Generates interpolations of 2D slices. More...

#include <mitkSliceBasedInterpolationController.h>

Inheritance diagram for mitk::SliceBasedInterpolationController:

Collaboration diagram for mitk::SliceBasedInterpolationController:

[legend]

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

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

Pointer	Clone () const

void	SetWorkingImage (LabelSetImage *image)
	Initialize with a whole volume. More...

void	SetReferenceImage (Image *image)
	Set a reference image (original patient image) - optional. More...

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

Image::Pointer	Interpolate (unsigned int sliceDimension, unsigned int sliceIndex, const mitk::PlaneGeometry *currentPlane, unsigned int timeStep)
	Update after changing the whole working image. More...

void	ResetLabelCount ()
	Initializes the internal container with the number of voxels per label. More...

Static Public Member Functions
static Pointer	New ()

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

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

typedef std::vector< LabelCounterVectorType >	LabelCounterSliceVectorType

typedef std::vector< std::vector< LabelCounterSliceVectorType > >	LabelCounterSliceTimeVectorType

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

Protected Member Functions
	SliceBasedInterpolationController ()

	~SliceBasedInterpolationController () override

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

template<typename TPixel , unsigned int VImageDimension>
void	ScanImageITKProcessing (itk::Image< TPixel, VImageDimension > *, unsigned int timeStep)
	internal scan of the whole image More...

Protected Attributes
LabelCounterSliceTimeVectorType	m_LabelCountInSlice

LabelSetImage::Pointer	m_WorkingImage

Image::Pointer	m_ReferenceImage

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::SliceBasedInterpolationController 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. SliceBasedInterpolationController 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 SliceBasedInterpolationController. 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.

SliceBasedInterpolationController 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 66 of file mitkSliceBasedInterpolationController.h.

Member Typedef Documentation

◆ InterpolatorMapType

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

protected

Definition at line 171 of file mitkSliceBasedInterpolationController.h.

◆ LabelCounterSliceTimeVectorType

typedef std::vector<std::vector<LabelCounterSliceVectorType> > mitk::SliceBasedInterpolationController::LabelCounterSliceTimeVectorType

protected

Definition at line 170 of file mitkSliceBasedInterpolationController.h.

◆ LabelCounterSliceVectorType

typedef std::vector<LabelCounterVectorType> mitk::SliceBasedInterpolationController::LabelCounterSliceVectorType

protected

Definition at line 169 of file mitkSliceBasedInterpolationController.h.

◆ LabelCounterVectorType

typedef std::vector<unsigned int> mitk::SliceBasedInterpolationController::LabelCounterVectorType

protected

Definition at line 168 of file mitkSliceBasedInterpolationController.h.

Constructor & Destructor Documentation

◆ SliceBasedInterpolationController()

mitk::SliceBasedInterpolationController::SliceBasedInterpolationController ( )

protected

Definition at line 44 of file mitkSliceBasedInterpolationController.cpp.

◆ ~SliceBasedInterpolationController()

mitk::SliceBasedInterpolationController::~SliceBasedInterpolationController ( )

overrideprotected

Definition at line 49 of file mitkSliceBasedInterpolationController.cpp.

References s_InterpolatorForImage.

Member Function Documentation

◆ Clone()

Pointer mitk::SliceBasedInterpolationController::Clone ( ) const

◆ Interpolate()

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

Update after changing the whole working image.

Parameters

image	is a 3D 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).
timeStep	Which time step is changed Generates an interpolated image for the given 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 to use

Definition at line 290 of file mitkSliceBasedInterpolationController.cpp.

References mitk::PlaneGeometry::Clone(), mitk::BaseGeometry::GetOrigin(), m_LabelCountInSlice, m_WorkingImage, MITK_ERROR, mitk::ShapeBasedInterpolationAlgorithm::New(), and mitk::ExtractSliceFilter::New().

◆ InterpolatorForImage()

mitk::SliceBasedInterpolationController * mitk::SliceBasedInterpolationController::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 30 of file mitkSliceBasedInterpolationController.cpp.

References s_InterpolatorForImage.

◆ mitkClassMacroItkParent()

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

◆ New()

static Pointer mitk::SliceBasedInterpolationController::New ( )

static

◆ ResetLabelCount()

void mitk::SliceBasedInterpolationController::ResetLabelCount ( )

Initializes the internal container with the number of voxels per label.

Definition at line 63 of file mitkSliceBasedInterpolationController.cpp.

References m_LabelCountInSlice, and m_WorkingImage.

Referenced by SetWorkingImage().

◆ ScanImageITKProcessing()

template<typename TPixel , unsigned int VImageDimension>

void mitk::SliceBasedInterpolationController::ScanImageITKProcessing	(	itk::Image< TPixel, VImageDimension > *	input,
		unsigned int	timeStep
	)

protected

internal scan of the whole image

Definition at line 241 of file mitkSliceBasedInterpolationController.cpp.

References m_LabelCountInSlice, and m_WorkingImage.

Referenced by SetWorkingImage().

◆ ScanSliceITKProcessing()

template<typename PixelType >

void mitk::SliceBasedInterpolationController::ScanSliceITKProcessing	(	const itk::Image< PixelType, 2 > *	input,
		const SetChangedSliceOptions &	options
	)

protected

internal scan of a single slice

Definition at line 197 of file mitkSliceBasedInterpolationController.cpp.

References mitk::SliceBasedInterpolationController::SetChangedSliceOptions::dim0, mitk::SliceBasedInterpolationController::SetChangedSliceOptions::dim1, m_LabelCountInSlice, m_WorkingImage, mitk::SliceBasedInterpolationController::SetChangedSliceOptions::sliceDimension, mitk::SliceBasedInterpolationController::SetChangedSliceOptions::sliceIndex, and mitk::SliceBasedInterpolationController::SetChangedSliceOptions::timeStep.

Referenced by SetChangedSlice().

◆ SetChangedSlice()

void mitk::SliceBasedInterpolationController::SetChangedSlice	(	const Image *	image,
		unsigned int	sliceDimension,
		unsigned int	sliceIndex,
		unsigned int	timeStep
	)

Update after changing a single slice in the working image.

Parameters

image	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 150 of file mitkSliceBasedInterpolationController.cpp.

References AccessFixedDimensionByItk_1, mitk::Image::GetDimension(), m_LabelCountInSlice, m_WorkingImage, and ScanSliceITKProcessing().

◆ SetReferenceImage()

void mitk::SliceBasedInterpolationController::SetReferenceImage ( Image * image )

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

If this image 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 121 of file mitkSliceBasedInterpolationController.cpp.

References m_ReferenceImage, m_WorkingImage, and MITK_WARN.

◆ SetWorkingImage()

void mitk::SliceBasedInterpolationController::SetWorkingImage ( LabelSetImage * image )

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 86 of file mitkSliceBasedInterpolationController.cpp.

References AccessFixedDimensionByItk_1, m_WorkingImage, ResetLabelCount(), s_InterpolatorForImage, and ScanImageITKProcessing().

Member Data Documentation

◆ m_LabelCountInSlice

LabelCounterSliceTimeVectorType mitk::SliceBasedInterpolationController::m_LabelCountInSlice

protected

An array that 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 191 of file mitkSliceBasedInterpolationController.h.

Referenced by Interpolate(), ResetLabelCount(), ScanImageITKProcessing(), ScanSliceITKProcessing(), and SetChangedSlice().