#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. |
1.3.9.1