ProgVolumeStructureFactor Class Reference

Inheritance diagram for ProgVolumeStructureFactor:

Collaboration diagram for ProgVolumeStructureFactor:

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

Protected Attributes
FileName	fnVol
FileName	fnStructure
double	sampling
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 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 ()
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Detailed Description

Definition at line 31 of file volume_structure_factor.cpp.

Member Function Documentation

defineParams()

void ProgVolumeStructureFactor::defineParams ( )

inlineprotectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 37 of file volume_structure_factor.cpp.

    {
        //Usage
        addUsageLine("Calculate the structure factor and the Guinier plot of a volume");
        //Parameters
        addParamsLine("-i <volume>           : Volume to analyze");
        addParamsLine("[-o <structure=\"\">] : Metadata with the structure factor and the Guinier plot");
        addParamsLine("                      : If no name is given, then volume_structure.xmd");
        addParamsLine("[--sampling <T=1>]    : Sampling rate in Angstroms/pixel");
    }

readParams()

void ProgVolumeStructureFactor::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 48 of file volume_structure_factor.cpp.

    {
        fnVol=getParam("-i");
        fnStructure=getParam("-o");
        if (fnStructure=="")
            fnStructure=fnVol.removeAllExtensions()+"_structure.xmd";
        sampling=getDoubleParam("--sampling");
    }

run()

void ProgVolumeStructureFactor::run ( )

inlineprotectedvirtual

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

Reimplemented from XmippProgram.

Definition at line 66 of file volume_structure_factor.cpp.

    {
        show();

        Image<double> V;
        FourierTransformer transformer;
        MultidimArray< std::complex<double> > VFourier;
        MultidimArray<double> VFourierMag, spectrum;

        V.read(fnVol);
        transformer.FourierTransform(V(),VFourier,false);
        FFT_magnitude(VFourier,VFourierMag);
        getSpectrum(VFourierMag,spectrum,POWER_SPECTRUM);

        MetaDataVec MDout;
        FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY1D(spectrum)
        {
            if (i==0 || A1D_ELEM(spectrum,i)==0)
                continue;
            size_t id=MDout.addObject();
            double f;
            FFT_IDX2DIGFREQ(i,XSIZE(V()),f);
            if (f>0.5)
                continue;
            f/=sampling;
            double fA=1/f;
            double f2=f*f;

            MDout.setValue(MDL_RESOLUTION_FREQ,f,id);
            MDout.setValue(MDL_RESOLUTION_FREQREAL,fA,id);
            MDout.setValue(MDL_RESOLUTION_FREQ2,f2,id);
            MDout.setValue(MDL_RESOLUTION_STRUCTURE_FACTOR,A1D_ELEM(spectrum,i),id);
            double aux=0;
            if (A1D_ELEM(spectrum,i)>0)
                aux=log(A1D_ELEM(spectrum,i));
            MDout.setValue(MDL_RESOLUTION_LOG_STRUCTURE_FACTOR,aux,id);
        }
        MDout.write(fnStructure);
    }

show()

void ProgVolumeStructureFactor::show ( )

inlineprotected

Definition at line 57 of file volume_structure_factor.cpp.

    {
        std::cout
        << "Input volume:     " << fnVol       << std::endl
        << "Output structure: " << fnStructure << std::endl
        << "Sampling:         " << sampling    << std::endl
        ;
    }

Member Data Documentation

fnStructure

FileName ProgVolumeStructureFactor::fnStructure

protected

Definition at line 34 of file volume_structure_factor.cpp.

fnVol

FileName ProgVolumeStructureFactor::fnVol

protected

Definition at line 34 of file volume_structure_factor.cpp.

sampling

double ProgVolumeStructureFactor::sampling

protected

Definition at line 35 of file volume_structure_factor.cpp.

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

• xmipp/libraries/reconstruction/volume_structure_factor.cpp