bico.cpp File Reference

Program to analyze icosahedral subtomograms. More...

#include "mg_processing.h"
#include "mg_reconstruct.h"
#include "rwmg.h"
#include "rwimg.h"
#include "rwsymop.h"
#include "symmetry.h"
#include "linked_list.h"
#include "utilities.h"
#include "options.h"
#include "timer.h"

Functions
Bimage *	img_vertex_reconstruct (Bproject *project, Vector3< long > size, double maxres)
long	project_ico_worst_vertex (Bproject *project, Bimage *pref, Bimage *pmask, Bimage *pfsmask, double hires, double lores)
	Determines the special vertex for icosahedral symmetry and returns two maps. More...
long	project_ico_opposite_vertex (Bproject *project, Bimage *pmask, Bimage *pfsmask, double hires, double lores)
	Determines the special vertex for icosahedral symmetry and returns two maps. More...
long	project_ico_best_c5 (Bproject *project, Bimage *pref, Bimage *pmask, Bimage *pfsmask, double hires, double lores)
	Determines the best 5-fold orientation of the vertex wrt a reference. More...
long	project_assign_special_vertex_orientations (Bproject *project, Bproject *project_specvert)
long	project_analyze_vertices (Bproject *project, double threshold)
long	project_analyze_vertices2 (Bproject *project, double significance)
long	project_analyze_vertices3 (Bproject *project, long maxcut)
int	main (int argc, char **argv)
Bimage *	img_read_orient_mask (Bstring &filename, Bimage *pmask, View view)
double	img_cc (Bimage *p1, Bimage *p2, Bimage *pfsmask, double hires, double lores)
long	particle_worst_vertex (Bparticle *vert, Bimage *pref, Bimage *pmask, Bimage *pfsmask, double hires, double lores)
long	particle_cc_opposite_vertices (Bparticle *vert, Bimage *pmask, Bimage *pfsmask, double hires, double lores)
long	particle_worst_opposite_vertex (Bparticle *vert, Bimage *pref, Bimage *pmask, Bimage *pfsmask, double hires, double lores)
long	particle_best_c5 (Bparticle *part, Bimage *pref, Bimage *pmask, Bimage *pfsmask, double hires, double lores)

Variables
int	verbose
fft_plan	planf
fft_plan	planb
const char *	use []

Detailed Description

Program to analyze icosahedral subtomograms.

Author

Bernard Heymann

Date

Created: 20180427

Modified: 20201124

Function Documentation

img_cc()

double img_cc	(	Bimage *	p1,
		Bimage *	p2,
		Bimage *	pfsmask,
		double	hires,
		double	lores
	)

img_read_orient_mask()

Bimage * img_read_orient_mask	(	Bstring &	filename,
		Bimage *	pmask,
		View	view
	)

img_vertex_reconstruct()

Bimage * img_vertex_reconstruct	(	Bproject *	project,
		Vector3< long >	size,
		double	maxres
	)

main()

int main	(	int	argc,
		char **	argv
	)

particle_best_c5()

long particle_best_c5	(	Bparticle *	part,
		Bimage *	pref,
		Bimage *	pmask,
		Bimage *	pfsmask,
		double	hires,
		double	lores
	)

particle_cc_opposite_vertices()

long particle_cc_opposite_vertices	(	Bparticle *	vert,
		Bimage *	pmask,
		Bimage *	pfsmask,
		double	hires,
		double	lores
	)

particle_worst_opposite_vertex()

long particle_worst_opposite_vertex	(	Bparticle *	vert,
		Bimage *	pref,
		Bimage *	pmask,
		Bimage *	pfsmask,
		double	hires,
		double	lores
	)

particle_worst_vertex()

long particle_worst_vertex	(	Bparticle *	vert,
		Bimage *	pref,
		Bimage *	pmask,
		Bimage *	pfsmask,
		double	hires,
		double	lores
	)

project_analyze_vertices()

long project_analyze_vertices	(	Bproject *	project,
		double	threshold
	)

project_analyze_vertices2()

long project_analyze_vertices2	(	Bproject *	project,
		double	significance
	)

project_analyze_vertices3()

long project_analyze_vertices3	(	Bproject *	project,
		long	maxcut
	)

project_assign_special_vertex_orientations()

long project_assign_special_vertex_orientations	(	Bproject *	project,
		Bproject *	project_specvert
	)

project_ico_best_c5()

long project_ico_best_c5	(	Bproject *	project,
		Bimage *	pref,
		Bimage *	pmask,
		Bimage *	pfsmask,
		double	hires,
		double	lores
	)

Determines the best 5-fold orientation of the vertex wrt a reference.

Parameters

*project	parameter structure with all parameters.
*pref	reference map.
*pmask	real space mask.
*pfsmask	frequency space mask.
hires	maximum resolution for correlation.
lores	minimum resolution for correlation.

Returns

long 1 if done, 0 on error.

The function compares opposite vertices of the twelve for every particle
to identify the pair that is most dissimilar. 
One of these is a candidate for the special vertex.
A reference map is then calculated from all the rest of the vertices.
The previously selected pair is then correlated agiants the reference
and the one with the worst coefficient selected as final candidate.
Two averages are calculated, the first for the non-special vertices,
and the second for the special vertices.

project_ico_opposite_vertex()

long project_ico_opposite_vertex	(	Bproject *	project,
		Bimage *	pmask,
		Bimage *	pfsmask,
		double	hires,
		double	lores
	)

Determines the special vertex for icosahedral symmetry and returns two maps.

Parameters

*project	parameter structure with all parameters.
*pmask	real space mask.
*pfsmask	frequency space mask.
hires	maximum resolution for correlation.
lores	minimum resolution for correlation.

Returns

long 1 if done, 0 on error.

The function compares opposite vertices of the twelve for every particle
to identify the pair that is most dissimilar. 
One of these is a candidate for the special vertex.
A reference map is then calculated from all the rest of the vertices.
The previously selected pair is then correlated agiants the reference
and the one with the worst coefficient selected as final candidate.
Two averages are calculated, the first for the non-special vertices,
and the second for the special vertices.

project_ico_worst_vertex()

long project_ico_worst_vertex	(	Bproject *	project,
		Bimage *	pref,
		Bimage *	pmask,
		Bimage *	pfsmask,
		double	hires,
		double	lores
	)

Determines the special vertex for icosahedral symmetry and returns two maps.

Parameters

*project	parameter structure with all parameters.
*pref	reference map.
*pmask	real space mask.
*pfsmask	frequency space mask.
hires	maximum resolution for correlation.
lores	minimum resolution for correlation.

Returns

long 1 if done, 0 on error.

The function correlates each vertex with the reference, and selects the one
out of the twelve for each particle with the worst coefficient as the 
likely special vertex.
Two averages are calculated, the first for the non-special vertices,
and the second for the special vertices.

Variable Documentation

planb

fft_plan planb

planf

fft_plan planf

use

const char* use[]

Initial value:

= {
" ",
"Usage: bico [options] tomo.star",
"-------------------------------",
"Analyzes icosahedral subtomograms.",
" ",
"Actions:",
"-find opp                Type of correlation: worst, opposite, c5.",
"-analyze 0.1             Calculate statistics for vertices.",
" ",
"Parameters:",
"-verbose 7               Verbosity of output.",
"-resolution 15.6,200     Resolution limits for cross-correlation (default 0,inf).",
"-maxresolution 9.5       Maximum reconstruction resolution limit (default Nyquist).",
" ",
"Input:",
"-reference image.map     Reference for cross-correlation.",
"-mask image.map          Real space mask.",
"-Mask fsmask.mrc         Frequency space mask (missing data).",
"-special vert.star       Parameter file with special vertex orientations.",
" ",
"Output:",
"-output file.star        Output parameter file.",
"-reconstruction file.ext Reconstruction file name.",
" ",
NULL
}

verbose

int verbose

extern