Alignment::AProgAlignSignificant< T > Class Template Reference

#include <aalign_significant.h>

Inheritance diagram for Alignment::AProgAlignSignificant< T >:

Collaboration diagram for Alignment::AProgAlignSignificant< T >:

Classes
struct	Assignment
struct	Settings

Public Member Functions
virtual void	readParams () override
virtual void	defineParams () override
virtual void	show () const override
virtual void	run () override
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	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 ()

Protected Member Functions
virtual void	check () const
const Settings &	getSettings ()
virtual std::vector< AlignmentEstimation >	align (const T *ref, const T *others)=0
virtual void	updateRefs (T *refs, const T *others, const std::vector< Assignment > &assignments)=0
ctpl::thread_pool &	getThreadPool ()
void	updateRefXmd (size_t refIndex, std::vector< Assignment > &images)
Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Additional Inherited Members
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug
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

template<typename T>
class Alignment::AProgAlignSignificant< T >

Definition at line 46 of file aalign_significant.h.

Member Function Documentation

align()

template<typename T >

virtual std::vector<AlignmentEstimation> Alignment::AProgAlignSignificant< T >::align ( const T *  ref, const T *  others  )

protectedpure virtual

Implemented in Alignment::ProgAlignSignificantGPU< T >.

check()

template<typename T >

void Alignment::AProgAlignSignificant< T >::check ( ) const

protectedvirtual

Definition at line 206 of file aalign_significant.cpp.

                                           {
    if ( ! m_referenceImages.dims.equalExceptNPadded(m_imagesToAlign.dims)) {
        REPORT_ERROR(ERR_LOGIC_ERROR, "Dimensions of the images to align and reference images do not match");
    }
    if (m_noOfBestToKeep > m_referenceImages.dims.n()) {
        REPORT_ERROR(ERR_LOGIC_ERROR, "--keepBestN is higher than number of references");
    }
    if (m_referenceImages.dims.n() <= 1) {
        REPORT_ERROR(ERR_LOGIC_ERROR, "We need at least two references");
    }
}

defineParams()

template<typename T >

void Alignment::AProgAlignSignificant< T >::defineParams ( )

overridevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Reimplemented in Alignment::ProgAlignSignificantGPU< T >.

Definition at line 32 of file aalign_significant.cpp.

                                            {
    addUsageLine("Find alignment of the experimental images in respect to a set of references");

    addParamsLine("   -i <md_file>                    : Metadata file with the experimental images");
    addParamsLine("   -r <md_file>                    : Metadata file with the reference images");
    addParamsLine("   -o <md_file>                    : Resulting metadata file with the aligned images");
    addParamsLine("   [--thr <N=-1>]                  : Maximal number of the processing CPU threads");
    addParamsLine("   [--angDistance <a=10>]          : Angular distance");
    addParamsLine("   [--odir <outputDir=\".\">]      : Output directory");
    addParamsLine("   [--keepBestN <N=1>]             : For each image, store N best alignments to references. N must be smaller than no. of references");
    addParamsLine("   [--allowInputSwap]              : Allow swapping reference and experimental images");
    addParamsLine("   [--useWeightInsteadOfCC]        : Select the best reference using weight, instead of CC");
    addParamsLine("   [--oUpdatedRefs <baseName=\"\">]: Update references using assigned experimental images. Store result here");
}

getSettings()

template<typename T >

const Settings& Alignment::AProgAlignSignificant< T >::getSettings ( )

inlineprotected

Definition at line 73 of file aalign_significant.h.

                                  {
        return m_settings;
    }

getThreadPool()

template<typename T >

ctpl::thread_pool& Alignment::AProgAlignSignificant< T >::getThreadPool ( )

inlineprotected

Definition at line 79 of file aalign_significant.h.

                                     {
        return m_threadPool;
    }

readParams()

template<typename T >

void Alignment::AProgAlignSignificant< T >::readParams ( )

overridevirtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippProgram.

Reimplemented in Alignment::ProgAlignSignificantGPU< T >.

Definition at line 48 of file aalign_significant.cpp.

                                          {
    m_imagesToAlign.fn = getParam("-i");
    m_referenceImages.fn = getParam("-r");
    auto outDir = FileName(getParam("--odir"));
    if ( ! outDir.exists()) {
        if (outDir.makePath()) {
            REPORT_ERROR(ERR_IO_NOWRITE, "cannot create " + outDir);
        }
    }
    m_fnOut = outDir + "/" + std::string(getParam("-o"));
    m_angDistance = getDoubleParam("--angDistance");
    m_noOfBestToKeep = getIntParam("--keepBestN");
    m_allowDataSwap = checkParam("--allowInputSwap");
    m_useWeightInsteadOfCC = checkParam("--useWeightInsteadOfCC");
    m_updateHelper.doUpdate = checkParam("--oUpdatedRefs");
    if (m_updateHelper.doUpdate) {
        FileName base = outDir + "/" + std::string(getParam("--oUpdatedRefs"));
        m_updateHelper.fnStk = base + ".stk";
        m_updateHelper.fnXmd = base + ".xmd";
    }

    int threads = getIntParam("--thr");
    if (-1 == threads) {
        m_settings.cpuThreads = CPU::findCores();
    } else {
        m_settings.cpuThreads = threads;
    }
}

run()

template<typename T >

void Alignment::AProgAlignSignificant< T >::run ( )

overridevirtual

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

Reimplemented from XmippProgram.

Definition at line 575 of file aalign_significant.cpp.

                                   {
    show();
    m_threadPool.resize(getSettings().cpuThreads);
    // load data
    load<false>(m_imagesToAlign);
    load<true>(m_referenceImages);

    bool hasMoreReferences = m_allowDataSwap
            && (m_referenceImages.dims.n() > m_imagesToAlign.dims.n());
    if (hasMoreReferences) {
        std::cerr << "We are swapping reference images and experimental images. "
                "This will enhance the performance. This might lead to worse results if the experimental "
                "images are not well centered. Use it with care!\n";
        std::swap(m_referenceImages, m_imagesToAlign);
    }

    // for each reference, get alignment of all images
    updateSettings();
    check();
    auto alignment = align(m_referenceImages.data.get(), m_imagesToAlign.data.get());

    // process the alignment and store
    if (hasMoreReferences) {
        std::swap(m_referenceImages, m_imagesToAlign);
        computeWeights<true>(alignment);
        if (m_useWeightInsteadOfCC) {
            computeAssignment<true, true>(alignment);
        } else {
            computeAssignment<true, false>(alignment);
        }
    } else {
        computeWeights<false>(alignment);
        if (m_useWeightInsteadOfCC) {
            computeAssignment<false, true>(alignment);
        } else {
            computeAssignment<false, false>(alignment);
        }
    }
    // at this moment, we can release some memory
    m_weights.clear();
    alignment.clear();

    if (m_useWeightInsteadOfCC) {
        storeAlignedImages<true>();
    } else {
        storeAlignedImages<false>();
    }

    if (m_updateHelper.doUpdate) {
        updateRefs();
    }
}

show()

template<typename T >

void Alignment::AProgAlignSignificant< T >::show ( ) const

overridevirtual

Show parameters

Reimplemented from XmippProgram.

Reimplemented in Alignment::ProgAlignSignificantGPU< T >.

Definition at line 78 of file aalign_significant.cpp.

                                          {
    if (verbose < 1) return;

    std::cout << "Input metadata              : " << m_imagesToAlign.fn << "\n";
    std::cout << "Reference metadata          : " << m_referenceImages.fn <<  "\n";
    std::cout << "Output metadata             : " << m_fnOut <<  "\n";
    std::cout << "Angular distance            : " << m_angDistance <<  "\n";
    std::cout << "Best references kept        : " << m_noOfBestToKeep << "\n";
    if (m_updateHelper.doUpdate) {
    std::cout << "Updated references          : " << m_updateHelper.fnXmd << "\n";
    }
    std::cout.flush();
}

updateRefs()

template<typename T >

virtual void Alignment::AProgAlignSignificant< T >::updateRefs ( T *  refs, const T *  others, const std::vector< Assignment > &  assignments  )

protectedpure virtual

Implemented in Alignment::ProgAlignSignificantGPU< T >.

updateRefXmd()

template<typename T >

void Alignment::AProgAlignSignificant< T >::updateRefXmd ( size_t  refIndex, std::vector< Assignment > &  images  )

protected

Definition at line 511 of file aalign_significant.cpp.

                                                                                          {
    static std::mutex mutex;
    std::lock_guard<std::mutex> lk(mutex); // released at the end of scope

    const size_t indexInStk = refIndex + 1; // within metadata file, index images from one (1)
    FileName refName;
    auto &refMeta = m_updateHelper.refBlock;
    // name of the reference
    refName.compose(indexInStk, m_updateHelper.fnStk);
    // some info about it
    auto refRow = MDRowVec();
    assert(std::numeric_limits<int>::max() >= refIndex);
    refRow.setValue(MDL_REF, getRefMetaIndex(refIndex), true);
    refRow.setValue(MDL_IMAGE, refName, true);
    refRow.setValue(MDL_CLASS_COUNT, images.size(), true);
    refMeta.addRows({refRow});

    // create image description block
    std::sort(images.begin(), images.end(), [](const Assignment &l, const Assignment &r) {
       return l.imgIndex < r.imgIndex; // sort by image index
    });

    const size_t noOfImages = images.size();
    if (0 != noOfImages) {
        std::vector<MDRowVec> rows(noOfImages);
        for (size_t i = 0; i < noOfImages; ++i) {
            auto &row = rows.at(i);
            const auto &a = images.at(i);
            getImgRow(row, a.imgIndex);
            fillRow(row, a.pose, refIndex, a.weight, a.imgIndex);
        }
        const auto& labels = rows.at(0).labels();
        if (0 == m_updateHelper.imgBlocks.size()) {
            m_updateHelper.imgBlocks.resize(m_referenceImages.dims.n(), labels);
        }
        auto &md = m_updateHelper.imgBlocks.at(refIndex);
        md.addRows(rows);
    }
}

---

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

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