ProgAlign2d Class Reference

#include <align2d.h>

Inheritance diagram for ProgAlign2d:

Collaboration diagram for ProgAlign2d:

Public Member Functions
void	readParams ()
	Read argument. More...
void	show ()
	Show. More...
void	defineParams ()
	Define parameters. More...
void	alignPairs (MetaData &MDin, MetaData &MDout, int level)
	Align pairs. More...
void	do_pspc ()
	Pyramidal combination of images to construct a reference. More...
void	computeMean ()
	Compute mean. More...
void	refinement ()
	Alignment of all images by iterative refinement. More...
void	run ()
	Main routine. More...
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	fnSel
FileName	fnRef
FileName	fnRoot
int	Niter
bool	dont_mirror
bool	pspc
MetaDataVec	SF
Image< double >	Iref
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

Align2D parameters.

Definition at line 36 of file align2d.h.

Member Function Documentation

alignPairs()

void ProgAlign2d::alignPairs	(	MetaData &	MDin,
		MetaData &	MDout,
		int	level
	)

Align pairs.

Definition at line 74 of file align2d.cpp.

{
    // Compute output stack size
    size_t imax=MDin.size()/2;
    size_t remaining=MDin.size()-2*imax;
    size_t Xdim, Ydim, Zdim, Ndim;
    getImageSize(MDin,Xdim,Ydim,Zdim,Ndim);
    if (Zdim!=1 || Ndim!=1)
        REPORT_ERROR(ERR_MATRIX_DIM,"Files in metadata are not 2D images");
    FileName fnOutputStack=fnRoot+"_level_"+integerToString(level,2)+".stk";
    fnOutputStack.deleteFile();
    createEmptyFile(fnOutputStack,Xdim,Ydim,1,imax+remaining,true,WRITE_REPLACE);

    // Align all pairs
    auto mdIdIter(MDin.ids().begin());
    Image<double> I1, I2;
    Matrix2D<double> M;
    FileName fnOut;
    AlignmentAux aux1;
    CorrelationAux aux2;
    RotationalCorrelationAux aux3;
    std::cerr << "Aligning level " << level << std::endl;
    init_progress_bar(imax);
    for (size_t i=0; i<imax; i++)
    {
        // Read the two input images
        I1.readApplyGeo(MDin, *mdIdIter);
        ++mdIdIter;
        I2.readApplyGeo(MDin, *mdIdIter);
        ++mdIdIter;

        // Align images
        MultidimArray<double> &I1m=I1();
        MultidimArray<double> &I2m=I2();
        if (dont_mirror)
            alignImages(I1m,I2m,M);
        else
            alignImagesConsideringMirrors(I1m,I2m,M,aux1,aux2,aux3);
        FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(I1m)
            DIRECT_MULTIDIM_ELEM(I1m,n)=0.5*(DIRECT_MULTIDIM_ELEM(I1m,n)+
                                             DIRECT_MULTIDIM_ELEM(I2m,n));
        centerImage(I1m,aux2,aux3);

        // Write to output stack
        fnOut.compose(i+1,fnOutputStack);
        I1.write(fnOut);
        size_t objId=MDout.addObject();
        MDout.setValue(MDL_IMAGE,fnOut,objId);

#ifdef DEBUG
        I1.write("PPPI1.xmp");
        I2.write("PPPI2.xmp");
        std::cout << "M=" << M;
        std::cout << "Press any key\n";
        char c;
        std::cin >> c;
#endif
        if (i%100==0)
            progress_bar(i);
    }
    progress_bar(imax);

    if (remaining)
    {
        I1.readApplyGeo(MDin, *mdIdIter);
        ++mdIdIter;
        fnOut.compose(imax+1,fnOutputStack);
        I1.write(fnOut);
    }
}

computeMean()

void ProgAlign2d::computeMean

(

)

Compute mean.

Definition at line 166 of file align2d.cpp.

{
    size_t Xdim, Ydim, Zdim, Ndim;
    getImageSize(SF,Xdim,Ydim,Zdim,Ndim);
    if (Zdim!=1 || Ndim!=1)
        REPORT_ERROR(ERR_MATRIX_DIM,"Files in metadata are not 2D images");
    Iref().initZeros(Ydim,Xdim);
    Image<double> I;
    FileName fnImg;
    size_t N=SF.size();
    std::cerr << "Computing average of images ...\n";
    init_progress_bar(N);
    int i=0;
    for (size_t objId : SF.ids())
    {
        I.readApplyGeo(SF, objId);
        Iref()+=I();
        if ((++i)%100==0)
            progress_bar(i);
    }
    progress_bar(N);
    Iref()*=1.0/N;
    CorrelationAux aux;
    RotationalCorrelationAux aux2;
    centerImage(Iref(),aux,aux2);
}

defineParams()

void ProgAlign2d::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 61 of file align2d.cpp.

{
    addUsageLine("Aligns a set of images");
    addParamsLine("  -i <selfile>             : Selfile containing images to be aligned");
    addParamsLine("  --oroot <rootname>       : Output rootname");
    addParamsLine(" [--ref <image=\"\">]      : reference image; if none: pyramidal combination of subset of images");
    addParamsLine(" [--iter <N=5>]            : Number of iterations to perform");
    addParamsLine(" [--do_not_check_mirrors]  : Do not consider mirrors when aligning");
    addParamsLine(" [--pspc]                  : Compute first reference by pspc");
}

do_pspc()

void ProgAlign2d::do_pspc

(

)

Pyramidal combination of images to construct a reference.

Definition at line 146 of file align2d.cpp.

{
    int level=0;
    MetaDataVec SFlevel = SF;
    MetaDataVec SFlevel_1;
    while (SFlevel.size()>1)
    {
        alignPairs(SFlevel,SFlevel_1,level);
        if (level>=1)
            unlink((fnRoot+"_level_"+integerToString(level-1,2)+".stk").c_str());
        level++;
        SFlevel=SFlevel_1;
        SFlevel_1.clear();
    }
    size_t objId=SFlevel.firstRowId();
    Iref.readApplyGeo(SFlevel,objId);
    unlink((fnRoot+"_level_"+integerToString(level-1,2)+".stk").c_str());
    Iref.write(fnRoot+"_pspc.xmp");
}

readParams()

void ProgAlign2d::readParams ( )

virtual

Read argument.

Reimplemented from XmippProgram.

Definition at line 35 of file align2d.cpp.

{
    fnSel = getParam("-i");
    fnRoot = getParam("--oroot");
    fnRef = getParam("--ref");
    Niter = getIntParam("--iter");
    dont_mirror = checkParam("--do_not_check_mirrors");
    pspc = checkParam("--pspc");
}

refinement()

void ProgAlign2d::refinement

(

)

Alignment of all images by iterative refinement.

Definition at line 195 of file align2d.cpp.

{
    Image<double> I;
    size_t N=SF.size();
    double lambda=1.0/(N/2.0);
    double lambdap=1-lambda;
    init_progress_bar(N);
    int i=0;
    MultidimArray<double> &Irefm=Iref();
    Matrix2D<double> M;
    int centerCount=0;
    FileName fnImg;
    AlignmentAux aux1;
    CorrelationAux aux2;
    RotationalCorrelationAux aux3;
    for (size_t objId : SF.ids())
    {
        SF.getValue(MDL_IMAGE, fnImg, objId);
        I.read(fnImg);
        I().setXmippOrigin();
        MultidimArray<double> Ibackup, Ialigned;
        Ibackup=I();

        // Align images
        MultidimArray<double> &Im=I();
        double corr;
        if (dont_mirror)
            corr=alignImages(Irefm,Im,M);
        else
            corr=alignImagesConsideringMirrors(Irefm,Im,M,aux1,aux2,aux3);
        applyGeometry(xmipp_transformation::LINEAR, Ialigned, Ibackup, M, xmipp_transformation::IS_NOT_INV, xmipp_transformation::WRAP);
        Im=Ialigned;

        // Save alignment
        bool flip;
        double scale, shiftX, shiftY, psi;
        transformationMatrix2Parameters2D(M, flip, scale, shiftX, shiftY, psi);
        SF.setValue(MDL_SHIFT_X, shiftX, objId);
        SF.setValue(MDL_SHIFT_Y, shiftY, objId);
        SF.setValue(MDL_ANGLE_PSI, psi, objId);
        SF.setValue(MDL_FLIP, flip, objId);
        SF.setValue(MDL_MAXCC, corr, objId);

        // Update reference
        FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(Irefm)
            DIRECT_MULTIDIM_ELEM(Irefm,n)=lambdap*DIRECT_MULTIDIM_ELEM(Irefm,n)+
                                          lambda*DIRECT_MULTIDIM_ELEM(Im,n);

        // From time to time, recenter the reference
        if ((++centerCount)%10==0)
        {
            centerImage(Irefm,aux2,aux3);
            centerCount=0;
        }

        if ((++i)%100==0)
            progress_bar(i);
#ifdef DEBUG
        Iref.write("PPPref.xmp");
        I.write("PPPexp.xmp");
        std::cout << "Press any key\n";
        char c;
        std::cin >> c;
#endif
    }
    progress_bar(N);
    Iref.write(fnRoot+"_ref.xmp");
    SF.write(fnRoot+"_alignment.xmd");
}

run()

void ProgAlign2d::run ( )

virtual

Main routine.

Reimplemented from XmippProgram.

Definition at line 267 of file align2d.cpp.

{
    // Read the input metadata
    SF.read(fnSel);

    // Get Reference
    if (fnRef != "")
        Iref.read(fnRef);
    else
    {
        if (pspc)
            do_pspc();
        else
            computeMean();
    }
    Iref().setXmippOrigin();

    // Circular mask the reference image
    MultidimArray<int> mask;
    mask.resize(Iref());
    mask.setXmippOrigin();
    BinaryCircularMask(mask,XSIZE(Iref())/2);
    apply_binary_mask(mask, Iref(), Iref());

    // Refine
    std::cout << "Refining ...\n";
    for (int n=0; n<Niter; n++)
    {
        std::cerr << "Refinement iteration " << n << std::endl;
        refinement();
    }
}

show()

void ProgAlign2d::show

(

)

Show.

Definition at line 46 of file align2d.cpp.

{
    if (verbose==0)
        return;
    std::cerr
    << "Input selfile:        " << fnSel       << std::endl
    << "Input reference:      " << fnRef       << std::endl
    << "Output rootname:       " << fnRoot      << std::endl
    << "Number of iterations: " << Niter       << std::endl
    << "Do not check mirrors: " << dont_mirror << std::endl
    << "PSPC:                 " << pspc        << std::endl
    ;
}

Member Data Documentation

dont_mirror

bool ProgAlign2d::dont_mirror

Do not check mirrors

Definition at line 48 of file align2d.h.

fnRef

FileName ProgAlign2d::fnRef

Filename reference image

Definition at line 42 of file align2d.h.

fnRoot

FileName ProgAlign2d::fnRoot

Filename output root

Definition at line 44 of file align2d.h.

fnSel

FileName ProgAlign2d::fnSel

Filename selection file containing the images

Definition at line 40 of file align2d.h.

Iref

Image<double> ProgAlign2d::Iref

Definition at line 55 of file align2d.h.

Niter

int ProgAlign2d::Niter

Integer number of iterations to perform

Definition at line 46 of file align2d.h.

pspc

bool ProgAlign2d::pspc

Do pspc

Definition at line 50 of file align2d.h.

SF

MetaDataVec ProgAlign2d::SF

Definition at line 53 of file align2d.h.

---

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

• xmipp/libraries/reconstruction/align2d.h
• xmipp/libraries/reconstruction/align2d.cpp