endoreg-db 0.8.9.32__py3-none-any.whl
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- endoreg_db/__init__.py +0 -0
- endoreg_db/_version.py +34 -0
- endoreg_db/admin.py +97 -0
- endoreg_db/api/serializers/finding_descriptions.py +0 -0
- endoreg_db/api/views/finding_descriptions.py +0 -0
- endoreg_db/api_urls.py +4 -0
- endoreg_db/apps.py +17 -0
- endoreg_db/assets/dummy_model.ckpt +1 -0
- endoreg_db/authz/auth.py +78 -0
- endoreg_db/authz/backends.py +168 -0
- endoreg_db/authz/management/commands/list_routes.py +20 -0
- endoreg_db/authz/middleware.py +84 -0
- endoreg_db/authz/permissions.py +138 -0
- endoreg_db/authz/policy.py +224 -0
- endoreg_db/authz/settings.py +64 -0
- endoreg_db/authz/views_auth.py +70 -0
- endoreg_db/codemods/readme.md +88 -0
- endoreg_db/codemods/rename_datetime_fields.py +99 -0
- endoreg_db/config/__init__.py +0 -0
- endoreg_db/config/env.py +106 -0
- endoreg_db/config/settings/__init__.py +6 -0
- endoreg_db/config/settings/base.py +148 -0
- endoreg_db/config/settings/case_gen.py +32 -0
- endoreg_db/config/settings/dev.py +108 -0
- endoreg_db/config/settings/keycloak.py +177 -0
- endoreg_db/config/settings/prod.py +66 -0
- endoreg_db/config/settings/test.py +72 -0
- endoreg_db/data/__init__.py +135 -0
- endoreg_db/data/ai_model/data.yaml +7 -0
- endoreg_db/data/ai_model_label/label/data.yaml +88 -0
- endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
- endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
- endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
- endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
- endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
- endoreg_db/data/ai_model_type/data.yaml +7 -0
- endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
- endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
- endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
- endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
- endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
- endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
- endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
- endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
- endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
- endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
- endoreg_db/data/case_template/rule_value/.init +0 -0
- endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
- endoreg_db/data/case_template/template/base.yaml +8 -0
- endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
- endoreg_db/data/case_template/tmp/_rule_value +13 -0
- endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
- endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
- endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
- endoreg_db/data/center/data.yaml +99 -0
- endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
- endoreg_db/data/center_shift/ukw.yaml +9 -0
- endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
- endoreg_db/data/contraindication/bleeding.yaml +11 -0
- endoreg_db/data/db_summary.csv +58 -0
- endoreg_db/data/db_summary.xlsx +0 -0
- endoreg_db/data/disease/cardiovascular.yaml +37 -0
- endoreg_db/data/disease/hepatology.yaml +5 -0
- endoreg_db/data/disease/misc.yaml +5 -0
- endoreg_db/data/disease/renal.yaml +5 -0
- endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
- endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
- endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
- endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
- endoreg_db/data/distribution/date/patient.yaml +7 -0
- endoreg_db/data/distribution/multiple_categorical/.init +0 -0
- endoreg_db/data/distribution/numeric/data.yaml +14 -0
- endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
- endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
- endoreg_db/data/endoscope/data.yaml +93 -0
- endoreg_db/data/endoscope_type/data.yaml +11 -0
- endoreg_db/data/endoscopy_processor/data.yaml +50 -0
- endoreg_db/data/event/cardiology.yaml +15 -0
- endoreg_db/data/event/neurology.yaml +14 -0
- endoreg_db/data/event/surgery.yaml +13 -0
- endoreg_db/data/event/thrombembolism.yaml +20 -0
- endoreg_db/data/event_classification/data.yaml +4 -0
- endoreg_db/data/event_classification_choice/data.yaml +9 -0
- endoreg_db/data/examination/examinations/data.yaml +172 -0
- endoreg_db/data/examination/time/data.yaml +48 -0
- endoreg_db/data/examination/time-type/data.yaml +5 -0
- endoreg_db/data/examination/type/data.yaml +17 -0
- endoreg_db/data/examination_indication/endoscopy.yaml +359 -0
- endoreg_db/data/examination_indication_classification/endoscopy.yaml +90 -0
- endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +97 -0
- endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
- endoreg_db/data/finding/00_generic.yaml +35 -0
- endoreg_db/data/finding/00_generic_complication.yaml +9 -0
- endoreg_db/data/finding/01_gastroscopy_baseline.yaml +88 -0
- endoreg_db/data/finding/01_gastroscopy_observation.yaml +113 -0
- endoreg_db/data/finding/02_colonoscopy_baseline.yaml +53 -0
- endoreg_db/data/finding/02_colonoscopy_hidden.yaml +119 -0
- endoreg_db/data/finding/02_colonoscopy_observation.yaml +152 -0
- endoreg_db/data/finding_classification/00_generic.yaml +44 -0
- endoreg_db/data/finding_classification/00_generic_histology.yaml +28 -0
- endoreg_db/data/finding_classification/00_generic_lesion.yaml +52 -0
- endoreg_db/data/finding_classification/02_colonoscopy_baseline.yaml +83 -0
- endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml +13 -0
- endoreg_db/data/finding_classification/02_colonoscopy_other.yaml +12 -0
- endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml +101 -0
- endoreg_db/data/finding_classification_choice/00_generic.yaml +15 -0
- endoreg_db/data/finding_classification_choice/00_generic_baseline.yaml +23 -0
- endoreg_db/data/finding_classification_choice/00_generic_complication.yaml +15 -0
- endoreg_db/data/finding_classification_choice/00_generic_histology.yaml +21 -0
- endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml +158 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_bowel_preparation.yaml +49 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_generic.yaml +19 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_histology.yaml +20 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_location.yaml +248 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_other.yaml +34 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_advanced_imaging.yaml +76 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_morphology.yaml +75 -0
- endoreg_db/data/finding_classification_choice/02_colonoscopy_size.yaml +27 -0
- endoreg_db/data/finding_classification_type/00_generic.yaml +53 -0
- endoreg_db/data/finding_classification_type/02_colonoscopy.yaml +9 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy.yaml +59 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_ablation.yaml +44 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_bleeding.yaml +55 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_resection.yaml +85 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_stenosis.yaml +17 -0
- endoreg_db/data/finding_intervention/00_generic_endoscopy_stent.yaml +9 -0
- endoreg_db/data/finding_intervention/01_gastroscopy.yaml +19 -0
- endoreg_db/data/finding_intervention/04_eus.yaml +39 -0
- endoreg_db/data/finding_intervention/05_ercp.yaml +3 -0
- endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
- endoreg_db/data/finding_type/data.yaml +39 -0
- endoreg_db/data/gender/data.yaml +42 -0
- endoreg_db/data/information_source/annotation.yaml +6 -0
- endoreg_db/data/information_source/data.yaml +30 -0
- endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
- endoreg_db/data/information_source/medication.yaml +6 -0
- endoreg_db/data/information_source/prediction.yaml +7 -0
- endoreg_db/data/information_source_type/data.yaml +8 -0
- endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
- endoreg_db/data/lab_value/coagulation.yaml +54 -0
- endoreg_db/data/lab_value/electrolytes.yaml +228 -0
- endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
- endoreg_db/data/lab_value/hematology.yaml +184 -0
- endoreg_db/data/lab_value/hormones.yaml +59 -0
- endoreg_db/data/lab_value/lipids.yaml +53 -0
- endoreg_db/data/lab_value/misc.yaml +76 -0
- endoreg_db/data/lab_value/renal_function.yaml +12 -0
- endoreg_db/data/log_type/data.yaml +57 -0
- endoreg_db/data/lx_client_tag/base.yaml +54 -0
- endoreg_db/data/lx_client_type/base.yaml +30 -0
- endoreg_db/data/lx_permission/base.yaml +24 -0
- endoreg_db/data/lx_permission/endoreg.yaml +52 -0
- endoreg_db/data/material/material.yaml +91 -0
- endoreg_db/data/medication/anticoagulation.yaml +65 -0
- endoreg_db/data/medication/tah.yaml +70 -0
- endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
- endoreg_db/data/medication_indication_type/data.yaml +11 -0
- endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
- endoreg_db/data/medication_intake_time/base.yaml +31 -0
- endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
- endoreg_db/data/medication_schedule/ass.yaml +12 -0
- endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
- endoreg_db/data/names_first/first_names.yaml +54 -0
- endoreg_db/data/names_last/last_names.yaml +51 -0
- endoreg_db/data/network_device/data.yaml +59 -0
- endoreg_db/data/network_device_type/data.yaml +12 -0
- endoreg_db/data/organ/data.yaml +29 -0
- endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
- endoreg_db/data/pdf_type/data.yaml +46 -0
- endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
- endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
- endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
- endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
- endoreg_db/data/profession/data.yaml +70 -0
- endoreg_db/data/qualification/endoscopy.yaml +36 -0
- endoreg_db/data/qualification/m2.yaml +39 -0
- endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
- endoreg_db/data/qualification/sonography.yaml +36 -0
- endoreg_db/data/qualification_type/base.yaml +29 -0
- endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
- endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
- endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
- endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
- endoreg_db/data/requirement/01_patient_data.yaml +93 -0
- endoreg_db/data/requirement/old/colon_polyp_intervention.yaml +49 -0
- endoreg_db/data/requirement/old/colonoscopy_baseline_austria.yaml +45 -0
- endoreg_db/data/requirement/old/coloreg_colon_polyp.yaml +49 -0
- endoreg_db/data/requirement/old/disease_cardiovascular.yaml +79 -0
- endoreg_db/data/requirement/old/disease_classification_choice_cardiovascular.yaml +41 -0
- endoreg_db/data/requirement/old/disease_hepatology.yaml +12 -0
- endoreg_db/data/requirement/old/disease_misc.yaml +12 -0
- endoreg_db/data/requirement/old/disease_renal.yaml +96 -0
- endoreg_db/data/requirement/old/endoscopy_bleeding_risk.yaml +59 -0
- endoreg_db/data/requirement/old/event_cardiology.yaml +251 -0
- endoreg_db/data/requirement/old/event_requirements.yaml +145 -0
- endoreg_db/data/requirement/old/finding_colon_polyp.yaml +50 -0
- endoreg_db/data/requirement/old/gender.yaml +0 -0
- endoreg_db/data/requirement/old/lab_value.yaml +441 -0
- endoreg_db/data/requirement/old/medication.yaml +93 -0
- endoreg_db/data/requirement_operator/_old/age.yaml +13 -0
- endoreg_db/data/requirement_operator/_old/lab_operators.yaml +129 -0
- endoreg_db/data/requirement_operator/_old/model_operators.yaml +96 -0
- endoreg_db/data/requirement_operator/new_operators.yaml +36 -0
- endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +65 -0
- endoreg_db/data/requirement_set/01_laboratory.yaml +13 -0
- endoreg_db/data/requirement_set/02_endoscopy_bleeding_risk.yaml +46 -0
- endoreg_db/data/requirement_set/90_coloreg.yaml +190 -0
- endoreg_db/data/requirement_set/_old_ +109 -0
- endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
- endoreg_db/data/requirement_set_type/data.yaml +41 -0
- endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
- endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
- endoreg_db/data/risk/bleeding.yaml +26 -0
- endoreg_db/data/risk/thrombosis.yaml +37 -0
- endoreg_db/data/risk_type/data.yaml +27 -0
- endoreg_db/data/setup_config.yaml +38 -0
- endoreg_db/data/shift/endoscopy.yaml +21 -0
- endoreg_db/data/shift/m2.yaml +0 -0
- endoreg_db/data/shift_type/base.yaml +35 -0
- endoreg_db/data/tag/requirement_set_tags.yaml +32 -0
- endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
- endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
- endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
- endoreg_db/data/unit/concentration.yaml +115 -0
- endoreg_db/data/unit/data.yaml +17 -0
- endoreg_db/data/unit/length.yaml +31 -0
- endoreg_db/data/unit/misc.yaml +20 -0
- endoreg_db/data/unit/rate.yaml +6 -0
- endoreg_db/data/unit/time.yaml +48 -0
- endoreg_db/data/unit/volume.yaml +35 -0
- endoreg_db/data/unit/weight.yaml +38 -0
- endoreg_db/data/waste/data.yaml +12 -0
- endoreg_db/exceptions.py +24 -0
- endoreg_db/export/frames/export.py +6 -0
- endoreg_db/export/frames/export_frames_with_labels.py +616 -0
- endoreg_db/factories/__init__.py +0 -0
- endoreg_db/forms/__init__.py +4 -0
- endoreg_db/forms/examination_form.py +12 -0
- endoreg_db/forms/patient_finding_intervention_form.py +40 -0
- endoreg_db/forms/patient_form.py +23 -0
- endoreg_db/forms/questionnaires/__init__.py +1 -0
- endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
- endoreg_db/forms/settings/__init__.py +11 -0
- endoreg_db/forms/unit.py +7 -0
- endoreg_db/helpers/__init__.py +0 -0
- endoreg_db/helpers/count_db.py +48 -0
- endoreg_db/helpers/data_loader.py +280 -0
- endoreg_db/helpers/default_objects.py +414 -0
- endoreg_db/helpers/download_segmentation_model.py +32 -0
- endoreg_db/helpers/interact.py +1 -0
- endoreg_db/helpers/test_video_helper.py +127 -0
- endoreg_db/import_files/__init__.py +27 -0
- endoreg_db/import_files/context/__init__.py +7 -0
- endoreg_db/import_files/context/default_sensitive_meta.py +83 -0
- endoreg_db/import_files/context/ensure_center.py +17 -0
- endoreg_db/import_files/context/file_lock.py +66 -0
- endoreg_db/import_files/context/import_context.py +42 -0
- endoreg_db/import_files/context/validate_directories.py +57 -0
- endoreg_db/import_files/file_storage/__init__.py +15 -0
- endoreg_db/import_files/file_storage/create_report_file.py +99 -0
- endoreg_db/import_files/file_storage/create_video_file.py +104 -0
- endoreg_db/import_files/file_storage/sensitive_meta_storage.py +42 -0
- endoreg_db/import_files/file_storage/state_management.py +463 -0
- endoreg_db/import_files/file_storage/storage.py +42 -0
- endoreg_db/import_files/import_service.md +26 -0
- endoreg_db/import_files/processing/__init__.py +11 -0
- endoreg_db/import_files/processing/report_processing/report_anonymization.py +99 -0
- endoreg_db/import_files/processing/sensitive_meta_adapter.py +51 -0
- endoreg_db/import_files/processing/video_processing/video_anonymization.py +107 -0
- endoreg_db/import_files/pseudonymization/__init__.py +0 -0
- endoreg_db/import_files/pseudonymization/fake.py +52 -0
- endoreg_db/import_files/pseudonymization/k_anonymity.py +181 -0
- endoreg_db/import_files/pseudonymization/k_pseudonymity.py +139 -0
- endoreg_db/import_files/pseudonymization/pseudonymize.py +0 -0
- endoreg_db/import_files/report_import_service.py +147 -0
- endoreg_db/import_files/video_import_service.py +154 -0
- endoreg_db/logger_conf.py +156 -0
- endoreg_db/management/__init__.py +1 -0
- endoreg_db/management/commands/__init__.py +1 -0
- endoreg_db/management/commands/anonymize_video.py +0 -0
- endoreg_db/management/commands/check_auth.py +132 -0
- endoreg_db/management/commands/create_model_meta_from_huggingface.py +177 -0
- endoreg_db/management/commands/create_multilabel_model_meta.py +419 -0
- endoreg_db/management/commands/export_frame_annot.py +196 -0
- endoreg_db/management/commands/fix_missing_patient_data.py +206 -0
- endoreg_db/management/commands/fix_video_paths.py +186 -0
- endoreg_db/management/commands/import_report.py +361 -0
- endoreg_db/management/commands/list_routes.py +20 -0
- endoreg_db/management/commands/load_ai_model_data.py +83 -0
- endoreg_db/management/commands/load_ai_model_label_data.py +60 -0
- endoreg_db/management/commands/load_base_db_data.py +63 -0
- endoreg_db/management/commands/load_center_data.py +68 -0
- endoreg_db/management/commands/load_contraindication_data.py +39 -0
- endoreg_db/management/commands/load_disease_classification_choices_data.py +38 -0
- endoreg_db/management/commands/load_disease_classification_data.py +38 -0
- endoreg_db/management/commands/load_disease_data.py +59 -0
- endoreg_db/management/commands/load_distribution_data.py +63 -0
- endoreg_db/management/commands/load_endoscope_data.py +58 -0
- endoreg_db/management/commands/load_event_data.py +39 -0
- endoreg_db/management/commands/load_examination_data.py +78 -0
- endoreg_db/management/commands/load_examination_indication_data.py +85 -0
- endoreg_db/management/commands/load_finding_data.py +115 -0
- endoreg_db/management/commands/load_gender_data.py +37 -0
- endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +142 -0
- endoreg_db/management/commands/load_information_source.py +46 -0
- endoreg_db/management/commands/load_lab_value_data.py +52 -0
- endoreg_db/management/commands/load_legacy_data.py +303 -0
- endoreg_db/management/commands/load_medication_data.py +104 -0
- endoreg_db/management/commands/load_name_data.py +36 -0
- endoreg_db/management/commands/load_organ_data.py +39 -0
- endoreg_db/management/commands/load_pdf_type_data.py +58 -0
- endoreg_db/management/commands/load_profession_data.py +40 -0
- endoreg_db/management/commands/load_qualification_data.py +56 -0
- endoreg_db/management/commands/load_report_reader_flag_data.py +40 -0
- endoreg_db/management/commands/load_requirement_data.py +207 -0
- endoreg_db/management/commands/load_requirement_set_tags.py +95 -0
- endoreg_db/management/commands/load_risk_data.py +57 -0
- endoreg_db/management/commands/load_shift_data.py +57 -0
- endoreg_db/management/commands/load_tag_data.py +54 -0
- endoreg_db/management/commands/load_unit_data.py +40 -0
- endoreg_db/management/commands/load_user_groups.py +26 -0
- endoreg_db/management/commands/model_input.py +169 -0
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- endoreg_db/utils/check_video_files.py +175 -0
- endoreg_db/utils/cropping.py +30 -0
- endoreg_db/utils/dataloader.py +285 -0
- endoreg_db/utils/dates.py +59 -0
- endoreg_db/utils/defaults/set_default_center.py +33 -0
- endoreg_db/utils/env.py +37 -0
- endoreg_db/utils/extract_specific_frames.py +87 -0
- endoreg_db/utils/file_operations.py +70 -0
- endoreg_db/utils/fix_video_path_direct.py +157 -0
- endoreg_db/utils/frame_anonymization_utils.py +463 -0
- endoreg_db/utils/hashs.py +138 -0
- endoreg_db/utils/links/__init__.py +0 -0
- endoreg_db/utils/links/requirement_link.py +237 -0
- endoreg_db/utils/mime_types.py +0 -0
- endoreg_db/utils/names.py +82 -0
- endoreg_db/utils/ocr.py +195 -0
- endoreg_db/utils/operation_log.py +87 -0
- endoreg_db/utils/parse_and_generate_yaml.py +45 -0
- endoreg_db/utils/paths.py +159 -0
- endoreg_db/utils/permissions.py +160 -0
- endoreg_db/utils/pipelines/Readme.md +235 -0
- endoreg_db/utils/pipelines/__init__.py +0 -0
- endoreg_db/utils/pipelines/process_video_dir.py +144 -0
- endoreg_db/utils/product/__init__.py +0 -0
- endoreg_db/utils/product/sum_emissions.py +22 -0
- endoreg_db/utils/product/sum_weights.py +20 -0
- endoreg_db/utils/pydantic_models/__init__.py +5 -0
- endoreg_db/utils/pydantic_models/db_config.py +57 -0
- endoreg_db/utils/requirement_helpers.py +0 -0
- endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
- endoreg_db/utils/requirement_operator_logic/_old/lab_value_operators.py +678 -0
- endoreg_db/utils/requirement_operator_logic/_old/model_evaluators.py +842 -0
- endoreg_db/utils/requirement_operator_logic/new_operator_logic.py +114 -0
- endoreg_db/utils/setup_config.py +196 -0
- endoreg_db/utils/storage.py +117 -0
- endoreg_db/utils/translation.py +31 -0
- endoreg_db/utils/uuid.py +5 -0
- endoreg_db/utils/validate_endo_roi.py +33 -0
- endoreg_db/utils/validate_subcategory_dict.py +93 -0
- endoreg_db/utils/validate_video_detailed.py +415 -0
- endoreg_db/utils/video/__init__.py +30 -0
- endoreg_db/utils/video/extract_frames.py +100 -0
- endoreg_db/utils/video/ffmpeg_wrapper.py +996 -0
- endoreg_db/utils/video/names.py +47 -0
- endoreg_db/utils/video/streaming_processor.py +386 -0
- endoreg_db/utils/video/video_splitter.py +105 -0
- endoreg_db/versioning.md +79 -0
- endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +247 -0
- endoreg_db/views/__init__.py +157 -0
- endoreg_db/views/anonymization/__init__.py +31 -0
- endoreg_db/views/anonymization/media_management.py +486 -0
- endoreg_db/views/anonymization/overview.py +307 -0
- endoreg_db/views/anonymization/validate.py +310 -0
- endoreg_db/views/auth/__init__.py +13 -0
- endoreg_db/views/auth/keycloak.py +146 -0
- endoreg_db/views/examination/__init__.py +30 -0
- endoreg_db/views/examination/examination.py +37 -0
- endoreg_db/views/examination/examination_manifest_cache.py +26 -0
- endoreg_db/views/examination/get_finding_classification_choices.py +62 -0
- endoreg_db/views/examination/get_finding_classifications.py +38 -0
- endoreg_db/views/examination/get_findings.py +39 -0
- endoreg_db/views/examination/get_instruments.py +19 -0
- endoreg_db/views/examination/get_interventions.py +14 -0
- endoreg_db/views/finding/__init__.py +9 -0
- endoreg_db/views/finding/finding.py +116 -0
- endoreg_db/views/finding/get_classifications.py +14 -0
- endoreg_db/views/finding/get_interventions.py +17 -0
- endoreg_db/views/finding_classification/__init__.py +13 -0
- endoreg_db/views/finding_classification/base.py +0 -0
- endoreg_db/views/finding_classification/finding_classification.py +41 -0
- endoreg_db/views/finding_classification/get_classification_choices.py +54 -0
- endoreg_db/views/media/__init__.py +32 -0
- endoreg_db/views/media/pdf_media.py +411 -0
- endoreg_db/views/media/sensitive_metadata.py +372 -0
- endoreg_db/views/media/video_media.py +275 -0
- endoreg_db/views/meta/__init__.py +7 -0
- endoreg_db/views/meta/sensitive_meta_list.py +102 -0
- endoreg_db/views/meta/sensitive_meta_verification.py +74 -0
- endoreg_db/views/misc/__init__.py +29 -0
- endoreg_db/views/misc/center.py +14 -0
- endoreg_db/views/misc/csrf.py +8 -0
- endoreg_db/views/misc/gender.py +15 -0
- endoreg_db/views/misc/stats.py +255 -0
- endoreg_db/views/misc/upload_views.py +241 -0
- endoreg_db/views/patient/__init__.py +3 -0
- endoreg_db/views/patient/patient.py +253 -0
- endoreg_db/views/patient_examination/__init__.py +11 -0
- endoreg_db/views/patient_examination/patient_examination.py +141 -0
- endoreg_db/views/patient_examination/patient_examination_create.py +58 -0
- endoreg_db/views/patient_examination/patient_examination_detail.py +63 -0
- endoreg_db/views/patient_examination/patient_examination_list.py +72 -0
- endoreg_db/views/patient_examination/video.py +228 -0
- endoreg_db/views/patient_finding/__init__.py +7 -0
- endoreg_db/views/patient_finding/base.py +0 -0
- endoreg_db/views/patient_finding/patient_finding.py +71 -0
- endoreg_db/views/patient_finding/patient_finding_optimized.py +291 -0
- endoreg_db/views/patient_finding_classification/__init__.py +5 -0
- endoreg_db/views/patient_finding_classification/pfc_create.py +75 -0
- endoreg_db/views/report/__init__.py +7 -0
- endoreg_db/views/report/reimport.py +177 -0
- endoreg_db/views/report/report_stream.py +191 -0
- endoreg_db/views/requirement/__init__.py +11 -0
- endoreg_db/views/requirement/evaluate.py +278 -0
- endoreg_db/views/requirement/lookup.py +380 -0
- endoreg_db/views/requirement/lookup_store.py +183 -0
- endoreg_db/views/requirement/requirement_utils.py +87 -0
- endoreg_db/views/requirement_lookup/lookup.py +0 -0
- endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
- endoreg_db/views/stats/__init__.py +13 -0
- endoreg_db/views/stats/stats_views.py +266 -0
- endoreg_db/views/video/__init__.py +49 -0
- endoreg_db/views/video/ai/__init__.py +8 -0
- endoreg_db/views/video/ai/label.py +159 -0
- endoreg_db/views/video/correction.py +529 -0
- endoreg_db/views/video/reimport.py +230 -0
- endoreg_db/views/video/segments_crud.py +709 -0
- endoreg_db/views/video/video_apply_mask.py +49 -0
- endoreg_db/views/video/video_correction.py +22 -0
- endoreg_db/views/video/video_download_processed.py +58 -0
- endoreg_db/views/video/video_examination_viewset.py +242 -0
- endoreg_db/views/video/video_metadata.py +101 -0
- endoreg_db/views/video/video_processing_history.py +25 -0
- endoreg_db/views/video/video_remove_frames.py +49 -0
- endoreg_db/views/video/video_stream.py +334 -0
- endoreg_db-0.8.9.32.dist-info/METADATA +404 -0
- endoreg_db-0.8.9.32.dist-info/RECORD +787 -0
- endoreg_db-0.8.9.32.dist-info/WHEEL +4 -0
- endoreg_db-0.8.9.32.dist-info/licenses/LICENSE +674 -0
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# endoreg_db/utils/ai/model_training/trainer_gastronet_multilabel.py
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from __future__ import annotations
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import json
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import random
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from pathlib import Path
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from typing import Dict, List, Optional, Sequence, Tuple
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import torch
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from torch.utils.data import DataLoader
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from torch.optim.lr_scheduler import CosineAnnealingLR
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from django.db import models
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from endoreg_db.models import AIDataSet
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from endoreg_db.utils.ai.data_loader_for_model_input import build_dataset_for_training
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from endoreg_db.utils.ai.model_training.config import (
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TrainingConfig,
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RUNS_DIR,
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)
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from endoreg_db.utils.ai.model_training.dataset import EndoMultiLabelDataset
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from endoreg_db.utils.ai.model_training.losses import (
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compute_class_weights,
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focal_loss_with_mask,
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)
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from endoreg_db.utils.ai.model_training.metrics import compute_metrics
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from endoreg_db.utils.ai.model_training.model_backbones import (
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create_multilabel_model,
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)
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# ---------------------------------------------------------------------
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# HELPER: FILTER LABELS BY LABELSET VERSION
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# ---------------------------------------------------------------------
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def filter_labels_by_labelset_version(
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labels: Sequence[models.Model],
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label_vectors: Sequence[Sequence[Optional[int]]],
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label_masks: Sequence[Sequence[int]],
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target_version: int,
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) -> Tuple[
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List[List[Optional[int]]],
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List[List[int]],
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List[models.Model],
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List[int],
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]:
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"""
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From the full label list + vectors, keep ONLY those labels that belong
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to ANY LabelSet with version == target_version.
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labels: list[Label]
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label_vectors: list[list[0/1/None]] (len = N samples)
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label_masks: list[list[0/1]] (len = N samples)
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target_version: integer LabelSet.version to filter by.
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Returns:
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filtered_label_vectors,
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filtered_label_masks,
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filtered_labels,
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kept_indices (original label indices kept)
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"""
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kept_indices: List[int] = []
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for idx, lbl in enumerate(labels):
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# lbl.label_sets is the M2M relation "LabelSet.labels"
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if lbl.label_sets.filter(version=target_version).exists():
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kept_indices.append(idx)
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if not kept_indices:
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raise ValueError(
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f"No labels in this dataset belong to any LabelSet with version={target_version}. "
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"Check your LabelSet configuration or change labelset_version_to_train "
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"in config.py."
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)
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# Slice vectors + masks to keep only the chosen label indices
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filtered_vectors: List[List[Optional[int]]] = []
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filtered_masks: List[List[int]] = []
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for vec, mask in zip(label_vectors, label_masks):
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new_vec = [vec[j] for j in kept_indices]
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new_mask = [mask[j] for j in kept_indices]
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filtered_vectors.append(new_vec)
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filtered_masks.append(new_mask)
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filtered_labels = [labels[j] for j in kept_indices]
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return filtered_vectors, filtered_masks, filtered_labels, kept_indices
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# ---------------------------------------------------------------------
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# GROUP-WISE SPLIT BY old_examination_id
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# ---------------------------------------------------------------------
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def groupwise_split_indices_by_examination(
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frame_ids: Sequence[int],
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old_examination_ids: Sequence[Optional[int]],
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val_split: float,
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test_split: float,
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seed: int = 42,
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) -> Tuple[List[int], List[int], List[int]]:
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"""
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Split sample indices into train / val / test based on old_examination_id.
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All frames sharing the same old_examination_id go into the same split.
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If old_examination_id is None, we treat each frame as its own group.
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Returns:
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train_indices, val_indices, test_indices
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"""
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assert len(frame_ids) == len(old_examination_ids)
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# 1) Build mapping: group_id -> list of sample indices
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groups: Dict[object, List[int]] = {}
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for idx, (fid, exam_id) in enumerate(zip(frame_ids, old_examination_ids)):
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group_key = exam_id if exam_id is not None else f"no_exam_{fid}"
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groups.setdefault(group_key, []).append(idx)
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group_ids = list(groups.keys())
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rng = random.Random(seed)
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rng.shuffle(group_ids)
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n_groups = len(group_ids)
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n_test = int(round(test_split * n_groups))
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n_val = int(round(val_split * n_groups))
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n_train = n_groups - n_val - n_test
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train_group_ids = group_ids[:n_train]
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val_group_ids = group_ids[n_train : n_train + n_val]
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test_group_ids = group_ids[n_train + n_val :]
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train_indices: List[int] = []
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val_indices: List[int] = []
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test_indices: List[int] = []
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for gid in train_group_ids:
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train_indices.extend(groups[gid])
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for gid in val_group_ids:
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val_indices.extend(groups[gid])
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for gid in test_group_ids:
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test_indices.extend(groups[gid])
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# Sort indices for reproducibility
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train_indices.sort()
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val_indices.sort()
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test_indices.sort()
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print(
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f"[TRAIN] Group-wise split by old_examination_id: "
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f"#groups={n_groups}, train_groups={len(train_group_ids)}, "
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f"val_groups={len(val_group_ids)}, test_groups={len(test_group_ids)}"
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)
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return train_indices, val_indices, test_indices
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# ---------------------------------------------------------------------
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# MAIN TRAINING FUNCTION
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# ---------------------------------------------------------------------
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def train_gastronet_multilabel(config: TrainingConfig) -> Dict:
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"""
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High-level training entry point.
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Pipeline:
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1. Load AIDataSet from DB and build raw dataset via build_dataset_for_training.
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2. Filter labels by LabelSet.version == config.labelset_version_to_train.
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3. Optionally convert unlabeled → negative (Option A).
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4. Compute dataset statistics (positives per label, etc.).
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5. Group-wise split by old_examination_id into train/val/test.
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6. Wrap in PyTorch Dataset + DataLoaders.
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7. Build GastroNet-ResNet50 backbone + new head.
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8. Train with focal loss + class weights (+ mask).
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9. LR schedule: warm-up + cosine decay (if enabled).
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10. Save model + metadata in model_training/runs.
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"""
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# ------------------------------------------------------------------
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# 1. Load dataset from DB
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# ------------------------------------------------------------------
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dataset_obj = AIDataSet.objects.get(id=config.dataset_id)
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data = build_dataset_for_training(dataset_obj)
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image_paths: List[str] = data["image_paths"]
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label_vectors: List[List[Optional[int]]] = data["label_vectors"]
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label_masks: List[List[int]] = data["label_masks"]
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labels = data["labels"] # list[Label]
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labelset = data["labelset"]
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frame_ids: List[int] = data.get("frame_ids", [])
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old_exam_ids: List[Optional[int]] = data.get("old_examination_ids", [])
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num_samples_raw = len(image_paths)
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num_labels_raw = len(labels)
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print(f"[TRAIN] AIDataSet id={dataset_obj.id}")
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print(
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f"[TRAIN] #samples (raw) = {num_samples_raw}, #labels (raw) = {num_labels_raw}"
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)
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print(
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f"[TRAIN] LabelSet id={labelset.id}, "
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f"name={labelset.name}, version={labelset.version}"
|
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206
|
+
)
|
|
207
|
+
print("[TRAIN] Labels (raw):")
|
|
208
|
+
for idx, lbl in enumerate(labels):
|
|
209
|
+
print(f" [{idx}] {lbl.name}")
|
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210
|
+
|
|
211
|
+
# ------------------------------------------------------------------
|
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212
|
+
# 2. Filter labels by LabelSet.version == config.labelset_version_to_train
|
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213
|
+
# ------------------------------------------------------------------
|
|
214
|
+
target_version = config.labelset_version_to_train
|
|
215
|
+
print(
|
|
216
|
+
f"[TRAIN] Filtering labels to those belonging to ANY LabelSet with version={target_version}..."
|
|
217
|
+
)
|
|
218
|
+
|
|
219
|
+
(
|
|
220
|
+
label_vectors,
|
|
221
|
+
label_masks,
|
|
222
|
+
labels,
|
|
223
|
+
kept_indices,
|
|
224
|
+
) = filter_labels_by_labelset_version(
|
|
225
|
+
labels=labels,
|
|
226
|
+
label_vectors=label_vectors,
|
|
227
|
+
label_masks=label_masks,
|
|
228
|
+
target_version=target_version,
|
|
229
|
+
)
|
|
230
|
+
|
|
231
|
+
num_labels_filtered = len(labels)
|
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232
|
+
print(
|
|
233
|
+
f"[TRAIN] Label filtering done. "
|
|
234
|
+
f"Kept {num_labels_filtered} / {num_labels_raw} labels."
|
|
235
|
+
)
|
|
236
|
+
print("[TRAIN] Kept labels (new index -> original index -> name):")
|
|
237
|
+
for new_idx, orig_idx in enumerate(kept_indices):
|
|
238
|
+
print(f" [{new_idx}] (orig {orig_idx}) {labels[new_idx].name}")
|
|
239
|
+
|
|
240
|
+
# ------------------------------------------------------------------
|
|
241
|
+
# 2b. OPTION A: treat UNLABELED v2 labels as NEGATIVE (0) + KNOWN
|
|
242
|
+
# ------------------------------------------------------------------
|
|
243
|
+
# After filtering to the target version, we decide how to interpret
|
|
244
|
+
# unlabeled entries:
|
|
245
|
+
#
|
|
246
|
+
# If treat_unlabeled_as_negative == True:
|
|
247
|
+
# vec[j] == 1 -> positive, mask[j] = 1
|
|
248
|
+
# vec[j] is None -> assume 0 (negative), mask[j] = 1
|
|
249
|
+
#
|
|
250
|
+
# If False:
|
|
251
|
+
# vec[j] is None -> value 0, but mask[j] = 0 (ignored)
|
|
252
|
+
#
|
|
253
|
+
# In your current setup you want Option A (True).
|
|
254
|
+
if config.treat_unlabeled_as_negative:
|
|
255
|
+
for i in range(len(label_vectors)):
|
|
256
|
+
vec = label_vectors[i]
|
|
257
|
+
mask = label_masks[i]
|
|
258
|
+
|
|
259
|
+
new_vec = []
|
|
260
|
+
new_mask = []
|
|
261
|
+
for x in vec:
|
|
262
|
+
if x is None:
|
|
263
|
+
# unlabeled -> assume negative but KNOWN
|
|
264
|
+
new_vec.append(0)
|
|
265
|
+
new_mask.append(1)
|
|
266
|
+
else:
|
|
267
|
+
# explicit label (1 or 0) -> keep value, mark as known
|
|
268
|
+
new_vec.append(int(x))
|
|
269
|
+
new_mask.append(1)
|
|
270
|
+
|
|
271
|
+
label_vectors[i] = new_vec
|
|
272
|
+
label_masks[i] = new_mask
|
|
273
|
+
else:
|
|
274
|
+
# Respect original semantics: None = unknown -> mask=0
|
|
275
|
+
cleaned_vectors = []
|
|
276
|
+
cleaned_masks = []
|
|
277
|
+
for vec, mask in zip(label_vectors, label_masks):
|
|
278
|
+
v = []
|
|
279
|
+
m = []
|
|
280
|
+
for x, ms in zip(vec, mask):
|
|
281
|
+
if x is None:
|
|
282
|
+
v.append(0) # value won't be used
|
|
283
|
+
m.append(0) # unknown -> ignore in loss/metrics
|
|
284
|
+
else:
|
|
285
|
+
v.append(int(x)) # 0 or 1
|
|
286
|
+
m.append(int(ms))
|
|
287
|
+
cleaned_vectors.append(v)
|
|
288
|
+
cleaned_masks.append(m)
|
|
289
|
+
|
|
290
|
+
label_vectors = cleaned_vectors
|
|
291
|
+
label_masks = cleaned_masks
|
|
292
|
+
|
|
293
|
+
# ------------------------------------------------------------------
|
|
294
|
+
# 3. Dataset statistics AFTER filtering + Option A conversion
|
|
295
|
+
# ------------------------------------------------------------------
|
|
296
|
+
labels_arr = []
|
|
297
|
+
masks_arr = []
|
|
298
|
+
for vec, mask in zip(label_vectors, label_masks):
|
|
299
|
+
v = [int(x) for x in vec] # now guaranteed 0/1
|
|
300
|
+
m = [int(x) for x in mask] # typically 1
|
|
301
|
+
labels_arr.append(v)
|
|
302
|
+
masks_arr.append(m)
|
|
303
|
+
|
|
304
|
+
labels_tensor = torch.tensor(labels_arr, dtype=torch.float32)
|
|
305
|
+
masks_tensor = torch.tensor(masks_arr, dtype=torch.float32)
|
|
306
|
+
|
|
307
|
+
total_known = masks_tensor.sum().item()
|
|
308
|
+
total_pos = (labels_tensor * masks_tensor).sum().item()
|
|
309
|
+
|
|
310
|
+
print("[DEBUG] Dataset statistics AFTER label filtering:")
|
|
311
|
+
print(f" #samples = {len(image_paths)}")
|
|
312
|
+
print(f" #labels = {num_labels_filtered}")
|
|
313
|
+
print(f" total known entries= {total_known}")
|
|
314
|
+
print(f" total positive labels (over known) = {total_pos}")
|
|
315
|
+
|
|
316
|
+
pos_per_label = (labels_tensor * masks_tensor).sum(dim=0).tolist()
|
|
317
|
+
print("[DEBUG] Positives per label (index: count):")
|
|
318
|
+
for idx, c in enumerate(pos_per_label):
|
|
319
|
+
print(f" [{idx}] = {int(c)}")
|
|
320
|
+
|
|
321
|
+
# ------------------------------------------------------------------
|
|
322
|
+
# 4. Group-wise split by old_examination_id (train/val/test)
|
|
323
|
+
# ------------------------------------------------------------------
|
|
324
|
+
if not frame_ids or not old_exam_ids:
|
|
325
|
+
frame_ids = list(range(len(image_paths)))
|
|
326
|
+
old_exam_ids = [None] * len(image_paths)
|
|
327
|
+
|
|
328
|
+
train_indices, val_indices, test_indices = groupwise_split_indices_by_examination(
|
|
329
|
+
frame_ids=frame_ids,
|
|
330
|
+
old_examination_ids=old_exam_ids,
|
|
331
|
+
val_split=config.val_split,
|
|
332
|
+
test_split=config.test_split,
|
|
333
|
+
seed=config.random_seed,
|
|
334
|
+
)
|
|
335
|
+
|
|
336
|
+
print(
|
|
337
|
+
f"[TRAIN] Train size: {len(train_indices)}, "
|
|
338
|
+
f"Val size: {len(val_indices)}, "
|
|
339
|
+
f"Test size: {len(test_indices)}"
|
|
340
|
+
)
|
|
341
|
+
|
|
342
|
+
# ------------------------------------------------------------------
|
|
343
|
+
# 5. Build PyTorch datasets + loaders
|
|
344
|
+
# ------------------------------------------------------------------
|
|
345
|
+
full_ds = EndoMultiLabelDataset(
|
|
346
|
+
image_paths=image_paths,
|
|
347
|
+
label_vectors=label_vectors,
|
|
348
|
+
label_masks=label_masks,
|
|
349
|
+
image_size=224,
|
|
350
|
+
)
|
|
351
|
+
|
|
352
|
+
def subset_dataset(
|
|
353
|
+
ds: EndoMultiLabelDataset, indices: List[int]
|
|
354
|
+
) -> EndoMultiLabelDataset:
|
|
355
|
+
sub_image_paths = [ds.image_paths[i] for i in indices]
|
|
356
|
+
sub_labels = ds.labels[indices]
|
|
357
|
+
sub_masks = ds.masks[indices]
|
|
358
|
+
|
|
359
|
+
sub_label_vectors = sub_labels.tolist()
|
|
360
|
+
sub_label_masks = sub_masks.tolist()
|
|
361
|
+
return EndoMultiLabelDataset(
|
|
362
|
+
image_paths=sub_image_paths,
|
|
363
|
+
label_vectors=sub_label_vectors,
|
|
364
|
+
label_masks=sub_label_masks,
|
|
365
|
+
image_size=ds.image_size,
|
|
366
|
+
)
|
|
367
|
+
|
|
368
|
+
train_ds = subset_dataset(full_ds, train_indices)
|
|
369
|
+
val_ds = subset_dataset(full_ds, val_indices)
|
|
370
|
+
test_ds = subset_dataset(full_ds, test_indices)
|
|
371
|
+
|
|
372
|
+
train_loader = DataLoader(
|
|
373
|
+
train_ds,
|
|
374
|
+
batch_size=config.batch_size,
|
|
375
|
+
shuffle=True,
|
|
376
|
+
num_workers=4,
|
|
377
|
+
pin_memory=True,
|
|
378
|
+
)
|
|
379
|
+
val_loader = DataLoader(
|
|
380
|
+
val_ds,
|
|
381
|
+
batch_size=config.batch_size,
|
|
382
|
+
shuffle=False,
|
|
383
|
+
num_workers=4,
|
|
384
|
+
pin_memory=True,
|
|
385
|
+
)
|
|
386
|
+
test_loader = DataLoader(
|
|
387
|
+
test_ds,
|
|
388
|
+
batch_size=config.batch_size,
|
|
389
|
+
shuffle=False,
|
|
390
|
+
num_workers=4,
|
|
391
|
+
pin_memory=True,
|
|
392
|
+
)
|
|
393
|
+
|
|
394
|
+
# ------------------------------------------------------------------
|
|
395
|
+
# 6. Build model
|
|
396
|
+
# ------------------------------------------------------------------
|
|
397
|
+
if config.device == "auto":
|
|
398
|
+
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
|
|
399
|
+
else:
|
|
400
|
+
device = torch.device(config.device)
|
|
401
|
+
|
|
402
|
+
"""backbone_ckpt = (
|
|
403
|
+
Path(config.backbone_checkpoint)
|
|
404
|
+
if config.backbone_checkpoint is not None
|
|
405
|
+
else None
|
|
406
|
+
)
|
|
407
|
+
|
|
408
|
+
model = GastroNetResNet50MultiLabel(
|
|
409
|
+
num_labels=num_labels_filtered,
|
|
410
|
+
backbone_checkpoint=backbone_ckpt,
|
|
411
|
+
freeze_backbone=True, # start with head-only training
|
|
412
|
+
)
|
|
413
|
+
model.to(device)"""
|
|
414
|
+
|
|
415
|
+
backbone_ckpt = (
|
|
416
|
+
Path(config.backbone_checkpoint)
|
|
417
|
+
if config.backbone_checkpoint is not None
|
|
418
|
+
else None
|
|
419
|
+
)
|
|
420
|
+
|
|
421
|
+
model = create_multilabel_model(
|
|
422
|
+
backbone_name=config.backbone_name,
|
|
423
|
+
num_labels=num_labels_filtered,
|
|
424
|
+
backbone_checkpoint=backbone_ckpt,
|
|
425
|
+
freeze_backbone=config.freeze_backbone,
|
|
426
|
+
)
|
|
427
|
+
model.to(device)
|
|
428
|
+
|
|
429
|
+
# ------------------------------------------------------------------
|
|
430
|
+
# 7. Class weights from full (filtered) dataset
|
|
431
|
+
# ------------------------------------------------------------------
|
|
432
|
+
class_weights = compute_class_weights(full_ds.labels, full_ds.masks).to(device)
|
|
433
|
+
print("[TRAIN] Computed class weights per label:", class_weights.cpu().tolist())
|
|
434
|
+
print(
|
|
435
|
+
"[DEBUG] class_weights range: "
|
|
436
|
+
f"min={float(class_weights.min()):.6f}, max={float(class_weights.max()):.6f}"
|
|
437
|
+
)
|
|
438
|
+
|
|
439
|
+
# ------------------------------------------------------------------
|
|
440
|
+
# 8. Optimizer + LR SCHEDULER (warm-up + cosine)
|
|
441
|
+
# ------------------------------------------------------------------
|
|
442
|
+
head_params = list(model.classifier.parameters())
|
|
443
|
+
backbone_params = [p for p in model.backbone.parameters() if p.requires_grad]
|
|
444
|
+
|
|
445
|
+
optimizer = torch.optim.AdamW(
|
|
446
|
+
[
|
|
447
|
+
{"params": head_params, "lr": config.lr_head},
|
|
448
|
+
{"params": backbone_params, "lr": config.lr_backbone},
|
|
449
|
+
]
|
|
450
|
+
)
|
|
451
|
+
|
|
452
|
+
# Store base LRs for warm-up
|
|
453
|
+
base_lrs = [config.lr_head, config.lr_backbone]
|
|
454
|
+
|
|
455
|
+
if config.use_scheduler:
|
|
456
|
+
total_epochs = config.num_epochs
|
|
457
|
+
warmup_epochs = max(config.warmup_epochs, 0)
|
|
458
|
+
# We apply cosine decay AFTER warm-up
|
|
459
|
+
t_max = max(total_epochs - warmup_epochs, 1)
|
|
460
|
+
|
|
461
|
+
scheduler = CosineAnnealingLR(
|
|
462
|
+
optimizer,
|
|
463
|
+
T_max=t_max,
|
|
464
|
+
eta_min=config.min_lr,
|
|
465
|
+
)
|
|
466
|
+
print(
|
|
467
|
+
f"[LR] Using warm-up + cosine decay: warmup_epochs={warmup_epochs}, "
|
|
468
|
+
f"T_max={t_max}, min_lr={config.min_lr}"
|
|
469
|
+
)
|
|
470
|
+
else:
|
|
471
|
+
scheduler = None
|
|
472
|
+
warmup_epochs = 0
|
|
473
|
+
print("[LR] No LR scheduler used (fixed learning rate).")
|
|
474
|
+
|
|
475
|
+
# ------------------------------------------------------------------
|
|
476
|
+
# 9. Training loop
|
|
477
|
+
# ------------------------------------------------------------------
|
|
478
|
+
history = {"train_loss": [], "val_loss": [], "test_loss": None}
|
|
479
|
+
|
|
480
|
+
# One-time debug of first batch
|
|
481
|
+
first_batch = next(iter(train_loader))
|
|
482
|
+
imgs_dbg, y_dbg, m_dbg = first_batch
|
|
483
|
+
print("[DEBUG] First training batch shapes:")
|
|
484
|
+
print(" imgs:", imgs_dbg.shape)
|
|
485
|
+
print(" y: ", y_dbg.shape)
|
|
486
|
+
print(" m: ", m_dbg.shape)
|
|
487
|
+
print("[DEBUG] First sample labels (y[0]):")
|
|
488
|
+
print(y_dbg[0].tolist())
|
|
489
|
+
print("[DEBUG] First sample mask (m[0]):")
|
|
490
|
+
print(m_dbg[0].tolist())
|
|
491
|
+
|
|
492
|
+
model.eval()
|
|
493
|
+
with torch.no_grad():
|
|
494
|
+
logits_dbg = model(imgs_dbg.to(device))
|
|
495
|
+
probs_dbg = torch.sigmoid(logits_dbg)
|
|
496
|
+
print("[DEBUG] First sample logits:")
|
|
497
|
+
print(logits_dbg[0].cpu().tolist())
|
|
498
|
+
print("[DEBUG] First sample probs (sigmoid):")
|
|
499
|
+
print(probs_dbg[0].cpu().tolist())
|
|
500
|
+
|
|
501
|
+
for epoch in range(1, config.num_epochs + 1):
|
|
502
|
+
# ----------------- LR SCHEDULER: warm-up + cosine ----------------
|
|
503
|
+
if scheduler is not None:
|
|
504
|
+
if warmup_epochs > 0 and epoch <= warmup_epochs:
|
|
505
|
+
# Linear warm-up: start from 0 → base_lr over warmup_epochs
|
|
506
|
+
warmup_factor = epoch / float(warmup_epochs)
|
|
507
|
+
for i, pg in enumerate(optimizer.param_groups):
|
|
508
|
+
pg["lr"] = base_lrs[i] * warmup_factor
|
|
509
|
+
else:
|
|
510
|
+
# After warm-up, step cosine scheduler once per epoch
|
|
511
|
+
scheduler.step()
|
|
512
|
+
|
|
513
|
+
current_lrs = [pg["lr"] for pg in optimizer.param_groups]
|
|
514
|
+
print(
|
|
515
|
+
f"[LR] Epoch {epoch:03d}: "
|
|
516
|
+
f"head_lr={current_lrs[0]:.6g}, backbone_lr={current_lrs[1]:.6g}"
|
|
517
|
+
)
|
|
518
|
+
|
|
519
|
+
# ----------------- TRAIN PHASE -----------------------------------
|
|
520
|
+
model.train()
|
|
521
|
+
train_loss_sum = 0.0
|
|
522
|
+
train_batches = 0
|
|
523
|
+
|
|
524
|
+
for imgs, y, m in train_loader:
|
|
525
|
+
imgs = imgs.to(device, non_blocking=True)
|
|
526
|
+
y = y.to(device, non_blocking=True)
|
|
527
|
+
m = m.to(device, non_blocking=True)
|
|
528
|
+
|
|
529
|
+
optimizer.zero_grad()
|
|
530
|
+
logits = model(imgs)
|
|
531
|
+
|
|
532
|
+
loss = focal_loss_with_mask(
|
|
533
|
+
logits=logits,
|
|
534
|
+
targets=y,
|
|
535
|
+
masks=m,
|
|
536
|
+
class_weights=class_weights,
|
|
537
|
+
alpha=config.alpha_focal,
|
|
538
|
+
gamma=config.gamma_focal,
|
|
539
|
+
)
|
|
540
|
+
loss.backward()
|
|
541
|
+
optimizer.step()
|
|
542
|
+
|
|
543
|
+
train_loss_sum += loss.item()
|
|
544
|
+
train_batches += 1
|
|
545
|
+
|
|
546
|
+
train_loss = train_loss_sum / max(train_batches, 1)
|
|
547
|
+
history["train_loss"].append(train_loss)
|
|
548
|
+
|
|
549
|
+
# ----------------- VALIDATION PHASE ------------------------------
|
|
550
|
+
model.eval()
|
|
551
|
+
val_loss_sum = 0.0
|
|
552
|
+
val_batches = 0
|
|
553
|
+
|
|
554
|
+
all_val_logits = []
|
|
555
|
+
all_val_targets = []
|
|
556
|
+
all_val_masks = []
|
|
557
|
+
|
|
558
|
+
with torch.no_grad():
|
|
559
|
+
for imgs, y, m in val_loader:
|
|
560
|
+
imgs = imgs.to(device, non_blocking=True)
|
|
561
|
+
y = y.to(device, non_blocking=True)
|
|
562
|
+
m = m.to(device, non_blocking=True)
|
|
563
|
+
|
|
564
|
+
logits = model(imgs)
|
|
565
|
+
loss = focal_loss_with_mask(
|
|
566
|
+
logits=logits,
|
|
567
|
+
targets=y,
|
|
568
|
+
masks=m,
|
|
569
|
+
class_weights=class_weights,
|
|
570
|
+
alpha=config.alpha_focal,
|
|
571
|
+
gamma=config.gamma_focal,
|
|
572
|
+
)
|
|
573
|
+
val_loss_sum += loss.item()
|
|
574
|
+
val_batches += 1
|
|
575
|
+
|
|
576
|
+
all_val_logits.append(logits)
|
|
577
|
+
all_val_targets.append(y)
|
|
578
|
+
all_val_masks.append(m)
|
|
579
|
+
|
|
580
|
+
val_loss = val_loss_sum / max(val_batches, 1)
|
|
581
|
+
history["val_loss"].append(val_loss)
|
|
582
|
+
|
|
583
|
+
all_val_logits = torch.cat(all_val_logits, dim=0)
|
|
584
|
+
all_val_targets = torch.cat(all_val_targets, dim=0)
|
|
585
|
+
all_val_masks = torch.cat(all_val_masks, dim=0)
|
|
586
|
+
|
|
587
|
+
val_metrics = compute_metrics(
|
|
588
|
+
logits=all_val_logits,
|
|
589
|
+
targets=all_val_targets,
|
|
590
|
+
masks=all_val_masks,
|
|
591
|
+
threshold=0.5,
|
|
592
|
+
)
|
|
593
|
+
|
|
594
|
+
print(
|
|
595
|
+
f"[VAL METRICS] "
|
|
596
|
+
f"Precision={val_metrics['precision']:.4f} "
|
|
597
|
+
f"Recall={val_metrics['recall']:.4f} "
|
|
598
|
+
f"F1={val_metrics['f1']:.4f} "
|
|
599
|
+
f"Acc={val_metrics['accuracy']:.4f} "
|
|
600
|
+
f"TP={val_metrics['tp']} FP={val_metrics['fp']} "
|
|
601
|
+
f"TN={val_metrics['tn']} FN={val_metrics['fn']}"
|
|
602
|
+
)
|
|
603
|
+
|
|
604
|
+
print(
|
|
605
|
+
f"[EPOCH {epoch:03d}/{config.num_epochs:03d}] "
|
|
606
|
+
f"train_loss={train_loss:.4f} val_loss={val_loss:.4f}"
|
|
607
|
+
)
|
|
608
|
+
|
|
609
|
+
# Print table of per-label metrics
|
|
610
|
+
print("\n[VAL PER-LABEL METRICS]")
|
|
611
|
+
print(f"{'Label':20s} {'Prec':>8s} {'Rec':>8s} {'F1':>8s} {'Support':>8s}")
|
|
612
|
+
print("-" * 60)
|
|
613
|
+
|
|
614
|
+
for j, stats in enumerate(val_metrics["per_label"]):
|
|
615
|
+
name = labels[j].name
|
|
616
|
+
p = stats["precision"]
|
|
617
|
+
r = stats["recall"]
|
|
618
|
+
f = stats["f1"]
|
|
619
|
+
sup = stats["support"]
|
|
620
|
+
|
|
621
|
+
if p is None:
|
|
622
|
+
print(f"{name:20s} {'N/A':>8} {'N/A':>8} {'N/A':>8} {sup:8d}")
|
|
623
|
+
else:
|
|
624
|
+
print(f"{name:20s} {p:8.4f} {r:8.4f} {f:8.4f} {sup:8d}")
|
|
625
|
+
|
|
626
|
+
print("-" * 60)
|
|
627
|
+
|
|
628
|
+
# ------------------------------------------------------------------
|
|
629
|
+
# 10. Final test loss + metrics
|
|
630
|
+
# ------------------------------------------------------------------
|
|
631
|
+
model.eval()
|
|
632
|
+
test_loss_sum = 0.0
|
|
633
|
+
test_batches = 0
|
|
634
|
+
|
|
635
|
+
all_test_logits = []
|
|
636
|
+
all_test_targets = []
|
|
637
|
+
all_test_masks = []
|
|
638
|
+
|
|
639
|
+
with torch.no_grad():
|
|
640
|
+
for imgs, y, m in test_loader:
|
|
641
|
+
imgs = imgs.to(device, non_blocking=True)
|
|
642
|
+
y = y.to(device, non_blocking=True)
|
|
643
|
+
m = m.to(device, non_blocking=True)
|
|
644
|
+
|
|
645
|
+
logits = model(imgs)
|
|
646
|
+
loss = focal_loss_with_mask(
|
|
647
|
+
logits=logits,
|
|
648
|
+
targets=y,
|
|
649
|
+
masks=m,
|
|
650
|
+
class_weights=class_weights,
|
|
651
|
+
alpha=config.alpha_focal,
|
|
652
|
+
gamma=config.gamma_focal,
|
|
653
|
+
)
|
|
654
|
+
test_loss_sum += loss.item()
|
|
655
|
+
test_batches += 1
|
|
656
|
+
|
|
657
|
+
all_test_logits.append(logits)
|
|
658
|
+
all_test_targets.append(y)
|
|
659
|
+
all_test_masks.append(m)
|
|
660
|
+
|
|
661
|
+
test_loss = test_loss_sum / max(test_batches, 1)
|
|
662
|
+
history["test_loss"] = test_loss
|
|
663
|
+
print(f"[TEST] test_loss={test_loss:.4f}")
|
|
664
|
+
|
|
665
|
+
all_test_logits = torch.cat(all_test_logits, dim=0)
|
|
666
|
+
all_test_targets = torch.cat(all_test_targets, dim=0)
|
|
667
|
+
all_test_masks = torch.cat(all_test_masks, dim=0)
|
|
668
|
+
|
|
669
|
+
test_metrics = compute_metrics(
|
|
670
|
+
logits=all_test_logits,
|
|
671
|
+
targets=all_test_targets,
|
|
672
|
+
masks=all_test_masks,
|
|
673
|
+
threshold=0.5,
|
|
674
|
+
)
|
|
675
|
+
|
|
676
|
+
print(
|
|
677
|
+
f"[TEST METRICS] "
|
|
678
|
+
f"Precision={test_metrics['precision']:.4f} "
|
|
679
|
+
f"Recall={test_metrics['recall']:.4f} "
|
|
680
|
+
f"F1={test_metrics['f1']:.4f} "
|
|
681
|
+
f"Acc={test_metrics['accuracy']:.4f} "
|
|
682
|
+
f"TP={test_metrics['tp']} FP={test_metrics['fp']} "
|
|
683
|
+
f"TN={test_metrics['tn']} FN={test_metrics['fn']}"
|
|
684
|
+
)
|
|
685
|
+
|
|
686
|
+
# Print table of per-label metrics
|
|
687
|
+
print("\n[VAL PER-LABEL METRICS]")
|
|
688
|
+
print(f"{'Label':20s} {'Prec':>8s} {'Rec':>8s} {'F1':>8s} {'Support':>8s}")
|
|
689
|
+
print("-" * 60)
|
|
690
|
+
|
|
691
|
+
for j, stats in enumerate(val_metrics["per_label"]):
|
|
692
|
+
name = labels[j].name
|
|
693
|
+
p = stats["precision"]
|
|
694
|
+
r = stats["recall"]
|
|
695
|
+
f = stats["f1"]
|
|
696
|
+
sup = stats["support"]
|
|
697
|
+
|
|
698
|
+
if p is None:
|
|
699
|
+
print(f"{name:20s} {'N/A':>8} {'N/A':>8} {'N/A':>8} {sup:8d}")
|
|
700
|
+
else:
|
|
701
|
+
print(f"{name:20s} {p:8.4f} {r:8.4f} {f:8.4f} {sup:8d}")
|
|
702
|
+
|
|
703
|
+
print("-" * 60)
|
|
704
|
+
|
|
705
|
+
# ------------------------------------------------------------------
|
|
706
|
+
# 11. Save model + metadata
|
|
707
|
+
# ------------------------------------------------------------------
|
|
708
|
+
backbone_tag = config.backbone_name.replace(" ", "_")
|
|
709
|
+
|
|
710
|
+
"""'run_name = (
|
|
711
|
+
f"aidataset_{config.dataset_id}_"
|
|
712
|
+
f"RN50_GastroNet1M_DINO_v{config.labelset_version_to_train}_multilabel"
|
|
713
|
+
)"""
|
|
714
|
+
|
|
715
|
+
# Keep the old name for the GastroNet RN50 backbone
|
|
716
|
+
if getattr(config, "backbone_name", "gastro_rn50") == "gastro_rn50":
|
|
717
|
+
run_name = (
|
|
718
|
+
f"aidataset_{config.dataset_id}_"
|
|
719
|
+
f"RN50_GastroNet1M_DINO_v{config.labelset_version_to_train}_multilabel"
|
|
720
|
+
)
|
|
721
|
+
else:
|
|
722
|
+
# For all other backbones, use a generic name that includes backbone_name
|
|
723
|
+
backbone_tag = config.backbone_name.replace(" ", "_")
|
|
724
|
+
run_name = (
|
|
725
|
+
f"aidataset_{config.dataset_id}_"
|
|
726
|
+
f"{backbone_tag}_v{config.labelset_version_to_train}_multilabel"
|
|
727
|
+
)
|
|
728
|
+
|
|
729
|
+
model_path = RUNS_DIR / f"{run_name}.pth"
|
|
730
|
+
meta_path = RUNS_DIR / f"{run_name}_meta.json"
|
|
731
|
+
|
|
732
|
+
torch.save(model.state_dict(), model_path)
|
|
733
|
+
|
|
734
|
+
meta = {
|
|
735
|
+
"config": {
|
|
736
|
+
"dataset_id": config.dataset_id,
|
|
737
|
+
"labelset_version_to_train": config.labelset_version_to_train,
|
|
738
|
+
"backbone_checkpoint": config.backbone_checkpoint,
|
|
739
|
+
"num_epochs": config.num_epochs,
|
|
740
|
+
"batch_size": config.batch_size,
|
|
741
|
+
"val_split": config.val_split,
|
|
742
|
+
"test_split": config.test_split,
|
|
743
|
+
"lr_head": config.lr_head,
|
|
744
|
+
"lr_backbone": config.lr_backbone,
|
|
745
|
+
"gamma_focal": config.gamma_focal,
|
|
746
|
+
"alpha_focal": config.alpha_focal,
|
|
747
|
+
"device": config.device,
|
|
748
|
+
"random_seed": config.random_seed,
|
|
749
|
+
"treat_unlabeled_as_negative": config.treat_unlabeled_as_negative,
|
|
750
|
+
"use_scheduler": config.use_scheduler,
|
|
751
|
+
"warmup_epochs": config.warmup_epochs,
|
|
752
|
+
"min_lr": config.min_lr,
|
|
753
|
+
},
|
|
754
|
+
"original_labelset_id": labelset.id,
|
|
755
|
+
"original_labelset_name": labelset.name,
|
|
756
|
+
"original_labelset_version": labelset.version,
|
|
757
|
+
"used_label_names": [lbl.name for lbl in labels],
|
|
758
|
+
"used_label_indices_original": kept_indices,
|
|
759
|
+
"history": history,
|
|
760
|
+
}
|
|
761
|
+
with meta_path.open("w", encoding="utf-8") as f:
|
|
762
|
+
json.dump(meta, f, indent=2)
|
|
763
|
+
|
|
764
|
+
print("[TRAIN] Saved model to:", model_path)
|
|
765
|
+
print("[TRAIN] Saved metadata to:", meta_path)
|
|
766
|
+
|
|
767
|
+
return {
|
|
768
|
+
"model_path": str(model_path),
|
|
769
|
+
"meta_path": str(meta_path),
|
|
770
|
+
"history": history,
|
|
771
|
+
}
|