Class for filtering volume images. More...

#include <cmtkFilterVolume.h>

Public Types
typedef Types::DataItem	CoupeBlock [COUPE_BLOCK_SIZE]
Static Public Member Functions
static TypedArray::SmartPtr	GaussianFilter (const UniformVolume volume, const Units::GaussianSigma &width, const Types::Coordinate radius=1.0, const TypedArray maskData=NULL)
	Apply Gaussian filter.
static TypedArray::SmartPtr	CoupeFilter (const UniformVolume *volume, const int windowRadius, const float beta=0.5)
	Apply Coupe denoising filter.
static TypedArray::SmartPtr	RohlfingFilter (const UniformVolume volume, const TypedArray subjectData, const TypedArray *maskData, const Units::GaussianSigma &iFilterSigma, const Units::GaussianSigma &filterWidth, const Types::Coordinate filterRadius)
	Apply Torsten Rohlfing's single-image intensity-consistent Gaussian filter.
static TypedArray::SmartPtr	StudholmeFilter (const UniformVolume volume, const TypedArray subjectData, const TypedArray averageData, const TypedArray maskData, std::list< TypedArray::SmartPtr > imgList, const Types::DataItem binWidth, const Units::GaussianSigma &filterWidth, const Types::Coordinate filterRadius)
	Apply Colin Studholme's Gaussian filter with registration-based weights.
static TypedArray::SmartPtr	StudholmeFilter (const UniformVolume volume, std::list< TypedArray::SmartPtr > subjectData, const TypedArray averageData, const TypedArray *maskData, std::list< TypedArray::SmartPtr > imgList, const Types::DataItem binWidth, const Units::GaussianSigma &filterWidth, const Types::Coordinate filterRadius)
	Apply Colin Studholme's Gaussian filter using multiple time points.
Static Private Member Functions
static Types::DataItem	Mean (CoupeBlock items)
	Return the mean value of a vector of Types::DataItems.
static Types::DataItem	Variance (CoupeBlock items, const Types::DataItem mean)
	Return the variance of a vector of Types::DataItems.
static void	GetCoupeBlock (CoupeBlock block, const TypedArray data, const int dims, const int x, const int y, const int z)
	Fill a CoupeBlock with the block centered around a given voxel.
static double	ComputeCoupeWeight (const Types::DataItem smoothingParam, CoupeBlock centerBlock, CoupeBlock outerBlock)
	Compute the NL-weighting factor between two blocks.
static void	BlockAddInPlace (CoupeBlock v1, CoupeBlock v2)
	Add two blocks, in-place on the first block.
static void	BlockSubtract (CoupeBlock diff, CoupeBlock v1, CoupeBlock v2)
	Subtract two blocks.
static void	BlockConstMult (CoupeBlock prod, CoupeBlock items, const Types::DataItem mult)
	Return the product of the input vector multiplied by a constant float.
static double	BlockSquaredDistance (CoupeBlock centerBlock, CoupeBlock outerBlock)
	Return the squared Euclidean distance between two blocks.
static void	ComputeNLWithinWindow (CoupeBlock NL, const TypedArray blockLocations, const TypedArray data, const int dims, const Types::DataItem smoothingParam, const int x, const int y, const int z, const int windowRadius, const float beta, const TypedArray localMeansMap, const TypedArray *localVariancesMap, CoupeBlock centerBlock)
	Process a window for NL-means accumulation.

Detailed Description

Class for filtering volume images.

Definition at line 53 of file cmtkFilterVolume.h.

Member Typedef Documentation

typedef Types::DataItem cmtk::FilterVolume::CoupeBlock[COUPE_BLOCK_SIZE]

Definition at line 57 of file cmtkFilterVolume.h.

Member Function Documentation

void cmtk::FilterVolume::BlockAddInPlace	(	CoupeBlock	v1,
		CoupeBlock	v2
	)		`[static, private]`

Add two blocks, in-place on the first block.

Parameters:

v1	First vector addend, becomes the sum
v2	Second vector addend

Definition at line 61 of file cmtkFilterVolume_Coupe.cxx.

References COUPE_BLOCK_SIZE.

void cmtk::FilterVolume::BlockConstMult	(	CoupeBlock	prod,
		CoupeBlock	items,
		const Types::DataItem	mult
	)		`[static, private]`

Return the product of the input vector multiplied by a constant float.

Parameters:

prod	An block to store the product
items	An block containing the items to be multiplied
mult	The constant to multiply by

Definition at line 78 of file cmtkFilterVolume_Coupe.cxx.

References COUPE_BLOCK_SIZE.

double cmtk::FilterVolume::BlockSquaredDistance	(	CoupeBlock	centerBlock,
		CoupeBlock	outerBlock
	)		`[static, private]`

Return the squared Euclidean distance between two blocks.

Definition at line 86 of file cmtkFilterVolume_Coupe.cxx.

References COUPE_BLOCK_SIZE.

void cmtk::FilterVolume::BlockSubtract	(	CoupeBlock	diff,
		CoupeBlock	v1,
		CoupeBlock	v2
	)		`[static, private]`

Subtract two blocks.

Parameters:

diff	Block to contain the difference between v1 and v2
v1	First block subtrahend
v2	Second block subtrahend

Definition at line 70 of file cmtkFilterVolume_Coupe.cxx.

References COUPE_BLOCK_SIZE.

double cmtk::FilterVolume::ComputeCoupeWeight	(	const Types::DataItem	smoothingParam,
		CoupeBlock	centerBlock,
		CoupeBlock	outerBlock
	)		`[static, private]`

Compute the NL-weighting factor between two blocks.

Parameters:

smoothingParam	Smoothing parameter for the weighting function
centerBlock	The block to be restored using NL-means
outerBlock	A block to contribute to the restoration of centerBlock

Definition at line 122 of file cmtkFilterVolume_Coupe.cxx.

void cmtk::FilterVolume::ComputeNLWithinWindow	(	CoupeBlock	NL,
		const TypedArray *	blockLocations,
		const TypedArray *	data,
		const int *	dims,
		const Types::DataItem	smoothingParam,
		const int	x,
		const int	y,
		const int	z,
		const int	windowRadius,
		const float	beta,
		const TypedArray *	localMeansMap,
		const TypedArray *	localVariancesMap,
		CoupeBlock	centerBlock
	)		`[static, private]`

Process a window for NL-means accumulation.

Parameters:

NL	Block in which to put the NL computation
blockLocations	UNDOCUMENTED
data	Data array from input 3D image.
dims	Dimensions of the input 3D image.
smoothingParam	Smoothing parameter for the weighting function
x	X-coordinate of volume center.
y	Y-coordinate of volume center.
z	Z-coordinate of volume center.
windowRadius	Distance from center voxel to outer edge of window
beta	Smoothing adjustment parameter
localMeansMap	Mean intensity values at each block
localVariancesMap	Variance of the intensities of the center block
centerBlock	The block to be restored using NL-means

Definition at line 138 of file cmtkFilterVolume_Coupe.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, COUPE_BLOCK_RADIUS, COUPE_BLOCK_SIZE, and cmtk::TypedArray::Get().

TypedArray::SmartPtr cmtk::FilterVolume::CoupeFilter	(	const UniformVolume *	volume,
		const int	windowRadius,
		const float	beta = `0.5`
	)		`[static]`

Apply Coupe denoising filter.

Parameters:

volume	Input 3D image.
beta	Smoothing adjustment parameter
windowRadius	Distance from center voxel to outer edge of window

Returns:: A newly allocated TypedArray object that can be used, for example, to replace the one held by the input image. The data type of the array is identical to the input array.

Definition at line 311 of file cmtkFilterVolume_Coupe.cxx.

References cmtk::AXIS_X, cmtk::AXIS_Y, cmtk::AXIS_Z, COUPE_BLOCK_RADIUS, COUPE_BLOCK_SIZE, cmtk::TypedArray::Get(), cmtk::TypedArray::GetDataSize(), cmtk::DataGrid::GetDims(), cmtk::TypedArray::GetType(), NULL, cmtk::TYPE_DOUBLE, and cmtk::TYPE_INT.

void cmtk::FilterVolume::GetCoupeBlock	(	CoupeBlock	block,
		const TypedArray *	data,
		const int *	dims,
		const int	x,
		const int	y,
		const int	z
	)		`[static, private]`

Fill a CoupeBlock with the block centered around a given voxel.

Note that this routine will only include existing voxels. So asking for a block near the edge of a volume will produce a truncated block.

Parameters:

block	To store the newly-fetched block
data	Data array from input 3D image.
dims	Dimensions of the input 3D image.
x	X-coordinate of block center.
y	Y-coordinate of block center.
z	Z-coordinate of block center.