back=0

//////// load needed templates////////////
if(!back){ load_file("nrngui.hoc")               }
if(!back){ load_file("template/ObliquePath.hoc") }
if(!back){ load_file("template/BasalPath.hoc"  ) }

objref econ,f1,f2,f3,ss,cvode
f1= new File()
f2= new File()
f3= new File()
ss=new SaveState()                                                                  
cvode = new CVode(1)
x=cvode.active(1)

restart=0
v_init=-70

strdef morphology_location, morpho_path, ObliqueTrunkSection, BasalTrunkSection
objref vRP, vAPEX

proc xopen_morphology(){
	sprint(morpho_path,"%s/%s",morphology_location,$s1)
	xopen(morpho_path)
}

// Carmen
morphology_location = "pc2b"
ObliqueTrunkSection = "trunk[17]"
BasalTrunkSection   = "trunk[7]"

xopen_morphology("cell.hoc")				//reads morpholofy from the file
xopen_morphology("cell-analysis-simple.hoc") //reads simplified version of CA 


			// --------------- Creating lists-----------------

xopen("lib/TP-lib.hoc")
Tip_sections(apical_non_trunk_list,apical_trunk_list,"Apical")		
objref apical_tip_list
apical_tip_list=TP_list							// Apical Tip list

print "apical_tip_list"
apical_tip_list.printnames()
print  "END apical_tip_list"

objref tmp_pl[num_tips],pl[num_tips],opl[num_tips],degree_apical_tip,peri_trunk_list
objref bl[num_tips],obl[num_tips],degree_basal_tip
xopen("lib/Oblique-lib.hoc")
oblique_sections(apical_tip_list,apical_trunk_list,num_tips)		// apical dendrite path lists and degree of tips

xopen("lib/vector-distance.hoc")

//-----------------------------------------------------------------------------------------------------
printf("Setting up cell\n")                                         // load cell-setup to
xopen("cell_setup_pc2b_CCh.hoc") 


///////////////////Load File//////////////////////
if(!back) { load_file("ca_conc_trpm4_dend.ses") }
//if(!back) load_file("kca.ses")

/*cvode_active(1)*/

//////   Spike counter//////////

objref apc, v1

proc insert_APC() {
	apc = new APCount(0.5)
	apc.thresh = $1
	v1 = new Vector()
	apc.record(v1)
}

proc init() {
	if(restart){
		f1.ropen("state.old")
		ss.fread(f1)
		f1.close
		finitialize(v_init)
		ss.restore()
		t=0
		fcurrent()
		cvode.re_init()
	} else {
		finitialize(v_init)
		fcurrent()
	}
}




            
////////////////////Main///////////////////
nsyn=10
objref  s[nsyn], rsyn[nsyn], nc[nsyn]
objref rsynmda[nsyn], ncnmda[nsyn]

objref rect,recv,reci,savv,savi,savt, recI1, recC1, savI1, savC1
objref tvec,ampvec,iclamp
proc main(){

	recv =new Vector()
	rect =new Vector()
	reci =new Vector()
	recI1= new Vector()
	recC1= new Vector()

	//tol=cvode.atolscale(&soma.v(0.5),1e-5)
	period=95.75
	phase0=67.8234
	dur=3
	amp2=0.0
	tstop=16000

	in=0

	th=-14
	access soma
	insert_APC(th)

	f3.wopen("spike.dat")
	current=0.0 // 0.18
	del=50
	npulse = 10
	pulsdur = 1000
	pulsamp = 0.35//0.58//0.35//
	starttime = 13000
        curbase = 0.06//0.06//0.11//

	trunk[10] {
		iclamp = new IClamp( 0.5 )
		tvec	= new Vector(5 )
		ampvec = new Vector(5 )
	}

	iclamp.del = 0
	iclamp.dur = 1e9
		tvec.x[0 ] = 0
		tvec.x[1 ] = starttime
		tvec.x[2 ] = starttime + pulsdur
		tvec.x[3 ] = starttime + 2*pulsdur
		tvec.x[4 ] = tstop
		ampvec.x[0  ] = curbase
		ampvec.x[1  ] = curbase
		ampvec.x[2  ] = curbase + pulsamp
		ampvec.x[3  ] = curbase
		ampvec.x[4  ] = curbase
	ampvec.play(&iclamp.amp,tvec,1)
	access trunk[10]
	recv.record(&v(0.5))
	rect.record(&t)
	reci.record(&iclamp.i)
	recI1.record(&I1_na16a(0.5))
	recC1.record(&C1_na16a(0.5))
	
	//if(!back) { load_file("dendstates.ses") }
	//////////////run//////////////////////// 
	run()
	/////////////////////////////////////
	savv= new File()
	savt= new File()
	savi = new File()
	savI1 = new File()
	savC1 = new File()

	savv.wopen("dv.txt")
	savt.wopen("dtime.txt")
	savi.wopen("di.txt")
	
	savI1.wopen("I1.txt")
	savC1.wopen("C1.txt")
	
	recv.printf(savv)
	rect.printf(savt)
	reci.printf(savi)
	recI1.printf(savI1)
	recC1.printf(savC1)
	
	savv.close
	savt.close
	savi.close
	savI1.close
	savC1.close
	
	// print the spike number 
	if(!back) printf("\n Current: %.4f nA | # Spikes: %d\n", current,  apc.n)
	if(!back) printf("___________________\n")
	v1.printf(f3)

	f3.close
	f2.wopen("state.new")
	ss.save
	ss.fwrite(f2)
	f2.close
}


main()
/********    end file    ******/