Selection of single particle parameters from multiple files for classification. More...

#include "mg_processing.h"
#include "mg_img_proc.h"
#include "mg_select.h"
#include "mg_particle_select.h"
#include "rwmg.h"
#include "Matrix.h"
#include "linked_list.h"
#include "utilities.h"

Functions
long	project_check_same_number_particles (Bproject *project_list)

Bproject *	project_multi_merge (Bstring *file_list, int fom_index, int flags)
	Merges multiple projects. More...

long	project_multi_add (Bproject project, Bstring file_list, int fom_index)
	Merges multiple projects with an existing one. More...

Bproject *	project_multi_add_particles (Bstring *file_list)
	Adds particles from a list of projects to the first one. More...

long	project_multi_adjust_FOM (Bproject *project_list, int fom_index)
	Adjusts FOM to the avergae of the first project. More...

long	project_multi_select_best_FOM (Bproject *project_list, double fom_cut, int fom_index, int fom_def_flag)
	Selects the best particle orientations from multiple parameter files. More...

long	project_multi_selection_stats (Bproject *project_list)
	Counts particle assignment distributions using selection arrays. More...

long	project_multi_select_low_variance (Bproject *project_list, Bsymmetry &sym, double origin_dev, double view_dev, double angle_dev, double mag_dev)
	Selects the best particle orientations from multiple parameter files. More...

long	project_multi_select_low_difference (Bproject project1, Bproject project2, Bsymmetry &sym, double origin_err, double view_err, double angle_err, double mag_err)
	Selects the best particle orientations from two parameter files. More...

long	project_multi_select_low_rmsd (Bproject project1, Bproject project2, Bsymmetry &sym, double origin_rmsd, double view_rmsd, double angle_rmsd, double mag_rmsd, int flag)
	Selects the best particle orientations from two parameter files. More...

long	project_multi_selection_compare (Bproject project1, Bproject project2)
	Calculates the number of selections that are the same. More...

Variables
int	verbose

Detailed Description

Selection of single particle parameters from multiple files for classification.

Author: Bernard Heymann

Date: Created: 20010319; Modified: 20220831

Function Documentation

◆ project_check_same_number_particles()

long project_check_same_number_particles ( Bproject * project_list )

◆ project_multi_add()

long project_multi_add	(	Bproject *	project,
		Bstring *	file_list,
		int	fom_index
	)

Merges multiple projects with an existing one.

Parameters

*project	project to add/merge to.
*file_list	linked list of parameter file names.
fom_index	index of FOM to select on.

Returns

long selected particles.

The selected particles are merged with existing ones.
Requirement: The project component ID's must correspond.

◆ project_multi_add_particles()

Bproject * project_multi_add_particles ( Bstring * file_list )

Adds particles from a list of projects to the first one.

Parameters

*file_list linked list of parameter file names.

Returns

Bproject* project with renumbered particles.

The particles from other files are added to existing ones in the first file.
Where project component ID's correspond the particles are added,
otherwise new components are added.
Particles are renumbered and the references to old particle files removed.

◆ project_multi_adjust_FOM()

long project_multi_adjust_FOM	(	Bproject *	project_list,
		int	fom_index
	)

Adjusts FOM to the avergae of the first project.

Parameters

*project_list	linked list of project structures with all parameters.
fom_index	index of FOM to select on.

Returns

long number of particles selected.

Requirement: The project structures must be of identical form.

◆ project_multi_merge()

Bproject * project_multi_merge	(	Bstring *	file_list,
		int	fom_index,
		int	flags
	)

Merges multiple projects.

Parameters

*file_list	linked list of parameter file names.
fom_index	index of FOM to select on.
flags	flags: 1=rec, 2=template, 4=reset.

Returns

Bproject* merged project.

The selected particles are merged.
Requirement: The project component ID's must correspond.
If bit 2 of the flag is set (2), it signifies a template and the FOM's of the template
are set to zero.

◆ project_multi_select_best_FOM()

long project_multi_select_best_FOM	(	Bproject *	project_list,
		double	fom_cut,
		int	fom_index,
		int	fom_def_flag
	)

Selects the best particle orientations from multiple parameter files.

Parameters

*project_list	linked list of project structures with all parameters.
fom_cut	FOM cutoff to eliminate bad particles.
fom_index	index of FOM to select on.
fom_def_flag	flag to adjust the cutoff for defocus.

Returns

long number of particles selected.

The orientation parameters for each particle is selected from
the file with the highest FOM. The selection flag gets the number 
of the file from which the particle was selected, with the first
file getting the number 1. If the best FOM is under the cutoff,
the selection flag is set to zero. The selected orientation
parameters are written into the first micrograph parameter
structure.
Requirement: The project structures must be of identical form.

◆ project_multi_select_low_difference()

long project_multi_select_low_difference	(	Bproject *	project1,
		Bproject *	project2,
		Bsymmetry &	sym,
		double	origin_err,
		double	view_err,
		double	angle_err,
		double	mag_err
	)

Selects the best particle orientations from two parameter files.

Parameters

*project1	first project structure with all parameters.
*project2	second project structure with all parameters.
*sym	symmetry.
origin_err	cutoff to accept origins (pixels).
view_err	cutoff to accept views (radians).
angle_err	cutoff to accept rotation angles (radians).
mag_err	cutoff to accept magnifications (fraction).

Returns

long number of particles selected.

The error is calculated between parameters. 
Requirement: The origin, view and rotation angle (or Euler angle), 
    and magnification arrays in the micrographs must be defined.

◆ project_multi_select_low_rmsd()

long project_multi_select_low_rmsd	(	Bproject *	project1,
		Bproject *	project2,
		Bsymmetry &	sym,
		double	origin_rmsd,
		double	view_rmsd,
		double	angle_rmsd,
		double	mag_rmsd,
		int	flag
	)

Selects the best particle orientations from two parameter files.

Parameters

*project1	first project structure with all parameters.
*project2	second project structure with all parameters.
*sym	symmetry.
origin_rmsd	cutoff to accept origins (pixels).
view_rmsd	cutoff to accept views (radians).
angle_rmsd	cutoff to accept rotation angles (radians).
mag_rmsd	cutoff to accept magnifications (fraction).
flag	0=RMSD, 1=MSD

Returns

long number of particles selected.

The error is calculated between parameters. 
Requirement: The origin, view and rotation angle (or Euler angle), 
    and magnification arrays in the micrographs must be defined.

◆ project_multi_select_low_variance()

long project_multi_select_low_variance	(	Bproject *	project_list,
		Bsymmetry &	sym,
		double	origin_dev,
		double	view_dev,
		double	angle_dev,
		double	mag_dev
	)

Selects the best particle orientations from multiple parameter files.

Parameters

*project_list	linked list of project structures with all parameters.
*sym	symmetry.
origin_dev	cutoff to accept origins (pixels).
view_dev	cutoff to accept views (radians).
angle_dev	cutoff to accept rotation angles (radians).
mag_dev	cutoff to accept magnifications (fraction).

Returns

long number of particles selected.

The standard deviations of particle parameters are calculated as 
follows:
    origin_std = sqrt(var(origin_x) + var(origin_y))
    view_std = sqrt(var(view_x) + var(view_y) + var(view_z))
    angle_std = sqrt(var(angle))
    size_std = sqrt(var(magnification))
Requirement: The origin, view and rotation angle (or Euler angle), 
    and magnification arrays in the micrographs must be defined.

◆ project_multi_selection_compare()

long project_multi_selection_compare	(	Bproject *	project1,
		Bproject *	project2
	)

Calculates the number of selections that are the same.

Parameters

*project1	first project structure with all parameters.
*project2	second project structure with all parameters.

Returns: long number of particles selections the same.

◆ project_multi_selection_stats()

long project_multi_selection_stats ( Bproject * project_list )

Counts particle assignment distributions using selection arrays.

Parameters

*project_list linked list of project structures with all parameters.

Returns

long number of particles selected.

Requirement: The project structures must be of identical form.

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ project_check_same_number_particles()

◆ project_multi_add()

◆ project_multi_add_particles()

◆ project_multi_adjust_FOM()

◆ project_multi_merge()

◆ project_multi_select_best_FOM()

◆ project_multi_select_low_difference()

◆ project_multi_select_low_rmsd()

◆ project_multi_select_low_variance()

◆ project_multi_selection_compare()

◆ project_multi_selection_stats()

Variable Documentation

◆ verbose