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itkFEMConformalMap.cxx
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itkFEMConformalMap.cxx
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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Copyright (c) 2002 Insight Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for detailm_Solver.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef _FEMConformalMap_hxx
#define _FEMConformalMap_hxx
#include "vtkFeatureEdges.h"
#include "vtkPointLocator.h"
#include "vtkCellLocator.h"
#include "vtkTriangleFilter.h"
#include "vtkCleanPolyData.h"
#include "vtkPolyDataConnectivityFilter.h"
#include <vcl_compiler.h>
#include <iostream>
#include <cmath>
#include <iostream>
#include <vnl/vnl_real_polynomial.h>
#include <vnl/vnl_vector.h>
#include <vnl/vnl_vector_fixed.h>
#include <itkMath.h>
#include "itkFEMConformalMap.h"
#include "itkFEMLoadNode.h"
namespace itk
{
vtkPolyData *
vtkGenSmoothMesh(vtkPolyData * vds)
{
float fai = 45;
vtkSmoothPolyDataFilter * polySmoother = vtkSmoothPolyDataFilter::New();
// polySmoother->SetInput(decimator->GetOutput());
polySmoother->SetInput(vds);
polySmoother->SetNumberOfIterations(100);
polySmoother->SetRelaxationFactor(0.01);
polySmoother->SetFeatureAngle(fai);
polySmoother->FeatureEdgeSmoothingOff();
polySmoother->BoundarySmoothingOff();
polySmoother->Update();
return polySmoother->GetOutput();
}
template <typename TSurface, typename TImage, unsigned int TDimension>
FEMConformalMap<TSurface, TImage, TDimension>::FEMConformalMap()
{
m_Sigma = 2.0e-4;
m_ParameterFileName = "";
m_NorthPole = 0;
m_SouthPole = 1;
m_VtkSurfaceMesh = nullptr;
m_Pi = 3.14159265358979323846;
m_ReadFromFile = true;
m_Debug = false;
m_FindingRealSolution = true;
m_SurfaceMesh = nullptr;
m_Image = nullptr;
m_SphereImage = nullptr;
for (int i = 0; i < 7; i++)
{
m_PoleElementsGN[i] = 0;
}
}
template <typename TSurface, typename TImage, unsigned int TDimension>
bool
FEMConformalMap<TSurface, TImage, TDimension>::GenerateSystemFromVtkSurfaceMesh()
{
if (!m_VtkSurfaceMesh)
{
::std::cout << " NO MESH";
return false;
}
::std::cout << " Generate system from surface mesh " << std::endl;
vtkTriangleFilter * fltTriangle = vtkTriangleFilter::New();
fltTriangle->SetInput(m_VtkSurfaceMesh);
cout << " converting mesh to triangles " << endl;
fltTriangle->Update();
// Clean the data
vtkCleanPolyData * fltCleaner = vtkCleanPolyData::New();
fltCleaner->SetInput(fltTriangle->GetOutput());
fltCleaner->SetTolerance(0);
fltCleaner->ConvertPolysToLinesOn();
cout << " cleaning up triangle mesh " << endl;
fltCleaner->Update();
// Go through and delete the cells that are of the wrong type
vtkPolyData * clean = fltCleaner->GetOutput();
for (vtkIdType i = clean->GetNumberOfCells(); i > 0; i--)
{
if (clean->GetCellType(i - 1) != VTK_TRIANGLE)
{
clean->DeleteCell(i - 1);
}
}
clean->BuildCells();
m_VtkSurfaceMesh = clean;
// create a material
// Choose the material properties
typename MaterialType::Pointer m;
m = MaterialType::New();
m->GN = 0; // Global number of the material ///
m->E = m_Sigma; // Young modulus -- used in the membrane ///
m->A = 0.0; // Crossection area ///
m->h = 0.0; // Crossection area ///
m->I = 0.0; // Moment of inertia ///
m->nu = 0.; // .0; // poissons -- DONT CHOOSE 1.0!!///
m->RhoC = 0.0;
// Create the element type
ElementType::Pointer e1 = ElementType::New();
e1->m_mat = dynamic_cast<MaterialType *>(m);
vtkPoints * vtkpoints = m_VtkSurfaceMesh->GetPoints();
int numPoints = vtkpoints->GetNumberOfPoints();
int foundnum = 0;
for (int i = 0; i < numPoints; i++)
{
double * pt = vtkpoints->GetPoint(i);
typename NodeType::Pointer n;
n = new NodeType(pt[0], pt[1], pt[2]);
n->GN = i;
m_Solver.node.push_back(itk::fem::FEMP<NodeType>(n));
foundnum++;
}
::std::cout << " foundnum " << foundnum << std::endl;
typename NodeType::Pointer * narr = new NodeType::Pointer[numPoints];
for (int i = 0; i < numPoints; i++)
{
narr[i] = m_Solver.node.Find(i);
}
vtkCellArray * vtkcells = m_VtkSurfaceMesh->GetPolys();
vtkIdType npts;
vtkIdType * pts;
unsigned long i = 0;
unsigned long toti = vtkcells->GetNumberOfCells();
// ::std::cout << " progress ";
::std::cout << " DONE: NUMBER OF CELLS start " << toti << std::endl;
for (vtkcells->InitTraversal(); vtkcells->GetNextCell(npts, pts);)
{
ElementType::Pointer e;
e = dynamic_cast<ElementType *>(e1->Clone());
e->SetNode(2, narr[pts[0]]);
e->SetNode(1, narr[pts[1]]);
e->SetNode(0, narr[pts[2]]);
e->GN = i;
m_Solver.el.push_back(itk::fem::FEMP<itk::fem::Element>(e));
i++;
}
::std::cout << " DONE: NUMBER OF CELLS " << i << std::endl;
return true;
}
template <typename TSurface, typename TImage, unsigned int TDimension>
bool
FEMConformalMap<TSurface, TImage, TDimension>::GenerateSystemFromSurfaceMesh()
{
if (!m_SurfaceMesh)
{
return false;
}
// create a material
// Choose the material properties
typename MaterialType::Pointer m;
m = MaterialType::New();
m->GN = 0; // Global number of the material ///
m->E = m_Sigma; // Young modulus -- used in the membrane ///
m->A = 0.0; // Crossection area ///
m->h = 0.0; // Crossection area ///
m->I = 0.0; // Moment of inertia ///
m->nu = 0.; // .0; // poissons -- DONT CHOOSE 1.0!!///
m->RhoC = 0.0;
// 3.e-4 prolly good
// ::std::cout << " input E "; std::cin >> m->E;
// Create the element type
ElementType::Pointer e1 = ElementType::New();
e1->m_mat = dynamic_cast<MaterialType *>(m);
PointType * pt_ptr;
PointType pt;
pt_ptr = &pt;
for (int i = 0; i < m_SurfaceMesh->GetNumberOfPoints(); i++)
{
m_SurfaceMesh->GetPoint(i, pt_ptr);
if (m_Debug)
{
::std::cout << "Point: " << i << " coords " << pt[0] << ", " << pt[1] << ", " << pt[2] << std::endl;
}
// turn the point into a node
{
// Create nodes
typename NodeType::Pointer n;
n = new NodeType(pt[0], pt[1], pt[2]);
n->GN = i;
m_Solver.node.push_back(itk::fem::FEMP<NodeType>(n));
}
}
InputCellsContainerPointer cellList = m_SurfaceMesh->GetCells();
InputCellsContainerIterator cells = cellList->Begin();
for (int i = 0; i < m_SurfaceMesh->GetNumberOfCells(); i++)
{
const unsigned long * tp;
typename SurfaceType::CellType * cellPtr = cells.Value();
tp = cellPtr->GetPointIds();
if (m_Debug)
{
::std::cout << " pt 1 id " << tp[0] << " pt 2 id " << tp[1] << " pt 3 id " << tp[2] << std::endl;
}
cells++;
// turn the cell into an element
{
// Create elements
ElementType::Pointer e;
e = dynamic_cast<ElementType *>(e1->Clone());
e->SetNode(0, m_Solver.node.Find(tp[0]));
e->SetNode(1, m_Solver.node.Find(tp[1]));
e->SetNode(2, m_Solver.node.Find(tp[2]));
e->GN = i;
m_Solver.el.push_back(itk::fem::FEMP<itk::fem::Element>(e));
}
}
return true;
}
template <typename TSurface, typename TImage, unsigned int TDimension>
void
FEMConformalMap<TSurface, TImage, TDimension>::MapImageToSphere(TImage * img, float rad)
{
typename ImageType::SizeType imageSize = img->GetLargestPossibleRegion().GetSize();
vnl_vector<float> Pos; // solution at the point
vnl_vector<float> Sol; // solution at the local point
vnl_vector<float> Gpt; // global position given by local point
Sol.set_size(ImageDimension);
Gpt.set_size(ImageDimension);
Pos.set_size(ImageDimension);
VectorType disp;
disp.set_size(3);
disp.fill(0.0);
float WIDTH = rad * 2.1;
float HEIGHT = rad * 2.1;
float DEPTH = rad * 2.1;
typename ImageType::SizeType size;
size[0] = WIDTH;
size[1] = HEIGHT;
size[2] = DEPTH;
typename ImageType::IndexType start;
start.Fill(0);
typename ImageType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
m_SphereImage = ImageType::New();
m_SphereImage->SetRegions(region);
m_SphereImage->Allocate();
int center = (int)WIDTH / 2;
typename ImageType::PixelType backgroundValue = 0;
itk::ImageRegionIteratorWithIndex<ImageType> it(m_SphereImage, region);
it.GoToBegin();
typename ImageType::IndexType rindex = it.GetIndex();
typename ImageType::IndexType sindex = it.GetIndex();
while (!it.IsAtEnd())
{
rindex = it.GetIndex();
float dist = 0;
for (int ii = 0; ii < ImageDimension; ii++)
{
dist += (float)(rindex[ii] - center) * (float)(rindex[ii] - center);
}
dist = sqrt(dist);
if (dist > rad)
{
it.Set(backgroundValue);
}
else
{
it.Set(1);
}
++it;
}
PointType * pt_ptr;
PointType pt;
pt_ptr = &pt;
bool inimage;
for (itk::fem::Element::ArrayType::iterator elt = m_Solver.el.begin(); elt != m_Solver.el.end(); ++elt)
{
unsigned int Nnodes = (*elt)->GetNumberOfNodes();
inimage = true;
for (unsigned int nd = 0; nd < Nnodes; nd++)
{
for (unsigned int f = 0; f < ImageDimension; f++)
{
float x;
if ((*elt)->GetNumberOfDegreesOfFreedomPerNode() == 3)
{
Sol[f] = m_Solver.GetLinearSystemWrapper()->GetSolutionValue((*elt)->GetNode(nd)->GetDegreeOfFreedom(f), 0);
x = (*elt)->GetNode(nd)->GetCoordinates()[f];
}
else
{
Sol[f] = (*elt)->GetNode(nd)->GetCoordinates()(f);
m_SurfaceMesh->GetPoint((*elt)->GetNode(nd)->GN, pt_ptr);
x = pt[f];
}
// get img index
long int temp;
if (x != 0)
{
temp = (long int)((x) + 0.5);
}
else
{
temp = 0; // round
}
rindex[f] = temp;
// get sphr index
disp[f] = (float)((float)center) + rad * Sol[f];
x = disp[f];
if (x != 0)
{
temp = (long int)((x) + 0.5);
}
else
{
temp = 0; // round
}
sindex[f] = temp;
}
if (inimage)
{
m_SphereImage->SetPixel(sindex, img->GetPixel(rindex) + 1.0); // *100. +110.0);
}
}
} // end of elt array loop
}
template <typename TSurface, typename TImage, unsigned int TDimension>
void
FEMConformalMap<TSurface, TImage, TDimension>::MapCheckerboardToImage(float increment)
{
typedef float Float;
if (increment < 0)
{
increment = 0;
}
if (increment > 1)
{
increment = 1;
}
float phiinc = m_Pi * increment;
float thetainc = m_Pi * increment;
vnl_vector<Float> Sol; // solution at the local point
typename ImageType::SpacingType spacing = m_Image->GetSpacing();
typename ImageType::SizeType imageSize = m_Image->GetLargestPossibleRegion().GetSize();
::std::cout << " size " << imageSize << std::endl;
VectorType disp;
disp.set_size(3);
disp.fill(0.0);
// Float solval,posval;
bool inimage;
float phi;
float theta;
float s;
float t;
float gridval;
ImageRegionIteratorWithIndex<ImageType> wimIter(m_Image, m_Image->GetLargestPossibleRegion());
wimIter.GoToBegin();
for (; !wimIter.IsAtEnd(); ++wimIter)
{
wimIter.Set(0.0);
}
typename ImageType::IndexType rindex = wimIter.GetIndex();
Sol.set_size(ImageDimension);
PointType * pt_ptr;
PointType pt;
pt_ptr = &pt;
for (itk::fem::Element::ArrayType::iterator elt = m_Solver.el.begin(); elt != m_Solver.el.end(); ++elt)
{
unsigned int Nnodes = (*elt)->GetNumberOfNodes();
inimage = true;
for (unsigned int nd = 0; nd < Nnodes; nd++)
{
for (unsigned int f = 0; f < ImageDimension; f++)
{
Float x;
Sol[f] = (*elt)->GetNode(nd)->GetCoordinates()(f);
m_SurfaceMesh->GetPoint((*elt)->GetNode(nd)->GN, pt_ptr);
x = pt[f];
long int temp;
if (x != 0)
{
temp = (long int)((x) + 0.5);
}
else
{
temp = 0; // round
}
rindex[f] = temp / spacing[f];
disp[f] = (Float)1.0 * Sol[f];
if (temp < 0 || temp > (long int)imageSize[f] - 1)
{
inimage = false;
}
}
// convert the cartesian coordinates to theta and phi spherical coords
phi = acos(Sol[2]);
theta = acos(Sol[0] / sin(phi));
s = phi / phiinc;
t = theta / thetainc;
gridval;
if ((((int)t) + ((int)s)) % 2 == 0)
{
gridval = 100;
}
else
{
gridval = 200;
}
if (inimage)
{
m_Image->SetPixel(rindex, gridval); // *100. +110.0);
}
}
} // end of elt array loop
}
template <typename TSurface, typename TImage, unsigned int TDimension>
void
FEMConformalMap<TSurface, TImage, TDimension>::MapStereographicCoordinatesToImage(int cdim)
{
typedef float Float;
vnl_vector<Float> Pos; // solution at the point
vnl_vector<Float> Sol; // solution at the local point
vnl_vector<Float> Gpt; // global position given by local point
typename ImageType::SpacingType spacing = m_Image->GetSpacing();
typename ImageType::SizeType imageSize = m_Image->GetLargestPossibleRegion().GetSize();
VectorType disp;
disp.set_size(3);
disp.fill(0.0);
bool inimage;
ImageRegionIteratorWithIndex<ImageType> wimIter(m_Image, m_Image->GetLargestPossibleRegion());
wimIter.GoToBegin();
for (; !wimIter.IsAtEnd(); ++wimIter)
{
wimIter.Set(0.0);
}
typename ImageType::IndexType rindex = wimIter.GetIndex();
Sol.set_size(ImageDimension);
Gpt.set_size(ImageDimension);
Pos.set_size(ImageDimension);
PointType * pt_ptr;
PointType pt;
pt_ptr = &pt;
for (itk::fem::Element::ArrayType::iterator elt = m_Solver.el.begin(); elt != m_Solver.el.end(); ++elt)
{
unsigned int Nnodes = (*elt)->GetNumberOfNodes();
inimage = true;
for (unsigned int nd = 0; nd < Nnodes; nd++)
{
for (unsigned int f = 0; f < ImageDimension; f++)
{
Float x;
if ((*elt)->GetNumberOfDegreesOfFreedomPerNode() == 3)
{
Sol[f] = m_Solver.GetLinearSystemWrapper()->GetSolutionValue((*elt)->GetNode(nd)->GetDegreeOfFreedom(f), 0);
x = (*elt)->GetNode(nd)->GetCoordinates()[f];
}
else
{
Sol[f] = (*elt)->GetNode(nd)->GetCoordinates()(f);
m_SurfaceMesh->GetPoint((*elt)->GetNode(nd)->GN, pt_ptr);
x = pt[f];
}
long int temp;
if (x != 0)
{
temp = (long int)((x) + 0.5);
}
else
{
temp = 0; // round
}
rindex[f] = temp / spacing[f];
disp[f] = (Float)1.0 * Sol[f];
if (temp < 0 || temp > (long int)imageSize[f] - 1)
{
inimage = false;
}
}
if (inimage)
{
m_Image->SetPixel(rindex, disp[cdim] + 2.0); // *100. +110.0);
}
}
} // end of elt array loop
}
template <typename TSurface, typename TImage, unsigned int TDimension>
void
FEMConformalMap<TSurface, TImage, TDimension>::FindPoles(int dim)
{
// find node with min x coord and its elt -> use as north pole (apply forces there)
// find node with max x coord and its elt -> use as south pole (fix solution to zero)
if (dim < 0)
{
return;
}
vnl_vector<float> minx(3, 9.e9);
vnl_vector<float> maxx(3, 0.0);
itk::fem::Element::VectorType minv;
itk::fem::Element::VectorType maxv;
itk::fem::Element::ArrayType::iterator elt = m_Solver.el.begin();
unsigned int Nnodes = (*elt)->GetNumberOfNodes();
for (; elt != m_Solver.el.end(); ++elt)
{
for (unsigned int nd = 0; nd < Nnodes; nd++)
{
for (unsigned int dd = 0; dd < ImageDimension; dd++)
{
float x = ((*elt)->GetNode(nd)->GetCoordinates()[dd]);
if (x <= minx[dd])
{
// ::std::cout << " x " << x << " minx " << minx << std::endl;
m_PoleElementsGN[dd * 2] = (*elt)->GN;
minv = (*elt)->GetNode(nd)->GetCoordinates();
minx[dd] = x;
}
else if (x >= maxx[dd])
{
// ::std::cout << " x " << x << " maxx " << maxx << std::endl;
m_PoleElementsGN[dd * 2 + 1] = (*elt)->GN;
maxv = (*elt)->GetNode(nd)->GetCoordinates();
maxx[dd] = x;
}
}
}
}
for (int jj = 0; jj < 3; jj++)
{
::std::cout << " Element " << m_PoleElementsGN[jj * 2] << " is north " << jj << std::endl;
::std::cout << " Element " << m_PoleElementsGN[jj * 2 + 1] << " is south " << jj << std::endl;
}
}
template <typename TSurface, typename TImage, unsigned int TDimension>
void
FEMConformalMap<TSurface, TImage, TDimension>::FixPoles(int dim)
{
// if (dim > 3 || dim < -3 || dim == 0 ) return;
if (dim == m_NorthPole)
{
return;
}
itk::fem::Element::ArrayType::iterator elt = m_Solver.el.begin();
unsigned int dofs = (*elt)->GetNumberOfDegreesOfFreedomPerNode();
{
float fixval;
itk::fem::LoadBC::Pointer l1;
itk::fem::LoadBC::Pointer l2;
itk::fem::LoadBC::Pointer l3;
itk::fem::LoadBC::Pointer l4;
itk::fem::LoadBC::Pointer l5;
// itk::fem::LoadBC::Pointer l6;
int absdim = abs(dim);
float oc = 2.0;
::std::cout << " Fixing BC " << absdim << std::endl;
switch (absdim)
{
case 0:
{
for (int i = 0; i < dofs; i++)
{
fixval = 0;
l1 = itk::fem::LoadBC::New();
l1->m_element = m_Solver.el[m_PoleElementsGN[0]];
l1->m_dof = i;
l1->m_value = vnl_vector<double>(1, fixval);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*l1));
}
}
break;
case 1:
{
for (int i = 0; i < dofs; i++)
{
fixval = 0;
l1 = itk::fem::LoadBC::New();
l1->m_element = m_Solver.el[m_PoleElementsGN[1]];
l1->m_dof = i;
l1->m_value = vnl_vector<double>(1, fixval);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*l1));
}
}
break;
case 2:
{
for (int i = 0; i < dofs; i++)
{
if (m_FindingRealSolution)
{
fixval = 0;
}
else
{
fixval = oc;
}
l2 = itk::fem::LoadBC::New();
l2->m_element = m_Solver.el[m_PoleElementsGN[2]];
l2->m_dof = i;
l2->m_value = vnl_vector<double>(1, fixval);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*l2));
}
}
break;
case 3:
{
for (int i = 0; i < dofs; i++)
{
if (m_FindingRealSolution)
{
fixval = 0;
}
else
{
fixval = -1.0 * oc; // was -2.0
}
l3 = itk::fem::LoadBC::New();
l3->m_element = m_Solver.el[m_PoleElementsGN[3]];
l3->m_dof = i;
l3->m_value = vnl_vector<double>(1, fixval);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*l3));
}
}
break;
case 4:
{
for (int i = 0; i < dofs; i++)
{
if (m_FindingRealSolution)
{
fixval = oc;
}
else
{
fixval = 0.0;
}
l4 = itk::fem::LoadBC::New();
l4->m_element = m_Solver.el[m_PoleElementsGN[4]];
l4->m_dof = i;
l4->m_value = vnl_vector<double>(1, fixval);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*l4));
}
}
break;
case 5:
{
for (int i = 0; i < dofs; i++)
{
if (m_FindingRealSolution)
{
fixval = -1.0 * oc;
}
else
{
fixval = 0.0;
}
l5 = itk::fem::LoadBC::New();
l5->m_element = m_Solver.el[m_PoleElementsGN[5]];
l5->m_dof = i;
l5->m_value = vnl_vector<double>(1, fixval);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*l5));
}
}
break;
}
}
}
template <typename TSurface, typename TImage, unsigned int TDimension>
void
FEMConformalMap<TSurface, TImage, TDimension>::ApplyRealForces(int dim)
{
if (dim > 6)
{
dim = 6;
}
// loop over all elements, applying forces to the nodes 0 and 1 (real forces are zero on the 3rd node)
// for( ::itk::fem::Solver::ElementArray::iterator e = m_Solver.el.begin(); e!=m_Solver.el.end(); e++)
{
itk::fem::Element::Pointer e = m_Solver.el[m_PoleElementsGN[dim]];
int na = 0;
int nb = 1;
int nc = 2;
{
VectorType A = (e)->GetNode(na)->GetCoordinates();
VectorType B = (e)->GetNode(nb)->GetCoordinates();
VectorType C = (e)->GetNode(nc)->GetCoordinates();
VectorType BA = B - A;
VectorType AC = A - C;
VectorType CB = C - B;
float bamag = BA.magnitude();
float cbmag = CB.magnitude();
float acmag = AC.magnitude();
if (bamag > cbmag && bamag > acmag)
{
na = 0;
nb = 1;
nc = 2;
}
if (cbmag > bamag && cbmag > acmag)
{
na = 1;
nb = 2;
nc = 0;
}
if (acmag > bamag && acmag > cbmag)
{
na = 2;
nb = 0;
nc = 1;
}
}
VectorType A = (e)->GetNode(na)->GetCoordinates();
VectorType B = (e)->GetNode(nb)->GetCoordinates();
VectorType C = (e)->GetNode(nc)->GetCoordinates();
VectorType BA = B - A;
VectorType CA = C - A;
VectorType CB = C - B;
float bamag = BA.magnitude();
float theta = (CA[0] * BA[0] + CA[1] * BA[1] + CA[2] * BA[2]) / bamag * bamag;
if (theta > 1)
{
::std::cout << " theta " << theta << std::endl;
}
VectorType E = A + BA * theta;
VectorType CE = C - E;
// load node 0
{
itk::fem::LoadNode::Pointer load = itk::fem::LoadNode::New();
load->m_pt = na;
load->F.set_size(3);
load->F.fill(-1.0 / bamag);
load->m_element = (e);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*load));
}
// load node 1
{
itk::fem::LoadNode::Pointer load = itk::fem::LoadNode::New();
load->m_pt = nb;
load->F.set_size(3);
load->F.fill(1.0 / bamag);
load->m_element = (e);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*load));
}
return;
}
}
template <typename TSurface, typename TImage, unsigned int TDimension>
void
FEMConformalMap<TSurface, TImage, TDimension>::ApplyImaginaryForces(int dim)
{
if (dim > 6)
{
dim = 6;
}
// loop over all elements, applying forces to the nodes 0 and 1 (real forces are zero on the 3rd node)
// for( ::itk::fem::Solver::ElementArray::iterator e = m_Solver.el.begin(); e!=m_Solver.el.end(); e++)
{
itk::fem::Element::Pointer e = m_Solver.el[m_PoleElementsGN[dim]];
/*
VectorType A=(e)->GetNode(0)->GetCoordinates();
VectorType B=(e)->GetNode(1)->GetCoordinates();
VectorType C=(e)->GetNode(2)->GetCoordinates();
VectorType BA =B-A;
VectorType CA =C-A;
float bamag=BA.magnitude();
float theta=(CA[0]*BA[0]+CA[1]*BA[1]+CA[2]*BA[2])/bamag*bamag;
if (theta > 1) ::std::cout << " theta " << theta << std::endl;
VectorType E = A+BA*theta;
VectorType CE =C-E;
float cemag=CE.magnitude();
*/
int na = 0;
int nb = 1;
int nc = 2;
{
VectorType A = (e)->GetNode(na)->GetCoordinates();
VectorType B = (e)->GetNode(nb)->GetCoordinates();
VectorType C = (e)->GetNode(nc)->GetCoordinates();
VectorType BA = B - A;
VectorType AC = A - C;
VectorType CB = C - B;
float bamag = BA.magnitude();
float cbmag = CB.magnitude();
float acmag = AC.magnitude();
if (bamag > cbmag && bamag > acmag)
{
na = 0;
nb = 1;
nc = 2;
}
if (cbmag > bamag && cbmag > acmag)
{
na = 1;
nb = 2;
nc = 0;
}
if (acmag > bamag && acmag > cbmag)
{
na = 2;
nb = 0;
nc = 1;
}
}
VectorType A = (e)->GetNode(na)->GetCoordinates();
VectorType B = (e)->GetNode(nb)->GetCoordinates();
VectorType C = (e)->GetNode(nc)->GetCoordinates();
VectorType BA = B - A;
VectorType CA = C - A;
VectorType CB = C - B;
float bamag = BA.magnitude();
float theta = (CA[0] * BA[0] + CA[1] * BA[1] + CA[2] * BA[2]) / bamag * bamag;
if (theta > 1 || theta < 0)
{
// ::std::cout << " ERROR : theta from non-acute angle " << theta << std::endl;
// throw;
// return;
}
VectorType E = A + BA * theta;
VectorType CE = C - E;
float cemag = CE.magnitude();
// load node 0
{
itk::fem::LoadNode::Pointer load = itk::fem::LoadNode::New();
load->m_pt = na;
load->F.set_size(3);
load->F.fill((1.0 - theta) / cemag);
load->m_element = (e);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*load));
}
// load node 1
{
itk::fem::LoadNode::Pointer load = itk::fem::LoadNode::New();
load->m_pt = nb;
load->F.set_size(3);
load->F.fill((theta) / cemag);
load->m_element = (e);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*load));
}
// load node 2
{
itk::fem::LoadNode::Pointer load = itk::fem::LoadNode::New();
load->m_pt = nc;
load->F.set_size(3);
load->F.fill(-1.0 / cemag);
load->m_element = (e);
m_Solver.load.push_back(itk::fem::FEMP<itk::fem::Load>(&*load));
}
return;
}
}
template <typename TSurface, typename TImage, unsigned int TDimension>
void
FEMConformalMap<TSurface, TImage, TDimension>::ComputeStereographicCoordinates()
{
::std::cout << " coords on unit sphere : " << std::endl;
float radsq; // radius squared
float c1, c2, c3; // stereographic coordinates
unsigned int dof;
for (::itk::fem::Solver::NodeArray::iterator n = m_Solver.node.begin(); n != m_Solver.node.end(); ++n)
{
dof = (*n)->GetDegreeOfFreedom(0);
float x = m_RealSolution[dof];
float y = m_ImagSolution[dof];
radsq = x * x + y * y;
c1 = 2.0 * x / (1.0 + radsq);
c2 = 2.0 * y / (1.0 + radsq);
c3 = 2.0 * radsq / (1.0 + radsq) - 1.0;
// ::std::cout << c1 << " " << c2 << " " << c3 << " mag " << sqrt(c1*c1+c2*c2+c3*c3) << std::endl;
VectorType coord = (*n)->GetCoordinates();
coord[0] = c1;
coord[1] = c2;
coord[2] = c3;
// / (*n)->SetCoordinates(coord);
}
::std::cout << " coords on unit sphere done " << std::endl;
}
template <typename TSurface, typename TImage, unsigned int TDimension>
void
FEMConformalMap<TSurface, TImage, TDimension>::ConformalMap()
{
m_Solver.load.clear();
m_Solver.node.clear();
m_Solver.el.clear();
/**
* Open the file and assign it to stream object f
*/
if (m_ReadFromFile)
{
const char * filename = m_ParameterFileName.c_str();