int main(int argc, char* argv[])
{
PARSE_ARGS;
if(fiberFile == "")
{
std::cerr << "A fiber file has to be specified" << std::endl;
return EXIT_FAILURE;
}
vtkSmartPointer<vtkPolyDataReader> reader = vtkSmartPointer<vtkPolyDataReader>::New();
std::cout << "Reading " << fiberFile<< std::endl;
reader->SetFileName(fiberFile.c_str());
reader->Update();
// Extract the polydata
vtkSmartPointer<vtkPolyData> polydata =
reader->GetOutput();
DeformationImageType::Pointer deformationfield(NULL);
if(hField != "")
deformationfield = readDeformationField(hField, HField);
else if(displacementField != "")
deformationfield = readDeformationField(displacementField, Displacement);
else
deformationfield = NULL;
typedef itk::VectorLinearInterpolateImageFunction<DeformationImageType, double> DeformationInterpolateType;
DeformationInterpolateType::Pointer definterp(NULL);
if(deformationfield)
{
definterp = DeformationInterpolateType::New();
definterp->SetInputImage(deformationfield);
} else {
std::cout << "A deformation field has to be specified" << std::endl;
return EXIT_FAILURE;
}
typedef DeformationInterpolateType::ContinuousIndexType ContinuousIndexType;
ContinuousIndexType ci, origci;
// For each point along the fiber
vtkIdType numPoints= polydata->GetNumberOfPoints();
vtkPoints* inPts = polydata->GetPoints();
vtkPoints * points = vtkPoints::New();
typedef DTIPointType::PointType PointType;
PointType fiberpoint;
double fiberpointtemp[3];
for(int i=0;i<numPoints;i++)
{
inPts->GetPoint( i, fiberpointtemp );
//convert RAS to LPS (vtk)
fiberpoint[0] = - fiberpointtemp[0];
fiberpoint[1] = - fiberpointtemp[1];
fiberpoint[2] = + fiberpointtemp[2];
deformationfield->TransformPhysicalPointToContinuousIndex(fiberpoint,ci);
if( !deformationfield->GetLargestPossibleRegion().IsInside( ci ) )
{
std::cerr << "Fiber is outside deformation field image. Deformation field has to be in the fiber space. Warning: Original position will be used" << std::endl ;
}
DeformationPixelType warp(definterp->EvaluateAtContinuousIndex(ci).GetDataPointer());
for(unsigned int j =0; j < 3; j++)
fiberpoint[j] +=warp[j];
//convert LPS to RAS (vtk)
fiberpoint[0] = - fiberpoint[0];
fiberpoint[1] = - fiberpoint[1];
fiberpoint[2] = + fiberpoint[2];
points->InsertPoint(i,fiberpoint[0],fiberpoint[1],fiberpoint[2]);
}
polydata->SetPoints(points);
if(fiberOutput != "")
{
std::cout<<std::endl;
std::cout<<"Saving fibers...."<<std::endl;
std::cout<<fiberOutput<<std::endl;
vtkPolyDataWriter * fiberwriter = vtkPolyDataWriter::New();
fiberwriter->SetFileName(fiberOutput.c_str());
fiberwriter->SetInput(polydata);
fiberwriter->Update();
try
{
fiberwriter->Write();
std::cout<<"Done!"<<std::endl;
std::cout<<"Number of fibers saved: "<<polydata->GetNumberOfLines()<<std::endl;
}
catch(...)
{
std::cout << "Error while saving fiber file." << std::endl;
throw;
}
}
return EXIT_SUCCESS;
}
int averageDeformationField(parameters list )
{
//read the reference volume
typedef itk::Image< unsigned char , 3 > ImageType ;
typedef itk::ImageFileReader< ImageType > ReaderType ;
typedef typename ReaderType::Pointer ReaderTypePointer ;
ReaderTypePointer readerReference ;
readerReference = ReaderType::New() ;
readerReference->SetFileName( list.referenceVolume.c_str() ) ;
readerReference->UpdateOutputInformation() ;
//set the size, origin, spacing,direction of the reference volume
itk::Point< double , 3 > m_Origin ;
itk::Vector< double , 3 > m_Spacing ;
itk::Size< 3 > m_Size ;
itk::Matrix< double , 3 , 3 > m_Direction;
m_Spacing = readerReference->GetOutput()->GetSpacing() ;
m_Size= readerReference->GetOutput()->GetLargestPossibleRegion().GetSize() ;
m_Origin = readerReference->GetOutput()->GetOrigin() ;
m_Direction = readerReference->GetOutput()->GetDirection() ;
int n=list.deffieldtoaverage.size();
typename DeformationImageType::Pointer fieldPointer1 ;
DeformationFieldType dftype1 = HField ;
if( !list.typeOfField[0].compare( "displacement" ) )
{
dftype1 = Displacement ;
}
//reads deformation field and if it is a h-field, it transforms it to a displacement field
fieldPointer1 = readDeformationField( list.deffieldtoaverage[0] , dftype1 ) ;
//Resample the deformation field so that it has the same properties as the reference image
ResampleDeformationField( fieldPointer1 ,m_Origin , m_Spacing ,m_Size ,m_Direction) ;
typedef itk::ImageRegionIterator< DeformationImageType > DeformationConstIteratorType;
DeformationConstIteratorType it1 (fieldPointer1,fieldPointer1->GetLargestPossibleRegion());
//walk through all other deformation field volumes
for(int i=1;i<n;i++)
{
typename DeformationImageType::Pointer fieldPointer2 ;
//set if the field is a displacement or a H- field
DeformationFieldType dftype2 = HField ;
if( !list.typeOfField[i].compare( "displacement" ) )
{
dftype2 = Displacement ;
}
//reads deformation field and if it is a h-field, it transforms it to a displacement field
fieldPointer2 = readDeformationField( list.deffieldtoaverage[i] , dftype2 ) ;
//Resample the deformation field so that it has the same properties as the reference image
ResampleDeformationField( fieldPointer2 ,m_Origin ,m_Spacing , m_Size ,m_Direction) ;
it1.GoToBegin();
DeformationConstIteratorType it2 (fieldPointer2,fieldPointer2->GetLargestPossibleRegion());
it2.GoToBegin();
itk::Vector<double,3> sum;sum[0]=0;sum[1]=0;sum[2]=0;
while(!it1.IsAtEnd() && !it2.IsAtEnd())
{
sum+=(it1.Get())+(it2.Get());//sum displacements together
it1.Set(sum);
sum[0]=0;sum[1]=0;sum[2]=0;
++it1;++it2;
}
}
it1.GoToBegin();
itk::Vector<double,3> temp;
while(!it1.IsAtEnd())
{
temp=(it1.Get())/n;//compute the average of displacements
it1.Set(temp);
++it1;
}
//Save HField
typedef itk::ImageFileWriter< DeformationImageType > HFieldWriterType ;
typedef typename HFieldWriterType::Pointer HFieldWriterTypePointer ;
HFieldWriterTypePointer hfwriterAvg = HFieldWriterType::New() ;
hfwriterAvg->SetInput( fieldPointer1 ) ;
hfwriterAvg->SetFileName( list.outputAvg ) ;
hfwriterAvg->UseCompressionOn();
try
{
hfwriterAvg->Update() ;
}
catch( itk::ExceptionObject & Except )
{
std::cerr << "Writing output HField: Exception caught!"
<< std::endl ;
std::cerr << Except << std::endl ;
return EXIT_FAILURE ;
}
return EXIT_SUCCESS ;
}