ProgFindCenter2D Class Reference

Inheritance diagram for ProgFindCenter2D:

Collaboration diagram for ProgFindCenter2D:

Public Member Functions
void	defineParams ()
	Define parameters. More...
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	fnIn
	Filenames. More...
FileName	fnOroot
double	_r1
	Radii. More...
double	_r2
double	_r3
double	_r4
double	x0
	Starting center. More...
double	y0
int	_ncic
	Harmonic. More...
int	_indmul
	Optimization type. More...
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 592 of file image_find_center.cpp.

Member Function Documentation

defineParams()

void ProgFindCenter2D::defineParams ( )

inlinevirtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 611 of file image_find_center.cpp.

    {
        addUsageLine("Find the best symmetry of rotation of an image or collection of images");
        addUsageLine("+It is very useful when you want to calculate the rotational symmetry of ");
        addUsageLine("+a set of images (in fact it computes the center of the average image). ");
        addUsageLine("+Image dimensions must be less than 512x512.");
        addSeeAlsoLine("xmipp_image_rotational_spectrum");
        addParamsLine(" -i <file>          : Image, image stack or image selfile");
        addParamsLine(" --oroot <rootname> : Rootname for output files");
        addParamsLine("                    :+ <rootname>_center.xmd contains the image center");
        addParamsLine("                    :+ <rootname>_analyzed_image.xmp (if verbose>=2) contains the image that was actually analyzed");
        addParamsLine("[--r1+ <radius=15>]  : Lowest integration radius (% of the image radius)");
        addParamsLine("[--r2+ <radius=80>]  : Highest integration radius (% of the image radius)");
        addParamsLine("[--r3+ <radius=90>]  : Lowest smoothing radius (% of the image radius)");
        addParamsLine("[--r4+ <radius=100>] : Highest smoothing radius (% of the image radius)");
        addParamsLine("[--x0 <x>]          : Initial center of rotation");
        addParamsLine("[--y0 <y>]          : Initial center of rotation");
        addParamsLine("[--harm+ <n=1>]      : Harmonic to optimize");
        addParamsLine("[--opt+ <opt=-1>]    : Type of optimization (-1=minimize, +1=maximize)");
        addExampleLine("xmipp_image_find_center -i image.xmp");
    }

readParams()

void ProgFindCenter2D::readParams ( )

inlinevirtual

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 633 of file image_find_center.cpp.

    {
        fnIn=getParam("-i");
        fnOroot=getParam("--oroot");
        _r1=getDoubleParam("--r1");
        _r2=getDoubleParam("--r2");
        _r3=getDoubleParam("--r3");
        _r4=getDoubleParam("--r4");
        if (checkParam("--x0"))
            x0=getDoubleParam("--x0");
        else
            x0=-1;
        if (checkParam("--y0"))
            y0=getDoubleParam("--y0");
        else
            y0=-1;
        _ncic=getIntParam("--harm");
        _indmul=getIntParam("--opt");
    }

run()

void ProgFindCenter2D::run ( )

inlinevirtual

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

Reimplemented from XmippProgram.

Definition at line 669 of file image_find_center.cpp.

    {
        show();
        size_t id;
        // Get the input image or the average of the input images
        Image<double> I, Iaux;
        if (fnIn.isMetaData())
        {
            MetaDataVec MD(fnIn);
            int N=0;
            for (size_t objId : MD.ids())
            {
                Iaux.readApplyGeo(MD, objId);
                if (N==0)
                    I()=Iaux();
                else
                    I()+=Iaux();
                ++N;
            }
            I()/=N;
        }
        else
        {
            I.read(fnIn, HEADER);
            size_t Xdim, Ydim, Zdim, Ndim;
            I.getDimensions(Xdim, Ydim, Zdim, Ndim);
            I.clear();
            if (Ndim>1)
            {
                for (size_t  n = FIRST_IMAGE; n <= Ndim; n++)
                {
                    Iaux.read(fnIn,DATA,n);
                    if (n == FIRST_IMAGE)
                        I=Iaux;
                    else
                        I()+=Iaux();
                }
                I()/=Ndim;
            }
            else
                I.read(fnIn);
        }
        I().rangeAdjust(0,255);
        if (verbose==2)
            I.write(fnOroot+"_analyzed_image.xmp");

        // Adapt to old code
        if ((imagen = (unsigned char **)imalloc(YSIZE(I()) + 1, XSIZE(I()) + 1, NATURAL)) == NULL)
            REPORT_ERROR(ERR_MEM_NOTENOUGH,"");
        FOR_ALL_ELEMENTS_IN_ARRAY2D(I())
        imagen[i+1][j+1]=(unsigned char)IMGPIXEL(I,i,j);
        if (x0>=0)
            xc0=(float)x0+1; //+1 because of Fortran indexing
        else
            xc0=XSIZE(I())/2+1;
        if (y0>=0)
            yc0=(float)y0+1;
        else
            yc0=YSIZE(I())/2+1;
        r1=(float)(_r1/100.0*XSIZE(I())/2.0);
        r2=(float)(_r2/100.0*XSIZE(I())/2.0);
        r3=1;
        rbajo=(float)(_r3/100.0*XSIZE(I())/2.0);
        ralto=(float)(_r4/100.0*XSIZE(I())/2.0);
        ncic=_ncic;
        indmul=_indmul;
        del = DEF_DEL;
        in = DEF_IN;
        ni = DEF_IT;
        mu = (int)(PI / 2 * r2 / ncic);
        if (mu < 3)
            REPORT_ERROR(ERR_ARG_INCORRECT,"A higher integration radius is needed (r2>6*harm/pi)");
        largo=YSIZE(I());
        lancho=XSIZE(I());
        busca();
        MetaDataVec MD;
        id=MD.addObject();
        if (yc0>0)
        {
            MD.setValue(MDL_X,(double)(yc0-1),id);
            MD.setValue(MDL_Y,(double)(xc0-1),id);
        }
        else
        {
            MD.setValue(MDL_X,(double)(XSIZE(I())/2),id);
            MD.setValue(MDL_Y,(double)(YSIZE(I())/2),id);
        }
        MD.write(fnOroot+"_center.xmd");
        imfree((char**)imagen, YSIZE(I()) + 1, XSIZE(I()) + 1, NATURAL);
    }

show()

void ProgFindCenter2D::show ( )

inline

Definition at line 653 of file image_find_center.cpp.

    {
        if (verbose==0)
            return;
        std::cout << "Input:          " << fnIn    << std::endl
        << "Output root:    " << fnOroot << std::endl
        << "R1:             " << _r1     << std::endl
        << "R2:             " << _r2     << std::endl
        << "R3:             " << _r3     << std::endl
        << "R4:             " << _r4     << std::endl
        << "Harmonic:       " << _ncic   << std::endl
        << "Opt:            " << _indmul << std::endl
        << "Initial center: (" << x0 << "," << y0 << ")\n"
        ;
    }

Member Data Documentation

_indmul

int ProgFindCenter2D::_indmul

Optimization type.

Definition at line 608 of file image_find_center.cpp.

_ncic

int ProgFindCenter2D::_ncic

Harmonic.

Definition at line 605 of file image_find_center.cpp.

_r1

double ProgFindCenter2D::_r1

Radii.

Definition at line 599 of file image_find_center.cpp.

_r2

double ProgFindCenter2D::_r2

Definition at line 599 of file image_find_center.cpp.

_r3

double ProgFindCenter2D::_r3

Definition at line 599 of file image_find_center.cpp.

_r4

double ProgFindCenter2D::_r4

Definition at line 599 of file image_find_center.cpp.

fnIn

FileName ProgFindCenter2D::fnIn

Filenames.

Definition at line 596 of file image_find_center.cpp.

fnOroot

FileName ProgFindCenter2D::fnOroot

Definition at line 596 of file image_find_center.cpp.

x0

double ProgFindCenter2D::x0

Starting center.

Definition at line 602 of file image_find_center.cpp.

y0

double ProgFindCenter2D::y0

Definition at line 602 of file image_find_center.cpp.

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

• xmipp/libraries/reconstruction/image_find_center.cpp