neurochat.nc_lfp module

This module implements NLfp Class for NeuroChaT software.

@author: Md Nurul Islam; islammn at tcd dot ie

class neurochat.nc_lfp.NLfp(**kwargs)

Bases: neurochat.nc_base.NBase

This data class contains information about the neural LFP signal.

It decodes data from different formats and analyses LFP signal in the recording.

_file_tag

The tag of the lfp data.

Type:str

_channel_id

The id of the channel the lfp data came from.

Type:int

_samples

Array of lfp samples.

Type:np.ndarray

_timestamp

Array of timestamps of the lfp samples.

Type:np.ndarray

__str__()

Return a friendly string representation of the object.

add_lfp(lfp=None, **kwargs)

Add new LFP node to current NLfp() object.

Parameters:lfp (NLfp) – NLfp object. If None, new object is created Returns:` (obj:Nlfp`) – A new NLfp() object

add_spike(spike=None, **kwargs)

Add new spike node to current NLfp() object.

Parameters:spike (NSpikes) – NSPike object. If None, new object is created Returns:` (obj:NSpike()`) – A new NSpike() object

bandpower(band, **kwargs)

Compute the average power of the signal x in a specific frequency band.

Modified from excellent article at https://raphaelvallat.com/bandpower.html

Parameters:

band (list) – Lower and upper frequencies of the band of interest. [lower, upper].

Keyword Arguments:  

• method (string) – Periodogram method. Only ‘welch’ is currently supported.
• window_sec (float) – Length of each window in seconds. If None, window_sec = (1 / min(band)) * 2.
• band_total (bool) – Whether to band the total power Default False
• total_band (List) – low and high frequency values for the filter on total band. Default [1.5, 90]
• unit (str) – Currently support micro and milli. The scale to return Volts in. Defaults to micro.

Returns:

bp (Dict) – “bandpower”, “total_power” and “relative_power”.

bandpower_ratio(first_band, second_band, win_sec, **kwargs)

Calculate the ratio in power between two bandpass filtered signals.

Note that common ranges are: delta (1.5–4 Hz), theta (5-11 Hz)

Parameters:

• first_band (1d array) – lower and upper bands
• second_band (1d array) – lower and upper bands
• win_sec (float) – length of the windows to bin lfp into in seconds. recommend 4 for eg.

Keyword Arguments:  

• first_name (str) – name of band 1, default “Band 1”
• second_name (str) – name of band 2, default “Band 2”

Returns:

float – the ratio between the power signals.

See also

nc_lfp.NLfp()

event_trig_average(event_stamp=None, **kwargs)

Averaging event-triggered LFP signals.

Parameters:

• event_stamp (ndarray) – Timestamps of the events or the spiking activities for measuring the event triggered average of the LFP signal
• **kwargs – Keywrod arguments

Returns:

dict – Graphical data of the analysis

find_artf(sd_thresh=3, min_artf_freq=8)

Obtain locations of signal above threshold in windows.

Note

This function is still a work in progress and may see future changes.

Parameters:

• sd_thresh (float) – threshold to exclude artf
• min_artf_freq (float) – minimum artf freq - Used to locate artf blocks eg. 250 Hz sampling rate, 40Hz min_artf_freq: locates artf within 9 samples of each other

get_bytes_per_sample()

Return the number of bytes to represent each LFP waveform sample.

Parameters:None – Returns:int – Number of bytes to represent each sample of the LFP waveform

get_channel_id()

Return the electrode channels ID.

Parameters:None – Returns:str – LFP channel ID

get_file_tag()

Return the file tag or extension for the LFP dataset.

For example, Axona recordings usually have file tags like ‘eeg’ or ‘eeg8’ etc.

Parameters:None – Returns:str – File tag or extension for the LFP dataset

get_fullscale_mv()

Return the fullscale value of the ADC in mV.

Parameters:None – Returns:int – Fullscale ADC value in mV

get_recording_time()

Return the recording time in seconds.

Parameters:None – Returns:int – Recording time in seconds

get_samples()

Return LFP waveform samples.

Parameters:None – Returns:ndarray – Samples of the LFP signal

get_sampling_rate()

Return the sampling rate of spike waveforms.

Parameters:None – Returns:int – Sampling rate for spike waveforms

get_timestamp()

Return the timestamps of the LFP waveform.

Parameters:None – Returns:ndarray – Timestamps of the LFP signal

get_timestamp_bytes()

Return number of bytes to represent each timestamp in the binary file.

Parameters:None – Returns:int – Number of bytes to represent timestamps

get_total_channel()

Return total number of electrode channels in the LFP data file.

Parameters:None – Returns:int – Total number of electrode channels

get_total_samples()

Return total number of LFP samples.

Parameters:None – Returns:ndarray – Total number of LFP samples

get_type()

Return the type of object. For NLfp, this is always lfp type.

Parameters:None – Returns:str

load(filename=None, system=None)

Load LFP datasets.

Parameters:

• filename (str) – Name of the spike datafile
• system (str) – Recording system or format of the spike data file

Returns:

None

See also

load_lfp_axona(), load_lfp_NLX(), load_lfp_NWB()

load_lfp(names=None)

Load datasets of the LFP nodes.

The name of each node is used for obtaining the filenames.

Parameters:names (list of str) – Names of the nodes to load. If all, all LFP nodes are loaded Returns:None

load_lfp_Axona(file_name)

Decode LFP data from Axona file format.

Parameters:file_name (str) – Full file directory for the lfp data Returns:None

load_lfp_NWB(file_name)

Decode LFP data from NWB (HDF5) file format.

Parameters:file_name (str) – Full file directory for the lfp data Returns:None

load_lfp_Neuralynx(file_name)

Decode LFP data from Neuralynx file format.

Parameters:file_name (str) – Full file directory for the lfp data Returns:None

load_spike(names='all')

Load datasets of the spike nodes.

The name of each node is used for obtaining the filenames.

Parameters:names (list of str) – Names of the nodes to load. If None, current NSpike() object is loaded Returns:None

phase_at_events(event_stamps, **kwargs)

Phase based on times.

Parameters:

• event_stamps (array) – an array of event times
• **kwargs – keyword arguments

Returns:

• (array)
• Phase values for each position

phase_dist(event_stamp, **kwargs)

Analysis of spike to LFP phase distribution.

Parameters:

• event_stamp (ndarray) – Timestamps of the events of spiking activities for measuring the phase distribution.
• **kwargs – Keyword arguments

Returns:

dict – Graphical data of the analysis

plv(event_stamp, **kwargs)

Calculate phase-locking value of the spike train to underlying LFP signal.

When ‘mode’= None in the input kwargs, it calculates the PLV and SFC over the entire spike-train.

If ‘mode’= ‘bs’, it bootstraps the spike-timestamps and calculates the locking values for each set of new spike timestamps.

If ‘mode’= ‘tr’, a time-resolved phase-locking analysis is performed where the LFP signal is split into overlapped segments for each calculation.

Parameters:

• evnet_stamp (ndarray) – Timestamps of the events or the spiking activities for measuring the phase locking
• **kwargs – Keyword arguments

Returns:

dict – Graphical data of the analysis

save_to_hdf5(file_name=None, system=None)

Store NLfp() object to HDF5 file.

Parameters:

• file_name (str) – Full file directory for the lfp data
• system (str) – Recoring system or data format

Returns:

• None
• Also see
• ——–
• nc_hdf.Nhdf().save_lfp()

set_channel_id(channel_id='')

Set the electrode channels ID.

Parameters:channel_id (str) – Channel ID for the LFP data Returns:None

set_file_tag(file_tag)

Set the file tag or extension for the LFP dataset.

For example, Axona recordings usually have file tags like ‘eeg’ or ‘eeg8’ etc.

Parameters:file_tag (str) – File tag or extension for the LFP dataset Returns:None

sharp_wave_ripples(in_range=None, **kwargs)

Detect SWR events in the lfp, optionally in a given range.

This method is based on finding peaks in the Root mean square envelope of a filtered signal between 100 and 250Hz (default params). Peaks that are above the peak_percentile keyword argument are returned.

Parameters:

• in_range (tuple) – A range in seconds
• kwargs –
• ------ –
• swr_lower (float) – Lower band in hz
• swr_upper (float) – Upper band in hz
• rms_window_size_ms (int) – Size of the rms window in ms
• percentile (float) – The percentile threshold for a peak

Returns:

dict – lfp times, lfp samples, swr times, lfp sample rate

spectrum(**kwargs)

Analyse frequency spectrum of the LFP signal.

Parameters:**kwargs – Keyword arguments Returns:dict – Graphical data of the analysis

spike_lfp_causality(spike=None, **kwargs)

(Not implemented yet).

Analyses spike to underlying LFP causality

Parameters:

• spike (NSpike) – Spike dataset which is used for the causality analysis
• **kwargs – Keywrod arguments

Returns:

dict – Should return graphical data of the analysis. The function is not implemented yet.

subsample(sample_range=None)

Extract a time range from the lfp.

Parameters:sample_range (tuple) – the time in seconds to extract from the lfp as (lower, upper) Returns:NLfp – subsampled version of initial lfp object