extract pulses and add to recording data

Author: BryonLewis

bats_ai/core/tasks/tasks.py

@@ -228,6 +228,15 @@ def recording_compute_spectrogram(self, recording_id: int):  # noqa: C901, PLR09
                         pulse_metadata_obj.contours = []
                     pulse_metadata_obj.save()
 
+            from bats_ai.core.utils.batbot_annotations import (
+                create_pulse_annotations_from_batbot_segments,
+            )
+
+            create_pulse_annotations_from_batbot_segments(
+                recording,
+                compressed["segments"],
+            )
+
         if processing_task:
             processing_task.status = ProcessingTask.Status.COMPLETE
             processing_task.save()

bats_ai/core/utils/batbot_annotations.py

@@ -0,0 +1,69 @@
+from __future__ import annotations
+
+import logging
+from typing import TYPE_CHECKING
+
+from bats_ai.core.models import Annotations, Configuration
+
+if TYPE_CHECKING:
+    from bats_ai.core.models import Recording
+    from bats_ai.core.utils.batbot_metadata import BatBotMetadataCurve
+
+logger = logging.getLogger(__name__)
+
+BATBOT_ANNOTATION_MODEL = "batbot"
+
+
+def _segment_bounds(
+    segment: BatBotMetadataCurve,
+) -> tuple[float, float, float, float] | None:
+    curve = segment.get("curve_hz_ms") or []
+    if not curve:
+        return None
+
+    times = [pt[1] for pt in curve]
+    freqs = [pt[0] for pt in curve]
+    return min(times), max(times), min(freqs), max(freqs)
+
+
+def create_pulse_annotations_from_batbot_segments(
+    recording: Recording,
+    segments: list[BatBotMetadataCurve],
+) -> int:
+    """Create pulse annotations from BatBot segments when enabled in Configuration."""
+    config = Configuration.objects.first()
+    if not config or not config.create_pulse_annotations_from_batbot:
+        return 0
+
+    Annotations.objects.filter(
+        recording=recording,
+        model=BATBOT_ANNOTATION_MODEL,
+    ).delete()
+
+    created = 0
+    for segment in segments:
+        bounds = _segment_bounds(segment)
+        if bounds is None:
+            segment_index = segment.get("segment_index")
+            logger.warning(
+                "Skipping BatBot pulse annotation for recording=%s segment_index=%s: no bbox",
+                recording.pk,
+                segment_index,
+            )
+            continue
+
+        t_start, t_end, f_lo, f_hi = bounds
+        Annotations.objects.create(
+            recording=recording,
+            owner=recording.owner,
+            start_time=t_start,
+            end_time=t_end,
+            low_freq=f_lo,
+            high_freq=f_hi,
+            type="pulse",
+            model=BATBOT_ANNOTATION_MODEL,
+            comments="",
+        )
+        created += 1
+
+    return created

bats_ai/core/views/recording.py

@@ -178,12 +178,12 @@ class RecordingPaginatedResponse(Schema):
 
 
 class AnnotationSchema(Schema):
-    start_time: int
-    end_time: int
-    low_freq: int
-    high_freq: int
+    start_time: float
+    end_time: float
+    low_freq: float
+    high_freq: float
     species: list[SpeciesSchema]
-    comments: str
+    comments: str = ""
     type: str | None = None
     id: int | None = None
     owner_email: str = None
@@ -196,18 +196,18 @@ def from_orm(cls, obj: Annotations, owner_email=None):
             low_freq=obj.low_freq,
             high_freq=obj.high_freq,
             species=[SpeciesSchema.from_orm(species) for species in obj.species.all()],
-            comments=obj.comments,
+            comments=obj.comments or "",
             id=obj.id,
             type=obj.type,
             owner_email=owner_email,  # Include owner_email in the schema
         )
 
 
 class UpdateAnnotationsSchema(Schema):
-    start_time: int | None
-    end_time: int | None
-    low_freq: int | None
-    high_freq: int | None
+    start_time: float | None
+    end_time: float | None
+    low_freq: float | None
+    high_freq: float | None
     species: list[SpeciesSchema] | None
     comments: str | None
     type: str | None
@@ -278,10 +278,10 @@ def linestring_to_list(ls):
 
 class SequenceAnnotationSchema(Schema):
     id: int
-    start_time: int
-    end_time: int
+    start_time: float
+    end_time: float
     type: str | None
-    comments: str
+    comments: str = ""
     species: list[SpeciesSchema] | None
     owner_email: str = None
 
@@ -292,15 +292,15 @@ def from_orm(cls, obj, owner_email=None):
             end_time=obj.end_time,
             type=obj.type,
             species=[SpeciesSchema.from_orm(species) for species in obj.species.all()],
-            comments=obj.comments,
+            comments=obj.comments or "",
             id=obj.id,
             owner_email=owner_email,  # Include owner_email in the schema
         )
 
 
 class UpdateSequenceAnnotationSchema(Schema):
-    start_time: int = None
-    end_time: int = None
+    start_time: float = None
+    end_time: float = None
     type: str | None = None
     comments: str | None = None