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EMAN::nn4_rectReconstructor Class Reference

Direct Fourier inversion Reconstructor for extremly rectangular object. More...

#include <reconstructor.h>

Inheritance diagram for EMAN::nn4_rectReconstructor:

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Collaboration diagram for EMAN::nn4_rectReconstructor:

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List of all members.

Public Member Functions

 nn4_rectReconstructor ()
 nn4_rectReconstructor (const string &symmetry, int size, int npad)
virtual ~nn4_rectReconstructor ()
virtual void setup ()
 Initialize the reconstructor.
virtual int insert_slice (const EMData *const slice, const Transform &euler, const float weight=1.0)
 Insert an image slice to the reconstructor.
virtual EMDatafinish (bool doift=true)
 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
void setup (const string &symmetry, int size, int npad)
int insert_padfft_slice (EMData *padded, const Transform &trans, int mult=1)

Static Public Member Functions

ReconstructorNEW ()

Static Public Attributes

const string NAME = "nn4_rect"

Private Member Functions

void buildFFTVolume ()
void buildNormVolume ()
void load_default_settings ()

Private Attributes

EMDatam_volume
EMDatam_wptr
EMDatam_result
bool m_delete_volume
bool m_delete_weight
string m_symmetry
int m_weighting
int m_vnx
int m_vny
int m_vnz
int m_npad
int m_nsym
int m_ndim
int m_vnzp
int m_vnyp
int m_vnxp
int m_vnzc
int m_vnyc
int m_vnxc
int m_count
float m_xratio
float m_yratio
float m_zratio
float m_xscale
float m_yscale
int m_sizeofprojection
float m_wghta
float m_wghtb
float m_osnr

Detailed Description

Direct Fourier inversion Reconstructor for extremly rectangular object.

Definition at line 821 of file reconstructor.h.


Constructor & Destructor Documentation

nn4_rectReconstructor::nn4_rectReconstructor  ) 
 

Definition at line 2399 of file reconstructor.cpp.

References m_result, m_volume, and m_wptr.

02400 {
02401         m_volume = NULL;
02402         m_wptr   = NULL;
02403         m_result = NULL;
02404 }

nn4_rectReconstructor::nn4_rectReconstructor const string &  symmetry,
int  size,
int  npad
 

Definition at line 2406 of file reconstructor.cpp.

References load_default_settings(), m_result, m_volume, m_wptr, EMAN::Reconstructor::print_params(), and setup().

02407 {
02408         m_volume = NULL;
02409         m_wptr   = NULL;
02410         m_result = NULL;
02411         setup( symmetry, size, npad );
02412         load_default_settings();
02413         print_params();
02414 }

nn4_rectReconstructor::~nn4_rectReconstructor  )  [virtual]
 

Definition at line 2416 of file reconstructor.cpp.

References checked_delete(), m_result, m_volume, and m_wptr.

02417 {
02418         if( m_delete_volume ) checked_delete(m_volume);
02419 
02420         if( m_delete_weight ) checked_delete( m_wptr );
02421 
02422         checked_delete( m_result );
02423 }


Member Function Documentation

void nn4_rectReconstructor::buildFFTVolume  )  [private]
 

Definition at line 2496 of file reconstructor.cpp.

References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), m_delete_volume, m_npad, m_vnxp, m_vnyp, m_vnzp, m_volume, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_attr(), EMAN::EMData::set_complex(), EMAN::EMData::set_fftodd(), EMAN::EMData::set_fftpad(), EMAN::EMData::set_nxc(), EMAN::EMData::set_ri(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero().

Referenced by setup().

02496                                            {
02497         int offset = 2 - m_vnxp%2;
02498 
02499         if( params.has_key("fftvol") ) {
02500                 m_volume = params["fftvol"];
02501                 m_delete_volume = false;
02502         } else {
02503                 m_volume = new EMData();
02504                 m_delete_volume = true;
02505         }
02506 
02507         if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
02508                 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
02509                 m_volume->to_zero();
02510         }
02511         // ----------------------------------------------------------------
02512         // Added by Zhengfan Yang on 03/15/07
02513         // Original author: please check whether my revision is correct and
02514         // other Reconstructor need similiar revision.
02515         if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
02516         else                    m_volume->set_fftodd(1);
02517         // ----------------------------------------------------------------
02518 
02519         m_volume->set_nxc(m_vnxp/2);
02520         m_volume->set_complex(true);
02521         m_volume->set_ri(true);
02522         m_volume->set_fftpad(true);
02523         m_volume->set_attr("npad", m_npad);
02524         m_volume->set_array_offsets(0,1,1);
02525 }

void nn4_rectReconstructor::buildNormVolume  )  [private]
 

Definition at line 2527 of file reconstructor.cpp.

References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), m_delete_weight, m_vnxc, m_vnyp, m_vnzp, m_wptr, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero().

Referenced by setup().

02527                                             {
02528 
02529         if( params.has_key("weight") ) {
02530                 m_wptr = params["weight"];
02531                 m_delete_weight = false;
02532         } else {
02533                 m_wptr = new EMData();
02534                 m_delete_weight = true;
02535         }
02536 
02537         if( m_wptr->get_xsize() != m_vnxc+1 &&
02538                 m_wptr->get_ysize() != m_vnyp &&
02539                 m_wptr->get_zsize() != m_vnzp ) {
02540                 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
02541                 m_wptr->to_zero();
02542         }
02543 
02544         m_wptr->set_array_offsets(0,1,1);
02545 }

EMData * nn4_rectReconstructor::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 2752 of file reconstructor.cpp.

References abs, circumf_rect(), EMAN::EMData::copy(), EMAN::EMData::depad(), EMAN::EMData::do_ift_inplace(), EMAN::EMData::get_attr(), m_ndim, m_result, m_vnyc, m_vnyp, m_volume, m_weighting, m_wghta, m_wptr, max, max2d(), max3d(), EMAN::EMData::set_array_offsets(), and EMAN::EMData::symplane0_rect().

02753 {
02754         
02755         if( m_ndim==3 ) {
02756                 m_volume->symplane0_rect(m_wptr);
02757         } else {
02758                 for( int i=1; i <= m_vnyp; ++i ) {
02759 
02760                         if( (*m_wptr)(0, i, 1)==0.0 ) {
02761                                 int j = m_vnyp + 1 - i;
02762                                 (*m_wptr)(0, i, 1) = (*m_wptr)(0, j, 1);
02763                                 (*m_volume)(0, i, 1) = (*m_volume)(0, j, 1);
02764                                 (*m_volume)(1, i, 1) = (*m_volume)(1, j, 1);
02765                         }
02766                 }
02767         }
02768 
02769 
02770         int box = 7;
02771         int kc = (box-1)/2;
02772         vector< float > pow_a( m_ndim*kc+1, 1.0 );
02773         for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
02774         pow_a.back()=0.0;
02775 
02776         float alpha = 0.0;
02777         if( m_ndim==3) {
02778                 int vol = box*box*box;
02779                 float max = max3d( kc, pow_a );
02780                 alpha = ( 1.0f - 1.0f/(float)vol ) / max;
02781         } else {
02782                 int ara = box*box;
02783                 float max = max2d( kc, pow_a );
02784                 alpha = ( 1.0f - 1.0f/(float)ara ) / max;
02785         }
02786 
02787         int ix,iy,iz;
02788         for (iz = 1; iz <= m_vnzp; iz++) {
02789                 for (iy = 1; iy <= m_vnyp; iy++) {
02790                         for (ix = 0; ix <= m_vnxc; ix++) {
02791                                 if ( (*m_wptr)(ix,iy,iz) > 0) {//(*v) should be treated as complex!!
02792                                         float tmp;
02793                                         tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+m_osnr);
02794                                         
02795                                         if( m_weighting == ESTIMATE ) {
02796                                                 int cx = ix;
02797                                                 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
02798                                                 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
02799                                                 float sum = 0.0;
02800                                                 for( int ii = -kc; ii <= kc; ++ii ) {
02801                                                         int nbrcx = cx + ii;
02802                                                         if( nbrcx >= m_vnxc ) continue;
02803                                                         for( int jj= -kc; jj <= kc; ++jj ) {
02804                                                                 int nbrcy = cy + jj;
02805                                                                 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
02806 
02807                                                                 int kcz = (m_ndim==3) ? kc : 0;
02808                                                                 for( int kk = -kcz; kk <= kcz; ++kk ) {
02809                                                                         int nbrcz = cz + kk;
02810                                                                         if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
02811                                                                         if( nbrcx < 0 ) {
02812                                                                                 nbrcx = -nbrcx;
02813                                                                                 nbrcy = -nbrcy;
02814                                                                                 nbrcz = -nbrcz;
02815                                                                         }
02816                                                                         int nbrix = nbrcx;
02817                                                                         int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
02818                                                                         int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
02819                                                                         if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
02820                                                                                 int c = m_ndim*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
02821                                                                                 sum = sum + pow_a[c];
02822                                                                         }
02823                                                                 }
02824                                                         }
02825                                                 }
02826                                                 float wght = 1.0f / ( 1.0f - alpha * sum );
02827                                                 tmp = tmp * wght;
02828                                         }
02829                                         (*m_volume)(2*ix,iy,iz)   *= tmp;
02830                                         (*m_volume)(2*ix+1,iy,iz) *= tmp;
02831                                 }
02832                         }
02833                 }
02834         }
02835 
02836         //if(m_ndim==2) printImage( m_volume );
02837 
02838         // back fft
02839         m_volume->do_ift_inplace();
02840 
02841         
02842         int npad = m_volume->get_attr("npad");
02843         m_volume->depad();
02844         circumf_rect( m_volume, npad );
02845         //circumf_rect_new( m_volume, npad,m_xratio,m_yratio);
02846         m_volume->set_array_offsets( 0, 0, 0 );
02847 
02848         m_result = m_volume->copy();
02849         return m_result;
02850 }

virtual string EMAN::nn4_rectReconstructor::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 849 of file reconstructor.h.

00850                 {
00851                         return "Direct Fourier inversion routine";
00852                 }

virtual string EMAN::nn4_rectReconstructor::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 844 of file reconstructor.h.

00845                 {
00846                         return NAME;
00847                 }

virtual TypeDict EMAN::nn4_rectReconstructor::get_param_types  )  const [inline, virtual]
 

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

Implements EMAN::FactoryBase.

Definition at line 859 of file reconstructor.h.

References EMAN::TypeDict::put().

00860                 {
00861                         TypeDict d;
00862                         d.put("sizeprojection", EMObject::INT);
00863                         d.put("sizex",          EMObject::INT);
00864                         d.put("sizey",          EMObject::INT);
00865                         d.put("sizez",          EMObject::INT);
00866                         d.put("xratio",         EMObject::FLOAT);
00867                         d.put("yratio",         EMObject::FLOAT);
00868                         d.put("npad",           EMObject::INT);
00869                         d.put("sign",           EMObject::INT);
00870                         d.put("ndim",           EMObject::INT);
00871                         d.put("snr",            EMObject::FLOAT);
00872                         d.put("symmetry",       EMObject::STRING);
00873                         d.put("snr",            EMObject::FLOAT);
00874                         d.put("fftvol",         EMObject::EMDATA);
00875                         d.put("weight",         EMObject::EMDATA);
00876                         d.put("weighting",      EMObject::INT);
00877                         return d;
00878                 }

int nn4_rectReconstructor::insert_padfft_slice EMData padded,
const Transform trans,
int  mult = 1
 

Definition at line 2656 of file reconstructor.cpp.

References Assert, EMAN::Transform::get_sym(), EMAN::EMData::insert_rect_slice(), m_npad, m_sizeofprojection, m_symmetry, m_volume, m_wptr, m_xratio, m_yratio, mult(), and t.

02657 {
02658         Assert( padded != NULL );
02659         
02660 
02661         for( int isym=0; isym < m_nsym; isym++) {
02662                 Transform tsym = t.get_sym( m_symmetry, isym );
02663                  m_volume->insert_rect_slice(m_wptr, padded, t, m_sizeofprojection, m_xratio, m_yratio, m_npad, mult);
02664                 }
02665 
02666         return 0;
02667 
02668 }

virtual int EMAN::nn4_rectReconstructor::insert_slice const EMData *const   slice,
const Transform euler,
const float  weight = 1.0
[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.

void EMAN::nn4_rectReconstructor::load_default_settings  )  [inline, private]
 

Definition at line 909 of file reconstructor.h.

Referenced by nn4_rectReconstructor().

00910                 {
00911                         //params["use_weights"] = false;
00912                 }

Reconstructor* EMAN::nn4_rectReconstructor::NEW  )  [inline, static]
 

Definition at line 854 of file reconstructor.h.

00855                 {
00856                         return new nn4_rectReconstructor();
00857                 }

void nn4_rectReconstructor::setup const string &  symmetry,
int  size,
int  npad
 

Definition at line 2445 of file reconstructor.cpp.

References buildFFTVolume(), buildNormVolume(), EMAN::Transform::get_nsym(), EMAN::Dict::has_key(), m_ndim, m_npad, m_nsym, m_symmetry, m_vnx, m_vnxc, m_vnxp, m_vny, m_vnyc, m_vnyp, m_vnz, m_vnzc, m_vnzp, m_weighting, m_wghta, m_xratio, and m_yratio.

02446 {
02447         m_weighting = ESTIMATE;
02448         m_wghta = 0.2f;
02449         m_symmetry = symmetry;
02450         m_npad = npad;
02451         m_nsym = Transform::get_nsym(m_symmetry);
02452 
02453         if( params.has_key("sizex") )  m_vnx = params["sizex"];
02454         else if(params.has_key("xratio")) 
02455                 {
02456                 float temp=params["xratio"];
02457                 m_vnx=int(float(sizeprojection)*temp);
02458                 }
02459         else                           m_vnx=sizeprojection;
02460 
02461         if( params.has_key("sizey") )  m_vny = params["sizey"];
02462         else if (params.has_key("yratio"))  
02463                {
02464                 float temp=params["yratio"];
02465                  m_vny=int(float(sizeprojection)*temp);
02466                 }
02467         else m_vny=sizeprojection;
02468 
02469         if( params.has_key("sizez") ) 
02470                 m_vnz = params["sizez"];
02471         else                          
02472                 m_vnz = (m_ndim==3) ? sizeprojection : 1;
02473         
02474         m_xratio=float(m_vnx)/float(sizeprojection);    
02475         m_yratio=float(m_vny)/float(sizeprojection);
02476 
02477         //std::cout<<"dim==="<<m_ndim<<"xratio=="<<m_xratio<<"yratio=="<<m_yratio<<std::endl;
02478         //std::cout<<"sx=="<<m_vnx<<"sy=="<<m_vny<<"sz=="<<m_vnz<<std::endl;
02479         
02480 
02481         m_vnxp = m_vnx*npad;
02482         m_vnyp = m_vny*npad;
02483         m_vnzp = (m_ndim==3) ? m_vnz*npad : 1;
02484 
02485         m_vnxc = m_vnxp/2;
02486         m_vnyc = m_vnyp/2;
02487         m_vnzc = (m_ndim==3) ? m_vnzp/2 : 1;
02488 
02489         buildFFTVolume();
02490         buildNormVolume();
02491 
02492 
02493 }

void nn4_rectReconstructor::setup  )  [virtual]
 

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 2426 of file reconstructor.cpp.

References EMAN::Dict::has_key(), m_count, m_ndim, m_osnr, and m_sizeofprojection.

Referenced by nn4_rectReconstructor().

02427 {
02428         m_sizeofprojection = params["sizeprojection"];
02429         int npad = params["npad"];
02430         m_count=0;
02431 
02432         string symmetry;
02433         if( params.has_key("symmetry") )  symmetry = params["symmetry"].to_str();
02434         else                               symmetry = "c1";
02435 
02436         if( params.has_key("ndim") )  m_ndim = params["ndim"];             
02437         else                            m_ndim = 3;
02438     
02439         if( params.has_key( "snr" ) )  m_osnr = 1.0f/float( params["snr"] );
02440         else                           m_osnr = 0.0;
02441 
02442         setup( symmetry, m_sizeofprojection, npad );
02443 }


Member Data Documentation

int EMAN::nn4_rectReconstructor::m_count [private]
 

Definition at line 900 of file reconstructor.h.

Referenced by setup().

bool EMAN::nn4_rectReconstructor::m_delete_volume [private]
 

Definition at line 890 of file reconstructor.h.

Referenced by buildFFTVolume().

bool EMAN::nn4_rectReconstructor::m_delete_weight [private]
 

Definition at line 891 of file reconstructor.h.

Referenced by buildNormVolume().

int EMAN::nn4_rectReconstructor::m_ndim [private]
 

Definition at line 897 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4_rectReconstructor::m_npad [private]
 

Definition at line 895 of file reconstructor.h.

Referenced by buildFFTVolume(), insert_padfft_slice(), and setup().

int EMAN::nn4_rectReconstructor::m_nsym [private]
 

Definition at line 896 of file reconstructor.h.

Referenced by setup().

float EMAN::nn4_rectReconstructor::m_osnr [private]
 

Definition at line 908 of file reconstructor.h.

Referenced by setup().

EMData* EMAN::nn4_rectReconstructor::m_result [private]
 

Definition at line 889 of file reconstructor.h.

Referenced by finish(), nn4_rectReconstructor(), and ~nn4_rectReconstructor().

int EMAN::nn4_rectReconstructor::m_sizeofprojection [private]
 

Definition at line 903 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

string EMAN::nn4_rectReconstructor::m_symmetry [private]
 

Definition at line 892 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

int EMAN::nn4_rectReconstructor::m_vnx [private]
 

Definition at line 894 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_rectReconstructor::m_vnxc [private]
 

Definition at line 899 of file reconstructor.h.

Referenced by buildNormVolume(), and setup().

int EMAN::nn4_rectReconstructor::m_vnxp [private]
 

Definition at line 898 of file reconstructor.h.

Referenced by buildFFTVolume(), and setup().

int EMAN::nn4_rectReconstructor::m_vny [private]
 

Definition at line 894 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_rectReconstructor::m_vnyc [private]
 

Definition at line 899 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4_rectReconstructor::m_vnyp [private]
 

Definition at line 898 of file reconstructor.h.

Referenced by buildFFTVolume(), buildNormVolume(), finish(), and setup().

int EMAN::nn4_rectReconstructor::m_vnz [private]
 

Definition at line 894 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_rectReconstructor::m_vnzc [private]
 

Definition at line 899 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_rectReconstructor::m_vnzp [private]
 

Definition at line 898 of file reconstructor.h.

Referenced by buildFFTVolume(), buildNormVolume(), and setup().

EMData* EMAN::nn4_rectReconstructor::m_volume [private]
 

Definition at line 887 of file reconstructor.h.

Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nn4_rectReconstructor(), and ~nn4_rectReconstructor().

int EMAN::nn4_rectReconstructor::m_weighting [private]
 

Definition at line 893 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4_rectReconstructor::m_wghta [private]
 

Definition at line 906 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4_rectReconstructor::m_wghtb [private]
 

Definition at line 907 of file reconstructor.h.

EMData* EMAN::nn4_rectReconstructor::m_wptr [private]
 

Definition at line 888 of file reconstructor.h.

Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nn4_rectReconstructor(), and ~nn4_rectReconstructor().

float EMAN::nn4_rectReconstructor::m_xratio [private]
 

Definition at line 901 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

float EMAN::nn4_rectReconstructor::m_xscale [private]
 

Definition at line 902 of file reconstructor.h.

float EMAN::nn4_rectReconstructor::m_yratio [private]
 

Definition at line 901 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

float EMAN::nn4_rectReconstructor::m_yscale [private]
 

Definition at line 902 of file reconstructor.h.

float EMAN::nn4_rectReconstructor::m_zratio [private]
 

Definition at line 901 of file reconstructor.h.

const string nn4_rectReconstructor::NAME = "nn4_rect" [static]
 

Definition at line 82 of file reconstructor.cpp.


The documentation for this class was generated from the following files:
Generated on Mon Mar 7 18:21:34 2011 for EMAN2 by  doxygen 1.3.9.1