The spectral unmixing filter base is designed as superclass for several spectral unmixing filter eg. Eigen- or Vigrabased ones. One can add wavelengths and chromophores and get a unmixed output images out of one MITK input image using algorithms from the subclasses. More...

#include <mitkPASpectralUnmixingFilterBase.h>

Inheritance diagram for mitk::pa::SpectralUnmixingFilterBase:

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Collaboration diagram for mitk::pa::SpectralUnmixingFilterBase:

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Public Member Functions
	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...

Public Attributes
ofstream	myfile

Protected Member Functions
	SpectralUnmixingFilterBase ()
	Constructor creats proptery calculater smart pointer new() More...

	~SpectralUnmixingFilterBase () override

virtual Eigen::VectorXf	SpectralUnmixingAlgorithm (Eigen::Matrix< float, Eigen::Dynamic, Eigen::Dynamic > endmemberMatrix, Eigen::VectorXf inputVector)=0
	The subclasses will override the mehtod to calculate the spectral unmixing result vector. 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

Protected Attributes
bool	m_Verbose

bool	m_RelativeError

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

std::vector< int >	m_Wavelength

std::vector< int >	m_RelativeErrorSettings

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 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 ()

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

The spectral unmixing filter base is designed as superclass for several spectral unmixing filter eg. Eigen- or Vigrabased ones. One can add wavelengths and chromophores and get a unmixed output images out of one MITK input image using algorithms from the subclasses.

Input: The unmixing input has to be a 3D MITK image where the XY-plane is a image and the Z-direction represents recordings for different wavelengths. Herein a XY-plane for a specific Z-direction will be called "image". Every image has to be assigned to a certain wavelength. The "AddWavelength" uses "push_back" to write float values into a vector. The first wavelength will correspond to the first image!!! If there a more input images 'I' then added wavelengths 'w' the filter base interprets the next x images as repetition sequence of the same wavelengths. If I % w !=0 the surplus image(s) will be dropped. Addtionaly one has to add chromophores from the property calculator class enum "ChromophoreType" with the "AddChromophore" method. This method as well uses "push_back" but the chosen (arbitary) order will be the order of the outputs.

Output: The output will be one MITK image per chosen chromophore. Where the XY-plane is a image and the Z-direction represents recordings for different sequences. Furthermore it is possible to creat an output image that contains the information about the relative error between unmixing result and the input image.

Subclasses:

mitkPASpectralUnmixingFilterVigra
mitkPALinearSpectralUnmixingFilter (uses Eigen algorithms)
mitkPASpectralUnmixingFilterSimplex

Possible exceptions:

"PIXELTYPE ERROR! FLOAT 32 REQUIRED": The MITK input image has to consist out of floats.
"ERROR! REMOVE WAVELENGTHS!": One needs at least the same amount of images (z-dimension) then added wavelengths.
"ADD MORE WAVELENGTHS!": One needs at least the same amount of wavelengths then added chromophores.
"WAVELENGTH XXX nm NOT SUPPORTED!": The wavelength is not part of the proptery calculater data base. The data base can be found @ [...].dat
"ADD OUTPUTS HAS TO BE LARGER THEN ZERO!"
"NO WAVELENGHTS/CHROMOPHORES SELECZED! - "INDEX ERROR! NUMBER OF OUTPUTS DOESN'T FIT TO OTHER SETTIGNS!"

Definition at line 63 of file mitkPASpectralUnmixingFilterBase.h.

Constructor & Destructor Documentation

◆ SpectralUnmixingFilterBase()

mitk::pa::SpectralUnmixingFilterBase::SpectralUnmixingFilterBase ( )

protected

Constructor creats proptery calculater smart pointer new()

Definition at line 23 of file mitkPASpectralUnmixingFilterBase.cpp.

References mitk::pa::PropertyCalculator::New().

◆ ~SpectralUnmixingFilterBase()

mitk::pa::SpectralUnmixingFilterBase::~SpectralUnmixingFilterBase ( )

overrideprotected

Definition at line 28 of file mitkPASpectralUnmixingFilterBase.cpp.

Member Function Documentation

◆ AddChromophore()

void mitk::pa::SpectralUnmixingFilterBase::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!

Parameters

chromophore has to be element of porperty calculater enum chromophore type

Returns: for wavelength smaller then 300nm and larger then 1000nm the return will be 0, because not at the data base (2018/06/19)

Definition at line 47 of file mitkPASpectralUnmixingFilterBase.cpp.

References m_Chromophore.

◆ AddOutputs()

void mitk::pa::SpectralUnmixingFilterBase::AddOutputs ( unsigned int outputs )

virtual

AddOutputs takes an integer and sets indexed outputs.

Parameters

outputs integer correponds to the number of output images

Exceptions

if	outputs == 0

Definition at line 33 of file mitkPASpectralUnmixingFilterBase.cpp.

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

◆ AddRelativeErrorSettings()

void mitk::pa::SpectralUnmixingFilterBase::AddRelativeErrorSettings ( int value )

virtual

AddRelativeErrorSettings takes integers and writes them at the end of the m_RelativeErrorSettings vector.

Parameters

value has to be a integer

Definition at line 62 of file mitkPASpectralUnmixingFilterBase.cpp.

References mitk::ImageWriteAccessor::GetData(), mitk::ImageAccessorBase::GetData(), mitk::Image::GetDimensions(), mitk::ImageToImageFilter::GetInput(), mitk::ImageSource::GetOutput(), m_Chromophore, m_RelativeError, m_RelativeErrorSettings, m_Verbose, m_Wavelength, MITK_INFO, MITK_WARN, mitkThrow, myfile, and SpectralUnmixingAlgorithm().

◆ AddWavelength()

void mitk::pa::SpectralUnmixingFilterBase::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.

Parameters

wavelength database supports integers between 300 and 1000 nm

Definition at line 42 of file mitkPASpectralUnmixingFilterBase.cpp.

References m_Wavelength.

◆ mitkClassMacro()

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

◆ RelativeError()

void mitk::pa::SpectralUnmixingFilterBase::RelativeError ( bool relativeError )

virtual

Definition at line 57 of file mitkPASpectralUnmixingFilterBase.cpp.

References m_RelativeError.

◆ SpectralUnmixingAlgorithm()

virtual Eigen::VectorXf mitk::pa::SpectralUnmixingFilterBase::SpectralUnmixingAlgorithm	(	Eigen::Matrix< float, Eigen::Dynamic, Eigen::Dynamic >	endmemberMatrix,
		Eigen::VectorXf	inputVector
	)

protectedpure virtual

The subclasses will override the mehtod to calculate the spectral unmixing result vector.

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