EMAN::Ctf Class Reference

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

#include <ctf.h>

Inheritance diagram for EMAN::Ctf:

Inheritance graph
[legend]
List of all members.

Public Types

 CTF_AMP
 CTF_SIGN
 CTF_BACKGROUND
 CTF_SNR
 CTF_SNR_SMOOTH
 CTF_WIENER_FILTER
 CTF_TOTAL
 CTFOS = 5
enum  CtfType {
  CTF_AMP, CTF_SIGN, CTF_BACKGROUND, CTF_SNR,
  CTF_SNR_SMOOTH, CTF_WIENER_FILTER, CTF_TOTAL
}
enum  { CTFOS = 5 }

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

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 63 of file ctf.h.


Member Enumeration Documentation

anonymous enum

Enumerator:
CTFOS 

Definition at line 105 of file ctf.h.

00106                 { CTFOS = 5 };

enum EMAN::Ctf::CtfType

Enumerator:
CTF_AMP 
CTF_SIGN 
CTF_BACKGROUND 
CTF_SNR 
CTF_SNR_SMOOTH 
CTF_WIENER_FILTER 
CTF_TOTAL 

Definition at line 67 of file ctf.h.

00068                 {
00069                         CTF_AMP,                        // ctf ampltidue only
00070                         CTF_SIGN,                       // ctf sign (+-1)
00071                         CTF_BACKGROUND,         // Background, no ctf oscillation
00072                         CTF_SNR,                        // Signal to noise ratio
00073                         CTF_SNR_SMOOTH,         // Signal to noise ratio, smoothed, algorithm may vary, but this should be more suitable for weighting
00074                         CTF_WIENER_FILTER,      // Weiner Filter = 1/(1+1/snr)
00075                         CTF_TOTAL                       // AMP*AMP+NOISE
00076                 };


Constructor & Destructor Documentation

virtual EMAN::Ctf::~Ctf (  )  [inline, virtual]

Definition at line 78 of file ctf.h.

00079                 {
00080                 }


Member Function Documentation

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

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

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

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

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

virtual void EMAN::Ctf::copy_from ( const Ctf new_ctf  )  [pure virtual]

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

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().

virtual void EMAN::Ctf::from_dict ( const Dict dict  )  [pure virtual]

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

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::MrcIO::read_ctf(), EMAN::ImagicIO2::read_ctf(), and EMAN::ImagicIO::read_ctf().

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

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

Referenced by EMAN::EMData::get_ctf().

virtual Dict EMAN::Ctf::to_dict (  )  const [pure virtual]

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

Referenced by EMAN::file_store::add_image(), EMAN::newfile_store::add_image(), ctf_store_new::init(), and ctf_store::init().

virtual string EMAN::Ctf::to_string (  )  const [pure virtual]

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

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

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

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

Referenced by EMAN::EMData::set_ctf().


Member Data Documentation

float EMAN::Ctf::apix

Definition at line 86 of file ctf.h.

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

float EMAN::Ctf::bfactor

Definition at line 83 of file ctf.h.

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

float EMAN::Ctf::cs

Definition at line 85 of file ctf.h.

Referenced by EMAN::EMAN2Ctf::calc_g1(), EMAN::EMAN1Ctf::calc_g1(), EMAN::EMAN2Ctf::copy_from(), EMAN::EMAN1Ctf::copy_from(), EMAN::EMAN1Ctf::EMAN1Ctf(), EMAN::EMAN2Ctf::EMAN2Ctf(), EMAN::EMAN2Ctf::equal(), EMAN::EMAN1Ctf::equal(), EMAN::EMAN2Ctf::from_dict(), EMAN::EMAN1Ctf::from_dict(), EMAN::EMAN2Ctf::from_string(), EMAN::EMAN1Ctf::from_string(), EMAN::EMAN2Ctf::from_vector(), EMAN::EMAN1Ctf::from_vector(), EMAN::CtfSimProcessor::process(), EMAN::EMAN2Ctf::to_dict(), EMAN::EMAN1Ctf::to_dict(), EMAN::EMAN2Ctf::to_string(), EMAN::EMAN1Ctf::to_string(), EMAN::EMAN2Ctf::to_vector(), and EMAN::EMAN1Ctf::to_vector().

float EMAN::Ctf::defocus

Definition at line 82 of file ctf.h.

Referenced by EMAN::EMAN2Ctf::calc_g2(), EMAN::EMAN1Ctf::calc_g2(), EMAN::EMAN2Ctf::copy_from(), EMAN::EMAN1Ctf::copy_from(), EMAN::EMAN1Ctf::EMAN1Ctf(), EMAN::EMAN2Ctf::EMAN2Ctf(), EMAN::EMAN2Ctf::equal(), EMAN::EMAN1Ctf::equal(), EMAN::EMAN2Ctf::from_dict(), EMAN::EMAN1Ctf::from_dict(), EMAN::EMAN2Ctf::from_string(), EMAN::EMAN1Ctf::from_string(), EMAN::EMAN2Ctf::from_vector(), EMAN::EMAN1Ctf::from_vector(), EMAN::EMAN1Ctf::get_defocus(), EMAN::CtfSimProcessor::process(), EMAN::EMAN2Ctf::to_dict(), EMAN::EMAN1Ctf::to_dict(), EMAN::EMAN2Ctf::to_string(), EMAN::EMAN1Ctf::to_string(), EMAN::EMAN2Ctf::to_vector(), and EMAN::EMAN1Ctf::to_vector().

float EMAN::Ctf::voltage

Definition at line 84 of file ctf.h.

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


The documentation for this class was generated from the following file:
Generated on Tue Jun 11 12:43:00 2013 for EMAN2 by  doxygen 1.4.7