CTFDescription Class Reference

#include <ctf.h>

Inheritance diagram for CTFDescription:

Collaboration diagram for CTFDescription:

Public Member Functions
	CTFDescription ()
	CTFDescription (CTFDescription1D copy)
void	read (const FileName &fn, bool disable_if_not_K=true)
void	readFromMetadataRow (const MetaData &MD, size_t id, bool disable_if_not_K=true)
void	readFromMdRow (const MDRow &row, bool disable_if_not_K=true)
void	setRow (MDRow &row) const
void	write (const FileName &fn)
void	readParams (XmippProgram *program)
	Read parameters from the command line. More...
void	clear ()
	Clear. More...
void	clearNoise ()
	Clear noise. More...
void	clearPureCtf ()
	Clear pure CTF. More...
void	changeSamplingRate (double newTm)
void	produceSideInfo ()
	Produce Side information. More...
void	precomputeValues (double X, double Y)
	Precompute values for a given frequency. More...
void	precomputeValues (const MultidimArray< double > &cont_x_freq, const MultidimArray< double > &cont_y_freq)
	Precompute values for an image. More...
void	precomputeValues (int i, int j)
	Precompute values for a given frequency. More...
double	getValueAt (bool show=false) const
	Compute CTF at (U,V). Continuous frequencies. More...
double	getValueArgument (bool show=false) const
	Compute pure CTF without damping at (U,V). Continuous frequencies. More...
double	getPhaseAt () const
	Get Phase of the CTF. More...
double	getValuePureNoPrecomputedAtxy (double X, double Y, bool show=false) const
	Compute CTF pure at (U,V). Continuous frequencies. More...
double	getValuePureNoDampingNoPrecomputedAt (double X, double Y) const
	Compute CTF pure at (U,V). Continuous frequencies. More...
double	getDeltafNoPrecomputed (double X, double Y) const
	Deltaf at a given direction. More...
double	getValueNoiseAt (bool show=false) const
	Compute noise at (X,Y). Continuous frequencies, notice it is squared. More...
void	lookFor (int n, const Matrix1D< double > &u, Matrix1D< double > &freq, int iwhat=0)
void	applyCTF (MultidimArray< std::complex< double > > &FFTI, const MultidimArray< double > &I, double Ts, bool absPhase=false)
	Apply CTF to an image. More...
void	applyCTF (MultidimArray< double > &I, double Ts, bool absPhase=false)
	Apply CTF to an image. More...
void	correctPhase (MultidimArray< std::complex< double > > &FFTI, const MultidimArray< double > &I, double Ts)
	Correct phase flip of an image. More...
void	correctPhase (MultidimArray< double > &I, double Ts)
	Correct phase flip of an image. More...
template<class T1 , class T2 >
void	generateCTF (const MultidimArray< T1 > &sample_image, MultidimArray< T2 > &CTF, double Ts=-1)
void	getProfile (double angle, double fmax, int nsamples, MultidimArray< double > &profiles)
void	getAverageProfile (double fmax, int nsamples, MultidimArray< double > &profiles)
template<class T >
void	generateCTF (int Ydim, int Xdim, MultidimArray< T > &CTF, double Ts=-1)
	Generate CTF image. More...
template<class T >
void	generateCTFWithoutDamping (int Ydim, int Xdim, MultidimArray< T > &CTF, double Ts=-1)
template<class T >
void	generateEnvelope (int Ydim, int Xdim, MultidimArray< T > &CTF, double Ts=-1)
bool	hasPhysicalMeaning ()
void	forcePhysicalMeaning ()
Public Member Functions inherited from CTFDescription1D
	CTFDescription1D ()
void	read (const FileName &fn, bool disable_if_not_K=true)
void	readFromMetadataRow (const MetaData &MD, size_t id, bool disable_if_not_K=true)
void	readFromMdRow (const MDRow &row, bool disable_if_not_K=true)
void	setRow (MDRow &row) const
void	write (const FileName &fn)
void	readParams (XmippProgram *program)
	Read parameters from the command line. More...
void	clear ()
	Clear. More...
void	clearNoise ()
	Clear noise. More...
void	clearPureCtf ()
	Clear pure CTF. More...
void	changeSamplingRate (double newTm)
void	produceSideInfo ()
	Produce Side information. More...
void	precomputeValues (double X)
	Precompute values for a given frequency. More...
void	precomputeValues (const MultidimArray< double > &cont_x_freq)
	Precompute values for an image. More...
void	precomputeValues (int i)
	Precompute values for a given frequency. More...
double	getValueAt (bool show=false) const
	Compute CTF at (U,V). Continuous frequencies. More...
double	getValueDampingAt (bool show=false) const
	Compute CTF damping at (U,V). Continuous frequencies. More...
double	getValuePureAt (bool show=false) const
	Compute CTF pure at (U,V). Continuous frequencies. More...
double	getValuePureNoKAt () const
	Compute CTF pure at (U,V). Continuous frequencies. More...
double	getValueNoiseAt (bool show=false) const
	Compute noise at (X,Y). Continuous frequencies, notice it is squared. More...
double	getValuePureWithoutDampingAt (bool show=false) const
	Compute pure CTF without damping at (U,V). Continuous frequencies. More...
void	getSineAndCosineParts (double &sine_part, double &cosine_part, double E, double u2, double deltaf, bool show) const
double	getValuePureNoPrecomputedAt (double X, bool show=false) const
	Compute CTF pure at (U,V). Continuous frequencies. More...
void	lookFor (int n, const Matrix1D< double > &u, Matrix1D< double > &freq, int iwhat=0)
void	applyCTF (MultidimArray< std::complex< double > > &FFTI, const MultidimArray< double > &I, double Ts, bool absPhase=false)
	Apply CTF to an image. More...
void	applyCTF (MultidimArray< double > &I, double Ts, bool absPhase=false)
	Apply CTF to an image. More...
void	correctPhase (MultidimArray< std::complex< double > > &FFTI, const MultidimArray< double > &I, double Ts)
	Correct phase flip of an image. More...
void	correctPhase (MultidimArray< double > &I, double Ts)
	Correct phase flip of an image. More...
template<class T1 , class T2 >
void	generateCTF (const MultidimArray< T1 > &sample_image, MultidimArray< T2 > &CTF, double Ts=-1)
void	getProfile (double fmax, int nsamples, MultidimArray< double > &profiles)
void	getAverageProfile (double fmax, int nsamples, MultidimArray< double > &profiles)
template<class T >
double	initCTF (int Ydim, int Xdim, MultidimArray< T > &CTF, double Ts=-1) const
	Function to initialize CTF to avoid duplicated code. More...
template<class T >
void	generateCTF (int Ydim, int Xdim, MultidimArray< T > &CTF, double Ts=-1)
	Generate CTF image. More...
template<class T >
void	generateCTFWithoutDamping (int Ydim, int Xdim, MultidimArray< T > &CTF, double Ts=-1)
bool	hasPhysicalMeaning ()
void	forcePhysicalMeaning ()

Static Public Member Functions
static void	defineParams (XmippProgram *program)
	Define parameters in the command line. More...
Static Public Member Functions inherited from CTFDescription1D
static void	defineParams (XmippProgram *program)
	Define parameters in the command line. More...

Public Attributes
double	rad_azimuth
double	defocus_average
double	defocus_deviation
double	rad_gaussian
double	rad_gaussian2
double	rad_sqrt
double	DeltafU
	Global gain. By default, 1. More...
double	DeltafV
	Defocus in V (in Angstroms). Negative values are underfocused. More...
double	azimuthal_angle
	Azimuthal angle (between X and U) in degrees. More...
double	sigmaU
	Spherical aberration (in milimeters). Typical value 5.6. More...
double	sigmaV
	Gaussian width V. More...
double	cU
	Gaussian center for U. More...
double	cV
	Gaussian center for V. More...
double	gaussian_angle
	Gaussian angle. More...
double	sqU
	Gain for the square root term. More...
double	sqV
	Sqrt width V. More...
double	sqrt_angle
	Sqrt angle. More...
double	sigmaU2
	Second Gaussian width U. More...
double	sigmaV2
	Second Gaussian width V. More...
double	cU2
	Second Gaussian center for U. More...
double	cV2
	Second Gaussian center for V. More...
double	gaussian_angle2
	Second Gaussian angle. More...
Public Attributes inherited from CTFDescription1D
double	lambda
double	K1
double	K2
double	K3
double	K4
double	K5
double	K6
double	K7
double	Ksin
double	Kcos
double	D
PrecomputedForCTF	precomputed
std::vector< PrecomputedForCTF >	precomputedImage
int	precomputedImageXdim
double	K
	Global gain. By default, 1. More...
double	Tm
	Sampling rate (A/pixel) More...
double	kV
	Accelerating Voltage (in KiloVolts) More...
double	Defocus
	Defocus (in Angstroms). Negative values are underfocused. More...
double	Cs
	Spherical aberration (in milimeters). Typical value 5.6. More...
double	Ca
	Chromatic aberration (in milimeters). Typical value 2. More...
double	espr
double	ispr
	Objective lens stability (deltaI/I) (ppm). Typical value 1. More...
double	alpha
	Convergence cone semiangle (in mrad). Typical value 0.5. More...
double	DeltaF
	Longitudinal mechanical displacement (ansgtrom). Typical value 100. More...
double	DeltaR
	Transversal mechanical displacement (ansgtrom). Typical value 3. More...
double	Q0
	Factor for the importance of the Amplitude contrast. More...
double	x0
	In the case of local CTF determination x0,xF,y0,yF determines the region where the CTF is determined. More...
double	xF
	In the case of local CTF determination x0,xF,y0,yF determines the region where the CTF is determined. More...
double	y0
	In the case of local CTF determination x0,xF,y0,yF determines the region where the CTF is determined. More...
double	yF
	In the case of local CTF determination x0,xF,y0,yF determines the region where the CTF is determined. More...
bool	isLocalCTF
	Local CTF determination. More...
bool	enable_CTFnoise
	Enable CTFnoise part. More...
bool	enable_CTF
	Enable CTF part. More...
double	base_line
	Global base_line. More...
double	gaussian_K
	Gain for the gaussian term. More...
double	sigma1
	Gaussian width. More...
double	Gc1
	Gaussian center. More...
double	sqrt_K
	Gain for the square root term. More...
double	sq
	Sqrt width. More...
double	gaussian_K2
	Gain for the second Gaussian term. More...
double	sigma2
	Second Gaussian width. More...
double	Gc2
	Second Gaussian center. More...
double	bgR1
double	bgR2
double	bgR3
double	envR0
double	envR1
double	envR2
double	freq_max
double	phase_shift
double	VPP_radius

Friends
std::ostream &	operator<< (std::ostream &out, const CTFDescription &ctf)
	Show. More...

Detailed Description

Definition at line 782 of file ctf.h.

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

• xmipp/libraries/data/ctf.h
• xmipp/libraries/data/ctf.cpp