def read_i2b2(txt, con):
"""
read_i2b2()
@param txt. A file path for the tokenized medical record
@param con. A file path for the i2b2 annotated concepts for txt
"""
tokenized_sents = []
sent_tokenize = lambda text: text.split('\n')
word_tokenize = lambda text: text.split(' ')
# Read in the medical text
with open(txt) as f:
try:
# Original text file
text = f.read().strip('\n')
# text = f.read()
except:
f = open(txt, encoding="utf8")
text = f.read().strip('\n')
f.close()
# tokenize
sentences = sent_tokenize(text)
# print(sentences)
'''
['DATE OF ADMISSION : MM/DD/YYYY', 'DATE OF DISCHARGE : MM/DD/YYYY', 'DISCHARGE DIAGNOSES :', '1 . Vasovagal syncope , status post fall .', '2 . Traumatic arthritis , right knee .', '3 .
Hypertension .', '4 ]
'''
for sentence in sentences:
sent = clean_text(sentence.rstrip())
# lowercase
sent = sent.lower()
toks = word_tokenize(sent)
# normalize tokens
normed_toks = normalize_tokens(toks)
#for w in normed_toks:
# print(w)
#print()
tokenized_sents.append(normed_toks)
# If an accompanying concept file was specified, read it
tok_concepts = []
if con:
with open(con) as f:
for line in f.readlines():
# Empty line
if not line.strip():
continue
# parse concept line
concept_regex = '^c="(.*)" (\d+):(\d+) (\d+):(\d+)\|\|t="(.*)"$'
match = re.search(concept_regex, line.strip())
groups = match.groups()
# retrieve regex info
concept_text = groups[0]
start_lineno = int(groups[1])
start_tok_ind = int(groups[2])
end_lineno = int(groups[3])
end_tok_ind = int(groups[4])
concept_label = groups[5]
# pre-process text for error-check
#matching_line = tokenized_sents[start_lineno-1]
#matching_toks = matching_line[start_tok_ind:end_tok_ind+1]
#matching_text = ' '.join(matching_toks).lower()
#concept_text = ' '.join(word_tokenize(concept_text))
# error-check info
assert start_lineno == end_lineno, 'concept must span single line'
#assert concept_text==matching_text, 'something wrong with inds'
# add the concept info
tup = (concept_label, start_lineno, start_tok_ind, end_tok_ind)
tok_concepts.append(tup)
# Safe guard against concept file having duplicate entries
tok_concepts = list(set(tok_concepts))
# Concept file does not guarantee ordering by line number
tok_concepts = sorted(tok_concepts, key=lambda t: t[1:])
# Ensure no overlapping concepts (that would be bad)
for i in range(len(tok_concepts) - 1):
c1 = tok_concepts[i]
c2 = tok_concepts[i + 1]
if c1[1] == c2[1]:
if c1[2] <= c2[2] and c2[2] <= c1[3]:
fname = os.path.basename(con)
error1 = '%s has overlapping entities on line %d' % (fname,
c1[1])
error2 = "It can't be processed until you remove one"
error3 = 'Please modify this file: %s' % con
error4 = '\tentity 1: c="%s" %d:%d %d:%d||t="%s"' % (
' '.join(tokenized_sents[c1[1] - 1][c1[2]:c1[3] + 1]),
c1[1], c1[2], c1[1], c1[3], c1[0])
error5 = '\tentity 2: c="%s" %d:%d %d:%d||t="%s"' % (
' '.join(tokenized_sents[c2[1] - 1][c2[2]:c2[3] + 1]),
c2[1], c2[2], c2[1], c2[3], c2[0])
error_msg = '\n\n%s\n%s\n\n%s\n\n%s\n%s\n' % (
error1, error2, error3, error4, error5)
raise DocumentException(error_msg)
# print(tok_concepts) # ('treatment', 48, 2, 2), ('treatment', 49, 5, 5)]
return tokenized_sents, tok_concepts
def read_i2b2(txt, con):
"""
read_i2b2()
@param txt. A file path for the tokenized medical record
@param con. A file path for the i2b2 annotated concepts for txt
"""
tokenized_sents = []
sent_tokenize = lambda text: text.split('\n')
word_tokenize = lambda text: text.split(' ')
# Read in the medical text
with open(txt) as f:
# Original text file
text = f.read().strip('\n')
# tokenize
sentences = sent_tokenize(text)
for sentence in sentences:
sent = clean_text(sentence.rstrip())
# lowercase
sent = sent.lower()
toks = word_tokenize(sent)
# normalize tokens
normed_toks = normalize_tokens(toks)
#for w in normed_toks:
# print w
#print
tokenized_sents.append(normed_toks)
# If an accompanying concept file was specified, read it
tok_concepts = []
if con:
with open(con) as f:
for line in f.readlines():
# Empty line
if not line.strip():
continue
# parse concept line
concept_regex = '^c="(.*)" (\d+):(\d+) (\d+):(\d+)\|\|t="(.*)"$'
match = re.search(concept_regex, line.strip())
groups = match.groups()
# retrieve regex info
concept_text = groups[0]
start_lineno = int(groups[1])
start_tok_ind = int(groups[2])
end_lineno = int(groups[3])
end_tok_ind = int(groups[4])
concept_label = groups[5]
# pre-process text for error-check
#matching_line = tokenized_sents[start_lineno-1]
#matching_toks = matching_line[start_tok_ind:end_tok_ind+1]
#matching_text = ' '.join(matching_toks).lower()
#concept_text = ' '.join(word_tokenize(concept_text))
# error-check info
assert start_lineno == end_lineno, 'concept must span single line'
#assert concept_text==matching_text, 'something wrong with inds'
# add the concept info
tup = (concept_label, start_lineno, start_tok_ind, end_tok_ind)
tok_concepts.append(tup)
# Safe guard against concept file having duplicate entries
tok_concepts = list(set(tok_concepts))
# Concept file does not guarantee ordering by line number
tok_concepts = sorted(tok_concepts, cmp=classification_cmp)
# Ensure no overlapping concepts (that would be bad)
for i in range(len(tok_concepts) - 1):
c1 = tok_concepts[i]
c2 = tok_concepts[i + 1]
if c1[1] == c2[1]:
if c1[2] <= c2[2] and c2[2] <= c1[3]:
fname = os.path.basenme(con)
error1 = '%s has overlapping entities on line %d' % (fname,
c1[1])
error2 = "It can't be processed until you remove one"
error_msg = '%s\n%s' % (error1, error2)
raise DocumentException(error_msg)
return tokenized_sents, tok_concepts
def readDocs(txt, concept):
tokenizedSentences = []
sentTokenize = lambda text: text.split('\n')
wordTokenize = lambda text: text.split(' ')
with open(txt) as foo:
text = foo.read().strip('\n')
sentences = sentTokenize(text)
for s in sentences:
sent = clean_text(s.rstrip())
sent = sent.lower()
tokens = wordTokenize(sent)
normedTokens = normalize_tokens(tokens)
tokenizedSentences.append(normedTokens)
tokenizedConcepts = []
if concept:
with open(concept) as foo:
for l in foo.readlines():
if not l.strip():
continue
conceptRegex = '^c="(.*)" (\d+):(\d+) (\d+):(\d+)\|\|t="(.*)"$'
match = re.search(conceptRegex, l.strip())
groups = match.groups()
concept_text = groups[0]
beginLineNum = int(groups[1])
beginTokenIndex = int(groups[2])
lastLineNum = int(groups[3])
lastTokenIndex = int(groups[4])
conceptLabel = groups[5]
assert beginLineNum == lastLineNum, 'concept must span single line'
tup = (conceptLabel, beginLineNum, beginTokenIndex,
lastTokenIndex)
tokenizedConcepts.append(tup)
tokenizedConcepts = list(set(tokenizedConcepts))
tokenizedConcepts = sorted(tokenizedConcepts, key=lambda t: t[1:])
# Ensure no overlapping concepts (that would be bad)
for i in range(len(tokenizedConcepts) - 1):
c1 = tokenizedConcepts[i]
c2 = tokenizedConcepts[i + 1]
if c1[1] == c2[1]:
if c1[2] <= c2[2] and c2[2] <= c1[3]:
fname = os.path.basename(con)
error1 = '%s has overlapping entities on line %d' % (fname,
c1[1])
error2 = "It can't be processed until you remove one"
error3 = 'Please modify this file: %s' % con
error4 = '\tentity 1: c="%s" %d:%d %d:%d||t="%s"' % (
' '.join(
tokenizedSentences[c1[1] - 1][c1[2]:c1[3] + 1]),
c1[1], c1[2], c1[1], c1[3], c1[0])
error5 = '\tentity 2: c="%s" %d:%d %d:%d||t="%s"' % (
' '.join(
tokenizedSentences[c2[1] - 1][c2[2]:c2[3] + 1]),
c2[1], c2[2], c2[1], c2[3], c2[0])
error_msg = '\n\n%s\n%s\n\n%s\n\n%s\n%s\n' % (
error1, error2, error3, error4, error5)
raise DocumentException(error_msg)
return tokenizedSentences, tokenizedConcepts
def read_i2b2(txt, con):
"""
read_i2b2()
@param txt. A file path for the tokenized medical record
@param con. A file path for the i2b2 annotated concepts for txt
"""
tokenized_sents = []
sent_tokenize = lambda text: text.split('\n')
word_tokenize = lambda text: text.split(' ')
# Read in the medical text
with open(txt) as f:
# Original text file
text = f.read().strip('\n')
# tokenize
sentences = sent_tokenize(text)
for sentence in sentences:
sent = clean_text(sentence.rstrip())
# lowercase (like word2vec preprocessing)
sent = sent.lower()
toks = word_tokenize(sent)
# normalize tokens
normed_toks = normalize_tokens(toks)
#for w in normed_toks:
# print w
#print
tokenized_sents.append(normed_toks)
# If an accompanying concept file was specified, read it
tok_concepts = []
if con:
with open(con) as f:
for line in f.readlines():
# Empty line
if not line.strip():
continue
# parse concept line
concept_regex = '^c="(.*)" (\d+):(\d+) (\d+):(\d+)\|\|t="(.*)"$'
match = re.search(concept_regex, line.strip())
groups = match.groups()
# retrieve regex info
concept_text = groups[0]
start_lineno = int(groups[1])
start_tok_ind = int(groups[2])
end_lineno = int(groups[3])
end_tok_ind = int(groups[4])
concept_label = groups[5]
# pre-process text for error-check
#matching_line = tokenized_sents[start_lineno-1]
#matching_toks = matching_line[start_tok_ind:end_tok_ind+1]
#matching_text = ' '.join(matching_toks).lower()
#concept_text = ' '.join(word_tokenize(concept_text))
# error-check info
assert start_lineno==end_lineno, 'concept must span single line'
#assert concept_text==matching_text, 'something wrong with inds'
# add the concept info
tup = (concept_label, start_lineno, start_tok_ind, end_tok_ind)
tok_concepts.append(tup)
# Safe guard against concept file having duplicate entries
tok_concepts = list(set(tok_concepts))
# Concept file does not guarantee ordering by line number
tok_concepts = sorted(tok_concepts, cmp=classification_cmp)
# Ensure no overlapping concepts (that would be bad)
for i in range(len(tok_concepts)-1):
c1 = tok_concepts[i]
c2 = tok_concepts[i+1]
if c1[1] == c2[1]:
if c1[2] <= c2[2] and c2[2] <= c1[3]:
fname = os.path.basenme(con)
error1='%s has overlapping entities on line %d'%(fname,c1[1])
error2="It can't be processed until you remove one"
error_msg = '%s\n%s' % (error1,error2)
raise DocumentException(error_msg)
return tokenized_sents, tok_concepts
