This filter is subclass of the spectral unmixing filter base. All algorithms in this class are based on the vigra open source c++ library. It takes a multispectral pixel as input and returns a vector with the unmixing result. More...

#include <mitkPASpectralUnmixingFilterVigra.h>

Inheritance diagram for mitk::pa::SpectralUnmixingFilterVigra:

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Collaboration diagram for mitk::pa::SpectralUnmixingFilterVigra:

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Public Types
enum	VigraAlgortihmType { LARS, GOLDFARB, WEIGHTED, LS }
	Contains all implemented Vigra algorithms for spectral unmixing. For detailed information of the algorithms look at the mitkPASpectralUnmixingFilterVigra.h documentation (section Algorithms). More...

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
	mitkClassMacro (SpectralUnmixingFilterVigra, SpectralUnmixingFilterBase)

void	AddWeight (unsigned int weight)
	AddWeight takes integers and writes them at the end of the weightsvec vector. The first call of the method then corresponds to the first input image/wavelength and so on. More...

void	SetAlgorithm (VigraAlgortihmType inputAlgorithmName)
	Takes a mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType and fix it for usage at the "SpectralUnmixingAlgorithm" method. More...

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

void	AddChromophore (mitk::pa::PropertyCalculator::ChromophoreType chromophore)
	AddChromophore takes mitk::pa::PropertyCalculator::ChromophoreType and writes them at the end of the m_Chromophore vector. The call of the method sets the order of the GetOutput method! More...

void	AddWavelength (int wavelength)
	AddWavelength takes integers and writes them at the end of the m_Wavelength vector. The first call of the method then corresponds to the first input image and so on. More...

virtual void	Verbose (bool verbose)

virtual void	AddOutputs (unsigned int outputs)
	AddOutputs takes an integer and sets indexed outputs. More...

virtual void	RelativeError (bool relativeError)

virtual void	AddRelativeErrorSettings (int value)
	AddRelativeErrorSettings takes integers and writes them at the end of the m_RelativeErrorSettings vector. 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
	SpectralUnmixingFilterVigra ()

	~SpectralUnmixingFilterVigra () override

Eigen::VectorXf	SpectralUnmixingAlgorithm (Eigen::Matrix< float, Eigen::Dynamic, Eigen::Dynamic > EndmemberMatrix, Eigen::VectorXf inputVector) override
	overrides the baseclass method with a mehtod to calculate the spectral unmixing result vector. Herain it first converts the Eigen inputs to the Vigra class. Afterwards the class performs the algorithm set by the "SetAlgorithm" method and writes the result into a Eigen vector which is the return value. More...

Protected Member Functions inherited from mitk::pa::SpectralUnmixingFilterBase
	SpectralUnmixingFilterBase ()
	Constructor creats proptery calculater smart pointer new() More...

	~SpectralUnmixingFilterBase () override

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 Attributes inherited from mitk::pa::SpectralUnmixingFilterBase
ofstream	myfile

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 ()

Protected Attributes inherited from mitk::pa::SpectralUnmixingFilterBase
bool	m_Verbose

bool	m_RelativeError

std::vector< mitk::pa::PropertyCalculator::ChromophoreType >	m_Chromophore

std::vector< int >	m_Wavelength

std::vector< int >	m_RelativeErrorSettings

Detailed Description

This filter is subclass of the spectral unmixing filter base. All algorithms in this class are based on the vigra open source c++ library. It takes a multispectral pixel as input and returns a vector with the unmixing result.

Input:

endmemberMatrix Eigen Matrix with number of chromophores colums and number of wavelengths rows so matrix element (i,j) contains the absorbtion of chromophore j @ wavelength i taken from the database by PropertyElement method.
inputVector Eigen Vector containing values of one pixel of XY-plane image with number of wavelength rows (z-dimension of a sequenece) so the pixelvalue of the first wavelength is stored in inputVector[0] and so on.

Output:

Eigen vector with unmixing result of one multispectral pixel. The ith element of the vector corresponds to the ith entry of the m_Chromophore vector.

Algorithms (see VigraAlgortihmType enum):

LARS algorithm minimizes (A*x-b)^2 s.t. x>=0 using least angle regression
GOLDFARB minimizes (A*x-b)^2 s.t. x>=0 using the Goldfarb-Idnani algorithm
WEIGHTED minimizes transpose(A*x-b)*diag(weights)*(A*x-b) using QR decomposition
LS minimizes (A*x-b)^2 using QR decomposition

Possible exceptions:

"404 VIGRA ALGORITHM NOT FOUND": Algorithm not implemented

Definition at line 49 of file mitkPASpectralUnmixingFilterVigra.h.

Member Enumeration Documentation

◆ VigraAlgortihmType

enum mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType

Contains all implemented Vigra algorithms for spectral unmixing. For detailed information of the algorithms look at the mitkPASpectralUnmixingFilterVigra.h documentation (section Algorithms).

Enumerator
LARS
GOLDFARB
WEIGHTED
LS

Definition at line 59 of file mitkPASpectralUnmixingFilterVigra.h.

Constructor & Destructor Documentation

◆ SpectralUnmixingFilterVigra()

mitk::pa::SpectralUnmixingFilterVigra::SpectralUnmixingFilterVigra ( )

protected

Definition at line 24 of file mitkPASpectralUnmixingFilterVigra.cpp.

◆ ~SpectralUnmixingFilterVigra()

mitk::pa::SpectralUnmixingFilterVigra::~SpectralUnmixingFilterVigra ( )

overrideprotected

Definition at line 28 of file mitkPASpectralUnmixingFilterVigra.cpp.

Member Function Documentation

◆ AddWeight()

void mitk::pa::SpectralUnmixingFilterVigra::AddWeight ( unsigned int weight )

AddWeight takes integers and writes them at the end of the weightsvec vector. The first call of the method then corresponds to the first input image/wavelength and so on.

Parameters

weight is a percentage (integer) between 1 and 100

Definition at line 37 of file mitkPASpectralUnmixingFilterVigra.cpp.

◆ mitkClassMacro()

mitk::pa::SpectralUnmixingFilterVigra::mitkClassMacro	(	SpectralUnmixingFilterVigra	,
		SpectralUnmixingFilterBase
	)

◆ New()

static Pointer mitk::pa::SpectralUnmixingFilterVigra::New ( )

static

Referenced by GetFilterInstance().

◆ SetAlgorithm()

void mitk::pa::SpectralUnmixingFilterVigra::SetAlgorithm ( VigraAlgortihmType inputAlgorithmName )

Takes a mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType and fix it for usage at the "SpectralUnmixingAlgorithm" method.

Parameters

algorithmName has to be a mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType

Definition at line 32 of file mitkPASpectralUnmixingFilterVigra.cpp.

◆ SpectralUnmixingAlgorithm()

Eigen::VectorXf mitk::pa::SpectralUnmixingFilterVigra::SpectralUnmixingAlgorithm	(	Eigen::Matrix< float, Eigen::Dynamic, Eigen::Dynamic >	EndmemberMatrix,
		Eigen::VectorXf	inputVector
	)

overrideprotectedvirtual

overrides the baseclass method with a mehtod to calculate the spectral unmixing result vector. Herain it first converts the Eigen inputs to the Vigra class. Afterwards the class performs the algorithm set by the "SetAlgorithm" method and writes the result into a Eigen vector which is the return value.

Parameters

endmemberMatrix	Matrix with number of chromophores colums and number of wavelengths rows so matrix element (i,j) contains the absorbtion of chromophore j @ wavelength i taken from the database by PropertyElement method.
inputVector	Vector containing values of one pixel of XY-plane image with number of wavelength rows (z-dimension of a sequenece) so the pixelvalue of the first wavelength is stored in inputVector[0] and so on.

Exceptions

if	the algorithmName is not a member of the enum VigraAlgortihmType

Implements mitk::pa::SpectralUnmixingFilterBase.

Definition at line 43 of file mitkPASpectralUnmixingFilterVigra.cpp.

References k(), and mitkThrow.

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ VigraAlgortihmType

Constructor & Destructor Documentation

◆ SpectralUnmixingFilterVigra()

◆ ~SpectralUnmixingFilterVigra()

Member Function Documentation

◆ AddWeight()

◆ mitkClassMacro()

◆ New()

◆ SetAlgorithm()

◆ SpectralUnmixingAlgorithm()