rwmgSerialEM.cpp File Reference

Converts between a SerialEM MDOC file and a micrograph parameter file. More...

#include "rwmgSerialEM.h"
#include "mg_img_proc.h"
#include "mg_tomography.h"
#include "rwmg.h"
#include "rwimg.h"
#include "mdoc.h"

Functions
int	read_project_serialem (Bstring &filename, Bproject *project, int flag)
	Creates a project structure using SerialEM MDOC parameters. More...
int	write_project_serialem (Bstring &filename, Bproject *project)
	Creates SerialEM MDOC files from a project structure. More...

Variables
int	verbose

Detailed Description

Converts between a SerialEM MDOC file and a micrograph parameter file.

Author

Bernard Heymann

Date

Created: 20190109

Modified: 20210728

Function Documentation

read_project_serialem()

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

Creates a project structure using SerialEM MDOC parameters.

Parameters

filename	SerialEM MDOC file name.
*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_serialem()

int write_project_serialem	(	Bstring &	filename,
		Bproject *	project
	)

Creates SerialEM MDOC files from a project structure.

Parameters

filename	SerialEM MDOC file name.
project	project structure.

Returns

int 0.

Variable Documentation

verbose

int verbose

extern