// THIS SCRIPT ASSIGNS ANNOTATION TO SPECIFIC SUBCELLULAR COMPARTMENTS.

forall {
	
	insert id
	
	for (x) {
		isTerm_id(x) = 0
		isTuft_id(x) = 0
		isObl_id(x) = 0
		isBas_id(x) = 0
		isPrim_id(x) = 0
	}
}

objref soma
objref basalList,obliqueList,primList,apicalList,tuftList,dendList,cellList,ca3List
	
apicalList = new SectionList() // apical list
basalList = new SectionList() // basal list
obliqueList = new SectionList() // oblique list
primList = new SectionList() // primary apical list
tuftList = new SectionList()
dendList = new SectionList() // list of all dendrites
cellList = new SectionList()
ca3List = new SectionList() // list of places that CA3 cells would contact CA1 (SO + SR)
	
Cell[0].dend[72] {soma = new SectionRef()}

// Populate apical list.
Cell[0].dend[11] { apicalList.subtree() }

// Populate primary apical list.
Cell[0].dend[11] { primList.append() }
Cell[0].dend[74] { primList.append() }
Cell[0].dend[75] { primList.append() }
Cell[0].dend[76] { primList.append() }
Cell[0].dend[77] { primList.append() } // right before twin bifurcation
Cell[0].dend[78] { primList.append() } // left twin apical
Cell[0].dend[79] { primList.append() }
Cell[0].dend[80] { primList.append() }
Cell[0].dend[82] { primList.append() }
Cell[0].dend[83] { primList.append() }
Cell[0].dend[84] { primList.append() }
Cell[0].dend[85] { primList.append() }
Cell[0].dend[86] { primList.append() }
Cell[0].dend[151] { primList.append() } // right twin apical
Cell[0].dend[154] { primList.append() }
Cell[0].dend[155] { primList.append() }
Cell[0].dend[157] { primList.append() }
Cell[0].dend[160] { primList.append() }
Cell[0].dend[161] { primList.append() }

// By eye, these were the beginning of sections that define the tuft.
Cell[0].dend[87] { tuftList.subtree() }
Cell[0].dend[162] { tuftList.subtree() }
Cell[0].dend[163] { tuftList.subtree() }

// Populate obliques.  By previous definitions, this is simply the
// whole apical dendrite less the tuft and the primary apical.
forsec apicalList { obliqueList.append() }
forsec tuftList { obliqueList.remove() }
forsec primList { obliqueList.remove() }


	
// Populate basals.  By previous definitions, this is simply the
// whole tree less the apical dendrite and the soma.
forall { basalList.append() }
forsec apicalList { basalList.remove() }
soma.sec { basalList.remove () }


// Populate all dendrites.  This is everything minus the soma.
forall { dendList.append() }
soma.sec { dendList.remove() }

// Populate the whole cell.  This is everything.
forall { cellList.append() }

// Populate sections which would contact CA3 axons.
forsec basalList {ca3List.append()}
forsec primList {ca3List.append()}
forsec obliqueList {ca3List.append()}
soma.sec {ca3List.append()}

// Declare a function that looks at whether a given SectionRef instance 
// (argument 1) is found in a given SectionList (argument 2).
// $o1: SectionRef instance to match.
// $o2: SectionList instance to search over.
// Returns logical of whether section is in list.
func sectionRefInList() {local isInList
	isInList = 0
	
	strdef tempSecName
	
	$o1.sec { tempSecName = secname() }
	
	forsec $o2 {
		if(abs(strcmp(secname(),tempSecName))<(1e-5)){
			isInList=1
		}
	}

	return isInList
}

objref theSec
forall {
	theSec = new SectionRef()
	for (x){
		isTuft_id(x) = sectionRefInList(theSec,tuftList)
		isPrim_id(x) = sectionRefInList(theSec,primList)
		isObl_id(x) = sectionRefInList(theSec,obliqueList)
		isBas_id(x) = sectionRefInList(theSec,basalList)
		brOrd_id(x) = -1
	}
}

// Assign distances from bifurcation of apical trunk.  Note this is used solely
// for obliques, so all other locations get assigned a -1 value.

forall {
	insert dists
	
}

// Generate a function that point out how far something is from main apical.
// INPUT: a SectionRef instance that refers to an oblique branch.
// OUTPUT: the distance from the initial bifurcation of this branch from the
//	primary apical branch.  [ note : to be consistent with AT data, this 
//	may not be the distance of the branch itself, but rather from a
//	parent branch that stems directly off of the primary apical ]
func oblDist(){localobj theSec,tempParSec
	theSec = $o1 // a SectionRef instance
	
	// Traverse down branch until hit parent branch that stems directly
	// off the main apical.
	
	// Identify parent.
	strdef strPar
	while(1){
		theSec.parent{	
			strPar = secname()	
		}
		
		inList = 0
		
		// Is parent in the obliques list?
		forsec obliqueList {
			curDist = abs(strcmp(secname(),strPar))
			if(curDist<0.0001){
				inList = 1
				tempParSec = new SectionRef()
			}
		}
		if(inList){
			// Repeat; update parent section.
			tempParSec.sec { theSec = new SectionRef() }
		}else{
			break
		}
	}
	
	// Get the distance from this parent branch to the soma.
	soma.sec {
		distance()
	}
	
	theSec.sec {
		theDist = distance(0)
	}
			
	return theDist
}

// Generate a function that point out how far along the main apical a given
// section (with associated x value) is.
// INPUT: a SectionRef instance that refers to an main apical branch, and a 
//	variable (0<= , <=1) corresponding to the x value.
// OUTPUT: the distance of the _middle_ of the section from the soma, divided
//	by the distance of the total main apical dendrite
func primDist(){local tuftDist,somaDist,outDist,theX localobj theSec,allTuftDists
	theSec = $o1 // a SectionRef instance
	theX = $2
	allTuftDists = new Vector()
	
	// Calculate minimum distance from tuft to selected section.
	theSec.sec { distance() }
	forsec tuftList {
		tuftDist = distance(0)
		allTuftDists.append(tuftDist)
	}
	tuftDist = allTuftDists.min() 
	
	// Calculate distance from selected section to soma.
	soma.sec { distance() }
	theSec.sec { somaDist = distance(theX) }

	outDist = somaDist/(somaDist+tuftDist)	
	return outDist
}

// Assign main bifurcation distances to obliques, as well as normalised
// primary apical distances.
forall {
	for(x) {
		theSec = new SectionRef()
		
		// Main bifurcation distance.
		if(sectionRefInList(theSec,obliqueList)){
			mainbif_dists = oblDist(theSec)
		}else{
			mainbif_dists = -1
		}
		
		// Norm prim apical distance.
		if(sectionRefInList(theSec,primList)){
			normprim_dists(x) = primDist(theSec,x)
		}else{
			normprim_dists = -1
		}
	}
}

forall {
	insert syns
	npyAt_syns = 0
	npyUnif_syns = 0
	sstAt_syns = 0
	sstUnif_syns = 0
	vlsAt_syns = 0
	exc_syns = 0
}