Some extensions related with Xmipp programs

Collaboration diagram for Some extensions related with Xmipp programs:

Functions
void	runSystem (const String &program, const String &arguments, bool useSystem=true)
int	runProgram (XmippProgram *program, const String &arguments, bool destroy=true)
int	runProgram (const String &programName, const String &arguments)
XmippProgram *	getProgramByName (const String &programName)

Detailed Description

Program extension routines.

Here you will find some routines which might help you to use programs from other programs. Also providing an accesible interface for binding with Python and/or Java.

Function Documentation

getProgramByName()

XmippProgram* getProgramByName

(

const String &

programName

)

This function will create a pointer to XmippProgram taking the program name. If the name is invalid, it will return NULL. This function will be hardcoded since C++ has not easy way to do reflection, so it need to be updated for new programs.

Definition at line 69 of file program_extension.cpp.

{
    //  if (programName == "xmipp_tranform_filter")
    //    return new ProgFilter();

    if (programName == "xmipp_volume_from_pdb")
        return new ProgPdbConverter();

    if (programName == "xmipp_angular_project_library")
        return new ProgAngularProjectLibrary();

    if (programName == "xmipp_angular_projection_matching")
        return new ProgAngularProjectionMatching();

    if (programName == "xmipp_mask")
        return new ProgMask();

    if (programName == "xmipp_angular_discrete_assign")
        return new ProgAngularDiscreteAssign();

    if (programName == "xmipp_angular_continuous_assign")
        return new ProgAngularContinuousAssign();

    if (programName == "xmipp_pdb_nma_deform")
        return new ProgPdbNmaDeform();
    
    if (programName == "xmipp_pdb_sph_deform")
        return new ProgPdbSphDeform();

    if (programName == "xmipp_micrograph_automatic_picking")
        return new ProgMicrographAutomaticPicking2();

    if (programName == "xmipp_classify_analyze_cluster")
        return new ProgAnalyzeCluster();

    if (programName == "xmipp_transform_filter")
        return new ProgFilter();

    return nullptr;
}

runProgram() [1/2]

int runProgram	(	XmippProgram *	program,
		const String &	arguments,
		bool	destroy = true
	)

Run a program passing some arguments. The program will be supplied as a pointer of XmippProgram if destroy is true the program pointer will be freed

Definition at line 52 of file program_extension.cpp.

{
    if (program == nullptr)
        REPORT_ERROR(ERR_PARAM_INCORRECT, "Received a NULL as program pointer");
    program->read(arguments);
    int retCode = program->tryRun();
    if (destroy)
        delete program;
    return retCode;
}

runProgram() [2/2]

int runProgram	(	const String &	programName,
		const String &	arguments
	)

Run a program providing the program name. Also the arguments should be supplied in a String.

Definition at line 63 of file program_extension.cpp.

{
    XmippProgram * program = getProgramByName(programName);
    return runProgram(program, arguments);
}

runSystem()

void runSystem	(	const String &	program,
		const String &	arguments,
		bool	useSystem = true
	)

Run a program either as a system call or as an internal call

Definition at line 42 of file program_extension.cpp.

                                                                               {
    if (useSystem) {
        String cmd = formatString("%s %s", program.c_str(), arguments.c_str());
        if (system(cmd.c_str())==-1)
            REPORT_ERROR(ERR_UNCLASSIFIED,"Cannot open shell");
    } else {
        runProgram(program, arguments);
    }
}