#include <reconstructor.h>
Inheritance diagram for EMAN::nnSSNR_Reconstructor:
Public Member Functions | |
nnSSNR_Reconstructor () | |
nnSSNR_Reconstructor (const string &symmetry, int size, int npad) | |
~nnSSNR_Reconstructor () | |
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) |
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 = "nnSSNR" |
Private Member Functions | |
void | buildFFTVolume () |
void | buildNormVolume () |
void | buildNorm2Volume () |
Private Attributes | |
EMData * | m_volume |
EMData * | m_wptr |
EMData * | m_wptr2 |
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 |
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Definition at line 2826 of file reconstructor.cpp. References m_volume, m_wptr, and m_wptr2.
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Definition at line 2833 of file reconstructor.cpp. References m_volume, m_wptr, m_wptr2, and setup(). 02834 { 02835 m_volume = NULL; 02836 m_wptr = NULL; 02837 m_wptr2 = NULL; 02838 02839 setup( symmetry, size, npad ); 02840 }
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Definition at line 2842 of file reconstructor.cpp. 02843 { 02844 //if( m_delete_volume ) checked_delete(m_volume); 02845 02846 //if( m_delete_weight ) checked_delete( m_wptr ); 02847 02848 //if( m_delete_weight2 ) checked_delete( m_wptr2 ); 02849 02850 //checked_delete( m_result ); 02851 }
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Definition at line 2894 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(). 02894 { 02895 02896 m_volume = params["fftvol"]; 02897 m_volume->set_size(m_vnxp+ 2 - m_vnxp%2,m_vnyp,m_vnzp); 02898 m_volume->to_zero(); 02899 if ( m_vnxp % 2 == 0 ) m_volume->set_fftodd(0); 02900 else m_volume->set_fftodd(1); 02901 02902 m_volume->set_nxc(m_vnxc); 02903 m_volume->set_complex(true); 02904 m_volume->set_ri(true); 02905 m_volume->set_fftpad(true); 02906 m_volume->set_attr("npad", m_npad); 02907 m_volume->set_array_offsets(0,1,1); 02908 }
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Definition at line 2918 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(). 02918 { 02919 02920 m_wptr2 = params["weight2"]; 02921 m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02922 m_wptr2->to_zero(); 02923 m_wptr2->set_array_offsets(0,1,1); 02924 }
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Definition at line 2910 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(). 02910 { 02911 02912 m_wptr = params["weight"]; 02913 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02914 m_wptr->to_zero(); 02915 m_wptr->set_array_offsets(0,1,1); 02916 }
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(*SSNR)(i,0,0) = nom[i]/denom[i] - 1;/// Reimplemented from EMAN::Reconstructor. Definition at line 2969 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, 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::symplane1(), EMAN::EMData::to_zero(), and EMAN::EMData::update(). 02970 { 02971 /* 02972 I changed the code on 05/15 so it only returns variance. 02973 Lines commented out are marked by //# 02974 The version prior to the currect changes is r1.190 02975 PAP 02976 */ 02977 int kz, ky; 02978 //#int iix, iiy, iiz; 02979 int box = 7; 02980 int kc = (box-1)/2; 02981 float alpha = 0.0; 02982 float argx, argy, argz; 02983 vector< float > pow_a( 3*kc+1, 1.0 ); 02984 float w = params["w"]; 02985 EMData* SSNR = params["SSNR"]; 02986 //#EMData* vol_ssnr = new EMData(); 02987 //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp); 02988 //#vol_ssnr->to_zero(); 02989 //# new line follow 02990 EMData* vol_ssnr = params["vol_ssnr"]; 02991 vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp); 02992 vol_ssnr->to_zero(); 02993 if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0); 02994 else vol_ssnr->set_fftodd(1); 02995 vol_ssnr->set_nxc(m_vnxc); 02996 vol_ssnr->set_complex(true); 02997 vol_ssnr->set_ri(true); 02998 vol_ssnr->set_fftpad(false); 02999 //# 03000 03001 float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc); 03002 float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc); 03003 #ifdef _WIN32 03004 float dz2 = 1.0f/_cpp_max(float(m_vnzc),1.0f)/_cpp_max(float(m_vnzc),1.0f); 03005 int inc = Util::round(float(_cpp_max(_cpp_max(m_vnxc,m_vnyc),m_vnzc))/w); 03006 #else 03007 float dz2 = 1.0f/std::max(float(m_vnzc),1.0f)/std::max(float(m_vnzc),1.0f); 03008 int inc = Util::round(float(std::max(std::max(m_vnxc,m_vnyc),m_vnzc))/w); 03009 #endif //_WIN32 03010 SSNR->set_size(inc+1,4,1); 03011 03012 float *nom = new float[inc+1]; 03013 float *denom = new float[inc+1]; 03014 int *nn = new int[inc+1]; 03015 int *ka = new int[inc+1]; 03016 float wght = 1.0f; 03017 for (int i = 0; i <= inc; i++) { 03018 nom[i] = 0.0f; 03019 denom[i] = 0.0f; 03020 nn[i] = 0; 03021 ka[i] = 0; 03022 } 03023 03024 m_volume->symplane1(m_wptr, m_wptr2); 03025 03026 if ( m_weighting == ESTIMATE ) { 03027 int vol = box*box*box; 03028 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 03029 pow_a[3*kc] = 0.0; 03030 float max = max3d( kc, pow_a ); 03031 alpha = ( 1.0f - 1.0f/(float)vol ) / max; 03032 } 03033 03034 for (int iz = 1; iz <= m_vnzp; iz++) { 03035 if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1; 03036 argz = float(kz*kz)*dz2; 03037 for (int iy = 1; iy <= m_vnyp; iy++) { 03038 if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1; 03039 argy = argz + float(ky*ky)*dy2; 03040 for (int ix = 0; ix <= m_vnxc; ix++) { 03041 float Kn = (*m_wptr)(ix,iy,iz); 03042 argx = std::sqrt(argy + float(ix*ix)*dx2); 03043 int r = Util::round(float(inc)*argx); 03044 if ( r >= 0 && Kn > 4.5f ) { 03045 if ( m_weighting == ESTIMATE ) { 03046 int cx = ix; 03047 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 03048 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 03049 03050 float sum = 0.0; 03051 for( int ii = -kc; ii <= kc; ++ii ) { 03052 int nbrcx = cx + ii; 03053 if( nbrcx >= m_vnxc ) continue; 03054 for ( int jj= -kc; jj <= kc; ++jj ) { 03055 int nbrcy = cy + jj; 03056 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 03057 for( int kk = -kc; kk <= kc; ++kk ) { 03058 int nbrcz = cz + jj; 03059 if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 03060 if( nbrcx < 0 ) { 03061 nbrcx = -nbrcx; 03062 nbrcy = -nbrcy; 03063 nbrcz = -nbrcz; 03064 } 03065 int nbrix = nbrcx; 03066 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 03067 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 03068 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) { 03069 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 03070 sum = sum + pow_a[c]; 03071 } 03072 } 03073 } 03074 } 03075 wght = 1.0f / ( 1.0f - alpha * sum ); 03076 } // end of ( m_weighting == ESTIMATE ) 03077 float nominator = std::norm(m_volume->cmplx(ix,iy,iz))/Kn; 03078 float denominator = ((*m_wptr2)(ix,iy,iz)-nominator)/(Kn-1.0f); 03079 // Skip Friedel related values 03080 if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) { 03081 if ( r <= inc ) { 03082 nom[r] += nominator*wght; 03083 denom[r] += denominator/Kn*wght; 03084 nn[r] += 2; 03085 ka[r] += int(Kn); 03086 } 03087 /* 03088 #ifdef _WIN32 03089 //#float tmp = _cpp_max(nominator/denominator/Kn-1.0f,0.0f); 03090 #else 03091 //#float tmp = std::max(nominator/denominator/Kn-1.0f,0.0f); 03092 #endif //_WIN32 03093 // Create SSNR as a 3D array (-n/2:n/2+n%2-1) 03094 iix = m_vnxc + ix; iiy = m_vnyc + ky; iiz = m_vnzc + kz; 03095 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 03096 (*vol_ssnr)(iix, iiy, iiz) = tmp; 03097 // Friedel part 03098 iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz; 03099 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 03100 (*vol_ssnr)(iix, iiy, iiz) = tmp; 03101 */ 03102 03103 } 03104 (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght; 03105 //(*vol_ssnr)(2*ix, iy-1, iz-1) = real(m_volume->cmplx(ix,iy,iz))*wght/Kn; 03106 //(*vol_ssnr)(2*ix+1, iy-1, iz-1) = imag(m_volume->cmplx(ix,iy,iz))*wght/Kn; 03107 } // end of Kn>4.5 03108 } 03109 } 03110 } 03111 03112 for (int i = 0; i <= inc; i++) { 03113 (*SSNR)(i,0,0) = nom[i]; 03114 (*SSNR)(i,1,0) = denom[i]; // variance 03115 (*SSNR)(i,2,0) = static_cast<float>(nn[i]); 03116 (*SSNR)(i,3,0) = static_cast<float>(ka[i]); 03117 } 03118 vol_ssnr->update(); 03119 03120 delete[] nom; 03121 delete[] denom; 03122 delete[] nn; 03123 delete[] ka; 03124 03125 return 0; 03126 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 944 of file reconstructor.h. 00945 { 00946 return "Reconstruction by nearest neighbor with 3D SSNR"; 00947 }
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Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase. Definition at line 939 of file reconstructor.h. 00940 {
00941 return NAME;
00942 }
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Implements EMAN::FactoryBase. Definition at line 954 of file reconstructor.h. References EMAN::TypeDict::put(). 00955 { 00956 TypeDict d; 00957 d.put("size", EMObject::INT); 00958 d.put("npad", EMObject::INT); 00959 d.put("symmetry", EMObject::STRING); 00960 d.put("fftvol", EMObject::EMDATA); 00961 d.put("weight", EMObject::EMDATA); 00962 d.put("weight2", EMObject::EMDATA); 00963 d.put("SSNR", EMObject::EMDATA); 00964 d.put("vol_ssnr", EMObject::EMDATA); 00965 d.put("w", EMObject::FLOAT); 00966 return d; 00967 }
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Definition at line 2956 of file reconstructor.cpp. References Assert, EMAN::Transform::get_sym(), m_symmetry, m_volume, m_wptr, m_wptr2, mult(), EMAN::EMData::nn_SSNR(), and t. 02957 { 02958 Assert( padfft != NULL ); 02959 // insert slice for all symmetry related positions 02960 for (int isym=0; isym < m_nsym; isym++) { 02961 Transform tsym = t.get_sym(m_symmetry, isym); 02962 m_volume->nn_SSNR( m_wptr, m_wptr2, padfft, tsym, mult); 02963 } 02964 return 0; 02965 }
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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. |
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Definition at line 949 of file reconstructor.h. 00950 { 00951 return new nnSSNR_Reconstructor(); 00952 }
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Definition at line 2865 of file reconstructor.cpp. References buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), EMAN::Transform::get_nsym(), 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, m_wghta, and m_wghtb. 02866 { 02867 02868 m_weighting = ESTIMATE; 02869 m_wghta = 0.2f; 02870 m_wghtb = 0.004f; 02871 02872 m_symmetry = symmetry; 02873 m_npad = npad; 02874 m_nsym = Transform::get_nsym(m_symmetry); 02875 02876 m_vnx = size; 02877 m_vny = size; 02878 m_vnz = size; 02879 02880 m_vnxp = size*npad; 02881 m_vnyp = size*npad; 02882 m_vnzp = size*npad; 02883 02884 m_vnxc = m_vnxp/2; 02885 m_vnyc = m_vnyp/2; 02886 m_vnzc = m_vnzp/2; 02887 02888 buildFFTVolume(); 02889 buildNormVolume(); 02890 buildNorm2Volume(); 02891 02892 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 2853 of file reconstructor.cpp. References EMAN::Dict::has_key(). Referenced by nnSSNR_Reconstructor(). 02854 { 02855 int size = params["size"]; 02856 int npad = params["npad"]; 02857 02858 string symmetry; 02859 if( params.has_key("symmetry") ) symmetry = params["symmetry"].to_str(); 02860 else symmetry = "c1"; 02861 02862 setup( symmetry, size, npad ); 02863 }
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Definition at line 982 of file reconstructor.h. Referenced by buildFFTVolume(), and setup(). |
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Definition at line 983 of file reconstructor.h. Referenced by setup(). |
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Definition at line 979 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 981 of file reconstructor.h. Referenced by setup(). |
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Definition at line 985 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 984 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), and setup(). |
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Definition at line 981 of file reconstructor.h. Referenced by setup(). |
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Definition at line 985 of file reconstructor.h. |
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Definition at line 984 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 981 of file reconstructor.h. Referenced by setup(). |
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Definition at line 985 of file reconstructor.h. |
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Definition at line 984 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 976 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), and nnSSNR_Reconstructor(). |
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Definition at line 980 of file reconstructor.h. |
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Definition at line 989 of file reconstructor.h. |
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Definition at line 990 of file reconstructor.h. Referenced by setup(). |
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Definition at line 977 of file reconstructor.h. Referenced by buildNormVolume(), finish(), insert_padfft_slice(), and nnSSNR_Reconstructor(). |
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Definition at line 978 of file reconstructor.h. Referenced by buildNorm2Volume(), finish(), insert_padfft_slice(), and nnSSNR_Reconstructor(). |
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Definition at line 83 of file reconstructor.cpp. |