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postprocessing.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Postprocessing Text Data, Saving Matrices, Corpora and LDA Models
*****************************************************************
Functions of this module are for **postprocessing purpose**. You can save \
`document-term matrices <https://en.wikipedia.org/wiki/Document-term_matrix>`_, \
`tokenized corpora <https://en.wikipedia.org/wiki/Tokenization_(lexical_analysis)>`_ \
and `LDA models <https://en.wikipedia.org/wiki/Latent_Dirichlet_allocation>`_, \
access topics, topic probabilites for documents, and word probabilities \
for each topic. All matrix variants provided in :func:`preprocessing.create_document_term_matrix()`_ \
are supported, as well as `lda <https://pypi.python.org/pypi/lda>`_, `Gensim <https://radimrehurek.com/gensim/>`_ \
and `MALLET <http://mallet.cs.umass.edu/topics.php>`_ models or output, respectively. \
Recurrent variable names are based on the following conventions:
* ``topics`` means a pandas DataFrame containing the top words for each \
topic and any Dirichlet parameters.
* ``document_topics`` means a pandas DataFrame containing topic proportions per \
document, at the end of the iterations.
* ``word_weights`` means unnormalized weights for every topic and word type.
* ``keys`` means the top *n* tokens of a topic.
Contents
********
* :func:`doc2bow()`
* :func:`save_document_term_matrix()` writes a document-term matrix to a `CSV <https://en.wikipedia.org/wiki/Comma-separated_values>`_
file or to a `Matrix Market <http://math.nist.gov/MatrixMarket/formats.html#MMformat>`_ file, respectively.
* :func:`save_model()` saves a LDA model (except MALLET models, which will be saved \
by specifying a parameter of :func:`mallet.create_mallet_model()`).
* :func:`save_tokenized_corpus()` writes tokens of a tokenized corpus to plain text \
files per document.
* :func:`show_document_topics()` shows topic probabilities for each document.
* :func:`show_topics()` shows topics generated by a LDA model.
* :func:`show_word_weights()` shows word probabilities for each topic.
"""
import itertools
import operator
import os
import numpy as np
import pandas as pd
import pickle
import logging
log = logging.getLogger(__name__)
log.addHandler(logging.NullHandler())
logging.basicConfig(level=logging.WARNING,
format='%(levelname)s %(name)s: %(message)s')
def doc2bow(document_term_matrix):
"""Creates a `doc2bow` pandas Series for Gensim.
With this function you can create a `doc2bow` pandas Series as input for Gensim, e.g. \
to instantiate the :class:`gensim.models.LdaModel` class or get topic distributions \
with :func:`gensim.models.LdaModel.get_document_topics()`.
Args:
document_term_matrix (pandas.DataFrame): A document-term matrix **designed
for large corpora**.
Returns:
List of lists containing tuples.
Todo:
* Improve efficiency.
Example:
>>> from dariah_topics import preprocessing
>>> tokenized_corpus = [['this', 'is', 'document', 'one'], ['this', 'is', 'document', 'two']]
>>> document_labels = ['document_one', 'document_two']
>>> document_term_matrix, _, _ = preprocessing.create_document_term_matrix(tokenized_corpus, document_labels, True)
>>> isinstance(doc2bow(document_term_matrix), pd.Series)
True
"""
doc2bow = pd.Series()
for n, document in enumerate(document_term_matrix.index.groupby(document_term_matrix.index.get_level_values('document_id'))):
doc2bow[str(n)] = [(token, freq) for token, freq in zip(document_term_matrix.loc[document].index, document_term_matrix.loc[document][0])]
return doc2bow
def save_document_term_matrix(document_term_matrix, path, document_ids=None, type_ids=None, matrix_market=False):
"""Saves document-term matrix.
Writes a ``document_term_matrix`` and, in case of a large corpus matrix, \
``document_ids`` and ``type_ids``, which have to be specified, to comma-separated \
values (CSV) files. Furthermore, if ``document_term_matrix`` is designed for \
large corpora and ``matrix_market`` is True, the matrix will be saved in the \
`Matrix Market format <http://math.nist.gov/MatrixMarket/formats.html#MMformat>`_ (`.mm`). \
Libraries like `scipy <https://www.scipy.org>`_ and `gensim <https://radimrehurek.com/gensim/>`_ \
are able to read and process the Matrix Market format.
Use the function :func:`preprocessing.create_document_term_matrix()` to create a
document-term matrix.
Args:
document_term_matrix (pandas.DataFrame): Document-term matrix with rows
corresponding to ``document_labels`` and columns corresponding to types
(unique tokens in the corpus). The single values of the matrix are
type frequencies. Will be saved as ``document_term_matrix.csv`` or
``document_term_matrix.mm``, respectively.
path (str): Path to the output directory.
document_ids (dict, optional): Dictionary containing ``document_labels`` as
keys and an unique identifier as value. Only required, if
``document_term_matrix`` is designed for large corpora. Will be saved
as ``document_ids.csv``. Defaults to None.
type_ids (dict, optional): Dictionary containing types as keys and an
unique identifier as value. Only required, if ``document_term_matrix``
is designed for large corpora. Will be saved as ``type_ids.csv``. Defaults
to None.
matrix_market (bool, optional): If True, matrix will be saved in Matrix
Market format. Only for the large corpus variant of ``document_term_matrix``
available. Defaults to False.
Returns:
None.
Example:
>>> from dariah_topics import preprocessing
>>> import os
>>> path = 'tmp'
>>> tokenized_corpus = [['this', 'is', 'document', 'one'], ['this', 'is', 'document', 'two']]
>>> document_labels = ['document_one', 'document_two']
>>> document_term_matrix = preprocessing.create_document_term_matrix(tokenized_corpus, document_labels)
>>> save_document_term_matrix(document_term_matrix=document_term_matrix, path=path)
>>> preprocessing.read_document_term_matrix(os.path.join(path, 'document_term_matrix.csv')) #doctest +NORMALIZE_WHITESPACE
this is document two one
document_one 1.0 1.0 1.0 0.0 1.0
document_two 1.0 1.0 1.0 1.0 0.0
>>> document_term_matrix, document_ids, type_ids = preprocessing.create_document_term_matrix(tokenized_corpus, document_labels, True)
>>> save_document_term_matrix(document_term_matrix, path, document_ids, type_ids)
>>> isinstance(preprocessing.read_document_term_matrix(os.path.join(path, 'document_term_matrix.csv')), pd.DataFrame)
True
"""
if not os.path.exists(path):
log.info("Creating directory {} ...".format(path))
os.makedirs(path)
if not matrix_market:
log.info("Saving document_term_matrix.csv to {} ...".format(path))
document_term_matrix.to_csv(os.path.join(path, 'document_term_matrix.csv'))
if isinstance(document_term_matrix.index, pd.MultiIndex) and not matrix_market:
if document_ids and type_ids is not None:
log.info("Saving document_ids.csv to {} ...".format(path))
pd.Series(document_ids).to_csv(os.path.join(path, 'document_ids.csv'))
log.info("Saving type_ids.csv to {} ...".format(path))
pd.Series(type_ids).to_csv(os.path.join(path, 'type_ids.csv'))
else:
raise ValueError("You have to pass document_ids and type_ids as parameters.")
elif isinstance(document_term_matrix.index, pd.MultiIndex) and matrix_market:
_save_matrix_market(document_term_matrix, path)
return None
def save_model(model, filepath):
"""Saves a LDA model.
With this function you can save a LDA model using :module:`pickle`. If you want \
to save MALLET models, you have to specify a parameter of the function :func:`mallet.create_mallet_model()`.
Args:
model: Fitted LDA model produced by `Gensim <https://radimrehurek.com/gensim/>`_
or `lda <https://pypi.python.org/pypi/lda>`_.
filepath (str): Path to LDA model, e.g. ``/home/models/model.pickle``.
Returns:
None.
Example:
>>> from lda import LDA
>>> from gensim.models import LdaModel
>>> from dariah_topics import preprocessing
>>> save_model(LDA, 'model.pickle')
>>> preprocessing.read_model('model.pickle') == LDA
True
>>> save_model(LdaModel, 'model.pickle')
>>> preprocessing.read_model('model.pickle') == LdaModel
True
"""
with open(filepath, 'wb') as file:
pickle.dump(model, file, protocol=pickle.HIGHEST_PROTOCOL)
return None
def save_tokenized_corpus(tokenized_corpus, document_labels, path):
"""Writes a tokenized corpus to text files.
With this function you can write tokens of a `tokenized_corpus` to plain text \
files per document to ``path``. Every file will be named after its ``document_label``. \
Depending on the used tokenizer, ``tokenized_corpus`` does normally not contain \
any punctuations or one-letter words.
Use the function :func:`preprocessing.tokenize()` to tokenize a corpus.
Args:
tokenized_corpus (list): Tokenized corpus containing one or more
iterables containing tokens.
document_labels (list): Name of each `tokenized_document` in `tokenized_corpus`.
path (str): Path to the output directory.
Returns:
None
Example:
>>> tokenized_corpus = [['this', 'is', 'a', 'tokenized', 'document']]
>>> document_labels = ['document_label']
>>> path = 'tmp'
>>> save_tokenized_corpus(tokenized_corpus, document_labels, path)
>>> with open(os.path.join(path, 'document_label.txt'), 'r', encoding='utf-8') as file:
... file.read()
'this\\nis\\na\\ntokenized\\ndocument'
"""
log.info("Saving tokenized corpus to {} ...".format(path))
if not os.path.exists(path):
log.info("Creating directory {} ...".format(path))
os.makedirs(path)
for tokenized_document, document_label in zip(tokenized_corpus, document_labels):
log.debug("Current file: {}".format(document_label))
with open(os.path.join(path, '{}.txt'.format(document_label)), 'w', encoding='utf-8') as file:
file.write('\n'.join(tokenized_document))
return None
def show_document_topics(topics, model=None, document_labels=None, doc_topics_file=None, doc2bow=None, num_keys=3):
"""Shows topic distribution for each document.
With this function you can show the topic distributions for all documents in a pandas DataFrame. \
For each topic, the top ``num_keys`` keys will be considered. If you have a
* `lda <https://pypi.python.org/pypi/lda>`_ model, you have to pass the model \
as ``model`` and the document-term matrix vocabulary as ``vocabulary``.
* `Gensim <https://radimrehurek.com/gensim/>`_ model, you have to pass only the model \
as ``model``.
* `MALLET <http://mallet.cs.umass.edu/topics.php>`_ based workflow, you have to\
pass only the ``doc_topics_file``.
Args:
topics (pandas.DataFrame, optional): Only for lda models. A pandas DataFrame
containing all topics.
model (optional): lda or Gensim model.
document_labels (list, optional): An list of all document labels.
doc_topics_file (str, optional): Only for MALLET. Path to the doc-topics file.
doc2bow (list, optional): A list of lists containing tuples of ``type_id`` and
frequency.
num_keys (int, optional): Number of top keys for each topic.
Returns:
A pandas DataFrame with rows corresponding to topics and columns corresponding
to keys.
Example:
"""
from lda.lda import LDA
from gensim.models import LdaModel, LdaMulticore
index = [' '.join(keys[:num_keys]) for keys in topics.values]
if isinstance(model, LDA):
return _show_lda_document_topics(model, document_labels, index)
elif isinstance(model, LdaModel) or isinstance(model, LdaMulticore):
return _show_gensim_document_topics(doc2bow, model, document_labels, index)
elif doc_topics_file is not None:
return _show_mallet_document_topics(doc_topics_file, index)
def show_topics(model=None, vocabulary=None, topic_keys_file=None, num_keys=10):
"""Shows topics of LDA model.
With this function you can show all topics of a LDA model in a pandas DataFrame. \
For each topic, the top ``num_keys`` keys will be considered. If you have a
* `lda <https://pypi.python.org/pypi/lda>`_ model, you have to pass the model \
as ``model`` and the document-term matrix vocabulary as ``vocabulary``.
* `Gensim <https://radimrehurek.com/gensim/>`_ model, you have to pass only the model \
as ``model``.
* `MALLET <http://mallet.cs.umass.edu/topics.php>`_ based workflow, you have to\
pass only the ``topic_keys_file``.
Args:
model (optional): lda or Gensim model.
vocabulary (list, optional): Only for lda. The vocabulary of the
document-term matrix.
topic_keys_file (str): Only for MALLET. Path to the topic keys file.
num_keys (int, optional): Number of top keys for each topic.
Returns:
A pandas DataFrame with rows corresponding to topics and columns corresponding
to keys.
Example:
"""
from lda.lda import LDA
from gensim.models import LdaModel, LdaMulticore
if isinstance(model, LDA):
return _show_lda_topics(model, vocabulary, num_keys)
elif isinstance(model, LdaModel) or isinstance(model, LdaMulticore):
return _show_gensim_topics(model, num_keys)
elif topic_keys_file is not None:
return _show_mallet_topics(topic_keys_file)
def show_word_weights(word_weights_file, num_tokens):
"""Read Mallet word_weigths file
Description:
Reads Mallet word_weigths into pandas DataFrame.
Args:
word_weigts_file: Word_weights_file created with Mallet
Returns: Pandas DataFrame
Todo:
* Adapt for ``lda`` and ``gensim`` output.
Example:
>>> import tempfile
>>> with tempfile.NamedTemporaryFile(suffix='.txt') as tmpfile:
... tmpfile.write(b'0\\tthis\\t0.5\\n0\\tis\\t0.4\\n0\\ta\\t0.3\\n0\\tdocument\\t0.2') and True
... tmpfile.flush()
... show_word_weights(tmpfile.name, 2) #doctest: +NORMALIZE_WHITESPACE
True
document token weight
0 0 this 0.5
1 0 is 0.4
"""
word_weights = pd.read_table(word_weights_file, header=None, sep='\t', names=['document', 'token', 'weight'])
return word_weights.sort_values('weight', ascending=False)[:num_tokens]
def _grouper(n, iterable, fillvalue=None):
"""Collects data into fixed-length chunks or blocks.
This private function is wrapped in :func:`_show_mallet_document_topics()`.
Args:
n (int): Length of chunks or blocks
iterable (object): Iterable object
fillvalue (boolean): If iterable can not be devided into evenly-sized chunks fill chunks with value.
Returns: n-sized chunks
"""
args = [iter(iterable)] * n
return itertools.zip_longest(*args, fillvalue=fillvalue)
def _show_gensim_document_topics(doc2bow, model, document_labels, index):
"""Creates a document-topic-matrix.
Description:
With this function you can create a doc-topic-maxtrix for gensim
output.
Args:
corpus (mmCorpus): Gensim corpus.
model: Gensim LDA model
doc_labels (list): List of document labels.
Returns:
Doc_topic-matrix as DataFrame
Example:
>>> from gensim.models import LdaModel
>>> from gensim.corpora import Dictionary
>>> document_labels = ['document_one', 'document_two']
>>> tokenized_corpus = [['this', 'is', 'the', 'first', 'document'], ['this', 'is', 'the', 'second', 'document']]
>>> id2word = Dictionary(tokenized_corpus)
>>> corpus = [id2word.doc2bow(document) for document in tokenized_corpus]
>>> model = LdaModel(corpus=corpus, id2word=id2word, iterations=1, passes=1, num_topics=2)
>>> topics = _show_gensim_topics(model, 5)
>>> index = [' '.join(keys[:2]) for keys in topics.values]
>>> isinstance(_show_gensim_document_topics(corpus, model, document_labels, index), pd.DataFrame)
True
"""
num_topics = model.num_topics
num_documents = len(document_labels)
document_topics = np.zeros((num_topics, num_documents))
for n, document in enumerate(doc2bow):
for distribution in model.get_document_topics(document):
document_topics[distribution[0]][n] = distribution[1]
return pd.DataFrame(document_topics, index=index, columns=document_labels)
def _show_gensim_topics(model, num_keys=10):
"""Converts gensim output to DataFrame.
Description:
With this function you can convert gensim output (usually a list of
tuples) to a DataFrame, a more convenient datastructure.
Args:
model: Gensim LDA model.
num_keys (int): Number of top keywords for topic.
Returns:
DataFrame.
ToDo:
Example:
>>> from gensim.models import LdaModel
>>> from gensim.corpora import Dictionary
>>> tokenized_corpus = [['this', 'is', 'the', 'first', 'document'], ['this', 'is', 'the', 'second', 'document']]
>>> id2word = Dictionary(tokenized_corpus)
>>> corpus = [id2word.doc2bow(document) for document in tokenized_corpus]
>>> model = LdaModel(corpus=corpus, id2word=id2word, iterations=1, passes=1, num_topics=2)
>>> isinstance(_show_gensim_topics(model, 5), pd.DataFrame)
True
"""
log.info("Accessing topics from Gensim model ...")
topics = []
for n, topic in model.show_topics(formatted=False, num_words=num_keys):
topics.append([key[0] for key in topic])
index = ['Topic {}'.format(n) for n in range(len(topics))]
columns = ['Key {}'.format(n) for n in range(num_keys)]
return pd.DataFrame(topics, index=index, columns=columns)
def _show_lda_document_topics(model, document_labels, index):
"""Creates a doc_topic_matrix for lda output.
Description:
With this function you can convert lda output to a DataFrame,
a more convenient datastructure.
Use 'lda2DataFrame()' to get topics.
Note:
Args:
model: Gensim LDA model.
topics: DataFrame.
doc_labels (list[str]): List of doc labels as string.
Returns:
DataFrame
Example:
>>> import lda
>>> from dariah_topics import preprocessing
>>> tokenized_corpus = [['this', 'is', 'the', 'first', 'document'], ['this', 'is', 'the', 'second', 'document']]
>>> document_labels = ['document_one', 'document_two']
>>> document_term_matrix = preprocessing.create_document_term_matrix(tokenized_corpus, document_labels)
>>> vocabulary = document_term_matrix.columns
>>> model = lda.LDA(n_topics=2, n_iter=1)
>>> model = model.fit(document_term_matrix.as_matrix().astype(int))
>>> topics = _show_lda_topics(model, vocabulary, num_keys=5)
>>> index = [' '.join(keys[:3]) for keys in topics.values]
>>> isinstance(_show_lda_document_topics(model, document_labels, index), pd.DataFrame)
True
"""
return pd.DataFrame(model.doc_topic_, index=document_labels, columns=index).T
def _show_lda_topics(model, vocabulary, num_keys):
"""Converts lda output to a DataFrame
Description:
With this function you can convert lda output to a DataFrame,
a more convenient datastructure.
Note:
Args:
model: LDA model.
vocab (list[str]): List of strings containing corpus vocabulary.
num_keys (int): Number of top keywords for topic
Returns:
DataFrame
Example:
>>> import lda
>>> from dariah_topics import preprocessing
>>> tokenized_corpus = [['this', 'is', 'the', 'first', 'document'], ['this', 'is', 'the', 'second', 'document']]
>>> document_labels = ['document_one', 'document_two']
>>> document_term_matrix = preprocessing.create_document_term_matrix(tokenized_corpus, document_labels)
>>> vocabulary = document_term_matrix.columns
>>> model = lda.LDA(n_topics=2, n_iter=1)
>>> model = model.fit(document_term_matrix.as_matrix().astype(int))
>>> isinstance(_show_lda_topics(model, vocabulary, num_keys=5), pd.DataFrame)
True
"""
log.info("Accessing topics from lda model ...")
topics = []
topic_word = model.topic_word_
for i, topic_distribution in enumerate(topic_word):
topics.append(np.array(vocabulary)[np.argsort(topic_distribution)][:-num_keys-1:-1])
index = ['Topic {}'.format(n) for n in range(len(topics))]
columns = ['Key {}'.format(n) for n in range(num_keys)]
return pd.DataFrame(topics, index=index, columns=columns)
def _show_mallet_document_topics(doc_topics_file, index):
"""Shows document-topic-mapping.
Args:
outfolder (str): Folder for MALLET output.
doc_topics (str): Name of MALLET's doc_topic file. Defaults to 'doc_topics.txt'.
topic_keys (str): Name of MALLET's topic_keys file. Defaults to 'topic_keys.txt'.
ToDo: Prettify docnames
Example:
>>> import tempfile
>>> index = ['first topic', 'second topic']
>>> with tempfile.NamedTemporaryFile(suffix='.txt') as tmpfile:
... tmpfile.write(b'0\\tdocument_one.txt\\t0.1\\t0.2\\n1\\tdocument_two.txt\\t0.4\\t0.5') and True
... tmpfile.flush()
... _show_mallet_document_topics(tmpfile.name, index) #doctest: +NORMALIZE_WHITESPACE
True
document_one document_two
first topic 0.1 0.4
second topic 0.2 0.5
"""
document_topics_triples = []
document_labels = []
topics = []
with open(doc_topics_file, 'r', encoding='utf-8') as file:
for line in file:
l = line.lstrip()
if l.startswith('#'):
lines = file.readlines()
for line in lines:
documet_number, document_label, *values = line.rstrip().split('\t')
document_labels.append(os.path.splitext(os.path.basename(document_label))[0])
for topic, share in _grouper(2, values):
triple = (document_label, int(topic), float(share))
topics.append(int(topic))
document_topics_triples.append(triple)
else:
easy_file_format = True
break
if easy_file_format:
document_topics = pd.read_table(doc_topics_file, sep='\t', header=None)
document_topics.index = [os.path.splitext(os.path.basename(document_label))[0] for document_label in document_topics[1]]
document_topics = document_topics.drop([0, 1], axis=1)
document_topics.columns = index
return document_topics.T
else:
document_topics_triples = sorted(document_topics_triples, key=operator.itemgetter(0, 1))
document_labels = sorted(document_labels)
num_documents = len(document_labels)
num_topics = len(topics)
document_topics = np.zeros((num_documents, num_topics))
for triple in document_topics_triples:
document_label, topic, share = triple
index_num = document_labels.index(document_label)
document_topics[index_num, topic] = share
return pd.DataFrame(document_topics, index=index, columns=columns.T)
def _show_mallet_topics(path_to_topic_keys_file):
"""Show topic-key-mapping.
Args:
outfolder (str): Folder for Mallet output,
topicsKeyFile (str): Name of Mallets' topic_key file, default "topic_keys"
#topic-model-mallet
Note: FBased on DARIAH-Tutorial -> https://de.dariah.eu/tatom/topic_model_mallet.html
ToDo: Prettify index
Example:
>>> import tempfile
>>> with tempfile.NamedTemporaryFile(suffix='.txt') as tmpfile:
... tmpfile.write(b'0\\t0.5\\tthis is the first document\\n1\\t0.5\\tthis is the second document') and True
... tmpfile.flush()
... _show_mallet_topics(tmpfile.name)
True
Key 0 Key 1 Key 2 Key 3 Key 4
Topic 0 this is the first document
Topic 1 this is the second document
"""
log.info("Accessing topics from MALLET model ...")
topics = []
with open(path_to_topic_keys_file, 'r', encoding='utf-8') as file:
for line in file.readlines():
_, _, keys = line.split('\t')
keys = keys.rstrip().split(' ')
topics.append(keys)
index = ['Topic {}'.format(n) for n in range(len(topics))]
columns = ['Key {}'.format(n) for n in range(len(topics[0]))]
return pd.DataFrame(topics, index=index, columns=columns)
def _save_matrix_market(document_term_matrix, path):
"""
Writes a `document_term_matrix` designed for large corpora to `Matrix Market <http://math.nist.gov/MatrixMarket/formats.html#MMformat>`_ file (`.mm`). Libraries like `scipy <https://www.scipy.org>`_
and `gensim <https://radimrehurek.com/gensim/>`_ are able to read and process
the Matrix Market format. This private function is wrapped in `save_document_term_matrix()`.
**Use the function `preprocessing.create_document_term_matrix()` to create a
document-term matrix.**
Args:
document_term_matrix (pandas.DataFrame): Document-term matrix with only
one column corresponding to type frequencies and a pandas MultiIndex
with `document_ids` for level 0 and `type_ids` for level 1. Will be
saved as `document_term_matrix.mm`.
path (str): Path to the output directory.
Returns:
None.
Example:
"""
num_docs = document_term_matrix.index.get_level_values('document_id').max()
num_types = document_term_matrix.index.get_level_values('type_id').max()
sum_counts = document_term_matrix[0].sum()
header = "{} {} {}\n".format(num_docs, num_types, sum_counts)
with open(os.path.join(path, 'document_term_matrix.mm'), 'w', encoding='utf-8') as file:
file.write("%%MatrixMarket matrix coordinate real general\n")
file.write(header)
document_term_matrix.to_csv(file, sep=' ', header=None)
return None