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
@@ -0,0 +1,193 @@
1
+ from typing import List, Optional, TYPE_CHECKING # Modified import
2
+
3
+ from pydantic import BaseModel, Field
4
+
5
+ from endoreg_db.models import (
6
+ PatientDisease, Disease, DiseaseClassificationChoice,
7
+ Event,
8
+ PatientEvent, Examination, ExaminationIndication, ExaminationIndicationClassificationChoice,
9
+ PatientExamination, PatientExaminationIndication,
10
+ PatientFinding,
11
+ Finding,
12
+ FindingIntervention,
13
+ FindingClassification,
14
+ FindingClassificationChoice,
15
+ LabValue,
16
+ PatientLabValue,
17
+ PatientLabSample,
18
+ PatientLabSampleType,
19
+ PatientMedication, # Added
20
+ PatientMedicationSchedule, # Added
21
+ Medication, # Added
22
+ MedicationIndication, # Added
23
+ MedicationIntakeTime, # Added
24
+ MedicationSchedule, # Added
25
+ )
26
+ if TYPE_CHECKING: # Added for Patient import
27
+ from endoreg_db.models.administration.person.patient import Patient
28
+
29
+ class RequirementLinks(BaseModel):
30
+ """
31
+ A class representing a dictionary of models related to a requirement.
32
+
33
+ Attributes:
34
+ # requirement_types (List[RequirementType]): A List of requirement types.
35
+ # operators (List[RequirementOperator]): A List of operators.
36
+ # requirement_sets (List[RequirementSet]): A List of requirement sets.
37
+ examinations (List[Examination]): A List of examinations.
38
+ examination_indications (List[ExaminationIndication]): A List of examination indications.
39
+ lab_values (List[LabValue]): A List of lab values.
40
+ diseases (List[Disease]): A List of diseases.
41
+ disease_classification_choices (List[DiseaseClassificationChoice]): A List of disease classification choices.
42
+ events (List[Event]): A List of events.
43
+ findings (List[Finding]): A List of findings.
44
+ finding_morphology_classification_choices (List[FindingMorphologyClassificationChoice]): A List of finding morphology classification choices.
45
+ finding_location_classification_choices (List[FindingLocationClassificationChoice]): A List of finding location classification choices.
46
+ finding_interventions (List[FindingIntervention]): A List of finding interventions.
47
+ """
48
+ model_config = {"arbitrary_types_allowed": True}
49
+ #
50
+ # requirement_types: Optional[List["RequirementType"]] = None
51
+ # operators: Optional[List["RequirementOperator"]] = None
52
+ # The following model import causes circular import
53
+ #requirement_sets: Optional[List["RequirementSet"]] = None
54
+ examinations: List["Examination"] = Field(default_factory=list)
55
+ examination_indications: List["ExaminationIndication"] = Field(default_factory=list)
56
+ examination_indication_classification_choices: List["ExaminationIndicationClassificationChoice"] = Field(default_factory=list)
57
+ patient_examinations: List["PatientExamination"] = Field(default_factory=list)
58
+
59
+ patient_examination_indication: List["PatientExaminationIndication"] = Field(default_factory=list)
60
+ lab_values: List["LabValue"] = Field(default_factory=list)
61
+ patient_lab_values: List["PatientLabValue"] = Field(default_factory=list)
62
+ patient_lab_samples: List["PatientLabSample"] = Field(default_factory=list)
63
+ patient_diseases: List["PatientDisease"] = Field(default_factory=list)
64
+ diseases: List["Disease"] = Field(default_factory=list)
65
+ disease_classification_choices: List["DiseaseClassificationChoice"] = Field(default_factory=list)
66
+ events: List["Event"] = Field(default_factory=list)
67
+ patient_events: List["PatientEvent"] = Field(default_factory=list)
68
+ patient_findings: List["PatientFinding"] = Field(default_factory=list)
69
+ findings: List["Finding"] = Field(default_factory=list)
70
+ finding_classification_choices: List["FindingClassificationChoice"] = Field(default_factory=list)
71
+ finding_classifications: List["FindingClassification"] = Field(default_factory=list) # Added for direct classification checks if needed
72
+ finding_interventions: List["FindingIntervention"] = Field(default_factory=list)
73
+ patient_lab_sample_types: List["PatientLabSampleType"] = Field(default_factory=list)
74
+ patient_medications: List["PatientMedication"] = Field(default_factory=list) # Added
75
+ patient_medication_schedules: List["PatientMedicationSchedule"] = Field(default_factory=list) # Added
76
+ # Added direct medication-related fields
77
+ medications: List["Medication"] = Field(default_factory=list)
78
+ medication_indications: List["MedicationIndication"] = Field(default_factory=list)
79
+ medication_intake_times: List["MedicationIntakeTime"] = Field(default_factory=list)
80
+ medication_schedules: List["MedicationSchedule"] = Field(default_factory=list)
81
+
82
+ def get_first_patient(self) -> Optional["Patient"]:
83
+ """
84
+ Retrieves the first Patient instance found through the linked patient-specific models.
85
+ Iterates through various patient-related lists and returns the .patient attribute
86
+ from the first relevant object found.
87
+ """
88
+ if self.patient_lab_values:
89
+ for plv in self.patient_lab_values:
90
+ if hasattr(plv, 'sample') and plv.sample and \
91
+ hasattr(plv.sample, 'patient') and plv.sample.patient:
92
+ return plv.sample.patient
93
+ if self.patient_lab_samples:
94
+ for pls in self.patient_lab_samples:
95
+ if hasattr(pls, 'patient') and pls.patient:
96
+ return pls.patient
97
+ if self.patient_examinations:
98
+ for pe in self.patient_examinations:
99
+ if hasattr(pe, 'patient') and pe.patient:
100
+ return pe.patient
101
+ if self.patient_diseases:
102
+ for pd in self.patient_diseases:
103
+ if hasattr(pd, 'patient') and pd.patient:
104
+ return pd.patient
105
+ if self.patient_events:
106
+ for pev in self.patient_events:
107
+ if hasattr(pev, 'patient') and pev.patient:
108
+ return pev.patient
109
+ if self.patient_findings:
110
+ for pf in self.patient_findings:
111
+ if hasattr(pf, 'patient') and pf.patient:
112
+ return pf.patient
113
+ # Check PatientMedication
114
+ if self.patient_medications:
115
+ for pm in self.patient_medications:
116
+ if hasattr(pm, 'patient') and pm.patient:
117
+ return pm.patient
118
+ # Check PatientMedicationSchedule
119
+ if self.patient_medication_schedules:
120
+ for pms in self.patient_medication_schedules:
121
+ if hasattr(pms, 'patient') and pms.patient:
122
+ return pms.patient
123
+ return None
124
+
125
+ @property
126
+ def data_model_dict(self):
127
+ """
128
+ Provides access to the data model dictionary used for requirement type parsing.
129
+
130
+ Returns:
131
+ The `data_model_dict` imported from the requirement type parser module.
132
+ """
133
+ from endoreg_db.models.requirement.requirement_evaluation.requirement_type_parser import data_model_dict
134
+ return data_model_dict
135
+
136
+ @property
137
+ def data_model_dict_reverse(self):
138
+ """
139
+ Provides a reverse mapping dictionary for data model types used in requirement evaluation.
140
+
141
+ Returns:
142
+ The `data_model_dict_reverse` dictionary imported from the requirement type parser module.
143
+ """
144
+ from endoreg_db.models.requirement.requirement_evaluation.requirement_type_parser import data_model_dict_reverse
145
+
146
+ return data_model_dict_reverse
147
+
148
+ def match_any(self, other:"RequirementLinks") -> bool:
149
+ """
150
+ Determines if any linked model in this instance is also present in another RequirementLinks instance.
151
+
152
+ Compares each list attribute of both instances and returns True if any element in any list overlaps.
153
+ """
154
+
155
+ other_dict = other.model_dump()
156
+ self_dict = self.model_dump()
157
+ for key in self_dict:
158
+ # print(f"Checking key: {key}") # This is a debug print, can be removed
159
+ if key in other_dict and self_dict[key] and other_dict[key]:
160
+ if any(item in other_dict[key] for item in self_dict[key]):
161
+ return True
162
+ return False # Ensure False is returned if no match is found
163
+
164
+ def active(self) -> dict[str, list]:
165
+ """
166
+ Returns a dictionary of all non-empty linked model lists.
167
+
168
+ Only attributes with non-empty lists are included in the returned dictionary.
169
+ """
170
+ active_links_dict = {}
171
+ # Use model_dump() to iterate field data reliably (pydantic v2)
172
+ for field_name, field_value in self.model_dump().items():
173
+ if isinstance(field_value, list) and field_value:
174
+ active_links_dict[field_name] = field_value
175
+ return active_links_dict
176
+
177
+ def __repr__(self):
178
+ """
179
+ Returns a concise string summarizing the counts of each linked model list in the instance.
180
+ """
181
+ data = self.model_dump()
182
+ fields = [
183
+ 'examinations', 'examination_indications', 'patient_examinations',
184
+ 'lab_values', 'patient_lab_values', 'patient_diseases', 'diseases',
185
+ 'disease_classification_choices', 'events', 'patient_events', 'findings',
186
+ 'patient_findings', 'finding_classification_choices', 'finding_interventions',
187
+ 'patient_medications', 'patient_medication_schedules', 'medications',
188
+ 'medication_indications', 'medication_intake_times', 'medication_schedules'
189
+ ]
190
+ parts = [f"{f}={len(data.get(f, []))}" for f in fields]
191
+ return f"RequirementLinks({', '.join(parts)})"
192
+
193
+
File without changes
@@ -0,0 +1,76 @@
1
+ # Use faker library to generate fake names by gender
2
+ # Use german names by default
3
+
4
+ from faker import Faker
5
+ import gender_guesser.detector as gender_detector
6
+
7
+
8
+ def create_mock_examiner_name() -> tuple[str, str]:
9
+ """
10
+ Generate a mock examiner's name using the Faker library.
11
+ This function creates a tuple with a first name and a last name for a mock examiner. It utilizes the "de_DE" locale for generating German names.
12
+ Returns:
13
+ tuple[str, str]: A tuple containing the first name and the last name.
14
+ """
15
+
16
+ fake = Faker("de_DE")
17
+ first_name = fake.first_name()
18
+ last_name = fake.last_name()
19
+ return first_name, last_name
20
+
21
+
22
+ def create_mock_patient_name(gender: str) -> tuple[str, str]:
23
+ """
24
+ Generate a mock patient's name based on the provided gender using the Faker library.
25
+ This function creates a tuple with a first name and a last name for a mock patient. It utilizes the "de_DE" locale for generating German names. When the input gender string is checked:
26
+ - If it contains "male", a male name is generated.
27
+ - If it contains "female", a female name is generated.
28
+ - Otherwise, a generic name is generated without considering gender.
29
+ Parameters:
30
+ gender (str): A string indicating the gender to be used for generating the name.
31
+ Returns:
32
+ tuple[str, str]: A tuple containing the first name and the last name.
33
+ """
34
+
35
+ fake = Faker("de_DE")
36
+
37
+ if "male" in gender.lower():
38
+ gender = "male"
39
+ elif "female" in gender.lower():
40
+ gender = "female"
41
+
42
+ if gender == "male":
43
+ first_name = fake.first_name_male()
44
+ last_name = fake.last_name_male()
45
+
46
+ elif gender == "female":
47
+ first_name = fake.first_name_female()
48
+ last_name = fake.last_name_female()
49
+
50
+ else:
51
+ first_name = fake.first_name()
52
+ last_name = fake.last_name()
53
+
54
+ return first_name, last_name
55
+
56
+
57
+ def guess_name_gender(name: str) -> str:
58
+ """
59
+ Guesses the gender for a given name by using a gender detector and retrieving the corresponding Gender model instance.
60
+ Parameters:
61
+ name (str): The name for which the gender is to be determined.
62
+ Returns:
63
+ Gender: The Gender object corresponding to the detected gender name.
64
+ Raises:
65
+ Gender.DoesNotExist: If no Gender object matching the detected gender is found.
66
+ Exception: For any other exceptions that occur during gender detection or database lookup.
67
+ """
68
+
69
+ from endoreg_db.models import Gender
70
+
71
+ detector = gender_detector.Detector(case_sensitive=False)
72
+ gender_name = detector.get_gender(name)
73
+ gender = Gender.objects.get(name=gender_name)
74
+ if not gender:
75
+ gender = Gender.objects.get(name="unknown")
76
+ return gender
@@ -0,0 +1,190 @@
1
+ import pytesseract
2
+ from PIL import Image, ImageOps, ImageFilter
3
+ import os
4
+ from collections import Counter
5
+ from tempfile import TemporaryDirectory
6
+ import re
7
+ from datetime import datetime
8
+ from typing import Dict, List
9
+ import numpy as np
10
+ from endoreg_db.utils.cropping import crop_and_insert
11
+
12
+
13
+
14
+ N_FRAMES_MEAN_OCR = 2
15
+
16
+ # Helper function to process date strings
17
+ def process_date_text(date_text):
18
+ """
19
+ Processes a string of text that represents a date and returns a datetime.date object.
20
+
21
+ Args:
22
+ date_text (str): A string of text that represents a date.
23
+
24
+ Returns:
25
+ datetime.date: A datetime.date object representing the parsed date, or None if the text cannot be parsed.
26
+ """
27
+ try:
28
+ # Remove any non-digit characters
29
+ date_text_clean = re.sub(r'\D', '', date_text)
30
+ # Reformat to 'ddmmyyyy' if necessary
31
+ if len(date_text_clean) == 8:
32
+ return datetime.strptime(date_text_clean, "%d%m%Y").date()
33
+ elif len(date_text_clean) == 14:
34
+ return datetime.strptime(date_text_clean, "%d%m%Y%H%M%S").date()
35
+ except ValueError:
36
+ # Return None if the text cannot be parsed into a date
37
+ # set date to 1/1/1900
38
+ return datetime.strptime("01011900", "%d%m%Y").date()
39
+
40
+ # Helper function to process patient names
41
+ def process_name_text(name_text):
42
+ """
43
+ Remove all numbers, punctuation, and whitespace from a string of text and return the result.
44
+ """
45
+ name = re.sub(r'[0-9!"#$%&\'()*+,-./:;<=>?@[\\]^_`{|}~\s]+', '', name_text).strip()
46
+ # capitalize first letter of each word
47
+ name = ' '.join([word.capitalize() for word in name.split()])
48
+ return name
49
+
50
+
51
+ # Helper function to process endoscope type text
52
+ def process_general_text(endoscope_text):
53
+ """
54
+ This function takes in a string of text from an endoscope and returns a cleaned version of the text.
55
+ """
56
+ return ' '.join(endoscope_text.split())
57
+
58
+ def roi_values_valid(roi):
59
+ """
60
+ Check if all values in an ROI dictionary are valid (>=0).
61
+ """
62
+ return all([value >= 0 for value in roi.values()])
63
+
64
+ # Function to extract text from ROIs
65
+ def extract_text_from_rois(image_path, processor):
66
+ """
67
+ Extracts text from regions of interest (ROIs) in an image using OCR.
68
+
69
+ Args:
70
+ image_path (str): The path to the image file.
71
+ processor (EndoscopyProcessor): An instance of the EndoscopyProcessor class.
72
+
73
+ Returns:
74
+ dict: A dictionary containing the extracted text for each ROI.
75
+ """
76
+ # Read the image using Pillow
77
+ image = Image.open(image_path)
78
+ image_dimensions = image.size # (width, height)
79
+
80
+ ####### Adjust Image #######
81
+ # Convert to grayscale
82
+ gray = image.convert('L')
83
+
84
+ # Invert colors for white text on black background
85
+ inverted = ImageOps.invert(gray)
86
+
87
+ # Initialize the dictionary to hold the extracted text
88
+ extracted_texts = {}
89
+
90
+ # Define your ROIs and their corresponding post-processing functions in tuples
91
+ rois_with_postprocessing = [
92
+ ('examination_date', processor.get_roi_examination_date, process_date_text),
93
+ ("patient_first_name", processor.get_roi_patient_first_name, process_name_text),
94
+ ('patient_last_name', processor.get_roi_patient_last_name, process_name_text),
95
+ ('patient_dob', processor.get_roi_patient_dob, process_date_text),
96
+ ('endoscope_type', processor.get_roi_endoscope_type, process_general_text),
97
+ ('endoscope_sn', processor.get_roi_endoscopy_sn, process_general_text),
98
+ ]
99
+
100
+ # Extract and post-process text for each ROI
101
+ for roi_name, roi_function, post_process in rois_with_postprocessing:
102
+ # Get the ROI dictionary
103
+ roi = roi_function()
104
+
105
+ # Check if the ROI has values
106
+
107
+ if roi_values_valid(roi):
108
+ x, y, w, h = roi['x'], roi['y'], roi['width'], roi['height']
109
+
110
+ # Get white image with original shape and just the roi remaining
111
+ roi_image = crop_and_insert(inverted, x,y,h,w)
112
+
113
+ # OCR configuration: Recognize white text on black background without corrections
114
+ config = '--psm 10 -c tessedit_char_whitelist=0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ-üöäÜÖÄß'
115
+
116
+ # Use pytesseract to do OCR on the preprocessed ROI
117
+ text = pytesseract.image_to_string(roi_image, config=config).strip()
118
+
119
+ # Post-process extracted text
120
+ processed_text = post_process(text)
121
+
122
+ extracted_texts[roi_name] = processed_text
123
+
124
+ else:
125
+ pass
126
+
127
+ return extracted_texts
128
+
129
+ def get_most_frequent_values(rois_texts: Dict[str, List[str]]) -> Dict[str, str]:
130
+ """
131
+ Given a dictionary of ROIs and their corresponding texts, returns a dictionary of the most frequent text for each ROI.
132
+
133
+ Args:
134
+ rois_texts: A dictionary where the keys are the names of the ROIs and the values are lists of texts.
135
+
136
+ Returns:
137
+ A dictionary where the keys are the names of the ROIs and the values are the most frequent text for each ROI.
138
+ """
139
+ most_frequent = {}
140
+ for key in rois_texts.keys():
141
+ counter = Counter([text for text in rois_texts[key] if text])
142
+ most_frequent[key], _ = counter.most_common(1)[0] if counter else (None, None)
143
+ return most_frequent
144
+
145
+ def process_video(video_path, processor):
146
+ """
147
+ Processes a video file by extracting text from regions of interest (ROIs) in each frame.
148
+
149
+ Args:
150
+ video_path (str): The path to the video file to process.
151
+ processor (OCRProcessor): An instance of the OCRProcessor class that defines the ROIs to extract text from.
152
+
153
+ Returns:
154
+ dict: A dictionary containing the most frequent text values extracted from each ROI.
155
+ """
156
+ # Create a temporary directory to store frames
157
+ with TemporaryDirectory() as temp_dir:
158
+ # Capture the video
159
+ video = cv2.VideoCapture(video_path)
160
+ success, frame_number = True, 0
161
+ rois_texts = {roi_name: [] for roi_name in processor.get_rois().keys()}
162
+ frames_for_mean_extraction = 0
163
+
164
+ while success:
165
+ success, frame = video.read()
166
+
167
+ # Check if this is the 200th frame
168
+ if frame_number % 1000 == 0 and success:
169
+ frame_path = os.path.join(temp_dir, f"frame_{frame_number}.jpg")
170
+ cv2.imwrite(frame_path, frame) # Save the frame as a JPEG file
171
+ # cv2.imwrite(f"_tmp/frame_{frame_number}.jpg", frame)
172
+
173
+ # Extract text from ROIs
174
+ extracted_texts = extract_text_from_rois(frame_path, processor)
175
+
176
+ # Store the extracted text from each ROI
177
+ for key, text in extracted_texts.items():
178
+ rois_texts[key].append(text)
179
+ frames_for_mean_extraction += 1
180
+
181
+ frame_number += 1
182
+
183
+ if frames_for_mean_extraction >= N_FRAMES_MEAN_OCR: break
184
+
185
+ # Release the video capture object
186
+ video.release()
187
+
188
+ # Get the most frequent values for each ROI
189
+ return get_most_frequent_values(rois_texts)
190
+
@@ -0,0 +1,46 @@
1
+ import yaml
2
+ from pathlib import Path
3
+
4
+ # get this files path
5
+ file_path = Path(__file__)
6
+ module_root = file_path.parent.parent
7
+ data_dir = module_root / "data"
8
+
9
+
10
+ def collect_center_names(
11
+ ):
12
+ input_file_path = data_dir / "center/data.yaml"
13
+ fist_name_dir = data_dir / "names_first"
14
+ last_name_dir = data_dir / "names_last"
15
+ # Load the input YAML file
16
+ with open(input_file_path, 'r', encoding='utf-8') as file:
17
+ data = yaml.safe_load(file)
18
+
19
+ # Containers for first and last names
20
+ first_names_set = set()
21
+ last_names_set = set()
22
+
23
+ # Extract first and last names from the YAML data
24
+ for entry in data:
25
+ fields = entry.get('fields', {})
26
+ first_names_set.update(fields.get('first_names', []))
27
+ last_names_set.update(fields.get('last_names', []))
28
+
29
+ # Create a list of dictionaries for first and last names
30
+ first_names_data = [
31
+ {"model": "endoreg_db.first_name", "fields": {"name": name}}
32
+ for name in sorted(first_names_set)
33
+ ]
34
+ last_names_data = [
35
+ {"model": "endoreg_db.last_name", "fields": {"name": name}}
36
+ for name in sorted(last_names_set)
37
+ ]
38
+
39
+ # Write the data to separate YAML files
40
+ with open(fist_name_dir/"first_names.yaml", "w", encoding='utf-8') as first_file:
41
+ yaml.dump(first_names_data, first_file, allow_unicode=True, sort_keys=False)
42
+
43
+ with open(last_name_dir/"last_names.yaml", "w", encoding='utf-8') as last_file:
44
+ yaml.dump(last_names_data, last_file, allow_unicode=True, sort_keys=False)
45
+
46
+ # print("Generated first_names.yaml and last_names.yaml successfully.")
@@ -0,0 +1,95 @@
1
+ """
2
+ Centralizes path management for the application.
3
+
4
+ This module sets up all necessary directories for storage and import operations.
5
+ It provides a unified dictionary 'data_paths' for accessing all path objects.
6
+ """
7
+
8
+ from logging import getLogger
9
+
10
+ from sphinx.search import no
11
+ logger = getLogger(__name__)
12
+
13
+ from pathlib import Path
14
+ from typing import Dict
15
+ import os
16
+ # Alternative approach using env_path helper, deprecated since monorepo setup. Alright for single install, env is always preferred.
17
+ #from endoreg_db.config.env import env_path
18
+
19
+ STORAGE_DIR = Path(os.getenv("STORAGE_DIR", "storage"))
20
+
21
+ storage_dir_env = os.getenv("STORAGE_DIR")
22
+ if storage_dir_env is None:
23
+ raise RuntimeError("STORAGE_DIR environment variable is not set.")
24
+ storage_dir_str = Path(storage_dir_env)
25
+ STORAGE_DIR = storage_dir_str
26
+ if not STORAGE_DIR.exists():
27
+ STORAGE_DIR.mkdir(parents=True, exist_ok=True)
28
+
29
+ PREFIX_RAW = "raw_"
30
+ IMPORT_DIR_NAME = "import"
31
+ EXPORT_DIR_NAME = "export"
32
+
33
+ VIDEO_DIR_NAME = "videos"
34
+ ANONYM_VIDEO_DIR_NAME = "anonym_videos" # Added for processed videos
35
+ FRAME_DIR_NAME = "frames"
36
+ PDF_DIR_NAME = "pdfs" # Changed from reports
37
+ WEIGHTS_DIR_NAME = "model_weights"
38
+ EXAMINATION_DIR_NAME = "examinations"
39
+
40
+ RAW_VIDEO_DIR_NAME = f"{PREFIX_RAW}videos"
41
+ RAW_FRAME_DIR_NAME = f"{PREFIX_RAW}frames"
42
+ RAW_PDF_DIR_NAME = f"{PREFIX_RAW}pdfs" # Changed from reports
43
+
44
+ # Define data subdirectories under STORAGE_DIR
45
+ VIDEO_DIR = STORAGE_DIR / VIDEO_DIR_NAME
46
+ ANONYM_VIDEO_DIR = STORAGE_DIR / ANONYM_VIDEO_DIR_NAME # Added
47
+ FRAME_DIR = STORAGE_DIR / FRAME_DIR_NAME
48
+ PDF_DIR = STORAGE_DIR / PDF_DIR_NAME # Changed
49
+ WEIGHTS_DIR = STORAGE_DIR / WEIGHTS_DIR_NAME
50
+ RAW_VIDEO_DIR = STORAGE_DIR / RAW_VIDEO_DIR_NAME
51
+ RAW_FRAME_DIR = STORAGE_DIR / RAW_FRAME_DIR_NAME
52
+ RAW_PDF_DIR = STORAGE_DIR / RAW_PDF_DIR_NAME # Changed
53
+
54
+ IMPORT_DIR = STORAGE_DIR / IMPORT_DIR_NAME
55
+ VIDEO_IMPORT_DIR = IMPORT_DIR / VIDEO_DIR_NAME
56
+ FRAME_IMPORT_DIR = IMPORT_DIR / FRAME_DIR_NAME
57
+ PDF_IMPORT_DIR = IMPORT_DIR / PDF_DIR_NAME # Changed
58
+ WEIGHTS_IMPORT_DIR = IMPORT_DIR / WEIGHTS_DIR_NAME
59
+
60
+ EXPORT_DIR = STORAGE_DIR / EXPORT_DIR_NAME
61
+
62
+ data_paths:Dict[str,Path] = {
63
+ "storage": STORAGE_DIR,
64
+ "video": VIDEO_DIR,
65
+ "anonym_video": ANONYM_VIDEO_DIR, # Added
66
+ "frame": FRAME_DIR,
67
+ "pdf": PDF_DIR, # Changed
68
+ "import": IMPORT_DIR,
69
+ "video_import": VIDEO_IMPORT_DIR,
70
+ "frame_import": FRAME_IMPORT_DIR,
71
+ "pdf_import": PDF_IMPORT_DIR, # Changed
72
+ "raw_video": RAW_VIDEO_DIR,
73
+ "raw_frame": RAW_FRAME_DIR,
74
+ "raw_pdf": RAW_PDF_DIR, # Changed
75
+ "weights": WEIGHTS_DIR,
76
+ "weights_import": WEIGHTS_IMPORT_DIR,
77
+ "export": EXPORT_DIR,
78
+ "video_export": EXPORT_DIR / VIDEO_DIR_NAME,
79
+ "anonym_video_export": EXPORT_DIR / ANONYM_VIDEO_DIR_NAME, # Added
80
+ "frame_export": EXPORT_DIR / FRAME_DIR_NAME,
81
+ "pdf_export": EXPORT_DIR / PDF_DIR_NAME, # Changed
82
+ "weights_export": EXPORT_DIR / WEIGHTS_DIR_NAME,
83
+ "examination_export": EXPORT_DIR / EXAMINATION_DIR_NAME,
84
+ "raw_video_export": EXPORT_DIR / RAW_VIDEO_DIR_NAME,
85
+ "raw_frame_export": EXPORT_DIR / RAW_FRAME_DIR_NAME,
86
+ "raw_pdf_export": EXPORT_DIR / RAW_PDF_DIR_NAME, # Changed
87
+ }
88
+
89
+ logger.info(f"Storage directory: {STORAGE_DIR.resolve()}")
90
+ logger.info(f"Export directory: {EXPORT_DIR.resolve()}")
91
+
92
+ # for key, path in data_paths.items():
93
+ # path.mkdir(parents=True, exist_ok=True)
94
+
95
+ # logger.info(f"{key.capitalize()} directory: {path.resolve()}")