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duct.cxx
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duct.cxx
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/*! \file duct.cxx
* \brief breastPhantom duct
* \author Christian G. Graff
* \version 1.0
* \date 2018
*
* \copyright To the extent possible under law, the author(s) have
* dedicated all copyright and related and neighboring rights to this
* software to the public domain worldwide. This software is
* distributed without any warranty. You should have received a copy
* of the CC0 Public Domain Dedication along with this software.
* If not, see <http://creativecommons.org/publicdomain/zero/1.0/>.
*
*/
#include "duct.hxx"
using namespace std;
namespace po = boost::program_options;
// default constructor for ductTree
ductTree::ductTree(po::variables_map o, ductTreeInit *init):
randGen(init->seed),
u01(randGen),
radiusDist(o["ductSeg.radiusBetaA"].as<double>(),o["ductSeg.radiusBetaB"].as<double>()){
opt = o;
// assign id and update number of ducts
#pragma omp critical
{
id = num;
num += 1;
}
fill = vtkImageData::New();
double spacing[3];
for(int i=0; i<3; i++){
spacing[i] = (init->endPos[i] - init->startPos[i])/(init->nFill[i]);
}
fill->SetSpacing(spacing);
fill->SetExtent(0, init->nFill[0]-1, 0, init->nFill[1]-1, 0, init->nFill[2]-1);
double origin[3];
for(int i=0; i<3; i++){
origin[i] = init->startPos[i]+spacing[i]/2.0;
}
fill->SetOrigin(origin);
#if VTK_MAJOR_VERSION <= 5
fill->SetNumberOfScalarComponents(1);
fill->SetScalarTypeToDouble();
fill->AllocateScalars();
#else
fill->AllocateScalars(VTK_DOUBLE,1);
#endif
numBranch = 0;
maxBranch = o["ductTree.maxBranch"].as<uint>();
baseLength = o["ductTree.baseLength"].as<double>();
boundBox = init->boundBox;
compartmentId = init->compartmentId;
tissue = init->tissue;
for(int i=0; i<3; i++){
prefDir[i] = init->prefDir[i];
}
breast = init->breast;
TDLUloc = init->TDLUloc;
TDLUattr = init->TDLUattr;
// temporarily set head branch pointer
head = nullptr;
}
// destructor
ductTree::~ductTree(){
fill->Delete();
}
// constructor for first branch (the root)
ductBr::ductBr(double* spos, double* sdir, double r, ductTree *owner){
double pos[3];
int invox[3];
bool failSeg = false; // failed to create a valid segment
bool edgeSeg = false; // segment at boundary of ROI
for(int i=0; i<3; i++){
startPos[i] = spos[i];
startDir[i] = sdir[i];
}
startRad = r;
myTree = owner;
// no parent or sibling branches
parent = nullptr;
sibBranch = nullptr;
// root branch has id 0 and level 0 and generation 0
id = 0;
level = 0;
gen = 0;
// increment tree branch count
myTree->numBranch += 1;
// determine length of branch
length = setLength();
curLength = 0.0;
// generate segments to fill branch
firstSeg = new ductSeg(this);
lastSeg = firstSeg;
// update length
curLength += firstSeg->length;
if (firstSeg->length == 0.0){
failSeg = true;
}
// check if at ROI boundary by seeing if any neighboring voxels are outside ROI
double* thePos = lastSeg->endPos;
double pcoords[3];
myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
for(int a=-1; a<=1; a++){
for(int b=-1; b<=1; b++){
for(int c=-1; c<=1; c++){
unsigned char* p =
static_cast<unsigned char*>(myTree->breast->GetScalarPointer(invox[0]+a,invox[1]+b,invox[2]+c));
if(p[0] != myTree->compartmentId && p[0] != myTree->tissue->duct){
edgeSeg = true;
}
}
}
}
// generate more segments until proper length
while(curLength < length && !failSeg && !edgeSeg){
lastSeg->nextSeg = new ductSeg(lastSeg);
// the lastSeg in parenthesis is used to fill variables including prevSeg ptr
lastSeg = lastSeg->nextSeg;
curLength += lastSeg->length;
if(lastSeg->length == 0.0){
failSeg = true;
//std::cout << "Zero length segment created\n";
}
// check if at ROI boundary
thePos = lastSeg->endPos;
myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
for(int a=-1; a<=1; a++){
for(int b=-1; b<=1; b++){
for(int c=-1; c<=1; c++){
unsigned char* p =
static_cast<unsigned char*>(myTree->breast->GetScalarPointer(invox[0]+a,invox[1]+b,invox[2]+c));
if(p[0] != myTree->compartmentId && p[0] != myTree->tissue->duct){
edgeSeg = true;
std::cout << "A segment hit the boundary\n";
}
}
}
}
}
// fill in end of branch variables
for(int i=0; i<3; i++){
endPos[i] = lastSeg->endPos[i];
endDir[i] = lastSeg->endDir[i];
}
endRad = lastSeg->endRad;
length = curLength;
// set number of children and generate them
nChild = setChild();
if(failSeg){
nChild = 0;
std::cout << "Segment generation failure for branch" << id << std::endl;
}
if(edgeSeg){
std::cout << "ROI edge collision for branch " << id << std::endl;
}
if (nChild == 0){
firstChild = nullptr;
secondChild = nullptr;
// TDLU creation
// check branch length is long enough
if(length >= myTree->opt["TDLU.minLength"].as<double>()){
// long enough
// pick sizes
double minLen = myTree->opt["TDLU.minLength"].as<double>();
double maxLen = myTree->opt["TDLU.maxLength"].as<double>();
double minWid = myTree->opt["TDLU.minWidth"].as<double>();
double maxWid = myTree->opt["TDLU.maxWidth"].as<double>();
if(length < maxLen){
maxLen = length;
}
double len = minLen + (maxLen-minLen)*myTree->u01();
double wid = minWid + (maxWid-minWid)*myTree->u01();
// save position
myTree->TDLUloc->InsertNextPoint(endPos);
// save attributes (length width and principle direction)
double att[5];
att[0] = len;
att[1] = wid;
for(int j=0; j<3; j++){
att[j+2] = endDir[j];
}
myTree->TDLUattr->InsertNextTuple(att);
// segment TDLU
vtkVector3d axis[3];
vtkVector3d v2;
double innerProd;
// coordinate system
// first vector
for(int j=0; j<3; j++){
axis[0][j] = endDir[j];
}
// calculate second vector based on direction to coordinate origin
for(int j=0; j<3; j++){
v2[j] = endPos[j];
}
innerProd = v2.Dot(axis[0]);
for(int j=0; j<3; j++){
axis[1][j] = v2[j] - innerProd*axis[0][j];
}
axis[1].Normalize();
// calculate 3rd vector based on cross product
axis[2] = axis[0].Cross(axis[1]);
// have 3 unit vectors
double imgRes = myTree->opt["base.imgRes"].as<double>();
int searchRad = (int)(ceil(len/imgRes));
#pragma omp parallel for collapse(3)
for(int a=-searchRad; a<=searchRad; a++){
for(int b=-searchRad; b<=searchRad; b++){
for(int c=-searchRad; c<=searchRad; c++){
double curPos[3] = {endPos[0]+a*imgRes, endPos[1]+b*imgRes, endPos[2]+c*imgRes};
int index[3];
double pcoords[3];
// structure coordinates, check if in breast
if(myTree->breast->ComputeStructuredCoordinates(curPos, index, pcoords)){
// in breast extent
// get tissue type, if not duct,skin,nipple,TDLU,outside breast: proceed
unsigned char* p = static_cast<unsigned char*>(myTree->breast->GetScalarPointer(index));
if(p[0] != myTree->tissue->bg && p[0] != myTree->tissue->skin && p[0] != myTree->tissue->nipple &&
p[0] != myTree->tissue->TDLU && p[0] != myTree->tissue->duct){
// check if in oval
// compute position in local coordinate system
vtkVector3d rvec;
vtkVector3d lCoords;
for(int m=0; m<3; m++){
rvec[m] = curPos[m]-endPos[m];
}
for(int m=0; m<3; m++){
lCoords[m] = rvec.Dot(axis[m]);
}
// inside oval?
if(lCoords[0]*lCoords[0]/len/len+lCoords[1]*lCoords[1]/wid/wid+lCoords[2]*lCoords[2]/wid/wid < 1.0){
p[0] = myTree->tissue->TDLU;
}
}
}
}
}
}
}
} else {
// bifurcate
// pick radii
double radii[2];
double thetas[2];
setRadiiThetas(radii,thetas);
// setup first child with level equal to current level
firstChild = new ductBr(this,level,gen+1,radii[0],thetas[0]);
firstChild->sibBranch = new ductBr(this,firstChild,level+1,gen+1,radii[1],thetas[1]);
secondChild = firstChild->sibBranch;
}
}
// constructor for first child branch of a parent branch
ductBr::ductBr(ductBr* par, unsigned int lev, unsigned int g, double r, double theta){
bool failSeg = false;
bool edgeSeg = false;
int invox[3];
// pointers
parent = par;
sibBranch = nullptr;
for(int i=0; i<3; i++){
startPos[i] = parent->endPos[i];
}
startRad = r;
level = lev;
gen = g;
myTree = parent->myTree;
id = myTree->numBranch;
myTree->numBranch += 1;
setDir(startDir,theta);
// determine length of branch
length = setLength();
curLength = 0.0;
// generate segments to fill branch
firstSeg = new ductSeg(this);
lastSeg = firstSeg;
// update length
curLength += firstSeg->length;
if (firstSeg->length == 0.0){
failSeg = true;
}
// check if at ROI boundary
double* thePos = lastSeg->endPos;
double pcoords[3];
myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
for(int a=-1; a<=1; a++){
for(int b=-1; b<=1; b++){
for(int c=-1; c<=1; c++){
unsigned char* p =
static_cast<unsigned char*>(myTree->breast->GetScalarPointer(invox[0]+a,invox[1]+b,invox[2]+c));
if(p[0] != myTree->compartmentId && p[0] != myTree->tissue->duct){
edgeSeg = true;
}
}
}
}
// generate more segments until proper length
while(curLength < length && !failSeg && !edgeSeg){
lastSeg->nextSeg = new ductSeg(lastSeg);
// the lastSeg in parenthesis is used to fill variables including prevSeg ptr
lastSeg = lastSeg->nextSeg;
curLength += lastSeg->length;
if(lastSeg->length == 0.0){
failSeg = true;
}
// check if at ROI boundary
thePos = lastSeg->endPos;
myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
for(int a=-1; a<=1; a++){
for(int b=-1; b<=1; b++){
for(int c=-1; c<=1; c++){
unsigned char* p =
static_cast<unsigned char*>(myTree->breast->GetScalarPointer(invox[0]+a,invox[1]+b,invox[2]+c));
if(p[0] != myTree->compartmentId && p[0] != myTree->tissue->duct){
edgeSeg = true;
}
}
}
}
}
// fill in end of branch variables
for(int i=0; i<3; i++){
endPos[i] = lastSeg->endPos[i];
endDir[i] = lastSeg->endDir[i];
}
endRad = lastSeg->endRad;
length = curLength;
// set number of children and generate them
nChild = setChild();
if(failSeg){
nChild = 0;
//std::cout << "Segment generation failure for branch" << id << std::endl;
}
if(edgeSeg){
nChild = 0;
}
if (nChild == 0){
firstChild = nullptr;
secondChild = nullptr;
// TDLU creation
// check branch length is long enough
if(length >= myTree->opt["TDLU.minLength"].as<double>()){
// long enough
// pick sizes
double minLen = myTree->opt["TDLU.minLength"].as<double>();
double maxLen = myTree->opt["TDLU.maxLength"].as<double>();
double minWid = myTree->opt["TDLU.minWidth"].as<double>();
double maxWid = myTree->opt["TDLU.maxWidth"].as<double>();
if(length < maxLen){
maxLen = length;
}
double len = minLen + (maxLen-minLen)*myTree->u01();
double wid = minWid + (maxWid-minWid)*myTree->u01();
// save position
myTree->TDLUloc->InsertNextPoint(endPos);
// save attributes (length width and principle direction)
double att[5];
att[0] = len;
att[1] = wid;
for(int j=0; j<3; j++){
att[j+2] = endDir[j];
}
myTree->TDLUattr->InsertNextTuple(att);
// segment TDLU
vtkVector3d axis[3];
vtkVector3d v2;
double innerProd;
// coordinate system
// first vector
for(int j=0; j<3; j++){
axis[0][j] = endDir[j];
}
// calculate second vector based on direction to coordinate origin
for(int j=0; j<3; j++){
v2[j] = endPos[j];
}
innerProd = v2.Dot(axis[0]);
for(int j=0; j<3; j++){
axis[1][j] = v2[j] - innerProd*axis[0][j];
}
axis[1].Normalize();
// calculate 3rd vector based on cross product
axis[2] = axis[0].Cross(axis[1]);
// have 3 unit vectors
double imgRes = myTree->opt["base.imgRes"].as<double>();
int searchRad = (int)(ceil(len/imgRes));
#pragma omp parallel for collapse(3)
for(int a=-searchRad; a<=searchRad; a++){
for(int b=-searchRad; b<=searchRad; b++){
for(int c=-searchRad; c<=searchRad; c++){
double curPos[3] = {endPos[0]+a*imgRes, endPos[1]+b*imgRes, endPos[2]+c*imgRes};
int index[3];
double pcoords[3];
// structure coordinates, check if in breast
if(myTree->breast->ComputeStructuredCoordinates(curPos, index, pcoords)){
// in breast extent
// get tissue type, if not duct,skin,nipple,TDLU,outside breast: proceed
unsigned char* p = static_cast<unsigned char*>(myTree->breast->GetScalarPointer(index));
if(p[0] != myTree->tissue->bg && p[0] != myTree->tissue->skin && p[0] != myTree->tissue->nipple &&
p[0] != myTree->tissue->TDLU && p[0] != myTree->tissue->duct){
// check if in oval
// compute position in local coordinate system
vtkVector3d rvec;
vtkVector3d lCoords;
for(int m=0; m<3; m++){
rvec[m] = curPos[m]-endPos[m];
}
for(int m=0; m<3; m++){
lCoords[m] = rvec.Dot(axis[m]);
}
// inside oval?
if(lCoords[0]*lCoords[0]/len/len+lCoords[1]*lCoords[1]/wid/wid+lCoords[2]*lCoords[2]/wid/wid < 1.0){
p[0] = myTree->tissue->TDLU;
}
}
}
}
}
}
}
} else {
// pick radii and thetas
double radii[2];
double thetas[2];
setRadiiThetas(radii,thetas);
// setup first child with level equal to current level
firstChild = new ductBr(this,level,gen+1,radii[0],thetas[0]);
firstChild->sibBranch = new ductBr(this,firstChild,level+1,gen+1,radii[1],thetas[1]);
secondChild = firstChild->sibBranch;
}
}
// constructor for subsequent children (not first child) of a parent branch
ductBr::ductBr(ductBr* par, ductBr* par2, unsigned int lev, unsigned int g, double r, double theta){
bool failSeg = false;
bool edgeSeg = false;
int invox[3];
// pointers
parent = par;
sibBranch = par2;
for(int i=0; i<3; i++){
startPos[i] = parent->endPos[i];
}
startRad = r;
level = lev;
gen = g;
myTree = parent->myTree;
id = myTree->numBranch;
myTree->numBranch += 1;
// set starting direction
setDir(startDir,theta);
// determine length of branch
length = setLength();
curLength = 0.0;
// generate segments to fill branch
firstSeg = new ductSeg(this);
lastSeg = firstSeg;
// update length
curLength += firstSeg->length;
if (firstSeg->length == 0.0){
failSeg = true;
}
// check if at ROI boundary
double* thePos = lastSeg->endPos;
double pcoords[3];
myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
for(int a=-1; a<=1; a++){
for(int b=-1; b<=1; b++){
for(int c=-1; c<=1; c++){
unsigned char* p =
static_cast<unsigned char*>(myTree->breast->GetScalarPointer(invox[0]+a,invox[1]+b,invox[2]+c));
if(p[0] != myTree->compartmentId && p[0] != myTree->tissue->duct){
edgeSeg = true;
}
}
}
}
// generate more segments until proper length
while(curLength < length && !failSeg && !edgeSeg){
lastSeg->nextSeg = new ductSeg(lastSeg);
// the lastSeg in parenthesis is used to fill variables including prevSeg ptr
lastSeg = lastSeg->nextSeg;
curLength += lastSeg->length;
if(lastSeg->length == 0.0){
failSeg = true;
}
// check if at ROI boundary
thePos = lastSeg->endPos;
myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
for(int a=-1; a<=1; a++){
for(int b=-1; b<=1; b++){
for(int c=-1; c<=1; c++){
unsigned char* p =
static_cast<unsigned char*>(myTree->breast->GetScalarPointer(invox[0]+a,invox[1]+b,invox[2]+c));
if(p[0] != myTree->compartmentId && p[0] != myTree->tissue->duct){
edgeSeg = true;
}
}
}
}
}
// fill in end of branch variables
for(int i=0; i<3; i++){
endPos[i] = lastSeg->endPos[i];
endDir[i] = lastSeg->endDir[i];
}
endRad = lastSeg->endRad;
length = curLength;
// set number of children and generate them
nChild = setChild();
if(failSeg){
nChild = 0;
//std::cout << "Segment generation failure for branch" << id << std::endl;
}
if(edgeSeg){
nChild = 0;
}
if (nChild == 0){
firstChild = nullptr;
secondChild = nullptr;
// TDLU creation
// check branch length is long enough
if(length >= myTree->opt["TDLU.minLength"].as<double>()){
// long enough
//std::cout << "Adding TDLU" << std::endl;
// pick sizes
double minLen = myTree->opt["TDLU.minLength"].as<double>();
double maxLen = myTree->opt["TDLU.maxLength"].as<double>();
double minWid = myTree->opt["TDLU.minWidth"].as<double>();
double maxWid = myTree->opt["TDLU.maxWidth"].as<double>();
if(length < maxLen){
maxLen = length;
}
double len = minLen + (maxLen-minLen)*myTree->u01();
double wid = minWid + (maxWid-minWid)*myTree->u01();
// save position
myTree->TDLUloc->InsertNextPoint(endPos);
// save attributes (length width and principle direction)
double att[5];
att[0] = len;
att[1] = wid;
for(int j=0; j<3; j++){
att[j+2] = endDir[j];
}
myTree->TDLUattr->InsertNextTuple(att);
// segment TDLU
vtkVector3d axis[3];
vtkVector3d v2;
double innerProd;
// coordinate system
// first vector
for(int j=0; j<3; j++){
axis[0][j] = endDir[j];
}
// calculate second vector based on direction to coordinate origin
for(int j=0; j<3; j++){
v2[j] = endPos[j];
}
innerProd = v2.Dot(axis[0]);
for(int j=0; j<3; j++){
axis[1][j] = v2[j] - innerProd*axis[0][j];
}
axis[1].Normalize();
// calculate 3rd vector based on cross product
axis[2] = axis[0].Cross(axis[1]);
// have 3 unit vectors
double imgRes = myTree->opt["base.imgRes"].as<double>();
int searchRad = (int)(ceil(len/imgRes));
#pragma omp parallel for collapse(3)
for(int a=-searchRad; a<=searchRad; a++){
for(int b=-searchRad; b<=searchRad; b++){
for(int c=-searchRad; c<=searchRad; c++){
double curPos[3] = {endPos[0]+a*imgRes, endPos[1]+b*imgRes, endPos[2]+c*imgRes};
int index[3];
double pcoords[3];
// structure coordinates, check if in breast
if(myTree->breast->ComputeStructuredCoordinates(curPos, index, pcoords)){
// in breast extent
// get tissue type, if not duct,skin,nipple,TDLU,outside breast: proceed
unsigned char* p = static_cast<unsigned char*>(myTree->breast->GetScalarPointer(index));
if(p[0] != myTree->tissue->bg && p[0] != myTree->tissue->skin && p[0] != myTree->tissue->nipple &&
p[0] != myTree->tissue->TDLU && p[0] != myTree->tissue->duct){
// check if in oval
// compute position in local coordinate system
vtkVector3d rvec;
vtkVector3d lCoords;
for(int m=0; m<3; m++){
rvec[m] = curPos[m]-endPos[m];
}
for(int m=0; m<3; m++){
lCoords[m] = rvec.Dot(axis[m]);
}
// inside oval?
if(lCoords[0]*lCoords[0]/len/len+lCoords[1]*lCoords[1]/wid/wid+lCoords[2]*lCoords[2]/wid/wid < 1.0){
p[0] = myTree->tissue->TDLU;
}
}
}
}
}
}
}
} else {
// pick radii
double radii[2];
double thetas[2];
setRadiiThetas(radii,thetas);
// setup first child with level equal to current level
firstChild = new ductBr(this,level,gen+1,radii[0],thetas[0]);
firstChild->sibBranch = new ductBr(this,firstChild,level+1,gen+1,radii[1],thetas[1]);
secondChild = firstChild->sibBranch;
}
}
double ductBr::setLength(void){
// set length using random distribution and level
double len;
double randVal = myTree->u01();
double baseLen = myTree->baseLength;
double lenShrink = myTree->opt["ductBr.lenShrink"].as<double>();
double lenRange = myTree->opt["ductBr.lenRange"].as<double>();
len = baseLen*pow(lenShrink,level);
// add variability +/- lenRange fraction of len
len = len - lenRange*len + randVal*2*lenRange*len;
return(len);
}
unsigned int ductBr::setChild(void){
// determine number of child branches
// cumulative probabilities of having 0-4 children based on level
//unsigned int maxChild = myTree->opt["ductBr.maxChild"].as<uint>();
//unsigned int levBound = myTree->opt["ductBr.childLevBound"].as<uint>();
//ostringstream var;
//double *prob = (double *)malloc((levBound+1)*maxChild*sizeof(double));
//for(int a=0; a<=levBound; a++){
// for(int b=0; b<maxChild; b++){
// var.str("");
// var.clear();
// var << "ductBr.child" << a << b;
// prob[a*maxChild+b] = myTree->opt[var.str()].as<double>();
// }
//}
// if small enough, no children
double minRad = myTree->opt["ductBr.childMinRad"].as<double>();
if(endRad < minRad){
//free(prob);
return(0);
}
// check for max number branches
if(myTree->numBranch >= myTree->maxBranch){
//free(prob);
return(0);
}
// define maximum generation
unsigned int maxGen = myTree->opt["ductTree.maxGen"].as<uint>();
if(gen > maxGen){
//free(prob);
return(0);
}
//double randVal = myTree->u01();
//
//for(int b=maxChild-1; b >= 0; b--){
// if(randVal > prob[std::min(level,levBound)*maxChild+b]){
// free(prob);
// return(b+1);
// }
//}
// default to no children
//free(prob);
// default 2 children
return(2);
}
void ductBr::setRadiiThetas(double* radii, double* thetas){
// set radii and angles of child branches based on the parent
double minFrac = myTree->opt["ductBr.minRadFrac"].as<double>();
double maxFrac = myTree->opt["ductBr.maxRadFrac"].as<double>();
double randVal = myTree->u01();
// first child radius
double myFrac = minFrac + randVal*(maxFrac-minFrac);
radii[0] = myFrac*endRad;
// second child radius based on Murray's law
double b = 1.0/myFrac;
double a = pow(pow(b,3.0)-1.0,1.0/3.0);
radii[1] = a*radii[0];
// first child theta
double lBound = (pow(b,4.0)+1.0-pow(a,4.0))/(2.0*pow(b,2.0));
double uBound = (pow(b,2.0)+1.0-pow(a,2.0))/(2.0*b);
randVal = myTree->u01();
double ctheta = lBound + randVal*(uBound-lBound);
thetas[0] = acos(ctheta);
// second child theta
lBound = (pow(b,4.0)+pow(a,4.0)-1.0)/(2*pow(a,2.0)*pow(b,2.0));
uBound = (pow(b,2.0)+pow(a,2.0)-1.0)/(2*a*b);
randVal = myTree->u01();
ctheta = lBound + randVal*(uBound-lBound);
thetas[1] = acos(ctheta);
}
void ductBr::setDir(double* sdir, double theta){
const double pi = boost::math::constants::pi<double>();
// set initial direction of branch
double dir[3];
double tempV[3];
double basis1[3];
double basis2[3];
double rotateJitter = myTree->opt["ductBr.rotateJitter"].as<double>();
double rotate;
if(sibBranch == nullptr){
// this is the first child
// random rotation about parent direction
rotate = 2*pi*myTree->u01();
azimuth = rotate;
} else {
// this is the second child
rotate = sibBranch->azimuth + pi;
double randVal = myTree->u01();
rotate = rotate - rotateJitter + randVal*2*rotateJitter;
azimuth = rotate;
}
// project origin onto plane perpendicular parent endDir
double dotProd = 0.0;
for(int i=0; i<3; i++){
dotProd += parent->endDir[i]*startPos[i];
}
for(int i=0; i<3; i++){
tempV[i] = dotProd*parent->endDir[i];
basis1[i] = tempV[i] - startPos[i];
}
// normalize basis1
double norm = 0.0;
for(int i=0; i<3; i++){
norm += basis1[i]*basis1[i];
}
norm = sqrt(norm);
for(int i=0; i<3; i++){
basis1[i] = basis1[i]/norm;
}
// find second basis vector using cross product
basis2[0] = parent->endDir[1]*basis1[2] - parent->endDir[2]*basis1[1];
basis2[1] = parent->endDir[2]*basis1[0] - parent->endDir[0]*basis1[2];
basis2[2] = parent->endDir[0]*basis1[1] - parent->endDir[1]*basis1[0];
for(int i=0; i<3; i++){
sdir[i] = cos(theta)*parent->endDir[i] + sin(theta)*(cos(rotate)*basis1[i] + sin(rotate)*basis2[i]);
}
}
// branch destructor that also deletes all child branches
ductBr::~ductBr(){
// delete segments
ductSeg* delSeg;
while(firstSeg != lastSeg){
delSeg = firstSeg;
firstSeg = firstSeg->nextSeg;
delete(delSeg);
}
delete(firstSeg);
// delete child branches
ductBr* delBranch;
while(firstChild != secondChild){
delBranch = firstChild;
firstChild = firstChild->secondChild;
delete(delBranch);
}
delete(firstChild);
}
// constructor for first segment
ductSeg::ductSeg(ductBr* br){
myBranch = br;
prevSeg = nullptr;
nextSeg = this;
for(int i=0; i<3; i++){
startPos[i] = myBranch->startPos[i];
startDir[i] = myBranch->startDir[i];
}
startRad = myBranch->startRad;
// keeping derivatives zero at nodes for now
startDeriv = 0.0;
// code to generate random segment
makeSeg();
}
// constructor for subsequent segments
ductSeg::ductSeg(ductSeg* pr){
prevSeg = pr;
myBranch = prevSeg->myBranch;
nextSeg = this;
for(int i=0; i<3; i++){
startPos[i] = prevSeg->endPos[i];
startDir[i] = prevSeg->endDir[i];
}
startRad = prevSeg->endRad;
startDeriv = prevSeg->endDeriv;
// code to generate random segment
makeSeg();
}
void ductSeg::makeSeg(){
const double pi = boost::math::constants::pi<double>();
double segFrac = myBranch->myTree->opt["ductSeg.segFrac"].as<double>();
unsigned int numTry = myBranch->myTree->opt["ductSeg.numTry"].as<uint>();
unsigned int maxTry = myBranch->myTree->opt["ductSeg.maxTry"].as<uint>();
unsigned int absMaxTry = myBranch->myTree->opt["ductSeg.absMaxTry"].as<uint>();
double maxRad = myBranch->myTree->opt["ductSeg.maxCurvRad"].as<double>();
double angleMax = pi*myBranch->myTree->opt["ductSeg.maxCurvFrac"].as<double>();
double roiStep = myBranch->myTree->opt["ductSeg.roiStep"].as<double>();
double densityWt = myBranch->myTree->opt["ductSeg.densityWt"].as<double>();
double angleWt = myBranch->myTree->opt["ductSeg.angleWt"].as<double>();
double prefDir[3]; // preferential direction of growth
for(int i=0; i<3; i++){
prefDir[i] = myBranch->myTree->prefDir[i];
}
double maxEndRad = myBranch->myTree->opt["ductSeg.maxEndRad"].as<double>();
double minEndRad = myBranch->myTree->opt["ductSeg.minEndRad"].as<double>();
int fillExtent[6]; // extents of fill
myBranch->myTree->fill->GetExtent(fillExtent);
double pos[3];
unsigned int invox[3];
unsigned int curTry; // number of valid segments tested so far
unsigned int totalTry; // number of test segments so far
unsigned int allTry; // total number of test segments overall
double lengthLB, lengthUB; // bounds on random length
double randVal, quantileVal; // for length random generator
double theta; // rotation of segment
double radius; // segment radius of curvature
double radLB,radUB; // min and max radius of curvature
double curv[3]; // point of rotation
double curvNorm; // stores norm(startPos-curv)
double basis1[3];
double basis2[3]; // basis vectors
double tempV[3];
double checkPos[3]; // checking if segment position in ROI
int myVoxel[3];
double pcoords[3];
double checkAngle;