mg_refine.h File Reference

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

#include "mg_processing.h"
#include "rwimg.h"
#include "symmetry.h"

Functions
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)

Detailed Description

Reciprocal space refinement of orientation parameters of particle images.

Author

Bernard Heymann

Date

Created: 20070115

Modified: 20190207

Function Documentation

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.

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
	)