distres = 5
objref postcellgids
speed = 1
strdef precellType_string, postcellType_string
proc makeConnections () {local precellType, distres, postcellType, precellStart, precellEnd, postcellStart, postcellEnd, i, j, r
// Attempt to connect all cells of each pre and post type
install_repeatconn()
for j = 0, numCellTypes-1 {
if (cellType[j].is_art()==0) { // ppstim cells are never the post synaptic cell in a connection, so exclude here
postcellType_string = cellType[j].cellType_string // Load cell type string used to grab connection-specific properties later
numpost = cellType[j].numThisHost
postcellgids = new Vector(numpost)
for r=0, numpost-1 {
postcellgids.x[r] = cellType[j].CellList[r].gid
}
newhighindex = 1+RandomSeedsConn
for i = 0, numCellTypes-1 {
//if (cellType[i].is_art()==0) {
precellType_string = cellType[i].cellType_string // Load cell type string used to grab connection-specific properties later
//print "precellType_string: ", precellType_string, " -> postcellType_string: ", postcellType_string
cellType[i].numCons.x[j]=connectCells (i, j, precellType_string, postcellType_string)
//}
}
cellType[j].LastHighIndex = newhighindex
}
}
if ((PrintTerminal>0)) {print "Host ", pc.id, " connected cells."}
}
objref params, conns2make
objref randnum, synRand
func connectCells () {local r, syn, distance, counter, precellType, postcellType, j, randSynNumber, pre_zpos, post_zpos , pre_xpos, post_xpos, pre_ypos, post_ypos, numSynTypes localobj cell
// Args: precellType, postcellType, precellType_string, postcellType_string
precellType = $1
postcellType = $2
counter=0
synWeight = cellType[$1].wgtConns.x[$2]
numSyns = cellType[$1].numSyns.x[$2]
numConns = cellType[$1].numConns.x[$2]
numConns = int(numConns/(Scale) + .5) // higher connectivity in smaller scale models
//getSynapseData($s3, $s4) // Given the pre and post cell types, look up the weight, delay,
// and probability of connection between these two types
if (PrintTerminal>1) {print "Host ", pc.id, " is connecting: ", $s3, "s to ", $s4, "s."}
//print "Host ", pc.id, " is connecting: ", $s3, "s to ", $s4, "s: numpost = ", numpost, ", numConns=", numConns
//if (numConns != 0 && synWeight != 0 && numpost !=0) {
if (numConns != 0 && numpost !=0) {
params = new Vector(27)
if (cellType[postcellType].numCells>=pc.nhost) {
connlength = int((numConns)/cellType[postcellType].numCells+.5)*int(cellType[postcellType].numCells/pc.nhost+1.5)+cellType[postcellType].numCells
} else {
connlength = int((numConns)/cellType[postcellType].numCells+.5)+cellType[postcellType].numCells
}
conns2make = new Vector(1+connlength*6)
params.x[0]=cellType[precellType].cellStartGid //gmin -- start gid of pre cell type
params.x[1]=cellType[precellType].cellEndGid //gmax -- end gid of pre cell type
params.x[2]= numConns/cellType[postcellType].numCells //nconn
params.x[3]= cellType[postcellType].numCells // number of cells of the postsynaptic type (total)
params.x[4]= numpost // number of cells of the postsynaptic type with gids on this computer
//print "gonna make ", params.x[2], " conns from ", $s3, "s to ", $s4, "s (", numpost, ")"
params.x[5]= sqrt(LongitudinalLength^2 + LayerVector.sum()^2 + TransverseLength^2)
//100 //maxd - the distance of the dimension for which the fit equation was designed (should add all three...), in um
// this also confusing because, right now, the equation calculates the overall distance (through all dimensions).
// If per dimension, should compare to distance in that dimension only
params.x[6]= distres //5 //steps - resolution of the fit , in number of steps to take
params.x[7]= cellType[precellType].dist.x[0] //a in the Gaussian fit // 5, .001, 30
params.x[8]= cellType[precellType].dist.x[1] //b in the Gaussian fit
params.x[9]= cellType[precellType].dist.x[2] //c in the Gaussian fit
params.x[10]= cellType[precellType].dentateXBins
params.x[11]= cellType[precellType].dentateYBins
params.x[12]= cellType[precellType].dentateZBins
params.x[13]= cellType[precellType].dentateXBinSize
params.x[14]= cellType[precellType].dentateYBinSize
params.x[15]= cellType[precellType].dentateZBinSize
addheight = 0
if (cellType[precellType].layerflag>0) {addheight=LayerVector.sum(0,cellType[precellType].layerflag-1)}
params.x[16]= addheight
params.x[17]= cellType[postcellType].dentateXBins
params.x[18]= cellType[postcellType].dentateYBins
params.x[19]= cellType[postcellType].dentateZBins
params.x[20]= cellType[postcellType].dentateXBinSize
params.x[21]= cellType[postcellType].dentateYBinSize
params.x[22]= cellType[postcellType].dentateZBinSize
addheight = 0
if (cellType[postcellType].layerflag>0) {addheight=LayerVector.sum(0,cellType[postcellType].layerflag-1)}
params.x[23]= addheight
params.x[24]= cellType[postcellType].cellStartGid
params.x[25]= newhighindex
params.x[26]= connlength
conns2make.repeatconn(params, postcellgids)
//print "host ", pc.id, " makes ", params.x[2], " conns from ", $s3, " to ", params.x[3], " ", $s4, " cells (connlength=", connlength, "), conns2make=", conns2make.x[0]
//newhighindex = newhighindex + cellType[precellType].numCells
newhighindex = newhighindex + int(conns2make.x[1]/1)+1
for r=1, int(conns2make.x[0]/1) {
if (pc.gid_exists(conns2make.x[r+1+connlength])) {
cell = pc.gid2cell(conns2make.x[r+1+connlength])
numSynTypes = cell.pre_list.o(precellType).count()
if (numSynTypes > 0) {
ransynlist.object(cell.randi).r.discunif(0,numSynTypes-1) // Create a uniform random INTEGER variable over the range specified (0 to # synapse types-1),
for s=1,numSyns {
randSynNumber = ransynlist.object(cell.randi).repick // Randomly pick a synapse type from the available synapse types
conDelay = 3 //sqrt(conns2make.x[r+2*connlength]/distres)*LongitudinalLength*speed+.1
//print $s3, "s to ", $s4, "s: nc_append ", s, "/", numSyns, " syns, ", r, "/", int(conns2make.x[0]/1), " conns, weight: ", synWeight
nc_append(conns2make.x[r+1], conns2make.x[r+1+connlength], precellType, randSynNumber, synWeight + (conns2make.x[r+1]+1)*1000, conDelay) // Make the connection // the latter part is for tracing the big bug, used by exp2sid mech (it will take away this extra part)
}
//if (conns2make.x[r+1+connlength]==5524) {print "pre ", $s3, ", gid ", conns2make.x[r+1], ", syn ", randSynNumber, ", wgt ", synWeight*numSyns}
counter +=1
}
} else {
print $s3, "s to ", $s4, "s:", " can't make gid ", conns2make.x[r+1+connlength], " which is r = ", r, " + connlength = ", connlength, " = ", r+1+connlength, " from x[r+1] = ", conns2make.x[r+1], " total conns = ", int(conns2make.x[0]/1)
}
}
}
return counter
}
objref f2
proc getSynapseData () { // Args: precelltype name, postcelltype name
strdef tempString
f2 = new File()
// Somehow, the program has switched the current directory to setupfiles (not sure where) so must get out of it
sprint(tempString,"../connections/%s.%s",$s1,$s2) // Get the file that specifies connection properties between these two cell types
f2.ropen(tempString)
if (f2.isopen) {
synWeight = f2.scanvar
numConns = f2.scanvar
numConns = int(numConns/(Scale)) // higher connectivity in smaller scale models
} else {
synWeight = 0
numConns = 0
}
if ((strcmp($s1,"granulecell")==0) && (strcmp($s2,"granulecell")==0)) {synProb = synProb * PercentAxonSprouting/100}
} // Reduce the probability of granule cell connection by the same degree as the sclerosis
// because mossy fibers connecting back to granule cells are subject to sclerosis (?)
makeConnections() // Try making connections between every type of cell
objref conns2make
//zzz = mallinfo(zzz, "objref conns2make")
//q()