EMAN::newfile_store Class Reference

#include <reconstructor.h>

List of all members.

Public Member Functions

 newfile_store (const string &prefix, int npad, bool ctf)
virtual ~newfile_store ()
void add_image (EMData *data, const Transform &tf)
void add_tovol (EMData *fftvol, EMData *wgtvol, const vector< int > &mults, int pbegin, int pend)
void get_image (int id, EMData *buf)
void read (int nprj)
void restart ()

Private Attributes

int m_npad
bool m_ctf
string m_bin_file
string m_txt_file
shared_ptr< std::ofstream > m_bin_of
shared_ptr< std::ofstream > m_txt_of
shared_ptr< std::ifstream > m_bin_if
vector< std::istream::off_type > m_offsets
vector< point_tm_points


Detailed Description

Definition at line 1285 of file reconstructor.h.


Constructor & Destructor Documentation

newfile_store::newfile_store ( const string &  prefix,
int  npad,
bool  ctf 
)

Definition at line 4065 of file reconstructor.cpp.

References m_ctf, and m_npad.

04066     : m_bin_file( filename + ".bin" ),
04067       m_txt_file( filename + ".txt" )
04068 {
04069         m_npad = npad;
04070         m_ctf = ctf;
04071 }

newfile_store::~newfile_store (  )  [virtual]

Definition at line 4073 of file reconstructor.cpp.

04074 {
04075 }


Member Function Documentation

void newfile_store::add_image ( EMData data,
const Transform tf 
)

Definition at line 4077 of file reconstructor.cpp.

References checked_delete(), EMAN::EMData::cmplx(), EMAN::point_t::ctf2, EMAN::EMData::get_attr(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::point_t::imag, m_bin_file, m_bin_of, m_ctf, m_npad, m_offsets, m_txt_file, m_txt_of, nx, ny, EMAN::padfft_slice(), EMAN::point_t::pos2, EMAN::point_t::real, sqrt(), tf(), and EMAN::Ctf::to_dict().

04078 {
04079         if( m_bin_of == NULL ) {
04080             m_bin_of = shared_ptr<ofstream>( new ofstream(m_bin_file.c_str(), std::ios::out|std::ios::binary) );
04081             m_txt_of = shared_ptr<ofstream>( new ofstream(m_txt_file.c_str()) );
04082         }
04083 
04084 
04085         EMData* padfft = padfft_slice( emdata, tf, m_npad );
04086 
04087         int nx = padfft->get_xsize();
04088         int ny = padfft->get_ysize();
04089         int n2 = ny / 2;
04090         int n = ny;
04091 
04092         float voltage=0.0f, pixel=0.0f, Cs=0.0f, ampcont=0.0f, bfactor=0.0f, defocus=0.0f;
04093 
04094         if( m_ctf ) {
04095                 Ctf* ctf = emdata->get_attr( "ctf" );
04096                 Dict params = ctf->to_dict();
04097                 voltage = params["voltage"];
04098                 pixel   = params["apix"];
04099                 Cs      = params["cs"];
04100                 ampcont = params["ampcont"];
04101                 bfactor = params["bfactor"];
04102                 defocus = params["defocus"];
04103                 if(ctf) {delete ctf; ctf=0;}
04104         }
04105 
04106         vector<point_t> points;
04107         for( int j=-ny/2+1; j <= ny/2; j++ ) {
04108                 int jp = (j>=0) ? j+1 : ny+j+1;
04109                 for( int i=0; i <= n2; ++i ) {
04110                         int r2 = i*i + j*j;
04111                         if( (r2<ny*ny/4) && !( (i==0) && (j<0) ) ) {
04112                                 float ctf;
04113                                 if( m_ctf ) {
04114                                         float ak = std::sqrt( r2/float(ny*ny) )/pixel;
04115                                         ctf = Util::tf( defocus, ak, voltage, Cs, ampcont, bfactor, 1);
04116                                 } else {
04117                                         ctf = 1.0;
04118                                 }
04119 
04120                                 float xnew = i*tf[0][0] + j*tf[1][0];
04121                                 float ynew = i*tf[0][1] + j*tf[1][1];
04122                                 float znew = i*tf[0][2] + j*tf[1][2];
04123                                 std::complex<float> btq;
04124                                 if (xnew < 0.) {
04125                                         xnew = -xnew;
04126                                         ynew = -ynew;
04127                                         znew = -znew;
04128                                         btq = conj(padfft->cmplx(i,jp-1));
04129                                 } else {
04130                                         btq = padfft->cmplx(i,jp-1);
04131                                 }
04132 
04133                                 int ixn = int(xnew + 0.5 + n) - n;
04134                                 int iyn = int(ynew + 0.5 + n) - n;
04135                                 int izn = int(znew + 0.5 + n) - n;
04136                                 if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2) && (izn >= -n2) && (izn <= n2)) {
04137                                         int ixf, iyf, izf;
04138                                         if (ixn >= 0) {
04139                                                 int iza, iya;
04140                                                 if (izn >= 0)
04141                                                     iza = izn + 1;
04142                                                 else
04143                                                     iza = n + izn + 1;
04144 
04145                                                 if (iyn >= 0)
04146                                                     iya = iyn + 1;
04147                                                 else
04148                                                     iya = n + iyn + 1;
04149 
04150                                                 ixf = ixn;
04151                                                 iyf = iya;
04152                                                 izf = iza;
04153                                         } else {
04154                                                 int izt, iyt;
04155                                                 if (izn > 0)
04156                                                     izt = n - izn + 1;
04157                                                 else
04158                                                     izt = -izn + 1;
04159 
04160                                                 if (iyn > 0)
04161                                                     iyt = n - iyn + 1;
04162                                                 else
04163                                                     iyt = -iyn + 1;
04164 
04165                                                 ixf = -ixn;
04166                                                 iyf = iyt;
04167                                                 izf = izt;
04168                                         }
04169 
04170 
04171                                         int pos2 = ixf + (iyf-1)*nx/2 + (izf-1)*ny*nx/2;
04172                                         float ctfv1 = btq.real() * ctf;
04173                                         float ctfv2 = btq.imag() * ctf;
04174                                         float ctf2 = ctf*ctf;
04175 
04176                                         point_t p;
04177                                         p.pos2 = pos2;
04178                                         p.real = ctfv1;
04179                                         p.imag = ctfv2;
04180                                         p.ctf2 = ctf2;
04181 
04182                                         points.push_back( p );
04183                                 }
04184                         }
04185                 }
04186         }
04187 
04188 
04189         int npoint = points.size();
04190         std::istream::off_type offset = (m_offsets.size()==0) ? 0 : m_offsets.back();
04191         offset += npoint*sizeof(point_t);
04192         m_offsets.push_back( offset );
04193 
04194         *m_txt_of << m_offsets.back() << std::endl;
04195         m_bin_of->write( (char*)(&points[0]), sizeof(point_t)*npoint );
04196         checked_delete( padfft );
04197 }

void newfile_store::add_tovol ( EMData fftvol,
EMData wgtvol,
const vector< int > &  mults,
int  pbegin,
int  pend 
)

Definition at line 4269 of file reconstructor.cpp.

References Assert, EMAN::EMData::get_data(), m_offsets, and m_points.

04270 {
04271         float* vdata = fftvol->get_data();
04272         float* wdata = wgtvol->get_data();
04273 
04274         int npoint = m_offsets[0]/sizeof(point_t);
04275 //    Assert( int(mults.size())==nprj );
04276         Assert( int(m_points.size())== (pend - pbegin)*npoint );
04277 
04278         for( int iprj=pbegin; iprj < pend; ++iprj ) {
04279                 int m = mults[iprj];
04280                 if( m==0 ) continue;
04281 
04282                 int ipt = (iprj-pbegin)*npoint;
04283                 for( int i=0; i < npoint; ++i )  {
04284                     int pos2 = m_points[ipt].pos2;
04285                     int pos1 = pos2*2;
04286 
04287                     wdata[pos2]   += m_points[ipt].ctf2*m;
04288                     vdata[pos1]   += m_points[ipt].real*m;
04289                     vdata[pos1+1] += m_points[ipt].imag*m;
04290                     ++ipt;
04291                 }
04292         }
04293 }

void newfile_store::get_image ( int  id,
EMData buf 
)

Definition at line 4199 of file reconstructor.cpp.

References Assert, data, EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), in, m_bin_file, m_bin_if, m_offsets, m_txt_file, EMAN::EMData::set_size(), and EMAN::EMData::update().

04200 {
04201         if( m_offsets.size()==0 ) {
04202                 ifstream is( m_txt_file.c_str() );
04203                 std::istream::off_type off;
04204                 while( is >> off ) {
04205                     m_offsets.push_back( off );
04206                 }
04207 
04208                 m_bin_if = shared_ptr<std::ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) );
04209         }
04210 
04211         Assert( m_bin_if != NULL );
04212 
04213         std::istream::off_type offset = (id==0) ? 0 : m_offsets[id-1];
04214         Assert( offset >= 0 );
04215         m_bin_if->seekg( offset, std::ios::beg );
04216 
04217 
04218         if( m_bin_if->bad() || m_bin_if->fail() || m_bin_if->eof() ) {
04219                 std::cout << "bad or fail or eof while fetching id, offset: " << id << " " << offset << std::endl;
04220                 throw std::logic_error( "bad happen" );
04221         }
04222 
04223         int bufsize = (m_offsets[id] - offset)/sizeof(float);
04224         if( buf->get_xsize() != bufsize ) {
04225                 buf->set_size( bufsize, 1, 1 );
04226         }
04227 
04228         char* data = (char*)(buf->get_data());
04229         m_bin_if->read( data, sizeof(float)*bufsize );
04230         buf->update();
04231 }

void newfile_store::read ( int  nprj  ) 

Definition at line 4233 of file reconstructor.cpp.

References in, m_bin_file, m_bin_if, m_offsets, m_points, and m_txt_file.

04234 {
04235         if( m_offsets.size()==0 ) {
04236             ifstream is( m_txt_file.c_str() );
04237             std::istream::off_type off;
04238             while( is >> off ) {
04239                 m_offsets.push_back( off );
04240             }
04241         }
04242 
04243         if( m_bin_if==NULL ) {
04244             m_bin_if = shared_ptr< ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) );
04245         }
04246 
04247 
04248         int npoint = m_offsets[0]/sizeof(point_t);
04249         std::ios::off_type prjsize = m_offsets[0];
04250 
04251         try {
04252             m_points.resize(nprj * npoint);
04253         }
04254         catch( std::exception& e ) {
04255             std::cout << "Error: " << e.what() << std::endl;
04256         }
04257 
04258         int ip = 0;
04259         for( int i=0; i < nprj; ++i ) {
04260                 m_bin_if->read( (char*)(&m_points[ip]), prjsize );
04261                 if( m_bin_if->bad() || m_bin_if->fail() || m_bin_if->eof() )  {
04262                         std::cout << "Error: file hander bad or fail or eof" << std::endl;
04263                         return;
04264                 }
04265                 ip += npoint;
04266         }
04267 }

void newfile_store::restart (  ) 

Definition at line 4295 of file reconstructor.cpp.

References in, m_bin_file, and m_bin_if.

04296 {
04297     m_bin_if = shared_ptr< ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) );
04298 }


Member Data Documentation

string EMAN::newfile_store::m_bin_file [private]

Definition at line 1307 of file reconstructor.h.

Referenced by add_image(), get_image(), read(), and restart().

shared_ptr<std::ifstream> EMAN::newfile_store::m_bin_if [private]

Definition at line 1312 of file reconstructor.h.

Referenced by get_image(), read(), and restart().

shared_ptr<std::ofstream> EMAN::newfile_store::m_bin_of [private]

Definition at line 1310 of file reconstructor.h.

Referenced by add_image().

bool EMAN::newfile_store::m_ctf [private]

Definition at line 1305 of file reconstructor.h.

Referenced by add_image(), and newfile_store().

int EMAN::newfile_store::m_npad [private]

Definition at line 1303 of file reconstructor.h.

Referenced by add_image(), and newfile_store().

vector< std::istream::off_type > EMAN::newfile_store::m_offsets [private]

Definition at line 1313 of file reconstructor.h.

Referenced by add_image(), add_tovol(), get_image(), and read().

vector< point_t > EMAN::newfile_store::m_points [private]

Definition at line 1315 of file reconstructor.h.

Referenced by add_tovol(), and read().

string EMAN::newfile_store::m_txt_file [private]

Definition at line 1308 of file reconstructor.h.

Referenced by add_image(), get_image(), and read().

shared_ptr<std::ofstream> EMAN::newfile_store::m_txt_of [private]

Definition at line 1311 of file reconstructor.h.

Referenced by add_image().


The documentation for this class was generated from the following files:
Generated on Tue Jul 12 13:50:00 2011 for EMAN2 by  doxygen 1.4.7