Real space 3D reconstruction using back projection. More...

#include <reconstructor.h>

Inheritance diagram for EMAN::BackProjectionReconstructor:

[legend]

Collaboration diagram for EMAN::BackProjectionReconstructor:

[legend]

Public Member Functions
	BackProjectionReconstructor ()

virtual	~BackProjectionReconstructor ()

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

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

virtual int	determine_slice_agreement (EMData *slice, const Transform &euler, const float weight=1.0, bool sub=true)
	Dummy function which always returns the same values. More...

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

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

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

virtual TypeDict	get_param_types () const

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

virtual	~Reconstructor ()

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...

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

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

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)

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

Dict	copy_relevant_params (const FactoryBase *const that) const

Public Member Functions inherited from EMAN::ReconstructorVolumeData
	ReconstructorVolumeData ()
	Only constructor All member variables are zeroed. More...

virtual	~ReconstructorVolumeData ()
	Destructor safely frees memory. More...

const EMData *	get_emdata ()
	Get the main image pointer, probably redundant (not used) More...

Static Public Member Functions
static Reconstructor *	NEW ()

Static Public Attributes
static const string	NAME = "back_projection"

Private Member Functions
	BackProjectionReconstructor (const BackProjectionReconstructor &that)

BackProjectionReconstructor &	operator= (const BackProjectionReconstructor &)

void	load_default_settings ()

EMData *	preprocess_slice (const EMData *const slice, const Transform &t)
	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...

Additional Inherited Members
Protected Member Functions inherited from EMAN::ReconstructorVolumeData
void	free_memory ()
	Free allocated memorys The inherited class may have allocated image of tmp_data In either case you can safely call this function to delete either of those pointers, even if they bdb:refine_03::threed_00are NULL. More...

virtual void	normalize_threed (const bool sqrt_damp=false, const bool wiener=false)
	Normalize on the assumption that image is a Fourier volume and that tmp_data is a volume of weights corresponding in size to this Fourier volume. More...

virtual void	zero_memory ()
	Sends the pixels in tmp_data and image to zero Convenience only. More...

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

Protected Attributes inherited from EMAN::ReconstructorVolumeData
EMData *	image
	Inheriting class allocates this, probably in setup(). More...

EMData *	tmp_data
	Inheriting class may allocate this, probably in setup() More...

int	nx

int	nx2

int	ny

int	ny2

int	nz

int	nz2

int	subnx

int	subny

int	subnz

int	subx0

int	suby0

int	subz0

Detailed Description

Real space 3D reconstruction using back projection.

Back-projection is a method of 3D reconstruction from 2D projections. It is based on superposing 3D functions ("back-projection bodies") obtained by translating the 2D projections along the directions of projection.

Definition at line 841 of file reconstructor.h.

Constructor & Destructor Documentation

◆ BackProjectionReconstructor() [1/2]

EMAN::BackProjectionReconstructor::BackProjectionReconstructor ( )

inline

Definition at line 844 of file reconstructor.h.

844{ load_default_settings(); }

EMAN::BackProjectionReconstructor::load_default_settings

void load_default_settings()

Definition: reconstructor.h:906

References load_default_settings().

Referenced by NEW().

◆ ~BackProjectionReconstructor()

virtual EMAN::BackProjectionReconstructor::~BackProjectionReconstructor ( )

inlinevirtual

Definition at line 846 of file reconstructor.h.

846{}

◆ BackProjectionReconstructor() [2/2]

EMAN::BackProjectionReconstructor::BackProjectionReconstructor ( const BackProjectionReconstructor & that )

private

Member Function Documentation

◆ determine_slice_agreement()

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

virtual

Dummy function which always returns the same values.

It could be implemented, but isn't, as this reconstructor is really just for testing.

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

NullPointerException	if the input EMData pointer is null
ImageFormatException	if the image is complex as opposed to real

Reimplemented from EMAN::Reconstructor.

Definition at line 2884 of file reconstructor.cpp.

{
        // Are these exceptions really necessary? (d.woolford)
        if (!input_slice) throw NullPointerException("EMData pointer (input image) is NULL");
 
        input_slice->set_attr("reconstruct_norm",1.0f);
        input_slice->set_attr("reconstruct_absqual",1.0f);
        input_slice->set_attr("reconstruct_weight",1.0f);
 
        return 0;
 
}

References NullPointerException.

◆ finish()

EMData * BackProjectionReconstructor::finish ( bool doift = true )

virtual

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 from EMAN::Reconstructor.

Definition at line 2897 of file reconstructor.cpp.

{
 
        Symmetry3D* sym = Factory<Symmetry3D>::get((string)params["sym"]);
        vector<Transform> syms = sym->get_syms();
 
        for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
 
//              it->printme();
                Transform t=*it;
                EMData *tmpcopy = image->process("xform",Dict("transform",(EMObject)&t));
                image->add(*tmpcopy);
                delete tmpcopy;
        }
 
        image->mult(1.0f/(float)sym->get_nsym());
        delete sym;
        if (image->get_xsize()==image->get_ysize() && image->get_ysize()==image->get_zsize()) {
                image->process_inplace("mask.sharp",Dict("outer_radius",image->get_xsize()/2-1));
        }
        else printf("No masking %d %d %d\n",image->get_xsize(),image->get_ysize(),image->get_zsize());
                
        EMData *ret = image;
        image = 0 ;
        return ret;
}

References EMAN::Factory< T >::get(), EMAN::Symmetry3D::get_nsym(), EMAN::Symmetry3D::get_syms(), EMAN::ReconstructorVolumeData::image, and EMAN::FactoryBase::params.

◆ get_desc()

virtual string EMAN::BackProjectionReconstructor::get_desc ( ) const

inlinevirtual

Get a clear, concise description of this class.

Returns: a clear, concise description of this class

Implements EMAN::FactoryBase.

Definition at line 878 of file reconstructor.h.

                {
                        return "Simple (unfiltered) back-projection reconstruction. Weighting by contributing particles in the class average is optional and default behaviour";
                }

◆ get_name()

virtual string EMAN::BackProjectionReconstructor::get_name ( ) const

inlinevirtual

Get the unique name of this class (especially for factory based instantiation access)

Returns: the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 873 of file reconstructor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::BackProjectionReconstructor::get_param_types ( ) const

inlinevirtual

Returns: a TypeDict defining and describing the feasible parameters of this class

Implements EMAN::FactoryBase.

Definition at line 888 of file reconstructor.h.

                {
                        TypeDict d;
                        d.put("size", EMObject::INTARRAY, "Required. The dimensions of the real-space output volume, including any padding (must be handled by the calling application). Assumed that apix x/y/z identical.");
                        d.put("weight", EMObject::FLOAT, "Optional. A temporary value set prior to slice insertion, indicative of the inserted slice's weight. Default sis 1.");
                        d.put("sym", EMObject::STRING, "Optional. The symmetry to impose on the final reconstruction. Default is c1");
                        d.put("verbose", EMObject::BOOL, "Optional. Toggles writing useful information to standard out. Default is false.");
                        return d;
                }

References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INTARRAY, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.

◆ insert_slice()

int BackProjectionReconstructor::insert_slice	(	const EMData *const	slice,
		const Transform &	euler,
		const float	weight
	)

virtual

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 from EMAN::Reconstructor.

Definition at line 2832 of file reconstructor.cpp.

{
        if (!input) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
 
        if (input->get_xsize() != input->get_ysize() || input->get_xsize() != nx) {
                LOGERR("tried to insert image that was not correction dimensions");
                return 1;
        }
 
//      Transform * transform;
//      if ( input->has_attr("xform.projection") ) {
//              transform = (Transform*) (input->get_attr("xform.projection")); // assignment operator
//      } else {
//              transform = new Transform(t); // assignment operator
//      }
        EMData* slice = preprocess_slice(input, t);
 
        // Clearly weight isn't a useful concept in back-projection without compensating with an exact-filter
//      float weight = params["weight"];
//      slice->mult(weight);
 
        EMData *tmp = new EMData();
        tmp->set_size(nx, ny, nz);
 
        float *slice_data = slice->get_data();
        float *tmp_data = tmp->get_data();
 
        size_t nxy = nx * ny;
        size_t nxy_size = nxy * sizeof(float);;
        for (int i = 0; i < nz; ++i) {
                memcpy(&tmp_data[nxy * i], slice_data, nxy_size);
        }
        tmp->update();
 
//      transform->set_scale(1.0);
//      transform->set_mirror(false);
//      transform->set_trans(0,0,0);
//      transform->invert();
 
        tmp->transform(t.inverse());            // This was incorrect. inverse() was missing
        image->add(*tmp);
 
//      if(transform) {delete transform; transform=0;}
        delete tmp;
        delete slice;
 
        return 0;
}

References EMAN::ReconstructorVolumeData::image, EMAN::Transform::inverse(), LOGERR, EMAN::ReconstructorVolumeData::nx, EMAN::ReconstructorVolumeData::ny, EMAN::ReconstructorVolumeData::nz, preprocess_slice(), EMAN::ReconstructorVolumeData::tmp_data, and EMAN::EMData::transform().

◆ load_default_settings()

void EMAN::BackProjectionReconstructor::load_default_settings ( )

inlineprivate

Definition at line 906 of file reconstructor.h.

                {
                        params["weight"] = 1.0;
                        params["use_weights"] = true;
                        params["sym"] = "c1";
                        params["verbose"] = false;
                }

References EMAN::FactoryBase::params.

Referenced by BackProjectionReconstructor().

◆ NEW()

static Reconstructor * EMAN::BackProjectionReconstructor::NEW ( )

inlinestatic

Definition at line 883 of file reconstructor.h.

                {
                        return new BackProjectionReconstructor();
                }

References BackProjectionReconstructor().

◆ operator=()

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

private

◆ preprocess_slice()

EMData * BackProjectionReconstructor::preprocess_slice	(	const EMData *const	slice,
		const Transform &	t
	)

privatevirtual

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 from EMAN::Reconstructor.

Definition at line 2806 of file reconstructor.cpp.

{
 
//      EMData* return_slice = slice->process("normalize.edgemean");
//      return_slice->process_inplace("filter.linearfourier");
 
        EMData* return_slice;
 
        return_slice = slice->process("filter.linearfourier");
//      return_slice = slice->copy();
        
//      Transform tmp(t);
//      tmp.set_rotation(Dict("type","eman")); // resets the rotation to 0 implicitly
//      Vec2f trans = tmp.get_trans_2d();
//      float scale = tmp.get_scale();
//      bool mirror = tmp.get_mirror();
//      if (trans[0] != 0 || trans[1] != 0 || scale != 1.0 ) {
//              return_slice->transform(tmp);
//      } 
//      if ( mirror == true ) {
//              return_slice->process_inplace("xform.flip",Dict("axis","x"));
//      }
 
        return return_slice;
}

Referenced by insert_slice().

◆ setup()

void BackProjectionReconstructor::setup ( )

virtual

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 2796 of file reconstructor.cpp.

{
        image = new EMData();
        vector<int> size=params["size"];
        nx = size[0];
        ny = size[1];
        nz = size[2];
        image->set_size(nx, ny, nz);
}

References EMAN::ReconstructorVolumeData::image, EMAN::ReconstructorVolumeData::nx, EMAN::ReconstructorVolumeData::ny, EMAN::ReconstructorVolumeData::nz, and EMAN::FactoryBase::params.

Member Data Documentation

◆ NAME

const string BackProjectionReconstructor::NAME = "back_projection"

static

Definition at line 898 of file reconstructor.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BackProjectionReconstructor() [1/2]

◆ ~BackProjectionReconstructor()

◆ BackProjectionReconstructor() [2/2]

Member Function Documentation

◆ determine_slice_agreement()

◆ finish()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ insert_slice()

◆ load_default_settings()

◆ NEW()

◆ operator=()

◆ preprocess_slice()

◆ setup()

Member Data Documentation

◆ NAME