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
@@ -0,0 +1,149 @@
1
+ from rest_framework.views import APIView
2
+ from rest_framework.response import Response
3
+ from rest_framework import status
4
+ from django.http import FileResponse, Http404
5
+ from ..models import RawVideoFile, Label
6
+ from ..serializers.video_segmentation import VideoFileSerializer,VideoListSerializer,LabelSerializer
7
+ import mimetypes
8
+ import os
9
+
10
+
11
+ class VideoView(APIView):
12
+ """
13
+ API endpoint to:
14
+ - Fetch video metadata (JSON)
15
+ - Serve the actual video file dynamically
16
+ """
17
+
18
+ def get(self, request, video_id=None):
19
+ """
20
+ Handles GET requests:
21
+ - If no `video_id` is provided, return a list of all videos for frontend dropdown.
22
+ - If `Accept: application/json` is in the request headers, return metadata for a specific video.
23
+ - Otherwise, return the video file.
24
+ """
25
+ if video_id is None:
26
+ return self.get_all_videos()
27
+ return self.get_video_details(request, video_id)
28
+
29
+ def get_all_videos(self):
30
+ """
31
+ Returns a list of all available videos along with available labels.
32
+ Used to populate the video selection dropdown in Vue.js.
33
+ """
34
+ videos = RawVideoFile.objects.all()
35
+ labels = Label.objects.all() # Fetch all labels
36
+
37
+ video_serializer = VideoListSerializer(videos, many=True)
38
+ label_serializer = LabelSerializer(labels, many=True) # Serialize labels
39
+
40
+ return Response({
41
+ "videos": video_serializer.data, # List of videos
42
+ "labels": label_serializer.data # List of labels
43
+ }, status=status.HTTP_200_OK)
44
+
45
+ def get_video_details(self, request, video_id):
46
+ """
47
+ Returns metadata for a specific video if `Accept: application/json` is set.
48
+ Otherwise, streams the video file.
49
+ """
50
+ try:
51
+ video_entry = RawVideoFile.objects.get(id=video_id)
52
+ serializer = VideoFileSerializer(video_entry, context={'request': request})
53
+
54
+ accept_header = request.headers.get('Accept', '')
55
+
56
+ if "application/json" in accept_header:
57
+ return Response(serializer.data, status=status.HTTP_200_OK)
58
+
59
+ return self.serve_video_file(video_entry)
60
+
61
+ except RawVideoFile.DoesNotExist:
62
+ return Response({"error": "Video not found in the database."}, status=status.HTTP_404_NOT_FOUND)
63
+ except Exception as e:
64
+ return Response({"error": f"Internal error: {str(e)}"}, status=status.HTTP_500_INTERNAL_SERVER_ERROR)
65
+
66
+ def serve_video_file(self, video_entry):
67
+ """
68
+ Serves the video file dynamically.
69
+ """
70
+ try:
71
+ full_video_path = video_entry.file.path # Get the correct file path
72
+
73
+ if not os.path.exists(full_video_path):
74
+ raise Http404("Video file not found.")
75
+
76
+ mime_type, _ = mimetypes.guess_type(full_video_path) # Determine the content type (e.g., video/mp4, video/avi)
77
+ response = FileResponse(open(full_video_path, "rb"), content_type=mime_type or "video/mp4")
78
+
79
+ # Enable video streaming and CORS
80
+ response["Access-Control-Allow-Origin"] = "*" # Allow frontend access
81
+ response["Access-Control-Allow-Credentials"] = "true"
82
+ response["Accept-Ranges"] = "bytes" # Enable seeking in video player
83
+ response["Content-Disposition"] = f'inline; filename="{os.path.basename(full_video_path)}"' # Instructs the browser to play the video instead of downloading it.
84
+
85
+ return response
86
+
87
+ except Exception as e:
88
+ return Response({"error": f"Internal error: {str(e)}"}, status=status.HTTP_500_INTERNAL_SERVER_ERROR)
89
+
90
+
91
+
92
+ from ..serializers.video_segmentation import VideoFileSerializer
93
+
94
+ class VideoLabelView(APIView):
95
+ """
96
+ API to fetch time segments (start & end times in seconds) for a specific label.
97
+ """
98
+
99
+ def get(self, request, video_id, label_name):
100
+ """
101
+ Handles GET request to return:
102
+ - Time segments for the selected label.
103
+ - Frame-wise predictions within those segments.
104
+ """
105
+ try:
106
+ video_entry = RawVideoFile.objects.get(id=video_id)
107
+
108
+ serializer = VideoFileSerializer(video_entry, context={'request': request})
109
+ label_data = serializer.get_label_time_segments(video_entry)
110
+
111
+ # Ensure the requested label exists
112
+ if label_name not in label_data:
113
+ return Response({"error": f"Label '{label_name}' not found"}, status=status.HTTP_404_NOT_FOUND)
114
+
115
+ return Response({
116
+ "label": label_name,
117
+ "time_segments": label_data[label_name]["time_ranges"],
118
+ "frame_predictions": label_data[label_name]["frame_predictions"]
119
+ }, status=status.HTTP_200_OK)
120
+
121
+ except RawVideoFile.DoesNotExist:
122
+ return Response({"error": "Video not found"}, status=status.HTTP_404_NOT_FOUND)
123
+
124
+ except Exception as e:
125
+ return Response({"error": f"Internal error: {str(e)}"}, status=status.HTTP_500_INTERNAL_SERVER_ERROR)
126
+
127
+
128
+ from ..serializers.video_segmentation import LabelSegmentUpdateSerializer, LabelSegmentSerializer
129
+
130
+ class UpdateLabelSegmentsView(APIView):
131
+ """
132
+ API to update or create label segments for a video.
133
+ """
134
+
135
+ def put(self, request, video_id, label_id):
136
+ """
137
+ Handles PUT request to update or create label segments.
138
+ """
139
+ serializer = LabelSegmentUpdateSerializer(data=request.data)
140
+
141
+ if serializer.is_valid():
142
+ result = serializer.save()
143
+ return Response({
144
+ "message": "Segments updated successfully",
145
+ "updated_segments": result["updated_segments"],
146
+ "new_segments": result["new_segments"]
147
+ }, status=status.HTTP_200_OK)
148
+
149
+ return Response(serializer.errors, status=status.HTTP_400_BAD_REQUEST)
@@ -0,0 +1,46 @@
1
+ from django.shortcuts import render, get_object_or_404
2
+ from ..models import RawVideoFile
3
+ import json
4
+ from ..serializers.video_segmentation import VideoFileSerializer
5
+
6
+ def video_timeline_view(request, video_id):
7
+ """
8
+ Fetches 'outside' label segments and passes their timestamps to the template.
9
+ """
10
+ video_entry = get_object_or_404(RawVideoFile, id=video_id)
11
+
12
+ # Get metadata (Assumes serializer method exists)
13
+ video_serializer = VideoFileSerializer(video_entry, context={'request': request})
14
+ label_segments = video_serializer.get_label_time_segments(video_entry)
15
+
16
+ segments = []
17
+ frame_markers = [] # Store frame timestamps
18
+ fps = 50 # Fixed FPS
19
+
20
+ # Ensure "outside" label exists
21
+ if "outside" in label_segments:
22
+ for segment in label_segments["outside"]["time_ranges"]:
23
+ segments.append({
24
+ "start_time": segment["start_time"],
25
+ "end_time": segment["end_time"]
26
+ })
27
+
28
+ # Extract frame timestamps for markers
29
+ for frame_num, _ in segment["frames"].items():
30
+ time_in_seconds = frame_num / fps
31
+ frame_markers.append(time_in_seconds)
32
+
33
+ # Set video duration correctly
34
+ video_duration = video_entry.duration if hasattr(video_entry, "duration") and video_entry.duration else 226 # Default to 226 seconds
35
+
36
+ print("Video ID:", video_id)
37
+ print("Segments:", segments)
38
+ print("Video Duration:", video_duration)
39
+
40
+ return render(request, "timeline.html", {
41
+ "video_id": video_id,
42
+ "video_url": video_serializer.get_video_url(video_entry),
43
+ "segments": json.dumps(segments), # Send segment start/end times
44
+ "frame_markers": json.dumps(frame_markers), # Send frame timestamps
45
+ "video_duration": video_duration,
46
+ })
@@ -1,10 +1,19 @@
1
- Metadata-Version: 2.2
1
+ Metadata-Version: 2.4
2
2
  Name: endoreg-db
3
- Version: 0.6.0
3
+ Version: 0.6.2
4
4
  Summary: EndoReg Db Django App
5
- Requires-Python: >=3.11
6
- Description-Content-Type: text/markdown
5
+ Project-URL: Homepage, https://info.coloreg.de
6
+ Project-URL: Repository, https://github.com/wg-lux/endoreg-db
7
+ Author: Max Hild, Hamza Zahid, Peter Kowalczyk
8
+ Author-email: "Thomas J. Lux" <lux_t1@ukw.de>
9
+ Maintainer: Max Hild, Hamza Zahid, Peter Kowalczyk
10
+ Maintainer-email: "Thomas J. Lux" <lux_t1@ukw.de>
7
11
  License-File: LICENSE
12
+ Classifier: Development Status :: 3 - Alpha
13
+ Classifier: Programming Language :: Python :: 3.11
14
+ Classifier: Programming Language :: Python :: 3.12
15
+ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
16
+ Requires-Python: >=3.11
8
17
  Requires-Dist: agl-report-reader>=0.4.0
9
18
  Requires-Dist: django-bootstrap5>=24.3
10
19
  Requires-Dist: django-cors-headers>=4.7.0
@@ -27,6 +36,7 @@ Requires-Dist: scipy>=1.14.1
27
36
  Requires-Dist: tesseract>=0.1.3
28
37
  Requires-Dist: tqdm>=4.67.0
29
38
  Requires-Dist: urllib3>=2.2.3
39
+ Description-Content-Type: text/markdown
30
40
 
31
41
  # EndoregDB - Professional Data Infrastructure for Clinical Research
32
42