StackSetMotionCorrector< T, T2, DistType > Class Template Reference

A class for stackSet motion correction. More...

#include <StackSetMotionCorrector.h>

List of all members.

Public Member Functions
	~StackSetMotionCorrector ()
	destructor
	StackSetMotionCorrector (StackSet< Stack< T, LinTransStack< float > > > &sss)
	constructor with sss, using initialization list
void	setMinStepSize (float m)
	Set _MSME_C_minStepSize.
void	setMinEdecrease (float m)
	Set _MSME_C_minEdecrement.
void	SIMC_BulkHead2Head_PW (unsigned int ref, unsigned int flo, SimpleTField< float > *mask=NULL, Tcomp stepsize=3.0)
	Bulk head-to-head alignment, using powell optimization.
void	SIMC_VB_MSME_C_CG (const SimpleTField< Tmask > *mask=NULL, const unsigned int init_n_basis=1, const unsigned int msiStep=2)
	Muti-scale motion, centered SIMC with volume blurred images, using conjugate gradient descent.
void	SIMC_C_ConjugateGradientDescent (SimpleTField< float > *mask=NULL)
	Centered conjugate gradient descent.
void	SetBlur (float sigma)
	Along-intersection blurring kernel.
template<>
const char	_versionID []
template<>
const char	_versionID []
template<>
const char	_versionID []
Static Public Member Functions
template<typename TStack , typename Tstf >
static void	VolumeBlurring (const TStack &ss, const float sigma, SimpleTField< Tstf > &stf, const SimpleTField< float > *mask=NULL)
	3D volume blurring function from a motion scattered stack
template<typename Tst1 , typename Tst2 , typename Tstf >
static void	Resample (const Stack< Tst1, Tst2 > &ssin, const SimpleTField< Tstf > &target, Stack< Tstf, Tst2 > &ssout)
	Resample a SimpleTField as a Stack. Currently Tstf=Tst1=Tst2 is needed.
static SimpleVTVec< float >	UpdateSliceQuality (StackSet< Stack< T, LinTransStack< float > > > &sss, const float thres=0.15f)
	Update slice quality by comparing the mean intensity with neighbors.
static SimpleVTVec< float >	UpdateSliceQualityIntx (StackSet< Stack< T, LinTransStack< float > > > &sss, const float thres=1.25f)
	Update slice quality by matching the slice intersection intensity profiles.
Static Public Attributes
static const char	_versionID []
Protected Types
typedef double	Tcomp
typedef float	Tmask
Protected Attributes
StackSet< Stack< T, LinTransStack< float > > > &	_sss
float	_sigmaBlur
float	_MSME_C_minStepSize
float	_MSME_C_minEdecrease

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Detailed Description

template<typename T = short, typename T2 = float, typename DistType = L2<T2>>
class StackSetMotionCorrector< T, T2, DistType >

A class for stackSet motion correction.

Author:

Kio Kim 2007-2011

Id:

SIMCBulkHeadEnergyFunction.h,v 1.3 2011/11/22 19:34:03 bicg Exp

Author:

Kio Kim 2007-2011

Id:

StackSetMotionCorrector.h,v 1.13 2012/02/21 01:57:47 kio Exp

---

Member Function Documentation

template<typename T = short, typename T2 = float, typename DistType = L2<T2>>

void StackSetMotionCorrector< T, T2, DistType >::SIMC_BulkHead2Head_PW	(	unsigned int	ref,
		unsigned int	flo,
		SimpleTField< float > *	mask = NULL,
		Tcomp	stepsize = 3.0
	)		[inline]

Bulk head-to-head alignment, using powell optimization.

Parameters:

[in]	factor	Slice quality threshold. If mean slice intersection energy of a slice against other slices is >factor*median, it is considered low quality.
[in]	mask	pointer to mask Given a reference stack, estimate the relative motion of the floating stack using the Powell's optimization in the head coordinate system.
[in]	ref	Stack index of the reference
[in]	flo	Stack index of the floating
[in]	mask	pointer to the mask file.
[in]	stepsize	Stepsize for Powell optimization

template<typename T = short, typename T2 = float, typename DistType = L2<T2>>

static SimpleVTVec<float> StackSetMotionCorrector< T, T2, DistType >::UpdateSliceQuality	(	StackSet< Stack< T, LinTransStack< float > > > &	sss,
		const float	thres = 0.15f
	)		[inline, static]

Update slice quality by comparing the mean intensity with neighbors.

Parameters:

[in]	sss	Input StackSet.
[in]	thres	Quality determination threshold (default =0.15)

Returns:

Quality Vector

template<typename T = short, typename T2 = float, typename DistType = L2<T2>>

template<typename TStack , typename Tstf >

static void StackSetMotionCorrector< T, T2, DistType >::VolumeBlurring	(	const TStack &	ss,
		const float	sigma,
		SimpleTField< Tstf > &	stf,
		const SimpleTField< float > *	mask = NULL
	)		[inline, static]

3D volume blurring function from a motion scattered stack

This function blurs a Stack of slices in 3D, accounting the location of individual slices.

Parameters:

[in]	ss	Input Stack object
[in]	sigma	sigma of the blurring Gaussian kernel size
[out]	stf	SimpleTField for the output
[in]	mask	Mask file is needed to specify the target region of blurring operation