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EMAN::nn4Reconstructor Class Reference

#include <reconstructor.h>

Inheritance diagram for EMAN::nn4Reconstructor:

Inheritance graph
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Collaboration diagram for EMAN::nn4Reconstructor:

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List of all members.

Public Member Functions

 nn4Reconstructor ()
 nn4Reconstructor (const string &symmetry, int size, int npad)
virtual ~nn4Reconstructor ()
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

static ReconstructorNEW ()

Static Public Attributes

static const string NAME = "nn4"

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
float m_wghta
float m_wghtb
float m_osnr

Detailed Description

Definition at line 792 of file reconstructor.h.


Constructor & Destructor Documentation

nn4Reconstructor::nn4Reconstructor  ) 
 

Definition at line 1988 of file reconstructor.cpp.

References m_result, m_volume, and m_wptr.

Referenced by NEW().

01989 {
01990     m_volume = NULL;
01991     m_wptr   = NULL;
01992     m_result = NULL;
01993 }

nn4Reconstructor::nn4Reconstructor const string &  symmetry,
int  size,
int  npad
 

Definition at line 1995 of file reconstructor.cpp.

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

01996 {
01997     m_volume = NULL;
01998     m_wptr   = NULL;
01999     m_result = NULL;
02000         setup( symmetry, size, npad );
02001         load_default_settings();
02002         print_params();
02003 }

nn4Reconstructor::~nn4Reconstructor  )  [virtual]
 

Definition at line 2005 of file reconstructor.cpp.

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

02006 {
02007     if( m_delete_volume )
02008         checked_delete(m_volume);
02009 
02010     if( m_delete_weight )
02011         checked_delete( m_wptr );
02012 
02013     checked_delete( m_result );
02014 }


Member Function Documentation

void nn4Reconstructor::buildFFTVolume  )  [private]
 

Definition at line 2109 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::FactoryBase::params, 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().

02109                                       {
02110         int offset = 2 - m_vnxp%2;
02111 
02112         if( params.has_key("fftvol") ) {
02113                 m_volume = params["fftvol"];
02114                 m_delete_volume = false;
02115         } else {
02116                 m_volume = new EMData();
02117                 m_delete_volume = true;
02118         }
02119 
02120         if( m_volume->get_xsize() != m_vnxp+offset &&
02121             m_volume->get_ysize() != m_vnyp &&
02122             m_volume->get_zsize() != m_vnzp ) {
02123                 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
02124                 m_volume->to_zero();
02125         }
02126         // ----------------------------------------------------------------
02127         // Added by Zhengfan Yang on 03/15/07
02128         // Original author: please check whether my revision is correct and
02129         // other Reconstructor need similiar revision.
02130         if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
02131         else                    m_volume->set_fftodd(1);
02132         // ----------------------------------------------------------------
02133 
02134         m_volume->set_nxc(m_vnxp/2);
02135         m_volume->set_complex(true);
02136         m_volume->set_ri(true);
02137         m_volume->set_fftpad(true);
02138         m_volume->set_attr("npad", m_npad);
02139         m_volume->set_array_offsets(0,1,1);
02140 }

void nn4Reconstructor::buildNormVolume  )  [private]
 

Definition at line 2142 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::FactoryBase::params, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero().

Referenced by setup().

02142                                        {
02143 
02144         if( params.has_key("weight") ) {
02145                 m_wptr = params["weight"];
02146                 m_delete_weight = false;
02147         } else {
02148                 m_wptr = new EMData();
02149                 m_delete_weight = true;
02150         }
02151 
02152         if( m_wptr->get_xsize() != m_vnxc+1 &&
02153                 m_wptr->get_ysize() != m_vnyp &&
02154                 m_wptr->get_zsize() != m_vnzp ) {
02155                 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
02156                 m_wptr->to_zero();
02157         }
02158 
02159         m_wptr->set_array_offsets(0,1,1);
02160 }

EMData * nn4Reconstructor::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 2294 of file reconstructor.cpp.

References abs, circumference(), EMAN::EMData::copy(), EMAN::EMData::depad(), EMAN::EMData::do_ift_inplace(), ESTIMATE, m_ndim, m_osnr, m_result, m_vnxc, m_vnyc, m_vnyp, m_vnzc, m_vnzp, m_volume, m_weighting, m_wghta, m_wptr, max, max2d(), max3d(), EMAN::EMData::set_array_offsets(), and EMAN::EMData::symplane0().

02295 {
02296         if( m_ndim==3 ) {
02297                 m_volume->symplane0(m_wptr);
02298         } else {
02299                 for( int i=1; i <= m_vnyp; ++i ) {
02300 
02301                         if( (*m_wptr)(0, i, 1)==0.0 ) {
02302                                 int j = m_vnyp + 1 - i;
02303                                 (*m_wptr)(0, i, 1) = (*m_wptr)(0, j, 1);
02304                                 (*m_volume)(0, i, 1) = (*m_volume)(0, j, 1);
02305                                 (*m_volume)(1, i, 1) = (*m_volume)(1, j, 1);
02306                         }
02307                 }
02308         }
02309 
02310 
02311         int box = 7;
02312         int kc = (box-1)/2;
02313         vector< float > pow_a( m_ndim*kc+1, 1.0 );
02314         for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
02315         pow_a.back()=0.0;
02316 
02317         float alpha = 0.0;
02318         if( m_ndim==3) {
02319                 int vol = box*box*box;
02320                 float max = max3d( kc, pow_a );
02321                 alpha = ( 1.0f - 1.0f/(float)vol ) / max;
02322         } else {
02323                 int ara = box*box;
02324                 float max = max2d( kc, pow_a );
02325                 alpha = ( 1.0f - 1.0f/(float)ara ) / max;
02326         }
02327 
02328         int ix,iy,iz;
02329         for (iz = 1; iz <= m_vnzp; iz++) {
02330                 for (iy = 1; iy <= m_vnyp; iy++) {
02331                         for (ix = 0; ix <= m_vnxc; ix++) {
02332                                 if ( (*m_wptr)(ix,iy,iz) > 0) {//(*v) should be treated as complex!!
02333                                         float tmp;
02334                                         tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+m_osnr);
02335 
02336                                         if( m_weighting == ESTIMATE ) {
02337                                                 int cx = ix;
02338                                                 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
02339                                                 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
02340                                                 float sum = 0.0;
02341                                                 for( int ii = -kc; ii <= kc; ++ii ) {
02342                                                         int nbrcx = cx + ii;
02343                                                         if( nbrcx >= m_vnxc ) continue;
02344                                                         for( int jj= -kc; jj <= kc; ++jj ) {
02345                                                                 int nbrcy = cy + jj;
02346                                                                 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
02347 
02348                                                                 int kcz = (m_ndim==3) ? kc : 0;
02349                                                                 for( int kk = -kcz; kk <= kcz; ++kk ) {
02350                                                                         int nbrcz = cz + kk;
02351                                                                         if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
02352                                                                         if( nbrcx < 0 ) {
02353                                                                                 nbrcx = -nbrcx;
02354                                                                                 nbrcy = -nbrcy;
02355                                                                                 nbrcz = -nbrcz;
02356                                                                         }
02357                                                                         int nbrix = nbrcx;
02358                                                                         int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
02359                                                                         int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
02360                                                                         if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
02361                                                                                 int c = m_ndim*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
02362                                                                                 sum = sum + pow_a[c];
02363                                                                         }
02364                                                                 }
02365                                                         }
02366                                                 }
02367                                                 float wght = 1.0f / ( 1.0f - alpha * sum );
02368                                                 tmp = tmp * wght;
02369                                         }
02370                                         (*m_volume)(2*ix,iy,iz) *= tmp;
02371                                         (*m_volume)(2*ix+1,iy,iz) *= tmp;
02372                                 }
02373                         }
02374                 }
02375         }
02376 
02377         //if(m_ndim==2) printImage( m_volume );
02378 
02379         // back fft
02380         m_volume->do_ift_inplace();
02381 
02382         // EMData* win = m_volume->window_center(m_vnx);
02383         m_volume->depad();
02384         circumference( m_volume );
02385         m_volume->set_array_offsets( 0, 0, 0 );
02386 
02387     m_result = m_volume->copy();
02388         return m_result;
02389 }

virtual string EMAN::nn4Reconstructor::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 820 of file reconstructor.h.

00821                 {
00822                         return "Direct Fourier inversion routine";
00823                 }

virtual string EMAN::nn4Reconstructor::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 815 of file reconstructor.h.

References NAME.

00816                 {
00817                         return NAME;
00818                 }

virtual TypeDict EMAN::nn4Reconstructor::get_param_types  )  const [inline, virtual]
 

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

Implements EMAN::FactoryBase.

Definition at line 830 of file reconstructor.h.

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

00831                 {
00832                         TypeDict d;
00833                         d.put("size",           EMObject::INT);
00834                         d.put("npad",           EMObject::INT);
00835                         d.put("sign",           EMObject::INT);
00836                         d.put("ndim",           EMObject::INT);
00837                         d.put("snr",            EMObject::FLOAT);
00838                         d.put("symmetry",       EMObject::STRING);
00839                         d.put("snr",            EMObject::FLOAT);
00840                         d.put("fftvol",         EMObject::EMDATA);
00841                         d.put("weight",         EMObject::EMDATA);
00842                         d.put("weighting",      EMObject::INT);
00843                         return d;
00844                 }

int nn4Reconstructor::insert_padfft_slice EMData padded,
const Transform trans,
int  mult = 1
 

Definition at line 2238 of file reconstructor.cpp.

References Assert, EMAN::Transform::get_sym(), m_nsym, m_symmetry, m_volume, m_wptr, and EMAN::EMData::nn().

Referenced by insert_slice().

02239 {
02240         Assert( padfft != NULL );
02241         // insert slice for all symmetry related positions
02242         for (int isym=0; isym < m_nsym; isym++) {
02243                 Transform tsym = t.get_sym(m_symmetry, isym);
02244                 m_volume->nn( m_wptr, padfft, tsym, mult);
02245         }
02246         return 0;
02247 }

int nn4Reconstructor::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.

Definition at line 2177 of file reconstructor.cpp.

References Assert, checked_delete(), EMAN::EMObject::f, EMAN::EMData::get_attr(), EMAN::EMData::get_attr_default(), EMAN::EMData::get_value_at(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), insert_padfft_slice(), LOGERR, m_ndim, m_npad, m_vnx, m_vnxc, m_vnxp, m_vnyp, mult(), and EMAN::padfft_slice().

02177                                                                                                     {
02178         // sanity checks
02179         if (!slice) {
02180                 LOGERR("try to insert NULL slice");
02181                 return 1;
02182         }
02183 
02184         int padffted= slice->get_attr_default( "padffted", 0 );
02185         if( m_ndim==3 ) {
02186                 if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  ) {
02187                         // FIXME: Why doesn't this throw an exception?
02188                         LOGERR("Tried to insert a slice that is the wrong size.");
02189                         return 1;
02190                 }
02191         } else {
02192                 Assert( m_ndim==2 );
02193                 if( slice->get_ysize() !=1 ) {
02194                         LOGERR( "for 2D reconstruction, a line is excepted" );
02195                         return 1;
02196                 }
02197         }
02198 
02199         EMData* padfft = NULL;
02200 
02201         if( padffted != 0 ) padfft = new EMData(*slice);
02202         else                padfft = padfft_slice( slice, t,  m_npad );
02203 
02204         int mult= slice->get_attr_default( "mult", 1 );
02205         Assert( mult > 0 );
02206 
02207         if( m_ndim==3 ) {
02208                 insert_padfft_slice( padfft, t, mult );
02209         } else {
02210                 float alpha = padfft->get_attr( "alpha" );
02211                 alpha = alpha/180.0f*M_PI;
02212                 for(int i=0; i < m_vnxc+1; ++i ) {
02213                         float xnew = i*cos(alpha);
02214                         float ynew = -i*sin(alpha);
02215                         float btqr = padfft->get_value_at( 2*i, 0, 0 );
02216                         float btqi = padfft->get_value_at( 2*i+1, 0, 0 );
02217                         if( xnew < 0.0 ) {
02218                                 xnew *= -1;
02219                                 ynew *= -1;
02220                                 btqi *= -1;
02221                         }
02222 
02223                         int ixn = int(xnew+0.5+m_vnxp) - m_vnxp;
02224                         int iyn = int(ynew+0.5+m_vnyp) - m_vnyp;
02225 
02226                         if(iyn < 0 ) iyn += m_vnyp;
02227 
02228                         (*m_volume)( 2*ixn, iyn+1, 1 ) += btqr *float(mult);
02229                         (*m_volume)( 2*ixn+1, iyn+1, 1 ) += btqi * float(mult);
02230                         (*m_wptr)(ixn,iyn+1, 1) += float(mult);
02231                 }
02232 
02233         }
02234         checked_delete( padfft );
02235         return 0;
02236 }

void EMAN::nn4Reconstructor::load_default_settings  )  [inline, private]
 

Definition at line 871 of file reconstructor.h.

Referenced by nn4Reconstructor().

00872                 {
00873                         //params["use_weights"] = false;
00874                 }

static Reconstructor* EMAN::nn4Reconstructor::NEW  )  [inline, static]
 

Definition at line 825 of file reconstructor.h.

References nn4Reconstructor().

00826                 {
00827                         return new nn4Reconstructor();
00828                 }

void nn4Reconstructor::setup const string &  symmetry,
int  size,
int  npad
 

Definition at line 2082 of file reconstructor.cpp.

References buildFFTVolume(), buildNormVolume(), ESTIMATE, EMAN::Transform::get_nsym(), 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, and m_wghta.

02083 {
02084         m_weighting = ESTIMATE;
02085         m_wghta = 0.2f;
02086 
02087         m_symmetry = symmetry;
02088         m_npad = npad;
02089         m_nsym = Transform::get_nsym(m_symmetry);
02090 
02091         m_vnx = size;
02092         m_vny = size;
02093         m_vnz = (m_ndim==3) ? size : 1;
02094 
02095         m_vnxp = size*npad;
02096         m_vnyp = size*npad;
02097         m_vnzp = (m_ndim==3) ? size*npad : 1;
02098 
02099         m_vnxc = m_vnxp/2;
02100         m_vnyc = m_vnyp/2;
02101         m_vnzc = (m_ndim==3) ? m_vnzp/2 : 1;
02102 
02103         buildFFTVolume();
02104         buildNormVolume();
02105 
02106 }

void nn4Reconstructor::setup  )  [virtual]
 

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 2054 of file reconstructor.cpp.

References EMAN::Dict::has_key(), m_ndim, m_osnr, and EMAN::FactoryBase::params.

Referenced by nn4Reconstructor().

02055 {
02056         int size = params["size"];
02057         int npad = params["npad"];
02058 
02059 
02060         string symmetry;
02061         if( params.has_key("symmetry") ) {
02062                 symmetry = params["symmetry"].to_str();
02063         } else {
02064                 symmetry = "c1";
02065         }
02066 
02067         if( params.has_key("ndim") ) {
02068             m_ndim = params["ndim"];
02069         } else {
02070                 m_ndim = 3;
02071         }
02072 
02073     if( params.has_key( "snr" ) ) {
02074         m_osnr = 1.0f/float( params["snr"] );
02075     } else {
02076         m_osnr = 0.0;
02077     }
02078 
02079         setup( symmetry, size, npad );
02080 }


Member Data Documentation

bool EMAN::nn4Reconstructor::m_delete_volume [private]
 

Definition at line 856 of file reconstructor.h.

Referenced by buildFFTVolume(), and ~nn4Reconstructor().

bool EMAN::nn4Reconstructor::m_delete_weight [private]
 

Definition at line 857 of file reconstructor.h.

Referenced by buildNormVolume(), and ~nn4Reconstructor().

int EMAN::nn4Reconstructor::m_ndim [private]
 

Definition at line 863 of file reconstructor.h.

Referenced by finish(), insert_slice(), and setup().

int EMAN::nn4Reconstructor::m_npad [private]
 

Definition at line 861 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_nsym [private]
 

Definition at line 862 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

float EMAN::nn4Reconstructor::m_osnr [private]
 

Definition at line 870 of file reconstructor.h.

Referenced by finish(), and setup().

EMData* EMAN::nn4Reconstructor::m_result [private]
 

Definition at line 855 of file reconstructor.h.

Referenced by finish(), nn4Reconstructor(), and ~nn4Reconstructor().

string EMAN::nn4Reconstructor::m_symmetry [private]
 

Definition at line 858 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

int EMAN::nn4Reconstructor::m_vnx [private]
 

Definition at line 860 of file reconstructor.h.

Referenced by insert_slice(), and setup().

int EMAN::nn4Reconstructor::m_vnxc [private]
 

Definition at line 865 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_vnxp [private]
 

Definition at line 864 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_vny [private]
 

Definition at line 860 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4Reconstructor::m_vnyc [private]
 

Definition at line 865 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4Reconstructor::m_vnyp [private]
 

Definition at line 864 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_vnz [private]
 

Definition at line 860 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4Reconstructor::m_vnzc [private]
 

Definition at line 865 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4Reconstructor::m_vnzp [private]
 

Definition at line 864 of file reconstructor.h.

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

EMData* EMAN::nn4Reconstructor::m_volume [private]
 

Definition at line 853 of file reconstructor.h.

Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nn4Reconstructor(), and ~nn4Reconstructor().

int EMAN::nn4Reconstructor::m_weighting [private]
 

Definition at line 859 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4Reconstructor::m_wghta [private]
 

Definition at line 868 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4Reconstructor::m_wghtb [private]
 

Definition at line 869 of file reconstructor.h.

EMData* EMAN::nn4Reconstructor::m_wptr [private]
 

Definition at line 854 of file reconstructor.h.

Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nn4Reconstructor(), and ~nn4Reconstructor().

const string nn4Reconstructor::NAME = "nn4" [static]
 

Definition at line 850 of file reconstructor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue May 25 17:38:04 2010 for EMAN2 by  doxygen 1.4.4