// -----------------------------------------------------------------------------------
// Authors: Ronald van Elburg
//
// Affiliations:
// Department of Artificial Intelligence
// Groningen University
//
// Department for Experimental Neurophysiology
// Vrije Universiteit Amsterdam
//
// Purpose: Overcoming the need to write standard for loops
// for parameter space exploration, generating output files
// and defining protocols.
//
// Author: Ronald van Elburg (RonaldAJ at vanElburg eu)
//
// This code was first published on http://senselab.med.yale.edu/modeldb/,
// accession number 114359 accompanying the paper:
// Ronald A.J. van Elburg and Arjen van Ooyen (2010) `Impact of dendritic size and
// dendritic topology on burst firing in pyramidal cells',
// PLoS Comput Biol 6(5): e1000781. doi:10.1371/journal.pcbi.1000781.
// Please cite both the paper and the ModelDB entry when you use
// this software to prepare a publication.
//
// This software is released under the GNU GPL version 3:
// http://www.gnu.org/copyleft/gpl.html
//
// Other Contributions:
// The file nrn_vread.m for reading neuron binaries into matlab was first
// published by Konstantin Miller on the Neuron forum.
//
// Other Files Loaded:
// MRC_all_in_list.hoc defines an iterator for lists
// MRC_Classes.hoc
//
//
// if nrngui.hoc is not loaded:
// nrngui.hoc standard GUI components
//
// Output: initial version: outputfiles defined by users
// later version: session files support
//
// Required Mechanisms:
// none
// Warnings:
//
// ----------------------------------------------------------------------------------//
loadedFromGui=1
MRC_debugmode=0 //MRC_debugmode=1 print debugging info, MRC_debugmode=0 don't.
if(name_declared("nrnmainmenu")==0){
printf("Not loaded from GUI, so we are in test mode and we need to load the GUI!\n")
// Load standard GUI components for testing
loadedFromGui=0
load_file("nrngui.hoc")
}
load_file("MRC_all_in_list.hoc")
load_file("MRC_Classes.hoc")
begintemplate MultipleRunControlGUI
public list, vbox, hbox , g, preparerun, printtofile,file_name
public map
objref list, sc,hbox[2] , vbox[6]
objref types_outpar, outpar
objref looppars, outpars
objref tobj, tobj1, this //reference for temporarily storing object
strdef tstr, tstr1, looppar_modestr, outpar_modestr, file_name
objref undefined_type
objref type, outpar_type
objref protocol
objref nil,this
strdef RemoveDialogText
strdef loopstr,loopstr2,loopindentstr
external all_in_list, MRC_debugmode,MRC_Run,MRC_PrepareModel, MRC_SliceNo
proc init() {
// Create list of loopparameters , list of outparameters, and a protocol object
looppars = new List()
outpars = new List()
protocol = new MRC_Protocol()
// Set default output filename
file_name="NRN_Outfile"
file_index_start=0
// Load handlers
types_outpar= new MRC_OutParamHandlerContainer()
undefined_type=types_outpar.get_undefined_type()
undefined_type_index=0
// Create a symbol chooser
sc = new SymChooser("Pick Input Parameter")
// Build the basic GUI-component, including vbox[0]
build()
if(0==numarg()){ // This check is made to allow creating the control without mapping it for use in session files
map()
}else if(4==numarg()){
map(0,$1,$2, $3, $4)
}
//auxilary variables
outpar_mode=0
index_in_outpars=0
semaphore=0
outpar_type_index=0
}
proc map() {
sprint(tstr, "%s", this)
if (numarg() > 0) {
vbox[0].map(tstr, $2, $3, $4, $5)
}else{
vbox[0].map(tstr)
}
}
proc build() {
credits()
vbox[0] = new VBox()
vbox[0].ref(this)
vbox[0].save("save()")
vbox[0].intercept(1)
//xpanel("",1)
//// xbutton("Credits", "credits()")
//xpanel()
xpanel("",1)
xbutton("Set Protocol", "protocol.edit()")
xbutton("Single Run", "MRC_PrepareModel() preparerun() MRC_Run() printtofile()")
xbutton("Loop Run", "looprun()")
xcheckbox("Start indices at 1 (default=0)",&file_index_start )
xpanel()
xpanel("",1)
xbutton("Set Basename for Output Files:","string_dialog(\"Basename for Output Files:\",file_name)")
xvarlabel(file_name)
xpanel()
hbox[1] = new HBox()
hbox[1] .intercept(1)
vbox[1] = new VBox()
vbox[1].intercept(1)
xpanel("",1)
xmenu("Loop Params")
xbutton("Add", "add_looppar() looppars.accept_action(\"\") looppar_modestr=\"...\"")
xbutton("Remove", "looppars.accept_action(\"remove_looppar(hoc_ac_)\") looppar_modestr=\"Remove\"")
xbutton("Toggle", "looppars.accept_action(\"toggle_looppar(hoc_ac_)\") looppar_modestr=\"Toggle\"")
xbutton("Edit","looppars.accept_action(\"edit_looppar(hoc_ac_)\") looppar_modestr=\"Edit\"")
xbutton("Up","looppars.accept_action(\"up_looppar(hoc_ac_)\") looppar_modestr=\"Move Up\"")
xbutton("Down","looppars.accept_action(\"down_looppar(hoc_ac_)\") looppar_modestr=\"MOve Down\"")
xmenu()
looppar_modestr="... "
xvarlabel(looppar_modestr)
xpanel()
looppars.browser("", "displaytext")
vbox[1].intercept(0)
vbox[1].map()
vbox[2] = new VBox()
vbox[2].intercept(1)
xpanel("",1)
xmenu("Out Params")
xbutton("Add", "if(0==semaphore){outpar_mode=0 setaction_outpar() }")
xradiobutton("Remove", "if(0==semaphore){outpar_mode=1 setaction_outpar() outpar_modestr=\"Remove\"}")
xradiobutton("Output Type", "if(0==semaphore){outpar_mode=2 setaction_outpar() outpar_modestr=\"Type\"}")
xradiobutton("Edit Output Var", "if(0==semaphore){outpar_mode=3 setaction_outpar() outpar_modestr=\"Edit\"}")
xradiobutton("Show Run Results", "if(0==semaphore){outpar_mode=4 setaction_outpar() outpar_modestr=\"Show\"}")
xradiobutton("Print to File", "if(0==semaphore){outpar_mode=5 setaction_outpar() outpar_modestr=\"Print to File\"}")
xradiobutton("Toggle Use", "if(0==semaphore){outpar_mode=7 setaction_outpar() outpar_modestr=\"Toggle\"}")
xbutton("Prepare Run", "if(0==semaphore){outpar_mode=6 setaction_outpar()}")
xmenu()
outpar_mode=0 outpar_modestr="... "
xvarlabel(outpar_modestr)
xpanel()
outpars.browser("", "displaytext")
vbox[2].intercept(0)
vbox[2].map()
hbox[1] .intercept(0)
hbox[1] .map()
vbox[0].intercept(0)
}
//Procedures used in the loopparameter browser for updating the information
//Procedure: update_browser_element
//Param1: List with active browser
//Param2: Index of elemenet that need to be redisplayed
proc update_browser_element(){local listcount
if(numarg()==2){
objref tobj
tobj=$o1.object($2)
$o1.remove($2)
$o1.insrt($2, tobj)
objref tobj
}
if(numarg()==3){
objref tobj
listcount=$o1.count()
if($2+$3 <= listcount-1 && $2+$3 >=0 ){
tobj=$o1.object($2)
$o1.remove($2)
$o1.insrt($2+$3, tobj)
}
objref tobj
}
}
//Procedure: add_looppar
//Create a symbol chooser to pick a new parameter for the loopparameter list.
proc add_looppar(){localobj loopparameter
if (sc.run()) {
sc.text(tstr)
loopparameter=new MRC_LoopParameter(tstr)
looppars.append(loopparameter)
}
}
//Procedure: remove_looppar
//Remove element with index Param1 from the loopparameter list, but
//only if confirmed in a dialog.
//Param1: Index of element to be removed.
proc remove_looppar(){
if($1<0){
return
}
dialog_outcome=0
sprint(RemoveDialogText,"Do you want to remove <%s> from the loopparameter list?",looppars.object($1).name)
vbox[3]=new VBox()
dialog_outcome=vbox[3].dialog(RemoveDialogText,"Yes","No")
if(dialog_outcome==0){
return
}else{
looppars.remove($1)
}
}
//Procedure: toggle_looppar
//Param1: Index of element to be toggled for using in parameter scan.
proc toggle_looppar(){
if($1<0){
return
}
looppars.object($1).toggle()
update_browser_element(looppars,$1)
}
//Procedure: edit_looppar
//Brings up a string_dialog for changing the limits and stepsize of a loopparameter
//Param1: Index of element to be edited
proc edit_looppar() {local lower_limit, upper_limit, stepsize,restart,restart_at,end_before localobj loopparameter
loopparameter = looppars.object($1)
loopparameter.get(&lower_limit, &upper_limit, &stepsize,&restart,&restart_at,&end_before)
sprint(tstr1, "Enter: lower limit upper limit and stepsize (restart (1=restart, 2=slice), restart_at, end_before) for %s .", loopparameter.name)
sprint(tstr, "%g %g %g %g %g %g", lower_limit, upper_limit, stepsize,restart,restart_at,end_before)
while (string_dialog(tstr1, tstr)) {
if (sscanf(tstr, "%g %g %g %g %g %g", &lower_limit, &upper_limit, &stepsize,&restart,&restart_at,&end_before) == 6) {
loopparameter.set(lower_limit, upper_limit, stepsize,restart,restart_at,end_before)
update_browser_element(looppars,$1)
break
}else{
sprint(tstr, "%g %g %g", lower_limit, upper_limit, stepsize)
continue_dialog("Must enter six space separated items, e.g. \"0.0 10.0 0.2 0 0 0\" ")
}
}
}
//Procedure: up_looppar
//Param1: Move element up.
proc up_looppar(){localobj looppar
if($1<0){
return
}
update_browser_element(looppars,$1,-1)
}
//Procedure: down_looppar
//Param1: Move element up.
proc down_looppar(){localobj looppar
if($1<0){
return
}
update_browser_element(looppars,$1,1)
}
//Procedure: setaction_outpar
proc setaction_outpar(){
outpars.accept_action("")
if(0==outpar_mode){
add_outpar()
}else if (1==outpar_mode){
outpars.accept_action("remove_outpar(hoc_ac_)")
}else if(2==outpar_mode){
outpars.accept_action("edittype_outpar(hoc_ac_)")
}else if(3==outpar_mode){
outpars.accept_action("edit_outpar(hoc_ac_)")
}else if(4==outpar_mode){
outpars.accept_action("show_outpar(hoc_ac_)")
}else if(5==outpar_mode){
outpars.accept_action("printtofile_outpar(hoc_ac_)")
}else if(6==outpar_mode){
preparerun()
}else if(7==outpar_mode){
outpars.accept_action("toggle_outpar(hoc_ac_)")
}else{
printf("A miracle happened because you shouldn't get to this position in function setaction_outpar() in MultipleRunControl.hoc ")
}
}
//Procedure: add_outpar
//Create a symbol chooser to pick a new parameter for the outparameter list.
proc add_outpar(){localobj outparameter
if(0==semaphore){
semaphore=1
sprint(tstr, "Enter a short reference name for display in the outparameter browser:")
tstr1=""
/*string_dialog(tstr, tstr1)*/
while (string_dialog(tstr, tstr1)) {
if (sscanf(tstr1, "%s", tstr) == 1) {
break
}else{
continue_dialog("Must enter one name without spaces!")
}
}
outparameter=new MRC_OutputVariable(tstr1,undefined_type,protocol)
outpars.append(outparameter)
semaphore=0
}
}
//Procedure: remove_outpar
//Remove element with index Param1 from the outparameter list, but
//only if confirmed in a dialog.
//Param1: Index of element to be removed.
proc remove_outpar(){
if(0==semaphore){
semaphore=1
if($1<0){
return
}
dialog_outcome=0
sprint(RemoveDialogText,"Do you want to remove <%s> from the outparameter list?",outpars.object($1).name)
vbox[3]=new VBox()
dialog_outcome=vbox[3].dialog(RemoveDialogText,"Yes","No")
if(dialog_outcome==0){
return
}else{
outpars.remove($1)
}
semaphore=0
}
}
//Procedure: edittype_outpar
//Brings up a radio_dialog for changing the outparameter output type
//@@Param1: Index of element to be edited
proc edittype_outpar() {local index , typecurrent, dialog_outcome
if(0==semaphore){
semaphore=1
index_in_outpars=$1
outpar =outpars.object(index_in_outpars)
outpar_type=outpar.gettype()
index =0
outpar_type_index=0
vbox[3]=new VBox()
vbox[3].intercept(1)
xpanel("")
for all_in_list(types_outpar,&index) {
type=types_outpar.object(index)
if(type==outpar_type){
typecurrent=1
outpar_type_index=index
}else{
typecurrent=0
}
sprint(tstr,"outpar_type_index=%d ",index)
type.gettypestr(tstr1)
if(1!=type.virtual){
xradiobutton(tstr1,tstr,typecurrent)
}
}
xpanel()
vbox[3].intercept(0)
doNotify()
dialog_outcome=vbox[3].dialog("Pick Type:","Accept","Cancel")
if(1==dialog_outcome){
type=types_outpar.object(outpar_type_index)
outpar.setprotocol(protocol)
outpar.settype(type)
update_browser_element(outpars,index_in_outpars)
}
semaphore=0
}
}
//Procedure: edit_outpar
//Acvtivates the handlers editform
//Param1: Index of element to be edited
proc edit_outpar() {local index localobj handler
if(0==semaphore){
semaphore=1
index_in_outpars=$1
outpar =outpars.object(index_in_outpars)
handler = outpar.gethandler()
if(nil!=handler){
handler.edit()
}
semaphore=0
}
}
//Procedure: printtofile_outpar
//Save output parameter to file
//Param1: Index of element to be edited
proc printtofile_outpar(){local index , typecurrent, dialog_outcome,outpar_type_index localobj handler
if(0==semaphore){
semaphore=1
index_in_outpars=$1
outpar =outpars.object(index_in_outpars)
handler = outpar.gethandler()
if(nil!=handler){
handler.printtofile(file_name)
}
semaphore=0
}
}
//Procedure: show_outpar
//Shows a graph of the output parameter
//Param1: Index of element to be edited
proc show_outpar(){local index , typecurrent, dialog_outcome,outpar_type_index localobj handler
if(0==semaphore){
semaphore=1
index_in_outpars=$1
outpar =outpars.object(index_in_outpars)
handler = outpar.gethandler()
if(nil!=handler){
handler.show()
}
semaphore=0
}
}
//Procedure: toggle_outpar
//Shows a graph of the output parameter
//Param1: Index of element to be edited
proc toggle_outpar(){local index
if(0==semaphore){
semaphore=1
index_in_outpars=$1
outpar =outpars.object(index_in_outpars)
outpar.toggle()
update_browser_element(outpars,$1)
semaphore=0
}
}
proc exprval() {
xpanel("", 1)
xbutton($s1, $s3)
xvarlabel($s2)
xpanel()
}
proc preparerun(){local index,index_in_outpars localobj handler
if(0==semaphore){
semaphore=1
for all_in_list ( outpars,&index_in_outpars){
outpar =outpars.object(index_in_outpars)
if(1==outpar.inuse()){
handler = outpar.gethandler()
if(nil!=handler){
handler.preparerun()
}
}
}
semaphore=0
}
}
proc printtofile(){local index,index_in_outpars localobj handler
if(0==semaphore){
semaphore=1
for all_in_list ( outpars,&index_in_outpars){
outpar =outpars.object(index_in_outpars)
if(1==outpar.inuse()){
handler = outpar.gethandler()
if(nil!=handler){
if(numarg()==1){
handler.printtofile($s1)
}else{
handler.printtofile(file_name)
}
}
}
}
semaphore=0
}
}
proc save() {local i,index
vbox[0].save("load_file(\"MultipleRunControl.hoc\",\"MultipleRunControlGUI\")\n}\n{")
vbox[0].save("ocbox_ = new MultipleRunControlGUI(1)")
vbox[0].save("}\n{object_push(ocbox_)}\n{")
sprint(tstr, "file_name=\"%s\"", file_name)
vbox[0].save(tstr)
sprint(tstr, "file_index_start=%d\n}", file_index_start)
vbox[0].save(tstr)
protocol.get_sessionstr(tstr,vbox[0])
vbox[0].save(tstr)
vbox[0].save("{protocol=tobj}")
for all_in_list(looppars, &index){
looppars.object(index).get_sessionstr(tstr,vbox[0])
vbox[0].save(tstr)
vbox[0].save("{looppars.append(tobj)}")
}
for all_in_list(outpars, &index){
outpars.object(index).get_sessionstr(tstr,vbox[0])
//print tstr
vbox[0].save(tstr)
vbox[0].save("{outpars.append(tobj)}")
}
vbox[0].save("{object_pop()}\n{")
}
proc load() {local i
}
//Well now its time to do the real work, and create a few loops
strdef MRC_LoopRunFileName
proc looprun(){local index,i, lower_limit, upper_limit, stepsize,restart,restart_at,end_before, lowerSliceLimit, upperSliceLimit localobj MRC_LoopRunFile, looppar
if(name_declared("MRC_Slice")==5){
MRC_bSliced=1
sprint(MRC_LoopRunFileName,"MRC_LoopRunFile_%g.hoc",MRC_SliceNo)
MRC_LoopRunFile=new File(MRC_LoopRunFileName)
}else{
sprint(MRC_LoopRunFileName,"MRC_LoopRunFile.hoc")
MRC_LoopRunFile=new File("MRC_LoopRunFile.hoc")
}
MRC_LoopRunFile.wopen()
MRC_LoopRunFile.printf("strdef loopstr\n")
MRC_LoopRunFile.printf("sprint(loopstr,\"%%s\",%s.file_name)\n",this)
for all_in_list(looppars,&index){
looppar=looppars.object(index)
loopstr2=looppar.name
looppar.get(&lower_limit, &upper_limit, &stepsize,&restart,&restart_at,&end_before)
if(1==looppar.use){
if(1==restart){
MRC_LoopRunFile.printf("%sMRC_bRestart%s=0\n",loopindentstr,loopstr2)
} else if(2==restart && MRC_bSliced==1){
MRC_LoopRunFile.printf("%sMRC_bSliced%s=0\n",loopindentstr,loopstr2)
} else if(2==restart){
MRC_LoopRunFile.printf("%sMRC_bRestart%s=0\n",loopindentstr,loopstr2)
}
}
}
for all_in_list(looppars,&index){
looppar=looppars.object(index)
loopstr2=looppar.name
looppar.get(&lower_limit, &upper_limit, &stepsize,&restart,&restart_at,&end_before)
if(1==looppar.use){
if(1==restart){
MRC_LoopRunFile.printf("%sfor(%s=%g; %s <= %g; %s=%s+%g){ \n",loopindentstr,loopstr2,lower_limit,loopstr2,upper_limit,loopstr2,loopstr2,stepsize)
MRC_LoopRunFile.printf("%sif(0==MRC_bRestart%s){%s=%g MRC_bRestart%s=1}\n",loopindentstr,loopstr2,loopstr2,restart_at,loopstr2)
}else if (2==restart){
lowerSliceLimit=lower_limit
upperSliceLimit=upper_limit
while(lowerSliceLimit<restart_at){lowerSliceLimit=lowerSliceLimit+stepsize}
while(upperSliceLimit>=end_before){upperSliceLimit=upperSliceLimit-stepsize}
MRC_LoopRunFile.printf("%sfor(%s=%g; %s <= %g; %s=%s+%g){ \n",loopindentstr,loopstr2,lowerSliceLimit,loopstr2,upperSliceLimit,loopstr2,loopstr2,stepsize)
}else{
MRC_LoopRunFile.printf("%sfor(%s=%g; %s <= %g; %s=%s+%g){ \n",loopindentstr,loopstr2,lower_limit,loopstr2,upper_limit,loopstr2,loopstr2,stepsize)
}
}
}
for all_in_list(looppars,&index){
looppar=looppars.object(index)
loopstr2=looppar.name
looppar.get(&lower_limit, &upper_limit, &stepsize,&restart,&restart_at,&end_before)
if(1==looppar.use){
MRC_LoopRunFile.printf("%ssprint(loopstr,\"%%s_%%d\",loopstr,int(%d+0.01+(%s-(%g))/%g))\n",loopindentstr,file_index_start,loopstr2,lower_limit,stepsize)
}
}
MRC_LoopRunFile.printf("%sMRC_PrepareModel()\n",loopindentstr)
MRC_LoopRunFile.printf("%s%s.preparerun()\n",loopindentstr,this)
MRC_LoopRunFile.printf("%sMRC_Run()\n",loopindentstr)
MRC_LoopRunFile.printf("%s%s.printtofile(loopstr)\n",loopindentstr,this)
MRC_LoopRunFile.printf("print loopstr\n",loopindentstr)
MRC_LoopRunFile.printf("%ssprint(loopstr,\"%%s\",%s.file_name)\n",loopindentstr,this)
for all_in_list(looppars,&index){
looppar=looppars.object(index)
if(1==looppar.use){
MRC_LoopRunFile.printf("%s}\n ",loopindentstr)
}
}
MRC_LoopRunFile.close()
load_file(1,MRC_LoopRunFileName)
}
proc credits(){
xpanel("Multiple Run Control Credits")
xlabel("Author: Ronald A.J. van Elburg (RonaldAJ at vanElburg eu)")
xlabel(" ")
xlabel(" This code was first published on http://senselab.med.yale.edu/modeldb/")
xlabel(" accession number 114359 accompanying the paper: ")
xlabel(" Ronald A.J. van Elburg and Arjen van Ooyen (2010) ")
xlabel(" `Impact of dendritic size and dendritic topology ")
xlabel(" on burst firing in pyramidal cells'")
xlabel(" PLoS Comput Biol 6(5): e1000781. doi:10.1371/journal.pcbi.1000781.")
xlabel(" ")
xlabel(" Please cite both the paper and the ModelDB entry when you used")
xlabel(" this software to prepare a publication.")
xlabel(" ")
xlabel(" This software is released under the GNU GPL version 3: ")
xlabel(" http://www.gnu.org/copyleft/gpl.html")
xpanel()
}
endtemplate MultipleRunControlGUI
objref tobj
proc makeMultipleRunControlGUI() {
tobj = new MultipleRunControlGUI($1,$2, $3, $4)
objref tobj
}
if(loadedFromGui==0){
// Not called from GUI, so we are in test mode
//load_file("TestCode/MultipleRunControlTests.hoc")
}
//makeMultipleRunControlGUI()