#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 |
EMData * | m_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 |
Definition at line 721 of file reconstructor.h.
nn4Reconstructor::nn4Reconstructor | ( | ) |
nn4Reconstructor::nn4Reconstructor | ( | const string & | symmetry, | |
int | size, | |||
int | npad | |||
) |
Definition at line 1874 of file reconstructor.cpp.
References load_default_settings(), m_result, m_volume, m_wptr, EMAN::Reconstructor::print_params(), and setup().
01875 { 01876 m_volume = NULL; 01877 m_wptr = NULL; 01878 m_result = NULL; 01879 setup( symmetry, size, npad ); 01880 load_default_settings(); 01881 print_params(); 01882 }
nn4Reconstructor::~nn4Reconstructor | ( | ) | [virtual] |
Definition at line 1884 of file reconstructor.cpp.
References checked_delete(), m_delete_volume, m_delete_weight, m_result, m_volume, and m_wptr.
01885 { 01886 if( m_delete_volume ) 01887 checked_delete(m_volume); 01888 01889 if( m_delete_weight ) 01890 checked_delete( m_wptr ); 01891 01892 checked_delete( m_result ); 01893 }
void nn4Reconstructor::buildFFTVolume | ( | ) | [private] |
Definition at line 1988 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().
01988 { 01989 int offset = 2 - m_vnxp%2; 01990 01991 if( params.has_key("fftvol") ) { 01992 m_volume = params["fftvol"]; 01993 m_delete_volume = false; 01994 } else { 01995 m_volume = new EMData(); 01996 m_delete_volume = true; 01997 } 01998 01999 if( m_volume->get_xsize() != m_vnxp+offset && 02000 m_volume->get_ysize() != m_vnyp && 02001 m_volume->get_zsize() != m_vnzp ) { 02002 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp); 02003 m_volume->to_zero(); 02004 } 02005 // ---------------------------------------------------------------- 02006 // Added by Zhengfan Yang on 03/15/07 02007 // Original author: please check whether my revision is correct and 02008 // other Reconstructor need similiar revision. 02009 if ( m_vnxp % 2 == 0 ) m_volume->set_fftodd(0); 02010 else m_volume->set_fftodd(1); 02011 // ---------------------------------------------------------------- 02012 02013 m_volume->set_nxc(m_vnxp/2); 02014 m_volume->set_complex(true); 02015 m_volume->set_ri(true); 02016 m_volume->set_fftpad(true); 02017 m_volume->set_attr("npad", m_npad); 02018 m_volume->set_array_offsets(0,1,1); 02019 }
void nn4Reconstructor::buildNormVolume | ( | ) | [private] |
Definition at line 2021 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().
02021 { 02022 02023 if( params.has_key("weight") ) { 02024 m_wptr = params["weight"]; 02025 m_delete_weight = false; 02026 } else { 02027 m_wptr = new EMData(); 02028 m_delete_weight = true; 02029 } 02030 02031 if( m_wptr->get_xsize() != m_vnxc+1 && 02032 m_wptr->get_ysize() != m_vnyp && 02033 m_wptr->get_zsize() != m_vnzp ) { 02034 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02035 m_wptr->to_zero(); 02036 } 02037 02038 m_wptr->set_array_offsets(0,1,1); 02039 }
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 2173 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().
02174 { 02175 if( m_ndim==3 ) { 02176 m_volume->symplane0(m_wptr); 02177 } else { 02178 for( int i=1; i <= m_vnyp; ++i ) { 02179 02180 if( (*m_wptr)(0, i, 1)==0.0 ) { 02181 int j = m_vnyp + 1 - i; 02182 (*m_wptr)(0, i, 1) = (*m_wptr)(0, j, 1); 02183 (*m_volume)(0, i, 1) = (*m_volume)(0, j, 1); 02184 (*m_volume)(1, i, 1) = (*m_volume)(1, j, 1); 02185 } 02186 } 02187 } 02188 02189 02190 int box = 7; 02191 int kc = (box-1)/2; 02192 vector< float > pow_a( m_ndim*kc+1, 1.0 ); 02193 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 02194 pow_a.back()=0.0; 02195 02196 float alpha = 0.0; 02197 if( m_ndim==3) { 02198 int vol = box*box*box; 02199 float max = max3d( kc, pow_a ); 02200 alpha = ( 1.0f - 1.0f/(float)vol ) / max; 02201 } else { 02202 int ara = box*box; 02203 float max = max2d( kc, pow_a ); 02204 alpha = ( 1.0f - 1.0f/(float)ara ) / max; 02205 } 02206 02207 int ix,iy,iz; 02208 for (iz = 1; iz <= m_vnzp; iz++) { 02209 for (iy = 1; iy <= m_vnyp; iy++) { 02210 for (ix = 0; ix <= m_vnxc; ix++) { 02211 if ( (*m_wptr)(ix,iy,iz) > 0) {//(*v) should be treated as complex!! 02212 float tmp; 02213 tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+m_osnr); 02214 02215 if( m_weighting == ESTIMATE ) { 02216 int cx = ix; 02217 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 02218 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 02219 float sum = 0.0; 02220 for( int ii = -kc; ii <= kc; ++ii ) { 02221 int nbrcx = cx + ii; 02222 if( nbrcx >= m_vnxc ) continue; 02223 for( int jj= -kc; jj <= kc; ++jj ) { 02224 int nbrcy = cy + jj; 02225 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 02226 02227 int kcz = (m_ndim==3) ? kc : 0; 02228 for( int kk = -kcz; kk <= kcz; ++kk ) { 02229 int nbrcz = cz + kk; 02230 if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 02231 if( nbrcx < 0 ) { 02232 nbrcx = -nbrcx; 02233 nbrcy = -nbrcy; 02234 nbrcz = -nbrcz; 02235 } 02236 int nbrix = nbrcx; 02237 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 02238 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 02239 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) { 02240 int c = m_ndim*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 02241 sum = sum + pow_a[c]; 02242 } 02243 } 02244 } 02245 } 02246 float wght = 1.0f / ( 1.0f - alpha * sum ); 02247 tmp = tmp * wght; 02248 } 02249 (*m_volume)(2*ix,iy,iz) *= tmp; 02250 (*m_volume)(2*ix+1,iy,iz) *= tmp; 02251 } 02252 } 02253 } 02254 } 02255 02256 //if(m_ndim==2) printImage( m_volume ); 02257 02258 // back fft 02259 m_volume->do_ift_inplace(); 02260 02261 // EMData* win = m_volume->window_center(m_vnx); 02262 m_volume->depad(); 02263 circumference( m_volume ); 02264 m_volume->set_array_offsets( 0, 0, 0 ); 02265 02266 m_result = m_volume->copy(); 02267 return m_result; 02268 }
virtual string EMAN::nn4Reconstructor::get_desc | ( | ) | const [inline, virtual] |
Get a clear, concise description of this class.
Implements EMAN::FactoryBase.
Definition at line 749 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 744 of file reconstructor.h.
References NAME.
00745 { 00746 return NAME; 00747 }
virtual TypeDict EMAN::nn4Reconstructor::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::FactoryBase.
Definition at line 759 of file reconstructor.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.
00760 { 00761 TypeDict d; 00762 d.put("size", EMObject::INT); 00763 d.put("npad", EMObject::INT); 00764 d.put("sign", EMObject::INT); 00765 d.put("ndim", EMObject::INT); 00766 d.put("snr", EMObject::FLOAT); 00767 d.put("symmetry", EMObject::STRING); 00768 d.put("snr", EMObject::FLOAT); 00769 d.put("fftvol", EMObject::EMDATA); 00770 d.put("weight", EMObject::EMDATA); 00771 d.put("weighting", EMObject::INT); 00772 return d; 00773 }
int nn4Reconstructor::insert_padfft_slice | ( | EMData * | padded, | |
const Transform & | trans, | |||
int | mult = 1 | |||
) |
Definition at line 2117 of file reconstructor.cpp.
References Assert, m_nsym, m_symmetry, m_volume, m_wptr, EMAN::EMData::nn(), and t.
Referenced by insert_slice().
02118 { 02119 Assert( padfft != NULL ); 02120 // insert slice for all symmetry related positions 02121 for (int isym=0; isym < m_nsym; isym++) { 02122 Transform tsym = t.get_sym(m_symmetry, isym); 02123 m_volume->nn( m_wptr, padfft, tsym, mult); 02124 } 02125 return 0; 02126 }
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 2056 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.
02056 { 02057 // sanity checks 02058 if (!slice) { 02059 LOGERR("try to insert NULL slice"); 02060 return 1; 02061 } 02062 02063 int padffted= slice->get_attr_default( "padffted", 0 ); 02064 if( m_ndim==3 ) { 02065 if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx) ) { 02066 // FIXME: Why doesn't this throw an exception? 02067 LOGERR("Tried to insert a slice that is the wrong size."); 02068 return 1; 02069 } 02070 } else { 02071 Assert( m_ndim==2 ); 02072 if( slice->get_ysize() !=1 ) { 02073 LOGERR( "for 2D reconstruction, a line is excepted" ); 02074 return 1; 02075 } 02076 } 02077 02078 EMData* padfft = NULL; 02079 02080 if( padffted != 0 ) padfft = new EMData(*slice); 02081 else padfft = padfft_slice( slice, t, m_npad ); 02082 02083 int mult= slice->get_attr_default( "mult", 1 ); 02084 Assert( mult > 0 ); 02085 02086 if( m_ndim==3 ) { 02087 insert_padfft_slice( padfft, t, mult ); 02088 } else { 02089 float alpha = padfft->get_attr( "alpha" ); 02090 alpha = alpha/180.0f*M_PI; 02091 for(int i=0; i < m_vnxc+1; ++i ) { 02092 float xnew = i*cos(alpha); 02093 float ynew = -i*sin(alpha); 02094 float btqr = padfft->get_value_at( 2*i, 0, 0 ); 02095 float btqi = padfft->get_value_at( 2*i+1, 0, 0 ); 02096 if( xnew < 0.0 ) { 02097 xnew *= -1; 02098 ynew *= -1; 02099 btqi *= -1; 02100 } 02101 02102 int ixn = int(xnew+0.5+m_vnxp) - m_vnxp; 02103 int iyn = int(ynew+0.5+m_vnyp) - m_vnyp; 02104 02105 if(iyn < 0 ) iyn += m_vnyp; 02106 02107 (*m_volume)( 2*ixn, iyn+1, 1 ) += btqr *float(mult); 02108 (*m_volume)( 2*ixn+1, iyn+1, 1 ) += btqi * float(mult); 02109 (*m_wptr)(ixn,iyn+1, 1) += float(mult); 02110 } 02111 02112 } 02113 checked_delete( padfft ); 02114 return 0; 02115 }
void EMAN::nn4Reconstructor::load_default_settings | ( | ) | [inline, private] |
static Reconstructor* EMAN::nn4Reconstructor::NEW | ( | ) | [inline, static] |
Definition at line 754 of file reconstructor.h.
References nn4Reconstructor().
00755 { 00756 return new nn4Reconstructor(); 00757 }
void nn4Reconstructor::setup | ( | const string & | symmetry, | |
int | size, | |||
int | npad | |||
) |
Definition at line 1961 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.
01962 { 01963 m_weighting = ESTIMATE; 01964 m_wghta = 0.2f; 01965 01966 m_symmetry = symmetry; 01967 m_npad = npad; 01968 m_nsym = Transform::get_nsym(m_symmetry); 01969 01970 m_vnx = size; 01971 m_vny = size; 01972 m_vnz = (m_ndim==3) ? size : 1; 01973 01974 m_vnxp = size*npad; 01975 m_vnyp = size*npad; 01976 m_vnzp = (m_ndim==3) ? size*npad : 1; 01977 01978 m_vnxc = m_vnxp/2; 01979 m_vnyc = m_vnyp/2; 01980 m_vnzc = (m_ndim==3) ? m_vnzp/2 : 1; 01981 01982 buildFFTVolume(); 01983 buildNormVolume(); 01984 01985 }
void nn4Reconstructor::setup | ( | ) | [virtual] |
Initialize the reconstructor.
Implements EMAN::Reconstructor.
Definition at line 1933 of file reconstructor.cpp.
References EMAN::Dict::has_key(), m_ndim, m_osnr, EMAN::FactoryBase::params, and EMAN::Gatan::to_str().
Referenced by nn4Reconstructor().
01934 { 01935 int size = params["size"]; 01936 int npad = params["npad"]; 01937 01938 01939 string symmetry; 01940 if( params.has_key("symmetry") ) { 01941 symmetry = params["symmetry"].to_str(); 01942 } else { 01943 symmetry = "c1"; 01944 } 01945 01946 if( params.has_key("ndim") ) { 01947 m_ndim = params["ndim"]; 01948 } else { 01949 m_ndim = 3; 01950 } 01951 01952 if( params.has_key( "snr" ) ) { 01953 m_osnr = 1.0f/float( params["snr"] ); 01954 } else { 01955 m_osnr = 0.0; 01956 } 01957 01958 setup( symmetry, size, npad ); 01959 }
bool EMAN::nn4Reconstructor::m_delete_volume [private] |
Definition at line 785 of file reconstructor.h.
Referenced by buildFFTVolume(), and ~nn4Reconstructor().
bool EMAN::nn4Reconstructor::m_delete_weight [private] |
Definition at line 786 of file reconstructor.h.
Referenced by buildNormVolume(), and ~nn4Reconstructor().
int EMAN::nn4Reconstructor::m_ndim [private] |
Definition at line 792 of file reconstructor.h.
Referenced by finish(), insert_slice(), and setup().
int EMAN::nn4Reconstructor::m_npad [private] |
Definition at line 790 of file reconstructor.h.
Referenced by buildFFTVolume(), insert_slice(), and setup().
int EMAN::nn4Reconstructor::m_nsym [private] |
float EMAN::nn4Reconstructor::m_osnr [private] |
EMData* EMAN::nn4Reconstructor::m_result [private] |
Definition at line 784 of file reconstructor.h.
Referenced by finish(), nn4Reconstructor(), and ~nn4Reconstructor().
string EMAN::nn4Reconstructor::m_symmetry [private] |
int EMAN::nn4Reconstructor::m_vnx [private] |
int EMAN::nn4Reconstructor::m_vnxc [private] |
Definition at line 794 of file reconstructor.h.
Referenced by buildNormVolume(), finish(), insert_slice(), and setup().
int EMAN::nn4Reconstructor::m_vnxp [private] |
Definition at line 793 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 793 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 793 of file reconstructor.h.
Referenced by buildFFTVolume(), buildNormVolume(), finish(), and setup().
EMData* EMAN::nn4Reconstructor::m_volume [private] |
Definition at line 782 of file reconstructor.h.
Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nn4Reconstructor(), and ~nn4Reconstructor().
int EMAN::nn4Reconstructor::m_weighting [private] |
float EMAN::nn4Reconstructor::m_wghta [private] |
float EMAN::nn4Reconstructor::m_wghtb [private] |
Definition at line 798 of file reconstructor.h.
EMData* EMAN::nn4Reconstructor::m_wptr [private] |
Definition at line 783 of file reconstructor.h.
Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nn4Reconstructor(), and ~nn4Reconstructor().
const string nn4Reconstructor::NAME = "nn4" [static] |