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 +1,699 @@
1
+ """Concrete model for video files, handling both raw and processed states."""
2
+
3
+ import logging
4
+ from pathlib import Path
5
+ import uuid
6
+ from typing import TYPE_CHECKING, Optional, Union, cast
7
+ import os
8
+
9
+ from django.db import models
10
+ from django.core.files import File
11
+ from django.db.models.fields.files import FieldFile
12
+ from django.core.validators import FileExtensionValidator
13
+ from django.db.models import F
14
+ from endoreg_db.utils.calc_duration_seconds import _calc_duration_vf
15
+
16
+ # --- Import model-specific function modules ---
17
+ from .create_from_file import _create_from_file
18
+ from .video_file_anonymize import (
19
+ _anonymize,
20
+ _create_anonymized_frame_files,
21
+ _cleanup_raw_assets,
22
+ )
23
+ from .video_file_meta import (
24
+ _update_text_metadata,
25
+ _update_video_meta,
26
+ _get_fps,
27
+ _get_endo_roi,
28
+ _get_crop_template,
29
+ _initialize_video_specs,
30
+ )
31
+ from .video_file_frames import (
32
+ _extract_frames,
33
+ _initialize_frames,
34
+ _delete_frames,
35
+ _get_frame_path,
36
+ _get_frame_paths,
37
+ _get_frame_number,
38
+ _get_frames,
39
+ _get_frame,
40
+ _get_frame_range,
41
+ _create_frame_object,
42
+ _bulk_create_frames,
43
+ )
44
+ # Update import aliases for clarity and to use as helpers
45
+ from .video_file_frames._manage_frame_range import _extract_frame_range as _extract_frame_range_helper
46
+ from .video_file_frames._manage_frame_range import _delete_frame_range as _delete_frame_range_helper
47
+ from .video_file_io import (
48
+ _delete_with_file,
49
+ _get_base_frame_dir,
50
+ _set_frame_dir,
51
+ _get_frame_dir_path,
52
+ _get_temp_anonymized_frame_dir,
53
+ _get_target_anonymized_video_path,
54
+ _get_raw_file_path,
55
+ _get_processed_file_path,
56
+ )
57
+ from .video_file_ai import (
58
+ _predict_video_pipeline,
59
+ _extract_text_from_video_frames,
60
+ )
61
+
62
+ from .pipe_1 import _pipe_1, _test_after_pipe_1
63
+ from .pipe_2 import _pipe_2
64
+
65
+ from ...utils import VIDEO_DIR, ANONYM_VIDEO_DIR
66
+ from ...state import VideoState
67
+ from ...label import LabelVideoSegment, Label
68
+
69
+
70
+ # Configure logging
71
+ logger = logging.getLogger(__name__) # Changed from "video_file"
72
+
73
+ if TYPE_CHECKING:
74
+ from endoreg_db.models import (
75
+ Center,
76
+ Frame,
77
+ SensitiveMeta,
78
+ EndoscopyProcessor,
79
+ VideoMeta,
80
+ PatientExamination,
81
+ Patient,
82
+ VideoState,
83
+ ModelMeta,
84
+ VideoImportMeta,
85
+ FFMpegMeta,
86
+ )
87
+ class VideoQuerySet(models.QuerySet):
88
+ def next_after(self, last_id=None):
89
+ """
90
+ Return the next VideoFile instance with a primary key greater than the given last_id.
91
+
92
+ Parameters:
93
+ last_id (int or None): The primary key to start after. If None or invalid, returns the first instance.
94
+
95
+ Returns:
96
+ VideoFile or None: The next VideoFile instance, or None if not found.
97
+ """
98
+ if last_id is not None:
99
+ try:
100
+ last_id = int(last_id)
101
+ except (ValueError, TypeError):
102
+ return None
103
+ q = self if last_id is None else self.filter(pk__gt=last_id)
104
+ return q.order_by("pk").first()
105
+
106
+ class VideoFile(models.Model):
107
+ uuid = models.UUIDField(default=uuid.uuid4, editable=False, unique=True)
108
+
109
+ objects = VideoQuerySet.as_manager()
110
+
111
+ raw_file = models.FileField(
112
+ upload_to=VIDEO_DIR.name, # Use .name for relative path
113
+ validators=[FileExtensionValidator(allowed_extensions=["mp4"])],
114
+ null=True,
115
+ blank=True,
116
+ )
117
+ processed_file = models.FileField(
118
+ upload_to=ANONYM_VIDEO_DIR.name, # Use .name for relative path
119
+ validators=[FileExtensionValidator(allowed_extensions=["mp4"])],
120
+ null=True,
121
+ blank=True,
122
+ )
123
+
124
+ video_hash = models.CharField(max_length=255, unique=True, help_text="Hash of the raw video file.")
125
+ processed_video_hash = models.CharField(
126
+ max_length=255, unique=True, null=True, blank=True, help_text="Hash of the processed video file, unique if not null."
127
+ )
128
+
129
+ sensitive_meta = models.OneToOneField(
130
+ "SensitiveMeta", on_delete=models.SET_NULL, null=True, blank=True, related_name="video_file"
131
+ ) # type: ignore
132
+ center = models.ForeignKey("Center", on_delete=models.PROTECT) # type: ignore
133
+ processor = models.ForeignKey(
134
+ "EndoscopyProcessor", on_delete=models.PROTECT, blank=True, null=True
135
+ ) # type: ignore
136
+ video_meta = models.OneToOneField(
137
+ "VideoMeta", on_delete=models.SET_NULL, null=True, blank=True, related_name="video_file"
138
+ ) # type: ignore
139
+ examination = models.ForeignKey(
140
+ "PatientExamination",
141
+ on_delete=models.SET_NULL,
142
+ blank=True,
143
+ null=True,
144
+ related_name="video_files",
145
+ ) # type: ignore
146
+ patient = models.ForeignKey(
147
+ "Patient",
148
+ on_delete=models.SET_NULL,
149
+ blank=True,
150
+ null=True,
151
+ related_name="video_files",
152
+ ) # type: ignore
153
+ ai_model_meta = models.ForeignKey(
154
+ "ModelMeta", on_delete=models.SET_NULL, blank=True, null=True
155
+ ) # type: ignore
156
+ state = models.OneToOneField(
157
+ "VideoState", on_delete=models.SET_NULL, null=True, blank=True, related_name="video_file"
158
+ ) # type: ignore
159
+ import_meta = models.OneToOneField(
160
+ "VideoImportMeta", on_delete=models.CASCADE, blank=True, null=True
161
+ ) # type: ignore
162
+
163
+ original_file_name = models.CharField(max_length=255, blank=True, null=True)
164
+ uploaded_at = models.DateTimeField(auto_now_add=True)
165
+ frame_dir = models.CharField(max_length=512, blank=True, help_text="Path to frames extracted from the raw video.")
166
+ fps = models.FloatField(blank=True, null=True)
167
+ duration = models.FloatField(blank=True, null=True)
168
+ frame_count = models.IntegerField(blank=True, null=True)
169
+ width = models.IntegerField(blank=True, null=True)
170
+ height = models.IntegerField(blank=True, null=True)
171
+ suffix = models.CharField(max_length=10, blank=True, null=True)
172
+ sequences = models.JSONField(default=dict, blank=True, help_text="AI prediction sequences based on raw frames.")
173
+ date = models.DateField(blank=True, null=True)
174
+ meta = models.JSONField(blank=True, null=True)
175
+ date_created = models.DateTimeField(auto_now_add=True)
176
+ date_modified = models.DateTimeField(auto_now=True)
177
+
178
+ if TYPE_CHECKING:
179
+ label_video_segments: "models.QuerySet[LabelVideoSegment]"
180
+ frames: "models.QuerySet[Frame]"
181
+ center: "Center"
182
+ processor: "EndoscopyProcessor"
183
+ video_meta: "VideoMeta"
184
+ examination: "PatientExamination"
185
+ patient: "Patient"
186
+ sensitive_meta: "SensitiveMeta"
187
+ state: "VideoState"
188
+ ai_model_meta: "ModelMeta"
189
+ import_meta: "VideoImportMeta"
190
+
191
+
192
+ @property
193
+ def ffmpeg_meta(self) -> "FFMpegMeta":
194
+ """
195
+ Return the associated FFMpegMeta instance for this video, initializing video specs if necessary.
196
+
197
+ Returns:
198
+ FFMpegMeta: The FFMpegMeta object containing metadata for this video.
199
+ """
200
+ from endoreg_db.models import FFMpegMeta
201
+ if self.video_meta is not None:
202
+ if self.video_meta.ffmpeg_meta is not None:
203
+ return self.video_meta.ffmpeg_meta
204
+ raise AssertionError("Expected FFMpegMeta instance.")
205
+ else:
206
+ self.initialize_video_specs()
207
+ ffmpeg_meta = self.video_meta.ffmpeg_meta if self.video_meta else None
208
+ assert isinstance(ffmpeg_meta, FFMpegMeta), "Expected FFMpegMeta instance."
209
+ return ffmpeg_meta
210
+
211
+
212
+ # Exception message constants
213
+ NO_ACTIVE_FILE = "Has no raw file"
214
+ NO_FILE_ASSOCIATED = "Active file has no associated file."
215
+
216
+ @property
217
+ def active_raw_file(self) -> File:
218
+ """Return the raw file if available, otherwise raise ValueError."""
219
+ if self.has_raw:
220
+ return self.raw_file
221
+ raise ValueError(self.NO_ACTIVE_FILE)
222
+
223
+ @property
224
+ def active_raw_file_url(self) -> str:
225
+ """Return the URL of the active raw file, or raise ValueError if unavailable."""
226
+ _file = self.active_raw_file
227
+ assert _file is not None, self.NO_ACTIVE_FILE
228
+ if not _file or not _file.name:
229
+ raise ValueError(self.NO_FILE_ASSOCIATED)
230
+ return _file.url
231
+
232
+ # Pipeline Functions
233
+ pipe_1 = _pipe_1
234
+ test_after_pipe_1 = _test_after_pipe_1
235
+ pipe_2 = _pipe_2
236
+
237
+ # Metadata Funtions
238
+ update_video_meta = _update_video_meta
239
+ initialize_video_specs = _initialize_video_specs
240
+ get_fps = _get_fps
241
+ get_endo_roi = _get_endo_roi
242
+ get_crop_template = _get_crop_template
243
+ update_text_metadata = _update_text_metadata
244
+
245
+ extract_frames = _extract_frames
246
+ initialize_frames = _initialize_frames
247
+ delete_frames = _delete_frames
248
+ get_frame_path = _get_frame_path
249
+ get_frame_paths = _get_frame_paths
250
+ get_frame_number = _get_frame_number
251
+ get_frames = _get_frames
252
+ get_frame = _get_frame
253
+ get_frame_range = _get_frame_range
254
+ get_duration = _calc_duration_vf
255
+ create_frame_object = _create_frame_object
256
+ bulk_create_frames = _bulk_create_frames
257
+
258
+
259
+
260
+ # Define new methods that call the helper functions
261
+ def extract_specific_frame_range(self, start_frame: int, end_frame: int, overwrite: bool = False, **kwargs) -> bool:
262
+ """
263
+ Extract frames from the video within the specified frame range.
264
+
265
+ Parameters:
266
+ start_frame (int): The starting frame number (inclusive).
267
+ end_frame (int): The ending frame number (exclusive).
268
+ overwrite (bool): Whether to overwrite existing frames in the range.
269
+
270
+ Returns:
271
+ bool: True if frame extraction was successful, False otherwise.
272
+
273
+ Additional keyword arguments:
274
+ quality (int, optional): Quality setting for extracted frames.
275
+ ext (str, optional): File extension for extracted frames.
276
+ verbose (bool, optional): Whether to enable verbose output.
277
+ """
278
+ quality = kwargs.get('quality', 2)
279
+ ext = kwargs.get('ext', "jpg")
280
+ verbose = kwargs.get('verbose', False)
281
+
282
+ # Log if unexpected kwargs are passed, beyond those used by the helper
283
+ expected_helper_kwargs = {'quality', 'ext', 'verbose'}
284
+ unexpected_kwargs = {k: v for k, v in kwargs.items() if k not in expected_helper_kwargs}
285
+ if unexpected_kwargs:
286
+ logger.warning(f"Unexpected keyword arguments for extract_specific_frame_range, will be ignored by helper: {unexpected_kwargs}")
287
+
288
+ return _extract_frame_range_helper(
289
+ video=self,
290
+ start_frame=start_frame,
291
+ end_frame=end_frame,
292
+ quality=quality,
293
+ overwrite=overwrite,
294
+ ext=ext,
295
+ verbose=verbose
296
+ )
297
+
298
+ def delete_specific_frame_range(self, start_frame: int, end_frame: int) -> None:
299
+ """
300
+ Deletes frame files for a specific range [start_frame, end_frame).
301
+ """
302
+ _delete_frame_range_helper(
303
+ video=self,
304
+ start_frame=start_frame,
305
+ end_frame=end_frame
306
+ )
307
+
308
+ delete_with_file = _delete_with_file
309
+ get_base_frame_dir = _get_base_frame_dir
310
+ set_frame_dir = _set_frame_dir
311
+ get_frame_dir_path = _get_frame_dir_path
312
+ get_temp_anonymized_frame_dir = _get_temp_anonymized_frame_dir
313
+ get_target_anonymized_video_path = _get_target_anonymized_video_path
314
+ get_raw_file_path = _get_raw_file_path
315
+ get_processed_file_path = _get_processed_file_path
316
+
317
+ anonymize = _anonymize
318
+ _create_anonymized_frame_files = _create_anonymized_frame_files
319
+ _cleanup_raw_assets = _cleanup_raw_assets
320
+
321
+ predict_video = _predict_video_pipeline
322
+ extract_text_from_frames = _extract_text_from_video_frames
323
+
324
+
325
+
326
+ @classmethod
327
+ def check_hash_exists(cls, video_hash: str) -> bool:
328
+ """
329
+ Checks if a VideoFile with the given raw video hash already exists.
330
+ """
331
+ return cls.objects.filter(video_hash=video_hash).exists()
332
+
333
+ @property
334
+ def is_processed(self) -> bool:
335
+ return bool(self.processed_file and self.processed_file.name)
336
+
337
+ @property
338
+ def has_raw(self) -> bool:
339
+ """
340
+ Return True if a raw video file is associated with this instance.
341
+ """
342
+ return bool(self.raw_file and self.raw_file.name)
343
+
344
+
345
+ @property
346
+ def active_file(self) -> FieldFile:
347
+ """
348
+ Return the active video file, preferring the processed file if available.
349
+
350
+ Returns:
351
+ File: The processed file if present; otherwise, the raw file.
352
+
353
+ Raises:
354
+ ValueError: If neither a processed nor a raw file is available.
355
+ """
356
+ processed = self.processed_file
357
+ if isinstance(processed, FieldFile) and processed.name:
358
+ return processed
359
+
360
+ raw = self.raw_file
361
+ if isinstance(raw, FieldFile) and raw.name:
362
+ return raw
363
+
364
+ raise ValueError("No active file available. VideoFile has neither raw nor processed file.")
365
+
366
+
367
+ @property
368
+ def active_file_path(self) -> Path:
369
+ """
370
+ Return the filesystem path of the active video file.
371
+
372
+ Returns:
373
+ Path: The path to the processed file if available, otherwise the raw file.
374
+
375
+ Raises:
376
+ ValueError: If neither a processed nor raw file is present.
377
+ """
378
+ active = self.active_file
379
+ if active is self.processed_file:
380
+ path = _get_processed_file_path(self)
381
+ elif active is self.raw_file:
382
+ path = _get_raw_file_path(self)
383
+ else:
384
+ raise ValueError("No active file path available. VideoFile has neither raw nor processed file.")
385
+
386
+ if path is None:
387
+ raise ValueError("Active file path could not be resolved.")
388
+ return path
389
+
390
+
391
+ @classmethod
392
+ def create_from_file(cls, file_path: Union[str, Path], center_name: str, **kwargs) -> Optional["VideoFile"]:
393
+ # Ensure file_path is a Path object
394
+ if isinstance(file_path, str):
395
+ file_path = Path(file_path)
396
+ # Pass center_name and other kwargs to the helper function
397
+ if not center_name:
398
+ try:
399
+ center_name = os.environ["CENTER_NAME"]
400
+ except KeyError:
401
+ logger.error("Center name must be provided to create VideoFile from file. You can set CENTER_NAME in environment variables.")
402
+ return None
403
+ return _create_from_file(cls, file_path, center_name=center_name, **kwargs)
404
+
405
+ @classmethod
406
+ def create_from_file_initialized(
407
+ cls,
408
+ file_path: Union[str, Path],
409
+ center_name:str,
410
+ processor_name: Optional[str] = None,
411
+ delete_source:bool = False,
412
+ save_video_file:bool = True, # Add this line
413
+ ):
414
+ """
415
+ Creates a VideoFile instance from a given video file path.
416
+ Handles transcoding (if necessary), hashing, file storage, and database record creation.
417
+ Raises exceptions on failure.
418
+ """
419
+ # Ensure file_path is a Path object
420
+ if isinstance(file_path, str):
421
+ file_path = Path(file_path)
422
+
423
+ # Call the helper function to create the VideoFile instance
424
+ video_file = _create_from_file(
425
+ cls_model=VideoFile,
426
+ file_path=file_path,
427
+ center_name=center_name,
428
+ processor_name=processor_name,
429
+ delete_source=delete_source,
430
+ save=save_video_file, # Add this line
431
+ )
432
+
433
+ video_file = video_file.initialize()
434
+ return video_file
435
+
436
+ def delete(self, using=None, keep_parents=False) -> tuple[int, dict[str, int]]:
437
+ """
438
+ Delete the VideoFile instance, including associated files and frames.
439
+
440
+ Overrides the default delete method to ensure proper cleanup of related resources.
441
+ """
442
+ # Ensure frames are deleted before the main instance
443
+ _delete_frames(self)
444
+
445
+ # Call the original delete method to remove the instance from the database
446
+ active_path = self.active_file_path
447
+ logger.info(f"Deleting VideoFile: {self.uuid} - {active_path}")
448
+
449
+ # Delete associated files if they exist
450
+ if active_path.exists():
451
+ active_path.unlink(missing_ok=True)
452
+
453
+
454
+ # Delete file storage
455
+ if self.raw_file and self.raw_file.storage.exists(self.raw_file.name):
456
+ self.raw_file.storage.delete(self.raw_file.name)
457
+ if self.processed_file and self.processed_file.storage.exists(self.processed_file.name):
458
+ self.processed_file.storage.delete(self.processed_file.name)
459
+
460
+ # Use proper database connection
461
+ if using is None:
462
+ using = 'default'
463
+
464
+ raw_file_path = self.get_raw_file_path()
465
+ if raw_file_path:
466
+ raw_file_path = Path(raw_file_path)
467
+ lock_path = raw_file_path.with_suffix(raw_file_path.suffix + ".lock")
468
+ if lock_path.exists():
469
+ try:
470
+ lock_path.unlink()
471
+ logger.info(f"Removed processing lock: {lock_path}")
472
+ except Exception as e:
473
+ logger.warning(f"Could not remove processing lock {lock_path}: {e}")
474
+
475
+ try:
476
+ # Call parent delete with proper parameters
477
+ result = super().delete(using=using, keep_parents=keep_parents)
478
+ logger.info(f"VideoFile {self.uuid} deleted successfully.")
479
+ return result
480
+ except Exception as e:
481
+ logger.error(f"Error deleting VideoFile {self.uuid}: {e}")
482
+ raise
483
+
484
+ def validate_metadata_annotation(self, extracted_data_dict: Optional[dict] = None) -> bool:
485
+ """
486
+ Validate the metadata of the VideoFile instance.
487
+
488
+ Called after annotation in the frontend, this method deletes the associated active file, updates the sensitive meta data with the user annotated data.
489
+ It also ensures the video file is properly saved after the metadata update.
490
+ """
491
+ from endoreg_db.models import SensitiveMeta
492
+ if not self.sensitive_meta:
493
+ self.sensitive_meta = SensitiveMeta.objects.create(center=self.center)
494
+
495
+ # Delete the active file to ensure it is reprocessed with the new metadata
496
+ if self.active_file_path.exists():
497
+ self.active_file_path.unlink(missing_ok=True)
498
+
499
+ # Update sensitive metadata with user annotations
500
+ sensitive_meta = _update_text_metadata(self, extracted_data_dict, overwrite=True)
501
+
502
+ if sensitive_meta:
503
+ # Mark as processed after validation
504
+ self.get_or_create_state().mark_sensitive_meta_processed(save=True)
505
+ # Save the VideoFile instance to persist changes
506
+ self.save()
507
+ logger.info(f"Metadata annotation validated and saved for video {self.uuid}.")
508
+ return True
509
+ else:
510
+ logger.error(f"Failed to validate metadata annotation for video {self.uuid}.")
511
+ return False
512
+
513
+
514
+
515
+ def initialize(self):
516
+ """
517
+ Initialize the VideoFile instance by updating metadata, setting up video specs, assigning frame directory, ensuring related state and sensitive metadata exist, saving the instance, and initializing frames.
518
+
519
+ Returns:
520
+ VideoFile: The initialized VideoFile instance.
521
+ """
522
+
523
+ self.update_video_meta()
524
+ # Initialize video specs
525
+ self.initialize_video_specs(use_raw=True)
526
+
527
+ # Set the frame directory
528
+ self.set_frame_dir()
529
+
530
+ # Create a new state if it doesn't exist
531
+ self.state = self.get_or_create_state()
532
+
533
+ self.sensitive_meta = self.get_or_create_sensitive_meta()
534
+ self.save()
535
+ # Initialize frames based on the video specs
536
+ self.initialize_frames()
537
+
538
+
539
+ return self
540
+
541
+ def __str__(self):
542
+ """
543
+ Return a human-readable string summarizing the video's state, active file name, and UUID.
544
+ """
545
+ active_path = self.active_file_path
546
+ file_name = active_path.name if active_path else "No file"
547
+ state = "Processed" if self.is_processed else ("Raw" if self.has_raw else "No File")
548
+ return f"VideoFile ({state}): {file_name} (UUID: {self.uuid})"
549
+
550
+ # --- Convenience state/meta helpers used in tests and admin workflows ---
551
+ def mark_sensitive_meta_processed(self, *, save: bool = True) -> "VideoFile":
552
+ """
553
+ Mark this video's processing state as having its sensitive meta fully processed.
554
+ This proxies to the related VideoState and persists by default.
555
+ """
556
+ state = self.get_or_create_state()
557
+ state.mark_sensitive_meta_processed(save=save)
558
+ return self
559
+
560
+ def mark_sensitive_meta_verified(self) -> "VideoFile":
561
+ """
562
+ Mark the associated SensitiveMeta as verified by setting both DOB and names as verified.
563
+ Ensures the SensitiveMeta and its state exist.
564
+ """
565
+ sm = self.get_or_create_sensitive_meta()
566
+ # Use SensitiveMeta methods to update underlying SensitiveMetaState
567
+ sm.mark_dob_verified()
568
+ sm.mark_names_verified()
569
+ return self
570
+
571
+ def save(self, *args, **kwargs):
572
+ # Ensure state exists or is created before the main save operation
573
+ # Now call the original save method
574
+ """
575
+ Saves the VideoFile instance to the database.
576
+
577
+ Overrides the default save method to persist changes to the VideoFile model.
578
+ """
579
+ super().save(*args, **kwargs)
580
+
581
+ def get_or_create_state(self) -> "VideoState":
582
+ """Ensure this video has a persisted ``VideoState`` and return it."""
583
+
584
+ state = self.state
585
+
586
+ # When tests reuse cached instances across database flushes, ``state`` may reference
587
+ # a row that no longer exists. Guard against that by validating persistence.
588
+ state_pk = getattr(state, "pk", None)
589
+ if state is not None and state_pk is not None:
590
+ if not VideoState.objects.filter(pk=state_pk).exists():
591
+ state = None
592
+
593
+ if state is None:
594
+ # Create a fresh state to avoid refresh_from_db() failures on unsaved instances.
595
+ state = VideoState.objects.create()
596
+ self.state = state
597
+
598
+ # Persist the relation immediately if the VideoFile already exists in the DB so
599
+ # later refreshes see the association without requiring additional saves.
600
+ if self.pk:
601
+ self.save(update_fields=["state"])
602
+
603
+ return state
604
+
605
+ def get_or_create_sensitive_meta(self) -> "SensitiveMeta":
606
+ """
607
+ Retrieve the associated SensitiveMeta instance for this video, creating and assigning one if it does not exist.
608
+
609
+ Returns:
610
+ SensitiveMeta: The related SensitiveMeta instance.
611
+ """
612
+ from endoreg_db.models import SensitiveMeta
613
+ if self.sensitive_meta is None:
614
+ self.sensitive_meta = SensitiveMeta.objects.create(center = self.center)
615
+ # Do not mark processed here; it will be set after extraction/validation steps
616
+ return self.sensitive_meta
617
+
618
+ def get_outside_segments(self, only_validated: bool = False) -> models.QuerySet["LabelVideoSegment"]:
619
+ """
620
+ Return all video segments labeled as "outside" for this video.
621
+
622
+ Parameters:
623
+ only_validated (bool): If True, only segments with a validated state are included.
624
+
625
+ Returns:
626
+ QuerySet: A queryset of LabelVideoSegment instances labeled as "outside". Returns an empty queryset if the label does not exist or an error occurs.
627
+ """
628
+ try:
629
+ outside_label = Label.objects.get(name__iexact="outside")
630
+ segments = self.label_video_segments.filter(label=outside_label)
631
+
632
+ if only_validated:
633
+ # Filter based on the is_validated field in the related state object
634
+ segments = segments.filter(state__is_validated=True)
635
+
636
+ return segments
637
+ except Label.DoesNotExist:
638
+ logger.warning("Outside label not found in the database.")
639
+ return self.label_video_segments.none()
640
+ except Exception as e:
641
+ logger.error("Error getting outside segments for video %s: %s", self.uuid, e, exc_info=True)
642
+ return self.label_video_segments.none()
643
+
644
+ @classmethod
645
+ def get_all_videos(cls) -> models.QuerySet["VideoFile"]:
646
+ """
647
+ Returns a queryset containing all VideoFile records.
648
+
649
+ This class method retrieves every VideoFile instance in the database without filtering.
650
+ """
651
+ return cast(models.QuerySet["VideoFile"], cls.objects.all())
652
+
653
+ def count_unmodified_others(self) -> int:
654
+ """
655
+ Count the number of other VideoFile instances that have not been modified since creation.
656
+
657
+ Returns:
658
+ int: The count of VideoFile records, excluding this instance, where the modification timestamp matches the creation timestamp.
659
+ """
660
+ return (
661
+ VideoFile.objects
662
+ .filter(date_modified=F('date_created')) # compare the two fields in SQL
663
+ .exclude(pk=self.pk) # exclude this instance
664
+ .count() # run a fast COUNT(*) on the filtered set
665
+ )
666
+
667
+
668
+ def frame_number_to_s(self, frame_number: int) -> float:
669
+ """
670
+ Convert a frame number to its corresponding time in seconds based on the video's frames per second (FPS).
671
+
672
+ Parameters:
673
+ frame_number (int): The frame number to convert.
674
+
675
+ Returns:
676
+ float: The time in seconds corresponding to the given frame number.
677
+
678
+ Raises:
679
+ ValueError: If the video's FPS is not set or is less than or equal to zero.
680
+ """
681
+ fps = self.get_fps()
682
+ if fps is None or fps <= 0:
683
+ raise ValueError("FPS must be set and greater than zero.")
684
+ return frame_number / fps
685
+
686
+ def get_video_by_id(self, video_id: int) -> "VideoFile":
687
+ """
688
+ Retrieve a VideoFile instance by its primary key (ID).
689
+
690
+ Parameters:
691
+ video_id (int): The primary key of the VideoFile to retrieve.
692
+
693
+ Returns:
694
+ VideoFile: The VideoFile instance with the specified ID.
695
+
696
+ Raises:
697
+ VideoFile.DoesNotExist: If no VideoFile with the given ID exists.
698
+ """
699
+ return self.objects.get(pk=video_id)