Reconstructor class defines a way to do 3D recontruction. More...

#include <reconstructor.h>

Inheritance diagram for EMAN::Reconstructor:

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Collaboration diagram for EMAN::Reconstructor:

Public Member Functions
	Reconstructor ()

virtual	~Reconstructor ()

virtual void	setup ()=0
	Initialize the reconstructor. More...

virtual void	setup_seed (EMData *seed, float seed_weight)
	Initialize the reconstructor with a seed volume. More...

virtual void	setup_seedandweights (EMData seed, EMData weight)
	Initialize the reconstructor with a seed volume, as above. More...

virtual EMData *	preprocess_slice (const EMData *const slice, const Transform &t=Transform())
	While you can just insert unprocessed slices, if you call preprocess_slice yourself, and insert the returned slice instead, repeatedly, it can save a fair bit of computation. More...

virtual int	insert_slice (const EMData *const slice, const Transform &euler, const float weight)
	Insert an image slice to the reconstructor. More...

int	insert_slice (const EMData *const slice, const Transform &euler)

virtual int	determine_slice_agreement (EMData *slice, const Transform &euler, const float weight=1.0, bool sub=true)
	Compares a slice to the current reconstruction volume and computes a normalization factor and quality. More...

virtual EMData *	projection (const Transform &euler, int ret_fourier=1)
	This will create a projection from the current reconstruction. More...

virtual EMData *	finish (bool doift=true)
	Finish reconstruction and return the complete model. More...

virtual void	clear ()
	set the volume and tmp_volume data to zero, for use in Monte Carlo reconstructors More...

void	print_params () const
	Print the current parameters to std::out. More...

EMObject &	operator[] (const string &key)

Public Member Functions inherited from EMAN::FactoryBase
	FactoryBase ()

virtual	~FactoryBase ()

virtual string	get_name () const =0
	Get the unique name of this class (especially for factory based instantiation access) More...

virtual string	get_desc () const =0
	Get a clear, concise description of this class. More...

Dict	get_params () const
	get a copy of the parameters of this class More...

void	set_params (const Dict &new_params)
	Set new parameters. More...

void	set_param (const string key, const EMObject val)

virtual TypeDict	get_param_types () const =0

void	insert_params (const Dict &new_params)
	Insert parameters. More...

Dict	copy_relevant_params (const FactoryBase *const that) const

Private Member Functions
	Reconstructor (const Reconstructor &that)

Reconstructor &	operator= (const Reconstructor &)

Additional Inherited Members
Protected Attributes inherited from EMAN::FactoryBase
Dict	params
	This is the dictionary the stores the parameters of the object. More...

Detailed Description

Reconstructor class defines a way to do 3D recontruction.

A reconstruction is done by 3 steps:

set up.
insert all image slices.
finish up. The last step will return the result.

Reconstructor class is the base class for all reconstructors. Each specific Reconstructor class has a unique ID name. This name is used to create a Reconstructor instance or do a reconstruction.

All Reconstructor classes in EMAN are managed by a Factory
pattern. So each Reconstructor class must define:
  - a unique name to idenfity itself in the factory.
  - a static method to register itself in the factory.

Typical usages of Reconstructors are as follows:

How to get all the Reconstructor names:
vector<string> all_reconstructors = Factory<Reconstructor>::get_list();

EMAN::Factory::get_list
static vector< string > get_list()
Definition: emobject.h:837
How to use a Reconstructor
Reconstructor* r = Factory<Reconstructor>::get("fourier");

r->setup();

r->determine_slice_agreement(slice,euler,weight,true);

...

r->insert_slice(slice, euler, weight);

...

EMData* result = r->finish();

EMAN::Factory::get
static T * get(const string &instance_name)
Definition: emobject.h:781

EMAN::Reconstructor::Reconstructor
Reconstructor()
Definition: reconstructor.h:111
How to define a new Reconstructor type
A new XYZReconstructor class must implement the following functions: (Please replace 'XYZ' with your own class name).
void setup();

int insert_slice(const EMData* const slice, const Transform & t);

EMData * finish();

string get_name() const { return "xyz"; }

static Reconstructor *NEW() { return new XYZReconstructor(); }

TypeDict get_param_types() const;

EMAN::FactoryBase::get_param_types
virtual TypeDict get_param_types() const =0

EMAN::FactoryBase::get_name
virtual string get_name() const =0
Get the unique name of this class (especially for factory based instantiation access)

EMAN::Reconstructor::setup
virtual void setup()=0
Initialize the reconstructor.

EMAN::Reconstructor::insert_slice
virtual int insert_slice(const EMData *const slice, const Transform &euler, const float weight)
Insert an image slice to the reconstructor.
Definition: reconstructor.h:147

EMAN::Reconstructor::finish
virtual EMData * finish(bool doift=true)
Finish reconstruction and return the complete model.
Definition: reconstructor.h:180

Definition at line 108 of file reconstructor.h.

Constructor & Destructor Documentation

◆ Reconstructor() [1/2]

EMAN::Reconstructor::Reconstructor ( )

inline

Definition at line 111 of file reconstructor.h.

111{}

◆ ~Reconstructor()

virtual EMAN::Reconstructor::~Reconstructor ( )

inlinevirtual

Definition at line 112 of file reconstructor.h.

112{}

◆ Reconstructor() [2/2]

EMAN::Reconstructor::Reconstructor ( const Reconstructor & that )

private

Member Function Documentation

◆ clear()

virtual void EMAN::Reconstructor::clear ( )

inlinevirtual

set the volume and tmp_volume data to zero, for use in Monte Carlo reconstructors

Reimplemented in EMAN::FourierReconstructor, and EMAN::FourierIterReconstructor.

Definition at line 184 of file reconstructor.h.

184{throw; }

◆ determine_slice_agreement()

virtual int EMAN::Reconstructor::determine_slice_agreement	(	EMData *	slice,
		const Transform &	euler,
		const float	weight = `1.0`,
		bool	sub = `true`
	)

inlinevirtual

Compares a slice to the current reconstruction volume and computes a normalization factor and quality.

Normalization and quality are returned via attributes set in the passed slice. You may freely mix calls to determine_slice_agreement with calls to insert_slice, but note that determine_slice_agreement can only use information from slices that have already been inserted. reconstruct_norm contains the relative normalization factor which should be applied before inserting the slice reconstruct_qual contains a quality factor (larger better) for this slice as compared to the existing reconstruction

Parameters

input_slice	The EMData slice to be compared
euler	The orientation of the slice as a Transform object
weight	A weighting factor for this slice, generally the number of particles in a class-average. May be ignored by some reconstructors
sub	Flag indicating whether to subtract the slice from the volume before comparing. May be ignored by some reconstructors

Returns: 0 if OK. 1 if error.

Exceptions

Reimplemented in EMAN::FourierReconstructor, EMAN::WienerFourierReconstructor, EMAN::FourierIterReconstructor, EMAN::BackProjectionReconstructor, and EMAN::RealMedianReconstructor.

Definition at line 163 of file reconstructor.h.

163{ throw; }

◆ finish()

virtual EMData * EMAN::Reconstructor::finish ( bool doift = true )

inlinevirtual

Finish reconstruction and return the complete model.

Parameters

doift A flag indicating whether the returned object should be guaranteed to be in real-space (true) or should be left in whatever space the reconstructor generated

Returns: The result 3D model.

Reimplemented in EMAN::nn4_ctfwReconstructor, EMAN::nn4_ctfwsReconstructor, EMAN::XYZReconstructor, EMAN::FourierReconstructorSimple2D, EMAN::FourierReconstructor, EMAN::WienerFourierReconstructor, EMAN::FourierIterReconstructor, EMAN::BackProjectionReconstructor, EMAN::RealMedianReconstructor, EMAN::nn4Reconstructor, EMAN::nn4_rectReconstructor, EMAN::nnSSNR_Reconstructor, EMAN::nn4_ctfReconstructor, EMAN::nn4_ctf_rectReconstructor, and EMAN::nnSSNR_ctfReconstructor.

Definition at line 180 of file reconstructor.h.

180{ throw; }

◆ insert_slice() [1/2]

int EMAN::Reconstructor::insert_slice	(	const EMData *const	slice,
		const Transform &	euler
	)

inline

Definition at line 148 of file reconstructor.h.

148{ return this->insert_slice(slice, euler, 1.0f); }

References insert_slice().

Referenced by insert_slice().

◆ insert_slice() [2/2]

virtual int EMAN::Reconstructor::insert_slice	(	const EMData *const	slice,
		const Transform &	euler,
		const float	weight
	)

inlinevirtual

Insert an image slice to the reconstructor.

To insert multiple image slices, call this function multiple times.

Parameters

slice	Image slice.
euler	Euler angle of this image slice.
weight	A weighting factor for this slice, generally the number of particles in a class-average. May be ignored by some reconstructors

Returns: 0 if OK. 1 if error.

Reimplemented in EMAN::XYZReconstructor, EMAN::FourierReconstructorSimple2D, EMAN::FourierReconstructor, EMAN::WienerFourierReconstructor, EMAN::FourierIterReconstructor, EMAN::BackProjectionReconstructor, EMAN::RealMedianReconstructor, EMAN::nn4Reconstructor, EMAN::nn4_rectReconstructor, EMAN::nnSSNR_Reconstructor, EMAN::nn4_ctfReconstructor, EMAN::nn4_ctfwReconstructor, EMAN::nn4_ctfwsReconstructor, EMAN::nn4_ctf_rectReconstructor, and EMAN::nnSSNR_ctfReconstructor.

Definition at line 147 of file reconstructor.h.

147{throw;}

◆ operator=()

Reconstructor & EMAN::Reconstructor::operator= ( const Reconstructor & )

private

◆ operator[]()

EMObject & EMAN::Reconstructor::operator[] ( const string & key )

inline

Definition at line 199 of file reconstructor.h.

199{ return params[key]; }

EMAN::FactoryBase::params

Dict params

This is the dictionary the stores the parameters of the object.

Definition: emobject.h:953

References EMAN::FactoryBase::params.

◆ preprocess_slice()

virtual EMData * EMAN::Reconstructor::preprocess_slice	(	const EMData *const	slice,
		const Transform &	t = `Transform()`
	)

inlinevirtual

While you can just insert unprocessed slices, if you call preprocess_slice yourself, and insert the returned slice instead, repeatedly, it can save a fair bit of computation.

The default operation just returns a copy of the image, as the preprocessing is reconstructor-specific.

Returns: the processed slice

Parameters

slice	the slice to be prepocessed
t	transform

Exceptions

InvalidValueException when the specified padding value is less than the size of the images

Reimplemented in EMAN::BackProjectionReconstructor, EMAN::FourierReconstructor, EMAN::FourierIterReconstructor, and EMAN::RealMedianReconstructor.

Definition at line 137 of file reconstructor.h.

137{ EMData *ret=slice->copy(); ret->set_attr("reconstruct_preproc",(int)1); return ret; }

◆ print_params()

void EMAN::Reconstructor::print_params ( ) const

inline

Print the current parameters to std::out.

Definition at line 188 of file reconstructor.h.

                {
                        std::cout << "Printing reconstructor params" << std::endl;
                        for ( Dict::const_iterator it = params.begin(); it != params.end(); ++it )
                        {
                                std::cout << (it->first) << " " << (it->second).to_str() << std::endl;
                        }
                        std::cout << "Done printing reconstructor params" << std::endl;
                }

References EMAN::Dict::begin(), EMAN::Dict::end(), and EMAN::FactoryBase::params.

Referenced by EMAN::nn4_rectReconstructor::nn4_rectReconstructor().

◆ projection()

virtual EMData * EMAN::Reconstructor::projection	(	const Transform &	euler,
		int	ret_fourier = `1`
	)

inlinevirtual

This will create a projection from the current reconstruction.

Only valid before finish() is called. may not be implemented for all Reconstructors. If the reconstructor implements padding, the projection will also be padded. The euler parameter will ignore translation and mirroring

Parameters

euler	The orientation of the slice as a Transform object
ret_fourier	If set returns the Fourier transform of the projection. For many reconstructors this may be less expensive.

Returns: 0 if OK. 1 if error.

Exceptions

Reimplemented in EMAN::FourierReconstructor.

Definition at line 173 of file reconstructor.h.

173{ throw; }

◆ setup()

virtual void EMAN::Reconstructor::setup ( )

pure virtual

Initialize the reconstructor.

Implemented in EMAN::XYZReconstructor, EMAN::FourierReconstructorSimple2D, EMAN::FourierReconstructor, EMAN::FourierIterReconstructor, EMAN::BackProjectionReconstructor, EMAN::RealMedianReconstructor, EMAN::nn4Reconstructor, EMAN::nn4_rectReconstructor, EMAN::nnSSNR_Reconstructor, EMAN::nn4_ctfReconstructor, EMAN::nn4_ctfwReconstructor, EMAN::nn4_ctfwsReconstructor, EMAN::nn4_ctf_rectReconstructor, and EMAN::nnSSNR_ctfReconstructor.

◆ setup_seed()

virtual void EMAN::Reconstructor::setup_seed	(	EMData *	seed,
		float	seed_weight
	)

inlinevirtual

Initialize the reconstructor with a seed volume.

This can be used to provide some 'default' value when there is missing data in Fourier space. The passed 'seed' must be of the appropriate padded size, must be in Fourier space. The seed is copied on input. The seed_weight determines how 'strong' the seed volume should be as compared to other inserted slices in Fourier space. Raises an exception if not supported by the Reconstructor, or if there is an error with the size.

Reimplemented in EMAN::FourierReconstructor, and EMAN::FourierIterReconstructor.

Definition at line 122 of file reconstructor.h.

122{throw;}

◆ setup_seedandweights()

virtual void EMAN::Reconstructor::setup_seedandweights	(	EMData *	seed,
		EMData *	weight
	)

inlinevirtual

Initialize the reconstructor with a seed volume, as above.

In this case the initial weight map is also provided explicitly, rather than a single weight value.

Reimplemented in EMAN::FourierReconstructor, and EMAN::FourierIterReconstructor.

Definition at line 126 of file reconstructor.h.

126{throw;}

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

reconstructor.h

Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Reconstructor() [1/2]

◆ ~Reconstructor()

◆ Reconstructor() [2/2]

Member Function Documentation

◆ clear()

◆ determine_slice_agreement()

◆ finish()

◆ insert_slice() [1/2]

◆ insert_slice() [2/2]

◆ operator=()

◆ operator[]()

◆ preprocess_slice()

◆ print_params()

◆ projection()

◆ setup()

◆ setup_seed()

◆ setup_seedandweights()