rwmg.cpp File Reference

Library routines to read and write micrograph parameters. More...

#include "rwmg.h"
#include "mg_processing.h"
#include "mg_img_proc.h"
#include "mg_ctf.h"
#include "mg_tags.h"
#include "rwmgSTAR.h"
#include "rwmgXML.h"
#include "rwmgEMX.h"
#include "rwmgRELION.h"
#include "rwmgIMOD.h"
#include "rwmgSerialEM.h"
#include "file_util.h"
#include "utilities.h"

Functions
int	project_check (Bproject *project, int flags=0)
int	project_display_counts (Bproject *project)
int	field_resolve_file_access (Bfield *field, Bmicrograph *mg, Bstring filename, int flags)
int	reconstruction_resolve_file_access (Breconstruction *rec, Bstring filename, int flags)
int	project_resolve_file_access (Bproject *project, Bstring filename, int flags)
Bproject *	read_project (const char *filename, int flags)
	Reading micrograph parameters from files. More...
Bproject *	read_project (Bstring &filename, int flags)
Bproject *	read_project (Bstring &filename, Bstring &xsdfile, int flags)
Bproject *	read_project (Bstring *file_list, int flags)
Bproject *	read_project (Bstring *file_list, Bstring &xsdfile, int flags)
long	append_project (Bproject *project, Bstring *file_list, Bstring &xsdfile, int flags)
Bparticle *	read_particle (Bstring &filename, Bparticle **partlist, FOMType fom_tag[NFOM])
int	write_project (const char *filename, Bproject *project)
	Writing micrograph parameters to a file. More...
int	write_project (Bstring &filename, Bproject *project, int mg_select, int rec_select)
	Writing micrograph parameters to a file. More...
int	write_project (Bstring &filename, Bproject *project, int flags)
	Writing micrograph parameters to a file. More...
long	write_particle_list (Bstring &filename, Bproject *project, int flags)
	Writing particle coordinates to a file. More...
int	write_particle (Bstring &filename, Bparticle *part, int euler_flag, int omega_flag, FOMType fom_tag[NFOM])
Bstring	ppx_filename (Bstring &id, int part_id)
int	ppx_exists (Bparticle *part, int flag)
int	ppx_check (Bparticle *part, FOMType fom_tag[NFOM])
int	ppx_check (Bparticle *part)
Bparticle *	project_find_particle (Bproject *project, Bstring &fn)
	Finds a particle associated with a file name. More...
long	project_update_from_ppx (Bproject *project)
	Updates a project with ppx files. More...
long	project_list_ppx (Bproject *project, int flag)
	Lists existing ppx files for a project. More...
int	project_split_write (Bstring &filename, Bproject *project)
	Splits a project into sets of particle selections and write the files. More...
int	project_split_field_write (Bproject *project)
	Splits a project into sets of particle selections and write the files. More...

Variables
int	verbose
string	command

Detailed Description

Library routines to read and write micrograph parameters.

Author

Bernard Heymann

Date

Created: 20030418

Modified: 20220406

Function Documentation

append_project()

long append_project	(	Bproject *	project,
		Bstring *	file_list,
		Bstring &	xsdfile,
		int	flags
	)

field_resolve_file_access()

int field_resolve_file_access	(	Bfield *	field,
		Bmicrograph *	mg,
		Bstring	filename,
		int	flags
	)

ppx_check() [1/2]

int ppx_check

(

Bparticle *

part

)

ppx_check() [2/2]

int ppx_check	(	Bparticle *	part,
		FOMType	fom_tag[NFOM]
	)

ppx_exists()

int ppx_exists	(	Bparticle *	part,
		int	flag
	)

ppx_filename()

Bstring ppx_filename	(	Bstring &	id,
		int	part_id
	)

project_check()

int project_check	(	Bproject *	project,
		int	flags = 0
	)

project_display_counts()

int project_display_counts

(

Bproject *

project

)

project_find_particle()

Bparticle * project_find_particle	(	Bproject *	project,
		Bstring &	fn
	)

Finds a particle associated with a file name.

Parameters

*project	micrograph processing parameter structure.
fn	filename to search for.

Returns

Bparticle* particle structure if found, otherwise NULL.

The file name to search for is altered to represent an accurate path.

project_list_ppx()

long project_list_ppx	(	Bproject *	project,
		int	flag
	)

Lists existing ppx files for a project.

Parameters

*project	project parameter structure.
flag	select: 0 = all, 1 = existing, 2 = absent.

Returns

long number of particles updated.

project_resolve_file_access()

int project_resolve_file_access	(	Bproject *	project,
		Bstring	filename,
		int	flags
	)

project_split_field_write()

int project_split_field_write

(

Bproject *

project

)

Splits a project into sets of particle selections and write the files.

Parameters

*project

the project.

Returns

int number of field files generated.

The relevant micrographs are selected for each particle selection number
and written into a file.

project_split_write()

int project_split_write	(	Bstring &	filename,
		Bproject *	project
	)

Splits a project into sets of particle selections and write the files.

Parameters

&filename	base filename modified to include the particle selection number.
*project	the project.

Returns

int number of sets generated.

The relevant micrographs are selected for each particle selection number
and written into a file.

project_update_from_ppx()

long project_update_from_ppx

(

Bproject *

project

)

Updates a project with ppx files.

Parameters

*project

project parameter structure.

Returns

long number of particles updated.

read_particle()

Bparticle * read_particle	(	Bstring &	filename,
		Bparticle **	partlist,
		FOMType	fom_tag[NFOM]
	)

read_project() [1/5]

Bproject * read_project	(	Bstring &	filename,
		Bstring &	xsdfile,
		int	flags
	)

read_project() [2/5]

Bproject * read_project	(	Bstring &	filename,
		int	flags
	)

read_project() [3/5]

Bproject * read_project	(	Bstring *	file_list,
		Bstring &	xsdfile,
		int	flags
	)

read_project() [4/5]

Bproject * read_project	(	Bstring *	file_list,
		int	flags
	)

read_project() [5/5]

Bproject * read_project	(	const char *	filename,
		int	flags
	)

Reading micrograph parameters from files.

Parameters

&filename	file name (or comma-delimited list).
flags	flags to modify behavior.

Returns

Bproject* project structure, NULL if reading failed.

Flags (bits):
1   check particle images against images.
8   warn if files not found.
16  delete file names of files not found.
32  update micrograph intensities.
64  update STAR tags.

reconstruction_resolve_file_access()

int reconstruction_resolve_file_access	(	Breconstruction *	rec,
		Bstring	filename,
		int	flags
	)

write_particle()

int write_particle	(	Bstring &	filename,
		Bparticle *	part,
		int	euler_flag,
		int	omega_flag,
		FOMType	fom_tag[NFOM]
	)

write_particle_list()

long write_particle_list	(	Bstring &	filename,
		Bproject *	project,
		int	flags
	)

Writing particle coordinates to a file.

Parameters

&filename	file name (or comma-delimited list).
*project	project structure.
flags	bits: 1=in angstrom

Returns

int error code (<0 means failure).

write_project() [1/3]

int write_project	(	Bstring &	filename,
		Bproject *	project,
		int	flags
	)

Writing micrograph parameters to a file.

Parameters

&filename	file name (or comma-delimited list).
*project	project structure.
flags	flags to modify behavior.

Returns

int error code (<0 means failure).

Flags (bits):
1.  check particle images.
2.  write only selected micrographs.
4.  write only selected reconstructions.
8.  warn if files not found.
16. delete file names of files not found.
32. update micrograph intensities.

write_project() [2/3]

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

Writing micrograph parameters to a file.

Parameters

*filename	file name (or comma-delimited list).
*project	project structure.
mg_select	flag to only write selected micrographs.
rec_select	flag to only write selected reconstructions.

Returns

int error code (<0 means failure).

write_project() [3/3]

int write_project	(	const char *	filename,
		Bproject *	project
	)

Writing micrograph parameters to a file.

Parameters

*filename	file name (or comma-delimited list).
*project	project structure.

Returns

int error code (<0 means failure).

Variable Documentation

command

string command

extern

verbose

int verbose

extern