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BirdNET on the river

This commit is contained in:
Samuel Ortion 2022-08-12 18:01:01 +02:00
parent 8f7af9da13
commit bd8a7bcbd6
23 changed files with 1156 additions and 1 deletions
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.env Normal file
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CUDA_VISIBLE_DEVICES=""

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.gitignore vendored Normal file
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var/
/.venv/
/analyzer/

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.gitmodules vendored Normal file
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[submodule "BirdNET-Analyzer"]
path = analyzer
url = git@github.com:kahst/BirdNET-Analyzer.git

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.ideas/create_database.sh Executable file
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#! /usr/bin/env bash
# Load config file
config_filepath="./config/analyzer.conf"
if [ -f "$config_filepath" ]; then
source "$config_filepath"
else
echo "Config file not found: $config_filepath"
exit 1
fi
# Check if database location is specified
if [ -z "$DATABASE" ]; then
echo "DATABASE location not specified"
echo "Defaults to ./var/db.sqlite"
DATABASE="./var/db.sqlite"
fi
# Create database according to schema in structure.sql
sqlite3 "$DATABASE" < ./daemon/database/structure.sql

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70
.ideas/fill_taxa.sh Executable file
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#! /usr/bin/env bash
set -e
# Load config file
config_filepath="./config/analyzer.conf"
if [ -f "$config_filepath" ]; then
source "$config_filepath"
else
echo "Config file not found: $config_filepath"
exit 1
fi
# Check if database location is specified
if [ -z "$DATABASE" ]; then
echo "DATABASE location not specified"
echo "Defaults to ./var/db.sqlite"
DATABASE="./var/db.sqlite"
fi
# Check if species list is specified
if [ -z "$SPECIES_LIST" ]; then
echo "SPECIES_LIST location not specified"
exit 1
fi
function insert_taxa()
{
for taxon in "$(cat $SPECIES_LIST)"; do
taxon_scientific_name=$(echo $taxon | cut -d'_' -f1)
taxon_common_name=$(echo $taxon | cut -d'_' -f2)
if $(taxon_exists $taxon_scientific_name); then
echo "Taxon already exists: $taxon_scientific_name"
else
echo "Inserting taxon: $taxon_scientific_name"
statement="INSERT INTO taxon (scientific_name, common_name) VALUES ('$taxon_scientific_name', '$taxon_common_name')"
echo $statement
result=$(sqlite3 "$DATABASE" "$statement")
echo "$result"
fi
done
}
function taxon_exists()
{
taxon_scientific_name="$1"
statement="SELECT scientific_name FROM taxon WHERE scientific_name='$taxon_scientific_name'"
result=$(sqlite3 "$DATABASE" "$statement")
if [ -z "$result" ]; then
return 1
else
return 0
fi
}
function purge_taxa()
{
statement="DELETE FROM taxon"
result=$(sqlite3 "$DATABASE" "$statement")
echo "$result"
}
function main()
{
purge_taxa
insert_taxa
}
main

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.ideas/insert_observation.sh Normal file
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#! /usr/bin/env bash
# Load config file
config_filepath="./config/analyzer.conf"
if [ -f "$config_filepath" ]; then
source "$config_filepath"
else
echo "Config file not found: $config_filepath"
exit 1
fi
# Check if database location is specified
if [ -z "$DATABASE" ]; then
echo "DATABASE location not specified"
echo "Defaults to ./var/db.sqlite"
DATABASE="./var/db.sqlite"
fi
function insert_observation()
{
# Insert observation into database
template=$(cat ./daemon/database/observation_template.sql)
statement=$(echo "$template" | sed "s/:taxon_id/$1/g" | sed "s/:location_id/$2/g" | sed "s/:date/$3/g" | sed "s/:time/$4/g" | sed "s/:confidence/$5/g" | sed "s/:notes/$6/g")
result=$(sqlite3 "$DATABASE" $statement)
echo "$result"
}
function get_taxon_id()
{
# Get taxon id from database
statement="SELECT taxon_id FROM taxon WHERE scientific_name='$1'"
result=$(sqlite3 "$DATABASE" "$statement")
echo "$result"
}
function test()
{
taxon_scientific_name="Erithacus rubecula"
taxon_id=$(get_taxon_id "$taxon_scientific_name")
}

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.ideas/observation_template.sql Normal file
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/** Observation database entry template */
INSERT INTO observation (taxon_id, locality_id, date, time, confidence) VALUES (:taxon_id, :locality_id, :date, :time, :confidence);

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INSTALL.md Normal file
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# Installation Guide for BirdNET-stream
## Requirements
- git
- ffmpeg
- python3
## Install process
### Install python requirements
```bash
sudo apt-get update
sudo apt-get install python3-dev python3-pip
sudo pip3 install --upgrade pip
```
### Install ffmpeg
```bash
sudo apt-get install ffmpeg
```
### Clone BirdNET-stream repository
```bash
git clone https://forge.chapril.org/UncleSamulus/BirdNET-stream.git
### Setup python virtualenv and packages
```bash
python3 -m venv .venv/birdnet-stream
source .venv/birdnet-stream
pip install -r requirements.txt
```

13
README.md
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# BirdNET-stream
BirdNET powered soundscape analysis for bird song identification
<div>
<img src="./media/logo.svg" alt="BirdNET-stream logo image IA generated">
</div>
Realtime BirdNET powered soundscape analysis for bird song identification.
## Acknoledgements
- [BirdNET](https://birdnet.cornell.edu) on which this project relies
- [BirdNET-Pi](https://birdnetpi.com) the great inspiration of this project

1
analyzer Submodule

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Subproject commit 08f031585265e5bc22e86a60ecbb0310c937a29b

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config/analyzer.conf Normal file
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# Configuration file for BirdNET Analyzer
# Coordinates of the recorder
LATITUDE="47.87842"
LONGITUDE="0.21826"
LOCATION="Maison ORTION - Saint-Gervais-en-Belin"
# Species selection list
SPECIES_LIST="./config/species_list.txt"
# Minimal confidence threshold
CONFIDENCE=0.25
# Recording duration (in seconds)
RECORDING_DURATION=15
# Chunk folder location
CHUNK_FOLDER="./var/chunks"
# Audio recording device (pulseaudio)
AUDIO_DEVICE="default"
# Virtual env for BirdNET AI with required packages
PYTHON_VENV="./.venv/birdnet-stream"
# Database location
DATABASE="./var/db.sqlite"

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config/species_list.txt Normal file
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Acanthis cabaret_Lesser Redpoll
Accipiter nisus_Eurasian Sparrowhawk
Acrocephalus palustris_Marsh Warbler
Acrocephalus schoenobaenus_Sedge Warbler
Acrocephalus scirpaceus_Eurasian Reed Warbler
Actitis hypoleucos_Common Sandpiper
Aegithalos caudatus_Long-tailed Tit
Aix galericulata_Mandarin Duck
Alauda arvensis_Eurasian Skylark
Alcedo atthis_Common Kingfisher
Alectoris rufa_Red-legged Partridge
Alopochen aegyptiaca_Egyptian Goose
Anas acuta_Northern Pintail
Anas crecca_Green-winged Teal
Anas platyrhynchos_Mallard
Anser albifrons_Greater White-fronted Goose
Anser anser_Graylag Goose
Anthus petrosus_Rock Pipit
Anthus pratensis_Meadow Pipit
Anthus spinoletta_Water Pipit
Anthus trivialis_Tree Pipit
Apus apus_Common Swift
Aquila chrysaetos_Golden Eagle
Ardea alba_Great Egret
Ardea cinerea_Gray Heron
Ardea purpurea_Purple Heron
Arenaria interpres_Ruddy Turnstone
Aythya ferina_Common Pochard
Aythya fuligula_Tufted Duck
Aythya marila_Greater Scaup
Branta bernicla_Brant
Branta canadensis_Canada Goose
Bubulcus ibis_Cattle Egret
Bucephala clangula_Common Goldeneye
Buteo buteo_Common Buzzard
Calidris alpina_Dunlin
Calidris melanotos_Pectoral Sandpiper
Calidris pugnax_Ruff
Carduelis carduelis_European Goldfinch
Certhia brachydactyla_Short-toed Treecreeper
Certhia familiaris_Eurasian Treecreeper
Cettia cetti_Cetti's Warbler
Charadrius dubius_Little Ringed Plover
Charadrius hiaticula_Common Ringed Plover
Chlidonias hybrida_Whiskered Tern
Chloris chloris_European Greenfinch
Chroicocephalus ridibundus_Black-headed Gull
Ciconia ciconia_White Stork
Cinclus cinclus_White-throated Dipper
Circaetus gallicus_Short-toed Snake-Eagle
Circus aeruginosus_Eurasian Marsh-Harrier
Circus pygargus_Montagu's Harrier
Cisticola juncidis_Zitting Cisticola
Coccothraustes coccothraustes_Hawfinch
Columba livia_Rock Pigeon
Columba oenas_Stock Dove
Columba palumbus_Common Wood-Pigeon
Corvus corax_Common Raven
Corvus corone_Carrion Crow
Corvus frugilegus_Rook
Corvus monedula_Eurasian Jackdaw
Coturnix coturnix_Common Quail
Cuculus canorus_Common Cuckoo
Curruca communis_Greater Whitethroat
Curruca curruca_Lesser Whitethroat
Curruca undata_Dartford Warbler
Cyanistes caeruleus_Eurasian Blue Tit
Cygnus olor_Mute Swan
Delichon urbicum_Common House-Martin
Dendrocopos major_Great Spotted Woodpecker
Dendrocoptes medius_Middle Spotted Woodpecker
Dryobates minor_Lesser Spotted Woodpecker
Dryocopus martius_Black Woodpecker
Egretta garzetta_Little Egret
Emberiza calandra_Corn Bunting
Emberiza cirlus_Cirl Bunting
Emberiza citrinella_Yellowhammer
Emberiza schoeniclus_Reed Bunting
Erithacus rubecula_European Robin
Falco peregrinus_Peregrine Falcon
Falco subbuteo_Eurasian Hobby
Falco tinnunculus_Eurasian Kestrel
Ficedula hypoleuca_European Pied Flycatcher
Fringilla coelebs_Common Chaffinch
Fringilla montifringilla_Brambling
Fulica atra_Eurasian Coot
Gallinago gallinago_Common Snipe
Gallinula chloropus_Eurasian Moorhen
Garrulus glandarius_Eurasian Jay
Grus grus_Common Crane
Haematopus ostralegus_Eurasian Oystercatcher
Himantopus himantopus_Black-winged Stilt
Hippolais polyglotta_Melodious Warbler
Hirundo rustica_Barn Swallow
Ichthyaetus melanocephalus_Mediterranean Gull
Lanius collurio_Red-backed Shrike
Larus argentatus_Herring Gull
Larus canus_Common Gull
Larus fuscus_Lesser Black-backed Gull
Larus marinus_Great Black-backed Gull
Larus michahellis_Yellow-legged Gull
Limosa lapponica_Bar-tailed Godwit
Limosa limosa_Black-tailed Godwit
Linaria cannabina_Eurasian Linnet
Locustella naevia_Common Grasshopper-Warbler
Lophophanes cristatus_Crested Tit
Loxia curvirostra_Red Crossbill
Lullula arborea_Wood Lark
Luscinia megarhynchos_Common Nightingale
Luscinia svecica_Bluethroat
Mareca penelope_Eurasian Wigeon
Mareca strepera_Gadwall
Mergus merganser_Common Merganser
Milvus migrans_Black Kite
Milvus milvus_Red Kite
Morus bassanus_Northern Gannet
Motacilla alba_White Wagtail
Motacilla cinerea_Gray Wagtail
Motacilla flava_Western Yellow Wagtail
Muscicapa striata_Spotted Flycatcher
Numenius arquata_Eurasian Curlew
Nycticorax nycticorax_Black-crowned Night-Heron
Oenanthe oenanthe_Northern Wheatear
Oriolus oriolus_Eurasian Golden Oriole
Pandion haliaetus_Osprey
Panurus biarmicus_Bearded Reedling
Parus major_Great Tit
Passer domesticus_House Sparrow
Passer montanus_Eurasian Tree Sparrow
Perdix perdix_Gray Partridge
Periparus ater_Coal Tit
Pernis apivorus_European Honey-buzzard
Phalacrocorax carbo_Great Cormorant
Phasianus colchicus_Ring-necked Pheasant
Phoenicurus ochruros_Black Redstart
Phoenicurus phoenicurus_Common Redstart
Phylloscopus bonelli_Western Bonelli's Warbler
Phylloscopus collybita_Common Chiffchaff
Phylloscopus ibericus_Iberian Chiffchaff
Phylloscopus trochilus_Willow Warbler
Pica pica_Eurasian Magpie
Picus viridis_Eurasian Green Woodpecker
Pluvialis apricaria_European Golden-Plover
Pluvialis squatarola_Black-bellied Plover
Podiceps cristatus_Great Crested Grebe
Poecile montanus_Willow Tit
Poecile palustris_Marsh Tit
Prunella modularis_Dunnock
Psittacula krameri_Rose-ringed Parakeet
Pyrrhocorax pyrrhocorax_Red-billed Chough
Pyrrhula pyrrhula_Eurasian Bullfinch
Rallus aquaticus_Water Rail
Recurvirostra avosetta_Pied Avocet
Regulus ignicapilla_Common Firecrest
Regulus regulus_Goldcrest
Remiz pendulinus_Eurasian Penduline-Tit
Riparia riparia_Bank Swallow
Saxicola rubetra_Whinchat
Saxicola rubicola_European Stonechat
Serinus serinus_European Serin
Sitta europaea_Eurasian Nuthatch
Spatula clypeata_Northern Shoveler
Spatula querquedula_Garganey
Spinus spinus_Eurasian Siskin
Sterna hirundo_Common Tern
Sternula albifrons_Little Tern
Streptopelia decaocto_Eurasian Collared-Dove
Streptopelia turtur_European Turtle-Dove
Strix aluco_Tawny Owl
Sturnus vulgaris_European Starling
Sylvia atricapilla_Eurasian Blackcap
Sylvia borin_Garden Warbler
Tachybaptus ruficollis_Little Grebe
Tadorna tadorna_Common Shelduck
Thalasseus sandvicensis_Sandwich Tern
Tringa erythropus_Spotted Redshank
Tringa glareola_Wood Sandpiper
Tringa nebularia_Common Greenshank
Tringa ochropus_Green Sandpiper
Tringa totanus_Common Redshank
Troglodytes troglodytes_Eurasian Wren
Turdus iliacus_Redwing
Turdus merula_Eurasian Blackbird
Turdus philomelos_Song Thrush
Turdus pilaris_Fieldfare
Turdus viscivorus_Mistle Thrush
Tyto alba_Barn Owl
Uria aalge_Common Murre
Vanellus vanellus_Northern Lapwing

90
daemon/analyze-stream.sh Executable file
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#! /usr/bin/env bash
set -e
config_filepath="./config/analyzer.conf"
if [ -f "$config_filepath" ]; then
source "$config_filepath"
else
echo "Config file not found: $config_filepath"
exit 1
fi
PYTHON_EXECUTABLE="${PYTHON_VENV}/bin/python3"
check_prerequisites() {
if [[ -z ${LATITUDE} ]]; then
echo "LATITUDE is not set"
exit 1
fi
if [[ -z ${LONGITUDE} ]]; then
echo "LONGITUDE is not set"
exit 1
fi
if [[ -z ${CHUNK_FOLDER} ]]; then
echo "CHUNK_FOLDER is not set"
exit 1
else
if [[ ! -d "${CHUNK_FOLDER}" ]]; then
echo "CHUNK_FOLDER does not exist: ${CHUNK_FOLDER}"
exit 1
else
if [[ ! -d "${CHUNK_FOLDER}/in" ]]; then
echo "Input dir does not exist: ${CHUNK_FOLDER}/in"
exit 1
else
if [[ ! -d "${CHUNK_FOLDER}/out" ]]; then
echo "Output dir does not exist: ${CHUNK_FOLDER}/out"
echo "Creating output dir"
mkdir -p "${CHUNK_FOLDER}/out"
fi
fi
fi
fi
fi
if [[ -z ${SPECIES_LIST} ]];
then
echo "SPECIES_LIST is not set"
exit 1
fi
if [[ -f $PYTHON_EXECUTABLE ]];
then
if $verbose; then
echo "Python executable found: $PYTHON_EXECUTABLE"
fi
else
echo "Python executable not found: $PYTHON_EXECUTABLE"
exit 1
fi
}
# Get array of audio chunks to be processed
get_chunk_list() {
find "$CHUNK_FOLDER/in" -type f -name '*.wav' -exec basename {} \; ! -size 0 | sort
}
# Perform audio chunk analysis on one chunk
analyze_chunk() {
chunk_name=$1
chunk_path="$CHUNK_FOLDER/in/$chunk_name"
output_dir="$CHUNK_FOLDER/out/$chunk_name.d"
mkdir -p "$output_dir"
date=$(echo $chunk_name | cut -d'_' -f2)
week=$(./daemon/weekof.sh $date)
$PYTHON_EXECUTABLE ./analyzer/analyze.py --i $chunk_path --o "$output_dir/model.out.csv" --lat $LATITUDE --lon $LONGITUDE --week $week --min_conf $CONFIDENCE --threads 4 --rtype csv
}
# Perform audio chunk analysis on all recorded chunks
analyze_chunks() {
for chunk_name in $(get_chunk_list); do
analyze_chunk $chunk_name
chunk_path="$CHUNK_FOLDER/in/$chunk_name"
mv $chunk_path "$CHUNK_FOLDER/out/$chunk_name"
done
}
# Get list of current chunk in working directory
chunks=$(get_chunk_list)
# Analyze all chunks in working directory
analyze_chunks $chunks

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daemon/database/scripts/database.py Executable file
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#! /usr/bin/env python3
import sqlite3
import os
verbose = False
"""Load config"""
def load_conf():
with open("./config/analyzer.conf", "r") as f:
conf = f.readlines()
res = dict(map(str.strip, sub.split('=', 1)) for sub in conf if '=' in sub)
return res
# Singleton database instance
database = None
def get_database():
global database
if database is None:
database = sqlite3.connect(CONFIG["DATABASE"])
return database
"""Create the database if it doesn't exist"""
def create_database():
# Create the database
database =
database = get_database()
cursor = database.cursor()
with open("./daemon/database/structure.sql", "r") as f:
cursor.executescript(f.read())
database.commit()
"""Insert an observation into the database"""
def insert_observation(observation):
database = get_database()
cursor = database.cursor()
cursor.execute(f"INSERT INTO observation (taxon_id, locality_id, date, time, confidence) VALUES ({observation['taxon_id']}, {observation['locality_id']}, {observation['date']}, {observation['time']}, {observation['confidence']});")
database.commit()
"""Insert a taxon in database"""
def insert_taxon(taxon):
database = get_database()
cursor = database.cursor()
cursor.execute(f"INSERT INTO taxon (scientific_name, common_name) VALUES ('{taxon['scientific_name']}', '{taxon['common_name']}');")
database.commit()
"""Insert a location into database"""
def insert_locality(locality):
database = get_database()
cursor = database.cursor()
cursor.execute(f"INSERT INTO locality (name, latitude, longitude) VALUES ('{locality['name']}', {locality['latitude']}, {locality['longitude']});")
database.commit()
"""Insert all species from list into database"""
def insert_all_species(species):
database = get_database()
cursor = database.cursor()
for sp in species:
# Check if the species already exists in the database
cursor.execute(f"SELECT * FROM taxon WHERE scientific_name = '{sp[0]}';")
# If it doesn't exist, insert it
if cursor.fetchone() is None:
cursor.execute(f"INSERT INTO taxon (scientific_name, common_name) VALUES ('{sp[0]}', '{sp[1]}');")
database.commit()
CONFIG = load_conf()
def main():
# Create the database if it doesn't exist
if not os.path.exists(CONFIG["DATABASE"]):
create_database()
else:
print("Database already exists")
# Open species list file
with open(CONFIG["SPECIES_LIST"], "r") as f:
species = f.readlines()
species = [sp.split("_") for sp in species]
if __name__ == "__main__":
main()
database.close()

29
daemon/database/structure.sql Normal file
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/** Database structure for BirdNET-stream SQLite*/
/** Taxon table */
CREATE TABLE IF NOT EXISTS taxon (
taxon_id INTEGER PRIMARY KEY,
scientific_name TEXT NOT NULL,
common_name TEXT NOT NULL
);
/** Locality table */
CREATE TABLE IF NOT EXISTS locality (
locality_id INTEGER PRIMARY KEY,
name TEXT NOT NULL,
latitude REAL NOT NULL,
longitude REAL NOT NULL
);
/** Observation table */
CREATE TABLE IF NOT EXISTS observation (
observation_id INTEGER PRIMARY KEY,
taxon_id INTEGER NOT NULL,
locality_id INTEGER NOT NULL,
date TEXT NOT NULL,
time TEXT NOT NULL,
notes TEXT,
confidence REAL NOT NULL,
FOREIGN KEY(taxon_id) REFERENCES taxon(taxon_id),
FOREIGN KEY(locality_id) REFERENCES locality(locality_id)
);

0
daemon/dist/birdnet-stream.service vendored Normal file
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35
daemon/miner.sh Normal file
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# !/bin/bash
# Extract data generated with BirdNET on record to get relevant informations and record data in sqlite
# Load config file
config_filepath="./config/analyzer.conf"
if [ -f "$config_filepath" ]; then
source "$config_filepath"
else
echo "Config file not found: $config_filepath"
exit 1
fi
# Verify needed prerequisites
if [[ -z ${CHUNK_FOLDER} ]]; then
echo "CHUNK_FOLDER is not set"
exit 1
else
if [[ ! -d "${CHUNK_FOLDER}" ]]; then
echo "CHUNK_FOLDER does not exist: ${CHUNK_FOLDER}"
exit 1
else
if [[ ! -d "${CHUNK_FOLDER}/out" ]]; then
echo "Output dir does not exist: ${CHUNK_FOLDER}/out"
echo "Cannot mine data"
exit 1
fi
fi
fi
fi
function list_all_model_outputs()
{
}

28
daemon/record-chunks.sh Executable file
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#! /usr/bin/env bash
record_chunk()
{
DEVICE=$1
DURATION=$2
ffmpeg -f pulse -i ${DEVICE} -t ${DURATION} -vn -acodec pcm_s16le -ac 1 -ar 48000 file:${CHUNK_FOLDER}/in/birdnet_$(date "+%Y%m%d_%H%M%S").wav
}
config_filepath="./config/analyzer.conf"
if [ -f "$config_filepath" ]; then
source "$config_filepath"
else
echo "Config file not found: $config_filepath"
exit 1
fi
[ -z $RECORDING_DURATION ] && RECORDING_DURATION=15
if [[ -z $AUDIO_DEVICE ]]; then
echo "AUDIO_DEVICE is not set"
exit 1
fi
while true; do
record_chunk $AUDIO_DEVICE $RECORDING_DURATION
done

9
daemon/weekof.sh Executable file
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#! /usr/bin/env bash
function weekof()
{
local date=$1
date -d "$date" +%W
}
weekof $1

231
media/logo.svg Normal file
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24
requirements.txt Normal file
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appdirs==1.4.4
audioread==2.1.9
certifi==2022.6.15
cffi==1.15.1
charset-normalizer==2.1.0
decorator==5.1.1
idna==3.3
joblib==1.1.0
librosa==0.9.2
llvmlite==0.39.0
numba==0.56.0
numpy==1.22.4
packaging==21.3
pooch==1.6.0
pycparser==2.21
pyparsing==3.0.9
requests==2.28.1
resampy==0.3.1
scikit-learn==1.1.2
scipy==1.9.0
SoundFile==0.10.3.post1
tflite-runtime==2.9.1
threadpoolctl==3.1.0
urllib3==1.26.11

24
utils/purge.sh Executable file
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#! /usr/bin/env bash
# Load config file
config_filepath="./config/analyzer.conf"
if [ -f "$config_filepath" ]; then
source "$config_filepath"
else
echo "Config file not found: $config_filepath"
exit 1
fi
# Remove all files from the temporary record directory
function clean_record_dir()
{
rm -rf "$CHUNK_FOLDER/in/*.wav"
}
function remove_empty_records()
{
find $CHUNK_FOLDER/in -maxdepth 1 -name '*wav' -type f -size 0 -delete
}
remove_empty_records