ProgImageVectorize Class Reference

Inheritance diagram for ProgImageVectorize:

Collaboration diagram for ProgImageVectorize:

Public Member Functions
void	defineParams ()
void	readParams ()
void	show ()
void	run ()
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	fnIn
FileName	fnOut
Mask	mask
bool	apply_mask
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 30 of file image_vectorize.cpp.

Member Function Documentation

defineParams()

void ProgImageVectorize::defineParams ( )

inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 37 of file image_vectorize.cpp.

    {
        addUsageLine("Convert an image/volume to data and viceversa.");
        addUsageLine("Data is the file format used by KerDenSOM and other classification programs");
        addParamsLine("   -i <file> : If Image->Vector: Input Single image/volume/stack or selfile");
        addParamsLine("             : If Vector->Image: Input Vector metadata");
        addParamsLine("   -o <file> : If Image->Vector: Output vector metadata");
        addParamsLine("             : If Vector->Image: Output stack");
        mask.defineParams(this,INT_MASK,nullptr,"Extract pixel values from a mask area.");
        addExampleLine("Produce vectors from images or volumes",false);
        addExampleLine("xmipp_image_vectorize -i projections.sel -o vectors.xmd");
        addExampleLine("Produce images from vectors",false);
        addExampleLine("xmipp_image_vectorize -i vectors.xmd -o images.stk");
        addExampleLine("Produce vectors from images or volumes with a mask",false);
        addExampleLine("xmipp_image_vectorize -i projections.sel -o vectors.xmd --mask circular -16");
        addExampleLine("Produce images from vectors that were defined using a mask",false);
        addExampleLine("xmipp_image_vectorize -i vectors.xmd -o images.stk --mask circular -16");
    }

readParams()

void ProgImageVectorize::readParams ( )

inlinevirtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippProgram.

Definition at line 56 of file image_vectorize.cpp.

    {
        fnIn = getParam("-i");
        fnOut = getParam("-o");
        mask.allowed_data_types = INT_MASK;
        if ((apply_mask = checkParam("--mask")))
            mask.readParams(this);
    }

run()

void ProgImageVectorize::run ( )

inlinevirtual

This function will be start running the program. it also should be implemented by derived classes.

Reimplemented from XmippProgram.

Definition at line 76 of file image_vectorize.cpp.

    {
        StringVector blockList;
        getBlocksInMetaDataFile(fnIn, blockList);
        bool headerFound=false;
        for (size_t i=0; i<blockList.size(); i++)
            if (blockList[i]=="vectorHeader")
            {
                headerFound=true;
                break;
            }
        if (!headerFound)
        {
            // Image -> Vector
            MetaDataVec SF(fnIn);
            MetaDataVec vectorContent, vectorHeader;
            vectorHeader.setColumnFormat(false);
            Image<double> img;
            bool first=true;
            size_t order=0;
            FileName fnImg;
            float *buffer=nullptr;
            FileName fnOutRaw=formatString("%s.vec",fnOut.withoutExtension().c_str());
            std::ofstream fhOutRaw(fnOutRaw.c_str(),std::ios::binary);
            if (!fhOutRaw)
                REPORT_ERROR(ERR_IO_NOWRITE,fnOutRaw);
            size_t vectorSize;

            for (auto& row : SF)
            {
                img.readApplyGeo(SF, row.id());

                // Create header
                if (first)
                {
                    if (apply_mask)
                    {
                        mask.generate_mask(ZSIZE(img()),YSIZE(img()),XSIZE(img()));
                        // Make sure that the mask is between 0 and 1
                        MultidimArray<int> &imask=mask.get_binary_mask();
                        FOR_ALL_ELEMENTS_IN_ARRAY2D(imask)
                            A2D_ELEM(imask,i,j)=(A2D_ELEM(imask,i,j)!=0)?1:0;
                        vectorSize=(int)imask.sum();
                    }
                    else
                        vectorSize=MULTIDIM_SIZE(img());
                    size_t outId=vectorHeader.addObject();
                    vectorHeader.setValue(MDL_XSIZE,XSIZE(img()),outId);
                    vectorHeader.setValue(MDL_YSIZE,YSIZE(img()),outId);
                    vectorHeader.setValue(MDL_ZSIZE,ZSIZE(img()),outId);
                    vectorHeader.setValue(MDL_COUNT,SF.size(),outId);
                    vectorHeader.setValue(MDL_CLASSIFICATION_DATA_SIZE,vectorSize,outId);
                    vectorHeader.write(formatString("vectorHeader@%s",fnOut.c_str()));
                    buffer=new float[vectorSize];
                    first=false;
                }

                // Save this image in the output metadata
                row.setValue(MDL_ORDER, order++);
                vectorContent.addRow(dynamic_cast<const MDRowVec&>(row));

                // Save raw values
                const MultidimArray<double> &mimg=img();
                const MultidimArray<int> &mmask=mask.get_binary_mask();
                int ii=0;
                if (apply_mask)
                {
                    FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mimg)
                    if (DIRECT_MULTIDIM_ELEM(mmask,n))
                        buffer[ii++]=(float)DIRECT_MULTIDIM_ELEM(mimg,n);
                }
                else
                {
                    FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mimg)
                    buffer[ii++]=(float)DIRECT_MULTIDIM_ELEM(mimg,n);
                }
                fhOutRaw.write((char*)buffer,vectorSize*sizeof(float));
            }
            fhOutRaw.close();
            vectorContent.write(formatString("vectorContent@%s",fnOut.c_str()),MD_APPEND);
            delete []buffer;
        }
        else
        {
            // Vector -> Image
            fnOut.deleteFile();

            MetaDataVec vectorHeader(formatString("vectorHeader@%s",fnIn.c_str()));
            MetaDataVec vectorContent(formatString("vectorContent@%s",fnIn.c_str()));

            // Read header
            size_t headerId=vectorHeader.firstRowId();
            size_t Xdim, Ydim, Zdim, vectorSize, imgNo;
            vectorHeader.getValue(MDL_XSIZE,Xdim,headerId);
            vectorHeader.getValue(MDL_YSIZE,Ydim,headerId);
            vectorHeader.getValue(MDL_ZSIZE,Zdim,headerId);
            vectorHeader.getValue(MDL_COUNT,imgNo,headerId);
            vectorHeader.getValue(MDL_CLASSIFICATION_DATA_SIZE,vectorSize,headerId);
            if (apply_mask)
                mask.generate_mask(Zdim,Ydim,Xdim);
            const MultidimArray<int> &mmask=mask.get_binary_mask();

            // Process all images
            Image<double> img;
            img().resizeNoCopy(Zdim,Ydim,Xdim);
            const MultidimArray<double> &mimg=img();
            FileName fnImg, fnIdx;
            auto *buffer=new float[vectorSize];
            FileName fnInRaw=formatString("%s.vec",fnIn.withoutExtension().c_str());
            std::ifstream fhInRaw(fnInRaw.c_str(),std::ios::binary);
            if (!fhInRaw)
                REPORT_ERROR(ERR_IO_NOTEXIST,fnInRaw);
            size_t order;
            size_t idx=1;

            for (size_t objId : vectorContent.ids())
            {
                vectorContent.getValue(MDL_IMAGE, fnImg, objId);
                vectorContent.getValue(MDL_ORDER, order, objId);

                // Read raw values
                fhInRaw.seekg(order*vectorSize*sizeof(float));
                fhInRaw.read((char*)buffer,vectorSize*sizeof(float));
                if (!fhInRaw)
                    REPORT_ERROR(ERR_IO_NOREAD,
                                 formatString("Could not read image %lu from %s",
                                              order,fnInRaw.c_str()));
                int ii=0;
                if (apply_mask)
                {
                    FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mimg)
                    if (DIRECT_MULTIDIM_ELEM(mmask,n))
                        DIRECT_MULTIDIM_ELEM(mimg,n)=buffer[ii++];
                }
                else
                {
                    FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mimg)
                    DIRECT_MULTIDIM_ELEM(mimg,n)=buffer[ii++];
                }

                // Write image
                fnIdx.compose(idx++,fnOut);
                img.write(fnIdx);
            }
            fhInRaw.close();
            delete []buffer;
        }
    }

show()

void ProgImageVectorize::show ( )

inline

Definition at line 65 of file image_vectorize.cpp.

    {
        if (verbose==0)
            return;
        std::cout
        << "Input:   " << fnIn    << std::endl
        << "Output:  " << fnOut << std::endl
        ;
    }

Member Data Documentation

apply_mask

bool ProgImageVectorize::apply_mask

Definition at line 36 of file image_vectorize.cpp.

fnIn

FileName ProgImageVectorize::fnIn

Definition at line 33 of file image_vectorize.cpp.

fnOut

FileName ProgImageVectorize::fnOut

Definition at line 34 of file image_vectorize.cpp.

mask

Mask ProgImageVectorize::mask

Definition at line 35 of file image_vectorize.cpp.

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

• xmipp/libraries/reconstruction/image_vectorize.cpp