mg_helix.cpp File Reference

Functions to process helical data. More...

#include "Bimage.h"
#include "mg_processing.h"
#include "mg_img_proc.h"
#include "mg_helix.h"
#include "mg_extract.h"
#include "spline.h"
#include "linked_list.h"
#include "Complex.h"
#include "utilities.h"
#include "timer.h"

Functions
double *	filament_profile (Bfilnode *fnode, Bimage *p, long img_num, int id, double width, long &n)
	Calculates a filament profile and node profile. More...
double	nodes_center (Bfilnode *fnode, Bimage *p, long img_num, int width)
double	filaments_center (Bfilament *fillist, Bimage *p, long img_num, int filament_width)
	Centers filament nodes in a micrograph. More...
double	project_center_filaments (Bproject *project, int filament_width)
	Centers filament nodes in all micrographs in a project. More...
int	project_filament_powerspectrum (Bproject *project, int pad, int rotated, Bstring &path)
	Calculates and average power spectrum from filaments. More...
Bimage *	project_filament_density (Bproject *project, int filament_width)
	Extracts filament images from micrographs defined in a project and estimates their density per length. More...
int	mg_generate_layer_lines (Bmicrograph *mg, int rad_lim)
	Generates layer lines given the unit cell vectors. More...
int	img_mask_layer_lines (Bimage *p, Blayerline *layer_line, float helix_axis, float width)
	Masks the image using the list of layer lines. More...
double *	img_extract_layer_line (Bimage *p, Blayerline *line, float helix_axis, int length)
	Extracts one layer line from an image. More...
int	mg_extract_show_layer_lines (Bmicrograph *mg, int length, int show)
	Extracts and prints layer lines from an image with corresponding Bessel functions. More...

Variables
int	verbose

Detailed Description

Functions to process helical data.

Author

Bernard Heymann

Date

Created: 20061110

Modified: 20170623

Function Documentation

filament_profile()

double * filament_profile	(	Bfilnode *	fnode,
		Bimage *	p,
		long	img_num,
		int	id,
		double	width,
		long &	n
	)

Calculates a filament profile and node profile.

Parameters

*fnode	node list.
*p	image with filament.
img_num	sub-image number.
id	identifier of selected node.
width	width of box around filament.
&n	number of elements in the profile.

Returns

double* two profile arrays, each length n.

A filament image is extracted from the micrograph along a spline through
the nodes. The overall profile and the profile around a specified node
are calculated and returned in a single array.
It only works for 2D images.

filaments_center()

double filaments_center	(	Bfilament *	fillist,
		Bimage *	p,
		long	img_num,
		int	filament_width
	)

Centers filament nodes in a micrograph.

Parameters

*fillist	list of filaments.
*p	image with filament.
img_num	sub-image number.
filament_width	width of box around filament.

Returns

double average correlation coefficient.

The profile for each node is calculated and centered by cross-correlation
with the mirrored profile.

img_extract_layer_line()

double * img_extract_layer_line	(	Bimage *	p,
		Blayerline *	line,
		float	helix_axis,
		int	length
	)

Extracts one layer line from an image.

Parameters

*p	power spectrum.
*line	layer line.
helix_axis	helix axis angle.
length	length of line.

Returns

double* array with line values.

img_mask_layer_lines()

int img_mask_layer_lines	(	Bimage *	p,
		Blayerline *	layer_line,
		float	helix_axis,
		float	width
	)

Masks the image using the list of layer lines.

Parameters

*p	complex image.
*layer_line	layer line list.
helix_axis	helix axis angle.
width	width of mask for a line.

Returns

int number of lines or error code.

mg_extract_show_layer_lines()

int mg_extract_show_layer_lines	(	Bmicrograph *	mg,
		int	length,
		int	show
	)

Extracts and prints layer lines from an image with corresponding Bessel functions.

Parameters

*mg	micrograph.
length	length of line.
show	show: 1=extracted layer lines, 2=Bessel functions, 3=both

Returns

int 0.

mg_generate_layer_lines()

int mg_generate_layer_lines	(	Bmicrograph *	mg,
		int	rad_lim
	)

Generates layer lines given the unit cell vectors.

Parameters

*mg	micrograph.
rad_lim	layer line radial limit.

Returns

int number of layer lines generated, <0 on error.

The structure factor location is given by:
    x = uh + vk
where u and v are the unit cell vectors,
and h and k are the associated Miller indices.

nodes_center()

double nodes_center	(	Bfilnode *	fnode,
		Bimage *	p,
		long	img_num,
		int	width
	)

project_center_filaments()

double project_center_filaments	(	Bproject *	project,
		int	filament_width
	)

Centers filament nodes in all micrographs in a project.

Parameters

*project	project object.
filament_width	width of box around filament.

Returns

double average correlation coefficient.

The profile for each node is calculated and centered by cross-correlation
with the mirrored profile.

project_filament_density()

Bimage * project_filament_density	(	Bproject *	project,
		int	filament_width
	)

Extracts filament images from micrographs defined in a project and estimates their density per length.

Parameters

*project	micrograph project.
filament_width	extracted filament width.

Returns

Bimage* image with all densities.

project_filament_powerspectrum()

int project_filament_powerspectrum	(	Bproject *	project,
		int	pad,
		int	rotated,
		Bstring &	path
	)

Calculates and average power spectrum from filaments.

Parameters

*project	project parameter structure.
pad	additional padding before transformation.
rotated	flag to indicate if particles are already rotated.
&path	path to write power spectra.

Returns

int 0.

Particles derived from picked filaments are extracted and transformed
to orient the helical axis along the x-axis. These images are then
Fourier transformed and their power spectra averaged.
One average per micrograph is calculated.
Requirements: The filaments must be picked and converted to particle locations.

Variable Documentation

verbose

int verbose

extern