96 lines
3.1 KiB
Bash
Executable File
96 lines
3.1 KiB
Bash
Executable File
#! /usr/bin/env bash
|
|
# Extract observations from a model output file into SQL database
|
|
#
|
|
|
|
DEBUG=${DEBUG:-1}
|
|
set -e
|
|
# set -x
|
|
DEBUG=${DEBUG:-1}
|
|
debug() {
|
|
[[ $DEBUG -eq 1 ]] && echo "$@"
|
|
}
|
|
|
|
# Load bash library to deal with BirdNET-stream database
|
|
source ./daemon/database/scripts/database.sh
|
|
|
|
# Load config
|
|
source ./config/birdnet.conf
|
|
# Check config
|
|
|
|
if [[ -z ${LATITUDE} ]]; then
|
|
echo "LATITUDE is not set"
|
|
exit 1
|
|
fi
|
|
|
|
if [[ -z ${LONGITUDE} ]]; then
|
|
echo "LONGITUDE is not set"
|
|
exit 1
|
|
fi
|
|
|
|
source_wav() {
|
|
model_output_path=$1
|
|
model_output_dir=$(dirname $model_output_path)
|
|
source_wav=$(basename $model_output_dir | rev | cut --complement -d"." -f1 | rev)
|
|
echo $source_wav
|
|
}
|
|
|
|
record_datetime() {
|
|
source_wav=$1
|
|
source_base=$(basename $source_wav .wav)
|
|
record_date=$(echo $source_base | cut -d"_" -f2)
|
|
record_time=$(echo $source_base | cut -d"_" -f3)
|
|
YYYY=$(echo $record_date | cut -c 1-4)
|
|
MM=$(echo $record_date | cut -c 5-6)
|
|
DD=$(echo $record_date | cut -c 7-8)
|
|
HH=$(echo $record_time | cut -c 1-2)
|
|
MI=$(echo $record_time | cut -c 3-4)
|
|
SS=$(echo $record_time | cut -c 5-6)
|
|
SSS="000"
|
|
date="$YYYY-$MM-$DD $HH:$MI:$SS.$SSS"
|
|
echo $date
|
|
}
|
|
|
|
save_observations() {
|
|
model_output_path=$1
|
|
source_audio=$(source_wav $model_output_path)
|
|
debug "Audio source: $source_audio"
|
|
observations=$(cat $model_output_path | tail -n +2)
|
|
IFS=$'\n'
|
|
for observation in $observations; do
|
|
if [[ -z "$observation" ]]; then
|
|
continue
|
|
fi
|
|
# debug "Observation: $observation"
|
|
start=$(echo "$observation" | cut -d"," -f1)
|
|
end=$(echo "$observation" | cut -d"," -f2)
|
|
scientific_name=$(echo "$observation" | cut -d"," -f3)
|
|
common_name=$(echo "$observation" | cut -d"," -f4)
|
|
confidence=$(echo "$observation" | cut -d"," -f5)
|
|
debug "Observation: $scientific_name ($common_name) from $start to $end with confidence $confidence"
|
|
taxon_id=$(get_taxon_id "$scientific_name")
|
|
if [[ -z $taxon_id ]]; then
|
|
debug "Taxon not found: $scientific_name"
|
|
debug "Inserting taxon..."
|
|
insert_taxon "$scientific_name" "$common_name"
|
|
taxon_id=$(get_taxon_id "$scientific_name")
|
|
fi
|
|
location_id=$(get_location_id "$LATITUDE" "$LONGITUDE")
|
|
if [[ -z $location_id ]]; then
|
|
debug "Location not found: $LATITUDE, $LONGITUDE"
|
|
debug "Inserting location..."
|
|
insert_location "$LATITUDE" "$LONGITUDE"
|
|
location_id=$(get_location_id "$LATITUDE" "$LONGITUDE")
|
|
fi
|
|
datetime=$(record_datetime $source_audio)
|
|
if [[ $(observation_exists "$source_audio" "$start" "$end" "$taxon_id" "$location_id") -eq 1 ]]; then
|
|
debug "Observation already exists: $source_audio, $start, $end, $taxon_id, $location_id"
|
|
else
|
|
debug "Inserting observation: $source_audio, $start, $end, $taxon_id, $location_id, $datetime"
|
|
insert_observation "$source_audio" "$start" "$end" "$taxon_id" "$location_id" "$confidence" "$datetime"
|
|
fi
|
|
done
|
|
}
|
|
|
|
model_output_path="$1"
|
|
|
|
save_observations $model_output_path |