StArrayFile.h

Classes

StManArrayFile -- Read/write array in external format for a storage manager (full description)

class StManArrayFile

Interface

Public Members
StManArrayFile (const String& name, ByteIO::OpenOption, uInt version=0, Bool bigEndian=True, uInt bufferSize=65536)
~StManArrayFile()
Bool flush (Bool fsync)
void reopenRW()
void resync()
Int64 length()
uInt putShape (const IPosition& shape, Int64& fileOffset, const Bool* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Char* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const uChar* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Short* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const uShort* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Int* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const uInt* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Int64* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const uInt64* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Float* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Double* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Complex* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const DComplex* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const String* dummy)
uInt getRefCount (Int64 offset)
void putRefCount (uInt refCount, Int64 offset)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Bool*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Char*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const uChar*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Short*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const uShort*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Int*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const uInt*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Int64*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const uInt64*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Float*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Double*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Complex*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const DComplex*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const String*)
uInt getShape (Int64 fileOffset, IPosition& shape)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Bool*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Char*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, uChar*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Short*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, uShort*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Int*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, uInt*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Int64*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, uInt64*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Float*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Double*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Complex*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, DComplex*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, String*)
void copyArrayBool (Int64 to, Int64 from, uInt nr)
void copyArrayChar (Int64 to, Int64 from, uInt nr)
void copyArrayuChar (Int64 to, Int64 from, uInt nr)
void copyArrayShort (Int64 to, Int64 from, uInt nr)
void copyArrayuShort (Int64 to, Int64 from, uInt nr)
void copyArrayInt (Int64 to, Int64 from, uInt nr)
void copyArrayuInt (Int64 to, Int64 from, uInt nr)
void copyArrayInt64 (Int64 to, Int64 from, uInt nr)
void copyArrayuInt64 (Int64 to, Int64 from, uInt nr)
void copyArrayFloat (Int64 to, Int64 from, uInt nr)
void copyArrayDouble (Int64 to, Int64 from, uInt nr)
void copyArrayComplex (Int64 to, Int64 from, uInt nr)
void copyArrayDComplex (Int64 to, Int64 from, uInt nr)
void copyArrayString (Int64 to, Int64 from, uInt nr)
Private Members
uInt put (const Int&)
uInt put (const uInt&)
uInt putRes (const IPosition& shape, Int64& fileOffset, float lenElem)
uInt get (Int&)
uInt get (uInt&)
void copyData (Int64 to, Int64 from, uInt length)
void setpos (Int64 offset)

Description

Prerequisite

Etymology

StManArrayFile is a class used by table storage managers to store indirect arrays in a file.

Synopsis

StManArrayFile is for use by the table storage manager, in particular to read/write indirectly stored arrays. Instead of holding the data in memory, they are written directly into a file. It also allows to access a part of an array, which is needed for the table system to access an array section. It does not use a cache of its own, but it is relying on the underlying system routines to cache and buffer adequately.

This class could in principle also be used for other array purposes, for example, to implement a paged array class for really huge arrays.

An StManArrayFile object is connected to one file. It is possible to hold multiple arrays in the file, each with its own shape. An array is stored as its shape followed by the actual data (all in canonical format). An array of strings is written as an array of offsets pointing to the actual strings. When a string gets a new value, the new value is written at the end of the file and the file space with the old value is lost.

Currently only the basic types are supported, but arbitrary types could also be supported by writing/reading an element in the normal way into the AipsIO buffer. It would only require that AipsIO would contain a function to get its buffers and to restart them.

Example

    void writeArray (const Array<Bool>& array)
    {
        // Construct object and update file StArray.dat.
        StManArrayFile arrayFile("StArray.dat, ByteIO::New);
        // Reserve space for an array with the given shape and data type.
        // This writes the shape at the end of the file and reserves
        // space the hold the entire Bool array.
        // It fills in the file offset where the shape is stored
        // and returns the length of the shape in the file.
        Int64 offset;
        uInt shapeLength = arrayFile.putShape (array.shape(), offset, static_cast<Bool*>(0));
        // Now put the actual array.
        // This has to be put at the returned file offset plus the length
        // of the shape in the file.
        Bool deleteIt;
        const Bool* dataPtr = array.getStorage (deleteIt);
        arrayFile.put (offset+shapeLength, 0, array.nelements(), dataPtr);
        array.freeStorage (dataPtr, deleteIt);
    }

Motivation

The AipsIO class was not suitable for indirect table arrays, because it uses memory to hold the data. Furthermore it is not possible to access part of the data in AipsIO.

To Do

Member Description

StManArrayFile (const String& name, ByteIO::OpenOption, uInt version=0, Bool bigEndian=True, uInt bufferSize=65536)

Construct the object and attach it to the give file. The OpenOption determines how the file is opened (e.g. ByteIO::New for a new file). The buffersize is used to allocate a buffer of a proper size for the underlying filebuf object (see iostream package).

~StManArrayFile()

Close the possibly opened file.

Bool flush (Bool fsync)

Flush and optionally fsync the data. It returns True when any data was written since the last flush.

void reopenRW()

Reopen the file for read/write access.

void resync()

Resync the file (i.e. clear possible cache information).

Int64 length()

Return the current file length (merely a debug tool).

uInt putShape (const IPosition& shape, Int64& fileOffset, const Complex* dummy)

Put the array shape and store its file offset into the offset argument. Reserve file space for the associated array. The length of the shape part in the file is returned. The file offset plus the shape length is the starting offset of the actual array data (which can be used by get and put). Space is reserved to store the reference count.

uInt putShape (const IPosition& shape, Int64& fileOffset, const Bool* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Char* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const uChar* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Short* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const uShort* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Int* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const uInt* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Int64* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const uInt64* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Float* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const Double* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const DComplex* dummy)
uInt putShape (const IPosition& shape, Int64& fileOffset, const String* dummy)

Put the array shape and store its file offset into the offset argument. Reserve file space for the associated array. The length of the shape part in the file is returned. The file offset plus the shape length is the starting offset of the actual array data (which can be used by get and put). Space is reserved to store the reference count.

uInt getRefCount (Int64 offset)

Get the reference count.

void putRefCount (uInt refCount, Int64 offset)

Put the reference count. An exception is thrown if a value other than 1 is put for version 0.

void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Complex*)

Put nr elements at the given file offset and array offset. The file offset of the first array element is the file offset of the shape plus the length of the shape in the file. The array offset is counted in number of elements. It can be used to put only a (contiguous) section of the array.

void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Bool*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Char*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const uChar*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Short*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const uShort*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Int*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const uInt*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Int64*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const uInt64*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Float*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const Double*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const DComplex*)
void put (Int64 fileOffset, uInt arrayOffset, uInt nr, const String*)

Put nr elements at the given file offset and array offset. The file offset of the first array element is the file offset of the shape plus the length of the shape in the file. The array offset is counted in number of elements. It can be used to put only a (contiguous) section of the array.

uInt getShape (Int64 fileOffset, IPosition& shape)

Get the shape at the given file offset. It will reshape the IPosition vector when needed. It returns the length of the shape in the file.

void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Complex*)

Get nr elements at the given file offset and array offset. The file offset of the first array element is the file offset of the shape plus the length of the shape in the file. The array offset is counted in number of elements. It can be used to get only a (contiguous) section of the array.

void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Bool*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Char*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, uChar*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Short*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, uShort*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Int*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, uInt*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Int64*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, uInt64*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Float*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, Double*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, DComplex*)
void get (Int64 fileOffset, uInt arrayOffset, uInt nr, String*)

Get nr elements at the given file offset and array offset. The file offset of the first array element is the file offset of the shape plus the length of the shape in the file. The array offset is counted in number of elements. It can be used to get only a (contiguous) section of the array.

void copyArrayComplex (Int64 to, Int64 from, uInt nr)

Copy the array with nr elements from one file offset to another.

void copyArrayBool (Int64 to, Int64 from, uInt nr)
void copyArrayChar (Int64 to, Int64 from, uInt nr)
void copyArrayuChar (Int64 to, Int64 from, uInt nr)
void copyArrayShort (Int64 to, Int64 from, uInt nr)
void copyArrayuShort (Int64 to, Int64 from, uInt nr)
void copyArrayInt (Int64 to, Int64 from, uInt nr)
void copyArrayuInt (Int64 to, Int64 from, uInt nr)
void copyArrayInt64 (Int64 to, Int64 from, uInt nr)
void copyArrayuInt64 (Int64 to, Int64 from, uInt nr)
void copyArrayFloat (Int64 to, Int64 from, uInt nr)
void copyArrayDouble (Int64 to, Int64 from, uInt nr)
void copyArrayDComplex (Int64 to, Int64 from, uInt nr)
void copyArrayString (Int64 to, Int64 from, uInt nr)

Copy the array with nr elements from one file offset to another.

uInt put (const Int&)
uInt put (const uInt&)

Put a single value at the current file offset. It returns the length of the value in the file.

uInt putRes (const IPosition& shape, Int64& fileOffset, float lenElem)

Put the array shape at the end of the file and reserve space for nr elements (each lenElem bytes long). It fills the file offset of the shape. It returns the length of the shape in the file.

uInt get (Int&)
uInt get (uInt&)

Get a single value at the current file offset. It returns the length of the value in the file.

void copyData (Int64 to, Int64 from, uInt length)

Copy data with the given length from one file offset to another.

void setpos (Int64 offset)

Position the file on the given offset.