#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 | |
Reconstructor * | NEW () |
Static Public Attributes | |
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 |
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Definition at line 1871 of file reconstructor.cpp. References m_result, m_volume, and m_wptr.
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Definition at line 1878 of file reconstructor.cpp. References load_default_settings(), m_result, m_volume, m_wptr, EMAN::Reconstructor::print_params(), and setup(). 01879 { 01880 m_volume = NULL; 01881 m_wptr = NULL; 01882 m_result = NULL; 01883 setup( symmetry, size, npad ); 01884 load_default_settings(); 01885 print_params(); 01886 }
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Definition at line 1888 of file reconstructor.cpp. References checked_delete(), m_result, m_volume, and m_wptr. 01889 { 01890 if( m_delete_volume ) checked_delete(m_volume); 01891 01892 if( m_delete_weight ) checked_delete( m_wptr ); 01893 01894 checked_delete( m_result ); 01895 }
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Definition at line 1981 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::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(). 01981 { 01982 int offset = 2 - m_vnxp%2; 01983 01984 if( params.has_key("fftvol") ) { 01985 m_volume = params["fftvol"]; 01986 m_delete_volume = false; 01987 } else { 01988 m_volume = new EMData(); 01989 m_delete_volume = true; 01990 } 01991 01992 if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) { 01993 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp); 01994 m_volume->to_zero(); 01995 } 01996 // ---------------------------------------------------------------- 01997 // Added by Zhengfan Yang on 03/15/07 01998 // Original author: please check whether my revision is correct and 01999 // other Reconstructor need similiar revision. 02000 if ( m_vnxp % 2 == 0 ) m_volume->set_fftodd(0); 02001 else m_volume->set_fftodd(1); 02002 // ---------------------------------------------------------------- 02003 02004 m_volume->set_nxc(m_vnxp/2); 02005 m_volume->set_complex(true); 02006 m_volume->set_ri(true); 02007 m_volume->set_fftpad(true); 02008 m_volume->set_attr("npad", m_npad); 02009 m_volume->set_array_offsets(0,1,1); 02010 }
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Definition at line 2012 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::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero(). Referenced by setup(). 02012 { 02013 02014 if( params.has_key("weight") ) { 02015 m_wptr = params["weight"]; 02016 m_delete_weight = false; 02017 } else { 02018 m_wptr = new EMData(); 02019 m_delete_weight = true; 02020 } 02021 02022 if( m_wptr->get_xsize() != m_vnxc+1 && 02023 m_wptr->get_ysize() != m_vnyp && 02024 m_wptr->get_zsize() != m_vnzp ) { 02025 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02026 m_wptr->to_zero(); 02027 } 02028 02029 m_wptr->set_array_offsets(0,1,1); 02030 }
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Finish reconstruction and return the complete model.
Reimplemented from EMAN::Reconstructor. Definition at line 2197 of file reconstructor.cpp. References abs, circumf(), EMAN::EMData::copy(), EMAN::EMData::depad(), EMAN::EMData::do_ift_inplace(), EMAN::EMData::get_attr(), m_ndim, m_result, m_vnyc, m_vnyp, m_volume, m_weighting, m_wghta, m_wptr, max, max2d(), max3d(), EMAN::EMData::set_array_offsets(), and EMAN::EMData::symplane0(). 02198 { 02199 if( m_ndim==3 ) { 02200 m_volume->symplane0(m_wptr); 02201 } else { 02202 for( int i=1; i <= m_vnyp; ++i ) { 02203 02204 if( (*m_wptr)(0, i, 1)==0.0 ) { 02205 int j = m_vnyp + 1 - i; 02206 (*m_wptr)(0, i, 1) = (*m_wptr)(0, j, 1); 02207 (*m_volume)(0, i, 1) = (*m_volume)(0, j, 1); 02208 (*m_volume)(1, i, 1) = (*m_volume)(1, j, 1); 02209 } 02210 } 02211 } 02212 02213 02214 int box = 7; 02215 int kc = (box-1)/2; 02216 vector< float > pow_a( m_ndim*kc+1, 1.0 ); 02217 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 02218 pow_a.back()=0.0; 02219 02220 float alpha = 0.0; 02221 if( m_ndim==3) { 02222 int vol = box*box*box; 02223 float max = max3d( kc, pow_a ); 02224 alpha = ( 1.0f - 1.0f/(float)vol ) / max; 02225 } else { 02226 int ara = box*box; 02227 float max = max2d( kc, pow_a ); 02228 alpha = ( 1.0f - 1.0f/(float)ara ) / max; 02229 } 02230 02231 int ix,iy,iz; 02232 for (iz = 1; iz <= m_vnzp; iz++) { 02233 for (iy = 1; iy <= m_vnyp; iy++) { 02234 for (ix = 0; ix <= m_vnxc; ix++) { 02235 if ( (*m_wptr)(ix,iy,iz) > 0) {//(*v) should be treated as complex!! 02236 float tmp; 02237 tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+m_osnr); 02238 02239 if( m_weighting == ESTIMATE ) { 02240 int cx = ix; 02241 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 02242 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 02243 float sum = 0.0; 02244 for( int ii = -kc; ii <= kc; ++ii ) { 02245 int nbrcx = cx + ii; 02246 if( nbrcx >= m_vnxc ) continue; 02247 for( int jj= -kc; jj <= kc; ++jj ) { 02248 int nbrcy = cy + jj; 02249 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 02250 02251 int kcz = (m_ndim==3) ? kc : 0; 02252 for( int kk = -kcz; kk <= kcz; ++kk ) { 02253 int nbrcz = cz + kk; 02254 if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 02255 if( nbrcx < 0 ) { 02256 nbrcx = -nbrcx; 02257 nbrcy = -nbrcy; 02258 nbrcz = -nbrcz; 02259 } 02260 int nbrix = nbrcx; 02261 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 02262 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 02263 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) { 02264 int c = m_ndim*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 02265 sum = sum + pow_a[c]; 02266 } 02267 } 02268 } 02269 } 02270 float wght = 1.0f / ( 1.0f - alpha * sum ); 02271 tmp = tmp * wght; 02272 } 02273 (*m_volume)(2*ix,iy,iz) *= tmp; 02274 (*m_volume)(2*ix+1,iy,iz) *= tmp; 02275 } 02276 } 02277 } 02278 } 02279 02280 //if(m_ndim==2) printImage( m_volume ); 02281 02282 // back fft 02283 m_volume->do_ift_inplace(); 02284 02285 // EMData* win = m_volume->window_center(m_vnx); 02286 int npad = m_volume->get_attr("npad"); 02287 m_volume->depad(); 02288 circumf( m_volume, npad ); 02289 m_volume->set_array_offsets( 0, 0, 0 ); 02290 02291 m_result = m_volume->copy(); 02292 return m_result; 02293 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 749 of file reconstructor.h. 00750 { 00751 return "Direct Fourier inversion routine"; 00752 }
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Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase. Definition at line 744 of file reconstructor.h. 00745 {
00746 return NAME;
00747 }
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Implements EMAN::FactoryBase. Definition at line 759 of file reconstructor.h. References EMAN::TypeDict::put(). 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 }
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Definition at line 2108 of file reconstructor.cpp. References Assert, EMAN::Transform::get_sym(), m_symmetry, m_volume, m_wptr, mult(), EMAN::EMData::nn(), and t. Referenced by insert_slice(). 02109 { 02110 Assert( padfft != NULL ); 02111 // insert slice for all symmetry related positions 02112 02113 for (int isym=0; isym < m_nsym; isym++) { 02114 Transform tsym = t.get_sym(m_symmetry, isym); 02115 02116 m_volume->nn( m_wptr, padfft, tsym, mult); 02117 } 02118 return 0; 02119 }
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Insert an image slice to the reconstructor. To insert multiple image slices, call this function multiple times.
Reimplemented from EMAN::Reconstructor. Definition at line 2047 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_vnxc, m_vnxp, m_vnyp, mult(), EMAN::padfft_slice(), and t. 02047 { 02048 // sanity checks 02049 if (!slice) { 02050 LOGERR("try to insert NULL slice"); 02051 return 1; 02052 } 02053 02054 int padffted= slice->get_attr_default( "padffted", 0 ); 02055 if( m_ndim==3 ) { 02056 if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx) ) { 02057 // FIXME: Why doesn't this throw an exception? 02058 LOGERR("Tried to insert a slice that is the wrong size."); 02059 return 1; 02060 } 02061 } else { 02062 Assert( m_ndim==2 ); 02063 if( slice->get_ysize() !=1 ) { 02064 LOGERR( "for 2D reconstruction, a line is excepted" ); 02065 return 1; 02066 } 02067 } 02068 02069 EMData* padfft = NULL; 02070 02071 if( padffted != 0 ) padfft = new EMData(*slice); 02072 else padfft = padfft_slice( slice, t, m_npad ); 02073 02074 int mult= slice->get_attr_default( "mult", 1 ); 02075 Assert( mult > 0 ); 02076 02077 if( m_ndim==3 ) { 02078 insert_padfft_slice( padfft, t, mult ); 02079 } else { 02080 float alpha = padfft->get_attr( "alpha" ); 02081 alpha = alpha/180.0f*M_PI; 02082 for(int i=0; i < m_vnxc+1; ++i ) { 02083 float xnew = i*cos(alpha); 02084 float ynew = -i*sin(alpha); 02085 float btqr = padfft->get_value_at( 2*i, 0, 0 ); 02086 float btqi = padfft->get_value_at( 2*i+1, 0, 0 ); 02087 if( xnew < 0.0 ) { 02088 xnew *= -1; 02089 ynew *= -1; 02090 btqi *= -1; 02091 } 02092 02093 int ixn = int(xnew+0.5+m_vnxp) - m_vnxp; 02094 int iyn = int(ynew+0.5+m_vnyp) - m_vnyp; 02095 02096 if(iyn < 0 ) iyn += m_vnyp; 02097 02098 (*m_volume)( 2*ixn, iyn+1, 1 ) += btqr *float(mult); 02099 (*m_volume)( 2*ixn+1, iyn+1, 1 ) += btqi * float(mult); 02100 (*m_wptr)(ixn,iyn+1, 1) += float(mult); 02101 } 02102 02103 } 02104 checked_delete( padfft ); 02105 return 0; 02106 }
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Definition at line 800 of file reconstructor.h. Referenced by nn4Reconstructor(). 00801 {
00802 //params["use_weights"] = false;
00803 }
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Definition at line 754 of file reconstructor.h. 00755 { 00756 return new nn4Reconstructor(); 00757 }
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Definition at line 1954 of file reconstructor.cpp. References buildFFTVolume(), buildNormVolume(), 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. 01955 { 01956 m_weighting = ESTIMATE; 01957 m_wghta = 0.2f; 01958 01959 m_symmetry = symmetry; 01960 m_npad = npad; 01961 m_nsym = Transform::get_nsym(m_symmetry); 01962 01963 m_vnx = size; 01964 m_vny = size; 01965 m_vnz = (m_ndim==3) ? size : 1; 01966 01967 m_vnxp = size*npad; 01968 m_vnyp = size*npad; 01969 m_vnzp = (m_ndim==3) ? size*npad : 1; 01970 01971 m_vnxc = m_vnxp/2; 01972 m_vnyc = m_vnyp/2; 01973 m_vnzc = (m_ndim==3) ? m_vnzp/2 : 1; 01974 01975 buildFFTVolume(); 01976 buildNormVolume(); 01977 01978 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 1935 of file reconstructor.cpp. References EMAN::Dict::has_key(), m_ndim, and m_osnr. Referenced by nn4Reconstructor(). 01936 { 01937 int size = params["size"]; 01938 int npad = params["npad"]; 01939 01940 01941 string symmetry; 01942 if( params.has_key("symmetry") ) symmetry = params["symmetry"].to_str(); 01943 else symmetry = "c1"; 01944 01945 if( params.has_key("ndim") ) m_ndim = params["ndim"]; 01946 else m_ndim = 3; 01947 01948 if( params.has_key( "snr" ) ) m_osnr = 1.0f/float( params["snr"] ); 01949 else m_osnr = 0.0; 01950 01951 setup( symmetry, size, npad ); 01952 }
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Definition at line 785 of file reconstructor.h. Referenced by buildFFTVolume(). |
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Definition at line 786 of file reconstructor.h. Referenced by buildNormVolume(). |
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Definition at line 792 of file reconstructor.h. Referenced by finish(), insert_slice(), and setup(). |
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Definition at line 790 of file reconstructor.h. Referenced by buildFFTVolume(), insert_slice(), and setup(). |
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Definition at line 791 of file reconstructor.h. Referenced by setup(). |
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Definition at line 799 of file reconstructor.h. Referenced by setup(). |
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Definition at line 784 of file reconstructor.h. Referenced by finish(), nn4Reconstructor(), and ~nn4Reconstructor(). |
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Definition at line 787 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 789 of file reconstructor.h. Referenced by setup(). |
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Definition at line 794 of file reconstructor.h. Referenced by buildNormVolume(), insert_slice(), and setup(). |
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Definition at line 793 of file reconstructor.h. Referenced by buildFFTVolume(), insert_slice(), and setup(). |
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Definition at line 789 of file reconstructor.h. Referenced by setup(). |
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Definition at line 794 of file reconstructor.h. |
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Definition at line 793 of file reconstructor.h. Referenced by buildFFTVolume(), buildNormVolume(), finish(), insert_slice(), and setup(). |
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Definition at line 789 of file reconstructor.h. Referenced by setup(). |
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Definition at line 794 of file reconstructor.h. Referenced by setup(). |
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Definition at line 793 of file reconstructor.h. Referenced by buildFFTVolume(), buildNormVolume(), and setup(). |
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Definition at line 782 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nn4Reconstructor(), and ~nn4Reconstructor(). |
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Definition at line 788 of file reconstructor.h. |
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Definition at line 797 of file reconstructor.h. |
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Definition at line 798 of file reconstructor.h. |
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Definition at line 783 of file reconstructor.h. Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nn4Reconstructor(), and ~nn4Reconstructor(). |
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Definition at line 77 of file reconstructor.cpp. |