Frefresh NABat Integration

bats_ai/core/admin/nabat/admin.py

@@ -1,6 +1,8 @@
 from __future__ import annotations
 
+from django import forms
 from django.contrib import admin
+from django.contrib.gis.db import models as gis_models
 from django.utils.html import format_html_join
 
 from bats_ai.core.models.nabat import (
@@ -9,6 +11,7 @@
     NABatRecordingAnnotation,
     NABatSpectrogram,
 )
+from bats_ai.core.models.nabat.nabat_pulse_metadata import NABatPulseMetadata
 
 
 # Register models for the NaBat category
@@ -88,7 +91,28 @@ class NABatRecordingAdmin(admin.ModelAdmin):
         "comments",
         "recording_location",
         "grts_cell_id",
-        "grts_cell",
+        "sample_frame_id",
     ]
     search_fields = ["name", "recording_id", "recording_location"]
     list_filter = ["name", "recording_id", "recording_location"]
+
+
+@admin.register(NABatPulseMetadata)
+class NABatPulseMetadataAdmin(admin.ModelAdmin):
+    formfield_overrides = {
+        gis_models.GeometryField: {
+            "widget": forms.Textarea(attrs={"rows": 4, "cols": 80}),
+        },
+    }
+
+    list_display = [
+        "nabat_recording",
+        "index",
+        "bounding_box",
+        "curve",
+        "char_freq",
+        "knee",
+        "heel",
+        "slopes",
+    ]
+    list_select_related = True

bats_ai/core/migrations/0041_rename_grts_cell_nabatrecording_sample_frame_id_and_more.py

@@ -0,0 +1,70 @@
+# Generated by Django 6.0.7 on 2026-08-05 20:08
+
+from __future__ import annotations
+
+import django.contrib.gis.db.models.fields
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("core", "0040_alter_grtscells_id"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="nabatrecording",
+            old_name="grts_cell",
+            new_name="sample_frame_id",
+        ),
+        migrations.CreateModel(
+            name="NABatPulseMetadata",
+            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)),
+                (
+                    "curve",
+                    django.contrib.gis.db.models.fields.LineStringField(
+                        blank=True, null=True, srid=4326
+                    ),
+                ),
+                (
+                    "char_freq",
+                    django.contrib.gis.db.models.fields.PointField(
+                        blank=True, null=True, srid=4326
+                    ),
+                ),
+                (
+                    "knee",
+                    django.contrib.gis.db.models.fields.PointField(
+                        blank=True, null=True, srid=4326
+                    ),
+                ),
+                (
+                    "heel",
+                    django.contrib.gis.db.models.fields.PointField(
+                        blank=True, null=True, srid=4326
+                    ),
+                ),
+                ("slopes", models.JSONField(blank=True, null=True)),
+                (
+                    "nabat_recording",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE, to="core.nabatrecording"
+                    ),
+                ),
+            ],
+            options={
+                "verbose_name": "NABat Pulse Metadata",
+                "verbose_name_plural": "NABat Pulse Metadata",
+            },
+        ),
+    ]

bats_ai/core/models/nabat/__init__.py

@@ -1,12 +1,14 @@
 from __future__ import annotations
 
 from .nabat_compressed_spectrogram import NABatCompressedSpectrogram
+from .nabat_pulse_metadata import NABatPulseMetadata
 from .nabat_recording import NABatRecording
 from .nabat_recording_annotation import NABatRecordingAnnotation
 from .nabat_spectrogram import NABatSpectrogram
 
 __all__ = [
     "NABatCompressedSpectrogram",
+    "NABatPulseMetadata",
     "NABatRecording",
     "NABatRecordingAnnotation",
     "NABatSpectrogram",

bats_ai/core/models/nabat/nabat_pulse_metadata.py

@@ -0,0 +1,21 @@
+from __future__ import annotations
+
+from django.contrib.gis.db import models
+
+from .nabat_recording import NABatRecording
+
+
+class NABatPulseMetadata(models.Model):
+    nabat_recording = models.ForeignKey(NABatRecording, 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)
+    curve = models.LineStringField(null=True, blank=True)
+    char_freq = models.PointField(null=True, blank=True)
+    knee = models.PointField(null=True, blank=True)
+    heel = models.PointField(null=True, blank=True)
+    slopes = models.JSONField(null=True, blank=True)
+
+    class Meta:
+        verbose_name = "NABat Pulse Metadata"
+        verbose_name_plural = "NABat Pulse Metadata"

bats_ai/core/models/nabat/nabat_recording.py

@@ -20,7 +20,7 @@ class NABatRecording(TimeStampedModel, models.Model):
     comments = models.TextField(blank=True, null=True)
     recording_location = models.GeometryField(srid=4326, blank=True, null=True)
     grts_cell_id = models.IntegerField(blank=True, null=True)
-    grts_cell = models.IntegerField(blank=True, null=True)
+    sample_frame_id = models.IntegerField(blank=True, null=True)
     public = models.BooleanField(default=False)
     software_name = models.TextField(blank=True, null=True)
     software_developer = models.TextField(blank=True, null=True)

bats_ai/core/tasks/nabat/tasks.py

@@ -9,7 +9,8 @@
 from django.contrib.gis.geos import LineString, Point, Polygon
 import requests
 
-from bats_ai.core.models import ProcessingTask, PulseMetadata
+from bats_ai.core.models import ProcessingTask
+from bats_ai.core.models.nabat import NABatPulseMetadata
 from bats_ai.utils.spectrogram_utils import (
     generate_nabat_compressed_spectrogram,
     generate_nabat_spectrogram,
@@ -66,8 +67,8 @@ def generate_spectrograms(  # noqa: C901, PLR0915
         segment_index_map = {}
         contour_segments = compressed.get("contours", {}).get("segments", [])
         for segment in contour_segments:
-            pulse_metadata_obj, _ = PulseMetadata.objects.get_or_create(
-                recording=compressed_obj.recording,
+            pulse_metadata_obj, _ = NABatPulseMetadata.objects.get_or_create(
+                nabat_recording=compressed_obj.nabat_recording,
                 index=segment["segment_index"],
                 defaults={
                     "contours": segment["contours"],
@@ -92,7 +93,7 @@ def generate_spectrograms(  # noqa: C901, PLR0915
                     "heel": Point(segment["heel_ms"], segment["heel_hz"]),
                     "slopes": segment.get("slopes"),
                 }
-                # `PulseMetadata.bounding_box` is non-nullable, so always populate it
+                # `NABatPulseMetadata.bounding_box` is non-nullable, so always populate it
                 # for rows not created from `compressed["contours"]`.
                 segment_bbox = segment.get("bbox")
                 if segment_bbox and len(segment_bbox) == 4:
@@ -121,8 +122,8 @@ def generate_spectrograms(  # noqa: C901, PLR0915
                 if not settings.BATAI_SAVE_SPECTROGRAM_CONTOURS:
                     defaults["contours"] = []
 
-                PulseMetadata.objects.update_or_create(
-                    recording=compressed_obj.recording,
+                NABatPulseMetadata.objects.update_or_create(
+                    nabat_recording=compressed_obj.nabat_recording,
                     index=segment["segment_index"],
                     defaults=defaults,
                 )

bats_ai/core/views/species.py

@@ -2,19 +2,13 @@
 
 from typing import TYPE_CHECKING
 
-from django.db.models import (
-    BooleanField,
-    Case,
-    Exists,
-    OuterRef,
-    Value,
-    When,
-)
+from django.db.models import BooleanField, Case, Exists, OuterRef, Value, When
 from django.shortcuts import get_object_or_404
 from ninja import Query, Router, Schema
 
 from bats_ai.core.constants import DEFAULT_SAMPLE_FRAME_ID
 from bats_ai.core.models import GRTSCells, Recording, Species, SpeciesRange
+from bats_ai.core.models.nabat.nabat_recording import NABatRecording
 from bats_ai.core.utils.grts_utils import normalize_sample_frame_id
 
 if TYPE_CHECKING:
@@ -40,20 +34,29 @@ class SpeciesSchema(Schema):
     in_range: bool | None = None
 
 
+class SpeciesQuerySchema(Schema):
+    grts_cell_id: int | None = None
+    sample_frame_id: int = DEFAULT_SAMPLE_FRAME_ID
+    recording_id: int | None = None
+    nabat: bool | None = None
+
+
 @router.get("/", response=list[SpeciesSchema], auth=None)
-def get_species(
-    request: HttpRequest,
-    grts_cell_id: int | None = Query(None),
-    sample_frame_id: int = Query(DEFAULT_SAMPLE_FRAME_ID),
-    recording_id: int | None = Query(None),
-):
-    sample_frame_id = normalize_sample_frame_id(sample_frame_id)
+def get_species(request: HttpRequest, q: Query[SpeciesQuerySchema]):
+    grts_cell_id = q.grts_cell_id
+    sample_frame_id = normalize_sample_frame_id(q.sample_frame_id)
 
-    if recording_id is not None:
-        recording = get_object_or_404(
-            Recording.objects.only("grts_cell_id", "sample_frame_id"),
-            pk=recording_id,
-        )
+    if q.recording_id is not None:
+        recording = None
+        if not q.nabat:
+            recording = get_object_or_404(
+                Recording.objects.only("grts_cell_id", "sample_frame_id"),
+                pk=q.recording_id,
+            )
+        else:
+            recording = get_object_or_404(
+                NABatRecording.objects.only("grts_cell_id", "sample_frame_id"), pk=q.recording_id
+            )
         grts_cell_id = recording.grts_cell_id
         sample_frame_id = normalize_sample_frame_id(
             recording.sample_frame_id

client/src/api/NABatApi.ts

@@ -5,6 +5,7 @@ import {
   type ProcessingTask,
   type Spectrogram,
   type UpdateFileAnnotation,
+  type Species,
 } from "./api";
 
 export interface NABatRecordingCompleteResponse {
@@ -85,6 +86,25 @@ async function getNABatFileAnnotations(recordingId: number) {
   );
 }
 
+async function getNABatSpecies({
+  recordingId,
+  grtsCellId,
+  sampleFrameId,
+}: {
+  recordingId?: number;
+  grtsCellId?: number;
+  sampleFrameId?: number;
+}) {
+  return axiosInstance.get<Species[]>("/species/", {
+    params: {
+      recording_id: recordingId,
+      grts_cell_id: grtsCellId,
+      sample_frame_id: sampleFrameId,
+      nabat: true,
+    },
+  });
+}
+
 async function getNABatFileAnnotationDetails(
   recordingId: number,
   apiToken?: string,
@@ -261,6 +281,7 @@ export {
   getNABatSpectrogramCompressed,
   getNABatRecordingFileAnnotations,
   getNABatFileAnnotations,
+  getNABatSpecies,
   getNABatFileAnnotationDetails,
   putNABatFileAnnotation,
   patchNABatFileAnnotationLocal,

client/src/views/NABat/NABatSpectrogram.vue

@@ -1,9 +1,10 @@
 <script lang="ts">
 import { defineComponent, onMounted, type Ref, ref, watch } from "vue";
-import { getSpecies, type Species } from "@api/api";
+import { type Species } from "@api/api";
 import {
   getNABatSpectrogram,
   getNABatSpectrogramCompressed,
+  getNABatSpecies,
 } from "@api/NABatApi";
 import SpectrogramViewer from "@components/SpectrogramViewer.vue";
 import { spectroXToTime, type SpectroInfo } from "@components/geoJS/geoJSUtils";
@@ -119,7 +120,7 @@ export default defineComponent({
           spectroInfo.value.end_times = response.data.compressed.end_times;
           viewCompressedOverlay.value = false;
         }
-        const speciesResponse = await getSpecies({
+        const speciesResponse = await getNABatSpecies({
           recordingId: parseInt(props.id),
         });
         // Removing NOISE species from list and any duplicates