casacore
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#include <HDF5Lattice.h>
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 §ion) |
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... | |
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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 §ion, 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 §ion, 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 §ion, 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... | |
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 | |
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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 > &) |
void | handleMathTo (Lattice< Bool > &, int) const |
A Lattice that is read from or written to an HDF5 dataset.
Public interface
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):
Class PagedArray contains some more info and examples.
Create a HDF5Lattice of Floats of shape [1024,1024,4,256] in a file called "myData_tmp.array" and initialize it to zero.
There was a need to be able to use HDF5 files to hold image data.
Definition at line 109 of file HDF5Lattice.h.
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.
casacore::HDF5Lattice< T >::HDF5Lattice | ( | const TiledShape & | shape, |
const String & | filename, | ||
const String & | arrayName = "array" , |
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const String & | groupName = String() |
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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.
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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.
casacore::HDF5Lattice< T >::HDF5Lattice | ( | const TiledShape & | shape, |
const CountedPtr< HDF5File > & | file, | ||
const String & | arrayName, | ||
const String & | groupName = String() |
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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.
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explicit |
Reconstruct from a pre-existing HDF5Lattice in the HDF5 file and group with the given names.
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explicit |
Reconstruct from a pre-existing HDF5Lattice in the HDF5 file and group with the given name.
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.
casacore::HDF5Lattice< T >::~HDF5Lattice | ( | ) |
The destructor flushes the HDF5Lattice's contents to disk.
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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 >.
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inline |
Returns the current HDF5DataSet object.
Definition at line 197 of file HDF5Lattice.h.
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inline |
Returns the name of this HDF5Lattice.
Definition at line 201 of file HDF5Lattice.h.
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private |
Check if the file is writable.
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virtual |
Make a copy of the object (reference semantics).
Implements casacore::Lattice< T >.
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Do the actual getting of an array of values.
Implements casacore::Lattice< T >.
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Get the best cursor shape.
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virtual |
Do the actual getting of an array of values.
Implements casacore::Lattice< T >.
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inline |
Return the current HDF5File object.
Definition at line 189 of file HDF5Lattice.h.
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virtual |
Flush the data (but do not unlock).
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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 >.
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inline |
Return the current HDF5Group object.
Definition at line 193 of file HDF5Lattice.h.
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virtual |
A HDF5Lattice is always paged to disk.
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A HDF5Lattice is always persistent.
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Is the HDF5Lattice writable?
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private |
Make the Array in the HDF5 file and group.
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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 >.
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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.
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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.
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private |
Open the Array in the HDF5 file and group.
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.
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Put the value of a single element.
Reimplemented from casacore::Lattice< T >.
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Set the cache size as to "fit" the indicated access pattern.
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Set the actual cache size for this Array to be big enough for the indicated number of tiles.
This cache is not shared with other HDF5Lattices, Tiles are cached using an LRU algorithm.
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Returns the shape of the HDF5Lattice.
IPosition casacore::HDF5Lattice< T >::tileShape | ( | ) | const |
Returns the current tile shape for this HDF5Lattice.
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Definition at line 268 of file HDF5Lattice.h.
Referenced by casacore::HDF5Lattice< Bool >::array(), and casacore::HDF5Lattice< Bool >::arrayName().
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Definition at line 266 of file HDF5Lattice.h.
Referenced by casacore::HDF5Lattice< Bool >::file().
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Definition at line 267 of file HDF5Lattice.h.
Referenced by casacore::HDF5Lattice< Bool >::group().
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Definition at line 269 of file HDF5Lattice.h.