SThprotocell.hoc

//
// The prototype STh cell class
//

print " "
print "loading STh cell data structures..."
print " "

begintemplate SThproto
 public ntrees,ntree0,ntree1,somadiam,somaL,PI
 public ref,child,diam,L,nseg,Ra,Cm

 objref f
 objref tree0ref,tree0c1,tree0c2,tree0diam,tree0L,tree0nseg,tree0dist,tree0var
 objref tree1ref,tree1c1,tree1c2,tree1diam,tree1L,tree1nseg,tree1dist,tree1var

 proc init() {local i, j, me, child1, child2

  somaL = 18.8
  somadiam = 18.3112
  
  nsegscale = 1

  ntrees = 2
  tc=0
  PI=3.14159265358979

  printf("  %d trees\n",ntrees)

  // TREE 1

  ntree0=23
  tree0ref  = new Vector(ntree0)
  tree0c1   = new Vector(ntree0)
  tree0c2   = new Vector(ntree0)
  tree0diam = new Vector(ntree0)
  tree0L    = new Vector(ntree0)
  tree0nseg = new Vector(ntree0)
  tree0dist = new Vector(ntree0)
  tree0var  = new Vector(ntree0)

  f = new File()
  f.ropen("sth-data/tree0-nom.dat")
  i=0
  while (!f.eof()) {
   if (i<ntree0) {
    tree0ref.x[i]  = f.scanvar()-1 // myref
    tree0c1.x[i]   = f.scanvar()-1 // child1
    tree0c2.x[i]   = f.scanvar()-1 // child2
    tree0diam.x[i] = f.scanvar()   // diam
    tree0L.x[i]    = f.scanvar()   // L
    tree0nseg.x[i] = nsegscale*f.scanvar()   // nseg
   }
   i=i+1
  }
  if (i!=ntree0) printf("WARNING file tree0ns.dat is inconsistent expecting %d branches got %d \n",ntree0,i)

  // sort Vectors

  sortv(ntree0,tree0ref,tree0c1,tree0c2,tree0diam,tree0L,tree0nseg)

  printf("  loaded tree 0 (%d branches)\n",ntree0)
  f.close()

  // TREE 2

  ntree1=11
  tree1ref  = new Vector(ntree1)
  tree1c1   = new Vector(ntree1)
  tree1c2   = new Vector(ntree1)
  tree1diam = new Vector(ntree1)
  tree1L    = new Vector(ntree1)
  tree1nseg = new Vector(ntree1)
  tree1dist = new Vector(ntree1)
  tree1var  = new Vector(ntree1)

  f = new File()
  f.ropen("sth-data/tree1-nom.dat")
  i=0
  while (!f.eof()) {
   if (i<ntree1) {
    tree1ref.x[i]  = f.scanvar()-1 // myref
    tree1c1.x[i]   = f.scanvar()-1 // child1
    tree1c2.x[i]   = f.scanvar()-1 // child2
    tree1diam.x[i] = f.scanvar()   // diam
    tree1L.x[i]    = f.scanvar()   // L
    tree1nseg.x[i] = nsegscale*f.scanvar()   // nseg
   }
   i=i+1
  }
  if (i!=ntree1) printf("WARNING file tree0ns.dat is inconsistent expecting %d branches got %d \n",ntree1,i)

  // sort Vectors

  sortv(ntree1,tree1ref,tree1c1,tree1c2,tree1diam,tree1L,tree1nseg)

  printf("  loaded tree 1 (%d branches)\n",ntree1)
  f.close()
 }

 // sortv - sort the vectors into index reference order!

 proc sortv() {local i, j, tmp
               // arg1 is the number of branches
	       // arg2,3,4,5,6,7 are the vectors to sort

 for i=0,$1-1 {
   j=i
   while (j<$1) {
     if (($o2.x[j]==i) && (j!=i)) {
       // swap jth line with ith
       tmp = $o2.x[i]
       $o2.x[i] = $o2.x[j]
       $o2.x[j] = tmp
       tmp = $o3.x[i]
       $o3.x[i] = $o3.x[j]
       $o3.x[j] = tmp
       tmp = $o4.x[i]
       $o4.x[i] = $o4.x[j]
       $o4.x[j] = tmp
       tmp = $o5.x[i]
       $o5.x[i] = $o5.x[j]
       $o5.x[j] = tmp
       tmp = $o6.x[i]
       $o6.x[i] = $o6.x[j]
       $o6.x[j] = tmp
       tmp = $o7.x[i]
       $o7.x[i] = $o7.x[j]
       $o7.x[j] = tmp
     }
     j=j+1
    }
  }
 }
  
 // ref(tree,branch) returns the recorded ref

 func ref() {local res

  res=0

  if (($1==0) && ($2<ntree0)){
    res=tree0ref.x[$2]
  }
  if (($1==1) && ($2<ntree1)){
    res=tree1ref.x[$2]
  }
  return res
 }

 // diam(tree,branch) returns the recorded diam

 func diam() {local res

  res=0
  
  if ($1==-1) {
    res=somadiam
  }
  if (($1==0) && ($2<ntree0)){
    res=tree0diam.x[$2]
  }
  if (($1==1) && ($2<ntree1)){
    res=tree1diam.x[$2]
  }

  return res
 }

 // L(tree,branch) returns the recorded L

 func L() {local res

  res=0

  if ($1==-1) {
    res=somaL
  }
  if (($1==0) && ($2<ntree0)){
    res=tree0L.x[$2]
  }
  if (($1==1) && ($2<ntree1)){
    res=tree1L.x[$2]
  }

  return res
 }

 // Ra(tree) returns the recorded Ra

 func Ra() {local res

  return 150.224
  
}

 // Cm(tree) returns the recorded membrane capacitance Cm [uF/cm^2]

 func Cm() {local res

  return 1.0

 }

 // nseg(tree,branch) returns the recorded nseg

 func nseg() {local res

  res=1
  
  if (($1==0) && ($2<ntree0)){
    res=tree0nseg.x[$2]
  }
  if (($1==1) && ($2<ntree1)){
    res=tree1nseg.x[$2]
  }

  return res
 }
   
 // child(tree,branch,0|1) returns the child ref 

 func child() {local res

  res=0

  if ($3==0){
   if (($1==0) && ($2<ntree0)){
     res=tree0c1.x[$2]
   }
   if (($1==1) && ($2<ntree1)){
     res=tree1c1.x[$2]
   }
  }

  if ($3==1){
   if (($1==0) && ($2<ntree0)){
     res=tree0c2.x[$2]
   }
   if (($1==1) && ($2<ntree1)){
     res=tree1c2.x[$2]
   }
  }

  return res
 }

endtemplate SThproto

//
//  THE STh CELL OBJECT
//

begintemplate SThcell
 public soma, dend0, dend1

 // declare the variables we will be using

 create soma, dend0[1], dend1[1]

 objref sthtype

 strdef cmd

 proc init() {local i, j, me, child1, child2

   // $1   = cell reference number
   // $o2  = cell prototype
   
   cellref = $1
   
   sthtype = $o2

   SThndend0  = sthtype.ntree0
   SThndend1  = sthtype.ntree1

   create soma, dend0[SThndend0], dend1[SThndend1]

   soma {
     nseg = sthtype.nseg(-1,-1)
     Ra = sthtype.Ra(-1)
     diam = sthtype.diam(-1,-1)
     L = sthtype.L(-1,-1)
     cm = sthtype.Cm(-1)

     // channels
     
     insert STh
     insert Na
     insert NaL
     insert KDR
     insert Kv31
     insert Ih
     insert Cacum
     insert sKCa
     insert CaT
     insert HVA
   }

   for i = 0,SThndend0-1 {
     
     me = sthtype.ref(0,i)
     child1 = sthtype.child(0,i,0)
     child2 = sthtype.child(0,i,1)

     dend0[me] {

       if (child1 >= 0) {
        connect dend0[child1](0), 1
       }

       if (child2 >= 0) {
        connect dend0[child2](0), 1
       }

       diam = sthtype.diam(0,i)
       L = sthtype.L(0,i)
       Ra = sthtype.Ra(0)
       nseg = sthtype.nseg(0,i)
       cm = sthtype.Cm(0)
       
       // channels
       
       insert STh
       insert Na
       insert NaL
       insert KDR
       insert Kv31
       insert Ih
       insert Cacum
       insert sKCa       
       insert CaT
       insert HVA
     }
   }

   for i = 0,SThndend1-1 {

     me = sthtype.ref(1,i)
     child1 = sthtype.child(1,i,0)
     child2 = sthtype.child(1,i,1)

     dend1[me] {

       if (child1 >= 0) {
        connect dend1[child1](0), 1
       }

       if (child2 >= 0) {
        connect dend1[child2](0), 1
       }

       diam = sthtype.diam(1,i)
       L = sthtype.L(1,i)
       Ra = sthtype.Ra(1)
       nseg = sthtype.nseg(1,i)
       cm = sthtype.Cm(0)       
 
       // channels
       
       insert STh
       insert Na
       insert NaL
       insert KDR
       insert Kv31
       insert Ih
       insert Cacum
       insert sKCa       
       insert CaT
       insert HVA
     }
   }

   // connect trees to soma

   connect dend0[0](0), soma(1)
   connect dend1[0](0), soma(0)
 }

endtemplate SThcell