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breastCompress.cxx
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breastCompress.cxx
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/*! \file breastCompress.cxx
* \brief breastCompress main file
* \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 "breastCompress.hxx"
namespace po = boost::program_options;
int main(int argc, char* argv[]){
double pi = vtkMath::Pi();
// breast tissue parameters
// Young's modulus, Poisson ratio, density
double fatModulus = 5.0; // kPa (equivalent to kg/(mm*s^2))
double fatPoisson = 0.49;
double fatDensity = 0.000001; // kg/mm^3
double glandModulus = 15.0; // kPa
double glandPoisson = 0.49;
double glandDensity = 0.000001; // kg/mm^3
double massModulus = 20.0; // kPa
double massPoisson = 0.49;
double massDensity = 0.00001; // kg/mm^3
tissueStruct tissue;
tissue.bg = 0;
tissue.skin = 2;
tissue.nipple = 33;
tissue.fat = 1;
tissue.cooper = 88;
tissue.gland = 29;
tissue.TDLU = 95;
tissue.duct = 125;
tissue.artery = 150;
tissue.vein = 225 ;
tissue.muscle = 40;
tissue.mass = 200;
tissue.calc = 250;
tissue.paddle = 50;
// command line parameters
po::options_description opts("All options");
opts.add_options()
("seed,s", po::value<int>()->required(), "input breast seed")
("febiopath,f", po::value<std::string>(), "FeBiO path")
("angle,a", po::value<double>()->default_value(0.0), "compression paddle angle (degrees)")
("thickness,t", po::value<double>()->required(), "final thickness (mm)")
// 0 -> autoremesh, else number of meshes
("meshes,m", po::value<int>()->default_value(0), "Number of times to (re)mesh")
("dir,d", po::value<std::string>()->default_value("."),"work directory")
("tetvolume,v", po::value<double>()->default_value(25.0), "maximum tetrahedral volume")
("decimateFrac,r", po::value<double>()->default_value(0.99), "surface mesh decimation fraction")
("help,h", "print help message")
;
po::variables_map vm;
// get command line arguments
po::store(parse_command_line(argc,argv,opts), vm);
if (vm.count("help")) {
cout << "\n";
cout << "breastCompress - breast phantom compression simulation\n\n";
cout << opts << "\n";
return 1;
}
// determine FeBiO path
char febioPath[256];
if(vm.count("febiopath")){
// specified on command line
std::string febio = vm["febiopath"].as<std::string>();
strcpy(febioPath, febio.c_str());
} else {
// check environment variable
const char* svar = getenv("FEBIO_PATH");
if(svar == NULL){
cout << "Error: FeBiO path not specified\n";
return(EXIT_FAILURE);
} else {
strcpy(febioPath, svar);
}
}
if(!vm.count("seed") || !vm.count("thickness")){
cout << "Command line options missing\n" ;
cout << opts << "\n";
return(EXIT_FAILURE);
}
int seed = vm["seed"].as<int>();
// compression angle converted to radians
double angle = vm["angle"].as<double>();
angle = angle*pi/180.0;
bool rotate = false;
if(fabs(angle) > 1e-9){
rotate = true;
}
double thickness = vm["thickness"].as<double>();
// check for nonsensical thickness
if(thickness < 10.0 || thickness > 200.0){
cerr << "Compressed thickness should be between 10 and 200 mm.\n";
return(1);
}
int numMeshes = vm["meshes"].as<int>();
bool autoRemesh = (numMeshes==0);
// mesh parameters
//double decimateFrac = 0.99;
double decimateFrac = vm["decimateFrac"].as<double>();
if(decimateFrac < 0.0 || decimateFrac >= 1.0){
cerr << "Invalid mesh decimation fraction.\n";
return(1);
}
tetgenbehavior tetPar;
tetPar.plc = 1;
tetPar.quality = 1;
tetPar.coarsen = 1;
tetPar.fixedvolume = 1;
//tetPar.maxvolume = 25.0;
tetPar.maxvolume = vm["tetvolume"].as<double>();
tetPar.optlevel = 10;
//tetPar.nobisect = 1;
tetPar.neighout = 2; // trigger calculation of boundary face parents
// tetPar.nomergevertex = 1;
int paddleNh = 18;
int paddleNl = 25;
int paddleNw = 25;
std::string workDir = vm["dir"].as<std::string>();
bool done = false;
double minimumFinalThicknessSoFar = 99999.9; // Dummy value.
double prevTopPaddleCenterDerotated[3] = {0.0,0.0,0.0};
double prevBotPaddleCenterDerotated[3] = {0.0,0.0,0.0};
double origPaddleWidth = 0.0;
double origPaddleLength = 0.0;
double paddleDist = 0.0;
int meshCount = 0;
const int MAX_MESHES = 18;
// main loop
while((autoRemesh && !done && (meshCount < MAX_MESHES))
||(!autoRemesh && (meshCount < numMeshes))){
char inputHdrFilename[256];
char inputgzFilename[256];
char inputLocFilename[256];
vtkSmartPointer<vtkImageData> input =
vtkSmartPointer<vtkImageData>::New();
if(meshCount == 0){
sprintf(inputHdrFilename, "%s/p_%d.mhd", workDir.c_str(), seed);
sprintf(inputLocFilename, "%s/p_%d.loc", workDir.c_str(), seed);
sprintf(inputgzFilename, "%s/p_%d.raw.gz", workDir.c_str(), seed);
} else {
sprintf(inputHdrFilename, "%s/p_%d_%d.mhd", workDir.c_str(), seed, meshCount-1);
sprintf(inputLocFilename, "%s/p_%d_%d.loc", workDir.c_str(), seed, meshCount-1);
sprintf(inputgzFilename, "%s/p_%d_%d.raw.gz", workDir.c_str(), seed, meshCount-1);
}
// parse header
double inputSpacing[3];
int inputDim[3];
double inputOrigin[3];
FILE *inputHdr = fopen(inputHdrFilename,"r");
if(inputHdr == NULL){
cerr << "Unable to open header file " << inputHdrFilename << "\n";
return(EXIT_FAILURE);
} else {
char hdrString[256];
// dummy variable to receive fgets return val
char *sReturn;
for(int i=0; i<6; i++){
sReturn = fgets(hdrString, 256, inputHdr);
}
sReturn = fgets(hdrString, 256, inputHdr);
sscanf(hdrString, "%*s %*s %lf %lf %lf", &inputOrigin[0], &inputOrigin[1], &inputOrigin[2]);
sReturn = fgets(hdrString, 256, inputHdr);
sReturn = fgets(hdrString, 256, inputHdr);
sscanf(hdrString,"%*s %*s %lf %lf %lf",&inputSpacing[0], &inputSpacing[1], &inputSpacing[2]);
sReturn = fgets(hdrString, 256, inputHdr);
sscanf(hdrString,"%*s %*s %d %d %d",&inputDim[0], &inputDim[1], &inputDim[2]);
fclose(inputHdr);
}
input->SetDimensions(inputDim);
input->SetSpacing(inputSpacing);
input->SetOrigin(inputOrigin);
// allocate memory and load from gz file
input->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
gzFile gzf = gzopen(inputgzFilename, "rb");
if(gzf == NULL){
cerr << "Unable to open gz data file" << inputgzFilename << "\n";
return(EXIT_FAILURE);
} else {
unsigned char *p = static_cast<unsigned char *>(input->GetScalarPointer());
unsigned char *buffer;
int bytesRead;
long long int totalBytesRead = 0;
buffer = (unsigned char *)malloc(inputDim[1]*inputDim[2]*sizeof(char));
gzbuffer(gzf, inputDim[1]*inputDim[2]);
for(int i=0; i<inputDim[0]; i++){
bytesRead = gzread(gzf, buffer, inputDim[1]*inputDim[2]);
if(bytesRead < 0){
cout << gzerror(gzf, &bytesRead) << "\n";
} else {
totalBytesRead += bytesRead;
}
memcpy(p, buffer, inputDim[1]*inputDim[2]);
p+=inputDim[1]*inputDim[2];
}
gzclose(gzf);
free(buffer);
cout << "Total bytes read = " << totalBytesRead << "\n";
}
// create list of lesion insertion locations
vtkSmartPointer<vtkPoints> lesionLoc =
vtkSmartPointer<vtkPoints>::New();
FILE *inLocFile = fopen(inputLocFilename, "rt");
char line[128];
while(fgets(line, 128, inLocFile) != NULL){
double pt[3];
char *sp;
sp = strtok(line, " ,");
for(int i=0; i<3; i++){
pt[i] = atof(sp);
sp = strtok(NULL, " ,");
}
lesionLoc->InsertNextPoint(pt);
}
fclose(inLocFile);
int numLesionLoc = lesionLoc->GetNumberOfPoints();
// create lower resolution mask for boundary meshing
vtkSmartPointer<vtkImageData> mask =
vtkSmartPointer<vtkImageData>::New();
double voxelSize = 1.0;
mask->SetSpacing(voxelSize,voxelSize,voxelSize);
double inputBounds[6];
input->GetBounds(inputBounds);
//std::cout<<"\nBegining mask search of breast surface.\n\n";
int maskDim[3];
// pad mask around breast
for(int i=0; i<3; i++){
maskDim[i] = (int)ceil((inputBounds[2*i+1]-inputBounds[2*i])/voxelSize)+(int)ceil(75.0/voxelSize);
}
mask->SetExtent(0,maskDim[0]-1,0,maskDim[1]-1,0,maskDim[2]-1);
double maskOrigin[3];
input->GetOrigin(maskOrigin);
// Needed so that breast is completely enclosed on all sides by background
for(int i=0; i<3; i++){
maskOrigin[i] -= 75.0/2;
}
mask->SetOrigin(maskOrigin);
mask->AllocateScalars(VTK_UNSIGNED_CHAR,1);
#pragma omp parallel for collapse(3)
for(int k=0; k<maskDim[2]; k++){
for(int j=0; j<maskDim[1]; j++){
for(int i=0; i<maskDim[0]; i++){
unsigned char *q = static_cast<unsigned char *>(mask->GetScalarPointer(i,j,k));
bool foundIn = false;
// check 27 points on voxel surface to check if any intersection with phantom
for(int a = -1; a <= 1; a++){
for(int b = -1; b <= 1; b++){
for(int c = -1; c <= 1; c++){
double pt[3] = {maskOrigin[0] + i*voxelSize + a*voxelSize/2,
maskOrigin[1] + j*voxelSize + b*voxelSize/2,
maskOrigin[2] + k*voxelSize + c*voxelSize/2};
int abc[3];
double pcoords[3];
int inVol = input->ComputeStructuredCoordinates(pt, abc, pcoords);
if(inVol){
unsigned char *p = static_cast<unsigned char *>(input->GetScalarPointer(abc));
if(*p != tissue.bg && *p != tissue.paddle){
*q = 2;
foundIn = true;
}
}
}
}
}
if(!foundIn){
*q = 0;
}
}
}
}
// create bounding surface using discrete marching cubes
vtkSmartPointer<vtkDiscreteMarchingCubes> surfaceMaker =
vtkSmartPointer<vtkDiscreteMarchingCubes>::New();
surfaceMaker->SetInputData(mask);
//surfaceMaker->ComputeNormalsOn();
surfaceMaker->SetNumberOfContours(1);
surfaceMaker->SetValue(0, 2);
surfaceMaker->Update();
vtkSmartPointer<vtkWindowedSincPolyDataFilter> smoother =
vtkSmartPointer<vtkWindowedSincPolyDataFilter>::New();
smoother->SetInputConnection(surfaceMaker->GetOutputPort());
smoother->SetNumberOfIterations(20);
smoother->BoundarySmoothingOff();
smoother->FeatureEdgeSmoothingOff();
smoother->SetFeatureAngle(120.0);
smoother->SetPassBand(0.001);
smoother->NonManifoldSmoothingOn();
smoother->NormalizeCoordinatesOn();
smoother->Update();
// clean mesh
vtkSmartPointer<vtkCleanPolyData> cleanPoly =
vtkSmartPointer<vtkCleanPolyData>::New();
//cleanPoly->PointMergingOn();
//cleanPoly->SetTolerance(0.002);
cleanPoly->SetInputConnection(smoother->GetOutputPort());
// decimate mesh
vtkSmartPointer<vtkQuadricDecimation> decimate =
vtkSmartPointer<vtkQuadricDecimation>::New();
decimate->SetTargetReduction(decimateFrac);
decimate->SetInputConnection(cleanPoly->GetOutputPort());
decimate->Update();
vtkSmartPointer<vtkPolyData> breastMeshPoly =
vtkSmartPointer<vtkPolyData>::New();
breastMeshPoly->ShallowCopy(decimate->GetOutput());
/**********************
* meshing with Tetgen
*********************/
std::cout << "\nMeshing with Tetgen\n\n";
tetgenio tetin, tetout;
tetin.firstnumber = 0;
tetin.numberofpoints = breastMeshPoly->GetNumberOfPoints();
tetin.pointlist = new REAL[tetin.numberofpoints*3];
// populate node list
for(int i=0; i<breastMeshPoly->GetNumberOfPoints(); i++){
double thisPoint[3];
breastMeshPoly->GetPoint(i, thisPoint);
tetin.pointlist[i*3] = thisPoint[0];
tetin.pointlist[i*3+1] = thisPoint[1];
tetin.pointlist[i*3+2] = thisPoint[2];
}
// populate input surface mesh
tetgenio::facet *tetfacet;
tetgenio::polygon *tetpoly;
tetin.numberoffacets = breastMeshPoly->GetNumberOfPolys();
tetin.facetlist = new tetgenio::facet[tetin.numberoffacets];
//tetin.facetmarkerlist = new int[tetin.numberoffacets];
for(int i=0; i<breastMeshPoly->GetNumberOfPolys(); i++){
vtkCell *thiscell = breastMeshPoly->GetCell(i);
tetfacet = &tetin.facetlist[i];
tetfacet->numberofpolygons = 1;
tetfacet->polygonlist = new tetgenio::polygon[tetfacet->numberofpolygons];
tetfacet->numberofholes = 0;
tetfacet->holelist = nullptr;
tetpoly = &tetfacet->polygonlist[0];
tetpoly->numberofvertices = thiscell->GetNumberOfPoints();
tetpoly->vertexlist = new int[tetpoly->numberofvertices];
for(int j=0; j<tetpoly->numberofvertices; j++){
tetpoly->vertexlist[j] = thiscell->GetPointId(j);
double thisPt[3];
breastMeshPoly->GetPoint(tetpoly->vertexlist[j], thisPt);
}
}
tetrahedralize(&tetPar, &tetin, &tetout);
/***************************
* setup FEBio simulation
**************************/
// calculate bounds
double phantomBounds[6];
int phantomExtent[6];
input->GetExtent(phantomExtent);
if(meshCount ==0){
// find phantom bounds - only needed on first iteration
//std::cout << "Searching for breast bounds\n";
#pragma omp sections
{
#pragma omp section
// back
{
bool foundBreast = false;
for(int i=phantomExtent[0]; i<=phantomExtent[1]; i++){
if(!foundBreast){
for(int j=phantomExtent[2]; j<=phantomExtent[3]; j++){
for(int k=phantomExtent[4]; k<=phantomExtent[5]; k++){
unsigned char* p = static_cast<unsigned char*>(input->GetScalarPointer(i,j,k));
if(p[0] != tissue.bg && !foundBreast){
double pos[3];
int ijk[3] = {i, j, k};
input->GetPoint(input->ComputePointId(ijk),pos);
phantomBounds[0] = pos[0];
foundBreast = true;
}
}
}
}
}
}
#pragma omp section
// front
{
bool foundBreast = false;
for(int i=phantomExtent[1]; i>=phantomExtent[0]; i--){
if(!foundBreast){
for(int j=phantomExtent[2]; j<=phantomExtent[3]; j++){
for(int k=phantomExtent[4]; k<=phantomExtent[5]; k++){
unsigned char* p = static_cast<unsigned char*>(input->GetScalarPointer(i,j,k));
if(p[0] != tissue.bg && !foundBreast){
double pos[3];
int ijk[3] = {i, j, k};
input->GetPoint(input->ComputePointId(ijk),pos);
phantomBounds[1] = pos[0];
foundBreast = true;
}
}
}
}
}
}
#pragma omp section
// left
{
bool foundBreast = false;
for(int j=phantomExtent[2]; j<=phantomExtent[3]; j++){
if(!foundBreast){
for(int i=phantomExtent[0]; i<=phantomExtent[1]; i++){
for(int k=phantomExtent[4]; k<=phantomExtent[5]; k++){
unsigned char* p = static_cast<unsigned char*>(input->GetScalarPointer(i,j,k));
if(p[0] != tissue.bg && !foundBreast){
double pos[3];
int ijk[3] = {i, j, k};
input->GetPoint(input->ComputePointId(ijk),pos);
phantomBounds[2] = pos[1];
foundBreast = true;
}
}
}
}
}
}
#pragma omp section
// right
{
bool foundBreast = false;
for(int j=phantomExtent[3]; j>=phantomExtent[2]; j--){
if(!foundBreast){
for(int i=phantomExtent[0]; i<=phantomExtent[1]; i++){
for(int k=phantomExtent[4]; k<=phantomExtent[5]; k++){
unsigned char* p = static_cast<unsigned char*>(input->GetScalarPointer(i,j,k));
if(p[0] != tissue.bg && !foundBreast){
double pos[3];
int ijk[3] = {i, j, k};
input->GetPoint(input->ComputePointId(ijk),pos);
phantomBounds[3] = pos[1];
foundBreast = true;
}
}
}
}
}
}
#pragma omp section
// bottom
{
bool foundBreast = false;
for(int k=phantomExtent[4]; k<=phantomExtent[5]; k++){
if(!foundBreast){
for(int i=phantomExtent[0]; i<=phantomExtent[1]; i++){
for(int j=phantomExtent[2]; j<=phantomExtent[3]; j++){
unsigned char* p = static_cast<unsigned char*>(input->GetScalarPointer(i,j,k));
if(p[0] != tissue.bg && !foundBreast){
double pos[3];
int ijk[3] = {i, j, k};
input->GetPoint(input->ComputePointId(ijk),pos);
phantomBounds[4] = pos[2];
foundBreast = true;
}
}
}
}
}
}
#pragma omp section
// top
{
bool foundBreast = false;
for(int k=phantomExtent[5]; k>=phantomExtent[4]; k--){
if(!foundBreast){
for(int i=phantomExtent[0]; i<=phantomExtent[1]; i++){
for(int j=phantomExtent[2]; j<=phantomExtent[3]; j++){
unsigned char* p = static_cast<unsigned char*>(input->GetScalarPointer(i,j,k));
if(p[0] != tissue.bg && !foundBreast){
double pos[3];
int ijk[3] = {i, j, k};
input->GetPoint(input->ComputePointId(ijk),pos);
phantomBounds[5] = pos[2];
foundBreast = true;
}
}
}
}
}
}
} // end parallel sections
}
//Update nipple position each iteration
//std::cout<<"Searching for nipple position.\n";
double nipplePos[3];
bool foundNipple = false;
for(int i=phantomExtent[1]; i>=phantomExtent[0]; i--){
if(!foundNipple){
int voxCount = 0;
double nippleSum[3] = {0.0, 0.0, 0.0};
for(int j=phantomExtent[2]; j<=phantomExtent[3]; j++){
for(int k=phantomExtent[4]; k<=phantomExtent[5]; k++){
unsigned char* p = static_cast<unsigned char*>(input->GetScalarPointer(i,j,k));
// position is mean position in plane farthest from chest wall
if(p[0] == tissue.nipple){
double pos[3];
int ijk[3] = {i, j, k};
input->GetPoint(input->ComputePointId(ijk),pos);
voxCount += 1;
for(int m=0; m<3; m++){
nippleSum[m] += pos[m];
}
}
}
}
if(voxCount > 0){
foundNipple = true;
for(int m=0; m<3; m++){
nipplePos[m] = nippleSum[m]/voxCount;
}
}
}
}
double topPaddleCenter[3];
double bottomPaddleCenter[3];
double paddleHeight = 1.0;
if(meshCount == 0){
origPaddleWidth = (phantomBounds[3]-phantomBounds[2])*1.75;
origPaddleLength = (phantomBounds[1]-phantomBounds[0])*1.75;
}
double paddleWidth = origPaddleWidth;
double paddleLength = origPaddleLength;
double paddleEdgeRadius = 3.0;
double paddleLipHeight = 15.0; // must be greater than paddleEdgeRadius
// paddle retreat after remeshing
double retreatDist = 10.0*paddleHeight;
if(meshCount == 0){
topPaddleCenter[0] = paddleLength/2.0 + (phantomBounds[1]-phantomBounds[0])*0.125;
topPaddleCenter[1] = nipplePos[1];
if(!rotate){
topPaddleCenter[2] = phantomBounds[5] + 4*paddleHeight/2.0;
} else {
topPaddleCenter[2] = phantomBounds[5] + 30*paddleHeight/2.0;
}
bottomPaddleCenter[0] = paddleLength/2.0 + (phantomBounds[1]-phantomBounds[0])*0.1;
bottomPaddleCenter[1] = nipplePos[1];
if(!rotate){
bottomPaddleCenter[2] = phantomBounds[4] - 4*paddleHeight/2.0;
} else {
bottomPaddleCenter[2] = phantomBounds[4] - 30*paddleHeight/2.0;
}
} else {
// use previous interation's paddle position plus a retreat
for(int i=0; i<3; i++){
topPaddleCenter[i] = prevTopPaddleCenterDerotated[i];
bottomPaddleCenter[i] = prevBotPaddleCenterDerotated[i];
}
topPaddleCenter[2] += retreatDist;
bottomPaddleCenter[2] -= retreatDist;
}
if(autoRemesh){
// try to complete full compression
paddleDist = ((topPaddleCenter[2]-bottomPaddleCenter[2] -
paddleHeight - thickness)/2.0);
} else {
if(numMeshes >= 3)
{
// paddle distance must be greater for every iteration past the first one to
// account for the distancing done when resuming from the last iteration.
if(meshCount == 0){
paddleDist = ((topPaddleCenter[2]-bottomPaddleCenter[2] -
paddleHeight - thickness)/2.0)*0.4;
} else if(meshCount == 1) {
paddleDist = paddleDist/2;
paddleDist += retreatDist;
} else {
paddleDist -= retreatDist;
paddleDist = (paddleDist*2)/(numMeshes-2);
paddleDist += retreatDist;
}
} else {
// 1 or 2 meshes
if(meshCount==0) {
paddleDist = ((topPaddleCenter[2]-bottomPaddleCenter[2] -
paddleHeight - thickness)/2.0)/numMeshes;
} else if (meshCount==1) {
paddleDist+=retreatDist;
}
}
}
if(paddleDist < 0.0){
cerr << "Paddle travel distance error.\n";
return(1);
}
vtkSmartPointer<vtkDoubleArray> bottomPaddleNodes =
vtkSmartPointer<vtkDoubleArray>::New();
bottomPaddleNodes->SetNumberOfComponents(3);
vtkSmartPointer<vtkIntArray> bottomPaddleHexElements =
vtkSmartPointer<vtkIntArray>::New();
bottomPaddleHexElements->SetNumberOfComponents(8);
vtkSmartPointer<vtkIntArray> bottomPaddlePentElements =
vtkSmartPointer<vtkIntArray>::New();
bottomPaddlePentElements->SetNumberOfComponents(6);
vtkSmartPointer<vtkIntArray> bottomPaddleContactSurface =
vtkSmartPointer<vtkIntArray>::New();
bottomPaddleContactSurface->SetNumberOfComponents(4);
vtkSmartPointer<vtkIntArray> breastBackNodes =
vtkSmartPointer<vtkIntArray>::New();
breastBackNodes->SetNumberOfComponents(1);
double paddleDy = paddleWidth/paddleNw;
double paddleDx = (paddleLength-2.0*paddleEdgeRadius)/(paddleNl-1);
vtkIdType nodes[8];
vtkIdType pnodes[6];
// create main part of bottom paddle
for(int j=0; j<paddleNl-1; j++){
double xpos = bottomPaddleCenter[0]+paddleLength/2.0 - j*paddleDx;
for(int i=0; i<paddleNw; i++){
double ypos = bottomPaddleCenter[1]-paddleWidth/2.0 + i*paddleDy;
double loc[3];
// add nodes
if(i==0 && j==0){
// add all 8 nodes
loc[0] = xpos;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]-paddleHeight/2.0;
nodes[0] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]-paddleHeight/2.0;
nodes[1] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos-paddleDx;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]-paddleHeight/2.0;
nodes[2] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos-paddleDx;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]-paddleHeight/2.0;
nodes[3] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
nodes[4] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
nodes[5] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos-paddleDx;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
nodes[6] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos-paddleDx;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
nodes[7] = bottomPaddleNodes->InsertNextTuple(loc);
} else if(j==0){
// add 4 nodes
nodes[0] = nodes[1];
loc[0] = xpos;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]-paddleHeight/2.0;
nodes[1] = bottomPaddleNodes->InsertNextTuple(loc);
nodes[3] = nodes[2];
loc[0] = xpos-paddleDx;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]-paddleHeight/2.0;
nodes[2] = bottomPaddleNodes->InsertNextTuple(loc);
nodes[4] = nodes[5];
loc[0] = xpos;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
nodes[5] = bottomPaddleNodes->InsertNextTuple(loc);
nodes[7] = nodes[6];
loc[0] = xpos-paddleDx;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
nodes[6] = bottomPaddleNodes->InsertNextTuple(loc);
} else if(i==0){
// add 4 nodes
loc[0] = xpos-paddleDx;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]-paddleHeight/2.0;
nodes[2] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos-paddleDx;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]-paddleHeight/2.0;
nodes[3] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos-paddleDx;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
nodes[6] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos-paddleDx;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
nodes[7] = bottomPaddleNodes->InsertNextTuple(loc);
// get left neighbor nodes
double leftN[8];
bottomPaddleHexElements->GetTuple((j-1)*(paddleNw), leftN);
nodes[0] = (int)leftN[3]-1;
nodes[1] = (int)leftN[2]-1;
nodes[4] = (int)leftN[7]-1;
nodes[5] = (int)leftN[6]-1;
} else {
// add 2 nodes
nodes[0] = nodes[1];
nodes[3] = nodes[2];
nodes[4] = nodes[5];
nodes[7] = nodes[6];
loc[0] = xpos-paddleDx;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]-paddleHeight/2.0;
nodes[2] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos-paddleDx;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
nodes[6] = bottomPaddleNodes->InsertNextTuple(loc);
// get left neighbor nodes
double *leftN;
leftN = bottomPaddleHexElements->GetTuple((j-1)*(paddleNw)+i);
nodes[1] = (int)leftN[2]-1;
nodes[5] = (int)leftN[6]-1;
}
// add element
double nodesD[8];
for(int a=0; a<8; a++){
nodesD[a] = (double)(nodes[a]+1);
}
bottomPaddleHexElements->InsertNextTuple(nodesD);
// add surface
bottomPaddleContactSurface->InsertNextTuple4(nodesD[4],nodesD[5],nodesD[6],nodesD[7]);
}
}
int saveTop;
// curved section
for(int i=0; i<paddleNw; i++){
double ypos = bottomPaddleCenter[1]-paddleWidth/2.0 + i*paddleDy;
double xpos = bottomPaddleCenter[0]+paddleLength/2.0 - (paddleNl-1)*paddleDx;
// middle pentahedral
double leftN[8];
double loc[3];
bottomPaddleHexElements->GetTuple((paddleNl-2)*(paddleNw)+i, leftN);
if(i==0){
loc[0] = xpos-paddleEdgeRadius;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0-paddleEdgeRadius;
pnodes[5] = bottomPaddleNodes->InsertNextTuple(loc);
} else {
pnodes[5] = pnodes[0];
}
loc[0] = xpos-paddleEdgeRadius;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0-paddleEdgeRadius;
pnodes[2] = bottomPaddleNodes->InsertNextTuple(loc);
pnodes[3] = (int)leftN[3]-1;
pnodes[4] = (int)leftN[7]-1;
pnodes[0] = (int)leftN[2]-1;
pnodes[1] = (int)leftN[6]-1;
// save 2 nodes for top pent
int nodSave[2];
nodSave[0] = pnodes[1];
nodSave[1] = pnodes[4];
double pnodesD[6];
for(int a=0; a<6; a++){
pnodesD[a] = (double)(pnodes[a]+1);
}
bottomPaddlePentElements->InsertNextTuple(pnodesD);
// bottom pentahedral
// 0 and 3 the same
pnodes[1] = pnodes[2];
pnodes[4] = pnodes[5];
loc[0] = xpos-paddleEdgeRadius;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0-paddleLipHeight;
pnodes[2] = bottomPaddleNodes->InsertNextTuple(loc);
if(i == 0){
loc[0] = xpos-paddleEdgeRadius;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0-paddleLipHeight;
pnodes[5] = bottomPaddleNodes->InsertNextTuple(loc);
} else {
// from previous edge hex
pnodes[5] = nodes[1];
}
for(int a=0; a<6; a++){
pnodesD[a] = (double)(pnodes[a]+1);
}
bottomPaddlePentElements->InsertNextTuple(pnodesD);
// bottom edge hex
nodes[0] = pnodes[5];
nodes[4] = pnodes[4];
nodes[1] = pnodes[2];
nodes[5] = pnodes[1];
if(i==0) {
loc[0] = xpos-paddleEdgeRadius-paddleEdgeRadius;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0-paddleLipHeight;
nodes[3] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos-paddleEdgeRadius-paddleEdgeRadius;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0-paddleEdgeRadius;
nodes[7] = bottomPaddleNodes->InsertNextTuple(loc);
} else {
nodes[3] = nodes[2];
nodes[7] = nodes[6];
}
loc[0] = xpos-paddleEdgeRadius-paddleEdgeRadius;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0-paddleLipHeight;
nodes[2] = bottomPaddleNodes->InsertNextTuple(loc);
loc[0] = xpos-paddleEdgeRadius-paddleEdgeRadius;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0-paddleEdgeRadius;
nodes[6] = bottomPaddleNodes->InsertNextTuple(loc);
double nodesD[8];
for(int a=0; a<8; a++){
nodesD[a] = (double)(nodes[a]+1);
}
bottomPaddleHexElements->InsertNextTuple(nodesD);
// the edge
bottomPaddleContactSurface->InsertNextTuple4(nodesD[3],nodesD[7],nodesD[6],nodesD[2]);
// add the bottom edge as well
bottomPaddleContactSurface->InsertNextTuple4(nodesD[3],nodesD[2],nodesD[1],nodesD[0]);
// top pentahedral
// pnodes 1,4 same
pnodes[2] = nodSave[0];
pnodes[5] = nodSave[1];
if(i==0){
loc[0] = xpos-paddleEdgeRadius;
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
pnodes[3] = bottomPaddleNodes->InsertNextTuple(loc);
} else {
pnodes[3] = saveTop;
}
loc[0] = xpos-paddleEdgeRadius;
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0;
pnodes[0] = bottomPaddleNodes->InsertNextTuple(loc);
saveTop = pnodes[0];
for(int a=0; a<6; a++){
pnodesD[a] = (double)(pnodes[a]+1);
}
bottomPaddlePentElements->InsertNextTuple(pnodesD);
// the edge
bottomPaddleContactSurface->InsertNextTuple4(pnodesD[5],pnodesD[2],pnodesD[0],pnodesD[3]);
// the fan
for(int j=0; j<paddleNh; j++){
if(j==0){
// from top pent
pnodes[1] = pnodes[0];
pnodes[4] = pnodes[3];
pnodes[0] = nodes[5];
pnodes[3] = nodes[4];
} else {
pnodes[1] = pnodes[2];
pnodes[4] = pnodes[5];
}
double theta = 3.141592654/2.0/(paddleNh)*(j+1);
if(j == paddleNh-1){
pnodes[2] = nodes[6];
} else {
loc[0] = xpos-paddleEdgeRadius-paddleEdgeRadius*sin(theta);
loc[1] = ypos+paddleDy;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0-paddleEdgeRadius + paddleEdgeRadius*cos(theta);
pnodes[2] = bottomPaddleNodes->InsertNextTuple(loc);
}
if(i==0 && j<paddleNh-1){
loc[0] = xpos-paddleEdgeRadius-paddleEdgeRadius*sin(theta);
loc[1] = ypos;
loc[2] = bottomPaddleCenter[2]+paddleHeight/2.0-paddleEdgeRadius + paddleEdgeRadius*cos(theta);
pnodes[5] = bottomPaddleNodes->InsertNextTuple(loc);
} else if(j<paddleNh-1){
double *leftP;