This is the generic base class for 2D transformations. More...

#include <mia/2d/transform.hh>

Inheritance diagram for C2DTransformation:

Collaboration diagram for C2DTransformation:

Data Structures
class	const_iterator

class	iterator_impl
	Base of the implementation of an iterator over the transformation domain This iterator takes care of iterating over the transformation range. X is the fastest changing index. Some methods are abstract and must be defined in derived classes by using the specific transformation model. More...

Public Types
typedef C2DImage	Data
	generic name for the data used by this transformation More...

typedef C2DInterpolatorFactory	InterpolatorFactory
	generic name for the interpolation factory used by this transformation More...

typedef std::shared_ptr< C2DTransformation >	Pointer
	pointer type of this transformation More...

typedef C2DBounds	Size
	generic name for the size type used by this transformation More...

typedef C2DTransformation	type
	generic name for this transformation type More...

typedef C2DFVector	Vector
	generic name for the vector type used by this transformation More...

Public Types inherited from Transformation< C2DImage, C2DInterpolatorFactory >
typedef C2DImage	Data
	typedef for the data type to be transformed by this transformation More...

typedef C2DInterpolatorFactory	InterpolatorFactory
	type of the interpolator used by this transformation More...

Public Member Functions
virtual C2DFVector	apply (const C2DFVector &x) const __attribute__((deprecated))

virtual const_iterator	begin () const =0

	C2DTransformation (const C2DInterpolatorFactory &ipf)

virtual C2DTransformation *	clone () const __attribute__((warn_unused_result))

virtual size_t	degrees_of_freedom () const =0

virtual C2DFMatrix	derivative_at (const C2DFVector &x) const =0

virtual C2DFMatrix	derivative_at (int x, int y) const =0

virtual const_iterator	end () const =0

const std::string &	get_creator_string () const

virtual C2DFVector	get_displacement_at (const C2DFVector &x) const =0

virtual float	get_jacobian (const C2DFVectorfield &v, float delta) const =0

virtual float	get_max_transform () const =0

virtual C2DBounds	get_minimal_supported_image_size () const

virtual CDoubleVector	get_parameters () const =0

virtual const C2DBounds &	get_size () const =0

virtual C2DTransformation *	invert () const __attribute__((warn_unused_result))=0

virtual C2DFVector	operator() (const C2DFVector &x) const =0

virtual float	pertuberate (C2DFVectorfield &v) const =0

virtual bool	refine ()

void	set_creator_string (const std::string &s)

virtual void	set_identity ()=0

virtual void	set_parameters (const CDoubleVector &params)=0

virtual void	translate (const C2DFVectorfield &gradient, CDoubleVector &params) const =0

virtual void	update (float step, const C2DFVectorfield &a)=0

Pointer	upscale (const C2DBounds &size) const

Public Member Functions inherited from Transformation< C2DImage, C2DInterpolatorFactory >
double	get_energy_penalty () const

double	get_energy_penalty_and_gradient (CDoubleVector &gradient) const

bool	has_energy_penalty () const

std::shared_ptr< C2DImage >	operator() (const C2DImage &input) const

std::shared_ptr< C2DImage >	operator() (const C2DImage &input, const C2DInterpolatorFactory &ipf_override) const

void	set_interpolator_factory (const C2DInterpolatorFactory &ipf)

	Transformation (const C2DInterpolatorFactory &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 const char *	data_descr
	plug-in search path element "type" More...

static const char *	dim_descr
	plug-in search path element "data" More...

static constexpr const char *	input_spacing_attr = "in-pixel-spacing"

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

Static Public Attributes inherited from Transformation< C2DImage, C2DInterpolatorFactory >
static const char *	type_descr
	interface type for plugin implementation and search More...

Additional Inherited Members
Protected Member Functions inherited from Transformation< C2DImage, C2DInterpolatorFactory >
const C2DInterpolatorFactory &	get_interpolator_factory () const

Detailed Description

This is the generic base class for 2D transformations.

This class defines the generic interface for a 2D transformation. Most methods are pure abstract and need to be implemented by a "real" transformation. Actual implementations are provided as plug-ins.

Definition at line 45 of file 2d/transform.hh.

Member Typedef Documentation

◆ Data

typedef C2DImage C2DTransformation::Data

generic name for the data used by this transformation

Definition at line 48 of file 2d/transform.hh.

◆ InterpolatorFactory

typedef C2DInterpolatorFactory C2DTransformation::InterpolatorFactory

generic name for the interpolation factory used by this transformation

Definition at line 57 of file 2d/transform.hh.

◆ Pointer

typedef std::shared_ptr<C2DTransformation > C2DTransformation::Pointer

pointer type of this transformation

Definition at line 63 of file 2d/transform.hh.

◆ Size

typedef C2DBounds C2DTransformation::Size

generic name for the size type used by this transformation

Definition at line 51 of file 2d/transform.hh.

◆ type

typedef C2DTransformation C2DTransformation::type

generic name for this transformation type

Definition at line 60 of file 2d/transform.hh.

◆ Vector

typedef C2DFVector C2DTransformation::Vector

generic name for the vector type used by this transformation

Definition at line 54 of file 2d/transform.hh.

Constructor & Destructor Documentation

◆ C2DTransformation()

C2DTransformation::C2DTransformation ( const C2DInterpolatorFactory & ipf )

Standard constructor place holder

Member Function Documentation

◆ apply()

virtual C2DFVector C2DTransformation::apply ( const C2DFVector & x ) const

inlinevirtual

Returns: the displacement at coordinate x

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

Definition at line 341 of file 2d/transform.hh.

◆ begin()

virtual const_iterator C2DTransformation::begin ( ) const

pure virtual

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

◆ clone()

virtual C2DTransformation* C2DTransformation::clone ( ) const

virtual

Returns: a newly allocated copy of the actual transformation

◆ degrees_of_freedom()

virtual size_t C2DTransformation::degrees_of_freedom ( ) const

pure virtual

Returns: the number of free parameters this transformation provides

◆ derivative_at() [1/2]

virtual C2DFMatrix C2DTransformation::derivative_at ( const C2DFVector & x ) const

pure virtual

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

Parameters

x

Returns: 2x2 matrix of the derivative

◆ derivative_at() [2/2]

virtual C2DFMatrix C2DTransformation::derivative_at	(	int	x,
		int	y
	)		const

pure virtual

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

Parameters

x
y

Returns: 2x2 matrix of the derivative

◆ end()

virtual const_iterator C2DTransformation::end ( ) const

pure virtual

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

◆ get_creator_string()

const std::string& C2DTransformation::get_creator_string ( ) const

Returns: the description string used to create this transformations

◆ get_displacement_at()

virtual C2DFVector C2DTransformation::get_displacement_at ( const C2DFVector & x ) const

pure virtual

Returns: the displacement at coordinate x

◆ get_jacobian()

virtual float C2DTransformation::get_jacobian	(	const C2DFVectorfield &	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

◆ get_max_transform()

virtual float C2DTransformation::get_max_transform ( ) const

pure virtual

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

◆ get_minimal_supported_image_size()

virtual C2DBounds C2DTransformation::get_minimal_supported_image_size ( ) const

virtual

Returns: the minimal image size that makes sense for the transformation. Usually this is (1,1), but for spline based transformation the image must be larger.

◆ get_parameters()

virtual CDoubleVector C2DTransformation::get_parameters ( ) const

pure virtual

Returns: the transformation parameters as a flat value array

◆ get_size()

virtual const C2DBounds& C2DTransformation::get_size ( ) const

pure virtual

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

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

◆ invert()

virtual C2DTransformation* C2DTransformation::invert ( ) const

pure virtual

Returns: a the inverse transform

◆ operator()()

virtual C2DFVector C2DTransformation::operator() ( const C2DFVector & x ) const

pure virtual

apply the actual transformation to point x

Returns: transformed point

◆ pertuberate()

virtual float C2DTransformation::pertuberate ( C2DFVectorfield & 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

◆ refine()

virtual bool C2DTransformation::refine ( )

virtual

If applicaple the transformation model is refined (e.g. splines are converted to a denser coefficient distribution.

Returns: true if refinement was applied, and false otherwise

◆ set_creator_string()

void C2DTransformation::set_creator_string ( const std::string & s )

Set the descrition string that was used to create this transformstion

Parameters

s

◆ set_identity()

virtual void C2DTransformation::set_identity ( )

pure virtual

set the transformation to be the identity transform

◆ set_parameters()

virtual void C2DTransformation::set_parameters ( const CDoubleVector & params )

pure virtual

sets the transformation parameters from a flat value array

◆ translate()

virtual void C2DTransformation::translate	(	const C2DFVectorfield &	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

◆ update()

virtual void C2DTransformation::update	(	float	step,
		const C2DFVectorfield &	a
	)

pure virtual

update a transformation by using a vector field

Remarks: this is too specialized and should go away

◆ upscale()

Pointer C2DTransformation::upscale ( const C2DBounds & size ) const

Transforation upscaling to new image size

Parameters

size	new size of the transformation

Returns: shared pointer to upscaled transformation

Field Documentation

◆ data_descr

const char* C2DTransformation::data_descr

static

plug-in search path element "type"

Definition at line 66 of file 2d/transform.hh.

◆ dim_descr

const char* C2DTransformation::dim_descr

static

plug-in search path element "data"

Definition at line 69 of file 2d/transform.hh.

◆ input_spacing_attr

constexpr const char* C2DTransformation::input_spacing_attr = "in-pixel-spacing"

static

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

Definition at line 374 of file 2d/transform.hh.

◆ output_spacing_attr

constexpr const char* C2DTransformation::output_spacing_attr = "out-pixel-spacing"

static

This attribute defines the output voxel spacing of this transform.

Definition at line 379 of file 2d/transform.hh.

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

2d/transform.hh

Data Structures

Public Types

Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Data

◆ InterpolatorFactory

◆ Pointer

◆ Size

◆ type

◆ Vector

Constructor & Destructor Documentation

◆ C2DTransformation()

Member Function Documentation

◆ apply()

◆ begin()

◆ clone()

◆ degrees_of_freedom()

◆ derivative_at() [1/2]

◆ derivative_at() [2/2]

◆ end()

◆ get_creator_string()

◆ get_displacement_at()

◆ get_jacobian()

◆ get_max_transform()

◆ get_minimal_supported_image_size()

◆ get_parameters()

◆ get_size()

◆ invert()

◆ operator()()

◆ pertuberate()

◆ refine()

◆ set_creator_string()

◆ set_identity()

◆ set_parameters()

◆ translate()

◆ update()

◆ upscale()

Field Documentation

◆ data_descr

◆ dim_descr

◆ input_spacing_attr

◆ output_spacing_attr