image=raw_image)
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67
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68 df['it'] = np.arange(len(regions))
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70 if add_patch:
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71 df['image'] = df['it'].map(lambda ait: regions[ait].image.astype(np.float).tolist())
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72 df['intensity_image'] = df['it'].map(lambda ait: regions[ait].intensity_image.astype(np.float).tolist())
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73
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74 #TODO no matrix features, but split in own rows?
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75 if args.add_label or args.all_features:
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76 df['label'] = df['it'].map(lambda ait: regions[ait].label)
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77
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78 if raw_image is not None:
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79 if args.max_intensity or args.all_features:
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80 df['max_intensity'] = df['it'].map(lambda ait: regions[ait].max_intensity)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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81 if args.mean_intensity or args.all_features:
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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82 df['mean_intensity'] = df['it'].map(lambda ait: regions[ait].mean_intensity)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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83 if args.min_intensity or args.all_features:
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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84 df['min_intensity'] = df['it'].map(lambda ait: regions[ait].min_intensity)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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85 if args.moments_hu or args.all_features:
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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86 df['moments_hu'] = df['it'].map(lambda ait: regions[ait].moments_hu)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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87
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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88 if args.centroid or args.all_features:
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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89 df['centroid'] = df['it'].map(lambda ait: regions[ait].centroid)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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90 if args.bbox or args.all_features:
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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91 df['bbox'] = df['it'].map(lambda ait: regions[ait].bbox)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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92 if args.area or args.all_features:
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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93 df['area'] = df['it'].map(lambda ait: regions[ait].area)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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94 if args.filled_area or args.all_features:
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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95 df['filled_area'] = df['it'].map(lambda ait: regions[ait].filled_area)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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96 if args.convex_area or args.all_features:
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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97 df['convex_area'] = df['it'].map(lambda ait: regions[ait].convex_area)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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98 if args.perimeter or args.all_features:
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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99 df['perimeter'] = df['it'].map(lambda ait: regions[ait].perimeter)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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100 if args.extent or args.all_features:
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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101 df['extent'] = df['it'].map(lambda ait: regions[ait].extent)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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102 if args.eccentricity or args.all_features:
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103 df['eccentricity'] = df['it'].map(lambda ait: regions[ait].eccentricity)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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104 if args.equivalent_diameter or args.all_features:
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105 df['equivalent_diameter'] = df['it'].map(lambda ait: regions[ait].equivalent_diameter)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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106 if args.euler_number or args.all_features:
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107 df['euler_number'] = df['it'].map(lambda ait: regions[ait].euler_number)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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108 if args.inertia_tensor_eigvals or args.all_features:
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109 df['inertia_tensor_eigvals'] = df['it'].map(lambda ait: regions[ait].inertia_tensor_eigvals)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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110 if args.major_axis_length or args.all_features:
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111 df['major_axis_length'] = df['it'].map(lambda ait: regions[ait].major_axis_length)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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112 if args.minor_axis_length or args.all_features:
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113 df['minor_axis_length'] = df['it'].map(lambda ait: regions[ait].minor_axis_length)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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114 if args.orientation or args.all_features:
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115 df['orientation'] = df['it'].map(lambda ait: regions[ait].orientation)
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116 if args.solidity or args.all_features:
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117 df['solidity'] = df['it'].map(lambda ait: regions[ait].solidity)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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118 if args.moments or args.all_features:
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119 df['moments'] = df['it'].map(lambda ait: regions[ait].moments)
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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120 if args.convexity or args.all_features:
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121 df['convexity'] = df.area/(df.perimeter*df.perimeter)
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122
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123 del df['it']
96909b9d1df1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_feature_extraction/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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124 df.to_csv(out_file, sep='\t', line_terminator='\n', index=False)