/*
*
* A neuroConstruct helper file of some simple utilities for checking the
* morphologies of cells loaded into NEURON
*
* Some of these functions provide GENESIS like output, for comparing models in each simulator
* Some functions need a little more tweaking
*
*/
objectvar nil
/*
* Provides information on the morphology of the current accessed section
*/
proc morph() {
totalarea = 0
print "Currently addressed section: ", secname()
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
print "+ Number of 3D info points: ", n3d()
for i=0,n3d()-1{
delx = x3d(i)-lastx
dely = y3d(i)-lasty
delz = z3d(i)-lastz
len = sqrt((delx*delx)+(dely*dely)+(delz*delz))
if (i==0){
delx = dely = delz = len = 0
}
print "+ ", secname(), " ", i, ": (", x3d(i), ", ", y3d(i), ", ", z3d(i),") diam: ", diam3d(i), " del: (", delx,", ", dely,", ", delz,") len: ", len
lastx = x3d(i)
lasty = y3d(i)
lastz = z3d(i)
}
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
print "+ Number of segments (nseg): ", nseg
for i=0,nseg+1{
print "+ ", secname(), " ", i/(nseg+1), " diam: ", diam((i/(nseg+1))), " area: ", area((i/(nseg+1))), " um^2"
totalarea = totalarea + area((i/(nseg+1)))
}
print "+ Total area: ", totalarea
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
print ""
}
/*
* Provides information on the total area, etc.
* Useful as a simple test for comparing cells
*/
proc areainfo(){
totalnum = 0
totalarea = 0
forall totalnum = totalnum +1
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
print "+"
forall {
totalsecarea = 0
for i=0,n3d()-1 print "+ ", secname(), " ", i, ": (", x3d(i), ", ", y3d(i), ", ", z3d(i), ") diam: ", diam3d(i)
for i=0,nseg+1{
//print "+ ", secname(), " ", i/(nseg+1), " diam: ", diam((i/(nseg+1))), " area: ", area((i/(nseg+1))), " um^2"
totalsecarea = totalsecarea + area((i/(nseg+1)))
}
print "+ Total section area in ",secname(), ": ", totalsecarea
totalarea = totalarea + totalsecarea
}
print "+"
print "+ Number of sections: ", totalnum
print "+ Total all sections: ", totalarea, " um^2"
print "+ Total all sections: ", totalarea/(1000000*1000000), " m^2"
print "+ Total all sections: ", totalarea/(10000*10000), " cm^2"
print "+"
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
/*
* Prints voltage of all of the created compartments
*/
proc allv(){
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
forall {
if (nseg ==1) {
print secname(), ": ", v
} else {
print secname(), " (nseg = ",nseg,"): "
for i=0,nseg+1{
strdef ind
sprint(ind, " %f: ", (i/(nseg+1)))
print ind, "\t\t ", v((i/(nseg+1)))
}
}
}
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
/*
* Prints ca conc of all of the created compartments
*/
proc allca(){
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
forall {
if (ismembrane("ca_ion")) {
if (nseg ==1) {
print secname(), ": ", cai
} else {
print secname(), " (nseg = ",nseg,"): "
for i=0,nseg+1{
strdef ind
sprint(ind, " %f: ", (i/(nseg+1)))
print ind, "\t\t ", cai((i/(nseg+1)))
}
}
}
}
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
/*
* Prints info on network connections
*/
proc allsyns() {
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
for i=0,allCells.count()-1 {
allCells.o[i].netInfo()
}
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
/*
* Prints info on all cells
*/
proc allcells() {
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
for i=0,allCells.count()-1 {
allCells.o[i].toString()
}
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
/*
* Provides information on the current section similar to that produced
* with "showfield *" in GENESIS
*/
proc gen() {
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
totalarea = 0
totalRa = 0
print ""
print secname()
print ""
print "Voltage = ", v
for i=0,nseg+1{
thisPoint = i/(nseg+1)
nextPoint = (i+1)/(nseg+1)
halfWay = thisPoint
areaHere = area(halfWay)
RaHere = ri(halfWay)
print " - Section from ", thisPoint, " to ", nextPoint, ", area: ", areaHere
print " Ra to end of this length = ", RaHere*1000, " ohm"
totalarea = totalarea + areaHere
if (i>0){
totalRa = totalRa + RaHere
}
}
print "Total area = ", totalarea
print "Total Ra = ", totalRa*1000 , " ohm"
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
/*
* Provides information on the current section, like an expanded psection()
*/
proc secinfo() {
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
totalarea = 0
totalRa = 0
print ""
print secname()
print ""
print "Voltage = ", v
print "nseg = ", nseg
for i=1,nseg+1{
thisPoint = i/(nseg+1)
nextPoint = (i+1)/(nseg+1)
halfWay = thisPoint
areaHere = area(halfWay)
RaHere = ri(halfWay)
print " - Section from ", thisPoint, ", to ", nextPoint, ", area: ", areaHere
print " Ra = ", RaHere*1000, " ohm"
totalarea = totalarea + areaHere
totalRa = totalRa + RaHere
}
print "Total area = ", totalarea
print "Total Ra = ", totalRa*1000 , " ohm (Note that this doesn't have any physical meaning)"
print "++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
objectvar listNcSyn
objectvar listNcPre
proc netConnInfo() {
netConInfo()
}
/*
* Helper functions for getting more info on NetConn objects
*/
proc netConInfo() {
print "-- ",hostid,"---------------------------------------------------------"
print "-- ",hostid,"-- NetConn: ", $o1
if ($o1!=nil) {
print "-- ",hostid,"-- Pre: ",$o1.precell(),", Syn: ",$o1.syn,"(",$o1.postcell, ")", ", Active: ",$o1.active(),", Valid: ",$o1.valid()
/*
// Doesn't seem to work with section in template...
if ($o1.precell()!=nil) {
print "-- ",hostid,"-- From: ", $o1.precell().toString()
loc = $o1.preloc()
print "-- ",hostid,"-- Section: ", secname(), " - ", loc
pop_section()
}*/
if ($o1.postcell()!=nil) { print "-- ",hostid,"-- To: ", $o1.postcell().toString() }
print "-- ",hostid,"-- Weight: ",$o1.weight, ", Delay: ",$o1.delay, ", Thresh: ",$o1.threshold
listNcSyn = $o1.synlist()
for i=0,listNcSyn.count()-1 {
print "-- ",hostid,"-- NetConns sharing syn: ", listNcSyn.o(i)
}
listNcPre = $o1.precelllist()
for i=0,listNcPre.count()-1 {
print "-- ",hostid,"-- NetConns sharing pre cell: ", listNcPre.o(i)
}
}
print "-- ",hostid,"---------------------------------------------------------"
}
proc netConInfoParallel() {
netConInfo($o1)
if ($o1!=nil) {
print "-- ",hostid,"----------------------- Src gid: ", $o1.srcgid
}
print " "
}
// Some utilities for automating testing of generated NEURON
numTestsPassed = 0
numTestsFailed = 0
proc testEquals() {
if ($1 != $2) {
print "Test failed: ", $1, " != ", $2
numTestsFailed = numTestsFailed + 1
} else {
numTestsPassed = numTestsPassed + 1
}
}
objref testResultFile
proc createTestReport() {
print "------------------------------------------------------------------------------"
print " Finished tests. Number of passed tests: ", numTestsPassed, ", number of failed tests: ", numTestsFailed
{testResultFile = new File()}
if(numTestsFailed == 0) {
testResultFile.wopen("passed")
} else {
testResultFile.wopen("failed")
}
{testResultFile.printf("numPassed=%g\n", numTestsPassed)}
{testResultFile.printf("numFailed=%g\n", numTestsFailed)}
{testResultFile.close()}
print "------------------------------------------------------------------------------"
}