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 988 of file reconstructor.h.


Constructor & Destructor Documentation

nnSSNR_ctfReconstructor::nnSSNR_ctfReconstructor (  ) 

Definition at line 2907 of file reconstructor.cpp.

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

Referenced by NEW().

02908 {
02909     m_volume  = NULL;
02910     m_wptr    = NULL;
02911     m_wptr2   = NULL;
02912     m_wptr3   = NULL;
02913     m_result  = NULL;
02914 }

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

Definition at line 2916 of file reconstructor.cpp.

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

02917 {
02918     m_volume  = NULL;
02919     m_wptr    = NULL;
02920     m_wptr2   = NULL;
02921     m_wptr3   = NULL;
02922     m_result  = NULL;
02923 
02924     setup( symmetry, size, npad, snr, sign );
02925 }

nnSSNR_ctfReconstructor::~nnSSNR_ctfReconstructor (  ) 

Definition at line 2927 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.

02928 {
02929 
02930    if( m_delete_volume )
02931         checked_delete(m_volume);
02932    if( m_delete_weight )
02933         checked_delete( m_wptr );
02934    if ( m_delete_weight2 )
02935         checked_delete( m_wptr2 );
02936    if ( m_delete_weight3 )
02937         checked_delete( m_wptr3 );
02938    checked_delete( m_result );
02939 }


Member Function Documentation

void nnSSNR_ctfReconstructor::buildFFTVolume (  )  [private]

Definition at line 2988 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().

02988                                              {
02989 
02990         int offset = 2 - m_vnxp%2;
02991         if( params.has_key("fftvol") ) {
02992                 m_volume = params["fftvol"]; /* volume should be defined in python when PMI is turned on*/
02993                 m_delete_volume = false;
02994     } else {
02995                 m_volume = new EMData();
02996                 m_delete_volume = true;
02997         }
02998 
02999         m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
03000         m_volume->to_zero();
03001 
03002         if ( m_vnxp % 2 == 0 ) {
03003                 m_volume->set_fftodd(0);
03004         } else {
03005                 m_volume->set_fftodd(1);
03006         }
03007 
03008         m_volume->set_nxc(m_vnxc);
03009         m_volume->set_complex(true);
03010         m_volume->set_ri(true); //(real, imaginary) instead of polar coordinate
03011         m_volume->set_fftpad(true);
03012         m_volume->set_attr("npad", m_npad);
03013         m_volume->set_array_offsets(0,1,1);
03014 }

void nnSSNR_ctfReconstructor::buildNorm2Volume (  )  [private]

Definition at line 3031 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().

03031                                                {
03032 
03033         if( params.has_key("weight2") ) {
03034                 m_wptr2          = params["weight2"];
03035                 m_delete_weight2 = false;
03036         } else {
03037                 m_wptr2 = new EMData();
03038                 m_delete_weight2 = true;
03039         }
03040         m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp);
03041         m_wptr2->to_zero();
03042         m_wptr2->set_array_offsets(0,1,1);
03043 }

void nnSSNR_ctfReconstructor::buildNorm3Volume (  )  [private]

Definition at line 3045 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().

03045                                                {
03046 
03047         if( params.has_key("weight3") ) {
03048                 m_wptr3          = params["weight3"];
03049                 m_delete_weight3 = false;
03050         } else {
03051                 m_wptr3 = new EMData();
03052                 m_delete_weight3 = true;
03053         }
03054         m_wptr3->set_size(m_vnxc+1,m_vnyp,m_vnzp);
03055         m_wptr3->to_zero();
03056         m_wptr3->set_array_offsets(0,1,1);
03057 }

void nnSSNR_ctfReconstructor::buildNormVolume (  )  [private]

Definition at line 3017 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().

03018 {
03019         if( params.has_key("weight") ) {
03020                  m_wptr          = params["weight"];
03021                  m_delete_weight = false;
03022         } else {
03023                 m_wptr = new EMData();
03024                 m_delete_weight = true;
03025         }
03026         m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
03027         m_wptr->to_zero();
03028         m_wptr->set_array_offsets(0,1,1);
03029 }

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 3101 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().

03102 {
03103 /*
03104   I changed the code on 05/15 so it only returns variance.
03105   Lines commented out are marked by //#
03106   The version prior to the currect changes is r1.190
03107   PAP
03108 */
03109         /***
03110             m_volume ctf*(P^2D->3D(F^3D))
03111             m_wptr   ctf^2
03112             m_wptr2  |P^2D->3D(F^3D)|^2
03113             m_wptr3  Kn
03114             nominator = sum_rot [ wght*signal ]
03115             denominator  = sum_rot[ wght*variance ]
03116                                                       ***/
03117         int kz, ky;
03118         int box = 7;
03119         int kc  = (box-1)/2;
03120         float alpha = 0.0;
03121         float argx, argy, argz;
03122         vector< float > pow_a( 3*kc+1, 1.0 );
03123         float w = params["w"];
03124         float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc);
03125         float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc);
03126 #ifdef  _WIN32
03127         float dz2 = 1.0f/_cpp_max(float(m_vnzc),1.0f)/_cpp_max(float(m_vnzc),1.0f);
03128         int inc = Util::round(float(_cpp_max(_cpp_max(m_vnxc,m_vnyc),m_vnzc))/w);
03129 #else
03130         float dz2 = 1.0f/std::max(float(m_vnzc),1.0f)/std::max(float(m_vnzc),1.0f);
03131         int inc = Util::round(float(std::max(std::max(m_vnxc,m_vnyc),m_vnzc))/w);
03132 #endif  //_WIN32
03133 
03134         EMData* SSNR = params["SSNR"];
03135         SSNR->set_size(inc+1,4,1);
03136         //#EMData* vol_ssnr = new EMData();
03137         //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp);
03138         //#vol_ssnr->to_zero();
03139         //#  new linea follow
03140         EMData* vol_ssnr = new EMData();
03141         vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp);
03142         vol_ssnr->to_zero();
03143         if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0);
03144         else                   vol_ssnr->set_fftodd(1);
03145         vol_ssnr->set_nxc(m_vnxc);
03146         vol_ssnr->set_complex(true);
03147         vol_ssnr->set_ri(true);
03148         vol_ssnr->set_fftpad(false);
03149         //#
03150         float *nom    = new float[inc+1];
03151         float *denom  = new float[inc+1];
03152         int  *ka     = new int[inc+1];
03153         int  *nn     = new int[inc+1];
03154         float wght = 1.f;
03155         for (int i = 0; i <= inc; i++) {
03156                 nom[i]   = 0.0f;
03157                 denom[i] = 0.0f;
03158                 nn[i]    = 0;
03159                 ka[i]    = 0;
03160         }
03161         m_volume->symplane2(m_wptr, m_wptr2, m_wptr3);
03162         if ( m_weighting == ESTIMATE ) {
03163                 int vol = box*box*box;
03164                 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
03165                 pow_a[3*kc] = 0.0;
03166                 float max = max3d( kc, pow_a );
03167                 alpha = ( 1.0f - 1.0f/(float)vol ) / max;
03168         }
03169         for (int iz = 1; iz <= m_vnzp; iz++) {
03170                 if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1;
03171                 argz = float(kz*kz)*dz2;
03172                 for (int iy = 1; iy <= m_vnyp; iy++) {
03173                         if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1;
03174                         argy = argz + float(ky*ky)*dy2;
03175                         for (int ix = 0; ix <= m_vnxc; ix++) {
03176                                 float Kn = (*m_wptr3)(ix,iy,iz);
03177                                 argx = std::sqrt(argy + float(ix*ix)*dx2);
03178                                 int r = Util::round(float(inc)*argx);
03179                                 if ( r >= 0 && Kn > 4.5f ) {
03180                                         if ( m_weighting == ESTIMATE ) {
03181                                                 int cx = ix;
03182                                                 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
03183                                                 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
03184                                                 float sum = 0.0;
03185                                                 for( int ii = -kc; ii <= kc; ++ii ) {
03186                                                         int nbrcx = cx + ii;
03187                                                         if( nbrcx >= m_vnxc ) continue;
03188                                                         for ( int jj= -kc; jj <= kc; ++jj ) {
03189                                                                 int nbrcy = cy + jj;
03190                                                                 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
03191                                                                 for( int kk = -kc; kk <= kc; ++kk ) {
03192                                                                         int nbrcz = cz + jj;
03193                                                                         if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
03194                                                                         if( nbrcx < 0 ) {
03195                                                                                 nbrcx = -nbrcx;
03196                                                                                 nbrcy = -nbrcy;
03197                                                                                 nbrcz = -nbrcz;
03198                                                                         }
03199                                                                         int nbrix = nbrcx;
03200                                                                         int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
03201                                                                         int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
03202                                                                         if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
03203                                                                                 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
03204                                                                                 sum = sum + pow_a[c];
03205                                                                         }
03206                                                                 }
03207                                                         }
03208                                                 }
03209 //                                              int r = std::abs(cx) + std::abs(cy) + std::abs(cz);
03210                                                 wght = 1.0f / ( 1.0f - alpha * sum );
03211                                         } // end of ( m_weighting == ESTIMATE )
03212                                         float nominator   = std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz);
03213                                         float denominator = ((*m_wptr2)(ix,iy,iz)-std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz))/(Kn-1.0f);
03214                                         // Skip Friedel related values
03215                                         if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) {
03216                                                 if ( r <= inc ) {
03217                                                         nom[r]   += nominator*wght;
03218                                                         denom[r] += denominator/(*m_wptr)(ix,iy,iz)*wght;
03219                                                         nn[r]    += 2;
03220                                                         ka[r]    += int(Kn);
03221                                                 }
03222 /*
03223 #ifdef  _WIN32
03224                                                 float  tmp = _cpp_max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f);
03225 #else
03226                                                 float  tmp = std::max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f);
03227 #endif  //_WIN32
03228                                                 //  Create SSNR as a 3D array (-n/2:n/2+n%2-1)
03229                                                 int iix = m_vnxc + ix; int iiy = m_vnyc + ky; int iiz = m_vnzc + kz;
03230                                                 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp )
03231                                                         (*vol_ssnr)(iix, iiy, iiz) = tmp;
03232                                                 // Friedel part
03233                                                 iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz;
03234                                                 if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp )
03235                                                         (*vol_ssnr)(iix, iiy, iiz) = tmp;
03236 */
03237                                         }
03238                                         (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght;
03239                                 } // end of Kn>4.5 or whatever
03240                         }
03241                 }
03242         }
03243         for (int i = 0; i <= inc; i++) {
03244                 (*SSNR)(i,0,0) = nom[i];
03245                 (*SSNR)(i,1,0) = denom[i];
03246                 (*SSNR)(i,2,0) = static_cast<float>(nn[i]);
03247                 (*SSNR)(i,3,0) = static_cast<float>(ka[i]);
03248         }
03249         vol_ssnr->update();
03250         return vol_ssnr;
03251 //      }
03252 }

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 1019 of file reconstructor.h.

01020                 {
01021                         return "Reconstruction by nearest neighbor with 3D SSNR with CTF";
01022                 }

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 1014 of file reconstructor.h.

References NAME.

01015                 {
01016                         return NAME;
01017                 }

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 1029 of file reconstructor.h.

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

01030                 {
01031                         TypeDict d;
01032                         d.put("size",     EMObject::INT);
01033                         d.put("npad",     EMObject::INT);
01034                         d.put("symmetry", EMObject::STRING);
01035                         d.put("fftvol",   EMObject::EMDATA);
01036                         d.put("fftwvol",  EMObject::EMDATA);
01037                         d.put("weight",   EMObject::EMDATA);
01038                         d.put("weight2",  EMObject::EMDATA);
01039                         d.put("weight3",  EMObject::EMDATA);
01040                         d.put("SSNR",     EMObject::EMDATA);
01041                         d.put("w",        EMObject::FLOAT);
01042                         d.put("sign",     EMObject::INT);
01043                         d.put("snr",      EMObject::FLOAT);
01044                         return d;
01045                 }

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

Definition at line 3087 of file reconstructor.cpp.

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

Referenced by insert_slice().

03088 {
03089         Assert( padfft != NULL );
03090 
03091         // insert slice for all symmetry related positions
03092         for (int isym=0; isym < m_nsym; isym++) {
03093                 Transform tsym = t.get_sym(m_symmetry, isym);
03094                 m_volume->nn_SSNR_ctf(m_wptr, m_wptr2, m_wptr3, padfft, tsym, mult);
03095         }
03096 
03097         return 0;
03098 }

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 3059 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(), EMAN::padfft_slice(), and t.

03059                                                                                                             {
03060         // sanity checks
03061         if (!slice) {
03062                 LOGERR("try to insert NULL slice");
03063                 return 1;
03064         }
03065         int padffted= slice->get_attr_default("padffted", 0);
03066         if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  ) {
03067                 // FIXME: Why doesn't this throw an exception?
03068                 LOGERR("Tried to insert a slice that is the wrong size.");
03069                 return 1;
03070         }
03071     EMData* padfft = NULL;
03072 
03073     if( padffted != 0 ) {
03074         padfft = new EMData(*slice);
03075     } else {
03076         padfft = padfft_slice( slice, t, m_npad );
03077     }
03078 
03079     int mult= slice->get_attr_default("mult", 1);
03080 
03081         Assert( mult > 0 );
03082         insert_padfft_slice( padfft, t, mult );
03083 
03084         checked_delete( padfft );
03085         return 0;
03086 }

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

Definition at line 1024 of file reconstructor.h.

References nnSSNR_ctfReconstructor().

01025                 {
01026                         return new nnSSNR_ctfReconstructor();
01027                 }

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

Definition at line 2955 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.

02956 {
02957 
02958     m_weighting = ESTIMATE;
02959     m_wghta     = 0.2f;
02960     m_wghtb     = 0.004f;
02961     wiener      = 1;
02962 
02963     m_symmetry  = symmetry;
02964     m_npad      = npad;
02965     m_nsym      = Transform::get_nsym(m_symmetry);
02966 
02967     m_sign      = sign;
02968     m_snr       = snr;
02969 
02970     m_vnx       = size;
02971     m_vny       = size;
02972     m_vnz       = size;
02973 
02974     m_vnxp      = size*npad;
02975     m_vnyp      = size*npad;
02976     m_vnzp      = size*npad;
02977 
02978     m_vnxc      = m_vnxp/2;
02979     m_vnyc      = m_vnyp/2;
02980     m_vnzc      = m_vnzp/2;
02981 
02982     buildFFTVolume();
02983     buildNormVolume();
02984     buildNorm2Volume();
02985     buildNorm3Volume();
02986 }

void nnSSNR_ctfReconstructor::setup (  )  [virtual]

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 2941 of file reconstructor.cpp.

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

Referenced by nnSSNR_ctfReconstructor().

02942 {
02943     int  size = params["size"];
02944     int  npad = params["npad"];
02945     int  sign = params["sign"];
02946     float snr = params["snr"];
02947     string symmetry;
02948     if( params.has_key("symmetry") ) {
02949                 symmetry = params["symmetry"].to_str();
02950     } else {
02951                 symmetry = "c1";
02952     }
02953     setup( symmetry, size, npad, snr, sign );
02954 }


Member Data Documentation

bool EMAN::nnSSNR_ctfReconstructor::m_delete_volume [private]

Definition at line 1058 of file reconstructor.h.

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

bool EMAN::nnSSNR_ctfReconstructor::m_delete_weight [private]

Definition at line 1059 of file reconstructor.h.

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

bool EMAN::nnSSNR_ctfReconstructor::m_delete_weight2 [private]

Definition at line 1060 of file reconstructor.h.

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

bool EMAN::nnSSNR_ctfReconstructor::m_delete_weight3 [private]

Definition at line 1061 of file reconstructor.h.

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

int EMAN::nnSSNR_ctfReconstructor::m_npad [private]

Definition at line 1065 of file reconstructor.h.

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

int EMAN::nnSSNR_ctfReconstructor::m_nsym [private]

Definition at line 1066 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

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

Definition at line 1057 of file reconstructor.h.

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

int EMAN::nnSSNR_ctfReconstructor::m_sign [private]

Definition at line 1075 of file reconstructor.h.

Referenced by setup().

float EMAN::nnSSNR_ctfReconstructor::m_snr [private]

Definition at line 1076 of file reconstructor.h.

Referenced by setup().

string EMAN::nnSSNR_ctfReconstructor::m_symmetry [private]

Definition at line 1062 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnx [private]

Definition at line 1064 of file reconstructor.h.

Referenced by insert_slice(), and setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnxc [private]

Definition at line 1068 of file reconstructor.h.

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

int EMAN::nnSSNR_ctfReconstructor::m_vnxp [private]

Definition at line 1067 of file reconstructor.h.

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

int EMAN::nnSSNR_ctfReconstructor::m_vny [private]

Definition at line 1064 of file reconstructor.h.

Referenced by setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnyc [private]

Definition at line 1068 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnyp [private]

Definition at line 1067 of file reconstructor.h.

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

int EMAN::nnSSNR_ctfReconstructor::m_vnz [private]

Definition at line 1064 of file reconstructor.h.

Referenced by setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnzc [private]

Definition at line 1068 of file reconstructor.h.

Referenced by finish(), and setup().

int EMAN::nnSSNR_ctfReconstructor::m_vnzp [private]

Definition at line 1067 of file reconstructor.h.

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

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

Definition at line 1053 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 1063 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nnSSNR_ctfReconstructor::m_wghta [private]

Definition at line 1073 of file reconstructor.h.

Referenced by finish(), and setup().

float EMAN::nnSSNR_ctfReconstructor::m_wghtb [private]

Definition at line 1074 of file reconstructor.h.

Referenced by setup().

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

Definition at line 1054 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 1055 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 1056 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 1050 of file reconstructor.h.

Referenced by get_name().

int EMAN::nnSSNR_ctfReconstructor::wiener [private]

Definition at line 1077 of file reconstructor.h.

Referenced by setup().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 12:44:28 2010 for EMAN2 by  doxygen 1.4.7