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

#include <mitkExtractSliceFilter.h>

Inheritance diagram for mitk::ExtractSliceFilter:

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Collaboration diagram for mitk::ExtractSliceFilter:

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Public Types
enum	ResliceInterpolation { RESLICE_NEAREST , RESLICE_LINEAR , RESLICE_CUBIC }

Public Types inherited from mitk::ImageToImageFilter
typedef Superclass::OutputImageRegionType	OutputImageRegionType
	Superclass typedefs. More...

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

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef SlicedData::RegionType	InputImageRegionType

Public Types inherited from mitk::ImageSource
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 BaseData	OutputType
	Output data type. More...

typedef itk::DataObject::DataObjectIdentifierType	DataObjectIdentifierType
	Identifier type for named data objects. More...

Public Member Functions
	mitkClassMacro (ExtractSliceFilter, ImageToImageFilter)

Pointer	Clone () const

	mitkNewMacro1Param (Self, vtkImageReslice *)

void	SetWorldGeometry (const PlaneGeometry *geometry)
	Set the plane geometry defining the reslice axis. More...

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

unsigned int	GetTimeStep ()
	Get the current time step. More...

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

void	SetResliceTransformByGeometry (const BaseGeometry *transform)
	Set a transform for the reslice axes. More...

void	SetInPlaneResampleExtentByGeometry (bool inPlaneResampleExtentByGeometry)
	Set whether the resampling grid is derived from image or world geometry. More...

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

void	SetOutputSpacingZDirection (double zSpacing)
	Set the spacing in z direction manually. More...

void	SetOutputExtentZDirection (int zMin, int zMax)
	Set the extent in pixels for the z direction manually. More...

bool	GetClippedPlaneBounds (double bounds[6])
	Get the bounding box of the slice [xMin, xMax, yMin, yMax, zMin, zMax]. 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. More...

vtkImageData *	GetVtkOutput ()
	Get the output as vtkImageData. More...

void	SetVtkOutputRequest (bool isRequested)
	Set VtkOutputRequest to suppress the conversion of the image. More...

vtkMatrix4x4 *	GetResliceAxes ()
	Get the reslice axes matrix. More...

void	SetBackgroundLevel (double backgroundLevel)
	Set the background level for areas outside the volume. More...

void	SetInterpolationMode (ExtractSliceFilter::ResliceInterpolation interpolation)
	Set the interpolation mode for reslicing. More...

Public Member Functions inherited from mitk::ImageToImageFilter
	mitkClassMacro (ImageToImageFilter, ImageSource)

Pointer	Clone () const

virtual void	SetInput (const InputImageType *image)
	Set the image input of this process object. More...

virtual void	SetInput (unsigned int idx, const InputImageType *image)
	Set the image input at the specified index. More...

InputImageType *	GetInput (void)
	Get the input image (non-const). More...

InputImageType *	GetInput (unsigned int idx)
	Get the input image at the specified index (non-const). More...

const InputImageType *	GetInput (void) const
	Get the input image (const). More...

const InputImageType *	GetInput (unsigned int idx) const
	Get the input image at the specified index (const). More...

Public Member Functions inherited from mitk::ImageSource
	mitkClassMacro (ImageSource, BaseDataSource)

Pointer	Clone () const

mitkBaseDataSourceGetOutputDeclarations itk::DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override
	Get the output data of this image source object. More...

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

virtual vtkImageData *	GetVtkImageData ()
	Get the output as VTK image data (non-const version). More...

virtual const vtkImageData *	GetVtkImageData () const
	Get the output as VTK image data (const version). More...

Public Member Functions inherited from mitk::BaseDataSource
	mitkClassMacroItkParent (BaseDataSource, itk::ProcessObject)

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)
	Graft the specified base data object onto a named output. More...

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
	Check whether the pipeline is currently executing. More...

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from mitk::ImageToImageFilter
static Pointer	New ()
	Method for creation through the object factory. More...

Static Public Member Functions inherited from mitk::ImageSource
static Pointer	New ()
	Method for creation through the object factory. More...

Protected Member Functions
	ExtractSliceFilter (vtkImageReslice *reslicer=nullptr)
	Constructor. More...

	~ExtractSliceFilter () override
	Destructor. More...

void	GenerateData () override
	Perform the actual reslicing. More...

void	GenerateOutputInformation () override
	Compute output information (spacing, origin, extent) based on input and world geometry. More...

void	GenerateInputRequestedRegion () override
	Set the requested region on the input image. More...

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

	~ImageToImageFilter () override

void	PrintSelf (std::ostream &os, itk::Indent indent) const override
	Print self information to the given stream. More...

void	GenerateInputRequestedRegion () override
	Determine the input requested region to produce the output requested region. More...

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

	~ImageSource () override

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

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...

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 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 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 ()
	Constructor. More...

	~BaseDataSource () override
	Destructor. More...

Protected Attributes
PlaneGeometry::ConstPointer	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

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::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 arbitrary 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 nullptr (No transform is set).
time step 0.
component 0.
resample by geometry false (Corresponds to input image).

Definition at line 63 of file mitkExtractSliceFilter.h.

Member Enumeration Documentation

◆ ResliceInterpolation

enum mitk::ExtractSliceFilter::ResliceInterpolation

Enumerator
RESLICE_NEAREST
RESLICE_LINEAR
RESLICE_CUBIC

Definition at line 230 of file mitkExtractSliceFilter.h.

Constructor & Destructor Documentation

◆ ExtractSliceFilter()

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

protected

Constructor.

Parameters

reslicer Optional custom vtkImageReslice instance. If nullptr, a default one is created.

◆ ~ExtractSliceFilter()

mitk::ExtractSliceFilter::~ExtractSliceFilter ( )

overrideprotected

Destructor.

Member Function Documentation

◆ Clone()

Pointer mitk::ExtractSliceFilter::Clone ( ) const

◆ GenerateData()

void mitk::ExtractSliceFilter::GenerateData ( )

overrideprotected

Perform the actual reslicing.

◆ GenerateInputRequestedRegion()

void mitk::ExtractSliceFilter::GenerateInputRequestedRegion ( )

overrideprotected

Set the requested region on the input image.

◆ GenerateOutputInformation()

void mitk::ExtractSliceFilter::GenerateOutputInformation ( )

overrideprotected

Compute output information (spacing, origin, extent) based on input and world geometry.

◆ GetClippedPlaneBounds() [1/2]

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].

Parameters

boundingGeometry	The bounding geometry of the volume.
planeGeometry	The plane geometry defining the slice.
bounds	Output array of six doubles: [xMin, xMax, yMin, yMax, zMin, zMax].

Returns: true if bounds were successfully computed, false otherwise.

◆ GetClippedPlaneBounds() [2/2]

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.

Parameters

bounds Output array of six doubles: [xMin, xMax, yMin, yMax, zMin, zMax].

Returns: true if bounds were successfully computed, false otherwise.

◆ GetOutputSpacing()

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

Get the spacing of the slice.

Returns: Pointer to an array of two mitk::ScalarType values representing the x and y spacing.

◆ GetResliceAxes()

vtkMatrix4x4* mitk::ExtractSliceFilter::GetResliceAxes ( )

inline

Get the reslice axes matrix.

Note: The axes are recalculated when calling SetResliceTransformByGeometry.

Returns: The 4x4 reslice axes matrix.

Definition at line 222 of file mitkExtractSliceFilter.h.

◆ GetTimeStep()

unsigned int mitk::ExtractSliceFilter::GetTimeStep ( )

inline

Get the current time step.

Returns: The time step index currently set.

Definition at line 98 of file mitkExtractSliceFilter.h.

◆ GetVtkOutput()

vtkImageData* mitk::ExtractSliceFilter::GetVtkOutput ( )

inline

Get the 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.

Returns: The resliced output as vtkImageData.

Definition at line 197 of file mitkExtractSliceFilter.h.

◆ mitkClassMacro()

mitk::ExtractSliceFilter::mitkClassMacro	(	ExtractSliceFilter	,
		ImageToImageFilter
	)

◆ mitkNewMacro1Param()

mitk::ExtractSliceFilter::mitkNewMacro1Param	(	Self	,
		vtkImageReslice *
	)

◆ New()

static Pointer mitk::ExtractSliceFilter::New ( )

static

◆ SetBackgroundLevel()

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

inline

Set the background level for areas outside the volume.

Parameters

backgroundLevel The background intensity value.

Definition at line 229 of file mitkExtractSliceFilter.h.

◆ SetComponent()

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

inline

Set the component of a multi-component image to be extracted.

Parameters

component The zero-based component index.

Definition at line 105 of file mitkExtractSliceFilter.h.

◆ SetInPlaneResampleExtentByGeometry()

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

inline

Set whether the resampling grid is derived from image or world geometry.

Parameters

inPlaneResampleExtentByGeometry If false, resampling grid corresponds to the image; if true, it corresponds to the world geometry.

Definition at line 122 of file mitkExtractSliceFilter.h.

◆ SetInterpolationMode()

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

inline

Set the interpolation mode for reslicing.

Parameters

interpolation The interpolation mode (RESLICE_NEAREST, RESLICE_LINEAR, or RESLICE_CUBIC).

Definition at line 242 of file mitkExtractSliceFilter.h.

◆ SetOutputDimensionality()

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

inline

Set the output dimensionality of the slice.

Parameters

dimension The output dimension (typically 2 for a slice).

Definition at line 132 of file mitkExtractSliceFilter.h.

◆ SetOutputExtentZDirection()

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

inline

Set the extent in pixels for the z direction manually.

Required if the output dimension is > 2.

Parameters

zMin	Minimum z extent.
zMax	Maximum z extent.

Definition at line 151 of file mitkExtractSliceFilter.h.

◆ SetOutputSpacingZDirection()

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

inline

Set the spacing in z direction manually.

Required if the output dimension is > 2.

Parameters

zSpacing The spacing value in z direction.

Definition at line 141 of file mitkExtractSliceFilter.h.

◆ SetResliceTransformByGeometry()

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 (affects the reslice axis).

Parameters

transform The BaseGeometry whose transform is used.

Definition at line 114 of file mitkExtractSliceFilter.h.

◆ SetTimeStep()

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

inline

Set the time step in the 4D volume.

Parameters

timestep The time step index to extract.

Definition at line 91 of file mitkExtractSliceFilter.h.

◆ SetVtkOutputRequest()

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

inline

Set VtkOutputRequest to suppress the conversion 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.

Parameters

isRequested If true, output will be provided as vtkImageData.

Definition at line 213 of file mitkExtractSliceFilter.h.

◆ SetWorldGeometry()

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

inline

Set the plane geometry defining the reslice axis.

Parameters

geometry The PlaneGeometry that defines where to reslice.

Definition at line 77 of file mitkExtractSliceFilter.h.

Member Data Documentation

◆ m_BackgroundLevel

double mitk::ExtractSliceFilter::m_BackgroundLevel

protected

Definition at line 288 of file mitkExtractSliceFilter.h.

◆ m_Component

unsigned int mitk::ExtractSliceFilter::m_Component

protected

Definition at line 290 of file mitkExtractSliceFilter.h.

◆ m_InPlaneResampleExtentByGeometry

bool mitk::ExtractSliceFilter::m_InPlaneResampleExtentByGeometry

protected

Definition at line 282 of file mitkExtractSliceFilter.h.

◆ m_InterpolationMode

ResliceInterpolation mitk::ExtractSliceFilter::m_InterpolationMode

protected

Definition at line 280 of file mitkExtractSliceFilter.h.

◆ m_OutputDimension

unsigned int mitk::ExtractSliceFilter::m_OutputDimension

protected

Definition at line 272 of file mitkExtractSliceFilter.h.

◆ m_OutPutSpacing

mitk::ScalarType* mitk::ExtractSliceFilter::m_OutPutSpacing

protected

Definition at line 284 of file mitkExtractSliceFilter.h.

◆ m_Reslicer

vtkSmartPointer<vtkImageReslice> mitk::ExtractSliceFilter::m_Reslicer

protected

Definition at line 268 of file mitkExtractSliceFilter.h.

◆ m_TimeStep

unsigned int mitk::ExtractSliceFilter::m_TimeStep

protected

Definition at line 270 of file mitkExtractSliceFilter.h.

◆ m_VtkOutputRequested

bool mitk::ExtractSliceFilter::m_VtkOutputRequested

protected

Definition at line 286 of file mitkExtractSliceFilter.h.

◆ m_WorldGeometry

PlaneGeometry::ConstPointer mitk::ExtractSliceFilter::m_WorldGeometry

protected

Definition at line 267 of file mitkExtractSliceFilter.h.

◆ m_ZMax

int mitk::ExtractSliceFilter::m_ZMax

protected

Definition at line 278 of file mitkExtractSliceFilter.h.

◆ m_ZMin

int mitk::ExtractSliceFilter::m_ZMin

protected

Definition at line 276 of file mitkExtractSliceFilter.h.

◆ m_ZSpacing

double mitk::ExtractSliceFilter::m_ZSpacing

protected

Definition at line 274 of file mitkExtractSliceFilter.h.

The documentation for this class was generated from the following file:

mitkExtractSliceFilter.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ResliceInterpolation

Constructor & Destructor Documentation

◆ ExtractSliceFilter()

◆ ~ExtractSliceFilter()

Member Function Documentation

◆ Clone()

◆ GenerateData()

◆ GenerateInputRequestedRegion()

◆ GenerateOutputInformation()

◆ GetClippedPlaneBounds() [1/2]

◆ GetClippedPlaneBounds() [2/2]

◆ GetOutputSpacing()

◆ GetResliceAxes()

◆ GetTimeStep()

◆ GetVtkOutput()

◆ mitkClassMacro()

◆ mitkNewMacro1Param()

◆ New()

◆ SetBackgroundLevel()

◆ SetComponent()

◆ SetInPlaneResampleExtentByGeometry()

◆ SetInterpolationMode()

◆ SetOutputDimensionality()

◆ SetOutputExtentZDirection()

◆ SetOutputSpacingZDirection()

◆ SetResliceTransformByGeometry()

◆ SetTimeStep()

◆ SetVtkOutputRequest()

◆ SetWorldGeometry()

Member Data Documentation

◆ m_BackgroundLevel

◆ m_Component

◆ m_InPlaneResampleExtentByGeometry

◆ m_InterpolationMode

◆ m_OutputDimension

◆ m_OutPutSpacing

◆ m_Reslicer

◆ m_TimeStep

◆ m_VtkOutputRequested

◆ m_WorldGeometry

◆ m_ZMax

◆ m_ZMin

◆ m_ZSpacing