ProgSortImages Class Reference

Inheritance diagram for ProgSortImages:

Collaboration diagram for ProgSortImages:

Public Member Functions
	ProgSortImages (int argc, char **argv)
	MPI constructor. More...
	ProgSortImages (const ProgSortImages &)=delete
	ProgSortImages (const ProgSortImages &&)=delete
	~ProgSortImages ()
	MPI destructor. More...
ProgSortImages &	operator= (const ProgSortImages &)=delete
ProgSortImages &	operator= (const ProgSortImages &&)=delete
void	readParams ()
	Read argument from command line. More...
void	show ()
	Show. More...
void	defineParams ()
	Usage. More...
void	produceSideInfo (int rank)
	Produce side info. More...
void	chooseNextImage (int rank, int Nproc)
	Choose next image. 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	fnRoot
MpiNode *	node
FileName	fnStack
bool	center
MetaDataVec	SFout
std::vector< MDRowVec >	toClassify
Matrix1D< int >	stillToDo
Image< double >	lastImage
MultidimArray< int >	mask
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 35 of file mpi_image_sort.cpp.

Constructor & Destructor Documentation

ProgSortImages() [1/3]

ProgSortImages::ProgSortImages ( int  argc, char **  argv  )

inline

MPI constructor.

Definition at line 68 of file mpi_image_sort.cpp.

    {
        node=new MpiNode(argc,argv);
        if (!node->isMaster())
            verbose=0;
    }

ProgSortImages() [2/3]

ProgSortImages::ProgSortImages ( const ProgSortImages &  )

delete

ProgSortImages() [3/3]

ProgSortImages::ProgSortImages ( const ProgSortImages &&  )

delete

~ProgSortImages()

ProgSortImages::~ProgSortImages ( )

inline

MPI destructor.

Definition at line 79 of file mpi_image_sort.cpp.

    {
        delete node;
    }

Member Function Documentation

chooseNextImage()

void ProgSortImages::chooseNextImage ( int  rank, int  Nproc  )

inline

Choose next image.

Definition at line 194 of file mpi_image_sort.cpp.

    {
        Image<double> bestImage, I;
        Matrix2D<double> M;
        double bestCorr=-1;
        int bestIdx=-1;
        int count=0;
        FileName fnImageStack, fnImg;
        AlignmentAux aux;
        CorrelationAux aux2;
        RotationalCorrelationAux aux3;
        FOR_ALL_ELEMENTS_IN_MATRIX1D(stillToDo)
        {
            if (!VEC_ELEM(stillToDo,i))
                continue;
            if ((count+1)%Nproc!=rank)
            {
                ++count;
                continue;
            }
            toClassify[i].getValue(MDL_IMAGE,fnImg);
            I.read(fnImg);
            I().setXmippOrigin();
            double corr=alignImagesConsideringMirrors(lastImage(),I(),M,aux,aux2,aux3,&mask);
            if (center)
                centerImage(I(),aux2,aux3);
            if (corr>bestCorr)
            {
                bestCorr=corr;
                bestImage()=I();
                bestIdx=i;
            }
            ++count;
        }

        // Rank 0 receives from the other nodes their best image
        double buffer[2];
        if (rank==0)
        {
            MPI_Status status;
            for (int n=1; n<Nproc; ++n)
            {
                MPI_Recv(buffer, 2, MPI_DOUBLE, n, 0, MPI_COMM_WORLD, &status);
                if (buffer[1]>bestCorr)
                {
                    bestIdx=(int)buffer[0];
                    bestCorr=buffer[1];
                }
            }
            std::cout << "Images to go=" << stillToDo.sum()-1 << " current correlation= " << bestCorr << std::endl;
        }
        else
        {
            buffer[0]=bestIdx;
            buffer[1]=bestCorr;
            MPI_Send(buffer, 2, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD);
        }

        // Now rank 0 redistributes the best image
        if (rank==0)
        {
            buffer[0]=bestIdx;
            MPI_Bcast(buffer, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
        }
        else
        {
            MPI_Bcast(buffer, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
            bestIdx=(int)buffer[0];
        }

        // All compute the best image
        toClassify[bestIdx].getValue(MDL_IMAGE,fnImg);
        I.read(fnImg);
        I().setXmippOrigin();
        bestCorr=alignImagesConsideringMirrors(lastImage(),I(),M,aux,aux2,aux3,&mask);
        if (center)
            centerImage(I(),aux2,aux3);
        lastImage()=bestImage()=I();

        if (rank==0)
        {
            int idxStack=SFout.size();
            fnImageStack.compose(idxStack+1,fnStack);
            bestImage.write(fnStack,idxStack,true,WRITE_APPEND);
            MDRowVec &row = toClassify[bestIdx];
            FileName fnImgOrig;
            row.getValue(MDL_IMAGE,fnImgOrig);
            row.setValue(MDL_IMAGE_ORIGINAL,fnImgOrig);
            row.setValue(MDL_IMAGE,fnImageStack);
            row.setValue(MDL_MAXCC,bestCorr);
            SFout.addRow(row);
        }
        VEC_ELEM(stillToDo,bestIdx)=0;
    }

defineParams()

void ProgSortImages::defineParams ( )

inlinevirtual

Usage.

Reimplemented from XmippProgram.

Definition at line 107 of file mpi_image_sort.cpp.

    {
        addUsageLine("Sort a set of images by local similarity");
        addUsageLine("+The program takes the first image of the input selfile as reference.");
        addUsageLine("+Then, it looks for the image among the remaining ones that is most similar to it once they have been aligned.");
        addUsageLine("+Now, the most similar image is aligned to the reference image (the first one) and is added to the list of sorted images.");
        addUsageLine("+The second image acts now as the reference, and the most similar image among the remaining images is added to the list of sorted images.");
        addUsageLine("+This process is repeated until no image is left.");
        addUsageLine("+");
        addUsageLine("+Note that only the MPI version of this program exists");
        addParamsLine("   -i <selfile>        : selfile of images");
        addParamsLine("   --oroot <rootname>  : output rootname");
        addParamsLine("                       : rootname.stk contains the list of aligned images.");
        addParamsLine("                       : rootname.xmd contains the correspondence between aligned images ");
        addParamsLine("                       : and the original images as well as the correlation coefficient ");
        addParamsLine("                       : between the aligned image and its predecessor in the list of ");
        addParamsLine("                       : aligned images.");
        addParamsLine("   [--dont_center]     : Do not center images as they are sorted");
        addExampleLine("mpirun -np 8 `which xmipp_mpi_image_sort` -i images.xmd --oroot sorted");
    }

operator=() [1/2]

ProgSortImages& ProgSortImages::operator= ( const ProgSortImages &  )

delete

operator=() [2/2]

ProgSortImages& ProgSortImages::operator= ( const ProgSortImages &&  )

delete

produceSideInfo()

void ProgSortImages::produceSideInfo ( int  rank )

inline

Produce side info.

Definition at line 129 of file mpi_image_sort.cpp.

    {
        fnStack = fnRoot + ".stk";

        if (rank == 0)
            fnStack.deleteFile();

        // Read input selfile and reference
        MetaDataVec SF;
        SF.read(fnSel);
        FileName fnImg;
        toClassify.reserve(SF.size());
        FileName fnImageStack;
        CorrelationAux aux;
        RotationalCorrelationAux aux2;
        bool thereIsClassCount=SF.containsLabel(MDL_CLASS_COUNT);
        bool firstSelected=false;

        for (auto& row : SF)
        {
            bool proceed=true;
            if (thereIsClassCount)
            {
                size_t classCount;
                row.getValue(MDL_CLASS_COUNT,classCount);
                if (classCount==0)
                    proceed=false;
            }
            if (proceed)
            {
                row.detach(); // so that we can copy it outside of the metadata
                toClassify.emplace_back(dynamic_cast<MDRowVec&>(row));
                row.getValue(MDL_IMAGE,fnImg);
                if (!firstSelected)
                {
                    row.getValue(MDL_IMAGE,fnImg);
                    lastImage.read(fnImg);
                    if (center)
                        centerImage(lastImage(),aux,aux2);
                    if (rank==0)
                        lastImage.write(fnStack,0,true,WRITE_APPEND);
                    fnImageStack.compose(1,fnStack);
                    if (rank==0)
                    {
                        row.setValue(MDL_IMAGE_ORIGINAL,fnImg);
                        row.setValue(MDL_MAXCC,1.0);
                        SFout.addRow(dynamic_cast<MDRowVec&>(row));
                    }
                    firstSelected=true;
                }
            }
        }
        if (toClassify.size()==0)
            return;
        stillToDo.resizeNoCopy(toClassify.size());
        stillToDo.initConstant(1);
        VEC_ELEM(stillToDo,0)=0;

        // Prepare mask
        mask.resize(lastImage());
        mask.setXmippOrigin();
        BinaryCircularMask(mask,XSIZE(lastImage())/2, INNER_MASK);
    }

readParams()

void ProgSortImages::readParams ( )

inlinevirtual

Read argument from command line.

Reimplemented from XmippProgram.

Definition at line 88 of file mpi_image_sort.cpp.

    {
        fnSel  = getParam("-i");
        fnRoot = getParam("--oroot");
        center = !checkParam("--dont_center");
    }

run()

void ProgSortImages::run ( )

inlinevirtual

Main routine.

Reimplemented from XmippProgram.

Definition at line 290 of file mpi_image_sort.cpp.

    {
        show();
        produceSideInfo(node->rank);
        while (stillToDo.sum()>0)
            chooseNextImage(node->rank,node->size);
        if (node->rank==0)
            SFout.write(fnRoot+".xmd");
    }

show()

void ProgSortImages::show ( )

inline

Show.

Definition at line 96 of file mpi_image_sort.cpp.

    {
        if (!verbose)
            return;
        std::cerr << "Input selfile:    " << fnSel           << std::endl
        << "Output rootname:  " << fnRoot          << std::endl
        << "Center: " << center << std::endl
        ;
    }

Member Data Documentation

center

bool ProgSortImages::center

Center

Definition at line 50 of file mpi_image_sort.cpp.

fnRoot

FileName ProgSortImages::fnRoot

Filename output rootname

Definition at line 42 of file mpi_image_sort.cpp.

fnSel

FileName ProgSortImages::fnSel

Filename selection file containing the images

Definition at line 39 of file mpi_image_sort.cpp.

fnStack

FileName ProgSortImages::fnStack

Filename of the output stack

Definition at line 47 of file mpi_image_sort.cpp.

lastImage

Image<double> ProgSortImages::lastImage

Definition at line 62 of file mpi_image_sort.cpp.

mask

MultidimArray<int> ProgSortImages::mask

Definition at line 65 of file mpi_image_sort.cpp.

node

MpiNode* ProgSortImages::node

Definition at line 44 of file mpi_image_sort.cpp.

SFout

MetaDataVec ProgSortImages::SFout

Definition at line 53 of file mpi_image_sort.cpp.

stillToDo

Matrix1D<int> ProgSortImages::stillToDo

Definition at line 59 of file mpi_image_sort.cpp.

toClassify

std::vector< MDRowVec > ProgSortImages::toClassify

Definition at line 56 of file mpi_image_sort.cpp.

---

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

• xmipp/libraries/parallel/mpi_image_sort.cpp