mg_extract.cpp File Reference

Functions to extract particles from micrographs. More...

#include "mg_extract.h"
#include "mg_select.h"
#include "linked_list.h"
#include "spline.h"
#include "utilities.h"
#include <sys/stat.h>

Functions
int	mask_filament_particles (Bstring &filename, Bparticle *partlist, int mask_width)
int	rotate_mask_filament_particles (Bstring &filename, Bparticle *partlist, int rotation_axis, int back_flag, int mask_width)
int	particle_setup_filenames (Bparticle *part, Bstring filename, Bstring partpath)
	Sets up individual particle file names for extraction. More...
int	filament_setup_filenames (Bfilament *fil, Bstring filename, Bstring filpath)
	Sets up individual filament file names for extraction. More...
Vector3< double > *	vector3_spline_from_nodes (Bfilnode *fnode, long &nspline)
	Calculates a spline curve from a set of filament nodes. More...
long	project_extract_particles (Bproject *project, double scale, int back_flag, int norm_flag, int fill_type, double fill, int mask_width, int split, Bstring &partbase, Bstring &partpath, Bstring &partext)
	Extracts particle images from micrographs defined in a project. More...
long	micrograph_extract_particles (Bmicrograph *mg, Bimage *p, double scale, int back_flag, int norm_flag, double fill, int mask_width)
	Extracts particle images from a micrograph. More...
long	reconstruction_extract_particles (Breconstruction *rec, Bimage *p, double scale, int back_flag, int norm_flag, double fill, int mask_width)
	Extracts particle images from a reconstruction. More...
Bparticle *	reconstruction_project_extract_particles (Breconstruction *rec, Bimage *p, double scale, int back_flag, int norm_flag, double fill, int mask_width)
	Extracts and projects 3D particle images from a reconstruction and return a 2D list. More...
Bimage *	particle_extract (Bparticle *particles, Bbadarea *bad_areas, Bimage *p, Vector3< long > size, double scale, double bad_radius, int back_flag, int norm_flag, double fill, int mask_width)
	Extracts particle images from an image. More...
Bimage *	micrograph_extract_gold (Bmicrograph *mg, Bimage *p, double radius)
	Extracts gold particle images from a micrograph. More...
Bimage *	reconstruction_extract_gold (Breconstruction *rec, Bimage *p, double radius)
	Extracts gold particle images from a reconstruction. More...
Bimage *	marker_extract_gold (Bmarker *marker_list, Bimage *p, int img_num, double radius)
	Extracts gold particle images from an image. More...
long	project_extract_filaments (Bproject *project, int filament_width, int axis, Bstring &base, Bstring &path, Bstring &ext, int split)
	Extracts filament images from micrographs defined in a project. More...
long	micrograph_extract_filaments (Bmicrograph *mg, Bimage *p, double width, int axis)
	Extracts filament images from a micrograph. More...
long	reconstruction_extract_filaments (Breconstruction *rec, Bimage *p, double width, int axis)
	Extracts filament images from a micrograph. More...
Bimage *	filament_extract (Bfilament *filaments, Bimage *p, double width, int axis)
	Extracts filament images from a micrograph. More...
int	project_filaments_to_particles (Bproject *project, Vector3< long > box_size, double boxing_interval, double rise, double angle)
	Converts filaments to sets of particles. More...
int	micrograph_filaments_to_particles (Bmicrograph *mg, Vector3< long > box_size, double boxing_interval, double rise, double angle)
	Converts filaments to sets of particles. More...
int	reconstruction_filaments_to_particles (Breconstruction *rec, Vector3< long > box_size, double boxing_interval, double rise, double angle)
	Converts filaments to sets of particles. More...
Bparticle *	filaments_to_particles (Bfilament *filaments, Vector3< double > pixel_size, Vector3< long > box_size, double boxing_interval, double rise, double angle)
	Converts filaments to sets of particles. More...
int	project_mask_filament_particles (Bproject *project, int mask_width)
	Masks particles extracted from filaments. More...
int	project_rotate_mask_filament_particles (Bproject *project, int rotation_axis, int back_flag, int mask_width)
	Rotates and masks particles extracted from filaments. More...

Variables
int	verbose

Detailed Description

Functions to extract particles from micrographs.

Author

Bernard Heymann

Date

Created: 20040406

Modified: 20200616

Function Documentation

filament_extract()

Bimage * filament_extract	(	Bfilament *	filaments,
		Bimage *	p,
		double	width,
		int	axis
	)

Extracts filament images from a micrograph.

Parameters

*filaments	filament parameters.
*p	image.
width	width of box around filament to extract.
axis	helical axis alignment: x=1, y=2, z=3.

Returns

Bimage* multi-filament image.

If the file names for individual filaments are specified, they are
used to write individual filaments to files.
Default axis alignment (for axis==0):
    2D images:  x-axis (1)
    3D images:  z-axis (3)

filament_setup_filenames()

int filament_setup_filenames	(	Bfilament *	fil,
		Bstring	filename,
		Bstring	filpath
	)

Sets up individual filament file names for extraction.

Parameters

*fil	filament list.
filename	filament file name base.
filpath	filament path with optional wild card characters.

Returns

long number of filaments.

The filament path can have wildcard characters ('?') that specify
the number of digits to use to insert numbers in the path and
the file name.

filaments_to_particles()

Bparticle * filaments_to_particles	(	Bfilament *	filaments,
		Vector3< double >	pixel_size,
		Vector3< long >	box_size,
		double	boxing_interval,
		double	rise,
		double	angle
	)

Converts filaments to sets of particles.

Parameters

*filaments	filament parameters.
pixel_size	sampling.
box_size	size of particle box.
boxing_interval	step size between boxes.
rise	rise per asymmetric unit in angstrom.
angle	angular rotation per asymmetric unit in radians.

Returns

Bparticle* pointer to new list of particles.

Particle coordinates are calculated along a spline curve through
the filament nodes, separated by half the given width.
Different filaments in a micrograph are indicated by the selection number.

marker_extract_gold()

Bimage * marker_extract_gold	(	Bmarker *	marker_list,
		Bimage *	p,
		int	img_num,
		double	radius
	)

Extracts gold particle images from an image.

Parameters

*marker_list	marker parameters.
*p	image.
img_num	sub-image number.
radius	radius of gold particle.

Returns

Bimage* multi-particle image.

mask_filament_particles()

int mask_filament_particles	(	Bstring &	filename,
		Bparticle *	partlist,
		int	mask_width
	)

micrograph_extract_filaments()

long micrograph_extract_filaments	(	Bmicrograph *	mg,
		Bimage *	p,
		double	width,
		int	axis
	)

Extracts filament images from a micrograph.

Parameters

*mg	micrograph parameters.
*p	micrograph image.
width	width of box around filament to extract.
axis	helical axis alignment: x=1, y=2, z=3.

Returns

long number of filaments.

micrograph_extract_gold()

Bimage * micrograph_extract_gold	(	Bmicrograph *	mg,
		Bimage *	p,
		double	radius
	)

Extracts gold particle images from a micrograph.

Parameters

*mg	micrograph parameters.
*p	micrograph image.
radius	radius of gold particle.

Returns

Bimage* multi-particle image.

micrograph_extract_particles()

long micrograph_extract_particles	(	Bmicrograph *	mg,
		Bimage *	p,
		double	scale,
		int	back_flag,
		int	norm_flag,
		double	fill,
		int	mask_width
	)

Extracts particle images from a micrograph.

Parameters

*mg	micrograph parameters.
*p	micrograph image.
scale	scale to extract (usually 1).
back_flag	background correction flag.
norm_flag	normalization flag.
fill	value to fill in new regions.
mask_width	filament mask width, if 0, don't apply.

Returns

long number of particles.

micrograph_filaments_to_particles()

int micrograph_filaments_to_particles	(	Bmicrograph *	mg,
		Vector3< long >	box_size,
		double	boxing_interval,
		double	rise,
		double	angle
	)

Converts filaments to sets of particles.

Parameters

*mg	micrograph parameters.
box_size	size of particle box.
boxing_interval	step size between boxes.
rise	rise per asymmetric unit in angstrom.
angle	angular rotation per asymmetric unit in radians.

Returns

int number of filaments converted.

Particle coordinates are calculated along a spline curve through
the filament nodes, separated by half the given width.
Different filaments in a micrograph are indicated by the selection number.

particle_extract()

Bimage * particle_extract	(	Bparticle *	particles,
		Bbadarea *	bad_areas,
		Bimage *	p,
		Vector3< long >	size,
		double	scale,
		double	bad_radius,
		int	back_flag,
		int	norm_flag,
		double	fill,
		int	mask_width
	)

Extracts particle images from an image.

Parameters

*particles	particle parameters.
*bad_areas	bad area parameters.
*p	image.
size	size of box to extract.
scale	scale to extract (usually 1).
bad_radius	radius of bad area.
back_flag	background correction flag.
norm_flag	normalization flag.
fill	value to fill in new regions.
mask_width	filament mask width, if 0, don't apply.

Returns

Bimage* multi-particle image.

If the background flag is specified, the particle mask is set in the 
background, defined as outside the inscribing circle.
The mask is set within every bad area in the micrograph and
transferred to the mask for a particle where it overlaps.

particle_setup_filenames()

int particle_setup_filenames	(	Bparticle *	part,
		Bstring	filename,
		Bstring	partpath
	)

Sets up individual particle file names for extraction.

Parameters

*part	particle list.
filename	particle file name base.
partpath	particle path with optional wild card characters.

Returns

long number of particles.

The particle path can have wildcard characters ('?') that specify
the number of digits to use to insert numbers in the path and
the file name.

project_extract_filaments()

long project_extract_filaments	(	Bproject *	project,
		int	filament_width,
		int	axis,
		Bstring &	base,
		Bstring &	path,
		Bstring &	ext,
		int	split
	)

Extracts filament images from micrographs defined in a project.

Parameters

*project	micrograph project.
filament_width	extracted filament width.
axis	helical axis alignment: x=1, y=2, z=3.
&base	file name base.
&path	path to filament file.
&ext	filament file extension.
split	flag to split filaments into individual files.

Returns

long number of filaments, <0 on error.

project_extract_particles()

long project_extract_particles	(	Bproject *	project,
		double	scale,
		int	back_flag,
		int	norm_flag,
		int	fill_type,
		double	fill,
		int	mask_width,
		int	split,
		Bstring &	partbase,
		Bstring &	partpath,
		Bstring &	partext
	)

Extracts particle images from micrographs defined in a project.

Parameters

*project	micrograph project.
scale	scale to extract (usually 1).
back_flag	background correction flag.
norm_flag	normalization flag.
fill_type	FILL_AVERAGE, FILL_BACKGROUND, FILL_USER.
fill	value to fill in new regions.
mask_width	filament mask width, if 0, don't apply.
split	flag to split images into separate files.
&partbase	file name base.
&partpath	path to particle file.
&partext	particle file extension.

Returns

long number of particles, <0 on error.

project_filaments_to_particles()

int project_filaments_to_particles	(	Bproject *	project,
		Vector3< long >	box_size,
		double	boxing_interval,
		double	rise,
		double	angle
	)

Converts filaments to sets of particles.

Parameters

*project	project parameters.
box_size	size of particle box.
boxing_interval	step size between boxes.
rise	rise per asymmetric unit in angstrom.
angle	angular rotation per asymmetric unit in radians.

Returns

int number of filaments converted.

Particle coordinates are calculated along a spline curve through
the filament nodes, separated by half the given width.
Different filaments in a micrograph are indicated by the selection number.

project_mask_filament_particles()

int project_mask_filament_particles	(	Bproject *	project,
		int	mask_width
	)

Masks particles extracted from filaments.

Parameters

*project	project parameters.
mask_width	width of mask to apply.

Returns

int number of particles masked.

The orientation of the filament is inferred from the view angle and
the adjacent regions are set to the background.

project_rotate_mask_filament_particles()

int project_rotate_mask_filament_particles	(	Bproject *	project,
		int	rotation_axis,
		int	back_flag,
		int	mask_width
	)

Rotates and masks particles extracted from filaments.

Parameters

*project	project parameters.
rotation_axis	axis to rotate to: 1=x, 2=y, 3=z.
back_flag	background correction flag.
mask_width	width of mask to apply.

Returns

int number of particles masked.

The orientation of the filament is inferred from the view angle and
the particle is rotated to orient the filament axis along a cartesian axis. 
The mask is applied and adjacent regions are set to the background.

reconstruction_extract_filaments()

long reconstruction_extract_filaments	(	Breconstruction *	rec,
		Bimage *	p,
		double	width,
		int	axis
	)

Extracts filament images from a micrograph.

Parameters

*rec	reconstruction parameters.
*p	reconstruction image.
width	width of box around filament to extract.
axis	helical axis alignment: x=1, y=2, z=3.

Returns

long number of filaments.

reconstruction_extract_gold()

Bimage * reconstruction_extract_gold	(	Breconstruction *	rec,
		Bimage *	p,
		double	radius
	)

Extracts gold particle images from a reconstruction.

Parameters

*rec	reconstruction parameters.
*p	reconstruction image.
radius	radius of gold particle.

Returns

Bimage* multi-particle image.

reconstruction_extract_particles()

long reconstruction_extract_particles	(	Breconstruction *	rec,
		Bimage *	p,
		double	scale,
		int	back_flag,
		int	norm_flag,
		double	fill,
		int	mask_width
	)

Extracts particle images from a reconstruction.

Parameters

*rec	reconstruction parameters.
*p	micrograph image.
scale	scale to extract (usually 1).
back_flag	background correction flag.
norm_flag	normalization flag.
fill	value to fill in new regions.
mask_width	filament mask width, if 0, don't apply.

Returns

long number of particles.

reconstruction_filaments_to_particles()

int reconstruction_filaments_to_particles	(	Breconstruction *	rec,
		Vector3< long >	box_size,
		double	boxing_interval,
		double	rise,
		double	angle
	)

Converts filaments to sets of particles.

Parameters

*rec	reconstruction parameters.
box_size	size of particle box.
boxing_interval	step size between boxes.
rise	rise per asymmetric unit in angstrom.
angle	angular rotation per asymmetric unit in radians.

Returns

int number of filaments converted.

Particle coordinates are calculated along a spline curve through
the filament nodes, separated by half the given width.
Different filaments in a micrograph are indicated by the selection number.

reconstruction_project_extract_particles()

Bparticle * reconstruction_project_extract_particles	(	Breconstruction *	rec,
		Bimage *	p,
		double	scale,
		int	back_flag,
		int	norm_flag,
		double	fill,
		int	mask_width
	)

Extracts and projects 3D particle images from a reconstruction and return a 2D list.

Parameters

*rec	reconstruction parameters.
*p	micrograph image.
scale	scale to extract (usually 1).
back_flag	background correction flag.
norm_flag	normalization flag.
fill	value to fill in new regions.
mask_width	filament mask width, if 0, don't apply.

Returns

Bparticle* list of 2D particles.

The file name of the new particles is returned in the image file name.

rotate_mask_filament_particles()

int rotate_mask_filament_particles	(	Bstring &	filename,
		Bparticle *	partlist,
		int	rotation_axis,
		int	back_flag,
		int	mask_width
	)

vector3_spline_from_nodes()

Vector3< double > * vector3_spline_from_nodes	(	Bfilnode *	fnode,
		long &	nspline
	)

Calculates a spline curve from a set of filament nodes.

Parameters

*fnode	node list.
&nspline	number of elements in the spline array.

Returns

Vector3<double>* array of spline coordinates.

The node coordinates are copied into a new array used to calculate the spline array.

Variable Documentation

verbose

int verbose

extern