Processing focal series. More...

#include "rwimg.h"
#include "mg_ctf.h"
#include "mg_ctf_fit.h"
#include "mg_ctf_focal.h"
#include "simplex.h"
#include "utilities.h"

Functions
Bimage *	img_ctf_gradient (CTFparam &cp, double def_min, double def_max, double def_inc, Vector3< long > size, Vector3< double > sam, double lores, double hires)
	Calculates an aberration image. More...

Bimage *	img_ctf_focal_series (CTFparam &cp, double def_start, double def_end, double def_inc, Vector3< long > size, Vector3< double > sam, double lores, double hires)

Bimage *	img_extract_section (Bimage *p, int which)
	Extracts a transverse section from focal series power spectra. More...

double	img_ctf_section_fit (Bimage *p, CTFparam cp, double def, double hires, double lores)
	Calculates a fit for a defocus value to a section from focal series modified power spectra. More...

double	img_find_section_defocus (Bimage *p, CTFparam &cp, double hires, double lores)
	Determines average defocus from a transverse section of focal series power spectra. More...

Bimage *	img_ctf_section_calc (Bimage *p, CTFparam &cp, double res)
	Calculates a transverse section of focal series power spectra from CTF parameters. More...

double	focus_cs_amp_section_fit_R (Bsimplex &simp)

double	focus_fit_R (Bsimplex &simp)

double	focal_aberration_fit_R (Bsimplex &simp)

double	img_ctf_fit_section (Bimage *p, CTFparam &cp, double hires, double lores, double Bfactor, long maxiter)
	Fits 3 CTF parameters to a transverse section of focal series power spectra. More...

double	img_ctf_fit_astigmatism (Bimage *p, CTFparam &cp, double hires, double lores, double Bfactor, long maxiter)
	Fits defocus and astigmatism to focal series power spectra. More...

double	img_ctf_fit_aberration (Bimage *p, double wl, map< pair< long, long >, double > &wa, map< pair< long, long >, double > wd, double hires, double lores, double Bfactor, long maxiter)
	Fits aberration parameters to focal series power spectra. More...

double	img_ctf_fit_even5 (Bimage *p, CTFparam &cp, double hires, double lores, double Bfactor, long maxiter)
	Fits 5 even aberration parameters to focal series power spectra. More...

double	img_ctf_fit_even9 (Bimage *p, CTFparam &cp, double hires, double lores, double Bfactor, long maxiter)
	Fits 9 even aberration parameters to focal series power spectra. More...

Bimage *	img_ctf_focal_fit (Bimage *p, CTFparam &cp, double hires, double lores, double Bfactor, long maxiter)
	Fits the CTF to focal series power spectra. More...

Bimage *	img_fspace_extract_sphere (Bimage *p, double volt)
	Extracts a sphere corresponding to a given acceleration voltage. More...

Variables
int	verbose

Detailed Description

Processing focal series.

Author: Bernard Heymann

Date: Created: 20220808; Modified: 20230127

Function Documentation

◆ focal_aberration_fit_R()

double focal_aberration_fit_R ( Bsimplex & simp )

◆ focus_cs_amp_section_fit_R()

double focus_cs_amp_section_fit_R ( Bsimplex & simp )

◆ focus_fit_R()

double focus_fit_R ( Bsimplex & simp )

◆ img_ctf_fit_aberration()

double img_ctf_fit_aberration	(	Bimage *	p,
		double	wl,
		map< pair< long, long >, double > &	wa,
		map< pair< long, long >, double >	wd,
		double	hires,
		double	lores,
		double	Bfactor,
		long	maxiter
	)

Fits aberration parameters to focal series power spectra.

Parameters

*p	Focal series.
wl	Electron wavelength.
&wa	Aberration weights (replaced).
wd	Aberration weight limits for fitting.
hires	High resolution limit.
lores	Low resolution limit.
Bfactor	B-factor for weighting.
maxiter	Maximum number of iterations.

Returns: double Correlation coefficient.

◆ img_ctf_fit_astigmatism()

double img_ctf_fit_astigmatism	(	Bimage *	p,
		CTFparam &	cp,
		double	hires,
		double	lores,
		double	Bfactor,
		long	maxiter
	)

Fits defocus and astigmatism to focal series power spectra.

Parameters

*p	Focal series.
&cp	CTF parameters.
hires	High resolution limit.
lores	Low resolution limit.
Bfactor	B-factor for weighting.
maxiter	Maximum number of iterations.

Returns

double Correlation coefficient.

The constant phase shift and spherical aberration are fixed at initial values.

◆ img_ctf_fit_even5()

double img_ctf_fit_even5	(	Bimage *	p,
		CTFparam &	cp,
		double	hires,
		double	lores,
		double	Bfactor,
		long	maxiter
	)

Fits 5 even aberration parameters to focal series power spectra.

Parameters

*p	Focal series.
&cp	CTF parameters.
hires	High resolution limit.
lores	Low resolution limit.
Bfactor	B-factor for weighting.
maxiter	Maximum number of iterations.

Returns: double Correlation coefficient.

◆ img_ctf_fit_even9()

double img_ctf_fit_even9	(	Bimage *	p,
		CTFparam &	cp,
		double	hires,
		double	lores,
		double	Bfactor,
		long	maxiter
	)

Fits 9 even aberration parameters to focal series power spectra.

Parameters

*p	Focal series.
&cp	CTF parameters.
hires	High resolution limit.
lores	Low resolution limit.
Bfactor	B-factor for weighting.
maxiter	Maximum number of iterations.

Returns: double Correlation coefficient.

◆ img_ctf_fit_section()

double img_ctf_fit_section	(	Bimage *	p,
		CTFparam &	cp,
		double	hires,
		double	lores,
		double	Bfactor,
		long	maxiter
	)

Fits 3 CTF parameters to a transverse section of focal series power spectra.

Parameters

*p	Transverse section.
&cp	CTF parameters.
hires	High resolution limit.
lores	Low resolution limit.
Bfactor	B-factor for weighting.
maxiter	Maximum number of iterations.

Returns

double Correlation coefficient.

The x axis is the original x or y axis from the power spectra.
The y axis is the original series with focus change specified in sampling.

The 3 parameters are the isotropic aberrations:
    constant phase shift (amplitude contrast)
    defocus
    spherical aberration

◆ img_ctf_focal_fit()

Bimage * img_ctf_focal_fit	(	Bimage *	p,
		CTFparam &	cp,
		double	hires,
		double	lores,
		double	Bfactor,
		long	maxiter
	)

Fits the CTF to focal series power spectra.

Parameters

*p	Focal series.
&cp	CTF parameters.
hires	High resolution limit.
lores	Low resolution limit.
Bfactor	B-factor for weighting.
maxiter	Maximum number of iterations.

Returns

double Correlation coefficient.

The image should be 3D with the third sampling interval the
change in focus per 2D image.

◆ img_ctf_focal_series()

Bimage * img_ctf_focal_series	(	CTFparam &	cp,
		double	def_start,
		double	def_end,
		double	def_inc,
		Vector3< long >	size,
		Vector3< double >	sam,
		double	lores,
		double	hires
	)

◆ img_ctf_gradient()

Bimage * img_ctf_gradient	(	CTFparam &	cp,
		double	def_min,
		double	def_max,
		double	def_inc,
		Vector3< long >	size,
		Vector3< double >	sam,
		double	lores,
		double	hires
	)

Calculates an aberration image.

Parameters

cp	CTF & aberration parameters.
def_min	Minimum defocus.
def_max	Maximum defocus.
def_inc	Defocus increment.
size	new image size.
sam	new image pixel size.
lores	low resolution limit.
hires	high resolution limit.

Returns

Bimage* new complex CTF function image.

Functions:
    angle = atan(y/x)
    s2 = x*x + y*y
    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)
Note: Defocus is positive for underfocus and negative for overfocus.

◆ img_ctf_section_calc()

Bimage * img_ctf_section_calc	(	Bimage *	p,
		CTFparam &	cp,
		double	res
	)

Calculates a transverse section of focal series power spectra from CTF parameters.

Parameters

*p	Transverse section.
&cp	CTF parameters.
res	High resolution limit.

Returns

Bimage* Transverse section.

The x axis is the original x or y axis from the power spectra.
The y axis is the original series with focus change specified in sampling.

◆ img_ctf_section_fit()

double img_ctf_section_fit	(	Bimage *	p,
		CTFparam	cp,
		double	def,
		double	hires,
		double	lores
	)

Calculates a fit for a defocus value to a section from focal series modified power spectra.

Parameters

*p	Section.
cp	CTF parameters.
def	defocus to test for.
hires	High resolution limit.
lores	Low resolution limit.

Returns

double correlation coefficient.

The x axis is the original x or y axis from the power spectra.
The y axis is the original series with focus change specified in sampling.

◆ img_extract_section()

Bimage * img_extract_section	(	Bimage *	p,
		int	which
	)

Extracts a transverse section from focal series power spectra.

Parameters

*p	Focal series.
which	0=x, 1=y.

Returns

Bimage* transverse section.

The x axis is the original x or y axis from the power spectra.
The y axis is the original series with focus change specified in sampling.

◆ img_find_section_defocus()

double img_find_section_defocus	(	Bimage *	p,
		CTFparam &	cp,
		double	hires,
		double	lores
	)

Determines average defocus from a transverse section of focal series power spectra.

Parameters

*p	Transverse section.
&cp	CTF parameters.
hires	High resolution limit.
lores	Low resolution limit.

Returns

double Correlation coefficient.

The x axis is the original x or y axis from the power spectra.
The y axis is the original series with focus change specified in sampling.

◆ img_fspace_extract_sphere()

Bimage * img_fspace_extract_sphere	(	Bimage *	p,
		double	volt
	)

Extracts a sphere corresponding to a given acceleration voltage.

Parameters

*p	Focal series.
volt	Acceleration voltage (V).

Returns: Bimage* Image with data from the sphere.

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ focal_aberration_fit_R()

◆ focus_cs_amp_section_fit_R()

◆ focus_fit_R()

◆ img_ctf_fit_aberration()

◆ img_ctf_fit_astigmatism()

◆ img_ctf_fit_even5()

◆ img_ctf_fit_even9()

◆ img_ctf_fit_section()

◆ img_ctf_focal_fit()

◆ img_ctf_focal_series()

◆ img_ctf_gradient()

◆ img_ctf_section_calc()

◆ img_ctf_section_fit()

◆ img_extract_section()

◆ img_find_section_defocus()

◆ img_fspace_extract_sphere()

Variable Documentation

◆ verbose