raab/GP2023_chirp_detection
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added unfiltered envelope in main plot

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weygoldt 2023-01-14 22:26:36 +01:00 committed by sprause
parent 658b5011fd
commit 0f1fca8b18
4 changed files with 46 additions and 40 deletions
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3
.vscode/settings.json vendored Normal file
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@ -0,0 +1,3 @@
{
"python.formatting.provider": "autopep8"
}

33
code/chirpdetection.py
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@ -11,6 +11,9 @@ from thunderfish.powerspectrum import spectrogram, decibel
from modules.filters import bandpass_filter, envelope, highpass_filter
from modules.filehandling import ConfLoader, LoadData
from modules.plotstyle import PlotStyle
ps = PlotStyle()
def instantaneos_frequency(
@ -275,19 +278,19 @@ def main(datapath: str) -> None:
)
# compute envelopes
baseline_envelope = envelope(
baseline_envelope_unfiltered = envelope(
baseline, data.raw_rate, config.envelope_cutoff)
search_envelope = envelope(
search, data.raw_rate, config.envelope_cutoff)
# highpass filter envelopes
baseline_envelope = highpass_filter(
baseline_envelope,
baseline_envelope_unfiltered,
data.raw_rate,
config.envelope_highpass_cutoff
)
baseline_envelope = np.abs(baseline_envelope)
# baseline_envelope = np.abs(baseline_envelope)
# search_envelope = highpass_filter(
# search_envelope,
# data.raw_rate,
@ -323,6 +326,7 @@ def main(datapath: str) -> None:
int(window_edge), len(baseline_envelope) -
int(window_edge)
)
baseline_envelope_unfiltered = baseline_envelope_unfiltered[valid]
baseline_envelope = baseline_envelope[valid]
search_envelope = search_envelope[valid]
@ -374,23 +378,22 @@ def main(datapath: str) -> None:
# plot baseline instantaneos frequency
axs[1, i].plot(baseline_freq_time, baseline_freq -
np.median(baseline_freq), marker=".")
np.median(baseline_freq))
# plot waveform of filtered signal
axs[2, i].plot(time_oi, baseline, c="k")
axs[2, i].plot(time_oi, baseline, c=ps.green)
# plot narrow filtered baseline
# plot broad filtered baseline
axs[2, i].plot(
time_oi,
baseline_envelope,
c="orange",
broad_baseline,
)
# plot broad filtered baseline
# plot narrow filtered baseline envelope
axs[2, i].plot(
time_oi,
broad_baseline,
c="green",
baseline_envelope_unfiltered,
c=ps.red
)
# plot waveform of filtered search signal
@ -400,7 +403,7 @@ def main(datapath: str) -> None:
axs[3, i].plot(
time_oi,
search_envelope,
c="orange",
c=ps.red
)
# plot filtered and rectified envelope
@ -408,7 +411,7 @@ def main(datapath: str) -> None:
axs[4, i].scatter(
(time_oi)[baseline_peaks],
baseline_envelope[baseline_peaks],
c="red",
c=ps.red,
)
# plot envelope of search signal
@ -416,7 +419,7 @@ def main(datapath: str) -> None:
axs[5, i].scatter(
(time_oi)[search_peaks],
search_envelope[search_peaks],
c="red",
c=ps.red,
)
# plot filtered instantaneous frequency
@ -424,7 +427,7 @@ def main(datapath: str) -> None:
axs[6, i].scatter(
baseline_freq_time[inst_freq_peaks],
np.abs(inst_freq_filtered)[inst_freq_peaks],
c="red",
c=ps.red,
)
axs[6, i].set_xlabel("Time [s]")

2
code/chirpdetector_conf.yml
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@ -13,7 +13,7 @@ search_boundary: 100
envelope_cutoff: 25
# Cutoff frequency for envelope highpass filter
envelope_highpass_cutoff: 5
envelope_highpass_cutoff: 4
# Cutoff frequency for envelope of envelope
envelope_envelope_cutoff: 5

48
code/modules/plotstyle.py
View File

@ -18,17 +18,17 @@ def PlotStyle() -> None:
black = "#111116"
white = "#e0e4f7"
gray = "#6c6e7d"
pink = "#f5c2e7"
purple = "#cba6f7"
red = "#f38ba8"
maroon = "#eba0ac"
orange = "#fab387"
yellow = "#f9e2af"
green = "#a6e3a1"
teal = "#94e2d5"
sky = "#89dceb"
sapphire = "#74c7ec"
blue = "#89b4fa"
sapphire = "#74c7ec"
sky = "#89dceb"
teal = "#94e2d5"
green = "#a6e3a1"
yellow = "#f9e2af"
orange = "#fab387"
maroon = "#eba0ac"
red = "#f38ba8"
purple = "#cba6f7"
pink = "#f5c2e7"
lavender = "#b4befe"
@classmethod
@ -218,7 +218,7 @@ def PlotStyle() -> None:
plt.rcParams["image.cmap"] = 'cmo.haline'
# plt.rcParams["axes.xmargin"] = 0.1
# plt.rcParams["axes.ymargin"] = 0.15
plt.rcParams["axes.titlelocation"] = "center"
plt.rcParams["axes.titlelocation"] = "left"
plt.rcParams["axes.titlesize"] = BIGGER_SIZE
# plt.rcParams["axes.titlepad"] = -10
plt.rcParams["legend.frameon"] = False
@ -244,8 +244,8 @@ def PlotStyle() -> None:
plt.rcParams["text.color"] = white
plt.rcParams["axes.facecolor"] = black # axes background color
plt.rcParams["axes.edgecolor"] = gray # axes edge color
plt.rcParams["axes.grid"] = True # display grid or not
plt.rcParams["axes.grid.axis"] = "y" # which axis the grid is applied to
# plt.rcParams["axes.grid"] = True # display grid or not
# plt.rcParams["axes.grid.axis"] = "y" # which axis the grid is applied to
plt.rcParams["axes.labelcolor"] = white
plt.rcParams["axes.axisbelow"] = True # draw axis gridlines and ticks:
plt.rcParams["axes.spines.left"] = True # display axis spines
@ -254,18 +254,18 @@ def PlotStyle() -> None:
plt.rcParams["axes.spines.right"] = False
plt.rcParams["axes.prop_cycle"] = cycler(
'color', [
'#f5c2e7',
'#cba6f7',
'#f38ba8',
'#eba0ac',
'#fab387',
'#f9e2af',
'#a6e3a1',
'#94e2d5',
'#89dceb',
'#74c7ec',
'#89b4fa',
'#b4befe',
'#89b4fa',
'#74c7ec',
'#89dceb',
'#94e2d5',
'#a6e3a1',
'#f9e2af',
'#fab387',
'#eba0ac',
'#f38ba8',
'#cba6f7',
'#f5c2e7',
])
plt.rcParams["xtick.color"] = gray # color of the ticks
plt.rcParams["ytick.color"] = gray # color of the ticks