SoftNegativeFilter Class Reference

#include <fourier_filter.h>

Inheritance diagram for SoftNegativeFilter:

Collaboration diagram for SoftNegativeFilter:

Public Member Functions
void	readParams (XmippProgram *program)
void	apply (MultidimArray< double > &img)
Public Member Functions inherited from XmippFilter
virtual	~XmippFilter ()
virtual void	show ()

Static Public Member Functions
static void	defineParams (XmippProgram *program)

Public Attributes
double	K
FileName	fnFSC
Image< int >	mask
double	Ts

Detailed Description

Definition at line 211 of file fourier_filter.h.

Member Function Documentation

apply()

void SoftNegativeFilter::apply ( MultidimArray< double > &  img )

virtual

Apply the filter to an image or volume

Implements XmippFilter.

Definition at line 879 of file fourier_filter.cpp.

{
    // Invert the mask and measure stddev outside the mask
    MultidimArray<int> &mMask=mask();
    mMask.setXmippOrigin();
    img.setXmippOrigin();
    double sum=0;
    double sum2=0;
    double N=0;
    auto R2max=(double)((XSIZE(img)/2)*(XSIZE(img)/2));
    FOR_ALL_ELEMENTS_IN_ARRAY3D(mMask)
    {
        A3D_ELEM(mMask,k,i,j)=1-A3D_ELEM(mMask,k,i,j);
        if (A3D_ELEM(mMask,k,i,j))
        {
            double R2=i*i+j*j+k*k;
            if (R2<R2max)
            {
                double val=A3D_ELEM(img,k,i,j);
                sum+=val;
                sum2+=val*val;
                N+=1;
            }
        }
    }
    double avg=sum/N;
    double stddev=sqrt(sum2/N-avg*avg);

    // Measure the stddev outside the structure
    // double avg, stddev;
    // img.computeAvgStdev_within_binary_mask(mMask,avg,stddev);

    // Find the too negative values
    double threshold=-K*stddev;
    if (avg<0)
        threshold+=avg;
    // std::cout << "avg=" << avg << " sigma=" << stddev << " threshold=" << threshold << std::endl;
    MultidimArray<double> softMask;
    MultidimArray<double> imgThresholded;
    softMask.initZeros(mMask);
    imgThresholded.initZeros(mMask);
    FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mMask)
        if (DIRECT_MULTIDIM_ELEM(img,n)>=threshold)
        {
            DIRECT_MULTIDIM_ELEM(softMask,n)=1;
            DIRECT_MULTIDIM_ELEM(imgThresholded,n)=DIRECT_MULTIDIM_ELEM(img,n);
        }
    mask.clear(); // Free memory
//  Image<double> save;
//  save()=softMask; save.write("PPPsoftmask.vol");

    FourierFilter filter;
    filter.FilterBand=filter.FilterShape=FSCPROFILE;
    filter.fnFSC=fnFSC;
    filter.sampling_rate=Ts;
    filter.generateMask(softMask);
    filter.applyMaskSpace(softMask);
    filter.applyMaskSpace(imgThresholded);
    softMask+=1;
//  save()=softMask; save.write("PPPsoftmaskFiltered.vol");
//  save()=imgThresholded; save.write("PPPthresholded.vol");

    FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(img)
    {
        DIRECT_MULTIDIM_ELEM(softMask,n)=CLIP(DIRECT_MULTIDIM_ELEM(softMask,n),0,1);
        DIRECT_MULTIDIM_ELEM(img,n)=DIRECT_MULTIDIM_ELEM(softMask,n)*DIRECT_MULTIDIM_ELEM(img,n)+
           (1-DIRECT_MULTIDIM_ELEM(softMask,n))*DIRECT_MULTIDIM_ELEM(imgThresholded,n);
    }
//  save()=softMask; save.write("PPPsoftmaskFilteredClipped.vol");
}

defineParams()

void SoftNegativeFilter::defineParams ( XmippProgram *  program )

static

Define the parameters for use inside an Xmipp program

Definition at line 861 of file fourier_filter.cpp.

{
    program->addParamsLine("== Soft negative pixels ==");
    program->addParamsLine(
        "  [ --softnegative <mask_file> <fsc> <Ts=1> <K=2>] : Removes strong negative values inside the mask");
    program->addParamsLine(" : Ts is the sampling rate in A/pix");
}

readParams()

void SoftNegativeFilter::readParams ( XmippProgram *  program )

virtual

Read from program command line

Reimplemented from XmippFilter.

Definition at line 870 of file fourier_filter.cpp.

{
    mask.read(program->getParam("--softnegative",0));
    fnFSC=program->getParam("--softnegative",1);
    Ts = program->getDoubleParam("--softnegative",2);
    K = program->getDoubleParam("--softnegative",3);
}

Member Data Documentation

fnFSC

FileName SoftNegativeFilter::fnFSC

Definition at line 215 of file fourier_filter.h.

K

double SoftNegativeFilter::K

Definition at line 214 of file fourier_filter.h.

mask

Image<int> SoftNegativeFilter::mask

Definition at line 216 of file fourier_filter.h.

Ts

double SoftNegativeFilter::Ts

Definition at line 217 of file fourier_filter.h.

---

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

• xmipp/libraries/data/fourier_filter.h
• xmipp/libraries/data/fourier_filter.cpp