endoreg-db 0.3.6__py3-none-any.whl → 0.8.6.1__py3-none-any.whl
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- endoreg_db/admin.py +92 -3
- endoreg_db/api_urls.py +4 -0
- endoreg_db/apps.py +18 -6
- endoreg_db/assets/dummy_model.ckpt +1 -0
- endoreg_db/codemods/readme.md +88 -0
- endoreg_db/codemods/rename_datetime_fields.py +92 -0
- endoreg_db/config/env.py +101 -0
- endoreg_db/data/__init__.py +144 -65
- endoreg_db/data/ai_model/data.yaml +7 -0
- endoreg_db/data/{label → ai_model_label}/label/data.yaml +88 -62
- 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/{label → ai_model_label}/label-type/data.yaml +6 -6
- endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
- endoreg_db/data/{model_type → ai_model_type}/data.yaml +6 -6
- 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 -167
- endoreg_db/data/case_template/rule/01_patient-set-age.yaml +7 -7
- endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +8 -8
- endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +22 -22
- endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +18 -18
- endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +18 -18
- endoreg_db/data/case_template/rule/19_create_patient.yaml +16 -16
- endoreg_db/data/case_template/rule_type/base_types.yaml +35 -35
- endoreg_db/data/case_template/rule_value_type/base_types.yaml +58 -58
- endoreg_db/data/case_template/template/base.yaml +7 -7
- endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +2 -2
- endoreg_db/data/case_template/tmp/_rule_value +13 -13
- endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -21
- endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +9 -9
- endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +6 -6
- endoreg_db/data/center/data.yaml +90 -59
- endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -144
- endoreg_db/data/center_shift/ukw.yaml +9 -0
- endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -48
- 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 -37
- endoreg_db/data/disease/hepatology.yaml +4 -4
- endoreg_db/data/disease/misc.yaml +5 -6
- endoreg_db/data/disease/renal.yaml +4 -4
- endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -6
- endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +5 -5
- endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -41
- endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +19 -19
- endoreg_db/data/distribution/date/patient.yaml +6 -6
- endoreg_db/data/distribution/numeric/data.yaml +14 -0
- endoreg_db/data/distribution/single_categorical/patient.yaml +6 -6
- endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -132
- endoreg_db/data/endoscope/data.yaml +93 -0
- endoreg_db/data/endoscope_type/data.yaml +10 -10
- endoreg_db/data/endoscopy_processor/data.yaml +50 -45
- endoreg_db/data/event/cardiology.yaml +15 -28
- endoreg_db/data/event/neurology.yaml +13 -13
- endoreg_db/data/event/surgery.yaml +12 -12
- endoreg_db/data/event/thrombembolism.yaml +19 -19
- endoreg_db/data/examination/examinations/data.yaml +72 -66
- endoreg_db/data/examination/time/data.yaml +47 -47
- endoreg_db/data/examination/time-type/data.yaml +7 -7
- endoreg_db/data/examination/type/data.yaml +17 -5
- endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
- endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
- endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
- endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
- endoreg_db/data/finding/anatomy_colon.yaml +128 -0
- endoreg_db/data/finding/colonoscopy.yaml +40 -0
- endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
- endoreg_db/data/finding/complication.yaml +16 -0
- endoreg_db/data/finding/data.yaml +105 -0
- endoreg_db/data/finding/examination_setting.yaml +16 -0
- endoreg_db/data/finding/medication_related.yaml +18 -0
- endoreg_db/data/finding/outcome.yaml +12 -0
- endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
- endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
- endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
- endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
- endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
- endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
- endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
- endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
- endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
- endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
- endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
- endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
- endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
- endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
- endoreg_db/data/finding_classification/medication_related.yaml +23 -0
- endoreg_db/data/finding_classification/visualized.yaml +33 -0
- endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
- endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
- endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
- endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
- endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
- endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
- endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
- endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
- endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
- endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
- endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
- endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
- endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
- endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
- endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
- endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
- endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
- endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
- endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
- endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
- endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
- endoreg_db/data/finding_type/data.yaml +43 -0
- endoreg_db/data/gender/data.yaml +42 -18
- endoreg_db/data/information_source/annotation.yaml +6 -0
- endoreg_db/data/information_source/data.yaml +30 -30
- endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
- endoreg_db/data/information_source/medication.yaml +5 -5
- 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 -31
- endoreg_db/data/lab_value/coagulation.yaml +54 -49
- endoreg_db/data/lab_value/electrolytes.yaml +228 -190
- endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -121
- endoreg_db/data/lab_value/hematology.yaml +184 -169
- endoreg_db/data/lab_value/hormones.yaml +59 -53
- endoreg_db/data/lab_value/lipids.yaml +53 -44
- endoreg_db/data/lab_value/misc.yaml +76 -30
- endoreg_db/data/lab_value/renal_function.yaml +12 -11
- 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/medication/anticoagulation.yaml +64 -64
- endoreg_db/data/medication/tah.yaml +69 -69
- endoreg_db/data/medication_indication/anticoagulation.yaml +115 -120
- endoreg_db/data/medication_indication_type/data.yaml +10 -10
- endoreg_db/data/medication_indication_type/thrombembolism.yaml +40 -40
- endoreg_db/data/medication_intake_time/base.yaml +30 -30
- endoreg_db/data/medication_schedule/apixaban.yaml +94 -94
- endoreg_db/data/medication_schedule/ass.yaml +12 -12
- endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -26
- 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 +5 -5
- endoreg_db/data/pdf_type/data.yaml +46 -28
- endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -66
- endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -33
- endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -308
- endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -88
- endoreg_db/data/profession/data.yaml +70 -70
- 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 -55
- endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
- endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -26
- endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -19
- endoreg_db/data/requirement/age.yaml +26 -0
- endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
- endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
- endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
- endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
- endoreg_db/data/requirement/disease_misc.yaml +12 -0
- endoreg_db/data/requirement/disease_renal.yaml +96 -0
- endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
- endoreg_db/data/requirement/event_cardiology.yaml +251 -0
- endoreg_db/data/requirement/event_requirements.yaml +145 -0
- endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
- endoreg_db/data/requirement/gender.yaml +25 -0
- endoreg_db/data/requirement/lab_value.yaml +441 -0
- endoreg_db/data/requirement/medication.yaml +93 -0
- endoreg_db/data/requirement_operator/age.yaml +13 -0
- endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
- endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
- endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
- endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
- endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
- endoreg_db/data/requirement_set_type/data.yaml +20 -0
- endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
- endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -15
- 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 +11 -0
- endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -12
- endoreg_db/data/unit/concentration.yaml +115 -92
- endoreg_db/data/unit/data.yaml +17 -17
- endoreg_db/data/unit/length.yaml +30 -30
- endoreg_db/data/unit/misc.yaml +19 -19
- endoreg_db/data/unit/rate.yaml +5 -5
- endoreg_db/data/unit/time.yaml +48 -13
- endoreg_db/data/unit/volume.yaml +35 -35
- endoreg_db/data/unit/weight.yaml +37 -37
- endoreg_db/data/waste/data.yaml +11 -11
- endoreg_db/exceptions.py +19 -0
- endoreg_db/factories/__init__.py +0 -0
- endoreg_db/forms/__init__.py +5 -3
- endoreg_db/forms/examination_form.py +11 -0
- endoreg_db/forms/patient_finding_intervention_form.py +18 -0
- endoreg_db/forms/patient_form.py +27 -0
- endoreg_db/forms/questionnaires/__init__.py +1 -1
- endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -23
- endoreg_db/forms/settings/__init__.py +8 -8
- endoreg_db/forms/unit.py +5 -5
- endoreg_db/helpers/__init__.py +0 -0
- endoreg_db/helpers/count_db.py +45 -0
- endoreg_db/helpers/data_loader.py +208 -0
- endoreg_db/helpers/default_objects.py +378 -0
- endoreg_db/helpers/download_segmentation_model.py +31 -0
- endoreg_db/helpers/interact.py +6 -0
- endoreg_db/helpers/test_video_helper.py +119 -0
- endoreg_db/logger_conf.py +140 -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 +125 -0
- endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
- endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
- endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
- endoreg_db/management/commands/fix_video_paths.py +165 -0
- endoreg_db/management/commands/import_fallback_video.py +203 -0
- endoreg_db/management/commands/import_report.py +298 -0
- endoreg_db/management/commands/import_video.py +423 -0
- endoreg_db/management/commands/import_video_with_classification.py +367 -0
- endoreg_db/management/commands/init_default_ai_model.py +112 -0
- endoreg_db/management/commands/load_ai_model_data.py +77 -45
- endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
- endoreg_db/management/commands/load_base_db_data.py +192 -128
- endoreg_db/management/commands/load_center_data.py +68 -43
- endoreg_db/management/commands/{load_medication_intake_time_data.py → load_contraindication_data.py} +40 -40
- endoreg_db/management/commands/load_disease_classification_choices_data.py +40 -40
- endoreg_db/management/commands/load_disease_classification_data.py +40 -40
- endoreg_db/management/commands/load_disease_data.py +61 -39
- endoreg_db/management/commands/load_distribution_data.py +65 -65
- endoreg_db/management/commands/{load_endoscope_type_data.py → load_endoscope_data.py} +67 -44
- endoreg_db/management/commands/load_event_data.py +40 -40
- endoreg_db/management/commands/load_examination_data.py +74 -74
- endoreg_db/management/commands/load_examination_indication_data.py +86 -0
- endoreg_db/management/commands/load_finding_data.py +128 -0
- endoreg_db/management/commands/load_gender_data.py +43 -43
- endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +131 -132
- endoreg_db/management/commands/load_information_source.py +50 -44
- endoreg_db/management/commands/load_lab_value_data.py +49 -49
- endoreg_db/management/commands/load_medication_data.py +103 -41
- endoreg_db/management/commands/load_name_data.py +37 -0
- endoreg_db/management/commands/{load_medication_indication_type_data.py → load_organ_data.py} +42 -40
- endoreg_db/management/commands/load_pdf_type_data.py +60 -60
- endoreg_db/management/commands/load_profession_data.py +43 -43
- endoreg_db/management/commands/load_qualification_data.py +59 -0
- endoreg_db/management/commands/{load_report_reader_flag.py → load_report_reader_flag_data.py} +45 -45
- endoreg_db/management/commands/load_requirement_data.py +180 -0
- endoreg_db/management/commands/load_risk_data.py +56 -0
- endoreg_db/management/commands/load_shift_data.py +60 -0
- endoreg_db/management/commands/load_tag_data.py +57 -0
- endoreg_db/management/commands/load_unit_data.py +45 -45
- endoreg_db/management/commands/load_user_groups.py +28 -28
- endoreg_db/management/commands/register_ai_model.py +64 -65
- endoreg_db/management/commands/reset_celery_schedule.py +9 -9
- endoreg_db/management/commands/setup_endoreg_db.py +381 -0
- endoreg_db/management/commands/start_filewatcher.py +106 -0
- endoreg_db/management/commands/storage_management.py +548 -0
- endoreg_db/management/commands/summarize_db_content.py +189 -0
- endoreg_db/management/commands/validate_video.py +204 -0
- endoreg_db/management/commands/validate_video_files.py +161 -0
- endoreg_db/management/commands/video_validation.py +22 -0
- endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
- endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
- endoreg_db/mermaid/binary_classification_annotation.md +50 -0
- endoreg_db/mermaid/classification.md +8 -0
- endoreg_db/mermaid/examination.md +8 -0
- endoreg_db/mermaid/findings.md +7 -0
- endoreg_db/mermaid/image_classification.md +28 -0
- endoreg_db/mermaid/interventions.md +8 -0
- endoreg_db/mermaid/morphology.md +8 -0
- endoreg_db/mermaid/patient_creation.md +14 -0
- endoreg_db/mermaid/video_segmentation_annotation.md +17 -0
- endoreg_db/migrations/0001_initial.py +1857 -582
- endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
- endoreg_db/migrations/0003_add_center_display_name.py +30 -0
- endoreg_db/models/__init__.py +359 -74
- endoreg_db/models/administration/__init__.py +116 -0
- endoreg_db/models/administration/ai/__init__.py +9 -0
- endoreg_db/models/administration/ai/active_model.py +35 -0
- endoreg_db/models/administration/ai/ai_model.py +156 -0
- endoreg_db/models/{ai_model → administration/ai}/model_type.py +41 -26
- endoreg_db/models/administration/case/__init__.py +19 -0
- endoreg_db/models/administration/case/case.py +114 -0
- endoreg_db/models/{case_template → administration/case/case_template}/__init__.py +15 -6
- endoreg_db/models/{case_template → administration/case/case_template}/case_template.py +125 -81
- endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule.py +269 -276
- endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule_value.py +86 -73
- endoreg_db/models/{case_template → administration/case/case_template}/case_template_type.py +26 -28
- endoreg_db/models/{center → administration/center}/__init__.py +13 -4
- endoreg_db/models/administration/center/center.py +67 -0
- endoreg_db/models/administration/center/center_product.py +64 -0
- endoreg_db/models/administration/center/center_resource.py +49 -0
- endoreg_db/models/administration/center/center_shift.py +88 -0
- endoreg_db/models/administration/center/center_waste.py +30 -0
- endoreg_db/models/administration/permissions/__init__.py +44 -0
- endoreg_db/models/administration/person/__init__.py +24 -0
- endoreg_db/models/administration/person/employee/__init__.py +3 -0
- endoreg_db/models/administration/person/employee/employee.py +35 -0
- endoreg_db/models/administration/person/employee/employee_qualification.py +39 -0
- endoreg_db/models/administration/person/employee/employee_type.py +42 -0
- endoreg_db/models/administration/person/examiner/__init__.py +4 -0
- endoreg_db/models/administration/person/examiner/examiner.py +54 -0
- endoreg_db/models/administration/person/names/__init__.py +0 -0
- endoreg_db/models/{persons → administration/person/names}/first_name.py +18 -18
- endoreg_db/models/{persons → administration/person/names}/last_name.py +18 -19
- endoreg_db/models/administration/person/patient/__init__.py +5 -0
- endoreg_db/models/administration/person/patient/patient.py +460 -0
- endoreg_db/models/{persons → administration/person}/person.py +31 -31
- endoreg_db/models/administration/person/profession/__init__.py +24 -0
- endoreg_db/models/administration/person/user/__init__.py +5 -0
- endoreg_db/models/administration/person/user/portal_user_information.py +37 -0
- endoreg_db/models/administration/product/__init__.py +14 -0
- endoreg_db/models/administration/product/product.py +97 -0
- endoreg_db/models/administration/product/product_group.py +39 -0
- endoreg_db/models/administration/product/product_material.py +54 -0
- endoreg_db/models/{product → administration/product}/product_weight.py +47 -26
- endoreg_db/models/{product → administration/product}/reference_product.py +130 -99
- endoreg_db/models/administration/qualification/__init__.py +7 -0
- endoreg_db/models/administration/qualification/qualification.py +37 -0
- endoreg_db/models/administration/qualification/qualification_type.py +35 -0
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- endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
- endoreg_db/models/label/label.py +83 -84
- endoreg_db/models/label/label_set.py +53 -0
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- endoreg_db/models/label/video_segmentation_label.py +31 -0
- endoreg_db/models/label/video_segmentation_labelset.py +27 -0
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- endoreg_db/models/media/frame/__init__.py +3 -0
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- endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
- endoreg_db/models/{report_reader → media/pdf/report_reader}/report_reader_flag.py +19 -19
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- endoreg_db/models/media/video/pipe_2.py +105 -0
- endoreg_db/models/media/video/refactor_plan.md +0 -0
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- endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
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- endoreg_db/models/medical/finding/finding_type.py +35 -0
- endoreg_db/models/medical/hardware/__init__.py +8 -0
- endoreg_db/models/medical/hardware/endoscope.py +65 -0
- endoreg_db/models/{hardware → medical/hardware}/endoscopy_processor.py +182 -143
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- endoreg_db/models/medical/laboratory/lab_value.py +419 -0
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- endoreg_db/models/medical/medication/medication_schedule.py +45 -0
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- endoreg_db/models/other/transport_route.py +33 -21
- endoreg_db/models/{unit.py → other/unit.py} +32 -22
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- endoreg_db/models/{rules → rule}/rule_applicator.py +224 -224
- endoreg_db/models/{rules → rule}/rule_attribute_dtype.py +16 -18
- endoreg_db/models/{rules → rule}/rule_type.py +19 -21
- endoreg_db/models/{rules → rule}/ruleset.py +17 -19
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- endoreg_db/models/state/abstract.py +11 -0
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- /endoreg_db/{models/persons/patient/case/__init__.py → api/serializers/finding_descriptions.py} +0 -0
- /endoreg_db/{queries/get/annotation.py → api/views/finding_descriptions.py} +0 -0
- /endoreg_db/{queries/get/prediction.py → config/__init__.py} +0 -0
- /endoreg_db/{queries/get/video_import_meta.py → data/case_template/rule_value/.init} +0 -0
- /endoreg_db/{queries/get/video_prediction_meta.py → data/distribution/multiple_categorical/.init} +0 -0
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2
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from pathlib import Path
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3
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from collections import defaultdict, Counter
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4
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5
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from endoreg_db.utils.hashs import get_video_hash
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6
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from endoreg_db.utils.file_operations import get_uuid_filename
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7
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from endoreg_db.utils.ocr import extract_text_from_rois
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8
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9
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import shutil
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import os
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import subprocess
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13
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from ..metadata import VideoMeta, SensitiveMeta
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14
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15
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class RawVideoFile(models.Model):
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uuid = models.UUIDField()
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file = models.FileField(upload_to="raw_data/")
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19
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sensitive_meta = models.OneToOneField(
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"SensitiveMeta", on_delete=models.CASCADE, blank=True, null=True
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)
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22
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23
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center = models.ForeignKey("Center", on_delete=models.CASCADE)
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processor = models.ForeignKey(
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"EndoscopyProcessor", on_delete=models.CASCADE, blank=True, null=True
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)
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video_meta = models.OneToOneField(
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"VideoMeta", on_delete=models.CASCADE, blank=True, null=True
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)
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30
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original_file_name = models.CharField(max_length=255)
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video_hash = models.CharField(max_length=255, unique=True)
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uploaded_at = models.DateTimeField(auto_now_add=True)
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33
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34
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# Frame Extraction States
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state_frames_required = models.BooleanField(default=True)
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state_frames_extracted = models.BooleanField(default=False)
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37
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38
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# Video
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39
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## Prediction
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40
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state_initial_prediction_required = models.BooleanField(default=True)
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41
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state_initial_prediction_completed = models.BooleanField(default=False)
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42
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state_initial_prediction_import_required = models.BooleanField(default=True)
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43
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state_initial_prediction_import_completed = models.BooleanField(default=False)
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44
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## OCR
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45
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state_ocr_required = models.BooleanField(default=True)
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46
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state_ocr_completed = models.BooleanField(default=False)
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47
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## Validation
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48
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state_outside_validated = models.BooleanField(default=False)
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49
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state_ocr_result_validated = models.BooleanField(default=False)
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50
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51
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state_sensitive_data_retrieved = models.BooleanField(default=False)
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52
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53
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# Dataset complete?
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54
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state_histology_required = models.BooleanField(blank=True, null=True)
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55
|
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state_histology_available = models.BooleanField(default=False)
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56
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state_follow_up_intervention_required = models.BooleanField(blank=True, null=True)
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57
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state_follow_up_intervention_available = models.BooleanField(default=False)
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58
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state_dataset_complete = models.BooleanField(default=False)
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59
|
-
|
|
60
|
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# Finalizing for Upload
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61
|
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state_anonym_video_required = models.BooleanField(default=True)
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62
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state_anonym_video_performed = models.BooleanField(default=False)
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63
|
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state_original_reports_deleted = models.BooleanField(default=False)
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64
|
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state_original_video_deleted = models.BooleanField(default=False)
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65
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state_finalized = models.BooleanField(default=False)
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66
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67
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frame_dir = models.CharField(max_length=255)
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68
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prediction_dir = models.CharField(max_length=255)
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69
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|
70
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@classmethod
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|
71
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def create_from_file(
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72
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cls,
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73
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file_path: Path,
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74
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video_dir: Path,
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75
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center_name: str,
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76
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processor_name: str,
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77
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frame_dir_parent: Path,
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78
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save: bool = True,
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79
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):
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|
80
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from endoreg_db.models import Center, EndoscopyProcessor
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81
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|
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82
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print(f"Creating RawVideoFile from {file_path}")
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83
|
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original_file_name = file_path.name
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|
84
|
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# Rename and and move
|
|
85
|
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|
|
86
|
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new_file_name, uuid = get_uuid_filename(file_path)
|
|
87
|
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framedir: Path = frame_dir_parent / str(uuid)
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88
|
-
|
|
89
|
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if not framedir.exists():
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90
|
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framedir.mkdir(parents=True, exist_ok=True)
|
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91
|
-
|
|
92
|
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if not video_dir.exists():
|
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93
|
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video_dir.mkdir(parents=True, exist_ok=True)
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|
94
|
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|
|
95
|
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video_hash = get_video_hash(file_path)
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|
96
|
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|
|
97
|
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center = Center.objects.get(name=center_name)
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|
98
|
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assert center is not None, "Center must exist"
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|
99
|
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|
|
100
|
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processor = EndoscopyProcessor.objects.get(name=processor_name)
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|
101
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assert processor is not None, "Processor must exist"
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102
|
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|
|
103
|
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new_filepath = video_dir / new_file_name
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|
104
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|
|
105
|
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print(f"Moving {file_path} to {new_filepath}")
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106
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shutil.move(file_path.resolve().as_posix(), new_filepath.resolve().as_posix())
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107
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print(f"Moved to {new_filepath}")
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108
|
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|
|
109
|
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# Make sure file was transferred correctly and hash is correct
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|
110
|
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if not new_filepath.exists():
|
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111
|
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print(f"File {file_path} was not transferred correctly to {new_filepath}")
|
|
112
|
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return None
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|
113
|
-
|
|
114
|
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new_hash = get_video_hash(new_filepath)
|
|
115
|
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if new_hash != video_hash:
|
|
116
|
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print(f"Hash of file {file_path} is not correct")
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|
117
|
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return None
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|
118
|
-
|
|
119
|
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# make sure that no other file with the same hash exists
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|
120
|
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if cls.objects.filter(video_hash=video_hash).exists():
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|
121
|
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# log and print warnint
|
|
122
|
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print(f"File with hash {video_hash} already exists")
|
|
123
|
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return None
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|
124
|
-
|
|
125
|
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else:
|
|
126
|
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print(center)
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|
127
|
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# Create a new instance of RawVideoFile
|
|
128
|
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raw_video_file = cls(
|
|
129
|
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uuid=uuid,
|
|
130
|
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file=new_filepath.resolve().as_posix(),
|
|
131
|
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center=center,
|
|
132
|
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processor=processor,
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|
133
|
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original_file_name=original_file_name,
|
|
134
|
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video_hash=video_hash,
|
|
135
|
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frame_dir=framedir.as_posix(),
|
|
136
|
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)
|
|
137
|
-
|
|
138
|
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# Save the instance to the database
|
|
139
|
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raw_video_file.save()
|
|
140
|
-
|
|
141
|
-
return raw_video_file
|
|
142
|
-
|
|
143
|
-
def __str__(self):
|
|
144
|
-
return self.file.name
|
|
145
|
-
|
|
146
|
-
def get_endo_roi(self):
|
|
147
|
-
endo_roi = self.video_meta.get_endo_roi()
|
|
148
|
-
return endo_roi
|
|
149
|
-
|
|
150
|
-
# video meta should be created when video file is created
|
|
151
|
-
def save(self, *args, **kwargs):
|
|
152
|
-
if self.video_meta is None:
|
|
153
|
-
center = self.center
|
|
154
|
-
processor = self.processor
|
|
155
|
-
self.video_meta = VideoMeta.objects.create(
|
|
156
|
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center=center, processor=processor
|
|
157
|
-
)
|
|
158
|
-
self.video_meta.initialize_ffmpeg_meta(self.file.path)
|
|
159
|
-
super(RawVideoFile, self).save(*args, **kwargs)
|
|
160
|
-
|
|
161
|
-
def extract_frames(
|
|
162
|
-
self,
|
|
163
|
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quality: int = 2,
|
|
164
|
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frame_dir: Path = None,
|
|
165
|
-
overwrite: bool = False,
|
|
166
|
-
ext="jpg",
|
|
167
|
-
):
|
|
168
|
-
"""
|
|
169
|
-
Extract frames from the video file and save them to the frame_dir.
|
|
170
|
-
For this, ffmpeg must be available in in the current environment.
|
|
171
|
-
"""
|
|
172
|
-
if frame_dir is None:
|
|
173
|
-
frame_dir = Path(self.frame_dir)
|
|
174
|
-
else:
|
|
175
|
-
frame_dir = Path(frame_dir)
|
|
176
|
-
|
|
177
|
-
if not frame_dir.exists():
|
|
178
|
-
frame_dir.mkdir(parents=True, exist_ok=True)
|
|
179
|
-
|
|
180
|
-
if not overwrite and len(list(frame_dir.glob("*.jpg"))) > 0:
|
|
181
|
-
print(f"Frames already extracted for {self.file.name}")
|
|
182
|
-
return
|
|
183
|
-
|
|
184
|
-
video_path = Path(self.file.path).resolve().as_posix()
|
|
185
|
-
|
|
186
|
-
frame_path_string = frame_dir.resolve().as_posix()
|
|
187
|
-
command = [
|
|
188
|
-
"ffmpeg",
|
|
189
|
-
"-i",
|
|
190
|
-
video_path, #
|
|
191
|
-
"-q:v",
|
|
192
|
-
str(quality),
|
|
193
|
-
os.path.join(frame_path_string, f"frame_%07d.{ext}"),
|
|
194
|
-
]
|
|
195
|
-
|
|
196
|
-
# Ensure FFmpeg is available
|
|
197
|
-
if not shutil.which("ffmpeg"):
|
|
198
|
-
raise EnvironmentError(
|
|
199
|
-
"FFmpeg could not be found. Ensure it is installed and in your PATH."
|
|
200
|
-
)
|
|
201
|
-
|
|
202
|
-
# Extract frames from the video file
|
|
203
|
-
# Execute the command
|
|
204
|
-
result = subprocess.run(command, capture_output=True, text=True)
|
|
205
|
-
if result.returncode != 0:
|
|
206
|
-
raise Exception(f"Error extracting frames: {result.stderr}")
|
|
207
|
-
|
|
208
|
-
self.state_frames_extracted = True
|
|
209
|
-
|
|
210
|
-
return f"Frames extracted to {frame_dir} ({frame_path_string}) with quality {quality}"
|
|
211
|
-
|
|
212
|
-
def delete_frames(self):
|
|
213
|
-
"""
|
|
214
|
-
Delete frames extracted from the video file.
|
|
215
|
-
"""
|
|
216
|
-
frame_dir = Path(self.frame_dir)
|
|
217
|
-
if frame_dir.exists():
|
|
218
|
-
shutil.rmtree(frame_dir)
|
|
219
|
-
self.state_frames_extracted = False
|
|
220
|
-
self.save()
|
|
221
|
-
return f"Frames deleted from {frame_dir}"
|
|
222
|
-
else:
|
|
223
|
-
return f"No frames to delete for {self.file.name}"
|
|
224
|
-
|
|
225
|
-
def get_frame_path(self, n: int = 0):
|
|
226
|
-
"""
|
|
227
|
-
Get the path to the n-th frame extracted from the video file.
|
|
228
|
-
Note that the frame numbering starts at 1 in our naming convention.
|
|
229
|
-
"""
|
|
230
|
-
# Adjust index
|
|
231
|
-
n = n + 1
|
|
232
|
-
|
|
233
|
-
frame_dir = Path(self.frame_dir)
|
|
234
|
-
return frame_dir / f"frame_{n:07d}.jpg"
|
|
235
|
-
|
|
236
|
-
def get_frame_paths(self):
|
|
237
|
-
if not self.state_frames_extracted:
|
|
238
|
-
return None
|
|
239
|
-
frame_dir = Path(self.frame_dir)
|
|
240
|
-
paths = [p for p in frame_dir.glob('*')]
|
|
241
|
-
indices = [int(p.stem.split("_")[1]) for p in paths]
|
|
242
|
-
path_index_tuples = list(zip(paths, indices))
|
|
243
|
-
# sort ascending by index
|
|
244
|
-
path_index_tuples.sort(key=lambda x: x[1])
|
|
245
|
-
paths, indices = zip(*path_index_tuples)
|
|
246
|
-
|
|
247
|
-
return paths
|
|
248
|
-
|
|
249
|
-
def get_prediction_dir(self):
|
|
250
|
-
return Path(self.prediction_dir)
|
|
251
|
-
|
|
252
|
-
def get_predictions_path(self, suffix = ".json"):
|
|
253
|
-
pred_dir = self.get_prediction_dir()
|
|
254
|
-
return pred_dir.joinpath("predictions").with_suffix(suffix)
|
|
255
|
-
|
|
256
|
-
def get_smooth_predictions_path(self, suffix = ".json"):
|
|
257
|
-
pred_dir = self.get_prediction_dir()
|
|
258
|
-
return pred_dir.joinpath("smooth_predictions").with_suffix(suffix)
|
|
259
|
-
|
|
260
|
-
def get_binary_predictions_path(self, suffix = ".json"):
|
|
261
|
-
pred_dir = self.get_prediction_dir()
|
|
262
|
-
return pred_dir.joinpath("binary_predictions").with_suffix(suffix)
|
|
263
|
-
|
|
264
|
-
def get_raw_sequences_path(self, suffix = ".json"):
|
|
265
|
-
pred_dir = self.get_prediction_dir()
|
|
266
|
-
return pred_dir.joinpath("raw_sequences").with_suffix(suffix)
|
|
267
|
-
|
|
268
|
-
def get_filtered_sequences_path(self, suffix=".json"):
|
|
269
|
-
pred_dir = self.get_prediction_dir()
|
|
270
|
-
return pred_dir.joinpath("filtered_sequences").with_suffix(suffix)
|
|
271
|
-
|
|
272
|
-
def extract_text_information(self, frame_fraction: float = 0.001):
|
|
273
|
-
"""
|
|
274
|
-
Extract text information from the video file.
|
|
275
|
-
Makes sure that frames are extracted and then processes the frames.
|
|
276
|
-
gets all frames from frame_dir and selects a fraction of them to process (at least 1)
|
|
277
|
-
"""
|
|
278
|
-
if not self.state_frames_extracted:
|
|
279
|
-
print(f"Frames not extracted for {self.file.name}")
|
|
280
|
-
return None
|
|
281
|
-
|
|
282
|
-
processor = self.processor
|
|
283
|
-
|
|
284
|
-
frame_dir = Path(self.frame_dir)
|
|
285
|
-
frames = list(frame_dir.glob("*"))
|
|
286
|
-
n_frames = len(frames)
|
|
287
|
-
n_frames_to_process = max(1, int(frame_fraction * n_frames))
|
|
288
|
-
|
|
289
|
-
# Select evenly spaced frames
|
|
290
|
-
frames = frames[:: n_frames // n_frames_to_process]
|
|
291
|
-
|
|
292
|
-
# extract text from each frame and store the value to
|
|
293
|
-
# defaultdict of lists.
|
|
294
|
-
# Then, extract the most frequent value from each list
|
|
295
|
-
# Finally, return the dictionary of most frequent values
|
|
296
|
-
|
|
297
|
-
# Create a defaultdict to store the extracted text from each ROI
|
|
298
|
-
rois_texts = defaultdict(list)
|
|
299
|
-
|
|
300
|
-
print(f"Processing {n_frames_to_process} frames from {self.file.name}")
|
|
301
|
-
# Process frames
|
|
302
|
-
for frame_path in frames[:n_frames_to_process]:
|
|
303
|
-
extracted_texts = extract_text_from_rois(frame_path, processor)
|
|
304
|
-
for roi, text in extracted_texts.items():
|
|
305
|
-
rois_texts[roi].append(text)
|
|
306
|
-
|
|
307
|
-
# Get the most frequent text values for each ROI using Counter
|
|
308
|
-
for key in rois_texts.keys():
|
|
309
|
-
counter = Counter([text for text in rois_texts[key] if text])
|
|
310
|
-
rois_texts[key] = counter.most_common(1)[0][0] if counter else None
|
|
311
|
-
|
|
312
|
-
return rois_texts
|
|
313
|
-
|
|
314
|
-
def update_text_metadata(self, ocr_frame_fraction=0.001):
|
|
315
|
-
print(f"Updating metadata for {self.file.name}")
|
|
316
|
-
texts = self.extract_text_information(ocr_frame_fraction)
|
|
317
|
-
|
|
318
|
-
self.sensitive_meta = SensitiveMeta.create_from_dict(texts)
|
|
319
|
-
self.state_sensitive_data_retrieved = True
|
|
320
|
-
self.save()
|
|
321
|
-
|
|
322
|
-
# Resulting dict depends on defined ROIs for this processor type!
|
|
323
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def update_video_meta(self):
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video_meta = self.video_meta
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video_path = Path(self.file.path)
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if video_meta is None:
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video_meta = VideoMeta.create_from_video(video_path)
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self.video_meta = video_meta
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self.save()
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else:
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video_meta.update_meta(video_path)
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def get_fps(self):
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if self.video_meta is None:
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self.update_video_meta()
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340
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if self.video_meta.ffmpeg_meta is None:
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self.video_meta.initialize_ffmpeg_meta(self.file.path)
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return self.video_meta.get_fps()
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@@ -1,31 +0,0 @@
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from django.db import models
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2
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3
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class SensitiveMeta(models.Model):
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4
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examination_date = models.DateField(blank=True, null=True)
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5
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patient_first_name = models.CharField(max_length=255, blank=True, null=True)
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6
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patient_last_name = models.CharField(max_length=255, blank=True, null=True)
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7
|
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patient_dob = models.DateField(blank=True, null=True)
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8
|
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endoscope_type = models.CharField(max_length=255, blank=True, null=True)
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9
|
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endoscope_sn = models.CharField(max_length=255, blank=True, null=True)
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10
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11
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@classmethod
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12
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def create_from_dict(cls, data: dict):
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# data can contain more fields than the model has
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field_names = [_.name for _ in cls._meta.fields]
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selected_data = {k: v for k, v in data.items() if k in field_names}
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17
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return cls.objects.create(**selected_data)
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19
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def update_from_dict(self, data: dict):
|
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# data can contain more fields than the model has
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21
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field_names = [_.name for _ in self._meta.fields]
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selected_data = {k: v for k, v in data.items() if k in field_names}
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for k, v in selected_data.items():
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setattr(self, k, v)
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27
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self.save()
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29
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def __str__(self):
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|
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return f"SensitiveMeta: {self.examination_date} {self.patient_first_name} {self.patient_last_name} (*{self.patient_dob})"
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|
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@@ -1,133 +0,0 @@
|
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|
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from django.db import models
|
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2
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import ffmpeg
|
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3
|
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from pathlib import Path
|
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4
|
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|
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5
|
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# import endoreg_center_id from django settings
|
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6
|
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from django.conf import settings
|
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7
|
-
|
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8
|
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# check if endoreg_center_id is set
|
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9
|
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if not hasattr(settings, 'ENDOREG_CENTER_ID'):
|
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10
|
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ENDOREG_CENTER_ID = 9999
|
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11
|
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else:
|
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12
|
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ENDOREG_CENTER_ID = settings.ENDOREG_CENTER_ID
|
|
13
|
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|
|
14
|
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# VideoMeta
|
|
15
|
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class VideoMeta(models.Model):
|
|
16
|
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processor = models.ForeignKey('EndoscopyProcessor', on_delete=models.CASCADE, blank=True, null=True)
|
|
17
|
-
endoscope = models.ForeignKey('Endoscope', on_delete=models.CASCADE, blank=True, null=True)
|
|
18
|
-
center = models.ForeignKey('Center', on_delete=models.CASCADE)
|
|
19
|
-
import_meta = models.OneToOneField('VideoImportMeta', on_delete=models.CASCADE, blank=True, null=True)
|
|
20
|
-
ffmpeg_meta = models.OneToOneField('FFMpegMeta', on_delete=models.CASCADE, blank=True, null=True)
|
|
21
|
-
|
|
22
|
-
def __str__(self):
|
|
23
|
-
|
|
24
|
-
processor_name = self.processor.name if self.processor is not None else "None"
|
|
25
|
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endoscope_name = self.endoscope.name if self.endoscope is not None else "None"
|
|
26
|
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center_name = self.center.name if self.center is not None else "None"
|
|
27
|
-
|
|
28
|
-
result_html = ""
|
|
29
|
-
|
|
30
|
-
result_html += f"Processor: {processor_name}<br>"
|
|
31
|
-
result_html += f"Endoscope: {endoscope_name}<br>"
|
|
32
|
-
result_html += f"Center: {center_name}<br>"
|
|
33
|
-
|
|
34
|
-
return result_html
|
|
35
|
-
|
|
36
|
-
# import meta should be created when video meta is created
|
|
37
|
-
def save(self, *args, **kwargs):
|
|
38
|
-
if self.import_meta is None:
|
|
39
|
-
self.import_meta = VideoImportMeta.objects.create()
|
|
40
|
-
super(VideoMeta, self).save(*args, **kwargs)
|
|
41
|
-
|
|
42
|
-
def initialize_ffmpeg_meta(self, file_path):
|
|
43
|
-
"""Initializes FFMpeg metadata for the video file if not already done."""
|
|
44
|
-
self.ffmpeg_meta = FFMpegMeta.create_from_file(Path(file_path))
|
|
45
|
-
self.save()
|
|
46
|
-
|
|
47
|
-
def update_meta(self, file_path):
|
|
48
|
-
"""Updates the video metadata from the file."""
|
|
49
|
-
self.initialize_ffmpeg_meta(file_path)
|
|
50
|
-
self.save()
|
|
51
|
-
|
|
52
|
-
def get_endo_roi(self):
|
|
53
|
-
endo_roi = self.processor.get_roi_endoscope_image()
|
|
54
|
-
return endo_roi
|
|
55
|
-
|
|
56
|
-
def get_fps(self):
|
|
57
|
-
if not self.ffmpeg_meta:
|
|
58
|
-
return None
|
|
59
|
-
|
|
60
|
-
return self.ffmpeg_meta.frame_rate
|
|
61
|
-
|
|
62
|
-
|
|
63
|
-
class FFMpegMeta(models.Model):
|
|
64
|
-
# Existing fields
|
|
65
|
-
duration = models.FloatField(blank=True, null=True)
|
|
66
|
-
width = models.IntegerField(blank=True, null=True)
|
|
67
|
-
height = models.IntegerField(blank=True, null=True)
|
|
68
|
-
frame_rate = models.FloatField(blank=True, null=True)
|
|
69
|
-
|
|
70
|
-
# New fields for comprehensive information
|
|
71
|
-
video_codec = models.CharField(max_length=50, blank=True, null=True)
|
|
72
|
-
audio_codec = models.CharField(max_length=50, blank=True, null=True)
|
|
73
|
-
audio_channels = models.IntegerField(blank=True, null=True)
|
|
74
|
-
audio_sample_rate = models.IntegerField(blank=True, null=True)
|
|
75
|
-
|
|
76
|
-
# Existing __str__ method can be updated to include new fields
|
|
77
|
-
|
|
78
|
-
@classmethod
|
|
79
|
-
def create_from_file(cls, file_path: Path):
|
|
80
|
-
"""Creates an FFMpegMeta instance from a video file using ffmpeg probe."""
|
|
81
|
-
try:
|
|
82
|
-
probe = ffmpeg.probe(file_path.resolve().as_posix())
|
|
83
|
-
except: # ffmpeg.Error as e:
|
|
84
|
-
# print(e.stderr)
|
|
85
|
-
print(f"Error while probing {file_path}")
|
|
86
|
-
return None
|
|
87
|
-
|
|
88
|
-
video_stream = next((stream for stream in probe['streams'] if stream['codec_type'] == 'video'), None)
|
|
89
|
-
audio_streams = [stream for stream in probe['streams'] if stream['codec_type'] == 'audio']
|
|
90
|
-
|
|
91
|
-
# Check for the existence of a video stream
|
|
92
|
-
if video_stream is None:
|
|
93
|
-
print(f"No video stream found in {file_path}")
|
|
94
|
-
return None
|
|
95
|
-
|
|
96
|
-
# Extract and store video metadata
|
|
97
|
-
metadata = {
|
|
98
|
-
'duration': float(video_stream.get('duration', 0)),
|
|
99
|
-
'width': int(video_stream.get('width', 0)),
|
|
100
|
-
'height': int(video_stream.get('height', 0)),
|
|
101
|
-
'frame_rate': float(next(iter(video_stream.get('avg_frame_rate', '').split('/')), 0)),
|
|
102
|
-
'video_codec': video_stream.get('codec_name', ''),
|
|
103
|
-
}
|
|
104
|
-
|
|
105
|
-
# If there are audio streams, extract and store audio metadata from the first stream
|
|
106
|
-
if audio_streams:
|
|
107
|
-
first_audio_stream = audio_streams[0]
|
|
108
|
-
metadata.update({
|
|
109
|
-
'audio_codec': first_audio_stream.get('codec_name', ''),
|
|
110
|
-
'audio_channels': int(first_audio_stream.get('channels', 0)),
|
|
111
|
-
'audio_sample_rate': int(first_audio_stream.get('sample_rate', 0)),
|
|
112
|
-
})
|
|
113
|
-
|
|
114
|
-
# Create and return the FFMpegMeta instance
|
|
115
|
-
return cls.objects.create(**metadata)
|
|
116
|
-
|
|
117
|
-
class VideoImportMeta(models.Model):
|
|
118
|
-
|
|
119
|
-
video_anonymized = models.BooleanField(default=False)
|
|
120
|
-
video_patient_data_detected = models.BooleanField(default=False)
|
|
121
|
-
outside_detected = models.BooleanField(default=False)
|
|
122
|
-
patient_data_removed = models.BooleanField(default=False)
|
|
123
|
-
outside_removed = models.BooleanField(default=False)
|
|
124
|
-
|
|
125
|
-
def __str__(self):
|
|
126
|
-
result_html = ""
|
|
127
|
-
|
|
128
|
-
result_html += f"Video anonymized: {self.video_anonymized}<br>"
|
|
129
|
-
result_html += f"Video patient data detected: {self.video_patient_data_detected}<br>"
|
|
130
|
-
result_html += f"Outside detected: {self.outside_detected}<br>"
|
|
131
|
-
result_html += f"Patient data removed: {self.patient_data_removed}<br>"
|
|
132
|
-
result_html += f"Outside removed: {self.outside_removed}<br>"
|
|
133
|
-
return result_html
|
|
@@ -1,89 +0,0 @@
|
|
|
1
|
-
from django.db import models
|
|
2
|
-
from ..center import Center
|
|
3
|
-
import hashlib
|
|
4
|
-
from datetime import date, time
|
|
5
|
-
|
|
6
|
-
class ReportFile(models.Model):
|
|
7
|
-
pdf = models.FileField(upload_to="raw_report_pdfs", blank=True, null=True)
|
|
8
|
-
pdf_hash = models.CharField(max_length=255, unique=True)
|
|
9
|
-
center = models.ForeignKey(Center, on_delete=models.CASCADE)
|
|
10
|
-
meta = models.JSONField(blank=True, null=True)
|
|
11
|
-
text = models.TextField(blank=True, null=True)
|
|
12
|
-
text_anonymized = models.TextField(blank=True, null=True)
|
|
13
|
-
patient = models.ForeignKey("Patient", on_delete=models.CASCADE, blank=True, null=True)
|
|
14
|
-
examiner = models.ForeignKey("Examiner", on_delete=models.CASCADE, blank=True, null=True)
|
|
15
|
-
date = models.DateField(blank=True, null=True)
|
|
16
|
-
time = models.TimeField(blank=True, null=True)
|
|
17
|
-
|
|
18
|
-
def get_pdf_hash(self):
|
|
19
|
-
#FIXME should use endoreg_db.utils.get_pdf_hash in future
|
|
20
|
-
pdf = self.pdf
|
|
21
|
-
pdf_hash = None
|
|
22
|
-
|
|
23
|
-
if pdf:
|
|
24
|
-
# Open the file in binary mode and read its contents
|
|
25
|
-
with pdf.open(mode='rb') as f:
|
|
26
|
-
pdf_contents = f.read()
|
|
27
|
-
# Create a hash object using SHA-256 algorithm
|
|
28
|
-
hash_object = hashlib.sha256(pdf_contents, usedforsecurity=False)
|
|
29
|
-
# Get the hexadecimal representation of the hash
|
|
30
|
-
pdf_hash = hash_object.hexdigest()
|
|
31
|
-
assert len(pdf_hash) <= 255, "Hash length exceeds 255 characters"
|
|
32
|
-
|
|
33
|
-
return pdf_hash
|
|
34
|
-
|
|
35
|
-
def initialize_metadata_in_db(self, report_meta=None):
|
|
36
|
-
if not report_meta:
|
|
37
|
-
report_meta = self.meta
|
|
38
|
-
self.set_examination_date_and_time(report_meta)
|
|
39
|
-
self.patient, created = self.get_or_create_patient(report_meta)
|
|
40
|
-
self.examiner, created = self.get_or_create_examiner(report_meta)
|
|
41
|
-
self.save()
|
|
42
|
-
|
|
43
|
-
def get_or_create_patient(self, report_meta=None):
|
|
44
|
-
from ..persons import Patient
|
|
45
|
-
if not report_meta:
|
|
46
|
-
report_meta = self.meta
|
|
47
|
-
patient_first_name = report_meta['patient_first_name']
|
|
48
|
-
patient_last_name = report_meta['patient_last_name']
|
|
49
|
-
patient_dob = report_meta['patient_dob']
|
|
50
|
-
|
|
51
|
-
patient, created = Patient.objects.get_or_create(
|
|
52
|
-
first_name=patient_first_name,
|
|
53
|
-
last_name=patient_last_name,
|
|
54
|
-
dob=patient_dob
|
|
55
|
-
)
|
|
56
|
-
|
|
57
|
-
return patient, created
|
|
58
|
-
|
|
59
|
-
def get_or_create_examiner(self, report_meta= None):
|
|
60
|
-
from ..persons import Examiner
|
|
61
|
-
if not report_meta:
|
|
62
|
-
report_meta = self.meta
|
|
63
|
-
examiner_first_name = report_meta['examiner_first_name']
|
|
64
|
-
examiner_last_name = report_meta['examiner_last_name']
|
|
65
|
-
examiner_center = self.center
|
|
66
|
-
|
|
67
|
-
examiner, created = Examiner.objects.get_or_create(
|
|
68
|
-
first_name=examiner_first_name,
|
|
69
|
-
last_name=examiner_last_name,
|
|
70
|
-
center=examiner_center
|
|
71
|
-
)
|
|
72
|
-
|
|
73
|
-
return examiner, created
|
|
74
|
-
|
|
75
|
-
def set_examination_date_and_time(self, report_meta=None):
|
|
76
|
-
if not report_meta:
|
|
77
|
-
report_meta = self.meta
|
|
78
|
-
examination_date_str = report_meta['examination_date']
|
|
79
|
-
examination_time_str = report_meta['examination_time']
|
|
80
|
-
|
|
81
|
-
if examination_date_str:
|
|
82
|
-
# TODO: get django DateField compatible date from string (e.g. "2021-01-01")
|
|
83
|
-
self.date = date.fromisoformat(examination_date_str)
|
|
84
|
-
if examination_time_str:
|
|
85
|
-
# TODO: get django TimeField compatible time from string (e.g. "12:00")
|
|
86
|
-
self.time = time.fromisoformat(examination_time_str)
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
|
|
@@ -1,25 +0,0 @@
|
|
|
1
|
-
# from django.db import models
|
|
2
|
-
|
|
3
|
-
# class VideoImportMeta(models.Model):
|
|
4
|
-
# processor = models.ForeignKey('EndoscopyProcessor', on_delete=models.CASCADE)
|
|
5
|
-
# endoscope = models.ForeignKey('Endoscope', on_delete=models.CASCADE, blank=True, null=True)
|
|
6
|
-
# center = models.ForeignKey('Center', on_delete=models.CASCADE)
|
|
7
|
-
# video_anonymized = models.BooleanField(default=False)
|
|
8
|
-
# video_patient_data_detected = models.BooleanField(default=False)
|
|
9
|
-
# outside_detected = models.BooleanField(default=False)
|
|
10
|
-
# patient_data_removed = models.BooleanField(default=False)
|
|
11
|
-
# outside_removed = models.BooleanField(default=False)
|
|
12
|
-
|
|
13
|
-
# def __str__(self):
|
|
14
|
-
# result_html = ""
|
|
15
|
-
|
|
16
|
-
# result_html += f"Processor: {self.processor.name}<br>"
|
|
17
|
-
# result_html += f"Endoscope: {self.endoscope.name}<br>"
|
|
18
|
-
# result_html += f"Center: {self.center.name}<br>"
|
|
19
|
-
# result_html += f"Video anonymized: {self.video_anonymized}<br>"
|
|
20
|
-
# result_html += f"Video patient data detected: {self.video_patient_data_detected}<br>"
|
|
21
|
-
# result_html += f"Outside detected: {self.outside_detected}<br>"
|
|
22
|
-
# result_html += f"Patient data removed: {self.patient_data_removed}<br>"
|
|
23
|
-
# result_html += f"Outside removed: {self.outside_removed}<br>"
|
|
24
|
-
# return result_html
|
|
25
|
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from ..base_classes import AbstractVideo
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from django.db import models
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from endoreg_db.models.data_file.frame import Frame
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from endoreg_db.models.data_file.frame import LegacyFrame
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BATCH_SIZE = 1000
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class Video(AbstractVideo):
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import_meta = models.OneToOneField('VideoImportMeta', on_delete=models.CASCADE, blank=True, null=True)
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def get_video_model(self):
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return Video
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def get_frame_model(self):
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return Frame
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class LegacyVideo(AbstractVideo):
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file = models.FileField(upload_to="legacy_videos", blank=True, null=True)
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def get_video_model(self):
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return LegacyVideo
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def get_frame_model(self):
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return LegacyFrame
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