class RasterView(MarkerSizeMixin, BaseColorView, BaseGlobalView, ManualClusteringView):
"""This view shows a raster plot of all clusters.
Constructor
-----------
spike_times : array-like
An `(n_spikes,)` array with the spike times, in seconds.
spike_clusters : array-like
An `(n_spikes,)` array with the spike-cluster assignments.
cluster_ids : array-like
The list of all clusters to show initially.
"""
_default_position = 'right'
default_shortcuts = {
'change_marker_size': 'alt+wheel',
'switch_color_scheme': 'shift+wheel',
'decrease_marker_size': 'ctrl+shift+-',
'increase_marker_size': 'ctrl+shift++',
'select_cluster': 'ctrl+click',
'select_more': 'shift+click',
}
def __init__(self, spike_times, spike_clusters, cluster_ids=None, **kwargs):
self.spike_times = spike_times
self.n_spikes = len(spike_times)
self.duration = spike_times[-1] * 1.01
self.n_clusters = 1
assert len(spike_clusters) == self.n_spikes
self.set_spike_clusters(spike_clusters)
self.set_cluster_ids(cluster_ids)
super(RasterView, self).__init__(**kwargs)
self.canvas.set_layout('stacked', origin='top', n_plots=self.n_clusters, has_clip=False)
self.canvas.enable_axes()
self.visual = ScatterVisual(
marker='vbar',
marker_scaling='''
point_size = v_size * u_zoom.y + 5.;
float width = 0.2;
float height = 0.5;
vec2 marker_size = point_size * vec2(width, height);
marker_size.x = clamp(marker_size.x, 1, 20);
''',
)
self.visual.inserter.insert_vert('''
gl_PointSize = a_size * u_zoom.y + 5.0;
''', 'end')
self.canvas.add_visual(self.visual)
self.canvas.panzoom.set_constrain_bounds((-1, -2, +1, +2))
# Data-related functions
# -------------------------------------------------------------------------
def set_spike_clusters(self, spike_clusters):
"""Set the spike clusters for all spikes."""
self.spike_clusters = spike_clusters
def set_cluster_ids(self, cluster_ids):
"""Set the shown clusters, which can be filtered and in any order (from top to bottom)."""
if cluster_ids is None or not len(cluster_ids):
return
self.all_cluster_ids = cluster_ids
self.n_clusters = len(self.all_cluster_ids)
# Only keep spikes that belong to the selected clusters.
self.spike_ids = np.isin(self.spike_clusters, self.all_cluster_ids)
# Internal plotting functions
# -------------------------------------------------------------------------
def _get_x(self):
"""Return the x position of the spikes."""
return self.spike_times[self.spike_ids]
def _get_y(self):
"""Return the y position of the spikes, given the relative position of the clusters."""
return np.zeros(np.sum(self.spike_ids))
def _get_box_index(self):
"""Return, for every spike, its row in the raster plot. This depends on the ordering
in self.cluster_ids."""
cl = self.spike_clusters[self.spike_ids]
# Sanity check.
# assert np.all(np.in1d(cl, self.cluster_ids))
return _index_of(cl, self.all_cluster_ids)
def _get_color(self, box_index, selected_clusters=None):
"""Return, for every spike, its color, based on its box index."""
cluster_colors = self.get_cluster_colors(self.all_cluster_ids, alpha=.75)
# Selected cluster colors.
if selected_clusters is not None:
cluster_colors = _add_selected_clusters_colors(
selected_clusters, self.all_cluster_ids, cluster_colors)
return cluster_colors[box_index, :]
# Main methods
# -------------------------------------------------------------------------
def _get_data_bounds(self):
"""Bounds of the raster plot view."""
return (0, 0, self.duration, self.n_clusters)
def update_cluster_sort(self, cluster_ids):
"""Update the order of all clusters."""
self.all_cluster_ids = cluster_ids
self.visual.set_box_index(self._get_box_index())
self.canvas.update()
def update_color(self):
"""Update the color of the spikes, depending on the selected clusters."""
box_index = self._get_box_index()
color = self._get_color(box_index, selected_clusters=self.cluster_ids)
self.visual.set_color(color)
self.canvas.update()
@property
def status(self):
return 'Color scheme: %s' % self.color_scheme
def plot(self, **kwargs):
"""Make the raster plot."""
if not len(self.spike_clusters):
return
x = self._get_x() # spike times for the selected spikes
y = self._get_y() # just 0
box_index = self._get_box_index()
color = self._get_color(box_index)
assert x.shape == y.shape == box_index.shape
assert color.shape[0] == len(box_index)
self.data_bounds = self._get_data_bounds()
self.visual.set_data(
x=x, y=y, color=color, size=self.marker_size,
data_bounds=(0, -1, self.duration, 1))
self.visual.set_box_index(box_index)
self.canvas.stacked.n_boxes = self.n_clusters
self._update_axes()
# self.canvas.stacked.add_boxes(self.canvas)
self.canvas.update()
def attach(self, gui):
"""Attach the view to the GUI."""
super(RasterView, self).attach(gui)
self.actions.add(self.increase_marker_size)
self.actions.add(self.decrease_marker_size)
self.actions.separator()
def on_select(self, *args, **kwargs):
super(RasterView, self).on_select(*args, **kwargs)
self.update_color()
def zoom_to_time_range(self, interval):
"""Zoom to a time interval."""
if not interval:
return
t0, t1 = interval
w = .5 * (t1 - t0) # half width
tm = .5 * (t0 + t1)
w = min(5, w) # minimum 5s time range
t0, t1 = tm - w, tm + w
x0 = -1 + 2 * t0 / self.duration
x1 = -1 + 2 * t1 / self.duration
box = (x0, -1, x1, +1)
self.canvas.panzoom.set_range(box)
# Interactivity
# -------------------------------------------------------------------------
def on_mouse_click(self, e):
"""Select a cluster by clicking in the raster plot."""
if 'Control' not in e.modifiers:
return
b = e.button
# Get mouse position in NDC.
cluster_idx, _ = self.canvas.stacked.box_map(e.pos)
cluster_id = self.all_cluster_ids[cluster_idx]
logger.debug("Click on cluster %d with button %s.", cluster_id, b)
if 'Shift' in e.modifiers:
emit('select_more', self, [cluster_id])
else:
emit('request_select', self, [cluster_id])
class RasterView(MarkerSizeMixin, BaseGlobalView, ManualClusteringView):
"""This view shows a raster plot of all clusters.
Constructor
-----------
spike_times : array-like
An `(n_spikes,)` array with the spike times, in seconds.
spike_clusters : array-like
An `(n_spikes,)` array with the spike-cluster assignments.
cluster_ids : array-like
The list of all clusters to show initially.
cluster_color_selector : ClusterColorSelector
The object managing the color mapping.
"""
_default_position = 'right'
default_shortcuts = {
'change_marker_size': 'ctrl+wheel',
'decrease': 'ctrl+shift+-',
'increase': 'ctrl+shift++',
'select_cluster': 'ctrl+click',
}
def __init__(
self, spike_times, spike_clusters, cluster_ids=None, cluster_color_selector=None,
**kwargs):
self.spike_times = spike_times
self.n_spikes = len(spike_times)
self.duration = spike_times[-1] * 1.01
self.n_clusters = 1
assert len(spike_clusters) == self.n_spikes
self.set_spike_clusters(spike_clusters)
self.set_cluster_ids(cluster_ids if cluster_ids is not None else None)
self.cluster_color_selector = cluster_color_selector
super(RasterView, self).__init__(**kwargs)
self.canvas.set_layout('stacked', origin='top', n_plots=self.n_clusters, has_clip=False)
self.canvas.enable_axes()
self.visual = ScatterVisual(marker='vbar')
self.canvas.add_visual(self.visual)
# Data-related functions
# -------------------------------------------------------------------------
def set_spike_clusters(self, spike_clusters):
"""Set the spike clusters for all spikes."""
self.spike_clusters = spike_clusters
def set_cluster_ids(self, cluster_ids):
"""Set the shown clusters, which can be filtered and in any order (from top to bottom)."""
if cluster_ids is None or not len(cluster_ids):
return
self.all_cluster_ids = cluster_ids
self.n_clusters = len(self.all_cluster_ids)
# Only keep spikes that belong to the selected clusters.
self.spike_ids = np.isin(self.spike_clusters, self.all_cluster_ids)
# Internal plotting functions
# -------------------------------------------------------------------------
def _get_x(self):
"""Return the x position of the spikes."""
return self.spike_times[self.spike_ids]
def _get_y(self):
"""Return the y position of the spikes, given the relative position of the clusters."""
return np.zeros(np.sum(self.spike_ids))
def _get_box_index(self):
"""Return, for every spike, its row in the raster plot. This depends on the ordering
in self.cluster_ids."""
cl = self.spike_clusters[self.spike_ids]
# Sanity check.
# assert np.all(np.in1d(cl, self.cluster_ids))
return _index_of(cl, self.all_cluster_ids)
def _get_color(self, box_index, selected_clusters=None):
"""Return, for every spike, its color, based on its box index."""
cluster_colors = self.cluster_color_selector.get_colors(self.all_cluster_ids, alpha=.75)
# Selected cluster colors.
if selected_clusters is not None:
cluster_colors = _add_selected_clusters_colors(
selected_clusters, self.all_cluster_ids, cluster_colors)
return cluster_colors[box_index, :]
# Main methods
# -------------------------------------------------------------------------
def _get_data_bounds(self):
"""Bounds of the raster plot view."""
return (0, 0, self.duration, self.n_clusters)
def update_cluster_sort(self, cluster_ids):
"""Update the order of all clusters."""
self.all_cluster_ids = cluster_ids
self.visual.set_box_index(self._get_box_index())
self.canvas.update()
def update_color(self, selected_clusters=None):
"""Update the color of the spikes, depending on the selected clustersd."""
box_index = self._get_box_index()
color = self._get_color(box_index, selected_clusters=selected_clusters)
self.visual.set_color(color)
self.canvas.update()
def plot(self, **kwargs):
"""Make the raster plot."""
if not len(self.spike_clusters):
return
x = self._get_x() # spike times for the selected spikes
y = self._get_y() # just 0
box_index = self._get_box_index()
color = self._get_color(box_index)
assert x.shape == y.shape == box_index.shape
assert color.shape[0] == len(box_index)
self.data_bounds = self._get_data_bounds()
self.visual.set_data(
x=x, y=y, color=color, size=self.marker_size,
data_bounds=(0, -1, self.duration, 1))
self.visual.set_box_index(box_index)
self.canvas.stacked.n_boxes = self.n_clusters
self._update_axes()
self.canvas.update()
def attach(self, gui):
"""Attach the view to the GUI."""
super(RasterView, self).attach(gui)
self.actions.add(self.increase)
self.actions.add(self.decrease)
self.actions.separator()
def on_mouse_click(self, e):
"""Select a cluster by clicking in the raster plot."""
b = e.button
if 'Control' in e.modifiers:
# Get mouse position in NDC.
cluster_idx, _ = self.canvas.stacked.box_map(e.pos)
cluster_id = self.all_cluster_ids[cluster_idx]
logger.debug("Click on cluster %d with button %s.", cluster_id, b)
emit('cluster_click', self, cluster_id, button=b)