mg_ctf.cpp File Reference

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

#include "rwimg.h"
#include "mg_ctf.h"
#include "mg_ctf_fit.h"
#include "ps_plot.h"
#include "ps_ctf_plot.h"
#include "mg_processing.h"
#include "zernike.h"
#include "utilities.h"
#include "timer.h"
#include <sys/stat.h>

Functions
Bimage *	img_ctf_calculate (CTFparam &cp, bool flip, double wiener, Vector3< long > size, Vector3< double > sam, double lores, double hires)
	Calculates an aberration image. More...
Bimage *	img_ctf_calculate (CTFparam cp, int action, double wiener, Vector3< long > size, Vector3< double > sam, double lores, double hires)
	Calculates a CTF image. More...
double	aberration (long n, long m, double s, double p)
vector< double >	aberration_terms (map< pair< long, long >, double > &wa, double u, double v)
vector< double >	aberration_terms (long nt, double u, double v)
vector< double >	aberration_even_terms (long nt, double u, double v)
vector< double >	aberration_odd_terms (long nt, double u, double v)
map< pair< long, long >, double >	aberration_weights (vector< double > v, int flag)
string	aberration_weight_string (map< pair< long, long >, double > &weights)
int	img_aberration_basis (Bimage *p, int flag)
int	img_create_aberration (Bimage *p, map< pair< long, long >, double > &weights, int flag)
int	img_create_aberration (Bimage *p, vector< map< pair< long, long >, double > > &weights, int flag)
int	img_create_aberration (Bimage *p, CTFparam cp, int flag)
int	img_create_aberration (Bimage *p, map< string, CTFparam > &cpa, int flag)
Bimage *	img_wave_aberration (CTFparam cp, Vector3< long > size, Vector3< double > sam)
	Calculates a wave aberration function. More...
int	img_ctf_apply (Bimage *p, CTFparam em_ctf, int action, double wiener, double lores, double hires, bool invert)
	Applies or corrects for the contrast transfer function (CTF). More...
int	img_ctf_apply (Bimage *p, CTFparam em_ctf, int action, double wiener, double lores, double hires, bool invert, fft_plan planf_2D, fft_plan planb_2D)
int	img_ctf_apply_complex (Bimage *p, CTFparam &cp, bool flip, double wiener, double lores, double hires)
	Applies or corrects for the contrast transfer function (CTF). More...
int	img_apply_phase_aberration (Bimage *p, CTFparam em_ctf)
int	img_ttf_apply_one (Bimage *p, long nn, CTFparam ctf, int action, double wiener, double def, double res_lo, double res_hi, bool invert, Vector3< long > psize, fft_plan planf, fft_plan planb)
int	img_ctf_apply_to_proj (Bimage *proj, CTFparam em_ctf, double defocus, double res_lo, double res_hi, bool invert, fft_plan planf_2D, fft_plan planb_2D)
	Applies a CTF to a projection image. More...
int	img_ttf_apply (Bimage *p, CTFparam ctf, int action, double wiener, Vector3< long > tile_size, double tilt, double axis, double res_lo, double res_hi, int invert)
	Applies or corrects for the tilted contrast transfer function (TTF). More...
int	mg_ps_name (Bmicrograph *mg, int img_num, Bstring &path, Bstring &newname, Bstring insert)
Bimage *	mg_ctf_prepare (Bmicrograph *mg, int action, double lores, double hires, Vector3< long > tile_size, double def_start, double def_end, double def_inc, int flags)
int	rec_ctf_prepare (Breconstruction *rec, int action, double lores, double hires, Vector3< long > tile_size, double def_start, double def_end, double def_inc, Bstring &newname, int flags)
int	project_ctf_prepare (Bproject *project, int action, double lores, double hires, Vector3< long > tile_size, double def_start, double def_end, double def_inc, Bstring &path, Bstring &newname, int flags)
	Calculates power spectra and optionally fits CTF curves. More...
int	part_ctf (Bparticle *partlist, int action, double lores, double hires, double wiener, DataType datatype, Bstring &partpath, Bstring &newname, int flags)
int	mg_ctf (Bmicrograph *mg, Bimage *pmg, int action, double lores, double hires, double wiener, Vector3< long > tile_size, DataType datatype, Bstring &newname, int flags)
int	rec_ctf (Breconstruction *rec, int action, double lores, double hires, double wiener, DataType datatype, Bstring &newname, int flags)
int	project_ctf (Bproject *project, int action, double lores, double hires, Vector3< long > tile_size, double wiener, DataType datatype, Bstring &partpath, Bstring &newname, int flags)
	Calculates or fits CTF curves to multiple power spectra. More...
double	img_ctf_isotropy (Bimage *p, long n, CTFparam &em_ctf, double lores, double hires)
	Calculates the isotropy of the power spectrum adjusted for astigmatism. More...
double	sinc_find_argument (double v)
int	project_powerspectrum_isotropy (Bproject *project, double lores, double hires)
	Calculates the isotropy at the CTF maxima. More...
JSvalue	project_defocus_range (Bproject *project)
	Determines the minimum and maximum defocus values. More...
int	project_ctf_average (Bproject *project, Bstring &psname)
	Calculates or fits CTF curves to multiple power spectra. More...
Bimage *	project_powerspectrum_average (Bproject *project, double deftarget)
	Averages multiple power spectra based on defocus estimates. More...
int	project_merge_CTF_parameters (Bproject *project, Bproject *ctfproject)
	Puts CTF parameters from one project into another. More...
int	project_CTF_to_part (Bproject *project)
	Transfers CTF parameters from micrographs to particles. More...
int	project_set_defocus (Bproject *project, double def_avg, double def_dev, double ast_angle)
	Sets the defocus values of all the micrographs. More...
int	project_set_astigmatism (Bproject *project, double def_dev, double ast_angle)
	Sets the defocus deviation and astigmatism angle of all the micrographs. More...
int	project_update_ctf (Bproject *project, JSvalue &jsctf)
	Updates the CTF parameters of all the micrographs. More...
int	project_set_volts (Bproject *project, double volts)
	Sets the acceleration voltage of all the micrographs. More...
int	project_set_Cs (Bproject *project, double Cs)
	Sets the spherical aberation constant of all the micrographs. More...
int	project_set_amp_shift (Bproject *project, double amp_shift)
	Sets the amplitude contribution of all the micrographs. More...
int	project_set_focal_length (Bproject *project, double focal_length)
	Sets the focal length of all the micrographs. More...
int	project_set_aperture (Bproject *project, double aperture)
	Sets the objective aperture of all the micrographs. More...
int	project_set_slit_width (Bproject *project, double slit)
	Sets the energy filter slit width of all the micrographs. More...
int	project_set_alpha (Bproject *project, double alpha)
	Sets the beam source size/divergence angle of all the micrographs. More...
int	project_set_envelope_type (Bproject *project, int type)
	Sets the envelope type of all the micrographs. More...
int	project_set_envelope (Bproject *project, int type, vector< double > &coeff)
	Sets the envelope equations of all the micrographs. More...
int	project_set_coherence_envelope (Bproject *project)
	Replaces envelope equations with those based on partial coherence in all micrographs. More...
int	project_set_baseline_type (Bproject *project, int type)
	Sets the baseline type of all the micrographs. More...
int	project_set_baseline (Bproject *project, int type, vector< double > &coeff)
	Sets the baseline equations of all the micrographs. More...
map< string, CTFparam >	project_ctf_optics_groups (Bproject *project)
	Retrieves unique optics groups as CTF parameters. More...
long	project_update_ctf_aberration (Bproject *project, map< string, CTFparam > &cpa, int flag)
	Updates the aberration weights for all optics groups. More...
int	project_aberration_compare (Bproject *project, Bproject *project2)
	Compares the aberration parameters from two projects. More...
int	project_delete_aberration (Bproject *project, int which)
	Deletes the aberration parameters of all the micrographs. More...
int	project_update_first_zero (Bproject *project)
	Updates the first zero from the defocus average for all the micrographs. More...
int	project_plot_ctf (Bproject *project, Bstring &filename)
	Plots the CTF curves. More...
long	project_ctf_statistics (Bproject *project)
	Calculates CTF parameter statistics. More...

Variables
int	verbose

Detailed Description

Functions for CTF (contrast transfer function) processing.

Author

Bernard Heymann

Date

Created: 19970715

Modified: 20230105

Function Documentation

aberration()

double aberration	(	long	n,
		long	m,
		double	s,
		double	p
	)

aberration_even_terms()

vector< double > aberration_even_terms	(	long	nt,
		double	u,
		double	v
	)

aberration_odd_terms()

vector< double > aberration_odd_terms	(	long	nt,
		double	u,
		double	v
	)

aberration_terms() [1/2]

vector< double > aberration_terms	(	long	nt,
		double	u,
		double	v
	)

aberration_terms() [2/2]

vector< double > aberration_terms	(	map< pair< long, long >, double > &	wa,
		double	u,
		double	v
	)

aberration_weight_string()

string aberration_weight_string

(

map< pair< long, long >, double > &

weights

)

aberration_weights()

map< pair< long, long >, double > aberration_weights	(	vector< double >	v,
		int	flag
	)

img_aberration_basis()

int img_aberration_basis	(	Bimage *	p,
		int	flag
	)

img_apply_phase_aberration()

int img_apply_phase_aberration	(	Bimage *	p,
		CTFparam	em_ctf
	)

img_create_aberration() [1/4]

int img_create_aberration	(	Bimage *	p,
		CTFparam	cp,
		int	flag
	)

img_create_aberration() [2/4]

int img_create_aberration	(	Bimage *	p,
		map< pair< long, long >, double > &	weights,
		int	flag
	)

img_create_aberration() [3/4]

int img_create_aberration	(	Bimage *	p,
		map< string, CTFparam > &	cpa,
		int	flag
	)

img_create_aberration() [4/4]

int img_create_aberration	(	Bimage *	p,
		vector< map< pair< long, long >, double > > &	weights,
		int	flag
	)

img_ctf_apply() [1/2]

int img_ctf_apply	(	Bimage *	p,
		CTFparam	em_ctf,
		int	action,
		double	wiener,
		double	lores,
		double	hires,
		bool	invert
	)

Applies or corrects for the contrast transfer function (CTF).

Parameters

*p	image (modified).
em_ctf	CTF parameter structure.
action	action to be taken.
wiener	Wiener factor (fraction).
lores	low resolution limit.
hires	high resolution limit.
invert	phase flip to invert contrast.

Returns

int 0, <0 on error.

The actions for this funtion are:
1   flip phase (multiply by the sign of the CTF)
2   apply a CTF (multiply with the CTF)
3   correct for the CTF: ctf/(ctf^2 + wiener_factor)
4   correct for the CTF: env*ctf/((env*ctf)^2 + noise^2)
5   correct for the CTF with baseline: ctf/(ctf^2*noise^2 + wiener_factor)
6   correct for the CTF with baseline: 1/(ctf*noise + sign*wiener_factor)

img_ctf_apply() [2/2]

int img_ctf_apply	(	Bimage *	p,
		CTFparam	em_ctf,
		int	action,
		double	wiener,
		double	lores,
		double	hires,
		bool	invert,
		fft_plan	planf_2D,
		fft_plan	planb_2D
	)

img_ctf_apply_complex()

int img_ctf_apply_complex	(	Bimage *	p,
		CTFparam &	cp,
		bool	flip,
		double	wiener,
		double	lores,
		double	hires
	)

Applies or corrects for the contrast transfer function (CTF).

Parameters

*p	image (modified).
cp	CTF & aberration parameters.
flip	Flip phases of even aberrations.
wiener	Wiener factor (fraction), if 0, flip phases.
lores	low resolution limit.
hires	high resolution limit.

Returns

int 0, <0 on error.

img_ctf_apply_to_proj()

int img_ctf_apply_to_proj	(	Bimage *	proj,
		CTFparam	em_ctf,
		double	defocus,
		double	res_lo,
		double	res_hi,
		bool	invert,
		fft_plan	planf_2D,
		fft_plan	planb_2D
	)

Applies a CTF to a projection image.

Parameters

*proj	projection image.
em_ctf	CTF parameters.
defocus	defocus.
res_lo	low resolution limit (angstrom).
res_hi	high resolution limit (angstrom).
invert	phase flip to invert contrast.
planf_2D	2D forward fourier transform plan.
planb_2D	2D backward fourier transform plan.

Returns

int error code.

img_ctf_calculate() [1/2]

Bimage * img_ctf_calculate	(	CTFparam &	cp,
		bool	flip,
		double	wiener,
		Vector3< long >	size,
		Vector3< double >	sam,
		double	lores,
		double	hires
	)

Calculates an aberration image.

Parameters

cp	CTF & aberration parameters.
flip	Flip phases of even aberrations.
wiener	Wiener factor (fraction), if 0, flip phases.
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_calculate() [2/2]

Bimage * img_ctf_calculate	(	CTFparam	cp,
		int	action,
		double	wiener,
		Vector3< long >	size,
		Vector3< double >	sam,
		double	lores,
		double	hires
	)

Calculates a CTF image.

Parameters

cp	CTF parameters.
action	type of CTF calculated (1-8).
wiener	Wiener factor (fraction).
size	new image size.
sam	new image pixel size.
lores	low resolution limit.
hires	high resolution limit.

Returns

Bimage* new 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_isotropy()

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

Calculates the isotropy of the power spectrum adjusted for astigmatism.

Parameters

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

Returns

double radial average std/avg ratio.

A power spectrum with its origin at the center.

img_ttf_apply()

int img_ttf_apply	(	Bimage *	p,
		CTFparam	ctf,
		int	action,
		double	wiener,
		Vector3< long >	tile_size,
		double	tilt,
		double	axis,
		double	res_lo,
		double	res_hi,
		int	invert
	)

Applies or corrects for the tilted contrast transfer function (TTF).

Parameters

*p	image (modified).
ctf	CTF parameter structure.
action	action to be taken.
wiener	Wiener factor (fraction).
tile_size	tile size for tilted CTF operations.
tilt	tilt angle (radians).
axis	tilt axis angle (radians).
res_lo	high resolution limit.
res_hi	low resolution limit.
invert	phase flip to invert contrast.

Returns

int 0, <0 on error.

The actions for this funtion are:
1   flip phase (multiply by the sign of the CTF)
2   apply a CTF (multiply with the CTF)
3   correct for the CTF: ctf/(ctf^2 + wiener_factor)
4   correct for the CTF: env*ctf/((env*ctf)^2 + noise^2)
5   correct for the CTF with baseline: ctf/(ctf^2*noise^2 + wiener_factor)
6   correct for the CTF with baseline: 1/(ctf*noise + sign*wiener_factor)

img_ttf_apply_one()

int img_ttf_apply_one	(	Bimage *	p,
		long	nn,
		CTFparam	ctf,
		int	action,
		double	wiener,
		double	def,
		double	res_lo,
		double	res_hi,
		bool	invert,
		Vector3< long >	psize,
		fft_plan	planf,
		fft_plan	planb
	)

img_wave_aberration()

Bimage * img_wave_aberration	(	CTFparam	cp,
		Vector3< long >	size,
		Vector3< double >	sam
	)

Calculates a wave aberration function.

Parameters

cp	CTF parameters.
size	new image size.
sam	new image pixel size.

Returns

Bimage* new wave aberration 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;
Note: Defocus is positive for underfocus and negative for overfocus.

mg_ctf()

int mg_ctf	(	Bmicrograph *	mg,
		Bimage *	pmg,
		int	action,
		double	lores,
		double	hires,
		double	wiener,
		Vector3< long >	tile_size,
		DataType	datatype,
		Bstring &	newname,
		int	flags
	)

mg_ctf_prepare()

Bimage * mg_ctf_prepare	(	Bmicrograph *	mg,
		int	action,
		double	lores,
		double	hires,
		Vector3< long >	tile_size,
		double	def_start,
		double	def_end,
		double	def_inc,
		int	flags
	)

mg_ps_name()

int mg_ps_name	(	Bmicrograph *	mg,
		int	img_num,
		Bstring &	path,
		Bstring &	newname,
		Bstring	insert
	)

part_ctf()

int part_ctf	(	Bparticle *	partlist,
		int	action,
		double	lores,
		double	hires,
		double	wiener,
		DataType	datatype,
		Bstring &	partpath,
		Bstring &	newname,
		int	flags
	)

project_aberration_compare()

int project_aberration_compare	(	Bproject *	project,
		Bproject *	project2
	)

Compares the aberration parameters from two projects.

Parameters

*project	project parameter structure.
*project2	second project parameter structure.

Returns

int 0.

project_ctf()

int project_ctf	(	Bproject *	project,
		int	action,
		double	lores,
		double	hires,
		Vector3< long >	tile_size,
		double	wiener,
		DataType	datatype,
		Bstring &	partpath,
		Bstring &	newname,
		int	flags
	)

Calculates or fits CTF curves to multiple power spectra.

Parameters

*project	project parameter structure.
action	CTF processing action.
lores	low resolution limit for CTF operations.
hires	high resolution limit for CTF operations.
tile_size	tile size for tilted CTF operations.
wiener	Wiener factor.
datatype	corrected particle file data type.
&partpath	corrected particle file path.
&newname	new file name for output.
flags	1=use mg or rec, 2=filter, 4=background, 8=astigmatism, 16=use frames, 32=invert

Returns

int 0, <0 on error.

The default is to use the particle file. If the particle file is not
specified, the micrograph is used. The selection can also be done with
the use_mg flag.

project_ctf_average()

int project_ctf_average	(	Bproject *	project,
		Bstring &	psname
	)

Calculates or fits CTF curves to multiple power spectra.

Parameters

*project	project parameter structure.
&psname	postscript file name for output.

Returns

int 0, <0 on error.

The default is to use the particle file. If the particle file is not
specified, the micrograph is used. The selection can also be done with
the use_mg flag.

project_ctf_optics_groups()

map< string, CTFparam > project_ctf_optics_groups

(

Bproject *

project

)

Retrieves unique optics groups as CTF parameters.

Parameters

*project

project parameter structure.

Returns

map<string,CTFparam> list of CTF instances.

project_ctf_prepare()

int project_ctf_prepare	(	Bproject *	project,
		int	action,
		double	lores,
		double	hires,
		Vector3< long >	tile_size,
		double	def_start,
		double	def_end,
		double	def_inc,
		Bstring &	path,
		Bstring &	newname,
		int	flags
	)

Calculates power spectra and optionally fits CTF curves.

Parameters

*project	project parameter structure.
action	CTF processing action.
lores	low resolution limit for CTF operations.
hires	high resolution limit for CTF operations.
tile_size	tile size for power spectrum generation.
def_start	defocus search start (default 1e3).
def_end	defocus search end (default 2e5).
def_inc	defocus search increment (default 1e3).
&path	new power spectrum directory for output.
&newname	new file name for output.
flags	1=use mg or rec, 2=filter, 4=background, 8=astigmatism, 16=frames, 32=aberration fit

Returns

int 0, <0 on error.

The default is to use the particle file. If the particle file is not
specified, the micrograph is used.

project_ctf_statistics()

long project_ctf_statistics

(

Bproject *

project

)

Calculates CTF parameter statistics.

Parameters

*project

project parameter structure.

Returns

long number of micrographs.

project_CTF_to_part()

int project_CTF_to_part

(

Bproject *

project

)

Transfers CTF parameters from micrographs to particles.

Parameters

*project

project parameter structure with all parameters.

Returns

int 0.

project_defocus_range()

JSvalue project_defocus_range

(

Bproject *

project

)

Determines the minimum and maximum defocus values.

Parameters

*project

project parameter structure.

Returns

JSvalue JSON object with the minimum and maximum values.

project_delete_aberration()

int project_delete_aberration	(	Bproject *	project,
		int	which
	)

Deletes the aberration parameters of all the micrographs.

Parameters

*project	project parameter structure.
which	0=all, 1=odd, 2=even.

Returns

int 0.

project_merge_CTF_parameters()

int project_merge_CTF_parameters	(	Bproject *	project,
		Bproject *	ctfproject
	)

Puts CTF parameters from one project into another.

Parameters

*project	project parameter structure with all parameters.
*ctfproject	project parameter structure with CTF parameters.

Returns

int 0.

project_plot_ctf()

int project_plot_ctf	(	Bproject *	project,
		Bstring &	filename
	)

Plots the CTF curves.

Parameters

*project	project parameter structure.
&filename	Postscript file name.

Returns

int 0.

project_powerspectrum_average()

Bimage * project_powerspectrum_average	(	Bproject *	project,
		double	deftarget
	)

Averages multiple power spectra based on defocus estimates.

Parameters

*project	project parameter structure.
deftarget	target defocus (angstrom).

Returns

Bimage* average power spectrum.

project_powerspectrum_isotropy()

int project_powerspectrum_isotropy	(	Bproject *	project,
		double	lores,
		double	hires
	)

Calculates the isotropy at the CTF maxima.

Parameters

*project	project parameter structure.
lores	low resolution limit.
hires	high resolution limit

Returns

int 0.

project_set_alpha()

int project_set_alpha	(	Bproject *	project,
		double	alpha
	)

Sets the beam source size/divergence angle of all the micrographs.

Parameters

*project	project parameter structure.
alpha	beam source size/divergence angle (radians).

Returns

int 0.

project_set_amp_shift()

int project_set_amp_shift	(	Bproject *	project,
		double	amp_shift
	)

Sets the amplitude contribution of all the micrographs.

Parameters

*project	project parameter structure.
amp_shift	amplitude contribution phase shift.

Returns

int 0.

project_set_aperture()

int project_set_aperture	(	Bproject *	project,
		double	aperture
	)

Sets the objective aperture of all the micrographs.

Parameters

*project	project parameter structure.
aperture	objective aperture in angstrom.

Returns

int 0.

project_set_astigmatism()

int project_set_astigmatism	(	Bproject *	project,
		double	def_dev,
		double	ast_angle
	)

Sets the defocus deviation and astigmatism angle of all the micrographs.

Parameters

*project	project parameter structure.
def_dev	defocus deviation.
ast_angle	astigmatism angle.

Returns

int 0.

project_set_baseline()

int project_set_baseline	(	Bproject *	project,
		int	type,
		vector< double > &	coeff
	)

Sets the baseline equations of all the micrographs.

Parameters

*project	project parameter structure.
type	baseline type.
&coeff	5 baseline coefficients.

Returns

int 0.

project_set_baseline_type()

int project_set_baseline_type	(	Bproject *	project,
		int	type
	)

Sets the baseline type of all the micrographs.

Parameters

*project	project parameter structure.
type	baseline type.

Returns

int 0.

project_set_coherence_envelope()

int project_set_coherence_envelope

(

Bproject *

project

)

Replaces envelope equations with those based on partial coherence in all micrographs.

Parameters

*project

project parameter structure.

Returns

int 0.

Partial coherence envelope:
    env = amp*exp(-(pi*alpha*defocus*s)^2)
The amplitude, defocus and alpha values are taken from the fields 
in each micrograph. The defocus must already be determined.

project_set_Cs()

int project_set_Cs	(	Bproject *	project,
		double	Cs
	)

Sets the spherical aberation constant of all the micrographs.

Parameters

*project	project parameter structure.
Cs	spherical aberation constant in angstrom.

Returns

int 0.

project_set_defocus()

int project_set_defocus	(	Bproject *	project,
		double	def_avg,
		double	def_dev,
		double	ast_angle
	)

Sets the defocus values of all the micrographs.

Parameters

*project	project parameter structure.
def_avg	defocus average.
def_dev	defocus deviation.
ast_angle	astigmatism angle.

Returns

int 0.

project_set_envelope()

int project_set_envelope	(	Bproject *	project,
		int	type,
		vector< double > &	coeff
	)

Sets the envelope equations of all the micrographs.

Parameters

*project	project parameter structure.
type	envelope type.
&coeff	5 envelope coefficients.

Returns

int 0.

project_set_envelope_type()

int project_set_envelope_type	(	Bproject *	project,
		int	type
	)

Sets the envelope type of all the micrographs.

Parameters

*project	project parameter structure.
type	envelope type.

Returns

int 0.

project_set_focal_length()

int project_set_focal_length	(	Bproject *	project,
		double	focal_length
	)

Sets the focal length of all the micrographs.

Parameters

*project	project parameter structure.
focal_length	focal length in angstrom.

Returns

int 0.

project_set_slit_width()

int project_set_slit_width	(	Bproject *	project,
		double	slit
	)

Sets the energy filter slit width of all the micrographs.

Parameters

*project	project parameter structure.
slit	slit width in eV.

Returns

int 0.

project_set_volts()

int project_set_volts	(	Bproject *	project,
		double	volts
	)

Sets the acceleration voltage of all the micrographs.

Parameters

*project	project parameter structure.
volts	acceleration voltage.

Returns

int 0.

project_update_ctf()

int project_update_ctf	(	Bproject *	project,
		JSvalue &	jsctf
	)

Updates the CTF parameters of all the micrographs.

Parameters

*project	project parameter structure.
jsctf	JSON parameters to be updated.

Returns

int 0.

project_update_ctf_aberration()

long project_update_ctf_aberration	(	Bproject *	project,
		map< string, CTFparam > &	cpa,
		int	flag
	)

Updates the aberration weights for all optics groups.

Parameters

*project	project parameter structure.
&cpa	list of CTF parameters for the optics groups.
flag	0=replace, 1=add

Returns

long number of optics groups not found.

project_update_first_zero()

int project_update_first_zero

(

Bproject *

project

)

Updates the first zero from the defocus average for all the micrographs.

Parameters

*project

project parameter structure.

Returns

int 0.

rec_ctf()

int rec_ctf	(	Breconstruction *	rec,
		int	action,
		double	lores,
		double	hires,
		double	wiener,
		DataType	datatype,
		Bstring &	newname,
		int	flags
	)

rec_ctf_prepare()

int rec_ctf_prepare	(	Breconstruction *	rec,
		int	action,
		double	lores,
		double	hires,
		Vector3< long >	tile_size,
		double	def_start,
		double	def_end,
		double	def_inc,
		Bstring &	newname,
		int	flags
	)

sinc_find_argument()

double sinc_find_argument

(

double

v

)

Variable Documentation

verbose

int verbose

extern