megadetector 5.0.7__py3-none-any.whl → 5.0.9__py3-none-any.whl

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  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
data_management/importers/prepare_zsl_imerit.py CHANGED
@@ -1,10 +1,10 @@
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- ########
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- #
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- # prepare_zsl_imerit.py
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- #
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- # Prepare ZSL Borneo data for annotation (convert input data to iMerit-friendly format).
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- #
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- ########
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+ """
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+
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+ prepare_zsl_imerit.py
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+
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+ Prepare ZSL Borneo data for annotation (convert input data to iMerit-friendly format).
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+
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+ """
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  #%% Imports and constants
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data_management/importers/rspb_to_json.py CHANGED
@@ -1,11 +1,11 @@
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- ########
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- #
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- # rspb_to_json.py
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- #
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- # Convert the .csv file provided for the RSPB data set to a
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- # COCO-camera-traps .json file
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- #
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- ########
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+ """
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+
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+ rspb_to_json.py
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+
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+ Convert the .csv file provided for the RSPB data set to a
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+ COCO-camera-traps .json file
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+
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+ """
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  #%% Constants and environment
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data_management/importers/save_the_elephants_survey_A.py CHANGED
@@ -1,11 +1,11 @@
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- ########
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- #
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- # save_the_elephants_survey_A.py
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- #
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- # Convert the .csv file provided for the Save the Elephants Survey A data set to a
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- # COCO-camera-traps .json file
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- #
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- ########
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+ """
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+
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+ save_the_elephants_survey_A.py
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+
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+ Convert the .csv file provided for the Save the Elephants Survey A data set to a
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+ COCO-camera-traps .json file
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+
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+ """
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  #%% Constants and environment
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data_management/importers/save_the_elephants_survey_B.py CHANGED
@@ -1,11 +1,11 @@
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- ########
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- #
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- # save_the_elephants_survey_B.py
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- #
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- # Convert the .csv file provided for the Save the Elephants Survey B data set to a
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- # COCO-camera-traps .json file
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- #
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- ########
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+ """
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+
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+ save_the_elephants_survey_B.py
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+
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+ Convert the .csv file provided for the Save the Elephants Survey B data set to a
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+ COCO-camera-traps .json file
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+
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+ """
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  #%% Constants and environment
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@@ -205,7 +205,7 @@ for image_name in tqdm(list(filenames_to_rows.keys())):
205
205
  if (isinstance(species,float) or \
206
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  (isinstance(species,str) and (len(species) == 0))):
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  category_name = 'empty'
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- elif species.startswith('?')
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+ elif species.startswith('?'):
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  category_name = 'unknown'
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  else:
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  category_name = species
data_management/importers/snapshot_safari_importer.py CHANGED
@@ -1,29 +1,29 @@
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- ########
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- #
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- # Import a Snapshot Safari project (one project, one season)
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- #
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- # Before running this script:
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- #
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- # * Mount the blob container where the images live, or copy the
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- # images to local storage
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- #
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- # What this script does:
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- #
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- # * Creates a .json file
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- # * Creates zip archives of the season without humans.
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- # * Copies animals and humans to separate folders
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- #
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- # After running this script:
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- #
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- # * Create or update LILA page
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- # * Push zipfile and unzipped images to LILA
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- # * Push unzipped humans to wildlifeblobssc
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- # * Delete images from UMN upload storage
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- #
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- # Snapshot Serengeti is handled specially, because we're dealing with bounding
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- # boxes too. See snapshot_serengeti_lila.py.
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- #
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- ########
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+ """
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+
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+ Import a Snapshot Safari project (one project, one season)
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+
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+ Before running this script:
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+
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+ * Mount the blob container where the images live, or copy the
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+ images to local storage
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+
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+ What this script does:
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+
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+ * Creates a .json file
13
+ * Creates zip archives of the season without humans.
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+ * Copies animals and humans to separate folders
15
+
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+ After running this script:
17
+
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+ * Create or update LILA page
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+ * Push zipfile and unzipped images to LILA
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+ * Push unzipped humans to wildlifeblobssc
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+ * Delete images from UMN upload storage
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+
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+ Snapshot Serengeti is handled specially, because we're dealing with bounding
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+ boxes too. See snapshot_serengeti_lila.py.
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+
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+ """
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27
 
28
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  #%% Imports
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