#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 2755 of file reconstructor.cpp. References m_result, m_volume, m_wptr, and m_wptr2. 02756 { 02757 m_volume = NULL; 02758 m_wptr = NULL; 02759 m_wptr2 = NULL; 02760 m_result = NULL; 02761 }
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Definition at line 2763 of file reconstructor.cpp. References m_result, m_volume, m_wptr, m_wptr2, and setup(). 02764 { 02765 m_volume = NULL; 02766 m_wptr = NULL; 02767 m_wptr2 = NULL; 02768 m_result = NULL; 02769 02770 setup( symmetry, size, npad ); 02771 }
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Definition at line 2773 of file reconstructor.cpp. References checked_delete(), m_result, m_volume, m_wptr, and m_wptr2. 02774 { 02775 if( m_delete_volume ) checked_delete(m_volume); 02776 02777 if( m_delete_weight ) checked_delete( m_wptr ); 02778 02779 if( m_delete_weight2 ) checked_delete( m_wptr2 ); 02780 02781 checked_delete( m_result ); 02782 }
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Definition at line 2862 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(). 02862 { 02863 02864 if( params.has_key("weight2") ) { 02865 m_wptr2 = params["weight2"]; 02866 m_delete_weight2 = false; 02867 } else { 02868 m_wptr2 = new EMData(); 02869 m_delete_weight2 = true; 02870 } 02871 m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02872 m_wptr2->to_zero(); 02873 m_wptr2->set_array_offsets(0,1,1); 02874 }
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Definition at line 2847 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(). 02847 { 02848 if( params.has_key("weight") ) { 02849 m_wptr = params["weight"]; 02850 m_delete_weight = false; 02851 } else { 02852 m_wptr = new EMData(); 02853 m_delete_weight = true; 02854 } 02855 02856 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02857 m_wptr->to_zero(); 02858 02859 m_wptr->set_array_offsets(0,1,1); 02860 }
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(*SSNR)(i,0,0) = nom[i]/denom[i] - 1;/// Reimplemented from EMAN::Reconstructor. Definition at line 2919 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(). 02920 { 02921 /* 02922 I changed the code on 05/15 so it only returns variance. 02923 Lines commented out are marked by //# 02924 The version prior to the currect changes is r1.190 02925 PAP 02926 */ 02927 int kz, ky; 02928 //#int iix, iiy, iiz; 02929 int box = 7; 02930 int kc = (box-1)/2; 02931 float alpha = 0.0; 02932 float argx, argy, argz; 02933 vector< float > pow_a( 3*kc+1, 1.0 ); 02934 float w = params["w"]; 02935 EMData* SSNR = params["SSNR"]; 02936 //#EMData* vol_ssnr = new EMData(); 02937 //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp); 02938 //#vol_ssnr->to_zero(); 02939 //# new line follow 02940 EMData* vol_ssnr = new EMData(); 02941 vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp); 02942 vol_ssnr->to_zero(); 02943 if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0); 02944 else vol_ssnr->set_fftodd(1); 02945 vol_ssnr->set_nxc(m_vnxc); 02946 vol_ssnr->set_complex(true); 02947 vol_ssnr->set_ri(true); 02948 vol_ssnr->set_fftpad(false); 02949 //# 02950 02951 float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc); 02952 float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc); 02953 #ifdef _WIN32 02954 float dz2 = 1.0f/_cpp_max(float(m_vnzc),1.0f)/_cpp_max(float(m_vnzc),1.0f); 02955 int inc = Util::round(float(_cpp_max(_cpp_max(m_vnxc,m_vnyc),m_vnzc))/w); 02956 #else 02957 float dz2 = 1.0f/std::max(float(m_vnzc),1.0f)/std::max(float(m_vnzc),1.0f); 02958 int inc = Util::round(float(std::max(std::max(m_vnxc,m_vnyc),m_vnzc))/w); 02959 #endif //_WIN32 02960 SSNR->set_size(inc+1,4,1); 02961 02962 float *nom = new float[inc+1]; 02963 float *denom = new float[inc+1]; 02964 int *nn = new int[inc+1]; 02965 int *ka = new int[inc+1]; 02966 float wght = 1.0f; 02967 for (int i = 0; i <= inc; i++) { 02968 nom[i] = 0.0f; 02969 denom[i] = 0.0f; 02970 nn[i] = 0; 02971 ka[i] = 0; 02972 } 02973 02974 m_volume->symplane1(m_wptr, m_wptr2); 02975 02976 if ( m_weighting == ESTIMATE ) { 02977 int vol = box*box*box; 02978 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 02979 pow_a[3*kc] = 0.0; 02980 float max = max3d( kc, pow_a ); 02981 alpha = ( 1.0f - 1.0f/(float)vol ) / max; 02982 } 02983 02984 for (int iz = 1; iz <= m_vnzp; iz++) { 02985 if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1; 02986 argz = float(kz*kz)*dz2; 02987 for (int iy = 1; iy <= m_vnyp; iy++) { 02988 if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1; 02989 argy = argz + float(ky*ky)*dy2; 02990 for (int ix = 0; ix <= m_vnxc; ix++) { 02991 float Kn = (*m_wptr)(ix,iy,iz); 02992 argx = std::sqrt(argy + float(ix*ix)*dx2); 02993 int r = Util::round(float(inc)*argx); 02994 if ( r >= 0 && Kn > 4.5f ) { 02995 if ( m_weighting == ESTIMATE ) { 02996 int cx = ix; 02997 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 02998 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 02999 03000 float sum = 0.0; 03001 for( int ii = -kc; ii <= kc; ++ii ) { 03002 int nbrcx = cx + ii; 03003 if( nbrcx >= m_vnxc ) continue; 03004 for ( int jj= -kc; jj <= kc; ++jj ) { 03005 int nbrcy = cy + jj; 03006 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 03007 for( int kk = -kc; kk <= kc; ++kk ) { 03008 int nbrcz = cz + jj; 03009 if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 03010 if( nbrcx < 0 ) { 03011 nbrcx = -nbrcx; 03012 nbrcy = -nbrcy; 03013 nbrcz = -nbrcz; 03014 } 03015 int nbrix = nbrcx; 03016 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 03017 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 03018 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) { 03019 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 03020 sum = sum + pow_a[c]; 03021 } 03022 } 03023 } 03024 } 03025 wght = 1.0f / ( 1.0f - alpha * sum ); 03026 } // end of ( m_weighting == ESTIMATE ) 03027 float nominator = std::norm(m_volume->cmplx(ix,iy,iz))/Kn; 03028 float denominator = ((*m_wptr2)(ix,iy,iz)-nominator)/(Kn-1.0f); 03029 // Skip Friedel related values 03030 if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) { 03031 if ( r <= inc ) { 03032 nom[r] += nominator*wght; 03033 denom[r] += denominator/Kn*wght; 03034 nn[r] += 2; 03035 ka[r] += int(Kn); 03036 } 03037 /* 03038 #ifdef _WIN32 03039 //#float tmp = _cpp_max(nominator/denominator/Kn-1.0f,0.0f); 03040 #else 03041 //#float tmp = std::max(nominator/denominator/Kn-1.0f,0.0f); 03042 #endif //_WIN32 03043 // Create SSNR as a 3D array (-n/2:n/2+n%2-1) 03044 iix = m_vnxc + ix; iiy = m_vnyc + ky; iiz = m_vnzc + kz; 03045 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 03046 (*vol_ssnr)(iix, iiy, iiz) = tmp; 03047 // Friedel part 03048 iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz; 03049 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 03050 (*vol_ssnr)(iix, iiy, iiz) = tmp; 03051 */ 03052 03053 } 03054 (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght; 03055 //(*vol_ssnr)(2*ix, iy-1, iz-1) = real(m_volume->cmplx(ix,iy,iz))*wght/Kn; 03056 //(*vol_ssnr)(2*ix+1, iy-1, iz-1) = imag(m_volume->cmplx(ix,iy,iz))*wght/Kn; 03057 } // end of Kn>4.5 03058 } 03059 } 03060 } 03061 03062 for (int i = 0; i <= inc; i++) { 03063 (*SSNR)(i,0,0) = nom[i]; 03064 (*SSNR)(i,1,0) = denom[i]; // variance 03065 (*SSNR)(i,2,0) = static_cast<float>(nn[i]); 03066 (*SSNR)(i,3,0) = static_cast<float>(ka[i]); 03067 } 03068 vol_ssnr->update(); 03069 return vol_ssnr; 03070 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 940 of file reconstructor.h. 00941 { 00942 return "Reconstruction by nearest neighbor with 3D SSNR"; 00943 }
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Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase. Definition at line 935 of file reconstructor.h. 00936 {
00937 return NAME;
00938 }
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Implements EMAN::FactoryBase. Definition at line 950 of file reconstructor.h. References EMAN::TypeDict::put(). 00951 { 00952 TypeDict d; 00953 d.put("size", EMObject::INT); 00954 d.put("npad", EMObject::INT); 00955 d.put("symmetry", EMObject::STRING); 00956 d.put("fftvol", EMObject::EMDATA); 00957 d.put("weight", EMObject::EMDATA); 00958 d.put("weight2", EMObject::EMDATA); 00959 d.put("SSNR", EMObject::EMDATA); 00960 d.put("w", EMObject::FLOAT); 00961 return d; 00962 }
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Definition at line 2906 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. Referenced by insert_slice(). 02907 { 02908 Assert( padfft != NULL ); 02909 // insert slice for all symmetry related positions 02910 for (int isym=0; isym < m_nsym; isym++) { 02911 Transform tsym = t.get_sym(m_symmetry, isym); 02912 m_volume->nn_SSNR( m_wptr, m_wptr2, padfft, tsym, mult); 02913 } 02914 return 0; 02915 }
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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 2877 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. 02877 { 02878 // sanity checks 02879 if (!slice) { 02880 LOGERR("try to insert NULL slice"); 02881 return 1; 02882 } 02883 02884 int padffted=slice->get_attr_default( "padffted", 0 ); 02885 02886 if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx) ) { 02887 // FIXME: Why doesn't this throw an exception? 02888 LOGERR("Tried to insert a slice that has wrong size."); 02889 return 1; 02890 } 02891 02892 EMData* padfft = NULL; 02893 02894 if( padffted != 0 ) padfft = new EMData(*slice); 02895 else padfft = padfft_slice( slice, t, m_npad ); 02896 02897 int mult = slice->get_attr_default("mult", 1); 02898 02899 Assert( mult > 0 ); 02900 insert_padfft_slice( padfft, t, mult ); 02901 02902 checked_delete( padfft ); 02903 return 0; 02904 }
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Definition at line 945 of file reconstructor.h. 00946 { 00947 return new nnSSNR_Reconstructor(); 00948 }
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Definition at line 2796 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. 02797 { 02798 02799 m_weighting = ESTIMATE; 02800 m_wghta = 0.2f; 02801 m_wghtb = 0.004f; 02802 02803 m_symmetry = symmetry; 02804 m_npad = npad; 02805 m_nsym = Transform::get_nsym(m_symmetry); 02806 02807 m_vnx = size; 02808 m_vny = size; 02809 m_vnz = size; 02810 02811 m_vnxp = size*npad; 02812 m_vnyp = size*npad; 02813 m_vnzp = size*npad; 02814 02815 m_vnxc = m_vnxp/2; 02816 m_vnyc = m_vnyp/2; 02817 m_vnzc = m_vnzp/2; 02818 02819 buildFFTVolume(); 02820 buildNormVolume(); 02821 buildNorm2Volume(); 02822 02823 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 2784 of file reconstructor.cpp. References EMAN::Dict::has_key(). Referenced by nnSSNR_Reconstructor(). 02785 { 02786 int size = params["size"]; 02787 int npad = params["npad"]; 02788 02789 string symmetry; 02790 if( params.has_key("symmetry") ) symmetry = params["symmetry"].to_str(); 02791 else symmetry = "c1"; 02792 02793 setup( symmetry, size, npad ); 02794 }
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Definition at line 975 of file reconstructor.h. Referenced by buildFFTVolume(). |
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Definition at line 976 of file reconstructor.h. Referenced by buildNormVolume(). |
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Definition at line 977 of file reconstructor.h. Referenced by buildNorm2Volume(). |
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Definition at line 981 of file reconstructor.h. Referenced by buildFFTVolume(), insert_slice(), and setup(). |
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Definition at line 982 of file reconstructor.h. Referenced by setup(). |
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Definition at line 974 of file reconstructor.h. Referenced by nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 978 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 980 of file reconstructor.h. Referenced by setup(). |
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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 983 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), and setup(). |
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Definition at line 980 of file reconstructor.h. Referenced by setup(). |
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Definition at line 984 of file reconstructor.h. |
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Definition at line 983 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 setup(). |
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Definition at line 984 of file reconstructor.h. |
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Definition at line 983 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 971 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 979 of file reconstructor.h. |
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Definition at line 988 of file reconstructor.h. |
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Definition at line 989 of file reconstructor.h. Referenced by setup(). |
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Definition at line 972 of file reconstructor.h. Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 973 of file reconstructor.h. Referenced by buildNorm2Volume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 79 of file reconstructor.cpp. |