#include <reconstructor.h>
Inheritance diagram for EMAN::nn4Reconstructor:
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 EMData * | finish (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 Reconstructor * | NEW () |
Static Public Attributes | |
static const string | NAME = "nn4" |
Private Member Functions | |
void | buildFFTVolume () |
void | buildNormVolume () |
void | load_default_settings () |
Private Attributes | |
EMData * | m_volume |
EMData * | m_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 |
Definition at line 731 of file reconstructor.h.
nn4Reconstructor::nn4Reconstructor | ( | ) |
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 }
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.
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 |
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.
Implements EMAN::FactoryBase.
Definition at line 759 of file reconstructor.h.
virtual string EMAN::nn4Reconstructor::get_name | ( | ) | const [inline, virtual] |
Get the unique name of this class (especially for factory based instantiation access).
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] |
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.
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 |
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] |
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 }
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] |
float EMAN::nn4Reconstructor::m_osnr [private] |
string EMAN::nn4Reconstructor::m_symmetry [private] |
int EMAN::nn4Reconstructor::m_vnx [private] |
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] |
int EMAN::nn4Reconstructor::m_vnyc [private] |
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] |
int EMAN::nn4Reconstructor::m_vnzc [private] |
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] |
float EMAN::nn4Reconstructor::m_wghta [private] |
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] |