distri_synapse.hoc

/* assumes
1. sections to be innervated have been appended to a SectionList called seclist
2. synaptic density is in units of number/(length in um)
3. geometry specification has been completed, including spatial discretization
4. total number of synapses to distribute is called NUMSYN
*/

////////use: aSynapseList = distSyns(numberOfSynapses,listOfSections,randomseed)
obfunc distSyns() { local NUMSYN,seedl localobj mvec,nvec,synlist,r

numsegs = 0 // will be total number of segments
forsec $o2 {numsegs+=nseg}
//objref mvec
mvec = new Vector(numsegs) // will hold cumulative sums of segment length
// each element in mvec corresponds to a segment in seclist

ii = 0 // to iterate over mvec
mtotal = 0 // will be total length in seclist
forsec $o2 {
  for (x,0) { // iterate over internal nodes of current section
    mtotal += L/nseg // or area(x) if density is in (number)/area
    mvec.x[ii] = mtotal
    ii += 1
  }
}
/*
now mvec.x[ii] is the sum of segment lengths (or areas)
for all segments up to and including segment ii
*/

//objref nvec
nvec = new Vector(numsegs, 0) // fill elements with 0
// each element in nvec corresponds to a segment in seclist
// when done, each element will hold the number of synaptic mechanisms
// that are to be attached to the corresponding segment
seedl = $3
 r = new Random(seedl)
 r.uniform(0,mtotal)
 
 NUMSYN = $1
for ii=1,NUMSYN {
  x = r.repick() //value drawn from uniform distribution over [0,mtotal]
  jj = mvec.indwhere(">=", x) // the first element in mvec that is >=x 
  // this is the index of the segment that should get the synapse
  nvec.x[jj] += 1
}

//objref synlist
synlist = new List()
ii = 0
forsec $o2 {
  for (x, 0) {
    num = nvec.x[ii]
    if (num>0) {
      for jj=1,num {print x, secname() synlist.append(new syn2(x))}
      // to keep this entirely generic
      // defer param specification until later
    }
    ii += 1 // we're moving on to the next segment,
      // so move on to the next element of nvec
  }
}
    return synlist
}