endoreg-db 0.8.5.1__py3-none-any.whl

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  1. endoreg_db/__init__.py +0 -0
  2. endoreg_db/admin.py +92 -0
  3. endoreg_db/api/serializers/finding_descriptions.py +0 -0
  4. endoreg_db/api/views/finding_descriptions.py +0 -0
  5. endoreg_db/api_urls.py +4 -0
  6. endoreg_db/apps.py +18 -0
  7. endoreg_db/assets/dummy_model.ckpt +1 -0
  8. endoreg_db/codemods/readme.md +88 -0
  9. endoreg_db/codemods/rename_datetime_fields.py +92 -0
  10. endoreg_db/config/__init__.py +0 -0
  11. endoreg_db/config/env.py +101 -0
  12. endoreg_db/data/__init__.py +144 -0
  13. endoreg_db/data/ai_model/data.yaml +7 -0
  14. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  15. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  16. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  17. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  18. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  19. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  20. endoreg_db/data/ai_model_type/data.yaml +7 -0
  21. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  22. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  23. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  24. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  25. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  26. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  27. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  28. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  29. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  30. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  31. endoreg_db/data/case_template/rule_value/.init +0 -0
  32. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  33. endoreg_db/data/case_template/template/base.yaml +8 -0
  34. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  35. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  36. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  37. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  38. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  39. endoreg_db/data/center/data.yaml +91 -0
  40. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  41. endoreg_db/data/center_shift/ukw.yaml +9 -0
  42. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  43. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  44. endoreg_db/data/db_summary.csv +58 -0
  45. endoreg_db/data/db_summary.xlsx +0 -0
  46. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  47. endoreg_db/data/disease/hepatology.yaml +5 -0
  48. endoreg_db/data/disease/misc.yaml +5 -0
  49. endoreg_db/data/disease/renal.yaml +5 -0
  50. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  51. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  52. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  53. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  54. endoreg_db/data/distribution/date/patient.yaml +7 -0
  55. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  56. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  57. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  58. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  59. endoreg_db/data/endoscope/data.yaml +93 -0
  60. endoreg_db/data/endoscope_type/data.yaml +11 -0
  61. endoreg_db/data/endoscopy_processor/data.yaml +50 -0
  62. endoreg_db/data/event/cardiology.yaml +15 -0
  63. endoreg_db/data/event/neurology.yaml +14 -0
  64. endoreg_db/data/event/surgery.yaml +13 -0
  65. endoreg_db/data/event/thrombembolism.yaml +20 -0
  66. endoreg_db/data/examination/examinations/data.yaml +72 -0
  67. endoreg_db/data/examination/time/data.yaml +48 -0
  68. endoreg_db/data/examination/time-type/data.yaml +8 -0
  69. endoreg_db/data/examination/type/data.yaml +17 -0
  70. endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
  71. endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
  72. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  73. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  74. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  75. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  76. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  77. endoreg_db/data/finding/complication.yaml +16 -0
  78. endoreg_db/data/finding/data.yaml +105 -0
  79. endoreg_db/data/finding/examination_setting.yaml +16 -0
  80. endoreg_db/data/finding/medication_related.yaml +18 -0
  81. endoreg_db/data/finding/outcome.yaml +12 -0
  82. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  83. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  84. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  85. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  86. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  87. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  88. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  89. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  90. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  91. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  92. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  93. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  94. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  95. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  96. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  97. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  98. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  99. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  100. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  101. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  102. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
  103. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  104. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  105. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  106. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
  107. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
  108. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
  109. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  110. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
  111. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
  112. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  113. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  114. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  115. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  116. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  117. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  118. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  119. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  120. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  121. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  122. endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
  123. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
  124. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
  125. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
  126. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
  127. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
  128. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  129. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  130. endoreg_db/data/finding_type/data.yaml +43 -0
  131. endoreg_db/data/gender/data.yaml +42 -0
  132. endoreg_db/data/information_source/annotation.yaml +6 -0
  133. endoreg_db/data/information_source/data.yaml +30 -0
  134. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  135. endoreg_db/data/information_source/medication.yaml +6 -0
  136. endoreg_db/data/information_source/prediction.yaml +7 -0
  137. endoreg_db/data/information_source_type/data.yaml +8 -0
  138. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  139. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  140. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  141. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  142. endoreg_db/data/lab_value/hematology.yaml +184 -0
  143. endoreg_db/data/lab_value/hormones.yaml +59 -0
  144. endoreg_db/data/lab_value/lipids.yaml +53 -0
  145. endoreg_db/data/lab_value/misc.yaml +76 -0
  146. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  147. endoreg_db/data/log_type/data.yaml +57 -0
  148. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  149. endoreg_db/data/lx_client_type/base.yaml +30 -0
  150. endoreg_db/data/lx_permission/base.yaml +24 -0
  151. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  152. endoreg_db/data/material/material.yaml +91 -0
  153. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  154. endoreg_db/data/medication/tah.yaml +70 -0
  155. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  156. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  157. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  158. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  159. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  160. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  161. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  162. endoreg_db/data/names_first/first_names.yaml +54 -0
  163. endoreg_db/data/names_last/last_names.yaml +51 -0
  164. endoreg_db/data/network_device/data.yaml +59 -0
  165. endoreg_db/data/network_device_type/data.yaml +12 -0
  166. endoreg_db/data/organ/data.yaml +29 -0
  167. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  168. endoreg_db/data/pdf_type/data.yaml +46 -0
  169. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  170. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  171. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  172. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  173. endoreg_db/data/profession/data.yaml +70 -0
  174. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  175. endoreg_db/data/qualification/m2.yaml +39 -0
  176. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  177. endoreg_db/data/qualification/sonography.yaml +36 -0
  178. endoreg_db/data/qualification_type/base.yaml +29 -0
  179. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  180. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  181. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  182. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
  183. endoreg_db/data/requirement/age.yaml +26 -0
  184. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  185. endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
  186. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
  187. endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
  188. endoreg_db/data/requirement/disease_misc.yaml +12 -0
  189. endoreg_db/data/requirement/disease_renal.yaml +96 -0
  190. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
  191. endoreg_db/data/requirement/event_cardiology.yaml +251 -0
  192. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  193. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  194. endoreg_db/data/requirement/gender.yaml +25 -0
  195. endoreg_db/data/requirement/lab_value.yaml +441 -0
  196. endoreg_db/data/requirement/medication.yaml +93 -0
  197. endoreg_db/data/requirement_operator/age.yaml +13 -0
  198. endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
  199. endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
  200. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  201. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  202. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
  203. endoreg_db/data/requirement_set_type/data.yaml +20 -0
  204. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  205. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  206. endoreg_db/data/risk/bleeding.yaml +26 -0
  207. endoreg_db/data/risk/thrombosis.yaml +37 -0
  208. endoreg_db/data/risk_type/data.yaml +27 -0
  209. endoreg_db/data/setup_config.yaml +38 -0
  210. endoreg_db/data/shift/endoscopy.yaml +21 -0
  211. endoreg_db/data/shift/m2.yaml +0 -0
  212. endoreg_db/data/shift_type/base.yaml +35 -0
  213. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  214. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  215. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  216. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  217. endoreg_db/data/unit/concentration.yaml +115 -0
  218. endoreg_db/data/unit/data.yaml +17 -0
  219. endoreg_db/data/unit/length.yaml +31 -0
  220. endoreg_db/data/unit/misc.yaml +20 -0
  221. endoreg_db/data/unit/rate.yaml +6 -0
  222. endoreg_db/data/unit/time.yaml +48 -0
  223. endoreg_db/data/unit/volume.yaml +35 -0
  224. endoreg_db/data/unit/weight.yaml +38 -0
  225. endoreg_db/data/waste/data.yaml +12 -0
  226. endoreg_db/exceptions.py +19 -0
  227. endoreg_db/factories/__init__.py +0 -0
  228. endoreg_db/forms/__init__.py +5 -0
  229. endoreg_db/forms/examination_form.py +11 -0
  230. endoreg_db/forms/patient_finding_intervention_form.py +18 -0
  231. endoreg_db/forms/patient_form.py +27 -0
  232. endoreg_db/forms/questionnaires/__init__.py +1 -0
  233. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  234. endoreg_db/forms/settings/__init__.py +8 -0
  235. endoreg_db/forms/unit.py +6 -0
  236. endoreg_db/helpers/__init__.py +0 -0
  237. endoreg_db/helpers/count_db.py +45 -0
  238. endoreg_db/helpers/data_loader.py +208 -0
  239. endoreg_db/helpers/default_objects.py +378 -0
  240. endoreg_db/helpers/download_segmentation_model.py +31 -0
  241. endoreg_db/helpers/interact.py +6 -0
  242. endoreg_db/helpers/test_video_helper.py +119 -0
  243. endoreg_db/logger_conf.py +140 -0
  244. endoreg_db/management/__init__.py +1 -0
  245. endoreg_db/management/commands/__init__.py +1 -0
  246. endoreg_db/management/commands/anonymize_video.py +0 -0
  247. endoreg_db/management/commands/check_auth.py +125 -0
  248. endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
  249. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  250. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  251. endoreg_db/management/commands/fix_video_paths.py +165 -0
  252. endoreg_db/management/commands/import_fallback_video.py +203 -0
  253. endoreg_db/management/commands/import_report.py +298 -0
  254. endoreg_db/management/commands/import_video.py +423 -0
  255. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  256. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  257. endoreg_db/management/commands/load_ai_model_data.py +77 -0
  258. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  259. endoreg_db/management/commands/load_base_db_data.py +192 -0
  260. endoreg_db/management/commands/load_center_data.py +68 -0
  261. endoreg_db/management/commands/load_contraindication_data.py +41 -0
  262. endoreg_db/management/commands/load_disease_classification_choices_data.py +41 -0
  263. endoreg_db/management/commands/load_disease_classification_data.py +41 -0
  264. endoreg_db/management/commands/load_disease_data.py +62 -0
  265. endoreg_db/management/commands/load_distribution_data.py +66 -0
  266. endoreg_db/management/commands/load_endoscope_data.py +68 -0
  267. endoreg_db/management/commands/load_event_data.py +41 -0
  268. endoreg_db/management/commands/load_examination_data.py +75 -0
  269. endoreg_db/management/commands/load_examination_indication_data.py +86 -0
  270. endoreg_db/management/commands/load_finding_data.py +128 -0
  271. endoreg_db/management/commands/load_gender_data.py +44 -0
  272. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +132 -0
  273. endoreg_db/management/commands/load_information_source.py +51 -0
  274. endoreg_db/management/commands/load_lab_value_data.py +50 -0
  275. endoreg_db/management/commands/load_medication_data.py +103 -0
  276. endoreg_db/management/commands/load_name_data.py +37 -0
  277. endoreg_db/management/commands/load_organ_data.py +43 -0
  278. endoreg_db/management/commands/load_pdf_type_data.py +61 -0
  279. endoreg_db/management/commands/load_profession_data.py +44 -0
  280. endoreg_db/management/commands/load_qualification_data.py +59 -0
  281. endoreg_db/management/commands/load_report_reader_flag_data.py +46 -0
  282. endoreg_db/management/commands/load_requirement_data.py +180 -0
  283. endoreg_db/management/commands/load_risk_data.py +56 -0
  284. endoreg_db/management/commands/load_shift_data.py +60 -0
  285. endoreg_db/management/commands/load_tag_data.py +57 -0
  286. endoreg_db/management/commands/load_unit_data.py +46 -0
  287. endoreg_db/management/commands/load_user_groups.py +28 -0
  288. endoreg_db/management/commands/register_ai_model.py +64 -0
  289. endoreg_db/management/commands/reset_celery_schedule.py +9 -0
  290. endoreg_db/management/commands/setup_endoreg_db.py +381 -0
  291. endoreg_db/management/commands/start_filewatcher.py +106 -0
  292. endoreg_db/management/commands/storage_management.py +548 -0
  293. endoreg_db/management/commands/summarize_db_content.py +189 -0
  294. endoreg_db/management/commands/validate_video.py +204 -0
  295. endoreg_db/management/commands/validate_video_files.py +161 -0
  296. endoreg_db/management/commands/video_validation.py +22 -0
  297. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  298. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  299. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
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  607. endoreg_db/tasks/video_processing_tasks.py +327 -0
  608. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  609. endoreg_db/templates/admin/start_examination.html +12 -0
  610. endoreg_db/templates/timeline.html +176 -0
  611. endoreg_db/urls/__init__.py +70 -0
  612. endoreg_db/urls/anonymization.py +32 -0
  613. endoreg_db/urls/auth.py +16 -0
  614. endoreg_db/urls/classification.py +39 -0
  615. endoreg_db/urls/examination.py +54 -0
  616. endoreg_db/urls/files.py +6 -0
  617. endoreg_db/urls/label_video_segment_validate.py +33 -0
  618. endoreg_db/urls/label_video_segments.py +44 -0
  619. endoreg_db/urls/media.py +226 -0
  620. endoreg_db/urls/patient.py +19 -0
  621. endoreg_db/urls/report.py +48 -0
  622. endoreg_db/urls/requirements.py +13 -0
  623. endoreg_db/urls/sensitive_meta.py +0 -0
  624. endoreg_db/urls/stats.py +46 -0
  625. endoreg_db/urls/upload.py +20 -0
  626. endoreg_db/urls/video.py +61 -0
  627. endoreg_db/urls.py +9 -0
  628. endoreg_db/utils/__init__.py +88 -0
  629. endoreg_db/utils/ai/__init__.py +9 -0
  630. endoreg_db/utils/ai/get.py +5 -0
  631. endoreg_db/utils/ai/inference_dataset.py +52 -0
  632. endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
  633. endoreg_db/utils/ai/postprocess.py +63 -0
  634. endoreg_db/utils/ai/predict.py +291 -0
  635. endoreg_db/utils/ai/preprocess.py +68 -0
  636. endoreg_db/utils/calc_duration_seconds.py +24 -0
  637. endoreg_db/utils/case_generator/__init__.py +0 -0
  638. endoreg_db/utils/case_generator/case_generator.py +159 -0
  639. endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
  640. endoreg_db/utils/case_generator/utils.py +30 -0
  641. endoreg_db/utils/check_video_files.py +148 -0
  642. endoreg_db/utils/cropping.py +29 -0
  643. endoreg_db/utils/dataloader.py +175 -0
  644. endoreg_db/utils/dates.py +60 -0
  645. endoreg_db/utils/env.py +33 -0
  646. endoreg_db/utils/extract_specific_frames.py +72 -0
  647. endoreg_db/utils/file_operations.py +58 -0
  648. endoreg_db/utils/fix_video_path_direct.py +141 -0
  649. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  650. endoreg_db/utils/hashs.py +153 -0
  651. endoreg_db/utils/links/__init__.py +0 -0
  652. endoreg_db/utils/links/requirement_link.py +193 -0
  653. endoreg_db/utils/mime_types.py +0 -0
  654. endoreg_db/utils/names.py +76 -0
  655. endoreg_db/utils/ocr.py +190 -0
  656. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  657. endoreg_db/utils/paths.py +95 -0
  658. endoreg_db/utils/permissions.py +143 -0
  659. endoreg_db/utils/pipelines/Readme.md +235 -0
  660. endoreg_db/utils/pipelines/__init__.py +0 -0
  661. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  662. endoreg_db/utils/product/__init__.py +0 -0
  663. endoreg_db/utils/product/sum_emissions.py +20 -0
  664. endoreg_db/utils/product/sum_weights.py +18 -0
  665. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  666. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  667. endoreg_db/utils/requirement_helpers.py +0 -0
  668. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  669. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  670. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  671. endoreg_db/utils/setup_config.py +177 -0
  672. endoreg_db/utils/translation.py +27 -0
  673. endoreg_db/utils/uuid.py +4 -0
  674. endoreg_db/utils/validate_endo_roi.py +19 -0
  675. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  676. endoreg_db/utils/validate_video_detailed.py +357 -0
  677. endoreg_db/utils/video/__init__.py +26 -0
  678. endoreg_db/utils/video/extract_frames.py +88 -0
  679. endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
  680. endoreg_db/utils/video/names.py +42 -0
  681. endoreg_db/utils/video/streaming_processor.py +312 -0
  682. endoreg_db/utils/video/video_splitter.py +94 -0
  683. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  684. endoreg_db/views/__init__.py +272 -0
  685. endoreg_db/views/anonymization/__init__.py +27 -0
  686. endoreg_db/views/anonymization/media_management.py +454 -0
  687. endoreg_db/views/anonymization/overview.py +216 -0
  688. endoreg_db/views/anonymization/validate.py +107 -0
  689. endoreg_db/views/auth/__init__.py +13 -0
  690. endoreg_db/views/auth/keycloak.py +113 -0
  691. endoreg_db/views/examination/__init__.py +33 -0
  692. endoreg_db/views/examination/examination.py +37 -0
  693. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  694. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  695. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  696. endoreg_db/views/examination/get_findings.py +41 -0
  697. endoreg_db/views/examination/get_instruments.py +18 -0
  698. endoreg_db/views/examination/get_interventions.py +14 -0
  699. endoreg_db/views/finding/__init__.py +9 -0
  700. endoreg_db/views/finding/finding.py +112 -0
  701. endoreg_db/views/finding/get_classifications.py +14 -0
  702. endoreg_db/views/finding/get_interventions.py +17 -0
  703. endoreg_db/views/finding_classification/__init__.py +13 -0
  704. endoreg_db/views/finding_classification/base.py +0 -0
  705. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  706. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  707. endoreg_db/views/label/__init__.py +5 -0
  708. endoreg_db/views/label/label.py +15 -0
  709. endoreg_db/views/label_video_segment/__init__.py +16 -0
  710. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  711. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  712. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  713. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  714. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  715. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  716. endoreg_db/views/label_video_segment/validate.py +226 -0
  717. endoreg_db/views/media/__init__.py +45 -0
  718. endoreg_db/views/media/pdf_media.py +386 -0
  719. endoreg_db/views/media/segments.py +71 -0
  720. endoreg_db/views/media/sensitive_metadata.py +314 -0
  721. endoreg_db/views/media/video_media.py +272 -0
  722. endoreg_db/views/media/video_segments.py +524 -0
  723. endoreg_db/views/meta/__init__.py +15 -0
  724. endoreg_db/views/meta/available_files_list.py +146 -0
  725. endoreg_db/views/meta/report_meta.py +53 -0
  726. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  727. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  728. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  729. endoreg_db/views/misc/__init__.py +63 -0
  730. endoreg_db/views/misc/center.py +13 -0
  731. endoreg_db/views/misc/csrf.py +7 -0
  732. endoreg_db/views/misc/gender.py +14 -0
  733. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  734. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  735. endoreg_db/views/misc/secure_url_validate.py +79 -0
  736. endoreg_db/views/misc/stats.py +220 -0
  737. endoreg_db/views/misc/translation.py +182 -0
  738. endoreg_db/views/misc/upload_views.py +240 -0
  739. endoreg_db/views/patient/__init__.py +5 -0
  740. endoreg_db/views/patient/patient.py +210 -0
  741. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  742. endoreg_db/views/patient_examination/__init__.py +11 -0
  743. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  744. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  745. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  746. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  747. endoreg_db/views/patient_examination/video.py +194 -0
  748. endoreg_db/views/patient_finding/__init__.py +7 -0
  749. endoreg_db/views/patient_finding/base.py +0 -0
  750. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  751. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  752. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  753. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  754. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  755. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  756. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  757. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  758. endoreg_db/views/pdf/__init__.py +11 -0
  759. endoreg_db/views/pdf/pdf_media.py +239 -0
  760. endoreg_db/views/pdf/pdf_stream_views.py +127 -0
  761. endoreg_db/views/pdf/reimport.py +161 -0
  762. endoreg_db/views/report/__init__.py +9 -0
  763. endoreg_db/views/report/report_list.py +112 -0
  764. endoreg_db/views/report/report_with_secure_url.py +28 -0
  765. endoreg_db/views/report/start_examination.py +7 -0
  766. endoreg_db/views/requirement/__init__.py +10 -0
  767. endoreg_db/views/requirement/evaluate.py +279 -0
  768. endoreg_db/views/requirement/lookup.py +483 -0
  769. endoreg_db/views/requirement/lookup_store.py +252 -0
  770. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  771. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  772. endoreg_db/views/stats/__init__.py +13 -0
  773. endoreg_db/views/stats/stats_views.py +229 -0
  774. endoreg_db/views/video/__init__.py +61 -0
  775. endoreg_db/views/video/correction.py +530 -0
  776. endoreg_db/views/video/reimport.py +195 -0
  777. endoreg_db/views/video/segmentation.py +274 -0
  778. endoreg_db/views/video/task_status.py +49 -0
  779. endoreg_db/views/video/timeline.py +46 -0
  780. endoreg_db/views/video/video_analyze.py +52 -0
  781. endoreg_db/views/video/video_apply_mask.py +48 -0
  782. endoreg_db/views/video/video_correction.py +21 -0
  783. endoreg_db/views/video/video_download_processed.py +58 -0
  784. endoreg_db/views/video/video_examination_viewset.py +329 -0
  785. endoreg_db/views/video/video_media.py +158 -0
  786. endoreg_db/views/video/video_meta.py +29 -0
  787. endoreg_db/views/video/video_processing_history.py +24 -0
  788. endoreg_db/views/video/video_remove_frames.py +48 -0
  789. endoreg_db/views/video/video_stream.py +306 -0
  790. endoreg_db/views.py +0 -0
  791. endoreg_db-0.8.5.1.dist-info/METADATA +383 -0
  792. endoreg_db-0.8.5.1.dist-info/RECORD +794 -0
  793. endoreg_db-0.8.5.1.dist-info/WHEEL +4 -0
  794. endoreg_db-0.8.5.1.dist-info/licenses/LICENSE +674 -0
endoreg_db/data/finding/anatomy_colon.yaml ADDED
@@ -0,0 +1,128 @@
1
+ - model: endoreg_db.finding
2
+ fields:
3
+ name: "cecum"
4
+ description: "Anatomical structure: Cecum"
5
+ examinations:
6
+ [
7
+ "colonoscopy",
8
+ "colonoscopy_austria_screening",
9
+ ]
10
+
11
+ finding_types: ["anatomy", "anatomy_colon"]
12
+
13
+ - model: endoreg_db.finding
14
+ fields:
15
+ name: "terminal_ileum"
16
+ description: "Anatomical structure: Terminal ileum"
17
+ examinations:
18
+ [
19
+ "colonoscopy",
20
+ "colonoscopy_austria_screening",
21
+ ]
22
+ finding_types: ["anatomy", "anatomy_colon"]
23
+
24
+ - model: endoreg_db.finding
25
+ fields:
26
+ name: "ileocecal_valve"
27
+ description: "Anatomical structure: Ileocecal valve"
28
+ examinations:
29
+ [
30
+ "colonoscopy",
31
+ "colonoscopy_austria_screening",
32
+ ]
33
+ finding_types: ["anatomy", "anatomy_colon"]
34
+
35
+ - model: endoreg_db.finding
36
+ fields:
37
+ name: "ascending_colon"
38
+ description: "Anatomical structure: Ascending colon"
39
+ examinations:
40
+ [
41
+ "colonoscopy",
42
+ "colonoscopy_austria_screening",
43
+ ]
44
+ finding_types: ["anatomy", "anatomy_colon"]
45
+
46
+ # "right_flexure",
47
+ - model: endoreg_db.finding
48
+ fields:
49
+ name: "right_flexure"
50
+ description: "Anatomical structure: Right flexure"
51
+ examinations:
52
+ [
53
+ "colonoscopy",
54
+ "colonoscopy_austria_screening",
55
+ ]
56
+ finding_types: ["anatomy", "anatomy_colon"]
57
+
58
+ # "transverse_colon",
59
+ - model: endoreg_db.finding
60
+ fields:
61
+ name: "transverse_colon"
62
+ description: "Anatomical structure: Transverse colon"
63
+ examinations:
64
+ [
65
+ "colonoscopy",
66
+ "colonoscopy_austria_screening",
67
+ ]
68
+ finding_types: ["anatomy", "anatomy_colon"]
69
+
70
+ # "left_flexure",
71
+ - model: endoreg_db.finding
72
+ fields:
73
+ name: "left_flexure"
74
+ description: "Anatomical structure: Left flexure"
75
+ examinations:
76
+ [
77
+ "colonoscopy",
78
+ "colonoscopy_austria_screening",
79
+ ]
80
+ finding_types: ["anatomy", "anatomy_colon"]
81
+
82
+ # "descending_colon",
83
+ - model: endoreg_db.finding
84
+ fields:
85
+ name: "descending_colon"
86
+ description: "Anatomical structure: Descending colon"
87
+ examinations:
88
+ [
89
+ "colonoscopy",
90
+ "colonoscopy_austria_screening",
91
+ ]
92
+ finding_types: ["anatomy", "anatomy_colon"]
93
+
94
+ # "sigmoid_colon",
95
+ - model: endoreg_db.finding
96
+ fields:
97
+ name: "sigmoid_colon"
98
+ description: "Anatomical structure: Sigmoid colon"
99
+ examinations:
100
+ [
101
+ "colonoscopy",
102
+ "colonoscopy_austria_screening",
103
+ ]
104
+ finding_types: ["anatomy", "anatomy_colon"]
105
+
106
+ # "rectum",
107
+ - model: endoreg_db.finding
108
+ fields:
109
+ name: "rectum"
110
+ description: "Anatomical structure: Rectum"
111
+ examinations:
112
+ [
113
+ "colonoscopy",
114
+ "colonoscopy_austria_screening",
115
+ ]
116
+ finding_types: ["anatomy", "anatomy_colon"]
117
+
118
+ # "rectum_anus",
119
+ - model: endoreg_db.finding
120
+ fields:
121
+ name: "rectum_anus"
122
+ description: "Anatomical structure: Rectum and anus"
123
+ examinations:
124
+ [
125
+ "colonoscopy",
126
+ "colonoscopy_austria_screening",
127
+ ]
128
+ finding_types: ["anatomy", "anatomy_colon"]
endoreg_db/data/finding/colonoscopy.yaml ADDED
@@ -0,0 +1,40 @@
1
+ - model: endoreg_db.finding
2
+ fields:
3
+ name: "colon_polyp"
4
+ name_de: "Kolonpolyp"
5
+ name_en: "Colon Polyp"
6
+
7
+ finding_interventions:
8
+ [
9
+ "colon_lesion_polypectomy_cold_snare",
10
+ "colon_lesion_polypectomy_hot_snare",
11
+ "colon_lesion_injection_liftup",
12
+ "colon_lesion_injection_vasoactive",
13
+ "colon_lesion_biopsy",
14
+ "colon_lesion_emr",
15
+ "colon_lesion_esd",
16
+ "colon_lesion_eftr",
17
+ "colon_lesion_clip",
18
+ ]
19
+ examinations: ["colonoscopy", "colonoscopy_austria_screening"]
20
+
21
+ finding_types: ["macroscopic"]
22
+
23
+ - model: endoreg_db.finding
24
+ fields:
25
+ name: "colonoscopy_complete"
26
+ examinations:
27
+ [
28
+ "colonoscopy",
29
+ "colonoscopy_austria_screening",
30
+ ]
31
+ finding_types: ["summary"]
32
+
33
+ - model: endoreg_db.finding
34
+ fields:
35
+ name: "colonoscopy_austria_screening_findings_summary"
36
+ examinations:
37
+ [
38
+ "colonoscopy_austria_screening",
39
+ ]
40
+ finding_types: ["summary"]
endoreg_db/data/finding/colonoscopy_bowel_prep.yaml ADDED
@@ -0,0 +1,56 @@
1
+ - model: endoreg_db.finding
2
+ fields:
3
+ name: "bowel_preparation_lc"
4
+ name_de: "Darmvorbereitung (Linkes Kolon)"
5
+ name_en: "Bowel Preparation (Left Colon)"
6
+ examinations:
7
+ [
8
+ "colonoscopy",
9
+ ]
10
+
11
+ finding_types: ["macroscopic"]
12
+
13
+ - model: endoreg_db.finding
14
+ fields:
15
+ name: "bowel_preparation_tc"
16
+ name_de: "Darmvorbereitung (Kolon Transversum)"
17
+ name_en: "Bowel Preparation (Transverse Colon)"
18
+ examinations:
19
+ [
20
+ "colonoscopy",
21
+ ]
22
+
23
+ finding_types: ["macroscopic"]
24
+
25
+ - model: endoreg_db.finding
26
+ fields:
27
+ name: "bowel_preparation_rc"
28
+ name_de: "Darmvorbereitung (Rechtes Kolon)"
29
+ name_en: "Bowel Preparation (Right Colon)"
30
+ examinations:
31
+ [
32
+ "colonoscopy",
33
+ ]
34
+
35
+ finding_types: ["macroscopic"]
36
+
37
+ - model: endoreg_db.finding
38
+ fields:
39
+ name: "bowel_preparation_simplified"
40
+ name_de: "Darmvorbereitung (Vereinfacht)"
41
+ name_en: "Bowel Preparation (Simplified)"
42
+ examinations:
43
+ [
44
+ "colonoscopy",
45
+ ]
46
+
47
+ finding_types: ["macroscopic"]
48
+
49
+ - model: endoreg_db.finding
50
+ fields:
51
+ name: "bowel_prep_screening_austria"
52
+ examinations:
53
+ [
54
+ "colonoscopy_austria_screening",
55
+ ]
56
+ finding_types: ["macroscopic"]
endoreg_db/data/finding/complication.yaml ADDED
@@ -0,0 +1,16 @@
1
+ - model: endoreg_db.finding
2
+ fields:
3
+ name: "complication"
4
+ examinations: [
5
+ "gastroscopy",
6
+ "endosonography_upper_gi",
7
+ "endosonography_lower_gi",
8
+ "ercp",
9
+ "small_bowel_endoscopy",
10
+ "capsule_endoscopy",
11
+ "percutaneous_transhepatic_biliary_drainage",
12
+ "colonoscopy",
13
+ "colonoscopy_austria_screening",
14
+ ]
15
+
16
+ finding_types: ["complication"]
endoreg_db/data/finding/data.yaml ADDED
@@ -0,0 +1,105 @@
1
+ - model: endoreg_db.finding
2
+ fields:
3
+ name: "placeholder"
4
+ name_de: "Platzhalter"
5
+ name_en: "Placeholder"
6
+ description: "This is a placeholder finding."
7
+
8
+ - model: endoreg_db.finding
9
+ fields:
10
+ name: "post-intervention-wound"
11
+ name_de: "Postinterventionelle Wunde"
12
+ finding_interventions: ["colon_lesion_clip"]
13
+ examinations: [
14
+ "colonoscopy"
15
+ ]
16
+
17
+ finding_types: ["macroscopic"]
18
+
19
+ - model: endoreg_db.finding
20
+ fields:
21
+ name: "tumor"
22
+ name_de: "Tumor"
23
+ name_en: "Tumor"
24
+ finding_interventions: []
25
+ examinations:
26
+ [
27
+ "colonoscopy",
28
+ "endosonography_upper_gi",
29
+ "endosonography_lower_gi",
30
+ "ercp",
31
+ "small_bowel_endoscopy",
32
+ "capsule_endoscopy",
33
+ ]
34
+
35
+ finding_types: ["macroscopic"]
36
+
37
+ - model: endoreg_db.finding
38
+ fields:
39
+ name: "inflammation"
40
+ name_de: "Entzündung"
41
+ name_en: "Inflammation"
42
+ finding_interventions: []
43
+ examinations:
44
+ [
45
+ "colonoscopy",
46
+ "endosonography_upper_gi",
47
+ "endosonography_lower_gi",
48
+ "ercp",
49
+ "small_bowel_endoscopy",
50
+ "capsule_endoscopy",
51
+ ]
52
+ finding_types: ["macroscopic"]
53
+
54
+ - model: endoreg_db.finding
55
+ fields:
56
+ name: "erosion"
57
+ name_de: "Erosion"
58
+ name_en: "Erosion"
59
+ finding_interventions: []
60
+ examinations:
61
+ [
62
+ "colonoscopy",
63
+ "endosonography_upper_gi",
64
+ "endosonography_lower_gi",
65
+ "ercp",
66
+ "small_bowel_endoscopy",
67
+ "capsule_endoscopy",
68
+ ]
69
+
70
+ finding_types: ["macroscopic"]
71
+
72
+ - model: endoreg_db.finding
73
+ fields:
74
+ name: "ulcer"
75
+ name_de: "Ulcus"
76
+ name_en: "Ulcer"
77
+ finding_interventions: []
78
+ examinations:
79
+ [
80
+ "colonoscopy",
81
+ "endosonography_upper_gi",
82
+ "endosonography_lower_gi",
83
+ "ercp",
84
+ "small_bowel_endoscopy",
85
+ "capsule_endoscopy",
86
+ ]
87
+ finding_types: ["macroscopic"]
88
+
89
+ - model: endoreg_db.finding
90
+ fields:
91
+ name: "scar"
92
+ name_de: "Narbe"
93
+ name_en: "Scar"
94
+ finding_interventions: []
95
+ examinations:
96
+ [
97
+ "colonoscopy",
98
+ "endosonography_upper_gi",
99
+ "endosonography_lower_gi",
100
+ "ercp",
101
+ "small_bowel_endoscopy",
102
+ "capsule_endoscopy",
103
+ ]
104
+
105
+ finding_types: ["macroscopic"]
endoreg_db/data/finding/examination_setting.yaml ADDED
@@ -0,0 +1,16 @@
1
+ - model: endoreg_db.finding
2
+ fields:
3
+ name: "examination_setting"
4
+ examinations: [
5
+ "gastroscopy",
6
+ "endosonography_upper_gi",
7
+ "endosonography_lower_gi",
8
+ "ercp",
9
+ "small_bowel_endoscopy",
10
+ "capsule_endoscopy",
11
+ "percutaneous_transhepatic_biliary_drainage",
12
+ "colonoscopy",
13
+ "colonoscopy_austria_screening",
14
+ ]
15
+
16
+ finding_types: ["summary"]
endoreg_db/data/finding/medication_related.yaml ADDED
@@ -0,0 +1,18 @@
1
+ - model: endoreg_db.finding
2
+ fields:
3
+ name: "sedation"
4
+ description: "Sedation during an examination"
5
+ examinations:
6
+ [
7
+ "gastroscopy",
8
+ "endosonography_upper_gi",
9
+ "endosonography_lower_gi",
10
+ "ercp",
11
+ "small_bowel_endoscopy",
12
+ "capsule_endoscopy",
13
+ "percutaneous_transhepatic_biliary_drainage",
14
+ "colonoscopy",
15
+ "colonoscopy_austria_screening",
16
+ ]
17
+
18
+ finding_types: ["medication_related"]
endoreg_db/data/finding/outcome.yaml ADDED
@@ -0,0 +1,12 @@
1
+ - model: endoreg_db.finding
2
+ fields:
3
+ name: "colonoscopy_austria_screening_outcome"
4
+ description: "Outcome of colonoscopy Austria screening."
5
+ examinations:
6
+ [
7
+ "colonoscopy_austria_screening",
8
+ ]
9
+ finding_types:
10
+ [
11
+ "summary"
12
+ ]
endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml ADDED
@@ -0,0 +1,95 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "bowel_prep_boston"
4
+ classification_types: [
5
+ "bowel_prep"
6
+ ]
7
+ name_de: "Boston Bowel Preparation Scale"
8
+ name_en: "Boston Bowel Preparation Scale"
9
+ examinations: [
10
+ "colonoscopy"
11
+ ]
12
+ findings: [
13
+ "bowel_preparation_lc",
14
+ "bowel_preparation_tc",
15
+ "bowel_preparation_rc",
16
+
17
+ ]
18
+ choices: [
19
+ "bowel_prep_boston_0",
20
+ "bowel_prep_boston_1",
21
+ "bowel_prep_boston_2",
22
+ "bowel_prep_boston_3"
23
+ ]
24
+
25
+ - model: endoreg_db.finding_classification
26
+ fields:
27
+ name: "bowel_prep_boston_simplified"
28
+ classification_types: [
29
+ "bowel_prep"
30
+ ]
31
+ name_de: "Boston Bowel Preparation Scale"
32
+ name_en: "Boston Bowel Preparation Scale"
33
+ examinations: [
34
+ "colonoscopy"
35
+ ]
36
+ findings: [
37
+ "bowel_preparation_simplified"
38
+ ]
39
+ choices: [
40
+ "bowel_prep_boston_0",
41
+ "bowel_prep_boston_1",
42
+ "bowel_prep_boston_2",
43
+ "bowel_prep_boston_3"
44
+ ]
45
+
46
+
47
+ #Aronchick
48
+ - model: endoreg_db.finding_classification
49
+ fields:
50
+ name: "bowel_prep_aronchick"
51
+ classification_types: [
52
+ "bowel_prep"
53
+ ]
54
+ name_de: "Aronchick Bowel Preparation Scale"
55
+ name_en: "Aronchick Bowel Preparation Scale"
56
+ examinations: [
57
+ "colonoscopy"
58
+ ]
59
+ findings: [
60
+ "bowel_preparation_lc",
61
+ "bowel_preparation_tc",
62
+ "bowel_preparation_rc",
63
+ ]
64
+ choices: [
65
+ "bowel_prep_aronchick_0",
66
+ "bowel_prep_aronchick_1",
67
+ "bowel_prep_aronchick_2",
68
+ "bowel_prep_aronchick_3"
69
+ ]
70
+
71
+ # Screening Austria
72
+ # Choices are "bowel_prep_perfect", "bowel_prep_good",
73
+ # "bowel_prep_fair", "bowel_prep_poor", "bowel_prep_poor_in_rc_only"
74
+
75
+ - model: endoreg_db.finding_classification
76
+ fields:
77
+ name: "bowel_prep_screening_austria"
78
+ classification_types: [
79
+ "bowel_prep"
80
+ ]
81
+ name_de: "Darmvorbereitung Screening Österreich"
82
+ name_en: "Bowel Preparation Screening Austria"
83
+ examinations: [
84
+ "colonoscopy_austria_screening"
85
+ ]
86
+ findings: [
87
+ "bowel_prep_screening_austria"
88
+ ]
89
+ choices: [
90
+ "bowel_prep_perfect",
91
+ "bowel_prep_good",
92
+ "bowel_prep_fair",
93
+ "bowel_prep_poor",
94
+ "bowel_prep_poor_in_rc_only"
95
+ ]
endoreg_db/data/finding_classification/colonoscopy_jnet.yaml ADDED
@@ -0,0 +1,22 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "colon_lesion_jnet"
5
+ name_de: "Kolonläsion - JNET"
6
+ name_en: "Colon lesion - JNET"
7
+ classification_types: [
8
+ "morphology",
9
+ "colon_lesion_advanced_imaging",
10
+ ]
11
+ examinations: [
12
+ "colonoscopy"
13
+ ]
14
+ findings: [
15
+ "colon_polyp",
16
+ ]
17
+ choices: [
18
+ "colon_lesion_jnet_1",
19
+ "colon_lesion_jnet_2a",
20
+ "colon_lesion_jnet_2b",
21
+ "colon_lesion_jnet_3",
22
+ ]
endoreg_db/data/finding_classification/colonoscopy_kudo.yaml ADDED
@@ -0,0 +1,25 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "colon_lesion_kudo"
5
+ classification_types: [
6
+ "colon_lesion_advanced_imaging",
7
+ "morphology"
8
+ ]
9
+ name_de: "Oberflächenklassifikation Kolonläsion"
10
+ name_en: "Colon Lesion Surface Classification"
11
+ examinations: [
12
+ "colonoscopy"
13
+ ]
14
+ findings: [
15
+ "colon_polyp",
16
+ ]
17
+ choices: [
18
+ "colon_lesion_kudo_1",
19
+ "colon_lesion_kudo_2",
20
+ "colon_lesion_kudo_3s",
21
+ "colon_lesion_kudo_3l",
22
+ "colon_lesion_kudo_4",
23
+ "colon_lesion_kudo_5i",
24
+ "colon_lesion_kudo_5n",
25
+ ]
endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml ADDED
@@ -0,0 +1,20 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "colon_lesion_circularity_default"
5
+ name_de: "Kolonläsion - Zirkularität"
6
+ name_en: "Colon lesion - circularity"
7
+ classification_types: [
8
+ "colon_lesion_circularity",
9
+ "morphology"
10
+ ]
11
+ examinations: [
12
+ "colonoscopy"
13
+ ]
14
+ findings: [
15
+ "colon_polyp",
16
+ ]
17
+ choices: [
18
+ "colon_lesion_circularity_false",
19
+ "colon_lesion_circularity_true"
20
+ ]
endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml ADDED
@@ -0,0 +1,24 @@
1
+
2
+ - model: endoreg_db.finding_classification
3
+ fields:
4
+ name: "colon_lesion_planarity_default"
5
+ classification_types: [
6
+ "colon_lesion_planarity",
7
+ "morphology"
8
+ ]
9
+ name_de: "Planaritätsklassifikation Kolonläsion"
10
+ name_en: "Colon Lesion Planarity Classification"
11
+ examinations: [
12
+ "colonoscopy"
13
+ ]
14
+ findings: [
15
+ "colon_polyp",
16
+ ]
17
+ choices: [
18
+ "colon_lesion_planarity_flat",
19
+ "colon_lesion_planarity_flat_elevated",
20
+ "colon_lesion_planarity_sessile",
21
+ "colon_lesion_planarity_pedunculated",
22
+ "colon_lesion_planarity_excavated",
23
+ "colon_lesion_planarity_unknown"
24
+ ]
endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml ADDED
@@ -0,0 +1,68 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "colon_lesion_size_categorical"
4
+ classification_types: [
5
+ "colon_lesion_size",
6
+ "morphology"
7
+ ]
8
+ name_de: "Größenklassifikation Kolonläsion (kategorisch)"
9
+ name_en: "Colon Lesion Size Classification (categorical)"
10
+ examinations: [
11
+ "colonoscopy"
12
+ ]
13
+ findings: [
14
+ "colon_polyp",
15
+ "tumor",
16
+ "erosion",
17
+ "ulcer",
18
+ "scar"
19
+ ]
20
+ choices: [
21
+ "colon_lesion_size_categorical_diminutive",
22
+ "colon_lesion_size_categorical_small",
23
+ "colon_lesion_size_categorical_medium",
24
+ "colon_lesion_size_categorical_large"
25
+ ]
26
+
27
+ - model: endoreg_db.finding_classification
28
+ fields:
29
+ name: "colon_lesion_size_mm"
30
+ classification_types: [
31
+ "colon_lesion_size",
32
+ "morphology"
33
+ ]
34
+ name_de: "Größenklassifikation Kolonläsion (numerisch)"
35
+ name_en: "Colon Lesion Size Classification (numerical)"
36
+ examinations: [
37
+ "colonoscopy"
38
+ ]
39
+ findings: [
40
+ "colon_polyp",
41
+ "tumor",
42
+ "erosion",
43
+ "ulcer",
44
+ "scar"
45
+ ]
46
+ choices: [
47
+ "colon_lesion_size_oval_mm"
48
+ ]
49
+
50
+ - model: endoreg_db.finding_classification
51
+ fields:
52
+ name: "colon_lesion_size_austria_categorical"
53
+ classification_types: [
54
+ "colon_lesion_size",
55
+ "morphology"
56
+ ]
57
+ examinations: [
58
+ "colonoscopy_austria_screening"
59
+ ]
60
+ findings: [
61
+ "colon_polyp",
62
+ ]
63
+ choices: [
64
+ "colon_lesion_size_austria_categorical_0_5",
65
+ "colon_lesion_size_austria_categorical_6_9",
66
+ "colon_lesion_size_austria_categorical_10_20",
67
+ "colon_lesion_size_austria_categorical_21_x"
68
+ ]
endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml ADDED
@@ -0,0 +1,20 @@
1
+ - model: endoreg_db.finding_classification
2
+ fields:
3
+ name: "colon_lesion_surface_intact_default"
4
+ classification_types: [
5
+ "colon_lesion_surface_intact",
6
+ "morphology"
7
+ ]
8
+ name_de: "Oberflächenklassifikation Kolonläsion"
9
+ name_en: "Colon Lesion Surface Classification"
10
+ examinations: [
11
+ "colonoscopy"
12
+ ]
13
+ findings: [
14
+ "colon_polyp",
15
+ ]
16
+ choices: [
17
+ "colon_lesion_surface_intact",
18
+ "colon_lesion_surface_eroded",
19
+ "colon_lesion_surface_ulcerated"
20
+ ]