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

endoreg_db/models/hardware/endoscopy_processor.py

@@ -1,143 +0,0 @@
-from django.db import models
-
-class EndoscopyProcessorManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class EndoscopyProcessor(models.Model):
-    objects = EndoscopyProcessorManager()
-
-    name = models.CharField(max_length=255)
-    image_width = models.IntegerField()
-    image_height = models.IntegerField()
-    # image_fps = models.IntegerField()
-
-    # Roi for endoscope image
-    endoscope_image_x = models.IntegerField()
-    endoscope_image_y = models.IntegerField()
-    endoscope_image_width = models.IntegerField()
-    endoscope_image_height = models.IntegerField()
-
-    # Roi for examination date
-    examination_date_x = models.IntegerField()
-    examination_date_y = models.IntegerField()
-    examination_date_width = models.IntegerField()
-    examination_date_height = models.IntegerField()
-
-    # Roi for examination time
-    examination_time_x = models.IntegerField(blank=True, null=True)
-    examination_time_y = models.IntegerField(blank=True, null=True)
-    examination_time_width = models.IntegerField(blank=True, null=True)
-    examination_time_height = models.IntegerField(blank=True, null=True)
-
-    # Roi for patient first name
-    patient_first_name_x = models.IntegerField()
-    patient_first_name_y = models.IntegerField()
-    patient_first_name_width = models.IntegerField()
-    patient_first_name_height = models.IntegerField()
-
-    # Roi for patient name
-    patient_last_name_x = models.IntegerField()
-    patient_last_name_y = models.IntegerField()
-    patient_last_name_width = models.IntegerField()
-    patient_last_name_height = models.IntegerField()
-
-    # Roi for patient dob
-    patient_dob_x = models.IntegerField()
-    patient_dob_y = models.IntegerField()
-    patient_dob_width = models.IntegerField()
-    patient_dob_height = models.IntegerField()
-
-    # Roi for endoscope type
-    endoscope_type_x = models.IntegerField(blank=True, null=True)
-    endoscope_type_y = models.IntegerField(blank=True, null=True)
-    endoscope_type_width = models.IntegerField(blank=True, null=True)
-    endoscope_type_height = models.IntegerField(blank=True, null=True)
-
-    # Roi for endoscopy sn
-    endoscope_sn_x = models.IntegerField(blank=True, null=True)
-    endoscope_sn_y = models.IntegerField(blank=True, null=True)
-    endoscope_sn_width = models.IntegerField(blank=True, null=True)
-    endoscope_sn_height = models.IntegerField(blank=True, null=True)
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-    
-    def get_roi_endoscope_image(self):
-        return {
-            "x": self.endoscope_image_x,
-            "y": self.endoscope_image_y,
-            "width": self.endoscope_image_width,
-            "height": self.endoscope_image_height
-        }
-    
-    def get_roi_examination_date(self):
-        return {
-            "x": self.examination_date_x,
-            "y": self.examination_date_y,
-            "width": self.examination_date_width,
-            "height": self.examination_date_height
-        }
-    
-    def get_roi_examination_time(self):
-        return {
-            "x": self.examination_time_x,
-            "y": self.examination_time_y,
-            "width": self.examination_time_width,
-            "height": self.examination_time_height
-        }
-    
-    def get_roi_patient_last_name(self):
-        return {
-            "x": self.patient_last_name_x,
-            "y": self.patient_last_name_y,
-            "width": self.patient_last_name_width,
-            "height": self.patient_last_name_height
-        }
-    
-    def get_roi_patient_first_name(self):
-        return {
-            "x": self.patient_first_name_x,
-            "y": self.patient_first_name_y,
-            "width": self.patient_first_name_width,
-            "height": self.patient_first_name_height
-        }
-    
-    def get_roi_patient_dob(self):
-        return {
-            "x": self.patient_dob_x,
-            "y": self.patient_dob_y,
-            "width": self.patient_dob_width,
-            "height": self.patient_dob_height
-        }
-    
-    def get_roi_endoscope_type(self):
-        return {
-            "x": self.endoscope_type_x,
-            "y": self.endoscope_type_y,
-            "width": self.endoscope_type_width,
-            "height": self.endoscope_type_height
-        }
-    
-    def get_roi_endoscopy_sn(self):
-        return {
-            "x": self.endoscope_sn_x,
-            "y": self.endoscope_sn_y,
-            "width": self.endoscope_sn_width,
-            "height": self.endoscope_sn_height
-        }
-    
-    def get_rois(self):
-        return {
-            "endoscope_image": self.get_roi_endoscope_image(),
-            "examination_date": self.get_roi_examination_date(),
-            "examination_time": self.get_roi_examination_time(),
-            "patient_first_name": self.get_roi_patient_first_name(),
-            "patient_last_name": self.get_roi_patient_last_name(),
-            "patient_dob": self.get_roi_patient_dob(),
-            "endoscope_type": self.get_roi_endoscope_type(),
-            "endoscope_sn": self.get_roi_endoscopy_sn()
-        }

endoreg_db/models/information_source.py

@@ -1,29 +0,0 @@
-from django.db import models
-
-def get_prediction_information_source():
-    _source = InformationSource.objects.get(name="prediction")
-
-    # make sure to return only one object
-    assert _source, "No prediction information source found"
-    return _source
-
-class InformationSourceManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class InformationSource(models.Model):
-    objects = InformationSourceManager()
-
-    name = models.CharField(max_length=100)
-    name_de = models.CharField(max_length=100, blank=True, null=True)
-    name_en = models.CharField(max_length=100, blank=True, null=True)
-
-    url = models.URLField(blank=True, null=True)
-    description = models.TextField(blank=True, null=True)
-    date = models.DateField(blank=True, null=True)
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name

endoreg_db/models/label/__init__.py

@@ -1 +0,0 @@
-from .label import Label, LabelType, LabelSet

endoreg_db/models/label/label.py

@@ -1,84 +0,0 @@
-from django.db import models
-
-class LabelTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class LabelType(models.Model):
-    """
-    A class representing a label type.
-
-    Attributes:
-        name (str): The name of the label type.
-        description (str): A description of the label type.
-
-    """
-    name = models.CharField(max_length=255)
-    description = models.TextField(blank=True, null=True)
-
-    objects = LabelTypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-
-
-class LabelManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class Label(models.Model):
-    """
-    A class representing a label.
-
-    Attributes:
-        name (str): The name of the label.
-        label_type (LabelType): The type of the label.
-        description (str): A description of the label.
-
-    """
-    name = models.CharField(max_length=255)
-    label_type = models.ForeignKey("LabelType", on_delete=models.CASCADE, related_name="labels")
-    description = models.TextField(blank=True, null=True)
-
-    objects = LabelManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-
-class LabelSetManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class LabelSet(models.Model):
-    """
-    A class representing a label set.
-
-    Attributes:
-        name (str): The name of the label set.
-        description (str): A description of the label set.
-
-    """
-    name = models.CharField(max_length=255)
-    description = models.TextField(blank=True, null=True)
-    version = models.IntegerField()
-    labels = models.ManyToManyField("Label", related_name="labels")
-    
-    objects = LabelSetManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-    def get_labels_in_order(self):
-        """
-        Get all labels in this label set as list in the correct order.
-        """
-        return list(self.labels.all().order_by('id'))

endoreg_db/models/laboratory/__init__.py

@@ -1 +0,0 @@
-from .lab_value import LabValue

endoreg_db/models/laboratory/lab_value.py

@@ -1,102 +0,0 @@
-from django.db import models
-import warnings
-
-LANG = "de"
-
-class LabValueManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class LabValue(models.Model):
-    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)
-    abbreviation = models.CharField(max_length=10, blank=True, null=True)
-    default_unit = models.ForeignKey('Unit', on_delete=models.CASCADE, blank=True, null=True)
-    numeric_precision = models.IntegerField(default=3)
-    default_single_categorical_value_distribution = models.ForeignKey(
-        'SingleCategoricalValueDistribution',
-        on_delete=models.CASCADE,
-        blank=True, null=True,
-        related_name='default_single_categorical_value_distribution'
-    )
-    default_numerical_value_distribution = models.ForeignKey(
-        'NumericValueDistribution',
-        on_delete=models.CASCADE,
-        blank=True, null=True,
-        related_name='default_numerical_value_distribution'
-    )
-    default_multiple_categorical_value_distribution = models.ForeignKey(
-        'MultipleCategoricalValueDistribution',
-        on_delete=models.CASCADE,
-        blank=True, null=True,
-        related_name='default_multiple_categorical_value_distribution'
-    )
-    default_date_value_distribution = models.ForeignKey(
-        'DateValueDistribution',
-        on_delete=models.CASCADE,
-        blank=True, null=True,
-        related_name='default_date_value_distribution'
-    )
-    default_normal_range = models.JSONField(blank=True, null=True)
-    normal_range_age_dependent = models.BooleanField(default=False)
-    normal_range_gender_dependent = models.BooleanField(default=False)
-    normal_range_special_case = models.BooleanField(default=False)
-    objects = LabValueManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-    def get_default_default_distribution(self):
-        if self.default_single_categorical_value_distribution:
-            return self.default_single_categorical_value_distribution
-        elif self.default_numerical_value_distribution:
-            return self.default_numerical_value_distribution
-        elif self.default_multiple_categorical_value_distribution:
-            return self.default_multiple_categorical_value_distribution
-        elif self.default_date_value_distribution:
-            return self.default_date_value_distribution
-        else:
-            warnings.warn("No default distribution set for lab value")
-            return None
-    
-    def get_normal_range(self, age=None, gender=None):
-        age_dependent = self.normal_range_age_dependent
-        gender_dependent = self.normal_range_gender_dependent
-        special_case = self.normal_range_special_case
-
-        min_value = None
-        max_value = None
-
-        if not age_dependent and \
-        not gender_dependent and \
-        not special_case:
-            min_value = self.default_normal_range.get('min', None)
-            max_value = self.default_normal_range.get('max', None)
-
-        if age_dependent: 
-            # get normal range for age)
-            warnings.warn("Age dependent normal range not implemented yet")
-            pass
-        
-        if gender_dependent:
-            if not gender:
-                warnings.warn("Calling get_normal_range with gender_dependent=True requires gender to be set, choosing by random")
-                # set gender to either "male" or "female"
-                from random import choice
-                choices = ["male", "female"]
-                gender = choice(choices)
-
-            default_range_dict = self.default_normal_range.get(gender, {})
-            min_value = default_range_dict.get('min', None)
-            max_value = default_range_dict.get('max', None)
-
-        if special_case:
-            # get normal range for special case
-            warnings.warn("Special case normal range not implemented yet")
-
-        return min_value, max_value
-

endoreg_db/models/legacy_data/__init__.py

@@ -1,3 +0,0 @@
-from ..data_file.frame import LegacyFrame
-from .image import LegacyImage
-from ..data_file.video import LegacyVideo

endoreg_db/models/legacy_data/image.py

@@ -1,34 +0,0 @@
-from django.db import models
-from ..label.label import Label
-from ..annotation.image_classification import ImageClassificationAnnotation
-
-class LegacyImage(models.Model):
-    # Add any other fields you need to store frame-related information
-    image = models.ImageField(upload_to="legacy_images")  # Or some other field type, depending on how you're storing the frame
-    suffix = models.CharField(max_length=255)
-    # ImageClassificationAnnotation has a foreign key to this model (related name: image_classification_annotations)
-
-    def get_classification_annotations(self):
-        """
-        Get all image classification annotations for this image.
-        """
-        return ImageClassificationAnnotation.objects.filter(legacy_image=self)
-    
-    def get_classification_annotations_by_label(self, label:Label):
-        """
-        Get all image classification annotations for this image with the given label.
-        """
-        return ImageClassificationAnnotation.objects.filter(legacy_image=self, label=label)
-    
-    def get_classification_annotations_by_value(self, value:bool):
-        """
-        Get all image classification annotations for this image with the given value.
-        """
-        return ImageClassificationAnnotation.objects.filter(legacy_image=self, value=value)
-    
-    def get_classification_annotations_by_label_and_value(self, label:Label, value:bool):
-        """
-        Get all image classification annotations for this image with the given label and value.
-        """
-        return ImageClassificationAnnotation.objects.filter(legacy_image=self, label=label, value=value)
-    

endoreg_db/models/logging/__init__.py

@@ -1,4 +0,0 @@
-from .base import AbstractLogEntry
-from .network_device import NetworkDeviceLogEntry
-from .log_type import LogType
-from .agl_service import AglServiceLogEntry

endoreg_db/models/logging/agl_service.py

@@ -1,19 +0,0 @@
-from django.db import models
-from .base import AbstractLogEntry
-
-class AglServiceLogEntry(AbstractLogEntry):
-    """
-    Model for log entries related to AGL services.
-    """
-    service = models.ForeignKey("AglService", on_delete=models.CASCADE)
-    device = models.ForeignKey(
-        "NetworkDevice", on_delete=models.CASCADE, null=True, blank=True
-    )
-    log_type = models.ForeignKey("LogType", on_delete=models.CASCADE, null=True, blank=True)
-
-    class Meta:
-        verbose_name = "AGL Service Log Entry"
-        verbose_name_plural = "AGL Service Log Entries"
-
-    def __str__(self):
-        return f"{self.timestamp} - {self.user} - {self.ip_address} - {self.service} - {self.message}"

endoreg_db/models/logging/base.py

@@ -1,22 +0,0 @@
-# django model for logging, first define an abstract base model
-from django.db import models
-from django.conf import settings
-
-class AbstractLogEntry(models.Model):
-    """
-    Abstract base model for log entries.
-    """
-
-    class Meta:
-        abstract = True
-
-    timestamp = models.DateTimeField(auto_now_add=True)
-    user = models.ForeignKey(settings.AUTH_USER_MODEL, on_delete=models.SET_NULL, null=True, blank=True)
-    ip_address = models.GenericIPAddressField(null=True, blank=True)
-    user_agent = models.CharField(max_length=256, null=True, blank=True)
-    message = models.TextField()
-    json_content = models.JSONField(null=True, blank=True)
-    
-
-    def __str__(self):
-        return f"{self.timestamp} - {self.user} - {self.ip_address} - {self.message}"

endoreg_db/models/logging/log_type.py

@@ -1,23 +0,0 @@
-from django.db import models
-
-class LogTypeManager(models.Manager):
-    # Custom manager for LogType; defines name as natural key
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-
-class LogType(models.Model):
-    name = models.CharField(max_length=255)
-    description = models.CharField(max_length=255)
-    created = models.DateTimeField(auto_now_add=True)
-    updated = models.DateTimeField(auto_now=True)
-    objects = LogTypeManager()
-    
-    def __str__(self):
-        return self.name
-    
-    class Meta:
-        ordering = ['name']
-        
-    def natural_key(self):
-        return (self.name,)

endoreg_db/models/logging/network_device.py

@@ -1,27 +0,0 @@
-from django.db import models
-from .base import AbstractLogEntry
-
-class NetworkDeviceLogEntry(AbstractLogEntry):
-    """
-    Model for log entries related to network devices.
-    """
-    device = models.ForeignKey("NetworkDevice", on_delete=models.CASCADE)
-    log_type = models.ForeignKey("LogType", on_delete=models.CASCADE, null=True, blank=True)
-
-    datetime = models.DateTimeField(default=None, null=True, blank=True)
-    # hostname = models.CharField(max_length=255, null=True, blank=True)
-    aglnet_ip = models.GenericIPAddressField(null=True, blank=True)
-    vpn_service_status = models.CharField(max_length=255, null=True, blank=True)
-    vpn_service_restart_attempt = models.BooleanField(default=False)
-    vpn_service_restart_success = models.BooleanField(null=True, blank=True)
-    ping_vpn = models.BooleanField(default=False)
-    ping_www = models.BooleanField(default=False)
-    transferred_to_host = models.BooleanField(default=False)
-
-    class Meta:
-        verbose_name = "Network Device Log Entry"
-        verbose_name_plural = "Network Device Log Entries"
-
-    def __str__(self):
-        return f"{self.timestamp} - {self.user} - {self.ip_address} - {self.device} - {self.message}"
-

endoreg_db/models/medication/__init__.py

@@ -1 +0,0 @@
-from .medication import *

endoreg_db/models/medication/medication.py

@@ -1,148 +0,0 @@
-from django.db import models
-
-class MedicationManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class Medication(models.Model):
-    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)
-    adapt_to_renal_function = models.BooleanField(default = False)
-    adapt_to_hepatic_function = models.BooleanField(default=False)
-    adapt_to_indication = models.BooleanField(default=False)
-    adapt_to_age = models.BooleanField(default=False)
-    adapt_to_weight = models.BooleanField(default=False)
-    adapt_to_risk = models.BooleanField(default=False)
-    default_unit = models.ForeignKey('Unit', on_delete=models.CASCADE)
-
-
-    objects = MedicationManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-class MedicationScheduleManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class MedicationSchedule(models.Model):
-    name = models.CharField(max_length=255)
-    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)
-    medication = models.ForeignKey("Medication", on_delete=models.CASCADE)
-    unit = models.ForeignKey("Unit", on_delete=models.CASCADE)
-    therapy_duration_d = models.FloatField(blank=True, null=True)
-    dose = models.FloatField()
-    intake_times = models.ManyToManyField(
-        "MedicationIntakeTime", 
-    )
-
-    objects = MedicationScheduleManager()
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-    
-    
-class MedicationIntakeTimeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class MedicationIntakeTime(models.Model):
-    name = models.CharField(max_length=255)
-    name_de = models.CharField(max_length=255, blank=True, null=True)
-    name_en = models.CharField(max_length=255, blank=True, null=True)
-    repeats = models.CharField(max_length=20, default = "daily")
-    time = models.TimeField()
-
-    objects = MedicationIntakeTimeManager()
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-
-# IMPLEMENT MEDICATION INDICATION TYPE
-class MedicationIndicationTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class MedicationIndicationType(models.Model):
-    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)
-
-    objects = MedicationIndicationTypeManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-    @classmethod
-    def get_random_indication_by_type(cls, name) -> "MedicationIndication":
-        return cls.objects.get(name=name).medication_indications.order_by('?').first()
-    
-
-    def get_random_medication_indication(self):
-        from endoreg_db.models import MedicationIndication
-        return MedicationIndication.objects.filter(indication_type=self).order_by('?').first()
-
-
-class MedicationIndicationManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class MedicationIndication(models.Model):
-    name = models.CharField(max_length=255, unique=True)
-    indication_type = models.ForeignKey(
-        "MedicationIndicationType", on_delete=models.CASCADE, related_name="medication_indications"
-    )
-    medication_schedules = models.ManyToManyField(
-        "MedicationSchedule"
-    )
-    diseases = models.ManyToManyField(
-        "Disease"
-    )
-    events = models.ManyToManyField(
-        "Event"
-    )
-    classification_choices = models.ManyToManyField(
-        "DiseaseClassificationChoice"
-    )
-    sources = models.ManyToManyField(
-        "InformationSource"
-    )
-
-    def get_indication_links(self):
-        links = {
-            "medication_schedules": self.medication_schedules,
-            "diseases": self.diseases,
-            "events": self.events,
-            "classification_choices": self.classification_choices
-        }
-
-    objects = MedicationIndicationManager()
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-    
-    def create_patient_medication_schedules(self, patient):
-        from endoreg_db.models import PatientMedicationSchedule
-        for medication_schedule in self.medication_schedules.all():
-            PatientMedicationSchedule.objects.create(
-                patient=patient,
-                medication_schedule=medication_schedule
-            )

endoreg_db/models/network/__init__.py

@@ -1,3 +0,0 @@
-from .network_device import NetworkDevice
-from .network_device_type import NetworkDeviceType
-from .agl_service import AglService