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// Make range variable and put it into vector
objectvar rvp
rvp = new RangeVarPlot("v")
soma rvp.end(1)
apic[79] rvp.begin(1)
//rvp.origin(11.387)
objref yspacevect, disspacevect
yspacevect=new Vector()
disspacevect=new Vector()
rvp.to_vector(yspacevect,disspacevect)
print "yspacevector is ", yspacevect
print "disspacevector is ", disspacevect 

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objref savdata2,tempmatrix2
savdata2=new File()
savdata2.wopen("dataspaceplot.dat")
savdata2.printf("distance y\n")

tempmatrix2=new Matrix()
tempmatrix2.resize(disspacevect.size(),2)
tempmatrix2.setcol(0,disspacevect)
tempmatrix2.setcol(1,yspacevect)
tempmatrix2.fprint(savdata2,"%g")
savdata2.close()

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soma rvp.end(1)
apic[79] rvp.begin(1)

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proc run() {
  stdinit()
  open_output_file()
  continuerun(tstop)
  close_output_file()
}

proc open_output_file() {
  // open the output file
  // append values to file
  // leave the file open 
}

proc close_output_file() {
  // close the output file
}

proc advance() {
  fadvance()
  // if output file is open, append values to it
  // note: by testing for an open output file, you avoid generating an error message
  // if you ever decide to explore by doing some single steps or continuerun
  // after the end of a "formal" simulation
}

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// start at termination and walk backward from child to parent until we reach origin
strdef origin
dendrite_1[8] origin = secname() // so we can tell when we have reached the origin of the path

objref this // the section to be checked to see if it is the origin
dendrite_1[13] this = new SectionRef()

objref path // will be the SectionList that contains the sections in the path

proc trace_to_origin() {
  path = new SectionList()
  this.sec path.append() // add termination to the list
  while (isorigin(this)!=1) { // if this is not the origin
    this = parsr(this) // go to the parent
    this.sec path.append() // and add parent to the list
  }
}

func isorigin() { local x  // return 1 if $o1.sec is the origin of the path
// $o1.sec print secname() // if you want to see it working
  $o1.sec x=issection(origin)
  return x
}

obfunc parsr() { localobj tobj // return SectionRef of parent of $o1.sec
  $o1.parent tobj = new SectionRef()
  return tobj
}

trace_to_origin()
forsec path print secname() // just to show that it worked

// now color the sections in path
objref ps
ps = new PlotShape()
ps.color_list(path,2) // make them red

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objref savdata2,tempmatrix2

proc open_outputfile_RangeVar(){
    tempmatrix2=new Matrix()
    tempmatrix2.resize(disspacevect.size(),int(tstop/dt)+1)
    tempmatrix2.setcol(0,disspacevect)
}

proc close_outputfile_RangeVar(){
    savdata2=new File()
    savdata2.wopen("dataspaceplottest.dat")
    savdata2.printf("distance y\n")
    tempmatrix2.fprint(savdata2,"%-g")
    savdata2.close()
}

proc advance(){
  fadvance()
  rvp.to_vector(yspacevect,disspacevect)
  tempmatrix2.setcol(int(t/dt)+1,yspacevect)
}

proc run(){
  stdinit()
  open_outputfile_RangeVar()
  continuerun(tstop)
  //frecord.init() neccessary ??
  //cvode.re_init() neccessary??
  close_outputfile_RangeVar()
}

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objref path
path = new SectionList()
rvp.list(path)

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objref path
path = new SectionList()
rvp.list(path)

objref veclist

proc buildveclist() { localobj tobj
  forsec path { // iterate over each section along the path
    for (x,0) { // iterate over each internal node in the current section
      tobj = new Vector()
      tobj.record(&v(x)) // or whatever other range variable you want to capture
      veclist.append(tobj)
    }
  }
}

buildveclist()

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proc run() {
  stdinit()
  continuerun(tstop)
  save_results()
}

proc save_results() { local i, j
  . . . open output file . . .
  // there are veclist.count() Vectors
  // the number of values in each Vector is veclist.o(0).size--
  // one value for each point in time at which a solution was computed
  for i=0,veclist.o(0).size-1 { // iterate over each point in time
    for j=0,veclist.count()-1 { // iterate over each point in space
      . . . print veclist.o(j).x[i] to the file . . .
    }
    . . . print \n to the file . . .
  }
  . . . close output file . . .
}

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  for i=0,veclist.count()-1 { // iterate over each point in space
    . . . use the Vector class's printf() method to print veclist.o(i) to the file . . .
    . . . print \n to the file . . .
  }
  . . . close output file . . .