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EMAN::nn4_ctfReconstructor Class Reference

nn4_ctf Direct Fourier Inversion Reconstructor More...

#include <reconstructor.h>

Inheritance diagram for EMAN::nn4_ctfReconstructor:

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Collaboration diagram for EMAN::nn4_ctfReconstructor:

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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 EMDatafinish (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

ReconstructorNEW ()

Static Public Attributes

const string NAME = "nn4_ctf"

Private Member Functions

void buildFFTVolume ()
void buildNormVolume ()

Private Attributes

EMDatam_volume
EMDatam_result
EMDatam_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 996 of file reconstructor.h.


Constructor & Destructor Documentation

nn4_ctfReconstructor::nn4_ctfReconstructor  ) 
 

Definition at line 3079 of file reconstructor.cpp.

References m_result, m_volume, and m_wptr.

03080 {
03081         m_volume  = NULL;
03082         m_wptr    = NULL;
03083         m_result  = NULL;
03084 }

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

Definition at line 3086 of file reconstructor.cpp.

References setup(), and sign.

03087 {
03088         setup( symmetry, size, npad, snr, sign );
03089 }

nn4_ctfReconstructor::~nn4_ctfReconstructor  )  [virtual]
 

Definition at line 3091 of file reconstructor.cpp.

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

03092 {
03093         if( m_delete_volume ) checked_delete(m_volume);
03094 
03095         if( m_delete_weight ) checked_delete( m_wptr );
03096 
03097         checked_delete( m_result );
03098 }


Member Function Documentation

void nn4_ctfReconstructor::buildFFTVolume  )  [private]
 

Definition at line 3153 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::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().

03153                                           {
03154         int offset = 2 - m_vnxp%2;
03155         if( params.has_key("fftvol") ) {
03156                 m_volume = params["fftvol"];
03157                 m_delete_volume = false;
03158         } else {
03159                 m_volume = new EMData();
03160                 m_delete_volume = true;
03161         }
03162 
03163         if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
03164                 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
03165                 m_volume->to_zero();
03166         }
03167 
03168         m_volume->set_nxc(m_vnxp/2);
03169         m_volume->set_complex(true);
03170         m_volume->set_ri(true);
03171         m_volume->set_fftpad(true);
03172         m_volume->set_attr("npad", m_npad);
03173         m_volume->set_array_offsets(0,1,1);
03174 }

void nn4_ctfReconstructor::buildNormVolume  )  [private]
 

Definition at line 3176 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::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero().

Referenced by setup().

03177 {
03178         if( params.has_key("weight") ) {
03179                 m_wptr = params["weight"];
03180                 m_delete_weight = false;
03181         } else {
03182                 m_wptr = new EMData();
03183                 m_delete_weight = true;
03184         }
03185 
03186         if( m_wptr->get_xsize() != m_vnxc+1 && m_wptr->get_ysize() != m_vnyp && m_wptr->get_zsize() != m_vnzp ) {
03187                m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
03188                m_wptr->to_zero();
03189         }
03190 
03191         m_wptr->set_array_offsets(0,1,1);
03192 
03193 }

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 3275 of file reconstructor.cpp.

References abs, circumf(), EMAN::EMData::copy(), EMAN::EMData::depad(), EMAN::EMData::do_ift_inplace(), EMAN::EMData::get_attr(), m_result, m_vnyc, m_vnyp, m_vnzp, m_volume, m_weighting, m_wghta, m_wptr, max, max3d(), EMAN::EMData::set_array_offsets(), sqrt(), and EMAN::EMData::symplane0_ctf().

03276 {
03277         m_volume->set_array_offsets(0, 1, 1);
03278         m_wptr->set_array_offsets(0, 1, 1);
03279         m_volume->symplane0_ctf(m_wptr);
03280 
03281         int box = 7;
03282         int vol = box*box*box;
03283         int kc = (box-1)/2;
03284         vector< float > pow_a( 3*kc+1, 1.0 );
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 
03288 
03289         float max = max3d( kc, pow_a );
03290         float alpha = ( 1.0f - 1.0f/(float)vol ) / max;
03291         float osnr = 1.0f/m_snr;
03292 
03293         // normalize
03294         int ix,iy,iz;
03295         for (iz = 1; iz <= m_vnzp; iz++) {
03296                 for (iy = 1; iy <= m_vnyp; iy++) {
03297                         for (ix = 0; ix <= m_vnxc; ix++) {
03298                                 if ( (*m_wptr)(ix,iy,iz) > 0.0f) {//(*v) should be treated as complex!!
03299                     int iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
03300                     int izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
03301                     float tmp=0.0;
03302                     if( m_varsnr )
03303                     {
03304                                             float freq = sqrt( (float)(ix*ix+iyp*iyp+izp*izp) );
03305                         tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr)*m_sign;
03306                     }
03307                     else
03308                     {
03309                         tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+osnr)*m_sign;
03310                     }
03311 
03312                                         if( m_weighting == ESTIMATE ) {
03313                                                 int cx = ix;
03314                                                 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
03315                                                 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
03316                                                 float sum = 0.0;
03317                                                 for( int ii = -kc; ii <= kc; ++ii ) {
03318                                                         int nbrcx = cx + ii;
03319                                                         if( nbrcx >= m_vnxc ) continue;
03320                                                         for( int jj= -kc; jj <= kc; ++jj ) {
03321                                                                 int nbrcy = cy + jj;
03322                                                                 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
03323                                                                 for( int kk = -kc; kk <= kc; ++kk ) {
03324                                                                         int nbrcz = cz + jj;
03325                                                                         if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
03326                                                                         if( nbrcx < 0 ) {
03327                                                                                 nbrcx = -nbrcx;
03328                                                                                 nbrcy = -nbrcy;
03329                                                                                 nbrcz = -nbrcz;
03330                                                                         }
03331 
03332                                                                         int nbrix = nbrcx;
03333                                                                         int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
03334                                                                         int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
03335                                                                         if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0.0 ) {
03336                                                                                 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
03337                                                                                 sum = sum + pow_a[c];
03338                                                                                   // if(ix%20==0 && iy%20==0 && iz%20==0)
03339                                                                                  //   std::cout << boost::format( "%4d %4d %4d %4d %10.3f" ) % nbrix % nbriy % nbriz % c % sum << std::endl;
03340                                                                         }
03341                                                                 }
03342                                                         }
03343                                                 }
03344                                                 float wght = 1.0f / ( 1.0f - alpha * sum );
03345 /*
03346                         if(ix%10==0 && iy%10==0)
03347                         {
03348                             std::cout << boost::format( "%4d %4d %4d " ) % ix % iy %iz;
03349                             std::cout << boost::format( "%10.3f %10.3f %10.3f " )  % tmp % wght % sum;
03350                             std::  << boost::format( "%10.3f %10.3e " ) % pow_b[r] % alpha;
03351                             std::cout << std::endl;
03352                         }
03353  */
03354                                                 tmp = tmp * wght;
03355                                         }
03356                                         (*m_volume)(2*ix,iy,iz) *= tmp;
03357                                         (*m_volume)(2*ix+1,iy,iz) *= tmp;
03358                                 }
03359                         }
03360                 }
03361         }
03362 
03363         // back fft
03364         m_volume->do_ift_inplace();
03365         int npad = m_volume->get_attr("npad");
03366         m_volume->depad();
03367         circumf( m_volume, npad );
03368         m_volume->set_array_offsets( 0, 0, 0 );
03369         m_result = m_volume->copy();
03370         return m_result;
03371 }

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 1025 of file reconstructor.h.

01026                 {
01027                         return "Direct Fourier inversion reconstruction routine";
01028                 }

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 1020 of file reconstructor.h.

01021                 {
01022                         return NAME;
01023                 }

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 1036 of file reconstructor.h.

References EMAN::TypeDict::put().

01037                 {
01038                         TypeDict d;
01039                         d.put("size",           EMObject::INT);
01040                         d.put("npad",           EMObject::INT);
01041                         d.put("sign",           EMObject::INT);
01042                         d.put("symmetry",       EMObject::STRING);
01043                         d.put("snr",            EMObject::FLOAT);
01044                         d.put("fftvol",         EMObject::EMDATA);
01045                         d.put("weight",         EMObject::EMDATA);
01046             d.put("weighting",  EMObject::INT);
01047             d.put("varsnr",     EMObject::INT);
01048                         return d;
01049                 }

int nn4_ctfReconstructor::insert_buffed_slice const EMData buffer,
int  mult
 

Definition at line 3233 of file reconstructor.cpp.

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

Referenced by insert_slice().

03234 {
03235         const float* bufdata = buffed->get_data();
03236         float* cdata = m_volume->get_data();
03237         float* wdata = m_wptr->get_data();
03238 
03239         int npoint = buffed->get_xsize()/4;
03240         for( int i=0; i < npoint; ++i ) {
03241 
03242                 int pos2 = int( bufdata[4*i] );
03243                 int pos1 = pos2 * 2;
03244                 cdata[pos1  ] += bufdata[4*i+1]*mult;
03245                 cdata[pos1+1] += bufdata[4*i+2]*mult;
03246                 wdata[pos2  ] += bufdata[4*i+3]*mult;
03247 /*
03248         std::cout << "pos1, pos2, ctfv1, ctfv2, ctf2: ";
03249         std::cout << pos1 << " " << bufdata[5*i+1] << " " << bufdata[5*i+2] << " ";
03250         std::cout << pos2 << " " << bufdata[5*i+4] << std::endl;
03251  */
03252         }
03253         return 0;
03254 }

int nn4_ctfReconstructor::insert_padfft_slice EMData padfft,
const Transform trans,
int  mult = 1
 

Definition at line 3256 of file reconstructor.cpp.

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

Referenced by insert_slice().

03257 {
03258         Assert( padfft != NULL );
03259         float tmp = padfft->get_attr("ctf_applied");
03260         int   ctf_applied = (int) tmp;
03261 
03262         for( int isym=0; isym < m_nsym; isym++) {
03263                 Transform tsym = t.get_sym( m_symmetry, isym );
03264 
03265                 if(ctf_applied) m_volume->nn_ctf_applied(m_wptr, padfft, tsym, mult);
03266                                 
03267                 else            m_volume->nn_ctf(m_wptr, padfft, tsym, mult);
03268         }
03269 
03270         return 0;
03271 
03272 }

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 3195 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, mult(), EMAN::padfft_slice(), and t.

03196 {
03197         // sanity checks
03198         if (!slice) {
03199                 LOGERR("try to insert NULL slice");
03200                 return 1;
03201         }
03202 
03203         int buffed = slice->get_attr_default( "buffed", 0 );
03204         if( buffed > 0 ) {
03205                 int mult = slice->get_attr_default( "mult", 1 );
03206                 insert_buffed_slice( slice, mult );
03207                 return 0;
03208         }
03209 
03210         int padffted= slice->get_attr_default("padffted", 0);
03211         if( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  )
03212         {
03213                 // FIXME: Why doesn't this throw an exception?
03214                 LOGERR("Tried to insert a slice that is the wrong size.");
03215                 return 1;
03216         }
03217 
03218         EMData* padfft = NULL;
03219 
03220         if( padffted != 0 ) padfft = new EMData(*slice);
03221         else                padfft = padfft_slice( slice, t, m_npad );
03222 
03223         int mult= slice->get_attr_default("mult", 1);
03224 
03225         Assert( mult > 0 );
03226         insert_padfft_slice( padfft, t, mult );
03227 
03228         checked_delete( padfft );
03229 
03230         return 0;
03231 }

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

Definition at line 1030 of file reconstructor.h.

01031                 {
01032                         return new nn4_ctfReconstructor();
01033                 }

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

Definition at line 3117 of file reconstructor.cpp.

References buildFFTVolume(), buildNormVolume(), 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, and m_wghtb.

03118 {
03119         m_weighting = ESTIMATE;
03120         if( params.has_key("weighting") ) {
03121                 int tmp = int( params["weighting"] );
03122                 if( tmp==0 ) m_weighting = NONE;
03123         }
03124 
03125 
03126 
03127         m_wghta = 0.2f;
03128         m_wghtb = 0.004f;
03129 
03130         m_symmetry = symmetry;
03131         m_npad = npad;
03132         m_sign = sign;
03133         m_nsym = Transform::get_nsym(m_symmetry);
03134 
03135         m_snr = snr;
03136 
03137         m_vnx = size;
03138         m_vny = size;
03139         m_vnz = size;
03140 
03141         m_vnxp = size*npad;
03142         m_vnyp = size*npad;
03143         m_vnzp = size*npad;
03144 
03145         m_vnxc = m_vnxp/2;
03146         m_vnyc = m_vnyp/2;
03147         m_vnzc = m_vnzp/2;
03148 
03149         buildFFTVolume();
03150         buildNormVolume();
03151 }

void nn4_ctfReconstructor::setup  )  [virtual]
 

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 3100 of file reconstructor.cpp.

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

Referenced by nn4_ctfReconstructor().

03101 {
03102         if( ! params.has_key("size") ) throw std::logic_error("Error: image size is not given");
03103 
03104         int size = params["size"];
03105         int npad = params.has_key("npad") ? int(params["npad"]) : 4;
03106         // int sign = params.has_key("sign") ? int(params["sign"]) : 1;
03107         int sign = 1;
03108         string symmetry = params.has_key("symmetry")? params["symmetry"].to_str() : "c1";
03109 
03110         float snr = params["snr"];
03111 
03112         m_varsnr = params.has_key("varsnr") ? int(params["varsnr"]) : 0;
03113         setup( symmetry, size, npad, snr, sign );
03114 
03115 }


Member Data Documentation

bool EMAN::nn4_ctfReconstructor::m_delete_volume [private]
 

Definition at line 1063 of file reconstructor.h.

Referenced by buildFFTVolume().

bool EMAN::nn4_ctfReconstructor::m_delete_weight [private]
 

Definition at line 1064 of file reconstructor.h.

Referenced by buildNormVolume().

int EMAN::nn4_ctfReconstructor::m_npad [private]
 

Definition at line 1068 of file reconstructor.h.

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

int EMAN::nn4_ctfReconstructor::m_nsym [private]
 

Definition at line 1075 of file reconstructor.h.

Referenced by setup().

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

Definition at line 1061 of file reconstructor.h.

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

int EMAN::nn4_ctfReconstructor::m_sign [private]
 

Definition at line 1069 of file reconstructor.h.

Referenced by setup().

float EMAN::nn4_ctfReconstructor::m_snr [private]
 

Definition at line 1073 of file reconstructor.h.

Referenced by setup().

string EMAN::nn4_ctfReconstructor::m_symmetry [private]
 

Definition at line 1074 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

int EMAN::nn4_ctfReconstructor::m_varsnr [private]
 

Definition at line 1070 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_ctfReconstructor::m_vnx [private]
 

Definition at line 1065 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_ctfReconstructor::m_vnxc [private]
 

Definition at line 1067 of file reconstructor.h.

Referenced by buildNormVolume(), and setup().

int EMAN::nn4_ctfReconstructor::m_vnxp [private]
 

Definition at line 1066 of file reconstructor.h.

Referenced by buildFFTVolume(), and setup().

int EMAN::nn4_ctfReconstructor::m_vny [private]
 

Definition at line 1065 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_ctfReconstructor::m_vnyc [private]
 

Definition at line 1067 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nn4_ctfReconstructor::m_vnyp [private]
 

Definition at line 1066 of file reconstructor.h.

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

int EMAN::nn4_ctfReconstructor::m_vnz [private]
 

Definition at line 1065 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_ctfReconstructor::m_vnzc [private]
 

Definition at line 1067 of file reconstructor.h.

Referenced by setup().

int EMAN::nn4_ctfReconstructor::m_vnzp [private]
 

Definition at line 1066 of file reconstructor.h.

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

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

Definition at line 1060 of file reconstructor.h.

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

int EMAN::nn4_ctfReconstructor::m_weighting [private]
 

Definition at line 1071 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4_ctfReconstructor::m_wghta [private]
 

Definition at line 1072 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nn4_ctfReconstructor::m_wghtb [private]
 

Definition at line 1072 of file reconstructor.h.

Referenced by setup().

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

Definition at line 1062 of file reconstructor.h.

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

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

Definition at line 80 of file reconstructor.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Dec 9 13:48:35 2010 for EMAN2 by  doxygen 1.3.9.1