megadetector 5.0.8__py3-none-any.whl → 5.0.9__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of megadetector might be problematic. Click here for more details.

Files changed (190) hide show
  1. api/__init__.py +0 -0
  2. api/batch_processing/__init__.py +0 -0
  3. api/batch_processing/api_core/__init__.py +0 -0
  4. api/batch_processing/api_core/batch_service/__init__.py +0 -0
  5. api/batch_processing/api_core/batch_service/score.py +0 -1
  6. api/batch_processing/api_core/server_job_status_table.py +0 -1
  7. api/batch_processing/api_core_support/__init__.py +0 -0
  8. api/batch_processing/api_core_support/aggregate_results_manually.py +0 -1
  9. api/batch_processing/api_support/__init__.py +0 -0
  10. api/batch_processing/api_support/summarize_daily_activity.py +0 -1
  11. api/batch_processing/data_preparation/__init__.py +0 -0
  12. api/batch_processing/data_preparation/manage_local_batch.py +65 -65
  13. api/batch_processing/data_preparation/manage_video_batch.py +8 -8
  14. api/batch_processing/integration/digiKam/xmp_integration.py +0 -1
  15. api/batch_processing/integration/eMammal/test_scripts/push_annotations_to_emammal.py +0 -1
  16. api/batch_processing/postprocessing/__init__.py +0 -0
  17. api/batch_processing/postprocessing/add_max_conf.py +12 -12
  18. api/batch_processing/postprocessing/categorize_detections_by_size.py +32 -14
  19. api/batch_processing/postprocessing/combine_api_outputs.py +68 -54
  20. api/batch_processing/postprocessing/compare_batch_results.py +113 -43
  21. api/batch_processing/postprocessing/convert_output_format.py +41 -16
  22. api/batch_processing/postprocessing/load_api_results.py +16 -17
  23. api/batch_processing/postprocessing/md_to_coco.py +31 -21
  24. api/batch_processing/postprocessing/md_to_labelme.py +52 -22
  25. api/batch_processing/postprocessing/merge_detections.py +14 -14
  26. api/batch_processing/postprocessing/postprocess_batch_results.py +246 -174
  27. api/batch_processing/postprocessing/remap_detection_categories.py +32 -25
  28. api/batch_processing/postprocessing/render_detection_confusion_matrix.py +60 -27
  29. api/batch_processing/postprocessing/repeat_detection_elimination/find_repeat_detections.py +53 -44
  30. api/batch_processing/postprocessing/repeat_detection_elimination/remove_repeat_detections.py +25 -14
  31. api/batch_processing/postprocessing/repeat_detection_elimination/repeat_detections_core.py +242 -158
  32. api/batch_processing/postprocessing/separate_detections_into_folders.py +159 -114
  33. api/batch_processing/postprocessing/subset_json_detector_output.py +146 -169
  34. api/batch_processing/postprocessing/top_folders_to_bottom.py +77 -43
  35. api/synchronous/__init__.py +0 -0
  36. api/synchronous/api_core/animal_detection_api/__init__.py +0 -0
  37. api/synchronous/api_core/animal_detection_api/api_backend.py +0 -2
  38. api/synchronous/api_core/animal_detection_api/api_frontend.py +266 -268
  39. api/synchronous/api_core/animal_detection_api/config.py +35 -35
  40. api/synchronous/api_core/tests/__init__.py +0 -0
  41. api/synchronous/api_core/tests/load_test.py +109 -109
  42. classification/__init__.py +0 -0
  43. classification/aggregate_classifier_probs.py +21 -24
  44. classification/analyze_failed_images.py +11 -13
  45. classification/cache_batchapi_outputs.py +51 -51
  46. classification/create_classification_dataset.py +69 -68
  47. classification/crop_detections.py +54 -53
  48. classification/csv_to_json.py +97 -100
  49. classification/detect_and_crop.py +105 -105
  50. classification/evaluate_model.py +43 -42
  51. classification/identify_mislabeled_candidates.py +47 -46
  52. classification/json_to_azcopy_list.py +10 -10
  53. classification/json_validator.py +72 -71
  54. classification/map_classification_categories.py +44 -43
  55. classification/merge_classification_detection_output.py +68 -68
  56. classification/prepare_classification_script.py +157 -154
  57. classification/prepare_classification_script_mc.py +228 -228
  58. classification/run_classifier.py +27 -26
  59. classification/save_mislabeled.py +30 -30
  60. classification/train_classifier.py +20 -20
  61. classification/train_classifier_tf.py +21 -22
  62. classification/train_utils.py +10 -10
  63. data_management/__init__.py +0 -0
  64. data_management/annotations/__init__.py +0 -0
  65. data_management/annotations/annotation_constants.py +18 -31
  66. data_management/camtrap_dp_to_coco.py +238 -0
  67. data_management/cct_json_utils.py +102 -59
  68. data_management/cct_to_md.py +176 -158
  69. data_management/cct_to_wi.py +247 -219
  70. data_management/coco_to_labelme.py +272 -263
  71. data_management/coco_to_yolo.py +79 -58
  72. data_management/databases/__init__.py +0 -0
  73. data_management/databases/add_width_and_height_to_db.py +20 -16
  74. data_management/databases/combine_coco_camera_traps_files.py +35 -31
  75. data_management/databases/integrity_check_json_db.py +62 -24
  76. data_management/databases/subset_json_db.py +24 -15
  77. data_management/generate_crops_from_cct.py +27 -45
  78. data_management/get_image_sizes.py +188 -162
  79. data_management/importers/add_nacti_sizes.py +8 -8
  80. data_management/importers/add_timestamps_to_icct.py +78 -78
  81. data_management/importers/animl_results_to_md_results.py +158 -158
  82. data_management/importers/auckland_doc_test_to_json.py +9 -9
  83. data_management/importers/auckland_doc_to_json.py +8 -8
  84. data_management/importers/awc_to_json.py +7 -7
  85. data_management/importers/bellevue_to_json.py +15 -15
  86. data_management/importers/cacophony-thermal-importer.py +13 -13
  87. data_management/importers/carrizo_shrubfree_2018.py +8 -8
  88. data_management/importers/carrizo_trail_cam_2017.py +8 -8
  89. data_management/importers/cct_field_adjustments.py +9 -9
  90. data_management/importers/channel_islands_to_cct.py +10 -10
  91. data_management/importers/eMammal/copy_and_unzip_emammal.py +1 -0
  92. data_management/importers/ena24_to_json.py +7 -7
  93. data_management/importers/filenames_to_json.py +8 -8
  94. data_management/importers/helena_to_cct.py +7 -7
  95. data_management/importers/idaho-camera-traps.py +7 -7
  96. data_management/importers/idfg_iwildcam_lila_prep.py +10 -10
  97. data_management/importers/jb_csv_to_json.py +9 -9
  98. data_management/importers/mcgill_to_json.py +8 -8
  99. data_management/importers/missouri_to_json.py +18 -18
  100. data_management/importers/nacti_fieldname_adjustments.py +10 -10
  101. data_management/importers/noaa_seals_2019.py +7 -7
  102. data_management/importers/pc_to_json.py +7 -7
  103. data_management/importers/plot_wni_giraffes.py +7 -7
  104. data_management/importers/prepare-noaa-fish-data-for-lila.py +359 -359
  105. data_management/importers/prepare_zsl_imerit.py +7 -7
  106. data_management/importers/rspb_to_json.py +8 -8
  107. data_management/importers/save_the_elephants_survey_A.py +8 -8
  108. data_management/importers/save_the_elephants_survey_B.py +9 -9
  109. data_management/importers/snapshot_safari_importer.py +26 -26
  110. data_management/importers/snapshot_safari_importer_reprise.py +665 -665
  111. data_management/importers/snapshot_serengeti_lila.py +14 -14
  112. data_management/importers/sulross_get_exif.py +8 -9
  113. data_management/importers/timelapse_csv_set_to_json.py +11 -11
  114. data_management/importers/ubc_to_json.py +13 -13
  115. data_management/importers/umn_to_json.py +7 -7
  116. data_management/importers/wellington_to_json.py +8 -8
  117. data_management/importers/wi_to_json.py +9 -9
  118. data_management/importers/zamba_results_to_md_results.py +181 -181
  119. data_management/labelme_to_coco.py +65 -24
  120. data_management/labelme_to_yolo.py +8 -8
  121. data_management/lila/__init__.py +0 -0
  122. data_management/lila/add_locations_to_island_camera_traps.py +9 -9
  123. data_management/lila/add_locations_to_nacti.py +147 -147
  124. data_management/lila/create_lila_blank_set.py +13 -13
  125. data_management/lila/create_lila_test_set.py +8 -8
  126. data_management/lila/create_links_to_md_results_files.py +106 -106
  127. data_management/lila/download_lila_subset.py +44 -110
  128. data_management/lila/generate_lila_per_image_labels.py +55 -42
  129. data_management/lila/get_lila_annotation_counts.py +18 -15
  130. data_management/lila/get_lila_image_counts.py +11 -11
  131. data_management/lila/lila_common.py +96 -33
  132. data_management/lila/test_lila_metadata_urls.py +132 -116
  133. data_management/ocr_tools.py +173 -128
  134. data_management/read_exif.py +110 -97
  135. data_management/remap_coco_categories.py +83 -83
  136. data_management/remove_exif.py +58 -62
  137. data_management/resize_coco_dataset.py +30 -23
  138. data_management/wi_download_csv_to_coco.py +246 -239
  139. data_management/yolo_output_to_md_output.py +86 -73
  140. data_management/yolo_to_coco.py +300 -60
  141. detection/__init__.py +0 -0
  142. detection/detector_training/__init__.py +0 -0
  143. detection/process_video.py +85 -33
  144. detection/pytorch_detector.py +43 -25
  145. detection/run_detector.py +157 -72
  146. detection/run_detector_batch.py +179 -113
  147. detection/run_inference_with_yolov5_val.py +108 -48
  148. detection/run_tiled_inference.py +111 -40
  149. detection/tf_detector.py +51 -29
  150. detection/video_utils.py +606 -521
  151. docs/source/conf.py +43 -0
  152. md_utils/__init__.py +0 -0
  153. md_utils/azure_utils.py +9 -9
  154. md_utils/ct_utils.py +228 -68
  155. md_utils/directory_listing.py +59 -64
  156. md_utils/md_tests.py +968 -871
  157. md_utils/path_utils.py +460 -134
  158. md_utils/process_utils.py +157 -133
  159. md_utils/sas_blob_utils.py +20 -20
  160. md_utils/split_locations_into_train_val.py +45 -32
  161. md_utils/string_utils.py +33 -10
  162. md_utils/url_utils.py +176 -60
  163. md_utils/write_html_image_list.py +40 -33
  164. md_visualization/__init__.py +0 -0
  165. md_visualization/plot_utils.py +102 -109
  166. md_visualization/render_images_with_thumbnails.py +34 -34
  167. md_visualization/visualization_utils.py +597 -291
  168. md_visualization/visualize_db.py +76 -48
  169. md_visualization/visualize_detector_output.py +61 -42
  170. {megadetector-5.0.8.dist-info → megadetector-5.0.9.dist-info}/METADATA +13 -7
  171. megadetector-5.0.9.dist-info/RECORD +224 -0
  172. {megadetector-5.0.8.dist-info → megadetector-5.0.9.dist-info}/top_level.txt +1 -0
  173. taxonomy_mapping/__init__.py +0 -0
  174. taxonomy_mapping/map_lila_taxonomy_to_wi_taxonomy.py +342 -335
  175. taxonomy_mapping/map_new_lila_datasets.py +154 -154
  176. taxonomy_mapping/prepare_lila_taxonomy_release.py +142 -134
  177. taxonomy_mapping/preview_lila_taxonomy.py +591 -591
  178. taxonomy_mapping/retrieve_sample_image.py +12 -12
  179. taxonomy_mapping/simple_image_download.py +11 -11
  180. taxonomy_mapping/species_lookup.py +10 -10
  181. taxonomy_mapping/taxonomy_csv_checker.py +18 -18
  182. taxonomy_mapping/taxonomy_graph.py +47 -47
  183. taxonomy_mapping/validate_lila_category_mappings.py +83 -76
  184. data_management/cct_json_to_filename_json.py +0 -89
  185. data_management/cct_to_csv.py +0 -140
  186. data_management/databases/remove_corrupted_images_from_db.py +0 -191
  187. detection/detector_training/copy_checkpoints.py +0 -43
  188. megadetector-5.0.8.dist-info/RECORD +0 -205
  189. {megadetector-5.0.8.dist-info → megadetector-5.0.9.dist-info}/LICENSE +0 -0
  190. {megadetector-5.0.8.dist-info → megadetector-5.0.9.dist-info}/WHEEL +0 -0
data_management/importers/prepare_zsl_imerit.py CHANGED
@@ -1,10 +1,10 @@
1
- ########
2
- #
3
- # prepare_zsl_imerit.py
4
- #
5
- # Prepare ZSL Borneo data for annotation (convert input data to iMerit-friendly format).
6
- #
7
- ########
1
+ """
2
+
3
+ prepare_zsl_imerit.py
4
+
5
+ Prepare ZSL Borneo data for annotation (convert input data to iMerit-friendly format).
6
+
7
+ """
8
8
 
9
9
  #%% Imports and constants
10
10
 
data_management/importers/rspb_to_json.py CHANGED
@@ -1,11 +1,11 @@
1
- ########
2
- #
3
- # rspb_to_json.py
4
- #
5
- # Convert the .csv file provided for the RSPB data set to a
6
- # COCO-camera-traps .json file
7
- #
8
- ########
1
+ """
2
+
3
+ rspb_to_json.py
4
+
5
+ Convert the .csv file provided for the RSPB data set to a
6
+ COCO-camera-traps .json file
7
+
8
+ """
9
9
 
10
10
  #%% Constants and environment
11
11
 
data_management/importers/save_the_elephants_survey_A.py CHANGED
@@ -1,11 +1,11 @@
1
- ########
2
- #
3
- # save_the_elephants_survey_A.py
4
- #
5
- # Convert the .csv file provided for the Save the Elephants Survey A data set to a
6
- # COCO-camera-traps .json file
7
- #
8
- ########
1
+ """
2
+
3
+ save_the_elephants_survey_A.py
4
+
5
+ Convert the .csv file provided for the Save the Elephants Survey A data set to a
6
+ COCO-camera-traps .json file
7
+
8
+ """
9
9
 
10
10
  #%% Constants and environment
11
11
 
data_management/importers/save_the_elephants_survey_B.py CHANGED
@@ -1,11 +1,11 @@
1
- ########
2
- #
3
- # save_the_elephants_survey_B.py
4
- #
5
- # Convert the .csv file provided for the Save the Elephants Survey B data set to a
6
- # COCO-camera-traps .json file
7
- #
8
- ########
1
+ """
2
+
3
+ save_the_elephants_survey_B.py
4
+
5
+ Convert the .csv file provided for the Save the Elephants Survey B data set to a
6
+ COCO-camera-traps .json file
7
+
8
+ """
9
9
 
10
10
  #%% Constants and environment
11
11
 
@@ -205,7 +205,7 @@ for image_name in tqdm(list(filenames_to_rows.keys())):
205
205
  if (isinstance(species,float) or \
206
206
  (isinstance(species,str) and (len(species) == 0))):
207
207
  category_name = 'empty'
208
- elif species.startswith('?')
208
+ elif species.startswith('?'):
209
209
  category_name = 'unknown'
210
210
  else:
211
211
  category_name = species
data_management/importers/snapshot_safari_importer.py CHANGED
@@ -1,29 +1,29 @@
1
- ########
2
- #
3
- # Import a Snapshot Safari project (one project, one season)
4
- #
5
- # Before running this script:
6
- #
7
- # * Mount the blob container where the images live, or copy the
8
- # images to local storage
9
- #
10
- # What this script does:
11
- #
12
- # * Creates a .json file
13
- # * Creates zip archives of the season without humans.
14
- # * Copies animals and humans to separate folders
15
- #
16
- # After running this script:
17
- #
18
- # * Create or update LILA page
19
- # * Push zipfile and unzipped images to LILA
20
- # * Push unzipped humans to wildlifeblobssc
21
- # * Delete images from UMN upload storage
22
- #
23
- # Snapshot Serengeti is handled specially, because we're dealing with bounding
24
- # boxes too. See snapshot_serengeti_lila.py.
25
- #
26
- ########
1
+ """
2
+
3
+ Import a Snapshot Safari project (one project, one season)
4
+
5
+ Before running this script:
6
+
7
+ * Mount the blob container where the images live, or copy the
8
+ images to local storage
9
+
10
+ What this script does:
11
+
12
+ * Creates a .json file
13
+ * Creates zip archives of the season without humans.
14
+ * Copies animals and humans to separate folders
15
+
16
+ After running this script:
17
+
18
+ * Create or update LILA page
19
+ * Push zipfile and unzipped images to LILA
20
+ * Push unzipped humans to wildlifeblobssc
21
+ * Delete images from UMN upload storage
22
+
23
+ Snapshot Serengeti is handled specially, because we're dealing with bounding
24
+ boxes too. See snapshot_serengeti_lila.py.
25
+
26
+ """
27
27
 
28
28
  #%% Imports
29
29