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#!/usr/bin/python
# preprocess.py
#
# Author: Yuanbin Wu
# National University of Singapore (NUS)
# Date: 12 Mar 2013
# Version: 1.0
#
# Contact: wuyb@comp.nus.edu.sg
#
# This script is distributed to support the CoNLL-2013 Shared Task.
# It is free for research and educational purposes.
#
# Usage: python preprocess.py OPTIONS sgmlFileName conllFileName annotationFileName m2FileName
# Options:
# -o generate conllFile, annotationFile, m2File from sgmlFile, with parser info.
# -l generate conllFile, annotationFile, m2File from sgmlFile, without parser info.
import parser_feature
from nuclesgmlparser import nuclesgmlparser
from nucle_doc import *
import nltk.data
from nltk import word_tokenize
import cPickle as pickle
import re
import sys
import os
import getopt
class PreProcessor:
def __init__(self):
self.sentenceTokenizer = nltk.data.load('tokenizers/punkt/english.pickle')
self.sentenceDumpedFile = 'sentence_file'
self.docsDumpedFileName = 'docs'
self.parsingDumpedFileName = 'parse_file'
def readNUCLE(self, fn):
f = open(fn, 'r')
parser = nuclesgmlparser()
filestr = f.read()
filestr = filestr.decode('utf-8')
#Fix Reference tag
p = re.compile(r'(<REFERENCE>\n<P>\n.*\n)<P>')
filestr = p.sub(r'\1</P>', filestr)
parser.feed(filestr)
f.close()
parser.close()
return parser.docs
def sentenceSplit(self, docs):
for doc in docs:
for par in doc.paragraphs:
doc.sentences.append([])
for s in self.sentenceTokenizer.tokenize(par):
doc.buildSentence(s, [], '', [], [])
return docs
def featureGeneration(self, docs, option):
# build parsing feature
# the sentence for parsing is dump to self.sentenceDumpedFile
f = open(self.sentenceDumpedFile, 'w')
for doc in docs:
for par in doc.paragraphs:
doc.sentences.append([])
for s in self.sentenceTokenizer.tokenize(par):
sent = nucle_sent(s, [], '', [], [])
doc.addSentence(sent)
tokenizedSentStr = ' '.join(sent.getWords()) + '\n'
f.write(tokenizedSentStr.encode('utf-8'))
f.close()
if option == 0:
nodelist = parser_feature.DependTree_Batch(self.sentenceDumpedFile, self.parsingDumpedFileName)
elif option == 1 :
nodelist = parser_feature.DependTree_Batch_Parsefile(self.parsingDumpedFileName)
else:
return
i = 0
for doc in docs:
for slist in doc.sentences:
for s in slist:
if s.sentstr.strip() == '':
continue
s.setDpNode(nodelist[i][0])
s.setConstituentStr(nodelist[i][1])
s.setPOSList(nodelist[i][2])
s.buildConstituentList()
i += 1
f = file(self.docsDumpedFileName,'w')
pickle.dump(docs, f)
f.close()
return docs
def conllFileGeneration(self, docs, conllFileName, annotationFileName, m2FileName):
fcolumn = open(conllFileName, 'w')
fannotation = open(annotationFileName, 'w')
fm2 = open(m2FileName, 'w')
for doc in docs:
for slistIndex in xrange(len(doc.sentences)):
slist = doc.sentences[slistIndex]
for sentid in xrange(len(slist)):
sent = slist[sentid]
# annotation string list
annotationList = []
# m2 format annotation string list
m2AnnotationList = []
# build colums
table = sent.getConllFormat(doc, slistIndex, sentid)
tokenizedSentStr = ' '.join(sent.getWords())
#Add annotation info
sentoffset = doc.paragraphs[slistIndex].index(sent.sentstr)
for m in doc.mistakes:
if m['start_par'] != slistIndex or \
m['start_par'] != m['end_par'] or \
m['start_off'] < sentoffset or \
m['start_off'] >= sentoffset + len(sent.sentstr) or \
m['end_off'] <sentoffset or \
m['end_off'] > sentoffset + len(sent.sentstr):
continue
wordsoffset = 0
wdstart = 0
startInWord = 0
headText = ''
endInWord = 0
tailText = ''
words = sent.getWords()
while wdstart < len(words):
word = words[wdstart]
nextstart = sent.sentstr.find(word, wordsoffset)
if nextstart == -1:
# may not find word, due to relpacement
print >> sys.stderr, "Warning in building conll format: can not find word"
print >> sys.stderr, word.encode('utf-8')
wordsoffset += 1
else:
wordsoffset = nextstart
if wordsoffset >= m['start_off']-sentoffset:
break
elif wordsoffset + len(word) > m['start_off']-sentoffset:
# annotation starts at the middle of a word
startInWord = 1
headText = sent.sentstr[wordsoffset: m['start_off']-sentoffset]
break
wordsoffset += len(word)
wdstart += 1
if wdstart == len(words):
print >> sys.stderr, 'Warning in building conll format: start_off overflow'
print >> sys.stderr, m, sent.sentstr.encode('utf-8')
continue
wdend = wdstart
while wdend < len(words):
word = words[wdend]
nextstart = sent.sentstr.find(word, wordsoffset)
if nextstart == -1:
print >> sys.stderr, "Warning in building conll format: can not find word"
print >> sys.stderr, word.encode('utf-8')
wordsoffset += 1
else:
wordsoffset = nextstart
if wordsoffset >= m['end_off']-sentoffset:
# annotation ends at the middle of a word
if wordsoffset - len(words[wdend-1]) - 1 < m['end_off']-sentoffset:
endInWord = 1
tailText = sent.sentstr[m['end_off']-sentoffset : wordsoffset].strip()
break
wordsoffset += len(word)
wdend += 1
correctionTokenizedStr = self.tokenizeCorrectionStr(headText + m['correction'] + tailText, wdstart, wdend, words)
#Shrink the correction string, wdstart, wdend
correctionTokenizedStr, wdstart, wdend = self.shrinkCorrectionStr(correctionTokenizedStr, wdstart, wdend, words)
if wdstart == wdend and len(correctionTokenizedStr) == 0:
continue
# build annotation string for .conll.ann file
annotationStr = '<MISTAKE '
annotationStr += 'nid="' + table[0][0] + '" ' #nid
annotationStr += 'pid="' + str(table[0][1]) + '" ' #start_par
annotationStr += 'sid="' + str(sentid) + '" ' #sentence id
annotationStr += 'start_token="' + str(wdstart) + '" ' #start_token
annotationStr += 'end_token="' + str(wdend) + '">\n' #end_token
annotationStr += '<TYPE>' + m['type'] + '</TYPE>\n'
annotationStr += '<CORRECTION>' + correctionTokenizedStr + '</CORRECTION>\n'
annotationStr += '</MISTAKE>\n'
annotationList.append(annotationStr)
# build annotation string for .conll.m2 file
m2AnnotationStr = 'A '
m2AnnotationStr += str(wdstart) + ' '
m2AnnotationStr += str(wdend) + '|||'
m2AnnotationStr += m['type'] + '|||'
m2AnnotationStr += correctionTokenizedStr.replace('\n', '') + '|||'
m2AnnotationStr += 'REQUIRED|||-NONE-|||0\n'
m2AnnotationList.append(m2AnnotationStr)
# write .conll file
for row in table:
output = ''
for record in row:
if type(record) == type(1):
output = output + str(record) + '\t'
else:
output = output + record + '\t'
fcolumn.write((output.strip() + '\n').encode('utf-8'))
fcolumn.write(('\n').encode('utf-8'))
# write .conll.ann file
if len(annotationList) != 0:
annotationSent = '<ANNOTATION>\n' + ''.join(annotationList) + '</ANNOTATION>\n'
fannotation.write((annotationSent + '\n').encode('utf-8'))
# write .conll.m2 file
m2AnnotationSent = 'S ' + tokenizedSentStr + '\n'
m2AnnotationSent += ''.join(m2AnnotationList) + '\n'
fm2.write(m2AnnotationSent.encode('utf-8'))
fcolumn.close()
fannotation.close()
fm2.close()
def tokenizeCorrectionStr(self, correctionStr, wdstart, wdend, words):
correctionTokenizedStr = ''
pseudoSent = correctionStr
if wdstart != 0:
pseudoSent = words[wdstart-1] + ' ' + pseudoSent
if wdend < len(words) - 1:
pseudoSent = pseudoSent + ' ' + words[wdend]
elif wdend == len(words) - 1:
pseudoSent = pseudoSent + words[wdend]
pseudoWordsList = []
sentList = self.sentenceTokenizer.tokenize(pseudoSent)
for sent in sentList:
pseudoWordsList += word_tokenize(sent)
start = 0
if wdstart != 0:
s = ''
for i in xrange(len(pseudoWordsList)):
s += pseudoWordsList[i]
if s == words[wdstart-1]:
start = i + 1
break
if start == 0:
print >> sys.stderr, 'Can not find words[wdstart-1]'
else:
start = 0
end = len(pseudoWordsList)
if wdend != len(words):
s = ''
for i in xrange(len(pseudoWordsList)):
s = pseudoWordsList[len(pseudoWordsList) - i - 1] + s
if s == words[wdend]:
end = len(pseudoWordsList) - i - 1
break
if end == len(pseudoWordsList):
print >> sys.stderr, 'Can not find words[wdend]'
else:
end = len(pseudoWordsList)
correctionTokenizedStr = ' '.join(pseudoWordsList[start:end])
return correctionTokenizedStr
def shrinkCorrectionStr(self, correctionTokenizedStr, wdstart, wdend, words):
correctionWords = correctionTokenizedStr.split(' ')
originalWords = words[wdstart: wdend]
wdstartNew = wdstart
wdendNew = wdend
cstart = 0
cend = len(correctionWords)
i = 0
while i < len(originalWords) and i < len(correctionWords):
if correctionWords[i] == originalWords[i]:
i += 1
wdstartNew = i + wdstart
cstart = i
else:
break
i = 1
while i <= len(originalWords) - cstart and i <= len(correctionWords) - cstart:
if correctionWords[len(correctionWords)-i] == originalWords[len(originalWords)-i]:
wdendNew = wdend - i
cend = len(correctionWords) - i
i += 1
else:
break
return ' '.join(correctionWords[cstart:cend]), wdstartNew, wdendNew
def usage_debug():
u = '\nUsage: python preprocess.py options \n\n'
u += '-g sgmlFileName -d useDumpedFile\n'
u += ' generate sentence features and dump the results \n'
u += ' sgmlFileName: the nucle sgml files \n'
u += ' useDumpedFile = 0, don\'t use dumped files, will parse nucle sgml file (Default) \n'
u += ' useDumpedFile = 1, reuse previous dumped parse files \n\n'
u += '-c conllFileName annotationFileName m2FileName \n'
u += ' generate conllFile, annotationFile, m2File \n\n'
u += '-l sgmlFileName conllFileName annotationFileName m2FileName \n'
u += ' generate conllFile, annotationFile, m2FileName from sgmlFile, without parser info.\n'
print u
def usage_release():
u = '\nUsage: python preprocess.py OPTIONS sgmlFileName conllFileName annotationFileName m2FileName \n\n'
u += '-o generate conllFile, annotationFile, m2File from sgmlFile, with parser info.\n'
u += '-l generate conllFile, annotationFile, m2File from sgmlFile, without parser info.\n'
print u
if __name__ == '__main__':
ppr = PreProcessor()
debug = False
try:
if debug == True:
opts, args = getopt.getopt(sys.argv[1:],'g:d:c:l:h')
else:
opts, args = getopt.getopt(sys.argv[1:],'l:o:h')
except getopt.GetoptError:
if debug == True:
usage_debug()
else:
usage_release()
sys.exit(2)
option = {}
option['-g'] = 0
option['-c'] = 0
option['-l'] = 0
option['-o'] = 0
option['useDumpedFile'] = 0
option['sgmlFileName'] = None
option['conllFileName'] = None
option['annotationFileName'] = None
option['m2FileName'] = None
for opt, arg in opts:
if opt == '-g':
if os.path.isfile(arg) == False:
print >> sys.stderr, 'can not find sgml file'
sys.exit(2)
else:
option['sgmlFileName'] = arg
option['-g'] = 1
elif opt == '-d':
if arg not in ('1', '0'):
print >> sys.stderr, '-d option should be 0 or 1'
sys.exit(2)
else:
option['useDumpedFile'] = int(arg)
elif opt == '-c':
if len(args) != 2:
print >> sys.stderr, '-c option need 3 args'
sys.exit(2)
else:
option['conllFileName'] = arg
option['annotationFileName'] = args[0]
option['m2FileName'] = args[1]
option['-c'] = 1
elif opt == '-l':
if len(args) != 3:
print >> sys.stderr, '-l option need 4 args'
sys.exit(2)
else:
if os.path.isfile(arg) == False:
print >> sys.stderr, 'can not find sgml file'
sys.exit(2)
else:
option['sgmlFileName'] = arg
option['conllFileName'] = args[0]
option['annotationFileName'] = args[1]
option['m2FileName'] = args[2]
option['-l'] = 1
elif opt == '-o':
if len(args) != 3:
print >> sys.stderr, '-o option need 4 args'
sys.exit(2)
else:
if os.path.isfile(arg) == False:
print >> sys.stderr, 'can not find sgml file'
sys.exit(2)
else:
option['sgmlFileName'] = arg
option['conllFileName'] = args[0]
option['annotationFileName'] = args[1]
option['m2FileName'] = args[2]
option['useDumpedFile'] = 0
option['-o'] = 1
elif opt == '-h':
if debug == True:
usage_debug()
else:
usage_release()
sys.exit()
if option['-g'] + option['-c'] + option['-l'] + option['-o'] > 1:
print >> sys.stderr, 'only one option among -g, -c, -l, -o is allowed'
sys.exit(2)
elif option['-g'] + option['-c'] + option['-l'] + option['-o'] == 0:
print >> sys.stderr, 'no option given'
sys.exit(2)
if option['-g'] == 1:
docs = ppr.readNUCLE(option['sgmlFileName'])
ppr.featureGeneration(docs, option['useDumpedFile'])
elif option['-c'] == 1:
if os.path.isfile(ppr.docsDumpedFileName) == False:
print >> sys.stderr, '-c option needs dumped \'docs\' file. Please use -g option first. '
sys.exit(2)
f = file(ppr.docsDumpedFileName, 'r')
docs = pickle.load(f)
f.close()
ppr.conllFileGeneration(docs, option['conllFileName'], option['annotationFileName'], option['m2FileName'])
elif option['-l'] == 1:
docs = ppr.sentenceSplit(ppr.readNUCLE(option['sgmlFileName']))
ppr.conllFileGeneration(docs, option['conllFileName'], option['annotationFileName'], option['m2FileName'])
elif option['-o'] == 1:
docs = ppr.readNUCLE(option['sgmlFileName'])
docs = ppr.featureGeneration(docs, 0)
ppr.conllFileGeneration(docs, option['conllFileName'], option['annotationFileName'], option['m2FileName'])
os.remove(ppr.sentenceDumpedFile)
os.remove(ppr.docsDumpedFileName)
os.remove(ppr.parsingDumpedFileName)
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