// Author: Etay Hay, 2011
//    Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of
//    Dendritic and Perisomatic Active Properties
//    (Hay et al., PLoS Computational Biology, 2011) 
//
// Template for models of L5 Pyramidal Cell
load_file("L5PCbiophys3Passive.hoc")

begintemplate L5PCtemplatePassive
  public init
  public locateSites, getLongestBranch
  public soma, dend, apic, axon, getAbsSecIndex
  public all, somatic, apical, axonal, basal, nSecSoma, nSecApical, nSecBasal, nSecAxonal, nSecAll, nSecAxonalOrig, SecSyn, distribute_channels
  objref SecSyn, this
  objref all, somatic, apical, axonal, basal
  strdef tstr

//$s1 - morphology file name
proc init() {localobj nl,import
	all = new SectionList()
	somatic = new SectionList()
	basal = new SectionList()
	apical = new SectionList()
	axonal = new SectionList()
	forall delete_section()
    
  nl = new Import3d_Neurolucida3()
  nl.quiet = 1
  nl.input("../biophys_components/morphologies/cell1.asc")
  import = new Import3d_GUI(nl, 0)
  import.instantiate(this)
  geom_nseg()
  biophys()
	forsec this.all {
		if(diam == 0){
	    diam =  1
	    printf("Error : Morphology problem with section [%s] 0 diam \n", secname())
		}
  }
}

create soma[1], dend[1], apic[1], axon[1]

proc geom() {
}

proc geom_nseg() {local nSec, L1, L2, D1, D2, nSeg1, nSeg2
  soma area(.5) // make sure diam reflects 3d points
  nSec = 0
  forsec all {
    //nseg = 1 + 2*int(L/40)
    nseg = 1 + 2*int(L/10)
    nSec = nSec + 1
  }

  nSecAll = nSec
  nSec = 0
  forsec somatic { nSec = nSec + 1}
  nSecSoma	= 	nSec
  nSec = 0
  forsec apical { nSec = nSec + 1}
  nSecApical= 	nSec
  nSec = 0
  forsec basal { nSec = nSec + 1}
  nSecBasal	= 	nSec
  nSec = 0
  forsec axonal { nSec = nSec + 1}
  nSecAxonalOrig = nSecAxonal	= 	nSec
}

proc biophys() {localobj bp
	delete_axon()
	area(0.5)
	distance()
	access soma

  bp = new L5PCbiophysPassive()
  bp.biophys(this)
}

// deleting axon, keeping only first 60 micrometers
proc delete_axon(){
    forsec axonal{delete_section()}
    create axon[2]
    access axon[0]{
      L= 30
      diam = 1
      //nseg = 1+2*int(L/40)
      nseg = 1+2*int(L/10)
      all.append()
      axonal.append()
    }
    access axon[1]{
      L= 30
      diam = 1
      //nseg = 1+2*int(L/40)
      nseg = 1+2*int(L/10)
      all.append()
      axonal.append()
    }

  nSecAxonal = 2
  connect axon(0), soma(0.5)
  connect axon[1](0), axon[0](1) 
  define_shape()
  access soma
}

proc distribute_channels()	{local dist,val,base,maxLength
	base = $8
	soma distance()
	maxLength = getLongestBranch($s1)

	forsec $s1		{
		if(0==strcmp($s2,"Ra")){
			Ra = $8
		} else {
			for(x) {
				if ($3==3) {
					dist = distance(x)
				} else {
					dist = distance(x)/maxLength
				}
				val = calculate_distribution($3,dist,$4,$5,$6,$7,$8)
				sprint(tstr,"%s(%-5.10f) = %-5.10f",$s2,x,val)
				execute(tstr)
			}
		}
	}
}

// $1 is the distribution type:
//     0 linear, 1 sigmoid, 2 exponential
//     3 step for absolute distance (in microns)
func calculate_distribution()	{local value
	if ($1==0)	{value = $3 + $2*$4}
	if ($1==1) {value = $3 + ($4/(1+exp(($2-$5)/$6)))}
  	if ($1==2) {value = $3 + $6*exp($4*($2-$5))}
	if ($1==3) {
		if (($2 > $5) && ($2 < $6)) {
			value = $3
		} else {
			value = $4
		}
	}
	value = value*$7
	return value
}

// $s1 section
func getLongestBranch(){local maxL,d localobj distallist,sref
    sprint(tstr,"%s distance()",$s1)
    execute(tstr,this)    
    
  	if(0==strcmp($s1,"axon")){
      sprint(tstr,"%s[0] distance(1)",$s1)
      execute(tstr,this)    
  	}

		maxL = 0
		d = 0
		distallist = new SectionList()
		forsec $s1 {
			sref = new SectionRef()
			if (sref.nchild==0) distallist.append()
		}
		forsec distallist{
			d = distance(1)
			if(maxL<d) maxL = d
		}
		// for the soma case
		if (maxL == 0) {
      $s1 {
        maxL = L
      }
    }
		return maxL
	}

// $s1 section
// $2 distance x in micrometers
// return list of [1,2] vectors  - of the appropriate section and the location in each vector
obfunc locateSites() {local maxL,site,d0,d1,siteX,i localobj vv,ll
	ll = new List()

  sprint(tstr,"%s distance()",$s1)
  execute(tstr,this)    
    
	if(0==strcmp($s1,"axon")){
    sprint(tstr,"%s[0] distance(1)",$s1)
    execute(tstr,this)    
	}

	maxL = getLongestBranch($s1)
	site = $2
	i = 0
	forsec $s1 {
    if (distance(0) < distance(1)) {
  		d0 = distance(0)
  		d1 = distance(1)
  	} else {
  		d1 = distance(0)
  		d0 = distance(1)
  	}

    if (site <= d1 && site >= d0) {
      siteX = (site-d0)/(d1-d0)
      secNum = i
      vv = new Vector()
      ll.append(vv.append(secNum,siteX))
		}
		i = i+1
	}
  return ll
}

func getAbsSecIndex(){ local nAbsInd, index  localobj str,strObj
    strObj  =  new StringFunctions()
    str     =  new String()
    nAbsInd = 0
    index   = 0
    if(strObj.substr($s1, "soma") > 0) {
        strObj.tail($s1, "soma", str.s)
        if(sscanf(str.s, "%*c%d", &index) < 0) {
            index = 0
        }
        nAbsInd = index
    }else if (strObj.substr($s1, "axon") >0) {
        strObj.tail($s1, "axon", str.s)
        if(sscanf(str.s, "%*c%d", &index) < 0) {
            index = 0
        }
        nAbsInd = nSecSoma + index
    }else if (strObj.substr($s1, "dend") >0) {
        strObj.tail($s1, "dend", str.s)
        if(sscanf(str.s, "%*c%d", &index) < 0) {
            index = 0
        }
        nAbsInd = nSecSoma + nSecAxonalOrig + index
    }else if (strObj.substr($s1, "apic") > 0) {
        strObj.tail($s1, "apic", str.s)
        if(sscanf(str.s, "%*c%d", &index) < 0) {
            index = 0
        }
        nAbsInd = nSecSoma + nSecAxonalOrig + nSecBasal + index
    }
    return nAbsInd
}


endtemplate L5PCtemplatePassive