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Enable mask images and batbot metadata in NABat #530

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82 changes: 82 additions & 0 deletions bats_ai/core/views/nabat/nabat_recording.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import base64
import json
import logging
from typing import TYPE_CHECKING, Any

from django.conf import settings
from django.db import transaction
Expand All @@ -17,12 +18,17 @@
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
from bats_ai.core.views.species import SpeciesSchema

if TYPE_CHECKING:
from bats_ai.core.views.recording import PulseMetadataSlopesSchema


logger = logging.getLogger(__name__)
router = RouterPaginated()

Expand Down Expand Up @@ -590,3 +596,79 @@ 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]
20 changes: 20 additions & 0 deletions client/src/api/NABatApi.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@ import {
type Spectrogram,
type UpdateFileAnnotation,
type Species,
type ComputedPulseContour,
type PulseMetadata,
} from "./api";

export interface NABatRecordingCompleteResponse {
Expand Down Expand Up @@ -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,
Expand All @@ -292,4 +310,6 @@ export {
getNABatConfigurationRecordings,
exportNABatAnnotations,
adminNaBatUpdateSpecies,
getNabatPulseContours,
getNabatPulseMetadata,
};
12 changes: 11 additions & 1 deletion client/src/components/PulseMetadataButton.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -22,6 +23,7 @@ export default defineComponent({
viewPulseMetadataLayer,
toggleViewPulseMetadataLayer,
loadPulseMetadata,
loadNabatPulseMetadata,
pulseMetadataList,
pulseMetadataLoading,
pulseMetadataLineColor,
Expand All @@ -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();
};
Expand Down
36 changes: 24 additions & 12 deletions client/src/components/SpectrogramViewer.vue
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Expand Up @@ -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: () => [],
Expand Down Expand Up @@ -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);
Expand Down
42 changes: 27 additions & 15 deletions client/src/components/ThumbnailViewer.vue
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Expand Up @@ -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: () => [],
Expand Down Expand Up @@ -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);
Expand Down
19 changes: 17 additions & 2 deletions client/src/components/geoJS/LayerManager.vue
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Expand Up @@ -101,13 +101,17 @@ export default defineComponent({
contoursEnabled,
contourOpacity,
loadContours,
loadNabatContours,
isNaBat,
nabatApiToken,
computedPulseContours,
transparencyThreshold,
} = useState();
const {
viewPulseMetadataLayer,
pulseMetadataList,
loadPulseMetadata,
loadNabatPulseMetadata,
clearPulseMetadata,
pulseMetadataLineColor,
pulseMetadataLineSize,
Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down
14 changes: 14 additions & 0 deletions client/src/use/usePulseMetadata.ts
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@@ -1,5 +1,6 @@
import { ref, type Ref, watch } from "vue";
import { getPulseMetadata, type PulseMetadata } from "../api/api";
import { getNabatPulseMetadata } from "@/api/NABatApi";

const STORAGE_KEY = "pulseMetadata";

Expand Down Expand Up @@ -79,6 +80,18 @@ async function loadPulseMetadata(recordingId: number) {
}
}

async function loadNabatPulseMetadata(recordingId: string, apiToken: string) {
pulseMetadataLoading.value = true;
try {
pulseMetadataList.value = await getNabatPulseMetadata(
recordingId,
apiToken,
);
} finally {
pulseMetadataLoading.value = false;
}
}

function clearPulseMetadata() {
pulseMetadataList.value = [];
}
Expand Down Expand Up @@ -144,6 +157,7 @@ export default function usePulseMetadata() {
pulseMetadataList,
pulseMetadataLoading,
loadPulseMetadata,
loadNabatPulseMetadata,
clearPulseMetadata,
viewPulseMetadataLayer,
toggleViewPulseMetadataLayer,
Expand Down
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