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BatBot initial testing and integration #305

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f1c3782
initial testing and integration
BryonLewis Jan 16, 2026
db3834a
batbot metadata parser
BryonLewis Jan 16, 2026
4253365
Merge branch 'main' into batbot-integration
BryonLewis Jan 19, 2026
5c3d9a8
batbot spectrogram generation
BryonLewis Jan 22, 2026
1c24339
remove old spectrogram generation code
BryonLewis Jan 22, 2026
8878620
swap back to using the github installation for batbot
BryonLewis Jan 26, 2026
e96da72
Merge branch 'batbot-integration' of https://github.com/Kitware/batai…
BryonLewis Jan 26, 2026
9623991
use temp branch for start/stop fixes
BryonLewis Jan 27, 2026
a1d5eed
increase accuracy for spectrograms and annotations
BryonLewis Jan 27, 2026
a438016
thumbnail centering fixes
BryonLewis Jan 27, 2026
b1ae312
add noise filter
BryonLewis Jan 28, 2026
4aa3016
contour testing
BryonLewis Jan 28, 2026
02d6d27
update batbot
BryonLewis Jan 29, 2026
439dae3
Merge branch 'main' into batbot-integration
BryonLewis Jan 30, 2026
d95e58b
fix NABat spectrogram generation
BryonLewis Jan 30, 2026
0bed12a
client linting
BryonLewis Jan 30, 2026
dacd997
removing integration notes
BryonLewis Jan 30, 2026
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2 changes: 1 addition & 1 deletion bats_ai/core/management/commands/generateNABat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,10 @@

from bats_ai.core.models import Species
from bats_ai.core.models.nabat import NABatRecording, NABatRecordingAnnotation
from bats_ai.core.utils.batbot_metadata import generate_spectrogram_assets
from bats_ai.utils.spectrogram_utils import (
generate_nabat_compressed_spectrogram,
generate_nabat_spectrogram,
generate_spectrogram_assets,
)

fake = Faker()
Expand Down
163 changes: 163 additions & 0 deletions bats_ai/core/migrations/0026_alter_annotations_end_time_and_more.py
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@@ -0,0 +1,163 @@
# Generated by Django 4.2.23 on 2026-01-27 18:11

import django.contrib.postgres.fields
from django.db import migrations, models


class Migration(migrations.Migration):
dependencies = [
('core', '0025_configuration_mark_annotations_completed_enabled_and_more'),
]

operations = [
migrations.AlterField(
model_name='annotations',
name='end_time',
field=models.FloatField(blank=True, null=True),
),
migrations.AlterField(
model_name='annotations',
name='high_freq',
field=models.FloatField(blank=True, null=True),
),
migrations.AlterField(
model_name='annotations',
name='low_freq',
field=models.FloatField(blank=True, null=True),
),
migrations.AlterField(
model_name='annotations',
name='start_time',
field=models.FloatField(blank=True, null=True),
),
migrations.AlterField(
model_name='compressedspectrogram',
name='length',
field=models.FloatField(),
),
migrations.AlterField(
model_name='compressedspectrogram',
name='starts',
field=django.contrib.postgres.fields.ArrayField(
base_field=django.contrib.postgres.fields.ArrayField(
base_field=models.FloatField(), size=None
),
size=None,
),
),
migrations.AlterField(
model_name='compressedspectrogram',
name='stops',
field=django.contrib.postgres.fields.ArrayField(
base_field=django.contrib.postgres.fields.ArrayField(
base_field=models.FloatField(), size=None
),
size=None,
),
),
migrations.AlterField(
model_name='compressedspectrogram',
name='widths',
field=django.contrib.postgres.fields.ArrayField(
base_field=django.contrib.postgres.fields.ArrayField(
base_field=models.FloatField(), size=None
),
size=None,
),
),
migrations.AlterField(
model_name='nabatcompressedspectrogram',
name='length',
field=models.FloatField(),
),
migrations.AlterField(
model_name='nabatcompressedspectrogram',
name='starts',
field=django.contrib.postgres.fields.ArrayField(
base_field=django.contrib.postgres.fields.ArrayField(
base_field=models.FloatField(), size=None
),
size=None,
),
),
migrations.AlterField(
model_name='nabatcompressedspectrogram',
name='stops',
field=django.contrib.postgres.fields.ArrayField(
base_field=django.contrib.postgres.fields.ArrayField(
base_field=models.FloatField(), size=None
),
size=None,
),
),
migrations.AlterField(
model_name='nabatcompressedspectrogram',
name='widths',
field=django.contrib.postgres.fields.ArrayField(
base_field=django.contrib.postgres.fields.ArrayField(
base_field=models.FloatField(), size=None
),
size=None,
),
),
migrations.AlterField(
model_name='nabatspectrogram',
name='duration',
field=models.FloatField(),
),
migrations.AlterField(
model_name='nabatspectrogram',
name='frequency_max',
field=models.FloatField(),
),
migrations.AlterField(
model_name='nabatspectrogram',
name='frequency_min',
field=models.FloatField(),
),
migrations.AlterField(
model_name='nabatspectrogram',
name='height',
field=models.FloatField(),
),
migrations.AlterField(
model_name='nabatspectrogram',
name='width',
field=models.FloatField(),
),
migrations.AlterField(
model_name='sequenceannotations',
name='end_time',
field=models.FloatField(blank=True, null=True),
),
migrations.AlterField(
model_name='sequenceannotations',
name='start_time',
field=models.FloatField(blank=True, null=True),
),
migrations.AlterField(
model_name='spectrogram',
name='duration',
field=models.FloatField(),
),
migrations.AlterField(
model_name='spectrogram',
name='frequency_max',
field=models.FloatField(),
),
migrations.AlterField(
model_name='spectrogram',
name='frequency_min',
field=models.FloatField(),
),
migrations.AlterField(
model_name='spectrogram',
name='height',
field=models.FloatField(),
),
migrations.AlterField(
model_name='spectrogram',
name='width',
field=models.FloatField(),
),
]
8 changes: 4 additions & 4 deletions bats_ai/core/models/annotations.py
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Expand Up @@ -10,10 +10,10 @@
class Annotations(TimeStampedModel, models.Model):
recording = models.ForeignKey(Recording, on_delete=models.CASCADE)
owner = models.ForeignKey(User, on_delete=models.CASCADE)
start_time = models.IntegerField(blank=True, null=True)
end_time = models.IntegerField(blank=True, null=True)
low_freq = models.IntegerField(blank=True, null=True)
high_freq = models.IntegerField(blank=True, null=True)
start_time = models.FloatField(blank=True, null=True)
end_time = models.FloatField(blank=True, null=True)
low_freq = models.FloatField(blank=True, null=True)
high_freq = models.FloatField(blank=True, null=True)
type = models.TextField(blank=True, null=True)
species = models.ManyToManyField(Species)
comments = models.TextField(blank=True, null=True)
Expand Down
8 changes: 4 additions & 4 deletions bats_ai/core/models/compressed_spectrogram.py
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Expand Up @@ -15,11 +15,11 @@
class CompressedSpectrogram(TimeStampedModel, models.Model):
recording = models.ForeignKey(Recording, on_delete=models.CASCADE)
spectrogram = models.ForeignKey(Spectrogram, on_delete=models.CASCADE)
length = models.IntegerField()
length = models.FloatField()
images = GenericRelation(SpectrogramImage)
starts = ArrayField(ArrayField(models.IntegerField()))
stops = ArrayField(ArrayField(models.IntegerField()))
widths = ArrayField(ArrayField(models.IntegerField()))
starts = ArrayField(ArrayField(models.FloatField()))
stops = ArrayField(ArrayField(models.FloatField()))
widths = ArrayField(ArrayField(models.FloatField()))
cache_invalidated = models.BooleanField(default=True)

@property
Expand Down
8 changes: 4 additions & 4 deletions bats_ai/core/models/nabat/nabat_compressed_spectrogram.py
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Expand Up @@ -17,10 +17,10 @@ class NABatCompressedSpectrogram(TimeStampedModel, models.Model):
nabat_recording = models.ForeignKey(NABatRecording, on_delete=models.CASCADE)
spectrogram = models.ForeignKey(NABatSpectrogram, on_delete=models.CASCADE)
images = GenericRelation(SpectrogramImage)
length = models.IntegerField()
starts = ArrayField(ArrayField(models.IntegerField()))
stops = ArrayField(ArrayField(models.IntegerField()))
widths = ArrayField(ArrayField(models.IntegerField()))
length = models.FloatField()
starts = ArrayField(ArrayField(models.FloatField()))
stops = ArrayField(ArrayField(models.FloatField()))
widths = ArrayField(ArrayField(models.FloatField()))
cache_invalidated = models.BooleanField(default=True)

@property
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10 changes: 5 additions & 5 deletions bats_ai/core/models/nabat/nabat_spectrogram.py
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Expand Up @@ -18,11 +18,11 @@
class NABatSpectrogram(TimeStampedModel, models.Model):
nabat_recording = models.ForeignKey(NABatRecording, on_delete=models.CASCADE)
images = GenericRelation(SpectrogramImage)
width = models.IntegerField() # pixels
height = models.IntegerField() # pixels
duration = models.IntegerField() # milliseconds
frequency_min = models.IntegerField() # hz
frequency_max = models.IntegerField() # hz
width = models.FloatField() # pixels
height = models.FloatField() # pixels
Comment on lines +21 to +22
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@naglepuff naglepuff Feb 2, 2026

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For these two fields specifically, which I believe are just a pixel count, would it make sense to just keep them as integers?

duration = models.FloatField() # milliseconds
frequency_min = models.FloatField() # hz
frequency_max = models.FloatField() # hz

@property
def image_url_list(self):
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4 changes: 2 additions & 2 deletions bats_ai/core/models/sequence_annotations.py
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Expand Up @@ -8,8 +8,8 @@
class SequenceAnnotations(models.Model):
recording = models.ForeignKey(Recording, on_delete=models.CASCADE)
owner = models.ForeignKey(User, on_delete=models.CASCADE)
start_time = models.IntegerField(blank=True, null=True)
end_time = models.IntegerField(blank=True, null=True)
start_time = models.FloatField(blank=True, null=True)
end_time = models.FloatField(blank=True, null=True)
type = models.TextField(blank=True, null=True)
comments = models.TextField(blank=True, null=True)
species = models.ManyToManyField(Species)
10 changes: 5 additions & 5 deletions bats_ai/core/models/spectrogram.py
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Expand Up @@ -12,11 +12,11 @@
class Spectrogram(TimeStampedModel, models.Model):
recording = models.ForeignKey(Recording, on_delete=models.CASCADE)
images = GenericRelation(SpectrogramImage)
width = models.IntegerField() # pixels
height = models.IntegerField() # pixels
duration = models.IntegerField() # milliseconds
frequency_min = models.IntegerField() # hz
frequency_max = models.IntegerField() # hz
width = models.FloatField() # pixels
height = models.FloatField() # pixels
Comment on lines +15 to +16
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@naglepuff naglepuff Feb 2, 2026

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Same question here. Would it be more accurate to use integers for height/width?

duration = models.FloatField() # milliseconds
frequency_min = models.FloatField() # hz
frequency_max = models.FloatField() # hz

@property
def image_url_list(self):
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5 changes: 3 additions & 2 deletions bats_ai/core/tasks/nabat/tasks.py
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Expand Up @@ -6,10 +6,10 @@

from bats_ai.core.models import Configuration, ProcessingTask, Species
from bats_ai.core.models.nabat import NABatRecording, NABatRecordingAnnotation
from bats_ai.core.utils.batbot_metadata import generate_spectrogram_assets
from bats_ai.utils.spectrogram_utils import (
generate_nabat_compressed_spectrogram,
generate_nabat_spectrogram,
generate_spectrogram_assets,
predict_from_compressed,
)

Expand Down Expand Up @@ -60,7 +60,8 @@ def generate_spectrograms(

try:
config = Configuration.objects.first()
if config and config.run_inference_on_upload:
# TODO: Disabled until prediction is in batbot
if config and config.run_inference_on_upload and False:
Comment on lines +63 to +64
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@naglepuff naglepuff Feb 2, 2026

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Is there an issue in batbot or BatAI tracking this? It would be nice to have a link to an issue in either of the GH repos here while we wait for this feature.

It might also be nice to add some sort of banner in the UI somewhere that tells users that prediction is disabled for now.

self.update_state(
state='Progress',
meta={'description': 'Running Prediction on Spectrogram'},
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17 changes: 14 additions & 3 deletions bats_ai/core/tasks/tasks.py
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@@ -1,5 +1,6 @@
import logging
import os
import shutil
import tempfile

from django.contrib.contenttypes.models import ContentType
Expand All @@ -15,7 +16,8 @@
Spectrogram,
SpectrogramImage,
)
from bats_ai.utils.spectrogram_utils import generate_spectrogram_assets, predict_from_compressed
from bats_ai.core.utils.batbot_metadata import generate_spectrogram_assets
from bats_ai.utils.spectrogram_utils import predict_from_compressed

logging.basicConfig(level=logging.INFO)
logger = logging.getLogger('NABatDataRetrieval')
Expand All @@ -26,7 +28,15 @@ def recording_compute_spectrogram(recording_id: int):
recording = Recording.objects.get(pk=recording_id)

with tempfile.TemporaryDirectory() as tmpdir:
results = generate_spectrogram_assets(recording.audio_file, tmpdir)
# Copy the audio file from FileField to a temporary file
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@naglepuff naglepuff Feb 2, 2026

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Is this needed because of how batbot handles spectrogram generation?

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@BryonLewis BryonLewis Feb 2, 2026

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yeah it no longer is using a fileHandle or something like that it. It needs a real file.

audio_filename = os.path.basename(recording.audio_file.name)
temp_audio_path = os.path.join(tmpdir, audio_filename)

with recording.audio_file.open('rb') as source_file:
with open(temp_audio_path, 'wb') as dest_file:
shutil.copyfileobj(source_file, dest_file)

results = generate_spectrogram_assets(temp_audio_path, output_folder=tmpdir)
# Create or get Spectrogram
spectrogram, _ = Spectrogram.objects.get_or_create(
recording=recording,
Expand Down Expand Up @@ -79,7 +89,8 @@ def recording_compute_spectrogram(recording_id: int):
)

config = Configuration.objects.first()
if config and config.run_inference_on_upload:
# TODO: Disabled until prediction is in batbot
if config and config.run_inference_on_upload and False:
Comment on lines +92 to +93
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@naglepuff naglepuff Feb 2, 2026

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Same idea here about a linked issue/visibility for users on the front-end web side.

predict_results = predict_from_compressed(compressed_obj)
label = predict_results['label']
score = predict_results['score']
Expand Down
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