void mitk::SliceBasedInterpolationController::SetWorkingImage(LabelSetImage *newImage)
{
if (m_WorkingImage != newImage)
{
// delete the current working image from the list of interpolators
InterpolatorMapType::iterator iter = s_InterpolatorForImage.find(m_WorkingImage);
if (iter != s_InterpolatorForImage.end())
{
s_InterpolatorForImage.erase(iter);
}
m_WorkingImage = newImage;
s_InterpolatorForImage.insert(std::make_pair(m_WorkingImage, this));
}
this->ResetLabelCount();
AccessFixedDimensionByItk_1(m_WorkingImage, ScanImageITKProcessing, 3, 0);
// for all timesteps, scan whole image: TODO: enable this again for 3D+time
/*
for (unsigned int timeStep = 0; timeStep < m_WorkingImage->GetTimeSteps(); ++timeStep)
{
ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
timeSelector->SetInput( m_WorkingImage );
timeSelector->SetTimeNr( timeStep );
timeSelector->UpdateLargestPossibleRegion();
Image::Pointer segmentation3D = timeSelector->GetOutput();
this->SetChangedVolume( segmentation3D.GetPointer(), timeStep );
}
*/
// this->Modified();
}
void mitk::SegmentationInterpolationController::SetChangedSlice( const Image* sliceDiff, unsigned int sliceDimension, unsigned int sliceIndex, unsigned int timeStep )
{
if ( !sliceDiff ) return;
if ( sliceDimension > 2 ) return;
if ( timeStep >= m_SegmentationCountInSlice.size() ) return;
if ( sliceIndex >= m_SegmentationCountInSlice[timeStep][sliceDimension].size() ) return;
unsigned int dim0(0);
unsigned int dim1(1);
// determine the other two dimensions
switch (sliceDimension)
{
default:
case 2:
dim0 = 0; dim1 = 1; break;
case 1:
dim0 = 0; dim1 = 2; break;
case 0:
dim0 = 1; dim1 = 2; break;
}
//mitkIpPicDescriptor* rawSlice = const_cast<Image*>(sliceDiff)->GetSliceData()->GetPicDescriptor(); // we promise not to change anything!
unsigned char* rawSlice = (unsigned char*) const_cast<Image*>(sliceDiff)->GetData();
if (!rawSlice) return;
AccessFixedDimensionByItk_1( sliceDiff, ScanChangedSlice, 2, SetChangedSliceOptions(sliceDimension, sliceIndex, dim0, dim1, timeStep, rawSlice) );
//PrintStatus();
Modified();
}
void mitk::SegmentationInterpolationController::SetChangedVolume( const Image* sliceDiff, unsigned int timeStep )
{
if ( !sliceDiff ) return;
if ( sliceDiff->GetDimension() != 3 ) return;
AccessFixedDimensionByItk_1( sliceDiff, ScanChangedVolume, 3, timeStep );
//PrintStatus();
Modified();
}
void mitk::CorrectorAlgorithm::CalculateDifferenceImage( Image* modifiedImage, Image* originalImage )
{
/*
* modifiedImage has ipMITKSegmentationTYPE
* originalImage may be any type
*
* --> we calculate a diff image using ITK, switching for the correct type of originalImage
*/
m_DifferenceImage = NULL;
Image::Pointer tmpPtr = originalImage;
AccessFixedDimensionByItk_1( tmpPtr, ItkCalculateDifferenceImage, 2, modifiedImage );
}
void mitk::SurfaceInterpolationController::SetCurrentInterpolationSession(mitk::Image::Pointer currentSegmentationImage)
{
if (currentSegmentationImage.GetPointer() == m_SelectedSegmentation)
return;
m_ReduceFilter->Reset();
m_NormalsFilter->Reset();
m_InterpolateSurfaceFilter->Reset();
if (currentSegmentationImage.IsNull())
{
m_SelectedSegmentation = 0;
return;
}
ContourListMap::iterator it = m_ListOfInterpolationSessions.find(currentSegmentationImage.GetPointer());
m_SelectedSegmentation = currentSegmentationImage.GetPointer();
itk::ImageBase<3>::Pointer itkImage = itk::ImageBase<3>::New();
AccessFixedDimensionByItk_1( m_SelectedSegmentation, GetImageBase, 3, itkImage );
m_InterpolateSurfaceFilter->SetReferenceImage( itkImage.GetPointer() );
if (it == m_ListOfInterpolationSessions.end())
{
ContourPositionPairList newList;
m_ListOfInterpolationSessions.insert(std::pair<mitk::Image*, ContourPositionPairList>(m_SelectedSegmentation, newList));
m_InterpolationResult = 0;
m_CurrentNumberOfReducedContours = 0;
itk::MemberCommand<SurfaceInterpolationController>::Pointer command = itk::MemberCommand<SurfaceInterpolationController>::New();
command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted);
m_SegmentationObserverTags.insert( std::pair<mitk::Image*, unsigned long>( m_SelectedSegmentation, m_SelectedSegmentation->AddObserver( itk::DeleteEvent(), command ) ) );
}
else
{
for (unsigned int i = 0; i < m_ListOfInterpolationSessions[m_SelectedSegmentation].size(); i++)
{
m_ReduceFilter->SetInput(i, m_ListOfInterpolationSessions[m_SelectedSegmentation].at(i).contour);
}
m_ReduceFilter->Update();
m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs();
for (unsigned int i = 0; i < m_CurrentNumberOfReducedContours; i++)
{
m_NormalsFilter->SetInput(i, m_ReduceFilter->GetOutput(i));
m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i));
}
}
Modified();
}
mitk::Image::Pointer
mitk::ShapeBasedInterpolationAlgorithm::Interpolate(
Image::ConstPointer lowerSlice, unsigned int lowerSliceIndex,
Image::ConstPointer upperSlice, unsigned int upperSliceIndex,
unsigned int requestedIndex,
unsigned int /*sliceDimension*/, // commented variables are not used
Image::Pointer resultImage,
unsigned int /*timeStep*/,
Image::ConstPointer /*referenceImage*/)
{
mitk::Image::Pointer lowerDistanceImage = mitk::Image::New();
AccessFixedDimensionByItk_1(lowerSlice, ComputeDistanceMap, 2, lowerDistanceImage);
mitk::Image::Pointer upperDistanceImage = mitk::Image::New();
AccessFixedDimensionByItk_1(upperSlice, ComputeDistanceMap, 2, upperDistanceImage);
// calculate where the current slice is in comparison to the lower and upper neighboring slices
float ratio = (float)(requestedIndex - lowerSliceIndex) / (float)(upperSliceIndex - lowerSliceIndex);
AccessFixedDimensionByItk_3(resultImage, InterpolateIntermediateSlice, 2, upperDistanceImage, lowerDistanceImage, ratio);
return resultImage;
}
void mitk::SurfaceInterpolationController::ReinitializeInterpolation()
{
// If session has changed reset the pipeline
m_ReduceFilter->Reset();
m_NormalsFilter->Reset();
m_InterpolateSurfaceFilter->Reset();
itk::ImageBase<3>::Pointer itkImage = itk::ImageBase<3>::New();
if ( m_SelectedSegmentation )
{
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput( m_SelectedSegmentation );
timeSelector->SetTimeNr( m_CurrentTimeStep );
timeSelector->SetChannelNr( 0 );
timeSelector->Update();
mitk::Image::Pointer refSegImage = timeSelector->GetOutput();
AccessFixedDimensionByItk_1( refSegImage, GetImageBase, 3, itkImage );
m_InterpolateSurfaceFilter->SetReferenceImage(itkImage.GetPointer());
unsigned int numTimeSteps = m_SelectedSegmentation->GetTimeSteps();
unsigned int size = m_ListOfInterpolationSessions[m_SelectedSegmentation].size();
if ( size != numTimeSteps )
{
m_ListOfInterpolationSessions[m_SelectedSegmentation].resize( numTimeSteps );
}
if ( m_CurrentTimeStep < numTimeSteps )
{
unsigned int numContours = m_ListOfInterpolationSessions[m_SelectedSegmentation][m_CurrentTimeStep].size();
for ( unsigned int c = 0; c < numContours; ++c )
{
m_ReduceFilter->SetInput(c, m_ListOfInterpolationSessions[m_SelectedSegmentation][m_CurrentTimeStep][c].contour);
}
m_ReduceFilter->Update();
m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs();
for (unsigned int i = 0; i < m_CurrentNumberOfReducedContours; i++)
{
m_NormalsFilter->SetInput(i, m_ReduceFilter->GetOutput(i));
m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i));
}
}
Modified();
}
}
bool mitk::ImageLiveWireContourModelFilter::CreateDynamicCostMap(mitk::ContourModel* path)
{
mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image*>(this->GetInput());
if(!input) return false;
try
{
AccessFixedDimensionByItk_1(input,CreateDynamicCostMapByITK, 2, path);
}
catch( itk::ExceptionObject & e )
{
MITK_INFO << "Exception caught during dynamic cost map alculation: " << e;
return false;
}
return true;
}
void mitk::SliceBasedInterpolationController::SetChangedSlice(const Image *slice,
unsigned int sliceDimension,
unsigned int sliceIndex,
unsigned int timeStep)
{
if (!slice)
return;
if (slice->GetDimension() != 2)
return;
if (sliceDimension > 2)
return;
if (m_WorkingImage.IsNull())
return;
// check if the number of labels has changed
int numberOfLabels = m_WorkingImage->GetNumberOfLabels();
if (m_LabelCountInSlice[0][0][0].size() != numberOfLabels)
return;
unsigned int dim0(0);
unsigned int dim1(1);
// determine the other two dimensions
switch (sliceDimension)
{
default:
case 2:
dim0 = 0;
dim1 = 1;
break;
case 1:
dim0 = 0;
dim1 = 2;
break;
case 0:
dim0 = 1;
dim1 = 2;
break;
}
AccessFixedDimensionByItk_1(
slice, ScanSliceITKProcessing, 2, SetChangedSliceOptions(sliceDimension, sliceIndex, dim0, dim1, timeStep));
// this->Modified();
}
void mitk::AutoCropImageFilter::GenerateData()
{
mitk::Image::ConstPointer input = this->GetInput();
mitk::Image::Pointer output = this->GetOutput();
if(input.IsNull())
return;
if(input->GetDimension() <= 2)
{
MITK_ERROR << "Only 3D and 4D images supported";
return;
}
if((output->IsInitialized()==false) )
return;
if( m_TimeSelector.IsNull() ) m_TimeSelector = mitk::ImageTimeSelector::New();
m_TimeSelector->SetInput(input);
mitk::SlicedData::RegionType outputRegion = input->GetRequestedRegion();
int tstart = outputRegion.GetIndex(3);
int tmax = tstart + outputRegion.GetSize(3);
for( int timestep=tstart;timestep<tmax;++timestep )
{
m_TimeSelector->SetTimeNr(timestep);
m_TimeSelector->UpdateLargestPossibleRegion();
AccessFixedDimensionByItk_1( m_TimeSelector->GetOutput(), ITKCrop3DImage, 3, timestep );
}
// this->GetOutput()->Update(); // Not sure if this is necessary...
m_TimeOfHeaderInitialization.Modified();
}
void mitk::DWIHeadMotionCorrectionFilter<DiffusionPixelType>
::GenerateData()
{
typedef itk::SplitDWImageFilter< DiffusionPixelType, DiffusionPixelType> SplitFilterType;
DiffusionImageType* input = const_cast<DiffusionImageType*>(this->GetInput(0));
unsigned int numberOfSteps = input->GetVectorImage()->GetNumberOfComponentsPerPixel () ;
m_Steps = numberOfSteps;
//
// (1) Extract the b-zero images to a 3d+t image, register them by NCorr metric and
// rigid registration : they will then be used are reference image for registering
// the gradient images
//
typedef itk::B0ImageExtractionToSeparateImageFilter< DiffusionPixelType, DiffusionPixelType> B0ExtractorType;
typename B0ExtractorType::Pointer b0_extractor = B0ExtractorType::New();
b0_extractor->SetInput( input->GetVectorImage() );
b0_extractor->SetDirections( input->GetDirections() );
b0_extractor->Update();
mitk::Image::Pointer b0Image = mitk::Image::New();
b0Image->InitializeByItk( b0_extractor->GetOutput() );
b0Image->SetImportChannel( b0_extractor->GetOutput()->GetBufferPointer(),
mitk::Image::CopyMemory );
// (2.1) Use the extractor to access the extracted b0 volumes
mitk::ImageTimeSelector::Pointer t_selector =
mitk::ImageTimeSelector::New();
t_selector->SetInput( b0Image );
t_selector->SetTimeNr(0);
t_selector->Update();
// first unweighted image as reference space for the registration
mitk::Image::Pointer b0referenceImage = t_selector->GetOutput();
mitk::PyramidImageRegistrationMethod::Pointer registrationMethod = mitk::PyramidImageRegistrationMethod::New();
registrationMethod->SetFixedImage( b0referenceImage );
registrationMethod->SetTransformToRigid();
// the unweighted images are of same modality
registrationMethod->SetCrossModalityOff();
// use the advanced (windowed sinc) interpolation
registrationMethod->SetUseAdvancedInterpolation(true);
// Initialize the temporary output image
mitk::Image::Pointer registeredB0Image = b0Image->Clone();
const unsigned int numberOfb0Images = b0Image->GetTimeSteps();
if( numberOfb0Images > 1)
{
mitk::ImageTimeSelector::Pointer t_selector2 =
mitk::ImageTimeSelector::New();
t_selector2->SetInput( b0Image );
for( unsigned int i=1; i<numberOfb0Images; i++)
{
m_CurrentStep = i + 1;
if( m_AbortRegistration == true) {
m_IsInValidState = false;
mitkThrow() << "Stopped by user.";
};
t_selector2->SetTimeNr(i);
t_selector2->Update();
registrationMethod->SetMovingImage( t_selector2->GetOutput() );
try
{
MITK_INFO << " === (" << i <<"/"<< numberOfb0Images-1 << ") :: Starting registration";
registrationMethod->Update();
}
catch( const itk::ExceptionObject& e)
{
m_IsInValidState = false;
mitkThrow() << "Failed to register the b0 images, the PyramidRegistration threw an exception: \n" << e.what();
}
// import volume to the inter-results
mitk::ImageWriteAccessor imac(registrationMethod->GetResampledMovingImage());
registeredB0Image->SetImportVolume( imac.GetData(),
i, 0, mitk::Image::ReferenceMemory );
}
// use the accumulateImageFilter as provided by the ItkAccumulateFilter method in the header file
AccessFixedDimensionByItk_1(registeredB0Image, ItkAccumulateFilter, (4), b0referenceImage );
}
//
// (2) Split the diffusion image into a 3d+t regular image, extract only the weighted images
//
typename SplitFilterType::Pointer split_filter = SplitFilterType::New();
split_filter->SetInput (input->GetVectorImage() );
split_filter->SetExtractAllAboveThreshold(20, input->GetB_ValueMap() );
try
{
split_filter->Update();
}
catch( const itk::ExceptionObject &e)
{
m_IsInValidState = false;
mitkThrow() << " Caught exception from SplitImageFilter : " << e.what();
}
mitk::Image::Pointer splittedImage = mitk::Image::New();
splittedImage->InitializeByItk( split_filter->GetOutput() );
splittedImage->SetImportChannel( split_filter->GetOutput()->GetBufferPointer(),
mitk::Image::CopyMemory );
//
// (3) Use again the time-selector to access the components separately in order
// to perform the registration of Image -> unweighted reference
//
mitk::PyramidImageRegistrationMethod::Pointer weightedRegistrationMethod
= mitk::PyramidImageRegistrationMethod::New();
weightedRegistrationMethod->SetTransformToAffine();
weightedRegistrationMethod->SetCrossModalityOn();
//
// - (3.1) Set the reference image
// - a single b0 image
// - average over the registered b0 images if multiple present
//
weightedRegistrationMethod->SetFixedImage( b0referenceImage );
// use the advanced (windowed sinc) interpolation
weightedRegistrationMethod->SetUseAdvancedInterpolation(true);
//
// - (3.2) Register all timesteps in the splitted image onto the first reference
//
unsigned int maxImageIdx = splittedImage->GetTimeSteps();
mitk::TimeGeometry* tsg = splittedImage->GetTimeGeometry();
mitk::ProportionalTimeGeometry* ptg = dynamic_cast<ProportionalTimeGeometry*>(tsg);
ptg->Expand(maxImageIdx+1);
ptg->SetTimeStepGeometry( ptg->GetGeometryForTimeStep(0), maxImageIdx );
mitk::Image::Pointer registeredWeighted = mitk::Image::New();
registeredWeighted->Initialize( splittedImage->GetPixelType(0), *tsg );
// insert the first unweighted reference as the first volume
mitk::ImageWriteAccessor imac(b0referenceImage);
registeredWeighted->SetImportVolume( imac.GetData(),
0,0, mitk::Image::CopyMemory );
// mitk::Image::Pointer registeredWeighted = splittedImage->Clone();
// this time start at 0, we have only gradient images in the 3d+t file
// the reference image comes form an other image
mitk::ImageTimeSelector::Pointer t_selector_w =
mitk::ImageTimeSelector::New();
t_selector_w->SetInput( splittedImage );
// store the rotation parts of the transformations in a vector
typedef mitk::PyramidImageRegistrationMethod::TransformMatrixType MatrixType;
std::vector< MatrixType > estimated_transforms;
for( unsigned int i=0; i<maxImageIdx; i++)
{
m_CurrentStep = numberOfb0Images + i + 1;
if( m_AbortRegistration == true) {
m_IsInValidState = false;
mitkThrow() << "Stopped by user.";
};
t_selector_w->SetTimeNr(i);
t_selector_w->Update();
weightedRegistrationMethod->SetMovingImage( t_selector_w->GetOutput() );
try
{
MITK_INFO << " === (" << i+1 <<"/"<< maxImageIdx << ") :: Starting registration";
weightedRegistrationMethod->Update();
}
catch( const itk::ExceptionObject& e)
{
m_IsInValidState = false;
mitkThrow() << "Failed to register the b0 images, the PyramidRegistration threw an exception: \n" << e.what();
}
// allow expansion
mitk::ImageWriteAccessor imac(weightedRegistrationMethod->GetResampledMovingImage());
registeredWeighted->SetImportVolume( imac.GetData(),
i+1, 0, mitk::Image::CopyMemory);
estimated_transforms.push_back( weightedRegistrationMethod->GetLastRotationMatrix() );
}
//
// (4) Cast the resulting image back to an diffusion weighted image
//
typename DiffusionImageType::GradientDirectionContainerType *gradients = input->GetDirections();
typename DiffusionImageType::GradientDirectionContainerType::Pointer gradients_new =
DiffusionImageType::GradientDirectionContainerType::New();
typename DiffusionImageType::GradientDirectionType bzero_vector;
bzero_vector.fill(0);
// compose the direction vector
// - no direction for the first image
// - correct ordering of the directions based on the index list
gradients_new->push_back( bzero_vector );
typename SplitFilterType::IndexListType index_list = split_filter->GetIndexList();
typename SplitFilterType::IndexListType::const_iterator lIter = index_list.begin();
while( lIter != index_list.end() )
{
gradients_new->push_back( gradients->at( *lIter ) );
++lIter;
}
typename mitk::ImageToDiffusionImageSource< DiffusionPixelType >::Pointer caster =
mitk::ImageToDiffusionImageSource< DiffusionPixelType >::New();
caster->SetImage( registeredWeighted );
caster->SetBValue( input->GetB_Value() );
caster->SetGradientDirections( gradients_new.GetPointer() );
try
{
caster->Update();
}
catch( const itk::ExceptionObject& e)
{
m_IsInValidState = false;
MITK_ERROR << "Casting back to diffusion image failed: ";
mitkThrow() << "Subprocess failed with exception: " << e.what();
}
//
// (5) Adapt the gradient directions according to the estimated transforms
//
typedef mitk::DiffusionImageCorrectionFilter< DiffusionPixelType > CorrectionFilterType;
typename CorrectionFilterType::Pointer corrector = CorrectionFilterType::New();
OutputImagePointerType output = caster->GetOutput();
corrector->SetImage( output );
corrector->CorrectDirections( estimated_transforms );
//
// (6) Pass the corrected image to the filters output port
//
m_CurrentStep += 1;
this->GetOutput()->SetVectorImage(output->GetVectorImage());
this->GetOutput()->SetB_Value(output->GetB_Value());
this->GetOutput()->SetDirections(output->GetDirections());
this->GetOutput()->SetMeasurementFrame(output->GetMeasurementFrame());
this->GetOutput()->InitializeFromVectorImage();
this->GetOutput()->Modified();
}
void mitk::CLUtil::CreateCheckerboardMask(mitk::Image::Pointer image, mitk::Image::Pointer & outimage)
{
AccessFixedDimensionByItk_1(image, mitk::CLUtil::itkCreateCheckerboardMask,3, outimage);
}
void mitk::CLUtil::FillHoleGrayscale(mitk::Image::Pointer & image, mitk::Image::Pointer & outimage)
{
AccessFixedDimensionByItk_1(image, mitk::CLUtil::itkFillHoleGrayscale, 3, outimage);
}
mitk::Image::Pointer mitk::PlanarFigureSegmentationController::GetInterpolationResult()
{
m_SegmentationAsImage = NULL;
if ( m_PlanarFigureList.size() == 0 )
{
m_SegmentationAsImage = mitk::Image::New();
m_SegmentationAsImage->Initialize(mitk::MakeScalarPixelType<unsigned char>() , *m_ReferenceImage->GetTimeGeometry());
return m_SegmentationAsImage;
}
itk::ImageBase<3>::Pointer itkImage;
AccessFixedDimensionByItk_1( m_ReferenceImage.GetPointer(), GetImageBase, 3, itkImage );
m_DistanceImageCreator->SetReferenceImage( itkImage.GetPointer() );
m_ReduceFilter->Update();
m_NormalsFilter->Update();
m_DistanceImageCreator->Update();
mitk::Image::Pointer distanceImage = m_DistanceImageCreator->GetOutput();
// Cleanup the pipeline
distanceImage->DisconnectPipeline();
m_DistanceImageCreator = NULL;
m_NormalsFilter = NULL;
m_ReduceFilter = NULL;
itkImage = NULL;
// If this bool flag is true, the distanceImage will be written to the
// filesystem as nrrd-image and as surface-representation.
bool debugOutput(false);
if ( debugOutput )
{
mitk::ImageWriter::Pointer imageWriter = mitk::ImageWriter::New();
imageWriter->SetInput( distanceImage );
imageWriter->SetExtension( ".nrrd" );
imageWriter->SetFileName( "v:/DistanceImage" );
imageWriter->Update();
}
mitk::ImageToSurfaceFilter::Pointer imageToSurfaceFilter = mitk::ImageToSurfaceFilter::New();
imageToSurfaceFilter->SetInput( distanceImage );
imageToSurfaceFilter->SetThreshold( 0 );
imageToSurfaceFilter->Update();
mitk::Surface::Pointer segmentationAsSurface = imageToSurfaceFilter->GetOutput();
// Cleanup the pipeline
segmentationAsSurface->DisconnectPipeline();
imageToSurfaceFilter = NULL;
if ( debugOutput )
{
mitk::SurfaceVtkWriter<vtkPolyDataWriter>::Pointer surfaceWriter = mitk::SurfaceVtkWriter<vtkPolyDataWriter>::New();
surfaceWriter->SetInput( segmentationAsSurface );
surfaceWriter->SetExtension( ".vtk" );
surfaceWriter->SetFileName( "v:/DistanceImageAsSurface.vtk" );
surfaceWriter->Update();
}
mitk::SurfaceToImageFilter::Pointer surfaceToImageFilter = mitk::SurfaceToImageFilter::New();
surfaceToImageFilter->SetInput( segmentationAsSurface );
surfaceToImageFilter->SetImage( m_ReferenceImage );
surfaceToImageFilter->SetMakeOutputBinary(true);
surfaceToImageFilter->Update();
m_SegmentationAsImage = surfaceToImageFilter->GetOutput();
// Cleanup the pipeline
m_SegmentationAsImage->DisconnectPipeline();
return m_SegmentationAsImage;
}
template <typename ItkOutputImageType> void CastToItkImage(const mitk::Image * mitkImage, itk::SmartPointer<ItkOutputImageType>& itkOutputImage)
{
AccessFixedDimensionByItk_1(mitkImage, _CastToItkImage2Access, ::itk::GetImageDimension<ItkOutputImageType>::ImageDimension, itkOutputImage);
}
void mitk::SurfaceStampImageFilter::SurfaceStamp(int time)
{
mitk::Image::Pointer inputImage = this->GetInput();
const mitk::TimeGeometry *surfaceTimeGeometry = GetInput()->GetTimeGeometry();
const mitk::TimeGeometry *imageTimeGeometry = inputImage->GetTimeGeometry();
// Convert time step from image time-frame to surface time-frame
mitk::TimePointType matchingTimePoint = imageTimeGeometry->TimeStepToTimePoint(time);
mitk::TimeStepType surfaceTimeStep = surfaceTimeGeometry->TimePointToTimeStep(matchingTimePoint);
vtkPolyData *polydata = m_Surface->GetVtkPolyData(surfaceTimeStep);
if (!polydata)
mitkThrow() << "Polydata is null.";
vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
transformFilter->SetInputData(polydata);
// transformFilter->ReleaseDataFlagOn();
vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New();
BaseGeometry::Pointer geometry = surfaceTimeGeometry->GetGeometryForTimeStep(surfaceTimeStep);
transform->PostMultiply();
transform->Concatenate(geometry->GetVtkTransform()->GetMatrix());
// take image geometry into account. vtk-Image information will be changed to unit spacing and zero origin below.
BaseGeometry::Pointer imageGeometry = imageTimeGeometry->GetGeometryForTimeStep(time);
transform->Concatenate(imageGeometry->GetVtkTransform()->GetLinearInverse());
transformFilter->SetTransform(transform);
transformFilter->Update();
polydata = transformFilter->GetOutput();
if (!polydata || !polydata->GetNumberOfPoints())
mitkThrow() << "Polydata retrieved from transformation is null or has no points.";
MeshType::Pointer mesh = MeshType::New();
mesh->SetCellsAllocationMethod(MeshType::CellsAllocatedDynamicallyCellByCell);
unsigned int numberOfPoints = polydata->GetNumberOfPoints();
mesh->GetPoints()->Reserve(numberOfPoints);
vtkPoints *points = polydata->GetPoints();
MeshType::PointType point;
for (unsigned int i = 0; i < numberOfPoints; i++)
{
double *aux = points->GetPoint(i);
point[0] = aux[0];
point[1] = aux[1];
point[2] = aux[2];
mesh->SetPoint(i, point);
}
// Load the polygons into the itk::Mesh
typedef MeshType::CellAutoPointer CellAutoPointerType;
typedef MeshType::CellType CellType;
typedef itk::TriangleCell<CellType> TriangleCellType;
typedef MeshType::PointIdentifier PointIdentifierType;
typedef MeshType::CellIdentifier CellIdentifierType;
// Read the number of polygons
CellIdentifierType numberOfPolygons = 0;
numberOfPolygons = polydata->GetNumberOfPolys();
PointIdentifierType numberOfCellPoints = 3;
CellIdentifierType i = 0;
for (i = 0; i < numberOfPolygons; i++)
{
vtkIdList *cellIds;
vtkCell *vcell = polydata->GetCell(i);
cellIds = vcell->GetPointIds();
CellAutoPointerType cell;
auto *triangleCell = new TriangleCellType;
PointIdentifierType k;
for (k = 0; k < numberOfCellPoints; k++)
{
triangleCell->SetPointId(k, cellIds->GetId(k));
}
cell.TakeOwnership(triangleCell);
mesh->SetCell(i, cell);
}
if (!mesh->GetNumberOfPoints())
mitkThrow() << "Generated itk mesh is empty.";
if (m_MakeOutputBinary)
{
this->SurfaceStampBinaryOutputProcessing(mesh);
}
else
{
AccessFixedDimensionByItk_1(inputImage, SurfaceStampProcessing, 3, mesh);
}
}