EMAN::Ctf Class Reference

Ctf is the base class for all CTF model. More...

#include <ctf.h>

Inheritance diagram for EMAN::Ctf:

Public Types
enum	CtfType {   CTF_AMP , CTF_SIGN , CTF_BACKGROUND , CTF_SNR ,   CTF_SNR_SMOOTH , CTF_WIENER_FILTER , CTF_TOTAL , CTF_FITREF ,   CTF_NOISERATIO , CTF_INTEN , CTF_POWEVAL , CTF_ALIFILT ,   CTF_ABS }

Public Member Functions
virtual	~Ctf ()
virtual int	from_string (const string &ctf)=0
virtual string	to_string () const =0
virtual void	from_dict (const Dict &dict)=0
virtual Dict	to_dict () const =0
virtual void	from_vector (const vector< float > &vctf)=0
virtual vector< float >	to_vector () const =0
virtual float	zero (int n) const =0
virtual vector< float >	compute_1d (int size, float ds, CtfType t, XYData *struct_factor=0)=0
virtual vector< float >	compute_1d_fromimage (int size, float ds, EMData *image)=0
virtual void	compute_2d_real (EMData *img, CtfType t, XYData *struct_factor=0)=0
virtual void	compute_2d_complex (EMData *img, CtfType t, XYData *struct_factor=0)=0
virtual void	copy_from (const Ctf *new_ctf)=0
virtual bool	equal (const Ctf *ctf1) const =0
virtual float	get_phase () const =0
virtual void	set_phase (float phase)=0

Public Attributes
float	defocus
float	bfactor
float	voltage
float	cs
float	apix

Detailed Description

Ctf is the base class for all CTF model.

Contrast transfer function (CTF) is the function that describes the transfer of information from the object to the contrast observed in the image for electron microscopy.

Definition at line 59 of file ctf.h.

Member Enumeration Documentation

CtfType

enum EMAN::Ctf::CtfType

Enumerator
CTF_AMP
CTF_SIGN
CTF_BACKGROUND
CTF_SNR
CTF_SNR_SMOOTH
CTF_WIENER_FILTER
CTF_TOTAL
CTF_FITREF
CTF_NOISERATIO
CTF_INTEN
CTF_POWEVAL
CTF_ALIFILT
CTF_ABS

Definition at line 63 of file ctf.h.

                {
                        CTF_AMP,                        // ctf ampltidue only
                        CTF_SIGN,                       // ctf sign (+-1)
                        CTF_BACKGROUND,         // Background, no ctf oscillation
                        CTF_SNR,                        // Signal to noise ratio
                        CTF_SNR_SMOOTH,         // Signal to noise ratio, smoothed, algorithm may vary, but this should be more suitable for weighting
                        CTF_WIENER_FILTER,      // Weiner Filter = 1/(1+1/snr)
                        CTF_TOTAL,                      // AMP*AMP+NOISE
                        CTF_FITREF,                     // CTF amplitude squared without B-factor and low resolution zeroed
                        CTF_NOISERATIO,         // 1-Noise/Total, when a particle is filtered with this it will still have noise, but the structure factor will look as if it's noise-free
                        CTF_INTEN,                      // ctf intensity only (no background or envelope)
                        CTF_POWEVAL,            // ctf intensity, no B-factor and filtered below 20 A
                        CTF_ALIFILT,                    // ctf intensity -> mean subtracted to cause phase-flipping near zeroes, used to focus alignment on Thon rings
                        CTF_ABS                         // ctf ampltidue only (abs value)
                };

Constructor & Destructor Documentation

~Ctf()

virtual EMAN::Ctf::~Ctf ( )

inlinevirtual

Definition at line 80 of file ctf.h.

                {
                }

Member Function Documentation

compute_1d()

virtual vector< float > EMAN::Ctf::compute_1d ( int  size, float  ds, CtfType  t, XYData *  struct_factor = 0  )

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

Referenced by EMAN::PhaseCmp::cmp(), EMAN::FRCCmp::cmp(), and EMAN::SNRProcessor::process_inplace().

compute_1d_fromimage()

virtual vector< float > EMAN::Ctf::compute_1d_fromimage ( int  size, float  ds, EMData *  image  )

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

compute_2d_complex()

virtual void EMAN::Ctf::compute_2d_complex ( EMData *  img, CtfType  t, XYData *  struct_factor = 0  )

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

Referenced by EMAN::CtfWtAverager::add_image(), EMAN::CtfWtFiltAverager::add_image(), EMAN::CtfCAutoAverager::add_image(), EMAN::CtfCWautoAverager::add_image(), EMAN::Wiener2DFourierProcessor::process(), and EMAN::SubtractOptProcessor::process().

compute_2d_real()

virtual void EMAN::Ctf::compute_2d_real ( EMData *  img, CtfType  t, XYData *  struct_factor = 0  )

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

copy_from()

virtual void EMAN::Ctf::copy_from ( const Ctf *  new_ctf )

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

equal()

virtual bool EMAN::Ctf::equal ( const Ctf *  ctf1 ) const

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

Referenced by EMAN::EMUtil::is_same_ctf().

from_dict()

virtual void EMAN::Ctf::from_dict ( const Dict &  dict )

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

from_string()

virtual int EMAN::Ctf::from_string ( const string &  ctf )

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

Referenced by EMAN::EMObject::operator Ctf *(), EMAN::ImagicIO2::read_ctf(), EMAN::ImagicIO::read_ctf(), and EMAN::MrcIO::read_ctf().

from_vector()

virtual void EMAN::Ctf::from_vector ( const vector< float > &  vctf )

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

get_phase()

virtual float EMAN::Ctf::get_phase ( ) const

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

set_phase()

virtual void EMAN::Ctf::set_phase ( float  phase )

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

to_dict()

virtual Dict EMAN::Ctf::to_dict ( ) const

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

Referenced by EMAN::newfile_store::add_image(), EMAN::file_store::add_image(), ctf_store_real::init(), EMAN::nn4_ctfReconstructor::insert_slice(), EMAN::nn4_ctfwReconstructor::insert_slice(), and EMAN::nn4_ctfwsReconstructor::insert_slice().

to_string()

virtual string EMAN::Ctf::to_string ( ) const

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

Referenced by EMAN::MrcIO::write_ctf(), EMAN::ImagicIO::write_ctf(), and EMAN::ImagicIO2::write_ctf().

to_vector()

virtual vector< float > EMAN::Ctf::to_vector ( ) const

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

zero()

virtual float EMAN::Ctf::zero ( int  n ) const

pure virtual

Implemented in EMAN::EMAN1Ctf, and EMAN::EMAN2Ctf.

Member Data Documentation

apix

float EMAN::Ctf::apix

Definition at line 88 of file ctf.h.

Referenced by EMAN::PhaseCmp::cmp(), EMAN::FRCCmp::cmp(), EMAN::EMAN1Ctf::compute_2d_complex(), EMAN::EMAN2Ctf::compute_2d_complex(), EMAN::EMAN1Ctf::copy_from(), EMAN::EMAN2Ctf::copy_from(), EMAN::SetSFProcessor::create_radial_func(), EMAN::EMAN1Ctf::EMAN1Ctf(), EMAN::EMAN2Ctf::EMAN2Ctf(), EMAN::EMAN1Ctf::equal(), EMAN::EMAN2Ctf::equal(), EMAN::EMAN1Ctf::from_dict(), EMAN::EMAN2Ctf::from_dict(), EMAN::EMAN1Ctf::from_string(), EMAN::EMAN2Ctf::from_string(), EMAN::EMAN1Ctf::from_vector(), EMAN::EMAN2Ctf::from_vector(), EMAN::CtfSimProcessor::process(), EMAN::CTFCorrProcessor::process_inplace(), EMAN::SNRProcessor::process_inplace(), EMAN::SetIsoPowProcessor::process_inplace(), scale_pixel(), EMAN::EMAN1Ctf::to_dict(), EMAN::EMAN2Ctf::to_dict(), EMAN::EMAN1Ctf::to_string(), EMAN::EMAN2Ctf::to_string(), EMAN::EMAN1Ctf::to_vector(), and EMAN::EMAN2Ctf::to_vector().

bfactor

float EMAN::Ctf::bfactor

Definition at line 85 of file ctf.h.

Referenced by EMAN::CtfWtAverager::add_image(), EMAN::CtfWtFiltAverager::add_image(), EMAN::CtfCAutoAverager::add_image(), EMAN::CtfCWautoAverager::add_image(), EMAN::EMAN1Ctf::calc_ctf1(), EMAN::EMAN2Ctf::compute_1d(), EMAN::EMAN2Ctf::compute_2d_complex(), EMAN::EMAN1Ctf::copy_from(), EMAN::EMAN2Ctf::copy_from(), EMAN::EMAN1Ctf::EMAN1Ctf(), EMAN::EMAN2Ctf::EMAN2Ctf(), EMAN::EMAN1Ctf::equal(), EMAN::EMAN2Ctf::equal(), EMAN::EMAN1Ctf::from_dict(), EMAN::EMAN2Ctf::from_dict(), EMAN::EMAN1Ctf::from_string(), EMAN::EMAN2Ctf::from_string(), EMAN::EMAN1Ctf::from_vector(), EMAN::EMAN2Ctf::from_vector(), EMAN::EMAN1Ctf::get_bfactor(), EMAN::CtfSimProcessor::process(), EMAN::CTFCorrProcessor::process_inplace(), EMAN::EMAN1Ctf::to_dict(), EMAN::EMAN2Ctf::to_dict(), EMAN::EMAN1Ctf::to_string(), EMAN::EMAN2Ctf::to_string(), EMAN::EMAN1Ctf::to_vector(), and EMAN::EMAN2Ctf::to_vector().

cs

float EMAN::Ctf::cs

Definition at line 87 of file ctf.h.

Referenced by EMAN::EMAN1Ctf::calc_g1(), EMAN::EMAN2Ctf::compute_1d(), EMAN::EMAN2Ctf::compute_2d_complex(), EMAN::EMAN1Ctf::copy_from(), EMAN::EMAN2Ctf::copy_from(), EMAN::EMAN1Ctf::EMAN1Ctf(), EMAN::EMAN2Ctf::EMAN2Ctf(), EMAN::EMAN1Ctf::equal(), EMAN::EMAN2Ctf::equal(), EMAN::EMAN1Ctf::from_dict(), EMAN::EMAN2Ctf::from_dict(), EMAN::EMAN1Ctf::from_string(), EMAN::EMAN2Ctf::from_string(), EMAN::EMAN1Ctf::from_vector(), EMAN::EMAN2Ctf::from_vector(), EMAN::CtfSimProcessor::process(), EMAN::CTFCorrProcessor::process_inplace(), EMAN::EMAN2Ctf::stos2(), EMAN::EMAN1Ctf::to_dict(), EMAN::EMAN2Ctf::to_dict(), EMAN::EMAN1Ctf::to_string(), EMAN::EMAN2Ctf::to_string(), EMAN::EMAN1Ctf::to_vector(), EMAN::EMAN2Ctf::to_vector(), and EMAN::EMAN2Ctf::zero().

defocus

float EMAN::Ctf::defocus

Definition at line 84 of file ctf.h.

Referenced by EMAN::EMAN1Ctf::calc_g2(), EMAN::EMAN2Ctf::compute_1d(), EMAN::EMAN2Ctf::compute_2d_complex(), EMAN::EMAN1Ctf::copy_from(), EMAN::EMAN2Ctf::copy_from(), EMAN::EMAN2Ctf::df(), EMAN::EMAN1Ctf::EMAN1Ctf(), EMAN::EMAN2Ctf::EMAN2Ctf(), EMAN::EMAN1Ctf::equal(), EMAN::EMAN2Ctf::equal(), EMAN::EMAN1Ctf::from_dict(), EMAN::EMAN2Ctf::from_dict(), EMAN::EMAN1Ctf::from_string(), EMAN::EMAN2Ctf::from_string(), EMAN::EMAN1Ctf::from_vector(), EMAN::EMAN2Ctf::from_vector(), EMAN::EMAN1Ctf::get_defocus(), EMAN::CtfSimProcessor::process(), EMAN::CTFCorrProcessor::process_inplace(), EMAN::EMAN2Ctf::stos2(), EMAN::EMAN1Ctf::to_dict(), EMAN::EMAN2Ctf::to_dict(), EMAN::EMAN1Ctf::to_string(), EMAN::EMAN2Ctf::to_string(), EMAN::EMAN1Ctf::to_vector(), EMAN::EMAN2Ctf::to_vector(), and EMAN::EMAN2Ctf::zero().

voltage

float EMAN::Ctf::voltage

Definition at line 86 of file ctf.h.

Referenced by EMAN::EMAN1Ctf::calc_lambda(), EMAN::EMAN1Ctf::copy_from(), EMAN::EMAN2Ctf::copy_from(), EMAN::EMAN1Ctf::EMAN1Ctf(), EMAN::EMAN2Ctf::EMAN2Ctf(), EMAN::EMAN1Ctf::equal(), EMAN::EMAN2Ctf::equal(), EMAN::EMAN1Ctf::from_dict(), EMAN::EMAN2Ctf::from_dict(), EMAN::EMAN1Ctf::from_string(), EMAN::EMAN2Ctf::from_string(), EMAN::EMAN1Ctf::from_vector(), EMAN::EMAN2Ctf::from_vector(), EMAN::EMAN2Ctf::lambda(), EMAN::CtfSimProcessor::process(), EMAN::CTFCorrProcessor::process_inplace(), EMAN::EMAN1Ctf::to_dict(), EMAN::EMAN2Ctf::to_dict(), EMAN::EMAN1Ctf::to_string(), EMAN::EMAN2Ctf::to_string(), EMAN::EMAN1Ctf::to_vector(), and EMAN::EMAN2Ctf::to_vector().

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

• ctf.h