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artery.cxx
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/*! \file artery.cxx
* \brief breastPhantom artery
* \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 "artery.hxx"
using namespace std;
namespace po = boost::program_options;
// default constructor for arteryTree
arteryTree::arteryTree(po::variables_map o, arteryTreeInit *init):
randGen(init->seed),
u01(randGen),
radiusDist(o["vesselSeg.radiusBetaA"].as<double>(),o["vesselSeg.radiusBetaB"].as<double>()){
opt = o;
// assign id and update number of arteries
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["vesselTree.maxBranch"].as<uint>();
baseLength = o["vesselTree.baseLength"].as<double>();
boundBox = init->boundBox;
tissue = init->tissue;
for(int i=0; i<3; i++){
nipplePos[i] = init->nipplePos[i];
}
breast = init->breast;
// temporarily set head branch pointer
head = nullptr;
}
// destructor
arteryTree::~arteryTree(){
fill->Delete();
}
// constructor for first branch (the root)
arteryBr::arteryBr(double* spos, double* sdir, double r, arteryTree *owner){
double pos[3];
int invox[3];
bool failSeg = false; // failed to create a valid segment
bool edgeSeg = false; // segment at boundary of ROI
myTree = owner;
int fillExtent[6]; // extents of fill
myTree->fill->GetExtent(fillExtent);
for(int i=0; i<3; i++){
startPos[i] = spos[i];
startDir[i] = sdir[i];
}
startRad = r;
// 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 arterySeg(this);
lastSeg = firstSeg;
// update length
curLength += firstSeg->length;
if (firstSeg->length == 0.0){
failSeg = true;
}
int breastExtent[6];
myTree->breast->GetExtent(breastExtent);
// check if at ROI boundary by seeing if any neighboring voxels are outside ROI
double* thePos = lastSeg->endPos;
double pcoords[3];
int inVol;
inVol = myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
if(inVol){
// check if near phantom boundary
if(invox[0] <= breastExtent[0] || invox[0] >= breastExtent[1] ||
invox[1] <= breastExtent[2] || invox[1] >= breastExtent[3] ||
invox[2] <= breastExtent[4] || invox[2] >= breastExtent[5]){
failSeg = true;
}
} else {
failSeg = true;
}
if(!failSeg){
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->tissue->skin || p[0] == myTree->tissue->bg){
edgeSeg = true;
}
}
}
}
}
// generate more segments until proper length
while(curLength < length && !failSeg && !edgeSeg){
lastSeg->nextSeg = new arterySeg(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;
inVol = myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
if(inVol){
if(invox[0] <= breastExtent[0] || invox[0] >=breastExtent[1]||
invox[1] <= breastExtent[2] || invox[1] >=breastExtent[3] ||
invox[2] <= breastExtent[4] || invox[2] >=breastExtent[5]){
failSeg = true;
}
} else {
failSeg = true;
}
if(!failSeg){
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->tissue->skin || p[0] == myTree->tissue->bg){
edgeSeg = true;
}
}
}
}
}
}
// insert segments into phantom and update fill map
arterySeg* mySeg = firstSeg;
arterySeg* prevSeg;
do{
mySeg->updateMap();
#pragma omp parallel for collapse(3)
for(int a=fillExtent[0]; a<=fillExtent[1]; a++){
for(int b=fillExtent[2]; b<=fillExtent[3]; b++){
for(int c=fillExtent[4]; c<=fillExtent[5]; c++){
double* v = static_cast<double*>(myTree->fill->GetScalarPointer(a,b,c));
if(v[0] > 0.0){
double dist;
// voxel in ROI
// voxel location
vtkIdType id;
int coord[3];
coord[0] = a;
coord[1] = b;
coord[2] = c;
id = myTree->fill->ComputePointId(coord);
// get spatial coordinates of point
double pos[3];
myTree->fill->GetPoint(id,pos);
dist = vtkMath::Distance2BetweenPoints(mySeg->endPos, pos);
if(dist < v[0]){
// update minimum distance
v[0] = dist;
}
}
}
}
}
prevSeg = mySeg;
mySeg = mySeg->nextSeg;
} while(prevSeg != mySeg);
// 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;
}
if(edgeSeg){
nChild = 0;
std::cout << "ROI edge collision for branch " << id << std::endl;
}
if (nChild == 0){
firstChild = nullptr;
secondChild = nullptr;
} else {
// bifurcate
// pick radii
double radii[2];
double thetas[2];
setRadiiThetas(radii,thetas);
// setup first child with level equal to current level
firstChild = new arteryBr(this,level,gen+1,radii[0],thetas[0]);
firstChild->sibBranch = new arteryBr(this,firstChild,level+1,gen+1,radii[1],thetas[1]);
secondChild = firstChild->sibBranch;
}
}
// constructor for first child branch of a parent branch
arteryBr::arteryBr(arteryBr* par, unsigned int lev, unsigned int g, double r, double theta){
int maxSegTry = 10;
int numSegTry = 0;
bool failSeg = false;
bool edgeSeg = false;
int invox[3];
parent = par;
sibBranch = nullptr;
myTree = parent->myTree;
int fillExtent[6]; // extents of fill
myTree->fill->GetExtent(fillExtent);
for(int i=0; i<3; i++){
startPos[i] = parent->endPos[i];
}
startRad = r;
level = lev;
gen = g;
id = myTree->numBranch;
myTree->numBranch += 1;
length = setLength();
bool segSuccess = false;
int breastExtent[6];
myTree->breast->GetExtent(breastExtent);
do{
numSegTry++;
setDir(startDir, theta);
curLength = 0.0;
// generate segments to fill branch
firstSeg = new arterySeg(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];
int inVol;
inVol = myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
if(inVol){
if(invox[0] <= breastExtent[0] || invox[0] >= breastExtent[1] ||
invox[1] <= breastExtent[2] || invox[1] >= breastExtent[3] ||
invox[2] <= breastExtent[4] || invox[2] >= breastExtent[5]){
failSeg = true;
}
} else {
failSeg = true;
}
if(!failSeg){
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->tissue->skin || p[0] == myTree->tissue->bg || p[0] == myTree->tissue->muscle){
edgeSeg = true;
}
}
}
}
}
// generate more segments until proper length
while(curLength < length && !failSeg && !edgeSeg){
lastSeg->nextSeg = new arterySeg(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;
inVol = myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
if(inVol){
if(invox[0] <= breastExtent[0] || invox[0] >= breastExtent[1] ||
invox[1] <= breastExtent[2] || invox[1] >= breastExtent[3] ||
invox[2] <= breastExtent[4] || invox[2] >= breastExtent[5]){
failSeg = true;
}
} else {
failSeg = true;
}
if(!failSeg){
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->tissue->skin || p[0] == myTree->tissue->bg || p[0] == myTree->tissue->muscle){
edgeSeg = true;
}
}
}
}
}
}
if(failSeg || edgeSeg){
// delete current segments and try again
arterySeg* delSeg;
while(firstSeg != lastSeg){
delSeg = firstSeg;
firstSeg = firstSeg->nextSeg;
delete(delSeg);
}
delete(firstSeg);
} else {
segSuccess = true;
}
} while(!segSuccess && numSegTry < maxSegTry);
// insert segments into phantom and update fill map
arterySeg* mySeg = firstSeg;
arterySeg* prevSeg;
do{
mySeg->updateMap();
#pragma omp parallel for collapse(3)
for(int a=fillExtent[0]; a<=fillExtent[1]; a++){
for(int b=fillExtent[2]; b<=fillExtent[3]; b++){
for(int c=fillExtent[4]; c<=fillExtent[5]; c++){
double* v = static_cast<double*>(myTree->fill->GetScalarPointer(a,b,c));
if(v[0] > 0.0){
double dist;
// voxel in ROI
// voxel location
vtkIdType id;
int coord[3];
coord[0] = a;
coord[1] = b;
coord[2] = c;
id = myTree->fill->ComputePointId(coord);
// get spatial coordinates of point
double pos[3];
myTree->fill->GetPoint(id,pos);
dist = vtkMath::Distance2BetweenPoints(mySeg->endPos, pos);
if(dist < v[0]){
// update minimum distance
v[0] = dist;
}
}
}
}
}
prevSeg = mySeg;
mySeg = mySeg->nextSeg;
} while(prevSeg != mySeg);
// 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(!segSuccess){
nChild = 0;
}
if (nChild == 0){
firstChild = nullptr;
secondChild = nullptr;
} else {
// pick radii
double radii[2];
double thetas[2];
setRadiiThetas(radii,thetas);
// setup first child with level equal to current level
firstChild = new arteryBr(this,level,gen+1,radii[0],thetas[0]);
firstChild->sibBranch = new arteryBr(this,level+1,gen+1,radii[1],radii[1]);
secondChild = firstChild->sibBranch;
}
}
// constructor for subsequent children (not first child) of a parent branch
arteryBr::arteryBr(arteryBr* par, arteryBr* par2, unsigned int lev, unsigned int g, double r, double theta){
int maxSegTry = 10;
int numSegTry = 0;
bool failSeg = false;
bool edgeSeg = false;
int invox[3];
parent = par;
sibBranch = par2;
myTree = parent->myTree;
int fillExtent[6]; // extents of fill
myTree->fill->GetExtent(fillExtent);
for(int i=0; i<3; i++){
startPos[i] = parent->endPos[i];
}
startRad = r;
level = lev;
gen = g;
id = myTree->numBranch;
myTree->numBranch += 1;
length = setLength();
bool segSuccess = false;
int breastExtent[6];
myTree->breast->GetExtent(breastExtent);
do{
numSegTry++;
setDir(startDir, theta);
curLength = 0.0;
// generate segments to fill branch
firstSeg = new arterySeg(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];
int inVol;
inVol = myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
if(inVol){
if(invox[0] <= breastExtent[0] || invox[0] >= breastExtent[1] ||
invox[1] <= breastExtent[2] || invox[1] >= breastExtent[3] ||
invox[2] <= breastExtent[4] || invox[2] >= breastExtent[5]){
failSeg = true;
}
} else {
failSeg = true;
}
if(!failSeg){
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->tissue->skin || p[0] == myTree->tissue->bg || p[0] == myTree->tissue->muscle){
edgeSeg = true;
}
}
}
}
}
// generate more segments until proper length
while(curLength < length && !failSeg && !edgeSeg){
lastSeg->nextSeg = new arterySeg(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;
inVol = myTree->breast->ComputeStructuredCoordinates(thePos, invox, pcoords);
if(inVol){
if(invox[0] <= breastExtent[0] || invox[0] >= breastExtent[1] ||
invox[1] <= breastExtent[2] || invox[1] >= breastExtent[3] ||
invox[2] <= breastExtent[4] || invox[2] >= breastExtent[5]){
failSeg = true;
}
} else {
failSeg = true;
}
if(!failSeg){
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->tissue->skin || p[0] == myTree->tissue->bg || p[0] == myTree->tissue->muscle){
edgeSeg = true;
}
}
}
}
}
}
if(failSeg || edgeSeg){
// delete current segments and try again
arterySeg* delSeg;
while(firstSeg != lastSeg){
delSeg = firstSeg;
firstSeg = firstSeg->nextSeg;
delete(delSeg);
}
delete(firstSeg);
} else {
segSuccess = true;
}
} while(!segSuccess && numSegTry < maxSegTry);
// insert segments into phantom and update fill map
arterySeg* mySeg = firstSeg;
arterySeg* prevSeg;
do{
mySeg->updateMap();
// update density map
#pragma omp parallel for collapse(3)
for(int a=fillExtent[0]; a<=fillExtent[1]; a++){
for(int b=fillExtent[2]; b<=fillExtent[3]; b++){
for(int c=fillExtent[4]; c<=fillExtent[5]; c++){
double* v = static_cast<double*>(myTree->fill->GetScalarPointer(a,b,c));
if(v[0] > 0.0){
double dist;
// voxel in ROI
// voxel location
vtkIdType id;
int coord[3];
coord[0] = a;
coord[1] = b;
coord[2] = c;
id = myTree->fill->ComputePointId(coord);
// get spatial coordinates of point
double pos[3];
myTree->fill->GetPoint(id,pos);
dist = vtkMath::Distance2BetweenPoints(mySeg->endPos, pos);
if(dist < v[0]){
// update minimum distance
v[0] = dist;
}
}
}
}
}
prevSeg = mySeg;
mySeg = mySeg->nextSeg;
} while(prevSeg != mySeg);
// 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(!segSuccess){
nChild = 0;
}
if (nChild == 0){
firstChild = nullptr;
secondChild = nullptr;
} else {
// pick radii and angles
double radii[2];
double thetas[2];
setRadiiThetas(radii, thetas);
// setup first child with level equal to current level
firstChild = new arteryBr(this,level,gen+1,radii[0],thetas[0]);
firstChild->sibBranch = new arteryBr(this,level+1,gen+1,radii[1],thetas[1]);
secondChild = firstChild->sibBranch;
}
}
double arteryBr::setLength(void){
double len;
double randVal = myTree->u01();
double baseLen = myTree->baseLength;
double lenShrink = myTree->opt["vesselBr.lenShrink"].as<double>();
double lenRange = myTree->opt["vesselBr.lenRange"].as<double>();
len = baseLen*pow(lenShrink,level);
len = len - lenRange*len + randVal*2*lenRange*len;
return(len);
}
unsigned int arteryBr::setChild(void){
// determine number of child branches
// if small enough, no children
double minRad = myTree->opt["vesselBr.childMinRad"].as<double>();
if(endRad < minRad){
return(0);
}
// check for max number branches
if(myTree->numBranch >= myTree->maxBranch){
return(0);
}
// define maximum generation
unsigned int maxGen = myTree->opt["vesselTree.maxGen"].as<uint>();
if(gen > maxGen){
return(0);
}
// default to 2 children
return(2);
}
void arteryBr::setRadiiThetas(double* radii, double* thetas){
// set radii of child branches based on radii of the parent
double minFrac = myTree->opt["vesselBr.minRadFrac"].as<double>();
double maxFrac = myTree->opt["vesselBr.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 arteryBr::setDir(double* sdir, double theta){
const double pi = boost::math::constants::pi<double>();
// set initial direction of child branches
double dir[3];
double tempV[3];
double basis1[3];
double basis2[3];
double rotateJitter = myTree->opt["ductBr.rotateJitter"].as<double>();
double rotate;
double minAngleSep = 0.1;
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, keep away from sibling
do{
rotate = 2*pi*myTree->u01();
} while(fabs(rotate-sibBranch->azimuth) < minAngleSep);
//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
arteryBr::~arteryBr(){
// delete segments
arterySeg* delSeg;
while(firstSeg != lastSeg){
delSeg = firstSeg;
firstSeg = firstSeg->nextSeg;
delete(delSeg);
}
delete(firstSeg);
// delete child branches
arteryBr* delBranch;
while(firstChild != secondChild){
delBranch = firstChild;
firstChild = firstChild->secondChild;
delete(delBranch);
}
delete(firstChild);
}
// constructor for first segment
arterySeg::arterySeg(arteryBr* 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
arterySeg::arterySeg(arterySeg* 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 arterySeg::makeSeg(){
const double pi = boost::math::constants::pi<double>();
double segFrac = myBranch->myTree->opt["ductSeg.segFrac"].as<double>();
unsigned int numTry = myBranch->myTree->opt["vesselSeg.numTry"].as<uint>();
unsigned int maxTry = myBranch->myTree->opt["vesselSeg.maxTry"].as<uint>();
unsigned int absMaxTry = myBranch->myTree->opt["vesselSeg.absMaxTry"].as<uint>();
double maxRad = myBranch->myTree->opt["vesselSeg.maxCurvRad"].as<double>();
maxRad = maxRad/(myBranch->level+1.0);
double angleMax = pi*myBranch->myTree->opt["vesselSeg.maxCurvFrac"].as<double>();
double roiStep = myBranch->myTree->opt["vesselSeg.roiStep"].as<double>();
double densityWt = myBranch->myTree->opt["vesselSeg.densityWt"].as<double>();
double angleWt = myBranch->myTree->opt["vesselSeg.angleWt"].as<double>();
double dirWt = myBranch->myTree->opt["vesselSeg.dirWt"].as<double>();
double prefDir[3]; // preferential direction of growth
for(int i=0; i<3; i++){
prefDir[i] = myBranch->myTree->nipplePos[i] - startPos[i];
}
vtkMath::Normalize(prefDir);
double maxEndRad = myBranch->myTree->opt["vesselSeg.maxEndRad"].as<double>();
double minEndRad = myBranch->myTree->opt["vesselSeg.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;
double checkLength;
double currentDir[3]; // unit vector in current direction
double angleStep; // angular step size for checking in ROI for segment
bool foundSeg = false; // have we found a good segment yet?
bool inROI; // is current test segment in ROI?
bool inFOV; // is current segment in FOV?
int inVol; // Structured coordinates check
double travelDist;
double travelStep = 1.0;
// breast FOV for checking if segment in FOV
double breastOrigin[3];
double breastSpacing[3];
int breastDim[3];
double breastFOV[6];
int breastExtent[6];
myBranch->myTree->breast->GetOrigin(breastOrigin);
myBranch->myTree->breast->GetSpacing(breastSpacing);
//myBranch->myTree->breast->GetDimensions(breastDim);
myBranch->myTree->breast->GetExtent(breastExtent);
for(int i=0; i<3; i++){
breastFOV[2*i] = breastOrigin[i]+(double)breastExtent[2*i]*breastSpacing[i]-breastSpacing[i]/2.0;
breastFOV[2*i+1] = breastOrigin[i]+(double)breastExtent[2*i+1]*breastSpacing[i]+breastSpacing[i]/2.0;
}
double bestCurv[3]; // best center of curvature found so far
double bestRadius;
double bestCost; // best cost found so far
double cost; // current cost
double density; // change in density of artery structure due to new segment
// determine proposed segment length
length = myBranch->length*segFrac;
if(length > (myBranch->length - myBranch->curLength)){
// truncate
length = myBranch->length - myBranch->curLength;
}
allTry = 0;
while (!foundSeg && allTry < absMaxTry){
curTry = 0;
while (curTry < numTry){
totalTry = 0;
inROI = false;
inFOV = false;
while (!inROI && !inFOV && totalTry < maxTry){
allTry++;
// generate random segment
theta = 2*pi*myBranch->myTree->u01();
radUB = maxRad;
radLB = length/angleMax;
// use beta distribution to pick radius
randVal = myBranch->myTree->u01();
quantileVal = boost::math::quantile(myBranch->myTree->radiusDist, randVal);
// scale to radius range
radius = quantileVal*(radUB-radLB) + radLB;
totalTry += 1;
// checking if in ROI
// need basis vectors in plane perpendicular to startDir
// project origin (0,0,0) onto plane perpendicular to startDir
vtkMath::ProjectVector(startPos, startDir, tempV);
vtkMath::Subtract(tempV, startPos, basis1);
// normalize it
vtkMath::Normalize(basis1);
// find second basis vector using cross product
vtkMath::Cross(startDir,basis1,basis2);
// calculate curvature
for(int i=0; i<3; i++){
curv[i] = startPos[i] + radius*(basis1[i]*cos(theta) + basis2[i]*sin(theta));
}
// calculate norm(startPos-curv)
curvNorm = 0.0;
for(int i=0; i<3; i++){
curvNorm += (startPos[i]-curv[i])*(startPos[i]-curv[i]);
}
curvNorm = sqrt(curvNorm);
// check if in ROI
angleStep = roiStep/radius;
checkAngle = 0.0;
checkLength = 0.0;
inROI = true;
inFOV = true;
while (checkLength < length && inROI && inFOV){
for(int i=0; i<3; i++){
checkPos[i] = curv[i] + radius*((startPos[i]-curv[i])/curvNorm*cos(checkAngle)+startDir[i]*sin(checkAngle));
}
// is point in FOV and in ROI?
// check FOV first