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setup.hoc
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setup.hoc
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// Salto
// (c) Charles CH Cohen, 2014-present
// this software is released to the public under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0
// International license (CC BY-NC-ND 4.0, in English).
// for any questions, please email [email protected]
print "Salto – Setup"
print "Simulation setup details"
print "Run once per cell"
// ------------------------------Directories---------------------------------------
strdef root, lib, ses
root = getcwd()
sprint(lib, "%s%s", root, "lib/")
sprint(ses, "%s%s", root, "ses/")
// --------------------------------------------------------------------------------
// -------------------------------Libraries----------------------------------------
load_file("stdgui.hoc")
chdir(lib)
load_file("startlib.hoc")
// --------------------------------------------------------------------------------
// --------------------------------------------------------------------------------
// cell type
setcelltype()
// Is there recording data?
strdef idataqstr
sprint(idataqstr, "%s", "Is there current-clamp recording data?\t[y/n]")
idata = sred(idataqstr, "y", "ny")
writebit(ses, "idata.dat", idata)
// --------------------------------------------------------------------------------
// --------------------------------------------------------------------------------
if (idata) {
print "\n-------------------Import Recorded Data-----------------------"
// Recording temperature
strdef tempqstr
sprint(tempqstr, "%s", "Please enter recording temperature (degrees celsius):\t")
temprec = xred(tempqstr, 35.3, 0, 100)
writenum(ses, "temprec.dat", temprec)
// Bessel filter setting
strdef bessqstr
bessqstr = "Please enter Bessel filter (\"Vm filter\") setting on the recording amplifier (kHz):\t"
bess = xred(bessqstr, 10, 1, 30)
writenum(ses, "bessfil.dat", bess)
// Recording location data
importreclocdata()
// Passive or active data?
strdef modeqstr
modeqstr = "\nDo you wish to set up passive conditions only, active conditions only, or both? Currently requires recording data for each condition.\nPassive = 0\nActive = 1\nBoth = 2\t"
ans = xred(modeqstr, 2, 0, 2)
if (ans == 2) {
print "\nPlease import passive data:\n"
mode_ = 0
writebit(ses, "mode.dat", mode_)
setfilestr(mode_, idata)
// delay before current injection (ms)
strdef idelqstr
idelqstr = "Please enter delay to injection start (ms):\t"
idel = xred(idelqstr, 9.375, 0, 1000)
writenum(ses, idelfilestr, idel)
// duration of current injection (ms)
strdef idurqstr
idurqstr = "Please enter duration of current injections (ms):\t"
idur = xred(idurqstr, 1.875, 0, 1000)
writenum(ses, idurfilestr, idur)
// import injection and recorded voltage data
importdata()
writenum(ses, "iamp-pas.dat", iampvec.x[0])
print "\nPlease import active data:\n"
mode_ = 1
writebit(ses, "mode.dat", mode_)
setfilestr(mode_, idata)
// delay before current injection (ms)
strdef idelqstr
idelqstr = "Please enter delay to injection start (ms):\t"
idel = xred(idelqstr, 5, 0, 1000)
writenum(ses, idelfilestr, idel)
// duration of current injection (ms)
strdef idurqstr
idurqstr = "Please enter duration of current injections (ms):\t"
idur = xred(idurqstr, 3, 0, 1000)
writenum(ses, idurfilestr, idur)
// import injection amplitudes and recorded voltage
importdata()
writenum(ses, "iamp-act.dat", iampvec.x[0])
writebit(ses, "mode.dat", 0)
}
if (ans == 0) {
print "\nPlease import passive data:\n"
mode_ = 0
writebit(ses, "mode.dat", mode_)
setfilestr(mode_, idata)
// delay before current injection (ms)
strdef idelqstr
idelqstr = "Please enter delay to injection start (ms):\t"
idel = xred(idelqstr, 9.375, 0, 1000)
writenum(ses, idelfilestr, idel)
// duration of current injection (ms)
strdef idurqstr
idurqstr = "Please enter duration of current injections (ms):\t"
idur = xred(idurqstr, 1.875, 0, 1000)
writenum(ses, idurfilestr, idur)
// import injection amplitudes and recorded voltage
importdata()
writenum(ses, "iamp-pas.dat", iampvec.x[0])
}
if (ans == 1) {
print "\nPlease import active data:\n"
mode_ = 1
writebit(ses, "mode.dat", 1)
setfilestr(mode_, idata)
// delay before current injection (ms)
strdef idelqstr
idelqstr = "Please enter delay to injection start (ms):\t"
idel = xred(idelqstr, 5, 0, 1000)
writenum(ses, idelfilestr, idel)
// duration of current injection (ms)
strdef idurqstr
idurqstr = "Please enter duration of current injections (ms):\t"
idur = xred(idurqstr, 3, 0, 1000)
writenum(ses, idurfilestr, idur)
// import injection amplitudes and recorded voltage
importdata()
writenum(ses, "iamp-act.dat", iampvec.x[0])
}
}
// --------------------------------------------------------------------------------
// --------------------------------------------------------------------------------
// Morphological detail
// get AIS sections
importaisloc()
// Define axon type
strdef axonqstr
axonqstr = "\nPlease select an axon type:\n1 = no myelin\n2 = single cable\n3 = double cable without paranodes\n4 = double cable with paranodes\t"
axontype = xred(axonqstr, 4, 1, 4)
writebit(ses, "axontype.dat", axontype)
if (axontype > 1) {
strdef grqstr
grqstr = "\nPlease enter expected g ratio:\t"
gr = xred(grqstr, 0.7, 0.001, 0.999)
writenum(ses, "gr.dat", gr)
strdef mintqstr
mintqstr = "\nPlease enter minimum internode length:\t"
mint = xred(mintqstr, 15, 10, 500)
writenum(ses, "mint.dat", mint)
strdef blebqstr
blebqstr = "\nPlease indicate whether the final section of the principal axon is myelinated:\t[y/n]"
bleb = sred(blebqstr, "n", "ny")
writebit(ses, "axbleb_exists.dat", !bleb)
if (!bleb) {
importblebdata()
}
}
// simulation time
set_maxtime()
// --------------------------------------------------------------------------------
// --------------------------------------------------------------------------------
print "\n-----------------------------------------------------------"
print "Model setup complete..."
print "\nYou may now open the model via openmodel.hoc (after compilation)."
print "-----------------------------------------------------------\n"
// --------------------------------------------------------------------------------
// --------------------------------------------------------------------------------
strdef compilemodqstr
sprint(compilemodqstr, "%s", "Do you wish to compile the required mod files now?\t[y/n]")
ans = sred(compilemodqstr, "y", "ny")
if (ans) {
loadfile(root, "compilemod.hoc")
}
// --------------------------------------------------------------------------------