ProgVolumeToWeb Class Reference

Inheritance diagram for ProgVolumeToWeb:

Collaboration diagram for ProgVolumeToWeb:

Public Member Functions
void	readParams ()
	Read parameters from command line. More...
void	defineParams ()
	define 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	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	fnVol
	Volume to convert. More...
FileName	fnCentralSlices
	Output central slices. More...
FileName	fnProjections
	Output projections. More...
int	Nslices
	Number of slices. More...
int	maxWidth
	Maximum Width. More...
int	sep
	Separation. More...
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

Definition at line 29 of file volume_to_web.cpp.

Member Function Documentation

defineParams()

void ProgVolumeToWeb::defineParams ( )

inlinevirtual

define parameters

Reimplemented from XmippProgram.

Definition at line 66 of file volume_to_web.cpp.

    {
        addUsageLine("Creates a representation for the web of the input volume");
        addParamsLine("   -i <volume>                        : Input volume");
        addParamsLine("  [--central_slices <imgFile> <n=-1>] : Output central slices (normally jpg); n=-1 for all slices");
        addParamsLine("  [--projections <imgFile>]           : Output projections (normally jpg)");
        addParamsLine("  [--maxWidth <w=800>]                : Maximum image width");
        addParamsLine("  [--separation <s=2>]                : Separation in pixels between slices");
        addExampleLine("xmipp_volume_to_web -i volume.vol --central_slices central_slices.jpg --projections projections.jpg");
    }

readParams()

void ProgVolumeToWeb::readParams ( )

inlinevirtual

Read parameters from command line.

Reimplemented from XmippProgram.

Definition at line 51 of file volume_to_web.cpp.

    {
        fnVol=getParam("-i");
        if (checkParam("--central_slices"))
        {
            fnCentralSlices=getParam("--central_slices");
            Nslices=getIntParam("--central_slices",1);
        }
        if (checkParam("--projections"))
            fnProjections=getParam("--projections");
        maxWidth=getIntParam("--maxWidth");
        sep=getIntParam("--separation");
    }

run()

void ProgVolumeToWeb::run ( )

inlinevirtual

Run.

Reimplemented from XmippProgram.

Definition at line 78 of file volume_to_web.cpp.

    {
        Image<double> V;
        V.read(fnVol);
        MultidimArray<double> &mV=V();

        Image<double> I;
        if (!fnCentralSlices.empty())
        {
            // Choose the starting and finishing slice
            if (Nslices==-1)
                Nslices=ZSIZE(mV);
            int kmiddle=ZSIZE(mV)/2;
            int k0=kmiddle-Nslices/2;
            int kF=k0+Nslices-1;

            // Resize the output image
            int NslicesPerRow=maxWidth/XSIZE(mV);
            if (NslicesPerRow==0)
                NslicesPerRow=1;
            else if (NslicesPerRow>Nslices)
                NslicesPerRow=Nslices;
            auto Nrows=(int)ceil(((float)Nslices)/NslicesPerRow);
            if (Nrows==0)
                Nrows=1;
            I().resizeNoCopy(Nrows*YSIZE(mV)+(Nrows-1)*sep,NslicesPerRow*XSIZE(mV)+(NslicesPerRow-1)*sep);
            I().initConstant(mV.computeMax());

            // Copy the slices into the output image
            int outI=0, outJ=0;
            for (int k=k0; k<=kF; ++k)
            {
                int outi=outI*(YSIZE(mV)+sep);
                int outj=outJ*(XSIZE(mV)+sep);
                for (size_t i=0; i<YSIZE(mV); ++i, ++outi)
                    memcpy(&IMGPIXEL(I,outi,outj),&A3D_ELEM(mV,k,i,0),XSIZE(mV)*sizeof(double));
                outJ++;
                if (outJ==NslicesPerRow)
                {
                    outJ=0;
                    outI++;
                }
            }
            I().rangeAdjust(0,255);
            I.write(fnCentralSlices);
        }
        if (fnProjections!="")
        {
            // Take projections
            MultidimArray<double> pXY, pYZ, pXZ;
            pXY.initZeros(YSIZE(mV),XSIZE(mV));
            pXZ.initZeros(ZSIZE(mV),XSIZE(mV));
            pYZ.initZeros(ZSIZE(mV),YSIZE(mV));
            double maxVal=-1e38;
            FOR_ALL_ELEMENTS_IN_ARRAY3D(mV)
            {
                double v=A3D_ELEM(mV,k,i,j);
                A2D_ELEM(pXY,i,j)+=v;
                A2D_ELEM(pXZ,k,j)+=v;
                A2D_ELEM(pYZ,k,i)+=v;
                maxVal=std::max(A2D_ELEM(pXY,i,j),maxVal);
                maxVal=std::max(A2D_ELEM(pXZ,k,j),maxVal);
                maxVal=std::max(A2D_ELEM(pYZ,k,i),maxVal);
            }

            // Now produce output image
            I().resizeNoCopy(XMIPP_MAX(YSIZE(mV),ZSIZE(mV)),2*(XSIZE(mV)+sep)+YSIZE(mV));
            I().initConstant(maxVal);
            int outi=0, outj=0;
            for (size_t i=0; i<YSIZE(pXY); ++i, ++outi)
                memcpy(&IMGPIXEL(I,outi,outj),&A2D_ELEM(pXY,i,0),XSIZE(pXY)*sizeof(double));

            outi=0;
            outj=XSIZE(mV)+sep;
            for (size_t i=0; i<YSIZE(pXZ); ++i, ++outi)
                memcpy(&IMGPIXEL(I,outi,outj),&A2D_ELEM(pXZ,i,0),XSIZE(pXZ)*sizeof(double));

            outi=0;
            outj=2*(XSIZE(mV)+sep);
            for (size_t i=0; i<YSIZE(pYZ); ++i, ++outi)
                memcpy(&IMGPIXEL(I,outi,outj),&A2D_ELEM(pYZ,i,0),XSIZE(pYZ)*sizeof(double));

            I().rangeAdjust(0,255);
            I.write(fnProjections);
        }
    }

Member Data Documentation

fnCentralSlices

FileName ProgVolumeToWeb::fnCentralSlices

Output central slices.

Definition at line 36 of file volume_to_web.cpp.

fnProjections

FileName ProgVolumeToWeb::fnProjections

Output projections.

Definition at line 39 of file volume_to_web.cpp.

fnVol

FileName ProgVolumeToWeb::fnVol

Volume to convert.

Definition at line 33 of file volume_to_web.cpp.

maxWidth

int ProgVolumeToWeb::maxWidth

Maximum Width.

Definition at line 45 of file volume_to_web.cpp.

Nslices

int ProgVolumeToWeb::Nslices

Number of slices.

Definition at line 42 of file volume_to_web.cpp.

sep

int ProgVolumeToWeb::sep

Separation.

Definition at line 48 of file volume_to_web.cpp.

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

• xmipp/libraries/reconstruction/volume_to_web.cpp