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EMAN::nnSSNR_ctfReconstructor Class Reference

#include <reconstructor.h>

Inheritance diagram for EMAN::nnSSNR_ctfReconstructor:

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Collaboration diagram for EMAN::nnSSNR_ctfReconstructor:

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List of all members.

Public Member Functions

 nnSSNR_ctfReconstructor ()
 nnSSNR_ctfReconstructor (const string &symmetry, int size, int npad, float snr, int sign)
 ~nnSSNR_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 *padded, const Transform &trans, int mult=1)

Static Public Member Functions

static ReconstructorNEW ()

Static Public Attributes

static const string NAME = "nnSSNR_ctf"

Private Member Functions

void buildFFTVolume ()
void buildNormVolume ()
void buildNorm2Volume ()
void buildNorm3Volume ()

Private Attributes

EMDatam_volume
EMDatam_wptr
EMDatam_wptr2
EMDatam_wptr3
EMDatam_result
bool m_delete_volume
bool m_delete_weight
bool m_delete_weight2
bool m_delete_weight3
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
int m_sign
float m_snr
int wiener

Detailed Description

Definition at line 1058 of file reconstructor.h.


Constructor & Destructor Documentation

nnSSNR_ctfReconstructor::nnSSNR_ctfReconstructor  ) 
 

Definition at line 3028 of file reconstructor.cpp.

References m_result, m_volume, m_wptr, m_wptr2, and m_wptr3.

Referenced by NEW().

03029 {
03030     m_volume  = NULL;
03031     m_wptr    = NULL;
03032     m_wptr2   = NULL;
03033     m_wptr3   = NULL;
03034     m_result  = NULL;
03035 }

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

Definition at line 3037 of file reconstructor.cpp.

References m_result, m_volume, m_wptr, m_wptr2, m_wptr3, and setup().

03038 {
03039     m_volume  = NULL;
03040     m_wptr    = NULL;
03041     m_wptr2   = NULL;
03042     m_wptr3   = NULL;
03043     m_result  = NULL;
03044 
03045     setup( symmetry, size, npad, snr, sign );
03046 }

nnSSNR_ctfReconstructor::~nnSSNR_ctfReconstructor  ) 
 

Definition at line 3048 of file reconstructor.cpp.

References checked_delete(), m_delete_volume, m_delete_weight, m_delete_weight2, m_delete_weight3, m_result, m_volume, m_wptr, m_wptr2, and m_wptr3.

03049 {
03050 
03051    if( m_delete_volume )
03052         checked_delete(m_volume);
03053    if( m_delete_weight )
03054         checked_delete( m_wptr );
03055    if ( m_delete_weight2 )
03056         checked_delete( m_wptr2 );
03057    if ( m_delete_weight3 )
03058         checked_delete( m_wptr3 );
03059    checked_delete( m_result );
03060 }


Member Function Documentation

void nnSSNR_ctfReconstructor::buildFFTVolume  )  [private]
 

Definition at line 3109 of file reconstructor.cpp.

References EMAN::Dict::has_key(), m_delete_volume, m_npad, m_vnxc, 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_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().

03109                                              {
03110 
03111         int offset = 2 - m_vnxp%2;
03112         if( params.has_key("fftvol") ) {
03113                 m_volume = params["fftvol"]; /* volume should be defined in python when PMI is turned on*/
03114                 m_delete_volume = false;
03115     } else {
03116                 m_volume = new EMData();
03117                 m_delete_volume = true;
03118         }
03119 
03120         m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
03121         m_volume->to_zero();
03122 
03123         if ( m_vnxp % 2 == 0 ) {
03124                 m_volume->set_fftodd(0);
03125         } else {
03126                 m_volume->set_fftodd(1);
03127         }
03128 
03129         m_volume->set_nxc(m_vnxc);
03130         m_volume->set_complex(true);
03131         m_volume->set_ri(true); //(real, imaginary) instead of polar coordinate
03132         m_volume->set_fftpad(true);
03133         m_volume->set_attr("npad", m_npad);
03134         m_volume->set_array_offsets(0,1,1);
03135 }

void nnSSNR_ctfReconstructor::buildNorm2Volume  )  [private]
 

Definition at line 3152 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().

03152                                                {
03153 
03154         if( params.has_key("weight2") ) {
03155                 m_wptr2          = params["weight2"];
03156                 m_delete_weight2 = false;
03157         } else {
03158                 m_wptr2 = new EMData();
03159                 m_delete_weight2 = true;
03160         }
03161         m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp);
03162         m_wptr2->to_zero();
03163         m_wptr2->set_array_offsets(0,1,1);
03164 }

void nnSSNR_ctfReconstructor::buildNorm3Volume  )  [private]
 

Definition at line 3166 of file reconstructor.cpp.

References EMAN::Dict::has_key(), m_delete_weight3, m_vnxc, m_vnyp, m_vnzp, m_wptr3, EMAN::FactoryBase::params, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero().

Referenced by setup().

03166                                                {
03167 
03168         if( params.has_key("weight3") ) {
03169                 m_wptr3          = params["weight3"];
03170                 m_delete_weight3 = false;
03171         } else {
03172                 m_wptr3 = new EMData();
03173                 m_delete_weight3 = true;
03174         }
03175         m_wptr3->set_size(m_vnxc+1,m_vnyp,m_vnzp);
03176         m_wptr3->to_zero();
03177         m_wptr3->set_array_offsets(0,1,1);
03178 }

void nnSSNR_ctfReconstructor::buildNormVolume  )  [private]
 

Definition at line 3138 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().

03139 {
03140         if( params.has_key("weight") ) {
03141                  m_wptr          = params["weight"];
03142                  m_delete_weight = false;
03143         } else {
03144                 m_wptr = new EMData();
03145                 m_delete_weight = true;
03146         }
03147         m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
03148         m_wptr->to_zero();
03149         m_wptr->set_array_offsets(0,1,1);
03150 }

EMData * nnSSNR_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 3222 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, m_wptr3, 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::symplane2(), EMAN::EMData::to_zero(), and EMAN::EMData::update().

03223 {
03224 /*
03225   I changed the code on 05/15 so it only returns variance.
03226   Lines commented out are marked by //#
03227   The version prior to the currect changes is r1.190
03228   PAP
03229 */
03230         /***
03231             m_volume ctf*(P^2D->3D(F^3D))
03232             m_wptr   ctf^2
03233             m_wptr2  |P^2D->3D(F^3D)|^2
03234             m_wptr3  Kn
03235             nominator = sum_rot [ wght*signal ]
03236             denominator  = sum_rot[ wght*variance ]
03237                                                       ***/
03238         int kz, ky;
03239         int box = 7;
03240         int kc  = (box-1)/2;
03241         float alpha = 0.0;
03242         float argx, argy, argz;
03243         vector< float > pow_a( 3*kc+1, 1.0 );
03244         float w = params["w"];
03245         float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc);
03246         float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc);
03247 #ifdef  _WIN32
03248         float dz2 = 1.0f/_cpp_max(float(m_vnzc),1.0f)/_cpp_max(float(m_vnzc),1.0f);
03249         int inc = Util::round(float(_cpp_max(_cpp_max(m_vnxc,m_vnyc),m_vnzc))/w);
03250 #else
03251         float dz2 = 1.0f/std::max(float(m_vnzc),1.0f)/std::max(float(m_vnzc),1.0f);
03252         int inc = Util::round(float(std::max(std::max(m_vnxc,m_vnyc),m_vnzc))/w);
03253 #endif  //_WIN32
03254 
03255         EMData* SSNR = params["SSNR"];
03256         SSNR->set_size(inc+1,4,1);
03257         //#EMData* vol_ssnr = new EMData();
03258         //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp);
03259         //#vol_ssnr->to_zero();
03260         //#  new linea follow
03261         EMData* vol_ssnr = new EMData();
03262         vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp);
03263         vol_ssnr->to_zero();
03264         if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0);
03265         else                   vol_ssnr->set_fftodd(1);
03266         vol_ssnr->set_nxc(m_vnxc);
03267         vol_ssnr->set_complex(true);
03268         vol_ssnr->set_ri(true);
03269         vol_ssnr->set_fftpad(false);
03270         //#
03271         float *nom    = new float[inc+1];
03272         float *denom  = new float[inc+1];
03273         int  *ka     = new int[inc+1];
03274         int  *nn     = new int[inc+1];
03275         float wght = 1.f;
03276         for (int i = 0; i <= inc; i++) {
03277                 nom[i]   = 0.0f;
03278                 denom[i] = 0.0f;
03279                 nn[i]    = 0;
03280                 ka[i]    = 0;
03281         }
03282         m_volume->symplane2(m_wptr, m_wptr2, m_wptr3);
03283         if ( m_weighting == ESTIMATE ) {
03284                 int vol = box*box*box;
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                 float max = max3d( kc, pow_a );
03288                 alpha = ( 1.0f - 1.0f/(float)vol ) / max;
03289         }
03290         for (int iz = 1; iz <= m_vnzp; iz++) {
03291                 if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1;
03292                 argz = float(kz*kz)*dz2;
03293                 for (int iy = 1; iy <= m_vnyp; iy++) {
03294                         if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1;
03295                         argy = argz + float(ky*ky)*dy2;
03296                         for (int ix = 0; ix <= m_vnxc; ix++) {
03297                                 float Kn = (*m_wptr3)(ix,iy,iz);
03298                                 argx = std::sqrt(argy + float(ix*ix)*dx2);
03299                                 int r = Util::round(float(inc)*argx);
03300                                 if ( r >= 0 && Kn > 4.5f ) {
03301                                         if ( m_weighting == ESTIMATE ) {
03302                                                 int cx = ix;
03303                                                 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
03304                                                 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
03305                                                 float sum = 0.0;
03306                                                 for( int ii = -kc; ii <= kc; ++ii ) {
03307                                                         int nbrcx = cx + ii;
03308                                                         if( nbrcx >= m_vnxc ) continue;
03309                                                         for ( int jj= -kc; jj <= kc; ++jj ) {
03310                                                                 int nbrcy = cy + jj;
03311                                                                 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
03312                                                                 for( int kk = -kc; kk <= kc; ++kk ) {
03313                                                                         int nbrcz = cz + jj;
03314                                                                         if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
03315                                                                         if( nbrcx < 0 ) {
03316                                                                                 nbrcx = -nbrcx;
03317                                                                                 nbrcy = -nbrcy;
03318                                                                                 nbrcz = -nbrcz;
03319                                                                         }
03320                                                                         int nbrix = nbrcx;
03321                                                                         int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
03322                                                                         int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
03323                                                                         if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
03324                                                                                 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
03325                                                                                 sum = sum + pow_a[c];
03326                                                                         }
03327                                                                 }
03328                                                         }
03329                                                 }
03330 //                                              int r = std::abs(cx) + std::abs(cy) + std::abs(cz);
03331                                                 wght = 1.0f / ( 1.0f - alpha * sum );
03332                                         } // end of ( m_weighting == ESTIMATE )
03333                                         float nominator   = std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz);
03334                                         float denominator = ((*m_wptr2)(ix,iy,iz)-std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz))/(Kn-1.0f);
03335                                         // Skip Friedel related values
03336                                         if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) {
03337                                                 if ( r <= inc ) {
03338                                                         nom[r]   += nominator*wght;
03339                                                         denom[r] += denominator/(*m_wptr)(ix,iy,iz)*wght;
03340                                                         nn[r]    += 2;
03341                                                         ka[r]    += int(Kn);
03342                                                 }
03343 /*
03344 #ifdef  _WIN32
03345                                                 float  tmp = _cpp_max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f);
03346 #else
03347                                                 float  tmp = std::max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f);
03348 #endif  //_WIN32
03349                                                 //  Create SSNR as a 3D array (-n/2:n/2+n%2-1)
03350                                                 int iix = m_vnxc + ix; int iiy = m_vnyc + ky; int iiz = m_vnzc + kz;
03351                                                 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp )
03352                                                         (*vol_ssnr)(iix, iiy, iiz) = tmp;
03353                                                 // Friedel part
03354                                                 iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz;
03355                                                 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp )
03356                                                         (*vol_ssnr)(iix, iiy, iiz) = tmp;
03357 */
03358                                         }
03359                                         (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght;
03360                                 } // end of Kn>4.5 or whatever
03361                         }
03362                 }
03363         }
03364         for (int i = 0; i <= inc; i++) {
03365                 (*SSNR)(i,0,0) = nom[i];
03366                 (*SSNR)(i,1,0) = denom[i];
03367                 (*SSNR)(i,2,0) = static_cast<float>(nn[i]);
03368                 (*SSNR)(i,3,0) = static_cast<float>(ka[i]);
03369         }
03370         vol_ssnr->update();
03371         return vol_ssnr;
03372 //      }
03373 }

virtual string EMAN::nnSSNR_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 1089 of file reconstructor.h.

01090                 {
01091                         return "Reconstruction by nearest neighbor with 3D SSNR with CTF";
01092                 }

virtual string EMAN::nnSSNR_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 1084 of file reconstructor.h.

References NAME.

01085                 {
01086                         return NAME;
01087                 }

TypeDict EMAN::nnSSNR_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 1099 of file reconstructor.h.

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

01100                 {
01101                         TypeDict d;
01102                         d.put("size",     EMObject::INT);
01103                         d.put("npad",     EMObject::INT);
01104                         d.put("symmetry", EMObject::STRING);
01105                         d.put("fftvol",   EMObject::EMDATA);
01106                         d.put("fftwvol",  EMObject::EMDATA);
01107                         d.put("weight",   EMObject::EMDATA);
01108                         d.put("weight2",  EMObject::EMDATA);
01109                         d.put("weight3",  EMObject::EMDATA);
01110                         d.put("SSNR",     EMObject::EMDATA);
01111                         d.put("w",        EMObject::FLOAT);
01112                         d.put("sign",     EMObject::INT);
01113                         d.put("snr",      EMObject::FLOAT);
01114                         return d;
01115                 }

int nnSSNR_ctfReconstructor::insert_padfft_slice EMData padded,
const Transform trans,
int  mult = 1
 

Definition at line 3208 of file reconstructor.cpp.

References Assert, EMAN::Transform::get_sym(), m_nsym, m_symmetry, m_volume, m_wptr, m_wptr2, m_wptr3, and EMAN::EMData::nn_SSNR_ctf().

Referenced by insert_slice().

03209 {
03210         Assert( padfft != NULL );
03211 
03212         // insert slice for all symmetry related positions
03213         for (int isym=0; isym < m_nsym; isym++) {
03214                 Transform tsym = t.get_sym(m_symmetry, isym);
03215                 m_volume->nn_SSNR_ctf(m_wptr, m_wptr2, m_wptr3, padfft, tsym, mult);
03216         }
03217 
03218         return 0;
03219 }

int nnSSNR_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 3180 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().

03180                                                                                                             {
03181         // sanity checks
03182         if (!slice) {
03183                 LOGERR("try to insert NULL slice");
03184                 return 1;
03185         }
03186         int padffted= slice->get_attr_default("padffted", 0);
03187         if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  ) {
03188                 // FIXME: Why doesn't this throw an exception?
03189                 LOGERR("Tried to insert a slice that is the wrong size.");
03190                 return 1;
03191         }
03192     EMData* padfft = NULL;
03193 
03194     if( padffted != 0 ) {
03195         padfft = new EMData(*slice);
03196     } else {
03197         padfft = padfft_slice( slice, t, m_npad );
03198     }
03199 
03200     int mult= slice->get_attr_default("mult", 1);
03201 
03202         Assert( mult > 0 );
03203         insert_padfft_slice( padfft, t, mult );
03204 
03205         checked_delete( padfft );
03206         return 0;
03207 }

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

Definition at line 1094 of file reconstructor.h.

References nnSSNR_ctfReconstructor().

01095                 {
01096                         return new nnSSNR_ctfReconstructor();
01097                 }

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

Definition at line 3076 of file reconstructor.cpp.

References buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), ESTIMATE, EMAN::Transform::get_nsym(), 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, and wiener.

03077 {
03078 
03079     m_weighting = ESTIMATE;
03080     m_wghta     = 0.2f;
03081     m_wghtb     = 0.004f;
03082     wiener      = 1;
03083 
03084     m_symmetry  = symmetry;
03085     m_npad      = npad;
03086     m_nsym      = Transform::get_nsym(m_symmetry);
03087 
03088     m_sign      = sign;
03089     m_snr       = snr;
03090 
03091     m_vnx       = size;
03092     m_vny       = size;
03093     m_vnz       = size;
03094 
03095     m_vnxp      = size*npad;
03096     m_vnyp      = size*npad;
03097     m_vnzp      = size*npad;
03098 
03099     m_vnxc      = m_vnxp/2;
03100     m_vnyc      = m_vnyp/2;
03101     m_vnzc      = m_vnzp/2;
03102 
03103     buildFFTVolume();
03104     buildNormVolume();
03105     buildNorm2Volume();
03106     buildNorm3Volume();
03107 }

void nnSSNR_ctfReconstructor::setup  )  [virtual]
 

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 3062 of file reconstructor.cpp.

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

Referenced by nnSSNR_ctfReconstructor().

03063 {
03064     int  size = params["size"];
03065     int  npad = params["npad"];
03066     int  sign = params["sign"];
03067     float snr = params["snr"];
03068     string symmetry;
03069     if( params.has_key("symmetry") ) {
03070                 symmetry = params["symmetry"].to_str();
03071     } else {
03072                 symmetry = "c1";
03073     }
03074     setup( symmetry, size, npad, snr, sign );
03075 }


Member Data Documentation

bool EMAN::nnSSNR_ctfReconstructor::m_delete_volume [private]
 

Definition at line 1128 of file reconstructor.h.

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

bool EMAN::nnSSNR_ctfReconstructor::m_delete_weight [private]
 

Definition at line 1129 of file reconstructor.h.

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

bool EMAN::nnSSNR_ctfReconstructor::m_delete_weight2 [private]
 

Definition at line 1130 of file reconstructor.h.

Referenced by buildNorm2Volume(), and ~nnSSNR_ctfReconstructor().

bool EMAN::nnSSNR_ctfReconstructor::m_delete_weight3 [private]
 

Definition at line 1131 of file reconstructor.h.

Referenced by buildNorm3Volume(), and ~nnSSNR_ctfReconstructor().

int EMAN::nnSSNR_ctfReconstructor::m_npad [private]
 

Definition at line 1135 of file reconstructor.h.

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

int EMAN::nnSSNR_ctfReconstructor::m_nsym [private]
 

Definition at line 1136 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

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

Definition at line 1127 of file reconstructor.h.

Referenced by nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor().

int EMAN::nnSSNR_ctfReconstructor::m_sign [private]
 

Definition at line 1145 of file reconstructor.h.

Referenced by setup().

float EMAN::nnSSNR_ctfReconstructor::m_snr [private]
 

Definition at line 1146 of file reconstructor.h.

Referenced by setup().

string EMAN::nnSSNR_ctfReconstructor::m_symmetry [private]
 

Definition at line 1132 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnx [private]
 

Definition at line 1134 of file reconstructor.h.

Referenced by insert_slice(), and setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnxc [private]
 

Definition at line 1138 of file reconstructor.h.

Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnxp [private]
 

Definition at line 1137 of file reconstructor.h.

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

int EMAN::nnSSNR_ctfReconstructor::m_vny [private]
 

Definition at line 1134 of file reconstructor.h.

Referenced by setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnyc [private]
 

Definition at line 1138 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnyp [private]
 

Definition at line 1137 of file reconstructor.h.

Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnz [private]
 

Definition at line 1134 of file reconstructor.h.

Referenced by setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnzc [private]
 

Definition at line 1138 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnzp [private]
 

Definition at line 1137 of file reconstructor.h.

Referenced by buildFFTVolume(), buildNorm2Volume(), buildNorm3Volume(), buildNormVolume(), finish(), and setup().

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

Definition at line 1123 of file reconstructor.h.

Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor().

int EMAN::nnSSNR_ctfReconstructor::m_weighting [private]
 

Definition at line 1133 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nnSSNR_ctfReconstructor::m_wghta [private]
 

Definition at line 1143 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nnSSNR_ctfReconstructor::m_wghtb [private]
 

Definition at line 1144 of file reconstructor.h.

Referenced by setup().

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

Definition at line 1124 of file reconstructor.h.

Referenced by buildNormVolume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor().

EMData* EMAN::nnSSNR_ctfReconstructor::m_wptr2 [private]
 

Definition at line 1125 of file reconstructor.h.

Referenced by buildNorm2Volume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor().

EMData* EMAN::nnSSNR_ctfReconstructor::m_wptr3 [private]
 

Definition at line 1126 of file reconstructor.h.

Referenced by buildNorm3Volume(), finish(), insert_padfft_slice(), nnSSNR_ctfReconstructor(), and ~nnSSNR_ctfReconstructor().

const string nnSSNR_ctfReconstructor::NAME = "nnSSNR_ctf" [static]
 

Definition at line 1120 of file reconstructor.h.

Referenced by get_name().

int EMAN::nnSSNR_ctfReconstructor::wiener [private]
 

Definition at line 1147 of file reconstructor.h.

Referenced by setup().


The documentation for this class was generated from the following files:
Generated on Tue May 25 17:38:05 2010 for EMAN2 by  doxygen 1.4.4