raab/GP2023_chirp_detection
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

removing logger output and adding tqdm

Browse Source
This commit is contained in:
wendtalexander 2023-01-18 17:58:33 +01:00
parent 501172f30d
commit a79fc86ab9
2 changed files with 17 additions and 13 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

28
code/chirpdetection.py
View File

@ -2,6 +2,7 @@ from itertools import combinations, compress
from dataclasses import dataclass
import numpy as np
from tqdm import tqdm
from IPython import embed
import matplotlib.pyplot as plt
from scipy.signal import find_peaks
@ -77,14 +78,17 @@ class PlotBuffer:
# plot spectrogram
plot_spectrogram(axs[0], data_oi, self.data.raw_rate, self.t0)
# plot baseline instantaneos frequency
axs[1].plot(self.frequency_time, self.frequency)
for chirp in chirps:
axs[0].scatter(chirp, np.median(self.frequency), c=ps.red)
# plot waveform of filtered signal
axs[2].plot(self.time, self.baseline, c=ps.green)
axs[1].plot(self.time, self.baseline, c=ps.green)
# plot waveform of filtered search signal
axs[3].plot(self.time, self.search)
axs[2].plot(self.time, self.search)
# plot baseline instantaneos frequency
axs[3].plot(self.frequency_time, self.frequency)
# plot filtered and rectified envelope
axs[4].plot(self.time, self.baseline_envelope)
@ -109,12 +113,12 @@ class PlotBuffer:
self.frequency_filtered[self.frequency_peaks],
c=ps.red,
)
axs[0].set_ylim(np.max(self.frequency)-200, top=np.max(self.frequency)+200)
axs[6].set_xlabel("Time [s]")
axs[0].set_title("Spectrogram")
axs[1].set_title("Fitered baseline instanenous frequency")
axs[2].set_title("Fitered baseline")
axs[3].set_title("Fitered above")
axs[1].set_title("Fitered baseline")
axs[2].set_title("Fitered above")
axs[3].set_title("Fitered baseline instanenous frequency")
axs[4].set_title("Filtered envelope of baseline envelope")
axs[5].set_title("Search envelope")
axs[6].set_title(
@ -275,7 +279,7 @@ def main(datapath: str, plot: str) -> None:
raw_time = np.arange(data.raw.shape[0]) / data.raw_rate
# # good chirp times for data: 2022-06-02-10_00
# t0 = (3 * 60 * 60 + 6 * 60 + 43.5) * data.raw_rate
#t0 = (3 * 60 * 60 + 6 * 60 + 43.5) * data.raw_rate
# dt = 60 * data.raw_rate
t0 = 0
@ -297,7 +301,8 @@ def main(datapath: str, plot: str) -> None:
chirps = []
fish_ids = []
for st, start_index in enumerate(window_starts):
for st, start_index in tqdm(enumerate(window_starts)):
#print(f"Processing window {st/data.raw_rate} of {len(window_starts/data.raw_rate)}")
logger.debug(f"Processing window {st} of {len(window_starts)}")
@ -328,7 +333,6 @@ def main(datapath: str, plot: str) -> None:
logger.debug(f"Processing track {tr} of {len(track_ids)}")
print(f"Track ID: {track_id}")
# get index of track data in this time window
window_idx = np.arange(len(data.idx))[
@ -425,7 +429,7 @@ def main(datapath: str, plot: str) -> None:
else:
search_freq = config.default_search_freq
print(f"Search frequency: {search_freq}")
#print(f"Search frequency: {search_freq}")
# ----------- chrips on the two best electrodes-----------
chirps_electrodes = []
electrodes_of_chirps = []

2
code/modules/logger.py
View File

@ -17,7 +17,7 @@ def makeLogger(name: str):
# create stream handler for terminal output
console_handler = logging.StreamHandler()
console_handler.setFormatter(console_formatter)
console_handler.setLevel(logging.DEBUG)
console_handler.setLevel(logging.INFO)
# create script specific logger
logger = logging.getLogger(name)