#include <reconstructor.h>
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_t > | m_points |
Definition at line 1502 of file reconstructor.h.
newfile_store::newfile_store | ( | const string & | prefix, | |
int | npad, | |||
bool | ctf | |||
) |
Definition at line 4089 of file reconstructor.cpp.
04090 : m_bin_file( filename + ".bin" ), 04091 m_txt_file( filename + ".txt" ) 04092 { 04093 m_npad = npad; 04094 m_ctf = ctf; 04095 }
newfile_store::~newfile_store | ( | ) | [virtual] |
Definition at line 4101 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().
04102 { 04103 if( m_bin_of == NULL ) { 04104 m_bin_of = shared_ptr<ofstream>( new ofstream(m_bin_file.c_str(), std::ios::out|std::ios::binary) ); 04105 m_txt_of = shared_ptr<ofstream>( new ofstream(m_txt_file.c_str()) ); 04106 } 04107 04108 04109 EMData* padfft = padfft_slice( emdata, tf, m_npad ); 04110 04111 int nx = padfft->get_xsize(); 04112 int ny = padfft->get_ysize(); 04113 int n2 = ny / 2; 04114 int n = ny; 04115 04116 float voltage=0.0f, pixel=0.0f, Cs=0.0f, ampcont=0.0f, bfactor=0.0f, defocus=0.0f; 04117 04118 if( m_ctf ) { 04119 Ctf* ctf = emdata->get_attr( "ctf" ); 04120 Dict params = ctf->to_dict(); 04121 voltage = params["voltage"]; 04122 pixel = params["apix"]; 04123 Cs = params["cs"]; 04124 ampcont = params["ampcont"]; 04125 bfactor = params["bfactor"]; 04126 defocus = params["defocus"]; 04127 if(ctf) {delete ctf; ctf=0;} 04128 } 04129 04130 vector<point_t> points; 04131 for( int j=-ny/2+1; j <= ny/2; j++ ) { 04132 int jp = (j>=0) ? j+1 : ny+j+1; 04133 for( int i=0; i <= n2; ++i ) { 04134 int r2 = i*i + j*j; 04135 if( (r2<ny*ny/4) && !( (i==0) && (j<0) ) ) { 04136 float ctf; 04137 if( m_ctf ) { 04138 float ak = std::sqrt( r2/float(ny*ny) )/pixel; 04139 ctf = Util::tf( defocus, ak, voltage, Cs, ampcont, bfactor, 1); 04140 } else { 04141 ctf = 1.0; 04142 } 04143 04144 float xnew = i*tf[0][0] + j*tf[1][0]; 04145 float ynew = i*tf[0][1] + j*tf[1][1]; 04146 float znew = i*tf[0][2] + j*tf[1][2]; 04147 std::complex<float> btq; 04148 if (xnew < 0.) { 04149 xnew = -xnew; 04150 ynew = -ynew; 04151 znew = -znew; 04152 btq = conj(padfft->cmplx(i,jp-1)); 04153 } else { 04154 btq = padfft->cmplx(i,jp-1); 04155 } 04156 04157 int ixn = int(xnew + 0.5 + n) - n; 04158 int iyn = int(ynew + 0.5 + n) - n; 04159 int izn = int(znew + 0.5 + n) - n; 04160 if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2) && (izn >= -n2) && (izn <= n2)) { 04161 int ixf, iyf, izf; 04162 if (ixn >= 0) { 04163 int iza, iya; 04164 if (izn >= 0) 04165 iza = izn + 1; 04166 else 04167 iza = n + izn + 1; 04168 04169 if (iyn >= 0) 04170 iya = iyn + 1; 04171 else 04172 iya = n + iyn + 1; 04173 04174 ixf = ixn; 04175 iyf = iya; 04176 izf = iza; 04177 } else { 04178 int izt, iyt; 04179 if (izn > 0) 04180 izt = n - izn + 1; 04181 else 04182 izt = -izn + 1; 04183 04184 if (iyn > 0) 04185 iyt = n - iyn + 1; 04186 else 04187 iyt = -iyn + 1; 04188 04189 ixf = -ixn; 04190 iyf = iyt; 04191 izf = izt; 04192 } 04193 04194 04195 int pos2 = ixf + (iyf-1)*nx/2 + (izf-1)*ny*nx/2; 04196 float ctfv1 = btq.real() * ctf; 04197 float ctfv2 = btq.imag() * ctf; 04198 float ctf2 = ctf*ctf; 04199 04200 point_t p; 04201 p.pos2 = pos2; 04202 p.real = ctfv1; 04203 p.imag = ctfv2; 04204 p.ctf2 = ctf2; 04205 04206 points.push_back( p ); 04207 } 04208 } 04209 } 04210 } 04211 04212 04213 int npoint = points.size(); 04214 std::istream::off_type offset = (m_offsets.size()==0) ? 0 : m_offsets.back(); 04215 offset += npoint*sizeof(point_t); 04216 m_offsets.push_back( offset ); 04217 04218 *m_txt_of << m_offsets.back() << std::endl; 04219 m_bin_of->write( (char*)(&points[0]), sizeof(point_t)*npoint ); 04220 checked_delete( padfft ); 04221 }
void newfile_store::add_tovol | ( | EMData * | fftvol, | |
EMData * | wgtvol, | |||
const vector< int > & | mults, | |||
int | pbegin, | |||
int | pend | |||
) |
Definition at line 4293 of file reconstructor.cpp.
References Assert, EMAN::EMData::get_data(), m_offsets, and m_points.
04294 { 04295 float* vdata = fftvol->get_data(); 04296 float* wdata = wgtvol->get_data(); 04297 04298 int npoint = m_offsets[0]/sizeof(point_t); 04299 // Assert( int(mults.size())==nprj ); 04300 Assert( int(m_points.size())== (pend - pbegin)*npoint ); 04301 04302 for( int iprj=pbegin; iprj < pend; ++iprj ) { 04303 int m = mults[iprj]; 04304 if( m==0 ) continue; 04305 04306 int ipt = (iprj-pbegin)*npoint; 04307 for( int i=0; i < npoint; ++i ) { 04308 int pos2 = m_points[ipt].pos2; 04309 int pos1 = pos2*2; 04310 04311 wdata[pos2] += m_points[ipt].ctf2*m; 04312 vdata[pos1] += m_points[ipt].real*m; 04313 vdata[pos1+1] += m_points[ipt].imag*m; 04314 ++ipt; 04315 } 04316 } 04317 }
void newfile_store::get_image | ( | int | id, | |
EMData * | buf | |||
) |
Definition at line 4223 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().
04224 { 04225 if( m_offsets.size()==0 ) { 04226 ifstream is( m_txt_file.c_str() ); 04227 std::istream::off_type off; 04228 while( is >> off ) { 04229 m_offsets.push_back( off ); 04230 } 04231 04232 m_bin_if = shared_ptr<std::ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) ); 04233 } 04234 04235 Assert( m_bin_if != NULL ); 04236 04237 std::istream::off_type offset = (id==0) ? 0 : m_offsets[id-1]; 04238 Assert( offset >= 0 ); 04239 m_bin_if->seekg( offset, std::ios::beg ); 04240 04241 04242 if( m_bin_if->bad() || m_bin_if->fail() || m_bin_if->eof() ) { 04243 std::cout << "bad or fail or eof while fetching id, offset: " << id << " " << offset << std::endl; 04244 throw std::logic_error( "bad happen" ); 04245 } 04246 04247 int bufsize = (m_offsets[id] - offset)/sizeof(float); 04248 if( buf->get_xsize() != bufsize ) { 04249 buf->set_size( bufsize, 1, 1 ); 04250 } 04251 04252 char* data = (char*)(buf->get_data()); 04253 m_bin_if->read( data, sizeof(float)*bufsize ); 04254 buf->update(); 04255 }
void newfile_store::read | ( | int | nprj | ) |
Definition at line 4257 of file reconstructor.cpp.
References in, m_bin_file, m_bin_if, m_offsets, m_points, and m_txt_file.
04258 { 04259 if( m_offsets.size()==0 ) { 04260 ifstream is( m_txt_file.c_str() ); 04261 std::istream::off_type off; 04262 while( is >> off ) { 04263 m_offsets.push_back( off ); 04264 } 04265 } 04266 04267 if( m_bin_if==NULL ) { 04268 m_bin_if = shared_ptr< ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) ); 04269 } 04270 04271 04272 int npoint = m_offsets[0]/sizeof(point_t); 04273 std::ios::off_type prjsize = m_offsets[0]; 04274 04275 try { 04276 m_points.resize(nprj * npoint); 04277 } 04278 catch( std::exception& e ) { 04279 std::cout << "Error: " << e.what() << std::endl; 04280 } 04281 04282 int ip = 0; 04283 for( int i=0; i < nprj; ++i ) { 04284 m_bin_if->read( (char*)(&m_points[ip]), prjsize ); 04285 if( m_bin_if->bad() || m_bin_if->fail() || m_bin_if->eof() ) { 04286 std::cout << "Error: file hander bad or fail or eof" << std::endl; 04287 return; 04288 } 04289 ip += npoint; 04290 } 04291 }
void newfile_store::restart | ( | ) |
Definition at line 4319 of file reconstructor.cpp.
References in, m_bin_file, and m_bin_if.
04320 { 04321 m_bin_if = shared_ptr< ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) ); 04322 }
string EMAN::newfile_store::m_bin_file [private] |
Definition at line 1524 of file reconstructor.h.
Referenced by add_image(), get_image(), read(), and restart().
shared_ptr<std::ifstream> EMAN::newfile_store::m_bin_if [private] |
shared_ptr<std::ofstream> EMAN::newfile_store::m_bin_of [private] |
bool EMAN::newfile_store::m_ctf [private] |
int EMAN::newfile_store::m_npad [private] |
vector< std::istream::off_type > EMAN::newfile_store::m_offsets [private] |
Definition at line 1530 of file reconstructor.h.
Referenced by add_image(), add_tovol(), get_image(), and read().
vector< point_t > EMAN::newfile_store::m_points [private] |
string EMAN::newfile_store::m_txt_file [private] |
Definition at line 1525 of file reconstructor.h.
Referenced by add_image(), get_image(), and read().
shared_ptr<std::ofstream> EMAN::newfile_store::m_txt_of [private] |