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// $Id: initbatser.hoc,v 1.9 2011/06/15 05:10:48 ted Exp ted $
// Serial batch implementation
// for stimulus current i iterating over a range of values
// run a simulation and report spike frequency
// save i & corresponding f to a file
// optionally plot fi curve
load_file("stdgui.hoc") // load standard library but don't open NMM toolbar
///// Simulation parameters
PLOTRESULTS = 1 // if 1, generates a graph that shows f-i curve
TSTOP = 500 // ms, more than long enough for 15 spikes at ISI = 25 ms
AMP0 = 0.1 // nA--minimum stimulus
D_AMP = 0.02 // nA--stim increment between runs
NRUNS = 30
///// Model specification
load_file("cell.hoc")
///// Instrumentation
// experimental manipulations
objref stim
soma stim = new IClamp(0.5)
stim.del = 1 // ms
stim.dur = 1e9
stim.amp = 0.1 // nA
// $1 is run #
// returns corresponding stimulus amplitude
func fstimamp() {
return AMP0 + $1*D_AMP
}
// sets stimulus amplitude to appropriate value for this run
proc setparams() {
stim.amp = fstimamp($1)
}
// data recording and analysis
objref nc, spvec, nil // to record spike times
// count only those spikes that get to distal end of dend
dend nc = new NetCon(&v(1), nil)
nc.threshold = -10 // mV
spvec = new Vector()
nc.record(spvec)
NSETTLE = 5 // ignore the first NSETTLE ISI (allow freq to stablize)
NINVL = 10 // # ISI from which frequency will be calculated
NMIN = NSETTLE + NINVL // ignore recordings with fewer than this # of ISIs
freq = 0
proc postproc() { local nspikes, t1, t2
freq = 0
nspikes = spvec.size()
if (nspikes > NMIN) {
t2 = spvec.x(nspikes-1) // last spike
t1 = spvec.x(nspikes-1-NINVL) // NINVL prior to last spike
freq = NINVL*1e3/(t2-t1) // t1 and t2 are separated by NINVL ISIs
}
}
///// Simulation control
tstop = TSTOP
// batch control
trun = startsw() // keep track of execution time past this point
objref svec, fvec
proc batchrun() { local ii
svec = new Vector()
fvec = new Vector()
for ii=0,$1-1 {
setparams(ii) // set parameters for this run
run()
postproc() // analyze the data
svec.append(stim.amp)
fvec.append(freq)
printf(".") // indicate progress
}
}
batchrun(NRUNS)
///// Reporting of results
proc saveresults() { local ii localobj file
file = new File($s1)
file.wopen()
file.printf("label:%s\n%d\n", "f", fvec.size)
for ii=0, fvec.size-1 {
file.printf("%g\t%g\n", svec.x[ii], fvec.x[ii])
}
file.close()
}
saveresults("fi.dat")
print " "
print startsw() - trun, "seconds" // report run time
objref fig
load_file("plotfi.hoc")
if (PLOTRESULTS==1) {
fig = plotfi(fvec, svec)
} else {
quit()
}
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