#include <reconstructor.h>
Inheritance diagram for EMAN::nnSSNR_ctfReconstructor:
Public Member Functions | |
nnSSNR_ctfReconstructor () | |
nnSSNR_ctfReconstructor (const string &symmetry, int size, int npad, float snr, int sign) | |
~nnSSNR_ctfReconstructor () | |
virtual void | setup () |
Initialize the reconstructor. | |
virtual int | insert_slice (const EMData *const slice, const Transform &euler, const float weight=1.0) |
Insert a slice into a 3D volume, in a given orientation. | |
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. | |
TypeDict | get_param_types () const |
void | setup (const string &symmetry, int size, int npad, float snr, int sign) |
int | insert_padfft_slice (EMData *padded, const Transform &trans, int mult=1) |
Static Public Member Functions | |
Reconstructor * | NEW () |
Static Public Attributes | |
const string | NAME = "nnSSNR_ctf" |
Private Member Functions | |
void | buildFFTVolume () |
void | buildNormVolume () |
void | buildNorm2Volume () |
void | buildNorm3Volume () |
Private Attributes | |
EMData * | m_volume |
EMData * | m_wptr |
EMData * | m_wptr2 |
EMData * | m_wptr3 |
EMData * | m_result |
bool | m_delete_volume |
bool | m_delete_weight |
bool | m_delete_weight2 |
bool | m_delete_weight3 |
string | m_symmetry |
int | m_weighting |
int | m_vnx |
int | m_vny |
int | m_vnz |
int | m_npad |
int | m_nsym |
int | m_vnzp |
int | m_vnyp |
int | m_vnxp |
int | m_vnzc |
int | m_vnyc |
int | m_vnxc |
float | m_wghta |
float | m_wghtb |
int | m_sign |
float | m_snr |
int | wiener |
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Definition at line 3700 of file reconstructor.cpp. References m_result, m_volume, m_wptr, m_wptr2, and m_wptr3. 03701 { 03702 m_volume = NULL; 03703 m_wptr = NULL; 03704 m_wptr2 = NULL; 03705 m_wptr3 = NULL; 03706 m_result = NULL; 03707 }
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Definition at line 3709 of file reconstructor.cpp. References m_result, m_volume, m_wptr, m_wptr2, m_wptr3, setup(), and sign. 03710 { 03711 m_volume = NULL; 03712 m_wptr = NULL; 03713 m_wptr2 = NULL; 03714 m_wptr3 = NULL; 03715 m_result = NULL; 03716 03717 setup( symmetry, size, npad, snr, sign ); 03718 }
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Definition at line 3720 of file reconstructor.cpp. References checked_delete(), m_result, m_volume, m_wptr, m_wptr2, and m_wptr3. 03721 { 03722 03723 if( m_delete_volume ) checked_delete(m_volume); 03724 if( m_delete_weight ) checked_delete( m_wptr ); 03725 if( m_delete_weight2 ) checked_delete( m_wptr2 ); 03726 if( m_delete_weight3 ) checked_delete( m_wptr3 ); 03727 checked_delete( m_result ); 03728 }
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Definition at line 3775 of file reconstructor.cpp. References EMAN::Dict::has_key(), m_delete_volume, m_npad, m_vnxc, 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(). 03775 { 03776 03777 int offset = 2 - m_vnxp%2; 03778 if( params.has_key("fftvol") ) { 03779 m_volume = params["fftvol"]; /* volume should be defined in python when PMI is turned on*/ 03780 m_delete_volume = false; 03781 } else { 03782 m_volume = new EMData(); 03783 m_delete_volume = true; 03784 } 03785 03786 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp); 03787 m_volume->to_zero(); 03788 03789 m_volume->set_fftodd(m_vnxp % 2); 03790 03791 m_volume->set_nxc(m_vnxc); 03792 m_volume->set_complex(true); 03793 m_volume->set_ri(true); //(real, imaginary) instead of polar coordinate 03794 m_volume->set_fftpad(true); 03795 m_volume->set_attr("npad", m_npad); 03796 m_volume->set_array_offsets(0,1,1); 03797 }
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Definition at line 3814 of file reconstructor.cpp. References EMAN::Dict::has_key(), m_delete_weight2, m_vnxc, m_vnyp, m_vnzp, m_wptr2, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero(). Referenced by setup(). 03814 { 03815 03816 if( params.has_key("weight2") ) { 03817 m_wptr2 = params["weight2"]; 03818 m_delete_weight2 = false; 03819 } else { 03820 m_wptr2 = new EMData(); 03821 m_delete_weight2 = true; 03822 } 03823 m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp); 03824 m_wptr2->to_zero(); 03825 m_wptr2->set_array_offsets(0,1,1); 03826 }
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Definition at line 3828 of file reconstructor.cpp. References EMAN::Dict::has_key(), m_delete_weight3, m_vnxc, m_vnyp, m_vnzp, m_wptr3, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero(). Referenced by setup(). 03828 { 03829 03830 if( params.has_key("weight3") ) { 03831 m_wptr3 = params["weight3"]; 03832 m_delete_weight3 = false; 03833 } else { 03834 m_wptr3 = new EMData(); 03835 m_delete_weight3 = true; 03836 } 03837 m_wptr3->set_size(m_vnxc+1,m_vnyp,m_vnzp); 03838 m_wptr3->to_zero(); 03839 m_wptr3->set_array_offsets(0,1,1); 03840 }
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Definition at line 3800 of file reconstructor.cpp. References 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(). 03801 { 03802 if( params.has_key("weight") ) { 03803 m_wptr = params["weight"]; 03804 m_delete_weight = false; 03805 } else { 03806 m_wptr = new EMData(); 03807 m_delete_weight = true; 03808 } 03809 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 03810 m_wptr->to_zero(); 03811 m_wptr->set_array_offsets(0,1,1); 03812 }
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Finish reconstruction and return the complete model.
Reimplemented from EMAN::Reconstructor. Definition at line 3881 of file reconstructor.cpp. References abs, EMAN::EMData::cmplx(), m_vnxc, m_vnxp, m_vnyc, m_vnyp, m_vnzc, m_vnzp, m_volume, m_weighting, m_wghta, m_wptr, m_wptr2, m_wptr3, max, max3d(), nn(), norm(), EMAN::Util::round(), EMAN::EMData::set_complex(), EMAN::EMData::set_fftodd(), EMAN::EMData::set_fftpad(), EMAN::EMData::set_nxc(), EMAN::EMData::set_ri(), EMAN::EMData::set_size(), sqrt(), EMAN::EMData::symplane2(), EMAN::EMData::to_zero(), and EMAN::EMData::update(). 03882 { 03883 /* 03884 I changed the code on 05/15 so it only returns variance. 03885 Lines commented out are marked by //# 03886 The version prior to the currect changes is r1.190 03887 PAP 03888 */ 03889 /*** 03890 m_volume ctf*(P^2D->3D(F^3D)) 03891 m_wptr ctf^2 03892 m_wptr2 |P^2D->3D(F^3D)|^2 03893 m_wptr3 Kn 03894 nominator = sum_rot [ wght*signal ] 03895 denominator = sum_rot[ wght*variance ] 03896 ***/ 03897 int kz, ky; 03898 int box = 7; 03899 int kc = (box-1)/2; 03900 float alpha = 0.0; 03901 float argx, argy, argz; 03902 vector< float > pow_a( 3*kc+1, 1.0 ); 03903 float w = params["w"]; 03904 float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc); 03905 float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc); 03906 #ifdef _WIN32 03907 float dz2 = 1.0f/_cpp_max(float(m_vnzc),1.0f)/_cpp_max(float(m_vnzc),1.0f); 03908 int inc = Util::round(float(_cpp_max(_cpp_max(m_vnxc,m_vnyc),m_vnzc))/w); 03909 #else 03910 float dz2 = 1.0f/std::max(float(m_vnzc),1.0f)/std::max(float(m_vnzc),1.0f); 03911 int inc = Util::round(float(std::max(std::max(m_vnxc,m_vnyc),m_vnzc))/w); 03912 #endif //_WIN32 03913 03914 EMData* SSNR = params["SSNR"]; 03915 SSNR->set_size(inc+1,4,1); 03916 //#EMData* vol_ssnr = new EMData(); 03917 //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp); 03918 //#vol_ssnr->to_zero(); 03919 //# new linea follow 03920 EMData* vol_ssnr = new EMData(); 03921 vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp); 03922 vol_ssnr->to_zero(); 03923 if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0); 03924 else vol_ssnr->set_fftodd(1); 03925 vol_ssnr->set_nxc(m_vnxc); 03926 vol_ssnr->set_complex(true); 03927 vol_ssnr->set_ri(true); 03928 vol_ssnr->set_fftpad(false); 03929 //# 03930 float *nom = new float[inc+1]; 03931 float *denom = new float[inc+1]; 03932 int *ka = new int[inc+1]; 03933 int *nn = new int[inc+1]; 03934 float wght = 1.f; 03935 for (int i = 0; i <= inc; i++) { 03936 nom[i] = 0.0f; 03937 denom[i] = 0.0f; 03938 nn[i] = 0; 03939 ka[i] = 0; 03940 } 03941 m_volume->symplane2(m_wptr, m_wptr2, m_wptr3); 03942 if ( m_weighting == ESTIMATE ) { 03943 int vol = box*box*box; 03944 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 03945 pow_a[3*kc] = 0.0; 03946 float max = max3d( kc, pow_a ); 03947 alpha = ( 1.0f - 1.0f/(float)vol ) / max; 03948 } 03949 for (int iz = 1; iz <= m_vnzp; iz++) { 03950 if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1; 03951 argz = float(kz*kz)*dz2; 03952 for (int iy = 1; iy <= m_vnyp; iy++) { 03953 if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1; 03954 argy = argz + float(ky*ky)*dy2; 03955 for (int ix = 0; ix <= m_vnxc; ix++) { 03956 float Kn = (*m_wptr3)(ix,iy,iz); 03957 argx = std::sqrt(argy + float(ix*ix)*dx2); 03958 int r = Util::round(float(inc)*argx); 03959 if ( r >= 0 && Kn > 4.5f ) { 03960 if ( m_weighting == ESTIMATE ) { 03961 int cx = ix; 03962 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 03963 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 03964 float sum = 0.0; 03965 for( int ii = -kc; ii <= kc; ++ii ) { 03966 int nbrcx = cx + ii; 03967 if( nbrcx >= m_vnxc ) continue; 03968 for ( int jj= -kc; jj <= kc; ++jj ) { 03969 int nbrcy = cy + jj; 03970 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 03971 for( int kk = -kc; kk <= kc; ++kk ) { 03972 int nbrcz = cz + jj; 03973 if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 03974 if( nbrcx < 0 ) { 03975 nbrcx = -nbrcx; 03976 nbrcy = -nbrcy; 03977 nbrcz = -nbrcz; 03978 } 03979 int nbrix = nbrcx; 03980 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 03981 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 03982 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) { 03983 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 03984 sum = sum + pow_a[c]; 03985 } 03986 } 03987 } 03988 } 03989 // int r = std::abs(cx) + std::abs(cy) + std::abs(cz); 03990 wght = 1.0f / ( 1.0f - alpha * sum ); 03991 } // end of ( m_weighting == ESTIMATE ) 03992 float nominator = std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz); 03993 float denominator = ((*m_wptr2)(ix,iy,iz)-std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz))/(Kn-1.0f); 03994 // Skip Friedel related values 03995 if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) { 03996 if ( r <= inc ) { 03997 nom[r] += nominator*wght; 03998 denom[r] += denominator/(*m_wptr)(ix,iy,iz)*wght; 03999 nn[r] += 2; 04000 ka[r] += int(Kn); 04001 } 04002 /* 04003 #ifdef _WIN32 04004 float tmp = _cpp_max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f); 04005 #else 04006 float tmp = std::max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f); 04007 #endif //_WIN32 04008 // Create SSNR as a 3D array (-n/2:n/2+n%2-1) 04009 int iix = m_vnxc + ix; int iiy = m_vnyc + ky; int iiz = m_vnzc + kz; 04010 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 04011 (*vol_ssnr)(iix, iiy, iiz) = tmp; 04012 // Friedel part 04013 iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz; 04014 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 04015 (*vol_ssnr)(iix, iiy, iiz) = tmp; 04016 */ 04017 } 04018 (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght; 04019 } // end of Kn>4.5 or whatever 04020 } 04021 } 04022 } 04023 for (int i = 0; i <= inc; i++) { 04024 (*SSNR)(i,0,0) = nom[i]; 04025 (*SSNR)(i,1,0) = denom[i]; 04026 (*SSNR)(i,2,0) = static_cast<float>(nn[i]); 04027 (*SSNR)(i,3,0) = static_cast<float>(ka[i]); 04028 } 04029 vol_ssnr->update(); 04030 return vol_ssnr; 04031 // } 04032 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 1219 of file reconstructor.h. 01220 { 01221 return "Reconstruction by nearest neighbor with 3D SSNR with CTF"; 01222 }
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Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase. Definition at line 1214 of file reconstructor.h. 01215 {
01216 return NAME;
01217 }
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Implements EMAN::FactoryBase. Definition at line 1229 of file reconstructor.h. References EMAN::TypeDict::put(). 01230 { 01231 TypeDict d; 01232 d.put("size", EMObject::INT); 01233 d.put("npad", EMObject::INT); 01234 d.put("symmetry", EMObject::STRING); 01235 d.put("fftvol", EMObject::EMDATA); 01236 d.put("fftwvol", EMObject::EMDATA); 01237 d.put("weight", EMObject::EMDATA); 01238 d.put("weight2", EMObject::EMDATA); 01239 d.put("weight3", EMObject::EMDATA); 01240 d.put("SSNR", EMObject::EMDATA); 01241 d.put("w", EMObject::FLOAT); 01242 d.put("sign", EMObject::INT); 01243 d.put("snr", EMObject::FLOAT); 01244 return d; 01245 }
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Definition at line 3867 of file reconstructor.cpp. References Assert, EMAN::Transform::get_sym(), m_symmetry, m_volume, m_wptr, m_wptr2, m_wptr3, mult(), EMAN::EMData::nn_SSNR_ctf(), and t. Referenced by insert_slice(). 03868 { 03869 Assert( padfft != NULL ); 03870 03871 // insert slice for all symmetry related positions 03872 for (int isym=0; isym < m_nsym; isym++) { 03873 Transform tsym = t.get_sym(m_symmetry, isym); 03874 m_volume->nn_SSNR_ctf(m_wptr, m_wptr2, m_wptr3, padfft, tsym, mult); 03875 } 03876 03877 return 0; 03878 }
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Insert a slice into a 3D volume, in a given orientation.
Reimplemented from EMAN::Reconstructor. Definition at line 3842 of file reconstructor.cpp. References Assert, checked_delete(), EMAN::EMData::get_attr_default(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), insert_padfft_slice(), LOGERR, m_npad, mult(), EMAN::padfft_slice(), and t. 03842 { 03843 // sanity checks 03844 if (!slice) { 03845 LOGERR("try to insert NULL slice"); 03846 return 1; 03847 } 03848 int padffted= slice->get_attr_default("padffted", 0); 03849 if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx) ) { 03850 // FIXME: Why doesn't this throw an exception? 03851 LOGERR("Tried to insert a slice that is the wrong size."); 03852 return 1; 03853 } 03854 EMData* padfft = NULL; 03855 03856 if( padffted != 0 ) padfft = new EMData(*slice); 03857 else padfft = padfft_slice( slice, t, m_npad ); 03858 03859 int mult= slice->get_attr_default("mult", 1); 03860 03861 Assert( mult > 0 ); 03862 insert_padfft_slice( padfft, t, mult ); 03863 03864 checked_delete( padfft ); 03865 return 0; 03866 }
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Definition at line 1224 of file reconstructor.h. 01225 { 01226 return new nnSSNR_ctfReconstructor(); 01227 }
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Definition at line 3742 of file reconstructor.cpp. References buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), EMAN::Transform::get_nsym(), m_npad, m_nsym, m_sign, m_snr, m_symmetry, m_vnx, m_vnxc, m_vnxp, m_vny, m_vnyc, m_vnyp, m_vnz, m_vnzc, m_vnzp, m_weighting, m_wghta, m_wghtb, and wiener. 03743 { 03744 03745 m_weighting = ESTIMATE; 03746 m_wghta = 0.2f; 03747 m_wghtb = 0.004f; 03748 wiener = 1; 03749 03750 m_symmetry = symmetry; 03751 m_npad = npad; 03752 m_nsym = Transform::get_nsym(m_symmetry); 03753 03754 m_sign = sign; 03755 m_snr = snr; 03756 03757 m_vnx = size; 03758 m_vny = size; 03759 m_vnz = size; 03760 03761 m_vnxp = size*npad; 03762 m_vnyp = size*npad; 03763 m_vnzp = size*npad; 03764 03765 m_vnxc = m_vnxp/2; 03766 m_vnyc = m_vnyp/2; 03767 m_vnzc = m_vnzp/2; 03768 03769 buildFFTVolume(); 03770 buildNormVolume(); 03771 buildNorm2Volume(); 03772 buildNorm3Volume(); 03773 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 3730 of file reconstructor.cpp. References EMAN::Dict::has_key(), and sign. Referenced by nnSSNR_ctfReconstructor(). 03731 { 03732 int size = params["size"]; 03733 int npad = params["npad"]; 03734 int sign = params["sign"]; 03735 float snr = params["snr"]; 03736 string symmetry; 03737 if( params.has_key("symmetry") ) symmetry = params["symmetry"].to_str(); 03738 else symmetry = "c1"; 03739 03740 setup( symmetry, size, npad, snr, sign ); 03741 }
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Definition at line 1258 of file reconstructor.h. Referenced by buildFFTVolume(). |
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Definition at line 1259 of file reconstructor.h. Referenced by buildNormVolume(). |
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Definition at line 1260 of file reconstructor.h. Referenced by buildNorm2Volume(). |
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Definition at line 1261 of file reconstructor.h. Referenced by buildNorm3Volume(). |
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Definition at line 1265 of file reconstructor.h. Referenced by buildFFTVolume(), insert_slice(), and setup(). |
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Definition at line 1266 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1257 of file reconstructor.h. Referenced by nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1275 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1276 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1262 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 1264 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1268 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 1267 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), and setup(). |
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Definition at line 1264 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1268 of file reconstructor.h. |
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Definition at line 1267 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 1264 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1268 of file reconstructor.h. |
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Definition at line 1267 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 1253 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1263 of file reconstructor.h. |
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Definition at line 1273 of file reconstructor.h. |
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Definition at line 1274 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1254 of file reconstructor.h. Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1255 of file reconstructor.h. Referenced by buildNorm2Volume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1256 of file reconstructor.h. Referenced by buildNorm3Volume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 82 of file reconstructor.cpp. |
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Definition at line 1277 of file reconstructor.h. Referenced by setup(). |