#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 2396 of file reconstructor.cpp. References m_result, m_volume, m_wptr, and m_wptr2. 02397 { 02398 m_volume = NULL; 02399 m_wptr = NULL; 02400 m_wptr2 = NULL; 02401 m_result = NULL; 02402 }
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Definition at line 2404 of file reconstructor.cpp. References m_result, m_volume, m_wptr, m_wptr2, and setup(). 02405 { 02406 m_volume = NULL; 02407 m_wptr = NULL; 02408 m_wptr2 = NULL; 02409 m_result = NULL; 02410 02411 setup( symmetry, size, npad ); 02412 }
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Definition at line 2414 of file reconstructor.cpp. References checked_delete(), m_result, m_volume, m_wptr, and m_wptr2. 02415 { 02416 if( m_delete_volume ) checked_delete(m_volume); 02417 02418 if( m_delete_weight ) checked_delete( m_wptr ); 02419 02420 if( m_delete_weight2 ) checked_delete( m_wptr2 ); 02421 02422 checked_delete( m_result ); 02423 }
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Definition at line 2503 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(). 02503 { 02504 02505 if( params.has_key("weight2") ) { 02506 m_wptr2 = params["weight2"]; 02507 m_delete_weight2 = false; 02508 } else { 02509 m_wptr2 = new EMData(); 02510 m_delete_weight2 = true; 02511 } 02512 m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02513 m_wptr2->to_zero(); 02514 m_wptr2->set_array_offsets(0,1,1); 02515 }
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Definition at line 2488 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(). 02488 { 02489 if( params.has_key("weight") ) { 02490 m_wptr = params["weight"]; 02491 m_delete_weight = false; 02492 } else { 02493 m_wptr = new EMData(); 02494 m_delete_weight = true; 02495 } 02496 02497 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 02498 m_wptr->to_zero(); 02499 02500 m_wptr->set_array_offsets(0,1,1); 02501 }
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(*SSNR)(i,0,0) = nom[i]/denom[i] - 1;/// Reimplemented from EMAN::Reconstructor. Definition at line 2560 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(). 02561 { 02562 /* 02563 I changed the code on 05/15 so it only returns variance. 02564 Lines commented out are marked by //# 02565 The version prior to the currect changes is r1.190 02566 PAP 02567 */ 02568 int kz, ky; 02569 //#int iix, iiy, iiz; 02570 int box = 7; 02571 int kc = (box-1)/2; 02572 float alpha = 0.0; 02573 float argx, argy, argz; 02574 vector< float > pow_a( 3*kc+1, 1.0 ); 02575 float w = params["w"]; 02576 EMData* SSNR = params["SSNR"]; 02577 //#EMData* vol_ssnr = new EMData(); 02578 //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp); 02579 //#vol_ssnr->to_zero(); 02580 //# new line follow 02581 EMData* vol_ssnr = new EMData(); 02582 vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp); 02583 vol_ssnr->to_zero(); 02584 if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0); 02585 else vol_ssnr->set_fftodd(1); 02586 vol_ssnr->set_nxc(m_vnxc); 02587 vol_ssnr->set_complex(true); 02588 vol_ssnr->set_ri(true); 02589 vol_ssnr->set_fftpad(false); 02590 //# 02591 02592 float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc); 02593 float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc); 02594 #ifdef _WIN32 02595 float dz2 = 1.0f/_cpp_max(float(m_vnzc),1.0f)/_cpp_max(float(m_vnzc),1.0f); 02596 int inc = Util::round(float(_cpp_max(_cpp_max(m_vnxc,m_vnyc),m_vnzc))/w); 02597 #else 02598 float dz2 = 1.0f/std::max(float(m_vnzc),1.0f)/std::max(float(m_vnzc),1.0f); 02599 int inc = Util::round(float(std::max(std::max(m_vnxc,m_vnyc),m_vnzc))/w); 02600 #endif //_WIN32 02601 SSNR->set_size(inc+1,4,1); 02602 02603 float *nom = new float[inc+1]; 02604 float *denom = new float[inc+1]; 02605 int *nn = new int[inc+1]; 02606 int *ka = new int[inc+1]; 02607 float wght = 1.0f; 02608 for (int i = 0; i <= inc; i++) { 02609 nom[i] = 0.0f; 02610 denom[i] = 0.0f; 02611 nn[i] = 0; 02612 ka[i] = 0; 02613 } 02614 02615 m_volume->symplane1(m_wptr, m_wptr2); 02616 02617 if ( m_weighting == ESTIMATE ) { 02618 int vol = box*box*box; 02619 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 02620 pow_a[3*kc] = 0.0; 02621 float max = max3d( kc, pow_a ); 02622 alpha = ( 1.0f - 1.0f/(float)vol ) / max; 02623 } 02624 02625 for (int iz = 1; iz <= m_vnzp; iz++) { 02626 if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1; 02627 argz = float(kz*kz)*dz2; 02628 for (int iy = 1; iy <= m_vnyp; iy++) { 02629 if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1; 02630 argy = argz + float(ky*ky)*dy2; 02631 for (int ix = 0; ix <= m_vnxc; ix++) { 02632 float Kn = (*m_wptr)(ix,iy,iz); 02633 argx = std::sqrt(argy + float(ix*ix)*dx2); 02634 int r = Util::round(float(inc)*argx); 02635 if ( r >= 0 && Kn > 4.5f ) { 02636 if ( m_weighting == ESTIMATE ) { 02637 int cx = ix; 02638 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 02639 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 02640 02641 float sum = 0.0; 02642 for( int ii = -kc; ii <= kc; ++ii ) { 02643 int nbrcx = cx + ii; 02644 if( nbrcx >= m_vnxc ) continue; 02645 for ( int jj= -kc; jj <= kc; ++jj ) { 02646 int nbrcy = cy + jj; 02647 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 02648 for( int kk = -kc; kk <= kc; ++kk ) { 02649 int nbrcz = cz + jj; 02650 if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 02651 if( nbrcx < 0 ) { 02652 nbrcx = -nbrcx; 02653 nbrcy = -nbrcy; 02654 nbrcz = -nbrcz; 02655 } 02656 int nbrix = nbrcx; 02657 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 02658 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 02659 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) { 02660 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 02661 sum = sum + pow_a[c]; 02662 } 02663 } 02664 } 02665 } 02666 wght = 1.0f / ( 1.0f - alpha * sum ); 02667 } // end of ( m_weighting == ESTIMATE ) 02668 float nominator = std::norm(m_volume->cmplx(ix,iy,iz))/Kn; 02669 float denominator = ((*m_wptr2)(ix,iy,iz)-nominator)/(Kn-1.0f); 02670 // Skip Friedel related values 02671 if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) { 02672 if ( r <= inc ) { 02673 nom[r] += nominator*wght; 02674 denom[r] += denominator/Kn*wght; 02675 nn[r] += 2; 02676 ka[r] += int(Kn); 02677 } 02678 /* 02679 #ifdef _WIN32 02680 //#float tmp = _cpp_max(nominator/denominator/Kn-1.0f,0.0f); 02681 #else 02682 //#float tmp = std::max(nominator/denominator/Kn-1.0f,0.0f); 02683 #endif //_WIN32 02684 // Create SSNR as a 3D array (-n/2:n/2+n%2-1) 02685 iix = m_vnxc + ix; iiy = m_vnyc + ky; iiz = m_vnzc + kz; 02686 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 02687 (*vol_ssnr)(iix, iiy, iiz) = tmp; 02688 // Friedel part 02689 iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz; 02690 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp ) 02691 (*vol_ssnr)(iix, iiy, iiz) = tmp; 02692 */ 02693 02694 } 02695 (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght; 02696 //(*vol_ssnr)(2*ix, iy-1, iz-1) = real(m_volume->cmplx(ix,iy,iz))*wght/Kn; 02697 //(*vol_ssnr)(2*ix+1, iy-1, iz-1) = imag(m_volume->cmplx(ix,iy,iz))*wght/Kn; 02698 } // end of Kn>4.5 02699 } 02700 } 02701 } 02702 02703 for (int i = 0; i <= inc; i++) { 02704 (*SSNR)(i,0,0) = nom[i]; 02705 (*SSNR)(i,1,0) = denom[i]; // variance 02706 (*SSNR)(i,2,0) = static_cast<float>(nn[i]); 02707 (*SSNR)(i,3,0) = static_cast<float>(ka[i]); 02708 } 02709 vol_ssnr->update(); 02710 return vol_ssnr; 02711 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 911 of file reconstructor.h. 00912 { 00913 return "Reconstruction by nearest neighbor with 3D SSNR"; 00914 }
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Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase. Definition at line 906 of file reconstructor.h. 00907 {
00908 return NAME;
00909 }
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Implements EMAN::FactoryBase. Definition at line 921 of file reconstructor.h. References EMAN::TypeDict::put(). 00922 { 00923 TypeDict d; 00924 d.put("size", EMObject::INT); 00925 d.put("npad", EMObject::INT); 00926 d.put("symmetry", EMObject::STRING); 00927 d.put("fftvol", EMObject::EMDATA); 00928 d.put("weight", EMObject::EMDATA); 00929 d.put("weight2", EMObject::EMDATA); 00930 d.put("SSNR", EMObject::EMDATA); 00931 d.put("w", EMObject::FLOAT); 00932 return d; 00933 }
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Definition at line 2547 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(). 02548 { 02549 Assert( padfft != NULL ); 02550 // insert slice for all symmetry related positions 02551 for (int isym=0; isym < m_nsym; isym++) { 02552 Transform tsym = t.get_sym(m_symmetry, isym); 02553 m_volume->nn_SSNR( m_wptr, m_wptr2, padfft, tsym, mult); 02554 } 02555 return 0; 02556 }
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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 2518 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. 02518 { 02519 // sanity checks 02520 if (!slice) { 02521 LOGERR("try to insert NULL slice"); 02522 return 1; 02523 } 02524 02525 int padffted=slice->get_attr_default( "padffted", 0 ); 02526 02527 if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx) ) { 02528 // FIXME: Why doesn't this throw an exception? 02529 LOGERR("Tried to insert a slice that has wrong size."); 02530 return 1; 02531 } 02532 02533 EMData* padfft = NULL; 02534 02535 if( padffted != 0 ) padfft = new EMData(*slice); 02536 else padfft = padfft_slice( slice, t, m_npad ); 02537 02538 int mult = slice->get_attr_default("mult", 1); 02539 02540 Assert( mult > 0 ); 02541 insert_padfft_slice( padfft, t, mult ); 02542 02543 checked_delete( padfft ); 02544 return 0; 02545 }
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Definition at line 916 of file reconstructor.h. 00917 { 00918 return new nnSSNR_Reconstructor(); 00919 }
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Definition at line 2437 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. 02438 { 02439 02440 m_weighting = ESTIMATE; 02441 m_wghta = 0.2f; 02442 m_wghtb = 0.004f; 02443 02444 m_symmetry = symmetry; 02445 m_npad = npad; 02446 m_nsym = Transform::get_nsym(m_symmetry); 02447 02448 m_vnx = size; 02449 m_vny = size; 02450 m_vnz = size; 02451 02452 m_vnxp = size*npad; 02453 m_vnyp = size*npad; 02454 m_vnzp = size*npad; 02455 02456 m_vnxc = m_vnxp/2; 02457 m_vnyc = m_vnyp/2; 02458 m_vnzc = m_vnzp/2; 02459 02460 buildFFTVolume(); 02461 buildNormVolume(); 02462 buildNorm2Volume(); 02463 02464 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 2425 of file reconstructor.cpp. References EMAN::Dict::has_key(). Referenced by nnSSNR_Reconstructor(). 02426 { 02427 int size = params["size"]; 02428 int npad = params["npad"]; 02429 02430 string symmetry; 02431 if( params.has_key("symmetry") ) symmetry = params["symmetry"].to_str(); 02432 else symmetry = "c1"; 02433 02434 setup( symmetry, size, npad ); 02435 }
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Definition at line 946 of file reconstructor.h. Referenced by buildFFTVolume(). |
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Definition at line 947 of file reconstructor.h. Referenced by buildNormVolume(). |
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Definition at line 948 of file reconstructor.h. Referenced by buildNorm2Volume(). |
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Definition at line 952 of file reconstructor.h. Referenced by buildFFTVolume(), insert_slice(), and setup(). |
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Definition at line 953 of file reconstructor.h. Referenced by setup(). |
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Definition at line 945 of file reconstructor.h. Referenced by nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 949 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 951 of file reconstructor.h. Referenced by setup(). |
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Definition at line 955 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 954 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), and setup(). |
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Definition at line 951 of file reconstructor.h. Referenced by setup(). |
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Definition at line 955 of file reconstructor.h. |
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Definition at line 954 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 951 of file reconstructor.h. Referenced by setup(). |
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Definition at line 955 of file reconstructor.h. |
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Definition at line 954 of file reconstructor.h. Referenced by buildFFTVolume(), buildNorm2Volume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 942 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 950 of file reconstructor.h. |
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Definition at line 959 of file reconstructor.h. |
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Definition at line 960 of file reconstructor.h. Referenced by setup(). |
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Definition at line 943 of file reconstructor.h. Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 944 of file reconstructor.h. Referenced by buildNorm2Volume(), finish(), insert_padfft_slice(), nnSSNR_Reconstructor(), and ~nnSSNR_Reconstructor(). |
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Definition at line 78 of file reconstructor.cpp. |