// $Id: network.hoc,v 1.352 2012/03/08 17:56:22 samn Exp $

//* Numbers and connectivity params

DOPE_INTF6=1
EDOPE_INTF6=1
ESTDP_INTF6 = ISTDP_INTF6 = 0

declare("scale",2)  // Sam had this on 4.
declare("colW",1,"colH",1)
declare("numcols",colW*colH)
declare("dbgcols",0) // whether to debug columns by making them have the same wiring and inputs
declare("colr",2) // maximal trans-column projection distance; 0 within col; 1 next col etc
declare("colnq","o[5]","lcol",new List())
declare("autotune",0) // 
declare("useSTDP",1) // 
{sprint(tstr,"o[%d]",numcols) declare("col",tstr)}
{sprint(tstr,"o[%d][%d]",colH,colW) declare("gcol",tstr)} // 2D column grid
double div[numcols][numcols][CTYPi][CTYPi]//div[i][j]==# of outputs from type i->j
double wmat[numcols][numcols][CTYPi][CTYPi][STYPi] // wmat[i][j][k]==weight from type i->j for synapse k
double delm[numcols][numcols][CTYPi][CTYPi]//avg. delay from type i->j
double deld[numcols][numcols][CTYPi][CTYPi]//delay variance from type i->j
double conv[numcols][numcols][CTYPi][CTYPi]
dosetpmat=name_declared("pmat")==0
{sprint(tstr,"d[%d][%d][%d][%d]",numcols,numcols,CTYPi,CTYPi) declare("pmat",tstr)}
double synloc[CTYPi][CTYPi]//location of synapses
declare("cedp",new List()) // list for DP cells

//* swire & related column variables
declare("colside",30) // column diameter in micrometers
declare("swire",0) // whether to use 'spatial' wiring, 2 means use swirecut, 3 means use swirecutfl  (Sam had set to 3)
declare("checkers",0) // whether to arrange cells in checkerboard pattern
declare("cxinc",3,"cyinc",3,"crad",1)
declare("EEsq",(colside/2)^2,"EIsq",(colside/2)^2,"IEsq",(colside/1)^2,"IIsq",(colside/2)^2) // params for swirecut
double dels[CTYPi][CTYPi]//[STYPi] //stdev of delays
double delv[CTYPi][CTYPi]//variance of delays
double vcond[CTYPi][CTYPi]//[STYPi] //conduction velocities
declare("layerzvar",25) // range of z location of cells in a layer (in micrometers)
declare("colxydist",50) // distance between adjacent columns (x,y)
declare("vlayerz",new Vector(CTYPi))
declare("pseed",4321)
declare("dvcond","d[2]") //intra layer conduction delays
declare("maxsfall",0.001) // max fall-off in prob of connection @ opposite side of column (used by swire)
declare("slambda",colside/3) // spatial length constant for probability of connections, used in swirecut
dvcond[0] = 1   //if presynaptic cell is excit, conduction delay == 1.0 m/s
dvcond[1] = 0.4 //if presynaptic cell is inhib, conduction delay == 0.4 m/s
declare("lambda",30,"hval",0)

//* other variables
declare("mknetnqss",1) // whether COLUMN should make connsnq,cellsnq
declare("fc",0.55)
declare("EEGain",fc*4*15/11,"EIGain",fc*15,"IEGain",fc*4*15/11,"IIGain",fc*4*15/11)
declare("NMAMR",0.1,"EENMGain",1)
declare("EIGainInterC0",0.125,"EIGainInterC1",1,"EEGainInterC0",1,"EEGainInterC1",0.25)
double EIGainInterC[2],EEGainInterC[2]
EIGainInterC[0] = EIGainInterC0 // 0->1
EIGainInterC[1] = EIGainInterC1
EEGainInterC[0] = EEGainInterC0
EEGainInterC[1] = EEGainInterC1
declare("TCNM",0) // whether TC->NM2 on
declare("NMUSCLES",4) // number of muscle groups in model
declare("sepDPpos",1) // whether to position DP cells in each group separately

if(autotune) {
  seadsetting_INTF6 = 2
  wsetting_INTF6 = 1 // use sywv during sim
} else if(useSTDP) {
  seadsetting_INTF6 = 3 // use plasticity
} else {
  seadsetting_INTF6 = 2 // fixed weights
}

declare("wnqstr","") // intracol wiring NQS (single column)

//* prdiv() - print div
proc prdiv () { local ii,jj,kk,ll
  for ii=0,numcols-1 for jj=0,numcols-1 for kk=0,CTYPi-1 for ll=0,CTYPi-1 if(div[ii][jj][kk][ll]) {
    printf("div[%d][%d][%s][%s]=%g\n",ii,jj,CTYP.o(kk).s,CTYP.o(ll).s,div[ii][jj][kk][ll])
  }
}

// %con (con/pre) = %div (div/post)
DEAD_DIV_INTF6=0
declare("jcn",1)
declare("disinhib",0) //iff==1 , turn off inhibition, by setting wmat[I%d][...]==0 in inhiboff()
declare("pmatscale",1) // scale for pmat - allows keeping it fixed while changing # of cells in network
declare("wmatscale",1) // scale for wmat - called after setwmat

batch_flag=declare("dstr",datestr,"setdviPT",NORM)
declare("params","not batch","ofile",output_file)
declare("dvseed",534023) // seed for wiring

dosetcpercol=name_declared("cpercol")==0 // whether to set values in cpercol or use user-supplied values
{sprint(tstr,"d[%d][%d]",numcols,CTYPi) declare("cpercol",tstr)} // cells of a specific type per column
{sprint(tstr,"o[%d]",numcols) declare("vcpercol",tstr)}
for i=0,numcols-1 vcpercol[i]=new Vector(CTYPi)
declare("DPESFeedForward",0.15) // level of feedforward connectivity from DP -> ES
// declare("DPESFeedForward",0.1) // level of feedforward connectivity from DP -> ES
declare("EMRecur",0.0) //declare("EMRecur",0.07) // level of recurrence between EM cells
declare("ESRecur",0.0)//declare("ESRecur",0.191)// level of recurrence between ES cells
declare("EMESFeedBack",0.0)//declare("EMESFeedBack",0.017)// level of feedback from EM -> ES
declare("ESEMFeedForward",0.08)// level of feedforward connectivity from ES -> EM

sprint(tstr,"d[%d][%d]",CTYPi,CTYPi)
if(!(i=name_declared("delmscale"))) {
  declare("delmscale",tstr) // scale delm values by this #
}
if(!i) {
  for i=0,CTYPi-1 for j=0,CTYPi-1 delmscale[i][j]=1
}

//** mklayerz -- get average z location of a layer, based on frana and tononi
// returns value in micrometers. 0 is at top (layer 1), max val
// is at layer 6 ... actual #s don't matter, only distances between
// the layers matters...
proc mkvlayerz () { local i,vl
  vlayerz.indgen(0,CTYPi-1,1)
  vlayerz.apply("layer")
  for vtr(&vl,vlayerz,&i) {
    if(vl == 2 || vl == 3){
      vlayerz.x(i)=1740 // average of 1540+1940 from frana
    } else if(vl == 4) {
      vlayerz.x(i) = (1740+1130) / 2
    } else if(vl == 5 ){
      vlayerz.x(i) = 1130
    } else if(vl == 6 ){
      vlayerz.x(i) = 488
    } else vlayerz.x(i) = 200
  }
}

//* setcpercol - set # of cells per column
proc setcpercol () { local i,j // (/u/samn/vcsim/notebook.dol_1:24562)(notebook.dol_1:24492)
  if(dosetcpercol) { // if user didn't supply values (default), set # of cells of a type per column

    cpercol[0][ES] =  int(48 * scale) // sensory layer
    cpercol[0][ISL] =      5 * scale 
    cpercol[0][IS]  =     11 * scale 

    cpercol[0][EM] =  int(48 * scale) // motor layer
    cpercol[0][IML] =      5 * scale 
    cpercol[0][IM]  =     11 * scale 

    cpercol[0][DP] = cpercol[0][ES] // arm-cell/spindle layer

    for i=0,CTYPi-1 if(cpercol[0][i]) cpercol[0][i]=int(cpercol[0][i]+0.5) // round

    //store values in vcpercol Vectors
    for i=0,numcols-1 {
      {vcpercol[i].resize(CTYPi) vcpercol[i].fill(0)} // store the values in a vector
      for j=0,CTYPi-1 vcpercol[i].x(j)=cpercol[i][j]
    }
  }
}

//* setpmat()
proc setpmat () { local pre,po,ii,jj,kk,ll
  if(!dosetpmat) return // if pmat setup by user (in notebook), then don't reset its values
  for ii=0,numcols-1 for jj=0,numcols-1 for kk=0,CTYPi-1 for ll=0,CTYPi-1 pmat[ii][jj][kk][ll]=0
  // intracol connections
  ii=0

  pmat[0][0][DP][ES]=DPESFeedForward // 0.1, DP = drawspike cells (muscle/arm layer)

  // sensory layer
  pmat[ii][ii][ES][EM]=ESEMFeedForward
  pmat[ii][ii][ES][ES]=ESRecur
  pmat[ii][ii][ES][ISL]=0.51
  pmat[ii][ii][ES][IS]=0.43
  pmat[ii][ii][ISL][ES]=0.35
  pmat[ii][ii][ISL][ISL]=0.09
  pmat[ii][ii][ISL][IS]=0.53
  pmat[ii][ii][IS][ES]=0.44
  pmat[ii][ii][IS][ISL]=0.34
  pmat[ii][ii][IS][IS]=0.62

  // motor layer
  pmat[ii][ii][EM][EM]=EMRecur
  pmat[ii][ii][EM][ES]=EMESFeedBack
  pmat[ii][ii][EM][IML]=0.51
  pmat[ii][ii][EM][IM]=0.43
  pmat[ii][ii][IML][EM]=0.35
  pmat[ii][ii][IML][IML]=0.09
  pmat[ii][ii][IML][IM]=0.53
  pmat[ii][ii][IM][EM]=0.44
  pmat[ii][ii][IM][IML]=0.34
  pmat[ii][ii][IM][IM]=0.62
}

//* scalepmat(fctr) - multiply values in pmat by fctr
proc scalepmat () { local fctr,from,to,c1,c2
  fctr=$1
  for c1=0,numcols-1 for c2=0,numcols-1 {
    for from=0,CTYPi-1 for to=0,CTYPi-1 pmat[c1][c2][from][to] *= fctr
  }
}

//* pmat2nq - return an NQS with info in pmat
obfunc pmat2nq () { local i,j,k,l localobj nqpmat
  nqpmat=new NQS("col1","col2","froms","tos","from","to","pij")
  {nqpmat.strdec("froms") nqpmat.strdec("tos")}
  for i=0,numcols-1 for j=0,numcols-1 for k=0,CTYPi-1 for l=0,CTYPi-1 if(pmat[i][j][k][l]) {
    nqpmat.append(i,j,CTYP.o(k).s,CTYP.o(l).s,k,l,pmat[i][j][k][l])
  }  
  return nqpmat
}

//* nq2pmat - load NQS ($o1) into pmat
proc nq2pmat () { local i,j,k,l localobj nq,vf,vto,vc1,vc2,vpij
  {nq=$o1 nq.tog("DB") vc1=nq.getcol("col1") vc2=nq.getcol("col2")}
  {vf=nq.getcol("from") vto=nq.getcol("to") vpij=nq.getcol("pij")}
  for i=0,numcols-1 for j=0,numcols-1 for k=0,CTYPi-1 for l=0,CTYPi-1 pmat[i][j][k][l]=0
  for i=0,vf.size-1 pmat[vc1.x(i)][vc2.x(i)][vf.x(i)][vto.x(i)]=vpij.x(i)
  print "loaded " , nq , " into pmat"
}

//* synapse locations DEND SOMA AXON
proc setsynloc () { local from,to
  for from=0,CTYPi-1 for to=0,CTYPi-1 {
    if(ice(from)) {
      if(IsLTS(from)) {
        synloc[from][to]=DEND // distal [GA2] - from LTS
      } else {
        synloc[from][to]=SOMA // proximal [GA] - from FS
      }
    } else {
      synloc[from][to]=DEND // E always distal. use AM2,NM2
    }
  }
}

//* setdelmats -- setup delm,deld
proc setdelmats () { local from,to,ii,jj,fcm,fcd
  for ii=0,numcols-1 for jj=0,numcols-1 {
    if(ii==jj) {
      fcm=fcd=1
    } else {fcm=3 fcd=6}
    for from=0,CTYPi-1 for to=0,CTYPi-1 {
      if(synloc[from][to]==DEND) {
        delm[ii][jj][from][to]=4 * delmscale[from][to] * fcm
        deld[ii][jj][from][to]=1 * fcd
      } else {
        delm[ii][jj][from][to]=2.0 * delmscale[from][to] * fcm
        deld[ii][jj][from][to]=0.2 * fcd
      }
    }
  }
}

//* weight params
//** delay all 2+/-0.02 within column for now
proc setwmat () { local from,to,sy,gn,c,ii,jj
  for ii=0,numcols-1 for jj=0,numcols-1 for from=0,CTYPi-1 for to=0,CTYPi-1 for sy=0,STYPi-1 wmat[ii][jj][from][to][sy]=0
  ii=0

  // wire DP directly to ES
  wmat[0][0][DP][ES][AM2]= 1.75 * 5.01 / EEGain // 1.67 

  // sensory layer
  wmat[ii][ii][ES][ES][AM2]=0.66
  wmat[ii][ii][ES][ISL][AM2]=0.23
  wmat[ii][ii][ES][IS][AM2]=0.23
  wmat[ii][ii][ES][EM][AM2]=0.88 * 2

  wmat[ii][ii][IS][ES][GA]=1.5
  wmat[ii][ii][IS][ISL][GA]=1.5
  wmat[ii][ii][IS][IS][GA]=1.5

  wmat[ii][ii][ISL][ES][GA2]=0.83
  wmat[ii][ii][ISL][ISL][GA2]=1.5
  wmat[ii][ii][ISL][IS][GA2]=1.5

  // motor layer
  wmat[ii][ii][EM][EM][AM2]=0.71
  wmat[ii][ii][EM][IML][AM2]=0.23
  wmat[ii][ii][EM][IM][AM2]=0.23
  wmat[ii][ii][EM][ES][AM2]=0.24

  wmat[ii][ii][IM][EM][GA]=1.5
  wmat[ii][ii][IM][IM][GA]=1.5
  wmat[ii][ii][IM][IML][GA]=1.5

  wmat[ii][ii][IML][EM][GA2]=0.83
  wmat[ii][ii][IML][IM][GA2]=1.5
  wmat[ii][ii][IML][IML][GA2]=1.5  

  //set NMDA weights
  for ii=0,numcols-1 for jj=0,numcols-1 {
    for from=0,CTYPi-1 for to=0,CTYPi-1 wmat[ii][jj][from][to][NM2]=NMAMR*wmat[ii][jj][from][to][AM2]
  }
  //gain control
  for ii=0,numcols-1 for jj=0,numcols-1 for from=0,CTYPi-1 for to=0,CTYPi-1 for sy=AM,GA2 if(wmat[ii][jj][from][to][sy]>0) {
    if(ice(from)) {
      if(ice(to)) {
        gn = IIGain
      } else {
        gn = IEGain
      }
      if(IsLTS(from) && !IsLTS(to)) gn *= 0.5
    } else {
      if(ice(to)) {
        gn = EIGain 
        if(IsLTS(to)) gn *= 0.5
      } else {
        gn = EEGain
        if(sy==NM || sy==NM2) gn *= EENMGain // E->E NMDA gain
      }
    }
    wmat[ii][jj][from][to][sy] *= gn 
  }
}

//* scalewmat(fctr) - multiply values in wmat by fctr
proc scalewmat () { local fctr,from,to,c1,c2,sy
  fctr=$1
  for c1=0,numcols-1 for c2=0,numcols-1 {
    for from=0,CTYPi-1 {
      if(from==DP || IsTHAL(from)) continue
      for to=0,CTYPi-1 {
        if(IsTHAL(to)) continue
        for sy=0,STYPi-1 wmat[c1][c2][from][to][sy] *= fctr
      }
    }
  }
}

//* %con (con/pre) = %div (div/post)
{sp = new NQS() cp = new NQS()}

//** gethublims(col,hubtype,hubfactor,numhubs,mode) 
// get a matrix of size CTYPi X CTYPi, specifying div with mat.x(hubtype,othertype)
// and conv with mat.x(othertype,hubtype)
// hubtype = type of hub. hubfactor = desired ratio of hub div/conv vs non-hub div/conv
// numhubs = # of hubs. col = COLUMN for which to set hubs.
// mode == 0 <-- hub div(conv) is set to hubfactor * original div(conv)
// mode == 1 <-- hub div(conv) is set so that final hub div = hubfactor * final non_hub div (same for conv)
//  formula is based on:  m / ((N-H*m) / (C-H)) = F , and then solving for m
//   m = div for the hubs,  F = desired ratio of final hub div to final non-hub div
//   N = # of synapses (links),  C = total # of postsynaptic cells (including hubs) , H = # of hubs
//   similarly done for conv , but replace N with appropriate values
//   (/u/samn/intfcol/notebook.dol_1:21933)
obfunc gethublims () { local ct,mode,from,to,lim,nc,nhubs,fctr localobj col,mat
  {col=$o1 ct=$2 fctr=$3 nhubs=$4 mode=$5 mat=new Matrix(CTYPi,CTYPi)}
  for to=0,CTYPi-1 if(col.numc[to] && col.div[ct][to]) {
    {nc=col.numc[to] if(ct==to)nc-=1} // deduct for self-link
    if(mode==0) {
      lim = int( 0.5 + col.div[ct][to]*fctr )
    } else {
      lim = int( 0.5 + col.div[ct][to]*col.numc[ct]*fctr/(col.numc[ct]-nhubs+fctr*nhubs) )
    }
    mat.x(ct,to) = MINxy(lim, nc) // at most div to all postsynaptic cells
  }
  for from=0,CTYPi-1 if(col.numc[from] && col.div[from][ct]) {
    {nc=col.numc[from] if(ct==from)nc-=1} // deduct for self-link
    if(mode==0) {
      lim = int( 0.5 + col.conv[from][ct]*fctr )
    } else {
      lim = int( 0.5 + col.div[from][ct]*col.numc[from]*fctr/(col.numc[ct]-nhubs+fctr*nhubs) )
    }
    mat.x(from,ct) = MAXxy(MINxy(lim, nc),1) // at most conv from all presynaptic cells, but at least 1
  }
  return mat
}

//** addhubs(column,cell-type,numhubs,scaling factor,skipI[,seed,allowz,hubmode,verbose])
// add hubs to the network by stealing wires from other neurons
// $o1 == column
// $2 == cell type of hub
// $3 == number of hubs to add
// $4 == scaling factor (should be > 1.0) for conv,div of hub
// $5 == skip div/conv of I cells
// $6 == seed - optional
// $7 == allowz - whether to allow pulling all links from/to another cell
// $8 == hubmode - which mode to use for gethublims (see above)
// $9 == verbose - optional
// function returns a Vector containing the ids of the cells selected as hubs (within column ids)
obfunc addhubs () { local a,ct,fctr,nhubs,idx,jdx,lseed,hubid,szorig,cursz,preid,poid,lim,skipI,to,from,vrb,changed,allowz,hmode\
                 localobj col,ce,vin,vout,nq,vd,vc,vdd,vdt,vddt,vpicked,vhubid,vw1,vw2,vsyn,vprob,vsynt,vtmp,vdsz,vcsz,mhlim
  col=$o1 ct=$2 nhubs=$3 fctr=$4 skipI=$5
  if(numarg()>5) lseed=$6 else lseed=1234
  if(numarg()>6) allowz=$7 else allowz=1
  if(numarg()>7) hmode=$8 else hmode=0
  if(numarg()>8) vrb=$9 else vrb=0
  {ce=col.ce hashseed_stats(lseed,lseed,lseed)}
  a=allocvecs(vin,vout,vd,vc,vdd,vdt,vddt,vpicked,vw1,vw2,vsyn,vprob,vsynt,vtmp,vdsz,vcsz)
  vrsz(col.allcells,vin,vout,vd,vc,vdd,vdt,vddt,vpicked,vw1,vw2,vsyn,vprob,vsynt,vdsz,vcsz,vtmp)
  mhlim=gethublims(col,ct,fctr,nhubs,hmode)
  //vin,vout = input/output markers. vd,vc = div/conv.
  //vdd div/conv delays, vdt div/conv temp. vddt=div/conv delay temp
  //vpicked=which cells already picked as hubs
  vhubid=new Vector()
  {vhubid.indgen(col.ix[ct],col.ixe[ct],1) vhubid.shuffle() vhubid.resize(nhubs)}
  if(vrb) vlk(vhubid)
  for idx=0,vhubid.size-1 vpicked.x(vhubid.x(idx))=1 
  for idx=0,vhubid.size-1 { hubid=vhubid.x(idx) 
    if(vrb) printf("hub%d id = %d\n",idx+1,hubid)
    {ce.o(hubid).getdvi(vd,vdd,vw1,vw2,vprob,vsyn) ce.o(hubid).getconv(vc)}//IDs of post/presynaptic cells
    {ce.o(hubid).getconv(1.2,vcsz) vdsz.resize(CTYPi) vdsz.fill(0)}//counts of post/pre types
    for jdx=0,vd.size-1 vdsz.x(ce.o(vd.x(jdx)).type)+=1
    {vout.fill(0) vin.fill(0)}     //init as 0
    for jdx=0,vd.size-1 vout.x(vd.x(jdx))=1 //mark current postsynaptic cells
    for jdx=0,vc.size-1 vin.x(vc.x(jdx))=1  //mark current presynaptic cells
    for to=0,CTYPi-1 if(col.numc[to] && col.div[ct][to] && (!skipI || !ice(to))) {
      cursz=szorig=vdsz.x(to) // update divergence
      if(vrb) print "\torig div -> " , CTYP.o(to).s, " = " , szorig
      {lim=mhlim.x(ct,to) changed=1}
      while(cursz<lim && changed==1) { changed=0
        for(preid=col.ix[ct];preid<=col.ixe[ct] && cursz<lim;preid+=1) {// pick same presynaptic type
          if(vpicked.x(preid)) continue //dont take from other hubs
          ce.o(preid).getdvi(vdt,vddt,vw1,vw2,vprob,vsynt) 
          vtmp.fill(0)
          for jdx=0,vdt.size-1 vtmp.x(ce.o(vdt.x(jdx)).type)+=1
          if(!allowz && vtmp.x(to)<=1)continue//dont want to turn div of another cell to 0
          for jdx=0,vdt.size-1 { poid=vdt.x(jdx) // go thru postsynaptic cells looking for target type            
            if(ce.o(poid).type==to && poid!=hubid && vout.x(poid)==0) { cursz+=1
              {vd.append(poid) vdd.append(vddt.x(jdx)) vsyn.append(vsynt.x(jdx))}
              {vdt.remove(jdx) vddt.remove(jdx) vsynt.remove(jdx)}
              ce.o(preid).setdvi(vdt,vddt,vsynt,1) // update presynaptic cell
              vout.x(poid)=changed=1 // this cell synapses on poid
              break
            }
          }
        }
      }
      if(vrb) print "\tnew div -> " , CTYP.o(to).s, " = " , cursz
    }
    ce.o(hubid).setdvi(vd,vdd,vsyn,1) // update hub dvi
    for from=0,CTYPi-1 if(col.numc[from] && col.div[from][ct] && (!skipI || !ice(from))) {
      cursz=szorig=vcsz.x(from) // update convergence
      {lim=mhlim.x(from,ct) changed=1}
      if(vrb) print "\torig conv <- ", CTYP.o(from).s, " = " , szorig
      while(cursz<lim && changed==1) { changed=0
        for(preid=col.ix[from];preid<=col.ixe[from]&&cursz<lim;preid+=1) {
          if(preid==hubid || vin.x(preid)) continue // don't make self or double-connects
          ce.o(preid).getdvi(vdt,vddt,vw1,vw2,vprob,vsynt)
          for jdx=0,vdt.size-1{
            poid = vdt.x(jdx)
            if(vpicked.x(poid)) continue // don't take wires from other hubs            
            if(ce.o(poid).type==ct){ ce.o(poid).getconv(1.2,vtmp)
              if(allowz || vtmp.x(from)>1) { // make sure not to remove all inputs of a type to a cell
                vdt.x( jdx ) = hubid // reassign input to hub
                ce.o(preid).setdvi(vdt,vddt,vsynt,1) // reset presynaptic cell's div
                vin.x( preid ) = changed = 1 // mark input
                cursz += 1
                break
              }
            }
          }
        }
      }
      if(vrb) print "\tnew conv <- " , CTYP.o(from).s, " = " , cursz
    }    
  }
  ce.o(0).finishdvir()
  {dealloc(a) return vhubid}
}

//* mkcolnqs - make an nqs with current pmat,wmat,delm,deld info for use by both COLUMNs(AREAS) for wiring
// "dist" represents distance between columns: dist==0 for intra-COLUMN setup, dist>0 for INTER-COLUMN setup
proc mkcolnqs () { local from,to,sy,i,j,d localobj froms,tos,sys
  for i=0,numcols-1 {
    {nqsdel(colnq[i]) colnq[i]=new NQS("froms","tos","sys","from","to","sy","w","pij","delm","deld","loc","dist")}
    colnq[i].strdec("froms","tos","sys")
    d=0 //intracol
    for from=0,CTYPi-1 { froms=CTYP.o(from)
      for to=0,CTYPi-1 { tos=CTYP.o(to)
        if(pmat[i][i][from][to]>0) for sy=0,STYPi-1 if(wmat[i][i][from][to][sy]>0) { sys=STYP.o(sy)
          colnq[i].append(froms.s,tos.s,sys.s,from,to,sy,wmat[i][i][from][to][sy],pmat[i][i][from][to],delm[i][i][from][to],deld[i][i][from][to],synloc[from][to],d)
        }
      }
    }
    for j=0,numcols-1 if(i!=j) { d=1 //intercol
      for from=0,CTYPi-1 { froms=CTYP.o(from)
        for to=0,CTYPi-1 { tos=CTYP.o(to)
          if(pmat[i][j][from][to]>0) for sy=0,STYPi-1 if(wmat[i][j][from][to][sy]>0) { sys=STYP.o(sy)
            colnq[i].append(froms.s,tos.s,sys.s,from,to,sy,wmat[i][j][from][to][sy],pmat[i][j][from][to],delm[i][j][from][to],deld[i][j][from][to],synloc[from][to],d)
          }
        }
      }
    }
  }
}

//** swirecut (col,EEsq,EIsq,IEsq,IIsq[,seed,slambda]) - spatial wiring: wires the column using pmat and cell positions
//                   (wiring probability effected by distance btwn cells)
// seed is random # seed
// lambda specifies length-constant for spatially-dependent fall-off in wiring probability
// at one lambda away, probability of connect is value in pmat
proc swirecut () { local x,y,z,ii,jj,a,del,prid,poid,prty,poty,dv,lseed,h,prob,slambda,dsq,dist,slambdasq,\
                  EEsq,EIsq,IEsq,IIsq,ic1,ic2,pdx\
               localobj col,ce,vidx,vdel,vdist,vwt1,vwt2,vtmp,opr,opo,st,rdm,vprob
  a=allocvecs(vidx,vdel,vtmp,vdist,vwt1,vwt2,vprob) z=0
  col=$o1 ce=col.ce EEsq=$2 EIsq=$3 IEsq=$4 IIsq=$5
  if (argtype(6)==0) lseed=$6 else lseed=1234  
  if(numarg()>6) slambda=$7 else slambda=10
  if(slambda<=0){
    printf("swirecut WARN: invalid slambda=%g, setting slambda to %g\n",colside/3)
    slambda=colside/3
  }
  slambdasq = slambda^2 // using squared distance
  vrsz(1e4,vidx,vdel,vdist,vtmp)
  rdm=new Random() rdm.ACG(lseed) // initdivrnd(lseed)//initialize random # generator
  rdm.uniform(0,1) vprob.resize(ce.count^2) vprob.setrand(rdm) pdx=0
  // Create the connectivity NQS table.
  if(col.mknetnqss) {nqsdel(col.connsnq) col.connsnq=new NQS("id1","id2","del","dist","wt1","wt2")}
  for y=0,ce.count-1 { opr=ce.o(y)
    vrsz(0,vidx,vdel,vdist,vwt1,vwt2)
    prid=opr.id prty=opr.type ic1=ice(opr.type)
    for poty=0,CTYPi-1 if (col.numc[poty]!=0 && (h=col.pmat[prty][poty])>0) {
      for poid=col.ix[poty],col.ixe[poty] if(prid!=poid) { // go thru postsynaptic cells
        opo = ce.o(poid) ic2=ice(ce.o(poid).type)
        dx = opr.xloc - opo.xloc
        dy = opr.yloc - opo.yloc
        dsq = dx^2 + dy^2        
        if(ic1 && ic2 && dsq > IIsq) { // check max dists
          continue
        } else if(!ic1 && !ic2 && dsq > EEsq) {
          continue
        } else if(!ic1 && ic2 && dsq > EIsq) {
          continue
        } else if(ic1 && !ic2 && dsq > IEsq) continue
        if(dsq <= slambdasq) {
          prob=h
        } else {
          prob = h * exp(1 - sqrt(dsq)/slambda) // probability of connect
          // print slambda,dx,dy,dsq,h,prob
        }
        if( prob >= vprob.x(pdx) ) { // rdm.uniform(0,1)
          del = rdm.uniform(col.delm[prty][poty]-col.deld[prty][poty],col.delm[prty][poty]+col.deld[prty][poty])
          {vidx.append(poid)          vdel.append(del)}
          if(synloc[prty][poty]==DEND) vdist.append(1) else vdist.append(0)
          if(col.mknetnqss || wsetting_INTF6==1) {
            if(col.syty1[prty][poty]>=0) vwt1.append(col.wmat[prty][poty][col.syty1[prty][poty]]) else vwt1.append(0)
            if(col.syty2[prty][poty]>=0) vwt2.append(col.wmat[prty][poty][col.syty2[prty][poty]]) else vwt2.append(0)
          }
        }
        pdx += 1
      }
    }
    if(vidx.size>0) {
      if(wsetting_INTF6==1) opr.setdvi(vidx,vdel,vdist,1,vwt1,vwt2) else opr.setdvi(vidx,vdel,vdist,1)
      if(col.mknetnqss) {
        for ii=0,vidx.size-1 col.connsnq.append(prid,vidx.x(ii),vdel.x(ii),vdist.x(ii),vwt1.x(ii),vwt2.x(ii))
      }
    }
  }
  dealloc(a)
  if(verbose) printf("\n")
}

//* conprob
func conprob () { // calculate connection probability using global slambda and hval
  if ($1<=slambda) return hval else return hval*exp(1-$1/slambda) // probability of connect
}

//** swirecutfl (col,EEsq,EIsq,IEsq,IIsq[,seed,slambda]) - spatial wiring: wires the column using pmat and cell positions
//                   (wiring probability effected by distance btwn cells)
// seed is random # seed
// slambda specifies length-constant for spatially-dependent fall-off in wiring probability
// at one slambda away, probability of connect is value in pmat
proc swirecutfl () { local x,y,z,ii,jj,a,del,prid,poid,prty,poty,dv,lseed,h,prob,slambda,dsq,dist,slambdasq,\
                  EEsq,EIsq,IEsq,IIsq,ic1,ic2,pdx,n,nn,maxd,rsz\
               localobj col,ce,vidx,vdel,vdist,vwt1,vwt2,vtmp,vpre,opr,opo,st,rdm,vprob,oq,ol,mmaxd
  oq=new NQS("id1","id2","del","dist","wt1","wt2","dist0","prob") oq.verbose=0 ol=new List() mmaxd=new Matrix(2,2)
  a=allocvecs(vidx,vdel,vtmp,vdist,vwt1,vwt2,vprob,vpre) z=0
  {ol.append(vpre) ol.append(vidx) ol.append(vdel) ol.append(vdist) ol.append(vwt1) ol.append(vwt2)}
  col=$o1 ce=col.ce EEsq=$2 EIsq=$3 IEsq=$4 IIsq=$5
  if (argtype(6)==0) lseed=$6 else lseed=1234  
  if(numarg()>6) slambda=$7 else slambda=10
  if(slambda<=0){
    printf("swirecut WARN: invalid slambda=%g, setting slambda to %g\n",colside/3)
    slambda=colside/3
  }
  slambdasq = slambda^2 // using squared distance
  vrsz(1e4,vidx,vdel,vdist,vtmp,vpre)
  rdm=new Random() rdm.ACG(lseed) // initdivrnd(lseed)//initialize random # generator
  rdm.uniform(0,1) rsz=ce.count^2 vprob.resize(rsz) vprob.setrand(rdm) pdx=0
  {mmaxd.x(0,0)=sqrt(EEsq) mmaxd.x(0,1)=sqrt(EIsq) mmaxd.x(1,0)=sqrt(IEsq) mmaxd.x(1,1)=sqrt(IIsq)}
  // Create the connectivity NQS table.
  if(col.mknetnqss) {nqsdel(col.connsnq) col.connsnq=new NQS("id1","id2","del","dist","wt1","wt2")}
  for y=0,ce.count-1 { opr=ce.o(y)
    vrsz(0,vidx,vdel,vdist,vwt1,vwt2)
    prid=opr.id prty=opr.type ic1=ice(opr.type)
    for poty=0,CTYPi-1 if (col.numc[poty]!=0 && (h=hval=col.pmat[prty][poty])>0) {
      ic2 = ice(poty)
      oq.clear()
      if ((n=opr.floc(opr.xloc,opr.yloc,1e9,oq.getcol("id2"),oq.getcol("dist"),mmaxd.x(ic1,ic2),poty))==0) {
        if(verbose) printf("swirecutfl: No possibilities for connections found from %d\n",opr.id)
      } else {
        oq.getcol("dist0").copy(oq.getcol("dist"))
        oq.pad(n)
        oq.getcol("dist0").apply("conprob") // turn distances into probabilities
        if (pdx+n>=rsz) { rdm.uniform(0,1) vprob.setrand(rdm) pdx=0 }
        oq.getcol("prob").copy(vprob,pdx,pdx+n-1)  // pick out some random probabilities to compare to
        pdx+=n 
        oq.calc("<dist0>.sub(<prob>)") 
        if ((nn=oq.select("dist0",">",0,"id2","!=",prid))==0) { // looks for dist_prob > prob
          if(verbose) printf("swirecutfl: No connections found from %d out of %d assayed\n",opr.id,n)
        } else {
          oq.cpout()
          //oq.fill("id1",prid)
          rdm.uniform(col.delm[prty][poty]-col.deld[prty][poty],col.delm[prty][poty]+col.deld[prty][poty])
          oq.getcol("del").setrand(rdm)
          if (col.syty1[prty][poty]>=0) oq.getcol("wt1").fill(col.wmat[prty][poty][col.syty1[prty][poty]]) else oq.getcol("wt1").fill(0)
          if (col.syty2[prty][poty]>=0) oq.getcol("wt2").fill(col.wmat[prty][poty][col.syty2[prty][poty]]) else oq.getcol("wt2").fill(0)
          {vwt1.append(oq.getcol("wt1")) vwt2.append(oq.getcol("wt2"))}
          {vidx.append(oq.getcol("id2")) vdel.append(oq.getcol("del"))}
          vdist.resize(vdist.size+nn)
          if(synloc[prty][poty]==DEND) vdist.fill(1,vdist.size-nn,vdist.size-1) else vdist.fill(0,vdist.size-nn,vdist.size-1)
        }
      }
    }
    if(vidx.size>0) {
      if(wsetting_INTF6==1) opr.setdvi(vidx,vdel,vdist,1,vwt1,vwt2) else opr.setdvi(vidx,vdel,vdist,1)
      if(col.mknetnqss){vpre.resize(vidx.size) vpre.fill(prid) col.connsnq.append(ol)}
//        for ii=0,vidx.size-1 col.connsnq.append(prid,vidx.x(ii),vdel.x(ii),vdist.x(ii),vwt1.x(ii),vwt2.x(ii))
    }
  }
  col.ce.o(0).finishdvir()
  dealloc(a)
  nqsdel(oq)
  if(verbose) printf("\n")
}

//* swireDPs(seed,slambda,) - wire the DP (muscle proprioceptive) cells - they're only in COLUMN[0] (sensory)
proc swireDPs () { local x,y,z,ii,jj,a,n,del,prid,poid,prty,poty,dv,lseed,prob,dsq,dist,ic1,ic2,pdx,rsz,cdx\
                  localobj cl,lce,vidx,vdel,vdend,vwt1,vwt2,vprob,vtmp,opr,opo,st,nc,oq,ol,rdm,vpoty
            //prid,poid,vdel.x[ii],vdist.x[ii],vwt1.x[ii],vwt2.x[ii]
  oq=new NQS("id1","id2","del","dist","wt1","wt2","dist0","prob") oq.verbose=0
  a=allocvecs(vprob,vpoty) ol=new List() 
  for ii=0,5 ol.append(oq.v[ii]) // will use ol for the appends
  vidx=oq.getcol("id1") // vdel,vdend,vwt1,vwt2,vtmp,vprob
  cdx=0
  cl=col[cdx] lce=cl.ce
  if (argtype(1)==0) lseed=$1 else lseed=1234  
  if(argtype(2)==0) slambda=$2 else slambda=10
  if(slambda<=0){slambda=colside/3 printf("swireDPs WARN: invalid lambda=%g, setting lambda to %g\n",slambda)}
  rdm=new Random() rdm.ACG(lseed) // initdivrnd(lseed)//initialize random # generator
  rdm.uniform(0,1) vprob.resize(rsz=lce.count^2) vprob.setrand(rdm) pdx=0
  vpoty.append(ES)
  //** wire in the DPs
  prty=DP
  for vtr(&poty,vpoty) {
    hval=pmat[cdx][cdx][prty][poty] 
    for ltr(opr,cedp,&ii) { prid=opr.id
      oq.clear()
      if ((n=col[cdx].ce.o(0).floc(opr.xloc,opr.yloc,1e9,oq.getcol("id2"),oq.getcol("dist"),4*slambda,poty))==0) {
        printf("swireDPs: No possibilities for connections found from %d\n",opr.id)
      } else {
        oq.getcol("dist0").copy(oq.getcol("dist"))
        oq.pad(n)
        oq.getcol("dist0").apply("conprob") // turn distances into probabilities
        if (pdx+n>=rsz) { vprob.setrand(rdm) pdx=0 }
        oq.getcol("prob").copy(vprob,pdx,pdx+n-1)  // pick out some random probabilities to compare to
        pdx+=n 
        oq.calc("<dist0>.sub(<prob>)") 
        if ((nn=oq.select("dist0",">",0))==0) { // looks for dist_prob > prob
          printf("swireDPs: No connections found from %d out of %d assayed\n",opr.id,n)
        } else {
          oq.cpout()
          oq.fill("id1",prid)
          rdm.uniform(cl.delm[prty][poty]-cl.deld[prty][poty],cl.delm[prty][poty]+cl.deld[prty][poty])
          oq.getcol("del").setrand(rdm)
          if (cl.syty1[prty][poty]>=0) oq.getcol("wt1").fill(cl.wmat[prty][poty][cl.syty1[prty][poty]]) else oq.getcol("wt1").fill(0)
          if (cl.syty2[prty][poty]>=0) oq.getcol("wt2").fill(cl.wmat[prty][poty][cl.syty2[prty][poty]]) else oq.getcol("wt2").fill(0)
          if (cl.mknetnqss) cl.connsnq.append(ol)
          for vtr(&poid,oq.out.getcol("id2"),&jj) {
            ncl.append(nc=new NetCon(opr.drspk,lce.o(poid)))
            nc.delay=oq.getcol("del").x[jj] 
            nc.weight[cl.syty1[prty][poty]]=oq.getcol("wt1").x[jj]
            nc.weight[cl.syty2[prty][poty]]=oq.getcol("wt2").x[jj]
          }
        }
      }
    }
  }
  dealloc(a)
  nqsdel(oq)
}

//* checkerpos(col,rad,xinc,yinc,seed) - arrange cells in checkerboard pattern
proc checkerpos () { local i,j,x,y,csz,xinc,yinc,seed,rad,a localobj col,ce,rdm,xo,nqc
  col=$o1 csz=col.cside rad=$2 xinc=$3 yinc=$4 rdm=new Random()
  if(numarg()>4) seed=$5 else seed=1234 rdm.ACG(seed) ce=col.ce nqc=new NQS("x","y")
  for(y=0;y<csz;y+=yinc) {
    if(y%2==0) {
      for(x=0;x<csz;x+=xinc) nqc.append(x,y)
    } else {
      for(x=xinc/2;x<csz;x+=xinc) nqc.append(x,y)
    }
  }
  if(verbose) {gvmarkflag=1 g.erase nqc.gr("y","x")}
  for ltr(xo,ce,&i) {
    r = rdm.discunif(0,nqc.v.size-1)
    x = nqc.v[0].x(r) + rdm.uniform(-rad,rad)
    y = nqc.v[1].x(r) + rdm.uniform(-rad,rad)
    while(x<0 || y<0 || x>=csz || y>=csz) {
      r = rdm.uniform(0,nqc.v.size-1)
      x = nqc.v[0].x(r) + rdm.uniform(-rad,rad)
      y = nqc.v[1].x(r) + rdm.uniform(-rad,rad)
    }
    {xo.xloc=x xo.yloc=y}
    if(col.cellsnq!=nil) {col.cellsnq.v[5].x(i)=xo.xloc col.cellsnq.v[6].x(i)=xo.yloc}
  }
  nqsdel(nqc)
}

//* mkcols - make the COLUMNs
proc mkcols () { local id,x,y,seed,svnum localobj nq
  id=nextGID_INTF6=0
  for y=0,colH-1 for x=0,colW-1 {
    if(dbgcols)seed=dvseed else seed=(id+1)*dvseed
    svnum=vcpercol[id].x[DP] vcpercol[id].x[DP]=0 // ==== REMOVE DPs so can create separately ====
    lcol.append(gcol[y][x]=new COLUMN(id,vcpercol[id],colnq[id],seed,x,y,setdviPT,mknetnqss,1))
    print "made COLUMN, wiring"
    // vcpercol[id].x[DP]=svnum // replace
    col[id]=gcol[y][x]
    col[id].verbose=verbose_INTF6
    nextGID_INTF6 += cpercol[0][DP] // inc by # of DPs
    if(strlen(wnqstr)>0 && id==1) { // wire from NQS
      nq=new NQS(wnqstr)
      col[id].wirenq(nq)
      nqsdel(nq)
    } else if(swire>0) { // spatial-wiring
      col[id].setcellpos(vlayerz,layerzvar,pseed*(id+1),colside)
      if(checkers) checkerpos(col[id],crad,cxinc,cyinc,pseed*(id+1))
      if(swire==1) {
        col[id].swire(col[id].wseed,maxsfall)
      } else if(swire==2) {
        swirecut(col[id],EEsq,EIsq,IEsq,IIsq,col[id].wseed,slambda)
      } else if(swire==3) {
        swirecutfl(col[id],EEsq,EIsq,IEsq,IIsq,col[id].wseed,slambda) // uses intf6::floc for speedup
      }
    } else col[id].wire(col[id].wseed) // random wiring (no spatial dependence)
    id+=1
  }
}

//** mkDPs() create and locate the Stimulators -- these are DRSPK cells rather than INTF6
proc mkDPs () { local ii,x,y,c,ndp,suty,rw,cl,rs,cs,pad,cdx localobj cellsnq,xo,rdm,ce
  cdx=0
  ndp=col[cdx].numc[DP]=cpercol[cdx][DP] // will be outside of col now
  col[cdx].ix[DP]=col[cdx].allcells col[cdx].ixe[DP]=col[cdx].allcells+ndp-1
  ce=col[cdx].ce gid=0 rs=2 cs=2 // 2 rows and 2 columns
  for ii=0,col[cdx].numc[DP]-1 cedp.append(new DPC()) // create the DPs
  rdm=new Random() rdm.ACG(pseed+DP)
  pad=colside/cs/8
  if (col[cdx].cellsnq==nil) c=-1 else { 
    cellsnq=col[cdx].cellsnq cellsnq.tog("DB") c=cellsnq.fi("xloc") 
    gid=cellsnq.applf(".max","gid")+1
    if(gid!=col[cdx].ix[DP]) {printf("mkDPS ERRA %d\n",gid) return }
  }
  if (gid==0) gid=col[cdx].ix[DP]
  //** assign DP identity
  for ltr(xo,cedp,&ii) { 
    xo.id=gid xo.type=DP suty=xo.subtype=int(xo.id%NMUSCLES) // which muscle it belongs to
    rw=int(suty/cs) cl=suty%cs  // xloc,yloc
    // print suty,rw,cl,cl*colside/cs,(cl+1)*colside/cs,rw*colside/cs,(rw+1)*colside/rs
    if(sepDPpos) { // each set of DP cells is spatially separated
      xo.xloc=x=rdm.uniform(cl*colside/cs+pad,(cl+1)*colside/cs-pad)
      xo.yloc=y=rdm.uniform(rw*colside/rs+pad,(rw+1)*colside/rs-pad)
    } else { // dont segregate DP cells 
      xo.xloc=x=rdm.uniform(0,colside)
      xo.yloc=y=rdm.uniform(0,colside)
    }
    xo.zloc=z=suty
    ce.o(col[cdx].ix[ES]+ii).zloc=ce.o(col[cdx].ix[EM]+ii).zloc=z//same group
    // add DPs to NQS; gid(0) id(1) col(2) ty(3) ice(4) xloc(5) yloc(6) zloc(7)
                              // gid id col   ty   ice x,y,z
    if(c!=-1) col[cdx].cellsnq.append(gid,xo.id,0,xo.type,0,x,y,suty) // use zloc to store muscle # 
    gid+=1
  }
}

//* wirecols - setup inter-COLUMN connectivity with NetCon
proc wirecols () { local i,j
  if(numcols==1) return
  for case(&i,0,1) if(EEGainInterC[i] || EIGainInterC[i]) {
    j = 1 - i
    gcol[0][i].wire2col(gcol[0][j],colnq[i],1,ncl) // unidirectional wiring
  }
}

//* intercoloff(c0,c1) - turn off all weights between COLUMNs
proc intercoloff () { local i,c0,c1 localobj xo
  c0=$1 c1=$2
  for ltr(xo,ncl) if(isojt(xo.pre,col.ce.o(0)) && isojt(xo.syn,col.ce.o(0))) {
    if(xo.pre.col!=c0 || xo.syn.col!=c1) continue
    for i=0,6 xo.weight(i)=0
  }
}

//* intercolmul(c0,c1,from,to,sy,w)
proc intercolsyw () { local c0,c1,from,to,sy,w localobj xo
  c0=$1 c1=$2 from=$3 to=$4 sy=$5 w=$6
  for ltr(xo,ncl) if(isojt(xo.pre,col.ce.o(0)) && isojt(xo.syn,col.ce.o(0))) {
    if(xo.pre.col!=c0 || xo.syn.col!=c1) continue
    if(xo.pre.type==from && xo.syn.type==to) xo.weight(sy)=w
  }
}

//** drdp() DP locations
proc drdp () { local cdx localobj nq
  nq=col[0].cellsnq gvmarkflag=1 ge(0)
  nq.marksym="o"
  for ii=0,5 if (nq.select("ty",DP,"zloc",ii)) nq.gr("yloc","xloc",0,ii+1,8)
}

//* drcelllocs - draw location of cells
proc drcelllocs () { local i,gvt,ty
  gvt=gvmarkflag
  {gvmarkflag=1 col[CDX].cellsnq.marksym="O"}
  if(numarg()>0) {
    if(col[CDX].cellsnq.select("ty",$1)) col[CDX].cellsnq.gr("yloc","xloc",0,1,3)
  } else for i=0,1 if(col[CDX].cellsnq.select("ice",i)) col[CDX].cellsnq.gr("yloc","xloc",0,i+2,3)
  gvmarkflag=gvt
}

//* drcelldiv(cellid[,skipI,skipE]) - draw outputs from a cell
proc drcelldiv () { local id1,id2,x1,y1,x2,y2,ic1,ic2,clr1,clr2,gvt,skipI,skipE localobj cnq,nq
  gvt=gvmarkflag gvmarkflag=1
  cnq=col[CDX].connsnq
  nq=col[CDX].cellsnq
  id1=$1 nq.verbose=0
  if(!nq.select(-1,"id",id1)) return
  if(numarg()>1) skipI=$2 else skipI=0
  if(numarg()>2) skipE=$3 else skipE=0
  x1=nq.v[5].x(nq.ind.x(0))
  y1=nq.v[6].x(nq.ind.x(0))
  ic1=nq.v[4].x(nq.ind.x(0))
  if(ic1) clr1=3 else clr1=2
  nq.select("id",id1)
  nq.gr("yloc","xloc",0,clr1,15)
  cnq.select(-1,"id1",id1)
  cnq.verbose=0
  for vtr(&i,cnq.ind) {
    id2 = cnq.v[1].x(i)
    if(nq.select("id",id2)) {
      x2=nq.fetch("xloc")
      y2=nq.fetch("yloc")
      ic2=nq.fetch("ice")
      if(ic2) {
        clr2=3
        if(skipI) continue
      } else {
        clr2=2
        if(skipE) continue
      }
      nq.gr("yloc","xloc",0,clr2,8)    
      drline(x1,y1,x2,y2,g,clr1,7)
    }
  }
  cnq.verbose=nq.verbose=1
  gvmarkflag=gvt
}

//* drcellconv(cellid) - draw inputs to a cell
proc drcellconv () { local id1,id2,x1,y1,x2,y2,ic1,ic2,clr1,clr2,gvt localobj cnq,nq
  gvt=gvmarkflag gvmarkflag=1
  cnq=col[CDX].connsnq
  nq=col[CDX].cellsnq
  id2=$1 nq.verbose=0
  nq.select(-1,"id",id2)
  x2=nq.v[5].x(nq.ind.x(0))
  y2=nq.v[6].x(nq.ind.x(0))
  ic2=nq.v[4].x(nq.ind.x(0))
  if(ic2) clr2=3 else clr2=2
  nq.select("id",id2)
  nq.gr("yloc","xloc",0,clr2,15)
  cnq.select(-1,"id2",id2) 
  cnq.verbose=0
  for vtr(&i,cnq.ind) {
    id1 = cnq.v[0].x(i)
    if(nq.select("id",id1)) {
      x1=nq.fetch("xloc")
      y1=nq.fetch("yloc")
      ic1=nq.fetch("ice")
      if(ic1) clr1=3 else clr1=2
      nq.gr("yloc","xloc",0,clr1,8)    
      drline(x1,y1,x2,y2,g,clr1,7)
    }
  }
  cnq.verbose=nq.verbose=1
  gvmarkflag=gvt
}

//* mkwgnq() - return nqs with intracolumnar weight info
obfunc mkwgnq () { local a,i,j,id1,id2,wg,ic,ty1,ty2,wt1,wt2,del,dist,c\
                localobj mycel,vwt1,vwt2,myv,myv1,myv2,myv3,myv4,myv5,myv6,wgnq,col
  a=allocvecs(vwt1,vwt2,myv,myv1,myv2,myv3,myv4,myv5,myv6) 
  {nqsdel(wgnq) wgnq=new NQS("col","id1","id2","wg","ice","ty1","ty2","wt1","wt2","del","dist")}
  for ltr(col,lcol,&c) for i=0,col.allcells-1 {
    mycel=col.ce.o(i)
    mycel.getdvi(myv,myv1,myv2,myv3,myv4,myv5,myv6)
    id1=i
    ic=ice(mycel.type)
    ty1=mycel.type
    vrsz(mycel.getdvi,vwt1,vwt2)
    if(wsetting_INTF6==1) {
      mycel.getsywv(vwt1,vwt2)
    } else {
      vwt1.copy(myv3)
      vwt2.copy(myv4)
    }
    for j=0,myv6.size-1 {
      id2=myv.x(j)
      ty2=col.ce.o(id2).type
      wg = myv6.x(j)
      wt1 = wg * vwt1.x(j)
      if(ic) wt2 = vwt2.x(j) else wt2 = wg * vwt2.x(j)
      del = myv1.x(j)
      dist = myv5.x(j)
      wgnq.append(c,id1,id2,wg,ic,ty1,ty2,wt1,wt2,del,dist)
    }
  }
  dealloc(a)
  return wgnq
}

//* function calls to setup network

//** z location of each layer in microns
mkvlayerz()

//** # of cells per column
setcpercol() 

//** setup pmat
if(name_declared("nqpmat")==2) { // read pmat from NQS if available, else set to default
  if(nqpmat!=nil) nq2pmat(nqpmat) else setpmat()
} else setpmat()
if(pmatscale!=1) scalepmat(pmatscale)

//** setup synapse locations,delays,wmat
setsynloc()
setdelmats()
setwmat() // new KMJ version
if(wmatscale!=1) scalewmat(wmatscale)

scrsz=50*1e3
double scr[scrsz]

//** make cells, columns, wire columns
{mkcolnqs() printf("finished mkcolnqs\n")}
{mkcols() printf("finished mkcols\n")}
wirecols(1) // only 1 col at present
{mkDPs() printf("finished mkDPs\n")}
{swireDPs(col[0].wseed,lambda) printf("finished swireDPs\n")}