endoreg-db 0.5.2__py3-none-any.whl → 0.6.0__py3-none-any.whl

endoreg_db/migrations/0002_anonymizedimagelabel_anonymousimageannotation_and_more.py

@@ -1,55 +0,0 @@
-# Generated by Django 4.2.15 on 2024-08-28 11:05
-
-import django.core.files.storage
-import django.core.validators
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('endoreg_db', '0001_initial'),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name='AnonymizedImageLabel',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('name', models.CharField(max_length=255, unique=True)),
-                ('description', models.TextField(blank=True, null=True)),
-            ],
-        ),
-        migrations.CreateModel(
-            name='AnonymousImageAnnotation',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('image_name', models.CharField(max_length=255)),
-                ('slug', models.SlugField(blank=True, null=True, unique=True)),
-                ('polyp_count', models.IntegerField()),
-                ('comments', models.CharField(max_length=255)),
-                ('gender', models.CharField(max_length=255)),
-                ('name_image_url', models.CharField(max_length=255)),
-                ('date_created', models.DateTimeField(auto_now_add=True)),
-                ('label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.label')),
-            ],
-        ),
-        migrations.AlterField(
-            model_name='rawpdffile',
-            name='file',
-            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(location='/home/agl-admin/agl-validator-backend/agl_validator_backend/erc_data/raw_pdf'), upload_to='raw_pdf/', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['pdf'])]),
-        ),
-        migrations.CreateModel(
-            name='DroppedName',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('name', models.CharField(max_length=255)),
-                ('gender', models.CharField(max_length=255)),
-                ('x', models.FloatField()),
-                ('y', models.FloatField()),
-                ('name_image_url', models.CharField(max_length=255)),
-                ('annotation', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='dropped_names', to='endoreg_db.anonymousimageannotation')),
-            ],
-        ),
-    ]

endoreg_db/migrations/0003_anonymousimageannotation_original_image_url_and_more.py

@@ -1,39 +0,0 @@
-# Generated by Django 4.2.15 on 2024-08-29 07:15
-
-from django.db import migrations, models
-import django.db.models.deletion
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('endoreg_db', '0002_anonymizedimagelabel_anonymousimageannotation_and_more'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='anonymousimageannotation',
-            name='original_image_url',
-            field=models.CharField(default='https://example.com/placeholder.jpg', max_length=255),
-        ),
-        migrations.AddField(
-            model_name='anonymousimageannotation',
-            name='processed',
-            field=models.BooleanField(default=False),
-        ),
-        migrations.AddField(
-            model_name='droppedname',
-            name='box_coordinates',
-            field=models.CharField(blank=True, max_length=255, null=True),
-        ),
-        migrations.AlterField(
-            model_name='anonymousimageannotation',
-            name='comments',
-            field=models.TextField(blank=True, null=True),
-        ),
-        migrations.AlterField(
-            model_name='anonymousimageannotation',
-            name='label',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.anonymizedimagelabel'),
-        ),
-    ]

endoreg_db/migrations/0004_alter_rawpdffile_file.py

@@ -1,20 +0,0 @@
-# Generated by Django 4.2.14 on 2024-09-04 19:48
-
-import django.core.files.storage
-import django.core.validators
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('endoreg_db', '0003_anonymousimageannotation_original_image_url_and_more'),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name='rawpdffile',
-            name='file',
-            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(location='/home/agl-admin/agl_anonymizer/agl_anonymizer/erc_data/raw_pdf'), upload_to='raw_pdf/', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['pdf'])]),
-        ),
-    ]

endoreg_db/migrations/0005_uploadedfile_alter_rawpdffile_file_anonymizedfile.py

@@ -1,40 +0,0 @@
-# Generated by Django 4.2.15 on 2024-09-17 11:46
-
-import django.core.files.storage
-import django.core.validators
-from django.db import migrations, models
-import django.db.models.deletion
-import django.utils.timezone
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('endoreg_db', '0004_alter_rawpdffile_file'),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name='UploadedFile',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('original_file', models.FileField(upload_to='uploads/original/')),
-                ('upload_date', models.DateTimeField(default=django.utils.timezone.now)),
-                ('description', models.TextField(blank=True, null=True)),
-            ],
-        ),
-        migrations.AlterField(
-            model_name='rawpdffile',
-            name='file',
-            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(location='/mnt/hdd-sensitive/Pseudo/import/pdf'), upload_to='raw_pdf/', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['pdf'])]),
-        ),
-        migrations.CreateModel(
-            name='AnonymizedFile',
-            fields=[
-                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('anonymized_file', models.FileField(upload_to='uploads/anonymized/')),
-                ('anonymization_date', models.DateTimeField(default=django.utils.timezone.now)),
-                ('original_file', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, related_name='anonymized_file', to='endoreg_db.uploadedfile')),
-            ],
-        ),
-    ]

endoreg_db/migrations/0006_alter_rawpdffile_file.py

@@ -1,20 +0,0 @@
-# Generated by Django 5.1.1 on 2024-10-01 16:31
-
-import django.core.files.storage
-import django.core.validators
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('endoreg_db', '0005_uploadedfile_alter_rawpdffile_file_anonymizedfile'),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name='rawpdffile',
-            name='file',
-            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(location='/home/agl-admin/dev/agl-monitor-flake/agl_monitor/erc_data/raw_pdf'), upload_to='raw_pdf/', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['pdf'])]),
-        ),
-    ]

endoreg_db/migrations/0007_networkdevicelogentry_datetime_and_more.py

@@ -1,43 +0,0 @@
-# Generated by Django 5.1.1 on 2024-10-12 15:28
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('endoreg_db', '0006_alter_rawpdffile_file'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='networkdevicelogentry',
-            name='datetime',
-            field=models.DateTimeField(blank=True, default=None, null=True),
-        ),
-        migrations.AddField(
-            model_name='networkdevicelogentry',
-            name='ping_vpn',
-            field=models.BooleanField(default=False),
-        ),
-        migrations.AddField(
-            model_name='networkdevicelogentry',
-            name='ping_www',
-            field=models.BooleanField(default=False),
-        ),
-        migrations.AddField(
-            model_name='networkdevicelogentry',
-            name='vpn_service_restart_attempt',
-            field=models.BooleanField(default=False),
-        ),
-        migrations.AddField(
-            model_name='networkdevicelogentry',
-            name='vpn_service_restart_success',
-            field=models.BooleanField(blank=True, null=True),
-        ),
-        migrations.AddField(
-            model_name='networkdevicelogentry',
-            name='vpn_service_status',
-            field=models.BooleanField(default=False),
-        ),
-    ]

endoreg_db/migrations/0008_networkdevicelogentry_aglnet_ip_and_more.py

@@ -1,28 +0,0 @@
-# Generated by Django 5.1.1 on 2024-10-12 16:13
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('endoreg_db', '0007_networkdevicelogentry_datetime_and_more'),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name='networkdevicelogentry',
-            name='aglnet_ip',
-            field=models.GenericIPAddressField(blank=True, null=True),
-        ),
-        migrations.AddField(
-            model_name='networkdevicelogentry',
-            name='hostname',
-            field=models.CharField(blank=True, max_length=255, null=True),
-        ),
-        migrations.AddField(
-            model_name='networkdevicelogentry',
-            name='transferred_to_host',
-            field=models.BooleanField(default=False),
-        ),
-    ]

endoreg_db/migrations/0009_alter_networkdevicelogentry_vpn_service_status.py

@@ -1,18 +0,0 @@
-# Generated by Django 5.1.1 on 2024-10-12 16:51
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('endoreg_db', '0008_networkdevicelogentry_aglnet_ip_and_more'),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name='networkdevicelogentry',
-            name='vpn_service_status',
-            field=models.CharField(blank=True, max_length=255, null=True),
-        ),
-    ]

endoreg_db/migrations/0010_remove_networkdevicelogentry_hostname.py

@@ -1,17 +0,0 @@
-# Generated by Django 5.1.1 on 2024-10-12 16:54
-
-from django.db import migrations
-
-
-class Migration(migrations.Migration):
-
-    dependencies = [
-        ('endoreg_db', '0009_alter_networkdevicelogentry_vpn_service_status'),
-    ]
-
-    operations = [
-        migrations.RemoveField(
-            model_name='networkdevicelogentry',
-            name='hostname',
-        ),
-    ]

endoreg_db/models/__init__.py

@@ -1,73 +0,0 @@
-from .unit import Unit
-from .information_source import InformationSource
-from .center import *
-from .report_reader import ReportReaderConfig, ReportReaderFlag
-from .emission import *
-from .persons import *
-from .network import *
-from .logging import *
-
-from .case_template import *
-# from .other.distribution import (
-#     SingleCategoricalValueDistribution,
-#     NumericValueDistribution,
-#     MultipleCategoricalValueDistribution,
-#     DateValueDistribution,
-# )
-from .rules import (
-    Rule,
-    RuleType,
-    Ruleset,
-    RuleApplicator,
-    Rule
-)
-
-from .disease import Disease, DiseaseClassification, DiseaseClassificationChoice
-from .event import Event
-from .laboratory import LabValue
-from .medication import *
-
-from .examination import (
-    Examination,
-    ExaminationType,
-    ExaminationTime,
-    ExaminationTimeType,
-)
-from .data_file import *
-
-from .patient_examination import PatientExamination
-
-from .label import Label, LabelType, LabelSet
-
-from .annotation import *
-
-from .legacy_data import (
-    LegacyImage,
-)
-
-from .other import *
-
-from .product import *
-
-from .ai_model import (
-    ModelMeta,
-    ModelType,
-    ActiveModel,
-)
-
-from .quiz import *
-
-from .prediction import (
-    ImageClassificationPrediction,
-    LegacyVideoPredictionMeta,
-    VideoPredictionMeta,
-)
-
-from .hardware import (
-    EndoscopyProcessor,
-    Endoscope,
-    EndoscopeType,
-)
-
-from .questionnaires import TtoQuestionnaire
-from .annotation import AnonymousImageAnnotation, AnonymizedImageLabel, DroppedName

endoreg_db/models/ai_model/__init__.py

@@ -1,3 +0,0 @@
-from .model_meta import ModelMeta
-from .model_type import ModelType
-from .active_model import ActiveModel

endoreg_db/models/ai_model/active_model.py

@@ -1,9 +0,0 @@
-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/model_meta.py

@@ -1,24 +0,0 @@
-from django.db import models
-
-class ModelMetaManager(models.Manager):
-    # natural key is name and version
-    def get_by_natural_key(self, name, version):
-        return self.get(name=name, version=version)
-
-class ModelMeta(models.Model):
-    name = models.CharField(max_length=255)
-    version = models.CharField(max_length=255)
-    type = models.ForeignKey("ModelType", on_delete=models.CASCADE, related_name="models")
-    labelset = models.ForeignKey("LabelSet", on_delete=models.CASCADE, related_name="models")
-    weights = models.FileField(upload_to='weights/')
-    
-    description = models.TextField(blank=True, null=True)
-    date_created = models.DateTimeField(auto_now_add=True)
-    objects = ModelMetaManager()
-
-    def natural_key(self):
-        return (self.name, self.version)
-
-    def __str__(self):
-        return f"{self.name} (v: {self.version})"
-

endoreg_db/models/ai_model/model_type.py

@@ -1,26 +0,0 @@
-from django.db import models
-from django.core import serializers
-
-class ModelTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class ModelType(models.Model):
-    """
-    A class representing a model type.
-
-    Attributes:
-        name (str): The name of the model type.
-        description (str): A description of the model type.
-
-    """
-    name = models.CharField(max_length=255)
-    description = models.TextField(blank=True, null=True)
-
-    objects = ModelTypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name

endoreg_db/models/ai_model/utils.py

@@ -1,8 +0,0 @@
-from .model_meta import ModelMeta
-
-# get latest model meta by model name
-
-# TODO MOVE THIS TO A QUERY FILE
-def get_latest_model_meta_by_model_name(model_name):
-    model_meta = ModelMeta.objects.filter(name=model_name).order_by('-version').first()
-    return model_meta

endoreg_db/models/annotation/__init__.py

@@ -1,3 +0,0 @@
-from .image_classification import ImageClassificationAnnotation
-from .binary_classification_annotation_task import LegacyBinaryClassificationAnnotationTask, BinaryClassificationAnnotationTask
-from .anonymized_image_annotation import AnonymousImageAnnotation, DroppedName, AnonymizedImageLabel, AnonymizedFile, UploadedFile

endoreg_db/models/annotation/anonymized_image_annotation.py

@@ -1,60 +0,0 @@
-from django.db import models
-from django.utils.text import slugify
-
-class AnonymizedImageLabel(models.Model):
-    name = models.CharField(max_length=255, unique=True)  # Ensuring label names are unique
-    description = models.TextField(blank=True, null=True)  # Optional description field
-
-    def __str__(self):
-        return self.name
-
-class AnonymousImageAnnotation(models.Model):
-    label = models.ForeignKey(AnonymizedImageLabel, on_delete=models.CASCADE)
-    image_name = models.CharField(max_length=255)
-    original_image_url = models.CharField(max_length=255, default='https://example.com/placeholder.jpg') # Field for the original image
-    slug = models.SlugField(unique=True, blank=True, null=True)
-    polyp_count = models.IntegerField()
-    comments = models.TextField(blank=True, null=True)  # Comments can be longer
-    gender = models.CharField(max_length=255)  # Overall gender (if applicable)
-    name_image_url = models.CharField(max_length=255)
-    date_created = models.DateTimeField(auto_now_add=True)
-    processed = models.BooleanField(default=False)  # Track if this annotation has been processed
-
-    def save(self, *args, **kwargs):
-        if not self.slug:
-            self.slug = slugify(f"{self.label}-{self.image_name}")
-        super().save(*args, **kwargs)
-
-    def __str__(self):
-        return f"{self.image_name} - {self.label}"
-
-class DroppedName(models.Model):
-    annotation = models.ForeignKey(AnonymousImageAnnotation, related_name='dropped_names', on_delete=models.CASCADE)
-    name = models.CharField(max_length=255)
-    gender = models.CharField(max_length=255)  # Gender of the individual name
-    x = models.FloatField()
-    y = models.FloatField()
-    name_image_url = models.CharField(max_length=255)
-    box_coordinates = models.CharField(max_length=255, blank=True, null=True)  # Store box coordinates if needed
-
-    def __str__(self):
-        return f"{self.name} ({self.gender}) at ({self.x}, {self.y})"
-
-from django.db import models
-from django.utils import timezone
-
-class UploadedFile(models.Model):
-    original_file = models.FileField(upload_to='uploads/original/')
-    upload_date = models.DateTimeField(default=timezone.now)
-    description = models.TextField(blank=True, null=True)
-    
-    def __str__(self):
-        return self.original_file.name
-    
-class AnonymizedFile(models.Model):
-    original_file = models.OneToOneField(UploadedFile, on_delete=models.CASCADE, related_name='anonymized_file')
-    anonymized_file = models.FileField(upload_to='uploads/anonymized/')
-    anonymization_date = models.DateTimeField(default=timezone.now)
-    
-    def __str__(self):
-        return f"Anonymized version of {self.original_file.original_file.name}"

endoreg_db/models/annotation/binary_classification_annotation_task.py

@@ -1,80 +0,0 @@
-from django.db import models
-from rest_framework import serializers
-from ..label import Label
-from ..data_file.video_segment import LegacyLabelVideoSegment
-from .image_classification import ImageClassificationAnnotation
-
-ANNOTATION_PER_S_THRESHOLD = 2
-
-def clear_finished_legacy_tasks():
-    # fetch all BinaryClassificationAnnotationTasks that are finished and delete them
-    tasks = LegacyBinaryClassificationAnnotationTask.objects.filter(finished=True)
-
-    # delete tasks with a bulk operation
-    tasks.delete()
-
-def get_legacy_binary_classification_annotation_tasks_by_label(label:Label, n:int=100, legacy=False):
-    clear_finished_legacy_tasks()
-
-    if legacy:
-        # fetch all LegacyLabelVideoSegments with the given label
-        _segments = LegacyLabelVideoSegment.objects.filter(label=label)
-        frames_for_tasks = []
-
-        for segment in _segments:
-            # check if the segment has already been annotated
-            annotations = list(ImageClassificationAnnotation.objects.filter(legacy_frame__in=segment.get_frames(), label=label))
-            segment_len_in_s = segment.get_segment_len_in_s()
-
-            target_annotation_number = segment_len_in_s * ANNOTATION_PER_S_THRESHOLD
-
-            if len(annotations) < target_annotation_number:
-                get_frame_number = int(target_annotation_number - len(annotations))
-                frames = segment.get_frames_without_annotation(get_frame_number)
-                frames_for_tasks.extend(frames)
-
-            if len(frames_for_tasks) >= n:
-                break
-
-        # create tasks
-        tasks = []
-        for frame in frames_for_tasks:
-
-            # get_or_create task
-            task, created = LegacyBinaryClassificationAnnotationTask.objects.get_or_create(
-                label=label,
-                image_path=frame.image.path,
-                frame_id=frame.pk,
-            )
-        
-
-class AbstractBinaryClassificationAnnotationTask(models.Model):
-    label = models.ForeignKey("Label", on_delete=models.CASCADE)
-    is_finished = models.BooleanField(default=False)
-    date_created = models.DateTimeField(auto_now_add=True)
-    date_finished = models.DateTimeField(blank=True, null=True)
-    image_path = models.CharField(max_length=255, blank=True, null=True)
-    image_type = models.CharField(max_length=255, blank=True, null=True)
-    frame_id = models.IntegerField(blank=True, null=True)
-    labelstudio_project_id = models.IntegerField(blank=True, null=True)
-    labelstudio_task_id = models.IntegerField(blank=True, null=True)
-
-    class Meta:
-        abstract = True
-
-class BinaryClassificationAnnotationTask(AbstractBinaryClassificationAnnotationTask):
-    frame = models.ForeignKey("Frame", on_delete=models.CASCADE, related_name="binary_classification_annotation_tasks")
-    image_type = models.CharField(max_length=255, default="frame")
-
-    def get_frame(self):
-        return self.video_segment.get_frame_by_id(self.frame_id)
-
-class LegacyBinaryClassificationAnnotationTask(AbstractBinaryClassificationAnnotationTask):
-    frame = models.ForeignKey("LegacyFrame", on_delete=models.CASCADE, related_name="binary_classification_annotation_tasks")
-    image_type = models.CharField(max_length=255, default="legacy")
-
-    def get_frame(self):
-        return self.frame
-
-
-

endoreg_db/models/annotation/image_classification.py

@@ -1,27 +0,0 @@
-from django.db import models
-
-class ImageClassificationAnnotation(models.Model):
-    """
-    A class representing an image classification annotation.
-
-    Attributes:
-        label (str): The label that was assigned to the image.
-        confidence (float): The confidence that the label is correct.
-        annotator (User): The user that created this annotation.
-        date (datetime.datetime): The date and time when this annotation was created.
-
-    """
-    # Foreign keys to Frame, LegacyFrame, and LegacyImage (only one of these should be set)
-    frame = models.ForeignKey("Frame", on_delete=models.CASCADE, blank=True, null=True, related_name="image_classification_annotations")
-    legacy_frame = models.ForeignKey("LegacyFrame", on_delete=models.CASCADE, blank=True, null=True, related_name="image_classification_annotations")
-    legacy_image = models.ForeignKey("LegacyImage", on_delete=models.CASCADE, blank=True, null=True, related_name="image_classification_annotations")
-
-    label = models.ForeignKey("Label", on_delete=models.CASCADE, related_name="image_classification_annotations")
-    value = models.BooleanField()
-    annotator = models.CharField(max_length=255)
-    date_created = models.DateTimeField(auto_now_add=True)
-    date_modified = models.DateTimeField(auto_now=True)
-
-    def __str__(self):
-        return self.label.name + " - " + str(self.value)
-    

endoreg_db/models/case_template/__init__.py

@@ -1,6 +0,0 @@
-# Django models to define CaseTemplate and CaseTemplateType models 
-# (each with "name" field which acts as a natural key)
-from .case_template_rule import CaseTemplateRule, CaseTemplateRuleType
-from .case_template_rule_value import CaseTemplateRuleValue, CaseTemplateRuleValueType
-from .case_template_type import CaseTemplateType
-from .case_template import CaseTemplate