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pyDAWG 1.0.0

Directed Acyclic Word Graph (DAWG) allows to store huge strings set in compacted form

Introduction

PyDAWG is a python module implements DAWG graph structure, which allow to store set of strings and check existence of a string in linear time (in terms of a string length).

DAWG is constructed by incremental algorithm described in Incremental algorithm for sorted data, Jan Daciuk, Stoyan Mihov, Bruce Watson, and Richard Watson, Computational Linguistics, 26(1), March 2000. Prof. Jan Daciuk offers also some useful documentation, presentations and even sample code on his site.

The algorithm asserts that input words are sorted in lexicographic order; default Python sort() orders strings correctly.

Also minimal perfect hashing (MPH) is supported, i.e. there is a function that maps words to unique number; this function is bidirectional, its possible to find number for given word or get word from number.


There are two versions of module:

  • C extension, compatible only with Python3;
  • pure python module, compatible with Python 2 and 3.

Python module implements subset of C extension API.

License

Library is licensed under very liberal three-clauses BSD license. Some portions has been released into public domain.

Full text of license is available in LICENSE file.

Installation

Compile time settings (can be change in setup.py):

  • DAWG_UNICODE — if defined, DAWG accepts and returns unicode strings, else bytes are supported
  • DAWG_PERFECT_HASHING — when defined, minimal perfect hashing is enabled (methods word2index and index2word are available)

Just run:

$ python setup.py install

If compilation succed, module is ready to use.

API

Module

Module pydawg provides class DAWG and following members:

Unicode and bytes

Type of strings accepted and returned by DAWG methods can be either unicode or bytes, depending on compile time settings (preprocessor definition DAWG_UNICODE). Value of module member unicode informs about chosen type.

DAWG class

DAWG class is picklable, and also provide independent way of marshaling with methods binload() and bindump().

Property

state [read-only integer]

Following values are possible:

  • pydawg.EMPTY — no words in a set;
  • pydawg.ACTIVE — there is at least one word in a set, and adding new words is possible (see add_word & add_word_unchecked);
  • pydawg.CLOSED — there is at least one word in a set, but adding new words is not allowed (see close/freeze).

Basic mathods

add_word(word) => bool
Add word, returns True if word didn’t exists in a set. Procedure checks if word is greater then previously added word (in lexicography order).
add_word_unchecked(word) => bool
Does the same thing as add_word but do not check word order. Method should be used if one is sure, that input data satisfy algorithm requirements, i.e. words order is valid.
exists(word) => bool or word in ...
Check if word is in set.
match(word) => bool
Check if word or any of its prefix is in a set.
longest_prefix(word) => int
Returns length of the longest prefix of word that exists in a set.
len() protocol
Returns number of distinct words.
words() => list
Returns list of all words.
find_all([word, [wildchar, [how]]]) => iterator

Returns iterator that match words depending on word argument.

find_all()
does the same job as iter()
find_all(prefix)
Yields words that share a prefix
find_all(pattern, wildchar, [how])

Yields words that match a pattern with given wildchar (wildchar matches any char). Parameter how controls which words are matched:

MATCH_EXACT_LENGTH
words with the same length as a pattern
MATCH_AT_LEAST_PREFIX
words of length not less then pattern
MATCH_AT_MOST_PREFIX
words of length no greater then pattern
clear()
Erase all words from set.
close() or freeze()

Don’t allow to add any new words, state value become pydawg.CLOSED. Also free memory occupied by a hash table used to perform incremental algorithm (see also get_hash_stats()).

Can be reverted only by clear().

Iterator

Class supports iter protocol, i.e. iter(DAWGobject) returns iterator, a lazy version of words() method.

Minimal perfect hashing

Minimal perfect hashing (MPH) allows to find unique number representing any word from DAWG, and also find word with given number. Numbers are in always in range 1 … len(DAWG).

Finally, this feature makes possible to perform fast lookups as in a regular dictionary.

Algorithm used for MPH is described in Applications of Finite Automata Representing Large Vocabularies, Claudio Lucchesi and Tomasz Kowaltowski, Software Practice and Experience, 23(1), pp. 15–30, Jan. 1993.

MPH feature is enabled during compilation time if preprocessor definition DAWG_PERFECT_HASHING exists. Module member perfect_hashing reflects this setting.

Warning

Words numbering is done for the whole DAWG. If new words are added with add_word or add_word_unchecked, then current numbering is lost and when method word2index or index2word is called, then DAWG is renumbered.

Because of that frequent mixing these two groups of method will degrade performance.

word2index(word) => index
Returns index of word, or None if word is not present in a DAWG.
index2word(index) => word
Returns words associated with index, or None if index isn’t valid.
Example
D = pydawg.DAWG()

# fill DAWG with keys
for key in sorted(dict):
        D.add_word_unchecked(key)

# prepare values array
V = [None] * len(D)

for key, value in dict.items():
        index = D.word2index(key)
        assert index is not None

        V[index - 1] = value


# lookups are possible now
for word in user_input:
        index = D.word2index(word)
        if index is not None:
                print(word, "=>", V[index - 1])

Other

dump() => (set of nodes, set of edges)

Returns sets describing DAWG, elements are tuples.

Node tuple:

  • unique id of node (number)
  • end of word marker

Edge tuple:

  • source node id
  • edge label — letter
  • destination node id

Distribution contains program dump2dot.py that shows how to convert output of this function to graphviz DOT language.

bindump() => bytes
Returns binary DAWG data.
binload(bytes)

Restore DAWG from binary data. Example:

import pydawg

A = pydawg.DAWG()
with open('dump', 'wb') as f:
        f.write(A.bindump())

B = pydawg.DAWG()
with open('dump', 'rb') as f:
        B.binload(f.read())
get_stats() => dict

Returns dictionary containing some statistics about underlaying data structure:

  • words_count — number of distinct words (same as len(dawg))
  • longest_word — length of the longest word
  • nodes_count — number of nodes
  • edges_count — number of edges
  • sizeof_node — size of single node (in bytes)
  • sizeof_edge — size of single node (in bytes)
  • graph_size — size of whole graph (in bytes); it’s about nodes_count * sizeof_node + edges_count * sizeof_edge
get_hash_stats() => dict

Returns some statistics about hash table used by DAWG.

  • table_size — number of table’s elements
  • element_size — size of single table item
  • items_count — number of items saved in a table
  • item_size — size of single item

Approx memory occupied by hash table is table_size * element_size + items_count * item_size.

 
File Type Py Version Uploaded on Size
pyDAWG-1.0.0.tar.gz (md5) Source 2014-11-26 25KB