endoreg-db 0.8.5.1__py3-none-any.whl

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  1. endoreg_db/__init__.py +0 -0
  2. endoreg_db/admin.py +92 -0
  3. endoreg_db/api/serializers/finding_descriptions.py +0 -0
  4. endoreg_db/api/views/finding_descriptions.py +0 -0
  5. endoreg_db/api_urls.py +4 -0
  6. endoreg_db/apps.py +18 -0
  7. endoreg_db/assets/dummy_model.ckpt +1 -0
  8. endoreg_db/codemods/readme.md +88 -0
  9. endoreg_db/codemods/rename_datetime_fields.py +92 -0
  10. endoreg_db/config/__init__.py +0 -0
  11. endoreg_db/config/env.py +101 -0
  12. endoreg_db/data/__init__.py +144 -0
  13. endoreg_db/data/ai_model/data.yaml +7 -0
  14. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  15. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  16. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  17. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  18. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  19. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  20. endoreg_db/data/ai_model_type/data.yaml +7 -0
  21. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  22. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  23. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  24. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  25. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  26. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  27. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  28. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  29. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  30. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  31. endoreg_db/data/case_template/rule_value/.init +0 -0
  32. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  33. endoreg_db/data/case_template/template/base.yaml +8 -0
  34. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  35. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  36. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  37. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  38. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  39. endoreg_db/data/center/data.yaml +91 -0
  40. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  41. endoreg_db/data/center_shift/ukw.yaml +9 -0
  42. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  43. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  44. endoreg_db/data/db_summary.csv +58 -0
  45. endoreg_db/data/db_summary.xlsx +0 -0
  46. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  47. endoreg_db/data/disease/hepatology.yaml +5 -0
  48. endoreg_db/data/disease/misc.yaml +5 -0
  49. endoreg_db/data/disease/renal.yaml +5 -0
  50. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  51. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  52. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  53. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  54. endoreg_db/data/distribution/date/patient.yaml +7 -0
  55. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  56. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  57. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  58. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  59. endoreg_db/data/endoscope/data.yaml +93 -0
  60. endoreg_db/data/endoscope_type/data.yaml +11 -0
  61. endoreg_db/data/endoscopy_processor/data.yaml +50 -0
  62. endoreg_db/data/event/cardiology.yaml +15 -0
  63. endoreg_db/data/event/neurology.yaml +14 -0
  64. endoreg_db/data/event/surgery.yaml +13 -0
  65. endoreg_db/data/event/thrombembolism.yaml +20 -0
  66. endoreg_db/data/examination/examinations/data.yaml +72 -0
  67. endoreg_db/data/examination/time/data.yaml +48 -0
  68. endoreg_db/data/examination/time-type/data.yaml +8 -0
  69. endoreg_db/data/examination/type/data.yaml +17 -0
  70. endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
  71. endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
  72. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  73. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  74. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  75. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  76. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  77. endoreg_db/data/finding/complication.yaml +16 -0
  78. endoreg_db/data/finding/data.yaml +105 -0
  79. endoreg_db/data/finding/examination_setting.yaml +16 -0
  80. endoreg_db/data/finding/medication_related.yaml +18 -0
  81. endoreg_db/data/finding/outcome.yaml +12 -0
  82. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  83. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  84. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  85. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  86. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  87. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  88. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  89. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  90. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  91. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  92. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  93. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  94. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  95. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  96. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  97. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  98. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  99. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  100. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  101. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  102. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
  103. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  104. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  105. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  106. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
  107. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
  108. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
  109. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  110. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
  111. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
  112. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  113. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  114. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  115. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  116. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  117. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  118. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  119. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  120. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  121. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  122. endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
  123. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
  124. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
  125. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
  126. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
  127. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
  128. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  129. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  130. endoreg_db/data/finding_type/data.yaml +43 -0
  131. endoreg_db/data/gender/data.yaml +42 -0
  132. endoreg_db/data/information_source/annotation.yaml +6 -0
  133. endoreg_db/data/information_source/data.yaml +30 -0
  134. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  135. endoreg_db/data/information_source/medication.yaml +6 -0
  136. endoreg_db/data/information_source/prediction.yaml +7 -0
  137. endoreg_db/data/information_source_type/data.yaml +8 -0
  138. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  139. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  140. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  141. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  142. endoreg_db/data/lab_value/hematology.yaml +184 -0
  143. endoreg_db/data/lab_value/hormones.yaml +59 -0
  144. endoreg_db/data/lab_value/lipids.yaml +53 -0
  145. endoreg_db/data/lab_value/misc.yaml +76 -0
  146. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  147. endoreg_db/data/log_type/data.yaml +57 -0
  148. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  149. endoreg_db/data/lx_client_type/base.yaml +30 -0
  150. endoreg_db/data/lx_permission/base.yaml +24 -0
  151. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  152. endoreg_db/data/material/material.yaml +91 -0
  153. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  154. endoreg_db/data/medication/tah.yaml +70 -0
  155. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  156. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  157. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  158. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  159. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  160. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  161. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  162. endoreg_db/data/names_first/first_names.yaml +54 -0
  163. endoreg_db/data/names_last/last_names.yaml +51 -0
  164. endoreg_db/data/network_device/data.yaml +59 -0
  165. endoreg_db/data/network_device_type/data.yaml +12 -0
  166. endoreg_db/data/organ/data.yaml +29 -0
  167. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  168. endoreg_db/data/pdf_type/data.yaml +46 -0
  169. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  170. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  171. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  172. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  173. endoreg_db/data/profession/data.yaml +70 -0
  174. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  175. endoreg_db/data/qualification/m2.yaml +39 -0
  176. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  177. endoreg_db/data/qualification/sonography.yaml +36 -0
  178. endoreg_db/data/qualification_type/base.yaml +29 -0
  179. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  180. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  181. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  182. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
  183. endoreg_db/data/requirement/age.yaml +26 -0
  184. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  185. endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
  186. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
  187. endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
  188. endoreg_db/data/requirement/disease_misc.yaml +12 -0
  189. endoreg_db/data/requirement/disease_renal.yaml +96 -0
  190. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
  191. endoreg_db/data/requirement/event_cardiology.yaml +251 -0
  192. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  193. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  194. endoreg_db/data/requirement/gender.yaml +25 -0
  195. endoreg_db/data/requirement/lab_value.yaml +441 -0
  196. endoreg_db/data/requirement/medication.yaml +93 -0
  197. endoreg_db/data/requirement_operator/age.yaml +13 -0
  198. endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
  199. endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
  200. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  201. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  202. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
  203. endoreg_db/data/requirement_set_type/data.yaml +20 -0
  204. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  205. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  206. endoreg_db/data/risk/bleeding.yaml +26 -0
  207. endoreg_db/data/risk/thrombosis.yaml +37 -0
  208. endoreg_db/data/risk_type/data.yaml +27 -0
  209. endoreg_db/data/setup_config.yaml +38 -0
  210. endoreg_db/data/shift/endoscopy.yaml +21 -0
  211. endoreg_db/data/shift/m2.yaml +0 -0
  212. endoreg_db/data/shift_type/base.yaml +35 -0
  213. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  214. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  215. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  216. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  217. endoreg_db/data/unit/concentration.yaml +115 -0
  218. endoreg_db/data/unit/data.yaml +17 -0
  219. endoreg_db/data/unit/length.yaml +31 -0
  220. endoreg_db/data/unit/misc.yaml +20 -0
  221. endoreg_db/data/unit/rate.yaml +6 -0
  222. endoreg_db/data/unit/time.yaml +48 -0
  223. endoreg_db/data/unit/volume.yaml +35 -0
  224. endoreg_db/data/unit/weight.yaml +38 -0
  225. endoreg_db/data/waste/data.yaml +12 -0
  226. endoreg_db/exceptions.py +19 -0
  227. endoreg_db/factories/__init__.py +0 -0
  228. endoreg_db/forms/__init__.py +5 -0
  229. endoreg_db/forms/examination_form.py +11 -0
  230. endoreg_db/forms/patient_finding_intervention_form.py +18 -0
  231. endoreg_db/forms/patient_form.py +27 -0
  232. endoreg_db/forms/questionnaires/__init__.py +1 -0
  233. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  234. endoreg_db/forms/settings/__init__.py +8 -0
  235. endoreg_db/forms/unit.py +6 -0
  236. endoreg_db/helpers/__init__.py +0 -0
  237. endoreg_db/helpers/count_db.py +45 -0
  238. endoreg_db/helpers/data_loader.py +208 -0
  239. endoreg_db/helpers/default_objects.py +378 -0
  240. endoreg_db/helpers/download_segmentation_model.py +31 -0
  241. endoreg_db/helpers/interact.py +6 -0
  242. endoreg_db/helpers/test_video_helper.py +119 -0
  243. endoreg_db/logger_conf.py +140 -0
  244. endoreg_db/management/__init__.py +1 -0
  245. endoreg_db/management/commands/__init__.py +1 -0
  246. endoreg_db/management/commands/anonymize_video.py +0 -0
  247. endoreg_db/management/commands/check_auth.py +125 -0
  248. endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
  249. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  250. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  251. endoreg_db/management/commands/fix_video_paths.py +165 -0
  252. endoreg_db/management/commands/import_fallback_video.py +203 -0
  253. endoreg_db/management/commands/import_report.py +298 -0
  254. endoreg_db/management/commands/import_video.py +423 -0
  255. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  256. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  257. endoreg_db/management/commands/load_ai_model_data.py +77 -0
  258. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  259. endoreg_db/management/commands/load_base_db_data.py +192 -0
  260. endoreg_db/management/commands/load_center_data.py +68 -0
  261. endoreg_db/management/commands/load_contraindication_data.py +41 -0
  262. endoreg_db/management/commands/load_disease_classification_choices_data.py +41 -0
  263. endoreg_db/management/commands/load_disease_classification_data.py +41 -0
  264. endoreg_db/management/commands/load_disease_data.py +62 -0
  265. endoreg_db/management/commands/load_distribution_data.py +66 -0
  266. endoreg_db/management/commands/load_endoscope_data.py +68 -0
  267. endoreg_db/management/commands/load_event_data.py +41 -0
  268. endoreg_db/management/commands/load_examination_data.py +75 -0
  269. endoreg_db/management/commands/load_examination_indication_data.py +86 -0
  270. endoreg_db/management/commands/load_finding_data.py +128 -0
  271. endoreg_db/management/commands/load_gender_data.py +44 -0
  272. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +132 -0
  273. endoreg_db/management/commands/load_information_source.py +51 -0
  274. endoreg_db/management/commands/load_lab_value_data.py +50 -0
  275. endoreg_db/management/commands/load_medication_data.py +103 -0
  276. endoreg_db/management/commands/load_name_data.py +37 -0
  277. endoreg_db/management/commands/load_organ_data.py +43 -0
  278. endoreg_db/management/commands/load_pdf_type_data.py +61 -0
  279. endoreg_db/management/commands/load_profession_data.py +44 -0
  280. endoreg_db/management/commands/load_qualification_data.py +59 -0
  281. endoreg_db/management/commands/load_report_reader_flag_data.py +46 -0
  282. endoreg_db/management/commands/load_requirement_data.py +180 -0
  283. endoreg_db/management/commands/load_risk_data.py +56 -0
  284. endoreg_db/management/commands/load_shift_data.py +60 -0
  285. endoreg_db/management/commands/load_tag_data.py +57 -0
  286. endoreg_db/management/commands/load_unit_data.py +46 -0
  287. endoreg_db/management/commands/load_user_groups.py +28 -0
  288. endoreg_db/management/commands/register_ai_model.py +64 -0
  289. endoreg_db/management/commands/reset_celery_schedule.py +9 -0
  290. endoreg_db/management/commands/setup_endoreg_db.py +381 -0
  291. endoreg_db/management/commands/start_filewatcher.py +106 -0
  292. endoreg_db/management/commands/storage_management.py +548 -0
  293. endoreg_db/management/commands/summarize_db_content.py +189 -0
  294. endoreg_db/management/commands/validate_video.py +204 -0
  295. endoreg_db/management/commands/validate_video_files.py +161 -0
  296. endoreg_db/management/commands/video_validation.py +22 -0
  297. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  298. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  299. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
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  607. endoreg_db/tasks/video_processing_tasks.py +327 -0
  608. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  609. endoreg_db/templates/admin/start_examination.html +12 -0
  610. endoreg_db/templates/timeline.html +176 -0
  611. endoreg_db/urls/__init__.py +70 -0
  612. endoreg_db/urls/anonymization.py +32 -0
  613. endoreg_db/urls/auth.py +16 -0
  614. endoreg_db/urls/classification.py +39 -0
  615. endoreg_db/urls/examination.py +54 -0
  616. endoreg_db/urls/files.py +6 -0
  617. endoreg_db/urls/label_video_segment_validate.py +33 -0
  618. endoreg_db/urls/label_video_segments.py +44 -0
  619. endoreg_db/urls/media.py +226 -0
  620. endoreg_db/urls/patient.py +19 -0
  621. endoreg_db/urls/report.py +48 -0
  622. endoreg_db/urls/requirements.py +13 -0
  623. endoreg_db/urls/sensitive_meta.py +0 -0
  624. endoreg_db/urls/stats.py +46 -0
  625. endoreg_db/urls/upload.py +20 -0
  626. endoreg_db/urls/video.py +61 -0
  627. endoreg_db/urls.py +9 -0
  628. endoreg_db/utils/__init__.py +88 -0
  629. endoreg_db/utils/ai/__init__.py +9 -0
  630. endoreg_db/utils/ai/get.py +5 -0
  631. endoreg_db/utils/ai/inference_dataset.py +52 -0
  632. endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
  633. endoreg_db/utils/ai/postprocess.py +63 -0
  634. endoreg_db/utils/ai/predict.py +291 -0
  635. endoreg_db/utils/ai/preprocess.py +68 -0
  636. endoreg_db/utils/calc_duration_seconds.py +24 -0
  637. endoreg_db/utils/case_generator/__init__.py +0 -0
  638. endoreg_db/utils/case_generator/case_generator.py +159 -0
  639. endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
  640. endoreg_db/utils/case_generator/utils.py +30 -0
  641. endoreg_db/utils/check_video_files.py +148 -0
  642. endoreg_db/utils/cropping.py +29 -0
  643. endoreg_db/utils/dataloader.py +175 -0
  644. endoreg_db/utils/dates.py +60 -0
  645. endoreg_db/utils/env.py +33 -0
  646. endoreg_db/utils/extract_specific_frames.py +72 -0
  647. endoreg_db/utils/file_operations.py +58 -0
  648. endoreg_db/utils/fix_video_path_direct.py +141 -0
  649. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  650. endoreg_db/utils/hashs.py +153 -0
  651. endoreg_db/utils/links/__init__.py +0 -0
  652. endoreg_db/utils/links/requirement_link.py +193 -0
  653. endoreg_db/utils/mime_types.py +0 -0
  654. endoreg_db/utils/names.py +76 -0
  655. endoreg_db/utils/ocr.py +190 -0
  656. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  657. endoreg_db/utils/paths.py +95 -0
  658. endoreg_db/utils/permissions.py +143 -0
  659. endoreg_db/utils/pipelines/Readme.md +235 -0
  660. endoreg_db/utils/pipelines/__init__.py +0 -0
  661. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  662. endoreg_db/utils/product/__init__.py +0 -0
  663. endoreg_db/utils/product/sum_emissions.py +20 -0
  664. endoreg_db/utils/product/sum_weights.py +18 -0
  665. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  666. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  667. endoreg_db/utils/requirement_helpers.py +0 -0
  668. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  669. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  670. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  671. endoreg_db/utils/setup_config.py +177 -0
  672. endoreg_db/utils/translation.py +27 -0
  673. endoreg_db/utils/uuid.py +4 -0
  674. endoreg_db/utils/validate_endo_roi.py +19 -0
  675. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  676. endoreg_db/utils/validate_video_detailed.py +357 -0
  677. endoreg_db/utils/video/__init__.py +26 -0
  678. endoreg_db/utils/video/extract_frames.py +88 -0
  679. endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
  680. endoreg_db/utils/video/names.py +42 -0
  681. endoreg_db/utils/video/streaming_processor.py +312 -0
  682. endoreg_db/utils/video/video_splitter.py +94 -0
  683. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  684. endoreg_db/views/__init__.py +272 -0
  685. endoreg_db/views/anonymization/__init__.py +27 -0
  686. endoreg_db/views/anonymization/media_management.py +454 -0
  687. endoreg_db/views/anonymization/overview.py +216 -0
  688. endoreg_db/views/anonymization/validate.py +107 -0
  689. endoreg_db/views/auth/__init__.py +13 -0
  690. endoreg_db/views/auth/keycloak.py +113 -0
  691. endoreg_db/views/examination/__init__.py +33 -0
  692. endoreg_db/views/examination/examination.py +37 -0
  693. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  694. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  695. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  696. endoreg_db/views/examination/get_findings.py +41 -0
  697. endoreg_db/views/examination/get_instruments.py +18 -0
  698. endoreg_db/views/examination/get_interventions.py +14 -0
  699. endoreg_db/views/finding/__init__.py +9 -0
  700. endoreg_db/views/finding/finding.py +112 -0
  701. endoreg_db/views/finding/get_classifications.py +14 -0
  702. endoreg_db/views/finding/get_interventions.py +17 -0
  703. endoreg_db/views/finding_classification/__init__.py +13 -0
  704. endoreg_db/views/finding_classification/base.py +0 -0
  705. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  706. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  707. endoreg_db/views/label/__init__.py +5 -0
  708. endoreg_db/views/label/label.py +15 -0
  709. endoreg_db/views/label_video_segment/__init__.py +16 -0
  710. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  711. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  712. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  713. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  714. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  715. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  716. endoreg_db/views/label_video_segment/validate.py +226 -0
  717. endoreg_db/views/media/__init__.py +45 -0
  718. endoreg_db/views/media/pdf_media.py +386 -0
  719. endoreg_db/views/media/segments.py +71 -0
  720. endoreg_db/views/media/sensitive_metadata.py +314 -0
  721. endoreg_db/views/media/video_media.py +272 -0
  722. endoreg_db/views/media/video_segments.py +524 -0
  723. endoreg_db/views/meta/__init__.py +15 -0
  724. endoreg_db/views/meta/available_files_list.py +146 -0
  725. endoreg_db/views/meta/report_meta.py +53 -0
  726. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  727. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  728. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  729. endoreg_db/views/misc/__init__.py +63 -0
  730. endoreg_db/views/misc/center.py +13 -0
  731. endoreg_db/views/misc/csrf.py +7 -0
  732. endoreg_db/views/misc/gender.py +14 -0
  733. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  734. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  735. endoreg_db/views/misc/secure_url_validate.py +79 -0
  736. endoreg_db/views/misc/stats.py +220 -0
  737. endoreg_db/views/misc/translation.py +182 -0
  738. endoreg_db/views/misc/upload_views.py +240 -0
  739. endoreg_db/views/patient/__init__.py +5 -0
  740. endoreg_db/views/patient/patient.py +210 -0
  741. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  742. endoreg_db/views/patient_examination/__init__.py +11 -0
  743. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  744. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  745. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  746. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  747. endoreg_db/views/patient_examination/video.py +194 -0
  748. endoreg_db/views/patient_finding/__init__.py +7 -0
  749. endoreg_db/views/patient_finding/base.py +0 -0
  750. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  751. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  752. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  753. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  754. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  755. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  756. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  757. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  758. endoreg_db/views/pdf/__init__.py +11 -0
  759. endoreg_db/views/pdf/pdf_media.py +239 -0
  760. endoreg_db/views/pdf/pdf_stream_views.py +127 -0
  761. endoreg_db/views/pdf/reimport.py +161 -0
  762. endoreg_db/views/report/__init__.py +9 -0
  763. endoreg_db/views/report/report_list.py +112 -0
  764. endoreg_db/views/report/report_with_secure_url.py +28 -0
  765. endoreg_db/views/report/start_examination.py +7 -0
  766. endoreg_db/views/requirement/__init__.py +10 -0
  767. endoreg_db/views/requirement/evaluate.py +279 -0
  768. endoreg_db/views/requirement/lookup.py +483 -0
  769. endoreg_db/views/requirement/lookup_store.py +252 -0
  770. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  771. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  772. endoreg_db/views/stats/__init__.py +13 -0
  773. endoreg_db/views/stats/stats_views.py +229 -0
  774. endoreg_db/views/video/__init__.py +61 -0
  775. endoreg_db/views/video/correction.py +530 -0
  776. endoreg_db/views/video/reimport.py +195 -0
  777. endoreg_db/views/video/segmentation.py +274 -0
  778. endoreg_db/views/video/task_status.py +49 -0
  779. endoreg_db/views/video/timeline.py +46 -0
  780. endoreg_db/views/video/video_analyze.py +52 -0
  781. endoreg_db/views/video/video_apply_mask.py +48 -0
  782. endoreg_db/views/video/video_correction.py +21 -0
  783. endoreg_db/views/video/video_download_processed.py +58 -0
  784. endoreg_db/views/video/video_examination_viewset.py +329 -0
  785. endoreg_db/views/video/video_media.py +158 -0
  786. endoreg_db/views/video/video_meta.py +29 -0
  787. endoreg_db/views/video/video_processing_history.py +24 -0
  788. endoreg_db/views/video/video_remove_frames.py +48 -0
  789. endoreg_db/views/video/video_stream.py +306 -0
  790. endoreg_db/views.py +0 -0
  791. endoreg_db-0.8.5.1.dist-info/METADATA +383 -0
  792. endoreg_db-0.8.5.1.dist-info/RECORD +794 -0
  793. endoreg_db-0.8.5.1.dist-info/WHEEL +4 -0
  794. endoreg_db-0.8.5.1.dist-info/licenses/LICENSE +674 -0
@@ -0,0 +1,174 @@
1
+ import logging
2
+ from endoreg_db.models.media.video.video_file_io import _get_frame_dir_path
3
+ from endoreg_db.utils.video.ffmpeg_wrapper import extract_frames as ffmpeg_extract_frames
4
+ from typing import TYPE_CHECKING
5
+
6
+ if TYPE_CHECKING:
7
+ from endoreg_db.models import VideoFile
8
+
9
+ from django.db import transaction
10
+
11
+
12
+ import shutil
13
+ logger = logging.getLogger(__name__)
14
+
15
+ def _extract_frames(
16
+ video: "VideoFile",
17
+ quality: int = 2,
18
+ overwrite: bool = False,
19
+ ext="jpg",
20
+ verbose=False,
21
+ ) -> bool:
22
+ """
23
+ Extract frames from a raw video file, update frame extraction status in the database, and manage related file system operations.
24
+
25
+ This function checks for existing extracted frames and skips extraction if appropriate, unless overwriting is requested. It handles deletion of existing frames when overwriting, invokes ffmpeg to extract frames, parses extracted frame numbers, updates corresponding database records, and manages video extraction state. Robust error handling ensures cleanup and state rollback on failure.
26
+
27
+ Parameters:
28
+ video (VideoFile): The video object from which frames are to be extracted.
29
+ quality (int, optional): Quality parameter for ffmpeg extraction. Defaults to 2.
30
+ overwrite (bool, optional): Whether to overwrite existing extracted frames. Defaults to False.
31
+ ext (str, optional): File extension for extracted frames. Defaults to "jpg".
32
+
33
+ Returns:
34
+ bool: True if extraction and updates succeed.
35
+
36
+ Raises:
37
+ FileNotFoundError: If the raw video file is missing.
38
+ RuntimeError: If extraction or database update fails.
39
+ ValueError: If the frame directory path cannot be determined.
40
+ """
41
+ from ._delete_frames import _delete_frames
42
+ from endoreg_db.models.media.frame import Frame
43
+
44
+ # Pre-validation checks (outside any transaction)
45
+ if not video.has_raw:
46
+ raise FileNotFoundError(f"Raw video file not available for {video.uuid}. Cannot extract frames.")
47
+
48
+ raw_file_path = video.get_raw_file_path()
49
+ if not raw_file_path or not raw_file_path.exists():
50
+ raise FileNotFoundError(f"Raw video file not found at {raw_file_path} for video {video.uuid}. Cannot extract frames.")
51
+
52
+ frame_dir = _get_frame_dir_path(video)
53
+ if not frame_dir:
54
+ raise ValueError(f"Cannot determine frame directory path for video {video.uuid}.")
55
+
56
+ state = video.get_or_create_state()
57
+ frames_exist_in_db = Frame.objects.filter(video=video).exists()
58
+ files_exist_on_disk = frame_dir.exists() and any(frame_dir.iterdir())
59
+
60
+ # Fast-path: if frames exist and we are not overwriting, update state and return.
61
+ if (state.frames_extracted or files_exist_on_disk) and not overwrite:
62
+ logger.info(
63
+ "Frames already extracted or files exist for video %s, and overwrite=False. Skipping extraction.",
64
+ video.uuid,
65
+ )
66
+ if state.frames_extracted and frames_exist_in_db:
67
+ with transaction.atomic():
68
+ updated_count = Frame.objects.filter(video=video, is_extracted=False).update(is_extracted=True)
69
+ if updated_count > 0:
70
+ logger.info(
71
+ "Marked %d existing Frame objects as extracted for video %s based on state.",
72
+ updated_count,
73
+ video.uuid,
74
+ )
75
+ elif not state.frames_extracted and files_exist_on_disk:
76
+ logger.warning(
77
+ "Files exist on disk for video %s but state.frames_extracted is False. Correcting state to match disk.",
78
+ video.uuid,
79
+ )
80
+ # Fix inconsistent state: files exist but state.frames_extracted is False
81
+ state.frames_extracted = True
82
+ state.save(update_fields=['frames_extracted'])
83
+
84
+ # Also update Frame objects to be consistent
85
+ with transaction.atomic():
86
+ updated_count = Frame.objects.filter(video=video, is_extracted=False).update(is_extracted=True)
87
+ if updated_count > 0:
88
+ logger.info(
89
+ "Marked %d existing Frame objects as extracted for video %s after state correction.",
90
+ updated_count,
91
+ video.uuid,
92
+ )
93
+ return True
94
+
95
+ # Overwrite: delete existing frames/files before re-extraction.
96
+ if overwrite:
97
+ logger.info("Overwrite=True. Preparing to delete existing frames/files for video %s before extraction.", video.uuid)
98
+ try:
99
+ _delete_frames(video)
100
+ with transaction.atomic():
101
+ updated_count = Frame.objects.filter(video=video, is_extracted=True).update(is_extracted=False)
102
+ if updated_count > 0:
103
+ logger.info(
104
+ "Reset %d Frame objects to is_extracted=False for video %s due to overwrite.",
105
+ updated_count,
106
+ video.uuid,
107
+ )
108
+ state.refresh_from_db()
109
+ except Exception as del_e:
110
+ logger.error("Failed to delete existing frames for video %s during overwrite: %s", video.uuid, del_e, exc_info=True)
111
+ raise RuntimeError(f"Failed to delete existing frames for video {video.uuid} during overwrite.") from del_e
112
+
113
+ frame_dir.mkdir(parents=True, exist_ok=True)
114
+
115
+ try:
116
+ logger.info("Starting frame extraction for video %s to %s", video.uuid, frame_dir)
117
+ # Step 1: Perform the long-running frame extraction outside any transaction.
118
+ extracted_paths = ffmpeg_extract_frames(raw_file_path, frame_dir, quality=quality, ext=ext)
119
+ if not extracted_paths:
120
+ logger.warning(
121
+ "ffmpeg_extract_frames returned no paths for video %s. Check video duration and ffmpeg logs.",
122
+ video.uuid,
123
+ )
124
+ if video.frame_count is not None and video.frame_count > 0:
125
+ raise RuntimeError(
126
+ f"ffmpeg_extract_frames returned no paths for video {video.uuid}, but {video.frame_count} frames were expected."
127
+ )
128
+
129
+ logger.info("Successfully extracted %d frames using ffmpeg for video %s.", len(extracted_paths), video.uuid)
130
+
131
+ extracted_frame_numbers = []
132
+ for frame_path in extracted_paths:
133
+ try:
134
+ frame_number = int(frame_path.stem.split('_')[-1])
135
+ extracted_frame_numbers.append(frame_number)
136
+ except (ValueError, IndexError) as e:
137
+ logger.warning("Could not parse frame number from extracted file %s: %s", frame_path.name, e)
138
+
139
+ # Step 2: Perform all the quick DB updates inside a minimal atomic transaction.
140
+ with transaction.atomic():
141
+ if extracted_frame_numbers:
142
+ try:
143
+ update_count = Frame.objects.filter(
144
+ video=video, frame_number__in=extracted_frame_numbers
145
+ ).update(is_extracted=True)
146
+ logger.info("Marked %d Frame objects as is_extracted=True for video %s.", update_count, video.uuid)
147
+ if update_count != len(extracted_frame_numbers):
148
+ logger.warning(
149
+ "Number of updated frames (%d) does not match number of parsed extracted files (%d) for video %s.",
150
+ update_count,
151
+ len(extracted_frame_numbers),
152
+ video.uuid,
153
+ )
154
+ except Exception as update_e:
155
+ logger.error("Failed to update is_extracted flag for frames of video %s: %s", video.uuid, update_e, exc_info=True)
156
+ if extracted_paths:
157
+ state.refresh_from_db()
158
+ state.mark_frames_extracted()
159
+ return True
160
+
161
+ except Exception as e:
162
+ logger.error("Frame extraction or update failed for video %s: %s", video.uuid, e, exc_info=True)
163
+ logger.warning("Cleaning up frame directory %s for video %s due to extraction error.", frame_dir, video.uuid)
164
+ shutil.rmtree(frame_dir, ignore_errors=True)
165
+ try:
166
+ with transaction.atomic():
167
+ Frame.objects.filter(video=video, is_extracted=True).update(is_extracted=False)
168
+ state.refresh_from_db()
169
+ if state.frames_extracted:
170
+ state.frames_extracted = False
171
+ state.save(update_fields=["frames_extracted"])
172
+ except Exception as db_err:
173
+ logger.error("Failed to reset flags/state in DB during error handling for video %s: %s", video.uuid, db_err)
174
+ raise RuntimeError(f"Frame extraction or update failed for video {video.uuid}.") from e
@@ -0,0 +1,28 @@
1
+ from typing import TYPE_CHECKING
2
+
3
+ import logging
4
+
5
+ if TYPE_CHECKING:
6
+ from endoreg_db.models import VideoFile, Frame
7
+
8
+ logger = logging.getLogger(__name__)
9
+
10
+
11
+
12
+
13
+ def _get_frame(video: "VideoFile", frame_number: int) -> "Frame":
14
+ """Gets a specific Frame object by its frame number."""
15
+ from endoreg_db.models import Frame
16
+ try:
17
+ # Access related manager directly
18
+ return video.frames.get(frame_number=frame_number)
19
+ except AttributeError:
20
+ logger.error("Could not access frame %d for video %s via related manager.", frame_number, video.uuid)
21
+ # Fallback query
22
+ return Frame.objects.get(video_file=video, frame_number=frame_number)
23
+ except Frame.DoesNotExist:
24
+ logger.error("Frame %d not found for video %s.", frame_number, video.uuid)
25
+ raise # Re-raise DoesNotExist
26
+ except Exception as e:
27
+ logger.error("Error getting frame %d for video %s: %s", frame_number, video.uuid, e, exc_info=True)
28
+ raise # Re-raise other exceptions
@@ -0,0 +1,27 @@
1
+
2
+ from typing import TYPE_CHECKING
3
+
4
+ import logging
5
+
6
+ if TYPE_CHECKING:
7
+ from endoreg_db.models import VideoFile
8
+
9
+ logger = logging.getLogger(__name__)
10
+
11
+
12
+
13
+
14
+ def _get_frame_number(video: "VideoFile") -> int:
15
+ """Counts the number of associated Frame objects in the database."""
16
+ try:
17
+ # Access related manager directly
18
+ return video.frames.count()
19
+ except AttributeError:
20
+ logger.error("Could not access frame count for video %s. 'frames' related manager not found.", str(video))
21
+ # Fallback query (less efficient)
22
+ frame_model = video.get_frame_model()
23
+ return frame_model.objects.filter(video_file=video).count()
24
+ except Exception as e:
25
+ logger.error("Error counting frames for video %s: %s", video.uuid, e, exc_info=True)
26
+ return 0
27
+
@@ -0,0 +1,20 @@
1
+ # --- Frame Creation/Deletion ---
2
+ import logging
3
+ from typing import TYPE_CHECKING, Optional
4
+ from pathlib import Path
5
+
6
+ if TYPE_CHECKING:
7
+ from endoreg_db.models import VideoFile
8
+
9
+ logger = logging.getLogger(__name__)
10
+
11
+ def _get_frame_path(video: "VideoFile", frame_number: int) -> Optional[Path]:
12
+ """Constructs the expected path for a given frame number."""
13
+ target_dir = video.get_frame_dir_path() # Use IO helper
14
+ if not target_dir:
15
+ logger.warning("Cannot get frame path for video %s: Frame directory not set.", video.uuid)
16
+ return None
17
+
18
+ frame_filename = f"frame_{frame_number:07d}.jpg"
19
+ path = target_dir / frame_filename
20
+ return path
@@ -0,0 +1,27 @@
1
+ from endoreg_db.models.media.video.video_file_io import _get_frame_dir_path
2
+
3
+ from pathlib import Path
4
+ import logging
5
+
6
+ from typing import TYPE_CHECKING, List
7
+ if TYPE_CHECKING:
8
+ from endoreg_db.models import VideoFile
9
+
10
+ logger = logging.getLogger(__name__)
11
+
12
+ def _get_frame_paths(video: "VideoFile") -> List[Path]:
13
+ """Returns a sorted list of Path objects for extracted frame image files."""
14
+ frame_dir = _get_frame_dir_path(video)
15
+ if not frame_dir or not frame_dir.exists():
16
+ logger.warning("Frame directory %s does not exist for video %s.", frame_dir, video.uuid)
17
+ return []
18
+
19
+ frame_paths = list(frame_dir.glob('frame_*.jpg'))
20
+
21
+ try:
22
+ frame_paths.sort(key=lambda p: int(p.stem.split('_')[-1]))
23
+ except (ValueError, IndexError) as e:
24
+ logger.error("Error sorting frame paths in %s: %s. Found paths: %s", frame_dir, e, [p.name for p in frame_paths], exc_info=True)
25
+ logger.warning("Falling back to unsorted frame paths to preserve available data.")
26
+ return frame_paths
27
+ return frame_paths
@@ -0,0 +1,34 @@
1
+
2
+ from typing import TYPE_CHECKING
3
+ from django.db.models import QuerySet
4
+ import logging
5
+
6
+ if TYPE_CHECKING:
7
+ from endoreg_db.models import VideoFile, Frame
8
+
9
+ logger = logging.getLogger(__name__)
10
+
11
+
12
+
13
+
14
+
15
+ def _get_frame_range(video: "VideoFile", start_frame_number: int, end_frame_number: int) -> "QuerySet[Frame]":
16
+ """Gets a QuerySet of Frame objects within a specific range, ordered by frame number."""
17
+ from endoreg_db.models import Frame
18
+ try:
19
+ # Access related manager directly
20
+ return video.frames.filter(
21
+ frame_number__gte=start_frame_number,
22
+ frame_number__lte=end_frame_number,
23
+ ).order_by("frame_number")
24
+ except AttributeError:
25
+ logger.error("Could not access frame range for video %s via related manager.", video.uuid)
26
+ # Fallback query
27
+ return Frame.objects.filter(
28
+ video_file=video,
29
+ frame_number__gte=start_frame_number,
30
+ frame_number__lte=end_frame_number,
31
+ ).order_by("frame_number")
32
+ except Exception as e:
33
+ logger.error("Error getting frame range (%d-%d) for video %s: %s", start_frame_number, end_frame_number, video.uuid, e, exc_info=True)
34
+ return Frame.objects.none() # Return empty queryset on error
@@ -0,0 +1,27 @@
1
+ from django.db.models import QuerySet
2
+
3
+ from typing import TYPE_CHECKING
4
+
5
+ import logging
6
+
7
+ if TYPE_CHECKING:
8
+ from endoreg_db.models import VideoFile, Frame
9
+
10
+ logger = logging.getLogger(__name__)
11
+
12
+
13
+
14
+
15
+ def _get_frames(video: "VideoFile") -> "QuerySet[Frame]":
16
+ """Gets a QuerySet of all associated Frame objects, ordered by frame number."""
17
+ from endoreg_db.models import Frame
18
+ try:
19
+ # Access related manager directly
20
+ return video.frames.order_by("frame_number")
21
+ except AttributeError:
22
+ logger.error("Could not access frames for video %s. 'frames' related manager not found.", video.uuid)
23
+ # Fallback query
24
+ return Frame.objects.filter(video_file=video).order_by("frame_number")
25
+ except Exception as e:
26
+ logger.error("Error getting frames for video %s: %s", video.uuid, e, exc_info=True)
27
+ return Frame.objects.none() # Return empty queryset on error
@@ -0,0 +1,129 @@
1
+ from tqdm import tqdm
2
+ from pathlib import Path
3
+ from typing import List
4
+ from typing import TYPE_CHECKING, Optional
5
+ import logging
6
+ from django.db import OperationalError
7
+ import time
8
+
9
+ if TYPE_CHECKING:
10
+ from endoreg_db.models import VideoFile
11
+
12
+ logger = logging.getLogger(__name__)
13
+
14
+
15
+ def _initialize_frames(video: "VideoFile", frame_paths: Optional[List[Path]] = None):
16
+ """
17
+ Initializes Frame objects in the database based on either provided existing
18
+ frame paths or the expected frame count from the video metadata.
19
+
20
+ If `frame_paths` is provided, Frame objects are created/updated and marked
21
+ as `is_extracted=True`.
22
+ If `frame_paths` is None, Frame objects are created based on `video.frame_count`
23
+ and marked as `is_extracted=False`.
24
+
25
+ Updates state.frames_initialized and state.frame_count.
26
+ Uses bulk_create with ignore_conflicts=True, so it won't fail if frames already exist.
27
+
28
+ Raises RuntimeError on failure to create/update frames or update state.
29
+
30
+ State Transitions:
31
+ - On Success: Sets state.frames_initialized=True, state.frame_count=N.
32
+ - On Failure: Does not change state (error is raised).
33
+ """
34
+ from endoreg_db.models import Frame
35
+ from endoreg_db.models.media.video.video_file_frames._bulk_create_frames import _bulk_create_frames
36
+ from endoreg_db.models.media.video.video_file_frames._create_frame_object import _create_frame_object
37
+
38
+
39
+ frames_to_create = []
40
+ num_expected_or_provided = 0
41
+ mark_as_extracted = False
42
+
43
+ if frame_paths:
44
+ logger.info("Initializing Frame objects based on %d provided paths for video %s.", len(frame_paths), video.uuid)
45
+ mark_as_extracted = True
46
+ num_expected_or_provided = len(frame_paths)
47
+ for frame_path in tqdm(frame_paths, desc=f"Initializing Frames from Paths {video.uuid}", unit="frame"):
48
+ try:
49
+ frame_number = int(frame_path.stem.split('_')[-1])
50
+ relative_path_str = frame_path.name
51
+ frames_to_create.append(
52
+ _create_frame_object(video, frame_number, relative_path_str, extracted=mark_as_extracted)
53
+ )
54
+ except (ValueError, IndexError) as e:
55
+ logger.warning("Could not parse frame number from %s: %s", frame_path.name, e)
56
+ continue
57
+ else:
58
+ expected_frame_count = video.frame_count
59
+ if expected_frame_count is None or expected_frame_count <= 0:
60
+ logger.warning("Cannot initialize frames for video %s: Frame count is %s.", video.uuid, expected_frame_count)
61
+ try:
62
+ state = video.get_or_create_state()
63
+ if state.frames_initialized or state.frame_count is not None:
64
+ state.frames_initialized = False
65
+ state.frame_count = None
66
+ state.save(update_fields=['frames_initialized', 'frame_count'])
67
+ except Exception as state_e:
68
+ logger.error("Failed to reset state during empty initialization for video %s: %s", video.uuid, state_e, exc_info=True)
69
+ return
70
+
71
+ logger.info("Initializing %d expected Frame objects for video %s (is_extracted=False).", expected_frame_count, video.uuid)
72
+ mark_as_extracted = False
73
+ num_expected_or_provided = expected_frame_count
74
+ for frame_number in tqdm(range(expected_frame_count), desc=f"Initializing Expected Frames {video.uuid}", unit="frame"):
75
+ relative_path_str = f"frame_{frame_number:07d}.jpg"
76
+ frames_to_create.append(
77
+ _create_frame_object(video, frame_number, relative_path_str, extracted=mark_as_extracted)
78
+ )
79
+
80
+ if frames_to_create:
81
+ for attempt in range(5):
82
+
83
+ try:
84
+ _bulk_create_frames(video, frames_to_create)
85
+ num_created_or_ignored = len(frames_to_create)
86
+ logger.info("Bulk create attempted for %d Frame objects for video %s (ignore_conflicts=True).", num_created_or_ignored, video.uuid)
87
+
88
+ if mark_as_extracted:
89
+ frame_numbers_to_update = [f.frame_number for f in frames_to_create]
90
+ if frame_numbers_to_update:
91
+ update_count = Frame.objects.filter(
92
+ video=video,
93
+ frame_number__in=frame_numbers_to_update,
94
+ is_extracted=False
95
+ ).update(is_extracted=True)
96
+ if update_count > 0:
97
+ logger.info("Marked %d existing Frame objects as is_extracted=True for video %s.", update_count, video.uuid)
98
+
99
+ try:
100
+ state = video.get_or_create_state()
101
+ state.frames_initialized = True
102
+ state.frame_count = num_expected_or_provided
103
+ state.save(update_fields=['frames_initialized', 'frame_count'])
104
+ logger.info("Set frames_initialized=True and frame_count=%d for video %s.", num_expected_or_provided, video.uuid)
105
+ except Exception as state_e:
106
+ logger.error("Failed to update state after frame initialization for video %s: %s", video.uuid, state_e, exc_info=True)
107
+ raise RuntimeError(f"Failed to update state after frame initialization for video {video.uuid}") from state_e
108
+
109
+ except OperationalError as e:
110
+ if "database is locked" in str(e):
111
+ logger.warning("Database is locked, retrying frame initialization for video %s (attempt %d/5).", video.uuid, attempt + 1)
112
+ time.sleep(2 ** attempt)
113
+ if attempt < 4:
114
+ continue
115
+ else:
116
+ raise RuntimeError(f"Failed to initialize frames for video {video.uuid}.") from e
117
+ logger.error("Error initializing frames for video %s: %s", video.uuid, e, exc_info=True)
118
+ raise RuntimeError(f"Failed to initialize frames for video {video.uuid}.") from e
119
+
120
+ else:
121
+ logger.warning("No valid frames found/generated to initialize for video %s.", video.uuid)
122
+ try:
123
+ state = video.get_or_create_state()
124
+ if state.frames_initialized or state.frame_count is not None:
125
+ state.frames_initialized = False
126
+ state.frame_count = None
127
+ state.save(update_fields=['frames_initialized', 'frame_count'])
128
+ except Exception as state_e:
129
+ logger.error("Failed to reset state during empty initialization for video %s: %s", video.uuid, state_e, exc_info=True)
@@ -0,0 +1,141 @@
1
+ import logging
2
+ import os
3
+ from typing import TYPE_CHECKING
4
+ from django.db import transaction
5
+
6
+ # Assuming ffmpeg_wrapper has or will have this function
7
+ from endoreg_db.utils.video.ffmpeg_wrapper import extract_frame_range as ffmpeg_extract_frame_range
8
+
9
+ from endoreg_db.models.media.video.video_file_io import _get_frame_dir_path
10
+
11
+ if TYPE_CHECKING:
12
+ from endoreg_db.models import VideoFile
13
+
14
+ logger = logging.getLogger(__name__)
15
+
16
+ def _delete_frame_range(video: "VideoFile", start_frame: int, end_frame: int):
17
+ """
18
+ Deletes frame image files within the specified range [start_frame, end_frame)
19
+ and updates their is_extracted status to False. Runs within the caller's transaction.
20
+ """
21
+
22
+ logger.info("Deleting frame files for video %s in range [%d, %d)", video.uuid, start_frame, end_frame)
23
+ frames_to_delete = video.frames.filter(
24
+ frame_number__gte=start_frame,
25
+ frame_number__lt=end_frame,
26
+ is_extracted=True
27
+ )
28
+
29
+ deleted_count = 0
30
+ paths_to_delete = [frame.file_path for frame in frames_to_delete] # Get paths before potential DB changes
31
+
32
+ # Update DB first
33
+ update_count = frames_to_delete.update(is_extracted=False)
34
+ logger.info("Marked %d Frame objects as is_extracted=False for video %s range [%d, %d).",
35
+ update_count, video.uuid, start_frame, end_frame)
36
+
37
+ # Then delete files
38
+ for frame_path in paths_to_delete:
39
+ try:
40
+ if frame_path.exists():
41
+ os.remove(frame_path)
42
+ deleted_count += 1
43
+ except Exception as e:
44
+ # Log warning but continue; DB state is already updated.
45
+ logger.warning("Could not delete frame file %s for video %s: %s", frame_path, video.uuid, e)
46
+
47
+ logger.info("Attempted deletion of %d files for video %s range [%d, %d). Actual deleted: %d.",
48
+ len(paths_to_delete), video.uuid, start_frame, end_frame, deleted_count)
49
+
50
+
51
+
52
+
53
+ @transaction.atomic
54
+ def _extract_frame_range(
55
+ video: "VideoFile",
56
+ start_frame: int,
57
+ end_frame: int,
58
+ quality: int = 2,
59
+ overwrite: bool = False,
60
+ ext="jpg",
61
+ verbose=False,
62
+ ) -> bool:
63
+ """
64
+ Extracts frames within the range [start_frame, end_frame) using ffmpeg.
65
+ Updates corresponding Frame objects' is_extracted flag.
66
+ Runs within the caller's transaction.
67
+ Does NOT update VideoState.frames_extracted.
68
+ """
69
+
70
+ if not video.has_raw:
71
+ raise FileNotFoundError(f"Raw video file not available for {video.uuid}. Cannot extract frame range.")
72
+
73
+ raw_file_path = video.get_raw_file_path()
74
+ if not raw_file_path or not raw_file_path.exists():
75
+ raise FileNotFoundError(f"Raw video file not found at {raw_file_path} for video {video.uuid}. Cannot extract frame range.")
76
+
77
+ frame_dir = _get_frame_dir_path(video)
78
+ if not frame_dir:
79
+ raise ValueError(f"Cannot determine frame directory path for video {video.uuid}.")
80
+
81
+ # Check frames within the range that might already exist
82
+ frames_in_range = video.frames.filter(
83
+ frame_number__gte=start_frame,
84
+ frame_number__lt=end_frame
85
+ )
86
+ existing_extracted_in_range = frames_in_range.filter(is_extracted=True)
87
+
88
+ if existing_extracted_in_range.exists():
89
+ if overwrite:
90
+ logger.info("Overwrite=True, deleting existing frame files in range [%d, %d) for video %s before extraction.", start_frame, end_frame, video.uuid)
91
+ _delete_frame_range(video, start_frame, end_frame)
92
+ else:
93
+ logger.info("Frames already exist in range [%d, %d) for video %s and overwrite=False. Skipping extraction for this range.", start_frame, end_frame, video.uuid)
94
+ updated_count = frames_in_range.filter(is_extracted=False).update(is_extracted=True)
95
+ if updated_count > 0:
96
+ logger.info("Marked %d existing Frame objects in range [%d, %d) as extracted for video %s.", updated_count, start_frame, end_frame, video.uuid)
97
+ return True # Indicate success as frames are considered present
98
+
99
+ frame_dir.mkdir(parents=True, exist_ok=True)
100
+ extracted_paths = []
101
+
102
+ try:
103
+ logger.info("Starting frame range extraction [%d, %d) for video %s to %s", start_frame, end_frame, video.uuid, frame_dir)
104
+ extracted_paths = ffmpeg_extract_frame_range(
105
+ raw_file_path, frame_dir, start_frame, end_frame, quality=quality, ext=ext
106
+ )
107
+
108
+ logger.info("ffmpeg extraction process completed for video %s range [%d, %d). Found %d files.", video.uuid, start_frame, end_frame, len(extracted_paths))
109
+
110
+ update_count = frames_in_range.update(is_extracted=True)
111
+ logger.info("Marked %d Frame objects in range [%d, %d) as is_extracted=True for video %s.", update_count, start_frame, end_frame, video.uuid)
112
+
113
+ return True
114
+
115
+ except FileNotFoundError as err:
116
+ logger.error(
117
+ "Frame range extraction [%d, %d) failed for video %s: %s",
118
+ start_frame,
119
+ end_frame,
120
+ video.uuid,
121
+ err,
122
+ exc_info=True,
123
+ )
124
+ raise
125
+
126
+ except Exception as e:
127
+ logger.error("Frame range extraction [%d, %d) or DB update failed for video %s: %s", start_frame, end_frame, video.uuid, e, exc_info=True)
128
+
129
+ logger.warning("Attempting file cleanup in range [%d, %d) for video %s due to extraction error.", start_frame, end_frame, video.uuid)
130
+ files_to_check = extracted_paths if 'extracted_paths' in locals() and extracted_paths else []
131
+ if not files_to_check:
132
+ files_to_check = [frame_dir / f"frame_{i:07d}.{ext}" for i in range(start_frame, end_frame)]
133
+
134
+ for potential_file in files_to_check:
135
+ if potential_file.exists():
136
+ try:
137
+ os.remove(potential_file)
138
+ except OSError as unlink_err:
139
+ logger.error("Failed to delete potential frame %s during cleanup: %s", potential_file, unlink_err)
140
+
141
+ raise RuntimeError(f"Frame range extraction or update failed for video {video.uuid} range [{start_frame}, {end_frame}).") from e