#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 |
| 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 3730 of file reconstructor.cpp. References m_volume, m_wptr, m_wptr2, and m_wptr3. 03731 {
03732 m_volume = NULL;
03733 m_wptr = NULL;
03734 m_wptr2 = NULL;
03735 m_wptr3 = NULL;
03736 }
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Definition at line 3738 of file reconstructor.cpp. References m_volume, m_wptr, m_wptr2, m_wptr3, setup(), and sign. 03739 {
03740 m_volume = NULL;
03741 m_wptr = NULL;
03742 m_wptr2 = NULL;
03743 m_wptr3 = NULL;
03744
03745 setup( symmetry, size, npad, snr, sign );
03746 }
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Definition at line 3748 of file reconstructor.cpp. 03749 {
03750
03751 //if( m_delete_volume ) checked_delete(m_volume);
03752 //if( m_delete_weight ) checked_delete( m_wptr );
03753 //if( m_delete_weight2 ) checked_delete( m_wptr2 );
03754 //if( m_delete_weight3 ) checked_delete( m_wptr3 );
03755 //checked_delete( m_result );
03756 }
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Definition at line 3803 of file reconstructor.cpp. References 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(). 03803 {
03804
03805 int offset = 2 - m_vnxp%2;
03806 m_volume = params["fftvol"];
03807
03808 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
03809 m_volume->to_zero();
03810
03811 m_volume->set_fftodd(m_vnxp % 2);
03812
03813 m_volume->set_nxc(m_vnxc);
03814 m_volume->set_complex(true);
03815 m_volume->set_ri(true); //(real, imaginary) instead of polar coordinate
03816 m_volume->set_fftpad(true);
03817 m_volume->set_attr("npad", m_npad);
03818 m_volume->set_array_offsets(0,1,1);
03819 }
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Definition at line 3830 of file reconstructor.cpp. References 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(). 03830 {
03831
03832 m_wptr2 = params["weight2"];
03833 m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp);
03834 m_wptr2->to_zero();
03835 m_wptr2->set_array_offsets(0,1,1);
03836 }
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Definition at line 3838 of file reconstructor.cpp. References 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(). 03838 {
03839
03840 m_wptr3 = params["weight3"];
03841 m_wptr3->set_size(m_vnxc+1,m_vnyp,m_vnzp);
03842 m_wptr3->to_zero();
03843 m_wptr3->set_array_offsets(0,1,1);
03844 }
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Definition at line 3822 of file reconstructor.cpp. References 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(). 03823 {
03824 m_wptr = params["weight"];
03825 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
03826 m_wptr->to_zero();
03827 m_wptr->set_array_offsets(0,1,1);
03828 }
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Finish reconstruction and return the complete model.
Reimplemented from EMAN::Reconstructor. Definition at line 3885 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(). 03886 {
03887 /*
03888 I changed the code on 05/15 so it only returns variance.
03889 Lines commented out are marked by //#
03890 The version prior to the currect changes is r1.190
03891 PAP
03892 */
03893 /***
03894 m_volume ctf*(P^2D->3D(F^3D))
03895 m_wptr ctf^2
03896 m_wptr2 |P^2D->3D(F^3D)|^2
03897 m_wptr3 Kn
03898 nominator = sum_rot [ wght*signal ]
03899 denominator = sum_rot[ wght*variance ]
03900 ***/
03901 int kz, ky;
03902 int box = 7;
03903 int kc = (box-1)/2;
03904 float alpha = 0.0;
03905 float argx, argy, argz;
03906 vector< float > pow_a( 3*kc+1, 1.0 );
03907 float w = params["w"];
03908 float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc);
03909 float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc);
03910 #ifdef _WIN32
03911 float dz2 = 1.0f/_cpp_max(float(m_vnzc),1.0f)/_cpp_max(float(m_vnzc),1.0f);
03912 int inc = Util::round(float(_cpp_max(_cpp_max(m_vnxc,m_vnyc),m_vnzc))/w);
03913 #else
03914 float dz2 = 1.0f/std::max(float(m_vnzc),1.0f)/std::max(float(m_vnzc),1.0f);
03915 int inc = Util::round(float(std::max(std::max(m_vnxc,m_vnyc),m_vnzc))/w);
03916 #endif //_WIN32
03917
03918 EMData* SSNR = params["SSNR"];
03919 SSNR->set_size(inc+1,4,1);
03920 //#EMData* vol_ssnr = new EMData();
03921 //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp);
03922 //#vol_ssnr->to_zero();
03923 //# new linea follow
03924 EMData* vol_ssnr = params["vol_ssnr"];
03925 vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp);
03926 vol_ssnr->to_zero();
03927 if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0);
03928 else vol_ssnr->set_fftodd(1);
03929 vol_ssnr->set_nxc(m_vnxc);
03930 vol_ssnr->set_complex(true);
03931 vol_ssnr->set_ri(true);
03932 vol_ssnr->set_fftpad(false);
03933 //#
03934 float *nom = new float[inc+1];
03935 float *denom = new float[inc+1];
03936 int *ka = new int[inc+1];
03937 int *nn = new int[inc+1];
03938 float wght = 1.f;
03939 for (int i = 0; i <= inc; i++) {
03940 nom[i] = 0.0f;
03941 denom[i] = 0.0f;
03942 nn[i] = 0;
03943 ka[i] = 0;
03944 }
03945 m_volume->symplane2(m_wptr, m_wptr2, m_wptr3);
03946 if ( m_weighting == ESTIMATE ) {
03947 int vol = box*box*box;
03948 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
03949 pow_a[3*kc] = 0.0;
03950 float max = max3d( kc, pow_a );
03951 alpha = ( 1.0f - 1.0f/(float)vol ) / max;
03952 }
03953 for (int iz = 1; iz <= m_vnzp; iz++) {
03954 if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1;
03955 argz = float(kz*kz)*dz2;
03956 for (int iy = 1; iy <= m_vnyp; iy++) {
03957 if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1;
03958 argy = argz + float(ky*ky)*dy2;
03959 for (int ix = 0; ix <= m_vnxc; ix++) {
03960 float Kn = (*m_wptr3)(ix,iy,iz);
03961 argx = std::sqrt(argy + float(ix*ix)*dx2);
03962 int r = Util::round(float(inc)*argx);
03963 if ( r >= 0 && Kn > 4.5f ) {
03964 if ( m_weighting == ESTIMATE ) {
03965 int cx = ix;
03966 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
03967 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
03968 float sum = 0.0;
03969 for( int ii = -kc; ii <= kc; ++ii ) {
03970 int nbrcx = cx + ii;
03971 if( nbrcx >= m_vnxc ) continue;
03972 for ( int jj= -kc; jj <= kc; ++jj ) {
03973 int nbrcy = cy + jj;
03974 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
03975 for( int kk = -kc; kk <= kc; ++kk ) {
03976 int nbrcz = cz + jj;
03977 if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
03978 if( nbrcx < 0 ) {
03979 nbrcx = -nbrcx;
03980 nbrcy = -nbrcy;
03981 nbrcz = -nbrcz;
03982 }
03983 int nbrix = nbrcx;
03984 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
03985 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
03986 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
03987 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
03988 sum = sum + pow_a[c];
03989 }
03990 }
03991 }
03992 }
03993 // int r = std::abs(cx) + std::abs(cy) + std::abs(cz);
03994 wght = 1.0f / ( 1.0f - alpha * sum );
03995 } // end of ( m_weighting == ESTIMATE )
03996 float nominator = std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz);
03997 float denominator = ((*m_wptr2)(ix,iy,iz)-std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz))/(Kn-1.0f);
03998 // Skip Friedel related values
03999 if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) {
04000 if ( r <= inc ) {
04001 nom[r] += nominator*wght;
04002 denom[r] += denominator/(*m_wptr)(ix,iy,iz)*wght;
04003 nn[r] += 2;
04004 ka[r] += int(Kn);
04005 }
04006 /*
04007 #ifdef _WIN32
04008 float tmp = _cpp_max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f);
04009 #else
04010 float tmp = std::max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f);
04011 #endif //_WIN32
04012 // Create SSNR as a 3D array (-n/2:n/2+n%2-1)
04013 int iix = m_vnxc + ix; int iiy = m_vnyc + ky; int 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 // Friedel part
04017 iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz;
04018 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp )
04019 (*vol_ssnr)(iix, iiy, iiz) = tmp;
04020 */
04021 }
04022 (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght;
04023 } // end of Kn>4.5 or whatever
04024 }
04025 }
04026 }
04027 for (int i = 0; i <= inc; i++) {
04028 (*SSNR)(i,0,0) = nom[i];
04029 (*SSNR)(i,1,0) = denom[i];
04030 (*SSNR)(i,2,0) = static_cast<float>(nn[i]);
04031 (*SSNR)(i,3,0) = static_cast<float>(ka[i]);
04032 }
04033 vol_ssnr->update();
04034
04035 delete[] nom;
04036 delete[] denom;
04037 delete[] nn;
04038 delete[] ka;
04039
04040 return 0;
04041 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 1213 of file reconstructor.h. 01214 {
01215 return "Reconstruction by nearest neighbor with 3D SSNR with CTF";
01216 }
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Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase. Definition at line 1208 of file reconstructor.h. 01209 {
01210 return NAME;
01211 }
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Implements EMAN::FactoryBase. Definition at line 1223 of file reconstructor.h. References EMAN::TypeDict::put(). 01224 {
01225 TypeDict d;
01226 d.put("size", EMObject::INT);
01227 d.put("npad", EMObject::INT);
01228 d.put("symmetry", EMObject::STRING);
01229 d.put("fftvol", EMObject::EMDATA);
01230 d.put("fftwvol", EMObject::EMDATA);
01231 d.put("weight", EMObject::EMDATA);
01232 d.put("weight2", EMObject::EMDATA);
01233 d.put("weight3", EMObject::EMDATA);
01234 d.put("SSNR", EMObject::EMDATA);
01235 d.put("vol_ssnr", EMObject::EMDATA);
01236 d.put("w", EMObject::FLOAT);
01237 d.put("sign", EMObject::INT);
01238 d.put("snr", EMObject::FLOAT);
01239 return d;
01240 }
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Definition at line 3871 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. 03872 {
03873 Assert( padfft != NULL );
03874
03875 // insert slice for all symmetry related positions
03876 for (int isym=0; isym < m_nsym; isym++) {
03877 Transform tsym = t.get_sym(m_symmetry, isym);
03878 m_volume->nn_SSNR_ctf(m_wptr, m_wptr2, m_wptr3, padfft, tsym, mult);
03879 }
03880
03881 return 0;
03882 }
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Insert a slice into a 3D volume, in a given orientation.
Reimplemented from EMAN::Reconstructor. |
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Definition at line 1218 of file reconstructor.h. 01219 {
01220 return new nnSSNR_ctfReconstructor();
01221 }
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Definition at line 3770 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. 03771 {
03772
03773 m_weighting = ESTIMATE;
03774 m_wghta = 0.2f;
03775 m_wghtb = 0.004f;
03776 wiener = 1;
03777
03778 m_symmetry = symmetry;
03779 m_npad = npad;
03780 m_nsym = Transform::get_nsym(m_symmetry);
03781
03782 m_sign = sign;
03783 m_snr = snr;
03784
03785 m_vnx = size;
03786 m_vny = size;
03787 m_vnz = size;
03788
03789 m_vnxp = size*npad;
03790 m_vnyp = size*npad;
03791 m_vnzp = size*npad;
03792
03793 m_vnxc = m_vnxp/2;
03794 m_vnyc = m_vnyp/2;
03795 m_vnzc = m_vnzp/2;
03796
03797 buildFFTVolume();
03798 buildNormVolume();
03799 buildNorm2Volume();
03800 buildNorm3Volume();
03801 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 3758 of file reconstructor.cpp. References EMAN::Dict::has_key(), and sign. Referenced by nnSSNR_ctfReconstructor(). 03759 {
03760 int size = params["size"];
03761 int npad = params["npad"];
03762 int sign = params["sign"];
03763 float snr = params["snr"];
03764 string symmetry;
03765 if( params.has_key("symmetry") ) symmetry = params["symmetry"].to_str();
03766 else symmetry = "c1";
03767
03768 setup( symmetry, size, npad, snr, sign );
03769 }
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Definition at line 1255 of file reconstructor.h. Referenced by buildFFTVolume(), and setup(). |
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Definition at line 1256 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1265 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1266 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1252 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 1254 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1258 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 1257 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), and setup(). |
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Definition at line 1254 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1258 of file reconstructor.h. |
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Definition at line 1257 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 1254 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1258 of file reconstructor.h. |
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Definition at line 1257 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 1248 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), and nnSSNR_ctfReconstructor(). |
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Definition at line 1253 of file reconstructor.h. |
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Definition at line 1263 of file reconstructor.h. |
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Definition at line 1264 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1249 of file reconstructor.h. Referenced by buildNormVolume(), finish(), insert_padfft_slice(), and nnSSNR_ctfReconstructor(). |
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Definition at line 1250 of file reconstructor.h. Referenced by buildNorm2Volume(), finish(), insert_padfft_slice(), and nnSSNR_ctfReconstructor(). |
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Definition at line 1251 of file reconstructor.h. Referenced by buildNorm3Volume(), finish(), insert_padfft_slice(), and nnSSNR_ctfReconstructor(). |
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Definition at line 86 of file reconstructor.cpp. |
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Definition at line 1267 of file reconstructor.h. Referenced by setup(). |
1.3.9.1