ProgMakeSpectra Class Reference

#include <image_rotational_spectra.h>

Inheritance diagram for ProgMakeSpectra:

Collaboration diagram for ProgMakeSpectra:

Public Member Functions
void	defineParams ()
void	readParams ()
void	show ()
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 ()

Public Attributes
FileName	fn_in
FileName	fn_out
Rotational_Spectrum	rot_spt
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

Make spectra parameters.

Definition at line 41 of file image_rotational_spectra.h.

Member Function Documentation

defineParams()

void ProgMakeSpectra::defineParams ( )

virtual

Define parameters

Reimplemented from XmippProgram.

Definition at line 30 of file image_rotational_spectra.cpp.

{
    addUsageLine("Computes the rotational spectrum of a set of images.");
    addUsageLine("+This program generates a Fourier-Bessel decomposition of each image listed ");
    addUsageLine("+in an image collection. For each one, it creates a vector with the armonic ");
    addUsageLine("+energy percentage as a function of the radius. ");
    addUsageLine("+ ");
    addUsageLine("+The rotational spectrum is computed around the point (x0,y0), by default the center of the image.");
    addUsageLine("+The length of the rotational spectrum is defined by the lowest and highest harmonic.");
    addUsageLine("+Each harmonic is calculated by the integration of the image over a ring defined by r1 and r2.");
    addUsageLine("+ ");
    addUsageLine("+The rotational spectrum was defined in Crowther, R.A., and Amos, L.A. ");
    addUsageLine("+Harmonic analysis of electron microscopy images with rotational symmetry.");
    addUsageLine("+J. Mol. Biol.: 60, 123-130 (1971).");
    addSeeAlsoLine("classify_kerdensom, image_vectorize");
    addParamsLine("   -i <file>                   : Input image, selfile or stack");
    addParamsLine("   -o <metadata>               : Output vector metadata");
    addParamsLine("  [--r1 <lowRadius=15>]        : Lowest Integration radius (as a percentage of the total radius)");
    addParamsLine("  [--r2 <highRadius=80>]       : Highest Integration radius (as a percentage of the total radius)");
    addParamsLine("  [--x0 <xcenter=-1>]          : In physical units.");
    addParamsLine("  [--y0 <ycenter=-1>]          : By default, the Xmipp origin");
    addParamsLine("  [--low  <lowerHarmonic=  1>] : Lower harmonic to compute");
    addParamsLine("  [--high <higherHarmonic=15>] : Higher harmonic to compute");
    addExampleLine("xmipp_image_rotational_spectra -i images.stk -o spectra.xmd");
}

readParams()

void ProgMakeSpectra::readParams ( )

virtual

Read parameters from command line.

Reimplemented from XmippProgram.

Definition at line 57 of file image_rotational_spectra.cpp.

{
    fn_in = getParam("-i");
    fn_out = getParam("-o");
    rot_spt.rl = getIntParam("--r1");
    rot_spt.rh = getIntParam("--r2");
    rot_spt.dr = 1;
    rot_spt.x0 = getDoubleParam("--x0");
    rot_spt.y0 = getDoubleParam("--y0");
    rot_spt.numin = getIntParam("--low");
    rot_spt.numax = getIntParam("--high");
}

run()

void ProgMakeSpectra::run ( )

virtual

Run.

Reimplemented from XmippProgram.

Definition at line 83 of file image_rotational_spectra.cpp.

{
    MetaDataVec vectorContent, vectorHeader;
    vectorHeader.setColumnFormat(false);
    bool first=true;
    size_t order=0;
    FileName fnImg;
    Image<double> I;
    MetaDataVec MD;
    MD.read(fn_in);
    std::ofstream fhOutRaw;
    MultidimArray<float> spectrum;
    FileName fnOutRaw=fn_out.withoutExtension()+".vec";
    fnOutRaw.deleteFile();

    // Convert the radii from percentages to actual pixels
    size_t Xdim, Ydim, Zdim, Ndim;
    getImageSize(MD,Xdim,Ydim,Zdim,Ndim);
    rot_spt.rl=(int)((rot_spt.rl/100.0)*Xdim/2);
    rot_spt.rh=(int)((rot_spt.rh/100.0)*Xdim/2);

    for (auto& row : MD)
    {
        MD.getValue(MDL_IMAGE,fnImg, row.id());
        I.readApplyGeo(fnImg,MD, row.id());
        rot_spt.compute_rotational_spectrum(I(), rot_spt.rl, rot_spt.rh,
                                            rot_spt.dr, rot_spt.rh - rot_spt.rl);
        fhOutRaw.open(fnOutRaw.c_str(),std::ios::app | std::ios::binary);
        if (!fhOutRaw)
            REPORT_ERROR(ERR_IO_NOWRITE,fnOutRaw);
        typeCast(rot_spt.rot_spectrum,spectrum);
        fhOutRaw.write((char*)MULTIDIM_ARRAY(spectrum),XSIZE(spectrum)*sizeof(float));
        fhOutRaw.close();

        // Create header
        if (first)
        {
            size_t vectorSize=MULTIDIM_SIZE(rot_spt.rot_spectrum);
            size_t outId=vectorHeader.addObject();
            vectorHeader.setValue(MDL_XSIZE,XSIZE(I()),outId);
            vectorHeader.setValue(MDL_YSIZE,YSIZE(I()),outId);
            vectorHeader.setValue(MDL_ZSIZE,ZSIZE(I()),outId);
            vectorHeader.setValue(MDL_COUNT,MD.size(),outId);
            vectorHeader.setValue(MDL_CLASSIFICATION_DATA_SIZE,vectorSize,outId);
            vectorHeader.write(formatString("vectorHeader@%s",fn_out.c_str()));
            first=false;
        }

        // Save this image in the output metadata
        row.setValue(MDL_ORDER, order++);
        vectorContent.addRow(dynamic_cast<MDRowVec&>(row));
    }
    vectorContent.write(formatString("vectorContent@%s",fn_out.c_str()),MD_APPEND);
}

show()

void ProgMakeSpectra::show

(

)

Show parameters.

Definition at line 71 of file image_rotational_spectra.cpp.

{
    if (verbose==0)
        return;
    std::cout
    << "Input file: " << fn_in << std::endl
    << "Output file: " << fn_out << std::endl
    ;
    std::cout << rot_spt << std::endl;
}

Member Data Documentation

fn_in

FileName ProgMakeSpectra::fn_in

Input file

Definition at line 45 of file image_rotational_spectra.h.

fn_out

FileName ProgMakeSpectra::fn_out

Output file

Definition at line 48 of file image_rotational_spectra.h.

rot_spt

Rotational_Spectrum ProgMakeSpectra::rot_spt

Rotational spectrum.

Definition at line 52 of file image_rotational_spectra.h.

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

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