raab/GP2023_chirp_detection
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reformatted

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This commit is contained in:
weygoldt 2023-01-20 17:54:51 +01:00
parent 16751a7006
commit 2dec8fd508
1 changed files with 32 additions and 21 deletions
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53
code/chirpdetection.py
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@ -63,19 +63,24 @@ class PlotBuffer:
# get index of track data in this time window # get index of track data in this time window
window_idx = np.arange(len(self.data.idx))[ window_idx = np.arange(len(self.data.idx))[
(self.data.ident == self.track_id) & (self.data.time[self.data.idx] >= self.t0) & ( (self.data.ident == self.track_id)
self.data.time[self.data.idx] <= (self.t0 + self.dt)) & (self.data.time[self.data.idx] >= self.t0)
& (self.data.time[self.data.idx] <= (self.t0 + self.dt))
] ]
# get tracked frequencies and their times # get tracked frequencies and their times
freq_temp = self.data.freq[window_idx] freq_temp = self.data.freq[window_idx]
time_temp = self.data.time[(self.data.time >= self.t0) & ( time_temp = self.data.time[
self.data.time <= (self.t0 + self.dt))] (self.data.time >= self.t0)
& (self.data.time <= (self.t0 + self.dt))
]
# remake the band we filtered in # remake the band we filtered in
q25, q50, q75 = np.percentile(freq_temp, [25, 50, 75]) q25, q50, q75 = np.percentile(freq_temp, [25, 50, 75])
search_upper, search_lower = q50 + self.search_frequency + self.config.minimal_bandwidth / \ search_upper, search_lower = (
2, q50 + self.search_frequency - self.config.minimal_bandwidth / 2 q50 + self.search_frequency + self.config.minimal_bandwidth / 2,
q50 + self.search_frequency - self.config.minimal_bandwidth / 2,
)
# get indices on raw data # get indices on raw data
start_idx = self.t0 * self.data.raw_rate start_idx = self.t0 * self.data.raw_rate
@ -85,16 +90,18 @@ class PlotBuffer:
# get raw data # get raw data
data_oi = self.data.raw[start_idx:stop_idx, self.electrode] data_oi = self.data.raw[start_idx:stop_idx, self.electrode]
self.time = (self.time - self.t0) self.time = self.time - self.t0
self.frequency_time = (self.frequency_time - self.t0) self.frequency_time = self.frequency_time - self.t0
chirps = (np.ararray(chirps) - self.t0) chirps = np.ararray(chirps) - self.t0
self.t0 = 0 self.t0 = 0
fig = plt.figure(figsize=(16 / 2.54, 24 / 2.54), fig = plt.figure(
constrained_layout=True) figsize=(16 / 2.54, 24 / 2.54), constrained_layout=True
)
grid = gr.GridSpec(9, 1, figure=fig, height_ratios=[ grid = gr.GridSpec(
4, 0.5, 1, 1, 1, 0.5, 1, 1, 1]) 9, 1, figure=fig, height_ratios=[4, 0.5, 1, 1, 1, 0.5, 1, 1, 1]
)
ax0 = fig.add_subplot(grid[0, 0]) ax0 = fig.add_subplot(grid[0, 0])
ax1 = fig.add_subplot(grid[2, 0], sharex=ax0) ax1 = fig.add_subplot(grid[2, 0], sharex=ax0)
@ -113,7 +120,8 @@ class PlotBuffer:
q50 + self.config.minimal_bandwidth / 2, q50 + self.config.minimal_bandwidth / 2,
color=ps.black, color=ps.black,
lw=0, lw=0,
alpha=0.2) alpha=0.2,
)
ax0.fill_between( ax0.fill_between(
np.arange(self.t0, self.t0 + self.dt, 1 / self.data.raw_rate), np.arange(self.t0, self.t0 + self.dt, 1 / self.data.raw_rate),
@ -121,7 +129,8 @@ class PlotBuffer:
search_upper, search_upper,
color=ps.black, color=ps.black,
lw=0, lw=0,
alpha=0.2) alpha=0.2,
)
for chirp in chirps: for chirp in chirps:
ax0.scatter( ax0.scatter(
@ -372,8 +381,7 @@ def find_searchband(
for j, check_track_id in enumerate(check_track_ids): for j, check_track_id in enumerate(check_track_ids):
q1, q2 = np.percentile( q1, q2 = np.percentile(
data.freq[data.ident == check_track_id], data.freq[data.ident == check_track_id], [25, 75]
[25, 75]
) )
print(q1, q2) print(q1, q2)
@ -751,7 +759,9 @@ def main(datapath: str, plot: str) -> None:
baseline_peak_timestamps = current_raw_time[ baseline_peak_timestamps = current_raw_time[
baseline_peak_indices baseline_peak_indices
] ]
search_peak_timestamps = current_raw_time[search_peak_indices] search_peak_timestamps = current_raw_time[
search_peak_indices]
frequency_peak_timestamps = baseline_frequency_time[ frequency_peak_timestamps = baseline_frequency_time[
frequency_peak_indices frequency_peak_indices
] ]
@ -853,9 +863,10 @@ def main(datapath: str, plot: str) -> None:
multiwindow_chirps.append(multielectrode_chirps_validated) multiwindow_chirps.append(multielectrode_chirps_validated)
multiwindow_ids.append(track_id) multiwindow_ids.append(track_id)
logger.debug( logger.info(
"Found %d chirps, starting plotting ... " "Found %d chirps for fish %d"
% len(multielectrode_chirps_validated) % len(multielectrode_chirps_validated),
track_id,
) )
# if chirps are detected and the plot flag is set, plot the # if chirps are detected and the plot flag is set, plot the
# chirps, otheswise try to delete the buffer if it exists # chirps, otheswise try to delete the buffer if it exists