AbstractFileArray: Class representing a persistent array stored in a file

In R.huge: Methods for Accessing Huge Amounts of Data [deprecated]

Class representing a persistent array stored in a file

Description

Package: R.huge
Class AbstractFileArray

Object
~~|
~~+--AbstractFileArray

Directly known subclasses:
FileByteMatrix, FileByteVector, FileDoubleMatrix, FileDoubleVector, FileFloatMatrix, FileFloatVector, FileIntegerMatrix, FileIntegerVector, FileMatrix, FileShortMatrix, FileShortVector, FileVector

public static class AbstractFileArray
extends Object

Note that this is an abstract class, i.e. it is not possible to create an object of this class but only from one of its subclasses. For a vector data type, see FileVector. For a matrix data type, see FileMatrix.

Usage

AbstractFileArray(filename=NULL, path=NULL, storageMode=c("integer", "double"),
  bytesPerCell=1, dim=NULL, dimnames=NULL, dimOrder=NULL, comments=NULL,
  nbrOfFreeBytes=4096)

Arguments

filename	The name of the file storing the data.
path	An optional path where data should be stored.
storageMode	The storage mode() of the data elements.
bytesPerCell	The number of bytes each element (cell) takes up on the file system. If NULL, it is inferred from the storageMode argument.
dim	A numeric vector specifying the dimensions of the array.
dimnames	An optional list of dimension names.
dimOrder	The order of the dimensions.
comments	An optional character string of arbitrary length.
nbrOfFreeBytes	The number of "spare" bytes after the comments before the data section begins.

Details

The purpose of this class is to be able to work with large arrays in R without being limited by the amount of memory available. Data is kept on the file system and elements are read and written whenever queried.

Fields and Methods

Methods:

	as.character	Returns a short string describing the file array.
	as.vector	Returns the elements of a file array as an R vector.
	clone	Clones a file array.
	close	Closes a connection to the data file of the file array.
	delete	Deletes the file array from the file system.
	dim	Gets the dimension of the file array.
	dimnames	Gets the dimension names of a file array.
	finalize	Internal: Clean up when file array is deallocated from memory.
	flush	Internal: Flushes the write buffer.
	getBasename	Gets the basename (filename) of the data file.
	getBytesPerCell	Gets the number of bytes per element in a file array.
	getCloneNumber	Gets the clone number of the file array.
	getComments	Gets the comments for this file array.
	getDataOffset	Gets file position of the data section in a file array.
	getDimensionOrder	Gets the order of dimension.
	getExtension	Gets the filename extension of the file array.
	getFileSize	Gets the size of the file array.
	getName	Gets the name of the file array.
	getPath	Gets the path (directory) where the data file lives.
	getPathname	Gets the full pathname to the data file.
	getSizeOfComments	Gets the number of bytes the comments occupies.
	getSizeOfData	Gets the size of the data section in bytes.
	getStorageMode	Gets the storage mode of the file array.
	isOpen	Checks whether the data file of the file array is open or not.
	length	Gets the number of elements in a file array.
	open	Opens a connection to the data file of the file array.
	readAllValues	Reads all values in the file array.
	readContiguousValues	Reads sets of contiguous values in the file array.
	readHeader	Read the header of a file array data file.
	readValues	Reads individual values in the file array.
	setComments	Sets the comments for this file array.
	writeAllValues	Writes all values to a file array.
	writeEmptyData	Writes an empty data section to the data file of a file array.
	writeHeader	Writes the header of a file array to file.
	writeHeaderComments	-
	writeValues	Writes values to a file array.

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save

Maximum number of elements

It is only the header that is kept in memory, not the data, and therefore the maximum length of a array that can be allocate, is limited by the amount of available space on the file system. Since element names (optional) are stored in the header, these may also be a limiting factor.

Element names

The element names are stored in the header and are currently read and written to file one by one. This may slow down the performance substantially if the dimensions are large. For optimal opening performance, avoid names.

For now, do not change names after file has been allocated.

File format

The file format consist of a header section and a data section. The header contains information about the file format, the length and element names of the array, as well as data type (storage mode()), the size of each element. The data section, which follows immediately after the header section, consists of all data elements with non-assigned elements being pre-allocated with zeros.

For more details, see the source code.

Limitations

The size of the array in bytes is limited by the maximum file size of the file system. For instance, the maximum file size on a Windows FAT32 system is 4GB (2GB?). On Windows NTFS the limit is in practice ~16TB.

Author(s)

Henrik Bengtsson

References

[1] New Technology File System (NTFS), Wikipedia, 2006 https://en.wikipedia.org/wiki/NTFS.

R.huge documentation built on July 9, 2023, 6:24 p.m.