#include <ctf.h>

Public Member Functions
	CTFparam ()

	CTFparam (string s)

	CTFparam (double v, double sa, double ac)

int	update (CTFparam *ctf)

int	update (CTFparam &ctf)
	Updates a CTF structure from another. More...

void	identifier (string s)

string &	identifier ()

long	select ()

void	select (long i)

double	volt ()

void	volt (double v)

double	focal_length ()

void	focal_length (double v)

double	Cc ()

void	Cc (double v)

double	alpha ()

void	alpha (double v)

double	dE ()

void	dE (double v)

double	aberration_weight (long n, long m)

void	aberration_weight (long n, long m, double v)

void	add_aberration_weight (long n, long m, double v)

map< pair< long, long >, double > &	aberration_weights ()

void	aberration_weights (map< pair< long, long >, double > &wa)

void	update_aberration_weights (map< pair< long, long >, double > &wa)

double	objective_aperture ()

void	objective_aperture (double v)

double	slit_width ()

void	slit_width (double v)

double	amp_shift ()

void	amp_shift (double v)

double	beam_tiltX ()

double	beam_tiltY ()

void	beam_tiltX (double v)

void	beam_tiltY (double v)

void	beam_tilt (double x, double y)

double	defocus_average ()

void	defocus_average (double v)

double	defocus_deviation ()

double	astigmatism_angle ()

void	astigmatism (double dev, double ang)

double	Cs ()

void	Cs (double v)

long	baseline_type ()

void	baseline_type (long t)

vector< double > &	baseline ()

double	baseline (int i)

void	baseline (int i, double d)

void	baseline (double *b)

void	baseline (vector< double > &b)

void	baseline (long t, vector< double > &b)

long	envelope_type ()

void	envelope_type (long t)

vector< double > &	envelope ()

double	envelope (int i)

void	envelope (int i, double d)

void	envelope (double *v)

void	envelope (vector< double > &v)

void	envelope (long t, vector< double > &v)

double	fom ()

void	fom (double v)

double	aberration_coefficient (long n, long m)

double	aberration_coefficient (pair< long, long > a)

string	aberration_weight_string ()

vector< double >	aberration_even ()

vector< double >	aberration_even_difference ()

void	aberration_even (vector< double > &v)

void	aberration_even_update (vector< double > &v)

vector< double >	aberration_odd ()

void	aberration_odd (vector< double > &v)

void	aberration_odd_update (vector< double > &v)

void	convert_zernike ()

void	add_zernike_even (vector< double > &v)

void	add_zernike_odd (vector< double > &v)

vector< double >	zernike_even ()

vector< double >	zernike_odd ()

void	delete_aberration (int which=3)

bool	check_defocus ()

double	lambda ()

double	frequency_cutoff ()

long double	calculate_aberration_even (double s2, double angle)

long double	calculate_aberration_odd (double s2, double angle)

Complex< double >	aberration_odd_complex (double s2, double angle)

long double	delta_phi (double s2, double angle)

long double	calculate (double s2, double angle)

vector< double >	calculate (int nrad, int npsi, double step_size)
	Calculates a CTF curve. More...

Complex< double >	calculate_complex (double s2, double angle)

double	calc_baseline (double s)

double	calc_envelope (double s)

vector< double >	zeroes (double max_s)
	Calculates the zeroes of a CTF curve on the spatial frequency scale. More...

vector< double >	maxima (double max_s)
	Calculates the maxima of a CTF curve on the spatial frequency scale. More...

Bstring	baseline_equation ()
	Generates a baseline equation string from 4 to 10 coefficients. More...

Bstring	envelope_equation ()
	Generates an envelope equation string from 4 coefficients. More...

int	parse_baseline_equation (Bstring base_eq)
	Extracts the coefficients from the baseline string. More...

int	parse_envelope_equation (Bstring env_eq)
	Extracts the coefficients from the envelope string. More...

double	partial_coherence (double s)
	Calculates the envelope curve based on partial coherence. More...

vector< double >	envelope_partial_coherence (long n, double freq_step)
	Calculates the envelope curve based on partial coherence. More...

double	energy_spread (double s2)
	Calculates the envelope curve based on energy spread. More...

vector< double >	envelope_energy_spread (long n, double freq_step)
	Calculates the envelope curve based on energy spread. More...

double	partial_coherence_and_energy_spread (double s2)
	Calculates the envelope curve based on partial coherence and energy spread. More...

double	zero (int i)

double	defocus_for_first_zero (double s)

void	show ()

void	show_aberration ()

void	show_baseline ()

void	show_envelope ()

Constructor & Destructor Documentation

◆ CTFparam() [1/3]

CTFparam::CTFparam ( )

inline

◆ CTFparam() [2/3]

CTFparam::CTFparam ( string s )

inline

◆ CTFparam() [3/3]

CTFparam::CTFparam	(	double	v,
		double	sa,
		double	ac
	)

inline

Member Function Documentation

◆ aberration_coefficient() [1/2]

double CTFparam::aberration_coefficient	(	long	n,
		long	m
	)

inline

◆ aberration_coefficient() [2/2]

double CTFparam::aberration_coefficient ( pair< long, long > a )

inline

◆ aberration_even() [1/2]

vector< double > CTFparam::aberration_even ( )

inline

◆ aberration_even() [2/2]

void CTFparam::aberration_even ( vector< double > & v )

inline

◆ aberration_even_difference()

vector< double > CTFparam::aberration_even_difference ( )

inline

◆ aberration_even_update()

void CTFparam::aberration_even_update ( vector< double > & v )

inline

◆ aberration_odd() [1/2]

vector< double > CTFparam::aberration_odd ( )

inline

◆ aberration_odd() [2/2]

void CTFparam::aberration_odd ( vector< double > & v )

inline

◆ aberration_odd_complex()

Complex< double > CTFparam::aberration_odd_complex	(	double	s2,
		double	angle
	)

inline

◆ aberration_odd_update()

void CTFparam::aberration_odd_update ( vector< double > & v )

inline

◆ aberration_weight() [1/2]

double CTFparam::aberration_weight	(	long	n,
		long	m
	)

inline

◆ aberration_weight() [2/2]

void CTFparam::aberration_weight	(	long	n,
		long	m,
		double	v
	)

inline

◆ aberration_weight_string()

string CTFparam::aberration_weight_string ( )

inline

◆ aberration_weights() [1/2]

map< pair< long, long >, double > & CTFparam::aberration_weights ( )

inline

◆ aberration_weights() [2/2]

void CTFparam::aberration_weights ( map< pair< long, long >, double > & wa )

inline

◆ add_aberration_weight()

void CTFparam::add_aberration_weight	(	long	n,
		long	m,
		double	v
	)

inline

◆ add_zernike_even()

void CTFparam::add_zernike_even ( vector< double > & v )

inline

◆ add_zernike_odd()

void CTFparam::add_zernike_odd ( vector< double > & v )

inline

◆ alpha() [1/2]

double CTFparam::alpha ( )

inline

◆ alpha() [2/2]

void CTFparam::alpha ( double v )

inline

◆ amp_shift() [1/2]

double CTFparam::amp_shift ( )

inline

◆ amp_shift() [2/2]

void CTFparam::amp_shift ( double v )

inline

◆ astigmatism()

void CTFparam::astigmatism	(	double	dev,
		double	ang
	)

inline

◆ astigmatism_angle()

double CTFparam::astigmatism_angle ( )

inline

◆ baseline() [1/6]

vector< double > & CTFparam::baseline ( )

inline

◆ baseline() [2/6]

void CTFparam::baseline ( double * b )

inline

◆ baseline() [3/6]

double CTFparam::baseline ( int i )

inline

◆ baseline() [4/6]

void CTFparam::baseline	(	int	i,
		double	d
	)

inline

◆ baseline() [5/6]

void CTFparam::baseline	(	long	t,
		vector< double > &	b
	)

inline

◆ baseline() [6/6]

void CTFparam::baseline ( vector< double > & b )

inline

◆ baseline_equation()

Bstring CTFparam::baseline_equation ( )

Generates a baseline equation string from 4 to 10 coefficients.

Returns

Bstring baseline equation.

The baseline string is constructed from the 4 to 10 coefficients
according to the specified type.

◆ baseline_type() [1/2]

long CTFparam::baseline_type ( )

inline

◆ baseline_type() [2/2]

void CTFparam::baseline_type ( long t )

inline

◆ beam_tilt()

void CTFparam::beam_tilt	(	double	x,
		double	y
	)

inline

◆ beam_tiltX() [1/2]

double CTFparam::beam_tiltX ( )

inline

◆ beam_tiltX() [2/2]

void CTFparam::beam_tiltX ( double v )

inline

◆ beam_tiltY() [1/2]

double CTFparam::beam_tiltY ( )

inline

◆ beam_tiltY() [2/2]

void CTFparam::beam_tiltY ( double v )

inline

◆ calc_baseline()

double CTFparam::calc_baseline ( double s )

inline

◆ calc_envelope()

double CTFparam::calc_envelope ( double s )

inline

◆ calculate() [1/2]

long double CTFparam::calculate	(	double	s2,
		double	angle
	)

inline

◆ calculate() [2/2]

vector< double > CTFparam::calculate	(	int	nrad,
		int	npsi,
		double	step_size
	)

Calculates a CTF curve.

Parameters

nrad	number of radii.
npsi	number of angular segments.
step_size	reciprocal space step size (1/angstrom).

Returns

vector<double> new CTF array.

Defocus values are positive for underfocus.
Functions:
    angle = atan(y/x)
    s2 = reciprocal space distance squared
    defocus_average = (defocus_max + defocus_min)/2
    defocus_deviation = (defocus_max - defocus_min)/2
    defocus = defocus_average + defocus_deviation*cos(2*(angle - astigmatism_angle))
    phase = 0.5*PI*lambda*lambda*lambda*Cs*s2*s2 - PI*lambda*defocus*s2 - amp_shift;
    CTF = sin(phase)
The new CTF curve is returned.

◆ calculate_aberration_even()

long double CTFparam::calculate_aberration_even	(	double	s2,
		double	angle
	)

inline

◆ calculate_aberration_odd()

long double CTFparam::calculate_aberration_odd	(	double	s2,
		double	angle
	)

inline

◆ calculate_complex()

Complex< double > CTFparam::calculate_complex	(	double	s2,
		double	angle
	)

inline

◆ Cc() [1/2]

double CTFparam::Cc ( )

inline

◆ Cc() [2/2]

void CTFparam::Cc ( double v )

inline

◆ check_defocus()

bool CTFparam::check_defocus ( )

inline

◆ convert_zernike()

void CTFparam::convert_zernike ( )

inline

◆ Cs() [1/2]

double CTFparam::Cs ( )

inline

◆ Cs() [2/2]

void CTFparam::Cs ( double v )

inline

◆ dE() [1/2]

double CTFparam::dE ( )

inline

◆ dE() [2/2]

void CTFparam::dE ( double v )

inline

◆ defocus_average() [1/2]

double CTFparam::defocus_average ( )

inline

◆ defocus_average() [2/2]

void CTFparam::defocus_average ( double v )

inline

◆ defocus_deviation()

double CTFparam::defocus_deviation ( )

inline

◆ defocus_for_first_zero()

double CTFparam::defocus_for_first_zero ( double s )

inline

◆ delete_aberration()

void CTFparam::delete_aberration ( int which = 3 )

inline

◆ delta_phi()

long double CTFparam::delta_phi	(	double	s2,
		double	angle
	)

inline

◆ energy_spread()

double CTFparam::energy_spread ( double s2 )

Calculates the envelope curve based on energy spread.

Parameters

s2	spatial frequency squared.

Returns: double amplitude.

The curve is calculated at frequency s as: Ees(s) = exp(-0.5*(pi*lambda*Cc*(dE/V)*s^2)^2) where Cc: Chromatic aberation (~2e7 A) dE: Energy spread (~1 eV) V: Acceleration voltage (~1e5 V) lamda: electron wavelength (~0.03 A)

References: Freitag et al. (2005) Ultramicroscopy 102, 209-14. Zhu et al. (1997) JSB 118, 197-219.

◆ envelope() [1/6]

vector< double > & CTFparam::envelope ( )

inline

◆ envelope() [2/6]

void CTFparam::envelope ( double * v )

inline

◆ envelope() [3/6]

double CTFparam::envelope ( int i )

inline

◆ envelope() [4/6]

void CTFparam::envelope	(	int	i,
		double	d
	)

inline

◆ envelope() [5/6]

void CTFparam::envelope	(	long	t,
		vector< double > &	v
	)

inline

◆ envelope() [6/6]

void CTFparam::envelope ( vector< double > & v )

inline

◆ envelope_energy_spread()

vector< double > CTFparam::envelope_energy_spread	(	long	n,
		double	freq_step
	)

Calculates the envelope curve based on energy spread.

Parameters

n	number of spatial frequency steps.
freq_step	size of spatial frequency step.

Returns: vector<double> curve.

The curve is calculated at frequency s as: Ees(s) = exp(-0.5*(pi*lambda*Cc*(dE/V)*s^2)^2) where Cc: Chromatic aberation (~2e7 A) dE: Energy spread (~1 eV) V: Acceleration voltage (~1e5 V) lamda: electron wavelength (~0.03 A)

References: Freitag et al. (2005) Ultramicroscopy 102, 209-14. Zhu et al. (1997) JSB 118, 197-219.

◆ envelope_equation()

Bstring CTFparam::envelope_equation ( )

Generates an envelope equation string from 4 coefficients.

Returns

Bstring envelope equation.

The envelope string is constructed from the 4 double gaussian parameters.

◆ envelope_partial_coherence()

vector< double > CTFparam::envelope_partial_coherence	(	long	n,
		double	freq_step
	)

Calculates the envelope curve based on partial coherence.

Parameters

n	number of spatial frequency steps.
freq_step	size of spatial frequency step.

Returns: vector<double> curve.

The curve is calculated at frequency s as: Epc(s) = exp(-(pi*alpha*(Cs*lamda^2*s^2 - def)*s)^2) where Cs: Spherical aberation (~2e7 A) alpha: Beam spread/source size (~0.1 mrad) def: Defocus (~1e4 A) lamda: electron wavelength (~0.03 A)

References: Zhu et al. (1997) JSB 118, 197-219.

◆ envelope_type() [1/2]

long CTFparam::envelope_type ( )

inline

◆ envelope_type() [2/2]

void CTFparam::envelope_type ( long t )

inline

◆ focal_length() [1/2]

double CTFparam::focal_length ( )

inline

◆ focal_length() [2/2]

void CTFparam::focal_length ( double v )

inline

◆ fom() [1/2]

double CTFparam::fom ( )

inline

◆ fom() [2/2]

void CTFparam::fom ( double v )

inline

◆ frequency_cutoff()

double CTFparam::frequency_cutoff ( )

inline

◆ identifier() [1/2]

string & CTFparam::identifier ( )

inline

◆ identifier() [2/2]

void CTFparam::identifier ( string s )

inline

◆ lambda()

double CTFparam::lambda ( )

inline

◆ maxima()

vector< double > CTFparam::maxima ( double max_s )

Calculates the maxima of a CTF curve on the spatial frequency scale.

Parameters

max_s maximum spatial frequency.

Returns

vector<double> array of spatial frequencies for maxima, NULL on error.

Thus uses the zeroes function to find the maxima.
Defocus values are positive for underfocus.
The array returned start with the first zero at index 0.

◆ objective_aperture() [1/2]

double CTFparam::objective_aperture ( )

inline

◆ objective_aperture() [2/2]

void CTFparam::objective_aperture ( double v )

inline

◆ parse_baseline_equation()

int CTFparam::parse_baseline_equation ( Bstring base_eq )

Extracts the coefficients from the baseline string.

Parameters

base_eq baseline equation string.

Returns

int equation type.

The baseline string is scanned in one of the three supported formats.

◆ parse_envelope_equation()

int CTFparam::parse_envelope_equation ( Bstring env_eq )

Extracts the coefficients from the envelope string.

Parameters

env_eq envelope equation string.

Returns

int 0.

The envelope string is scanned to get the 4 double gaussian parameters.

◆ partial_coherence()

double CTFparam::partial_coherence ( double s )

Calculates the envelope curve based on partial coherence.

Parameters

s	spatial frequency.

Returns: double amplitude.

The curve is calculated at frequency s as: Epc(s) = exp(-(pi*alpha*(Cs*lamda^2*s^2 - def)*s)^2) where Cs: Spherical aberation (~2e7 A) alpha: Beam spread/source size (~0.1 mrad) def: Defocus (~1e4 A) lamda: electron wavelength (~0.03 A)

References: Zhu et al. (1997) JSB 118, 197-219.

◆ partial_coherence_and_energy_spread()

double CTFparam::partial_coherence_and_energy_spread ( double s2 )

Calculates the envelope curve based on partial coherence and energy spread.

Parameters

s2	spatial frequency squared.

Returns: double amplitude.

References: Freitag et al. (2005) Ultramicroscopy 102, 209-14. Zhu et al. (1997) JSB 118, 197-219.

◆ select() [1/2]

long CTFparam::select ( )

inline

◆ select() [2/2]

void CTFparam::select ( long i )

inline

◆ show()

void CTFparam::show ( )

inline

◆ show_aberration()

void CTFparam::show_aberration ( )

inline

◆ show_baseline()

void CTFparam::show_baseline ( )

inline

◆ show_envelope()

void CTFparam::show_envelope ( )

inline

◆ slit_width() [1/2]

double CTFparam::slit_width ( )

inline

◆ slit_width() [2/2]

void CTFparam::slit_width ( double v )

inline

◆ update() [1/2]

int CTFparam::update ( CTFparam & ctf )

Updates a CTF structure from another.

Parameters

ctf	CTF structure with new information.

Returns: int 0, <0 on error.

◆ update() [2/2]

int CTFparam::update ( CTFparam * ctf )

inline

◆ update_aberration_weights()

void CTFparam::update_aberration_weights ( map< pair< long, long >, double > & wa )

inline

◆ volt() [1/2]

double CTFparam::volt ( )

inline

◆ volt() [2/2]

void CTFparam::volt ( double v )

inline

◆ zernike_even()

vector< double > CTFparam::zernike_even ( )

inline

◆ zernike_odd()

vector< double > CTFparam::zernike_odd ( )

inline

◆ zero()

double CTFparam::zero ( int i )

inline

◆ zeroes()

vector< double > CTFparam::zeroes ( double max_s )

Calculates the zeroes of a CTF curve on the spatial frequency scale.

Parameters

max_s maximum spatial frequency.

Returns

vector<double> array of spatial frequencies for zeroes, NULL on error.

The nth zero is given by the reciprocal space distance where the
phase shift term is equal to -n*PI:
phase = 0.5*PI*lambda^3*Cs*s^4 - PI*lambda*defocus*s^2 = -n*PI
ctf_fz = defocus/(Cs*lambda^2)
zero(n) = sqrt(ctf_fz - sqrt(ctf_fz^2 - 2.0*n/(Cs*lambda^3)))
Defocus values are positive for underfocus.
The array returned start with the first zero at index 0.

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

/Users/heymannb/b20/bsoft/include/ctf.h
/Users/heymannb/b20/bsoft/src/util/ctf.cpp

Public Member Functions

Constructor & Destructor Documentation

◆ CTFparam() [1/3]

◆ CTFparam() [2/3]

◆ CTFparam() [3/3]

Member Function Documentation

◆ aberration_coefficient() [1/2]

◆ aberration_coefficient() [2/2]

◆ aberration_even() [1/2]

◆ aberration_even() [2/2]

◆ aberration_even_difference()

◆ aberration_even_update()

◆ aberration_odd() [1/2]

◆ aberration_odd() [2/2]

◆ aberration_odd_complex()

◆ aberration_odd_update()

◆ aberration_weight() [1/2]

◆ aberration_weight() [2/2]

◆ aberration_weight_string()

◆ aberration_weights() [1/2]

◆ aberration_weights() [2/2]

◆ add_aberration_weight()

◆ add_zernike_even()

◆ add_zernike_odd()

◆ alpha() [1/2]

◆ alpha() [2/2]

◆ amp_shift() [1/2]

◆ amp_shift() [2/2]

◆ astigmatism()

◆ astigmatism_angle()

◆ baseline() [1/6]

◆ baseline() [2/6]

◆ baseline() [3/6]

◆ baseline() [4/6]

◆ baseline() [5/6]

◆ baseline() [6/6]

◆ baseline_equation()

◆ baseline_type() [1/2]

◆ baseline_type() [2/2]

◆ beam_tilt()

◆ beam_tiltX() [1/2]

◆ beam_tiltX() [2/2]

◆ beam_tiltY() [1/2]

◆ beam_tiltY() [2/2]

◆ calc_baseline()

◆ calc_envelope()

◆ calculate() [1/2]

◆ calculate() [2/2]

◆ calculate_aberration_even()

◆ calculate_aberration_odd()

◆ calculate_complex()

◆ Cc() [1/2]

◆ Cc() [2/2]

◆ check_defocus()

◆ convert_zernike()

◆ Cs() [1/2]

◆ Cs() [2/2]

◆ dE() [1/2]

◆ dE() [2/2]

◆ defocus_average() [1/2]

◆ defocus_average() [2/2]

◆ defocus_deviation()

◆ defocus_for_first_zero()

◆ delete_aberration()

◆ delta_phi()

◆ energy_spread()

◆ envelope() [1/6]

◆ envelope() [2/6]

◆ envelope() [3/6]

◆ envelope() [4/6]

◆ envelope() [5/6]

◆ envelope() [6/6]

◆ envelope_energy_spread()

◆ envelope_equation()

◆ envelope_partial_coherence()

◆ envelope_type() [1/2]

◆ envelope_type() [2/2]

◆ focal_length() [1/2]

◆ focal_length() [2/2]

◆ fom() [1/2]