ImageGeneric Class Reference

#include <xmipp_image_generic.h>

Collaboration diagram for ImageGeneric:

Public Member Functions
	ImageGeneric ()
	ImageGeneric (DataType _datatype)
	ImageGeneric (const FileName &filename)
	ImageGeneric (const ImageGeneric &img)
	~ImageGeneric ()
void	init ()
void	clear ()
void	copy (const ImageGeneric &img)
void	clearHeader ()
void	initGeometry (const size_t n=0)
MDRow &	getGeometry (const size_t n=0)
void	getDimensions (size_t &Xdim, size_t &Ydim, size_t &Zdim, size_t &Ndim) const
void	getDimensions (size_t &Xdim, size_t &Ydim, size_t &Zdim) const
void	getDimensions (ArrayDim &aDim) const
size_t	getSize () const
void	getEulerAngles (double &rot, double &tilt, double &psi, size_t n=0)
double	tilt (const size_t n=0) const
void	resize (int Xdim, int Ydim, int Zdim, size_t Ndim, bool copy=true)
void	setDatatype (DataType _datatype)
void	setDatatype (const FileName &name, ImageInfo &imgInf)
void	setDatatype (const FileName &name)
void	setDataMode (DataMode mode)
DataType	getDatatype () const
void	getInfo (ImageInfo &imgInfo) const
int	getDatatypeDepth () const
bool	isMapped ()
int	read (const FileName &name, DataMode datamode=DATA, size_t select_img=ALL_IMAGES, bool mapData=false)
int	readApplyGeo (const FileName &name, const MDRow &row, const ApplyGeoParams &params=DefaultApplyGeoParams)
int	readApplyGeo (const FileName &name, const MetaData &md, size_t objId, const ApplyGeoParams &params=DefaultApplyGeoParams)
int	readApplyGeo (const MetaData &md, size_t objId, const ApplyGeoParams &params=DefaultApplyGeoParams)
void	applyGeo (const MetaData &md, size_t objId, const ApplyGeoParams &params=DefaultApplyGeoParams)
void	mirrorY (void)
int	readMapped (const FileName &name, size_t select_img=ALL_IMAGES, int mode=WRITE_READONLY)
int	readOrReadMapped (const FileName &name, size_t select_img=ALL_IMAGES, int mode=WRITE_READONLY)
int	readPreview (const FileName &name, size_t Xdim, size_t Ydim=0, int select_slice=CENTRAL_SLICE, size_t select_img=FIRST_IMAGE)
int	readOrReadPreview (const FileName &name, size_t Xdim, size_t Ydim=0, int select_slice=CENTRAL_SLICE, size_t select_img=FIRST_IMAGE, bool mapData=false, bool wrap=true)
void	getPreview (ImageGeneric &imgOut, int Xdim, int Ydim=-1, int select_slice=CENTRAL_SLICE, size_t select_img=FIRST_IMAGE)
int	readPreviewFourier (const FileName &name, size_t Xdim, size_t Ydim=0, int select_slice=CENTRAL_SLICE, size_t select_img=FIRST_IMAGE)
int	readPreviewSmooth (const FileName &name, size_t Xdim, size_t Ydim=0, int select_slice=CENTRAL_SLICE, size_t select_img=FIRST_IMAGE)
void	write (const FileName &name="", size_t select_img=ALL_IMAGES, bool isStack=false, int mode=WRITE_OVERWRITE, CastWriteMode castMode=CW_CAST, int _swapWrite=0)
void	mapFile2Write (int Xdim, int Ydim, int Zdim, const FileName &_filename, bool createTempFile=false, size_t select_img=APPEND_IMAGE, bool isStack=false, int mode=WRITE_OVERWRITE, int _swapWrite=0)
void	movePointerTo (int select_slice=ALL_SLICES, size_t select_img=ALL_IMAGES)
MultidimArrayGeneric &	operator() ()
const MultidimArrayGeneric &	operator() () const
ImageGeneric &	operator= (const ImageGeneric &img)
bool	operator== (const ImageGeneric &i1) const
void	convert2Datatype (DataType datatype, CastWriteMode castMode=CW_CONVERT)
void	reslice (AxisView view)
void	reslice (AxisView view, ImageGeneric &out)
bool	equal (const ImageGeneric &i1, double accuracy=XMIPP_EQUAL_ACCURACY) const
double	getPixel (unsigned long n, int k, int i, int j) const
double	getPixel (int i, int j) const
void	setPixel (unsigned long n, int k, int i, int j, double value) const
void	setPixel (int i, int j, double value) const
void	initConstant (double value) const
void	initRandom (double op1, double op2, RandomMode mode=RND_UNIFORM) const
void	print () const
void	toString (String &s) const
void	add (const ImageGeneric &img)
void	subtract (const ImageGeneric &img)
void	multiply (const double value)
void	multiply (const ImageGeneric &img)
void	divide (const ImageGeneric &img)
void	divide (const double value)

Public Attributes
ImageBase *	image
DataType	datatype
MultidimArrayGeneric *	data

Protected Attributes
bool	swap

Friends
std::ostream &	operator<< (std::ostream &o, const ImageGeneric &I)

Detailed Description

ImageGeneric class to handle images with independence of data type

Definition at line 47 of file xmipp_image_generic.h.

Constructor & Destructor Documentation

ImageGeneric() [1/4]

ImageGeneric::ImageGeneric ( )

inline

Empty constructor.

No internal image class is declared.

Definition at line 65 of file xmipp_image_generic.h.

    {
        init();
    }

ImageGeneric() [2/4]

ImageGeneric::ImageGeneric

(

DataType

_datatype

)

Constructor passing the data type of the image.

Defines the data type of the image and then declares the internal image class.

Definition at line 41 of file xmipp_image_generic.cpp.

{
    init();
    setDatatype(_datatype);
}

ImageGeneric() [3/4]

ImageGeneric::ImageGeneric

(

const FileName &

filename

)

Constructor for reading the image

This constructor will be useful for perfom construction and read in a single step.

Definition at line 47 of file xmipp_image_generic.cpp.

{
    init();
    read(filename);
}

ImageGeneric() [4/4]

ImageGeneric::ImageGeneric

(

const ImageGeneric &

img

)

Copy Constructor

Definition at line 53 of file xmipp_image_generic.cpp.

{
    init();
    copy(img);
}

~ImageGeneric()

ImageGeneric::~ImageGeneric

(

)

Destructor.

Definition at line 59 of file xmipp_image_generic.cpp.

{
    delete image;
    delete data;
}

Member Function Documentation

add()

void ImageGeneric::add

(

const ImageGeneric &

img

)

Addition of the passed image to the internal's

Definition at line 543 of file xmipp_image_generic.cpp.

{
    if (datatype != img.datatype)
        REPORT_ERROR(ERR_TYPE_INCORRECT, "Images have different datatypes");

#define ADD(type) MultidimArray<type> & kk = *((MultidimArray<type>*) data->im);\
                     MultidimArray<type> & pp = *((MultidimArray<type>*) img.data->im);\
                     kk += pp;

    SWITCHDATATYPE(datatype, ADD);
#undef ADD

}

applyGeo()

void ImageGeneric::applyGeo	(	const MetaData &	md,
		size_t	objId,
		const ApplyGeoParams &	params = DefaultApplyGeoParams
	)

Apply geometry in referring metadata to the image

Definition at line 407 of file xmipp_image_generic.cpp.

{
    image->applyGeo(md, objId, params);
}

clear()

void ImageGeneric::clear

(

)

Clear the parameters and initialize them.

Definition at line 72 of file xmipp_image_generic.cpp.

{
    if (image != NULL)
    {
        image->clear();
        delete image;
        delete data;
        init();
    }
}

clearHeader()

void ImageGeneric::clearHeader ( )

inline

Clear the image header

Definition at line 101 of file xmipp_image_generic.h.

    {
        image->clearHeader();
    }

convert2Datatype()

void ImageGeneric::convert2Datatype	(	DataType	datatype,
		CastWriteMode	castMode = CW_CONVERT
	)

Convert the datatype of the object and cast the image

Definition at line 414 of file xmipp_image_generic.cpp.

{
    if (_datatype == datatype || _datatype == DT_Unknown)
        return;

    ArrayDim aDim;
    data->getDimensions(aDim);

    ImageBase * newImage;
    MultidimArrayGeneric * newMAG;

#define CONVERTTYPE(type) Image<type> *imT = new Image<type>; \
        newImage = imT;\
        newMAG = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), _datatype);\
        MultidimArray<type>* pMAG;\
        newMAG->getMultidimArrayPointer(pMAG);\
        if (castMode == CW_CAST)\
         data->getImage(*pMAG);\
        else\
        {\
         pMAG->resize(aDim);\
         double min, max;\
         data->computeDoubleMinMax(min, max);\
         ((Image<double>*) image)->getCastConvertPageFromT(0, (char*)pMAG->data, _datatype, aDim.nzyxdim, min, max, castMode);\
        }\

    SWITCHDATATYPE(_datatype, CONVERTTYPE)

#undef CONVERTTYPE

    /* aDimFile must be set in order to movePointerTo can be used.
     * If movePointerTo has been used before convert2Datatype, then
     * only the pointed image/slice is converted, and the images/slices left
     * are lost. This is why we set the new dimensions to the new ImageGeneric Object*/
    newImage->setADimFile(aDim);

    clear();
    datatype = _datatype;
    image = newImage;
    data = newMAG;
}

copy()

void ImageGeneric::copy

(

const ImageGeneric &

img

)

Copy data from other ImageGeneric

Definition at line 83 of file xmipp_image_generic.cpp.

{
    if (img.datatype != DT_Unknown)
    {
        setDatatype(img.datatype);
#define COPY(type) (*(Image<type>*)image) = (*(Image<type>*)img.image);

        SWITCHDATATYPE(datatype, COPY);
#undef COPY

    }

}

divide() [1/2]

void ImageGeneric::divide

(

const ImageGeneric &

img

)

Division of the internal image by another image

Definition at line 594 of file xmipp_image_generic.cpp.

{

#define DIVIDEIMG(type) MultidimArray<type> & kk = *((MultidimArray<type>*) data->im);\
                     MultidimArray<type> & pp = *((MultidimArray<type>*) img.data->im);\
                     kk /= pp;

    SWITCHDATATYPE(datatype, DIVIDEIMG);
#undef DIVIDEIMG

}

divide() [2/2]

void ImageGeneric::divide

(

const double

value

)

Division if the internal image by a constant

Definition at line 606 of file xmipp_image_generic.cpp.

{

#define DIVIDE(type) MultidimArray<type> & kk = *((MultidimArray<type>*) data->im);\
                     kk /= value;

    SWITCHDATATYPE(datatype, DIVIDE);
#undef DIVIDE

}

equal()

bool ImageGeneric::equal ( const ImageGeneric &  i1, double  accuracy = XMIPP_EQUAL_ACCURACY  ) const

inline

equal for doubles

Definition at line 354 of file xmipp_image_generic.h.

    {
        return data->equal(MULTIDIM_ARRAY_GENERIC(i1),accuracy);
    }

getDatatype()

DataType ImageGeneric::getDatatype ( ) const

inline

Get the data type

Definition at line 170 of file xmipp_image_generic.h.

    {
        return datatype;
    }

getDatatypeDepth()

int ImageGeneric::getDatatypeDepth ( ) const

inline

Get the data type

Definition at line 181 of file xmipp_image_generic.h.

    {
        switch (datatype)
        {
        case DT_Float:
        case DT_UInt:
            return 32;
        case DT_Int:
            return 31;
        case DT_Short:
            return 15;
        case DT_UShort:
        case DT_HalfFloat:
            return 16;
        case DT_SChar:
            return 7;
        case DT_UHalfByte:
        case DT_UChar:
            return 8;
        default:
            REPORT_ERROR(ERR_TYPE_INCORRECT,"Do not know how to handle this type at this point");
        }
    }

getDimensions() [1/3]

void ImageGeneric::getDimensions	(	size_t &	Xdim,
		size_t &	Ydim,
		size_t &	Zdim,
		size_t &	Ndim
	)		const

Get Image dimensions

Definition at line 103 of file xmipp_image_generic.cpp.

{
    image->getDimensions(xdim, ydim, Zdim, Ndim);
}

getDimensions() [2/3]

void ImageGeneric::getDimensions	(	size_t &	Xdim,
		size_t &	Ydim,
		size_t &	Zdim
	)		const

Definition at line 97 of file xmipp_image_generic.cpp.

{
    size_t Ndim;
    image->getDimensions(xdim, ydim, Zdim, Ndim);
}

getDimensions() [3/3]

void ImageGeneric::getDimensions

(

ArrayDim &

aDim

)

const

Definition at line 108 of file xmipp_image_generic.cpp.

{
    image->getDimensions(aDim);
}

getEulerAngles()

void ImageGeneric::getEulerAngles ( double &  rot, double &  tilt, double &  psi, size_t  n = 0  )

inline

Get Euler angles from image header

Definition at line 131 of file xmipp_image_generic.h.

    {
        image->getEulerAngles(rot, tilt, psi, n);
    }

getGeometry()

MDRow& ImageGeneric::getGeometry ( const size_t  n = 0 )

inline

Return geometry row

Definition at line 111 of file xmipp_image_generic.h.

    {
        return *(image->MD[n]);
    }

getInfo()

void ImageGeneric::getInfo

(

ImageInfo &

imgInfo

)

const

Get basic information from already read image file

Definition at line 113 of file xmipp_image_generic.cpp.

{
    image->getInfo(imgInfo);
}

getPixel() [1/2]

double ImageGeneric::getPixel ( unsigned long  n, int  k, int  i, int  j  ) const

inline

Get pixel value

Definition at line 360 of file xmipp_image_generic.h.

    {
        double ret;
#define GETVALUE(type) ret = NZYX_ELEM(*(MultidimArray<type>*)data->im,n,k,i,j);
        SWITCHDATATYPE(datatype,GETVALUE)
#undef GETVALUE
        return ret;
    }

getPixel() [2/2]

double ImageGeneric::getPixel ( int  i, int  j  ) const

inline

Get pixel value

Definition at line 371 of file xmipp_image_generic.h.

    {
        double ret;
#define GETVALUE(type) ret = (double) A2D_ELEM(*(MultidimArray<type>*)data->im,i,j);
        SWITCHDATATYPE(datatype,GETVALUE)
#undef GETVALUE
        return ret;
    }

getPreview()

void ImageGeneric::getPreview	(	ImageGeneric &	imgOut,
		int	Xdim,
		int	Ydim = -1,
		int	select_slice = CENTRAL_SLICE,
		size_t	select_img = FIRST_IMAGE
	)

Returns an image with a lower resolution as a preview image. If Zdim parameter is not passed, then all slices are rescaled. If Ydim is not passed, then Ydim is rescaled same factor as Xdim.

Definition at line 303 of file xmipp_image_generic.cpp.

{
    imgOut.setDatatype(getDatatype());
    image->getPreview(imgOut.image, xdim, ydim, select_slice, select_img);
}

getSize()

size_t ImageGeneric::getSize ( ) const

inline

Get number of elements in image

Definition at line 124 of file xmipp_image_generic.h.

    {
        return NZYXSIZE(*(data->im));
    }

init()

void ImageGeneric::init

(

void

)

Initialize the parameters.

Definition at line 65 of file xmipp_image_generic.cpp.

{
    image = NULL;
    data = NULL;
    datatype = DT_Unknown;
}

initConstant()

void ImageGeneric::initConstant ( double  value ) const

inline

Init constant

Definition at line 403 of file xmipp_image_generic.h.

    {
#define INITCONS(type) (*(MultidimArray<type>*)(data->im)).initConstant((type) value);
        CHECK_IMG(SWITCHDATATYPE(datatype,INITCONS))
#undef INITCONS

    }

initGeometry()

void ImageGeneric::initGeometry

(

const size_t

n = 0

)

Init geometry transformation with defaults values

Definition at line 36 of file xmipp_image_generic.cpp.

{
    MDL::emptifyHeader(*(image->MD[n]));
}

initRandom()

void ImageGeneric::initRandom ( double  op1, double  op2, RandomMode  mode = RND_UNIFORM  ) const

inline

Init random

Definition at line 413 of file xmipp_image_generic.h.

    {
#define INITRND(type) (*(MultidimArray<type>*)(data->im)).initRandom(op1, op2, mode);
        CHECK_IMG(SWITCHDATATYPE(datatype,INITRND))
#undef INITRND

    }

isMapped()

bool ImageGeneric::isMapped ( )

inline

Check if image is mapped on file

Definition at line 207 of file xmipp_image_generic.h.

    {
        return image->isMapped();
    }

mapFile2Write()

void ImageGeneric::mapFile2Write	(	int	Xdim,
		int	Ydim,
		int	Zdim,
		const FileName &	_filename,
		bool	createTempFile = false,
		size_t	select_img = APPEND_IMAGE,
		bool	isStack = false,
		int	mode = WRITE_OVERWRITE,
		int	_swapWrite = 0
	)

Definition at line 360 of file xmipp_image_generic.cpp.

{
    image->setDataMode(HEADER); // Use this to ask rw* which datatype to use
    if (swapWrite > 0)
        image->swapOnWrite();
    image->mapFile2Write(xdim,ydim,Zdim,_filename,createTempFile, select_img, isStack, mode);

    DataType writeDT = image->datatype();

    if ( writeDT != datatype)
    {
        setDatatype(writeDT);

        image->mapFile2Write(xdim,ydim,Zdim,_filename,createTempFile, select_img, isStack, mode);
    }
}

mirrorY()

void ImageGeneric::mirrorY

(

void

)

Definition at line 392 of file xmipp_image_generic.cpp.

{
    return image->mirrorY();
}

movePointerTo()

void ImageGeneric::movePointerTo ( int  select_slice = ALL_SLICES, size_t  select_img = ALL_IMAGES  )

inline

It changes the behavior of the internal multidimarray so it points to a specific slice/image from a stack, volume or stack of volumes. No information is deallocated from memory, so it is also possible to repoint to the whole stack,volume... (passing select_slice = ALL_SLICES and selec_img = ALL_IMAGES).

The options for select_slice are:

• a slice number,
• CENTRAL_SLICE, to automatically select the central slice of the volume,
• ALL_SLICES, to recover the whole volume.

The options for selec_img are:

• a image number of the stack,
• ALL_IMAGES, to recover the whole stack.

If a specific slice number is selected, then a specific image from the stack must be also selected. Otherwise, FIRST_IMAGE is proposed.

If Image Object is read using readPreview method, movePointerTo only works when rescaling the image in X-Y plane only, but all slices must be read.

Definition at line 312 of file xmipp_image_generic.h.

    {
        image->movePointerTo(select_slice, select_img);
    }

multiply() [1/2]

void ImageGeneric::multiply

(

const double

value

)

Multiplication of the internal image by a constant

Definition at line 583 of file xmipp_image_generic.cpp.

{

#define MULTIPLY(type) MultidimArray<type> & kk = *((MultidimArray<type>*) data->im);\
                     kk *= value;

    SWITCHDATATYPE(datatype, MULTIPLY);
#undef MULTIPLY

}

multiply() [2/2]

void ImageGeneric::multiply

(

const ImageGeneric &

img

)

Multiplication of the internal image by another image

Definition at line 571 of file xmipp_image_generic.cpp.

{

#define MULTIPLYIMG(type) MultidimArray<type> & kk = *((MultidimArray<type>*) data->im);\
                     MultidimArray<type> & pp = *((MultidimArray<type>*) img.data->im);\
                     kk *= pp;

    SWITCHDATATYPE(datatype, MULTIPLYIMG);
#undef MULTIPLYIMG

}

operator()() [1/2]

MultidimArrayGeneric& ImageGeneric::operator() ( )

inline

Definition at line 320 of file xmipp_image_generic.h.

    {
        return *data;
    }

operator()() [2/2]

const MultidimArrayGeneric& ImageGeneric::operator() ( ) const

inline

Definition at line 325 of file xmipp_image_generic.h.

    {
        return *data;
    }

operator=()

ImageGeneric & ImageGeneric::operator=

(

const ImageGeneric &

img

)

assign operator

Definition at line 515 of file xmipp_image_generic.cpp.

{
    copy(img);
    return *this;
}

operator==()

bool ImageGeneric::operator==

(

const ImageGeneric &

i1

)

const

equal operator

Definition at line 521 of file xmipp_image_generic.cpp.

{
    return(*(this->data) == *(i1.data));
}

print()

void ImageGeneric::print

(

)

const

Print image information

Definition at line 526 of file xmipp_image_generic.cpp.

{
    String s;
    toString(s);
    std::cout << s <<std::endl;
}

read()

int ImageGeneric::read	(	const FileName &	name,
		DataMode	datamode = DATA,
		size_t	select_img = ALL_IMAGES,
		bool	mapData = false
	)

Read image from file.

Definition at line 229 of file xmipp_image_generic.cpp.

{
    SET_DATATYPE(name);
    return image->read(name, datamode, select_img, mapData && !imgInf.swap);
}

readApplyGeo() [1/3]

int ImageGeneric::readApplyGeo	(	const FileName &	name,
		const MDRow &	row,
		const ApplyGeoParams &	params = DefaultApplyGeoParams
	)

Read image from file with a header applied.

Definition at line 378 of file xmipp_image_generic.cpp.

{
    setDatatype(name);
    return image->readApplyGeo(name, row, params);
}

readApplyGeo() [2/3]

int ImageGeneric::readApplyGeo	(	const FileName &	name,
		const MetaData &	md,
		size_t	objId,
		const ApplyGeoParams &	params = DefaultApplyGeoParams
	)

Read image from file.

Definition at line 385 of file xmipp_image_generic.cpp.

{
    setDatatype(name);
    return image->readApplyGeo(name, md, objId, params);
}

readApplyGeo() [3/3]

int ImageGeneric::readApplyGeo	(	const MetaData &	md,
		size_t	objId,
		const ApplyGeoParams &	params = DefaultApplyGeoParams
	)

Read an image from metadata, filename is taken from MDL_IMAGE

Definition at line 397 of file xmipp_image_generic.cpp.

{
    FileName name;
    md.getValue(MDL_IMAGE, name, objId/*md.firstObject()*/);
    setDatatype(name);
    return image->readApplyGeo(name, md, objId, params);
}

readMapped()

int ImageGeneric::readMapped	(	const FileName &	name,
		size_t	select_img = ALL_IMAGES,
		int	mode = WRITE_READONLY
	)

Read image mapped from file.

Definition at line 236 of file xmipp_image_generic.cpp.

{
    SET_DATATYPE(name);
    return image->read(name, DATA, select_img, !imgInf.swap, mode);
}

readOrReadMapped()

int ImageGeneric::readOrReadMapped	(	const FileName &	name,
		size_t	select_img = ALL_IMAGES,
		int	mode = WRITE_READONLY
	)

Definition at line 242 of file xmipp_image_generic.cpp.

{
    try
    {
        return read(name, DATA, select_img, false);
    }
    catch (XmippError &xe)
    {
        if (xe.__errno == ERR_MEM_NOTENOUGH)
        {
            reportWarning("ImageBase::readOrReadMapped: Not enough memory to allocate. \n"
                          " Proceeding to map image from file.");
            return readMapped(name, select_img, mode);
        }
        else
            throw xe;
    }
}

readOrReadPreview()

int ImageGeneric::readOrReadPreview	(	const FileName &	name,
		size_t	Xdim,
		size_t	Ydim = 0,
		int	select_slice = CENTRAL_SLICE,
		size_t	select_img = FIRST_IMAGE,
		bool	mapData = false,
		bool	wrap = true
	)

This function allows to read the original image or a preview of it also allowing to select either a specific image from the stack or a slice from a volume.

In the case of reading images in its real dimensions it is also possible to image map from file.

Definition at line 291 of file xmipp_image_generic.cpp.

{
    SET_DATATYPE(name);
    double scale = getScale(imgInf, xdim, ydim);
    //std::cerr << "DEBUG_JM: readOrReadPreview, scale: " << scale << std::endl;

    if (scale < 0.1)
      return readPreviewSmooth(name, xdim, ydim, select_slice, select_img);
    return image->readOrReadPreview(name, xdim, ydim, select_slice, select_img, !imgInf.swap && mapData);
}

readPreview()

int ImageGeneric::readPreview	(	const FileName &	name,
		size_t	Xdim,
		size_t	Ydim = 0,
		int	select_slice = CENTRAL_SLICE,
		size_t	select_img = FIRST_IMAGE
	)

Definition at line 280 of file xmipp_image_generic.cpp.

{
    SET_DATATYPE(name);
    double scale = getScale(imgInf, xdim, ydim);
    //std::cerr << "DEBUG_JM: readPreview, scale: " << scale << std::endl;

    if (scale < 0.1)
      return readPreviewSmooth(name, xdim, ydim, select_slice, select_img);
    return image->readPreview(name, xdim, ydim, select_slice, select_img);
}

readPreviewFourier()

int ImageGeneric::readPreviewFourier	(	const FileName &	name,
		size_t	Xdim,
		size_t	Ydim = 0,
		int	select_slice = CENTRAL_SLICE,
		size_t	select_img = FIRST_IMAGE
	)

Definition at line 310 of file xmipp_image_generic.cpp.

{
    ImageGeneric ig;
    int result = ig.read(name, DATA, select_img);
    ImageInfo ii;
    ig.getInfo(ii);
    setDatatype(ii.datatype);
    switch (select_slice)
    {
    case CENTRAL_SLICE:
    case ALL_SLICES:
        select_slice = (int)((float)ii.adim.zdim / 2.0);
        break;
    default:
        select_slice--;
        break;
    }

    getScale(ii, xdim, ydim);

    ig().getSlice(select_slice, data);


    data->setXmippOrigin();
    selfScaleToSizeFourier((int)ydim, (int)xdim, *data, 1);
    return result;
}

readPreviewSmooth()

int ImageGeneric::readPreviewSmooth	(	const FileName &	name,
		size_t	Xdim,
		size_t	Ydim = 0,
		int	select_slice = CENTRAL_SLICE,
		size_t	select_img = FIRST_IMAGE
	)

Definition at line 338 of file xmipp_image_generic.cpp.

{
  //std::cerr << "DEBUG_JM: readPreviewSmooth" << std::endl;
    ImageGeneric ig;
    int result = ig.read(name, DATA, select_img);
    ig.convert2Datatype(DT_UChar);
    ImageInfo ii;
    ig.getInfo(ii);

    getScale(ii, xdim, ydim);

    setDatatype(DT_UChar);
    resize(xdim, ydim, 1, 1, false);

    byte *inputArray = (byte*) MULTIDIM_ARRAY_GENERIC(ig).getArrayPointer();
    byte *outputArray = (byte*) MULTIDIM_ARRAY_GENERIC(*this).getArrayPointer();

    SmoothResize(inputArray, outputArray, ii.adim.xdim, ii.adim.ydim, xdim, ydim);
    return result;
}

resize()

void ImageGeneric::resize ( int  Xdim, int  Ydim, int  Zdim, size_t  Ndim, bool  copy = true  )

inline

Resizes image dimensions

Definition at line 146 of file xmipp_image_generic.h.

    {
        image->setDimensions(Xdim, Ydim, Zdim, Ndim);
        data->resize(Ndim, Zdim, Ydim, Xdim, copy);
    }

reslice() [1/2]

void ImageGeneric::reslice

(

AxisView

view

)

Definition at line 502 of file xmipp_image_generic.cpp.

{
    ImageGeneric imgOut;
    reslice(face, imgOut);
    clear();
    datatype = imgOut.getDatatype();
    image = imgOut.image;
    data = imgOut.data;
    imgOut.image = NULL;
    imgOut.data = NULL;
}

reslice() [2/2]

void ImageGeneric::reslice	(	AxisView	view,
		ImageGeneric &	out
	)

Definition at line 457 of file xmipp_image_generic.cpp.

{
    ArrayDim aDim, aDimOut;
    data->getDimensions(aDim);

    char axis;
    bool reverse;

    aDimOut = aDim;

    if (face == VIEW_Y_NEG || face == VIEW_Y_POS)
    {
        axis = 'Y';
        aDimOut.ydim = aDim.zdim;
        aDimOut.zdim = aDim.ydim;
        reverse = (face == VIEW_Y_NEG);
    }
    else if (face == VIEW_X_NEG || face == VIEW_X_POS)
    {
        axis = 'X';
        aDimOut.xdim = aDim.zdim;
        aDimOut.zdim = aDim.xdim;
        reverse = (face == VIEW_X_NEG);
    }
    else
      REPORT_ERROR(ERR_VALUE_INCORRECT, formatString("reslice: not supported view %d", (int)face));

    DataType dtype = getDatatype();
    imgOut.setDatatype(dtype);
    imgOut().resize(aDimOut, false);
    imgOut.image->setADimFile(aDimOut);

    MultidimArrayGeneric imTemp;

    int index;

    for (size_t k = 0; k < aDimOut.zdim; k++)
    {
        imTemp.aliasSlice(MULTIDIM_ARRAY_GENERIC(imgOut), k);
        index = k + (aDimOut.zdim - 1 - 2*k) * (int)reverse;
        MULTIDIM_ARRAY_GENERIC(*this).getSlice(index, &imTemp, axis, !reverse);
    }

}

setDataMode()

void ImageGeneric::setDataMode ( DataMode  mode )

inline

Set image dataMode

Definition at line 163 of file xmipp_image_generic.h.

    {
        image->setDataMode(mode);
    }

setDatatype() [1/3]

void ImageGeneric::setDatatype

(

DataType

_datatype

)

Set the data type for the generic image

Definition at line 118 of file xmipp_image_generic.cpp.

{
    if (imgType == datatype)
        return;

    clear();
    datatype = imgType;
    switch (datatype)
    {
    case DT_Float:
        {
            Image<float> *imT = new Image<float>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_Double:
        {
            Image<double> *imT = new Image<double>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_UInt:
        {
            Image<unsigned int> *imT = new Image<unsigned int>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_Int:
        {
            Image<int> *imT = new Image<int>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_UShort:
        {
            Image<unsigned short> *imT = new Image<unsigned short>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_Short:
        {
            Image<short> *imT = new Image<short>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_UHalfByte:
    case DT_UChar:
        {
            Image<unsigned char> *imT = new Image<unsigned char>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_SChar:
        {
            Image<char> *imT = new Image<char>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_ULong:
        {
            Image<unsigned long> *imT = new Image<unsigned long>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_Long:
        {
            Image<long> *imT = new Image<long>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_HalfFloat:
        {
            Image<half_float::half> *imT = new Image<half_float::half>;
            image = imT;
            data = new MultidimArrayGeneric((MultidimArrayBase*) &(imT->data), datatype);
        }
        break;
    case DT_Unknown:
        REPORT_ERROR(ERR_IMG_UNKNOWN,"Datatype of the image file is unknown.");
        break;
    default:
        REPORT_ERROR(ERR_NOT_IMPLEMENTED, "Datatype not implemented.");
        break;
    }
}

setDatatype() [2/3]

void ImageGeneric::setDatatype	(	const FileName &	name,
		ImageInfo &	imgInf
	)

Set the data type according to the image file, checking if file size is correct.

Definition at line 214 of file xmipp_image_generic.cpp.

{
    getImageInfo(name, imgInf);
    checkImageFileSize(name, imgInf, true);
    setDatatype(imgInf.datatype);

}

setDatatype() [3/3]

void ImageGeneric::setDatatype

(

const FileName &

name

)

Definition at line 224 of file xmipp_image_generic.cpp.

{
    SET_DATATYPE(name);
}

setPixel() [1/2]

void ImageGeneric::setPixel ( unsigned long  n, int  k, int  i, int  j, double  value  ) const

inline

Set pixel value

Definition at line 382 of file xmipp_image_generic.h.

    {
#define SETVALUE(type) NZYX_ELEM(*(MultidimArray<type>*)data->im,n,k,i,j) = (type) value;
        SWITCHDATATYPE(datatype,SETVALUE)
#undef SETVALUE

    }

setPixel() [2/2]

void ImageGeneric::setPixel ( int  i, int  j, double  value  ) const

inline

Set pixel value

Definition at line 392 of file xmipp_image_generic.h.

    {

#define SETVALUE(type) A2D_ELEM(*(MultidimArray<type>*)data->im,i,j) = (type) value;
        CHECK_IMG(SWITCHDATATYPE(datatype,SETVALUE))
#undef SETVALUE

    }

subtract()

void ImageGeneric::subtract

(

const ImageGeneric &

img

)

Subtraction of the passed image to the internal's

Definition at line 557 of file xmipp_image_generic.cpp.

{
    if (datatype != img.datatype)
        REPORT_ERROR(ERR_TYPE_INCORRECT, "Images have different datatypes");

#define MINUS(type) MultidimArray<type> & kk = *((MultidimArray<type>*) data->im);\
                     MultidimArray<type> & pp = *((MultidimArray<type>*) img.data->im);\
                     kk -= pp;

    SWITCHDATATYPE(datatype, MINUS);
#undef MINUS

}

tilt()

double ImageGeneric::tilt ( const size_t  n = 0 ) const

inline

Get Tilt angle from image header

Definition at line 139 of file xmipp_image_generic.h.

    {
        return image->tilt(n);
    }

toString()

void ImageGeneric::toString

(

String &

s

)

const

Add to string the image information

Definition at line 533 of file xmipp_image_generic.cpp.

{
    std::stringstream ss;
    if (image == NULL)
        ss << "Xmipp::ImageGeneric: Uninitialized image";
    else
        ss << *image;
    s = ss.str();
}

write()

void ImageGeneric::write ( const FileName &  name = "", size_t  select_img = ALL_IMAGES, bool  isStack = false, int  mode = WRITE_OVERWRITE, CastWriteMode  castMode = CW_CAST, int  _swapWrite = 0  )

inline

Write image to file.

Definition at line 278 of file xmipp_image_generic.h.

    {
        image->write(name,select_img,isStack,mode,castMode,_swapWrite);
    }

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  o, const ImageGeneric &  I  )

friend

Definition at line 429 of file xmipp_image_generic.h.

    {
        o << I.image;
        return o;
    }

Member Data Documentation

data

MultidimArrayGeneric* ImageGeneric::data

Definition at line 53 of file xmipp_image_generic.h.

datatype

DataType ImageGeneric::datatype

Definition at line 52 of file xmipp_image_generic.h.

image

ImageBase* ImageGeneric::image

Definition at line 51 of file xmipp_image_generic.h.

swap

bool ImageGeneric::swap

protected

Definition at line 57 of file xmipp_image_generic.h.

---

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

• xmippCore/core/xmipp_image_generic.h
• xmippCore/core/xmipp_image_generic.cpp