endoreg-db 0.3.6__py3-none-any.whl → 0.8.6.1__py3-none-any.whl

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  1. endoreg_db/admin.py +92 -3
  2. endoreg_db/api_urls.py +4 -0
  3. endoreg_db/apps.py +18 -6
  4. endoreg_db/assets/dummy_model.ckpt +1 -0
  5. endoreg_db/codemods/readme.md +88 -0
  6. endoreg_db/codemods/rename_datetime_fields.py +92 -0
  7. endoreg_db/config/env.py +101 -0
  8. endoreg_db/data/__init__.py +144 -65
  9. endoreg_db/data/ai_model/data.yaml +7 -0
  10. endoreg_db/data/{label → ai_model_label}/label/data.yaml +88 -62
  11. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  12. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  13. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  14. endoreg_db/data/{label → ai_model_label}/label-type/data.yaml +6 -6
  15. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  16. endoreg_db/data/{model_type → ai_model_type}/data.yaml +6 -6
  17. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  18. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  19. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -167
  20. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +7 -7
  21. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +8 -8
  22. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +22 -22
  23. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +18 -18
  24. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +18 -18
  25. endoreg_db/data/case_template/rule/19_create_patient.yaml +16 -16
  26. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -35
  27. endoreg_db/data/case_template/rule_value_type/base_types.yaml +58 -58
  28. endoreg_db/data/case_template/template/base.yaml +7 -7
  29. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +2 -2
  30. endoreg_db/data/case_template/tmp/_rule_value +13 -13
  31. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -21
  32. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +9 -9
  33. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +6 -6
  34. endoreg_db/data/center/data.yaml +90 -59
  35. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -144
  36. endoreg_db/data/center_shift/ukw.yaml +9 -0
  37. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -48
  38. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  39. endoreg_db/data/db_summary.csv +58 -0
  40. endoreg_db/data/db_summary.xlsx +0 -0
  41. endoreg_db/data/disease/cardiovascular.yaml +37 -37
  42. endoreg_db/data/disease/hepatology.yaml +4 -4
  43. endoreg_db/data/disease/misc.yaml +5 -6
  44. endoreg_db/data/disease/renal.yaml +4 -4
  45. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -6
  46. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +5 -5
  47. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -41
  48. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +19 -19
  49. endoreg_db/data/distribution/date/patient.yaml +6 -6
  50. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  51. endoreg_db/data/distribution/single_categorical/patient.yaml +6 -6
  52. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -132
  53. endoreg_db/data/endoscope/data.yaml +93 -0
  54. endoreg_db/data/endoscope_type/data.yaml +10 -10
  55. endoreg_db/data/endoscopy_processor/data.yaml +50 -45
  56. endoreg_db/data/event/cardiology.yaml +15 -28
  57. endoreg_db/data/event/neurology.yaml +13 -13
  58. endoreg_db/data/event/surgery.yaml +12 -12
  59. endoreg_db/data/event/thrombembolism.yaml +19 -19
  60. endoreg_db/data/examination/examinations/data.yaml +72 -66
  61. endoreg_db/data/examination/time/data.yaml +47 -47
  62. endoreg_db/data/examination/time-type/data.yaml +7 -7
  63. endoreg_db/data/examination/type/data.yaml +17 -5
  64. endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
  65. endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
  66. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  67. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  68. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  69. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  70. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  71. endoreg_db/data/finding/complication.yaml +16 -0
  72. endoreg_db/data/finding/data.yaml +105 -0
  73. endoreg_db/data/finding/examination_setting.yaml +16 -0
  74. endoreg_db/data/finding/medication_related.yaml +18 -0
  75. endoreg_db/data/finding/outcome.yaml +12 -0
  76. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  77. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  78. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  79. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  80. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  81. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  82. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  83. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  84. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  85. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  86. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  87. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  88. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  89. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  90. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  91. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  92. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  93. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  94. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  95. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  96. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
  97. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  98. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  99. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  100. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
  101. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
  102. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
  103. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  104. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
  105. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
  106. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  107. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  108. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  109. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  110. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  111. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  112. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  113. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  114. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  115. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  116. endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
  117. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
  118. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
  119. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
  120. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
  121. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
  122. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  123. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  124. endoreg_db/data/finding_type/data.yaml +43 -0
  125. endoreg_db/data/gender/data.yaml +42 -18
  126. endoreg_db/data/information_source/annotation.yaml +6 -0
  127. endoreg_db/data/information_source/data.yaml +30 -30
  128. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  129. endoreg_db/data/information_source/medication.yaml +5 -5
  130. endoreg_db/data/information_source/prediction.yaml +7 -0
  131. endoreg_db/data/information_source_type/data.yaml +8 -0
  132. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -31
  133. endoreg_db/data/lab_value/coagulation.yaml +54 -49
  134. endoreg_db/data/lab_value/electrolytes.yaml +228 -190
  135. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -121
  136. endoreg_db/data/lab_value/hematology.yaml +184 -169
  137. endoreg_db/data/lab_value/hormones.yaml +59 -53
  138. endoreg_db/data/lab_value/lipids.yaml +53 -44
  139. endoreg_db/data/lab_value/misc.yaml +76 -30
  140. endoreg_db/data/lab_value/renal_function.yaml +12 -11
  141. endoreg_db/data/log_type/data.yaml +57 -0
  142. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  143. endoreg_db/data/lx_client_type/base.yaml +30 -0
  144. endoreg_db/data/lx_permission/base.yaml +24 -0
  145. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  146. endoreg_db/data/medication/anticoagulation.yaml +64 -64
  147. endoreg_db/data/medication/tah.yaml +69 -69
  148. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -120
  149. endoreg_db/data/medication_indication_type/data.yaml +10 -10
  150. endoreg_db/data/medication_indication_type/thrombembolism.yaml +40 -40
  151. endoreg_db/data/medication_intake_time/base.yaml +30 -30
  152. endoreg_db/data/medication_schedule/apixaban.yaml +94 -94
  153. endoreg_db/data/medication_schedule/ass.yaml +12 -12
  154. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -26
  155. endoreg_db/data/names_first/first_names.yaml +54 -0
  156. endoreg_db/data/names_last/last_names.yaml +51 -0
  157. endoreg_db/data/network_device/data.yaml +59 -0
  158. endoreg_db/data/network_device_type/data.yaml +12 -0
  159. endoreg_db/data/organ/data.yaml +29 -0
  160. endoreg_db/data/patient_lab_sample_type/generic.yaml +5 -5
  161. endoreg_db/data/pdf_type/data.yaml +46 -28
  162. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -66
  163. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -33
  164. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -308
  165. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -88
  166. endoreg_db/data/profession/data.yaml +70 -70
  167. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  168. endoreg_db/data/qualification/m2.yaml +39 -0
  169. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  170. endoreg_db/data/qualification/sonography.yaml +36 -0
  171. endoreg_db/data/qualification_type/base.yaml +29 -0
  172. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -55
  173. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  174. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -26
  175. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -19
  176. endoreg_db/data/requirement/age.yaml +26 -0
  177. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  178. endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
  179. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
  180. endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
  181. endoreg_db/data/requirement/disease_misc.yaml +12 -0
  182. endoreg_db/data/requirement/disease_renal.yaml +96 -0
  183. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
  184. endoreg_db/data/requirement/event_cardiology.yaml +251 -0
  185. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  186. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  187. endoreg_db/data/requirement/gender.yaml +25 -0
  188. endoreg_db/data/requirement/lab_value.yaml +441 -0
  189. endoreg_db/data/requirement/medication.yaml +93 -0
  190. endoreg_db/data/requirement_operator/age.yaml +13 -0
  191. endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
  192. endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
  193. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  194. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  195. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
  196. endoreg_db/data/requirement_set_type/data.yaml +20 -0
  197. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  198. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -15
  199. endoreg_db/data/risk/bleeding.yaml +26 -0
  200. endoreg_db/data/risk/thrombosis.yaml +37 -0
  201. endoreg_db/data/risk_type/data.yaml +27 -0
  202. endoreg_db/data/setup_config.yaml +38 -0
  203. endoreg_db/data/shift/endoscopy.yaml +21 -0
  204. endoreg_db/data/shift/m2.yaml +0 -0
  205. endoreg_db/data/shift_type/base.yaml +35 -0
  206. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  207. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -12
  208. endoreg_db/data/unit/concentration.yaml +115 -92
  209. endoreg_db/data/unit/data.yaml +17 -17
  210. endoreg_db/data/unit/length.yaml +30 -30
  211. endoreg_db/data/unit/misc.yaml +19 -19
  212. endoreg_db/data/unit/rate.yaml +5 -5
  213. endoreg_db/data/unit/time.yaml +48 -13
  214. endoreg_db/data/unit/volume.yaml +35 -35
  215. endoreg_db/data/unit/weight.yaml +37 -37
  216. endoreg_db/data/waste/data.yaml +11 -11
  217. endoreg_db/exceptions.py +19 -0
  218. endoreg_db/factories/__init__.py +0 -0
  219. endoreg_db/forms/__init__.py +5 -3
  220. endoreg_db/forms/examination_form.py +11 -0
  221. endoreg_db/forms/patient_finding_intervention_form.py +18 -0
  222. endoreg_db/forms/patient_form.py +27 -0
  223. endoreg_db/forms/questionnaires/__init__.py +1 -1
  224. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -23
  225. endoreg_db/forms/settings/__init__.py +8 -8
  226. endoreg_db/forms/unit.py +5 -5
  227. endoreg_db/helpers/__init__.py +0 -0
  228. endoreg_db/helpers/count_db.py +45 -0
  229. endoreg_db/helpers/data_loader.py +208 -0
  230. endoreg_db/helpers/default_objects.py +378 -0
  231. endoreg_db/helpers/download_segmentation_model.py +31 -0
  232. endoreg_db/helpers/interact.py +6 -0
  233. endoreg_db/helpers/test_video_helper.py +119 -0
  234. endoreg_db/logger_conf.py +140 -0
  235. endoreg_db/management/__init__.py +1 -0
  236. endoreg_db/management/commands/__init__.py +1 -0
  237. endoreg_db/management/commands/anonymize_video.py +0 -0
  238. endoreg_db/management/commands/check_auth.py +125 -0
  239. endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
  240. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  241. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  242. endoreg_db/management/commands/fix_video_paths.py +165 -0
  243. endoreg_db/management/commands/import_fallback_video.py +203 -0
  244. endoreg_db/management/commands/import_report.py +298 -0
  245. endoreg_db/management/commands/import_video.py +423 -0
  246. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  247. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  248. endoreg_db/management/commands/load_ai_model_data.py +77 -45
  249. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  250. endoreg_db/management/commands/load_base_db_data.py +192 -128
  251. endoreg_db/management/commands/load_center_data.py +68 -43
  252. endoreg_db/management/commands/{load_medication_intake_time_data.py → load_contraindication_data.py} +40 -40
  253. endoreg_db/management/commands/load_disease_classification_choices_data.py +40 -40
  254. endoreg_db/management/commands/load_disease_classification_data.py +40 -40
  255. endoreg_db/management/commands/load_disease_data.py +61 -39
  256. endoreg_db/management/commands/load_distribution_data.py +65 -65
  257. endoreg_db/management/commands/{load_endoscope_type_data.py → load_endoscope_data.py} +67 -44
  258. endoreg_db/management/commands/load_event_data.py +40 -40
  259. endoreg_db/management/commands/load_examination_data.py +74 -74
  260. endoreg_db/management/commands/load_examination_indication_data.py +86 -0
  261. endoreg_db/management/commands/load_finding_data.py +128 -0
  262. endoreg_db/management/commands/load_gender_data.py +43 -43
  263. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +131 -132
  264. endoreg_db/management/commands/load_information_source.py +50 -44
  265. endoreg_db/management/commands/load_lab_value_data.py +49 -49
  266. endoreg_db/management/commands/load_medication_data.py +103 -41
  267. endoreg_db/management/commands/load_name_data.py +37 -0
  268. endoreg_db/management/commands/{load_medication_indication_type_data.py → load_organ_data.py} +42 -40
  269. endoreg_db/management/commands/load_pdf_type_data.py +60 -60
  270. endoreg_db/management/commands/load_profession_data.py +43 -43
  271. endoreg_db/management/commands/load_qualification_data.py +59 -0
  272. endoreg_db/management/commands/{load_report_reader_flag.py → load_report_reader_flag_data.py} +45 -45
  273. endoreg_db/management/commands/load_requirement_data.py +180 -0
  274. endoreg_db/management/commands/load_risk_data.py +56 -0
  275. endoreg_db/management/commands/load_shift_data.py +60 -0
  276. endoreg_db/management/commands/load_tag_data.py +57 -0
  277. endoreg_db/management/commands/load_unit_data.py +45 -45
  278. endoreg_db/management/commands/load_user_groups.py +28 -28
  279. endoreg_db/management/commands/register_ai_model.py +64 -65
  280. endoreg_db/management/commands/reset_celery_schedule.py +9 -9
  281. endoreg_db/management/commands/setup_endoreg_db.py +381 -0
  282. endoreg_db/management/commands/start_filewatcher.py +106 -0
  283. endoreg_db/management/commands/storage_management.py +548 -0
  284. endoreg_db/management/commands/summarize_db_content.py +189 -0
  285. endoreg_db/management/commands/validate_video.py +204 -0
  286. endoreg_db/management/commands/validate_video_files.py +161 -0
  287. endoreg_db/management/commands/video_validation.py +22 -0
  288. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  289. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  290. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
  291. endoreg_db/mermaid/classification.md +8 -0
  292. endoreg_db/mermaid/examination.md +8 -0
  293. endoreg_db/mermaid/findings.md +7 -0
  294. endoreg_db/mermaid/image_classification.md +28 -0
  295. endoreg_db/mermaid/interventions.md +8 -0
  296. endoreg_db/mermaid/morphology.md +8 -0
  297. endoreg_db/mermaid/patient_creation.md +14 -0
  298. endoreg_db/mermaid/video_segmentation_annotation.md +17 -0
  299. endoreg_db/migrations/0001_initial.py +1857 -582
  300. endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
  301. endoreg_db/migrations/0003_add_center_display_name.py +30 -0
  302. endoreg_db/models/__init__.py +359 -74
  303. endoreg_db/models/administration/__init__.py +116 -0
  304. endoreg_db/models/administration/ai/__init__.py +9 -0
  305. endoreg_db/models/administration/ai/active_model.py +35 -0
  306. endoreg_db/models/administration/ai/ai_model.py +156 -0
  307. endoreg_db/models/{ai_model → administration/ai}/model_type.py +41 -26
  308. endoreg_db/models/administration/case/__init__.py +19 -0
  309. endoreg_db/models/administration/case/case.py +114 -0
  310. endoreg_db/models/{case_template → administration/case/case_template}/__init__.py +15 -6
  311. endoreg_db/models/{case_template → administration/case/case_template}/case_template.py +125 -81
  312. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule.py +269 -276
  313. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule_value.py +86 -73
  314. endoreg_db/models/{case_template → administration/case/case_template}/case_template_type.py +26 -28
  315. endoreg_db/models/{center → administration/center}/__init__.py +13 -4
  316. endoreg_db/models/administration/center/center.py +67 -0
  317. endoreg_db/models/administration/center/center_product.py +64 -0
  318. endoreg_db/models/administration/center/center_resource.py +49 -0
  319. endoreg_db/models/administration/center/center_shift.py +88 -0
  320. endoreg_db/models/administration/center/center_waste.py +30 -0
  321. endoreg_db/models/administration/permissions/__init__.py +44 -0
  322. endoreg_db/models/administration/person/__init__.py +24 -0
  323. endoreg_db/models/administration/person/employee/__init__.py +3 -0
  324. endoreg_db/models/administration/person/employee/employee.py +35 -0
  325. endoreg_db/models/administration/person/employee/employee_qualification.py +39 -0
  326. endoreg_db/models/administration/person/employee/employee_type.py +42 -0
  327. endoreg_db/models/administration/person/examiner/__init__.py +4 -0
  328. endoreg_db/models/administration/person/examiner/examiner.py +54 -0
  329. endoreg_db/models/administration/person/names/__init__.py +0 -0
  330. endoreg_db/models/{persons → administration/person/names}/first_name.py +18 -18
  331. endoreg_db/models/{persons → administration/person/names}/last_name.py +18 -19
  332. endoreg_db/models/administration/person/patient/__init__.py +5 -0
  333. endoreg_db/models/administration/person/patient/patient.py +460 -0
  334. endoreg_db/models/{persons → administration/person}/person.py +31 -31
  335. endoreg_db/models/administration/person/profession/__init__.py +24 -0
  336. endoreg_db/models/administration/person/user/__init__.py +5 -0
  337. endoreg_db/models/administration/person/user/portal_user_information.py +37 -0
  338. endoreg_db/models/administration/product/__init__.py +14 -0
  339. endoreg_db/models/administration/product/product.py +97 -0
  340. endoreg_db/models/administration/product/product_group.py +39 -0
  341. endoreg_db/models/administration/product/product_material.py +54 -0
  342. endoreg_db/models/{product → administration/product}/product_weight.py +47 -26
  343. endoreg_db/models/{product → administration/product}/reference_product.py +130 -99
  344. endoreg_db/models/administration/qualification/__init__.py +7 -0
  345. endoreg_db/models/administration/qualification/qualification.py +37 -0
  346. endoreg_db/models/administration/qualification/qualification_type.py +35 -0
  347. endoreg_db/models/administration/shift/__init__.py +9 -0
  348. endoreg_db/models/administration/shift/scheduled_days.py +69 -0
  349. endoreg_db/models/administration/shift/shift.py +51 -0
  350. endoreg_db/models/administration/shift/shift_type.py +108 -0
  351. endoreg_db/models/label/__init__.py +24 -1
  352. endoreg_db/models/label/annotation/__init__.py +12 -0
  353. endoreg_db/models/label/annotation/image_classification.py +84 -0
  354. endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
  355. endoreg_db/models/label/label.py +83 -84
  356. endoreg_db/models/label/label_set.py +53 -0
  357. endoreg_db/models/label/label_type.py +29 -0
  358. endoreg_db/models/label/label_video_segment/__init__.py +3 -0
  359. endoreg_db/models/label/label_video_segment/_create_from_video.py +41 -0
  360. endoreg_db/models/label/label_video_segment/label_video_segment.py +511 -0
  361. endoreg_db/models/label/video_segmentation_label.py +31 -0
  362. endoreg_db/models/label/video_segmentation_labelset.py +27 -0
  363. endoreg_db/models/media/__init__.py +16 -0
  364. endoreg_db/models/media/frame/__init__.py +3 -0
  365. endoreg_db/models/media/frame/frame.py +111 -0
  366. endoreg_db/models/media/pdf/__init__.py +11 -0
  367. endoreg_db/models/media/pdf/raw_pdf.py +757 -0
  368. endoreg_db/models/media/pdf/report_file.py +162 -0
  369. endoreg_db/models/media/pdf/report_reader/__init__.py +7 -0
  370. endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
  371. endoreg_db/models/{report_reader → media/pdf/report_reader}/report_reader_flag.py +19 -19
  372. endoreg_db/models/media/video/__init__.py +8 -0
  373. endoreg_db/models/media/video/create_from_file.py +358 -0
  374. endoreg_db/models/media/video/pipe_1.py +213 -0
  375. endoreg_db/models/media/video/pipe_2.py +105 -0
  376. endoreg_db/models/media/video/refactor_plan.md +0 -0
  377. endoreg_db/models/media/video/video_file.py +825 -0
  378. endoreg_db/models/media/video/video_file_ai.py +443 -0
  379. endoreg_db/models/media/video/video_file_anonymize.py +349 -0
  380. endoreg_db/models/media/video/video_file_frames/__init__.py +47 -0
  381. endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +22 -0
  382. endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
  383. endoreg_db/models/media/video/video_file_frames/_delete_frames.py +104 -0
  384. endoreg_db/models/media/video/video_file_frames/_extract_frames.py +174 -0
  385. endoreg_db/models/media/video/video_file_frames/_get_frame.py +28 -0
  386. endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +27 -0
  387. endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +20 -0
  388. endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +27 -0
  389. endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +34 -0
  390. endoreg_db/models/media/video/video_file_frames/_get_frames.py +27 -0
  391. endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +129 -0
  392. endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +141 -0
  393. endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +65 -0
  394. endoreg_db/models/media/video/video_file_frames.py +0 -0
  395. endoreg_db/models/media/video/video_file_io.py +168 -0
  396. endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
  397. endoreg_db/models/media/video/video_file_meta/get_crop_template.py +45 -0
  398. endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
  399. endoreg_db/models/media/video/video_file_meta/get_fps.py +147 -0
  400. endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +143 -0
  401. endoreg_db/models/media/video/video_file_meta/text_meta.py +134 -0
  402. endoreg_db/models/media/video/video_file_meta/video_meta.py +70 -0
  403. endoreg_db/models/media/video/video_file_segments.py +209 -0
  404. endoreg_db/models/media/video/video_metadata.py +65 -0
  405. endoreg_db/models/media/video/video_processing.py +152 -0
  406. endoreg_db/models/medical/__init__.py +146 -0
  407. endoreg_db/models/medical/contraindication/__init__.py +17 -0
  408. endoreg_db/models/medical/disease.py +156 -0
  409. endoreg_db/models/medical/event.py +137 -0
  410. endoreg_db/models/medical/examination/__init__.py +9 -0
  411. endoreg_db/models/medical/examination/examination.py +148 -0
  412. endoreg_db/models/medical/examination/examination_indication.py +278 -0
  413. endoreg_db/models/medical/examination/examination_time.py +49 -0
  414. endoreg_db/models/medical/examination/examination_time_type.py +41 -0
  415. endoreg_db/models/medical/examination/examination_type.py +48 -0
  416. endoreg_db/models/medical/finding/__init__.py +18 -0
  417. endoreg_db/models/medical/finding/finding.py +96 -0
  418. endoreg_db/models/medical/finding/finding_classification.py +142 -0
  419. endoreg_db/models/medical/finding/finding_intervention.py +52 -0
  420. endoreg_db/models/medical/finding/finding_type.py +35 -0
  421. endoreg_db/models/medical/hardware/__init__.py +8 -0
  422. endoreg_db/models/medical/hardware/endoscope.py +65 -0
  423. endoreg_db/models/{hardware → medical/hardware}/endoscopy_processor.py +182 -143
  424. endoreg_db/models/medical/laboratory/__init__.py +5 -0
  425. endoreg_db/models/medical/laboratory/lab_value.py +419 -0
  426. endoreg_db/models/medical/medication/__init__.py +19 -0
  427. endoreg_db/models/medical/medication/medication.py +31 -0
  428. endoreg_db/models/medical/medication/medication_indication.py +50 -0
  429. endoreg_db/models/medical/medication/medication_indication_type.py +39 -0
  430. endoreg_db/models/medical/medication/medication_intake_time.py +44 -0
  431. endoreg_db/models/medical/medication/medication_schedule.py +45 -0
  432. endoreg_db/models/medical/organ/__init__.py +35 -0
  433. endoreg_db/models/medical/patient/__init__.py +56 -0
  434. endoreg_db/models/medical/patient/medication_examples.py +38 -0
  435. endoreg_db/models/medical/patient/patient_disease.py +63 -0
  436. endoreg_db/models/medical/patient/patient_event.py +75 -0
  437. endoreg_db/models/medical/patient/patient_examination.py +249 -0
  438. endoreg_db/models/medical/patient/patient_examination_indication.py +44 -0
  439. endoreg_db/models/medical/patient/patient_finding.py +357 -0
  440. endoreg_db/models/medical/patient/patient_finding_classification.py +207 -0
  441. endoreg_db/models/medical/patient/patient_finding_intervention.py +40 -0
  442. endoreg_db/models/medical/patient/patient_lab_sample.py +148 -0
  443. endoreg_db/models/{persons → medical}/patient/patient_lab_value.py +222 -176
  444. endoreg_db/models/medical/patient/patient_medication.py +104 -0
  445. endoreg_db/models/medical/patient/patient_medication_schedule.py +136 -0
  446. endoreg_db/models/medical/risk/__init__.py +7 -0
  447. endoreg_db/models/medical/risk/risk.py +72 -0
  448. endoreg_db/models/medical/risk/risk_type.py +51 -0
  449. endoreg_db/models/metadata/__init__.py +19 -0
  450. endoreg_db/models/metadata/frame_ocr_result.py +0 -0
  451. endoreg_db/models/metadata/model_meta.py +206 -0
  452. endoreg_db/models/metadata/model_meta_logic.py +343 -0
  453. endoreg_db/models/{data_file/metadata → metadata}/pdf_meta.py +89 -70
  454. endoreg_db/models/metadata/sensitive_meta.py +288 -0
  455. endoreg_db/models/metadata/sensitive_meta_logic.py +1048 -0
  456. endoreg_db/models/metadata/video_meta.py +332 -0
  457. endoreg_db/models/metadata/video_prediction_logic.py +190 -0
  458. endoreg_db/models/metadata/video_prediction_meta.py +270 -0
  459. endoreg_db/models/other/__init__.py +40 -5
  460. endoreg_db/models/other/distribution/__init__.py +44 -0
  461. endoreg_db/models/other/distribution/base_value_distribution.py +20 -0
  462. endoreg_db/models/other/distribution/date_value_distribution.py +89 -0
  463. endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +32 -0
  464. endoreg_db/models/other/distribution/numeric_value_distribution.py +125 -0
  465. endoreg_db/models/other/distribution/single_categorical_value_distribution.py +22 -0
  466. endoreg_db/models/other/emission/__init__.py +5 -0
  467. endoreg_db/models/other/emission/emission_factor.py +94 -0
  468. endoreg_db/models/{persons → other}/gender.py +27 -22
  469. endoreg_db/models/other/information_source.py +159 -0
  470. endoreg_db/models/other/material.py +28 -16
  471. endoreg_db/models/other/resource.py +21 -17
  472. endoreg_db/models/other/tag.py +27 -0
  473. endoreg_db/models/other/transport_route.py +33 -21
  474. endoreg_db/models/{unit.py → other/unit.py} +32 -22
  475. endoreg_db/models/other/waste.py +27 -20
  476. endoreg_db/models/requirement/__init__.py +11 -0
  477. endoreg_db/models/requirement/requirement.py +767 -0
  478. endoreg_db/models/requirement/requirement_evaluation/__init__.py +6 -0
  479. endoreg_db/models/requirement/requirement_evaluation/get_values.py +40 -0
  480. endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +9 -0
  481. endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +95 -0
  482. endoreg_db/models/requirement/requirement_operator.py +176 -0
  483. endoreg_db/models/requirement/requirement_set.py +287 -0
  484. endoreg_db/models/rule/__init__.py +13 -0
  485. endoreg_db/models/{rules → rule}/rule.py +27 -24
  486. endoreg_db/models/{rules → rule}/rule_applicator.py +224 -224
  487. endoreg_db/models/{rules → rule}/rule_attribute_dtype.py +16 -18
  488. endoreg_db/models/{rules → rule}/rule_type.py +19 -21
  489. endoreg_db/models/{rules → rule}/ruleset.py +17 -19
  490. endoreg_db/models/state/__init__.py +12 -0
  491. endoreg_db/models/state/abstract.py +11 -0
  492. endoreg_db/models/state/audit_ledger.py +150 -0
  493. endoreg_db/models/state/label_video_segment.py +22 -0
  494. endoreg_db/models/state/raw_pdf.py +187 -0
  495. endoreg_db/models/state/sensitive_meta.py +46 -0
  496. endoreg_db/models/state/video.py +232 -0
  497. endoreg_db/models/upload_job.py +99 -0
  498. endoreg_db/models/utils.py +135 -0
  499. endoreg_db/queries/__init__.py +4 -4
  500. endoreg_db/queries/annotations/__init__.py +2 -2
  501. endoreg_db/queries/annotations/legacy.py +158 -159
  502. endoreg_db/renames.yml +8 -0
  503. endoreg_db/root_urls.py +9 -0
  504. endoreg_db/schemas/__init__.py +0 -0
  505. endoreg_db/schemas/examination_evaluation.py +27 -0
  506. endoreg_db/serializers/Frames_NICE_and_PARIS_classifications.py +775 -0
  507. endoreg_db/serializers/__init__.py +118 -10
  508. endoreg_db/serializers/_old/raw_pdf_meta_validation.py +223 -0
  509. endoreg_db/serializers/_old/raw_video_meta_validation.py +179 -0
  510. endoreg_db/serializers/_old/video.py +71 -0
  511. endoreg_db/serializers/administration/__init__.py +14 -0
  512. endoreg_db/serializers/administration/ai/__init__.py +10 -0
  513. endoreg_db/serializers/administration/ai/active_model.py +10 -0
  514. endoreg_db/serializers/administration/ai/ai_model.py +18 -0
  515. endoreg_db/serializers/administration/ai/model_type.py +10 -0
  516. endoreg_db/serializers/administration/center.py +9 -0
  517. endoreg_db/serializers/administration/gender.py +9 -0
  518. endoreg_db/serializers/anonymization.py +69 -0
  519. endoreg_db/serializers/evaluation/examination_evaluation.py +1 -0
  520. endoreg_db/serializers/examination/__init__.py +10 -0
  521. endoreg_db/serializers/examination/base.py +46 -0
  522. endoreg_db/serializers/examination/dropdown.py +21 -0
  523. endoreg_db/serializers/examination_serializer.py +12 -0
  524. endoreg_db/serializers/finding/__init__.py +5 -0
  525. endoreg_db/serializers/finding/finding.py +54 -0
  526. endoreg_db/serializers/finding_classification/__init__.py +7 -0
  527. endoreg_db/serializers/finding_classification/choice.py +19 -0
  528. endoreg_db/serializers/finding_classification/classification.py +13 -0
  529. endoreg_db/serializers/label/__init__.py +7 -0
  530. endoreg_db/serializers/label/image_classification_annotation.py +62 -0
  531. endoreg_db/serializers/label/label.py +15 -0
  532. endoreg_db/serializers/label_video_segment/__init__.py +7 -0
  533. endoreg_db/serializers/label_video_segment/_lvs_create.py +149 -0
  534. endoreg_db/serializers/label_video_segment/_lvs_update.py +138 -0
  535. endoreg_db/serializers/label_video_segment/_lvs_validate.py +149 -0
  536. endoreg_db/serializers/label_video_segment/label_video_segment.py +344 -0
  537. endoreg_db/serializers/label_video_segment/label_video_segment_annotation.py +99 -0
  538. endoreg_db/serializers/label_video_segment/label_video_segment_update.py +163 -0
  539. endoreg_db/serializers/meta/__init__.py +19 -0
  540. endoreg_db/serializers/meta/pdf_file_meta_extraction.py +115 -0
  541. endoreg_db/serializers/meta/report_meta.py +53 -0
  542. endoreg_db/serializers/meta/sensitive_meta_detail.py +162 -0
  543. endoreg_db/serializers/meta/sensitive_meta_update.py +148 -0
  544. endoreg_db/serializers/meta/sensitive_meta_verification.py +59 -0
  545. endoreg_db/serializers/meta/video_meta.py +39 -0
  546. endoreg_db/serializers/misc/__init__.py +14 -0
  547. endoreg_db/serializers/misc/file_overview.py +182 -0
  548. endoreg_db/serializers/misc/sensitive_patient_data.py +120 -0
  549. endoreg_db/serializers/misc/stats.py +33 -0
  550. endoreg_db/serializers/misc/translatable_field_mix_in.py +44 -0
  551. endoreg_db/serializers/misc/upload_job.py +71 -0
  552. endoreg_db/serializers/patient/__init__.py +11 -0
  553. endoreg_db/serializers/patient/patient.py +86 -0
  554. endoreg_db/serializers/patient/patient_dropdown.py +27 -0
  555. endoreg_db/serializers/patient_examination/__init__.py +7 -0
  556. endoreg_db/serializers/patient_examination/patient_examination.py +141 -0
  557. endoreg_db/serializers/patient_finding/__init__.py +15 -0
  558. endoreg_db/serializers/patient_finding/patient_finding.py +31 -0
  559. endoreg_db/serializers/patient_finding/patient_finding_classification.py +39 -0
  560. endoreg_db/serializers/patient_finding/patient_finding_detail.py +53 -0
  561. endoreg_db/serializers/patient_finding/patient_finding_intervention.py +26 -0
  562. endoreg_db/serializers/patient_finding/patient_finding_list.py +41 -0
  563. endoreg_db/serializers/patient_finding/patient_finding_write.py +126 -0
  564. endoreg_db/serializers/pdf/__init__.py +5 -0
  565. endoreg_db/serializers/pdf/anony_text_validation.py +85 -0
  566. endoreg_db/serializers/report/__init__.py +9 -0
  567. endoreg_db/serializers/report/mixins.py +45 -0
  568. endoreg_db/serializers/report/report.py +105 -0
  569. endoreg_db/serializers/report/report_list.py +22 -0
  570. endoreg_db/serializers/report/secure_file_url.py +26 -0
  571. endoreg_db/serializers/requirements/requirement_schema.py +25 -0
  572. endoreg_db/serializers/requirements/requirement_sets.py +29 -0
  573. endoreg_db/serializers/sensitive_meta_serializer.py +282 -0
  574. endoreg_db/serializers/video/__init__.py +7 -0
  575. endoreg_db/serializers/video/segmentation.py +263 -0
  576. endoreg_db/serializers/video/video_file_brief.py +10 -0
  577. endoreg_db/serializers/video/video_file_detail.py +83 -0
  578. endoreg_db/serializers/video/video_file_list.py +67 -0
  579. endoreg_db/serializers/video/video_metadata.py +105 -0
  580. endoreg_db/serializers/video/video_processing_history.py +153 -0
  581. endoreg_db/serializers/video_examination.py +198 -0
  582. endoreg_db/services/__init__.py +5 -0
  583. endoreg_db/services/anonymization.py +223 -0
  584. endoreg_db/services/examination_evaluation.py +149 -0
  585. endoreg_db/services/finding_description_service.py +0 -0
  586. endoreg_db/services/lookup_service.py +411 -0
  587. endoreg_db/services/lookup_store.py +266 -0
  588. endoreg_db/services/pdf_import.py +1382 -0
  589. endoreg_db/services/polling_coordinator.py +288 -0
  590. endoreg_db/services/pseudonym_service.py +89 -0
  591. endoreg_db/services/requirements_object.py +147 -0
  592. endoreg_db/services/segment_sync.py +155 -0
  593. endoreg_db/services/storage_aware_video_processor.py +344 -0
  594. endoreg_db/services/video_import.py +1259 -0
  595. endoreg_db/tasks/upload_tasks.py +207 -0
  596. endoreg_db/tasks/video_ingest.py +157 -0
  597. endoreg_db/tasks/video_processing_tasks.py +327 -0
  598. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  599. endoreg_db/templates/admin/start_examination.html +12 -0
  600. endoreg_db/templates/timeline.html +176 -0
  601. endoreg_db/urls/__init__.py +83 -0
  602. endoreg_db/urls/anonymization.py +32 -0
  603. endoreg_db/urls/auth.py +16 -0
  604. endoreg_db/urls/classification.py +39 -0
  605. endoreg_db/urls/examination.py +54 -0
  606. endoreg_db/urls/files.py +6 -0
  607. endoreg_db/urls/label_video_segment_validate.py +33 -0
  608. endoreg_db/urls/label_video_segments.py +46 -0
  609. endoreg_db/urls/media.py +227 -0
  610. endoreg_db/urls/patient.py +19 -0
  611. endoreg_db/urls/report.py +48 -0
  612. endoreg_db/urls/requirements.py +13 -0
  613. endoreg_db/urls/sensitive_meta.py +0 -0
  614. endoreg_db/urls/stats.py +46 -0
  615. endoreg_db/urls/upload.py +20 -0
  616. endoreg_db/urls/video.py +61 -0
  617. endoreg_db/urls.py +9 -0
  618. endoreg_db/utils/__init__.py +88 -1
  619. endoreg_db/utils/ai/__init__.py +9 -0
  620. endoreg_db/{models/ai_model/utils.py → utils/ai/get.py} +5 -8
  621. endoreg_db/utils/ai/inference_dataset.py +52 -0
  622. endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
  623. endoreg_db/utils/ai/postprocess.py +63 -0
  624. endoreg_db/utils/ai/predict.py +291 -0
  625. endoreg_db/utils/ai/preprocess.py +68 -0
  626. endoreg_db/utils/calc_duration_seconds.py +24 -0
  627. endoreg_db/utils/case_generator/__init__.py +0 -0
  628. endoreg_db/utils/case_generator/case_generator.py +159 -0
  629. endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
  630. endoreg_db/utils/case_generator/utils.py +30 -0
  631. endoreg_db/utils/check_video_files.py +148 -0
  632. endoreg_db/utils/cropping.py +28 -28
  633. endoreg_db/utils/dataloader.py +175 -92
  634. endoreg_db/utils/dates.py +60 -0
  635. endoreg_db/utils/env.py +33 -0
  636. endoreg_db/utils/extract_specific_frames.py +72 -0
  637. endoreg_db/utils/file_operations.py +58 -30
  638. endoreg_db/utils/fix_video_path_direct.py +141 -0
  639. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  640. endoreg_db/utils/hashs.py +153 -34
  641. endoreg_db/utils/links/__init__.py +0 -0
  642. endoreg_db/utils/links/requirement_link.py +193 -0
  643. endoreg_db/utils/mime_types.py +0 -0
  644. endoreg_db/utils/names.py +76 -0
  645. endoreg_db/utils/ocr.py +190 -197
  646. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  647. endoreg_db/utils/paths.py +95 -0
  648. endoreg_db/utils/permissions.py +143 -0
  649. endoreg_db/utils/pipelines/Readme.md +235 -0
  650. endoreg_db/utils/pipelines/__init__.py +0 -0
  651. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  652. endoreg_db/utils/product/__init__.py +0 -0
  653. endoreg_db/utils/product/sum_emissions.py +20 -0
  654. endoreg_db/utils/product/sum_weights.py +18 -0
  655. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  656. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  657. endoreg_db/utils/requirement_helpers.py +0 -0
  658. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  659. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  660. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  661. endoreg_db/utils/setup_config.py +177 -0
  662. endoreg_db/utils/translation.py +27 -0
  663. endoreg_db/utils/uuid.py +4 -4
  664. endoreg_db/utils/validate_endo_roi.py +19 -0
  665. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  666. endoreg_db/utils/validate_video_detailed.py +357 -0
  667. endoreg_db/utils/video/__init__.py +26 -0
  668. endoreg_db/utils/video/extract_frames.py +88 -0
  669. endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
  670. endoreg_db/utils/video/names.py +42 -0
  671. endoreg_db/utils/video/streaming_processor.py +312 -0
  672. endoreg_db/utils/video/video_splitter.py +94 -0
  673. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  674. endoreg_db/views/__init__.py +275 -0
  675. endoreg_db/views/anonymization/__init__.py +27 -0
  676. endoreg_db/views/anonymization/media_management.py +454 -0
  677. endoreg_db/views/anonymization/overview.py +216 -0
  678. endoreg_db/views/anonymization/validate.py +107 -0
  679. endoreg_db/views/auth/__init__.py +13 -0
  680. endoreg_db/views/auth/keycloak.py +113 -0
  681. endoreg_db/views/examination/__init__.py +33 -0
  682. endoreg_db/views/examination/examination.py +37 -0
  683. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  684. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  685. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  686. endoreg_db/views/examination/get_findings.py +41 -0
  687. endoreg_db/views/examination/get_instruments.py +18 -0
  688. endoreg_db/views/examination/get_interventions.py +14 -0
  689. endoreg_db/views/finding/__init__.py +9 -0
  690. endoreg_db/views/finding/finding.py +112 -0
  691. endoreg_db/views/finding/get_classifications.py +14 -0
  692. endoreg_db/views/finding/get_interventions.py +17 -0
  693. endoreg_db/views/finding_classification/__init__.py +13 -0
  694. endoreg_db/views/finding_classification/base.py +0 -0
  695. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  696. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  697. endoreg_db/views/label/__init__.py +5 -0
  698. endoreg_db/views/label/label.py +15 -0
  699. endoreg_db/views/label_video_segment/__init__.py +16 -0
  700. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  701. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  702. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  703. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  704. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  705. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  706. endoreg_db/views/label_video_segment/validate.py +226 -0
  707. endoreg_db/views/media/__init__.py +45 -0
  708. endoreg_db/views/media/pdf_media.py +388 -0
  709. endoreg_db/views/media/segments.py +71 -0
  710. endoreg_db/views/media/sensitive_metadata.py +314 -0
  711. endoreg_db/views/media/video_media.py +272 -0
  712. endoreg_db/views/media/video_segments.py +524 -0
  713. endoreg_db/views/meta/__init__.py +15 -0
  714. endoreg_db/views/meta/available_files_list.py +146 -0
  715. endoreg_db/views/meta/report_meta.py +53 -0
  716. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  717. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  718. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  719. endoreg_db/views/misc/__init__.py +63 -0
  720. endoreg_db/views/misc/center.py +13 -0
  721. endoreg_db/views/misc/csrf.py +7 -0
  722. endoreg_db/views/misc/gender.py +14 -0
  723. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  724. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  725. endoreg_db/views/misc/secure_url_validate.py +79 -0
  726. endoreg_db/views/misc/stats.py +220 -0
  727. endoreg_db/views/misc/translation.py +182 -0
  728. endoreg_db/views/misc/upload_views.py +240 -0
  729. endoreg_db/views/patient/__init__.py +5 -0
  730. endoreg_db/views/patient/patient.py +210 -0
  731. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  732. endoreg_db/views/patient_examination/__init__.py +11 -0
  733. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  734. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  735. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  736. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  737. endoreg_db/views/patient_examination/video.py +194 -0
  738. endoreg_db/views/patient_finding/__init__.py +7 -0
  739. endoreg_db/views/patient_finding/base.py +0 -0
  740. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  741. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  742. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  743. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  744. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  745. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  746. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  747. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  748. endoreg_db/views/pdf/__init__.py +8 -0
  749. endoreg_db/views/pdf/pdf_stream.py +187 -0
  750. endoreg_db/views/pdf/reimport.py +177 -0
  751. endoreg_db/views/report/__init__.py +9 -0
  752. endoreg_db/views/report/report_list.py +112 -0
  753. endoreg_db/views/report/report_with_secure_url.py +28 -0
  754. endoreg_db/views/report/start_examination.py +7 -0
  755. endoreg_db/views/requirement/__init__.py +10 -0
  756. endoreg_db/views/requirement/evaluate.py +279 -0
  757. endoreg_db/views/requirement/lookup.py +367 -0
  758. endoreg_db/views/requirement/lookup_store.py +252 -0
  759. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  760. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  761. endoreg_db/views/stats/__init__.py +13 -0
  762. endoreg_db/views/stats/stats_views.py +229 -0
  763. endoreg_db/views/video/__init__.py +59 -0
  764. endoreg_db/views/video/correction.py +530 -0
  765. endoreg_db/views/video/reimport.py +195 -0
  766. endoreg_db/views/video/segmentation.py +274 -0
  767. endoreg_db/views/video/task_status.py +49 -0
  768. endoreg_db/views/video/timeline.py +46 -0
  769. endoreg_db/views/video/video_analyze.py +52 -0
  770. endoreg_db/views/video/video_apply_mask.py +48 -0
  771. endoreg_db/views/video/video_correction.py +21 -0
  772. endoreg_db/views/video/video_download_processed.py +58 -0
  773. endoreg_db/views/video/video_examination_viewset.py +242 -0
  774. endoreg_db/views/video/video_meta.py +29 -0
  775. endoreg_db/views/video/video_processing_history.py +24 -0
  776. endoreg_db/views/video/video_remove_frames.py +48 -0
  777. endoreg_db/views/video/video_stream.py +306 -0
  778. endoreg_db/views.py +0 -3
  779. endoreg_db-0.8.6.1.dist-info/METADATA +383 -0
  780. endoreg_db-0.8.6.1.dist-info/RECORD +793 -0
  781. {endoreg_db-0.3.6.dist-info → endoreg_db-0.8.6.1.dist-info}/WHEEL +1 -1
  782. {endoreg_db-0.3.6.dist-info → endoreg_db-0.8.6.1.dist-info/licenses}/LICENSE +674 -674
  783. endoreg_db/data/active_model/data.yaml +0 -3
  784. endoreg_db/data/label/label-set/data.yaml +0 -18
  785. endoreg_db/management/commands/_load_model_template.py +0 -41
  786. endoreg_db/management/commands/delete_all.py +0 -18
  787. endoreg_db/management/commands/delete_legacy_images.py +0 -19
  788. endoreg_db/management/commands/delete_legacy_videos.py +0 -17
  789. endoreg_db/management/commands/extract_legacy_video_frames.py +0 -18
  790. endoreg_db/management/commands/fetch_legacy_image_dataset.py +0 -32
  791. endoreg_db/management/commands/fix_auth_permission.py +0 -20
  792. endoreg_db/management/commands/import_legacy_images.py +0 -94
  793. endoreg_db/management/commands/import_legacy_videos.py +0 -76
  794. endoreg_db/management/commands/load_active_model_data.py +0 -45
  795. endoreg_db/management/commands/load_endoscopy_processor_data.py +0 -45
  796. endoreg_db/management/commands/load_g_play_data.py +0 -113
  797. endoreg_db/management/commands/load_label_data.py +0 -67
  798. endoreg_db/management/commands/load_medication_indication_data.py +0 -63
  799. endoreg_db/management/commands/load_medication_schedule_data.py +0 -55
  800. endoreg_db/migrations/0002_rawvideofile.py +0 -26
  801. endoreg_db/migrations/0003_rawvideofile_frames_required.py +0 -18
  802. endoreg_db/migrations/0004_rename_hash_rawvideofile_video_hash.py +0 -18
  803. endoreg_db/migrations/0005_ffmpegmeta_remove_videoimportmeta_center_and_more.py +0 -56
  804. endoreg_db/migrations/0006_rawvideofile_center_alter_videometa_processor.py +0 -25
  805. endoreg_db/migrations/0007_rawvideofile_processor.py +0 -19
  806. endoreg_db/migrations/0008_rename_frames_required_rawvideofile_state_frames_required.py +0 -18
  807. endoreg_db/migrations/0009_sensitivemeta_rawvideofile_sensitive_meta.py +0 -31
  808. endoreg_db/migrations/0010_rename_endoscope_serial_number_sensitivemeta_endoscope_sn.py +0 -18
  809. endoreg_db/migrations/0011_rawvideofile_state_sensitive_data_retrieved.py +0 -18
  810. endoreg_db/migrations/0012_rawvideofile_prediction_dir_and_more.py +0 -109
  811. endoreg_db/migrations/0013_rawpdffile.py +0 -31
  812. endoreg_db/migrations/0014_pdftype_alter_rawpdffile_file_pdfmeta.py +0 -38
  813. endoreg_db/migrations/0015_rename_report_processed_rawpdffile_state_report_processed_and_more.py +0 -31
  814. endoreg_db/migrations/0016_rawpdffile_state_report_processing_required.py +0 -18
  815. endoreg_db/migrations/0017_firstname_lastname_center_first_names_and_more.py +0 -37
  816. endoreg_db/migrations/0018_reportreaderflag_reportreaderconfig.py +0 -37
  817. endoreg_db/migrations/0019_pdftype_cut_off_above_lines_and_more.py +0 -42
  818. endoreg_db/migrations/0020_rename_endoscopy_info_line_pdftype_endoscope_info_line.py +0 -18
  819. endoreg_db/migrations/0021_alter_pdftype_endoscope_info_line.py +0 -19
  820. endoreg_db/migrations/0022_alter_pdftype_endoscope_info_line.py +0 -19
  821. endoreg_db/migrations/0023_ttoquestionnaire_alter_pdftype_endoscope_info_line.py +0 -59
  822. endoreg_db/migrations/0024_remove_ttoquestionnaire_infections_and_more.py +0 -27
  823. endoreg_db/migrations/0025_event_alter_rawpdffile_file_patientevent.py +0 -42
  824. endoreg_db/migrations/0026_disease_diseaseclassification_and_more.py +0 -166
  825. endoreg_db/migrations/0027_labvalue_abbreviation_labvalue_default_normal_range_and_more.py +0 -38
  826. endoreg_db/migrations/0028_alter_unit_abbreviation.py +0 -18
  827. endoreg_db/migrations/0029_medicationintaketime_and_more.py +0 -75
  828. endoreg_db/migrations/0030_medicationindicationtype_and_more.py +0 -101
  829. endoreg_db/migrations/0031_rename_adapt_to_liver_function_medication_adapt_to_age_and_more.py +0 -38
  830. endoreg_db/migrations/0032_alter_medicationschedule_therapy_duration_d.py +0 -18
  831. endoreg_db/migrations/0033_medicationindication_sources.py +0 -18
  832. endoreg_db/migrations/0034_alter_rawpdffile_file.py +0 -20
  833. endoreg_db/migrations/0035_alter_medicationindication_sources.py +0 -18
  834. endoreg_db/migrations/0036_alter_rawpdffile_file.py +0 -20
  835. endoreg_db/migrations/0037_alter_medicationindication_sources.py +0 -18
  836. endoreg_db/migrations/0038_emissionfactor_material_product_productgroup_and_more.py +0 -164
  837. endoreg_db/migrations/0039_referenceproduct_name.py +0 -19
  838. endoreg_db/migrations/0040_quizanswertype_quizquestiontype_quizquestion_and_more.py +0 -50
  839. endoreg_db/migrations/0041_gender_patientmedication_medication_indication_and_more.py +0 -40
  840. endoreg_db/migrations/0042_casetemplateruletype_casetemplaterulevalue_and_more.py +0 -74
  841. endoreg_db/migrations/0043_casetemplatetype_name_de_casetemplatetype_name_en.py +0 -23
  842. endoreg_db/migrations/0044_casetemplateruletype_name_de_and_more.py +0 -23
  843. endoreg_db/migrations/0045_casetemplaterulevalue_value_type.py +0 -19
  844. endoreg_db/migrations/0046_casetemplaterulevalue_target_field.py +0 -18
  845. endoreg_db/migrations/0047_casetemplaterule_target_model.py +0 -18
  846. endoreg_db/migrations/0048_remove_casetemplaterule_chained_rules_and_more.py +0 -22
  847. endoreg_db/migrations/0049_remove_casetemplaterule_rule_values.py +0 -17
  848. endoreg_db/migrations/0050_casetemplaterule_rule_values.py +0 -18
  849. endoreg_db/migrations/0051_remove_casetemplaterule_calling_rules_and_more.py +0 -27
  850. endoreg_db/migrations/0052_rename_case_template_type_casetemplate_template_type.py +0 -18
  851. endoreg_db/migrations/0053_patientlabsampletype_patientlabsample_and_more.py +0 -38
  852. endoreg_db/migrations/0054_multiplecategoricalvaluedistribution_and_more.py +0 -69
  853. endoreg_db/migrations/0055_remove_casetemplaterule_rule_values_and_more.py +0 -59
  854. endoreg_db/migrations/0056_datevaluedistribution_and_more.py +0 -32
  855. endoreg_db/migrations/0057_remove_datevaluedistribution_max_date_and_more.py +0 -72
  856. endoreg_db/migrations/0058_datevaluedistribution_description_and_more.py +0 -28
  857. endoreg_db/migrations/0059_casetemplaterule_rule_values.py +0 -18
  858. endoreg_db/migrations/0060_labvalue__default_date_value_distribution_and_more.py +0 -44
  859. endoreg_db/migrations/0061_remove_patientlabvalue_date_patientlabvalue_datetime.py +0 -24
  860. endoreg_db/migrations/0062_labvalue_numeric_precision.py +0 -18
  861. endoreg_db/migrations/0063_alter_labvalue_numeric_precision.py +0 -18
  862. endoreg_db/migrations/0064_casetemplaterule_extra_parameters_and_more.py +0 -23
  863. endoreg_db/migrations/0065_rename__date_value_distribution_casetemplaterule_date_value_distribution_and_more.py +0 -58
  864. endoreg_db/migrations/0066_alter_patientlabvalue_patient_and_more.py +0 -29
  865. endoreg_db/migrations/0067_alter_medicationindication_indication_type.py +0 -19
  866. endoreg_db/models/ai_model/__init__.py +0 -3
  867. endoreg_db/models/ai_model/active_model.py +0 -9
  868. endoreg_db/models/ai_model/model_meta.py +0 -24
  869. endoreg_db/models/annotation/__init__.py +0 -2
  870. endoreg_db/models/annotation/binary_classification_annotation_task.py +0 -80
  871. endoreg_db/models/annotation/image_classification.py +0 -27
  872. endoreg_db/models/center/center.py +0 -25
  873. endoreg_db/models/center/center_product.py +0 -34
  874. endoreg_db/models/center/center_resource.py +0 -19
  875. endoreg_db/models/center/center_waste.py +0 -11
  876. endoreg_db/models/data_file/__init__.py +0 -6
  877. endoreg_db/models/data_file/base_classes/__init__.py +0 -2
  878. endoreg_db/models/data_file/base_classes/abstract_frame.py +0 -51
  879. endoreg_db/models/data_file/base_classes/abstract_video.py +0 -201
  880. endoreg_db/models/data_file/frame.py +0 -45
  881. endoreg_db/models/data_file/import_classes/__init__.py +0 -32
  882. endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +0 -35
  883. endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +0 -28
  884. endoreg_db/models/data_file/import_classes/processing_functions/video.py +0 -260
  885. endoreg_db/models/data_file/import_classes/raw_pdf.py +0 -188
  886. endoreg_db/models/data_file/import_classes/raw_video.py +0 -343
  887. endoreg_db/models/data_file/metadata/__init__.py +0 -3
  888. endoreg_db/models/data_file/metadata/sensitive_meta.py +0 -31
  889. endoreg_db/models/data_file/metadata/video_meta.py +0 -133
  890. endoreg_db/models/data_file/report_file.py +0 -89
  891. endoreg_db/models/data_file/video/__init__.py +0 -7
  892. endoreg_db/models/data_file/video/import_meta.py +0 -25
  893. endoreg_db/models/data_file/video/video.py +0 -25
  894. endoreg_db/models/data_file/video_segment.py +0 -107
  895. endoreg_db/models/disease.py +0 -56
  896. endoreg_db/models/emission/__init__.py +0 -1
  897. endoreg_db/models/emission/emission_factor.py +0 -20
  898. endoreg_db/models/event.py +0 -22
  899. endoreg_db/models/examination/__init__.py +0 -4
  900. endoreg_db/models/examination/examination.py +0 -26
  901. endoreg_db/models/examination/examination_time.py +0 -27
  902. endoreg_db/models/examination/examination_time_type.py +0 -24
  903. endoreg_db/models/examination/examination_type.py +0 -18
  904. endoreg_db/models/hardware/__init__.py +0 -2
  905. endoreg_db/models/hardware/endoscope.py +0 -44
  906. endoreg_db/models/information_source.py +0 -29
  907. endoreg_db/models/laboratory/__init__.py +0 -1
  908. endoreg_db/models/laboratory/lab_value.py +0 -102
  909. endoreg_db/models/legacy_data/__init__.py +0 -3
  910. endoreg_db/models/legacy_data/image.py +0 -34
  911. endoreg_db/models/medication/__init__.py +0 -1
  912. endoreg_db/models/medication/medication.py +0 -148
  913. endoreg_db/models/other/distribution.py +0 -215
  914. endoreg_db/models/patient_examination/__init__.py +0 -35
  915. endoreg_db/models/permissions/__init__.py +0 -44
  916. endoreg_db/models/persons/__init__.py +0 -7
  917. endoreg_db/models/persons/examiner/__init__.py +0 -2
  918. endoreg_db/models/persons/examiner/examiner.py +0 -16
  919. endoreg_db/models/persons/examiner/examiner_type.py +0 -2
  920. endoreg_db/models/persons/patient/__init__.py +0 -8
  921. endoreg_db/models/persons/patient/case/case.py +0 -30
  922. endoreg_db/models/persons/patient/patient.py +0 -216
  923. endoreg_db/models/persons/patient/patient_disease.py +0 -16
  924. endoreg_db/models/persons/patient/patient_event.py +0 -22
  925. endoreg_db/models/persons/patient/patient_lab_sample.py +0 -106
  926. endoreg_db/models/persons/patient/patient_medication.py +0 -44
  927. endoreg_db/models/persons/patient/patient_medication_schedule.py +0 -28
  928. endoreg_db/models/persons/portal_user_information.py +0 -27
  929. endoreg_db/models/prediction/__init__.py +0 -2
  930. endoreg_db/models/prediction/image_classification.py +0 -37
  931. endoreg_db/models/prediction/video_prediction_meta.py +0 -244
  932. endoreg_db/models/product/__init__.py +0 -5
  933. endoreg_db/models/product/product.py +0 -97
  934. endoreg_db/models/product/product_group.py +0 -19
  935. endoreg_db/models/product/product_material.py +0 -24
  936. endoreg_db/models/questionnaires/__init__.py +0 -114
  937. endoreg_db/models/quiz/__init__.py +0 -2
  938. endoreg_db/models/quiz/quiz_answer.py +0 -41
  939. endoreg_db/models/quiz/quiz_question.py +0 -54
  940. endoreg_db/models/report_reader/__init__.py +0 -2
  941. endoreg_db/models/report_reader/report_reader_config.py +0 -53
  942. endoreg_db/models/rules/__init__.py +0 -5
  943. endoreg_db/queries/get/__init__.py +0 -6
  944. endoreg_db/queries/get/center.py +0 -42
  945. endoreg_db/queries/get/model.py +0 -13
  946. endoreg_db/queries/get/patient.py +0 -14
  947. endoreg_db/queries/get/patient_examination.py +0 -20
  948. endoreg_db/queries/get/report_file.py +0 -33
  949. endoreg_db/queries/get/video.py +0 -31
  950. endoreg_db/serializers/ai_model.py +0 -19
  951. endoreg_db/serializers/annotation.py +0 -17
  952. endoreg_db/serializers/center.py +0 -11
  953. endoreg_db/serializers/examination.py +0 -33
  954. endoreg_db/serializers/frame.py +0 -13
  955. endoreg_db/serializers/hardware.py +0 -21
  956. endoreg_db/serializers/label.py +0 -22
  957. endoreg_db/serializers/patient.py +0 -10
  958. endoreg_db/serializers/prediction.py +0 -15
  959. endoreg_db/serializers/report_file.py +0 -7
  960. endoreg_db/serializers/video.py +0 -27
  961. endoreg_db/tests.py +0 -3
  962. endoreg_db/utils/legacy_ocr.py +0 -201
  963. endoreg_db/utils/video_metadata.py +0 -87
  964. endoreg_db-0.3.6.dist-info/METADATA +0 -33
  965. endoreg_db-0.3.6.dist-info/RECORD +0 -357
  966. /endoreg_db/{models/persons/patient/case/__init__.py → api/serializers/finding_descriptions.py} +0 -0
  967. /endoreg_db/{queries/get/annotation.py → api/views/finding_descriptions.py} +0 -0
  968. /endoreg_db/{queries/get/prediction.py → config/__init__.py} +0 -0
  969. /endoreg_db/{queries/get/video_import_meta.py → data/case_template/rule_value/.init} +0 -0
  970. /endoreg_db/{queries/get/video_prediction_meta.py → data/distribution/multiple_categorical/.init} +0 -0
@@ -0,0 +1,775 @@
1
+ from endoreg_db.utils.extract_specific_frames import extract_selected_frames
2
+ from rest_framework import serializers
3
+ from endoreg_db.models import Label, LabelVideoSegment
4
+ from itertools import combinations
5
+ from pathlib import Path
6
+ from django.conf import settings
7
+ # === CONFIGURABLE PARAMETERS - ForNiceClassificationSerializer ===
8
+ POLYP_LABEL_NAME = "polyp"
9
+ CHROMO_LABEL_NAMES = ["digital_chromo_endoscopy", "nbi"]
10
+ FPS = 50 # Frames per second- should fetch dynamically from videofile table
11
+ # Sequence-level filtering
12
+ MIN_SEQUENCE_GAP_SECONDS = 0.5 # Enforce diversity between sequences
13
+ MIN_SEQUENCE_GAP_FRAMES = FPS * MIN_SEQUENCE_GAP_SECONDS # Convert to frame count
14
+ # Minimum length of a segment in seconds
15
+ MIN_SEGMENT_LENGTH_SECONDS = 0.5
16
+ MIN_SEGMENT_LENGTH_FRAMES = FPS * MIN_SEGMENT_LENGTH_SECONDS
17
+
18
+ # Frame-level selection within a sequence
19
+ MIN_FRAME_GAP_SECONDS = 1 # Minimum gap between selected frames in seconds
20
+ MIN_FRAME_GAP_IN_SEQUENCE = FPS * MIN_FRAME_GAP_SECONDS # Convert to frame count
21
+ FRAMES_PER_SEQUENCE = 3 # Number of frames to select per matched sequence
22
+
23
+
24
+ # === Frame Filtering Rules ===
25
+ # All rules must return True to accept the frame
26
+ FRAME_SELECTION_RULES = [
27
+ lambda pred: pred.get("low_quality", 1.0) < 0.1,
28
+ lambda pred: pred.get("outside", 1.0) < 0.1,
29
+ lambda pred: pred.get("snare", 1.0) < 0.1,
30
+
31
+ # Add more rules easily here
32
+ ]
33
+
34
+ REQUIRED_FRAME_KEYS = ["low_quality", "outside", "snare"] # need tp update when adding rules
35
+
36
+ POLYP_CONFIDENCE_THRESHOLDS = [0.9, 0.8, 0.7] # basically this is the prediction value/score, we are using for frame selection
37
+ INSTRUMENT_LABEL_NAMES = ["instrument", "snare", "needle"] # Add more as needed later
38
+
39
+
40
+ class BaseClassificationSerializer(serializers.Serializer):
41
+ """
42
+ Base class for NICE and PARIS serializers.
43
+ Handles label lookup, chromo/instrument segment filtering, and shared utilities.
44
+ """
45
+ #TODO add create method
46
+ #TODO add update method
47
+ LABEL_NAME = "polyp" # default (can be overridden)
48
+ INSTRUMENT_LABEL_NAME = "instrument" #TODO @Hamzaukw we should define frequently used labels in a utils file
49
+
50
+
51
+ def get_label_id_by_name(self, label_name):
52
+ """
53
+ Get the ID of a label by its name.
54
+ Raises a validation error if not found.
55
+ """
56
+ try:
57
+ label = Label.objects.get(name=label_name)
58
+ return label.id
59
+ except Label.DoesNotExist:
60
+ raise serializers.ValidationError({
61
+ "error": f"Label with name '{label_name}' does not exist."
62
+ })
63
+
64
+ def get_label_ids_by_names(self, label_names):
65
+ """
66
+ Get a list of label IDs for a given list of label names.
67
+ Ensures all names exist in the database.
68
+ """
69
+ labels = Label.objects.filter(name__in=label_names)
70
+ label_map = {label.name: label.id for label in labels}
71
+
72
+ missing = set(label_names) - set(label_map.keys())
73
+ if missing:
74
+ raise serializers.ValidationError({
75
+ "error": f"Labels not found: {', '.join(missing)}"
76
+ })
77
+
78
+ return list(label_map.values())
79
+
80
+ def get_chromo_segments(self, video_id):
81
+ """
82
+ Fetch all segments that match chromo-like labels (e.g., chromo or NBI).
83
+ Used in both NICE and PARIS, but interpreted differently:
84
+ - NICE: chromo overlap is required
85
+ - PARIS: chromo overlap is disqualifying
86
+ """
87
+ chromo_label_ids = self.get_label_ids_by_names(CHROMO_LABEL_NAMES)
88
+ return LabelVideoSegment.objects.filter(label_id__in=chromo_label_ids, video_file_id=video_id)
89
+
90
+
91
+
92
+ def get_filtered_polyp_segments(self, video_id):
93
+ """
94
+ Return polyp segments that do NOT overlap with 'instrument' segments.
95
+ """
96
+ polyp_label_id = self.get_label_id_by_name(self.LABEL_NAME)
97
+ instrument_label_id = self.get_label_id_by_name(self.INSTRUMENT_LABEL_NAME)
98
+
99
+ print("polyp label id is :-", polyp_label_id,"and - instrument_label_id is ,", instrument_label_id)
100
+
101
+ polyp_segments = LabelVideoSegment.objects.filter(
102
+ label_id=polyp_label_id, video_file_id=video_id
103
+ )
104
+
105
+ instrument_segments = LabelVideoSegment.objects.filter(
106
+ label_id=instrument_label_id, video_file_id=video_id
107
+ )
108
+ print("------------------------ --------------------------------- -------------------------------")
109
+ print("polyp label id is :-", polyp_label_id,"and - instrument_label_id is ,", instrument_label_id)
110
+ print("polyp segments are",polyp_segments , "instrument_segments are", instrument_segments)
111
+
112
+ def overlaps(seg1, seg2):
113
+ return seg1.start_frame_number <= seg2.end_frame_number and seg1.end_frame_number >= seg2.start_frame_number
114
+
115
+ filtered_polyp_segments = []
116
+ for polyp_seg in polyp_segments:
117
+ if not any(overlaps(polyp_seg, instr_seg) for instr_seg in instrument_segments):
118
+ filtered_polyp_segments.append(polyp_seg)
119
+
120
+ return filtered_polyp_segments
121
+
122
+ def get_polyp_segments(self, video_id):
123
+ polyp_label_id = self.get_label_id_by_name(self.LABEL_NAME)
124
+ return LabelVideoSegment.objects.filter(label_id=polyp_label_id, video_file_id=video_id)
125
+
126
+ def apply_sequence_diversity(self, matching_segments):
127
+ if not matching_segments:
128
+ return []
129
+
130
+ matching_segments.sort(key=lambda seg: seg['polyp'].start_frame_number)
131
+
132
+ valid_segments = [
133
+ seg for seg in matching_segments
134
+ if (seg['polyp'].end_frame_number - seg['polyp'].start_frame_number) >= MIN_SEGMENT_LENGTH_FRAMES
135
+ ]
136
+
137
+ if len(valid_segments) < 3:
138
+ valid_segments.sort(
139
+ key=lambda seg: seg['polyp'].end_frame_number - seg['polyp'].start_frame_number,
140
+ reverse=True
141
+ )
142
+ return valid_segments[:3]
143
+
144
+ best_combo = None
145
+ best_gap_sum = -1
146
+
147
+ for combo in combinations(valid_segments, 3):
148
+ sorted_combo = sorted(combo, key=lambda seg: seg['polyp'].start_frame_number)
149
+ s1, s2, s3 = sorted_combo
150
+ s1_end = s1['polyp'].end_frame_number
151
+ s2_start = s2['polyp'].start_frame_number
152
+ s2_end = s2['polyp'].end_frame_number
153
+ s3_start = s3['polyp'].start_frame_number
154
+ gap1 = s2_start - s1_end
155
+ gap2 = s3_start - s2_end
156
+
157
+ if gap1 >= MIN_SEQUENCE_GAP_FRAMES and gap2 >= MIN_SEQUENCE_GAP_FRAMES:
158
+ total_gap = gap1 + gap2
159
+ if total_gap > best_gap_sum:
160
+ best_gap_sum = total_gap
161
+ best_combo = sorted_combo
162
+
163
+ if best_combo:
164
+ return list(best_combo)
165
+
166
+ valid_segments.sort(
167
+ key=lambda seg: seg['polyp'].end_frame_number - seg['polyp'].start_frame_number,
168
+ reverse=True
169
+ )
170
+ return valid_segments[:3]
171
+
172
+ def select_frames_for_sequence(self, sequence):
173
+ """
174
+ Selects evenly spaced representative frames from a polyp segment.
175
+
176
+ Frames are chosen from the segment's frame range, ensuring a minimum gap between selected frames. Returns a list of dictionaries containing frame numbers and their corresponding file paths. If the video's frame directory is unavailable, returns an empty list.
177
+ """
178
+ polyp_sequence = sequence['polyp']
179
+ video = polyp_sequence.video_file
180
+
181
+ start_frame = polyp_sequence.start_frame_number
182
+ end_frame = polyp_sequence.end_frame_number
183
+
184
+ frame_dir = getattr(video, "frame_dir", "")
185
+
186
+ if not frame_dir:
187
+ return []
188
+
189
+ # Just create frames assuming predictions aren't available
190
+ segment_frames = [
191
+ {
192
+ "frame_number": idx,
193
+ "frame_path": f"{frame_dir}/frame_{str(idx).zfill(7)}.png"
194
+ }
195
+ for idx in range(start_frame, end_frame + 1)
196
+ ]
197
+
198
+ selected_frames = []
199
+ last_selected_frame = -float('inf')
200
+
201
+ for frame in segment_frames:
202
+ if len(selected_frames) >= FRAMES_PER_SEQUENCE:
203
+ break
204
+
205
+ if frame["frame_number"] - last_selected_frame >= MIN_FRAME_GAP_IN_SEQUENCE:
206
+ selected_frames.append({
207
+ "frame_number": frame["frame_number"],
208
+ "frame_path": frame["frame_path"]
209
+ })
210
+ last_selected_frame = frame["frame_number"]
211
+
212
+ return selected_frames
213
+
214
+ def extract_and_save_selected_frames(self, video, frame_numbers, classification_type: str):
215
+ """
216
+ Extract specific frames from the original video file and save them
217
+ into a structured folder path based on the classification type.
218
+
219
+ Args:
220
+ video (VideoFile): Video object with `original_file_name` and `frame_dir`.
221
+ frame_numbers (List[int]): List of frame numbers to extract.
222
+ classification_type (str): Either "nice" or "paris".
223
+ """
224
+ # Resolve the path to the original video
225
+ original_path = Path(video.original_file_name)
226
+ if not original_path.is_absolute():
227
+ base_video_dir = settings.BASE_DIR.parent.parent / "production_test" / "endoreg-db" / "data" / "coloreg_first_test_batch"
228
+ original_path = base_video_dir / original_path
229
+
230
+ # Define output directory based on classification and video ID
231
+ output_path = Path(video.frame_dir) / classification_type / f"video_{video.id}"
232
+
233
+ # Extract frames using the shared utility
234
+ extract_selected_frames(
235
+ video_path=original_path,
236
+ frame_numbers=frame_numbers,
237
+ output_dir=output_path,
238
+ fps=FPS
239
+ )
240
+
241
+
242
+ ''' # # If any error occurs in this function, use the commented one below(fallback:select_frames_for_sequence).
243
+ def select_frames_for_sequence(self, sequence):
244
+ # Extract the polyp segment from the current sequence
245
+ polyp_sequence = sequence['polyp']
246
+ video = polyp_sequence.video
247
+
248
+ # Get the start and end frame numbers of the segment/sequence
249
+ start_frame = polyp_sequence.start_frame_number
250
+ end_frame = polyp_sequence.end_frame_number
251
+
252
+ # here we aregetting the predictions and frame directory from the video object
253
+ predictions = getattr(video, "readable_predictions", [])
254
+ frame_dir = getattr(video, "frame_dir", "") #need to check
255
+
256
+ # If either predictions or frame_dir is missing, return an empty list
257
+ if not predictions or not frame_dir:
258
+ return []
259
+
260
+ # Build a list of prediction dictionaries for each frame in the segment
261
+ # Each entry includes frame number, selected prediction keys, path, and full prediction
262
+ segment_predictions = [
263
+ {
264
+ "frame_number": idx,
265
+ **{key: pred.get(key, 1.0) for key in REQUIRED_FRAME_KEYS + ["polyp"]},
266
+ "frame_path": f"{frame_dir}/frame_{str(idx).zfill(7)}.jpg",
267
+ "prediction": pred
268
+ }
269
+ for idx, pred in enumerate(predictions[start_frame:end_frame + 1], start=start_frame)
270
+ if isinstance(pred, dict)
271
+ ]
272
+
273
+ # Sort the frames by lowest 'low_quality' value first,# for higher quality images// changeable,
274
+ segment_predictions.sort(key=lambda x: x["low_quality"])
275
+
276
+ # Try frame selection with decreasing polyp confidence thresholds
277
+ #for polyp_threshold in [0.9, 0.8, 0.7]:
278
+ for polyp_threshold in POLYP_CONFIDENCE_THRESHOLDS:
279
+
280
+ # Filter frames that meet the current polyp threshold
281
+ candidate_frames = [
282
+ frame for frame in segment_predictions
283
+ if frame["prediction"].get("polyp", 0.0) > polyp_threshold
284
+ ]
285
+
286
+ # If no candidates at this threshold, try the next lower threshold
287
+ if not candidate_frames:
288
+ continue
289
+
290
+ # Initialize list of selected frames and track last selected frame number
291
+ selected_frames = []
292
+ last_selected_frame = -float('inf')
293
+
294
+ # Iterate through the candidate frames
295
+ for frame in candidate_frames:
296
+ # Stop if we've already selected enough frames
297
+ if len(selected_frames) >= FRAMES_PER_SEQUENCE:
298
+ break
299
+
300
+ # Apply the standard filtering rules and spacing condition
301
+ if (
302
+ frame["prediction"].get("low_quality", 1.0) < 0.1 and
303
+ frame["prediction"].get("outside", 1.0) < 0.1 and
304
+ frame["prediction"].get("snare", 1.0) < 0.1 and
305
+ frame["frame_number"] - last_selected_frame >= MIN_FRAME_GAP_IN_SEQUENCE
306
+ ):
307
+ # Frame passes all filters and spacing rule, so select it
308
+ selected_frames.append({
309
+ "frame_number": frame["frame_number"],
310
+ "low_quality": frame["low_quality"],
311
+ "polyp_score": frame["prediction"]["polyp"],
312
+ "frame_path": frame["frame_path"]
313
+ })
314
+ last_selected_frame = frame["frame_number"]
315
+
316
+ # If we found enough valid frames at this threshold, return them
317
+ if len(selected_frames) >= FRAMES_PER_SEQUENCE:
318
+ return selected_frames
319
+
320
+ # If no threshold yielded enough frames, return what was found in the last attempt (could be empty)
321
+ return selected_frames if selected_frames else []'''
322
+
323
+
324
+ # fallback:select_frames_for_sequence
325
+ '''
326
+ def select_frames_for_sequence(self, sequence):
327
+ print("----------------------in selected_frames fro sequnces funtion ----------------------------------------")
328
+ polyp_sequence = sequence['polyp']
329
+ video = polyp_sequence.video
330
+ start_frame = polyp_sequence.start_frame_number
331
+ end_frame = polyp_sequence.end_frame_number
332
+ predictions = getattr(video, "readable_predictions", [])
333
+ frame_dir = getattr(video, "frame_dir", "")
334
+
335
+ if not predictions or not frame_dir:
336
+ return []
337
+
338
+ segment_predictions = [
339
+ {
340
+ "frame_number": idx,
341
+ **{key: pred.get(key, 1.0) for key in REQUIRED_FRAME_KEYS},
342
+ "frame_path": f"{frame_dir}/frame_{str(idx).zfill(7)}.jpg",
343
+ "prediction": pred
344
+ }
345
+ for idx, pred in enumerate(predictions[start_frame:end_frame + 1], start=start_frame)
346
+ if isinstance(pred, dict)
347
+ ]
348
+
349
+
350
+ segment_predictions.sort(key=lambda x: x["low_quality"])
351
+
352
+ selected_frames = []
353
+ last_selected_frame = -float('inf')
354
+
355
+ for frame in segment_predictions:
356
+ if len(selected_frames) >= FRAMES_PER_SEQUENCE:
357
+ break
358
+
359
+ if all(rule(frame["prediction"]) for rule in FRAME_SELECTION_RULES):
360
+ if frame["frame_number"] - last_selected_frame >= MIN_FRAME_GAP_IN_SEQUENCE:
361
+ selected_frames.append({
362
+ "frame_number": frame["frame_number"],
363
+ "low_quality": frame["low_quality"],
364
+ "frame_path": frame["frame_path"]
365
+ })
366
+ last_selected_frame = frame["frame_number"]
367
+
368
+ return selected_frames'''
369
+ class ForNiceClassificationSerializer(BaseClassificationSerializer):
370
+ """
371
+ NICE classification logic:
372
+ - Requires polyp segments
373
+ - Filters out any overlap with instrument labels
374
+ - Requires overlap with chromo-like labels (chromo/NBI)
375
+ - Selects diverse sequences and representative frames from each
376
+ """
377
+ def get_matching_sequences(self, video_id):
378
+ """
379
+ 1. Fetch all polyp segments in a video
380
+ 2. Remove parts overlapping with any instrument-type labels
381
+ 3. Keep only parts that still overlap with chromo/NBI
382
+ 4. Trim segments accordingly and return valid subsegments
383
+ """
384
+ polyp_label_id = self.get_label_id_by_name(self.LABEL_NAME)
385
+ instrument_label_ids = self.get_label_ids_by_names(INSTRUMENT_LABEL_NAMES)
386
+ #chromo_label_id = self.get_label_id_by_name(CHROMO_LABEL_NAME)
387
+ chromo_segments = self.get_chromo_segments(video_id)
388
+
389
+
390
+ polyp_segments = LabelVideoSegment.objects.filter(label_id=polyp_label_id, video_file_id=video_id)
391
+ instrument_segments = LabelVideoSegment.objects.filter(label_id__in=instrument_label_ids, video_file_id=video_id)
392
+
393
+ #chromo_segments = LabelVideoSegment.objects.filter(label_id=chromo_label_id, video_file_id=video_id)
394
+ print("polyp_label_id is", polyp_label_id, "and ployp_segment is ", polyp_segments)
395
+ print("instrument_segments is", instrument_segments)
396
+ #print("chromo_segments is ",chromo_segments)
397
+
398
+ def overlaps(seg1, seg2):
399
+ return seg1.start_frame_number <= seg2.end_frame_number and seg1.end_frame_number >= seg2.start_frame_number
400
+
401
+ def subtract_overlap(seg, overlaps):
402
+ start = seg.start_frame_number
403
+ end = seg.end_frame_number
404
+ blocks = [(o.start_frame_number, o.end_frame_number) for o in overlaps]
405
+ blocks.sort()
406
+
407
+ safe_ranges = []
408
+ curr = start
409
+
410
+ for o_start, o_end in blocks:
411
+ if o_end < curr:
412
+ continue
413
+ if o_start > end:
414
+ break
415
+ if o_start > curr:
416
+ safe_ranges.append((curr, min(o_start - 1, end)))
417
+ curr = max(curr, o_end + 1)
418
+
419
+ if curr <= end:
420
+ safe_ranges.append((curr, end))
421
+
422
+ return safe_ranges
423
+
424
+ matching_segments = []
425
+
426
+ for polyp in polyp_segments:
427
+ overlapping_instr = [seg for seg in instrument_segments if overlaps(polyp, seg)]
428
+ safe_ranges = subtract_overlap(polyp, overlapping_instr)
429
+
430
+ for start, end in safe_ranges:
431
+ if end - start + 1 < MIN_SEGMENT_LENGTH_FRAMES:
432
+ continue
433
+
434
+ for chromo in chromo_segments:
435
+ if chromo.start_frame_number <= end and chromo.end_frame_number >= start:
436
+ overlap_start = max(start, chromo.start_frame_number)
437
+ overlap_end = min(end, chromo.end_frame_number)
438
+
439
+ if overlap_end - overlap_start + 1 >= MIN_SEGMENT_LENGTH_FRAMES:
440
+ overlapping_segment = LabelVideoSegment(
441
+ video_file=polyp.video_file,
442
+ start_frame_number=overlap_start,
443
+ end_frame_number=overlap_end
444
+ )
445
+ matching_segments.append({'polyp': overlapping_segment})
446
+
447
+ return matching_segments
448
+
449
+ def to_representation(self, videos):
450
+ """
451
+ Processes a list of videos:
452
+ - Applies NICE/PARIS rules to find segments
453
+ - Applies sequence diversity logic
454
+ - Selects frames per segment
455
+ - Extracts all frames for a video in a single call
456
+ - Returns structured output with messages per video
457
+ """
458
+ results = []
459
+
460
+ for video in videos:
461
+ try:
462
+ video_id = video.id
463
+ print("video-id is", video_id)
464
+
465
+ matching_segments = self.get_matching_sequences(video_id)
466
+ print("matching_segments are", matching_segments)
467
+ if not matching_segments:
468
+ results.append({
469
+ "video_id": video_id,
470
+ "message": "No valid polyp segments overlapping with chromo and not overlapping with instrument."
471
+ })
472
+ continue
473
+
474
+ diverse_segments = self.apply_sequence_diversity(matching_segments)
475
+ if not diverse_segments:
476
+ results.append({
477
+ "video_id": video_id,
478
+ "message": "No diverse NICE sequences found — either too short or too close together."
479
+ })
480
+ continue
481
+
482
+ # Collect all frame numbers to extract only once per video
483
+ all_frames = []
484
+ segment_results = []
485
+
486
+ for segment in diverse_segments:
487
+ frames = self.select_frames_for_sequence(segment)
488
+
489
+ if not frames:
490
+ segment_results.append({
491
+ "video_id": video_id,
492
+ "segment_start": segment['polyp'].start_frame_number,
493
+ "segment_end": segment['polyp'].end_frame_number,
494
+ "message": "No valid frames passed filtering rules (low_quality, outside, snare)."
495
+ })
496
+ else:
497
+ segment_results.append({
498
+ "video_id": video_id,
499
+ "segment_start": segment['polyp'].start_frame_number,
500
+ "segment_end": segment['polyp'].end_frame_number,
501
+ "frames": frames
502
+ })
503
+ all_frames.extend(frames)
504
+
505
+ # Extract once per video
506
+ if all_frames:
507
+ unique_frame_numbers = sorted({f["frame_number"] for f in all_frames})
508
+ classification_type = "nice" if isinstance(self, ForNiceClassificationSerializer) else "paris"
509
+ self.extract_and_save_selected_frames(video, unique_frame_numbers, classification_type)
510
+
511
+ results.extend(segment_results)
512
+
513
+ except Exception as e:
514
+ results.append({
515
+ "video_id": video.id,
516
+ "error": str(e)
517
+ })
518
+
519
+ if not results:
520
+ return [{
521
+ "message": "No classification data generated for any videos."
522
+ }]
523
+
524
+ return {
525
+ "message": "NICE classification data generated." if isinstance(self, ForNiceClassificationSerializer)
526
+ else "PARIS classification data generated.",
527
+ "data": results
528
+ }
529
+
530
+
531
+
532
+
533
+
534
+ class ForParisClassificationSerializer(BaseClassificationSerializer):
535
+ """
536
+ PARIS classification logic:
537
+ - Requires polyp segments
538
+ - Excludes any region overlapping with instruments or chromo/NBI
539
+ - Keeps remaining 'clean' subsegments
540
+ - Enforces minimum length and sequence diversity
541
+ - Selects frames from each valid segment
542
+ """
543
+
544
+ def get_filtered_polyp_segments(self, video_id):
545
+ """
546
+ 1. Fetch all polyp segments
547
+ 2. Subtract any overlap with chromo or instrument segments
548
+ 3. Keep only trimmed segments longer than the minimum threshold
549
+ """
550
+
551
+ polyp_label_id = self.get_label_id_by_name(self.LABEL_NAME)
552
+ instrument_label_ids = self.get_label_ids_by_names(INSTRUMENT_LABEL_NAMES)
553
+ #chromo_label_id = self.get_label_id_by_name(CHROMO_LABEL_NAME)
554
+
555
+ polyp_segments = LabelVideoSegment.objects.filter(label_id=polyp_label_id, video_file_id=video_id)
556
+ instrument_segments = LabelVideoSegment.objects.filter(label_id__in=instrument_label_ids, video_file_id=video_id)
557
+ #chromo_segments = LabelVideoSegment.objects.filter(label_id=chromo_label_id, video_file_id=video_id)
558
+ chromo_segments = self.get_chromo_segments(video_id)
559
+
560
+
561
+ def overlaps(seg1, seg2):
562
+ return seg1.start_frame_number <= seg2.end_frame_number and seg1.end_frame_number >= seg2.start_frame_number
563
+
564
+ def subtract_overlap(seg, overlaps):
565
+ """
566
+ Given a base segment and list of overlapping segments,
567
+ returns list of non-overlapping sub-segments.
568
+ """
569
+ start = seg.start_frame_number
570
+ end = seg.end_frame_number
571
+ blocks = [(o.start_frame_number, o.end_frame_number) for o in overlaps]
572
+ blocks.sort()
573
+
574
+ safe_ranges = []
575
+ curr = start
576
+
577
+ for o_start, o_end in blocks:
578
+ if o_end < curr:
579
+ continue
580
+ if o_start > end:
581
+ break
582
+ if o_start > curr:
583
+ safe_ranges.append((curr, min(o_start - 1, end)))
584
+ curr = max(curr, o_end + 1)
585
+
586
+ if curr <= end:
587
+ safe_ranges.append((curr, end))
588
+
589
+ return safe_ranges
590
+
591
+ # Final valid sub-segments
592
+ trimmed_segments = []
593
+
594
+ for polyp_seg in polyp_segments:
595
+ # Collect all overlapping regions with instrument or chromo
596
+ overlapping = [
597
+ seg for seg in (list(instrument_segments) + list(chromo_segments))
598
+ if overlaps(polyp_seg, seg)
599
+ ]
600
+
601
+ safe_ranges = subtract_overlap(polyp_seg, overlapping)
602
+
603
+ for start, end in safe_ranges:
604
+ if end - start + 1 >= MIN_SEGMENT_LENGTH_FRAMES:
605
+ trimmed_segments.append(LabelVideoSegment(
606
+ video_file=polyp_seg.video_file,
607
+ start_frame_number=start,
608
+ end_frame_number=end
609
+ ))
610
+
611
+ return trimmed_segments
612
+
613
+ filtered_segments = []
614
+ for polyp_seg in polyp_segments:
615
+ if not any(overlaps(polyp_seg, instr_seg) for instr_seg in instrument_segments) and \
616
+ not any(overlaps(polyp_seg, chromo_seg) for chromo_seg in chromo_segments):
617
+ filtered_segments.append(polyp_seg)
618
+
619
+ return filtered_segments
620
+
621
+ def get_matching_sequences(self, video_id):
622
+ """
623
+ Wraps all valid polyp subsegments into a uniform data structure.
624
+ This is needed for consistent downstream processing.
625
+ """
626
+ segments = self.get_filtered_polyp_segments(video_id)
627
+ return [{'polyp': seg} for seg in segments]
628
+
629
+
630
+ def to_representation(self, videos):
631
+ """
632
+ Processes videos for PARIS classification.
633
+ Filters segments, selects diverse sequences, and picks valid frames.
634
+ Extracts all selected frames once per video.
635
+ Returns detailed per-video feedback or results.
636
+ """
637
+ results = []
638
+
639
+ for video in videos:
640
+ try:
641
+ video_id = video.id
642
+ matching_segments = self.get_matching_sequences(video_id)
643
+
644
+ if not matching_segments:
645
+ results.append({
646
+ "video_id": video_id,
647
+ "message": "No matching polyp segments found — possibly filtered due to overlap with 'instrument' label."
648
+ })
649
+ continue
650
+
651
+ diverse_segments = self.apply_sequence_diversity(matching_segments)
652
+ if not diverse_segments:
653
+ results.append({
654
+ "video_id": video_id,
655
+ "message": "No diverse sequences found — either too short or too close to each other."
656
+ })
657
+ continue
658
+
659
+ all_frames = []
660
+ segment_results = []
661
+
662
+ for segment in diverse_segments:
663
+ frames = self.select_frames_for_sequence(segment)
664
+
665
+ if not frames:
666
+ segment_results.append({
667
+ "video_id": video_id,
668
+ "segment_start": segment['polyp'].start_frame_number,
669
+ "segment_end": segment['polyp'].end_frame_number,
670
+ "message": "No valid frames selected due to prediction rules (e.g., quality, outside, snare)."
671
+ })
672
+ else:
673
+ segment_results.append({
674
+ "video_id": video_id,
675
+ "segment_start": segment['polyp'].start_frame_number,
676
+ "segment_end": segment['polyp'].end_frame_number,
677
+ "frames": frames
678
+ })
679
+ all_frames.extend(frames)
680
+
681
+ if all_frames:
682
+ unique_frame_numbers = sorted({f["frame_number"] for f in all_frames})
683
+ self.extract_and_save_selected_frames(video, unique_frame_numbers, classification_type="paris")
684
+
685
+ results.extend(segment_results)
686
+
687
+ except Exception as e:
688
+ results.append({
689
+ "video_id": video.id,
690
+ "error": str(e)
691
+ })
692
+
693
+ if not results:
694
+ return [{
695
+ "message": "No valid classification results could be generated for any video."
696
+ }]
697
+
698
+ return {
699
+ "message": "PARIS classification data generated.",
700
+ "data": results
701
+ }
702
+
703
+
704
+
705
+ """
706
+ NICE Classification Serializer
707
+ ------------------------------
708
+
709
+ This serializer identifies clean polyp segments for NICE classification:
710
+ - Filters out segments overlapping with instruments
711
+ - Requires overlap with digital chromo or NBI
712
+ - Applies sequence diversity and selects clean frames
713
+
714
+ Configurable via:
715
+ - INSTRUMENT_LABEL_NAMES: defines what tools to exclude
716
+ - CHROMO_LABEL_NAMES: defines what chromo types to include
717
+
718
+ Returns:
719
+ {
720
+ "video_id": int,
721
+ "segment_start": int,
722
+ "segment_end": int,
723
+ "frames": [{ frame_number, frame_path }]
724
+ }
725
+ """
726
+
727
+
728
+ """
729
+ PARIS Classification Serializer
730
+ -------------------------------
731
+
732
+ This serializer identifies clean polyp segments for PARIS classification:
733
+ - Filters out segments that overlap with any instrument-type labels
734
+ - Also excludes any segments that overlap with digital chromo or NBI imaging
735
+ - Trims overlapping regions and returns only clean, usable subsegments
736
+ - Applies sequence diversity to avoid redundant or closely positioned segments
737
+ - Selects clean, representative frames from each remaining valid segment
738
+
739
+ Configurable via:
740
+ - INSTRUMENT_LABEL_NAMES: defines all instrument labels that must be excluded (e.g., 'instrument', 'snare', 'needle')
741
+ - CHROMO_LABEL_NAMES: defines chromo-like labels that should also be excluded (e.g., 'digital_chromo_endoscopy', 'nbi')
742
+
743
+ Returns:
744
+ {
745
+ "video_id": int,
746
+ "segment_start": int,
747
+ "segment_end": int,
748
+ "frames": [{ frame_number: int, frame_path: str }]
749
+ }
750
+ """
751
+
752
+
753
+
754
+
755
+
756
+ '''
757
+ await import('https://cdn.jsdelivr.net/npm/axios/dist/axios.min.js');
758
+ const fetchNiceClassification = async () => {
759
+ try {
760
+ const response = await axios.get("http://localhost:8000/videos/nice-classification/", {
761
+ headers: { "Accept": "application/json" }
762
+ });
763
+
764
+ console.log(" NICE Classification Response:", response.data);
765
+ alert("NICE Classification data fetched!");
766
+ return response.data;
767
+ } catch (error) {
768
+ console.error(" Error fetching NICE classification:", error.response?.data || error);
769
+ alert("Failed to fetch NICE classification data.");
770
+ return error.response?.data || { error: "Unknown error" };
771
+ }
772
+ };
773
+
774
+ fetchNiceClassification().then(data => console.log("Final Output:", data));
775
+ '''