void QmitkDeformableRegistrationView::ApplyDeformationField()
{
ImageReaderType::Pointer reader = ImageReaderType::New();
reader->SetFileName( m_Controls.m_QmitkBSplineRegistrationViewControls->m_Controls.m_DeformationField->text().toStdString() );
reader->Update();
DeformationFieldType::Pointer deformationField = reader->GetOutput();
mitk::Image * mimage = dynamic_cast<mitk::Image*> (m_MovingNode->GetData());
mitk::Image * fimage = dynamic_cast<mitk::Image*> (m_FixedNode->GetData());
typedef itk::Image<float, 3> FloatImageType;
FloatImageType::Pointer itkMovingImage = FloatImageType::New();
FloatImageType::Pointer itkFixedImage = FloatImageType::New();
mitk::CastToItkImage(mimage, itkMovingImage);
mitk::CastToItkImage(fimage, itkFixedImage);
typedef itk::WarpImageFilter<
FloatImageType,
FloatImageType,
DeformationFieldType > WarperType;
typedef itk::LinearInterpolateImageFunction<
FloatImageType,
double > InterpolatorType;
WarperType::Pointer warper = WarperType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
warper->SetInput( itkMovingImage );
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( itkFixedImage->GetSpacing() );
warper->SetOutputOrigin( itkFixedImage->GetOrigin() );
warper->SetOutputDirection (itkFixedImage->GetDirection() );
warper->SetDisplacementField( deformationField );
warper->Update();
FloatImageType::Pointer outputImage = warper->GetOutput();
mitk::Image::Pointer result = mitk::Image::New();
mitk::CastToMitkImage(outputImage, result);
// Create new DataNode
mitk::DataNode::Pointer newNode = mitk::DataNode::New();
newNode->SetData( result );
newNode->SetProperty( "name", mitk::StringProperty::New("warped image") );
// add the new datatree node to the datatree
this->GetDefaultDataStorage()->Add(newNode);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
//Image::Pointer outputImage = this->GetOutput();
//mitk::CastToMitkImage( warper->GetOutput(), outputImage );
}
void TractAnalyzer::MakeRoi()
{
m_CostSum = 0.0;
int n = 0;
if(m_PointSetNode.IsNotNull())
{
n = m_PointSetNode->GetSize();
if(n==0)
{
QMessageBox msgBox;
msgBox.setText("No points have been set yet.");
msgBox.exec();
}
}
else{
QMessageBox msgBox;
msgBox.setText("No points have been set yet.");
msgBox.exec();
}
std::string pathDescription = "";
std::vector< itk::Index<3> > totalPath;
if(n>0)
{
for(int i=0; i<n-1; ++i)
{
mitk::ProgressBar::GetInstance()->Progress();
mitk::Point3D p = m_PointSetNode->GetPoint(i);
mitk::Point3D p2 = m_PointSetNode->GetPoint(i+1);
itk::Index<3> startPoint;
itk::Index<3> endPoint;
m_InputImage->GetGeometry()->WorldToIndex(p,startPoint);
m_InputImage->GetGeometry()->WorldToIndex(p2,endPoint);
MITK_INFO << "create roi";
std::vector< itk::Index<3> > path = CreateSegment(startPoint, endPoint);
for(std::vector< itk::Index<3> >::iterator it = path.begin();
it != path.end(); it++)
{
itk::Index<3> ix = *it;
if (!(ix==endPoint))
{
mitk::ProgressBar::GetInstance()->Progress();
totalPath.push_back(ix);
std::stringstream ss;
ss << ix[0] << " " << ix[1] << " " << ix[2] << "\n";
pathDescription += ss.str();
}
else
{
// Only when dealing with the last segment the last point should be added. This one will not occur
// as the first point of the next roi segment.
if(i == (n-2))
{
totalPath.push_back(endPoint);
std::stringstream ss;
ss << endPoint[0] << " " << endPoint[1] << " " << endPoint[2] << "\n";
pathDescription += ss.str();
}
}
}
}
// save pathDescription to m_PathDescription
m_PathDescription = pathDescription;
FloatImageType::Pointer itkImg = FloatImageType::New();
mitk::CastToItkImage(m_InputImage, itkImg);
CharImageType::Pointer roiImg = CharImageType::New();
roiImg->SetRegions(itkImg->GetLargestPossibleRegion().GetSize());
roiImg->SetOrigin(itkImg->GetOrigin());
roiImg->SetSpacing(itkImg->GetSpacing());
roiImg->SetDirection(itkImg->GetDirection());
roiImg->Allocate();
roiImg->FillBuffer(0);
std::vector< itk::Index<3> > roi;
std::vector< itk::Index<3> >::iterator it;
for(it = totalPath.begin();
it != totalPath.end();
it++)
{
itk::Index<3> ix = *it;
roiImg->SetPixel(ix, 1);
roi.push_back(ix);
}
m_TbssRoi = mitk::TbssRoiImage::New();
m_TbssRoi->SetRoi(roi);
m_TbssRoi->SetImage(roiImg);
m_TbssRoi->InitializeFromImage();
}
}