Class implementing a mitk::ImageToImageFilter for PAUS motion correction. More...

#include <mitkPhotoacousticMotionCorrectionFilter.h>

Inheritance diagram for mitk::PhotoacousticMotionCorrectionFilter:

Collaboration diagram for mitk::PhotoacousticMotionCorrectionFilter:

Public Member Functions
	mitkClassMacro (PhotoacousticMotionCorrectionFilter, ImageToImageFilter)

virtual void	SetBatchSize (unsigned int _arg)

virtual void	SetPyrScale (double _arg)

virtual void	SetLevels (unsigned int _arg)

virtual void	SetWinSize (unsigned int _arg)

virtual void	SetIterations (unsigned int _arg)

virtual void	SetPolyN (unsigned int _arg)

virtual void	SetPolySigma (double _arg)

virtual void	SetFlags (unsigned int _arg)

virtual unsigned int	GetBatchSize () const

virtual double	GetPyrScale () const

virtual unsigned int	GetLevels () const

virtual unsigned int	GetWinSize () const

virtual unsigned int	GetIterations () const

virtual unsigned int	GetPolyN () const

virtual double	GetPolySigma () const

virtual unsigned int	GetFlags () const

void	SetPaInput (mitk::Image::Pointer)
	Wrapper which sets the photoacoustic image as the correct input. More...

mitk::Image::Pointer	GetPaInput ()
	Wrapper which gets the photoacoustic image out of the correct input. More...

void	SetUsInput (mitk::Image::Pointer)
	Wrapper which sets the ultrasonic image as the correct input. More...

mitk::Image::Pointer	GetUsInput ()
	Wrapper which gets the ultrasonic image out of the correct input. More...

mitk::Image::Pointer	GetPaOutput ()
	Wrapper which gets the photoacoustic image out of the correct output. More...

mitk::Image::Pointer	GetUsOutput ()
	Wrapper which gets the ultrasonic image out of the correct output. More...

Public Member Functions inherited from mitk::ImageToImageFilter
virtual std::vector< std::string >	GetClassHierarchy () const override

virtual const char *	GetClassName () const

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

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

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 Pointer	New ()

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
	PhotoacousticMotionCorrectionFilter ()

	~PhotoacousticMotionCorrectionFilter () override

void	GenerateData () override
	Apply OpenCV algorithm to compensate motion in a 2d image time series. More...

void	CheckInput (mitk::Image::Pointer paImage, mitk::Image::Pointer usImage)
	Validate the input images. More...

void	InitializeOutputIfNecessary (mitk::Image::Pointer paInput, mitk::Image::Pointer usInput, mitk::Image::Pointer paOutput, mitk::Image::Pointer usOutput)
	Assure that the output images have the same dimensions as the input images. More...

void	InitializeOutput (mitk::Image::Pointer input, mitk::Image::Pointer output)
	Copy the image data from the input image to the output image. More...

void	PerformCorrection (mitk::Image::Pointer paInput, mitk::Image::Pointer usInput, mitk::Image::Pointer paOutput, mitk::Image::Pointer usOutput)
	This method performs the actual motion compensation. More...

cv::Mat	GetMatrix (const mitk::Image::Pointer input, unsigned int i)
	Extract a 2d slice as OpenCV matrix. More...

cv::Mat	FitMatrixToChar (cv::Mat mat)
	Rescale matrix such that the values lie between 0 and 255. More...

void	InsertMatrixAsSlice (cv::Mat mat, mitk::Image::Pointer output, unsigned int i)
	Insert a OpenCV matrix as a slice into an image. More...

cv::Mat	ComputeFlowMap (cv::Mat)
	Compute the remapping map from an optical flow. More...

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

	~ImageToImageFilter () override

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

void	GenerateInputRequestedRegion () override

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 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 ()

	~BaseDataSource () override

Additional Inherited Members
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

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

Class implementing a mitk::ImageToImageFilter for PAUS motion correction.

The filter takes a stack of PA and US images. It then computes the optical flow within the US image and compensates the PA and US images for the flow. Afterwards it returns the stack of PA and US images.

See also: https://docs.opencv.org/3.0-beta/modules/video/doc/motion_analysis_and_object_tracking.html#calcopticalflowfarneback

Definition at line 52 of file mitkPhotoacousticMotionCorrectionFilter.h.

Constructor & Destructor Documentation

◆ PhotoacousticMotionCorrectionFilter()

mitk::PhotoacousticMotionCorrectionFilter::PhotoacousticMotionCorrectionFilter ( )

protected

Definition at line 17 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References mitk::Image::New(), and ~PhotoacousticMotionCorrectionFilter().

◆ ~PhotoacousticMotionCorrectionFilter()

mitk::PhotoacousticMotionCorrectionFilter::~PhotoacousticMotionCorrectionFilter ( )

overrideprotected

Definition at line 40 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

Referenced by PhotoacousticMotionCorrectionFilter().

Member Function Documentation

◆ CheckInput()

void mitk::PhotoacousticMotionCorrectionFilter::CheckInput	(	mitk::Image::Pointer	paImage,
		mitk::Image::Pointer	usImage
	)

protected

Validate the input images.

The input images have to be non-empty, 3d and have to coincide in the length in each dimension. If any of these conditions are violated, the method will throw an invalid_argument exception.

Parameters

paImage	A mitk image
usImage	A mitk image

Warning: If the two images are not 3d and do not coincide in the length in each dimension, this method will throw an invalid_argument exception.

Exceptions

invalid_argument

Definition at line 68 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References IMAGE_DIMENSION, and MITK_ERROR.

Referenced by GenerateData().

◆ ComputeFlowMap()

cv::Mat mitk::PhotoacousticMotionCorrectionFilter::ComputeFlowMap ( cv::Mat flow )

protected

Compute the remapping map from an optical flow.

The optical flow cannot be used directly to compensate an image. Instead we have to generate an appropriate map.

Parameters

flow	The optical flow which is the base for the remapping.

Returns: The remapping map.

Definition at line 163 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References mitk::ImageMappingHelper::map().

Referenced by PerformCorrection().

◆ FitMatrixToChar()

cv::Mat mitk::PhotoacousticMotionCorrectionFilter::FitMatrixToChar ( cv::Mat mat )

protected

Rescale matrix such that the values lie between 0 and 255.

This method rescales the matrix such that its values lie between 0 and 255. In order to do that it uses the maximum and the minimum of the input ultrasonic image.

Warning: This is a specialized method which does not perform the operation in general, but only if the matrix stems from the right ultrasonic image. Therefore, the method should only be called internally.

Parameters

mat	The OpenCV matrix to be rescaled

Returns: The rescaled OpenCV matrix

Definition at line 176 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References MAX_MATRIX.

Referenced by PerformCorrection().

◆ GenerateData()

void mitk::PhotoacousticMotionCorrectionFilter::GenerateData ( )

overrideprotected

Apply OpenCV algorithm to compensate motion in a 2d image time series.

This method uses two 3d mitk images. Both will be interpreted as time series of 2d images. GetInput(0) should be a photoacoustic image whereas GetInput(1) should be an ultrasound image. The input will be validated and then converted to OpenCV matrices. In the end the Farneback algorithm will be used to compute the optical flow in consecutive images and compensate for this flow. The Output will be two 3d mitk images of the same dimensions as the input containing the compensated data.

Warning: The input images need to be 3-dimensional (with the same size in each dimension). Otherwise, an invalid_argument exception will be thrown.

Exceptions

invalid_argument

Definition at line 212 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References CheckInput(), mitk::ImageToImageFilter::GetInput(), mitk::ImageSource::GetOutput(), InitializeOutputIfNecessary(), MITK_INFO, and PerformCorrection().

◆ GetBatchSize()

virtual unsigned int mitk::PhotoacousticMotionCorrectionFilter::GetBatchSize ( ) const

virtual

◆ GetFlags()

virtual unsigned int mitk::PhotoacousticMotionCorrectionFilter::GetFlags ( ) const

virtual

◆ GetIterations()

virtual unsigned int mitk::PhotoacousticMotionCorrectionFilter::GetIterations ( ) const

virtual

◆ GetLevels()

virtual unsigned int mitk::PhotoacousticMotionCorrectionFilter::GetLevels ( ) const

virtual

◆ GetMatrix()

cv::Mat mitk::PhotoacousticMotionCorrectionFilter::GetMatrix	(	const mitk::Image::Pointer	input,
		unsigned int	i
	)

protected

Extract a 2d slice as OpenCV matrix.

This method extracts slice i from the 3-dimensional image input and converts it to a OpenCV matrix. Internally, the mitkImageToOpenCVImageFilter is used.

Parameters

input	A 3d image from which a slice is extracted as a 2d OpenCV matrix.
i	Determines the slice to be extracted.

Returns: returns a OpenCV matrix containing the 2d slice.

Definition at line 186 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References IMAGE_DIMENSION, and mitk::Image::New().

Referenced by PerformCorrection().

◆ GetPaInput()

mitk::Image::Pointer mitk::PhotoacousticMotionCorrectionFilter::GetPaInput ( )

Wrapper which gets the photoacoustic image out of the correct input.

This method is a wrapper around the GetInput method. It is implemented for convenience such that you do not have to remember which input is for which image.

Returns: The photoacoustic image

Definition at line 47 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References mitk::ImageToImageFilter::GetInput().

◆ GetPaOutput()

mitk::Image::Pointer mitk::PhotoacousticMotionCorrectionFilter::GetPaOutput ( )

Wrapper which gets the photoacoustic image out of the correct output.

This method is a wrapper around the GetOutput method. It is implemented for convenience such that you do not have to remember which output is for which image.

Returns: The photoacoustic image

Definition at line 60 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References mitk::ImageSource::GetOutput().

◆ GetPolyN()

virtual unsigned int mitk::PhotoacousticMotionCorrectionFilter::GetPolyN ( ) const

virtual

◆ GetPolySigma()

virtual double mitk::PhotoacousticMotionCorrectionFilter::GetPolySigma ( ) const

virtual

◆ GetPyrScale()

virtual double mitk::PhotoacousticMotionCorrectionFilter::GetPyrScale ( ) const

virtual

◆ GetUsInput()

mitk::Image::Pointer mitk::PhotoacousticMotionCorrectionFilter::GetUsInput ( )

Wrapper which gets the ultrasonic image out of the correct input.

This method is a wrapper around the GetInput method. It is implemented for convenience such that you do not have to remember which input is for which image.

Returns: The ultrasonic image

Definition at line 56 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References mitk::ImageToImageFilter::GetInput().

◆ GetUsOutput()

mitk::Image::Pointer mitk::PhotoacousticMotionCorrectionFilter::GetUsOutput ( )

Wrapper which gets the ultrasonic image out of the correct output.

This method is a wrapper around the GetOutput method. It is implemented for convenience such that you do not have to remember which output is for which image.

Returns: The ultrasonic image

Definition at line 64 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References mitk::ImageSource::GetOutput().

◆ GetWinSize()

virtual unsigned int mitk::PhotoacousticMotionCorrectionFilter::GetWinSize ( ) const

virtual

◆ InitializeOutput()

void mitk::PhotoacousticMotionCorrectionFilter::InitializeOutput	(	mitk::Image::Pointer	input,
		mitk::Image::Pointer	output
	)

protected

Copy the image data from the input image to the output image.

This method copys the image data from input to output. This method assumes that the dimensions of the two images match and will not test this.

Parameters

input	A mitk image
output	A mitk image

Definition at line 111 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References mitk::ImageAccessorBase::GetData().

Referenced by InitializeOutputIfNecessary().

◆ InitializeOutputIfNecessary()

void mitk::PhotoacousticMotionCorrectionFilter::InitializeOutputIfNecessary	(	mitk::Image::Pointer	paInput,
		mitk::Image::Pointer	usInput,
		mitk::Image::Pointer	paOutput,
		mitk::Image::Pointer	usOutput
	)

protected

Assure that the output images have the same dimensions as the input images.

The output images need to have the same dimensions as the input images. This will be checked here. If the dimensions do not match, the output will be reinitialized and the image data from the input images will be copied to the output images (in order to make sure that they have a valid data pointer).

Parameters

paInput	Pointer to the photoacoustic input image
usInput	Pointer to the ultrasonic input image
paOutput	Pointer to the photoacoustic output image
usOutput	Pointer to the ultrasonic output image

Definition at line 94 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References IMAGE_DIMENSION, and InitializeOutput().

Referenced by GenerateData().

◆ InsertMatrixAsSlice()

void mitk::PhotoacousticMotionCorrectionFilter::InsertMatrixAsSlice	(	cv::Mat	mat,
		mitk::Image::Pointer	output,
		unsigned int	i
	)

protected

Insert a OpenCV matrix as a slice into an image.

This method converts the 2d OpenCV matrix mat into an mitk image using the mitkOpenCVToMitkImageFilter. Afterwards it inserts the image as slice i into the 3d mitk image output.

Parameters

mat	The matrix to be inserted as a slice
output	The 3d image the matrix is inserted into
i	The index of the slice to be replaced.

Definition at line 200 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References mitk::ImageAccessorBase::GetData().

Referenced by PerformCorrection().

◆ mitkClassMacro()

mitk::PhotoacousticMotionCorrectionFilter::mitkClassMacro	(	PhotoacousticMotionCorrectionFilter	,
		ImageToImageFilter
	)

◆ New()

static Pointer mitk::PhotoacousticMotionCorrectionFilter::New ( )

static

◆ PerformCorrection()

void mitk::PhotoacousticMotionCorrectionFilter::PerformCorrection	(	mitk::Image::Pointer	paInput,
		mitk::Image::Pointer	usInput,
		mitk::Image::Pointer	paOutput,
		mitk::Image::Pointer	usOutput
	)

protected

This method performs the actual motion compensation.

This method uses the ultrasonic input image usInput to compute the optical flow in the time series of 2d images. Then it compensates both the usInput and paInput for it and saves the result in usOutput and paOutput respectively. In the background the OpenCV Farneback algorithm is used for the flow determination.

Parameters

paInput	The photoacoustic input image
usInput	The ultrasonic input image
paOutput	The photoacoustic output image
usOutput	The ultrasonic output image

Definition at line 118 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References ComputeFlowMap(), FitMatrixToChar(), GetMatrix(), IMAGE_DIMENSION, and InsertMatrixAsSlice().

Referenced by GenerateData().

◆ SetBatchSize()

virtual void mitk::PhotoacousticMotionCorrectionFilter::SetBatchSize ( unsigned int _arg )

virtual

◆ SetFlags()

virtual void mitk::PhotoacousticMotionCorrectionFilter::SetFlags ( unsigned int _arg )

virtual

◆ SetIterations()

virtual void mitk::PhotoacousticMotionCorrectionFilter::SetIterations ( unsigned int _arg )

virtual

◆ SetLevels()

virtual void mitk::PhotoacousticMotionCorrectionFilter::SetLevels ( unsigned int _arg )

virtual

◆ SetPaInput()

void mitk::PhotoacousticMotionCorrectionFilter::SetPaInput ( mitk::Image::Pointer input )

Wrapper which sets the photoacoustic image as the correct input.

This method is a wrapper around the SetInput method. It is implemented for convenience such that you do not have to remember which input is for which image.

Parameters

input The photoacoustic image

Definition at line 42 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References mitk::ImageToImageFilter::SetInput().

◆ SetPolyN()

virtual void mitk::PhotoacousticMotionCorrectionFilter::SetPolyN ( unsigned int _arg )

virtual

◆ SetPolySigma()

virtual void mitk::PhotoacousticMotionCorrectionFilter::SetPolySigma ( double _arg )

virtual

◆ SetPyrScale()

virtual void mitk::PhotoacousticMotionCorrectionFilter::SetPyrScale ( double _arg )

virtual

◆ SetUsInput()

void mitk::PhotoacousticMotionCorrectionFilter::SetUsInput ( mitk::Image::Pointer input )

Wrapper which sets the ultrasonic image as the correct input.

This method is a wrapper around the SetInput method. It is implemented for convenience such that you do not have to remember which input is for which image.

Parameters

input The ultrasonic image

Definition at line 51 of file mitkPhotoacousticMotionCorrectionFilter.cpp.

References mitk::ImageToImageFilter::SetInput().

◆ SetWinSize()

virtual void mitk::PhotoacousticMotionCorrectionFilter::SetWinSize ( unsigned int _arg )

virtual

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PhotoacousticMotionCorrectionFilter()

◆ ~PhotoacousticMotionCorrectionFilter()

Member Function Documentation

◆ CheckInput()

◆ ComputeFlowMap()

◆ FitMatrixToChar()

◆ GenerateData()

◆ GetBatchSize()

◆ GetFlags()

◆ GetIterations()

◆ GetLevels()

◆ GetMatrix()

◆ GetPaInput()

◆ GetPaOutput()

◆ GetPolyN()

◆ GetPolySigma()

◆ GetPyrScale()

◆ GetUsInput()

◆ GetUsOutput()

◆ GetWinSize()

◆ InitializeOutput()

◆ InitializeOutputIfNecessary()

◆ InsertMatrixAsSlice()

◆ mitkClassMacro()

◆ New()

◆ PerformCorrection()

◆ SetBatchSize()

◆ SetFlags()

◆ SetIterations()

◆ SetLevels()

◆ SetPaInput()

◆ SetPolyN()

◆ SetPolySigma()

◆ SetPyrScale()

◆ SetUsInput()

◆ SetWinSize()