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|
begintemplate ModelViewSegment
public proximal, distal, id
proc init() {
proximal = $2
distal = $3
id = $1
}
endtemplate ModelViewSegment
begintemplate ModelViewSection
public name, segmentList, getName, addSegment
objref segmentList
objref strobj
strdef name
proc init() {
segmentList = new List()
name = $s1
}
proc addSegment() {
segmentList.append($o1)
}
func getName() {
return name
}
func hashCode() {local hash, length, i
strobj = new StringFunctions()
length = strobj.len(name)
for i = 0, len - 1 {
}
return 0
}
endtemplate ModelViewSection
begintemplate ModelViewXML
public selected
public selsub, selsec, disp, xportLevel1, xportLevel2
public subsets, prependname, mview, unlink
public exportNeuroML
external nil, hoc_sf_
objref tobj, tobj1, mview, secref, cellref, fileref
objref dmech, dparm, dpelm, dmlist
objref storecm, pointvec, segmentvec
objref ksstate, ksgate, kstrans
strdef tstr
strdef nameForGroupWithAll
strdef singleSecGroupPrefix
objref singleSecGroupsCreated
proc init() {local i
mview = $o1
nameForGroupWithAll = ""
singleSecGroupPrefix = "OneSecGrp_"
}
proc unlink() {local i
if (dmlist != nil) for i=0, dmlist.count - 1 {
dmlist.object(i).unlink()
}
objref tobj, tobj1, mview
objref parmsubsets, parmsecs, parminhomos, dmech, dmlist
}
proc selected() {
if ($4 == -2) {
}else if ($4 == -1) {
}else if ($4 > -1) {
}
xport()
}
proc xportLevel1() {
if (numarg() == 1) {
fileref = new File($s1)
xport1(1)
return
}
fileref = new File()
fileref.chooser("w", "Save model in NeuroML v1.8.1 Level 1 file", "*.xml")
if (fileref.chooser()) {
xport1(1)
}
}
proc xportLevel2() {
if (numarg() == 1) {
fileref = new File($s1)
xport1(2)
return
}
fileref = new File()
fileref.chooser("w", "Save model in NeuroML v1.8.1 Level 2 file", "*.xml")
if (fileref.chooser()) {
xport1(2)
}
}
proc xport1() {
exportNeuroML(fileref.getname, $1)
}
// Takes args: fileName, level
proc exportNeuroML() {local ok
fileref = new File($s1)
level = $2
print "Exporting NeuroML Level ", level, "into: ",fileref.getname
ok = fileref.wopen()
if (!ok) {
printf("could not open %s\n", fileref.getname)
return
}
fileref.printf("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
header(fileref, level)
xmlwrite(fileref, level)
fileref.printf("</neuroml>\n")
fileref.close()
}
proc header() {
$o1.printf("<neuroml xmlns=\"http://morphml.org/neuroml/schema\"\n")
$o1.printf(" xmlns:mml=\"http://morphml.org/morphml/schema\"\n")
$o1.printf(" xmlns:meta=\"http://morphml.org/metadata/schema\"\n")
$o1.printf(" xmlns:bio=\"http://morphml.org/biophysics/schema\"\n")
$o1.printf(" xmlns:cml=\"http://morphml.org/channelml/schema\"\n")
$o1.printf(" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n")
$o1.printf(" xsi:schemaLocation=\"http://morphml.org/neuroml/schema http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd\"\n", $2)
$o1.printf(" name = \"NeuroML Level %d file exported from NEURON\"\n", $2)
$o1.printf(" lengthUnits=\"micron\">\n\n")
}
// store cell number in cm of first seg of root of cell (and restore original cm
proc assoc_cell_number() {local i, j, pointcount
i = 0
pointcount = 0
forsec mview.dparm.sall {
tobj = new SectionRef()
if ($1 == 1) {
storecm.x[i] = cm(.00001)
cm(.00001) = i
pointvec.x[i] = pointcount + 1
segmentvec.x[i] = pointcount + 1 - i
for j = 0, n3d() - 1 {
pointcount += 1
// $o2.printf(" <point id=\"%d\" x=\"%g\" y=\"%g\" z=\"%g\" diam=\"%g\"/>\n", pointcount, x3d(j), y3d(j), z3d(j), diam3d(j))
// $o2.printf(" <point id=\"%d\"><x=\"%g\"/><y=\"%g\"/><z=\"%g\"/><diam=\"%g\"/></point>\n", pointcount, x3d(j), y3d(j), z3d(j), diam3d(j))
}
} else {
cm(.00001) = storecm.x[i]
}
i += 1
}
}
proc xmlwrite() {local proximalid, pointcount, segmentcount, sectioncount, i, j, k, l, m
strdef date
///////$o1.printf("<!-- %s -->\n", $o1.getname())
$o1.printf("<meta:notes>NeuroML Level %d file generated from ModelView by: %s\n", $2, nrnversion())
$o1.printf("Authors: Michael Hines, Sushil Kambampati and Padraig Gleeson,\n")
$o1.printf("Yale University and UCL</meta:notes>\n\n")
proximalid = 0
pointcount = 0
sectioncount = 0
forsec mview.dparm.sall {sectioncount += 1}
pointvec = new Vector(sectioncount)
segmentvec = new Vector(sectioncount)
storecm = new Vector(sectioncount)
// go over all points in all sections in all cells
assoc_cell_number(1, $o1)
$o1.printf("<cells>\n")
totalnumcells = 0
oldidrootseg = -1
for mview.realcells(cellref) {
totalnumcells =totalnumcells+1
}
for mview.realcells(cellref) {
strdef cellName
cellName = cellref.name
if (hoc_sf_.substr(cellName,"[")>=0 && hoc_sf_.substr(cellName,"]")>=0) {
hoc_sf_.left(cellName, hoc_sf_.substr(cellName,"]"))
strdef index
index = cellName
hoc_sf_.left(cellName, hoc_sf_.substr(cellName,"["))
hoc_sf_.right(index, hoc_sf_.substr(index,"[")+1)
sprint(cellName, "%s_%s", cellName, index)
}
$o1.printf(" <cell name=\"%s\">\n", cellName)
$o1.printf(" <meta:notes>Cell: %s exported from NEURON ModelView</meta:notes>\n", cellName)
$o1.printf(" <segments xmlns=\"http://morphml.org/morphml/schema\"> <!-- Changing the namespace from neuroml to morphml-->\n")
forsec cellref.secanal.allseclist {
$o1.printf("<!-- Section: %s which has %d 3D points, so %d segment(s)-->\n", secname(), n3d(), (n3d() - 1))
sectioncount = cm(.00001)
tobj = new SectionRef()
proximalid = pointvec.x[sectioncount]
pointcount = pointvec.x[sectioncount]
segmentcount = segmentvec.x[sectioncount]
for i = 1, n3d() - 1 {
strdef newSec
newSec = secname()
hoc_sf_.right(newSec, hoc_sf_.substr(newSec, ".")+1)
thissegid = segmentcount
if (i == 1 && totalnumcells == 1 && !tobj.has_parent){ // i.e. the first seg of parentless sec on only cell
oldidrootseg = thissegid
thissegid = 0
}
$o1.printf(" <segment id=\"%d\"", thissegid)
if (hoc_sf_.substr(newSec,"[")>=0 && hoc_sf_.substr(newSec,"]")>=0) {
hoc_sf_.left(newSec, hoc_sf_.substr(newSec,"]"))
strdef index
index = newSec
hoc_sf_.left(newSec, hoc_sf_.substr(newSec,"["))
hoc_sf_.right(index, hoc_sf_.substr(index,"[")+1)
sprint(newSec, "%s_%s", newSec, index)
}
$o1.printf(" name = \"Seg%d_%s\"", i-1, newSec)
strdef parentNameInfo
parentNameInfo = ""
if (i == 1) {
if (tobj.has_parent) {
tobj.parent {
fract = -1
tobj.sec {fract = parent_connection()}
if (fract==1) {
sprint(parentNameInfo, " <!-- Parent section: %s -->", secname())
parentsegid = segmentvec.x[cm(.00001)] + n3d() - 2
if (parentsegid == oldidrootseg) {parentsegid = 0}
$o1.printf(" parent=\"%d\"", parentsegid)
} else {
parentSeg = -1
sprint(parentNameInfo, " <!-- Connected at %g on parent section: %s -->",fract, secname())
for pointIndex = 1, n3d() - 1 {
if (parentSeg<0) {
arcFract = arc3d(pointIndex)/L
if (arcFract>=fract) {
parentSeg = segmentvec.x[cm(.00001)] + pointIndex -2
}
}
}
if (parentSeg == oldidrootseg) {parentSeg = 0}
$o1.printf(" parent=\"%d\"", parentSeg)
}
}
}
} else {
parentsegid = segmentcount - 1
if (parentsegid == oldidrootseg) {parentsegid = 0}
$o1.printf(" parent=\"%d\"", parentsegid)
}
$o1.printf(" cable = \"%d\">%s\n", sectioncount, parentNameInfo)
if (i == 1) {
$o1.printf(" <proximal x=\"%g\" y=\"%g\" z=\"%g\" diameter=\"%g\"/>\n", \
x3d(i-1), y3d(i-1), z3d(i-1), diam3d(i-1))
}
$o1.printf(" <distal x=\"%g\" y=\"%g\" z=\"%g\" diameter=\"%g\"/>\n", \
x3d(i), y3d(i), z3d(i), diam3d(i))
$o1.printf(" </segment>\n")
pointcount += 1
segmentcount += 1
}
}
$o1.printf(" </segments>\n")
$o1.printf(" <cables xmlns=\"http://morphml.org/morphml/schema\"> <!-- Changing namespace from neuroml to morphml-->\n")
totalNumCables = 0
forsec cellref.secanal.allseclist {
sectioncount = cm(.00001)
tobj = new SectionRef()
strdef newSectionName
newSectionName = secname()
hoc_sf_.right(newSectionName, hoc_sf_.substr(newSectionName, ".")+1)
if (hoc_sf_.substr(newSectionName,"[")>=0 && hoc_sf_.substr(newSectionName,"]")>=0) {
hoc_sf_.left(newSectionName, hoc_sf_.substr(newSectionName,"]"))
strdef index
index = newSectionName
hoc_sf_.left(newSectionName, hoc_sf_.substr(newSectionName,"["))
hoc_sf_.right(index, hoc_sf_.substr(index,"[")+1)
sprint(newSectionName, "%s_%s", newSectionName, index)
}
$o1.printf(" <cable id = \"%d\" name = \"%s\"",sectioncount, newSectionName)
if (parent_connection() != 1) {
$o1.printf(" fract_along_parent = \"%g\"", parent_connection())
}
if (nseg > 1) {
$o1.printf(">\n")
$o1.printf(" <meta:properties>\n <meta:property>\n")
$o1.printf(" <meta:tag>numberInternalDivisions</meta:tag> <!-- Discetization of model at time of export. Can be overridden by importing application-->\n <meta:value>%d</meta:value>\n", nseg)
$o1.printf(" </meta:property>\n </meta:properties>\n")
$o1.printf(" </cable>\n")
} else {
$o1.printf("/>\n")
}
totalNumCables = totalNumCables + 1
}
if (object_id(cellref.secanal.parmsubsets) == 0) {
cellref.secanal.analyse()
}
if (cellref.secanal.parmsubsets.subsets.count >= 1) {
for i=0, cellref.secanal.parmsubsets.subsets.count-1 {
tobj1 = cellref.secanal.parmsubsets.subsets.object(i)
strdef groupName
sprint(groupName, "%s", tobj1)
strdef comment
comment = ""
if (hoc_sf_.substr(groupName,"[")>=0 && hoc_sf_.substr(groupName,"]")>=0) {
hoc_sf_.left(groupName, hoc_sf_.substr(groupName,"]"))
strdef index
index = groupName
hoc_sf_.left(groupName, hoc_sf_.substr(groupName,"["))
hoc_sf_.right(index, hoc_sf_.substr(index,"[")+1)
sprint(groupName, "%s_%s", groupName, index)
}
if (hoc_sf_.len(nameForGroupWithAll)==0 && tobj1.subset.size== totalNumCables) {
nameForGroupWithAll = groupName
groupName = "all"
sprint(comment, "<!-- Replacing subset name %s with all, as it contains all sections -->", nameForGroupWithAll)
}
$o1.printf(" <cablegroup name=\"%s\"> %s\n", groupName, comment)
for j=0, tobj1.subset.size - 1 {
secref = cellref.secanal.all.object(tobj1.subset.x(j))
$o1.printf(" <cable id = \"%d\"/>\n",secref.sec.cm(.00001))
}
$o1.printf(" </cablegroup>\n")
}
} else {
$o1.printf(" <!-- No cable groups present -->\n")
}
/// Must check if there is an easier way of doing this!!!
singleSecGroupsCreated = new Vector()
for i=0, cellref.secanal.dmlist.count - 1 {
dmech = cellref.secanal.dmlist.object(i)
if (object_id(dmech.location) == 0) { continue }
for dmech.parmiter(dparm) {
for dparm.parmiter(dpelm) {
for l=0, dpelm.parms.count - 1 {
///printparmval($o1, cellref.secanal.all, "", dpelm.parms.object(l), 1) // Converting ohm cm (NEURON units) to Kohm cm (Phys units)
trySingleSecGroup = 1
if (dpelm.parms.object(l).type() == 1){
if (dpelm.parms.object(l).location.type() == 8) { trySingleSecGroup = 0}
}
if(trySingleSecGroup==1) {
secref = cellref.secanal.all.object(dpelm.parms.object(l).location.isec)
strdef groupName
sprint(groupName, "%s%s", singleSecGroupPrefix, secref)
if (hoc_sf_.substr(groupName,"[")>=0 && hoc_sf_.substr(groupName,"]")>=0) {
hoc_sf_.left(groupName, hoc_sf_.substr(groupName,"]"))
strdef index
index = groupName
hoc_sf_.left(groupName, hoc_sf_.substr(groupName,"["))
hoc_sf_.right(index, hoc_sf_.substr(index,"[")+1)
sprint(groupName, "%s_%s", groupName, index)
}
strdef currsecname
secref.sec {currsecname = secname()}
cableid = secref.sec.cm(.00001)
sprint(comment, "<!-- Creating a group containing a single section: %s... -->", currsecname)
if (!singleSecGroupsCreated.contains(cableid)) { // so no repeats...
$o1.printf(" <cablegroup name=\"%s\"> %s\n", groupName, comment)
$o1.printf(" <cable id = \"%d\"/>\n", cableid)
$o1.printf(" </cablegroup>\n")
}
singleSecGroupsCreated.append(cableid)
}
}
}
}
}
$o1.printf(" </cables>\n")
// biophysics element for THIS cell. Only include if level > 1
if ($2 > 1) { // i.e. Level 2 of NeuroML or greater
$o1.printf(" <biophysics units = \"Physiological Units\"> <!-- Note: values of cond dens are different in NEURON and phy units-->\n")
for mview.dparm.kschans(tobj) {
kschan_xmlwrite($o1, tobj)
}
///////////for mview.realcells(cellref) {
// to distinguish b/w toplevel and encapsulated real cells
if (object_id(cellref.secanal.parmsubsets) == 0) {
continue
}
//////////////$o1.printf("<cell name=\"%s\">\n", cellref.name)
for i=0, cellref.secanal.dmlist.count - 1 {
dmech = cellref.secanal.dmlist.object(i)
// TODO: for tobj.mechs(dmech) { }
if (dmech.parms.count > 0) {
}
if (object_id(dmech.location) == 0) { continue }
if (strcmp(dmech.name,"capacitance") != 0 && strcmp(dmech.name,"Ra") != 0 && hoc_sf_.substr(dmech.name, "_ion") == -1) {
strdef passiveAttr
passiveAttr = ""
// If mech name is built in passive conductance in NEURON
if (strcmp(dmech.name,"pas") == 0) {
passiveAttr = " passive_conductance=\"true\""
}
// If mech name is default passive conductance from neuroConstruct
if (strcmp(dmech.name,"LeakConductance") == 0) {
passiveAttr = " passive_conductance=\"true\""
}
$o1.printf(" <bio:mechanism name=\"%s\" type=\"Channel Mechanism\"%s>\n", dmech.name, passiveAttr)
for j=0, dmech.location.subset.size()-1 {
secref = cellref.secanal.all.object(dmech.location.subset.x(j))
// printsec($o1, secref)
}
for dmech.parmiter(dparm) {
for dparm.parmiter(dpelm) {
for l=0, dpelm.parms.count - 1 {
strdef paramNameToUse
paramNameToUse = dparm.name
strdef comment
comment = ""
// strip suffix
if (hoc_sf_.substr(paramNameToUse, "_")>=0) {
hoc_sf_.left(paramNameToUse, hoc_sf_.substr(paramNameToUse, "_"))
}
if (strcmp(dparm.name,"g_pas") == 0) {
paramNameToUse = "gmax"
sprint(comment, "<!-- Assuming parameter g_pas refers to passive maximum cond density, so replacing it with gmax -->", paramNameToUse)
}
if (strcmp(paramNameToUse,"g") == 0) {
paramNameToUse = "gmax"
sprint(comment, "<!-- Assuming parameter g refers to passive maximum cond density, so replacing it with gmax -->", paramNameToUse)
} else if (hoc_sf_.substr(paramNameToUse, "g")==0 && hoc_sf_.substr(paramNameToUse, "bar")>=1) {
sprint(comment, "<!-- Assuming parameter %s refers to the maximum cond density, so replacing it with gmax -->", paramNameToUse)
paramNameToUse = "gmax"
} else if (strcmp(paramNameToUse,"gl") == 0) {
paramNameToUse = "gmax"
sprint(comment, "<!-- Assuming parameter gl refers to the maximum cond density, so replacing it with gmax -->", paramNameToUse)
} else if (hoc_sf_.substr(dmech.name, "_") >= 0) {
strdef paramNameSuspect
paramNameSuspect = dmech.name
hoc_sf_.left(paramNameSuspect, hoc_sf_.substr(paramNameSuspect, "_"))
sprint(paramNameSuspect, "g%s", paramNameSuspect)
print "Suspecting: ",paramNameSuspect
if (strcmp(paramNameToUse,paramNameSuspect) == 0) {
sprint(comment, "Assuming parameter %s refers to the maximum cond density, so replacing it with gmax", paramNameToUse)
paramNameToUse = "gmax"
}
}
//print "Checking param: ",paramNameToUse, " in ", dmech.name
//print comment
factor = 1
if (hoc_sf_.substr(paramNameToUse,"gmax") >= 0) {
factor = 1000 /// converting S cm-2 (NEURON units) to mS cm-2 (Phys units)
}
printparmval($o1, cellref.secanal.all, paramNameToUse, dpelm.parms.object(l), factor, comment, dmech.name)
}
}
}
$o1.printf(" </bio:mechanism>\n")
}
}
strdef noComment
noComment = ""
for i=0, cellref.secanal.dmlist.count - 1 {
dmech = cellref.secanal.dmlist.object(i)
if (object_id(dmech.location) == 0) { continue }
if (strcmp(dmech.name,"capacitance") == 0) {
$o1.printf(" <bio:spec_capacitance>\n")
for dmech.parmiter(dparm) {
for dparm.parmiter(dpelm) {
for l=0, dpelm.parms.count - 1 {
printparmval($o1, cellref.secanal.all, "", dpelm.parms.object(l), 1, noComment, dmech.name) // Converting μF cm-2 (NEURON units) to μF cm-2 (Phys units)
}
}
}
$o1.printf(" </bio:spec_capacitance>\n")
}
}
for i=0, cellref.secanal.dmlist.count - 1 {
dmech = cellref.secanal.dmlist.object(i)
if (object_id(dmech.location) == 0) { continue }
if (strcmp(dmech.name,"Ra") == 0) {
$o1.printf(" <bio:spec_axial_resistance>\n")
for dmech.parmiter(dparm) {
for dparm.parmiter(dpelm) {
for l=0, dpelm.parms.count - 1 {
printparmval($o1, cellref.secanal.all, "", dpelm.parms.object(l), 0.001, noComment, dmech.name) // Converting ohm cm (NEURON units) to Kohm cm (Phys units)
}
}
}
$o1.printf(" </bio:spec_axial_resistance>\n")
}
}
//////////// ion_xmlwrite($o1)
$o1.printf(" </biophysics>\n")
}
$o1.printf(" </cell>\n")
}
$o1.printf("</cells>\n")
assoc_cell_number(0, $o1)
////////PG: not required //// $o1.printf("</morphml>\n")
/*
if (parmsubsets.subsets.count > 1) {
sprint(tstr, "%d subsets with constant parameters", parmsubsets.subsets.count)
disp1 = new TreeViewItem(disp, tstr, this, -1)
}else{
disp1 = disp
}
for i=0, parmsubsets.subsets.count-1 {
tobj = parmsubsets.subsets.object(i)
sprint(tstr, "%s (%d sections)", tobj, tobj.subset.size)
msub = new TreeViewItem(disp1, tstr, tobj, -1)
prsub(tobj.subset)
for j=0, tobj.parmlist.count-1 {
tobj1 = tobj.parmlist.object(j)
sprint(tstr, "%s = %g", tobj1.parmelm.name, tobj1.value)
msub.append(tstr, tobj, j)
}
}
if (parmsecs.count + parminhomos.count > 1) {
sprint(tstr, "%d sections with unique parameters", parmsecs.count + parminhomos.count)
disp1 = new TreeViewItem(disp, tstr)
}else{
disp1 = disp
}
for i=0, parmsecs.count-1 {
tobj = parmsecs.object(i)
all.object(tobj.isec).sec sprint(tstr, "%s {", secname())
msub = new TreeViewItem(disp1, tstr, tobj, -1)
for j=0, tobj.parmlist.count-1 {
tobj1 = tobj.parmlist.object(j)
sprint(tstr, " %s = %g", tobj1.parmelm.name, tobj1.value)
msub.append(tstr, tobj, j)
}
msub.append("}", tobj, j)
}
for i=0, parminhomos.count-1 {
tobj = parminhomos.object(i)
all.object(tobj.isec).sec sprint(tstr, "%s {", secname())
msub = new TreeViewItem(disp1, tstr, tobj, -1)
for j=0, tobj.parmlist.count-1 {
tobj1 = tobj.parmlist.object(j)
sprint(tstr, " %s =", tobj1.parmelm.name)
for k=0, tobj1.vec.size-1 {
sprint(tstr, " %s %g", tstr, tobj1.vec.x[k])
}
msub.append(tstr, tobj, j)
}
msub.append("}", tobj, j)
}
*/
artcell($o1)
// $o1.printf("</model>\n")
}
proc artcell() {local i,j,l
for i=0, mview.acview.alist.count-1 {
dmech = mview.acview.alist.object(i)
$o1.printf(" <mechanism name=\"%s\">\n", dmech.name)
for j=0, dmech.parms.count-1 {
dparm = dmech.parms.object(j)
for dparm.parmiter(dpelm) {
for l=0, dpelm.parms.count - 1 {
tobj = dpelm.parms.object(l)
// 1 is ModelViewParmVal, 2 is ModelViewParmVec
if (tobj.type() == 1) {
$o1.printf(" <parameter name=\"%s\" value=\"%g\"/>\n", dpelm.name, tobj.value)
}
}
}
}
$o1.printf(" </mechanism>\n")
}
}
proc printparmval() {
// 1 is ModelViewParmVal, 2 is ModelViewParmVec
if ($o4.type() == 1) {
strdef nameattr
nameattr = ""
strdef comment
comment = ""
if (hoc_sf_.len($s3)>0) { // only incl if $s3 is set
strdef newParamName
newParamName = $s3
sprint(nameattr, " name=\"%s\"", newParamName)
}
$o1.printf(" <bio:parameter%s value=\"%g\"> %s\n", nameattr, $o4.value * $5, $s6)
// 8 is ModelViewParmSubset, 9 is ModelViewParmSec
if ($o4.location.type() == 8) {
// for m=0, $o4.location.subset.size()-1 {
// secref = $o2.object($o4.location.subset.x(m))
// printsec($o1, secref)
// }
strdef groupName
sprint(groupName, "%s", $o4.location)
if (hoc_sf_.substr(groupName,"[")>=0 && hoc_sf_.substr(groupName,"]")>=0) {
hoc_sf_.left(groupName, hoc_sf_.substr(groupName,"]"))
strdef index
index = groupName
hoc_sf_.left(groupName, hoc_sf_.substr(groupName,"["))
hoc_sf_.right(index, hoc_sf_.substr(index,"[")+1)
sprint(groupName, "%s_%s", groupName, index)
}
if (strcmp(groupName,nameForGroupWithAll) == 0) {
groupName = "all"
}
$o1.printf(" <bio:group>%s</bio:group>\n", groupName)
} else {
secref = $o2.object($o4.location.isec)
//printsec($o1, secref)
strdef groupName
sprint(groupName, "%s%s", singleSecGroupPrefix, secref)
if (hoc_sf_.substr(groupName,"[")>=0 && hoc_sf_.substr(groupName,"]")>=0) {
hoc_sf_.left(groupName, hoc_sf_.substr(groupName,"]"))
strdef index
index = groupName
hoc_sf_.left(groupName, hoc_sf_.substr(groupName,"["))
hoc_sf_.right(index, hoc_sf_.substr(index,"[")+1)
sprint(groupName, "%s_%s", groupName, index)
}
$o1.printf(" <bio:group>%s</bio:group>\n", groupName)
}
$o1.printf(" </bio:parameter>\n")
} else if ($o4.type() == 2) { // ModelViewParmVec
secref = $o2.object($o4.location.isec)
strdef groupName
sprint(groupName, "%s%s", singleSecGroupPrefix, secref)
if (hoc_sf_.substr(groupName,"[")>=0 && hoc_sf_.substr(groupName,"]")>=0) {
hoc_sf_.left(groupName, hoc_sf_.substr(groupName,"]"))
strdef index
index = groupName
hoc_sf_.left(groupName, hoc_sf_.substr(groupName,"["))
hoc_sf_.right(index, hoc_sf_.substr(index,"[")+1)
sprint(groupName, "%s_%s", groupName, index)
}
strdef currsecname
secref.sec {currsecname = secname()}
$o1.printf(" <!-- There is an inhomogenous parameter: %s present for mechanism: %s on group: %s for section: %s! -->\n", $s3, $s7, groupName, currsecname)
avgVal = 0
strdef infoVals
infoVals = ""
for i=0, $o4.vec.size - 1 {
sprint(infoVals, "%s %g, ", infoVals, $o4.vec.x(i))
avgVal = avgVal + $o4.vec.x(i)
}
avgVal = avgVal / $o4.vec.size
$o1.printf(" <!-- Actual values along section (in NEURON units): %s but using average: %g -->\n", infoVals, avgVal)
//printvecvals($o1, $o4)
$o1.printf(" <bio:parameter name=\"%s\" value=\"%g\"> \n", $s3, avgVal * $5)
$o1.printf(" <bio:group>%s</bio:group>\n", groupName)
$o1.printf(" </bio:parameter>\n")
}
}
proc printsec() {
$o2.sec {
$o1.printf(" <section name=\"%s\"/>\n", secname())
}
}
proc printvecvals() {local i
$o2.location.realcell.all.object($o2.location.isec).sec {
$o1.printf(" <!-- NOTE: this mechanism is present on %s but has non uniform values. Expression for generating values cannot be retrieved! -->\n", secname())
///$o1.printf(" <section name=\"%s\">\n", secname())
}
for i=0, $o2.vec.size - 1 {
//$o1.printf(" <value>%g</value>\n", $o2.vec.x(i))
$o1.printf(" <!-- Value %g: %g -->\n", i, $o2.vec.x(i))
}
//$o1.printf(" </section>\n")
}
proc ion_xmlwrite() {
for mview.dparm.mechs(tobj) {
if (hoc_sf_.head(tobj.name, "_ion", tstr) != -1) {
$o1.printf(" <bio:ion name=\"%s\" charge=\"%d\"/>\n", tstr, ion_charge(tobj.name))
}
}
}
proc kschan_xmlwrite() {local i, j
$o1.printf(" <channel_type name=\"%s\"", $o2.name)
if ($o2.is_point) {
$o1.printf(" density=\"no\"")
}else{
$o1.printf(" density=\"yes\"")
}
$o1.printf(">\n")
$o1.printf(" <current_voltage_relation>\n")
if ($o2.iv_type == 0) {
if (strcmp($o2.ion, "NonSpecific") == 0) {
$o1.printf(" <ohmic NonSpecific=\"yes\" default_erev=\"%g\">\n", $o2.erev)
}else{
$o1.printf(" <ohmic ion=\"%s\">\n", $o2.ion)
}
$o1.printf(" <conductance default_gmax=\"%g\">\n", $o2.gmax)
kschan_cond_xmlwrite($o1, $o2)
$o1.printf(" </conductance>\n")
}else{
$o1.printf(" <Goldman_Hodgkin_Katz ion=\"%s\">\n", $o2.ion)
$o1.printf(" <permeability default_pmax=\"%g\">\n", $o2.gmax)
kschan_cond_xmlwrite($o1, $o2)
$o1.printf(" </permeability>\n")
}
if ($o2.iv_type == 0) {
$o1.printf(" </ohmic>\n")
}else{
$o1.printf(" </Goldman_Hodgkin_Katz>\n")
}
$o1.printf(" </current_voltage_relation>\n")
for i=0, $o2.ngate-1 {
ksgate = $o2.gate(i)
if (ksgate.nstate == 1) {
ksstate = $o2.state(ksgate.sindex)
$o1.printf(" <hh_gate state=\"%s\">\n", ksstate.name)
kstrans = $o2.trans(i)
kstrans1($o1, $o2, kstrans)
$o1.printf(" </hh_gate>\n")
}else{
$o1.printf(" <ks_gate>\n")
for j=0, ksgate.nstate-1 {
ksstate = $o2.state(ksgate.sindex + j)
$o1.printf(" <state name=\"%s\"/>\n", ksstate.name)
}
for j=0, $o2.ntrans-1 {
kstrans = $o2.trans(j)
if (kstrans.src.gate.index == i) {
kstrans1($o1, $o2, kstrans)
}
}
$o1.printf(" </ks_gate>\n")
}
}
$o1.printf(" </channel_type>\n")
}
proc kschan_cond_xmlwrite() {local i, j
for i=0, $o2.ngate-1 {
ksgate = $o2.gate(i)
$o1.printf(" <gate power=\"%g\">\n", ksgate.power)
for j=0, ksgate.nstate-1 {
ksstate = $o2.state(ksgate.sindex + j)
if (ksstate.frac != 0) {
$o1.printf(" <state name=\"%s\" fraction=\"%g\"/>\n", ksstate.name, ksstate.frac)
}
}
$o1.printf(" </gate>\n")
}
}
proc kstrans1() {
if ($o3.src == $o3.target) {
$o1.printf(" <transition>\n")
}else{
$o1.printf(" <transition src=\"%s\" target=\"%s\">\n", $o3.src.name, $o3.target.name)
}
if ($o3.type <= 1) {
$o1.printf(" <voltage_gate>\n")
if($o3.type == 0) {
kstrans2($o1, "alpha", $o3.ftype(0), $o3.parm(0))
kstrans2($o1, "beta", $o3.ftype(1), $o3.parm(1))
}else{
kstrans2($o1, "infinity", $o3.ftype(0), $o3.parm(0))
kstrans2($o1, "tau", $o3.ftype(1), $o3.parm(1))
}
$o1.printf(" </voltage_gate>\n")
}else if ($o3.type > 1) {
if ($o3.type == 2) { tstr = "no" } else { tstr = "yes" }
$o1.printf(" <ligand_gate ligand=\"%s\" inside=\"%s\">\n", $o3.ligand, tstr)
kstrans2($o1, "alpha", $o3.ftype(0), $o3.parm(0))
kstrans2($o1, "beta", $o3.ftype(1), $o3.parm(1))
$o1.printf(" </ligand_gate>\n")
}
$o1.printf(" </transition>\n")
}
proc kstrans2() {local i
$o1.printf(" <%s>\n", $s2)
$o1.printf(" <parameterised_hh")
if ($3 == 1) {
$o1.printf(" type=\"constant\" value=\"%g\"/>", $o4.x[0])
return
}else if ($3 == 2) {
$o1.printf(" type=\"exponential\" expr=\"A*exp(k*(v-d))\"")
}else if ($3 == 3) {
$o1.printf(" type=\"linoid\" expr=\"A*x/(1 - exp(-x)) where x = k*v-d)\"")
}else if ($3 == 4) {
$o1.printf(" type=\"sigmoid\" expr=\"A/(1 + exp(-k*(d-v))\"")
}
$o1.printf(">\n")
$o1.printf(" <parameter name=\"A\" value=\"%g\"/>\n", $o4.x[0])
$o1.printf(" <parameter name=\"k\" value=\"%g\"/>\n", $o4.x[1])
$o1.printf(" <parameter name=\"d\" value=\"%g\"/>\n", $o4.x[2])
$o1.printf(" </parameterised_hh>\n")
$o1.printf(" </%s>\n", $s2)
}
endtemplate ModelViewXML
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