megadetector 5.0.28__py3-none-any.whl → 10.0.0__py3-none-any.whl

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  1. megadetector/api/batch_processing/integration/digiKam/xmp_integration.py +2 -2
  2. megadetector/api/batch_processing/integration/eMammal/test_scripts/push_annotations_to_emammal.py +1 -1
  3. megadetector/api/batch_processing/integration/eMammal/test_scripts/select_images_for_testing.py +1 -1
  4. megadetector/classification/aggregate_classifier_probs.py +3 -3
  5. megadetector/classification/analyze_failed_images.py +5 -5
  6. megadetector/classification/cache_batchapi_outputs.py +5 -5
  7. megadetector/classification/create_classification_dataset.py +11 -12
  8. megadetector/classification/crop_detections.py +10 -10
  9. megadetector/classification/csv_to_json.py +8 -8
  10. megadetector/classification/detect_and_crop.py +13 -15
  11. megadetector/classification/efficientnet/model.py +8 -8
  12. megadetector/classification/efficientnet/utils.py +6 -5
  13. megadetector/classification/evaluate_model.py +7 -7
  14. megadetector/classification/identify_mislabeled_candidates.py +6 -6
  15. megadetector/classification/json_to_azcopy_list.py +1 -1
  16. megadetector/classification/json_validator.py +29 -32
  17. megadetector/classification/map_classification_categories.py +9 -9
  18. megadetector/classification/merge_classification_detection_output.py +12 -9
  19. megadetector/classification/prepare_classification_script.py +19 -19
  20. megadetector/classification/prepare_classification_script_mc.py +26 -26
  21. megadetector/classification/run_classifier.py +4 -4
  22. megadetector/classification/save_mislabeled.py +6 -6
  23. megadetector/classification/train_classifier.py +1 -1
  24. megadetector/classification/train_classifier_tf.py +9 -9
  25. megadetector/classification/train_utils.py +10 -10
  26. megadetector/data_management/annotations/annotation_constants.py +1 -2
  27. megadetector/data_management/camtrap_dp_to_coco.py +79 -46
  28. megadetector/data_management/cct_json_utils.py +103 -103
  29. megadetector/data_management/cct_to_md.py +49 -49
  30. megadetector/data_management/cct_to_wi.py +33 -33
  31. megadetector/data_management/coco_to_labelme.py +75 -75
  32. megadetector/data_management/coco_to_yolo.py +210 -193
  33. megadetector/data_management/databases/add_width_and_height_to_db.py +86 -12
  34. megadetector/data_management/databases/combine_coco_camera_traps_files.py +40 -40
  35. megadetector/data_management/databases/integrity_check_json_db.py +228 -200
  36. megadetector/data_management/databases/subset_json_db.py +33 -33
  37. megadetector/data_management/generate_crops_from_cct.py +88 -39
  38. megadetector/data_management/get_image_sizes.py +54 -49
  39. megadetector/data_management/labelme_to_coco.py +133 -125
  40. megadetector/data_management/labelme_to_yolo.py +159 -73
  41. megadetector/data_management/lila/create_lila_blank_set.py +81 -83
  42. megadetector/data_management/lila/create_lila_test_set.py +32 -31
  43. megadetector/data_management/lila/create_links_to_md_results_files.py +18 -18
  44. megadetector/data_management/lila/download_lila_subset.py +21 -24
  45. megadetector/data_management/lila/generate_lila_per_image_labels.py +365 -107
  46. megadetector/data_management/lila/get_lila_annotation_counts.py +35 -33
  47. megadetector/data_management/lila/get_lila_image_counts.py +22 -22
  48. megadetector/data_management/lila/lila_common.py +73 -70
  49. megadetector/data_management/lila/test_lila_metadata_urls.py +28 -19
  50. megadetector/data_management/mewc_to_md.py +344 -340
  51. megadetector/data_management/ocr_tools.py +262 -255
  52. megadetector/data_management/read_exif.py +249 -227
  53. megadetector/data_management/remap_coco_categories.py +90 -28
  54. megadetector/data_management/remove_exif.py +81 -21
  55. megadetector/data_management/rename_images.py +187 -187
  56. megadetector/data_management/resize_coco_dataset.py +588 -120
  57. megadetector/data_management/speciesnet_to_md.py +41 -41
  58. megadetector/data_management/wi_download_csv_to_coco.py +55 -55
  59. megadetector/data_management/yolo_output_to_md_output.py +248 -122
  60. megadetector/data_management/yolo_to_coco.py +333 -191
  61. megadetector/detection/change_detection.py +832 -0
  62. megadetector/detection/process_video.py +340 -337
  63. megadetector/detection/pytorch_detector.py +358 -278
  64. megadetector/detection/run_detector.py +399 -186
  65. megadetector/detection/run_detector_batch.py +404 -377
  66. megadetector/detection/run_inference_with_yolov5_val.py +340 -327
  67. megadetector/detection/run_tiled_inference.py +257 -249
  68. megadetector/detection/tf_detector.py +24 -24
  69. megadetector/detection/video_utils.py +332 -295
  70. megadetector/postprocessing/add_max_conf.py +19 -11
  71. megadetector/postprocessing/categorize_detections_by_size.py +45 -45
  72. megadetector/postprocessing/classification_postprocessing.py +468 -433
  73. megadetector/postprocessing/combine_batch_outputs.py +23 -23
  74. megadetector/postprocessing/compare_batch_results.py +590 -525
  75. megadetector/postprocessing/convert_output_format.py +106 -102
  76. megadetector/postprocessing/create_crop_folder.py +347 -147
  77. megadetector/postprocessing/detector_calibration.py +173 -168
  78. megadetector/postprocessing/generate_csv_report.py +508 -499
  79. megadetector/postprocessing/load_api_results.py +48 -27
  80. megadetector/postprocessing/md_to_coco.py +133 -102
  81. megadetector/postprocessing/md_to_labelme.py +107 -90
  82. megadetector/postprocessing/md_to_wi.py +40 -40
  83. megadetector/postprocessing/merge_detections.py +92 -114
  84. megadetector/postprocessing/postprocess_batch_results.py +319 -301
  85. megadetector/postprocessing/remap_detection_categories.py +91 -38
  86. megadetector/postprocessing/render_detection_confusion_matrix.py +214 -205
  87. megadetector/postprocessing/repeat_detection_elimination/find_repeat_detections.py +57 -57
  88. megadetector/postprocessing/repeat_detection_elimination/remove_repeat_detections.py +27 -28
  89. megadetector/postprocessing/repeat_detection_elimination/repeat_detections_core.py +704 -679
  90. megadetector/postprocessing/separate_detections_into_folders.py +226 -211
  91. megadetector/postprocessing/subset_json_detector_output.py +265 -262
  92. megadetector/postprocessing/top_folders_to_bottom.py +45 -45
  93. megadetector/postprocessing/validate_batch_results.py +70 -70
  94. megadetector/taxonomy_mapping/map_lila_taxonomy_to_wi_taxonomy.py +52 -52
  95. megadetector/taxonomy_mapping/map_new_lila_datasets.py +18 -19
  96. megadetector/taxonomy_mapping/prepare_lila_taxonomy_release.py +54 -33
  97. megadetector/taxonomy_mapping/preview_lila_taxonomy.py +67 -67
  98. megadetector/taxonomy_mapping/retrieve_sample_image.py +16 -16
  99. megadetector/taxonomy_mapping/simple_image_download.py +8 -8
  100. megadetector/taxonomy_mapping/species_lookup.py +156 -74
  101. megadetector/taxonomy_mapping/taxonomy_csv_checker.py +14 -14
  102. megadetector/taxonomy_mapping/taxonomy_graph.py +10 -10
  103. megadetector/taxonomy_mapping/validate_lila_category_mappings.py +13 -13
  104. megadetector/utils/ct_utils.py +1049 -211
  105. megadetector/utils/directory_listing.py +21 -77
  106. megadetector/utils/gpu_test.py +22 -22
  107. megadetector/utils/md_tests.py +632 -529
  108. megadetector/utils/path_utils.py +1520 -431
  109. megadetector/utils/process_utils.py +41 -41
  110. megadetector/utils/split_locations_into_train_val.py +62 -62
  111. megadetector/utils/string_utils.py +148 -27
  112. megadetector/utils/url_utils.py +489 -176
  113. megadetector/utils/wi_utils.py +2658 -2526
  114. megadetector/utils/write_html_image_list.py +137 -137
  115. megadetector/visualization/plot_utils.py +34 -30
  116. megadetector/visualization/render_images_with_thumbnails.py +39 -74
  117. megadetector/visualization/visualization_utils.py +487 -435
  118. megadetector/visualization/visualize_db.py +232 -198
  119. megadetector/visualization/visualize_detector_output.py +82 -76
  120. {megadetector-5.0.28.dist-info → megadetector-10.0.0.dist-info}/METADATA +5 -2
  121. megadetector-10.0.0.dist-info/RECORD +139 -0
  122. {megadetector-5.0.28.dist-info → megadetector-10.0.0.dist-info}/WHEEL +1 -1
  123. megadetector/api/batch_processing/api_core/__init__.py +0 -0
  124. megadetector/api/batch_processing/api_core/batch_service/__init__.py +0 -0
  125. megadetector/api/batch_processing/api_core/batch_service/score.py +0 -439
  126. megadetector/api/batch_processing/api_core/server.py +0 -294
  127. megadetector/api/batch_processing/api_core/server_api_config.py +0 -97
  128. megadetector/api/batch_processing/api_core/server_app_config.py +0 -55
  129. megadetector/api/batch_processing/api_core/server_batch_job_manager.py +0 -220
  130. megadetector/api/batch_processing/api_core/server_job_status_table.py +0 -149
  131. megadetector/api/batch_processing/api_core/server_orchestration.py +0 -360
  132. megadetector/api/batch_processing/api_core/server_utils.py +0 -88
  133. megadetector/api/batch_processing/api_core_support/__init__.py +0 -0
  134. megadetector/api/batch_processing/api_core_support/aggregate_results_manually.py +0 -46
  135. megadetector/api/batch_processing/api_support/__init__.py +0 -0
  136. megadetector/api/batch_processing/api_support/summarize_daily_activity.py +0 -152
  137. megadetector/api/batch_processing/data_preparation/__init__.py +0 -0
  138. megadetector/api/synchronous/__init__.py +0 -0
  139. megadetector/api/synchronous/api_core/animal_detection_api/__init__.py +0 -0
  140. megadetector/api/synchronous/api_core/animal_detection_api/api_backend.py +0 -151
  141. megadetector/api/synchronous/api_core/animal_detection_api/api_frontend.py +0 -263
  142. megadetector/api/synchronous/api_core/animal_detection_api/config.py +0 -35
  143. megadetector/api/synchronous/api_core/tests/__init__.py +0 -0
  144. megadetector/api/synchronous/api_core/tests/load_test.py +0 -110
  145. megadetector/data_management/importers/add_nacti_sizes.py +0 -52
  146. megadetector/data_management/importers/add_timestamps_to_icct.py +0 -79
  147. megadetector/data_management/importers/animl_results_to_md_results.py +0 -158
  148. megadetector/data_management/importers/auckland_doc_test_to_json.py +0 -373
  149. megadetector/data_management/importers/auckland_doc_to_json.py +0 -201
  150. megadetector/data_management/importers/awc_to_json.py +0 -191
  151. megadetector/data_management/importers/bellevue_to_json.py +0 -272
  152. megadetector/data_management/importers/cacophony-thermal-importer.py +0 -793
  153. megadetector/data_management/importers/carrizo_shrubfree_2018.py +0 -269
  154. megadetector/data_management/importers/carrizo_trail_cam_2017.py +0 -289
  155. megadetector/data_management/importers/cct_field_adjustments.py +0 -58
  156. megadetector/data_management/importers/channel_islands_to_cct.py +0 -913
  157. megadetector/data_management/importers/eMammal/copy_and_unzip_emammal.py +0 -180
  158. megadetector/data_management/importers/eMammal/eMammal_helpers.py +0 -249
  159. megadetector/data_management/importers/eMammal/make_eMammal_json.py +0 -223
  160. megadetector/data_management/importers/ena24_to_json.py +0 -276
  161. megadetector/data_management/importers/filenames_to_json.py +0 -386
  162. megadetector/data_management/importers/helena_to_cct.py +0 -283
  163. megadetector/data_management/importers/idaho-camera-traps.py +0 -1407
  164. megadetector/data_management/importers/idfg_iwildcam_lila_prep.py +0 -294
  165. megadetector/data_management/importers/import_desert_lion_conservation_camera_traps.py +0 -387
  166. megadetector/data_management/importers/jb_csv_to_json.py +0 -150
  167. megadetector/data_management/importers/mcgill_to_json.py +0 -250
  168. megadetector/data_management/importers/missouri_to_json.py +0 -490
  169. megadetector/data_management/importers/nacti_fieldname_adjustments.py +0 -79
  170. megadetector/data_management/importers/noaa_seals_2019.py +0 -181
  171. megadetector/data_management/importers/osu-small-animals-to-json.py +0 -364
  172. megadetector/data_management/importers/pc_to_json.py +0 -365
  173. megadetector/data_management/importers/plot_wni_giraffes.py +0 -123
  174. megadetector/data_management/importers/prepare_zsl_imerit.py +0 -131
  175. megadetector/data_management/importers/raic_csv_to_md_results.py +0 -416
  176. megadetector/data_management/importers/rspb_to_json.py +0 -356
  177. megadetector/data_management/importers/save_the_elephants_survey_A.py +0 -320
  178. megadetector/data_management/importers/save_the_elephants_survey_B.py +0 -329
  179. megadetector/data_management/importers/snapshot_safari_importer.py +0 -758
  180. megadetector/data_management/importers/snapshot_serengeti_lila.py +0 -1067
  181. megadetector/data_management/importers/snapshotserengeti/make_full_SS_json.py +0 -150
  182. megadetector/data_management/importers/snapshotserengeti/make_per_season_SS_json.py +0 -153
  183. megadetector/data_management/importers/sulross_get_exif.py +0 -65
  184. megadetector/data_management/importers/timelapse_csv_set_to_json.py +0 -490
  185. megadetector/data_management/importers/ubc_to_json.py +0 -399
  186. megadetector/data_management/importers/umn_to_json.py +0 -507
  187. megadetector/data_management/importers/wellington_to_json.py +0 -263
  188. megadetector/data_management/importers/wi_to_json.py +0 -442
  189. megadetector/data_management/importers/zamba_results_to_md_results.py +0 -180
  190. megadetector/data_management/lila/add_locations_to_island_camera_traps.py +0 -101
  191. megadetector/data_management/lila/add_locations_to_nacti.py +0 -151
  192. megadetector/utils/azure_utils.py +0 -178
  193. megadetector/utils/sas_blob_utils.py +0 -509
  194. megadetector-5.0.28.dist-info/RECORD +0 -209
  195. /megadetector/{api/batch_processing/__init__.py → __init__.py} +0 -0
  196. {megadetector-5.0.28.dist-info → megadetector-10.0.0.dist-info}/licenses/LICENSE +0 -0
  197. {megadetector-5.0.28.dist-info → megadetector-10.0.0.dist-info}/top_level.txt +0 -0
@@ -2,7 +2,7 @@
2
2
 
3
3
  test_lila_metadata_urls.py
4
4
 
5
- Test that all the metadata URLs for LILA camera trap datasets are valid, including MegaDetector
5
+ Test that all the metadata URLs for LILA camera trap datasets are valid, including MegaDetector
6
6
  results files.
7
7
 
8
8
  Also pick an arbitrary image from each dataset and make sure that URL is valid.
@@ -18,6 +18,7 @@ import os
18
18
 
19
19
  from megadetector.data_management.lila.lila_common import read_lila_metadata,\
20
20
  read_metadata_file_for_dataset, read_lila_taxonomy_mapping
21
+ from megadetector.utils.url_utils import test_urls
21
22
 
22
23
  # We'll write images, metadata downloads, and temporary files here
23
24
  lila_local_base = os.path.expanduser('~/lila')
@@ -31,7 +32,7 @@ os.makedirs(metadata_dir,exist_ok=True)
31
32
  md_results_dir = os.path.join(lila_local_base,'md_results')
32
33
  os.makedirs(md_results_dir,exist_ok=True)
33
34
 
34
- md_results_keys = ['mdv4_results_raw','mdv5a_results_raw','mdv5b_results_raw',
35
+ md_results_keys = ['mdv5a_results_raw','mdv5b_results_raw',
35
36
  'md1000-redwood_results_raw','md_results_with_rde']
36
37
 
37
38
  preferred_cloud = None # 'gcp' # 'azure', 'aws'
@@ -53,19 +54,21 @@ print('Loaded metadata URLs for {} datasets'.format(len(metadata_table)))
53
54
 
54
55
  #%% Download and extract metadata and MD results for each dataset
55
56
 
56
- # Takes ~60 seconds if everything needs to be downloaded and unzipped
57
+ # Takes ~10 minutes if everything needs to be downloaded and unzipped
57
58
 
58
- for ds_name in metadata_table.keys():
59
+ for ds_name in metadata_table.keys():
59
60
 
60
61
  # Download the main metadata file for this dataset
61
62
  metadata_table[ds_name]['json_filename'] = \
62
63
  read_metadata_file_for_dataset(ds_name=ds_name,
63
64
  metadata_dir=metadata_dir,
64
65
  metadata_table=metadata_table,
65
- force_download=force_download)
66
-
66
+ force_download=force_download,
67
+ preferred_cloud=preferred_cloud)
68
+
67
69
  # Download MD results for this dataset
68
70
  for k in md_results_keys:
71
+
69
72
  md_results_url = metadata_table[ds_name][k]
70
73
  if md_results_url is None:
71
74
  metadata_table[ds_name][k + '_filename'] = None
@@ -74,7 +77,10 @@ for ds_name in metadata_table.keys():
74
77
  read_metadata_file_for_dataset(ds_name=ds_name,
75
78
  metadata_dir=md_results_dir,
76
79
  json_url=md_results_url,
77
- force_download=force_download)
80
+ force_download=force_download,
81
+ preferred_cloud=preferred_cloud)
82
+
83
+ # ...for each MD results file
78
84
 
79
85
  # ...for each dataset
80
86
 
@@ -93,13 +99,13 @@ image_index = 2000
93
99
  #
94
100
  # ds_name = list(metadata_table.keys())[0]
95
101
  for ds_name in metadata_table.keys():
96
-
102
+
97
103
  if 'bbox' in ds_name:
98
104
  print('Skipping bbox dataset {}'.format(ds_name))
99
105
  continue
100
106
 
101
107
  print('Processing dataset {}'.format(ds_name))
102
-
108
+
103
109
  json_filename = metadata_table[ds_name]['json_filename']
104
110
  with open(json_filename, 'r') as f:
105
111
  data = json.load(f)
@@ -108,21 +114,23 @@ for ds_name in metadata_table.keys():
108
114
  clouds = [preferred_cloud]
109
115
  else:
110
116
  clouds = ['gcp','aws','azure']
111
-
117
+
112
118
  for cloud in clouds:
113
-
119
+
114
120
  image_base_url = metadata_table[ds_name]['image_base_url_' + cloud]
115
121
  assert not image_base_url.endswith('/')
116
-
122
+
117
123
  # Download a test image
118
124
  test_image_relative_path = data['images'][image_index]['file_name']
119
125
  test_image_url = image_base_url + '/' + test_image_relative_path
120
-
126
+
121
127
  url_to_source[test_image_url] = ds_name + ' metadata ({})'.format(cloud)
122
-
128
+
129
+ # ...for each cloud
130
+
123
131
  # Grab an image from the MegaDetector results
124
-
125
- # k = md_results_keys[2]
132
+
133
+ # k = md_results_keys[0]
126
134
  for k in md_results_keys:
127
135
  k_fn = k + '_filename'
128
136
  if metadata_table[ds_name][k_fn] is not None:
@@ -133,14 +141,12 @@ for ds_name in metadata_table.keys():
133
141
  url_to_source[md_image_url] = ds_name + ' ' + k
134
142
  del md_results
135
143
  del data
136
-
144
+
137
145
  # ...for each dataset
138
146
 
139
147
 
140
148
  #%% Test URLs
141
149
 
142
- from megadetector.utils.url_utils import test_urls
143
-
144
150
  urls_to_test = sorted(url_to_source.keys())
145
151
  urls_to_test = [fn.replace('\\','/') for fn in urls_to_test]
146
152
 
@@ -154,3 +160,6 @@ for i_url,url in enumerate(urls_to_test):
154
160
  if status_codes[i_url] != 200:
155
161
  print('Status {} for {} ({})'.format(
156
162
  status_codes[i_url],url,url_to_source[url]))
163
+
164
+ print('Tested {} URLs'.format(len(urls_to_test)))
165
+