Issue 239 generate smooth svg

bats_ai/core/admin/__init__.py

@@ -11,13 +11,15 @@
     NABatSpectrogramAdmin,
 )
 from .processing_task import ProcessingTaskAdmin
+from .pulse_annotation import ComputedPulseAnnotationAdmin
 from .recording import RecordingAdmin
 from .recording_annotations import RecordingAnnotationAdmin
 from .recording_tag import RecordingTagAdmin
 from .sequence_annotations import SequenceAnnotationsAdmin
 from .species import SpeciesAdmin
 from .spectrogram import SpectrogramAdmin
 from .spectrogram_image import SpectrogramImageAdmin
+from .spectrogram_svg import SpectrogramSvgAdmin
 
 __all__ = [
     'AnnotationsAdmin',
@@ -34,9 +36,11 @@
     'ConfigurationAdmin',
     'ExportedAnnotationFileAdmin',
     'SpectrogramImageAdmin',
+    'SpectrogramSvgAdmin',
     # NABat Models
     'NABatRecordingAnnotationAdmin',
     'NABatCompressedSpectrogramAdmin',
     'NABatSpectrogramAdmin',
     'NABatRecordingAdmin',
+    'ComputedPulseAnnotationAdmin',
 ]

bats_ai/core/admin/pulse_annotation.py

@@ -0,0 +1,13 @@
+from django.contrib import admin
+
+from bats_ai.core.models import ComputedPulseAnnotation
+
+
+@admin.register(ComputedPulseAnnotation)
+class ComputedPulseAnnotationAdmin(admin.ModelAdmin):
+    list_display = [
+        'id',
+        'recording',
+        'bounding_box',
+    ]
+    list_select_related = True

bats_ai/core/admin/spectrogram_svg.py

@@ -0,0 +1,22 @@
+from django.contrib import admin
+
+from bats_ai.core.models import SpectrogramSvg
+
+
+@admin.register(SpectrogramSvg)
+class SpectrogramSvgAdmin(admin.ModelAdmin):
+    list_display = [
+        'pk',
+        'content_type',
+        'object_id',
+        'index',
+        'image_file',
+    ]
+    list_select_related = True
+    readonly_fields = [
+        'pk',
+        'content_type',
+        'object_id',
+        'index',
+        'image_file',
+    ]

bats_ai/core/migrations/0024_spectrogramsvg_computedpulseannotation.py

@@ -0,0 +1,41 @@
+# Generated by Django 4.2.23 on 2025-12-08 22:19
+
+import bats_ai.core.models.spectrogram_vector
+import django.contrib.gis.db.models.fields
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('contenttypes', '0002_remove_content_type_name'),
+        ('core', '0023_recordingtag_recording_tags_and_more'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='SpectrogramSvg',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('object_id', models.PositiveIntegerField()),
+                ('type', models.CharField(choices=[('spectrogram', 'Spectrogram'), ('compressed', 'Compressed')], default='spectrogram', max_length=20)),
+                ('index', models.PositiveIntegerField()),
+                ('image_file', models.FileField(upload_to=bats_ai.core.models.spectrogram_vector.spectrogram_svg_upload_to)),
+                ('content_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='contenttypes.contenttype')),
+            ],
+            options={
+                'ordering': ['index'],
+            },
+        ),
+        migrations.CreateModel(
+            name='ComputedPulseAnnotation',
+            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()),
+                ('recording', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.recording')),
+            ],
+        ),
+    ]

bats_ai/core/models/__init__.py

@@ -5,13 +5,15 @@
 from .grts_cells import GRTSCells
 from .image import Image
 from .processing_task import ProcessingTask, ProcessingTaskType
+from .pulse_annotation import ComputedPulseAnnotation
 from .recording import Recording, RecordingTag
 from .recording_annotation import RecordingAnnotation
 from .recording_annotation_status import RecordingAnnotationStatus
 from .sequence_annotations import SequenceAnnotations
 from .species import Species
 from .spectrogram import Spectrogram
 from .spectrogram_image import SpectrogramImage
+from .spectrogram_vector import SpectrogramSvg
 
 __all__ = [
     'Annotations',
@@ -30,4 +32,6 @@
     'ProcessingTaskType',
     'ExportedAnnotationFile',
     'SpectrogramImage',
+    'SpectrogramSvg',
+    'ComputedPulseAnnotation',
 ]

bats_ai/core/models/compressed_spectrogram.py

@@ -9,6 +9,7 @@
 from .recording import Recording
 from .spectrogram import Spectrogram
 from .spectrogram_image import SpectrogramImage
+from .spectrogram_vector import SpectrogramSvg
 
 
 # TimeStampedModel also provides "created" and "modified" fields
@@ -17,6 +18,7 @@ class CompressedSpectrogram(TimeStampedModel, models.Model):
     spectrogram = models.ForeignKey(Spectrogram, on_delete=models.CASCADE)
     length = models.IntegerField()
     images = GenericRelation(SpectrogramImage)
+    vector_images = GenericRelation(SpectrogramSvg)
     starts = ArrayField(ArrayField(models.IntegerField()))
     stops = ArrayField(ArrayField(models.IntegerField()))
     widths = ArrayField(ArrayField(models.IntegerField()))
@@ -28,6 +30,11 @@ 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 vector_url_list(self):
+        images = self.vector_images.filter(type='compressed').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."""

bats_ai/core/models/pulse_annotation.py

@@ -0,0 +1,10 @@
+from django.contrib.gis.db import models
+
+from .recording import Recording
+
+
+class ComputedPulseAnnotation(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()

bats_ai/core/models/spectrogram.py

@@ -7,11 +7,13 @@
 
 from .recording import Recording
 from .spectrogram_image import SpectrogramImage
+from .spectrogram_vector import SpectrogramSvg
 
 
 class Spectrogram(TimeStampedModel, models.Model):
     recording = models.ForeignKey(Recording, on_delete=models.CASCADE)
     images = GenericRelation(SpectrogramImage)
+    vector_images = GenericRelation(SpectrogramSvg)
     width = models.IntegerField()  # pixels
     height = models.IntegerField()  # pixels
     duration = models.IntegerField()  # milliseconds
@@ -24,6 +26,11 @@ def image_url_list(self):
         images = self.images.filter(type='spectrogram').order_by('index')
         return [default_storage.url(img.image_file.name) for img in images]
 
+    @property
+    def vector_url_list(self):
+        images = self.vector_images.filter(type='spectrogram').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."""

bats_ai/core/models/spectrogram_vector.py

@@ -0,0 +1,43 @@
+from django.contrib.contenttypes.fields import GenericForeignKey
+from django.contrib.contenttypes.models import ContentType
+from django.db import models
+from django.dispatch import receiver
+
+
+def spectrogram_svg_upload_to(instance, filename):
+    related = instance.content_object
+
+    recording = getattr(related, 'recording', None) or getattr(related, 'nabat_recording', None)
+    recording_id = getattr(recording, 'id', None)
+
+    if not recording_id:
+        raise ValueError('Related content must have a recording or nabat_recording.')
+
+    return f'recording_{recording_id}/{instance.type}/svg_{instance.index}_{filename}'
+
+
+class SpectrogramSvg(models.Model):
+    SPECTROGRAM_TYPE_CHOICES = [
+        ('spectrogram', 'Spectrogram'),
+        ('compressed', 'Compressed'),
+    ]
+    content_object = GenericForeignKey('content_type', 'object_id')
+
+    content_type = models.ForeignKey(ContentType, on_delete=models.CASCADE)
+    object_id = models.PositiveIntegerField()
+    type = models.CharField(
+        max_length=20,
+        choices=SPECTROGRAM_TYPE_CHOICES,
+        default='spectrogram',
+    )
+    index = models.PositiveIntegerField()
+    image_file = models.FileField(upload_to=spectrogram_svg_upload_to)
+
+    class Meta:
+        ordering = ['index']
+
+
+@receiver(models.signals.pre_delete, sender=SpectrogramSvg)
+def delete_content(sender, instance, **kwargs):
+    if instance.image_file:
+        instance.image_file.delete(save=False)

bats_ai/core/views/recording.py

@@ -1,7 +1,7 @@
 from datetime import datetime
 import json
 import logging
-from typing import List, Optional
+from typing import Any, List, Optional
 
 from django.contrib.auth.models import User
 from django.contrib.gis.geos import Point
@@ -16,6 +16,7 @@
 from bats_ai.core.models import (
     Annotations,
     CompressedSpectrogram,
+    ComputedPulseAnnotation,
     Recording,
     RecordingAnnotation,
     RecordingTag,
@@ -127,6 +128,22 @@ class UpdateAnnotationsSchema(Schema):
     id: int | None
 
 
+class ComputedPulseAnnotationSchema(Schema):
+    id: int | None
+    index: int
+    bounding_box: Any
+    contours: list
+
+    @classmethod
+    def from_orm(cls, obj: ComputedPulseAnnotation):
+        return cls(
+            id=obj.id,
+            index=obj.index,
+            contours=obj.contours,
+            bounding_box=json.loads(obj.bounding_box.geojson)
+        )
+
+
 @router.post('/')
 def create_recording(
     request: HttpRequest,
@@ -373,6 +390,7 @@ def get_spectrogram(request: HttpRequest, id: int):
 
     spectro_data = {
         'urls': spectrogram.image_url_list,
+        'vectors': spectrogram.vector_url_list,
         'spectroInfo': {
             'spectroId': spectrogram.pk,
             'width': spectrogram.width,
@@ -443,6 +461,7 @@ def get_spectrogram_compressed(request: HttpRequest, id: int):
 
     spectro_data = {
         'urls': compressed_spectrogram.image_url_list,
+        'vectors': compressed_spectrogram.vector_url_list,
         'spectroInfo': {
             'spectroId': compressed_spectrogram.pk,
             'width': compressed_spectrogram.spectrogram.width,
@@ -526,6 +545,26 @@ def get_annotations(request: HttpRequest, id: int):
         return {'error': 'Recording not found'}
 
 
+@router.get('/{id}/pulse_data')
+def get_pulse_data(request: HttpRequest, id: int):
+    try:
+        recording = Recording.objects.get(pk=id)
+        if recording.owner == request.user or recording.public:
+            computed_pulse_annotation_qs = ComputedPulseAnnotation.objects.filter(
+                recording=recording
+            ).order_by('index')
+            return [
+                ComputedPulseAnnotationSchema.from_orm(pulse)
+                for pulse in computed_pulse_annotation_qs.all()
+            ]
+        else:
+            return {
+                'error': 'Permission denied. You do not own this recording, and it is not public.'
+            }
+    except Recording.DoesNotExist:
+        return {'error': 'Recording not found'}
+
+
 @router.get('/{id}/annotations/other_users')
 def get_other_user_annotations(request: HttpRequest, id: int):
     try: