#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 | |
static Reconstructor * | NEW () |
Static Public Attributes | |
static 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 |
EMData * | m_result |
bool | m_delete_volume |
bool | m_delete_weight |
bool | m_delete_weight2 |
bool | m_delete_weight3 |
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 |
Definition at line 1058 of file reconstructor.h.
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Definition at line 3028 of file reconstructor.cpp. References m_result, m_volume, m_wptr, m_wptr2, and m_wptr3. Referenced by NEW(). 03029 { 03030 m_volume = NULL; 03031 m_wptr = NULL; 03032 m_wptr2 = NULL; 03033 m_wptr3 = NULL; 03034 m_result = NULL; 03035 }
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Definition at line 3037 of file reconstructor.cpp. References m_result, m_volume, m_wptr, m_wptr2, m_wptr3, and setup(). 03038 { 03039 m_volume = NULL; 03040 m_wptr = NULL; 03041 m_wptr2 = NULL; 03042 m_wptr3 = NULL; 03043 m_result = NULL; 03044 03045 setup( symmetry, size, npad, snr, sign ); 03046 }
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Definition at line 3048 of file reconstructor.cpp. References checked_delete(), m_delete_volume, m_delete_weight, m_delete_weight2, m_delete_weight3, m_result, m_volume, m_wptr, m_wptr2, and m_wptr3. 03049 { 03050 03051 if( m_delete_volume ) 03052 checked_delete(m_volume); 03053 if( m_delete_weight ) 03054 checked_delete( m_wptr ); 03055 if ( m_delete_weight2 ) 03056 checked_delete( m_wptr2 ); 03057 if ( m_delete_weight3 ) 03058 checked_delete( m_wptr3 ); 03059 checked_delete( m_result ); 03060 }
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Definition at line 3152 of file reconstructor.cpp. References EMAN::Dict::has_key(), m_delete_weight2, m_vnxc, m_vnyp, m_vnzp, m_wptr2, EMAN::FactoryBase::params, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero(). Referenced by setup(). 03152 { 03153 03154 if( params.has_key("weight2") ) { 03155 m_wptr2 = params["weight2"]; 03156 m_delete_weight2 = false; 03157 } else { 03158 m_wptr2 = new EMData(); 03159 m_delete_weight2 = true; 03160 } 03161 m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp); 03162 m_wptr2->to_zero(); 03163 m_wptr2->set_array_offsets(0,1,1); 03164 }
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Definition at line 3166 of file reconstructor.cpp. References EMAN::Dict::has_key(), m_delete_weight3, m_vnxc, m_vnyp, m_vnzp, m_wptr3, EMAN::FactoryBase::params, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero(). Referenced by setup(). 03166 { 03167 03168 if( params.has_key("weight3") ) { 03169 m_wptr3 = params["weight3"]; 03170 m_delete_weight3 = false; 03171 } else { 03172 m_wptr3 = new EMData(); 03173 m_delete_weight3 = true; 03174 } 03175 m_wptr3->set_size(m_vnxc+1,m_vnyp,m_vnzp); 03176 m_wptr3->to_zero(); 03177 m_wptr3->set_array_offsets(0,1,1); 03178 }
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Definition at line 3138 of file reconstructor.cpp. References EMAN::Dict::has_key(), m_delete_weight, m_vnxc, m_vnyp, m_vnzp, m_wptr, EMAN::FactoryBase::params, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero(). Referenced by setup(). 03139 { 03140 if( params.has_key("weight") ) { 03141 m_wptr = params["weight"]; 03142 m_delete_weight = false; 03143 } else { 03144 m_wptr = new EMData(); 03145 m_delete_weight = true; 03146 } 03147 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 03148 m_wptr->to_zero(); 03149 m_wptr->set_array_offsets(0,1,1); 03150 }
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Finish reconstruction and return the complete model.
Reimplemented from EMAN::Reconstructor. Definition at line 3222 of file reconstructor.cpp. References abs, EMAN::EMData::cmplx(), ESTIMATE, 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::FactoryBase::params, 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(). 03223 { 03224 /* 03225 I changed the code on 05/15 so it only returns variance. 03226 Lines commented out are marked by //# 03227 The version prior to the currect changes is r1.190 03228 PAP 03229 */ 03230 /*** 03231 m_volume ctf*(P^2D->3D(F^3D)) 03232 m_wptr ctf^2 03233 m_wptr2 |P^2D->3D(F^3D)|^2 03234 m_wptr3 Kn 03235 nominator = sum_rot [ wght*signal ] 03236 denominator = sum_rot[ wght*variance ] 03237 ***/ 03238 int kz, ky; 03239 int box = 7; 03240 int kc = (box-1)/2; 03241 float alpha = 0.0; 03242 float argx, argy, argz; 03243 vector< float > pow_a( 3*kc+1, 1.0 ); 03244 float w = params["w"]; 03245 float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc); 03246 float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc); 03247 #ifdef _WIN32 03248 float dz2 = 1.0f/_cpp_max(float(m_vnzc),1.0f)/_cpp_max(float(m_vnzc),1.0f); 03249 int inc = Util::round(float(_cpp_max(_cpp_max(m_vnxc,m_vnyc),m_vnzc))/w); 03250 #else 03251 float dz2 = 1.0f/std::max(float(m_vnzc),1.0f)/std::max(float(m_vnzc),1.0f); 03252 int inc = Util::round(float(std::max(std::max(m_vnxc,m_vnyc),m_vnzc))/w); 03253 #endif //_WIN32 03254 03255 EMData* SSNR = params["SSNR"]; 03256 SSNR->set_size(inc+1,4,1); 03257 //#EMData* vol_ssnr = new EMData(); 03258 //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp); 03259 //#vol_ssnr->to_zero(); 03260 //# new linea follow 03261 EMData* vol_ssnr = new EMData(); 03262 vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp); 03263 vol_ssnr->to_zero(); 03264 if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0); 03265 else vol_ssnr->set_fftodd(1); 03266 vol_ssnr->set_nxc(m_vnxc); 03267 vol_ssnr->set_complex(true); 03268 vol_ssnr->set_ri(true); 03269 vol_ssnr->set_fftpad(false); 03270 //# 03271 float *nom = new float[inc+1]; 03272 float *denom = new float[inc+1]; 03273 int *ka = new int[inc+1]; 03274 int *nn = new int[inc+1]; 03275 float wght = 1.f; 03276 for (int i = 0; i <= inc; i++) { 03277 nom[i] = 0.0f; 03278 denom[i] = 0.0f; 03279 nn[i] = 0; 03280 ka[i] = 0; 03281 } 03282 m_volume->symplane2(m_wptr, m_wptr2, m_wptr3); 03283 if ( m_weighting == ESTIMATE ) { 03284 int vol = box*box*box; 03285 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 03286 pow_a[3*kc] = 0.0; 03287 float max = max3d( kc, pow_a ); 03288 alpha = ( 1.0f - 1.0f/(float)vol ) / max; 03289 } 03290 for (int iz = 1; iz <= m_vnzp; iz++) { 03291 if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1; 03292 argz = float(kz*kz)*dz2; 03293 for (int iy = 1; iy <= m_vnyp; iy++) { 03294 if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1; 03295 argy = argz + float(ky*ky)*dy2; 03296 for (int ix = 0; ix <= m_vnxc; ix++) { 03297 float Kn = (*m_wptr3)(ix,iy,iz); 03298 argx = std::sqrt(argy + float(ix*ix)*dx2); 03299 int r = Util::round(float(inc)*argx); 03300 if ( r >= 0 && Kn > 4.5f ) { 03301 if ( m_weighting == ESTIMATE ) { 03302 int cx = ix; 03303 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 03304 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 03305 float sum = 0.0; 03306 for( int ii = -kc; ii <= kc; ++ii ) { 03307 int nbrcx = cx + ii; 03308 if( nbrcx >= m_vnxc ) continue; 03309 for ( int jj= -kc; jj <= kc; ++jj ) { 03310 int nbrcy = cy + jj; 03311 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 03312 for( int kk = -kc; kk <= kc; ++kk ) { 03313 int nbrcz = cz + jj; 03314 if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 03315 if( nbrcx < 0 ) { 03316 nbrcx = -nbrcx; 03317 nbrcy = -nbrcy; 03318 nbrcz = -nbrcz; 03319 } 03320 int nbrix = nbrcx; 03321 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 03322 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 03323 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) { 03324 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 03325 sum = sum + pow_a[c]; 03326 } 03327 } 03328 } 03329 } 03330 // int r = std::abs(cx) + std::abs(cy) + std::abs(cz); 03331 wght = 1.0f / ( 1.0f - alpha * sum ); 03332 } // end of ( m_weighting == ESTIMATE ) 03333 float nominator = std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz); 03334 float denominator = ((*m_wptr2)(ix,iy,iz)-std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz))/(Kn-1.0f); 03335 // Skip Friedel related values 03336 if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) { 03337 if ( r <= inc ) { 03338 nom[r] += nominator*wght; 03339 denom[r] += denominator/(*m_wptr)(ix,iy,iz)*wght; 03340 nn[r] += 2; 03341 ka[r] += int(Kn); 03342 } 03343 /* 03344 #ifdef _WIN32 03345 float tmp = _cpp_max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f); 03346 #else 03347 float tmp = std::max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f); 03348 #endif //_WIN32 03349 // Create SSNR as a 3D array (-n/2:n/2+n%2-1) 03350 int iix = m_vnxc + ix; int iiy = m_vnyc + ky; int iiz = m_vnzc + kz; 03351 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 03352 (*vol_ssnr)(iix, iiy, iiz) = tmp; 03353 // Friedel part 03354 iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz; 03355 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 03356 (*vol_ssnr)(iix, iiy, iiz) = tmp; 03357 */ 03358 } 03359 (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght; 03360 } // end of Kn>4.5 or whatever 03361 } 03362 } 03363 } 03364 for (int i = 0; i <= inc; i++) { 03365 (*SSNR)(i,0,0) = nom[i]; 03366 (*SSNR)(i,1,0) = denom[i]; 03367 (*SSNR)(i,2,0) = static_cast<float>(nn[i]); 03368 (*SSNR)(i,3,0) = static_cast<float>(ka[i]); 03369 } 03370 vol_ssnr->update(); 03371 return vol_ssnr; 03372 // } 03373 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 1089 of file reconstructor.h.
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Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase. Definition at line 1084 of file reconstructor.h. References NAME. 01085 { 01086 return NAME; 01087 }
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Implements EMAN::FactoryBase. Definition at line 1099 of file reconstructor.h. References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING. 01100 { 01101 TypeDict d; 01102 d.put("size", EMObject::INT); 01103 d.put("npad", EMObject::INT); 01104 d.put("symmetry", EMObject::STRING); 01105 d.put("fftvol", EMObject::EMDATA); 01106 d.put("fftwvol", EMObject::EMDATA); 01107 d.put("weight", EMObject::EMDATA); 01108 d.put("weight2", EMObject::EMDATA); 01109 d.put("weight3", EMObject::EMDATA); 01110 d.put("SSNR", EMObject::EMDATA); 01111 d.put("w", EMObject::FLOAT); 01112 d.put("sign", EMObject::INT); 01113 d.put("snr", EMObject::FLOAT); 01114 return d; 01115 }
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Definition at line 3208 of file reconstructor.cpp. References Assert, EMAN::Transform::get_sym(), m_nsym, m_symmetry, m_volume, m_wptr, m_wptr2, m_wptr3, and EMAN::EMData::nn_SSNR_ctf(). Referenced by insert_slice(). 03209 { 03210 Assert( padfft != NULL ); 03211 03212 // insert slice for all symmetry related positions 03213 for (int isym=0; isym < m_nsym; isym++) { 03214 Transform tsym = t.get_sym(m_symmetry, isym); 03215 m_volume->nn_SSNR_ctf(m_wptr, m_wptr2, m_wptr3, padfft, tsym, mult); 03216 } 03217 03218 return 0; 03219 }
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Insert a slice into a 3D volume, in a given orientation.
Reimplemented from EMAN::Reconstructor. Definition at line 3180 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, m_vnx, mult(), and EMAN::padfft_slice(). 03180 { 03181 // sanity checks 03182 if (!slice) { 03183 LOGERR("try to insert NULL slice"); 03184 return 1; 03185 } 03186 int padffted= slice->get_attr_default("padffted", 0); 03187 if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx) ) { 03188 // FIXME: Why doesn't this throw an exception? 03189 LOGERR("Tried to insert a slice that is the wrong size."); 03190 return 1; 03191 } 03192 EMData* padfft = NULL; 03193 03194 if( padffted != 0 ) { 03195 padfft = new EMData(*slice); 03196 } else { 03197 padfft = padfft_slice( slice, t, m_npad ); 03198 } 03199 03200 int mult= slice->get_attr_default("mult", 1); 03201 03202 Assert( mult > 0 ); 03203 insert_padfft_slice( padfft, t, mult ); 03204 03205 checked_delete( padfft ); 03206 return 0; 03207 }
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Definition at line 1094 of file reconstructor.h. References nnSSNR_ctfReconstructor(). 01095 { 01096 return new nnSSNR_ctfReconstructor(); 01097 }
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Definition at line 3076 of file reconstructor.cpp. References buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), ESTIMATE, 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. 03077 { 03078 03079 m_weighting = ESTIMATE; 03080 m_wghta = 0.2f; 03081 m_wghtb = 0.004f; 03082 wiener = 1; 03083 03084 m_symmetry = symmetry; 03085 m_npad = npad; 03086 m_nsym = Transform::get_nsym(m_symmetry); 03087 03088 m_sign = sign; 03089 m_snr = snr; 03090 03091 m_vnx = size; 03092 m_vny = size; 03093 m_vnz = size; 03094 03095 m_vnxp = size*npad; 03096 m_vnyp = size*npad; 03097 m_vnzp = size*npad; 03098 03099 m_vnxc = m_vnxp/2; 03100 m_vnyc = m_vnyp/2; 03101 m_vnzc = m_vnzp/2; 03102 03103 buildFFTVolume(); 03104 buildNormVolume(); 03105 buildNorm2Volume(); 03106 buildNorm3Volume(); 03107 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 3062 of file reconstructor.cpp. References EMAN::Dict::has_key(), EMAN::FactoryBase::params, and sign. Referenced by nnSSNR_ctfReconstructor(). 03063 { 03064 int size = params["size"]; 03065 int npad = params["npad"]; 03066 int sign = params["sign"]; 03067 float snr = params["snr"]; 03068 string symmetry; 03069 if( params.has_key("symmetry") ) { 03070 symmetry = params["symmetry"].to_str(); 03071 } else { 03072 symmetry = "c1"; 03073 } 03074 setup( symmetry, size, npad, snr, sign ); 03075 }
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Definition at line 1128 of file reconstructor.h. Referenced by buildFFTVolume(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1129 of file reconstructor.h. Referenced by buildNormVolume(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1130 of file reconstructor.h. Referenced by buildNorm2Volume(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1131 of file reconstructor.h. Referenced by buildNorm3Volume(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1135 of file reconstructor.h. Referenced by buildFFTVolume(), insert_slice(), and setup(). |
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Definition at line 1136 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 1127 of file reconstructor.h. Referenced by nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1145 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1146 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1132 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 1134 of file reconstructor.h. Referenced by insert_slice(), and setup(). |
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Definition at line 1138 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 1137 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), and setup(). |
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Definition at line 1134 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1138 of file reconstructor.h. |
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Definition at line 1137 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 1134 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1138 of file reconstructor.h. |
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Definition at line 1137 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 1123 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1133 of file reconstructor.h. |
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Definition at line 1143 of file reconstructor.h. |
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Definition at line 1144 of file reconstructor.h. Referenced by setup(). |
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Definition at line 1124 of file reconstructor.h. Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1125 of file reconstructor.h. Referenced by buildNorm2Volume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1126 of file reconstructor.h. Referenced by buildNorm3Volume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor(). |
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Definition at line 1120 of file reconstructor.h. Referenced by get_name(). |
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Definition at line 1147 of file reconstructor.h. Referenced by setup(). |