Functions to assess the resoltion of a tomographic tilt series. More...

#include "mg_tomo_resol.h"
#include "mg_tomo_rec.h"
#include "mg_reconstruct.h"
#include "rwimg.h"
#include "mg_ctf.h"
#include "Complex.h"
#include "linked_list.h"
#include "utilities.h"

Functions
Bplot *	img_calculate_FRC_curve (vector< Bimage * > parr, double hi_res, double sampling_ratio)
	Calculates the FRC/FSC for a micrograph or particle image in a series. More...

double	plot_calculate_resolution (Bplot *plot, double cutoff)
	Calculates the resolution estimate from a FRC/FSC curve. More...

int	plot_resolution (Bplot *plot, double hi_res, Bstring &psfile, Bstring &title)
	Plots the resolution curve in a plot structure. More...

int	img_pack_2D_into_central_section_old (Bimage p, Bimage prec, Bimage *prec2, long ft_size, int zsize, double scale, double hi_res, Matrix3 matr, Matrix3 mat, int inplane)

vector< Bimage * >	mg_tomo_res_reconstruct (Bproject *project, int micrograph_id, double hi_res, double sampling_ratio, double scale, Vector3< long > size, double fast_angle, int action, double wiener)
	Estimating the resolution of one micrograph in an aligned tilt series. More...

Bimage *	mg_tomo_resolution (Bproject *project, int micrograph_id, double hi_res, double sampling_ratio, double scale, Vector3< long > size, double fast_angle, int action, double wiener, double cutoff, Bstring &psfile)
	Estimating the resolution of one micrograph in an aligned tilt series. More...

int	plot_nloo3d (Bplot *plot)

vector< Bplot * >	project_tomo_resolution (Bproject *project, double hi_res, double sampling_ratio, double scale, Vector3< long > size, double fast_angle, int action, double wiener, double cutoff)
	Estimating the resolution of the tomogram from an aligned tilt series. More...

Bplot *	project_tomo_particle_resolution (Bproject *project, double hi_res, double sampling_ratio, double fast_angle, double cutoff)
	Estimates the resolution for each particle image in each micrograph. More...

long	img_pack_2D_into_central_section (Bimage p, Bimage prec, Bimage *prec2, long ft_size, double scale, double hi_res, Matrix3 matr, Matrix3 mat, int inplane)
	Packs a 2D Fourier transform into a 3D reciprocal space volume. More...

Bplot *	plot_tilt_resolution (Bproject *project)
	Plots the estimated resolution against the tilt angle. More...

Variables
int	verbose

Detailed Description

Functions to assess the resoltion of a tomographic tilt series.

Author: Bernard Heymann

Date: Created: 20031205; Modified: 20190221

Function Documentation

◆ img_calculate_FRC_curve()

Bplot * img_calculate_FRC_curve	(	vector< Bimage * >	parr,
		double	hi_res,
		double	sampling_ratio
	)

Calculates the FRC/FSC for a micrograph or particle image in a series.

Parameters

parr	image array with 2D Fourier transform, 3D central section, 3D LOO central section
hi_res	high resolution limit.
sampling_ratio	ratio for averaging window.

Returns: Bplot* plot structure with FRC/FSC curve.

◆ img_pack_2D_into_central_section()

long img_pack_2D_into_central_section	(	Bimage *	p,
		Bimage *	prec,
		Bimage *	prec2,
		long	ft_size,
		double	scale,
		double	hi_res,
		Matrix3	matr,
		Matrix3	mat,
		int	inplane
	)

Packs a 2D Fourier transform into a 3D reciprocal space volume.

Parameters

*p	2D Fourier transform.
*prec	3D central section.
*prec2	3D central section with in-plane micrograph omitted.
ft_size	Fourier transform size.
scale	reconstruction scale.
hi_res	high resolution limit.
matr	in plane or reference matrix.
mat	matrix of image being packed.
inplane	flag to indicate an in plane image.

Returns

long number voxels packed.

The rotation matrix is used to determine the plane in reciprocal space
to which the 2D transform data is added. The map is assumed to be cubic
and the 2D transform square. The orientation parameters must be written
into the image structure. The real space 2D image must be supplied.
This is then padded to more than twice its original size, fourier
transformed, and packed into the 3D reciprocal space block.

◆ img_pack_2D_into_central_section_old()

int img_pack_2D_into_central_section_old	(	Bimage *	p,
		Bimage *	prec,
		Bimage *	prec2,
		long	ft_size,
		int	zsize,
		double	scale,
		double	hi_res,
		Matrix3	matr,
		Matrix3	mat,
		int	inplane
	)

◆ mg_tomo_res_reconstruct()

vector< Bimage * > mg_tomo_res_reconstruct	(	Bproject *	project,
		int	micrograph_id,
		double	hi_res,
		double	sampling_ratio,
		double	scale,
		Vector3< long >	size,
		double	fast_angle,
		int	action,
		double	wiener
	)

Estimating the resolution of one micrograph in an aligned tilt series.

Parameters

*project	image processing parameter structure.
micrograph_id	micrograph number to use for resolution test.
hi_res	high resolution limit.
sampling_ratio	ratio for averaging window.
scale	reconstruction scale.
size	reconstruction size.
fast_angle	angle to select micrographs for reconstruction.
action	flag to apply CTF to projections.
wiener	Wiener factor.

Returns

vector<Bimage*> array of three images, length of zero on error.

The orientation parameters, view vector, angle of rotation and origin,
must all be set. Each image is padded to at least two times its size
and its Fourier transform packed into 3D reciprocal space.
The figure-of-merit calculated for each reciprocal space voxel is:
           sum(w*re)^2 + sum(w*im)^2
    FOM = ---------------------------
          sum(w)*sum(w*(re^2 + im^2))
where
    re  real part
    im  imaginary part
    w   weight (inverse distance of image pixel to closest grid point)
For voxels with only one data pixel contributing to it, FOM(0).
An image is used in the reconstruction if its selection flag has been set.
If the selection number is less than zero, all particles with selection flags
greater than zero are used. If the selection number is zero or above, all
particles with the selection flag set to the same number are used.
Three images are returned: micrograph, full reconstruction, leave-one-out reconstruction.

◆ mg_tomo_resolution()

Bimage * mg_tomo_resolution	(	Bproject *	project,
		int	micrograph_id,
		double	hi_res,
		double	sampling_ratio,
		double	scale,
		Vector3< long >	size,
		double	fast_angle,
		int	action,
		double	wiener,
		double	cutoff,
		Bstring &	psfile
	)

Estimating the resolution of one micrograph in an aligned tilt series.

Parameters

*project	image processing parameter structure.
micrograph_id	micrograph number to use for resolution test.
hi_res	high resolution limit.
sampling_ratio	ratio for averaging window.
scale	reconstruction scale.
size	reconstruction size.
fast_angle	angle to select micrographs for reconstruction.
action	flag to apply CTF to projections.
wiener	Wiener factor.
cutoff	FRC cutoff.
&psfile	postscript output file name.

Returns

Bimage* micrograph reconstruction, NULL on error.

The orientation parameters, view vector, angle of rotation and origin,
must all be set. Each image is padded to at least two times its size 
and its Fourier transform packed into 3D reciprocal space.
The figure-of-merit calculated for each reciprocal space voxel is:
           sum(w*re)^2 + sum(w*im)^2
    FOM = ---------------------------
          sum(w)*sum(w*(re^2 + im^2))
where
    re  real part
    im  imaginary part
    w   weight (inverse distance of image pixel to closest grid point)
For voxels with only one data pixel contributing to it, FOM(0).
An image is used in the reconstruction if its selection flag has been set.
If the selection number is less than zero, all particles with selection flags
greater than zero are used. If the selection number is zero or above, all
particles with the selection flag set to the same number are used.

◆ plot_calculate_resolution()

double plot_calculate_resolution	(	Bplot *	plot,
		double	cutoff
	)

Calculates the resolution estimate from a FRC/FSC curve.

Parameters

*plot	plot structure.
cutoff	FRC/FSC cutoff to use.

Returns: double estimated resolution.

◆ plot_nloo3d()

int plot_nloo3d ( Bplot * plot )

◆ plot_resolution()

int plot_resolution	(	Bplot *	plot,
		double	hi_res,
		Bstring &	psfile,
		Bstring &	title
	)

Plots the resolution curve in a plot structure.

Parameters

*plot	plot structure.
hi_res	high resolution limit.
&psfile	postscript output file name.
&title	plot title.

Returns: int 0.

◆ plot_tilt_resolution()

Bplot * plot_tilt_resolution ( Bproject * project )

Plots the estimated resolution against the tilt angle.

Parameters

*project project structure.

Returns

*plot new plot.

The resolution estimates must be encoded in the micrograph FOM's.

◆ project_tomo_particle_resolution()

Bplot * project_tomo_particle_resolution	(	Bproject *	project,
		double	hi_res,
		double	sampling_ratio,
		double	fast_angle,
		double	cutoff
	)

Estimates the resolution for each particle image in each micrograph.

Parameters

*project	micrograph project.
hi_res	high resolution limit for resolution estimation.
sampling_ratio	ratio for averaging window.
fast_angle	angle to select micrographs for reconstruction.
cutoff	FRC cutoff to use.

Returns

Bplot* plot with average particle resolutions.

Requires the particles to be defined in all micrographs.
The NLOO algorithm is used for each particle.

◆ project_tomo_resolution()

vector< Bplot * > project_tomo_resolution	(	Bproject *	project,
		double	hi_res,
		double	sampling_ratio,
		double	scale,
		Vector3< long >	size,
		double	fast_angle,
		int	action,
		double	wiener,
		double	cutoff
	)

Estimating the resolution of the tomogram from an aligned tilt series.

Parameters

*project	image processing parameter structure.
hi_res	high resolution limit.
sampling_ratio	ratio for averaging window.
scale	reconstruction scale.
size	reconstruction size.
fast_angle	angle to select micrographs for reconstruction.
action	flag to apply CTF to projections.
wiener	Wiener factor.
cutoff	FRC cutoff.

Returns

vector<Bplot*> Two plots: Tilt-resolution and NLOO-3D.

The orientation parameters, view vector, angle of rotation and origin,
must all be set. Each image is padded to at least two times its size
and its Fourier transform packed into 3D reciprocal space.
The figure-of-merit calculated for each reciprocal space voxel is:
           sum(w*re)^2 + sum(w*im)^2
    FOM = ---------------------------
          sum(w)*sum(w*(re^2 + im^2))
where
    re  real part
    im  imaginary part
    w   weight (inverse distance of image pixel to closest grid point)
For voxels with only one data pixel contributing to it, FOM(0).
An image is used in the reconstruction if its selection flag has been set.
If the selection number is less than zero, all particles with selection flags
greater than zero are used. If the selection number is zero or above, all
particles with the selection flag set to the same number are used.

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ img_calculate_FRC_curve()

◆ img_pack_2D_into_central_section()

◆ img_pack_2D_into_central_section_old()

◆ mg_tomo_res_reconstruct()

◆ mg_tomo_resolution()

◆ plot_calculate_resolution()

◆ plot_nloo3d()

◆ plot_resolution()

◆ plot_tilt_resolution()

◆ project_tomo_particle_resolution()

◆ project_tomo_resolution()

Variable Documentation

◆ verbose