change detect spikes approach
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a.ott
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e84ac53657
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f7ffdcc66f
@ -313,7 +313,7 @@ def calculate_vector_strength_from_v1_trace(times, eods, v1_traces):
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print("-----LENGTH OF TIMES = 0")
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for recording in range(len(times)):
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spiketime_idices = detect_spikes_indices(v1_traces[recording])
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spiketime_idices = detect_spike_indices(v1_traces[recording])
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rel_spikes, eod_durs = eods_around_spikes(times[recording], eods[recording], spiketime_idices)
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relative_spike_times.extend(rel_spikes)
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eod_durations.extend(eod_durs)
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@ -332,7 +332,7 @@ def calculate_vector_strength_from_spiketimes(time, eod, spiketimes, sampling_in
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return __vector_strength__(rel_spikes, eod_durs)
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def detect_spikes_indices(v1, split=20, threshold=3):
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def detect_spike_indices(v1, split=20, threshold=3.0):
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total = len(v1)
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all_peaks = []
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@ -350,19 +350,86 @@ def detect_spikes_indices(v1, split=20, threshold=3):
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return all_peaks
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def detect_spiketimes(time, v1, split=20, threshold=3):
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all_peak_indicies = detect_spikes_indices(v1, split, threshold)
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def detect_spike_indices_automatic_split(v1, min_length=3000, threshold=3.0):
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split_start = 0
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step_size = 250
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break_threshold = 0.1
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splits = []
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return [time[p_idx] for p_idx in all_peak_indicies]
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if len(v1) < min_length:
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splits = [(0, len(v1))]
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else:
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last_max = max(v1[0:min_length])
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last_min = min(v1[0:min_length])
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idx = min_length
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while idx < len(v1):
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if idx + step_size > len(v1):
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splits.append((split_start, len(v1)))
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break
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# max_dif = abs((max(v1[idx:idx+step_size]) / last_max) - 1)
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# min_dif = abs((min(v1[idx:idx+step_size]) / last_min) - 1)
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# print("last_max: {:.2f}, current_max: {:.2f}".format(last_max, max(v1[idx:idx+step_size])))
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# print("max_dif: {:.2f}, min_dif: {:.2f}".format(max_dif, min_dif))
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max_similar = abs((max(v1[idx:idx+step_size]) / last_max) - 1) < break_threshold
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min_similar = abs((min(v1[idx:idx+step_size]) / last_min) - 1) < break_threshold
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if not max_similar or not min_similar:
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# print("new split")
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end_idx = np.argmin(v1[idx-20:idx+21]) - 20
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splits.append((split_start, idx+end_idx))
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split_start = idx+end_idx
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last_max = max(v1[split_start:split_start + min_length])
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last_min = min(v1[split_start:split_start + min_length])
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idx = split_start + min_length
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continue
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else:
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pass
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# print("elongated!")
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idx += step_size
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if splits[-1][1] != len(v1):
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splits.append((split_start, len(v1)))
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# plt.plot(v1)
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#
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# for s in splits:
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# plt.plot(s, (max(v1[s[0]:s[1]]), max(v1[s[0]:s[1]])))
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# plt.show()
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all_peaks = []
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for s in splits:
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first_index = s[0]
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last_index = s[1]
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std = np.std(v1[first_index:last_index])
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peaks, _ = detect_peaks(v1[first_index:last_index], std * threshold)
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peaks = peaks + first_index
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# plt.plot(peaks, [np.mean(v1[first_index:last_index]) for _ in peaks], 'o')
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all_peaks.extend(peaks)
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# plt.show()
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all_peaks = np.array(all_peaks)
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return all_peaks
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def calculate_phases(relative_spike_times, eod_durations):
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phase_times = np.zeros(len(relative_spike_times))
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def detect_spiketimes(time, v1, split=80, threshold=2.8):
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# all_peak_indicies = detect_spikes_indices(v1, split, threshold)
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all_peak_indicies = detect_spike_indices_automatic_split(v1, threshold=threshold)
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return [time[p_idx] for p_idx in all_peak_indicies]
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for i in range(len(relative_spike_times)):
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phase_times[i] = (relative_spike_times[i] / eod_durations[i]) * 2 * np.pi
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return phase_times
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# def calculate_phases(relative_spike_times, eod_durations):
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# phase_times = np.zeros(len(relative_spike_times))
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#
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# for i in range(len(relative_spike_times)):
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# phase_times[i] = (relative_spike_times[i] / eod_durations[i]) * 2 * np.pi
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#
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# return phase_times
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def eods_around_spikes(time, eod, spiketime_idices):
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@ -396,48 +463,48 @@ def eods_around_spikes(time, eod, spiketime_idices):
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return np.array(relative_spike_times), np.array(eod_durations)
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def search_eod_start_and_end_times(time, eod, index):
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# TODO might break if a spike is in the cut off first or last eod!
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# search start_time:
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previous = index
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working_idx = index-1
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while True:
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if eod[working_idx] < 0 < eod[previous]:
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first_value = eod[working_idx]
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second_value = eod[previous]
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dif = second_value - first_value
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part = np.abs(first_value/dif)
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time_dif = np.abs(time[previous] - time[working_idx])
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start_time = time[working_idx] + time_dif*part
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break
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previous = working_idx
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working_idx -= 1
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# search end_time
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previous = index
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working_idx = index + 1
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while True:
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if eod[previous] < 0 < eod[working_idx]:
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first_value = eod[previous]
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second_value = eod[working_idx]
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dif = second_value - first_value
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part = np.abs(first_value / dif)
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time_dif = np.abs(time[previous] - time[working_idx])
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end_time = time[working_idx] + time_dif * part
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break
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previous = working_idx
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working_idx += 1
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return start_time, end_time
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# def search_eod_start_and_end_times(time, eod, index):
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# # TODO might break if a spike is in the cut off first or last eod!
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#
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# # search start_time:
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# previous = index
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# working_idx = index-1
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# while True:
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# if eod[working_idx] < 0 < eod[previous]:
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# first_value = eod[working_idx]
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# second_value = eod[previous]
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#
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# dif = second_value - first_value
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# part = np.abs(first_value/dif)
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#
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# time_dif = np.abs(time[previous] - time[working_idx])
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# start_time = time[working_idx] + time_dif*part
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#
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# break
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#
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# previous = working_idx
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# working_idx -= 1
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#
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# # search end_time
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# previous = index
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# working_idx = index + 1
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# while True:
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# if eod[previous] < 0 < eod[working_idx]:
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# first_value = eod[previous]
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# second_value = eod[working_idx]
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#
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# dif = second_value - first_value
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# part = np.abs(first_value / dif)
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#
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# time_dif = np.abs(time[previous] - time[working_idx])
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# end_time = time[working_idx] + time_dif * part
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#
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# break
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#
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# previous = working_idx
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# working_idx += 1
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#
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# return start_time, end_time
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def __vector_strength__(relative_spike_times: np.ndarray, eod_durations: np.ndarray):
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@ -455,12 +522,12 @@ def __vector_strength__(relative_spike_times: np.ndarray, eod_durations: np.ndar
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def detect_f_zero_in_frequency_trace(time, frequency, stimulus_start, sampling_interval, peak_buffer_percent=0.05, buffer=0.025):
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freq_before = frequency[int(time[0]+buffer/sampling_interval):int((stimulus_start - time[0] - buffer) / sampling_interval)]
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if len(freq_before) < 3:
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print("Length of reference frequency before the stimulus too short (< 3 points)")
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if time[0] + 2*buffer > stimulus_start:
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print("F_zero detection: Not enough frequency trace before start of the stimulus.")
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return 0
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freq_before = frequency[int(time[0]+buffer/sampling_interval):int((stimulus_start - time[0] - buffer) / sampling_interval)]
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min_before = min(freq_before)
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max_before = max(freq_before)
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mean_before = np.mean(freq_before)
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@ -468,6 +535,10 @@ def detect_f_zero_in_frequency_trace(time, frequency, stimulus_start, sampling_i
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# time where the f-zero is searched in
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start_idx, end_idx = time_window_detect_f_zero(time[0], stimulus_start, sampling_interval, buffer)
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if start_idx < 0:
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raise ValueError("Time window to detect f_zero starts in an negative index!")
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min_during_start_of_stim = min(frequency[start_idx:end_idx])
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max_during_start_of_stim = max(frequency[start_idx:end_idx])
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