endoreg-db 0.6.4__py3-none-any.whl → 0.8.2__py3-none-any.whl
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- endoreg_db/admin.py +26 -26
- endoreg_db/api_urls.py +4 -0
- endoreg_db/apps.py +12 -0
- 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 +12 -0
- endoreg_db/data/ai_model/data.yaml +1 -1
- endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
- endoreg_db/data/ai_model_label/label-set/data.yaml +20 -1
- endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
- endoreg_db/data/center/data.yaml +13 -12
- endoreg_db/data/center_shift/ukw.yaml +9 -0
- endoreg_db/data/db_summary.csv +58 -0
- endoreg_db/data/db_summary.xlsx +0 -0
- endoreg_db/data/disease/misc.yaml +1 -2
- endoreg_db/data/endoscopy_processor/data.yaml +3 -0
- endoreg_db/data/event/cardiology.yaml +0 -13
- endoreg_db/data/examination/examinations/data.yaml +14 -9
- endoreg_db/data/examination_indication/endoscopy.yaml +30 -30
- endoreg_db/data/examination_indication_classification/endoscopy.yaml +11 -11
- 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 +3 -46
- 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_morphology_classification_choice → finding_classification_choice}/colon_lesion_circularity_default.yaml +0 -2
- 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_morphology_classification_choice → finding_classification_choice}/colon_lesion_nice.yaml +4 -7
- endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_paris.yaml +0 -8
- endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_planarity_default.yaml +6 -13
- endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
- endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_surface_intact_default.yaml +3 -6
- endoreg_db/data/{finding_location_classification_choice/colonoscopy.yaml → finding_classification_choice/colonoscopy_location.yaml} +11 -22
- 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_colonoscopy.yaml +8 -3
- endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +6 -6
- endoreg_db/data/finding_type/data.yaml +23 -10
- endoreg_db/data/gender/data.yaml +8 -1
- endoreg_db/data/information_source/annotation.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/misc.yaml +43 -0
- endoreg_db/data/medication/anticoagulation.yaml +5 -5
- endoreg_db/data/medication/tah.yaml +5 -5
- endoreg_db/data/medication_intake_time/base.yaml +4 -4
- endoreg_db/data/names_first/first_names.yaml +3 -0
- endoreg_db/data/pdf_type/data.yaml +26 -2
- 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/report_reader_flag/rkh-histology-generic.yaml +10 -0
- endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +5 -0
- 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 +6 -6
- endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +9 -6
- endoreg_db/data/requirement/disease_hepatology.yaml +1 -1
- endoreg_db/data/requirement/disease_misc.yaml +3 -3
- endoreg_db/data/requirement/disease_renal.yaml +18 -2
- endoreg_db/data/requirement/{colonoscopy_indications.yaml → endoscopy_bleeding_risk.yaml} +6 -3
- endoreg_db/data/requirement/event_cardiology.yaml +17 -17
- 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 +352 -31
- 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 +36 -35
- endoreg_db/data/requirement_operator/model_operators.yaml +13 -7
- 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 +42 -2
- endoreg_db/data/requirement_type/requirement_types.yaml +82 -0
- endoreg_db/data/shift/endoscopy.yaml +21 -0
- endoreg_db/data/shift_type/base.yaml +35 -0
- endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
- endoreg_db/data/unit/concentration.yaml +23 -0
- endoreg_db/exceptions.py +19 -0
- endoreg_db/forms/patient_finding_intervention_form.py +4 -5
- endoreg_db/forms/patient_form.py +7 -6
- endoreg_db/forms/questionnaires/__init__.py +1 -1
- endoreg_db/forms/questionnaires/tto_questionnaire.py +19 -19
- endoreg_db/helpers/count_db.py +45 -0
- endoreg_db/helpers/data_loader.py +208 -0
- endoreg_db/helpers/default_objects.py +359 -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_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 +422 -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 +2 -7
- endoreg_db/management/commands/load_base_db_data.py +1 -0
- endoreg_db/management/commands/load_endoscope_data.py +2 -2
- endoreg_db/management/commands/load_examination_indication_data.py +2 -3
- endoreg_db/management/commands/load_finding_data.py +49 -92
- endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +0 -1
- endoreg_db/management/commands/load_information_source.py +13 -7
- endoreg_db/management/commands/load_name_data.py +37 -0
- endoreg_db/management/commands/load_qualification_data.py +59 -0
- endoreg_db/management/commands/load_requirement_data.py +30 -6
- endoreg_db/management/commands/load_shift_data.py +60 -0
- endoreg_db/management/commands/load_tag_data.py +57 -0
- endoreg_db/management/commands/register_ai_model.py +1 -1
- 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/migrations/0001_initial.py +625 -813
- endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
- endoreg_db/models/__init__.py +270 -307
- endoreg_db/models/administration/__init__.py +116 -0
- endoreg_db/models/{ai_model → administration/ai}/__init__.py +6 -1
- 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 +6 -1
- 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}/case_template.py +3 -3
- endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule.py +3 -10
- endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule_value.py +2 -4
- endoreg_db/models/{case_template → administration/case/case_template}/case_template_type.py +1 -3
- endoreg_db/models/{center → administration/center}/__init__.py +3 -1
- endoreg_db/models/administration/center/center.py +61 -0
- endoreg_db/models/administration/center/center_product.py +64 -0
- endoreg_db/models/{center → administration/center}/center_resource.py +19 -3
- 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 +1 -1
- endoreg_db/models/{persons → administration/person/names}/last_name.py +2 -3
- endoreg_db/models/administration/person/patient/__init__.py +5 -0
- endoreg_db/models/administration/person/patient/patient.py +460 -0
- 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/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 +9 -0
- endoreg_db/models/{product → administration/product}/reference_product.py +26 -11
- 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
- endoreg_db/models/administration/shift/__init__.py +9 -0
- endoreg_db/models/administration/shift/scheduled_days.py +69 -0
- endoreg_db/models/administration/shift/shift.py +51 -0
- endoreg_db/models/administration/shift/shift_type.py +108 -0
- endoreg_db/models/label/__init__.py +24 -1
- endoreg_db/models/label/annotation/__init__.py +12 -0
- endoreg_db/models/label/annotation/image_classification.py +84 -0
- endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
- endoreg_db/models/label/label.py +45 -74
- endoreg_db/models/label/label_set.py +53 -0
- endoreg_db/models/label/label_type.py +29 -0
- endoreg_db/models/label/label_video_segment/__init__.py +3 -0
- endoreg_db/models/label/label_video_segment/_create_from_video.py +41 -0
- endoreg_db/models/label/label_video_segment/label_video_segment.py +511 -0
- endoreg_db/models/label/video_segmentation_label.py +31 -0
- endoreg_db/models/{annotation → label}/video_segmentation_labelset.py +7 -0
- endoreg_db/models/media/__init__.py +14 -0
- endoreg_db/models/media/frame/__init__.py +3 -0
- endoreg_db/models/media/frame/frame.py +111 -0
- endoreg_db/models/media/pdf/__init__.py +11 -0
- endoreg_db/models/media/pdf/raw_pdf.py +608 -0
- endoreg_db/models/media/pdf/report_file.py +162 -0
- endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
- endoreg_db/models/media/video/__init__.py +4 -0
- endoreg_db/models/media/video/create_from_file.py +336 -0
- endoreg_db/models/media/video/pipe_1.py +207 -0
- endoreg_db/models/media/video/pipe_2.py +105 -0
- endoreg_db/models/media/video/refactor_plan.md +0 -0
- endoreg_db/models/media/video/video_file.py +680 -0
- endoreg_db/models/media/video/video_file_ai.py +443 -0
- endoreg_db/models/media/video/video_file_anonymize.py +348 -0
- endoreg_db/models/media/video/video_file_frames/__init__.py +47 -0
- endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +22 -0
- endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
- endoreg_db/models/media/video/video_file_frames/_delete_frames.py +104 -0
- endoreg_db/models/media/video/video_file_frames/_extract_frames.py +174 -0
- endoreg_db/models/media/video/video_file_frames/_get_frame.py +28 -0
- endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +27 -0
- endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +20 -0
- endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +27 -0
- endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +34 -0
- endoreg_db/models/media/video/video_file_frames/_get_frames.py +27 -0
- endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +129 -0
- endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +129 -0
- endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +65 -0
- endoreg_db/models/media/video/video_file_frames.py +0 -0
- endoreg_db/models/media/video/video_file_io.py +166 -0
- endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
- endoreg_db/models/media/video/video_file_meta/get_crop_template.py +45 -0
- endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
- endoreg_db/models/media/video/video_file_meta/get_fps.py +147 -0
- endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +143 -0
- endoreg_db/models/media/video/video_file_meta/text_meta.py +134 -0
- endoreg_db/models/media/video/video_file_meta/video_meta.py +70 -0
- endoreg_db/models/media/video/video_file_meta.py +11 -0
- endoreg_db/models/media/video/video_file_segments.py +209 -0
- endoreg_db/models/medical/__init__.py +146 -0
- endoreg_db/models/{contraindication → medical/contraindication}/__init__.py +1 -5
- endoreg_db/models/{disease.py → medical/disease.py} +60 -52
- endoreg_db/models/{event.py → medical/event.py} +31 -54
- endoreg_db/models/{examination → medical/examination}/__init__.py +1 -1
- endoreg_db/models/medical/examination/examination.py +148 -0
- endoreg_db/models/{examination → medical/examination}/examination_indication.py +64 -35
- endoreg_db/models/{examination → medical/examination}/examination_time.py +0 -4
- endoreg_db/models/{examination → medical/examination}/examination_time_type.py +1 -8
- endoreg_db/models/{examination → medical/examination}/examination_type.py +1 -7
- endoreg_db/models/medical/finding/__init__.py +18 -0
- endoreg_db/models/medical/finding/finding.py +96 -0
- endoreg_db/models/medical/finding/finding_classification.py +142 -0
- endoreg_db/models/{finding → medical/finding}/finding_intervention.py +2 -10
- endoreg_db/models/medical/finding/finding_type.py +35 -0
- endoreg_db/models/medical/hardware/__init__.py +8 -0
- endoreg_db/models/{hardware → medical/hardware}/endoscope.py +28 -23
- endoreg_db/models/medical/laboratory/__init__.py +5 -0
- endoreg_db/models/medical/laboratory/lab_value.py +419 -0
- endoreg_db/models/{medication → medical/medication}/medication.py +1 -3
- endoreg_db/models/{medication → medical/medication}/medication_indication_type.py +8 -3
- endoreg_db/models/{medication → medical/medication}/medication_intake_time.py +21 -3
- endoreg_db/models/{medication → medical/medication}/medication_schedule.py +13 -5
- endoreg_db/models/{organ → medical/organ}/__init__.py +3 -6
- endoreg_db/models/medical/patient/__init__.py +56 -0
- endoreg_db/models/medical/patient/medication_examples.py +38 -0
- endoreg_db/models/medical/patient/patient_disease.py +63 -0
- endoreg_db/models/medical/patient/patient_event.py +75 -0
- endoreg_db/models/medical/patient/patient_examination.py +249 -0
- endoreg_db/models/{persons → medical}/patient/patient_examination_indication.py +21 -9
- endoreg_db/models/medical/patient/patient_finding.py +357 -0
- endoreg_db/models/medical/patient/patient_finding_classification.py +207 -0
- endoreg_db/models/{patient → medical/patient}/patient_finding_intervention.py +15 -1
- endoreg_db/models/medical/patient/patient_lab_sample.py +148 -0
- endoreg_db/models/{persons → medical}/patient/patient_lab_value.py +40 -15
- endoreg_db/models/medical/patient/patient_medication.py +104 -0
- endoreg_db/models/medical/patient/patient_medication_schedule.py +136 -0
- endoreg_db/models/{risk → medical/risk}/risk_type.py +0 -4
- endoreg_db/models/{data_file/metadata → metadata}/__init__.py +6 -0
- endoreg_db/models/metadata/frame_ocr_result.py +0 -0
- endoreg_db/models/metadata/model_meta.py +193 -0
- endoreg_db/models/metadata/model_meta_logic.py +236 -0
- endoreg_db/models/{data_file/metadata → metadata}/pdf_meta.py +28 -13
- endoreg_db/models/metadata/sensitive_meta.py +288 -0
- endoreg_db/models/metadata/sensitive_meta_logic.py +643 -0
- endoreg_db/models/metadata/video_meta.py +332 -0
- endoreg_db/models/metadata/video_prediction_logic.py +190 -0
- endoreg_db/models/metadata/video_prediction_meta.py +270 -0
- endoreg_db/models/other/__init__.py +17 -0
- endoreg_db/models/other/distribution/date_value_distribution.py +0 -2
- endoreg_db/models/other/distribution/numeric_value_distribution.py +30 -2
- endoreg_db/models/{emission → other/emission}/emission_factor.py +15 -6
- endoreg_db/models/{persons → other}/gender.py +8 -3
- endoreg_db/models/other/information_source.py +159 -0
- endoreg_db/models/other/material.py +10 -2
- endoreg_db/models/other/resource.py +6 -2
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- endoreg_db/models/{rules → rule}/ruleset.py +0 -2
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- endoreg_db/models/data_file/base_classes/prepare_bulk_frames.py +0 -19
- endoreg_db/models/data_file/base_classes/utils.py +0 -58
- endoreg_db/models/data_file/frame.py +0 -29
- endoreg_db/models/data_file/import_classes/__init__.py +0 -18
- endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +0 -35
- endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +0 -28
- endoreg_db/models/data_file/import_classes/processing_functions/video.py +0 -260
- endoreg_db/models/data_file/import_classes/raw_pdf.py +0 -254
- endoreg_db/models/data_file/import_classes/raw_video.py +0 -290
- endoreg_db/models/data_file/metadata/sensitive_meta.py +0 -290
- endoreg_db/models/data_file/metadata/video_meta.py +0 -199
- endoreg_db/models/data_file/report_file.py +0 -56
- endoreg_db/models/data_file/video/__init__.py +0 -11
- endoreg_db/models/data_file/video/import_meta.py +0 -25
- endoreg_db/models/data_file/video/video.py +0 -196
- endoreg_db/models/data_file/video_segment.py +0 -214
- endoreg_db/models/examination/examination.py +0 -67
- endoreg_db/models/finding/__init__.py +0 -11
- endoreg_db/models/finding/finding.py +0 -75
- endoreg_db/models/finding/finding_location_classification.py +0 -94
- endoreg_db/models/finding/finding_morphology_classification.py +0 -89
- endoreg_db/models/finding/finding_type.py +0 -22
- endoreg_db/models/hardware/__init__.py +0 -2
- endoreg_db/models/information_source.py +0 -65
- endoreg_db/models/laboratory/__init__.py +0 -1
- endoreg_db/models/laboratory/lab_value.py +0 -162
- endoreg_db/models/logging/__init__.py +0 -11
- endoreg_db/models/logging/agl_service.py +0 -19
- endoreg_db/models/logging/base.py +0 -22
- endoreg_db/models/logging/log_type.py +0 -23
- endoreg_db/models/logging/network_device.py +0 -27
- endoreg_db/models/lx/__init__.py +0 -4
- endoreg_db/models/lx/client.py +0 -57
- endoreg_db/models/lx/identity.py +0 -34
- endoreg_db/models/lx/permission.py +0 -18
- endoreg_db/models/lx/user.py +0 -16
- endoreg_db/models/network/__init__.py +0 -9
- endoreg_db/models/network/agl_service.py +0 -38
- endoreg_db/models/network/network_device.py +0 -58
- endoreg_db/models/network/network_device_type.py +0 -23
- endoreg_db/models/other/distribution.py +0 -5
- endoreg_db/models/patient/__init__.py +0 -24
- endoreg_db/models/patient/patient_examination.py +0 -182
- endoreg_db/models/patient/patient_finding.py +0 -143
- endoreg_db/models/patient/patient_finding_location.py +0 -120
- endoreg_db/models/patient/patient_finding_morphology.py +0 -166
- endoreg_db/models/permissions/__init__.py +0 -44
- endoreg_db/models/persons/__init__.py +0 -34
- endoreg_db/models/persons/examiner/__init__.py +0 -2
- endoreg_db/models/persons/examiner/examiner.py +0 -60
- endoreg_db/models/persons/examiner/examiner_type.py +0 -2
- endoreg_db/models/persons/patient/__init__.py +0 -8
- endoreg_db/models/persons/patient/patient.py +0 -389
- endoreg_db/models/persons/patient/patient_disease.py +0 -22
- endoreg_db/models/persons/patient/patient_event.py +0 -52
- endoreg_db/models/persons/patient/patient_lab_sample.py +0 -108
- endoreg_db/models/persons/patient/patient_medication.py +0 -59
- endoreg_db/models/persons/patient/patient_medication_schedule.py +0 -88
- endoreg_db/models/persons/portal_user_information.py +0 -27
- endoreg_db/models/prediction/__init__.py +0 -8
- endoreg_db/models/prediction/image_classification.py +0 -51
- endoreg_db/models/prediction/video_prediction_meta.py +0 -306
- endoreg_db/models/product/product.py +0 -110
- endoreg_db/models/product/product_group.py +0 -27
- endoreg_db/models/product/product_material.py +0 -28
- endoreg_db/models/questionnaires/__init__.py +0 -114
- endoreg_db/models/quiz/__init__.py +0 -9
- endoreg_db/models/quiz/quiz_answer.py +0 -41
- endoreg_db/models/quiz/quiz_question.py +0 -54
- endoreg_db/models/report_reader/report_reader_config.py +0 -53
- endoreg_db/models/rules/__init__.py +0 -5
- endoreg_db/queries/get/__init__.py +0 -6
- endoreg_db/queries/get/center.py +0 -42
- endoreg_db/queries/get/model.py +0 -13
- endoreg_db/queries/get/patient.py +0 -14
- endoreg_db/queries/get/patient_examination.py +0 -20
- endoreg_db/queries/get/report_file.py +0 -33
- endoreg_db/queries/get/video.py +0 -31
- endoreg_db/serializers/ai_model.py +0 -19
- endoreg_db/serializers/annotation.py +0 -14
- endoreg_db/serializers/center.py +0 -11
- endoreg_db/serializers/examination.py +0 -33
- endoreg_db/serializers/frame.py +0 -9
- endoreg_db/serializers/hardware.py +0 -21
- endoreg_db/serializers/label.py +0 -22
- endoreg_db/serializers/patient.py +0 -33
- endoreg_db/serializers/prediction.py +0 -10
- endoreg_db/serializers/raw_pdf_anony_text_validation.py +0 -137
- endoreg_db/serializers/report_file.py +0 -7
- endoreg_db/serializers/video.py +0 -20
- endoreg_db/serializers/video_segmentation.py +0 -574
- endoreg_db/tests.py +0 -3
- endoreg_db/utils/legacy_ocr.py +0 -201
- endoreg_db/utils/video/transcode_videofile.py +0 -111
- endoreg_db/views/patient_views.py +0 -90
- endoreg_db/views/raw_pdf_anony_text_validation_views.py +0 -95
- endoreg_db/views/raw_pdf_meta_validation_views.py +0 -111
- endoreg_db/views/raw_video_meta_validation_views.py +0 -148
- endoreg_db/views/report_views.py +0 -96
- endoreg_db/views/video_segmentation_views.py +0 -166
- endoreg_db-0.6.4.dist-info/METADATA +0 -161
- endoreg_db-0.6.4.dist-info/RECORD +0 -470
- /endoreg_db/{case_generator/__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 → data/shift/m2.yaml} +0 -0
- /endoreg_db/{queries/get/video_import_meta.py → factories/__init__.py} +0 -0
- /endoreg_db/{queries/get/video_prediction_meta.py → helpers/__init__.py} +0 -0
- /endoreg_db/models/{case_template → administration/case/case_template}/__init__.py +0 -0
- /endoreg_db/models/{persons → administration/person}/person.py +0 -0
- /endoreg_db/models/{product → administration/product}/__init__.py +0 -0
- /endoreg_db/models/{report_reader → media/pdf/report_reader}/__init__.py +0 -0
- /endoreg_db/models/{report_reader → media/pdf/report_reader}/report_reader_flag.py +0 -0
- /endoreg_db/models/{hardware → medical/hardware}/endoscopy_processor.py +0 -0
- /endoreg_db/models/{medication → medical/medication}/__init__.py +0 -0
- /endoreg_db/models/{medication → medical/medication}/medication_indication.py +0 -0
- /endoreg_db/models/{risk → medical/risk}/__init__.py +0 -0
- /endoreg_db/models/{risk → medical/risk}/risk.py +0 -0
- /endoreg_db/models/{emission → other/emission}/__init__.py +0 -0
- /endoreg_db/models/{rules → rule}/rule_applicator.py +0 -0
- /endoreg_db/{case_generator → utils/case_generator}/case_generator.py +0 -0
- /endoreg_db/{case_generator → utils/case_generator}/lab_sample_factory.py +0 -0
- /endoreg_db/{case_generator → utils/case_generator}/utils.py +0 -0
- /endoreg_db/views/{csrf.py → misc/csrf.py} +0 -0
- {endoreg_db-0.6.4.dist-info → endoreg_db-0.8.2.dist-info}/WHEEL +0 -0
- {endoreg_db-0.6.4.dist-info → endoreg_db-0.8.2.dist-info}/licenses/LICENSE +0 -0
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""" """
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from django.db import models
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from collections import defaultdict, Counter
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import shutil
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import os
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from icecream import ic
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from endoreg_db.utils.hashs import get_video_hash
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from endoreg_db.utils.file_operations import get_uuid_filename
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from endoreg_db.utils.ocr import extract_text_from_rois
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from ....utils.video import (
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transcode_videofile,
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transcode_videofile_if_required,
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initialize_frame_objects,
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extract_frames,
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)
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from ..metadata import VideoMeta, SensitiveMeta
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from ....utils import (
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STORAGE_DIR,
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VIDEO_DIR,
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FRAME_DIR,
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)
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if TYPE_CHECKING:
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from endoreg_db.models import (
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VideoPredictionMeta,
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Video,
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RawVideoFile,
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RawVideoPredictionMeta,
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LabelRawVideoSegment,
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LabelVideoSegment,
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ModelMeta,
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Center,
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EndoscopyProcessor,
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VideoMeta,
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Frame,
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RawFrame,
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PatientExamination,
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) #
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ic("-----\nTEST RUN ENABLED\n-----")
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class AbstractVideoFile(models.Model):
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Abstract base class for video files.
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self: Union["RawVideoFile", "Video"]
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label_video_segments: Union[
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"QuerySet[LabelRawVideoSegment]",
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examination: "PatientExamination"
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video_meta: "VideoMeta"
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processor: "EndoscopyProcessor"
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center: "Center"
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ai_model_meta: "ModelMeta"
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sensitive_meta: "SensitiveMeta"
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frames: Union["QuerySet[RawFrame]", "QuerySet[Frame]"]
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class Meta:
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def transcode_videofile(cls, filepath: Path, transcoded_path: Path):
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""" """
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def check_hash_exists(cls, video_hash: str):
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@classmethod
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def create_from_file( # TODO Rename to get_or_create_from_file
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video.save()
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video.save()
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return video
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def get_video_model(self):
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from endoreg_db.models import RawVideoFile, Video
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if self.is_raw:
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return RawVideoFile
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return Video
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def get_frame_model(self):
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from endoreg_db.models import RawFrame, Frame
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if self.is_raw_video_file():
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return RawFrame
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return Frame
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def get_label_segment_model(self):
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from endoreg_db.models import LabelVideoSegment, LabelRawVideoSegment # pylint: disable=import-outside-toplevel
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if self.is_raw:
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return LabelRawVideoSegment
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return LabelVideoSegment
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def sequences_to_label_video_segments(
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self,
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video_prediction_meta: Union["VideoPredictionMeta", "RawVideoPredictionMeta"],
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):
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"""
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Convert sequences to label video segments.
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"""
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from endoreg_db.models import Label, InformationSource
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label_video_segment_model = self.get_label_segment_model()
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for label, sequences in self.sequences.items():
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label = Label.objects.get(name=label)
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for sequence in sequences:
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start_frame_number = sequence[0]
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end_frame_number = sequence[1]
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label_video_segment = label_video_segment_model.objects.create(
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video=self,
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prediction_meta=video_prediction_meta,
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label=label,
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start_frame_number=start_frame_number,
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end_frame_number=end_frame_number,
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)
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label_video_segment.save()
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def get_frame_number(self):
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"""
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Get the number of frames in the video.
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"""
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frame_model = self.get_frame_model()
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framecount = frame_model.objects.filter(video=self).count()
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return framecount
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def set_frames_extracted(self, value: bool = True):
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self.state_frames_extracted = value
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self.save()
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def get_frames(self):
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"""
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Retrieve all frames for this video in the correct order.
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"""
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frame_model = self.get_frame_model()
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return frame_model.objects.filter(video=self).order_by("frame_number")
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271
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def get_frame(self, frame_number):
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"""
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Retrieve a specific frame for this video.
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"""
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frame_model = self.get_frame_model()
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return frame_model.objects.get(video=self, frame_number=frame_number)
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|
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def get_frame_range(self, start_frame_number: int, end_frame_number: int):
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"""
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Expects numbers of start and stop frame.
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Returns all frames of this video within the given range in ascending order.
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"""
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frame_model = self.get_frame_model()
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return frame_model.objects.filter(
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video=self,
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frame_number__gte=start_frame_number,
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frame_number__lte=end_frame_number,
|
|
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|
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).order_by("frame_number")
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|
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290
|
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def is_raw_video_file(self):
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if self.__class__.__name__ == "RawVideoFile":
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return True
|
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return False
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|
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295
|
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def get_prediction_meta_model(self):
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from endoreg_db.models import VideoPredictionMeta, RawVideoPredictionMeta
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|
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298
|
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if self.is_raw_video_file():
|
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return RawVideoPredictionMeta
|
|
300
|
-
return VideoPredictionMeta
|
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301
|
-
|
|
302
|
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def predict_video(
|
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|
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self,
|
|
304
|
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model_meta_name: str,
|
|
305
|
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dataset_name: str = "inference_dataset",
|
|
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|
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model_meta_version: Optional[int] = None,
|
|
307
|
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smooth_window_size_s: int = 1,
|
|
308
|
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binarize_threshold: float = 0.5,
|
|
309
|
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anonymized_frames: bool = True,
|
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310
|
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img_suffix: str = ".jpg",
|
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311
|
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test_run: bool = TEST_RUN,
|
|
312
|
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n_test_frames: int = TEST_RUN_FRAME_NUMBER,
|
|
313
|
-
):
|
|
314
|
-
"""
|
|
315
|
-
WARNING: When using with Video Objects "anonymous_frames" should be set to False
|
|
316
|
-
Predict the video file using the given model.
|
|
317
|
-
Frames should be extracted and anonymized frames should be generated before prediction.
|
|
318
|
-
"""
|
|
319
|
-
from endoreg_db.models import (
|
|
320
|
-
RawVideoFile,
|
|
321
|
-
Video,
|
|
322
|
-
ModelMeta,
|
|
323
|
-
AiModel,
|
|
324
|
-
) # pylint: disable=import-outside-toplevel
|
|
325
|
-
#TODO Create issue to movie this function to the endo-ai module
|
|
326
|
-
#endoreg-db is our "base" module, so it should not depend "upstream" models
|
|
327
|
-
from endo_ai.predictor.inference_dataset import InferenceDataset # pylint: disable=import-outside-toplevel
|
|
328
|
-
from endo_ai.predictor.model_loader import MultiLabelClassificationNet
|
|
329
|
-
from endo_ai.predictor.predict import Classifier
|
|
330
|
-
from endo_ai.predictor.postprocess import (
|
|
331
|
-
concat_pred_dicts,
|
|
332
|
-
make_smooth_preds,
|
|
333
|
-
find_true_pred_sequences,
|
|
334
|
-
)
|
|
335
|
-
|
|
336
|
-
if TEST_RUN:
|
|
337
|
-
test_run = True
|
|
338
|
-
|
|
339
|
-
datasets = {
|
|
340
|
-
"inference_dataset": InferenceDataset,
|
|
341
|
-
}
|
|
342
|
-
|
|
343
|
-
if isinstance(self, RawVideoFile):
|
|
344
|
-
self: "RawVideoFile"
|
|
345
|
-
elif isinstance(self, Video):
|
|
346
|
-
self: "Video"
|
|
347
|
-
else:
|
|
348
|
-
raise Exception("Invalid instance type")
|
|
349
|
-
|
|
350
|
-
dataset_model_class = datasets[dataset_name]
|
|
351
|
-
|
|
352
|
-
if anonymized_frames and self.is_raw:
|
|
353
|
-
try:
|
|
354
|
-
frame_dir = self.get_anonymized_frame_dir()
|
|
355
|
-
except: # FIXME
|
|
356
|
-
frame_dir = Path(self.frame_dir)
|
|
357
|
-
assert self.state_frames_extracted, "Frames not extracted"
|
|
358
|
-
|
|
359
|
-
else:
|
|
360
|
-
frame_dir = Path(self.frame_dir)
|
|
361
|
-
assert self.state_frames_extracted, "Frames not extracted"
|
|
362
|
-
|
|
363
|
-
model_meta = ModelMeta.get_by_name(model_meta_name, model_meta_version)
|
|
364
|
-
model: AiModel = model_meta.model
|
|
365
|
-
|
|
366
|
-
ic(f"Model: {model}, Model Meta: {model_meta}")
|
|
367
|
-
|
|
368
|
-
model_type = model.model_type
|
|
369
|
-
model_subtype = model.model_subtype
|
|
370
|
-
|
|
371
|
-
ic(f"Model type: {model_type}, Model subtype: {model_subtype}")
|
|
372
|
-
ic(f"self: {self}, Type: {type(self)}")
|
|
373
|
-
|
|
374
|
-
prediction_meta_model = self.get_prediction_meta_model()
|
|
375
|
-
|
|
376
|
-
ic(
|
|
377
|
-
f"Prediction Meta Model: {prediction_meta_model}, Type: {type(prediction_meta_model)}"
|
|
378
|
-
)
|
|
379
|
-
|
|
380
|
-
video_prediction_meta, _created = prediction_meta_model.objects.get_or_create(
|
|
381
|
-
video=self, model_meta=model_meta
|
|
382
|
-
)
|
|
383
|
-
|
|
384
|
-
video_prediction_meta.save()
|
|
385
|
-
|
|
386
|
-
ic(video_prediction_meta)
|
|
387
|
-
|
|
388
|
-
paths = self.get_frame_paths()
|
|
389
|
-
ic(f"Found {len(paths)} images in {frame_dir}")
|
|
390
|
-
|
|
391
|
-
# frame names in format "frame_{index}.jpg"
|
|
392
|
-
indices = [int(p.stem.split("_")[1]) for p in paths]
|
|
393
|
-
path_index_tuples = list(zip(paths, indices))
|
|
394
|
-
# sort ascending by index
|
|
395
|
-
path_index_tuples.sort(key=lambda x: x[1])
|
|
396
|
-
paths, indices = zip(*path_index_tuples)
|
|
397
|
-
|
|
398
|
-
crop_template = self.get_crop_template()
|
|
399
|
-
|
|
400
|
-
string_paths = [p.resolve().as_posix() for p in paths]
|
|
401
|
-
crops = [crop_template for _ in paths]
|
|
402
|
-
|
|
403
|
-
ic(f"Detected {len(paths)} frames")
|
|
404
|
-
|
|
405
|
-
if test_run: # only use the first 10 frames
|
|
406
|
-
ic(f"Running in test mode, using only the first {n_test_frames} frames")
|
|
407
|
-
paths = paths[:n_test_frames]
|
|
408
|
-
indices = indices[:n_test_frames]
|
|
409
|
-
string_paths = string_paths[:n_test_frames]
|
|
410
|
-
crops = crops[:n_test_frames]
|
|
411
|
-
|
|
412
|
-
assert paths, f"No images found in {frame_dir}"
|
|
413
|
-
|
|
414
|
-
ds_config = model_meta.get_inference_dataset_config()
|
|
415
|
-
|
|
416
|
-
# Create dataset
|
|
417
|
-
ds = dataset_model_class(string_paths, crops, config=ds_config)
|
|
418
|
-
ic(f"Dataset length: {len(ds)}")
|
|
419
|
-
|
|
420
|
-
# Get a sample image
|
|
421
|
-
sample = ds[0]
|
|
422
|
-
ic("Shape:", sample.shape) # e.g., torch.Size([3, 716, 716])
|
|
423
|
-
|
|
424
|
-
# unorm = get_unorm(ds_config)
|
|
425
|
-
|
|
426
|
-
weights_path = model_meta.weights.path
|
|
427
|
-
|
|
428
|
-
ic(f"Model path: {weights_path}")
|
|
429
|
-
|
|
430
|
-
# FIXME implement support for different model types
|
|
431
|
-
ai_model_instance = MultiLabelClassificationNet.load_from_checkpoint(
|
|
432
|
-
checkpoint_path=weights_path,
|
|
433
|
-
)
|
|
434
|
-
|
|
435
|
-
_ = ai_model_instance.cuda()
|
|
436
|
-
_ = ai_model_instance.eval()
|
|
437
|
-
classifier = Classifier(ai_model_instance, verbose=True)
|
|
438
|
-
|
|
439
|
-
ic("Starting inference")
|
|
440
|
-
predictions = classifier.pipe(string_paths, crops)
|
|
441
|
-
|
|
442
|
-
ic("Creating Prediction Dict")
|
|
443
|
-
prediction_dict = classifier.get_prediction_dict(predictions, string_paths)
|
|
444
|
-
self.predictions = prediction_dict
|
|
445
|
-
|
|
446
|
-
ic("Creating Readable Predictions")
|
|
447
|
-
readable_predictions = [classifier.readable(p) for p in predictions]
|
|
448
|
-
self.readable_predictions = readable_predictions
|
|
449
|
-
|
|
450
|
-
ic("Creating Merged Predictions")
|
|
451
|
-
merged_predictions = concat_pred_dicts(readable_predictions)
|
|
452
|
-
|
|
453
|
-
fps = self.get_fps()
|
|
454
|
-
ic(
|
|
455
|
-
f"Creating Smooth Merged Predictions; FPS: {fps}, \
|
|
456
|
-
Smooth Window Size: {smooth_window_size_s}"
|
|
457
|
-
)
|
|
458
|
-
|
|
459
|
-
smooth_merged_predictions = {}
|
|
460
|
-
for key in merged_predictions.keys():
|
|
461
|
-
smooth_merged_predictions[key] = make_smooth_preds(
|
|
462
|
-
prediction_array=merged_predictions[key],
|
|
463
|
-
window_size_s=smooth_window_size_s,
|
|
464
|
-
fps=fps,
|
|
465
|
-
)
|
|
466
|
-
|
|
467
|
-
ic(
|
|
468
|
-
"Creating Binary Smooth Merged Predictions; Binarize Threshold: ",
|
|
469
|
-
binarize_threshold,
|
|
470
|
-
)
|
|
471
|
-
binary_smooth_merged_predictions = {}
|
|
472
|
-
for key in smooth_merged_predictions.keys(): # pylint: disable=consider-using-dict-items
|
|
473
|
-
binary_smooth_merged_predictions[key] = (
|
|
474
|
-
smooth_merged_predictions[key] > binarize_threshold
|
|
475
|
-
)
|
|
476
|
-
|
|
477
|
-
ic("Creating Sequences")
|
|
478
|
-
sequences = {}
|
|
479
|
-
for label, prediction_array in binary_smooth_merged_predictions.items():
|
|
480
|
-
sequences[label] = find_true_pred_sequences(prediction_array)
|
|
481
|
-
|
|
482
|
-
self.sequences = sequences
|
|
483
|
-
|
|
484
|
-
self.sequences_to_label_video_segments(
|
|
485
|
-
video_prediction_meta=video_prediction_meta
|
|
486
|
-
)
|
|
487
|
-
|
|
488
|
-
ic("Finished inference")
|
|
489
|
-
ic("Saving predictions to DB")
|
|
490
|
-
ic(sequences)
|
|
491
|
-
self.state_initial_prediction_required = False
|
|
492
|
-
self.state_initial_prediction_completed = True
|
|
493
|
-
self.save()
|
|
494
|
-
|
|
495
|
-
def get_outside_segments(self, outside_label_name: str = "outside"):
|
|
496
|
-
"""
|
|
497
|
-
Get sequences of outside frames.
|
|
498
|
-
"""
|
|
499
|
-
from endoreg_db.models import Label # pylint: disable=import-outside-toplevel
|
|
500
|
-
|
|
501
|
-
outside_label = Label.objects.get(name="outside")
|
|
502
|
-
assert outside_label is not None
|
|
503
|
-
|
|
504
|
-
outside_segments = self.label_video_segments.filter(label=outside_label)
|
|
505
|
-
|
|
506
|
-
ic(f"Getting outside sequences using label: {outside_label}")
|
|
507
|
-
|
|
508
|
-
return outside_segments
|
|
509
|
-
|
|
510
|
-
def get_outside_frames(self) -> List["Frame"]:
|
|
511
|
-
"""
|
|
512
|
-
Get outside frames.
|
|
513
|
-
"""
|
|
514
|
-
outside_segments = self.get_outside_segments()
|
|
515
|
-
frames = []
|
|
516
|
-
for segment in outside_segments:
|
|
517
|
-
frames.extend(segment.get_frames())
|
|
518
|
-
return frames
|
|
519
|
-
|
|
520
|
-
def get_outside_frame_paths(self):
|
|
521
|
-
"""
|
|
522
|
-
Get paths to outside frames.
|
|
523
|
-
"""
|
|
524
|
-
frames = self.get_outside_frames()
|
|
525
|
-
|
|
526
|
-
frame_paths = [Path(frame.image.path) for frame in frames]
|
|
527
|
-
|
|
528
|
-
return frame_paths
|
|
529
|
-
|
|
530
|
-
def __str__(self):
|
|
531
|
-
return self.file.name
|
|
532
|
-
|
|
533
|
-
def delete_with_file(self):
|
|
534
|
-
file_path = Path(self.file.path)
|
|
535
|
-
if file_path.exists():
|
|
536
|
-
file_path.unlink()
|
|
537
|
-
self.delete_frames()
|
|
538
|
-
self.delete_frames_anonymized()
|
|
539
|
-
self.delete()
|
|
540
|
-
return f"Deleted {self.file.name}; Deleted frames; Deleted anonymized frames"
|
|
541
|
-
|
|
542
|
-
def get_endo_roi(self):
|
|
543
|
-
"""
|
|
544
|
-
Fetches the endoscope ROI from the video meta.
|
|
545
|
-
Returns a dictionary with keys "x", "y", "width", "height"
|
|
546
|
-
"""
|
|
547
|
-
endo_roi = self.video_meta.get_endo_roi()
|
|
548
|
-
return endo_roi
|
|
549
|
-
|
|
550
|
-
def get_crop_template(self):
|
|
551
|
-
"""
|
|
552
|
-
Creates a crop template (e.g., [0, 1080, 550, 1920 - 20] for a 1080p frame) from the endoscope ROI.
|
|
553
|
-
"""
|
|
554
|
-
endo_roi = self.get_endo_roi()
|
|
555
|
-
x = endo_roi["x"]
|
|
556
|
-
y = endo_roi["y"]
|
|
557
|
-
width = endo_roi["width"]
|
|
558
|
-
height = endo_roi["height"]
|
|
559
|
-
|
|
560
|
-
crop_template = [y, y + height, x, x + width]
|
|
561
|
-
return crop_template
|
|
562
|
-
|
|
563
|
-
def set_frame_dir(self):
|
|
564
|
-
self.frame_dir = f"{FRAME_DIR}/{self.uuid}"
|
|
565
|
-
|
|
566
|
-
# video meta should be created when video file is created
|
|
567
|
-
def save(self, *args, **kwargs):
|
|
568
|
-
assert self.processor is not None, "Processor must be set"
|
|
569
|
-
if not self.fps:
|
|
570
|
-
self.fps = self.get_fps()
|
|
571
|
-
if self.is_raw_video_file():
|
|
572
|
-
self.is_raw = True
|
|
573
|
-
if self.video_meta is None:
|
|
574
|
-
center = self.center
|
|
575
|
-
processor = self.processor
|
|
576
|
-
self.video_meta = VideoMeta.objects.create(
|
|
577
|
-
center=center, processor=processor
|
|
578
|
-
)
|
|
579
|
-
self.video_meta.initialize_ffmpeg_meta(self.file.path)
|
|
580
|
-
|
|
581
|
-
if not self.frame_dir:
|
|
582
|
-
self.set_frame_dir()
|
|
583
|
-
|
|
584
|
-
sm = self.sensitive_meta
|
|
585
|
-
if sm:
|
|
586
|
-
self.patient = sm.pseudo_patient
|
|
587
|
-
self.patient_examination = sm.pseudo_examination
|
|
588
|
-
|
|
589
|
-
super(AbstractVideoFile, self).save(*args, **kwargs)
|
|
590
|
-
|
|
591
|
-
def extract_frames(
|
|
592
|
-
self,
|
|
593
|
-
quality: int = 2,
|
|
594
|
-
overwrite: bool = False,
|
|
595
|
-
ext="jpg",
|
|
596
|
-
verbose=False,
|
|
597
|
-
) -> List[Path]:
|
|
598
|
-
"""
|
|
599
|
-
Extract frames from the video file and save them to the frame_dir.
|
|
600
|
-
For this, ffmpeg must be available in in the current environment.
|
|
601
|
-
"""
|
|
602
|
-
|
|
603
|
-
return extract_frames(
|
|
604
|
-
video=self,
|
|
605
|
-
quality=quality,
|
|
606
|
-
overwrite=overwrite,
|
|
607
|
-
ext=ext,
|
|
608
|
-
verbose=verbose,
|
|
609
|
-
)
|
|
610
|
-
|
|
611
|
-
def initialize_frames(self, paths: List[Path]):
|
|
612
|
-
"""
|
|
613
|
-
Initialize frame objects for the video file.
|
|
614
|
-
"""
|
|
615
|
-
initialize_frame_objects(self, paths)
|
|
616
|
-
|
|
617
|
-
def delete_frames(self):
|
|
618
|
-
"""
|
|
619
|
-
Delete frames extracted from the video file.
|
|
620
|
-
"""
|
|
621
|
-
frame_dir = Path(self.frame_dir)
|
|
622
|
-
if frame_dir.exists():
|
|
623
|
-
shutil.rmtree(frame_dir)
|
|
624
|
-
self.state_frames_extracted = False
|
|
625
|
-
self.save()
|
|
626
|
-
return f"Frames deleted from {frame_dir}"
|
|
627
|
-
else:
|
|
628
|
-
return f"No frames to delete for {self.file.name}"
|
|
629
|
-
|
|
630
|
-
def delete_frames_anonymized(self):
|
|
631
|
-
"""
|
|
632
|
-
Delete anonymized frames extracted from the video file.
|
|
633
|
-
"""
|
|
634
|
-
frame_dir = Path(self.frame_dir)
|
|
635
|
-
anonymized_frame_dir = frame_dir.parent / f"anonymized_{self.uuid}"
|
|
636
|
-
if anonymized_frame_dir.exists():
|
|
637
|
-
shutil.rmtree(anonymized_frame_dir)
|
|
638
|
-
return f"Anonymized frames deleted from {anonymized_frame_dir}"
|
|
639
|
-
else:
|
|
640
|
-
return f"No anonymized frames to delete for {self.file.name}"
|
|
641
|
-
|
|
642
|
-
def get_frame_path(self, n: int = 0, anonymized=False):
|
|
643
|
-
"""
|
|
644
|
-
Get the path to the n-th frame extracted from the video file.
|
|
645
|
-
Note that the frame numbering starts at 1 in our naming convention.
|
|
646
|
-
"""
|
|
647
|
-
# Adjust index
|
|
648
|
-
n = n + 1
|
|
649
|
-
|
|
650
|
-
if anonymized:
|
|
651
|
-
_frame_dir = Path(self.frame_dir)
|
|
652
|
-
frame_dir = _frame_dir.parent / f"anonymized_{_frame_dir.name}"
|
|
653
|
-
else:
|
|
654
|
-
frame_dir = Path(self.frame_dir)
|
|
655
|
-
return frame_dir / f"frame_{n:07d}.jpg"
|
|
656
|
-
|
|
657
|
-
def get_frame_paths(self):
|
|
658
|
-
"""
|
|
659
|
-
Get paths to frames extracted from the video file.
|
|
660
|
-
"""
|
|
661
|
-
frames = self.frames.filter(extracted=True).order_by("frame_number")
|
|
662
|
-
|
|
663
|
-
paths = [Path(frame.image.path) for frame in frames]
|
|
664
|
-
return paths
|
|
665
|
-
|
|
666
|
-
def get_prediction_dir(self):
|
|
667
|
-
return Path(self.prediction_dir)
|
|
668
|
-
|
|
669
|
-
def get_predictions_path(self, suffix=".json"):
|
|
670
|
-
pred_dir = self.get_prediction_dir()
|
|
671
|
-
return pred_dir.joinpath("predictions").with_suffix(suffix)
|
|
672
|
-
|
|
673
|
-
def get_smooth_predictions_path(self, suffix=".json"):
|
|
674
|
-
pred_dir = self.get_prediction_dir()
|
|
675
|
-
return pred_dir.joinpath("smooth_predictions").with_suffix(suffix)
|
|
676
|
-
|
|
677
|
-
def get_binary_predictions_path(self, suffix=".json"):
|
|
678
|
-
pred_dir = self.get_prediction_dir()
|
|
679
|
-
return pred_dir.joinpath("binary_predictions").with_suffix(suffix)
|
|
680
|
-
|
|
681
|
-
def get_raw_sequences_path(self, suffix=".json"):
|
|
682
|
-
pred_dir = self.get_prediction_dir()
|
|
683
|
-
return pred_dir.joinpath("raw_sequences").with_suffix(suffix)
|
|
684
|
-
|
|
685
|
-
def get_filtered_sequences_path(self, suffix=".json"):
|
|
686
|
-
pred_dir = self.get_prediction_dir()
|
|
687
|
-
return pred_dir.joinpath("filtered_sequences").with_suffix(suffix)
|
|
688
|
-
|
|
689
|
-
def extract_text_information(self, frame_fraction: float = 0.001):
|
|
690
|
-
"""
|
|
691
|
-
Extract text information from the video file.
|
|
692
|
-
Makes sure that frames are extracted and then processes the frames.
|
|
693
|
-
gets all frames from frame_dir and selects a fraction of them to process (at least 1)
|
|
694
|
-
"""
|
|
695
|
-
if not self.state_frames_extracted:
|
|
696
|
-
print(f"Frames not extracted for {self.file.name}")
|
|
697
|
-
return None
|
|
698
|
-
|
|
699
|
-
processor = self.processor
|
|
700
|
-
|
|
701
|
-
frame_paths = self.get_frame_paths()
|
|
702
|
-
n_frames = len(frame_paths)
|
|
703
|
-
n_frames_to_process = max(1, int(frame_fraction * n_frames))
|
|
704
|
-
|
|
705
|
-
# Select evenly spaced frames
|
|
706
|
-
frame_paths = frame_paths[:: n_frames // n_frames_to_process]
|
|
707
|
-
|
|
708
|
-
# extract text from each frame and store the value to
|
|
709
|
-
# defaultdict of lists.
|
|
710
|
-
# Then, extract the most frequent value from each list
|
|
711
|
-
# Finally, return the dictionary of most frequent values
|
|
712
|
-
|
|
713
|
-
# Create a defaultdict to store the extracted text from each ROI
|
|
714
|
-
rois_texts = defaultdict(list)
|
|
715
|
-
|
|
716
|
-
print(f"Processing {n_frames_to_process} frames from {self.file.name}")
|
|
717
|
-
# Process frames
|
|
718
|
-
for frame_path in frame_paths[:n_frames_to_process]:
|
|
719
|
-
extracted_texts = extract_text_from_rois(frame_path, processor)
|
|
720
|
-
for roi, text in extracted_texts.items():
|
|
721
|
-
rois_texts[roi].append(text)
|
|
722
|
-
|
|
723
|
-
# Get the most frequent text values for each ROI using Counter
|
|
724
|
-
for key in rois_texts.keys(): # pylint: disable=consider-using-dict-items
|
|
725
|
-
counter = Counter([text for text in rois_texts[key] if text])
|
|
726
|
-
rois_texts[key] = counter.most_common(1)[0][0] if counter else None
|
|
727
|
-
|
|
728
|
-
return rois_texts
|
|
729
|
-
|
|
730
|
-
def update_text_metadata(self, ocr_frame_fraction=0.001):
|
|
731
|
-
ic(f"Updating metadata for {self.file.name}")
|
|
732
|
-
extracted_data_dict = self.extract_text_information(ocr_frame_fraction)
|
|
733
|
-
if extracted_data_dict is None:
|
|
734
|
-
ic("No text extracted; skipping metadata update.")
|
|
735
|
-
return
|
|
736
|
-
extracted_data_dict["center_name"] = self.center.name
|
|
737
|
-
|
|
738
|
-
ic(extracted_data_dict)
|
|
739
|
-
|
|
740
|
-
extracted_data_dict["center_name"] = self.center.name
|
|
741
|
-
|
|
742
|
-
ic("____________")
|
|
743
|
-
ic(extracted_data_dict)
|
|
744
|
-
ic("____________")
|
|
745
|
-
|
|
746
|
-
self.sensitive_meta = SensitiveMeta.create_from_dict(extracted_data_dict)
|
|
747
|
-
self.state_sensitive_data_retrieved = True # pylint: disable=attribute-defined-outside-init
|
|
748
|
-
self.save()
|
|
749
|
-
|
|
750
|
-
# Resulting dict depends on defined ROIs for this processor type!
|
|
751
|
-
|
|
752
|
-
def update_video_meta(self):
|
|
753
|
-
video_meta = self.video_meta
|
|
754
|
-
video_path = Path(self.file.path)
|
|
755
|
-
center = self.center
|
|
756
|
-
assert self.processor
|
|
757
|
-
|
|
758
|
-
if video_meta is None:
|
|
759
|
-
video_meta = VideoMeta.create_from_file(
|
|
760
|
-
video_path,
|
|
761
|
-
center=center,
|
|
762
|
-
processor=self.processor,
|
|
763
|
-
)
|
|
764
|
-
self.video_meta = video_meta
|
|
765
|
-
self.save()
|
|
766
|
-
|
|
767
|
-
else:
|
|
768
|
-
video_meta.update_meta(video_path)
|
|
769
|
-
|
|
770
|
-
def get_fps(self):
|
|
771
|
-
# # FIXME
|
|
772
|
-
# fps = 50
|
|
773
|
-
# return fps
|
|
774
|
-
|
|
775
|
-
if self.video_meta is None:
|
|
776
|
-
self.update_video_meta()
|
|
777
|
-
|
|
778
|
-
if self.video_meta.ffmpeg_meta is None:
|
|
779
|
-
self.video_meta.initialize_ffmpeg_meta(self.file.path)
|
|
780
|
-
|
|
781
|
-
return self.video_meta.get_fps()
|
|
782
|
-
|
|
783
|
-
def create_frame_object(
|
|
784
|
-
self, frame_number, image_file=None, extracted: bool = False
|
|
785
|
-
):
|
|
786
|
-
"""
|
|
787
|
-
Returns a frame instance with the image_file set.
|
|
788
|
-
"""
|
|
789
|
-
frame_model = self.get_frame_model()
|
|
790
|
-
return frame_model(
|
|
791
|
-
video=self,
|
|
792
|
-
frame_number=frame_number,
|
|
793
|
-
image=image_file,
|
|
794
|
-
extracted=extracted,
|
|
795
|
-
)
|
|
796
|
-
|
|
797
|
-
def bulk_create_frames(self, frames_to_create):
|
|
798
|
-
"""
|
|
799
|
-
Bulk create frames, then save their images to storage.
|
|
800
|
-
"""
|
|
801
|
-
frame_model = self.get_frame_model()
|
|
802
|
-
created = frame_model.objects.bulk_create(frames_to_create)
|
|
803
|
-
# for frame in created:
|
|
804
|
-
# frame_name = f"frame_{frame.frame_number:07d}.jpg"
|
|
805
|
-
# frame.image.save(frame_name, frame.image)
|
|
806
|
-
# frame.save()
|