Is there an error while calculating the period in Python code？
benzimidazole opened this issue · comments
In python code, i find that period is defined as follows:
period = df_samples['sample_next_trough'] - df_samples['sample_last_trough'];
`"""Compute shape features for individual cycles."""
import numpy as np
import pandas as pd
from neurodsp.timefrequency import amp_by_time
from bycycle.utils import rename_extrema_df, check_param
from bycycle.features.cyclepoints import compute_cyclepoints
###################################################################################################
###################################################################################################
def compute_shape_features(sig, fs, f_range, center_extrema='peak',
find_extrema_kwargs=None, n_cycles=3):
"""Compute shape features for each cycle.
Parameters
----------
sig : 1d array
Time series.
fs : float
Sampling rate, in Hz.
f_range : tuple of (float, float)
Frequency range for narrowband signal of interest (Hz).
center_extrema : {'peak', 'trough'}
The center extrema in the cycle.
- 'peak' : cycles are defined trough-to-trough
- 'trough' : cycles are defined peak-to-peak
find_extrema_kwargs : dict, optional, default: None
Keyword arguments for function to find peaks and troughs (:func:`~.find_extrema`)
to change filter parameters or boundary. By default, the filter length is set to three
cycles of the low cutoff frequency (``f_range[0]``).
n_cycles : int, optional, default: 3
Length of filter, in number of cycles, at the lower cutoff frequency.
Returns
-------
df_shape_features : pandas.DataFrame
Dataframe containing cycle shape features. Each row is one cycle. Columns:
- ``period`` : period of the cycle
- ``time_decay`` : time between peak and next trough
- ``time_rise`` : time between peak and previous trough
- ``time_peak`` : time between rise and decay zero-crosses
- ``time_trough`` : duration of previous trough estimated by zero-crossings
- ``volt_decay`` : voltage change between peak and next trough
- ``volt_rise`` : voltage change between peak and previous trough
- ``volt_amp`` : average of rise and decay voltage
- ``volt_peak`` : voltage at the peak
- ``volt_trough`` : voltage at the last trough
- ``time_rdsym`` : fraction of cycle in the rise period
- ``time_ptsym`` : fraction of cycle in the peak period
- ``band_amp`` : average analytic amplitude of the oscillation
- ``sample_peak`` : sample at which the peak occurs
- ``sample_zerox_decay`` : sample of the decaying zero-crossing
- ``sample_zerox_rise`` : sample of the rising zero-crossing
- ``sample_last_trough`` : sample of the last trough
- ``sample_next_trough`` : sample of the next trough
Notes
-----
Peak vs trough centering:
- By default, the first extrema analyzed will be a peak, and the final one a trough.
- In order to switch the preference, the signal is simply inverted and columns are renamed.
- Columns are slightly different dependent on ``center_extrema`` being 'peak' or 'trough'.
Examples
--------
Compute shape features:
>>> from neurodsp.sim import sim_bursty_oscillation
>>> fs = 500
>>> sig = sim_bursty_oscillation(10, fs, freq=10)
>>> df_shapes = compute_shape_features(sig, fs, f_range=(8, 12))
"""
# Ensure arguments are within valid ranges
check_param(fs, 'fs', (0, np.inf))
check_param(n_cycles, 'n_cycles', (0, np.inf))
# Set defaults if user input is None
if find_extrema_kwargs is None:
find_extrema_kwargs = {'filter_kwargs': {'n_cycles': n_cycles}}
elif 'first_extrema' in find_extrema_kwargs.keys():
raise ValueError("This function has been designed to assume that the first extrema "
"identified will be a peak. This cannot be overwritten at this time.")
# Negate signal if set to analyze trough-centered cycles
if center_extrema == 'peak':
pass
elif center_extrema == 'trough':
sig = -sig
else:
raise ValueError('Parameter "center_extrema" must be either "peak" or "trough"')
# For each cycle, identify the sample of each extrema and zero-crossing
df_samples = compute_cyclepoints(sig, fs, f_range, **find_extrema_kwargs)
# Compute durations of period, peaks, and troughs
period, time_peak, time_trough = compute_durations(df_samples)
# Compute extrema voltage
volt_peak, volt_trough = compute_extrema_voltage(df_samples, sig)
# Compute rise-decay and peak-trough features and characteristics
sym_features = compute_symmetry(df_samples, sig, period=period,
time_peak=time_peak, time_trough=time_trough)
# Compute average oscillatory amplitude estimate during cycle
band_amp = compute_band_amp(df_samples, sig, fs, f_range, n_cycles=n_cycles)
# Organize shape features into a dataframe
shape_features = {}
shape_features['period'] = period
shape_features['time_peak'] = time_peak
shape_features['time_trough'] = time_trough
shape_features['volt_peak'] = volt_peak
shape_features['volt_trough'] = volt_trough
shape_features['time_decay'] = sym_features['time_decay']
shape_features['time_rise'] = sym_features['time_rise']
shape_features['volt_decay'] = sym_features['volt_decay']
shape_features['volt_rise'] = sym_features['volt_rise']
shape_features['volt_amp'] = sym_features['volt_amp']
shape_features['time_rdsym'] = sym_features['time_rdsym']
shape_features['time_ptsym'] = sym_features['time_ptsym']
shape_features['band_amp'] = band_amp
df_shape_features = pd.DataFrame.from_dict(shape_features)
df_shape_features = pd.concat((df_shape_features, df_samples), axis=1)
# Rename the dataframe if trough centered
df_shape_features = rename_extrema_df(center_extrema, df_shape_features)
return df_shape_features
def compute_durations(df_samples):
"""Compute the time durations of periods, peaks, and troughs.
Parameters
---------
df_samples : pandas.DataFrame
Dataframe containing sample indices of cyclepoints.
Returns
-------
period : 1d array
The period of each cycle.
time_peak : 1d array
Time between peak and next trough.
time_trough : 1d array
Time between peak and previous trough.
Examples
--------
Compute the durations of periods, peaks, and troughs:
>>> from bycycle.features import compute_cyclepoints
>>> from neurodsp.sim import sim_bursty_oscillation
>>> fs = 500
>>> sig = sim_bursty_oscillation(10, fs, freq=10)
>>> df_samples = compute_cyclepoints(sig, fs, f_range=(8, 12))
>>> period, time_peak, time_trough = compute_durations(df_samples)
"""
**period = df_samples['sample_next_trough'] - df_samples['sample_last_trough']**
time_peak = df_samples['sample_zerox_decay'] - df_samples['sample_zerox_rise']
time_trough = df_samples['sample_zerox_rise'] - df_samples['sample_last_zerox_decay']
return period, time_peak, time_trough
def compute_extrema_voltage(df_samples, sig):
"""Compute the voltage of peaks and troughs.
Parameters
---------
df_samples : pandas.DataFrame
Dataframe containing sample indices of cyclepoints.
sig : 1d array
Time series.
Returns
-------
volt_peak : 1d array
Voltage at the peak.
volt_trough : 1d array
Voltage at the last trough.
Examples
--------
Compute the voltage at peaks and troughs:
>>> from bycycle.features import compute_cyclepoints
>>> from neurodsp.sim import sim_bursty_oscillation
>>> fs = 500
>>> sig = sim_bursty_oscillation(10, fs, freq=10)
>>> df_samples = compute_cyclepoints(sig, fs, f_range=(8, 12))
>>> volt_peak, volt_trough = compute_extrema_voltage(df_samples, sig)
"""
volt_peak = sig[df_samples['sample_peak']]
volt_trough = sig[df_samples['sample_last_trough']]
return volt_peak, volt_trough
def compute_symmetry(df_samples, sig, period=None, time_peak=None, time_trough=None):
"""Compute rise-decay and peak-trough characteristics.
Parameters
---------
df_samples : pandas.DataFrame
Dataframe containing sample indices of cyclepoints.
sig : 1d array
Time series.
period : 1d array, optional, default: None
The period of each cycle.
time_peak : 1d array, optional, default: None
Time between peak and next trough.
time_trough : 1d array, optional, default: None
Time between peak and previous trough
Returns
-------
sym_features : dict
Contains 1d arrays of symmetry features. Keys include:
- time_decay : time between peak and next trough
- time_rise : time between peak and previous trough
- volt_decay : voltage change between peak and next trough
- volt_rise : voltage change between peak and previous trough
- volt_amp : average of rise and decay voltage
- time_rdsym : fraction of cycle in the rise period
- time_ptsym : fraction of cycle in the peak period
Examples
--------
Compute cycle symmetry characteristics:
>>> from bycycle.features import compute_cyclepoints
>>> from neurodsp.sim import sim_bursty_oscillation
>>> fs = 500
>>> sig = sim_bursty_oscillation(10, fs, freq=10)
>>> df_samples = compute_cyclepoints(sig, fs, f_range=(8, 12))
>>> sym_features = compute_symmetry(df_samples, sig)
"""
# Determine rise and decay characteristics
sym_features = {}
time_decay = df_samples['sample_next_trough'] - df_samples['sample_peak']
time_rise = df_samples['sample_peak'] - df_samples['sample_last_trough']
volt_decay = sig[df_samples['sample_peak']] - sig[df_samples['sample_next_trough']]
volt_rise = sig[df_samples['sample_peak']] - sig[df_samples['sample_last_trough']]
volt_amp = (volt_decay + volt_rise) / 2
# Compute rise-decay symmetry features
if period is None or time_peak is None or time_trough is None:
period, time_peak, time_trough = compute_durations(df_samples)
time_rdsym = time_rise / period
# Compute peak-trough symmetry features
time_ptsym = time_peak / (time_peak + time_trough)
sym_features['time_decay'] = time_decay
sym_features['time_rise'] = time_rise
sym_features['volt_decay'] = volt_decay
sym_features['volt_rise'] = volt_rise
sym_features['volt_amp'] = volt_amp
sym_features['time_rdsym'] = time_rdsym
sym_features['time_ptsym'] = time_ptsym
return sym_features
def compute_band_amp(df_samples, sig, fs, f_range, n_cycles=3):
"""Compute the average amplitude of each oscillation.
Parameters
----------
sig : 1d array
Time series.
fs : float
Sampling rate, in Hz.
f_range : tuple of (float, float)
Frequency range for narrowband signal of interest (Hz).
n_cycles : int, optional, default: 3
Length of filter, in number of cycles, at the lower cutoff frequency.
Returns
-------
band_amp : 1d array
Average analytic amplitude of the oscillation.
Examples
--------
Compute the mean amplitude for each cycle:
>>> from bycycle.features import compute_cyclepoints
>>> from neurodsp.sim import sim_bursty_oscillation
>>> fs = 500
>>> sig = sim_bursty_oscillation(10, fs, freq=10)
>>> df_samples = compute_cyclepoints(sig, fs, f_range=(8, 12))
>>> band_amp = compute_band_amp(df_samples, sig, fs, f_range=(8, 12))
"""
# Ensure arguments are within valid ranges
check_param(fs, 'fs', (0, np.inf))
check_param(n_cycles, 'n_cycles', (0, np.inf))
amp = amp_by_time(sig, fs, f_range, remove_edges=False, n_cycles=n_cycles)
troughs = np.append(df_samples['sample_last_trough'].values[0],
df_samples['sample_next_trough'].values)
band_amp = [np.mean(amp[troughs[sig_idx]:troughs[sig_idx + 1]]) for
sig_idx in range(len(df_samples['sample_peak']))]
return band_amp
`
but in the paper, "The period is defined as the time between the two peaks". So which is the correct definition?
This depends on the center_extrema argument. If it is equal to 'peak' (default), the period is from trough to trough. If set to 'trough', it is defined from peak to peak.
ok, i know! thank you!