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casacore::MaskedLattice< T > Class Template Referenceabstract

A templated, abstract base class for array-like objects with masks. More...

#include <LatticeUtilities.h>

Inheritance diagram for casacore::MaskedLattice< T >:
casacore::Lattice< T > casacore::LatticeBase casacore::CurvedLattice2D< T > casacore::ExtendLattice< T > casacore::ImageInterface< T > casacore::LatticeConcat< T > casacore::LatticeExpr< T > casacore::RebinLattice< T > casacore::SubLattice< T > casacore::ImageInterface< casacore::Complex > casacore::ImageInterface< Complex > casacore::ImageInterface< DComplex > casacore::ImageInterface< Double > casacore::ImageInterface< float > casacore::ImageInterface< Float > casacore::LatticeExpr< Bool >

Public Member Functions

 MaskedLattice ()
 Default constructor. More...
 
 MaskedLattice (const MaskedLattice< T > &)
 Copy constructor. More...
 
virtual ~MaskedLattice ()
 a virtual destructor is needed so that it will use the actual destructor in the derived class More...
 
virtual MaskedLattice< T > * cloneML () const =0
 Make a copy of the object (reference semantics). More...
 
virtual Lattice< T > * clone () const
 Make a copy of the derived object (reference semantics). More...
 
virtual Bool isMasked () const
 Has the object really a mask? The default implementation returns True if the MaskedLattice has a region with a mask. More...
 
virtual Bool hasPixelMask () const
 Does the lattice have a pixelmask? The default implementation returns False. More...
 
virtual const Lattice< Bool > & pixelMask () const
 Get access to the pixelmask. More...
 
virtual Lattice< Bool > & pixelMask ()
 
const LatticeRegionregion () const
 Get the region used. More...
 
Bool getMask (COWPtr< Array< Bool > > &buffer, Bool removeDegenerateAxes=False) const
 Get the mask or a slice from the mask. More...
 
Bool getMaskSlice (COWPtr< Array< Bool > > &buffer, const Slicer &section, Bool removeDegenerateAxes=False) const
 
Bool getMaskSlice (COWPtr< Array< Bool > > &buffer, const IPosition &start, const IPosition &shape, Bool removeDegenerateAxes=False) const
 
Bool getMaskSlice (COWPtr< Array< Bool > > &buffer, const IPosition &start, const IPosition &shape, const IPosition &stride, Bool removeDegenerateAxes=False) const
 
Bool getMask (Array< Bool > &buffer, Bool removeDegenerateAxes=False)
 
Bool getMaskSlice (Array< Bool > &buffer, const Slicer &section, Bool removeDegenerateAxes=False)
 
Bool getMaskSlice (Array< Bool > &buffer, const IPosition &start, const IPosition &shape, Bool removeDegenerateAxes=False)
 
Bool getMaskSlice (Array< Bool > &buffer, const IPosition &start, const IPosition &shape, const IPosition &stride, Bool removeDegenerateAxes=False)
 
Array< BoolgetMask (Bool removeDegenerateAxes=False) const
 
Array< BoolgetMaskSlice (const Slicer &section, Bool removeDegenerateAxes=False) const
 
Array< BoolgetMaskSlice (const IPosition &start, const IPosition &shape, Bool removeDegenerateAxes=False) const
 
Array< BoolgetMaskSlice (const IPosition &start, const IPosition &shape, const IPosition &stride, Bool removeDegenerateAxes=False) const
 
virtual Bool doGetMaskSlice (Array< Bool > &buffer, const Slicer &section)
 The function (in the derived classes) doing the actual work. More...
 
- Public Member Functions inherited from casacore::Lattice< T >
virtual ~Lattice ()
 a virtual destructor is needed so that it will use the actual destructor in the derived class More...
 
virtual DataType dataType () const
 Get the data type of the lattice. More...
 
operator() (const IPosition &where) const
 Return the value of the single element located at the argument IPosition. More...
 
virtual T getAt (const IPosition &where) const
 
virtual void putAt (const T &value, const IPosition &where)
 Put the value of a single element. More...
 
Bool get (COWPtr< Array< T > > &buffer, Bool removeDegenerateAxes=False) const
 Functions which extract an Array of values from a Lattice. More...
 
Bool getSlice (COWPtr< Array< T > > &buffer, const Slicer &section, Bool removeDegenerateAxes=False) const
 
Bool getSlice (COWPtr< Array< T > > &buffer, const IPosition &start, const IPosition &shape, Bool removeDegenerateAxes=False) const
 
Bool getSlice (COWPtr< Array< T > > &buffer, const IPosition &start, const IPosition &shape, const IPosition &stride, Bool removeDegenerateAxes=False) const
 
Bool get (Array< T > &buffer, Bool removeDegenerateAxes=False)
 
Bool getSlice (Array< T > &buffer, const Slicer &section, Bool removeDegenerateAxes=False)
 
Bool getSlice (Array< T > &buffer, const IPosition &start, const IPosition &shape, Bool removeDegenerateAxes=False)
 
Bool getSlice (Array< T > &buffer, const IPosition &start, const IPosition &shape, const IPosition &stride, Bool removeDegenerateAxes=False)
 
Array< T > get (Bool removeDegenerateAxes=False) const
 
Array< T > getSlice (const Slicer &section, Bool removeDegenerateAxes=False) const
 
Array< T > getSlice (const IPosition &start, const IPosition &shape, Bool removeDegenerateAxes=False) const
 
Array< T > getSlice (const IPosition &start, const IPosition &shape, const IPosition &stride, Bool removeDegenerateAxes=False) const
 
void putSlice (const Array< T > &sourceBuffer, const IPosition &where, const IPosition &stride)
 A function which places an Array of values within this instance of the Lattice at the location specified by the IPosition "where", incrementing by "stride". More...
 
void putSlice (const Array< T > &sourceBuffer, const IPosition &where)
 
void put (const Array< T > &sourceBuffer)
 
virtual void set (const T &value)
 Set all elements in the Lattice to the given value. More...
 
virtual void apply (T(*function)(T))
 Replace every element, x, of the Lattice with the result of f(x). More...
 
virtual void apply (T(*function)(const T &))
 
virtual void apply (const Functional< T, T > &function)
 
void operator+= (const Lattice< T > &other)
 Add, subtract, multiple, or divide by another Lattice. More...
 
void operator-= (const Lattice< T > &other)
 
void operator*= (const Lattice< T > &other)
 
void operator/= (const Lattice< T > &other)
 
virtual void copyData (const Lattice< T > &from)
 Copy the data from the given lattice to this one. More...
 
virtual void copyDataTo (Lattice< T > &to) const
 Copy the data from this lattice to the given lattice. More...
 
virtual uInt advisedMaxPixels () const
 This function returns the advised maximum number of pixels to include in the cursor of an iterator. More...
 
virtual LatticeIterInterface< T > * makeIter (const LatticeNavigator &navigator, Bool useRef) const
 These functions are used by the LatticeIterator class to generate an iterator of the correct type for a specified Lattice. More...
 
virtual Bool doGetSlice (Array< T > &buffer, const Slicer &section)=0
 The functions (in the derived classes) doing the actual work. More...
 
virtual void doPutSlice (const Array< T > &buffer, const IPosition &where, const IPosition &stride)=0
 
- Public Member Functions inherited from casacore::LatticeBase
virtual ~LatticeBase ()
 A virtual destructor is needed so that it will use the actual destructor in the derived class. More...
 
virtual String imageType () const
 Get the image type (returns name of derived class). More...
 
virtual Bool isPersistent () const
 Is the lattice persistent and can it be loaded by other processes as well? That is the case for a PagedArray or PagedImage and for an ImageExpr which does not use transient lattices or regions. More...
 
virtual Bool isPaged () const
 Is the lattice paged to disk?
The default implementation returns False. More...
 
virtual Bool canReferenceArray () const
 Can the lattice data be referenced as an array section? That is the case for an ArrayLattice or a Temp/SubLattice using it. More...
 
virtual Bool isWritable () const
 Is the lattice writable?
The default implementation returns True. More...
 
virtual void save (const String &fileName) const
 Save the image in an AipsIO file with the given name. More...
 
virtual Bool lock (FileLocker::LockType, uInt nattempts)
 It is strongly recommended to use class LatticeLocker to handle lattice locking. More...
 
virtual void unlock ()
 
virtual Bool hasLock (FileLocker::LockType) const
 
virtual void resync ()
 Resynchronize the Lattice object with the lattice file. More...
 
virtual void flush ()
 Flush the data (but do not unlock). More...
 
virtual void tempClose ()
 Temporarily close the lattice. More...
 
virtual void reopen ()
 Explicitly reopen the temporarily closed lattice. More...
 
virtual String name (Bool stripPath=False) const
 Return the name of the current Lattice object. More...
 
virtual IPosition shape () const =0
 Return the shape of the Lattice including all degenerate axes (ie. More...
 
virtual uInt ndim () const
 Return the number of axes in this Lattice. More...
 
virtual size_t nelements () const
 Return the total number of elements in this Lattice. More...
 
size_t size () const
 
Bool conform (const LatticeBase &other) const
 Return a value of "True" if this instance of Lattice and 'other' have the same shape, otherwise returns a value of "False". More...
 
virtual LELCoordinates lelCoordinates () const
 Return the coordinates of the lattice. More...
 
IPosition niceCursorShape (uInt maxPixels) const
 Returns a recommended cursor shape for iterating through all the pixels in the Lattice. More...
 
IPosition niceCursorShape () const
 
virtual Bool ok () const
 Check class internals - used for debugging. More...
 
virtual IPosition doNiceCursorShape (uInt maxPixels) const
 The function (in the derived classes) doing the actual work. More...
 
virtual uInt maximumCacheSize () const
 Maximum cache size - not necessarily all used. More...
 
virtual void setMaximumCacheSize (uInt howManyPixels)
 Set the maximum (allowed) cache size as indicated. More...
 
virtual void setCacheSizeInTiles (uInt howManyTiles)
 Set the actual cache size for this Array to be big enough for the indicated number of tiles. More...
 
virtual void setCacheSizeFromPath (const IPosition &sliceShape, const IPosition &windowStart, const IPosition &windowLength, const IPosition &axisPath)
 Set the cache size as to "fit" the indicated path. More...
 
virtual void clearCache ()
 Clears and frees up the caches, but the maximum allowed cache size is unchanged from when setCacheSize was called. More...
 
virtual void showCacheStatistics (ostream &os) const
 Report on cache success. More...
 

Protected Member Functions

MaskedLattice< T > & operator= (const MaskedLattice< T > &)
 Assignment can only be used by derived classes. More...
 
virtual const LatticeRegiongetRegionPtr () const =0
 Get a pointer to the region used. More...
 
- Protected Member Functions inherited from casacore::Lattice< T >
 Lattice ()
 Define default constructor to satisfy compiler. More...
 
virtual void handleMath (const Lattice< T > &from, int oper)
 Handle the Math operators (+=, -=, *=, /=). More...
 
virtual void handleMathTo (Lattice< T > &to, int oper) const
 
 Lattice (const Lattice< T > &)
 Copy constructor and assignment can only be used by derived classes. More...
 
Lattice< T > & operator= (const Lattice< T > &)
 
template<>
void handleMathTo (Lattice< Bool > &, int) const
 
- Protected Member Functions inherited from casacore::LatticeBase
 LatticeBase ()
 Define default constructor to be used by derived classes. More...
 
 LatticeBase (const LatticeBase &)
 Copy constructor and assignment can only be used by derived classes. More...
 
LatticeBaseoperator= (const LatticeBase &)
 
void throwBoolMath () const
 Throw an exception for arithmetic on a Bool Lattice. More...
 

Private Attributes

LatticeRegionitsDefRegPtr
 

Detailed Description

template<class T>
class casacore::MaskedLattice< T >

A templated, abstract base class for array-like objects with masks.

Intended use:

Public interface

Review Status

Date Reviewed:
yyyy/mm/dd
Demo programs:
dLattice

Prerequisite

Etymology

Lattice: "A regular, periodic configuration of points, particles, or objects, throughout an area of a space..." (American Heritage Directory) This definition matches our own: an n-dimensional arrangement of items, on regular orthogonal axes.

Synopsis

This pure abstract base class defines the operations which may be performed on any concrete class derived from it. It has only a few non-pure virtual member functions. The fundamental contribution of this class, therefore, is that it defines the operations derived classes must provide:


Tip: Lattices are always zero origined;

Example

Because Lattice is an abstract base class, an actual instance of this class cannot be constructed. However the interface it defines can be used inside a function. This is always recommended as it allows Functions which have Lattices as arguments to work for any derived class.

I will give a few examples here and then refer the reader to the ArrayLattice class (a memory resident Lattice) and the PagedArray class (a disk based Lattice) which contain further examples with concrete classes (rather than an abstract one). All the examples shown below are used in the dLattice.cc demo program.

Example 1:

This example calculates the mean of the Lattice. Because Lattices can be too large to fit into physical memory it is not good enough to simply use getSlice to read all the elements into an Array. Instead the Lattice is accessed in chunks which can fit into memory (the size is determined by the maxPixels and niceCursorShape functions). The LatticeIterator::cursor() function then returns each of these chunks as an Array and the standard Array based functions are used to calculate the mean on each of these chunks. Functions like this one are the recommended way to access Lattices as the LatticeIterator will correctly setup any required caches.

Complex latMean(const Lattice<Complex>& lat) {
const uInt cursorSize = lat.advisedMaxPixels();
const IPosition cursorShape = lat.niceCursorShape(cursorSize);
const IPosition latticeShape = lat.shape();
Complex currentSum = 0.0f;
size_t nPixels = 0;
RO_LatticeIterator<Complex> iter(lat,
LatticeStepper(latticeShape, cursorShape));
for (iter.reset(); !iter.atEnd(); iter++){
currentSum += sum(iter.cursor());
nPixels += iter.cursor().nelements();
}
return currentSum/nPixels;
}

Example 2:

Sometimes it will be neccesary to access slices of a Lattice in a nearly random way. Often this can be done using the subSection commands in the LatticeStepper class. But it is also possible to use the getSlice and putSlice functions. The following example does a two-dimensional Real to Complex Fourier transform. This example is restricted to four-dimensional Arrays (unlike the previous example) and does not set up any caches (caching is currently only used with PagedArrays). So only use getSlice and putSlice when things cannot be done using LatticeIterators.

void FFT2DReal2Complex(Lattice<Complex>& result,
const Lattice<Float>& input){
AlwaysAssert(input.ndim() == 4, AipsError);
const IPosition shape = input.shape();
const uInt nx = shape(0);
AlwaysAssert (nx > 1, AipsError);
const uInt ny = shape(1);
AlwaysAssert (ny > 1, AipsError);
const uInt npol = shape(2);
const uInt nchan = shape(3);
const IPosition resultShape = result.shape();
AlwaysAssert(resultShape.nelements() == 4, AipsError);
AlwaysAssert(resultShape(3) == nchan, AipsError);
AlwaysAssert(resultShape(2) == npol, AipsError);
AlwaysAssert(resultShape(1) == ny, AipsError);
AlwaysAssert(resultShape(0) == nx/2 + 1, AipsError);
const IPosition inputSliceShape(4,nx,ny,1,1);
const IPosition resultSliceShape(4,nx/2+1,ny,1,1);
COWPtr<Array<Float> >
inputArrPtr(new Array<Float>(inputSliceShape.nonDegenerate()));
Array<Complex> resultArray(resultSliceShape.nonDegenerate());
FFTServer<Float, Complex> FFT2D(inputSliceShape.nonDegenerate());
IPosition start(4,0);
Bool isARef;
for (uInt c = 0; c < nchan; c++){
for (uInt p = 0; p < npol; p++){
isARef = input.getSlice(inputArrPtr,
Slicer(start,inputSliceShape), True);
FFT2D.fft(resultArray, *inputArrPtr);
result.putSlice(resultArray, start);
start(2) += 1;
}
start(2) = 0;
start(3) += 1;
}
}

Example 3:

Occasionally you may want to access a few elements of a Lattice without all the difficulty involved in setting up Iterators or calling getSlice and putSlice. This is demonstrated in the example below and uses the parenthesis operator, along with the LatticeValueRef companion class. Using these functions to access many elements of a Lattice is not recommended as this is the slowest access method.

In this example an ideal point spread function will be inserted into an empty Lattice. As with the previous examples all the action occurs inside a function because Lattice is an interface (abstract) class.

void makePsf(Lattice<Float>& psf) {
const IPosition centrePos = psf.shape()/2;
psf.set(0.0f); // this sets all the elements to zero
// As it uses a LatticeIterator it is efficient
psf(centrePos) = 1; // This sets just the centre element to one
AlwaysAssert(near(psf(centrePos), 1.0f, 1E-6), AipsError);
AlwaysAssert(near(psf(centrePos*0), 0.0f, 1E-6), AipsError);
}

Motivation

Creating an abstract base class which provides a common interface between memory and disk based arrays has a number of advantages.

Definition at line 37 of file LatticeUtilities.h.

Constructor & Destructor Documentation

template<class T>
casacore::MaskedLattice< T >::MaskedLattice ( )
inline

Default constructor.

Definition at line 226 of file MaskedLattice.h.

template<class T>
casacore::MaskedLattice< T >::MaskedLattice ( const MaskedLattice< T > &  )

Copy constructor.

template<class T>
virtual casacore::MaskedLattice< T >::~MaskedLattice ( )
virtual

a virtual destructor is needed so that it will use the actual destructor in the derived class

Member Function Documentation

template<class T>
virtual Lattice<T>* casacore::MaskedLattice< T >::clone ( ) const
virtual

Make a copy of the derived object (reference semantics).

Implements casacore::Lattice< T >.

template<class T>
virtual MaskedLattice<T>* casacore::MaskedLattice< T >::cloneML ( ) const
pure virtual
template<class T>
virtual Bool casacore::MaskedLattice< T >::doGetMaskSlice ( Array< Bool > &  buffer,
const Slicer section 
)
virtual

The function (in the derived classes) doing the actual work.

These functions are public, so they can be used internally in the various Lattice classes.
However, doGetMaskSlice does not call Slicer::inferShapeFromSource to fill in possible unspecified section values. Therefore one should normally use one of the getMask(Slice) functions. doGetMaskSlice should be used with care and only when performance is an issue.
The default implementation gets the mask from the region and fills the buffer with True values if there is no region.

Reimplemented in casacore::SubLattice< T >, casacore::SubLattice< casacore::Float >, casacore::ImageConcat< T >, casacore::LatticeConcat< T >, casacore::LatticeConcat< casacore::Float >, casacore::SubImage< T >, casacore::LatticeExpr< T >, casacore::LatticeExpr< Bool >, casacore::CurvedImage2D< T >, casacore::ExtendLattice< T >, casacore::CurvedLattice2D< T >, casacore::TempImage< T >, casacore::TempImage< casacore::DComplex >, casacore::TempImage< casacore::Float >, casacore::TempImage< casacore::Complex >, casa::ComponentListImage, casacore::ImageExpr< T >, casacore::ImageExpr< Bool >, casacore::MIRIADImage, casacore::FITSImage, casacore::RebinImage< T >, casacore::RebinLattice< T >, casacore::ExtendImage< T >, and casacore::FITSQualityImage.

template<class T>
Bool casacore::MaskedLattice< T >::getMask ( COWPtr< Array< Bool > > &  buffer,
Bool  removeDegenerateAxes = False 
) const

Get the mask or a slice from the mask.

This is the mask formed by combination of the possible pixelmask of the lattice and the possible mask of the region taken from the lattice. If there is no mask, it still works fine. In that case it sizes the buffer correctly and sets it to True.

template<class T>
Bool casacore::MaskedLattice< T >::getMask ( Array< Bool > &  buffer,
Bool  removeDegenerateAxes = False 
)
template<class T>
Array<Bool> casacore::MaskedLattice< T >::getMask ( Bool  removeDegenerateAxes = False) const
template<class T>
Bool casacore::MaskedLattice< T >::getMaskSlice ( COWPtr< Array< Bool > > &  buffer,
const Slicer section,
Bool  removeDegenerateAxes = False 
) const
template<class T>
Bool casacore::MaskedLattice< T >::getMaskSlice ( COWPtr< Array< Bool > > &  buffer,
const IPosition start,
const IPosition shape,
Bool  removeDegenerateAxes = False 
) const
template<class T>
Bool casacore::MaskedLattice< T >::getMaskSlice ( COWPtr< Array< Bool > > &  buffer,
const IPosition start,
const IPosition shape,
const IPosition stride,
Bool  removeDegenerateAxes = False 
) const
template<class T>
Bool casacore::MaskedLattice< T >::getMaskSlice ( Array< Bool > &  buffer,
const Slicer section,
Bool  removeDegenerateAxes = False 
)
template<class T>
Bool casacore::MaskedLattice< T >::getMaskSlice ( Array< Bool > &  buffer,
const IPosition start,
const IPosition shape,
Bool  removeDegenerateAxes = False 
)
template<class T>
Bool casacore::MaskedLattice< T >::getMaskSlice ( Array< Bool > &  buffer,
const IPosition start,
const IPosition shape,
const IPosition stride,
Bool  removeDegenerateAxes = False 
)
template<class T>
Array<Bool> casacore::MaskedLattice< T >::getMaskSlice ( const Slicer section,
Bool  removeDegenerateAxes = False 
) const
template<class T>
Array<Bool> casacore::MaskedLattice< T >::getMaskSlice ( const IPosition start,
const IPosition shape,
Bool  removeDegenerateAxes = False 
) const
template<class T>
Array<Bool> casacore::MaskedLattice< T >::getMaskSlice ( const IPosition start,
const IPosition shape,
const IPosition stride,
Bool  removeDegenerateAxes = False 
) const
template<class T>
virtual const LatticeRegion* casacore::MaskedLattice< T >::getRegionPtr ( ) const
protectedpure virtual
template<class T>
virtual Bool casacore::MaskedLattice< T >::hasPixelMask ( ) const
virtual
template<class T>
virtual Bool casacore::MaskedLattice< T >::isMasked ( ) const
virtual
template<class T>
MaskedLattice<T>& casacore::MaskedLattice< T >::operator= ( const MaskedLattice< T > &  )
protected

Assignment can only be used by derived classes.

template<class T>
virtual const Lattice<Bool>& casacore::MaskedLattice< T >::pixelMask ( ) const
virtual
template<class T>
virtual Lattice<Bool>& casacore::MaskedLattice< T >::pixelMask ( )
virtual
template<class T>
const LatticeRegion& casacore::MaskedLattice< T >::region ( ) const

Get the region used.

This is in principle the region pointed to by getRegionPtr. However, if that pointer is 0, it returns a LatticeRegion for the full image.

Member Data Documentation

template<class T>
LatticeRegion* casacore::MaskedLattice< T >::itsDefRegPtr
mutableprivate

Definition at line 321 of file MaskedLattice.h.


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