//genesis
/*********************************************************************/
/**begin to draw :) **/
// function make_xcell(xcell,tmax)
// str xcell
// float tmax
// create xform /{xcell} [200,50,800,800]
// create xlabel /{xcell}/label [10,0,95%,25] \
// -label " CA1 SPINE" \
// -fg red
// create xgraph /{xcell}/v [10,10:label.bottom, 50%, 45%] \
// -title "Memberaine Potential" \
// -bg white
// create xgraph /{xcell}/syncurrents [10,10:v.bottom,50%,45%] \
// -title "Synaptic currents" \
// -bg white
// create xgraph /{xcell}/Ca [10:v.right,10:label.bottom,50%,45%] \
// -title "Calcium Concentration" \
// -bg white
// create xgraph /{xcell}/channels [10:syncurrents.right,10:Ca.bottom,48%,45%] \
// -title "Channel Currents" \
// -bg white
// setfield /{xcell}/v xmax {tmax+0.8} ymin -0.1 ymax 0.05
// setfield /{xcell}/Ca xmax {tmax+0.8} ymin 1e-6 ymax 1e-2
// setfield /{xcell}/syncurrents xmax {tmax+0.8} ymin 0 ymax 5.0e-12
// setfield /{xcell}/channels xmax {tmax+0.8} ymin -1e-9 ymax 1e-9
// useclock /{xcell}/v 1
// useclock /{xcell}/Ca 1
// useclock /{xcell}/syncurrents 1
// useclock /{xcell}/channels 1
// xshow /{xcell}
// reset
// end
function make_xcells(xcell, label, title1,title2,title3,title4,tmin,tmax)
str xcell,label, title1,title2,title3,title4
float tmin,tmax
create xform /{xcell} [200,50,800,800]
create xlabel /{xcell}/{label} [10,0,95%,25] \
-label {label} \
-fg red
create xgraph /{xcell}/{title1} [10,10:{label}.bottom, 50%, 45%] \
-title {title1} \
-bg white
create xgraph /{xcell}/{title2} [10,10:{title1}.bottom,50%,45%] \
-title {title2} \
-bg white
create xgraph /{xcell}/{title3} [10:{title1}.right,10:{label}.bottom,50%,45%] \
-title {title3} \
-bg white
create xgraph /{xcell}/{title4} [10:{title2}.right,10:{title3}.bottom,48%,45%] \
-title {title4} \
-bg white
setfield /{xcell}/{title1} xmin {tmin} xmax {tmax}
setfield /{xcell}/{title2} xmin {tmin} xmax {tmax}
setfield /{xcell}/{title3} xmin {tmin} xmax {tmax}
setfield /{xcell}/{title4} xmin {tmin} xmax {tmax}
useclock /{xcell}/{title1} 1
useclock /{xcell}/{title2} 1
useclock /{xcell}/{title3} 1
useclock /{xcell}/{title4} 1
xshow /{xcell}
reset
end
function make_VerticalXcells(xcell, label, allTitles,tmin,tmax)
str xcell,label, allTitles,title1,title_old
float tmin,tmax, height
int num,n0
echo allTitles is {allTitles}
num = {getarg {arglist {allTitles}} -count} // number of the xgraphs that is going to draw
n0 = 1
height = 90.0/num
create xform /{xcell} [620,50,400,400]
create xlabel /{xcell}/{label} [10,0,100%,5] \
-label {label} \
-fg red
foreach title1 ({arglist {allTitles}})
echo title1 is {title1}
if (n0 == 1 )
create xgraph /{xcell}/{title1} [10,10:{label}.bottom, 95%, {height}%] \
-title {title1} \
-bg white
else
title_old = {getarg {arglist {allTitles}} -arg {(n0-1)}}
echo title_old is {title_old} and n0 is {n0}
create xgraph /{xcell}/{title1} [10,10:{title_old}.bottom, 95%, {height}%] \
-title {title1} \
-bg white
end // end of if....
setfield /{xcell}/{title1} xmin {tmin} xmax {tmax}
useclock /{xcell}/{title1} 1
n0 = n0+1
end // foreach...
xshow /{xcell}
reset
end
function record_channel(cellpath,compt,channel,xcell,label, name,color,ymin,ymax)
str cellpath,compt,xcell,channel, path, color,label,name
int chanmode // hsolve : 1
// normal : 0
float ymin,ymax
// echo the cellpath is {cellpath}
// echo the compatment is {compt}
// echo the ion channel is {channel}
// echo the xcell is {xcell}
// echo th chanmode is {chanmode}
if(!{exists {cellpath}})
echo the cell {cellpath} does not exist! Please check the cellpath
return
end
if(!{exists {cellpath}/{compt}})
echo the compartment {cellpath}/{compt} does not exist!
return
end
if(!{exists {cellpath}/{compt}/{channel}})
echo the channel {cellpath}/{compt}/{channel} does not exist!
return
end
if(!{exists /{xcell}})
echo the xcell {xcell} does not exist!
return
end
if (!{isa xform /{xcell}})
echo the xcell is not the "xform" object that we want!!
return
end
path = {cellpath}@"/"@{compt}@"/"@{channel}
// if ({channel}=="Ca_difshell_1"||{channel}=="Ca_difshell_2"||{channel}=="Ca_difshell_3")
if( {isa difshell {path}})
addmsg {cellpath}/{compt}/{channel} /{xcell}/{label} PLOT C *{path} *{color}
echo add {path} successfully!
elif( {isa Ca_concen {path}})
addmsg {cellpath}/{compt}/{channel} /{xcell}/{label} PLOT Ca *{path} *{color}
echo add {path} successfully!
// end
else // for synaptic and ion channels
addmsg {cellpath}/{compt}/{channel} /{xcell}/{label} PLOT Ik *{name} *{color}
echo add {path} successfully!
end
setfield /{xcell}/{label} ymin {ymin} ymax {ymax}
end
function record_channel_Gk(cellpath,compt,channel,xcell,label, color,ymin,ymax)
str cellpath,compt,xcell,channel, path, color,label
int chanmode // hsolve : 1
// normal : 0
float ymin,ymax
// echo the cellpath is {cellpath}
// echo the compatment is {compt}
// echo the ion channel is {channel}
// echo the xcell is {xcell}
// echo th chanmode is {chanmode}
if(!{exists {cellpath}})
echo the cell {cellpath} does not exist! Please check the cellpath
return
end
if(!{exists {cellpath}/{compt}})
echo the compartment {cellpath}/{compt} does not exist!
return
end
if(!{exists {cellpath}/{compt}/{channel}})
echo the channel {cellpath}/{compt}/{channel} does not exist!
return
end
if(!{exists /{xcell}})
echo the xcell {xcell} does not exist!
return
end
if (!{isa xform /{xcell}})
echo the xcell is not the "xform" object that we want!!
return
end
path = {cellpath}@"/"@{compt}@"/"@{channel}
addmsg {cellpath}/{compt}/{channel} /{xcell}/{label} PLOT Gk *{channel} *{color}
echo add {path} successfully!
setfield /{xcell}/{label} ymin {ymin} ymax {ymax}
end
function record_voltage (cellpath, compt, xcell,title,volt_label,color,ymin,ymax,chanmode)
str cellpath,compt,xcell,path,path1,color,title,volt_label
int chanmode
float ymin,ymax
if(!{exists {cellpath}})
echo the cell {cellpath} does not exist! Please check the cellpath
return
end
if(!{exists {cellpath}/{compt}})
echo the compartment {cellpath}/{compt} does not exist!
return
end
if(!{exists /{xcell}})
echo the xcell {xcell} does not exist!
return
end
if (!{isa xform /{xcell}})
echo the xcell is not the "xform" object that we want!!
return
end
if ({{chanmode} == 1} || {chanmode}==0 )
path = {getpath {compt} -tail}
addmsg {cellpath}/{compt} /{xcell}/{title} PLOT Vm *{volt_label} *{color}
elif ({chanmode} == 4)
path = {getpath {compt} -tail}
path1 = {findsolvefield {cellpath}/solve {path} Vm}
addmsg {cellpath} /{xcell}/{title} PLOT {path1} *{volt_label} *{color}
else
echo The function record_channel currently does not support the chanmode {chanmode}!
echo only chanmode 0, 1 and 4 are available!
return
end
setfield /{xcell}/{title} ymin {ymin} ymax {ymax}
echo the title is {title}
end
function increaseXcellDia(cellpath,compt_list,factor)
str cellpath,compt_list,compt
float dia,factor,dia_new
foreach compt ({arglist {compt_list}})
compt = {cellpath}@"/"@{compt}
dia = {getfield {compt} dia}
dia_new = dia*factor
setfield {compt} dia {dia_new}
//echo the old dia of {compt} is {dia} and the new dia is {dia_new}
end
end
function makeColorCode(cellpath,compt_list,field,value)
str cellpath,compt_list,compt,field
float value
foreach compt ({arglist {compt_list}})
compt = {cellpath}@"/"@{compt}
setfield {compt} {field} {value}
end
end
// the file contains many numbers (such as "Ri") as the color codes
// "the_num": which specific line in the file should be taken as the color code?
function readColorData(cellpath,compt_list,field,filepath,the_num)
str cellpath,compt_list,compt,field,filepath
int the_num,n0
float value
foreach compt ({arglist {compt_list}})
n0 = 1
openfile {filepath}/{compt}".txt" r
while(n0<=the_num)
value = {readfile {filepath}/{compt}".txt"}
if (n0 == the_num)
setfield {cellpath}/{compt} {field} {value}
end
n0 = n0+1
end // end of while
closefile {filepath}/{compt}".txt"
//echo the {compt} field {field} is {value}
end // end of foreach
end
function makeSpheres(cellpath, compt_list,xdrawPath,xsphere_name,color,dia)
str cellpath,compt_list,compt,color,xsphere_name
float x,y,z,dia
int i=1
pushe {xdrawPath}
foreach compt ({arglist {compt_list}})
x = {getfield {cellpath}/{compt} x}
y = {getfield {cellpath}/{compt} y}
z = {getfield {cellpath}/{compt} z}
if ({exists {xsphere_name}"_"{i}})
delete {xsphere_name}"_"{i}
end
create xsphere {xsphere_name}"_"{i} -fg {color} -tx {x} -ty {y} -tz {z} -r {dia}
i=i+1
end // end of foreach
pope
end
// delete the existed spheres first
function makeSpheres_del(cellpath, compt_list,xdrawPath,xsphere_name,color,dia)
str cellpath,compt_list,compt,color,xsphere_name
float x,y,z,dia
int i=1
if ({exists {xdrawPath}/xphere})
delete {xdrawPath}/xphere
end
create neutral {xdrawPath}/xphere
pushe {xdrawPath}/xphere
foreach compt ({arglist {compt_list}})
x = {getfield {cellpath}/{compt} x}
y = {getfield {cellpath}/{compt} y}
z = {getfield {cellpath}/{compt} z}
if ({exists {xsphere_name}"_"{i}})
delete {xsphere_name}"_"{i}
end
create xsphere {xsphere_name}"_"{i} -fg {color} -tx {x} -ty {y} -tz {z} -r {dia}
i=i+1
end // end of foreach
pope
end
function plotActiveSynByTime(cellpath,spikeList,drawPath,xsphere_name,color,dia,tmin,tmax,ISI)
str spikeList, drawPath, list, list1,cellpath,xsphere_name,color
float tmin,tmax,ISI, dur, dt , t0,t1,dia
int maxN,n
dur = tmax - tmin
int maxN = dur/ISI
for (n=1;n<=maxN;n=n+1)
t0 = tmin+(n-2)*ISI
t1 = tmin +(n-1)*ISI
echo t0 is {t0}, t1 is {t1}
list1 = ""
foreach list ({arglist {spikeList}})
list1=list1@" "@{findActivatedRandSyn {list} {t0} {t1}}
end // end of foreach...
makeSpheres_del {cellpath} {list1} {drawPath} {xsphere_name} {color} {dia}
echo list1 is {list1}
step {ISI} -time
end // end of for ...
end
