/usr/include/relion-1.3/src/multidim_array.h is in librelion-dev-common 1.3+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* This complete copyright notice must be included in any revised version of the
* source code. Additional authorship citations may be added, but existing
* author citations must be preserved.
***************************************************************************/
/***************************************************************************
*
* Authors: Carlos Oscar S. Sorzano (coss@cnb.csic.es)
*
* Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
* 02111-1307 USA
*
* All comments concerning this program package may be sent to the
* e-mail address 'xmipp@cnb.csic.es'
***************************************************************************/
#ifndef MULTIDIM_ARRAY_H
#define MULTIDIM_ARRAY_H
#include <typeinfo>
#include <sys/mman.h>
#include <fcntl.h>
#include <unistd.h>
#include "src/funcs.h"
#include "src/error.h"
#include "src/args.h"
#include "src/matrix1d.h"
#include "src/matrix2d.h"
#include "src/complex.h"
extern int bestPrecision(float F, int _width);
extern std::string floatToString(float F, int _width, int _prec);
/// @defgroup MultidimensionalArrays Multidimensional Arrays
/// @ingroup DataLibrary
//@{
/** @name MultidimArraysSpeedUp Speed up macros
*
* This macros are defined to allow high speed in critical parts of your
* program. They shouldn't be used systematically as usually there is no
* checking on the correctness of the operation you are performing. Speed comes
* from three facts: first, they are macros and no function call is performed
* (although most of the critical functions are inline functions), there is no
* checking on the correctness of the operation (it could be wrong and you are
* not warned of it), and destination vectors are not returned saving time in
* the copy constructor and in the creation/destruction of temporary vectors.
*/
//@{
/** Returns the first X valid logical index
*/
#define STARTINGX(v) ((v).xinit)
/** Returns the last X valid logical index
*/
#define FINISHINGX(v) ((v).xinit + (v).xdim - 1)
/** Returns the first Y valid logical index
*/
#define STARTINGY(v) ((v).yinit)
/** Returns the last Y valid logical index
*/
#define FINISHINGY(v) ((v).yinit + (v).ydim - 1)
/** Returns the first Z valid logical index
*/
#define STARTINGZ(v) ((v).zinit)
/** Returns the last Z valid logical index
*/
#define FINISHINGZ(v) ((v).zinit + (v).zdim - 1)
/** Access to X dimension (size)
*/
#define XSIZE(v) ((v).xdim)
/** Access to Y dimension (size)
*/
#define YSIZE(v) ((v).ydim)
/** Access to Z dimension (size)
*/
#define ZSIZE(v) ((v).zdim)
/** Access to N dimension (size)
*/
#define NSIZE(v) ((v).ndim)
/** Access to XY dimension (Ysize*Xsize)
*/
#define YXSIZE(v) ((v).yxdim)
/** Access to XYZ dimension (Zsize*Ysize*Xsize)
*/
#define ZYXSIZE(v) ((v).zyxdim)
/** Access to XYZN dimension (Nsize*Zsize*Ysize*Xsize)
*/
#define MULTIDIM_SIZE(v) ((v).nzyxdim)
/** Access to XYZN dimension (Nsize*Zsize*Ysize*Xsize)
*/
#define NZYXSIZE(v) ((v).nzyxdim)
/** Array access.
*
* This macro gives you access to the array (T **)
*/
#ifndef MULTIDIM_ARRAY
#define MULTIDIM_ARRAY(v) ((v).data)
#endif
/** Access to a direct element.
* v is the array, l is the image, k is the slice, i is the Y index and j is the X index.
* i and j) within the slice.
*/
#define DIRECT_NZYX_ELEM(v, l, k, i, j) ((v).data[(l)*ZYXSIZE(v)+(k)*YXSIZE(v)+((i)*XSIZE(v))+(j)])
/** Multidim element: Logical access.
*/
#define NZYX_ELEM(v, l, k, i, j) \
DIRECT_NZYX_ELEM((v), (l), (k) - STARTINGZ(v), (i) - STARTINGY(v), (j) - STARTINGX(v))
/** Access to a direct element.
* v is the array, k is the slice and n is the number of the pixel (combined i and j)
* within the slice.
*/
#define DIRECT_MULTIDIM_ELEM(v,n) ((v).data[(n)])
/** For all direct elements in the array
*
* This macro is used to generate loops for the array in an easy manner. It
* defines an internal index 'n' which goes over the slices and 'n' that
* goes over the pixels in each slice.
*
* @code
* FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(v)
* {
* std::cout << DIRECT_MULTIDIM_ELEM(v,n) << " ";
* }
* @endcode
*/
#define FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(v) \
for (long int n=0; n<NZYXSIZE(v); ++n)
/** For all direct elements in the array
*
* This macro is used to generate loops for the array in an easy
* manner. It defines internal indexes 'l', 'k','i' and 'j' which
* ranges over the n volume using its physical definition.
*
* @code
* FOR_ALL_DIRECT_NZYX_ELEMENTS_IN_MULTIDIMARRAY(v)
* {
* std::cout << DIRECT_NZYX_ELEM(v,l, k, i, j) << " ";
* }
* @endcode
*/
#define FOR_ALL_DIRECT_NZYX_ELEMENTS_IN_MULTIDIMARRAY(V) \
for (long int l=0; l<NSIZE(V); l++) \
for (long int k=0; k<ZSIZE(V); k++) \
for (long int i=0; i<YSIZE(V); i++) \
for (long int j=0; j<XSIZE(V); j++)
/** For all direct elements in the array
*
* This macro is used to generate loops for the array in an easy
* manner. It defines internal indexes 'l', 'k','i' and 'j' which
* ranges over the n volume using its logical definition.
*
* @code
* FOR_ALL_NZYX_ELEMENTS_IN_MULTIDIMARRAY(v)
* {
* std::cout << NZYX_ELEM(v,l, k, i, j) << " ";
* }
* @endcode
*/
#define FOR_ALL_NZYX_ELEMENTS_IN_MULTIDIMARRAY(V) \
for (long int l=0; l<NSIZE(V); l++) \
for (long int k=STARTINGZ(V); k<=FINISHINGZ(V); k++) \
for (long int i=STARTINGY(V); i<=FINISHINGY(V); i++) \
for (long int j=STARTINGX(V); j<=FINISHINGX(V); j++)
/** For all direct elements in the array, pointer version
*
* This macro is used to generate loops for the array in an easy manner. It
* defines an internal index 'k' which goes over the slices and 'n' that
* goes over the pixels in each slice. Each element can be accessed through
* an external pointer called ptr.
*
* @code
* T* ptr=NULL;
* long int n;
* FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(v,n,ptr)
* {
* std::cout << *ptr << " ";
* }
* @endcode
*/
#define FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(v,n,ptr) \
for ((n)=0, (ptr)=(v).data; (n)<NZYXSIZE(v); ++(n), ++(ptr))
/** Access to a direct element.
* v is the array, k is the slice (Z), i is the Y index and j is the X index.
*/
#define DIRECT_A3D_ELEM(v,k,i,j) ((v).data[(k)*YXSIZE(v)+((i)*XSIZE(v))+(j)])
/** A short alias for the previous function.
*
*/
#define dAkij(V, k, i, j) DIRECT_A3D_ELEM(V, k, i, j)
/** Volume element: Logical access.
*
* @code
* A3D_ELEM(V, -1, -2, 1) = 1;
* val = A3D_ELEM(V, -1, -2, 1);
* @endcode
*/
#define A3D_ELEM(V, k, i, j) \
DIRECT_A3D_ELEM((V),(k) - STARTINGZ(V), (i) - STARTINGY(V), (j) - STARTINGX(V))
/** For all elements in the array.
*
* This macro is used to generate loops for the volume in an easy way. It
* defines internal indexes 'k','i' and 'j' which ranges the volume using its
* mathematical definition (ie, logical access).
*
* @code
* FOR_ALL_ELEMENTS_IN_ARRAY3D(V)
* {
* std::cout << V(k, i, j) << " ";
* }
* @endcode
*/
#define FOR_ALL_ELEMENTS_IN_ARRAY3D(V) \
for (long int k=STARTINGZ(V); k<=FINISHINGZ(V); k++) \
for (long int i=STARTINGY(V); i<=FINISHINGY(V); i++) \
for (long int j=STARTINGX(V); j<=FINISHINGX(V); j++)
/** For all elements in common.
*
* This macro is used to generate loops for all the elements logically in common
* between two volumes in an easy manner. Then k, i and j (locally defined)
* range from
*
* MAX(STARTINGZ(V1),STARTINGZ(V2)) to MIN(FINISHINGZ(V1),FINISHINGZ(V2)),
* MAX(STARTINGY(V1),STARTINGY(V2)) to MIN(FINISHINGY(V1),FINISHINGY(V2)),
* MAX(STARTINGX(V1),STARTINGX(V2)) to MIN(FINISHINGX(V1),FINISHINGX(V2))
*
* (included limits) respectively. You need to define SPEED_UP_temps.
*
* @code
* SPEED_UP_temps;
* MultidimArray< double > V1(10, 10, 10), V2(20, 20, 20);
* V1.setXmippOrigin();
* V2.setXmippOrigin();
*
* FOR_ALL_ELEMENTS_IN_COMMON_IN_ARRAY3D(V1, V2)
* {
* // ...
* }
* @endcode
*/
#define FOR_ALL_ELEMENTS_IN_COMMON_IN_ARRAY3D(V1, V2) \
ispduptmp0 = XMIPP_MAX(STARTINGZ(V1), STARTINGZ(V2)); \
ispduptmp1 = XMIPP_MIN(FINISHINGZ(V1),FINISHINGZ(V2)); \
ispduptmp2 = XMIPP_MAX(STARTINGY(V1), STARTINGY(V2)); \
ispduptmp3 = XMIPP_MIN(FINISHINGY(V1),FINISHINGY(V2)); \
ispduptmp4 = XMIPP_MAX(STARTINGX(V1), STARTINGX(V2)); \
ispduptmp5 = XMIPP_MIN(FINISHINGX(V1),FINISHINGX(V2)); \
for (long int k=ispduptmp0; k<=ispduptmp1; k++) \
for (long int i=ispduptmp2; i<=ispduptmp3; i++) \
for (long int j=ispduptmp4; j<=ispduptmp5; j++)
/** For all direct elements in the array.
*
* This macro is used to generate loops for the volume in an easy way. It
* defines internal indexes 'k','i' and 'j' which ranges the volume using its
* physical definition.
*
* @code
* FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY3D(V)
* {
* std::cout << DIRECT_A3D_ELEM(m, k, i, j) << " ";
* }
* @endcode
*/
#define FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY3D(V) \
for (long int k=0; k<ZSIZE(V); k++) \
for (long int i=0; i<YSIZE(V); i++) \
for (long int j=0; j<XSIZE(V); j++)
/** Access to a direct element of a matrix.
* v is the array, i and j define the element v_ij.
*
* Be careful because this is physical access, usually matrices follow the C
* convention of starting index==0 (X and Y). This function should not be used
* as it goes against the vector library philosophy unless you explicitly want
* to access directly to any value in the matrix without taking into account its
* logical position
*
* @code
* DIRECT_A2D_ELEM(m, 0, 0) = 1;
* val = DIRECT_A2D_ELEM(m, 0, 0);
* @endcode
*/
#define DIRECT_A2D_ELEM(v,i,j) ((v).data[(i)*(v).xdim+(j)])
/** Short alias for DIRECT_A2D_ELEM
*/
#define dAij(M, i, j) DIRECT_A2D_ELEM(M, i, j)
/** Matrix element: Logical access
*
* @code
* A2D_ELEM(m, -2, 1) = 1;
* val = A2D_ELEM(m, -2, 1);
* @endcode
*/
#define A2D_ELEM(v, i, j) \
DIRECT_A2D_ELEM(v, (i) - STARTINGY(v), (j) - STARTINGX(v))
/** TRUE if both arrays have the same shape
*
* Two arrays have the same shape if they have the same size and the same
* starting point. Be aware that this is a macro which simplifies to a boolean.
*/
#define SAME_SHAPE2D(v1, v2) \
(XSIZE(v1) == XSIZE(v2) && \
YSIZE(v1) == YSIZE(v2) && \
STARTINGX(v1) == STARTINGX(v2) && \
STARTINGY(v1) == STARTINGY(v2))
/** For all elements in the array
*
* This macro is used to generate loops for the matrix in an easy way. It
* defines internal indexes 'i' and 'j' which ranges the matrix using its
* mathematical definition (ie, logical access).
*
* @code
* FOR_ALL_ELEMENTS_IN_ARRAY2D(m)
* {
* std::cout << m(i, j) << " ";
* }
* @endcode
*/
#define FOR_ALL_ELEMENTS_IN_ARRAY2D(m) \
for (long int i=STARTINGY(m); i<=FINISHINGY(m); i++) \
for (long int j=STARTINGX(m); j<=FINISHINGX(m); j++)
/** For all elements in the array, accessed physically
*
* This macro is used to generate loops for the matrix in an easy way using
* physical indexes. It defines internal indexes 'i' and 'j' which ranges the
* matrix using its physical definition.
*
* @code
* FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D(m)
* {
* std::cout << DIRECT_A2D_ELEM(m, i, j) << " ";
* }
* @endcode
*/
#define FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D(m) \
for (long int i=0; i<YSIZE(m); i++) \
for (long int j=0; j<XSIZE(m); j++)
/** Vector element: Physical access
*
* Be careful because this is physical access, usually vectors follow the C
* convention of starting index==0. This function should not be used as it goes
* against the vector library philosophy unless you explicitly want to access
* directly to any value in the vector without taking into account its logical
* position.
*
* @code
* DIRECT_A1D_ELEM(v, 0) = 1;
* val = DIRECT_A1D_ELEM(v, 0);
* @endcode
*/
#define DIRECT_A1D_ELEM(v, i) ((v).data[(i)])
/** A short alias to previous function
*/
#define dAi(v, i) DIRECT_A1D_ELEM(v, i)
/** Vector element: Logical access
*
* @code
* A1D_ELEM(v, -2) = 1;
* val = A1D_ELEM(v, -2);
* @endcode
*/
#define A1D_ELEM(v, i) DIRECT_A1D_ELEM(v, (i) - ((v).xinit))
/** For all elements in the array
*
* This macro is used to generate loops for the vector in an easy manner. It
* defines an internal index 'i' which ranges the vector using its mathematical
* definition (ie, logical access).
*
* @code
* FOR_ALL_ELEMENTS_IN_ARRAY1D(v)
* {
* std::cout << v(i) << " ";
* }
* @endcode
*/
#define FOR_ALL_ELEMENTS_IN_ARRAY1D(v) \
for (long int i=STARTINGX(v); i<=FINISHINGX(v); i++)
/** For all elements in the array, accessed physically
*
* This macro is used to generate loops for the vector in an easy way using
* physical indexes. It defines internal the index 'i' which ranges the vector
* using its physical definition.
*
* @code
* FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY1D(v)
* {
* std::cout << DIRECT_A1D_ELEM(v, i) << " ";
* }
* @endcode
*/
#define FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY1D(v) \
for (long int i=0; i<v.xdim; i++)
//@}
// Forward declarations ====================================================
template<typename T>
class MultidimArray;
template<typename T>
void coreArrayByScalar(const MultidimArray<T>& op1, const T& op2,
MultidimArray<T>& result, char operation);
template<typename T>
void coreScalarByArray(const T& op1, const MultidimArray<T>& op2,
MultidimArray<T>& result, char operation);
template<typename T>
void coreArrayByArray(const MultidimArray<T>& op1, const MultidimArray<T>& op2,
MultidimArray<T>& result, char operation);
/** Template class for Xmipp arrays.
* This class provides physical and logical access.
*/
template<typename T>
class MultidimArray
{
public:
/* The array itself.
The array is always a 3D array (Z,Y,X). For vectors the size of the array
is (1,1,X) and for matrices (1,Y,X). The pixel (i,j) (y,x) is at the
position data[i*Xdim+j] or data[y*Xdim+x]
*/
T* data;
// Destroy data
bool destroyData;
// Number of images
long int ndim;
// Number of elements in Z
long int zdim;
// Number of elements in Y
long int ydim;
// Number of elements in X
long int xdim;
// Number of elements in YX
long int yxdim;
// Number of elements in ZYX
long int zyxdim;
// Number of elements in NZYX
long int nzyxdim;
// Z init
long int zinit;
// Y init
long int yinit;
// X init
long int xinit;
//Alloc memory or map to a file
bool mmapOn;
// Mapped File name
FileName mapFile;
//Mapped file handler
int mFd;
// Number of elements in NZYX in allocated memory
long int nzyxdimAlloc;
public:
/// @name Constructors
//@{
/** Empty constructor.
* The empty constructor creates an array with no memory associated,
* size=0.
*/
MultidimArray()
{
coreInit();
}
/** Size constructor with 4D size.
* The Size constructor creates an array with memory associated,
* and fills it with zeros.
*/
MultidimArray(long int Ndim, long int Zdim, long int Ydim, long int Xdim)
{
coreInit();
resize(Ndim, Zdim, Ydim, Xdim);
}
/** Size constructor with 3D size.
* The Size constructor creates an array with memory associated,
* and fills it with zeros.
*/
MultidimArray(long int Zdim, long int Ydim, long int Xdim)
{
coreInit();
resize(1, Zdim, Ydim, Xdim);
}
/** Size constructor with 2D size.
* The Size constructor creates an array with memory associated,
* and fills it with zeros.
*/
MultidimArray(long int Ydim, long int Xdim)
{
coreInit();
resize(1, 1, Ydim, Xdim);
}
/** Size constructor with 1D size.
* The Size constructor creates an array with memory associated,
* and fills it with zeros.
*/
MultidimArray(long int Xdim)
{
coreInit();
resize(1, 1, 1, Xdim);
}
/** Copy constructor
*
* The created volume is a perfect copy of the input array but with a
* different memory assignment.
*
* @code
* MultidimArray< double > V2(V1);
* @endcode
*/
MultidimArray(const MultidimArray<T>& V)
{
coreInit();
*this = V;
}
/** Copy constructor from a Matrix1D.
* The Size constructor creates an array with memory associated,
* and fills it with zeros.
*/
MultidimArray(const Matrix1D<T>& V)
{
coreInit();
resize(1, 1, 1, V.size());
for (long int i = 0; i < V.size(); i++)
(*this)(i) = V(i);
}
/** Constructor from vector 1D
* This will create a MultidimArray 1D
* the size and elements will be copied from
* the std::vector
*/
MultidimArray(const std::vector<T> &vector)
{
coreInit();
resize(1, 1, 1, vector.size());
for (long int i = 0; i < vector.size(); i++)
(*this)(i) = vector[i];
}
/** Destructor.
*/
~MultidimArray()
{
coreDeallocate();
}
/** Clear.
*/
void clear()
{
coreDeallocate();
coreInit();
}
//@}
/// @name Core memory operations
//@{
/** Core init.
* Initialize everything to 0
*/
void coreInit()
{
xdim=0;
yxdim=0;
zyxdim=0;
nzyxdim=0;
ydim=1;
zdim=1;
ndim=1;
zinit=0;
yinit=0;
xinit=0;
data=NULL;
nzyxdimAlloc = 0;
destroyData=true;
mmapOn = false;
mFd=0;
}
/** Core allocate with dimensions.
*/
void coreAllocate(long int _ndim, long int _zdim, long int _ydim, long int _xdim)
{
if (_ndim <= 0 || _zdim <= 0 || _ydim<=0 || _xdim<=0)
{
clear();
return;
}
if(data!=NULL)
REPORT_ERROR( "do not allocate space for an image if you have not deallocate it first");
ndim=_ndim;
zdim=_zdim;
ydim=_ydim;
xdim=_xdim;
yxdim=ydim*xdim;
zyxdim=zdim*yxdim;
nzyxdim=ndim*zyxdim;
coreAllocate();
}
/** Core allocate without dimensions.
*
* It is supposed the dimensions are set previously with setXdim(x), setYdim(y)
* setZdim(z), setNdim(n) or with setDimensions(Xdim, Ydim, Zdim, Ndim);
*
*/
void coreAllocate()
{
if(data!=NULL)
REPORT_ERROR( "do not allocate space for an image if you have not deallocate it first");
if (nzyxdim < 0)
REPORT_ERROR("coreAllocate:Cannot allocate a negative number of bytes");
if (mmapOn)
{
mapFile.initRandom(8);
mapFile = mapFile.addExtension("tmp");
if ( ( mFd = open(mapFile.c_str(), O_RDWR | O_CREAT | O_TRUNC,S_IRUSR|S_IWUSR|S_IRGRP|S_IWGRP) ) == -1 )
REPORT_ERROR("MultidimArray::coreAllocate: Error creating map file.");
if ((lseek(mFd, nzyxdim*sizeof(T), SEEK_SET) == -1)|| (::write(mFd,"",1) == -1))// Use of :: to call write from global space due to confict with multidimarray::write
{
close(mFd);
REPORT_ERROR("MultidimArray::coreAllocate: Error 'stretching' the map file.");
}
if ( (data = (T*) mmap(0,nzyxdim*sizeof(T), PROT_READ | PROT_WRITE, MAP_SHARED, mFd, 0)) == (void*) -1 )
REPORT_ERROR("MultidimArray::coreAllocate: mmap failed.");
}
else
{
data = new T [nzyxdim];
if (data == NULL)
REPORT_ERROR( "Allocate: No space left");
}
nzyxdimAlloc = nzyxdim;
}
/** Core allocate without dimensions.
*
* It is supposed the dimensions are set previously with setXdim(x), setYdim(y)
* setZdim(z), setNdim(n) or with setDimensions(Xdim, Ydim, Zdim, Ndim);
*
*/
void coreAllocateReuse()
{
if(data != NULL && nzyxdim <= nzyxdimAlloc)
return;
else if (nzyxdim > nzyxdimAlloc)
coreDeallocate();
if (nzyxdim < 0)
REPORT_ERROR("coreAllocateReuse:Cannot allocate a negative number of bytes");
if (mmapOn)
{
mapFile.initRandom(8);
mapFile = mapFile.addExtension("tmp");
if ( ( mFd = open(mapFile.c_str(), O_RDWR | O_CREAT | O_TRUNC,S_IRUSR|S_IWUSR|S_IRGRP|S_IWGRP) ) == -1 )
REPORT_ERROR("MultidimArray::coreAllocateReuse: Error creating map file.");
if ((lseek(mFd, nzyxdim*sizeof(T), SEEK_SET) == -1) || (::write(mFd,"",1) == -1))// Use of :: to call write from global space due to confict with multidimarray::write
{
close(mFd);
REPORT_ERROR("MultidimArray::coreAllocateReuse: Error 'stretching' the map file.");
}
if ( (data = (T*) mmap(0,nzyxdim*sizeof(T), PROT_READ | PROT_WRITE, MAP_SHARED, mFd, 0)) == (void*) -1 )
REPORT_ERROR("MultidimArray::coreAllocateReuse: mmap failed.");
}
else
{
data = new T [nzyxdim];
if (data == NULL)
REPORT_ERROR( "Allocate: No space left");
}
nzyxdimAlloc = nzyxdim;
}
/** Sets mmap.
*
* Sets on/off mmap flag to allocate memory in a file.
*
*/
void setMmap(bool mmap)
{
mmapOn = mmap;
}
/** Core deallocate.
* Free all data.
*/
void coreDeallocate()
{
if (data != NULL && destroyData)
{
if (mmapOn)
{
munmap(data,nzyxdimAlloc*sizeof(T));
close(mFd);
remove(mapFile.c_str());
}
else
delete[] data;
}
data=NULL;
nzyxdimAlloc = 0;
}
/** Alias a multidimarray.
*
* Treat the multidimarray as if it were a volume. The data is not copied
* into new memory, but a pointer to the multidimarray is copied.
* You should not make any operation on this volume such that the
* memory locations are changed
*/
void alias(const MultidimArray<T> &m)
{
copyShape(m);
this->data=m.data;
this->destroyData=false;
}
//@}
/// @name Size
//@{
/** Sets new 4D dimensions.
*
* Note that the dataArray is NOT resized. This should be done separately with coreAllocate()
*
*/
void setDimensions(long int Xdim, long int Ydim, long int Zdim, long int Ndim)
{
ndim=Ndim;
zdim=Zdim;
ydim=Ydim;
xdim=Xdim;
yxdim=ydim*xdim;
zyxdim=zdim*yxdim;
nzyxdim=ndim*zyxdim;
}
/** Sets new N dimension.
*
* Note that the dataArray is NOT resized. This should be done separately with coreAllocate()
*
*/
void setNdim(long int Ndim)
{
ndim = Ndim;
nzyxdim=ndim*zyxdim;
}
/** Sets new Z dimension.
*
* Note that the dataArray is NOT resized. This should be done separately with coreAllocate()
*
*/
void setZdim(long int Zdim)
{
zdim = Zdim;
zyxdim=zdim*yxdim;
nzyxdim=ndim*zyxdim;
}
/** Sets new Y dimension.
*
* Note that the dataArray is NOT resized. This should be done separately with coreAllocate()
*
*/
void setYdim(long int Ydim)
{
ydim = Ydim;
yxdim=ydim*xdim;
zyxdim=zdim*yxdim;
nzyxdim=ndim*zyxdim;
}
/** Sets new X dimension.
*
* Note that the dataArray is NOT resized. This should be done separately with coreAllocate()
*
*/
void setXdim(long int Xdim)
{
xdim = Xdim;
yxdim=ydim*xdim;
zyxdim=zdim*yxdim;
nzyxdim=ndim*zyxdim;
}
/** Copy the shape parameters
*
*/
void copyShape(const MultidimArray<T> &m)
{
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;
}
/** 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.
*
* @code
* V1.resize(3, 3, 2);
* @endcode
*/
void resize(long int Ndim, long int Zdim, long int Ydim, long int Xdim)
{
if (Ndim*Zdim*Ydim*Xdim == nzyxdimAlloc && data != NULL)
return;
if (Xdim <= 0 || Ydim <= 0 || Zdim <= 0 || Ndim <= 0)
{
clear();
return;
}
// data can be NULL while xdim etc are set to non-zero values
// (This can happen for reading of images...)
// In that case, initialize data to zeros.
if (NZYXSIZE(*this) > 0 && data == NULL)
{
coreAllocate();
return;
}
// Ask for memory
size_t YXdim=Ydim*Xdim;
size_t ZYXdim=Zdim*YXdim;
size_t NZYXdim=Ndim*ZYXdim;
int new_mFd = 0;
FileName newMapFile;
T * new_data;
try
{
if (mmapOn)
{
newMapFile.initRandom(8);
newMapFile = newMapFile.addExtension("tmp");
if ( ( new_mFd = open(newMapFile.c_str(), O_RDWR | O_CREAT | O_TRUNC,S_IRUSR|S_IWUSR|S_IRGRP|S_IWGRP) ) == -1 )
REPORT_ERROR("MultidimArray::resize: Error creating map file.");
if ((lseek(new_mFd, NZYXdim*sizeof(T)-1, SEEK_SET) == -1) || (::write(new_mFd,"",1) == -1))
{
close(new_mFd);
REPORT_ERROR("MultidimArray::resize: Error 'stretching' the map file.");
}
if ( (new_data = (T*) mmap(0,NZYXdim*sizeof(T), PROT_READ | PROT_WRITE, MAP_SHARED, new_mFd, 0)) == (void*) -1 )
REPORT_ERROR("MultidimArray::resize: mmap failed.");
}
else
new_data = new T [NZYXdim];
}
catch (std::bad_alloc &)
{
REPORT_ERROR( "Allocate: No space left");
}
// Copy needed elements, fill with 0 if necessary
for (long int l = 0; l < Ndim; l++)
for (long int k = 0; k < Zdim; k++)
for (long int i = 0; i < Ydim; i++)
for (long int j = 0; j < Xdim; j++)
{
T val;
if (k >= ZSIZE(*this))
val = 0;
else if (i >= YSIZE(*this))
val = 0;
else if (j >= XSIZE(*this))
val = 0;
else
val = DIRECT_A3D_ELEM(*this, k, i, j);
new_data[l*ZYXdim + k*YXdim+i*Xdim+j] = val;
}
// deallocate old vector
coreDeallocate();
// assign *this vector to the newly created
data = new_data;
ndim = Ndim;
xdim = Xdim;
ydim = Ydim;
zdim = Zdim;
yxdim = Ydim * Xdim;
zyxdim = Zdim * yxdim;
nzyxdim = Ndim * zyxdim;
mFd = new_mFd;
mapFile = newMapFile;
nzyxdimAlloc = nzyxdim;
}
/** Resize a single 3D image
*
* This function assumes n is 1
* @code
* V1.resize(3, 3, 2);
* @endcode
*/
void resize(long int Zdim, long int Ydim, long int Xdim)
{
resize(1, Zdim, Ydim, Xdim);
}
/** Resize a single 2D image
*
* This function assumes n and z are 1
* @code
* V1.resize(3, 2);
* @endcode
*/
void resize(long int Ydim, long int Xdim)
{
resize(1, 1, Ydim, Xdim);
}
/** Resize a single 1D image
*
* This function assumes n and z and y are 1
* @code
* V1.resize(2);
* @endcode
*/
void resize(long int Xdim)
{
resize(1, 1, 1, Xdim);
}
/** Resize according to a pattern.
*
* This function resize the actual array to the same size and origin
* as the input pattern. If the actual array is larger than the pattern
* then the trailing values are lost, if it is smaller then 0's are
* added at the end
*
* @code
* v2.resize(v1);
* // v2 has got now the same structure as v1
* @endcode
*/
template<typename T1>
void resize(const MultidimArray<T1> &v)
{
if (NSIZE(*this) != NSIZE(v) || XSIZE(*this) != XSIZE(v) ||
YSIZE(*this) != YSIZE(v) || ZSIZE(*this) != ZSIZE(v) || data==NULL)
resize(NSIZE(v), ZSIZE(v), YSIZE(v), XSIZE(v));
STARTINGX(*this) = STARTINGX(v);
STARTINGY(*this) = STARTINGY(v);
STARTINGZ(*this) = STARTINGZ(v);
}
/** Returns the multidimArray N,Z, Y and X dimensions.
*
* @code
* V.getDimensions(Xdim, Ydim, Zdim, Ndim);
* @endcode
*/
void getDimensions(long int& Xdim, long int& Ydim, long int& Zdim, long int &Ndim) const
{
Xdim = XSIZE(*this);
Ydim = YSIZE(*this);
Zdim = ZSIZE(*this);
Ndim = NSIZE(*this);
}
/** Returns the total size of the multidimArray
*
* @code
* if (V.getSize() > 1) ...
* @endcode
*/
long int getSize() const
{
return NZYXSIZE(*this);
}
/** Returns the multidimArray dimension.
*
* @code
* int dim = V.getDim();
* @endcode
*/
inline int getDim() const
{
if (NZYXSIZE(*this) < 1)
return 0;
if (ZSIZE(*this) > 1)
return 3;
if (YSIZE(*this) > 1)
return 2;
else
return 1;
}
/** Check dimension.
*
* returns true if the dimension is equal to the argument and false otherwise
* It also prints an error message in the latter case.
*/
#define checkDimension(dim) checkDimensionWithDebug(dim,__FILE__,__LINE__)
void checkDimensionWithDebug(int dim, const char *file, int line) const
{
if (getDim() != dim)
{
std::cerr<<" Check for dimension: " << dim <<std::endl;
std::cerr << "MultidimArray shape: ";
printShape(std::cerr);
std::cerr << std::endl;
std::cerr << "Check called from file "<<file<<" line "<<line<<std::endl;
exit(1);
}
}
/** Get size.
*
* 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.
*/
void getSize(int* size) const
{
size[0] = xdim;
size[1] = ydim;
size[2] = zdim;
size[3] = ndim;
}
/** Generic window routine (dim independent)
*
* This function will call to 3D,2D or 1D specific window routines
*/
void window(long int n0, long int z0, long int y0, long int x0,
long int nF, long int zF, long int yF, long int xF,
T init_value = 0, long n = 0)
{
if (this->ndim >1)
REPORT_ERROR("stack windowing not implemented");
if (this->zdim >1)
{//call 3Dwindow
window( z0, y0, x0,
zF, yF, xF,
init_value ,n );
}
else if (this->ydim >1)
{//call 2Dwindow
window( y0, x0,
yF, xF,
init_value , n );
}
else if (this->xdim >1)
{//call 1Dwindow
window( x0,
xF,
init_value = 0, n );
}
}
/** Put a 3D window to the nth volume
*
* The volume is windowed within the two positions given to this function.
* Indexes always refer to logical indexes. If a position is outside the
* actual matrix range then the matrix is padded init_value until the
* new position is reached. In the following example suppose that m1
* is the following and that the origin is (-1,-1,-1).
*
* @code
* slice 0
* [01 02 03 [
* 04 05 06 04 05 06 0
* 07 08 09] 07 08 09 0]
*
* ----->
*
* slice 1
* [11 12 13 [
* 14 15 16 14 15 16 0
* 17 18 19] 17 18 19 0]
* @endcode
*
* @code
* V1.window(0, 0, -1, 1, 1, 2);
* @endcode
*/
void window(MultidimArray<T> &result, long int z0, long int y0, long int x0, long int zF, long int yF, long int xF,
T init_value = 0, long n = 0) const
{
result.resize(zF - z0 + 1, yF - y0 + 1, xF - x0 + 1);
result.zinit = z0;
result.yinit = y0;
result.xinit = x0;
for (long int k = z0; k <= zF; k++)
for (long int i = y0; i <= yF; i++)
for (long int j = x0; j <= xF; j++)
if ((k >= STARTINGZ(*this) && k <= FINISHINGZ(*this)) &&
(i >= STARTINGY(*this) && i <= FINISHINGY(*this)) &&
(j >= STARTINGX(*this) && j <= FINISHINGX(*this)))
A3D_ELEM(result, k, i, j) = NZYX_ELEM(*this, n, k, i, j);
else
A3D_ELEM(result, k, i, j) = init_value;
}
// As above but acts on itself
void window(long int z0, long int y0, long int x0, long int zF, long int yF, long int xF,
T init_value = 0, long n = 0)
{
MultidimArray<T> result;
window(result, z0, y0, x0, zF, yF, xF, init_value, n);
*this = result;
}
/** Put a 2D window to the nth matrix
*
* The matrix is windowed within the two positions given to this function.
* Indexes always refer to logical indexes. If a position is outside the
* actual matrix range then the matrix is padded with init_value until the
* new position is reached. In the following examples suppose that m1 is the
* following and that the origin is (-1,-1).
*
* @code
* [1 2 3 [1 2 3 0
* m1 = 4 5 6 ---> m1 = 4 5 6 0
* 7 8 9] 7 8 9 0]
*
* @endcode
*
* @code
* m1.window(-1, -1, 1, 2);
* @endcode
*/
void window(MultidimArray<T> &result, long int y0, long int x0, long int yF, long int xF, T init_value = 0, long n = 0) const
{
result.resize(yF - y0 + 1, xF - x0 + 1);
STARTINGY(result) = y0;
STARTINGX(result) = x0;
FOR_ALL_ELEMENTS_IN_ARRAY2D(result)
if (j >= STARTINGX(*this) && j <= FINISHINGX(*this) &&
i >= STARTINGY(*this) && i <= FINISHINGY(*this))
A2D_ELEM(result, i, j) = NZYX_ELEM(*this, n, 0, i, j);
else
A2D_ELEM(result, i, j) = init_value;
}
// As above but acts on itself
void window(long int y0, long int x0, long int yF, long int xF, T init_value = 0, long n = 0)
{
MultidimArray<T> result;
window(result, y0, x0, yF, xF, init_value, n);
*this = result;
}
/** Put a 1D window to the nth vector
*
* The vector is windowed within the two indexes given to this function.
* Indexes always refer to logical indexes. If an index is outside the
* actual vector range then the vector is padded winit_value. In the
* following examples suppose that v1=[-2 -1 0 1 2] and that the origin is
* -2.
*
* @code
* v1.window(-1, 2); // v1=[-1 0 1 2]; v1.startingX() == -1
*
* v1.window(-3, 1); // v1=[0 -2 -1 0 1]; v1.startingX() == -3
* @endcode
*/
void window(MultidimArray<T> &result, long int x0, long int xF, T init_value = 0, long n = 0) const
{
result.resize(xF - x0 + 1);
STARTINGX(result) = x0;
for (long int j = x0; j <= xF; j++)
if (j >= STARTINGX(*this) && j <= FINISHINGX(*this))
A1D_ELEM(result, j) = NZYX_ELEM(*this, n, 0, 0, j);
else
A1D_ELEM(result, j) = init_value;
}
// As above but acts on itself
void window(long int x0, long int xF, T init_value = 0, long n = 0)
{
MultidimArray<T> result;
window(result, x0, xF, init_value, n);
*this = result;
}
/** 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.
*
* @code
* v.printShape();
*
* std::ofstream fh;
* ...;
* v.printShape(fh);
* @endcode
*/
void printShape(std::ostream& out = std::cout) const
{
if (NSIZE(*this) > 1)
out << " Number of images = "<<NSIZE(*this);
int dim = getDim();
if (dim == 3)
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 (dim == 2)
out<< " Size(Y,X): " << YSIZE(*this) << "x" << XSIZE(*this)
<< " i=[" << STARTINGY(*this) << ".." << FINISHINGY(*this) << "]"
<< " j=[" << STARTINGX(*this) << ".." << FINISHINGX(*this) << "]";
else if (dim == 1)
out<< " Size(X): " << XSIZE(*this)
<< " j=[" << STARTINGX(*this) << ".." << FINISHINGX(*this) << "]";
else
out << " Empty MultidimArray!";
out<<"\n";
}
/** Same shape.
*
* Returns true if this object has got the same shape (origin and size)
* than the argument
*/
template <typename T1>
inline bool sameShape(const MultidimArray<T1>& op) const
{
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));
}
/** Outside for 3D matrices
*
* TRUE if the logical index given is outside the definition region of this
* array.
*/
bool outside(long int k, long int i, long int j) const
{
return (j < STARTINGX(*this) || j > FINISHINGX(*this) ||
i < STARTINGY(*this) || i > FINISHINGY(*this) ||
k < STARTINGZ(*this) || k > FINISHINGZ(*this));
}
/** Outside for 2D matrices
*
* TRUE if the logical index given is outside the definition region of this
* array.
*/
bool outside(long int i, long int j) const
{
return (j < STARTINGX(*this) || j > FINISHINGX(*this) ||
i < STARTINGY(*this) || i > FINISHINGY(*this));
}
/** Outside for 1D matrices
*
* TRUE if the logical index given is outside the definition region of this
* array.
*/
bool outside(long int i) const
{
return (i < STARTINGX(*this) || i > FINISHINGX(*this));
}
/** Outside
*
* TRUE if the logical index given is outside the definition region of this
* array.
*/
bool outside(const Matrix1D<double> &r) const
{
if (r.size() < 1)
{
REPORT_ERROR( "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("Outside: index vector has too many components");
}
/** Returns Y dimension.
*/
inline long int rowNumber() const
{
return ydim;
}
/** Returns X dimension.
*/
inline long int colNumber() const
{
return xdim;
}
/** 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.
*
* @code
* V.setXmippOrigin();
* @endcode
*/
void setXmippOrigin()
{
zinit = FIRST_XMIPP_INDEX(zdim);
yinit = FIRST_XMIPP_INDEX(ydim);
xinit = FIRST_XMIPP_INDEX(xdim);
}
/** 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.
*
*/
void moveOriginTo(long int k, long int i, long int j)
{
zinit = k + FIRST_XMIPP_INDEX(zdim);
yinit = i + FIRST_XMIPP_INDEX(ydim);
xinit = j + FIRST_XMIPP_INDEX(xdim);
}
/** 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.
*
*/
void moveOriginTo(long int i, long int j)
{
yinit = i + FIRST_XMIPP_INDEX(ydim);
xinit = j + FIRST_XMIPP_INDEX(xdim);
}
/** Returns the first valid logical Z index.
*/
inline long int startingZ() const
{
return zinit;
}
/** Returns the last valid logical Z index.
*/
inline long int finishingZ() const
{
return zinit + zdim - 1;
}
/** Returns the first valid logical Y index.
*/
inline long int startingY() const
{
return yinit;
}
/** Returns the last valid logical Y index.
*/
inline long int finishingY() const
{
return yinit + ydim - 1;
}
/** Returns the first valid logical X index.
*/
inline long int startingX() const
{
return xinit;
}
/** Returns the last valid logical X index.
*/
inline long int finishingX() const
{
return xinit + xdim - 1;
}
/** IsCorner (in 2D or 3D matrix)
*
* TRUE if the logical index given is a corner of the definition region of this
* array.
*/
bool isCorner(const Matrix1D< double >& v) const
{
if (v.size() < 2)
REPORT_ERROR( "isCorner: index vector has got not enough components");
else if (XSIZE(*this)==2)
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 (XSIZE(*this)==3)
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( "isCorner: index vector has too many components");
}
//@}
///@name Access to the pixel values
//@{
/** Volume element access via double vector.
*
* Returns the value of a matrix logical position, but this time the
* element position is determined by a R3 vector. The elements can be used
* either by value or by reference. An exception is thrown if the index is
* outside the logical range. Pay attention in the following example that
* we are accessing the same element as in the previous function but, now
* we have to give first the X position because we are building first a
* vector of the form (x,y,z).
*
* @code
* V(vectorR3(1, -2, 0)) = 1;
* val = V(vectorR3(1, -2, 0));
* @endcode
*/
T& operator()(const Matrix1D< double >& v) const
{
switch (VEC_XSIZE(v))
{
case 1:
return A1D_ELEM((*this), ROUND(XX(v)));
case 2:
return A2D_ELEM((*this), ROUND(YY(v)), ROUND(XX(v)));
case 3:
return A3D_ELEM((*this), ROUND(ZZ(v)), ROUND(YY(v)), ROUND(XX(v)));
}
}
/** Volume element access via integer vector.
*/
T& operator()(const Matrix1D< long int >& v) const
{
switch (VEC_XSIZE(v))
{
case 1:
return A1D_ELEM((*this), XX(v));
case 2:
return A2D_ELEM((*this), YY(v), XX(v));
case 3:
return A3D_ELEM((*this), ZZ(v), YY(v), XX(v));
}
}
/** 4D element access via index.
*
* Returns the value of a matrix logical position. In our example we could
* access from v(0, 0,-2,-1) to v(0, 1,2,1). The elements can be used either by
* value or by reference. An exception is thrown if the index is outside
* the logical range. Be careful that the argument order is (Z,Y,X).
*
* @code
* V(0, 0, -2, 1) = 1;
* val = V(0, 0, -2, 1);
* @endcode
*/
inline T& operator()(long n, long int k, long int i, long int j) const
{
return NZYX_ELEM(*this, n, k, i, j);
}
/** 3D element access via index.
*
* Returns the value of a matrix logical position. In our example we could
* access from v(0,-2,-1) to v(1,2,1). The elements can be used either by
* value or by reference. An exception is thrown if the index is outside
* the logical range. Be careful that the argument order is (Z,Y,X).
*
* @code
* V(0, -2, 1) = 1;
* val = V(0, -2, 1);
* @endcode
*/
inline T& operator()(long int k, long int i, long int j) const
{
return A3D_ELEM(*this, k, i, j);
}
/** 3D element access via index (getVoxel).
*
* Same function as operator() but with a name. Needed by swig.
*
*/
inline T getVoxel(long int k, long int i, long int j) const
{
return A3D_ELEM(*this, k, i, j);
}
/** 3D element access via index (setVoxel).
*
* Same function as operator() but with a name. Needed by swig.
*
*/
inline void setVoxel(long int k, long int i, long int j, T newval)
{
A3D_ELEM(*this, k, i, j)=newval;
}
/** Matrix element access via index
*
* Returns the value of a matrix logical position. In our example we could
* access from v(-2,-1) to v(2,1). The elements can be used either by value
* or by reference. An exception is thrown if the index is outside the
* logical range. The first argument is the Y position and the second the X
* position.
*
* @code
* m(-2, 1) = 1;
* val = m(-2, 1);
* @endcode
*/
inline T& operator()(long int i, long int j) const
{
return A2D_ELEM(*this, i, j);
}
/** Vector element access
*
* Returns the value of a vector logical position. In our example we could
* access from v(-2) to v(2). The elements can be used either by value or by
* reference. An exception is thrown if the index is outside the logical
* range.
*
* @code
* v(-2) = 1;
* val = v(-2);
* @endcode
*/
inline T& operator()(long int i) const
{
return A1D_ELEM(*this, i);
}
/** Get a single 1,2 or 3D image from a multi-image array
*
* This function extracts a single-image array from a multi-image one.
* @code
* V.getImage(0, m);
* @endcode
*/
void getImage(long n, MultidimArray<T>& M) const
{
if (XSIZE(*this) == 0)
{
M.clear();
return;
}
if (n > NSIZE(*this))
REPORT_ERROR(" Multidimarray getImage: n larger than NSIZE");
M.resize(1, ZSIZE(*this), YSIZE(*this), XSIZE(*this));
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY3D(M)
DIRECT_A2D_ELEM(M, i, j) = DIRECT_NZYX_ELEM(*this, n, k, i, j);
STARTINGX(M) = STARTINGX(*this);
STARTINGY(M) = STARTINGY(*this);
STARTINGZ(M) = STARTINGZ(*this);
}
/** Set a single 1,2 or 3D image in a multi-image array
*
* This function sets a single-image array in a multi-image one.
* @code
* V.setImage(0, m);
* @endcode
*/
void setImage(long n, MultidimArray<T>& M) const
{
if (xdim == 0)
return;
if (n < 0 || n > NSIZE(*this))
REPORT_ERROR( "setImage: MultidimArray subscript (n) out of range");
if ( ZSIZE(M) != ZSIZE(*this) || YSIZE(M) != YSIZE(*this) || XSIZE(M) != XSIZE(*this))
REPORT_ERROR( "setImage: MultidimArray dimensions different from the input image ones");
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY3D(M)
DIRECT_NZYX_ELEM(*this, n, k, i, j) = DIRECT_A3D_ELEM(M, k, i, j);
}
/** 2D Slice access for reading.
*
* This function returns a slice (a 2D matrix) corresponding to the choosen
* slice inside the nth 3D matrix, the numbering of the slices is also logical not
* physical. This function differs from the previous one in that this one
* cuts and assign in a single step instead of in two steps, as in
* the previous example.
*
* @code
* V.slice(0, m);
* @endcode
*/
void getSlice(long int k, MultidimArray<T>& M, char axis = 'Z', long n = 0) const
{
if (XSIZE(*this) == 0)
{
M.clear();
return;
}
switch (axis)
{
case 'Z':
if (k < STARTINGZ(*this) || k > FINISHINGZ(*this))
REPORT_ERROR( "Slice: Multidim subscript (k) out of range");
k = k - STARTINGZ(*this);
M.resize(1, 1, YSIZE(*this), XSIZE(*this));
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D(M)
DIRECT_A2D_ELEM(M, i, j) = DIRECT_NZYX_ELEM(*this, n, k, i, j);
STARTINGX(M) = STARTINGX(*this);
STARTINGY(M) = STARTINGY(*this);
break;
case 'Y':
if (k < STARTINGY(*this) || k > FINISHINGY(*this))
REPORT_ERROR( "Slice: Multidim subscript (i) out of range");
k = k - STARTINGY(*this);
M.resize(ZSIZE(*this), XSIZE(*this));
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D(M)
DIRECT_A2D_ELEM(M, i, j) = DIRECT_NZYX_ELEM(*this, n, i, k, j);
STARTINGX(M) = STARTINGX(*this);
STARTINGY(M) = STARTINGZ(*this);
break;
case 'X':
if (k < STARTINGX(*this) || k > FINISHINGX(*this))
REPORT_ERROR( "Slice: Multidim subscript (j) out of range");
k = k - STARTINGX(*this);
M.resize(ZSIZE(*this), YSIZE(*this));
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D(M)
DIRECT_A2D_ELEM(M, i, j) = DIRECT_NZYX_ELEM(*this, n, i, j, k);
STARTINGX(M) = STARTINGY(*this);
STARTINGY(M) = STARTINGZ(*this);
break;
default:
REPORT_ERROR( (std::string) "Slice: not supported axis " + axis);
}
}
/** Slice access for writing.
*
* This function sets a 2D matrix corresponding to the choosen slice inside the nth
* volume, the numbering of the slices is also logical not physical.
*
* @code
* // Copies slice 0 in slice 1
* V.setSlice(1, (V.slice(0)));
* @endcode
*/
void setSlice(long int k, const MultidimArray<T>& v, long n = 0)
{
if (xdim == 0)
return;
if (k < STARTINGZ(*this) || k > FINISHINGZ(*this))
REPORT_ERROR( "setSlice: MultidimArray subscript (k) out of range");
if (v.rowNumber() != YSIZE(*this) || v.colNumber() != XSIZE(*this))
REPORT_ERROR( "setSlice: MultidimArray dimensions different from the matrix ones");
k = k - STARTINGZ(*this);
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D(v)
DIRECT_NZYX_ELEM(*this, n, k, i, j) = DIRECT_A2D_ELEM(v, i, j);
}
/** Get Column
*
* This function returns a column vector corresponding to the
* choosen column.
*
* @code
* std::vector< double > v;
* m.getCol(-1, v);
* @endcode
*/
void getCol(long int j, MultidimArray<T>& v) const
{
if (xdim == 0 || ydim == 0)
{
v.clear();
return;
}
if (j < 0 || j >= xdim)
REPORT_ERROR("getCol: Matrix subscript (j) greater than matrix dimension");
v.resize(ydim);
for (long int i = 0; i < ydim; i++)
v(i) = (*this)(i, j);
}
/** Set Column
*
* This function sets a column vector corresponding to the choosen column
* inside matrix.
*
* @code
* m.setCol(0, (m.row(1)).transpose()); // Copies row 1 in column 0
* @endcode
*/
void setCol(long int j, const MultidimArray<T>& v)
{
if (xdim == 0 || ydim == 0)
REPORT_ERROR( "setCol: Target matrix is empty");
if (j < 0 || j>= xdim)
REPORT_ERROR( "setCol: Matrix subscript (j) out of range");
if (v.xdim != ydim)
REPORT_ERROR( "setCol: Vector dimension different from matrix one");
for (long int i = 0; i < ydim; i++)
(*this)(i, j) = v(i);
}
/** Get row
*
* This function returns a row vector corresponding to the choosen
* row inside the nth 2D matrix, the numbering of the rows is also
* logical not physical.
*
* @code
* std::vector< double > v;
* m.getRow(-2, v);
* @endcode
*/
void getRow(long int i, MultidimArray<T>& v) const
{
if (xdim == 0 || ydim == 0)
{
v.clear();
return;
}
if (i < 0 || i >= ydim)
REPORT_ERROR( "getRow: Matrix subscript (i) greater than matrix dimension");
v.resize(xdim);
for (long int j = 0; j < xdim; j++)
v(j) = (*this)(i, j);
}
/** Set Row
*
* This function sets a row vector corresponding to the choosen row in the 2D Matrix
*
* @code
* m.setRow(-2, m.row(1)); // Copies row 1 in row -2
* @endcode
*/
void setRow(long int i, const MultidimArray<T>& v)
{
if (xdim == 0 || ydim == 0)
REPORT_ERROR( "setRow: Target matrix is empty");
if (i < 0 || i >= ydim)
REPORT_ERROR( "setRow: Matrix subscript (i) out of range");
if (v.xdim != xdim)
REPORT_ERROR( "setRow: Vector dimension different from matrix one");
for (long int j = 0; j < xdim; j++)
(*this)(i, j) = v(j);
}
/** 3D Logical to physical index translation.
*
* This function returns the physical position of a logical one.
*
* @code
* m.toPhysical(k_log, i_log, j_log, k_phys, i_phys, j_phys);
* @endcode
*/
void toPhysical(long int k_log, long int i_log, long int j_log,
long int& k_phys, long int& i_phys, long int& j_phys) const
{
k_phys = k_log - STARTINGZ(*this);
i_phys = i_log - STARTINGY(*this);
j_phys = j_log - STARTINGX(*this);
}
/** 3D Physical to logical index translation.
*
* This function returns the logical position of a physical one.
*
* @code
* m.toLogical(i_phys, j_phys, i_log, j_log);
* @endcode
*/
void toLogical(long int k_phys, long int i_phys, long int j_phys,
long int& k_log, long int& i_log, long int& j_log) const
{
k_log = k_phys + STARTINGZ(*this);
i_log = i_phys + STARTINGY(*this);
j_log = j_phys + STARTINGX(*this);
}
/** 2D Logical to physical index translation
*
* This function returns the physical position of a logical one.
*
* @code
* m.toPhysical(i_log, j_log, i_phys, j_phys);
* @endcode
*/
void toPhysical(long int i_log, long int j_log, long int& i_phys, long int& j_phys) const
{
i_phys = i_log - STARTINGY(*this);
j_phys = j_log - STARTINGX(*this);
}
/** 2D Physical to logical index translation
*
* This function returns the logical position of a physical one.
*
* @code
* m.toLogical(i_phys, j_phys, i_log, j_log);
* @endcode
*/
void toLogical(long int i_phys, long int j_phys, long int &i_log, long int& j_log) const
{
i_log = i_phys + STARTINGY(*this);
j_log = j_phys + STARTINGX(*this);
}
/** 1D Logical to physical index translation
*
* This function returns the physical position of a logical one.
*
* @code
* v.toPhysical(i_log, i_phys);
* @endcode
*/
void toPhysical(long int i_log, long int& i_phys) const
{
i_phys = i_log - STARTINGX(*this);
}
/** 1D Physical to logical index translation.
*
* This function returns the logical position of a physical one.
*
* @code
* v.toLogical(i_phys, i_log);
* @endcode
*/
void toLogical(long int i_phys, long int& i_log) const
{
i_log = i_phys + STARTINGX(*this);
}
/** Interpolates the value of the nth 3D matrix M at the point (x,y,z).
*
* (x,y,z) are in logical coordinates.
*/
T interpolatedElement3D(double x, double y, double z, T outside_value = (T) 0, long int n = 0)
{
long int x0 = FLOOR(x);
double fx = x - x0;
long int x1 = x0 + 1;
long int y0 = FLOOR(y);
double fy = y - y0;
long int y1 = y0 + 1;
long int z0 = FLOOR(z);
double fz = z - z0;
long int z1 = z0 + 1;
T d000 = (outside(z0, y0, x0)) ? outside_value : NZYX_ELEM(*this, n, z0, y0, x0);
T d001 = (outside(z0, y0, x1)) ? outside_value : NZYX_ELEM(*this, n, z0, y0, x1);
T d010 = (outside(z0, y1, x0)) ? outside_value : NZYX_ELEM(*this, n, z0, y1, x0);
T d011 = (outside(z0, y1, x1)) ? outside_value : NZYX_ELEM(*this, n, z0, y1, x1);
T d100 = (outside(z1, y0, x0)) ? outside_value : NZYX_ELEM(*this, n, z1, y0, x0);
T d101 = (outside(z1, y0, x1)) ? outside_value : NZYX_ELEM(*this, n, z1, y0, x1);
T d110 = (outside(z1, y1, x0)) ? outside_value : NZYX_ELEM(*this, n, z1, y1, x0);
T d111 = (outside(z1, y1, x1)) ? outside_value : NZYX_ELEM(*this, n, z1, y1, x1);
double dx00 = LIN_INTERP(fx, (double) d000, (double) d001);
double dx01 = LIN_INTERP(fx, (double) d100, (double) d101);
double dx10 = LIN_INTERP(fx, (double) d010, (double) d011);
double dx11 = LIN_INTERP(fx, (double) d110, (double) d111);
double dxy0 = LIN_INTERP(fy, (double) dx00, (double) dx10);
double dxy1 = LIN_INTERP(fy, (double) dx01, (double) dx11);
return (T) LIN_INTERP(fz, dxy0, dxy1);
}
/** Interpolates the value of the nth 2D matrix M at the point (x,y)
*
* Bilinear interpolation. (x,y) are in logical coordinates.
*/
inline T interpolatedElement2D(double x, double y, T outside_value = (T) 0, long int n = 0) const
{
long int x0 = FLOOR(x);
double fx = x - x0;
long int x1 = x0 + 1;
long int y0 = FLOOR(y);
double fy = y - y0;
long int y1 = y0 + 1;
T d00 = outside(y0, x0) ? outside_value : NZYX_ELEM(*this, n, 0, y0, x0);
T d10 = outside(y1, x0) ? outside_value : NZYX_ELEM(*this, n, 0, y1, x0);
T d11 = outside(y1, x1) ? outside_value : NZYX_ELEM(*this, n, 0, y1, x1);
T d01 = outside(y0, x1) ? outside_value : NZYX_ELEM(*this, n, 0, y0, x1);
double d0 = (T) LIN_INTERP(fx, (double) d00, (double) d01);
double d1 = (T) LIN_INTERP(fx, (double) d10, (double) d11);
return (T) LIN_INTERP(fy, d0, d1);
}
//@}
/// @name Statistics functions
//@{
/** Print statistics in current line.
*
* No end of line character is written after this print out.
*
* @code
* a.computeStats();
* std::cout << "Statistics of variable a ";
* a.printStats();
* std::cout << std::endl;
* @endcode
*/
void printStats(std::ostream& out = std::cout) const
{
T minval, maxval;
double avgval, devval;
computeStats(avgval, devval, minval, maxval);
out.setf(std::ios::showpoint);
int old_prec = out.precision(7);
out << " min= ";
out.width(9);
out << minval;
out << " max= ";
out.width(9);
out << maxval;
out << " avg= ";
out.width(9);
out << avgval;
out << " dev= ";
out.width(9);
out << devval;
out.precision(old_prec);
}
/** Maximum of the values in the array.
*
* The returned value is of the same type as the type of the array.
*/
T computeMax() const
{
if (NZYXSIZE(*this) <= 0)
return static_cast< T >(0);
T maxval = data[0];
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
if (*ptr > maxval)
maxval = *ptr;
return maxval;
}
/** Minimum of the values in the array.
*
* The returned value is of the same type as the type of the array.
*/
T computeMin() const
{
if (NZYXSIZE(*this) <= 0)
return static_cast< T >(0);
T minval = data[0];
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
if (*ptr < minval)
minval = *ptr;
return minval;
}
/** 4D Indices for the minimum element.
*
* This function returns the index of the minimum element of an array.
* array(l,k,i,j). Returns -1 if the array is empty
*/
void minIndex(long int &lmin, long int& kmin, long int& imin, long int& jmin) const
{
if (XSIZE(*this) == 0)
{
lmin = kmin = imin = jmin = -1;
return;
}
kmin = STARTINGZ(*this);
imin = STARTINGY(*this);
jmin = STARTINGX(*this);
lmin = 0;
T minval = NZYX_ELEM(*this, lmin, kmin, imin, jmin);
FOR_ALL_NZYX_ELEMENTS_IN_MULTIDIMARRAY(*this)
if (NZYX_ELEM(*this, l, k, i, j) > minval)
{
minval = NZYX_ELEM(*this, l, k, i, j);
lmin = l;
kmin = k;
imin = i;
jmin = j;
}
}
/** 3D Indices for the minimum element.
*
* This function just calls to the 4D function
*/
void minIndex(long int& kmin, long int& imin, long int& jmin) const
{
long int zeroInt=0;
minIndex(zeroInt,kmin,imin,jmin);
}
/** 2D Indices for the minimum element.
*
* This function just calls to the 4D function
*/
void minIndex(long int& imin, long int& jmin) const
{
long int zeroInt=0;
minIndex(zeroInt,zeroInt,imin,jmin);
}
/** 1D Indices for the minimum element.
*
* This function just calls to the 4D function
*/
void minIndex(long int& jmin) const
{
long int zeroInt=0;
minIndex(zeroInt,zeroInt,zeroInt,jmin);
}
/** 4D Indices for the maximum element.
*
* This function returns the index of the maximum element of an array.
* array(l,k,i,j). Returns -1 if the array is empty
*/
void maxIndex(long int &lmax, long int& kmax, long int& imax, long int& jmax) const
{
if (XSIZE(*this) == 0)
{
lmax = kmax = imax = jmax = -1;
return;
}
kmax = STARTINGZ(*this);
imax = STARTINGY(*this);
jmax = STARTINGX(*this);
lmax = 0;
T maxval = NZYX_ELEM(*this, lmax, kmax, imax, jmax);
FOR_ALL_NZYX_ELEMENTS_IN_MULTIDIMARRAY(*this)
if (NZYX_ELEM(*this, l, k, i, j) > maxval)
{
maxval = NZYX_ELEM(*this, l, k, i, j);
lmax = l;
kmax = k;
imax = i;
jmax = j;
}
}
/** 3D Indices for the maximum element.
*
* This function just calls to the 4D function
*/
void maxIndex(long int& kmax, long int& imax, long int& jmax) const
{
long int dum;
maxIndex(dum, kmax, imax, jmax);
}
/** 2D Indices for the maximum element.
*
* This function just calls to the 4D function
*/
void maxIndex(long int& imax, long int& jmax) const
{
long int dum;
maxIndex(dum, dum, imax, jmax);
}
/** 1D Indices for the maximum element.
*
* This function just calls to the 4D function
*/
void maxIndex(long int& jmax) const
{
long int dum;
maxIndex(dum, dum, dum, jmax);
}
/** Minimum and maximum of the values in the array.
*
* As doubles.
*/
void computeDoubleMinMax(double& minval, double& maxval) const
{
if (NZYXSIZE(*this) <= 0)
return;
minval = maxval = static_cast< double >(data[0]);
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
{
T val=*ptr;
if (val < minval)
minval = static_cast< double >(val);
else if (val > maxval)
maxval = static_cast< double >(val);
}
}
/** Average of the values in the array.
*
* The returned value is always double, independently of the type of the
* array.
*/
double computeAvg() const
{
if (NZYXSIZE(*this) <= 0)
return 0;
double sum = 0;
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
sum += static_cast< double >(*ptr);
return sum / NZYXSIZE(*this);
}
/** Standard deviation of the values in the array.
*
* Be careful that the standard deviation and NOT the variance is returned.
* The returned value is always double, independently of the type of the
* array.
*/
double computeStddev() const
{
if (NZYXSIZE(*this) <= 1)
return 0;
double avg = 0, stddev = 0;
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
{
double val=static_cast< double >(*ptr);
avg += val;
stddev += val * val;
}
avg /= NZYXSIZE(*this);
stddev = stddev / NZYXSIZE(*this) - avg * avg;
stddev *= NZYXSIZE(*this) / (NZYXSIZE(*this) - 1);
// Foreseeing numerical instabilities
stddev = sqrt(static_cast<double>((ABS(stddev))));
return stddev;
}
/** Compute statistics.
*
* The average, standard deviation, minimum and maximum value are
* returned.
*/
void computeStats(double& avg, double& stddev, T& minval, T& maxval) const
{
if (NZYXSIZE(*this) <= 0)
return;
avg = 0;
stddev = 0;
minval = maxval = data[0];
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
{
T Tval=*ptr;
double val=static_cast< double >(Tval);
avg += val;
stddev += val * val;
if (Tval > maxval)
maxval = Tval;
else if (Tval < minval)
minval = Tval;
}
avg /= NZYXSIZE(*this);
if (NZYXSIZE(*this) > 1)
{
stddev = stddev / NZYXSIZE(*this) - avg * avg;
stddev *= NZYXSIZE(*this) / (NZYXSIZE(*this) - 1);
// Foreseeing numerical instabilities
stddev = sqrt(static_cast< double >(ABS(stddev)));
}
else
stddev = 0;
}
/** Median
*
* Calculate the median element.
*
* @code
* med = v1.computeMedian();
* @endcode
*/
double computeMedian() const
{
if (XSIZE(*this) == 0)
return 0;
if (XSIZE(*this) == 1)
return DIRECT_MULTIDIM_ELEM(*this,0);
// Initialise data
MultidimArray< double > temp(*this);
// Sort indexes
temp.sort();
// Get median
if (NZYXSIZE(*this)%2==0)
return 0.5*(DIRECT_MULTIDIM_ELEM(temp,NZYXSIZE(*this)/2-1)+
DIRECT_MULTIDIM_ELEM(temp,NZYXSIZE(*this)/2 ));
else
return DIRECT_MULTIDIM_ELEM(temp,NZYXSIZE(*this)/2);
}
/** Adjust the range of the array to a given one.
*
* A linear operation is performed on the values of the array such that
* after it, the values of the array are comprissed between the two values
* set. The actual array is modified itself
*
* @code
* v.rangeAdjust(0, 1);
* // The array is now ranging from 0 to 1
* @endcode
*/
void rangeAdjust(T minF, T maxF)
{
if (NZYXSIZE(*this) <= 0)
return;
double min0, max0;
computeDoubleMinMax(min0, max0);
// If max0==min0, it means that the vector is a constant one, so the
// only possible transformation is to a fixed minF
double slope;
if (max0 != min0)
slope = static_cast< double >(maxF - minF) /
static_cast< double >(max0 - min0);
else
slope = 0;
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = minF + static_cast< T >(slope *
static_cast< double >(*ptr - min0));
}
/** Adjust the range of the array to a given one within a mask.
*
* A linear operation is performed on the values of the array such that
* after it, the values of the array are comprissed between the two values
* set. The actual array is modified itself. The linear transformation
* is computed within the mask, but it is applied everywhere.
*
* @code
* v.rangeAdjust(0, 1, mask);
* // The array is now ranging from 0 to 1
* @endcode
*/
// This function must be explictly implemented outside
void rangeAdjust(T minF, T maxF, MultidimArray<int> &mask)
{
if (MULTIDIM_SIZE(*this) <= 0)
return;
double min0, max0;
bool first=true;
T* ptr=NULL;
long int n;
int * ptrMask=MULTIDIM_ARRAY(mask);
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
{
if (*ptrMask)
{
T val= *ptr;
if (first)
{
min0=max0=(double)val;
first=false;
}
else
{
min0=XMIPP_MIN(min0,val);
max0=XMIPP_MAX(max0,val);
}
}
ptrMask++;
}
// If max0==min0, it means that the vector is a constant one, so the
// only possible transformation is to a fixed minF
double slope;
if (max0 != min0)
slope = static_cast< double >(maxF - minF) /
static_cast< double >(max0 - min0);
else
slope = 0;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = minF + static_cast< T >(slope *
static_cast< double >(*ptr - min0));
}
/** Adjust the range of the array to the range of another array in
a least squares sense.
*
* A linear operation is performed on the values of the array such that
* after it, the values of the self array are as similar as possible
* (L2 sense) to the values of the array shown as sample
*/
//As written this will only work for T=double
//nevertheless since this is used is better
//to use T than double or will create problem for int multidim arrays
void rangeAdjust(const MultidimArray<T> &example,
const MultidimArray<int> *mask=NULL)
{
if (NZYXSIZE(*this) <= 0)
return;
// y=a+bx
double sumx=0, sumy=0, sumxy=0, sumx2=0;
T* ptrExample=MULTIDIM_ARRAY(example);
int* ptrMask=NULL;
if (mask!=NULL)
ptrMask=MULTIDIM_ARRAY(*mask);
T* ptr=NULL;
long int n;
double N=0;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
{
bool process=true;
if (mask!=NULL)
if (*ptrMask==0)
process=false;
if (process)
{
T x=*ptr;
T y=*ptrExample;
sumy+=y;
sumxy+=x*y;
sumx+=x;
sumx2+=x*x;
N++;
}
ptrExample++;
if (mask!=NULL)
ptrMask++;
}
double b=(N*sumxy-sumx*sumy)/(N*sumx2-sumx*sumx);
double a=sumy/N-b*sumx/N;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = static_cast< double >(a+b * static_cast< double > (*ptr));
}
/** Adjust the average and stddev of the array to given values.
*
* A linear operation is performed on the values of the array such
* that after it, the average and standard deviation of the array
* are the two values set. The actual array is modified itself
*
* @code
* v.statisticsAdjust(0,1);
* // The array has got now 0 mean and stddev=1
* @endcode
*/
// This function must be explictly implemented outside.
void statisticsAdjust(double avgF, double stddevF)
{
double avg0, stddev0;
double a, b;
if (NZYXSIZE(*this) == 0)
return;
T minval, maxval;
computeStats(avg0, stddev0, minval, maxval);
if (stddev0 != 0)
a = static_cast< double >(stddevF) / static_cast< double >(stddev0);
else
a = 0;
b = static_cast< double >(avgF) - a * static_cast< double >(avg0);
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = static_cast< T >(a * static_cast< double > (*ptr) + b);
}
//@}
/** @name Array "by" array operations.
*
* These are operations that are performed between 2 arrays of the
* SAME type (two integer vectors, two double matrices, ...). If they
* are not of the same type you can convert one of the arrays to the
* desired type using the function typeCast. The result must have been
* defined to be of the same type as the operands.
*
* In this kind of operations each element of array 1 is operated with its
* homologous in array 2, it is very important that both have got the
* same size and starting origins. The result has also got the same
* shape as the two operated arrays and its former content is lost.
*/
//@{
/** Core array by array operation.
*
* It assumes that the result is already resized.
*/
inline friend void coreArrayByArray(const MultidimArray<T>& op1,
const MultidimArray<T>& op2, MultidimArray<T>& result,
char operation)
{
T* ptrResult=NULL;
T* ptrOp1=NULL;
T* ptrOp2=NULL;
long int n;
for (n=0, ptrResult=result.data, ptrOp1=op1.data,ptrOp2=op2.data;
n<op1.zyxdim; ++n, ++ptrResult, ++ptrOp1, ++ptrOp2)
switch (operation)
{
case '+':
*ptrResult = *ptrOp1 + *ptrOp2;
break;
case '-':
*ptrResult = *ptrOp1 - *ptrOp2;
break;
case '*':
*ptrResult = *ptrOp1 * *ptrOp2;
break;
case '/':
*ptrResult = *ptrOp1 / *ptrOp2;
break;
}
}
/** Array by array
*
* This function must take two vectors of the same size, and operate element
* by element according to the operation required. This is the function
* which really implements the operations. Simple calls to it perform much
* faster than calls to the corresponding operators. Although it is supposed
* to be a hidden function not useable by normal programmers.
*
*/
inline friend void arrayByArray(const MultidimArray<T>& op1,
const MultidimArray<T>& op2, MultidimArray<T>& result,
char operation)
{
if (!op1.sameShape(op2))
REPORT_ERROR( (std::string) "Array_by_array: different shapes (" +
operation + ")");
if (result.data == NULL || !result.sameShape(op1))
result.resize(op1);
coreArrayByArray(op1, op2, result, operation);
}
/** v3 = v1 + v2.
*/
MultidimArray<T> operator+(const MultidimArray<T>& op1) const
{
MultidimArray<T> tmp;
arrayByArray(*this, op1, tmp, '+');
return tmp;
}
/** v3 = v1 - v2.
*/
MultidimArray<T> operator-(const MultidimArray<T>& op1) const
{
MultidimArray<T> tmp;
arrayByArray(*this, op1, tmp, '-');
return tmp;
}
/** v3 = v1 * v2.
*/
MultidimArray<T> operator*(const MultidimArray<T>& op1) const
{
MultidimArray<T> tmp;
arrayByArray(*this, op1, tmp, '*');
return tmp;
}
/** v3 = v1 / v2.
*/
MultidimArray<T> operator/(const MultidimArray<T>& op1) const
{
MultidimArray<T> tmp;
arrayByArray(*this, op1, tmp, '/');
return tmp;
}
/** v3 += v2.
*/
void operator+=(const MultidimArray<T>& op1)
{
arrayByArray(*this, op1, *this, '+');
}
/** v3 -= v2.
*/
void operator-=(const MultidimArray<T>& op1)
{
arrayByArray(*this, op1, *this, '-');
}
/** v3 *= v2.
*/
void operator*=(const MultidimArray<T>& op1)
{
arrayByArray(*this, op1, *this, '*');
}
/** v3 /= v2.
*/
void operator/=(const MultidimArray<T>& op1)
{
arrayByArray(*this, op1, *this, '/');
}
//@}
/** @name Array "by" scalar operations
*
* These operations are between an array and a scalar (of the same type as
* the array). The result must have been defined to be of the same type as
* the operands.
*
* In this kind of operations each element of array 1 is operated with the
* given constant. The result has also got the same shape as the input
* array and its former content is lost
*/
//@{
/** Core array by scalar operation.
*
* It assumes that the result is already resized.
*
* This function is not ported to Python.
*/
inline friend void coreArrayByScalar(const MultidimArray<T>& op1,
const T& op2,
MultidimArray<T>& result,
char operation)
{
T* ptrResult=NULL;
T* ptrOp1=NULL;
long int n;
for (n=0, ptrResult=result.data, ptrOp1=op1.data;
n<op1.zyxdim; ++n, ++ptrResult, ++ptrOp1)
switch (operation)
{
case '+':
*ptrResult = *ptrOp1 + op2;
break;
case '-':
*ptrResult = *ptrOp1 - op2;
break;
case '*':
*ptrResult = *ptrOp1 * op2;
break;
case '/':
*ptrResult = *ptrOp1 / op2;
break;
}
}
/** Array by scalar.
*
* This function must take one vector and a constant, and operate element
* by element according to the operation required. This is the function
* which really implements the operations. Simple calls to it perform much
* faster than calls to the corresponding operators. Although it is
* supposed to be a hidden function not useable by normal programmers.
*
* This function is not ported to Python.
*/
inline friend void arrayByScalar(const MultidimArray<T>& op1,
T op2,
MultidimArray<T>& result,
char operation)
{
if (result.data == NULL || !result.sameShape(op1))
result.resize(op1);
coreArrayByScalar(op1, op2, result, operation);
}
/** v3 = v1 + k.
*/
MultidimArray<T> operator+(T op1) const
{
MultidimArray<T> tmp;
arrayByScalar(*this, op1, tmp, '+');
return tmp;
}
/** v3 = v1 - k.
*/
MultidimArray<T> operator-(T op1) const
{
MultidimArray<T> tmp;
arrayByScalar(*this, op1, tmp, '-');
return tmp;
}
/** v3 = v1 * k.
*/
MultidimArray<T> operator*(T op1) const
{
MultidimArray<T> tmp;
arrayByScalar(*this, op1, tmp, '*');
return tmp;
}
/** v3 = v1 / k.
*/
MultidimArray<T> operator/(T op1) const
{
MultidimArray<T> tmp;
arrayByScalar(*this, op1, tmp, '/');
return tmp;
}
/** v3 += k.
*
* This function is not ported to Python.
*/
void operator+=(const T& op1)
{
arrayByScalar(*this, op1, *this, '+');
}
/** v3 -= k.
*
* This function is not ported to Python.
*/
void operator-=(const T& op1)
{
arrayByScalar(*this, op1, *this, '-');
}
/** v3 *= k.
*
* This function is not ported to Python.
*/
void operator*=(const T& op1)
{
arrayByScalar(*this, op1, *this, '*');
}
/** v3 /= k.
*
* This function is not ported to Python.
*/
void operator/=(const T& op1)
{
arrayByScalar(*this, op1, *this, '/');
}
//@}
/** @name Scalar "by" array operations
*
* These operations are between a scalar (of the same type as the array)
* and an array. The result must have been defined to be of the same type
* as the operand. The former content of the result array is lost after
* the operation.
*
* In this kind of operations the constant is operated with each element
* of array 2. The result has also got the same shape as the input array
* and its former content is lost
*/
//@{
/** Core array by scalar operation.
*
* It assumes that the result is already resized.
*
* This function is not ported to Python.
*/
inline friend void coreScalarByArray(const T& op1,
const MultidimArray<T>& op2,
MultidimArray<T>& result,
char operation)
{
T* ptrResult=NULL;
T* ptrOp2=NULL;
long int n;
for (n=0, ptrResult=result.data, ptrOp2=op2.data;
n<op2.zyxdim; ++n, ++ptrResult, ++ptrOp2)
switch (operation)
{
case '+':
*ptrResult = op1 + *ptrOp2;
break;
case '-':
*ptrResult = op1 - *ptrOp2;
break;
case '*':
*ptrResult = op1 * *ptrOp2;
break;
case '/':
*ptrResult = op1 / *ptrOp2;
break;
}
}
/** Scalar by array.
*
* This function must take one scalar and a vector, and operate element by
* element according to the operation required. This is the function which
* really implements the operations. Simple calls to it perform much faster
* than calls to the corresponding operators. Although it is supposed to
* be a hidden function not useable by normal programmers.
*
* This function is not ported to Python.
*/
inline friend void scalarByArray(T op1,
const MultidimArray<T>& op2,
MultidimArray<T>& result,
char operation)
{
if (result.data == NULL || !result.sameShape(op2))
result.resize(op2);
coreScalarByArray(op1, op2, result, operation);
}
/** v3 = k + v2.
*/
friend MultidimArray<T> operator+(T op1, const MultidimArray<T>& op2)
{
MultidimArray<T> tmp;
scalarByArray(op1, op2, tmp, '+');
return tmp;
}
/** v3 = k - v2.
*/
friend MultidimArray<T> operator-(T op1, const MultidimArray<T>& op2)
{
MultidimArray<T> tmp;
scalarByArray(op1, op2, tmp, '-');
return tmp;
}
/** v3 = k * v2.
*/
friend MultidimArray<T> operator*(T op1, const MultidimArray<T>& op2)
{
MultidimArray<T> tmp;
scalarByArray(op1, op2, tmp, '*');
return tmp;
}
/** v3 = k / v2
*/
friend MultidimArray<T> operator/(T op1, const MultidimArray<T>& op2)
{
MultidimArray<T> tmp;
scalarByArray(op1, op2, tmp, '/');
return tmp;
}
//@}
/// @name Initialization
/// @{
/** Same value in all components.
*
* The constant must be of a type compatible with the array type, ie,
* you cannot assign a double to an integer array without a casting.
* It is not an error if the array is empty, then nothing is done.
*
* @code
* v.initConstant(3.14);
* @endcode
*/
void initConstant(T val)
{
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = val;
}
/** Initialize to zeros following a pattern.
*
* All values are set to 0, and the origin and size of the pattern are
* adopted.
*
* @code
* v2.initZeros(v1);
* @endcode
*/
template <typename T1>
void initZeros(const MultidimArray<T1>& op)
{
if (data == NULL || !sameShape(op))
resize(op);
memset(data,0,nzyxdim*sizeof(T));
}
/** Initialize to zeros with current size.
*
* All values are set to 0. The current size and origin are kept. It is not
* an error if the array is empty, then nothing is done.
*
* @code
* v.initZeros();
* @endcode
*/
inline void initZeros()
{
memset(data,0,nzyxdim*sizeof(T));
}
/** Initialize to zeros with a given size.
*/
inline void initZeros(long int Ndim, long int Zdim, long int Ydim, long int Xdim)
{
if (xdim!=Xdim || ydim!=Ydim || zdim!=Zdim || ndim!=Ndim)
resize(Ndim, Zdim,Ydim,Xdim);
memset(data,0,nzyxdim*sizeof(T));
}
/** Initialize to zeros with a given size.
*/
void initZeros(long int Xdim)
{
initZeros(1, 1, 1, Xdim);
}
/** Initialize to zeros with a given size.
*/
void initZeros(long int Ydim, long int Xdim)
{
initZeros(1, 1, Ydim, Xdim);
}
/** Initialize to zeros with a given size.
*/
void initZeros(long int Zdim, long int Ydim, long int Xdim)
{
initZeros(1, Zdim, Ydim, Xdim);
}
/** Linear initialization (only for 1D)
*
* The 1D vector is filled with values increasing/decreasing linearly within a
* range or at given steps.
*
* Increment functionality: The default increment is 1, the initial point is
* incremented by this value until the upper limit is reached. This is the
* default working mode for the function.
*
* @code
* v1.initLinear(1, 3); // v1=[1 2 3]
* v1.initLinear(1.5, 3.1); // v1=[1.5 2.5]
* v1.initLinear(0, 10, 3); // v1=[0 3 6 9]
* v1.initLinear(0, 10, 3, "incr"); // v1=[0 3 6 9]
* @endcode
*
* Step functionality: The given range is divided in as many points as
* indicated (in the example 6 points).
*
* @code
* v1.initLinear(0, 10, 6, "steps"); // v1=[0 2 4 6 8 10]
* @endcode
*/
void initLinear(T minF, T maxF, int n = 1, const std::string& mode = "incr")
{
double slope;
int steps;
if (mode == "incr")
{
steps = 1 + (int) FLOOR((double) ABS((maxF - minF)) / ((double) n));
slope = n * SGN(maxF - minF);
}
else if (mode == "steps")
{
steps = n;
slope = (maxF - minF) / (steps - 1);
}
else
REPORT_ERROR( "Init_linear: Mode not supported (" + mode + ")");
if (steps == 0)
clear();
else
{
resize(steps);
for (int i = 0; i < steps; i++)
A1D_ELEM(*this, i) = (T)((double) minF + slope * i);
}
}
/** Initialize with random values.
*
* This function allows you to initialize the array with a set of random
* values picked from a uniform random distribution or a gaussian one. You
* must choose two parameters for each, for the uniform distribution they
* mean the range where to generate the random numbers, while in the
* gaussian case they are the mean and the standard deviation. By default
* the uniform distribution is selected. The size and origin of the array
* are not modified.
*
* @code
* v.initRandom(0, 1);
* // uniform distribution between 0 and 1
*
* v.initRandom(0, 1, "uniform");
* // the same
*
* v.initRandom(0, 1, "gaussian");
* // gaussian distribution with 0 mean and stddev=1
* @endcode
*/
void initRandom(double op1, double op2, const std::string& mode = "uniform")
{
T* ptr=NULL;
long int n;
if (mode == "uniform")
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = static_cast< T >(rnd_unif(op1, op2));
else if (mode == "gaussian")
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = static_cast< T >(rnd_gaus(op1, op2));
else
REPORT_ERROR( static_cast< std::string >("InitRandom: Mode not supported (" +
mode + ")"));
}
/** Add noise to actual values.
*
* This function add some noise to the actual values of the array according
* to a certain random distribution. You must choose two parameters for
* each, for the uniform distribution they mean the range where to generate
* the random numbers, while in the gaussian case they are the mean and the
* standard deviation. By default the uniform distribution is selected. The
* size and origin of the array are not modified. The array itself is
* modified.
*
* @code
* v1.addNoise(0, 1);
* // uniform distribution between 0 and 1
*
* v1.addNoise(0, 1, "uniform");
* // the same
*
* v1.addNoise(0, 1, "gaussian");
* // gaussian distribution with 0 mean and stddev=1
*
* v1.addNoise(0, 1, "student", 3);
* // t-student distribution with 0 mean and stddev=1, and 3 degrees of freedom
*
* @endcode
*/
void addNoise(double op1,
double op2,
const std::string& mode = "uniform",
double df = 3.) const
{
T* ptr=NULL;
unsigned long int n;
if (mode == "uniform")
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr += static_cast< T >(rnd_unif(op1, op2));
else if (mode == "gaussian")
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr += static_cast< T >(rnd_gaus(op1, op2));
else if (mode == "student")
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr += static_cast< T >(rnd_student_t(df, op1, op2));
else
REPORT_ERROR( static_cast< std::string >("AddNoise: Mode not supported (" +
mode + ")"));
}
//@}
/** @name Utilities
*
* Here you have several easy functions to manage the values of
* the array.
*/
//@{
/** Produce a 3D array suitable for working with Numerical Recipes.
*
* This function must be used only as a preparation for routines which need
* that the first physical index is 1 and not 0 as it usually is in C. New
* memory is needed to hold the new double pointer array.
*/
T*** adaptForNumericalRecipes3D(long int n = 0) const
{
T*** m = NULL;
ask_Tvolume(m, 1, ZSIZE(*this), 1, YSIZE(*this), 1, XSIZE(*this));
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY3D(*this)
m[k+1][i+1][j+1] = DIRECT_NZYX_ELEM(*this, n, k, i, j);
return m;
}
/** Kill a 3D array produced for numerical recipes.
*/
void killAdaptationForNumericalRecipes3D(T*** m) const
{
free_Tvolume(m, 1, ZSIZE(*this), 1, YSIZE(*this), 1, XSIZE(*this));
}
/** Produce a 2D array suitable for working with Numerical Recipes
*
* This function must be used only as a preparation for routines which need
* that the first physical index is 1 and not 0 as it usually is in C. New
* memory is needed to hold the new double pointer array.
*/
T** adaptForNumericalRecipes2D(long int n = 0) const
{
T** m = NULL;
ask_Tmatrix(m, 1, YSIZE(*this), 1, XSIZE(*this));
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D(*this)
m[i+1][j+1] = DIRECT_NZYX_ELEM(*this, n, 0, i, j);
return m;
}
/** Produce a 1D pointer suitable for working with Numerical Recipes (2)
*
* This function meets the same goal as the one before, however this one
* work with 2D arrays as a single pointer. The first element of the array
* is pointed by result[1*Xdim+1], and in general result[i*Xdim+j]
*/
T* adaptForNumericalRecipes22D() const
{
return MULTIDIM_ARRAY(*this) - 1 - XSIZE(*this);
}
/** Load 2D array from numerical recipes result.
*/
void loadFromNumericalRecipes2D(T** m, long int Ydim, long int Xdim)
{
resize(Ydim, Xdim);
for (long int i = 1; i <= Ydim; i++)
for (long int j = 1; j <= Xdim; j++)
(*this)(i - 1, j - 1) = m[i][j];
}
/** Kill a 2D array produced for numerical recipes
*
* The allocated memory is freed.
*/
void killAdaptationForNumericalRecipes2D(T** m) const
{
free_Tmatrix(m, 1, YSIZE(*this), 1, XSIZE(*this));
}
/** Kill a 2D array produced for numerical recipes, 2.
*
* Nothing needs to be done.
*/
void killAdaptationForNumericalRecipes22D(T** m) const
{}
/** Produce a 1D array suitable for working with Numerical Recipes
*
* This function must be used only as a preparation for routines which need
* that the first physical index is 1 and not 0 as it usually is in C. In
* fact the vector provided for Numerical recipes is exactly this same one
* but with the indexes changed.
*
* This function is not ported to Python.
*/
T* adaptForNumericalRecipes1D() const
{
return MULTIDIM_ARRAY(*this) - 1;
}
/** Kill a 1D array produced for Numerical Recipes.
*
* Nothing needs to be done in fact.
*
* This function is not ported to Python.
*/
void killAdaptationForNumericalRecipes1D(T* m) const
{}
/** Computes the center of mass of the nth array
*/
void centerOfMass(Matrix1D< double >& center, void * mask=NULL, long int n = 0)
{
center.initZeros(3);
double mass = 0;
MultidimArray< int >* imask = (MultidimArray< int >*) mask;
FOR_ALL_ELEMENTS_IN_ARRAY3D(*this)
{
if ((imask == NULL || NZYX_ELEM(*imask, n, k, i, j)) &&
A3D_ELEM(*this, k, i, j) > 0)
{
XX(center) += j * NZYX_ELEM(*this, n, k, i, j);
YY(center) += i * NZYX_ELEM(*this, n, k, i, j);
ZZ(center) += k * NZYX_ELEM(*this, n, k, i, j);
mass += NZYX_ELEM(*this, n, k, i, j);
}
}
if (mass != 0)
center /= mass;
// resize center to the correct dimensionality
if (getDim() == 2)
center.resize(2);
else if (getDim() == 1)
center.resize(1);
}
/** Sort 1D vector elements
*
* Sort in ascending order the vector elements. You can use the "selfReverseX"
* function to sort in descending order.
*
* @code
* v1.sort();
* @endcode
*/
void sort()
{
checkDimension(1);
std::sort(MULTIDIM_ARRAY(*this), MULTIDIM_ARRAY(*this) + xdim);
}
/** Get the indices that sort the 1D vector elements (original array intact)
*
* @code
* MultidimArray<long int> idx(v1.size());
* v1.sorted_index(idx);
* @endcode
*/
// TODO: check this function!
void sorted_index(MultidimArray<long> &idx) const
{
checkDimension(1);
//Set up a vector of pairs
std::vector<std::pair<T,long int> > vp;
vp.reserve(XSIZE(*this));
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(*this)
{
vp.push_back(std::make_pair(DIRECT_MULTIDIM_ELEM(*this,n), n));
}
// Sort on the first elements of the pairs
std::sort(vp.begin(), vp.end());
idx.resize(XSIZE(*this));
// Fill the output array with the second elements of the sorted vp
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(idx)
{
DIRECT_MULTIDIM_ELEM(idx, n) = vp[n].second;
}
}
/** Several thresholding.
*
* Apply a threshold to the array, the object is modified itself. There
* are several kinds of thresholding and you must specify it, the values
* given in the fuction have different meanings according to the threshold
* applied.
*
* abs_above: if |x|>a => x=b
* abs_below: if |x|<a => x=b
* above: if x >a => x=b
* below: if x <a => x=b
* range: if x <a => x=a and if x>b => x=b
*
* @code
* v.threshold("abs_above", 10, 10);
* // any value whose absolute value is above 10 will be substituted by
* // -10 (if it is negative) or 10 (if it is positive)
*
* v.threshold("abs_below", 0.1, 0);
* // any value whose absolute value is below 0.1 will be substituted by
* // -0 (if it is negative) or 0 (if it is positive)
*
* v.threshold("above", 10, 10);
* // any value above 10 will be substituted by 10
*
* v.threshold("below", -10, -10);
* // any value below -10 will be substituted by -10
*
* v.threshold("range", 0, 1);
* // v is "saturated" by values 0 and 1, any value outside this range
* // will be substituted by its nearest border
* @endcode
*/
void threshold(const std::string& type,
T a,
T b,
MultidimArray<int> * mask = NULL )
{
int mode;
if (type == "abs_above")
mode = 1;
else if (type == "abs_below")
mode = 2;
else if (type == "above")
mode = 3;
else if (type == "below")
mode = 4;
else if (type == "range")
mode = 5;
else
REPORT_ERROR( static_cast< std::string >("Threshold: mode not supported (" +
type + ")"));
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
{
if (mask == NULL || DIRECT_MULTIDIM_ELEM(*mask,n) > 0 )
{
switch (mode)
{
case 1:
if (ABS(*ptr) > a)
*ptr = SGN(*ptr) * b;
break;
case 2:
if (ABS(*ptr) < a)
*ptr = SGN(*ptr) * b;
break;
case 3:
if (*ptr > a)
*ptr = b;
break;
case 4:
if (*ptr < a)
*ptr = b;
break;
case 5:
if (*ptr < a)
*ptr = a;
else if (*ptr > b)
*ptr = b;
break;
}
}
}
}
/** Count with threshold.
*
* This function returns the number of elements meeting the threshold
* condition.
*/
long int countThreshold(const std::string& type,
T a,
T b,
MultidimArray<int> * mask = NULL )
{
int mode;
if (type == "abs_above")
mode = 1;
else if (type == "abs_below")
mode = 2;
else if (type == "above")
mode = 3;
else if (type == "below")
mode = 4;
else if (type == "range")
mode = 5;
else
REPORT_ERROR( static_cast< std::string >("CountThreshold: mode not supported (" +
type + ")"));
long int ret = 0;
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
if (mask == NULL || DIRECT_MULTIDIM_ELEM(*mask,n) > 0 )
{
switch (mode)
{
case 1:
if (ABS(*ptr) > a)
ret++;
break;
case 2:
if (ABS(*ptr) < a)
ret++;
break;
case 3:
if (*ptr > a)
ret++;
break;
case 4:
if (*ptr < a)
ret++;
break;
case 5:
if (*ptr >= a && *ptr <= b)
ret++;
break;
}
}
return ret;
}
/** Substitute a value by another.
*
* Substitute an old value by a new one. The accuracy is used to say if
* the value in the array is equal to the old value. Set it to 0 for
* perfect accuracy.
*/
void substitute(T oldv,
T newv,
double accuracy = XMIPP_EQUAL_ACCURACY,
MultidimArray<int> * mask = NULL )
{
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
if (mask == NULL || DIRECT_MULTIDIM_ELEM(*mask,n) > 0 )
if (ABS(*ptr - oldv) <= accuracy)
*ptr = newv;
}
/** Substitute a given value by a sample from a Gaussian distribution.
*
* Substitute a given value by a sample from a Gaussian distribution.
* The accuracy is used to say if the value in the array is equal
* to the old value. Set it to 0 for perfect accuracy.
*/
void randomSubstitute(T oldv,
T avgv,
T sigv,
double accuracy = XMIPP_EQUAL_ACCURACY,
MultidimArray<int> * mask = NULL )
{
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
if (mask == NULL || DIRECT_MULTIDIM_ELEM(*mask,n) > 0 )
if (ABS(*ptr - oldv) <= accuracy)
*ptr = rnd_gaus(avgv, sigv);
}
/** Binarize.
*
* This functions substitutes all values in a volume which are greater
* than val+accuracy by 1 and the rest are set to 0. Use threshold to get a
* very powerful binarization.
*/
void binarize(double val = 0,
double accuracy = XMIPP_EQUAL_ACCURACY,
MultidimArray<int> * mask = NULL )
{
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
if ((mask == NULL) || (DIRECT_MULTIDIM_ELEM(*mask,n) > 0) )
{
if (*ptr <= val + accuracy)
{
*ptr = 0;
}
else
{
*ptr = 1;
}
}
}
/** ROUND
*
* Applies a ROUND (look for the nearest integer) to each array element.
*/
void selfROUND()
{
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = ROUND(*ptr);
}
/** CEILING
*
* Applies a CEILING (look for the nearest larger integer) to each
* array element.
*/
void selfCEIL()
{
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = CEIL(*ptr);
}
/** FLOOR
*
* Applies a FLOOR (look for the nearest larger integer) to each
* array element.
*/
void selfFLOOR()
{
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = FLOOR(*ptr);
}
/** ABS
*
* Applies an ABS (absolute value) to each array element.
*/
void selfABS()
{
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = ABS(*ptr);
}
/** MAX
*
* Each component of the result is the maximum of the correspoing
* components of the two input arrays. They must have the same shape, if
* not an exception is thrown
*/
friend void MAX(const MultidimArray<T>& v1, const MultidimArray<T>& v2,
MultidimArray<T>& result)
{
if (!v1.sameShape(v2))
REPORT_ERROR( "MAX: arrays of different shape");
result.resize(v1);
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(result)
DIRECT_MULTIDIM_ELEM(result,n) = XMIPP_MAX(
DIRECT_MULTIDIM_ELEM(v1,n),
DIRECT_MULTIDIM_ELEM(v2,n));
}
/** MIN
*
* Each component of the result is the minimum of the correspoing
* components of the two input arrays. They must have the same shape, if
* not an exception is thrown
*/
friend void MIN(const MultidimArray<T>& v1, const MultidimArray<T>& v2,
MultidimArray<T>& result)
{
if (!v1.sameShape(v2))
REPORT_ERROR( "MIN: arrays of different shape");
result.resize(v1);
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(result)
DIRECT_MULTIDIM_ELEM(result,n) = XMIPP_MIN(
DIRECT_MULTIDIM_ELEM(v1,n),
DIRECT_MULTIDIM_ELEM(v2,n));
}
/** Sqrt.
*
* Each component of the result is the square root of the original
* component.
*/
void selfSQRT()
{
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = static_cast< T >(sqrt(static_cast< double >(*ptr)));
}
/** Sum of matrix values.
*
* This function returns the sum of all internal values.
*
* @code
* double sum = m.sum();
* @endcode
*/
double sum() const
{
double sum = 0;
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
sum += *ptr;
return sum;
}
/** Sum of squared vector values.
*
* This function returns the sum of all internal values to the second
* power_class.
*
* @code
* double sum2 = m.sum2();
* @endcode
*/
double sum2() const
{
double sum = 0;
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
sum += *ptr * *ptr;
return sum;
}
/** Log10.
*
* Each component of the result is the log10 of the original components.
*/
void selfLog10()
{
T* ptr=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this,n,ptr)
*ptr = static_cast< T >(log10(static_cast< double >(*ptr)));
}
/** Reverse matrix values over X axis, keep in this object.
*
* Maybe better with an example:
*
* @code
* slice 0
* [01 02 03 [07 08 09
* 04 05 06 04 05 06
* 07 08 09] 01 02 03]
*
* ----->
*
* slice 1
* [11 12 13 [17 18 19
* 14 15 16 14 15 16
* 17 18 19] 11 12 13]
* @endcode
*
*/
void selfReverseX()
{
long int xsize = XSIZE(*this);
long int halfSizeX = (long int)(xsize-1)/2;
long int ysize = YSIZE(*this);
long int zsize = ZSIZE(*this);
long int nsize = NSIZE(*this);
//0 column should be handled in a different way
//for even and odd matrices
long int start_x = ((xsize%2) ? 0: 1);
for (long int l = 0; l < nsize; l++)
for (long int k = 0; k < zsize; k++)
for (long int i = 0; i < ysize; i++)
for (long int j = start_x; j <= halfSizeX; j++)
{
T aux;
SWAP(DIRECT_NZYX_ELEM(*this, l, k, i, j),
DIRECT_NZYX_ELEM(*this, l, k, i, xsize - j),
aux);
}
//NOTE: line x=0 should not be modified since gets itself by wrapping
//NOTE center hyper-plane (dimx/2,y,z) should remain unchanged
}
/** Reverse matrix values over Y axis, keep in this object.
*
* Maybe better with an example:
*
* @code
* slice 0
* [01 02 03 [03 02 01
* 04 05 06 06 05 04
* 07 08 09] 09 08 07]
*
* ----->
*
* slice 1
* [11 12 13 [13 12 11
* 14 15 16 16 15 14
* 17 18 19] 19 18 17]
* @endcode
*
*/
void selfReverseY()
{
long int xsize = XSIZE(*this);
long int ysize = YSIZE(*this);
long int halfSizeY = (long int)(ysize-1)/2;
long int zsize = ZSIZE(*this);
long int nsize = NSIZE(*this);
//0 column should be handled in a different way
//for even and odd matrices
long int start_y = ((ysize%2) ? 0: 1);
for (long int l = 0; l < nsize; l++)
for (long int k = 0; k < zsize; k++)
for (long int i = start_y; i <= halfSizeY; i++)
for (long int j = 0; j < xsize; j++)
{
T aux;
SWAP(DIRECT_NZYX_ELEM(*this, l, k, i, j),
DIRECT_NZYX_ELEM(*this, l, k, ysize - i, j),
aux);
}
STARTINGY(*this) = -FINISHINGY(*this);
}
/** Reverse matrix values over Z axis, keep in this object.
*
* Maybe better with an example:
*
* @code
* slice 0
* [01 02 03 [11 12 13
* 04 05 06 14 15 16
* 07 08 09] 17 18 19]
*
* ----->
*
* slice 1
* [11 12 13 [01 02 03
* 14 15 16 04 05 06
* 17 18 19] 07 08 09]
* @endcode
*
*/
void selfReverseZ()
{
long int xsize = XSIZE(*this);
long int ysize = YSIZE(*this);
long int zsize = ZSIZE(*this);
long int halfSizeZ = (long int)(zsize-1)/2;
long int nsize = NSIZE(*this);
//0 column should be handled in a different way
//for even and odd matrices
long int start_z = ((zsize%2) ? 0: 1);
for (int l = 0; l < nsize; l++)
for (int k = start_z; k <= halfSizeZ; k++)
for (int i = 0; i <ysize; i++)
for (int j = 0; j < xsize; j++)
{
T aux;
SWAP(DIRECT_NZYX_ELEM(*this, l, k, i, j),
DIRECT_NZYX_ELEM(*this, l, zsize- k, i, j),
aux);
}
STARTINGZ(*this) = -FINISHINGZ(*this);
}
/** Extracts the 1D profile between two points in a 2D array
*
* Given two logical indexes, this function returns samples of the line that
* joins them. This is done by bilinear interpolation. The number of samples
* in the line is N.
*/
void profile(long int x0, long int y0, long int xF, long int yF, long int N,
MultidimArray< double >& profile) const
{
checkDimension(2);
profile.initZeros(N);
double tx_step = (double)(xF - x0) / (N - 1);
double ty_step = (double)(yF - y0) / (N - 1);
double tx = x0, ty = y0;
for (long int i = 0; i < N; i++)
{
profile(i) = interpolatedElement2D(tx, ty);
tx += tx_step;
ty += ty_step;
}
}
/** Show using gnuplot
*
* This function uses gnuplot to plot this vector. You must supply the
* xlabel, ylabel, and title.
*/
void showWithGnuPlot(const std::string& xlabel, const std::string& title)
{
checkDimension(1);
FileName fn_tmp;
fn_tmp.initRandom(10);
MultidimArray<T>::write(static_cast<std::string>("PPP") +
fn_tmp + ".txt");
std::ofstream fh_gplot;
fh_gplot.open((static_cast<std::string>("PPP") + fn_tmp +
".gpl").c_str());
if (!fh_gplot)
REPORT_ERROR( static_cast<std::string>("vector::showWithGnuPlot: Cannot open PPP")
+ fn_tmp + ".gpl for output");
fh_gplot << "set xlabel \"" + xlabel + "\"\n";
fh_gplot << "plot \"PPP" + fn_tmp + ".txt\" title \"" + title +
"\" w l\n";
fh_gplot << "pause 300 \"\"\n";
fh_gplot.close();
system((static_cast<std::string>("(gnuplot PPP") + fn_tmp +
".gpl; rm PPP" + fn_tmp + ".txt PPP" + fn_tmp + ".gpl) &").c_str());
}
/** Edit with xmipp_editor.
*
* This function generates a random filename starting with PPP and
* edits it with xmipp_editor. After closing the editor the file is
* removed.
*/
void edit()
{
FileName nam;
nam.initRandom(15);
nam = static_cast< std::string >("PPP" + nam + ".txt");
write(nam);
system((static_cast< std::string >("xmipp_edit -i " + nam +
" -remove &").c_str()));
}
/* Write to a binary file
*/
void writeBinary(const FileName& fn) const
{
std::ofstream out;
out.open(fn.c_str(), std::ios::out | std::ios::binary);
if (!out)
REPORT_ERROR(static_cast< std::string >("MultidimArray::write: File " + fn + " cannot be opened for output"));
T* ptr;
unsigned long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this, n, ptr)
out.write(reinterpret_cast< char* >(ptr), sizeof(T));
out.close();
}
/** Read from a binary file.
* The array must be previously resized to the correct size.
*/
void readBinary(const FileName& fn)
{
std::ifstream in;
in.open(fn.c_str(), std::ios::in | std::ios::binary);
if (!in)
REPORT_ERROR(static_cast< std::string>("MultidimArray::read: File " + fn + " not found"));
T* ptr;
unsigned long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this, n, ptr)
in.read(reinterpret_cast< char* >(ptr), sizeof(T));
in.close();
}
/** Read from a binary file, while summing to the existing array
* The array must be previously resized to the correct size.
*/
void readBinaryAndSum(const FileName& fn)
{
std::ifstream in;
in.open(fn.c_str(), std::ios::in | std::ios::binary);
if (!in)
REPORT_ERROR(static_cast< std::string>("MultidimArray::read: File " + fn + " not found"));
T* ptr;
T val;
unsigned long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(*this, n, ptr)
{
in.read(reinterpret_cast< char* >(&val), sizeof(T));
*ptr += val;
}
in.close();
}
/** Write to an ASCII file.
*/
void write(const FileName& fn) const
{
std::ofstream out;
out.open(fn.c_str(), std::ios::out);
if (!out)
REPORT_ERROR( static_cast< std::string >("MultidimArray::write: File " + fn + " cannot be opened for output"));
out << *this;
out.close();
}
/** Read from an ASCII file.
*/
void read(const FileName& fn) const
{
std::ofstream in;
in.open(fn.c_str(), std::ios::in);
if (!in)
REPORT_ERROR( static_cast< std::string >("MultidimArray::read: Cannot read File " + fn));
in >> *this;
in.close();
}
//@}
/// @name Operators
/// @{
/** Assignment.
*
* You can build as complex assignment expressions as you like. Multiple
* assignment is allowed.
*
* @code
* v1 = v2 + v3;
* v1 = v2 = v3;
* @endcode
*
* This function is ported to Python as assign.
*/
MultidimArray<T>& operator=(const MultidimArray<T>& op1)
{
if (&op1 != this)
{
if (data == NULL || !sameShape(op1))
resize(op1);
memcpy(data,op1.data,MULTIDIM_SIZE(op1)*sizeof(T));
}
return *this;
}
/** Unary minus.
*
* It is used to build arithmetic expressions. You can make a minus
* of anything as long as it is correct semantically.
*
* @code
* v1 = -v2;
* v1 = -v2.transpose();
* @endcode
*/
MultidimArray<T> operator-() const
{
MultidimArray<T> tmp(*this);
T* ptr;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(tmp,n,ptr)
*ptr = -(*ptr);
return tmp;
}
/** Input from input stream.
*
* Actual size of the array is used to know how many values must be read.
*
* @code
* v.<3);
* std::cin >> v;
* @endcode
*
* This function is not ported to Python.
*/
friend std::istream& operator>>(std::istream& in, MultidimArray<T>& v)
{
T* ptr;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(v,n,ptr)
in >> *ptr;
return in;
}
/** Equality.
*
* Returns true if this object has got the same shape (origin and size)
* than the argument and the same values (within accuracy).
*/
bool equal(const MultidimArray<T>& op,
double accuracy = XMIPP_EQUAL_ACCURACY) const
{
if (!sameShape(op) || data==NULL || op.data == NULL)
return false;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(*this)
if (ABS(DIRECT_MULTIDIM_ELEM(*this,n) -
DIRECT_MULTIDIM_ELEM(op,n)) > accuracy)
return false;
return true;
}
//@}
};
/// @name Functions for all multidimensional arrays
/// @{
/** Conversion from one type to another.
*
* If we have an integer array and we need a double one, we can use this
* function. The conversion is done through a type casting of each element
* If n >= 0, only the nth volumes will be converted, otherwise all NSIZE volumes
*/
template<typename T1, typename T2>
void typeCast(const MultidimArray<T1>& v1, MultidimArray<T2>& v2, long n = -1)
{
if (NZYXSIZE(v1) == 0)
{
v2.clear();
return;
}
if (n < 0)
{
v2.resize(v1);
T1* ptr1=NULL;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(v1,n,ptr1)
DIRECT_MULTIDIM_ELEM(v2,n) = static_cast< T2 >(*ptr1);
}
else
{
v2.resize(ZSIZE(v1),YSIZE(v1),XSIZE(v1));
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY3D(v2)
DIRECT_A3D_ELEM(v2,k,i,j) = static_cast< T2 >DIRECT_NZYX_ELEM(v1,n,k,i,j);
}
}
/** Force positive.
* A median filter is applied at those negative values. Positive values are untouched.
*/
void forcePositive(MultidimArray<double> &V);
/** MultidimArray equality.*/
template<typename T>
bool operator==(const MultidimArray<T>& op1, const MultidimArray<T>& op2)
{
return op1.equal(op2);
}
/** MultidimArray inequality.*/
template<typename T>
bool operator!=(const MultidimArray<T>& op1, const MultidimArray<T>& op2)
{
return !(op1==op2);
}
/** Reduce both volumes to a common size.
*
* Search the range of logical indexes for which both volumes have got valid
* values, and cut both to that size, the corresponding origin is automatically
* computed.
*
* @code
* MultidimArray< double > V1(4, 5, 3);
* V1.startingX() = -2;
* V1.startingY() = -2;
* V1.startingZ() = -2;
*
* MultidimArray< double > V2(4, 2, 3);
* V2.startingX() = 0;
* V2.startingY() = 0;
* V2.startingZ() = 0;
*
* // V1 and V2 range from (0,0,0)=(z,y,x) to (1,1,0)
* cutToCommonSize(V1, V2);
* @endcode
*/
template<typename T>
void cutToCommonSize(MultidimArray<T>& V1, MultidimArray<T>& V2)
{
long int z0 = XMIPP_MAX(STARTINGZ(V1), STARTINGZ(V2));
long int zF = XMIPP_MIN(FINISHINGZ(V1), FINISHINGZ(V2));
long int y0 = XMIPP_MAX(STARTINGY(V1), STARTINGY(V2));
long int yF = XMIPP_MIN(FINISHINGY(V1), FINISHINGY(V2));
long int x0 = XMIPP_MAX(STARTINGX(V1), STARTINGX(V2));
long int xF = XMIPP_MIN(FINISHINGX(V1), FINISHINGX(V2));
V1.window(z0, y0, x0, zF, yF, xF);
V2.window(z0, y0, x0, zF, yF, xF);
}
/** Output to output stream.
* This function is not ported to Python.
*/
template <typename T>
std::ostream& operator<< (std::ostream& ostrm, const MultidimArray<T>& v)
{
if (v.xdim == 0)
ostrm << "NULL Array\n";
else
ostrm << std::endl;
double max_val = ABS(DIRECT_A3D_ELEM(v , 0, 0, 0));
T* ptr;
long int n;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY_ptr(v,n,ptr)
max_val = XMIPP_MAX(max_val, ABS(*ptr));
int prec = bestPrecision(max_val, 10);
if (YSIZE(v)==1 && ZSIZE(v)==1)
{
for (long int j = STARTINGX(v); j <= FINISHINGX(v); j++)
ostrm << floatToString((double) A3D_ELEM(v, 0, 0, j), 10, prec)
<< std::endl;
}
else
{
for (long int l = 0; l < NSIZE(v); l++)
{
if (NSIZE(v)>1)
ostrm << "Image No. " << l << std::endl;
for (long int k = STARTINGZ(v); k <= FINISHINGZ(v); k++)
{
if (ZSIZE(v)>1)
ostrm << "Slice No. " << k << std::endl;
for (long int i = STARTINGY(v); i <= FINISHINGY(v); i++)
{
for (long int j = STARTINGX(v); j <= FINISHINGX(v); j++)
{
ostrm << floatToString((double) A3D_ELEM(v, k, i, j), 10, prec) << ' ';
}
ostrm << std::endl;
}
}
}
}
return ostrm;
}
//@}
// Specializations cases for complex numbers
template<>
std::ostream& operator<<(std::ostream& ostrm, const MultidimArray< Complex >& v);
//@}
#endif
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