Analyzes and manipulates single particle images. More...

#include "mg_processing.h"
#include "mg_particles.h"
#include "mg_particle_select.h"
#include "mg_select.h"
#include "mg_img_proc.h"
#include "mg_ctf.h"
#include "rwimg.h"
#include "matrix_linear.h"
#include "file_util.h"
#include "utilities.h"
#include "timer.h"
#include <sys/stat.h>

Functions
int	project_align_particles (Bproject *project, int part_select, double nuavg, double nustd)
	Aligns single particle images based on orientation parameters. More...

int	project_center_particles (Bproject *project, int part_select, double nuavg, double nustd)
	Centers single particle images based on the parametric center. More...

int	project_set_particle_centers (Bproject project, Bimage pref, int part_select, double hires, double lores)
	Calculates centers of single particle images by cross-correlation with a reference. More...

long	project_find_part_centers_in_mgs (Bproject *project, double hires, double lores, int filter_flag)
	Finds the centers of picked particles within a micrograph. More...

long	mg_find_part_centers (Bmicrograph *mg, double hires, double lores, int filter_flag)
	Finds the centers of picked particles within a micrograph. More...

Bimage *	project_find_particle_centers (Bproject *project, int max_iter, int part_select, double hires, double lores)
	Calculates centers of single particle images. More...

long	particles_mask (Bmicrograph mg, Bimage pmask, Bstring &partpath)

long	project_mask_particles (Bproject project, Bimage pmask, Bstring &partpath)
	Calculates centers of single particle images. More...

long	project_compare_particles (Bproject project, Bproject projcomp)
	Compares the coordinates of particles between two files. More...

double	project_tilt_from_particle_defocus (Bproject *project)
	Finds the tilt axis from refined particle defocus values. More...

long	project_set_particle_defocus_from_tilt (Bproject *project, double axis, double tilt)
	Finds the tilt axis from refined particle defocus values. More...

Bimage *	particle_correlation_sum (Bparticle part, Bimage pref, double hires, FSI_Kernel *kernel, fft_plan planf)

Bimage *	project_correlation_sum (Bproject project, Bimage pref, double hires, FSI_Kernel *kernel)
	Correlates each particle with the CTF applied reference projection and sum the correlations. More...

int	img_add_aberration_terms (Bimage psum, Bimage psec, Bimage *ppart, CTFparam &cp)

Bimage *	particle_aberration_sum (Bparticle part, Bimage pref, double hires, FSI_Kernel *kernel, fft_plan planf)

int	img_check_contrast (Bimage *psum)

Bimage *	img_calculate_phase_differences (Bimage *psum)

Bimage *	project_aberration_phase_difference (Bproject project, Bimage pref, double hires, FSI_Kernel *kernel)
	Calculates the aberration phase difference from a set of particles. More...

Variables
int	verbose

Detailed Description

Analyzes and manipulates single particle images.

Author: Bernard Heymann

Date: Created: 20080424; Modified: 20221130

Function Documentation

◆ img_add_aberration_terms()

int img_add_aberration_terms	(	Bimage *	psum,
		Bimage *	psec,
		Bimage *	ppart,
		CTFparam &	cp
	)

◆ img_calculate_phase_differences()

Bimage * img_calculate_phase_differences ( Bimage * psum )

◆ img_check_contrast()

int img_check_contrast ( Bimage * psum )

◆ mg_find_part_centers()

long mg_find_part_centers	(	Bmicrograph *	mg,
		double	hires,
		double	lores,
		int	filter_flag
	)

Finds the centers of picked particles within a micrograph.

Parameters

*mg	micrograph parameter structure.
hires	high resolution limit.
lores	low resolution limit.
filter_flag	flag to filter extremes in particles.

Returns

long number of particles.

An image processing parameter structure loaded with micrograph
information is used to extract particle images from the micrograph
image using the particle coordinates in the parameter structure.
The extracted particle images are each rotated by PI and the shift
found by cross-correlation between the unrotated and rotated images.
The particle coordinates in the parameter structure are updated with
the shift.

◆ particle_aberration_sum()

Bimage * particle_aberration_sum	(	Bparticle *	part,
		Bimage *	pref,
		double	hires,
		FSI_Kernel *	kernel,
		fft_plan	planf
	)

◆ particle_correlation_sum()

Bimage * particle_correlation_sum	(	Bparticle *	part,
		Bimage *	pref,
		double	hires,
		FSI_Kernel *	kernel,
		fft_plan	planf
	)

◆ particles_mask()

long particles_mask	(	Bmicrograph *	mg,
		Bimage *	pmask,
		Bstring &	partpath
	)

◆ project_aberration_phase_difference()

Bimage * project_aberration_phase_difference	(	Bproject *	project,
		Bimage *	pref,
		double	hires,
		FSI_Kernel *	kernel
	)

Calculates the aberration phase difference from a set of particles.

Parameters

*project	project parameter structure.
*pref	reference map.
hires	high resolution limit (angstrom).
*kernel	frequency space interpolation kernel lookup table.

Returns

Bimage* aberration phase differences as a complex image.

Uses the method as described in Zivanov et al (2020).
The return image is complex with the even and odd phase differences
in real and imaginary parts, respectively.

◆ project_align_particles()

int project_align_particles	(	Bproject *	project,
		int	part_select,
		double	nuavg,
		double	nustd
	)

Aligns single particle images based on orientation parameters.

Parameters

*project	micrograph processing parameter structure.
part_select	selection number from the selection column.
nuavg	rescale to new average.
nustd	rescale to new standard deviation.

Returns

int 0.

Each selected particle image is rotated and shifted.

◆ project_center_particles()

int project_center_particles	(	Bproject *	project,
		int	part_select,
		double	nuavg,
		double	nustd
	)

Centers single particle images based on the parametric center.

Parameters

*project	micrograph processing parameter structure.
part_select	selection number from the selection column.
nuavg	rescale to new average.
nustd	rescale to new standard deviation.

Returns

int 0.

Each particle image is shifted to center the origin.

◆ project_compare_particles()

long project_compare_particles	(	Bproject *	project,
		Bproject *	projcomp
	)

Compares the coordinates of particles between two files.

Parameters

*project	project parameter structure.
*projcomp	comparable project parameter structure.

Returns

long number of common particles.

The coordinates of particles in one parameter file is compared to
that of a reference parameter file.
The two parameter files must have the same field and micrograph ID's.

◆ project_correlation_sum()

Bimage * project_correlation_sum	(	Bproject *	project,
		Bimage *	pref,
		double	hires,
		FSI_Kernel *	kernel
	)

Correlates each particle with the CTF applied reference projection and sum the correlations.

Parameters

*project	project parameter structure.
*pref	reference map.
hires	high resolution limit (angstrom).
*kernel	frequency space interpolation kernel lookup table.

Returns: Bimage* sum of cross-correlations.

◆ project_find_part_centers_in_mgs()

long project_find_part_centers_in_mgs	(	Bproject *	project,
		double	hires,
		double	lores,
		int	filter_flag
	)

Finds the centers of picked particles within a micrograph.

Parameters

*project	project parameter structure.
hires	high resolution limit.
lores	low resolution limit.
filter_flag	flag to filter extremes in particles.

Returns

int 0.

An image processing parameter structure loaded with micrograph
information is used to extract particle images from the micrograph
image using the particle coordinates in the parameter structure.
The extracted particle images are each rotated by PI and the shift
found by cross-correlation between the unrotated and rotated images.
The particle coordinates in the parameter structure are updated with
the shift.

◆ project_find_particle_centers()

Bimage * project_find_particle_centers	(	Bproject *	project,
		int	max_iter,
		int	part_select,
		double	hires,
		double	lores
	)

Calculates centers of single particle images.

Parameters

*project	image processing parameter structure.
max_iter	maximum number of iterations.
part_select	selection number from the selection column.
hires	high resolution limit.
lores	low resolution limit.

Returns

Bimage* final image composite reference.

A composite image is generated from the selected particles and radially
symmetrized. Each image shift is then determined by cross correlation.
This is repeated until the chnage in image shifts decreases below
a threshold.

◆ project_mask_particles()

long project_mask_particles	(	Bproject *	project,
		Bimage *	pmask,
		Bstring &	partpath
	)

Calculates centers of single particle images.

Parameters

*project	image processing parameter structure.
*pmask	3D volume mask to be projected.
&partpath	new path to particle files.

Returns

long number of particles masked.

A 3D mask is projected into each particle view and the particle image masked.

◆ project_set_particle_centers()

int project_set_particle_centers	(	Bproject *	project,
		Bimage *	pref,
		int	part_select,
		double	hires,
		double	lores
	)

Calculates centers of single particle images by cross-correlation with a reference.

Parameters

*project	micrograph processing parameter structure.
*pref	reference image.
part_select	selection number from the selection column.
hires	high resolution limit.
lores	low resolution limit.

Returns

int 0.

Each particle image shift is determined by cross correlation with
the reference image.
The reference must be the same size as the particle images.

◆ project_set_particle_defocus_from_tilt()

long project_set_particle_defocus_from_tilt	(	Bproject *	project,
		double	axis,
		double	tilt
	)

Finds the tilt axis from refined particle defocus values.

Parameters

*project	project parameter structure.
axis	tilt axis angle (radians).
tilt	tilt angle (radians).

Returns: long number of selected particles.

◆ project_tilt_from_particle_defocus()

double project_tilt_from_particle_defocus ( Bproject * project )

Finds the tilt axis from refined particle defocus values.

Parameters

*project project parameter structure.

Returns: double average tilt axis.

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ img_add_aberration_terms()

◆ img_calculate_phase_differences()

◆ img_check_contrast()

◆ mg_find_part_centers()

◆ particle_aberration_sum()

◆ particle_correlation_sum()

◆ particles_mask()

◆ project_aberration_phase_difference()

◆ project_align_particles()

◆ project_center_particles()

◆ project_compare_particles()

◆ project_correlation_sum()

◆ project_find_part_centers_in_mgs()

◆ project_find_particle_centers()

◆ project_mask_particles()

◆ project_set_particle_centers()

◆ project_set_particle_defocus_from_tilt()

◆ project_tilt_from_particle_defocus()

Variable Documentation

◆ verbose