rwmgIMOD.h File Reference

Converts between IMOD files and a micrograph parameter file. More...

#include "mg_processing.h"

Classes
struct	IMOD
struct	OBJT
struct	CONT

Macros
#define	IMODSIZE   232
#define	OBJTSIZE   176
#define	CONTSIZE   16

Functions
int	read_imod_tlt (Bstring &filename, Bproject *project)
int	read_project_imod (Bstring *file_list, Bproject *project, int flag)
	Creates a project structure using IMOD parameters. More...
int	write_project_imod (Bstring &imodfile, Bproject *project)
	Creates IMOD parameter files from a project structure. More...

Detailed Description

Converts between IMOD files and a micrograph parameter file.

Author

Bernard Heymann

Date

Created: 20070501

Modified: 20170120

Macro Definition Documentation

CONTSIZE

#define CONTSIZE   16

IMODSIZE

#define IMODSIZE   232

OBJTSIZE

#define OBJTSIZE   176

Function Documentation

read_imod_tlt()

int read_imod_tlt	(	Bstring &	filename,
		Bproject *	project
	)

read_project_imod()

int read_project_imod	(	Bstring *	file_list,
		Bproject *	project,
		int	flag
	)

Creates a project structure using IMOD parameters.

Parameters

*file_list	list of IMOD parameter file names.
*project	initialized project structure.
flag	flag to indicate conversion of the image file.

Returns

int error code (<0 means failure).

Requirements:
    Tilt series micrograph image (if 3D then converted to multi-2D)
    2D transform file (.xf)
    Tilt angle file (.tlt)
Calculations:
    Tilt angle: from tilt angle file
    Tilt axis: ta = (atan2(-A11, A12) + atan2(-A22, -A21))/2
    Mg origin: o = on - Ad
where
    A:  2x2 transformation matrix
    ta: tilt axis angle
    on: nominal micrograph origin (center of mg)
    o:  aligned micrograph origin
    d:  shift for micrograph

write_project_imod()

int write_project_imod	(	Bstring &	imodfile,
		Bproject *	project
	)

Creates IMOD parameter files from a project structure.

Parameters

imodfile	IMOD parameter file name.
project	project structure.

Returns

int 0.

Writes both .xf, .tlt and .xyz files.
Calculations:
    Tilt angle: from micrograph tilt angle
    Matrix: A = {cos(ta), -sin(ta), sin(ta), cos(ta)}
    Shift:  d = o - on
where
    A:  2x2 transformation matrix
    ta: tilt axis angle
    on: nominal micrograph origin (center of mg)
    o:  aligned micrograph origin
    d:  shift for micrograph