This is the generic base class for 3D transformations. More...

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

Inheritance diagram for C3DTransformation:

Collaboration diagram for C3DTransformation:

Data Structures
class	const_iterator

class	iterator_impl

Public Member Functions
virtual C3DFVector	apply (const C3DFVector &x) const __attribute__((deprecated))

virtual const_iterator	begin () const =0

virtual const_iterator	begin_range (const C3DBounds &begin, const C3DBounds &end) const =0

	C3DTransformation (const C3DInterpolatorFactory &ipf)

virtual C3DTransformation *	clone () const

virtual size_t	degrees_of_freedom () const =0

virtual C3DFMatrix	derivative_at (int x, int y, int z) const =0

virtual C3DFMatrix	derivative_at (const C3DFVector &x) const =0

virtual const_iterator	end () const =0

virtual const_iterator	end_range (const C3DBounds &begin, const C3DBounds &end) const =0

const std::string &	get_creator_string () const

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

virtual float	get_jacobian (const C3DFVectorfield &v, float delta) const =0

virtual float	get_max_transform () const =0

virtual C3DBounds	get_minimal_supported_image_size () const

virtual CDoubleVector	get_parameters () const =0

virtual const C3DBounds &	get_size () const =0

virtual C3DTransformation *	invert () const =0

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

virtual float	pertuberate (C3DFVectorfield &v) const =0

virtual bool	refine ()

virtual void	reinit () const

void	set_creator_string (const std::string &s)

void	set_debug ()

virtual void	set_identity ()=0

virtual void	set_parameters (const CDoubleVector &params)=0

virtual void	translate (const C3DFVectorfield &gradient, CDoubleVector &params) const =0

virtual void	update (float step, const C3DFVectorfield &a)=0

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)

Static Public Attributes
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
bool	get_debug () const

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

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...

Detailed Description

This is the generic base class for 3D transformations.

This class defines the interface for 3D transformations. Most methods are pure abstract and need to be implemented by a "real" transformation.

Definition at line 53 of file 3d/transform.hh.

Constructor & Destructor Documentation

◆ C3DTransformation()

C3DTransformation::C3DTransformation ( const C3DInterpolatorFactory & ipf )

Standard constructor place holder

Member Function Documentation

◆ apply()

virtual C3DFVector C3DTransformation::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 in C3DLinearTransform.

◆ begin()

virtual const_iterator C3DTransformation::begin ( ) const

pure virtual

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

Implemented in C3DLinearTransform.

◆ begin_range()

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

pure virtual

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

Implemented in C3DLinearTransform.

◆ clone()

virtual C3DTransformation* C3DTransformation::clone ( ) const

virtual

Returns: a newly allocated copy of the actual transformation

◆ degrees_of_freedom()

virtual size_t C3DTransformation::degrees_of_freedom ( ) const

pure virtual

Returns: the number of free parameters this transformation provides

Implemented in C3DLinearTransform.

◆ derivative_at() [1/2]

virtual C3DFMatrix C3DTransformation::derivative_at	(	int	x,
		int	y,
		int	z
	)		const

pure virtual

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

Parameters

x
y
z

Returns: 3x3 matrix of the derivative

Implemented in C3DLinearTransform.

◆ derivative_at() [2/2]

virtual C3DFMatrix C3DTransformation::derivative_at ( const C3DFVector & x ) const

pure virtual

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

Parameters

x

Returns: 3x3 matrix of the derivative

Implemented in C3DLinearTransform.

◆ end()

virtual const_iterator C3DTransformation::end ( ) const

pure virtual

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

Implemented in C3DLinearTransform.

◆ end_range()

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

pure virtual

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

Implemented in C3DLinearTransform.

◆ get_creator_string()

const std::string& C3DTransformation::get_creator_string ( ) const

Returns: the description string used to create this transformations

◆ get_debug()

bool C3DTransformation::get_debug ( ) const

protected

Returns: information about the debug state

◆ get_displacement_at()

virtual C3DFVector C3DTransformation::get_displacement_at ( const C3DFVector & x ) const

pure virtual

Returns the displacement of the transformation at a given coordinate

Parameters

x	coordinate

Returns: actual displacement

◆ get_jacobian()

virtual float C3DTransformation::get_jacobian	(	const C3DFVectorfield &	v,
		float	delta
	)		const

pure 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

Implemented in C3DLinearTransform.

◆ get_max_transform()

virtual float C3DTransformation::get_max_transform ( ) const

pure virtual

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

Implemented in C3DLinearTransform.

◆ get_minimal_supported_image_size()

virtual C3DBounds C3DTransformation::get_minimal_supported_image_size ( ) const

virtual

◆ get_parameters()

virtual CDoubleVector C3DTransformation::get_parameters ( ) const

pure virtual

Returns: the transformation parameters as a flat value array

Implemented in C3DLinearTransform.

◆ get_size()

virtual const C3DBounds& C3DTransformation::get_size ( ) const

pure 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

Implemented in C3DLinearTransform.

◆ invert()

virtual C3DTransformation* C3DTransformation::invert ( ) const

pure virtual

Returns: a the inverse transform

Implemented in C3DLinearTransform.

◆ operator()()

virtual C3DFVector C3DTransformation::operator() ( const C3DFVector & x ) const

pure virtual

apply the actual transformation to point x

Returns: transformed point

Implemented in C3DLinearTransform.

◆ pertuberate()

virtual float C3DTransformation::pertuberate ( C3DFVectorfield & v ) const

pure 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

Implemented in C3DLinearTransform.

◆ refine()

virtual bool C3DTransformation::refine ( )

virtual

Increase the number of coefficients along the axis according to the maximum given by the c-rate. This is the complemantary step to upscaling the transformation.

Returns: true if an actual refinment was done.

◆ reinit()

virtual void C3DTransformation::reinit ( ) const

virtual

Placeholder for transformations that might need special initializations like the B-spline based transformation

◆ set_creator_string()

void C3DTransformation::set_creator_string ( const std::string & s )

Set the descrition string that was used to create this transformstion

Parameters

s

◆ set_debug()

void C3DTransformation::set_debug ( )

Enable some additional debugging.

◆ set_identity()

virtual void C3DTransformation::set_identity ( )

pure virtual

set the transformation to be the identity transform

Implemented in C3DLinearTransform.

◆ set_parameters()

virtual void C3DTransformation::set_parameters ( const CDoubleVector & params )

pure virtual

sets the transformation parameters from a flat value array

Implemented in C3DLinearTransform.

◆ translate()

virtual void C3DTransformation::translate	(	const C3DFVectorfield &	gradient,
		CDoubleVector &	params
	)		const

pure 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

Implemented in C3DLinearTransform.

◆ update()

virtual void C3DTransformation::update	(	float	step,
		const C3DFVectorfield &	a
	)

pure virtual

update a transformation by using a vector field

Remarks: this is too specialized and should go away

Implemented in C3DLinearTransform.

◆ upscale()

P3DTransformation C3DTransformation::upscale ( const C3DBounds & size ) const

Transforation upscaling to new image size

Parameters

size	new size of the transformation

Returns: shared pointer to upscaled transformation

Field Documentation

◆ input_spacing_attr

constexpr const char* C3DTransformation::input_spacing_attr = "in-voxel-spacing"

static

This attribute defines the voxel spacing of the input data of this transform.

Definition at line 364 of file 3d/transform.hh.

◆ output_spacing_attr

constexpr const char* C3DTransformation::output_spacing_attr = "out-voxel-spacing"

static

This attribute defines the output voxel spacing of this transform.

Definition at line 369 of file 3d/transform.hh.

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

3d/transform.hh

Data Structures

Public Member Functions

Static Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ C3DTransformation()

Member Function Documentation

◆ apply()

◆ begin()

◆ begin_range()

◆ clone()

◆ degrees_of_freedom()

◆ derivative_at() [1/2]

◆ derivative_at() [2/2]

◆ end()

◆ end_range()

◆ get_creator_string()

◆ get_debug()

◆ get_displacement_at()

◆ get_jacobian()

◆ get_max_transform()

◆ get_minimal_supported_image_size()

◆ get_parameters()

◆ get_size()

◆ invert()

◆ operator()()

◆ pertuberate()

◆ refine()

◆ reinit()

◆ set_creator_string()

◆ set_debug()

◆ set_identity()

◆ set_parameters()

◆ translate()

◆ update()

◆ upscale()

Field Documentation

◆ input_spacing_attr

◆ output_spacing_attr