endoreg-db 0.3.4__py3-none-any.whl → 0.3.6__py3-none-any.whl

endoreg_db/models/data_file/video/__init__.py

@@ -1,7 +1,7 @@
-from .video import (
-    Video,
-    LegacyVideo,
-)
-from ..metadata import (
-    VideoImportMeta,
+from .video import (
+    Video,
+    LegacyVideo,
+)
+from ..metadata import (
+    VideoImportMeta,
 )

endoreg_db/models/data_file/video/import_meta.py

@@ -1,25 +1,25 @@
-# from django.db import models
-
-# class VideoImportMeta(models.Model):
-#     processor = models.ForeignKey('EndoscopyProcessor', on_delete=models.CASCADE)
-#     endoscope = models.ForeignKey('Endoscope', on_delete=models.CASCADE, blank=True, null=True)
-#     center = models.ForeignKey('Center', on_delete=models.CASCADE)
-#     video_anonymized = models.BooleanField(default=False)
-#     video_patient_data_detected = models.BooleanField(default=False)
-#     outside_detected = models.BooleanField(default=False)
-#     patient_data_removed = models.BooleanField(default=False)
-#     outside_removed = models.BooleanField(default=False)
-
-#     def __str__(self):
-#         result_html = ""
-
-#         result_html += f"Processor: {self.processor.name}<br>"
-#         result_html += f"Endoscope: {self.endoscope.name}<br>"
-#         result_html += f"Center: {self.center.name}<br>"
-#         result_html += f"Video anonymized: {self.video_anonymized}<br>"
-#         result_html += f"Video patient data detected: {self.video_patient_data_detected}<br>"
-#         result_html += f"Outside detected: {self.outside_detected}<br>"
-#         result_html += f"Patient data removed: {self.patient_data_removed}<br>"
-#         result_html += f"Outside removed: {self.outside_removed}<br>"
-#         return result_html
-    
+# from django.db import models
+
+# class VideoImportMeta(models.Model):
+#     processor = models.ForeignKey('EndoscopyProcessor', on_delete=models.CASCADE)
+#     endoscope = models.ForeignKey('Endoscope', on_delete=models.CASCADE, blank=True, null=True)
+#     center = models.ForeignKey('Center', on_delete=models.CASCADE)
+#     video_anonymized = models.BooleanField(default=False)
+#     video_patient_data_detected = models.BooleanField(default=False)
+#     outside_detected = models.BooleanField(default=False)
+#     patient_data_removed = models.BooleanField(default=False)
+#     outside_removed = models.BooleanField(default=False)
+
+#     def __str__(self):
+#         result_html = ""
+
+#         result_html += f"Processor: {self.processor.name}<br>"
+#         result_html += f"Endoscope: {self.endoscope.name}<br>"
+#         result_html += f"Center: {self.center.name}<br>"
+#         result_html += f"Video anonymized: {self.video_anonymized}<br>"
+#         result_html += f"Video patient data detected: {self.video_patient_data_detected}<br>"
+#         result_html += f"Outside detected: {self.outside_detected}<br>"
+#         result_html += f"Patient data removed: {self.patient_data_removed}<br>"
+#         result_html += f"Outside removed: {self.outside_removed}<br>"
+#         return result_html
+    

endoreg_db/models/data_file/video/video.py

@@ -1,25 +1,25 @@
-from ..base_classes import AbstractVideo
-from django.db import models
-
-from endoreg_db.models.data_file.frame import Frame
-from endoreg_db.models.data_file.frame import LegacyFrame
-
-BATCH_SIZE = 1000
-
-class Video(AbstractVideo):
-    import_meta = models.OneToOneField('VideoImportMeta', on_delete=models.CASCADE, blank=True, null=True)
-    def get_video_model(self):
-        return Video
-
-    def get_frame_model(self):
-        return Frame
-
-
-class LegacyVideo(AbstractVideo):
-    file = models.FileField(upload_to="legacy_videos", blank=True, null=True)
-
-    def get_video_model(self):
-        return LegacyVideo
-
-    def get_frame_model(self):
-        return LegacyFrame
+from ..base_classes import AbstractVideo
+from django.db import models
+
+from endoreg_db.models.data_file.frame import Frame
+from endoreg_db.models.data_file.frame import LegacyFrame
+
+BATCH_SIZE = 1000
+
+class Video(AbstractVideo):
+    import_meta = models.OneToOneField('VideoImportMeta', on_delete=models.CASCADE, blank=True, null=True)
+    def get_video_model(self):
+        return Video
+
+    def get_frame_model(self):
+        return Frame
+
+
+class LegacyVideo(AbstractVideo):
+    file = models.FileField(upload_to="legacy_videos", blank=True, null=True)
+
+    def get_video_model(self):
+        return LegacyVideo
+
+    def get_frame_model(self):
+        return LegacyFrame

endoreg_db/models/data_file/video_segment.py

@@ -1,107 +1,107 @@
-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
+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

@@ -0,0 +1,56 @@
+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

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

endoreg_db/models/emission/emission_factor.py

@@ -0,0 +1,20 @@
+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

@@ -0,0 +1,22 @@
+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 +1,4 @@
-from .examination import Examination
-from .examination_type import ExaminationType
-from .examination_time import ExaminationTime
+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 +1,26 @@
-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']
-
+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 +1,27 @@
-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']
-
+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 +1,24 @@
-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']
-
+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 +1,18 @@
-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,)
-    
+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 +1,2 @@
-from .endoscopy_processor import EndoscopyProcessor
+from .endoscopy_processor import EndoscopyProcessor
 from .endoscope import Endoscope, EndoscopeType