endoreg-db 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

endoreg_db/migrations/0002_alter_frame_image_alter_rawframe_image.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.1.6 on 2025-03-11 08:41
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='frame',
+            name='image',
+            field=models.ImageField(blank=True, null=True, upload_to=''),
+        ),
+        migrations.AlterField(
+            model_name='rawframe',
+            name='image',
+            field=models.ImageField(blank=True, null=True, upload_to=''),
+        ),
+    ]

endoreg_db/migrations/0003_alter_frame_image_alter_rawframe_image.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.1.6 on 2025-03-11 09:24
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0002_alter_frame_image_alter_rawframe_image'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='frame',
+            name='image',
+            field=models.ImageField(blank=True, null=True, upload_to='db_frames'),
+        ),
+        migrations.AlterField(
+            model_name='rawframe',
+            name='image',
+            field=models.ImageField(blank=True, null=True, upload_to='db_raw_frames'),
+        ),
+    ]

endoreg_db/migrations/0004_alter_rawvideofile_file_alter_video_file.py

@@ -0,0 +1,25 @@
+# Generated by Django 5.1.6 on 2025-03-12 05:05
+
+import django.core.files.storage
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0003_alter_frame_image_alter_rawframe_image'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='rawvideofile',
+            name='file',
+            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(location='/home/admin/test-data'), upload_to='db_raw_videos', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['mp4'])]),
+        ),
+        migrations.AlterField(
+            model_name='video',
+            name='file',
+            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(location='/home/admin/test-data'), upload_to='db_videos', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['mp4'])]),
+        ),
+    ]

endoreg_db/migrations/0005_rawvideofile_frame_count_and_more.py

@@ -0,0 +1,33 @@
+# Generated by Django 5.1.6 on 2025-03-12 06:40
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0004_alter_rawvideofile_file_alter_video_file'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='rawvideofile',
+            name='frame_count',
+            field=models.IntegerField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='rawvideofile',
+            name='state_frames_initialized',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name='video',
+            name='frame_count',
+            field=models.IntegerField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='video',
+            name='state_frames_initialized',
+            field=models.BooleanField(default=False),
+        ),
+    ]

endoreg_db/migrations/0006_frame_extracted_rawframe_extracted.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.1.6 on 2025-03-13 08:27
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0005_rawvideofile_frame_count_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='frame',
+            name='extracted',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name='rawframe',
+            name='extracted',
+            field=models.BooleanField(default=False),
+        ),
+    ]

endoreg_db/migrations/0007_rename_pseudo_patient_video_patient_and_more.py

@@ -0,0 +1,24 @@
+# Generated by Django 5.1.6 on 2025-03-13 12:00
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0006_frame_extracted_rawframe_extracted'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='video',
+            old_name='pseudo_patient',
+            new_name='patient',
+        ),
+        migrations.AddField(
+            model_name='rawpdffile',
+            name='patient',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='raw_pdf_files', to='endoreg_db.patient'),
+        ),
+    ]

endoreg_db/migrations/0008_remove_reportfile_patient_examination_and_more.py

@@ -0,0 +1,48 @@
+# Generated by Django 5.1.6 on 2025-03-13 14:15
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0007_rename_pseudo_patient_video_patient_and_more'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='reportfile',
+            name='patient_examination',
+        ),
+        migrations.AddField(
+            model_name='rawpdffile',
+            name='examination',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='endoreg_db.patientexamination'),
+        ),
+        migrations.AddField(
+            model_name='rawpdffile',
+            name='examiner',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='endoreg_db.examiner'),
+        ),
+        migrations.AddField(
+            model_name='rawvideofile',
+            name='examination',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='endoreg_db.patientexamination'),
+        ),
+        migrations.AddField(
+            model_name='reportfile',
+            name='examination',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='endoreg_db.patientexamination'),
+        ),
+        migrations.AlterField(
+            model_name='reportfile',
+            name='examiner',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='endoreg_db.examiner'),
+        ),
+        migrations.AlterField(
+            model_name='reportfile',
+            name='patient',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='endoreg_db.patient'),
+        ),
+    ]

endoreg_db/models/__init__.py

@@ -0,0 +1,376 @@
+# Utility
+from .unit import Unit
+from .information_source import InformationSource
+from .emission import EmissionFactor
+
+# Center
+from .center import (
+    Center,
+    CenterProduct,
+    CenterResource,
+    CenterWaste,
+)
+
+# Persons
+from .persons import (
+    Gender,
+    Person,
+    Patient,
+    PatientForm,
+    PatientEvent,
+    PatientDisease,
+    PatientLabSample,
+    PatientLabSampleType,
+    PatientLabValue,
+    PatientMedication,
+    PatientMedicationSchedule,
+    PatientExaminationIndication,
+    Examiner,
+    ExaminerSerializer,
+    PortalUserInfo,
+    Profession,
+    FirstName,
+    LastName,
+)
+
+# Network
+from .network import (
+    NetworkDevice,
+    NetworkDeviceType,
+    AglService,
+)
+
+# Logging
+from .logging import (
+    AbstractLogEntry,
+    NetworkDeviceLogEntry,
+    LogType,
+    AglServiceLogEntry,
+)
+
+# Patient
+from .patient import (
+    PatientExamination,
+    PatientFinding,
+    PatientFindingLocation,
+    PatientFindingMorphology,
+    PatientFindingIntervention,
+)
+
+# Organ
+from .organ import Organ
+
+# LX
+from .lx import (
+    LxClientType,
+    LxClientTag,
+    LxClient,
+    LxIdentity,
+    LxIdentityType,
+    LxPermission,
+    LxUser,
+)
+
+# Contraindication
+from .contraindication import Contraindication
+
+# Finding
+from .finding import (
+    Finding,
+    FindingType,
+    FindingLocationClassification,
+    FindingLocationClassificationChoice,
+    FindingMorphologyClassificationType,
+    FindingMorphologyClassificationChoice,
+    FindingMorphologyClassification,
+    FindingIntervention,
+    FindingInterventionType,
+)
+
+# Case template
+from .case_template import (
+    CaseTemplate,
+    CaseTemplateType,
+    CaseTemplateRule,
+    CaseTemplateRuleType,
+    CaseTemplateRuleValue,
+    CaseTemplateRuleValueType,
+)
+
+# Rules
+from .rules import (
+    Rule,
+    RuleType,
+    Ruleset,
+    RuleApplicator,
+)
+
+# Disease
+from .disease import Disease, DiseaseClassification, DiseaseClassificationChoice
+
+# Event
+from .event import Event, EventClassification, EventClassificationChoice
+
+# Laboratory
+from .laboratory import LabValue
+
+# Medication
+from .medication import (
+    Medication,
+    MedicationSchedule,
+    MedicationIntakeTime,
+    MedicationIndication,
+    MedicationIndicationType,
+)
+
+# Examination
+from .examination import (
+    Examination,
+    ExaminationType,
+    ExaminationTime,
+    ExaminationTimeType,
+    ExaminationIndication,
+    ExaminationIndicationClassification,
+    ExaminationIndicationClassificationChoice,
+)
+
+# Report Reader
+from .report_reader import (
+    ReportReaderConfig,
+    ReportReaderFlag,
+)
+
+# Data file
+from .data_file import (
+    Frame,
+    ReportFile,
+    Video,
+    LabelVideoSegment,
+    LabelRawVideoSegment,
+    SensitiveMeta,
+    PdfMeta,
+    PdfType,
+    VideoMeta,
+    RawFrame,
+    FFMpegMeta,
+    VideoImportMeta,
+    RawPdfFile,
+    RawVideoFile,
+)
+
+# Label
+from .label import Label, LabelType, LabelSet
+
+# Annotation
+from .annotation import (
+    ImageClassificationAnnotation,
+    BinaryClassificationAnnotationTask,
+    AnonymousImageAnnotation,
+    DroppedName,
+    AnonymizedImageLabel,
+    AnonymizedFile,
+    UploadedFile,
+    VideoSegmentationLabel,
+    VideoSegmentationAnnotation,
+    VideoSegmentationLabelSet,
+)
+
+# Other
+from .other import (
+    Material,
+    Resource,
+    TransportRoute,
+    Waste,
+    BaseValueDistribution,
+    NumericValueDistribution,
+    SingleCategoricalValueDistribution,
+    MultipleCategoricalValueDistribution,
+    DateValueDistribution,
+)
+
+# Product
+from .product import (
+    Product,
+    ProductMaterial,
+    ProductGroup,
+    ReferenceProduct,
+    ProductWeight,
+)
+
+# AI models
+from .ai_model import (
+    ModelMeta,
+    ModelType,
+    ActiveModel,
+    AiModel,
+)
+
+# Quiz
+from .quiz import (
+    QuizAnswer,
+    QuizAnswerType,
+    QuizQuestion,
+    QuizQuestionType,
+)
+
+# Prediction
+from .prediction import (
+    ImageClassificationPrediction,
+    VideoPredictionMeta,
+    RawVideoPredictionMeta,
+)
+
+# Hardware
+from .hardware import (
+    EndoscopyProcessor,
+    Endoscope,
+    EndoscopeType,
+)
+
+# Questionnaires
+from .questionnaires import TtoQuestionnaire
+
+__all__ = [
+    "ReportReaderConfig",
+    "ReportReaderFlag",
+    "Unit",
+    "InformationSource",
+    "EmissionFactor",
+    "Center",
+    "CenterProduct",
+    "CenterResource",
+    "CenterWaste",
+    "RawVideoPredictionMeta",
+    "Gender",
+    "Person",
+    "Patient",
+    "PatientForm",
+    "PatientEvent",
+    "PatientDisease",
+    "PatientLabSample",
+    "PatientLabSampleType",
+    "PatientLabValue",
+    "PatientMedication",
+    "PatientMedicationSchedule",
+    "PatientExaminationIndication",
+    "Examiner",
+    "ExaminerSerializer",
+    "PortalUserInfo",
+    "RawFrame",
+    "Profession",
+    "FirstName",
+    "LastName",
+    "NetworkDevice",
+    "NetworkDeviceType",
+    "AglService",
+    "AbstractLogEntry",
+    "NetworkDeviceLogEntry",
+    "LogType",
+    "AglServiceLogEntry",
+    "PatientExamination",
+    "PatientFinding",
+    "PatientFindingLocation",
+    "PatientFindingMorphology",
+    "PatientFindingIntervention",
+    "Organ",
+    "LxClientType",
+    "LxClientTag",
+    "LxClient",
+    "LxIdentity",
+    "LxIdentityType",
+    "LxPermission",
+    "LxUser",
+    "Contraindication",
+    "Finding",
+    "FindingType",
+    "FindingLocationClassification",
+    "FindingLocationClassificationChoice",
+    "FindingMorphologyClassificationType",
+    "FindingMorphologyClassificationChoice",
+    "FindingMorphologyClassification",
+    "FindingIntervention",
+    "FindingInterventionType",
+    "CaseTemplate",
+    "CaseTemplateType",
+    "CaseTemplateRule",
+    "CaseTemplateRuleType",
+    "CaseTemplateRuleValue",
+    "CaseTemplateRuleValueType",
+    "Rule",
+    "RuleType",
+    "Ruleset",
+    "RuleApplicator",
+    "Disease",
+    "DiseaseClassification",
+    "DiseaseClassificationChoice",
+    "Event",
+    "EventClassification",
+    "EventClassificationChoice",
+    "LabValue",
+    "Medication",
+    "MedicationSchedule",
+    "MedicationIntakeTime",
+    "MedicationIndication",
+    "MedicationIndicationType",
+    "Examination",
+    "ExaminationType",
+    "ExaminationTime",
+    "ExaminationTimeType",
+    "ExaminationIndication",
+    "ExaminationIndicationClassification",
+    "ExaminationIndicationClassificationChoice",
+    "Label",
+    "LabelType",
+    "LabelSet",
+    "LabelRawVideoSegment",
+    "ImageClassificationAnnotation",
+    "BinaryClassificationAnnotationTask",
+    "AnonymousImageAnnotation",
+    "DroppedName",
+    "AnonymizedImageLabel",
+    "AnonymizedFile",
+    "UploadedFile",
+    "VideoSegmentationLabel",
+    "VideoSegmentationAnnotation",
+    "Material",
+    "Resource",
+    "TransportRoute",
+    "Waste",
+    "BaseValueDistribution",
+    "NumericValueDistribution",
+    "SingleCategoricalValueDistribution",
+    "MultipleCategoricalValueDistribution",
+    "DateValueDistribution",
+    "Product",
+    "ProductMaterial",
+    "ProductGroup",
+    "ReferenceProduct",
+    "ProductWeight",
+    "ModelMeta",
+    "ModelType",
+    "ActiveModel",
+    "AiModel",
+    "QuizAnswer",
+    "QuizAnswerType",
+    "QuizQuestion",
+    "QuizQuestionType",
+    "ImageClassificationPrediction",
+    "VideoPredictionMeta",
+    "EndoscopyProcessor",
+    "Endoscope",
+    "EndoscopeType",
+    "TtoQuestionnaire",
+    "Frame",
+    "ReportFile",
+    "Video",
+    "LabelVideoSegment",
+    "SensitiveMeta",
+    "PdfMeta",
+    "PdfType",
+    "VideoMeta",
+    "FFMpegMeta",
+    "VideoImportMeta",
+    "RawPdfFile",
+    "RawVideoFile",
+    "VideoSegmentationLabelSet",
+]

endoreg_db/models/ai_model/__init__.py

@@ -0,0 +1,4 @@
+from .model_meta import ModelMeta
+from .model_type import ModelType
+from .active_model import ActiveModel
+from .ai_model import AiModel

endoreg_db/models/ai_model/active_model.py

@@ -0,0 +1,9 @@
+from django.db import models
+
+class ActiveModelManager(models.Manager):
+    def get_by_natural_key(self, name):
+        return self.get(name=name)
+    
+class ActiveModel(models.Model):
+    name = models.CharField(max_length=255, unique=True)
+    model_meta = models.OneToOneField('ModelMeta', on_delete=models.SET_NULL, blank=True, null=True)

endoreg_db/models/ai_model/ai_model.py

@@ -0,0 +1,103 @@
+"""
+Django model for AI models.
+"""
+
+from pathlib import Path
+import os
+from django.db import models
+from icecream import ic
+
+PSEUDO_DIR = Path(os.environ.get("DJANGO_PSEUDO_DIR", Path("./erc_data")))
+
+STORAGE_LOCATION = PSEUDO_DIR
+WEIGHTS_DIR_NAME = "db_model_weights"
+WEIGHTS_DIR = STORAGE_LOCATION / WEIGHTS_DIR_NAME
+
+if not WEIGHTS_DIR.exists():
+    WEIGHTS_DIR.mkdir(parents=True)
+
+
+class AiModelManager(models.Manager):
+    """
+    Manager for AI models with custom query methods.
+    """
+
+    def get_by_natural_key(self, name: str) -> "AiModel":
+        """
+        Return the model with the given name.
+        """
+        return self.get(name=name)
+
+
+class AiModel(models.Model):
+    """
+    Represents a generic AiModel.
+    ModelMeta objects have a foreign key to this model.
+    Here we gather high-level information about the model.
+    this contains the name, description, labels, and version of the model.
+
+    Attributes:
+        name (str): The name of the model.
+        name_de (str): The German name of the model.
+        name_en (str): The English name of the model.
+        description (str): A description of the model.
+        model_type (str): The type of the model.
+        model_subtype (str): The subtype of the model.
+        video_segmentation_labels (QuerySet): The labels for video segmentation.
+    """
+
+    objects = AiModelManager()
+
+    name = models.CharField(max_length=255, unique=True)
+    name_de = models.CharField(max_length=255, blank=True, null=True)
+    name_en = models.CharField(max_length=255, blank=True, null=True)
+    description = models.TextField(blank=True, null=True)
+    model_type = models.CharField(max_length=255, blank=True, null=True)
+    model_subtype = models.CharField(max_length=255, blank=True, null=True)
+    video_segmentation_labelset = models.ForeignKey(
+        "VideoSegmentationLabelSet",
+        on_delete=models.CASCADE,
+        related_name="ai_models",
+        blank=True,
+        null=True,
+    )
+    active_meta = models.ForeignKey(
+        "ModelMeta",
+        on_delete=models.SET_NULL,
+        related_name="active_model",
+        blank=True,
+        null=True,
+    )
+
+    @classmethod
+    def set_active_model_meta(cls, model_name: str, meta_name: str, meta_version: int):
+        """
+        Set the active model.
+        """
+        from endoreg_db.models import ModelMeta
+
+        model = cls.objects.get(name=model_name)
+        assert model is not None, "Model not found"
+
+        ic(f"Getting model meta for {model_name} {meta_name} {meta_version}")
+
+        model_meta = ModelMeta.objects.get(
+            name=meta_name, model=model, version=meta_version
+        )
+        assert model_meta is not None, "ModelMeta not found"
+
+        model.active_meta = model_meta
+        model.save()
+
+        ic(
+            f"Set active model meta for {model_name} to {meta_name} version {meta_version}"
+        )
+
+    def natural_key(self):
+        """
+        Return the natural key for this model.
+        """
+        return (self.name,)
+
+    def __str__(self):
+        return str(self.name)

endoreg_db/models/ai_model/lightning/__init__.py

@@ -0,0 +1,3 @@
+from .inference_dataset import InferenceDataset
+from .multilabel_classification_net import MultiLabelClassificationNet
+from .predict import Classifier