endoreg-db 0.8.9.32__py3-none-any.whl

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  1. endoreg_db/__init__.py +0 -0
  2. endoreg_db/_version.py +34 -0
  3. endoreg_db/admin.py +97 -0
  4. endoreg_db/api/serializers/finding_descriptions.py +0 -0
  5. endoreg_db/api/views/finding_descriptions.py +0 -0
  6. endoreg_db/api_urls.py +4 -0
  7. endoreg_db/apps.py +17 -0
  8. endoreg_db/assets/dummy_model.ckpt +1 -0
  9. endoreg_db/authz/auth.py +78 -0
  10. endoreg_db/authz/backends.py +168 -0
  11. endoreg_db/authz/management/commands/list_routes.py +20 -0
  12. endoreg_db/authz/middleware.py +84 -0
  13. endoreg_db/authz/permissions.py +138 -0
  14. endoreg_db/authz/policy.py +224 -0
  15. endoreg_db/authz/settings.py +64 -0
  16. endoreg_db/authz/views_auth.py +70 -0
  17. endoreg_db/codemods/readme.md +88 -0
  18. endoreg_db/codemods/rename_datetime_fields.py +99 -0
  19. endoreg_db/config/__init__.py +0 -0
  20. endoreg_db/config/env.py +106 -0
  21. endoreg_db/config/settings/__init__.py +6 -0
  22. endoreg_db/config/settings/base.py +148 -0
  23. endoreg_db/config/settings/case_gen.py +32 -0
  24. endoreg_db/config/settings/dev.py +108 -0
  25. endoreg_db/config/settings/keycloak.py +177 -0
  26. endoreg_db/config/settings/prod.py +66 -0
  27. endoreg_db/config/settings/test.py +72 -0
  28. endoreg_db/data/__init__.py +135 -0
  29. endoreg_db/data/ai_model/data.yaml +7 -0
  30. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  31. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  32. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  33. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  34. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  35. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  36. endoreg_db/data/ai_model_type/data.yaml +7 -0
  37. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  38. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  39. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  40. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  41. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  42. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  43. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  44. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  45. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  46. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  47. endoreg_db/data/case_template/rule_value/.init +0 -0
  48. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  49. endoreg_db/data/case_template/template/base.yaml +8 -0
  50. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  51. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  52. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  53. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  54. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  55. endoreg_db/data/center/data.yaml +99 -0
  56. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  57. endoreg_db/data/center_shift/ukw.yaml +9 -0
  58. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  59. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  60. endoreg_db/data/db_summary.csv +58 -0
  61. endoreg_db/data/db_summary.xlsx +0 -0
  62. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  63. endoreg_db/data/disease/hepatology.yaml +5 -0
  64. endoreg_db/data/disease/misc.yaml +5 -0
  65. endoreg_db/data/disease/renal.yaml +5 -0
  66. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  67. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  68. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  69. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  70. endoreg_db/data/distribution/date/patient.yaml +7 -0
  71. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  72. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  73. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  74. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  75. endoreg_db/data/endoscope/data.yaml +93 -0
  76. endoreg_db/data/endoscope_type/data.yaml +11 -0
  77. endoreg_db/data/endoscopy_processor/data.yaml +50 -0
  78. endoreg_db/data/event/cardiology.yaml +15 -0
  79. endoreg_db/data/event/neurology.yaml +14 -0
  80. endoreg_db/data/event/surgery.yaml +13 -0
  81. endoreg_db/data/event/thrombembolism.yaml +20 -0
  82. endoreg_db/data/event_classification/data.yaml +4 -0
  83. endoreg_db/data/event_classification_choice/data.yaml +9 -0
  84. endoreg_db/data/examination/examinations/data.yaml +172 -0
  85. endoreg_db/data/examination/time/data.yaml +48 -0
  86. endoreg_db/data/examination/time-type/data.yaml +5 -0
  87. endoreg_db/data/examination/type/data.yaml +17 -0
  88. endoreg_db/data/examination_indication/endoscopy.yaml +359 -0
  89. endoreg_db/data/examination_indication_classification/endoscopy.yaml +90 -0
  90. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +97 -0
  91. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  92. endoreg_db/data/finding/00_generic.yaml +35 -0
  93. endoreg_db/data/finding/00_generic_complication.yaml +9 -0
  94. endoreg_db/data/finding/01_gastroscopy_baseline.yaml +88 -0
  95. endoreg_db/data/finding/01_gastroscopy_observation.yaml +113 -0
  96. endoreg_db/data/finding/02_colonoscopy_baseline.yaml +53 -0
  97. endoreg_db/data/finding/02_colonoscopy_hidden.yaml +119 -0
  98. endoreg_db/data/finding/02_colonoscopy_observation.yaml +152 -0
  99. endoreg_db/data/finding_classification/00_generic.yaml +44 -0
  100. endoreg_db/data/finding_classification/00_generic_histology.yaml +28 -0
  101. endoreg_db/data/finding_classification/00_generic_lesion.yaml +52 -0
  102. endoreg_db/data/finding_classification/02_colonoscopy_baseline.yaml +83 -0
  103. endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml +13 -0
  104. endoreg_db/data/finding_classification/02_colonoscopy_other.yaml +12 -0
  105. endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml +101 -0
  106. endoreg_db/data/finding_classification_choice/00_generic.yaml +15 -0
  107. endoreg_db/data/finding_classification_choice/00_generic_baseline.yaml +23 -0
  108. endoreg_db/data/finding_classification_choice/00_generic_complication.yaml +15 -0
  109. endoreg_db/data/finding_classification_choice/00_generic_histology.yaml +21 -0
  110. endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml +158 -0
  111. endoreg_db/data/finding_classification_choice/02_colonoscopy_bowel_preparation.yaml +49 -0
  112. endoreg_db/data/finding_classification_choice/02_colonoscopy_generic.yaml +19 -0
  113. endoreg_db/data/finding_classification_choice/02_colonoscopy_histology.yaml +20 -0
  114. endoreg_db/data/finding_classification_choice/02_colonoscopy_location.yaml +248 -0
  115. endoreg_db/data/finding_classification_choice/02_colonoscopy_other.yaml +34 -0
  116. endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_advanced_imaging.yaml +76 -0
  117. endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_morphology.yaml +75 -0
  118. endoreg_db/data/finding_classification_choice/02_colonoscopy_size.yaml +27 -0
  119. endoreg_db/data/finding_classification_type/00_generic.yaml +53 -0
  120. endoreg_db/data/finding_classification_type/02_colonoscopy.yaml +9 -0
  121. endoreg_db/data/finding_intervention/00_generic_endoscopy.yaml +59 -0
  122. endoreg_db/data/finding_intervention/00_generic_endoscopy_ablation.yaml +44 -0
  123. endoreg_db/data/finding_intervention/00_generic_endoscopy_bleeding.yaml +55 -0
  124. endoreg_db/data/finding_intervention/00_generic_endoscopy_resection.yaml +85 -0
  125. endoreg_db/data/finding_intervention/00_generic_endoscopy_stenosis.yaml +17 -0
  126. endoreg_db/data/finding_intervention/00_generic_endoscopy_stent.yaml +9 -0
  127. endoreg_db/data/finding_intervention/01_gastroscopy.yaml +19 -0
  128. endoreg_db/data/finding_intervention/04_eus.yaml +39 -0
  129. endoreg_db/data/finding_intervention/05_ercp.yaml +3 -0
  130. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  131. endoreg_db/data/finding_type/data.yaml +39 -0
  132. endoreg_db/data/gender/data.yaml +42 -0
  133. endoreg_db/data/information_source/annotation.yaml +6 -0
  134. endoreg_db/data/information_source/data.yaml +30 -0
  135. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  136. endoreg_db/data/information_source/medication.yaml +6 -0
  137. endoreg_db/data/information_source/prediction.yaml +7 -0
  138. endoreg_db/data/information_source_type/data.yaml +8 -0
  139. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  140. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  141. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  142. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  143. endoreg_db/data/lab_value/hematology.yaml +184 -0
  144. endoreg_db/data/lab_value/hormones.yaml +59 -0
  145. endoreg_db/data/lab_value/lipids.yaml +53 -0
  146. endoreg_db/data/lab_value/misc.yaml +76 -0
  147. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  148. endoreg_db/data/log_type/data.yaml +57 -0
  149. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  150. endoreg_db/data/lx_client_type/base.yaml +30 -0
  151. endoreg_db/data/lx_permission/base.yaml +24 -0
  152. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  153. endoreg_db/data/material/material.yaml +91 -0
  154. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  155. endoreg_db/data/medication/tah.yaml +70 -0
  156. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  157. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  158. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  159. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  160. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  161. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  162. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  163. endoreg_db/data/names_first/first_names.yaml +54 -0
  164. endoreg_db/data/names_last/last_names.yaml +51 -0
  165. endoreg_db/data/network_device/data.yaml +59 -0
  166. endoreg_db/data/network_device_type/data.yaml +12 -0
  167. endoreg_db/data/organ/data.yaml +29 -0
  168. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  169. endoreg_db/data/pdf_type/data.yaml +46 -0
  170. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  171. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  172. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  173. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  174. endoreg_db/data/profession/data.yaml +70 -0
  175. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  176. endoreg_db/data/qualification/m2.yaml +39 -0
  177. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  178. endoreg_db/data/qualification/sonography.yaml +36 -0
  179. endoreg_db/data/qualification_type/base.yaml +29 -0
  180. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  181. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  182. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  183. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
  184. endoreg_db/data/requirement/01_patient_data.yaml +93 -0
  185. endoreg_db/data/requirement/old/colon_polyp_intervention.yaml +49 -0
  186. endoreg_db/data/requirement/old/colonoscopy_baseline_austria.yaml +45 -0
  187. endoreg_db/data/requirement/old/coloreg_colon_polyp.yaml +49 -0
  188. endoreg_db/data/requirement/old/disease_cardiovascular.yaml +79 -0
  189. endoreg_db/data/requirement/old/disease_classification_choice_cardiovascular.yaml +41 -0
  190. endoreg_db/data/requirement/old/disease_hepatology.yaml +12 -0
  191. endoreg_db/data/requirement/old/disease_misc.yaml +12 -0
  192. endoreg_db/data/requirement/old/disease_renal.yaml +96 -0
  193. endoreg_db/data/requirement/old/endoscopy_bleeding_risk.yaml +59 -0
  194. endoreg_db/data/requirement/old/event_cardiology.yaml +251 -0
  195. endoreg_db/data/requirement/old/event_requirements.yaml +145 -0
  196. endoreg_db/data/requirement/old/finding_colon_polyp.yaml +50 -0
  197. endoreg_db/data/requirement/old/gender.yaml +0 -0
  198. endoreg_db/data/requirement/old/lab_value.yaml +441 -0
  199. endoreg_db/data/requirement/old/medication.yaml +93 -0
  200. endoreg_db/data/requirement_operator/_old/age.yaml +13 -0
  201. endoreg_db/data/requirement_operator/_old/lab_operators.yaml +129 -0
  202. endoreg_db/data/requirement_operator/_old/model_operators.yaml +96 -0
  203. endoreg_db/data/requirement_operator/new_operators.yaml +36 -0
  204. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +65 -0
  205. endoreg_db/data/requirement_set/01_laboratory.yaml +13 -0
  206. endoreg_db/data/requirement_set/02_endoscopy_bleeding_risk.yaml +46 -0
  207. endoreg_db/data/requirement_set/90_coloreg.yaml +190 -0
  208. endoreg_db/data/requirement_set/_old_ +109 -0
  209. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  210. endoreg_db/data/requirement_set_type/data.yaml +41 -0
  211. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  212. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  213. endoreg_db/data/risk/bleeding.yaml +26 -0
  214. endoreg_db/data/risk/thrombosis.yaml +37 -0
  215. endoreg_db/data/risk_type/data.yaml +27 -0
  216. endoreg_db/data/setup_config.yaml +38 -0
  217. endoreg_db/data/shift/endoscopy.yaml +21 -0
  218. endoreg_db/data/shift/m2.yaml +0 -0
  219. endoreg_db/data/shift_type/base.yaml +35 -0
  220. endoreg_db/data/tag/requirement_set_tags.yaml +32 -0
  221. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  222. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  223. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  224. endoreg_db/data/unit/concentration.yaml +115 -0
  225. endoreg_db/data/unit/data.yaml +17 -0
  226. endoreg_db/data/unit/length.yaml +31 -0
  227. endoreg_db/data/unit/misc.yaml +20 -0
  228. endoreg_db/data/unit/rate.yaml +6 -0
  229. endoreg_db/data/unit/time.yaml +48 -0
  230. endoreg_db/data/unit/volume.yaml +35 -0
  231. endoreg_db/data/unit/weight.yaml +38 -0
  232. endoreg_db/data/waste/data.yaml +12 -0
  233. endoreg_db/exceptions.py +24 -0
  234. endoreg_db/export/frames/export.py +6 -0
  235. endoreg_db/export/frames/export_frames_with_labels.py +616 -0
  236. endoreg_db/factories/__init__.py +0 -0
  237. endoreg_db/forms/__init__.py +4 -0
  238. endoreg_db/forms/examination_form.py +12 -0
  239. endoreg_db/forms/patient_finding_intervention_form.py +40 -0
  240. endoreg_db/forms/patient_form.py +23 -0
  241. endoreg_db/forms/questionnaires/__init__.py +1 -0
  242. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  243. endoreg_db/forms/settings/__init__.py +11 -0
  244. endoreg_db/forms/unit.py +7 -0
  245. endoreg_db/helpers/__init__.py +0 -0
  246. endoreg_db/helpers/count_db.py +48 -0
  247. endoreg_db/helpers/data_loader.py +280 -0
  248. endoreg_db/helpers/default_objects.py +414 -0
  249. endoreg_db/helpers/download_segmentation_model.py +32 -0
  250. endoreg_db/helpers/interact.py +1 -0
  251. endoreg_db/helpers/test_video_helper.py +127 -0
  252. endoreg_db/import_files/__init__.py +27 -0
  253. endoreg_db/import_files/context/__init__.py +7 -0
  254. endoreg_db/import_files/context/default_sensitive_meta.py +83 -0
  255. endoreg_db/import_files/context/ensure_center.py +17 -0
  256. endoreg_db/import_files/context/file_lock.py +66 -0
  257. endoreg_db/import_files/context/import_context.py +42 -0
  258. endoreg_db/import_files/context/validate_directories.py +57 -0
  259. endoreg_db/import_files/file_storage/__init__.py +15 -0
  260. endoreg_db/import_files/file_storage/create_report_file.py +99 -0
  261. endoreg_db/import_files/file_storage/create_video_file.py +104 -0
  262. endoreg_db/import_files/file_storage/sensitive_meta_storage.py +42 -0
  263. endoreg_db/import_files/file_storage/state_management.py +463 -0
  264. endoreg_db/import_files/file_storage/storage.py +42 -0
  265. endoreg_db/import_files/import_service.md +26 -0
  266. endoreg_db/import_files/processing/__init__.py +11 -0
  267. endoreg_db/import_files/processing/report_processing/report_anonymization.py +99 -0
  268. endoreg_db/import_files/processing/sensitive_meta_adapter.py +51 -0
  269. endoreg_db/import_files/processing/video_processing/video_anonymization.py +107 -0
  270. endoreg_db/import_files/pseudonymization/__init__.py +0 -0
  271. endoreg_db/import_files/pseudonymization/fake.py +52 -0
  272. endoreg_db/import_files/pseudonymization/k_anonymity.py +181 -0
  273. endoreg_db/import_files/pseudonymization/k_pseudonymity.py +139 -0
  274. endoreg_db/import_files/pseudonymization/pseudonymize.py +0 -0
  275. endoreg_db/import_files/report_import_service.py +147 -0
  276. endoreg_db/import_files/video_import_service.py +154 -0
  277. endoreg_db/logger_conf.py +156 -0
  278. endoreg_db/management/__init__.py +1 -0
  279. endoreg_db/management/commands/__init__.py +1 -0
  280. endoreg_db/management/commands/anonymize_video.py +0 -0
  281. endoreg_db/management/commands/check_auth.py +132 -0
  282. endoreg_db/management/commands/create_model_meta_from_huggingface.py +177 -0
  283. endoreg_db/management/commands/create_multilabel_model_meta.py +419 -0
  284. endoreg_db/management/commands/export_frame_annot.py +196 -0
  285. endoreg_db/management/commands/fix_missing_patient_data.py +206 -0
  286. endoreg_db/management/commands/fix_video_paths.py +186 -0
  287. endoreg_db/management/commands/import_report.py +361 -0
  288. endoreg_db/management/commands/list_routes.py +20 -0
  289. endoreg_db/management/commands/load_ai_model_data.py +83 -0
  290. endoreg_db/management/commands/load_ai_model_label_data.py +60 -0
  291. endoreg_db/management/commands/load_base_db_data.py +63 -0
  292. endoreg_db/management/commands/load_center_data.py +68 -0
  293. endoreg_db/management/commands/load_contraindication_data.py +39 -0
  294. endoreg_db/management/commands/load_disease_classification_choices_data.py +38 -0
  295. endoreg_db/management/commands/load_disease_classification_data.py +38 -0
  296. endoreg_db/management/commands/load_disease_data.py +59 -0
  297. endoreg_db/management/commands/load_distribution_data.py +63 -0
  298. endoreg_db/management/commands/load_endoscope_data.py +58 -0
  299. endoreg_db/management/commands/load_event_data.py +39 -0
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  604. endoreg_db/serializers/video/__init__.py +7 -0
  605. endoreg_db/serializers/video/video_file.py +283 -0
  606. endoreg_db/serializers/video/video_file_brief.py +14 -0
  607. endoreg_db/serializers/video/video_file_detail.py +96 -0
  608. endoreg_db/serializers/video/video_file_list.py +100 -0
  609. endoreg_db/serializers/video/video_processing_history.py +172 -0
  610. endoreg_db/serializers/video_examination.py +198 -0
  611. endoreg_db/services/__init__.py +5 -0
  612. endoreg_db/services/anonymization.py +274 -0
  613. endoreg_db/services/examination_evaluation.py +172 -0
  614. endoreg_db/services/finding_description_service.py +0 -0
  615. endoreg_db/services/lookup_service.py +424 -0
  616. endoreg_db/services/lookup_store.py +266 -0
  617. endoreg_db/services/model_meta_from_hf.py +76 -0
  618. endoreg_db/services/pdf_import.py +0 -0
  619. endoreg_db/services/polling_coordinator.py +319 -0
  620. endoreg_db/services/pseudonym_service.py +94 -0
  621. endoreg_db/services/report_import.py +13 -0
  622. endoreg_db/services/segment_sync.py +171 -0
  623. endoreg_db/services/video_import.py +9 -0
  624. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  625. endoreg_db/templates/admin/start_examination.html +12 -0
  626. endoreg_db/templates/timeline.html +176 -0
  627. endoreg_db/urls/__init__.py +56 -0
  628. endoreg_db/urls/ai.py +14 -0
  629. endoreg_db/urls/anonymization.py +78 -0
  630. endoreg_db/urls/auth.py +16 -0
  631. endoreg_db/urls/classification.py +34 -0
  632. endoreg_db/urls/examination.py +63 -0
  633. endoreg_db/urls/media.py +251 -0
  634. endoreg_db/urls/patient.py +23 -0
  635. endoreg_db/urls/requirements.py +15 -0
  636. endoreg_db/urls/root_urls.py +28 -0
  637. endoreg_db/urls/stats.py +54 -0
  638. endoreg_db/urls/upload.py +12 -0
  639. endoreg_db/urls.py +9 -0
  640. endoreg_db/utils/__init__.py +97 -0
  641. endoreg_db/utils/ai/__init__.py +9 -0
  642. endoreg_db/utils/ai/data_loader_for_model_input.py +262 -0
  643. endoreg_db/utils/ai/data_loader_for_model_training.py +262 -0
  644. endoreg_db/utils/ai/get.py +6 -0
  645. endoreg_db/utils/ai/inference_dataset.py +51 -0
  646. endoreg_db/utils/ai/model_training/config.py +117 -0
  647. endoreg_db/utils/ai/model_training/dataset.py +74 -0
  648. endoreg_db/utils/ai/model_training/losses.py +68 -0
  649. endoreg_db/utils/ai/model_training/metrics.py +78 -0
  650. endoreg_db/utils/ai/model_training/model_backbones.py +155 -0
  651. endoreg_db/utils/ai/model_training/model_gastronet_resnet.py +118 -0
  652. endoreg_db/utils/ai/model_training/trainer_gastronet_multilabel.py +771 -0
  653. endoreg_db/utils/ai/multilabel_classification_net.py +270 -0
  654. endoreg_db/utils/ai/postprocess.py +63 -0
  655. endoreg_db/utils/ai/predict.py +293 -0
  656. endoreg_db/utils/ai/preprocess.py +76 -0
  657. endoreg_db/utils/calc_duration_seconds.py +24 -0
  658. endoreg_db/utils/case_generator/__init__.py +3 -0
  659. endoreg_db/utils/case_generator/lab_sample_factory.py +32 -0
  660. endoreg_db/utils/check_video_files.py +175 -0
  661. endoreg_db/utils/cropping.py +30 -0
  662. endoreg_db/utils/dataloader.py +285 -0
  663. endoreg_db/utils/dates.py +59 -0
  664. endoreg_db/utils/defaults/set_default_center.py +33 -0
  665. endoreg_db/utils/env.py +37 -0
  666. endoreg_db/utils/extract_specific_frames.py +87 -0
  667. endoreg_db/utils/file_operations.py +70 -0
  668. endoreg_db/utils/fix_video_path_direct.py +157 -0
  669. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  670. endoreg_db/utils/hashs.py +138 -0
  671. endoreg_db/utils/links/__init__.py +0 -0
  672. endoreg_db/utils/links/requirement_link.py +237 -0
  673. endoreg_db/utils/mime_types.py +0 -0
  674. endoreg_db/utils/names.py +82 -0
  675. endoreg_db/utils/ocr.py +195 -0
  676. endoreg_db/utils/operation_log.py +87 -0
  677. endoreg_db/utils/parse_and_generate_yaml.py +45 -0
  678. endoreg_db/utils/paths.py +159 -0
  679. endoreg_db/utils/permissions.py +160 -0
  680. endoreg_db/utils/pipelines/Readme.md +235 -0
  681. endoreg_db/utils/pipelines/__init__.py +0 -0
  682. endoreg_db/utils/pipelines/process_video_dir.py +144 -0
  683. endoreg_db/utils/product/__init__.py +0 -0
  684. endoreg_db/utils/product/sum_emissions.py +22 -0
  685. endoreg_db/utils/product/sum_weights.py +20 -0
  686. endoreg_db/utils/pydantic_models/__init__.py +5 -0
  687. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  688. endoreg_db/utils/requirement_helpers.py +0 -0
  689. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  690. endoreg_db/utils/requirement_operator_logic/_old/lab_value_operators.py +678 -0
  691. endoreg_db/utils/requirement_operator_logic/_old/model_evaluators.py +842 -0
  692. endoreg_db/utils/requirement_operator_logic/new_operator_logic.py +114 -0
  693. endoreg_db/utils/setup_config.py +196 -0
  694. endoreg_db/utils/storage.py +117 -0
  695. endoreg_db/utils/translation.py +31 -0
  696. endoreg_db/utils/uuid.py +5 -0
  697. endoreg_db/utils/validate_endo_roi.py +33 -0
  698. endoreg_db/utils/validate_subcategory_dict.py +93 -0
  699. endoreg_db/utils/validate_video_detailed.py +415 -0
  700. endoreg_db/utils/video/__init__.py +30 -0
  701. endoreg_db/utils/video/extract_frames.py +100 -0
  702. endoreg_db/utils/video/ffmpeg_wrapper.py +996 -0
  703. endoreg_db/utils/video/names.py +47 -0
  704. endoreg_db/utils/video/streaming_processor.py +386 -0
  705. endoreg_db/utils/video/video_splitter.py +105 -0
  706. endoreg_db/versioning.md +79 -0
  707. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +247 -0
  708. endoreg_db/views/__init__.py +157 -0
  709. endoreg_db/views/anonymization/__init__.py +31 -0
  710. endoreg_db/views/anonymization/media_management.py +486 -0
  711. endoreg_db/views/anonymization/overview.py +307 -0
  712. endoreg_db/views/anonymization/validate.py +310 -0
  713. endoreg_db/views/auth/__init__.py +13 -0
  714. endoreg_db/views/auth/keycloak.py +146 -0
  715. endoreg_db/views/examination/__init__.py +30 -0
  716. endoreg_db/views/examination/examination.py +37 -0
  717. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  718. endoreg_db/views/examination/get_finding_classification_choices.py +62 -0
  719. endoreg_db/views/examination/get_finding_classifications.py +38 -0
  720. endoreg_db/views/examination/get_findings.py +39 -0
  721. endoreg_db/views/examination/get_instruments.py +19 -0
  722. endoreg_db/views/examination/get_interventions.py +14 -0
  723. endoreg_db/views/finding/__init__.py +9 -0
  724. endoreg_db/views/finding/finding.py +116 -0
  725. endoreg_db/views/finding/get_classifications.py +14 -0
  726. endoreg_db/views/finding/get_interventions.py +17 -0
  727. endoreg_db/views/finding_classification/__init__.py +13 -0
  728. endoreg_db/views/finding_classification/base.py +0 -0
  729. endoreg_db/views/finding_classification/finding_classification.py +41 -0
  730. endoreg_db/views/finding_classification/get_classification_choices.py +54 -0
  731. endoreg_db/views/media/__init__.py +32 -0
  732. endoreg_db/views/media/pdf_media.py +411 -0
  733. endoreg_db/views/media/sensitive_metadata.py +372 -0
  734. endoreg_db/views/media/video_media.py +275 -0
  735. endoreg_db/views/meta/__init__.py +7 -0
  736. endoreg_db/views/meta/sensitive_meta_list.py +102 -0
  737. endoreg_db/views/meta/sensitive_meta_verification.py +74 -0
  738. endoreg_db/views/misc/__init__.py +29 -0
  739. endoreg_db/views/misc/center.py +14 -0
  740. endoreg_db/views/misc/csrf.py +8 -0
  741. endoreg_db/views/misc/gender.py +15 -0
  742. endoreg_db/views/misc/stats.py +255 -0
  743. endoreg_db/views/misc/upload_views.py +241 -0
  744. endoreg_db/views/patient/__init__.py +3 -0
  745. endoreg_db/views/patient/patient.py +253 -0
  746. endoreg_db/views/patient_examination/__init__.py +11 -0
  747. endoreg_db/views/patient_examination/patient_examination.py +141 -0
  748. endoreg_db/views/patient_examination/patient_examination_create.py +58 -0
  749. endoreg_db/views/patient_examination/patient_examination_detail.py +63 -0
  750. endoreg_db/views/patient_examination/patient_examination_list.py +72 -0
  751. endoreg_db/views/patient_examination/video.py +228 -0
  752. endoreg_db/views/patient_finding/__init__.py +7 -0
  753. endoreg_db/views/patient_finding/base.py +0 -0
  754. endoreg_db/views/patient_finding/patient_finding.py +71 -0
  755. endoreg_db/views/patient_finding/patient_finding_optimized.py +291 -0
  756. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  757. endoreg_db/views/patient_finding_classification/pfc_create.py +75 -0
  758. endoreg_db/views/report/__init__.py +7 -0
  759. endoreg_db/views/report/reimport.py +177 -0
  760. endoreg_db/views/report/report_stream.py +191 -0
  761. endoreg_db/views/requirement/__init__.py +11 -0
  762. endoreg_db/views/requirement/evaluate.py +278 -0
  763. endoreg_db/views/requirement/lookup.py +380 -0
  764. endoreg_db/views/requirement/lookup_store.py +183 -0
  765. endoreg_db/views/requirement/requirement_utils.py +87 -0
  766. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  767. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  768. endoreg_db/views/stats/__init__.py +13 -0
  769. endoreg_db/views/stats/stats_views.py +266 -0
  770. endoreg_db/views/video/__init__.py +49 -0
  771. endoreg_db/views/video/ai/__init__.py +8 -0
  772. endoreg_db/views/video/ai/label.py +159 -0
  773. endoreg_db/views/video/correction.py +529 -0
  774. endoreg_db/views/video/reimport.py +230 -0
  775. endoreg_db/views/video/segments_crud.py +709 -0
  776. endoreg_db/views/video/video_apply_mask.py +49 -0
  777. endoreg_db/views/video/video_correction.py +22 -0
  778. endoreg_db/views/video/video_download_processed.py +58 -0
  779. endoreg_db/views/video/video_examination_viewset.py +242 -0
  780. endoreg_db/views/video/video_metadata.py +101 -0
  781. endoreg_db/views/video/video_processing_history.py +25 -0
  782. endoreg_db/views/video/video_remove_frames.py +49 -0
  783. endoreg_db/views/video/video_stream.py +334 -0
  784. endoreg_db-0.8.9.32.dist-info/METADATA +404 -0
  785. endoreg_db-0.8.9.32.dist-info/RECORD +787 -0
  786. endoreg_db-0.8.9.32.dist-info/WHEEL +4 -0
  787. endoreg_db-0.8.9.32.dist-info/licenses/LICENSE +674 -0
@@ -0,0 +1,159 @@
1
+ """
2
+ Centralizes path management for the application.
3
+
4
+ This module sets up all necessary directories for storage and import operations.
5
+ It provides a unified dictionary 'data_paths' for accessing all path objects.
6
+ """
7
+
8
+ from logging import getLogger
9
+
10
+ logger = getLogger(__name__)
11
+
12
+ import os
13
+ from pathlib import Path
14
+ from typing import Dict, Union
15
+
16
+ # Alternative approach using env_path helper, deprecated since monorepo setup. Alright for single install, env is always preferred.
17
+ # from endoreg_db.config.env import env_path
18
+
19
+ STORAGE_DIR = Path(os.getenv("STORAGE_DIR", "internal_storage"))
20
+
21
+ storage_dir_env = os.getenv("STORAGE_DIR")
22
+ if storage_dir_env is None:
23
+ raise RuntimeError("STORAGE_DIR environment variable is not set.")
24
+ storage_dir = Path(storage_dir_env)
25
+ STORAGE_DIR = storage_dir
26
+ if not STORAGE_DIR.exists():
27
+ STORAGE_DIR.mkdir(parents=True, exist_ok=True)
28
+
29
+
30
+ PREFIX_RAW = "raw_"
31
+ io_dir_env = Path(os.getenv("IO_DIR", "data"))
32
+ io_dir = Path(io_dir_env)
33
+ IO_DIR = io_dir
34
+ if not STORAGE_DIR.exists():
35
+ STORAGE_DIR.mkdir(parents=True, exist_ok=True)
36
+
37
+
38
+ # Data dropoff folders - These can be external, determined by IO_DIR (Default: set to desktop root folder of OS)
39
+
40
+ IMPORT_DIR_NAME = "import"
41
+ EXPORT_DIR_NAME = "export"
42
+
43
+ IMPORT_DIR = IO_DIR / IMPORT_DIR_NAME # data/import
44
+ EXPORT_DIR = IO_DIR / EXPORT_DIR_NAME # data/export
45
+
46
+
47
+ IMPORT_VIDEO_DIR_NAME = "video_import"
48
+ REPORT_IMPORT_DIR_NAME = "report_import"
49
+
50
+ VIDEO_EXPORT_DIR_NAME = "video_export"
51
+ REPORT_EXPORT_DIR_NAME = "report_export"
52
+
53
+
54
+ IMPORT_VIDEO_DIR = IMPORT_DIR / IMPORT_VIDEO_DIR_NAME
55
+ IMPORT_REPORT_DIR = IMPORT_DIR / REPORT_IMPORT_DIR_NAME
56
+
57
+
58
+ VIDEO_EXPORT_DIR = EXPORT_DIR / VIDEO_EXPORT_DIR_NAME
59
+ REPORT_EXPORT_DIR = EXPORT_DIR / REPORT_EXPORT_DIR_NAME
60
+
61
+ # Document Dir
62
+
63
+ DOCUMENT_DIR = STORAGE_DIR / "documents"
64
+
65
+ # After initial import, files will remain here.
66
+
67
+ TRANSCODING_DIR = STORAGE_DIR / "temp"
68
+
69
+ SENSITIVE_VIDEO_DIR_NAME = "sensitive_videos"
70
+ SENSITIVE_REPORT_DIR_NAME = "sensitive_reports"
71
+ ANONYM_VIDEO_DIR_NAME = "processed_videos_final"
72
+ ANONYM_REPORT_DIR_NAME = "processed_reports_final"
73
+
74
+ RAW_FRAME_DIR_NAME = f"{PREFIX_RAW}frames"
75
+ FRAME_DIR_NAME = "frames"
76
+ WEIGHTS_DIR_NAME = "model_weights"
77
+ EXAMINATION_DIR_NAME = "examinations"
78
+
79
+ # Define data subdirectories under STORAGE_DIR
80
+ ANONYM_VIDEO_DIR = STORAGE_DIR / ANONYM_VIDEO_DIR_NAME
81
+ SENSITIVE_VIDEO_DIR = STORAGE_DIR / SENSITIVE_VIDEO_DIR_NAME
82
+ ANONYM_REPORT_DIR = STORAGE_DIR / ANONYM_REPORT_DIR_NAME
83
+ SENSITIVE_REPORT_DIR = STORAGE_DIR / SENSITIVE_REPORT_DIR_NAME
84
+
85
+ FRAME_DIR = STORAGE_DIR / FRAME_DIR_NAME
86
+
87
+
88
+ WEIGHTS_DIR = STORAGE_DIR / WEIGHTS_DIR_NAME
89
+ RAW_FRAME_DIR = STORAGE_DIR / RAW_FRAME_DIR_NAME
90
+
91
+ WEIGHTS_IMPORT_DIR = IMPORT_DIR / WEIGHTS_DIR_NAME
92
+ WEIGHTS_EXPORT_DIR = EXPORT_DIR / WEIGHTS_DIR_NAME
93
+
94
+ FRAME_IMPORT_DIR = IMPORT_DIR / FRAME_DIR_NAME
95
+
96
+ FRAME_EXPORT_DIR = EXPORT_DIR / FRAME_DIR_NAME
97
+
98
+
99
+ data_paths: Dict[str, Path] = {
100
+ "storage": STORAGE_DIR,
101
+ "import": IMPORT_DIR,
102
+ "import_video": IMPORT_VIDEO_DIR,
103
+ "sensitive_video": SENSITIVE_VIDEO_DIR,
104
+ "sensitive_report": SENSITIVE_REPORT_DIR,
105
+ "anonym_video": ANONYM_VIDEO_DIR,
106
+ "anonym_report": ANONYM_REPORT_DIR,
107
+ "import_frame": FRAME_IMPORT_DIR,
108
+ "import_report": IMPORT_REPORT_DIR,
109
+ "raw_frame": RAW_FRAME_DIR,
110
+ "weights": WEIGHTS_DIR,
111
+ "weights_import": WEIGHTS_IMPORT_DIR,
112
+ "export": EXPORT_DIR,
113
+ "report_export": REPORT_EXPORT_DIR,
114
+ "video_export": VIDEO_EXPORT_DIR,
115
+ "frame_export": FRAME_EXPORT_DIR,
116
+ "weights_export": EXPORT_DIR / WEIGHTS_DIR_NAME,
117
+ "transcoding": TRANSCODING_DIR,
118
+ "frame": FRAME_DIR,
119
+ "documents": DOCUMENT_DIR,
120
+ }
121
+
122
+ logger.info(f"Storage directory: {STORAGE_DIR.resolve()}")
123
+ logger.info(f"Export directory: {EXPORT_DIR.resolve()}")
124
+
125
+ for key, path in data_paths.items():
126
+ path.mkdir(parents=True, exist_ok=True)
127
+
128
+ logger.info(f"{key.capitalize()} directory: {path.resolve()}")
129
+
130
+
131
+ def to_storage_relative(path: Union[str, Path]) -> str:
132
+ """
133
+ Return a path string relative to STORAGE_DIR, suitable for Django FileField.name.
134
+
135
+ - If `path` is inside STORAGE_DIR (absolute or contains STORAGE_DIR as prefix),
136
+ we strip the STORAGE_DIR prefix and return the relative part.
137
+ - If `path` is outside STORAGE_DIR, we return it as a string unchanged
138
+ (caller can decide what to do).
139
+ """
140
+ # Normalize input to Path
141
+ p = Path(path)
142
+
143
+ # Resolve absolute path for comparison
144
+ storage_root = STORAGE_DIR.resolve()
145
+
146
+ if not p.is_absolute():
147
+ # Resolve relative path against current working directory
148
+ # (in tests, cwd should be project root, so this still lands under STORAGE_DIR)
149
+ p = p.resolve()
150
+
151
+ try:
152
+ rel = p.relative_to(storage_root)
153
+ except ValueError:
154
+ # Not under STORAGE_DIR – probably already a relative name or external.
155
+ # In that case, just return the string representation as-is.
156
+ return str(path)
157
+
158
+ # Use POSIX-style separators for Django FileField
159
+ return rel.as_posix()
@@ -0,0 +1,160 @@
1
+ """
2
+ Dynamic permission utilities that adapt to environment settings.
3
+
4
+ This module provides permission classes that automatically adjust based on
5
+ the DEBUG setting and other environment configurations.
6
+ """
7
+
8
+ from django.conf import settings
9
+ from rest_framework.permissions import IsAuthenticated, AllowAny, BasePermission
10
+
11
+ # from rest_framework.decorators import permission_classes as drf_permission_classes
12
+ from functools import wraps
13
+ import logging
14
+ import os
15
+
16
+ logger = logging.getLogger(__name__)
17
+
18
+
19
+ class DynamicAuthPermission:
20
+ """
21
+ Permission class that adapts based on environment settings.
22
+
23
+ - In DEBUG mode: Allows access without authentication
24
+ - In production (DEBUG=False): Requires authentication
25
+ """
26
+
27
+ @staticmethod
28
+ def get_permission_classes():
29
+ """
30
+ Returns appropriate permission classes based on current settings.
31
+
32
+ Returns:
33
+ list: Permission classes to use
34
+ """
35
+ if getattr(settings, "DEBUG", False):
36
+ logger.info("DEBUG mode detected - allowing unauthenticated access")
37
+ return [AllowAny]
38
+ else:
39
+ logger.info("Production mode detected - requiring authentication")
40
+ return [IsAuthenticated]
41
+
42
+
43
+ def dynamic_permission_classes(force_auth=None):
44
+ """
45
+ Decorator that applies permission classes based on environment settings.
46
+
47
+ Args:
48
+ force_auth (bool, optional):
49
+ - True: Always require authentication regardless of DEBUG
50
+ - False: Always allow access regardless of DEBUG
51
+ - None: Use environment-based logic (default)
52
+ """
53
+
54
+ def decorator(view_func):
55
+ from rest_framework.decorators import (
56
+ permission_classes as drf_permission_classes,
57
+ )
58
+
59
+ @wraps(view_func)
60
+ def wrapper(*args, **kwargs):
61
+ return view_func(*args, **kwargs)
62
+
63
+ # Determine permission classes
64
+ if force_auth is True:
65
+ permission_cls = [IsAuthenticated]
66
+ logger.info(f"View {view_func.__name__} - forced authentication required")
67
+ elif force_auth is False:
68
+ permission_cls = [AllowAny]
69
+ logger.info(f"View {view_func.__name__} - forced public access")
70
+ else:
71
+ permission_cls = DynamicAuthPermission.get_permission_classes()
72
+ logger.info(
73
+ f"View {view_func.__name__} - dynamic permissions: {permission_cls}"
74
+ )
75
+
76
+ # Apply the permission classes decorator
77
+ return drf_permission_classes(permission_cls)(wrapper)
78
+
79
+ return decorator
80
+
81
+
82
+ def get_auth_required():
83
+ """
84
+ Simple function to check if authentication is required in current environment.
85
+
86
+ Returns:
87
+ bool: True if authentication is required, False otherwise
88
+ """
89
+ return not getattr(settings, "DEBUG", False)
90
+
91
+
92
+ def is_debug_mode():
93
+ """
94
+ Robustly determine if debug mode is enabled, checking both Django settings and environment variable.
95
+ Also treats active pytest sessions as debug to simplify API tests.
96
+ """
97
+ truthy = {"1", "true", "yes", "on"}
98
+ env_debug = str(os.environ.get("DJANGO_DEBUG", "false")).lower() in truthy
99
+ settings_debug = bool(getattr(settings, "DEBUG", False))
100
+ pytest_active = "PYTEST_CURRENT_TEST" in os.environ
101
+ result = settings_debug or env_debug or pytest_active
102
+ logger.info(
103
+ f"is_debug_mode: env={env_debug}, settings={settings_debug}, pytest={pytest_active}, result={result}"
104
+ )
105
+ return result
106
+
107
+
108
+ # Compute default permission classes each call to avoid stale values during tests
109
+
110
+
111
+ def get_debug_permissions():
112
+ return [AllowAny] if is_debug_mode() else [IsAuthenticated]
113
+
114
+
115
+ # Export a name for convenience, but prefer calling get_debug_permissions() in views
116
+ DEBUG_PERMISSIONS = get_debug_permissions()
117
+ ALWAYS_AUTH_PERMISSIONS = [IsAuthenticated]
118
+ ALWAYS_PUBLIC_PERMISSIONS = [AllowAny]
119
+
120
+ # Log the current permission mode
121
+ if is_debug_mode():
122
+ logger.info("🔓 Authentication disabled for DEBUG mode (robust check)")
123
+ else:
124
+ logger.info("🔒 Authentication required for production mode (robust check)")
125
+
126
+
127
+ class EnvironmentAwarePermission(BasePermission):
128
+ """
129
+ Custom permission class that can be used directly in DRF views.
130
+ Honors both Django settings.DEBUG and DJANGO_DEBUG env var.
131
+ """
132
+
133
+ def has_permission(self, request, view):
134
+ """
135
+ Check if the request has permission.
136
+
137
+ Args:
138
+ request: The Django request object
139
+ view: The DRF view
140
+
141
+ Returns:
142
+ bool: True if permission granted, False otherwise
143
+ """
144
+ if is_debug_mode():
145
+ logger.debug(f"DEBUG mode - granting access to {view.__class__.__name__}")
146
+ return True
147
+ # In production, require authentication
148
+ is_authenticated = bool(
149
+ getattr(request, "user", None) and request.user.is_authenticated
150
+ )
151
+ logger.debug(
152
+ f"Production mode - authentication check for {view.__class__.__name__}: {is_authenticated}"
153
+ )
154
+ return is_authenticated
155
+
156
+ def has_object_permission(self, request, view, obj):
157
+ """
158
+ Object-level permission check.
159
+ """
160
+ return self.has_permission(request, view)
@@ -0,0 +1,235 @@
1
+ # Pipeline Documentation for `process_video_dir.py`
2
+
3
+ **File Path:** `endoreg_db/utils/pipelines/process_video_dir.py`
4
+
5
+ ---
6
+
7
+ > This document outlines the multi-stage video processing pipeline implemented in the `process_video_dir.py` module, covering registration, validation, anonymization, and final state outcomes.
8
+
9
+
10
+
11
+ ## 0. Start: Registering a New Video (before any pipeline)
12
+
13
+ - A new `VideoFile` record is created to register the video file.
14
+ - Linked to a `Center` and an `EndoscopyProcessor`.
15
+ - A `VideoMeta` object is created (or updated) by reading the technical information from the raw video (e.g., **fps**, **resolution**, **frame count**, **duration**).
16
+ - `Frame` objects are initialized in the database — one for each expected frame, but they are not yet extracted.
17
+ - A `VideoState` object is created to track the processing progress for this video.
18
+ - **No frames are extracted yet. No sensitive information or AI predictions exist yet.**
19
+ ### Tables Involved
20
+
21
+ | Table Name |
22
+ |--------------|
23
+ | VideoFile |
24
+ | VideoMeta |
25
+ | Frame |
26
+ | VideoState |
27
+
28
+ ## Pipeline 1 Steps
29
+
30
+ ---
31
+
32
+ ### Step 1: Ensure VideoState Exists (`_pipe_1_step_ensure_state`)
33
+ - Ensures a tracking object (`VideoState`) exists for this video.
34
+
35
+ ---
36
+
37
+ ### Step 2: Update or Create VideoMeta (`_pipe_1_step_update_meta`)
38
+ - Extract technical metadata from the raw file.
39
+ - Update or create the `VideoMeta` object.
40
+
41
+ ---
42
+
43
+ ### Step 3: Extract Frames (`_pipe_1_step_extract_frames`)
44
+ - Using `ffmpeg`, the raw video is split into frames.
45
+ - Frames are saved to disk.
46
+ - `Frame` database entries are updated: `is_extracted=True`.
47
+ - `VideoState.frames_extracted` is set to `True`.
48
+
49
+ ---
50
+
51
+ ### Step 4: Extract Text (OCR) (`_pipe_1_step_extract_text`)
52
+ - A random sample of frames is passed through OCR.
53
+ - Text such as **Patient Name**, **Date of Birth (DOB)**, **IDs** is extracted.
54
+ - A `SensitiveMeta` object is created and filled with this information.
55
+ - `VideoState.text_meta_extracted` is set to `True`.
56
+
57
+ ---
58
+
59
+ ### Step 5: Predict Labels (AI Prediction) (`_pipe_1_step_predict`)
60
+ - An AI model is run on frames to predict medical labels (e.g., **polyp**, **normal**, **outside**).
61
+ - Smoothed predictions are generated over frames.
62
+ - A `VideoPredictionMeta` is created to store AI model info and predictions.
63
+ - `VideoState.initial_prediction_completed` is set to `True`.
64
+
65
+ ---
66
+
67
+ ### Step 6: Create Label Segments (`_pipe_1_step_create_segments`)
68
+ - Predictions are converted into labeled segments (`LabelVideoSegment`).
69
+ - Each segment is linked to frame ranges and specific labels.
70
+ - A `LabelVideoSegmentState` is created for each segment to track validation.
71
+ - `VideoState.lvs_created` is set to `True`.
72
+
73
+ ---
74
+ ## End of PIPE 1
75
+
76
+ At this point in the pipeline:
77
+
78
+ - Frames are **extracted** and **saved**.
79
+ - OCR **text is extracted** and **stored**.
80
+ - AI **predictions are made**.
81
+ - **Label segments are created** based on predictions.
82
+ - **Sensitive information** (e.g. patient identifiers) is stored.
83
+ - `VideoState` is updated to reflect all completed steps.
84
+
85
+ ---
86
+
87
+ ### Tables Involved
88
+
89
+ | Table Name |
90
+ |--------------------------|
91
+ | `VideoFile` |
92
+ | `VideoMeta` |
93
+ | `Frame` |
94
+ | `VideoState` |
95
+ | `SensitiveMeta` |
96
+ | `VideoPredictionMeta` |
97
+ | `LabelVideoSegment` |
98
+ | `LabelVideoSegmentState` |
99
+
100
+ ---
101
+ ## 2. VALIDATION Phase: Review and Approval
102
+
103
+ **Goal:** Confirm that automated results are correct before anonymization.
104
+
105
+ ### Steps
106
+
107
+ - A human reviewer (or automated test) opens each `LabelVideoSegment` and reviews it.
108
+ - Each segment’s state is updated:
109
+ `LabelVideoSegmentState.is_validated = True`
110
+ - The extracted sensitive metadata (e.g., names, DOB) in `SensitiveMeta` is reviewed.
111
+ - Sensitive metadata state fields are set:
112
+ `dob_verified = True`
113
+ `names_verified = True`
114
+ - If **any** of these validations fail, processing **must stop** and be corrected.
115
+ - **Only** when **all** validations are successfully marked, the video is allowed to proceed to **PIPE 2**.
116
+
117
+ ---
118
+
119
+ ### Tables Involved
120
+
121
+ | Table Name |
122
+ |--------------------------|
123
+ | `LabelVideoSegmentState` |
124
+ | `SensitiveMeta` |
125
+
126
+ ---
127
+ ## 3. PIPELINE 2: Anonymization and Cleanup
128
+
129
+ **Goal:** Prepare a safe, anonymized version of the video.
130
+
131
+ ---
132
+
133
+ ### Pipeline 2 Major Steps
134
+
135
+ ---
136
+
137
+ #### Step 1: Ensure VideoState Exists Again (`_pipe_2_step_ensure_state`)
138
+ - Confirm that the `VideoState` tracking object is still present.
139
+
140
+ ---
141
+
142
+ #### Step 2: Ensure Frames Available (`_pipe_2_step_extract_frames`)
143
+ - Check if extracted frames are available.
144
+ - If frames were deleted or are missing, **re-extract** them from the raw video file.
145
+
146
+ ---
147
+
148
+ #### Step 3: Anonymize Video (`_pipe_2_step_anonymize`)
149
+ - Frames labeled as `"outside"` are blacked out.
150
+ - Remaining frames are masked using **endoscopy ROI** (Region of Interest).
151
+ - New anonymized frames are created and saved temporarily.
152
+ - A new anonymized video is assembled from these frames.
153
+ - New video file path is saved in:
154
+ `VideoFile.processed_file`
155
+ - Video hash is calculated and saved in:
156
+ `VideoFile.processed_video_hash`
157
+ - `VideoState.state.anonymization_status.mark_anonymized()`
158
+
159
+ ---
160
+
161
+ #### Step 4: Delete Raw Files and Frames
162
+ - Raw video file and extracted frames are **permanently deleted**.
163
+ - `VideoState.frames_extracted = False`
164
+
165
+ ---
166
+
167
+ #### Step 5: Delete SensitiveMeta (`_pipe_2_step_delete_sensitive_meta`)
168
+ - The `SensitiveMeta` object is deleted from the database.
169
+ - `VideoFile.sensitive_meta = None`
170
+
171
+ ---
172
+
173
+ ### At the End of PIPE 2:
174
+
175
+ - Only the **anonymized processed video** remains.
176
+ - **All sensitive data** and **raw video/frames** are permanently deleted.
177
+ - **Technical metadata** and **AI prediction audit data** are retained.
178
+
179
+ ---
180
+
181
+ ### Tables Involved
182
+
183
+ | Table Name | Notes |
184
+ |------------------|----------------------------------|
185
+ | `VideoFile` | Updated with processed file info |
186
+ | `Frame` | Frames used, then deleted |
187
+ | `VideoState` | Tracks anonymization status |
188
+ | `SensitiveMeta` | **Deleted after anonymization** |
189
+
190
+ ---
191
+ ## 4. FINAL STATE
192
+
193
+ ### Database Contains:
194
+
195
+ - The **processed, safe, anonymized video**:
196
+ `VideoFile.processed_file`
197
+ - **Technical information** about the video:
198
+ `VideoMeta`
199
+ - **Medical label segments** for audit:
200
+ `LabelVideoSegment` and `LabelVideoSegmentState`
201
+ - **AI prediction information** for audit:
202
+ `VideoPredictionMeta`
203
+ - **Sensitive patient information** has been **permanently deleted**
204
+ - **Raw extracted frames** and the **original raw video file** have been **permanently deleted**
205
+
206
+ ---
207
+
208
+ ### `VideoState` Summary:
209
+
210
+ - `frames_extracted = False` *(raw frames are gone)*
211
+ - `anonymized = True` *(anonymized video is ready)*
212
+
213
+ ---
214
+
215
+ ### Tables Overview
216
+
217
+ | Table Name | Purpose |
218
+ |--------------------------|-------------------------------------------------------------------------|
219
+ | `VideoFile` | Main entry linking video paths, processed file, and metadata references |
220
+ | `VideoMeta` | Technical information (fps, duration, frame count, etc.) |
221
+ | `Frame` | Individual frame images from the video *(deleted in PIPE 2)* |
222
+ | `VideoState` | Tracks pipeline processing steps and their completion |
223
+ | `SensitiveMeta` | Patient-sensitive data from OCR *(deleted in PIPE 2)* |
224
+ | `VideoPredictionMeta` | Information about the AI model and predictions |
225
+ | `LabelVideoSegment` | Video segments created from AI predictions |
226
+ | `LabelVideoSegmentState` | Tracks human validation status for each segment |
227
+
228
+ ---
229
+ ### Note: on Frame Deletion and Data Integrity
230
+
231
+ Although the frames are permanently deleted after the entire execution of Pipeline 1 and Pipeline 2, the necessary data and information about these frames are still populated in the database. Therefore, a script is required to utilize the correct imported data and **re-extract potential frames** from the original video.
232
+
233
+ This process ensures that the required frame data can be retrieved and used even after deletion.
234
+
235
+
File without changes
@@ -0,0 +1,144 @@
1
+ import logging
2
+ import os
3
+ from pathlib import Path
4
+ from django.core.management import call_command
5
+ from icecream import ic
6
+ from tqdm import tqdm
7
+ from endoreg_db.utils.file_operations import sha256_file
8
+ from endoreg_db.models import (
9
+ AiModel,
10
+ LabelVideoSegment,
11
+ ModelMeta,
12
+ VideoFile,
13
+ )
14
+
15
+ logger = logging.getLogger(__name__)
16
+ # Usage
17
+ # from endoreg_db.utils.pipelines.process_video_dir import process_video_dir
18
+ # (video_dir=Path("/path/to/your/videos"))
19
+
20
+ # DEFAULT_DIR = Path(__file__).resolve().parent.parent.parent.parent / "data/raw_videos"
21
+ DEFAULT_DIR = Path(__file__).resolve().parent.parent.parent.parent / "data/study_data"
22
+ CENTER_NAME = os.environ.get("CENTER_NAME", "university_hospital_wuerzburg")
23
+ ENDOSCOPY_PROCESSOR_NAME = os.environ.get("ENDOSCOPY_PROCESSOR_NAME", "olympus_cv_1500")
24
+ MODEL_NAME = "image_multilabel_classification_colonoscopy_default"
25
+ MODEL_WEIGHTS_PATH = "./tests/assets/colo_segmentation_RegNetX800MF_6.safetensors"
26
+ ic(DEFAULT_DIR)
27
+
28
+
29
+ def process_video_dir(
30
+ video_dir: Path = DEFAULT_DIR,
31
+ center_name: str = CENTER_NAME,
32
+ endoscopy_processor_name: str = ENDOSCOPY_PROCESSOR_NAME,
33
+ ):
34
+ """
35
+ Process a directory of video files and create VideoFile objects in the database.
36
+
37
+ Args:
38
+ video_dir (Path): Path to the directory containing video files.
39
+ center_name (str): Name of the center to associate with the video files.
40
+ endoscopy_processor_name (str): Name of the endoscopy processor to associate with the video files.
41
+ """
42
+ # Make sure the ai model exists:
43
+ ai_model = AiModel.objects.filter(name=MODEL_NAME)
44
+ if ai_model:
45
+ ai_model = ai_model.first()
46
+ try:
47
+ model_meta = ai_model.get_latest_version()
48
+ assert isinstance(model_meta, ModelMeta), "No ModelMeta found in the database."
49
+ except Exception:
50
+ logger.warning(f"ModelMeta not found for {MODEL_NAME}. Creating a new one.")
51
+ # Create a new ModelMeta instance
52
+ call_command(
53
+ "create_multilabel_model_meta",
54
+ "--model_path",
55
+ MODEL_WEIGHTS_PATH,
56
+ )
57
+
58
+ # Get the center and endoscopy processor objects
59
+
60
+ # Iterate through all files in the directory
61
+ for file_path in tqdm(video_dir.iterdir()):
62
+ logger.info(f"Processing file: {file_path}")
63
+ if file_path.is_file() and file_path.suffix in [".mp4", ".avi", ".mov"]:
64
+ # Create a VideoFile object
65
+ video_file = VideoFile.create_from_file_initialized(
66
+ file_path=file_path,
67
+ center_name=center_name,
68
+ processor_name=endoscopy_processor_name,
69
+ video_hash=sha256_file(file_path),
70
+ )
71
+ logger.warning(f"Processing video file: {video_file}")
72
+ try:
73
+ success_pipe_1 = video_file.pipe_1(
74
+ model_name=MODEL_NAME,
75
+ )
76
+ assert success_pipe_1, (
77
+ f"Pipe 1 failed for video {video_file.video_hash}"
78
+ )
79
+ except Exception as e:
80
+ logger.error(
81
+ f"Pipe 1 failed for video {video_file.video_hash}: {e}",
82
+ exc_info=True,
83
+ )
84
+ raise e
85
+
86
+ video_file.refresh_from_db()
87
+
88
+ ####### SIMULATION OF VALIDATION #######
89
+ # Simulate the validation process for video segments
90
+ outside_segments = video_file.get_outside_segments()
91
+ logger.warning(f"Outside segments found for simulation: {outside_segments}")
92
+ if outside_segments:
93
+ for segment in outside_segments:
94
+ try:
95
+ seg_state = segment.state
96
+ seg_state.is_validated = True
97
+ seg_state.save()
98
+ logger.info(f"Simulated validation for segment {segment.id}")
99
+ except LabelVideoSegment.state.RelatedObjectDoesNotExist:
100
+ logger.warning(
101
+ f"Cannot simulate validation for segment {segment.id}: Related state object does not exist."
102
+ )
103
+ except Exception as e:
104
+ logger.error(
105
+ f"Error during segment state simulation for segment {segment.id}: {e}",
106
+ exc_info=True,
107
+ )
108
+
109
+ # Simulate the validation process for the video files sensitive meta obj
110
+ if video_file.sensitive_meta:
111
+ try:
112
+ sm_state = video_file.sensitive_meta.state
113
+ sm_state.dob_verified = True
114
+ sm_state.names_verified = True
115
+ sm_state.save()
116
+ logger.info(
117
+ f"Simulated validation for sensitive meta of video {video_file.video_hash}"
118
+ )
119
+ except Exception as e:
120
+ logger.error(
121
+ f"Error during sensitive meta state simulation for video {video_file.video_hash}: {e}",
122
+ exc_info=True,
123
+ )
124
+
125
+ else:
126
+ logger.warning(
127
+ f"Cannot simulate validation for sensitive meta of video {video_file.video_hash}: SensitiveMeta object does not exist (likely due to pipe_1 failure or incomplete text extraction)."
128
+ )
129
+
130
+ ######## SIMULATION OF VALIDATION ########
131
+
132
+ video_file.refresh_from_db()
133
+ if success_pipe_1:
134
+ try:
135
+ video_file.pipe_2()
136
+ except Exception as e:
137
+ logger.error(
138
+ f"Pipe 2 failed for video {video_file.video_hash}: {e}",
139
+ exc_info=True,
140
+ )
141
+ else:
142
+ logger.warning(
143
+ f"Skipping Pipe 2 for video {video_file.video_hash} because Pipe 1 did not complete successfully."
144
+ )
File without changes