/*======================================================================
A GENESIS GUI for network models, with a control panel, a graph with
axis scaling, and a network view to visualize Vm in each cell
======================================================================*/
//=========================================
// Function definitions used by GUI
//=========================================
function overlaytoggle(widget)
str widget
setfield /##[TYPE=xgraph] overlay {getfield {widget} state}
end
function change_stepsize(dialog)
str dialog
dt = {getfield {dialog} value}
setclock 0 {dt}
echo "Changing step size to "{dt}
end
/*
function inj_toggle // toggles current injection ON/OFF
if ({getfield /control/injtoggle state} == 1)
setfield /injectpulse level1 1.0 // ON
else
setfield /injectpulse level1 0.0 // OFF
end
end
function add_injection
int cell_no
cell_no = ({getfield /control/cell_no value})
if (cell_no > {NX*NY-1})
echo "There are only "{NX*NY}" cells - numbering begins with 0"
return
end
InjCell = cell_no
if (({getmsg /injectpulse/injcurr -outgoing -count}) > 0)
deletemsg /injectpulse/injcurr 0 -outgoing // only outgoing message
end
addmsg /injectpulse/injcurr /SPnetwork/cell[{cell_no}]/soma INJECT output
echo "Current injection is to cell number "{cell_no}
end
function set_injection
str dialog = "/control"
set_inj_timing {getfield {dialog}/injectdelay value} \
{getfield {dialog}/width value} {getfield {dialog}/interval value}
setfield /injectpulse/injcurr gain {getfield {dialog}/inject value}
echo "Injection current = "{getfield {dialog}/inject value}
echo "Injection pulse delay = "{getfield {dialog}/injectdelay value}" sec"
echo "Injection pulse width = "{getfield {dialog}/width value}" sec"
echo "Injection pulse interval = "{getfield {dialog}/interval value}" sec"
end
*/
/* A subset of the functions defined in genesis/startup/xtools.g
These are used to provide a "scale" button to graphs.
"makegraphscale path_to_graph" creates the button and the popup
menu to change the graph scale.
*/
function setgraphscale(graph)
str graph
str form = graph @ "_scaleform"
str xmin = {getfield {form}/xmin value}
str xmax = {getfield {form}/xmax value}
str ymin = {getfield {form}/ymin value}
str ymax = {getfield {form}/ymax value}
setfield {graph} xmin {xmin} xmax {xmax} ymin {ymin} ymax {ymax}
xhide {form}
end
function showgraphscale(form)
str form
str x, y
// find the parent form
str parent = {el {form}/..}
while (!{isa xform {parent}})
parent = {el {parent}/..}
end
x = {getfield {parent} xgeom}
y = {getfield {parent} ygeom}
setfield {form} xgeom {x} ygeom {y}
xshow {form}
end
function makegraphscale(graph)
if ({argc} < 1)
echo usage: makegraphscale graph
return
end
str graph
str graphName = {getpath {graph} -tail}
float x, y
str form = graph @ "_scaleform"
str parent = {el {graph}/..}
while (!{isa xform {parent}})
parent = {el {parent}/..}
end
x = {getfield {graph} x}
y = {getfield {graph} y}
create xbutton {graph}_scalebutton \
[{getfield {graph} xgeom},{getfield {graph} ygeom},50,25] \
-title scale -script "showgraphscale "{form}
create xform {form} [{x},{y},180,170] -nolabel
disable {form}
pushe {form}
create xbutton DONE [10,5,55,25] -script "setgraphscale "{graph}
create xbutton CANCEL [70,5,55,25] -script "xhide "{form}
create xdialog xmin [10,35,160,25] -value {getfield {graph} xmin}
create xdialog xmax [10,65,160,25] -value {getfield {graph} xmax}
create xdialog ymin [10,95,160,25] -value {getfield {graph} ymin}
create xdialog ymax [10,125,160,25] -value {getfield {graph} ymax}
pope
end
/* Add some interesting colors to any widgets that have been created */
function colorize
setfield /##[ISA=xlabel] fg white bg blue3
setfield /##[ISA=xbutton] offbg rosybrown1 onbg rosybrown1
setfield /##[ISA=xtoggle] onfg red offbg cadetblue1 onbg cadetblue1
setfield /##[ISA=xdialog] bg palegoldenrod
setfield /##[ISA=xgraph] bg ivory
end
//==================================
// Functions to set up the GUI
//==================================
//str graphlabel = "Network of Spiny Projection neurons with Fast Spiking interneuronal input"
str graphlabel = "Control w/ 20Hz GABA"
float tmax = 3 // simulation time
float dt = 50e-6 // simulation time step
float SEP_X = 500e-6 // 500 um
float SEP_Y = 500e-6
float syn_weight = 6 // synaptic weight, effectively multiplies gmax
float cond_vel = 0.5 // m/sec - GABA and the Basal Ganglia by Tepper et al
float syn_weight2 = 4 // synaptic weight, effectively multiplies gmax
float cond_vel2 = 1.4 // m/sec - GABA and the Basal Ganglia by Tepper et al
int NI_X = 3
int NI_Y = 3
int NI_Z = 3
int NX = 3 //{sqrt {getglobal numCells_{net}}} number of cells = NX*NY
int NY = NX
int NZ = NX
float CI_X = 25e-6
float CI_Y = 25e-6
float prop_delay = {CI_X}/{cond_vel}
float prop_delay2 = {SEP_X}/{cond_vel2}
float gmax = 4e-9 // 1 nS - possibly a little small for this cell
float gmax2 = 4e-9
int num_inter_connections = 100
function make_control
create xform /control [10,50,250,460]
pushe /control
create xlabel label -hgeom 25 -bg cyan -label "CONTROL PANEL"
create xbutton RESET -wgeom 25% -script reset
create xbutton RUN -xgeom 0:RESET -ygeom 0:label -wgeom 25% \
-script step_tmax
create xbutton STOP -xgeom 0:RUN -ygeom 0:label -wgeom 25% \
-script stop
create xbutton QUIT -xgeom 0:STOP -ygeom 0:label -wgeom 25% -script quit
create xdialog stepsize -title "dt (sec)" -value {dt} \
-script "change_stepsize <widget>"
create xtoggle overlay -script "overlaytoggle <widget>"
setfield overlay offlabel "Overlay OFF" onlabel "Overlay ON" state 0
create xlabel connlabel -label "Connection Parameters"
create xdialog Inter_connection -label "Number of interconnections per neuron" -value {num_inter_connections}
create xdialog gmax -label "Inhchan gmax (S)" -value {gmax} \
-script "setfield /network/cell[]/soma/Inh_channel gmax <v>"
create xdialog gmax2 -label "Exchan gmax (S)" -value {gmax2} \
-script "setfield /network/cell[]/soma/Ex_channel gmax <v>"
create xdialog weight -label " Cortical input Weight" -wgeom 50% \
-value {syn_weight} -script "set_weights <v>"
create xdialog weight2 -label "SP network Weight" -wgeom 50% \
-value {syn_weight} -script "set_weights2 <v>"
create xdialog propdelay -label "Cortical input Delay" -wgeom 50% -xgeom 0:weight \
-ygeom 0:gmax -value {prop_delay} -script "set_delays <v>"
create xdialog propdelay2 -label "SP network Delay" -wgeom 50% -xgeom 0:weight \
-ygeom 0:gmax -value {prop_delay} -script "set_delays2 <v>"
/* create xlabel stimlabel -label "Stimulation Parameters"
create xtoggle injtoggle -label "" -script inj_toggle
setfield injtoggle offlabel "Current Injection OFF"
setfield injtoggle onlabel "Current Injection ON" state 1
inj_toggle // initialize
create xlabel numbering -label "Lower Left = 0; Center = "{middlecell}
create xdialog cell_no -label "Inject Cell:" -value {InjCell} \
-script "add_injection"
create xdialog inject -label "Injection (Amp)" -value {injcurrent} \
-script "set_injection"
create xdialog injectdelay -label "Delay (sec)" -value {injdelay} \
-script "set_injection"
create xdialog width -label "Width (sec)" -value {injwidth} \
-script "set_injection"
create xdialog interval -label "Interval (sec)" -value {injinterval} \
-script "set_injection"
*/
create xlabel randact -label "Random background activation"
create xdialog randfreq -label "Frequency (Hz)" -value 0 \
-script "set_frequency <v>"
pope
xshow /control
end
function make_Vmgraph
float vmin = -0.1
float vmax = 0.15
create xform /data [265,50,400,460]
create xlabel /data/label -hgeom 5% -label {graphlabel}
create xgraph /data/voltage -hgeom 80% -title "Membrane Potential" -bg white
setfield ^ XUnits sec YUnits V
setfield ^ xmax {tmax} ymin {vmin} ymax {vmax}
makegraphscale /data/voltage
create xgraph /data/spike -hgeom 15% -ygeom 0:voltage \
-title "Spike" -bg white
setfield ^ XUnits sec YUnits A
setfield ^ xmax {tmax} ymin {0} ymax {1e-9}
makegraphscale /data/spike
/* Set up plotting messages, with offsets */
// middlecell is a middle point (exactly, if NX and NY are odd)
/*
addmsg /SPnetwork/SPcell[0]/soma /data/voltage PLOTSCALE \
Vm *"0" *black 1 0
addmsg /SPnetwork/SPcell[1]/soma /data/voltage PLOTSCALE \
Vm *"1" *blue 1 0
addmsg /SPnetwork/SPcell[2]/soma /data/voltage PLOTSCALE \
Vm *"2" *red 1 0
addmsg /SPnetwork/SPcell[3]/soma /data/voltage PLOTSCALE \
Vm *"3" *black 1 0.05
addmsg /SPnetwork/SPcell[4]/soma /data/voltage PLOTSCALE \
Vm *"4" *blue 1 0.05
addmsg /SPnetwork/SPcell[5]/soma /data/voltage PLOTSCALE \
Vm *"5" *red 1 0.05
addmsg /SPnetwork/SPcell[6]/soma /data/voltage PLOTSCALE \
Vm *"6" *black 1 0.1
addmsg /SPnetwork/SPcell[7]/soma /data/voltage PLOTSCALE \
Vm *"7" *blue 1 0.1
addmsg /SPnetwork/SPcell[8]/soma /data/voltage PLOTSCALE \
Vm *"8" *red 1 0.1
*/
addmsg /SPnetwork/SPcell[0]/soma /data/voltage PLOTSCALE \
Vm *"L corner 0 " *black 1 0
//addmsg /SPnetwork/SPcell[{{round {(NY-1)/2}}*NX}]/soma /data/voltage \
// PLOTSCALE Vm *"R edge "{{round {(NY-1)/2}}*NX} *blue 1 0
addmsg /SPnetwork/SPcell[49]/soma /data/voltage PLOTSCALE \
Vm *"center 49" *blue 1 0.05
addmsg /SPnetwork/SPcell[99]/soma /data/voltage PLOTSCALE \
Vm *"R corner 99" *red 1 0.1
/*
addmsg /FSnetwork/FScell[0]/soma /data/voltage PLOTSCALE \
Vm *"L corner 0 " *black 1 0
//addmsg /SPnetwork/SPcell[{{round {(NY-1)/2}}*NX}]/soma /data/voltage \
// PLOTSCALE Vm *"R edge "{{round {(NY-1)/2}}*NX} *blue 1 0
addmsg /FSnetwork/FScell[12]/soma /data/voltage PLOTSCALE \
Vm *"center 49" *blue 1 0.05
addmsg /FSnetwork/FScell[24]/soma /data/voltage PLOTSCALE \
Vm *"R corner 99" *red 1 0.1
*/
/*
addmsg /SPnetwork/SPcell[1]/soma /data/voltage PLOTSCALE \
Vm *"L corner 1 " *black 1 0
//addmsg /SPnetwork/SPcell[{{round {(NY-1)/2}}*NX}]/soma /data/voltage \
// PLOTSCALE Vm *"R edge "{{round {(NY-1)/2}}*NX} *blue 1 0
addmsg /SPnetwork/SPcell[4]/soma /data/voltage PLOTSCALE \
Vm *"center 4" *blue 1 0.05
addmsg /SPnetwork/SPcell[3]/soma /data/voltage PLOTSCALE \
Vm *"center 3" *green 1 0.05
addmsg /SPnetwork/SPcell[5]/soma /data/voltage PLOTSCALE \
Vm *"center 5" *black 1 0.05
addmsg /SPnetwork/SPcell[8]/soma /data/voltage PLOTSCALE \
Vm *"R corner 8" *red 1 0.1
*/
//addmsg /injectpulse/injcurr /data/injection PLOT output *injection *black
xshow /data
end
function make_Cagraph
float vmin = -0.1
float vmax = 0.15
create xform /Cadata [265,50,400,460]
create xlabel /Cadata/label -hgeom 5% -label {graphlabel}
create xgraph /Cadata/Calevel -hgeom 80% -title "Ca2+ level" -bg white
setfield ^ XUnits sec YUnits M
//setfield ^ xmax {tmax} ymin {vmin} ymax {vmax}
makegraphscale /Cadata/Calevel
//create xgraph /data/spike -hgeom 15% -ygeom 0:voltage \
// -title "Spike" -bg white
// setfield ^ XUnits sec YUnits A
// setfield ^ xmax {tmax} ymin {0} ymax {1e-9}
// makegraphscale /data/spike
/* Set up plotting messages, with offsets */
// middlecell is a middle point (exactly, if NX and NY are odd)
/*
addmsg /SPnetwork/SPcell[0]/soma /data/voltage PLOTSCALE \
Vm *"0" *black 1 0
addmsg /SPnetwork/SPcell[1]/soma /data/voltage PLOTSCALE \
Vm *"1" *blue 1 0
addmsg /SPnetwork/SPcell[2]/soma /data/voltage PLOTSCALE \
Vm *"2" *red 1 0
addmsg /SPnetwork/SPcell[3]/soma /data/voltage PLOTSCALE \
Vm *"3" *black 1 0.05
addmsg /SPnetwork/SPcell[4]/soma /data/voltage PLOTSCALE \
Vm *"4" *blue 1 0.05
addmsg /SPnetwork/SPcell[5]/soma /data/voltage PLOTSCALE \
Vm *"5" *red 1 0.05
addmsg /SPnetwork/SPcell[6]/soma /data/voltage PLOTSCALE \
Vm *"6" *black 1 0.1
addmsg /SPnetwork/SPcell[7]/soma /data/voltage PLOTSCALE \
Vm *"7" *blue 1 0.1
addmsg /SPnetwork/SPcell[8]/soma /data/voltage PLOTSCALE \
Vm *"8" *red 1 0.1
*/
addmsg /SPnetwork/SPcell[0]/soma /data/voltage PLOTSCALE \
Vm *"L corner 0 " *black 1 0
//addmsg /SPnetwork/SPcell[{{round {(NY-1)/2}}*NX}]/soma /data/voltage \
// PLOTSCALE Vm *"R edge "{{round {(NY-1)/2}}*NX} *blue 1 0
addmsg /SPnetwork/SPcell[49]/soma /data/voltage PLOTSCALE \
Vm *"center 49" *blue 1 0.05
addmsg /SPnetwork/SPcell[99]/soma /data/voltage PLOTSCALE \
Vm *"R corner 99" *red 1 0.1
/*
addmsg /FSnetwork/FScell[0]/soma /data/voltage PLOTSCALE \
Vm *"L corner 0 " *black 1 0
//addmsg /SPnetwork/SPcell[{{round {(NY-1)/2}}*NX}]/soma /data/voltage \
// PLOTSCALE Vm *"R edge "{{round {(NY-1)/2}}*NX} *blue 1 0
addmsg /FSnetwork/FScell[12]/soma /data/voltage PLOTSCALE \
Vm *"center 49" *blue 1 0.05
addmsg /FSnetwork/FScell[24]/soma /data/voltage PLOTSCALE \
Vm *"R corner 99" *red 1 0.1
*/
/*
addmsg /SPnetwork/SPcell[1]/soma /data/voltage PLOTSCALE \
Vm *"L corner 1 " *black 1 0
//addmsg /SPnetwork/SPcell[{{round {(NY-1)/2}}*NX}]/soma /data/voltage \
// PLOTSCALE Vm *"R edge "{{round {(NY-1)/2}}*NX} *blue 1 0
addmsg /SPnetwork/SPcell[4]/soma /data/voltage PLOTSCALE \
Vm *"center 4" *blue 1 0.05
addmsg /SPnetwork/SPcell[3]/soma /data/voltage PLOTSCALE \
Vm *"center 3" *green 1 0.05
addmsg /SPnetwork/SPcell[5]/soma /data/voltage PLOTSCALE \
Vm *"center 5" *black 1 0.05
addmsg /SPnetwork/SPcell[8]/soma /data/voltage PLOTSCALE \
Vm *"R corner 8" *red 1 0.1
*/
//addmsg /injectpulse/injcurr /data/injection PLOT output *injection *black
xshow /data
end
function make_netview // sets up xview widget to display Vm of each cell
create xform /netview [670,50,300,300]
create xdraw /netview/draw [0%,0%,100%, 100%]
// Make the display region a little larger than the cell array
setfield /netview/draw xmin {-SEP_X} xmax {NX*SEP_X} \
ymin {-SEP_Y} ymax {NY*SEP_Y}
create xview /netview/draw/view
setfield /netview/draw/view path /SPnetwork/SPcell[]/soma field Vm \
value_min -0.08 value_max 0.03 viewmode colorview sizescale {SEP_X}
xshow /netview
end
function make_inview // sets up xview widget to display Vm of each cell
create xform /inview [1070,50,300,300]
create xdraw /inview/draw [0%,0%,100%, 100%]
// Make the display region a little larger than the cell array
setfield /inview/draw xmin {-CI_X} xmax {NI_X*CI_X} \
ymin {-CI_Y} ymax {NI_Y*CI_Y}
create xview /inview/draw/view
setfield /inview/draw/view path /in/input[] field state \
value_min -0.08 value_max 0.03 viewmode colorview sizescale {CI_X}
xshow /inview
end