daemon: Remove birdnet_miner and call birdnet_output_to_sql at each new model execution

This commit is contained in:
Samuel Ortion 2022-08-24 11:58:15 +02:00
parent 39233fe937
commit 4f09a2dd4e
12 changed files with 248 additions and 188 deletions

View File

@ -3,8 +3,9 @@
- Add docker compose port
- Improve install script
- Add base uninstall script (need deeper work)
- Add ttyd for systemd logging
## v0.0.1-rc
## v0.0.1-rc (2022-08-18)
- Integrate BirdNET-Analyzer as submodule
- Add birdnet_recording service

View File

@ -129,7 +129,7 @@ sudo mv /composer.phar /usr/local/bin/composer
```bash
cd www
composer install
composer install --no-dev --prefer-dist --optimize-autoloader
```
### Install nodejs and npm
@ -147,7 +147,7 @@ nvm use 16
```
```bash
sudo dnf install npm
sudo apt-get install npm
```
```bash

View File

@ -3,9 +3,7 @@ set -e
DEBUG=${DEBUG:-1}
debug() {
if [ $DEBUG -eq 1 ]; then
echo "$1"
fi
[[ $DEBUG -eq 1 ]] && echo "$@"
}
config_filepath="./config/birdnet.conf"
@ -64,7 +62,9 @@ check_prerequisites() {
# Get array of audio chunks to be processed
get_chunk_list() {
find "${CHUNK_FOLDER}/in" -type f -name '*.wav' -exec basename {} \; ! -size 0 | sort
chunk_list=($(ls ${CHUNK_FOLDER}/in))
echo "${chunk_list}"
# find "${CHUNK_FOLDER}/in" -type f -name '*.wav' -exec basename {} \; ! -size 0 | sort
}
# Perform audio chunk analysis on one chunk
@ -75,13 +75,22 @@ analyze_chunk() {
mkdir -p "$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 $CONFIDENCE --threads 4 --rtype csv
if [[ ! -z "${THREADS}" ]]; then
threads="--threads ${THREADS}"
else
threads=""
fi
$PYTHON_EXECUTABLE ./analyzer/analyze.py --i $chunk_path --o "$output_dir/model.out.csv" --lat $LATITUDE --lon $LONGITUDE --week $week --min_conf $CONFIDENCE $threads --rtype csv
debug "Model output written to $output_dir/model.out.csv"
bash ./daemon/birdnet_output_to_sql.sh "$output_dir/model.out.csv"
debug "Dumped to SQL database"
}
# Perform audio chunk analysis on all recorded chunks
analyze_chunks() {
for chunk_name in $(get_chunk_list); do
local chunks
chunks="${1}"
for chunk_name in "${chunks}"; do
if [[ -f "${CHUNK_FOLDER}/out/$chunk_name.d/model.out.csv" ]]; then
debug "Skipping $chunk_name, as it has already been analyzed"
else
@ -98,4 +107,4 @@ check_prerequisites
chunks=$(get_chunk_list)
# Analyze all chunks in working directory
analyze_chunks $chunks
analyze_chunks "$chunks"

View File

@ -1,15 +1,13 @@
#! /usr/bin/env bash
# Extract observations from a model output folder
# Extract observations from a model output file into SQL database
#
DEBUG=${DEBUG:-1}
set -e
# set -x
DEBUG=${DEBUG:-1}
debug() {
if [ $DEBUG -eq 1 ]; then
echo "$1"
fi
[[ $DEBUG -eq 1 ]] && echo "$@"
}
# Load bash library to deal with BirdNET-stream database
@ -18,16 +16,6 @@ source ./daemon/database/scripts/database.sh
# Load config
source ./config/birdnet.conf
# Check config
if [[ -z ${CHUNK_FOLDER} ]]; then
echo "CHUNK_FOLDER is not set"
exit 1
else
if [[ ! -d ${CHUNK_FOLDER}/out ]]; then
echo "CHUNK_FOLDER does not exist: ${CHUNK_FOLDER}/out"
echo "Cannot extract observations."
exit 1
fi
fi
if [[ -z ${LATITUDE} ]]; then
echo "LATITUDE is not set"
@ -39,10 +27,6 @@ if [[ -z ${LONGITUDE} ]]; then
exit 1
fi
model_outputs() {
ls ${CHUNK_FOLDER}/out/*/model.out.csv
}
source_wav() {
model_output_path=$1
model_output_dir=$(dirname $model_output_path)
@ -107,13 +91,6 @@ save_observations() {
done
}
main() {
# # Remove all junk observations
# ./daemon/birdnet_clean.sh
# Get model outputs
for model_output in $(model_outputs); do
save_observations $model_output
done
}
model_output_path="$1"
main
save_observations $model_output_path

View File

@ -6,31 +6,44 @@ import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
import seaborn as sns
from datetime import datetime
import os
import glob
CONFIG = {
"readings": 10,
"palette": "Greens",
"db": "./var/db.sqlite",
"date": datetime.now().strftime("%Y-%m-%d")
# "date": "2022-08-15"
"date": datetime.now().strftime("%Y-%m-%d"),
"charts_dir": "./var/charts"
}
db = sqlite3.connect(CONFIG['db'])
db = None
df = pd.read_sql_query("""SELECT common_name, date, location_id, confidence
def get_database():
global db
if db is None:
db = sqlite3.connect(CONFIG["db"])
return db
def chart(date):
db = get_database()
df = pd.read_sql_query(f"""SELECT common_name, date, location_id, confidence
FROM observation
INNER JOIN taxon
ON observation.taxon_id = taxon.taxon_id""", db)
ON observation.taxon_id = taxon.taxon_id
WHERE STRFTIME("%Y-%m-%d", `date`) = '{date}'""", db)
df['date'] = pd.to_datetime(df['date'])
df['hour'] = df['date'].dt.hour
df['date'] = df['date'].dt.date
df['date'] = df['date'].astype(str)
df_on_date = df[df['date'] == CONFIG['date']]
df_on_date = df[df['date'] == date]
top_on_date = (df_on_date['common_name'].value_counts()[:CONFIG['readings']])
if top_on_date.empty:
print("No observations on {}".format(CONFIG['date']))
exit()
print("No observations on {}".format(date))
return
else:
print(f"Found observations on {date}")
df_top_on_date = df_on_date[df_on_date['common_name'].isin(top_on_date.index)]
@ -90,6 +103,22 @@ plot.set(xlabel="Hour of day")
plt.suptitle(f"Top {CONFIG['readings']} species on {CONFIG['date']}", fontsize=14)
plt.text(15, 11, f"(Updated on {datetime.now().strftime('%Y/%m-%d %H:%M')})")
plt.savefig(f"./var/charts/chart_{CONFIG['date']}.png", dpi=300)
print(f"Plot for {date} saved.")
plt.close()
def main():
done_charts = glob.glob(f"{CONFIG['charts_dir']}/*.png")
last_modified = max(done_charts, key=os.path.getctime)
last_modified_date = last_modified.split("_")[-1].split(".")[0]
missing_dates = pd.date_range(start=last_modified_date, end=CONFIG['date'], freq='D')
print(missing_dates)
for missing_date in missing_dates:
date = missing_date.strftime("%Y-%m-%d")
chart(date)
chart(CONFIG['date'])
if db is not None:
db.close()
print("Done.")
if __name__ == "__main__":
main()

View File

@ -1,13 +0,0 @@
[Unit]
Description=BirdNET-stream miner service
[Service]
Type=simple
User=<USER>
Group=<GROUP>
WorkingDirectory=<DIR>
ExecStart=bash ./daemon/birdnet_miner.sh
RemainAfterExit=yes
[Install]
WantedBy=multi-user.target

View File

@ -1,9 +0,0 @@
[Unit]
Description=BirdNET-stream miner Timer
[Timer]
OnCalendar=*:0/15
Unit=birdnet_miner.service
[Install]
WantedBy=timers.target

View File

@ -34,10 +34,13 @@ Then, create your dotenv file and populate it with your own configuration (for i
cp .env.example .env
```
Then, run docker-compose:
You may need to adapt the listening ports of the services or other configuration parameters.
In general all variables stated with ${VARIABLE:-default} inside [../docker-compose.yml](../docker-compose.yml) can be override in the .env file using `VARIABLE=value`.
Once that is done, you can build and start docker services:
```bash
# Build image (first time only)
# Build images (first time only)
docker compose build
# Run
docker compose up # add `-d`, to run in background

View File

@ -67,7 +67,7 @@ install_birdnetstream_services() {
DIR="$WORKDIR"
cd "$WORKDIR"
debug "Setting up BirdNET stream systemd services"
services="birdnet_recording.service birdnet_analyzis.service birdnet_miner.timer birdnet_miner.service birdnet_plotter.service birdnet_plotter.timer"
services="birdnet_recording.service birdnet_analyzis.service birdnet_plotter.service birdnet_plotter.timer"
read -r -a services_array <<<"$services"
for service in ${services_array[@]}; do
sudo cp "daemon/systemd/templates/$service" "/etc/systemd/system/"
@ -78,7 +78,7 @@ install_birdnetstream_services() {
done
sudo sed -i "s|<VENV>|$WORKDIR/$PYTHON_VENV|g" "/etc/systemd/system/birdnet_plotter.service"
sudo systemctl daemon-reload
enabled_services="birdnet_recording.service birdnet_analyzis.service birdnet_miner.timer birdnet_plotter.timer"
enabled_services="birdnet_recording.service birdnet_analyzis.service birdnet_plotter.timer"
read -r -a services_array <<<"$services"
for service in ${services_array[@]}; do
debug "Enabling $service"
@ -163,7 +163,7 @@ setup_http_server() {
fi
debug "Enable birdnet.lan domain"
sudo ln -s /etc/nginx/sites-available/birdnet-stream.conf /etc/nginx/sites-enabled/birdnet-stream.conf
debug "Info: Please edit /etc/nginx/sites-available/birdnet-stream.conf to set the correct server name and paths"
debug "INFO: Please edit /etc/nginx/sites-available/birdnet-stream.conf to set the correct server name and paths"
debug "Setup nginx variables the best way possible"
sudo sed -i "s|<SYMFONY_PUBLIC>|$WORKDIR/www/public/|g" /etc/nginx/sites-available/birdnet-stream.conf
sudo sed -i "s|<RECORDS_DIR>|$CHUNK_FOLDER/out|g" /etc/nginx/sites-available/birdnet-stream.conf

View File

@ -38,3 +38,12 @@ uninstall_webapp() {
sudo unlink /etc/nginx/sites-enabled/birdnet-stream.conf
sudo systemctl restart nginx
}
main() {
echo "WARNING: This will remove all BirdNET-stream related files and services. \
Note that it may forget some special configuration."
uninstall_webapp
uninstall_birdnet_services
}
main

View File

@ -25,11 +25,15 @@ class HomeController extends AbstractController
* @Route("", name="home")
* @Route("/{_locale<%app.supported_locales%>}/", name="home_i18n")
*/
public function index()
public function index(Request $request)
{
$date = $request->get("on");
if ($date == null) {
$date = date("Y-m-d");
}
return $this->render('index.html.twig', [
"stats" => $this->get_stats(),
"charts" => $this->last_chart_generated(),
"stats" => $this->get_stats($date),
"charts" => $this->last_chart_generated($date),
]);
}
@ -42,11 +46,12 @@ class HomeController extends AbstractController
return $this->render('about/index.html.twig', []);
}
private function get_stats()
private function get_stats($date)
{
$stats = array();
$stats["most-recorded-species"] = $this->get_most_recorded_species();
$stats["last-detected-species"] = $this->get_last_recorded_species();
$stats["number-of-species-detected"] = $this->get_number_of_species_detected($date);
return $stats;
}
@ -86,6 +91,27 @@ class HomeController extends AbstractController
return $species;
}
private function get_number_of_species_detected($date)
{
$count = 0;
$sql = "SELECT COUNT(`taxon_id`) AS contact_count
FROM `observation`
WHERE STRFTIME('%Y-%m-%d', `date`) = :date
GROUP BY `taxon_id`";
try {
$stmt = $this->connection->prepare($sql);
$stmt->bindValue(":date", $date);
$result = $stmt->executeQuery();
$output = $result->fetchAllAssociative();
if ($output != null) {
$count = $output[0]["contact_count"];
}
} catch (\Exception $e) {
$this->logger->error($e->getMessage());
}
return $count;
}
private function last_chart_generated()
{
$files = glob($this->getParameter('kernel.project_dir') . '/../var/charts/*.png');

View File

@ -1,49 +1,77 @@
<div id="stats">
<h2>{{ "Quick Stats" | trans }}</h2>
<h2>
{{ 'Quick Stats'|trans }}
</h2>
<ul>
<li class="most-recorded-species">
{{ "Most recorded species" | trans }}:
{% if stats["most-recorded-species"] is defined and stats["most-recorded-species"]|length > 0 %}
<li class="stat">
{{ 'Most recorded species'|trans }}:{% if
stats['most-recorded-species'] is defined
and (stats['most-recorded-species']|length) > 0 %}
<span class="scientific-name">
{{ stats["most-recorded-species"]["scientific_name"] }}
{{ stats['most-recorded-species']['scientific_name'] }}
</span>
(<span class="common_name">{{ stats["most-recorded-species"]["common_name"] }}</span>)
{{ "with" | trans }}
(<span class="common_name">
{{ stats['most-recorded-species']['common_name'] }}
</span>)
{{ 'with'|trans }}
<span class="observation-count">
{{ stats["most-recorded-species"]["contact_count"] }}
{{ stats['most-recorded-species']['contact_count'] }}
</span>
{{ "contacts" | trans }}.
{{ 'contacts'|trans }}.
{% else %}
{{ "No species in database." | trans }}
{{ 'No species in database.'|trans }}
{% endif %}
</li>
<li class="last-recorded-species">
{{ "Last detected species" | trans }}:
{% if stats["last-detected-species"] is defined and stats["last-detected-species"]|length > 0 %}
<li class="stat">
{{ 'Last detected species'|trans }}:{% if
stats['last-detected-species'] is defined
and (stats['last-detected-species']|length) > 0 %}
<span class="scientific-name">
{{ stats["last-detected-species"]["scientific_name"] }}
{{ stats['last-detected-species']['scientific_name'] }}
</span>
(<span class="common_name">{{ stats["last-detected-species"]["common_name"] }}</span>)
{{ "with" | trans }}
(<span class="common_name">
{{ stats['last-detected-species']['common_name'] }}
</span>)
{{ 'with'|trans }}
<span class="confidence">
{{ stats["last-detected-species"]["confidence"] }}
{{ stats['last-detected-species']['confidence'] }}
</span>
{{ "AI confidence" | trans }}
{{ 'AI confidence'|trans }}
<span class="datetime">
{% set date = stats["last-detected-species"]["date"] %}
{% if date | date("Y-m-d") == "now" | date("Y-m-d") %}
{{ "today" | trans }}
{% set date = stats['last-detected-species']['date'] %}
{% if (date|date('Y-m-d')) == ('now'|date('Y-m-d')) %}
{{ 'today'|trans }}
{% else %}
{{ "on" | trans }}
{{ date | format_datetime("full", "none") }}
{% endif %}
at
<span class="time">
{{ date | date("H:i") }}
</span>
{{ 'on'|trans }}
{{ date|format_datetime('full', 'none') }}
{% endif %}at
<span class="time">{{ date|date('H:i') }}</span>
</span>.
{% else %}
{{ "No species in database" | trans }}
{{ 'No species in database'|trans }}
{% endif %}
</li>
<li class="stat">
{% set today = 'now'|date('Y-m-d') %}
{% set date = app.request.get('on') %}
{% if
stats['number-of-species-detected'] is defined
and stats['number-of-species-detected'] > 0 %}
{% if today == date %}
{{ 'Number of species detected today: '|trans }}
{% else %}
{{ 'Number of species detected on '|trans }}
{{ date|format_datetime('full', 'none') }}:
{% endif %}
<span>{{ stats['number-of-species-detected'] }}</span>.
{% else %}
{# {{ 'No species detected today'|trans }} #}
{% if today == date %}
{{ 'No species detected today.'|trans }}
{% else %}
{{ 'No species detected on '|trans }}
{{ date|format_datetime('full', 'none') }}
{% endif %}
{% endif %}
</li>
</ul>