// This function makes a list with all dendritic sections in the apical trunk
// written by Yiota Poirazi, July 2001, poirazi@LNC.usc.edu

strdef origin
objref apical_trunk_list,apical_endtosoma
objref this
apical_trunk_list=new SectionList()
apical_endtosoma=new List()

// PREVIOUS VERSION, THIS FUCNTION TRACES BACK TO ORIGIN AND PUTS ITS IN A SECTIONLIST ( IN STEAD OF LIST)
//obfunc trace_to_origin() { localobj path
//  path = new SectionList()
//  while (isorigin(this)!=1) { // if this is not the origin
//    this.sec path.append() // Add current accessed segment this to the path
//    this = parsr(this) // the new this is the parent of the previous this
//  }
//  return path
//}

obfunc reverse_listtrunk(){ localobj revlist,reftemp
  revlist=new SectionList()
  for(i=$o1.count()-1;i>=0;i=i-1) {
    reftemp=$o1.o(i)
    reftemp.sec revlist.append()
  }
  return revlist
}

obfunc trace_to_origin() { localobj path
  path = new List()
  while (isorigin(this)!=1) { // if this is not the origin
    path.append(this)
    this = parsr(this) // the new this is the parent of the previous this
  }
  return path
}

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
} 

//all paths are traced to the soma
soma origin = secname() // so we can tell when we have reached the origin of the path

//determine path from apical_dendrite[104]
strdef tmp_string
apical_dendrite[104] this = new SectionRef()
apical_endtosoma=trace_to_origin()
apical_trunk_list=reverse_listtrunk(apical_endtosoma)
forsec apical_trunk_list{ 
  //sprint(tmp_string,"access %s",secname())
  //execute1(tmp_string)
  print secname() // just to show that it worked
}
print "above is given the apical_trunk"

/* OLD CODE: ADJUSTED BY MARTINE ROSA GROEN TO IMPLEMENT MULTIPLE MORPHOLOGIES
apical_dendrite[0]  apical_trunk_list.append() // 13.40  microns from soma 
apical_dendrite[4]  apical_trunk_list.append() // 46.03 (vertical distance)
apical_dendrite[6]  apical_trunk_list.append() // 45.75
apical_dendrite[14] apical_trunk_list.append() // 52.53
apical_dendrite[15] apical_trunk_list.append() // 58.97
apical_dendrite[16] apical_trunk_list.append() // 70.89
apical_dendrite[22] apical_trunk_list.append() // 72.93
apical_dendrite[23] apical_trunk_list.append() // 74.48
apical_dendrite[25] apical_trunk_list.append() // 93.56
apical_dendrite[26] apical_trunk_list.append() // 98.55
apical_dendrite[27] apical_trunk_list.append() // 121.89
apical_dendrite[41] apical_trunk_list.append() // 144.46
apical_dendrite[42] apical_trunk_list.append() // 142.81
apical_dendrite[46] apical_trunk_list.append() // 156.96
apical_dendrite[48] apical_trunk_list.append() // 162.99
apical_dendrite[56] apical_trunk_list.append() // 179.58
apical_dendrite[58] apical_trunk_list.append() // 180.11
apical_dendrite[60] apical_trunk_list.append() // 210.33
apical_dendrite[62] apical_trunk_list.append() // 222.80
apical_dendrite[64] apical_trunk_list.append() // 233.67
apical_dendrite[65] apical_trunk_list.append() // 252.71
apical_dendrite[69] apical_trunk_list.append() // 292.06
apical_dendrite[71] apical_trunk_list.append() // 324.53 
apical_dendrite[81] apical_trunk_list.append() // 346.84
apical_dendrite[83] apical_trunk_list.append() // 387.00
apical_dendrite[95] apical_trunk_list.append() // 413.05
apical_dendrite[103] apical_trunk_list.append() // 417.73
apical_dendrite[104] apical_trunk_list.append() // 423.75
*/ //END OLD CODE COMMENTED OUT

/* Make a shape graph with apical trunk sections

objref apical_trunk_list_shape
apical_trunk_list_shape=new Shape()
color_index=3
apical_trunk_list_shape.color_list(apical_trunk_list,color_index)
apical_trunk_list_shape.printfile("apical-trunk-list.eps")
*/