ProgPSFXrCreate Class Reference

Inheritance diagram for ProgPSFXrCreate:

Collaboration diagram for ProgPSFXrCreate:

Public Member Functions
void	run ()
Public Member Functions inherited from XmippProgram
const char *	getParam (const char *param, int arg=0)
const char *	getParam (const char *param, const char *subparam, int arg=0)
int	getIntParam (const char *param, int arg=0)
int	getIntParam (const char *param, const char *subparam, int arg=0)
double	getDoubleParam (const char *param, int arg=0)
double	getDoubleParam (const char *param, const char *subparam, int arg=0)
float	getFloatParam (const char *param, int arg=0)
float	getFloatParam (const char *param, const char *subparam, int arg=0)
void	getListParam (const char *param, StringVector &list)
int	getCountParam (const char *param)
bool	checkParam (const char *param)
bool	existsParam (const char *param)
void	addParamsLine (const String &line)
void	addParamsLine (const char *line)
ParamDef *	getParamDef (const char *param) const
virtual void	quit (int exit_code=0) const
virtual int	tryRun ()
void	initProgress (size_t total, size_t stepBin=60)
void	setProgress (size_t value=0)
void	endProgress ()
void	processDefaultComment (const char *param, const char *left)
void	setDefaultComment (const char *param, const char *comment)
virtual void	initComments ()
void	setProgramName (const char *name)
void	addUsageLine (const char *line, bool verbatim=false)
void	clearUsage ()
void	addExampleLine (const char *example, bool verbatim=true)
void	addSeeAlsoLine (const char *seeAlso)
void	addKeywords (const char *keywords)
const char *	name () const
virtual void	usage (int verb=0) const
virtual void	usage (const String &param, int verb=2)
int	version () const
virtual void	show () const
virtual void	read (int argc, const char **argv, bool reportErrors=true)
virtual void	read (int argc, char **argv, bool reportErrors=true)
void	read (const String &argumentsLine)
	XmippProgram ()
	XmippProgram (int argc, const char **argv)
virtual	~XmippProgram ()

Protected Member Functions
void	defineParams ()
void	readParams ()
Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Attributes
FileName	fnParam
	Filename with the Microscope Parameters. More...
FileName	fnPSF
int	nThr
	Number of threads;. More...
XRayPSF	psf
	PSF. More...
Protected Attributes inherited from XmippProgram
int	errorCode
ProgramDef *	progDef
	Program definition and arguments parser. More...
std::map< String, CommentList >	defaultComments
int	argc
	Original command line arguments. More...
const char **	argv

Additional Inherited Members
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Detailed Description

Definition at line 29 of file xray_psf_create.cpp.

Member Function Documentation

defineParams()

void ProgPSFXrCreate::defineParams ( )

inlineprotectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 40 of file xray_psf_create.cpp.

    {
        //Usage
        addUsageLine("Create a volume with the 3D PSF of an X-ray microscope.");
        addUsageLine("A param file can be passed or directly setting the microscope parameters.");
        addUsageLine("The program generates a PSF volume file and its associated info file.");
        //See Also
        addParamsLine("[-i <psf_param_file>] : XRay-Microscope parameters file.");
        addParamsLine(" alias --input;");
        addParamsLine("[-o <output_name_file>]  : Name for output files. It creates a PSF volume file and a PSF parameters file.");
        addParamsLine(" alias --output;");
        psf.defineParams(this);
        // Examples
        addExampleLine("The parameters are in a file",false);
        addExampleLine("xmipp_xray_psf_create -i psf560.xmd -o psf560.vol");
        addExampleLine("The parameters are given in the command line",false);
        addExampleLine("xmipp_xray_psf_create -o psf900.vol -lambda 2.5 -zones 900");
        addExampleLine("In the following link you can find an example of X-ray microscope parameters file:",false);
        addExampleLine(" ",false);
        addExampleLine("http://sourceforge.net/p/testxmipp/code/ci/3.0/tree/input/xray_psf.xmd",false);
    }

readParams()

void ProgPSFXrCreate::readParams ( )

inlineprotectedvirtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippProgram.

Definition at line 62 of file xray_psf_create.cpp.

    {
        psf.verbose = verbose;

        if (checkParam("-i"))
        {
            fnParam = getParam("-i");
            /* This forces always the creation of the PSF Volume file, even if the input already includes the
             name of a volume in the "image" label
             */
            psf.read(fnParam, false);
        }
        else
            psf.readParams(this);

        if (checkParam("-o"))
            fnPSF = getParam("-o");
        else
            fnPSF = fnParam;
    }

run()

void ProgPSFXrCreate::run ( )

inlinevirtual

This function will be start running the program. it also should be implemented by derived classes.

Reimplemented from XmippProgram.

Definition at line 85 of file xray_psf_create.cpp.

    {
        psf.generatePSF();
        psf.write(fnPSF);
    }

Member Data Documentation

fnParam

FileName ProgPSFXrCreate::fnParam

protected

Filename with the Microscope Parameters.

Definition at line 34 of file xray_psf_create.cpp.

fnPSF

FileName ProgPSFXrCreate::fnPSF

protected

Definition at line 34 of file xray_psf_create.cpp.

nThr

int ProgPSFXrCreate::nThr

protected

Number of threads;.

Definition at line 36 of file xray_psf_create.cpp.

psf

XRayPSF ProgPSFXrCreate::psf

protected

PSF.

Definition at line 38 of file xray_psf_create.cpp.

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The documentation for this class was generated from the following file:

• xmipp/legacy/libraries/reconstruction/xray_psf_create.cpp