#include <reconstructor.h>
Inheritance diagram for EMAN::nn4_rectReconstructor:


Public Member Functions | |
| nn4_rectReconstructor () | |
| nn4_rectReconstructor (const string &symmetry, int size, int npad) | |
| virtual | ~nn4_rectReconstructor () |
| 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) |
| 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. | |
| 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 = "nn4_rect" |
Private Member Functions | |
| void | buildFFTVolume () |
| void | buildNormVolume () |
| void | load_default_settings () |
Private Attributes | |
| EMData * | m_volume |
| EMData * | m_wptr |
| string | m_symmetry |
| int | m_weighting |
| int | m_vnx |
| int | m_vny |
| int | m_vnz |
| int | m_npad |
| int | m_nsym |
| int | m_ndim |
| int | m_vnzp |
| int | m_vnyp |
| int | m_vnxp |
| int | m_vnzc |
| int | m_vnyc |
| int | m_vnxc |
| int | m_count |
| float | m_xratio |
| float | m_yratio |
| float | m_zratio |
| float | m_xscale |
| float | m_yscale |
| int | m_sizeofprojection |
| float | m_wghta |
| float | m_wghtb |
| float | m_osnr |
Definition at line 819 of file reconstructor.h.
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Definition at line 2393 of file reconstructor.cpp. References m_volume, and m_wptr.
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Definition at line 2399 of file reconstructor.cpp. References load_default_settings(), m_volume, m_wptr, EMAN::Reconstructor::print_params(), and setup(). 02400 {
02401 m_volume = NULL;
02402 m_wptr = NULL;
02403 setup( symmetry, size, npad );
02404 load_default_settings();
02405 print_params();
02406 }
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Definition at line 2408 of file reconstructor.cpp. 02409 {
02410 //if( m_delete_volume ) checked_delete(m_volume);
02411
02412 //if( m_delete_weight ) checked_delete( m_wptr );
02413
02414 //checked_delete( m_result );
02415 }
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Definition at line 2482 of file reconstructor.cpp. References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), m_npad, 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(). 02482 {
02483 int offset = 2 - m_vnxp%2;
02484
02485 m_volume = params["fftvol"];
02486
02487 if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
02488 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
02489 m_volume->to_zero();
02490 }
02491 // ----------------------------------------------------------------
02492 // Added by Zhengfan Yang on 03/15/07
02493 // Original author: please check whether my revision is correct and
02494 // other Reconstructor need similiar revision.
02495 if ( m_vnxp % 2 == 0 ) m_volume->set_fftodd(0);
02496 else m_volume->set_fftodd(1);
02497 // ----------------------------------------------------------------
02498
02499 m_volume->set_nxc(m_vnxp/2);
02500 m_volume->set_complex(true);
02501 m_volume->set_ri(true);
02502 m_volume->set_fftpad(true);
02503 m_volume->set_attr("npad", m_npad);
02504 m_volume->set_array_offsets(0,1,1);
02505 }
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Definition at line 2507 of file reconstructor.cpp. References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), 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(). 02507 {
02508
02509 m_wptr = params["weight"];
02510
02511 if( m_wptr->get_xsize() != m_vnxc+1 &&
02512 m_wptr->get_ysize() != m_vnyp &&
02513 m_wptr->get_zsize() != m_vnzp ) {
02514 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
02515 m_wptr->to_zero();
02516 }
02517
02518 m_wptr->set_array_offsets(0,1,1);
02519 }
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Finish reconstruction and return the complete model.
Reimplemented from EMAN::Reconstructor. Definition at line 2722 of file reconstructor.cpp. References abs, circumf_rect(), EMAN::EMData::depad(), EMAN::EMData::do_ift_inplace(), EMAN::EMData::get_attr(), m_ndim, m_vnyc, m_vnyp, m_volume, m_weighting, m_wghta, m_wptr, max, max2d(), max3d(), EMAN::EMData::set_array_offsets(), and EMAN::EMData::symplane0_rect(). 02723 {
02724
02725 if( m_ndim==3 ) {
02726 m_volume->symplane0_rect(m_wptr);
02727 } else {
02728 for( int i=1; i <= m_vnyp; ++i ) {
02729
02730 if( (*m_wptr)(0, i, 1)==0.0 ) {
02731 int j = m_vnyp + 1 - i;
02732 (*m_wptr)(0, i, 1) = (*m_wptr)(0, j, 1);
02733 (*m_volume)(0, i, 1) = (*m_volume)(0, j, 1);
02734 (*m_volume)(1, i, 1) = (*m_volume)(1, j, 1);
02735 }
02736 }
02737 }
02738
02739
02740 int box = 7;
02741 int kc = (box-1)/2;
02742 vector< float > pow_a( m_ndim*kc+1, 1.0 );
02743 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
02744 pow_a.back()=0.0;
02745
02746 float alpha = 0.0;
02747 if( m_ndim==3) {
02748 int vol = box*box*box;
02749 float max = max3d( kc, pow_a );
02750 alpha = ( 1.0f - 1.0f/(float)vol ) / max;
02751 } else {
02752 int ara = box*box;
02753 float max = max2d( kc, pow_a );
02754 alpha = ( 1.0f - 1.0f/(float)ara ) / max;
02755 }
02756
02757 int ix,iy,iz;
02758 for (iz = 1; iz <= m_vnzp; iz++) {
02759 for (iy = 1; iy <= m_vnyp; iy++) {
02760 for (ix = 0; ix <= m_vnxc; ix++) {
02761 if ( (*m_wptr)(ix,iy,iz) > 0) {//(*v) should be treated as complex!!
02762 float tmp;
02763 tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+m_osnr);
02764
02765 if( m_weighting == ESTIMATE ) {
02766 int cx = ix;
02767 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
02768 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
02769 float sum = 0.0;
02770 for( int ii = -kc; ii <= kc; ++ii ) {
02771 int nbrcx = cx + ii;
02772 if( nbrcx >= m_vnxc ) continue;
02773 for( int jj= -kc; jj <= kc; ++jj ) {
02774 int nbrcy = cy + jj;
02775 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
02776
02777 int kcz = (m_ndim==3) ? kc : 0;
02778 for( int kk = -kcz; kk <= kcz; ++kk ) {
02779 int nbrcz = cz + kk;
02780 if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
02781 if( nbrcx < 0 ) {
02782 nbrcx = -nbrcx;
02783 nbrcy = -nbrcy;
02784 nbrcz = -nbrcz;
02785 }
02786 int nbrix = nbrcx;
02787 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
02788 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
02789 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
02790 int c = m_ndim*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
02791 sum = sum + pow_a[c];
02792 }
02793 }
02794 }
02795 }
02796 float wght = 1.0f / ( 1.0f - alpha * sum );
02797 tmp = tmp * wght;
02798 }
02799 (*m_volume)(2*ix,iy,iz) *= tmp;
02800 (*m_volume)(2*ix+1,iy,iz) *= tmp;
02801 }
02802 }
02803 }
02804 }
02805
02806 //if(m_ndim==2) printImage( m_volume );
02807
02808 // back fft
02809 m_volume->do_ift_inplace();
02810
02811
02812 int npad = m_volume->get_attr("npad");
02813 m_volume->depad();
02814 circumf_rect( m_volume, npad );
02815 //circumf_rect_new( m_volume, npad,m_xratio,m_yratio);
02816 m_volume->set_array_offsets( 0, 0, 0 );
02817
02818 return 0;
02819 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 847 of file reconstructor.h. 00848 {
00849 return "Direct Fourier inversion routine";
00850 }
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Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase. Definition at line 842 of file reconstructor.h. 00843 {
00844 return NAME;
00845 }
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Implements EMAN::FactoryBase. Definition at line 857 of file reconstructor.h. References EMAN::TypeDict::put(). 00858 {
00859 TypeDict d;
00860 d.put("sizeprojection", EMObject::INT);
00861 d.put("sizex", EMObject::INT);
00862 d.put("sizey", EMObject::INT);
00863 d.put("sizez", EMObject::INT);
00864 d.put("xratio", EMObject::FLOAT);
00865 d.put("yratio", EMObject::FLOAT);
00866 d.put("npad", EMObject::INT);
00867 d.put("sign", EMObject::INT);
00868 d.put("ndim", EMObject::INT);
00869 d.put("snr", EMObject::FLOAT);
00870 d.put("symmetry", EMObject::STRING);
00871 d.put("snr", EMObject::FLOAT);
00872 d.put("fftvol", EMObject::EMDATA);
00873 d.put("weight", EMObject::EMDATA);
00874 d.put("weighting", EMObject::INT);
00875 return d;
00876 }
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Definition at line 2628 of file reconstructor.cpp. References Assert, EMAN::Transform::get_sym_proj(), EMAN::EMData::insert_rect_slice(), m_npad, m_sizeofprojection, m_symmetry, m_volume, m_wptr, m_xratio, m_yratio, mult(), and t. 02629 {
02630 Assert( padded != NULL );
02631
02632 vector<Transform> tsym = t.get_sym_proj(m_symmetry);
02633 for (unsigned int isym=0; isym < tsym.size(); isym++) {
02634 m_volume->insert_rect_slice(m_wptr, padded, tsym[isym], m_sizeofprojection, m_xratio, m_yratio, m_npad, mult);
02635 }
02636
02637
02638 return 0;
02639
02640 }
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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 904 of file reconstructor.h. Referenced by nn4_rectReconstructor(). 00905 {
00906 //params["use_weights"] = false;
00907 }
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Definition at line 852 of file reconstructor.h. 00853 {
00854 return new nn4_rectReconstructor();
00855 }
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Definition at line 2437 of file reconstructor.cpp. References buildFFTVolume(), buildNormVolume(), EMAN::Transform::get_nsym(), EMAN::Dict::has_key(), m_ndim, 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, m_xratio, and m_yratio. 02438 {
02439 m_weighting = ESTIMATE;
02440 m_wghta = 0.2f;
02441 m_symmetry = symmetry;
02442 m_npad = npad;
02443 m_nsym = Transform::get_nsym(m_symmetry);
02444
02445 if( params.has_key("sizex") ) m_vnx = params["sizex"];
02446 else if(params.has_key("xratio"))
02447 {
02448 float temp=params["xratio"];
02449 m_vnx=int(float(sizeprojection)*temp);
02450 }
02451 else m_vnx=sizeprojection;
02452
02453 if( params.has_key("sizey") ) m_vny = params["sizey"];
02454 else if (params.has_key("yratio"))
02455 {
02456 float temp=params["yratio"];
02457 m_vny=int(float(sizeprojection)*temp);
02458 }
02459 else m_vny=sizeprojection;
02460
02461 if( params.has_key("sizez") )
02462 m_vnz = params["sizez"];
02463 else
02464 m_vnz = (m_ndim==3) ? sizeprojection : 1;
02465
02466 m_xratio=float(m_vnx)/float(sizeprojection);
02467 m_yratio=float(m_vny)/float(sizeprojection);
02468
02469 m_vnxp = m_vnx*npad;
02470 m_vnyp = m_vny*npad;
02471 m_vnzp = (m_ndim==3) ? m_vnz*npad : 1;
02472
02473 m_vnxc = m_vnxp/2;
02474 m_vnyc = m_vnyp/2;
02475 m_vnzc = (m_ndim==3) ? m_vnzp/2 : 1;
02476
02477 buildFFTVolume();
02478 buildNormVolume();
02479 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 2418 of file reconstructor.cpp. References EMAN::Dict::has_key(), m_count, m_ndim, m_osnr, and m_sizeofprojection. Referenced by nn4_rectReconstructor(). 02419 {
02420 m_sizeofprojection = params["sizeprojection"];
02421 int npad = params["npad"];
02422 m_count=0;
02423
02424 string symmetry;
02425 if( params.has_key("symmetry") ) symmetry = params["symmetry"].to_str();
02426 else symmetry = "c1";
02427
02428 if( params.has_key("ndim") ) m_ndim = params["ndim"];
02429 else m_ndim = 3;
02430
02431 if( params.has_key( "snr" ) ) m_osnr = 1.0f/float( params["snr"] );
02432 else m_osnr = 0.0;
02433
02434 setup( symmetry, m_sizeofprojection, npad );
02435 }
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Definition at line 895 of file reconstructor.h. Referenced by setup(). |
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Definition at line 892 of file reconstructor.h. |
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Definition at line 890 of file reconstructor.h. Referenced by buildFFTVolume(), insert_padfft_slice(), and setup(). |
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Definition at line 891 of file reconstructor.h. Referenced by setup(). |
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Definition at line 903 of file reconstructor.h. Referenced by setup(). |
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Definition at line 898 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 887 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 889 of file reconstructor.h. Referenced by setup(). |
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Definition at line 894 of file reconstructor.h. Referenced by buildNormVolume(), and setup(). |
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Definition at line 893 of file reconstructor.h. Referenced by buildFFTVolume(), and setup(). |
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Definition at line 889 of file reconstructor.h. Referenced by setup(). |
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Definition at line 894 of file reconstructor.h. |
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Definition at line 893 of file reconstructor.h. Referenced by buildFFTVolume(), buildNormVolume(), finish(), and setup(). |
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Definition at line 889 of file reconstructor.h. Referenced by setup(). |
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Definition at line 894 of file reconstructor.h. Referenced by setup(). |
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Definition at line 893 of file reconstructor.h. Referenced by buildFFTVolume(), buildNormVolume(), and setup(). |
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Definition at line 885 of file reconstructor.h. Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), and nn4_rectReconstructor(). |
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Definition at line 888 of file reconstructor.h. |
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Definition at line 901 of file reconstructor.h. |
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Definition at line 902 of file reconstructor.h. |
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Definition at line 886 of file reconstructor.h. Referenced by buildNormVolume(), finish(), insert_padfft_slice(), and nn4_rectReconstructor(). |
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Definition at line 896 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 897 of file reconstructor.h. |
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Definition at line 896 of file reconstructor.h. Referenced by insert_padfft_slice(), and setup(). |
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Definition at line 897 of file reconstructor.h. |
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Definition at line 896 of file reconstructor.h. |
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Definition at line 82 of file reconstructor.cpp. |
1.3.9.1