def load(self,
channel_colors=None,
channel_groups=None,
channel_names=None,
group_colors=None,
group_names=None,
background={}):
if group_names is None or channel_colors is None:
return
# Create the tree.
# go through all groups
for groupidx, groupname in group_names.iteritems():
groupitem = self.add_group_node(groupidx=groupidx,
name=groupname,
color=select(
group_colors, groupidx))
# go through all channels
for channelidx, color in channel_colors.iteritems():
# add channel
bgcolor = background.get(channelidx, None)
channelitem = self.add_channel(name=channel_names[channelidx],
channelidx=channelidx,
color=color,
bgcolor=None,
parent=self.get_group(
select(channel_groups,
channelidx)))
def test_select_array():
# All spikes in cluster 1.
indices = [10, 20, 25]
# Indices in data excerpt.
indices_data = [5, 10, 15, 20]
# Generate clusters and data.
clusters = generate_clusters(indices)
data_raw = generate_data2D()
data = pd.DataFrame(data_raw)
# Excerpt of the data.
data_excerpt = select(data, indices_data)
# Get all spike indices in cluster 1.
spikes_inclu1 = get_spikes_in_clusters([1], clusters)
# We want to select all clusters in cluster 1 among those in data excerpt.
data_excerpt_inclu1 = select(data_excerpt, spikes_inclu1)
# There should be two rows: 4 in the excerpt, among which two are in
# cluster 1.
assert data_excerpt_inclu1.shape == (2, 5)
def split_clusters_undo(self, clusters, clusters_old, cluster_groups,
cluster_colors, clusters_new):
if not hasattr(clusters, '__len__'):
clusters = [clusters]
spikes = get_indices(clusters_old)
# Find groups and colors of old clusters.
cluster_indices_old = np.unique(clusters_old)
cluster_indices_new = np.unique(clusters_new)
# Add clusters that were removed after the split operation.
clusters_empty = sorted(set(cluster_indices_old) -
set(cluster_indices_new))
self.loader.add_clusters(
clusters_empty,
select(cluster_groups, clusters_empty),
# select(cluster_colors, clusters_empty),
)
# Set the new clusters to the corresponding spikes.
self.loader.set_cluster(spikes, clusters_old)
# Remove empty clusters.
clusters_empty = self.loader.remove_empty_clusters()
self.loader.unselect()
return dict(clusters_to_split=clusters,
clusters_split=get_array(cluster_indices_new),
# clusters_empty=clusters_empty
)
def split_clusters_undo(self, clusters, clusters_old, cluster_groups,
cluster_colors, clusters_new):
if not hasattr(clusters, '__len__'):
clusters = [clusters]
spikes = get_indices(clusters_old)
# Find groups and colors of old clusters.
cluster_indices_old = np.unique(clusters_old)
cluster_indices_new = np.unique(clusters_new)
# Add clusters that were removed after the split operation.
clusters_empty = sorted(
set(cluster_indices_old) - set(cluster_indices_new))
self.loader.add_clusters(
clusters_empty,
select(cluster_groups, clusters_empty),
# select(cluster_colors, clusters_empty),
)
# Set the new clusters to the corresponding spikes.
self.loader.set_cluster(spikes, clusters_old)
# Remove empty clusters.
clusters_empty = self.loader.remove_empty_clusters()
self.loader.unselect()
return dict(
clusters_to_split=clusters,
clusters_split=get_array(cluster_indices_new),
# clusters_empty=clusters_empty
)
def test_select_pytables():
a = np.random.randn(100, 10)
path = generate_earray(a)
f = tb.openFile(path, 'r')
arr = f.root.arr
s = select(arr, slice(0, 10, 2))
assert isinstance(s, pd.DataFrame)
assert s.shape == (5, 10)
assert np.array_equal(select(arr, 10), arr[[10], :])
assert np.array_equal(select(arr, [10]), arr[[10], :])
assert np.array_equal(select(arr, [10, 20]), arr[[10, 20], :])
assert np.array_equal(select(arr, slice(10, 20)), arr[10:20, :])
f.close()
os.remove(path)
def cluster_quality(waveforms, features, clusters, masks,
clusters_selected=None):
# clusters = select(clusters, spikes)
# features = select(features, spikes)
# waveforms = select(waveforms, spikes)
# masks = select(masks, spikes)
nspikes, nsamples, nchannels = waveforms.shape
quality = {}
for cluster in clusters_selected:
spikes = get_spikes_in_clusters(cluster, clusters)
w = select(waveforms, spikes)
m = select(masks, spikes)
q = 1. / nsamples * ((w ** 2).sum(axis=1) * 1).mean(axis=1).max()
quality[cluster] = q
return quality
def test_select_pytables():
a = np.random.randn(100, 10)
path = generate_earray(a)
f = tb.openFile(path, 'r')
arr = f.root.arr
s = select(arr, slice(0, 10, 2))
assert isinstance(s, pd.DataFrame)
assert s.shape == (5, 10)
assert np.array_equal(select(arr, 10), arr[[10], :])
assert np.array_equal(select(arr, [10]), arr[[10], :])
assert np.array_equal(select(arr, [10, 20]), arr[[10, 20], :])
assert np.array_equal(select(arr, slice(10, 20)), arr[10:20, :])
f.close()
os.remove(path)
def cluster_quality(waveforms, features, clusters, masks,
clusters_selected=None):
# clusters = select(clusters, spikes)
# features = select(features, spikes)
# waveforms = select(waveforms, spikes)
# masks = select(masks, spikes)
nspikes, nsamples, nchannels = waveforms.shape
quality = {}
for cluster in clusters_selected:
spikes = get_spikes_in_clusters(cluster, clusters)
w = select(waveforms, spikes)
m = select(masks, spikes)
q = 1. / nsamples * ((w ** 2).sum(axis=1) * 1).mean(axis=1).max()
quality[cluster] = q
return quality
def load(self,
cluster_colors=None,
cluster_groups=None,
group_colors=None,
group_names=None,
cluster_sizes=None,
cluster_quality=None,
background={}):
if group_names is None or cluster_colors is None:
return
# Create the tree.
# go through all groups
for groupidx, groupname in group_names.iteritems():
spkcount = np.sum(cluster_sizes[cluster_groups == groupidx])
groupitem = self.add_group_node(
groupidx=groupidx,
name=groupname,
# color=group_colors[groupidx], spkcount=spkcount)
color=select(group_colors, groupidx),
spkcount=spkcount)
# go through all clusters
for clusteridx, color in cluster_colors.iteritems():
if cluster_quality is not None:
try:
quality = get_array(select(cluster_quality, clusteridx))[0]
except IndexError:
quality = 0.
else:
quality = 0.
# add cluster
bgcolor = background.get(clusteridx, None)
clusteritem = self.add_cluster(
clusteridx=clusteridx,
# name=info.names[clusteridx],
color=color,
bgcolor=bgcolor,
quality=quality,
# spkcount=cluster_sizes[clusteridx],
spkcount=select(cluster_sizes, clusteridx),
# assign the group as a parent of this cluster
parent=self.get_group(select(cluster_groups, clusteridx)))
def auto_projection(self, target):
fet = get_array(select(self.data_manager.features,
self.data_manager.clusters == target))
n = fet.shape[1]
fet = np.abs(fet[:,0:n-self.nextrafet:self.fetdim]).mean(axis=0)
channels_best = np.argsort(fet)[::-1]
channel0 = channels_best[0]
channel1 = channels_best[1]
self.set_projection(0, channel0, 0)
self.set_projection(1, channel1, 0)
self.parent.projectionChanged.emit(0, channel0, 0)
self.parent.projectionChanged.emit(1, channel1, 0)
def auto_projection(self, target):
fet = select(self.data_manager.features,
self.data_manager.clusters == target)
n = fet.shape[1]
fet = np.abs(fet.values[:,
0:n - self.nextrafet:self.fetdim]).mean(axis=0)
channels_best = np.argsort(fet)[::-1]
channel0 = channels_best[0]
channel1 = channels_best[1]
self.set_projection(0, channel0, 0)
self.set_projection(1, channel1, 0)
self.parent.projectionChanged.emit(0, channel0, 0)
self.parent.projectionChanged.emit(1, channel1, 0)
def load(self, channel_colors=None, channel_groups=None,
channel_names=None, group_colors=None, group_names=None,
background={}):
if group_names is None or channel_colors is None:
return
# Create the tree.
# go through all groups
for groupidx, groupname in group_names.iteritems():
groupitem = self.add_group_node(groupidx=groupidx, name=groupname,
color=select(group_colors, groupidx))
# go through all channels
for channelidx, color in channel_colors.iteritems():
# add channel
bgcolor = background.get(channelidx, None)
channelitem = self.add_channel(
name=channel_names[channelidx],
channelidx=channelidx,
color=color,
bgcolor=None,
parent=self.get_group(select(channel_groups, channelidx)))
def load(self, cluster_colors=None, cluster_groups=None,
group_colors=None, group_names=None, cluster_sizes=None,
cluster_quality=None, background={}):
if group_names is None or cluster_colors is None:
return
# Create the tree.
# go through all groups
for groupidx, groupname in group_names.iteritems():
spkcount = np.sum(cluster_sizes[cluster_groups == groupidx])
groupitem = self.add_group_node(groupidx=groupidx, name=groupname,
# color=group_colors[groupidx], spkcount=spkcount)
color=select(group_colors, groupidx), spkcount=spkcount)
# go through all clusters
for clusteridx, color in cluster_colors.iteritems():
if cluster_quality is not None:
try:
quality = select(cluster_quality, clusteridx)
except IndexError:
quality = 0.
else:
quality = 0.
# add cluster
bgcolor = background.get(clusteridx, None)
clusteritem = self.add_cluster(
clusteridx=clusteridx,
# name=info.names[clusteridx],
color=color,
bgcolor=bgcolor,
quality=quality,
# spkcount=cluster_sizes[clusteridx],
spkcount=select(cluster_sizes, clusteridx),
# assign the group as a parent of this cluster
parent=self.get_group(select(cluster_groups, clusteridx)))
def test_select_pandas():
indices = [10, 20, 25]
clusters = generate_clusters(indices)
# test selection of Series (1D)
clusters = pd.Series(clusters)
assert np.array_equal(select(clusters, [9, 11]), [0, 0])
assert np.array_equal(select(clusters, [10, 99]), [1, 0])
assert np.array_equal(select(clusters, [20, 25, 25]), [1, 1, 1])
# test selection of Series (3D)
clusters = pd.DataFrame(clusters)
assert np.array_equal(np.array(select(clusters, [9, 11])).ravel(), [0, 0])
assert np.array_equal(np.array(select(clusters, [10, 99])).ravel(), [1, 0])
assert np.array_equal(np.array(select(clusters, [20, 25, 25])).ravel(), [1, 1, 1])
# test selection of Panel (4D)
clusters = pd.Panel(np.expand_dims(clusters, 3))
assert np.array_equal(np.array(select(clusters, [9, 11])).ravel(), [0, 0])
assert np.array_equal(np.array(select(clusters, [10, 99])).ravel(), [1, 0])
def test_select_pandas():
indices = [10, 20, 25]
clusters = generate_clusters(indices)
# test selection of Series (1D)
clusters = pd.Series(clusters)
assert np.array_equal(select(clusters, [9, 11]), [0, 0])
assert np.array_equal(select(clusters, [10, 99]), [1, 0])
assert np.array_equal(select(clusters, [20, 25, 25]), [1, 1, 1])
# test selection of Series (3D)
clusters = pd.DataFrame(clusters)
assert np.array_equal(np.array(select(clusters, [9, 11])).ravel(), [0, 0])
assert np.array_equal(np.array(select(clusters, [10, 99])).ravel(), [1, 0])
assert np.array_equal(
np.array(select(clusters, [20, 25, 25])).ravel(), [1, 1, 1])
# test selection of Panel (4D)
clusters = pd.Panel(np.expand_dims(clusters, 3))
assert np.array_equal(np.array(select(clusters, [9, 11])).ravel(), [0, 0])
assert np.array_equal(np.array(select(clusters, [10, 99])).ravel(), [1, 0])
def set_data(self,
waveforms=None,
masks=None,
clusters=None,
# list of clusters that are selected, the order matters
clusters_selected=None,
cluster_colors=None,
geometrical_positions=None,
keep_order=None,
autozoom=None,
):
self.autozoom = autozoom
if clusters_selected is None:
clusters_selected = []
if waveforms is None:
waveforms = np.zeros((0, 1, 1))
masks = np.zeros((0, 1))
clusters = np.zeros(0, dtype=np.int32)
cluster_colors = np.zeros(0, dtype=np.int32)
clusters_selected = []
self.keep_order = keep_order
# Not all waveforms have been selected, so select the appropriate
# samples in clusters and masks.
self.waveform_indices = get_indices(waveforms)
self.waveform_indices_array = get_array(self.waveform_indices)
masks = select(masks, self.waveform_indices)
clusters = select(clusters, self.waveform_indices)
# Convert from Pandas into raw NumPy arrays.
self.waveforms_array = get_array(waveforms)
self.masks_array = get_array(masks)
self.clusters_array = get_array(clusters)
# Relative indexing.
if len(clusters_selected) > 0:
self.clusters_rel = np.array(np.digitize(self.clusters_array,
sorted(clusters_selected)) - 1, dtype=np.int32)
self.clusters_rel_ordered = (np.argsort(clusters_selected)
[self.clusters_rel]).astype(np.int32)
else:
self.clusters_rel = np.zeros(0, dtype=np.int32)
self.clusters_rel_ordered = np.zeros(0, dtype=np.int32)
if self.keep_order:
self.clusters_rel_ordered2 = self.clusters_rel_ordered
self.cluster_colors_array = get_array(cluster_colors, dosort=True)[np.argsort(clusters_selected)]
self.clusters_selected2 = clusters_selected
else:
self.clusters_rel_ordered2 = self.clusters_rel
self.cluster_colors_array = get_array(cluster_colors, dosort=True)
self.clusters_selected2 = sorted(clusters_selected)
self.nspikes, self.nsamples, self.nchannels = self.waveforms_array.shape
self.npoints = self.waveforms_array.size
self.geometrical_positions = geometrical_positions
self.clusters_selected = clusters_selected
self.clusters_unique = sorted(clusters_selected)
self.nclusters = len(clusters_selected)
self.waveforms = waveforms
self.clusters = clusters
# self.cluster_colors = cluster_colors
self.masks = masks
# Prepare GPU data.
self.data = self.prepare_waveform_data()
self.masks_full = np.repeat(self.masks_array.T.ravel(), self.nsamples)
self.clusters_full = np.tile(np.repeat(self.clusters_rel_ordered2, self.nsamples), self.nchannels)
self.clusters_full_depth = np.tile(np.repeat(self.clusters_rel_ordered, self.nsamples), self.nchannels)
self.channels_full = np.repeat(np.arange(self.nchannels, dtype=np.int32), self.nspikes * self.nsamples)
# Compute average waveforms.
self.data_avg = self.prepare_average_waveform_data()
self.masks_full_avg = np.repeat(self.masks_avg.T.ravel(), self.nsamples_avg)
self.clusters_full_avg = np.tile(np.repeat(self.clusters_rel_ordered_avg2, self.nsamples_avg), self.nchannels_avg)
self.clusters_full_depth_avg = np.tile(np.repeat(self.clusters_rel_ordered_avg, self.nsamples_avg), self.nchannels_avg)
self.channels_full_avg = np.repeat(np.arange(self.nchannels_avg, dtype=np.int32), self.nspikes_avg * self.nsamples_avg)
# position waveforms
self.position_manager.set_info(self.nchannels, self.nclusters,
geometrical_positions=self.geometrical_positions,)
# update the highlight manager
self.highlight_manager.initialize()
def test_select_single():
indices = [10, 20, 25]
clusters = generate_clusters(indices)
assert select(clusters, 10) == 1
def test_select_numpy():
indices = [10, 20, 25]
clusters = generate_clusters(indices)
assert np.array_equal(select(clusters, [9, 11]), [0, 0])
assert np.array_equal(select(clusters, [10, 99]), [1, 0])
assert np.array_equal(select(clusters, [20, 25, 25]), [1, 1, 1])
def test_select_numpy():
indices = [10, 20, 25]
clusters = generate_clusters(indices)
assert np.array_equal(select(clusters, [9, 11]), [0, 0])
assert np.array_equal(select(clusters, [10, 99]), [1, 0])
assert np.array_equal(select(clusters, [20, 25, 25]), [1, 1, 1])
def test_select_single():
indices = [10, 20, 25]
clusters = generate_clusters(indices)
assert select(clusters, 10) == 1
def set_data(self,
waveforms=None,
channels=None,
masks=None,
clusters=None,
# list of clusters that are selected, the order matters
clusters_selected=None,
cluster_colors=None,
geometrical_positions=None,
keep_order=None,
autozoom=None,
):
self.autozoom = autozoom
if clusters_selected is None:
clusters_selected = []
if waveforms is None:
waveforms = np.zeros((0, 1, 1))
masks = np.zeros((0, 1))
clusters = np.zeros(0, dtype=np.int32)
cluster_colors = np.zeros(0, dtype=np.int32)
clusters_selected = []
self.keep_order = keep_order
# Not all waveforms have been selected, so select the appropriate
# samples in clusters and masks.
self.waveform_indices = get_indices(waveforms)
self.waveform_indices_array = get_array(self.waveform_indices)
masks = select(masks, self.waveform_indices)
clusters = select(clusters, self.waveform_indices)
# Convert from Pandas into raw NumPy arrays.
self.waveforms_array = get_array(waveforms)
self.masks_array = get_array(masks)
self.clusters_array = get_array(clusters)
# Relative indexing.
if len(clusters_selected) > 0 and len(self.waveform_indices) > 0:
self.clusters_rel = np.array(np.digitize(self.clusters_array,
sorted(clusters_selected)) - 1, dtype=np.int32)
self.clusters_rel_ordered = (np.argsort(clusters_selected)
[self.clusters_rel]).astype(np.int32)
else:
self.clusters_rel = np.zeros(0, dtype=np.int32)
self.clusters_rel_ordered = np.zeros(0, dtype=np.int32)
if self.keep_order:
self.clusters_rel_ordered2 = self.clusters_rel_ordered
self.cluster_colors_array = get_array(cluster_colors, dosort=True)[np.argsort(clusters_selected)]
self.clusters_selected2 = clusters_selected
else:
self.clusters_rel_ordered2 = self.clusters_rel
self.cluster_colors_array = get_array(cluster_colors, dosort=True)
self.clusters_selected2 = sorted(clusters_selected)
self.nspikes, self.nsamples, self.nchannels = self.waveforms_array.shape
if channels is None:
channels = range(self.nchannels)
self.channels = channels
self.npoints = self.waveforms_array.size
self.geometrical_positions = geometrical_positions
self.clusters_selected = clusters_selected
self.clusters_unique = sorted(clusters_selected)
self.nclusters = len(clusters_selected)
self.waveforms = waveforms
self.clusters = clusters
# self.cluster_colors = cluster_colors
self.masks = masks
# Prepare GPU data.
self.data = self.prepare_waveform_data()
self.masks_full = np.repeat(self.masks_array.T.ravel(), self.nsamples)
self.clusters_full = np.tile(np.repeat(self.clusters_rel_ordered2, self.nsamples), self.nchannels)
self.clusters_full_depth = np.tile(np.repeat(self.clusters_rel_ordered, self.nsamples), self.nchannels)
self.channels_full = np.repeat(np.arange(self.nchannels, dtype=np.int32), self.nspikes * self.nsamples)
# Compute average waveforms.
self.data_avg = self.prepare_average_waveform_data()
self.masks_full_avg = np.repeat(self.masks_avg.T.ravel(), self.nsamples_avg)
self.clusters_full_avg = np.tile(np.repeat(self.clusters_rel_ordered_avg2, self.nsamples_avg), self.nchannels_avg)
self.clusters_full_depth_avg = np.tile(np.repeat(self.clusters_rel_ordered_avg, self.nsamples_avg), self.nchannels_avg)
self.channels_full_avg = np.repeat(np.arange(self.nchannels_avg, dtype=np.int32), self.nspikes_avg * self.nsamples_avg)
# position waveforms
self.position_manager.set_info(self.nchannels, self.nclusters,
geometrical_positions=self.geometrical_positions,)
# update the highlight manager
self.highlight_manager.initialize()
def prepare_average_waveform_data(self):
waveforms_avg = np.zeros((self.nclusters, self.nsamples, self.nchannels))
waveforms_std = np.zeros((self.nclusters, self.nsamples, self.nchannels))
self.masks_avg = np.zeros((self.nclusters, self.nchannels))
for i, cluster in enumerate(self.clusters_unique):
spike_indices = get_spikes_in_clusters(cluster, self.clusters)
w = select(self.waveforms, spike_indices)
m = select(self.masks, spike_indices)
waveforms_avg[i,...] = w.mean(axis=0)
waveforms_std[i,...] = w.std(axis=0).mean()
self.masks_avg[i,...] = m.mean(axis=0)
# create X coordinates
X = np.tile(np.linspace(-1., 1., self.nsamples),
(self.nchannels * self.nclusters, 1))
# create Y coordinates
if self.nclusters == 0:
Y = np.array([], dtype=np.float32)
thickness = np.array([], dtype=np.float32)
else:
Y = np.vstack(waveforms_avg)
thickness = np.vstack(waveforms_std).T.ravel()
# concatenate data
data = np.empty((X.size, 2), dtype=np.float32)
data[:,0] = X.ravel()
data[:,1] = Y.T.ravel()
if self.nclusters > 0:
# thicken
w = thickness.reshape((-1, 1))
n = waveforms_avg.size
Y = np.zeros((2 * n, 2))
u = np.zeros((n, 2))
u[1:,0] = -np.diff(data[:,1])
u[1:,1] = data[1,0] - data[0,0]
u[0,:] = u[1,:]
r = (u[:,0] ** 2 + u[:,1] ** 2) ** .5
r[r == 0.] = 1
u[:,0] /= r
u[:,1] /= r
Y[::2,:] = data - w * u
Y[1::2,:] = data + w * u
data_thickened = Y
else:
n = 0
data_thickened = data
self.nsamples_avg = self.nsamples * 2
self.npoints_avg = waveforms_avg.size * 2
self.nspikes_avg = self.nclusters
self.nclusters_avg = self.nclusters
self.nchannels_avg = self.nchannels
self.clusters_rel_avg = np.arange(self.nclusters, dtype=np.int32)
self.clusters_rel_ordered_avg = np.argsort(self.clusters_selected)[self.clusters_rel_avg]
if self.keep_order:
self.clusters_rel_ordered_avg2 = self.clusters_rel_ordered_avg
else:
self.clusters_rel_ordered_avg2 = self.clusters_rel_avg
return data_thickened
def prepare_average_waveform_data(self):
waveforms_avg = np.zeros((self.nclusters, self.nsamples, self.nchannels))
waveforms_std = np.zeros((self.nclusters, self.nsamples, self.nchannels))
self.masks_avg = np.zeros((self.nclusters, self.nchannels))
for i, cluster in enumerate(self.clusters_unique):
spike_indices = get_spikes_in_clusters(cluster, self.clusters)
w = select(self.waveforms, spike_indices)
m = select(self.masks, spike_indices)
waveforms_avg[i,...] = w.mean(axis=0)
waveforms_std[i,...] = w.std(axis=0).mean()
self.masks_avg[i,...] = m.mean(axis=0)
# create X coordinates
X = np.tile(np.linspace(-1., 1., self.nsamples),
(self.nchannels * self.nclusters, 1))
# create Y coordinates
if self.nclusters == 0:
Y = np.array([], dtype=np.float32)
thickness = np.array([], dtype=np.float32)
else:
Y = np.vstack(waveforms_avg)
thickness = np.vstack(waveforms_std).T.ravel()
# concatenate data
data = np.empty((X.size, 2), dtype=np.float32)
data[:,0] = X.ravel()
data[:,1] = Y.T.ravel()
if self.nclusters > 0:
# thicken
w = thickness.reshape((-1, 1))
n = waveforms_avg.size
Y = np.zeros((2 * n, 2))
u = np.zeros((n, 2))
u[1:,0] = -np.diff(data[:,1])
u[1:,1] = data[1,0] - data[0,0]
u[0,:] = u[1,:]
r = (u[:,0] ** 2 + u[:,1] ** 2) ** .5
r[r == 0.] = 1
u[:,0] /= r
u[:,1] /= r
Y[::2,:] = data - w * u
Y[1::2,:] = data + w * u
data_thickened = Y
else:
n = 0
data_thickened = data
self.nsamples_avg = self.nsamples * 2
self.npoints_avg = waveforms_avg.size * 2
self.nspikes_avg = self.nclusters
self.nclusters_avg = self.nclusters
self.nchannels_avg = self.nchannels
self.clusters_rel_avg = np.arange(self.nclusters, dtype=np.int32)
self.clusters_rel_ordered_avg = np.argsort(self.clusters_selected)[self.clusters_rel_avg]
if self.keep_order:
self.clusters_rel_ordered_avg2 = self.clusters_rel_ordered_avg
else:
self.clusters_rel_ordered_avg2 = self.clusters_rel_avg
return data_thickened
def set_data(self,
features=None,
features_background=None,
spiketimes=None, # a subset of all spikes, disregarding cluster
masks=None, # masks for all spikes in selected clusters
clusters=None, # clusters for all spikes in selected clusters
clusters_selected=None,
cluster_colors=None,
fetdim=None,
nchannels=None,
channels=None,
nextrafet=None,
autozoom=None, # None, or the target cluster
duration=None,
freq=None,
alpha_selected=.75,
alpha_background=.25,
time_unit=None,
):
if features is None:
features = np.zeros((0, 2))
features_background = np.zeros((0, 2))
masks = np.zeros((0, 1))
clusters = np.zeros(0, dtype=np.int32)
clusters_selected = []
cluster_colors = np.zeros(0, dtype=np.int32)
fetdim = 2
nchannels = 1
nextrafet = 0
if features.shape[1] == 1:
features = np.tile(features, (1, 4))
if features_background.shape[1] == 1:
features_background = np.tile(features_background, (1, 4))
assert fetdim is not None
self.duration = duration
self.spiketimes = spiketimes
self.freq = freq
self.interaction_manager.get_processor('grid').update_viewbox()
# Feature background alpha value.
self.alpha_selected = alpha_selected
self.alpha_background = alpha_background
# can be 'second' or 'samples'
self.time_unit = time_unit
# Extract the relevant spikes, but keep the other ones in features_full
self.clusters = clusters
# Contains all spikes, needed for splitting.
self.features_full = features
self.features_full_array = get_array(features)
# Keep a subset of all spikes in the view.
self.nspikes_full = len(features)
# > features_nspikes_per_cluster_max spikes ==> take a selection
nspikes_max = USERPREF.get('features_nspikes_per_cluster_max', 1000)
k = self.nspikes_full // nspikes_max + 1
# self.features = features[::k]
subsel = slice(None, None, k)
self.features = select(features, subsel)
self.features_array = get_array(self.features)
# self.features_background contains all non-selected spikes
self.features_background = features_background
self.features_background_array = get_array(self.features_background)
# Background spikes are those which do not belong to the selected clusters
self.npoints_background = self.features_background_array.shape[0]
self.nspikes_background = self.npoints_background
if channels is None:
channels = range(nchannels)
self.nspikes, self.ndim = self.features.shape
self.fetdim = fetdim
self.nchannels = nchannels
self.channels = channels
self.nextrafet = nextrafet
self.npoints = self.features.shape[0]
if masks is None:
masks = np.ones_like(self.features, dtype=np.float32)
self.masks = masks
# Subselection
self.masks = select(self.masks, subsel)
self.masks_array = get_array(self.masks)
if self.spiketimes is not None:
self.spiketimes = select(self.spiketimes, subsel)
self.clusters = select(self.clusters, subsel)
self.clusters_array = get_array(self.clusters)
self.feature_indices = get_indices(self.features)
self.feature_full_indices = get_indices(self.features_full)
self.feature_indices_array = get_array(self.feature_indices)
self.cluster_colors = get_array(cluster_colors, dosort=True)
# Relative indexing.
if self.npoints > 0:
self.clusters_rel = np.digitize(self.clusters_array, sorted(clusters_selected)) - 1
self.clusters_rel_ordered = np.argsort(clusters_selected)[self.clusters_rel]
else:
self.clusters_rel = np.zeros(0, dtype=np.int32)
self.clusters_rel_ordered = np.zeros(0, dtype=np.int32)
self.clusters_unique = sorted(clusters_selected)
self.nclusters = len(clusters_selected)
self.masks_full = self.masks_array.T.ravel()
self.clusters_full_depth = self.clusters_rel_ordered
self.clusters_full = self.clusters_rel
# prepare GPU data
self.data = np.empty((self.nspikes, 2), dtype=np.float32)
self.data_full = np.empty((self.nspikes_full, 2), dtype=np.float32)
self.data_background = np.empty((self.nspikes_background, 2),
dtype=np.float32)
# set initial projection
self.projection_manager.set_data()
self.autozoom = autozoom
if autozoom is None:
self.projection_manager.reset_projection()
else:
self.projection_manager.auto_projection(autozoom)
# update the highlight manager
self.highlight_manager.initialize()
self.selection_manager.initialize()
self.selection_manager.cancel_selection()