ctf.h File Reference

Header file for CTF (contrast transfer function) functions. More...

#include <cmath>
#include <vector>
#include "Bstring.h"
#include "Complex.h"
#include "json.h"
#include "utilities.h"

Classes
class	CTFparam

Macros
#define	NCTFPARAM   10
#define	_CTFparam_

Functions
JSvalue	ctf_to_json (CTFparam &cp)
	Converts microscope parameters to a JSON object list. More...
CTFparam	ctf_from_json (JSvalue &js)
	Converts a JSON object list to microscope parameters. More...
CTFparam	ctf_from_json (string filename)
	Converts a JSON object list to microscope parameters. More...
int	ctf_update_from_json (CTFparam &cp, JSvalue &js)
	Converts a JSON object list to microscope parameters. More...
double	electron_wavelength (double volt)
	Calculates the wavelength in angstrom from the acceleration voltage. More...
double	beta2 (double volt)
	Calculates the square of the relative electron velocity. More...
double	beta (double volt)
	Calculates the relative electron velocity. More...
vector< double >	C_curve (long n, double freq_step)
	Calculates the carbon scattering curve. More...
vector< double >	defocus_range_profile (CTFparam &ctf, double freq_step, double def_min, double def_max, double def_step)
	Calculates a weighting profile associated with a range of defocus values. More...
double	defocus_factor (CTFparam &ctf, double def_min, double def_max, double def_step)
	Calculates an integrated defocus weighting factor for a range of defocus values. More...

Detailed Description

Header file for CTF (contrast transfer function) functions.

Author

Bernard Heymann

Date

Created: 20000426

Modified: 20230105

Macro Definition Documentation

_CTFparam_

#define _CTFparam_

NCTFPARAM

#define NCTFPARAM   10

Function Documentation

beta()

double beta

(

double

volt

)

Calculates the relative electron velocity.

Parameters

volt	acceleration voltage.

Returns

double relative electron velocity.

                          1
beta = sqrt(1 - ---------------------)
                (1+e*volt/(me*c^2))^2

beta2()

double beta2

(

double

volt

)

Calculates the square of the relative electron velocity.

Parameters

volt	acceleration voltage.

Returns

double square of the relative electron velocity.

                     1
beta2 = 1 - ---------------------
            (1+e*volt/(me*c^2))^2

C_curve()

vector< double > C_curve	(	long	n,
		double	freq_step
	)

Calculates the carbon scattering curve.

Parameters

n	length of curve.
freq_step	frequency step size.

Returns

vector<double> array with C-curve.

The curve is based on the sum of five Gaussians.

ctf_from_json() [1/2]

CTFparam ctf_from_json

(

JSvalue &

js

)

Converts a JSON object list to microscope parameters.

Parameters

&js	JSON object list.

Returns

CTFparam microscope parameter structure.

ctf_from_json() [2/2]

CTFparam ctf_from_json

(

string

filename

)

Converts a JSON object list to microscope parameters.

Parameters

filename

JSON file name.

Returns

CTFparam microscope parsmeter structure.

ctf_to_json()

JSvalue ctf_to_json

(

CTFparam &

cp

)

Converts microscope parameters to a JSON object list.

Parameters

&cp	microscope parsmeter structure.

Returns

JSvalue JSON object list.

ctf_update_from_json()

int ctf_update_from_json	(	CTFparam &	cp,
		JSvalue &	js
	)

Converts a JSON object list to microscope parameters.

Parameters

&cp	CTF parameter structure.
&js	JSON object list.

Returns

int 0.

defocus_factor()

double defocus_factor	(	CTFparam &	ctf,
		double	def_min,
		double	def_max,
		double	def_step
	)

Calculates an integrated defocus weighting factor for a range of defocus values.

Parameters

&ctf	CTF parameters.
def_min	minimum defocus.
def_max	maximum defocus.
def_step	defocus step.

Returns

vector<double> sum of all CTF curves.

The CTF curves are calculated up to the frequency cutoff determined by the objective aperture.

defocus_range_profile()

vector< double > defocus_range_profile	(	CTFparam &	ctf,
		double	freq_step,
		double	def_min,
		double	def_max,
		double	def_step
	)

Calculates a weighting profile associated with a range of defocus values.

Parameters

&ctf	CTF parameters.
freq_step	frequency step size.
def_min	minimum defocus.
def_max	maximum defocus.
def_step	defocus step.

Returns

vector<double> sum of all CTF curves.

The CTF curves are calculated up to the frequency cutoff determined by the objective aperture.

electron_wavelength()

double electron_wavelength

(

double

volt

)

Calculates the wavelength in angstrom from the acceleration voltage.

Parameters

volt	acceleration voltage.

Returns

double wavelength in angstrom, <0 on error.

                   12.26
lambda = ----------------------------
         sqrt(volt*(1+volt*0.9788e-6)
                       1e10 * h
lambda = ---------------------------------------
         sqrt(2*me*e*volt*(1+e*volt/(2*me*c^2)))