neurochat.nc_clust module

This module implements NClust Class for NeuroChaT software.

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

class neurochat.nc_clust.NClust(**kwargs)

Bases: neurochat.nc_base.NBase

This class facilitates clustering-related operations.

Although no clustering algorithm is implemented in this class, it can be subclassed to create such algorithms.

Many of the functions in this class are delegated to the spike attr.

spike

An object of NSpike() class.

Type:NSpike

add_spike(spike=None, **kwargs)

Add new spike node to current NSpike() object.

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

align_wave_peak(reach=300, factor=2)

Align the waves by their peaks.

Parameters:

• reach (int) – Maximum allowed time-shift in microsecond
• factors (int) – Resampling factor

Returns:

None

burst(burst_thresh=5, ibi_thresh=50)

Burst analysis of spike-train.

Delegates to NSpike().burst()

Parameters:

• burst_thresh (int) – Minimum ISI between consecutive spikes in a burst
• ibi_thresh (int) – Minimum inter-burst interval between two bursting groups of spikes

Returns:

None

See also

nc_spike.NSpike()

cluster_separation(unit_no=0)

Measure the separation of a specific unit from other clusters.

This is performed quantitatively using the following: 1. Bhattacharyya coefficient 2. Hellinger distance

Parameters:unit_no (int) – Unit of interest. If ‘0’, pairwise comparison of all units are returned. Returns:

• (bc, dh) ((ndarray, ndarray))
• bc (ndarray) – Bhattacharyya coefficient
• dh (ndarray) – Hellinger distance

cluster_similarity(nclust=None, unit_1=None, unit_2=None)

Measure the similarity or distance of units in a cluster.

This is performed on one unit in a spike dataset to cluster of another unit in another dataset.

This is performed quantitatively using the following: 1. Bhattacharyya coefficient 2. Hellinger distance

Parameters:

• nclust (Nclust) – NClust object whose unit is under comparison
• unit_1 (int) – Unit of current Nclust object
• unit_2 (int) – Unit of another NClust object under comparison

Returns:

• (bc, dh) ((ndarray, ndarray))
• bc (ndarray) – Bhattacharyya coefficient
• dh (ndarray) – Hellinger distance

get_channel_ids()

Return the identities of individual channels.

Parameters:None – Returns:list – Identities of individual channels

get_feat(npc=2)

Return the spike-waveform features.

Parameters:npc (int) – Number of principle components in each channel. Returns:feat (ndarray) – Matrix of size (number_spike X number_features)

get_feat_by_unit(unit_no=None)

Return the spike-waveform features for a particular unit.

Parameters:unit_no (int) – Unit of interest Returns:feat (ndarray) – Matrix of size (number_spike X number_features)

get_max_energy_chan()

Return the maximum energy of the spike waveforms.

Parameters:None – Returns:ndarray – Maximum energy of the spikes

get_max_wave_chan()

Return the maximum of waveform peaks among the electrode groups.

Parameters:None – Returns:

• (max_wave_val, max_wave_chan, peak_loc) ((ndarray, ndarray, ndarray))
• max_wave_val (ndarray) – Maximum value of the peaks of the waveforms
• max_wave_chan (ndarray) – Channel of the electrode group where a spike waveform is strongest
• peak_loc (ndarray) – Peak location in the channel with strongest waveform

get_min_wave_chan()

Return the maximum of waveform peaks among the electrode groups.

Parameters:None – Returns:(min_val, min_index) ((ndarray, ndarray)) –

min_val : ndarray

Minimum value of the waveform at channels with peak value

min_index : ndarray

Index of minimum values

get_samples_per_spike()

Return the number of bytes to represent each timestamp.

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

get_sampling_rate()

Return the sampling rate of spike waveforms.

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

get_timebase()

Return the timebase for spike event timestamps.

Parameters:None – Returns:int – Timebase for spike event timestamps

get_timestamp(unit_no=None)

Return the timestamps of the spike-waveforms of specified unit.

Parameters:unit_no (int) – Unit whose timestamps are to be returned Returns:ndarray – Timestamps of the spiking waveforms

get_total_channels()

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

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

get_total_spikes()

Return total number of spikes in the recording.

Parameters:None – Returns:int – Total number of spikes

get_unit_list()

Return the list of units in a spike dataset.

Parameters:None – Returns:list – List of units

get_unit_spikes_count(unit_no=None)

Return the total number of spikes in a specified unit.

Parameters:unit_no (int) – Unit whose count is returned Returns:int – Total number of spikes in the unit

get_unit_tags()

Return tags of the spiking waveforms from clustering.

Parameters:None – Returns:None

get_unit_waves(unit_no=None)

Return spike waveforms of a specific unit.

Parameters:unit_no (int) – Unit whose waveforms are returned Returns:dict – Spike waveforms in each channel of the electrode group

get_wave_energy()

Energy of the spike waveforms.

This is measured as the summation of the square of samples.

Parameters:None – Returns:energy (ndarray) – Energy of spikes (num_spike X num_channels)

get_wave_min()

Return the minimum values of the spike-waveforms.

Parameters:None – Returns:(min_w, min_loc) ((ndarray, ndarray)) –

min_w : ndarray

Minimum value of the waveforms

min_loc : ndarray

Index of minimum value

get_wave_pc(npc=2)

Return the Principle Components of the waveforms.

Parameters:npc (int) – Number of principle components from waveforms of each channel Returns:pc (ndarray) – Principle components (num_waves X npc*num_channels)

get_wave_peaks()

Return the peaks of the spike-waveforms.

Parameters:None – Returns:(peak, peak_loc) ((ndarray, ndarray)) –

peak:

Spike waveform peaks in all the electrode channels Shape is (num_waves X num_channels)

peak_loc :

Index of peak locations

get_wave_timestamp()

Return the temporal resolution to represent samples of spike-waves.

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

get_waveform()

Return the waveforms in the spike dataset.

Parameters:None – Returns:dict – Each key represents one channel of the electrode group. Each value represents the waveforms of the spikes in a matrix form (no_samples x no_spikes)

get_wavetime()

Return the timestamps of the waveforms, not the spiking-event.

Parameters:None – Returns:Timestamps of the spike-waveforms

isi(bins='auto', bound=None, density=False)

Calculate the ISI histogram of the spike train.

Delegates to NSpike().isi()

Parameters:

• bins (str or int) – Number of ISI histogram bins. If ‘auto’, NumPy default is used
• bound (int) – Length of the ISI histogram in msec
• density (bool) – If true, normalized histogram is calculated

Returns:

dict – Graphical data of the analysis

See also

NSpike()

isi_corr(**kwargs)

Analysis of ISI autocorrelation histogram.

Delegates to NSpike().isi_auto_corr()

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

See also

nc_spike.NSpike()

load(filename=None, system=None)

Load spike dataset from the file.

Parameters:

• filename (str) – Name of the spike file
• system (str) – Name of the recording format or system.

Returns:

None

See also

nc_spike.NSpike()

load_spike(names=None)

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

psth(event_stamp, **kwargs)

Calculate peri-stimulus time histogram (PSTH).

Delegates to NSpike().psth()

Parameters:

• event_stamp (ndarray) – Event timestamps
• **kwargs – Keyword arguments

Returns:

dict – Graphical data of the analysis

See also

nc_spike.NSpike()

remove_null_chan()

Remove the channel from the electrode group that has no spike in it.

Parameters:None – Returns:off_chan (int) – Channel number that has been removed

resample_wave(factor=2)

Resample spike waveforms using spline interpolation.

Parameters:factor (int) – Resampling factor Returns:

• wave (dict) – Upsampled waveforms
• uptime ndarray – Upsampled wave timestamps

resample_wavetime(factor=2)

Resample the timestamps of spike-waveforms.

Parameters:factor (int) – Resampling factor Returns:Resampled timestamps

save_to_hdf5()

Store NSpike() object to HDF5 file.

Delegates to NSPike().save_to_hdf5()

Parameters:None – Returns:

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

set_unit_tags(new_tags=None)

Return tags of the spiking waveforms from clustering.

Parameters:new_tags (ndarray) – Array that contains the tags for spike-waveforms which is based on the cluster number. Returns:None

wave_property()

Calculate different waveform properties for currently set unit.

Delegates to NSpike().wave_property()

Parameters:None – Returns:dict – Graphical data of the analysis

See also

NSpike()