ExtractSliceFilter extracts a 2D abitrary oriented slice from a 3D volume. More...

#include <mitkExtractSliceFilter.h>

Inheritance diagram for mitk::ExtractSliceFilter:

Collaboration diagram for mitk::ExtractSliceFilter:

Public Types
enum	ResliceInterpolation { RESLICE_NEAREST, RESLICE_LINEAR, RESLICE_CUBIC }

typedef ExtractSliceFilter	Self

typedef ImageToImageFilter	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

Public Types inherited from mitk::ImageToImageFilter
typedef ImageToImageFilter	Self

typedef ImageSource	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef mitk::Image	InputImageType

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef SlicedData::RegionType	InputImageRegionType

Public Types inherited from mitk::ImageSource
typedef ImageSource	Self

typedef BaseDataSource	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef mitk::Image	OutputImageType
	Some convenient typedefs. More...

typedef OutputImageType	OutputType

typedef OutputImageType::Pointer	OutputImagePointer

typedef SlicedData::RegionType	OutputImageRegionType

Public Types inherited from mitk::BaseDataSource
typedef BaseDataSource	Self

typedef itk::ProcessObject	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef BaseData	OutputType

typedef itk::DataObject::DataObjectIdentifierType	DataObjectIdentifierType

Public Member Functions
virtual std::vector< std::string >	GetClassHierarchy () const override

virtual const char *	GetClassName () const

Pointer	Clone () const

void	SetWorldGeometry (const PlaneGeometry *geometry)
	Set the axis where to reslice at. More...

void	SetTimeStep (unsigned int timestep)
	Set the time step in the 4D volume. More...

unsigned int	GetTimeStep ()

void	SetComponent (unsigned int component)
	Set the component of an image to be extracted. More...

void	SetResliceTransformByGeometry (const BaseGeometry *transform)
	Set a transform for the reslice axes. This transform is needed if the image volume itself is transformed. (Effects the reslice axis) More...

void	SetInPlaneResampleExtentByGeometry (bool inPlaneResampleExtentByGeometry)
	Resampling grid corresponds to: false->image true->worldgeometry. More...

void	SetOutputDimensionality (unsigned int dimension)
	Sets the output dimension of the slice. More...

void	SetOutputSpacingZDirection (double zSpacing)
	Set the spacing in z direction manually. Required if the outputDimension is > 2. More...

void	SetOutputExtentZDirection (int zMin, int zMax)
	Set the extent in pixel for direction z manualy. Required if the output dimension is > 2. More...

bool	GetClippedPlaneBounds (double bounds[6])
	Get the bounding box of the slice [xMin, xMax, yMin, yMax, zMin, zMax] The method uses the input of the filter to calculate the bounds. It is recommended to use GetClippedPlaneBounds(const BaseGeometry, const PlaneGeometry, double*) if you are not sure about the input. More...

bool	GetClippedPlaneBounds (const BaseGeometry boundingGeometry, const PlaneGeometry planeGeometry, double *bounds)
	Get the bounding box of the slice [xMin, xMax, yMin, yMax, zMin, zMax]. More...

mitk::ScalarType *	GetOutputSpacing ()
	Get the spacing of the slice. returns mitk::ScalarType[2]. More...

vtkImageData *	GetVtkOutput ()
	Get Output as vtkImageData. Note: SetVtkOutputRequest(true) has to be called at least once before GetVtkOutput(). Otherwise the output is empty for the first update step. More...

void	SetVtkOutputRequest (bool isRequested)

vtkMatrix4x4 *	GetResliceAxes ()
	Get the reslices axis matrix. Note: the axis are recalculated when calling SetResliceTransformByGeometry. More...

void	SetBackgroundLevel (double backgroundLevel)

void	SetInterpolationMode (ExtractSliceFilter::ResliceInterpolation interpolation)

Public Member Functions inherited from mitk::ImageToImageFilter
Pointer	Clone () const

virtual void	SetInput (const InputImageType *image)

virtual void	SetInput (unsigned int, const InputImageType *image)

InputImageType *	GetInput (void)

InputImageType *	GetInput (unsigned int idx)

const InputImageType *	GetInput (void) const

const InputImageType *	GetInput (unsigned int idx) const

Public Member Functions inherited from mitk::ImageSource
Pointer	Clone () const

OutputType *	GetOutput ()
	Get the output data of this image source object. More...

const OutputType *	GetOutput () const

OutputType *	GetOutput (DataObjectPointerArraySizeType idx)

const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const

virtual itk::DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override
	Make a DataObject of the correct type to used as the specified output. More...

virtual itk::DataObject::Pointer	MakeOutput (const DataObjectIdentifierType &name) override

virtual vtkImageData *	GetVtkImageData ()

virtual const vtkImageData *	GetVtkImageData () const

Public Member Functions inherited from mitk::BaseDataSource
OutputType *	GetOutput ()

const OutputType *	GetOutput () const

OutputType *	GetOutput (DataObjectPointerArraySizeType idx)

const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const

virtual void	GraftOutput (OutputType *output)
	Graft the specified BaseData onto this BaseDataSource's output. More...

virtual void	GraftOutput (const DataObjectIdentifierType &key, OutputType *output)

virtual void	GraftNthOutput (unsigned int idx, OutputType *output)
	Graft the specified base data object onto this BaseDataSource's idx'th output. More...

bool	Updating () const
	Access itk::ProcessObject::m_Updating. More...

Static Public Member Functions
static const char *	GetStaticNameOfClass ()

static Pointer	New ()

static Pointer	New (vtkImageReslice *_arg)

Static Public Member Functions inherited from mitk::ImageToImageFilter
static const char *	GetStaticNameOfClass ()

static Pointer	New ()

Static Public Member Functions inherited from mitk::ImageSource
static const char *	GetStaticNameOfClass ()

static Pointer	New ()
	Method for creation through the object factory. More...

Static Public Member Functions inherited from mitk::BaseDataSource
static const char *	GetStaticNameOfClass ()

Protected Member Functions
	ExtractSliceFilter (vtkImageReslice *reslicer=nullptr)

virtual	~ExtractSliceFilter ()

virtual void	GenerateData () override
	A version of GenerateData() specific for image processing filters. More...

virtual void	GenerateOutputInformation () override

virtual void	GenerateInputRequestedRegion () override

Protected Member Functions inherited from mitk::ImageToImageFilter
	ImageToImageFilter ()

virtual	~ImageToImageFilter ()

virtual void	PrintSelf (std::ostream &os, itk::Indent indent) const override

Protected Member Functions inherited from mitk::ImageSource
	ImageSource ()

virtual	~ImageSource ()

virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, itk::ThreadIdType threadId)
	If an imaging filter can be implemented as a multithreaded algorithm, the filter will provide an implementation of ThreadedGenerateData(). More...

virtual void	PrepareOutputs () override
	This method is intentionally left blank. More...

virtual void	AllocateOutputs ()
	The GenerateData method normally allocates the buffers for all of the outputs of a filter. More...

virtual void	BeforeThreadedGenerateData ()
	If an imaging filter needs to perform processing after the buffer has been allocated but before threads are spawned, the filter can can provide an implementation for BeforeThreadedGenerateData(). More...

virtual void	AfterThreadedGenerateData ()
	If an imaging filter needs to perform processing after all processing threads have completed, the filter can can provide an implementation for AfterThreadedGenerateData(). More...

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)
	Split the output's RequestedRegion into "num" pieces, returning region "i" as "splitRegion". More...

Protected Member Functions inherited from mitk::BaseDataSource
	BaseDataSource ()

virtual	~BaseDataSource ()

Protected Attributes
const PlaneGeometry *	m_WorldGeometry

vtkSmartPointer< vtkImageReslice >	m_Reslicer

unsigned int	m_TimeStep

unsigned int	m_OutputDimension

double	m_ZSpacing

int	m_ZMin

int	m_ZMax

ResliceInterpolation	m_InterpolationMode

BaseGeometry::ConstPointer	m_ResliceTransform

bool	m_InPlaneResampleExtentByGeometry

mitk::ScalarType *	m_OutPutSpacing

bool	m_VtkOutputRequested

double	m_BackgroundLevel

unsigned int	m_Component

Additional Inherited Members
Static Protected Member Functions inherited from mitk::ImageSource
static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)
	Static function used as a "callback" by the MultiThreader. More...

Static Protected Member Functions inherited from mitk::BaseDataSource
static Pointer	New ()

Detailed Description

ExtractSliceFilter extracts a 2D abitrary oriented slice from a 3D volume.

The filter can reslice in all orthogonal planes such as sagittal, coronal and axial, and is also able to reslice an arbitrary oriented oblique plane. Curved planes are specified via an AbstractTransformGeometry as the input worldgeometry.

Additionally the filter extracts the specified component of a multi-component input image. This is done only if the caller requests an mitk::Image output ('m_VtkOutputRequested' set to false). The default component to be extracted is '0'.

The convenient workflow is:

Set an image as input.
Set the worldPlaneGeometry. This defines a grid where the slice is being extracted
And then start the pipeline.

There are a few more properties that can be set to modify the behavior of the slicing. The properties are:

interpolation mode either Nearestneighbor, Linear or Cubic.
a transform this is a convenient way to adapt the reslice axis for the case that the image is transformed e.g. rotated.
time step the time step in a times volume.
the component to extract from a multi-component input image
vtkoutputrequested, to define whether an mitk::image should be initialized
resample by geometry whether the resampling grid corresponds to the specs of the worldgeometry or is directly derived from the input image

By default the properties are set to:

interpolation mode Nearestneighbor.
a transform NULL (No transform is set).
time step 0.
component 0.
resample by geometry false (Corresponds to input image).

Definition at line 67 of file mitkExtractSliceFilter.h.

Member Typedef Documentation

typedef itk::SmartPointer<const Self> mitk::ExtractSliceFilter::ConstPointer

Definition at line 70 of file mitkExtractSliceFilter.h.

typedef itk::SmartPointer<Self> mitk::ExtractSliceFilter::Pointer

Definition at line 70 of file mitkExtractSliceFilter.h.

typedef ExtractSliceFilter mitk::ExtractSliceFilter::Self

Definition at line 70 of file mitkExtractSliceFilter.h.

typedef ImageToImageFilter mitk::ExtractSliceFilter::Superclass

Definition at line 70 of file mitkExtractSliceFilter.h.

Member Enumeration Documentation

enum mitk::ExtractSliceFilter::ResliceInterpolation

Enumerator
RESLICE_NEAREST
RESLICE_LINEAR
RESLICE_CUBIC

Definition at line 153 of file mitkExtractSliceFilter.h.

Constructor & Destructor Documentation

mitk::ExtractSliceFilter::ExtractSliceFilter ( vtkImageReslice * reslicer = nullptr )

protected

Definition at line 28 of file mitkExtractSliceFilter.cpp.

References m_BackgroundLevel, m_Component, m_InPlaneResampleExtentByGeometry, m_InterpolationMode, m_OutputDimension, m_OutPutSpacing, m_Reslicer, m_ResliceTransform, m_TimeStep, m_VtkOutputRequested, m_ZMax, m_ZMin, m_ZSpacing, mitk::New(), and RESLICE_NEAREST.

mitk::ExtractSliceFilter::~ExtractSliceFilter ( )

protectedvirtual

Definition at line 54 of file mitkExtractSliceFilter.cpp.

Member Function Documentation

Pointer mitk::ExtractSliceFilter::Clone ( ) const

void mitk::ExtractSliceFilter::GenerateData ( )

overrideprotectedvirtual

A version of GenerateData() specific for image processing filters.

This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.

See also: ThreadedGenerateData()

Reimplemented from mitk::ImageSource.

Definition at line 90 of file mitkExtractSliceFilter.cpp.

References mitk::BaseGeometry::GetAxisVector(), mitk::TimeGeometry::GetGeometryForTimeStep(), mitk::PlaneGeometry::GetNormal(), mitk::BaseGeometry::GetOrigin(), mitk::AbstractTransformGeometry::GetParametricExtent(), mitk::AbstractTransformGeometry::GetParametricExtentInMM(), mitk::AbstractTransformGeometry::GetPlane(), mitk::AbstractTransformGeometry::GetVtkAbstractTransform(), mitk::Image::GetVtkImageData(), mitk::TimeGeometry::IsValidTimeStep(), mitk::Image::IsVolumeSet(), mitk::itk2vtk(), max(), MITK_ERROR, mitk::New(), and mitk::vnl2vtk().

void mitk::ExtractSliceFilter::GenerateInputRequestedRegion ( )

overrideprotectedvirtual

What is the input requested region that is required to produce the output requested region? The base assumption for image processing filters is that the input requested region can be set to match the output requested region. If a filter requires more input (for instance a filter that uses neighborhoods needs more input than output to avoid introducing artificial boundary conditions) or less input (for instance a magnify filter) will have to override this method. In doing so, it should call its superclass' implementation as its first step. Note that this imaging filters operate differently than the classes to this point in the class hierachy. Up till now, the base assumption has been that the largest possible region will be requested of the input.

See also: ProcessObject::GenerateInputRequestedRegion(), ImageSource::GenerateInputRequestedRegion()

Reimplemented from mitk::ImageToImageFilter.

Definition at line 74 of file mitkExtractSliceFilter.cpp.

void mitk::ExtractSliceFilter::GenerateOutputInformation ( )

overrideprotectedvirtual

Definition at line 61 of file mitkExtractSliceFilter.cpp.

virtual std::vector<std::string> mitk::ExtractSliceFilter::GetClassHierarchy ( ) const

inlineoverridevirtual

Reimplemented from mitk::ImageToImageFilter.

Definition at line 70 of file mitkExtractSliceFilter.h.

virtual const char* mitk::ExtractSliceFilter::GetClassName ( ) const

virtual

Reimplemented from mitk::ImageToImageFilter.

bool mitk::ExtractSliceFilter::GetClippedPlaneBounds ( double bounds[6] )

Get the bounding box of the slice [xMin, xMax, yMin, yMax, zMin, zMax] The method uses the input of the filter to calculate the bounds. It is recommended to use GetClippedPlaneBounds(const BaseGeometry*, const PlaneGeometry*, double*) if you are not sure about the input.

Definition at line 464 of file mitkExtractSliceFilter.cpp.

bool mitk::ExtractSliceFilter::GetClippedPlaneBounds	(	const BaseGeometry *	boundingGeometry,
		const PlaneGeometry *	planeGeometry,
		double *	bounds
	)

Get the bounding box of the slice [xMin, xMax, yMin, yMax, zMin, zMax].

Definition at line 473 of file mitkExtractSliceFilter.cpp.

References mitk::PlaneClipping::CalculateClippedPlaneBounds().

mitk::ScalarType * mitk::ExtractSliceFilter::GetOutputSpacing ( )

Get the spacing of the slice. returns mitk::ScalarType[2].

Definition at line 85 of file mitkExtractSliceFilter.cpp.

vtkMatrix4x4* mitk::ExtractSliceFilter::GetResliceAxes ( )

inline

Get the reslices axis matrix. Note: the axis are recalculated when calling SetResliceTransformByGeometry.

Definition at line 151 of file mitkExtractSliceFilter.h.

static const char* mitk::ExtractSliceFilter::GetStaticNameOfClass ( )

inlinestatic

Definition at line 70 of file mitkExtractSliceFilter.h.

unsigned int mitk::ExtractSliceFilter::GetTimeStep ( )

inline

Definition at line 84 of file mitkExtractSliceFilter.h.

vtkImageData* mitk::ExtractSliceFilter::GetVtkOutput ( )

inline

Get Output as vtkImageData. Note: SetVtkOutputRequest(true) has to be called at least once before GetVtkOutput(). Otherwise the output is empty for the first update step.

Definition at line 135 of file mitkExtractSliceFilter.h.

static Pointer mitk::ExtractSliceFilter::New ( )

static

Referenced by QmitkSliceBasedInterpolatorWidget::AcceptAllInterpolations(), QmitkSlicesInterpolator::AcceptAllInterpolations(), mitk::DiffSliceOperationApplier::ExecuteOperation(), mitk::ContourModelSetToImageFilter::GenerateData(), mitk::LabelSetImageVtkMapper2D::GenerateDataForRenderer(), mitk::SegTool2D::GetAffectedImageSliceAs2DImage(), QmitkSliceBasedInterpolatorWidget::GetWorkingSlice(), mitk::SliceBasedInterpolationController::Interpolate(), mitk::SegmentationInterpolationController::Interpolate(), mitk::RegEvaluationMapper2D::LocalStorage::LocalStorage(), mitk::ImageVtkMapper2D::LocalStorage::LocalStorage(), mitk::DoseImageVtkMapper2D::LocalStorage::LocalStorage(), mitkRotatedSlice4DTest(), QmitkSliceBasedInterpolatorWidget::OnAcceptInterpolationClicked(), QmitkSlicesInterpolator::OnAcceptInterpolationClicked(), and mitk::SegTool2D::WriteSliceToVolume().

static Pointer mitk::ExtractSliceFilter::New ( vtkImageReslice * _arg )

inlinestatic

Definition at line 73 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetBackgroundLevel ( double backgroundLevel )

inline

Definition at line 152 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetComponent ( unsigned int component )

inline

Set the component of an image to be extracted.

Definition at line 87 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetInPlaneResampleExtentByGeometry ( bool inPlaneResampleExtentByGeometry )

inline

Resampling grid corresponds to: false->image true->worldgeometry.

Definition at line 94 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetInterpolationMode ( ExtractSliceFilter::ResliceInterpolation interpolation )

inline

Definition at line 160 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetOutputDimensionality ( unsigned int dimension )

inline

Sets the output dimension of the slice.

Definition at line 100 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetOutputExtentZDirection	(	int	zMin,
		int	zMax
	)

inline

Set the extent in pixel for direction z manualy. Required if the output dimension is > 2.

Definition at line 108 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetOutputSpacingZDirection ( double zSpacing )

inline

Set the spacing in z direction manually. Required if the outputDimension is > 2.

Definition at line 104 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetResliceTransformByGeometry ( const BaseGeometry * transform )

inline

Set a transform for the reslice axes. This transform is needed if the image volume itself is transformed. (Effects the reslice axis)

Definition at line 92 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetTimeStep ( unsigned int timestep )

inline

Set the time step in the 4D volume.

Definition at line 83 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetVtkOutputRequest ( bool isRequested )

inline

Set VtkOutPutRequest to suppress the convertion of the image. It is suggested to use this with GetVtkOutput(). Note: SetVtkOutputRequest(true) has to be called at least once before GetVtkOutput(). Otherwise the output is empty for the first update step.

Definition at line 147 of file mitkExtractSliceFilter.h.

void mitk::ExtractSliceFilter::SetWorldGeometry ( const PlaneGeometry * geometry )

inline

Set the axis where to reslice at.

Definition at line 76 of file mitkExtractSliceFilter.h.