PyTables User's Guide

Francesc Alted • Scott Prater

PyTables User's Guide

Hierarchical datasets in Python
Release 0.8

Copyright Notice and Statement for PyTables Software Library and Utilities

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Copyright Notice and Statement for NCSA Hierarchical Data Format (HDF) Software Library and Utilities

See more information about the terms of this license at:
http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html

1	Introduction
	1.1	Main Features
	1.2	The Object Tree

2	Installation
	2.1	Installation from source
		2.1.1	Prerequisites
		2.1.2	`PyTables` package installation
	2.2	Binary installation (Windows)
		2.2.1	Windows prerequisites
		2.2.2	`PyTables` package installation

3	Tutorials
	3.1	Getting started
		3.1.1	Importing `tables` objects
		3.1.2	Declaring a Column Descriptor
		3.1.3	Creating a `PyTables` file from scratch
		3.1.4	Creating a new group
		3.1.5	Creating a new table
		3.1.6	Reading (and selecting) data in a table
		3.1.7	Creating new array objects
		3.1.8	Closing the file and looking at its content
	3.2	Browsing the object tree and appending to tables
		3.2.1	Traversing the object tree
		3.2.2	Setting and getting user attributes
		3.2.3	Getting object metadata
		3.2.4	Reading data from `Array` objects
		3.2.5	Appending data to an existing table
		3.2.6	And finally... how to delete rows from a table
	3.3	Multidimensional table cells and automatic sanity checks
		3.3.1	Shape checking
		3.3.2	Field name checking
		3.3.3	Data type checking

4	Library Reference
	4.1	`tables` variables and functions
		4.1.1	Global variables
		4.1.2	Global functions
	4.2	The `File` class
		4.2.1	`File` instance variables
		4.2.2	`File` methods
		4.2.3	`File` special methods
	4.3	The `Group` class
		4.3.1	`Group` instance variables
		4.3.2	`Group` methods
		4.3.3	`Group` special methods
	4.4	The `Leaf` class
		4.4.1	`Leaf` instance variables
		4.4.2	`Leaf` methods
	4.5	The `Table` class
		4.5.1	`Table` instance variables
		4.5.2	`Table` methods
		4.5.3	`Table` special methods
		4.5.4	The `Row` class
		4.5.5	The `Cols` class
		4.5.6	The `Column` class
	4.6	The `Array` class
		4.6.1	`Array` instance variables
		4.6.2	`Array` methods
		4.6.3	`Array` special methods
	4.7	The `EArray` class
		4.7.1	`EArray` instance variables
		4.7.2	`EArray` methods
	4.8	The `VLArray` class
		4.8.1	`VLArray` instance variables
		4.8.2	`VLArray` methods
		4.8.3	`VLArray` special methods
	4.9	The `UnImplemented` class
	4.10	The `AttributeSet` class
		4.10.1	`AttributeSet` instance variables
		4.10.2	`AttributeSet` methods
	4.11	Declarative classes
		4.11.1	The `IsDescription` class
		4.11.2	The `Col` class and its descendants
		4.11.3	The `Atom` class and its descendants.
	4.12	Helper classes
		4.12.1	The `Filters` class

5	Optimization tips
	5.1	Taking advantage of Psyco
	5.2	Compression issues
	5.3	Shuffling (or how to make the compression process more effective)
	5.4	Informing `PyTables` about expected number of rows in tables
	5.5	Selecting an User Entry Point (UEP) in your tree
	5.6	Compacting your `PyTables` files

A	Supported data types in `PyTables`

B	`PyTables` File Format
	B.1	Mandatory attributes for a `File`
	B.2	Mandatory attributes for a `Group`
	B.3	Mandatory attributes, storage layout and supported datatypes for `Leaves`
		B.3.1	`Table` format
		B.3.2	`Array` format
		B.3.3	`EArray` format
		B.3.4	`VLArray` format

C	Utilities
	C.1	ptdump
		C.1.1	Usage
		C.1.2	A small tutorial on `ptdump`
	C.2	ptrepack
		C.2.1	Usage
		C.2.2	A small tutorial on `ptrepack`

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