// Author: Ronald van Elburg  (RonaldAJ at vanElburg eu)
//	
// Affiliation:
//           Department of Artificial Intelligence
//           Groningen University
//
// NEURON scripts 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_[3]
objectvar ocbox_, ocbox_list_, scene_, scene_list_
{ocbox_list_ = new List()  scene_list_ = new List()}

//Load MultipleRunControlGUI[0] code
{
    load_file("../hoc/mrc/MultipleRunControl.hoc","MultipleRunControlGUI")
}


// Begin of manually added code (the rest is a session file)
    interactive=0
    load_file("../modelCellReConstruction.hoc")
    /* AdjustModel() */
    remove_basal    =   0
    passive_basal   =   1
    passive_apical  =   0
    passive_soma    =   0
    remove_axon     =   0
    modBasalChannelDensity=0
    remCaDepChannelsFromSoma=0
    pruneDend11=0
    
    ST_AMP=0.2
    ST_DEL=400     
    tstop = 10000
    ST_DUR=tstop
    aspiny = 1
    
    // Dendritic Stimulation
    ra=80
    synaptic_density=0.05
    mean_interval=1000              // milliseconds   
    globSynapseStrength=0.0024      // Bernander 1994
    total_area=0
    L_total=0
    objref KSyn, KSynList
    
    bDendriticStimulation=1   
    proc createSynapses(){
        objref KSyn, KSynList
        KSynList=new List()   
        
        total_area=0
        unmod_area=67698.57
        
        forsec "dend"{	
            for (x,0) {                
                total_area+=area(x)
            }
        }
        
        compensation_factor=unmod_area/total_area
        
        forsec "dend"{
            //L_total+=L	
            for (x,0) {                
                KSyn= new SynAlphaPoisson(x)
                //total_area+=area(x)       
                KSyn.mean=mean_interval/(area(x)*synaptic_density*compensation_factor)
                KSyn.tau=0.5
                KSyn.offset=tstop-0.1
                KSyn.stim=globSynapseStrength
                KSynList.append(KSyn)
            }
        }
    }

    // Tree Topologies
    bMoveBranches=1
    bPrintTree=0
    TreeNumber=0
    proc movextoy(){
            dend11[$1] disconnect()
            connect dend11[$1](0), dend11[$2](1)
    }

    proc moveBranches(){
        
        // Standard tree
        if(TreeNumber==0){ 
            //Do Nothing
    	}
    
       // Non Bursting with 0.2 somatic stim
        if(TreeNumber==1) { 
            movextoy(24,39)
            movextoy(51,40)
            movextoy(48,23)
            
            movextoy(58,39)
            movextoy(40,22)
    	}
    
        if(TreeNumber==2) { 
            movextoy(24,39)
            movextoy(51,40)
            movextoy(48,23)
           
            movextoy(58,39)
            movextoy(40,22)
            
            movextoy(59,24)
            movextoy(25,58)
            
            
            movextoy(32,51)
            movextoy(52,24)
    	}
        
        if(TreeNumber==3) { 
            movextoy(24,39)
            movextoy(51,40)
            movextoy(48,23)
            
            movextoy(58,39)
            movextoy(40,22)
            
            movextoy(59,24)
            movextoy(25,58)
            
            movextoy(32,22)
            movextoy(40,24)
            
            movextoy(59,40)
            movextoy(51,24)   
            
            movextoy(59,71)
            movextoy(72,40)     
            
            movextoy(34,40)
            movextoy(72,32)         
        }
    
        // Bursting with 0.2 somatic stim        
        if(TreeNumber==4) { 
            movextoy(24,39)
            movextoy(51,40)
            movextoy(48,23)
            movextoy(58,23)
            movextoy(48,22)
    	}
    
        if(TreeNumber==5) { 
            movextoy(24,39)
            movextoy(51,40)
            movextoy(48,23)
            movextoy(59,24)
            movextoy(25,58)
    	}
    
        if(TreeNumber==6) { 
            movextoy(58,23)
            movextoy(24,22)
            movextoy(59,24)
            movextoy(32,58)
        }
    
        sh.exec_menu("Show Diam")
        sh.exec_menu("View = plot")
        doNotify()
        sh.exec_menu("View = plot")
        doEvents()
        sh.exec_menu("View = plot")
        doNotify()
        sh.exec_menu("View = plot")
        doEvents()
    } 


    proc customModifications(){
        
        
        if(bMoveBranches==1){
            moveBranches()
        }
    
        if(bDendriticStimulation==1){
            createSynapses()
            st.amp=0
            st.dur=0
        }else{
            st.amp=ST_AMP
            st.del=ST_DEL    
            st.dur=tstop
        }
    }

// End of  manually added code

//Begin MultipleRunControlGUI[0]
{
ocbox_ = new MultipleRunControlGUI(1)
}
{object_push(ocbox_)}
{
file_name="ReReconstructedCells/Results/Sim"
file_index_start=1
}
{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="TreeNumber"
		lower_limit=0
		upper_limit=6
		stepsize=1
		use=1
		setdisplaytext()
	}
	{object_pop()}
{looppars.append(tobj)}

{tobj=new MRC_LoopParameter()}
	{object_push(tobj)}
	{
		name="bDendriticStimulation"
		lower_limit=0
		upper_limit=0
		stepsize=1
        restart=0
        restart_at=0
        end_before=0
		use=1
		setdisplaytext()
	}
	{object_pop()}
{looppars.append(tobj)}


{tobj1=types_outpar.gettypefromindex(2)}
{tobj=new MRC_OutputVariable("j4a_spikes",tobj1,protocol)}
	{object_push(tobj)}
	{
		use=1
		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="j4a_spikes"
	}
	{object_pop()}

{outpars.append(tobj)}
{tobj1=types_outpar.gettypefromindex(1)}
{tobj=new MRC_OutputVariable("j4a_vtrace_soma",tobj1,protocol)}
	{object_push(tobj)}
	{
		use=1
		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="j4a_vtrace_soma"
	}
	{object_pop()}

{outpars.append(tobj)}
{tobj1=types_outpar.gettypefromindex(1)}
{tobj=new MRC_OutputVariable("j4a_vtrace_dend",tobj1,protocol)}
	{object_push(tobj)}
	{
		use=0
		setdisplaytext()
	}
	{object_pop()}
{tobj1=tobj.gethandler()}
	{object_push(tobj1)}
	{
		record_start=0
		record_stop=9000
		sectionname="dend11[82]"
		membername="v(0.5)"
		useindexing=0
		isart=0
		shortname="j4a_vtrace_dend"
	}
	{object_pop()}

{outpars.append(tobj)}
{object_pop()}
{
ocbox_.map("MultipleRunControlGUI[0]", 840, 132, 392.4, 342)
}
objref ocbox_
//End MultipleRunControlGUI[0]

objectvar scene_vector_[1]
{doNotify()}