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/finding_classification/00_generic.yaml ADDED
@@ -0,0 +1,44 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "visualized"
4
+ classification_types:
5
+ - inferrable
6
+ choices:
7
+ - "yes"
8
+ - "no"
9
+
10
+ - model: endoreg_db.finding_classification
11
+ fields:
12
+ name: "examination_setting_generic_location"
13
+ classification_types: []
14
+ choices:
15
+ - examination_setting_generic_location_inpatient
16
+ - examination_setting_generic_location_outpatient
17
+
18
+ - model: endoreg_db.finding_classification
19
+ fields:
20
+ name: "sedation_performed"
21
+ classification_types: []
22
+ choices:
23
+ - "yes"
24
+ - "no"
25
+
26
+ - model: endoreg_db.finding_classification
27
+ fields:
28
+ name: "examination_setting_generic_sedation"
29
+ classification_types: []
30
+ choices:
31
+ - "sedation_propofol"
32
+ - "sedation_midazolam"
33
+ - "sedation_propofol_midazolam"
34
+ - "sedation_other"
35
+
36
+ - model: endoreg_db.finding_classification
37
+ fields:
38
+ name: "complication_generic_type"
39
+ classification_types: []
40
+ choices:
41
+ - complication_generic_type_cardiorespiratory
42
+ - complication_generic_type_bleeding
43
+ - complication_generic_type_perforation
44
+ - complication_generic_type_other
endoreg_db/data/finding_classification/00_generic_histology.yaml ADDED
@@ -0,0 +1,28 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "histology_dysplasia_default"
4
+ classification_types:
5
+ - histology
6
+ choices:
7
+ - histology_dysplasia_none
8
+ - histology_dysplasia_low_grade
9
+ - histology_dysplasia_high_grade
10
+
11
+ - model: endoreg_db.finding_classification
12
+ fields:
13
+ name: "histology_dignity_default"
14
+ classification_types:
15
+ - histology
16
+ choices:
17
+ - histology_dignity_benign
18
+ - histology_dignity_malign
19
+
20
+ - model: endoreg_db.finding_classification_choice
21
+ fields:
22
+ name: "histology_in_sano_default"
23
+ classification_types:
24
+ - histology
25
+ choices:
26
+ - "yes"
27
+ - "no"
28
+ - "na"
endoreg_db/data/finding_classification/00_generic_lesion.yaml ADDED
@@ -0,0 +1,52 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "lesion_size_mm"
4
+ classification_types: ["size"]
5
+ name_de: "Größe (mm)"
6
+ name_en: "Size (mm)"
7
+ choices: ["lesion_size_oval_mm"]
8
+
9
+ - model: endoreg_db.finding_classification
10
+ fields:
11
+ name: "lesion_length_mm"
12
+ classification_types: ["size"]
13
+ name_de: "Länge (mm)"
14
+ name_en: "Length (mm)"
15
+ choices:
16
+ - lesion_length_mm #TODO
17
+
18
+ - model: endoreg_db.finding_classification
19
+ fields:
20
+ name: "lesion_planarity_default"
21
+ classification_types: ["planarity", "morphology"]
22
+ name_de: "Planaritätsklassifikation Kolonläsion"
23
+ name_en: "Colon Lesion Planarity Classification"
24
+ choices:
25
+ - lesion_planarity_flat
26
+ - lesion_planarity_flat_elevated
27
+ - lesion_planarity_sessile
28
+ - lesion_planarity_pedunculated
29
+ - lesion_planarity_excavated
30
+ - lesion_planarity_unknown
31
+
32
+ - model: endoreg_db.finding_classification
33
+ fields:
34
+ name: "lesion_surface_intact_default"
35
+ classification_types:
36
+ - morphology
37
+ name_de: "Oberflächenklassifikation Kolonläsion"
38
+ name_en: "Colon Lesion Surface Classification"
39
+ choices:
40
+ - lesion_surface_intact
41
+ - lesion_surface_eroded
42
+ - lesion_surface_ulcerated
43
+
44
+ - model: endoreg_db.finding_classification
45
+ fields:
46
+ name: "lesion_circularity_default"
47
+ name_de: "Zirkularität"
48
+ name_en: "Circularity"
49
+ classification_types: ["morphology"]
50
+ choices:
51
+ - lesion_circularity_false
52
+ - lesion_circularity_true
endoreg_db/data/finding_classification/02_colonoscopy_baseline.yaml ADDED
@@ -0,0 +1,83 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "colonoscopy_location_default"
4
+ name_de: "Koloskopie Standard"
5
+ name_en: "Colonoscopy Default"
6
+ classification_types: ["location"]
7
+ choices:
8
+ [
9
+ "terminal_ileum",
10
+ "cecum",
11
+ "ascending_colon",
12
+ "right_flexure",
13
+ "transverse_colon",
14
+ "left_flexure",
15
+ "descending_colon",
16
+ "sigmoid_colon",
17
+ "rectum",
18
+ "anal_canal",
19
+ ]
20
+
21
+ - model: endoreg_db.finding_classification
22
+ fields:
23
+ name: "colonoscopy_location_coarse"
24
+ name_de: "Koloskopie Grob"
25
+ name_en: "Colonoscopy Coarse"
26
+ classification_types: ["location"]
27
+ choices: ["left_colon", "right_colon", "rectum"]
28
+
29
+ - model: endoreg_db.finding_classification
30
+ fields:
31
+ name: "bowel_prep_boston"
32
+ classification_types: ["bowel_prep"]
33
+ name_de: "Boston Bowel Preparation Scale"
34
+ name_en: "Boston Bowel Preparation Scale"
35
+ choices:
36
+ [
37
+ "bowel_prep_boston_0",
38
+ "bowel_prep_boston_1",
39
+ "bowel_prep_boston_2",
40
+ "bowel_prep_boston_3",
41
+ ]
42
+
43
+ - model: endoreg_db.finding_classification
44
+ fields:
45
+ name: "bowel_prep_boston_simplified"
46
+ classification_types: ["bowel_prep"]
47
+ name_de: "Boston Bowel Preparation Scale"
48
+ name_en: "Boston Bowel Preparation Scale"
49
+ choices:
50
+ [
51
+ "bowel_prep_boston_0",
52
+ "bowel_prep_boston_1",
53
+ "bowel_prep_boston_2",
54
+ "bowel_prep_boston_3",
55
+ ]
56
+
57
+ #Aronchick
58
+ - model: endoreg_db.finding_classification
59
+ fields:
60
+ name: "bowel_prep_aronchick"
61
+ classification_types: ["bowel_prep"]
62
+ name_de: "Aronchick Bowel Preparation Scale"
63
+ name_en: "Aronchick Bowel Preparation Scale"
64
+ choices:
65
+ [
66
+ "bowel_prep_aronchick_0",
67
+ "bowel_prep_aronchick_1",
68
+ "bowel_prep_aronchick_2",
69
+ "bowel_prep_aronchick_3",
70
+ ]
71
+
72
+ - model: endoreg_db.finding_classification
73
+ fields:
74
+ name: "colonoscopy_not_complete_reason"
75
+ classification_types: []
76
+ choices:
77
+ [
78
+ "colonoscopy_incomplete_insufficient_preparation",
79
+ "colonoscopy_incomplete_complication",
80
+ "colonoscopy_incomplete_pain",
81
+ "colonoscopy_incomplete_stenosis",
82
+ "colonoscopy_incomplete_other",
83
+ ]
endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml ADDED
@@ -0,0 +1,13 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "colonoscopy_polyp_histology"
4
+ classification_types:
5
+ - histology
6
+ choices: [
7
+ "histology_polyp_hyperplastic",
8
+ "histology_polyp_adenoma_tubular",
9
+ "histology_polyp_adenoma_tubulovillous",
10
+ "histology_polyp_adenoma_villous",
11
+ "histology_polyp_sessile_serrated_lesion",
12
+ # unknown?
13
+ ]
endoreg_db/data/finding_classification/02_colonoscopy_other.yaml ADDED
@@ -0,0 +1,12 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "hemorrhoids_grade"
4
+ classification_types: []
5
+ choices:
6
+ [
7
+ "hemorrhoids_grade_0_no_hemorrhoids",
8
+ "hemorrhoids_grade_1",
9
+ "hemorrhoids_grade_2",
10
+ "hemorrhoids_grade_3",
11
+ "hemorrhoids_grade_4",
12
+ ]
endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml ADDED
@@ -0,0 +1,101 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "colon_lesion_paris"
4
+ classification_types: ["shape", "morphology"]
5
+ name_de: "Formklassifikation Kolonläsion"
6
+ name_en: "Colon Lesion Shape Classification"
7
+ choices: [
8
+ "colon_lesion_paris_Is", # maps to colon_lesion_planarity_sessile
9
+ "colon_lesion_paris_Ip", # colon_lesion_planarity_pedunculated
10
+ "colon_lesion_paris_IIa",
11
+ "colon_lesion_paris_IIb",
12
+ "colon_lesion_paris_IIc",
13
+ "colon_lesion_paris_III",
14
+ "colon_lesion_paris_IIa_IIc",
15
+ "colon_lesion_paris_IIb_IIc",
16
+ ]
17
+
18
+ - model: endoreg_db.finding_classification
19
+ fields:
20
+ name: "colon_lesion_sano"
21
+ classification_types: ["capillary_pattern", "morphology"]
22
+ name_de: "Oberflächenklassifikation Kolonläsion"
23
+ name_en: "Colon Lesion Surface Classification"
24
+ choices:
25
+ [
26
+ "colon_lesion_sano_1",
27
+ "colon_lesion_sano_2",
28
+ "colon_lesion_sano_3a",
29
+ "colon_lesion_sano_3b",
30
+ ]
31
+
32
+ - model: endoreg_db.finding_classification
33
+ fields:
34
+ name: "colon_lesion_size_categorical"
35
+ classification_types: ["size", "morphology"]
36
+ name_de: "Größenklassifikation Kolonläsion (kategorisch)"
37
+ name_en: "Colon Lesion Size Classification (categorical)"
38
+ choices: [
39
+ "colon_lesion_size_categorical_diminutive", # 0 - 5 mm
40
+ "colon_lesion_size_categorical_small", # 6 - 9 mm
41
+ "colon_lesion_size_categorical_medium", # 10 - 20 mm
42
+ "colon_lesion_size_categorical_large", # 21+ mm
43
+ ]
44
+
45
+ - model: endoreg_db.finding_classification
46
+ fields:
47
+ name: "colon_lesion_lst"
48
+ classification_types: ["shape", "morphology"]
49
+ name_de: "Oberflächenklassifikation Kolonläsion"
50
+ name_en: "Colon Lesion Surface Classification"
51
+ choices:
52
+ [
53
+ "colon_lesion_lst_granular_homogeneous",
54
+ "colon_lesion_lst_granular_nodular_mixed",
55
+ "colon_lesion_lst_non_granular_flat_elevated",
56
+ "colon_lesion_lst_non_granular_pseudodepressed",
57
+ ]
58
+
59
+ - model: endoreg_db.finding_classification
60
+ fields:
61
+ name: "colon_lesion_kudo"
62
+ classification_types: ["colon_lesion_advanced_imaging", "morphology"]
63
+ name_de: "Oberflächenklassifikation Kolonläsion"
64
+ name_en: "Colon Lesion Surface Classification"
65
+ choices:
66
+ [
67
+ "colon_lesion_kudo_1",
68
+ "colon_lesion_kudo_2",
69
+ "colon_lesion_kudo_3s",
70
+ "colon_lesion_kudo_3l",
71
+ "colon_lesion_kudo_4",
72
+ "colon_lesion_kudo_5i",
73
+ "colon_lesion_kudo_5n",
74
+ ]
75
+
76
+ - model: endoreg_db.finding_classification
77
+ fields:
78
+ name: "colon_lesion_jnet"
79
+ name_de: "Kolonläsion - JNET"
80
+ name_en: "Colon lesion - JNET"
81
+ classification_types: ["morphology", "colon_lesion_advanced_imaging"]
82
+ choices:
83
+ [
84
+ "colon_lesion_jnet_1",
85
+ "colon_lesion_jnet_2a",
86
+ "colon_lesion_jnet_2b",
87
+ "colon_lesion_jnet_3",
88
+ ]
89
+
90
+ - model: endoreg_db.finding_classification
91
+ fields:
92
+ name: "colon_lesion_nice"
93
+ classification_types: ["colon_lesion_advanced_imaging", "morphology"]
94
+ name_de: "Kolonläsion - NICE"
95
+ name_en: "Colon lesion - NICE"
96
+ choices:
97
+ [
98
+ "colon_lesion_NICE_type_1",
99
+ "colon_lesion_NICE_type_2",
100
+ "colon_lesion_NICE_type_3",
101
+ ]
endoreg_db/data/finding_classification_choice/00_generic.yaml ADDED
@@ -0,0 +1,15 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "yes"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "no"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "na"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "unknown"
endoreg_db/data/finding_classification_choice/00_generic_baseline.yaml ADDED
@@ -0,0 +1,23 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "examination_setting_generic_location_inpatient"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "examination_setting_generic_location_outpatient"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "sedation_propofol"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "sedation_midazolam"
16
+
17
+ - model: endoreg_db.finding_classification_choice
18
+ fields:
19
+ name: "sedation_propofol_midazolam"
20
+
21
+ - model: endoreg_db.finding_classification_choice
22
+ fields:
23
+ name: "sedation_other"
endoreg_db/data/finding_classification_choice/00_generic_complication.yaml ADDED
@@ -0,0 +1,15 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "complication_generic_type_cardiorespiratory"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "complication_generic_type_bleeding"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "complication_generic_type_perforation"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "complication_generic_type_other"
endoreg_db/data/finding_classification_choice/00_generic_histology.yaml ADDED
@@ -0,0 +1,21 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "histology_dysplasia_none"
4
+ description: "Histology: No dysplasia"
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "histology_dysplasia_low_grade"
8
+ description: "Histology: Low-grade dysplasia"
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "histology_dysplasia_high_grade"
12
+ description: "Histology: High-grade dysplasia"
13
+
14
+ - model: endoreg_db.finding_classification_choice
15
+ fields:
16
+ name: "histology_dignity_benign"
17
+ description: "Histology: Benign"
18
+ - model: endoreg_db.finding_classification_choice
19
+ fields:
20
+ name: "histology_dignity_malign"
21
+ description: "Histology: Malign"
endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml ADDED
@@ -0,0 +1,158 @@
1
+ # Planarity of lesions
2
+ - model: endoreg_db.finding_classification_choice
3
+ fields:
4
+ name: "lesion_planarity_flat"
5
+ name_de: "Planarität flach"
6
+ name_en: "planarity flat"
7
+ description: "Category for flat lesions"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "lesion_planarity_flat_elevated"
12
+ name_de: "Planarität flach-erhaben"
13
+ name_en: "planarity flat-elevated"
14
+ description: "Category for flat-elevated lesions (surface +/- 2 mm)"
15
+
16
+ - model: endoreg_db.finding_classification_choice
17
+ fields:
18
+ name: "lesion_planarity_sessile"
19
+ name_de: "Planarität sessil"
20
+ name_en: "planarity sessile"
21
+ description: "Category for sessile lesions (surface > 2 mm)"
22
+
23
+ - model: endoreg_db.finding_classification_choice
24
+ fields:
25
+ name: "lesion_planarity_pedunculated"
26
+ name_de: "Planarität gestielt"
27
+ name_en: "planarity pedunculated"
28
+ description: "Category for pedunculated lesions (surface on a stalk)"
29
+
30
+ - model: endoreg_db.finding_classification_choice
31
+ fields:
32
+ name: "lesion_planarity_excavated"
33
+ name_de: "Planarität exkaviert"
34
+ name_en: "planarity excavated"
35
+ description: "Category for excavated lesions (surface below surrounding mucosa)"
36
+ subcategories:
37
+ description:
38
+ choices: ["unspecified", "focal", "diffuse", "total"]
39
+ probability: [0.5, 0.2, 0.2, 0.1]
40
+ default: "unspecified"
41
+ required: true
42
+
43
+ - model: endoreg_db.finding_classification_choice
44
+ fields:
45
+ name: "lesion_planarity_unknown"
46
+ name_de: "Planarität unbekannt"
47
+ name_en: "planarity unknown"
48
+
49
+ # Circularity of lesions
50
+ - model: endoreg_db.finding_classification_choice
51
+ fields:
52
+ name: "lesion_circularity_false"
53
+ name_de: "Zirkularität"
54
+ name_en: "Circularity"
55
+ description: "Category for non-circular lesions"
56
+
57
+ - model: endoreg_db.finding_classification_choice
58
+ fields:
59
+ name: "lesion_circularity_true"
60
+ name_de: "Zirkularität"
61
+ name_en: "Circularity"
62
+ description: "Category for circular lesions"
63
+ numerical_descriptors:
64
+ length:
65
+ unit: "milimeter"
66
+ min: 0
67
+ max: 100
68
+ default: null
69
+ distribution: "uniform"
70
+ description: "Length of the lesion in mm"
71
+ required: true
72
+ circumference:
73
+ unit: "percent"
74
+ min: 33
75
+ max: 100
76
+ mean: 50
77
+ std: 10
78
+ default: null
79
+ distribution: "normal"
80
+ description: "Circumference of the lesion in %"
81
+ required: true
82
+
83
+ # Size of oval lesions
84
+ - model: endoreg_db.finding_classification_choice
85
+ fields:
86
+ name: "lesion_size_oval_mm"
87
+ name_de: "Größe Ovaler Läsionen (mm)"
88
+ name_en: "Size of Oval Lesions (mm)"
89
+ description: "oval lesions"
90
+ numerical_descriptors:
91
+ largest_diameter_mm:
92
+ unit: "mm"
93
+ min: 0
94
+ max: 35
95
+ distribution: "normal"
96
+ mean: 5
97
+ std: 3
98
+ description: "Largest diameter of the lesion in mm"
99
+ required: true
100
+ perpendicular_diameter_mm:
101
+ unit: "mm"
102
+ min: 0
103
+ max: 35
104
+ description: "Perpendicular diameter of the lesion in mm"
105
+ required: false
106
+
107
+ - model: endoreg_db.finding_classification_choice
108
+ fields:
109
+ name: "lesion_length_mm"
110
+ name_de: "Länge Läsion (mm)"
111
+ name_en: "Length of lesions (mm)"
112
+ description: "Length of lesions"
113
+ numerical_descriptors:
114
+ value:
115
+ unit: "mm"
116
+ min: 0
117
+ max: 100
118
+ distribution: "normal"
119
+ mean: 5
120
+ std: 3
121
+ description: "Largest diameter of the lesion in mm"
122
+ required: true
123
+
124
+ # Surface of lesions
125
+ - model: endoreg_db.finding_classification_choice
126
+ fields:
127
+ name: "lesion_surface_intact"
128
+ name_de: "Oberfläche intakt"
129
+ name_en: "surface intact"
130
+ description: "Category for intact lesion surfaces"
131
+
132
+ # eroded
133
+ - model: endoreg_db.finding_classification_choice
134
+ fields:
135
+ name: "lesion_surface_eroded"
136
+ name_de: "Oberfläche erodiert"
137
+ name_en: "surface eroded"
138
+ description: "Category for eroded lesion surfaces"
139
+ subcategories:
140
+ description:
141
+ choices: ["unspecified", "focal", "diffuse"]
142
+ default: "unspecified"
143
+ probability: [0.5, 0.2, 0.3]
144
+ required: true
145
+
146
+ # ulcerated
147
+ - model: endoreg_db.finding_classification_choice
148
+ fields:
149
+ name: "lesion_surface_ulcerated"
150
+ name_de: "Oberfläche ulzeriert"
151
+ name_en: "surface ulcerated"
152
+ description: "Category for ulcerated lesion surfaces"
153
+ subcategories:
154
+ description:
155
+ choices: ["unspecified", "focal", "diffuse"]
156
+ default: "unspecified"
157
+ probability: [0.5, 0.2, 0.3]
158
+ required: true
endoreg_db/data/finding_classification_choice/02_colonoscopy_bowel_preparation.yaml ADDED
@@ -0,0 +1,49 @@
1
+ # Boston
2
+ - model: endoreg_db.finding_classification_choice
3
+ fields:
4
+ name: "bowel_prep_boston_0"
5
+ name_de: "0"
6
+ name_en: "bowel_prep_boston_0"
7
+
8
+ - model: endoreg_db.finding_classification_choice
9
+ fields:
10
+ name: "bowel_prep_boston_1"
11
+ name_de: "1"
12
+ name_en: "bowel_prep_boston_1"
13
+
14
+ - model: endoreg_db.finding_classification_choice
15
+ fields:
16
+ name: "bowel_prep_boston_2"
17
+ name_de: "2"
18
+ name_en: "bowel_prep_boston_2"
19
+
20
+ - model: endoreg_db.finding_classification_choice
21
+ fields:
22
+ name: "bowel_prep_boston_3"
23
+ name_de: "3"
24
+ name_en: "bowel_prep_boston_3"
25
+
26
+ # Aronchick
27
+ - model: endoreg_db.finding_classification_choice
28
+ fields:
29
+ name: "bowel_prep_aronchick_0"
30
+ name_de: "Inadäquat"
31
+ name_en: "Inadequate"
32
+
33
+ - model: endoreg_db.finding_classification_choice
34
+ fields:
35
+ name: "bowel_prep_aronchick_1"
36
+ name_en: "Fair"
37
+ name_de: "Ausreichend"
38
+
39
+ - model: endoreg_db.finding_classification_choice
40
+ fields:
41
+ name: "bowel_prep_aronchick_2"
42
+ name_en: "Good"
43
+ name_de: "Gut"
44
+
45
+ - model: endoreg_db.finding_classification_choice
46
+ fields:
47
+ name: "bowel_prep_aronchick_3"
48
+ name_en: "Excellent"
49
+ name_de: "Exzellent"
endoreg_db/data/finding_classification_choice/02_colonoscopy_generic.yaml ADDED
@@ -0,0 +1,19 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "colonoscopy_incomplete_insufficient_preparation"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "colonoscopy_incomplete_complication"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "colonoscopy_incomplete_pain"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "colonoscopy_incomplete_stenosis"
16
+
17
+ - model: endoreg_db.finding_classification_choice
18
+ fields:
19
+ name: "colonoscopy_incomplete_other"
endoreg_db/data/finding_classification_choice/02_colonoscopy_histology.yaml ADDED
@@ -0,0 +1,20 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "histology_polyp_hyperplastic"
4
+ description: "Histology: Hyperplastic polyp"
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "histology_polyp_adenoma_tubular"
8
+ description: "Histology: Tubular adenoma"
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "histology_polyp_adenoma_tubulovillous"
12
+ description: "Histology: Tubulovillous adenoma"
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "histology_polyp_adenoma_villous"
16
+ description: "Histology: Villous adenoma"
17
+ - model: endoreg_db.finding_classification_choice
18
+ fields:
19
+ name: "histology_polyp_sessile_serrated_lesion"
20
+ description: "Histology: Sessile serrated lesion"