#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 | |
static Reconstructor * | NEW () |
Static Public Attributes | |
static 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 |
Definition at line 812 of file reconstructor.h.
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Definition at line 2275 of file reconstructor.cpp. References m_result, m_volume, m_wptr, and m_wptr2. Referenced by NEW(). 02276 { 02277 m_volume = NULL; 02278 m_wptr = NULL; 02279 m_wptr2 = NULL; 02280 m_result = NULL; 02281 }
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Definition at line 2283 of file reconstructor.cpp. References m_result, m_volume, m_wptr, m_wptr2, and setup(). 02284 { 02285 m_volume = NULL; 02286 m_wptr = NULL; 02287 m_wptr2 = NULL; 02288 m_result = NULL; 02289 02290 setup( symmetry, size, npad ); 02291 }
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Definition at line 2293 of file reconstructor.cpp. References checked_delete(), m_delete_volume, m_delete_weight, m_delete_weight2, m_result, m_volume, m_wptr, and m_wptr2. 02294 { 02295 if( m_delete_volume ) checked_delete(m_volume); 02296 02297 if( m_delete_weight ) checked_delete( m_wptr ); 02298 02299 if( m_delete_weight2 ) checked_delete( m_wptr2 ); 02300 02301 checked_delete( m_result ); 02302 }
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Definition at line 2382 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(). 02382 { 02383 02384 if( params.has_key("weight2") ) { 02385 m_wptr2 = params["weight2"]; 02386 m_delete_weight2 = false; 02387 } else { 02388 m_wptr2 = new EMData(); 02389 m_delete_weight2 = true; 02390 } 02391 m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02392 m_wptr2->to_zero(); 02393 m_wptr2->set_array_offsets(0,1,1); 02394 }
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Definition at line 2367 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(). 02367 { 02368 if( params.has_key("weight") ) { 02369 m_wptr = params["weight"]; 02370 m_delete_weight = false; 02371 } else { 02372 m_wptr = new EMData(); 02373 m_delete_weight = true; 02374 } 02375 02376 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02377 m_wptr->to_zero(); 02378 02379 m_wptr->set_array_offsets(0,1,1); 02380 }
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(*SSNR)(i,0,0) = nom[i]/denom[i] - 1;/// Reimplemented from EMAN::Reconstructor. Definition at line 2439 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, 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::symplane1(), EMAN::EMData::to_zero(), and EMAN::EMData::update(). 02440 { 02441 /* 02442 I changed the code on 05/15 so it only returns variance. 02443 Lines commented out are marked by //# 02444 The version prior to the currect changes is r1.190 02445 PAP 02446 */ 02447 int kz, ky; 02448 //#int iix, iiy, iiz; 02449 int box = 7; 02450 int kc = (box-1)/2; 02451 float alpha = 0.0; 02452 float argx, argy, argz; 02453 vector< float > pow_a( 3*kc+1, 1.0 ); 02454 float w = params["w"]; 02455 EMData* SSNR = params["SSNR"]; 02456 //#EMData* vol_ssnr = new EMData(); 02457 //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp); 02458 //#vol_ssnr->to_zero(); 02459 //# new line follow 02460 EMData* vol_ssnr = new EMData(); 02461 vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp); 02462 vol_ssnr->to_zero(); 02463 if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0); 02464 else vol_ssnr->set_fftodd(1); 02465 vol_ssnr->set_nxc(m_vnxc); 02466 vol_ssnr->set_complex(true); 02467 vol_ssnr->set_ri(true); 02468 vol_ssnr->set_fftpad(false); 02469 //# 02470 02471 float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc); 02472 float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc); 02473 #ifdef _WIN32 02474 float dz2 = 1.0f/_cpp_max(float(m_vnzc),1.0f)/_cpp_max(float(m_vnzc),1.0f); 02475 int inc = Util::round(float(_cpp_max(_cpp_max(m_vnxc,m_vnyc),m_vnzc))/w); 02476 #else 02477 float dz2 = 1.0f/std::max(float(m_vnzc),1.0f)/std::max(float(m_vnzc),1.0f); 02478 int inc = Util::round(float(std::max(std::max(m_vnxc,m_vnyc),m_vnzc))/w); 02479 #endif //_WIN32 02480 SSNR->set_size(inc+1,4,1); 02481 02482 float *nom = new float[inc+1]; 02483 float *denom = new float[inc+1]; 02484 int *nn = new int[inc+1]; 02485 int *ka = new int[inc+1]; 02486 float wght = 1.0f; 02487 for (int i = 0; i <= inc; i++) { 02488 nom[i] = 0.0f; 02489 denom[i] = 0.0f; 02490 nn[i] = 0; 02491 ka[i] = 0; 02492 } 02493 02494 m_volume->symplane1(m_wptr, m_wptr2); 02495 02496 if ( m_weighting == ESTIMATE ) { 02497 int vol = box*box*box; 02498 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 02499 pow_a[3*kc] = 0.0; 02500 float max = max3d( kc, pow_a ); 02501 alpha = ( 1.0f - 1.0f/(float)vol ) / max; 02502 } 02503 02504 for (int iz = 1; iz <= m_vnzp; iz++) { 02505 if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1; 02506 argz = float(kz*kz)*dz2; 02507 for (int iy = 1; iy <= m_vnyp; iy++) { 02508 if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1; 02509 argy = argz + float(ky*ky)*dy2; 02510 for (int ix = 0; ix <= m_vnxc; ix++) { 02511 float Kn = (*m_wptr)(ix,iy,iz); 02512 argx = std::sqrt(argy + float(ix*ix)*dx2); 02513 int r = Util::round(float(inc)*argx); 02514 if ( r >= 0 && Kn > 4.5f ) { 02515 if ( m_weighting == ESTIMATE ) { 02516 int cx = ix; 02517 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 02518 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 02519 02520 float sum = 0.0; 02521 for( int ii = -kc; ii <= kc; ++ii ) { 02522 int nbrcx = cx + ii; 02523 if( nbrcx >= m_vnxc ) continue; 02524 for ( int jj= -kc; jj <= kc; ++jj ) { 02525 int nbrcy = cy + jj; 02526 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 02527 for( int kk = -kc; kk <= kc; ++kk ) { 02528 int nbrcz = cz + jj; 02529 if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 02530 if( nbrcx < 0 ) { 02531 nbrcx = -nbrcx; 02532 nbrcy = -nbrcy; 02533 nbrcz = -nbrcz; 02534 } 02535 int nbrix = nbrcx; 02536 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 02537 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 02538 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) { 02539 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 02540 sum = sum + pow_a[c]; 02541 } 02542 } 02543 } 02544 } 02545 wght = 1.0f / ( 1.0f - alpha * sum ); 02546 } // end of ( m_weighting == ESTIMATE ) 02547 float nominator = std::norm(m_volume->cmplx(ix,iy,iz))/Kn; 02548 float denominator = ((*m_wptr2)(ix,iy,iz)-nominator)/(Kn-1.0f); 02549 // Skip Friedel related values 02550 if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) { 02551 if ( r <= inc ) { 02552 nom[r] += nominator*wght; 02553 denom[r] += denominator/Kn*wght; 02554 nn[r] += 2; 02555 ka[r] += int(Kn); 02556 } 02557 /* 02558 #ifdef _WIN32 02559 //#float tmp = _cpp_max(nominator/denominator/Kn-1.0f,0.0f); 02560 #else 02561 //#float tmp = std::max(nominator/denominator/Kn-1.0f,0.0f); 02562 #endif //_WIN32 02563 // Create SSNR as a 3D array (-n/2:n/2+n%2-1) 02564 iix = m_vnxc + ix; iiy = m_vnyc + ky; iiz = m_vnzc + kz; 02565 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 02566 (*vol_ssnr)(iix, iiy, iiz) = tmp; 02567 // Friedel part 02568 iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz; 02569 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 02570 (*vol_ssnr)(iix, iiy, iiz) = tmp; 02571 */ 02572 02573 } 02574 (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght; 02575 //(*vol_ssnr)(2*ix, iy-1, iz-1) = real(m_volume->cmplx(ix,iy,iz))*wght/Kn; 02576 //(*vol_ssnr)(2*ix+1, iy-1, iz-1) = imag(m_volume->cmplx(ix,iy,iz))*wght/Kn; 02577 } // end of Kn>4.5 02578 } 02579 } 02580 } 02581 02582 for (int i = 0; i <= inc; i++) { 02583 (*SSNR)(i,0,0) = nom[i]; 02584 (*SSNR)(i,1,0) = denom[i]; // variance 02585 (*SSNR)(i,2,0) = static_cast<float>(nn[i]); 02586 (*SSNR)(i,3,0) = static_cast<float>(ka[i]); 02587 } 02588 vol_ssnr->update(); 02589 return vol_ssnr; 02590 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 841 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 836 of file reconstructor.h. References NAME. 00837 { 00838 return NAME; 00839 }
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Implements EMAN::FactoryBase. Definition at line 851 of file reconstructor.h. References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING. 00852 { 00853 TypeDict d; 00854 d.put("size", EMObject::INT); 00855 d.put("npad", EMObject::INT); 00856 d.put("symmetry", EMObject::STRING); 00857 d.put("fftvol", EMObject::EMDATA); 00858 d.put("weight", EMObject::EMDATA); 00859 d.put("weight2", EMObject::EMDATA); 00860 d.put("SSNR", EMObject::EMDATA); 00861 d.put("w", EMObject::FLOAT); 00862 return d; 00863 }
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Definition at line 2426 of file reconstructor.cpp. References Assert, EMAN::Transform::get_sym(), m_nsym, m_symmetry, m_volume, m_wptr, m_wptr2, and EMAN::EMData::nn_SSNR(). Referenced by insert_slice(). 02427 { 02428 Assert( padfft != NULL ); 02429 // insert slice for all symmetry related positions 02430 for (int isym=0; isym < m_nsym; isym++) { 02431 Transform tsym = t.get_sym(m_symmetry, isym); 02432 m_volume->nn_SSNR( m_wptr, m_wptr2, padfft, tsym, mult); 02433 } 02434 return 0; 02435 }
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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 2397 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(). 02397 { 02398 // sanity checks 02399 if (!slice) { 02400 LOGERR("try to insert NULL slice"); 02401 return 1; 02402 } 02403 02404 int padffted=slice->get_attr_default( "padffted", 0 ); 02405 02406 if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx) ) { 02407 // FIXME: Why doesn't this throw an exception? 02408 LOGERR("Tried to insert a slice that has wrong size."); 02409 return 1; 02410 } 02411 02412 EMData* padfft = NULL; 02413 02414 if( padffted != 0 ) padfft = new EMData(*slice); 02415 else padfft = padfft_slice( slice, t, m_npad ); 02416 02417 int mult = slice->get_attr_default("mult", 1); 02418 02419 Assert( mult > 0 ); 02420 insert_padfft_slice( padfft, t, mult ); 02421 02422 checked_delete( padfft ); 02423 return 0; 02424 }
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Definition at line 846 of file reconstructor.h. References nnSSNR_Reconstructor(). 00847 { 00848 return new nnSSNR_Reconstructor(); 00849 }
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Definition at line 2316 of file reconstructor.cpp. References buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), ESTIMATE, 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. 02317 { 02318 02319 m_weighting = ESTIMATE; 02320 m_wghta = 0.2f; 02321 m_wghtb = 0.004f; 02322 02323 m_symmetry = symmetry; 02324 m_npad = npad; 02325 m_nsym = Transform::get_nsym(m_symmetry); 02326 02327 m_vnx = size; 02328 m_vny = size; 02329 m_vnz = size; 02330 02331 m_vnxp = size*npad; 02332 m_vnyp = size*npad; 02333 m_vnzp = size*npad; 02334 02335 m_vnxc = m_vnxp/2; 02336 m_vnyc = m_vnyp/2; 02337 m_vnzc = m_vnzp/2; 02338 02339 buildFFTVolume(); 02340 buildNormVolume(); 02341 buildNorm2Volume(); 02342 02343 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 2304 of file reconstructor.cpp. References EMAN::Dict::has_key(), and EMAN::FactoryBase::params. Referenced by nnSSNR_Reconstructor(). 02305 { 02306 int size = params["size"]; 02307 int npad = params["npad"]; 02308 02309 string symmetry; 02310 if( params.has_key("symmetry") ) symmetry = params["symmetry"].to_str(); 02311 else symmetry = "c1"; 02312 02313 setup( symmetry, size, npad ); 02314 }
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Definition at line 876 of file reconstructor.h. Referenced by buildFFTVolume(), and ~nnSSNR_Reconstructor(). |
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Definition at line 877 of file reconstructor.h. Referenced by buildNormVolume(), and ~nnSSNR_Reconstructor(). |
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Definition at line 878 of file reconstructor.h. Referenced by buildNorm2Volume(), and ~nnSSNR_Reconstructor(). |
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Definition at line 882 of file reconstructor.h. Referenced by buildFFTVolume(), insert_slice(), and setup(). |
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Definition at line 883 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 875 of file reconstructor.h. Referenced by nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 879 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 881 of file reconstructor.h. Referenced by insert_slice(), and setup(). |
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Definition at line 885 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 884 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), and setup(). |
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Definition at line 881 of file reconstructor.h. Referenced by setup(). |
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Definition at line 885 of file reconstructor.h. |
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Definition at line 884 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 881 of file reconstructor.h. Referenced by setup(). |
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Definition at line 885 of file reconstructor.h. |
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Definition at line 884 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 872 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 880 of file reconstructor.h. |
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Definition at line 889 of file reconstructor.h. |
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Definition at line 890 of file reconstructor.h. Referenced by setup(). |
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Definition at line 873 of file reconstructor.h. Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 874 of file reconstructor.h. Referenced by buildNorm2Volume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 869 of file reconstructor.h. Referenced by get_name(). |