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