rwmgSTAR.cpp File Reference

Library routines to read and write micrograph parameters in STAR format. More...

#include "mg_processing.h"
#include "rwmgSTAR.h"
#include "star.h"
#include "mg_tags.h"
#include "linked_list.h"
#include "utilities.h"

Functions
int	star_to_project (Bstar &star, Bproject *project, int flag)
int	project_to_star (Bproject *project, Bstar &star, int mg_select, int rec_select)
int	read_project_star (Bstring &filename, Bproject *project, int flag)
	Reading micrograph parameters from STAR files. More...
int	write_project_star (const char *filename, Bproject *project, int mg_select, int rec_select)
	Writing micrograph parameters to a STAR file. More...
int	write_project_star (Bstring &filename, Bproject *project, int mg_select, int rec_select)
int	mg_star_update_tags (Bstar &star)
	Replacing old STAR tags with new ones. More...
Bframe *	frame_from_starblock (BstarBlock &block)
int	project_get_fom_tags (Bstar star, FOMType *fom_tag)
Bparticle *	particle_from_starblock (BstarBlock &block, FOMType fom_tag[NFOM])
Bfilament *	filament_from_starblock (BstarBlock &block)
Bbadarea *	badarea_from_starblock (BstarBlock &block)
Bmarker *	marker_from_starblock (BstarBlock &block)
Bstrucfac *	strucfac_from_starblock (BstarBlock &block)
Blayerline *	layerline_from_starblock (BstarBlock &block)
CTFparam *	ctf_from_starblock (BstarBlock &block)
Bmicrograph *	micrograph_from_starblock (BstarBlock &block, Bstring &mgid, FOMType fom_tag[NFOM])
Breconstruction *	reconstruction_from_starblock (BstarBlock &block, FOMType fom_tag[NFOM])
int	frame_to_starblock (Bframe *frame, BstarBlock &block)
int	particle_to_starblock (Bparticle *part, BstarBlock &block, FOMType fom_tag[NFOM], int euler_flag, int omega_flag)
int	badarea_to_starblock (Bbadarea *bad, BstarBlock &block)
int	filament_to_starblock (Bfilament *fil, BstarBlock &block)
int	marker_to_starblock (Bmarker *mark, BstarBlock &block)
int	strucfac_to_starblock (Bstrucfac *sf, BstarBlock &block)
int	layerline_to_starblock (Blayerline *line, BstarBlock &block)
int	ctf_to_starblock (CTFparam *ctf, BstarBlock &block)
int	micrograph_to_starblock (Bmicrograph *mg, BstarBlock &block, FOMType fom_tag[NFOM], int euler_flag, int omega_flag)
int	reconstruction_to_starblock (Breconstruction *rec, BstarBlock &block, FOMType fom_tag[NFOM], int euler_flag, int omega_flag)

Variables
int	verbose

Detailed Description

Library routines to read and write micrograph parameters in STAR format.

Author

Bernard Heymann

Date

Created: 20010206

Modified: 20220113

Function Documentation

badarea_from_starblock()

Bbadarea * badarea_from_starblock

(

BstarBlock &

block

)

badarea_to_starblock()

int badarea_to_starblock	(	Bbadarea *	bad,
		BstarBlock &	block
	)

ctf_from_starblock()

CTFparam * ctf_from_starblock

(

BstarBlock &

block

)

ctf_to_starblock()

int ctf_to_starblock	(	CTFparam *	ctf,
		BstarBlock &	block
	)

filament_from_starblock()

Bfilament * filament_from_starblock

(

BstarBlock &

block

)

filament_to_starblock()

int filament_to_starblock	(	Bfilament *	fil,
		BstarBlock &	block
	)

frame_from_starblock()

Bframe * frame_from_starblock

(

BstarBlock &

block

)

frame_to_starblock()

int frame_to_starblock	(	Bframe *	frame,
		BstarBlock &	block
	)

layerline_from_starblock()

Blayerline * layerline_from_starblock

(

BstarBlock &

block

)

layerline_to_starblock()

int layerline_to_starblock	(	Blayerline *	line,
		BstarBlock &	block
	)

marker_from_starblock()

Bmarker * marker_from_starblock

(

BstarBlock &

block

)

marker_to_starblock()

int marker_to_starblock	(	Bmarker *	mark,
		BstarBlock &	block
	)

mg_star_update_tags()

int mg_star_update_tags

(

Bstar &

star

)

Replacing old STAR tags with new ones.

Parameters

&star

STAR database.

Returns

int 0.

micrograph_from_starblock()

Bmicrograph * micrograph_from_starblock	(	BstarBlock &	block,
		Bstring &	mgid,
		FOMType	fom_tag[NFOM]
	)

micrograph_to_starblock()

int micrograph_to_starblock	(	Bmicrograph *	mg,
		BstarBlock &	block,
		FOMType	fom_tag[NFOM],
		int	euler_flag,
		int	omega_flag
	)

particle_from_starblock()

Bparticle * particle_from_starblock	(	BstarBlock &	block,
		FOMType	fom_tag[NFOM]
	)

particle_to_starblock()

int particle_to_starblock	(	Bparticle *	part,
		BstarBlock &	block,
		FOMType	fom_tag[NFOM],
		int	euler_flag,
		int	omega_flag
	)

project_get_fom_tags()

int project_get_fom_tags	(	Bstar	star,
		FOMType *	fom_tag
	)

project_to_star()

int project_to_star	(	Bproject *	project,
		Bstar &	star,
		int	mg_select,
		int	rec_select
	)

read_project_star()

int read_project_star	(	Bstring &	filename,
		Bproject *	project,
		int	flag
	)

Reading micrograph parameters from STAR files.

Parameters

&filename	file name (or comma-delimited list).
*project	initialized project structure.
flag	update tags.

Returns

int error code (<0 means failure).

reconstruction_from_starblock()

Breconstruction * reconstruction_from_starblock	(	BstarBlock &	block,
		FOMType	fom_tag[NFOM]
	)

reconstruction_to_starblock()

int reconstruction_to_starblock	(	Breconstruction *	rec,
		BstarBlock &	block,
		FOMType	fom_tag[NFOM],
		int	euler_flag,
		int	omega_flag
	)

star_to_project()

int star_to_project	(	Bstar &	star,
		Bproject *	project,
		int	flag
	)

strucfac_from_starblock()

Bstrucfac * strucfac_from_starblock

(

BstarBlock &

block

)

strucfac_to_starblock()

int strucfac_to_starblock	(	Bstrucfac *	sf,
		BstarBlock &	block
	)

write_project_star() [1/2]

int write_project_star	(	Bstring &	filename,
		Bproject *	project,
		int	mg_select,
		int	rec_select
	)

write_project_star() [2/2]

int write_project_star	(	const char *	filename,
		Bproject *	project,
		int	mg_select,
		int	rec_select
	)

Writing micrograph parameters to a STAR file.

Parameters

&filename	file name.
*project	project structure.
mg_select	flag to only write selected micrographs.
rec_select	flag to only convert selected reconstructions.

Returns

int error code (<0 means failure).

Variable Documentation

verbose

int verbose

extern