Mercurial > repos > imgteam > 2d_feature_extraction

comparison 2d_feature_extraction.py @ 5:2436a8807ad1 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:23:23 +0000
parents 0a53256b48c6
children 5bc8cdc17fd0
comparison
equal deleted inserted replaced
4:0a53256b48c6 5:2436a8807ad1
6 import skimage.io 6 import skimage.io
7 import skimage.measure 7 import skimage.measure
8 import skimage.morphology 8 import skimage.morphology
9 import skimage.segmentation 9 import skimage.segmentation
10 10
11 # TODO make importable by python script
12 11
13 parser = argparse.ArgumentParser(description='Extract Features 2D') 12 if __name__ == '__main__':
14 13
15 # TODO create factory for boilerplate code 14 parser = argparse.ArgumentParser(description='Extract image features')
16 features = parser.add_argument_group('compute features')
17 features.add_argument('--all', dest='all_features', action='store_true')
18 features.add_argument('--label', dest='add_label', action='store_true')
19 features.add_argument('--patches', dest='add_roi_patches', action='store_true')
20 features.add_argument('--max_intensity', dest='max_intensity', action='store_true')
21 features.add_argument('--mean_intensity', dest='mean_intensity', action='store_true')
22 features.add_argument('--min_intensity', dest='min_intensity', action='store_true')
23 features.add_argument('--moments_hu', dest='moments_hu', action='store_true')
24 features.add_argument('--centroid', dest='centroid', action='store_true')
25 features.add_argument('--bbox', dest='bbox', action='store_true')
26 features.add_argument('--area', dest='area', action='store_true')
27 features.add_argument('--filled_area', dest='filled_area', action='store_true')
28 features.add_argument('--convex_area', dest='convex_area', action='store_true')
29 features.add_argument('--perimeter', dest='perimeter', action='store_true')
30 features.add_argument('--extent', dest='extent', action='store_true')
31 features.add_argument('--eccentricity', dest='eccentricity', action='store_true')
32 features.add_argument('--equivalent_diameter', dest='equivalent_diameter', action='store_true')
33 features.add_argument('--euler_number', dest='euler_number', action='store_true')
34 features.add_argument('--inertia_tensor_eigvals', dest='inertia_tensor_eigvals', action='store_true')
35 features.add_argument('--major_axis_length', dest='major_axis_length', action='store_true')
36 features.add_argument('--minor_axis_length', dest='minor_axis_length', action='store_true')
37 features.add_argument('--orientation', dest='orientation', action='store_true')
38 features.add_argument('--solidity', dest='solidity', action='store_true')
39 features.add_argument('--moments', dest='moments', action='store_true')
40 features.add_argument('--convexity', dest='convexity', action='store_true')
41 15
42 parser.add_argument('--label_file_binary', dest='label_file_binary', action='store_true') 16 # TODO create factory for boilerplate code
17 features = parser.add_argument_group('compute features')
18 features.add_argument('--all', dest='all_features', action='store_true')
19 features.add_argument('--label', dest='add_label', action='store_true')
20 features.add_argument('--patches', dest='add_roi_patches', action='store_true')
21 features.add_argument('--max_intensity', dest='max_intensity', action='store_true')
22 features.add_argument('--mean_intensity', dest='mean_intensity', action='store_true')
23 features.add_argument('--min_intensity', dest='min_intensity', action='store_true')
24 features.add_argument('--moments_hu', dest='moments_hu', action='store_true')
25 features.add_argument('--centroid', dest='centroid', action='store_true')
26 features.add_argument('--bbox', dest='bbox', action='store_true')
27 features.add_argument('--area', dest='area', action='store_true')
28 features.add_argument('--filled_area', dest='filled_area', action='store_true')
29 features.add_argument('--convex_area', dest='convex_area', action='store_true')
30 features.add_argument('--perimeter', dest='perimeter', action='store_true')
31 features.add_argument('--extent', dest='extent', action='store_true')
32 features.add_argument('--eccentricity', dest='eccentricity', action='store_true')
33 features.add_argument('--equivalent_diameter', dest='equivalent_diameter', action='store_true')
34 features.add_argument('--euler_number', dest='euler_number', action='store_true')
35 features.add_argument('--inertia_tensor_eigvals', dest='inertia_tensor_eigvals', action='store_true')
36 features.add_argument('--major_axis_length', dest='major_axis_length', action='store_true')
37 features.add_argument('--minor_axis_length', dest='minor_axis_length', action='store_true')
38 features.add_argument('--orientation', dest='orientation', action='store_true')
39 features.add_argument('--solidity', dest='solidity', action='store_true')
40 features.add_argument('--moments', dest='moments', action='store_true')
41 features.add_argument('--convexity', dest='convexity', action='store_true')
43 42
44 parser.add_argument('--raw', dest='raw_file', type=argparse.FileType('r'), 43 parser.add_argument('--label_file_binary', dest='label_file_binary', action='store_true')
45 help='Original input file', required=False)
46 parser.add_argument('label_file', type=argparse.FileType('r'),
47 help='Label input file')
48 parser.add_argument('output_file', type=argparse.FileType('w'),
49 help='Tabular output file')
50 args = parser.parse_args()
51 44
52 label_file_binary = args.label_file_binary 45 parser.add_argument('--raw', dest='raw_file', type=argparse.FileType('r'),
53 label_file = args.label_file.name 46 help='Original input file', required=False)
54 out_file = args.output_file.name 47 parser.add_argument('label_file', type=argparse.FileType('r'),
55 add_patch = args.add_roi_patches 48 help='Label input file')
49 parser.add_argument('output_file', type=argparse.FileType('w'),
50 help='Tabular output file')
51 args = parser.parse_args()
56 52
57 raw_image = None 53 label_file_binary = args.label_file_binary
58 if args.raw_file is not None: 54 label_file = args.label_file.name
59 raw_image = skimage.io.imread(args.raw_file.name) 55 out_file = args.output_file.name
56 add_patch = args.add_roi_patches
60 57
61 raw_label_image = skimage.io.imread(label_file) 58 raw_image = None
59 if args.raw_file is not None:
60 raw_image = skimage.io.imread(args.raw_file.name)
62 61
63 df = pd.DataFrame() 62 raw_label_image = skimage.io.imread(label_file)
64 if label_file_binary:
65 raw_label_image = skimage.measure.label(raw_label_image)
66 regions = skimage.measure.regionprops(raw_label_image, intensity_image=raw_image)
67 63
68 df['it'] = np.arange(len(regions)) 64 df = pd.DataFrame()
65 if label_file_binary:
66 raw_label_image = skimage.measure.label(raw_label_image)
67 regions = skimage.measure.regionprops(raw_label_image, intensity_image=raw_image)
69 68
70 if add_patch: 69 df['it'] = np.arange(len(regions))
71 df['image'] = df['it'].map(lambda ait: regions[ait].image.astype(np.float).tolist())
72 df['intensity_image'] = df['it'].map(lambda ait: regions[ait].intensity_image.astype(np.float).tolist())
73 70
74 # TODO no matrix features, but split in own rows? 71 if add_patch:
75 if args.add_label or args.all_features: 72 df['image'] = df['it'].map(lambda ait: regions[ait].image.astype(np.float).tolist())
76 df['label'] = df['it'].map(lambda ait: regions[ait].label) 73 df['intensity_image'] = df['it'].map(lambda ait: regions[ait].intensity_image.astype(np.float).tolist())
77 74
78 if raw_image is not None: 75 # TODO no matrix features, but split in own rows?
79 if args.max_intensity or args.all_features: 76 if args.add_label or args.all_features:
80 df['max_intensity'] = df['it'].map(lambda ait: regions[ait].max_intensity) 77 df['label'] = df['it'].map(lambda ait: regions[ait].label)
81 if args.mean_intensity or args.all_features:
82 df['mean_intensity'] = df['it'].map(lambda ait: regions[ait].mean_intensity)
83 if args.min_intensity or args.all_features:
84 df['min_intensity'] = df['it'].map(lambda ait: regions[ait].min_intensity)
85 if args.moments_hu or args.all_features:
86 df['moments_hu'] = df['it'].map(lambda ait: regions[ait].moments_hu)
87 78
88 if args.centroid or args.all_features: 79 if raw_image is not None:
89 df['centroid'] = df['it'].map(lambda ait: regions[ait].centroid) 80 if args.max_intensity or args.all_features:
90 if args.bbox or args.all_features: 81 df['max_intensity'] = df['it'].map(lambda ait: regions[ait].max_intensity)
91 df['bbox'] = df['it'].map(lambda ait: regions[ait].bbox) 82 if args.mean_intensity or args.all_features:
92 if args.area or args.all_features: 83 df['mean_intensity'] = df['it'].map(lambda ait: regions[ait].mean_intensity)
93 df['area'] = df['it'].map(lambda ait: regions[ait].area) 84 if args.min_intensity or args.all_features:
94 if args.filled_area or args.all_features: 85 df['min_intensity'] = df['it'].map(lambda ait: regions[ait].min_intensity)
95 df['filled_area'] = df['it'].map(lambda ait: regions[ait].filled_area) 86 if args.moments_hu or args.all_features:
96 if args.convex_area or args.all_features: 87 df['moments_hu'] = df['it'].map(lambda ait: regions[ait].moments_hu)
97 df['convex_area'] = df['it'].map(lambda ait: regions[ait].convex_area)
98 if args.perimeter or args.all_features:
99 df['perimeter'] = df['it'].map(lambda ait: regions[ait].perimeter)
100 if args.extent or args.all_features:
101 df['extent'] = df['it'].map(lambda ait: regions[ait].extent)
102 if args.eccentricity or args.all_features:
103 df['eccentricity'] = df['it'].map(lambda ait: regions[ait].eccentricity)
104 if args.equivalent_diameter or args.all_features:
105 df['equivalent_diameter'] = df['it'].map(lambda ait: regions[ait].equivalent_diameter)
106 if args.euler_number or args.all_features:
107 df['euler_number'] = df['it'].map(lambda ait: regions[ait].euler_number)
108 if args.inertia_tensor_eigvals or args.all_features:
109 df['inertia_tensor_eigvals'] = df['it'].map(lambda ait: regions[ait].inertia_tensor_eigvals)
110 if args.major_axis_length or args.all_features:
111 df['major_axis_length'] = df['it'].map(lambda ait: regions[ait].major_axis_length)
112 if args.minor_axis_length or args.all_features:
113 df['minor_axis_length'] = df['it'].map(lambda ait: regions[ait].minor_axis_length)
114 if args.orientation or args.all_features:
115 df['orientation'] = df['it'].map(lambda ait: regions[ait].orientation)
116 if args.solidity or args.all_features:
117 df['solidity'] = df['it'].map(lambda ait: regions[ait].solidity)
118 if args.moments or args.all_features:
119 df['moments'] = df['it'].map(lambda ait: regions[ait].moments)
120 if args.convexity or args.all_features:
121 perimeter = df['it'].map(lambda ait: regions[ait].perimeter)
122 area = df['it'].map(lambda ait: regions[ait].area)
123 df['convexity'] = area / (perimeter * perimeter)
124 88
125 del df['it'] 89 if args.centroid or args.all_features:
126 df.to_csv(out_file, sep='\t', line_terminator='\n', index=False) 90 df['centroid'] = df['it'].map(lambda ait: regions[ait].centroid)
91 if args.bbox or args.all_features:
92 df['bbox'] = df['it'].map(lambda ait: regions[ait].bbox)
93 if args.area or args.all_features:
94 df['area'] = df['it'].map(lambda ait: regions[ait].area)
95 if args.filled_area or args.all_features:
96 df['filled_area'] = df['it'].map(lambda ait: regions[ait].filled_area)
97 if args.convex_area or args.all_features:
98 df['convex_area'] = df['it'].map(lambda ait: regions[ait].convex_area)
99 if args.perimeter or args.all_features:
100 df['perimeter'] = df['it'].map(lambda ait: regions[ait].perimeter)
101 if args.extent or args.all_features:
102 df['extent'] = df['it'].map(lambda ait: regions[ait].extent)
103 if args.eccentricity or args.all_features:
104 df['eccentricity'] = df['it'].map(lambda ait: regions[ait].eccentricity)
105 if args.equivalent_diameter or args.all_features:
106 df['equivalent_diameter'] = df['it'].map(lambda ait: regions[ait].equivalent_diameter)
107 if args.euler_number or args.all_features:
108 df['euler_number'] = df['it'].map(lambda ait: regions[ait].euler_number)
109 if args.inertia_tensor_eigvals or args.all_features:
110 df['inertia_tensor_eigvals'] = df['it'].map(lambda ait: regions[ait].inertia_tensor_eigvals)
111 if args.major_axis_length or args.all_features:
112 df['major_axis_length'] = df['it'].map(lambda ait: regions[ait].major_axis_length)
113 if args.minor_axis_length or args.all_features:
114 df['minor_axis_length'] = df['it'].map(lambda ait: regions[ait].minor_axis_length)
115 if args.orientation or args.all_features:
116 df['orientation'] = df['it'].map(lambda ait: regions[ait].orientation)
117 if args.solidity or args.all_features:
118 df['solidity'] = df['it'].map(lambda ait: regions[ait].solidity)
119 if args.moments or args.all_features:
120 df['moments'] = df['it'].map(lambda ait: regions[ait].moments)
121 if args.convexity or args.all_features:
122 perimeter = df['it'].map(lambda ait: regions[ait].perimeter)
123 area = df['it'].map(lambda ait: regions[ait].area)
124 df['convexity'] = area / (perimeter * perimeter)
125
126 del df['it']
127 df.to_csv(out_file, sep='\t', line_terminator='\n', index=False)