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
endoreg_db/data/__init__.py ADDED
@@ -0,0 +1,135 @@
1
+ from pathlib import Path
2
+
3
+ DATA_DIR = Path(__file__).parent
4
+
5
+ INFORMATION_DATA_DIR = DATA_DIR / "information_source"
6
+ INFORMATION_SOURCE_TYPE_DATA_DIR = DATA_DIR / "information_source_type"
7
+ UNIT_DATA_DIR = DATA_DIR / "unit"
8
+ CENTER_DATA_DIR = DATA_DIR / "center"
9
+ EXAMINATION_DATA_DIR = DATA_DIR / "examination"
10
+ MODEL_TYPE_DATA_DIR = DATA_DIR / "ai_model_type"
11
+ ENDOSCOPY_PROCESSOR_DATA_DIR = DATA_DIR / "endoscopy_processor"
12
+ ENDOSCOPE_TYPE_DATA_DIR = DATA_DIR / "endoscope_type"
13
+ ENDOSCOPE_DATA_DIR = DATA_DIR / "endoscope"
14
+ ACTIVE_MODEL_DATA_DIR = DATA_DIR / "active_model"
15
+ PROFESSION_DATA_DIR = DATA_DIR / "profession"
16
+ REPORT_TYPE_DATA_DIR = DATA_DIR / "pdf_type"
17
+ REPORT_READER_FLAG_DATA_DIR = DATA_DIR / "report_reader_flag"
18
+ EVENT_DATA_DIR = DATA_DIR / "event"
19
+ GENDER_DATA_DIR = DATA_DIR / "gender"
20
+ ORGAN_DATA_DIR = DATA_DIR / "organ"
21
+ NAMES_FIRST_DATA_DIR = DATA_DIR / "names_first"
22
+ NAMES_LAST_DATA_DIR = DATA_DIR / "names_last"
23
+
24
+
25
+ # Contraindication
26
+ CONTRAINDICATION_DATA_DIR = DATA_DIR / "contraindication"
27
+
28
+ # Examination
29
+ EXAMINATION_INDICATION_DATA_DIR = DATA_DIR / "examination_indication"
30
+ EXAMINATION_INDICATION_CLASSIFICATION_DATA_DIR = (
31
+ DATA_DIR / "examination_indication_classification"
32
+ )
33
+ EXAMINATION_INDICATION_CLASSIFICATION_CHOICE_DATA_DIR = (
34
+ DATA_DIR / "examination_indication_classification_choice"
35
+ )
36
+
37
+ # Finding
38
+ FINDING_TYPE_DATA_DIR = DATA_DIR / "finding_type"
39
+ FINDING_DATA_DIR = DATA_DIR / "finding"
40
+ FINDING_LOCATION_CLASSIFICATION_DATA_DIR = DATA_DIR / "finding_location_classification"
41
+ FINDING_LOCATION_CLASSIFICATION_CHOICE_DATA_DIR = (
42
+ DATA_DIR / "finding_location_classification_choice"
43
+ )
44
+ FINDING_MORPHOLOGY_CLASSIFICATION_DATA_DIR = (
45
+ DATA_DIR / "finding_morphology_classification"
46
+ )
47
+ FINDING_MORPHOLOGY_CLASSIFICATION_CHOICE_DATA_DIR = (
48
+ DATA_DIR / "finding_morphology_classification_choice"
49
+ )
50
+ FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR = (
51
+ DATA_DIR / "finding_morphology_classification_type"
52
+ )
53
+ FINDING_INTERVETION_DATA_DIR = DATA_DIR / "finding_intervention"
54
+ FINIDNG_INTERVENTION_TYPE_DATA_DIR = DATA_DIR / "finding_intervention_type"
55
+
56
+
57
+ FINDING_CLASSIFICATION_TYPE_DATA_DIR = DATA_DIR / "finding_classification_type"
58
+ FINDING_CLASSIFICATION_DATA_DIR = DATA_DIR / "finding_classification"
59
+ FINDING_CLASSIFICATION_CHOICE_DATA_DIR = DATA_DIR / "finding_classification_choice"
60
+
61
+ # Green Endoscopy Dashboard Stuffs
62
+ CENTER_RESOURCE_DATA_DIR = DATA_DIR / "center_resource"
63
+ CENTER_WASTE_DATA_DIR = DATA_DIR / "center_waste"
64
+ EMISSION_FACTOR_DATA_DIR = DATA_DIR / "emission_factor"
65
+ MATERIAL_DATA_DIR = DATA_DIR / "material"
66
+ PRODUCT_DATA_DIR = DATA_DIR / "product"
67
+ PRODUCT_GROUP_DATA_DIR = DATA_DIR / "product_group"
68
+ PRODUCT_MATERIAL_DATA_DIR = DATA_DIR / "product_material"
69
+ PRODUCT_WEIGHT_DATA_DIR = DATA_DIR / "product_weight"
70
+ REFERENCE_PRODUCT_DATA_DIR = DATA_DIR / "reference_product"
71
+ RESOURCE_DATA_DIR = DATA_DIR / "resource"
72
+ WASTE_DATA_DIR = DATA_DIR / "waste"
73
+ TRANSPORT_ROUTE_DATA_DIR = DATA_DIR / "transport_route"
74
+ DISEASE_CLASSIFICATION_DATA_DIR = DATA_DIR / "disease_classification"
75
+ DISEASE_CLASSIFICATION_CHOICE_DATA_DIR = DATA_DIR / "disease_classification_choice"
76
+ DISEASE_DATA_DIR = DATA_DIR / "disease"
77
+ MEDICATION_DATA_DIR = DATA_DIR / "medication"
78
+ MEDICATION_INDICATION_DATA_DIR = DATA_DIR / "medication_indication"
79
+ MEDICATION_INDICATION_TYPE_DATA_DIR = DATA_DIR / "medication_indication_type"
80
+
81
+ DISTRIBUTION_BASE_DIR = DATA_DIR / "distribution"
82
+ DISTRIBUTION_SINGLE_CATEGORICAL_DATA_DIR = DISTRIBUTION_BASE_DIR / "single_categorical"
83
+ DISTRIBUTION_NUMERIC_DATA_DIR = DISTRIBUTION_BASE_DIR / "numeric"
84
+ DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR = (
85
+ DISTRIBUTION_BASE_DIR / "multiple_categorical"
86
+ )
87
+ DISTRIBUTION_DATE_DATA_DIR = DISTRIBUTION_BASE_DIR / "date"
88
+
89
+ # NETWORK
90
+ NETWORK_DEVICE_DATA_DIR = DATA_DIR / "network_device"
91
+ NETWORK_DEVICE_TYPE_DATA_DIR = DATA_DIR / "network_device_type"
92
+ AGL_SERVICE_DATA_DIR = DATA_DIR / "agl_service"
93
+
94
+ # LOGS
95
+ LOG_TYPE_DATA_DIR = DATA_DIR / "log_type"
96
+
97
+ # AI STUFFS
98
+ AI_MODEL_DATA_DIR = DATA_DIR / "ai_model"
99
+ AI_MODEL_TYPE_DATA_DIR = DATA_DIR / "ai_model_type"
100
+ AI_MODEL_META_DATA_DIR = DATA_DIR / "ai_model_meta"
101
+ LABEL_DATA_DIR = DATA_DIR / "ai_model_label"
102
+ VIDEO_SEGMENTATION_LABEL_DATA_DIR = DATA_DIR / "ai_model_video_segmentation_label"
103
+ VIDEO_SEGMENTATION_LABELSET_DATA_DIR = DATA_DIR / "ai_model_video_segmentation_labelset"
104
+
105
+ # RISK
106
+ RISK_DATA_DIR = DATA_DIR / "risk"
107
+ RISK_TYPE_DATA_DIR = DATA_DIR / "risk_type"
108
+
109
+ # REQUIREMENT
110
+ REQUIREMENT_DATA_DIR = DATA_DIR / "requirement"
111
+ REQUIREMENT_OPERATOR_DATA_DIR = DATA_DIR / "requirement_operator"
112
+ REQUIREMENT_SET_DATA_DIR = DATA_DIR / "requirement_set"
113
+ REQUIREMENT_SET_TYPE_DATA_DIR = DATA_DIR / "requirement_set_type"
114
+ REQUIREMENT_TYPE_DATA_DIR = DATA_DIR / "requirement_type"
115
+
116
+ # To Do
117
+ LAB_VALUE_DATA_DIR = DATA_DIR / "lab_value"
118
+ PATIENT_LAB_SAMPLE_TYPE_DATA_DIR = DATA_DIR / "patient_lab_sample_type"
119
+ MEDICATION_SCHEDULE_DATA_DIR = DATA_DIR / "medication_schedule"
120
+ MEDICATION_INTAKE_TIME_DATA_DIR = DATA_DIR / "medication_intake_time"
121
+
122
+
123
+ RULE_TYPE_DATA_DIR = DATA_DIR / "rule_type"
124
+ RULE_ATTRIBUTE_DTYPE_DATA_DIR = DATA_DIR / "rule_attribute_dtype"
125
+ RULESET_DATA_DIR = DATA_DIR / "ruleset"
126
+
127
+ LX_PERMISSION_DATA_DIR = DATA_DIR / "lx_permission"
128
+ LX_CLIENT_TAG_DATA_DIR = DATA_DIR / "lx_client_tag"
129
+ LX_CLIENT_TYPE_DATA_DIR = DATA_DIR / "lx_client_type"
130
+
131
+ QUALIFICATION_DATA_DIR = DATA_DIR / "qualification"
132
+
133
+ TAG_DATA_DIR = DATA_DIR / "tag"
134
+
135
+ EXAMINATION_REQUIREMENT_SET_DATA_DIR = DATA_DIR / "examination_requirement_set"
endoreg_db/data/ai_model/data.yaml ADDED
@@ -0,0 +1,7 @@
1
+ - model: endoreg_db.ai_model
2
+ fields:
3
+ name: "image_multilabel_classification_colonoscopy_default"
4
+ description: "Image multilabel classification model"
5
+ model_type: "multilabel_classification"
6
+ model_subtype: "multilabel"
7
+ video_segmentation_labelset: "colonoscopy_video_segmentation_raw"
endoreg_db/data/ai_model_label/label/data.yaml ADDED
@@ -0,0 +1,88 @@
1
+ # labels are: "appendix", "ileocecal_valve", "polyp", "water_jet", "digital_chromo_endoscopy", "instrument", "wound", "blood", "ileum", "low_quality", "clip", "outside"
2
+
3
+ - model: endoreg_db.Label
4
+ fields:
5
+ name: "appendix"
6
+ label_type: "classification"
7
+
8
+ - model: endoreg_db.Label
9
+ fields:
10
+ name: "ileocaecalvalve"
11
+ label_type: "classification"
12
+
13
+ - model: endoreg_db.Label
14
+ fields:
15
+ name: "polyp"
16
+ label_type: "classification"
17
+
18
+ - model: endoreg_db.Label
19
+ fields:
20
+ name: "water_jet"
21
+ label_type: "classification"
22
+
23
+ - model: endoreg_db.Label
24
+ fields:
25
+ name: "digital_chromo_endoscopy"
26
+ label_type: "classification"
27
+
28
+ - model: endoreg_db.Label
29
+ fields:
30
+ name: "instrument"
31
+ label_type: "classification"
32
+
33
+ - model: endoreg_db.Label
34
+ fields:
35
+ name: "wound"
36
+ label_type: "classification"
37
+
38
+ - model: endoreg_db.Label
39
+ fields:
40
+ name: "blood"
41
+ label_type: "classification"
42
+
43
+ - model: endoreg_db.Label
44
+ fields:
45
+ name: "ileum"
46
+ label_type: "classification"
47
+
48
+ - model: endoreg_db.Label
49
+ fields:
50
+ name: "low_quality"
51
+ label_type: "classification"
52
+
53
+ - model: endoreg_db.Label
54
+ fields:
55
+ name: "clip"
56
+ label_type: "classification"
57
+
58
+ - model: endoreg_db.Label
59
+ fields:
60
+ name: "outside"
61
+ label_type: "classification"
62
+
63
+ - model: endoreg_db.Label
64
+ fields:
65
+ name: "diverticule"
66
+ label_type: "classification"
67
+
68
+ - model: endoreg_db.Label
69
+ fields:
70
+ name: "grasper"
71
+ label_type: "classification"
72
+
73
+ - model: endoreg_db.Label
74
+ fields:
75
+ name: "nbi"
76
+ label_type: "classification"
77
+
78
+ # needle
79
+ - model: endoreg_db.Label
80
+ fields:
81
+ name: "needle"
82
+ label_type: "classification"
83
+
84
+ # snare
85
+ - model: endoreg_db.Label
86
+ fields:
87
+ name: "snare"
88
+ label_type: "classification"
endoreg_db/data/ai_model_label/label/polyp_classification.yaml ADDED
@@ -0,0 +1,52 @@
1
+ # Paris
2
+ - model: endoreg_db.Label
3
+ fields:
4
+ name: "paris_1s"
5
+ label_type: "classification"
6
+
7
+ - model: endoreg_db.Label
8
+ fields:
9
+ name: "paris_1p"
10
+ label_type: "classification"
11
+
12
+ - model: endoreg_db.Label
13
+ fields:
14
+ name: "paris_2a"
15
+ label_type: "classification"
16
+
17
+ - model: endoreg_db.Label
18
+ fields:
19
+ name: "paris_2b"
20
+ label_type: "classification"
21
+
22
+ - model: endoreg_db.Label
23
+ fields:
24
+ name: "paris_2c"
25
+ label_type: "classification"
26
+
27
+ - model: endoreg_db.Label
28
+ fields:
29
+ name: "paris_3"
30
+ label_type: "classification"
31
+
32
+ # NICE Classification
33
+ - model: endoreg_db.Label
34
+ fields:
35
+ name: "nice_1"
36
+ label_type: "classification"
37
+
38
+ - model: endoreg_db.Label
39
+ fields:
40
+ name: "nice_2a"
41
+ label_type: "classification"
42
+
43
+ - model: endoreg_db.Label
44
+ fields:
45
+ name: "nice_2b"
46
+ label_type: "classification"
47
+
48
+ - model: endoreg_db.Label
49
+ fields:
50
+ name: "nice_3"
51
+ label_type: "classification"
52
+
endoreg_db/data/ai_model_label/label-set/data.yaml ADDED
@@ -0,0 +1,40 @@
1
+ - model: endoreg_db.label_set
2
+ fields:
3
+ name: "multilabel_classification_colonoscopy_default"
4
+ version: 1
5
+ labels:
6
+ [
7
+ "appendix",
8
+ "blood",
9
+ "diverticule",
10
+ "grasper",
11
+ "ileocaecalvalve",
12
+ "ileum",
13
+ "low_quality",
14
+ "nbi",
15
+ "needle",
16
+ "outside",
17
+ "polyp",
18
+ "snare",
19
+ "water_jet",
20
+ "wound",
21
+ ]
22
+
23
+ - model: endoreg_db.label_set
24
+ fields:
25
+ name: "multilabel_classification_colonoscopy_default"
26
+ version: 2
27
+ labels:
28
+ [
29
+ "appendix",
30
+ "blood",
31
+ "ileocaecalvalve",
32
+ "ileum",
33
+ "low_quality",
34
+ "instrument",
35
+ "digital_chromo_endoscopy",
36
+ "outside",
37
+ "polyp",
38
+ "water_jet",
39
+ "wound",
40
+ ]
endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml ADDED
@@ -0,0 +1,25 @@
1
+ - model: endoreg_db.LabelSet
2
+ fields:
3
+ name: "endoscopy_paris_classification"
4
+ version: 1
5
+ labels:
6
+ [
7
+ "paris_1s",
8
+ "paris_1p",
9
+ "paris_2a",
10
+ "paris_2b",
11
+ "paris_2c",
12
+ "paris_3",
13
+ ]
14
+
15
+ - model: endoreg_db.LabelSet
16
+ fields:
17
+ name: "endoscopy_nice_classification"
18
+ version: 1
19
+ labels:
20
+ [
21
+ "nice_1",
22
+ "nice_2a",
23
+ "nice_2b",
24
+ "nice_3",
25
+ ]
endoreg_db/data/ai_model_label/label-type/data.yaml ADDED
@@ -0,0 +1,7 @@
1
+ - model: endoreg_db.LabelType
2
+ fields:
3
+ name: "classification"
4
+
5
+ - model: endoreg_db.LabelType
6
+ fields:
7
+ name: "object_detection"
endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml ADDED
@@ -0,0 +1,27 @@
1
+ # Model metadata configuration with setup hints
2
+ - model: endoreg_db.model_meta
3
+ fields:
4
+ name: "image_multilabel_classification_colonoscopy_default"
5
+ version: "1"
6
+ model: "image_multilabel_classification_colonoscopy_default"
7
+ labelset: "multilabel_classification_colonoscopy_default"
8
+ labelset_version: 1
9
+ activation: "sigmoid"
10
+ mean: "0.485,0.456,0.406" # ImageNet defaults
11
+ std: "0.229,0.224,0.225" # ImageNet defaults
12
+ size_x: 224
13
+ size_y: 224
14
+ axes: "CHW"
15
+ batchsize: 32
16
+ num_workers: 4
17
+ description: "Default colonoscopy image multilabel classification model from YAML"
18
+ # Note: weights field intentionally left empty - will be set by setup command or model meta logic
19
+
20
+ # Setup configuration hints for this model
21
+ setup_config:
22
+ is_primary_model: true # Mark this as the primary model for setup
23
+ weight_filenames: # Specific weight file patterns for this model
24
+ - "colo_segmentation_RegNetX800MF_6.safetensors"
25
+ huggingface_fallback: # HF configuration for this model
26
+ repo_id: "wg-lux/colo_segmentation_RegNetX800MF_base"
27
+ filename: "colo_segmentation_RegNetX800MF_base.safetensors"
endoreg_db/data/ai_model_type/data.yaml ADDED
@@ -0,0 +1,7 @@
1
+ - model: endoreg_db.model_type
2
+ fields:
3
+ name: "multilabel_classification"
4
+
5
+ - model: endoreg_db.model_type
6
+ fields:
7
+ name: "object_detection"
endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml ADDED
@@ -0,0 +1,176 @@
1
+ - model: endoreg_db.video_segmentation_label
2
+ fields:
3
+ name: "upper_gi"
4
+ name_de: "Oberer GI-Trakt"
5
+ name_en: "Upper GI"
6
+ description: "Upper GI"
7
+ color: "#FF0000"
8
+
9
+ - model: endoreg_db.video_segmentation_label
10
+ fields:
11
+ name: "lower_gi"
12
+ name_de: "Unterer GI-Trakt"
13
+ name_en: "Lower GI"
14
+ description: "Lower GI"
15
+ color: "#00FF00"
16
+
17
+ - model: endoreg_db.video_segmentation_label
18
+ fields:
19
+ name: "esophagus"
20
+ name_de: "Ösophagus"
21
+ name_en: "Esophagus"
22
+ description: "Esophagus"
23
+ color: "#0000FF"
24
+
25
+ - model: endoreg_db.video_segmentation_label
26
+ fields:
27
+ name: "stomach"
28
+ name_de: "Magen"
29
+ name_en: "Stomach"
30
+ description: "Stomach"
31
+ color: "#FFFF00"
32
+
33
+ - model: endoreg_db.video_segmentation_label
34
+ fields:
35
+ name: "duodenum"
36
+ name_de: "Duodenum"
37
+ name_en: "Duodenum"
38
+ description: "Duodenum"
39
+ color: "#FF00FF"
40
+
41
+ - model: endoreg_db.video_segmentation_label
42
+ fields:
43
+ name: "colon"
44
+ name_de: "Kolon"
45
+ name_en: "Colon"
46
+ description: "Colon"
47
+ color: "#00FFFF"
48
+
49
+ - model: endoreg_db.video_segmentation_label
50
+ fields:
51
+ name: "ileum"
52
+ name_de: "Ileum"
53
+ name_en: "Ileum"
54
+ description: "Ileum"
55
+ color: "#800000"
56
+
57
+ - model: endoreg_db.video_segmentation_label
58
+ fields:
59
+ name: "outside"
60
+ name_de: "Außerhalb des Körpers"
61
+ name_en: "Out of Body"
62
+ description: "Out of Body"
63
+ color: "#008000"
64
+
65
+ - model: endoreg_db.video_segmentation_label
66
+ fields:
67
+ name: "bli"
68
+ name_de: "Blau-Licht-Imaging"
69
+ name_en: "Blue Light Imaging"
70
+ description: "Blue Light Imaging (high level for nbi and similar modes)"
71
+ color: "#000080"
72
+
73
+ - model: endoreg_db.video_segmentation_label
74
+ fields:
75
+ name: "low_quality"
76
+ name_de: "Niedrige Qualität"
77
+ name_en: "Low Quality"
78
+ description: "Low Quality"
79
+ color: "#800080"
80
+
81
+ - model: endoreg_db.video_segmentation_label
82
+ fields:
83
+ name: "instrument"
84
+ name_de: "Instrument"
85
+ name_en: "Instrument"
86
+ description: "Instrument"
87
+ color: "#808000"
88
+
89
+ # Appendix
90
+ - model: endoreg_db.video_segmentation_label
91
+ fields:
92
+ name: "appendix"
93
+ name_de: "Appendix"
94
+ name_en: "Appendix"
95
+ description: "Appendix"
96
+ color: "#FF0000"
97
+ # blood, diverticule, grasper, ileocaecalvalve, ileum, low_quality, nbi, needle, polyp, snare, water_jet, wound
98
+ - model: endoreg_db.video_segmentation_label
99
+ fields:
100
+ name: "blood"
101
+ name_de: "Blut"
102
+ name_en: "Blood"
103
+ description: "Blood"
104
+ color: "#00FF00"
105
+
106
+ - model: endoreg_db.video_segmentation_label
107
+ fields:
108
+ name: "diverticule"
109
+ name_de: "Divertikel"
110
+ name_en: "Diverticule"
111
+ description: "Diverticule"
112
+ color: "#0000FF"
113
+
114
+ - model: endoreg_db.video_segmentation_label
115
+ fields:
116
+ name: "grasper"
117
+ name_de: "Grasper"
118
+ name_en: "Grasper"
119
+ description: "Grasper"
120
+ color: "#FFFF00"
121
+
122
+ - model: endoreg_db.video_segmentation_label
123
+ fields:
124
+ name: "ileocaecalvalve"
125
+ name_de: "Ileocaecalvalve"
126
+ name_en: "Ileocaecalvalve"
127
+ description: "Ileocaecalvalve"
128
+ color: "#FF00FF"
129
+
130
+ - model: endoreg_db.video_segmentation_label
131
+ fields:
132
+ name: "nbi"
133
+ name_de: "Narrow Band Imaging"
134
+ name_en: "Narrow Band Imaging"
135
+ description: "Narrow Band Imaging"
136
+ color: "#00FFFF"
137
+
138
+ - model: endoreg_db.video_segmentation_label
139
+ fields:
140
+ name: "needle"
141
+ name_de: "Needle"
142
+ name_en: "Needle"
143
+ description: "Needle"
144
+ color: "#800000"
145
+
146
+ - model: endoreg_db.video_segmentation_label
147
+ fields:
148
+ name: "polyp"
149
+ name_de: "Polyp"
150
+ name_en: "Polyp"
151
+ description: "Polyp"
152
+ color: "#008000"
153
+
154
+ - model: endoreg_db.video_segmentation_label
155
+ fields:
156
+ name: "snare"
157
+ name_de: "Snare"
158
+ name_en: "Snare"
159
+ description: "Snare"
160
+ color: "#000080"
161
+
162
+ - model: endoreg_db.video_segmentation_label
163
+ fields:
164
+ name: "water_jet"
165
+ name_de: "Water Jet"
166
+ name_en: "Water Jet"
167
+ description: "Water Jet"
168
+ color: "#800080"
169
+
170
+ - model: endoreg_db.video_segmentation_label
171
+ fields:
172
+ name: "wound"
173
+ name_de: "Wound"
174
+ name_en: "Wound"
175
+ description: "Wound"
176
+ color: "#808000"
endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml ADDED
@@ -0,0 +1,20 @@
1
+ - model: endoreg_db.video_segmentation_label_set
2
+ fields:
3
+ name: "colonoscopy_video_segmentation_raw"
4
+ labels:
5
+ [
6
+ "appendix",
7
+ "blood",
8
+ "diverticule",
9
+ "grasper",
10
+ "ileocaecalvalve",
11
+ "ileum",
12
+ "low_quality",
13
+ "nbi",
14
+ "needle",
15
+ "outside",
16
+ "polyp",
17
+ "snare",
18
+ "water_jet",
19
+ "wound",
20
+ ]