def test_controller_misc():
l, c = load()
# Select three clusters
clusters = [2, 4, 6]
spikes = l.get_spikes(clusters=clusters)
cluster_spikes = l.get_clusters(clusters=clusters)
# Merge these clusters.
action, output = c.merge_clusters(clusters)
cluster_new = output['cluster_merged']
assert np.array_equal(l.get_spikes(cluster_new), spikes)
assert np.all(~np.in1d(clusters, get_indices(l.get_cluster_groups('all'))))
# Undo.
assert c.can_undo()
c.undo()
assert np.array_equal(l.get_spikes(cluster_new), [])
assert np.all(np.in1d(clusters, get_indices(l.get_cluster_groups('all'))))
assert np.array_equal(l.get_clusters(clusters=clusters), cluster_spikes)
# Move clusters.
action, output = c.move_clusters(clusters, 0)
assert action == 'move_clusters'
# assert np.array_equal(output['to_select'], [7])
assert np.all(l.get_cluster_groups(clusters) == 0)
assert c.can_undo()
assert not c.can_redo()
# Undo
action, output = c.undo()
assert action == 'move_clusters_undo'
# assert np.array_equal(output['to_select'], clusters)
assert np.all(l.get_cluster_groups(clusters) == 3)
assert not c.can_undo()
assert c.can_redo()
# Merge clusters.
c.merge_clusters(clusters)
assert c.can_undo()
assert not c.can_redo()
l.close()
def test_controller_merge():
l, c = load()
# Select three clusters
clusters = [2, 4, 6]
spikes = l.get_spikes(clusters=clusters)
cluster_spikes = l.get_clusters(clusters=clusters)
# Select half of the spikes in these clusters.
spikes_sample = spikes[::2]
# Merge these clusters.
action, output = c.merge_clusters(clusters)
cluster_new = output['cluster_merged']
assert action == 'merge_clusters'
assert np.array_equal(output['cluster_merged'], cluster_new)
assert np.array_equal(output['clusters_to_merge'],
sorted(set(clusters)))
assert np.array_equal(l.get_spikes(cluster_new), spikes)
assert np.all(~np.in1d(clusters, get_indices(l.get_cluster_groups('all'))))
# Undo.
assert c.can_undo()
action, output = c.undo()
assert action == 'merge_clusters_undo'
assert np.array_equal(output['cluster_merged'], cluster_new)
assert np.array_equal(output['clusters_to_merge'],
sorted(set(clusters)))
assert np.array_equal(l.get_spikes(cluster_new), [])
assert np.all(np.in1d(clusters, get_indices(l.get_cluster_groups('all'))))
assert np.array_equal(l.get_clusters(clusters=clusters), cluster_spikes)
# Redo.
assert c.can_redo()
action, output = c.redo()
assert action == 'merge_clusters'
assert np.array_equal(output['cluster_merged'], cluster_new)
assert np.array_equal(output['clusters_to_merge'],
sorted(set(clusters)))
assert np.array_equal(l.get_spikes(cluster_new), spikes)
assert np.all(~np.in1d(clusters, get_indices(l.get_cluster_groups('all'))))
l.close()
def test_clusterview():
keys = ('cluster_groups,group_colors,group_names,'
'cluster_sizes').split(',')
data = get_data()
kwargs = {k: data[k] for k in keys}
kwargs['cluster_colors'] = data['cluster_colors_full']
# kwargs['background'] = {5: 1, 7: 2}
clusters = get_indices(data['cluster_sizes'])
quality = pd.Series(np.random.rand(len(clusters)), index=clusters)
kwargs['cluster_quality'] = quality
kwargs['operators'] = [
lambda self: self.view.set_quality(quality),
lambda self: self.view.set_background({
5: 1,
7: 2
}),
lambda self: self.view.set_background({6: 3}),
lambda self: self.view.set_background({}),
lambda self: (self.close()
if USERPREF['test_auto_close'] != False else None),
]
# Show the view.
window = show_view(ClusterView, **kwargs)
def set_data(
self,
similarity_matrix=None,
cluster_colors_full=None,
clusters_hidden=[],
):
if similarity_matrix is None:
similarity_matrix = np.zeros(0)
cluster_colors_full = np.zeros(0)
if similarity_matrix.size == 0:
similarity_matrix = -np.ones((2, 2))
elif similarity_matrix.shape[0] == 1:
similarity_matrix = -np.ones((2, 2))
self.similarity_matrix = similarity_matrix
n = similarity_matrix.shape[0]
self.texture = colormap(similarity_matrix)
# similarity_matrix axes are originally (x, y) from the lower left corner
# but when displayed, they are (i, j) from the upper left corner
# so we need to transpose
self.texture = np.swapaxes(self.texture, 0, 1)[::-1, :, :]
# Hide some clusters.
tex0 = self.texture.copy()
for clu in clusters_hidden:
# Inversion of axes in the y axis
self.texture[-clu - 1, :, :] = tex0[-clu - 1, :, :] * .5
self.texture[:, clu, :] = tex0[:, clu, :] * .5
self.clusters_unique = get_indices(cluster_colors_full)
self.cluster_colors = cluster_colors_full
self.nclusters = len(self.clusters_unique)
def split_clusters(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)
# Get group and color of the new clusters, from the old clusters.
groups = self.loader.get_cluster_groups(cluster_indices_old)
# colors = self.loader.get_cluster_colors(cluster_indices_old)
# Add clusters.
for cluster_new, group in zip(cluster_indices_new,
groups):
self.loader.add_cluster(cluster_new, group, random_color())
# Set the new clusters to the corresponding spikes.
self.loader.set_cluster(spikes, clusters_new)
# Remove empty clusters.
clusters_empty = self.loader.remove_empty_clusters()
self.loader.unselect()
clusters_to_select = sorted(set(cluster_indices_old).union(
set(cluster_indices_new)) - set(clusters_empty))
return dict(clusters_to_split=clusters,
clusters_split=get_array(cluster_indices_new),
clusters_empty=clusters_empty)
def set_data(self, similarity_matrix=None,
cluster_colors_full=None,
clusters_hidden=[],
):
if similarity_matrix is None:
similarity_matrix = np.zeros(0)
cluster_colors_full = np.zeros(0)
if similarity_matrix.size == 0:
similarity_matrix = -np.ones((2, 2))
elif similarity_matrix.shape[0] == 1:
similarity_matrix = -np.ones((2, 2))
self.similarity_matrix = similarity_matrix
n = similarity_matrix.shape[0]
self.texture = colormap(self.similarity_matrix.copy())
# similarity_matrix axes are originally (x, y) from the lower left corner
# but when displayed, they are (i, j) from the upper left corner
# so we need to transpose
self.texture = np.swapaxes(self.texture, 0, 1)[::-1, :, :]
# Hide some clusters.
tex0 = self.texture.copy()
for clu in clusters_hidden:
# Inversion of axes in the y axis
self.texture[- clu - 1, :, :] = tex0[- clu - 1, :, :] * .5
self.texture[:, clu, :] = tex0[:, clu, :] * .5
self.clusters_unique = get_indices(cluster_colors_full)
self.cluster_colors = cluster_colors_full
self.nclusters = len(self.clusters_unique)
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 split_clusters(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)
# Get group and color of the new clusters, from the old clusters.
groups = self.loader.get_cluster_groups(cluster_indices_old)
# colors = self.loader.get_cluster_colors(cluster_indices_old)
# Add clusters.
self.loader.add_clusters(cluster_indices_new,
# HACK: take the group of the first cluster for all new clusters
get_array(groups)[0]*np.ones(len(cluster_indices_new)),
random_color(len(cluster_indices_new)))
# Set the new clusters to the corresponding spikes.
self.loader.set_cluster(spikes, clusters_new)
# Remove empty clusters.
clusters_empty = self.loader.remove_empty_clusters()
self.loader.unselect()
clusters_to_select = sorted(set(cluster_indices_old).union(
set(cluster_indices_new)) - set(clusters_empty))
return dict(clusters_to_split=clusters,
clusters_split=get_array(cluster_indices_new),
clusters_empty=clusters_empty)
def test_clusterview():
keys = ('cluster_groups,group_colors,group_names,'
'cluster_sizes').split(',')
data = get_data()
kwargs = {k: data[k] for k in keys}
kwargs['cluster_colors'] = data['cluster_colors_full']
# kwargs['background'] = {5: 1, 7: 2}
clusters = get_indices(data['cluster_sizes'])
quality = pd.Series(np.random.rand(len(clusters)), index=clusters)
kwargs['cluster_quality'] = quality
kwargs['operators'] = [
lambda self: self.view.set_quality(quality),
lambda self: self.view.set_background({5: 1, 7: 2}),
lambda self: self.view.set_background({6: 3}),
lambda self: self.view.set_background({}),
lambda self: (self.close()
if USERPREF['test_auto_close'] != False else None),
]
# Show the view.
window = show_view(ClusterView, **kwargs)
def merge_clusters(self, clusters_old, cluster_groups, cluster_colors,
cluster_merged):
# Get spikes in clusters to merge.
# spikes = self.loader.get_spikes(clusters=clusters_to_merge)
spikes = get_indices(clusters_old)
clusters_to_merge = get_indices(cluster_groups)
group = np.max(get_array(cluster_groups))
# color_old = get_array(cluster_colors)[0]
color_new = random_color()
self.loader.add_cluster(cluster_merged, group, color_new)
# Set the new cluster to the corresponding spikes.
self.loader.set_cluster(spikes, cluster_merged)
# Remove old clusters.
for cluster in clusters_to_merge:
self.loader.remove_cluster(cluster)
self.loader.unselect()
return dict(clusters_to_merge=clusters_to_merge,
cluster_merged=cluster_merged,
cluster_merged_colors=(color_new, color_new),)
def merge_clusters(self, clusters_old, cluster_groups, cluster_colors,
cluster_merged):
# Get spikes in clusters to merge.
# spikes = self.loader.get_spikes(clusters=clusters_to_merge)
spikes = get_indices(clusters_old)
clusters_to_merge = get_indices(cluster_groups)
group = np.max(get_array(cluster_groups))
# color_old = get_array(cluster_colors)[0]
color_new = random_color()
self.loader.add_cluster(cluster_merged, group, color_new)
# Set the new cluster to the corresponding spikes.
self.loader.set_cluster(spikes, cluster_merged)
# Remove old clusters.
for cluster in clusters_to_merge:
self.loader.remove_cluster(cluster)
self.loader.unselect()
return dict(clusters_to_merge=clusters_to_merge,
cluster_merged=cluster_merged,
cluster_merged_colors=(color_new, color_new),)
def set_data(self, cluster_groups=None, similarity_matrix=None):
"""Update the data."""
if cluster_groups is not None:
self.clusters_unique = get_array(get_indices(cluster_groups))
self.cluster_groups = get_array(cluster_groups)
if (similarity_matrix is not None and similarity_matrix.size > 0):
self.matrix = similarity_matrix
self.quality = np.diag(self.matrix)
assert len(self.cluster_groups) == self.matrix.shape[0]
def set_data(self, cluster_groups=None, similarity_matrix=None):
"""Update the data."""
if cluster_groups is not None:
self.clusters_unique = get_array(get_indices(cluster_groups))
self.cluster_groups = get_array(cluster_groups)
if (similarity_matrix is not None and similarity_matrix.size > 0):
self.matrix = similarity_matrix
self.quality = np.diag(self.matrix)
assert len(self.cluster_groups) == self.matrix.shape[0]
def set_data(self, cluster_groups=None, similarity_matrix=None):
"""Update the data."""
if cluster_groups is not None:
self.clusters_unique = get_array(get_indices(cluster_groups))
self.cluster_groups = get_array(cluster_groups)
if (similarity_matrix is not None and similarity_matrix.size > 0):
if len(get_array(cluster_groups)) != similarity_matrix.shape[0]:
log.warn(("Cannot update the wizard: cluster_groups "
"has {0:d} elements whereas the similarity matrix has {1:d}.").format(
len(get_array(cluster_groups)), similarity_matrix.shape[0]))
return
self.matrix = similarity_matrix
self.quality = np.diag(self.matrix)
def set_data(
self,
similarity_matrix=None,
cluster_colors_full=None,
clusters_hidden=[], # WARNING: relative indexing
):
if similarity_matrix is None:
similarity_matrix = np.zeros(0)
cluster_colors_full = np.zeros(0)
if similarity_matrix.size == 0:
similarity_matrix = -np.ones((2, 2))
elif similarity_matrix.shape[0] == 1:
similarity_matrix = -np.ones((2, 2))
self.similarity_matrix = similarity_matrix
n = similarity_matrix.shape[0]
self.texture = colormap(self.similarity_matrix.copy())
# similarity_matrix axes are originally (x, y) from the lower left corner
# but when displayed, they are (i, j) from the upper left corner
# so we need to transpose
self.texture = np.swapaxes(self.texture, 0, 1)
self.clusters_unique = get_indices(cluster_colors_full)
self.cluster_colors = cluster_colors_full
self.nclusters = len(self.clusters_unique)
# Remove hidden clusters.
indices = np.array(
sorted(set(range(self.nclusters)) - set(clusters_hidden)),
dtype=np.int32)
self.indices = indices
if len(indices) >= 2:
tex0 = self.texture.copy()
self.texture = tex0[[[_] for _ in (indices)], indices, :]
else:
indices = range(self.nclusters)
self.clusters_displayed = self.clusters_unique[indices]
self.nclusters_displayed = len(indices)
self.texture = self.texture[::-1, :, :]
def set_data(self, cluster_groups=None, similarity_matrix=None):
"""Update the data."""
if cluster_groups is not None:
self.clusters_unique = get_array(get_indices(cluster_groups))
self.cluster_groups = get_array(cluster_groups)
if (similarity_matrix is not None and similarity_matrix.size > 0):
if len(get_array(cluster_groups)) != similarity_matrix.shape[0]:
log.warn((
"Cannot update the wizard: cluster_groups "
"has {0:d} elements whereas the similarity matrix has {1:d}."
).format(len(get_array(cluster_groups)),
similarity_matrix.shape[0]))
return
self.matrix = similarity_matrix
self.quality = np.diag(self.matrix)
def set_data(self, similarity_matrix=None,
cluster_colors_full=None,
clusters_hidden=[], # WARNING: relative indexing
):
if similarity_matrix is None:
similarity_matrix = np.zeros(0)
cluster_colors_full = np.zeros(0)
if similarity_matrix.size == 0:
similarity_matrix = -np.ones((2, 2))
elif similarity_matrix.shape[0] == 1:
similarity_matrix = -np.ones((2, 2))
self.similarity_matrix = similarity_matrix
n = similarity_matrix.shape[0]
self.texture = colormap(self.similarity_matrix.copy())
# similarity_matrix axes are originally (x, y) from the lower left corner
# but when displayed, they are (i, j) from the upper left corner
# so we need to transpose
self.texture = np.swapaxes(self.texture, 0, 1)
self.clusters_unique = get_indices(cluster_colors_full)
self.cluster_colors = cluster_colors_full
self.nclusters = len(self.clusters_unique)
# Remove hidden clusters.
indices = np.array(sorted(set(range(self.nclusters)) - set(clusters_hidden)),
dtype=np.int32)
self.indices = indices
if len(indices) >= 2:
tex0 = self.texture.copy()
self.texture = tex0[[[_] for _ in (indices)],indices,:]
else:
indices = range(self.nclusters)
self.clusters_displayed = self.clusters_unique[indices]
self.nclusters_displayed = len(indices)
self.texture = self.texture[::-1,:,:]
def merge_clusters_undo(self, clusters_old, cluster_groups,
cluster_colors, cluster_merged):
# Get spikes in clusters to merge.
spikes = self.loader.get_spikes(clusters=cluster_merged)
clusters_to_merge = get_indices(cluster_groups)
# Add old clusters.
for cluster, group, color in zip(
clusters_to_merge, cluster_groups, cluster_colors):
self.loader.add_cluster(cluster, group, color)
# Set the new clusters to the corresponding spikes.
self.loader.set_cluster(spikes, clusters_old)
# Remove merged cluster.
self.loader.remove_cluster(cluster_merged)
self.loader.unselect()
color_old = self.loader.get_cluster_color(clusters_to_merge[0])
color_old2 = self.loader.get_cluster_color(clusters_to_merge[1])
return dict(clusters_to_merge=clusters_to_merge,
cluster_merged=cluster_merged,
cluster_to_merge_colors=(color_old, color_old2),
)
def merge_clusters_undo(self, clusters_old, cluster_groups,
cluster_colors, cluster_merged):
# Get spikes in clusters to merge.
spikes = self.loader.get_spikes(clusters=cluster_merged)
clusters_to_merge = get_indices(cluster_groups)
# Add old clusters.
for cluster, group, color in zip(
clusters_to_merge, cluster_groups, cluster_colors):
self.loader.add_cluster(cluster, group, color)
# Set the new clusters to the corresponding spikes.
self.loader.set_cluster(spikes, clusters_old)
# Remove merged cluster.
self.loader.remove_cluster(cluster_merged)
self.loader.unselect()
color_old = self.loader.get_cluster_color(clusters_to_merge[0])
color_old2 = self.loader.get_cluster_color(clusters_to_merge[1])
return dict(clusters_to_merge=clusters_to_merge,
cluster_merged=cluster_merged,
cluster_to_merge_colors=(color_old, color_old2),
)
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()
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 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 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,
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
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
# # Indices of all subset spikes.
# indices_all = get_indices(features)
# # Select only the clusters for subset of spikes.
# clusters = select(clusters, indices_all)
# # Indices of subset spikes in selected clusters.
# indices_selection = get_indices(clusters)
# # Indices of subset spikes that are not in selected clusters.
# indices_background = np.setdiff1d(indices_all, indices_selection, True)
# Extract the relevant spikes, but keep the other ones in features_full
self.clusters = clusters
self.clusters_array = get_array(self.clusters)
# self.features contains selected spikes.
# self.features = select(features, indices_selection)
self.features = features
self.features_array = get_array(self.features)
# self.features_background contains all non-selected spikes
# self.features_background = select(features, indices_background)
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
self.nspikes, self.ndim = self.features.shape
self.fetdim = fetdim
self.nchannels = nchannels
self.nextrafet = nextrafet
self.npoints = self.features.shape[0]
self.masks = masks
self.feature_indices = get_indices(self.features)
self.feature_indices_array = get_array(self.feature_indices)
self.masks_array = get_array(self.masks)
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_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()
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,
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
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
# # Indices of all subset spikes.
# indices_all = get_indices(features)
# # Select only the clusters for subset of spikes.
# clusters = select(clusters, indices_all)
# # Indices of subset spikes in selected clusters.
# indices_selection = get_indices(clusters)
# # Indices of subset spikes that are not in selected clusters.
# indices_background = np.setdiff1d(indices_all, indices_selection, True)
# Extract the relevant spikes, but keep the other ones in features_full
self.clusters = clusters
self.clusters_array = get_array(self.clusters)
# self.features contains selected spikes.
# self.features = select(features, indices_selection)
self.features = features
self.features_array = get_array(self.features)
# self.features_background contains all non-selected spikes
# self.features_background = select(features, indices_background)
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
self.nspikes, self.ndim = self.features.shape
self.fetdim = fetdim
self.nchannels = nchannels
self.nextrafet = nextrafet
self.npoints = self.features.shape[0]
self.masks = masks
self.feature_indices = get_indices(self.features)
self.feature_indices_array = get_array(self.feature_indices)
self.masks_array = get_array(self.masks)
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_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()