B-Spline-based resampling. More...

#include <aims/resampling/splineresampler.h>

Inheritance diagram for aims::SplineResampler< T >:

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Collaboration diagram for aims::SplineResampler< T >:

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Public Types
typedef carto::DataTypeTraits< T >::ChannelType	ChannelType

Public Types inherited from carto::RCObject
typedef int	RefCounterType

Public Member Functions
	SplineResampler ()

	~SplineResampler ()

virtual int	getOrder () const =0
	Spline order (1 to 7)

carto::VolumeRef< double >	getSplineCoef (const carto::Volume< T > &inVolume, int t=0, bool verbose=false)
	Computes spline coefficients corresponding to an input volume.

void	reset ()
	Clear the cache.

void	resample_inv_to_vox (const carto::Volume< T > &input_data, const soma::Transformation3d &inverse_transform_to_vox, const T &background, carto::Volume< T > &output_data, bool verbose=false) const CARTO_OVERRIDE
	Resample a volume into an existing output volume.

void	resample_channel_inv_to_vox (const carto::Volume< ChannelType > &inVolume, const soma::Transformation3d &inverse_transform_to_vox, const ChannelType &outBackground, carto::Volume< ChannelType > &outVolume, bool verbose) const

Public Member Functions inherited from aims::Resampler< T >
	Resampler ()

virtual	~Resampler ()

void	setVerboseStream (std::ostream &stream)
	write verbose progress information to this stream.

void	doit (const aims::AffineTransformation3d &transform, carto::Volume< T > &output_data) const
	Resample the input volume set with setRef() into an existing volume.

carto::VolumeRef< T >	doit (const aims::AffineTransformation3d &transform, int dimX, int dimY, int dimZ, const Point3df &voxel_size) const
	Resample the input volume set with setRef() in a newly allocated volume.

virtual void	resample (const carto::Volume< T > &input_data, const aims::AffineTransformation3d &transform, const T &background, carto::Volume< T > &output_data, bool verbose=false) const
	Resample a volume into an existing output volume.

void	resample (const carto::Volume< T > &input_data, const aims::AffineTransformation3d &transform, const T &background, const Point3df &output_location, T &output_value, int timestep) const
	Resample a volume at a single location.

void	resample_inv (const carto::Volume< T > &input_data, const soma::Transformation3d &inverse_transform_to_mm, const T &background, const Point3df &output_location, T &output_value, int timestep) const
	Resample a volume at a single location.

void	resample_inv (const carto::Volume< T > &input_data, const soma::Transformation3d &inverse_transform_to_mm, const T &background, carto::Volume< T > &output_data, bool verbose=false) const
	Resample a volume into an existing output volume.

void	resample_inv_to_vox (const carto::Volume< T > &input_data, const soma::Transformation3d &inverse_transform_to_vox, const T &background, const Point3df &output_location, T &output_value, int timestep) const
	Resample a volume at a single location.

void	setRef (const carto::rc_ptr< carto::Volume< T > > &ref)
	Set the input data to be resampled by the doit() methods.

const carto::rc_ptr< carto::Volume< T > > &	ref () const
	Input data to be resampled by the doit() methods.

void	setDefaultValue (T val)
	Set the background value to be used by the doit() methods.

const T &	defaultValue () const
	Background value used by the doit() methods.

Public Member Functions inherited from carto::RCObject
	RCObject ()

	RCObject (const RCObject &)

RCObject &	operator= (const RCObject &)

virtual	~RCObject ()

Protected Member Functions
void	doResample (const carto::Volume< T > &inVolume, const soma::Transformation3d &transform3d, const T &outBackground, const Point3df &outLocation, T &outValue, int t) const CARTO_OVERRIDE
	Resample a volume at a single location.

virtual void	doResampleChannel (const carto::Volume< ChannelType > &inVolume, const soma::Transformation3d &transform3d, const ChannelType &outBackground, const Point3df &outLocation, ChannelType &outValue, int t) const

void	updateParameters (const carto::Volume< T > &inVolume, int t, bool verbose) const CARTO_OVERRIDE
	Update the cache of spline coefficients if needed.

virtual void	updateParametersChannel (const carto::Volume< ChannelType > &inVolume, int t, bool verbose) const

void	iirConvolveMirror (std::vector< double > &data) const

int	getFold (int i, int size) const
	This method returns a mirror index when needed.

virtual double	getBSplineWeight (int i, double x) const =0
	Returns .

Protected Attributes
std::vector< double >	_poles

double	_gain

carto::VolumeRef< double >	_splineCoefficients

const carto::Volume< ChannelType > *	_lastvolume

int	_lasttime

Protected Attributes inherited from aims::Resampler< T >
carto::rc_ptr< carto::Volume< T > >	_ref

T	_defval

std::ostream *	_verbose_stream

Friends
template<bool, typename>
struct	MultiChannelResamplerSwitch

Detailed Description

template<class T>
class aims::SplineResampler< T >

B-Spline-based resampling.

This is the base class for all resamplers based on B-spline interpolation as described by Unser, Aldroubi & Eden in IEEE PAMI (1991). A class computing the actual spline coefficient is derived for each spline order (1 to 7).

The resampling API is described in the base class, Resampler.

See also: LinearResampler CubicResampler QuadraticResampler QuinticResampler SixthOrderResampler SeventhOrderResampler

Coefficients are computed through a recursive scheme from an input reference volume. This recursive algorithm is fast for whole volume resampling, but slower for single points. A cache mechanism has thus been implemented so that coefficients are not recomputed if the input volume did not change.

For an input volume inVolume of dimensions [dimX, dimY, dimZ], coefficients are double precision values stored in a volume of same dimensions. Any value $\mathrm{inVolume}(x, y, z)$ can then be interpolated through the formula:

$\mathrm{inVolume}(x, y, z) = \sum_i ( c_i * B^n(x - x_i) * B^n(y - y_i) * B^n(z - z_i) )$

with $ c_i$ the coefficients, $ B^n$ a $ n$ -th order B-spline and $ (x_i, y_i, z_i)$ the discrete input image points. Given that the support of $ B^n$ is $ ]-(n+1)/2, (n+1)/2[$ , only the $ (n+1)^d$ (with $ d$ the volume dimension in $[1,2,3]$ ) closest coefficients / discrete points are used to interpolate a given point.

Template Parameters

T	Voxel data type

Definition at line 88 of file splineresampler.h.

Member Typedef Documentation

◆ ChannelType

template<class T>

typedef carto::DataTypeTraits<T>::ChannelType aims::SplineResampler< T >::ChannelType

Definition at line 139 of file splineresampler.h.

Constructor & Destructor Documentation

◆ SplineResampler()

template<class T>

aims::SplineResampler< T >::SplineResampler ( )

Definition at line 56 of file splineresampler_d.h.

References _lasttime, _lastvolume, and aims::Resampler< T >::Resampler().

Referenced by aims::CubicResampler< T >::CubicResampler(), aims::LinearResampler< T >::LinearResampler(), aims::MajorityLabelResampler< T >::MajorityLabelResampler(), aims::MedianResampler< T >::MedianResampler(), aims::QuadraticResampler< T >::QuadraticResampler(), aims::QuarticResampler< T >::QuarticResampler(), aims::QuinticResampler< T >::QuinticResampler(), aims::SeventhOrderResampler< T >::SeventhOrderResampler(), and aims::SixthOrderResampler< T >::SixthOrderResampler().

◆ ~SplineResampler()

template<class T>

aims::SplineResampler< T >::~SplineResampler ( )

inline

Definition at line 93 of file splineresampler.h.

Member Function Documentation

◆ doResample()

template<class T>

void aims::SplineResampler< T >::doResample	(	const carto::Volume< T > &	input_data,
		const soma::Transformation3d &	inverse_transform,
		const T &	background,
		const Point3df &	output_location,
		T &	output_value,
		int	timestep ) const

protectedvirtual

Resample a volume at a single location.

Parameters

[in]	input_data	data to be resampled (its voxel size is not* taken into account)
[in]	inverse_transform	transformation from output coordinates to coordinates of the input volume (unit: voxels)
[in]	background	value set if the transformed point is outside of the input volume
[in]	output_location	coordinates in output space (source space of `transform`)
[out]	output_value	variable to be filled with resampled data
[in]	timestep	for 4D volume, time step to be used

Implements aims::Resampler< T >.

Definition at line 781 of file splineresampler_d.h.

References carto::DataTypeTraits< typename DataType >::is_multichannel, and MultiChannelResamplerSwitch.

◆ doResampleChannel()

template<class T>

void aims::SplineResampler< T >::doResampleChannel	(	const carto::Volume< ChannelType > &	inVolume,
		const soma::Transformation3d &	transform3d,
		const ChannelType &	outBackground,
		const Point3df &	outLocation,
		ChannelType &	outValue,
		int	t ) const

protectedvirtual

Reimplemented in aims::LinearResampler< T >, aims::MajorityLabelResampler< T >, and aims::MedianResampler< T >.

Definition at line 84 of file splineresampler_d.h.

References _lasttime.

Referenced by aims::MultiChannelResamplerSwitch< false, T >::doResample(), aims::MultiChannelResamplerSwitch< true, T >::doResample(), and resample_channel_inv_to_vox().

◆ getBSplineWeight()

template<class T>

virtual double aims::SplineResampler< T >::getBSplineWeight	(	int	i,
		double	x ) const

protectedpure virtual

Returns $ B^n( x - i )$ .

This method is defined by each nth order derived class

Implemented in aims::CubicResampler< T >, aims::LinearResampler< T >, aims::MajorityLabelResampler< T >, aims::MedianResampler< T >, aims::QuadraticResampler< T >, aims::QuarticResampler< T >, aims::QuinticResampler< T >, aims::SeventhOrderResampler< T >, and aims::SixthOrderResampler< T >.

◆ getFold()

template<class T>

int aims::SplineResampler< T >::getFold	(	int	i,
		int	size ) const

protected

This method returns a mirror index when needed.

Only inVolume's size spline coefficient are computed since "outside" coefficients are equal to their mirror inside the image domain. This method computes this mirror correspondance.

If i is in [0, size-1]: returns i
If i < 0: returns -1
If i >= size: returns size - (i - size) - 2

Definition at line 537 of file splineresampler_d.h.

References aims::mirrorCoeff().

Referenced by aims::LinearResampler< T >::doResampleChannel(), aims::MajorityLabelResampler< T >::doResampleChannel(), and aims::MedianResampler< T >::doResampleChannel().

◆ getOrder()

template<class T>

virtual int aims::SplineResampler< T >::getOrder ( ) const

pure virtual

Spline order (1 to 7)

Implemented in aims::CubicResampler< T >, aims::LinearResampler< T >, aims::MajorityLabelResampler< T >, aims::MedianResampler< T >, aims::QuadraticResampler< T >, aims::QuarticResampler< T >, aims::QuinticResampler< T >, aims::SeventhOrderResampler< T >, and aims::SixthOrderResampler< T >.

Referenced by updateParametersChannel().

◆ getSplineCoef()

template<class T>

carto::VolumeRef< double > aims::SplineResampler< T >::getSplineCoef	(	const carto::Volume< T > &	inVolume,
		int	t = 0,
		bool	verbose = false )

Computes spline coefficients corresponding to an input volume.

Spline coefficients are recomputed only if one of these conditions is satisfied:

inVolume is different from the last volume used for coefficients computation (in the sense that they share the same adress)
t is different from the last t used for coefficients computation
A call to reset() has previously been made

Parameters

inVolume	input image
t	volume to use in the T dimension in the case where inVolume is a time series.
verbose	print progress on stdout

Returns: Volume of double containing the coefficients in the image domain. Border coefficient need to be retrieved by mirror.

This method actually calls updateParameters() and returns the coeff container

Definition at line 72 of file splineresampler_d.h.

References _splineCoefficients, and updateParameters().

◆ iirConvolveMirror()

template<class T>

void aims::SplineResampler< T >::iirConvolveMirror ( std::vector< double > & data ) const

protected

Definition at line 421 of file splineresampler_d.h.

References _gain, _poles, and EPSILON.

Referenced by updateParametersChannel().

◆ resample_channel_inv_to_vox()

template<typename T>

void aims::SplineResampler< T >::resample_channel_inv_to_vox	(	const carto::Volume< ChannelType > &	inVolume,
		const soma::Transformation3d &	inverse_transform_to_vox,
		const ChannelType &	outBackground,
		carto::Volume< ChannelType > &	outVolume,
		bool	verbose ) const

Definition at line 547 of file splineresampler_d.h.

References carto::Volume< typename T >::at(), doResampleChannel(), carto::VolumeProxy< typename T >::getSizeT(), carto::VolumeProxy< typename T >::getSizeX(), carto::VolumeProxy< typename T >::getSizeY(), carto::VolumeProxy< typename T >::getSizeZ(), carto::VolumeProxy< typename T >::getVoxelSize(), aims::ProgressInfo< class T1, class T2 >::print(), and updateParametersChannel().

Referenced by aims::MultiChannelResamplerSwitch< true, T >::resample_inv_to_vox().

◆ resample_inv_to_vox()

template<class T>

void aims::SplineResampler< T >::resample_inv_to_vox	(	const carto::Volume< T > &	input_data,
		const soma::Transformation3d &	inverse_transform_to_vox,
		const T &	background,
		carto::Volume< T > &	output_data,
		bool	verbose = false ) const

virtual

Resample a volume into an existing output volume.

Parameters

[in]	input_data	data to be resampled (its voxel size is not** taken into account)
[in]	inverse_transform_to_vox	transformation from coordinates of the output volume (unit: mm), to coordinates of the input volume (unit: voxel)**
[in]	background	value set in output regions that are outside of the transformed input volume
[in,out]	output_data	existing volume to be filled with resampled data (its pre-existing dimensions and voxel size are used)
[in]	verbose	print progress to stdout

The transformations, referentials, and referential header attributes of output_data are not touched; it is up to the calling code to update them accordingly.

This method does not use the instance state set by setRef() or setDefaultValue().

Derived classes can override this method to optimize interpolation of a full volume. The base class method simply calls doResample for each point.

Reimplemented from aims::Resampler< T >.

Definition at line 764 of file splineresampler_d.h.

References carto::DataTypeTraits< typename DataType >::is_multichannel, and MultiChannelResamplerSwitch.