import java.io.*;
import java.text.*;
import java.util.*;
import swcparts.*;
import java.math.*;
public class lnded2_0 {
public static void main(String[] args) {
try {
//*****************************************************************************
//***********************Initialize global variables***************************
//*****************************************************************************
double DRconstant = 1;
double TRconstant = 1;
double PDRconstant = 1;
int SomaType = 1; //sets the type tag for soma
double PercentStep = .1;
int RandomSeed = 1;
Random myRand = new Random();
myRand.setSeed(RandomSeed);
//Parameter (.prn) file setable varialbes with default values
int typeToDo = 3; //Type tag to do, default (3) is dendrite/basal dendrite
int nToDo = 10; //number of virt trees to produce for each real one
int Binning = 85; //minimum number of points (TR) in each bin
double MinRad = .15;
boolean Debugging = false;
boolean SWCout = false;
boolean DendroOut = false;
boolean RealDendro = false;
//ratio of virtual to real bifurcations at which explosive growth is said to have occured and further growth is terminated
int explodeRatio = 20;
//Data arays, maximum sizes and subscript variables
int maxInFiles = 100;
int actualInFiles = 0;
int maxBiffLines = 10000;
double realBiffCount = 0;
int maxVirtBifLines = 20000;
int actualBiffLines = 0;
int maxStems = 1000;
int stemCount = 0;
int maxInputLines = 120;
int actualInputLines = 0;
int maxBins = 60;
int actualRDbins = 1;
int actualPLbins = 1;
int actualBObins = 1;
String[] inputLineArray = new String[maxInputLines];
String[] inputFileArray = new String[maxInFiles];
swcparts.SwcNeuron[] Neurons = new swcparts.SwcNeuron[maxInFiles];
swcparts.BiffLine[] BifsArray = new swcparts.BiffLine[maxBiffLines];
////
swcparts.BinnedBiffData[] BOTable = new swcparts.BinnedBiffData[maxBins];
swcparts.BinnedBiffData[] PLTable = new swcparts.BinnedBiffData[maxBins];
swcparts.BinnedBiffData[] RDTable = new swcparts.BinnedBiffData[maxBins];
////
int[] realBifs = new int[maxInFiles]; //real biffs per cell
int[] realTreeBifs = new int[maxStems]; //real bifs per tree
double[] realAsymetryArray = new double[maxStems];
double[] realSurfaceArray = new double[maxStems];
double[] realSurfaceAsymArray = new double[maxStems];
double[] stemRadArray = new double[maxStems];
int stemRadArrayCurveType = 0;
//cell parameter temporary values
double tempDSrad;
double tempDLrad;
//other variables
GammaDist gDist = new GammaDist();
String inFile = ""; //input file name from cmd line
String outFile = ""; //output file prefix from cmd line
double realBiffMean = 0; //computed as total over n trees (not counting biffs of each tree)
int tempBiff;
boolean BifsMismatch = false;
double stemMin = 0;
double stemMax = 0;
double stemMean = 0;
double stemStdev = 0;
double tempStemSum = 0;
double tempStemSqSum = 0;
double RealBifsSum = 0;
double RealBifsSqSum = 0;
double RealBifsMean = 0;
double RealBifsStdev = 0;
int RealBifsMax = 0;
double RealAsymSum = 0;
double RealAsymSqSum = 0;
double RealAsymMean = 0;
double RealAsymStdev = 0;
double RealSurfaceSum = 0;
double RealSurfaceSqSum = 0;
double RealSurfaceMean = 0;
double RealSurfaceStdev = 0;
double RealSurfaceAsymSum = 0;
double RealSurfaceAsymSqSum = 0;
double RealSurfaceAsymMean = 0;
double RealSurfaceAsymStdev = 0;
//set number output style
NumberFormat myFormat = NumberFormat.getInstance();
myFormat.setMinimumIntegerDigits(1);
myFormat.setMaximumFractionDigits(5);
myFormat.setMinimumFractionDigits(5);
//*****************************************************************************
//*****************Parse command line arguments********************************
//*****************************************************************************
//set input and out file names
if (args.length == 2) {
inFile = args[0];
outFile = args[1];
}
//too few or too many command line args
else {
System.out.println("Incorrect command line arguments.");
System.out.println("Format = [input file name], [output file prefix] ");
System.exit(1);
}
//*****************************************************************************
//*****************Open and parse .prn input file******************************
//*****************************************************************************
//open input file
FileInputStream fin = new FileInputStream(inFile);
BufferedInputStream bin = new BufferedInputStream(fin);
//character stream
BufferedReader r = new BufferedReader(new InputStreamReader(bin));
r.mark(1);
//Input comment lines into string array
for (int j = 1; 1 < maxInputLines; j++) {
inputLineArray[j] = new String();
inputLineArray[j] = r.readLine();
if (inputLineArray[j] != null) {
++actualInputLines;
}
else {
break;
}
}
r.close();
//set variables as given in input file
for (int j = 1; j <= actualInputLines; j++) {
if (inputLineArray[j].startsWith("TYPETODO")) {
typeToDo = Integer.parseInt(inputLineArray[ (j + 1)]);
}
if (inputLineArray[j].startsWith("NTODO")) {
nToDo = Integer.parseInt(inputLineArray[ (j + 1)]);
}
if (inputLineArray[j].startsWith("BINNING")) {
Binning = Integer.parseInt(inputLineArray[ (j + 1)]);
}
if (inputLineArray[j].startsWith("SEED")) {
RandomSeed = Integer.parseInt(inputLineArray[ (j + 1)]);
}
if (inputLineArray[j].startsWith("MINRAD")) {
MinRad = Double.parseDouble(inputLineArray[ (j + 1)]);
}
if (inputLineArray[j].startsWith("PERCENTSTEP")) {
PercentStep = Double.parseDouble(inputLineArray[ (j + 1)]);
}
if (inputLineArray[j].startsWith("DEBUGGING")) {
if (inputLineArray[ (j + 1)].startsWith("TRUE")) {
Debugging = true;
}
else if (inputLineArray[ (j + 1)].startsWith("FALSE")) {
Debugging = false;
}
else {
System.out.println(
"ERROR: Unrecognized value given for DEBUGGING. Only TRUE and FALSE accepted. Default value of " +
Debugging + " used.");
}
}
if (inputLineArray[j].startsWith("DENDRO")) {
if (inputLineArray[ (j + 1)].startsWith("TRUE")) {
DendroOut = true;
}
else if (inputLineArray[ (j + 1)].startsWith("FALSE")) {
DendroOut = false;
}
else {
System.out.println(
"ERROR: Unrecognized value given for DENDRO. Only TRUE and FALSE accepted. Default value of " +
Debugging + " used.");
}
}
if (inputLineArray[j].startsWith("REALDENDRO")) {
if (inputLineArray[ (j + 1)].startsWith("TRUE")) {
RealDendro = true;
}
else if (inputLineArray[ (j + 1)].startsWith("FALSE")) {
RealDendro = false;
}
else {
System.out.println(
"ERROR: Unrecognized value given for REALDENDRO. Only TRUE and FALSE accepted. Default value of " +
Debugging + " used.");
}
}
if (inputLineArray[j].startsWith("SWCOUT")) {
if (inputLineArray[ (j + 1)].startsWith("TRUE")) {
SWCout = true;
}
else if (inputLineArray[ (j + 1)].startsWith("FALSE")) {
SWCout = false;
}
else {
System.out.println(
"ERROR: Unrecognized value given for SWCOUT. Only TRUE and FALSE accepted. Default value of " +
SWCout + " used.");
}
}
if (inputLineArray[j].startsWith("INPUT")) {
actualInFiles = Integer.parseInt(inputLineArray[ (j + 1)]);
// System.out.println("infiles = " + actualInFiles);
if (actualInFiles > maxInFiles) {
System.out.println("Too many input files given. Only first " +
maxInFiles + " will be used.");
actualInFiles = maxInFiles;
}
if ( (actualInFiles + j + 2) > actualInputLines) {
System.out.println("Input File Error. Not enought input files given.");
System.exit( -1);
}
int infilecount = 0;
for (int k = j + 2; k <= j + actualInFiles + 2; k++) {
++infilecount;
inputFileArray[infilecount] = new String(inputLineArray[k]);
}
}
}
//*****************************************************************************
//***********************open and process SWC files****************************
//*****************************************************************************
//initialize output streams ****************************************************
//virtBifsOutFile : print NBifs for each virt tree
FileOutputStream ggg = new FileOutputStream("VirtBifs_" + outFile);
BufferedOutputStream hhh = new BufferedOutputStream(ggg);
PrintWriter virtBifsOutFile = new PrintWriter(hhh);
//inputInfoOutFile : print each real bif line for debugging
// FileOutputStream fo = new FileOutputStream("InputInfo_" + outFile);
// BufferedOutputStream bfot = new BufferedOutputStream(fo);
// PrintWriter inputInfoOutFile = new PrintWriter(bfot);
//tableOut : print table file for program
FileOutputStream fob = new FileOutputStream("Table_" + outFile);
BufferedOutputStream bfotb = new BufferedOutputStream(fob);
PrintWriter tableOut = new PrintWriter(bfotb);
//virtDetailsOut : print parameter details for each virt tree
FileOutputStream fod = new FileOutputStream("OutputInfo_" + outFile);
BufferedOutputStream dfot = new BufferedOutputStream(fod);
PrintWriter virtDetailsOut = new PrintWriter(dfot);
//virtAsymetryOut : print parameter details for each virt tree
FileOutputStream vays = new FileOutputStream("VirtAsymetry_" + outFile);
BufferedOutputStream dvays = new BufferedOutputStream(vays);
PrintWriter virtAsymetryFile = new PrintWriter(dvays);
//virtSurfaceOut : print parameter details for each virt tree
FileOutputStream says = new FileOutputStream("VirtSurface_" + outFile);
BufferedOutputStream dsays = new BufferedOutputStream(says);
PrintWriter virtSurfaceFile = new PrintWriter(dsays);
//virtSurfaceAsymetryOut : print parameter details for each virt tree
FileOutputStream gays = new FileOutputStream("VirtSurfaceAsym_" + outFile);
BufferedOutputStream dgays = new BufferedOutputStream(gays);
PrintWriter virtSurfaceAsymFile = new PrintWriter(dgays);
//open swc files and place them into an array of swcNeuron type
for (int j = 1; j <= actualInFiles; j++) {
Neurons[j] = new swcparts.SwcNeuron();
Neurons[j].InitSwcNeuron(inputFileArray[j]);
System.out.println("processing " + inputFileArray[j]);
Neurons[j].removeOtherTypeSideBranches(typeToDo);
}
//Put all bifurcation information into bifLineType array and all stem radius into array of doubles
for (int j = 1; j <= actualInFiles; j++) { //for each neuron
realBifs[j] = 0;
for (int k = 1; k <= Neurons[j].getSize(); k++) { //for every line
Neurons[j].setEuclidianDistancesToSoma();
if (Neurons[j].getType(k) == typeToDo) { //only wory about lines of correct type
// set initial diameters
if (k > 1) {
//count stems and get stem start radius
if (Neurons[j].getType(Neurons[j].getLink(k)) == SomaType) {
++stemCount;
stemRadArray[stemCount] = Neurons[j].getRad(k);
realTreeBifs[stemCount] = Neurons[j].getTreeSize(k,
typeToDo);
if (realTreeBifs[stemCount] > RealBifsMax) {
RealBifsMax = realTreeBifs[stemCount];
}
realAsymetryArray[stemCount] = Neurons[j].getTreeAsymetry(k,
typeToDo);
realSurfaceArray[stemCount] = Neurons[j].getTreeSurface(k,
typeToDo);
// System.out.println(realSurfaceArray[stemCount]);
realSurfaceAsymArray[stemCount] = Neurons[j].
getTreeSurfaceAsym(
k, typeToDo);
// System.out.println(" Neuron, Stem, Asymetry "+j+" "+k+" "+realAsymetryArray[stemCount]);
}
}
//count Bifs for this cell
if ( (Neurons[j].getNumDaughters(k) == 2)) {
++realBifs[j];
}
//initialize and populate BIFSarray with only those lines that are bifurcations or terminations
if ( (Neurons[j].getNumDaughters(k) == 2) ||
(Neurons[j].getNumDaughters(k) == 0)) {
++actualBiffLines;
BifsArray[actualBiffLines] = new swcparts.BiffLine();
tempBiff = 0;
tempDSrad = 0;
tempDLrad = 0;
//if bifurcation, set daughter diameters
if (Neurons[j].getNumDaughters(k) == 2) {
tempBiff = 1;
if (Neurons[j].getDaughter1rad(k) >
Neurons[j].getDaughter2rad(k)) {
tempDSrad = Neurons[j].getDaughter2rad(k);
tempDLrad = Neurons[j].getDaughter1rad(k);
}
else {
tempDSrad = Neurons[j].getDaughter1rad(k);
tempDLrad = Neurons[j].getDaughter2rad(k);
}
}
BifsArray[actualBiffLines].setAll(Neurons[j].getBranchOrder(k),
(Neurons[j].getTreeLength(k) -
Neurons[j].getBranchLength(k)),
Neurons[j].getTreeLength(k),
Neurons[j].getEDistanceToSoma(k), Neurons[j].getY(k),
Neurons[j].getRad(k), Neurons[j].getBranchStartRad(k),
Neurons[j].getBranchLength(k), tempBiff, tempDSrad,
tempDLrad);
}
}
}
realBiffCount = realBiffCount + realBifs[j];
}
realBiffMean = (realBiffCount / stemCount);
//**************Create input table for sampling virtual neurons****************
//compute initial stem diameter mean, stdev
if (stemCount <= 0) {
System.out.println("No tree stems found.");
System.exit(4);
}
else {
stemMin = stemRadArray[1];
stemMax = stemRadArray[1];
for (int i = 1; i <= stemCount; i++) { //for each stem
tempStemSum = tempStemSum + stemRadArray[i];
if (stemRadArray[i] < stemMin) {
stemMin = stemRadArray[i];
}
if (stemRadArray[i] > stemMax) {
stemMax = stemRadArray[i];
}
}
stemMean = tempStemSum / stemCount;
for (int i = 1; i <= stemCount; i++) { //for each stem
tempStemSqSum = tempStemSqSum +
( (stemRadArray[i] - stemMean) *
(stemRadArray[i] - stemMean));
}
stemStdev = java.lang.Math.sqrt(tempStemSqSum / (stemCount - 1)); ;
}
stemRadArrayCurveType = GammaDist.getCurveType(stemRadArray, stemCount, myRand);
double symetricStemMax = ( (stemMean * 2) - stemMin);
//populate input tables
BOTable = BiffLine.createBBDTable(BifsArray, actualBiffLines, "BO", Binning, myRand);
PLTable = BiffLine.createBBDTable(BifsArray, actualBiffLines, "PLS", Binning, myRand);
RDTable = BiffLine.createBBDTable(BifsArray, actualBiffLines, "RAD", Binning, myRand);
// if (Debugging) {
tableOut.println("Branch Order Table.");
BinnedBiffData.writeOutInputTable(BOTable, tableOut, BOTable[1].getArraySize());
tableOut.println("Path Length Table.");
BinnedBiffData.writeOutInputTable(PLTable, tableOut, PLTable[1].getArraySize());
tableOut.println("Radius Table.");
BinnedBiffData.writeOutInputTable(RDTable, tableOut, RDTable[1].getArraySize());
// inputInfoOutFile.close();
tableOut.close();
// }
//******************************************************************************
//******************************************************************************
//********************* END OF INPUT PROCESSING ********************
//********************* Generation of new trees ********************
//******************************************************************************
//******************************************************************************
virtBifsOutFile.println("inFile , outFile");
virtBifsOutFile.println(inFile + " , " + outFile);
virtAsymetryFile.println("inFile , outFile");
virtAsymetryFile.println(inFile + " , " + outFile);
virtSurfaceFile.println("inFile , outFile");
virtSurfaceFile.println(inFile + " , " + outFile);
virtSurfaceAsymFile.println("inFile , outFile");
virtSurfaceAsymFile.println(inFile + " , " + outFile);
int newTreeCount = stemCount * nToDo; //number of virtual trees to create
System.out.println("Creating " + newTreeCount + " virtual trees.");
if (Debugging) {
virtDetailsOut.println();
}
virtBifsOutFile.println(
"mean of group means , stdev of group means , , mean of group stdevs , stdev of group stdevs");
virtAsymetryFile.println(
"mean of group means , stdev of group means , , mean of group stdevs , stdev of group stdevs");
virtSurfaceFile.println(
"mean of group means , stdev of group means , , mean of group stdevs , stdev of group stdevs");
virtSurfaceAsymFile.println(
"mean of group means , stdev of group means , , mean of group stdevs , stdev of group stdevs");
//******************master loop for mixing of fundemental parameters********
double PLpercentDR = 0;
double RDpercentDR = 0;
double BOpercentDR = 0;
double PLpercentPDR = 0;
double RDpercentPDR = 0;
double BOpercentPDR = 0;
double PLpercentTR = 0;
double RDpercentTR = 0;
double BOpercentTR = 0;
double PLpercentBPL = 0;
double RDpercentBPL = 0;
double BOpercentBPL = 0;
double PLpercentBIFF = 0;
double RDpercentBIFF = 0;
double BOpercentBIFF = 0;
int groupN = 0;
for (int DRdeterminant = 1; DRdeterminant <= 3; DRdeterminant++) {
for (int PDRdeterminant = 1; PDRdeterminant <= 3; PDRdeterminant++) {
for (int TRdeterminant = 1; TRdeterminant <= 3; TRdeterminant++) {
for (int BPLdeterminant = 1; BPLdeterminant <= 3; BPLdeterminant++) {
for (int BIFFdeterminant = 1; BIFFdeterminant <= 3;
BIFFdeterminant++) {
++groupN;
//Variables to track and limit explosive growth
boolean doesExplodeGroup = false;
int explodeCount = 0;
int MaxBifs = explodeRatio * RealBifsMax;
switch (DRdeterminant) {
case 1:
PLpercentDR = 1;
RDpercentDR = 0;
BOpercentDR = 0;
System.out.print("DR = PL; ");
virtBifsOutFile.print("DR = PL; ");
virtAsymetryFile.print("DR = PL; ");
virtSurfaceFile.print("DR = PL; ");
virtSurfaceAsymFile.print("DR = PL; ");
break;
case 2:
PLpercentDR = 0;
RDpercentDR = 1;
BOpercentDR = 0;
System.out.print("DR = RD; ");
virtBifsOutFile.print("DR = RD; ");
virtAsymetryFile.print("DR = RD; ");
virtSurfaceFile.print("DR = RD; ");
virtSurfaceAsymFile.print("DR = RD; ");
break;
case 3:
PLpercentDR = 0;
RDpercentDR = 0;
BOpercentDR = 1;
System.out.print("DR = BO; ");
virtBifsOutFile.print("DR = BO; ");
virtAsymetryFile.print("DR = BO; ");
virtSurfaceFile.print("DR = BO; ");
virtSurfaceAsymFile.print("DR = BO; ");
break;
default:
System.out.println("switch error, value is : " +
DRdeterminant);
System.exit(44);
}
switch (PDRdeterminant) {
case 1:
PLpercentPDR = 1;
RDpercentPDR = 0;
BOpercentPDR = 0;
System.out.print("PDR = PL; ");
virtBifsOutFile.print("PDR = PL; ");
virtAsymetryFile.print("PDR = PL; ");
virtSurfaceFile.print("PDR = PL; ");
virtSurfaceAsymFile.print("PDR = PL; ");
break;
case 2:
PLpercentPDR = 0;
RDpercentPDR = 1;
BOpercentPDR = 0;
System.out.print("PDR = RD; ");
virtBifsOutFile.print("PDR = RD; ");
virtAsymetryFile.print("PDR = RD; ");
virtSurfaceFile.print("PDR = RD; ");
virtSurfaceAsymFile.print("PDR = RD; ");
break;
case 3:
PLpercentPDR = 0;
RDpercentPDR = 0;
BOpercentPDR = 1;
System.out.print("PDR = BO; ");
virtBifsOutFile.print("PDR = BO; ");
virtAsymetryFile.print("PDR = BO; ");
virtSurfaceFile.print("PDR = BO; ");
virtSurfaceAsymFile.print("PDR = BO; ");
break;
default:
System.out.println("switch error, value is : " +
PDRdeterminant);
System.exit(44);
}
switch (TRdeterminant) {
case 1:
PLpercentTR = 1;
RDpercentTR = 0;
BOpercentTR = 0;
System.out.print("TR = PL; ");
virtBifsOutFile.print("TR = PL; ");
virtAsymetryFile.print("TR = PL; ");
virtSurfaceFile.print("TR = PL; ");
virtSurfaceAsymFile.print("TR = PL; ");
break;
case 2:
PLpercentTR = 0;
RDpercentTR = 1;
BOpercentTR = 0;
System.out.print("TR = RD; ");
virtBifsOutFile.print("TR = RD; ");
virtAsymetryFile.print("TR = RD; ");
virtSurfaceFile.print("TR = RD; ");
virtSurfaceAsymFile.print("TR = RD; ");
break;
case 3:
PLpercentTR = 0;
RDpercentTR = 0;
BOpercentTR = 1;
System.out.print("TR = BO; ");
virtBifsOutFile.print("TR = BO; ");
virtAsymetryFile.print("TR = BO; ");
virtSurfaceFile.print("TR = BO; ");
virtSurfaceAsymFile.print("TR = BO; ");
break;
default:
System.out.println("switch error, value is : " +
TRdeterminant);
System.exit(44);
}
switch (BPLdeterminant) {
case 1:
PLpercentBPL = 1;
RDpercentBPL = 0;
BOpercentBPL = 0;
System.out.print("BPL = PL; ");
virtBifsOutFile.print("BPL = PL; ");
virtAsymetryFile.print("BPL = PL; ");
virtSurfaceFile.print("BPL = PL; ");
virtSurfaceAsymFile.print("BPL = PL; ");
break;
case 2:
PLpercentBPL = 0;
RDpercentBPL = 1;
BOpercentBPL = 0;
System.out.print("BPL = RD; ");
virtBifsOutFile.print("BPL = RD; ");
virtAsymetryFile.print("BPL = RD; ");
virtSurfaceFile.print("BPL = RD; ");
virtSurfaceAsymFile.print("BPL = RD; ");
break;
case 3:
PLpercentBPL = 0;
RDpercentBPL = 0;
BOpercentBPL = 1;
System.out.print("BPL = BO; ");
virtBifsOutFile.print("BPL = BO; ");
virtAsymetryFile.print("BPL = BO; ");
virtSurfaceFile.print("BPL = BO; ");
virtSurfaceAsymFile.print("BPL = BO; ");
break;
default:
System.out.println("switch error, value is : " +
BPLdeterminant);
System.exit(44);
}
switch (BIFFdeterminant) {
case 1:
PLpercentBIFF = 1;
RDpercentBIFF = 0;
BOpercentBIFF = 0;
System.out.println("BIFF = PL");
virtBifsOutFile.println("BIFF = PL");
virtAsymetryFile.println("BIFF = PL");
virtSurfaceFile.println("BIFF = PL");
virtSurfaceAsymFile.println("BIFF = PL");
break;
case 2:
PLpercentBIFF = 0;
RDpercentBIFF = 1;
BOpercentBIFF = 0;
System.out.println("BIFF = RD");
virtBifsOutFile.println("BIFF = RD");
virtAsymetryFile.println("BIFF = RD");
virtSurfaceFile.println("BIFF = RD");
virtSurfaceAsymFile.println("BIFF = RD");
break;
case 3:
PLpercentBIFF = 0;
RDpercentBIFF = 0;
BOpercentBIFF = 1;
System.out.println("BIFF = BO");
virtBifsOutFile.println("BIFF = BO");
virtAsymetryFile.println("BIFF = BO");
virtSurfaceFile.println("BIFF = BO");
virtSurfaceAsymFile.println("BIFF = BO");
break;
default:
System.out.println("switch error, value is : " +
BIFFdeterminant);
System.exit(44);
}
/*
for (double RDpercent = 0; RDpercent <= 1; RDpercent += PercentStep) {
for (double PLpercent = 0; PLpercent <= 1 - RDpercent;
PLpercent += PercentStep) {
double BOpercent = 1 - (RDpercent + PLpercent);
//lot of trouble to correctly round and cast a double to int
BigDecimal rdbd = new BigDecimal(RDpercent);
BigDecimal plbd = new BigDecimal(PLpercent);
BigDecimal bobd = new BigDecimal(BOpercent);
rdbd = rdbd.setScale(4, BigDecimal.ROUND_HALF_UP);
plbd = plbd.setScale(4, BigDecimal.ROUND_HALF_UP);
bobd = bobd.setScale(4, BigDecimal.ROUND_HALF_UP);
int intRDpercent = (int) (rdbd.doubleValue() * 100);
int intBOpercent = (int) (bobd.doubleValue() * 100);
int intPLpercent = (int) (plbd.doubleValue() * 100);
System.out.println(":rd% = " + intRDpercent + " pl% = " + intPLpercent +
" bo% = " + intBOpercent);
virtBifsOutFile.println(":rd% = " + intRDpercent + " pl% = " +
intPLpercent +
" bo% = " + intBOpercent);
virtAsymetryFile.println(":rd% = " + intRDpercent + " pl% = " +
intPLpercent +
" bo% = " + intBOpercent);
virtSurfaceFile.println(":rd% = " + intRDpercent + " pl% = " +
intPLpercent +
" bo% = " + intBOpercent);
virtSurfaceAsymFile.println(":rd% = " + intRDpercent + " pl% = " +
intPLpercent +
" bo% = " + intBOpercent);
if (Debugging) {
virtDetailsOut.println(":rd% = " + intRDpercent + " pl% = " +
intPLpercent +
" bo% = " + intBOpercent);
}
//
*/
actualRDbins = RDTable[1].getArraySize();
actualPLbins = PLTable[1].getArraySize();
actualBObins = BOTable[1].getArraySize();
boolean[] virtExplodeArray = new boolean[newTreeCount + 1];
int[] virtBifsArray = new int[newTreeCount + 1];
double[] virtAsymArray = new double[newTreeCount + 1];
double virtAsymSum = 0;
double[] virtSurfaceArray = new double[newTreeCount + 1];
double virtSurfaceSum = 0;
double[] virtSurfaceAsymArray = new double[newTreeCount + 1];
double virtSurfaceAsymSum = 0;
double BifsSum = 0;
double BifsMean = 0;
swcparts.BiffLine[] virtTreesArray = new swcparts.BiffLine[
maxVirtBifLines + 1];
for (int currentBranch = 1;
currentBranch <= maxVirtBifLines;
currentBranch++) {
virtTreesArray[currentBranch] = new swcparts.BiffLine();
}
double tempTP = 0;
double tempDR = 0;
double tempPDR = 0;
double tempBPL = 0;
int NBifs = 0;
if (Debugging) {
virtDetailsOut.println(
"Line , startRad, taperRate, endFP, branchPL, bif, termRand, random, PDR, DR, d1Rad, d2Rad ");
}
int treeSize = 0;
for (int currentTreeN = 1; currentTreeN <= newTreeCount;
currentTreeN++) { //for each virtual tree
treeSize = 0;
boolean doesExplodeTree = false;
if (Debugging) {
virtBifsOutFile.print(currentTreeN);
virtDetailsOut.println();
virtDetailsOut.println("Tree number : " +
currentTreeN);
}
NBifs = 0;
double idia = 0;
if (stemRadArrayCurveType == 1) {
idia = (myRand.nextDouble() *
(symetricStemMax - stemMin) +
stemMin);
}
else if (stemRadArrayCurveType == 2) {
while ( (idia < stemMin) ||
(idia > symetricStemMax)) {
idia = gDist.GetGammaMS(stemMean, stemStdev,
myRand);
}
}
else if (stemRadArrayCurveType == 3) {
idia = stemMin - 1;
while ( (idia < stemMin) || (idia > stemMax)) {
idia = (myRand.nextGaussian() * stemStdev) +
stemMean;
}
}
else {
System.out.println(
"stemRadArrayCurveType invalid: " +
stemRadArrayCurveType);
System.exit( -11);
}
if (Debugging) {
System.out.print("Tree " + currentTreeN +
" idia: " + idia);
}
virtTreesArray[1].setStartRAD(idia);
virtTreesArray[1].setBO(0);
virtTreesArray[1].setStartPLS(0);
virtTreesArray[1].setParrentNum( -1);
//go through each line of the new virt cell cell
int nextFreeBranchNum = 2;
int tempCurrnetBranchLoopMax = (maxVirtBifLines - 4) /
2;
double tempTermRand = 0;
double tempCompareRand = 0;
for (int currentBranch = 1;
currentBranch <= tempCurrnetBranchLoopMax;
currentBranch++) {
//find fundemental param bin for start of seg
int currentRDbin = actualRDbins;
int currentPLbin = actualPLbins;
int currentBObin = actualBObins;
for (int j = actualRDbins; j >= 1; j--) {
if (virtTreesArray[currentBranch].
getStartFundementalParamValue(
"RAD") <=
RDTable[j].getFPbinMax()) {
currentRDbin = j;
}
}
for (int j = actualPLbins; j >= 1; j--) {
if (virtTreesArray[currentBranch].
getStartFundementalParamValue(
"PLS") <=
PLTable[j].getFPbinMax()) {
currentPLbin = j;
}
}
for (int j = actualBObins; j >= 1; j--) {
if (virtTreesArray[currentBranch].
getStartFundementalParamValue(
"BO") <=
BOTable[j].getFPbinMax()) {
currentBObin = j;
}
}
//taper
//sample taper rate
if (virtTreesArray[currentBranch].
getStartRAD() <=
MinRad) {
tempTP = 1;
}
else {
double tempTPuf = ( (RDTable[
currentRDbin].
getTRuf() *
RDpercentTR) +
(PLTable[currentPLbin].getTRuf() *
PLpercentTR) +
(BOTable[currentBObin].getTRuf() *
BOpercentTR));
if (myRand.nextDouble() < tempTPuf) {
tempTP = TRconstant;
}
else {
// tempTP = ( (RDTable[currentRDbin].
// getParamValueCurve(
// "TP", myRand, gDist) *
// RDpercentTR) +
// (PLTable[currentPLbin].
// getParamValueCurve(
// "TP", myRand, gDist) *
// PLpercentTR) +
// (BOTable[currentBObin].
// getParamValueCurve(
// "TP", myRand, gDist) *
// BOpercentTR));
if (RDpercentTR == 1) {
tempTP = RDTable[currentRDbin].
getParamValueCurve("TP",
myRand, gDist);
}
else if (PLpercentTR == 1) {
tempTP = PLTable[currentPLbin].
getParamValueCurve("TP",
myRand, gDist);
}
else if (BOpercentTR == 1) {
tempTP = BOTable[currentBObin].
getParamValueCurve("TP",
myRand, gDist);
}
else {
System.out.println("TP error");
}
}
}
//set end rad to start rad * tp
virtTreesArray[currentBranch].setEndRAD(
virtTreesArray[currentBranch].
getStartRAD() /
tempTP);
// find branch path length
// tempBPL = ( (RDTable[currentRDbin].
// getParamValueCurve(
// "BPL", myRand, gDist) * RDpercentBPL) +
// (PLTable[currentPLbin].
// getParamValueCurve(
// "BPL", myRand, gDist) * PLpercentBPL) +
// (BOTable[currentBObin].
// getParamValueCurve(
// "BPL", myRand, gDist) * BOpercentBPL));
if (RDpercentBPL == 1) {
tempBPL = RDTable[currentRDbin].
getParamValueCurve(
"BPL", myRand, gDist);
}
else if (PLpercentBPL == 1) {
tempBPL = PLTable[currentPLbin].
getParamValueCurve(
"BPL", myRand, gDist);
}
else if (BOpercentBPL == 1) {
tempBPL = BOTable[currentBObin].
getParamValueCurve(
"BPL", myRand, gDist);
}
else {
System.out.println("BPL error");
}
//set bramch path length
virtTreesArray[currentBranch].setBPL(tempBPL);
virtTreesArray[currentBranch].setSurface(Math.PI *
(virtTreesArray[currentBranch].getStartRAD() +
virtTreesArray[currentBranch].getEndRAD()) *
tempBPL);
//set path length soma
virtTreesArray[currentBranch].setEndPLS(
virtTreesArray[currentBranch].
getStartPLS() +
tempBPL);
//reset current fundemental paramater bin with end value
currentRDbin = actualRDbins;
currentPLbin = actualPLbins;
currentBObin = actualBObins;
for (int j = actualRDbins; j >= 1; j--) {
if (virtTreesArray[currentBranch].
getEndFundementalParamValue(
"RAD") <=
RDTable[j].getFPbinMax()) {
currentRDbin = j;
}
}
for (int j = actualPLbins; j >= 1; j--) {
if (virtTreesArray[currentBranch].
getEndFundementalParamValue(
"PLS") <=
PLTable[j].getFPbinMax()) {
currentPLbin = j;
}
}
for (int j = actualBObins; j >= 1; j--) {
if (virtTreesArray[currentBranch].
getEndFundementalParamValue(
"BO") <=
BOTable[j].getFPbinMax()) {
currentBObin = j;
}
}
//Print out virtual cell details
if (Debugging) {
virtDetailsOut.print(currentBranch +
" , " +
virtTreesArray[currentBranch].
getStartRAD() +
" , " +
tempTP + " , " + tempBPL);
}
//Bif?
//sample bif prob
//if no, set bif to 0
virtTreesArray[currentBranch].setBIFF(1);
// tempTermRand = ( (RDTable[currentRDbin].
// getParamValueCurve(
// "BP", myRand, gDist) * RDpercentBIFF) +
// (PLTable[currentPLbin].
// getParamValueCurve(
// "BP", myRand, gDist) * PLpercentBIFF) +
// (BOTable[currentBObin].
// getParamValueCurve(
// "BP", myRand, gDist) * BOpercentBIFF));
if (RDpercentBIFF == 1) {
tempTermRand = RDTable[currentRDbin].
getParamValueCurve(
"BP", myRand, gDist);
}
else if (PLpercentBIFF == 1) {
tempTermRand = PLTable[currentPLbin].
getParamValueCurve(
"BP", myRand, gDist);
}
else if (BOpercentBIFF == 1) {
tempTermRand = BOTable[currentBObin].
getParamValueCurve(
"BP", myRand, gDist);
}
else {
System.out.println("BIFF error");
}
tempCompareRand = myRand.nextDouble();
// if ( (tempTermRand < tempCompareRand) ||
// (virtTreesArray[currentBranch].getEndFundementalParamValue(
// "RAD") <= MinRad)) {
// virtTreesArray[currentBranch].setBIFF(0);
// }
if ( (tempTermRand < tempCompareRand)) {
virtTreesArray[currentBranch].setBIFF(0);
}
// System.out.println("BO bin, tempTermRand, tempCompareRand, bif? " +currentBObin+" "+ tempTermRand+" "+ tempCompareRand+" "+virtTreesArray[currentBranch].getBIFF());
//Print out virtual Bif cell details
if (Debugging) {
virtDetailsOut.print(" , " +
virtTreesArray[currentBranch].
getBIFF() +
" , " + tempTermRand + " , " +
tempCompareRand);
}
//if yes, set bif to 1
if (virtTreesArray[currentBranch].getBIFF() ==
1) {
++NBifs;
double tempPDRuf = ( (RDTable[
currentRDbin].
getPDRuf() *
RDpercentPDR) +
(PLTable[currentPLbin].getPDRuf() *
PLpercentPDR) +
(BOTable[currentBObin].getPDRuf() *
BOpercentPDR));
if (myRand.nextDouble() < tempPDRuf) {
tempPDR = PDRconstant;
}
else {
// tempPDR = ( (RDTable[currentRDbin].
// getParamValueCurve(
// "PDR", myRand, gDist) *
// RDpercentPDR) +
// (PLTable[currentPLbin].
// getParamValueCurve(
// "PDR", myRand, gDist) *
// PLpercentPDR) +
// (BOTable[currentBObin].
// getParamValueCurve(
// "PDR", myRand, gDist) *
// BOpercentPDR));
if (RDpercentPDR == 1) {
tempPDR = RDTable[currentRDbin].
getParamValueCurve(
"PDR", myRand, gDist);
}
else if (PLpercentPDR == 1) {
tempPDR = PLTable[currentPLbin].
getParamValueCurve(
"PDR", myRand, gDist);
}
else if (BOpercentPDR == 1) {
tempPDR = BOTable[currentBObin].
getParamValueCurve(
"PDR", myRand, gDist);
}
else {
System.out.println("PDR error");
}
}
if ( (virtTreesArray[currentBranch].
getEndFundementalParamValue(
"RAD") <=
MinRad)) {
tempPDR = PDRconstant;
}
//Large Daughter rad = end rad / PDR
virtTreesArray[currentBranch].setDLRAD(
virtTreesArray[currentBranch].
getEndRAD() /
tempPDR);
double tempDRuf = ( (RDTable[
currentRDbin].
getDRuf() *
RDpercentDR) +
(PLTable[currentPLbin].getDRuf() *
PLpercentDR) +
(BOTable[currentBObin].getDRuf() *
BOpercentDR));
if (myRand.nextDouble() < tempDRuf) {
tempDR = DRconstant;
}
else {
// tempDR = ( (RDTable[currentRDbin].
// getParamValueCurve(
// "DR", myRand, gDist) *
// RDpercentDR) +
// (PLTable[currentPLbin].
// getParamValueCurve(
// "DR", myRand, gDist) *
// PLpercentDR) +
// (BOTable[currentBObin].
// getParamValueCurve(
// "DR", myRand, gDist) *
// BOpercentDR));
if (RDpercentDR == 1) {
tempDR = RDTable[currentRDbin].
getParamValueCurve(
"DR", myRand, gDist);
}
else if (PLpercentDR == 1) {
tempDR = PLTable[currentPLbin].
getParamValueCurve(
"DR", myRand, gDist);
}
else if (BOpercentDR == 1) {
tempDR = BOTable[currentBObin].
getParamValueCurve(
"DR", myRand, gDist);
}
else {
System.out.println("DR error");
}
}
if ( (virtTreesArray[currentBranch].
getEndFundementalParamValue(
"RAD") <=
MinRad)) {
tempDR = DRconstant;
}
//Samll Daughter Rad = Large Daughter Rad / DR
virtTreesArray[currentBranch].setDSRAD(
virtTreesArray[currentBranch].
getDLRAD() / tempDR);
//initialize new daughters
virtTreesArray[currentBranch].setD1num(
nextFreeBranchNum);
++nextFreeBranchNum;
virtTreesArray[currentBranch].setD2num(
nextFreeBranchNum);
++nextFreeBranchNum;
//set new daughter diameters
virtTreesArray[virtTreesArray[currentBranch].
getD1num()].
setStartRAD(
virtTreesArray[currentBranch].
getDLRAD());
virtTreesArray[virtTreesArray[currentBranch].
getD2num()].
setStartRAD(
virtTreesArray[currentBranch].
getDSRAD());
//set parrent number
virtTreesArray[virtTreesArray[currentBranch].
getD1num()].
setParrentNum(currentBranch);
virtTreesArray[virtTreesArray[currentBranch].
getD2num()].
setParrentNum(currentBranch);
//set branch orders
virtTreesArray[virtTreesArray[currentBranch].
getD1num()].
setBO(virtTreesArray[currentBranch].
getBO() + 1);
virtTreesArray[virtTreesArray[currentBranch].
getD2num()].
setBO(virtTreesArray[currentBranch].
getBO() + 1);
//set pls
virtTreesArray[virtTreesArray[currentBranch].
getD1num()].
setStartPLS(
virtTreesArray[currentBranch].
getEndPLS());
virtTreesArray[virtTreesArray[currentBranch].
getD2num()].
setStartPLS(
virtTreesArray[currentBranch].
getEndPLS());
}
treeSize = currentBranch;
if (currentBranch + 1 == (nextFreeBranchNum)) {
break;
}
if (Debugging) {
virtDetailsOut.println();
}
if (NBifs == MaxBifs) {
doesExplodeTree = true;
doesExplodeGroup = true;
explodeCount++;
break;
}
}
if (Debugging) {
System.out.println(" NBifs: " + NBifs);
virtBifsOutFile.println(" , " + NBifs);
if (currentTreeN % stemCount == 0) {
virtBifsOutFile.println(); // a space in between tree groups
}
}
if (doesExplodeTree) {
}
else {
virtExplodeArray[currentTreeN] = doesExplodeTree;
virtBifsArray[currentTreeN] = NBifs;
BifsSum = BifsSum + NBifs;
virtAsymArray[currentTreeN] = BiffLine.
getVirtualAsymetry(
virtTreesArray, treeSize);
if (virtAsymArray[currentTreeN] == -1) {
// ++undefinedAsymCount;
}
else {
virtAsymSum += virtAsymArray[currentTreeN];
}
virtSurfaceArray[currentTreeN] = BiffLine.
getVirtualSurface(
virtTreesArray, 1);
// System.out.println(virtSurfaceArray[currentTreeN]);
virtSurfaceSum += virtSurfaceArray[currentTreeN];
virtSurfaceAsymArray[currentTreeN] = BiffLine.
getVirtualSurfaceAsym(
virtTreesArray, treeSize);
if (virtSurfaceArray[currentTreeN] == -1) {
// ++virtSurfaceAsymSum;
}
else {
virtSurfaceAsymSum += virtSurfaceArray[
currentTreeN];
}
}
//******************************************************************************
//******************************************************************************
//***********************Output SWC Files***************************************
//******************************************************************************
//******************************************************************************
if (SWCout) {
//swcOut : output file stream for virtual swc files
FileOutputStream sod = new FileOutputStream(
"SWC_" +
outFile + ".group" + groupN + "tree" +
currentTreeN + ".swc");
BufferedOutputStream bossod = new BufferedOutputStream(
sod);
PrintWriter swcOut = new PrintWriter(bossod);
switch (DRdeterminant) {
case 1:
swcOut.print("# DR = PL; ");
break;
case 2:
swcOut.print("# DR = RD; ");
break;
case 3:
swcOut.print("# DR = BO; ");
break;
default:
System.out.println("switch error, value is : " +
DRdeterminant);
System.exit(44);
}
switch (PDRdeterminant) {
case 1:
swcOut.print("PDR = PL; ");
break;
case 2:
swcOut.print("PDR = RD; ");
break;
case 3:
swcOut.print("PDR = BO; ");
break;
default:
System.out.println("switch error, value is : " +
PDRdeterminant);
System.exit(44);
}
switch (TRdeterminant) {
case 1:
swcOut.print("TR = PL; ");
break;
case 2:
swcOut.print("TR = RD; ");
break;
case 3:
swcOut.print("TR = BO; ");
break;
default:
System.out.println(
"switch error, value is : " +
TRdeterminant);
System.exit(44);
}
switch (BPLdeterminant) {
case 1:
swcOut.print("BPL = PL; ");
break;
case 2:
swcOut.print("BPL = RD; ");
break;
case 3:
swcOut.print("BPL = BO; ");
break;
default:
System.out.println(
"switch error, value is : " +
BPLdeterminant);
System.exit(44);
}
switch (BIFFdeterminant) {
case 1:
swcOut.println("BIFF = PL");
break;
case 2:
swcOut.println("BIFF = RD");
break;
case 3:
swcOut.println("BIFF = BO");
break;
default:
System.out.println(
"switch error, value is : " +
BIFFdeterminant);
System.exit(44);
}
swcOut.println("# Tree Number : " + currentTreeN +
" out of: " + newTreeCount);
if (doesExplodeTree) {
swcOut.println("# Tree Explodes");
}
else {
swcOut.println("# Bifurcations: " +
virtBifsArray[currentTreeN]);
swcOut.println("# Asymmetry: " +
virtAsymArray[currentTreeN]);
swcOut.println("# Surface Area: " +
virtSurfaceArray[currentTreeN]);
swcOut.println("# Surface Asymmetry: " +
virtSurfaceAsymArray[currentTreeN]);
swcOut.println("# ");
swcOut.println("1 1 0 0 0 0 -1");
for (int i = 1; i <= treeSize; i++) {
if (i == 1) {
swcOut.println( ( (i * 2)) + " 3 0 " +
virtTreesArray[i].getStartPLS() +
" 0 " +
virtTreesArray[i].getStartRAD() +
" " +
1);
}
else {
swcOut.println( ( (i * 2)) + " 3 0 " +
virtTreesArray[i].getStartPLS() +
" 0 " +
virtTreesArray[i].getStartRAD() +
" " +
( (virtTreesArray[i].
getParrentNum() * 2) + 1));
}
swcOut.println( ( (i * 2) + 1) + " 3 0 " +
virtTreesArray[i].getEndPLS() +
" 0 " + virtTreesArray[i].getEndRAD() +
" " +
( (i * 2)));
}
}
swcOut.close();
}
//******************************************************************************
//******************************************************************************
}
if (doesExplodeGroup) {
System.out.println(explodeCount + " out of " +
newTreeCount +
" virtual trees exploded.");
}
//
//compute mean and stdev by cell group
int[] groupExplodes = new int[nToDo + 1];
double[] groupMeans = new double[nToDo + 1];
double[] groupSums = new double[nToDo + 1];
double[] groupStdevs = new double[nToDo + 1];
double[] groupSqSums = new double[nToDo + 1];
double meanOfGroupMeans = 0;
double sumOfGroupMeans = 0;
double sumOfGroupMeanSqSums = 0;
double meanOfGroupStdevs = 0;
double sumOfGroupStdevs = 0;
double stdevOfGroupMeans = 0;
double stdevOfGroupStdevs = 0;
double sumOfGroupStdevSqSums = 0;
int[] GroupUndefinedAsymCount = new int[nToDo + 1];
double[] groupAsymMeans = new double[nToDo + 1];
double[] groupAsymSums = new double[nToDo + 1];
double[] groupAsymStdevs = new double[nToDo + 1];
double[] groupAsymSqSums = new double[nToDo + 1];
double meanAsymOfGroupMeans = 0;
double sumAsymOfGroupMeans = 0;
double sumAsymOfGroupMeanSqSums = 0;
double meanAsymOfGroupStdevs = 0;
double sumAsymOfGroupStdevs = 0;
double stdevAsymOfGroupMeans = 0;
double stdevAsymOfGroupStdevs = 0;
double sumAsymOfGroupStdevSqSums = 0;
double[] groupSurfaceMeans = new double[nToDo + 1];
double[] groupSurfaceSums = new double[nToDo + 1];
double[] groupSurfaceStdevs = new double[nToDo + 1];
double[] groupSurfaceSqSums = new double[nToDo + 1];
double meanSurfaceOfGroupMeans = 0;
double sumSurfaceOfGroupMeans = 0;
double sumSurfaceOfGroupMeanSqSums = 0;
double meanSurfaceOfGroupStdevs = 0;
double sumSurfaceOfGroupStdevs = 0;
double stdevSurfaceOfGroupMeans = 0;
double stdevSurfaceOfGroupStdevs = 0;
double sumSurfaceOfGroupStdevSqSums = 0;
int[] GroupUndefinedSurfaceAsymCount = new int[nToDo + 1];
double[] groupSurfaceAsymMeans = new double[nToDo + 1];
double[] groupSurfaceAsymSums = new double[nToDo + 1];
double[] groupSurfaceAsymStdevs = new double[nToDo + 1];
double[] groupSurfaceAsymSqSums = new double[nToDo + 1];
double meanSurfaceAsymOfGroupMeans = 0;
double sumSurfaceAsymOfGroupMeans = 0;
double sumSurfaceAsymOfGroupMeanSqSums = 0;
double meanSurfaceAsymOfGroupStdevs = 0;
double sumSurfaceAsymOfGroupStdevs = 0;
double stdevSurfaceAsymOfGroupMeans = 0;
double stdevSurfaceAsymOfGroupStdevs = 0;
double sumSurfaceAsymOfGroupStdevSqSums = 0;
for (int i = 1; i <= nToDo; i++) {
//for each virtual tree group
groupExplodes[i] = 0;
GroupUndefinedSurfaceAsymCount[i] = 0;
GroupUndefinedAsymCount[i] = 0;
for (int j = 1; j <= stemCount; j++) {
//for each virtual tree in the grouip
int currentTree = ( (j - 1) * nToDo) + i;
//get the tree number
if (virtExplodeArray[currentTree]) {
//keep track of individual tree esplosions
groupExplodes[i]++;
}
else {
//if tree doesn't explode, add emergent prop values to running group sums
groupSums[i] += virtBifsArray[currentTree];
groupSurfaceSums[i] += virtSurfaceArray[
currentTree];
if (virtAsymArray[currentTree] == -1) {
//if asym is undefined, incriment count
++GroupUndefinedAsymCount[i];
}
else {
//otherwise add value to sum
groupAsymSums[i] += virtAsymArray[
currentTree];
}
if (virtSurfaceAsymArray[currentTree] == -1) {
//if surface asym is undefined, incriment count
++GroupUndefinedSurfaceAsymCount[i];
}
else {
groupSurfaceAsymSums[i] +=
virtSurfaceAsymArray[
currentTree];
}
}
}
//if all trees in group explode set means to undefined (-1)
if (groupExplodes[i] == stemCount) {
groupMeans[i] = -1;
groupAsymMeans[i] = -1;
groupSurfaceMeans[i] = -1;
groupSurfaceAsymMeans[i] = -1;
}
//otherwise compute means
else {
groupMeans[i] = groupSums[i] /
(stemCount - groupExplodes[i]);
if (stemCount >
(groupExplodes[i] +
GroupUndefinedAsymCount[i])) {
//if there are asym values which did not explode or return -1 compute the group mean
groupAsymMeans[i] = groupAsymSums[i] /
( (stemCount - groupExplodes[i]) -
GroupUndefinedAsymCount[i]);
}
else {
//otherwise set group mean to undefined (-1)
groupAsymMeans[i] = -1;
}
groupSurfaceMeans[i] = groupSurfaceSums[i] /
(stemCount - groupExplodes[i]);
if (stemCount >
groupExplodes[i] +
GroupUndefinedSurfaceAsymCount[i]) {
//if there are Surf asym values which did not explode or return -1 compute the group mean
groupSurfaceAsymMeans[i] =
groupSurfaceAsymSums[i] /
( (stemCount - groupExplodes[i]) -
GroupUndefinedSurfaceAsymCount[i]);
}
else {
//otherwise set group mean to undefined (-1)
groupSurfaceAsymMeans[i] = -1;
}
}
}
int BifGroups = nToDo;
int BifStdevGroups = nToDo;
int AsymGroups = nToDo;
int AsymStdevGroups = nToDo;
int SurfaceGroups = nToDo;
int SurfaceStdevGroups = nToDo;
int SurfaceAsymGroups = nToDo;
int SurfaceAsymStdevGroups = nToDo;
//Compute group stdevs
for (int i = 1; i <= nToDo; i++) {
//set n's to stem counts
int GroupBifs = stemCount;
int GroupAsyms = stemCount;
int GroupSurfaces = stemCount;
int GroupSurfaceAsyms = stemCount;
for (int j = 1; j <= stemCount; j++) {
int currentTree = ( (j - 1) * nToDo) + i;
if (virtExplodeArray[currentTree]) {
//if tree explodes, remove from stdev computation
--GroupBifs;
--GroupAsyms;
--GroupSurfaces;
--GroupSurfaceAsyms;
}
else {
if (groupMeans[i] == -1) {
//if group means undefined, decriment group counter
--BifGroups;
}
else {
//otherwise add to sqSum
groupSqSums[i] +=
( (virtBifsArray[currentTree] -
groupMeans[i]) *
(virtBifsArray[currentTree] -
groupMeans[i]));
}
if (groupAsymMeans[i] == -1) {
//if group means undefined, decriment group n's
--AsymGroups;
}
else {
//add to sq sum
if (virtAsymArray[currentTree] == -1) {
//if virt asym undefined, decriment group counter
--GroupAsyms;
}
else {
//otherwise add to sq sum
groupAsymSqSums[i] +=
( (virtAsymArray[
currentTree] -
groupAsymMeans[i]) *
(virtAsymArray[currentTree] -
groupAsymMeans[i]));
}
}
if (groupSurfaceMeans[i] == -1) {
// if undefined, decriment group n's
--SurfaceGroups;
}
else {
groupSurfaceSqSums[i] +=
( (virtSurfaceArray[currentTree] -
groupSurfaceMeans[i]) *
(virtSurfaceArray[currentTree] -
groupSurfaceMeans[i]));
}
if (groupSurfaceAsymMeans[i] == -1) {
//if group surf asym mean undevined, decriment number of groups
--SurfaceAsymGroups;
}
else {
if (virtSurfaceAsymArray[currentTree] ==
-1) {
//if virt surf asym undefined, decriment group counter
--GroupAsyms;
}
else {
//add tp surf sq sum
groupSurfaceAsymSqSums[i] +=
( (virtSurfaceAsymArray[
currentTree] -
groupSurfaceAsymMeans[i]) *
(virtSurfaceAsymArray[
currentTree] -
groupSurfaceAsymMeans[i]));
}
}
}
}
//////////////
if (GroupBifs >= 2) {
//if there are enough group bif values, compute stdev
groupStdevs[i] = java.lang.Math.sqrt(groupSqSums[
i] /
( (GroupBifs) - 1));
}
else {
//else, set group stdev to -1
groupStdevs[i] = -1;
}
if (groupMeans[i] == -1) {
// --BifGroups;, already done
}
else {
sumOfGroupMeans += groupMeans[i];
}
if (groupStdevs[i] == -1) {
--BifStdevGroups;
}
else {
sumOfGroupStdevs += groupStdevs[i];
}
/////////////////////
if (GroupAsyms >= 2) {
//if there are enough group asym values, compute stdev
groupAsymStdevs[i] = java.lang.Math.sqrt(
groupAsymSqSums[i] /
( (stemCount - groupExplodes[i]) - 1));
}
else {
groupAsymStdevs[i] = -1;
}
if (groupAsymMeans[i] == -1) {
//decriment already done
}
else {
sumAsymOfGroupMeans += groupAsymMeans[i];
}
if (groupAsymStdevs[i] == -1) {
--AsymStdevGroups;
}
else {
sumAsymOfGroupStdevs += groupAsymStdevs[i];
}
//////////////////////////////
if (GroupSurfaces >= 2) {
groupSurfaceStdevs[i] = java.lang.Math.sqrt(
groupSurfaceSqSums[
i] / ( (stemCount - groupExplodes[i]) - 1));
}
else {
//else, set group stdev to -1
groupSurfaceStdevs[i] = -1;
}
if (groupSurfaceMeans[i] == -1) {
//decriment alreadly done
}
else {
sumSurfaceOfGroupMeans += groupSurfaceMeans[i];
}
if (groupSurfaceStdevs[i] == -1) {
--SurfaceStdevGroups;
}
else {
sumSurfaceOfGroupStdevs += groupSurfaceStdevs[i];
}
//////////////
if (GroupSurfaceAsyms >= 2) {
groupSurfaceAsymStdevs[i] = java.lang.Math.sqrt(
groupSurfaceAsymSqSums[i] /
( (stemCount - groupExplodes[i]) - 1));
}
else {
//else, set group stdev to -1
groupSurfaceAsymStdevs[i] = -1;
}
if (groupSurfaceAsymMeans[i] == -1) {
//decriment alreadly done
}
else {
sumSurfaceAsymOfGroupMeans +=
groupSurfaceAsymMeans[i];
}
if (groupSurfaceAsymStdevs[i] == -1) {
--SurfaceAsymStdevGroups;
}
else {
sumSurfaceAsymOfGroupStdevs +=
groupSurfaceAsymStdevs[i];
}
} //compute global (group) means of means and stdevs
if (BifGroups >= 1) {
meanOfGroupMeans = sumOfGroupMeans / BifGroups;
}
else {
meanOfGroupMeans = -1;
}
if (BifStdevGroups >= 1) {
meanOfGroupStdevs = sumOfGroupStdevs / BifStdevGroups;
}
else {
meanOfGroupStdevs = -1;
}
if (AsymGroups >= 1) {
meanAsymOfGroupMeans = sumAsymOfGroupMeans /
AsymGroups;
}
else {
meanAsymOfGroupMeans = -1;
}
if (AsymStdevGroups >= 1) {
meanAsymOfGroupStdevs = sumAsymOfGroupStdevs /
AsymStdevGroups;
}
else {
meanAsymOfGroupStdevs = -1;
}
if (SurfaceGroups >= 1) {
meanSurfaceOfGroupMeans = sumSurfaceOfGroupMeans /
SurfaceGroups;
}
else {
meanSurfaceOfGroupMeans = -1;
}
if (SurfaceStdevGroups >= 1) {
meanSurfaceOfGroupStdevs = sumSurfaceOfGroupStdevs /
SurfaceStdevGroups;
}
else {
meanSurfaceOfGroupStdevs = -1;
}
if (SurfaceAsymGroups >= 1) {
meanSurfaceAsymOfGroupMeans =
sumSurfaceAsymOfGroupMeans /
SurfaceAsymGroups;
}
else {
meanSurfaceAsymOfGroupMeans = -1;
}
if (SurfaceAsymStdevGroups >= 1) {
meanSurfaceAsymOfGroupStdevs =
sumSurfaceAsymOfGroupStdevs /
SurfaceAsymStdevGroups;
}
else {
meanSurfaceAsymOfGroupStdevs = -1;
}
//Compute Stdevs of groups
int NgroupBifsStdevs = nToDo;
int NgroupAsymStdevs = nToDo;
int NgroupSurfStdevs = nToDo;
int NgroupSurfAsymStdevs = nToDo;
int NgroupBifsMeans = nToDo;
int NgroupAsymMeans = nToDo;
int NgroupSurfMeans = nToDo;
int NgroupSurfAsymMeans = nToDo;
/////////////////Bifs Stdevs
if (meanOfGroupStdevs == -1) {
stdevOfGroupStdevs = -1;
}
else {
for (int i = 1; i <= nToDo; i++) {
if (groupStdevs[i] == -1) {
--NgroupBifsStdevs;
}
else {
sumOfGroupStdevSqSums +=
( (groupStdevs[i] - meanOfGroupStdevs) *
(groupStdevs[i] - meanOfGroupStdevs));
}
}
if (NgroupBifsStdevs > 1) {
stdevOfGroupStdevs = java.lang.Math.sqrt(
sumOfGroupStdevSqSums /
(NgroupBifsStdevs - 1));
}
else {
stdevOfGroupStdevs = -1;
}
}
////////////////////Asym Stdevs
if (meanAsymOfGroupStdevs == -1) {
stdevAsymOfGroupStdevs = -1;
}
else {
for (int i = 1; i <= nToDo; i++) {
if (groupAsymStdevs[i] == -1) {
--NgroupAsymStdevs;
}
else {
sumAsymOfGroupStdevSqSums +=
( (groupAsymStdevs[i] -
meanAsymOfGroupStdevs) *
(groupAsymStdevs[i] -
meanAsymOfGroupStdevs));
}
}
if (NgroupAsymStdevs > 1) {
stdevAsymOfGroupStdevs = java.lang.Math.sqrt(
sumAsymOfGroupStdevSqSums /
(NgroupAsymStdevs - 1));
}
else {
stdevAsymOfGroupStdevs = -1;
}
}
////////////////////Surf Stdevs
if (meanSurfaceOfGroupStdevs == -1) {
stdevSurfaceOfGroupStdevs = -1;
}
else {
for (int i = 1; i <= nToDo; i++) {
if (groupSurfaceStdevs[i] == -1) {
--NgroupSurfStdevs;
}
else {
sumSurfaceOfGroupStdevSqSums +=
( (groupSurfaceStdevs[i] -
meanSurfaceOfGroupStdevs) *
(groupSurfaceStdevs[i] -
meanSurfaceOfGroupStdevs));
}
}
if (NgroupSurfStdevs > 1) {
stdevSurfaceOfGroupStdevs = java.lang.Math.sqrt(
sumSurfaceOfGroupStdevSqSums /
(NgroupSurfStdevs - 1));
}
else {
stdevSurfaceOfGroupStdevs = -1;
}
}
////////////////////SurfAsym Stdevs
if (meanSurfaceAsymOfGroupStdevs == -1) {
stdevSurfaceAsymOfGroupStdevs = -1;
}
else {
for (int i = 1; i <= nToDo; i++) {
if (groupSurfaceAsymStdevs[i] == -1) {
--NgroupSurfAsymStdevs;
}
else {
sumSurfaceAsymOfGroupStdevSqSums +=
( (groupSurfaceAsymStdevs[i] -
meanSurfaceAsymOfGroupStdevs) *
(groupSurfaceAsymStdevs[i] -
meanSurfaceAsymOfGroupStdevs));
}
}
if (NgroupSurfAsymStdevs > 1) {
stdevSurfaceAsymOfGroupStdevs = java.lang.Math.
sqrt(
sumSurfaceAsymOfGroupStdevSqSums /
(NgroupSurfAsymStdevs - 1));
}
else {
stdevSurfaceAsymOfGroupStdevs = -1;
}
}
/////////////////Bifs Means
if (meanOfGroupMeans == -1) {
stdevOfGroupMeans = -1;
}
else {
for (int i = 1; i <= nToDo; i++) {
if (groupMeans[i] == -1) {
--NgroupBifsMeans;
}
else {
sumOfGroupMeanSqSums +=
( (groupMeans[i] - meanOfGroupMeans) *
(groupMeans[i] - meanOfGroupMeans));
}
}
if (NgroupBifsMeans > 1) {
stdevOfGroupMeans = java.lang.Math.sqrt(
sumOfGroupMeanSqSums /
(NgroupBifsMeans - 1));
}
else {
stdevOfGroupMeans = -1;
}
}
////////////////////Asym Means
if (meanAsymOfGroupMeans == -1) {
stdevAsymOfGroupMeans = -1;
}
else {
for (int i = 1; i <= nToDo; i++) {
if (groupAsymMeans[i] == -1) {
--NgroupAsymMeans;
}
else {
sumAsymOfGroupMeanSqSums +=
( (groupAsymMeans[i] -
meanAsymOfGroupMeans) *
(groupAsymMeans[i] -
meanAsymOfGroupMeans));
}
}
if (NgroupAsymMeans > 1) {
stdevAsymOfGroupMeans = java.lang.Math.sqrt(
sumAsymOfGroupMeanSqSums /
(NgroupAsymMeans - 1));
}
else {
stdevAsymOfGroupMeans = -1;
}
}
////////////////////Surf Means
if (meanSurfaceOfGroupMeans == -1) {
stdevSurfaceOfGroupMeans = -1;
}
else {
for (int i = 1; i <= nToDo; i++) {
if (groupSurfaceMeans[i] == -1) {
--NgroupSurfMeans;
}
else {
sumSurfaceOfGroupMeanSqSums +=
( (groupSurfaceMeans[i] -
meanSurfaceOfGroupMeans) *
(groupSurfaceMeans[i] -
meanSurfaceOfGroupMeans));
}
}
if (NgroupSurfMeans > 1) {
stdevSurfaceOfGroupMeans = java.lang.Math.sqrt(
sumSurfaceOfGroupMeanSqSums /
(NgroupSurfMeans - 1));
}
else {
stdevSurfaceOfGroupStdevs = -1;
}
}
////////////////////SurfAsym Means
if (meanSurfaceAsymOfGroupMeans == -1) {
stdevSurfaceAsymOfGroupMeans = -1;
}
else {
for (int i = 1; i <= nToDo; i++) {
if (groupSurfaceAsymMeans[i] == -1) {
--NgroupSurfAsymMeans;
}
else {
sumSurfaceAsymOfGroupMeanSqSums +=
( (groupSurfaceAsymMeans[i] -
meanSurfaceAsymOfGroupMeans) *
(groupSurfaceAsymMeans[i] -
meanSurfaceAsymOfGroupMeans));
}
}
if (NgroupSurfAsymMeans > 1) {
stdevSurfaceAsymOfGroupMeans = java.lang.Math.
sqrt(
sumSurfaceAsymOfGroupMeanSqSums /
(NgroupSurfAsymMeans - 1));
}
else {
stdevSurfaceAsymOfGroupMeans = -1;
}
}
////////////////////Printing of virt emergent stuff
System.out.println("Mean and Stdev of Means = " +
meanOfGroupMeans +
" +- " + stdevOfGroupMeans + " , of Stdevs = " +
meanOfGroupStdevs + " +- " + stdevOfGroupStdevs);
virtBifsOutFile.println(meanOfGroupMeans + " , " +
stdevOfGroupMeans +
" ," + explodeCount + ", " + meanOfGroupStdevs +
" , " +
stdevOfGroupStdevs);
System.out.println("Mean and Stdev of Asyms = " +
meanAsymOfGroupMeans +
" +- " + stdevAsymOfGroupMeans +
" , of Stdevs = " +
meanAsymOfGroupStdevs + " +- " +
stdevAsymOfGroupStdevs);
virtAsymetryFile.println(meanAsymOfGroupMeans + " , " +
stdevAsymOfGroupMeans +
" ," + explodeCount + ", " + meanAsymOfGroupStdevs +
" , " +
stdevAsymOfGroupStdevs);
System.out.println("Mean and Stdev of Surfaces = " +
meanSurfaceOfGroupMeans +
" +- " + stdevSurfaceOfGroupMeans +
" , of Stdevs = " +
meanSurfaceOfGroupStdevs + " +- " +
stdevSurfaceOfGroupStdevs);
virtSurfaceFile.println(meanSurfaceOfGroupMeans + " , " +
stdevSurfaceOfGroupMeans +
" ," + explodeCount + ", " +
meanSurfaceOfGroupStdevs + " , " +
stdevSurfaceOfGroupStdevs);
System.out.println("Mean and Stdev of Surface Asymetry = " +
meanSurfaceAsymOfGroupMeans +
" +- " + stdevSurfaceAsymOfGroupMeans +
" , of Stdevs = " +
meanSurfaceAsymOfGroupStdevs + " +- " +
stdevSurfaceAsymOfGroupStdevs);
virtSurfaceAsymFile.println(meanSurfaceAsymOfGroupMeans +
" , " +
stdevSurfaceAsymOfGroupMeans +
" ," + explodeCount + ", " +
meanSurfaceAsymOfGroupStdevs +
" , " +
stdevSurfaceAsymOfGroupStdevs);
if (BifsMismatch) {
virtBifsOutFile.println("BifsMismatch");
}
}
}
}
}
}
//compute mean and stdev for real tree bifs and asymetry
RealBifsSum = 0;
RealBifsSqSum = 0;
RealBifsMean = 0;
RealBifsStdev = 0;
int NrealAsyms = stemCount;
RealAsymSum = 0;
RealAsymSqSum = 0;
RealAsymMean = 0;
RealAsymStdev = 0;
RealSurfaceSum = 0;
RealSurfaceSqSum = 0;
RealSurfaceMean = 0;
RealSurfaceStdev = 0;
int NrealSurfaceAsyms = stemCount;
RealSurfaceAsymSum = 0;
RealSurfaceAsymSqSum = 0;
RealSurfaceAsymMean = 0;
RealSurfaceAsymStdev = 0;
for (int i = 1; i <= stemCount; i++) {
RealBifsSum = RealBifsSum + realTreeBifs[i];
if (realAsymetryArray[i] == -1) {
--NrealAsyms;
}
else {
RealAsymSum = RealAsymSum + realAsymetryArray[i];
}
RealSurfaceSum = RealSurfaceSum + realSurfaceArray[i];
if (realSurfaceAsymArray[i] == -1) {
--NrealSurfaceAsyms;
}
else {
RealSurfaceAsymSum = RealSurfaceAsymSum + realSurfaceAsymArray[i];
}
if (Debugging) {
virtBifsOutFile.println(", , , ," + realTreeBifs[i]);
virtAsymetryFile.println(", , , ," + realAsymetryArray[i]);
virtSurfaceFile.println(", , , ," + realSurfaceArray[i]);
virtSurfaceAsymFile.println(", , , ," + realSurfaceAsymArray[i]);
}
}
RealBifsMean = RealBifsSum / stemCount;
if (NrealAsyms > 0) {
RealAsymMean = RealAsymSum / NrealAsyms;
}
else {
RealAsymMean = -1;
}
RealSurfaceMean = RealSurfaceSum / stemCount;
//System.out.println("lll "+RealSurfaceMean);
if (NrealSurfaceAsyms > 0) {
RealSurfaceAsymMean = RealSurfaceAsymSum / NrealSurfaceAsyms;
}
else {
RealSurfaceAsymMean = -1;
}
RealSurfaceAsymMean = RealSurfaceAsymSum / stemCount;
//compute real emergent param stdevs
for (int i = 1; i <= stemCount; i++) {
RealBifsSqSum = RealBifsSqSum + ( (realTreeBifs[i] - RealBifsMean) *
(realTreeBifs[i] - RealBifsMean));
RealSurfaceSqSum = RealSurfaceSqSum +
( (realSurfaceArray[i] - RealSurfaceMean) *
(realSurfaceArray[i] - RealSurfaceMean));
}
RealBifsStdev = java.lang.Math.sqrt(RealBifsSqSum / (stemCount - 1));
RealSurfaceStdev = java.lang.Math.sqrt(RealSurfaceSqSum / (stemCount - 1));
if (RealAsymMean == -1) {
RealAsymStdev = -1;
}
else {
for (int i = 1; i <= stemCount; i++) {
if (realAsymetryArray[i] == -1) {
// --NrealAsyms; already done
}
else {
RealAsymSqSum = RealAsymSqSum +
( (realAsymetryArray[i] - RealAsymMean) *
(realAsymetryArray[i] - RealAsymMean));
}
}
if (NrealAsyms > 1) {
RealAsymStdev = java.lang.Math.sqrt(RealAsymSqSum / (NrealAsyms - 1));
}
else {
RealAsymStdev = -1;
}
}
if (RealSurfaceAsymMean == -1) {
RealSurfaceAsymStdev = -1;
}
else {
for (int i = 1; i <= stemCount; i++) {
if (realSurfaceAsymArray[i] == -1) {
//
}
else {
RealSurfaceAsymSqSum = RealSurfaceAsymSqSum +
( (realSurfaceAsymArray[i] - RealSurfaceAsymMean) *
(realSurfaceAsymArray[i] - RealSurfaceAsymMean));
}
}
if (NrealSurfaceAsyms > 1) {
RealSurfaceAsymStdev = java.lang.Math.sqrt(RealSurfaceAsymSqSum /
(NrealSurfaceAsyms - 1));
}
else {
RealSurfaceAsymStdev = -1;
}
}
//RealBifsMean error check (as computed from tree bifs and individual bifs
if (RealBifsMean != realBiffMean) {
System.out.println("Real bifs do not match: " + RealBifsMean +
" vs " +
realBiffMean);
// System.exit(47);
BifsMismatch = true;
}
System.out.println(" Real Biff Mean and Stdev =" + RealBifsMean +
" +- " +
RealBifsStdev);
System.out.println(" Real Asym Mean and Stdev =" + RealAsymMean +
" +- " +
RealAsymStdev);
System.out.println(" Real Surface Mean and Stdev =" + RealSurfaceMean +
" +- " +
RealSurfaceStdev);
System.out.println(" Real SurfaceAsym Mean and Stdev =" + RealSurfaceAsymMean +
" +- " +
RealSurfaceAsymStdev);
virtBifsOutFile.println(" , , , Real Biff Mean, Stdev ," + RealBifsMean +
" , " +
RealBifsStdev);
virtAsymetryFile.println(" , , , Real Asym Mean, Stdev ," + RealAsymMean +
" , " +
RealAsymStdev);
virtSurfaceFile.println(" , , , Real Surface Mean, Stdev ," + RealSurfaceMean +
" , " +
RealSurfaceStdev);
virtSurfaceAsymFile.println(" , , , Real Surface Asym Mean, Stdev ," +
RealSurfaceAsymMean +
" , " +
RealSurfaceAsymStdev);
virtBifsOutFile.close();
virtDetailsOut.close();
virtAsymetryFile.close();
virtSurfaceFile.close();
virtSurfaceAsymFile.close();
}
catch (IOException e) {
System.out.println("error: " + e.getMessage());
System.out.println("Hit enter.");
char character;
try {
character = (char) System.in.read();
}
catch (IOException f) {}
}
}
}