def calculate_case_statistics():
"""Calculate statistics of patient cases."""
words = data.get_stopwords()
terms = data.get_medical_terms()
print("Case | Lines | Stopwords | Terms | Medical terms")
for code, case in sorted(PatientCase.ALL.items()):
print(' & '.join((code, str(len(case.text.split('\n'))),
str(len([i for i in case.text.split() if i in words])),
str(len(case.vector)),
str(len([i for i in case.vector.keys() if i in terms])))) + r' \\')
print()
def main(script):
"""Run all the functions in this module."""
data.main() # Populate all objects
# Generate a LaTeX table with all stopwords
_generate_columned_table(sorted(data.get_stopwords()),
6, 'stopwords', 'Norwegian stopwords')
# Generate a LaTeX table with all medical terms
_generate_columned_table(sorted(data.get_medical_terms()),
3, 'medicalterms', 'Medical terms')
generate_cases_table()
calculate_chapter_statistics()
calculate_case_statistics()
def parse_case_file(path, stopwords=get_stopwords()):
"""Read lines from case file in 'path'."""
# Read in lines from case files
with open(path) as f:
text = []
for line in f.readlines():
line = ' '.join(i for i in line.strip().split(' ')
if i.lower() not in stopwords)
if line:
if line[-1] == '.':
line = line[:-1] # Remove period from queries
text.append(line)
filename, ext = os.path.splitext(os.path.split(path)[1])
PatientCase(filename.replace('case', ''), '\n'.join(text))
from math import log
from whoosh.index import create_in, open_dir, exists_in
from whoosh.analysis import StandardAnalyzer
from whoosh.fields import Schema, TEXT, KEYWORD, ID, STORED
from whoosh.qparser import QueryParser, OrGroup
from data import ATC, ICD, PatientCase, Therapy, populate_all, get_stopwords
# Folder to store whoosh index in
INDEX_DIR = 'whooshindex'
# Analyzer which removes stopwords
ANALYZER = StandardAnalyzer(stoplist=get_stopwords())
# Schema for storing and indexing ATC codes in whoosh database
ATC_SCHEMA = Schema(code=ID(stored=True), title=TEXT(stored=True))
# Schema for storing and indexing ICD10 codes in whoosh database
ICD_SCHEMA = Schema(code=ID(stored=True), short=ID(stored=True),
label=TEXT(stored=True, analyzer=ANALYZER),
type=TEXT, icpc2_code=ID,
icpc2_label=TEXT, synonyms=TEXT, terms=TEXT,
inclusions=TEXT, exclusions=TEXT,
description=TEXT(analyzer=ANALYZER))
