120 lines
3.6 KiB
Bash
Executable File
120 lines
3.6 KiB
Bash
Executable File
#! /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:-1}
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set -e
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# set -x
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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/birdnet.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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ls ${CHUNK_FOLDER}/out/*/model.out.csv
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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 $record_time | cut -c 1-2)
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MI=$(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 $HH:$MI:$SS.$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") -eq 1 ]]; then
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debug "Observation already exists: $source_audio, $start, $end, $taxon_id, $location_id"
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else
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debug "Inserting observation: $source_audio, $start, $end, $taxon_id, $location_id, $datetime"
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insert_observation "$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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