Batbot contours

bats_ai/core/admin/__init__.py

@@ -10,6 +10,7 @@
     NABatSpectrogramAdmin,
 )
 from .processing_task import ProcessingTaskAdmin
+from .pulse_metadata import PulseMetadataAdmin
 from .recording import RecordingAdmin
 from .recording_annotations import RecordingAnnotationAdmin
 from .recording_tag import RecordingTagAdmin
@@ -34,6 +35,7 @@
     'ExportedAnnotationFileAdmin',
     'SpectrogramImageAdmin',
     'VettingDetailsAdmin',
+    'PulseMetadataAdmin',
     # NABat Models
     'NABatRecordingAnnotationAdmin',
     'NABatCompressedSpectrogramAdmin',

bats_ai/core/admin/compressed_spectrogram.py

@@ -15,6 +15,7 @@ class CompressedSpectrogramAdmin(admin.ModelAdmin):
         'starts',
         'stops',
         'image_url_list_display',
+        'mask_url_list_display',
     ]
     list_display_links = ['pk', 'recording', 'spectrogram']
     list_select_related = True
@@ -28,6 +29,7 @@ class CompressedSpectrogramAdmin(admin.ModelAdmin):
         'starts',
         'stops',
         'image_url_list_display',
+        'mask_url_list_display',
     ]
 
     @admin.display(description='Image URLs')
@@ -39,3 +41,13 @@ def image_url_list_display(self, obj):
         return format_html_join(
             '\n', '<div><a href="{}" target="_blank">{}</a></div>', ((url, url) for url in urls)
         )
+
+    @admin.display(description='Mask URLs')
+    def mask_url_list_display(self, obj):
+        """Render each mask URL as a clickable link in admin detail view."""
+        urls = obj.mask_url_list
+        if not urls:
+            return '(No masks)'
+        return format_html_join(
+            '\n', '<div><a href="{}" target="_blank">{}</a></div>', ((url, url) for url in urls)
+        )

bats_ai/core/admin/pulse_metadata.py

@@ -0,0 +1,9 @@
+from django.contrib import admin
+
+from bats_ai.core.models import PulseMetadata
+
+
+@admin.register(PulseMetadata)
+class PulseMetadataAdmin(admin.ModelAdmin):
+    list_display = ('recording', 'index', 'bounding_box')
+    list_select_related = True

bats_ai/core/migrations/0028_alter_spectrogramimage_type_pulsemetadata.py

@@ -0,0 +1,47 @@
+# Generated by Django 4.2.23 on 2026-02-04 17:02
+
+import django.contrib.gis.db.models.fields
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('core', '0027_alter_annotations_end_time_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='spectrogramimage',
+            name='type',
+            field=models.CharField(
+                choices=[
+                    ('spectrogram', 'Spectrogram'),
+                    ('compressed', 'Compressed'),
+                    ('masks', 'Masks'),
+                ],
+                default='spectrogram',
+                max_length=20,
+            ),
+        ),
+        migrations.CreateModel(
+            name='PulseMetadata',
+            fields=[
+                (
+                    'id',
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name='ID'
+                    ),
+                ),
+                ('index', models.IntegerField()),
+                ('bounding_box', django.contrib.gis.db.models.fields.PolygonField(srid=4326)),
+                ('contours', models.JSONField(blank=True, null=True)),
+                (
+                    'recording',
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE, to='core.recording'
+                    ),
+                ),
+            ],
+        ),
+    ]

bats_ai/core/models/__init__.py

@@ -4,6 +4,7 @@
 from .exported_file import ExportedAnnotationFile
 from .grts_cells import GRTSCells
 from .processing_task import ProcessingTask, ProcessingTaskType
+from .pulse_metadata import PulseMetadata
 from .recording import Recording, RecordingTag
 from .recording_annotation import RecordingAnnotation
 from .recording_annotation_status import RecordingAnnotationStatus
@@ -23,6 +24,7 @@
     'SequenceAnnotations',
     'GRTSCells',
     'CompressedSpectrogram',
+    'PulseMetadata',
     'RecordingAnnotation',
     'Configuration',
     'ProcessingTask',

bats_ai/core/models/compressed_spectrogram.py

@@ -28,12 +28,24 @@ def image_url_list(self):
         images = self.images.filter(type='compressed').order_by('index')
         return [default_storage.url(img.image_file.name) for img in images]
 
+    @property
+    def mask_url_list(self):
+        """Ordered list of mask image URLs for this spectrogram."""
+        images = self.images.filter(type='masks').order_by('index')
+        return [default_storage.url(img.image_file.name) for img in images]
+
     @property
     def image_pil_list(self):
         """List of PIL images in order."""
         images = self.images.filter(type='compressed').order_by('index')
         return [Image.open(img.image_file) for img in images]
 
+    @property
+    def mask_pil_list(self):
+        """List of PIL mask images in order."""
+        images = self.images.filter(type='masks').order_by('index')
+        return [Image.open(img.image_file) for img in images]
+
     @property
     def image_np(self):
         """Combined image as a single numpy array by horizontal stacking."""

bats_ai/core/models/nabat/nabat_compressed_spectrogram.py

@@ -29,12 +29,24 @@ def image_url_list(self):
         images = self.images.filter(type='compressed').order_by('index')
         return [default_storage.url(img.image_file.name) for img in images]
 
+    @property
+    def mask_url_list(self):
+        """Ordered list of mask image URLs for this spectrogram."""
+        images = self.images.filter(type='masks').order_by('index')
+        return [default_storage.url(img.image_file.name) for img in images]
+
     @property
     def image_pil_list(self):
         """List of PIL images in order."""
         images = self.images.filter(type='compressed').order_by('index')
         return [Image.open(img.image_file) for img in images]
 
+    @property
+    def mask_pil_list(self):
+        """List of PIL mask images in order."""
+        images = self.images.filter(type='masks').order_by('index')
+        return [Image.open(img.image_file) for img in images]
+
     @property
     def image_np(self):
         """Combined image as a single numpy array by horizontal stacking."""

bats_ai/core/models/pulse_metadata.py

@@ -0,0 +1,11 @@
+from django.contrib.gis.db import models
+
+from .recording import Recording
+
+
+class PulseMetadata(models.Model):
+    recording = models.ForeignKey(Recording, on_delete=models.CASCADE)
+    index = models.IntegerField(null=False, blank=False)
+    bounding_box = models.PolygonField(null=False, blank=False)
+    contours = models.JSONField(null=True, blank=True)
+    # TODO: Add in metadata from batbot

bats_ai/core/models/spectrogram_image.py

@@ -20,6 +20,7 @@ class SpectrogramImage(models.Model):
     SPECTROGRAM_TYPE_CHOICES = [
         ('spectrogram', 'Spectrogram'),
         ('compressed', 'Compressed'),
+        ('masks', 'Masks'),
     ]
     content_object = GenericForeignKey('content_type', 'object_id')
 

bats_ai/core/tasks/tasks.py

@@ -4,12 +4,14 @@
 import tempfile
 
 from django.contrib.contenttypes.models import ContentType
+from django.contrib.gis.geos import Polygon
 from django.core.files import File
 
 from bats_ai.celery import app
 from bats_ai.core.models import (
     CompressedSpectrogram,
     Configuration,
+    PulseMetadata,
     Recording,
     RecordingAnnotation,
     Species,
@@ -88,6 +90,38 @@ def recording_compute_spectrogram(recording_id: int):
                     },
                 )
 
+        # Save mask images (from batbot metadata mask_path)
+        for idx, mask_path in enumerate(compressed.get('masks', [])):
+            with open(mask_path, 'rb') as f:
+                SpectrogramImage.objects.get_or_create(
+                    content_type=ContentType.objects.get_for_model(compressed_obj),
+                    object_id=compressed_obj.id,
+                    index=idx,
+                    type='masks',
+                    defaults={
+                        'image_file': File(f, name=os.path.basename(mask_path)),
+                    },
+                )
+
+        # Create SpectrogramContour objects for each segment
+        for segment in results['segments']['segments']:
+            PulseMetadata.objects.update_or_create(
+                recording=compressed_obj.recording,
+                index=segment['segment_index'],
+                defaults={
+                    'contours': segment.get('contours', []),
+                    'bounding_box': Polygon(
+                        (
+                            (segment['start_ms'], segment['freq_max']),
+                            (segment['stop_ms'], segment['freq_max']),
+                            (segment['stop_ms'], segment['freq_min']),
+                            (segment['start_ms'], segment['freq_min']),
+                            (segment['start_ms'], segment['freq_max']),
+                        )
+                    ),
+                },
+            )
+
         config = Configuration.objects.first()
         # TODO: Disabled until prediction is in batbot
         # https://github.com/Kitware/batbot/issues/29

bats_ai/core/utils/batbot_metadata.py

@@ -7,12 +7,15 @@
 import batbot
 from pydantic import BaseModel, ConfigDict, Field, field_validator
 
+from .contour_utils import process_spectrogram_assets_for_contours
+
 
 class SpectrogramMetadata(BaseModel):
     """Metadata about the spectrogram."""
 
     uncompressed_path: list[str] = Field(alias='uncompressed.path')
     compressed_path: list[str] = Field(alias='compressed.path')
+    mask_path: list[str] = Field(alias='mask.path')
 
 
 class UncompressedSize(BaseModel):
@@ -227,19 +230,43 @@ class SpectrogramAssetResult(TypedDict):
 
 class SpectrogramCompressedAssetResult(TypedDict):
     paths: list[str]
+    masks: list[str]
     width: int
     height: int
     widths: list[float]
     starts: list[float]
     stops: list[float]
 
 
+class SpectrogramContour(TypedDict):
+    level: float
+    curve: list[list[float]]
+    index: int
+
+
+class SpectrogramContourSegment(TypedDict):
+    segment_index: int
+    contour_count: int
+    freq_min: float
+    freq_max: float
+    contours: list[SpectrogramContour]
+    width_px: float
+    start_ms: float
+    stop_ms: float
+
+
+class SpectrogramContours(TypedDict):
+    segments: list[SpectrogramContourSegment]
+    total_segments: int
+
+
 class SpectrogramAssets(TypedDict):
     duration: float
     freq_min: int
     freq_max: int
     normal: SpectrogramAssetResult
     compressed: SpectrogramCompressedAssetResult
+    segments: SpectrogramContours | None
 
 
 @contextmanager
@@ -261,6 +288,7 @@ def generate_spectrogram_assets(recording_path: str, output_folder: str):
     # from the metadata we should have the images that are used
     uncompressed_paths = metadata.spectrogram.uncompressed_path
     compressed_paths = metadata.spectrogram.compressed_path
+    mask_paths = metadata.spectrogram.mask_path
 
     metadata.frequencies.min_hz
     metadata.frequencies.max_hz
@@ -277,11 +305,16 @@ def generate_spectrogram_assets(recording_path: str, output_folder: str):
         },
         'compressed': {
             'paths': compressed_paths,
+            'masks': mask_paths,
             'width': metadata.size.compressed.width_px,
             'height': metadata.size.compressed.height_px,
             'widths': compressed_metadata.widths,
             'starts': compressed_metadata.starts,
             'stops': compressed_metadata.stops,
         },
     }
+
+    segments_data = process_spectrogram_assets_for_contours(result)
+    result['segments'] = segments_data
+
     return result