rework analysis
This commit is contained in:
frederik
@@ -0,0 +1,145 @@
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import logging
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import os
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import os.path
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import re
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import signal
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import sys
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import threading
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from queue import Queue
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import inotify.adapters
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from inotify.constants import IN_CLOSE_WRITE
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from utils.reporting import extract_detection, summary, write_to_file, write_to_db, apprise, bird_weather, heartbeat
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from server import load_global_model, run_analysis
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from utils.helpers import get_settings, ParseFileName, get_wav_files, write_settings, ANALYZING_NOW
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shutdown = False
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log = logging.getLogger(__name__)
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def sig_handler(sig_num, curr_stack_frame):
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global shutdown
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log.info('Caught shutdown signal %d', sig_num)
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shutdown = True
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def main():
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write_settings()
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load_global_model()
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conf = get_settings()
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i = inotify.adapters.Inotify()
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i.add_watch(os.path.join(conf['RECS_DIR'], 'StreamData'), mask=IN_CLOSE_WRITE)
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backlog = get_wav_files()
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report_queue = Queue()
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thread = threading.Thread(target=handle_reporting_queue, args=(report_queue, ))
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thread.start()
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log.info('backlog is %d', len(backlog))
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for file_name in backlog:
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process_file(file_name, report_queue)
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if shutdown:
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break
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log.info('backlog done')
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empty_count = 0
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for event in i.event_gen():
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if shutdown:
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break
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if event is None:
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if empty_count > (conf.getint('RECORDING_LENGTH') * 2):
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log.error('no more notifications: restarting...')
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break
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empty_count += 1
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continue
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(_, type_names, path, file_name) = event
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if re.search('.wav$', file_name) is None:
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continue
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log.debug("PATH=[%s] FILENAME=[%s] EVENT_TYPES=%s", path, file_name, type_names)
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file_path = os.path.join(path, file_name)
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if file_path in backlog:
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# if we're very lucky, the first event could be for the file in the backlog that finished
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# while running get_wav_files()
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backlog = []
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continue
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process_file(file_path, report_queue)
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empty_count = 0
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# we're all done
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report_queue.put(None)
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thread.join()
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report_queue.join()
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def process_file(file_name, report_queue):
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try:
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if os.path.getsize(file_name) == 0:
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os.remove(file_name)
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return
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log.info('Analyzing %s', file_name)
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with open(ANALYZING_NOW, 'w') as analyzing:
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analyzing.write(file_name)
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file = ParseFileName(file_name)
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detections = run_analysis(file)
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# we join() to make sure te reporting queue does not get behind
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if not report_queue.empty():
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log.warning('reporting queue not yet empty')
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report_queue.join()
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report_queue.put((file, detections))
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except BaseException as e:
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log.exception('Unexpected error:', exc_info=e)
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def handle_reporting_queue(queue):
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while True:
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msg = queue.get()
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# check for signal that we are done
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if msg is None:
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break
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file, detections = msg
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try:
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for detection in detections:
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detection.file_name_extr = extract_detection(file, detection)
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log.info('%s;%s', summary(file, detection), os.path.basename(detection.file_name_extr))
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write_to_file(file, detection)
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write_to_db(file, detection)
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apprise(file, detections)
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bird_weather(file, detections)
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heartbeat()
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os.remove(file.file_name)
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except BaseException as e:
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log.exception('Unexpected error:', exc_info=e)
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queue.task_done()
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# mark the 'None' signal as processed
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queue.task_done()
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log.info('handle_reporting_queue done')
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def setup_logging():
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logger = logging.getLogger()
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formatter = logging.Formatter("[%(name)s][%(levelname)s] %(message)s")
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handler = logging.StreamHandler(stream=sys.stdout)
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handler.setFormatter(formatter)
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logger.addHandler(handler)
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logger.setLevel(logging.INFO)
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global log
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log = logging.getLogger('birdnet_analysis')
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if __name__ == '__main__':
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signal.signal(signal.SIGINT, sig_handler)
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signal.signal(signal.SIGTERM, sig_handler)
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setup_logging()
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main()
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@@ -0,0 +1,110 @@
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import configparser
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import datetime
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import glob
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import os
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import stat
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import re
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import subprocess
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from itertools import chain
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from tzlocal import get_localzone
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_settings = None
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DB_PATH = os.path.expanduser('~/BirdNET-Pi/scripts/birds.db')
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THISRUN = os.path.expanduser('~/BirdNET-Pi/scripts/thisrun.txt')
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ANALYZING_NOW = os.path.expanduser('~/BirdNET-Pi/analyzing_now.txt')
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def _load_settings(settings_path='/etc/birdnet/birdnet.conf', force_reload=False):
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global _settings
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if _settings is None or force_reload:
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with open(settings_path) as f:
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parser = configparser.ConfigParser()
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# preserve case
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parser.optionxform = lambda option: option
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lines = chain(("[top]",), f)
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parser.read_file(lines)
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_settings = parser['top']
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return _settings
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def get_settings(settings_path='/etc/birdnet/birdnet.conf', force_reload=False):
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settings = _load_settings(settings_path, force_reload)
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return settings
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def write_settings(file_name=THISRUN):
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settings = _load_settings()
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with open(file_name, 'w') as configfile:
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for key, value in settings.items():
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configfile.write(f'{key}={value}\n')
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os.chmod(file_name, stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IWGRP)
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class Detection:
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def __init__(self, start_time, stop_time, species, confidence):
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self.start = float(start_time)
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self.stop = float(stop_time)
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self.confidence = float(confidence)
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self.confidence_pct = round(self.confidence * 100)
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self.species = species
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self.scientific_name = species.split('_')[0]
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self.common_name = species.split('_')[1]
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self.common_name_safe = self.common_name.replace("'", "").replace(" ", "_")
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self.file_name_extr = None
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class ParseFileName:
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def __init__(self, file_name):
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self.file_name = file_name
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name = os.path.splitext(os.path.basename(file_name))[0]
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date_created = re.search('^[0-9]+-[0-9]+-[0-9]+', name).group()
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time_created = re.search('[0-9]+:[0-9]+:[0-9]+$', name).group()
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self.file_date = datetime.datetime.strptime(f'{date_created}T{time_created}', "%Y-%m-%dT%H:%M:%S")
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self.root = name
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ident_match = re.search("RTSP_[0-9]+-", file_name)
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self.RTSP_id = ident_match.group() if ident_match is not None else ""
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@property
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def date(self):
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current_date = self.file_date.strftime("%Y-%m-%d")
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return current_date
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@property
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def time(self):
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current_time = self.file_date.strftime("%H:%M:%S")
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return current_time
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@property
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def iso8601(self):
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current_iso8601 = self.file_date.astimezone(get_localzone()).isoformat()
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return current_iso8601
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@property
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def week(self):
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week = self.file_date.isocalendar()[1]
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return week
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def get_open_files_in_dir(dir_name):
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result = subprocess.run(['lsof', '-Fn', '+D', f'{dir_name}'], check=False, capture_output=True)
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ret = result.stdout.decode('utf-8')
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err = result.stderr.decode('utf-8')
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if err:
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raise RuntimeError(f'{ret}:\n {err}')
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names = [line.lstrip('n') for line in ret.splitlines() if line.startswith('n')]
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return names
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def get_wav_files():
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conf = get_settings()
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files = (glob.glob(os.path.join(conf['RECS_DIR'], '*/*/*.wav')) +
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glob.glob(os.path.join(conf['RECS_DIR'], 'StreamData/*.wav')))
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files.sort()
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files = [os.path.join(conf['RECS_DIR'], file) for file in files]
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rec_dir = os.path.join(conf['RECS_DIR'], 'StreamData')
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open_recs = get_open_files_in_dir(rec_dir)
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files = [file for file in files if file not in open_recs]
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return files
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@@ -0,0 +1,189 @@
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import datetime
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import gzip
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import logging
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import os
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import sqlite3
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import subprocess
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from time import sleep
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import requests
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from tzlocal import get_localzone
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from .helpers import get_settings, ParseFileName, Detection, DB_PATH
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from .notifications import sendAppriseNotifications
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log = logging.getLogger(__name__)
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def get_safe_title(title):
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result = subprocess.run(['iconv', '-f', 'utf8', '-t', 'ascii//TRANSLIT'],
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check=True, input=title.encode('utf-8'), capture_output=True)
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ret = result.stdout.decode('utf-8')
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return ret
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def extract(in_file, out_file, start, stop):
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result = subprocess.run(['sox', '-V1', f'{in_file}', f'{out_file}', 'trim', f'={start}', f'={stop}'],
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check=True, capture_output=True)
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ret = result.stdout.decode('utf-8')
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err = result.stderr.decode('utf-8')
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if err:
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raise RuntimeError(f'{ret}:\n {err}')
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return ret
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def extract_safe(in_file, out_file, start, stop):
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conf = get_settings()
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# This section sets the SPACER that will be used to pad the audio clip with
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# context. If EXTRACTION_LENGTH is 10, for instance, 3 seconds are removed
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# from that value and divided by 2, so that the 3 seconds of the call are
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# within 3.5 seconds of audio context before and after.
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try:
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ex_len = conf.getint('EXTRACTION_LENGTH')
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except ValueError:
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ex_len = 6
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spacer = (ex_len - 3) / 2
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safe_start = max(0, start - spacer)
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safe_stop = min(conf.getint('RECORDING_LENGTH'), stop + spacer)
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extract(in_file, out_file, safe_start, safe_stop)
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def spectrogram(in_file, title, comment, raw=False):
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args = ['sox', '-V1', f'{in_file}', '-n', 'remix', '1', 'rate', '24k', 'spectrogram',
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'-t', f'{get_safe_title(title)}', '-c', f'{comment}', '-o', f'{in_file}.png']
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args += ['-r'] if raw else []
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result = subprocess.run(args, check=True, capture_output=True)
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ret = result.stdout.decode('utf-8')
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err = result.stderr.decode('utf-8')
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if err:
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raise RuntimeError(f'{ret}:\n {err}')
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return ret
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def extract_detection(file: ParseFileName, detection: Detection):
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conf = get_settings()
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new_file_name = f'{detection.common_name_safe}-{detection.confidence_pct}-{file.root}.{conf["AUDIOFMT"]}'
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new_dir = os.path.join(conf['EXTRACTED'], 'By_Date', f'{file.date}', f'{detection.common_name_safe}')
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new_file = os.path.join(new_dir, new_file_name)
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if os.path.isfile(new_file):
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log.warning('Extraction exists. Moving on: %s', new_file)
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else:
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os.makedirs(new_dir, exist_ok=True)
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extract_safe(file.file_name, new_file, detection.start, detection.stop)
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spectrogram(new_file, detection.common_name, new_file.replace(os.path.expanduser('~/'), ''))
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return new_file
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def write_to_db(file: ParseFileName, detection: Detection):
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conf = get_settings()
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# Connect to SQLite Database
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for attempt_number in range(3):
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try:
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con = sqlite3.connect(DB_PATH)
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cur = con.cursor()
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cur.execute("INSERT INTO detections VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)",
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(file.date, file.time, detection.scientific_name, detection.common_name, detection.confidence,
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conf['LATITUDE'], conf['LONGITUDE'], conf['CONFIDENCE'], str(file.week), conf['SENSITIVITY'],
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conf['OVERLAP'], os.path.basename(detection.file_name_extr)))
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# (Date, Time, Sci_Name, Com_Name, str(score),
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# Lat, Lon, Cutoff, Week, Sens,
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# Overlap, File_Name))
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con.commit()
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con.close()
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break
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except BaseException as e:
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log.warning("Database busy: %s", e)
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sleep(2)
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def summary(file: ParseFileName, detection: Detection):
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# Date;Time;Sci_Name;Com_Name;Confidence;Lat;Lon;Cutoff;Week;Sens;Overlap
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# 2023-03-03;12:48:01;Phleocryptes melanops;Wren-like Rushbird;0.76950216;-1;-1;0.7;9;1.25;0.0
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conf = get_settings()
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s = (f'{file.date};{file.time};{detection.scientific_name};{detection.common_name};'
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f'{detection.confidence};'
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f'{conf["LATITUDE"]};{conf["LONGITUDE"]};{conf["CONFIDENCE"]};{file.week};{conf["SENSITIVITY"]};'
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f'{conf["OVERLAP"]}')
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return s
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def write_to_file(file: ParseFileName, detection: Detection):
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with open(os.path.expanduser('~/BirdNET-Pi/BirdDB.txt'), 'a') as rfile:
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rfile.write(f'{summary(file, detection)}\n')
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def apprise(file: ParseFileName, detections: [Detection]):
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species_apprised_this_run = []
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conf = get_settings()
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for detection in detections:
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# Apprise of detection if not already alerted this run.
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if detection.species not in species_apprised_this_run:
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try:
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sendAppriseNotifications(detection.species, str(detection.confidence), str(detection.confidence_pct),
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os.path.basename(detection.file_name_extr), file.date, file.time, str(file.week),
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conf['LATITUDE'], conf['LONGITUDE'], conf['CONFIDENCE'], conf['SENSITIVITY'],
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conf['OVERLAP'], dict(conf), DB_PATH)
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except BaseException as e:
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log.exception('Error during Apprise:', exc_info=e)
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species_apprised_this_run.append(detection.species)
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def bird_weather(file: ParseFileName, detections: [Detection]):
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conf = get_settings()
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if conf['BIRDWEATHER_ID'] == "":
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return
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if detections:
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# POST soundscape to server
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soundscape_url = (f'https://app.birdweather.com/api/v1/stations/'
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f'{conf["BIRDWEATHER_ID"]}/soundscapes?timestamp={file.iso8601}')
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with open(file.file_name, 'rb') as f:
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wav_data = f.read()
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gzip_wav_data = gzip.compress(wav_data)
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try:
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response = requests.post(url=soundscape_url, data=gzip_wav_data, timeout=30,
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headers={'Content-Type': 'application/octet-stream', 'Content-Encoding': 'gzip'})
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log.info("Soundscape POST Response Status - %d", response.status_code)
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sdata = response.json()
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except BaseException as e:
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log.error("Cannot POST soundscape: %s", e)
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return
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if not sdata.get('success'):
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log.error(sdata.get('message'))
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return
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soundscape_id = sdata['soundscape']['id']
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for detection in detections:
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# POST detection to server
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detection_url = f'https://app.birdweather.com/api/v1/stations/{conf["BIRDWEATHER_ID"]}/detections'
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start = file.file_date + datetime.timedelta(seconds=detection.start)
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current_iso8601 = start.astimezone(get_localzone()).isoformat()
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data = {'timestamp': current_iso8601, 'lat': conf['LATITUDE'], 'lon': conf['LONGITUDE'],
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'soundscapeId': soundscape_id,
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'soundscapeStartTime': detection.start, 'soundscapeEndTime': detection.stop,
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'commonName': detection.common_name, 'scientificName': detection.scientific_name,
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'algorithm': '2p4' if conf['MODEL'] == 'BirdNET_GLOBAL_6K_V2.4_Model_FP16' else 'alpha',
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'confidence': detection.confidence}
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log.debug(data)
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try:
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response = requests.post(detection_url, json=data, timeout=20)
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log.info("Detection POST Response Status - %d", response.status_code)
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except BaseException as e:
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log.error("Cannot POST detection: %s", e)
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def heartbeat():
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conf = get_settings()
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if conf['HEARTBEAT_URL']:
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try:
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result = requests.get(url=conf['HEARTBEAT_URL'], timeout=10)
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log.info('Heartbeat: %s', result.text)
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except BaseException as e:
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log.error('Error during heartbeat: %s', e)
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Reference in New Issue
Block a user