def __init__(self, features=None, attributes=None, **kwargs):
super(FeatureView, self).__init__(**kwargs)
self.state_attrs += ('fixed_channels', 'feature_scaling')
assert features
self.features = features
self._lim = 1
self.grid_dim = _get_default_grid() # 2D array where every item a string like `0A,1B`
self.n_rows, self.n_cols = np.array(self.grid_dim).shape
self.canvas.set_layout('grid', shape=(self.n_rows, self.n_cols))
self.canvas.enable_lasso()
# Channels being shown.
self.channel_ids = None
# Attributes: extra features. This is a dictionary
# {name: array}
# where each array is a `(n_spikes,)` array.
self.attributes = attributes or {}
self.visual = ScatterVisual()
self.canvas.add_visual(self.visual)
self.text_visual = TextVisual()
self.canvas.add_visual(self.text_visual)
self.line_visual = LineVisual()
self.canvas.add_visual(self.line_visual)
def __init__(self,
correlograms=None,
firing_rate=None,
sample_rate=None,
**kwargs):
super(CorrelogramView, self).__init__(**kwargs)
self.state_attrs += ('bin_size', 'window_size', 'refractory_period',
'uniform_normalization')
self.local_state_attrs += ()
self.canvas.set_layout(layout='grid')
# Outside margin to show labels.
self.canvas.gpu_transforms.add(Scale(.9))
assert sample_rate > 0
self.sample_rate = float(sample_rate)
# Function clusters => CCGs.
self.correlograms = correlograms
# Function clusters => firing rates (same unit as CCG).
self.firing_rate = firing_rate
# Set the default bin and window size.
self._set_bin_window(bin_size=self.bin_size,
window_size=self.window_size)
self.correlogram_visual = HistogramVisual()
self.canvas.add_visual(self.correlogram_visual)
self.line_visual = LineVisual()
self.canvas.add_visual(self.line_visual)
self.text_visual = TextVisual(color=(1., 1., 1., 1.))
self.canvas.add_visual(self.text_visual)
def __init__(self, amplitudes=None, amplitude_name=None, duration=None):
super(AmplitudeView, self).__init__()
self.state_attrs += ('amplitude_name',)
self.canvas.enable_axes()
self.canvas.enable_lasso()
# Ensure amplitudes is a dictionary, even if there is a single amplitude.
if not isinstance(amplitudes, dict):
amplitudes = {'amplitude': amplitudes}
assert amplitudes
self.amplitudes = amplitudes
self.amplitude_names = list(amplitudes.keys())
# Current amplitude type.
self.amplitude_name = amplitude_name or self.amplitude_names[0]
assert self.amplitude_name in amplitudes
self.cluster_ids = ()
self.duration = duration or 1
# Histogram visual.
self.hist_visual = HistogramVisual()
self.hist_visual.transforms.add_on_gpu([
Range(NDC, (-1, -1, 1, -1 + 2 * self.histogram_scale)), Rotate('ccw')])
self.canvas.add_visual(self.hist_visual)
# Scatter plot.
self.visual = ScatterVisual()
self.canvas.add_visual(self.visual)
# Amplitude name.
self.text_visual = TextVisual()
self.canvas.add_visual(self.text_visual, exclude_origins=(self.canvas.panzoom,))
def __init__(self,
waveforms=None,
waveforms_type=None,
sample_rate=None,
**kwargs):
self._overlap = False
self.do_show_labels = True
self.channel_ids = None
self.filtered_tags = ()
self.wave_duration = 0. # updated in the plotting method
self.data_bounds = None
self.sample_rate = sample_rate
self._status_suffix = ''
assert sample_rate > 0., "The sample rate must be provided to the waveform view."
# Initialize the view.
super(WaveformView, self).__init__(**kwargs)
self.state_attrs += ('waveforms_type', 'overlap', 'do_show_labels')
self.local_state_attrs += ('box_scaling', 'probe_scaling')
# Box and probe scaling.
self.canvas.set_layout('boxed', box_pos=np.zeros((1, 2)))
# Ensure waveforms is a dictionary, even if there is a single waveforms type.
waveforms = waveforms or {}
waveforms = waveforms if isinstance(waveforms, dict) else {
'waveforms': waveforms
}
self.waveforms = waveforms
# Rotating property waveforms types.
self.waveforms_types = RotatingProperty()
for name, value in self.waveforms.items():
self.waveforms_types.add(name, value)
# Current waveforms type.
self.waveforms_types.set(waveforms_type)
assert self.waveforms_type in self.waveforms
self.text_visual = TextVisual()
self.canvas.add_visual(self.text_visual)
self.line_visual = LineVisual()
self.canvas.add_visual(self.line_visual)
self.tick_visual = UniformScatterVisual(marker='vbar',
color=self.ax_color,
size=self.tick_size)
self.canvas.add_visual(self.tick_visual)
# Two types of visuals: thin raw line visual for normal waveforms, thick antialiased
# agg plot visual for mean and template waveforms.
self.waveform_agg_visual = PlotAggVisual()
self.waveform_visual = PlotVisual()
self.canvas.add_visual(self.waveform_agg_visual)
self.canvas.add_visual(self.waveform_visual)
def __init__(
self, positions=None, best_channels=None, channel_labels=None,
dead_channels=None, **kwargs):
super(ProbeView, self).__init__(**kwargs)
self.state_attrs += ('do_show_labels',)
# Normalize positions.
assert positions.ndim == 2
assert positions.shape[1] == 2
positions = positions.astype(np.float32)
self.positions, self.data_bounds = _get_pos_data_bounds(positions)
self.n_channels = positions.shape[0]
self.best_channels = best_channels
self.channel_labels = channel_labels or [str(ch) for ch in range(self.n_channels)]
self.dead_channels = dead_channels if dead_channels is not None else ()
self.probe_visual = ScatterVisual()
self.canvas.add_visual(self.probe_visual)
# Probe visual.
color = np.ones((self.n_channels, 4))
color[:, :3] = .5
# Change alpha value for dead channels.
if len(self.dead_channels):
color[self.dead_channels, 3] = self.dead_channel_alpha
self.probe_visual.set_data(
pos=self.positions, data_bounds=self.data_bounds,
color=color, size=self.unselected_marker_size)
# Cluster visual.
self.cluster_visual = ScatterVisual()
self.canvas.add_visual(self.cluster_visual)
# Text visual
color[:] = 1
color[self.dead_channels, :3] = self.dead_channel_alpha * 2
self.text_visual = TextVisual()
self.text_visual.inserter.insert_vert('uniform float n_channels;', 'header')
self.text_visual.inserter.add_varying(
'float', 'v_discard',
'float((n_channels >= 200 * u_zoom.y) && '
'(mod(int(a_string_index), int(n_channels / (200 * u_zoom.y))) >= 1))')
self.text_visual.inserter.insert_frag('if (v_discard > 0) discard;', 'end')
self.canvas.add_visual(self.text_visual)
self.text_visual.set_data(
pos=self.positions, text=self.channel_labels, anchor=[0, -1],
data_bounds=self.data_bounds, color=color
)
self.text_visual.program['n_channels'] = self.n_channels
self.canvas.update()
def __init__(self, cluster_stat=None):
super(HistogramView, self).__init__()
self.state_attrs += self._state_attrs
self.local_state_attrs += self._local_state_attrs
self.canvas.set_layout(layout='stacked', n_plots=1)
self.canvas.enable_axes()
self.cluster_stat = cluster_stat
self.visual = HistogramVisual()
self.canvas.add_visual(self.visual)
self.plot_visual = PlotVisual()
self.canvas.add_visual(self.plot_visual)
self.text_visual = TextVisual(color=(1., 1., 1., 1.))
self.canvas.add_visual(self.text_visual)
def _create_visuals(self):
self.canvas.set_layout('stacked', n_plots=self.n_channels)
self.canvas.enable_axes(show_y=False)
self.trace_visual = UniformPlotVisual()
self.canvas.add_visual(self.trace_visual)
self.waveform_visual = PlotVisual()
self.canvas.add_visual(self.waveform_visual)
self.text_visual = TextVisual()
_fix_coordinate_in_visual(self.text_visual, 'x')
self.text_visual.inserter.add_varying(
'float', 'v_discard',
'float((n_boxes >= 50 * u_zoom.y) && '
'(mod(int(a_box_index), int(n_boxes / (50 * u_zoom.y))) >= 1))')
self.text_visual.inserter.insert_frag('if (v_discard > 0) discard;', 'end')
self.canvas.add_visual(self.text_visual)
def __init__(self,
cluster_ids=None,
cluster_info=None,
bindings=None,
**kwargs):
super(ClusterScatterView, self).__init__(**kwargs)
self.state_attrs += (
'scaling',
'x_axis',
'y_axis',
'size',
'x_axis_log_scale',
'y_axis_log_scale',
'size_log_scale',
)
self.local_state_attrs += ()
self.canvas.enable_axes()
self.canvas.enable_lasso()
bindings = bindings or {}
self.cluster_info = cluster_info
# update self.x_axis, y_axis, size
self.__dict__.update({(k, v)
for k, v in bindings.items() if k in self._dims})
# Size range computed initially so that it doesn't change during the course of the session.
self._size_min = self._size_max = None
# Full list of clusters.
self.all_cluster_ids = cluster_ids
self.visual = ScatterVisual()
self.canvas.add_visual(self.visual)
self.label_visual = TextVisual()
self.canvas.add_visual(self.label_visual,
exclude_origins=(self.canvas.panzoom, ))
self.marker_positions = self.marker_colors = self.marker_sizes = None
def __init__(self, waveforms=None, waveforms_type=None, **kwargs):
self._overlap = False
self.do_show_labels = True
self.channel_ids = None
self.filtered_tags = ()
# Initialize the view.
super(WaveformView, self).__init__(**kwargs)
self.state_attrs += ('waveforms_type', 'overlap', 'do_show_labels')
self.local_state_attrs += ('box_scaling', 'probe_scaling')
# Box and probe scaling.
self.canvas.set_layout('boxed', box_bounds=[[-1, -1, +1, +1]])
self.canvas.enable_axes()
self._box_scaling = (1., 1.)
self._probe_scaling = (1., 1.)
self.box_pos = np.array(self.canvas.boxed.box_pos)
self.box_size = np.array(self.canvas.boxed.box_size)
self._update_boxes()
# Ensure waveforms is a dictionary, even if there is a single waveforms type.
waveforms = waveforms if isinstance(waveforms, dict) else {
'waveforms': waveforms
}
assert waveforms
self.waveforms = waveforms
self.waveforms_types = list(waveforms.keys())
# Current waveforms type.
self.waveforms_type = waveforms_type or self.waveforms_types[0]
assert self.waveforms_type in waveforms
assert 'waveforms' in waveforms
self.text_visual = TextVisual()
self.canvas.add_visual(self.text_visual)
self.waveform_visual = PlotVisual()
self.canvas.add_visual(self.waveform_visual)
def _create_visuals(self):
self.canvas.set_layout('stacked', n_plots=self.n_channels)
self.canvas.enable_axes(show_y=False)
self.trace_visual = UniformPlotVisual()
# Gradient of color for the traces.
if self.trace_color_0 and self.trace_color_1:
self.trace_visual.inserter.insert_frag(
'gl_FragColor.rgb = mix(vec3%s, vec3%s, (v_signal_index / %d));' % (
self.trace_color_0, self.trace_color_1, self.n_channels), 'end')
self.canvas.add_visual(self.trace_visual)
self.waveform_visual = PlotVisual()
self.canvas.add_visual(self.waveform_visual)
self.text_visual = TextVisual()
_fix_coordinate_in_visual(self.text_visual, 'x')
self.text_visual.inserter.add_varying(
'float', 'v_discard',
'float((n_boxes >= 50 * u_zoom.y) && '
'(mod(int(a_box_index), int(n_boxes / (50 * u_zoom.y))) >= 1))')
self.text_visual.inserter.insert_frag('if (v_discard > 0) discard;', 'end')
self.canvas.add_visual(self.text_visual)
def __init__(self, model=None):
super(WaveformClusteringView, self).__init__()
self.canvas.enable_axes()
self.canvas.enable_lasso()
self.text_visual = TextVisual()
self.canvas.add_visual(self.text_visual, exclude_origins=(self.canvas.panzoom,))
self.model = model
self.gain = 0.195
self.Fs = 30 # kHz
self.visual = PlotVisual()
self.canvas.add_visual(self.visual)
self.canvas.panzoom.zoom = self.canvas.panzoom._default_zoom = (.97, .95)
self.canvas.panzoom.pan = self.canvas.panzoom._default_pan = (-.01, 0)
self.cluster_ids = None
self.cluster_id = None
self.channel_ids = None
self.wavefs = None
self.current_channel_idx = None
class AmplitudeView(MarkerSizeMixin, LassoMixin, ManualClusteringView):
"""This view displays an amplitude plot for all selected clusters.
Constructor
-----------
amplitudes : function
Maps `cluster_ids` to a list `[Bunch(amplitudes, spike_ids), ...]` for each cluster.
Use `cluster_id=None` for background amplitudes.
"""
_default_position = 'right'
# Alpha channel of the markers in the scatter plot.
marker_alpha = 1.
# Number of bins in the histogram.
n_bins = 100
# Alpha channel of the histogram in the background.
histogram_alpha = .5
# Quantile used for scaling of the amplitudes (less than 1 to avoid outliers).
quantile = .99
# Size of the histogram, between 0 and 1.
histogram_scale = .25
default_shortcuts = {
'change_marker_size': 'ctrl+wheel',
'next_amplitude_type': 'a',
'previous_amplitude_type': 'shift+a',
'select_x_dim': 'alt+left click',
'select_y_dim': 'alt+right click',
}
def __init__(self, amplitudes=None, amplitude_name=None, duration=None):
super(AmplitudeView, self).__init__()
self.state_attrs += ('amplitude_name',)
self.canvas.enable_axes()
self.canvas.enable_lasso()
# Ensure amplitudes is a dictionary, even if there is a single amplitude.
if not isinstance(amplitudes, dict):
amplitudes = {'amplitude': amplitudes}
assert amplitudes
self.amplitudes = amplitudes
self.amplitude_names = list(amplitudes.keys())
# Current amplitude type.
self.amplitude_name = amplitude_name or self.amplitude_names[0]
assert self.amplitude_name in amplitudes
self.cluster_ids = ()
self.duration = duration or 1
# Histogram visual.
self.hist_visual = HistogramVisual()
self.hist_visual.transforms.add_on_gpu([
Range(NDC, (-1, -1, 1, -1 + 2 * self.histogram_scale)), Rotate('ccw')])
self.canvas.add_visual(self.hist_visual)
# Scatter plot.
self.visual = ScatterVisual()
self.canvas.add_visual(self.visual)
# Amplitude name.
self.text_visual = TextVisual()
self.canvas.add_visual(self.text_visual, exclude_origins=(self.canvas.panzoom,))
def _get_data_bounds(self, bunchs):
"""Compute the data bounds."""
if not bunchs: # pragma: no cover
return (0, 0, self.duration, 1)
m = min(np.quantile(bunch.amplitudes, 1 - self.quantile) for bunch in bunchs)
m = min(0, m) # ensure ymin <= 0
M = max(np.quantile(bunch.amplitudes, self.quantile) for bunch in bunchs)
return (0, m, self.duration, M)
def _add_histograms(self, bunchs):
# We do this after get_clusters_data because we need x_max.
for bunch in bunchs:
bunch.histogram = _compute_histogram(
bunch.amplitudes,
x_min=self.data_bounds[1],
x_max=self.data_bounds[3],
n_bins=self.n_bins,
normalize=False,
ignore_zeros=True,
)
return bunchs
def _plot_cluster(self, bunch):
"""Make the scatter plot."""
ms = self._marker_size
# Histogram in the background.
self.hist_visual.add_batch_data(
hist=bunch.histogram,
ylim=self._ylim,
color=add_alpha(bunch.color, self.histogram_alpha))
# Scatter plot.
self.visual.add_batch_data(
pos=bunch.pos, color=bunch.color, size=ms, data_bounds=self.data_bounds)
def _plot_amplitude_name(self):
"""Show the amplitude name."""
self.text_visual.add_batch_data(pos=[0, 1], anchor=[0, -1], text=self.amplitude_name)
def get_clusters_data(self, load_all=None):
"""Return a list of Bunch instances, with attributes pos and spike_ids."""
if not len(self.cluster_ids):
return
cluster_ids = list(self.cluster_ids)
# Don't need the background when splitting.
if not load_all:
# Add None cluster which means background spikes.
cluster_ids = [None] + cluster_ids
bunchs = self.amplitudes[self.amplitude_name](cluster_ids, load_all=load_all) or ()
# Add a pos attribute in bunchs in addition to x and y.
for i, (cluster_id, bunch) in enumerate(zip(cluster_ids, bunchs)):
spike_ids = _as_array(bunch.spike_ids)
spike_times = _as_array(bunch.spike_times)
amplitudes = _as_array(bunch.amplitudes)
assert spike_ids.shape == spike_times.shape == amplitudes.shape
# Ensure that bunch.pos exists, as it used by the LassoMixin.
bunch.pos = np.c_[spike_times, amplitudes]
assert bunch.pos.ndim == 2
bunch.cluster_id = cluster_id
bunch.color = (
selected_cluster_color(i - 1, self.marker_alpha)
# Background amplitude color.
if cluster_id is not None else (.5, .5, .5, .5))
return bunchs
def plot(self, **kwargs):
"""Update the view with the current cluster selection."""
bunchs = self.get_clusters_data()
if not bunchs:
return
self.data_bounds = self._get_data_bounds(bunchs)
bunchs = self._add_histograms(bunchs)
# Use the same scale for all histograms.
self._ylim = max(bunch.histogram.max() for bunch in bunchs) if bunchs else 1.
self.visual.reset_batch()
self.hist_visual.reset_batch()
self.text_visual.reset_batch()
for bunch in bunchs:
self._plot_cluster(bunch)
self._plot_amplitude_name()
self.canvas.update_visual(self.visual)
self.canvas.update_visual(self.hist_visual)
self.canvas.update_visual(self.text_visual)
self._update_axes()
self.canvas.update()
def attach(self, gui):
"""Attach the view to the GUI."""
super(AmplitudeView, self).attach(gui)
self.actions.add(self.next_amplitude_type, set_busy=True)
self.actions.add(self.previous_amplitude_type, set_busy=True)
def _change_amplitude_type(self, dir=+1):
i = self.amplitude_names.index(self.amplitude_name)
n = len(self.amplitude_names)
self.amplitude_name = self.amplitude_names[(i + dir) % n]
logger.debug("Switch to amplitude type: %s.", self.amplitude_name)
self.plot()
def next_amplitude_type(self):
"""Switch to the next amplitude type."""
self._change_amplitude_type(+1)
def previous_amplitude_type(self):
"""Switch to the previous amplitude type."""
self._change_amplitude_type(-1)
class HistogramView(ScalingMixin, ManualClusteringView):
"""This view displays a histogram for every selected cluster, along with a possible plot
and some text. To be overriden.
Constructor
-----------
cluster_stat : function
Maps `cluster_id` to `Bunch(data (1D array), plot (1D array), text)`.
"""
_default_position = 'right'
cluster_ids = ()
# Number of bins in the histogram.
n_bins = 100
# Minimum value on the x axis (determines the range of the histogram)
# If None, then `data.min()` is used.
x_min = None
# Maximum value on the x axis (determines the range of the histogram)
# If None, then `data.max()` is used.
x_max = None
# Unit of the bin in the set_bin_size, set_x_min, set_x_max actions.
bin_unit = 's' # s (seconds) or ms (milliseconds)
# The snippet to update this view are `hn` to change the number of bins, and `hm` to
# change the maximum value on the x axis. The character `h` can be customized by child classes.
alias_char = 'h'
default_shortcuts = {
'change_window_size': 'ctrl+wheel',
}
default_snippets = {
'set_n_bins': '%sn' % alias_char,
'set_bin_size (%s)' % bin_unit: '%sb' % alias_char,
'set_x_min (%s)' % bin_unit: '%smin' % alias_char,
'set_x_max (%s)' % bin_unit: '%smax' % alias_char,
}
_state_attrs = ('n_bins', 'x_min', 'x_max')
_local_state_attrs = ()
def __init__(self, cluster_stat=None):
super(HistogramView, self).__init__()
self.state_attrs += self._state_attrs
self.local_state_attrs += self._local_state_attrs
self.canvas.set_layout(layout='stacked', n_plots=1)
self.canvas.enable_axes()
self.cluster_stat = cluster_stat
self.visual = HistogramVisual()
self.canvas.add_visual(self.visual)
self.plot_visual = PlotVisual()
self.canvas.add_visual(self.plot_visual)
self.text_visual = TextVisual(color=(1., 1., 1., 1.))
self.canvas.add_visual(self.text_visual)
def _plot_cluster(self, bunch):
assert bunch
n_bins = self.n_bins
assert n_bins >= 0
# Update the visual's data.
self.visual.add_batch_data(
hist=bunch.histogram, ylim=bunch.ylim, color=bunch.color, box_index=bunch.index)
# Plot.
plot = bunch.get('plot', None)
if plot is not None:
x = np.linspace(self.x_min, self.x_max, len(plot))
self.plot_visual.add_batch_data(
x=x, y=plot, color=(1, 1, 1, 1), data_bounds=self.data_bounds,
box_index=bunch.index,
)
text = bunch.get('text', None)
if not text:
return
# Support multiline text.
text = text.splitlines()
n = len(text)
self.text_visual.add_batch_data(
text=text, pos=[(-1, .8)] * n, anchor=[(1, -1 - 2 * i) for i in range(n)],
box_index=bunch.index,
)
def get_clusters_data(self, load_all=None):
bunchs = []
for i, cluster_id in enumerate(self.cluster_ids):
bunch = self.cluster_stat(cluster_id)
if not bunch.data.size:
continue
bmin, bmax = bunch.data.min(), bunch.data.max()
# Update self.x_max if it was not set before.
self.x_min = self.x_min or bunch.get('x_min', None) or bmin
self.x_max = self.x_max or bunch.get('x_max', None) or bmax
self.x_min = min(self.x_min, self.x_max)
assert self.x_min is not None
assert self.x_max is not None
assert self.x_min <= self.x_max
# Compute the histogram.
bunch.histogram = _compute_histogram(
bunch.data, x_min=self.x_min, x_max=self.x_max, n_bins=self.n_bins)
bunch.ylim = bunch.histogram.max()
bunch.color = selected_cluster_color(i)
bunch.index = i
bunch.cluster_id = cluster_id
bunchs.append(bunch)
return bunchs
def _get_data_bounds(self, bunchs):
# Get the axes data bounds (the last subplot's extended n_cluster times on the y axis).
ylim = max(bunch.ylim for bunch in bunchs) if bunchs else 1
return (self.x_min, 0, self.x_max, ylim * len(self.cluster_ids))
def plot(self, **kwargs):
"""Update the view with the selected clusters."""
bunchs = self.get_clusters_data()
self.data_bounds = self._get_data_bounds(bunchs)
self.canvas.stacked.n_boxes = len(self.cluster_ids)
self.visual.reset_batch()
self.plot_visual.reset_batch()
self.text_visual.reset_batch()
for bunch in bunchs:
self._plot_cluster(bunch)
self.canvas.update_visual(self.visual)
self.canvas.update_visual(self.plot_visual)
self.canvas.update_visual(self.text_visual)
self._update_axes()
self.canvas.update()
self.update_status()
def attach(self, gui):
"""Attach the view to the GUI."""
super(HistogramView, self).attach(gui)
self.actions.add(
self.set_n_bins, alias=self.alias_char + 'n',
prompt=True, prompt_default=lambda: self.n_bins)
self.actions.add(
self.set_bin_size, alias=self.alias_char + 'b',
prompt=True, prompt_default=lambda: self.bin_size)
self.actions.add(
self.set_x_min, alias=self.alias_char + 'min',
prompt=True, prompt_default=lambda: self.x_min)
self.actions.add(
self.set_x_max, alias=self.alias_char + 'max',
prompt=True, prompt_default=lambda: self.x_max)
self.actions.separator()
@property
def status(self):
f = 1 if self.bin_unit == 's' else 1000
return '[{:.1f}{u}, {:.1f}{u:s}]'.format(
(self.x_min or 0) * f, (self.x_max or 0) * f, u=self.bin_unit)
# Histogram parameters
# -------------------------------------------------------------------------
def _get_scaling_value(self):
return self.x_max
def _set_scaling_value(self, value):
if self.bin_unit == 'ms':
value *= 1000
self.set_x_max(value)
def set_n_bins(self, n_bins):
"""Set the number of bins in the histogram."""
self.n_bins = n_bins
logger.debug("Change number of bins to %d for %s.", n_bins, self.__class__.__name__)
self.plot()
@property
def bin_size(self):
"""Return the bin size (in seconds or milliseconds depending on `self.bin_unit`)."""
bs = (self.x_max - self.x_min) / self.n_bins
if self.bin_unit == 'ms':
bs *= 1000
return bs
def set_bin_size(self, bin_size):
"""Set the bin size in the histogram."""
assert bin_size > 0
if self.bin_unit == 'ms':
bin_size /= 1000
self.n_bins = np.round((self.x_max - self.x_min) / bin_size)
logger.debug("Change number of bins to %d for %s.", self.n_bins, self.__class__.__name__)
self.plot()
def set_x_min(self, x_min):
"""Set the minimum value on the x axis for the histogram."""
if self.bin_unit == 'ms':
x_min /= 1000
x_min = min(x_min, self.x_max)
if x_min == self.x_max:
return
self.x_min = x_min
logger.debug("Change x min to %s for %s.", x_min, self.__class__.__name__)
self.plot()
def set_x_max(self, x_max):
"""Set the maximum value on the x axis for the histogram."""
if self.bin_unit == 'ms':
x_max /= 1000
x_max = max(x_max, self.x_min)
if x_max == self.x_min:
return
self.x_max = x_max
logger.debug("Change x max to %s for %s.", x_max, self.__class__.__name__)
self.plot()
class CorrelogramView(ScalingMixin, ManualClusteringView):
"""A view showing the autocorrelogram of the selected clusters, and all cross-correlograms
of cluster pairs.
Constructor
-----------
correlograms : function
Maps `(cluster_ids, bin_size, window_size)` to an `(n_clusters, n_clusters, n_bins) array`.
firing_rate : function
Maps `(cluster_ids, bin_size)` to an `(n_clusters, n_clusters) array`
"""
# Do not show too many clusters.
max_n_clusters = 20
_default_position = 'left'
cluster_ids = ()
# Bin size, in seconds.
bin_size = 1e-3
# Window size, in seconds.
window_size = 50e-3
# Refactory period, in seconds
refractory_period = 2e-3
# Whether the normalization is uniform across entire rows or not.
uniform_normalization = False
default_shortcuts = {
'change_window_size': 'ctrl+wheel',
'change_bin_size': 'alt+wheel',
}
default_snippets = {
'set_bin': 'cb',
'set_window': 'cw',
'set_refractory_period': 'cr',
}
def __init__(self,
correlograms=None,
firing_rate=None,
sample_rate=None,
**kwargs):
super(CorrelogramView, self).__init__(**kwargs)
self.state_attrs += ('bin_size', 'window_size', 'refractory_period',
'uniform_normalization')
self.local_state_attrs += ()
self.canvas.set_layout(layout='grid')
# Outside margin to show labels.
self.canvas.gpu_transforms.add(Scale(.9))
assert sample_rate > 0
self.sample_rate = float(sample_rate)
# Function clusters => CCGs.
self.correlograms = correlograms
# Function clusters => firing rates (same unit as CCG).
self.firing_rate = firing_rate
# Set the default bin and window size.
self._set_bin_window(bin_size=self.bin_size,
window_size=self.window_size)
self.correlogram_visual = HistogramVisual()
self.canvas.add_visual(self.correlogram_visual)
self.line_visual = LineVisual()
self.canvas.add_visual(self.line_visual)
self.text_visual = TextVisual(color=(1., 1., 1., 1.))
self.canvas.add_visual(self.text_visual)
# -------------------------------------------------------------------------
# Internal methods
# -------------------------------------------------------------------------
def _iter_subplots(self, n_clusters):
for i in range(n_clusters):
for j in range(n_clusters):
yield i, j
def get_clusters_data(self, load_all=None):
ccg = self.correlograms(self.cluster_ids, self.bin_size,
self.window_size)
fr = self.firing_rate(self.cluster_ids,
self.bin_size) if self.firing_rate else None
assert ccg.ndim == 3
n_bins = ccg.shape[2]
bunchs = []
m = ccg.max()
for i, j in self._iter_subplots(len(self.cluster_ids)):
b = Bunch()
b.correlogram = ccg[i, j, :]
if not self.uniform_normalization:
# Normalization row per row.
m = ccg[i, j, :].max()
b.firing_rate = fr[i, j] if fr is not None else None
b.data_bounds = (0, 0, n_bins, m)
b.pair_index = i, j
b.color = selected_cluster_color(i, 1)
if i != j:
b.color = add_alpha(_override_hsv(b.color[:3], s=.1, v=1))
bunchs.append(b)
return bunchs
def _plot_pair(self, bunch):
# Plot the histogram.
self.correlogram_visual.add_batch_data(hist=bunch.correlogram,
color=bunch.color,
ylim=bunch.data_bounds[3],
box_index=bunch.pair_index)
# Plot the firing rate.
gray = (.25, .25, .25, 1.)
if bunch.firing_rate is not None:
# Line.
pos = np.array([[
0, bunch.firing_rate, bunch.data_bounds[2], bunch.firing_rate
]])
self.line_visual.add_batch_data(pos=pos,
color=gray,
data_bounds=bunch.data_bounds,
box_index=bunch.pair_index)
# # Text.
# self.text_visual.add_batch_data(
# pos=[bunch.data_bounds[2], bunch.firing_rate],
# text='%.2f' % bunch.firing_rate,
# anchor=(-1, 0),
# box_index=bunch.pair_index,
# data_bounds=bunch.data_bounds,
# )
# Refractory period.
xrp0 = round(
(self.window_size * .5 - self.refractory_period) / self.bin_size)
xrp1 = round((self.window_size * .5 + self.refractory_period) /
self.bin_size) + 1
ylim = bunch.data_bounds[3]
pos = np.array([[xrp0, 0, xrp0, ylim], [xrp1, 0, xrp1, ylim]])
self.line_visual.add_batch_data(pos=pos,
color=gray,
data_bounds=bunch.data_bounds,
box_index=bunch.pair_index)
def _plot_labels(self):
n = len(self.cluster_ids)
# Display the cluster ids in the subplots.
for k in range(n):
self.text_visual.add_batch_data(
pos=[-1, 0],
text=str(self.cluster_ids[k]),
anchor=[-1.25, 0],
data_bounds=None,
box_index=(k, 0),
)
self.text_visual.add_batch_data(
pos=[0, -1],
text=str(self.cluster_ids[k]),
anchor=[0, -1.25],
data_bounds=None,
box_index=(n - 1, k),
)
# # Display the window size in the bottom right subplot.
# self.text_visual.add_batch_data(
# pos=[1, -1],
# anchor=[1.25, 1],
# text='%.1f ms' % (1000 * .5 * self.window_size),
# box_index=(n - 1, n - 1),
# )
def plot(self, **kwargs):
"""Update the view with the current cluster selection."""
self.canvas.grid.shape = (len(self.cluster_ids), len(self.cluster_ids))
bunchs = self.get_clusters_data()
self.correlogram_visual.reset_batch()
self.line_visual.reset_batch()
self.text_visual.reset_batch()
for bunch in bunchs:
self._plot_pair(bunch)
self._plot_labels()
self.canvas.update_visual(self.correlogram_visual)
self.canvas.update_visual(self.line_visual)
self.canvas.update_visual(self.text_visual)
self.canvas.update()
# -------------------------------------------------------------------------
# Public methods
# -------------------------------------------------------------------------
def toggle_normalization(self, checked):
"""Change the normalization of the correlograms."""
self.uniform_normalization = checked
self.plot()
def toggle_labels(self, checked):
"""Show or hide all labels."""
if checked:
self.text_visual.show()
else:
self.text_visual.hide()
self.canvas.update()
def attach(self, gui):
"""Attach the view to the GUI."""
super(CorrelogramView, self).attach(gui)
self.actions.add(self.toggle_normalization,
shortcut='n',
checkable=True)
self.actions.add(self.toggle_labels, checkable=True, checked=True)
self.actions.separator()
self.actions.add(self.set_bin,
prompt=True,
prompt_default=lambda: self.bin_size * 1000)
self.actions.add(self.set_window,
prompt=True,
prompt_default=lambda: self.window_size * 1000)
self.actions.add(self.set_refractory_period,
prompt=True,
prompt_default=lambda: self.refractory_period * 1000)
self.actions.separator()
# -------------------------------------------------------------------------
# Methods for changing the parameters
# -------------------------------------------------------------------------
def _set_bin_window(self, bin_size=None, window_size=None):
"""Set the bin and window sizes (in seconds)."""
bin_size = bin_size or self.bin_size
window_size = window_size or self.window_size
bin_size = _clip(bin_size, 1e-6, 1e3)
window_size = _clip(window_size, 1e-6, 1e3)
assert 1e-6 <= bin_size <= 1e3
assert 1e-6 <= window_size <= 1e3
assert bin_size < window_size
self.bin_size = bin_size
self.window_size = window_size
self.update_status()
@property
def status(self):
b, w = self.bin_size * 1000, self.window_size * 1000
return '{:.1f} ms ({:.1f} ms)'.format(w, b)
def set_refractory_period(self, value):
"""Set the refractory period (in milliseconds)."""
self.refractory_period = _clip(value, .1, 100) * 1e-3
self.plot()
def set_bin(self, bin_size):
"""Set the correlogram bin size (in milliseconds).
Example: `1`
"""
self._set_bin_window(bin_size=bin_size * 1e-3)
self.plot()
def set_window(self, window_size):
"""Set the correlogram window size (in milliseconds).
Example: `100`
"""
self._set_bin_window(window_size=window_size * 1e-3)
self.plot()
def increase(self):
"""Increase the window size."""
self.set_window(1000 * self.window_size * 1.1)
def decrease(self):
"""Decrease the window size."""
self.set_window(1000 * self.window_size / 1.1)
def on_mouse_wheel(self, e): # pragma: no cover
"""Change the scaling with the wheel."""
super(CorrelogramView, self).on_mouse_wheel(e)
if e.modifiers == ('Alt', ):
self._set_bin_window(bin_size=self.bin_size * 1.1**e.delta)
self.plot()
class ClusterScatterView(MarkerSizeMixin, BaseColorView, BaseGlobalView,
ManualClusteringView):
"""This view shows all clusters in a customizable scatter plot.
Constructor
-----------
cluster_ids : array-like
cluster_info: function
Maps cluster_id => Bunch() with attributes.
bindings: dict
Maps plot dimension to cluster attributes.
"""
_default_position = 'right'
_scaling = 1.
_default_alpha = .75
_min_marker_size = 5.0
_max_marker_size = 30.0
_dims = ('x_axis', 'y_axis', 'size')
# NOTE: this is not the actual marker size, but a scaling factor for the normal marker size.
_marker_size = 1.
_default_marker_size = 1.
x_axis = ''
y_axis = ''
size = ''
x_axis_log_scale = False
y_axis_log_scale = False
size_log_scale = False
default_shortcuts = {
'change_marker_size': 'alt+wheel',
'switch_color_scheme': 'shift+wheel',
'select_cluster': 'click',
'select_more': 'shift+click',
'add_to_lasso': 'control+left click',
'clear_lasso': 'control+right click',
}
default_snippets = {
'set_x_axis': 'csx',
'set_y_axis': 'csy',
'set_size': 'css',
}
def __init__(self,
cluster_ids=None,
cluster_info=None,
bindings=None,
**kwargs):
super(ClusterScatterView, self).__init__(**kwargs)
self.state_attrs += (
'scaling',
'x_axis',
'y_axis',
'size',
'x_axis_log_scale',
'y_axis_log_scale',
'size_log_scale',
)
self.local_state_attrs += ()
self.canvas.enable_axes()
self.canvas.enable_lasso()
bindings = bindings or {}
self.cluster_info = cluster_info
# update self.x_axis, y_axis, size
self.__dict__.update({(k, v)
for k, v in bindings.items() if k in self._dims})
# Size range computed initially so that it doesn't change during the course of the session.
self._size_min = self._size_max = None
# Full list of clusters.
self.all_cluster_ids = cluster_ids
self.visual = ScatterVisual()
self.canvas.add_visual(self.visual)
self.label_visual = TextVisual()
self.canvas.add_visual(self.label_visual,
exclude_origins=(self.canvas.panzoom, ))
self.marker_positions = self.marker_colors = self.marker_sizes = None
def _update_labels(self):
self.label_visual.set_data(pos=[[-1, -1], [1, 1]],
text=[self.x_axis, self.y_axis],
anchor=[[1.25, 3], [-3, -1.25]])
# Data access
# -------------------------------------------------------------------------
@property
def bindings(self):
return {k: getattr(self, k) for k in self._dims}
def get_cluster_data(self, cluster_id):
"""Return the data of one cluster."""
data = self.cluster_info(cluster_id)
return {k: data.get(v, 0.) for k, v in self.bindings.items()}
def get_clusters_data(self, cluster_ids):
"""Return the data of a set of clusters, as a dictionary {cluster_id: Bunch}."""
return {
cluster_id: self.get_cluster_data(cluster_id)
for cluster_id in cluster_ids
}
def set_cluster_ids(self, all_cluster_ids):
"""Update the cluster data by specifying the list of all cluster ids."""
self.all_cluster_ids = all_cluster_ids
if len(all_cluster_ids) == 0:
return
self.prepare_position()
self.prepare_size()
self.prepare_color()
# Data preparation
# -------------------------------------------------------------------------
def set_fields(self):
data = self.cluster_info(self.all_cluster_ids[0])
self.fields = sorted(data.keys())
self.fields = [f for f in self.fields if not isinstance(data[f], str)]
def prepare_data(self):
"""Prepare the marker position, size, and color from the cluster information."""
self.prepare_position()
self.prepare_size()
self.prepare_color()
def prepare_position(self):
"""Compute the marker positions."""
self.cluster_data = self.get_clusters_data(self.all_cluster_ids)
# Get the list of fields returned by cluster_info.
self.set_fields()
# Create the x array.
x = np.array([
self.cluster_data[cluster_id]['x_axis'] or 0.
for cluster_id in self.all_cluster_ids
])
if self.x_axis_log_scale:
x = np.log(1.0 + x - x.min())
# Create the y array.
y = np.array([
self.cluster_data[cluster_id]['y_axis'] or 0.
for cluster_id in self.all_cluster_ids
])
if self.y_axis_log_scale:
y = np.log(1.0 + y - y.min())
self.marker_positions = np.c_[x, y]
# Update the data bounds.
self.data_bounds = (x.min(), y.min(), x.max(), y.max())
def prepare_size(self):
"""Compute the marker sizes."""
size = np.array([
self.cluster_data[cluster_id]['size'] or 1.
for cluster_id in self.all_cluster_ids
])
# Log scale for the size.
if self.size_log_scale:
size = np.log(1.0 + size - size.min())
# Find the size range.
if self._size_min is None:
self._size_min, self._size_max = size.min(), size.max()
m, M = self._size_min, self._size_max
# Normalize the marker size.
size = (size - m) / ((M - m) or 1.0) # size is in [0, 1]
ms, Ms = self._min_marker_size, self._max_marker_size
size = ms + size * (Ms - ms) # now, size is in [ms, Ms]
self.marker_sizes = size
def prepare_color(self):
"""Compute the marker colors."""
colors = self.get_cluster_colors(self.all_cluster_ids,
self._default_alpha)
self.marker_colors = colors
# Marker size
# -------------------------------------------------------------------------
@property
def marker_size(self):
"""Size of the spike markers, in pixels."""
return self._marker_size
@marker_size.setter
def marker_size(self, val):
# We override this method so as to use self._marker_size as a scaling factor, not
# as an actual fixed marker size.
self._marker_size = val
self._set_marker_size()
self.canvas.update()
def _set_marker_size(self):
if self.marker_sizes is not None:
self.visual.set_marker_size(self.marker_sizes * self._marker_size)
# Plotting functions
# -------------------------------------------------------------------------
def update_color(self):
"""Update the cluster colors depending on the current color scheme."""
self.prepare_color()
self.visual.set_color(self.marker_colors)
self.canvas.update()
def update_select_color(self):
"""Update the cluster colors after the cluster selection changes."""
if self.marker_colors is None:
return
selected_clusters = self.cluster_ids
if selected_clusters is not None and len(selected_clusters) > 0:
colors = _add_selected_clusters_colors(selected_clusters,
self.all_cluster_ids,
self.marker_colors.copy())
self.visual.set_color(colors)
self.canvas.update()
def plot(self, **kwargs):
"""Make the scatter plot."""
if self.marker_positions is None:
self.prepare_data()
self.visual.set_data(
pos=self.marker_positions,
color=self.marker_colors,
size=self.marker_sizes *
self._marker_size, # marker size scaling factor
data_bounds=self.data_bounds)
self.canvas.axes.reset_data_bounds(self.data_bounds)
self.canvas.update()
def change_bindings(self, **kwargs):
"""Change the bindings."""
# Ensure the specified fields are valid.
kwargs = {k: v for k, v in kwargs.items() if v in self.fields}
assert set(kwargs.keys()) <= set(self._dims)
# Reset the size scaling.
if 'size' in kwargs:
self._size_min = self._size_max = None
self.__dict__.update(kwargs)
self._update_labels()
self.update_status()
self.prepare_data()
self.plot()
def toggle_log_scale(self, dim, checked):
"""Toggle logarithmic scaling for one of the dimensions."""
self._size_min = None
setattr(self, '%s_log_scale' % dim, checked)
self.prepare_data()
self.plot()
self.canvas.update()
def set_x_axis(self, field):
"""Set the dimension for the x axis."""
self.change_bindings(x_axis=field)
def set_y_axis(self, field):
"""Set the dimension for the y axis."""
self.change_bindings(y_axis=field)
def set_size(self, field):
"""Set the dimension for the marker size."""
self.change_bindings(size=field)
# Misc functions
# -------------------------------------------------------------------------
def attach(self, gui):
"""Attach the GUI."""
super(ClusterScatterView, self).attach(gui)
def _make_action(dim, name):
def callback():
self.change_bindings(**{dim: name})
return callback
def _make_log_toggle(dim):
def callback(checked):
self.toggle_log_scale(dim, checked)
return callback
# Change the bindings.
for dim in self._dims:
view_submenu = 'Change %s' % dim
# Change to every cluster info.
for name in self.fields:
self.actions.add(_make_action(dim, name),
show_shortcut=False,
name='Change %s to %s' % (dim, name),
view_submenu=view_submenu)
# Toggle logarithmic scale.
self.actions.separator(view_submenu=view_submenu)
self.actions.add(_make_log_toggle(dim),
checkable=True,
view_submenu=view_submenu,
name='Toggle log scale for %s' % dim,
show_shortcut=False,
checked=getattr(self, '%s_log_scale' % dim))
self.actions.separator()
self.actions.add(self.set_x_axis,
prompt=True,
prompt_default=lambda: self.x_axis)
self.actions.add(self.set_y_axis,
prompt=True,
prompt_default=lambda: self.y_axis)
self.actions.add(self.set_size,
prompt=True,
prompt_default=lambda: self.size)
connect(self.on_select)
connect(self.on_cluster)
@connect(sender=self.canvas)
def on_lasso_updated(sender, polygon):
if len(polygon) < 3:
return
pos = range_transform([self.data_bounds], [NDC],
self.marker_positions)
ind = self.canvas.lasso.in_polygon(pos)
cluster_ids = self.all_cluster_ids[ind]
emit("request_select", self, list(cluster_ids))
@connect(sender=self)
def on_close_view(view_, gui):
"""Unconnect all events when closing the view."""
unconnect(self.on_select)
unconnect(self.on_cluster)
unconnect(on_lasso_updated)
if self.all_cluster_ids is not None:
self.set_cluster_ids(self.all_cluster_ids)
self._update_labels()
def on_select(self, *args, **kwargs):
super(ClusterScatterView, self).on_select(*args, **kwargs)
self.update_select_color()
def on_cluster(self, sender, up):
if 'all_cluster_ids' in up:
self.set_cluster_ids(up.all_cluster_ids)
self.plot()
@property
def status(self):
return 'Size: %s. Color scheme: %s.' % (self.size, self.color_scheme)
# Interactivity
# -------------------------------------------------------------------------
def on_mouse_click(self, e):
"""Select a cluster by clicking on its template waveform."""
if 'Control' in e.modifiers:
return
b = e.button
pos = self.canvas.window_to_ndc(e.pos)
marker_pos = range_transform([self.data_bounds], [NDC],
self.marker_positions)
cluster_rel = np.argmin(((marker_pos - pos)**2).sum(axis=1))
cluster_id = self.all_cluster_ids[cluster_rel]
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])
def on_view_attached(view, gui):
if isinstance(view, AmplitudeView):
# Create batch of vertical lines (full height)
self.line_visual = LineVisual()
_fix_coordinate_in_visual(self.line_visual, 'y')
view.canvas.add_visual(self.line_visual)
# Create batch of annotative text
self.text_visual = TextVisual(self.line_color)
_fix_coordinate_in_visual(self.text_visual, 'y')
self.text_visual.inserter.insert_vert(
'gl_Position.x += 0.001;', 'after_transforms')
view.canvas.add_visual(self.text_visual)
@view.actions.add(shortcut='alt+b',
checkable=True,
name='Toggle event markers')
def toggle(on):
"""Toggle event markers"""
# Use `show` and `hide` instead of `toggle` here in
# case synchronization issues
if on:
logger.debug('Toggle on markers.')
self.line_visual.show()
self.text_visual.show()
view.show_events = True
else:
logger.debug('Toggle off markers.')
self.line_visual.hide()
self.text_visual.hide()
view.show_events = False
view.canvas.update()
@view.actions.add(shortcut='shift+alt+e',
prompt=True,
name='Go to event',
alias='ge')
def Go_to_event(event_num):
trace_view = gui.get_view(TraceView)
if 0 < event_num <= events.size:
trace_view.go_to(events[event_num - 1])
# Disable the menu until events are successfully added
view.actions.disable('Go to event')
view.actions.disable('Toggle event markers')
if not hasattr(view, 'show_events'):
view.show_events = True
view.state_attrs += ('show_events', )
# Read event markers from file
filename = controller.dir_path / 'eventmarkers.txt'
try:
events = np.genfromtxt(filename, usecols=0, dtype=None)
except (FileNotFoundError, OSError):
logger.warn('Event marker file not found: `%s`.', filename)
view.show_events = False
return
# Create list of event names
labels = list(map(str, range(1, events.size + 1)))
# Read event names from file (if present)
filename = controller.dir_path / 'eventmarkernames.txt'
try:
eventnames = np.loadtxt(filename,
usecols=0,
dtype=str,
max_rows=events.size)
labels[:eventnames.size] = np.atleast_1d(eventnames)
except (FileNotFoundError, OSError):
logger.info(
'Event marker names file not found (optional):'
' `%s`. Fall back to numbering.', filename)
# Obtain seconds from samples
if events.dtype == int:
logger.debug('Converting input from samples to seconds.')
events = events / controller.model.sample_rate
logger.debug('Add event markers to amplitude view.')
# Obtain horizontal positions
x = -1 + 2 * events / view.duration
x = x.repeat(4, 0).reshape(-1, 4)
x[:, 1::2] = 1, -1
# Add lines and update view
self.line_visual.reset_batch()
self.line_visual.add_batch_data(pos=x, color=self.line_color)
view.canvas.update_visual(self.line_visual)
# Add text and update view
self.text_visual.reset_batch()
self.text_visual.add_batch_data(pos=x[:, :2],
anchor=(1, -1),
text=labels)
view.canvas.update_visual(self.text_visual)
# Finally enable the menu
logger.debug('Enable menu items.')
view.actions.enable('Go to event')
view.actions.enable('Toggle event markers')
if view.show_events:
view.actions.get('Toggle event markers').toggle()
else:
self.line_visual.hide()
self.text_visual.hide()
class FeatureView(MarkerSizeMixin, ScalingMixin, ManualClusteringView):
"""This view displays a 4x4 subplot matrix with different projections of the principal
component features. This view keeps track of which channels are currently shown.
Constructor
-----------
features : function
Maps `(cluster_id, channel_ids=None, load_all=False)` to
`Bunch(data, channel_ids, channel_labels, spike_ids , masks)`.
* `data` is an `(n_spikes, n_channels, n_features)` array
* `channel_ids` contains the channel ids of every row in `data`
* `channel_labels` contains the channel labels of every row in `data`
* `spike_ids` is a `(n_spikes,)` array
* `masks` is an `(n_spikes, n_channels)` array
This allows for a sparse format.
attributes : dict
Maps an attribute name to a 1D array with `n_spikes` numbers (for example, spike times).
"""
# Do not show too many clusters.
max_n_clusters = 8
_default_position = 'right'
cluster_ids = ()
# Whether to disable automatic selection of channels.
fixed_channels = False
feature_scaling = 1.
default_shortcuts = {
'change_marker_size': 'alt+wheel',
'increase': 'ctrl++',
'decrease': 'ctrl+-',
'add_lasso_point': 'ctrl+click',
'stop_lasso': 'ctrl+right click',
'toggle_automatic_channel_selection': 'c',
}
def __init__(self, features=None, attributes=None, **kwargs):
super(FeatureView, self).__init__(**kwargs)
self.state_attrs += ('fixed_channels', 'feature_scaling')
assert features
self.features = features
self._lim = 1
self.grid_dim = _get_default_grid() # 2D array where every item a string like `0A,1B`
self.n_rows, self.n_cols = np.array(self.grid_dim).shape
self.canvas.set_layout('grid', shape=(self.n_rows, self.n_cols))
self.canvas.enable_lasso()
# Channels being shown.
self.channel_ids = None
# Attributes: extra features. This is a dictionary
# {name: array}
# where each array is a `(n_spikes,)` array.
self.attributes = attributes or {}
self.visual = ScatterVisual()
self.canvas.add_visual(self.visual)
self.text_visual = TextVisual()
self.canvas.add_visual(self.text_visual)
self.line_visual = LineVisual()
self.canvas.add_visual(self.line_visual)
def set_grid_dim(self, grid_dim):
"""Change the grid dim dynamically.
Parameters
----------
grid_dim : array-like (2D)
`grid_dim[row, col]` is a string with two values separated by a comma. Each value
is the relative channel id (0, 1, 2...) followed by the PC (A, B, C...). For example,
`grid_dim[row, col] = 0B,1A`. Each value can also be an attribute name, for example
`time`. For example, `grid_dim[row, col] = time,2C`.
"""
self.grid_dim = grid_dim
self.n_rows, self.n_cols = np.array(grid_dim).shape
self.canvas.grid.shape = (self.n_rows, self.n_cols)
# Internal methods
# -------------------------------------------------------------------------
def _iter_subplots(self):
"""Yield (i, j, dim)."""
for i in range(self.n_rows):
for j in range(self.n_cols):
dim = self.grid_dim[i][j]
dim_x, dim_y = dim.split(',')
yield i, j, dim_x, dim_y
def _get_axis_label(self, dim):
"""Return the channel label from a dimension, if applicable."""
if str(dim[:-1]).isdecimal():
n = len(self.channel_ids)
channel_id = self.channel_ids[int(dim[:-1]) % n]
return self.channel_labels[channel_id] + dim[-1]
else:
return dim
def _get_channel_and_pc(self, dim):
"""Return the channel_id and PC of a dim."""
if self.channel_ids is None:
return
assert dim not in self.attributes # This is called only on PC data.
s = 'ABCDEFGHIJ'
# Channel relative index, typically just 0 or 1.
c_rel = int(dim[:-1])
# Get the channel_id from the currently-selected channels.
channel_id = self.channel_ids[c_rel % len(self.channel_ids)]
pc = s.index(dim[-1])
return channel_id, pc
def _get_axis_data(self, bunch, dim, cluster_id=None, load_all=None):
"""Extract the points from the data on a given dimension.
bunch is returned by the features() function.
dim is the string specifying the dimensions to extract for the data.
"""
if dim in self.attributes:
return self.attributes[dim](cluster_id, load_all=load_all)
masks = bunch.get('masks', None)
channel_id, pc = self._get_channel_and_pc(dim)
# Skip the plot if the channel id is not displayed.
if channel_id not in bunch.channel_ids: # pragma: no cover
return Bunch(data=np.zeros((bunch.data.shape[0],)))
# Get the column index of the current channel in data.
c = list(bunch.channel_ids).index(channel_id)
if masks is not None:
masks = masks[:, c]
return Bunch(data=self.feature_scaling * bunch.data[:, c, pc], masks=masks)
def _get_axis_bounds(self, dim, bunch):
"""Return the min/max of an axis."""
if dim in self.attributes:
# Attribute: specified lim, or compute the min/max.
vmin, vmax = bunch.get('lim', (0, 0))
assert vmin is not None
assert vmax is not None
return vmin, vmax
return (-self._lim, +self._lim)
def _plot_points(self, bunch, clu_idx=None):
if not bunch:
return
cluster_id = self.cluster_ids[clu_idx] if clu_idx is not None else None
for i, j, dim_x, dim_y in self._iter_subplots():
px = self._get_axis_data(bunch, dim_x, cluster_id=cluster_id)
py = self._get_axis_data(bunch, dim_y, cluster_id=cluster_id)
# Skip empty data.
if px is None or py is None: # pragma: no cover
logger.warning("Skipping empty data for cluster %d.", cluster_id)
return
assert px.data.shape == py.data.shape
xmin, xmax = self._get_axis_bounds(dim_x, px)
ymin, ymax = self._get_axis_bounds(dim_y, py)
assert xmin <= xmax
assert ymin <= ymax
data_bounds = (xmin, ymin, xmax, ymax)
masks = _get_masks_max(px, py)
# Prepare the batch visual with all subplots
# for the selected cluster.
self.visual.add_batch_data(
x=px.data, y=py.data,
color=_get_point_color(clu_idx),
# Reduced marker size for background features
size=self._marker_size,
masks=_get_point_masks(clu_idx=clu_idx, masks=masks),
data_bounds=data_bounds,
box_index=(i, j),
)
# Get the channel ids corresponding to the relative channel indices
# specified in the dimensions. Channel 0 corresponds to the first
# best channel for the selected cluster, and so on.
label_x = self._get_axis_label(dim_x)
label_y = self._get_axis_label(dim_y)
# Add labels.
self.text_visual.add_batch_data(
pos=[1, 1],
anchor=[-1, -1],
text=label_y,
data_bounds=None,
box_index=(i, j),
)
self.text_visual.add_batch_data(
pos=[0, -1.],
anchor=[0, 1],
text=label_x,
data_bounds=None,
box_index=(i, j),
)
def _plot_axes(self):
self.line_visual.reset_batch()
for i, j, dim_x, dim_y in self._iter_subplots():
self.line_visual.add_batch_data(
pos=[[-1., 0., +1., 0.],
[0., -1., 0., +1.]],
color=(.5, .5, .5, .5),
box_index=(i, j),
data_bounds=None,
)
self.canvas.update_visual(self.line_visual)
def _get_lim(self, bunchs):
if not bunchs: # pragma: no cover
return 1
m, M = min(bunch.data.min() for bunch in bunchs), max(bunch.data.max() for bunch in bunchs)
M = max(abs(m), abs(M))
return M
def _get_scaling_value(self):
return self.feature_scaling
def _set_scaling_value(self, value):
self.feature_scaling = value
self.plot(fixed_channels=True)
# Public methods
# -------------------------------------------------------------------------
def clear_channels(self):
"""Reset the current channels."""
self.channel_ids = None
self.plot()
def get_clusters_data(self, fixed_channels=None, load_all=None):
# Get the feature data.
# Specify the channel ids if these are fixed, otherwise
# choose the first cluster's best channels.
c = self.channel_ids if fixed_channels else None
bunchs = [self.features(cluster_id, channel_ids=c) for cluster_id in self.cluster_ids]
bunchs = [b for b in bunchs if b]
if not bunchs: # pragma: no cover
return []
for cluster_id, bunch in zip(self.cluster_ids, bunchs):
bunch.cluster_id = cluster_id
# Choose the channels based on the first selected cluster.
channel_ids = list(bunchs[0].get('channel_ids', [])) if bunchs else []
common_channels = list(channel_ids)
# Intersection (with order kept) of channels belonging to all clusters.
for bunch in bunchs:
common_channels = [c for c in bunch.get('channel_ids', []) if c in common_channels]
# The selected channels will be (1) the channels common to all clusters, followed
# by (2) remaining channels from the first cluster (excluding those already selected
# in (1)).
n = len(channel_ids)
not_common_channels = [c for c in channel_ids if c not in common_channels]
channel_ids = common_channels + not_common_channels[:n - len(common_channels)]
assert len(channel_ids) > 0
# Choose the channels automatically unless fixed_channels is set.
if (not fixed_channels or self.channel_ids is None):
self.channel_ids = channel_ids
assert len(self.channel_ids)
# Channel labels.
self.channel_labels = {}
for d in bunchs:
chl = d.get('channel_labels', ['%d' % ch for ch in d.get('channel_ids', [])])
self.channel_labels.update({
channel_id: chl[i] for i, channel_id in enumerate(d.get('channel_ids', []))})
return bunchs
def plot(self, **kwargs):
"""Update the view with the selected clusters."""
# Determine whether the channels should be fixed or not.
added = kwargs.get('up', {}).get('added', None)
# Fix the channels if the view updates after a cluster event
# and there are new clusters.
fixed_channels = (
self.fixed_channels or kwargs.get('fixed_channels', None) or added is not None)
# Get the clusters data.
bunchs = self.get_clusters_data(fixed_channels=fixed_channels)
bunchs = [b for b in bunchs if b]
if not bunchs:
return
self._lim = self._get_lim(bunchs)
# Get the background data.
background = self.features(channel_ids=self.channel_ids)
# Plot all features.
self._plot_axes()
# NOTE: the columns in bunch.data are ordered by decreasing quality
# of the associated channels. The channels corresponding to each
# column are given in bunch.channel_ids in the same order.
# Plot points.
self.visual.reset_batch()
self.text_visual.reset_batch()
self._plot_points(background) # background spikes
# Plot each cluster.
for clu_idx, bunch in enumerate(bunchs):
self._plot_points(bunch, clu_idx=clu_idx)
# Upload the data on the GPU.
self.canvas.update_visual(self.visual)
self.canvas.update_visual(self.text_visual)
self.canvas.update()
def attach(self, gui):
"""Attach the view to the GUI."""
super(FeatureView, self).attach(gui)
self.actions.add(
self.toggle_automatic_channel_selection,
checked=not self.fixed_channels, checkable=True)
self.actions.add(self.clear_channels)
self.actions.separator()
def toggle_automatic_channel_selection(self, checked):
"""Toggle the automatic selection of channels when the cluster selection changes."""
self.fixed_channels = not checked
@property
def status(self):
if self.channel_ids is None: # pragma: no cover
return ''
channel_labels = [self.channel_labels[ch] for ch in self.channel_ids[:2]]
return 'channels: %s' % ', '.join(channel_labels)
# Dimension selection
# -------------------------------------------------------------------------
def on_select_channel(self, sender=None, channel_id=None, key=None, button=None):
"""Respond to the click on a channel from another view, and update the
relevant subplots."""
channels = self.channel_ids
if channels is None:
return
if len(channels) == 1:
self.plot()
return
assert len(channels) >= 2
# Get the axis from the pressed button (1, 2, etc.)
if key is not None:
d = np.clip(len(channels) - 1, 0, key - 1)
else:
d = 0 if button == 'Left' else 1
# Change the first or second best channel.
old = channels[d]
# Avoid updating the view if the channel doesn't change.
if channel_id == old:
return
channels[d] = channel_id
# Ensure that the first two channels are different.
if channels[1 - min(d, 1)] == channel_id:
channels[1 - min(d, 1)] = old
assert channels[0] != channels[1]
# Remove duplicate channels.
self.channel_ids = _uniq(channels)
logger.debug("Choose channels %d and %d in feature view.", *channels[:2])
# Fix the channels temporarily.
self.plot(fixed_channels=True)
self.update_status()
def on_mouse_click(self, e):
"""Select a feature dimension by clicking on a box in the feature view."""
b = e.button
if 'Alt' in e.modifiers:
# Get mouse position in NDC.
(i, j), _ = self.canvas.grid.box_map(e.pos)
dim = self.grid_dim[i][j]
dim_x, dim_y = dim.split(',')
dim = dim_x if b == 'Left' else dim_y
other_dim = dim_y if b == 'Left' else dim_x
if dim not in self.attributes:
# When a regular (channel, PC) dimension is selected.
channel_pc = self._get_channel_and_pc(dim)
if channel_pc is None:
return
channel_id, pc = channel_pc
logger.debug("Click on feature dim %s, channel id %s, PC %s.", dim, channel_id, pc)
else:
# When the selected dimension is an attribute, e.g. "time".
pc = None
# Take the channel id in the other dimension.
channel_pc = self._get_channel_and_pc(other_dim)
channel_id = channel_pc[0] if channel_pc is not None else None
logger.debug("Click on feature dim %s.", dim)
emit('select_feature', self, dim=dim, channel_id=channel_id, pc=pc)
def on_request_split(self, sender=None):
"""Return the spikes enclosed by the lasso."""
if (self.canvas.lasso.count < 3 or not len(self.cluster_ids)): # pragma: no cover
return np.array([], dtype=np.int64)
assert len(self.channel_ids)
# Get the dimensions of the lassoed subplot.
i, j = self.canvas.layout.active_box
dim = self.grid_dim[i][j]
dim_x, dim_y = dim.split(',')
# Get all points from all clusters.
pos = []
spike_ids = []
for cluster_id in self.cluster_ids:
# Load all spikes.
bunch = self.features(cluster_id, channel_ids=self.channel_ids, load_all=True)
if not bunch:
continue
px = self._get_axis_data(bunch, dim_x, cluster_id=cluster_id, load_all=True)
py = self._get_axis_data(bunch, dim_y, cluster_id=cluster_id, load_all=True)
points = np.c_[px.data, py.data]
# Normalize the points.
xmin, xmax = self._get_axis_bounds(dim_x, px)
ymin, ymax = self._get_axis_bounds(dim_y, py)
r = Range((xmin, ymin, xmax, ymax))
points = r.apply(points)
pos.append(points)
spike_ids.append(bunch.spike_ids)
pos = np.vstack(pos)
spike_ids = np.concatenate(spike_ids)
# Find lassoed spikes.
ind = self.canvas.lasso.in_polygon(pos)
self.canvas.lasso.clear()
return np.unique(spike_ids[ind])
class TraceView(ScalingMixin, BaseColorView, ManualClusteringView):
"""This view shows the raw traces along with spike waveforms.
Constructor
-----------
traces : function
Maps a time interval `(t0, t1)` to a `Bunch(data, color, waveforms)` where
* `data` is an `(n_samples, n_channels)` array
* `waveforms` is a list of bunchs with the following attributes:
* `data`
* `color`
* `channel_ids`
* `start_time`
* `spike_id`
* `spike_cluster`
spike_times : function
Teturns the list of relevant spike times.
sample_rate : float
duration : float
n_channels : int
channel_positions : array-like
Positions of the channels, used for displaying the channels in the right y order
channel_labels : list
Labels of all shown channels. By default, this is just the channel ids.
"""
_default_position = 'left'
auto_update = True
auto_scale = True
interval_duration = .25 # default duration of the interval
shift_amount = .1
scaling_coeff_x = 1.25
trace_quantile = .01 # quantile for auto-scaling
default_trace_color = (.5, .5, .5, 1)
trace_color_0 = (.353, .161, .443)
trace_color_1 = (.133, .404, .396)
default_shortcuts = {
'change_trace_size': 'ctrl+wheel',
'switch_color_scheme': 'shift+wheel',
'navigate': 'alt+wheel',
'decrease': 'alt+down',
'increase': 'alt+up',
'go_left': 'alt+left',
'go_right': 'alt+right',
'jump_left': 'shift+alt+left',
'jump_right': 'shift+alt+right',
'go_to_start': 'alt+home',
'go_to_end': 'alt+end',
'go_to': 'alt+t',
'go_to_next_spike': 'alt+pgdown',
'go_to_previous_spike': 'alt+pgup',
'narrow': 'alt++',
'select_spike': 'ctrl+click',
'select_channel_pcA': 'shift+left click',
'select_channel_pcB': 'shift+right click',
'switch_origin': 'alt+o',
'toggle_highlighted_spikes': 'alt+s',
'toggle_show_labels': 'alt+l',
'widen': 'alt+-',
}
default_snippets = {
'go_to': 'tg',
'shift': 'ts',
}
def __init__(
self, traces=None, sample_rate=None, spike_times=None, duration=None,
n_channels=None, channel_positions=None, channel_labels=None, **kwargs):
self.do_show_labels = True
self.show_all_spikes = False
self.get_spike_times = spike_times
# Sample rate.
assert sample_rate > 0
self.sample_rate = float(sample_rate)
self.dt = 1. / self.sample_rate
# Traces and spikes.
assert hasattr(traces, '__call__')
self.traces = traces
# self.waveforms = None
assert duration >= 0
self.duration = duration
assert n_channels >= 0
self.n_channels = n_channels
# Channel y ranking.
self.channel_positions = (
channel_positions if channel_positions is not None else
np.c_[np.zeros(n_channels), np.arange(n_channels)])
# channel_y_ranks[i] is the position of channel #i in the trace view.
self.channel_y_ranks = np.argsort(np.argsort(self.channel_positions[:, 1]))
assert self.channel_y_ranks.shape == (n_channels,)
# Channel labels.
self.channel_labels = (
channel_labels if channel_labels is not None else
['%d' % ch for ch in range(n_channels)])
assert len(self.channel_labels) == n_channels
# Initialize the view.
super(TraceView, self).__init__(**kwargs)
self.state_attrs += ('origin', 'do_show_labels', 'show_all_spikes', 'auto_scale')
self.local_state_attrs += ('interval', 'scaling',)
# Visuals.
self._create_visuals()
# Initial interval.
self._interval = None
self.go_to(duration / 2.)
self._waveform_times = []
self.canvas.panzoom.set_constrain_bounds((-1, -2, +1, +2))
def _create_visuals(self):
self.canvas.set_layout('stacked', n_plots=self.n_channels)
self.canvas.enable_axes(show_y=False)
self.trace_visual = UniformPlotVisual()
# Gradient of color for the traces.
if self.trace_color_0 and self.trace_color_1:
self.trace_visual.inserter.insert_frag(
'gl_FragColor.rgb = mix(vec3%s, vec3%s, (v_signal_index / %d));' % (
self.trace_color_0, self.trace_color_1, self.n_channels), 'end')
self.canvas.add_visual(self.trace_visual)
self.waveform_visual = PlotVisual()
self.canvas.add_visual(self.waveform_visual)
self.text_visual = TextVisual()
_fix_coordinate_in_visual(self.text_visual, 'x')
self.text_visual.inserter.add_varying(
'float', 'v_discard',
'float((n_boxes >= 50 * u_zoom.y) && '
'(mod(int(a_box_index), int(n_boxes / (50 * u_zoom.y))) >= 1))')
self.text_visual.inserter.insert_frag('if (v_discard > 0) discard;', 'end')
self.canvas.add_visual(self.text_visual)
@property
def stacked(self):
return self.canvas.stacked
# Internal methods
# -------------------------------------------------------------------------
def _plot_traces(self, traces, color=None):
traces = traces.T
n_samples = traces.shape[1]
n_ch = self.n_channels
assert traces.shape == (n_ch, n_samples)
color = color or self.default_trace_color
t = self._interval[0] + np.arange(n_samples) * self.dt
t = np.tile(t, (n_ch, 1))
box_index = self.channel_y_ranks
box_index = np.repeat(box_index[:, np.newaxis], n_samples, axis=1)
assert t.shape == (n_ch, n_samples)
assert traces.shape == (n_ch, n_samples)
assert box_index.shape == (n_ch, n_samples)
self.trace_visual.color = color
self.canvas.update_visual(
self.trace_visual,
t, traces,
data_bounds=self.data_bounds,
box_index=box_index.ravel(),
)
def _plot_spike(self, bunch):
# The spike time corresponds to the first sample of the waveform.
n_samples, n_channels = bunch.data.shape
assert len(bunch.channel_ids) == n_channels
# Generate the x coordinates of the waveform.
t = bunch.start_time + self.dt * np.arange(n_samples)
t = np.tile(t, (n_channels, 1)) # (n_unmasked_channels, n_samples)
# Determine the spike color.
i = bunch.select_index
c = bunch.spike_cluster
cs = self.color_schemes.get()
color = selected_cluster_color(i, alpha=1) if i is not None else cs.get(c, alpha=1)
# We could tweak the color of each spike waveform depending on the template amplitude
# on each of its best channels.
# channel_amps = bunch.get('channel_amps', None)
# if channel_amps is not None:
# color = np.tile(color, (n_channels, 1))
# assert color.shape == (n_channels, 4)
# color[:, 3] = channel_amps
# The box index depends on the channel.
box_index = self.channel_y_ranks[bunch.channel_ids]
box_index = np.repeat(box_index[:, np.newaxis], n_samples, axis=0)
self.waveform_visual.add_batch_data(
box_index=box_index,
x=t, y=bunch.data.T, color=color,
data_bounds=self.data_bounds,
)
def _plot_waveforms(self, waveforms, **kwargs):
"""Plot the waveforms."""
# waveforms = self.waveforms
assert isinstance(waveforms, list)
if waveforms:
self.waveform_visual.show()
self.waveform_visual.reset_batch()
for w in waveforms:
self._plot_spike(w)
self._waveform_times.append(
(w.start_time, w.spike_id, w.spike_cluster, w.get('channel_ids', None)))
self.canvas.update_visual(self.waveform_visual)
else: # pragma: no cover
self.waveform_visual.hide()
def _plot_labels(self, traces):
self.text_visual.reset_batch()
for ch in range(self.n_channels):
bi = self.channel_y_ranks[ch]
ch_label = self.channel_labels[ch]
self.text_visual.add_batch_data(
pos=[self.data_bounds[0], 0],
text=ch_label,
anchor=[+1., 0],
data_bounds=self.data_bounds,
box_index=bi,
)
self.canvas.update_visual(self.text_visual)
# Public methods
# -------------------------------------------------------------------------
def _restrict_interval(self, interval):
start, end = interval
# Round the times to full samples to avoid subsampling shifts
# in the traces.
start = int(round(start * self.sample_rate)) / self.sample_rate
end = int(round(end * self.sample_rate)) / self.sample_rate
# Restrict the interval to the boundaries of the traces.
if start < 0:
end += (-start)
start = 0
elif end >= self.duration:
start -= (end - self.duration)
end = self.duration
start = np.clip(start, 0, end)
end = np.clip(end, start, self.duration)
assert 0 <= start < end <= self.duration
return start, end
def plot(self, update_traces=True, update_waveforms=True):
if update_waveforms:
# Load the traces in the interval.
traces = self.traces(self._interval)
if update_traces:
logger.log(5, "Redraw the entire trace view.")
start, end = self._interval
# Find the data bounds.
if self.auto_scale or getattr(self, 'data_bounds', NDC) == NDC:
ymin = np.quantile(traces.data, self.trace_quantile)
ymax = np.quantile(traces.data, 1. - self.trace_quantile)
else:
ymin, ymax = self.data_bounds[1], self.data_bounds[3]
self.data_bounds = (start, ymin, end, ymax)
# Used for spike click.
self._waveform_times = []
# Plot the traces.
self._plot_traces(
traces.data, color=traces.get('color', None))
# Plot the labels.
if self.do_show_labels:
self._plot_labels(traces.data)
if update_waveforms:
self._plot_waveforms(traces.get('waveforms', []))
self._update_axes()
self.canvas.update()
def set_interval(self, interval=None):
"""Display the traces and spikes in a given interval."""
if interval is None:
interval = self._interval
interval = self._restrict_interval(interval)
if interval != self._interval:
logger.log(5, "Redraw the entire trace view.")
self._interval = interval
emit('is_busy', self, True)
self.plot(update_traces=True, update_waveforms=True)
emit('is_busy', self, False)
emit('time_range_selected', self, interval)
self.update_status()
else:
self.plot(update_traces=False, update_waveforms=True)
def on_select(self, cluster_ids=None, **kwargs):
self.cluster_ids = cluster_ids
if not cluster_ids:
return
# Make sure we call again self.traces() when the cluster selection changes.
self.set_interval()
def attach(self, gui):
"""Attach the view to the GUI."""
super(TraceView, self).attach(gui)
self.actions.add(self.toggle_show_labels, checkable=True, checked=self.do_show_labels)
self.actions.add(
self.toggle_highlighted_spikes, checkable=True, checked=self.show_all_spikes)
self.actions.add(self.toggle_auto_scale, checkable=True, checked=self.auto_scale)
self.actions.add(self.switch_origin)
self.actions.separator()
self.actions.add(
self.go_to, prompt=True, prompt_default=lambda: str(self.time))
self.actions.separator()
self.actions.add(self.go_to_start)
self.actions.add(self.go_to_end)
self.actions.separator()
self.actions.add(self.shift, prompt=True)
self.actions.add(self.go_right)
self.actions.add(self.go_left)
self.actions.add(self.jump_right)
self.actions.add(self.jump_left)
self.actions.separator()
self.actions.add(self.widen)
self.actions.add(self.narrow)
self.actions.separator()
self.actions.add(self.go_to_next_spike)
self.actions.add(self.go_to_previous_spike)
self.actions.separator()
self.set_interval()
@property
def status(self):
a, b = self._interval
return '[{:.2f}s - {:.2f}s]. Color scheme: {}.'.format(a, b, self.color_scheme)
# Origin
# -------------------------------------------------------------------------
@property
def origin(self):
"""Whether to show the channels from top to bottom (`top` option, the default), or from
bottom to top (`bottom`)."""
return getattr(self.canvas.layout, 'origin', Stacked._origin)
@origin.setter
def origin(self, value):
if value is None:
return
if self.canvas.layout:
self.canvas.layout.origin = value
else: # pragma: no cover
logger.warning(
"Could not set origin to %s because the layout instance was not initialized yet.",
value)
def switch_origin(self):
"""Switch between top and bottom origin for the channels."""
self.origin = 'bottom' if self.origin == 'top' else 'top'
# Navigation
# -------------------------------------------------------------------------
@property
def time(self):
"""Time at the center of the window."""
return sum(self._interval) * .5
@property
def interval(self):
"""Interval as `(tmin, tmax)`."""
return self._interval
@interval.setter
def interval(self, value):
self.set_interval(value)
@property
def half_duration(self):
"""Half of the duration of the current interval."""
if self._interval is not None:
a, b = self._interval
return (b - a) * .5
else:
return self.interval_duration * .5
def go_to(self, time):
"""Go to a specific time (in seconds)."""
half_dur = self.half_duration
self.set_interval((time - half_dur, time + half_dur))
def shift(self, delay):
"""Shift the interval by a given delay (in seconds)."""
self.go_to(self.time + delay)
def go_to_start(self):
"""Go to the start of the recording."""
self.go_to(0)
def go_to_end(self):
"""Go to end of the recording."""
self.go_to(self.duration)
def go_right(self):
"""Go to right."""
start, end = self._interval
delay = (end - start) * .1
self.shift(delay)
def go_left(self):
"""Go to left."""
start, end = self._interval
delay = (end - start) * .1
self.shift(-delay)
def jump_right(self):
"""Jump to right."""
delay = self.duration * .1
self.shift(delay)
def jump_left(self):
"""Jump to left."""
delay = self.duration * .1
self.shift(-delay)
def _jump_to_spike(self, delta=+1):
"""Jump to next or previous spike from the selected clusters."""
spike_times = self.get_spike_times()
if spike_times is not None and len(spike_times):
ind = np.searchsorted(spike_times, self.time)
n = len(spike_times)
self.go_to(spike_times[(ind + delta) % n])
def go_to_next_spike(self, ):
"""Jump to the next spike from the first selected cluster."""
self._jump_to_spike(+1)
def go_to_previous_spike(self, ):
"""Jump to the previous spike from the first selected cluster."""
self._jump_to_spike(-1)
def toggle_highlighted_spikes(self, checked):
"""Toggle between showing all spikes or selected spikes."""
self.show_all_spikes = checked
self.set_interval()
def widen(self):
"""Increase the interval size."""
t, h = self.time, self.half_duration
h *= self.scaling_coeff_x
self.set_interval((t - h, t + h))
def narrow(self):
"""Decrease the interval size."""
t, h = self.time, self.half_duration
h /= self.scaling_coeff_x
self.set_interval((t - h, t + h))
# Misc
# -------------------------------------------------------------------------
def toggle_show_labels(self, checked):
"""Toggle the display of the channel ids."""
logger.debug("Set show labels to %s.", checked)
self.do_show_labels = checked
self.text_visual.toggle()
self.canvas.update()
def toggle_auto_scale(self, checked):
"""Toggle automatic scaling of the traces."""
logger.debug("Set auto scale to %s.", checked)
self.auto_scale = checked
def update_color(self):
"""Update the view when the color scheme changes."""
self.plot(update_traces=False, update_waveforms=True)
# Scaling
# -------------------------------------------------------------------------
@property
def scaling(self):
"""Scaling of the channel boxes."""
return self.stacked._box_scaling[1]
@scaling.setter
def scaling(self, value):
self.stacked._box_scaling = (self.stacked._box_scaling[0], value)
def _get_scaling_value(self):
return self.scaling
def _set_scaling_value(self, value):
self.scaling = value
self.stacked.update()
# Spike selection
# -------------------------------------------------------------------------
def on_mouse_click(self, e):
"""Select a cluster by clicking on a spike."""
if 'Control' in e.modifiers:
# Get mouse position in NDC.
box_id, _ = self.canvas.stacked.box_map(e.pos)
channel_id = np.nonzero(self.channel_y_ranks == box_id)[0]
# Find the spike and cluster closest to the mouse.
db = self.data_bounds
# Get the information about the displayed spikes.
wt = [(t, s, c, ch) for t, s, c, ch in self._waveform_times if channel_id in ch]
if not wt:
return
# Get the time coordinate of the mouse position.
mouse_pos = self.canvas.panzoom.window_to_ndc(e.pos)
mouse_time = Range(NDC, db).apply(mouse_pos)[0][0]
# Get the closest spike id.
times, spike_ids, spike_clusters, channel_ids = zip(*wt)
i = np.argmin(np.abs(np.array(times) - mouse_time))
# Raise the select_spike event.
spike_id = spike_ids[i]
cluster_id = spike_clusters[i]
emit('select_spike', self, channel_id=channel_id,
spike_id=spike_id, cluster_id=cluster_id)
if 'Shift' in e.modifiers:
# Get mouse position in NDC.
box_id, _ = self.canvas.stacked.box_map(e.pos)
channel_id = int(np.nonzero(self.channel_y_ranks == box_id)[0][0])
emit('select_channel', self, channel_id=channel_id, button=e.button)
def on_mouse_wheel(self, e): # pragma: no cover
"""Scroll through the data with alt+wheel."""
super(TraceView, self).on_mouse_wheel(e)
if e.modifiers == ('Alt',):
start, end = self._interval
delay = e.delta * (end - start) * .1
self.shift(-delay)
class ProbeView(ManualClusteringView):
"""This view displays the positions of all channels on the probe, highlighting channels
where the selected clusters belong.
Constructor
-----------
positions : array-like
An `(n_channels, 2)` array with the channel positions
best_channels : function
Maps `cluster_id` to the list of the best_channel_ids.
channel_labels : list
List of channel label strings.
dead_channels : list
List of dead channel ids.
"""
_default_position = 'right'
# Marker size of channels without selected clusters.
unselected_marker_size = 10
# Marker size of channels with selected clusters.
selected_marker_size = 15
# Alpha value of the dead channels.
dead_channel_alpha = .25
do_show_labels = False
def __init__(
self, positions=None, best_channels=None, channel_labels=None,
dead_channels=None, **kwargs):
super(ProbeView, self).__init__(**kwargs)
self.state_attrs += ('do_show_labels',)
# Normalize positions.
assert positions.ndim == 2
assert positions.shape[1] == 2
positions = positions.astype(np.float32)
self.positions, self.data_bounds = _get_pos_data_bounds(positions)
self.n_channels = positions.shape[0]
self.best_channels = best_channels
self.channel_labels = channel_labels or [str(ch) for ch in range(self.n_channels)]
self.dead_channels = dead_channels if dead_channels is not None else ()
self.probe_visual = ScatterVisual()
self.canvas.add_visual(self.probe_visual)
# Probe visual.
color = np.ones((self.n_channels, 4))
color[:, :3] = .5
# Change alpha value for dead channels.
if len(self.dead_channels):
color[self.dead_channels, 3] = self.dead_channel_alpha
self.probe_visual.set_data(
pos=self.positions, data_bounds=self.data_bounds,
color=color, size=self.unselected_marker_size)
# Cluster visual.
self.cluster_visual = ScatterVisual()
self.canvas.add_visual(self.cluster_visual)
# Text visual
color[:] = 1
color[self.dead_channels, :3] = self.dead_channel_alpha * 2
self.text_visual = TextVisual()
self.text_visual.inserter.insert_vert('uniform float n_channels;', 'header')
self.text_visual.inserter.add_varying(
'float', 'v_discard',
'float((n_channels >= 200 * u_zoom.y) && '
'(mod(int(a_string_index), int(n_channels / (200 * u_zoom.y))) >= 1))')
self.text_visual.inserter.insert_frag('if (v_discard > 0) discard;', 'end')
self.canvas.add_visual(self.text_visual)
self.text_visual.set_data(
pos=self.positions, text=self.channel_labels, anchor=[0, -1],
data_bounds=self.data_bounds, color=color
)
self.text_visual.program['n_channels'] = self.n_channels
self.canvas.update()
def _get_clu_positions(self, cluster_ids):
"""Get the positions of the channels containing selected clusters."""
# List of channels per cluster.
cluster_channels = {i: self.best_channels(cl) for i, cl in enumerate(cluster_ids)}
# List of clusters per channel.
clusters_per_channel = defaultdict(lambda: [])
for clu_idx, channels in cluster_channels.items():
for channel in channels:
clusters_per_channel[channel].append(clu_idx)
# Enumerate the discs for each channel.
w = self.data_bounds[2] - self.data_bounds[0]
clu_pos = []
clu_colors = []
for channel_id, (x, y) in enumerate(self.positions):
for i, clu_idx in enumerate(clusters_per_channel[channel_id]):
n = len(clusters_per_channel[channel_id])
# Translation.
t = .025 * w * (i - .5 * (n - 1))
x += t
alpha = 1.0 if channel_id not in self.dead_channels else self.dead_channel_alpha
clu_pos.append((x, y))
clu_colors.append(selected_cluster_color(clu_idx, alpha=alpha))
return np.array(clu_pos), np.array(clu_colors)
def on_select(self, cluster_ids=(), **kwargs):
"""Update the view with the selected clusters."""
self.cluster_ids = cluster_ids
if not cluster_ids:
return
pos, colors = self._get_clu_positions(cluster_ids)
self.cluster_visual.set_data(
pos=pos, color=colors, size=self.selected_marker_size, data_bounds=self.data_bounds)
self.canvas.update()
def attach(self, gui):
"""Attach the view to the GUI."""
super(ProbeView, self).attach(gui)
self.actions.add(self.toggle_show_labels, checkable=True, checked=self.do_show_labels)
if not self.do_show_labels:
self.text_visual.hide()
def toggle_show_labels(self, checked):
"""Toggle the display of the channel ids."""
logger.debug("Set show labels to %s.", checked)
self.do_show_labels = checked
self.text_visual._hidden = not checked
self.canvas.update()
class WaveformView(ScalingMixin, ManualClusteringView):
"""This view shows the waveforms of the selected clusters, on relevant channels,
following the probe geometry.
Constructor
-----------
waveforms : dict of functions
Every function maps a cluster id to a Bunch with the following attributes:
* `data` : a 3D array `(n_spikes, n_samples, n_channels_loc)`
* `channel_ids` : the channel ids corresponding to the third dimension in `data`
* `channel_labels` : a list of channel labels for every channel in `channel_ids`
* `channel_positions` : a 2D array with the coordinates of the channels on the probe
* `masks` : a 2D array `(n_spikes, n_channels)` with the waveforms masks
* `alpha` : the alpha transparency channel
The keys of the dictionary are called **waveform types**. The `next_waveforms_type`
action cycles through all available waveform types. The key `waveforms` is mandatory.
waveform_type : str
Default key of the waveforms dictionary to plot initially.
"""
_default_position = 'right'
cluster_ids = ()
default_shortcuts = {
'toggle_waveform_overlap': 'o',
'toggle_show_labels': 'ctrl+l',
'next_waveforms_type': 'w',
'toggle_mean_waveforms': 'm',
# Box scaling.
'widen': 'ctrl+right',
'narrow': 'ctrl+left',
'increase': 'ctrl+up',
'decrease': 'ctrl+down',
'change_box_size': 'ctrl+wheel',
# Probe scaling.
'extend_horizontally': 'shift+right',
'shrink_horizontally': 'shift+left',
'extend_vertically': 'shift+up',
'shrink_vertically': 'shift+down',
}
default_snippets = {
'change_n_spikes_waveforms': 'wn',
}
def __init__(self, waveforms=None, waveforms_type=None, **kwargs):
self._overlap = False
self.do_show_labels = True
self.channel_ids = None
self.filtered_tags = ()
# Initialize the view.
super(WaveformView, self).__init__(**kwargs)
self.state_attrs += ('waveforms_type', 'overlap', 'do_show_labels')
self.local_state_attrs += ('box_scaling', 'probe_scaling')
# Box and probe scaling.
self.canvas.set_layout('boxed', box_bounds=[[-1, -1, +1, +1]])
self.canvas.enable_axes()
self._box_scaling = (1., 1.)
self._probe_scaling = (1., 1.)
self.box_pos = np.array(self.canvas.boxed.box_pos)
self.box_size = np.array(self.canvas.boxed.box_size)
self._update_boxes()
# Ensure waveforms is a dictionary, even if there is a single waveforms type.
waveforms = waveforms if isinstance(waveforms, dict) else {
'waveforms': waveforms
}
assert waveforms
self.waveforms = waveforms
self.waveforms_types = list(waveforms.keys())
# Current waveforms type.
self.waveforms_type = waveforms_type or self.waveforms_types[0]
assert self.waveforms_type in waveforms
assert 'waveforms' in waveforms
self.text_visual = TextVisual()
self.canvas.add_visual(self.text_visual)
self.waveform_visual = PlotVisual()
self.canvas.add_visual(self.waveform_visual)
# Internal methods
# -------------------------------------------------------------------------
def _get_data_bounds(self, bunchs):
m = min(_min(b.data) for b in bunchs)
M = max(_max(b.data) for b in bunchs)
return [-1, m, +1, M]
def get_clusters_data(self):
bunchs = [
self.waveforms[self.waveforms_type](cluster_id)
for cluster_id in self.cluster_ids
]
clu_offsets = _get_clu_offsets(bunchs)
n_clu = max(clu_offsets) + 1
# Offset depending on the overlap.
for i, (bunch, offset) in enumerate(zip(bunchs, clu_offsets)):
bunch.index = i
bunch.offset = offset
bunch.n_clu = n_clu
bunch.color = selected_cluster_color(i, bunch.get('alpha', .75))
return bunchs
def _plot_cluster(self, bunch):
wave = bunch.data
if wave is None or not wave.size:
return
channel_ids_loc = bunch.channel_ids
n_channels = len(channel_ids_loc)
masks = bunch.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.
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)
t = _overlap_transform(t,
offset=bunch.offset,
n=bunch.n_clu,
overlap=self.overlap)
# 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.
masks *= .99999
# NOTE: we add the cluster index which is used for the
# computation of the depth on the GPU.
masks += bunch.index
# Generate the box index (one number per channel).
box_index = _index_of(channel_ids_loc, self.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.waveform_visual.add_batch_data(x=t,
y=wave,
color=bunch.color,
masks=masks,
box_index=box_index,
data_bounds=self.data_bounds)
def _plot_labels(self, channel_ids, n_clusters, channel_labels):
# Add channel labels.
if not self.do_show_labels:
return
self.text_visual.reset_batch()
for i, ch in enumerate(channel_ids):
label = channel_labels[ch]
self.text_visual.add_batch_data(
pos=[-1, 0],
text=str(label),
anchor=[-1.25, 0],
box_index=i,
)
self.canvas.update_visual(self.text_visual)
def plot(self, **kwargs):
"""Update the view with the current cluster selection."""
if not self.cluster_ids:
return
bunchs = self.get_clusters_data()
# All channel ids appearing in all selected clusters.
channel_ids = sorted(set(_flatten([d.channel_ids for d in bunchs])))
self.channel_ids = channel_ids
# Channel labels.
channel_labels = {}
for d in bunchs:
chl = d.get('channel_labels', ['%d' % ch for ch in d.channel_ids])
channel_labels.update({
channel_id: chl[i]
for i, channel_id in enumerate(d.channel_ids)
})
# Update the box bounds as a function of the selected channels.
if channel_ids:
self.canvas.boxed.box_bounds = _get_box_bounds(bunchs, channel_ids)
self.box_pos = np.array(self.canvas.boxed.box_pos)
self.box_size = np.array(self.canvas.boxed.box_size)
self._update_boxes()
self.data_bounds = self._get_data_bounds(bunchs)
self.waveform_visual.reset_batch()
for bunch in bunchs:
self._plot_cluster(bunch)
self.canvas.update_visual(self.waveform_visual)
self._plot_labels(channel_ids, len(self.cluster_ids), channel_labels)
self._update_axes(bunchs)
self.canvas.update()
def _update_axes(self, bunchs):
"""Update the axes."""
# Update the axes data bounds.
_, m, _, M = self.data_bounds
# Waveform duration, scaled by overlap factor if needed.
wave_dur = bunchs[0].get('waveform_duration', 1.)
wave_dur /= .5 * (1 + _overlap_transform(
1, n=len(self.cluster_ids), overlap=self.overlap))
x1, y1 = range_transform(self.canvas.boxed.box_bounds[0], NDC,
[wave_dur, M - m])
axes_data_bounds = (0, 0, x1, y1)
self.canvas.axes.reset_data_bounds(axes_data_bounds, do_update=True)
def attach(self, gui):
"""Attach the view to the GUI."""
super(WaveformView, self).attach(gui)
self.actions.add(self.toggle_waveform_overlap,
checkable=True,
checked=self.overlap)
self.actions.add(self.toggle_show_labels,
checkable=True,
checked=self.do_show_labels)
self.actions.add(self.next_waveforms_type)
self.actions.add(self.toggle_mean_waveforms, checkable=True)
self.actions.separator()
# Box scaling.
self.actions.add(self.widen)
self.actions.add(self.narrow)
self.actions.separator()
# Probe scaling.
self.actions.add(self.extend_horizontally)
self.actions.add(self.shrink_horizontally)
self.actions.separator()
self.actions.add(self.extend_vertically)
self.actions.add(self.shrink_vertically)
self.actions.separator()
@property
def boxed(self):
"""Layout instance."""
return self.canvas.boxed
# Overlap
# -------------------------------------------------------------------------
@property
def overlap(self):
"""Whether to overlap the waveforms belonging to different clusters."""
return self._overlap
@overlap.setter
def overlap(self, value):
self._overlap = value
self.plot()
def toggle_waveform_overlap(self, checked):
"""Toggle the overlap of the waveforms."""
self.overlap = checked
# Box scaling
# -------------------------------------------------------------------------
def _update_boxes(self):
self.canvas.boxed.update_boxes(self.box_pos * self.probe_scaling,
self.box_size)
def _apply_box_scaling(self):
self.canvas.layout.scaling = self._box_scaling
@property
def box_scaling(self):
"""Scaling of the channel boxes."""
return self._box_scaling
@box_scaling.setter
def box_scaling(self, value):
assert len(value) == 2
self._box_scaling = value
self._apply_box_scaling()
def widen(self):
"""Increase the horizontal scaling of the waveforms."""
w, h = self._box_scaling
self._box_scaling = (w * self._scaling_param_increment, h)
self._apply_box_scaling()
def narrow(self):
"""Decrease the horizontal scaling of the waveforms."""
w, h = self._box_scaling
self._box_scaling = (w / self._scaling_param_increment, h)
self._apply_box_scaling()
def _get_scaling_value(self):
return self._box_scaling[1]
def _set_scaling_value(self, value):
w, h = self._box_scaling
self.box_scaling = (w, value)
self._update_boxes()
# Probe scaling
# -------------------------------------------------------------------------
@property
def probe_scaling(self):
"""Scaling of the entire probe."""
return self._probe_scaling
@probe_scaling.setter
def probe_scaling(self, value):
assert len(value) == 2
self._probe_scaling = value
self._update_boxes()
def extend_horizontally(self):
"""Increase the horizontal scaling of the probe."""
w, h = self._probe_scaling
self._probe_scaling = (w * self._scaling_param_increment, h)
self._update_boxes()
def shrink_horizontally(self):
"""Decrease the horizontal scaling of the waveforms."""
w, h = self._probe_scaling
self._probe_scaling = (w / self._scaling_param_increment, h)
self._update_boxes()
def extend_vertically(self):
"""Increase the vertical scaling of the waveforms."""
w, h = self._probe_scaling
self._probe_scaling = (w, h * self._scaling_param_increment)
self._update_boxes()
def shrink_vertically(self):
"""Decrease the vertical scaling of the waveforms."""
w, h = self._probe_scaling
self._probe_scaling = (w, h / self._scaling_param_increment)
self._update_boxes()
# Navigation
# -------------------------------------------------------------------------
def toggle_show_labels(self, checked):
"""Whether to show the channel ids or not."""
self.do_show_labels = checked
self.text_visual.show() if checked else self.text_visual.hide()
self.canvas.update()
def on_mouse_click(self, e):
"""Select a channel by clicking on a box in the waveform view."""
b = e.button
nums = tuple('%d' % i for i in range(10))
if 'Control' in e.modifiers or e.key in nums:
key = int(e.key) if e.key in nums else None
# Get mouse position in NDC.
channel_idx, _ = self.canvas.boxed.box_map(e.pos)
channel_id = self.channel_ids[channel_idx]
logger.debug("Click on channel_id %d with key %s and button %s.",
channel_id, key, b)
emit('channel_click',
self,
channel_id=channel_id,
key=key,
button=b)
def next_waveforms_type(self):
"""Switch to the next waveforms type."""
i = self.waveforms_types.index(self.waveforms_type)
n = len(self.waveforms_types)
self.waveforms_type = self.waveforms_types[(i + 1) % n]
logger.debug("Switch to waveforms type %s.", self.waveforms_type)
self.plot()
def toggle_mean_waveforms(self, checked):
"""Switch to the `mean_waveforms` type, if it is available."""
if self.waveforms_type == 'mean_waveforms':
self.waveforms_type = 'waveforms'
self.plot()
elif 'mean_waveforms' in self.waveforms_types:
self.waveforms_type = 'mean_waveforms'
self.plot()
class TraceView(ScalingMixin, ManualClusteringView):
"""This view shows the raw traces along with spike waveforms.
Constructor
-----------
traces : function
Maps a time interval `(t0, t1)` to a `Bunch(data, color, waveforms)` where
* `data` is an `(n_samples, n_channels)` array
* `waveforms` is a list of bunchs with the following attributes:
* `data`
* `color`
* `channel_ids`
* `start_time`
* `spike_id`
* `spike_cluster`
spike_times : function
Teturns the list of relevant spike times.
sample_rate : float
duration : float
n_channels : int
channel_vertical_order : array-like
Permutation of the channels. This 1D array gives the channel id of all channels from
top to bottom (or conversely, depending on `origin=top|bottom`).
channel_labels : list
Labels of all shown channels. By default, this is just the channel ids.
"""
_default_position = 'left'
auto_update = True
auto_scale = True
interval_duration = .25 # default duration of the interval
shift_amount = .1
scaling_coeff_x = 1.25
trace_quantile = .01 # quantile for auto-scaling
default_trace_color = (.5, .5, .5, 1)
default_shortcuts = {
'change_trace_size': 'ctrl+wheel',
'decrease': 'alt+down',
'increase': 'alt+up',
'go_left': 'alt+left',
'go_right': 'alt+right',
'go_to_start': 'alt+home',
'go_to_end': 'alt+end',
'go_to': 'alt+t',
'go_to_next_spike': 'alt+pgdown',
'go_to_previous_spike': 'alt+pgup',
'narrow': 'alt++',
'select_spike': 'ctrl+click',
'switch_origin': 'alt+o',
'toggle_highlighted_spikes': 'alt+s',
'toggle_show_labels': 'alt+l',
'widen': 'alt+-',
}
default_snippets = {
'go_to': 'tg',
'shift': 'ts',
}
def __init__(
self, traces=None, sample_rate=None, spike_times=None, duration=None, n_channels=None,
channel_vertical_order=None, channel_labels=None, **kwargs):
self.do_show_labels = True
self.show_all_spikes = False
self._scaling = 1.
self.get_spike_times = spike_times
# Sample rate.
assert sample_rate > 0
self.sample_rate = float(sample_rate)
self.dt = 1. / self.sample_rate
# Traces and spikes.
assert hasattr(traces, '__call__')
self.traces = traces
self.waveforms = None
assert duration >= 0
self.duration = duration
assert n_channels >= 0
self.n_channels = n_channels
# Channel permutation.
self._channel_perm = (
np.arange(n_channels) if channel_vertical_order is None else channel_vertical_order)
assert self._channel_perm.shape == (n_channels,)
self._channel_perm = np.argsort(self._channel_perm)
# Channel labels.
self.channel_labels = (
channel_labels if channel_labels is not None else
['%d' % ch for ch in range(n_channels)])
assert len(self.channel_labels) == n_channels
# Box and probe scaling.
self._origin = None
# Initialize the view.
super(TraceView, self).__init__(**kwargs)
self.state_attrs += ('origin', 'do_show_labels', 'show_all_spikes', 'auto_scale')
self.local_state_attrs += ('interval', 'scaling',)
self.canvas.set_layout('stacked', origin=self.origin, n_plots=self.n_channels)
self.canvas.enable_axes(show_y=False)
# Visuals.
self.trace_visual = UniformPlotVisual()
self.canvas.add_visual(self.trace_visual)
self.waveform_visual = PlotVisual()
self.canvas.add_visual(self.waveform_visual)
self.text_visual = TextVisual()
_fix_coordinate_in_visual(self.text_visual, 'x')
self.canvas.add_visual(self.text_visual)
# Make a copy of the initial box pos and size. We'll apply the scaling
# to these quantities.
self.box_size = np.array(self.canvas.stacked.box_size)
# Initial interval.
self._interval = None
self.go_to(duration / 2.)
self._waveform_times = []
@property
def stacked(self):
return self.canvas.stacked
def _permute_channels(self, x, inv=False):
cp = self._channel_perm
cp = np.argsort(cp)
return cp[x]
# Internal methods
# -------------------------------------------------------------------------
def _plot_traces(self, traces, color=None):
traces = traces.T
n_samples = traces.shape[1]
n_ch = self.n_channels
assert traces.shape == (n_ch, n_samples)
color = color or self.default_trace_color
t = self._interval[0] + np.arange(n_samples) * self.dt
t = np.tile(t, (n_ch, 1))
box_index = self._permute_channels(np.arange(n_ch))
box_index = np.repeat(box_index[:, np.newaxis], n_samples, axis=1)
assert t.shape == (n_ch, n_samples)
assert traces.shape == (n_ch, n_samples)
assert box_index.shape == (n_ch, n_samples)
self.trace_visual.color = color
self.canvas.update_visual(
self.trace_visual,
t, traces,
data_bounds=self.data_bounds,
box_index=box_index.ravel(),
)
def _plot_spike(self, bunch):
# The spike time corresponds to the first sample of the waveform.
n_samples, n_channels = bunch.data.shape
assert len(bunch.channel_ids) == n_channels
# Generate the x coordinates of the waveform.
t = bunch.start_time + self.dt * np.arange(n_samples)
t = np.tile(t, (n_channels, 1)) # (n_unmasked_channels, n_samples)
# The box index depends on the channel.
box_index = self._permute_channels(bunch.channel_ids)
box_index = np.repeat(box_index[:, np.newaxis], n_samples, axis=0)
self.waveform_visual.add_batch_data(
box_index=box_index,
x=t, y=bunch.data.T, color=bunch.color,
data_bounds=self.data_bounds,
)
def _plot_labels(self, traces):
self.text_visual.reset_batch()
for ch in range(self.n_channels):
bi = self._permute_channels(ch)
ch_label = self.channel_labels[ch]
self.text_visual.add_batch_data(
pos=[self.data_bounds[0], 0],
text=ch_label,
anchor=[+1., 0],
data_bounds=self.data_bounds,
box_index=bi,
)
self.canvas.update_visual(self.text_visual)
# Public methods
# -------------------------------------------------------------------------
def _restrict_interval(self, interval):
start, end = interval
# Round the times to full samples to avoid subsampling shifts
# in the traces.
start = int(round(start * self.sample_rate)) / self.sample_rate
end = int(round(end * self.sample_rate)) / self.sample_rate
# Restrict the interval to the boundaries of the traces.
if start < 0:
end += (-start)
start = 0
elif end >= self.duration:
start -= (end - self.duration)
end = self.duration
start = np.clip(start, 0, end)
end = np.clip(end, start, self.duration)
assert 0 <= start < end <= self.duration
return start, end
def set_interval(self, interval=None, change_status=True):
"""Display the traces and spikes in a given interval."""
if interval is None:
interval = self._interval
interval = self._restrict_interval(interval)
# Load the traces.
traces = self.traces(interval)
self.waveforms = traces.get('waveforms', [])
if interval != self._interval:
logger.debug("Redraw the entire trace view.")
self._interval = interval
start, end = interval
# Set the status message.
if change_status:
self.set_status('Interval: {:.3f} s - {:.3f} s'.format(start, end))
# Find the data bounds.
if self.auto_scale or getattr(self, 'data_bounds', NDC) == NDC:
ymin = np.quantile(traces.data, self.trace_quantile)
ymax = np.quantile(traces.data, 1. - self.trace_quantile)
else:
ymin, ymax = self.data_bounds[1], self.data_bounds[3]
self.data_bounds = (start, ymin, end, ymax)
# Used for spike click.
self._waveform_times = []
# Plot the traces.
self._plot_traces(
traces.data, color=traces.get('color', None))
# Plot the labels.
if self.do_show_labels:
self._plot_labels(traces.data)
# Plot the waveforms.
self.plot()
def on_select(self, cluster_ids=None, **kwargs):
self.cluster_ids = cluster_ids
if not cluster_ids:
return
# Make sure we call again self.traces() when the cluster selection changes.
self.set_interval()
def plot(self, **kwargs):
"""Plot the waveforms."""
waveforms = self.waveforms
assert isinstance(waveforms, list)
if waveforms:
self.waveform_visual.show()
self.waveform_visual.reset_batch()
for w in waveforms:
self._plot_spike(w)
self._waveform_times.append(
(w.start_time, w.spike_id, w.spike_cluster, w.get('channel_ids', None)))
self.canvas.update_visual(self.waveform_visual)
else: # pragma: no cover
self.waveform_visual.hide()
self._update_axes()
self.canvas.update()
def attach(self, gui):
"""Attach the view to the GUI."""
super(TraceView, self).attach(gui)
self.actions.add(self.toggle_show_labels, checkable=True, checked=self.do_show_labels)
self.actions.add(
self.toggle_highlighted_spikes, checkable=True, checked=self.show_all_spikes)
self.actions.add(self.toggle_auto_scale, checkable=True, checked=self.auto_scale)
self.actions.add(self.switch_origin)
self.actions.separator()
self.actions.add(
self.go_to, prompt=True, prompt_default=lambda: str(self.time))
self.actions.separator()
self.actions.add(self.go_to_start)
self.actions.add(self.go_to_end)
self.actions.separator()
self.actions.add(self.shift, prompt=True)
self.actions.add(self.go_right)
self.actions.add(self.go_left)
self.actions.separator()
self.actions.add(self.widen)
self.actions.add(self.narrow)
self.actions.separator()
self.actions.add(self.go_to_next_spike)
self.actions.add(self.go_to_previous_spike)
self.actions.separator()
self.set_interval()
# Origin
# -------------------------------------------------------------------------
@property
def origin(self):
"""Whether to show the channels from top to bottom (`top` option, the default), or from
bottom to top (`bottom`)."""
return self._origin
@origin.setter
def origin(self, value):
self._origin = value
if self.canvas.layout:
self.canvas.layout.origin = value
def switch_origin(self):
"""Switch between top and bottom origin for the channels."""
self.origin = 'top' if self._origin in ('bottom', None) else 'bottom'
# Navigation
# -------------------------------------------------------------------------
@property
def time(self):
"""Time at the center of the window."""
return sum(self._interval) * .5
@property
def interval(self):
"""Interval as `(tmin, tmax)`."""
return self._interval
@interval.setter
def interval(self, value):
self.set_interval(value)
@property
def half_duration(self):
"""Half of the duration of the current interval."""
if self._interval is not None:
a, b = self._interval
return (b - a) * .5
else:
return self.interval_duration * .5
def go_to(self, time):
"""Go to a specific time (in seconds)."""
half_dur = self.half_duration
self.set_interval((time - half_dur, time + half_dur))
def shift(self, delay):
"""Shift the interval by a given delay (in seconds)."""
self.go_to(self.time + delay)
def go_to_start(self):
"""Go to the start of the recording."""
self.go_to(0)
def go_to_end(self):
"""Go to end of the recording."""
self.go_to(self.duration)
def go_right(self):
"""Go to right."""
start, end = self._interval
delay = (end - start) * .1
self.shift(delay)
def go_left(self):
"""Go to left."""
start, end = self._interval
delay = (end - start) * .1
self.shift(-delay)
def _jump_to_spike(self, delta=+1):
"""Jump to next or previous spike from the selected clusters."""
spike_times = self.get_spike_times()
if spike_times is not None and len(spike_times):
ind = np.searchsorted(spike_times, self.time)
n = len(spike_times)
self.go_to(spike_times[(ind + delta) % n])
def go_to_next_spike(self, ):
"""Jump to the next spike from the first selected cluster."""
self._jump_to_spike(+1)
def go_to_previous_spike(self, ):
"""Jump to the previous spike from the first selected cluster."""
self._jump_to_spike(-1)
def toggle_highlighted_spikes(self, checked):
"""Toggle between showing all spikes or selected spikes."""
self.show_all_spikes = checked
self.set_interval()
def widen(self):
"""Increase the interval size."""
t, h = self.time, self.half_duration
h *= self.scaling_coeff_x
self.set_interval((t - h, t + h))
def narrow(self):
"""Decrease the interval size."""
t, h = self.time, self.half_duration
h /= self.scaling_coeff_x
self.set_interval((t - h, t + h))
# Misc
# -------------------------------------------------------------------------
def toggle_show_labels(self, checked):
"""Toggle the display of the channel ids."""
logger.debug("Set show labels to %s.", checked)
self.do_show_labels = checked
self.set_interval()
def toggle_auto_scale(self, checked):
"""Toggle automatic scaling of the traces."""
logger.debug("Set auto scale to %s.", checked)
self.auto_scale = checked
# Scaling
# -------------------------------------------------------------------------
def _apply_scaling(self):
self.canvas.layout.scaling = (self.canvas.layout.scaling[0], self._scaling)
@property
def scaling(self):
"""Scaling of the channel boxes."""
return self._scaling
@scaling.setter
def scaling(self, value):
self._scaling = value
self._apply_scaling()
def _get_scaling_value(self):
return self.scaling
def _set_scaling_value(self, value):
self.scaling = value
# Spike selection
# -------------------------------------------------------------------------
def on_mouse_click(self, e):
"""Select a cluster by clicking on a spike."""
if 'Control' in e.modifiers:
# Get mouse position in NDC.
box_id, _ = self.canvas.stacked.box_map(e.pos)
channel_id = self._permute_channels(box_id, inv=True)
# Find the spike and cluster closest to the mouse.
db = self.data_bounds
# Get the information about the displayed spikes.
wt = [(t, s, c, ch) for t, s, c, ch in self._waveform_times if channel_id in ch]
if not wt:
return
# Get the time coordinate of the mouse position.
mouse_pos = self.canvas.panzoom.window_to_ndc(e.pos)
mouse_time = Range(NDC, db).apply(mouse_pos)[0][0]
# Get the closest spike id.
times, spike_ids, spike_clusters, channel_ids = zip(*wt)
i = np.argmin(np.abs(np.array(times) - mouse_time))
# Raise the spike_click event.
spike_id = spike_ids[i]
cluster_id = spike_clusters[i]
emit('spike_click', self, channel_id=channel_id,
spike_id=spike_id, cluster_id=cluster_id)
class WaveformClusteringView(LassoMixin,ManualClusteringView):
default_shortcuts = {
'next_channel': 'f',
'previous_channel': 'r',
}
def __init__(self, model=None):
super(WaveformClusteringView, self).__init__()
self.canvas.enable_axes()
self.canvas.enable_lasso()
self.text_visual = TextVisual()
self.canvas.add_visual(self.text_visual, exclude_origins=(self.canvas.panzoom,))
self.model = model
self.gain = 0.195
self.Fs = 30 # kHz
self.visual = PlotVisual()
self.canvas.add_visual(self.visual)
self.canvas.panzoom.zoom = self.canvas.panzoom._default_zoom = (.97, .95)
self.canvas.panzoom.pan = self.canvas.panzoom._default_pan = (-.01, 0)
self.cluster_ids = None
self.cluster_id = None
self.channel_ids = None
self.wavefs = None
self.current_channel_idx = None
def on_select(self, cluster_ids=(), **kwargs):
self.cluster_ids = cluster_ids
if not cluster_ids:
return
if self.cluster_id != cluster_ids[0]:
self.cluster_id = cluster_ids[0]
self.channel_ids = self.model.get_cluster_channels(self.cluster_id)
self.spike_ids = self.model.get_cluster_spikes(self.cluster_id)
self.wavefs = self.model.get_waveforms(self.spike_ids,channel_ids=self.channel_ids)
self.setChannelIdx(0)
def plotWaveforms(self):
Nspk,Ntime,Nchan = self.wavefs.shape
self.visual.reset_batch()
self.text_visual.reset_batch()
x = np.tile(np.linspace(-Ntime/2/self.Fs, Ntime/2/self.Fs, Ntime), (Nspk, 1))
M=np.max(np.abs(self.wavefs[:,:,self.current_channel_idx]))
#print(M*self.gain)
if M*self.gain<100:
M = 10*np.ceil(M*self.gain/10)
elif M*self.gain<1000:
M = 100*np.ceil(M*self.gain/100)
else:
M = 1000*np.floor(M*self.gain/1000)
self.data_bounds = (x[0][0], -M, x[0][-1], M)
colorwavef = selected_cluster_color(0)
colormedian = selected_cluster_color(3)#(1,156/256,0,.5)#selected_cluster_color(1)
colorstd = (0,1,0,1)#selected_cluster_color(2)
colorqtl = (1,1,0,1)
if Nspk>100:
medianCl = np.median(self.wavefs[:,:,self.current_channel_idx],axis=0)
stdCl = np.std(self.wavefs[:,:,self.current_channel_idx],axis=0)
q1 = np.quantile(self.wavefs[:,:,self.current_channel_idx],.01,axis=0,interpolation='higher')
q9 = np.quantile(self.wavefs[:,:,self.current_channel_idx],.99,axis=0,interpolation='lower')
self.visual.add_batch_data(
x=x, y=self.gain*self.wavefs[:,:,self.current_channel_idx], color=colorwavef, data_bounds=self.data_bounds, box_index=0)
#stats
if Nspk>100:
x1 = x[0]
self.visual.add_batch_data(
x=x1, y=self.gain*medianCl, color=colormedian, data_bounds=self.data_bounds, box_index=0)
self.visual.add_batch_data(
x=x1, y=self.gain*(medianCl+3*stdCl), color=colorstd, data_bounds=self.data_bounds, box_index=0)
self.visual.add_batch_data(
x=x1, y=self.gain*(medianCl-3*stdCl), color=colorstd, data_bounds=self.data_bounds, box_index=0)
self.visual.add_batch_data(
x=x1, y=self.gain*q1, color=colorqtl, data_bounds=self.data_bounds, box_index=0)
self.visual.add_batch_data(
x=x1, y=self.gain*q9, color=colorqtl, data_bounds=self.data_bounds, box_index=0)
#axes
self.text_visual.add_batch_data(
pos=[.9, .98],
text='[uV]',
anchor=[-1, -1],
box_index=0,
)
self.text_visual.add_batch_data(
pos=[-1, -.95],
text='[ms]',
anchor=[1, 1],
box_index=0,
)
label = 'Ch {a}'.format(a=self.channel_ids[self.current_channel_idx])
self.text_visual.add_batch_data(
pos=[-.98, .98],
text=str(label),
anchor=[1, -1],
box_index=0,
)
self.canvas.update_visual(self.visual)
self.canvas.update_visual(self.text_visual)
self.canvas.axes.reset_data_bounds(self.data_bounds)
self.canvas.update()
def setChannel(self,channel_id):
self.channel_ids
itemindex = np.where(self.channel_ids==channel_id)[0]
if len(itemindex):
self.setChannelIdx(itemindex[0])
def setChannelIdx(self,channel_idx):
self.current_channel_idx = channel_idx
self.plotWaveforms()
def setNextChannelIdx(self):
if self.current_channel_idx == len(self.channel_ids)-1:
return
self.setChannelIdx(self.current_channel_idx+1)
def setPrevChannelIdx(self):
if self.current_channel_idx == 0:
return
self.setChannelIdx(self.current_channel_idx-1)
def on_request_split(self, sender=None):
"""Return the spikes enclosed by the lasso."""
if (self.canvas.lasso.count < 3 or not len(self.cluster_ids)): # pragma: no cover
return np.array([], dtype=np.int64)
pos = []
spike_ids = []
Ntime = self.wavefs.shape[1]
x = np.linspace(-Ntime/2/self.Fs, Ntime/2/self.Fs, Ntime)
for idx,spike in enumerate(self.spike_ids):
points = np.c_[x,self.gain*self.wavefs[idx,:,self.current_channel_idx]]
pos.append(points)
spike_ids.append([spike]*len(x))
if not pos: # pragma: no cover
logger.warning("Empty lasso.")
return np.array([])
pos = np.vstack(pos)
pos = range_transform([self.data_bounds], [NDC], pos)
spike_ids = np.concatenate(spike_ids)
# Find lassoed spikes.
ind = self.canvas.lasso.in_polygon(pos)
self.canvas.lasso.clear()
# Return all spikes not lassoed, so the selected cluster is still the same we are working on
spikes_to_remove = np.unique(spike_ids[ind])
keepspikes=np.isin(self.spike_ids,spikes_to_remove,assume_unique=True,invert=True)
A=self.spike_ids[self.spike_ids != spikes_to_remove]
if len(A)>0:
return self.spike_ids[keepspikes]
else:
return np.array([], dtype=np.int64)
class WaveformView(ScalingMixin, ManualClusteringView):
"""This view shows the waveforms of the selected clusters, on relevant channels,
following the probe geometry.
Constructor
-----------
waveforms : dict of functions
Every function maps a cluster id to a Bunch with the following attributes:
* `data` : a 3D array `(n_spikes, n_samples, n_channels_loc)`
* `channel_ids` : the channel ids corresponding to the third dimension in `data`
* `channel_labels` : a list of channel labels for every channel in `channel_ids`
* `channel_positions` : a 2D array with the coordinates of the channels on the probe
* `masks` : a 2D array `(n_spikes, n_channels)` with the waveforms masks
* `alpha` : the alpha transparency channel
The keys of the dictionary are called **waveform types**. The `next_waveforms_type`
action cycles through all available waveform types. The key `waveforms` is mandatory.
waveforms_type : str
Default key of the waveforms dictionary to plot initially.
"""
# Do not show too many clusters.
max_n_clusters = 8
_default_position = 'right'
ax_color = (.75, .75, .75, 1.)
tick_size = 5.
cluster_ids = ()
default_shortcuts = {
'toggle_waveform_overlap': 'o',
'toggle_show_labels': 'ctrl+l',
'next_waveforms_type': 'w',
'previous_waveforms_type': 'shift+w',
'toggle_mean_waveforms': 'm',
# Box scaling.
'widen': 'ctrl+right',
'narrow': 'ctrl+left',
'increase': 'ctrl+up',
'decrease': 'ctrl+down',
'change_box_size': 'ctrl+wheel',
# Probe scaling.
'extend_horizontally': 'shift+right',
'shrink_horizontally': 'shift+left',
'extend_vertically': 'shift+up',
'shrink_vertically': 'shift+down',
}
default_snippets = {
'change_n_spikes_waveforms': 'wn',
}
def __init__(self,
waveforms=None,
waveforms_type=None,
sample_rate=None,
**kwargs):
self._overlap = False
self.do_show_labels = True
self.channel_ids = None
self.filtered_tags = ()
self.wave_duration = 0. # updated in the plotting method
self.data_bounds = None
self.sample_rate = sample_rate
self._status_suffix = ''
assert sample_rate > 0., "The sample rate must be provided to the waveform view."
# Initialize the view.
super(WaveformView, self).__init__(**kwargs)
self.state_attrs += ('waveforms_type', 'overlap', 'do_show_labels')
self.local_state_attrs += ('box_scaling', 'probe_scaling')
# Box and probe scaling.
self.canvas.set_layout('boxed', box_pos=np.zeros((1, 2)))
# Ensure waveforms is a dictionary, even if there is a single waveforms type.
waveforms = waveforms or {}
waveforms = waveforms if isinstance(waveforms, dict) else {
'waveforms': waveforms
}
self.waveforms = waveforms
# Rotating property waveforms types.
self.waveforms_types = RotatingProperty()
for name, value in self.waveforms.items():
self.waveforms_types.add(name, value)
# Current waveforms type.
self.waveforms_types.set(waveforms_type)
assert self.waveforms_type in self.waveforms
self.text_visual = TextVisual()
self.canvas.add_visual(self.text_visual)
self.line_visual = LineVisual()
self.canvas.add_visual(self.line_visual)
self.tick_visual = UniformScatterVisual(marker='vbar',
color=self.ax_color,
size=self.tick_size)
self.canvas.add_visual(self.tick_visual)
# Two types of visuals: thin raw line visual for normal waveforms, thick antialiased
# agg plot visual for mean and template waveforms.
self.waveform_agg_visual = PlotAggVisual()
self.waveform_visual = PlotVisual()
self.canvas.add_visual(self.waveform_agg_visual)
self.canvas.add_visual(self.waveform_visual)
# Internal methods
# -------------------------------------------------------------------------
@property
def _current_visual(self):
if self.waveforms_type == 'waveforms':
return self.waveform_visual
else:
return self.waveform_agg_visual
def _get_data_bounds(self, bunchs):
m = min(_min(b.data) for b in bunchs)
M = max(_max(b.data) for b in bunchs)
# Symmetrize on the y axis.
M = max(abs(m), abs(M))
return [-1, -M, +1, M]
def get_clusters_data(self):
if self.waveforms_type not in self.waveforms:
return
bunchs = [
self.waveforms_types.get()(cluster_id)
for cluster_id in self.cluster_ids
]
clu_offsets = _get_clu_offsets(bunchs)
n_clu = max(clu_offsets) + 1
# Offset depending on the overlap.
for i, (bunch, offset) in enumerate(zip(bunchs, clu_offsets)):
bunch.index = i
bunch.offset = offset
bunch.n_clu = n_clu
bunch.color = selected_cluster_color(i, bunch.get('alpha', .75))
return bunchs
def _plot_cluster(self, bunch):
wave = bunch.data
if wave is None or not wave.size:
return
channel_ids_loc = bunch.channel_ids
n_channels = len(channel_ids_loc)
masks = bunch.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.
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)
t = _overlap_transform(t,
offset=bunch.offset,
n=bunch.n_clu,
overlap=self.overlap)
# 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.
eps = .001
masks = eps + (1 - 2 * eps) * masks
# NOTE: we add the cluster index which is used for the
# computation of the depth on the GPU.
masks += bunch.index
# Generate the box index (one number per channel).
box_index = _index_of(channel_ids_loc, self.channel_ids)
box_index = np.tile(box_index, n_spikes_clu)
# Find the correct number of vertices depending on the current waveform visual.
if self._current_visual == self.waveform_visual:
# PlotVisual
box_index = np.repeat(box_index, n_samples)
assert box_index.size == n_spikes_clu * n_channels * n_samples
else:
# PlotAggVisual
box_index = np.repeat(box_index, 2 * (n_samples + 2))
assert box_index.size == n_spikes_clu * n_channels * 2 * (
n_samples + 2)
# Generate the waveform array.
wave = np.transpose(wave, (0, 2, 1))
nw = n_spikes_clu * n_channels
wave = wave.reshape((nw, n_samples))
assert self.data_bounds is not None
self._current_visual.add_batch_data(x=t,
y=wave,
color=bunch.color,
masks=masks,
box_index=box_index,
data_bounds=self.data_bounds)
# Waveform axes.
# --------------
# Horizontal y=0 lines.
ax_db = self.data_bounds
a, b = _overlap_transform(np.array([-1, 1]),
offset=bunch.offset,
n=bunch.n_clu,
overlap=self.overlap)
box_index = _index_of(channel_ids_loc, self.channel_ids)
box_index = np.repeat(box_index, 2)
box_index = np.tile(box_index, n_spikes_clu)
hpos = np.tile([[a, 0, b, 0]], (nw, 1))
assert box_index.size == hpos.shape[0] * 2
self.line_visual.add_batch_data(
pos=hpos,
color=self.ax_color,
data_bounds=ax_db,
box_index=box_index,
)
# Vertical ticks every millisecond.
steps = np.arange(np.round(self.wave_duration * 1000))
# A vline every millisecond.
x = .001 * steps
# Scale to [-1, 1], same coordinates as the waveform points.
x = -1 + 2 * x / self.wave_duration
# Take overlap into account.
x = _overlap_transform(x,
offset=bunch.offset,
n=bunch.n_clu,
overlap=self.overlap)
x = np.tile(x, len(channel_ids_loc))
# Generate the box index.
box_index = _index_of(channel_ids_loc, self.channel_ids)
box_index = np.repeat(box_index, x.size // len(box_index))
assert x.size == box_index.size
self.tick_visual.add_batch_data(
x=x,
y=np.zeros_like(x),
data_bounds=ax_db,
box_index=box_index,
)
def _plot_labels(self, channel_ids, n_clusters, channel_labels):
# Add channel labels.
if not self.do_show_labels:
return
self.text_visual.reset_batch()
for i, ch in enumerate(channel_ids):
label = channel_labels[ch]
self.text_visual.add_batch_data(
pos=[-1, 0],
text=str(label),
anchor=[-1.25, 0],
box_index=i,
)
self.canvas.update_visual(self.text_visual)
def plot(self, **kwargs):
"""Update the view with the current cluster selection."""
if not self.cluster_ids:
return
bunchs = self.get_clusters_data()
if not bunchs:
return
# All channel ids appearing in all selected clusters.
channel_ids = sorted(set(_flatten([d.channel_ids for d in bunchs])))
self.channel_ids = channel_ids
if bunchs[0].data is not None:
self.wave_duration = bunchs[0].data.shape[1] / float(
self.sample_rate)
else: # pragma: no cover
self.wave_duration = 1.
# Channel labels.
channel_labels = {}
for d in bunchs:
chl = d.get('channel_labels', ['%d' % ch for ch in d.channel_ids])
channel_labels.update({
channel_id: chl[i]
for i, channel_id in enumerate(d.channel_ids)
})
# Update the Boxed box positions as a function of the selected channels.
if channel_ids:
self.canvas.boxed.update_boxes(_get_box_pos(bunchs, channel_ids))
self.data_bounds = self.data_bounds or self._get_data_bounds(bunchs)
self._current_visual.reset_batch()
self.line_visual.reset_batch()
self.tick_visual.reset_batch()
for bunch in bunchs:
self._plot_cluster(bunch)
self.canvas.update_visual(self.tick_visual)
self.canvas.update_visual(self.line_visual)
self.canvas.update_visual(self._current_visual)
self._plot_labels(channel_ids, len(self.cluster_ids), channel_labels)
# Only show the current waveform visual.
if self._current_visual == self.waveform_visual:
self.waveform_visual.show()
self.waveform_agg_visual.hide()
elif self._current_visual == self.waveform_agg_visual:
self.waveform_agg_visual.show()
self.waveform_visual.hide()
self.canvas.update()
self.update_status()
def attach(self, gui):
"""Attach the view to the GUI."""
super(WaveformView, self).attach(gui)
self.actions.add(self.toggle_waveform_overlap,
checkable=True,
checked=self.overlap)
self.actions.add(self.toggle_show_labels,
checkable=True,
checked=self.do_show_labels)
self.actions.add(self.next_waveforms_type)
self.actions.add(self.previous_waveforms_type)
self.actions.add(self.toggle_mean_waveforms, checkable=True)
self.actions.separator()
# Box scaling.
self.actions.add(self.widen)
self.actions.add(self.narrow)
self.actions.separator()
# Probe scaling.
self.actions.add(self.extend_horizontally)
self.actions.add(self.shrink_horizontally)
self.actions.separator()
self.actions.add(self.extend_vertically)
self.actions.add(self.shrink_vertically)
self.actions.separator()
@property
def boxed(self):
"""Layout instance."""
return self.canvas.boxed
@property
def status(self):
return self.waveforms_type
# Overlap
# -------------------------------------------------------------------------
@property
def overlap(self):
"""Whether to overlap the waveforms belonging to different clusters."""
return self._overlap
@overlap.setter
def overlap(self, value):
self._overlap = value
self.plot()
def toggle_waveform_overlap(self, checked):
"""Toggle the overlap of the waveforms."""
self.overlap = checked
# Box scaling
# -------------------------------------------------------------------------
def widen(self):
"""Increase the horizontal scaling of the waveforms."""
self.boxed.expand_box_width()
def narrow(self):
"""Decrease the horizontal scaling of the waveforms."""
self.boxed.shrink_box_width()
@property
def box_scaling(self):
return self.boxed._box_scaling
@box_scaling.setter
def box_scaling(self, value):
self.boxed._box_scaling = value
def _get_scaling_value(self):
return self.boxed._box_scaling[1]
def _set_scaling_value(self, value):
w, h = self.boxed._box_scaling
self.boxed._box_scaling = (w, value)
self.boxed.update()
# Probe scaling
# -------------------------------------------------------------------------
@property
def probe_scaling(self):
return self.boxed._layout_scaling
@probe_scaling.setter
def probe_scaling(self, value):
self.boxed._layout_scaling = value
def extend_horizontally(self):
"""Increase the horizontal scaling of the probe."""
self.boxed.expand_layout_width()
def shrink_horizontally(self):
"""Decrease the horizontal scaling of the waveforms."""
self.boxed.shrink_layout_width()
def extend_vertically(self):
"""Increase the vertical scaling of the waveforms."""
self.boxed.expand_layout_height()
def shrink_vertically(self):
"""Decrease the vertical scaling of the waveforms."""
self.boxed.shrink_layout_height()
# Navigation
# -------------------------------------------------------------------------
def toggle_show_labels(self, checked):
"""Whether to show the channel ids or not."""
self.do_show_labels = checked
self.text_visual.show() if checked else self.text_visual.hide()
self.canvas.update()
def on_mouse_click(self, e):
"""Select a channel by clicking on a box in the waveform view."""
b = e.button
nums = tuple('%d' % i for i in range(10))
if 'Control' in e.modifiers or e.key in nums:
key = int(e.key) if e.key in nums else None
# Get mouse position in NDC.
channel_idx, _ = self.canvas.boxed.box_map(e.pos)
channel_id = self.channel_ids[channel_idx]
logger.debug("Click on channel_id %d with key %s and button %s.",
channel_id, key, b)
emit('select_channel',
self,
channel_id=channel_id,
key=key,
button=b)
@property
def waveforms_type(self):
return self.waveforms_types.current
@waveforms_type.setter
def waveforms_type(self, value):
self.waveforms_types.set(value)
def next_waveforms_type(self):
"""Switch to the next waveforms type."""
self.waveforms_types.next()
logger.debug("Switch to waveforms type %s.", self.waveforms_type)
self.plot()
def previous_waveforms_type(self):
"""Switch to the previous waveforms type."""
self.waveforms_types.previous()
logger.debug("Switch to waveforms type %s.", self.waveforms_type)
self.plot()
def toggle_mean_waveforms(self, checked):
"""Switch to the `mean_waveforms` type, if it is available."""
if self.waveforms_type == 'mean_waveforms' and 'waveforms' in self.waveforms:
self.waveforms_types.set('waveforms')
logger.debug("Switch to raw waveforms.")
self.plot()
elif 'mean_waveforms' in self.waveforms:
self.waveforms_types.set('mean_waveforms')
logger.debug("Switch to mean waveforms.")
self.plot()
def __init__(
self, traces=None, sample_rate=None, spike_times=None, duration=None, n_channels=None,
channel_vertical_order=None, channel_labels=None, **kwargs):
self.do_show_labels = True
self.show_all_spikes = False
self._scaling = 1.
self.get_spike_times = spike_times
# Sample rate.
assert sample_rate > 0
self.sample_rate = float(sample_rate)
self.dt = 1. / self.sample_rate
# Traces and spikes.
assert hasattr(traces, '__call__')
self.traces = traces
self.waveforms = None
assert duration >= 0
self.duration = duration
assert n_channels >= 0
self.n_channels = n_channels
# Channel permutation.
self._channel_perm = (
np.arange(n_channels) if channel_vertical_order is None else channel_vertical_order)
assert self._channel_perm.shape == (n_channels,)
self._channel_perm = np.argsort(self._channel_perm)
# Channel labels.
self.channel_labels = (
channel_labels if channel_labels is not None else
['%d' % ch for ch in range(n_channels)])
assert len(self.channel_labels) == n_channels
# Box and probe scaling.
self._origin = None
# Initialize the view.
super(TraceView, self).__init__(**kwargs)
self.state_attrs += ('origin', 'do_show_labels', 'show_all_spikes', 'auto_scale')
self.local_state_attrs += ('interval', 'scaling',)
self.canvas.set_layout('stacked', origin=self.origin, n_plots=self.n_channels)
self.canvas.enable_axes(show_y=False)
# Visuals.
self.trace_visual = UniformPlotVisual()
self.canvas.add_visual(self.trace_visual)
self.waveform_visual = PlotVisual()
self.canvas.add_visual(self.waveform_visual)
self.text_visual = TextVisual()
_fix_coordinate_in_visual(self.text_visual, 'x')
self.canvas.add_visual(self.text_visual)
# Make a copy of the initial box pos and size. We'll apply the scaling
# to these quantities.
self.box_size = np.array(self.canvas.stacked.box_size)
# Initial interval.
self._interval = None
self.go_to(duration / 2.)
self._waveform_times = []