ProgCTFShow Class Reference

#include <ctf_show.h>

Inheritance diagram for ProgCTFShow:

Collaboration diagram for ProgCTFShow:

Public Member Functions
void	defineParams ()
void	readParams ()
void	run ()
void	show ()
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
FileName	fn_in
FileName	fn_out
int	dim
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippProgram
void	defineCommons ()
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

Detailed Description

Definition at line 37 of file ctf_show.h.

Member Function Documentation

defineParams()

void ProgCTFShow::defineParams ( )

virtual

Define parameters

Reimplemented from XmippProgram.

Definition at line 30 of file ctf_show.cpp.

{
    addUsageLine("Convert parametric CTF into image");
    addParamsLine(" -i <file>               : parametric_CTF");
    addParamsLine(" -o <file>               : image CTF");
    addParamsLine(" --dim <xdim>               : image size");
    addExampleLine("Create CTF image from parametric CTF file ctf.param and with dimension 256 pixels:", false);
    addExampleLine("xmipp_ctf_show -i ctf.param -o 20.mrc --dim 256");
}

readParams()

void ProgCTFShow::readParams ( )

virtual

Read parameters

Reimplemented from XmippProgram.

Definition at line 40 of file ctf_show.cpp.

{
    fn_in   = getParam("-i");
    fn_out  = getParam("-o");
    dim     = getIntParam("--dim");
}

run()

void ProgCTFShow::run ( )

virtual

Do_all.

Reimplemented from XmippProgram.

Definition at line 58 of file ctf_show.cpp.

{
    show();

    // Read CTF
    CTFDescription ctf;
    ctf.clear();
    ctf.read(fn_in);
    ctf.produceSideInfo();

    Matrix1D<double> freq(2); // Frequencies for Fourier plane
    int yDim=dim;
    int xDim=dim;
    double iTm=1.0/ctf.Tm;
    Image<double> img(xDim,yDim);
    MultidimArray<double> &dummy = img.data;
    int x2Dim = xDim / 2 ;
    int y2Dim = yDim / 2 ;

    for (int i=0; i<yDim; ++i)
    {
        FFT_IDX2DIGFREQ(i, yDim, YY(freq));
        YY(freq) *= iTm;
        for (int j=0; j<xDim; ++j)
        {
            FFT_IDX2DIGFREQ(j, xDim, XX(freq));
            XX(freq) *= iTm;
            ctf.precomputeValues(XX(freq),YY(freq));
            DIRECT_A2D_ELEM(dummy,intWRAP(i+x2Dim,0,xDim-1),
                                  intWRAP(j+y2Dim,0,yDim-1))
                              =ctf.getValuePureWithoutDampingAt();
        }
    }

    // Perform inverse Fourier transform and finish
    img.write(fn_out);
}

show()

void ProgCTFShow::show

(

)

Show parameters.

Definition at line 48 of file ctf_show.cpp.

{
    if (verbose==0)
        return;
    std::cout
    << "parametric CTF:      " << fn_in    << std::endl
    << "image CTF:           " << fn_out << std::endl
    ;
}

Member Data Documentation

dim

int ProgCTFShow::dim

Image dim

Definition at line 45 of file ctf_show.h.

fn_in

FileName ProgCTFShow::fn_in

Input CTF param file

Definition at line 41 of file ctf_show.h.

fn_out

FileName ProgCTFShow::fn_out

Out CTF image

Definition at line 43 of file ctf_show.h.

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

• xmipp/legacy/libraries/reconstruction/ctf_show.h
• xmipp/legacy/libraries/reconstruction/ctf_show.cpp