Base class for all NiftyReg registrations. More...

#include "NiftyRegistration.h"

Inheritance diagram for sirf::NiftyRegistration< dataType >:

Public Member Functions
	NiftyRegistration ()
	Constructor.

virtual	~NiftyRegistration ()
	Destructor.

void	set_parameter_file (const std::string &parameter_filename)
	Set parameter file.

void	set_parameter (const std::string &par, const std::string &arg1="", const std::string &arg2="")

void	set_reference_mask (const std::shared_ptr< const ImageData > reference_mask_sptr)
	Set reference mask.

void	set_floating_mask (const std::shared_ptr< const ImageData > floating_mask_sptr)
	Set floating mask.

Public Member Functions inherited from sirf::NiftiBasedRegistration< dataType >
	NiftiBasedRegistration ()
	Constructor.

virtual	~NiftiBasedRegistration ()
	Destructor.

virtual const std::shared_ptr< const Transformation< dataType > >	get_displacement_field_forward_sptr (const unsigned idx=0) const
	Get forward displacement field image.

virtual const std::shared_ptr< const Transformation< dataType > >	get_displacement_field_inverse_sptr (const unsigned idx=0) const
	Get inverse displacement field image.

Public Member Functions inherited from sirf::Registration< dataType >
	Registration ()
	Constructor.

virtual	~Registration ()
	Destructor.

void	set_reference_image (const std::shared_ptr< const ImageData > reference_image_sptr)
	Set reference image.

void	set_floating_image (const std::shared_ptr< const ImageData > floating_image_sptr)
	Set floating image. Will clear any previous floating images.

void	add_floating_image (const std::shared_ptr< const ImageData > floating_image_sptr)
	Add floating image.

void	set_reference_image_filename (const std::string &filename)
	Set reference image filename. Will be read as NiftiImageData.

void	set_floating_image_filename (const std::string &filename)
	Set floating image filename. Will be read as NiftiImageData.

void	add_floating_image_filename (const std::string &filename)
	Add floating image filename. Will be read as NiftiImageData.

void	clear_floating_images ()
	Clear floating images.

virtual void	process ()=0
	Process.

virtual const std::shared_ptr< const ImageData >	get_output_sptr (const unsigned idx=0) const
	Get registered image.

virtual const std::shared_ptr< const Transformation< dataType > >	get_deformation_field_forward_sptr (const unsigned idx=0) const
	Get forward deformation field image.

virtual const std::shared_ptr< const Transformation< dataType > >	get_deformation_field_inverse_sptr (const unsigned idx=0) const =0
	Get inverse deformation field image.

Protected Member Functions
virtual void	parse_parameter_file ()=0
	Parse parameter file.

void	set_up_inputs ()
	Set up inputs.

virtual void	set_parameters ()=0
	Set any extra parameters.

Protected Member Functions inherited from sirf::Registration< dataType >
virtual void	check_parameters () const
	Check parameters.

Protected Attributes
std::vector< std::string >	_extra_params
	Store extra parameters. Only apply them after parsing.

std::string	_parameter_filename
	Parameter filename.

std::shared_ptr< const ImageData >	_floating_mask_sptr
	Floating mask.

std::shared_ptr< const ImageData >	_reference_mask_sptr
	Reference mask.

std::shared_ptr< const NiftiImageData3D< dataType > >	_floating_mask_nifti_sptr
	Floating mask (as NiftiImageData3D)

std::shared_ptr< const NiftiImageData3D< dataType > >	_reference_mask_nifti_sptr
	Reference mask (as NiftiImageData3D)

Protected Attributes inherited from sirf::NiftiBasedRegistration< dataType >
std::shared_ptr< const NiftiImageData3D< dataType > >	_reference_image_nifti_sptr
	Reference image (as NiftiImageData3D)

std::vector< std::shared_ptr< const NiftiImageData3D< dataType > > >	_floating_images_nifti
	Floating image (as NiftiImageData3D)

std::vector< std::shared_ptr< NiftiImageData3D< dataType > > >	_warped_images_nifti
	Output (as NiftiImageData3D)

Protected Attributes inherited from sirf::Registration< dataType >
std::shared_ptr< const ImageData >	_reference_image_sptr
	Reference image.

std::vector< std::shared_ptr< const ImageData > >	_floating_images
	Floating image.

std::vector< std::shared_ptr< ImageData > >	_warped_images
	Warped image.

std::vector< std::shared_ptr< Transformation< dataType > > >	_def_fwd_images
	Forward deformation field image.

std::string	_reference_image_filename = ""
	Reference image filename.

std::vector< std::string >	_floating_image_filenames
	Floating image filenames.

Additional Inherited Members
Static Public Member Functions inherited from sirf::NiftiBasedRegistration< dataType >
static void	convert_to_NiftiImageData_if_not_already (std::shared_ptr< const NiftiImageData3D< dataType > > &output_sptr, const std::shared_ptr< const ImageData > &input_sptr)
	Convert an ImageData to NiftiImageData. Try to dynamic pointer cast, else create new image.

Detailed Description

template<class dataType>
class sirf::NiftyRegistration< dataType >

Base class for all NiftyReg registrations.

Author: Richard Brown; SyneRBI

Member Function Documentation

◆ set_parameter()

template<class dataType >

void NiftyRegistration::set_parameter	(	const std::string &	par,
		const std::string &	arg1 = `""`,
		const std::string &	arg2 = `""`
	)

Set string parameter. Check if any set methods match the method given by par. If so, set the value given by arg. Convert to float/int etc., as necessary. Up to 2 arguments, leave blank if unneeded. These are applied after parsing the parameter file.

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

/home/sirfuser/devel/buildVM/sources/SIRF/src/Registration/cReg/include/sirf/Reg/NiftyRegistration.h
/home/sirfuser/devel/buildVM/sources/SIRF/src/Registration/cReg/NiftyRegistration.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

template<class dataType> class sirf::NiftyRegistration< dataType >

Member Function Documentation

◆ set_parameter()

template<class dataType>
class sirf::NiftyRegistration< dataType >