GENESIS: Documentation

Related Documentation:
Contributed By:
Dave Beeman (dbeeman@dogstar.colorado.edu)
Based on fplot.py for plotting the membrane potential from the G-3 implementation of tutorial4 written by Karthikeyan Subramanian (kartikznov@gmail.com)

G3Plot (Ver. 0.55)

This is a preliminary version of a collection of stand-alone Python-based graphical utilities for plotting the output of GENESIS simulations. The simulations use the asc_file object to write simulation variables to a file, with one line per step of the output clock. These scripts may also be useful as prototypes of graphical objects that could be more directly incorporated into the GENESIS GUI G-Tube.

These scripts make use of the powerful scientific graphics capability of Matplotlib, which easily generates a wide variety of plots, accompanied by a Navigation Toolbar that allows for panning and zooming of plots, and saving to publication quality PNG format images.

To run these scripts, you need Python Ver. 2.5 or later, and the Matplotlib library for Python. The installation instructions explain other requirememts, such as NumPy (numerical libraries for Python) that are usually installed along with Python on most Linux systems.

The main script of this package, G3Plot.py, also requires wxPython, the Python implemention of the wxWidgets widget set now used by GENESIS.

The use of these Python libraries is described in the Frontiers in Neuroinformatics special issue on Python in Neuroscience.

Python scripts

Brief description of the scripts and their usage:

• fplot.py
  Plot files of one (x,y) pair, or (time, V _m) pair per line from a single file given as the argument, e.g.

  fplot.py Vm.out

• plotVm.py
  An extended version of fplot.py that uses the Matplotlib object-oriented classes, instead of the Matlab-like pylab commands. It takes multiple wildcarded filenames as arguments, and plots them in different colors on the same axes, e.g.

  plotVm.py Vm.out pyr4*.out

  It has labels and scales specific for membrane potential plots, and is handy for quickly comparing the results of current injection simulations. The (x,y) coordinates of a point on the graph can be displayed in the Navigation Toolbar by positioning the cursor over it.

• rasterplot.py
  Similar to plotVm, but specialized for creating raster plots of firing times for a group of neurons. It takes a single filename as argument, with a line for each cell containing the spike times separated by spaces. The times are plotted as dots with the time on the x-axis and the cell number (the line number) on the y-axis.

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  Figure 1: G3Plot Raster Plot.

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  Figure 1 shows a plot generated with

  rasterplot.py spike_times.txt

• G3Plot.py
  Enhanced version of plotVm that wraps Matplotlib plots within a wxPython GUI. It has several fancy Help menu features and plotting options to illustrate the capabilities of wxWidgets as a GUI for displaying simulation results in Python. It can either take the filename list as arguments, or to be entered in a dialog from the File/Open menu selection.

  It addition to the usual Menu bar with File and Help menus, it has a Control Panel of colored buttons and toggles for clearing the plot, plotting, setting overlay ON or OFF, and toggling the Legend display. The Legend identifies each colored line on the graph with the filename in the same color.

  The HTML Usage help describes the use of the Matplotlib Toolbar that is used in all these programs, as well as Menu choices and Control Panel buttons. The Program Info scrolling message dialog gives information obtained from program documentation strings about the objects and functions, and the wxPython and matplotlib classes that are used here.

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  Figure 2: G3Plot GUI: Includes Usage and About panels.

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  Figure 2 shows a screen dump of the GUI with Usage and About help displayed with the plot.

  The screen dump was produced with the following command and arguments:

  G3Plot.py pyr4*.out Vm.out

• rowrateplot.py
  This is a utility for analyzing network activity by displaying a filled contour map of spike frequency vs. simulation time for groups of neurons. It takes a single filename as argument, with a line for each time step containing the simulation time, followed by the average spike frequency (firing rate) during that time step for each group of cells. Typically each cell group is a horizontal row of cells in the network that are receiving auditory input. Time is plotted on the x-axis, cell group (row) on the y-axis, with the average firing frequency of cells in that row at that time represented by a colored filled contour plot.

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  Figure 3: G3Plot Contour Plot.

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  Figure 3 (called freqplot-HD2500-11p.eps) shows the contour plot generated from

  rowrateplot.py spike_freq_HD2500-11p.txt

  The data file was produced from asc_file output of a G-2 layer 4 auditory cortex simulation. The parameters used for the connection weights in this run provided strong response to the random background input, and to a 220 Hz tone pulse with thalamic input to row 25 and nearby rows, lasting from 0.25–0.75 s. rowrateplot.py will be useful for tuning parameters to balance excitation and inhibition.

Other related files

• Vm.out
  Typical membrane potential from simplecell current injection.
• pyr4_Vm.out, pyr4a_Vm.out
  Membrane potential from 0.5 nA injection to soma of symmetric and asymmetric layer 4 pyramidal cell models.
• spike_times.txt
  Sample output for a raster plot, produced by raster_data.g.
• raster_data.g
  A G-2 script to generate sample spike time data for rasterplot.py. It creates an array of 128 unconnected single compartment cells based on basic-cell.p. The setrandfield command is used to provide injection currents randomly distributed within the range 0.27–0.33 nA. It uses XODUS graphics (which is optional) and some features of the table object that have not yet been implemented to produce the output file spike_times.txt.
• spike_freq_HD2500-11p.txt
  Output of network simulation run HD2500-11p for average spike frequency of each row vs. time.
• basic-cell.p The cell parameter file for the single compartment neuron.

BUGS and ‘features’

Under Fedora 12 Linux, the scripts plotVm.py and rasterplot.py produce the warning message:

G3Plot.py does not produce this warning, but does not show the (x,y) coordinates of the cursor in the Navigation Toolbar. This is a very handy feature of plotVm.py, when measuring action potential times and amplitudes.

Note: G3Plot.py uses the Matplotlib backend API for embedding in wxPython, matplotlib.backends.backend_wxagg NavigationToolbar2WxAgg. The other scripts, which do not use wxPython, use matplotlib.pyplot.figure, which has the Toolbar built in. Possibly, there is a setting to enable this feature hidden somewhere in NavigationToolbar2WxAgg.

References