A Lattice that is read from or written to an HDF5 dataset. More...

#include <HDF5Lattice.h>

Inheritance diagram for casacore::HDF5Lattice< T >:

Public Member Functions
	HDF5Lattice ()
	The default constructor creates an HDF5Lattice that is useless for just about everything, except that it can be assigned to with the assignment operator. More...

	HDF5Lattice (const TiledShape &shape, const String &filename, const String &arrayName="array", const String &groupName=String())
	Construct a new HDF5Lattice with the specified shape. More...

	HDF5Lattice (const TiledShape &shape)
	Construct a temporary HDF5Lattice with the specified shape. More...

	HDF5Lattice (const TiledShape &shape, const CountedPtr< HDF5File > &file, const String &arrayName, const String &groupName=String())
	Construct a new HDF5Lattice, with the specified shape, in the given HDF5 file. More...

	HDF5Lattice (const String &fileName, const String &arrayName="array", const String &groupName=String())
	Reconstruct from a pre-existing HDF5Lattice in the HDF5 file and group with the given names. More...

	HDF5Lattice (const CountedPtr< HDF5File > &file, const String &arrayName, const String &groupName=String())
	Reconstruct from a pre-existing HDF5Lattice in the HDF5 file and group with the given name. More...

	HDF5Lattice (const HDF5Lattice< T > &other)
	The copy constructor which uses reference semantics. More...

	~HDF5Lattice ()
	The destructor flushes the HDF5Lattice's contents to disk. More...

HDF5Lattice< T > &	operator= (const HDF5Lattice< T > &other)
	The assignment operator with reference semantics. More...

virtual Lattice< T > *	clone () const
	Make a copy of the object (reference semantics). More...

virtual Bool	isPersistent () const
	A HDF5Lattice is always persistent. More...

virtual Bool	isPaged () const
	A HDF5Lattice is always paged to disk. More...

virtual Bool	isWritable () const
	Is the HDF5Lattice writable? More...

virtual IPosition	shape () const
	Returns the shape of the HDF5Lattice. More...

virtual String	name (Bool stripPath=False) const
	Return the current HDF5 file name. More...

const CountedPtr< HDF5File > &	file () const
	Return the current HDF5File object. More...

const CountedPtr< HDF5Group > &	group () const
	Return the current HDF5Group object. More...

const CountedPtr< HDF5DataSet > &	array () const
	Returns the current HDF5DataSet object. More...

const String &	arrayName () const
	Returns the name of this HDF5Lattice. More...

IPosition	tileShape () const
	Returns the current tile shape for this HDF5Lattice. 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 access pattern. More...

virtual T	getAt (const IPosition &where) const
	Return the value of the single element located at the argument IPosition. More...

virtual void	putAt (const T &value, const IPosition &where)
	Put the value of a single element. More...

virtual Bool	ok () const
	A function which checks for internal consistency. More...

virtual LatticeIterInterface< T > *	makeIter (const LatticeNavigator &navigator, Bool useRef) const
	This function is 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)
	Do the actual getting of an array of values. More...

virtual void	doPutSlice (const Array< T > &sourceBuffer, const IPosition &where, const IPosition &stride)
	Do the actual getting of an array of values. More...

virtual uInt	advisedMaxPixels () const
	Returns the maximum recommended number of pixels for a cursor. More...

virtual IPosition	doNiceCursorShape (uInt maxPixels) const
	Get the best cursor shape. More...

virtual void	flush ()
	Flush the data (but do not unlock). 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...

T	operator() (const IPosition &where) const
	Return the value of the single element located at the argument IPosition. 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...

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	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 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	tempClose ()
	Temporarily close the lattice. More...

virtual void	reopen ()
	Explicitly reopen the temporarily closed lattice. 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 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	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...

Private Member Functions
void	makeArray (const TiledShape &shape, const String &arrayName, const String &groupName)
	Make the Array in the HDF5 file and group. More...

void	openArray (const String &arrayName, const String &groupName)
	Open the Array in the HDF5 file and group. More...

void	checkWritable () const
	Check if the file is writable. More...

Private Attributes
CountedPtr< HDF5File >	itsFile

CountedPtr< HDF5Group >	itsGroup

CountedPtr< HDF5DataSet >	itsDataSet

IPosition	itsTileShape

Additional Inherited Members
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...

LatticeBase &	operator= (const LatticeBase &)

void	throwBoolMath () const
	Throw an exception for arithmetic on a Bool Lattice. More...

Detailed Description

template<typename T>
class casacore::HDF5Lattice< T >

A Lattice that is read from or written to an HDF5 dataset.

Intended use:

Public interface

Review Status

Test programs:: tHDF5Lattice

Prerequisite

Synopsis

Astronomical data arrays (like images) have to be persistent. A Lattice is a templated abstract base class to hold any Casacore array. The PagedArray class is a Lattice specialization which stores the data in a Casacore table.
HDF5Lattice ia another Lattice specialization making it possible to store an array as a dataset in a group in an HDF5 file.

When you construct an HDF5Lattice you do not read any data into memory. Instead an HDF5 disk file is created, in a place you specify, to hold the data. This means you need to have enough disk space to hold the array. Constructing a new HDF5Lattice is equivalent to creating a data set in an HDF5 file.

To access the data in a HDF5Lattice you can (in order of preference):

Use a LatticeIterator
Use the getSlice and putSlice member functions
Use the parenthesis operator or getAt and putAt functions

Class PagedArray contains some more info and examples.

Example

Create a HDF5Lattice of Floats of shape [1024,1024,4,256] in a file called "myData_tmp.array" and initialize it to zero.

const IPosition arrayShape(4,1024,1024,4,256);
const String filename("myData_tmp.array");
HDF5Lattice<Float> diskArray(arrayShape, filename);
cout << "Created a HDF5Lattice of shape " << diskArray.shape() 
<< " (" << diskArray.shape().product()/1024/1024*sizeof(Float) 
<< " MBytes)" << endl
<< "in the table called " << diskArray.tableName() << endl;
diskArray.set(0.0f);
// Using the set function is an efficient way to initialize the HDF5Lattice
// as it uses a LatticeIterator internally. Note that the set function is
// defined in the Lattice class that HDF5Lattice is derived from. 

Motivation

There was a need to be able to use HDF5 files to hold image data.

Template Type Argument Requirements (T)

HDF5DataSet supports only a limited amount of types. This restricts the template argument to the types Bool, Int Float, Double, Complex, and DComplex.

Definition at line 109 of file HDF5Lattice.h.

Constructor & Destructor Documentation

template<typename T>

casacore::HDF5Lattice< T >::HDF5Lattice ( )

The default constructor creates an HDF5Lattice that is useless for just about everything, except that it can be assigned to with the assignment operator.

template<typename T>

casacore::HDF5Lattice< T >::HDF5Lattice	(	const TiledShape &	shape,
		const String &	filename,
		const String &	arrayName = `"array"`,
		const String &	groupName = `String()`
	)

Construct a new HDF5Lattice with the specified shape.

A new HDF5 file with the specified filename is constructed to hold the array. The file will remain on disk after the HDF5Lattice goes out of scope or is deleted. Optionally the name of an HDF5 group can be given to create the array in. The group is created if not existing yet.

template<typename T>

casacore::HDF5Lattice< T >::HDF5Lattice ( const TiledShape & shape )

explicit

Construct a temporary HDF5Lattice with the specified shape.

A scratch file is created in the current working directory to hold the array. This file will be deleted automatically when the HDF5Lattice goes out of scope or is deleted.

template<typename T>

casacore::HDF5Lattice< T >::HDF5Lattice	(	const TiledShape &	shape,
		const CountedPtr< HDF5File > &	file,
		const String &	arrayName,
		const String &	groupName = `String()`
	)

Construct a new HDF5Lattice, with the specified shape, in the given HDF5 file.

The array gets the given name. Optionally the name of an HDF5 group can be given to create the array in. The group is created if not existing yet.

template<typename T>

casacore::HDF5Lattice< T >::HDF5Lattice	(	const String &	fileName,
		const String &	arrayName = `"array"`,
		const String &	groupName = `String()`
	)

explicit

Reconstruct from a pre-existing HDF5Lattice in the HDF5 file and group with the given names.

template<typename T>

casacore::HDF5Lattice< T >::HDF5Lattice	(	const CountedPtr< HDF5File > &	file,
		const String &	arrayName,
		const String &	groupName = `String()`
	)

explicit

Reconstruct from a pre-existing HDF5Lattice in the HDF5 file and group with the given name.

template<typename T>

casacore::HDF5Lattice< T >::HDF5Lattice ( const HDF5Lattice< T > & other )

The copy constructor which uses reference semantics.

Copying by value doesn't make sense, because it would require the creation of a temporary (but possibly huge) file on disk.

template<typename T>

casacore::HDF5Lattice< T >::~HDF5Lattice ( )

The destructor flushes the HDF5Lattice's contents to disk.

Member Function Documentation

template<typename T>

virtual uInt casacore::HDF5Lattice< T >::advisedMaxPixels ( ) const

virtual

Returns the maximum recommended number of pixels for a cursor.

This is the number of pixels in a tile.

Reimplemented from casacore::Lattice< T >.

template<typename T>

const CountedPtr<HDF5DataSet>& casacore::HDF5Lattice< T >::array ( ) const

inline

Returns the current HDF5DataSet object.

Definition at line 197 of file HDF5Lattice.h.

template<typename T>

const String& casacore::HDF5Lattice< T >::arrayName ( ) const

inline

Returns the name of this HDF5Lattice.

Definition at line 201 of file HDF5Lattice.h.

template<typename T>

void casacore::HDF5Lattice< T >::checkWritable ( ) const

private

Check if the file is writable.

template<typename T>

virtual Lattice<T>* casacore::HDF5Lattice< T >::clone ( ) const

virtual

Make a copy of the object (reference semantics).

Implements casacore::Lattice< T >.

template<typename T>

virtual Bool casacore::HDF5Lattice< T >::doGetSlice	(	Array< T > &	buffer,
		const Slicer &	section
	)

virtual

Do the actual getting of an array of values.

Implements casacore::Lattice< T >.

template<typename T>

virtual IPosition casacore::HDF5Lattice< T >::doNiceCursorShape ( uInt maxPixels ) const

virtual

Get the best cursor shape.

Reimplemented from casacore::LatticeBase.

template<typename T>

virtual void casacore::HDF5Lattice< T >::doPutSlice	(	const Array< T > &	sourceBuffer,
		const IPosition &	where,
		const IPosition &	stride
	)

virtual

Do the actual getting of an array of values.

Implements casacore::Lattice< T >.

template<typename T>

const CountedPtr<HDF5File>& casacore::HDF5Lattice< T >::file ( ) const

inline

Return the current HDF5File object.

Definition at line 189 of file HDF5Lattice.h.

template<typename T>

virtual void casacore::HDF5Lattice< T >::flush ( )

virtual

Flush the data (but do not unlock).

Reimplemented from casacore::LatticeBase.

template<typename T>

virtual T casacore::HDF5Lattice< T >::getAt ( const IPosition & where ) const

virtual

Return the value of the single element located at the argument IPosition.

Note that Lattice::operator() can also be used.

Reimplemented from casacore::Lattice< T >.

template<typename T>

const CountedPtr<HDF5Group>& casacore::HDF5Lattice< T >::group ( ) const

inline

Return the current HDF5Group object.

Definition at line 193 of file HDF5Lattice.h.

template<typename T>

virtual Bool casacore::HDF5Lattice< T >::isPaged ( ) const

virtual

A HDF5Lattice is always paged to disk.

Reimplemented from casacore::LatticeBase.

template<typename T>

virtual Bool casacore::HDF5Lattice< T >::isPersistent ( ) const

virtual

A HDF5Lattice is always persistent.

Reimplemented from casacore::LatticeBase.

template<typename T>

virtual Bool casacore::HDF5Lattice< T >::isWritable ( ) const

virtual

Is the HDF5Lattice writable?

Reimplemented from casacore::LatticeBase.

template<typename T>

void casacore::HDF5Lattice< T >::makeArray	(	const TiledShape &	shape,
		const String &	arrayName,
		const String &	groupName
	)

private

Make the Array in the HDF5 file and group.

template<typename T>

virtual LatticeIterInterface<T>* casacore::HDF5Lattice< T >::makeIter	(	const LatticeNavigator &	navigator,
		Bool	useRef
	)		const

virtual

This function is used by the LatticeIterator class to generate an iterator of the correct type for a specified Lattice.

Not recommended for general use.

Reimplemented from casacore::Lattice< T >.

template<typename T>

virtual String casacore::HDF5Lattice< T >::name ( Bool stripPath = False ) const

virtual

Return the current HDF5 file name.

By default this includes the full path. The path preceeding the file name can be stripped off on request.

Reimplemented from casacore::LatticeBase.

template<typename T>

virtual Bool casacore::HDF5Lattice< T >::ok ( ) const

virtual

A function which checks for internal consistency.

Returns False if something nasty has happened to the HDF5Lattice. In that case it also throws an exception.

Reimplemented from casacore::LatticeBase.

template<typename T>

void casacore::HDF5Lattice< T >::openArray	(	const String &	arrayName,
		const String &	groupName
	)

private

Open the Array in the HDF5 file and group.

template<typename T>

HDF5Lattice<T>& casacore::HDF5Lattice< T >::operator= ( const HDF5Lattice< T > & other )

The assignment operator with reference semantics.

As with the copy constructor assigning by value does not make sense.

template<typename T>

virtual void casacore::HDF5Lattice< T >::putAt	(	const T &	value,
		const IPosition &	where
	)

virtual

Put the value of a single element.

Reimplemented from casacore::Lattice< T >.

template<typename T>

virtual void casacore::HDF5Lattice< T >::setCacheSizeFromPath	(	const IPosition &	sliceShape,
		const IPosition &	windowStart,
		const IPosition &	windowLength,
		const IPosition &	axisPath
	)