emodelrunner.GUI_utils.plotshape

Plot shape of neuron.

Functions

auto_aspect(ax)

Sets the x, y, and z range symmetric around the center.

get_color_from_cmap(val, val_min, val_max, cmap)

Return color.

get_morph_lines(ax, sim[, val_min, val_max, ...])

Plots a 3D shapeplot.

plot_shape(ax, xaxis, yaxis, zaxis, plot_3d, ...)

Plot shape and return line.

set_labels(ax, xaxis, yaxis, zaxis, plot_3d)

Set labels.
emodelrunner.GUI_utils.plotshape.auto_aspect(ax)[source]

Sets the x, y, and z range symmetric around the center.

Parameters:

ax (matplotlib.axes.Axes) – axis

emodelrunner.GUI_utils.plotshape.get_color_from_cmap(val, val_min, val_max, cmap)[source]

Return color.

Parameters:

  • val (float) – value to get color for from colormap (mV)

  • val_min (int) – minimum value of voltage for colormap (mV)

  • val_max (int) – minimum value of voltage for colormap (mV)

  • cmap (matplotlib.colors.Colormap) – colormap

Returns:

tuple of RGBA values indicating a color

Return type:

tuple

emodelrunner.GUI_utils.plotshape.get_morph_lines(ax, sim, val_min=-90, val_max=30, sections=None, variable='v', cmap=matplotlib.cm.plasma, do_plot=False, plot_3d=False, threshold_volt=4, threshold_volt_fine=25, old_vals=None, vals_last_draw=None, xaxis=2, yaxis=0, zaxis=1, linewidth=0.9)[source]

Plots a 3D shapeplot.

Parameters:

  • ax (matplotlib.axes.Axes) – axis

  • sim (bluepyopt.ephys.simulators.NrnSimulator) –

  • val_min (int) – minimum value of voltage for colormap (mV)

  • val_max (int) – minimum value of voltage for colormap (mV)

  • sections (list) list of h.Section() – If None, all sections are loaded.

  • variable (str) – variable to be plotted. ‘v’ for voltage.

  • cmap (matplotlib.colors.Colormap) – colormap

  • do_plot (bool) – True to plot data. False to get actualised data.

  • plot_3d (bool) – set to True to plot the shape in 3D

  • threshold_volt (int) – voltage difference from which color should be changed on the cell shape. (mV)

  • threshold_volt_fine (int) – voltage difference from which display should be updated after a small simulation time to fine display rapid changes. (mV)

  • old_vals (list) – variable values at the last display

  • vals_last_drawn (list) – variable values the last time the morphology has been drawn (and not blitted).

  • xaxis (int) – indicate which data to plot on the x-axis (0 for x, 1 for y, 2 for z)

  • yaxis (int) – indicate which data to plot on the y-axis (0 for x, 1 for y, 2 for z)

  • zaxis (int) – indicate which data to plot on the z-axis (0 for x, 1 for y, 2 for z)

  • linewidth (float) – width of line in shape plot

Returns:

tuple containing

  • list: line objects making up shapeplot to update in figure

  • list: voltages previously plotted (mV)

  • bool: True to force the draw of figure, False to blit the figure

emodelrunner.GUI_utils.plotshape.plot_shape(ax, xaxis, yaxis, zaxis, plot_3d, data, linewidth)[source]

Plot shape and return line.

Parameters:

  • ax (matplotlib.axes.Axes) – axis

  • xaxis (int) – indicate which data to plot on the x-axis (0 for x, 1 for y, 2 for z)

  • yaxis (int) – indicate which data to plot on the y-axis (0 for x, 1 for y, 2 for z)

  • zaxis (int) – indicate which data to plot on the z-axis (0 for x, 1 for y, 2 for z)

  • plot_3d (bool) – whether to plot in 3d or 2d

  • data (list) – list of (xs, ys, zs, diams) for each segment

  • linewidth (float) – width of line in shape plot

Returns:

the plotted line

Return type:

matplotlib.lines.Line2D

emodelrunner.GUI_utils.plotshape.set_labels(ax, xaxis, yaxis, zaxis, plot_3d)[source]

Set labels.

Parameters:

  • ax (matplotlib.axes.Axes) – axis

  • xaxis (int) – indicate which label to set on the x-axis (0 for x, 1 for y, 2 for z)

  • yaxis (int) – indicate which label to set on the y-axis (0 for x, 1 for y, 2 for z)

  • zaxis (int) – indicate which label to set on the z-axis (0 for x, 1 for y, 2 for z)

  • plot_3d (bool) – whether to plot in 3d or 2d