Plotting the simulation

NeuroDevSim can plot during simulations when run in jupyter notebooks by setting plot=True during Admin_agent initialization. Results can also be plotted afterwards from the stored database using the nds_plot or nds_movie commands. All these methods have common settings that are explained here.

Color settings

There are several parameters that control how structures in the simulation are colored, selecting from 13 standard colors. By default all somata are black and each neuron has a different color, but because of the small number of colors available several neurons will have the same color in networks with many neurons. The following settings control how colors are used in Admin_agent, nds_plot and nds_movie:

color_scheme : integer : has 4 possible settings:

• 0 : default, all neurons have different colors, limited by number of colors available. Colors are asigned in order of soma creation.

• 1 : color determined by neuron_types. All neurons of the same type have the same color, different types have different colors, limited by number of colors available. Useful in network simulations with many different neuron types.

• 2 : color determined by branch_name. Fronts with different branch_names have different colors, limited by number of colors available. Useful when simulating a single neuron.

• 3 : a continuous color scale is used (matplotlib ‘rainbow’) to color a scalar attribute. Additional information must be provided in color_data. All fronts that do not have the selected attribute are colored black. An example can be found in the Synapses notebook.

color_data : list with 3 entries : used only for color_scheme==3:

• attribute : string : the front attribute to be used for color selection.

• min value : float : mimimum value used for color scale (purple color).

• max value : float : maximum value used for color scale (red color).

soma_black : boolean : every soma is always colored black (default), used for color_scheme 0-2.

In addition, nds_plot and nds_movie also have a color_scheme==-1 setting. This allows the user to specify a specific color for each neuron in the simulation in a text file, which is defined in neuron_colors. The easiest way to do this is to first call the nds_get_color_dict method on the database, this will output a text file containing for each neuron a line with its name and the color selected for color_scheme==0 (optionally color_scheme==1). The user can then edit this text file, being careful to specify colors correctly as shown in the table below, and then run nds_plot or nds_movie with color_scheme==-1.

neuron_colors : string : name of text file containing dictionary info by neuron name that specifies color to use for color_scheme==-1 in nds_plot or nds_movie. Use nds_get_color_dict on the database to obtain a valid text file and then edit it.

Available colors and their names

These color names should be used in the neuron_color text file.

color	name used
black	‘k’
blue	‘tab:blue’
brown	‘tab:brown’
cyan	‘tab:cyan’
gray	‘tab:gray’
green	‘tab:green’
magenta	‘m’
olive	‘tab:olive’
orange	‘tab:orange’
pink	‘tab:pink’
purple	‘tab:purple’
red	‘tab:red’
yellow	‘y’

View settings

Properly setting orientation of the camera with azim and elev can improve visibility of relevant phenomena and in complex simulations it can also be helpful to zoom in with box. Finally visibility of small structures can be enhanced with radius_scale or sphere_scale.

azim : float : azimuth in degrees of camera, default -60.

box : list [[left, front, bottom], [right, back, top]]: subvolume to plot, allows to zoom in, default full sim_volume.

elev : float : elevation in degrees of camera, default 30.

radius_scale : float : change thickness of cylindrical fronts, default 1. size equals 2 * radius.

sphere_scale : float : change size of spherical fronts, default 1. size equals radius.

Axes settings

One can suppress axes with no_axis or change relative scaling of axes with scale_axis. The latter can be quite important as Matplotlib plots by default a cubic volume, so if not all axes have identical length the default setting will create a distorted plot with some axes compressed. This may, however, squeeze the axis ticks to unlegible text and in that case it is better to turn them off with axis_ticks.

axis_ticks : boolean : show axis ticks, default True.

no_axis : boolean : suppress drawing of axes, default False.

scale_axis : boolean or list of 3 floats : list as [1.0,1.0,1.0] decrease one or more values to change relative scaling of axes, value for largest axis should be close to 1.0; default False. Examples in Real Morphologies notebook.