Estimate the SSNR

Collaboration diagram for Estimate the SSNR:

Classes
class	ProgImageSSNR

Functions
void	ProgImageSSNR::defineParams ()
void	ProgImageSSNR::readParams ()
void	ProgImageSSNR::preProcess ()
void	ProgImageSSNR::processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut)
void	ProgImageSSNR::postProcess ()

Variables
double	ProgImageSSNR::R
double	ProgImageSSNR::Rwidth
double	ProgImageSSNR::fmin
double	ProgImageSSNR::fmax
double	ProgImageSSNR::sampling
double	ProgImageSSNR::ssnrcut
double	ProgImageSSNR::ssnrpercent
bool	ProgImageSSNR::normalizessnr
Image< double >	ProgImageSSNR::img
Image< double >	ProgImageSSNR::imgS
Image< double >	ProgImageSSNR::imgN
MultidimArray< double >	ProgImageSSNR::maskS
MultidimArray< double >	ProgImageSSNR::maskN
MultidimArray< double >	ProgImageSSNR::spectrumS
MultidimArray< double >	ProgImageSSNR::spectrumN
size_t	ProgImageSSNR::imin
size_t	ProgImageSSNR::imax

Detailed Description

Function Documentation

defineParams()

void ProgImageSSNR::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgImageSSNR >.

Definition at line 32 of file program_image_ssnr.cpp.

{
    produces_a_metadata = true;
    each_image_produces_an_output = false;
    keep_input_columns = true;
    remove_disabled = false;
    addUsageLine("Analyze image SSNR. For doing so, we estimate the SSNR of each particle defining as signal "\
                 "the part of the image within a certain radius, and as noise the part of the image outside.");
    XmippMetadataProgram::defineParams();
    addParamsLine(" [-R <r=-1>]: Particle radius, by default, half size of the image");
    addParamsLine(" [--Rwidth <r=3>]: Transition radius the mask is 1 till R-Rwidth, and zero from R+Rwidth");
    addParamsLine(" [--fmin <f=40>]: Minimum frequency (in Angstroms) to measure");
    addParamsLine(" [--fmax <f=3>]:  Maximum frequency (in Angstroms) to measure");
    addParamsLine(" [--sampling <Ts=1>]:  Sampling rate in Angstroms/pixel");
    addParamsLine(" [--ssnrcut <ssnr=-1>]:  Disable images whose SSNR is below this value");
    addParamsLine(" [--ssnrpercent <p=-1>]:  Disable images whose SSNR is below this percentage");
    addParamsLine(" [--normalizessnr]: Normalize the SSNR by dividing by the maximum SSNR");
    addExampleLine("xmipp_image_ssnr -i images.xmd -o imagesOut.xmd ");
}

postProcess()

void ProgImageSSNR::postProcess ( )

virtual

Reimplemented from XmippMetadataProgram.

Definition at line 153 of file program_image_ssnr.cpp.

{
    if (ssnrcut>0)
        thresholdSSNR(getOutputMd(), ssnrcut);

    if (ssnrpercent>0)
    {
        std::vector<double> ssnr;
        getOutputMd().getColumnValues(MDL_CUMULATIVE_SSNR,ssnr);
        std::sort(ssnr.begin(),ssnr.end());
        auto idx=(size_t)(ssnrpercent/100.0*ssnr.size());
        thresholdSSNR(getOutputMd(),ssnr[idx]);
    }

    if (normalizessnr)
        normalizeSSNR(getOutputMd());
    if (fn_out!="")
        getOutputMd().write(fn_out);
    else
        getOutputMd().write(fn_in);
}

preProcess()

void ProgImageSSNR::preProcess ( )

virtual

Reimplemented from XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgImageSSNR >.

Definition at line 65 of file program_image_ssnr.cpp.

{
    size_t Xdim, Ydim, Zdim, Ndim;
    getImageSize(*getInputMd(), Xdim, Ydim, Zdim, Ndim);
    maskS.initZeros(Ydim,Xdim);
    maskS.setXmippOrigin();

    if (R==-1)
        R=0.5*Xdim-Rwidth;
    RaisedCosineMask(maskS,R-Rwidth,R+Rwidth);
    maskN=1-maskS;

    imin=(size_t)std::max(3.0,0.5*Xdim*(sampling/fmin));
    imax=(size_t)std::min(Xdim-3.0,0.5*Xdim*(sampling/fmax));
}

processImage()

void ProgImageSSNR::processImage ( const FileName &  fnImg, const FileName &  fnImgOut, const MDRow &  rowIn, MDRow &  rowOut  )

virtual

Implements XmippMetadataProgram.

Definition at line 81 of file program_image_ssnr.cpp.

{
    // Copy Enabled
    int enabled;
    rowIn.getValue(MDL_ENABLED,enabled);
    rowOut.setValue(MDL_ENABLED,enabled);

    img.read(fnImg);
    img().setXmippOrigin();

    imgN()=imgS()=img();
    imgS()*=maskS;
    imgN()*=maskN;

    getSpectrum(imgS(),spectrumS,POWER_SPECTRUM);
    getSpectrum(imgN(),spectrumN,POWER_SPECTRUM);

    double SSNR=0;
    FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY1D(spectrumS)
    {
        if (i>=imin && i<=imax)
        {
            double S=DIRECT_A1D_ELEM(spectrumS,i);
            double N=DIRECT_A1D_ELEM(spectrumN,i);
            if (S>0 && N>0)
            SSNR+=log10(S)-log10(N);
        }
    }
    SSNR*=10.0/(imax-imin+1); // decibels
    rowOut.setValue(MDL_CUMULATIVE_SSNR,SSNR);

    //spectrumS.write("PPPS.txt");
    //spectrumN.write("PPPN.txt");
    //std::cout << fnImg << " SSNR=" << SSNR << std::endl;
    //std::cout << "Press any key\n";
    // char c; std::cin>> c;
}

readParams()

void ProgImageSSNR::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 XmippMetadataProgram.

Reimplemented in BasicMpiMetadataProgram< ProgImageSSNR >.

Definition at line 52 of file program_image_ssnr.cpp.

{
    XmippMetadataProgram::readParams();
    R=getDoubleParam("-R");
    Rwidth=getDoubleParam("--Rwidth");
    fmin=getDoubleParam("--fmin");
    fmax=getDoubleParam("--fmax");
    sampling=getDoubleParam("--sampling");
    ssnrcut=getDoubleParam("--ssnrcut");
    ssnrpercent=getDoubleParam("--ssnrpercent");
    normalizessnr=checkParam("--normalizessnr");
}

Variable Documentation

fmax

double ProgImageSSNR::fmax

Definition at line 37 of file program_image_ssnr.h.

fmin

double ProgImageSSNR::fmin

Definition at line 37 of file program_image_ssnr.h.

imax

size_t ProgImageSSNR::imax

Definition at line 50 of file program_image_ssnr.h.

img

Image<double> ProgImageSSNR::img

Definition at line 48 of file program_image_ssnr.h.

imgN

Image<double> ProgImageSSNR::imgN

Definition at line 48 of file program_image_ssnr.h.

imgS

Image<double> ProgImageSSNR::imgS

Definition at line 48 of file program_image_ssnr.h.

imin

size_t ProgImageSSNR::imin

Definition at line 50 of file program_image_ssnr.h.

maskN

MultidimArray<double> ProgImageSSNR::maskN

Definition at line 49 of file program_image_ssnr.h.

maskS

MultidimArray<double> ProgImageSSNR::maskS

Definition at line 49 of file program_image_ssnr.h.

normalizessnr

bool ProgImageSSNR::normalizessnr

Definition at line 40 of file program_image_ssnr.h.

R

double ProgImageSSNR::R

Definition at line 36 of file program_image_ssnr.h.

Rwidth

double ProgImageSSNR::Rwidth

Definition at line 36 of file program_image_ssnr.h.

sampling

double ProgImageSSNR::sampling

Definition at line 38 of file program_image_ssnr.h.

spectrumN

MultidimArray<double> ProgImageSSNR::spectrumN

Definition at line 49 of file program_image_ssnr.h.

spectrumS

MultidimArray<double> ProgImageSSNR::spectrumS

Definition at line 49 of file program_image_ssnr.h.

ssnrcut

double ProgImageSSNR::ssnrcut

Definition at line 39 of file program_image_ssnr.h.

ssnrpercent

double ProgImageSSNR::ssnrpercent

Definition at line 39 of file program_image_ssnr.h.