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 731 of file reconstructor.h.


Constructor & Destructor Documentation

nn4Reconstructor::nn4Reconstructor (  ) 

Definition at line 1980 of file reconstructor.cpp.

References m_volume, and m_wptr.

Referenced by NEW().

01981 {
01982         m_volume = NULL;
01983         m_wptr   = NULL;
01984 }

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

Definition at line 1986 of file reconstructor.cpp.

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

01987 {
01988         m_volume = NULL;
01989         m_wptr   = NULL;
01990         setup( symmetry, size, npad );
01991         load_default_settings();
01992         print_params();
01993 }

nn4Reconstructor::~nn4Reconstructor (  )  [virtual]

Definition at line 1995 of file reconstructor.cpp.

01996 {
01997         //if( m_delete_volume ) checked_delete(m_volume); 
01998 
01999         //if( m_delete_weight ) checked_delete( m_wptr );
02000 
02001         //checked_delete( m_result );
02002 }


Member Function Documentation

void nn4Reconstructor::buildFFTVolume (  )  [private]

Definition at line 2088 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().

02088                                       {
02089         int offset = 2 - m_vnxp%2;
02090 
02091         m_volume = params["fftvol"];
02092 
02093         if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
02094                 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
02095                 m_volume->to_zero();
02096         }
02097         // ----------------------------------------------------------------
02098         // Added by Zhengfan Yang on 03/15/07
02099         // Original author: please check whether my revision is correct and
02100         // other Reconstructor need similiar revision.
02101         if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
02102         else                    m_volume->set_fftodd(1);
02103         // ----------------------------------------------------------------
02104 
02105         m_volume->set_nxc(m_vnxp/2);
02106         m_volume->set_complex(true);
02107         m_volume->set_ri(true);
02108         m_volume->set_fftpad(true);
02109         m_volume->set_attr("npad", m_npad);
02110         m_volume->set_array_offsets(0,1,1);
02111 }

void nn4Reconstructor::buildNormVolume (  )  [private]

Definition at line 2113 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().

02113                                        {
02114 
02115         m_wptr = params["weight"];
02116 
02117         if( m_wptr->get_xsize() != m_vnxc+1 &&
02118                 m_wptr->get_ysize() != m_vnyp &&
02119                 m_wptr->get_zsize() != m_vnzp ) {
02120                 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
02121                 m_wptr->to_zero();
02122         }
02123         m_wptr->set_array_offsets(0,1,1);
02124 }

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, 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().

02294                                      {
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         int npad = m_volume->get_attr("npad");
02384         m_volume->depad();
02385         circumf( m_volume, npad );
02386         m_volume->set_array_offsets( 0, 0, 0 );
02387 
02388         return 0;
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 759 of file reconstructor.h.

00760                 {
00761                         return "Direct Fourier inversion routine";
00762                 }

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 754 of file reconstructor.h.

References NAME.

00755                 {
00756                         return NAME;
00757                 }

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 769 of file reconstructor.h.

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

00770                 {
00771                         TypeDict d;
00772                         d.put("size",           EMObject::INT);
00773                         d.put("npad",           EMObject::INT);
00774                         d.put("sign",           EMObject::INT);
00775                         d.put("ndim",           EMObject::INT);
00776                         d.put("snr",            EMObject::FLOAT);
00777                         d.put("symmetry",       EMObject::STRING);
00778                         d.put("snr",            EMObject::FLOAT);
00779                         d.put("fftvol",         EMObject::EMDATA);
00780                         d.put("weight",         EMObject::EMDATA);
00781                         d.put("weighting",      EMObject::INT);
00782                         return d;
00783                 }

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

Definition at line 2202 of file reconstructor.cpp.

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

Referenced by insert_slice().

02203 {
02204         Assert( padfft != NULL );
02205 
02206         vector<Transform> tsym = t.get_sym_proj(m_symmetry);
02207         for (unsigned int isym=0; isym < tsym.size(); isym++) {
02208                 m_volume->nn( m_wptr, padfft, tsym[isym], mult);
02209         }
02210         
02211         /*for (int isym=0; isym < m_nsym; isym++) {
02212                 Transform tsym = t.get_sym(m_symmetry, isym);
02213                 m_volume->nn( m_wptr, padfft, tsym, mult);
02214         }*/
02215         return 0;
02216 }

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 2141 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.

02141                                                                                              {
02142         // sanity checks
02143         if (!slice) {
02144                 LOGERR("try to insert NULL slice");
02145                 return 1;
02146         }
02147 
02148         int padffted= slice->get_attr_default( "padffted", 0 );
02149         if( m_ndim==3 ) {
02150                 if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  ) {
02151                         // FIXME: Why doesn't this throw an exception?
02152                         LOGERR("Tried to insert a slice that is the wrong size.");
02153                         return 1;
02154                 }
02155         } else {
02156                 Assert( m_ndim==2 );
02157                 if( slice->get_ysize() !=1 ) {
02158                         LOGERR( "for 2D reconstruction, a line is excepted" );
02159                         return 1;
02160                 }
02161         }
02162 
02163         EMData* padfft = NULL;
02164 
02165         if( padffted != 0 ) padfft = new EMData(*slice);
02166         else                padfft = padfft_slice( slice, t,  m_npad );
02167 
02168         int mult= slice->get_attr_default( "mult", 1 );
02169         Assert( mult > 0 );
02170 
02171         if( m_ndim==3 ) {
02172                 insert_padfft_slice( padfft, t, mult );
02173         } else {
02174                 float alpha = padfft->get_attr( "alpha" );
02175                 alpha = alpha/180.0f*M_PI;
02176                 for(int i=0; i < m_vnxc+1; ++i ) {
02177                         float xnew = i*cos(alpha);
02178                         float ynew = -i*sin(alpha);
02179                         float btqr = padfft->get_value_at( 2*i, 0, 0 );
02180                         float btqi = padfft->get_value_at( 2*i+1, 0, 0 );
02181                         if( xnew < 0.0 ) {
02182                                 xnew *= -1;
02183                                 ynew *= -1;
02184                                 btqi *= -1;
02185                         }
02186 
02187                         int ixn = int(xnew+0.5+m_vnxp) - m_vnxp;
02188                         int iyn = int(ynew+0.5+m_vnyp) - m_vnyp;
02189 
02190                         if(iyn < 0 ) iyn += m_vnyp;
02191 
02192                         (*m_volume)( 2*ixn, iyn+1, 1 ) += btqr *float(mult);
02193                         (*m_volume)( 2*ixn+1, iyn+1, 1 ) += btqi * float(mult);
02194                         (*m_wptr)(ixn,iyn+1, 1) += float(mult);
02195                 }
02196 
02197         }
02198         checked_delete( padfft );
02199         return 0;
02200 }

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

Definition at line 807 of file reconstructor.h.

Referenced by nn4Reconstructor().

00808                 {
00809                         //params["use_weights"] = false;
00810                 }

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

Definition at line 764 of file reconstructor.h.

References nn4Reconstructor().

00765                 {
00766                         return new nn4Reconstructor();
00767                 }

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

Definition at line 2061 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.

02062 {
02063         m_weighting = ESTIMATE;
02064         m_wghta = 0.2f;
02065 
02066         m_symmetry = symmetry;
02067         m_npad = npad;
02068         m_nsym = Transform::get_nsym(m_symmetry);
02069 
02070         m_vnx = size;
02071         m_vny = size;
02072         m_vnz = (m_ndim==3) ? size : 1;
02073 
02074         m_vnxp = size*npad;
02075         m_vnyp = size*npad;
02076         m_vnzp = (m_ndim==3) ? size*npad : 1;
02077 
02078         m_vnxc = m_vnxp/2;
02079         m_vnyc = m_vnyp/2;
02080         m_vnzc = (m_ndim==3) ? m_vnzp/2 : 1;
02081 
02082         buildFFTVolume();
02083         buildNormVolume();
02084         
02085 }

void nn4Reconstructor::setup (  )  [virtual]

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 2042 of file reconstructor.cpp.

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

Referenced by nn4Reconstructor().

02043 {
02044         int size = params["size"];
02045         int npad = params["npad"];
02046 
02047 
02048         string symmetry;
02049         if( params.has_key("symmetry") )  symmetry = params["symmetry"].to_str();
02050         else                               symmetry = "c1";
02051 
02052         if( params.has_key("ndim") )  m_ndim = params["ndim"];
02053         else                          m_ndim = 3;
02054 
02055         if( params.has_key( "snr" ) )  m_osnr = 1.0f/float( params["snr"] );
02056         else                           m_osnr = 0.0;
02057 
02058         setup( symmetry, size, npad );
02059 }


Member Data Documentation

int EMAN::nn4Reconstructor::m_ndim [private]

Definition at line 799 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_npad [private]

Definition at line 797 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_nsym [private]

Definition at line 798 of file reconstructor.h.

Referenced by setup().

float EMAN::nn4Reconstructor::m_osnr [private]

Definition at line 806 of file reconstructor.h.

Referenced by finish(), and setup().

string EMAN::nn4Reconstructor::m_symmetry [private]

Definition at line 794 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

int EMAN::nn4Reconstructor::m_vnx [private]

Definition at line 796 of file reconstructor.h.

Referenced by insert_slice(), and setup().

int EMAN::nn4Reconstructor::m_vnxc [private]

Definition at line 801 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_vnxp [private]

Definition at line 800 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_vny [private]

Definition at line 796 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4Reconstructor::m_vnyc [private]

Definition at line 801 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4Reconstructor::m_vnyp [private]

Definition at line 800 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_vnz [private]

Definition at line 796 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4Reconstructor::m_vnzc [private]

Definition at line 801 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4Reconstructor::m_vnzp [private]

Definition at line 800 of file reconstructor.h.

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

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

Definition at line 792 of file reconstructor.h.

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

int EMAN::nn4Reconstructor::m_weighting [private]

Definition at line 795 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4Reconstructor::m_wghta [private]

Definition at line 804 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4Reconstructor::m_wghtb [private]

Definition at line 805 of file reconstructor.h.

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

Definition at line 793 of file reconstructor.h.

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

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

Definition at line 789 of file reconstructor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue Jul 12 13:49:57 2011 for EMAN2 by  doxygen 1.4.7