endoreg-db 0.4.5__py3-none-any.whl → 0.8.6.3__py3-none-any.whl

endoreg_db/models/data_file/video_segment.py

@@ -1,107 +0,0 @@
-from django.db import models
-import numpy as np
-from ..annotation import ImageClassificationAnnotation
-
-def find_segments_in_prediction_array(prediction_array: np.array, min_frame_len: int):
-    """
-    Expects a prediction array of shape (num_frames) and a minimum frame length.
-    Returns a list of tuples (start_frame_number, end_frame_number) that represent the segments.
-    """
-    # Add False to the beginning and end to detect changes at the array boundaries
-    padded_prediction = np.pad(prediction_array, (1, 1), 'constant', constant_values=False)
-    
-    # Find the start points and end points of the segments
-    diffs = np.diff(padded_prediction.astype(int))
-    segment_starts = np.where(diffs == 1)[0]
-    segment_ends = np.where(diffs == -1)[0]
-    
-    # Filter segments based on min_frame_len
-    segments = [(start, end) for start, end in zip(segment_starts, segment_ends) if end - start >= min_frame_len]
-    
-    return segments
-
-class AbstractLabelVideoSegment(models.Model):
-    video = None # Placeholder for the video field, to be defined in derived classes
-    prediction_meta = None # Placeholder for the prediction_meta field, to be defined in derived classes
-    start_frame_number = models.IntegerField()
-    end_frame_number = models.IntegerField()
-    source = models.ForeignKey("InformationSource", on_delete=models.CASCADE)
-    label = models.ForeignKey("Label", on_delete=models.CASCADE)
-
-    class Meta:
-        abstract = True
-
-    def __str__(self):
-        return self.video.file.path + " Label - " + self.label.name + " - " + str(self.start_frame_number) + " - " + str(self.end_frame_number)
-    
-    def get_frames(self):
-        return self.video.get_frame_range(self.start_frame_number, self.end_frame_number)
-    
-    def get_annotations(self) -> ImageClassificationAnnotation.objects:
-        frames = self.get_frames()
-        annotations = ImageClassificationAnnotation.objects.filter(frame__in=frames, label=self.label)
-
-        return annotations
-    
-    def get_frames_without_annotation(self):
-        """
-        Get a frame without an annotation.
-        """
-        assert 1 == 2, "This method should be overridden in derived classes"
-
-    def get_segment_len_in_s(self):
-        return (self.end_frame_number - self.start_frame_number) / self.video.fps
-
-class LegacyLabelVideoSegment(AbstractLabelVideoSegment):
-    video = models.ForeignKey("LegacyVideo", on_delete=models.CASCADE)
-    prediction_meta = models.ForeignKey("LegacyVideoPredictionMeta", on_delete=models.CASCADE, related_name="video_segments")
-
-    def get_video_model(self):
-        from endoreg_db.models.data_file.video import LegacyVideo
-        return LegacyVideo
-
-    def get_annotations(self) -> ImageClassificationAnnotation.objects:
-        frames = self.get_frames()
-        annotations = ImageClassificationAnnotation.objects.filter(legacy_frame__in=frames, label=self.label)
-
-        return annotations
-
-    def get_frames_without_annotation(self, n_frames):
-        """
-        Get a frame without an annotation.
-        """
-        frames = self.get_frames()
-        annotations = ImageClassificationAnnotation.objects.filter(legacy_frame__in=frames, label=self.label)
-
-        annotated_frames = [annotation.legacy_frame for annotation in annotations]
-        frames_without_annotation = [frame for frame in frames if frame not in annotated_frames]
-
-        # draw n random frames
-        if len(frames_without_annotation) > n_frames:
-            frames_without_annotation = np.random.choice(frames_without_annotation, n_frames, replace=False)
-
-        return frames_without_annotation
-    
-class LabelVideoSegment(AbstractLabelVideoSegment):
-    video = models.ForeignKey("Video", on_delete=models.CASCADE)
-    prediction_meta = models.ForeignKey("VideoPredictionMeta", on_delete=models.CASCADE, related_name="video_segments")
-
-    def get_video_model(self):
-        from endoreg_db.models.data_file.video import Video
-        return Video
-
-    def get_frames_without_annotation(self, n_frames):
-        """
-        Get a frame without an annotation.
-        """
-        frames = self.get_frames()
-        annotations = ImageClassificationAnnotation.objects.filter(frame__in=frames, label=self.label)
-
-        annotated_frames = [annotation.frame for annotation in annotations]
-        frames_without_annotation = [frame for frame in frames if frame not in annotated_frames]
-
-        # draw n random frames
-        if len(frames_without_annotation) > n_frames:
-            frames_without_annotation = np.random.choice(frames_without_annotation, n_frames, replace=False)
-
-        return frames_without_annotation

endoreg_db/models/disease.py

@@ -1,56 +0,0 @@
-from django.db import models
-
-class DiseaseManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class Disease(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 = DiseaseManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-class DiseaseClassificationManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class DiseaseClassification(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)
-
-    disease = models.ForeignKey(Disease, on_delete=models.CASCADE)
-
-    objects = DiseaseClassificationManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name
-    
-class DiseaseClassificationChoiceManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class DiseaseClassificationChoice(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)
-
-    disease_classification = models.ForeignKey(DiseaseClassification, on_delete=models.CASCADE)
-
-    objects = DiseaseClassificationChoiceManager()
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name

endoreg_db/models/emission/__init__.py

@@ -1 +0,0 @@
-from .emission_factor import EmissionFactor

endoreg_db/models/emission/emission_factor.py

@@ -1,20 +0,0 @@
-from django.db import models
-
-class EmissionFactorManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class EmissionFactor(models.Model):
-    objects = EmissionFactorManager()
-
-    name = models.CharField(max_length=255)
-    name_de = models.CharField(max_length=255, null=True)
-    name_en = models.CharField(max_length=255, null=True)
-    unit = models.ForeignKey("Unit", on_delete=models.SET_NULL, null=True)
-    value = models.FloatField()
-    
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name

endoreg_db/models/event.py

@@ -1,22 +0,0 @@
-from django.db import models
-
-class Event(models.Model):
-    """
-    A class representing an event.
-
-    Attributes:
-        name (str): The name of the event.
-        name_de (str): The German name of the event.
-        name_en (str): The English name of the event.
-        description (str): A description of the event.
-    """
-    name = models.CharField(max_length=100, unique=True)
-    name_de = models.CharField(max_length=100, blank=True, null=True)
-    name_en = models.CharField(max_length=100, blank=True, null=True)
-    description = models.TextField(blank=True, null=True)
-
-    def natural_key(self):
-        return (self.name,)
-
-    def __str__(self):
-        return self.name

endoreg_db/models/examination/__init__.py

@@ -1,4 +0,0 @@
-from .examination import Examination
-from .examination_type import ExaminationType
-from .examination_time import ExaminationTime
-from .examination_time_type import ExaminationTimeType

endoreg_db/models/examination/examination.py

@@ -1,26 +0,0 @@
-from django.db import models
-
-class ExaminationManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class Examination(models.Model):
-    name = models.CharField(max_length=100, unique=True)
-    name_de = models.CharField(max_length=100, blank=True, null=True)
-    name_en = models.CharField(max_length=100, blank=True, null=True)
-    examination_types = models.ManyToManyField('ExaminationType', blank=True)
-    objects = ExaminationManager()
-    date = models.DateField(blank=True, null=True)
-    time = models.TimeField(blank=True, null=True)
-
-    def __str__(self):
-        return self.name
-    
-    def natural_key(self):
-        return (self.name,)
-
-    class Meta:
-        verbose_name = 'Examination'
-        verbose_name_plural = 'Examinations'
-        ordering = ['name']
-

endoreg_db/models/examination/examination_time.py

@@ -1,27 +0,0 @@
-from django.db import models
-from rest_framework import serializers
-
-class ExaminationTimeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class ExaminationTime(models.Model):
-    name = models.CharField(max_length=100, unique=True)
-    name_de = models.CharField(max_length=100, blank=True, null=True)
-    name_en = models.CharField(max_length=100, blank=True, null=True)
-    start_time = models.TimeField(blank=True, null=True)
-    time_types = models.ManyToManyField('ExaminationTimeType', blank=True)
-    end_time = models.TimeField(blank=True, null=True)
-    objects = ExaminationTimeManager()
-
-    def __str__(self):
-        return self.name
-    
-    def natural_key(self):
-        return (self.name,)
-
-    class Meta:
-        verbose_name = 'Examination Time'
-        verbose_name_plural = 'Examination Times'
-        ordering = ['name']
-

endoreg_db/models/examination/examination_time_type.py

@@ -1,24 +0,0 @@
-from django.db import models
-
-class ExaminationTimeTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class ExaminationTimeType(models.Model):
-    objects = ExaminationTimeTypeManager()
-    name = models.CharField(max_length=100, unique=True)
-    name_de = models.CharField(max_length=100, blank=True, null=True)
-    name_en = models.CharField(max_length=100, blank=True, null=True)
-    examinations = models.ManyToManyField('Examination', blank=True)
-
-    def __str__(self):
-        return self.name
-    
-    def natural_key(self):
-        return (self.name,)
-
-    class Meta:
-        verbose_name = 'Examination Time Type'
-        verbose_name_plural = 'Examination Time Types'
-        ordering = ['name']
-

endoreg_db/models/examination/examination_type.py

@@ -1,18 +0,0 @@
-from django.db import models
-
-class ExaminationTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class ExaminationType(models.Model):
-    objects = ExaminationTypeManager()
-    name = models.CharField(max_length=100, unique=True)
-    name_de = models.CharField(max_length=100, blank=True, null=True)
-    name_en = models.CharField(max_length=100, blank=True, null=True)
-
-    def __str__(self):
-        return self.name_en
-    
-    def natural_key(self):
-        return (self.name,)
-    

endoreg_db/models/hardware/__init__.py

@@ -1,2 +0,0 @@
-from .endoscopy_processor import EndoscopyProcessor
-from .endoscope import Endoscope, EndoscopeType

endoreg_db/models/hardware/endoscope.py

@@ -1,44 +0,0 @@
-from django.db import models
-
-class EndoscopeManager(models.Manager):
-    def get_by_natural_key(self, name, sn):
-        return self.get(name=name, sn=sn)
-    
-class Endoscope(models.Model):
-    objects = EndoscopeManager()
-    
-    name = models.CharField(max_length=255)
-    sn = models.CharField(max_length=255)
-    
-    def natural_key(self):
-        return (self.name, self.sn)
-    
-    def __str__(self):
-        return self.name
-    
-    class Meta:
-        ordering = ['name']
-        verbose_name = 'Endoscope'
-        verbose_name_plural = 'Endoscopes'
-
-class EndoscopeTypeManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-    
-class EndoscopeType(models.Model):
-    objects = EndoscopeTypeManager()
-    
-    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)
-    
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name
-    
-    class Meta:
-        ordering = ['name']
-        verbose_name = 'Endoscope Type'
-        verbose_name_plural = 'Endoscope Types'

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/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

@@ -1,24 +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)
-    vpn_service_status = models.BooleanField(default=False)
-    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)
-
-    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 *