Enable mask images and batbot metadata in NABat

bats_ai/core/views/guanometadata.py

@@ -1,10 +1,10 @@
 from __future__ import annotations
 
 import contextlib
+from datetime import datetime
 import logging
 import os
 import tempfile
-from typing import TYPE_CHECKING
 
 from django.http import HttpRequest, JsonResponse
 from ninja import File, Schema
@@ -15,10 +15,6 @@
 
 from bats_ai.core.utils.guano_utils import extract_guano_metadata
 
-if TYPE_CHECKING:
-    from datetime import datetime
-
-
 router = RouterPaginated()
 logger = logging.getLogger(__name__)
 

bats_ai/core/views/nabat/nabat_configuration.py

@@ -3,7 +3,8 @@
 from datetime import date, datetime, timedelta
 import json
 import logging
-from typing import TYPE_CHECKING, Any, Literal
+from typing import Any, Literal
+import uuid
 
 from django.contrib.gis.db.models import functions as gis_functions
 from django.contrib.gis.geos import Point, Polygon
@@ -20,9 +21,6 @@
 from bats_ai.core.tasks.nabat.nabat_export_task import export_nabat_annotations_task
 from bats_ai.core.tasks.nabat.nabat_update_species import update_nabat_species
 
-if TYPE_CHECKING:
-    import uuid
-
 logger = logging.getLogger(__name__)
 
 router = Router()

bats_ai/core/views/nabat/nabat_recording.py

@@ -3,6 +3,7 @@
 import base64
 import json
 import logging
+from typing import Any
 
 from django.conf import settings
 from django.db import transaction
@@ -17,10 +18,14 @@
 from bats_ai.core.models import ProcessingTask, ProcessingTaskType, Species
 from bats_ai.core.models.nabat import (
     NABatCompressedSpectrogram,
+    NABatPulseMetadata,
     NABatRecording,
     NABatRecordingAnnotation,
 )
 from bats_ai.core.tasks.nabat.nabat_data_retrieval import nabat_recording_initialize
+
+# Real (not TYPE_CHECKING) import: pydantic needs this at runtime to build NABatPulseMetadataSchema.
+from bats_ai.core.views.recording import PulseMetadataSlopesSchema
 from bats_ai.core.views.species import SpeciesSchema
 
 logger = logging.getLogger(__name__)
@@ -590,3 +595,79 @@ def delete_recording_annotation(
     # Check permission
     annotation.delete()
     return "Recording annotation deleted successfully."
+
+
+class NABatPulseContourSchema(Schema):
+    id: int | None
+    index: int
+    bounding_box: Any
+    contours: list
+
+    @classmethod
+    def from_orm(cls, obj: NABatPulseMetadata):
+        return cls(
+            id=obj.id,
+            index=obj.index,
+            contours=obj.contours if obj.contours is not None else [],
+            bounding_box=json.loads(obj.bounding_box.geojson),
+        )
+
+
+class NABatPulseMetadataSchema(Schema):
+    id: int | None
+    index: int
+    curve: list[list[float]] | None = None
+    char_freq: list[float] | None = None
+    knee: list[float] | None = None
+    heel: list[float] | None = None
+    slopes: PulseMetadataSlopesSchema | None = None
+
+    @classmethod
+    def from_orm(cls, obj: NABatPulseMetadata):
+        def point_to_list(pt):
+            if pt is None:
+                return None
+            return [pt.x, pt.y]
+
+        def linestring_to_list(ls):
+            if ls is None:
+                return None
+            return [[c[0], c[1]] for c in ls.coords]
+
+        return cls(
+            id=obj.id,
+            index=obj.index,
+            curve=linestring_to_list(obj.curve),
+            char_freq=point_to_list(obj.char_freq),
+            knee=point_to_list(obj.knee),
+            heel=point_to_list(obj.heel),
+            slopes=obj.slopes,
+        )
+
+
+@router.get("/{pk}/pulse_contours", auth=None)
+def get_pulse_contours(request: HttpRequest, pk: int, api_token: str):
+    recording = get_object_or_404(NABatRecording, pk=pk)
+
+    email_or_response = get_email_if_authorized(request, api_token, recording.recording_id)
+    if isinstance(email_or_response, JsonResponse):
+        return email_or_response
+
+    computed_pulse_annotation_qs = NABatPulseMetadata.objects.filter(
+        nabat_recording=recording
+    ).order_by("index")
+    return [NABatPulseContourSchema.from_orm(pulse) for pulse in computed_pulse_annotation_qs]
+
+
+@router.get("/{pk}/pulse_metadata", auth=None)
+def get_pulse_data(request: HttpRequest, pk: int, api_token: str):
+    recording = get_object_or_404(NABatRecording, pk=pk)
+
+    email_or_response = get_email_if_authorized(request, api_token, recording.recording_id)
+    if isinstance(email_or_response, JsonResponse):
+        return email_or_response
+
+    computed_pulse_annotation_qs = NABatPulseMetadata.objects.filter(
+        nabat_recording=recording
+    ).order_by("index")
+    return [NABatPulseMetadataSchema.from_orm(pulse) for pulse in computed_pulse_annotation_qs]

bats_ai/core/views/recording.py

@@ -31,13 +31,12 @@
 )
 from bats_ai.core.tasks.tasks import recording_compute_spectrogram
 from bats_ai.core.views.recording_location import _parse_bbox, filter_recordings_by_map_bbox
+from bats_ai.core.views.recording_tag import RecordingTagSchema
 from bats_ai.core.views.species import SpeciesSchema
 
 if TYPE_CHECKING:
     from django.http import HttpRequest
 
-    from bats_ai.core.views.recording_tag import RecordingTagSchema
-
 logger = logging.getLogger(__name__)
 
 

client/src/api/NABatApi.ts

@@ -6,6 +6,8 @@ import {
   type Spectrogram,
   type UpdateFileAnnotation,
   type Species,
+  type ComputedPulseContour,
+  type PulseMetadata,
 } from "./api";
 
 export interface NABatRecordingCompleteResponse {
@@ -275,6 +277,22 @@ async function exportNABatAnnotations(
   return response.data;
 }
 
+async function getNabatPulseContours(recordingId: string, apiToken: string) {
+  const result = await axiosInstance.get<ComputedPulseContour[]>(
+    `nabat/recording/${recordingId}/pulse_contours`,
+    { params: { api_token: apiToken } },
+  );
+  return result.data;
+}
+
+async function getNabatPulseMetadata(recordingId: string, apiToken: string) {
+  const result = await axiosInstance.get<PulseMetadata[]>(
+    `nabat/recording/${recordingId}/pulse_metadata`,
+    { params: { api_token: apiToken } },
+  );
+  return result.data;
+}
+
 export {
   postNABatRecording,
   getNABatSpectrogram,
@@ -292,4 +310,6 @@ export {
   getNABatConfigurationRecordings,
   exportNABatAnnotations,
   adminNaBatUpdateSpecies,
+  getNabatPulseContours,
+  getNabatPulseMetadata,
 };

client/src/components/PulseMetadataButton.vue

@@ -3,6 +3,7 @@ import { defineComponent, ref } from "vue";
 import usePulseMetadata, {
   PULSE_METADATA_LABELS_OPTIONS,
 } from "@use/usePulseMetadata";
+import useState from "@use/useState";
 
 export default defineComponent({
   name: "PulseMetadataButton",
@@ -22,6 +23,7 @@ export default defineComponent({
       viewPulseMetadataLayer,
       toggleViewPulseMetadataLayer,
       loadPulseMetadata,
+      loadNabatPulseMetadata,
       pulseMetadataList,
       pulseMetadataLoading,
       pulseMetadataLineColor,
@@ -35,10 +37,18 @@ export default defineComponent({
       pulseMetadataLabels,
       pulseMetadataDurationFreqLineColor,
     } = usePulseMetadata();
+    const { isNaBat, nabatApiToken } = useState();
 
     const togglePulseMetadata = async () => {
       if (pulseMetadataList.value.length === 0 && props.recordingId != null) {
-        await loadPulseMetadata(Number(props.recordingId));
+        if (isNaBat()) {
+          await loadNabatPulseMetadata(
+            String(props.recordingId),
+            nabatApiToken.value,
+          );
+        } else {
+          await loadPulseMetadata(Number(props.recordingId));
+        }
       }
       toggleViewPulseMetadataLayer();
     };

client/src/components/SpectrogramViewer.vue

@@ -41,6 +41,10 @@ export default defineComponent({
       type: Array as PropType<HTMLImageElement[]>,
       default: () => [],
     },
+    maskLoaded: {
+      type: Boolean,
+      default: false,
+    },
     waveplotImages: {
       type: Array as PropType<HTMLImageElement[]>,
       default: () => [],
@@ -496,18 +500,26 @@ export default defineComponent({
       }
     });
 
-    watch([viewMaskOverlay, maskOverlayOpacity, () => props.maskImages], () => {
-      if (viewMaskOverlay.value && props.maskImages.length) {
-        geoJS.drawMaskImages(
-          props.maskImages,
-          scaledWidth.value,
-          scaledHeight.value,
-          maskOverlayOpacity.value,
-        );
-      } else {
-        geoJS.clearMaskQuadFeatures(true);
-      }
-    });
+    watch(
+      [
+        viewMaskOverlay,
+        maskOverlayOpacity,
+        () => props.maskImages,
+        () => props.maskLoaded,
+      ],
+      () => {
+        if (viewMaskOverlay.value && props.maskImages.length) {
+          geoJS.drawMaskImages(
+            props.maskImages,
+            scaledWidth.value,
+            scaledHeight.value,
+            maskOverlayOpacity.value,
+          );
+        } else {
+          geoJS.clearMaskQuadFeatures(true);
+        }
+      },
+    );
 
     watch([showWaveplot], () => {
       resetViewerBounds(false);

client/src/components/ThumbnailViewer.vue

@@ -28,6 +28,10 @@ export default defineComponent({
       type: Array as PropType<HTMLImageElement[]>,
       default: () => [],
     },
+    maskLoaded: {
+      type: Boolean,
+      default: false,
+    },
     waveplotImages: {
       type: Array as PropType<HTMLImageElement[]>,
       default: () => [],
@@ -259,21 +263,29 @@ export default defineComponent({
       drawWaveplotIfEnabled(finalWidth, finalHeight);
     });
 
-    watch([viewMaskOverlay, maskOverlayOpacity, () => props.maskImages], () => {
-      const { width, height } = getImageDimensions(props.images);
-      const finalWidth = scaledWidth.value || width;
-      const finalHeight = scaledHeight.value || height;
-      if (viewMaskOverlay.value && props.maskImages.length) {
-        geoJS.drawMaskImages(
-          props.maskImages,
-          finalWidth,
-          finalHeight,
-          maskOverlayOpacity.value,
-        );
-      } else {
-        geoJS.clearMaskQuadFeatures(true);
-      }
-    });
+    watch(
+      [
+        viewMaskOverlay,
+        maskOverlayOpacity,
+        () => props.maskImages,
+        () => props.maskLoaded,
+      ],
+      () => {
+        const { width, height } = getImageDimensions(props.images);
+        const finalWidth = scaledWidth.value || width;
+        const finalHeight = scaledHeight.value || height;
+        if (viewMaskOverlay.value && props.maskImages.length) {
+          geoJS.drawMaskImages(
+            props.maskImages,
+            finalWidth,
+            finalHeight,
+            maskOverlayOpacity.value,
+          );
+        } else {
+          geoJS.clearMaskQuadFeatures(true);
+        }
+      },
+    );
 
     watch(viewWaveplot, () => {
       const { width, height } = getImageDimensions(props.images);

client/src/components/geoJS/LayerManager.vue

@@ -101,13 +101,17 @@ export default defineComponent({
       contoursEnabled,
       contourOpacity,
       loadContours,
+      loadNabatContours,
+      isNaBat,
+      nabatApiToken,
       computedPulseContours,
       transparencyThreshold,
     } = useState();
     const {
       viewPulseMetadataLayer,
       pulseMetadataList,
       loadPulseMetadata,
+      loadNabatPulseMetadata,
       clearPulseMetadata,
       pulseMetadataLineColor,
       pulseMetadataLineSize,
@@ -595,7 +599,11 @@ export default defineComponent({
         return;
       }
       if (computedPulseContours.value.length === 0) {
-        await loadContours(new Number(props.recordingId) as number);
+        if (isNaBat()) {
+          await loadNabatContours(props.recordingId);
+        } else {
+          await loadContours(new Number(props.recordingId) as number);
+        }
       }
       if (!contourLayer) {
         contourLayer = new ContourLayer(
@@ -636,7 +644,14 @@ export default defineComponent({
         if (!props.recordingId || !props.spectroInfo?.compressedWidth) return;
         if (viewPulseMetadataLayer.value) {
           if (pulseMetadataList.value.length === 0) {
-            await loadPulseMetadata(Number(props.recordingId));
+            if (isNaBat()) {
+              await loadNabatPulseMetadata(
+                props.recordingId,
+                nabatApiToken.value,
+              );
+            } else {
+              await loadPulseMetadata(Number(props.recordingId));
+            }
           }
           if (!pulseMetadataLayer) {
             pulseMetadataLayer = new PulseMetadataLayer(