def main():
# Read external parameters:
# - path and file: "/usr/xxx/data/XXX.xml"
# - temporal expression: "every two days"
#
#
temporal_expression = sys.argv[2]
path_and_file = sys.argv[1]
doc_analyser = DocumentAnalyser()
path = os.path.abspath(os.path.dirname(path_and_file)) + "/"
filename = os.path.basename(path_and_file)
clinical_note = doc_analyser.analyse(path, filename, True)
utterance_time = select_utterance_time(temporal_expression, clinical_note)
print normalise(temporal_expression, utterance_time, True)
def main():
# Read external parameters:
# - path and file: "/usr/xxx/data/XXX.xml"
# - temporal expression: "every two days"
#
#
temporal_expression = sys.argv[2]
path_and_file = sys.argv[1]
doc_analyser = DocumentAnalyser()
path = os.path.abspath(os.path.dirname(path_and_file)) + "/"
filename = os.path.basename(path_and_file)
clinical_note = doc_analyser.analyse(path, filename, True)
utterance_time = select_utterance_time(temporal_expression, clinical_note)
print normalise(temporal_expression, utterance_time, True)
def analyse(self, path, file, normalisation=False):
clinical_note = ClinicalDocument()
text = ''
file = codecs.open(path+file, 'rU')
for line in file.readlines():
if not re.match("^(?:\]\]>)?<(?:\?|/)?[A-Za-z]+", line):
text += line.lower()
file.close()
date_refs = [(match.start(), match.end()) for match in re.finditer(self.date_syntaxes[0], text)]
clinical_note.file_name = file.name
clinical_note.file_path = path
if normalisation:
clinical_note.admission_date = normalise(self.search_closest(self.admission_signals, date_refs, text, 'forward', 6))[2]
clinical_note.discharge_date = normalise(self.search_closest(self.discharge_signals, date_refs, text, 'forward', 6))[2]
if clinical_note.discharge_date == 'NONE':
clinical_note.discharge_date = normalise(self.search_closest(self.discharge_signals, date_refs, text, 'forward', 50))[2]
clinical_note.operation_date = normalise(self.search_closest(self.operation_signals, date_refs, text, 'both'), clinical_note.admission_date.replace('-', ''))[2]
clinical_note.transfer_date = normalise(self.search_closest(self.transfer_signals, date_refs, text, 'both'), clinical_note.admission_date.replace('-', ''))[2]
clinical_note.course_length = self.get_difference_from_normalised_dates(clinical_note.admission_date, clinical_note.discharge_date)
else:
clinical_note.admission_date = self.search_closest(self.admission_signals, date_refs, text, 'forward', 6)
clinical_note.discharge_date = self.search_closest(self.discharge_signals, date_refs, text, 'forward', 6)
if not clinical_note.discharge_date:
clinical_note.discharge_date = self.search_closest(self.discharge_signals, date_refs, text, 'forward', 50)
clinical_note.discharge_date_not_in_header = True
clinical_note.operation_date = self.search_closest(self.operation_signals, date_refs, text, 'both')
clinical_note.transfer_date = self.search_closest(self.transfer_signals, date_refs, text, 'both')
clinical_note.course_length = self.get_difference_from_normalised_dates(normalise(clinical_note.admission_date)[2], normalise(clinical_note.discharge_date)[2])
return clinical_note
