MultidimArrayBase Class Reference

#include <multidim_array_base.h>

Inheritance diagram for MultidimArrayBase:

Public Member Functions
virtual	~MultidimArrayBase ()
virtual void	clear ()=0
virtual void	selfReverseX ()=0
virtual void	selfReverseY ()=0
virtual void	selfReverseZ ()=0
virtual double	computeAvg () const =0
virtual void	computeDoubleMinMaxRange (double &minval, double &maxval, size_t offset, size_t size) const =0
virtual void	maxIndex (size_t &lmax, int &kmax, int &imax, int &jmax) const =0
virtual void	coreAllocateReuse ()=0
virtual void	coreDeallocate ()=0
virtual void *	getArrayPointer () const =0
int	getDim () const
void	setMmap (bool mmap)
void	maxIndex (ArrayCoord &pos) const
void	maxIndex (int &kmax, int &imax, int &jmax) const
void	maxIndex (int &imax, int &jmax) const
void	maxIndex (int &jmax) const
void	printShape (std::ostream &out=std::cout) const
Size
void	setNdim (int Ndim)
void	setZdim (int Zdim)
void	setYdim (int Ydim)
void	setXdim (int Xdim)
void	setDimensions (int Xdim, int Ydim, int Zdim, size_t Ndim)
void	setDimensions (ArrayDim &newDim)
void	getDimensions (size_t &Xdim, size_t &Ydim, size_t &Zdim, size_t &Ndim) const
void	getDimensions (ArrayDim &idim) const
ArrayDim	getDimensions () const
void	getDimensions (int *size) const
size_t	getSize () const
virtual void	resize (size_t Ndim, size_t Zdim, size_t Ydim, size_t Xdim, bool copy=true)=0
void	resize (size_t Zdim, size_t Ydim, size_t Xdim)
void	resize (size_t Ydim, size_t Xdim)
void	resize (size_t Xdim)
void	resize (ArrayDim &adim, bool copy=true)
void	resizeNoCopy (size_t Ndim, size_t Zdim, size_t Ydim, size_t Xdim)
void	resizeNoCopy (size_t Zdim, size_t Ydim, size_t Xdim)
void	resizeNoCopy (size_t Ydim, size_t Xdim)
void	resizeNoCopy (size_t Xdim)
size_t	rowNumber () const
size_t	colNumber () const
void	copyShape (const MultidimArrayBase &m)
bool	sameShape (const MultidimArrayBase &op) const
void	setXmippOrigin ()
void	resetOrigin ()
void	moveOriginTo (int k, int i, int j)
void	moveOriginTo (int i, int j)
int	startingZ () const
int	finishingZ () const
int	startingY () const
int	finishingY () const
int	startingX () const
int	finishingX () const
bool	isCorner (const Matrix1D< double > &v) const
bool	outside (int k, int i, int j) const
bool	outside (int i, int j) const
bool	outside (int i) const
bool	outside (const Matrix1D< double > &r) const

Public Attributes
bool	destroyData
size_t	ndim
size_t	zdim
size_t	ydim
size_t	xdim
size_t	yxdim
size_t	zyxdim
size_t	nzyxdim
int	zinit
int	yinit
int	xinit
bool	mmapOn
FILE *	mFd
size_t	nzyxdimAlloc

Detailed Description

Template class for Xmipp arrays. This class provides physical and logical access.

Definition at line 615 of file multidim_array_base.h.

Constructor & Destructor Documentation

~MultidimArrayBase()

virtual MultidimArrayBase::~MultidimArrayBase ( )

inlinevirtual

Definition at line 658 of file multidim_array_base.h.

    {}

Member Function Documentation

clear()

virtual void MultidimArrayBase::clear ( )

pure virtual

Implemented in Histogram2D, MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, MultidimArray< unsigned short int >, and Histogram1D.

colNumber()

size_t MultidimArrayBase::colNumber ( ) const

inline

Returns X dimension.

Definition at line 832 of file multidim_array_base.h.

    {
        return xdim;
    }

computeAvg()

virtual double MultidimArrayBase::computeAvg ( ) const

pure virtual

Implemented in MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, and MultidimArray< unsigned short int >.

computeDoubleMinMaxRange()

virtual void MultidimArrayBase::computeDoubleMinMaxRange ( double &  minval, double &  maxval, size_t  offset, size_t  size  ) const

pure virtual

Implemented in MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, and MultidimArray< unsigned short int >.

copyShape()

void MultidimArrayBase::copyShape

(

const MultidimArrayBase &

m

)

Copy the shape parameters

Definition at line 186 of file multidim_array_base.cpp.

{
    ndim=m.ndim;
    zdim=m.zdim;
    ydim=m.ydim;
    xdim=m.xdim;
    yxdim=m.yxdim;
    zyxdim=m.zyxdim;
    nzyxdim=m.nzyxdim;
    zinit=m.zinit;
    yinit=m.yinit;
    xinit=m.xinit;
}

coreAllocateReuse()

virtual void MultidimArrayBase::coreAllocateReuse ( )

pure virtual

Implemented in MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, and MultidimArray< unsigned short int >.

coreDeallocate()

virtual void MultidimArrayBase::coreDeallocate ( )

pure virtual

Implemented in MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, and MultidimArray< unsigned short int >.

finishingX()

int MultidimArrayBase::finishingX ( ) const

inline

Returns the last valid logical X index.

Definition at line 939 of file multidim_array_base.h.

    {
        return xinit + xdim - 1;
    }

finishingY()

int MultidimArrayBase::finishingY ( ) const

inline

Returns the last valid logical Y index.

Definition at line 925 of file multidim_array_base.h.

    {
        return yinit + ydim - 1;
    }

finishingZ()

int MultidimArrayBase::finishingZ ( ) const

inline

Returns the last valid logical Z index.

Definition at line 911 of file multidim_array_base.h.

    {
        return zinit + zdim - 1;
    }

getArrayPointer()

virtual void* MultidimArrayBase::getArrayPointer ( ) const

pure virtual

Implemented in MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, and MultidimArray< unsigned short int >.

getDim()

int MultidimArrayBase::getDim ( ) const

inline

Returns the multidimArray dimension.

int dim = V.getDim();

Definition at line 1000 of file multidim_array_base.h.

    {
        if (NZYXSIZE(*this) < 1)
            return 0;
        if (NSIZE(*this) > 1)
            return 4;
        if (ZSIZE(*this) > 1)
            return 3;
        if (YSIZE(*this) > 1)
            return 2;
        return 1;
    }

getDimensions() [1/4]

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

Get the array dimensions.

Returns the multidimArray N,Z, Y and X dimensions.

V.getDimensions(Xdim, Ydim, Zdim, Ndim);

Definition at line 114 of file multidim_array_base.cpp.

{
    Xdim = xdim;
    Ydim = ydim;
    Zdim = zdim;
    Ndim = ndim;
}

getDimensions() [2/4]

void MultidimArrayBase::getDimensions

(

ArrayDim &

idim

)

const

Definition at line 122 of file multidim_array_base.cpp.

{
    adim.xdim = xdim;
    adim.ydim = ydim;
    adim.zdim = zdim;
    adim.ndim = ndim;
    adim.yxdim = yxdim;
    adim.zyxdim = zyxdim;
    adim.nzyxdim = nzyxdim;
}

getDimensions() [3/4]

ArrayDim MultidimArrayBase::getDimensions

(

)

const

Definition at line 133 of file multidim_array_base.cpp.

{
    ArrayDim adim;
    adim.xdim = xdim;
    adim.ydim = ydim;
    adim.zdim = zdim;
    adim.ndim = ndim;
    adim.yxdim = yxdim;
    adim.zyxdim = zyxdim;
    adim.nzyxdim = nzyxdim;

    return adim;
}

getDimensions() [4/4]

void MultidimArrayBase::getDimensions

(

int *

size

)

const

Get dimensions.

Returns the size of the object in a 4D vector. If the object is a matrix or a vector, then the higher order dimensions will be set to 1, ie, (Xdim, 1, 1) or (Xdim, Ydim, 1).

This function is not ported to Python.

Definition at line 155 of file multidim_array_base.cpp.

{
    size[0] = xdim;
    size[1] = ydim;
    size[2] = zdim;
    size[3] = ndim;
}

getSize()

size_t MultidimArrayBase::getSize

(

)

const

Returns the total size of the multidimArray

if (V.getSize() > 1) ...

Definition at line 169 of file multidim_array_base.cpp.

{
    return nzyxdim;
}

isCorner()

bool MultidimArrayBase::isCorner

(

const Matrix1D< double > &

v

)

const

IsCorner (in 2D or 3D matrix)

TRUE if the logical index given is a corner of the definition region of this array.

IsCorner (in 2D or 3D matrix)

   TRUE if the logical index given is a corner of the definition region of this
   array.

Definition at line 230 of file multidim_array_base.cpp.

{

    if (v.size() < 2)
        REPORT_ERROR(ERR_MATRIX_SIZE, "isCorner: index vector has got not enough components");

    else if (ZSIZE(*this)==1)
        return ((XX(v) == STARTINGX(*this)  && YY(v) == STARTINGY(*this))  ||
                (XX(v) == STARTINGX(*this)  && YY(v) == FINISHINGY(*this)) ||
                (XX(v) == FINISHINGX(*this) && YY(v) == STARTINGY(*this))  ||
                (XX(v) == FINISHINGX(*this) && YY(v) == FINISHINGY(*this)));
    else if (ZSIZE(*this)>1)
        return ((XX(v) == STARTINGX(*this)  && YY(v) == STARTINGY(*this)  && ZZ(v) == STARTINGZ(*this)) ||
                (XX(v) == STARTINGX(*this)  && YY(v) == FINISHINGY(*this) && ZZ(v) == STARTINGZ(*this)) ||
                (XX(v) == FINISHINGX(*this) && YY(v) == STARTINGY(*this)  && ZZ(v) == STARTINGZ(*this))  ||
                (XX(v) == FINISHINGX(*this) && YY(v) == FINISHINGY(*this) && ZZ(v) == STARTINGZ(*this)) ||
                (XX(v) == STARTINGX(*this)  && YY(v) == STARTINGY(*this)  && ZZ(v) == FINISHINGZ(*this)) ||
                (XX(v) == STARTINGX(*this)  && YY(v) == FINISHINGY(*this) && ZZ(v) == FINISHINGZ(*this)) ||
                (XX(v) == FINISHINGX(*this) && YY(v) == STARTINGY(*this)  && ZZ(v) == FINISHINGZ(*this))  ||
                (XX(v) == FINISHINGX(*this) && YY(v) == FINISHINGY(*this) && ZZ(v) == FINISHINGZ(*this)));
    else
        REPORT_ERROR(ERR_MATRIX_SIZE, formatString("isCorner: index vector has too many components. dimV= %lu matrix dim = %i", v.size(), XSIZE(*this)));
}

maxIndex() [1/5]

virtual void MultidimArrayBase::maxIndex ( size_t &  lmax, int &  kmax, int &  imax, int &  jmax  ) const

pure virtual

Implemented in MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, and MultidimArray< unsigned short int >.

maxIndex() [2/5]

void MultidimArrayBase::maxIndex ( ArrayCoord &  pos ) const

inline

Definition at line 1024 of file multidim_array_base.h.

    {
        maxIndex(pos.n, pos.z, pos.y, pos.x);
    }

maxIndex() [3/5]

void MultidimArrayBase::maxIndex ( int &  kmax, int &  imax, int &  jmax  ) const

inline

3D Indices for the maximum element.

This function just calls to the 4D function

Definition at line 1033 of file multidim_array_base.h.

    {
        size_t dum;
        maxIndex(dum, kmax, imax, jmax);
    }

maxIndex() [4/5]

void MultidimArrayBase::maxIndex ( int &  imax, int &  jmax  ) const

inline

2D Indices for the maximum element.

This function just calls to the 4D function

Definition at line 1043 of file multidim_array_base.h.

    {
        size_t dum;
        int idum;
        maxIndex(dum, idum, imax, jmax);
    }

maxIndex() [5/5]

void MultidimArrayBase::maxIndex ( int &  jmax ) const

inline

1D Indices for the maximum element.

This function just calls to the 4D function

Definition at line 1054 of file multidim_array_base.h.

    {
        size_t dum;
        int idum;
        maxIndex(dum, idum, idum, jmax);
    }

moveOriginTo() [1/2]

void MultidimArrayBase::moveOriginTo	(	int	k,
		int	i,
		int	j
	)

Move origin to.

This function adjust logical indexes such that the Xmipp origin of the array moves to the specified position. For instance, an array whose x indexes go from -1 to 1, if we move the origin to 4, then the x indexes go from 3 to 5. This is very useful for convolution operations where you only need to move the logical starting of the array.

Definition at line 212 of file multidim_array_base.cpp.

{
    zinit = k + FIRST_XMIPP_INDEX(zdim);
    yinit = i + FIRST_XMIPP_INDEX(ydim);
    xinit = j + FIRST_XMIPP_INDEX(xdim);
}

moveOriginTo() [2/2]

void MultidimArrayBase::moveOriginTo	(	int	i,
		int	j
	)

Move origin to.

This function adjust logical indexes such that the Xmipp origin of the array moves to the specified position. For instance, an array whose x indexes go from -1 to 1, if we move the origin to 4, then the x indexes go from 3 to 5. This is very useful for convolution operations where you only need to move the logical starting of the array.

Definition at line 219 of file multidim_array_base.cpp.

{
    yinit = i + FIRST_XMIPP_INDEX(ydim);
    xinit = j + FIRST_XMIPP_INDEX(xdim);
}

outside() [1/4]

bool MultidimArrayBase::outside ( int  k, int  i, int  j  ) const

inline

Outside for 3D matrices

TRUE if the logical index given is outside the definition region of this array.

Definition at line 956 of file multidim_array_base.h.

    {
        return (j < STARTINGX(*this) || j > FINISHINGX(*this) ||
                i < STARTINGY(*this) || i > FINISHINGY(*this) ||
                k < STARTINGZ(*this) || k > FINISHINGZ(*this));
    }

outside() [2/4]

bool MultidimArrayBase::outside ( int  i, int  j  ) const

inline

Outside for 2D matrices

TRUE if the logical index given is outside the definition region of this array.

Definition at line 968 of file multidim_array_base.h.

    {
        return (j < STARTINGX(*this) || j > FINISHINGX(*this) ||
                i < STARTINGY(*this) || i > FINISHINGY(*this));
    }

outside() [3/4]

bool MultidimArrayBase::outside ( int  i ) const

inline

Outside for 1D matrices

TRUE if the logical index given is outside the definition region of this array.

Definition at line 979 of file multidim_array_base.h.

    {
        return (i < STARTINGX(*this) || i > FINISHINGX(*this));
    }

outside() [4/4]

bool MultidimArrayBase::outside

(

const Matrix1D< double > &

r

)

const

Outside

TRUE if the logical index given is outside the definition region of this array.

Definition at line 259 of file multidim_array_base.cpp.

{
    if (r.size() < 1)
    {
        REPORT_ERROR(ERR_MATRIX_SIZE, "Outside: index vector has not got enough components");
    }
    else if (r.size()==1)
    {
        return (XX(r) < STARTINGX(*this) || XX(r) > FINISHINGX(*this));
    }
    else if (r.size()==2)
    {
        return (XX(r) < STARTINGX(*this) || XX(r) > FINISHINGX(*this) ||
                YY(r) < STARTINGY(*this) || YY(r) > FINISHINGY(*this));
    }
    else if (r.size()==3)
    {
        return (XX(r) < STARTINGX(*this) || XX(r) > FINISHINGX(*this) ||
                YY(r) < STARTINGY(*this) || YY(r) > FINISHINGY(*this) ||
                ZZ(r) < STARTINGZ(*this) || ZZ(r) > FINISHINGZ(*this));
    }
    else
        REPORT_ERROR(ERR_MATRIX_SIZE,"Outside: index vector has too many components");
}

printShape()

void MultidimArrayBase::printShape

(

std::ostream &

out = std::cout

)

const

Print shape of multidimensional array.

This function shows the size, starting and finishing indexes of the given array. No end of line is printed neither at the beginning nor the end.

v.printShape();

std::ofstream fh;
...;
v.printShape(fh);

Definition at line 284 of file multidim_array_base.cpp.

{
    if (NSIZE(*this) > 1)
        out << " Number of images = "<<NSIZE(*this);

    if (ZSIZE(*this)>1)
        out<< " Size(Z,Y,X): " << ZSIZE(*this) << "x" << YSIZE(*this) << "x" << XSIZE(*this)
        << " k=[" << STARTINGZ(*this) << ".." << FINISHINGZ(*this) << "]"
        << " i=[" << STARTINGY(*this) << ".." << FINISHINGY(*this) << "]"
        << " j=[" << STARTINGX(*this) << ".." << FINISHINGX(*this) << "]";
    else if (YSIZE(*this)>1)
        out<< " Size(Y,X): " << YSIZE(*this) << "x" << XSIZE(*this)
        << " i=[" << STARTINGY(*this) << ".." << FINISHINGY(*this) << "]"
        << " j=[" << STARTINGX(*this) << ".." << FINISHINGX(*this) << "]";
    else if (XSIZE(*this)>1)
        out<< " Size(X): " << XSIZE(*this)
        << " j=[" << STARTINGX(*this) << ".." << FINISHINGX(*this) << "]";
    else
        out << " Empty MultidimArray!";
    out<<"\n";
}

resetOrigin()

void MultidimArrayBase::resetOrigin

(

)

Reset logical origin to zeros.

This function adjust the starting points in the array such that upper left corner begins in zero.

V.resetOrigin();

Definition at line 207 of file multidim_array_base.cpp.

{
    zinit = yinit = xinit = 0;
}

resize() [1/5]

virtual void MultidimArrayBase::resize ( size_t  Ndim, size_t  Zdim, size_t  Ydim, size_t  Xdim, bool  copy = true  )

pure virtual

Resize to a given size

This function resize the actual array to the given size. The origin is not modified. If the actual array is larger than the pattern then the values outside the new size are lost, if it is smaller then 0's are added. An exception is thrown if there is no memory.

V1.resize(3, 3, 2);

Implemented in MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, and MultidimArray< unsigned short int >.

resize() [2/5]

void MultidimArrayBase::resize ( size_t  Zdim, size_t  Ydim, size_t  Xdim  )

inline

Resize a single 3D image

This function assumes n is 1

V1.resize(3, 3, 2);

Definition at line 761 of file multidim_array_base.h.

    {
        resize(1, Zdim, Ydim, Xdim);
    }

resize() [3/5]

void MultidimArrayBase::resize ( size_t  Ydim, size_t  Xdim  )

inline

Resize a single 2D image

This function assumes n and z are 1

V1.resize(3, 2);

Definition at line 773 of file multidim_array_base.h.

    {
        resize(1, 1, Ydim, Xdim);
    }

resize() [4/5]

void MultidimArrayBase::resize ( size_t  Xdim )

inline

Resize a single 1D image

This function assumes n and z and y are 1

V1.resize(2);

Definition at line 785 of file multidim_array_base.h.

    {
        resize(1, 1, 1, Xdim);
    }

resize() [5/5]

void MultidimArrayBase::resize	(	ArrayDim &	adim,
		bool	copy = true
	)

Resize an image using the dimensions from an ArrayDim structure.

Resize the multidimarray from an ArrayDim struct

Definition at line 177 of file multidim_array_base.cpp.

{
    setDimensions(adim);
    resize(adim.ndim, adim.zdim, adim.ydim, adim.xdim, copy);
}

resizeNoCopy() [1/4]

void MultidimArrayBase::resizeNoCopy ( size_t  Ndim, size_t  Zdim, size_t  Ydim, size_t  Xdim  )

inline

Resize with no copy a single 3D image

Definition at line 797 of file multidim_array_base.h.

    {
        resize(Ndim, Zdim, Ydim, Xdim, false);
    }

resizeNoCopy() [2/4]

void MultidimArrayBase::resizeNoCopy ( size_t  Zdim, size_t  Ydim, size_t  Xdim  )

inline

Resize with no copy a single 3D image

Definition at line 804 of file multidim_array_base.h.

    {
        resize(1, Zdim, Ydim, Xdim, false);
    }

resizeNoCopy() [3/4]

void MultidimArrayBase::resizeNoCopy ( size_t  Ydim, size_t  Xdim  )

inline

Resize a single 2D image with no copy

Definition at line 811 of file multidim_array_base.h.

    {
        resize(1, 1, Ydim, Xdim, false);
    }

resizeNoCopy() [4/4]

void MultidimArrayBase::resizeNoCopy ( size_t  Xdim )

inline

Resize a single 1D image with no copy

Definition at line 818 of file multidim_array_base.h.

    {
        resize(1, 1, 1, Xdim, false);
    }

rowNumber()

size_t MultidimArrayBase::rowNumber ( ) const

inline

Returns Y dimension.

Definition at line 825 of file multidim_array_base.h.

    {
        return ydim;
    }

sameShape()

bool MultidimArrayBase::sameShape ( const MultidimArrayBase &  op ) const

inline

Same shape.

Returns true if this object has got the same shape (origin and size) than the argument

Definition at line 847 of file multidim_array_base.h.

    {
        return (NSIZE(*this) == NSIZE(op) &&
                XSIZE(*this) == XSIZE(op) &&
                YSIZE(*this) == YSIZE(op) &&
                ZSIZE(*this) == ZSIZE(op) &&
                STARTINGX(*this) == STARTINGX(op) &&
                STARTINGY(*this) == STARTINGY(op) &&
                STARTINGZ(*this) == STARTINGZ(op));
    }

selfReverseX()

virtual void MultidimArrayBase::selfReverseX ( )

pure virtual

Implemented in MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, and MultidimArray< unsigned short int >.

selfReverseY()

virtual void MultidimArrayBase::selfReverseY ( )

pure virtual

Implemented in MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, and MultidimArray< unsigned short int >.

selfReverseZ()

virtual void MultidimArrayBase::selfReverseZ ( )

pure virtual

Implemented in MultidimArray< T >, MultidimArray< long >, MultidimArray< double >, MultidimArray< float >, MultidimArray< int >, MultidimArray< unsigned int >, MultidimArray< short int >, MultidimArray< size_t >, MultidimArray< unsigned char >, MultidimArray< std::complex< double > >, MultidimArray< char >, MultidimArray< bool >, and MultidimArray< unsigned short int >.

setDimensions() [1/2]

void MultidimArrayBase::setDimensions	(	int	Xdim,
		int	Ydim,
		int	Zdim,
		size_t	Ndim
	)

Sets new 4D dimensions. Note that the dataArray is NOT resized. This should be done separately with coreAllocate()

Definition at line 78 of file multidim_array_base.cpp.

{
    if (((size_t)Xdim)*Ydim*Zdim*Ndim < 1)
        REPORT_ERROR(ERR_MULTIDIM_SIZE, "Dimensions' size cannot be zero nor negative.");
    ndim=Ndim;
    zdim=Zdim;
    ydim=Ydim;
    xdim=Xdim;
    yxdim=ydim*xdim;
    zyxdim=zdim*yxdim;
    nzyxdim=ndim*zyxdim;
}

setDimensions() [2/2]

void MultidimArrayBase::setDimensions

(

ArrayDim &

newDim

)

Sets new 4D dimensions. Note that the dataArray is NOT resized. This should be done separately with coreAllocate()

Definition at line 94 of file multidim_array_base.cpp.

{
    if (newDim.ndim*newDim.zdim*newDim.ydim*newDim.xdim < 1)
        REPORT_ERROR(ERR_MULTIDIM_SIZE, "Dimensions' size cannot be zero nor negative.");
    ndim = newDim.ndim;
    zdim = newDim.zdim;
    ydim = newDim.ydim;
    xdim = newDim.xdim;

    newDim.yxdim   = yxdim   = ydim*xdim;
    newDim.zyxdim  = zyxdim  = zdim*yxdim;
    newDim.nzyxdim = nzyxdim = ndim*zyxdim;
}

setMmap()

void MultidimArrayBase::setMmap ( bool  mmap )

inline

Sets mmap.

Sets on/off mmap flag to allocate memory in a file.

Definition at line 1018 of file multidim_array_base.h.

    {
        coreDeallocate();
        mmapOn = mmap;
    }

setNdim()

void MultidimArrayBase::setNdim

(

int

Ndim

)

Sets new N dimension.

Note that the dataArray is NOT resized. This should be done separately with coreAllocate()

Definition at line 31 of file multidim_array_base.cpp.

{
    ndim = Ndim;
    nzyxdim=zyxdim*ndim;
}

setXdim()

void MultidimArrayBase::setXdim

(

int

Xdim

)

Sets new X dimension.

Note that the dataArray is NOT resized. This should be done separately with coreAllocate()

Definition at line 67 of file multidim_array_base.cpp.

{
    xdim = Xdim;
    yxdim=(size_t)ydim*xdim;
    zyxdim=yxdim*zdim;
    nzyxdim=zyxdim*ndim;
}

setXmippOrigin()

void MultidimArrayBase::setXmippOrigin

(

)

Set logical origin in Xmipp fashion.

This function adjust the starting points in the array such that the center of the array is defined in the Xmipp fashion.

V.setXmippOrigin();

Definition at line 200 of file multidim_array_base.cpp.

{
    zinit = FIRST_XMIPP_INDEX(zdim);
    yinit = FIRST_XMIPP_INDEX(ydim);
    xinit = FIRST_XMIPP_INDEX(xdim);
}

setYdim()

void MultidimArrayBase::setYdim

(

int

Ydim

)

Sets new Y dimension.

Note that the dataArray is NOT resized. This should be done separately with coreAllocate()

Definition at line 54 of file multidim_array_base.cpp.

{
    ydim = Ydim;
    yxdim=(size_t)ydim*xdim;
    zyxdim=yxdim*zdim;
    nzyxdim=zyxdim*ndim;
}

setZdim()

void MultidimArrayBase::setZdim

(

int

Zdim

)

Sets new Z dimension.

Note that the dataArray is NOT resized. This should be done separately with coreAllocate()

Definition at line 42 of file multidim_array_base.cpp.

{
    zdim = Zdim;
    zyxdim=yxdim*zdim;
    nzyxdim=zyxdim*ndim;
}

startingX()

int MultidimArrayBase::startingX ( ) const

inline

Returns the first valid logical X index.

Definition at line 932 of file multidim_array_base.h.

    {
        return xinit;
    }

startingY()

int MultidimArrayBase::startingY ( ) const

inline

Returns the first valid logical Y index.

Definition at line 918 of file multidim_array_base.h.

    {
        return yinit;
    }

startingZ()

int MultidimArrayBase::startingZ ( ) const

inline

Returns the first valid logical Z index.

Definition at line 904 of file multidim_array_base.h.

    {
        return zinit;
    }

Member Data Documentation

destroyData

bool MultidimArrayBase::destroyData

Definition at line 619 of file multidim_array_base.h.

mFd

FILE* MultidimArrayBase::mFd

Definition at line 654 of file multidim_array_base.h.

mmapOn

bool MultidimArrayBase::mmapOn

Definition at line 652 of file multidim_array_base.h.

ndim

size_t MultidimArrayBase::ndim

Definition at line 622 of file multidim_array_base.h.

nzyxdim

size_t MultidimArrayBase::nzyxdim

Definition at line 640 of file multidim_array_base.h.

nzyxdimAlloc

size_t MultidimArrayBase::nzyxdimAlloc

Definition at line 656 of file multidim_array_base.h.

xdim

size_t MultidimArrayBase::xdim

Definition at line 631 of file multidim_array_base.h.

xinit

int MultidimArrayBase::xinit

Definition at line 649 of file multidim_array_base.h.

ydim

size_t MultidimArrayBase::ydim

Definition at line 628 of file multidim_array_base.h.

yinit

int MultidimArrayBase::yinit

Definition at line 646 of file multidim_array_base.h.

yxdim

size_t MultidimArrayBase::yxdim

Definition at line 634 of file multidim_array_base.h.

zdim

size_t MultidimArrayBase::zdim

Definition at line 625 of file multidim_array_base.h.

zinit

int MultidimArrayBase::zinit

Definition at line 643 of file multidim_array_base.h.

zyxdim

size_t MultidimArrayBase::zyxdim

Definition at line 637 of file multidim_array_base.h.

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

• xmippCore/core/multidim_array_base.h
• xmippCore/core/multidim_array_base.cpp