Coverage for dariah_topics/mallet.py : 32%

#!/usr/bin/env python3 

# -*- coding: utf-8 -*- 

"""MALLET wrapper for Python. 

This module contains various `MALLET`_ related functions for Topic Modeling 

provided by `DARIAH-DE`_. 

.. _MALLET: 

http://mallet.cs.umass.edu/ 

.. _DARIAH-DE: 

https://de.dariah.eu 

https://github.com/DARIAH-DE 

""" 

__author__ = "DARIAH-DE" 

__authors__ = "Steffen Pielstroem, Sina Bock, Severin Simmler" 

__email__ = "pielstroem@biozentrum.uni-wuerzburg.de" 

__date__ = "2017-03-28" 

import itertools 

import logging 

import numpy as np 

import operator 

import os 

import pandas as pd 

from platform import system 

from subprocess import Popen, PIPE 

log = logging.getLogger('mallet') 

log.addHandler(logging.NullHandler()) 

logging.basicConfig(level=logging.INFO, 

format='%(levelname)s %(name)s: %(message)s') 

def create_mallet_binary(outfile='binary.mallet', outfolder='mallet_output', 

path_to_file=False, path_to_corpus=os.path.join(os.path.abspath('.'), 'corpus_txt'), 

path_to_mallet="mallet", keep_sequence=False, preserve_case=False, 

remove_stopwords=True, stoplist=None, token_regex=False, use_pipe_from=False, 

replacement_files=False, deletion_files=False, extra_stopwords=False): 

"""Creates a MALLET binary file. 

Args: 

outfile (str): Name of the MALLET file that will be generated. Defaults to 'binary.mallet'. 

outfolder (str): Folder for output. 

path_to_file (str): Absolute path to text file, e.g. '/home/workspace/testfile.txt'. 

path_to_corpus (str): Absolute path to corpus folder, e.g. '/home/workspace/corpus_txt'. 

path_to_mallet (str): Path to MALLET. Defaults to 'mallet'. 

If MALLET is not properly installed use absolute path, e.g. '/home/workspace/mallet/bin/mallet'. 

keep_sequence (bool): Preserves the document as a sequence of word features, 

rather than a vector of word feature counts. Use this 

option for sequence labeling tasks. MALLET also requires 

feature sequences rather than feature vectors. Defaults 

to False. 

preserve_case (bool): Converts all word features to lowercase. Defaults to False. 

remove_stopwords (bool): Ignores a standard list of very common tokens. Defaults to True. 

stoplist (str): Absolute path to plain text stopword list. Defaults to None. 

token_regex (str): Divides documents into tokens using a regular expression. 

Defaults to False. 

use_pipe_from (str): Use the pipe and alphabets from a previously created vectors file. 

Allows the creation, for example, of a test set of vectors that are 

compatible with a previously created set of training vectors. Defaults to False. 

replacement_files (str): Files containing string replacements, one per line: 

'A B [tab] C' replaces A B with C, 

'A B' replaces A B with A_B 

deletion_files (str): Files containing strings to delete after replacements but before 

tokenization (i.e. multiword stop terms). 

Returns: 

String. Absolute path to created MALLET binary file. 

""" 

if system() == 'Windows': 

shell = True 

else: 

shell = False 

path_to_binary = os.path.join(outfolder, outfile) 

if not os.path.exists(outfolder): 

log.info("Creating output folder ...") 

os.makedirs(outfolder) 

param = [path_to_mallet] 

if not path_to_file: 

param.append('import-dir') 

param.append('--input') 

param.append(path_to_corpus) 

else: 

param.append('import-file') 

param.append('--input') 

param.append(path_to_file) 

if preserve_case: 

param.append('--preserve-case') 

if remove_stopwords: 

param.append('--remove-stopwords') 

if stoplist is not None: 

param.append('--stoplist-file') 

param.append(stoplist) 

if token_regex is not False: 

param.append('--token-regex') 

param.append(token_regex) 

if use_pipe_from: 

param.append('--use-pipe-from') 

param.append(use_pipe_from) 

if replacement_files: 

param.append('--replacement-files') 

param.append(replacement_files) 

if deletion_files: 

param.append('--deletion-files') 

param.append(deletion_files) 

if extra_stopwords: 

param.append('--extra-stopwords') 

param.append(extra_stopwords) 

param.append('--output') 

param.append(os.path.join(path_to_binary)) 

param.append('--keep-sequence') 

try: 

log.info("Accessing MALLET with %s ...", param) 

p = Popen(param, stdout=PIPE, stderr=PIPE, shell=shell) 

out = p.communicate()[0].decode('utf-8') 

log.debug(out) 

except KeyboardInterrupt: 

p.terminate() 

log.error(out) 

return path_to_binary 

def create_mallet_model(path_to_binary, outfolder, path_to_mallet='mallet', num_topics=False, 

num_top_words=False, num_iterations=False, num_threads=False, 

num_icm_iterations=False, no_inference=False, random_seed=False, 

optimize_interval=False, optimize_burn_in=False, use_symmetric_alpha=False, 

alpha=False, beta=False, output_topic_keys=True, topic_word_weights_file=True, 

word_topic_counts_file=True, diagnostics_file=True, xml_topic_report=True, 

xml_topic_phrase_report=False, output_topic_docs=False, num_top_docs=False, 

output_doc_topics=True, doc_topics_threshold=False, output_model=True, 

output_state=True, doc_topics_max=False): 

"""Creates MALLET model. 

Note: Use `create_mallet_binary()` to create `path_to_binary`. 

Args: 

path_to_binary (str): Path to MALLET binary. 

outfolder (str): Folder for MALLET output. 

path_to_mallet (str): Path to MALLET. Defaults to 'mallet'. 

If MALLET is not properly installed use absolute path, e.g. '/home/workspace/mallet/bin/mallet'. 

num_topics (int): Number of topics. Defaults to False. 

num_interations (int): Number of iterations. Defaults to False. 

num_top_words (int): Number of keywords for each topic. Defaults to False. 

num_threads (int): Number of threads for parallel training. Defaults to False. 

num_icm_iterations (int): Number of iterations of iterated conditional modes (topic maximization). Defaults to False.. 

no_inference (bool): Load a saved model and create a report. Equivalent to `num_iterations = 0`. Defaults to False. 

random_seed (int): Random seed for the Gibbs sampler. Defaults to False. 

optimize_interval (int): Number of iterations between reestimating dirichlet hyperparameters. Defaults to False. 

optimize_burn_in (int): Number of iterations to run before first estimating dirichlet hyperparameters. Defaults to False. 

use_symmetric_alpha (bool): Only optimize the concentration parameter of the prior over document-topic 

distributions. This may reduce the number of very small, poorly estimated 

topics, but may disperse common words over several topics. Defaults to False. 

alpha (float): Sum over topics of smoothing over doc-topic distributions. alpha_k = [this value] / [num topics]. Defaults to False. 

beta (float): Smoothing parameter for each topic-word. Defaults to False. 

output_topic_keys (bool): Write the top words for each topic and any Dirichlet parameters. Defaults to True. 

topic_word_weights_file (bool): Write unnormalized weights for every topic and word type. Defaults to False. 

word_topic_counts_file (bool): Write a sparse representation of topic-word assignments. By default this is 

null, indicating that no file will be written. Defaults to False. 

diagnostics_file (bool): Write measures of topic quality, in XML format. By default this is null, 

indicating that no file will be written. Defaults to False. 

xml_topic_report (bool): Write the top words for each topic and any Dirichlet parameters in XML format. Defaults to False. 

xml_topic_phrase_report (bool): Write the top words and phrases for each topic and any Dirichlet parameters in XML format. Defaults to False. 

output_topic_docs (bool): Write the most prominent documents for each topic, at the end of the iterations. Defaults to False. 

num_top_docs (int): Number of top documents for `output_topic_docs`. Defaults to False. 

output_doc_topics (bool): Write the topic proportions per document, at the end of the iterations. Defaults to True. 

doc_topics_threshold (float): Do not print topics with proportions less than this threshold value within `output_doc_topics`. Defaults to False. 

doc_topics_max (int): Do not print more than `int` number of topics. A negative value indicates that all topics should be printed. Defaults to False. 

output_model (bool): Write a serialized MALLET topic trainer object. This type of output is appropriate for pausing 

and restarting training, but does not produce data that can easily be analyzed. Defaults to False. 

output_state (bool): Output a compressed text file containing the words in the corpus with their topic assignments. 

The file format can easily be parsed and used by non-Java-based software. Defaults to True. 

ToDo: 

Param 'output_topic_docs' is causing an internal error  

-> Exception in thread "main" java.lang.ClassCastException: java.net.URI cannot be cast to java.lang.String 

-> at cc.mallet.topics.ParallelTopicModel.printTopicDocuments(ParallelTopicModel.java:1773) 

-> at cc.mallet.topics.tui.TopicTrainer.main(TopicTrainer.java:281) 

Para, 'num_top_docs' is obsolete, refering to 'output_topic_docs' 

Returns: 

None 

""" 

if system() == 'Windows': 

log.debug(outfolder) 

shell = True 

else: 

log.debug(outfolder) 

shell = False 

outfolder = os.path.join(os.path.abspath('.'), outfolder) 

param = [path_to_mallet, 'train-topics', '--input', path_to_binary] 

# parameter: 

if num_topics is not False: 

param.append('--num-topics') 

param.append(str(num_topics)) 

if num_iterations is not False: 

param.append('--num-iterations') 

param.append(str(num_iterations)) 

if num_threads is not False: 

param.append('--num-threads') 

param.append(str(num_threads)) 

if num_top_words is not False: 

param.append('--num-top-words') 

param.append(str(num_top_words)) 

if num_icm_iterations is not False: 

param.append('--num-icm-iterations') 

param.append(str(num_icm_iterations)) 

if no_inference is not False: 

param.append('--no-inference') 

param.append(str(no_inference)) 

if random_seed is not False: 

param.append('--random-seed') 

param.append(str(random_seed)) 

# hyperparameter: 

if optimize_interval is not False: 

param.append('--optimize-interval') 

param.append(optimize_interval) 

if optimize_burn_in is not False: 

param.append('--optimize-burn-in') 

param.append(optimize_burn_in) 

if use_symmetric_alpha is not False: 

param.append('--use-symmetric-alpha') 

param.append(use_symmetric_alpha) 

if alpha is not False: 

param.append('--alpha') 

param.append(alpha) 

if beta is not False: 

param.append('--beta') 

param.append(beta) 

# output: 

if output_topic_keys: 

param.append('--output-topic-keys') 

param.append(os.path.join(outfolder, 'topic_keys.txt')) 

if topic_word_weights_file: 

param.append('--topic-word-weights-file') 

param.append(os.path.join(outfolder, 'topic_word_weights.txt')) 

if word_topic_counts_file: 

param.append('--word-topic-counts-file') 

param.append(os.path.join(outfolder, 'word_topic_counts.txt')) 

if diagnostics_file: 

param.append('--diagnostics-file') 

param.append(os.path.join(outfolder, 'diagnostics.txt')) 

if xml_topic_report: 

param.append('--xml-topic-report') 

param.append(os.path.join(outfolder, 'topic_report.xml')) 

if xml_topic_phrase_report: 

param.append('--xml-topic-phrase-report') 

param.append(os.path.join(outfolder, 'topic_phrase_report.xml')) 

#not yet working 

if output_topic_docs: 

param.append('--output-topic-docs') 

param.append(os.path.join(outfolder, 'topic_docs.txt')) 

if num_top_docs is not False: 

param.append('--num-top-docs') 

param.append(topic_word_weights_file) 

if output_doc_topics: 

param.append('--output-doc-topics') 

param.append(os.path.join(outfolder, 'doc_topics.txt')) 

if doc_topics_threshold: 

param.append('--doc-topics-threshold') 

param.append(topic_word_weights_file) 

if doc_topics_max: 

param.append('--doc-topics-max') 

param.append(topic_word_weights_file) 

if output_model: 

param.append('--output-model') 

param.append(os.path.join(outfolder, 'mallet.model')) 

if output_state: 

param.append('--output-state') 

param.append(os.path.join(outfolder, 'state.gz')) 

try: 

log.info("Accessing Mallet with %s ...", param) 

p = Popen(param, stdout=PIPE, stderr=PIPE, shell=shell) 

out = p.communicate()[1].decode('utf-8') 

log.debug(out) 

except KeyboardInterrupt: 

p.terminate() 

log.error(out) 

def _grouper(n, iterable, fillvalue=None): 

"""Collects data into fixed-length chunks or blocks. 

Args: 

Returns: 

""" 

args=[iter(iterable)] * n 

return itertools.zip_longest(*args, fillvalue=fillvalue) 

def show_doc_topic_matrix(output_folder, doc_topics='doc_topics.txt', topic_keys='topic_keys.txt', 

easy_file_format=False): 

"""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 

""" 

doc_topics=os.path.join(output_folder, doc_topics) 

assert doc_topics 

topic_keys=os.path.join(output_folder, topic_keys) 

assert topic_keys 

doctopic_triples=[] 

mallet_docnames=[] 

topics=[] 

df=pd.read_csv(topic_keys, sep='\t', header=None, encoding='utf-8') 

labels=[] 

for index, item in df.iterrows(): 

label=' '.join(item[2].split()[:3]) 

labels.append(label) 

with open(doc_topics, encoding='utf-8') as f: 

for line in f: 

li=line.lstrip() 

if li.startswith("#"): 

lines=f.readlines() 

for line in lines: 

docnum, docname, *values=line.rstrip().split('\t') 

mallet_docnames.append(docname) 

for topic, share in _grouper(2, values): 

triple=(docname, int(topic), float(share)) 

topics.append(int(topic)) 

doctopic_triples.append(triple) 

else: 

easy_file_format=True 

break 

if easy_file_format: 

newindex=[] 

doc_topic_matrix=pd.read_csv( 

doc_topics, sep='\t', names=labels[0:], encoding='utf-8') 

for eins, zwei in doc_topic_matrix.index: 

newindex.append(os.path.basename(zwei)) 

doc_topic_matrix.index=newindex 

else: 

# sort the triples 

# triple is (docname, topicnum, share) so sort(key=operator.itemgetter(0,1)) 

# sorts on (docname, topicnum) which is what we want 

doctopic_triples=sorted( 

doctopic_triples, key=operator.itemgetter(0, 1)) 

# sort the document names rather than relying on MALLET's ordering 

mallet_docnames=sorted(mallet_docnames) 

# collect into a document-term matrix 

num_docs=len(mallet_docnames) 

num_topics=max(topics) + 1 

# the following works because we know that the triples are in 

# sequential order 

data=np.zeros((num_docs, num_topics)) 

for triple in doctopic_triples: 

docname, topic, share=triple 

row_num=mallet_docnames.index(docname) 

data[row_num, topic]=share 

topicLabels=[] 

# creates list of topic lables consisting of the 3 most weighed topics 

df=pd.read_csv(topic_keys, sep='\t', header=None, encoding='utf-8') 

labels=[] 

for index, item in df.iterrows(): 

topicLabel=' '.join(item[2].split()[:3]) 

topicLabels.append(topicLabel) 

shortened_docnames=[] 

for item in mallet_docnames: 

shortened_docnames.append(os.path.basename(item)) 

''' 

for topic in range(max(topics)+1): 

topicLabels.append("Topic_" + str(topic)) 

''' 

doc_topic_matrix=pd.DataFrame(data=data[0:, 0:], 

index=shortened_docnames[0:], 

columns=topicLabels[0:]) 

return doc_topic_matrix.T 

def show_topics_keys(output_folder, topicsKeyFile="topic_keys.txt", num_topics=10): 

"""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 

""" 

path_to_topic_keys=os.path.join(output_folder, topicsKeyFile) 

assert path_to_topic_keys 

with open(path_to_topic_keys, encoding='utf-8') as input: 

topic_keys_lines=input.readlines() 

topic_keys=[] 

#topicLabels=[] 

for line in topic_keys_lines: 

_, _, words=line.split('\t') # tab-separated 

words=words.rstrip().split(' ') # remove the trailing '\n' 

topic_keys.append(words) 

topicKeysMatrix=pd.DataFrame(topic_keys) 

topicKeysMatrix.index=['Topic ' + str(x + 1) for x in range(num_topics)] 

topicKeysMatrix.columns=['Key ' + str(x + 1) for x in range(10)] 

return topicKeysMatrix