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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


Constructor & Destructor Documentation

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

Definition at line 4056 of file reconstructor.cpp.

References m_ctf, and m_npad.

04057     : m_bin_file( filename + ".bin" ),
04058       m_txt_file( filename + ".txt" )
04059 {
04060         m_npad = npad;
04061         m_ctf = ctf;
04062 }

newfile_store::~newfile_store  )  [virtual]
 

Definition at line 4064 of file reconstructor.cpp.

04065 {
04066 }


Member Function Documentation

void newfile_store::add_image EMData data,
const Transform tf
 

Definition at line 4068 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_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().

04069 {
04070         if( m_bin_of == NULL ) {
04071             m_bin_of = shared_ptr<ofstream>( new ofstream(m_bin_file.c_str(), std::ios::out|std::ios::binary) );
04072             m_txt_of = shared_ptr<ofstream>( new ofstream(m_txt_file.c_str()) );
04073         }
04074 
04075 
04076         EMData* padfft = padfft_slice( emdata, tf, m_npad );
04077 
04078         int nx = padfft->get_xsize();
04079         int ny = padfft->get_ysize();
04080         int n2 = ny / 2;
04081         int n = ny;
04082 
04083         float voltage=0.0f, pixel=0.0f, Cs=0.0f, ampcont=0.0f, bfactor=0.0f, defocus=0.0f;
04084 
04085         if( m_ctf ) {
04086                 Ctf* ctf = emdata->get_attr( "ctf" );
04087                 Dict params = ctf->to_dict();
04088                 voltage = params["voltage"];
04089                 pixel   = params["apix"];
04090                 Cs      = params["cs"];
04091                 ampcont = params["ampcont"];
04092                 bfactor = params["bfactor"];
04093                 defocus = params["defocus"];
04094                 if(ctf) {delete ctf; ctf=0;}
04095         }
04096 
04097         vector<point_t> points;
04098         for( int j=-ny/2+1; j <= ny/2; j++ ) {
04099                 int jp = (j>=0) ? j+1 : ny+j+1;
04100                 for( int i=0; i <= n2; ++i ) {
04101                         int r2 = i*i + j*j;
04102                         if( (r2<ny*ny/4) && !( (i==0) && (j<0) ) ) {
04103                                 float ctf;
04104                                 if( m_ctf ) {
04105                                         float ak = std::sqrt( r2/float(ny*ny) )/pixel;
04106                                         ctf = Util::tf( defocus, ak, voltage, Cs, ampcont, bfactor, 1);
04107                                 } else {
04108                                         ctf = 1.0;
04109                                 }
04110 
04111                                 float xnew = i*tf[0][0] + j*tf[1][0];
04112                                 float ynew = i*tf[0][1] + j*tf[1][1];
04113                                 float znew = i*tf[0][2] + j*tf[1][2];
04114                                 std::complex<float> btq;
04115                                 if (xnew < 0.) {
04116                                         xnew = -xnew;
04117                                         ynew = -ynew;
04118                                         znew = -znew;
04119                                         btq = conj(padfft->cmplx(i,jp-1));
04120                                 } else {
04121                                         btq = padfft->cmplx(i,jp-1);
04122                                 }
04123 
04124                                 int ixn = int(xnew + 0.5 + n) - n;
04125                                 int iyn = int(ynew + 0.5 + n) - n;
04126                                 int izn = int(znew + 0.5 + n) - n;
04127                                 if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2) && (izn >= -n2) && (izn <= n2)) {
04128                                         int ixf, iyf, izf;
04129                                         if (ixn >= 0) {
04130                                                 int iza, iya;
04131                                                 if (izn >= 0)
04132                                                     iza = izn + 1;
04133                                                 else
04134                                                     iza = n + izn + 1;
04135 
04136                                                 if (iyn >= 0)
04137                                                     iya = iyn + 1;
04138                                                 else
04139                                                     iya = n + iyn + 1;
04140 
04141                                                 ixf = ixn;
04142                                                 iyf = iya;
04143                                                 izf = iza;
04144                                         } else {
04145                                                 int izt, iyt;
04146                                                 if (izn > 0)
04147                                                     izt = n - izn + 1;
04148                                                 else
04149                                                     izt = -izn + 1;
04150 
04151                                                 if (iyn > 0)
04152                                                     iyt = n - iyn + 1;
04153                                                 else
04154                                                     iyt = -iyn + 1;
04155 
04156                                                 ixf = -ixn;
04157                                                 iyf = iyt;
04158                                                 izf = izt;
04159                                         }
04160 
04161 
04162                                         int pos2 = ixf + (iyf-1)*nx/2 + (izf-1)*ny*nx/2;
04163                                         float ctfv1 = btq.real() * ctf;
04164                                         float ctfv2 = btq.imag() * ctf;
04165                                         float ctf2 = ctf*ctf;
04166 
04167                                         point_t p;
04168                                         p.pos2 = pos2;
04169                                         p.real = ctfv1;
04170                                         p.imag = ctfv2;
04171                                         p.ctf2 = ctf2;
04172 
04173                                         points.push_back( p );
04174                                 }
04175                         }
04176                 }
04177         }
04178 
04179 
04180         int npoint = points.size();
04181         std::istream::off_type offset = (m_offsets.size()==0) ? 0 : m_offsets.back();
04182         offset += npoint*sizeof(point_t);
04183         m_offsets.push_back( offset );
04184 
04185         *m_txt_of << m_offsets.back() << std::endl;
04186         m_bin_of->write( (char*)(&points[0]), sizeof(point_t)*npoint );
04187         checked_delete( padfft );
04188 }

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

Definition at line 4260 of file reconstructor.cpp.

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

04261 {
04262         float* vdata = fftvol->get_data();
04263         float* wdata = wgtvol->get_data();
04264 
04265         int npoint = m_offsets[0]/sizeof(point_t);
04266 //    Assert( int(mults.size())==nprj );
04267         Assert( int(m_points.size())== (pend - pbegin)*npoint );
04268 
04269         for( int iprj=pbegin; iprj < pend; ++iprj ) {
04270                 int m = mults[iprj];
04271                 if( m==0 ) continue;
04272 
04273                 int ipt = (iprj-pbegin)*npoint;
04274                 for( int i=0; i < npoint; ++i )  {
04275                     int pos2 = m_points[ipt].pos2;
04276                     int pos1 = pos2*2;
04277 
04278                     wdata[pos2]   += m_points[ipt].ctf2*m;
04279                     vdata[pos1]   += m_points[ipt].real*m;
04280                     vdata[pos1+1] += m_points[ipt].imag*m;
04281                     ++ipt;
04282                 }
04283         }
04284 }

void newfile_store::get_image int  id,
EMData buf
 

Definition at line 4190 of file reconstructor.cpp.

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

04191 {
04192         if( m_offsets.size()==0 ) {
04193                 ifstream is( m_txt_file.c_str() );
04194                 std::istream::off_type off;
04195                 while( is >> off ) {
04196                     m_offsets.push_back( off );
04197                 }
04198 
04199                 m_bin_if = shared_ptr<std::ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) );
04200         }
04201 
04202         Assert( m_bin_if != NULL );
04203 
04204         std::istream::off_type offset = (id==0) ? 0 : m_offsets[id-1];
04205         Assert( offset >= 0 );
04206         m_bin_if->seekg( offset, std::ios::beg );
04207 
04208 
04209         if( m_bin_if->bad() || m_bin_if->fail() || m_bin_if->eof() ) {
04210                 std::cout << "bad or fail or eof while fetching id, offset: " << id << " " << offset << std::endl;
04211                 throw std::logic_error( "bad happen" );
04212         }
04213 
04214         int bufsize = (m_offsets[id] - offset)/sizeof(float);
04215         if( buf->get_xsize() != bufsize ) {
04216                 buf->set_size( bufsize, 1, 1 );
04217         }
04218 
04219         char* data = (char*)(buf->get_data());
04220         m_bin_if->read( data, sizeof(float)*bufsize );
04221         buf->update();
04222 }

void newfile_store::read int  nprj  ) 
 

Definition at line 4224 of file reconstructor.cpp.

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

04225 {
04226         if( m_offsets.size()==0 ) {
04227             ifstream is( m_txt_file.c_str() );
04228             std::istream::off_type off;
04229             while( is >> off ) {
04230                 m_offsets.push_back( off );
04231             }
04232         }
04233 
04234         if( m_bin_if==NULL ) {
04235             m_bin_if = shared_ptr< ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) );
04236         }
04237 
04238 
04239         int npoint = m_offsets[0]/sizeof(point_t);
04240         std::ios::off_type prjsize = m_offsets[0];
04241 
04242         try {
04243             m_points.resize(nprj * npoint);
04244         }
04245         catch( std::exception& e ) {
04246             std::cout << "Error: " << e.what() << std::endl;
04247         }
04248 
04249         int ip = 0;
04250         for( int i=0; i < nprj; ++i ) {
04251                 m_bin_if->read( (char*)(&m_points[ip]), prjsize );
04252                 if( m_bin_if->bad() || m_bin_if->fail() || m_bin_if->eof() )  {
04253                         std::cout << "Error: file hander bad or fail or eof" << std::endl;
04254                         return;
04255                 }
04256                 ip += npoint;
04257         }
04258 }

void newfile_store::restart  ) 
 

Definition at line 4286 of file reconstructor.cpp.

References m_bin_file, and m_bin_if.

04287 {
04288     m_bin_if = shared_ptr< ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) );
04289 }


Member Data Documentation

string EMAN::newfile_store::m_bin_file [private]
 

Definition at line 1317 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 1322 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 1320 of file reconstructor.h.

Referenced by add_image().

bool EMAN::newfile_store::m_ctf [private]
 

Definition at line 1315 of file reconstructor.h.

Referenced by newfile_store().

int EMAN::newfile_store::m_npad [private]
 

Definition at line 1313 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 1323 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 1325 of file reconstructor.h.

Referenced by add_tovol(), and read().

string EMAN::newfile_store::m_txt_file [private]
 

Definition at line 1318 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 1321 of file reconstructor.h.

Referenced by add_image().


The documentation for this class was generated from the following files:
Generated on Thu Dec 9 13:48:36 2010 for EMAN2 by  doxygen 1.3.9.1