Revert "Adding Flake8 Github Action for Python Linting "
This commit is contained in:
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name: CI Jobs
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on: pull_request
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jobs:
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python-lint:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Setup Python
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uses: actions/setup-python@v3
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with:
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python-version: '3.9.x'
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cache: 'pip'
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architecture: 'x64'
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- name: Install flake8
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run: pip install flake8
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- name: Run Flake8 Lint
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uses: py-actions/flake8@v2
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+16
-72
@@ -1,16 +1,3 @@
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#!/usr/bin/env python3
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"""
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# Example calls
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python3 analyze.py --i 'example/XC558716 - Soundscape.mp3' \
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--lat 35.4244 --lon -120.7463 --week 18
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python3 analyze.py --i 'example/XC563936 - Soundscape.mp3' \
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--lat 47.6766 --lon -122.294 --week 11 \
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--overlap 1.5 --min_conf 0.25 --sensitivity 1.25 \
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--custom_list 'example/custom_species_list.txt'
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"""
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import argparse
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import argparse
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import socket
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import socket
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@@ -24,7 +11,6 @@ ADDR = (SERVER, PORT)
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client = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
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client = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
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client.connect(ADDR)
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client.connect(ADDR)
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def send(msg):
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def send(msg):
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message = msg.encode(FORMAT)
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message = msg.encode(FORMAT)
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msg_length = len(message)
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msg_length = len(message)
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@@ -34,7 +20,6 @@ def send(msg):
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client.send(message)
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client.send(message)
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print(client.recv(2048).decode(FORMAT))
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print(client.recv(2048).decode(FORMAT))
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def main():
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def main():
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global INCLUDE_LIST
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global INCLUDE_LIST
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@@ -42,62 +27,17 @@ def main():
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# Parse passed arguments
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# Parse passed arguments
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parser = argparse.ArgumentParser()
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parser = argparse.ArgumentParser()
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parser.add_argument(
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parser.add_argument('--i', help='Path to input file.')
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'--i',
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parser.add_argument('--o', default='result.csv', help='Path to output file. Defaults to result.csv.')
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help='Path to input file.')
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parser.add_argument('--lat', type=float, default=-1, help='Recording location latitude. Set -1 to ignore.')
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parser.add_argument(
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parser.add_argument('--lon', type=float, default=-1, help='Recording location longitude. Set -1 to ignore.')
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'--o',
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parser.add_argument('--week', type=int, default=-1, help='Week of the year when the recording was made. Values in [1, 48] (4 weeks per month). Set -1 to ignore.')
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default='result.csv',
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parser.add_argument('--overlap', type=float, default=0.0, help='Overlap in seconds between extracted spectrograms. Values in [0.0, 2.9]. Defaults tp 0.0.')
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help='Path to output file. Defaults to result.csv.')
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parser.add_argument('--sensitivity', type=float, default=1.0, help='Detection sensitivity; Higher values result in higher sensitivity. Values in [0.5, 1.5]. Defaults to 1.0.')
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parser.add_argument(
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parser.add_argument('--min_conf', type=float, default=0.1, help='Minimum confidence threshold. Values in [0.01, 0.99]. Defaults to 0.1.')
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'--lat',
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parser.add_argument('--include_list', default='null', help='Path to text file containing a list of included species. Not used if not provided.')
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type=float,
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parser.add_argument('--exclude_list', default='null', help='Path to text file containing a list of excluded species. Not used if not provided.')
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default=-1,
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parser.add_argument('--birdweather_id', default='99999', help='Private Station ID for BirdWeather.')
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help='Recording location latitude. Set -1 to ignore.')
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parser.add_argument(
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'--lon',
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type=float,
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default=-1,
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help='Recording location longitude. Set -1 to ignore.')
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parser.add_argument(
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'--week',
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type=int,
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default=-1,
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help='''Week of the year when the recording was made.
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Values in [1, 48] (4 weeks per month). Set -1 to ignore.''')
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parser.add_argument(
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'--overlap',
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type=float,
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default=0.0,
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help='''Overlap in seconds between extracted spectrograms.
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Values in [0.0, 2.9]. Defaults tp 0.0.''')
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parser.add_argument(
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'--sensitivity',
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type=float,
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default=1.0,
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help='''Detection sensitivity;
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Higher values result in higher sensitivity.
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Values in [0.5, 1.5]. Defaults to 1.0.''')
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parser.add_argument(
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'--min_conf',
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type=float,
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default=0.1,
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help='''Minimum confidence threshold.
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Values in [0.01, 0.99]. Defaults to 0.1.''')
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parser.add_argument(
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'--include_list',
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default='null',
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help='''Path to text file containing a list of included species.
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Not used if not provided.''')
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parser.add_argument(
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'--exclude_list',
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default='null',
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help='''Path to text file containing a list of excluded species.
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Not used if not provided.''')
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parser.add_argument(
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'--birdweather_id',
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default='99999',
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help='Private Station ID for BirdWeather.')
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args = parser.parse_args()
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args = parser.parse_args()
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@@ -133,6 +73,10 @@ def main():
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###############################################################################
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###############################################################################
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###############################################################################
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###############################################################################
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if __name__ == '__main__':
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if __name__ == '__main__':
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main()
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main()
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# Example calls
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# python3 analyze.py --i 'example/XC558716 - Soundscape.mp3' --lat 35.4244 --lon -120.7463 --week 18
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# python3 analyze.py --i 'example/XC563936 - Soundscape.mp3' --lat 47.6766 --lon -122.294 --week 11 --overlap 1.5 --min_conf 0.25 --sensitivity 1.25 --custom_list 'example/custom_species_list.txt'
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+26
-92
@@ -1,5 +1,6 @@
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import sqlite3
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import sqlite3
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import os
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import os
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import configparser
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import pandas as pd
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import pandas as pd
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import seaborn as sns
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import seaborn as sns
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import matplotlib.pyplot as plt
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import matplotlib.pyplot as plt
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@@ -11,8 +12,7 @@ userDir = os.path.expanduser('~')
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conn = sqlite3.connect(userDir + '/BirdNET-Pi/scripts/birds.db')
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conn = sqlite3.connect(userDir + '/BirdNET-Pi/scripts/birds.db')
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df = pd.read_sql_query("SELECT * from detections", conn)
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df = pd.read_sql_query("SELECT * from detections", conn)
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cursor = conn.cursor()
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cursor = conn.cursor()
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cursor.execute(
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cursor.execute('SELECT * FROM detections WHERE Date = DATE(\'now\', \'localtime\')')
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'SELECT * FROM detections WHERE Date = DATE(\'now\', \'localtime\')')
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table_rows = cursor.fetchall()
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table_rows = cursor.fetchall()
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@@ -37,29 +37,17 @@ df_plt_today = df_plt[df_plt['Date'] == now.strftime("%Y-%m-%d")]
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readings=10
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readings=10
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plt_top10_today = (df_plt_today['Com_Name'].value_counts()[:readings])
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plt_top10_today = (df_plt_today['Com_Name'].value_counts()[:readings])
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df_plt_top10_today = df_plt_today[df_plt_today.Com_Name.isin(
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df_plt_top10_today = df_plt_today[df_plt_today.Com_Name.isin(plt_top10_today.index)]
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plt_top10_today.index)]
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#Set Palette for graphics
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#Set Palette for graphics
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pal = "Greens"
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pal = "Greens"
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#Set up plot axes and titles
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#Set up plot axes and titles
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f, axs = plt.subplots(
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f, axs = plt.subplots(1, 2, figsize = (10, 4), gridspec_kw=dict(width_ratios=[3, 6]), facecolor='#77C487')
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1, 2, figsize=(
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plt.subplots_adjust(left=None, bottom=None, right=None, top=None, wspace=0, hspace=0)
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10, 4), gridspec_kw=dict(
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width_ratios=[
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3, 6]), facecolor='#77C487')
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plt.subplots_adjust(
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left=None,
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bottom=None,
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right=None,
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top=None,
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wspace=0,
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hspace=0)
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#generate y-axis order for all figures based on frequency
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#generate y-axis order for all figures based on frequency
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freq_order = pd.value_counts(
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freq_order = pd.value_counts(df_plt_top10_today['Com_Name']).iloc[:readings].index
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df_plt_top10_today['Com_Name']).iloc[:readings].index
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#make color for max confidence --> this groups by name and calculates max conf
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#make color for max confidence --> this groups by name and calculates max conf
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confmax = df_plt_top10_today.groupby('Com_Name')['Confidence'].max()
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confmax = df_plt_top10_today.groupby('Com_Name')['Confidence'].max()
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@@ -71,28 +59,21 @@ norm = plt.Normalize(confmax.values.min(), confmax.values.max())
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colors = plt.cm.Greens(norm(confmax))
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colors = plt.cm.Greens(norm(confmax))
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#Generate frequency plot
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#Generate frequency plot
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plot = sns.countplot(
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plot=sns.countplot(y='Com_Name', data = df_plt_top10_today, palette = colors, order=freq_order, ax=axs[0])
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y='Com_Name',
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data=df_plt_top10_today,
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palette=colors,
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order=freq_order,
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ax=axs[0])
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# Try plot grid lines between bars - problem at the moment plots grid
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# lines on bars - want between bars
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#Try plot grid lines between bars - problem at the moment plots grid lines on bars - want between bars
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z=plot.get_ymajorticklabels()
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z=plot.get_ymajorticklabels()
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plot.set_yticklabels(['\n'.join(textwrap.wrap(ticklabel.get_text(), 15))
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plot.set_yticklabels(['\n'.join(textwrap.wrap(ticklabel.get_text(),15)) for ticklabel in plot.get_yticklabels()], fontsize = 10)
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for ticklabel in plot.get_yticklabels()], fontsize=10)
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plot.set(ylabel=None)
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plot.set(ylabel=None)
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plot.set(xlabel="Detections")
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plot.set(xlabel="Detections")
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#Generate crosstab matrix for heatmap plot
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#Generate crosstab matrix for heatmap plot
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heat = pd.crosstab(
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heat = pd.crosstab(df_plt_top10_today['Com_Name'],df_plt_top10_today['Hour of Day'])
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df_plt_top10_today['Com_Name'],
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df_plt_top10_today['Hour of Day'])
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#Order heatmap Birds by frequency of occurrance
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#Order heatmap Birds by frequency of occurrance
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heat.index = pd.CategoricalIndex(heat.index, categories = freq_order)
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heat.index = pd.CategoricalIndex(heat.index, categories = freq_order)
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heat.sort_index(level=0, inplace=True)
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heat.sort_index(level=0, inplace=True)
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@@ -103,20 +84,7 @@ heat_frame = pd.DataFrame(data=0, index=heat.index, columns=hours_in_day)
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heat=(heat+heat_frame).fillna(0)
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heat=(heat+heat_frame).fillna(0)
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#Generatie heatmap plot
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#Generatie heatmap plot
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plot = sns.heatmap(
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plot = sns.heatmap(heat, norm=LogNorm(), annot=True, annot_kws={"fontsize":7}, fmt="g", cmap = pal , square = False, cbar=False, linewidths = 0.5, linecolor = "Grey", ax=axs[1], yticklabels = False)
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heat,
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norm=LogNorm(),
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annot=True,
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annot_kws={
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"fontsize": 7},
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fmt="g",
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cmap=pal,
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square=False,
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cbar=False,
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linewidths=0.5,
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linecolor="Grey",
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ax=axs[1],
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yticklabels=False)
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plot.set_xticklabels(plot.get_xticklabels(), rotation = 0, size = 7)
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plot.set_xticklabels(plot.get_xticklabels(), rotation = 0, size = 7)
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# Set heatmap border
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# Set heatmap border
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@@ -131,8 +99,7 @@ plt.suptitle("Top 10 Last Updated: " + str(now.strftime("%Y-%m-%d %H:%M")))
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#Save combined plot
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#Save combined plot
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userDir = os.path.expanduser('~')
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userDir = os.path.expanduser('~')
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savename = userDir + '/BirdSongs/Extracted/Charts/Combo-' + \
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savename=userDir + '/BirdSongs/Extracted/Charts/Combo-'+str(now.strftime("%Y-%m-%d"))+'.png'
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str(now.strftime("%Y-%m-%d")) + '.png'
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plt.savefig(savename)
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plt.savefig(savename)
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plt.show()
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plt.show()
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plt.close()
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plt.close()
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@@ -140,30 +107,18 @@ plt.close()
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# Get Bottom detection frequency
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# Get Bottom detection frequency
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plt_Bot10_today = (df_plt_today['Com_Name'].value_counts()[-readings:])
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plt_Bot10_today = (df_plt_today['Com_Name'].value_counts()[-readings:])
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df_plt_Bot10_today = df_plt_today[df_plt_today.Com_Name.isin(
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df_plt_Bot10_today = df_plt_today[df_plt_today.Com_Name.isin(plt_Bot10_today.index)]
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plt_Bot10_today.index)]
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#Set Palette for graphics
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#Set Palette for graphics
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pal = "Reds"
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pal = "Reds"
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#Set up plot axes and titles
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#Set up plot axes and titles
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f, axs = plt.subplots(
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f, axs = plt.subplots(1, 2, figsize = (10, 4), gridspec_kw=dict(width_ratios=[3, 6]), facecolor='#77C487')
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1, 2, figsize=(
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plt.subplots_adjust(left=None, bottom=None, right=None, top=None, wspace=0, hspace=0)
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10, 4), gridspec_kw=dict(
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width_ratios=[
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3, 6]), facecolor='#77C487')
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plt.subplots_adjust(
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left=None,
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bottom=None,
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right=None,
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top=None,
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wspace=0,
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hspace=0)
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#generate y-axis order for all figures based on frequency
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#generate y-axis order for all figures based on frequency
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freq_order = pd.value_counts(
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freq_order = pd.value_counts(df_plt_Bot10_today['Com_Name']).iloc[-readings:].index
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df_plt_Bot10_today['Com_Name']).iloc[-readings:].index
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#make color for max confidence --> this groups by name and calculates max conf
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#make color for max confidence --> this groups by name and calculates max conf
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confmax = df_plt_Bot10_today.groupby('Com_Name')['Confidence'].max()
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confmax = df_plt_Bot10_today.groupby('Com_Name')['Confidence'].max()
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@@ -174,27 +129,20 @@ norm = plt.Normalize(confmax.values.min(), confmax.values.max())
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colors = plt.cm.Reds(norm(confmax))
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colors = plt.cm.Reds(norm(confmax))
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#Generate frequency plot
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#Generate frequency plot
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plot = sns.countplot(
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plot=sns.countplot(y='Com_Name', data = df_plt_Bot10_today, palette = colors, order=freq_order, ax=axs[0])
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y='Com_Name',
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data=df_plt_Bot10_today,
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palette=colors,
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order=freq_order,
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ax=axs[0])
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# Try plot grid lines between bars - problem at the moment plots grid
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# lines on bars - want between bars
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#Try plot grid lines between bars - problem at the moment plots grid lines on bars - want between bars
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z=plot.get_ymajorticklabels()
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z=plot.get_ymajorticklabels()
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plot.set_yticklabels(['\n'.join(textwrap.wrap(ticklabel.get_text(), 15))
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plot.set_yticklabels(['\n'.join(textwrap.wrap(ticklabel.get_text(),15)) for ticklabel in plot.get_yticklabels()], fontsize = 10)
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for ticklabel in plot.get_yticklabels()], fontsize=10)
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plot.set(ylabel=None)
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plot.set(ylabel=None)
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plot.set(xlabel="Detections")
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plot.set(xlabel="Detections")
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#Generate crosstab matrix for heatmap plot
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#Generate crosstab matrix for heatmap plot
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heat = pd.crosstab(
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heat = pd.crosstab(df_plt_Bot10_today['Com_Name'],df_plt_Bot10_today['Hour of Day'])
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df_plt_Bot10_today['Com_Name'],
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df_plt_Bot10_today['Hour of Day'])
|
|
||||||
#Order heatmap Birds by frequency of occurrance
|
#Order heatmap Birds by frequency of occurrance
|
||||||
heat.index = pd.CategoricalIndex(heat.index, categories = freq_order)
|
heat.index = pd.CategoricalIndex(heat.index, categories = freq_order)
|
||||||
heat.sort_index(level=0, inplace=True)
|
heat.sort_index(level=0, inplace=True)
|
||||||
@@ -205,20 +153,7 @@ heat_frame = pd.DataFrame(data=0, index=heat.index, columns=hours_in_day)
|
|||||||
heat=(heat+heat_frame).fillna(0)
|
heat=(heat+heat_frame).fillna(0)
|
||||||
|
|
||||||
#Generatie heatmap plot
|
#Generatie heatmap plot
|
||||||
plot = sns.heatmap(
|
plot = sns.heatmap(heat, norm=LogNorm(), annot=True, fmt="g", annot_kws={"fontsize":7}, cmap = pal , square = False, cbar=False, linewidths = 0.5, linecolor = "Grey", ax=axs[1], yticklabels = False)
|
||||||
heat,
|
|
||||||
norm=LogNorm(),
|
|
||||||
annot=True,
|
|
||||||
fmt="g",
|
|
||||||
annot_kws={
|
|
||||||
"fontsize": 7},
|
|
||||||
cmap=pal,
|
|
||||||
square=False,
|
|
||||||
cbar=False,
|
|
||||||
linewidths=0.5,
|
|
||||||
linecolor="Grey",
|
|
||||||
ax=axs[1],
|
|
||||||
yticklabels=False)
|
|
||||||
plot.set_xticklabels(plot.get_xticklabels(), rotation = 0, size = 7)
|
plot.set_xticklabels(plot.get_xticklabels(), rotation = 0, size = 7)
|
||||||
|
|
||||||
# Set heatmap border
|
# Set heatmap border
|
||||||
@@ -232,8 +167,7 @@ f.subplots_adjust(top=0.9)
|
|||||||
plt.suptitle("Bottom 10 Last Updated: "+ str(now.strftime("%Y-%m-%d %H:%M")))
|
plt.suptitle("Bottom 10 Last Updated: "+ str(now.strftime("%Y-%m-%d %H:%M")))
|
||||||
|
|
||||||
#Save combined plot
|
#Save combined plot
|
||||||
savename = userDir + '/BirdSongs/Extracted/Charts/Combo2-' + \
|
savename=userDir + '/BirdSongs/Extracted/Charts/Combo2-'+str(now.strftime("%Y-%m-%d"))+'.png'
|
||||||
str(now.strftime("%Y-%m-%d")) + '.png'
|
|
||||||
plt.savefig(savename)
|
plt.savefig(savename)
|
||||||
plt.show()
|
plt.show()
|
||||||
plt.close()
|
plt.close()
|
||||||
|
|||||||
+12
-20
@@ -4,7 +4,8 @@ import pandas as pd
|
|||||||
import numpy as np
|
import numpy as np
|
||||||
import plotly.graph_objects as go
|
import plotly.graph_objects as go
|
||||||
from plotly.subplots import make_subplots
|
from plotly.subplots import make_subplots
|
||||||
from datetime import timedelta
|
from datetime import timedelta, datetime
|
||||||
|
from pathlib import Path
|
||||||
import sqlite3
|
import sqlite3
|
||||||
from sqlite3 import Connection
|
from sqlite3 import Connection
|
||||||
|
|
||||||
@@ -41,7 +42,6 @@ def get_data(conn: Connection):
|
|||||||
df1=pd.read_sql("SELECT * FROM detections", con=conn)
|
df1=pd.read_sql("SELECT * FROM detections", con=conn)
|
||||||
return df1
|
return df1
|
||||||
|
|
||||||
|
|
||||||
conn = get_connection(URI_SQLITE_DB)
|
conn = get_connection(URI_SQLITE_DB)
|
||||||
# Read in the cereal data
|
# Read in the cereal data
|
||||||
# df = load_data()
|
# df = load_data()
|
||||||
@@ -51,6 +51,7 @@ df2['DateTime'] = pd.to_datetime(df2['Date'] + " " + df2['Time'])
|
|||||||
df2=df2.set_index('DateTime')
|
df2=df2.set_index('DateTime')
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
# Filter on date range
|
# Filter on date range
|
||||||
# Date as calendars
|
# Date as calendars
|
||||||
# Start_Date = pd.to_datetime(st.sidebar.date_input('Which date do you want to start?', value = df2.index.min()))
|
# Start_Date = pd.to_datetime(st.sidebar.date_input('Which date do you want to start?', value = df2.index.min()))
|
||||||
@@ -67,6 +68,7 @@ Date_Slider = st.slider('Date Range',
|
|||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
filt = (df2.index >= pd.Timestamp(Date_Slider[0])) & (df2.index <= pd.Timestamp(Date_Slider[1]+timedelta(days=1)))
|
filt = (df2.index >= pd.Timestamp(Date_Slider[0])) & (df2.index <= pd.Timestamp(Date_Slider[1]+timedelta(days=1)))
|
||||||
df2 = df2[filt]
|
df2 = df2[filt]
|
||||||
|
|
||||||
@@ -92,10 +94,7 @@ top_N = cols1.slider(
|
|||||||
top_N_species = (df2['Com_Name'].value_counts()[:top_N])
|
top_N_species = (df2['Com_Name'].value_counts()[:top_N])
|
||||||
|
|
||||||
|
|
||||||
specie = cols2.selectbox(
|
specie = cols2.selectbox('Which bird would you like to explore for the dates '+str(Date_Slider[0])+' to '+str(Date_Slider[1])+'?', species,
|
||||||
'Which bird would you like to explore for the dates ' +
|
|
||||||
str(Date_Slider[0]) + ' to ' + str(Date_Slider[1]) + '?',
|
|
||||||
species,
|
|
||||||
index=species.index(list(top_N_species.index)[0]))
|
index=species.index(list(top_N_species.index)[0]))
|
||||||
|
|
||||||
|
|
||||||
@@ -109,17 +108,11 @@ df_counts = df2[filt].resample('D').count()
|
|||||||
|
|
||||||
fig = make_subplots(
|
fig = make_subplots(
|
||||||
rows=3, cols =2,
|
rows=3, cols =2,
|
||||||
specs=[[{"type": "xy", "rowspan": 3}, {"type": "polar", "rowspan": 2}], [
|
specs= [[{"type":"xy","rowspan":3}, {"type":"polar","rowspan":2}], [{"rowspan":1}, {"rowspan":1} ], [None, {"type":"xy","rowspan":1}]],
|
||||||
{"rowspan": 1}, {"rowspan": 1}], [None, {"type": "xy", "rowspan": 1}]],
|
subplot_titles=('<b>Top '+ str(top_N) + ' Species in Date Range '+str(Date_Slider[0])+' to '+str(Date_Slider[1])+'</b>',
|
||||||
subplot_titles=(
|
|
||||||
'<b>Top ' + str(top_N) +
|
|
||||||
' Species in Date Range ' + str(Date_Slider[0]) +
|
|
||||||
' to ' + str(Date_Slider[1]) +
|
|
||||||
'</b>',
|
|
||||||
'Total Detect:'+str('{:,}'.format(sum(df_counts.Time)))+
|
'Total Detect:'+str('{:,}'.format(sum(df_counts.Time)))+
|
||||||
' Confidence Max:'+str('{:.2f}%'.format(max(df2[df2['Com_Name']==specie]['Confidence'])*100))+
|
' Confidence Max:'+str('{:.2f}%'.format(max(df2[df2['Com_Name']==specie]['Confidence'])*100))+
|
||||||
' ' + ' Median:' +
|
' '+' Median:'+str('{:.2f}%'.format(np.median(df2[df2['Com_Name']==specie]['Confidence'])*100))
|
||||||
str('{:.2f}%'.format(np.median(df2[df2['Com_Name'] == specie]['Confidence']) * 100))
|
|
||||||
)
|
)
|
||||||
)
|
)
|
||||||
fig.layout.annotations[1].update(x=0.7,y=0.25, font_size=15)
|
fig.layout.annotations[1].update(x=0.7,y=0.25, font_size=15)
|
||||||
@@ -154,16 +147,15 @@ fig.update_layout(
|
|||||||
rotation = -90,
|
rotation = -90,
|
||||||
direction = 'clockwise',
|
direction = 'clockwise',
|
||||||
tickmode='array',
|
tickmode='array',
|
||||||
tickvals=[0, 15, 35, 45, 60, 75, 90, 105, 120, 135, 150, 165,
|
tickvals=[0,15,35,45,60,75,90,105,120,135,150,165,180,195,210,225,240,255,270,285,300,315,330,345],
|
||||||
180, 195, 210, 225, 240, 255, 270, 285, 300, 315, 330, 345],
|
ticktext=['12am','1am','2am','3am','4am','5am', '6am','7am','8am','9am','10am','11am','12pm','1pm','2pm','3pm','4pm','5pm', '6pm','7pm','8pm','9pm','10pm','11pm'],
|
||||||
ticktext=['12am', '1am', '2am', '3am', '4am', '5am', '6am', '7am', '8am', '9am', '10am', '11am',
|
|
||||||
'12pm', '1pm', '2pm', '3pm', '4pm', '5pm', '6pm', '7pm', '8pm', '9pm', '10pm', '11pm'],
|
|
||||||
hoverformat = "#%{theta}: <br>Popularity: %{percent} </br> %{r}"
|
hoverformat = "#%{theta}: <br>Popularity: %{percent} </br> %{r}"
|
||||||
),
|
),
|
||||||
),
|
),
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
daily=pd.crosstab(df2['Com_Name'],df2.index.date, dropna=False)
|
daily=pd.crosstab(df2['Com_Name'],df2.index.date, dropna=False)
|
||||||
|
|
||||||
fig.add_trace(go.Bar(x=daily.columns, y=daily.loc[specie]), row=3, col=2)
|
fig.add_trace(go.Bar(x=daily.columns, y=daily.loc[specie]), row=3, col=2)
|
||||||
@@ -176,6 +168,6 @@ st.plotly_chart(fig, use_container_width=True) # , config=config)
|
|||||||
#
|
#
|
||||||
# extract_date=Date_Slider
|
# extract_date=Date_Slider
|
||||||
#
|
#
|
||||||
# audio_file = open('/home/*/BirdSongs/Extracted/By_Date/2022-03-22/Yellow-streaked_Greenbul/Yellow-streaked_Greenbul-77-2022-03-22-birdnet-15:04:28.mp3', 'rb') # noqa: E501
|
# audio_file = open('/home/*/BirdSongs/Extracted/By_Date/2022-03-22/Yellow-streaked_Greenbul/Yellow-streaked_Greenbul-77-2022-03-22-birdnet-15:04:28.mp3', 'rb')
|
||||||
# audio_bytes = audio_file.read()
|
# audio_bytes = audio_file.read()
|
||||||
# cols4.audio(audio_bytes, format='audio/mp3')
|
# cols4.audio(audio_bytes, format='audio/mp3')
|
||||||
|
|||||||
+45
-106
@@ -1,27 +1,32 @@
|
|||||||
import os
|
|
||||||
import socket
|
import socket
|
||||||
import threading
|
import threading
|
||||||
import operator
|
import os
|
||||||
import librosa
|
|
||||||
import numpy as np
|
|
||||||
import math
|
|
||||||
import time
|
|
||||||
import json
|
|
||||||
import requests
|
|
||||||
import sqlite3
|
|
||||||
import datetime
|
|
||||||
from tzlocal import get_localzone
|
|
||||||
from pathlib import Path
|
|
||||||
import apprise
|
|
||||||
|
|
||||||
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
|
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
|
||||||
os.environ['CUDA_VISIBLE_DEVICES'] = ''
|
os.environ['CUDA_VISIBLE_DEVICES'] = ''
|
||||||
|
|
||||||
try:
|
try:
|
||||||
import tflite_runtime.interpreter as tflite
|
import tflite_runtime.interpreter as tflite
|
||||||
except BaseException:
|
except:
|
||||||
from tensorflow import lite as tflite
|
from tensorflow import lite as tflite
|
||||||
|
|
||||||
|
import argparse
|
||||||
|
import operator
|
||||||
|
import librosa
|
||||||
|
import numpy as np
|
||||||
|
import math
|
||||||
|
import time
|
||||||
|
from decimal import Decimal
|
||||||
|
import json
|
||||||
|
import requests
|
||||||
|
import sqlite3
|
||||||
|
import datetime
|
||||||
|
from time import sleep
|
||||||
|
import pytz
|
||||||
|
from tzlocal import get_localzone
|
||||||
|
from pathlib import Path
|
||||||
|
import apprise
|
||||||
|
|
||||||
|
|
||||||
HEADER = 64
|
HEADER = 64
|
||||||
PORT = 5050
|
PORT = 5050
|
||||||
SERVER = socket.gethostbyname(socket.gethostname())
|
SERVER = socket.gethostbyname(socket.gethostname())
|
||||||
@@ -32,18 +37,18 @@ DISCONNECT_MESSAGE = "!DISCONNECT"
|
|||||||
server = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
|
server = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
|
||||||
try:
|
try:
|
||||||
server.bind(ADDR)
|
server.bind(ADDR)
|
||||||
except BaseException:
|
except:
|
||||||
print("Waiting on socket")
|
print("Waiting on socket")
|
||||||
time.sleep(5)
|
time.sleep(5)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
# Open most recent Configuration and grab DB_PWD as a python variable
|
# Open most recent Configuration and grab DB_PWD as a python variable
|
||||||
userDir = os.path.expanduser('~')
|
userDir = os.path.expanduser('~')
|
||||||
with open(userDir + '/BirdNET-Pi/scripts/thisrun.txt', 'r') as f:
|
with open(userDir + '/BirdNET-Pi/scripts/thisrun.txt', 'r') as f:
|
||||||
this_run = f.readlines()
|
this_run = f.readlines()
|
||||||
audiofmt = "." + str(str(str([i for i in this_run if i.startswith('AUDIOFMT')]).split('=')[1]).split('\\')[0])
|
audiofmt = "." + str(str(str([i for i in this_run if i.startswith('AUDIOFMT')]).split('=')[1]).split('\\')[0])
|
||||||
priv_thresh = float(
|
priv_thresh = float("." + str(str(str([i for i in this_run if i.startswith('PRIVACY_THRESHOLD')]).split('=')[1]).split('\\')[0]))/10
|
||||||
"." + str(str(str([i for i in this_run if i.startswith('PRIVACY_THRESHOLD')]).split('=')[1]).split('\\')[0])) / 10
|
|
||||||
|
|
||||||
|
|
||||||
def loadModel():
|
def loadModel():
|
||||||
@@ -80,7 +85,6 @@ def loadModel():
|
|||||||
|
|
||||||
return myinterpreter
|
return myinterpreter
|
||||||
|
|
||||||
|
|
||||||
def loadCustomSpeciesList(path):
|
def loadCustomSpeciesList(path):
|
||||||
|
|
||||||
slist = []
|
slist = []
|
||||||
@@ -91,7 +95,6 @@ def loadCustomSpeciesList(path):
|
|||||||
|
|
||||||
return slist
|
return slist
|
||||||
|
|
||||||
|
|
||||||
def splitSignal(sig, rate, overlap, seconds=3.0, minlen=1.5):
|
def splitSignal(sig, rate, overlap, seconds=3.0, minlen=1.5):
|
||||||
|
|
||||||
# Split signal with overlap
|
# Split signal with overlap
|
||||||
@@ -113,7 +116,6 @@ def splitSignal(sig, rate, overlap, seconds=3.0, minlen=1.5):
|
|||||||
|
|
||||||
return sig_splits
|
return sig_splits
|
||||||
|
|
||||||
|
|
||||||
def readAudioData(path, overlap, sample_rate=48000):
|
def readAudioData(path, overlap, sample_rate=48000):
|
||||||
|
|
||||||
print('READING AUDIO DATA...', end=' ', flush=True)
|
print('READING AUDIO DATA...', end=' ', flush=True)
|
||||||
@@ -128,7 +130,6 @@ def readAudioData(path, overlap, sample_rate=48000):
|
|||||||
|
|
||||||
return chunks
|
return chunks
|
||||||
|
|
||||||
|
|
||||||
def convertMetadata(m):
|
def convertMetadata(m):
|
||||||
|
|
||||||
# Convert week to cosine
|
# Convert week to cosine
|
||||||
@@ -146,11 +147,9 @@ def convertMetadata(m):
|
|||||||
|
|
||||||
return np.concatenate([m, mask])
|
return np.concatenate([m, mask])
|
||||||
|
|
||||||
|
|
||||||
def custom_sigmoid(x, sensitivity=1.0):
|
def custom_sigmoid(x, sensitivity=1.0):
|
||||||
return 1 / (1.0 + np.exp(-sensitivity * x))
|
return 1 / (1.0 + np.exp(-sensitivity * x))
|
||||||
|
|
||||||
|
|
||||||
def predict(sample, sensitivity):
|
def predict(sample, sensitivity):
|
||||||
global INTERPRETER
|
global INTERPRETER
|
||||||
# Make a prediction
|
# Make a prediction
|
||||||
@@ -182,7 +181,6 @@ def predict(sample, sensitivity):
|
|||||||
|
|
||||||
return p_sorted[:human_cutoff]
|
return p_sorted[:human_cutoff]
|
||||||
|
|
||||||
|
|
||||||
def analyzeAudioData(chunks, lat, lon, week, sensitivity, overlap,):
|
def analyzeAudioData(chunks, lat, lon, week, sensitivity, overlap,):
|
||||||
global INTERPRETER
|
global INTERPRETER
|
||||||
|
|
||||||
@@ -215,7 +213,7 @@ def analyzeAudioData(chunks, lat, lon, week, sensitivity, overlap,):
|
|||||||
pred_end = pred_start + 3.0
|
pred_end = pred_start + 3.0
|
||||||
|
|
||||||
#If human detected set all detections to human to make sure voices are not saved
|
#If human detected set all detections to human to make sure voices are not saved
|
||||||
if HUMAN_DETECTED is True:
|
if HUMAN_DETECTED == True:
|
||||||
p=[('Human_Human',0.0)]*10
|
p=[('Human_Human',0.0)]*10
|
||||||
|
|
||||||
detections[str(pred_start) + ';' + str(pred_end)] = p
|
detections[str(pred_start) + ';' + str(pred_end)] = p
|
||||||
@@ -226,17 +224,14 @@ def analyzeAudioData(chunks, lat, lon, week, sensitivity, overlap,):
|
|||||||
# print('DETECTIONS:::::',detections)
|
# print('DETECTIONS:::::',detections)
|
||||||
return detections
|
return detections
|
||||||
|
|
||||||
|
|
||||||
def sendAppriseNotifications(species,confidence):
|
def sendAppriseNotifications(species,confidence):
|
||||||
if os.path.exists(userDir + '/BirdNET-Pi/apprise.txt') and os.path.getsize(userDir + '/BirdNET-Pi/apprise.txt') > 0:
|
if os.path.exists(userDir + '/BirdNET-Pi/apprise.txt') and os.path.getsize(userDir + '/BirdNET-Pi/apprise.txt') > 0:
|
||||||
with open(userDir + '/BirdNET-Pi/scripts/thisrun.txt', 'r') as f:
|
with open(userDir + '/BirdNET-Pi/scripts/thisrun.txt', 'r') as f:
|
||||||
this_run = f.readlines()
|
this_run = f.readlines()
|
||||||
title = str(str(str([i for i in this_run if i.startswith('APPRISE_NOTIFICATION_TITLE')]
|
title = str(str(str([i for i in this_run if i.startswith('APPRISE_NOTIFICATION_TITLE')]).split('=')[1]).split('\\')[0]).replace('"', '')
|
||||||
).split('=')[1]).split('\\')[0]).replace('"', '')
|
body = str(str(str([i for i in this_run if i.startswith('APPRISE_NOTIFICATION_BODY')]).split('=')[1]).split('\\')[0]).replace('"', '')
|
||||||
body = str(str(str([i for i in this_run if i.startswith('APPRISE_NOTIFICATION_BODY')]
|
|
||||||
).split('=')[1]).split('\\')[0]).replace('"', '')
|
|
||||||
|
|
||||||
if str(str(str([i for i in this_run if i.startswith('APPRISE_NOTIFY_EACH_DETECTION')]).split('=')[1]).split('\\')[0]) == "1": # noqa E501
|
if str(str(str([i for i in this_run if i.startswith('APPRISE_NOTIFY_EACH_DETECTION')]).split('=')[1]).split('\\')[0]) == "1":
|
||||||
|
|
||||||
apobj = apprise.Apprise()
|
apobj = apprise.Apprise()
|
||||||
config = apprise.AppriseConfig()
|
config = apprise.AppriseConfig()
|
||||||
@@ -244,17 +239,10 @@ def sendAppriseNotifications(species, confidence):
|
|||||||
apobj.add(config)
|
apobj.add(config)
|
||||||
|
|
||||||
apobj.notify(
|
apobj.notify(
|
||||||
body=body.replace(
|
body=body.replace("$sciname",species.split("_")[0]).replace("$comname",species.split("_")[1]).replace("$confidence",confidence),
|
||||||
"$sciname",
|
|
||||||
species.split("_")[0]).replace(
|
|
||||||
"$comname",
|
|
||||||
species.split("_")[1]).replace(
|
|
||||||
"$confidence",
|
|
||||||
confidence),
|
|
||||||
title=title,
|
title=title,
|
||||||
)
|
)
|
||||||
|
|
||||||
|
|
||||||
def writeResultsToFile(detections, min_conf, path):
|
def writeResultsToFile(detections, min_conf, path):
|
||||||
|
|
||||||
print('WRITING RESULTS TO', path, '...', end=' ')
|
print('WRITING RESULTS TO', path, '...', end=' ')
|
||||||
@@ -263,15 +251,13 @@ def writeResultsToFile(detections, min_conf, path):
|
|||||||
rfile.write('Start (s);End (s);Scientific name;Common name;Confidence\n')
|
rfile.write('Start (s);End (s);Scientific name;Common name;Confidence\n')
|
||||||
for d in detections:
|
for d in detections:
|
||||||
for entry in detections[d]:
|
for entry in detections[d]:
|
||||||
if entry[1] >= min_conf and ((entry[0] in INCLUDE_LIST or len(INCLUDE_LIST) == 0)
|
if entry[1] >= min_conf and ((entry[0] in INCLUDE_LIST or len(INCLUDE_LIST) == 0) and (entry[0] not in EXCLUDE_LIST or len(EXCLUDE_LIST) == 0) ):
|
||||||
and (entry[0] not in EXCLUDE_LIST or len(EXCLUDE_LIST) == 0)):
|
sendAppriseNotifications(str(entry[0]),str(entry[1]));
|
||||||
sendAppriseNotifications(str(entry[0]), str(entry[1]))
|
|
||||||
rfile.write(d + ';' + entry[0].replace('_', ';') + ';' + str(entry[1]) + '\n')
|
rfile.write(d + ';' + entry[0].replace('_', ';') + ';' + str(entry[1]) + '\n')
|
||||||
rcnt += 1
|
rcnt += 1
|
||||||
print('DONE! WROTE', rcnt, 'RESULTS.')
|
print('DONE! WROTE', rcnt, 'RESULTS.')
|
||||||
return
|
return
|
||||||
|
|
||||||
|
|
||||||
def handle_client(conn, addr):
|
def handle_client(conn, addr):
|
||||||
global INCLUDE_LIST
|
global INCLUDE_LIST
|
||||||
global EXCLUDE_LIST
|
global EXCLUDE_LIST
|
||||||
@@ -302,6 +288,7 @@ def handle_client(conn, addr):
|
|||||||
args.lat = -1
|
args.lat = -1
|
||||||
args.lon = -1
|
args.lon = -1
|
||||||
|
|
||||||
|
|
||||||
for line in msg.split('||'):
|
for line in msg.split('||'):
|
||||||
inputvars = line.split('=')
|
inputvars = line.split('=')
|
||||||
if inputvars[0] == 'i':
|
if inputvars[0] == 'i':
|
||||||
@@ -327,6 +314,8 @@ def handle_client(conn, addr):
|
|||||||
elif inputvars[0] == 'lon':
|
elif inputvars[0] == 'lon':
|
||||||
args.lon = float(inputvars[1])
|
args.lon = float(inputvars[1])
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
# Load custom species lists - INCLUDED and EXCLUDED
|
# Load custom species lists - INCLUDED and EXCLUDED
|
||||||
if not args.include_list == 'null':
|
if not args.include_list == 'null':
|
||||||
INCLUDE_LIST = loadCustomSpeciesList(args.include_list)
|
INCLUDE_LIST = loadCustomSpeciesList(args.include_list)
|
||||||
@@ -382,14 +371,13 @@ def handle_client(conn, addr):
|
|||||||
for i in detections:
|
for i in detections:
|
||||||
myReturn += str(i) + '-' + str(detections[i][0]) + '\n'
|
myReturn += str(i) + '-' + str(detections[i][0]) + '\n'
|
||||||
|
|
||||||
|
|
||||||
with open(userDir + '/BirdNET-Pi/BirdDB.txt', 'a') as rfile:
|
with open(userDir + '/BirdNET-Pi/BirdDB.txt', 'a') as rfile:
|
||||||
for d in detections:
|
for d in detections:
|
||||||
for entry in detections[d]:
|
for entry in detections[d]:
|
||||||
if entry[1] >= min_conf and ((entry[0] in INCLUDE_LIST or len(INCLUDE_LIST) == 0) and (
|
if entry[1] >= min_conf and ((entry[0] in INCLUDE_LIST or len(INCLUDE_LIST) == 0) and (entry[0] not in EXCLUDE_LIST or len(EXCLUDE_LIST) == 0) ):
|
||||||
entry[0] not in EXCLUDE_LIST or len(EXCLUDE_LIST) == 0)):
|
rfile.write(str(current_date) + ';' + str(current_time) + ';' + entry[0].replace('_', ';') + ';' \
|
||||||
rfile.write(str(current_date) + ';' + str(current_time) + ';' + entry[0].replace('_', ';') + ';'
|
+ str(entry[1]) +";" + str(args.lat) + ';' + str(args.lon) + ';' + str(min_conf) + ';' + str(week) + ';' \
|
||||||
+ str(entry[1]) + ";" + str(args.lat) + ';' + str(args.lon) +
|
|
||||||
';' + str(min_conf) + ';' + str(week) + ';'
|
|
||||||
+ str(args.sensitivity) +';' + str(args.overlap) + '\n')
|
+ str(args.sensitivity) +';' + str(args.overlap) + '\n')
|
||||||
|
|
||||||
Date = str(current_date)
|
Date = str(current_date)
|
||||||
@@ -413,78 +401,34 @@ def handle_client(conn, addr):
|
|||||||
try:
|
try:
|
||||||
con = sqlite3.connect(userDir + '/BirdNET-Pi/scripts/birds.db')
|
con = sqlite3.connect(userDir + '/BirdNET-Pi/scripts/birds.db')
|
||||||
cur = con.cursor()
|
cur = con.cursor()
|
||||||
cur.execute(
|
cur.execute("INSERT INTO detections VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)", (Date, Time, Sci_Name, Com_Name, str(score), Lat, Lon, Cutoff, Week, Sens, Overlap, File_Name))
|
||||||
"INSERT INTO detections VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)",
|
|
||||||
(Date,
|
|
||||||
Time,
|
|
||||||
Sci_Name,
|
|
||||||
Com_Name,
|
|
||||||
str(score),
|
|
||||||
Lat,
|
|
||||||
Lon,
|
|
||||||
Cutoff,
|
|
||||||
Week,
|
|
||||||
Sens,
|
|
||||||
Overlap,
|
|
||||||
File_Name))
|
|
||||||
|
|
||||||
con.commit()
|
con.commit()
|
||||||
con.close()
|
con.close()
|
||||||
break
|
break
|
||||||
except BaseException:
|
except:
|
||||||
print("Database busy")
|
print("Database busy")
|
||||||
time.sleep(2)
|
time.sleep(2)
|
||||||
|
|
||||||
print(str(current_date) +
|
print(str(current_date) + ';' + str(current_time) + ';' + entry[0].replace('_', ';') + ';' + str(entry[1]) + ';' + str(args.lat) + ';' + str(args.lon) + ';' + str(min_conf) + ';' + str(week) + ';' + str(args.sensitivity) +';' + str(args.overlap) + Com_Name.replace(" ", "_") + '-' + str(score) + '-' + str(current_date) + '-birdnet-' + str(current_time) + audiofmt + '\n')
|
||||||
';' +
|
|
||||||
str(current_time) +
|
|
||||||
';' +
|
|
||||||
entry[0].replace('_', ';') +
|
|
||||||
';' +
|
|
||||||
str(entry[1]) +
|
|
||||||
';' +
|
|
||||||
str(args.lat) +
|
|
||||||
';' +
|
|
||||||
str(args.lon) +
|
|
||||||
';' +
|
|
||||||
str(min_conf) +
|
|
||||||
';' +
|
|
||||||
str(week) +
|
|
||||||
';' +
|
|
||||||
str(args.sensitivity) +
|
|
||||||
';' +
|
|
||||||
str(args.overlap) +
|
|
||||||
Com_Name.replace(" ", "_") +
|
|
||||||
'-' +
|
|
||||||
str(score) +
|
|
||||||
'-' +
|
|
||||||
str(current_date) +
|
|
||||||
'-birdnet-' +
|
|
||||||
str(current_time) +
|
|
||||||
audiofmt +
|
|
||||||
'\n')
|
|
||||||
|
|
||||||
if birdweather_id != "99999":
|
if birdweather_id != "99999":
|
||||||
try:
|
try:
|
||||||
|
|
||||||
if soundscape_uploaded is False:
|
if soundscape_uploaded is False:
|
||||||
# POST soundscape to server
|
# POST soundscape to server
|
||||||
soundscape_url = "https://app.birdweather.com/api/v1/stations/" + \
|
soundscape_url = "https://app.birdweather.com/api/v1/stations/" + birdweather_id + "/soundscapes" + "?timestamp=" + current_iso8601
|
||||||
birdweather_id + "/soundscapes" + "?timestamp=" + current_iso8601
|
|
||||||
|
|
||||||
with open(args.i, 'rb') as f:
|
with open(args.i, 'rb') as f:
|
||||||
wav_data = f.read()
|
wav_data = f.read()
|
||||||
response = requests.post(
|
response = requests.post(url=soundscape_url, data=wav_data, headers={'Content-Type': 'application/octet-stream'})
|
||||||
url=soundscape_url, data=wav_data, headers={
|
|
||||||
'Content-Type': 'application/octet-stream'})
|
|
||||||
print("Soundscape POST Response Status - ", response.status_code)
|
print("Soundscape POST Response Status - ", response.status_code)
|
||||||
sdata = response.json()
|
sdata = response.json()
|
||||||
soundscape_id = sdata['soundscape']['id']
|
soundscape_id = sdata['soundscape']['id']
|
||||||
soundscape_uploaded = True
|
soundscape_uploaded = True
|
||||||
|
|
||||||
# POST detection to server
|
# POST detection to server
|
||||||
detection_url = "https://app.birdweather.com/api/v1/stations/" + \
|
detection_url = "https://app.birdweather.com/api/v1/stations/" + birdweather_id + "/detections"
|
||||||
birdweather_id + "/detections"
|
|
||||||
start_time = d.split(';')[0]
|
start_time = d.split(';')[0]
|
||||||
end_time = d.split(';')[1]
|
end_time = d.split(';')[1]
|
||||||
post_begin = "{ "
|
post_begin = "{ "
|
||||||
@@ -502,15 +446,11 @@ def handle_client(conn, addr):
|
|||||||
post_confidence = "\"confidence\": " + str(entry[1])
|
post_confidence = "\"confidence\": " + str(entry[1])
|
||||||
post_end = " }"
|
post_end = " }"
|
||||||
|
|
||||||
post_json = post_begin + \
|
post_json = post_begin + post_timestamp + post_lat + post_lon + post_soundscape_id + post_soundscape_start_time + post_soundscape_end_time + post_commonName + post_scientificName + post_algorithm + post_confidence + post_end
|
||||||
post_timestamp + post_lat + post_lon + \
|
|
||||||
post_soundscape_id + post_soundscape_start_time + \
|
|
||||||
post_soundscape_end_time + post_commonName + post_scientificName + \
|
|
||||||
post_algorithm + post_confidence + post_end
|
|
||||||
print(post_json)
|
print(post_json)
|
||||||
response = requests.post(detection_url, json=json.loads(post_json))
|
response = requests.post(detection_url, json=json.loads(post_json))
|
||||||
print("Detection POST Response Status - ", response.status_code)
|
print("Detection POST Response Status - ", response.status_code)
|
||||||
except BaseException:
|
except:
|
||||||
print("Cannot POST right now")
|
print("Cannot POST right now")
|
||||||
conn.send(myReturn.encode(FORMAT))
|
conn.send(myReturn.encode(FORMAT))
|
||||||
|
|
||||||
@@ -518,7 +458,6 @@ def handle_client(conn, addr):
|
|||||||
|
|
||||||
conn.close()
|
conn.close()
|
||||||
|
|
||||||
|
|
||||||
def start():
|
def start():
|
||||||
# Load model
|
# Load model
|
||||||
global INTERPRETER, INCLUDE_LIST, EXCLUDE_LIST
|
global INTERPRETER, INCLUDE_LIST, EXCLUDE_LIST
|
||||||
|
|||||||
Reference in New Issue
Block a user