Mercurial > repos > imgteam > 2d_feature_extraction

comparison 2d_feature_extraction.py @ 4:a4bc9dfde846 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
author imgteam
date Wed, 17 Dec 2025 11:20:49 +0000
parents f4bcb0207519
children
comparison
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3:f4bcb0207519 4:a4bc9dfde846
1 import argparse 1 import argparse
2
3 import giatools.io
2 import numpy as np 4 import numpy as np
3 import pandas as pd 5 import pandas as pd
4 import skimage.io 6 import skimage.feature
5 import skimage.measure 7 import skimage.measure
6 import skimage.feature 8 import skimage.morphology
7 import skimage.segmentation 9 import skimage.segmentation
8 import skimage.morphology
9 10
10 #TODO make importable by python script
11 11
12 parser = argparse.ArgumentParser(description='Extract Features 2D') 12 if __name__ == '__main__':
13 13
14 #TODO create factory for boilerplate code 14 parser = argparse.ArgumentParser(description='Extract image features')
15 features = parser.add_argument_group('compute features')
16 features.add_argument('--all', dest='all_features', action='store_true')
17 features.add_argument('--label', dest='add_label', action='store_true')
18 features.add_argument('--patches', dest='add_roi_patches', action='store_true')
19 features.add_argument('--max_intensity', dest='max_intensity', action='store_true')
20 features.add_argument('--mean_intensity', dest='mean_intensity', action='store_true')
21 features.add_argument('--min_intensity', dest='min_intensity', action='store_true')
22 features.add_argument('--moments_hu', dest='moments_hu', action='store_true')
23 features.add_argument('--centroid', dest='centroid', action='store_true')
24 features.add_argument('--bbox', dest='bbox', action='store_true')
25 features.add_argument('--area', dest='area', action='store_true')
26 features.add_argument('--filled_area', dest='filled_area', action='store_true')
27 features.add_argument('--convex_area', dest='convex_area', action='store_true')
28 features.add_argument('--perimeter', dest='perimeter', action='store_true')
29 features.add_argument('--extent', dest='extent', action='store_true')
30 features.add_argument('--eccentricity', dest='eccentricity', action='store_true')
31 features.add_argument('--equivalent_diameter', dest='equivalent_diameter', action='store_true')
32 features.add_argument('--euler_number', dest='euler_number', action='store_true')
33 features.add_argument('--inertia_tensor_eigvals', dest='inertia_tensor_eigvals', action='store_true')
34 features.add_argument('--major_axis_length', dest='major_axis_length', action='store_true')
35 features.add_argument('--minor_axis_length', dest='minor_axis_length', action='store_true')
36 features.add_argument('--orientation', dest='orientation', action='store_true')
37 features.add_argument('--solidity', dest='solidity', action='store_true')
38 features.add_argument('--moments', dest='moments', action='store_true')
39 features.add_argument('--convexity', dest='convexity', action='store_true')
40 15
41 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')
42 42
43 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')
44 help='Original input file', required=False)
45 parser.add_argument('label_file', type=argparse.FileType('r'),
46 help='Label input file')
47 parser.add_argument('output_file', type=argparse.FileType('w'),
48 help='Tabular output file')
49 args = parser.parse_args()
50
51 label_file_binary = args.label_file_binary
52 label_file = args.label_file.name
53 out_file = args.output_file.name
54 add_patch = args.add_roi_patches
55 44
56 raw_image = None 45 parser.add_argument('--raw', dest='raw_file', type=argparse.FileType('r'),
57 if args.raw_file is not None: 46 help='Original input file', required=False)
58 raw_image = skimage.io.imread(args.raw_file.name) 47 parser.add_argument('label_file', type=argparse.FileType('r'),
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()
59 52
60 raw_label_image = skimage.io.imread(label_file) 53 label_file_binary = args.label_file_binary
54 label_file = args.label_file.name
55 out_file = args.output_file.name
56 add_patch = args.add_roi_patches
61 57
62 df = pd.DataFrame() 58 raw_image = None
63 if label_file_binary: 59 if args.raw_file is not None:
64 raw_label_image = skimage.measure.label(raw_label_image) 60 raw_image = giatools.io.imread(args.raw_file.name)
65 regions = skimage.measure.regionprops(raw_label_image, intensity_image=raw_image)
66 61
67 df['it'] = np.arange(len(regions)) 62 raw_label_image = giatools.io.imread(label_file)
68 63
69 if add_patch: 64 df = pd.DataFrame()
70 df['image'] = df['it'].map(lambda ait: regions[ait].image.astype(np.float).tolist()) 65 if label_file_binary:
71 df['intensity_image'] = df['it'].map(lambda ait: regions[ait].intensity_image.astype(np.float).tolist()) 66 raw_label_image = skimage.measure.label(raw_label_image)
67 regions = skimage.measure.regionprops(raw_label_image, intensity_image=raw_image)
72 68
73 #TODO no matrix features, but split in own rows? 69 df['it'] = np.arange(len(regions))
74 if args.add_label or args.all_features:
75 df['label'] = df['it'].map(lambda ait: regions[ait].label)
76 70
77 if raw_image is not None: 71 if add_patch:
78 if args.max_intensity or args.all_features: 72 df['image'] = df['it'].map(lambda ait: regions[ait].image.astype(np.float).tolist())
79 df['max_intensity'] = df['it'].map(lambda ait: regions[ait].max_intensity) 73 df['intensity_image'] = df['it'].map(lambda ait: regions[ait].intensity_image.astype(np.float).tolist())
80 if args.mean_intensity or args.all_features:
81 df['mean_intensity'] = df['it'].map(lambda ait: regions[ait].mean_intensity)
82 if args.min_intensity or args.all_features:
83 df['min_intensity'] = df['it'].map(lambda ait: regions[ait].min_intensity)
84 if args.moments_hu or args.all_features:
85 df['moments_hu'] = df['it'].map(lambda ait: regions[ait].moments_hu)
86 74
87 if args.centroid or args.all_features: 75 # TODO no matrix features, but split in own rows?
88 df['centroid'] = df['it'].map(lambda ait: regions[ait].centroid) 76 if args.add_label or args.all_features:
89 if args.bbox or args.all_features: 77 df['label'] = df['it'].map(lambda ait: regions[ait].label)
90 df['bbox'] = df['it'].map(lambda ait: regions[ait].bbox)
91 if args.area or args.all_features:
92 df['area'] = df['it'].map(lambda ait: regions[ait].area)
93 if args.filled_area or args.all_features:
94 df['filled_area'] = df['it'].map(lambda ait: regions[ait].filled_area)
95 if args.convex_area or args.all_features:
96 df['convex_area'] = df['it'].map(lambda ait: regions[ait].convex_area)
97 if args.perimeter or args.all_features:
98 df['perimeter'] = df['it'].map(lambda ait: regions[ait].perimeter)
99 if args.extent or args.all_features:
100 df['extent'] = df['it'].map(lambda ait: regions[ait].extent)
101 if args.eccentricity or args.all_features:
102 df['eccentricity'] = df['it'].map(lambda ait: regions[ait].eccentricity)
103 if args.equivalent_diameter or args.all_features:
104 df['equivalent_diameter'] = df['it'].map(lambda ait: regions[ait].equivalent_diameter)
105 if args.euler_number or args.all_features:
106 df['euler_number'] = df['it'].map(lambda ait: regions[ait].euler_number)
107 if args.inertia_tensor_eigvals or args.all_features:
108 df['inertia_tensor_eigvals'] = df['it'].map(lambda ait: regions[ait].inertia_tensor_eigvals)
109 if args.major_axis_length or args.all_features:
110 df['major_axis_length'] = df['it'].map(lambda ait: regions[ait].major_axis_length)
111 if args.minor_axis_length or args.all_features:
112 df['minor_axis_length'] = df['it'].map(lambda ait: regions[ait].minor_axis_length)
113 if args.orientation or args.all_features:
114 df['orientation'] = df['it'].map(lambda ait: regions[ait].orientation)
115 if args.solidity or args.all_features:
116 df['solidity'] = df['it'].map(lambda ait: regions[ait].solidity)
117 if args.moments or args.all_features:
118 df['moments'] = df['it'].map(lambda ait: regions[ait].moments)
119 if args.convexity or args.all_features:
120 perimeter = df['it'].map(lambda ait: regions[ait].perimeter)
121 area = df['it'].map(lambda ait: regions[ait].area)
122 df['convexity'] = area/(perimeter*perimeter)
123 78
124 del df['it'] 79 if raw_image is not None:
125 df.to_csv(out_file, sep='\t', line_terminator='\n', index=False) 80 if args.max_intensity or args.all_features:
81 df['max_intensity'] = df['it'].map(lambda ait: regions[ait].max_intensity)
82 if args.mean_intensity or args.all_features:
83 df['mean_intensity'] = df['it'].map(lambda ait: regions[ait].mean_intensity)
84 if args.min_intensity or args.all_features:
85 df['min_intensity'] = df['it'].map(lambda ait: regions[ait].min_intensity)
86 if args.moments_hu or args.all_features:
87 df['moments_hu'] = df['it'].map(lambda ait: regions[ait].moments_hu)
88
89 if args.centroid or args.all_features:
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', lineterminator='\n', index=False)