This is a specialized viewer for computing the value of a cubic B-Spline interpolation from the parameters. Thus the input to the constructor or setArray must be a parameter image. More...

#include <accessors.h>

Inherits npl::NDView< T >.

Public Member Functions
	BSplineView (std::shared_ptr< MRImage > params, BoundaryConditionT bound=ZEROFLUX)

	BSplineView ()

void	createOverlay (ptr< const MRImage > overlay, double bspace)

bool	get (size_t len, const double *point, int dir, double &val, double &dval)
	Samples the BSpline function at the specified point. More...

double	get (size_t len, double *point)
	Simple sample function, just retrieve value at point, does not perform derivative. More...

ptr< MRImage >	reconstruct (ptr< const MRImage > input)
	Perform full-on reconstruction in the space of the input image. More...

ptr< MRImage >	reconstructNotAligned (ptr< const MRImage > input)

ptr< MRImage >	reconstructAligned (ptr< const MRImage > input)

double	thinPlateEnergy ()

double	thinPlateEnergy (size_t len, double *grad)

double	jacobianDet (int dir)
	Computes the regularization term by integrating over the entire space for each knot. Thankfully integrals can be pre-computed (vConv, dvConv, ddvConv). See equations 66-71 in docs/bspline/fmri_dist_correct_2013-12-06.pdf. More...

double	jacobianDet (int dir, size_t len, double *grad)
	Computes the gradient of regularization for each of the knots. Thankfully integrals can be pre-computed (uConv, duConv, dduConv). See equations 54-59 in docs/bspline/fmri_dist_correct_2013-12-06.pdf. More...

ptr< MRImage >	getParams ()
	Return the parameter image. More...

void	setArray (ptr< NDArray > in)

T	operator[] (int64_t index)
	Gets value linear position in array, then casts to T. More...

T	operator[] (const std::vector< int64_t > &index)
	Gets value at array index and then casts to T. More...

T	get (const std::vector< int64_t > &index)
	Gets value at array index and then casts to T. More...

T	get (size_t len, int64_t *index)
	Gets value at array index and then casts to T. More...

void	set (size_t len, const int64_t *index, T v)
	Casts to the appropriate type then sets array at given index. More...

void	set (const std::vector< int64_t > &index, T v)
	Casts to the appropriate type then sets array at given index. More...

void	set (int64_t index, T v)
	Casts to the appropriate type then sets array at given index. More...

int64_t	tlen ()

Public Attributes
BoundaryConditionT	m_boundmethod
	How to handle boundaries (ZEROFLUX for constant outside bounds, ZERO for outside to be 0 and WRAP to wrap values, this might also be called periodic) More...

bool	m_ras
	if true, then this assumes the inputs are RAS coordinates rather than indexes. Default is false More...

double	vConv [5][5]

double	dvConv [5][5]

double	ddvConv [5][5]

double	U200 [9][9][9]

double	U110 [9][9][9]

double	U100 [9][9][9]

Static Protected Member Functions
template<typename U >
static T	castgetStatic (void *ptr)
	This is a wrapper function that will be called to safely cast from the underlying type. More...

template<typename U >
static void	castsetStatic (void *ptr, const T &val)
	This is a wrapper function that will be called to safely cast to the underlying type. More...

Protected Attributes
std::shared_ptr< NDArray >	parent
	Where to get the dat a from. Also the shared_ptr prevents dealloc. More...

T(*	castget )(void *ptr)
	Function pointer to the correct function for casting from the underlying type. More...

void(*	castset )(void *ptr, const T &v)
	Function pointer to the correct function for casting to the underlying type. This should be set during construction. More...

Detailed Description

template<typename T>
class npl::BSplineView< T >

This is a specialized viewer for computing the value of a cubic B-Spline interpolation from the parameters. Thus the input to the constructor or setArray must be a parameter image.

estimate(in) will generate the parameters that minimize the least squares difference from the given image (in).

createOverlay(in) will create a new parameter array in params that extends for two knots outside the input image (in)

Template Parameters

T	Value to interpolate as

Definition at line 2049 of file accessors.h.

Constructor & Destructor Documentation

template<typename T >

npl::BSplineView< T >::BSplineView	(	std::shared_ptr< MRImage >	params,
		BoundaryConditionT	bound = `ZEROFLUX`
	)

inline

Definition at line 2052 of file accessors.h.

template<typename T >

npl::BSplineView< T >::BSplineView ( )

inline

Definition at line 2057 of file accessors.h.

Member Function Documentation

template<typename T >

template<typename U >

static T npl::NDView< T >::castgetStatic ( void * ptr )

inlinestaticprotectedinherited

This is a wrapper function that will be called to safely cast from the underlying type.

Template Parameters

U	Underlying type of pixel, figured out in the constructor

Parameters

ptr	Pointer to memory where the pixel is.

Returns: Correctly cast value

Definition at line 272 of file accessors.h.

template<typename T >

template<typename U >

static void npl::NDView< T >::castsetStatic	(	void *	ptr,
		const T &	val
	)

inlinestaticprotectedinherited

This is a wrapper function that will be called to safely cast to the underlying type.

Template Parameters

U	Underlying type of pixel, figured out in the constructor

Parameters

ptr	Pointer to memory where the pixel is.
val	new value to write

Definition at line 287 of file accessors.h.

template<typename T >

void npl::BSplineView< T >::createOverlay	(	ptr< const MRImage >	overlay,
		double	bspace
	)

inline

Definition at line 2059 of file accessors.h.

template<typename T >

T npl::NDView< T >::get ( const std::vector< int64_t > & index )

inlineinherited

Gets value at array index and then casts to T.

Parameters

index n-d index to access

Returns: value

Definition at line 170 of file accessors.h.

template<typename T >

T npl::NDView< T >::get	(	size_t	len,
		int64_t *	index
	)

inlineinherited

Gets value at array index and then casts to T.

Parameters

len	length of index array
index	n-d index to access

Returns: value

Definition at line 186 of file accessors.h.

template<typename T >

bool npl::BSplineView< T >::get	(	size_t	len,
		const double *	point,
		int	dir,
		double &	val,
		double &	dval
	)

inline

Samples the BSpline function at the specified point.

Parameters

len	Length of point vector
point	Point (if m_ras) or continuous index in parameter space
dir	Dimension to take derivative in, must be >= 0
val	Return value at specified point
dval	Return derivative of Bspline in dir direction

Returns: true if the specified point used boundary conditions (outside values)

Definition at line 2108 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::get	(	size_t	len,
		double *	point
	)

inline

Simple sample function, just retrieve value at point, does not perform derivative.

Parameters

len	Length of point array
point	Point (or if m_ras = false, then continuous index in parameter space)

Returns: Value at point

Definition at line 2198 of file accessors.h.

template<typename T >

ptr<MRImage> npl::BSplineView< T >::getParams ( )

inline

Return the parameter image.

Returns

Definition at line 2630 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::jacobianDet ( int dir )

inline

Computes the regularization term by integrating over the entire space for each knot. Thankfully integrals can be pre-computed (vConv, dvConv, ddvConv). See equations 66-71 in docs/bspline/fmri_dist_correct_2013-12-06.pdf.

Returns: regularization value

Definition at line 2508 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::jacobianDet	(	int	dir,
		size_t	len,
		double *	grad
	)

inline

Computes the gradient of regularization for each of the knots. Thankfully integrals can be pre-computed (uConv, duConv, dduConv). See equations 54-59 in docs/bspline/fmri_dist_correct_2013-12-06.pdf.

Parameters

dir	Direction of distortion/deformation
len	Length of grad vector
grad	Vector of values, one for each parameter in the B-spline

Definition at line 2565 of file accessors.h.

template<typename T >

T npl::NDView< T >::operator[] ( int64_t index )

inlineinherited

Gets value linear position in array, then casts to T.

Returns: value

Definition at line 155 of file accessors.h.

template<typename T >

T npl::NDView< T >::operator[] ( const std::vector< int64_t > & index )

inlineinherited

Gets value at array index and then casts to T.

Parameters

index n-d index to access

Returns: value

Definition at line 201 of file accessors.h.

template<typename T >

ptr<MRImage> npl::BSplineView< T >::reconstruct ( ptr< const MRImage > input )

inline

Perform full-on reconstruction in the space of the input image.

Parameters

input

Returns

Definition at line 2274 of file accessors.h.

template<typename T >

ptr<MRImage> npl::BSplineView< T >::reconstructAligned ( ptr< const MRImage > input )

inline

Definition at line 2292 of file accessors.h.

template<typename T >

ptr<MRImage> npl::BSplineView< T >::reconstructNotAligned ( ptr< const MRImage > input )

inline

Definition at line 2284 of file accessors.h.

template<typename T >

void npl::NDView< T >::set	(	size_t	len,
		const int64_t *	index,
		T	v
	)

inlineinherited

Casts to the appropriate type then sets array at given index.

Parameters

len	length of index array
index	n-d index to access
v	value to set at index

Returns: current value

Definition at line 218 of file accessors.h.

template<typename T >

void npl::NDView< T >::set	(	const std::vector< int64_t > &	index,
		T	v
	)

inlineinherited

Casts to the appropriate type then sets array at given index.

Parameters

v	value to set at index
index	n-d index to access

Returns: current value

Definition at line 234 of file accessors.h.

template<typename T >

void npl::NDView< T >::set	(	int64_t	index,
		T	v
	)

inlineinherited

Casts to the appropriate type then sets array at given index.

Parameters

v	value to set at index
index	n-d index to access

Returns: current value

Definition at line 250 of file accessors.h.

template<typename T >

void npl::NDView< T >::setArray ( ptr< NDArray > in )

inlineinherited

Definition at line 73 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::thinPlateEnergy ( )

inline

Definition at line 2349 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::thinPlateEnergy	(	size_t	len,
		double *	grad
	)

inline

Definition at line 2408 of file accessors.h.

template<typename T >

int64_t npl::NDView< T >::tlen ( )

inlineinherited

Definition at line 258 of file accessors.h.

Member Data Documentation

template<typename T >

T(* npl::NDView< T >::castget) (void *ptr)

protectedinherited

Function pointer to the correct function for casting from the underlying type.

Parameters

ptr	location in memory where the pixel is stored

Definition at line 303 of file accessors.h.

template<typename T >

void(* npl::NDView< T >::castset) (void *ptr, const T &v)

protectedinherited

Function pointer to the correct function for casting to the underlying type. This should be set during construction.

Parameters

ptr	pointer to memory
v	value to cast and write

Definition at line 313 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::ddvConv[5][5]

Initial value:

= {
        {0.041666666666666664,0.,-0.125,0.08333333333333333,0.},
        {0.,0.4166666666666667,-0.75,0.25,0.08333333333333333},
        {-0.125,-0.75,1.75,-0.75,-0.125},
        {0.08333333333333333,0.25,-0.75,0.4166666666666667,0.},
        {0.,0.08333333333333333,-0.125,0.,0.041666666666666664}}

Definition at line 2657 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::dvConv[5][5]

Initial value:

= {
        {0.0015625,0.013541666666666667,-0.0109375,-0.004166666666666667,0.},
        {0.013541666666666667,0.24479166666666666,-0.07604166666666666,-0.178125,-0.004166666666666667},
        {-0.0109375,-0.07604166666666666,0.17395833333333333,-0.07604166666666666,-0.0109375},
        {-0.004166666666666667,-0.178125,-0.07604166666666666,0.24479166666666666,0.013541666666666667},
        {0.,-0.004166666666666667,-0.0109375,0.013541666666666667,0.0015625}}

Definition at line 2651 of file accessors.h.

template<typename T >

BoundaryConditionT npl::BSplineView< T >::m_boundmethod

How to handle boundaries (ZEROFLUX for constant outside bounds, ZERO for outside to be 0 and WRAP to wrap values, this might also be called periodic)

Definition at line 2630 of file accessors.h.

template<typename T >

bool npl::BSplineView< T >::m_ras

if true, then this assumes the inputs are RAS coordinates rather than indexes. Default is false

Definition at line 2643 of file accessors.h.

template<typename T >

std::shared_ptr<NDArray> npl::NDView< T >::parent

protectedinherited

Where to get the dat a from. Also the shared_ptr prevents dealloc.

Definition at line 290 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::U100[9][9][9]

Definition at line 3614 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::U110[9][9][9]

Definition at line 3139 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::U200[9][9][9]

Definition at line 2664 of file accessors.h.

template<typename T >

double npl::BSplineView< T >::vConv[5][5]

Initial value:

= {
        {0.000031001984126984125,0.0010788690476190477,0.0013950892857142857,0.0000992063492063492,0.},
        {0.0010788690476190477,0.058643353174603174,0.11707589285714286,0.02101934523809524,0.0000992063492063492},
        {0.0013950892857142857,0.11707589285714286,0.362016369047619,0.11707589285714286,0.0013950892857142857},
        {0.0000992063492063492,0.02101934523809524,0.11707589285714286,0.058643353174603174,0.0010788690476190477},
        {0.,0.0000992063492063492,0.0013950892857142857,0.0010788690476190477,0.000031001984126984125}}

Definition at line 2645 of file accessors.h.

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

/home/micahc/coding/npl/lib/accessors.h

Public Member Functions

Public Attributes

Static Protected Member Functions

Protected Attributes

Detailed Description

template<typename T> class npl::BSplineView< T >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<typename T>
class npl::BSplineView< T >