EMAN::nn4Reconstructor Class Reference

#include <reconstructor.h>

Inheritance diagram for EMAN::nn4Reconstructor:

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Collaboration diagram for EMAN::nn4Reconstructor:

Collaboration graph
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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
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 947 of file reconstructor.h.


Constructor & Destructor Documentation

nn4Reconstructor::nn4Reconstructor (  ) 

Definition at line 1996 of file reconstructor.cpp.

References m_volume, and m_wptr.

Referenced by NEW().

01997 {
01998         m_volume = NULL;
01999         m_wptr   = NULL;
02000 }

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

Definition at line 2002 of file reconstructor.cpp.

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

02003 {
02004         m_volume = NULL;
02005         m_wptr   = NULL;
02006         setup( symmetry, size, npad );
02007         load_default_settings();
02008         print_params();
02009 }

nn4Reconstructor::~nn4Reconstructor (  )  [virtual]

Definition at line 2011 of file reconstructor.cpp.

02012 {
02013         //if( m_delete_volume ) checked_delete(m_volume); 
02014 
02015         //if( m_delete_weight ) checked_delete( m_wptr );
02016 
02017         //checked_delete( m_result );
02018 }


Member Function Documentation

void nn4Reconstructor::buildFFTVolume (  )  [private]

Definition at line 2104 of file reconstructor.cpp.

References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), 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().

02104                                       {
02105         int offset = 2 - m_vnxp%2;
02106 
02107         m_volume = params["fftvol"];
02108 
02109         if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
02110                 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
02111                 m_volume->to_zero();
02112         }
02113         // ----------------------------------------------------------------
02114         // Added by Zhengfan Yang on 03/15/07
02115         // Original author: please check whether my revision is correct and
02116         // other Reconstructor need similiar revision.
02117         if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
02118         else                    m_volume->set_fftodd(1);
02119         // ----------------------------------------------------------------
02120 
02121         m_volume->set_nxc(m_vnxp/2);
02122         m_volume->set_complex(true);
02123         m_volume->set_ri(true);
02124         m_volume->set_fftpad(true);
02125         m_volume->set_attr("npad", m_npad);
02126         m_volume->set_array_offsets(0,1,1);
02127 }

void nn4Reconstructor::buildNormVolume (  )  [private]

Definition at line 2129 of file reconstructor.cpp.

References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), 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().

02129                                        {
02130 
02131         m_wptr = params["weight"];
02132 
02133         if( m_wptr->get_xsize() != m_vnxc+1 &&
02134                 m_wptr->get_ysize() != m_vnyp &&
02135                 m_wptr->get_zsize() != m_vnzp ) {
02136                 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
02137                 m_wptr->to_zero();
02138         }
02139         m_wptr->set_array_offsets(0,1,1);
02140 }

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 2310 of file reconstructor.cpp.

References abs, circumf(), EMAN::EMData::depad(), EMAN::EMData::do_ift_inplace(), ESTIMATE, EMAN::EMData::get_attr(), m_ndim, m_osnr, 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().

02310                                      {
02311 
02312         if( m_ndim==3 ) {
02313                 m_volume->symplane0(m_wptr);
02314         } else {
02315                 for( int i=1; i <= m_vnyp; ++i ) {
02316 
02317                         if( (*m_wptr)(0, i, 1)==0.0 ) {
02318                                 int j = m_vnyp + 1 - i;
02319                                 (*m_wptr)(0, i, 1) = (*m_wptr)(0, j, 1);
02320                                 (*m_volume)(0, i, 1) = (*m_volume)(0, j, 1);
02321                                 (*m_volume)(1, i, 1) = (*m_volume)(1, j, 1);
02322                         }
02323                 }
02324         }
02325 
02326 
02327         int box = 7;
02328         int kc = (box-1)/2;
02329         vector< float > pow_a( m_ndim*kc+1, 1.0 );
02330         for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
02331         pow_a.back()=0.0;
02332 
02333         float alpha = 0.0;
02334         if( m_ndim==3) {
02335                 int vol = box*box*box;
02336                 float max = max3d( kc, pow_a );
02337                 alpha = ( 1.0f - 1.0f/(float)vol ) / max;
02338         } else {
02339                 int ara = box*box;
02340                 float max = max2d( kc, pow_a );
02341                 alpha = ( 1.0f - 1.0f/(float)ara ) / max;
02342         }
02343 
02344         int ix,iy,iz;
02345         for (iz = 1; iz <= m_vnzp; iz++) {
02346                 for (iy = 1; iy <= m_vnyp; iy++) {
02347                         for (ix = 0; ix <= m_vnxc; ix++) {
02348                                 if ( (*m_wptr)(ix,iy,iz) > 0) {//(*v) should be treated as complex!!
02349                                         float tmp;
02350                                         tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+m_osnr);
02351 
02352                                         if( m_weighting == ESTIMATE ) {
02353                                                 int cx = ix;
02354                                                 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
02355                                                 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
02356                                                 float sum = 0.0;
02357                                                 for( int ii = -kc; ii <= kc; ++ii ) {
02358                                                         int nbrcx = cx + ii;
02359                                                         if( nbrcx >= m_vnxc ) continue;
02360                                                         for( int jj= -kc; jj <= kc; ++jj ) {
02361                                                                 int nbrcy = cy + jj;
02362                                                                 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
02363 
02364                                                                 int kcz = (m_ndim==3) ? kc : 0;
02365                                                                 for( int kk = -kcz; kk <= kcz; ++kk ) {
02366                                                                         int nbrcz = cz + kk;
02367                                                                         if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
02368                                                                         if( nbrcx < 0 ) {
02369                                                                                 nbrcx = -nbrcx;
02370                                                                                 nbrcy = -nbrcy;
02371                                                                                 nbrcz = -nbrcz;
02372                                                                         }
02373                                                                         int nbrix = nbrcx;
02374                                                                         int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
02375                                                                         int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
02376                                                                         if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
02377                                                                                 int c = m_ndim*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
02378                                                                                 sum = sum + pow_a[c];
02379                                                                         }
02380                                                                 }
02381                                                         }
02382                                                 }
02383                                                 float wght = 1.0f / ( 1.0f - alpha * sum );
02384                                                 tmp = tmp * wght;
02385                                         }
02386                                         (*m_volume)(2*ix,iy,iz)   *= tmp;
02387                                         (*m_volume)(2*ix+1,iy,iz) *= tmp;
02388                                 }
02389                         }
02390                 }
02391         }
02392 
02393         //if(m_ndim==2) printImage( m_volume );
02394 
02395         // back fft
02396         m_volume->do_ift_inplace();
02397 
02398         // EMData* win = m_volume->window_center(m_vnx);
02399         int npad = m_volume->get_attr("npad");
02400         m_volume->depad();
02401         circumf( m_volume, npad );
02402         m_volume->set_array_offsets( 0, 0, 0 );
02403 
02404         return 0;
02405 }

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 975 of file reconstructor.h.

00976                 {
00977                         return "Direct Fourier inversion routine";
00978                 }

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 970 of file reconstructor.h.

References NAME.

00971                 {
00972                         return NAME;
00973                 }

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 985 of file reconstructor.h.

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

00986                 {
00987                         TypeDict d;
00988                         d.put("size",           EMObject::INT);
00989                         d.put("npad",           EMObject::INT);
00990                         d.put("sign",           EMObject::INT);
00991                         d.put("ndim",           EMObject::INT);
00992                         d.put("snr",            EMObject::FLOAT);
00993                         d.put("symmetry",       EMObject::STRING);
00994                         d.put("snr",            EMObject::FLOAT);
00995                         d.put("fftvol",         EMObject::EMDATA);
00996                         d.put("weight",         EMObject::EMDATA);
00997                         d.put("weighting",      EMObject::INT);
00998                         return d;
00999                 }

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

Definition at line 2218 of file reconstructor.cpp.

References Assert, m_symmetry, m_volume, m_wptr, EMAN::EMData::nn(), and t.

Referenced by insert_slice().

02219 {
02220         Assert( padfft != NULL );
02221 
02222         vector<Transform> tsym = t.get_sym_proj(m_symmetry);
02223         for (unsigned int isym=0; isym < tsym.size(); isym++) {
02224                 m_volume->nn( m_wptr, padfft, tsym[isym], mult);
02225         }
02226         
02227         /*for (int isym=0; isym < m_nsym; isym++) {
02228                 Transform tsym = t.get_sym(m_symmetry, isym);
02229                 m_volume->nn( m_wptr, padfft, tsym, mult);
02230         }*/
02231         return 0;
02232 }

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 2157 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(), EMAN::padfft_slice(), and t.

02157                                                                                              {
02158         // sanity checks
02159         if (!slice) {
02160                 LOGERR("try to insert NULL slice");
02161                 return 1;
02162         }
02163 
02164         int padffted= slice->get_attr_default( "padffted", 0 );
02165         if( m_ndim==3 ) {
02166                 if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  ) {
02167                         // FIXME: Why doesn't this throw an exception?
02168                         LOGERR("Tried to insert a slice that is the wrong size.");
02169                         return 1;
02170                 }
02171         } else {
02172                 Assert( m_ndim==2 );
02173                 if( slice->get_ysize() !=1 ) {
02174                         LOGERR( "for 2D reconstruction, a line is excepted" );
02175                         return 1;
02176                 }
02177         }
02178 
02179         EMData* padfft = NULL;
02180 
02181         if( padffted != 0 ) padfft = new EMData(*slice);
02182         else                padfft = padfft_slice( slice, t,  m_npad );
02183 
02184         int mult= slice->get_attr_default( "mult", 1 );
02185         Assert( mult > 0 );
02186 
02187         if( m_ndim==3 ) {
02188                 insert_padfft_slice( padfft, t, mult );
02189         } else {
02190                 float alpha = padfft->get_attr( "alpha" );
02191                 alpha = alpha/180.0f*M_PI;
02192                 for(int i=0; i < m_vnxc+1; ++i ) {
02193                         float xnew = i*cos(alpha);
02194                         float ynew = -i*sin(alpha);
02195                         float btqr = padfft->get_value_at( 2*i, 0, 0 );
02196                         float btqi = padfft->get_value_at( 2*i+1, 0, 0 );
02197                         if( xnew < 0.0 ) {
02198                                 xnew *= -1;
02199                                 ynew *= -1;
02200                                 btqi *= -1;
02201                         }
02202 
02203                         int ixn = int(xnew+0.5+m_vnxp) - m_vnxp;
02204                         int iyn = int(ynew+0.5+m_vnyp) - m_vnyp;
02205 
02206                         if(iyn < 0 ) iyn += m_vnyp;
02207 
02208                         (*m_volume)( 2*ixn, iyn+1, 1 ) += btqr *float(mult);
02209                         (*m_volume)( 2*ixn+1, iyn+1, 1 ) += btqi * float(mult);
02210                         (*m_wptr)(ixn,iyn+1, 1) += float(mult);
02211                 }
02212 
02213         }
02214         checked_delete( padfft );
02215         return 0;
02216 }

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

Definition at line 1023 of file reconstructor.h.

Referenced by nn4Reconstructor().

01024                 {
01025                         //params["use_weights"] = false;
01026                 }

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

Definition at line 980 of file reconstructor.h.

References nn4Reconstructor().

00981                 {
00982                         return new nn4Reconstructor();
00983                 }

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

Definition at line 2077 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.

02078 {
02079         m_weighting = ESTIMATE;
02080         m_wghta = 0.2f;
02081 
02082         m_symmetry = symmetry;
02083         m_npad = npad;
02084         m_nsym = Transform::get_nsym(m_symmetry);
02085 
02086         m_vnx = size;
02087         m_vny = size;
02088         m_vnz = (m_ndim==3) ? size : 1;
02089 
02090         m_vnxp = size*npad;
02091         m_vnyp = size*npad;
02092         m_vnzp = (m_ndim==3) ? size*npad : 1;
02093 
02094         m_vnxc = m_vnxp/2;
02095         m_vnyc = m_vnyp/2;
02096         m_vnzc = (m_ndim==3) ? m_vnzp/2 : 1;
02097 
02098         buildFFTVolume();
02099         buildNormVolume();
02100         
02101 }

void nn4Reconstructor::setup (  )  [virtual]

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 2058 of file reconstructor.cpp.

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

Referenced by nn4Reconstructor().

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


Member Data Documentation

int EMAN::nn4Reconstructor::m_ndim [private]

Definition at line 1015 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_npad [private]

Definition at line 1013 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_nsym [private]

Definition at line 1014 of file reconstructor.h.

Referenced by setup().

float EMAN::nn4Reconstructor::m_osnr [private]

Definition at line 1022 of file reconstructor.h.

Referenced by finish(), and setup().

string EMAN::nn4Reconstructor::m_symmetry [private]

Definition at line 1010 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

int EMAN::nn4Reconstructor::m_vnx [private]

Definition at line 1012 of file reconstructor.h.

Referenced by insert_slice(), and setup().

int EMAN::nn4Reconstructor::m_vnxc [private]

Definition at line 1017 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_vnxp [private]

Definition at line 1016 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_vny [private]

Definition at line 1012 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4Reconstructor::m_vnyc [private]

Definition at line 1017 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4Reconstructor::m_vnyp [private]

Definition at line 1016 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_vnz [private]

Definition at line 1012 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4Reconstructor::m_vnzc [private]

Definition at line 1017 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4Reconstructor::m_vnzp [private]

Definition at line 1016 of file reconstructor.h.

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

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

Definition at line 1008 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_weighting [private]

Definition at line 1011 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4Reconstructor::m_wghta [private]

Definition at line 1020 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4Reconstructor::m_wghtb [private]

Definition at line 1021 of file reconstructor.h.

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

Definition at line 1009 of file reconstructor.h.

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

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

Definition at line 1005 of file reconstructor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 12:45:00 2013 for EMAN2 by  doxygen 1.4.7