ProgTomoRemoveFluctuations Class Reference

#include <tomo_remove_fluctuations.h>

Inheritance diagram for ProgTomoRemoveFluctuations:

Collaboration diagram for ProgTomoRemoveFluctuations:

Public Member Functions
void	readParams ()
	Read parameters from command line. More...
void	defineParams ()
	Define params. More...
void	produceSideInfo ()
	Produce side info. More...
void	show () const
	Show parameters. More...
void	run ()
	Run. 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	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	fnIn
	Input images. More...
FileName	fnOut
	Rootname for the output. More...
double	maxFreq
	Cutoff frequency of the lowpass filter (<0.5) More...
MetaDataVec	SF
Image< double >	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

Parameters for the program removing the fluctuations

Definition at line 38 of file tomo_remove_fluctuations.h.

Member Function Documentation

defineParams()

void ProgTomoRemoveFluctuations::defineParams ( )

virtual

Define params.

Reimplemented from XmippProgram.

Definition at line 39 of file tomo_remove_fluctuations.cpp.

{
    addUsageLine("Remove the flickering in a tilt series. This is a phenomenon rather ");
    addUsageLine("common in X-ray microscopy. For doing so, a low-pass filter of a given ");
    addUsageLine("frequency (normalized to 0.5) is applied across the time series, i.e., a ");
    addUsageLine("line is formed with all the lines at the same position along the tilt series. ");
    addUsageLine("This time series is the filtered and put back into the tilt series. ");
    addParamsLine("  -i <file>                 : Input images (selfile or stack)");
    addParamsLine("  -o <outputStack>          : Output stack");
    addParamsLine(" [--lpf <f=0.25>]           : Low pass filter");
    addParamsLine("                            : Frequency is normalized to 0.5");
}

produceSideInfo()

void ProgTomoRemoveFluctuations::produceSideInfo

(

)

Produce side info.

Definition at line 53 of file tomo_remove_fluctuations.cpp.

{
    // Read the selfile into a volume
    SF.read(fnIn);
    size_t Zdim, dummy, Ydim, Xdim, Ndim;
    Zdim=SF.size();
    getImageSize(SF,Xdim,Ydim,dummy,Ndim);
    V().setMmap(true);
    V().initZeros(Zdim,Ydim,Xdim);
    int k=0;
    Image<double> I;
    FileName fnImg;
    for (size_t objId : SF.ids())
    {
        SF.getValue(MDL_IMAGE,fnImg,objId);
        I.read(fnImg);
        V().setSlice(k,I());
        k++;
    }
}

readParams()

void ProgTomoRemoveFluctuations::readParams ( )

virtual

Read parameters from command line.

Reimplemented from XmippProgram.

Definition at line 31 of file tomo_remove_fluctuations.cpp.

{
    fnIn  = getParam("-i");
    fnOut = getParam("-o");
    maxFreq = getDoubleParam("--lpf");
}

run()

void ProgTomoRemoveFluctuations::run ( )

virtual

Run.

Reimplemented from XmippProgram.

Definition at line 87 of file tomo_remove_fluctuations.cpp.

{
    produceSideInfo();

    // Filter each line in the series
    MultidimArray<double> &mV=V();
    int maxPixel=CEIL(ZSIZE(mV)*maxFreq);
    FourierTransformer transformer;
    if (verbose>=1)
        init_progress_bar(YSIZE(mV));
    MultidimArray<double> line;
    MultidimArray< std::complex<double> > lineFourier;
    std::complex<double> zero=0;
    line.initZeros(ZSIZE(mV));
    for (size_t i=0; i<YSIZE(mV); i++)
    {
        for (size_t j=0; j<XSIZE(mV); j++)
        {
            // Get line
            for (size_t k=0; k<ZSIZE(mV); k++)
                DIRECT_A1D_ELEM(line,k)=DIRECT_A3D_ELEM(mV,k,i,j);

            // Fourier transform
            transformer.setReal(line);
            transformer.FourierTransform();

            // Filter
            transformer.getFourierAlias(lineFourier);
            for (size_t k=maxPixel; k<XSIZE(lineFourier); k++)
                DIRECT_A1D_ELEM(lineFourier,k)=zero;

            // Inverse Fourier transform and back to the volume
            transformer.inverseFourierTransform();
            for (size_t k=0; k<ZSIZE(mV); k++)
                DIRECT_A3D_ELEM(mV,k,i,j)=DIRECT_A1D_ELEM(line,k);
        }
        if (verbose>=1)
            progress_bar(i+1);
    }
    if (verbose>=1)
        progress_bar(YSIZE(mV));

    // Write the results
    mV.setDimensions(XSIZE(mV),YSIZE(mV),1,ZSIZE(mV));
    V.write(fnOut,ALL_IMAGES,true);
}

show()

void ProgTomoRemoveFluctuations::show ( ) const

virtual

Show parameters.

Reimplemented from XmippProgram.

Definition at line 75 of file tomo_remove_fluctuations.cpp.

{
    if (verbose==0)
        return;
    std::cout << "Removing fluctuations from a tilt series\n";
    std::cout << "Input series:   " << fnIn    << std::endl
              << "Output root:    " << fnOut   << std::endl
              << "Max freq (LPF): " << maxFreq << std::endl
    ;
}

Member Data Documentation

fnIn

FileName ProgTomoRemoveFluctuations::fnIn

Input images.

Definition at line 42 of file tomo_remove_fluctuations.h.

fnOut

FileName ProgTomoRemoveFluctuations::fnOut

Rootname for the output.

Definition at line 45 of file tomo_remove_fluctuations.h.

maxFreq

double ProgTomoRemoveFluctuations::maxFreq

Cutoff frequency of the lowpass filter (<0.5)

Definition at line 48 of file tomo_remove_fluctuations.h.

SF

MetaDataVec ProgTomoRemoveFluctuations::SF

Definition at line 51 of file tomo_remove_fluctuations.h.

V

Image<double> ProgTomoRemoveFluctuations::V

Definition at line 54 of file tomo_remove_fluctuations.h.

---

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

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