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

endoreg_db/models/metadata/video_meta.py

@@ -0,0 +1,332 @@
+from django.db import models
+import logging
+from pathlib import Path
+from typing import Optional, TYPE_CHECKING
+
+# import endoreg_center_id from django settings
+from django.conf import settings
+
+# check if endoreg_center_id is set
+if not hasattr(settings, "ENDOREG_CENTER_ID"):
+    ENDOREG_CENTER_ID = 9999
+else:
+    ENDOREG_CENTER_ID = settings.ENDOREG_CENTER_ID
+
+# Import the new utility function
+from ...utils.video import ffmpeg_wrapper
+
+logger = logging.getLogger(__name__)
+
+if TYPE_CHECKING:
+    from ..administration import Center
+    from ..medical.hardware import EndoscopyProcessor, Endoscope
+
+
+# VideoMeta
+class VideoMeta(models.Model):
+    """
+    Stores technical and contextual metadata related to a video file.
+
+    Links to hardware (processor, endoscope), center, import details, and FFmpeg technical specs.
+    """
+    processor = models.ForeignKey(
+        "EndoscopyProcessor", on_delete=models.CASCADE, blank=True, null=True
+    )
+    endoscope = models.ForeignKey(
+        "Endoscope", on_delete=models.CASCADE, blank=True, null=True
+    )
+    center = models.ForeignKey("Center", on_delete=models.CASCADE)
+    import_meta = models.OneToOneField(
+        "VideoImportMeta", on_delete=models.CASCADE, blank=True, null=True
+    )
+    ffmpeg_meta = models.OneToOneField(
+        "FFMpegMeta", on_delete=models.CASCADE, blank=True, null=True
+    )
+
+    @classmethod
+    def create_from_file(
+        cls,
+        video_path: Path,
+        center: "Center",
+        processor: Optional["EndoscopyProcessor"] = None,
+        endoscope: Optional["Endoscope"] = None,
+        save_instance: bool = True,
+    ) -> "VideoMeta":
+        """
+        Create a new VideoMeta from a video file path, initializing FFMpegMeta.
+        Raises FileNotFoundError, TypeError, or RuntimeError on failure.
+        """
+        if not isinstance(video_path, Path):
+            raise TypeError("video_path must be a Path object")
+        if not video_path.exists():
+            raise FileNotFoundError(f"Video file not found at {video_path}")
+
+        meta = cls(center=center, processor=processor, endoscope=endoscope)
+        try:
+            # initialize_ffmpeg_meta now raises exceptions on failure
+            meta.initialize_ffmpeg_meta(video_path)
+        except Exception as e:
+            # Re-raise exceptions from ffmpeg meta initialization
+            logger.error("Failed during FFMpegMeta initialization within create_from_file for %s: %s", video_path.name, e, exc_info=True)
+            raise RuntimeError(f"Failed to initialize FFMpeg metadata for {video_path.name}") from e
+
+        if save_instance:
+            meta.save() # This ensures VideoImportMeta is created too
+            logger.info("Created and saved VideoMeta instance PK %s from %s", meta.pk, video_path.name)
+        else:
+            logger.info("Instantiated VideoMeta from %s (not saved yet)", video_path.name)
+
+        return meta
+
+    def __str__(self):
+        """Returns a string summary of the video metadata."""
+        processor_name = self.processor.name if self.processor is not None else "None"
+        endoscope_name = self.endoscope.name if self.endoscope is not None else "None"
+        center_name = self.center.name if self.center is not None else "None"
+        ffmpeg_meta_str = self.ffmpeg_meta.__str__()
+        import_meta_str = self.import_meta.__str__()
+
+        result_html = ""
+
+        result_html += f"Processor: {processor_name}\n"
+        result_html += f"Endoscope: {endoscope_name}\n"
+        result_html += f"Center: {center_name}\n"
+        result_html += f"FFMpeg Meta: {ffmpeg_meta_str}\n"
+        result_html += f"Import Meta: {import_meta_str}\n"
+
+        return result_html
+
+    def save(self, *args, **kwargs):
+        """Ensures VideoImportMeta exists before saving."""
+        if self.import_meta is None:
+            self.import_meta = VideoImportMeta.objects.create()
+        super(VideoMeta, self).save(*args, **kwargs)
+
+    def initialize_ffmpeg_meta(self, video_path: Path):
+        """
+        Initializes FFMpeg metadata for the video file if not already done.
+        Raises RuntimeError if FFMpegMeta creation fails.
+        """
+        if self.ffmpeg_meta:
+            logger.debug("FFMpegMeta already exists for VideoMeta PK %s. Skipping initialization.", self.pk)
+            return
+
+        logger.info("Initializing FFMpegMeta for VideoMeta PK %s from %s", self.pk if self.pk else "(unsaved)", video_path.name)
+        try:
+            # FFMpegMeta.create_from_file now raises exceptions on failure
+            ffmpeg_instance = FFMpegMeta.create_from_file(video_path)
+            # If create_from_file succeeds, link it. No need to check for None.
+            self.ffmpeg_meta = ffmpeg_instance
+            # If the VideoMeta instance is already saved, save the link immediately.
+            # Otherwise, the link will be saved when VideoMeta itself is saved.
+            if self.pk:
+                self.save(update_fields=['ffmpeg_meta'])
+            logger.info("Successfully created and linked FFMpegMeta PK %s", self.ffmpeg_meta.pk)
+
+        except Exception as e:
+            # Log the error and re-raise it
+            logger.error("Failed to create or link FFMpegMeta from %s: %s", video_path, e, exc_info=True)
+            raise RuntimeError(f"Failed to create FFMpeg metadata from {video_path}") from e
+
+    def update_meta(self, video_path: Path):
+        """
+        Updates the FFMpeg metadata from the file, replacing existing data.
+        Raises RuntimeError if FFMpegMeta creation fails.
+        """
+        logger.info("Updating FFMpegMeta for VideoMeta PK %s from %s", self.pk, video_path.name)
+        existing_ffmpeg_pk = None
+        if self.ffmpeg_meta:
+            existing_ffmpeg_pk = self.ffmpeg_meta.pk
+            logger.debug("Deleting existing FFMpegMeta PK %s before update.", existing_ffmpeg_pk)
+            # Nullify the relation first before deleting the related object
+            self.ffmpeg_meta = None
+            self.save(update_fields=['ffmpeg_meta']) # Save the null relation
+            FFMpegMeta.objects.filter(pk=existing_ffmpeg_pk).delete() # Delete the old object
+
+        # initialize_ffmpeg_meta handles creation, linking, saving the link, and raises exceptions
+        self.initialize_ffmpeg_meta(video_path)
+
+    def get_endo_roi(self):
+        """Retrieves the endoscope region of interest (ROI) from the associated processor."""
+        from ..medical.hardware import EndoscopyProcessor
+
+        processor: EndoscopyProcessor = self.processor
+        endo_roi = processor.get_roi_endoscope_image()
+        return endo_roi
+
+    @property
+    def fps(self) -> Optional[float]:
+        """Returns the frame rate (FPS) from the linked FFMpegMeta."""
+        if not self.ffmpeg_meta:
+            logger.warning("FFMpegMeta not linked for VideoMeta PK %s. Cannot get FPS.", self.pk)
+            return None
+        return self.ffmpeg_meta.fps
+
+    @property
+    def duration(self) -> Optional[float]:
+        """Returns the duration in seconds from the linked FFMpegMeta."""
+        return self.ffmpeg_meta.duration if self.ffmpeg_meta else None
+
+    @property
+    def width(self) -> Optional[int]:
+        """Returns the video width in pixels from the linked FFMpegMeta."""
+        return self.ffmpeg_meta.width if self.ffmpeg_meta else None
+
+    @property
+    def height(self) -> Optional[int]:
+        """Returns the video height in pixels from the linked FFMpegMeta."""
+        return self.ffmpeg_meta.height if self.ffmpeg_meta else None
+
+    @property
+    def frame_count(self) -> Optional[int]:
+        """Calculates frame count based on duration and FPS from FFMpegMeta."""
+        if self.ffmpeg_meta and self.ffmpeg_meta.duration is not None and self.ffmpeg_meta.fps is not None and self.ffmpeg_meta.fps > 0:
+            return int(self.ffmpeg_meta.duration * self.ffmpeg_meta.fps)
+        return None
+
+
+class FFMpegMeta(models.Model):
+    """
+    Stores technical video stream information extracted using FFmpeg (ffprobe).
+    """
+    width = models.IntegerField(null=True, blank=True)
+    height = models.IntegerField(null=True, blank=True)
+    duration = models.FloatField(null=True, blank=True)  # Duration in seconds
+    frame_rate_num = models.IntegerField(null=True, blank=True)  # Numerator for frame rate
+    frame_rate_den = models.IntegerField(null=True, blank=True)  # Denominator for frame rate
+    codec_name = models.CharField(max_length=50, null=True, blank=True)
+    pixel_format = models.CharField(max_length=50, null=True, blank=True)
+    bit_rate = models.BigIntegerField(null=True, blank=True)  # Bit rate in bits per second
+    raw_probe_data = models.JSONField(null=True, blank=True)  # Store the full JSON output for debugging or future use
+
+    @property
+    def fps(self) -> Optional[float]:
+        """Calculates and returns the frames per second (FPS) if possible."""
+        if self.frame_rate_num is not None and self.frame_rate_den is not None and self.frame_rate_den != 0:
+            return self.frame_rate_num / self.frame_rate_den
+        return None
+
+    @classmethod
+    def create_from_file(cls, file_path: Path):
+        """
+        Creates an FFMpegMeta instance by running ffprobe on the given file path.
+        Raises RuntimeError on failure.
+        """
+        logger.info("Running ffprobe on %s", file_path)
+        try:
+            probe_data = ffmpeg_wrapper.get_stream_info(file_path)  # Use the new utility
+        except Exception as probe_err:
+            logger.error("ffprobe execution failed for %s: %s", file_path, probe_err, exc_info=True)
+            raise RuntimeError(f"ffprobe execution failed for {file_path}") from probe_err
+
+
+        if not probe_data or "streams" not in probe_data:
+            logger.error("Failed to get valid stream info from ffprobe for %s", file_path)
+            # Raise exception instead of returning None
+            raise RuntimeError(f"Invalid stream info from ffprobe for {file_path}")
+
+        video_stream = next((s for s in probe_data["streams"] if s.get("codec_type") == "video"), None)
+
+        if not video_stream:
+            logger.warning("No video stream found in ffprobe output for %s", file_path)
+            # Raise exception instead of returning None
+            raise RuntimeError(f"No video stream found in {file_path}")
+
+        # Extract data safely using .get()
+        width = video_stream.get("width")
+        height = video_stream.get("height")
+        duration_str = video_stream.get("duration")
+        # --- FIX: Handle potential format key ---
+        if duration_str is None and 'format' in probe_data and 'duration' in probe_data['format']:
+            duration_str = probe_data['format']['duration']
+            logger.debug("Using duration from format block: %s", duration_str)
+        # --- End Fix ---
+        duration = float(duration_str) if duration_str else None
+
+        # Frame rate can be tricky, often represented as "num/den"
+        frame_rate_str = video_stream.get("r_frame_rate")
+        # --- FIX: Fallback to avg_frame_rate if r_frame_rate is invalid ---
+        if not frame_rate_str or frame_rate_str == "0/0":
+            frame_rate_str = video_stream.get("avg_frame_rate")
+            logger.debug("Using avg_frame_rate as fallback: %s", frame_rate_str)
+        # --- End Fix ---
+        frame_rate_num, frame_rate_den = None, None
+        if frame_rate_str and "/" in frame_rate_str:
+            try:
+                num_str, den_str = frame_rate_str.split('/')
+                frame_rate_num = int(num_str)
+                frame_rate_den = int(den_str)
+                if frame_rate_den == 0: # Avoid division by zero
+                    logger.warning("Invalid frame rate denominator (0) for %s", file_path)
+                    frame_rate_num, frame_rate_den = None, None
+            except ValueError:
+                logger.warning("Could not parse frame rate '%s' for %s", frame_rate_str, file_path)
+                frame_rate_num, frame_rate_den = None, None
+
+        codec_name = video_stream.get("codec_name")
+        pixel_format = video_stream.get("pix_fmt")
+        bit_rate_str = video_stream.get("bit_rate")
+        # --- FIX: Handle potential format key for bit_rate ---
+        if bit_rate_str is None and 'format' in probe_data and 'bit_rate' in probe_data['format']:
+            bit_rate_str = probe_data['format']['bit_rate']
+            logger.debug("Using bit_rate from format block: %s", bit_rate_str)
+        # --- End Fix ---
+        bit_rate = int(bit_rate_str) if bit_rate_str else None
+
+        try:
+            instance = cls.objects.create(
+                width=width,
+                height=height,
+                duration=duration,
+                frame_rate_num=frame_rate_num,
+                frame_rate_den=frame_rate_den,
+                codec_name=codec_name,
+                pixel_format=pixel_format,
+                bit_rate=bit_rate,
+                raw_probe_data=probe_data,
+            )
+            logger.info("Successfully created FFMpegMeta for %s (ID: %d)", file_path.name, instance.pk)
+            return instance
+        except Exception as e:
+            logger.error("Error creating FFMpegMeta DB record from %s: %s", file_path.name, e, exc_info=True)
+            # Raise exception instead of returning None
+            raise RuntimeError(f"Database error creating FFMpegMeta for {file_path.name}") from e
+
+    def __str__(self):
+        """Returns a string summary of the FFmpeg metadata."""
+        result_html = ""
+
+        result_html += f"Width: {self.width}\n"
+        result_html += f"Height: {self.height}\n"
+        result_html += f"Duration: {self.duration}\n"
+        result_html += f"Frame Rate: {self.fps}\n"
+        result_html += f"Codec Name: {self.codec_name}\n"
+        result_html += f"Pixel Format: {self.pixel_format}\n"
+        result_html += f"Bit Rate: {self.bit_rate}\n"
+
+        return result_html
+
+
+class VideoImportMeta(models.Model):
+    """
+    Stores metadata related to the import and processing status of a video.
+    """
+    file_name = models.CharField(max_length=255, blank=True, null=True)
+    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):
+        """Returns a string summary of the import metadata."""
+        result_html = ""
+
+        result_html += f"Video anonymized: {self.video_anonymized}\n"
+        result_html += (
+            f"Video patient data detected: {self.video_patient_data_detected}\n"
+        )
+        result_html += f"Outside detected: {self.outside_detected}\n"
+        result_html += f"Patient data removed: {self.patient_data_removed}\n"
+        result_html += f"Outside removed: {self.outside_removed}\n"
+        return result_html

endoreg_db/models/metadata/video_prediction_logic.py

@@ -0,0 +1,190 @@
+import logging
+from typing import TYPE_CHECKING, List, Tuple, Optional
+import numpy as np
+
+# Import necessary models and utils used by the logic
+from ..utils import find_segments_in_prediction_array
+from ..label.label_video_segment import LabelVideoSegment
+
+
+logger = logging.getLogger(__name__)
+
+DEFAULT_WINDOW_SIZE_IN_SECONDS_FOR_RUNNING_MEAN = 1.5
+DEFAULT_VIDEO_SEGMENT_LENGTH_THRESHOLD_IN_S = 1.0
+
+if TYPE_CHECKING:
+    from .video_prediction_meta import VideoPredictionMeta
+    from ..label import Label
+
+
+def apply_running_mean_logic(instance: "VideoPredictionMeta", confidence_array: np.ndarray, window_size_in_seconds: Optional[float] = None) -> np.ndarray:
+    """
+    Apply a running mean filter to the confidence array for smoothing.
+    """
+    video_obj = instance.get_video()
+    fps = video_obj.get_fps()
+
+    if fps is None or fps <= 0:
+        logger.warning(f"Invalid FPS ({fps}) for {video_obj}. Cannot apply running mean. Returning original array.")
+        return confidence_array
+
+    if window_size_in_seconds is None:
+        window_size_in_seconds = DEFAULT_WINDOW_SIZE_IN_SECONDS_FOR_RUNNING_MEAN
+
+    window_size_in_frames = int(window_size_in_seconds * fps)
+    window_size_in_frames = max(window_size_in_frames, 1)
+
+    window = np.ones(window_size_in_frames) / window_size_in_frames
+    pad_size = window_size_in_frames // 2
+
+    padded_confidences = np.pad(
+        confidence_array,
+        (pad_size, pad_size),
+        "constant",
+        constant_values=(0.5, 0.5),
+    )
+
+    running_mean = np.convolve(padded_confidences, window, mode="same")
+    start_index = pad_size
+    end_index = start_index + len(confidence_array)
+    running_mean = running_mean[start_index:end_index]
+
+    if running_mean.shape != confidence_array.shape:
+        logger.warning(f"Running mean output shape {running_mean.shape} differs from input {confidence_array.shape}. Check padding/slicing.")
+        # Return original array on shape mismatch to avoid downstream errors
+        return confidence_array
+
+    return running_mean
+
+
+def calculate_prediction_array_logic(instance: "VideoPredictionMeta", window_size_in_seconds: Optional[float] = None) -> Optional[np.ndarray]:
+    """
+    Fetches predictions, applies smoothing, and returns the binary prediction array.
+    Does not save the array itself.
+    """
+    from ..label import ImageClassificationAnnotation
+    video_obj = instance.get_video()
+    model_meta = instance.model_meta
+    label_list = instance.get_label_list()
+    num_frames = video_obj.frame_count
+
+    if num_frames is None or num_frames <= 0:
+        logger.warning(f"Cannot calculate prediction array for {video_obj} with invalid frame count ({num_frames}).")
+        return None
+
+    if not label_list:
+        logger.warning(f"No labels found for model {model_meta}. Cannot calculate prediction array.")
+        return None
+
+    prediction_array = np.zeros((num_frames, len(label_list)))
+
+    base_pred_qs = ImageClassificationAnnotation.objects.filter(
+        model_meta=model_meta,
+        frame__video_file=video_obj
+    )
+
+    for i, label in enumerate(label_list):
+        predictions = base_pred_qs.filter(label=label).order_by("frame__frame_number").values_list(
+            "frame__frame_number", "confidence"
+        )
+
+        # Initialize with 0.5 (neutral confidence)
+        confidences = np.full(num_frames, 0.5)
+        found_predictions = False
+        for frame_num, confidence in predictions:
+            if 0 <= frame_num < num_frames:
+                confidences[frame_num] = confidence
+                found_predictions = True
+            else:
+                logger.warning(f"Prediction found for out-of-bounds frame number {frame_num} (max: {num_frames-1}). Skipping.")
+
+        if not found_predictions:
+            logger.warning(f"No predictions found for label '{label.name}' in {video_obj}. Using default confidence.")
+
+        smooth_confidences = apply_running_mean_logic(
+            instance, confidences, window_size_in_seconds
+        )
+        # Threshold smoothed confidences
+        binary_predictions = smooth_confidences > 0.5
+        prediction_array[:, i] = binary_predictions
+
+    return prediction_array
+
+
+def create_video_segments_for_label_logic(instance: "VideoPredictionMeta", segments: List[Tuple[int, int]], label: "Label"):
+    """
+    Creates LabelVideoSegment instances for the given label and segments.
+    """
+    from ..other import InformationSource
+    video_obj = instance.get_video()
+    information_source, _ = InformationSource.objects.get_or_create(name="prediction")
+
+    segments_to_create = []
+    for start_frame, end_frame in segments:
+        segment_data = {
+            "start_frame_number": start_frame,
+            "end_frame_number": end_frame,
+            "source": information_source,
+            "label": label,
+            "prediction_meta": instance,
+            "video_file": video_obj,
+        }
+        # Check for existence before creating the object instance
+        if not LabelVideoSegment.objects.filter(
+            video_file=video_obj,
+            prediction_meta=instance,
+            label=label,
+            start_frame_number=start_frame,
+            end_frame_number=end_frame
+        ).exists():
+            segments_to_create.append(LabelVideoSegment(**segment_data))
+
+    if segments_to_create:
+        LabelVideoSegment.objects.bulk_create(segments_to_create)
+        logger.info(f"Created {len(segments_to_create)} video segments for label '{label.name}' in {video_obj}.")
+    else:
+        logger.info(f"No new video segments needed for label '{label.name}' in {video_obj}.")
+
+
+def create_video_segments_logic(instance: "VideoPredictionMeta", segment_length_threshold_in_s: Optional[float] = None):
+    """
+    Generates LabelVideoSegments based on the stored prediction array.
+    """
+    if segment_length_threshold_in_s is None:
+        segment_length_threshold_in_s = DEFAULT_VIDEO_SEGMENT_LENGTH_THRESHOLD_IN_S
+
+    video_obj = instance.get_video()
+    fps = video_obj.get_fps()
+
+    if fps is None or fps <= 0:
+        logger.warning(f"Cannot create video segments for {video_obj} with invalid FPS ({fps}).")
+        return
+
+    min_frame_length = int(segment_length_threshold_in_s * fps)
+    min_frame_length = max(min_frame_length, 1) # Ensure minimum length is at least 1
+
+    label_list = instance.get_label_list()
+    if not label_list:
+        logger.warning(f"No labels associated with {instance}. Cannot create segments.")
+        return
+
+    prediction_array = instance.get_prediction_array()
+    if prediction_array is None:
+        logger.info(f"Prediction array not found for {instance}. Calculating...")
+        instance.calculate_prediction_array() # This will save the array internally
+        prediction_array = instance.get_prediction_array() # Fetch again
+        if prediction_array is None:
+            logger.error(f"Failed to get or calculate prediction array for {instance}. Cannot create segments.")
+            return
+
+    if prediction_array.shape[1] != len(label_list):
+        logger.warning(f"Prediction array shape {prediction_array.shape} incompatible with label list length {len(label_list)} for {instance}.")
+        return
+
+    logger.info(f"Creating video segments for {instance} (min length: {min_frame_length} frames)...")
+    for i, label in enumerate(label_list):
+        binary_predictions = prediction_array[:, i].astype(bool)
+        segments = find_segments_in_prediction_array(binary_predictions, min_frame_length)
+        if segments:
+            create_video_segments_for_label_logic(instance, segments, label)
+    logger.info(f"Finished creating video segments for {instance}.")