Source code for brainbox.singlecell

'''
Computes properties of single-cells, e.g. the autocorrelation and firing rate.
'''

import numpy as np
from scipy.signal import convolve, gaussian
from iblutil.util import Bunch
from brainbox.population.decode import xcorr


[docs]def acorr(spike_times, bin_size=None, window_size=None): """Compute the auto-correlogram of a neuron. Parameters ---------- :param spike_times: Spike times in seconds. :type spike_times: array-like :param bin_size: Size of the bin, in seconds. :type bin_size: float :param window_size: Size of the window, in seconds. :type window_size: float Returns an `(winsize_samples,)` array with the auto-correlogram. """ xc = xcorr(spike_times, np.zeros_like(spike_times, dtype=np.int32), bin_size=bin_size, window_size=window_size) return xc[0, 0, :]
[docs]def calculate_peths( spike_times, spike_clusters, cluster_ids, align_times, pre_time=0.2, post_time=0.5, bin_size=0.025, smoothing=0.025, return_fr=True): """ Calcluate peri-event time histograms; return means and standard deviations for each time point across specified clusters :param spike_times: spike times (in seconds) :type spike_times: array-like :param spike_clusters: cluster ids corresponding to each event in `spikes` :type spike_clusters: array-like :param cluster_ids: subset of cluster ids for calculating peths :type cluster_ids: array-like :param align_times: times (in seconds) to align peths to :type align_times: array-like :param pre_time: time (in seconds) to precede align times in peth :type pre_time: float :param post_time: time (in seconds) to follow align times in peth :type post_time: float :param bin_size: width of time windows (in seconds) to bin spikes :type bin_size: float :param smoothing: standard deviation (in seconds) of Gaussian kernel for smoothing peths; use `smoothing=0` to skip smoothing :type smoothing: float :param return_fr: `True` to return (estimated) firing rate, `False` to return spike counts :type return_fr: bool :return: peths, binned_spikes :rtype: peths: Bunch({'mean': peth_means, 'std': peth_stds, 'tscale': ts, 'cscale': ids}) :rtype: binned_spikes: np.array (n_align_times, n_clusters, n_bins) """ # initialize containers n_offset = 5 * int(np.ceil(smoothing / bin_size)) # get rid of boundary effects for smoothing n_bins_pre = int(np.ceil(pre_time / bin_size)) + n_offset n_bins_post = int(np.ceil(post_time / bin_size)) + n_offset n_bins = n_bins_pre + n_bins_post binned_spikes = np.zeros(shape=(len(align_times), len(cluster_ids), n_bins)) # build gaussian kernel if requested if smoothing > 0: w = n_bins - 1 if n_bins % 2 == 0 else n_bins window = gaussian(w, std=smoothing / bin_size) # half (causal) gaussian filter # window[int(np.ceil(w/2)):] = 0 window /= np.sum(window) binned_spikes_conv = np.copy(binned_spikes) ids = np.unique(cluster_ids) # filter spikes outside of the loop idxs = np.bitwise_and(spike_times >= np.min(align_times) - (n_bins_pre + 1) * bin_size, spike_times <= np.max(align_times) + (n_bins_post + 1) * bin_size) idxs = np.bitwise_and(idxs, np.isin(spike_clusters, cluster_ids)) spike_times = spike_times[idxs] spike_clusters = spike_clusters[idxs] # compute floating tscale tscale = np.arange(-n_bins_pre, n_bins_post + 1) * bin_size # bin spikes for i, t_0 in enumerate(align_times): # define bin edges ts = tscale + t_0 # filter spikes idxs = np.bitwise_and(spike_times >= ts[0], spike_times <= ts[-1]) i_spikes = spike_times[idxs] i_clusters = spike_clusters[idxs] # bin spikes similar to bincount2D: x = spike times, y = spike clusters xscale = ts xind = (np.floor((i_spikes - np.min(ts)) / bin_size)).astype(np.int64) yscale, yind = np.unique(i_clusters, return_inverse=True) nx, ny = [xscale.size, yscale.size] ind2d = np.ravel_multi_index(np.c_[yind, xind].transpose(), dims=(ny, nx)) r = np.bincount(ind2d, minlength=nx * ny, weights=None).reshape(ny, nx) # store (ts represent bin edges, so there are one fewer bins) bs_idxs = np.isin(ids, yscale) binned_spikes[i, bs_idxs, :] = r[:, :-1] # smooth if smoothing > 0: idxs = np.where(bs_idxs)[0] for j in range(r.shape[0]): binned_spikes_conv[i, idxs[j], :] = convolve( r[j, :], window, mode='same', method='auto')[:-1] # average if smoothing > 0: binned_spikes_ = np.copy(binned_spikes_conv) else: binned_spikes_ = np.copy(binned_spikes) if return_fr: binned_spikes_ /= bin_size peth_means = np.mean(binned_spikes_, axis=0) peth_stds = np.std(binned_spikes_, axis=0) if smoothing > 0: peth_means = peth_means[:, n_offset:-n_offset] peth_stds = peth_stds[:, n_offset:-n_offset] binned_spikes = binned_spikes[:, :, n_offset:-n_offset] tscale = tscale[n_offset:-n_offset] # package output tscale = (tscale[:-1] + tscale[1:]) / 2 peths = Bunch({'means': peth_means, 'stds': peth_stds, 'tscale': tscale, 'cscale': ids}) return peths, binned_spikes
[docs]def firing_rate(ts, hist_win=0.01, fr_win=0.5): ''' Computes the instantaneous firing rate of a unit over time by computing a histogram of spike counts over a specified window of time, and summing this histogram over a sliding window of specified time over a specified period of total time. Parameters ---------- ts : ndarray The spike timestamps from which to compute the firing rate.. hist_win : float The time window (in s) to use for computing spike counts. fr_win : float The time window (in s) to use as a moving slider to compute the instantaneous firing rate. Returns ------- fr : ndarray The instantaneous firing rate over time (in hz). See Also -------- metrics.firing_rate_cv metrics.firing_rate_fano_factor plot.firing_rate Examples -------- 1) Compute the firing rate for unit 1 from the time of its first to last spike. >>> import brainbox as bb >>> import alf.io as aio >>> import ibllib.ephys.spikes as e_spks (*Note, if there is no 'alf' directory, make 'alf' directory from 'ks2' output directory): >>> e_spks.ks2_to_alf(path_to_ks_out, path_to_alf_out) # Load a spikes bunch and get the timestamps for unit 1, and calculate the instantaneous # firing rate. >>> spks_b = aio.load_object(path_to_alf_out, 'spikes') >>> unit_idxs = np.where(spks_b['clusters'] == 1)[0] >>> ts = spks_b['times'][unit_idxs] >>> fr = bb.singlecell.firing_rate(ts) ''' # Compute histogram of spike counts. t_tot = ts[-1] - ts[0] n_bins_hist = int(t_tot / hist_win) counts = np.histogram(ts, n_bins_hist)[0] # Compute moving average of spike counts to get instantaneous firing rate in s. n_bins_fr = int(t_tot / fr_win) step_sz = int(len(counts) / n_bins_fr) fr = np.convolve(counts, np.ones(step_sz)) / fr_win fr = fr[step_sz - 1:- step_sz] return fr