#include <reconstructor.h>
Public Member Functions | |
file_store (const string &filename, int npad, int write, bool CTF) | |
virtual | ~file_store () |
void | add_image (EMData *data, const Transform &tf) |
void | get_image (int id, EMData *padfft) |
void | restart () |
Private Attributes | |
shared_ptr< std::ifstream > | m_ihandle |
shared_ptr< std::ofstream > | m_bin_ohandle |
shared_ptr< std::ofstream > | m_txt_ohandle |
string | m_bin_file |
string | m_txt_file |
int | m_ctf |
int | m_npad |
int | m_prev |
int | m_x_out |
int | m_y_out |
int | m_z_out |
int | m_write |
std::istream::off_type | m_totsize |
float | m_Cs |
float | m_pixel |
float | m_voltage |
float | m_ctf_applied |
float | m_amp_contrast |
vector< float > | m_defocuses |
vector< float > | m_phis |
vector< float > | m_thetas |
vector< float > | m_psis |
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Definition at line 4291 of file reconstructor.cpp. References m_ctf, m_npad, m_prev, and m_write. 04292 : m_bin_file(filename + ".bin"), 04293 m_txt_file(filename + ".txt") 04294 { 04295 m_ctf = ctf; 04296 m_prev = -1; 04297 m_npad = npad; 04298 m_write = write; 04299 }
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Definition at line 4301 of file reconstructor.cpp. 04302 { 04303 }
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Definition at line 4305 of file reconstructor.cpp. References checked_delete(), data, EMAN::Dict::get(), EMAN::EMData::get_attr(), EMAN::EMData::get_data(), EMAN::Transform::get_rotation(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), m_amp_contrast, m_bin_file, m_bin_ohandle, m_Cs, m_ctf_applied, m_defocuses, m_npad, m_phis, m_pixel, m_psis, m_thetas, m_totsize, m_txt_file, m_txt_ohandle, m_voltage, m_write, m_x_out, m_y_out, m_z_out, EMAN::padfft_slice(), phi, and EMAN::Ctf::to_dict(). 04306 { 04307 04308 EMData* padfft = padfft_slice( emdata, tf, m_npad ); 04309 04310 float* data = padfft->get_data(); 04311 04312 if( m_write && m_bin_ohandle == NULL ) 04313 { 04314 m_bin_ohandle = shared_ptr< ofstream >( new ofstream(m_bin_file.c_str(), std::ios::out | std::ios::binary) ); 04315 m_txt_ohandle = shared_ptr< ofstream >( new ofstream(m_txt_file.c_str() ) ); 04316 if( m_ctf ) 04317 *m_txt_ohandle << "Cs pixel voltage ctf_applied amp_contrast defocus "; 04318 04319 *m_txt_ohandle << "phi theta psi" << std::endl; 04320 } 04321 04322 m_x_out = padfft->get_xsize(); 04323 m_y_out = padfft->get_ysize(); 04324 m_z_out = padfft->get_zsize(); 04325 m_totsize = m_x_out*m_y_out*m_z_out; 04326 04327 if( m_ctf ) 04328 { 04329 Ctf* ctf = padfft->get_attr( "ctf" ); 04330 Dict ctf_params = ctf->to_dict(); 04331 04332 m_ctf_applied = padfft->get_attr( "ctf_applied" ); 04333 04334 m_Cs = ctf_params["cs"]; 04335 m_pixel = ctf_params["apix"]; 04336 m_voltage = ctf_params["voltage"]; 04337 m_amp_contrast = ctf_params["ampcont"]; 04338 m_defocuses.push_back( ctf_params["defocus"] ); 04339 if(ctf) {delete ctf; ctf=0;} 04340 } 04341 04342 Dict params = tf.get_rotation( "spider" ); 04343 float phi = params.get( "phi" ); 04344 float tht = params.get( "theta" ); 04345 float psi = params.get( "psi" ); 04346 04347 04348 m_phis.push_back( phi ); 04349 m_thetas.push_back( tht ); 04350 m_psis.push_back( psi ); 04351 04352 if( m_write ) 04353 { 04354 m_bin_ohandle->write( (char*)data, sizeof(float)*m_totsize ); 04355 04356 if( m_ctf ) 04357 { 04358 *m_txt_ohandle << m_Cs << " "; 04359 *m_txt_ohandle << m_pixel << " "; 04360 *m_txt_ohandle << m_voltage << " "; 04361 *m_txt_ohandle << m_ctf_applied << " "; 04362 *m_txt_ohandle << m_amp_contrast << " "; 04363 *m_txt_ohandle << m_defocuses.back() << " "; 04364 } 04365 *m_txt_ohandle << m_phis.back() << " "; 04366 *m_txt_ohandle << m_thetas.back() << " "; 04367 *m_txt_ohandle << m_psis.back() << " "; 04368 *m_txt_ohandle << m_x_out << " "; 04369 *m_txt_ohandle << m_y_out << " "; 04370 *m_txt_ohandle << m_z_out << " "; 04371 *m_txt_ohandle << m_totsize << std::endl; 04372 } 04373 04374 checked_delete(padfft); 04375 04376 }
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Definition at line 4378 of file reconstructor.cpp. References Assert, data, EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), m_amp_contrast, m_Cs, m_ctf_applied, m_defocuses, m_ihandle, m_phis, m_pixel, m_psis, m_thetas, m_totsize, m_txt_file, m_voltage, m_x_out, m_y_out, m_z_out, phi, EMAN::EMData::set_attr(), EMAN::EMData::set_size(), theta, and EMAN::EMData::update(). 04379 { 04380 04381 if( m_phis.size() == 0 ) { 04382 ifstream m_txt_ifs( m_txt_file.c_str() ); 04383 04384 if( !m_txt_ifs ) 04385 { 04386 std::cerr << "Error: file " << m_txt_file << " does not exist" << std::endl; 04387 } 04388 04389 string line; 04390 std::getline( m_txt_ifs, line ); 04391 04392 float first, defocus, phi, theta, psi; 04393 04394 04395 04396 while( m_txt_ifs >> first ) { 04397 04398 if( m_ctf ) 04399 { 04400 m_Cs = first; 04401 m_txt_ifs >> m_pixel >> m_voltage; 04402 m_txt_ifs >> m_ctf_applied >> m_amp_contrast; 04403 m_txt_ifs >> defocus >> phi >> theta >> psi; 04404 m_defocuses.push_back( defocus ); 04405 } 04406 else 04407 { 04408 phi = first; 04409 m_txt_ifs >> theta >> psi; 04410 } 04411 04412 m_txt_ifs >> m_x_out >> m_y_out >> m_z_out >> m_totsize; 04413 m_phis.push_back( phi ); 04414 m_thetas.push_back( theta ); 04415 m_psis.push_back( psi ); 04416 } 04417 } 04418 04419 Assert( m_ihandle != NULL ); 04420 04421 std::istream::off_type offset = id*sizeof(float)*m_totsize; 04422 Assert( offset >= 0 ); 04423 04424 if( offset > 0 ) 04425 { 04426 m_ihandle->seekg(offset, std::ios::beg); 04427 } 04428 04429 if( m_ihandle->bad() ) 04430 { 04431 std::cout << "bad while fetching id, offset: " << id << " " << offset << std::endl; 04432 throw std::logic_error( "bad happen" ); 04433 } 04434 04435 if( m_ihandle->fail() ) 04436 { 04437 std::cout << "fail while fetching id, offset, curoff: " << id << " " << offset << std::endl; 04438 throw std::logic_error( "fail happen" ); 04439 } 04440 04441 if( m_ihandle->eof() ) 04442 { 04443 std::cout << "eof while fetching id, offset: " << id << " " << offset << std::endl; 04444 throw std::logic_error( "eof happen" ); 04445 } 04446 04447 if( padfft->get_xsize() != m_x_out || 04448 padfft->get_ysize() != m_y_out || 04449 padfft->get_zsize() != m_z_out ) 04450 { 04451 padfft->set_size(m_x_out, m_y_out, m_z_out); 04452 } 04453 04454 char* data = (char*)(padfft->get_data()); 04455 m_ihandle->read( data, sizeof(float)*m_totsize ); 04456 padfft->update(); 04457 04458 if( m_ctf ) 04459 { 04460 padfft->set_attr( "Cs", m_Cs ); 04461 padfft->set_attr( "Pixel_size", m_pixel ); 04462 padfft->set_attr( "voltage", m_voltage ); 04463 padfft->set_attr( "ctf_applied", m_ctf_applied ); 04464 padfft->set_attr( "amp_contrast", m_amp_contrast ); 04465 padfft->set_attr( "defocus", m_defocuses[id] ); 04466 } 04467 04468 padfft->set_attr( "padffted", 1 ); 04469 padfft->set_attr( "phi", m_phis[id] ); 04470 padfft->set_attr( "theta", m_thetas[id] ); 04471 padfft->set_attr( "psi", m_psis[id] ); 04472 04473 }
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Definition at line 4475 of file reconstructor.cpp. References m_bin_file, and m_ihandle. 04476 { 04477 if( m_ihandle == NULL ) 04478 { 04479 m_ihandle = shared_ptr< ifstream >( new ifstream(m_bin_file.c_str(), std::ios::in | std::ios::binary) ); 04480 } 04481 04482 if( m_ihandle->bad() || m_ihandle->fail() || m_ihandle->eof() ) 04483 { 04484 m_ihandle->open( m_bin_file.c_str(), std::ios::binary ); 04485 } 04486 04487 m_ihandle->seekg( 0, std::ios::beg ); 04488 }
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Definition at line 1358 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1344 of file reconstructor.h. Referenced by add_image(), and restart(). |
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Definition at line 1342 of file reconstructor.h. Referenced by add_image(). |
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Definition at line 1354 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1346 of file reconstructor.h. Referenced by file_store(). |
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Definition at line 1357 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1359 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1341 of file reconstructor.h. Referenced by get_image(), and restart(). |
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Definition at line 1347 of file reconstructor.h. Referenced by add_image(), and file_store(). |
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Definition at line 1360 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1355 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1348 of file reconstructor.h. Referenced by file_store(). |
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Definition at line 1362 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1361 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1353 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1345 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1343 of file reconstructor.h. Referenced by add_image(). |
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Definition at line 1356 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1352 of file reconstructor.h. Referenced by add_image(), and file_store(). |
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Definition at line 1349 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1350 of file reconstructor.h. Referenced by add_image(), and get_image(). |
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Definition at line 1351 of file reconstructor.h. Referenced by add_image(), and get_image(). |