Created
October 12, 2016 02:24
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Clean up radiology reports from EPIC data dump. Usage: python report_cleaner.py input_filename.csv
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#!/usr/bin/python | |
import re | |
import csv | |
import sys | |
# Usage: python report_cleaner.py input_file_name.csv | |
# This will write to input_filename_cleaned.csv | |
# Define how we clean up the reports after the lines | |
# have been collected. | |
def clean_report(report): | |
report = re.sub(r'\s+', ' ', report) | |
return report | |
# Read the data from the input file. | |
f = open(sys.argv[1],'rU') | |
data = csv.DictReader(f) | |
reports = {} | |
for row in data: | |
order_proc_id = row['ORDER_PROC_ID'] | |
if order_proc_id not in reports: | |
reports[order_proc_id] = { 'ORDER_PROC_ID': row['ORDER_PROC_ID'], \ | |
'PAT_ENC_CSN_ID': row['PAT_ENC_CSN_ID'], \ | |
'PROC_CODE': row['PROC_CODE'], \ | |
'RADIOLOGIST': row['RADIOLOGIST'],\ | |
'NARRATIVE': row['NARRATIVE'],\ | |
'DESCRIPTION': row['DESCRIPTION'],\ | |
'ORDER_TIME': row['ORDER_TIME']} | |
else: | |
reports[order_proc_id]['NARRATIVE'] += row['NARRATIVE'] | |
# Set up the output file | |
o = open(sys.argv[1][:-4] + '_cleaned.csv','wb') | |
fieldnames = ['ORDER_PROC_ID','PAT_ENC_CSN_ID','PROC_CODE','RADIOLOGIST','NARRATIVE','DESCRIPTION','ORDER_TIME'] | |
output = csv.DictWriter(o, fieldnames=fieldnames, delimiter=',', lineterminator='\n') | |
output.writeheader() | |
# Clean the report and write to file. | |
for report in reports: | |
if report: | |
reports[report]['NARRATIVE'] = clean_report(reports[report]['NARRATIVE']) | |
output.writerow(reports[report]) | |
print(reports[report]['NARRATIVE']) | |
o.close() |
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