ProgConstructPDBDictionary Class Reference

#include <pdb_construct_dictionary.h>

Inheritance diagram for ProgConstructPDBDictionary:

Collaboration diagram for ProgConstructPDBDictionary:

Public Member Functions
void	defineParams ()
void	readParams ()
void	show ()
void	run ()
Public Member Functions inherited from ProgPDBDictionary
void	extractPatch (const MultidimArray< double > &V, MultidimArray< double > &patch, int k, int i, int j)
void	insertPatch (MultidimArray< double > &Vhigh, MultidimArray< double > &weightHigh, const MultidimArray< double > &patchHigh, int k, int i, int j, double R2)
void	constructRotationGroup2D ()
void	constructRotationGroup3D ()
void	constructRotationGroup ()
size_t	canonicalOrientation2D (const MultidimArray< double > &patch, MultidimArray< double > &canonicalPatch, Matrix1D< double > &patchSignature)
size_t	canonicalOrientation3D (const MultidimArray< double > &patch, MultidimArray< double > &canonicalPatch, Matrix1D< double > &patchSignature)
bool	notInDictionary (const MultidimArray< double > &candidatePatch, MultidimArray< double > &canonicalPatch, Matrix1D< double > &canonicalSignature, size_t &canonicalIdx)
void	selectDictionaryPatches (const MultidimArray< double > &lowResolutionPatch, Matrix1D< double > &lowResolutionPatchSignature, std::vector< size_t > &selectedPatchesIdx, std::vector< double > &weight)
double	approximatePatch (const MultidimArray< double > &lowResolutionPatch, std::vector< size_t > &selectedPatchesIdx, std::vector< double > &weight, Matrix1D< double > &alpha)
void	reconstructPatch (size_t idxTransf, std::vector< size_t > &selectedPatchesIdx, Matrix1D< double > &alpha, MultidimArray< double > &highResolutionPatch)
void	loadDictionaries ()
void	saveDictionaries () const
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 ()

Additional Inherited Members
Public Attributes inherited from ProgPDBDictionary
FileName	fnRoot
int	patchSize
double	stdThreshold
double	angleThreshold
double	lambda
int	iterations
int	mode
std::vector< MultidimArray< double > >	dictionaryLow
std::vector< MultidimArray< double > >	dictionaryHigh
std::vector< Matrix1D< double > >	dictionarySignature
std::vector< Matrix2D< double > >	rotationGroup
MultidimArray< double >	auxPatch
Matrix1D< double >	auxSignature
Matrix2D< double >	Ui
Matrix2D< double >	UitUi
Matrix1D< double >	wi
Matrix1D< double >	v1
Matrix1D< double >	v2
Matrix1D< double >	y
Matrix1D< double >	yp
Matrix1D< double >	Uity
int	patchSize_2
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug
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

Construct Low and High resolution dictionary

Definition at line 137 of file pdb_construct_dictionary.h.

Member Function Documentation

defineParams()

void ProgConstructPDBDictionary::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented from ProgPDBDictionary.

Definition at line 541 of file pdb_construct_dictionary.cpp.

{
    // Usage
    addUsageLine("This program takes a set of PDB files at low and high resolution and constructs a dictionary for them.");

    // Parameters
    addParamsLine(" --low <metadata>      : Metadata with the low resolution volumes");
    addParamsLine(" --high <metadata>     : Metadata with the high resolution volumes");
    addParamsLine(" [--R2Threshold <s=0.99>] : Threshold in R2 to include a patch");
    addParamsLine(" [--oroot <root=dictionary>] : Rootname for the output files");
    addParamsLine(" [--patchSize <n=5>] : Patch size for the dictionary");
    ProgPDBDictionary::defineParams();
}

readParams()

void ProgConstructPDBDictionary::readParams ( )

virtual

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

Reimplemented from ProgPDBDictionary.

Definition at line 555 of file pdb_construct_dictionary.cpp.

{
    fnLow=getParam("--low");
    fnHigh=getParam("--high");
    fnRoot=getParam("--oroot");
    patchSize=getIntParam("--patchSize");
    R2threshold=getDoubleParam("--R2Threshold");
    ProgPDBDictionary::readParams();
}

run()

void ProgConstructPDBDictionary::run ( )

virtual

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

Implements ProgPDBDictionary.

Definition at line 581 of file pdb_construct_dictionary.cpp.

{
    show();
    if (fileExists(fnRoot+"_low.mrcs"))
        loadDictionaries();

    MetaDataVec mdlow, mdhigh;
    mdlow.read(fnLow);
    mdhigh.read(fnHigh);
    if (mode==0)
        constructRotationGroup3D();
    else
        constructRotationGroup2D();

    FileName fnVol;
    Image<double> Vlow, Vhigh;
#ifdef DEBUG
    Image<double>Vmask;
#endif
    MultidimArray<double> patchLow, patchHigh, canonicalPatch;
    Matrix1D<double> alpha, canonicalSignature;
    patchSize_2=patchSize/2;

    if (mode==0)
        patchLow.resize(patchSize,patchSize,patchSize);
    else
        patchLow.resize(patchSize,patchSize);
    patchLow.setXmippOrigin();
    patchHigh=patchLow;

    auto itIdLow = mdlow.ids().begin();
    auto itIdHigh = mdhigh.ids().end();
    for (; itIdLow != mdlow.ids().end(); ++itIdLow, ++itIdHigh)
    {
        // Read the low and high resolution volumes
        mdlow.getValue(MDL_IMAGE,fnVol, *itIdLow);
        Vlow.read(fnVol);
        std::cout << "Processing " << fnVol << " and ";
        mdhigh.getValue(MDL_IMAGE,fnVol, *itIdHigh);
        std::cout << fnVol << std::endl;
        Vhigh.read(fnVol);

        // Go through the volumes and decide whether to move into the dictionary
        const MultidimArray<double> &mVlow=Vlow();
        const MultidimArray<double> &mVhigh=Vhigh();

        double minLow, maxLow, meanLow, stdLow=0;
        double minHigh, maxHigh, meanHigh, stdHigh=0;
        mVlow.computeStats(meanLow,stdLow,minLow,maxLow);
        mVhigh.computeStats(meanHigh,stdHigh,minHigh,maxHigh);
#ifdef DEBUG
        Vmask().initZeros(Vhigh());
#endif

        std::vector< size_t > selectedPatchesIdx;
        std::vector<double> weight;
        size_t Npatches=0, NcandidatePatches=0, NsuccessfulPatches=0;
        init_progress_bar(ZSIZE(mVlow));
        for (int k=patchSize_2; k<(int)ZSIZE(mVlow)-patchSize_2; ++k)
        {
            for (int i=patchSize_2; i<(int)ZSIZE(mVlow)-patchSize_2; ++i)
                for (int j=patchSize_2; j<(int)ZSIZE(mVlow)-patchSize_2; ++j)
                {
                     ++Npatches;
                     extractPatch(mVlow,patchLow,k,i,j);
                     extractPatch(mVhigh,patchHigh,k,i,j);

                    double minPatchLow, maxPatchLow, meanPatchLow, stdPatchLow=0;
                    double minPatchHigh, maxPatchHigh, meanPatchHigh, stdPatchHigh=0;
                    patchLow.computeStats(meanPatchLow,stdPatchLow,minPatchLow,maxPatchLow);
                    patchHigh.computeStats(meanPatchHigh,stdPatchHigh,minPatchHigh,maxPatchHigh);

                    if (stdPatchLow > stdThreshold*stdLow && stdPatchHigh > stdThreshold*stdHigh)
                    {
                        ++NcandidatePatches;

                        // Candidate patch
                        double inormPatchLow=1.0/sqrt(patchLow.sum2());
                        patchLow*=inormPatchLow;
                        size_t canonicalIdx=0;
                        if (mode==0)
                            canonicalIdx=canonicalOrientation3D(patchLow,canonicalPatch,canonicalSignature);
                        else
                            canonicalIdx=canonicalOrientation2D(patchLow,canonicalPatch,canonicalSignature);
                        selectDictionaryPatches(canonicalPatch, canonicalSignature, selectedPatchesIdx, weight);
                        bool introduceInDictionary=(selectedPatchesIdx.size()==0);
#ifdef DEBUG
                        std::cout << "Evaluating " << k << "," << i << "," << j << " -> selectedPatches=" << selectedPatchesIdx.size() << std::endl;
#endif
                        double R2=-1;
                        if (!introduceInDictionary)
                        {
                            R2=approximatePatch(canonicalPatch,selectedPatchesIdx,weight,alpha);
#ifdef DEBUG
                        std::cout << "   R2=" << R2 << std::endl;
#endif
                            introduceInDictionary=(R2<R2threshold);
                        }
                        if (introduceInDictionary)
                        {
                            ++NsuccessfulPatches;
                            selfApplyGeometry(xmipp_transformation::LINEAR,patchHigh,rotationGroup[canonicalIdx],xmipp_transformation::IS_INV,xmipp_transformation::DONT_WRAP);

                            dictionaryLow.push_back(canonicalPatch);
                            patchHigh*=inormPatchLow;
                            dictionaryHigh.push_back(patchHigh);
                            dictionarySignature.push_back(canonicalSignature);
#ifdef DEBUG
                        std::cout << "   Introducing it into dictionary" << std::endl;
#endif
                        }

#ifdef DEBUG
                        Vmask(k,i,j)=1;
#endif
                    }
                }
            progress_bar(k);
        }
        progress_bar(ZSIZE(mVlow));
        std::cout << "Candidate patches =" << NcandidatePatches << "(" << ((double)NcandidatePatches)/Npatches*100 << "%)"
                  << "  successful=" << NsuccessfulPatches << "(" << ((double)NsuccessfulPatches)/NcandidatePatches*100 << "%)" << std::endl;
        saveDictionaries();
#ifdef DEBUG
        Vmask.write("PPPmask.vol");
        std::cout << "Press any key\n";
        char c; std::cin >> c;
#endif
    }
}

show()

void ProgConstructPDBDictionary::show ( )

virtual

Reimplemented from ProgPDBDictionary.

Definition at line 565 of file pdb_construct_dictionary.cpp.

{
    if (verbose)
    {
        std::cout
        << "Input low volumes:   " << fnLow     << std::endl
        << "Input high volumes:  " << fnHigh    << std::endl
        << "Output rootname:     " << fnRoot    << std::endl
        << "Patch size:          " << patchSize << std::endl
        << "R2 threshold:        " << R2threshold << std::endl
        ;
        ProgPDBDictionary::show();
    }
}

---

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

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