begintemplate CellCategoryInfo // Define a template that describes
// a class of celltype objects,
// where each celltype object
// holds type-specific parameters
// used in creating the network model
public setCellTypeParams, setCellTypeDist // Define variables and funcs that are
public cellType_string, technicalType, cellStartGid, cellEndGid // accessible from outside the class
public updateGidRange, addPosVec, layerflag, LastHighIndex // object
public dist, numCells, CellList, addCell, numCons, numConns, numSyns, wgtConns, numThisHost
public setBins, dentateYBins, dentateXBins, dentateZBins
public dentateYBinSize, dentateXBinSize, dentateZBinSize, is_art
objref dist, cellpos, f1, CellList, numCons, numConns, numSyns, wgtConns, ctype, this // Define objects, including
// 'this', which is this
// instance of the class
strdef cellType_string, technicalType, tempString, cmd, strtomax // Define strings
proc setCellTypeParams(){ // Define a proc to set the parameters
// corresponding to the celltype this
// member of the class describes
cellType_string = $s1 // Name of the cell type
technicalType = $s2
cellStartGid = $3 // First number in gid range (all cells
// of this type have consecutive numbers
// in the gid range)
numCells = $4 // Number of cells of this type
cellEndGid = $3 + $4 -1 // Last number in gid range
layerflag = $5 // Layer in which the somata of this cell type
// are found (order of the layers is a matter
// of convention, documented by YOU)
LastHighIndex = 0
ctype = new StringFunctions() // Create a new StringFunctions object
// for parsing the name of the celltype
is_art=$6 // if the cell type is artificial
objref CellList[numCells] // Create a new CellList for this celltype,
// the length of which equals the number
// of cells
numThisHost = 0
}
proc setCellTypeDist(){ // From a file, read in the constants
// for the Gaussian equation that describes
// the axonal distribution of this celltype
f1 = new File()
dist = new Vector(3) // Define a new vector, dist, which holds
// the constants
sprint(tempString,"../cells/dist_%s.hoc",cellType_string) //Specify file
f1.ropen(tempString) // Open the file
if (f1.isopen()) {
dist.scanf(f1) // Read in the values from the file
} else {
dist.x[0]=1
dist.x[1]=1
dist.x[2]=1
}
f1.close() // Close the file
}
proc updateGidRange() { // Define a proc that updates the range
// of gids used by this celltype. The range
// needs updating if this cell type was
// subject to cell loss (reducing the
// number of cells) or if any celltype
// earlier in the gid sequence was subject
// to cell loss (causing the StartGid to
// be moved earlier)
cellStartGid = $1 // Read in the start gid
cellEndGid = $1 + numCells -1 // Solve for the end gid given the
// number of cells
if (numCells>0) {
objref CellList[numCells] // Create a new CellList for this celltype,
}
}
proc setBins() {local runresult, toohigh, numtomin // Defines the proc setBins,
// which takes the arguments
// for the length of the
// brain region in X, Y, and Z,
// and determines how far apart
// the cells should be in each
// dimension to be evenly spaced
dentateZBins=int((numCells*($3)^2/($2*$1))^(1/3)) // Given the relative length of
// the Z dimension compared to
// the X and Y dimensions, solve
// for how many cells should be
// spaced along the z dimension
if (dentateZBins==0) {dentateZBins=1} // Make sure the Z dimension is at least one
// cell wide
dentateYBins=int(($2/$3)*(numCells*($3)^2/($2*$1))^(1/3)) // Given the relative
// length for Y...
if (dentateYBins==0) {dentateYBins=1} // Make sure the Y dimension is at least one
// cell wide
dentateXBins=int(($1/$3)*(numCells*($3)^2/($2*$1))^(1/3)) // Given the relative
// length for X...
if (dentateXBins==0) {dentateXBins=1} // Make sure the Z dimension is at least one
// cell wide
// The above code may result in there being slightly too few or too many positions
// set aside for cells. To make the final spacing along each dimension most closely,
// match the total number of cells of this type, we may either increase or decrease
// the number of cells assigned along each edge as follows
// Find the largest dimension (which is the ideal dimension to change if the number
// of cell assignments is too large or too small)
if ($3 >= $2 && $3 >= $1) {
strtomax="dentateZBins"
numtomin=dentateXBins*dentateYBins
} else {
if ($2 >= $3 && $2 >= $1) {
strtomax="dentateYBins"
numtomin=dentateXBins*dentateZBins
} else {
strtomax="dentateXBins"
numtomin=dentateYBins*dentateZBins
}
}
while (dentateXBins*dentateYBins*dentateZBins < numCells){ // If not enough cell
// positions are allotted
sprint(cmd, "%s=%s+1",strtomax,strtomax) // Add another slot to
// the largest dimension
runresult=execute1(cmd, this) // This command was written as a string so
// the dimension to increase doesn't have to be hard coded
}
toohigh=dentateXBins*dentateYBins*dentateZBins-numtomin
while (toohigh >= numCells){ // If too many cell positions were allotted
sprint(cmd, "%s=%s-1",strtomax,strtomax)// Remove one from the largest dimension
runresult=execute1(cmd, this) // This command was written as a string so
// the dimension to increase doesn't have to be hard coded
toohigh=dentateXBins*dentateYBins*dentateZBins-numtomin
}
dentateZBinSize = int($3/dentateZBins) // Length of each cell's 'personal space' (along Z dimension) in microns
dentateYBinSize = int($2/dentateYBins) // Length of each cell's 'personal space' (along Y dimension) in microns
dentateXBinSize = int($1/dentateXBins) // Length of each cell's 'personal space' (along X dimension) in microns
}
endtemplate CellCategoryInfo
