#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 |
EMData * | m_result |
bool | m_delete_volume |
bool | m_delete_weight |
bool | m_delete_weight2 |
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 2857 of file reconstructor.cpp. References m_result, m_volume, m_wptr, and m_wptr2. 02858 { 02859 m_volume = NULL; 02860 m_wptr = NULL; 02861 m_wptr2 = NULL; 02862 m_result = NULL; 02863 }
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Definition at line 2865 of file reconstructor.cpp. References m_result, m_volume, m_wptr, m_wptr2, and setup(). 02866 { 02867 m_volume = NULL; 02868 m_wptr = NULL; 02869 m_wptr2 = NULL; 02870 m_result = NULL; 02871 02872 setup( symmetry, size, npad ); 02873 }
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Definition at line 2875 of file reconstructor.cpp. References checked_delete(), m_result, m_volume, m_wptr, and m_wptr2. 02876 { 02877 if( m_delete_volume ) checked_delete(m_volume); 02878 02879 if( m_delete_weight ) checked_delete( m_wptr ); 02880 02881 if( m_delete_weight2 ) checked_delete( m_wptr2 ); 02882 02883 checked_delete( m_result ); 02884 }
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Definition at line 2964 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(). 02964 { 02965 02966 if( params.has_key("weight2") ) { 02967 m_wptr2 = params["weight2"]; 02968 m_delete_weight2 = false; 02969 } else { 02970 m_wptr2 = new EMData(); 02971 m_delete_weight2 = true; 02972 } 02973 m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02974 m_wptr2->to_zero(); 02975 m_wptr2->set_array_offsets(0,1,1); 02976 }
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Definition at line 2949 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(). 02949 { 02950 if( params.has_key("weight") ) { 02951 m_wptr = params["weight"]; 02952 m_delete_weight = false; 02953 } else { 02954 m_wptr = new EMData(); 02955 m_delete_weight = true; 02956 } 02957 02958 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02959 m_wptr->to_zero(); 02960 02961 m_wptr->set_array_offsets(0,1,1); 02962 }
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(*SSNR)(i,0,0) = nom[i]/denom[i] - 1;/// Reimplemented from EMAN::Reconstructor. Definition at line 3021 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(). 03022 { 03023 /* 03024 I changed the code on 05/15 so it only returns variance. 03025 Lines commented out are marked by //# 03026 The version prior to the currect changes is r1.190 03027 PAP 03028 */ 03029 int kz, ky; 03030 //#int iix, iiy, iiz; 03031 int box = 7; 03032 int kc = (box-1)/2; 03033 float alpha = 0.0; 03034 float argx, argy, argz; 03035 vector< float > pow_a( 3*kc+1, 1.0 ); 03036 float w = params["w"]; 03037 EMData* SSNR = params["SSNR"]; 03038 //#EMData* vol_ssnr = new EMData(); 03039 //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp); 03040 //#vol_ssnr->to_zero(); 03041 //# new line follow 03042 EMData* vol_ssnr = new EMData(); 03043 vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp); 03044 vol_ssnr->to_zero(); 03045 if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0); 03046 else vol_ssnr->set_fftodd(1); 03047 vol_ssnr->set_nxc(m_vnxc); 03048 vol_ssnr->set_complex(true); 03049 vol_ssnr->set_ri(true); 03050 vol_ssnr->set_fftpad(false); 03051 //# 03052 03053 float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc); 03054 float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc); 03055 #ifdef _WIN32 03056 float dz2 = 1.0f/_cpp_max(float(m_vnzc),1.0f)/_cpp_max(float(m_vnzc),1.0f); 03057 int inc = Util::round(float(_cpp_max(_cpp_max(m_vnxc,m_vnyc),m_vnzc))/w); 03058 #else 03059 float dz2 = 1.0f/std::max(float(m_vnzc),1.0f)/std::max(float(m_vnzc),1.0f); 03060 int inc = Util::round(float(std::max(std::max(m_vnxc,m_vnyc),m_vnzc))/w); 03061 #endif //_WIN32 03062 SSNR->set_size(inc+1,4,1); 03063 03064 float *nom = new float[inc+1]; 03065 float *denom = new float[inc+1]; 03066 int *nn = new int[inc+1]; 03067 int *ka = new int[inc+1]; 03068 float wght = 1.0f; 03069 for (int i = 0; i <= inc; i++) { 03070 nom[i] = 0.0f; 03071 denom[i] = 0.0f; 03072 nn[i] = 0; 03073 ka[i] = 0; 03074 } 03075 03076 m_volume->symplane1(m_wptr, m_wptr2); 03077 03078 if ( m_weighting == ESTIMATE ) { 03079 int vol = box*box*box; 03080 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 03081 pow_a[3*kc] = 0.0; 03082 float max = max3d( kc, pow_a ); 03083 alpha = ( 1.0f - 1.0f/(float)vol ) / max; 03084 } 03085 03086 for (int iz = 1; iz <= m_vnzp; iz++) { 03087 if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1; 03088 argz = float(kz*kz)*dz2; 03089 for (int iy = 1; iy <= m_vnyp; iy++) { 03090 if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1; 03091 argy = argz + float(ky*ky)*dy2; 03092 for (int ix = 0; ix <= m_vnxc; ix++) { 03093 float Kn = (*m_wptr)(ix,iy,iz); 03094 argx = std::sqrt(argy + float(ix*ix)*dx2); 03095 int r = Util::round(float(inc)*argx); 03096 if ( r >= 0 && Kn > 4.5f ) { 03097 if ( m_weighting == ESTIMATE ) { 03098 int cx = ix; 03099 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 03100 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 03101 03102 float sum = 0.0; 03103 for( int ii = -kc; ii <= kc; ++ii ) { 03104 int nbrcx = cx + ii; 03105 if( nbrcx >= m_vnxc ) continue; 03106 for ( int jj= -kc; jj <= kc; ++jj ) { 03107 int nbrcy = cy + jj; 03108 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 03109 for( int kk = -kc; kk <= kc; ++kk ) { 03110 int nbrcz = cz + jj; 03111 if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 03112 if( nbrcx < 0 ) { 03113 nbrcx = -nbrcx; 03114 nbrcy = -nbrcy; 03115 nbrcz = -nbrcz; 03116 } 03117 int nbrix = nbrcx; 03118 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 03119 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 03120 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) { 03121 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 03122 sum = sum + pow_a[c]; 03123 } 03124 } 03125 } 03126 } 03127 wght = 1.0f / ( 1.0f - alpha * sum ); 03128 } // end of ( m_weighting == ESTIMATE ) 03129 float nominator = std::norm(m_volume->cmplx(ix,iy,iz))/Kn; 03130 float denominator = ((*m_wptr2)(ix,iy,iz)-nominator)/(Kn-1.0f); 03131 // Skip Friedel related values 03132 if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) { 03133 if ( r <= inc ) { 03134 nom[r] += nominator*wght; 03135 denom[r] += denominator/Kn*wght; 03136 nn[r] += 2; 03137 ka[r] += int(Kn); 03138 } 03139 /* 03140 #ifdef _WIN32 03141 //#float tmp = _cpp_max(nominator/denominator/Kn-1.0f,0.0f); 03142 #else 03143 //#float tmp = std::max(nominator/denominator/Kn-1.0f,0.0f); 03144 #endif //_WIN32 03145 // Create SSNR as a 3D array (-n/2:n/2+n%2-1) 03146 iix = m_vnxc + ix; iiy = m_vnyc + ky; iiz = m_vnzc + kz; 03147 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 03148 (*vol_ssnr)(iix, iiy, iiz) = tmp; 03149 // Friedel part 03150 iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz; 03151 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 03152 (*vol_ssnr)(iix, iiy, iiz) = tmp; 03153 */ 03154 03155 } 03156 (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght; 03157 //(*vol_ssnr)(2*ix, iy-1, iz-1) = real(m_volume->cmplx(ix,iy,iz))*wght/Kn; 03158 //(*vol_ssnr)(2*ix+1, iy-1, iz-1) = imag(m_volume->cmplx(ix,iy,iz))*wght/Kn; 03159 } // end of Kn>4.5 03160 } 03161 } 03162 } 03163 03164 for (int i = 0; i <= inc; i++) { 03165 (*SSNR)(i,0,0) = nom[i]; 03166 (*SSNR)(i,1,0) = denom[i]; // variance 03167 (*SSNR)(i,2,0) = static_cast<float>(nn[i]); 03168 (*SSNR)(i,3,0) = static_cast<float>(ka[i]); 03169 } 03170 vol_ssnr->update(); 03171 return vol_ssnr; 03172 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 949 of file reconstructor.h. 00950 { 00951 return "Reconstruction by nearest neighbor with 3D SSNR"; 00952 }
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Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase. Definition at line 944 of file reconstructor.h. 00945 {
00946 return NAME;
00947 }
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Implements EMAN::FactoryBase. Definition at line 959 of file reconstructor.h. References EMAN::TypeDict::put(). 00960 { 00961 TypeDict d; 00962 d.put("size", EMObject::INT); 00963 d.put("npad", EMObject::INT); 00964 d.put("symmetry", EMObject::STRING); 00965 d.put("fftvol", EMObject::EMDATA); 00966 d.put("weight", EMObject::EMDATA); 00967 d.put("weight2", EMObject::EMDATA); 00968 d.put("SSNR", EMObject::EMDATA); 00969 d.put("w", EMObject::FLOAT); 00970 return d; 00971 }
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Definition at line 3008 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. 03009 { 03010 Assert( padfft != NULL ); 03011 // insert slice for all symmetry related positions 03012 for (int isym=0; isym < m_nsym; isym++) { 03013 Transform tsym = t.get_sym(m_symmetry, isym); 03014 m_volume->nn_SSNR( m_wptr, m_wptr2, padfft, tsym, mult); 03015 } 03016 return 0; 03017 }
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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 954 of file reconstructor.h. 00955 { 00956 return new nnSSNR_Reconstructor(); 00957 }
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Definition at line 2898 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. 02899 { 02900 02901 m_weighting = ESTIMATE; 02902 m_wghta = 0.2f; 02903 m_wghtb = 0.004f; 02904 02905 m_symmetry = symmetry; 02906 m_npad = npad; 02907 m_nsym = Transform::get_nsym(m_symmetry); 02908 02909 m_vnx = size; 02910 m_vny = size; 02911 m_vnz = size; 02912 02913 m_vnxp = size*npad; 02914 m_vnyp = size*npad; 02915 m_vnzp = size*npad; 02916 02917 m_vnxc = m_vnxp/2; 02918 m_vnyc = m_vnyp/2; 02919 m_vnzc = m_vnzp/2; 02920 02921 buildFFTVolume(); 02922 buildNormVolume(); 02923 buildNorm2Volume(); 02924 02925 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 2886 of file reconstructor.cpp. References EMAN::Dict::has_key(). Referenced by nnSSNR_Reconstructor(). 02887 { 02888 int size = params["size"]; 02889 int npad = params["npad"]; 02890 02891 string symmetry; 02892 if( params.has_key("symmetry") ) symmetry = params["symmetry"].to_str(); 02893 else symmetry = "c1"; 02894 02895 setup( symmetry, size, npad ); 02896 }
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Definition at line 984 of file reconstructor.h. Referenced by buildFFTVolume(). |
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Definition at line 985 of file reconstructor.h. Referenced by buildNormVolume(). |
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Definition at line 986 of file reconstructor.h. Referenced by buildNorm2Volume(). |
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Definition at line 990 of file reconstructor.h. Referenced by buildFFTVolume(), and setup(). |
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Definition at line 991 of file reconstructor.h. Referenced by setup(). |
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Definition at line 983 of file reconstructor.h. Referenced by nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 987 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 989 of file reconstructor.h. Referenced by setup(). |
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Definition at line 993 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 992 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), and setup(). |
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Definition at line 989 of file reconstructor.h. Referenced by setup(). |
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Definition at line 993 of file reconstructor.h. |
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Definition at line 992 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 989 of file reconstructor.h. Referenced by setup(). |
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Definition at line 993 of file reconstructor.h. |
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Definition at line 992 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 980 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 988 of file reconstructor.h. |
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Definition at line 997 of file reconstructor.h. |
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Definition at line 998 of file reconstructor.h. Referenced by setup(). |
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Definition at line 981 of file reconstructor.h. Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 982 of file reconstructor.h. Referenced by buildNorm2Volume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 83 of file reconstructor.cpp. |