// Author: Ronald van Elburg  (RonaldAJ at vanElburg eu)
//	
// Affiliation:
//           Department of Artificial Intelligence
//           Groningen University
//
// NEURON script for the paper:
//
//   Ronald A.J. van Elburg and Arjen van Ooyen (2010) `Impact of dendritic size and
//   dendritic topology on burst firing in pyramidal cells', 
//   PLoS Comput Biol 6(5): e1000781. doi:10.1371/journal.pcbi.1000781.
//
// Please consult readme.txt or instructions on the usage of this file.
//
// This software is released under the GNU GPL version 3: 
// http://www.gnu.org/copyleft/gpl.html

objectvar save_window_, rvp_
objectvar scene_vector_[4]
objectvar ocbox_, ocbox_list_, scene_, scene_list_

load_file("../modelSimplifiedCells.hoc")
tstop = 0.01
bStimSoma=1
bActiveDendrites=1

objref ImpedanceTool
func getic(){local ic
    
    soma {
        ImpedanceTool=new Impedance()
        ImpedanceTool.loc(0.5)
        ImpedanceTool.compute(0)
        ic=1/ImpedanceTool.input(0.5) // Units: 1/[MOhm]?
    }

    objref ImpedanceTool
    return ic
}


proc MRC_PrepareModel(){local sectionLength
    procName="MRC_PrepareModel"
    GenerateMessage(1,procName,"")
    create dend[2*noOfTerms-1]
    create soma
    sectionLength=totalDendriticLength/(2*noOfTerms-1)
    setLengths(sectionLength,somaLength)
    setSegmentation(dendNSegLength,somaNSeg)
    
    
    CellAssemble(noOfTerms,currentTopologyNo,terminalDiameter,useRall,rallPower,bconstantSurface)
    
    if(bStimSoma==0){
            createSynapses()
    }else{
            connectSomaStimulus()
    } 
    
    equipCells(bActiveDendrites)
    
}

func dend_area(){local myArea
    myArea=0
    
    forsec "dend"{	
        for (x,0) {                
            myArea+=area(x)
        }
    }

    return myArea
}

 

{ocbox_list_ = new List()  scene_list_ = new List()}
{
    xpanel("RunControl", 0)
        
        v_init = -70
        xvalue("Init","v_init", 1,"stdinit()", 1, 1 )
        
        xbutton("Init & Run","run()")
        
        xbutton("Stop","stoprun=1")
        
        runStopAt = 5
        xvalue("Continue til","runStopAt", 1,"{continuerun(runStopAt) stoprun=1}", 1, 1 )
        
        runStopIn = 1
        xvalue("Continue for","runStopIn", 1,"{continuerun(t + runStopIn) stoprun=1}", 1, 1 )
        
        xbutton("Single Step","steprun()")
        
        t = 0
        xvalue("t","t", 2 )
        
        xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
        
        dt = 0.025
        xvalue("dt","dt", 1,"setdt()", 0, 1 )
        
        steps_per_ms = 40
        xvalue("Points plotted/ms","steps_per_ms", 1,"setdt()", 0, 1 )
        
        screen_update_invl = 1
        xvalue("Scrn update invl","screen_update_invl", 1,"", 0, 1 )
        
        realtime = 0
        xvalue("Real Time","realtime", 0,"", 0, 1 )
    xpanel(-1,1500)
}
{
save_window_ = new Graph(0)
save_window_.size(0,1500,-80,40)
scene_vector_[3] = save_window_
{save_window_.view(0, -80, 1500, 120, 295, 661, 300.6, 200.8)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addexpr("v(.5)", 1, 1, 0.8, 0.9, 2)
}
{
save_window_ = new PlotShape(0)
save_window_.size(-346.486,1827.84,-58.5592,2115.77)
save_window_.variable("v")
scene_vector_[2] = save_window_
{save_window_.view(-346.486, -58.5592, 2174.33, 2174.33, 714, 661, 200.7, 200.8)}
fast_flush_list.append(save_window_)
save_window_.save_name("fast_flush_list.")
}

//Begin MultipleRunControlGUI[0]
{
load_file("../hoc/mrc/MultipleRunControl.hoc","MultipleRunControlGUI")
}
{
ocbox_ = new MultipleRunControlGUI(1)
}
{object_push(ocbox_)}
{
file_name="SimplifiedTopologies/Results/ICFull"
file_index_start=0
}

{tobj=new MRC_Protocol()}
	{object_push(tobj)}
	{
		output_matlab_mfile=1
		output_neuronbinary=1
		output_axontextfile=0
	}
	{object_pop()}

{protocol=tobj}

{tobj=new MRC_LoopParameter()}
	{object_push(tobj)}
	{
		name="currentTopologyNo"
		lower_limit=1
		upper_limit=23
		stepsize=1
		use=1
		setdisplaytext()
	}
	{object_pop()}
{looppars.append(tobj)}

{tobj=new MRC_LoopParameter()}
	{object_push(tobj)}
	{
		name="totalDendriticLength"
		lower_limit=1000
		upper_limit=4000
		stepsize=25
		use=1
		setdisplaytext()
	}
	{object_pop()}
{looppars.append(tobj)}

{tobj1=types_outpar.gettypefromindex(2)}
{tobj=new MRC_OutputVariable("spikes",tobj1,protocol)}
	{object_push(tobj)}
	{
		use=0
		setdisplaytext()
	}
	{object_pop()}
{tobj1=tobj.gethandler()}
	{object_push(tobj1)}
	{
		record_start=0
		record_stop=9000
		threshold=0
		listname="soma"
		sectionname=""
		membername="v(0.5)"
		listtype=2
		useindexing=0
		isart=0
		shortname="spikes"
	}
	{object_pop()}
{outpars.append(tobj)}

{tobj1=types_outpar.gettypefromindex(1)}
{tobj=new MRC_OutputVariable("vtrace_soma",tobj1,protocol)}
	{object_push(tobj)}
	{
		use=0
		setdisplaytext()
	}
	{object_pop()}
{tobj1=tobj.gethandler()}
	{object_push(tobj1)}
	{
		record_start=0
		record_stop=9000
		sectionname="soma"
		membername="v(0.5)"
		useindexing=0
		isart=0
		shortname="vtrace_soma"
	}
	{object_pop()}

{outpars.append(tobj)}


{tobj1=types_outpar.gettypefromindex(3)}
{tobj=new MRC_OutputVariable("v_membrane",tobj1,protocol)}
	{object_push(tobj)}
	{
		use=0
		setdisplaytext()
	}
	{object_pop()}
{tobj1=tobj.gethandler()}
	{object_push(tobj1)}
	{
		scalarname="soma.v( 0.5 )"
		shortname="vm"
	}
	{object_pop()}

{outpars.append(tobj)}

{tobj1=types_outpar.gettypefromindex(3)}
{tobj=new MRC_OutputVariable("dend_area",tobj1,protocol)}
	{object_push(tobj)}
	{
		use=1
		setdisplaytext()
	}
	{object_pop()}
{tobj1=tobj.gethandler()}
	{object_push(tobj1)}
	{
		scalarname="dend_area()"
		shortname="da"
	}
	{object_pop()}

{outpars.append(tobj)}


{tobj1=types_outpar.gettypefromindex(3)}
{tobj=new MRC_OutputVariable("input_conductance",tobj1,protocol)}
	{object_push(tobj)}
	{
		use=1
		setdisplaytext()
	}
	{object_pop()}
{tobj1=tobj.gethandler()}
	{object_push(tobj1)}
	{
		scalarname="getic()"
		shortname="ic"
	}
	{object_pop()}

{outpars.append(tobj)}

{tobj1=types_outpar.gettypefromindex(3)}
{tobj=new MRC_OutputVariable("mep",tobj1,protocol)}
	{object_push(tobj)}
	{
		use=1
		setdisplaytext()
	}
	{object_pop()}
{tobj1=tobj.gethandler()}
	{object_push(tobj1)}
	{
		scalarname="mep(\"dend\")"
		shortname="mep"
	}
	{object_pop()}

{outpars.append(tobj)}

{object_pop()}
{
ocbox_.map("MultipleRunControlGUI[0]", 931, 134, 399.6, 385.2)
}
objref ocbox_
//End MultipleRunControlGUI[0]

objectvar scene_vector_[1]
{doNotify()}