mg_pick.cpp File Reference

Functions for picking single particle images from a micrograph. More...

#include "mg_pick.h"
#include "mg_processing.h"
#include "mg_select.h"
#include "linked_list.h"
#include "utilities.h"

Functions
Bimage *	img_prepare_for_picking (Bimage *p, int flags, long sigma, long bin)
Bparticle *	particles_from_peaks (Bimage *pcc, long bin, double excl_dist, double part_ori, double &fommin, double fommax, long maxnum, double pix_min, double pix_max)
	Finds the peaks in a cross-correlation map corresponding to particles. More...
Bparticle *	particles_pick_cc (Bimage *p, Bimage *ptemp, Bimage *pmask, double hires, double lores, double fommin, double fommax, double excl_dist, long bin)
	Picks particles using cross-correlation. More...
double	gauss_find_intersection (long ngauss, vector< double > &gauss)
Bparticle *	particles_pick_var (Bimage *p, long avg_kernel, long var_kernel, double nsig, double part_ori, double excl_dist, long bin)
	Picks particles in variance map. More...
Bparticle *	particles_pick_var (Bimage *p, long avg_kernel, long var_kernel, double cutmin, double cutmax, double part_ori, double excl_dist, long bin)
Bparticle *	particles_pick_cc (Bstring &filename, long img_num, Bimage *ptemp, Bimage *pmask, double hires, double lores, double fommin, double fommax, double excl_dist, long bin)
	Picks particles using cross-correlation. More...
Bparticle *	particles_pick_var (Bstring &filename, long img_num, long avg_kernel, long var_kernel, double nsig, double part_ori, double excl_dist, long bin)
	Picks particles in variance map. More...
double	img_marker_set_difference_at_voxel (Bimage *p, long i, Bmarker *markin, Bmarker *markout)
Bimage *	img_marker_set_difference (Bimage *p, Bmarker *markin, Bmarker *markout, int contrast)
	Calculates the average difference between voxels tagged by two marker sets. More...
double	mg_pick_particles (Bmicrograph *mg, Bimage *p, Bmarker *markin, Bmarker *markout, int avg_kernel, int contrast)
	Locates particles using a fore/background difference measure. More...
double	project_pick_particles (Bproject *project, Bimage *ptemp, Bimage *pmask, double hires, double lores, double fommin, double fommax, double excl_dist, long bin)
	Picks particles using cross-correlation. More...
double	project_pick_particles (Bproject *project, long avg_kernel, long var_kernel, double nsig, double part_ori, double excl_dist, long bin)
	Picks particles in variance map. More...
long	project_pick_particles (Bproject *project, double din, double dout, int avg_kernel, double ainc, int flags, int contrast)
	Locates particles using a fore/background difference measure. More...
int	part_mask_particles (Bparticle *part, Bimage *pmask, long box_size)
int	img_mask_above_threshold (Bimage *pvar, Bimage *p, double threshold)
double	mg_pick_background (Bmicrograph *mg, Bimage *p, long number, long avg_kernel, long var_kernel, double excl_dist)
double	rec_pick_background (Breconstruction *rec, Bimage *p, long number, long avg_kernel, long var_kernel, double excl_dist)
long	project_pick_background (Bproject *project, long number, long avg_kernel, long var_kernel, double excl_dist)
	Picks background areas not overlapping existing particles. More...
Bparticle *	part_pick_sym_axis (Bparticle *part, Bsymmetry &sym, View &refview, Vector3< double > refori, double axis_dist)
long	project_pick_sym_axis (Bproject *project, Bsymmetry &sym, int sym_axis, double axis_dist)
	Picks subregions in 3D particles on the given symmetry axis. More...
Bimage *	img_prepare_projections (Bstring &tempfile, Bsymmetry &sym, double hires, long bin)
Bimage *	img_prepare_orientations (Bstring &tempfile, Bsymmetry &sym, double hires, long bin)
double	part_align (Bparticle *part, Bimage *p, Bimage *ptemp, double hires, double lores, double shift_limit, long bin, fft_plan planf, fft_plan planb)
long	mg_extract_orient_particles (Bmicrograph *mg, Bimage *ptemp, double hires, double lores, long bin, fft_plan planf, fft_plan planb)
	Finds the centers of picked particles within a micrograph. More...
long	rec_extract_orient_particles (Breconstruction *rec, Bimage *ptemp, double hires, double lores, long bin, fft_plan planf, fft_plan planb)
double	project_extract_orient_particles (Bproject *project, Bstring &tempfile, Bsymmetry &sym, double hires, double lores, long bin)
	Picks particles using cross-correlation. More...

Variables
int	verbose

Detailed Description

Functions for picking single particle images from a micrograph.

Author

Bernard Heymann

Date

Created: 20000505

Modified: 20210510

Function Documentation

gauss_find_intersection()

double gauss_find_intersection	(	long	ngauss,
		vector< double > &	gauss
	)

img_marker_set_difference()

Bimage * img_marker_set_difference	(	Bimage *	p,
		Bmarker *	markin,
		Bmarker *	markout,
		int	contrast
	)

Calculates the average difference between voxels tagged by two marker sets.

Parameters

*p	image.
*markin	inner marker set (relates to particle).
*markout	outer marker set (relates to background).
contrast	contrast direction (foreground: white=1, black=0).

Returns

Bimage* map with resultant differences.

The values in the image corresponding to the coordinates of the
inner marker set is subtracted from those of the outer marker set.

img_marker_set_difference_at_voxel()

double img_marker_set_difference_at_voxel	(	Bimage *	p,
		long	i,
		Bmarker *	markin,
		Bmarker *	markout
	)

img_mask_above_threshold()

int img_mask_above_threshold	(	Bimage *	pvar,
		Bimage *	p,
		double	threshold
	)

img_prepare_for_picking()

Bimage * img_prepare_for_picking	(	Bimage *	p,
		int	flags,
		long	sigma,
		long	bin
	)

img_prepare_orientations()

Bimage * img_prepare_orientations	(	Bstring &	tempfile,
		Bsymmetry &	sym,
		double	hires,
		long	bin
	)

img_prepare_projections()

Bimage * img_prepare_projections	(	Bstring &	tempfile,
		Bsymmetry &	sym,
		double	hires,
		long	bin
	)

mg_extract_orient_particles()

long mg_extract_orient_particles	(	Bmicrograph *	mg,
		Bimage *	ptemp,
		double	hires,
		double	lores,
		long	bin,
		fft_plan	planf,
		fft_plan	planb
	)

Finds the centers of picked particles within a micrograph.

Parameters

*mg	micrograph parameter structure.
*ptemp	template image.
hires	high resolution limit.
lores	low resolution limit.
bin	level of image binning.
planf	FFT forward plan.
planb	FFT backward plan.

Returns

long number of particles.

An image processing parameter structure loaded with micrograph
information is used to extract particle images from the micrograph
image using the particle coordinates in the parameter structure.
The extracted particle images are each rotated by PI and the shift
found by cross-correlation between the unrotated and rotated images.
The particle coordinates in the parameter structure are updated with
the shift.

mg_pick_background()

double mg_pick_background	(	Bmicrograph *	mg,
		Bimage *	p,
		long	number,
		long	avg_kernel,
		long	var_kernel,
		double	excl_dist
	)

mg_pick_particles()

double mg_pick_particles	(	Bmicrograph *	mg,
		Bimage *	p,
		Bmarker *	markin,
		Bmarker *	markout,
		int	avg_kernel,
		int	contrast
	)

Locates particles using a fore/background difference measure.

Parameters

*mg	micrograph parameter structure.
*p	micrograph image, if NULL, read from mg.
*markin	foreground marker set.
*markout	background marker set.
avg_kernel	averaging kernle to smooth difference map.
contrast	contrast direction (foreground: white=1, black=0).

Returns

double threshold used to accept peaks.

The two marker sets are used to calculate a difference
between the foreground and background as an estimate of the
presence of a particle.
The resultant image is smoothed by an averaging kernel and rescaled to [0,1].
This image is then scanned to identify particles.

part_align()

double part_align	(	Bparticle *	part,
		Bimage *	p,
		Bimage *	ptemp,
		double	hires,
		double	lores,
		double	shift_limit,
		long	bin,
		fft_plan	planf,
		fft_plan	planb
	)

part_mask_particles()

int part_mask_particles	(	Bparticle *	part,
		Bimage *	pmask,
		long	box_size
	)

part_pick_sym_axis()

Bparticle * part_pick_sym_axis	(	Bparticle *	part,
		Bsymmetry &	sym,
		View &	refview,
		Vector3< double >	refori,
		double	axis_dist
	)

particles_from_peaks()

Bparticle * particles_from_peaks	(	Bimage *	pcc,
		long	bin,
		double	excl_dist,
		double	part_ori,
		double &	fommin,
		double	fommax,
		long	maxnum,
		double	pix_min,
		double	pix_max
	)

Finds the peaks in a cross-correlation map corresponding to particles.

Parameters

*pcc	peak map (after binning).
bin	binning to speed up calculations.
excl_dist	distance between peaks.
part_ori	particle origin.
fommin	minimum threshold to accept peaks.
fommax	maximum threshold to accept peaks.
maxnum	maximum number of peaks to pick.
pix_min	minimum peak width.
pix_max	maximum peak width.

Returns

Bparticle* list of particles.

The map is searched in increments of the particle radius to identify
peaks above the threshold and within a box the size of the
particle radius. The identified peaks are further examined to eliminate 
ones that are too close to a higher scoring peak. The acceptable distance
between peaks is set to 1.8 times the particle radius.

particles_pick_cc() [1/2]

Bparticle * particles_pick_cc	(	Bimage *	p,
		Bimage *	ptemp,
		Bimage *	pmask,
		double	hires,
		double	lores,
		double	fommin,
		double	fommax,
		double	excl_dist,
		long	bin
	)

Picks particles using cross-correlation.

Parameters

*p	image to pick from.
*ptemp	template image.
*pmask	frequency space mask.
hires	high resolution limit.
lores	low resolution limit.
fommin	minimum FOM cutoff.
fommax	maximum FOM cutoff.
excl_dist	minimum distance between particles.
bin	level of image binning.

Returns

Bparticle* list of particles.

A template is cross-correlated with the input image including
bandpass filtering to target the size of the particle.

particles_pick_cc() [2/2]

Bparticle * particles_pick_cc	(	Bstring &	filename,
		long	img_num,
		Bimage *	ptemp,
		Bimage *	pmask,
		double	hires,
		double	lores,
		double	fommin,
		double	fommax,
		double	excl_dist,
		long	bin
	)

Picks particles using cross-correlation.

Parameters

&filename	image to pick from.
img_num	sub-image number.
*ptemp	template image.
*pmask	frequency space mask.
hires	high resolution limit.
lores	low resolution limit.
fommin	minimum FOM cutoff.
fommax	maximum FOM cutoff.
excl_dist	minimum distance between particles.
bin	level of image binning.

Returns

Bparticle* list of particles.

A template is cross-correlated with the input image including
bandpass filtering to target the size of the particle.
The template must have the correct pixel size.

particles_pick_var() [1/3]

Bparticle * particles_pick_var	(	Bimage *	p,
		long	avg_kernel,
		long	var_kernel,
		double	cutmin,
		double	cutmax,
		double	part_ori,
		double	excl_dist,
		long	bin
	)

particles_pick_var() [2/3]

Bparticle * particles_pick_var	(	Bimage *	p,
		long	avg_kernel,
		long	var_kernel,
		double	nsig,
		double	part_ori,
		double	excl_dist,
		long	bin
	)

Picks particles in variance map.

Parameters

*p	image to pick from.
avg_kernel	averaging kernel size.
var_kernel	variance kernel size.
nsig	multiple of sigma above variance average to accept peaks.
part_ori	particle origin.
excl_dist	minimum distance between particles.
bin	level of image binning.

Returns

Bparticle* list of particles.

A copy of the micrograph is filtered with an averaging kernel
and a variance map calculated. The variance map is then used to
find high variance peaks as candidate locations for particles.

particles_pick_var() [3/3]

Bparticle * particles_pick_var	(	Bstring &	filename,
		long	img_num,
		long	avg_kernel,
		long	var_kernel,
		double	nsig,
		double	part_ori,
		double	excl_dist,
		long	bin
	)

Picks particles in variance map.

Parameters

&filename	image to pick from.
img_num	sub-image number.
avg_kernel	averaging kernel size.
var_kernel	variance kernel size.
nsig	multiple of sigma above variance average to accept peaks.
part_ori	particle origin.
excl_dist	minimum distance between particles.
bin	level of image binning.

Returns

Bparticle* list of particles.

A copy of the micrograph is filtered with an averaging kernel
and a variance map calculated. The variance map is then used to
find high variance peaks as candidate locations for particles.

project_extract_orient_particles()

double project_extract_orient_particles	(	Bproject *	project,
		Bstring &	tempfile,
		Bsymmetry &	sym,
		double	hires,
		double	lores,
		long	bin
	)

Picks particles using cross-correlation.

Parameters

*project	project parameter structure.
&tempfile	template image.
sym	point group symmetry.
hires	high resolution limit.
lores	low resolution limit.
bin	level of image binning.

Returns

double minimum threshold used to accept peaks.

Each micrograph is cross-correlated with the template image including
bandpass filtering and frequency space masking.

project_pick_background()

long project_pick_background	(	Bproject *	project,
		long	number,
		long	avg_kernel,
		long	var_kernel,
		double	excl_dist
	)

Picks background areas not overlapping existing particles.

Parameters

*project	project parameter structure.
number	maximum number of background images to pick.
avg_kernel	averaging kernel to smooth the image.
var_kernel	kernel to calculate a local variance image.
excl_dist	exclusion distance between areas.

Returns

long number of background areas.

project_pick_particles() [1/3]

double project_pick_particles	(	Bproject *	project,
		Bimage *	ptemp,
		Bimage *	pmask,
		double	hires,
		double	lores,
		double	fommin,
		double	fommax,
		double	excl_dist,
		long	bin
	)

Picks particles using cross-correlation.

Parameters

*project	project parameter structure.
*ptemp	template image.
*pmask	frequency space mask.
hires	high resolution limit.
lores	low resolution limit.
fommin	minimum FOM cutoff.
fommax	maximum FOM cutoff.
excl_dist	minimum distance between particles.
bin	level of image binning.

Returns

double minimum threshold used to accept peaks.

Each micrograph is cross-correlated with the template image including
bandpass filtering and frequency space masking.

project_pick_particles() [2/3]

long project_pick_particles	(	Bproject *	project,
		double	din,
		double	dout,
		int	avg_kernel,
		double	ainc,
		int	flags,
		int	contrast
	)

Locates particles using a fore/background difference measure.

Parameters

*project	project parameter structure.
din	inner diameter corresponding to particle edge.
dout	outer diameter corresponding to background.
avg_kernel	averaging kernle to smooth difference map.
ainc	angular increment.
flags	flags: bit 1 = filter extremes.
contrast	contrast direction (foreground: white=1, black=0).

Returns

long number of particles.

Two marker sets are generated at the indicated diameters.
At each pixel, the marker sets are used to calculate a difference
between the foreground and background as an estimate of the
presence of a particle.

project_pick_particles() [3/3]

double project_pick_particles	(	Bproject *	project,
		long	avg_kernel,
		long	var_kernel,
		double	nsig,
		double	part_ori,
		double	excl_dist,
		long	bin
	)

Picks particles in variance map.

Parameters

*project	project parameter structure.
avg_kernel	averaging kernel size.
var_kernel	variance kernel size.
nsig	multiple of sigma above variance average to accept peaks.
part_ori	particle origin.
excl_dist	minimum distance between particles.
bin	level of image binning.

Returns

double minimum threshold used to accept peaks.

A copy of the micrograph is filtered with an averaging kernel
and a variance map calculated. The variance map is then used to
find high variance peaks as candidate locations for particles.

project_pick_sym_axis()

long project_pick_sym_axis	(	Bproject *	project,
		Bsymmetry &	sym,
		int	sym_axis,
		double	axis_dist
	)

Picks subregions in 3D particles on the given symmetry axis.

Parameters

*project	parameter structure with all parameters.
sym	point group symmetry.
sym_axis	symmetry axis to pick subregions.
axis_dist	distance along symmetry axis.

Returns

long number of new particles.

The existing particles are replaced by the new particles.

rec_extract_orient_particles()

long rec_extract_orient_particles	(	Breconstruction *	rec,
		Bimage *	ptemp,
		double	hires,
		double	lores,
		long	bin,
		fft_plan	planf,
		fft_plan	planb
	)

rec_pick_background()

double rec_pick_background	(	Breconstruction *	rec,
		Bimage *	p,
		long	number,
		long	avg_kernel,
		long	var_kernel,
		double	excl_dist
	)

Variable Documentation

verbose

int verbose

extern