megadetector 5.0.7__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 (191) 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 +93 -79
  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 +69 -55
  20. api/batch_processing/postprocessing/compare_batch_results.py +114 -44
  21. api/batch_processing/postprocessing/convert_output_format.py +62 -19
  22. api/batch_processing/postprocessing/load_api_results.py +17 -20
  23. api/batch_processing/postprocessing/md_to_coco.py +31 -21
  24. api/batch_processing/postprocessing/md_to_labelme.py +165 -68
  25. api/batch_processing/postprocessing/merge_detections.py +40 -15
  26. api/batch_processing/postprocessing/postprocess_batch_results.py +270 -186
  27. api/batch_processing/postprocessing/remap_detection_categories.py +170 -0
  28. api/batch_processing/postprocessing/render_detection_confusion_matrix.py +75 -39
  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 +244 -160
  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 +107 -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 -0
  71. data_management/coco_to_yolo.py +86 -62
  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 +130 -83
  76. data_management/databases/subset_json_db.py +25 -16
  77. data_management/generate_crops_from_cct.py +27 -45
  78. data_management/get_image_sizes.py +188 -144
  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 -160
  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 +8 -8
  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 +309 -159
  120. data_management/labelme_to_yolo.py +103 -60
  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 +114 -31
  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 +92 -90
  128. data_management/lila/generate_lila_per_image_labels.py +56 -43
  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 +103 -70
  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 +161 -99
  135. data_management/remap_coco_categories.py +84 -0
  136. data_management/remove_exif.py +58 -62
  137. data_management/resize_coco_dataset.py +32 -44
  138. data_management/wi_download_csv_to_coco.py +246 -0
  139. data_management/yolo_output_to_md_output.py +86 -73
  140. data_management/yolo_to_coco.py +535 -95
  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 +189 -114
  147. detection/run_inference_with_yolov5_val.py +118 -51
  148. detection/run_tiled_inference.py +113 -42
  149. detection/tf_detector.py +51 -28
  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 +249 -70
  155. md_utils/directory_listing.py +59 -64
  156. md_utils/md_tests.py +968 -862
  157. md_utils/path_utils.py +655 -155
  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 +208 -27
  163. md_utils/write_html_image_list.py +51 -35
  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 +908 -311
  168. md_visualization/visualize_db.py +109 -58
  169. md_visualization/visualize_detector_output.py +61 -42
  170. {megadetector-5.0.7.dist-info → megadetector-5.0.9.dist-info}/METADATA +21 -17
  171. megadetector-5.0.9.dist-info/RECORD +224 -0
  172. {megadetector-5.0.7.dist-info → megadetector-5.0.9.dist-info}/WHEEL +1 -1
  173. {megadetector-5.0.7.dist-info → megadetector-5.0.9.dist-info}/top_level.txt +1 -0
  174. taxonomy_mapping/__init__.py +0 -0
  175. taxonomy_mapping/map_lila_taxonomy_to_wi_taxonomy.py +342 -335
  176. taxonomy_mapping/map_new_lila_datasets.py +154 -154
  177. taxonomy_mapping/prepare_lila_taxonomy_release.py +142 -134
  178. taxonomy_mapping/preview_lila_taxonomy.py +591 -591
  179. taxonomy_mapping/retrieve_sample_image.py +12 -12
  180. taxonomy_mapping/simple_image_download.py +11 -11
  181. taxonomy_mapping/species_lookup.py +10 -10
  182. taxonomy_mapping/taxonomy_csv_checker.py +18 -18
  183. taxonomy_mapping/taxonomy_graph.py +47 -47
  184. taxonomy_mapping/validate_lila_category_mappings.py +83 -76
  185. data_management/cct_json_to_filename_json.py +0 -89
  186. data_management/cct_to_csv.py +0 -140
  187. data_management/databases/remove_corrupted_images_from_db.py +0 -191
  188. detection/detector_training/copy_checkpoints.py +0 -43
  189. md_visualization/visualize_megadb.py +0 -183
  190. megadetector-5.0.7.dist-info/RECORD +0 -202
  191. {megadetector-5.0.7.dist-info → megadetector-5.0.9.dist-info}/LICENSE +0 -0
@@ -1,12 +1,12 @@
1
- ########
2
- #
3
- # jb_csv_to_json.py
4
- #
5
- # Convert a particular .csv file to CCT format. Images were not available at
6
- # the time I wrote this script, so this is much shorter than other scripts
7
- # in this folder.
8
- #
9
- ########
1
+ """
2
+
3
+ jb_csv_to_json.py
4
+
5
+ Convert a particular .csv file to CCT format. Images were not available at
6
+ the time I wrote this script, so this is much shorter than other scripts
7
+ in this folder.
8
+
9
+ """
10
10
 
11
11
  #%% Constants and environment
12
12
 
@@ -1,11 +1,11 @@
1
- ########
2
- #
3
- # mcgill_to_json.py
4
- #
5
- # Convert the .csv file provided for the McGill test data set to a
6
- # COCO-camera-traps .json file
7
- #
8
- ########
1
+ """
2
+
3
+ mcgill_to_json.py
4
+
5
+ Convert the .csv file provided for the McGill test data set to a
6
+ COCO-camera-traps .json file
7
+
8
+ """
9
9
 
10
10
  #%% Constants and environment
11
11
 
@@ -1,21 +1,21 @@
1
- ########
2
- #
3
- # missouri_to_json.py
4
- #
5
- # Create .json files from the original source files for the Missouri Camera Traps
6
- # data set. Metadata was provided here in two formats:
7
- #
8
- # 1) In one subset of the data, folder names indicated species names. In Set 1,
9
- # there are no empty sequences. Set 1 has a metadata file to indicate image-level
10
- # bounding boxes.
11
- #
12
- # 2) A subset of the data (overlapping with (1)) was annotated with bounding
13
- # boxes, specified in a whitespace-delimited text file. In set 2, there are
14
- # some sequences omitted from the metadata file, which implied emptiness.
15
- #
16
- # In the end, set 2 labels were not reliable enough to publish, so LILA includes only set 1.
17
- #
18
- ########
1
+ """
2
+
3
+ missouri_to_json.py
4
+
5
+ Create .json files from the original source files for the Missouri Camera Traps
6
+ data set. Metadata was provided here in two formats:
7
+
8
+ 1) In one subset of the data, folder names indicated species names. In Set 1,
9
+ there are no empty sequences. Set 1 has a metadata file to indicate image-level
10
+ bounding boxes.
11
+
12
+ 2) A subset of the data (overlapping with (1)) was annotated with bounding
13
+ boxes, specified in a whitespace-delimited text file. In set 2, there are
14
+ some sequences omitted from the metadata file, which implied emptiness.
15
+
16
+ In the end, set 2 labels were not reliable enough to publish, so LILA includes only set 1.
17
+
18
+ """
19
19
 
20
20
  #%% Constants and imports
21
21
 
@@ -1,13 +1,13 @@
1
- ########
2
- #
3
- # nacti_fieldname_adjustments.py
4
- #
5
- # NACTI metadata was posted with "filename" in images instead of "file_name", and
6
- # used string (rather than int) category IDs (in categories, but not in annotations).
7
- #
8
- # This script fixes those issues and rev's the version number.
9
- #
10
- ########
1
+ """
2
+
3
+ nacti_fieldname_adjustments.py
4
+
5
+ NACTI metadata was posted with "filename" in images instead of "file_name", and
6
+ used string (rather than int) category IDs (in categories, but not in annotations).
7
+
8
+ This script fixes those issues and rev's the version number.
9
+
10
+ """
11
11
 
12
12
  #%% Constants and environment
13
13
 
@@ -1,10 +1,10 @@
1
- ########
2
- #
3
- # noaa_seals_2019.py
4
- #
5
- # Prepare the NOAA Arctic Seals 2019 metadata for LILA.
6
- #
7
- ########
1
+ """
2
+
3
+ noaa_seals_2019.py
4
+
5
+ Prepare the NOAA Arctic Seals 2019 metadata for LILA.
6
+
7
+ """
8
8
 
9
9
  #%% Imports and constants
10
10
 
@@ -165,7 +165,7 @@ for b in ir_boxes:
165
165
  use_normalized_coordinates=False,
166
166
  thickness=3)
167
167
 
168
- visualization_utils.show_images_in_a_row([img_rgb,img_ir])
168
+ # visualization_utils.show_images_in_a_row([img_rgb,img_ir])
169
169
 
170
170
 
171
171
  #%% Save images
@@ -1,10 +1,10 @@
1
- ########
2
- #
3
- # pc_to_json.py
4
- #
5
- # Convert a particular collection of .csv files from Parks Canada to CCT format.
6
- #
7
- ########
1
+ """
2
+
3
+ pc_to_json.py
4
+
5
+ Convert a particular collection of .csv files from Parks Canada to CCT format.
6
+
7
+ """
8
8
 
9
9
  #%% Constants and environment
10
10
 
@@ -1,10 +1,10 @@
1
- ########
2
- #
3
- # plot_wni_giraffes.py
4
- #
5
- # Plot keypoints on a random sample of images from the wni-giraffes data set.
6
- #
7
- ########
1
+ """
2
+
3
+ plot_wni_giraffes.py
4
+
5
+ Plot keypoints on a random sample of images from the wni-giraffes data set.
6
+
7
+ """
8
8
 
9
9
  #%% Constants and imports
10
10