Visualization
-------------
The WM GUI is activated by setting ``gui_flag`` to 1 in the .rsp file.
It opens with two windows, the *main* window and the
*connections* window. A third window, the *monitor* window,
can be used to view the response and stimulus during the execution of
the model. Some documentation can be listed in the shell (from which
'wm' was launched) by pressing **h** in the main window.
Examining connections
*********************
Some basic techniques for examining synaptic connections are described
here.
The main window shows icons for a population of cells and an icon list
(upper left) for all populations. Left-click on the icon list to
select which population is displayed in the main window. Right-click
on the icon list to select which population is displayed in the
connections window. Clicking left/right on one of the icons among the
2D grid of icons in the main window (not in the header) will cause the
pre/post synaptic connections with respect to the population in the
connections window to be displayed. The display in the connections
window can be binarized by pressing **b**, or normalized to max by
pressing **m**, in the main window. Pressing the same key again
will turn off the feature.
If an LGN population is displayed in the connections window, middle
clicking an LGN unit in the connections window will show its
post-synaptic targets in the main window.
Stimulus mode
*************
Pressing **s** while the focus is in the main window will turn on (or
off) the stimulus mode. This will display the stimulus in the
connections window. This is useful for verifying the stimulus,
examining how it overlaps with LGN inputs of a particular neuron, and
selecting the stimulus that will be used if the model is executed in
interactive mode. The following commands are relevant to stimulus
mode:
* **,.** - pressing comma and period: scroll forward and backword
through video frames of the stimulus.
* **> , <** - less-than and greater-than: scroll forward and backward
through the list of stimuli, if there are multiple stimuli specified
in the .stm file.
* **s** - enter or leave stimulus mode.
Interactive mode
****************
This mode allows execution of the model and visualization of the
output in real time. Interactive mode is initiated by pressing
**i**, which causes the *monitor* window to appear. This may
steal the focus from the main window, so it is necessary to click the
mouse back into the main window to issue commands.
The basics:
#. Press **i** to enter interactive mode (you can leave only by
exiting the model)
#. Be sure that the desired stimulus has been selected in stimulus
mode. You do not have to have stimulus mode turned on, once the
desired stimulus has been selected.
#. Verify that some cells are marked (with a dim white highlight)
for recording. Cells will be marked based on requested outputs in the
response (.rsp) file. You can mark cells in the GUI by clicking on
them, then pressing **f**, then highlighting the desired output
options, and using **ESC** (escape key) to quit.
#. Note, the spacebar is used to clear all requested output.
#. Press **r** to run the selected stimulus on the model.
Monitor Window
**************
The monitor window shows responses as they are computed during
simulation, and it can compute statistics of the traces that it
monitors, and print them to the shell from which 'wm' was launched.
Parameters that control the monitor configuration are listed below.
**Limitations**
The monitor window currently shows output and does not accept input.
The window can be resized with the mouse, but will not refresh
properly until the next stimulus is run by pressing **r** in the
main window.
Response file parameters
************************
These parameters control the configuration of the GUI from the .rsp
file.
*Main and connections windows*
* **gui_flag** - 0-do not activate GUI, 1-activate GUI.
* **gui_win_x** - x location of main window (pix)
* **gui_win_y** - y location of main window (pix)
* **gui_win_w** - width of gui main window (pix)
* **gui_win_h** - height of gui main window (pix)
* **gui_win2_x** - x location of connection window (pix)
* **gui_win2_y** - y location of connection window (pix)
* **gui_win2_w** - width of gui connection window (pix)
* **gui_win2_h** - height of gui connection window (pix)
* **gui_colormapflag** - 0-start w/o colormap, 1-w/ colormap
* **gui_stim_frame** - [0] initial frame index of stimulus (this is
the frame that will appear first when entering stimulus mode)
* **gui_stim_num** - [0] initial stimulus number in stimulus mode
*Monitor window*
* **mon_flag** - whether to show the monitor window (0 or 1)
* **mon_stim_flag** - show visual stimulus in monitor window (0 or 1)
* **mon_t** - temporal epoch (sec), use -1 for default time period
* **mon_dt** - update monitor plot this often (sec)
* **mon_winw** - monitor window width (pixels)
* **mon_winh** - monitor window height (pixels)
* **mon_mV_y0** - y-axis lower bound for mV (-90)
* **mon_mV_y1** - y-axis upper bound for mV (-20)
* **mon_nS_y0** - y-axis lower bound for nS (-20)
* **mon_nS_y1** - y-axis upper bound for nS ( 40)
*Statistics (mean, SD) for plots*
* **mon_stat_t0** - start of window for statistics (sec)
* **mon_stat_tn** - duration of window for statistics (sec), 0=off
A line in the .rsp file like the following can be used to monitor
spike trains from, for example, all inhibitory neurons that synapse
onto the specified excitatory neuron::
mon_presyn_layer_to_cell in exs 8 8 0 spikes # Monitor spikes from 'in' layer
Population Icons
****************
Population icons are defined in the ``pop`` objects within the
model parameter files (.moo). The following shapes are supported:
* **circle**
* **square**
* **polygon**
* **nside** [number_of_sides]
* **stellate**
* **npoint** [number_of_points]
* **cs** - Center/Surround, used for LGN
Example of a simple blue circle::
shape circle
r 0.4
g 0.4
b 0.8
Example of green 5-pointed star::
shape stellate
r 0.0
g 0.8
b 0.2
npoint 5