EMAN::nn4_ctfReconstructor Class Reference

nn4_ctf Direct Fourier Inversion Reconstructor More...

#include <reconstructor.h>

Inheritance diagram for EMAN::nn4_ctfReconstructor:

Collaboration diagram for EMAN::nn4_ctfReconstructor:

List of all members.

Public Member Functions

nn4_ctfReconstructor ()

nn4_ctfReconstructor (const string &symmetry, int size, int npad, float snr, int sign)

virtual ~nn4_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 *padfft, const Transform &trans, int mult=1)

int insert_buffed_slice (const EMData *buffer, int mult)

Static Public Member Functions

static Reconstructor * NEW ()

Static Public Attributes

static const string NAME = "nn4_ctf"

Private Member Functions

void buildFFTVolume ()

void buildNormVolume ()

Private Attributes

EMData * m_volume

EMData * m_result

EMData * m_wptr

bool m_delete_volume

bool m_delete_weight

int m_vnx

int m_vny

int m_vnz

int m_vnzp

int m_vnyp

int m_vnxp

int m_vnxc

int m_vnyc

int m_vnzc

int m_npad

int m_sign

int m_varsnr

int m_weighting

float m_wghta

float m_wghtb

float m_snr

string m_symmetry

int m_nsym

Detailed Description

nn4_ctf Direct Fourier Inversion Reconstructor

Definition at line 967 of file reconstructor.h.

Constructor & Destructor Documentation

nn4_ctfReconstructor::nn4_ctfReconstructor ( )

Definition at line 2720 of file reconstructor.cpp.

References m_result, m_volume, and m_wptr.

Referenced by NEW().

02721 {
02722         m_volume  = NULL;
02723         m_wptr    = NULL;
02724         m_result  = NULL;
02725 }

nn4_ctfReconstructor::nn4_ctfReconstructor	(	const string &	symmetry,
		int	size,
		int	npad,
		float	snr,
		int	sign
	)

Definition at line 2727 of file reconstructor.cpp.

References setup().

02728 {
02729         setup( symmetry, size, npad, snr, sign );
02730 }

nn4_ctfReconstructor::~nn4_ctfReconstructor ( ) [virtual]

Definition at line 2732 of file reconstructor.cpp.

References checked_delete(), m_delete_volume, m_delete_weight, m_result, m_volume, and m_wptr.

02733 {
02734         if( m_delete_volume ) checked_delete(m_volume);
02735 
02736         if( m_delete_weight ) checked_delete( m_wptr );
02737 
02738         checked_delete( m_result );
02739 }

Member Function Documentation

void nn4_ctfReconstructor::setup ( ) [virtual]

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 2741 of file reconstructor.cpp.

References EMAN::Dict::has_key(), m_varsnr, EMAN::FactoryBase::params, and sign.

Referenced by nn4_ctfReconstructor().

02742 {
02743         if( ! params.has_key("size") ) throw std::logic_error("Error: image size is not given");
02744 
02745         int size = params["size"];
02746         int npad = params.has_key("npad") ? int(params["npad"]) : 4;
02747         // int sign = params.has_key("sign") ? int(params["sign"]) : 1;
02748         int sign = 1;
02749         string symmetry = params.has_key("symmetry")? params["symmetry"].to_str() : "c1";
02750 
02751         float snr = params["snr"];
02752 
02753     m_varsnr = params.has_key("varsnr") ? int(params["varsnr"]) : 0;
02754         setup( symmetry, size, npad, snr, sign );
02755 
02756 }

int nn4_ctfReconstructor::insert_slice	(	const EMData *const	slice,
		const Transform &	euler,
		const float	weight = `1.0`
	)			`[virtual]`

Insert a slice into a 3D volume, in a given orientation.

Returns:: 0 if successful, 1 otherwise

Parameters:

	slice	the image slice to be inserted into the 3D volume
	euler	Euler angle of this image slice.
	weight	A weighting factor for this slice, generally the number of particles in a class-average. May be ignored by some reconstructors

Returns:: 0 if OK. 1 if error.

Exceptions:

	NullPointerException	if the input EMData pointer is null
	ImageFormatException	if the image is complex as opposed to real

Reimplemented from EMAN::Reconstructor.

Definition at line 2843 of file reconstructor.cpp.

References Assert, checked_delete(), EMAN::EMData::get_attr_default(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), insert_buffed_slice(), insert_padfft_slice(), LOGERR, m_npad, m_vnx, mult(), and EMAN::padfft_slice().

02844 {
02845         // sanity checks
02846         if (!slice) {
02847                 LOGERR("try to insert NULL slice");
02848                 return 1;
02849         }
02850 
02851         int buffed = slice->get_attr_default( "buffed", 0 );
02852         if( buffed > 0 )
02853         {
02854             int mult = slice->get_attr_default( "mult", 1 );
02855             insert_buffed_slice( slice, mult );
02856             return 0;
02857         }
02858 
02859         int padffted= slice->get_attr_default("padffted", 0);
02860         if( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  )
02861         {
02862                 // FIXME: Why doesn't this throw an exception?
02863                 LOGERR("Tried to insert a slice that is the wrong size.");
02864                 return 1;
02865         }
02866 
02867         EMData* padfft = NULL;
02868 
02869         if( padffted != 0 ) padfft = new EMData(*slice);
02870         else                padfft = padfft_slice( slice, t, m_npad );
02871 
02872         int mult= slice->get_attr_default("mult", 1);
02873 
02874         Assert( mult > 0 );
02875         insert_padfft_slice( padfft, t, mult );
02876 
02877         checked_delete( padfft );
02878 
02879         return 0;
02880 }

EMData * nn4_ctfReconstructor::finish ( bool doift = true ) [virtual]

Finish reconstruction and return the complete model.

Parameters:

doift

A flag indicating whether the returned object should be guaranteed to be in real-space (true) or should be left in whatever space the reconstructor generated

Returns:: The result 3D model.

Reimplemented from EMAN::Reconstructor.

Definition at line 2923 of file reconstructor.cpp.

References abs, circumference(), EMAN::EMData::copy(), EMAN::EMData::depad(), EMAN::EMData::do_ift_inplace(), ESTIMATE, m_result, m_sign, m_snr, m_varsnr, m_vnxc, m_vnyc, m_vnyp, m_vnzc, m_vnzp, m_volume, m_weighting, m_wghta, m_wptr, max, max3d(), EMAN::EMData::set_array_offsets(), sqrt(), and EMAN::EMData::symplane0_ctf().

02924 {
02925         m_volume->set_array_offsets(0, 1, 1);
02926         m_wptr->set_array_offsets(0, 1, 1);
02927         m_volume->symplane0_ctf(m_wptr);
02928 
02929         int box = 7;
02930         int vol = box*box*box;
02931         int kc = (box-1)/2;
02932         vector< float > pow_a( 3*kc+1, 1.0 );
02933         for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
02934         pow_a[3*kc]=0.0;
02935 
02936 
02937         float max = max3d( kc, pow_a );
02938         float alpha = ( 1.0f - 1.0f/(float)vol ) / max;
02939         float osnr = 1.0f/m_snr;
02940 
02941         // normalize
02942         int ix,iy,iz;
02943         for (iz = 1; iz <= m_vnzp; iz++) {
02944                 for (iy = 1; iy <= m_vnyp; iy++) {
02945                         for (ix = 0; ix <= m_vnxc; ix++) {
02946                                 if ( (*m_wptr)(ix,iy,iz) > 0.0f) {//(*v) should be treated as complex!!
02947                     int iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
02948                     int izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
02949                     float tmp=0.0;
02950                     if( m_varsnr )
02951                     {
02952                                             float freq = sqrt( (float)(ix*ix+iyp*iyp+izp*izp) );
02953                         tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr)*m_sign;
02954                     }
02955                     else
02956                     {
02957                         tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+osnr)*m_sign;
02958                     }
02959 
02960                                         if( m_weighting == ESTIMATE ) {
02961                                                 int cx = ix;
02962                                                 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
02963                                                 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
02964                                                 float sum = 0.0;
02965                                                 for( int ii = -kc; ii <= kc; ++ii ) {
02966                                                         int nbrcx = cx + ii;
02967                                                         if( nbrcx >= m_vnxc ) continue;
02968                                                         for( int jj= -kc; jj <= kc; ++jj ) {
02969                                                                 int nbrcy = cy + jj;
02970                                                                 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
02971                                                                 for( int kk = -kc; kk <= kc; ++kk ) {
02972                                                                         int nbrcz = cz + jj;
02973                                                                         if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
02974                                                                         if( nbrcx < 0 ) {
02975                                                                                 nbrcx = -nbrcx;
02976                                                                                 nbrcy = -nbrcy;
02977                                                                                 nbrcz = -nbrcz;
02978                                                                         }
02979 
02980                                                                         int nbrix = nbrcx;
02981                                                                         int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
02982                                                                         int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
02983                                                                         if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0.0 ) {
02984                                                                                 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
02985                                                                                 sum = sum + pow_a[c];
02986                                                                                   // if(ix%20==0 && iy%20==0 && iz%20==0)
02987                                                                                  //   std::cout << boost::format( "%4d %4d %4d %4d %10.3f" ) % nbrix % nbriy % nbriz % c % sum << std::endl;
02988                                                                         }
02989                                                                 }
02990                                                         }
02991                                                 }
02992                                                 float wght = 1.0f / ( 1.0f - alpha * sum );
02993 /*
02994                         if(ix%10==0 && iy%10==0)
02995                         {
02996                             std::cout << boost::format( "%4d %4d %4d " ) % ix % iy %iz;
02997                             std::cout << boost::format( "%10.3f %10.3f %10.3f " )  % tmp % wght % sum;
02998                             std::  << boost::format( "%10.3f %10.3e " ) % pow_b[r] % alpha;
02999                             std::cout << std::endl;
03000                         }
03001  */
03002                                                 tmp = tmp * wght;
03003                                         }
03004                                         (*m_volume)(2*ix,iy,iz) *= tmp;
03005                                         (*m_volume)(2*ix+1,iy,iz) *= tmp;
03006                                 }
03007                         }
03008                 }
03009         }
03010 
03011     // back fft
03012     m_volume->do_ift_inplace();
03013     m_volume->depad();
03014     circumference( m_volume );
03015     m_volume->set_array_offsets( 0, 0, 0 );
03016     m_result = m_volume->copy();
03017     return m_result;
03018 }

virtual string EMAN::nn4_ctfReconstructor::get_name ( ) const [inline, virtual]

Get the unique name of this class (especially for factory based instantiation access).

Returns:: the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 991 of file reconstructor.h.

References NAME.

00992                 {
00993                         return NAME;
00994                 }

virtual string EMAN::nn4_ctfReconstructor::get_desc ( ) const [inline, virtual]

Get a clear, concise description of this class.

Returns:: a clear, concise description of this class

Implements EMAN::FactoryBase.

Definition at line 996 of file reconstructor.h.

00997                 {
00998                         return "Direct Fourier inversion reconstruction routine";
00999                 }

static Reconstructor* EMAN::nn4_ctfReconstructor::NEW ( ) [inline, static]

Definition at line 1001 of file reconstructor.h.

References nn4_ctfReconstructor().

01002                 {
01003                         return new nn4_ctfReconstructor();
01004                 }

TypeDict EMAN::nn4_ctfReconstructor::get_param_types ( ) const [inline, virtual]

Returns:: a TypeDict defining and describing the feasible parameters of this class

Implements EMAN::FactoryBase.

Definition at line 1007 of file reconstructor.h.

References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.

01008                 {
01009                         TypeDict d;
01010                         d.put("size",           EMObject::INT);
01011                         d.put("npad",           EMObject::INT);
01012                         d.put("sign",           EMObject::INT);
01013                         d.put("symmetry",       EMObject::STRING);
01014                         d.put("snr",            EMObject::FLOAT);
01015                         d.put("fftvol",         EMObject::EMDATA);
01016                         d.put("weight",         EMObject::EMDATA);
01017             d.put("weighting",  EMObject::INT);
01018             d.put("varsnr",     EMObject::INT);
01019                         return d;
01020                 }

void nn4_ctfReconstructor::setup	(	const string &	symmetry,
		int	size,
		int	npad,
		float	snr,
		int	sign
	)

Definition at line 2758 of file reconstructor.cpp.

References buildFFTVolume(), buildNormVolume(), ESTIMATE, EMAN::Transform::get_nsym(), EMAN::Dict::has_key(), 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, NONE, and EMAN::FactoryBase::params.

02759 {
02760         m_weighting = ESTIMATE;
02761         if( params.has_key("weighting") ) {
02762                 int tmp = int( params["weighting"] );
02763                 if( tmp==0 ) m_weighting = NONE;
02764         }
02765 
02766 
02767 
02768         m_wghta = 0.2f;
02769         m_wghtb = 0.004f;
02770 
02771         m_symmetry = symmetry;
02772         m_npad = npad;
02773         m_sign = sign;
02774         m_nsym = Transform::get_nsym(m_symmetry);
02775 
02776         m_snr = snr;
02777 
02778         m_vnx = size;
02779         m_vny = size;
02780         m_vnz = size;
02781 
02782         m_vnxp = size*npad;
02783         m_vnyp = size*npad;
02784         m_vnzp = size*npad;
02785 
02786         m_vnxc = m_vnxp/2;
02787         m_vnyc = m_vnyp/2;
02788         m_vnzc = m_vnzp/2;
02789 
02790         buildFFTVolume();
02791         buildNormVolume();
02792 }

int nn4_ctfReconstructor::insert_padfft_slice	(	EMData *	padfft,
		const Transform &	trans,
		int	mult = `1`
	)

Definition at line 2905 of file reconstructor.cpp.

References Assert, EMAN::EMData::get_attr(), EMAN::Transform::get_sym(), m_nsym, m_symmetry, m_volume, m_wptr, EMAN::EMData::nn_ctf(), and EMAN::EMData::nn_ctf_applied().

Referenced by insert_slice().

02906 {
02907         Assert( padfft != NULL );
02908         float tmp = padfft->get_attr("ctf_applied");
02909         int   ctf_applied = (int) tmp;
02910 
02911         for( int isym=0; isym < m_nsym; isym++) {
02912                 Transform tsym = t.get_sym( m_symmetry, isym );
02913 
02914                 if(ctf_applied) m_volume->nn_ctf_applied(m_wptr, padfft, tsym, mult);
02915                 else            m_volume->nn_ctf(m_wptr, padfft, tsym, mult);
02916         }
02917 
02918         return 0;
02919 
02920 }

int nn4_ctfReconstructor::insert_buffed_slice	(	const EMData *	buffer,
		int	mult
	)

Definition at line 2882 of file reconstructor.cpp.

References EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), m_volume, and m_wptr.

Referenced by insert_slice().

02883 {
02884         const float* bufdata = buffed->get_data();
02885         float* cdata = m_volume->get_data();
02886         float* wdata = m_wptr->get_data();
02887 
02888         int npoint = buffed->get_xsize()/4;
02889         for( int i=0; i < npoint; ++i ) {
02890 
02891                int pos2 = int( bufdata[4*i] );
02892                int pos1 = pos2 * 2;
02893                cdata[pos1  ] += bufdata[4*i+1]*mult;
02894                cdata[pos1+1] += bufdata[4*i+2]*mult;
02895                wdata[pos2  ] += bufdata[4*i+3]*mult;
02896 /*
02897         std::cout << "pos1, pos2, ctfv1, ctfv2, ctf2: ";
02898         std::cout << pos1 << " " << bufdata[5*i+1] << " " << bufdata[5*i+2] << " ";
02899         std::cout << pos2 << " " << bufdata[5*i+4] << std::endl;
02900  */
02901         }
02902         return 0;
02903 }

void nn4_ctfReconstructor::buildFFTVolume ( ) [private]

Definition at line 2794 of file reconstructor.cpp.

References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), m_delete_volume, m_npad, m_vnxp, m_vnyp, m_vnzp, m_volume, EMAN::FactoryBase::params, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_attr(), EMAN::EMData::set_complex(), EMAN::EMData::set_fftpad(), EMAN::EMData::set_nxc(), EMAN::EMData::set_ri(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero().

Referenced by setup().

02794                                           {
02795         int offset = 2 - m_vnxp%2;
02796         if( params.has_key("fftvol") ) {
02797             m_volume = params["fftvol"];
02798             m_delete_volume = false;
02799         } else {
02800             m_volume = new EMData();
02801             m_delete_volume = true;
02802         }
02803 
02804         if( m_volume->get_xsize() != m_vnxp+offset &&
02805             m_volume->get_ysize() != m_vnyp &&
02806             m_volume->get_zsize() != m_vnzp )
02807         {
02808             m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
02809             m_volume->to_zero();
02810         }
02811 
02812         m_volume->set_nxc(m_vnxp/2);
02813         m_volume->set_complex(true);
02814         m_volume->set_ri(true);
02815         m_volume->set_fftpad(true);
02816         m_volume->set_attr("npad", m_npad);
02817         m_volume->set_array_offsets(0,1,1);
02818 }

void nn4_ctfReconstructor::buildNormVolume ( ) [private]

Definition at line 2820 of file reconstructor.cpp.

References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), 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().

02821 {
02822         if( params.has_key("weight") )
02823         {
02824             m_wptr = params["weight"];
02825             m_delete_weight = false;
02826         } else {
02827             m_wptr = new EMData();
02828             m_delete_weight = true;
02829         }
02830 
02831         if( m_wptr->get_xsize() != m_vnxc+1 &&
02832             m_wptr->get_ysize() != m_vnyp &&
02833             m_wptr->get_zsize() != m_vnzp )
02834         {
02835             m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
02836             m_wptr->to_zero();
02837         }
02838 
02839         m_wptr->set_array_offsets(0,1,1);
02840 
02841 }

Member Data Documentation

const string nn4_ctfReconstructor::NAME = "nn4_ctf" [static]

Definition at line 1028 of file reconstructor.h.

Referenced by get_name().

EMData* EMAN::nn4_ctfReconstructor::m_volume [private]

Definition at line 1031 of file reconstructor.h.

Referenced by buildFFTVolume(), finish(), insert_buffed_slice(), insert_padfft_slice(), nn4_ctfReconstructor(), and ~nn4_ctfReconstructor().

EMData* EMAN::nn4_ctfReconstructor::m_result [private]

Definition at line 1032 of file reconstructor.h.

Referenced by finish(), nn4_ctfReconstructor(), and ~nn4_ctfReconstructor().

EMData* EMAN::nn4_ctfReconstructor::m_wptr [private]

Definition at line 1033 of file reconstructor.h.

Referenced by buildNormVolume(), finish(), insert_buffed_slice(), insert_padfft_slice(), nn4_ctfReconstructor(), and ~nn4_ctfReconstructor().

bool EMAN::nn4_ctfReconstructor::m_delete_volume [private]

Definition at line 1034 of file reconstructor.h.

Referenced by buildFFTVolume(), and ~nn4_ctfReconstructor().

bool EMAN::nn4_ctfReconstructor::m_delete_weight [private]

Definition at line 1035 of file reconstructor.h.

Referenced by buildNormVolume(), and ~nn4_ctfReconstructor().

int EMAN::nn4_ctfReconstructor::m_vnx [private]

Definition at line 1036 of file reconstructor.h.

Referenced by insert_slice(), and setup().

int EMAN::nn4_ctfReconstructor::m_vny [private]

Definition at line 1036 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_ctfReconstructor::m_vnz [private]

Definition at line 1036 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_ctfReconstructor::m_vnzp [private]

Definition at line 1037 of file reconstructor.h.

Referenced by buildFFTVolume(), buildNormVolume(), finish(), and setup().

int EMAN::nn4_ctfReconstructor::m_vnyp [private]

Definition at line 1037 of file reconstructor.h.

Referenced by buildFFTVolume(), buildNormVolume(), finish(), and setup().

int EMAN::nn4_ctfReconstructor::m_vnxp [private]

Definition at line 1037 of file reconstructor.h.

Referenced by buildFFTVolume(), and setup().

int EMAN::nn4_ctfReconstructor::m_vnxc [private]

Definition at line 1038 of file reconstructor.h.

Referenced by buildNormVolume(), finish(), and setup().

int EMAN::nn4_ctfReconstructor::m_vnyc [private]

Definition at line 1038 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4_ctfReconstructor::m_vnzc [private]

Definition at line 1038 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4_ctfReconstructor::m_npad [private]

Definition at line 1039 of file reconstructor.h.

Referenced by buildFFTVolume(), insert_slice(), and setup().

int EMAN::nn4_ctfReconstructor::m_sign [private]

Definition at line 1040 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4_ctfReconstructor::m_varsnr [private]

Definition at line 1041 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4_ctfReconstructor::m_weighting [private]

Definition at line 1042 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4_ctfReconstructor::m_wghta [private]

Definition at line 1043 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4_ctfReconstructor::m_wghtb [private]

Definition at line 1043 of file reconstructor.h.

Referenced by setup().

float EMAN::nn4_ctfReconstructor::m_snr [private]

Definition at line 1044 of file reconstructor.h.

Referenced by finish(), and setup().

string EMAN::nn4_ctfReconstructor::m_symmetry [private]

Definition at line 1045 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

int EMAN::nn4_ctfReconstructor::m_nsym [private]

Definition at line 1046 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

The documentation for this class was generated from the following files:


Public Member Functions
	nn4_ctfReconstructor ()
	nn4_ctfReconstructor (const string &symmetry, int size, int npad, float snr, int sign)
virtual	~nn4_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 *padfft, const Transform &trans, int mult=1)
int	insert_buffed_slice (const EMData *buffer, int mult)
Static Public Member Functions
static Reconstructor *	NEW ()
Static Public Attributes
static const string	NAME = "nn4_ctf"
Private Member Functions
void	buildFFTVolume ()
void	buildNormVolume ()
Private Attributes
EMData *	m_volume
EMData *	m_result
EMData *	m_wptr
bool	m_delete_volume
bool	m_delete_weight
int	m_vnx
int	m_vny
int	m_vnz
int	m_vnzp
int	m_vnyp
int	m_vnxp
int	m_vnxc
int	m_vnyc
int	m_vnzc
int	m_npad
int	m_sign
int	m_varsnr
int	m_weighting
float	m_wghta
float	m_wghtb
float	m_snr
string	m_symmetry
int	m_nsym