endoreg-db 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

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  1. endoreg_db/case_generator/__init__.py +0 -0
  2. endoreg_db/case_generator/case_generator.py +159 -0
  3. endoreg_db/case_generator/lab_sample_factory.py +33 -0
  4. endoreg_db/case_generator/utils.py +30 -0
  5. endoreg_db/data/__init__.py +118 -0
  6. endoreg_db/data/agl_service/data.yaml +19 -0
  7. endoreg_db/data/ai_model/data.yaml +7 -0
  8. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  9. endoreg_db/data/ai_model_label/label-set/data.yaml +21 -0
  10. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  11. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +5 -0
  12. endoreg_db/data/ai_model_type/data.yaml +7 -0
  13. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  14. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  15. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  16. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  17. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  18. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  19. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  20. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  21. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  22. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  23. endoreg_db/data/case_template/rule_value/.init +0 -0
  24. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  25. endoreg_db/data/case_template/template/base.yaml +8 -0
  26. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  27. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  28. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  29. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  30. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  31. endoreg_db/data/center/data.yaml +90 -0
  32. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  33. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  34. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  35. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  36. endoreg_db/data/disease/hepatology.yaml +5 -0
  37. endoreg_db/data/disease/misc.yaml +6 -0
  38. endoreg_db/data/disease/renal.yaml +5 -0
  39. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  40. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  41. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  42. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  43. endoreg_db/data/distribution/date/patient.yaml +7 -0
  44. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  45. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  46. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  47. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  48. endoreg_db/data/endoscope/data.yaml +93 -0
  49. endoreg_db/data/endoscope_type/data.yaml +11 -0
  50. endoreg_db/data/endoscopy_processor/data.yaml +47 -0
  51. endoreg_db/data/event/cardiology.yaml +28 -0
  52. endoreg_db/data/event/neurology.yaml +14 -0
  53. endoreg_db/data/event/surgery.yaml +13 -0
  54. endoreg_db/data/event/thrombembolism.yaml +20 -0
  55. endoreg_db/data/examination/examinations/data.yaml +66 -0
  56. endoreg_db/data/examination/time/data.yaml +48 -0
  57. endoreg_db/data/examination/time-type/data.yaml +8 -0
  58. endoreg_db/data/examination/type/data.yaml +5 -0
  59. endoreg_db/data/examination_indication/endoscopy.yaml +8 -0
  60. endoreg_db/data/examination_indication_classification/endoscopy.yaml +8 -0
  61. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  62. endoreg_db/data/finding/data.yaml +141 -0
  63. endoreg_db/data/finding_intervention/endoscopy.yaml +138 -0
  64. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  65. endoreg_db/data/finding_location_classification/colonoscopy.yaml +46 -0
  66. endoreg_db/data/finding_location_classification_choice/colonoscopy.yaml +240 -0
  67. endoreg_db/data/finding_morphology_classification/colonoscopy.yaml +48 -0
  68. endoreg_db/data/finding_morphology_classification_choice/colon_lesion_circularity_default.yaml +34 -0
  69. endoreg_db/data/finding_morphology_classification_choice/colon_lesion_nice.yaml +20 -0
  70. endoreg_db/data/finding_morphology_classification_choice/colon_lesion_paris.yaml +65 -0
  71. endoreg_db/data/finding_morphology_classification_choice/colon_lesion_planarity_default.yaml +56 -0
  72. endoreg_db/data/finding_morphology_classification_choice/colon_lesion_surface_intact_default.yaml +39 -0
  73. endoreg_db/data/finding_morphology_classification_choice/colonoscopy_size.yaml +57 -0
  74. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  75. endoreg_db/data/finding_type/data.yaml +30 -0
  76. endoreg_db/data/gender/data.yaml +35 -0
  77. endoreg_db/data/information_source/data.yaml +30 -0
  78. endoreg_db/data/information_source/medication.yaml +6 -0
  79. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  80. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  81. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  82. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  83. endoreg_db/data/lab_value/hematology.yaml +184 -0
  84. endoreg_db/data/lab_value/hormones.yaml +59 -0
  85. endoreg_db/data/lab_value/lipids.yaml +53 -0
  86. endoreg_db/data/lab_value/misc.yaml +33 -0
  87. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  88. endoreg_db/data/log_type/data.yaml +57 -0
  89. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  90. endoreg_db/data/lx_client_type/base.yaml +30 -0
  91. endoreg_db/data/lx_permission/base.yaml +24 -0
  92. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  93. endoreg_db/data/material/material.yaml +91 -0
  94. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  95. endoreg_db/data/medication/tah.yaml +70 -0
  96. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  97. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  98. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  99. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  100. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  101. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  102. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  103. endoreg_db/data/names_first/first_names.yaml +51 -0
  104. endoreg_db/data/names_last/last_names.yaml +51 -0
  105. endoreg_db/data/network_device/data.yaml +59 -0
  106. endoreg_db/data/network_device_type/data.yaml +12 -0
  107. endoreg_db/data/organ/data.yaml +29 -0
  108. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  109. endoreg_db/data/pdf_type/data.yaml +29 -0
  110. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  111. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  112. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  113. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  114. endoreg_db/data/profession/data.yaml +70 -0
  115. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  116. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  117. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +19 -0
  118. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  119. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  120. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  121. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  122. endoreg_db/data/unit/concentration.yaml +92 -0
  123. endoreg_db/data/unit/data.yaml +17 -0
  124. endoreg_db/data/unit/length.yaml +31 -0
  125. endoreg_db/data/unit/misc.yaml +20 -0
  126. endoreg_db/data/unit/rate.yaml +6 -0
  127. endoreg_db/data/unit/time.yaml +13 -0
  128. endoreg_db/data/unit/volume.yaml +35 -0
  129. endoreg_db/data/unit/weight.yaml +38 -0
  130. endoreg_db/data/waste/data.yaml +12 -0
  131. endoreg_db/forms/__init__.py +5 -0
  132. endoreg_db/forms/examination_form.py +11 -0
  133. endoreg_db/forms/patient_finding_intervention_form.py +19 -0
  134. endoreg_db/forms/patient_form.py +26 -0
  135. endoreg_db/forms/questionnaires/__init__.py +1 -0
  136. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  137. endoreg_db/forms/settings/__init__.py +8 -0
  138. endoreg_db/forms/unit.py +6 -0
  139. endoreg_db/management/__init__.py +0 -0
  140. endoreg_db/management/commands/__init__.py +0 -0
  141. endoreg_db/management/commands/_load_model_template.py +41 -0
  142. endoreg_db/management/commands/delete_all.py +18 -0
  143. endoreg_db/management/commands/fetch_legacy_image_dataset.py +32 -0
  144. endoreg_db/management/commands/fix_auth_permission.py +20 -0
  145. endoreg_db/management/commands/load_active_model_data.py +45 -0
  146. endoreg_db/management/commands/load_ai_model_data.py +79 -0
  147. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  148. endoreg_db/management/commands/load_base_db_data.py +178 -0
  149. endoreg_db/management/commands/load_center_data.py +43 -0
  150. endoreg_db/management/commands/load_contraindication_data.py +41 -0
  151. endoreg_db/management/commands/load_disease_classification_choices_data.py +41 -0
  152. endoreg_db/management/commands/load_disease_classification_data.py +41 -0
  153. endoreg_db/management/commands/load_disease_data.py +62 -0
  154. endoreg_db/management/commands/load_distribution_data.py +66 -0
  155. endoreg_db/management/commands/load_endoscope_data.py +68 -0
  156. endoreg_db/management/commands/load_event_data.py +41 -0
  157. endoreg_db/management/commands/load_examination_data.py +75 -0
  158. endoreg_db/management/commands/load_examination_indication_data.py +65 -0
  159. endoreg_db/management/commands/load_finding_data.py +171 -0
  160. endoreg_db/management/commands/load_g_play_data.py +113 -0
  161. endoreg_db/management/commands/load_gender_data.py +44 -0
  162. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +133 -0
  163. endoreg_db/management/commands/load_information_source.py +45 -0
  164. endoreg_db/management/commands/load_lab_value_data.py +50 -0
  165. endoreg_db/management/commands/load_logging_data.py +39 -0
  166. endoreg_db/management/commands/load_lx_data.py +64 -0
  167. endoreg_db/management/commands/load_medication_data.py +103 -0
  168. endoreg_db/management/commands/load_medication_indication_data.py +63 -0
  169. endoreg_db/management/commands/load_medication_indication_type_data.py +41 -0
  170. endoreg_db/management/commands/load_medication_intake_time_data.py +41 -0
  171. endoreg_db/management/commands/load_medication_schedule_data.py +55 -0
  172. endoreg_db/management/commands/load_name_data.py +37 -0
  173. endoreg_db/management/commands/load_network_data.py +57 -0
  174. endoreg_db/management/commands/load_organ_data.py +43 -0
  175. endoreg_db/management/commands/load_pdf_type_data.py +61 -0
  176. endoreg_db/management/commands/load_profession_data.py +44 -0
  177. endoreg_db/management/commands/load_report_reader_flag_data.py +46 -0
  178. endoreg_db/management/commands/load_unit_data.py +46 -0
  179. endoreg_db/management/commands/load_user_groups.py +28 -0
  180. endoreg_db/management/commands/register_ai_model.py +64 -0
  181. endoreg_db/management/commands/reset_celery_schedule.py +9 -0
  182. endoreg_db/migrations/0001_initial.py +2045 -0
  183. endoreg_db/migrations/0002_alter_frame_image_alter_rawframe_image.py +23 -0
  184. endoreg_db/migrations/0003_alter_frame_image_alter_rawframe_image.py +23 -0
  185. endoreg_db/migrations/0004_alter_rawvideofile_file_alter_video_file.py +25 -0
  186. endoreg_db/migrations/0005_rawvideofile_frame_count_and_more.py +33 -0
  187. endoreg_db/migrations/0006_frame_extracted_rawframe_extracted.py +23 -0
  188. endoreg_db/migrations/0007_rename_pseudo_patient_video_patient_and_more.py +24 -0
  189. endoreg_db/migrations/0008_remove_reportfile_patient_examination_and_more.py +48 -0
  190. endoreg_db/migrations/__init__.py +0 -0
  191. endoreg_db/models/__init__.py +376 -0
  192. endoreg_db/models/ai_model/__init__.py +4 -0
  193. endoreg_db/models/ai_model/active_model.py +9 -0
  194. endoreg_db/models/ai_model/ai_model.py +103 -0
  195. endoreg_db/models/ai_model/lightning/__init__.py +3 -0
  196. endoreg_db/models/ai_model/lightning/inference_dataset.py +53 -0
  197. endoreg_db/models/ai_model/lightning/multilabel_classification_net.py +155 -0
  198. endoreg_db/models/ai_model/lightning/postprocess.py +53 -0
  199. endoreg_db/models/ai_model/lightning/predict.py +172 -0
  200. endoreg_db/models/ai_model/lightning/prediction_visualizer.py +55 -0
  201. endoreg_db/models/ai_model/lightning/preprocess.py +68 -0
  202. endoreg_db/models/ai_model/lightning/run_visualizer.py +21 -0
  203. endoreg_db/models/ai_model/model_meta.py +250 -0
  204. endoreg_db/models/ai_model/model_type.py +36 -0
  205. endoreg_db/models/ai_model/utils.py +8 -0
  206. endoreg_db/models/annotation/__init__.py +32 -0
  207. endoreg_db/models/annotation/anonymized_image_annotation.py +115 -0
  208. endoreg_db/models/annotation/binary_classification_annotation_task.py +117 -0
  209. endoreg_db/models/annotation/image_classification.py +86 -0
  210. endoreg_db/models/annotation/video_segmentation_annotation.py +52 -0
  211. endoreg_db/models/annotation/video_segmentation_labelset.py +20 -0
  212. endoreg_db/models/case/__init__.py +1 -0
  213. endoreg_db/models/case/case.py +34 -0
  214. endoreg_db/models/case_template/__init__.py +15 -0
  215. endoreg_db/models/case_template/case_template.py +125 -0
  216. endoreg_db/models/case_template/case_template_rule.py +276 -0
  217. endoreg_db/models/case_template/case_template_rule_value.py +88 -0
  218. endoreg_db/models/case_template/case_template_type.py +28 -0
  219. endoreg_db/models/center/__init__.py +11 -0
  220. endoreg_db/models/center/center.py +51 -0
  221. endoreg_db/models/center/center_product.py +33 -0
  222. endoreg_db/models/center/center_resource.py +33 -0
  223. endoreg_db/models/center/center_waste.py +16 -0
  224. endoreg_db/models/contraindication/__init__.py +21 -0
  225. endoreg_db/models/data_file/__init__.py +39 -0
  226. endoreg_db/models/data_file/base_classes/__init__.py +7 -0
  227. endoreg_db/models/data_file/base_classes/abstract_frame.py +100 -0
  228. endoreg_db/models/data_file/base_classes/abstract_pdf.py +136 -0
  229. endoreg_db/models/data_file/base_classes/abstract_video.py +807 -0
  230. endoreg_db/models/data_file/base_classes/frame_helpers.py +17 -0
  231. endoreg_db/models/data_file/base_classes/prepare_bulk_frames.py +19 -0
  232. endoreg_db/models/data_file/base_classes/utils.py +80 -0
  233. endoreg_db/models/data_file/frame.py +29 -0
  234. endoreg_db/models/data_file/import_classes/__init__.py +18 -0
  235. endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +35 -0
  236. endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +28 -0
  237. endoreg_db/models/data_file/import_classes/processing_functions/video.py +260 -0
  238. endoreg_db/models/data_file/import_classes/raw_pdf.py +260 -0
  239. endoreg_db/models/data_file/import_classes/raw_video.py +288 -0
  240. endoreg_db/models/data_file/metadata/__init__.py +13 -0
  241. endoreg_db/models/data_file/metadata/pdf_meta.py +74 -0
  242. endoreg_db/models/data_file/metadata/sensitive_meta.py +290 -0
  243. endoreg_db/models/data_file/metadata/video_meta.py +199 -0
  244. endoreg_db/models/data_file/report_file.py +56 -0
  245. endoreg_db/models/data_file/video/__init__.py +11 -0
  246. endoreg_db/models/data_file/video/import_meta.py +25 -0
  247. endoreg_db/models/data_file/video/video.py +196 -0
  248. endoreg_db/models/data_file/video_segment.py +214 -0
  249. endoreg_db/models/disease.py +79 -0
  250. endoreg_db/models/emission/__init__.py +5 -0
  251. endoreg_db/models/emission/emission_factor.py +85 -0
  252. endoreg_db/models/event.py +73 -0
  253. endoreg_db/models/examination/__init__.py +9 -0
  254. endoreg_db/models/examination/examination.py +67 -0
  255. endoreg_db/models/examination/examination_indication.py +170 -0
  256. endoreg_db/models/examination/examination_time.py +53 -0
  257. endoreg_db/models/examination/examination_time_type.py +48 -0
  258. endoreg_db/models/examination/examination_type.py +40 -0
  259. endoreg_db/models/finding/__init__.py +11 -0
  260. endoreg_db/models/finding/finding.py +75 -0
  261. endoreg_db/models/finding/finding_intervention.py +60 -0
  262. endoreg_db/models/finding/finding_location_classification.py +94 -0
  263. endoreg_db/models/finding/finding_morphology_classification.py +89 -0
  264. endoreg_db/models/finding/finding_type.py +22 -0
  265. endoreg_db/models/hardware/__init__.py +2 -0
  266. endoreg_db/models/hardware/endoscope.py +60 -0
  267. endoreg_db/models/hardware/endoscopy_processor.py +155 -0
  268. endoreg_db/models/information_source.py +29 -0
  269. endoreg_db/models/label/__init__.py +1 -0
  270. endoreg_db/models/label/label.py +112 -0
  271. endoreg_db/models/laboratory/__init__.py +1 -0
  272. endoreg_db/models/laboratory/lab_value.py +111 -0
  273. endoreg_db/models/logging/__init__.py +11 -0
  274. endoreg_db/models/logging/agl_service.py +19 -0
  275. endoreg_db/models/logging/base.py +22 -0
  276. endoreg_db/models/logging/log_type.py +23 -0
  277. endoreg_db/models/logging/network_device.py +27 -0
  278. endoreg_db/models/lx/__init__.py +4 -0
  279. endoreg_db/models/lx/client.py +57 -0
  280. endoreg_db/models/lx/identity.py +34 -0
  281. endoreg_db/models/lx/permission.py +18 -0
  282. endoreg_db/models/lx/user.py +16 -0
  283. endoreg_db/models/medication/__init__.py +19 -0
  284. endoreg_db/models/medication/medication.py +33 -0
  285. endoreg_db/models/medication/medication_indication.py +50 -0
  286. endoreg_db/models/medication/medication_indication_type.py +34 -0
  287. endoreg_db/models/medication/medication_intake_time.py +26 -0
  288. endoreg_db/models/medication/medication_schedule.py +37 -0
  289. endoreg_db/models/network/__init__.py +9 -0
  290. endoreg_db/models/network/agl_service.py +38 -0
  291. endoreg_db/models/network/network_device.py +58 -0
  292. endoreg_db/models/network/network_device_type.py +23 -0
  293. endoreg_db/models/organ/__init__.py +38 -0
  294. endoreg_db/models/other/__init__.py +23 -0
  295. endoreg_db/models/other/distribution/__init__.py +44 -0
  296. endoreg_db/models/other/distribution/base_value_distribution.py +20 -0
  297. endoreg_db/models/other/distribution/date_value_distribution.py +91 -0
  298. endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +32 -0
  299. endoreg_db/models/other/distribution/numeric_value_distribution.py +97 -0
  300. endoreg_db/models/other/distribution/single_categorical_value_distribution.py +22 -0
  301. endoreg_db/models/other/distribution.py +5 -0
  302. endoreg_db/models/other/material.py +20 -0
  303. endoreg_db/models/other/resource.py +18 -0
  304. endoreg_db/models/other/transport_route.py +22 -0
  305. endoreg_db/models/other/waste.py +20 -0
  306. endoreg_db/models/patient/__init__.py +24 -0
  307. endoreg_db/models/patient/patient_examination.py +182 -0
  308. endoreg_db/models/patient/patient_finding.py +143 -0
  309. endoreg_db/models/patient/patient_finding_intervention.py +26 -0
  310. endoreg_db/models/patient/patient_finding_location.py +120 -0
  311. endoreg_db/models/patient/patient_finding_morphology.py +166 -0
  312. endoreg_db/models/permissions/__init__.py +44 -0
  313. endoreg_db/models/persons/__init__.py +34 -0
  314. endoreg_db/models/persons/examiner/__init__.py +2 -0
  315. endoreg_db/models/persons/examiner/examiner.py +60 -0
  316. endoreg_db/models/persons/examiner/examiner_type.py +2 -0
  317. endoreg_db/models/persons/first_name.py +18 -0
  318. endoreg_db/models/persons/gender.py +22 -0
  319. endoreg_db/models/persons/last_name.py +20 -0
  320. endoreg_db/models/persons/patient/__init__.py +8 -0
  321. endoreg_db/models/persons/patient/patient.py +389 -0
  322. endoreg_db/models/persons/patient/patient_disease.py +22 -0
  323. endoreg_db/models/persons/patient/patient_event.py +52 -0
  324. endoreg_db/models/persons/patient/patient_examination_indication.py +32 -0
  325. endoreg_db/models/persons/patient/patient_lab_sample.py +108 -0
  326. endoreg_db/models/persons/patient/patient_lab_value.py +197 -0
  327. endoreg_db/models/persons/patient/patient_medication.py +59 -0
  328. endoreg_db/models/persons/patient/patient_medication_schedule.py +88 -0
  329. endoreg_db/models/persons/person.py +31 -0
  330. endoreg_db/models/persons/portal_user_information.py +27 -0
  331. endoreg_db/models/prediction/__init__.py +8 -0
  332. endoreg_db/models/prediction/image_classification.py +51 -0
  333. endoreg_db/models/prediction/video_prediction_meta.py +306 -0
  334. endoreg_db/models/product/__init__.py +14 -0
  335. endoreg_db/models/product/product.py +110 -0
  336. endoreg_db/models/product/product_group.py +27 -0
  337. endoreg_db/models/product/product_material.py +28 -0
  338. endoreg_db/models/product/product_weight.py +38 -0
  339. endoreg_db/models/product/reference_product.py +115 -0
  340. endoreg_db/models/questionnaires/__init__.py +114 -0
  341. endoreg_db/models/quiz/__init__.py +9 -0
  342. endoreg_db/models/quiz/quiz_answer.py +41 -0
  343. endoreg_db/models/quiz/quiz_question.py +54 -0
  344. endoreg_db/models/report_reader/__init__.py +7 -0
  345. endoreg_db/models/report_reader/report_reader_config.py +53 -0
  346. endoreg_db/models/report_reader/report_reader_flag.py +20 -0
  347. endoreg_db/models/rules/__init__.py +5 -0
  348. endoreg_db/models/rules/rule.py +24 -0
  349. endoreg_db/models/rules/rule_applicator.py +224 -0
  350. endoreg_db/models/rules/rule_attribute_dtype.py +19 -0
  351. endoreg_db/models/rules/rule_type.py +22 -0
  352. endoreg_db/models/rules/ruleset.py +19 -0
  353. endoreg_db/models/unit.py +22 -0
  354. endoreg_db/queries/__init__.py +5 -0
  355. endoreg_db/queries/annotations/__init__.py +3 -0
  356. endoreg_db/queries/annotations/legacy.py +158 -0
  357. endoreg_db/queries/get/__init__.py +6 -0
  358. endoreg_db/queries/get/annotation.py +0 -0
  359. endoreg_db/queries/get/center.py +42 -0
  360. endoreg_db/queries/get/model.py +13 -0
  361. endoreg_db/queries/get/patient.py +14 -0
  362. endoreg_db/queries/get/patient_examination.py +20 -0
  363. endoreg_db/queries/get/prediction.py +0 -0
  364. endoreg_db/queries/get/report_file.py +33 -0
  365. endoreg_db/queries/get/video.py +31 -0
  366. endoreg_db/queries/get/video_import_meta.py +0 -0
  367. endoreg_db/queries/get/video_prediction_meta.py +0 -0
  368. endoreg_db/queries/sanity/__init_.py +0 -0
  369. endoreg_db/serializers/__init__.py +10 -0
  370. endoreg_db/serializers/ai_model.py +19 -0
  371. endoreg_db/serializers/annotation.py +14 -0
  372. endoreg_db/serializers/center.py +11 -0
  373. endoreg_db/serializers/examination.py +33 -0
  374. endoreg_db/serializers/frame.py +9 -0
  375. endoreg_db/serializers/hardware.py +21 -0
  376. endoreg_db/serializers/label.py +22 -0
  377. endoreg_db/serializers/patient.py +33 -0
  378. endoreg_db/serializers/prediction.py +10 -0
  379. endoreg_db/serializers/raw_video_meta_validation.py +13 -0
  380. endoreg_db/serializers/report_file.py +7 -0
  381. endoreg_db/serializers/video.py +20 -0
  382. endoreg_db/serializers/video_segmentation.py +492 -0
  383. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  384. endoreg_db/templates/admin/start_examination.html +12 -0
  385. endoreg_db/templates/timeline.html +176 -0
  386. endoreg_db/utils/__init__.py +36 -0
  387. endoreg_db/utils/cropping.py +29 -0
  388. endoreg_db/utils/dataloader.py +118 -0
  389. endoreg_db/utils/dates.py +39 -0
  390. endoreg_db/utils/file_operations.py +30 -0
  391. endoreg_db/utils/hashs.py +152 -0
  392. endoreg_db/utils/legacy_ocr.py +201 -0
  393. endoreg_db/utils/names.py +74 -0
  394. endoreg_db/utils/ocr.py +190 -0
  395. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  396. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  397. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  398. endoreg_db/utils/uuid.py +4 -0
  399. endoreg_db/utils/validate_endo_roi.py +19 -0
  400. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  401. endoreg_db/utils/video/__init__.py +13 -0
  402. endoreg_db/utils/video/extract_frames.py +121 -0
  403. endoreg_db/utils/video/transcode_videofile.py +111 -0
  404. endoreg_db/views/__init__.py +2 -0
  405. endoreg_db/views/csrf.py +7 -0
  406. endoreg_db/views/patient_views.py +90 -0
  407. endoreg_db/views/raw_video_meta_validation_views.py +38 -0
  408. endoreg_db/views/report_views.py +96 -0
  409. endoreg_db/views/video_segmentation_views.py +149 -0
  410. endoreg_db/views/views_for_timeline.py +46 -0
  411. {endoreg_db-0.6.0.dist-info → endoreg_db-0.6.2.dist-info}/METADATA +14 -4
  412. endoreg_db-0.6.2.dist-info/RECORD +420 -0
  413. {endoreg_db-0.6.0.dist-info → endoreg_db-0.6.2.dist-info}/WHEEL +1 -2
  414. endoreg_db-0.6.0.dist-info/RECORD +0 -11
  415. endoreg_db-0.6.0.dist-info/top_level.txt +0 -1
  416. {endoreg_db-0.6.0.dist-info → endoreg_db-0.6.2.dist-info/licenses}/LICENSE +0 -0
File without changes
@@ -0,0 +1,159 @@
1
+ from endoreg_db.models import CaseTemplate, CaseTemplateRule, CaseTemplateRuleType
2
+ from endoreg_db.case_generator.lab_sample_factory import LabSampleFactory
3
+
4
+ DEFAULT_CASE_TEMPLATE_NAME = "pre_default_screening_colonoscopy"
5
+
6
+ class CaseGenerator:
7
+ """
8
+ Provides methods to generate cases based on a template.
9
+ """
10
+
11
+ def __init__(self, template: CaseTemplate = None):
12
+ """
13
+ Initializes the CaseGenerator with a template.
14
+
15
+ Args:
16
+ template (CaseTemplate, optional): The template to use for case generation. Defaults to the predefined template.
17
+ """
18
+ self.template = template or CaseTemplate.objects.get(name=DEFAULT_CASE_TEMPLATE_NAME)
19
+ self.lab_sample_factory = LabSampleFactory()
20
+
21
+ # Define available rule types
22
+ rule_type_names = [
23
+ "create-object",
24
+ "set-field-default",
25
+ "set-field-by-distribution",
26
+ "set-field-by-value",
27
+ "set-field-single-choice",
28
+ "set-field-multiple-choice",
29
+ ]
30
+ self.available_rule_types = CaseTemplateRuleType.objects.filter(name__in=rule_type_names)
31
+
32
+ def _validate_rule_type(self, rule_type: CaseTemplateRuleType):
33
+ """
34
+ Validates if the rule type is supported.
35
+
36
+ Args:
37
+ rule_type (CaseTemplateRuleType): The rule type to validate.
38
+
39
+ Raises:
40
+ ValueError: If the rule type is not supported.
41
+ """
42
+ if rule_type not in self.available_rule_types:
43
+ raise ValueError(f"Rule type {rule_type} is not supported.")
44
+
45
+ def _apply_create_object(self, rule: CaseTemplateRule, parent=None):
46
+ """
47
+ Applies a create-object rule to generate a model instance.
48
+
49
+ Args:
50
+ rule (CaseTemplateRule): The rule to apply.
51
+ parent (Optional[Model]): The parent object for the rule.
52
+
53
+ Returns:
54
+ Model: The created model instance.
55
+ """
56
+ target_model = rule.get_target_model()
57
+ extra_params = rule.extra_parameters or {}
58
+ create_method_info = extra_params.get("create_method", {})
59
+
60
+ assert create_method_info, "Create method must be set for a create-object rule."
61
+
62
+ create_method = getattr(target_model, create_method_info["name"])
63
+ kwargs = create_method_info.get("kwargs", {})
64
+
65
+ if parent:
66
+ kwargs[rule.parent_field] = parent
67
+
68
+ target_instance = create_method(**kwargs)
69
+ target_instance.save()
70
+
71
+ for action in extra_params.get("actions", []):
72
+ action_method = getattr(target_instance, action["name"])
73
+ action_kwargs = action.get("kwargs", {})
74
+ action_method(**action_kwargs)
75
+
76
+ for chained_rule in rule.chained_rules.all():
77
+ self.apply_rule(chained_rule, parent=target_instance)
78
+
79
+ return target_instance
80
+
81
+ def _apply_set_field_by_distribution(self, rule: CaseTemplateRule, parent):
82
+ """
83
+ Applies a set-field-by-distribution rule.
84
+
85
+ Args:
86
+ rule (CaseTemplateRule): The rule to apply.
87
+ parent (Model): The parent object for the rule.
88
+
89
+ Returns:
90
+ Model: The updated parent object.
91
+ """
92
+ assert parent, "Parent must be provided for set-field-by-distribution rules."
93
+ assert rule.target_field, "Target field must be specified for the rule."
94
+
95
+ distribution = rule.get_distribution()
96
+ value = distribution.generate_value()
97
+
98
+ setattr(parent, rule.target_field, value)
99
+ parent.save()
100
+ return parent
101
+
102
+ def apply_rule(self, rule: CaseTemplateRule, parent=None):
103
+ """
104
+ Applies a rule based on its type to generate a case.
105
+
106
+ Args:
107
+ rule (CaseTemplateRule): The rule to apply.
108
+ parent (Optional[Model]): The parent object for the rule.
109
+
110
+ Returns:
111
+ Model: The case by applying the rule.
112
+ """
113
+ self._validate_rule_type(rule.rule_type)
114
+
115
+ if rule.rule_type.name == "create-object":
116
+ return self._apply_create_object(rule, parent)
117
+
118
+ if rule.rule_type.name == "set-field-by-distribution":
119
+ return self._apply_set_field_by_distribution(rule, parent)
120
+
121
+ raise ValueError(f"Unsupported rule type: {rule.rule_type.name}")
122
+
123
+ def generate_case(self, case_template: CaseTemplate = None):
124
+ """
125
+ Generates a case based on the provided or default template.
126
+
127
+ Args:
128
+ case_template (CaseTemplate, optional): The template to use for case generation. Defaults to None.
129
+
130
+ Returns:
131
+ Tuple[Model, Model]: The generated patient and medication schedule.
132
+ """
133
+ case_template = case_template or CaseTemplate.objects.get(name=DEFAULT_CASE_TEMPLATE_NAME)
134
+
135
+ create_patient_rule = case_template.get_create_patient_rule()
136
+ patient = self.apply_rule(create_patient_rule)
137
+
138
+ medication_schedule_rule = case_template.get_create_patient_medication_schedule_rule()
139
+ medication_schedule = self.apply_rule(medication_schedule_rule, parent=patient)
140
+
141
+ return patient, medication_schedule
142
+
143
+ # if not create_new_patient:
144
+ # raise NotImplementedError("Only new patients are supported at the moment.")
145
+ # else:
146
+ # # TODO Implement patient rules
147
+ # patient_rules = None # all rules of type "create_patient"
148
+ # patient = self.generate_patient(patient_rules)
149
+
150
+ # # Generate case based on template
151
+ # rules = self.template.get_rules()
152
+ # chained_rules = set()
153
+
154
+ # for rule in rules:
155
+ # rule_chain = rule.get_all_downward_chained_rules()
156
+ # chained_rules.add(rule)
157
+ # chained_rules.update(rule_chain)
158
+
159
+ # return chained_rules
@@ -0,0 +1,33 @@
1
+ from datetime import datetime, timezone
2
+ from endoreg_db.models import Patient, PatientLabSample, PatientLabSampleType
3
+
4
+ class LabSampleFactory:
5
+ """
6
+ Provides methods to generate lab samples.
7
+ """
8
+
9
+ def __init__(self):
10
+ """
11
+ Initializes the LabSampleFactory.
12
+ """
13
+ pass
14
+
15
+ def create_generic_lab_sample(self, patient: Patient):
16
+ """
17
+ Generates a generic lab sample for a given patient.
18
+
19
+ Args:
20
+ patient (Patient): The patient for whom the lab sample is generated.
21
+
22
+ Returns:
23
+ PatientLabSample: The created lab sample instance.
24
+ """
25
+ sample_type = PatientLabSampleType.objects.get(name="generic")
26
+
27
+ lab_sample = PatientLabSample.objects.create(
28
+ patient=patient,
29
+ sample_type=sample_type,
30
+ date=datetime.now(tz=timezone.utc)
31
+ )
32
+
33
+ return lab_sample
@@ -0,0 +1,30 @@
1
+ from endoreg_db.models import CaseTemplate
2
+ from endoreg_db.case_generator.case_generator import CaseGenerator
3
+
4
+ # TEMPLATE_NAME = "pre_endo-anticoagulation-af-low_risk"
5
+ TEMPLATE_NAME = "pre_default_screening_colonoscopy"
6
+
7
+ def fetch_template(template_name: str = DEFAULT_TEMPLATE_NAME) -> CaseTemplate:
8
+ """
9
+ Fetches a CaseTemplate by name.
10
+
11
+ Args:
12
+ template_name (str): The name of the template to fetch. Defaults to DEFAULT_TEMPLATE_NAME.
13
+
14
+ Returns:
15
+ CaseTemplate: The fetched CaseTemplate instance.
16
+ """
17
+ return CaseTemplate.objects.get(name=template_name)
18
+
19
+ def initialize_case_generator(template_name: str = DEFAULT_TEMPLATE_NAME) -> CaseGenerator:
20
+ """
21
+ Initializes a CaseGenerator with the specified template.
22
+
23
+ Args:
24
+ template_name (str): The name of the template to use. Defaults to DEFAULT_TEMPLATE_NAME.
25
+
26
+ Returns:
27
+ CaseGenerator: An instance of CaseGenerator initialized with the template.
28
+ """
29
+ template = fetch_template(template_name)
30
+ return CaseGenerator(template)
@@ -0,0 +1,118 @@
1
+ from pathlib import Path
2
+
3
+ DATA_DIR = Path(__file__).parent
4
+
5
+ INFORMATION_DATA_DIR = DATA_DIR / "information_source"
6
+ UNIT_DATA_DIR = DATA_DIR / "unit"
7
+ CENTER_DATA_DIR = DATA_DIR / "center"
8
+ EXAMINATION_DATA_DIR = DATA_DIR / "examination"
9
+ MODEL_TYPE_DATA_DIR = DATA_DIR / "ai_model_type"
10
+ ENDOSCOPY_PROCESSOR_DATA_DIR = DATA_DIR / "endoscopy_processor"
11
+ ENDOSCOPE_TYPE_DATA_DIR = DATA_DIR / "endoscope_type"
12
+ ENDOSCOPE_DATA_DIR = DATA_DIR / "endoscope"
13
+ ACTIVE_MODEL_DATA_DIR = DATA_DIR / "active_model"
14
+ PROFESSION_DATA_DIR = DATA_DIR / "profession"
15
+ PDF_TYPE_DATA_DIR = DATA_DIR / "pdf_type"
16
+ REPORT_READER_FLAG_DATA_DIR = DATA_DIR / "report_reader_flag"
17
+ EVENT_DATA_DIR = DATA_DIR / "event"
18
+ GENDER_DATA_DIR = DATA_DIR / "gender"
19
+ ORGAN_DATA_DIR = DATA_DIR / "organ"
20
+
21
+ # Contraindication
22
+ CONTRAINDICATION_DATA_DIR = DATA_DIR / "contraindication"
23
+
24
+ # Examination
25
+ EXAMINATION_INDICATION_DATA_DIR = DATA_DIR / "examination_indication"
26
+ EXAMINATION_INDICATION_CLASSIFICATION_DATA_DIR = (
27
+ DATA_DIR / "examination_indication_classification"
28
+ )
29
+ EXAMINATION_INDICATION_CLASSIFICATION_CHOICE_DATA_DIR = (
30
+ DATA_DIR / "examination_indication_classification_choice"
31
+ )
32
+
33
+ # Finding
34
+ FINDING_TYPE_DATA_DIR = DATA_DIR / "finding_type"
35
+ FINDING_DATA_DIR = DATA_DIR / "finding"
36
+ FINDING_LOCATION_CLASSIFICATION_DATA_DIR = DATA_DIR / "finding_location_classification"
37
+ FINDING_LOCATION_CLASSIFICATION_CHOICE_DATA_DIR = (
38
+ DATA_DIR / "finding_location_classification_choice"
39
+ )
40
+ FINDING_MORPHOLOGY_CLASSIFICATION_DATA_DIR = (
41
+ DATA_DIR / "finding_morphology_classification"
42
+ )
43
+ FINDING_MORPHOLOGY_CLASSIFICATION_CHOICE_DATA_DIR = (
44
+ DATA_DIR / "finding_morphology_classification_choice"
45
+ )
46
+ FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR = (
47
+ DATA_DIR / "finding_morphology_classification_type"
48
+ )
49
+ FINDING_INTERVETION_DATA_DIR = DATA_DIR / "finding_intervention"
50
+ FINIDNG_INTERVENTION_TYPE_DATA_DIR = DATA_DIR / "finding_intervention_type"
51
+
52
+ # Green Endoscopy Dashboard Stuffs
53
+ CENTER_RESOURCE_DATA_DIR = DATA_DIR / "center_resource"
54
+ CENTER_WASTE_DATA_DIR = DATA_DIR / "center_waste"
55
+ EMISSION_FACTOR_DATA_DIR = DATA_DIR / "emission_factor"
56
+ MATERIAL_DATA_DIR = DATA_DIR / "material"
57
+ PRODUCT_DATA_DIR = DATA_DIR / "product"
58
+ PRODUCT_GROUP_DATA_DIR = DATA_DIR / "product_group"
59
+ PRODUCT_MATERIAL_DATA_DIR = DATA_DIR / "product_material"
60
+ PRODUCT_WEIGHT_DATA_DIR = DATA_DIR / "product_weight"
61
+ REFERENCE_PRODUCT_DATA_DIR = DATA_DIR / "reference_product"
62
+ RESOURCE_DATA_DIR = DATA_DIR / "resource"
63
+ WASTE_DATA_DIR = DATA_DIR / "waste"
64
+ TRANSPORT_ROUTE_DATA_DIR = DATA_DIR / "transport_route"
65
+ DISEASE_CLASSIFICATION_DATA_DIR = DATA_DIR / "disease_classification"
66
+ DISEASE_CLASSIFICATION_CHOICE_DATA_DIR = DATA_DIR / "disease_classification_choice"
67
+ DISEASE_DATA_DIR = DATA_DIR / "disease"
68
+ MEDICATION_DATA_DIR = DATA_DIR / "medication"
69
+ MEDICATION_INDICATION_DATA_DIR = DATA_DIR / "medication_indication"
70
+ MEDICATION_INDICATION_TYPE_DATA_DIR = DATA_DIR / "medication_indication_type"
71
+
72
+ DISTRIBUTION_BASE_DIR = DATA_DIR / "distribution"
73
+ DISTRIBUTION_SINGLE_CATEGORICAL_DATA_DIR = DISTRIBUTION_BASE_DIR / "single_categorical"
74
+ DISTRIBUTION_NUMERIC_DATA_DIR = DISTRIBUTION_BASE_DIR / "numeric"
75
+ DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR = (
76
+ DISTRIBUTION_BASE_DIR / "multiple_categorical"
77
+ )
78
+ DISTRIBUTION_DATE_DATA_DIR = DISTRIBUTION_BASE_DIR / "date"
79
+
80
+ # G-Play Stuffs
81
+ CASE_TEMPLATE_BASE_DIR = DATA_DIR / "case_template"
82
+ CASE_TEMPLATE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "template"
83
+ CASE_TEMPLATE_TYPE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "template_type"
84
+ CASE_TEMPLATE_RULE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule"
85
+ CASE_TEMPLATE_RULE_TYPE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule_type"
86
+ CASE_TEMPLATE_RULE_VALUE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule_value"
87
+ CASE_TEMPLATE_RULE_VALUE_TYPE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule_value_type"
88
+
89
+ # NETWORK
90
+ NETWORK_DEVICE_DATA_DIR = DATA_DIR / "network_device"
91
+ NETWORK_DEVICE_TYPE_DATA_DIR = DATA_DIR / "network_device_type"
92
+ AGL_SERVICE_DATA_DIR = DATA_DIR / "agl_service"
93
+
94
+ # LOGS
95
+ LOG_TYPE_DATA_DIR = DATA_DIR / "log_type"
96
+
97
+ # AI STUFFS
98
+ AI_MODEL_DATA_DIR = DATA_DIR / "ai_model"
99
+ AI_MODEL_TYPE_DATA_DIR = DATA_DIR / "ai_model_type"
100
+ AI_MODEL_META_DATA_DIR = DATA_DIR / "ai_model_meta"
101
+ LABEL_DATA_DIR = DATA_DIR / "ai_model_label"
102
+ VIDEO_SEGMENTATION_LABEL_DATA_DIR = DATA_DIR / "ai_model_video_segmentation_label"
103
+ VIDEO_SEGMENTATION_LABELSET_DATA_DIR = DATA_DIR / "ai_model_video_segmentation_labelset"
104
+
105
+ # To Do
106
+ LAB_VALUE_DATA_DIR = DATA_DIR / "lab_value"
107
+ PATIENT_LAB_SAMPLE_TYPE_DATA_DIR = DATA_DIR / "patient_lab_sample_type"
108
+ MEDICATION_SCHEDULE_DATA_DIR = DATA_DIR / "medication_schedule"
109
+ MEDICATION_INTAKE_TIME_DATA_DIR = DATA_DIR / "medication_intake_time"
110
+
111
+
112
+ RULE_TYPE_DATA_DIR = DATA_DIR / "rule_type"
113
+ RULE_ATTRIBUTE_DTYPE_DATA_DIR = DATA_DIR / "rule_attribute_dtype"
114
+ RULESET_DATA_DIR = DATA_DIR / "ruleset"
115
+
116
+ LX_PERMISSION_DATA_DIR = DATA_DIR / "lx_permission"
117
+ LX_CLIENT_TAG_DATA_DIR = DATA_DIR / "lx_client_tag"
118
+ LX_CLIENT_TYPE_DATA_DIR = DATA_DIR / "lx_client_type"
@@ -0,0 +1,19 @@
1
+ - model: endoreg_db.agl_service
2
+ fields:
3
+ name: "agl-home-django"
4
+ description: "AGL Home Django service"
5
+ devices: [
6
+ "agl-server-04",
7
+ ]
8
+ port: 9100
9
+ url: "https://home.endo-reg.net/"
10
+
11
+ - model: endoreg_db.agl_service
12
+ fields:
13
+ name: "endoreg-client-manager"
14
+ description: "AGL Home Django service"
15
+ devices: [
16
+ "agl-gpu-client-dev",
17
+ ]
18
+ port: 9000
19
+ url: "https://home.endo-reg.net/"
@@ -0,0 +1,7 @@
1
+ - model: endoreg_db.ai_model
2
+ fields:
3
+ name: "image_multilabel_classification_colonoscopy_default"
4
+ description: "Image multilabel classification model"
5
+ model_type: "image"
6
+ model_subtype: "multilabel"
7
+ video_segmentation_labelset: "colonoscopy_video_segmentation_raw"
@@ -0,0 +1,88 @@
1
+ # labels are: "appendix", "ileocecal_valve", "polyp", "water_jet", "digital_chromo_endoscopy", "instrument", "wound", "blood", "ileum", "low_quality", "clip", "outside"
2
+
3
+ - model: endoreg_db.Label
4
+ fields:
5
+ name: "appendix"
6
+ label_type: "classification"
7
+
8
+ - model: endoreg_db.Label
9
+ fields:
10
+ name: "ileocaecalvalve"
11
+ label_type: "classification"
12
+
13
+ - model: endoreg_db.Label
14
+ fields:
15
+ name: "polyp"
16
+ label_type: "classification"
17
+
18
+ - model: endoreg_db.Label
19
+ fields:
20
+ name: "water_jet"
21
+ label_type: "classification"
22
+
23
+ - model: endoreg_db.Label
24
+ fields:
25
+ name: "digital_chromo_endoscopy"
26
+ label_type: "classification"
27
+
28
+ - model: endoreg_db.Label
29
+ fields:
30
+ name: "instrument"
31
+ label_type: "classification"
32
+
33
+ - model: endoreg_db.Label
34
+ fields:
35
+ name: "wound"
36
+ label_type: "classification"
37
+
38
+ - model: endoreg_db.Label
39
+ fields:
40
+ name: "blood"
41
+ label_type: "classification"
42
+
43
+ - model: endoreg_db.Label
44
+ fields:
45
+ name: "ileum"
46
+ label_type: "classification"
47
+
48
+ - model: endoreg_db.Label
49
+ fields:
50
+ name: "low_quality"
51
+ label_type: "classification"
52
+
53
+ - model: endoreg_db.Label
54
+ fields:
55
+ name: "clip"
56
+ label_type: "classification"
57
+
58
+ - model: endoreg_db.Label
59
+ fields:
60
+ name: "outside"
61
+ label_type: "classification"
62
+
63
+ - model: endoreg_db.Label
64
+ fields:
65
+ name: "diverticule"
66
+ label_type: "classification"
67
+
68
+ - model: endoreg_db.Label
69
+ fields:
70
+ name: "grasper"
71
+ label_type: "classification"
72
+
73
+ - model: endoreg_db.Label
74
+ fields:
75
+ name: "nbi"
76
+ label_type: "classification"
77
+
78
+ # needle
79
+ - model: endoreg_db.Label
80
+ fields:
81
+ name: "needle"
82
+ label_type: "classification"
83
+
84
+ # snare
85
+ - model: endoreg_db.Label
86
+ fields:
87
+ name: "snare"
88
+ label_type: "classification"
@@ -0,0 +1,21 @@
1
+ - model: endoreg_db.LabelSet
2
+ fields:
3
+ name: "multilabel_classification_colonoscopy_default"
4
+ version: 1
5
+ labels:
6
+ [
7
+ "appendix",
8
+ "blood",
9
+ "diverticule",
10
+ "grasper",
11
+ "ileocaecalvalve",
12
+ "ileum",
13
+ "low_quality",
14
+ "nbi",
15
+ "needle",
16
+ "outside",
17
+ "polyp",
18
+ "snare",
19
+ "water_jet",
20
+ "wound",
21
+ ]
@@ -0,0 +1,7 @@
1
+ - model: endoreg_db.LabelType
2
+ fields:
3
+ name: "classification"
4
+
5
+ - model: endoreg_db.LabelType
6
+ fields:
7
+ name: "object_detection"
@@ -0,0 +1,5 @@
1
+ - model: endoreg_db.model_meta
2
+ fields:
3
+ name: "image_multilabel_classification_colonoscopy_default"
4
+ version: 1
5
+ labelset: "multilabel_classification_colonoscopy_default"
@@ -0,0 +1,7 @@
1
+ - model: endoreg_db.model_type
2
+ fields:
3
+ name: "multilabel_classification"
4
+
5
+ - model: endoreg_db.model_type
6
+ fields:
7
+ name: "object_detection"
@@ -0,0 +1,176 @@
1
+ - model: endoreg_db.video_segmentation_label
2
+ fields:
3
+ name: "upper_gi"
4
+ name_de: "Oberer GI-Trakt"
5
+ name_en: "Upper GI"
6
+ description: "Upper GI"
7
+ color: "#FF0000"
8
+
9
+ - model: endoreg_db.video_segmentation_label
10
+ fields:
11
+ name: "lower_gi"
12
+ name_de: "Unterer GI-Trakt"
13
+ name_en: "Lower GI"
14
+ description: "Lower GI"
15
+ color: "#00FF00"
16
+
17
+ - model: endoreg_db.video_segmentation_label
18
+ fields:
19
+ name: "esophagus"
20
+ name_de: "Ösophagus"
21
+ name_en: "Esophagus"
22
+ description: "Esophagus"
23
+ color: "#0000FF"
24
+
25
+ - model: endoreg_db.video_segmentation_label
26
+ fields:
27
+ name: "stomach"
28
+ name_de: "Magen"
29
+ name_en: "Stomach"
30
+ description: "Stomach"
31
+ color: "#FFFF00"
32
+
33
+ - model: endoreg_db.video_segmentation_label
34
+ fields:
35
+ name: "duodenum"
36
+ name_de: "Duodenum"
37
+ name_en: "Duodenum"
38
+ description: "Duodenum"
39
+ color: "#FF00FF"
40
+
41
+ - model: endoreg_db.video_segmentation_label
42
+ fields:
43
+ name: "colon"
44
+ name_de: "Kolon"
45
+ name_en: "Colon"
46
+ description: "Colon"
47
+ color: "#00FFFF"
48
+
49
+ - model: endoreg_db.video_segmentation_label
50
+ fields:
51
+ name: "ileum"
52
+ name_de: "Ileum"
53
+ name_en: "Ileum"
54
+ description: "Ileum"
55
+ color: "#800000"
56
+
57
+ - model: endoreg_db.video_segmentation_label
58
+ fields:
59
+ name: "outside"
60
+ name_de: "Außerhalb des Körpers"
61
+ name_en: "Out of Body"
62
+ description: "Out of Body"
63
+ color: "#008000"
64
+
65
+ - model: endoreg_db.video_segmentation_label
66
+ fields:
67
+ name: "bli"
68
+ name_de: "Blau-Licht-Imaging"
69
+ name_en: "Blue Light Imaging"
70
+ description: "Blue Light Imaging (high level for nbi and similar modes)"
71
+ color: "#000080"
72
+
73
+ - model: endoreg_db.video_segmentation_label
74
+ fields:
75
+ name: "low_quality"
76
+ name_de: "Niedrige Qualität"
77
+ name_en: "Low Quality"
78
+ description: "Low Quality"
79
+ color: "#800080"
80
+
81
+ - model: endoreg_db.video_segmentation_label
82
+ fields:
83
+ name: "instrument"
84
+ name_de: "Instrument"
85
+ name_en: "Instrument"
86
+ description: "Instrument"
87
+ color: "#808000"
88
+
89
+ # Appendix
90
+ - model: endoreg_db.video_segmentation_label
91
+ fields:
92
+ name: "appendix"
93
+ name_de: "Appendix"
94
+ name_en: "Appendix"
95
+ description: "Appendix"
96
+ color: "#FF0000"
97
+ # blood, diverticule, grasper, ileocaecalvalve, ileum, low_quality, nbi, needle, polyp, snare, water_jet, wound
98
+ - model: endoreg_db.video_segmentation_label
99
+ fields:
100
+ name: "blood"
101
+ name_de: "Blut"
102
+ name_en: "Blood"
103
+ description: "Blood"
104
+ color: "#00FF00"
105
+
106
+ - model: endoreg_db.video_segmentation_label
107
+ fields:
108
+ name: "diverticule"
109
+ name_de: "Divertikel"
110
+ name_en: "Diverticule"
111
+ description: "Diverticule"
112
+ color: "#0000FF"
113
+
114
+ - model: endoreg_db.video_segmentation_label
115
+ fields:
116
+ name: "grasper"
117
+ name_de: "Grasper"
118
+ name_en: "Grasper"
119
+ description: "Grasper"
120
+ color: "#FFFF00"
121
+
122
+ - model: endoreg_db.video_segmentation_label
123
+ fields:
124
+ name: "ileocaecalvalve"
125
+ name_de: "Ileocaecalvalve"
126
+ name_en: "Ileocaecalvalve"
127
+ description: "Ileocaecalvalve"
128
+ color: "#FF00FF"
129
+
130
+ - model: endoreg_db.video_segmentation_label
131
+ fields:
132
+ name: "nbi"
133
+ name_de: "Narrow Band Imaging"
134
+ name_en: "Narrow Band Imaging"
135
+ description: "Narrow Band Imaging"
136
+ color: "#00FFFF"
137
+
138
+ - model: endoreg_db.video_segmentation_label
139
+ fields:
140
+ name: "needle"
141
+ name_de: "Needle"
142
+ name_en: "Needle"
143
+ description: "Needle"
144
+ color: "#800000"
145
+
146
+ - model: endoreg_db.video_segmentation_label
147
+ fields:
148
+ name: "polyp"
149
+ name_de: "Polyp"
150
+ name_en: "Polyp"
151
+ description: "Polyp"
152
+ color: "#008000"
153
+
154
+ - model: endoreg_db.video_segmentation_label
155
+ fields:
156
+ name: "snare"
157
+ name_de: "Snare"
158
+ name_en: "Snare"
159
+ description: "Snare"
160
+ color: "#000080"
161
+
162
+ - model: endoreg_db.video_segmentation_label
163
+ fields:
164
+ name: "water_jet"
165
+ name_de: "Water Jet"
166
+ name_en: "Water Jet"
167
+ description: "Water Jet"
168
+ color: "#800080"
169
+
170
+ - model: endoreg_db.video_segmentation_label
171
+ fields:
172
+ name: "wound"
173
+ name_de: "Wound"
174
+ name_en: "Wound"
175
+ description: "Wound"
176
+ color: "#808000"