Add spectro webpage (not the audio of the server yet) & dataminer script
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0399fa085e
commit
6b37e1cfc5
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@ -7,7 +7,7 @@ LOCATION="Maison ORTION - Saint-Gervais-en-Belin"
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# Species selection list
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SPECIES_LIST="./config/species_list.txt"
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# Minimal confidence threshold
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CONFIDENCE=0.25
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CONFIDENCE=0.1
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# Recording duration (in seconds)
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RECORDING_DURATION=15
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# Chunk folder location
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@ -28,9 +28,9 @@ mem() {
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string=$2
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substring=$1
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if [[ "$string" == *"$substring"* ]]; then
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echo "true"
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true
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else
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echo "false"
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false
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fi
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}
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@ -49,7 +49,7 @@ junk() {
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# Get all empty treatment directories
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junk="$junk $(find ${CHUNK_FOLDER}/out -type d -empty)"
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# Get all empty record directories
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treatement_folder=$(find "${CHUNK_FOLDER}/out" -type d ! -empty)
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treatement_folder=$(find "${CHUNK_FOLDER}/out/*" -type d ! -empty)
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if [[ ! -z ${treatement_folder} ]]; then
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for folder in $treatement_folder; do
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echo $folder
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@ -0,0 +1,120 @@
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#! /usr/bin/env bash
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# Extract observations from a model output folder
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#
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DEBUG=${DEBUG:-0}
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set -e
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debug() {
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if [ $DEBUG -eq 1 ]; then
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echo "$1"
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fi
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}
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# Load bash library to deal with BirdNET-stream database
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source ./daemon/database/scripts/database.sh
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# Load config
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source ./config/analyzer.conf
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# Check config
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if [[ -z ${CHUNK_FOLDER} ]]; then
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echo "CHUNK_FOLDER is not set"
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exit 1
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else
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if [[ ! -d ${CHUNK_FOLDER}/out ]]; then
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echo "CHUNK_FOLDER does not exist: ${CHUNK_FOLDER}/out"
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echo "Cannot extract observations."
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exit 1
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fi
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fi
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if [[ -z ${LATITUDE} ]]; then
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echo "LATITUDE is not set"
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exit 1
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fi
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if [[ -z ${LONGITUDE} ]]; then
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echo "LONGITUDE is not set"
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exit 1
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fi
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model_outputs() {
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find -name "model.out.csv" -type f ! -empty
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}
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source_wav() {
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model_output_path=$1
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model_output_dir=$(dirname $model_output_path)
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source_wav=$(basename $model_output_dir | rev | cut --complement -d"." -f1 | rev)
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echo $source_wav
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}
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record_datetime() {
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source_wav=$1
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source_base=$(basename $source_wav .wav)
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record_date=$(echo $source_base | cut -d"_" -f2)
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record_time=$(echo $source_base | cut -d"_" -f3)
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YYYY=$(echo $record_date | cut -c 1-4)
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MM=$(echo $record_date | cut -c 5-6)
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DD=$(echo $record_date | cut -c 7-8)
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HH=$(echo $record_time | cut -c 1-2)
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MM=$(echo $record_time | cut -c 3-4)
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SS=$(echo $record_time | cut -c 5-6)
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SSS="000"
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date="$YYYY-$MM-$DD $HH:$MM:$SS.$SSS"
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echo $date
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}
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save_observations() {
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model_output_path=$1
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source_audio=$(source_wav $model_output_path)
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debug "Audio source: $source_audio"
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observations=$(cat $model_output_path | tail -n +2)
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IFS=$'\n'
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for observation in $observations; do
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if [[ -z "$observation" ]]; then
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continue
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fi
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# debug "Observation: $observation"
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start=$(echo "$observation" | cut -d"," -f1)
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end=$(echo "$observation" | cut -d"," -f2)
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scientific_name=$(echo "$observation" | cut -d"," -f3)
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common_name=$(echo "$observation" | cut -d"," -f4)
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confidence=$(echo "$observation" | cut -d"," -f5)
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debug "Observation: $scientific_name ($common_name) from $start to $end with confidence $confidence"
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taxon_id=$(get_taxon_id "$scientific_name")
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if [[ -z $taxon_id ]]; then
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debug "Taxon not found: $scientific_name"
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debug "Inserting taxon..."
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insert_taxon "$scientific_name" "$common_name"
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taxon_id=$(get_taxon_id "$scientific_name")
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fi
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location_id=$(get_location_id "$LATITUDE" "$LONGITUDE")
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if [[ -z $location_id ]]; then
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debug "Location not found: $LATITUDE, $LONGITUDE"
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debug "Inserting location..."
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insert_location "$LATITUDE" "$LONGITUDE"
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location_id=$(get_location_id "$LATITUDE" "$LONGITUDE")
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fi
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datetime=$(record_datetime $source_audio)
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if [[ $(observation_exists "$source_audio" "$start" "$end" "$taxon_id" "$location_id") = "true" ]]; then
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debug "Observation already exists: $source_audio, $start, $end, $taxon_id, $location_id"
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exit 1
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else
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debug "Inserting observation: $source_audio, $start, $end, $taxon_id, $location_id"
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insert_observation "$source_audio" "$start" "$end" "$taxon_id" "$location_id" "$confidence" "$datetime"
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fi
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done
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}
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main() {
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# Remove all junk observations
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./daemon/birdnet_clean.sh
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# Get model outputs
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for model_output in $(model_outputs); do
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save_observations $model_output
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done
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}
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main
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@ -32,7 +32,7 @@ record() {
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DEVICE=$1
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DURATION=$2
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debug "Recording from $DEVICE for $DURATION seconds"
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echo "" | ffmpeg -nostdin -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
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ffmpeg -nostdin -f pulse -i ${DEVICE} -t ${DURATION} -vn -acodec pcm_s16le -ac 1 -ar 48000 file:${CHUNK_FOLDER}/in/birdnet_$(date "+%Y%m%d_%H%M%S").wav
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}
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config_filepath="./config/analyzer.conf"
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@ -0,0 +1,36 @@
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#! /usr/bin/env bash
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# SQLite library to deal with BirdNET-stream database
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set -e
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source ./config/analyzer.conf
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# Create database in case it was not created yet
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./daemon/database/scripts/create.sh
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DATABASE=${DATABASE:-"./var/db.sqlite"}
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get_location_id() {
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sqlite3 $DATABASE "SELECT location_id FROM location WHERE latitude=$1 AND longitude=$2"
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}
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get_taxon_id() {
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sqlite3 $DATABASE "SELECT taxon_id FROM taxon WHERE scientific_name='$1'"
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}
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insert_taxon() {
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sqlite3 $DATABASE "INSERT INTO taxon (scientific_name, common_name) VALUES ('$1', '$2')"
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}
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insert_location() {
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sqlite3 $DATABASE "INSERT INTO location (latitude, longitude) VALUES ($1, $2)"
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}
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insert_observation() {
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sqlite3 $DATABASE "INSERT INTO observation (audio_file, start, end, taxon_id, location_id, confidence, date) VALUES ('$1', '$2', '$3', '$4', '$5', '$6', '$7')"
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}
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# Check if the observation already exists in the database
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observation_exists() {
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sqlite3 $DATABASE "SELECT EXISTS(SELECT observation_id FROM observation WHERE audio_file='$1' AND start='$2' AND end='$3' AND taxon_id='$4' AND location_id='$5')"
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}
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@ -7,23 +7,24 @@ CREATE TABLE IF NOT EXISTS taxon (
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common_name TEXT NOT NULL
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);
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/** Locality table */
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CREATE TABLE IF NOT EXISTS locality (
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locality_id INTEGER PRIMARY KEY,
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name TEXT NOT NULL,
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/** Location table */
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CREATE TABLE IF NOT EXISTS location (
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location_id INTEGER PRIMARY KEY,
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latitude REAL NOT NULL,
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longitude REAL NOT NULL
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);
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/** Observation table */
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CREATE TABLE IF NOT EXISTS observation (
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observation_id INTEGER PRIMARY KEY,
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taxon_id INTEGER NOT NULL,
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locality_id INTEGER NOT NULL,
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date TEXT NOT NULL,
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time TEXT NOT NULL,
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notes TEXT,
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confidence REAL NOT NULL,
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`observation_id` INTEGER PRIMARY KEY,
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`audio_file` TEXT NOT NULL,
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`start` REAL NOT NULL,
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`end` REAL NOT NULL,
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`taxon_id` INTEGER NOT NULL,
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`location_id` INTEGER NOT NULL,
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`date` TEXT NOT NULL,
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`notes` TEXT,
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`confidence` REAL NOT NULL,
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FOREIGN KEY(taxon_id) REFERENCES taxon(taxon_id),
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FOREIGN KEY(locality_id) REFERENCES locality(locality_id)
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FOREIGN KEY(location_id) REFERENCES location(location_id)
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);
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@ -43,12 +43,12 @@ install_birdnetstream() {
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workdir=$(pwd)
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if [ -d "$workdir/BirdNET-stream" ]; then
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debug "BirdNET-stream is already installed"
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return
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fi
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else
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# Clone BirdNET-stream
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debug "Cloning BirdNET-stream from $REPOSITORY"
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git clone --recurse-submodules $REPOSITORY
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# Install BirdNET-stream
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fi
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cd BirdNET-stream
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debug "Creating python3 virtual environment '$PYTHON_VENV'"
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python3 -m venv $PYTHON_VENV
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@ -10,3 +10,5 @@ import './styles/app.css';
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// start the Stimulus application
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import './bootstrap';
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import './utils/spectro';
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@ -81,3 +81,9 @@ nav ul li a:hover {
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box-shadow: 0px 8px 16px 0px rgba(0, 0, 0, 0.2);
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z-index: 1;
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}
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canvas {
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display: block;
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height: 100%;
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width: 100%;
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}
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@ -0,0 +1,63 @@
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/**
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* Credits to:
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* https://codepen.io/jakealbaugh/pen/jvQweW
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*/
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// UPDATE: there is a problem in chrome with starting audio context
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// before a user gesture. This fixes it.
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var started = false;
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var spectro_button = document.getElementById('spectro-button');
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spectro_button.addEventListener('click', () => {
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if (started) return;
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started = true;
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console.log("starting spectro");
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initialize();
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})
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function initialize() {
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const CVS = document.getElementById('spectro-canvas');
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const CTX = CVS.getContext('2d');
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const W = CVS.width = window.innerWidth;
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const H = CVS.height = window.innerHeight;
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const ACTX = new AudioContext();
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const ANALYSER = ACTX.createAnalyser();
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ANALYSER.fftSize = 4096;
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navigator.mediaDevices
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.getUserMedia({ audio: true })
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.then(process);
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function process(stream) {
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const SOURCE = ACTX.createMediaStreamSource(stream);
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SOURCE.connect(ANALYSER);
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const DATA = new Uint8Array(ANALYSER.frequencyBinCount);
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const LEN = DATA.length;
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const h = H / LEN;
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const x = W - 1;
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CTX.fillStyle = 'hsl(280, 100%, 10%)';
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CTX.fillRect(0, 0, W, H);
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loop();
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function loop() {
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window.requestAnimationFrame(loop);
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let imgData = CTX.getImageData(1, 0, W - 1, H);
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CTX.fillRect(0, 0, W, H);
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CTX.putImageData(imgData, 0, 0);
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ANALYSER.getByteFrequencyData(DATA);
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for (let i = 0; i < LEN; i++) {
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let rat = DATA[i] / 255;
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let hue = Math.round((rat * 120) + 280 % 360);
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let sat = '100%';
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let lit = 10 + (70 * rat) + '%';
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CTX.beginPath();
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CTX.strokeStyle = `hsl(${hue}, ${sat}, ${lit})`;
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CTX.moveTo(x, H - (i * h));
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CTX.lineTo(x, H - (i * h + h));
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CTX.stroke();
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}
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}
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}
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}
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@ -4,9 +4,8 @@ server {
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root /var/www/html;
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location / {
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return 302 https://$host$request_uri;
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return 302 https://$server_name$request_uri;
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}
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}
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server {
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@ -0,0 +1,21 @@
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<?php
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// src/Controller/AboutController.php
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namespace App\Controller;
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use Symfony\Component\HttpFoundation\Response;
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use Symfony\Component\HttpFoundation\Request;
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use Symfony\Component\Routing\Annotation\Route;
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use Symfony\Bundle\FrameworkBundle\Controller\AbstractController;
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class SpectroController extends AbstractController
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{
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/**
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* @Route("/spectro", name="spectro")
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*/
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public function about()
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{
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return $this->render('spectro/index.html.twig', [
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]);
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}
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}
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{% extends "base.html.twig" %}
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{% block content %}
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<h2>{{ "Spectrogram" | trans }}</h2>
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<div>
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<button id="spectro-button">{{ "Launch Live Spectrogram" | trans }}</button>
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<canvas id="spectro-canvas"></canvas>
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</div>
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{% endblock %}
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