Functions for CTF (contrast transfer function) processing. More...

#include "rwimg.h"
#include "mg_ctf.h"
#include "mg_ctf_fit.h"
#include "mg_processing.h"
#include "simplex.h"
#include "moving_average.h"
#include "utilities.h"
#include "timer.h"
#include <sys/stat.h>

Functions
double	ctf_fit_baseline (Bimage *prad, double real_size, CTFparam &em_ctf, double lores, double hires)

double	ctf_fit_envelope (Bimage *prad, double real_size, CTFparam &em_ctf, double lores, double hires)

double	img_aberration_phase_fit_iter (Bimage *p, long nn, double lores, double hires, int flag, long iter, map< pair< long, long >, double > &wa)

int	complete_weights (map< pair< long, long >, double > &w, int flag)

Bimage *	img_ctf_radial_average (Bimage *p, long n, CTFparam &em_ctf)
	Calculates the power spectrum radial average corrected for astigmatism. More...

double	img_ctf_fit_residual (Bimage *p, long n, CTFparam &em_ctf, double lores, double hires)

double	img_ctf_find_defocus2 (Bimage *p, long n, CTFparam &em_ctf, double lores, double hires, double def_start, double def_end, double def_inc)

int	img_manage_power_spectrum_peak (Bimage p, Bimage pb, long radius)

Bimage *	img_ctf_fit_prepare (Bimage *p, double sigma)

Bimage *	img_ctf_fit_prepare (Bimage *p, long n, double sigma)

double	img_ctf_fit_old (Bimage *p, long n, CTFparam &em_ctf, double lores, double hires, double def_start, double def_end, double def_inc, int flag)
	Determines the CTF parameters from a power spectrum. More...

double	img_ctf_fit (Bimage *p, long n, CTFparam &em_ctf, double lores, double hires, double def_start, double def_end, double def_inc, int flag)

double	img_ctf_fit_baseline (Bimage *p, long n, CTFparam &em_ctf, double lores, double hires)
	Fits only the baseline for a given CTF. More...

double	img_ctf_fit_envelope (Bimage *p, long n, CTFparam &em_ctf, double lores, double hires)
	Fits only the envelope for a given CTF. More...

double	ctf_test_defocus (CTFparam &em_ctf, double def, double step_size, vector< double > &r, long rmin, long rmax)

double	ctf_find_defocus (vector< double > &v, CTFparam &em_ctf, long rmin, long rmax, double step_size, double def_start, double def_end, double def_inc)

double	img_ctf_find_defocus (Bimage *p, long n, CTFparam &em_ctf, double lores, double hires, double def_start, double def_end, double def_inc)
	Searches for the defocus based on correlation. More...

Bimage *	img_ctf_radial_subtract_baseline (Bimage *prad, double real_size, CTFparam &em_ctf)

double	img_ctf_astigmatism_measure (Bimage *p, long n, double real_size, CTFparam &em_ctf, double lores, double hires)

double	img_ctf_fit_astigmatism (Bimage *p, long n, CTFparam &em_ctf, double lores, double hires)
	Fits the astigmatism with a given defocus, baseline and envelope. More...

map< pair< long, long >, double >	img_aberration_phase_fit (Bimage *p, long nn, double lores, double hires, int flag)
	Fits a phase image with aberration functions. More...

double	aberration_fit_R (Bsimplex &simp)

double	sine_aberration_fit_R (Bsimplex &simp)

double	cosine_aberration_fit_R (Bsimplex &simp)

double	img_aberration_phase_fit_iter_old (Bimage *p, long nn, double lores, double hires, int flag, long iter, map< pair< long, long >, double > &wa)

vector< map< pair< long, long >, double > >	img_aberration_phase_fit (Bimage *p, double lores, double hires, int flag, long iter)

vector< map< pair< long, long >, double > >	img_aberration_phase_fit (Bimage *p, double lores, double hires, vector< map< pair< long, long >, double > > &win, int flag, long iter)
	Fits a phase image with aberration terms. More...

double	img_ctf_fit_aberration (Bimage *p, long n, CTFparam &em_ctf, double lores, double hires)

double	img_water_ring_index (Bimage *p, long img_num, CTFparam &em_ctf)
	Calculates the water ring index from a power spectrum. More...

double	img_water_ring_index (Bimage *prad)
	Calculates the water ring index from a power spectrum. More...

double	water_ring_R (Bsimplex &simp)

vector< double >	img_fit_water_ring (Bimage *p)

double	gaussian_R (Bsimplex &simp)

double	gaussian_WR (Bsimplex &simp)

double	gaussian1_R (Bsimplex &simp)

double	double_gaussian_R (Bsimplex &simp)

double	double_gaussian_WR (Bsimplex &simp)

double	eman_baseline_R (Bsimplex &simp)

double	ctf_fit_double_gaussian_baseline (vector< double > &x, vector< double > &y, vector< double > &coeff)

double	ctf_fit_eman_to_baseline (vector< double > &x, vector< double > &y, vector< double > &coeff)

double	ctf_fit_gaussian (vector< double > &x, vector< double > &y, vector< double > &coeff)

double	ctf_fit_baseline_bump (vector< double > &x, vector< double > &y, vector< double > &coeff)

double	ctf_fit_double_gaussian_envelope (vector< double > &x, vector< double > &y, vector< double > &coeff)

Variables
int	verbose

Detailed Description

Functions for CTF (contrast transfer function) processing.

Author: Bernard Heymann

Date: Created: 19970715; Modified: 20221213

Function Documentation

◆ aberration_fit_R()

double aberration_fit_R ( Bsimplex & simp )

◆ complete_weights()

int complete_weights	(	map< pair< long, long >, double > &	w,
		int	flag
	)

◆ cosine_aberration_fit_R()

double cosine_aberration_fit_R ( Bsimplex & simp )

◆ ctf_find_defocus()

double ctf_find_defocus	(	vector< double > &	v,
		CTFparam &	em_ctf,
		long	rmin,
		long	rmax,
		double	step_size,
		double	def_start,
		double	def_end,
		double	def_inc
	)

◆ ctf_fit_baseline()

double ctf_fit_baseline	(	Bimage *	prad,
		double	real_size,
		CTFparam &	em_ctf,
		double	lores,
		double	hires
	)

◆ ctf_fit_baseline_bump()

double ctf_fit_baseline_bump	(	vector< double > &	x,
		vector< double > &	y,
		vector< double > &	coeff
	)

◆ ctf_fit_double_gaussian_baseline()

double ctf_fit_double_gaussian_baseline	(	vector< double > &	x,
		vector< double > &	y,
		vector< double > &	coeff
	)

◆ ctf_fit_double_gaussian_envelope()

double ctf_fit_double_gaussian_envelope	(	vector< double > &	x,
		vector< double > &	y,
		vector< double > &	coeff
	)

◆ ctf_fit_eman_to_baseline()

double ctf_fit_eman_to_baseline	(	vector< double > &	x,
		vector< double > &	y,
		vector< double > &	coeff
	)

◆ ctf_fit_envelope()

double ctf_fit_envelope	(	Bimage *	prad,
		double	real_size,
		CTFparam &	em_ctf,
		double	lores,
		double	hires
	)

◆ ctf_fit_gaussian()

double ctf_fit_gaussian	(	vector< double > &	x,
		vector< double > &	y,
		vector< double > &	coeff
	)

◆ ctf_test_defocus()

double ctf_test_defocus	(	CTFparam &	em_ctf,
		double	def,
		double	step_size,
		vector< double > &	r,
		long	rmin,
		long	rmax
	)

◆ double_gaussian_R()

double double_gaussian_R ( Bsimplex & simp )

◆ double_gaussian_WR()

double double_gaussian_WR ( Bsimplex & simp )

◆ eman_baseline_R()

double eman_baseline_R ( Bsimplex & simp )

◆ gaussian1_R()

double gaussian1_R ( Bsimplex & simp )

◆ gaussian_R()

double gaussian_R ( Bsimplex & simp )

◆ gaussian_WR()

double gaussian_WR ( Bsimplex & simp )

◆ img_aberration_phase_fit() [1/3]

vector< map< pair< long, long >, double > > img_aberration_phase_fit	(	Bimage *	p,
		double	lores,
		double	hires,
		int	flag,
		long	iter
	)

◆ img_aberration_phase_fit() [2/3]

vector< map< pair< long, long >, double > > img_aberration_phase_fit	(	Bimage *	p,
		double	lores,
		double	hires,
		vector< map< pair< long, long >, double > > &	win,
		int	flag,
		long	iter
	)

Fits a phase image with aberration terms.

Parameters

*p	phase image.
lores	low resolution limit.
hires	high resolution limit.
win	initial aberration parameters.
flag	0=full, 1=odd, 2=even.
iter	maximum number of iterations.

Returns: vector<map<pair<long,long>,double>> vector of aberration weights.

◆ img_aberration_phase_fit() [3/3]

map< pair< long, long >, double > img_aberration_phase_fit	(	Bimage *	p,
		long	nn,
		double	lores,
		double	hires,
		int	flag
	)

Fits a phase image with aberration functions.

Parameters

*p	image structure.
nn	sub-image number.
lores	low resolution limit.
hires	high resolution limit.
flag	0=full, 1=odd, 2=even.

Returns

map<pair<long,long>,double> aberration weights.

The aberration terms are calculated for each pixel and added to a symmetric matrix.
The matrix is inverted and the aberration weights calculated.
The origin of the image must be at {0,0}.

◆ img_aberration_phase_fit_iter()

double img_aberration_phase_fit_iter	(	Bimage *	p,
		long	nn,
		double	lores,
		double	hires,
		int	flag,
		long	iter,
		map< pair< long, long >, double > &	wa
	)

◆ img_aberration_phase_fit_iter_old()

double img_aberration_phase_fit_iter_old	(	Bimage *	p,
		long	nn,
		double	lores,
		double	hires,
		int	flag,
		long	iter,
		map< pair< long, long >, double > &	wa
	)

◆ img_ctf_astigmatism_measure()

double img_ctf_astigmatism_measure	(	Bimage *	p,
		long	n,
		double	real_size,
		CTFparam &	em_ctf,
		double	lores,
		double	hires
	)

◆ img_ctf_find_defocus()

double img_ctf_find_defocus	(	Bimage *	p,
		long	n,
		CTFparam &	em_ctf,
		double	lores,
		double	hires,
		double	def_start,
		double	def_end,
		double	def_inc
	)

Searches for the defocus based on correlation.

Parameters

*p	image structure.
n	sub-image number.
&em_ctf	CTF parameter structure.
lores	low resolution limit.
hires	high resolution limit.
def_start	defocus search start (default 1e3).
def_end	defocus search end (default 2e5).
def_inc	defocus search increment (default 1e3).

Returns

double R factor.

A radial power spectrum is calculated.
A range of defocus values is tested (1000-200000 angstrom, 0.1-20 um), 
and the best fitting value accepted.
The new parameters are written into the CTFparam structure.

◆ img_ctf_find_defocus2()

double img_ctf_find_defocus2	(	Bimage *	p,
		long	n,
		CTFparam &	em_ctf,
		double	lores,
		double	hires,
		double	def_start,
		double	def_end,
		double	def_inc
	)

◆ img_ctf_fit()

double img_ctf_fit	(	Bimage *	p,
		long	n,
		CTFparam &	em_ctf,
		double	lores,
		double	hires,
		double	def_start,
		double	def_end,
		double	def_inc,
		int	flag
	)

◆ img_ctf_fit_aberration()

double img_ctf_fit_aberration	(	Bimage *	p,
		long	n,
		CTFparam &	em_ctf,
		double	lores,
		double	hires
	)

◆ img_ctf_fit_astigmatism()

double img_ctf_fit_astigmatism	(	Bimage *	p,
		long	n,
		CTFparam &	em_ctf,
		double	lores,
		double	hires
	)

Fits the astigmatism with a given defocus, baseline and envelope.

Parameters

*p	image structure.
n	sub-image number.
&em_ctf	CTF parameter structure.
lores	low resolution limit.
hires	high resolution limit

Returns

double objective measure (larger is better).

A radial power spectrum is calculated and the baseline subtracted.
The defocus deviation starts from a low value to get an estimate of
the astigmatism angle. The defocus deviation is modified nased on
the direction of improvements in the fit, at each iteration 
narrowing the angular search for the astigmatism angle.
The new parameters are written into the CTFparam structure.

◆ img_ctf_fit_baseline()

double img_ctf_fit_baseline	(	Bimage *	p,
		long	n,
		CTFparam &	em_ctf,
		double	lores,
		double	hires
	)

Fits only the baseline for a given CTF.

Parameters

*p	image structure.
n	sub-image number.
&em_ctf	CTF parameter structure.
lores	low resolution limit.
hires	high resolution limit

Returns

double R factor.

A radial power spectrum is calculated incorporating astigmatism.
The baseline of the required type is fit.
The new parameters are written into the CTFparam structure.

◆ img_ctf_fit_envelope()

double img_ctf_fit_envelope	(	Bimage *	p,
		long	n,
		CTFparam &	em_ctf,
		double	lores,
		double	hires
	)

Fits only the envelope for a given CTF.

Parameters

*p	image structure.
n	sub-image number.
*em_ctf	CTF parameter structure.
lores	low resolution limit.
hires	high resolution limit

Returns

double R factor.

A radial power spectrum is calculated incorporating astigmatism.
The envelope is fit.
The new parameters are written into the CTFparam structure.

◆ img_ctf_fit_old()

double img_ctf_fit_old	(	Bimage *	p,
		long	n,
		CTFparam &	em_ctf,
		double	lores,
		double	hires,
		double	def_start,
		double	def_end,
		double	def_inc,
		int	flag
	)

Determines the CTF parameters from a power spectrum.

Parameters

*p	image structure.
n	sub-image number.
&em_ctf	CTF parameter structure.
lores	low resolution limit.
hires	high resolution limit
def_start	defocus search start (default 1e3).
def_end	defocus search end (default 2e5).
def_inc	defocus search increment (default 1e3).
flag	flag to determine astigmatism.

Returns

double water ring index.

Input: Power spectrum or its logarithm.
A radial power spectrum is calculated.
A range of defocus values is tested (100-200000 angstrom, 0.01-20 um), 
defining the baseline as passing through the zeroes for each defocus 
and fitting it to a 4th order polynomial.
The envelope function is a simple gaussian on top of the baseline and
fitted to minimize the RMSD between the calculated curve and the
radial power spectrum logarithm.
The fitting is limited to the spatial frequency range between the 
first and last zeroes.
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 parameters are written into the CTPparam structure.

◆ img_ctf_fit_prepare() [1/2]

Bimage * img_ctf_fit_prepare	(	Bimage *	p,
		double	sigma
	)

◆ img_ctf_fit_prepare() [2/2]

Bimage * img_ctf_fit_prepare	(	Bimage *	p,
		long	n,
		double	sigma
	)

◆ img_ctf_fit_residual()

double img_ctf_fit_residual	(	Bimage *	p,
		long	n,
		CTFparam &	em_ctf,
		double	lores,
		double	hires
	)

◆ img_ctf_radial_average()

Bimage * img_ctf_radial_average	(	Bimage *	p,
		long	n,
		CTFparam &	em_ctf
	)

Calculates the power spectrum radial average corrected for astigmatism.

Parameters

*p	image structure.
n	sub-image number.
&em_ctf	CTF parameter structure.

Returns

Bimage* radial average, NULL on error.

A power spectrum with its origin at the center.
Functions:
    angle = atan(y/x) - astigmatism_angle
    s2 = reciprocal space distance squared
    defocus_min = defocus_avg - defocus_dev
    defocus_max = defocus_avg + defocus_dev
    smin2 = 1 - defocus_dev/defocus_avg
    smax2 = 1 + defocus_dev/defocus_avg
    radius = sqrt(2*s2*(smax2*cos(angle)*cos(angle)+
                smin2*sin(angle)*sin(angle))/(smax2+smin2))
The radial average is returned as a new 1D image.

◆ img_ctf_radial_subtract_baseline()

Bimage * img_ctf_radial_subtract_baseline	(	Bimage *	prad,
		double	real_size,
		CTFparam &	em_ctf
	)

◆ img_fit_water_ring()

vector< double > img_fit_water_ring ( Bimage * p )

◆ img_manage_power_spectrum_peak()

int img_manage_power_spectrum_peak	(	Bimage *	p,
		Bimage *	pb,
		long	radius
	)

◆ img_water_ring_index() [1/2]

double img_water_ring_index	(	Bimage *	p,
		long	img_num,
		CTFparam &	em_ctf
	)

Calculates the water ring index from a power spectrum.

Parameters

*p	power spectrum.
img_num	sub-image number.
&em_ctf	CTF parameter structure.

Returns

double water ing index.

A radial power spectrum is calculated.
The the water ring index is defined as:
    wri = wp/b - 1
where wp is the intensity at s=0.26 (3.8 Å) and b is the background.
The background is estimated as the average of sections before and after 
the water peak:
    b1 between s=0.1 and s=0.2
    b2 between s=0.3 and s=0.4

◆ img_water_ring_index() [2/2]

double img_water_ring_index ( Bimage * prad )

Calculates the water ring index from a power spectrum.

Parameters

*prad radial power spectrum.

Returns

double water ing index.

The the water ring index is defined as:
    wri = wp/b - 1
where wp is the average intensity between 0.2 and 0.3, covering the 
peak at s=0.26 (3.8 Å).
The background, b, is estimated as the average of sections before and after 
the water peak:
    b1 between s=0.1 and s=0.2
    b2 between s=0.3 and s=0.4

◆ sine_aberration_fit_R()

double sine_aberration_fit_R ( Bsimplex & simp )

◆ water_ring_R()

double water_ring_R ( Bsimplex & simp )

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ aberration_fit_R()

◆ complete_weights()

◆ cosine_aberration_fit_R()

◆ ctf_find_defocus()

◆ ctf_fit_baseline()

◆ ctf_fit_baseline_bump()

◆ ctf_fit_double_gaussian_baseline()

◆ ctf_fit_double_gaussian_envelope()

◆ ctf_fit_eman_to_baseline()

◆ ctf_fit_envelope()

◆ ctf_fit_gaussian()

◆ ctf_test_defocus()

◆ double_gaussian_R()

◆ double_gaussian_WR()

◆ eman_baseline_R()

◆ gaussian1_R()

◆ gaussian_R()

◆ gaussian_WR()

◆ img_aberration_phase_fit() [1/3]

◆ img_aberration_phase_fit() [2/3]

◆ img_aberration_phase_fit() [3/3]

◆ img_aberration_phase_fit_iter()

◆ img_aberration_phase_fit_iter_old()

◆ img_ctf_astigmatism_measure()

◆ img_ctf_find_defocus()

◆ img_ctf_find_defocus2()

◆ img_ctf_fit()

◆ img_ctf_fit_aberration()

◆ img_ctf_fit_astigmatism()

◆ img_ctf_fit_baseline()

◆ img_ctf_fit_envelope()

◆ img_ctf_fit_old()

◆ img_ctf_fit_prepare() [1/2]

◆ img_ctf_fit_prepare() [2/2]

◆ img_ctf_fit_residual()

◆ img_ctf_radial_average()

◆ img_ctf_radial_subtract_baseline()

◆ img_fit_water_ring()

◆ img_manage_power_spectrum_peak()

◆ img_water_ring_index() [1/2]

◆ img_water_ring_index() [2/2]

◆ sine_aberration_fit_R()

◆ water_ring_R()

Variable Documentation

◆ verbose