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EMAN::file_store Class Reference

#include <reconstructor.h>

List of all members.

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


Constructor & Destructor Documentation

file_store::file_store const string &  filename,
int  npad,
int  write,
bool  CTF
 

Definition at line 4392 of file reconstructor.cpp.

References m_ctf, m_npad, m_prev, and m_write.

04393     : m_bin_file(filename + ".bin"),
04394       m_txt_file(filename + ".txt")
04395 {
04396     m_ctf = ctf;
04397     m_prev = -1;
04398     m_npad = npad;
04399     m_write = write;
04400 }

file_store::~file_store  )  [virtual]
 

Definition at line 4402 of file reconstructor.cpp.

04403 {
04404 }


Member Function Documentation

void file_store::add_image EMData data,
const Transform tf
 

Definition at line 4406 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().

04407 {
04408 
04409     EMData* padfft = padfft_slice( emdata, tf, m_npad );
04410 
04411     float* data = padfft->get_data();
04412 
04413     if( m_write && m_bin_ohandle == NULL )
04414     {
04415         m_bin_ohandle = shared_ptr< ofstream >( new ofstream(m_bin_file.c_str(), std::ios::out | std::ios::binary) );
04416         m_txt_ohandle = shared_ptr< ofstream >( new ofstream(m_txt_file.c_str() ) );
04417         if( m_ctf )
04418                  *m_txt_ohandle << "Cs pixel voltage ctf_applied amp_contrast defocus ";
04419 
04420         *m_txt_ohandle << "phi theta psi" << std::endl;
04421     }
04422 
04423     m_x_out = padfft->get_xsize();
04424     m_y_out = padfft->get_ysize();
04425     m_z_out = padfft->get_zsize();
04426     m_totsize = m_x_out*m_y_out*m_z_out;
04427 
04428     if( m_ctf )
04429     {
04430         Ctf* ctf = padfft->get_attr( "ctf" );
04431         Dict ctf_params = ctf->to_dict();
04432 
04433         m_ctf_applied = padfft->get_attr( "ctf_applied" );
04434 
04435         m_Cs = ctf_params["cs"];
04436         m_pixel = ctf_params["apix"];
04437         m_voltage = ctf_params["voltage"];
04438         m_amp_contrast = ctf_params["ampcont"];
04439         m_defocuses.push_back( ctf_params["defocus"] );
04440         if(ctf) {delete ctf; ctf=0;}
04441     }
04442 
04443     Dict params = tf.get_rotation( "spider" );
04444     float phi = params.get( "phi" );
04445     float tht = params.get( "theta" );
04446     float psi = params.get( "psi" );
04447 
04448 
04449     m_phis.push_back( phi );
04450     m_thetas.push_back( tht );
04451     m_psis.push_back( psi );
04452 
04453     if( m_write )
04454     {
04455         m_bin_ohandle->write( (char*)data, sizeof(float)*m_totsize );
04456 
04457         if( m_ctf )
04458         {
04459             *m_txt_ohandle << m_Cs << " ";
04460             *m_txt_ohandle << m_pixel << " ";
04461             *m_txt_ohandle << m_voltage << " ";
04462             *m_txt_ohandle << m_ctf_applied << " ";
04463             *m_txt_ohandle << m_amp_contrast << " ";
04464             *m_txt_ohandle << m_defocuses.back() << " ";
04465         }
04466         *m_txt_ohandle << m_phis.back() << " ";
04467         *m_txt_ohandle << m_thetas.back() << " ";
04468         *m_txt_ohandle << m_psis.back() << " ";
04469         *m_txt_ohandle << m_x_out << " ";
04470         *m_txt_ohandle << m_y_out << " ";
04471         *m_txt_ohandle << m_z_out << " ";
04472         *m_txt_ohandle << m_totsize << std::endl;
04473     }
04474 
04475     checked_delete(padfft);
04476 
04477 }

void file_store::get_image int  id,
EMData padfft
 

Definition at line 4479 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().

04480 {
04481 
04482     if( m_phis.size() == 0 ) {
04483         ifstream m_txt_ifs( m_txt_file.c_str() );
04484 
04485         if( !m_txt_ifs )
04486         {
04487             std::cerr << "Error: file " << m_txt_file << " does not exist" << std::endl;
04488         }
04489 
04490         string line;
04491         std::getline( m_txt_ifs, line );
04492 
04493         float first, defocus, phi, theta, psi;
04494 
04495 
04496 
04497         while( m_txt_ifs >> first ) {
04498 
04499             if( m_ctf )
04500             {
04501                 m_Cs = first;
04502                 m_txt_ifs >> m_pixel >> m_voltage;
04503                 m_txt_ifs >> m_ctf_applied >> m_amp_contrast;
04504                 m_txt_ifs >> defocus >> phi >> theta >> psi;
04505                 m_defocuses.push_back( defocus );
04506             }
04507             else
04508             {
04509                 phi = first;
04510                 m_txt_ifs >> theta >> psi;
04511             }
04512 
04513             m_txt_ifs >> m_x_out >> m_y_out >> m_z_out >> m_totsize;
04514             m_phis.push_back( phi );
04515             m_thetas.push_back( theta );
04516             m_psis.push_back( psi );
04517         }
04518     }
04519 
04520     Assert( m_ihandle != NULL );
04521 
04522     std::istream::off_type offset = id*sizeof(float)*m_totsize;
04523     Assert( offset >= 0 );
04524 
04525     if( offset > 0 )
04526     {
04527         m_ihandle->seekg(offset, std::ios::beg);
04528     }
04529 
04530     if( m_ihandle->bad() )
04531     {
04532         std::cout << "bad while fetching id, offset: " << id << " " << offset << std::endl;
04533         throw std::logic_error( "bad happen" );
04534     }
04535 
04536     if( m_ihandle->fail() )
04537     {
04538         std::cout << "fail while fetching id, offset, curoff: " << id << " " << offset << std::endl;
04539         throw std::logic_error( "fail happen" );
04540     }
04541 
04542     if( m_ihandle->eof() )
04543     {
04544         std::cout << "eof while fetching id, offset: " << id << " " << offset << std::endl;
04545         throw std::logic_error( "eof happen" );
04546     }
04547 
04548     if( padfft->get_xsize() != m_x_out ||
04549         padfft->get_ysize() != m_y_out ||
04550         padfft->get_zsize() != m_z_out )
04551     {
04552         padfft->set_size(m_x_out, m_y_out, m_z_out);
04553     }
04554 
04555     char* data = (char*)(padfft->get_data());
04556     m_ihandle->read( data, sizeof(float)*m_totsize );
04557     padfft->update();
04558 
04559     if( m_ctf )
04560     {
04561         padfft->set_attr( "Cs", m_Cs );
04562         padfft->set_attr( "Pixel_size", m_pixel );
04563         padfft->set_attr( "voltage", m_voltage );
04564         padfft->set_attr( "ctf_applied", m_ctf_applied );
04565         padfft->set_attr( "amp_contrast", m_amp_contrast );
04566         padfft->set_attr( "defocus", m_defocuses[id] );
04567     }
04568 
04569     padfft->set_attr( "padffted", 1 );
04570     padfft->set_attr( "phi", m_phis[id] );
04571     padfft->set_attr( "theta", m_thetas[id] );
04572     padfft->set_attr( "psi", m_psis[id] );
04573 
04574 }

void file_store::restart  ) 
 

Definition at line 4576 of file reconstructor.cpp.

References m_bin_file, and m_ihandle.

04577 {
04578     if( m_ihandle == NULL )
04579     {
04580         m_ihandle = shared_ptr< ifstream >( new ifstream(m_bin_file.c_str(), std::ios::in | std::ios::binary) );
04581     }
04582 
04583     if( m_ihandle->bad() || m_ihandle->fail() || m_ihandle->eof() )
04584     {
04585         m_ihandle->open( m_bin_file.c_str(), std::ios::binary );
04586     }
04587 
04588     m_ihandle->seekg( 0, std::ios::beg );
04589 }


Member Data Documentation

float EMAN::file_store::m_amp_contrast [private]
 

Definition at line 1367 of file reconstructor.h.

Referenced by add_image(), and get_image().

string EMAN::file_store::m_bin_file [private]
 

Definition at line 1353 of file reconstructor.h.

Referenced by add_image(), and restart().

shared_ptr<std::ofstream> EMAN::file_store::m_bin_ohandle [private]
 

Definition at line 1351 of file reconstructor.h.

Referenced by add_image().

float EMAN::file_store::m_Cs [private]
 

Definition at line 1363 of file reconstructor.h.

Referenced by add_image(), and get_image().

int EMAN::file_store::m_ctf [private]
 

Definition at line 1355 of file reconstructor.h.

Referenced by file_store().

float EMAN::file_store::m_ctf_applied [private]
 

Definition at line 1366 of file reconstructor.h.

Referenced by add_image(), and get_image().

vector< float > EMAN::file_store::m_defocuses [private]
 

Definition at line 1368 of file reconstructor.h.

Referenced by add_image(), and get_image().

shared_ptr<std::ifstream> EMAN::file_store::m_ihandle [private]
 

Definition at line 1350 of file reconstructor.h.

Referenced by get_image(), and restart().

int EMAN::file_store::m_npad [private]
 

Definition at line 1356 of file reconstructor.h.

Referenced by add_image(), and file_store().

vector< float > EMAN::file_store::m_phis [private]
 

Definition at line 1369 of file reconstructor.h.

Referenced by add_image(), and get_image().

float EMAN::file_store::m_pixel [private]
 

Definition at line 1364 of file reconstructor.h.

Referenced by add_image(), and get_image().

int EMAN::file_store::m_prev [private]
 

Definition at line 1357 of file reconstructor.h.

Referenced by file_store().

vector< float > EMAN::file_store::m_psis [private]
 

Definition at line 1371 of file reconstructor.h.

Referenced by add_image(), and get_image().

vector< float > EMAN::file_store::m_thetas [private]
 

Definition at line 1370 of file reconstructor.h.

Referenced by add_image(), and get_image().

std::istream::off_type EMAN::file_store::m_totsize [private]
 

Definition at line 1362 of file reconstructor.h.

Referenced by add_image(), and get_image().

string EMAN::file_store::m_txt_file [private]
 

Definition at line 1354 of file reconstructor.h.

Referenced by add_image(), and get_image().

shared_ptr<std::ofstream> EMAN::file_store::m_txt_ohandle [private]
 

Definition at line 1352 of file reconstructor.h.

Referenced by add_image().

float EMAN::file_store::m_voltage [private]
 

Definition at line 1365 of file reconstructor.h.

Referenced by add_image(), and get_image().

int EMAN::file_store::m_write [private]
 

Definition at line 1361 of file reconstructor.h.

Referenced by add_image(), and file_store().

int EMAN::file_store::m_x_out [private]
 

Definition at line 1358 of file reconstructor.h.

Referenced by add_image(), and get_image().

int EMAN::file_store::m_y_out [private]
 

Definition at line 1359 of file reconstructor.h.

Referenced by add_image(), and get_image().

int EMAN::file_store::m_z_out [private]
 

Definition at line 1360 of file reconstructor.h.

Referenced by add_image(), and get_image().


The documentation for this class was generated from the following files:
Generated on Mon Mar 7 18:21:36 2011 for EMAN2 by  doxygen 1.3.9.1