megadetector 5.0.11__py3-none-any.whl → 5.0.12__py3-none-any.whl

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  1. megadetector/api/__init__.py +0 -0
  2. megadetector/api/batch_processing/__init__.py +0 -0
  3. megadetector/api/batch_processing/api_core/__init__.py +0 -0
  4. megadetector/api/batch_processing/api_core/batch_service/__init__.py +0 -0
  5. megadetector/api/batch_processing/api_core/batch_service/score.py +439 -0
  6. megadetector/api/batch_processing/api_core/server.py +294 -0
  7. megadetector/api/batch_processing/api_core/server_api_config.py +98 -0
  8. megadetector/api/batch_processing/api_core/server_app_config.py +55 -0
  9. megadetector/api/batch_processing/api_core/server_batch_job_manager.py +220 -0
  10. megadetector/api/batch_processing/api_core/server_job_status_table.py +152 -0
  11. megadetector/api/batch_processing/api_core/server_orchestration.py +360 -0
  12. megadetector/api/batch_processing/api_core/server_utils.py +92 -0
  13. megadetector/api/batch_processing/api_core_support/__init__.py +0 -0
  14. megadetector/api/batch_processing/api_core_support/aggregate_results_manually.py +46 -0
  15. megadetector/api/batch_processing/api_support/__init__.py +0 -0
  16. megadetector/api/batch_processing/api_support/summarize_daily_activity.py +152 -0
  17. megadetector/api/batch_processing/data_preparation/__init__.py +0 -0
  18. megadetector/api/batch_processing/integration/digiKam/setup.py +6 -0
  19. megadetector/api/batch_processing/integration/digiKam/xmp_integration.py +465 -0
  20. megadetector/api/batch_processing/integration/eMammal/test_scripts/config_template.py +5 -0
  21. megadetector/api/batch_processing/integration/eMammal/test_scripts/push_annotations_to_emammal.py +126 -0
  22. megadetector/api/batch_processing/integration/eMammal/test_scripts/select_images_for_testing.py +55 -0
  23. megadetector/api/synchronous/__init__.py +0 -0
  24. megadetector/api/synchronous/api_core/animal_detection_api/__init__.py +0 -0
  25. megadetector/api/synchronous/api_core/animal_detection_api/api_backend.py +152 -0
  26. megadetector/api/synchronous/api_core/animal_detection_api/api_frontend.py +266 -0
  27. megadetector/api/synchronous/api_core/animal_detection_api/config.py +35 -0
  28. megadetector/api/synchronous/api_core/tests/__init__.py +0 -0
  29. megadetector/api/synchronous/api_core/tests/load_test.py +110 -0
  30. megadetector/classification/__init__.py +0 -0
  31. megadetector/classification/aggregate_classifier_probs.py +108 -0
  32. megadetector/classification/analyze_failed_images.py +227 -0
  33. megadetector/classification/cache_batchapi_outputs.py +198 -0
  34. megadetector/classification/create_classification_dataset.py +627 -0
  35. megadetector/classification/crop_detections.py +516 -0
  36. megadetector/classification/csv_to_json.py +226 -0
  37. megadetector/classification/detect_and_crop.py +855 -0
  38. megadetector/classification/efficientnet/__init__.py +9 -0
  39. megadetector/classification/efficientnet/model.py +415 -0
  40. megadetector/classification/efficientnet/utils.py +610 -0
  41. megadetector/classification/evaluate_model.py +520 -0
  42. megadetector/classification/identify_mislabeled_candidates.py +152 -0
  43. megadetector/classification/json_to_azcopy_list.py +63 -0
  44. megadetector/classification/json_validator.py +699 -0
  45. megadetector/classification/map_classification_categories.py +276 -0
  46. megadetector/classification/merge_classification_detection_output.py +506 -0
  47. megadetector/classification/prepare_classification_script.py +194 -0
  48. megadetector/classification/prepare_classification_script_mc.py +228 -0
  49. megadetector/classification/run_classifier.py +287 -0
  50. megadetector/classification/save_mislabeled.py +110 -0
  51. megadetector/classification/train_classifier.py +827 -0
  52. megadetector/classification/train_classifier_tf.py +725 -0
  53. megadetector/classification/train_utils.py +323 -0
  54. megadetector/data_management/__init__.py +0 -0
  55. megadetector/data_management/annotations/__init__.py +0 -0
  56. megadetector/data_management/annotations/annotation_constants.py +34 -0
  57. megadetector/data_management/camtrap_dp_to_coco.py +239 -0
  58. megadetector/data_management/cct_json_utils.py +395 -0
  59. megadetector/data_management/cct_to_md.py +176 -0
  60. megadetector/data_management/cct_to_wi.py +289 -0
  61. megadetector/data_management/coco_to_labelme.py +272 -0
  62. megadetector/data_management/coco_to_yolo.py +662 -0
  63. megadetector/data_management/databases/__init__.py +0 -0
  64. megadetector/data_management/databases/add_width_and_height_to_db.py +33 -0
  65. megadetector/data_management/databases/combine_coco_camera_traps_files.py +206 -0
  66. megadetector/data_management/databases/integrity_check_json_db.py +477 -0
  67. megadetector/data_management/databases/subset_json_db.py +115 -0
  68. megadetector/data_management/generate_crops_from_cct.py +149 -0
  69. megadetector/data_management/get_image_sizes.py +189 -0
  70. megadetector/data_management/importers/add_nacti_sizes.py +52 -0
  71. megadetector/data_management/importers/add_timestamps_to_icct.py +79 -0
  72. megadetector/data_management/importers/animl_results_to_md_results.py +158 -0
  73. megadetector/data_management/importers/auckland_doc_test_to_json.py +373 -0
  74. megadetector/data_management/importers/auckland_doc_to_json.py +201 -0
  75. megadetector/data_management/importers/awc_to_json.py +191 -0
  76. megadetector/data_management/importers/bellevue_to_json.py +273 -0
  77. megadetector/data_management/importers/cacophony-thermal-importer.py +796 -0
  78. megadetector/data_management/importers/carrizo_shrubfree_2018.py +269 -0
  79. megadetector/data_management/importers/carrizo_trail_cam_2017.py +289 -0
  80. megadetector/data_management/importers/cct_field_adjustments.py +58 -0
  81. megadetector/data_management/importers/channel_islands_to_cct.py +913 -0
  82. megadetector/data_management/importers/eMammal/copy_and_unzip_emammal.py +180 -0
  83. megadetector/data_management/importers/eMammal/eMammal_helpers.py +249 -0
  84. megadetector/data_management/importers/eMammal/make_eMammal_json.py +223 -0
  85. megadetector/data_management/importers/ena24_to_json.py +276 -0
  86. megadetector/data_management/importers/filenames_to_json.py +386 -0
  87. megadetector/data_management/importers/helena_to_cct.py +283 -0
  88. megadetector/data_management/importers/idaho-camera-traps.py +1407 -0
  89. megadetector/data_management/importers/idfg_iwildcam_lila_prep.py +294 -0
  90. megadetector/data_management/importers/jb_csv_to_json.py +150 -0
  91. megadetector/data_management/importers/mcgill_to_json.py +250 -0
  92. megadetector/data_management/importers/missouri_to_json.py +490 -0
  93. megadetector/data_management/importers/nacti_fieldname_adjustments.py +79 -0
  94. megadetector/data_management/importers/noaa_seals_2019.py +181 -0
  95. megadetector/data_management/importers/pc_to_json.py +365 -0
  96. megadetector/data_management/importers/plot_wni_giraffes.py +123 -0
  97. megadetector/data_management/importers/prepare-noaa-fish-data-for-lila.py +359 -0
  98. megadetector/data_management/importers/prepare_zsl_imerit.py +131 -0
  99. megadetector/data_management/importers/rspb_to_json.py +356 -0
  100. megadetector/data_management/importers/save_the_elephants_survey_A.py +320 -0
  101. megadetector/data_management/importers/save_the_elephants_survey_B.py +329 -0
  102. megadetector/data_management/importers/snapshot_safari_importer.py +758 -0
  103. megadetector/data_management/importers/snapshot_safari_importer_reprise.py +665 -0
  104. megadetector/data_management/importers/snapshot_serengeti_lila.py +1067 -0
  105. megadetector/data_management/importers/snapshotserengeti/make_full_SS_json.py +150 -0
  106. megadetector/data_management/importers/snapshotserengeti/make_per_season_SS_json.py +153 -0
  107. megadetector/data_management/importers/sulross_get_exif.py +65 -0
  108. megadetector/data_management/importers/timelapse_csv_set_to_json.py +490 -0
  109. megadetector/data_management/importers/ubc_to_json.py +399 -0
  110. megadetector/data_management/importers/umn_to_json.py +507 -0
  111. megadetector/data_management/importers/wellington_to_json.py +263 -0
  112. megadetector/data_management/importers/wi_to_json.py +442 -0
  113. megadetector/data_management/importers/zamba_results_to_md_results.py +181 -0
  114. megadetector/data_management/labelme_to_coco.py +547 -0
  115. megadetector/data_management/labelme_to_yolo.py +272 -0
  116. megadetector/data_management/lila/__init__.py +0 -0
  117. megadetector/data_management/lila/add_locations_to_island_camera_traps.py +97 -0
  118. megadetector/data_management/lila/add_locations_to_nacti.py +147 -0
  119. megadetector/data_management/lila/create_lila_blank_set.py +558 -0
  120. megadetector/data_management/lila/create_lila_test_set.py +152 -0
  121. megadetector/data_management/lila/create_links_to_md_results_files.py +106 -0
  122. megadetector/data_management/lila/download_lila_subset.py +178 -0
  123. megadetector/data_management/lila/generate_lila_per_image_labels.py +516 -0
  124. megadetector/data_management/lila/get_lila_annotation_counts.py +170 -0
  125. megadetector/data_management/lila/get_lila_image_counts.py +112 -0
  126. megadetector/data_management/lila/lila_common.py +300 -0
  127. megadetector/data_management/lila/test_lila_metadata_urls.py +132 -0
  128. megadetector/data_management/ocr_tools.py +874 -0
  129. megadetector/data_management/read_exif.py +681 -0
  130. megadetector/data_management/remap_coco_categories.py +84 -0
  131. megadetector/data_management/remove_exif.py +66 -0
  132. megadetector/data_management/resize_coco_dataset.py +189 -0
  133. megadetector/data_management/wi_download_csv_to_coco.py +246 -0
  134. megadetector/data_management/yolo_output_to_md_output.py +441 -0
  135. megadetector/data_management/yolo_to_coco.py +676 -0
  136. megadetector/detection/__init__.py +0 -0
  137. megadetector/detection/detector_training/__init__.py +0 -0
  138. megadetector/detection/detector_training/model_main_tf2.py +114 -0
  139. megadetector/detection/process_video.py +702 -0
  140. megadetector/detection/pytorch_detector.py +341 -0
  141. megadetector/detection/run_detector.py +779 -0
  142. megadetector/detection/run_detector_batch.py +1219 -0
  143. megadetector/detection/run_inference_with_yolov5_val.py +917 -0
  144. megadetector/detection/run_tiled_inference.py +934 -0
  145. megadetector/detection/tf_detector.py +189 -0
  146. megadetector/detection/video_utils.py +606 -0
  147. megadetector/postprocessing/__init__.py +0 -0
  148. megadetector/postprocessing/add_max_conf.py +64 -0
  149. megadetector/postprocessing/categorize_detections_by_size.py +163 -0
  150. megadetector/postprocessing/combine_api_outputs.py +249 -0
  151. megadetector/postprocessing/compare_batch_results.py +958 -0
  152. megadetector/postprocessing/convert_output_format.py +396 -0
  153. megadetector/postprocessing/load_api_results.py +195 -0
  154. megadetector/postprocessing/md_to_coco.py +310 -0
  155. megadetector/postprocessing/md_to_labelme.py +330 -0
  156. megadetector/postprocessing/merge_detections.py +401 -0
  157. megadetector/postprocessing/postprocess_batch_results.py +1902 -0
  158. megadetector/postprocessing/remap_detection_categories.py +170 -0
  159. megadetector/postprocessing/render_detection_confusion_matrix.py +660 -0
  160. megadetector/postprocessing/repeat_detection_elimination/find_repeat_detections.py +211 -0
  161. megadetector/postprocessing/repeat_detection_elimination/remove_repeat_detections.py +83 -0
  162. megadetector/postprocessing/repeat_detection_elimination/repeat_detections_core.py +1631 -0
  163. megadetector/postprocessing/separate_detections_into_folders.py +730 -0
  164. megadetector/postprocessing/subset_json_detector_output.py +696 -0
  165. megadetector/postprocessing/top_folders_to_bottom.py +223 -0
  166. megadetector/taxonomy_mapping/__init__.py +0 -0
  167. megadetector/taxonomy_mapping/map_lila_taxonomy_to_wi_taxonomy.py +491 -0
  168. megadetector/taxonomy_mapping/map_new_lila_datasets.py +150 -0
  169. megadetector/taxonomy_mapping/prepare_lila_taxonomy_release.py +142 -0
  170. megadetector/taxonomy_mapping/preview_lila_taxonomy.py +590 -0
  171. megadetector/taxonomy_mapping/retrieve_sample_image.py +71 -0
  172. megadetector/taxonomy_mapping/simple_image_download.py +219 -0
  173. megadetector/taxonomy_mapping/species_lookup.py +834 -0
  174. megadetector/taxonomy_mapping/taxonomy_csv_checker.py +159 -0
  175. megadetector/taxonomy_mapping/taxonomy_graph.py +346 -0
  176. megadetector/taxonomy_mapping/validate_lila_category_mappings.py +83 -0
  177. megadetector/utils/__init__.py +0 -0
  178. megadetector/utils/azure_utils.py +178 -0
  179. megadetector/utils/ct_utils.py +612 -0
  180. megadetector/utils/directory_listing.py +246 -0
  181. megadetector/utils/md_tests.py +968 -0
  182. megadetector/utils/path_utils.py +1044 -0
  183. megadetector/utils/process_utils.py +157 -0
  184. megadetector/utils/sas_blob_utils.py +509 -0
  185. megadetector/utils/split_locations_into_train_val.py +228 -0
  186. megadetector/utils/string_utils.py +92 -0
  187. megadetector/utils/url_utils.py +323 -0
  188. megadetector/utils/write_html_image_list.py +225 -0
  189. megadetector/visualization/__init__.py +0 -0
  190. megadetector/visualization/plot_utils.py +293 -0
  191. megadetector/visualization/render_images_with_thumbnails.py +275 -0
  192. megadetector/visualization/visualization_utils.py +1536 -0
  193. megadetector/visualization/visualize_db.py +550 -0
  194. megadetector/visualization/visualize_detector_output.py +405 -0
  195. {megadetector-5.0.11.dist-info → megadetector-5.0.12.dist-info}/METADATA +1 -1
  196. megadetector-5.0.12.dist-info/RECORD +199 -0
  197. megadetector-5.0.12.dist-info/top_level.txt +1 -0
  198. megadetector-5.0.11.dist-info/RECORD +0 -5
  199. megadetector-5.0.11.dist-info/top_level.txt +0 -1
  200. {megadetector-5.0.11.dist-info → megadetector-5.0.12.dist-info}/LICENSE +0 -0
  201. {megadetector-5.0.11.dist-info → megadetector-5.0.12.dist-info}/WHEEL +0 -0
@@ -0,0 +1,114 @@
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+ # Lint as: python3
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+ # Copyright 2020 The TensorFlow Authors. All Rights Reserved.
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+ #
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+ # Licensed under the Apache License, Version 2.0 (the "License");
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+ # you may not use this file except in compliance with the License.
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+ # You may obtain a copy of the License at
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+ #
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+ # http://www.apache.org/licenses/LICENSE-2.0
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+ #
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+ # Unless required by applicable law or agreed to in writing, software
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+ # distributed under the License is distributed on an "AS IS" BASIS,
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+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+ # See the License for the specific language governing permissions and
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+ # limitations under the License.
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+ # ==============================================================================
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+
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+ r"""Creates and runs TF2 object detection models.
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+ For local training/evaluation run:
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+ PIPELINE_CONFIG_PATH=path/to/pipeline.config
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+ MODEL_DIR=/tmp/model_outputs
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+ NUM_TRAIN_STEPS=10000
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+ SAMPLE_1_OF_N_EVAL_EXAMPLES=1
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+ python model_main_tf2.py -- \
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+ --model_dir=$MODEL_DIR --num_train_steps=$NUM_TRAIN_STEPS \
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+ --sample_1_of_n_eval_examples=$SAMPLE_1_OF_N_EVAL_EXAMPLES \
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+ --pipeline_config_path=$PIPELINE_CONFIG_PATH \
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+ --alsologtostderr
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+ """
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+ from absl import flags
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+ import tensorflow.compat.v2 as tf
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+ from object_detection import model_lib_v2
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+
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+ flags.DEFINE_string('pipeline_config_path', None, 'Path to pipeline config '
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+ 'file.')
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+ flags.DEFINE_integer('num_train_steps', None, 'Number of train steps.')
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+ flags.DEFINE_bool('eval_on_train_data', False, 'Enable evaluating on train '
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+ 'data (only supported in distributed training).')
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+ flags.DEFINE_integer('sample_1_of_n_eval_examples', None, 'Will sample one of '
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+ 'every n eval input examples, where n is provided.')
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+ flags.DEFINE_integer('sample_1_of_n_eval_on_train_examples', 5, 'Will sample '
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+ 'one of every n train input examples for evaluation, '
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+ 'where n is provided. This is only used if '
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+ '`eval_training_data` is True.')
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+ flags.DEFINE_string(
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+ 'model_dir', None, 'Path to output model directory '
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+ 'where event and checkpoint files will be written.')
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+ flags.DEFINE_string(
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+ 'checkpoint_dir', None, 'Path to directory holding a checkpoint. If '
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+ '`checkpoint_dir` is provided, this binary operates in eval-only mode, '
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+ 'writing resulting metrics to `model_dir`.')
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+
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+ flags.DEFINE_integer('eval_timeout', 3600, 'Number of seconds to wait for an'
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+ 'evaluation checkpoint before exiting.')
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+
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+ flags.DEFINE_bool('use_tpu', False, 'Whether the job is executing on a TPU.')
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+ flags.DEFINE_string(
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+ 'tpu_name',
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+ default=None,
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+ help='Name of the Cloud TPU for Cluster Resolvers.')
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+ flags.DEFINE_integer(
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+ 'num_workers', 1, 'When num_workers > 1, training uses '
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+ 'MultiWorkerMirroredStrategy. When num_workers = 1 it uses '
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+ 'MirroredStrategy.')
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+ flags.DEFINE_integer(
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+ 'checkpoint_every_n', 1000, 'Integer defining how often we checkpoint.')
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+ flags.DEFINE_boolean('record_summaries', True,
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+ ('Whether or not to record summaries defined by the model'
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+ ' or the training pipeline. This does not impact the'
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+ ' summaries of the loss values which are always'
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+ ' recorded.'))
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+
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+ FLAGS = flags.FLAGS
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+
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+
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+ def main(unused_argv):
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+ flags.mark_flag_as_required('model_dir')
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+ flags.mark_flag_as_required('pipeline_config_path')
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+ tf.config.set_soft_device_placement(True)
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+
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+ if FLAGS.checkpoint_dir:
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+ model_lib_v2.eval_continuously(
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+ pipeline_config_path=FLAGS.pipeline_config_path,
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+ model_dir=FLAGS.model_dir,
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+ train_steps=FLAGS.num_train_steps,
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+ sample_1_of_n_eval_examples=FLAGS.sample_1_of_n_eval_examples,
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+ sample_1_of_n_eval_on_train_examples=(
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+ FLAGS.sample_1_of_n_eval_on_train_examples),
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+ checkpoint_dir=FLAGS.checkpoint_dir,
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+ wait_interval=300, timeout=FLAGS.eval_timeout)
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+ else:
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+ if FLAGS.use_tpu:
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+ # TPU is automatically inferred if tpu_name is None and
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+ # we are running under cloud ai-platform.
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+ resolver = tf.distribute.cluster_resolver.TPUClusterResolver(
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+ FLAGS.tpu_name)
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+ tf.config.experimental_connect_to_cluster(resolver)
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+ tf.tpu.experimental.initialize_tpu_system(resolver)
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+ strategy = tf.distribute.experimental.TPUStrategy(resolver)
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+ elif FLAGS.num_workers > 1:
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+ strategy = tf.distribute.experimental.MultiWorkerMirroredStrategy()
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+ else:
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+ strategy = tf.compat.v2.distribute.MirroredStrategy()
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+
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+ with strategy.scope():
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+ model_lib_v2.train_loop(
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+ pipeline_config_path=FLAGS.pipeline_config_path,
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+ model_dir=FLAGS.model_dir,
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+ train_steps=FLAGS.num_train_steps,
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+ use_tpu=FLAGS.use_tpu,
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+ checkpoint_every_n=FLAGS.checkpoint_every_n,
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+ record_summaries=FLAGS.record_summaries)
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+
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+ if __name__ == '__main__':
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+ tf.compat.v1.app.run()