mg_refine.cpp File Reference

Reciprocal space refinement of orientation parameters of particle images. More...

#include "mg_processing.h"
#include "mg_refine.h"
#include "rwmg.h"
#include "mg_ctf.h"
#include "rwimg.h"
#include "Complex.h"
#include "Matrix3.h"
#include "linked_list.h"
#include "random_numbers.h"
#include "utilities.h"
#include <sys/stat.h>
#include <fcntl.h>

Functions
long	part_refine_orientation (Bparticle *part, Bstring &partfile, Bimage *pref, Bimage *pmask, Bsymmetry sym, int max_iter, double alpha_step, double accuracy, double shift_step, double shift_accuracy, double hi_res, double lo_res, int fom_type, vector< double > weight, double edge_radius, CTFparam *em_ctf, double def_std, double shift_std, double view_std, double max_angle, double max_mag, int flags, FSI_Kernel *kernel, fft_plan planf)
	Refine the orientation and origin of one particle with respect to a reference map. More...
double	img_refine_monte (Bimage *p, Bimage *pref, double hi_res, double lo_res, int flags, int max_iter, int fom_type, vector< double > &weight, CTFparam *em_ctf, double def_std, double shift_std, double view_std, double max_angle, double max_mag, FSI_Kernel *kernel, long &number)
	Refine the orientation and origin of one particle with respect to a reference map. More...
double	img_refine_grid (Bimage *p, Bimage *pref, double hi_res, double lo_res, int flags, double alpha_step, double accuracy, double shift_step, double shift_accuracy, double max_mag, int fom_type, vector< double > &weight, CTFparam *em_ctf, double def_std, FSI_Kernel *kernel, long &number)
	Refine the orientation and origin of one particle with respect to a reference map. More...
long	mg_refine_orientations (Bproject *project, Bstring &reffile, Bstring &maskfile, Bstring &sym_string, int part_select, int max_iter, double alpha_step, double accuracy, double shift_step, double shift_accuracy, int fom_type, vector< double > weight, double hi_res, double lo_res, int kernel_width, int kernel_power, double edge_radius, double def_std, double shift_std, double view_std, double max_angle, double max_mag, int flags)
	Refine the orientation and origin with respect to a reference map. More...
long	project_refine_orientations (Bproject *project, Bstring &reffile, Bstring &maskfile, Bstring &sym_string, int part_select, int max_iter, double alpha_step, double accuracy, double shift_step, double shift_accuracy, int fom_type, vector< double > weight, double hi_res, double lo_res, int kernel_width, int kernel_power, double edge_radius, double def_std, double shift_std, double view_std, double max_angle, double max_mag, int flags)
double	img_recip_space_fom (Bimage *p, Bimage *pref, double hi_res, double lo_res, int fom_type, vector< double > &weight, int flags, CTFparam *em_ctf)
double	img_fit_in_recip_space_monte (Bimage *p, Bimage *pref, double hi_res, double lo_res, int flags, int max_iter, int fom_type, vector< double > &weight, CTFparam *em_ctf, double def_std, double shift_std, FSI_Kernel *kernel, long &number)
double	img_fit_in_recip_space_grid (Bimage *p, Bimage *pref, double hi_res, double lo_res, int flags, double step, double accuracy, int fom_type, vector< double > &weight, CTFparam *em_ctf, double def_std, FSI_Kernel *kernel, long &number)

Variables
int	verbose

Detailed Description

Reciprocal space refinement of orientation parameters of particle images.

Author

Bernard Heymann

Date

Created: 20070115

Modified: 20220813

Function Documentation

img_fit_in_recip_space_grid()

double img_fit_in_recip_space_grid	(	Bimage *	p,
		Bimage *	pref,
		double	hi_res,
		double	lo_res,
		int	flags,
		double	step,
		double	accuracy,
		int	fom_type,
		vector< double > &	weight,
		CTFparam *	em_ctf,
		double	def_std,
		FSI_Kernel *	kernel,
		long &	number
	)

img_fit_in_recip_space_monte()

double img_fit_in_recip_space_monte	(	Bimage *	p,
		Bimage *	pref,
		double	hi_res,
		double	lo_res,
		int	flags,
		int	max_iter,
		int	fom_type,
		vector< double > &	weight,
		CTFparam *	em_ctf,
		double	def_std,
		double	shift_std,
		FSI_Kernel *	kernel,
		long &	number
	)

img_recip_space_fom()

double img_recip_space_fom	(	Bimage *	p,
		Bimage *	pref,
		double	hi_res,
		double	lo_res,
		int	fom_type,
		vector< double > &	weight,
		int	flags,
		CTFparam *	em_ctf
	)

img_refine_grid()

double img_refine_grid	(	Bimage *	p,
		Bimage *	pref,
		double	hi_res,
		double	lo_res,
		int	flags,
		double	alpha_step,
		double	accuracy,
		double	shift_step,
		double	shift_accuracy,
		double	max_mag,
		int	fom_type,
		vector< double > &	weight,
		CTFparam *	em_ctf,
		double	def_std,
		FSI_Kernel *	kernel,
		long &	number
	)

Refine the orientation and origin of one particle with respect to a reference map.

Parameters

*p	particle image.
*pref	reference map.
hi_res	high resolution limit (angstrom).
lo_res	low resolution limit (angstrom).
flags	APPLY_CTF, INVERT.
alpha_step	grid search angular step size.
accuracy	grid search accuracy.
shift_step	grid shift size.
shift_accuracy	grid shift accuracy.
max_mag	maximum magnification adjustment.
fom_type	type of resolution measure: 0=FRC, 1=DPR
weight	1D reciprocal space weight curve.
*em_ctf	CTF parameters (if NULL, not used).
def_std	defocus step size.
*kernel	interpolation kernel.
&number	number of comparisons.

Returns

double best figure-of-merit.

The orientation and origin are refined using a grid search
with selection based on the FSC or DPR.
The best result is returned in the orientation parameters of the image structure.
The FOM in the image structure is the first FOM determined, while the best
FOM is returned.

img_refine_monte()

double img_refine_monte	(	Bimage *	p,
		Bimage *	pref,
		double	hi_res,
		double	lo_res,
		int	flags,
		int	max_iter,
		int	fom_type,
		vector< double > &	weight,
		CTFparam *	em_ctf,
		double	def_std,
		double	shift_std,
		double	view_std,
		double	max_angle,
		double	max_mag,
		FSI_Kernel *	kernel,
		long &	number
	)

Refine the orientation and origin of one particle with respect to a reference map.

Parameters

*p	particle image.
*pref	reference map.
hi_res	high resolution limit (angstrom).
lo_res	low resolution limit (angstrom).
flags	APPLY_CTF, INVERT.
max_iter	maximum number of refining iterations.
fom_type	type of resolution measure: 0=FRC, 1=DPR
weight	1D reciprocal space weight curve.
*em_ctf	CTF parameters (if NULL, not used).
def_std	random defocus standard deviation
shift_std	random origin shift standard deviation.
view_std	random view shift standard deviation.
max_angle	maximum random rotation angle adjustment.
max_mag	maximum magnification adjustment.
*kernel	interpolation kernel.
&number	number of comparisons.

Returns

double best figure-of-merit.

The orientation and origin are iteratively modified in small random steps,
with selection based on the Fourier shell correlation.
The best result is returned in the orientation parameters of the image structure.
The FOM in the image structure is the first FOM determined, while the best
FOM is returned.

mg_refine_orientations()

long mg_refine_orientations	(	Bproject *	project,
		Bstring &	reffile,
		Bstring &	maskfile,
		Bstring &	sym_string,
		int	part_select,
		int	max_iter,
		double	alpha_step,
		double	accuracy,
		double	shift_step,
		double	shift_accuracy,
		int	fom_type,
		vector< double >	weight,
		double	hi_res,
		double	lo_res,
		int	kernel_width,
		int	kernel_power,
		double	edge_radius,
		double	def_std,
		double	shift_std,
		double	view_std,
		double	max_angle,
		double	max_mag,
		int	flags
	)

Refine the orientation and origin with respect to a reference map.

Parameters

*project	image processing parameter structure.
&reffile	file containing reference map.
&maskfile	file containing a real space mask (can be empty).
&sym_string	point group symmetry designator.
part_select	particle selection for processing.
max_iter	Monte Carlo maximum number of refining iterations.
alpha_step	grid search angular step size.
accuracy	grid search accuracy.
shift_step	grid shift size.
shift_accuracy	grid shift accuracy.
fom_type	type of resolution measure: 0=FRC, 1=DPR
weight	1D reciprocal space weight curve.
hi_res	high resolution limit (angstrom).
lo_res	low resolution limit (angstrom).
kernel_width	interpolation kernel width.
kernel_power	interpolation kernel power.
edge_radius	edge radius to mask background using previous origin.
def_std	random defocus standard deviation
shift_std	random origin shift standard deviation.
view_std	random view shift standard deviation.
max_angle	maximum random rotation angle adjustment.
max_mag	maximum magnification adjustment.
flags	option flags.

Returns

long number of comparisons, <0 on error.

The orientation, origin, magnitude and defocus are refined for each particle.
The default method uses a grid search around the existing view and origin.
Specifying the maximum number of iterations switches the algorithm to a
Monte Carlo search for the best parameters.
The FOM is either based on the FSC or the DPR.

part_refine_orientation()

long part_refine_orientation	(	Bparticle *	part,
		Bstring &	partfile,
		Bimage *	pref,
		Bimage *	pmask,
		Bsymmetry	sym,
		int	max_iter,
		double	alpha_step,
		double	accuracy,
		double	shift_step,
		double	shift_accuracy,
		double	hi_res,
		double	lo_res,
		int	fom_type,
		vector< double >	weight,
		double	edge_radius,
		CTFparam *	em_ctf,
		double	def_std,
		double	shift_std,
		double	view_std,
		double	max_angle,
		double	max_mag,
		int	flags,
		FSI_Kernel *	kernel,
		fft_plan	planf
	)

Refine the orientation and origin of one particle with respect to a reference map.

Parameters

*part	particle.
&partfile	particle filename.
*pref	reference map.
*pmask	mask.
*sym	symmetry structure.
max_iter	maximum number of refining iterations.
alpha_step	grid search angular step size.
accuracy	grid search accuracy.
shift_step	grid shift size.
shift_accuracy	grid shift accuracy.
hi_res	high resolution limit (angstrom).
lo_res	low resolution limit (angstrom).
fom_type	type of resolution measure: 0=FRC, 1=DPR
weight	1D reciprocal space weight curve.
edge_radius	edge radius to mask background using previous origin.
*em_ctf	CTF parameters (if NULL, not used).
def_std	random defocus standard deviation
shift_std	random origin shift standard deviation.
view_std	random view shift standard deviation.
max_angle	maximum random rotation angle adjustment.
max_mag	maximum magnification adjustment.
flags	option flags.
*kernel	interpolation kernel.
planf	FFT forward plan for 2D images.

Returns

long number of comparisons.

The orientation and origin are iteratively modified in small random steps,
with selection based on the Fourier shell correlation.

project_refine_orientations()

long project_refine_orientations	(	Bproject *	project,
		Bstring &	reffile,
		Bstring &	maskfile,
		Bstring &	sym_string,
		int	part_select,
		int	max_iter,
		double	alpha_step,
		double	accuracy,
		double	shift_step,
		double	shift_accuracy,
		int	fom_type,
		vector< double >	weight,
		double	hi_res,
		double	lo_res,
		int	kernel_width,
		int	kernel_power,
		double	edge_radius,
		double	def_std,
		double	shift_std,
		double	view_std,
		double	max_angle,
		double	max_mag,
		int	flags
	)

Variable Documentation

verbose

int verbose

extern