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ConformalMapping.cxx
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ConformalMapping.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 details.
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.
=========================================================================*/
#include "antsUtilities.h"
#include "antsAllocImage.h"
#include <algorithm>
#include <algorithm>
#include <string>
#include <math.h>
#include <time.h>
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIterator.h"
#include "itkMesh.h"
#include "itkSphereMeshSource.h"
#include "itkBinaryMask3DMeshSource.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkFEMConformalMap.h"
#include "itkFEMDiscConformalMap.h"
#include "BinaryImageToMeshFilter.h"
#include "vtkCallbackCommand.h"
#include "vtkPointPicker.h"
#include "vtkCellPicker.h"
#include "vtkPolyDataWriter.h"
#include "vtkPolyDataReader.h"
#include "ReadWriteData.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkSurfaceImageCurvature.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkImageRegionIterator.h"
#include "itkPointSet.h"
#include <vtkSmartPointer.h>
#include <vtkWindowedSincPolyDataFilter.h>
namespace ants
{
/*
OPEN QUESTIONS:
LOCAL FROM GLOBAL FOR TRIANGLE IN 3D (MARCELO)
USEFUL FOR INTERPOLATING STEREOGRAPHIC COORDS INTO IMAGE.
CURRENTLY JUST DENSELY INTERPOLATE ACROSS EACH TRIANGLE. -- Not necessary for triangle
TRIANGLE AREA IN 3D (D0NE : USING CROSS PRODUCT )
- need to insure we use the hypotneuse as the AB edge : so theta is <= 1.0;
- try to apply bcs to even out the map
- what is the effect of material param E?
*/
void Display(vtkUnstructuredGrid* vtkgrid, bool secondwin = false, bool delinter = true)
{
// Create the renderer and window stuff
std::cout << " second win " << secondwin << std::endl;
vtkRenderer* ren1 = vtkRenderer::New();
vtkRenderer* ren2 = vtkRenderer::New();
vtkRenderWindow* renWin = vtkRenderWindow::New();
renWin->AddRenderer(ren1);
if( secondwin )
{
renWin->AddRenderer(ren2);
}
vtkRenderWindowInteractor* inter = vtkRenderWindowInteractor::New();
inter->SetRenderWindow(renWin);
// vtkCellPicker* cpicker = vtkCellPicker::New();
vtkCallbackCommand *cbc = vtkCallbackCommand::New();
/*-------------------------------------------------------------------------
void vtkCompositeManagerExitInteractor(vtkObject *vtkNotUsed(o),
unsigned long vtkNotUsed(event),
void *clientData, void *)
{
vtkCompositeManager *self = (vtkCompositeManager *)clientData;
self->ExitInteractor();
}*/
// cbc=vectraEventHandler; //-> SetCallback(vectraEventHandler);
ren1->AddObserver(vtkCommand::KeyPressEvent, cbc);
vtkDataSetMapper* mapper = vtkDataSetMapper::New();
mapper->SetInput(vtkgrid);
mapper->SetScalarRange(0, 255);
vtkActor* actor = vtkActor::New();
actor->SetMapper(mapper);
vtkDataSetMapper* mapper2 = vtkDataSetMapper::New();
if( secondwin )
{
mapper2->SetInput(vtkgrid);
}
if( secondwin )
{
mapper2->SetScalarRange(0, 255);
}
vtkActor* actor2 = vtkActor::New();
if( secondwin )
{
actor2->SetMapper(mapper2);
}
if( secondwin )
{
ren1->SetViewport(0.0, 0.0, 0.5, 1.0);
ren2->SetViewport(0.5, 0.0, 1.0, 1.0);
}
else
{
ren1->SetViewport(0.0, 0.0, 1.0, 1.0);
}
if( secondwin )
{
ren2->AddActor(actor2);
}
// add the actor and start the render loop
ren1->AddActor(actor);
// this->InteractionPicker->Pick(x, y, 0.0, this->CurrentRenderer);
// this->InteractionPicker->GetPickPosition(this->DownPt);
renWin->Render();
inter->Start();
/*
int X, Y;
char keypressed = *(inter -> GetKeySym());
inter -> GetMousePosition(&X, &Y);
std::cout <<" X Y " << X << " " << Y << std::endl;
renWin->Render();
inter->Start();*/
/*
vtkPointPicker* picker=vtkPointPicker::New();
// vtkPoints *GetPickedPositions() {return this->PickedPositions;};
float x = inter->GetEventPosition()[0];
float y = inter->GetEventPosition()[1];
float z = 0.0;
picker->Pick(x,y,z,ren1);
std::cout <<" picked " << (*picker->GetPickedPositions()) << std::endl;*/
mapper->Delete();
actor->Delete();
ren1->Delete();
mapper2->Delete();
actor2->Delete();
ren2->Delete();
renWin->Delete();
if( delinter )
{
inter->Delete();
}
}
template <class TImage>
void MapToSphere(typename TImage::Pointer image, int fixdir, float e)
{
typedef TImage ImageType;
typedef unsigned char PixelType;
typedef itk::Mesh<float> MeshType;
typedef itk::BinaryMask3DMeshSource<ImageType, MeshType> MeshSourceType;
PixelType internalValue = 1;
typename MeshSourceType::Pointer meshSource = MeshSourceType::New();
meshSource->SetBinaryImage( image );
meshSource->SetObjectValue( internalValue );
try
{
meshSource->Update();
}
catch( itk::ExceptionObject & exp )
{
std::cout << "Exception thrown during Update() " << std::endl;
std::cout << exp << std::endl;
return;
}
meshSource->GetOutput();
std::cout << meshSource->GetNumberOfNodes() << std::endl;
std::cout << meshSource->GetNumberOfCells() << std::endl;
typedef itk::FEMConformalMap<MeshType, ImageType> ParamType;
typename ParamType::Pointer Parameterizer = ParamType::New();
Parameterizer->SetDebug(false);
// Parameterizer->SetDebug(true);
Parameterizer->SetReadFromFile(false);
Parameterizer->SetParameterFileName("");
Parameterizer->SetImage(image);
std::cout << " fixdir " << fixdir << " e " << e << " best e ~ 3.e-3 " << std::endl;
Parameterizer->SetNorthPole(fixdir);
Parameterizer->SetSigma(e);
Parameterizer->SetSurfaceMesh(meshSource->GetOutput() );
// Parameterizer->GenerateSystemFromSurfaceMesh();
std::cout << std::endl;
Parameterizer->ConformalMap();
Parameterizer->ComputeStereographicCoordinates();
if( Parameterizer->GetImage() )
{
std::cout << " writing param images " << std::endl;
{
Parameterizer->MapCheckerboardToImage(0.05);
typename itk::ImageFileWriter<ImageType>::Pointer writer;
writer = itk::ImageFileWriter<ImageType>::New();
std::string fn = "checker.nii";
writer->SetFileName(fn.c_str() );
writer->SetInput(Parameterizer->GetImage() );
writer->Write();
}
}
}
template <class TImage>
typename TImage::Pointer
SmoothImage( typename TImage::Pointer input, double var)
{
typedef TImage ImageType;
typedef typename ImageType::PixelType PixelType;
enum { ImageDimension = ImageType::ImageDimension };
typedef itk::Image<float, ImageDimension> realImageType;
typedef itk::DiscreteGaussianImageFilter<ImageType, ImageType> dgf;
typename dgf::Pointer filter = dgf::New();
filter->SetVariance(var);
filter->SetMaximumError(.01f);
filter->SetUseImageSpacingOn();
filter->SetInput(input);
filter->Update();
typedef itk::CastImageFilter<ImageType, ImageType> CasterType1;
typename CasterType1::Pointer caster1 = CasterType1::New();
caster1->SetInput(filter->GetOutput() );
caster1->Update();
return caster1->GetOutput();
}
float ComputeGenus(vtkPolyData* pd1)
{
vtkExtractEdges* edgeex = vtkExtractEdges::New();
edgeex->SetInput(pd1);
edgeex->Update();
vtkPolyData* edg1 = edgeex->GetOutput();
vtkIdType nedg = edg1->GetNumberOfCells();
vtkIdType vers = pd1->GetNumberOfPoints();
int nfac = pd1->GetNumberOfPolys();
float g = 0.5 * (2.0 - vers + nedg - nfac);
std::cout << " Genus " << g << std::endl;
std::cout << " face " << nfac << " edg " << nedg << " vert " << vers << std::endl;
return g;
}
float vtkComputeTopology(vtkPolyData* pd)
{
// Marching cubes
// std::cout << " Marching Cubes ";
// vtkMarchingCubes *marchingCubes = vtkMarchingCubes::New();
// vtkContourFilter *marchingCubes = vtkContourFilter::New();
// vtkKitwareContourFilter *marchingCubes = vtkKitwareContourFilter::New();
// marchingCubes->SetInput((vtkDataSet*) vds);
// marchingCubes->SetValue(0, hithresh);
// int nc;
// std::cout << " Input #conts "; std::cin >> nc;
// marchingCubes->SetNumberOfContours(2);
// marchingCubes->SetComputeScalars(false);
// marchingCubes->SetComputeGradients(false);
// marchingCubes->SetComputeNormals(false);
vtkPolyDataConnectivityFilter* con = vtkPolyDataConnectivityFilter::New();
con->SetExtractionModeToLargestRegion();
// con->SetInput(marchingCubes->GetOutput());
con->SetInput(pd);
// vtkUnstructuredGridToPolyDataFilter* gp = vtkUnstructuredGridToPolyDataFilter::New();
// gp->SetInput(con->GetOutput());
float g = ComputeGenus(con->GetOutput() );
// marchingCubes->Delete();
return g;
}
template <class TImage>
void GetMeshAndCurvature(typename TImage::Pointer image, float e, const char* filename)
{
typedef TImage ImageType;
typedef vtkPolyData MeshType;
double aaParm = 0.024;
typedef BinaryImageToMeshFilter<ImageType> FilterType;
typename FilterType::Pointer fltMesh = FilterType::New();
fltMesh->SetInput(image);
fltMesh->SetAntiAliasMaxRMSError(aaParm);
fltMesh->SetAntiAliasMaxRMSError( -1000.0 ); // to do nothing
fltMesh->Update();
vtkPolyData* vtkmesh = fltMesh->GetMesh();
// assign scalars to the original surface mesh
// Display((vtkUnstructuredGrid*)vtkmesh);
std::cout << " Genus " << vtkComputeTopology(vtkmesh) << std::endl;
typedef itk::SurfaceImageCurvature<ImageType> surfktype;
typename surfktype::Pointer surfk = surfktype::New();
// kappa=;
typedef itk::Image<float, 3> FloatImageType;
surfk->SetInput(image); // SmoothImage<ImageType>(image,1.0));
surfk->SetNeighborhoodRadius( 1.5 );
surfk->SetSigma(1.);
surfk->SetUseLabel(false);
surfk->SetUseGeodesicNeighborhood(false);
surfk->SetkSign(1.0);
surfk->ComputeFrameOverDomain( 3 );
typename FloatImageType::Pointer kappa = surfk->GetFunctionImage();
typedef itk::Image<unsigned char, 3> itype;
typedef itk::RescaleIntensityImageFilter<
FloatImageType,
itype> CastFilterType;
typename CastFilterType::Pointer caster = CastFilterType::New();
caster->SetInput( image );
caster->SetOutputMinimum( 0 );
caster->SetOutputMaximum( 255 );
std::string fn = std::string(filename);
fn = fn.substr(0, fn.length() - 4) + "kappa.nii";
typedef itk::ImageFileWriter<itype> writertype;
typename writertype::Pointer w = writertype::New();
typename itype::Pointer kimg = caster->GetOutput();
w->SetInput(kimg);
w->SetFileName(fn.c_str() );
w->Write();
typename itype::SpacingType spacing = image->GetSpacing();
vtkPoints* vtkpoints = vtkmesh->GetPoints();
int numPoints = vtkpoints->GetNumberOfPoints();
float mx = 0, mn = 9.e9, meank = 0;
for( int i = 0; i < numPoints; i++ )
{
typename ImageType::IndexType index;
for( int j = 0; j < 3; j++ )
{
index[j] = (int)(vtkpoints->GetPoint(i)[j] / spacing[j] + 0.5);
}
float temp = kimg->GetPixel(index);
// float temp=image->GetPixel(index);
if( fabs(temp) > mx )
{
mx = fabs(temp);
}
if( fabs(temp) < mn && mn > 0 )
{
mn = fabs(temp);
}
meank += fabs(temp);
}
std::cout << " max kap " << mx << " mn k " << mn << std::endl;
meank /= numPoints;
// mx=1.3;
// mx=2.0;
// bool done=false;
// while (!done)
{
vtkFloatArray * param = vtkFloatArray::New();
param->SetName("angle");
float dif = (mx - mn) * 0.25;
const float mx2 = meank + dif;
const float mn2 = meank - dif;
dif = mx2 - mn2;
for( int i = 0; i < numPoints; i++ )
{
typename ImageType::IndexType index;
for( int j = 0; j < 3; j++ )
{
index[j] = (int)(vtkpoints->GetPoint(i)[j] / spacing[j] + 0.5);
}
float temp = kimg->GetPixel(index);
// float temp=surfk->CurvatureAtIndex(index);
if( i % 1000 == 0 )
{
std::cout << " kappa " << temp << std::endl;
}
// =fabs(manifoldIntegrator->GetGraphNode(i)->GetTotalCost());
temp = fabs(temp);
param->InsertNextValue( (temp - mn2) * 255. / dif);
}
vtkmesh->GetPointData()->SetScalars(param);
// Display((vtkUnstructuredGrid*)vtkmesh);
// std::cout<<"DOne? "; std::cin >> done;
}
std::cout << " done with curvature map ";
vtkPolyDataWriter *writer = vtkPolyDataWriter::New();
writer->SetInput(vtkmesh);
std::string outnm = std::string(filename);
outnm = outnm.substr(0, outnm.length() - 4) + ".vtk";
std::cout << " writing " << outnm << std::endl;
// outnm="C:\\temp\\mesh.vtk";
writer->SetFileName(outnm.c_str() );
writer->SetFileTypeToBinary();
writer->Update();
std::cout << " done writing ";
return;
}
template <class TImage>
float GetImageTopology(typename TImage::Pointer image, float e, const char* filename)
{
typedef TImage ImageType;
typedef vtkPolyData MeshType;
double aaParm = 0.024;
typedef BinaryImageToMeshFilter<ImageType> FilterType;
typename FilterType::Pointer fltMesh = FilterType::New();
fltMesh->SetInput(image);
fltMesh->SetAntiAliasMaxRMSError(aaParm);
fltMesh->SetAntiAliasMaxRMSError( -1000.0 ); // to do nothing
fltMesh->Update();
vtkPolyData* vtkmesh = fltMesh->GetMesh();
// assign scalars to the original surface mesh
// Display((vtkUnstructuredGrid*)vtkmesh);
float genus = vtkComputeTopology(vtkmesh);
std::cout << " Genus " << genus << std::endl;
return genus;
}
template <class TImage>
void MapToDisc(vtkPolyData* vtkmesh, float e, std::string outfn)
{
typedef TImage ImageType;
typedef vtkPolyData MeshType;
typedef itk::FEMDiscConformalMap<MeshType, ImageType> ParamType;
typename ParamType::Pointer Parameterizer = ParamType::New();
Parameterizer->SetDebug(false);
// Parameterizer->SetDebug(true);
Parameterizer->SetReadFromFile(false);
Parameterizer->SetParameterFileName("");
Parameterizer->SetSigma(e);
Parameterizer->SetSurfaceMesh(vtkmesh);
ComputeGenus( (vtkPolyData *)Parameterizer->GetSurfaceMesh() );
Parameterizer->ExtractSurfaceDisc();
ComputeGenus( (vtkPolyData *)Parameterizer->GetSurfaceMesh() );
// Display((vtkUnstructuredGrid*)Parameterizer->GetSurfaceMesh());
std::cout << " begin conformal mapping ";
Parameterizer->ConformalMap();
std::cout << " display patch ";
// ComputeGenus((vtkPolyData*)Parameterizer->m_ExtractedSurfaceMesh);
// Display((vtkUnstructuredGrid*)Parameterizer->m_ExtractedSurfaceMesh);
// std::cout << " display flattened patch ";
// float step = 0.1;
// float maxt=0.0;
// for (float tt = 0.0; tt<=maxt; tt=tt+step)
{
// std::cout <<" Building at : " << tt << std::endl;
// / Parameterizer->BuildOutputMeshes(tt);
// if (tt == 0.)
{
vtkPolyDataWriter *writer = vtkPolyDataWriter::New();
writer->SetInput(Parameterizer->m_ExtractedSurfaceMesh);
std::string outnm; // =std::string(filename);
// outnm=outnm.substr(0,outnm.length()-4)+".vtk";
outnm = outfn + "mapspace.vtk";
std::cout << " writing " << outnm << std::endl;
writer->SetFileName(outnm.c_str() );
writer->SetFileTypeToBinary();
writer->Update();
}
{
vtkPolyDataWriter *writer = vtkPolyDataWriter::New();
writer->SetInput(Parameterizer->m_DiskSurfaceMesh);
std::string outnm;
outnm = outfn + "mapflat.vtk";
std::cout << " writing " << outnm << std::endl;
writer->SetFileName(outnm.c_str() );
writer->SetFileTypeToBinary();
writer->Update();
}
}
/*
for (float sig=0.4; sig<=1.0; sig=sig+0.1)
{
Parameterizer->SetSmooth(sig);
Parameterizer->ConjugateHarmonic();
// ComputeGenus((vtkPolyData*)Parameterizer->m_DiskSurfaceMesh);
Display((vtkUnstructuredGrid*)Parameterizer->m_DiskSurfaceMesh);
}
*/
typedef typename ParamType::FlatImageType imtype;
typename itk::ImageFileWriter<imtype>::Pointer writer;
writer = itk::ImageFileWriter<imtype>::New();
std::string fn = outfn + "flat.nii";
writer->SetFileName(fn.c_str() );
writer->SetInput(Parameterizer->m_FlatImage);
if( Parameterizer->m_FlatImage )
{
writer->Write();
}
std::cout << " done writing ";
}
/*
template <class TImage>
void MeshToImage(vtkPolyData* vtkmesh, int imagesize, std::string outfn)
{
const unsigned int Dimension = 2;
const int splineOrder = 3;
const int component = 0;
const char* dataname = "scalars";
typedef TImage ImageType;
typedef vtkPolyData MeshType;
typedef typename ImageType::PixelType PixelType;
typedef typename itk::Vector<PixelType, 1> FunctionalDataType;
typedef typename itk::Image<FunctionalDataType, Dimension> FunctionalImageType;
int numVertices = vtkmesh->GetNumberOfPoints();
vtkmesh->GetPointData()->SetActiveScalars( dataname );
std::cout << "#of vertices " << numVertices << " Fitting variable " << vtkmesh->GetPointData()->GetScalars()->GetName( ) << std::endl;
typedef itk::PointSet<FunctionalDataType, Dimension> FunctionalMapType;
typedef itk::BSplineScatteredDataPointSetToImageFilter
<FunctionalMapType, FunctionalImageType> BSplineFilterType;
typename FunctionalMapType::Pointer funcdataPoints =
FunctionalMapType::New();
typename BSplineFilterType::Pointer bspliner = BSplineFilterType::New();
FunctionalDataType data, data1;
typename FunctionalMapType::PointType point;
double bounds[6];
vtkPoints *meshpoints = vtkmesh->GetPoints();
meshpoints->ComputeBounds();
meshpoints->GetBounds( bounds );
for (int ID=0; ID < numVertices; ++ID)
{
data[0] = vtkmesh->GetPointData()->GetScalars()->GetComponent(ID, component);
for (int dir=0; dir < Dimension; ++dir)
point[dir] = meshpoints->GetPoint(ID)[dir];
//Debug
//data[0] = 1*point[0] + 0*point[1];
funcdataPoints->SetPointData( ID, data);
funcdataPoints->SetPoint( ID, point);
//std::cout << ID << " " << point[0] << " " << point[1] << " " << data[0] << std::endl;
}
std::cout << "Read all mesh data" << std::endl;
typename FunctionalImageType::PointType origin;
typename FunctionalImageType::SpacingType spacing;
typename FunctionalImageType::SizeType size;
float maxX, minX, maxY, minY;
maxX = static_cast<float>(bounds[1]);
minX = static_cast<float>(bounds[0]);
maxY = static_cast<float>(bounds[3]);
minY = static_cast<float>(bounds[2]);
std::cout << "minX " << minX << " maxX " << maxX << " minY " << minY << " maxY " << maxY << std::endl;
size[0] = imagesize;
size[1] = imagesize;
origin[0] = (minX + maxX)/2;
origin[1] = (minY + maxY)/2;
origin[0] = minX - (maxX-minX)*0.1;
origin[1] = minY - (maxY-minY)*0.1;
origin[0] = minX;
origin[1] = minY;
spacing[0] = 1.1*((((maxX-minX)>(maxY-minY))?(maxX-minX):(maxY-minY)))/imagesize;
spacing[1] = spacing[0];
std::cout << "size " << size << " origin " << origin << " spacing " << spacing << std::endl;
typename BSplineFilterType::ArrayType ncps;
ncps.Fill( splineOrder + 1 );
//const int numLevels = round((1/static_cast<double>(Dimension))*log(static_cast<double>(numVertices))/log(2.0));
const int numLevels = 13;
typename BSplineFilterType::ArrayType close;
close.Fill( false );
std::cout << "No. of levels " << numLevels << " splineOrder " << splineOrder << " #control points " << ncps << std::endl;
bspliner->SetOrigin( origin );
bspliner->SetSpacing( spacing );
bspliner->SetSize( size );
bspliner->SetGenerateOutputImage( true );
bspliner->SetNumberOfLevels( numLevels );
bspliner->SetSplineOrder( splineOrder );
bspliner->SetNumberOfControlPoints( ncps );
bspliner->SetCloseDimension( close );
bspliner->SetInput( funcdataPoints );
bspliner->DebugOn();
std::cout << "Entering BSpline" << std::endl;
bspliner->Update();
std::cout << "BSpline fitting done" << std::endl;
// ORIENTATION ALERT -- the original code here
// set the region, spacing, and origin without setting directions.
typename ImageType::Pointer outimage =
AllocImage<ImageType>(bspliner->GetOutput());
typename itk::ImageRegionIterator<ImageType>
ItO( outimage, outimage->GetRequestedRegion() );
typename itk::ImageRegionConstIterator<FunctionalImageType>
ItB( bspliner->GetOutput(), bspliner->GetOutput()->GetRequestedRegion() );
for ( ItB.GoToBegin(), ItO.GoToBegin(); !ItB.IsAtEnd(); ++ItB, ++ItO )
{
ItO.Set( static_cast<PixelType>( ItB.Get()[0] ) );
}
typename itk::ImageFileWriter<ImageType>::Pointer writer;
writer = itk::ImageFileWriter<ImageType>::New();
std::string fn=outfn+"flat.nii";
writer->SetFileName(fn.c_str());
writer->SetInput( outimage );
writer->Write();
*/
/*** Evaluate quality of fit ***/
/*
typedef typename itk::LinearInterpolateImageFunction< ImageType, float > InterpolatorType;
typename InterpolatorType::PointType testpoint;
typename InterpolatorType::Pointer interp = InterpolatorType::New();
interp->SetInputImage( outimage );
for (int ID=0; ID < numVertices; ++ID)
{
data[0] = vtkmesh->GetPointData()->GetScalars()->GetComponent(ID, component);
for (int dir=0; dir < Dimension; ++dir)
{
point[dir] = meshpoints->GetPoint(ID)[dir];
testpoint[dir] = point[dir] - origin[dir];
}
vtkmesh->GetPointData()->GetScalars()->SetComponent(ID, component, static_cast<int>(data[0]) - static_cast<int>(interp->Evaluate( testpoint )));
//vtkmesh->GetPointData()->GetScalars()->SetComponent(ID, component, interp->Evaluate( testpoint ));
data1[0] = vtkmesh->GetPointData()->GetScalars()->GetComponent(ID, component);
cout << "error " << data1[0] << " original " << data[0] << " at " << point << " interpolated " << interp->Evaluate( testpoint ) << " at " << testpoint << endl;
}
vtkPolyDataWriter *vtkwriter = vtkPolyDataWriter::New();
vtkwriter->SetInput( vtkmesh );
vtkwriter->SetFileName( "newmesh3.vtk" );
vtkwriter->Write();
*/
// }
template <class TImage>
typename TImage::Pointer
RemoveNaNs(typename TImage::Pointer image, float replaceval )
{
typedef itk::ImageRegionIteratorWithIndex<TImage> Iterator;
Iterator vfIter(image, image->GetLargestPossibleRegion() );
for( vfIter.GoToBegin(); !vfIter.IsAtEnd(); ++vfIter )
{
typename TImage::PixelType v1 = vfIter.Get();
if( vnl_math_isnan(v1) )
{
vfIter.Set(replaceval);
}
}
return image;
}
/*
template <class TImage>
void ImageToMesh(vtkPolyData* vtkmesh, typename TImage::Pointer image, std::string outfn)
{
const unsigned int Dimension = 2;
const int splineOrder = 3;
const int imagesize = 512;
const int component = 0;
const char* dataname = "points";
typedef TImage ImageType;
typedef vtkPolyData MeshType;
typedef typename ImageType::PixelType PixelType;
typedef typename itk::Vector<PixelType, 1> FunctionalDataType;
typedef typename itk::Image<FunctionalDataType, Dimension> FunctionalImageType;
float replaceval = 5;
image = RemoveNaNs<TImage>(image, replaceval);
int numVertices = vtkmesh->GetNumberOfPoints();
vtkmesh->GetPointData()->SetActiveScalars( dataname );
std::cout << "#of vertices " << numVertices << " Fitting variable " << vtkmesh->GetPointData()->GetScalars()->GetName( ) << std::endl;
typedef itk::PointSet<FunctionalDataType, Dimension> FunctionalMapType;
typedef itk::BSplineScatteredDataPointSetToImageFilter
<FunctionalMapType, FunctionalImageType> BSplineFilterType;
typename FunctionalMapType::Pointer funcdataPoints =
FunctionalMapType::New();
typename BSplineFilterType::Pointer bspliner = BSplineFilterType::New();
FunctionalDataType data;
typename FunctionalMapType::PointType point;
double bounds[6];
vtkPoints *meshpoints = vtkmesh->GetPoints();
meshpoints->ComputeBounds();
meshpoints->GetBounds( bounds );
for (int ID=0; ID < numVertices; ++ID)
{
data[0] = vtkmesh->GetPointData()->GetScalars()->GetComponent(ID, component);
for (int dir=0; dir < Dimension; ++dir)
point[dir] = meshpoints->GetPoint(ID)[dir];
//Debug
//data[0] = 1*point[0] + 0*point[1];
funcdataPoints->SetPointData( ID, data);
funcdataPoints->SetPoint( ID, point);
//std::cout << ID << " " << point[0] << " " << point[1] << " " << data[0] << std::endl;
}
std::cout << "Read all mesh data" << std::endl;
// Create new data array
vtkFloatArray *newdata;
newdata = vtkFloatArray::New();
newdata->SetName("atlas");
typename FunctionalImageType::PointType origin;
typename FunctionalImageType::SpacingType spacing;
typename FunctionalImageType::SizeType size;
float maxX, minX, maxY, minY;
maxX = static_cast<float>(bounds[1]);
minX = static_cast<float>(bounds[0]);
maxY = static_cast<float>(bounds[3]);
minY = static_cast<float>(bounds[2]);
std::cout << "minX " << minX << " maxX " << maxX << " minY " << minY << " maxY " << maxY << std::endl;
size[0] = imagesize;
size[1] = imagesize;
origin[0] = (minX + maxX)/2;
origin[1] = (minY + maxY)/2;
origin[0] = minX - (maxX-minX)*0.1;
origin[1] = minY - (maxY-minY)*0.1;
origin[0] = minX;
origin[1] = minY;
spacing[0] = 1.1*((((maxX-minX)>(maxY-minY))?(maxX-minX):(maxY-minY)))/imagesize;
spacing[1] = spacing[0];
std::cout << "size " << size << " origin " << origin << " spacing " << spacing << std::endl;
*/
/* bspline code -- not doing b-spline now
typename BSplineFilterType::ArrayType ncps;
ncps.Fill( splineOrder + 1 );
//const int numLevels = round((1/static_cast<double>(Dimension))*log(static_cast<double>(numVertices))/log(2.0));
const int numLevels = 13;
typename BSplineFilterType::ArrayType close;
close.Fill( false );
std::cout << "No. of levels " << numLevels << " splineOrder " << splineOrder << " #control points " << ncps << std::endl;
bspliner->SetOrigin( origin );
bspliner->SetSpacing( spacing );
bspliner->SetSize( size );
bspliner->SetGenerateOutputImage( true );
bspliner->SetNumberOfLevels( numLevels );
bspliner->SetSplineOrder( splineOrder );
bspliner->SetNumberOfControlPoints( ncps );
bspliner->SetCloseDimension( close );
bspliner->SetInput( funcdataPoints );
bspliner->DebugOn();
std::cout << "Entering BSpline" << std::endl;
bspliner->Update();
std::cout << "BSpline fitting done" << std::endl;
typename ImageType::Pointer outimage = ImageType::New();
outimage->SetSpacing( bspliner->GetOutput()->GetSpacing() );
outimage->SetOrigin( bspliner->GetOutput()->GetOrigin() );
outimage->SetRegions( bspliner->GetOutput()->GetLargestPossibleRegion() );
outimage->Allocate();
*/
/*
typename itk::ImageRegionIterator<ImageType>
ItO( image, image->GetRequestedRegion() );
// Evaluate quality of fit
//typedef typename itk::LinearInterpolateImageFunction< ImageType, float > InterpolatorType;
typedef typename itk::NearestNeighborInterpolateImageFunction< ImageType, float > InterpolatorType;
typename InterpolatorType::PointType testpoint;
typedef typename itk::ContinuousIndex< float, Dimension > ContinuousIndexType;
typename InterpolatorType::Pointer interp = InterpolatorType::New();
interp->SetInputImage( image );
ContinuousIndexType contind;
for (int ID=0; ID < numVertices; ++ID)
{
for (int dir=0; dir < Dimension; ++dir)
testpoint[dir] = meshpoints->GetPoint(ID)[dir] - origin[dir];
newdata->InsertNextValue( interp->Evaluate( testpoint ) );
//vtkmesh->GetPointData()->GetScalars()->SetComponent(ID, component, (interp->Evaluate( testpoint )));
//vtkmesh->GetPointData()->GetScalars()->SetComponent(ID, component, interp->Evaluate( testpoint ));
// cout << vtkmesh->GetPointData()->GetScalars()->GetComponent(ID, component) << " " << data[0] << " " << interp->Evaluate( testpoint ) << endl;
}
vtkmesh->GetPointData()->AddArray( newdata );
vtkPolyDataWriter *vtkwriter = vtkPolyDataWriter::New();
vtkwriter->SetInput( vtkmesh );
std::string fn=outfn+".vtk";
vtkwriter->SetFileName(fn.c_str());
vtkwriter->Write();
}
*/
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int ConformalMapping( std::vector<std::string> args, std::ostream* out_stream = NULL )
{
// put the arguments coming in as 'args' into standard (argc,argv) format;
// 'args' doesn't have the command name as first, argument, so add it manually;
// 'args' may have adjacent arguments concatenated into one argument,
// which the parser should handle
args.insert( args.begin(), "ConformalMapping" );
int argc = args.size();
char* * argv = new char *[args.size() + 1];
for( unsigned int i = 0; i < args.size(); ++i )
{
// allocate space for the string plus a null character
argv[i] = new char[args[i].length() + 1];
std::strncpy( argv[i], args[i].c_str(), args[i].length() );
// place the null character in the end
argv[i][args[i].length()] = '\0';
}
argv[argc] = 0;
// class to automatically cleanup argv upon destruction
class Cleanup_argv
{
public:
Cleanup_argv( char* * argv_, int argc_plus_one_ ) : argv( argv_ ), argc_plus_one( argc_plus_one_ )
{
}
~Cleanup_argv()
{
for( unsigned int i = 0; i < argc_plus_one; ++i )
{
delete[] argv[i];
}
delete[] argv;
}
private:
char* * argv;
unsigned int argc_plus_one;
};
Cleanup_argv cleanup_argv( argv, argc + 1 );
// antscout->set_stream( out_stream );
// Define the dimension of the images
const unsigned int Dimension = 3;
typedef float PixelType;
// Declare the types of the output images
typedef itk::Image<PixelType, Dimension> ImageType;
typedef itk::Image<PixelType, 2> Image2DType;
// Declare the type of the index,size and region to initialize images
typedef itk::Index<Dimension> IndexType;
typedef itk::Size<Dimension> SizeType;
typedef itk::ImageRegion<Dimension> RegionType;
typedef itk::ImageRegionIterator<ImageType> IteratorType;
// Declare the type of the Mesh
char* filename;
PixelType loth = 1;
PixelType hith = 256;
int fixdir = 1;
float param = 2.e-4;
std::string outfn;
std::cout << "to get mesh: ConformalMapping image.nii 1 255 1.e-3 0 outname " << std::endl;
std::cout << "to flatten mesh: ConformalMapping mesh.vtk 1 2 3 4 outname " << std::endl;
std::cout << "to view mesh: ConformalMapping mesh.vtk 1 2 3 1 outname " << std::endl;
std::cout << "to get image topology: ConformalMapping image.nii 1 255 1.e-3 5 outname " << std::endl;
std::cout << "to convert flattened mesh to image : ConformalMapping mesh.vtk 1 2 3 6 outname " << std::endl;
std::cout
<<
"to interpolate data in flattened image domain to original mesh: ConformalMapping image.nii 1 2 3 7 outname originalflatmesh.vtk"
<< std::endl;
std::cout << " to smooth a mesh --- ConformalMapping mesh.vtk 1 2 NumSmoothIts 8 outname " << std::endl;
if( argc >= 2 )
{
filename = argv[1];
loth = atof(argv[2]);
hith = atof(argv[3]);
param = atof(argv[4]);
fixdir = atoi(argv[5]);
outfn = std::string(argv[6]);
}
else
{
filename = (char *)"image.nii";
return 0;
}
if( fixdir == 0 )
{
typedef itk::ImageFileReader<ImageType> FileSourceType;
typedef ImageType::PixelType PixType;
FileSourceType::Pointer readfilter = FileSourceType::New();
readfilter->SetFileName( filename );
try
{
readfilter->Update();
}
catch( itk::ExceptionObject & e )
{
std::cout << "Exception caught during reference file reading " << std::endl;
std::cout << e << std::endl;
return -1;
}
ImageType::Pointer image = readfilter->GetOutput();
ImageType::Pointer thresh = BinaryThreshold<ImageType>(loth, hith, hith, image );
// Save the mesh
GetMeshAndCurvature<ImageType>(thresh, param, filename);
// MapToSphere<ImageType>(thresh,fixdir,e);
}
else if( fixdir == 5 )
{
typedef itk::ImageFileReader<ImageType> FileSourceType;
typedef ImageType::PixelType PixType;
FileSourceType::Pointer readfilter = FileSourceType::New();
readfilter->SetFileName( filename );
try
{
readfilter->Update();
}
catch( itk::ExceptionObject & e )
{
std::cout << "Exception caught during reference file reading " << std::endl;
std::cout << e << std::endl;
return -1;
}
ImageType::Pointer image = readfilter->GetOutput();