endoreg-db 0.8.9.2__py3-none-any.whl → 0.8.9.10__py3-none-any.whl

endoreg_db/models/media/video/video_file_segments.py

@@ -27,7 +27,11 @@ def _convert_sequences_to_db_segments(
     """
     from ...label import Label, LabelVideoSegment  # Local import for models
 
-    logger.info("Converting sequences to LabelVideoSegments for video %s, prediction meta %s", video.uuid, video_prediction_meta.pk)
+    logger.info(
+        "Converting sequences to LabelVideoSegments for video %s, prediction meta %s",
+        video.video_hash,
+        video_prediction_meta.pk,
+    )
     created_count = 0
     skipped_count = 0
     error_count = 0
@@ -45,14 +49,21 @@ def _convert_sequences_to_db_segments(
         try:
             label = Label.objects.get(name=label_name)  # require pre-existing label
         except Exception as e:
-            logger.error("Could not get or create Label '%s': %s", label_name, e, exc_info=True)
+            logger.error(
+                "Could not get or create Label '%s': %s", label_name, e, exc_info=True
+            )
             error_count += len(sequence_list)
             continue
 
         segments_to_create = []
         for start_frame, end_frame in sequence_list:
             if start_frame > end_frame or start_frame < 0:
-                logger.warning("Skipping invalid sequence for label '%s': start=%d, end=%d", label_name, start_frame, end_frame)
+                logger.warning(
+                    "Skipping invalid sequence for label '%s': start=%d, end=%d",
+                    label_name,
+                    start_frame,
+                    end_frame,
+                )
                 skipped_count += 1
                 continue
 
@@ -68,19 +79,34 @@ def _convert_sequences_to_db_segments(
 
         if segments_to_create:
             try:
-                LabelVideoSegment.objects.bulk_create(segments_to_create, ignore_conflicts=True)
+                LabelVideoSegment.objects.bulk_create(
+                    segments_to_create, ignore_conflicts=True
+                )
                 created_count += len(segments_to_create)
-                logger.debug("Bulk created %d segments for label '%s'", len(segments_to_create), label_name)
+                logger.debug(
+                    "Bulk created %d segments for label '%s'",
+                    len(segments_to_create),
+                    label_name,
+                )
             except Exception as e:
-                logger.error("Error bulk creating segments for label '%s': %s", label_name, e, exc_info=True)
+                logger.error(
+                    "Error bulk creating segments for label '%s': %s",
+                    label_name,
+                    e,
+                    exc_info=True,
+                )
                 error_count += len(segments_to_create)
 
-    newly_created_segments = LabelVideoSegment.objects.filter(video_file=video, prediction_meta=video_prediction_meta, label__name__in=processed_labels)
+    newly_created_segments = LabelVideoSegment.objects.filter(
+        video_file=video,
+        prediction_meta=video_prediction_meta,
+        label__name__in=processed_labels,
+    )
 
     logger.info(
         "Attempting to create state objects for %d potentially new segments (Video: %s, PredictionMeta: %s)",
         newly_created_segments.count(),
-        video.uuid,
+        video.video_hash,
         video_prediction_meta.pk,
     )
 
@@ -90,12 +116,18 @@ def _convert_sequences_to_db_segments(
             if created:
                 state_created_count += 1
         except Exception as e:
-            logger.error("Failed to get or create state for segment %s (Video: %s): %s", segment.pk, video.uuid, e, exc_info=True)
+            logger.error(
+                "Failed to get or create state for segment %s (Video: %s): %s",
+                segment.pk,
+                video.video_hash,
+                e,
+                exc_info=True,
+            )
             state_error_count += 1
 
     logger.info(
         "LabelVideoSegment conversion finished for video %s. Segments Created: %d, Skipped: %d, Errors: %d. States Created: %d, State Errors: %d",
-        video.uuid,
+        video.video_hash,
         created_count,
         skipped_count,
         error_count,
@@ -122,7 +154,9 @@ def _sequences_to_label_video_segments(
     )
 
 
-def _get_outside_segments(video: "VideoFile", outside_label_name: str = "outside") -> "QuerySet[LabelVideoSegment]":
+def _get_outside_segments(
+    video: "VideoFile", outside_label_name: str = "outside"
+) -> "QuerySet[LabelVideoSegment]":
     """Gets LabelVideoSegments marked with the 'outside' label."""
     from ...label import Label, LabelVideoSegment  # Local import for models
 
@@ -133,29 +167,52 @@ def _get_outside_segments(video: "VideoFile", outside_label_name: str = "outside
         logger.warning("Label '%s' not found in the database.", outside_label_name)
         return LabelVideoSegment.objects.none()
     except AttributeError:
-        logger.error("VideoFile instance does not have 'label_video_segments' related manager.")
+        logger.error(
+            "VideoFile instance does not have 'label_video_segments' related manager."
+        )
         return LabelVideoSegment.objects.none()
     except Exception as e:
-        logger.error("Error getting '%s' segments for video %s: %s", outside_label_name, video.uuid, e, exc_info=True)
+        logger.error(
+            "Error getting '%s' segments for video %s: %s",
+            outside_label_name,
+            video.video_hash,
+            e,
+            exc_info=True,
+        )
         return LabelVideoSegment.objects.none()
 
 
-def _get_outside_frame_numbers(video: "VideoFile", outside_label_name: str = "outside") -> Set[int]:
+def _get_outside_frame_numbers(
+    video: "VideoFile", outside_label_name: str = "outside"
+) -> Set[int]:
     """
     Gets a set of frame numbers corresponding to segments labeled as 'outside'.
     """
     outside_segments = _get_outside_segments(video, outside_label_name)
     frame_numbers = set()
     for segment in outside_segments:
-        frame_numbers.update(range(segment.start_frame_number, segment.end_frame_number + 1))
+        frame_numbers.update(
+            range(segment.start_frame_number, segment.end_frame_number + 1)
+        )
     if frame_numbers:
-        logger.info("Found %d frame numbers marked as '%s' for video %s.", len(frame_numbers), outside_label_name, video.uuid)
+        logger.info(
+            "Found %d frame numbers marked as '%s' for video %s.",
+            len(frame_numbers),
+            outside_label_name,
+            video.video_hash,
+        )
     else:
-        logger.info("No frame numbers marked as '%s' found for video %s.", outside_label_name, video.uuid)
+        logger.info(
+            "No frame numbers marked as '%s' found for video %s.",
+            outside_label_name,
+            video.video_hash,
+        )
     return frame_numbers
 
 
-def _get_outside_frames(video: "VideoFile", outside_label_name: str = "outside") -> "QuerySet[Frame]":
+def _get_outside_frames(
+    video: "VideoFile", outside_label_name: str = "outside"
+) -> "QuerySet[Frame]":
     """
     Gets a QuerySet of all unique Frame objects that fall within any segment
     labeled with the specified 'outside_label_name'.
@@ -168,7 +225,10 @@ def _get_outside_frames(video: "VideoFile", outside_label_name: str = "outside")
 
     q_objects: Q | None = None
     for segment in outside_segments:
-        clause = Q(frame_number__gte=segment.start_frame_number, frame_number__lt=segment.end_frame_number)
+        clause = Q(
+            frame_number__gte=segment.start_frame_number,
+            frame_number__lt=segment.end_frame_number,
+        )
         q_objects = clause if q_objects is None else q_objects | clause
 
     if q_objects is None:
@@ -177,11 +237,18 @@ def _get_outside_frames(video: "VideoFile", outside_label_name: str = "outside")
     try:
         return video.frames.filter(q_objects).distinct().order_by("frame_number")
     except Exception as e:
-        logger.error("Error filtering outside frames for video %s: %s", video.uuid, e, exc_info=True)
+        logger.error(
+            "Error filtering outside frames for video %s: %s",
+            video.video_hash,
+            e,
+            exc_info=True,
+        )
         return Frame.objects.none()
 
 
-def _get_outside_frame_paths(video: "VideoFile", outside_label_name: str = "outside") -> List["Path"]:
+def _get_outside_frame_paths(
+    video: "VideoFile", outside_label_name: str = "outside"
+) -> List["Path"]:
     """Gets the file paths of frames that fall within 'outside' segments."""
     from pathlib import Path  # Local import
 
@@ -191,16 +258,28 @@ def _get_outside_frame_paths(video: "VideoFile", outside_label_name: str = "outs
         try:
             frame_paths.append(Path(frame.relative_path))
         except Exception as e:
-            logger.warning("Could not get path for frame %s (Number: %d): %s", frame.pk, frame.frame_number, e)
+            logger.warning(
+                "Could not get path for frame %s (Number: %d): %s",
+                frame.pk,
+                frame.frame_number,
+                e,
+            )
             ic(f"Could not get path for frame {frame.pk}: {e}")
 
-    logger.info("Found %d frame paths within '%s' segments for video %s", len(frame_paths), outside_label_name, video.uuid)
+    logger.info(
+        "Found %d frame paths within '%s' segments for video %s",
+        len(frame_paths),
+        outside_label_name,
+        video.video_hash,
+    )
     return frame_paths
 
 
 def _label_segments_to_frame_annotations(video: "VideoFile"):
     """Generates frame annotations based on existing LabelVideoSegments."""
-    logger.info("Generating frame annotations from segments for video %s", video.uuid)
+    logger.info(
+        "Generating frame annotations from segments for video %s", video.video_hash
+    )
     processed_count = 0
     try:
         for lvs in video.label_video_segments.all():
@@ -210,7 +289,19 @@ def _label_segments_to_frame_annotations(video: "VideoFile"):
                     lvs.generate_annotations()
                     processed_count += 1
                 except Exception as e:
-                    logger.error("Error generating annotations for segment %s (Video %s): %s", lvs.pk, video.uuid, e)
-        logger.info("Processed %d segments for frame annotations for video %s", processed_count, video.uuid)
+                    logger.error(
+                        "Error generating annotations for segment %s (Video %s): %s",
+                        lvs.pk,
+                        video.video_hash,
+                        e,
+                    )
+        logger.info(
+            "Processed %d segments for frame annotations for video %s",
+            processed_count,
+            video.video_hash,
+        )
     except AttributeError:
-        logger.error("Could not generate frame annotations for video %s. 'label_video_segments' related manager not found.", video.uuid)
+        logger.error(
+            "Could not generate frame annotations for video %s. 'label_video_segments' related manager not found.",
+            video.video_hash,
+        )

endoreg_db/models/media/video/video_metadata.py

@@ -18,15 +18,34 @@ class VideoMetadata(models.Model):
     and provides metrics for the correction UI.
     """
 
-    video = models.OneToOneField(VideoFile, on_delete=models.CASCADE, related_name="metadata", help_text="Video file this metadata belongs to")
+    video = models.OneToOneField(
+        VideoFile,
+        on_delete=models.CASCADE,
+        related_name="metadata",
+        help_text="Video file this metadata belongs to",
+    )
 
     # Analysis Results
-    sensitive_frame_count = models.IntegerField(null=True, blank=True, help_text="Number of frames detected as containing sensitive information")
-    sensitive_ratio = models.FloatField(null=True, blank=True, help_text="Ratio of sensitive frames to total frames (0.0-1.0)")
-    sensitive_frame_ids = models.TextField(null=True, blank=True, help_text="JSON array of sensitive frame indices (0-based)")
+    sensitive_frame_count = models.IntegerField(
+        null=True,
+        blank=True,
+        help_text="Number of frames detected as containing sensitive information",
+    )
+    sensitive_ratio = models.FloatField(
+        null=True,
+        blank=True,
+        help_text="Ratio of sensitive frames to total frames (0.0-1.0)",
+    )
+    sensitive_frame_ids = models.TextField(
+        null=True,
+        blank=True,
+        help_text="JSON array of sensitive frame indices (0-based)",
+    )
 
     # Metadata
-    analyzed_at = models.DateTimeField(auto_now=True, help_text="Timestamp of last analysis")
+    analyzed_at = models.DateTimeField(
+        auto_now=True, help_text="Timestamp of last analysis"
+    )
 
     class Meta:
         db_table = "video_metadata"
@@ -34,7 +53,7 @@ class VideoMetadata(models.Model):
         verbose_name_plural = "Video Metadata"
 
     def __str__(self):
-        return f"Metadata for {self.video.uuid} ({self.sensitive_frame_count or 0} sensitive frames)"
+        return f"Metadata for {self.video.video_hash} ({self.sensitive_frame_count or 0} sensitive frames)"
 
     @property
     def has_analysis(self) -> bool:

endoreg_db/models/media/video/video_processing.py

@@ -53,26 +53,57 @@ class VideoProcessingHistory(models.Model):
         (STATUS_CANCELLED, "Cancelled"),
     ]
 
-    video = models.ForeignKey(VideoFile, on_delete=models.CASCADE, related_name="processing_history", help_text="Video file this operation was performed on")
-
-    operation = models.CharField(max_length=50, choices=OPERATION_CHOICES, help_text="Type of processing operation")
-
-    status = models.CharField(max_length=20, choices=STATUS_CHOICES, default=STATUS_PENDING, help_text="Current status of the operation")
+    video = models.ForeignKey(
+        VideoFile,
+        on_delete=models.CASCADE,
+        related_name="processing_history",
+        help_text="Video file this operation was performed on",
+    )
+
+    operation = models.CharField(
+        max_length=50,
+        choices=OPERATION_CHOICES,
+        help_text="Type of processing operation",
+    )
+
+    status = models.CharField(
+        max_length=20,
+        choices=STATUS_CHOICES,
+        default=STATUS_PENDING,
+        help_text="Current status of the operation",
+    )
 
     # Configuration & Results
-    config = models.JSONField(default=dict, help_text="Operation configuration (mask settings, frame list, etc.)")
+    config = models.JSONField(
+        default=dict,
+        help_text="Operation configuration (mask settings, frame list, etc.)",
+    )
 
-    output_file = models.CharField(max_length=500, blank=True, help_text="Path to output file (relative to MEDIA_ROOT)")
+    output_file = models.CharField(
+        max_length=500,
+        blank=True,
+        help_text="Path to output file (relative to MEDIA_ROOT)",
+    )
 
-    details = models.TextField(blank=True, help_text="Additional details or error messages")
+    details = models.TextField(
+        blank=True, help_text="Additional details or error messages"
+    )
 
     # Celery Integration
-    task_id = models.CharField(max_length=100, blank=True, help_text="Celery task ID for progress tracking")
+    task_id = models.CharField(
+        max_length=100, blank=True, help_text="Celery task ID for progress tracking"
+    )
 
     # Timestamps
-    created_at = models.DateTimeField(auto_now_add=True, help_text="When the operation was started")
+    created_at = models.DateTimeField(
+        auto_now_add=True, help_text="When the operation was started"
+    )
 
-    completed_at = models.DateTimeField(null=True, blank=True, help_text="When the operation completed (success or failure)")
+    completed_at = models.DateTimeField(
+        null=True,
+        blank=True,
+        help_text="When the operation completed (success or failure)",
+    )
 
     class Meta:
         db_table = "video_processing_history"
@@ -89,9 +120,11 @@ class VideoProcessingHistory(models.Model):
         operation_display = getattr(self, "get_operation_display", None)
         status_display = getattr(self, "get_status_display", None)
 
-        operation = operation_display() if callable(operation_display) else self.operation
+        operation = (
+            operation_display() if callable(operation_display) else self.operation
+        )
         status = status_display() if callable(status_display) else self.status
-        return f"{operation} on {self.video.uuid} - {status}"
+        return f"{operation} on {self.video.video_hash} - {status}"
 
     def mark_running(self, save=True):
         """Mark operation as running."""
@@ -130,7 +163,9 @@ class VideoProcessingHistory(models.Model):
         if details:
             self.details = details
         if save:
-            self.save(update_fields=["status", "completed_at", "output_file", "details"])
+            self.save(
+                update_fields=["status", "completed_at", "output_file", "details"]
+            )
 
     def mark_failure(self, error_message, save=True):
         """Mark operation as failed."""
@@ -150,4 +185,8 @@ class VideoProcessingHistory(models.Model):
     @property
     def is_complete(self) -> bool:
         """Check if operation is in a terminal state."""
-        return self.status in [self.STATUS_SUCCESS, self.STATUS_FAILURE, self.STATUS_CANCELLED]
+        return self.status in [
+            self.STATUS_SUCCESS,
+            self.STATUS_FAILURE,
+            self.STATUS_CANCELLED,
+        ]

endoreg_db/models/medical/__init__.py

@@ -1,5 +1,5 @@
-from .disease import (Disease, DiseaseClassification, DiseaseClassificationChoice)
-from .event import (Event, EventClassification, EventClassificationChoice)
+from .disease import Disease, DiseaseClassification, DiseaseClassificationChoice
+from .event import Event, EventClassification, EventClassificationChoice
 
 from .contraindication import Contraindication
 from .examination import (
@@ -72,15 +72,12 @@ __all__ = [
     "Disease",
     "DiseaseClassification",
     "DiseaseClassificationChoice",
-
     # Event
     "Event",
     "EventClassification",
     "EventClassificationChoice",
-
     # Contraindication
     "Contraindication",
-
     # Examination
     "Examination",
     "ExaminationRequirementSet",
@@ -90,7 +87,6 @@ __all__ = [
     "ExaminationIndicationClassification",
     "ExaminationTime",
     "ExaminationTimeType",
-    
     # Finding
     "Finding",
     "FindingClassificationType",
@@ -100,7 +96,6 @@ __all__ = [
     "FindingMorphologyClassification",
     "FindingIntervention",
     "FindingInterventionType",
-
     # Patient
     ## Disease
     "PatientDisease",
@@ -120,14 +115,11 @@ __all__ = [
     ## Medication
     "PatientMedication",
     "PatientMedicationSchedule",
-
     # Organ
     "Organ",
-
     # Risk
     "Risk",
     "RiskType",
-
     # Medication
     "Medication",
     "MedicationManager",
@@ -135,12 +127,10 @@ __all__ = [
     "MedicationIntakeTime",
     "MedicationIndicationType",
     "MedicationIndication",
-
     # Hardware
     "Endoscope",
     "EndoscopeType",
     "EndoscopyProcessor",
-
     # Laboratory
     "LabValue",
-]
+]

endoreg_db/models/medical/contraindication/__init__.py

@@ -18,7 +18,9 @@ class Contraindication(models.Model):
         from endoreg_db.models import FindingIntervention
 
         @property
-        def contraindicating_finding_interventions(self) -> "models.manager.RelatedManager[FindingIntervention]": ...
+        def contraindicating_finding_interventions(
+            self,
+        ) -> "models.manager.RelatedManager[FindingIntervention]": ...
 
     def natural_key(self):
         return (self.name,)

endoreg_db/models/medical/disease.py

@@ -38,7 +38,9 @@ class Disease(models.Model):
     if TYPE_CHECKING:
 
         @property
-        def disease_classifications(self) -> models.QuerySet["DiseaseClassification"]: ...
+        def disease_classifications(
+            self,
+        ) -> models.QuerySet["DiseaseClassification"]: ...
 
         @property
         def patient_diseases(self) -> models.QuerySet["PatientDisease"]: ...
@@ -58,7 +60,9 @@ class Disease(models.Model):
         Returns:
             List[DiseaseClassification]: A list of related disease classification objects.
         """
-        classifications: List[DiseaseClassification] = [_ for _ in self.disease_classifications.all()]
+        classifications: List[DiseaseClassification] = [
+            _ for _ in self.disease_classifications.all()
+        ]
         return classifications
 
 
@@ -85,7 +89,9 @@ class DiseaseClassification(models.Model):
 
     name = models.CharField(max_length=255, unique=True)
 
-    disease = models.ForeignKey(Disease, on_delete=models.CASCADE, related_name="disease_classifications")
+    disease = models.ForeignKey(
+        Disease, on_delete=models.CASCADE, related_name="disease_classifications"
+    )
 
     objects = DiseaseClassificationManager()
 
@@ -93,7 +99,9 @@ class DiseaseClassification(models.Model):
         disease: models.ForeignKey["Disease"]
 
         @property
-        def disease_classification_choices(self) -> models.manager.RelatedManager["DiseaseClassificationChoice"]: ...
+        def disease_classification_choices(
+            self,
+        ) -> models.manager.RelatedManager["DiseaseClassificationChoice"]: ...
 
     def natural_key(self):
         """Returns the natural key (name) as a tuple."""
@@ -110,7 +118,9 @@ class DiseaseClassification(models.Model):
         Returns:
             List[DiseaseClassificationChoice]: A list of related disease classification choices.
         """
-        choices: List[DiseaseClassificationChoice] = [_ for _ in self.disease_classification_choices.all()]
+        choices: List[DiseaseClassificationChoice] = [
+            _ for _ in self.disease_classification_choices.all()
+        ]
         return choices
 
 
@@ -151,7 +161,9 @@ class DiseaseClassificationChoice(models.Model):
         disease_classification: models.ForeignKey["DiseaseClassification"]
 
         @property
-        def patient_diseases(self) -> models.manager.RelatedManager["PatientDisease"]: ...
+        def patient_diseases(
+            self,
+        ) -> models.manager.RelatedManager["PatientDisease"]: ...
 
     def natural_key(self):
         """Returns the natural key (name) as a tuple."""

endoreg_db/models/medical/event.py

@@ -93,7 +93,9 @@ class EventClassification(models.Model):
         event: models.ForeignKey["Event"]
 
         @property
-        def event_classification_choices(self) -> models.QuerySet["EventClassificationChoice"]: ...
+        def event_classification_choices(
+            self,
+        ) -> models.QuerySet["EventClassificationChoice"]: ...
 
     def natural_key(self):
         """Returns the natural key (name) as a tuple."""
@@ -105,7 +107,9 @@ class EventClassification(models.Model):
 
     def get_choices(self) -> List["EventClassificationChoice"]:
         """Retrieves all choices associated with this classification."""
-        choices: List[EventClassificationChoice] = [_ for _ in self.event_classification_choices.all()]
+        choices: List[EventClassificationChoice] = [
+            _ for _ in self.event_classification_choices.all()
+        ]
         return choices
 
 

endoreg_db/models/medical/examination/__init__.py

@@ -1,5 +1,9 @@
 from .examination import Examination, ExaminationRequirementSet
-from .examination_indication import ExaminationIndication, ExaminationIndicationClassification, ExaminationIndicationClassificationChoice
+from .examination_indication import (
+    ExaminationIndication,
+    ExaminationIndicationClassification,
+    ExaminationIndicationClassificationChoice,
+)
 from .examination_time import ExaminationTime
 from .examination_time_type import ExaminationTimeType
 from .examination_type import ExaminationType

endoreg_db/models/medical/examination/examination.py

@@ -53,18 +53,34 @@ class Examination(models.Model):
     objects = ExaminationManager()
 
     if TYPE_CHECKING:
-        from endoreg_db.models import ExaminationIndication, ExaminationTime, Finding, FindingClassification, InformationSource
+        from endoreg_db.models import (
+            ExaminationIndication,
+            ExaminationTime,
+            Finding,
+            FindingClassification,
+            InformationSource,
+        )
 
-        indications = cast("models.manager.RelatedManager[ExaminationIndication]", indications)
-        examination_times = cast("models.manager.RelatedManager[ExaminationTime]", examination_times)
+        indications = cast(
+            "models.manager.RelatedManager[ExaminationIndication]", indications
+        )
+        examination_times = cast(
+            "models.manager.RelatedManager[ExaminationTime]", examination_times
+        )
         findings = cast("models.manager.RelatedManager[Finding]", findings)
-        information_sources = cast("models.manager.RelatedManager[InformationSource]", information_sources)
+        information_sources = cast(
+            "models.manager.RelatedManager[InformationSource]", information_sources
+        )
 
         @property
-        def finding_classifications(self) -> "models.manager.RelatedManager[FindingClassification]": ...
+        def finding_classifications(
+            self,
+        ) -> "models.manager.RelatedManager[FindingClassification]": ...
 
         @property
-        def exam_reqset_links(self) -> "models.manager.RelatedManager[ExaminationRequirementSet]": ...
+        def exam_reqset_links(
+            self,
+        ) -> "models.manager.RelatedManager[ExaminationRequirementSet]": ...
 
     @property
     def links(self) -> "RequirementLinks":