Generates interpolations of 2D slices. More...

#include <mitkSegmentationInterpolationController.h>

Inheritance diagram for mitk::SegmentationInterpolationController:

Collaboration diagram for mitk::SegmentationInterpolationController:

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Classes
class	SetChangedSliceOptions
	Protected class of mitk::SegmentationInterpolationController. Don't use (you shouldn't be able to do so)! More...

Public Member Functions
	mitkClassMacroItkParent (SegmentationInterpolationController, itk::Object)

Pointer	Clone () const

void	BlockModified (bool)
	Block reaction to an images Modified() events. More...

void	SetSegmentationVolume (const Image *segmentation)
	Initialize with a whole volume. More...

void	SetReferenceVolume (const Image *segmentation)
	Set a reference image (original patient image) - optional. More...

void	SetChangedSlice (const Image *sliceDiff, unsigned int sliceDimension, unsigned int sliceIndex, unsigned int timeStep)
	Update after changing a single slice. More...

void	SetChangedVolume (const Image *sliceDiff, unsigned int timeStep)

Image::Pointer	Interpolate (unsigned int sliceDimension, unsigned int sliceIndex, const mitk::PlaneGeometry *currentPlane, unsigned int timeStep)
	Generates an interpolated image for the given slice. More...

void	OnImageModified (const itk::EventObject &)

void	Activate2DInterpolation (bool)

Static Public Member Functions
static Pointer	New ()

static SegmentationInterpolationController *	InterpolatorForImage (const Image *)
	Find interpolator for a given image. More...

static SegmentationInterpolationController *	GetInstance ()
	Get existing instance or create a new one. More...

Protected Types
typedef std::vector< unsigned int >	DirtyVectorType

typedef std::vector< std::vector< DirtyVectorType > >	TimeResolvedDirtyVectorType

typedef std::map< const Image , SegmentationInterpolationController >	InterpolatorMapType

Protected Member Functions
	SegmentationInterpolationController ()

	~SegmentationInterpolationController () override

template<typename DATATYPE >
void	ScanChangedSlice (const itk::Image< DATATYPE, 2 > *, const SetChangedSliceOptions &options)
	internal scan of a single slice More...

template<typename TPixel , unsigned int VImageDimension>
void	ScanChangedVolume (const itk::Image< TPixel, VImageDimension > *, unsigned int timeStep)

template<typename DATATYPE >
void	ScanWholeVolume (const itk::Image< DATATYPE, 3 > , const Image volume, unsigned int timeStep)

void	PrintStatus ()

Protected Attributes
TimeResolvedDirtyVectorType	m_SegmentationCountInSlice

Image::ConstPointer	m_Segmentation

Image::ConstPointer	m_ReferenceImage

bool	m_BlockModified

bool	m_2DInterpolationActivated

Static Protected Attributes
static InterpolatorMapType	s_InterpolatorForImage

Detailed Description

Generates interpolations of 2D slices.

See also: QmitkSlicesInterpolator; QmitkInteractiveSegmentation

This class keeps track of the contents of a 3D segmentation image.

Attention: mitk::SegmentationInterpolationController assumes that the image contains pixel values of 0 and 1.

After you set the segmentation image using SetSegmentationVolume(), the whole image is scanned for pixels other than 0. SegmentationInterpolationController registers as an observer to the segmentation image, and repeats the scan whenvever the image is modified.

You can prevent this (time consuming) scan if you do the changes slice-wise and send difference images to SegmentationInterpolationController. For this purpose SetChangedSlice() should be used. mitk::OverwriteImageFilter already does this every time it changes a slice of an image. There is a static method InterpolatorForImage(), which can be used to find out if there already is an interpolator instance for a specified image. OverwriteImageFilter uses this to get to know its interpolator.

SegmentationInterpolationController needs to maintain some information about the image slices (in every dimension). This information is stored internally in m_SegmentationCountInSlice, which is basically three std::vectors (one for each dimension). Each item describes one image dimension, each vector item holds the count of pixels in "its" slice. This is perhaps better to understand from the following picture (where red items just mean to symbolize "there is some segmentation" - in reality there is an integer count).

$Author$

Definition at line 67 of file mitkSegmentationInterpolationController.h.

Member Typedef Documentation

◆ DirtyVectorType

typedef std::vector<unsigned int> mitk::SegmentationInterpolationController::DirtyVectorType

protected

Definition at line 178 of file mitkSegmentationInterpolationController.h.

◆ InterpolatorMapType

typedef std::map<const Image *, SegmentationInterpolationController *> mitk::SegmentationInterpolationController::InterpolatorMapType

protected

Definition at line 182 of file mitkSegmentationInterpolationController.h.

◆ TimeResolvedDirtyVectorType

typedef std::vector<std::vector<DirtyVectorType> > mitk::SegmentationInterpolationController::TimeResolvedDirtyVectorType

protected

Definition at line 181 of file mitkSegmentationInterpolationController.h.

Constructor & Destructor Documentation

◆ SegmentationInterpolationController()

mitk::SegmentationInterpolationController::SegmentationInterpolationController ( )

protected

Definition at line 45 of file mitkSegmentationInterpolationController.cpp.

◆ ~SegmentationInterpolationController()

mitk::SegmentationInterpolationController::~SegmentationInterpolationController ( )

overrideprotected

Definition at line 66 of file mitkSegmentationInterpolationController.cpp.

References s_InterpolatorForImage.

Member Function Documentation

◆ Activate2DInterpolation()

void mitk::SegmentationInterpolationController::Activate2DInterpolation ( bool status )

Activate/Deactivate the 2D interpolation.

Definition at line 50 of file mitkSegmentationInterpolationController.cpp.

References m_2DInterpolationActivated.

◆ BlockModified()

void mitk::SegmentationInterpolationController::BlockModified ( bool block )

Block reaction to an images Modified() events.

Blocking the scan of the whole image is especially useful when you are about to change a single slice of the image. Then you would send a difference image of this single slice to SegmentationInterpolationController but call image->Modified() anyway. Before calling image->Modified() you should block SegmentationInterpolationController's reactions to this modified by using this method.

Definition at line 87 of file mitkSegmentationInterpolationController.cpp.

References m_BlockModified.

Referenced by mitk::DiffImageApplier::ExecuteOperation(), and mitk::OverwriteSliceImageFilter::GenerateData().

◆ Clone()

Pointer mitk::SegmentationInterpolationController::Clone ( ) const

◆ GetInstance()

mitk::SegmentationInterpolationController * mitk::SegmentationInterpolationController::GetInstance ( )

static

Get existing instance or create a new one.

Definition at line 55 of file mitkSegmentationInterpolationController.cpp.

References New().

◆ Interpolate()

mitk::Image::Pointer mitk::SegmentationInterpolationController::Interpolate	(	unsigned int	sliceDimension,
		unsigned int	sliceIndex,
		const mitk::PlaneGeometry *	currentPlane,
		unsigned int	timeStep
	)

Generates an interpolated image for the given slice.

Parameters

sliceDimension	Number of the dimension which is constant for all pixels of the meant slice.
sliceIndex	Which slice to take, in the direction specified by sliceDimension. Count starts from 0.
timeStep	Which time step to use

Definition at line 432 of file mitkSegmentationInterpolationController.cpp.

References mitk::PlaneGeometry::Clone(), mitk::BaseGeometry::GetOrigin(), m_ReferenceImage, m_Segmentation, m_SegmentationCountInSlice, MITK_ERROR, mitk::ShapeBasedInterpolationAlgorithm::New(), and mitk::ExtractSliceFilter::New().

◆ InterpolatorForImage()

mitk::SegmentationInterpolationController * mitk::SegmentationInterpolationController::InterpolatorForImage ( const Image * image )

static

Find interpolator for a given image.

Returns: nullptr if there is no interpolator yet.

This method is useful if several "clients" modify the same image and want to access the interpolations. Then they can share the same object.

Definition at line 31 of file mitkSegmentationInterpolationController.cpp.

References s_InterpolatorForImage.

Referenced by mitk::DiffImageApplier::ExecuteOperation(), and mitk::OverwriteSliceImageFilter::GenerateData().

◆ mitkClassMacroItkParent()

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

◆ New()

static Pointer mitk::SegmentationInterpolationController::New ( )

static

Referenced by GetInstance().

◆ OnImageModified()

void mitk::SegmentationInterpolationController::OnImageModified ( const itk::EventObject & )

Definition at line 79 of file mitkSegmentationInterpolationController.cpp.

References m_2DInterpolationActivated, m_BlockModified, m_Segmentation, and SetSegmentationVolume().

Referenced by SetSegmentationVolume().

◆ PrintStatus()

void mitk::SegmentationInterpolationController::PrintStatus ( )

protected

Definition at line 373 of file mitkSegmentationInterpolationController.cpp.

References m_SegmentationCountInSlice, and MITK_INFO.

◆ ScanChangedSlice()

template<typename DATATYPE >

void mitk::SegmentationInterpolationController::ScanChangedSlice	(	const itk::Image< DATATYPE, 2 > *	,
		const SetChangedSliceOptions &	options
	)

protected

internal scan of a single slice

Definition at line 244 of file mitkSegmentationInterpolationController.cpp.

References mitk::SegmentationInterpolationController::SetChangedSliceOptions::dim0, mitk::SegmentationInterpolationController::SetChangedSliceOptions::dim1, m_SegmentationCountInSlice, mitk::SegmentationInterpolationController::SetChangedSliceOptions::pixelData, mitk::SegmentationInterpolationController::SetChangedSliceOptions::sliceDimension, mitk::SegmentationInterpolationController::SetChangedSliceOptions::sliceIndex, and mitk::SegmentationInterpolationController::SetChangedSliceOptions::timeStep.

Referenced by SetChangedSlice().

◆ ScanChangedVolume()

template<typename TPixel , unsigned int VImageDimension>

void mitk::SegmentationInterpolationController::ScanChangedVolume	(	const itk::Image< TPixel, VImageDimension > *	diffImage,
		unsigned int	timeStep
	)

protected

Definition at line 297 of file mitkSegmentationInterpolationController.cpp.

References m_SegmentationCountInSlice.

Referenced by SetChangedVolume().

◆ ScanWholeVolume()

template<typename DATATYPE >

void mitk::SegmentationInterpolationController::ScanWholeVolume	(	const itk::Image< DATATYPE, 3 > *	,
		const Image *	volume,
		unsigned int	timeStep
	)

protected

Definition at line 352 of file mitkSegmentationInterpolationController.cpp.

References mitk::Image::GetDimension(), mitk::Image::GetVolumeData(), and m_SegmentationCountInSlice.

Referenced by SetSegmentationVolume().

◆ SetChangedSlice()

void mitk::SegmentationInterpolationController::SetChangedSlice	(	const Image *	sliceDiff,
		unsigned int	sliceDimension,
		unsigned int	sliceIndex,
		unsigned int	timeStep
	)

Update after changing a single slice.

Parameters

sliceDiff	is a 2D image with the difference image of the slice determined by sliceDimension and sliceIndex. The difference is (pixel value in the new slice minus pixel value in the old slice).
sliceDimension	Number of the dimension which is constant for all pixels of the meant slice.
sliceIndex	Which slice to take, in the direction specified by sliceDimension. Count starts from 0.
timeStep	Which time step is changed

Definition at line 197 of file mitkSegmentationInterpolationController.cpp.

References AccessFixedDimensionByItk_1, mitk::ImageAccessorBase::GetData(), m_SegmentationCountInSlice, and ScanChangedSlice().

Referenced by mitk::DiffImageApplier::ExecuteOperation(), and mitk::OverwriteSliceImageFilter::GenerateData().

◆ SetChangedVolume()

void mitk::SegmentationInterpolationController::SetChangedVolume	(	const Image *	sliceDiff,
		unsigned int	timeStep
	)

Definition at line 184 of file mitkSegmentationInterpolationController.cpp.

References AccessFixedDimensionByItk_1, mitk::Image::GetDimension(), and ScanChangedVolume().

Referenced by mitk::DiffImageApplier::ExecuteOperation().

◆ SetReferenceVolume()

void mitk::SegmentationInterpolationController::SetReferenceVolume ( const Image * segmentation )

Set a reference image (original patient image) - optional.

If this volume is set (must exactly match the dimensions of the segmentation), the interpolation algorithm may consider image content to improve the interpolated (estimated) segmentation.

Definition at line 155 of file mitkSegmentationInterpolationController.cpp.

References m_ReferenceImage, m_Segmentation, and MITK_WARN.

Referenced by SetSegmentationVolume().

◆ SetSegmentationVolume()

void mitk::SegmentationInterpolationController::SetSegmentationVolume ( const Image * segmentation )

Initialize with a whole volume.

Will scan the volume for segmentation pixels (values other than 0) and fill some internal data structures. You don't have to call this method every time something changes, but only when several slices at once change.

When you change a single slice, call SetChangedSlice() instead.

Definition at line 92 of file mitkSegmentationInterpolationController.cpp.

References AccessFixedDimensionByItk_2, mitk::Image::GetDimension(), m_ReferenceImage, m_Segmentation, m_SegmentationCountInSlice, mitk::ImageTimeSelector::New(), OnImageModified(), s_InterpolatorForImage, ScanWholeVolume(), and SetReferenceVolume().

Referenced by OnImageModified().

Member Data Documentation

◆ m_2DInterpolationActivated

bool mitk::SegmentationInterpolationController::m_2DInterpolationActivated

protected

Definition at line 215 of file mitkSegmentationInterpolationController.h.

Referenced by Activate2DInterpolation(), and OnImageModified().

◆ m_BlockModified

bool mitk::SegmentationInterpolationController::m_BlockModified

protected

Definition at line 214 of file mitkSegmentationInterpolationController.h.

Referenced by BlockModified(), and OnImageModified().

◆ m_ReferenceImage

Image::ConstPointer mitk::SegmentationInterpolationController::m_ReferenceImage

protected

Definition at line 213 of file mitkSegmentationInterpolationController.h.

Referenced by Interpolate(), SetReferenceVolume(), and SetSegmentationVolume().

◆ m_Segmentation

Image::ConstPointer mitk::SegmentationInterpolationController::m_Segmentation

protected

Definition at line 212 of file mitkSegmentationInterpolationController.h.

Referenced by Interpolate(), OnImageModified(), SetReferenceVolume(), and SetSegmentationVolume().

◆ m_SegmentationCountInSlice

TimeResolvedDirtyVectorType mitk::SegmentationInterpolationController::m_SegmentationCountInSlice

protected

An array of flags. One for each dimension of the image. A flag is set, when a slice in a certain dimension has at least one pixel that is not 0 (which would mean that it has to be considered by the interpolation algorithm).

E.g. flags for axial slices are stored in m_SegmentationCountInSlice[0][index].

Enhanced with time steps it is now m_SegmentationCountInSlice[timeStep][0][index]

Definition at line 208 of file mitkSegmentationInterpolationController.h.

Referenced by Interpolate(), PrintStatus(), ScanChangedSlice(), ScanChangedVolume(), ScanWholeVolume(), SetChangedSlice(), and SetSegmentationVolume().

◆ s_InterpolatorForImage

mitk::SegmentationInterpolationController::InterpolatorMapType mitk::SegmentationInterpolationController::s_InterpolatorForImage

staticprotected

Definition at line 210 of file mitkSegmentationInterpolationController.h.

Referenced by InterpolatorForImage(), SetSegmentationVolume(), and ~SegmentationInterpolationController().

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

Classes

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Typedef Documentation

◆ DirtyVectorType

◆ InterpolatorMapType

◆ TimeResolvedDirtyVectorType

Constructor & Destructor Documentation

◆ SegmentationInterpolationController()

◆ ~SegmentationInterpolationController()

Member Function Documentation

◆ Activate2DInterpolation()

◆ BlockModified()

◆ Clone()

◆ GetInstance()

◆ Interpolate()

◆ InterpolatorForImage()

◆ mitkClassMacroItkParent()

◆ New()

◆ OnImageModified()

◆ PrintStatus()

◆ ScanChangedSlice()

◆ ScanChangedVolume()

◆ ScanWholeVolume()

◆ SetChangedSlice()

◆ SetChangedVolume()

◆ SetReferenceVolume()

◆ SetSegmentationVolume()

Member Data Documentation

◆ m_2DInterpolationActivated

◆ m_BlockModified

◆ m_ReferenceImage

◆ m_Segmentation

◆ m_SegmentationCountInSlice

◆ s_InterpolatorForImage