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

#include "rwmgIMOD.h"
#include "mg_img_proc.h"
#include "mg_tomography.h"
#include "rwmg.h"
#include "rwimg.h"
#include "linked_list.h"

Functions
int	read_imod_xf (Bstring &filename, Bproject *project)

int	read_imod_tlt (Bstring &filename, Bproject *project)

int	read_imod_xyz (Bstring &filename, Breconstruction *rec)

int	read_imod_fid (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_imod_xf (Bstring &imodfile, Bproject *project)

int	write_imod_tlt (Bstring &imodfile, Bproject *project)

int	write_imod_xyz (Bstring &imodfile, Bproject *project)

int	write_project_imod (Bstring &imodfile, Bproject *project)
	Creates IMOD parameter files from a project structure. More...

Variables
int	verbose

Detailed Description

Converts between IMOD files and a micrograph parameter file.

Author: Bernard Heymann

Date: Created: 20070501; Modified: 20170120

Function Documentation

◆ read_imod_fid()

int read_imod_fid	(	Bstring &	filename,
		Bproject *	project
	)

◆ read_imod_tlt()

int read_imod_tlt	(	Bstring &	filename,
		Bproject *	project
	)

◆ read_imod_xf()

int read_imod_xf	(	Bstring &	filename,
		Bproject *	project
	)

◆ read_imod_xyz()

int read_imod_xyz	(	Bstring &	filename,
		Breconstruction *	rec
	)

◆ 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_imod_tlt()

int write_imod_tlt	(	Bstring &	imodfile,
		Bproject *	project
	)

◆ write_imod_xf()

int write_imod_xf	(	Bstring &	imodfile,
		Bproject *	project
	)

◆ write_imod_xyz()

int write_imod_xyz	(	Bstring &	imodfile,
		Bproject *	project
	)

◆ 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

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables