EMAN::BackProjectionReconstructor Class Reference

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

#include <reconstructor.h>

Inheritance diagram for EMAN::BackProjectionReconstructor:

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List of all members.

Public Member Functions

 BackProjectionReconstructor ()
virtual ~BackProjectionReconstructor ()
virtual void setup ()
 Initialize the reconstructor.
virtual int insert_slice (const EMData *const slice, const Transform3D &euler)
 Insert an image slice to the reconstructor.
virtual int insert_slice (const EMData *const slice, const Transform &euler)
virtual EMData * finish ()
 Finish reconstruction and return the complete model.
virtual string get_name () const
 Get the unique name of this class (especially for factory based instantiation access).
virtual string get_desc () const
 Get a clear, concise description of this class.
virtual TypeDict get_param_types () const

Static Public Member Functions

static Reconstructor * NEW ()

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)

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 731 of file reconstructor.h.

Constructor & Destructor Documentation

EMAN::BackProjectionReconstructor::BackProjectionReconstructor (  )  [inline]

Definition at line 734 of file reconstructor.h.

References load_default_settings().

Referenced by NEW().

00734 { load_default_settings();  }

virtual EMAN::BackProjectionReconstructor::~BackProjectionReconstructor (  )  [inline, virtual]

Definition at line 736 of file reconstructor.h.

00736 {}

EMAN::BackProjectionReconstructor::BackProjectionReconstructor ( const BackProjectionReconstructor &  that  )  [private]

Member Function Documentation

void BackProjectionReconstructor::setup (  )  [virtual]

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 1923 of file reconstructor.cpp.

References EMAN::ReconstructorVolumeData::image, EMAN::ReconstructorVolumeData::nx, EMAN::ReconstructorVolumeData::ny, EMAN::ReconstructorVolumeData::nz, EMAN::FactoryBase::params, and EMAN::EMData::set_size().

01924 {
01925         int size = params["size"];
01926         image = new EMData();
01927         nx = size;
01928         ny = size;
01929         if ( (int) params["zsample"] != 0 ) nz = params["zsample"];
01930         else nz = size;
01931         image->set_size(nx, ny, nz);
01932 }

virtual int EMAN::BackProjectionReconstructor::insert_slice ( const EMData *const   slice,
const Transform3D &  euler 
) [inline, 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.
Returns:
0 if OK. 1 if error.

Reimplemented from EMAN::Reconstructor.

Definition at line 740 of file reconstructor.h.

References UnexpectedBehaviorException.

00740                                                                                                {
00741                         throw UnexpectedBehaviorException("Use of Tranform3D with BackProjection is deprecated"); }

int BackProjectionReconstructor::insert_slice ( const EMData *const   slice,
const Transform &  euler 
) [virtual]

Reimplemented from EMAN::Reconstructor.

Definition at line 1954 of file reconstructor.cpp.

References EMAN::EMData::add(), EMAN::EMData::get_attr(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::has_attr(), EMAN::ReconstructorVolumeData::image, EMAN::Transform::invert(), LOGERR, EMAN::EMData::mult(), EMAN::ReconstructorVolumeData::nx, EMAN::ReconstructorVolumeData::ny, EMAN::ReconstructorVolumeData::nz, EMAN::FactoryBase::params, preprocess_slice(), EMAN::Transform::set_mirror(), EMAN::Transform::set_scale(), EMAN::EMData::set_size(), EMAN::Transform::set_trans(), EMAN::ReconstructorVolumeData::tmp_data, EMAN::EMData::transform(), and weight.

01955 {
01956         if (!input) {
01957                 LOGERR("try to insert NULL slice");
01958                 return 1;
01959         }
01960 
01961         if (input->get_xsize() != input->get_ysize() || input->get_xsize() != nx) {
01962                 LOGERR("tried to insert image that was not correction dimensions");
01963                 return 1;
01964         }
01965 
01966         Transform * transform;
01967         if ( input->has_attr("xform.projection") ) {
01968                 transform = (Transform*) (input->get_attr("xform.projection")); // assignment operator
01969         } else {
01970                 transform = new Transform(t); // assignment operator
01971         }
01972         EMData* slice = preprocess_slice(input, t);
01973 
01974         float weight = params["weight"];
01975         slice->mult(weight);
01976 
01977         EMData *tmp = new EMData();
01978         tmp->set_size(nx, ny, nz);
01979 
01980         float *slice_data = slice->get_data();
01981         float *tmp_data = tmp->get_data();
01982 
01983         size_t nxy = nx * ny;
01984         size_t nxy_size = nxy * sizeof(float);;
01985         for (int i = 0; i < nz; ++i) {
01986                 memcpy(&tmp_data[nxy * i], slice_data, nxy_size);
01987         }
01988 
01989         transform->set_scale(1.0);
01990         transform->set_mirror(false);
01991         transform->set_trans(0,0,0);
01992         transform->invert();
01993 
01994         tmp->transform(*transform);
01995         image->add(*tmp);
01996 
01997         if(transform) {delete transform; transform=0;}
01998         delete tmp;
01999         delete slice;
02000 
02001         return 0;
02002 }

EMData * BackProjectionReconstructor::finish (  )  [virtual]

Finish reconstruction and return the complete model.

Returns:
The result 3D model.

Implements EMAN::Reconstructor.

Definition at line 2004 of file reconstructor.cpp.

References EMAN::EMData::add(), EMAN::Symmetry3D::get_nsym(), EMAN::Symmetry3D::get_syms(), EMAN::ReconstructorVolumeData::image, EMAN::EMData::mult(), EMAN::FactoryBase::params, and EMAN::EMData::transform().

02005 {
02006 
02007         Symmetry3D* sym = Factory<Symmetry3D>::get((string)params["sym"]);
02008         vector<Transform> syms = sym->get_syms();
02009 
02010         for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
02011 
02012                 EMData tmpcopy(*image);
02013                 tmpcopy.transform(*it);
02014                 image->add(tmpcopy);
02015         }
02016 
02017         image->mult(1.0f/(float)sym->get_nsym());
02018         delete sym;
02019         return image;
02020 }

virtual string EMAN::BackProjectionReconstructor::get_name (  )  const [inline, virtual]

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 747 of file reconstructor.h.

00748                 {
00749                         return "back_projection";
00750                 }

virtual string EMAN::BackProjectionReconstructor::get_desc (  )  const [inline, virtual]

Get a clear, concise description of this class.

Returns:
a clear, concise description of this class

Implements EMAN::FactoryBase.

Definition at line 752 of file reconstructor.h.

00753                 {
00754                         return "Simple (unfiltered) back-projection reconstruction. Weighting by contributing particles in the class average is optional and default behaviour";
00755                 }

static Reconstructor* EMAN::BackProjectionReconstructor::NEW (  )  [inline, static]

Definition at line 757 of file reconstructor.h.

References BackProjectionReconstructor().

00758                 {
00759                         return new BackProjectionReconstructor();
00760                 }

virtual TypeDict EMAN::BackProjectionReconstructor::get_param_types (  )  const [inline, virtual]

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

Implements EMAN::FactoryBase.

Definition at line 762 of file reconstructor.h.

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

00763                 {
00764                         TypeDict d;
00765                         d.put("size", EMObject::INT, "Necessary. The x and y dimensions of the input images.");
00766                         d.put("weight", EMObject::FLOAT, "Optional. A temporary value set prior to slice insertion, indicative of the inserted slice's weight. Default sis 1.");
00767                         d.put("sym", EMObject::STRING, "Optional. The symmetry to impose on the final reconstruction. Default is c1");
00768                         d.put("zsample", EMObject::INT, "Optional. The z dimensions of the reconstructed volume.");
00769                         return d;
00770                 }

BackProjectionReconstructor& EMAN::BackProjectionReconstructor::operator= ( const BackProjectionReconstructor &   )  [private]

void EMAN::BackProjectionReconstructor::load_default_settings (  )  [inline, private]

Definition at line 777 of file reconstructor.h.

References EMAN::FactoryBase::params.

Referenced by BackProjectionReconstructor().

00778                 {
00779                         params["weight"] = 1.0;
00780                         params["use_weights"] = true;
00781                         params["size"] = 0;
00782                         params["sym"] = "c1";
00783                         params["zsample"] = 0;
00784                 }

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

Definition at line 1934 of file reconstructor.cpp.

References EMAN::Transform::get_mirror(), EMAN::Transform::get_scale(), EMAN::Transform::get_trans_2d(), EMAN::EMData::process(), EMAN::EMData::process_inplace(), EMAN::Transform::set_rotation(), and EMAN::EMData::transform().

Referenced by insert_slice().

01935 {
01936 
01937         EMData* return_slice = slice->process("normalize.edgemean");
01938         return_slice->process_inplace("filter.linearfourier");
01939 
01940         Transform tmp(t);
01941         tmp.set_rotation(Dict("type","eman")); // resets the rotation to 0 implicitly
01942         Vec2f trans = tmp.get_trans_2d();
01943         float scale = tmp.get_scale();
01944         bool mirror = tmp.get_mirror();
01945         if (trans[0] != 0 || trans[1] != 0 || scale != 1.0 ) {
01946                 return_slice->transform(tmp);
01947         } else if ( mirror == true ) {
01948                 return_slice = slice->process("xform.flip",Dict("axis","x"));
01949         }
01950 
01951         return return_slice;
01952 }

The documentation for this class was generated from the following files:
Generated on Sat Nov 21 02:20:41 2009 for EMAN2 by  doxygen 1.5.6