def get_features(self, spike_ids, channel_ids):
"""Return sparse features for given spikes."""
data = self.features
_, n_channels_loc, n_pcs = data.shape
ns = len(spike_ids)
nc = len(channel_ids)
# Initialize the output array.
features = np.empty((ns, n_channels_loc, n_pcs))
features[:] = np.NAN
if self.features_rows is not None:
s = np.intersect1d(spike_ids, self.features_rows)
# Relative indices of the spikes in the self.features_spike_ids
# array, necessary to load features from all_features which only
# contains the subset of the spikes.
rows = _index_of(s, self.features_rows)
# Relative indices of the non-null rows in the output features
# array.
rows_out = _index_of(s, spike_ids)
else:
rows = spike_ids
rows_out = slice(None, None, None)
features[rows_out, ...] = data[rows]
if self.features_cols is not None:
assert self.features_cols.shape[1] == n_channels_loc
cols = self.features_cols[self.spike_templates[spike_ids]]
features = from_sparse(features, cols, channel_ids)
assert features.shape == (ns, nc, n_pcs)
return features
def get_template_features(self, spike_ids):
"""Return sparse template features for given spikes."""
data = self.template_features
_, n_templates_loc = data.shape
ns = len(spike_ids)
if self.template_features_rows is not None:
spike_ids = np.intersect1d(spike_ids, self.features_rows)
# Relative indices of the spikes in the self.features_spike_ids
# array, necessary to load features from all_features which only
# contains the subset of the spikes.
rows = _index_of(spike_ids, self.template_features_rows)
else:
rows = spike_ids
template_features = data[rows]
if self.template_features_cols is not None:
assert self.template_features_cols.shape[1] == n_templates_loc
cols = self.template_features_cols[self.spike_templates[spike_ids]]
template_features = from_sparse(template_features,
cols,
np.arange(self.n_templates),
)
assert template_features.shape[0] == ns
return template_features
def get_features(self, cluster_id, load_all=False):
# Overriden to take into account the sparse structure.
# Only keep spikes belonging to the features spike ids.
if self.features_spike_ids is not None:
# All spikes
spike_ids = self._select_spikes(cluster_id)
spike_ids = np.intersect1d(spike_ids, self.features_spike_ids)
# Relative indices of the spikes in the self.features_spike_ids
# array, necessary to load features from all_features which only
# contains the subset of the spikes.
spike_ids_rel = _index_of(spike_ids, self.features_spike_ids)
else:
spike_ids = self._select_spikes(
cluster_id, self.n_spikes_features if not load_all else None)
spike_ids_rel = spike_ids
st = self.spike_templates[spike_ids]
nc = self.n_channels
nfpc = self.n_features_per_channel
ns = len(spike_ids)
f = _densify(spike_ids_rel, self.all_features,
self.features_ind[st, :], self.n_channels)
f = np.transpose(f, (0, 2, 1))
assert f.shape == (ns, nc, nfpc)
b = Bunch()
# Normalize features.
m = self.get_feature_lim()
f = _normalize(f, -m, m)
b.data = f
b.spike_ids = spike_ids
b.spike_clusters = self.spike_clusters[spike_ids]
b.masks = self.all_masks[spike_ids]
return b
def get_features(self, cluster_id, load_all=False):
# Overriden to take into account the sparse structure.
# Only keep spikes belonging to the features spike ids.
if self.features_spike_ids is not None:
# All spikes
spike_ids = self._select_spikes(cluster_id)
spike_ids = np.intersect1d(spike_ids, self.features_spike_ids)
# Relative indices of the spikes in the self.features_spike_ids
# array, necessary to load features from all_features which only
# contains the subset of the spikes.
spike_ids_rel = _index_of(spike_ids, self.features_spike_ids)
else:
spike_ids = self._select_spikes(cluster_id,
self.n_spikes_features
if not load_all else None)
spike_ids_rel = spike_ids
st = self.spike_templates[spike_ids]
nc = self.n_channels
nfpc = self.n_features_per_channel
ns = len(spike_ids)
f = _densify(spike_ids_rel, self.all_features,
self.features_ind[st, :], self.n_channels)
f = np.transpose(f, (0, 2, 1))
assert f.shape == (ns, nc, nfpc)
b = Bunch()
# Normalize features.
m = self.get_feature_lim()
f = _normalize(f, -m, m)
b.data = f
b.spike_ids = spike_ids
b.spike_clusters = self.spike_clusters[spike_ids]
b.masks = self.all_masks[spike_ids]
return b
def from_sparse(data, cols, channel_ids):
"""Convert a sparse structure into a dense one.
Arguments:
data : array
A (n_spikes, n_channels_loc, ...) array with the data.
cols : array
A (n_spikes, n_channels_loc) array with the channel indices of
every row in data.
channel_ids : array
List of requested channel ids (columns).
"""
# The axis in the data that contains the channels.
if len(channel_ids) != len(np.unique(channel_ids)):
raise NotImplementedError("Multiple identical requested channels "
"in from_sparse().")
channel_axis = 1
shape = list(data.shape)
assert data.ndim >= 2
assert cols.ndim == 2
assert data.shape[:2] == cols.shape
n_spikes, n_channels_loc = shape[:2]
# NOTE: we ensure here that `col` contains integers.
c = cols.flatten().astype(np.int32)
# Remove columns that do not belong to the specified channels.
c[~np.in1d(c, channel_ids)] = -1
assert np.all(np.in1d(c, np.r_[channel_ids, -1]))
# Convert column indices to relative indices given the specified
# channel_ids.
cols_loc = _index_of(c, np.r_[channel_ids, -1]).reshape(cols.shape)
assert cols_loc.shape == (n_spikes, n_channels_loc)
n_channels = len(channel_ids)
# Shape of the output array.
out_shape = shape
# The channel dimension contains the number of requested channels.
# The last column contains irrelevant values.
out_shape[channel_axis] = n_channels + 1
out = np.zeros(out_shape, dtype=data.dtype)
x = np.tile(np.arange(n_spikes)[:, np.newaxis],
(1, n_channels_loc))
assert x.shape == cols_loc.shape == data.shape[:2]
out[x, cols_loc, ...] = data
# Remove the last column with values outside the specified
# channels.
out = out[:, :-1, ...]
return out
def on_select(self, cluster_ids=None):
super(ScatterView, self).on_select(cluster_ids)
cluster_ids = self.cluster_ids
n_clusters = len(cluster_ids)
if n_clusters == 0:
return
# Get the spike times and amplitudes
data = self.coords(cluster_ids)
if data is None:
self.clear()
return
spike_ids = data.spike_ids
spike_clusters = data.spike_clusters
x = data.x
y = data.y
n_spikes = len(spike_ids)
assert n_spikes > 0
assert spike_clusters.shape == (n_spikes, )
assert x.shape == (n_spikes, )
assert y.shape == (n_spikes, )
# Get the spike clusters.
sc = _index_of(spike_clusters, cluster_ids)
# Plot the amplitudes.
with self.building():
m = np.ones(n_spikes)
# Get the color of the markers.
color = _spike_colors(sc, masks=m)
assert color.shape == (n_spikes, 4)
ms = (self._default_marker_size if sc is not None else 1.)
self.scatter(
x=x,
y=y,
color=color,
size=ms * np.ones(n_spikes),
)
def on_select(self, cluster_ids=None):
super(ScatterView, self).on_select(cluster_ids)
cluster_ids = self.cluster_ids
n_clusters = len(cluster_ids)
if n_clusters == 0:
return
# Get the spike times and amplitudes
data = self.coords(cluster_ids)
if data is None:
self.clear()
return
spike_ids = data.spike_ids
spike_clusters = data.spike_clusters
x = data.x
y = data.y
n_spikes = len(spike_ids)
assert n_spikes > 0
assert spike_clusters.shape == (n_spikes,)
assert x.shape == (n_spikes,)
assert y.shape == (n_spikes,)
# Get the spike clusters.
sc = _index_of(spike_clusters, cluster_ids)
# Plot the amplitudes.
with self.building():
m = np.ones(n_spikes)
# Get the color of the markers.
color = _spike_colors(sc, masks=m)
assert color.shape == (n_spikes, 4)
ms = (self._default_marker_size if sc is not None else 1.)
self.scatter(x=x,
y=y,
color=color,
data_bounds=self.data_bounds,
size=ms * np.ones(n_spikes),
)
def _plot_waveforms(self, bunchs, bunchs_set, channel_ids, cluster_ids):
# Initialize the box scaling the first time.
if self.box_scaling[1] == 1.:
M = np.max([np.max(np.abs(b.data)) for b in bunchs])
self.box_scaling[1] = 1. / M
self._update_boxes()
clu_offsets = _get_clu_offsets(bunchs)
max_clu_offsets = max(clu_offsets) + 1
for i, d in enumerate(bunchs):
wave = d.data
alpha = d.get('alpha', .5)
channel_ids_loc = d.channel_ids
n_channels = len(channel_ids_loc)
masks = d.get('masks', np.ones((wave.shape[0], n_channels)))
# By default, this is 0, 1, 2 for the first 3 clusters.
# But it can be customized when displaying several sets
# of waveforms per cluster.
# i = cluster_ids.index(d.cluster_id) # 0, 1, 2, ...
n_spikes_clu, n_samples = wave.shape[:2]
assert wave.shape[2] == n_channels
assert masks.shape == (n_spikes_clu, n_channels)
# Find the x coordinates.
t = _get_linear_x(n_spikes_clu * n_channels, n_samples)
if not self.overlap:
# Determine the cluster offset.
offset = clu_offsets[i]
t = t + 2.5 * (offset - (max_clu_offsets - 1) / 2.)
# The total width should not depend on the number of
# clusters.
t /= max_clu_offsets
# Get the spike masks.
m = masks
# HACK: on the GPU, we get the actual masks with fract(masks)
# since we add the relative cluster index. We need to ensure
# that the masks is never 1.0, otherwise it is interpreted as
# 0.
m *= .99999
# NOTE: we add the cluster index which is used for the
# computation of the depth on the GPU.
m += i
color = tuple(_colormap(i)) + (alpha,)
assert len(color) == 4
# Generate the box index (one number per channel).
box_index = _index_of(channel_ids_loc, channel_ids)
box_index = np.repeat(box_index, n_samples)
box_index = np.tile(box_index, n_spikes_clu)
assert box_index.shape == (n_spikes_clu *
n_channels *
n_samples,)
# Generate the waveform array.
wave = np.transpose(wave, (0, 2, 1))
wave = wave.reshape((n_spikes_clu * n_channels, n_samples))
self.uplot(x=t,
y=wave,
color=color,
masks=m,
box_index=box_index,
data_bounds=None,
)
for i, d in enumerate(bunchs_set):
wave = d.data ##### Equivalent to the data of module CellTypes.py
clIds = str(cluster_ids).replace(' ', '')
color = tuple(_colormap(i)) + (alpha,)
color=color[:3]+(0.3,)
#np.save('/home/ms047/Desktop/waveform385%s.npy'%clIds, wave)
# Generate the waveform array.
plot_wvf_feat_vispy(self, wave, color, i)
def correlograms(spike_times,
spike_clusters,
cluster_ids=None,
sample_rate=1.,
bin_size=None,
window_size=None,
symmetrize=True,
):
"""Compute all pairwise cross-correlograms among the clusters appearing
in `spike_clusters`.
Parameters
----------
spike_times : array-like
Spike times in seconds.
spike_clusters : array-like
Spike-cluster mapping.
cluster_ids : array-like
The list of unique clusters, in any order. That order will be used
in the output array.
bin_size : float
Size of the bin, in seconds.
window_size : float
Size of the window, in seconds.
Returns
-------
correlograms : array
A `(n_clusters, n_clusters, winsize_samples)` array with all pairwise
CCGs.
"""
assert sample_rate > 0.
assert np.all(np.diff(spike_times) >= 0), ("The spike times must be "
"increasing.")
# Get the spike samples.
spike_times = np.asarray(spike_times, dtype=np.float64)
spike_samples = (spike_times * sample_rate).astype(np.int64)
spike_clusters = _as_array(spike_clusters)
assert spike_samples.ndim == 1
assert spike_samples.shape == spike_clusters.shape
# Find `binsize`.
bin_size = np.clip(bin_size, 1e-5, 1e5) # in seconds
binsize = int(sample_rate * bin_size) # in samples
assert binsize >= 1
# Find `winsize_bins`.
window_size = np.clip(window_size, 1e-5, 1e5) # in seconds
winsize_bins = 2 * int(.5 * window_size / bin_size) + 1
assert winsize_bins >= 1
assert winsize_bins % 2 == 1
# Take the cluster oder into account.
if cluster_ids is None:
clusters = _unique(spike_clusters)
else:
clusters = _as_array(cluster_ids)
n_clusters = len(clusters)
# Like spike_clusters, but with 0..n_clusters-1 indices.
spike_clusters_i = _index_of(spike_clusters, clusters)
# Shift between the two copies of the spike trains.
shift = 1
# At a given shift, the mask precises which spikes have matching spikes
# within the correlogram time window.
mask = np.ones_like(spike_samples, dtype=np.bool)
correlograms = _create_correlograms_array(n_clusters, winsize_bins)
# The loop continues as long as there is at least one spike with
# a matching spike.
while mask[:-shift].any():
# Number of time samples between spike i and spike i+shift.
spike_diff = _diff_shifted(spike_samples, shift)
# Binarize the delays between spike i and spike i+shift.
spike_diff_b = spike_diff // binsize
# Spikes with no matching spikes are masked.
mask[:-shift][spike_diff_b > (winsize_bins // 2)] = False
# Cache the masked spike delays.
m = mask[:-shift].copy()
d = spike_diff_b[m]
# # Update the masks given the clusters to update.
# m0 = np.in1d(spike_clusters[:-shift], clusters)
# m = m & m0
# d = spike_diff_b[m]
d = spike_diff_b[m]
# Find the indices in the raveled correlograms array that need
# to be incremented, taking into account the spike clusters.
indices = np.ravel_multi_index((spike_clusters_i[:-shift][m],
spike_clusters_i[+shift:][m],
d),
correlograms.shape)
# Increment the matching spikes in the correlograms array.
_increment(correlograms.ravel(), indices)
shift += 1
# Remove ACG peaks.
correlograms[np.arange(n_clusters),
np.arange(n_clusters),
0] = 0
if symmetrize:
return _symmetrize_correlograms(correlograms)
else:
return correlograms
def correlograms(
spike_times,
spike_clusters,
cluster_ids=None,
sample_rate=1.,
bin_size=None,
window_size=None,
symmetrize=True,
):
"""Compute all pairwise cross-correlograms among the clusters appearing
in `spike_clusters`.
Parameters
----------
spike_times : array-like
Spike times in seconds.
spike_clusters : array-like
Spike-cluster mapping.
cluster_ids : array-like
The list of unique clusters, in any order. That order will be used
in the output array.
bin_size : float
Size of the bin, in seconds.
window_size : float
Size of the window, in seconds.
Returns
-------
correlograms : array
A `(n_clusters, n_clusters, winsize_samples)` array with all pairwise
CCGs.
"""
assert sample_rate > 0.
assert np.all(np.diff(spike_times) >= 0), ("The spike times must be "
"increasing.")
# Get the spike samples.
spike_times = np.asarray(spike_times, dtype=np.float64)
spike_samples = (spike_times * sample_rate).astype(np.int64)
spike_clusters = _as_array(spike_clusters)
assert spike_samples.ndim == 1
assert spike_samples.shape == spike_clusters.shape
# Find `binsize`.
bin_size = np.clip(bin_size, 1e-5, 1e5) # in seconds
binsize = int(sample_rate * bin_size) # in samples
assert binsize >= 1
# Find `winsize_bins`.
window_size = np.clip(window_size, 1e-5, 1e5) # in seconds
winsize_bins = 2 * int(.5 * window_size / bin_size) + 1
assert winsize_bins >= 1
assert winsize_bins % 2 == 1
# Take the cluster oder into account.
if cluster_ids is None:
clusters = _unique(spike_clusters)
else:
clusters = _as_array(cluster_ids)
n_clusters = len(clusters)
# Like spike_clusters, but with 0..n_clusters-1 indices.
spike_clusters_i = _index_of(spike_clusters, clusters)
# Shift between the two copies of the spike trains.
shift = 1
# At a given shift, the mask precises which spikes have matching spikes
# within the correlogram time window.
mask = np.ones_like(spike_samples, dtype=np.bool)
correlograms = _create_correlograms_array(n_clusters, winsize_bins)
# The loop continues as long as there is at least one spike with
# a matching spike.
while mask[:-shift].any():
# Number of time samples between spike i and spike i+shift.
spike_diff = _diff_shifted(spike_samples, shift)
# Binarize the delays between spike i and spike i+shift.
spike_diff_b = spike_diff // binsize
# Spikes with no matching spikes are masked.
mask[:-shift][spike_diff_b > (winsize_bins // 2)] = False
# Cache the masked spike delays.
m = mask[:-shift].copy()
d = spike_diff_b[m]
# # Update the masks given the clusters to update.
# m0 = np.in1d(spike_clusters[:-shift], clusters)
# m = m & m0
# d = spike_diff_b[m]
d = spike_diff_b[m]
# Find the indices in the raveled correlograms array that need
# to be incremented, taking into account the spike clusters.
indices = np.ravel_multi_index(
(spike_clusters_i[:-shift][m], spike_clusters_i[+shift:][m], d),
correlograms.shape)
# Increment the matching spikes in the correlograms array.
_increment(correlograms.ravel(), indices)
shift += 1
# Remove ACG peaks.
correlograms[np.arange(n_clusters), np.arange(n_clusters), 0] = 0
if symmetrize:
return _symmetrize_correlograms(correlograms)
else:
return correlograms
def on_select(self, cluster_ids=None):
super(WaveformView, self).on_select(cluster_ids)
cluster_ids = self.cluster_ids
n_clusters = len(cluster_ids)
if n_clusters == 0:
return
# Load the waveform subset.
data = self.waveforms(cluster_ids)
# Take one element in the list.
data = data[self.data_index % len(data)]
alpha = data.get('alpha', .5)
spike_ids = data.spike_ids
spike_clusters = data.spike_clusters
w = data.data
masks = data.masks
n_spikes = len(spike_ids)
assert w.ndim == 3
n_samples = w.shape[1]
assert w.shape == (n_spikes, n_samples, self.n_channels)
assert masks.shape == (n_spikes, self.n_channels)
# Relative spike clusters.
spike_clusters_rel = _index_of(spike_clusters, cluster_ids)
assert spike_clusters_rel.shape == (n_spikes,)
# Fetch the waveforms.
t = _get_linear_x(n_spikes, n_samples)
# Overlap.
if not self.overlap:
t = t + 2.5 * (spike_clusters_rel[:, np.newaxis] -
(n_clusters - 1) / 2.)
# The total width should not depend on the number of clusters.
t /= n_clusters
# Plot all waveforms.
# OPTIM: avoid the loop.
with self.building():
for ch in range(self.n_channels):
m = masks[:, ch]
depth = _get_depth(m,
spike_clusters_rel=spike_clusters_rel,
n_clusters=n_clusters)
color = _spike_colors(spike_clusters_rel,
masks=m,
alpha=alpha,
)
self[ch].plot(x=t, y=w[:, :, ch],
color=color,
depth=depth,
data_bounds=self.data_bounds,
)
# Add channel labels.
self[ch].text(pos=[[t[0, 0], 0.]],
text=str(ch),
anchor=[-1.01, -.25],
data_bounds=self.data_bounds,
)
# Zoom on the best channels when selecting clusters.
channels = self.best_channels(cluster_ids)
if channels is not None and self.do_zoom_on_channels:
self.zoom_on_channels(channels)
def on_select(self, cluster_ids=None):
super(FeatureView, self).on_select(cluster_ids)
cluster_ids = self.cluster_ids
n_clusters = len(cluster_ids)
if n_clusters == 0:
return
# Get the spikes, features, masks.
data = self.features(cluster_ids)
spike_ids = data.spike_ids
spike_clusters = data.spike_clusters
f = data.data
masks = data.masks
assert f.ndim == 3
assert masks.ndim == 2
assert spike_ids.shape[0] == f.shape[0] == masks.shape[0]
# Get the spike clusters.
sc = _index_of(spike_clusters, cluster_ids)
# Get the background features.
data_bg = self.background_features
if data_bg is not None:
spike_ids_bg = data_bg.spike_ids
features_bg = data_bg.data
masks_bg = data_bg.masks
# Select the dimensions.
# Choose the channels automatically unless fixed_channels is set.
if (not self.fixed_channels or self.channels is None):
self.channels = self._get_channel_dims(cluster_ids)
tla = self.top_left_attribute
assert self.channels
x_dim, y_dim = _dimensions_matrix(self.channels,
n_cols=self.n_cols,
top_left_attribute=tla)
# Set the status message.
ch = ', '.join(map(str, self.channels))
self.set_status('Channels: {}'.format(ch))
# Set a non-time attribute as y coordinate in the top-left subplot.
attrs = sorted(self.attributes)
attrs.remove('time')
if attrs:
y_dim[0, 0] = attrs[0]
# Plot all features.
with self.building():
for i in range(self.n_cols):
for j in range(self.n_cols):
# Retrieve the x and y values for the subplot.
x = self._get_feature(x_dim[i, j], spike_ids, f)
y = self._get_feature(y_dim[i, j], spike_ids, f)
if data_bg is not None:
# Retrieve the x and y values for the background
# spikes.
x_bg = self._get_feature(x_dim[i, j], spike_ids_bg,
features_bg)
y_bg = self._get_feature(y_dim[i, j], spike_ids_bg,
features_bg)
# Background features.
self._plot_features(i, j, x_dim, y_dim, x_bg, y_bg,
masks=masks_bg)
# Cluster features.
self._plot_features(i, j, x_dim, y_dim, x, y,
masks=masks,
spike_clusters_rel=sc)
# Add axes.
self[i, j].lines(pos=[[-1., 0., +1., 0.],
[0., -1., 0., +1.]],
color=(.25, .25, .25, .5))
# Add the boxes.
self.grid.add_boxes(self, self.shape)
def _plot_waveforms(self, bunchs, channel_ids):
# Initialize the box scaling the first time.
if self.box_scaling[1] == 1.:
M = np.max([np.max(np.abs(b.data)) for b in bunchs])
self.box_scaling[1] = 1. / M
self._update_boxes()
clu_offsets = _get_clu_offsets(bunchs)
max_clu_offsets = max(clu_offsets) + 1
for i, d in enumerate(bunchs):
wave = d.data
alpha = d.get('alpha', .5)
channel_ids_loc = d.channel_ids
n_channels = len(channel_ids_loc)
masks = d.get('masks', np.ones((wave.shape[0], n_channels)))
# By default, this is 0, 1, 2 for the first 3 clusters.
# But it can be customized when displaying several sets
# of waveforms per cluster.
# i = cluster_ids.index(d.cluster_id) # 0, 1, 2, ...
n_spikes_clu, n_samples = wave.shape[:2]
assert wave.shape[2] == n_channels
assert masks.shape == (n_spikes_clu, n_channels)
# Find the x coordinates.
t = _get_linear_x(n_spikes_clu * n_channels, n_samples)
if not self.overlap:
# Determine the cluster offset.
offset = clu_offsets[i]
t = t + 2.5 * (offset - (max_clu_offsets - 1) / 2.)
# The total width should not depend on the number of
# clusters.
t /= max_clu_offsets
# Get the spike masks.
m = masks
# HACK: on the GPU, we get the actual masks with fract(masks)
# since we add the relative cluster index. We need to ensure
# that the masks is never 1.0, otherwise it is interpreted as
# 0.
m *= .99999
# NOTE: we add the cluster index which is used for the
# computation of the depth on the GPU.
m += i
color = tuple(_colormap(i)) + (alpha,)
assert len(color) == 4
# Generate the box index (one number per channel).
box_index = _index_of(channel_ids_loc, channel_ids)
box_index = np.repeat(box_index, n_samples)
box_index = np.tile(box_index, n_spikes_clu)
assert box_index.shape == (n_spikes_clu *
n_channels *
n_samples,)
# Generate the waveform array.
wave = np.transpose(wave, (0, 2, 1))
wave = wave.reshape((n_spikes_clu * n_channels, n_samples))
self.uplot(x=t,
y=wave,
color=color,
masks=m,
box_index=box_index,
data_bounds=None,
)