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//=================== creating cell object ==========================
load_file("stdlib.hoc") 
load_file("nrngui.hoc")
load_file("ranstream.hoc")

objref cvode
cvode = new CVode()
cvode.active(1)
load_file("import3d.hoc")

objref L5PC
strdef morphology_file
morphology_file = "../morphologies/cell1.asc"

load_file("../models/L5PCbiophys3.hoc")
load_file("../models/L5PCtemplate.hoc")
L5PC = new L5PCtemplate(morphology_file)

//-------------------parameters-----------------------//
v_init = -80 
eNSNUM = 15000       // how many NetStims to create (total, excite + inhib, so # of excitatory synapses is eNSNUM - iNSNUM)
iNSNUM = 4500         //nuber of inhibitory synapses
MAXSTREAM = 1000 
tstop = 3000      // length of simulation
dendnseg = 83      // as determind by the original model

//-------------------parameters for NetStim-----------//
// this generates a presynaptic train of stimuli
spikeint = 1000    // (ms) mean time between spikes, 1000(ms) to get 1 Hz 
i_spikeinit = 200 // inhibitory 200 (ms) to get 5 Hz
nspikes = 50     // average number of spikes, that NetStim will produce.
spikeonset = 500    // start time (ms) of first spike (delay)
noise = 1         // set to 1 for poisson mode

//-------------------parameters for Exp2Syn-----------//
// S = 1 / Ohms. G is in microOhms
// TAU1 and TAU2 parameters for L5PC in a paper
TAU1 = 0.20     
TAU2 = 1.7    
i_excite = 1      //current (nA), (original: 1), multiplier -> 10
e_excite = 0      //revesral potential

i_inhibit = 0.5   // current (nA), original (original: 0.5) multiplier -> 10
e_inhibit = -60   //leak reversal potential

//-------------------parameters for NetCon------------//
// not sure what parameters to set for this setion. arbitrarily picked
THRESHOLD =  10
DELAY = 0.8
WEIGHT = 0.1

//-------------------MODEL SETUP-----------------------//
objref nslist, rslist, eslist, nclist
nslist = new List()   // NetStim list
rslist = new List()   // RandStream list
eslist = new List()   // Exp2Syn list

//----- make_stims create excitatory synapses, all firing randomly-----//
proc syn_excite() { local i  localobj ns, rs, es, r
  nslist = new List()   
  rslist = new List()   
  eslist = new List()   

  random_stream_offset_ = MAXSTREAM

  for i = 0, $1-1 {
    ns = new NetStim()
    nslist.append(ns)
    rs = new RandomStream(i)
    rslist.append(rs)
    ns.noiseFromRandom(rs.r)
    rs.r.negexp(1)              // must specify negexp distribution with mean = 1
    rs.start()                  // makes random noise and writes results in list
  }

  r = new Random()
  
  for i = 0, $1-1 {
    s1dend= 1                        //s1 dendrite, in our case, we only have 1 dend
    s1comp= r.uniform(0, dendnseg)  //s1 compartment --- choose a random (discunif = discrete uniform) compartment of dendrites
    s1coord= s1comp / dendnseg       //s1 coordinate, remember dendnseg is 1 by original cell model

    L5PC.dend[s1dend] {
    es = new Exp2Syn(s1coord)         //places Exp2Syn on dend in compartment with coordinate s1
    eslist.append(es)
    }
  }
}

syn_excite(eNSNUM)

//this changes the last few EXP2SYN's parameters to be inhibitory (number of inhibitory synapses is iNSNUM)
proc setparams() {local i, j 

  for i = 0,nslist.count()-iNSNUM {
    nslist.o(i).interval = spikeint
    nslist.o(i).number = nspikes
    nslist.o(i).start = spikeonset
    nslist.o(i).noise = noise
  }
  
  for i = nslist.count()-iNSNUM, nslist.count()-1{
    nslist.o(i).interval = i_spikeinit
    nslist.o(i).number = nspikes
    nslist.o(i).start = spikeonset
    nslist.o(i).noise = noise
  }

  for i = 0,eslist.count()-iNSNUM {                        
    eslist.o(i).tau1 = TAU1    //rise time (ms)
    eslist.o(i).tau2 = TAU2    //delay time (ms)
    eslist.o(i).e = e_excite     //reversal potential, change this to make it inhibitory
    eslist.o(i).i = i_excite
  }

  for i = eslist.count()-iNSNUM, eslist.count()-1{
    eslist.o(i).tau1 = TAU1    //rise time (ms)
    eslist.o(i).tau2 = TAU2    //delay time (ms)
    eslist.o(i).e = e_inhibit     //reversal potential, change this to make it inhibitory
    eslist.o(i).i = i_inhibit 
  }
}

setparams()             // default is deterministic spike times (NOISE = 0)

//-------------------instrumentation-----------------------//
// this is where NetCon is caled and connects the NetStim and EXP2SYN

objref nclist, tvec, idvec
idvec = new Vector()
tvec = new Vector()
nclist = new List()

proc instrumentation() { local i  localobj nc, inc 
  for i = 0,nslist.count()-1 {
    nc = new NetCon(nslist.o(i), eslist.o(i), THRESHOLD, DELAY, WEIGHT)
    nclist.append(nc)
    nc.record(tvec, idvec, i)
  }
}
instrumentation()

//======================= plot settings ============================
objref gV, tempVec

gV = new Graph()
gV.size(0,tstop,-80,40)
graphList[0].append(gV)
gV.addvar("soma","L5PC.soma.v(0.5)",1,1)

objref vvec, r_tvec
vvec = new Vector()
r_tvec = new Vector()
cvode.record(&v(0.5), vvec, r_tvec)

//-------------------starting simulation-----------------------//
run()
print "done!"

//-------------------save settings----------------------------//
objref savv
strdef str1 

count = 16
savv = new File() 
sprint(str1,"v_cell_%d.txt", count)   
savv.wopen(str1)  
vvec.printf(savv) 
r_tvec.printf(savv)       
savv.close()