Batbot pulse annotations

bats_ai/core/admin/configuration.py

@@ -11,6 +11,7 @@ class ConfigurationAdmin(admin.ModelAdmin):
         "display_pulse_annotations",
         "display_sequence_annotations",
         "run_inference_on_upload",
+        "create_pulse_annotations_from_batbot",
         "spectrogram_x_stretch",
         "spectrogram_view",
     ]

bats_ai/core/management/commands/copy_batbot_pulse_annotations.py

@@ -0,0 +1,95 @@
+"""
+Management command to duplicate the batbot model's pulse annotations for a user.
+
+Useful for generating training data to improve Batbot's ability to detect pulses.
+"""
+
+from __future__ import annotations
+
+import logging
+
+from django.contrib.auth.models import User
+from django.core.management.base import CommandError
+import djclick as click
+
+from bats_ai.core.models import Annotations
+from bats_ai.core.utils.batbot_annotations import BATBOT_ANNOTATION_MODEL
+
+logger = logging.getLogger(__name__)
+
+COPY_COMMENT = "Copy of batbot pulse annotation"
+
+
+@click.command()
+@click.argument("username")
+@click.option("--batch-size", default=5000)
+def copy_batbot_pulse_annotations(username: str, batch_size: int = 5000):
+    logger.info("Finding user with username %s...", username)
+    new_owner = User.objects.filter(username=username).first()
+    if not new_owner:
+        raise CommandError(f"No user found with username {username}")
+
+    logger.info("Finding all pulse annotations created by batbot...")
+    batbot_pulse_annotations = (
+        Annotations.objects.filter(model=BATBOT_ANNOTATION_MODEL)
+        .order_by("recording_id")
+        .iterator(chunk_size=batch_size)
+    )
+
+    total_count = 0
+
+    copies = []
+    current_recording_id = None
+    skip_recording = False
+    for original in batbot_pulse_annotations:
+        if original.recording_id != current_recording_id:
+            current_recording_id = original.recording_id
+            # This check attempts to prevent multiple runs of this command
+            # from creating redundant copies for the given user. This is not
+            # perfect, since it relies on the editable "comments" field, and
+            # lazily checks for the existence of any annotation for the given
+            # recording that was created by a run of this command. There are 2
+            # existing concerns that are unlikely to cause trouble in the short
+            # term, but should be noted:
+            #
+            # 1. "comments" are editable. If a user edits all the comments
+            # for their copied annotations for a given recording, a re-run of
+            # this command will duplicate the annotations again.
+            #
+            # 2. If a run of this command is interrupted and a strict subset of
+            # annotations for a given recording has been saved, then whichever annotations
+            # for that recording have not been copied WILL NOT be copied by a subsequent run.
+            copied_already = Annotations.objects.filter(
+                owner=new_owner, comments=COPY_COMMENT, recording_id=current_recording_id
+            ).exists()
+            skip_recording = copied_already
+        if skip_recording:
+            continue
+        else:
+            # Create a new annotation object and add it to copies
+            copies.append(
+                Annotations(
+                    recording_id=original.recording_id,
+                    owner=new_owner,
+                    start_time=original.start_time,
+                    end_time=original.end_time,
+                    low_freq=original.low_freq,
+                    high_freq=original.high_freq,
+                    type=original.type,
+                    comments=COPY_COMMENT,
+                    model="",
+                    confidence=original.confidence,
+                )
+            )
+        if len(copies) >= batch_size:
+            logger.info("Saving %d copied annotations...", len(copies))
+            total_count += len(copies)
+            Annotations.objects.bulk_create(copies)
+            copies = []
+
+    if len(copies) > 0:
+        logger.info("Saving %d copied annotations...", len(copies))
+        total_count += len(copies)
+        Annotations.objects.bulk_create(copies)
+
+    logger.info("Done. Copied %d annotations.", total_count)

bats_ai/core/migrations/0042_configuration_create_pulse_annotations_from_batbot.py

@@ -0,0 +1,19 @@
+# Generated by Django 6.0.7 on 2026-08-10 18:29
+
+from __future__ import annotations
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("core", "0041_rename_grts_cell_nabatrecording_sample_frame_id_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="configuration",
+            name="create_pulse_annotations_from_batbot",
+            field=models.BooleanField(default=False),
+        ),
+    ]

bats_ai/core/models/configuration.py

@@ -22,6 +22,7 @@ class AvailableColorScheme(models.TextChoices):
     display_pulse_annotations = models.BooleanField(default=True)
     display_sequence_annotations = models.BooleanField(default=True)
     run_inference_on_upload = models.BooleanField(default=True)
+    create_pulse_annotations_from_batbot = models.BooleanField(default=False)
     spectrogram_x_stretch = models.DecimalField(default=2.5, max_digits=3, decimal_places=2)
     spectrogram_view = models.CharField(
         max_length=12, choices=SpectrogramViewMode, default=SpectrogramViewMode.COMPRESSED

bats_ai/core/tasks/tasks.py

@@ -78,9 +78,9 @@ def recording_compute_spectrogram(self, recording_id: int):  # noqa: C901, PLR09
                         content_type=ContentType.objects.get_for_model(spectrogram),
                         object_id=spectrogram.id,
                         index=idx,
+                        type="spectrogram",
                         defaults={
                             "image_file": File(f, name=os.path.basename(img_path)),
-                            "type": "spectrogram",
                         },
                     )
             for idx, img_path in enumerate(results["normal"].get("waveplot_paths", [])):
@@ -90,9 +90,9 @@ def recording_compute_spectrogram(self, recording_id: int):  # noqa: C901, PLR09
                     content_type=ContentType.objects.get_for_model(spectrogram),
                     object_id=spectrogram.id,
                     index=idx,
+                    type="waveform_uncompressed",
                     defaults={
                         "image_file": File(buf, name=f"{base}.png"),
-                        "type": "waveform_uncompressed",
                     },
                 )
             # Create or get CompressedSpectrogram
@@ -116,9 +116,9 @@ def recording_compute_spectrogram(self, recording_id: int):  # noqa: C901, PLR09
                         content_type=ContentType.objects.get_for_model(compressed_obj),
                         object_id=compressed_obj.id,
                         index=idx,
+                        type="compressed",
                         defaults={
                             "image_file": File(f, name=os.path.basename(img_path)),
-                            "type": "compressed",
                         },
                     )
 
@@ -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/configuration.py

@@ -26,6 +26,7 @@ class ConfigurationSchema(Schema):
     display_sequence_annotations: bool
     is_admin: bool | None = None
     run_inference_on_upload: bool
+    create_pulse_annotations_from_batbot: bool
     spectrogram_x_stretch: float
     spectrogram_view: Configuration.SpectrogramViewMode
     default_color_scheme: Configuration.AvailableColorScheme
@@ -44,6 +45,7 @@ def get_configuration(request):
         display_pulse_annotations=config.display_pulse_annotations,
         display_sequence_annotations=config.display_sequence_annotations,
         run_inference_on_upload=config.run_inference_on_upload,
+        create_pulse_annotations_from_batbot=config.create_pulse_annotations_from_batbot,
         spectrogram_x_stretch=config.spectrogram_x_stretch,
         spectrogram_view=config.spectrogram_view,
         default_color_scheme=config.default_color_scheme,
@@ -62,7 +64,7 @@ def update_configuration(request, payload: ConfigurationSchema):
     config = Configuration.objects.first()
     if not config:
         return JsonResponse({"error": "No configuration found"}, status=404)
-    for attr, value in payload.dict().items():
+    for attr, value in payload.dict(exclude={"is_admin"}).items():
         setattr(config, attr, value)
     config.save()
     return ConfigurationSchema.from_orm(config)

bats_ai/core/views/recording.py

@@ -178,15 +178,16 @@ 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
+    model: str | None = None
 
     @classmethod
     def from_orm(cls, obj: Annotations, owner_email=None):
@@ -196,18 +197,19 @@ 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
+            model=obj.model,
         )
 
 
 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 +280,10 @@ 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 +294,15 @@ 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
 

client/src/api/api.ts

@@ -66,6 +66,7 @@ export interface SpectrogramAnnotation {
   comments?: string;
   type?: string;
   owner_email?: string;
+  model?: string;
 }
 
 export interface SpectrogramSequenceAnnotation {
@@ -643,6 +644,7 @@ export interface ConfigurationSettings {
   display_pulse_annotations: boolean;
   display_sequence_annotations: boolean;
   run_inference_on_upload: boolean;
+  create_pulse_annotations_from_batbot: boolean;
   spectrogram_x_stretch: number;
   spectrogram_view: "compressed" | "uncompressed";
   is_admin?: boolean;