megadetector 5.0.11__py3-none-any.whl → 5.0.13__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 +97 -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 +149 -0
  11. megadetector/api/batch_processing/api_core/server_orchestration.py +360 -0
  12. megadetector/api/batch_processing/api_core/server_utils.py +88 -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 +125 -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 +263 -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 +607 -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 +237 -0
  58. megadetector/data_management/cct_json_utils.py +404 -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 +283 -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 +493 -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 +793 -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 +870 -0
  129. megadetector/data_management/read_exif.py +809 -0
  130. megadetector/data_management/remap_coco_categories.py +84 -0
  131. megadetector/data_management/remove_exif.py +66 -0
  132. megadetector/data_management/rename_images.py +187 -0
  133. megadetector/data_management/resize_coco_dataset.py +189 -0
  134. megadetector/data_management/wi_download_csv_to_coco.py +247 -0
  135. megadetector/data_management/yolo_output_to_md_output.py +446 -0
  136. megadetector/data_management/yolo_to_coco.py +676 -0
  137. megadetector/detection/__init__.py +0 -0
  138. megadetector/detection/detector_training/__init__.py +0 -0
  139. megadetector/detection/detector_training/model_main_tf2.py +114 -0
  140. megadetector/detection/process_video.py +846 -0
  141. megadetector/detection/pytorch_detector.py +355 -0
  142. megadetector/detection/run_detector.py +779 -0
  143. megadetector/detection/run_detector_batch.py +1219 -0
  144. megadetector/detection/run_inference_with_yolov5_val.py +1087 -0
  145. megadetector/detection/run_tiled_inference.py +934 -0
  146. megadetector/detection/tf_detector.py +192 -0
  147. megadetector/detection/video_utils.py +698 -0
  148. megadetector/postprocessing/__init__.py +0 -0
  149. megadetector/postprocessing/add_max_conf.py +64 -0
  150. megadetector/postprocessing/categorize_detections_by_size.py +165 -0
  151. megadetector/postprocessing/classification_postprocessing.py +716 -0
  152. megadetector/postprocessing/combine_api_outputs.py +249 -0
  153. megadetector/postprocessing/compare_batch_results.py +966 -0
  154. megadetector/postprocessing/convert_output_format.py +396 -0
  155. megadetector/postprocessing/load_api_results.py +195 -0
  156. megadetector/postprocessing/md_to_coco.py +310 -0
  157. megadetector/postprocessing/md_to_labelme.py +330 -0
  158. megadetector/postprocessing/merge_detections.py +412 -0
  159. megadetector/postprocessing/postprocess_batch_results.py +1908 -0
  160. megadetector/postprocessing/remap_detection_categories.py +170 -0
  161. megadetector/postprocessing/render_detection_confusion_matrix.py +660 -0
  162. megadetector/postprocessing/repeat_detection_elimination/find_repeat_detections.py +211 -0
  163. megadetector/postprocessing/repeat_detection_elimination/remove_repeat_detections.py +83 -0
  164. megadetector/postprocessing/repeat_detection_elimination/repeat_detections_core.py +1635 -0
  165. megadetector/postprocessing/separate_detections_into_folders.py +730 -0
  166. megadetector/postprocessing/subset_json_detector_output.py +700 -0
  167. megadetector/postprocessing/top_folders_to_bottom.py +223 -0
  168. megadetector/taxonomy_mapping/__init__.py +0 -0
  169. megadetector/taxonomy_mapping/map_lila_taxonomy_to_wi_taxonomy.py +491 -0
  170. megadetector/taxonomy_mapping/map_new_lila_datasets.py +150 -0
  171. megadetector/taxonomy_mapping/prepare_lila_taxonomy_release.py +142 -0
  172. megadetector/taxonomy_mapping/preview_lila_taxonomy.py +588 -0
  173. megadetector/taxonomy_mapping/retrieve_sample_image.py +71 -0
  174. megadetector/taxonomy_mapping/simple_image_download.py +219 -0
  175. megadetector/taxonomy_mapping/species_lookup.py +834 -0
  176. megadetector/taxonomy_mapping/taxonomy_csv_checker.py +159 -0
  177. megadetector/taxonomy_mapping/taxonomy_graph.py +346 -0
  178. megadetector/taxonomy_mapping/validate_lila_category_mappings.py +83 -0
  179. megadetector/utils/__init__.py +0 -0
  180. megadetector/utils/azure_utils.py +178 -0
  181. megadetector/utils/ct_utils.py +613 -0
  182. megadetector/utils/directory_listing.py +246 -0
  183. megadetector/utils/md_tests.py +1164 -0
  184. megadetector/utils/path_utils.py +1045 -0
  185. megadetector/utils/process_utils.py +160 -0
  186. megadetector/utils/sas_blob_utils.py +509 -0
  187. megadetector/utils/split_locations_into_train_val.py +228 -0
  188. megadetector/utils/string_utils.py +92 -0
  189. megadetector/utils/url_utils.py +323 -0
  190. megadetector/utils/write_html_image_list.py +225 -0
  191. megadetector/visualization/__init__.py +0 -0
  192. megadetector/visualization/plot_utils.py +293 -0
  193. megadetector/visualization/render_images_with_thumbnails.py +275 -0
  194. megadetector/visualization/visualization_utils.py +1536 -0
  195. megadetector/visualization/visualize_db.py +552 -0
  196. megadetector/visualization/visualize_detector_output.py +405 -0
  197. {megadetector-5.0.11.dist-info → megadetector-5.0.13.dist-info}/LICENSE +0 -0
  198. {megadetector-5.0.11.dist-info → megadetector-5.0.13.dist-info}/METADATA +2 -2
  199. megadetector-5.0.13.dist-info/RECORD +201 -0
  200. megadetector-5.0.13.dist-info/top_level.txt +1 -0
  201. megadetector-5.0.11.dist-info/RECORD +0 -5
  202. megadetector-5.0.11.dist-info/top_level.txt +0 -1
  203. {megadetector-5.0.11.dist-info → megadetector-5.0.13.dist-info}/WHEEL +0 -0
@@ -0,0 +1,219 @@
1
+ """
2
+
3
+ simple_image_download.py
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+
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+ Web image downloader, used in preview_lila_taxonomy.py
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+
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+ Slightly modified from:
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+
9
+ https://github.com/RiddlerQ/simple_image_download
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+
11
+ """
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+
13
+ #%% Imports
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+
15
+ import os
16
+ import urllib
17
+ import requests
18
+ import magic
19
+ import random
20
+
21
+ from urllib.parse import quote
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+
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+
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+ #%% Constants
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+
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+ BASE_URL = 'https://www.google.com/search?q='
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+ GOOGLE_PICTURE_ID = '''&biw=1536&bih=674&tbm=isch&sxsrf=ACYBGNSXXpS6YmAKUiLKKBs6xWb4uUY5gA:1581168823770&source=lnms&sa=X&ved=0ahUKEwioj8jwiMLnAhW9AhAIHbXTBMMQ_AUI3QUoAQ'''
28
+ HEADERS = {
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+ 'User-Agent':
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+ "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/77.0.3865.90 Safari/537.36"
31
+ }
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+ SCANNER_COUNTER = None
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+
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+
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+ #%% Support functions
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+
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+ def generate_search_url(keywords):
38
+ keywords_to_search = [str(item).strip() for item in keywords.split(',')][0].split()
39
+ keywords_count = len(keywords_to_search)
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+ return keywords_to_search, keywords_count
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+
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+
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+ def generate_urls(search):
44
+ """
45
+ Generate Google search URLs for all tokens in the list [search]
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+ """
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+
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+ return [(BASE_URL+quote(word)+GOOGLE_PICTURE_ID) for word in search]
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+
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+
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+ def check_webpage(url):
52
+ checked_url = None
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+ try:
54
+ request = requests.get(url, allow_redirects=True, timeout=10)
55
+ if 'html' not in str(request.content):
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+ checked_url = request
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+ except Exception as err:
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+ print(err)
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+ return checked_url
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+
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+
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+ def scan_webpage(webpage, extensions, timer):
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+ """
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+ Scan for pictures to download based on keywords
65
+ """
66
+
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+ global SCANNER_COUNTER
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+ scanner = webpage.find
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+ found = False
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+ counter = 0
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+ while counter < timer:
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+ new_line = scanner('"https://', SCANNER_COUNTER + 1) # How Many New lines
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+ SCANNER_COUNTER = scanner('"', new_line + 1) # Ends of line
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+ buffer = scanner('\\', new_line + 1, SCANNER_COUNTER)
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+ if buffer != -1:
76
+ object_raw = webpage[new_line + 1:buffer]
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+ else:
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+ object_raw = webpage[new_line + 1:SCANNER_COUNTER]
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+ if any(extension in object_raw for extension in extensions):
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+ found = True
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+ break
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+ counter += 1
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+ if found:
84
+ object_ready = check_webpage(object_raw)
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+ return object_ready
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+
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+
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+ #%% Main class
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+
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+ class Downloader:
91
+ """
92
+ Main Downloader
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+ ::param extension:iterable of Files extensions
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+ """
95
+ def __init__(self, extensions=None):
96
+ if extensions:
97
+ self._extensions = set(*[extensions])
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+ else:
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+ self._extensions = {'.jpg', '.png', '.ico', '.gif', '.jpeg'}
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+ self._directory = "simple_images/"
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+ self.get_dirs = set()
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+ self._cached_urls = {}
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+
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+ @property
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+ def directory(self):
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+ return self._directory
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+
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+ @directory.setter
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+ def directory(self, value):
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+ self._directory = value
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+
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+ @property
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+ def cached_urls(self):
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+ return self._cached_urls
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+
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+ @property
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+ def extensions(self):
118
+ return self._extensions
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+
120
+ @extensions.setter
121
+ def extensions(self, value):
122
+ self._extensions = set([value])
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+
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+
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+ def get_urls(self):
126
+ return [self._cached_urls[url][1].url
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+ for url in self._cached_urls]
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+
129
+ def _download_page(self, url):
130
+ req = urllib.request.Request(url, headers=HEADERS)
131
+ resp = urllib.request.urlopen(req)
132
+ resp_data = str(resp.read())
133
+ return resp_data
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+
135
+ def search_urls(self, keywords, limit=1, verbose=False, cache=True, timer=None):
136
+ cache_out = {}
137
+ search, count = generate_search_url(keywords)
138
+ urls_ = generate_urls(search)
139
+ timer = timer if timer else 1000
140
+ # max_progressbar = count * (list(range(limit+1))[-1]+1)
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+
142
+ # bar = progressbar.ProgressBar(maxval=max_progressbar,
143
+ # widgets=[progressbar.Bar('=', '[', ']'), ' ', progressbar.Percentage()]).start()
144
+ i = 0
145
+ while i < count:
146
+ global SCANNER_COUNTER
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+ SCANNER_COUNTER = -1
148
+ url = urls_[i]
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+ path = self.generate_dir(search[i])
150
+ raw_html = self._download_page(url) # Download the entire page from the google Picture search
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+ for _ in range(limit+1):
152
+ webpage_url = scan_webpage(raw_html, self._extensions, timer)
153
+ if webpage_url:
154
+ file_name = Downloader.gen_fn(webpage_url, search[i])
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+ cache_out[file_name] = [path, webpage_url]
156
+ else:
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+ pass
158
+ # bar.update(bar.currval + 1)
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+ i += 1
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+ # bar.finish()
161
+ if verbose:
162
+ for url in cache_out:
163
+ print(url)
164
+ if cache:
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+ self._cached_urls = cache_out
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+ if not cache_out:
167
+ print('==='*15 + ' < ' + 'NO PICTURES FOUND' + ' > ' + '==='*15)
168
+ return cache_out
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+
170
+ def download(self, keywords=None, limit=1, verbose=False, cache=True, download_cache=False,
171
+ timer=None):
172
+ if not download_cache:
173
+ content = self.search_urls(keywords, limit, verbose, cache, timer)
174
+ else:
175
+ content = self._cached_urls
176
+ if not content:
177
+ print('Downloader has not URLs saved in Memory yet, run Downloader.search_urls to find pics first')
178
+ paths = []
179
+ for name, (path, url) in content.items():
180
+ fullpath = os.path.join(path, name)
181
+ paths.append(fullpath)
182
+ with open(fullpath, 'wb') as file:
183
+ file.write(url.content)
184
+ if verbose:
185
+ print(f'File Name={name}, Downloaded from {url.url}')
186
+ return paths
187
+
188
+ def _create_directories(self, name):
189
+ dir_path = os.path.join(self._directory, name)
190
+ try:
191
+ if not os.path.exists(dir_path):
192
+ os.makedirs(dir_path)
193
+ except OSError:
194
+ raise
195
+ self.get_dirs.update([name])
196
+ return
197
+
198
+ def generate_dir(self, dir_name):
199
+ """Generate Path and Directory, also check if Directory exists or not """
200
+ dir_name = dir_name.replace(" ", "_")
201
+ if dir_name in self.get_dirs:
202
+ pass
203
+ else:
204
+ self._create_directories(dir_name)
205
+ return os.path.join(self._directory,dir_name)
206
+
207
+ @staticmethod
208
+ def gen_fn(check, name):
209
+ """Create a file name string and generate a random identifiers otherwise won't import same pic twice"""
210
+ id = str(hex(random.randrange(1000)))
211
+ mime = magic.Magic(mime=True)
212
+ file_type = mime.from_buffer(check.content)
213
+ file_extension = f'.{file_type.split("/")[1]}'
214
+ file_name = str(name) + "_" + id[2:] + file_extension
215
+ return file_name
216
+
217
+ def flush_cache(self):
218
+ """Clear the Downloader instance cache"""
219
+ self._cached_urls = set()