casacore::HDF5Image< T > Class Template Reference

Read, store, and manipulate astronomical images in HDF5 format. More...

#include <HDF5Image.h>

Inheritance diagram for casacore::HDF5Image< T >:

Public Member Functions
	HDF5Image (const TiledShape &mapShape, const CoordinateSystem &coordinateInfo, const String &nameOfNewFile)
	Construct a new Image from shape and coordinate information.
	HDF5Image (const String &fileName, MaskSpecifier=MaskSpecifier())
	Reconstruct an image from a pre-existing file.
	HDF5Image (const HDF5Image< T > &other)
	Copy constructor (reference semantics).
	~HDF5Image ()
HDF5Image< T > &	operator= (const HDF5Image< T > &other)
	Assignment operator (reference semantics).
virtual ImageInterface< T > *	cloneII () const
	Make a copy of the object (reference semantics).
virtual String	imageType () const
	Get the image type (returns name of derived class).
virtual String	name (Bool stripPath=False) const
	Return the current HDF5 file name.
virtual void	resize (const TiledShape &newShape)
	Function which changes the shape of the ImageExpr.
virtual Bool	ok () const
	Check for symmetry in data members.
virtual IPosition	shape () const
	Return the shape of the image.
virtual Bool	doGetSlice (Array< T > &buffer, const Slicer &theSlice)
	Function which extracts an array from the map.
virtual void	doPutSlice (const Array< T > &sourceBuffer, const IPosition &where, const IPosition &stride)
	Function to replace the values in the map with soureBuffer.
virtual const LatticeRegion *	getRegionPtr () const
	Get a pointer the default pixelmask object used with this image.
virtual Bool	isPersistent () const
	An HDF5Image is always persistent.
virtual Bool	isPaged () const
	An HDF5Image is always paged to disk.
virtual Bool	isWritable () const
	Is the HDF5Image writable?
virtual Bool	hasPixelMask () const
	Does the image object use a pixelmask?
virtual const Lattice< Bool > &	pixelMask () const
	Get access to the pixelmask used.
virtual Lattice< Bool > &	pixelMask ()
virtual void	setDefaultMask (const String &maskName)
	Set the default pixelmask to the mask with the given name (which has to exist in the "masks" group).
virtual void	useMask (MaskSpecifier=MaskSpecifier())
	Use the mask as specified.
virtual void	apply (T(*function)(T))
	Replace every element, x, of the lattice with the result of f(x).
virtual void	apply (T(*function)(const T &))
virtual void	apply (const Functional< T, T > &function)
HDF5Image< T > &	operator+= (const Lattice< T > &other)
	Add a lattice to this image.
virtual Bool	setUnits (const Unit &newUnits)
	Function which sets the units associated with the image pixels (i.e.
virtual Bool	setCoordinateInfo (const CoordinateSystem &coords)
	Flushes the new coordinate system to disk if the file is writable.
virtual T	getAt (const IPosition &where) const
	These are the true implementations of the paran operator.
virtual void	putAt (const T &value, const IPosition &where)
	Put the value of a single element.
virtual Bool	setMiscInfo (const RecordInterface &newInfo)
	Replace the miscinfo in the HDF5Image.
virtual Bool	setImageInfo (const ImageInfo &info)
	The ImageInfo object contains some miscellaneous information about the image, which unlike that stored in MiscInfo, has a standard list of things, such as the restoring beam.
virtual ImageAttrHandler &	attrHandler (Bool createHandler=False)
	Get access to the attribute handler.
virtual void	removeRegion (const String &name, RegionHandler::GroupType=RegionHandler::Any, Bool throwIfUnknown=True)
	Remove a region/mask belonging to the image from the given group (which can be Any).
virtual LatticeIterInterface< T > *	makeIter (const LatticeNavigator &navigator, Bool useRef) const
	This is the implementation of the letter for the envelope Iterator class; Note: Not for public use ;.
virtual uInt	advisedMaxPixels () const
	Returns the maximum recommended number of pixels for a cursor.
virtual IPosition	doNiceCursorShape (uInt maxPixels) const
	Help the user pick a cursor for most efficient access.
virtual void	flush ()
	Flush the data.
Private Member Functions
void	attach_logtable ()
	This must be called in every constructor and place where the image is attached to a new image.
void	open_logtable ()
void	restoreUnits (const RecordInterface &rec)
void	restoreMiscInfo (const RecordInterface &rec)
void	restoreImageInfo (const RecordInterface &rec)
	Restore the image info from the record.
void	restoreAll ()
void	check_conformance (const Lattice< T > &other)
void	applyMaskSpecifier (const MaskSpecifier &)
void	applyMask (const String &maskName)
Static Private Member Functions
static const CountedPtr < HDF5File > &	getFile (void *imagePtr)
	Function to return the internal HDF5File object to the RegionHandler.
Private Attributes
HDF5Lattice< T >	map_p
LatticeRegion *	regionPtr_p
ImageAttrHandlerHDF5	itsAttrHandler

Detailed Description

template<class T>
class casacore::HDF5Image< T >

Read, store, and manipulate astronomical images in HDF5 format.

Intended use:

Public interface

Review Status

Test programs:: tHDF5Image
Demo programs:: dHDF5Image

Prerequisite

Etymology

The HDF5Image name comes from its role as the Image class using HDF5.

Synopsis

All Casacore Images are Lattices. They may be treated like any other Lattice; getSlice(...), putSlice(...), LatticeIterator for iterating, etc..\. ArrayImages contain a map, a mask for that map, and coordinate information. This provides a Lattice interface for images and their respective coordinates. Additional functionality is defined by the ImageInterface class.

You can use the global function imagePixelType to determine what the pixel type of an image is before you open the image if your code can work with Images of many possible types, or for error checking.

Example

This example shows how to create a mask for an image, fill it, and make it known to the image.

 // Open the image (as readonly for the moment).
 HDF5Image<Float> myimage ("image.name");
 // Create a mask for the image.
 // The mask will be stored in a subtable of the image.
 LCPagedMask mask (RegionHandler::makeMask (myimage, "mask.name"));
 // Fill the mask with whatever values (e.g. all True).
 mask.set (True);
 // Make the mask known to the image (with name mask1).
 myimage.defineRegion ("mask1", mask, RegionHandler::Masks);
 // Make the mask the default mask for this image.
 myimage.setDefaultMask ("mask1");

It is possible to create as many masks as one likes. They can all be defined as masks for the image (with different names, of course). However, only one of them can be the default mask (the mask used by default when the image is opened). When another mask has to be used, one can do two things:

Use setDefaultMask to make the other mask the default mask. This is advisable when the change should be more or less permanent.
Open the HDF5Image without using a default mask. Thereafter a SubImage object can be created from the HDF5Image and the mask. This is advisable when it the mask has to be used only one time.

Motivation

The size of astronomical data can be very large. The ability to fit an entire image into random access memory cannot be guaranteed. Paging from disk pieces of the image appeared to be the way to deal with this problem.

Note: When you make a new HDF5Image, and you are transferring information from some other HDF5Image, be aware that you must copy, manually, things like miscInfo, imageInfo, units, logSink (history) to the new file;

Definition at line 122 of file HDF5Image.h.

Constructor & Destructor Documentation

template<class T>

casacore::HDF5Image< T >::HDF5Image	(	const TiledShape &	mapShape,
		const CoordinateSystem &	coordinateInfo,
		const String &	nameOfNewFile
	)

Construct a new Image from shape and coordinate information.

The image will be stored in the named file.

template<class T>

casacore::HDF5Image< T >::HDF5Image	(	const String &	fileName,
		MaskSpecifier	= `MaskSpecifier()`
	)			`[explicit]`

Reconstruct an image from a pre-existing file.

By default the default pixelmask (if available) is used.

template<class T>

casacore::HDF5Image< T >::HDF5Image ( const HDF5Image< T > & other )

Copy constructor (reference semantics).

template<class T>

casacore::HDF5Image< T >::~HDF5Image ( )

Member Function Documentation

template<class T>

virtual uInt casacore::HDF5Image< 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<class T>

virtual void casacore::HDF5Image< T >::apply ( const Functional< T, T > & function ) [virtual]

Reimplemented from casacore::Lattice< T >.

template<class T>

virtual void casacore::HDF5Image< T >::apply ( T(*)(const T &) function ) [virtual]

Reimplemented from casacore::Lattice< T >.

template<class T>

virtual void casacore::HDF5Image< T >::apply ( T(*)(T) function ) [virtual]

Replace every element, x, of the lattice with the result of f(x).

you must pass in the address of the function -- so the function must be declared and defined in the scope of your program. Both versions of apply require a function that accepts a single argument of type T (the Lattice template actual type) and returns a result of the same type. The first apply expects a function with an argument passed by value; the second expects the argument to be passed by const reference. The first form ought to run faster for the built-in types, which may be an issue for large Lattices stored in memory, where disk access is not an issue.

Reimplemented from casacore::Lattice< T >.

template<class T>

void casacore::HDF5Image< T >::applyMask ( const String & maskName ) [private]

template<class T>

void casacore::HDF5Image< T >::applyMaskSpecifier ( const MaskSpecifier & ) [private]

template<class T>

void casacore::HDF5Image< T >::attach_logtable ( ) [private]

This must be called in every constructor and place where the image is attached to a new image.

template<class T>

virtual ImageAttrHandler& casacore::HDF5Image< T >::attrHandler ( Bool createHandler = False ) [virtual]

Get access to the attribute handler.

If a handler keyword does not exist yet, it is created if createHandler is set. Otherwise the handler is empty and no groups can be created for it.

Reimplemented from casacore::ImageInterface< T >.

template<class T>

void casacore::HDF5Image< T >::check_conformance ( const Lattice< T > & other ) [private]

template<class T>

virtual ImageInterface<T>* casacore::HDF5Image< T >::cloneII ( ) const [virtual]

Make a copy of the object (reference semantics).

Implements casacore::ImageInterface< T >.

template<class T>

virtual Bool casacore::HDF5Image< T >::doGetSlice	(	Array< T > &	buffer,
		const Slicer &	theSlice
	)			`[virtual]`

Function which extracts an array from the map.

Implements casacore::Lattice< T >.

template<class T>

virtual IPosition casacore::HDF5Image< T >::doNiceCursorShape ( uInt maxPixels ) const [virtual]

Help the user pick a cursor for most efficient access.

Reimplemented from casacore::LatticeBase.

template<class T>

virtual void casacore::HDF5Image< T >::doPutSlice	(	const Array< T > &	sourceBuffer,
		const IPosition &	where,
		const IPosition &	stride
	)			`[virtual]`

Function to replace the values in the map with soureBuffer.

Implements casacore::Lattice< T >.

template<class T>

virtual void casacore::HDF5Image< T >::flush ( ) [virtual]

Flush the data.

Reimplemented from casacore::LatticeBase.

template<class T>

virtual T casacore::HDF5Image< T >::getAt ( const IPosition & where ) const [virtual]

These are the true implementations of the paran operator.

Note: Not for public use

Reimplemented from casacore::Lattice< T >.

template<class T>

static const CountedPtr<HDF5File>& casacore::HDF5Image< T >::getFile ( void * imagePtr ) [static, private]

Function to return the internal HDF5File object to the RegionHandler.

template<class T>

virtual const LatticeRegion* casacore::HDF5Image< T >::getRegionPtr ( ) const [virtual]

Get a pointer the default pixelmask object used with this image.

It returns 0 if no default pixelmask is used.

Implements casacore::MaskedLattice< T >.

template<class T>

virtual Bool casacore::HDF5Image< T >::hasPixelMask ( ) const [virtual]

Does the image object use a pixelmask?

Reimplemented from casacore::MaskedLattice< T >.

template<class T>

virtual String casacore::HDF5Image< T >::imageType ( ) const [virtual]

Get the image type (returns name of derived class).

Implements casacore::ImageInterface< T >.

template<class T>

virtual Bool casacore::HDF5Image< T >::isPaged ( ) const [virtual]

An HDF5Image is always paged to disk.

Reimplemented from casacore::LatticeBase.

template<class T>

virtual Bool casacore::HDF5Image< T >::isPersistent ( ) const [virtual]

An HDF5Image is always persistent.

Reimplemented from casacore::LatticeBase.

template<class T>

virtual Bool casacore::HDF5Image< T >::isWritable ( ) const [virtual]

Is the HDF5Image writable?

Reimplemented from casacore::LatticeBase.

template<class T>

virtual LatticeIterInterface<T>* casacore::HDF5Image< T >::makeIter	(	const LatticeNavigator &	navigator,
		Bool	useRef
	)			const `[virtual]`

This is the implementation of the letter for the envelope Iterator class;
Note: Not for public use
;.

Reimplemented from casacore::Lattice< T >.

template<class T>

virtual String casacore::HDF5Image< T >::name ( Bool stripPath = False ) const [virtual]

Return the current HDF5 file name.

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

Implements casacore::ImageInterface< T >.

template<class T>

virtual Bool casacore::HDF5Image< T >::ok ( ) const [virtual]

Check for symmetry in data members.

Implements casacore::ImageInterface< T >.

template<class T>

void casacore::HDF5Image< T >::open_logtable ( ) [private]

template<class T>

HDF5Image<T>& casacore::HDF5Image< T >::operator+= ( const Lattice< T > & other )

Add a lattice to this image.

template<class T>

HDF5Image<T>& casacore::HDF5Image< T >::operator= ( const HDF5Image< T > & other )

Assignment operator (reference semantics).

Reimplemented from casacore::ImageInterface< T >.

template<class T>

virtual Lattice<Bool>& casacore::HDF5Image< T >::pixelMask ( ) [virtual]

Reimplemented from casacore::MaskedLattice< T >.

template<class T>

virtual const Lattice<Bool>& casacore::HDF5Image< T >::pixelMask ( ) const [virtual]

Get access to the pixelmask used.

An exception is thrown if the image does not use a pixelmask.

Reimplemented from casacore::MaskedLattice< T >.

template<class T>

virtual void casacore::HDF5Image< T >::putAt	(	const T &	value,
		const IPosition &	where
	)			`[virtual]`

Put the value of a single element.

The default implementation uses putSlice.

Reimplemented from casacore::Lattice< T >.

template<class T>

virtual void casacore::HDF5Image< T >::removeRegion	(	const String &	name,
		RegionHandler::GroupType	= `RegionHandler::Any`,
		Bool	throwIfUnknown = `True`
	)			`[virtual]`

Remove a region/mask belonging to the image from the given group (which can be Any).

If a mask removed is the default mask, the image gets unmasked.
Optionally an exception is thrown if the region does not exist.

Reimplemented from casacore::ImageInterface< T >.

template<class T>

virtual void casacore::HDF5Image< T >::resize ( const TiledShape & newShape ) [virtual]

Function which changes the shape of the ImageExpr.

Throws an exception as an HDF5Image cannot be resized.

Implements casacore::ImageInterface< T >.

template<class T>

void casacore::HDF5Image< T >::restoreAll ( ) [private]

template<class T>

void casacore::HDF5Image< T >::restoreImageInfo ( const RecordInterface & rec ) [private]

Restore the image info from the record.

Reimplemented from casacore::ImageInterface< T >.

template<class T>

void casacore::HDF5Image< T >::restoreMiscInfo ( const RecordInterface & rec ) [private]

template<class T>

void casacore::HDF5Image< T >::restoreUnits ( const RecordInterface & rec ) [private]

template<class T>

virtual Bool casacore::HDF5Image< T >::setCoordinateInfo ( const CoordinateSystem & coords ) [virtual]

Flushes the new coordinate system to disk if the file is writable.

Reimplemented from casacore::ImageInterface< T >.

template<class T>

virtual void casacore::HDF5Image< T >::setDefaultMask ( const String & maskName ) [virtual]

Set the default pixelmask to the mask with the given name (which has to exist in the "masks" group).

If the image file is writable, the setting is persistent by writing the name as a keyword. If the given mask name is the empty string, the default pixelmask is unset.

Reimplemented from casacore::ImageInterface< T >.

template<class T>

virtual Bool casacore::HDF5Image< T >::setImageInfo ( const ImageInfo & info ) [virtual]

The ImageInfo object contains some miscellaneous information about the image, which unlike that stored in MiscInfo, has a standard list of things, such as the restoring beam.

Note that setImageInfo REPLACES the information with the new information. It can fail if, e.g., the underlying file is not writable.

Reimplemented from casacore::ImageInterface< T >.

template<class T>

virtual Bool casacore::HDF5Image< T >::setMiscInfo ( const RecordInterface & newInfo ) [virtual]