EMAN::file_store Class Reference

#include <reconstructor.h>

Collaboration diagram for EMAN::file_store:

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 1778 of file reconstructor.h.

Constructor & Destructor Documentation

file_store()

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

Definition at line 6533 of file reconstructor.cpp.

    : m_bin_file(filename + ".bin"),
      m_txt_file(filename + ".txt")
{
    m_ctf = ctf;
    m_prev = -1;
    m_npad = npad;
    m_write = write;
}

References m_ctf, m_npad, m_prev, and m_write.

~file_store()

file_store::~file_store ( )

virtual

Definition at line 6543 of file reconstructor.cpp.

{
}

Member Function Documentation

add_image()

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

Definition at line 6547 of file reconstructor.cpp.

{
 
    EMData* padfft = padfft_slice( emdata, tf, m_npad );
 
    float* data = padfft->get_data();
 
    if( m_write && m_bin_ohandle == NULL )
    {
        m_bin_ohandle = shared_ptr< ofstream >( new ofstream(m_bin_file.c_str(), std::ios::out | std::ios::binary) );
        m_txt_ohandle = shared_ptr< ofstream >( new ofstream(m_txt_file.c_str() ) );
        if( m_ctf )
                 *m_txt_ohandle << "Cs pixel voltage ctf_applied amp_contrast defocus ";
 
        *m_txt_ohandle << "phi theta psi" << std::endl;
    }
 
    m_x_out = padfft->get_xsize();
    m_y_out = padfft->get_ysize();
    m_z_out = padfft->get_zsize();
    m_totsize = m_x_out*m_y_out*m_z_out;
 
    if( m_ctf )
    {
        Ctf* ctf = padfft->get_attr( "ctf" );
        Dict ctf_params = ctf->to_dict();
 
        m_ctf_applied = padfft->get_attr( "ctf_applied" );
 
        m_Cs = ctf_params["cs"];
        m_pixel = ctf_params["apix"];
        m_voltage = ctf_params["voltage"];
        m_amp_contrast = ctf_params["ampcont"];
        m_defocuses.push_back( ctf_params["defocus"] );
        if(ctf) {delete ctf; ctf=0;}
    }
 
    Dict params = tf.get_rotation( "spider" );
    float phi = params.get( "phi" );
    float tht = params.get( "theta" );
    float psi = params.get( "psi" );
 
 
    m_phis.push_back( phi );
    m_thetas.push_back( tht );
    m_psis.push_back( psi );
 
    if( m_write )
    {
        m_bin_ohandle->write( (char*)data, sizeof(float)*m_totsize );
 
        if( m_ctf )
        {
            *m_txt_ohandle << m_Cs << " ";
            *m_txt_ohandle << m_pixel << " ";
            *m_txt_ohandle << m_voltage << " ";
            *m_txt_ohandle << m_ctf_applied << " ";
            *m_txt_ohandle << m_amp_contrast << " ";
            *m_txt_ohandle << m_defocuses.back() << " ";
        }
        *m_txt_ohandle << m_phis.back() << " ";
        *m_txt_ohandle << m_thetas.back() << " ";
        *m_txt_ohandle << m_psis.back() << " ";
        *m_txt_ohandle << m_x_out << " ";
        *m_txt_ohandle << m_y_out << " ";
        *m_txt_ohandle << m_z_out << " ";
        *m_txt_ohandle << m_totsize << std::endl;
    }
 
    checked_delete(padfft);
 
}

References checked_delete(), EMAN::Dict::get(), EMAN::Transform::get_rotation(), 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(), and EMAN::Ctf::to_dict().

get_image()

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

Definition at line 6620 of file reconstructor.cpp.

{
 
    if( m_phis.size() == 0 ) {
        ifstream m_txt_ifs( m_txt_file.c_str() );
 
                if( !m_txt_ifs ) std::cerr << "Error: file " << m_txt_file << " does not exist" << std::endl;
 
 
                string line;
                std::getline( m_txt_ifs, line );
 
                float first, defocus, phi, theta, psi;
 
 
 
                while( m_txt_ifs >> first ) {
 
                        if( m_ctf ) {
                                m_Cs = first;
                                m_txt_ifs >> m_pixel >> m_voltage;
                                m_txt_ifs >> m_ctf_applied >> m_amp_contrast;
                                m_txt_ifs >> defocus >> phi >> theta >> psi;
                                m_defocuses.push_back( defocus );
                        } else {
                                phi = first;
                                m_txt_ifs >> theta >> psi;
                        }
 
                        m_txt_ifs >> m_x_out >> m_y_out >> m_z_out >> m_totsize;
                        m_phis.push_back( phi );
                        m_thetas.push_back( theta );
                        m_psis.push_back( psi );
                }
        }
 
        Assert( m_ihandle != NULL );
 
        std::istream::off_type offset = id*sizeof(float)*m_totsize;
        Assert( offset >= 0 );
 
        if( offset > 0 ) m_ihandle->seekg(offset, std::ios::beg);
 
 
        if( m_ihandle->bad() )
        {
                std::cout << "bad while fetching id, offset: " << id << " " << offset << std::endl;
                throw std::logic_error( "bad happen" );
        }
 
        if( m_ihandle->fail() )
        {
                std::cout << "fail while fetching id, offset, curoff: " << id << " " << offset << std::endl;
                throw std::logic_error( "fail happen" );
        }
 
        if( m_ihandle->eof() )
        {
                std::cout << "eof while fetching id, offset: " << id << " " << offset << std::endl;
                throw std::logic_error( "eof happen" );
        }
 
        if( padfft->get_xsize() != m_x_out ||
                padfft->get_ysize() != m_y_out ||
                padfft->get_zsize() != m_z_out )
        {
                padfft->set_size(m_x_out, m_y_out, m_z_out);
        }
 
        char* data = (char*)(padfft->get_data());
        m_ihandle->read( data, sizeof(float)*m_totsize );
        padfft->update();
 
        if( m_ctf ) {
                padfft->set_attr( "Cs", m_Cs );
                padfft->set_attr( "Pixel_size", m_pixel );
                padfft->set_attr( "voltage", m_voltage );
                padfft->set_attr( "ctf_applied", m_ctf_applied );
                padfft->set_attr( "amp_contrast", m_amp_contrast );
                padfft->set_attr( "defocus", m_defocuses[id] );
        }
 
        padfft->set_attr( "padffted", 1 );
        padfft->set_attr( "phi", m_phis[id] );
        padfft->set_attr( "theta", m_thetas[id] );
        padfft->set_attr( "psi", m_psis[id] );
 
}

References Assert, 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, and m_z_out.

restart()

void file_store::restart

(

)

Definition at line 6709 of file reconstructor.cpp.

{
    if( m_ihandle == NULL ) m_ihandle = shared_ptr< ifstream >( new ifstream(m_bin_file.c_str(), std::ios::in | std::ios::binary) );
 
 
    if( m_ihandle->bad() || m_ihandle->fail() || m_ihandle->eof() ) m_ihandle->open( m_bin_file.c_str(), std::ios::binary );
 
    m_ihandle->seekg( 0, std::ios::beg );
}

References m_bin_file, and m_ihandle.

Member Data Documentation

m_amp_contrast

float EMAN::file_store::m_amp_contrast

private

Definition at line 1808 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_bin_file

string EMAN::file_store::m_bin_file

private

Definition at line 1794 of file reconstructor.h.

Referenced by add_image(), and restart().

m_bin_ohandle

shared_ptr<std::ofstream> EMAN::file_store::m_bin_ohandle

private

Definition at line 1792 of file reconstructor.h.

Referenced by add_image().

m_Cs

float EMAN::file_store::m_Cs

private

Definition at line 1804 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_ctf

int EMAN::file_store::m_ctf

private

Definition at line 1796 of file reconstructor.h.

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

m_ctf_applied

float EMAN::file_store::m_ctf_applied

private

Definition at line 1807 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_defocuses

vector< float > EMAN::file_store::m_defocuses

private

Definition at line 1809 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_ihandle

shared_ptr<std::ifstream> EMAN::file_store::m_ihandle

private

Definition at line 1791 of file reconstructor.h.

Referenced by get_image(), and restart().

m_npad

int EMAN::file_store::m_npad

private

Definition at line 1797 of file reconstructor.h.

Referenced by add_image(), and file_store().

m_phis

vector< float > EMAN::file_store::m_phis

private

Definition at line 1810 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_pixel

float EMAN::file_store::m_pixel

private

Definition at line 1805 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_prev

int EMAN::file_store::m_prev

private

Definition at line 1798 of file reconstructor.h.

Referenced by file_store().

m_psis

vector< float > EMAN::file_store::m_psis

private

Definition at line 1812 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_thetas

vector< float > EMAN::file_store::m_thetas

private

Definition at line 1811 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_totsize

std::istream::off_type EMAN::file_store::m_totsize

private

Definition at line 1803 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_txt_file

string EMAN::file_store::m_txt_file

private

Definition at line 1795 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_txt_ohandle

shared_ptr<std::ofstream> EMAN::file_store::m_txt_ohandle

private

Definition at line 1793 of file reconstructor.h.

Referenced by add_image().

m_voltage

float EMAN::file_store::m_voltage

private

Definition at line 1806 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_write

int EMAN::file_store::m_write

private

Definition at line 1802 of file reconstructor.h.

Referenced by add_image(), and file_store().

m_x_out

int EMAN::file_store::m_x_out

private

Definition at line 1799 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_y_out

int EMAN::file_store::m_y_out

private

Definition at line 1800 of file reconstructor.h.

Referenced by add_image(), and get_image().

m_z_out

int EMAN::file_store::m_z_out

private

Definition at line 1801 of file reconstructor.h.

Referenced by add_image(), and get_image().

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The documentation for this class was generated from the following files:

• reconstructor.h
• reconstructor.cpp