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


Detailed Description

Definition at line 1535 of file reconstructor.h.


Constructor & Destructor Documentation

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

Definition at line 4324 of file reconstructor.cpp.

References m_ctf, m_npad, m_prev, and m_write.

04325     : m_bin_file(filename + ".bin"),
04326       m_txt_file(filename + ".txt")
04327 {
04328     m_ctf = ctf;
04329     m_prev = -1;
04330     m_npad = npad;
04331     m_write = write;
04332 }

file_store::~file_store (  )  [virtual]

Definition at line 4334 of file reconstructor.cpp.

04335 {
04336 }


Member Function Documentation

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

Definition at line 4338 of file reconstructor.cpp.

References checked_delete(), data, EMAN::Dict::get(), EMAN::EMData::get_attr(), EMAN::EMData::get_data(), 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, 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, tf(), and EMAN::Ctf::to_dict().

04339 {
04340 
04341     EMData* padfft = padfft_slice( emdata, tf, m_npad );
04342 
04343     float* data = padfft->get_data();
04344 
04345     if( m_write && m_bin_ohandle == NULL )
04346     {
04347         m_bin_ohandle = shared_ptr< ofstream >( new ofstream(m_bin_file.c_str(), std::ios::out | std::ios::binary) );
04348         m_txt_ohandle = shared_ptr< ofstream >( new ofstream(m_txt_file.c_str() ) );
04349         if( m_ctf )
04350                  *m_txt_ohandle << "Cs pixel voltage ctf_applied amp_contrast defocus ";
04351 
04352         *m_txt_ohandle << "phi theta psi" << std::endl;
04353     }
04354 
04355     m_x_out = padfft->get_xsize();
04356     m_y_out = padfft->get_ysize();
04357     m_z_out = padfft->get_zsize();
04358     m_totsize = m_x_out*m_y_out*m_z_out;
04359 
04360     if( m_ctf )
04361     {
04362         Ctf* ctf = padfft->get_attr( "ctf" );
04363         Dict ctf_params = ctf->to_dict();
04364 
04365         m_ctf_applied = padfft->get_attr( "ctf_applied" );
04366 
04367         m_Cs = ctf_params["cs"];
04368         m_pixel = ctf_params["apix"];
04369         m_voltage = ctf_params["voltage"];
04370         m_amp_contrast = ctf_params["ampcont"];
04371         m_defocuses.push_back( ctf_params["defocus"] );
04372         if(ctf) {delete ctf; ctf=0;}
04373     }
04374 
04375     Dict params = tf.get_rotation( "spider" );
04376     float phi = params.get( "phi" );
04377     float tht = params.get( "theta" );
04378     float psi = params.get( "psi" );
04379 
04380 
04381     m_phis.push_back( phi );
04382     m_thetas.push_back( tht );
04383     m_psis.push_back( psi );
04384 
04385     if( m_write )
04386     {
04387         m_bin_ohandle->write( (char*)data, sizeof(float)*m_totsize );
04388 
04389         if( m_ctf )
04390         {
04391             *m_txt_ohandle << m_Cs << " ";
04392             *m_txt_ohandle << m_pixel << " ";
04393             *m_txt_ohandle << m_voltage << " ";
04394             *m_txt_ohandle << m_ctf_applied << " ";
04395             *m_txt_ohandle << m_amp_contrast << " ";
04396             *m_txt_ohandle << m_defocuses.back() << " ";
04397         }
04398         *m_txt_ohandle << m_phis.back() << " ";
04399         *m_txt_ohandle << m_thetas.back() << " ";
04400         *m_txt_ohandle << m_psis.back() << " ";
04401         *m_txt_ohandle << m_x_out << " ";
04402         *m_txt_ohandle << m_y_out << " ";
04403         *m_txt_ohandle << m_z_out << " ";
04404         *m_txt_ohandle << m_totsize << std::endl;
04405     }
04406 
04407     checked_delete(padfft);
04408 
04409 }

void file_store::get_image ( int  id,
EMData padfft 
)

Definition at line 4411 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, 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().

04412 {
04413 
04414     if( m_phis.size() == 0 ) {
04415         ifstream m_txt_ifs( m_txt_file.c_str() );
04416 
04417         if( !m_txt_ifs )
04418         {
04419             std::cerr << "Error: file " << m_txt_file << " does not exist" << std::endl;
04420         }
04421 
04422         string line;
04423         std::getline( m_txt_ifs, line );
04424 
04425         float first, defocus, phi, theta, psi;
04426 
04427 
04428 
04429         while( m_txt_ifs >> first ) {
04430 
04431             if( m_ctf )
04432             {
04433                 m_Cs = first;
04434                 m_txt_ifs >> m_pixel >> m_voltage;
04435                 m_txt_ifs >> m_ctf_applied >> m_amp_contrast;
04436                 m_txt_ifs >> defocus >> phi >> theta >> psi;
04437                 m_defocuses.push_back( defocus );
04438             }
04439             else
04440             {
04441                 phi = first;
04442                 m_txt_ifs >> theta >> psi;
04443             }
04444 
04445             m_txt_ifs >> m_x_out >> m_y_out >> m_z_out >> m_totsize;
04446             m_phis.push_back( phi );
04447             m_thetas.push_back( theta );
04448             m_psis.push_back( psi );
04449         }
04450     }
04451 
04452     Assert( m_ihandle != NULL );
04453 
04454     std::istream::off_type offset = id*sizeof(float)*m_totsize;
04455     Assert( offset >= 0 );
04456 
04457     if( offset > 0 )
04458     {
04459         m_ihandle->seekg(offset, std::ios::beg);
04460     }
04461 
04462     if( m_ihandle->bad() )
04463     {
04464         std::cout << "bad while fetching id, offset: " << id << " " << offset << std::endl;
04465         throw std::logic_error( "bad happen" );
04466     }
04467 
04468     if( m_ihandle->fail() )
04469     {
04470         std::cout << "fail while fetching id, offset, curoff: " << id << " " << offset << std::endl;
04471         throw std::logic_error( "fail happen" );
04472     }
04473 
04474     if( m_ihandle->eof() )
04475     {
04476         std::cout << "eof while fetching id, offset: " << id << " " << offset << std::endl;
04477         throw std::logic_error( "eof happen" );
04478     }
04479 
04480     if( padfft->get_xsize() != m_x_out ||
04481         padfft->get_ysize() != m_y_out ||
04482         padfft->get_zsize() != m_z_out )
04483     {
04484         padfft->set_size(m_x_out, m_y_out, m_z_out);
04485     }
04486 
04487     char* data = (char*)(padfft->get_data());
04488     m_ihandle->read( data, sizeof(float)*m_totsize );
04489     padfft->update();
04490 
04491     if( m_ctf )
04492     {
04493         padfft->set_attr( "Cs", m_Cs );
04494         padfft->set_attr( "Pixel_size", m_pixel );
04495         padfft->set_attr( "voltage", m_voltage );
04496         padfft->set_attr( "ctf_applied", m_ctf_applied );
04497         padfft->set_attr( "amp_contrast", m_amp_contrast );
04498         padfft->set_attr( "defocus", m_defocuses[id] );
04499     }
04500 
04501     padfft->set_attr( "padffted", 1 );
04502     padfft->set_attr( "phi", m_phis[id] );
04503     padfft->set_attr( "theta", m_thetas[id] );
04504     padfft->set_attr( "psi", m_psis[id] );
04505 
04506 }

void file_store::restart (  ) 

Definition at line 4508 of file reconstructor.cpp.

References in, m_bin_file, and m_ihandle.

04509 {
04510     if( m_ihandle == NULL )
04511     {
04512         m_ihandle = shared_ptr< ifstream >( new ifstream(m_bin_file.c_str(), std::ios::in | std::ios::binary) );
04513     }
04514 
04515     if( m_ihandle->bad() || m_ihandle->fail() || m_ihandle->eof() )
04516     {
04517         m_ihandle->open( m_bin_file.c_str(), std::ios::binary );
04518     }
04519 
04520     m_ihandle->seekg( 0, std::ios::beg );
04521 }


Member Data Documentation

float EMAN::file_store::m_amp_contrast [private]

Definition at line 1565 of file reconstructor.h.

Referenced by add_image(), and get_image().

string EMAN::file_store::m_bin_file [private]

Definition at line 1551 of file reconstructor.h.

Referenced by add_image(), and restart().

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

Definition at line 1549 of file reconstructor.h.

Referenced by add_image().

float EMAN::file_store::m_Cs [private]

Definition at line 1561 of file reconstructor.h.

Referenced by add_image(), and get_image().

int EMAN::file_store::m_ctf [private]

Definition at line 1553 of file reconstructor.h.

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

float EMAN::file_store::m_ctf_applied [private]

Definition at line 1564 of file reconstructor.h.

Referenced by add_image(), and get_image().

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

Definition at line 1566 of file reconstructor.h.

Referenced by add_image(), and get_image().

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

Definition at line 1548 of file reconstructor.h.

Referenced by get_image(), and restart().

int EMAN::file_store::m_npad [private]

Definition at line 1554 of file reconstructor.h.

Referenced by add_image(), and file_store().

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

Definition at line 1567 of file reconstructor.h.

Referenced by add_image(), and get_image().

float EMAN::file_store::m_pixel [private]

Definition at line 1562 of file reconstructor.h.

Referenced by add_image(), and get_image().

int EMAN::file_store::m_prev [private]

Definition at line 1555 of file reconstructor.h.

Referenced by file_store().

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

Definition at line 1569 of file reconstructor.h.

Referenced by add_image(), and get_image().

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

Definition at line 1568 of file reconstructor.h.

Referenced by add_image(), and get_image().

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

Definition at line 1560 of file reconstructor.h.

Referenced by add_image(), and get_image().

string EMAN::file_store::m_txt_file [private]

Definition at line 1552 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 1550 of file reconstructor.h.

Referenced by add_image().

float EMAN::file_store::m_voltage [private]

Definition at line 1563 of file reconstructor.h.

Referenced by add_image(), and get_image().

int EMAN::file_store::m_write [private]

Definition at line 1559 of file reconstructor.h.

Referenced by add_image(), and file_store().

int EMAN::file_store::m_x_out [private]

Definition at line 1556 of file reconstructor.h.

Referenced by add_image(), and get_image().

int EMAN::file_store::m_y_out [private]

Definition at line 1557 of file reconstructor.h.

Referenced by add_image(), and get_image().

int EMAN::file_store::m_z_out [private]

Definition at line 1558 of file reconstructor.h.

Referenced by add_image(), and get_image().


The documentation for this class was generated from the following files:
Generated on Thu Nov 17 12:47:18 2011 for EMAN2 by  doxygen 1.4.7