IDR Xray Tomography

Collaboration diagram for IDR Xray Tomography:

Classes
class	ProgIDRXrayTomo

Functions
int	reconsTomo3D (const MetaData &MD, const FileName &fnOut, const String &params="")
int	reconsTomo3D (const FileName &fnAngles, const FileName &fnProjs, const FileName &fnOut, const String &params="")

Detailed Description

Function Documentation

reconsTomo3D() [1/2]

int reconsTomo3D	(	const MetaData &	MD,
		const FileName &	fnOut,
		const String &	params = ""
	)

Reconstruct tomogram projections using external tomo3D

Parameters

MD	Includes tilt angle values and projections file names
fnOut	Reconstructed output volume name
params	Other parameters to be passed to tomo3D

Returns

True if external system call ran right. Otherwise False

Definition at line 311 of file idr_xray_tomo.cpp.

{
    // Saving angles in plain text to pass to tomo3D
    FileName fnAngles("idr_xray_tomo_to_tomo3d_angles.txt");
    std::vector<MDLabel> desiredLabels;
    desiredLabels.push_back(MDL_ANGLE_TILT);
    MD.writeText(fnAngles, &desiredLabels);

    FileName fnProjs;

    MD.getValue(MDL_IMAGE, fnProjs, MD.firstRowId());

    // Projections must be in an MRC stack to be passed
    if ( !(fnProjs.isInStack() && (fnProjs.contains("mrc") || fnProjs.contains("st"))))
    {
        //FIXME: To be implemented the conversion to an MRC stack

        REPORT_ERROR(ERR_IMG_NOREAD, "reconsTromo3D: Image format cannot be read by tomo3D.");
    }

    return reconsTomo3D(fnAngles, fnProjs.removePrefixNumber(), fnOut, params);
}

reconsTomo3D() [2/2]

int reconsTomo3D	(	const FileName &	fnAngles,
		const FileName &	fnProjs,
		const FileName &	fnOut,
		const String &	params = ""
	)

Reconstruct tomogram projections using external tomo3D

Parameters

fnAngles	Text file with angles sequence
fnProjs	MRC stack file with projections
fnOut	Reconstructed output volume name
params	Other parameters to be passed to tomo3D

Returns

True if external system call ran right. Otherwise False

Definition at line 334 of file idr_xray_tomo.cpp.

{
    String exec("tomo3d -n -f -v 0 -a "+fnAngles+" -i "+fnProjs.removeAllPrefixes()+" -o "+fnOut+" "+params);
    return system(exec.c_str());
}