mg_orient.cpp File Reference

Determines orientation angles and x,y origins of single particle images. More...

#include "mg_orient.h"
#include "mg_processing.h"
#include "rwmg.h"
#include "mg_particle_select.h"
#include "mg_ctf.h"
#include "symmetry.h"
#include "linked_list.h"
#include "rwimg.h"
#include "ps_views.h"
#include "utilities.h"
#include <fstream>
#include <sys/stat.h>
#include <fcntl.h>

Functions
int	part_determine_orientation (Bparticle *part, Bimage *proj, Bimage *part_mask, Bimage *prs_mask, Bsymmetry &sym, int bin, double res_lo, double res_hi, double res_polar, int ann_min, int ann_max, double shift_limit, double angle_limit, double edge_radius, int flags, fft_plan planf_1D, fft_plan planb_1D, fft_plan planf_2D, fft_plan planb_2D)
double	correlation_coefficient_adjust (double cc, double std)
Bimage *	project_prepare_2D_references (Bproject *project, long first, long number, int bin, int ctf_action, double wiener)
	Prepare reference images from particles. More...
Bimage *	img_prepare_projections (Bstring &filename, Bstring &mask_file, int bin, Bsymmetry &sym, double theta_step, double phi_step, double side_ang)
	Generate projections if a 3D file, otherwise clean projections. More...
Bimage *	img_read_projection (Bstring &proj_file, int multi_file, int proj_num)
int	project_determine_orientations (Bproject *project, Bimage *proj, Bstring &mask_file, int bin, Bsymmetry &sym, int part_select, vector< double > &band, double res_lo, double res_hi, double res_polar, int ann_min, int ann_max, double shift_limit, double angle_limit, double edge_radius, int flags)
	Find the orientation and origin of every image in a project. More...
Bparticle	part_compare (Bimage *p, Bimage *proj, Bimage *prs_mask, long k, int bin, CTFparam *ctf, double res_lo, double res_hi, double res_polar, long ann_min, long ann_max, double shift_limit, double angle_limit, double edge_radius, int flags, fft_plan planf_1D, fft_plan planb_1D, fft_plan planf_2D, fft_plan planb_2D)
int	part_determine_orientation2 (Bparticle *part, Bimage *proj, Bimage *part_mask, Bimage *prs_mask, Bsymmetry &sym, int bin, double res_lo, double res_hi, double res_polar, int ann_min, int ann_max, double shift_limit, double angle_limit, double edge_radius, int flags, fft_plan planf_1D, fft_plan planb_1D, fft_plan planf_2D, fft_plan planb_2D)
int	project_determine_orientations2 (Bproject *project, Bimage *proj, Bstring &mask_file, int bin, Bsymmetry &sym, int part_select, vector< double > &band, double res_lo, double res_hi, double res_polar, int ann_min, int ann_max, double shift_limit, double angle_limit, double edge_radius, int flags)
	Find the orientation and origin of every image in a project. More...
int	project_determine_origins (Bproject *project, Bimage *proj, int bin, Bsymmetry &sym, int part_select, double res_lo, double res_hi, double shift_limit, int flags)
	Find the origin of every image in a project. More...
double	img_cross_validate (Bimage *p, Bimage *pref, Bimage *prs_mask, fft_plan planf)
	Rotates and shifts a reference image and calculates a cross-validation coefficient. More...

Variables
int	verbose

Detailed Description

Determines orientation angles and x,y origins of single particle images.

Author

Bernard Heymann and David M. Belnap

Date

Created: 20010403

Modified: 20220813 (BH)

Function Documentation

correlation_coefficient_adjust()

double correlation_coefficient_adjust	(	double	cc,
		double	std
	)

img_cross_validate()

double img_cross_validate	(	Bimage *	p,
		Bimage *	pref,
		Bimage *	prs_mask,
		fft_plan	planf
	)

Rotates and shifts a reference image and calculates a cross-validation coefficient.

Parameters

*p	2D image.
*pref	reference 2D image.
*prs_mask	dual mask.
planf	FFT forward plan.

Returns

double cross-validation coefficient.

The reference image is first rotated by the difference in the angles
between the image and the reference, then shifted to the same origin
as the image. Both are then Fourier transformed, the negative values in
the mask used to select reciprocal space areas, and the complex product
calculated. The sum of the zeroeth pixel then gives the cross-validation
coefficient.
The input images must be equal-sized square 2D images.

img_prepare_projections()

Bimage * img_prepare_projections	(	Bstring &	filename,
		Bstring &	mask_file,
		int	bin,
		Bsymmetry &	sym,
		double	theta_step,
		double	phi_step,
		double	side_ang
	)

Generate projections if a 3D file, otherwise clean projections.

Parameters

&filename	file containing reference map or projections.
&mask_file	mask to apply to projections.
bin	data compression by binning.
*sym	point group symmetry structure.
theta_step	angular step size from primary symmetry axis (radians).
phi_step	angular step size around primary symmetry axis (radians).
side_ang	angular devaition from eqautor (radians).

Returns

Bimage* projection images, NULL on error.

If the input file is a 3D map, a set of projections are generated
given the point group symmetry.
Flags:
    FULL_ASU    projections for full asymmetric unit
    MULTI_FILE  projections in multiple files   

img_read_projection()

Bimage * img_read_projection	(	Bstring &	proj_file,
		int	multi_file,
		int	proj_num
	)

part_compare()

Bparticle part_compare	(	Bimage *	p,
		Bimage *	proj,
		Bimage *	prs_mask,
		long	k,
		int	bin,
		CTFparam *	ctf,
		double	res_lo,
		double	res_hi,
		double	res_polar,
		long	ann_min,
		long	ann_max,
		double	shift_limit,
		double	angle_limit,
		double	edge_radius,
		int	flags,
		fft_plan	planf_1D,
		fft_plan	planb_1D,
		fft_plan	planf_2D,
		fft_plan	planb_2D
	)

part_determine_orientation()

int part_determine_orientation	(	Bparticle *	part,
		Bimage *	proj,
		Bimage *	part_mask,
		Bimage *	prs_mask,
		Bsymmetry &	sym,
		int	bin,
		double	res_lo,
		double	res_hi,
		double	res_polar,
		int	ann_min,
		int	ann_max,
		double	shift_limit,
		double	angle_limit,
		double	edge_radius,
		int	flags,
		fft_plan	planf_1D,
		fft_plan	planb_1D,
		fft_plan	planf_2D,
		fft_plan	planb_2D
	)

part_determine_orientation2()

int part_determine_orientation2	(	Bparticle *	part,
		Bimage *	proj,
		Bimage *	part_mask,
		Bimage *	prs_mask,
		Bsymmetry &	sym,
		int	bin,
		double	res_lo,
		double	res_hi,
		double	res_polar,
		int	ann_min,
		int	ann_max,
		double	shift_limit,
		double	angle_limit,
		double	edge_radius,
		int	flags,
		fft_plan	planf_1D,
		fft_plan	planb_1D,
		fft_plan	planf_2D,
		fft_plan	planb_2D
	)

project_determine_orientations()

int project_determine_orientations	(	Bproject *	project,
		Bimage *	proj,
		Bstring &	mask_file,
		int	bin,
		Bsymmetry &	sym,
		int	part_select,
		vector< double > &	band,
		double	res_lo,
		double	res_hi,
		double	res_polar,
		int	ann_min,
		int	ann_max,
		double	shift_limit,
		double	angle_limit,
		double	edge_radius,
		int	flags
	)

Find the orientation and origin of every image in a project.

Parameters

*project	image processing parameter structure.
*proj	reference projections.
&mask_file	mask to apply to particles.
bin	data compression by binning.
*sym	point group symmetry structure.
part_select	particle selection for processing.
*band	array of reciprocal space bands.
res_lo	low resolution limit (angstrom).
res_hi	high resolution limit (angstrom).
res_polar	resolution limit for in-plane angular alignment (angstrom).
ann_min	minimum annulus (>=0).
ann_max	maximum annulus (< image radius).
shift_limit	maximum shift from nominal origin of box.
angle_limit	maximum rotation from original in-plane rotation angle.
edge_radius	edge radius to mask background using previous origin.
flags	option flags.

Returns

int error code.

The polar power spectrum (pps) of the reference projection is cross correlated
with that of the image in order to find the angle of rotation.  The image
is transformed using this angle and the shift found by cross correlation (cc).
A  second iterative comparison is done with real space polar images
to find the angle followed by cross correlation to find the shift.
How much of this second comparison is done depends on the mode flag:
    mode=0  pps     projection selected only based on pps comparison
    mode=1  scc     several projections selected based on cutoff for pps cc's
    mode=2  ccc     all projections selected
The angle and the x and y values are stored in the view_angle, and ox and oy 
arrays of the micrograph parameter structure.
The projections must already be binned.
Flags:
    MODE        projection matching mode
    APPLY_CTF   apply CTF to projections
    PART_LOG    write log files in log directory

project_determine_orientations2()

int project_determine_orientations2	(	Bproject *	project,
		Bimage *	proj,
		Bstring &	mask_file,
		int	bin,
		Bsymmetry &	sym,
		int	part_select,
		vector< double > &	band,
		double	res_lo,
		double	res_hi,
		double	res_polar,
		int	ann_min,
		int	ann_max,
		double	shift_limit,
		double	angle_limit,
		double	edge_radius,
		int	flags
	)

Find the orientation and origin of every image in a project.

Parameters

*project	image processing parameter structure.
*proj	reference projections.
&mask_file	mask to apply to particles.
bin	data compression by binning.
*sym	point group symmetry structure.
part_select	particle selection for processing.
*band	array of reciprocal space bands.
res_lo	low resolution limit (angstrom).
res_hi	high resolution limit (angstrom).
res_polar	resolution limit for in-plane angular alignment (angstrom).
ann_min	minimum annulus (>=0).
ann_max	maximum annulus (< image radius).
shift_limit	maximum shift from nominal origin of box.
angle_limit	maximum rotation from original in-plane rotation angle.
edge_radius	edge radius to mask background using previous origin.
flags	option flags.

Returns

int error code.

The polar power spectrum (pps) of the reference projection is cross correlated
with that of the image in order to find the angle of rotation.  The image
is transformed using this angle and the shift found by cross correlation (cc).
A  second iterative comparison is done with real space polar images
to find the angle followed by cross correlation to find the shift.
How much of this second comparison is done depends on the mode flag:
    mode=0  pps     projection selected only based on pps comparison
    mode=1  scc     several projections selected based on cutoff for pps cc's
    mode=2  ccc     all projections selected
The angle and the x and y values are stored in the view_angle, and ox and oy
arrays of the micrograph parameter structure.
The projections must already be binned.
Flags:
    MODE        projection matching mode
    APPLY_CTF   apply CTF to projections
    PART_LOG    write log files in log directory

project_determine_origins()

int project_determine_origins	(	Bproject *	project,
		Bimage *	proj,
		int	bin,
		Bsymmetry &	sym,
		int	part_select,
		double	res_lo,
		double	res_hi,
		double	shift_limit,
		int	flags
	)

Find the origin of every image in a project.

Parameters

*project	image processing parameter structure.
*proj	reference projections.
bin	data compression by binning.
sym	point group symmetry structure.
part_select	particle selection for processing.
res_lo	low resolution limit (angstrom).
res_hi	high resolution limit (angstrom).
shift_limit	maximum shift from nominal origin of box.
flags	option flags.

Returns

int error code.

The input view is used to find the corresponding reference projection.
This projection is then rotated by the input view angle and cross-correlated 
with the image to find the shift.
Flags:
    PART_LOG    write log files in log directory

project_prepare_2D_references()

Bimage * project_prepare_2D_references	(	Bproject *	project,
		long	first,
		long	number,
		int	bin,
		int	ctf_action,
		double	wiener
	)

Prepare reference images from particles.

Parameters

project	micrograph project structure.
first	first particle image to use.
number	number of particle images to use.
bin	data compression by binning.
ctf_action	flag to apply CTF to projections.
wiener	Wiener factor.

Returns

Bimage* reference images, NULL on error.

The particle images are shifted to center their origins.

Variable Documentation

verbose

int verbose

extern