#include <mia/3d/linear_transform.hh>

Inheritance diagram for C3DLinearTransform:

Collaboration diagram for C3DLinearTransform:

Data Structures
class	iterator_impl

Public Member Functions
virtual void	add (const C3DTransformation &a)
	these functions should be removed More...

virtual C3DFVector	apply (const C3DFVector &x) const

virtual C3DTransformation::const_iterator	begin () const

virtual C3DTransformation::const_iterator	begin_range (const C3DBounds &begin, const C3DBounds &end) const

	C3DLinearTransform ()

	C3DLinearTransform (const C3DBounds &size, const C3DInterpolatorFactory &ipf)

virtual float	curl () const

virtual size_t	degrees_of_freedom () const

virtual C3DFMatrix	derivative_at (const C3DFVector &x) const

virtual C3DFMatrix	derivative_at (int x, int y, int z) const

virtual float	divergence () const

virtual C3DTransformation::const_iterator	end () const

virtual C3DTransformation::const_iterator	end_range (const C3DBounds &begin, const C3DBounds &end) const

virtual double	get_divcurl_cost (double wd, double wr, CDoubleVector &gradient) const

double	get_divcurl_cost (double wd, double wr) const

virtual float	get_jacobian (const C3DFVectorfield &v, float delta) const

virtual float	get_max_transform () const

virtual CDoubleVector	get_parameters () const

virtual const C3DBounds &	get_size () const

virtual C3DTransformation *	invert () const

virtual C3DFVector	operator() (const C3DFVector &x) const

virtual float	pertuberate (C3DFVectorfield &v) const

virtual void	set_identity ()

virtual void	set_parameters (const CDoubleVector &params)

virtual void	translate (const C3DFVectorfield &gradient, CDoubleVector &params) const

virtual void	update (float step, const C3DFVectorfield &a)

Public Member Functions inherited from C3DTransformation
	C3DTransformation (const C3DInterpolatorFactory &ipf)

virtual C3DTransformation *	clone () const

const std::string &	get_creator_string () const

virtual C3DFVector	get_displacement_at (const C3DFVector &x) const =0

virtual C3DBounds	get_minimal_supported_image_size () const

virtual bool	refine ()

virtual void	reinit () const

void	set_creator_string (const std::string &s)

void	set_debug ()

P3DTransformation	upscale (const C3DBounds &size) const

Public Member Functions inherited from Transformation< C3DImage, C3DInterpolatorFactory >
double	get_energy_penalty () const

double	get_energy_penalty_and_gradient (CDoubleVector &gradient) const

bool	has_energy_penalty () const

std::shared_ptr< C3DImage >	operator() (const C3DImage &input) const

std::shared_ptr< C3DImage >	operator() (const C3DImage &input, const C3DInterpolatorFactory &ipf_override) const

void	set_interpolator_factory (const C3DInterpolatorFactory &ipf)

	Transformation (const C3DInterpolatorFactory &ipf)

virtual	~Transformation ()

Public Member Functions inherited from CIOData
const std::string &	get_source_format () const

void	set_source_format (const std::string &format)

Public Member Functions inherited from CAttributedData
CAttributeMap::const_iterator	begin_attributes () const

void	delete_attribute (const std::string &key)

CAttributeMap::const_iterator	end_attributes () const

const PAttribute	get_attribute (const std::string &key) const

template<typename T >
const T	get_attribute_as (const std::string &key) const

template<typename T >
const T	get_attribute_as (const std::string &key, T default_value) const

const std::string	get_attribute_as_string (const std::string &key) const
	returns the requested attribute as string, returns an empty string if attribute doesn't exist More...

bool	has_attribute (const std::string &key) const

CAttributedData &	operator= (const CAttributedData &org)
	Assignemt operator. More...

void	print (std::ostream &os) const

void	set_attribute (const std::string &key, PAttribute attr)

void	set_attribute (const std::string &key, const std::string &value)

template<typename T >
void	set_attribute (const std::string &key, const T &value)

void	set_attribute (const std::string &key, const char *value)

void	set_attributes (CAttributeMap::const_iterator begin, CAttributeMap::const_iterator end)

	CAttributedData ()

	CAttributedData (const CAttributedData &org)

	CAttributedData (PAttributeMap attr)

Additional Inherited Members
Public Types inherited from Transformation< C3DImage, C3DInterpolatorFactory >
typedef C3DImage	Data
	typedef for the data type to be transformed by this transformation More...

typedef C3DInterpolatorFactory	InterpolatorFactory
	type of the interpolator used by this transformation More...

Static Public Attributes inherited from C3DTransformation
static constexpr const char *	input_spacing_attr = "in-voxel-spacing"

static constexpr const char *	output_spacing_attr = "out-voxel-spacing"

Static Public Attributes inherited from Transformation< C3DImage, C3DInterpolatorFactory >
static const char *	type_descr
	interface type for plugin implementation and search More...

Protected Member Functions inherited from C3DTransformation
bool	get_debug () const

Protected Member Functions inherited from Transformation< C3DImage, C3DInterpolatorFactory >
const C3DInterpolatorFactory &	get_interpolator_factory () const

Detailed Description

Definition at line 29 of file linear_transform.hh.

Constructor & Destructor Documentation

◆ C3DLinearTransform() [1/2]

C3DLinearTransform::C3DLinearTransform ( )

◆ C3DLinearTransform() [2/2]

C3DLinearTransform::C3DLinearTransform	(	const C3DBounds &	size,
		const C3DInterpolatorFactory &	ipf
	)

Member Function Documentation

◆ add()

virtual void C3DLinearTransform::add ( const C3DTransformation & a )

virtual

these functions should be removed

◆ apply()

virtual C3DFVector C3DLinearTransform::apply ( const C3DFVector & x ) const

virtual

Returns: the displacement at coordinate x

Remarks: rename the function to something that explains better whats going on

Reimplemented from C3DTransformation.

◆ begin()

virtual C3DTransformation::const_iterator C3DLinearTransform::begin ( ) const

virtual

Returns: the start iterator of the transformation that iterates over the grid of the area the ransformation is defined on

Implements C3DTransformation.

◆ begin_range()

virtual C3DTransformation::const_iterator C3DLinearTransform::begin_range	(	const C3DBounds &	begin,
		const C3DBounds &	end
	)		const

virtual

Returns: the start iterator of the transformation that iterates over the grid of the area the ransformation is defined on

Implements C3DTransformation.

◆ curl()

virtual float C3DLinearTransform::curl ( ) const

virtual

◆ degrees_of_freedom()

virtual size_t C3DLinearTransform::degrees_of_freedom ( ) const

virtual

Returns: the number of free parameters this transformation provides

Implements C3DTransformation.

◆ derivative_at() [1/2]

virtual C3DFMatrix C3DLinearTransform::derivative_at ( const C3DFVector & x ) const

virtual

evaluate the derivative (Jacobian matrix) of the transformation at the given coordinates

Parameters

x

Returns: 3x3 matrix of the derivative

Implements C3DTransformation.

◆ derivative_at() [2/2]

virtual C3DFMatrix C3DLinearTransform::derivative_at	(	int	x,
		int	y,
		int	z
	)		const

virtual

evaluate the derivative (Jacobian matrix) of the transformation at the given grid coordinates

Parameters

x
y
z

Returns: 3x3 matrix of the derivative

Implements C3DTransformation.

◆ divergence()

virtual float C3DLinearTransform::divergence ( ) const

virtual

◆ end()

virtual C3DTransformation::const_iterator C3DLinearTransform::end ( ) const

virtual

Returns: the end iterator of the transformation that iterates over the grid of the area the ransformation is defined on

Implements C3DTransformation.

◆ end_range()

virtual C3DTransformation::const_iterator C3DLinearTransform::end_range	(	const C3DBounds &	begin,
		const C3DBounds &	end
	)		const

virtual

Returns: the end iterator of the transformation that iterates over the grid of the area the ransformation is defined on

Implements C3DTransformation.

◆ get_divcurl_cost() [1/2]

virtual double C3DLinearTransform::get_divcurl_cost	(	double	wd,
		double	wr,
		CDoubleVector &	gradient
	)		const

virtual

◆ get_divcurl_cost() [2/2]

double C3DLinearTransform::get_divcurl_cost	(	double	wd,
		double	wr
	)		const

◆ get_jacobian()

virtual float C3DLinearTransform::get_jacobian	(	const C3DFVectorfield &	v,
		float	delta
	)		const

virtual

Evaluate the Jacobian of the transformation when updated with vector field v by factor delta

Returns: Jacobian

Remarks: this only is used for fluid dynamics registration and should probably be moved elsewhere

Implements C3DTransformation.

◆ get_max_transform()

virtual float C3DLinearTransform::get_max_transform ( ) const

virtual

Returns: the (approximate) maximum absolute translation of the transformation over the whole domain

Implements C3DTransformation.

◆ get_parameters()

virtual CDoubleVector C3DLinearTransform::get_parameters ( ) const

virtual

Returns: the transformation parameters as a flat value array

Implements C3DTransformation.

◆ get_size()

virtual const C3DBounds& C3DLinearTransform::get_size ( ) const

virtual

A transformation is defined on [0,X-1]x[0.Y-1]y[0,Z-1].

Returns: the upper boundaries (X,Y,Z) of this range

Implements C3DTransformation.

◆ invert()

virtual C3DTransformation* C3DLinearTransform::invert ( ) const

virtual

Returns: a the inverse transform

Implements C3DTransformation.

◆ operator()()

virtual C3DFVector C3DLinearTransform::operator() ( const C3DFVector & x ) const

virtual

apply the actual transformation to point x

Returns: transformed point

Implements C3DTransformation.

◆ pertuberate()

virtual float C3DLinearTransform::pertuberate ( C3DFVectorfield & v ) const

virtual

evaluate the pertuberation of a vectorfield combined with this transformation

Parameters

[in,out] v vectorfield to be pertuberated

Returns: maximum value of the pertuberation

Remarks: this makes only sense for fluid dynamics registration and should be handled elsewhere

Implements C3DTransformation.

◆ set_identity()

virtual void C3DLinearTransform::set_identity ( )

virtual

set the transformation to be the identity transform

Implements C3DTransformation.

◆ set_parameters()

virtual void C3DLinearTransform::set_parameters ( const CDoubleVector & params )

virtual

sets the transformation parameters from a flat value array

Implements C3DTransformation.

◆ translate()

virtual void C3DLinearTransform::translate	(	const C3DFVectorfield &	gradient,
		CDoubleVector &	params
	)		const

virtual

Translate the input gradient to a vector field in the space of the transformation field

Remarks: this is too specialized and needs to be replaced by something

Implements C3DTransformation.

◆ update()

virtual void C3DLinearTransform::update	(	float	step,
		const C3DFVectorfield &	a
	)

virtual

update a transformation by using a vector field

Remarks: this is too specialized and should go away

Implements C3DTransformation.

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

linear_transform.hh

Data Structures

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ C3DLinearTransform() [1/2]

◆ C3DLinearTransform() [2/2]

Member Function Documentation

◆ add()

◆ apply()

◆ begin()

◆ begin_range()

◆ curl()

◆ degrees_of_freedom()

◆ derivative_at() [1/2]

◆ derivative_at() [2/2]

◆ divergence()

◆ end()

◆ end_range()

◆ get_divcurl_cost() [1/2]

◆ get_divcurl_cost() [2/2]

◆ get_jacobian()

◆ get_max_transform()

◆ get_parameters()

◆ get_size()

◆ invert()

◆ operator()()

◆ pertuberate()

◆ set_identity()

◆ set_parameters()

◆ translate()

◆ update()