//######################################
//
// util.hoc
// -------------
//
// Several function to work with LayerVrun
//
// Author: Konstantin Stadler
// Version: 20131108
//
//######################################
//
/*******************************************************************
** implemented functions and procedures **
*******************************************************************/
/*
start() PROC
opens most used windows to visualize the model run
inits a pointprocessmanager on the default section
optional parameter: Tstop
CCIV()
runs a cciv on the default section
parameter: CCIV(time_start, time_step, current_start, number_steps, step_size, save)
save ... 0 for don't save, otherwise yes
CCIVstand()
starts the CCIV() with standard parameter:
50ms start time without input current
1000ms stps from -0.3 to 0.7 nA with 50 pA step size
Result are saved in CCIVprot.txt and CCIV_AP.txt
*/
/*******************************************************************
** General objectref and global variables **
*******************************************************************/
//general
objectvar StartDefaultSection //pointer to the access section at start
StartDefaultSection = new SectionRef()
//start
objectvar save_window_, ocbox_
objectvar scene_vector_[7]
//record time
objectvar Time
Time = new Vector()
Time.record(&t) //saves the time of the current simulation
//record execution time
objref ParaCont
ParaCont = new ParallelContext()
CalcTimeStart = 0
CalcTimeEnd = 0
//CCIV
objref IStim, AktPotCount //pointmechnismen
objref IGraph, APGraph //graphs
objref ErgList, APVec, RecGes, SaveMatrix, ErgFile //lists,files and matrices to save data
strdef SaveFile, SaveFile_AP //SaveFile 's for the data, _AP for f/I
/*******************************************************************
** procedures **
*******************************************************************/
proc start() { //opens most used windows to visualize the model run
ExpTime = 2000 // duration of experiment in ms if not given as parameter
dt = 0.025
if (numarg()>0) {
ExpTime=$1
}
if (numarg()>1) {
dt=$2
}
//init PointProcessManager
{
load_file("pointman.hoc")
}
{
StartDefaultSection ocbox_ = new PointProcessManager(0)
}
{
ocbox_ = ocbox_.v1
ocbox_.map("PointProcessManager", 300, 654, 222.3, 371.7)
}
objref ocbox_
//end init PointProcessManager
//RunControl
xpanel("RunControl", 0)
v_init = -78
xvalue("Init","v_init", 1,"stdinit()", 1, 1 )
xbutton("Init & Run","run()")
xbutton("Stop","stoprun=1")
runStopAt = 5
xvalue("Continue til","runStopAt", 1,"{continuerun(runStopAt) stoprun=1}", 1, 1 )
runStopIn = 1
xvalue("Continue for","runStopIn", 1,"{continuerun(t + runStopIn) stoprun=1}", 1, 1 )
xbutton("Single Step","steprun()")
t = 0
xvalue("t","t", 2 )
tstop = ExpTime
xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
xvalue("dt","dt", 1,"setdt()", 0, 1 )
steps_per_ms = 1/dt
xvalue("Points plotted/ms","steps_per_ms", 1,"setdt()", 0, 1 )
screen_update_invl = 0.05
xvalue("Scrn update invl","screen_update_invl", 1,"", 0, 1 )
realtime = 0
xvalue("Real Time","realtime", 0,"", 0, 1 )
xpanel(1,654)
//end Runcontrol
//misc windows and graphs
{
save_window_ = new Graph(0)
save_window_.size(0,4200,-100,20)
scene_vector_[3] = save_window_
{save_window_.view(0, -100, ExpTime, 120, 819, 0, 602, 172)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addexpr("v(.5)", 1, 1, 0.8, 0.9, 2)
save_window_.label(0.1, 0.9, "Voltage at soma", 2, 1, 0, 0, 1)
}
{
save_window_ = new Graph(0)
save_window_.size(0,4200,-100,20)
scene_vector_[4] = save_window_
{save_window_.view(0, -100, ExpTime, 120, 819, 310, 602, 172)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addexpr("dend1[184].v(0.5)", 1, 1, 0.8, 0.9, 2) //dendrite 600 um from soma
save_window_.addexpr("dend1[669].v(0.5)", 1, 1, 0.8, 0.9, 2) //dendrite 1000um from soma
save_window_.label(0.1, 0.9, "Voltage at dendrites 600um and 1000um from soma", 2, 1, 0, 0, 1)
}
{
save_window_ = new PlotShape(0)
save_window_.size(-620.785,410.235,-148.192,925.442)
save_window_.variable("v")
/*save_window_.exec_menu("Shape Plot")*/
scene_vector_[5] = save_window_
{save_window_.view(-620.785, -148.192, 1031.02, 1073.63, 817, 617, 372.6, 388)}
fast_flush_list.append(save_window_)
scene_vector_[5].exec_menu("Shape Plot")
}
//end misc windows
}
func CCIV() { local tStart, tStep, IStartStep, Steps, Stepsize localobj Prot
// Simulation of a CCIV with IClamp on the access section with AP plot
// parameters:
// Required:
// TimeStart, TimeStep, IStartStep,
// Steps, Stepsize, Save(0...no, else yes)
// Optional:
// SaveFile, SaveFile_AP
//
// returns:
// -99 in case of errors
// 1 otherwise
CalcTimeStart = ParaCont.time()
if (numarg()<6) {
print "Wrong parameter..."
print "Required:"
print "TimeStart, TimeStep, IStartStep,"
print "Steps, Stepsize, Save(0...no, else yes)"
print "Optional:"
print "SaveFile, SaveFile_AP"
return -99
}
if (numarg()>6) {
SaveFile = $s7
} else {
SaveFile = "CCIVprot.txt"
}
if (numarg()==8) {
SaveFile_AP = $s8
} else {
SaveFile_AP = "CCIV_AP.txt"
}
tStart= $1
tStep = $2
IStartStep = $3
Steps = $4
Stepsize = $5
if (tStart<0 || tStep<=0 || Steps <0 ) {
print "Wrong parameter: times and steps must be positive"
return -99
}
if ( (tStart+tStep) > tstop ) {
print "experiment time shorter than pulse"
return -99
}
IStim = new IClamp(.5)
AktPotCount = new APCount(.5)
RecGes = new Vector()
ErgList = new List()
APVec = new Vector(Steps+1)
Prot = new Vector(Steps+1) //Saves the currents for the APGraph
IStim.del = tStart //start with I=0
IStim.dur = tStep //duration of the step
Min=0
Max=0 //saves max and min for visualization
print "CCIV calculation..."
for i=0, Steps {
IStim.amp = IStartStep + i*Stepsize
print "\nStep ", i, "of ", Steps
print "Input current: ", IStim.amp, " nA"
RecGes.record(&v(.5)) //voltage on the access section
run()
ErgList.append(RecGes.c) //Copy of the result vector
APVec.x[i] = AktPotCount.n()
Prot.x[i] = IStim.amp
if (RecGes.min() < Min) Min = RecGes.min()
if (RecGes.max() > Max) Max = RecGes.max()
}
print "\nCalculation finished, visualization:"
IGraph = new Graph(0)
IGraph.view(0, Min, tstop, (Max-Min), 720, 720, 500, 150)
// draws it on the screen (Axenskalierung: (Start, ymin, Ende, ymax=ymin+value)
// in a window with user-specified location (5th and 6th args)
// and size (last 2 args)
for i=0, ErgList.count()-1 {
ErgList.o(i).plot(IGraph, Time)
//Time vector as specified in general objectref at the beginning of that .hoc
IGraph.label(0.8, 0.8, "Voltage", 2, 1, 0, 0, 1)
}
APGraph = new Graph(0) //Plot of the FI curve
APGraph.view(IStartStep,0,abs(IStartStep)+i*Stepsize,APVec.max(),10,350,200,200)
APVec.plot(APGraph, Prot)
APGraph.label(0.8, 0.8, "F/I", 2, 1, 0, 0, 1)
if ($6!=0) { //6. parameter determines of the data will be saved
print "Save..."
SaveMatrix = new Matrix()
SaveMatrix.resize(Time.size(),ErgList.count()+1)
SaveMatrix.setcol(0,Time)
for i=0, ErgList.count()-1 SaveMatrix.setcol(1+i, ErgList.o(i))
//save to file
ErgFile = new File()
ErgFile.wopen(SaveFile)
SaveMatrix.fprint(ErgFile, "%-e ")
ErgFile.close()
ErgFile = new File()
ErgFile.wopen(SaveFile_AP)
APVec.printf(ErgFile)
ErgFile.close()
print "**Saved**"
}
IStim.del = 1e9 //wait 'eternally' for the next CCIV
CalcTimeEnd = ParaCont.time()
print "\nCCIV protocol finished"
print " Duration: ", CalcTimeEnd - CalcTimeStart," s"
return 1
}
proc CCIVstand() { //CCIV with standard parameters
//50 ms init, 1000 ms step, starts at -300 pA, 20 steps a 50 pA
//Result are saved in CCIVprot.txt and CCIV_AP.txt
SaveFile = "CCIVprot.txt"
SaveFile_AP = "CCIV_AP.txt"
if (numarg() > 0) SaveFile=$s1
if (numarg() > 1) SaveFile_AP=$s2
print SaveFile, SaveFile_AP
CCIV(50, 1000, -0.3, 20, 0.05, 1, SaveFile, SaveFile_AP)
}
