ProgCompareDensity Class Reference

#include <compare_density.h>

Inheritance diagram for ProgCompareDensity:

Collaboration diagram for ProgCompareDensity:

Public Member Functions
void	defineParams ()
	Define params. More...
void	readParams ()
	Read arguments from command line. More...
void	show ()
	Show. More...
void	run ()
	Run. More...
void	computeCorrImage (int i)
	Compute corr image. More...
void	compare (Image< double > &op1, const Image< double > &op2)
	Compare binary images. 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	fnVol1
	Volumes to compare. More...
FileName	fnVol2
FileName	fnImgOut
	Output corelation image. More...
double	degstep
	Degree step. More...
Image< double >	V1
	Images. More...
Image< double >	V2
Image< double >	CorrImg
std::vector< double >	tilt_v
	Rot and tilt vectors. More...
std::vector< double >	rot_v
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

Sph Alignment Parameters.

Definition at line 38 of file compare_density.h.

Member Function Documentation

compare()

void ProgCompareDensity::compare	(	Image< double > &	op1,
		const Image< double > &	op2
	)

Compare binary images.

Definition at line 140 of file compare_density.cpp.

{
    MultidimArray<double> &mOp1 = op1();
    const MultidimArray<double> &mOp2 = op2();
    FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mOp1)
    {
        dAi(mOp1, n) = dAi(mOp1, n) == dAi(mOp2, n) ? 0 : (dAi(mOp1, n) < dAi(mOp2, n) ? -1 : 1 );
    }
}

computeCorrImage()

void ProgCompareDensity::computeCorrImage

(

int

i

)

Compute corr image.

Definition at line 97 of file compare_density.cpp.

{
    Projection P1, P2;
    auto &mCorrImg = CorrImg();
    auto &mV1 = V1();
    auto &mV2 = V2();
    auto &mP1 = P1();
    auto &mP2 = P2();
    int size_x = XSIZE(mV1);
    int size_y = YSIZE(mV1);
    auto rot = rot_v[i];

    // Filter
    FourierFilter filter;
    filter.FilterBand=LOWPASS;
    filter.w1=1.0/12.0;
    filter.raised_w=0.02;

    for (int j = 0; j < tilt_v.size(); j++)
    {
        projectVolume(mV1, P1, size_y, size_x, rot, tilt_v[j], 0.);
        projectVolume(mV2, P2, size_y, size_x, rot, tilt_v[j], 0.);
        auto &mP1 = P1();
        auto &mP2 = P2();
        filter.applyMaskSpace(mP1);
        filter.applyMaskSpace(mP2);
        OtsuSegmentation(mP1);
        OtsuSegmentation(mP2);
        MultidimArray<double> cmP1 = mP1;
        MultidimArray<double> cmP2 = mP2;
        keepBiggestComponent(cmP1);
        keepBiggestComponent(cmP2);
        mP1 = mP1 - cmP1;
        mP2 = mP2 - cmP2;
        compare(P1, P2);
        double sum_cmp = mP1.sum();
        if (sum_cmp > 0.0)
            DIRECT_A2D_ELEM(mCorrImg, i, j) = 1.0;
        else if (sum_cmp < 0.0)
            DIRECT_A2D_ELEM(mCorrImg, i, j) = -1.0;
    }
}

defineParams()

void ProgCompareDensity::defineParams ( )

virtual

Define params.

Reimplemented from XmippProgram.

Definition at line 38 of file compare_density.cpp.

                                      {
    addUsageLine("Compute the deformation that properly fits two volumes using spherical harmonics");
    addParamsLine("   -v1 <volume>                        : First volume to compare");
    addParamsLine("   -v2 <volume>                        : Second volume to compare");
    addParamsLine("  [-o <image=\"\">]                    : Output correlation image");
    addParamsLine("  [--degstep <d=5.0>]                  : Degrees step size for rot and tilt angles");
    addParamsLine("  [--thr <N=-1>]                       : Maximal number of the processing CPU threads");
    addExampleLine("xmipp_compare_density -v1 vol1.vol -v2 vol2.vol -o corr_img.xmp");
}

readParams()

void ProgCompareDensity::readParams ( )

virtual

Read arguments from command line.

Reimplemented from XmippProgram.

Definition at line 49 of file compare_density.cpp.

                                    {
    std::string aux;
    fnVol1 = getParam("-v1");
    fnVol2 = getParam("-v2");
    fnImgOut = getParam("-o");
    degstep = getDoubleParam("--degstep");

    if (fnImgOut=="")
        fnImgOut="Rot_tilt_corr_map.xmp";

    V1.read(fnVol1);
    V1().setXmippOrigin();
    V2.read(fnVol2);
    V2().setXmippOrigin();

    // Update degstep to have evenly spaced points in the interval [0,180]
    degstep = 360. / ROUND(360./degstep);
    
    int size_rot = 360./degstep;
    int size_tlt = 180./degstep;
    tilt_v.resize(size_tlt + 1);
    rot_v.resize(size_rot + 1);
    CorrImg().initZeros(size_rot + 1, size_tlt + 1);
    CorrImg().setXmippOrigin();

    std::generate(tilt_v.begin(), tilt_v.end(), [&, n = -degstep] () mutable { return n+=degstep; });
    std::generate(rot_v.begin(), rot_v.end(), [&, n = -degstep] () mutable { return n+=degstep; });

    int threads = getIntParam("--thr");
    if (0 >= threads) {
        threads = CPU::findCores();
    }
    m_threadPool.resize(threads);
}

run()

void ProgCompareDensity::run ( )

virtual

Run.

Reimplemented from XmippProgram.

Definition at line 151 of file compare_density.cpp.

                             {
    auto futures = std::vector<std::future<void>>();
    futures.reserve(V1().zdim);

    auto routine = [this](int thrId, int i) {
        computeCorrImage(i);
    };

    for (int i=0; i<rot_v.size(); i++)
    {
        futures.emplace_back(m_threadPool.push(routine, i));
    }

    for (auto &f : futures) {
        f.get();
    }

    CorrImg.write(fnImgOut);
}

show()

void ProgCompareDensity::show

(

)

Show.

Definition at line 85 of file compare_density.cpp.

                              {
    if (verbose==0)
        return;
    std::cout
            << "First volume:         " << fnVol1         << std::endl
            << "Second volume:        " << fnVol2         << std::endl
            << "Output image:         " << fnImgOut       << std::endl
            << "Degree step:          " << degstep        << std::endl
    ;

}

Member Data Documentation

CorrImg

Image<double> ProgCompareDensity::CorrImg

Definition at line 53 of file compare_density.h.

degstep

double ProgCompareDensity::degstep

Degree step.

Definition at line 49 of file compare_density.h.

fnImgOut

FileName ProgCompareDensity::fnImgOut

Output corelation image.

Definition at line 46 of file compare_density.h.

fnVol1

FileName ProgCompareDensity::fnVol1

Volumes to compare.

Definition at line 42 of file compare_density.h.

fnVol2

FileName ProgCompareDensity::fnVol2

Definition at line 43 of file compare_density.h.

rot_v

std::vector<double> ProgCompareDensity::rot_v

Definition at line 56 of file compare_density.h.

tilt_v

std::vector<double> ProgCompareDensity::tilt_v

Rot and tilt vectors.

Definition at line 56 of file compare_density.h.

V1

Image<double> ProgCompareDensity::V1

Images.

Definition at line 53 of file compare_density.h.

V2

Image<double> ProgCompareDensity::V2

Definition at line 53 of file compare_density.h.

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

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