raab/GP2023_chirp_detection
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cleaned up a bit

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This commit is contained in:
weygoldt 2023-01-16 19:31:13 +01:00
parent 12d1c3c1af
commit b41e03c681
1 changed files with 41 additions and 22 deletions
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63
code/chirpdetection.py
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@ -138,7 +138,6 @@ def double_bandpass(
def main(datapath: str) -> None: def main(datapath: str) -> None:
# load raw file # load raw file
file = os.path.join(datapath, "traces-grid1.raw")
data = LoadData(datapath) data = LoadData(datapath)
# ititialize data collection # ititialize data collection
@ -223,11 +222,10 @@ def main(datapath: str) -> None:
print(f"Track ID: {track_id}") print(f"Track ID: {track_id}")
# get index of track data in this time window # get index of track data in this time window
window_index = np.arange(len(data.idx))[ window_index = np.arange(len(data.idx))[
(data.ident == track_id) & (data.time[data.idx] >= t0) & ( (data.ident == track_id) & (data.time[data.idx] >= t0) & (
data.time[data.idx] <= (t0 + dt)) data.time[data.idx] <= (t0 + dt))
] ]
# get tracked frequencies and their times # get tracked frequencies and their times
@ -257,8 +255,9 @@ def main(datapath: str) -> None:
powers_temp, axis=0))[-config.electrodes:] powers_temp, axis=0))[-config.electrodes:]
# frequency where second filter filters # frequency where second filter filters
search_window = np.arange(np.median(freq_temp)+config.search_df_lower, np.median( search_window = np.arange(
freq_temp)+config.search_df_upper, config.search_res) np.median(freq_temp)+config.search_df_lower, np.median(
freq_temp)+config.search_df_upper, config.search_res)
# search window in boolean # search window in boolean
search_window_bool = np.ones(len(search_window), dtype=bool) search_window_bool = np.ones(len(search_window), dtype=bool)
@ -273,7 +272,9 @@ def main(datapath: str) -> None:
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], config.search_freq_percentiles) data.freq[data.ident == check_track_id],
config.search_freq_percentiles
)
search_window_bool[(search_window > q1) & ( search_window_bool[(search_window > q1) & (
search_window < q2)] = False search_window < q2)] = False
@ -296,7 +297,9 @@ def main(datapath: str) -> None:
# if the last value is -1, the array ends with true, so a gap # if the last value is -1, the array ends with true, so a gap
if nonzeros[-1] == 1: if nonzeros[-1] == 1:
stops = np.append( stops = np.append(
search_window_indices[search_window_gaps == -1], len(search_window) - 1) search_window_indices[search_window_gaps == -1],
len(search_window) - 1
)
# else it starts with false, so no gap # else it starts with false, so no gap
if nonzeros[0] == 1: if nonzeros[0] == 1:
@ -306,7 +309,9 @@ def main(datapath: str) -> None:
# if the last value is -1, the array ends with true, so a gap # if the last value is -1, the array ends with true, so a gap
if nonzeros[-1] == 1: if nonzeros[-1] == 1:
stops = np.append( stops = np.append(
search_window_indices[search_window_gaps == -1], len(search_window)) search_window_indices[search_window_gaps == -1],
len(search_window)
)
# get the frequency ranges of the gaps # get the frequency ranges of the gaps
search_windows = [search_window[x:y] search_windows = [search_window[x:y]
@ -339,7 +344,10 @@ def main(datapath: str) -> None:
# filter baseline and above # filter baseline and above
baseline, search = double_bandpass( baseline, search = double_bandpass(
data_oi[:, electrode], data.raw_rate, freq_temp, search_freq data_oi[:, electrode],
data.raw_rate,
freq_temp,
search_freq
) )
# compute instantaneous frequency on broad signal # compute instantaneous frequency on broad signal
@ -399,14 +407,20 @@ def main(datapath: str) -> None:
valid_t1 = baseline_freq_time[-1] - \ valid_t1 = baseline_freq_time[-1] - \
(int(window_edge) / data.raw_rate) (int(window_edge) / data.raw_rate)
inst_freq_filtered = inst_freq_filtered[(baseline_freq_time >= valid_t0) & ( inst_freq_filtered = inst_freq_filtered[
baseline_freq_time <= valid_t1)] (baseline_freq_time >= valid_t0) & (
baseline_freq_time <= valid_t1)
]
baseline_freq = baseline_freq[(baseline_freq_time >= valid_t0) & ( baseline_freq = baseline_freq[
baseline_freq_time <= valid_t1)] (baseline_freq_time >= valid_t0) & (
baseline_freq_time <= valid_t1)
]
baseline_freq_time = baseline_freq_time[(baseline_freq_time >= valid_t0) & ( baseline_freq_time = baseline_freq_time[
baseline_freq_time <= valid_t1)] + t0 (baseline_freq_time >= valid_t0) & (
baseline_freq_time <= valid_t1)
] + t0
# overwrite raw time to valid region # overwrite raw time to valid region
time_oi = time_oi[valid] time_oi = time_oi[valid]
@ -436,18 +450,23 @@ def main(datapath: str) -> None:
# detect peaks inst_freq_filtered # detect peaks inst_freq_filtered
prominence = np.percentile( prominence = np.percentile(
inst_freq_filtered, config.instantaneous_prominence_percentile) inst_freq_filtered,
config.instantaneous_prominence_percentile
)
inst_freq_peaks, _ = find_peaks( inst_freq_peaks, _ = find_peaks(
np.abs(inst_freq_filtered), prominence=prominence) np.abs(inst_freq_filtered),
prominence=prominence
)
# SAVE DATA ---------------------------------------------------- # SAVE DATA ---------------------------------------------------
baseline_ts_subsub.append(time_oi[baseline_peaks].tolist()) baseline_ts_subsub.append(time_oi[baseline_peaks].tolist())
search_ts_subsub.append(time_oi[search_peaks].tolist()) search_ts_subsub.append(time_oi[search_peaks].tolist())
freq_ts_subsub.append(baseline_freq_time[inst_freq_peaks].tolist()) freq_ts_subsub.append(
baseline_freq_time[inst_freq_peaks].tolist())
electrodes_subsub.append(electrode) electrodes_subsub.append(electrode)
# PLOT ------------------------------------------------------------ # PLOT --------------------------------------------------------
# plot spectrogram # plot spectrogram
plot_spectrogram( plot_spectrogram(
@ -531,11 +550,11 @@ def main(datapath: str) -> None:
fish_ids.append(fish_ids_sub) fish_ids.append(fish_ids_sub)
electrodes.append(electrodes_sub) electrodes.append(electrodes_sub)
# reorder this mess of nested lists to make it understandable
num_snippets = len(window_starts)
embed() embed()
if __name__ == "__main__": if __name__ == "__main__":
datapath = "../data/2022-06-02-10_00/" datapath = "../data/2022-06-02-10_00/"
main(datapath) main(datapath)