def filterEEG(eeg_data, fs=250, f_range=(1, 50)):
sig_filt = filt.filter_signal(eeg_data, fs, 'bandpass', f_range, filter_type='iir', butterworth_order=2)
test_sig_filt = filt.filter_signal(sig_filt, fs, 'bandstop', (58, 62), n_seconds=1)
num_nans = sum(np.isnan(test_sig_filt))
sig_filt = np.concatenate(([0]*(num_nans // 2), sig_filt, [0]*(num_nans // 2)))
sig_filt = filt.filter_signal(sig_filt, fs, 'bandstop', (58, 62), n_seconds=1)
sig_filt = sig_filt[~np.isnan(sig_filt)]
return sig_filt
def get_bandpass_filter_signal(data, fs, f_range, passtype='bandpass'):
sig_filt = filt.filter_signal(data,
fs,
passtype,
f_range,
remove_edges=False)
return sig_filt
def bandpass_bandstop_filter(data,fs=250, lowcut=1, highcut=50, order = 2):
nyq = 0.5 * fs
low = lowcut / nyq
high = highcut / nyq
sos = butter(order, [low, high], analog = False, btype = 'band', output = 'sos')
filted_data = sosfiltfilt(sos, data)
filted_data = filt.filter_signal(filted_data, fs, 'bandstop', (58, 62), n_seconds=1)
filted_data = filted_data[~np.isnan(filted_data)]
return filted_data
def phase_by_time(sig,
fs,
f_range=None,
hilbert_increase_n=False,
remove_edges=True,
**filter_kwargs):
"""Compute the instantaneous phase of a time series.
Parameters
----------
sig : 1d array
Time series.
fs : float
Sampling rate, in Hz.
f_range : tuple of float or None, optional default: None
Filter range, in Hz, as (low, high). If None, no filtering is applied.
hilbert_increase_n : bool, optional, default: False
If True, zero pad the signal's length to the next power of 2 for the Hilbert transform.
This is because ``scipy.signal.hilbert`` can be very slow for some lengths of x.
remove_edges : bool, optional, default: True
If True, replace samples that are within half of the filter's length to the edge with nan.
This removes edge artifacts from the filtered signal. Only used if `f_range` is defined.
**filter_kwargs
Keyword parameters to pass to `filter_signal`.
Returns
-------
pha : 1d array
Instantaneous phase time series.
Examples
--------
Compute the instantaneous phase, for the alpha range:
>>> from neurodsp.sim import sim_combined
>>> sig = sim_combined(n_seconds=10, fs=500,
... components={'sim_powerlaw': {}, 'sim_oscillation': {'freq': 10}})
>>> pha = phase_by_time(sig, fs=500, f_range=(8, 12))
"""
if f_range:
sig, filter_kernel = filter_signal(sig,
fs,
infer_passtype(f_range),
f_range=f_range,
remove_edges=False,
return_filter=True,
**filter_kwargs)
pha = np.angle(robust_hilbert(sig, increase_n=hilbert_increase_n))
if f_range and remove_edges:
pha = remove_filter_edges(pha, len(filter_kernel))
return pha
def sim_powerlaw(n_seconds, fs, exponent=-2.0, f_range=None, **filter_kwargs):
"""Generate a power law time series with specified exponent by spectrally rotating white noise.
Parameters
----------
n_seconds : float
Simulation time, in seconds.
fs : float
Sampling rate of simulated signal, in Hz.
exponent : float
Desired power-law exponent, of the form P(f)=f^exponent.
f_range : list of [float, float] or None, optional
Frequency range to filter simulated data, as [f_lo, f_hi], in Hz.
**filter_kwargs : kwargs, optional
Keyword arguments to pass to `filter_signal`.
Returns
-------
sig: 1d array
Time-series with the desired power-law exponent.
"""
n_samples = int(n_seconds * fs)
sig = np.random.randn(n_samples)
# Compute the FFT
fft_output = np.fft.fft(sig)
freqs = np.fft.fftfreq(len(sig), 1. / fs)
# Rotate spectrum and invert, zscore to normalize.
# Note: the delta exponent to be applied is divided by two, as
# the FFT output is in units of amplitude not power
fft_output_rot = rotate_powerlaw(freqs, fft_output, -exponent/2)
sig = zscore(np.real(np.fft.ifft(fft_output_rot)))
if f_range is not None:
filter_signal(sig, fs, infer_passtype(f_range), f_range, **filter_kwargs)
return sig
def sim_powerlaw(n_seconds, fs, exponent=-2.0, f_range=None, **filter_kwargs):
"""Simulate a power law time series, with a specified exponent.
Parameters
----------
n_seconds : float
Simulation time, in seconds.
fs : float
Sampling rate of simulated signal, in Hz.
exponent : float, optional, default: -2
Desired power-law exponent, of the form P(f)=f^exponent.
f_range : list of [float, float] or None, optional
Frequency range to filter simulated data, as [f_lo, f_hi], in Hz.
**filter_kwargs : kwargs, optional
Keyword arguments to pass to `filter_signal`.
Returns
-------
sig: 1d array
Time-series with the desired power law exponent.
"""
# Get the number of samples to simulate for the signal
# If filter is to be filtered, with FIR, add extra to compensate for edges
if f_range and filter_kwargs.get('filter_type', None) != 'iir':
pass_type = infer_passtype(f_range)
filt_len = compute_filter_length(fs, pass_type,
*check_filter_definition(pass_type, f_range),
n_seconds=filter_kwargs.get('n_seconds', None),
n_cycles=filter_kwargs.get('n_cycles', 3))
n_samples = int(n_seconds * fs) + filt_len + 1
else:
n_samples = int(n_seconds * fs)
sig = _create_powerlaw(n_samples, fs, exponent)
if f_range is not None:
sig = filter_signal(sig, fs, infer_passtype(f_range), f_range,
remove_edges=True, **filter_kwargs)
# Drop the edges, that were compensated for, if not using IIR (using FIR)
if not filter_kwargs.get('filter_type', None) == 'iir':
sig, _ = remove_nans(sig)
return sig
def amp_by_time(sig, fs, f_range=None, remove_edges=True, **filter_kwargs):
"""Compute the instantaneous amplitude of a time series.
Parameters
----------
sig : 1d array
Time series.
fs : float
Sampling rate, in Hz.
f_range : tuple of float or None, optional default: None
Filter range, in Hz, as (low, high). If None, no filtering is applied.
remove_edges : bool, optional, default: True
If True, replace samples that are within half of the filter's length to the edge with nan.
This removes edge artifacts from the filtered signal. Only used if `f_range` is defined.
**filter_kwargs
Keyword parameters to pass to `filter_signal`.
Returns
-------
amp : 1d array
Instantaneous amplitude time series.
Examples
--------
Compute the instantaneous amplitude, for the alpha range:
>>> from neurodsp.sim import sim_combined
>>> sig = sim_combined(n_seconds=10, fs=500,
... components={'sim_powerlaw': {}, 'sim_oscillation' : {'freq': 10}})
>>> amp = amp_by_time(sig, fs=500, f_range=(8, 12))
"""
if f_range:
sig, filter_kernel = filter_signal(sig,
fs,
infer_passtype(f_range),
f_range=f_range,
remove_edges=False,
return_filter=True,
**filter_kwargs)
amp = np.abs(robust_hilbert(sig))
if f_range and remove_edges:
amp = remove_filter_edges(amp, len(filter_kernel))
return amp
def amp_by_time(sig,
fs,
f_range=None,
hilbert_increase_n=False,
remove_edges=True,
**filter_kwargs):
"""Compute the instantaneous amplitude of a time series.
Parameters
----------
sig : 1d array
Time series.
fs : float
Sampling rate, in Hz.
f_range : tuple of float or None, optional default: None
Filter range, in Hz, as (low, high). If None, no filtering is applied.
hilbert_increase_n : bool, optional, default: False
If True, zero pad the signal to length the next power of 2 when doing the Hilbert transform.
This is because :func:`scipy.signal.hilbert` can be very slow for some lengths of sig.
remove_edges : bool, optional, default: True
If True, replace samples that are within half of the filters length to the edge with np.nan.
This removes edge artifacts from the filtered signal. Only used if `f_range` is defined.
**filter_kwargs
Keyword parameters to pass to `filter_signal`.
Returns
-------
amp : 1d array
Instantaneous amplitude time series.
"""
if f_range:
sig, filter_kernel = filter_signal(sig,
fs,
infer_passtype(f_range),
f_range=f_range,
remove_edges=False,
return_filter=True,
**filter_kwargs)
amp = np.abs(robust_hilbert(sig, increase_n=hilbert_increase_n))
if f_range and remove_edges:
amp = remove_filter_edges(amp, len(filter_kernel))
return amp
def amp_by_time(sig,
fs,
f_range,
hilbert_increase_n=False,
remove_edges=True,
**filter_kwargs):
"""Calculate the amplitude time series.
Parameters
----------
sig : 1d array
Time series.
fs : float
Sampling rate, in Hz.
f_range : tuple of float
The frequency filtering range, in Hz, as (low, high).
hilbert_increase_n : bool, optional, default: False
If True, zeropad the signal to length the next power of 2 when doing the hilbert transform.
This is because scipy.signal.hilbert can be very slow for some lengths of sig.
remove_edges : bool, optional, default: True
If True, replace the samples that are within half a kernel's length to
the signal edge with np.nan.
**filter_kwargs
Keyword parameters to pass to `filter_signal`.
Returns
-------
amp : 1d array
Time series of amplitude.
"""
sig_filt, kernel = filter_signal(sig,
fs,
infer_passtype(f_range),
f_range=f_range,
remove_edges=False,
return_filter=True,
**filter_kwargs)
amp = np.abs(robust_hilbert(sig_filt, increase_n=hilbert_increase_n))
if remove_edges:
amp = remove_filter_edges(amp, len(kernel))
return amp
def test_detect_bursts_df_amp():
"""Test amplitude-threshold burst detection."""
# Load signal
sig = np.load(DATA_PATH + 'sim_bursting.npy')
fs = 1000
f_range = (6, 14)
sig_filt = filter_signal(sig,
fs,
'lowpass',
30,
n_seconds=.3,
remove_edges=False)
# Compute cycle-by-cycle df without burst detection column
df = compute_features(sig_filt,
fs,
f_range,
burst_detection_method='amp',
burst_detection_kwargs={
'amp_threshes': (1, 2),
'filter_kwargs': {
'n_seconds': .5
}
})
df.drop('is_burst', axis=1, inplace=True)
# Apply consistency burst detection
df_burst_amp = detect_bursts_df_amp(df,
sig_filt,
fs,
f_range,
amp_threshes=(.5, 1),
n_cycles_min=4,
filter_kwargs={'n_seconds': .5})
# Make sure that burst detection is only boolean
assert df_burst_amp.dtypes['is_burst'] == 'bool'
assert df_burst_amp['is_burst'].mean() > 0
assert df_burst_amp['is_burst'].mean() < 1
assert np.min([sum(1 for _ in group) for key, group \
in itertools.groupby(df_burst_amp['is_burst']) if key]) >= 4
def find_extrema(sig,
fs,
f_range,
boundary=0,
first_extrema='peak',
filter_kwargs=None,
pass_type='bandpass',
pad=True):
"""Identify peaks and troughs in a time series.
Parameters
----------
sig : 1d array
Time series.
fs : float
Sampling rate, in Hz.
f_range : tuple of (float, float)
Frequency range, in Hz, to narrowband filter the signal, used to find zero-crossings.
boundary : int, optional, default: 0
Number of samples from edge of the signal to ignore.
first_extrema: {'peak', 'trough', None}
If 'peak', then force the output to begin with a peak and end in a trough.
If 'trough', then force the output to begin with a trough and end in peak.
If None, force nothing.
filter_kwargs : dict, optional, default: None
Keyword arguments to :func:`~neurodsp.filt.filter.filter_signal`,
such as 'n_cycles' or 'n_seconds' to control filter length.
pass_type : str, optional, default: 'bandpass'
Which kind of filter pass_type is consistent with the frequency definition provided.
pad : bool, optional, default: True
Whether to pad ``sig`` with zeros to prevent missed cyclepoints at the edges.
Returns
-------
peaks : 1d array
Indices at which oscillatory peaks occur in the input ``sig``.
troughs : 1d array
Indices at which oscillatory troughs occur in the input ``sig``.
Notes
-----
This function assures that there are the same number of peaks and troughs
if the first extrema is forced to be either peak or trough.
Examples
--------
Find the locations of peaks and burst in a signal:
>>> from neurodsp.sim import sim_bursty_oscillation
>>> fs = 500
>>> sig = sim_bursty_oscillation(10, fs, freq=10)
>>> peaks, troughs = find_extrema(sig, fs, f_range=(8, 12))
"""
# Ensure arguments are within valid range
check_param_range(fs, 'fs', (0, np.inf))
# Set default filtering parameters
if filter_kwargs is None:
filter_kwargs = {}
# Get the original signal and filter lengths
sig_len = len(sig)
filt_len = 0
# Pad beginning of signal with zeros to prevent missing cyclepoints
if pad:
filt_len = compute_filter_length(
fs,
pass_type,
f_range[0],
f_range[1],
n_seconds=filter_kwargs.get('n_seconds', None),
n_cycles=filter_kwargs.get('n_cycles', 3))
# Pad the signal
sig = np.pad(sig, int(np.ceil(filt_len / 2)), mode='constant')
# Narrowband filter signal
sig_filt = filter_signal(sig,
fs,
pass_type,
f_range,
remove_edges=False,
**filter_kwargs)
# Find rising and decaying zero-crossings (narrowband)
rise_xs = find_flank_zerox(sig_filt, 'rise')
decay_xs = find_flank_zerox(sig_filt, 'decay')
# Compute number of peaks and troughs
if rise_xs[-1] > decay_xs[-1]:
n_peaks = len(rise_xs) - 1
n_troughs = len(decay_xs)
else:
n_peaks = len(rise_xs)
n_troughs = len(decay_xs) - 1
# Calculate peak samples
peaks = np.zeros(n_peaks, dtype=int)
for p_idx in range(n_peaks):
# Calculate the sample range between the most recent zero rise and the next zero decay
last_rise = rise_xs[p_idx]
next_decay = decay_xs[decay_xs > last_rise][0]
# Identify time of peak
peaks[p_idx] = np.argmax(sig[last_rise:next_decay]) + last_rise
# Calculate trough samples
troughs = np.zeros(n_troughs, dtype=int)
for t_idx in range(n_troughs):
# Calculate the sample range between the most recent zero decay and the next zero rise
last_decay = decay_xs[t_idx]
next_rise = rise_xs[rise_xs > last_decay][0]
# Identify time of trough
troughs[t_idx] = np.argmin(sig[last_decay:next_rise]) + last_decay
# Remove padding
peaks = peaks - int(np.ceil(filt_len / 2))
troughs = troughs - int(np.ceil(filt_len / 2))
# Remove peaks and trough outside the boundary limit
peaks = peaks[np.logical_and(peaks > boundary, peaks < sig_len - boundary)]
troughs = troughs[np.logical_and(troughs > boundary,
troughs < sig_len - boundary)]
# Force the first extrema to be as desired & assure equal # of peaks and troughs
if first_extrema == 'peak':
troughs = troughs[1:] if peaks[0] > troughs[0] else troughs
peaks = peaks[:-1] if peaks[-1] > troughs[-1] else peaks
elif first_extrema == 'trough':
peaks = peaks[1:] if troughs[0] > peaks[0] else peaks
troughs = troughs[:-1] if troughs[-1] > peaks[-1] else troughs
elif first_extrema is None:
pass
else:
raise ValueError('Parameter "first_extrema" is invalid')
return peaks, troughs
fs = 1000
# sampling frequency in Hz
times = rawdata['tx_14'] # time vector
times = (times).T
print(f"DATA: (n_trials, n_times)={data.shape}; SAMPLING FREQUENCY={fs}Hz; "
f"TIME VECTOR: n_times={len(times)}")
# Define a frequency range to filter the data
sig = np.mean(data, axis=0)
f_range = (2, 12)
# Bandpass filter the data, across the band of interest
sig_filt = filter_signal(sig,
fs,
'bandpass',
f_range,
filter_type='iir',
butterworth_order=4)
# Plot filtered signal
# fig = plt.figure(figsize=(14, 6))
plot_time_series(times, [sig, sig_filt], ['Raw', 'Filtered'])
# plt.show()
fig = plt.figure(figsize=(14, 6))
# adding the mean PSD over trials
# plt.subplot(1, 2, 1)
plt.plot(times, sig, color='black')
plt.plot(times, sig_filt, color='red', linewidth=5.0)
plt.ylim([-50, 50])
# plt.xlim([-1000, 0])
####################################################################################################
#
# Load simulated experiment of 10 patients and 10 controls
# --------------------------------------------------------
####################################################################################################
# Load experimental data
sigs = np.load('data/sim_experiment.npy')
fs = 1000 # Sampling rate
# Apply lowpass filter to each signal
for idx in range(len(sigs)):
sigs[idx] = filter_signal(sigs[idx],
fs,
'lowpass',
30,
n_seconds=.2,
remove_edges=False)
####################################################################################################
# Plot an example signal
n_signals = len(sigs)
n_seconds = len(sigs[0]) / fs
times = np.arange(0, n_seconds, 1 / fs)
plot_time_series(times, sigs[0], lw=2)
####################################################################################################
#
# Compute cycle-by-cycle features
def find_extrema(sig,
fs,
f_range,
boundary=None,
first_extrema='peak',
filter_kwargs=None):
"""Identify peaks and troughs in a time series.
Parameters
----------
sig : 1d array
Voltage time series.
fs : float
Sampling rate, in Hz.
f_range : tuple of (float, float)
Frequency range, in Hz, for narrowband signal of interest,
used to find zero-crossings of the oscillation.
boundary : int, optional
Number of samples from edge of recording to ignore.
first_extrema: {'peak', 'trough', None}
If 'peak', then force the output to begin with a peak and end in a trough.
If 'trough', then force the output to begin with a trough and end in peak.
If None, force nothing.
filter_kwargs : dict, optional
Keyword arguments to :func:`~neurodsp.filt.filter.filter_signal`, such as 'n_cycles' or
'n_seconds' to control filter length.
Returns
-------
ps : 1d array
Indices at which oscillatory peaks occur in the input ``sig``.
ts : 1d array
Indices at which oscillatory troughs occur in the input ``sig``.
Notes
-----
This function assures that there are the same number of peaks and troughs
if the first extrema is forced to be either peak or trough.
"""
# Set default filtering parameters
if filter_kwargs is None:
filter_kwargs = {}
# Default boundary value as 1 cycle length of low cutoff frequency
if boundary is None:
boundary = int(np.ceil(fs / float(f_range[0])))
# Narrowband filter signal
sig_filt = filter_signal(sig,
fs,
'bandpass',
f_range,
remove_edges=False,
**filter_kwargs)
# Find rising and falling zero-crossings (narrowband)
zerorise_n = _fzerorise(sig_filt)
zerofall_n = _fzerofall(sig_filt)
# Compute number of peaks and troughs
if zerorise_n[-1] > zerofall_n[-1]:
pl = len(zerorise_n) - 1
tl = len(zerofall_n)
else:
pl = len(zerorise_n)
tl = len(zerofall_n) - 1
# Calculate peak samples
ps = np.zeros(pl, dtype=int)
for p_idx in range(pl):
# Calculate the sample range between the most recent zero rise and the next zero fall
mrzerorise = zerorise_n[p_idx]
nfzerofall = zerofall_n[zerofall_n > mrzerorise][0]
# Identify time of peak
ps[p_idx] = np.argmax(sig[mrzerorise:nfzerofall]) + mrzerorise
# Calculate trough samples
ts = np.zeros(tl, dtype=int)
for t_idx in range(tl):
# Calculate the sample range between the most recent zero fall and the next zero rise
mrzerofall = zerofall_n[t_idx]
nfzerorise = zerorise_n[zerorise_n > mrzerofall][0]
# Identify time of trough
ts[t_idx] = np.argmin(sig[mrzerofall:nfzerorise]) + mrzerofall
# Remove peaks and troughs within the boundary limit
ps = ps[np.logical_and(ps > boundary, ps < len(sig) - boundary)]
ts = ts[np.logical_and(ts > boundary, ts < len(sig) - boundary)]
# Force the first extrema to be as desired
# Assure equal # of peaks and troughs
if first_extrema == 'peak':
if ps[0] > ts[0]:
ts = ts[1:]
if ps[-1] > ts[-1]:
ps = ps[:-1]
elif first_extrema == 'trough':
if ts[0] > ps[0]:
ps = ps[1:]
if ts[-1] > ps[-1]:
ts = ts[:-1]
elif first_extrema is None:
pass
else:
raise ValueError('Parameter "first_extrema" is invalid')
return ps, ts
#
###################################################################################################
# Using filter_signal
# ~~~~~~~~~~~~~~~~~~~
#
# In the above, we did a step-by-step procedure of designing, evaluating, and applying our filter.
#
# Note that all of these elements can also be done directly through the
# :func:`~.filter_signal` function.
#
###################################################################################################
sig_filt, sos = filter_signal(sig, fs, pass_type, f_range,
filter_type='iir', butterworth_order=butterworth_order,
plot_properties=True, print_transitions=True,
return_filter=True)
###################################################################################################
# Example Application: Line Noise Removal
# ---------------------------------------
#
# A common application of IIR filters is for line noise removal.
#
# In this example, a 3rd order Butterworth filter is applied to remove 60Hz noise.
#
###################################################################################################
# Generate a signal, with a low frequency oscillation and 60 Hz line noise
components = {'sim_oscillation' : [{'freq' : 6}, {'freq' : 60}]}
# Generate a signal for this example, with an oscillation and 60 Hz line noise
components = {'sim_oscillation' : [{'freq' : 6}, {'freq' : 60}]}
variances = [1, 0.2]
sig = sim_combined(n_seconds, fs, components, variances)
###################################################################################################
# Define filter settings
f_range = (58, 62)
passtype = 'bandstop'
###################################################################################################
# Apply a short filter, one that won't achieve our desired attenuation
sig_filt_short = filter_signal(sig, fs, passtype, f_range,
n_seconds=0.25, plot_properties=True)
###################################################################################################
#
# Notice that when we apply the filter above, with a short filter length, we get a
# warning about the filter attenuation. The filter we have defined does not get to a
# sufficient attenuation level.
#
###################################################################################################v
# This user warning disappears if we elongate the filter
sig_filt_long = filter_signal(sig, fs, passtype, f_range,
n_seconds=1, plot_properties=True)
###################################################################################################
# Simulation settings
n_seconds = 10
fs = 1000
components = {'sim_bursty_oscillation': {'freq': 10, 'enter_burst': .1, 'leave_burst': .1,
'cycle': 'asine', 'rdsym': 0.3},
'sim_powerlaw': {'f_range': (2, None)}}
sig = sim_combined(n_seconds, fs, components=components, component_variances=(2, 1))
# Filter settings
f_alpha = (8, 12)
n_seconds_filter = .5
# Compute amplitude and phase
sig_filt = filter_signal(sig, fs, 'bandpass', f_alpha, n_seconds=n_seconds_filter)
theta_amp = amp_by_time(sig, fs, f_alpha, n_seconds=n_seconds_filter)
theta_phase = phase_by_time(sig, fs, f_alpha, n_seconds=n_seconds_filter)
# Plot signal
times = create_times(n_seconds, fs)
xlim = (2, 6)
tidx = np.logical_and(times >= xlim[0], times < xlim[1])
fig, axes = plt.subplots(figsize=(15, 9), nrows=3)
# Plot the raw signal
plot_time_series(times[tidx], sig[tidx], ax=axes[0], ylabel='Voltage (mV)',
xlabel='', lw=2, labels='raw signal')
# Plot the filtered signal and oscillation amplitude
# # Extract signal within a specific frequency range (e.g. theta, 4-8 Hz). # ################################################################################################### # Generate an oscillation with noise fs = 1000 times = create_times(4, 1000) sig = np.random.randn(len(times)) + 5 * np.sin(times * 2 * np.pi * 6) ################################################################################################### # Filter the data, across a frequency band of interest f_range = (4, 8) sig_filt = filt.filter_signal(sig, fs, 'bandpass', f_range) ################################################################################################### # Plot filtered signal plot_time_series(times, [sig, sig_filt], ['Raw', 'Filtered']) ################################################################################################### # # Notice that the edges of the filtered signal are clipped (no red). # # Edge artifact removal is done by default in :func:`filter_signal`, because # the signal samples at the edges only experienced part of the filter. # # To bypass this feature, set `remove_edge_artifacts=False`, but at your own risk! #
def get_bandpass_filter_signal(data, fs, passtype, f_range):
sig_filt = filt.filter_signal(data, fs, passtype, f_range)
return sig_filt
def run_all(session):
# get data session path from mat file
path = get_session_path(session)
# load position data from .mat file
df = load_position(session)
# load xml which has channel & fs info
channels, fs, shank = loadXML(path)
# get good channels
good_ch = get_good_channels(shank)
# load .lfp
lfp, ts = loadLFP(glob.glob(path + '\*.lfp')[0],
n_channels=channels,
channel=good_ch,
frequency=fs,
precision='int16')
# interp speed of the animal
speed = np.interp(ts, df.ts, df.speed)
speed[np.isnan(speed)] = 0
# get filtered signal
print('filtering signal')
filtered_lfps = np.stack([
filter_signal(lfp_, fs, 'bandpass', (80, 250), remove_edges=False)
for lfp_ in lfp.T
])
filtered_lfps = filtered_lfps.T
# detect ripples
print('detecting ripples')
ripple_times = Karlsson_ripple_detector(ts, filtered_lfps, speed, fs)
# find ripple duration
ripple_times[
'ripple_duration'] = ripple_times.end_time - ripple_times.start_time
# check against emg (< 0.85)
ripple_times = emg_filter(session, ripple_times, shank)
# add ripple channel and peak amp
print('getting ripple channel')
ripple_times = get_ripple_channel(ripple_times,
stats.zscore(filtered_lfps, axis=0), ts,
fs)
# get instant phase, amp, and freq
print('get instant phase, amp, and freq')
phase, amp, freq = get_phase_amp_freq(filtered_lfps, fs)
# get ripple_map
print('getting ripple maps')
ripple_maps = get_ripple_maps(ripple_times, ts, lfp, filtered_lfps, phase,
amp, freq, fs)
# get ripple frequency
print('getting ripple frequency')
ripple_times['peak_freq'] = [
map[len(map) // 2] for map in ripple_maps['freq_map']
]
# filter out cliped signal
ripple_times, ripple_maps = clip_filter(ripple_times, ripple_maps)
# filter out very high amplitude ripples
#ripple_times,ripple_maps = filter_high_amp(ripple_times,ripple_maps)
# find ripples with a single large jump
#ripple_times,ripple_maps = filter_single_peaks(ripple_times,ripple_maps)
# save ripples for neuroscope inspection
save_ripples(ripple_times, path)
return ripple_times, lfp, filtered_lfps, ts, ripple_maps
def sim_powerlaw(n_seconds, fs, exponent=-2.0, f_range=None, **filter_kwargs):
"""Simulate a power law time series, with a specified exponent.
Parameters
----------
n_seconds : float
Simulation time, in seconds.
fs : float
Sampling rate of simulated signal, in Hz.
exponent : float, optional, default: -2
Desired power-law exponent, of the form P(f)=f^exponent.
f_range : list of [float, float] or None, optional
Frequency range to filter simulated data, as [f_lo, f_hi], in Hz.
**filter_kwargs : kwargs, optional
Keyword arguments to pass to `filter_signal`.
Returns
-------
sig : 1d array
Time-series with the desired power law exponent.
Notes
-----
- Powerlaw data with exponents is created by spectrally rotating white noise [1]_.
References
----------
.. [1] Timmer, J., & Konig, M. (1995). On Generating Power Law Noise.
Astronomy and Astrophysics, 300, 707–710.
Examples
--------
Simulate a power law signal, with an exponent of -2 (brown noise):
>>> sig = sim_powerlaw(n_seconds=1, fs=500, exponent=-2.0)
Simulate a power law signal, with a highpass filter applied at 2 Hz:
>>> sig = sim_powerlaw(n_seconds=1, fs=500, exponent=-1.5, f_range=(2, None))
"""
# Compute the number of samples for the simulated time series
n_samples = compute_nsamples(n_seconds, fs)
# Get the number of samples to simulate for the signal
# If signal is to be filtered, with FIR, add extra to compensate for edges
if f_range and filter_kwargs.get('filter_type', None) != 'iir':
pass_type = infer_passtype(f_range)
filt_len = compute_filter_length(
fs,
pass_type,
*check_filter_definition(pass_type, f_range),
n_seconds=filter_kwargs.get('n_seconds', None),
n_cycles=filter_kwargs.get('n_cycles', 3))
n_samples += filt_len + 1
# Simulate the powerlaw data
sig = _create_powerlaw(n_samples, fs, exponent)
if f_range is not None:
sig = filter_signal(sig,
fs,
infer_passtype(f_range),
f_range,
remove_edges=True,
**filter_kwargs)
# Drop the edges, that were compensated for, if not using FIR filter
if not filter_kwargs.get('filter_type', None) == 'iir':
sig, _ = remove_nans(sig)
return sig
####################################################################################################
# Only keep 60 seconds of data
n_seconds = 60
ca1_raw = ca1_raw[:int(n_seconds * fs)]
ec3_raw = ec3_raw[:int(n_seconds * fs)]
####################################################################################################
# Apply a lowpass filter at 25Hz
fc = 25
filter_seconds = .5
ca1 = filter_signal(ca1_raw,
fs,
'lowpass',
fc,
n_seconds=filter_seconds,
remove_edges=False)
ec3 = filter_signal(ec3_raw,
fs,
'lowpass',
fc,
n_seconds=filter_seconds,
remove_edges=False)
####################################################################################################
# Compute cycle-by-cycle features
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
####################################################################################################
pd.options.display.max_columns = 10
####################################################################################################
# Load data
sig = np.load('data/ca1.npy') / 1000
sig = sig[:125000]
fs = 1250
f_theta = (4, 10)
f_lowpass = 30
n_seconds = .1
# Lowpass filter
sig_low = filter_signal(sig,
fs,
'lowpass',
f_lowpass,
n_seconds=n_seconds,
remove_edges=False)
# Plot signal
times = np.arange(0, len(sig) / fs, 1 / fs)
xlim = (2, 5)
tidx = np.logical_and(times >= xlim[0], times < xlim[1])
plot_time_series(times[tidx], [sig[tidx], sig_low[tidx]],
colors=['k', 'k'],
alpha=[.5, 1],
lw=2)
####################################################################################################
#
'freq': 10
}, {
'freq': 60
}]
}
comp_vars = [0.5, 1, 1]
# Simulate a time series
sig = sim_combined(n_seconds, fs, components, comp_vars)
###################################################################################################
# Bandstop filter the signal to remove line noise frequencies
sig_filt = filter_signal(sig,
fs,
'bandstop', (57, 63),
n_seconds=2,
remove_edges=False)
###################################################################################################
# Compute a power spectrum of the simulated signal
freqs, powers_pre = trim_spectrum(*compute_spectrum(sig, fs), [3, 75])
freqs, powers_post = trim_spectrum(*compute_spectrum(sig_filt, fs), [3, 75])
###################################################################################################
# Plot the spectrum of the data, pre and post bandstop filtering
plot_spectra(freqs, [powers_pre, powers_post],
log_powers=True,
labels=['Pre-Filter', 'Post-Filter'])
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Now that we have a simulated signal, let's filter it into each of our frequency bands.
#
# To do so, we will loop across our band definitions, and plot the filtered version
# of the signal.
#
###################################################################################################
# Apply band-by-band filtering of our signal into each defined frequency band
_, axes = plt.subplots(len(bands), 1, figsize=(12, 15))
for ax, (label, f_range) in zip(axes, bands):
# Filter the signal to the current band definition
band_sig = filter_signal(sig, s_rate, 'bandpass', f_range)
# Plot the time series of the current band, and adjust plot aesthetics
plot_time_series(times, band_sig, title=label + ' ' + str(f_range), ax=ax,
xlim=(0, n_seconds), ylim=(-1, 1), xlabel='')
###################################################################################################
#
# As we can see, filtering a signal with aperiodic activity into arbitrary
# frequency ranges returns filtered signals that look like rhythmic activity.
#
# Also, because our simulated signal has some random variation, the filtered components
# also exhibit some fluctuations.
#
# Overall, we can see from filtering this signal that:
#
'sim_oscillation': {
'freq': 6
}
}
variances = [0.1, 1]
# Simulate our signal
sig = sim_combined(n_seconds, fs, components, variances)
###################################################################################################
# Define a frequency range to filter the data
f_range = (4, 8)
# Bandpass filter the data, across the band of interest
sig_filt = filter_signal(sig, fs, 'bandpass', f_range)
###################################################################################################
# Plot filtered signal
plot_time_series(times, [sig, sig_filt], ['Raw', 'Filtered'])
###################################################################################################
#
# Notice that the edges of the filtered signal are clipped (no red).
#
# Edge artifact removal is done by default in NeuroDSP filtering, because
# the signal samples at the edges only experienced part of the filter.
#
# To bypass this feature, set `remove_edges=False`, but at your own risk!
#
# Using filter_signal
# ~~~~~~~~~~~~~~~~~~~
#
# In the above, we did a step-by-step procedure of designing, evaluating, and applying our filter.
#
# Note that all of these elements can also be done directly through the
# :func:`~.filter_signal` function.
#
###################################################################################################
# Filter our signal, using the main filter function, with extra options
sig_filt2, filter_kernel = filter_signal(sig,
fs,
pass_type,
f_range,
filter_type='fir',
print_transitions=True,
plot_properties=True,
return_filter=True)
###################################################################################################
# Plot the signal and filtered version
plot_time_series(times, [sig, sig_filt2], ['Raw', 'Filtered'])
###################################################################################################
#
# You might notice in the above plot, the edges of the filtered version have been removed.
# This is done to remove edge artifacts. Data points at the edge of the signal don't get fully
# processed by the filter, and may contain some filtering artifacts.
#
