// Single branch, high frequency (50 Hz), synaptic stimulation of a group A of exciatory synapses
// and one inhibitory synapse within a single apical oblique. This experiment is used to show how 
// A+B type stimulation delivered on single branches can be sublinear, linear or supralinear depending
// on the strength and location of stimuli A, B

// Type of inhibition: one GABA_a/GABA_b synapse in the stimulated branch
 
// The variable "times" is used to select among a set of blockade cases to test
// times: 0 = control , 1 = block_A, 2 =  block_NMDA, 3 = block_A_NMDA, 4 = block_Na, 5 =  block_Ca

times = 0

//load_proc("nrnmainmenu")      
//load_template("ExperimentControl") // load needed templates
//load_template("EPSPTuning")
//load_template("RangeRef")
load_file("nrngui.hoc")
load_file("../../template/load_templates.hoc")

objref econ                        // initialize template parameters
show_errs=1
debug_lev=1
econ=new ExperimentControl(show_errs,debug_lev)
econ.self_define(econ)
econ.morphology_dir = "../../morphology/n123"        // set location for morphology files
econ.add_lib_dir("Terrence","../../lib")             // set location for library files
econ.generic_dir    = "../../experiment/"            // set location for cell-setup file
econ.data_dir       = "data"                                                 // set directory to store data
sprint(econ.syscmd, "mkdir -p %s", econ.data_dir)
system(econ.syscmd)

actual_resolution=75							     // maximum nseg number
desired_resolution=1

econ.xopen_geometry_dependent("cell")					     // load raw cell morphology	
econ.xopen_geometry_dependent("cell-analysis")				     // load user-defined semantics on morphology
cell_analysis(econ)

printf("Opening cell setup\n")						     // load cell-setup to	
econ.xopen_generic("cell-setup")					     // specify all mechanisms,	
printf("Opened. Setting up cell\n")					     // membrane properties etc	
maximum_segment_length=actual_resolution
cell_setup(econ)

// Set simulation parameters for the experiment 
 
econ.defvar("Simulation Control", "tstop", "250", "Defines when the simulation stops.")
econ.defvar("Simulation Control", "dt", "0.1", "Timestep")
econ.defvar("Simulation Control", "steps_per_ms", "10", "How many points are plotted per ms")
setdt()

// open files with NMDA/AMPA, GABA_A/AMPA and GABA_B/GABA_A ratios
econ.xopen_geometry_dependent("nmda-ampa-ratio")
econ.xopen_geometry_dependent("gabab-gabaa-uniform-ratio")

// Open file with tuned AMPA conductance values for all sections
objref tune_epsp_list
tune_epsp_list=new List()
strdef tunings_file, select
sprint(tunings_file, "%s", "tunings")
xopen("../tune-synapses/tunings.dat")

// Open library functions that will be needed
econ.xopen_library("Terrence","choose-secs")    // used to randomly select sections from a list
econ.xopen_library("Terrence","salloc")         // used to allocate synapses on sections
econ.xopen_library("Terrence","deduce-ratio")   // used to extract NMDA/AMPA, GABA_A/AMPA and GABA_B/GABA_B ratios
econ.xopen_library("Terrence","basic-graphics") // used to plot graphics 
econ.xopen_library("Terrence","spikecount")     // used to count spikes

synapses = 100                                  // maximum number of AMPA/NMDA synapses
gaba_synapses = 20			        // maximum number of GABA synapses

maxruns = 1                                     // max number of runs for each synapse group in section (averaging)
minsyn = 1                                      // minimum number of synapses in selected section
maxsyn = 10                                     // maximum number of synapses in selected section

Deadtime_GLU=dt
Deadtime_NMDA=dt
Deadtime_GABAa=dt
Deadtime_GABAb=dt
hertz=50				      // frequency of stimulation for all synapses
synch=0					      // synapses are stimulated randomly (NOT synchronously)
perio=0					      // spike trains for each synapse are NOT periodic
dendritic_spike_threshold = -25
somatic_spike_threshold = 0
      
objref rpid 
objref ampa[synapses], nmda[synapses], gabaa[gaba_synapses], gabab[gaba_synapses]
objref vrec, Cvrec, vf, dendrec, Cdendrec, meanvrec, maxvrec, meandendrec, maxdendrec, spikes, soma_spikes
objref somarecf, dendrecf

meanvrec = new Vector(maxruns)          // used to store the mean somatic depolarization in each run 
maxvrec = new Vector(maxruns)           // used to store the max somatic depolarization in each run 
meandendrec = new Vector(maxruns)       // used to store the mean dendritic depolarization in each run
maxdendrec = new Vector(maxruns)        // used to store the max dendritic depolarization in each run
spikes = new Vector(maxruns)            // used to store number of dendritic spikes per run 
soma_spikes = new Vector(maxruns)       // used to store number of somatic spikes per run 

//Proceedures for the different cases to be tested

proc Ca_block(){   // Block all Ca++ channels
  forall if(ismembrane("cat")) { 
     for (x) { gcatbar_cat(x) = 0 }
  }
  forall if(ismembrane("calH")) { 
     for (x) { gcalbar_calH(x) = 0 }
  }
  forall if(ismembrane("cal")) { 
     for (x) { gcalbar_cal(x) = 0 }
  }
  forall if(ismembrane("car")) { 
     for (x) { gcabar_car(x) = 0 }
  }
  forall if(ismembrane("somacar")) { 
     for (x) { gcabar_somacar(x) = 0 }
  }
}

proc Na_block(){  // Block all Na+ channels
  forall if(ismembrane("hha2")) { 
     for (x) { gnabar_hha2(x) = 0 }
  }
  forall if(ismembrane("hha_old")) { 
     for (x) { gnabar_hha_old(x) = 0 }
  }
}

proc NMDA_block(){  // Block NMDA current 
 for i=0, synapses -1 {
   nmda[i].gmax = 0  
 }
}

proc A_block() {  // Block all A-type K+ channels 
f = 0
forall if(ismembrane("kad")) { // distal conductances
     for(x) { gkabar_kad(x)= gkabar_kad(x)*f }
  } else if(ismembrane("kap")) { // proximal conductances
     for(x) { gkabar_kap(x)= gkabar_kap(x)*f }
  }
}

proc A_NMDA_block(){ // block both A-current and NMDA current
 NMDA_block()
 A_block()
}


objref splot, gaba_band_shape
strdef csec, syscmd,temp
objref all_branches
all_branches=new SectionList()

// Make a list with all terminal oblique  dendrites
forsec apical_tip_list { // list of all primary obliques
   all_branches.append()
}
forsec apical_tip_list_addendum {
   all_branches.append()   // list of all additional obliques
}


if (times == 0 || times == 2) {
  temporal_offset = 10
}else{
  temporal_offset = 120        // allow some time for equalibrium to be reached when channels are blocked
}
tstop = tstop+temporal_offset  // simulation time period


addgraph_2("soma.v(0.5)",0,tstop, -72,20) // plot voltage at the soma
 
forsec all_branches { 
    nseg = maxsyn  // number of segments in each section is set equal to max number of synapses
                   // to avoid inserting more than one synapses at the same location 

    for (synapses=minsyn; synapses<=maxsyn; synapses=synapses+1) { // for increasing number for synapses in the branch

        for runs = 0, maxruns-1 {  // number of averaging runs 

        rpid=new Random(runs+synapses)
        PID=int(rpid.repick())
        b = 0

        if (synapses == minsyn && runs == 0) {
           print secname(), "is where we assess potency."
           strdef recordsec           
           sprint(recordsec, "%s.v(0.5)",secname()) 
           addgraph_2(recordsec,0,tstop,-72,20) // plot trace at current branch
        }

//Add one inhibitory GABAa/ GABAb synapse on the current branch
//        posa = 0.5
//        posb = 0.5
//	gabaa[b] = new GABAa(posa)
//   	SALLOC_GABAa(gabaa[b],posa,1,0)        
//        gabab[b] = new GABAb(posa)
//        SALLOC_GABAb(gabab[b],posa,1,0)
//        gaba_synapses = 1 

        for si=1,synapses {
          posn=(2*si -1)/(2*synapses)     //explicitly specify synapse position  
          printf("ampa[%d] = new GLU(%g)\n", si-1, posn)
          ampa[si-1] = new GLU(posn)      // add an AMPA receptor at location posn
          nmda[si-1] = new NMDA(posn)     // add an NMDA receptor at location posn
          salloc(ampa[si-1],nmda[si-1],posn) // set pointers to mechanisms and plot on graph
 	}

//Plot all inhibitory synapses in a shape graph
        COLOR=4
        splot=new Shape()
        for i=0,synapses-1 {
          splot.point_mark(ampa[i],COLOR)
        }
//          for i = 0, gaba_synapses -1 {
//            splot.point_mark(gabaa[i],COLOR+1)
//            splot.point_mark(gabab[i],COLOR-1)
//          }
        splot.flush()
        splot.show(1)

        GABA_flag = 0              // Don't make both AMPA/NMDA and GABA trains in shiftsyn_init         
        // create the stimulation trains for AMPA & NMDA synapses
        econ.xopen_library("Terrence","shiftsyn-initA") 
        shiftsyn_init(synapses,tstop,dt,hertz,synch,perio,PID,temporal_offset, GABA_flag,"ampa","nmda")
        
        // Create the stimulation trains for GABA synapses
//        econ.xopen_library("Terrence","GABA_shiftsyn")  
//        gaba_shift(gaba_synapses,tstop,dt,hertz,synch,perio,PID,temporal_offset, "gabaa","gabab")
     
        vrec=new Vector(tstop/dt)    // prepare to record somatic voltage
        vrec.record(&soma.v(0.5))
        dendrec=new Vector(tstop/dt) // prepare to record dendritic voltage 
        dendrec.record(&v(0.5))
       
        // Execute current-blockade proceedure specified
 
        if (times == 0) {
             sprint(select, "%s", "control")}  
        if (times == 1 || times == 6) {
             A_block()
             sprint(select, "%s", "block_A")}
        if (times == 2 || times == 6) {
             NMDA_block() 
             sprint(select, "%s", "block_NMDA")}
        if (times == 3 || times == 6) {
             A_NMDA_block() 
             sprint(select, "%s", "block_A_NMDA")}
        if (times == 4 || times == 6) {
             Na_block()
             sprint(select, "%s", "block_Na")}
        if (times == 5) {
             Ca_block()
             sprint(select, "%s", "block_Ca")}

        print "case = ", select, " secname = ", secname(), " synapses = ", synapses, " runs =", runs 
        finitialize(v_init)
        fcurrent()
        run()
 
        meanvrec.x(runs) = vrec.mean(temporal_offset/dt,tstop/dt -1)      // mean somatic depolarization
        maxvrec.x(runs) = vrec.max(temporal_offset/dt,tstop/dt -1)        // max somatic depolarization
        meandendrec.x(runs)= dendrec.mean(temporal_offset/dt,tstop/dt -1) // mean dendritic depolarization
        maxdendrec.x(runs) = dendrec.max(temporal_offset/dt,tstop/dt -1)  // max dendritic depolarization

        Cvrec = new Vector((tstop-temporal_offset)/dt)
        Cdendrec = new Vector((tstop-temporal_offset)/dt)
        Cvrec = vrec.c(temporal_offset/dt,tstop/dt -1)                    // copy the current somatic voltage trace
        Cdendrec = dendrec.c(temporal_offset/dt,tstop/dt -1)              // copy the current dendritic voltage trace 
        spikes.x(runs) =  spikecount(Cdendrec, dendritic_spike_threshold) // count current number of dendritic spikes
        soma_spikes.x(runs) =  spikecount(Cvrec, somatic_spike_threshold) // count current number of somatic spikes
        }


        // Use only to print graphics to eps files
 //       econ.xopen_library("Terrence","verbose-system")         
 //       for i=0,windex {
 //          sprint(econ.tmp_str2, "data/%s/Apical_Tips/Freq/Single_Tips/%s/graph-%d-%d.eps", tunings_file, secname(), minsyn, i)      
 //          win[i].printfile(econ.tmp_str2)
 //       }

        // create the output file and prepare to write data
        sprint(econ.tmp_str, "data/%s/Apical_Tips/Freq/Single_Tips/%s/",tunings_file,secname())
        sprint(econ.syscmd,  "mkdir -p %s", econ.tmp_str)
        system(econ.syscmd)   
        sprint(econ.tmp_str2, "%s/%s_%d_%d", econ.tmp_str, select, minsyn, maxsyn) 
        vf=new File()
        vf.aopen(econ.tmp_str2)
         
        // print recordings and spike counts to the specified file 
        vf.printf("%d %g %g %g %g %g %g %g %g %g %g %g %g\n", synapses, meanvrec.mean(), meanvrec.stdev(), maxvrec.mean(), maxvrec.stdev(), meandendrec.mean(), meandendrec.stdev(), maxdendrec.mean(), maxdendrec.stdev(), spikes.mean(), spikes.stdev(), soma_spikes.mean(), soma_spikes.stdev())
        vf.close()
  
   //     sprint(econ.tmp_str, "data/%s/Apical_Tips/Freq/Single_Tips/%s/",tunings_file,secname())
   //     somarecf=new File()
   //     sprint(temp, "%s/Vsoma_%d", econ.tmp_str, synapses)
   //     somarecf.wopen(temp)
   //     vrec.printf(somarecf, "%g\n")
   //     somarecf.close()
        
   //     sprint(econ.tmp_str, "data/%s/Apical_Tips/Freq/Single_Tips/%s/",tunings_file,secname())
   //     dendrecf=new File()
   //     sprint(temp, "%s/Vdend_%d", econ.tmp_str, synapses)
   //     dendrecf.wopen(temp)
   //     dendrec.printf(dendrecf, "%g\n")
   //     dendrecf.close() 
               
   }
}