mitk::ImageStatisticsCalculator Class Reference

Class for calculating statistics and histogram for an (optionally masked) image. More...

#include <mitkImageStatisticsCalculator.h>

Inheritance diagram for mitk::ImageStatisticsCalculator:

Collaboration diagram for mitk::ImageStatisticsCalculator:

Classes
class	ImageExtrema
class	Statistics
	Class for common statistics, includig hotspot properties. More...
class	StatisticsContainer
	Container class for storing the computed image statistics. More...

Public Types
enum	{ MASKING_MODE_NONE, MASKING_MODE_IMAGE, MASKING_MODE_PLANARFIGURE }
	Enum for possible masking modi. More...
typedef ImageStatisticsCalculator	Self
typedef itk::Object	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer< const Self >	ConstPointer
typedef double	statisticsValueType
typedef std::map< std::string, statisticsValueType >	statisticsMapType
typedef itk::Statistics::Histogram< double >	HistogramType
typedef unsigned short	MaskPixelType
typedef itk::Statistics::Histogram< double >	HistogramType
typedef HistogramType::ConstIterator	HistogramConstIteratorType
typedef std::vector< HistogramType::ConstPointer >	HistogramContainer
typedef std::vector< Statistics >	StatisticsContainer
typedef std::map< int, double >	BinFrequencyType

Public Member Functions
virtual const char *	GetClassName () const
void	SetInputImage (mitk::Image::Pointer image)
	Set the image for which the statistics are to be computed. More...
void	SetMask (mitk::MaskGenerator::Pointer mask)
	Set the mask generator that creates the mask which is to be used to calculate statistics. If no more mask is desired simply set. More...
void	SetSecondaryMask (mitk::MaskGenerator::Pointer mask)
	Set this if more than one mask should be applied (for instance if a IgnorePixelValueMask were to be used alongside with a segmentation). Both masks are combined using pixel wise AND operation. The secondary mask does not have to be the same size than the primary but they need to have some overlap. More...
void	SetNBinsForHistogramStatistics (unsigned int nBins)
	Set number of bins to be used for histogram statistics. If Bin size is set after number of bins, bin size will be used instead! More...
unsigned int	GetNBinsForHistogramStatistics () const
	Retrieve the number of bins used for histogram statistics. Careful: The return value does not indicate whether NBins or BinSize is used. That solely depends on which parameter has been set last. More...
void	SetBinSizeForHistogramStatistics (double binSize)
	Set bin size to be used for histogram statistics. If nbins is set after bin size, nbins will be used instead! More...
double	GetBinSizeForHistogramStatistics () const
	Retrieve the bin size for histogram statistics. Careful: The return value does not indicate whether NBins or BinSize is used. That solely depends on which parameter has been set last. More...
StatisticsContainer::Pointer	GetStatistics (unsigned int timeStep=0, unsigned int label=1)
	Returns the statistics for label label and timeStep timeStep. If these requested statistics are not computed yet the computation is done as well. For performance reasons, statistics for all labels in the image are computed at once. More...
	mitkClassMacroItkParent (ImageStatisticsCalculator, itk::Object)
Pointer	Clone () const
void	SetUseDefaultBinSize (bool useDefault)
	Automatically calculate bin size to obtain 200 bins. More...
void	SetImage (const mitk::Image *image)
	Set image from which to compute statistics. More...
void	SetImageMask (const mitk::Image *imageMask)
	Set image for masking. More...
void	SetPlanarFigure (mitk::PlanarFigure *planarFigure)
	Set planar figure for masking. More...
void	SetMaskingMode (unsigned int mode)
	Set/Get operation mode for masking. More...
virtual unsigned int	GetMaskingMode ()
	Set/Get operation mode for masking. More...
void	SetMaskingModeToNone ()
	Set/Get operation mode for masking. More...
void	SetMaskingModeToImage ()
	Set/Get operation mode for masking. More...
void	SetMaskingModeToPlanarFigure ()
	Set/Get operation mode for masking. More...
void	SetIgnorePixelValue (double value)
	Set a pixel value for pixels that will be ignored in the statistics. More...
double	GetIgnorePixelValue ()
	Get the pixel value for pixels that will be ignored in the statistics. More...
void	SetDoIgnorePixelValue (bool doit)
	Set whether a pixel value should be ignored in the statistics. More...
bool	GetDoIgnorePixelValue ()
	Get whether a pixel value will be ignored in the statistics. More...
void	SetHistogramBinSize (double size)
	Set bin size for histogram resolution. More...
double	GetHistogramBinSize ()
	Get bin size for histogram resolution. More...
void	SetHotspotRadiusInMM (double hotspotRadiusInMM)
	Sets the radius for the hotspot. More...
double	GetHotspotRadiusInMM ()
	Returns the radius of the hotspot. More...
void	SetCalculateHotspot (bool calculateHotspot)
	Sets whether the hotspot should be calculated. More...
bool	IsHotspotCalculated ()
	Returns true whether the hotspot should be calculated, otherwise false. More...
void	SetHotspotMustBeCompletlyInsideImage (bool hotspotIsCompletlyInsideImage, bool warn=true)
	Sets flag whether hotspot is completly inside the image. Please note that if set to false it can be possible that statistics are calculated for which the whole hotspot is not inside the image! More...
bool	GetHotspotMustBeCompletlyInsideImage () const
	Returns true if hotspot has to be completly inside the image. More...
virtual bool	ComputeStatistics (unsigned int timeStep=0)
	Compute statistics (together with histogram) for the current masking mode. More...
const HistogramType *	GetHistogram (unsigned int timeStep=0, unsigned int label=0) const
	Retrieve the histogram depending on the current masking mode. More...
const HistogramContainer &	GetHistogramVector (unsigned int timeStep=0) const
	Retrieve the histogram depending on the current masking mode (for all image labels. More...
BinFrequencyType	GetBinsAndFreuqencyForHistograms (unsigned int timeStep=0, unsigned int label=0) const
const Statistics &	GetStatistics (unsigned int timeStep=0, unsigned int label=0) const
	Retrieve statistics depending on the current masking mode. More...
const StatisticsContainer &	GetStatisticsVector (unsigned int timeStep=0) const
	Retrieve statistics depending on the current masking mode (for all image labels). More...

Static Public Member Functions
static Pointer	New ()
static Pointer	New ()

Protected Types
typedef std::vector< HistogramContainer >	HistogramVector
typedef std::vector< StatisticsContainer >	StatisticsVector
typedef std::vector< itk::TimeStamp >	TimeStampVectorType
typedef std::vector< bool >	BoolVectorType
typedef itk::Image< unsigned short, 3 >	MaskImage3DType
typedef itk::Image< unsigned short, 2 >	MaskImage2DType

Protected Member Functions
	ImageStatisticsCalculator ()
	ImageStatisticsCalculator ()
virtual	~ImageStatisticsCalculator ()
void	ExtractImageAndMask (unsigned int timeStep=0)
	Depending on the masking mode, the image and mask from which to calculate statistics is extracted from the original input image and mask data. More...
template<typename TPixel , unsigned int VImageDimension>
void	GetMinAndMaxValue (double &minimum, double &maximum, int &counter, double &sigma, const itk::Image< TPixel, VImageDimension > *InputImage, itk::Image< unsigned short, VImageDimension > *MaskImageType)
bool	GetPrincipalAxis (const BaseGeometry *geometry, Vector3D vector, unsigned int &axis)
	If the passed vector matches any of the three principal axes of the passed geometry, the ínteger value corresponding to the axis is set and true is returned. More...
template<typename TPixel , unsigned int VImageDimension>
void	InternalCalculateStatisticsUnmasked (const itk::Image< TPixel, VImageDimension > *image, StatisticsContainer *statisticsContainer, HistogramContainer *histogramContainer)
template<typename TPixel , unsigned int VImageDimension>
void	InternalCalculateStatisticsMasked (const itk::Image< TPixel, VImageDimension > *image, itk::Image< unsigned short, VImageDimension > *maskImage, StatisticsContainer *statisticsContainer, HistogramContainer *histogramContainer)
template<typename TPixel , unsigned int VImageDimension>
void	InternalCalculateMaskFromPlanarFigure (const itk::Image< TPixel, VImageDimension > *image, unsigned int axis)
template<typename TPixel , unsigned int VImageDimension>
void	InternalMaskIgnoredPixels (const itk::Image< TPixel, VImageDimension > *image, itk::Image< unsigned short, VImageDimension > *maskImage)
template<typename TPixel , unsigned int VImageDimension>
ImageExtrema	CalculateExtremaWorld (const itk::Image< TPixel, VImageDimension > *inputImage, itk::Image< unsigned short, VImageDimension > *maskImage, double neccessaryDistanceToImageBorderInMM, unsigned int label)
	Calculates minimum, maximum, mean value and their corresponding indices in a given ROI. As input the function needs an image and a mask. Returns an ImageExtrema object. More...
template<typename TPixel , unsigned int VImageDimension>
Statistics	CalculateHotspotStatistics (const itk::Image< TPixel, VImageDimension > *inputImage, itk::Image< unsigned short, VImageDimension > *maskImage, double radiusInMM, bool &isHotspotDefined, unsigned int label)
	Calculates the hotspot statistics depending on masking mode. Hotspot statistics are calculated for a hotspot which is completly located inside the image by default. More...
template<typename ITK_Exporter , typename VTK_Importer >
void	ConnectPipelines (ITK_Exporter exporter, vtkSmartPointer< VTK_Importer > importer)
template<typename VTK_Exporter , typename ITK_Importer >
void	ConnectPipelines (vtkSmartPointer< VTK_Exporter > exporter, ITK_Importer importer)
void	UnmaskedStatisticsProgressUpdate ()
void	MaskedStatisticsProgressUpdate ()
template<unsigned int VImageDimension>
itk::Size< VImageDimension >	CalculateConvolutionKernelSize (double spacing[VImageDimension], double radiusInMM)
	Returns size of convolution kernel depending on spacing and radius. More...
template<unsigned int VImageDimension>
itk::SmartPointer< itk::Image< float, VImageDimension > >	GenerateHotspotSearchConvolutionKernel (double spacing[VImageDimension], double radiusInMM)
	Generates image of kernel which is needed for convolution. More...
template<typename TPixel , unsigned int VImageDimension>
itk::SmartPointer< itk::Image< TPixel, VImageDimension > >	GenerateConvolutionImage (const itk::Image< TPixel, VImageDimension > *inputImage)
	Convolves image with spherical kernel image. Used for hotspot calculation. More...
template<typename TPixel , unsigned int VImageDimension>
void	FillHotspotMaskPixels (itk::Image< TPixel, VImageDimension > *maskImage, itk::Point< double, VImageDimension > sphereCenter, double sphereRadiusInMM)
	Fills pixels of the spherical hotspot mask. More...

Protected Attributes
mitk::Image::ConstPointer	m_Image
mitk::Image::ConstPointer	m_ImageMask
mitk::PlanarFigure::Pointer	m_PlanarFigure
HistogramVector	m_ImageHistogramVector
HistogramVector	m_MaskedImageHistogramVector
HistogramVector	m_PlanarFigureHistogramVector
HistogramType::Pointer	m_EmptyHistogram
HistogramContainer	m_EmptyHistogramContainer
StatisticsVector	m_ImageStatisticsVector
StatisticsVector	m_MaskedImageStatisticsVector
StatisticsVector	m_PlanarFigureStatisticsVector
StatisticsVector	m_MaskedImageHotspotStatisticsVector
Statistics	m_EmptyStatistics
StatisticsContainer	m_EmptyStatisticsContainer
unsigned int	m_MaskingMode
bool	m_MaskingModeChanged
mitk::Image::ConstPointer	m_InternalImage
MaskImage3DType::Pointer	m_InternalImageMask3D
MaskImage2DType::Pointer	m_InternalImageMask2D
TimeStampVectorType	m_ImageStatisticsTimeStampVector
TimeStampVectorType	m_MaskedImageStatisticsTimeStampVector
TimeStampVectorType	m_PlanarFigureStatisticsTimeStampVector
BoolVectorType	m_ImageStatisticsCalculationTriggerVector
BoolVectorType	m_MaskedImageStatisticsCalculationTriggerVector
BoolVectorType	m_PlanarFigureStatisticsCalculationTriggerVector
double	m_IgnorePixelValue
bool	m_DoIgnorePixelValue
bool	m_IgnorePixelValueChanged
unsigned int	m_PlanarFigureAxis
unsigned int	m_PlanarFigureSlice
int	m_PlanarFigureCoordinate0
int	m_PlanarFigureCoordinate1
double	m_HistogramBinSize
bool	m_UseDefaultBinSize
	Bin size for histogram resoluion. More...
bool	m_UseBinSizeBasedOnVOIRegion
double	m_HotspotRadiusInMM
bool	m_CalculateHotspot
bool	m_HotspotRadiusInMMChanged
bool	m_HotspotMustBeCompletelyInsideImage

Detailed Description

Class for calculating statistics and histogram for an (optionally masked) image.

Images can be masked by either a label image (of the same dimensions as the original image) or by a closed mitk::PlanarFigure, e.g. a circle or polygon. When masking with a planar figure, the slice corresponding to the plane containing the figure is extracted and then clipped with contour defined by the figure. Planar figures need to be aligned along the main axes of the image (axial, sagittal, coronal). Planar figures on arbitrary rotated planes are not supported.

For each operating mode (no masking, masking by image, masking by planar figure), the calculated statistics and histogram are cached so that, when switching back and forth between operation modes without modifying mask or image, the information doesn't need to be recalculated.

The class also has the possibility to calculate the location and separate statistics for a region called "hotspot". The hotspot is a sphere of user-defined size and its location is chosen in a way that the average pixel value within the sphere is maximized.

Warning

Hotspot calculation does not work in case of 2D-images!

Note: currently time-resolved and multi-channel pictures are not properly supported.

Calculation of hotspot statistics

Since calculation of hotspot location and statistics is not straight-forward, the following paragraphs will describe it in more detail.

Note: Calculation of hotspot statistics is optional and set to off by default. Multilabel-masks are supported.

Hotspot Definition

The hotspot of an image is motivated from PET readings. It is defined as a spherical region of fixed size which maximizes the average pixel value within the region. The following image illustrates the concept: the colored areas are different image intensities and the hotspot is located in the hottest region of the image.

Note: Only hotspots are calculated for which the whole hotspot-sphere is inside the image by default. This behaviour can be changed by by calling SetHotspotMustBeCompletlyInsideImage().

Warning

Note that SetHotspotMustBeCompletlyInsideImage(false) may overrate "hot" regions at image borders, because they have a stronger influence on the mean value! Think clearly about this fact and make sure this is what you want/need in your application, before calling SetHotspotMustBeCompletlyInsideImage(false)!

Hotspot Calculation

Since only the size of the hotspot is known initially, we need to calculate two aspects (both implemented in CalculateHotspotStatistics() ):

• the hotspot location
• statistics of the pixels within the hotspot.

Finding the hotspot location requires to calculate the average value at each position. This is done by convolution of the image with a sperical kernel image which reflects partial volumes (important in the case of low-resolution PET images).

Once the hotspot location is known, calculating the actual statistics is a simple task which is implemented in CalculateHotspotStatistics() using a second instance of the ImageStatisticsCalculator.

Step 1: Finding the hotspot by image convolution

As described above, we use image convolution with a rasterized sphere to average the image at each position. To handle coarse resolutions, which would normally force us to decide for partially contained voxels whether to count them or not, we supersample the kernel image and use non-integer kernel values (see GenerateHotspotSearchConvolutionKernel()), which reflect the volume part that is contained in the sphere. For example, if three subvoxels are inside the sphere, the corresponding kernel voxel gets a value of 0.75 (3 out of 4 subvoxels, see 2D example below).

Convolution itself is done by means of the itkFFTConvolutionImageFilter. To find the hotspot location, we simply iterate the averaged image and find a maximum location (see CalculateExtremaWorld()). In case of images with multiple maxima the method returns value and corresponding index of the extrema that is found by the iterator first.

Step 2: Computation of hotspot statistics

Once the hotspot location is found, statistics for the region are calculated by simply iterating the input image and regarding all pixel centers inside the hotspot-sphere for statistics.

Warning

Index positions of maximum/minimum are not provided, because they are not necessarily unique

Tests

To check the correctness of the hotspot calculation, a special class (mitkImageStatisticsHotspotTest) has been created, which generates images with known hotspot location and statistics. A number of unit tests use this class to first generate an image of known properites and then verify that ImageStatisticsCalculator is able to reproduce the known statistics.

Definition at line 14 of file mitkImageStatisticsCalculator.h.

Member Typedef Documentation

typedef std::map<int, double> mitk::ImageStatisticsCalculator::BinFrequencyType

Definition at line 359 of file old/mitkImageStatisticsCalculator.h.

typedef std::vector< bool > mitk::ImageStatisticsCalculator::BoolVectorType

protected

Definition at line 382 of file old/mitkImageStatisticsCalculator.h.

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

Definition at line 21 of file mitkImageStatisticsCalculator.h.

typedef HistogramType::ConstIterator mitk::ImageStatisticsCalculator::HistogramConstIteratorType

Definition at line 172 of file old/mitkImageStatisticsCalculator.h.

typedef std::vector< HistogramType::ConstPointer > mitk::ImageStatisticsCalculator::HistogramContainer

Definition at line 267 of file old/mitkImageStatisticsCalculator.h.

typedef itk::Statistics::Histogram<double> mitk::ImageStatisticsCalculator::HistogramType

Definition at line 31 of file mitkImageStatisticsCalculator.h.

typedef itk::Statistics::Histogram<double> mitk::ImageStatisticsCalculator::HistogramType

Definition at line 171 of file old/mitkImageStatisticsCalculator.h.

typedef std::vector< HistogramContainer > mitk::ImageStatisticsCalculator::HistogramVector

protected

Definition at line 378 of file old/mitkImageStatisticsCalculator.h.

typedef itk::Image< unsigned short, 2 > mitk::ImageStatisticsCalculator::MaskImage2DType

protected

Definition at line 385 of file old/mitkImageStatisticsCalculator.h.

typedef itk::Image< unsigned short, 3 > mitk::ImageStatisticsCalculator::MaskImage3DType

protected

Definition at line 384 of file old/mitkImageStatisticsCalculator.h.

typedef unsigned short mitk::ImageStatisticsCalculator::MaskPixelType

Definition at line 32 of file mitkImageStatisticsCalculator.h.

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

Definition at line 20 of file mitkImageStatisticsCalculator.h.

typedef ImageStatisticsCalculator mitk::ImageStatisticsCalculator::Self

Standard Self typedef

Definition at line 18 of file mitkImageStatisticsCalculator.h.

typedef std::vector< Statistics > mitk::ImageStatisticsCalculator::StatisticsContainer

Definition at line 268 of file old/mitkImageStatisticsCalculator.h.

typedef std::map<std::string, statisticsValueType> mitk::ImageStatisticsCalculator::statisticsMapType

Definition at line 30 of file mitkImageStatisticsCalculator.h.

typedef double mitk::ImageStatisticsCalculator::statisticsValueType

Definition at line 29 of file mitkImageStatisticsCalculator.h.

typedef std::vector< StatisticsContainer > mitk::ImageStatisticsCalculator::StatisticsVector

protected

Definition at line 379 of file old/mitkImageStatisticsCalculator.h.

typedef itk::Object mitk::ImageStatisticsCalculator::Superclass

Definition at line 19 of file mitkImageStatisticsCalculator.h.

typedef std::vector< itk::TimeStamp > mitk::ImageStatisticsCalculator::TimeStampVectorType

protected

Definition at line 381 of file old/mitkImageStatisticsCalculator.h.

Member Enumeration Documentation

anonymous enum

Enum for possible masking modi.

Enumerator
MASKING_MODE_NONE
MASKING_MODE_IMAGE
MASKING_MODE_PLANARFIGURE

Definition at line 164 of file old/mitkImageStatisticsCalculator.h.

Constructor & Destructor Documentation

mitk::ImageStatisticsCalculator::ImageStatisticsCalculator ( )

inlineprotected

Definition at line 366 of file mitkImageStatisticsCalculator.h.

mitk::ImageStatisticsCalculator::ImageStatisticsCalculator ( )

protected

mitk::ImageStatisticsCalculator::~ImageStatisticsCalculator ( )

protectedvirtual

Definition at line 105 of file old/mitkImageStatisticsCalculator.cpp.

Member Function Documentation

template<unsigned int VImageDimension>

itk::Size< VImageDimension > mitk::ImageStatisticsCalculator::CalculateConvolutionKernelSize ( double  spacing[VImageDimension], double  radiusInMM  )

protected

Returns size of convolution kernel depending on spacing and radius.

Definition at line 1759 of file old/mitkImageStatisticsCalculator.cpp.

template<typename TPixel , unsigned int VImageDimension>

ImageStatisticsCalculator::ImageExtrema mitk::ImageStatisticsCalculator::CalculateExtremaWorld ( const itk::Image< TPixel, VImageDimension > *  inputImage, itk::Image< unsigned short, VImageDimension > *  maskImage, double  neccessaryDistanceToImageBorderInMM, unsigned int  label  )

protected

Calculates minimum, maximum, mean value and their corresponding indices in a given ROI. As input the function needs an image and a mask. Returns an ImageExtrema object.

Definition at line 1629 of file old/mitkImageStatisticsCalculator.cpp.

References mitk::ImageStatisticsCalculator::ImageExtrema::Defined, max(), mitk::ImageStatisticsCalculator::ImageExtrema::Max, mitk::ImageStatisticsCalculator::ImageExtrema::MaxIndex, min(), mitk::ImageStatisticsCalculator::ImageExtrema::Min, and mitk::ImageStatisticsCalculator::ImageExtrema::MinIndex.

Referenced by CalculateHotspotStatistics().

template<typename TPixel , unsigned int VImageDimension>

ImageStatisticsCalculator::Statistics mitk::ImageStatisticsCalculator::CalculateHotspotStatistics ( const itk::Image< TPixel, VImageDimension > *  inputImage, itk::Image< unsigned short, VImageDimension > *  maskImage, double  radiusInMM, bool &  isHotspotDefined, unsigned int  label  )

protected

Calculates the hotspot statistics depending on masking mode. Hotspot statistics are calculated for a hotspot which is completly located inside the image by default.

Definition at line 1946 of file old/mitkImageStatisticsCalculator.cpp.

References CalculateExtremaWorld(), mitk::ImageStatisticsCalculator::ImageExtrema::Defined, FillHotspotMaskPixels(), GenerateConvolutionImage(), mitk::ImageStatisticsCalculator::Statistics::GetMax(), mitk::ImageStatisticsCalculator::Statistics::GetMean(), mitk::ImageStatisticsCalculator::Statistics::GetMin(), mitk::ImageStatisticsCalculator::Statistics::GetSigma(), m_EmptyStatistics, m_HotspotMustBeCompletelyInsideImage, m_HotspotRadiusInMM, mitk::ImageStatisticsCalculator::ImageExtrema::Max, mitk::ImageStatisticsCalculator::ImageExtrema::MaxIndex, MITK_DEBUG, MITK_ERROR, mitk::New(), mitk::ImageStatisticsCalculator::Statistics::Reset(), mitk::ImageStatisticsCalculator::Statistics::SetHotspotIndex(), mitk::ImageStatisticsCalculator::Statistics::SetLabel(), mitk::ImageStatisticsCalculator::Statistics::SetMax(), mitk::ImageStatisticsCalculator::Statistics::SetMean(), mitk::ImageStatisticsCalculator::Statistics::SetMedian(), mitk::ImageStatisticsCalculator::Statistics::SetMin(), mitk::ImageStatisticsCalculator::Statistics::SetN(), mitk::ImageStatisticsCalculator::Statistics::SetRMS(), mitk::ImageStatisticsCalculator::Statistics::SetSigma(), and mitk::ImageStatisticsCalculator::Statistics::SetVariance().

Referenced by InternalCalculateStatisticsMasked(), and InternalCalculateStatisticsUnmasked().

Pointer mitk::ImageStatisticsCalculator::Clone

(

)

const

bool mitk::ImageStatisticsCalculator::ComputeStatistics ( unsigned int  timeStep = 0 )

virtual

Compute statistics (together with histogram) for the current masking mode.

Computation is not executed if statistics is already up to date. In this case, false is returned; otherwise, true.

Definition at line 593 of file old/mitkImageStatisticsCalculator.cpp.

References AccessFixedDimensionByItk_2, AccessFixedDimensionByItk_3, ExtractImageAndMask(), m_DoIgnorePixelValue, m_HotspotRadiusInMMChanged, m_IgnorePixelValueChanged, m_ImageHistogramVector, m_ImageMask, m_ImageStatisticsCalculationTriggerVector, m_ImageStatisticsTimeStampVector, m_ImageStatisticsVector, m_InternalImage, m_InternalImageMask2D, m_InternalImageMask3D, m_MaskedImageHistogramVector, m_MaskedImageStatisticsCalculationTriggerVector, m_MaskedImageStatisticsTimeStampVector, m_MaskedImageStatisticsVector, m_MaskingMode, m_MaskingModeChanged, m_PlanarFigure, m_PlanarFigureHistogramVector, m_PlanarFigureStatisticsCalculationTriggerVector, m_PlanarFigureStatisticsTimeStampVector, m_PlanarFigureStatisticsVector, MASKING_MODE_IMAGE, MASKING_MODE_NONE, MASKING_MODE_PLANARFIGURE, MITK_ERROR, and mitkThrow.

template<typename ITK_Exporter , typename VTK_Importer >

void mitk::ImageStatisticsCalculator::ConnectPipelines ( ITK_Exporter  exporter, vtkSmartPointer< VTK_Importer >  importer  )

inlineprotected

Connection from ITK to VTK

Definition at line 476 of file old/mitkImageStatisticsCalculator.h.

Referenced by InternalCalculateMaskFromPlanarFigure().

template<typename VTK_Exporter , typename ITK_Importer >

void mitk::ImageStatisticsCalculator::ConnectPipelines ( vtkSmartPointer< VTK_Exporter >  exporter, ITK_Importer  importer  )

inlineprotected

Connection from VTK to ITK

Definition at line 497 of file old/mitkImageStatisticsCalculator.h.

void mitk::ImageStatisticsCalculator::ExtractImageAndMask ( unsigned int  timeStep = 0 )

protected

Depending on the masking mode, the image and mask from which to calculate statistics is extracted from the original input image and mask data.

For example, a when using a PlanarFigure as mask, the 2D image slice corresponding to the PlanarFigure will be extracted from the original image. If masking is disabled, the original image is simply passed through.

Definition at line 892 of file old/mitkImageStatisticsCalculator.cpp.

References AccessFixedDimensionByItk_1, mitk::CastToItkImage(), mitk::Image::Clone(), mitk::PixelType::GetComponentType(), mitk::Image::GetDimension(), mitk::BaseData::GetGeometry(), mitk::PlaneGeometry::GetNormal(), mitk::BaseGeometry::GetOrigin(), mitk::Image::GetPixelType(), GetPrincipalAxis(), InternalCalculateMaskFromPlanarFigure(), InternalMaskIgnoredPixels(), m_DoIgnorePixelValue, m_ImageMask, m_InternalImage, m_InternalImageMask2D, m_InternalImageMask3D, m_MaskingMode, m_PlanarFigure, m_PlanarFigureAxis, m_PlanarFigureSlice, MASKING_MODE_IMAGE, MASKING_MODE_NONE, MASKING_MODE_PLANARFIGURE, mitk::ImageTimeSelector::New(), mitk::ExtractImageFilter::New(), and mitk::BaseGeometry::WorldToIndex().

Referenced by ComputeStatistics().

template<typename TPixel , unsigned int VImageDimension>

void mitk::ImageStatisticsCalculator::FillHotspotMaskPixels ( itk::Image< TPixel, VImageDimension > *  maskImage, itk::Point< double, VImageDimension >  sphereCenter, double  sphereRadiusInMM  )

protected

Fills pixels of the spherical hotspot mask.

Definition at line 1924 of file old/mitkImageStatisticsCalculator.cpp.

Referenced by CalculateHotspotStatistics().

template<typename TPixel , unsigned int VImageDimension>

itk::SmartPointer< itk::Image< TPixel, VImageDimension > > mitk::ImageStatisticsCalculator::GenerateConvolutionImage ( const itk::Image< TPixel, VImageDimension > *  inputImage )

protected

Convolves image with spherical kernel image. Used for hotspot calculation.

Definition at line 1878 of file old/mitkImageStatisticsCalculator.cpp.

References GetHotspotMustBeCompletlyInsideImage(), m_HotspotRadiusInMM, m_HotspotRadiusInMMChanged, MITK_DEBUG, and mitk::New().

Referenced by CalculateHotspotStatistics().

template<unsigned int VImageDimension>

itk::SmartPointer< itk::Image< float, VImageDimension > > mitk::ImageStatisticsCalculator::GenerateHotspotSearchConvolutionKernel ( double  spacing[VImageDimension], double  radiusInMM  )

protected

Generates image of kernel which is needed for convolution.

Definition at line 1781 of file old/mitkImageStatisticsCalculator.cpp.

References MITK_DEBUG, and mitk::New().

ImageStatisticsCalculator::BinFrequencyType mitk::ImageStatisticsCalculator::GetBinsAndFreuqencyForHistograms	(	unsigned int	timeStep = 0,
		unsigned int	label = 0
	)		const

Definition at line 763 of file old/mitkImageStatisticsCalculator.cpp.

References GetHistogram().

double mitk::ImageStatisticsCalculator::GetBinSizeForHistogramStatistics

(

)

const

Retrieve the bin size for histogram statistics. Careful: The return value does not indicate whether NBins or BinSize is used. That solely depends on which parameter has been set last.

Documentation

Definition at line 108 of file mitkImageStatisticsCalculator.cpp.

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

virtual

Runtime information support.

bool mitk::ImageStatisticsCalculator::GetDoIgnorePixelValue

(

)

Get whether a pixel value will be ignored in the statistics.

Definition at line 460 of file old/mitkImageStatisticsCalculator.cpp.

References m_DoIgnorePixelValue.

const ImageStatisticsCalculator::HistogramType * mitk::ImageStatisticsCalculator::GetHistogram	(	unsigned int	timeStep = 0,
		unsigned int	label = 0
	)		const

Retrieve the histogram depending on the current masking mode.

Parameters

label

The label for which to retrieve the histogram in multi-label situations (ascending order).

Definition at line 784 of file old/mitkImageStatisticsCalculator.cpp.

References m_DoIgnorePixelValue, m_ImageHistogramVector, m_MaskedImageHistogramVector, m_MaskingMode, m_PlanarFigureHistogramVector, MASKING_MODE_IMAGE, MASKING_MODE_NONE, and MASKING_MODE_PLANARFIGURE.

Referenced by GetBinsAndFreuqencyForHistograms().

double mitk::ImageStatisticsCalculator::GetHistogramBinSize

(

)

Get bin size for histogram resolution.

Definition at line 469 of file old/mitkImageStatisticsCalculator.cpp.

References m_HistogramBinSize.

const ImageStatisticsCalculator::HistogramContainer & mitk::ImageStatisticsCalculator::GetHistogramVector

(

unsigned int

timeStep = 0

)

const

Retrieve the histogram depending on the current masking mode (for all image labels.

Definition at line 811 of file old/mitkImageStatisticsCalculator.cpp.

References m_DoIgnorePixelValue, m_EmptyHistogramContainer, m_ImageHistogramVector, m_MaskedImageHistogramVector, m_MaskingMode, m_PlanarFigureHistogramVector, MASKING_MODE_IMAGE, MASKING_MODE_NONE, and MASKING_MODE_PLANARFIGURE.

bool mitk::ImageStatisticsCalculator::GetHotspotMustBeCompletlyInsideImage

(

)

const

Returns true if hotspot has to be completly inside the image.

Definition at line 518 of file old/mitkImageStatisticsCalculator.cpp.

References m_HotspotMustBeCompletelyInsideImage.

Referenced by GenerateConvolutionImage().

double mitk::ImageStatisticsCalculator::GetHotspotRadiusInMM

(

)

Returns the radius of the hotspot.

Definition at line 488 of file old/mitkImageStatisticsCalculator.cpp.

References m_HotspotRadiusInMM.

Referenced by InternalCalculateStatisticsMasked().

double mitk::ImageStatisticsCalculator::GetIgnorePixelValue

(

)

Get the pixel value for pixels that will be ignored in the statistics.

Definition at line 445 of file old/mitkImageStatisticsCalculator.cpp.

References m_IgnorePixelValue.

virtual unsigned int mitk::ImageStatisticsCalculator::GetMaskingMode ( )

virtual

Set/Get operation mode for masking.

template<typename TPixel , unsigned int VImageDimension>

void mitk::ImageStatisticsCalculator::GetMinAndMaxValue ( double &  minimum, double &  maximum, int &  counter, double &  sigma, const itk::Image< TPixel, VImageDimension > *  InputImage, itk::Image< unsigned short, VImageDimension > *  MaskImageType  )

protected

Definition at line 526 of file old/mitkImageStatisticsCalculator.cpp.

Referenced by InternalCalculateStatisticsMasked().

unsigned int mitk::ImageStatisticsCalculator::GetNBinsForHistogramStatistics

(

)

const

Retrieve the number of bins used for histogram statistics. Careful: The return value does not indicate whether NBins or BinSize is used. That solely depends on which parameter has been set last.

Documentation

Definition at line 88 of file mitkImageStatisticsCalculator.cpp.

bool mitk::ImageStatisticsCalculator::GetPrincipalAxis ( const BaseGeometry *  geometry, Vector3D  vector, unsigned int &  axis  )

protected

If the passed vector matches any of the three principal axes of the passed geometry, the ínteger value corresponding to the axis is set and true is returned.

Definition at line 1068 of file old/mitkImageStatisticsCalculator.cpp.

References mitk::eps, and mitk::BaseGeometry::GetAxisVector().

Referenced by ExtractImageAndMask().

ImageStatisticsCalculator::StatisticsContainer::Pointer mitk::ImageStatisticsCalculator::GetStatistics	(	unsigned int	timeStep = 0,
		unsigned int	label = 1
	)

Returns the statistics for label label and timeStep timeStep. If these requested statistics are not computed yet the computation is done as well. For performance reasons, statistics for all labels in the image are computed at once.

Documentation

Definition at line 113 of file mitkImageStatisticsCalculator.cpp.

References AccessByItk_1, MITK_WARN, mitkThrow, mitk::ImageTimeSelector::New(), and mitk::ImageStatisticsCalculator::StatisticsContainer::New().

const ImageStatisticsCalculator::Statistics & mitk::ImageStatisticsCalculator::GetStatistics	(	unsigned int	timeStep = 0,
		unsigned int	label = 0
	)		const

Retrieve statistics depending on the current masking mode.

Parameters

label

The label for which to retrieve the statistics in multi-label situations (ascending order).

Definition at line 839 of file old/mitkImageStatisticsCalculator.cpp.

References m_DoIgnorePixelValue, m_EmptyStatistics, m_ImageStatisticsVector, m_MaskedImageStatisticsVector, m_MaskingMode, m_PlanarFigureStatisticsVector, MASKING_MODE_IMAGE, MASKING_MODE_NONE, and MASKING_MODE_PLANARFIGURE.

const ImageStatisticsCalculator::StatisticsContainer & mitk::ImageStatisticsCalculator::GetStatisticsVector

(

unsigned int

timeStep = 0

)

const

Retrieve statistics depending on the current masking mode (for all image labels).

Definition at line 865 of file old/mitkImageStatisticsCalculator.cpp.

References m_DoIgnorePixelValue, m_EmptyStatisticsContainer, m_ImageStatisticsVector, m_MaskedImageStatisticsVector, m_MaskingMode, m_PlanarFigureStatisticsVector, MASKING_MODE_IMAGE, MASKING_MODE_NONE, and MASKING_MODE_PLANARFIGURE.

template<typename TPixel , unsigned int VImageDimension>

void mitk::ImageStatisticsCalculator::InternalCalculateMaskFromPlanarFigure ( const itk::Image< TPixel, VImageDimension > *  image, unsigned int  axis  )

protected

Definition at line 2045 of file old/mitkImageStatisticsCalculator.cpp.

References ConnectPipelines(), mitk::eps, mitk::BaseGeometry::IsInside(), m_InternalImageMask2D, m_PlanarFigure, m_PlanarFigureCoordinate0, m_PlanarFigureCoordinate1, mitk::PlaneGeometry::Map(), mitkThrow, mitk::New(), and mitk::BaseGeometry::WorldToIndex().

Referenced by ExtractImageAndMask().

template<typename TPixel , unsigned int VImageDimension>

void mitk::ImageStatisticsCalculator::InternalCalculateStatisticsMasked ( const itk::Image< TPixel, VImageDimension > *  image, itk::Image< unsigned short, VImageDimension > *  maskImage, StatisticsContainer *  statisticsContainer, HistogramContainer *  histogramContainer  )

protected

Definition at line 1275 of file old/mitkImageStatisticsCalculator.cpp.

References CalculateHotspotStatistics(), mitk::eps, mitk::ImageStatisticsCalculator::Statistics::GetHotspotIndex(), GetHotspotRadiusInMM(), mitk::ImageStatisticsCalculator::Statistics::GetHotspotStatistics(), mitk::ImageStatisticsCalculator::Statistics::GetMax(), mitk::ImageStatisticsCalculator::Statistics::GetMean(), mitk::ImageStatisticsCalculator::Statistics::GetMin(), GetMinAndMaxValue(), mitk::ImageStatisticsCalculator::Statistics::GetSigma(), mitk::ImageStatisticsCalculator::Statistics::HasHotspotStatistics(), IsHotspotCalculated(), m_EmptyHistogram, m_HistogramBinSize, m_MaskingMode, m_PlanarFigureAxis, m_PlanarFigureCoordinate0, m_PlanarFigureCoordinate1, m_PlanarFigureSlice, m_UseBinSizeBasedOnVOIRegion, m_UseDefaultBinSize, MaskedStatisticsProgressUpdate(), MASKING_MODE_PLANARFIGURE, MITK_DEBUG, MITK_ERROR, mitkThrow, mitk::New(), offset, mitk::ImageStatisticsCalculator::Statistics::SetEntropy(), mitk::ImageStatisticsCalculator::Statistics::SetHotspotIndex(), mitk::ImageStatisticsCalculator::Statistics::SetKurtosis(), mitk::ImageStatisticsCalculator::Statistics::SetLabel(), mitk::ImageStatisticsCalculator::Statistics::SetMax(), mitk::ImageStatisticsCalculator::Statistics::SetMaxIndex(), mitk::ImageStatisticsCalculator::Statistics::SetMean(), mitk::ImageStatisticsCalculator::Statistics::SetMedian(), mitk::ImageStatisticsCalculator::Statistics::SetMin(), mitk::ImageStatisticsCalculator::Statistics::SetMinIndex(), mitk::ImageStatisticsCalculator::Statistics::SetMPP(), mitk::ImageStatisticsCalculator::Statistics::SetN(), mitk::ImageStatisticsCalculator::Statistics::SetRMS(), mitk::ImageStatisticsCalculator::Statistics::SetSigma(), mitk::ImageStatisticsCalculator::Statistics::SetSkewness(), mitk::ImageStatisticsCalculator::Statistics::SetUniformity(), mitk::ImageStatisticsCalculator::Statistics::SetUPP(), and mitk::ImageStatisticsCalculator::Statistics::SetVariance().

template<typename TPixel , unsigned int VImageDimension>

void mitk::ImageStatisticsCalculator::InternalCalculateStatisticsUnmasked ( const itk::Image< TPixel, VImageDimension > *  image, StatisticsContainer *  statisticsContainer, HistogramContainer *  histogramContainer  )

protected

Definition at line 1096 of file old/mitkImageStatisticsCalculator.cpp.

References CalculateHotspotStatistics(), mitk::ImageStatisticsCalculator::Statistics::GetHotspotIndex(), mitk::ImageStatisticsCalculator::Statistics::GetHotspotStatistics(), mitk::ImageStatisticsCalculator::Statistics::GetMax(), mitk::ImageStatisticsCalculator::Statistics::GetMaxIndex(), mitk::ImageStatisticsCalculator::Statistics::GetMean(), mitk::ImageStatisticsCalculator::Statistics::GetMin(), mitk::ImageStatisticsCalculator::Statistics::GetMinIndex(), mitk::ImageStatisticsCalculator::Statistics::GetSigma(), mitk::ImageStatisticsCalculator::Statistics::HasHotspotStatistics(), IsHotspotCalculated(), m_HistogramBinSize, m_HotspotRadiusInMM, m_UseDefaultBinSize, MITK_DEBUG, MITK_ERROR, mitkThrow, mitk::New(), mitk::ImageStatisticsCalculator::Statistics::Reset(), mitk::ImageStatisticsCalculator::Statistics::SetEntropy(), mitk::ImageStatisticsCalculator::Statistics::SetHasHotspotStatistics(), mitk::ImageStatisticsCalculator::Statistics::SetHotspotIndex(), mitk::ImageStatisticsCalculator::Statistics::SetKurtosis(), mitk::ImageStatisticsCalculator::Statistics::SetLabel(), mitk::ImageStatisticsCalculator::Statistics::SetMax(), mitk::ImageStatisticsCalculator::Statistics::SetMean(), mitk::ImageStatisticsCalculator::Statistics::SetMedian(), mitk::ImageStatisticsCalculator::Statistics::SetMin(), mitk::ImageStatisticsCalculator::Statistics::SetMinIndex(), mitk::ImageStatisticsCalculator::Statistics::SetMPP(), mitk::ImageStatisticsCalculator::Statistics::SetN(), mitk::ImageStatisticsCalculator::Statistics::SetRMS(), mitk::ImageStatisticsCalculator::Statistics::SetSigma(), mitk::ImageStatisticsCalculator::Statistics::SetSkewness(), mitk::ImageStatisticsCalculator::Statistics::SetUniformity(), mitk::ImageStatisticsCalculator::Statistics::SetUPP(), mitk::ImageStatisticsCalculator::Statistics::SetVariance(), and UnmaskedStatisticsProgressUpdate().

template<typename TPixel , unsigned int VImageDimension>

void mitk::ImageStatisticsCalculator::InternalMaskIgnoredPixels ( const itk::Image< TPixel, VImageDimension > *  image, itk::Image< unsigned short, VImageDimension > *  maskImage  )

protected

Definition at line 1247 of file old/mitkImageStatisticsCalculator.cpp.

References m_IgnorePixelValue.

Referenced by ExtractImageAndMask().

bool mitk::ImageStatisticsCalculator::IsHotspotCalculated

(

)

Returns true whether the hotspot should be calculated, otherwise false.

Definition at line 504 of file old/mitkImageStatisticsCalculator.cpp.

References m_CalculateHotspot.

Referenced by InternalCalculateStatisticsMasked(), and InternalCalculateStatisticsUnmasked().

void mitk::ImageStatisticsCalculator::MaskedStatisticsProgressUpdate ( )

protected

Definition at line 2241 of file old/mitkImageStatisticsCalculator.cpp.

Referenced by InternalCalculateStatisticsMasked().

mitk::ImageStatisticsCalculator::mitkClassMacroItkParent	(	ImageStatisticsCalculator	,
		itk::Object
	)

static Pointer mitk::ImageStatisticsCalculator::New ( )

static

Method for creation through the object factory.

Referenced by compute_statistics(), ExtractImageStatistics(), mitk::FeatureBasedEdgeDetectionFilter::GenerateData(), and main().

static Pointer mitk::ImageStatisticsCalculator::New ( )

static

void mitk::ImageStatisticsCalculator::SetBinSizeForHistogramStatistics

(

double

binSize

)

Set bin size to be used for histogram statistics. If nbins is set after bin size, nbins will be used instead!

Documentation

Definition at line 93 of file mitkImageStatisticsCalculator.cpp.

void mitk::ImageStatisticsCalculator::SetCalculateHotspot

(

bool

calculateHotspot

)

Sets whether the hotspot should be calculated.

Definition at line 493 of file old/mitkImageStatisticsCalculator.cpp.

References m_CalculateHotspot, and m_HotspotRadiusInMMChanged.

void mitk::ImageStatisticsCalculator::SetDoIgnorePixelValue

(

bool

doit

)

Set whether a pixel value should be ignored in the statistics.

Definition at line 450 of file old/mitkImageStatisticsCalculator.cpp.

References m_DoIgnorePixelValue, and m_IgnorePixelValueChanged.

void mitk::ImageStatisticsCalculator::SetHistogramBinSize

(

double

size

)

Set bin size for histogram resolution.

Definition at line 465 of file old/mitkImageStatisticsCalculator.cpp.

References m_HistogramBinSize.

void mitk::ImageStatisticsCalculator::SetHotspotMustBeCompletlyInsideImage	(	bool	hotspotIsCompletlyInsideImage,
		bool	warn = true
	)

Sets flag whether hotspot is completly inside the image. Please note that if set to false it can be possible that statistics are calculated for which the whole hotspot is not inside the image!

Warning

regarding positions at the image centers may produce unexpected hotspot locations, please see Hotspot Definition

Definition at line 509 of file old/mitkImageStatisticsCalculator.cpp.

References m_HotspotMustBeCompletelyInsideImage, and MITK_WARN.

void mitk::ImageStatisticsCalculator::SetHotspotRadiusInMM

(

double

hotspotRadiusInMM

)

Sets the radius for the hotspot.

Definition at line 474 of file old/mitkImageStatisticsCalculator.cpp.

References m_CalculateHotspot, m_HotspotRadiusInMM, and m_HotspotRadiusInMMChanged.

void mitk::ImageStatisticsCalculator::SetIgnorePixelValue

(

double

value

)

Set a pixel value for pixels that will be ignored in the statistics.

Definition at line 432 of file old/mitkImageStatisticsCalculator.cpp.

References m_DoIgnorePixelValue, m_IgnorePixelValue, and m_IgnorePixelValueChanged.

void mitk::ImageStatisticsCalculator::SetImage

(

const mitk::Image *

image

)

Set image from which to compute statistics.

Definition at line 313 of file old/mitkImageStatisticsCalculator.cpp.

References mitk::BaseData::GetTimeSteps(), m_ImageHistogramVector, m_ImageStatisticsCalculationTriggerVector, m_ImageStatisticsTimeStampVector, m_ImageStatisticsVector, m_MaskedImageHistogramVector, m_MaskedImageStatisticsCalculationTriggerVector, m_MaskedImageStatisticsTimeStampVector, m_MaskedImageStatisticsVector, m_PlanarFigureHistogramVector, m_PlanarFigureStatisticsCalculationTriggerVector, m_PlanarFigureStatisticsTimeStampVector, and m_PlanarFigureStatisticsVector.

void mitk::ImageStatisticsCalculator::SetImageMask

(

const mitk::Image *

imageMask

)

Set image for masking.

Definition at line 347 of file old/mitkImageStatisticsCalculator.cpp.

References m_ImageMask, m_MaskedImageStatisticsCalculationTriggerVector, and m_MaskedImageStatisticsTimeStampVector.

void mitk::ImageStatisticsCalculator::SetInputImage

(

mitk::Image::Pointer

image

)

Set the image for which the statistics are to be computed.

Documentation

Definition at line 38 of file mitkImageStatisticsCalculator.cpp.

void mitk::ImageStatisticsCalculator::SetMask

(

mitk::MaskGenerator::Pointer

mask

)

Set the mask generator that creates the mask which is to be used to calculate statistics. If no more mask is desired simply set.

Documentation

Parameters

mask	to nullptr

Definition at line 50 of file mitkImageStatisticsCalculator.cpp.

void mitk::ImageStatisticsCalculator::SetMaskingMode

(

unsigned int

mode

)

Set/Get operation mode for masking.

Definition at line 389 of file old/mitkImageStatisticsCalculator.cpp.

References m_MaskingMode, and m_MaskingModeChanged.

void mitk::ImageStatisticsCalculator::SetMaskingModeToImage

(

)

Set/Get operation mode for masking.

Definition at line 411 of file old/mitkImageStatisticsCalculator.cpp.

References m_MaskingMode, m_MaskingModeChanged, and MASKING_MODE_IMAGE.

void mitk::ImageStatisticsCalculator::SetMaskingModeToNone

(

)

Set/Get operation mode for masking.

Definition at line 400 of file old/mitkImageStatisticsCalculator.cpp.

References m_MaskingMode, m_MaskingModeChanged, and MASKING_MODE_NONE.

void mitk::ImageStatisticsCalculator::SetMaskingModeToPlanarFigure

(

)

Set/Get operation mode for masking.

Definition at line 422 of file old/mitkImageStatisticsCalculator.cpp.

References m_MaskingMode, m_MaskingModeChanged, and MASKING_MODE_PLANARFIGURE.

void mitk::ImageStatisticsCalculator::SetNBinsForHistogramStatistics

(

unsigned int

nBins

)

Set number of bins to be used for histogram statistics. If Bin size is set after number of bins, bin size will be used instead!

Documentation

Definition at line 73 of file mitkImageStatisticsCalculator.cpp.

void mitk::ImageStatisticsCalculator::SetPlanarFigure

(

mitk::PlanarFigure *

planarFigure

)

Set planar figure for masking.

Definition at line 368 of file old/mitkImageStatisticsCalculator.cpp.

References m_PlanarFigure, m_PlanarFigureStatisticsCalculationTriggerVector, and m_PlanarFigureStatisticsTimeStampVector.

void mitk::ImageStatisticsCalculator::SetSecondaryMask

(

mitk::MaskGenerator::Pointer

mask

)

Set this if more than one mask should be applied (for instance if a IgnorePixelValueMask were to be used alongside with a segmentation). Both masks are combined using pixel wise AND operation. The secondary mask does not have to be the same size than the primary but they need to have some overlap.

Documentation

Definition at line 61 of file mitkImageStatisticsCalculator.cpp.

void mitk::ImageStatisticsCalculator::SetUseDefaultBinSize

(

bool

useDefault

)

Automatically calculate bin size to obtain 200 bins.

Definition at line 110 of file old/mitkImageStatisticsCalculator.cpp.

References m_UseDefaultBinSize.

void mitk::ImageStatisticsCalculator::UnmaskedStatisticsProgressUpdate ( )

protected

Definition at line 2229 of file old/mitkImageStatisticsCalculator.cpp.

Referenced by InternalCalculateStatisticsUnmasked().

Member Data Documentation

bool mitk::ImageStatisticsCalculator::m_CalculateHotspot

protected

Definition at line 595 of file old/mitkImageStatisticsCalculator.h.

Referenced by IsHotspotCalculated(), SetCalculateHotspot(), and SetHotspotRadiusInMM().

bool mitk::ImageStatisticsCalculator::m_DoIgnorePixelValue

protected

Definition at line 583 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), ExtractImageAndMask(), GetDoIgnorePixelValue(), GetHistogram(), GetHistogramVector(), GetStatistics(), GetStatisticsVector(), SetDoIgnorePixelValue(), and SetIgnorePixelValue().

HistogramType::Pointer mitk::ImageStatisticsCalculator::m_EmptyHistogram

protected

Definition at line 554 of file old/mitkImageStatisticsCalculator.h.

Referenced by InternalCalculateStatisticsMasked().

HistogramContainer mitk::ImageStatisticsCalculator::m_EmptyHistogramContainer

protected

Definition at line 555 of file old/mitkImageStatisticsCalculator.h.

Referenced by GetHistogramVector().

Statistics mitk::ImageStatisticsCalculator::m_EmptyStatistics

protected

Definition at line 563 of file old/mitkImageStatisticsCalculator.h.

Referenced by CalculateHotspotStatistics(), and GetStatistics().

StatisticsContainer mitk::ImageStatisticsCalculator::m_EmptyStatisticsContainer

protected

Definition at line 564 of file old/mitkImageStatisticsCalculator.h.

Referenced by GetStatisticsVector().

double mitk::ImageStatisticsCalculator::m_HistogramBinSize

protected

Definition at line 591 of file old/mitkImageStatisticsCalculator.h.

Referenced by GetHistogramBinSize(), InternalCalculateStatisticsMasked(), InternalCalculateStatisticsUnmasked(), and SetHistogramBinSize().

bool mitk::ImageStatisticsCalculator::m_HotspotMustBeCompletelyInsideImage

protected

Definition at line 597 of file old/mitkImageStatisticsCalculator.h.

Referenced by CalculateHotspotStatistics(), GetHotspotMustBeCompletlyInsideImage(), and SetHotspotMustBeCompletlyInsideImage().

double mitk::ImageStatisticsCalculator::m_HotspotRadiusInMM

protected

Definition at line 594 of file old/mitkImageStatisticsCalculator.h.

Referenced by CalculateHotspotStatistics(), GenerateConvolutionImage(), GetHotspotRadiusInMM(), InternalCalculateStatisticsUnmasked(), and SetHotspotRadiusInMM().

bool mitk::ImageStatisticsCalculator::m_HotspotRadiusInMMChanged

protected

Definition at line 596 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), GenerateConvolutionImage(), SetCalculateHotspot(), and SetHotspotRadiusInMM().

double mitk::ImageStatisticsCalculator::m_IgnorePixelValue

protected

Definition at line 582 of file old/mitkImageStatisticsCalculator.h.

Referenced by GetIgnorePixelValue(), InternalMaskIgnoredPixels(), and SetIgnorePixelValue().

bool mitk::ImageStatisticsCalculator::m_IgnorePixelValueChanged

protected

Definition at line 584 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), SetDoIgnorePixelValue(), and SetIgnorePixelValue().

mitk::Image::ConstPointer mitk::ImageStatisticsCalculator::m_Image

protected

m_Image contains the input image (e.g. 2D, 3D, 3D+t)

Definition at line 544 of file old/mitkImageStatisticsCalculator.h.

HistogramVector mitk::ImageStatisticsCalculator::m_ImageHistogramVector

protected

Definition at line 550 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), GetHistogram(), GetHistogramVector(), and SetImage().

mitk::Image::ConstPointer mitk::ImageStatisticsCalculator::m_ImageMask

protected

Definition at line 546 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), ExtractImageAndMask(), and SetImageMask().

BoolVectorType mitk::ImageStatisticsCalculator::m_ImageStatisticsCalculationTriggerVector

protected

Definition at line 578 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), and SetImage().

TimeStampVectorType mitk::ImageStatisticsCalculator::m_ImageStatisticsTimeStampVector

protected

Definition at line 574 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), and SetImage().

StatisticsVector mitk::ImageStatisticsCalculator::m_ImageStatisticsVector

protected

Definition at line 558 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), GetStatistics(), GetStatisticsVector(), and SetImage().

mitk::Image::ConstPointer mitk::ImageStatisticsCalculator::m_InternalImage

protected

m_InternalImage contains a image volume at one time step (e.g. 2D, 3D)

Definition at line 570 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), and ExtractImageAndMask().

MaskImage2DType::Pointer mitk::ImageStatisticsCalculator::m_InternalImageMask2D

protected

Definition at line 572 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), ExtractImageAndMask(), and InternalCalculateMaskFromPlanarFigure().

MaskImage3DType::Pointer mitk::ImageStatisticsCalculator::m_InternalImageMask3D

protected

Definition at line 571 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), and ExtractImageAndMask().

HistogramVector mitk::ImageStatisticsCalculator::m_MaskedImageHistogramVector

protected

Definition at line 551 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), GetHistogram(), GetHistogramVector(), and SetImage().

StatisticsVector mitk::ImageStatisticsCalculator::m_MaskedImageHotspotStatisticsVector

protected

Definition at line 561 of file old/mitkImageStatisticsCalculator.h.

BoolVectorType mitk::ImageStatisticsCalculator::m_MaskedImageStatisticsCalculationTriggerVector

protected

Definition at line 579 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), SetImage(), and SetImageMask().

TimeStampVectorType mitk::ImageStatisticsCalculator::m_MaskedImageStatisticsTimeStampVector

protected

Definition at line 575 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), SetImage(), and SetImageMask().

StatisticsVector mitk::ImageStatisticsCalculator::m_MaskedImageStatisticsVector

protected

Definition at line 559 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), GetStatistics(), GetStatisticsVector(), and SetImage().

unsigned int mitk::ImageStatisticsCalculator::m_MaskingMode

protected

Definition at line 566 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), ExtractImageAndMask(), GetHistogram(), GetHistogramVector(), GetStatistics(), GetStatisticsVector(), InternalCalculateStatisticsMasked(), SetMaskingMode(), SetMaskingModeToImage(), SetMaskingModeToNone(), and SetMaskingModeToPlanarFigure().

bool mitk::ImageStatisticsCalculator::m_MaskingModeChanged

protected

Definition at line 567 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), SetMaskingMode(), SetMaskingModeToImage(), SetMaskingModeToNone(), and SetMaskingModeToPlanarFigure().

mitk::PlanarFigure::Pointer mitk::ImageStatisticsCalculator::m_PlanarFigure

protected

Definition at line 548 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), ExtractImageAndMask(), InternalCalculateMaskFromPlanarFigure(), and SetPlanarFigure().

unsigned int mitk::ImageStatisticsCalculator::m_PlanarFigureAxis

protected

Definition at line 586 of file old/mitkImageStatisticsCalculator.h.

Referenced by ExtractImageAndMask(), and InternalCalculateStatisticsMasked().

int mitk::ImageStatisticsCalculator::m_PlanarFigureCoordinate0

protected

Definition at line 588 of file old/mitkImageStatisticsCalculator.h.

Referenced by InternalCalculateMaskFromPlanarFigure(), and InternalCalculateStatisticsMasked().

int mitk::ImageStatisticsCalculator::m_PlanarFigureCoordinate1

protected

Definition at line 589 of file old/mitkImageStatisticsCalculator.h.

Referenced by InternalCalculateMaskFromPlanarFigure(), and InternalCalculateStatisticsMasked().

HistogramVector mitk::ImageStatisticsCalculator::m_PlanarFigureHistogramVector

protected

Definition at line 552 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), GetHistogram(), GetHistogramVector(), and SetImage().

unsigned int mitk::ImageStatisticsCalculator::m_PlanarFigureSlice

protected

Definition at line 587 of file old/mitkImageStatisticsCalculator.h.

Referenced by ExtractImageAndMask(), and InternalCalculateStatisticsMasked().

BoolVectorType mitk::ImageStatisticsCalculator::m_PlanarFigureStatisticsCalculationTriggerVector

protected

Definition at line 580 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), SetImage(), and SetPlanarFigure().

TimeStampVectorType mitk::ImageStatisticsCalculator::m_PlanarFigureStatisticsTimeStampVector

protected

Definition at line 576 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), SetImage(), and SetPlanarFigure().

StatisticsVector mitk::ImageStatisticsCalculator::m_PlanarFigureStatisticsVector

protected

Definition at line 560 of file old/mitkImageStatisticsCalculator.h.

Referenced by ComputeStatistics(), GetStatistics(), GetStatisticsVector(), and SetImage().

bool mitk::ImageStatisticsCalculator::m_UseBinSizeBasedOnVOIRegion

protected

Definition at line 593 of file old/mitkImageStatisticsCalculator.h.

Referenced by InternalCalculateStatisticsMasked().

bool mitk::ImageStatisticsCalculator::m_UseDefaultBinSize

protected

Bin size for histogram resoluion.

Definition at line 592 of file old/mitkImageStatisticsCalculator.h.

Referenced by InternalCalculateStatisticsMasked(), InternalCalculateStatisticsUnmasked(), and SetUseDefaultBinSize().

---

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

• mitkImageStatisticsCalculator.h
• mitkImageStatisticsCalculator.cpp