spykeutils.plot package

This package contains various plotting functions for neo objects. The plots are created using guiqwt - if it is not installed, this package can not be used.

raster(*args, **kwargs)

Create a new plotting window with a rasterplot of spiketrains.

Parameters:

• trains (dict) – Dictionary of spike trains indexed by a Neo object (Unit or Segment).
• time_unit (Quantity) – Unit of X-Axis.
• show_lines (bool) – Determines if a horizontal line will be shown for each spike train.
• events (sequence) – A sequence of neo Event objects that will be marked on the plot.

cross_correlogram(*args, **kwargs)

Create (cross-)correlograms from a dictionary of spike train lists for different units.

Parameters:

• trains (dict) – Dictionary of neo.core.SpikeTrain lists.
• bin_size (Quantity scalar) – Bin size (time).
• max_lag (Quantity scalar) – Maximum time lag for which spikes are considered (end time of calculated correlogram).
• border_correction (bool) – Apply correction for less data at higher timelags.
• time_unit (Quantity) – Unit of X-Axis.
• progress (spykeutils.progress_indicator.ProgressIndicator) – Set this parameter to report progress.

isi(*args, **kwargs)

Create a plot dialog with an interspike interval histogram.

Parameters:

• trains (dict) – Dictionary with lists of spike trains indexed by units for which to display ISI histograms
• bin_size (Quantity scalar) – Bin size (time)
• cut_off – End of histogram (time)
• bar_plot (bool) – If True, create a bar ISI histogram for each index in trains. Else, create a line ISI histogram.
• time_unit (Quantity) – Unit of X-Axis.

psth(*args, **kwargs)

Create a peri stimulus time histogram.

The peri stimulus time histogram gives an estimate of the instantaneous rate.

Parameters:

• trains (dict) – A dictionary of neo.core.SpikeTrain lists.
• events (dict) – A dictionary of Event objects, indexed by segment. The events will be at time 0 on the plot. If None, spike trains are used unmodified.
• start (Quantity scalar) – The desired time for the start of the first bin. It will be recalculated if there are spike trains which start later than this time. This parameter can be negative (which could be useful when aligning on events).
• stop (Quantity scalar) – The desired time for the end of the last bin. It will be recalculated if there are spike trains which end earlier than this time.
• bin_size (Quantity scalar) – The bin size for the histogram.
• rate_correction (bool) – Determines if a rates (True) or counts (False) are shown.
• bar_plot (bool) – Determines if a bar plot (True) or a line plot (False) will be created. In case of a bar plot, one plot for each index in trains will be created.
• time_unit (Quantity) – Unit of X-Axis.
• progress (spykeutils.progress_indicator.ProgressIndicator) – Set this parameter to report progress.

sde(*args, **kwargs)

Create a spike density estimation plot.

The spike density estimations give an estimate of the instantaneous rate. Optionally finds optimal kernel size for given data.

Parameters:

• trains (dict) – A dictionary of neo.core.SpikeTrain lists.
• events (dict) – A dictionary (with the same indices as trains) of Event objects or lists of Event objects. In case of lists, the first event in the list will be used for alignment. The events will be at time 0 on the plot. If None, spike trains will are used unmodified.
• start (Quantity scalar) – The desired time for the start of the first bin. It will be recalculated if there are spike trains which start later than this time. This parameter can be negative (which could be useful when aligning on events).
• stop (Quantity scalar) – The desired time for the end of the last bin. It will be recalculated if there are spike trains which end earlier than this time.
• kernel_size (Quantity scalar) – A uniform kernel size for all spike trains. Only used if optimization of kernel sizes is not used (i.e. optimize_steps is 0).
• optimize_steps (int) – The number of different kernel sizes tried between minimum_kernel and maximum_kernel. If 0, kernel_size will be used.
• minimum_kernel (Quantity scalar) – The minimum kernel size to try in optimization.
• maximum_kernel (Quantity scalar) – The maximum kernel size to try in optimization.
• kernel_function – The kernel function to use, should accept two parameters: A ndarray of distances and a kernel size. The total area under the kernel function sould be 1. By default, a Gaussian kernel is used. Automatic optimization assumes a Gaussian kernel and will likely not produce optimal results for different kernels.
• time_unit (Quantity) – Unit of X-Axis.
• progress (spykeutils.progress_indicator.ProgressIndicator) – Set this parameter to report progress.

signals(*args, **kwargs)

Create a plot from a list of analog signals.

Parameters:

• signals (list) – The list of neo.core.AnalogSignal objects to plot.
• events (sequence) – A list of Event objects to be included in the plot.
• epochs (sequence) – A list of Epoch objects to be included in the plot.
• spike_trains (list) – A list of neo.core.SpikeTrain objects to be included in the plot. The unit property (if it exists) is used for color and legend entries.
• spikes (list) – A list neo.core.Spike objects to be included in the plot. The unit property (if it exists) is used for color and legend entries.
• show_waveforms (bool) – Determines if spikes from neo.core.Spike and neo.core.SpikeTrain objects are shown as waveforms (if available) or vertical lines.
• use_subplots (bool) – Determines if a separate subplot for is created each signal.
• subplot_names (bool) – Only valid if use_subplots is True. Determines if signal (or channel) names are shown for subplots.
• time_unit (Quantity) – The unit of the x axis.
• progress (spykeutils.progress_indicator.ProgressIndicator) – Set this parameter to report progress.

spike_amplitude_histogram(*args, **kwargs)

Create a spike amplitude histogram.

This plot is useful to assess the drift in spike amplitude over a longer recording. It shows histograms (one for each trains entry, e.g. segment) of maximum and minimum spike amplitudes.

Parameters:

• trains (list) – A list of lists of neo.core.SpikeTrain objects. Each entry of the outer list will be one point on the x-axis (they could correspond to segments), all amplitude occurences of spikes contained in the inner list will be added up.
• num_bins (int) – Number of bins for the histograms.
• uniform_y_scale (bool) – If True, the histogram for each channel will use the same bins. Otherwise, the minimum bin range is computed separately for each channel.
• x_unit (Quantity) – Unit of Y-Axis.
• progress (spykeutils.progress_indicator.ProgressIndicator) – Set this parameter to report progress.

Returns:

spikes(*args, **kwargs)

Create a plot dialog with spike waveforms.

Parameters:

• spikes (dict) – A dictionary of spike lists.
• axes_style (int) –

  Plotting mode. The following values are possible:

  • 1: Show each channel in a seperate plot, split vertically.
  • 2: Show each channel in a separate plot, split horizontally.
  • 3: Show each key of spikes in a separate plot, channels are split vertically.
  • 4: Show each key of spikes in a separate plot, channels are split horizontally.
  • 5: Show all channels in the same plot, split vertically.
  • 6: Show all channels in the same plot, split horizontally.
• anti_alias (bool) – Determines whether an antialiased plot is created.
• time_unit (Quantity) – Unit of X-Axis.
• progress (spykeutils.progress_indicator.ProgressIndicator) – Set this parameter to report progress.

dialog Module

Contains a helper class for creating windows containing guiqwt plots.

class PlotDialog(wintitle='Plot window', major_grid=True, minor_grid=False, toolbar=False, parent=None, panels=None, min_plot_width=100, min_plot_height=75)

Bases: QDialog, PlotManager

Implements a dialog to which an arbitrary number of plots can be added.

This class implements a QDialog with a number of plots on it. The axes of the plots can be arbitrarily synchronized and option checkboxes can be added which provide callbacks when the checkbox state changes.

Parameters:

• wintitle (str) – Title of the window.
• major_grid (bool) – Show major grid in plots.
• minor_grid (bool) – Show minor grid in plots.
• toolbar (bool) – Show toolbar.
• parent – Parent window.
• panels – A list of guiqwt panels to be added to the window.
• min_plot_width (int) – Default minimum width for plots.
• min_plot_height (int) – Default minimum height for plots.

add_color_legend(legend, show_option=None)

Create a legend on the right of the plots with colors and names.

Parameters:

• legend (sequence) – List of (color, text) tuples, where color is a Qt color name (e.g. ‘#ff0000’) and text is the corresponding text to display in the legend.
• show_option (bool) – Determines whether a toggle for the legend will be shown (if the parameter is not None) and if the legend is visible initially (True/False).

add_custom_curve_tools(antialiasing=True, activate_zoom=True, signal_stats=False)

Adds typically needed curve tools to the window.

Parameters:

• antialiasing (bool) – Determines if the antialiasing tool is added.
• activate_zoom (bool) – Determines if the zoom tool is activated initially (otherwise, the selection tool will be activated).
• signal_stats (bool) – Determines if the signal stats tool is available.

add_custom_image_tools(activate_zoom=True)

Adds typically needed image tools to the window.

add_custom_label(legend_string)

Add a label on the right of the plots

Parameters:legend_string (str) – An arbitrary string (which can contain newlines) to display on the right of the plots

add_legend_option(legends, active)

Create a user option to show or hide a list of legend objects.

Parameters:

• legends (sequence) – The legend objects affected by the option.
• active (bool) – Determines whether the legends will be visible initially.

add_option(name, change_callback, active=False)

Add an option (using a checkbox) to the window.

Parameters:

• name (str) – The name of the option.
• change_callback (func) – A function accepting the new state as a parameter. The function will be called whenever the state of the option changes.
• active (bool) – Determines if the option is activated initially.

add_plot_widget(plot_widget, plot_id, row=-1, column=0, min_plot_width=None, min_plot_height=None)

Adds a guiqwt plot to the window.

Parameters:

• plot_widget (guiqwt plot widget) – The plot to add.
• plot_id (int) – The id of the new plot.
• row (int) – The row of the new plot. If this is -1, the new plot will be added in a new row (if column is 0) or in the last row.
• column (int) – The column of the new plot.
• min_plot_width (int) – The minimum width of this plot. If None, the default minimum width for this dialog is used.
• max_plot_height (int) – The minimum height of this plot. If None, the default minimum height for this dialog is used.

add_unit_color(color, name='Unit color:')

Create a small legend on top of the window with only one entry.

Parameters:

• color (str) – A Qt color name (e.g. ‘#ff0000’)
• name (str) – The name of the legend item. It will be displayed on the left of the color.

add_x_synchronization_option(active, ids=None)

Offer an option for X axes synchronization. This method should be called after show(), so that a proper initial synchronization can be performed.

Parameters:

• active (bool) – Determines whether the axes are synchronized initially.
• ids (sequence) – List of plot ids to synchronize.

add_y_synchronization_option(active, ids=None)

Offer an option for Y axes synchronization. This method should be called after show(), so that a proper initial synchronization can be performed.

Parameters:

• active (bool) – Determines whether the axes are synchronized initially
• ids (sequence) – List of plot ids to synchronize.

replace_colors(replace_list)

Replace colors of items in all plots.

This can be useful when changing the background color to black and black items should be drawn in white: replace_colors([('#000000', '#ffffff']))

Parameters:replace_list (list) – A list of tuples of Qt color names. The first color in each tuple is replaced by the second color.

set_background_color(color)

Set the background color for all plots.

Parameters:color (str) – A Qt color name (e.g. ‘#ff0000’)

set_plot_title(plot, title)

Set the title of a guiqwt plot and use the same font as for the

rest of the window.

Parameters:

• plot – The plot for which the title is set.
• title (str) – The new title of the plot.

helper Module

This module contains some utility functions that are usefult in plot creation.

add_epochs(plot, epochs, units=None)

Add Epoch markers to a guiqwt plot.

Parameters:

• plot (guiqwt.baseplot.BasePlot) – The plot object.
• epochs (sequence) – The epochs (neo neo.Epoch objects).
• units – The x-scale of the plot. If this is None, the time unit of the events will be use.

add_events(plot, events, units=None)

Add Event markers to a guiqwt plot.

Parameters:

• plot (guiqwt.baseplot.BasePlot) – The plot object.
• events (sequence) – The events (neo neo.Event objects).
• units (Quantity) – The x-scale of the plot. If this is None, the time unit of the events will be use.

add_spikes(plot, train, color='k', spike_width=1, spike_height=20000, y_offset=0, name='', units=None)

Add all spikes from a spike train to a guiqwt plot as vertical lines.

Parameters:

• plot (guiqwt.baseplot.BasePlot) – The plot object.
• train (neo.core.SpikeTrain) – A spike train with the spike times to show.
• color (str) – The color for the spikes.
• spike_width (int) – The width of the shown spikes in pixels.
• spike_height (int) – The height of the shown spikes in pixels.
• y_offset (float) – An offset for the drawing position on the y-axis.
• name (str) – The name of the spike train.
• units (Quantity) – The x-scale of the plot. If this is None, the time unit of the events will be use.

Returns:

The plot item added for the spike train

get_color(entity_id)

Return a color for an int.

get_object_color(unit)

Return a color for a Neo object, based on the ‘unique_id’ annotation. If the annotation is not present, return a color based on the hash of the object.

make_window_legend(win, objects, show_option=None)

Create a legend in a PlotDialog for a given sequence of neo objects.

Parameters:

• win (spykeutils.plot.dialogs.PlotDialog) – The window where the legend will be added.
• objects (sequence) – A list of neo objects which will be included in the legend.
• show_option (bool) – Determines whether a toggle for the legend will be shown (if the parameter is not None) and if the legend is visible initially (True/False).

set_color_scheme(colors)

Set the color scheme used in plots.

Parameters:colors (sequence) – A list of strings with HTML-style color codes (e.g. '#ffffff' for white). If this is None or empty, the default color scheme will be set.

guiqwt_tools Module

Additional guiqwt tools to facilitate plot navigation.

class HelpTool(manager, toolbar_id=<MagicMock name='mock.DefaultToolbarID' id='124530064'>)

Bases: CommandTool

A help tool that includes a message what a single middle click does, otherwise identical to the guiqwt tool with the same name.

activate_command(plot, checked)

Activate tool

class HomeTool(manager, toolbar_id=<MagicMock name='mock.DefaultToolbarID' id='124530064'>)

Bases: CommandTool

A command to show all elements in the plot (same as pressing the middle mouse button).

activate_command(plot, checked)

Activate that command!

class PanTool

Bases: InteractiveTool

Allows panning with the left mouse button.