Fuzzy-Pacs

Note: This is our first attempt at open-sourcing our work. All feedback is appreciated and significant effort would be put into incorporating it.

Fuzzy Matching of PACS Data with HIS/RIS Data

This project is a continuation of a paper presented by us at the European Congress of Radiology, 2019. The video is available at: https://ecronline.myesr.org/ecr2019/index.php?p=recording&t=recorded&lecture=fuzzy-pacs-linking-large-unorganised-image-and-report-databases-for-development-and-validation-of-deep-learning-algorithms

It is a well known problem that in many parts of the world, integration between PACS and RIS/HIS systems is sub-optimal - i.e. there is no unique linker between images and reports, making it very time consuming and labour intensive to pull either images or reports of a large group of patients. FuzzyPACS, a simple combination of multiple dicom tools and Fuzzy String Matching, enables a user to link images and reports using an approximate match between the name of the patient as entered in PACS (Mr. John Smith) and Report (John Smith).

This project contains 2 scripts named script.py and match.py & Pynetdicom3 Module zip file

Prerequisites:

1. Python 3.+
2. Pynetdicom3,Pydicom, mysql.connector,datetime,fuzzywuzzy Module for python
3. Mysql 5.7+ server
4. Little knowledge of csv/tsv writing.
5. Active connection to PACS.

script.py:

This script helps to get data like (PatientName, StudyInstanceUID, StudyDescription, StudyDate etc.) from your PACS between specified date range as a csv file.

1. Enter a name for the output csv file. file = open('example.csv','w')
2. Enter Date range in (YYYYMMDD) format. rangestart = 20160101 rangeend = 20190418 Also, write date(rangeend +1 day) in this line while rangeend < 20190419:
3. Enter PACS details like AE-Title, IP Address & Port Number. assoc = ae.associate('127.0.0.1', 11112, 'AETITLE')
4. Run the script using python 3+.

After this you will get a csv file with all the data.

match.py:

This script needs both PACS data and HIS/RIS data to be stored in Mysql database seperately.

1. Enter the name for the output tsv file. file = open('example.tsv','w')
2. Enter the mysql database details: cnx = mysql.connector.connect(user='root', password='password', host='localhost', port="if-any", database='fuzzy')
3. Enter start date and end date in (YYYY,MM,DD) format start = date(2016, 5, 27) end = date(2019, 3, 9)
4. Please ensure the correct column names and table names query1 = ("SELECT NAME, testid, Date_Of_Registration, Department FROM his_data WHERE DATE(Date_Of_Registration) = ""
   • str(start.year) + "-" + str(start.month).zfill(2) + "-" + str(start.day).zfill(2) + """) query2 = ("SELECT Name, Modality, StudyInstanceUID, Date, Description FROM pacs_data WHERE Date = "" +str(start.year) + "-" + str(start.month).zfill(2) + "-" + str(start.day).zfill(2) + """)
5. Run the script using python 3+.