Resampling of data from a volume, applying a transformation. More...

#include <aims/resampling/resampler.h>

Inheritance diagram for aims::Resampler< T >:

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Collaboration diagram for aims::Resampler< T >:

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Public Member Functions
	Resampler ()

virtual	~Resampler ()

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

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

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

virtual 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
	Resample a volume into an existing output volume. More...

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

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

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

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

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

	RCObject (const RCObject &)

RCObject &	operator= (const RCObject &)

virtual	~RCObject ()

Protected Member Functions
virtual void	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 =0
	Resample a volume at a single location. More...

virtual void	updateParameters (const carto::Volume< T > &, int, bool) const
	Method called before doResample() for each time step. More...

Protected Attributes
carto::rc_ptr< carto::Volume< T > >	_ref

T	_defval

std::ostream *	_verbose_stream

Additional Inherited Members
Public Types inherited from carto::RCObject
typedef int	RefCounterType

Detailed Description

template<class T>
class aims::Resampler< T >

Resampling of data from a volume, applying a transformation.

The doit() and resample() methods can be used to apply an affine transformation (aims::AffineTransformation3d). They take a direct transformation, i.e. the transformation goes from the space of the input image (unit: mm) to the space of the output image (unit: mm). The transformation is inverted and normalized internally as needed, because the resamplers "pull" data by transforming output coordinates into input coordinates.

The doit() methods work on input data passed to the setRef() method. setDefaultValue() can also be called to set the background value.

The resample() methods provide stateless alternatives.

You can also use arbitrary non-affine transformations (inheriting soma::Transformation3d) by using the resample_inv() family of methods. In this case, you must pass the backward transformation (from output space to input space), because of the "pulling" mechanism described above.

Beware that contrary to the other methods, the resample_inv_to_vox() overloads take a transformation that maps to voxel coordinates of the input image. These methods can be slightly faster than resample_inv() because they map directly to the API that the actual resamplers are implementing (doResample()). The performance gain is especially noticeable for repeated calls to the overloads that perform resampling for a single point only.

Definition at line 75 of file resampler.h.

Constructor & Destructor Documentation

◆ Resampler()

template<typename T >

aims::Resampler< T >::Resampler

Definition at line 61 of file resampler_d.h.

◆ ~Resampler()

template<class T >

virtual aims::Resampler< T >::~Resampler ( )

inlinevirtual

Definition at line 80 of file resampler.h.

Member Function Documentation

◆ defaultValue()

template<class T >

const T& aims::Resampler< T >::defaultValue ( ) const

inline

Background value used by the doit() methods.

Definition at line 323 of file resampler.h.

References aims::Resampler< T >::_defval.

◆ doit() [1/2]

template<typename T >

void aims::Resampler< T >::doit	(	const aims::AffineTransformation3d &	transform,
		carto::Volume< T > &	output_data
	)		const

Resample the input volume set with setRef() into an existing volume.

Parameters

[in]	transform	transformation from coordinates of the input volume (unit: mm), to coordinates of the output* volume (unit: mm) (its inverse is used for resampling)
[in,out]	output_data	existing volume to be filled with resampled data (its pre-existing dimensions and voxel size are used)

Exceptions

std::runtime_error if no input volume has been set with setRef.

The background value (to be used for regions that are outside of the input volume) can be set with setDefaultValue().

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

The level of verbosity is taken from carto::verbose (i.e. the --verbose command-line argument is honoured).

Definition at line 226 of file resampler_d.h.

References carto::verbose.

Referenced by BlockMatching< T >::doit(), and aims::RoiStats::populate().

◆ doit() [2/2]

template<typename T >

carto::VolumeRef< T > aims::Resampler< 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.

Parameters

[in]	transform	transformation from coordinates of the input* volume (unit: mm), to coordinates of the output volume (unit: mm) (its inverse is used for resampling)
[in]	dimX,dimY,dimZ	dimensions of the newly allocated volume
[in]	voxel_size	voxel size of the newly allocated volume (unit: mm)

Returns: a newly allocated volume containing the resampled data (its size along the t axis is the same as the input volume).

Exceptions

std::runtime_error if no input volume has been set with setRef.

The background value (to be used for regions that are outside of the input volume) can be set with setDefaultValue().

The level of verbosity is taken from carto::verbose (i.e. the --verbose command-line argument is honoured).

The transformations, referentials, and referential header attributes of the new volume are reset if transform.isIdentity() is false:

the referential attribute is removed
each transformation in transformations is composed with transform so that the output volume still points to the original space. If that is not possible (e.g. the transformations attribute is missing or invalid), then a new transformation is added that points to the input volume.

Definition at line 237 of file resampler_d.h.

◆ doResample()

template<class T >

virtual void aims::Resampler< 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

protectedpure virtual

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

Implemented in aims::SplineResampler< T >, and aims::NearestNeighborResampler< T >.

Referenced by aims::Resampler< T >::resample_inv_to_vox().

◆ ref()

template<class T >

const carto::rc_ptr<carto::Volume<T> >& aims::Resampler< T >::ref ( ) const

inline

Input data to be resampled by the doit() methods.

Definition at line 317 of file resampler.h.

References aims::Resampler< T >::_ref.

◆ resample() [1/2]

template<typename T >

void aims::Resampler< T >::resample	(	const carto::Volume< T > &	input_data,
		const aims::AffineTransformation3d &	transform,
		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 taken into account)
[in]	transform	transformation from coordinates of the input volume (unit: mm), to coordinates of the output* volume (unit: mm) (its inverse is used for resampling)
[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.

Definition at line 179 of file resampler_d.h.

References carto::VolumeProxy< class >::getVoxelSize(), aims::AffineTransformation3d::inverse(), soma::AffineTransformation3dBase::scale(), and verbose.

◆ resample() [2/2]

template<typename T >

void aims::Resampler< T >::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.

Parameters

[in]	input_data	data to be resampled (its voxel size is taken into account)
[in]	transform	transformation from coordinates of the input* volume (unit: mm), to output coordinates (its inverse is used for resampling)
[in]	background	value set in output regions that are outside of the transformed input volume
[in]	output_location	coordinates in output space (destination space of `transform`)
[out]	output_value	variable to be filled with resampled data
[in]	timestep	for 4D volume, time step to be used

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

Definition at line 202 of file resampler_d.h.

References carto::VolumeProxy< class >::getVoxelSize(), aims::AffineTransformation3d::inverse(), soma::AffineTransformation3dBase::scale(), and carto::verbose.

◆ resample_inv() [1/2]

template<typename T >

void aims::Resampler< T >::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.

Parameters

[in]	input_data	data to be resampled (its voxel size is taken into account)
[in]	transform	transformation from coordinates of the output* volume (unit: mm), to coordinates of the input volume (unit: mm)
[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().

Definition at line 132 of file resampler_d.h.

References carto::VolumeProxy< class >::getVoxelSize().

◆ resample_inv() [2/2]

template<typename T >

void aims::Resampler< T >::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.

Parameters

[in]	input_data	data to be resampled (its voxel size is taken into account)
[in]	inverse_transform	transformation from output coordinates to coordinates of the input volume (unit: mm)
[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

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

Definition at line 154 of file resampler_d.h.

References carto::VolumeProxy< class >::getVoxelSize(), aims::TransformationChain3d::push_back(), and soma::AffineTransformation3dBase::scale().

◆ resample_inv_to_vox() [1/2]

template<typename T >

void aims::Resampler< 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 in aims::SplineResampler< T >.

Definition at line 68 of file resampler_d.h.

References carto::VolumeProxy< class >::getVoxelSize().

◆ resample_inv_to_vox() [2/2]

template<class T >

void aims::Resampler< T >::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

inline

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_to_vox	transformation from output coordinates to coordinates of the input volume (unit: voxel)
[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

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

Definition at line 271 of file resampler.h.

References aims::Resampler< T >::doResample(), aims::Resampler< T >::updateParameters(), and carto::verbose.

◆ setDefaultValue()

template<class T >

void aims::Resampler< T >::setDefaultValue ( T val )

inline

Set the background value to be used by the doit() methods.

Definition at line 320 of file resampler.h.

References aims::Resampler< T >::_defval.

◆ setRef()

template<typename T >

void aims::Resampler< T >::setRef ( const carto::rc_ptr< carto::Volume< T > > & ref )

Set the input data to be resampled by the doit() methods.

Definition at line 311 of file resampler_d.h.

References ref().

Referenced by BlockMatching< T >::doit(), and aims::RoiStats::populate().

◆ setVerboseStream()

template<class T >

void aims::Resampler< T >::setVerboseStream ( std::ostream & stream )

inline

write verbose progress information to this stream.

The default is std::cout.

Definition at line 84 of file resampler.h.

References aims::Resampler< T >::_verbose_stream.

◆ updateParameters()

template<class T >

virtual void aims::Resampler< T >::updateParameters	(	const carto::Volume< T > &	,
		int	,
		bool
	)		const

inlineprotectedvirtual

Method called before doResample() for each time step.

This method is called by all the resampling methods (resample() and doit()) before they call doResample for a given time point t.

The base class version of this method does nothing.

Reimplemented in aims::SplineResampler< T >.

Definition at line 354 of file resampler.h.

Referenced by aims::Resampler< T >::resample_inv_to_vox().

Member Data Documentation

◆ _defval

template<class T >

T aims::Resampler< T >::_defval

protected

Definition at line 359 of file resampler.h.

Referenced by aims::Resampler< T >::defaultValue(), and aims::Resampler< T >::setDefaultValue().

◆ _ref

template<class T >

carto::rc_ptr<carto::Volume<T> > aims::Resampler< T >::_ref

protected

Definition at line 358 of file resampler.h.

Referenced by aims::Resampler< T >::ref().

◆ _verbose_stream

template<class T >

std::ostream* aims::Resampler< T >::_verbose_stream

protected

Definition at line 360 of file resampler.h.

Referenced by aims::Resampler< T >::setVerboseStream().

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

aims/resampling/resampler.h
aims/resampling/resampler_d.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

template<class T> class aims::Resampler< T >

Constructor & Destructor Documentation

◆ Resampler()

◆ ~Resampler()

Member Function Documentation

◆ defaultValue()

◆ doit() [1/2]

◆ doit() [2/2]

◆ doResample()

◆ ref()

◆ resample() [1/2]

◆ resample() [2/2]

◆ resample_inv() [1/2]

◆ resample_inv() [2/2]

◆ resample_inv_to_vox() [1/2]

◆ resample_inv_to_vox() [2/2]

◆ setDefaultValue()

◆ setRef()

◆ setVerboseStream()

◆ updateParameters()

Member Data Documentation

◆ _defval

◆ _ref

◆ _verbose_stream

template<class T>
class aims::Resampler< T >