Program used to report patient data using pandas in Python
This program uses pandas and xlsxwriter in order to parse excel files in .xlsx and csv and renders report of patient 5 vitals, GCS, and prescription information. The files can be read individually or in batches based on subject data; the Sorter.py file runs the patient data individually, while the iSorter.py file runs the patient data in batches based on the file name provided.
There are a total of 46520 patient ChartEvents files provided along with matching prescription files that give information on the route and type of prescription the subject is taking. All subjects have a registered subject_id. These are available from the MIMIC-II database generously provided by physionet.
The project requires us to separate the patients batches by the 5 vitals: Heart Rate, Blood Pressure, Temperature, Respiratory Rate, and O2 Saturation. The item ids that are used to parse these data are listed below.
HEART RATE
- 220045, 211
BLOOD PRESSURE
- 220179, 455 -- "Systolic Blood Pressure"
- 220180, 8441 -- "Diastolic Blood Pressure"
TEMPERATURE
- 223762, 676 -- "Temperature Celsius"
- 223761, 678 -- "Temperature Fahrenheit"
RESPIRATORY RATE
- 220210, 618
O2 Saturation
- 220277, 646
The data are then sorted to form a dataframe with each of the vital's itemid and their corresponding chart time, and then merged into the visualization table which will be printed to the 'Visualization' sheet on the report. The data is then taken from the Visualization sheet and charted under a new 'Report' sheet. In the report sheet, the prescription and GCS table values are also listed.
The completed batch files will be stored in folders of their ICD9 disease values, which are listed below. The subjects which match these values can be found in the folders above.
ICD9 disease values:
- 460-466 Acute Respiratory Infections
- 470-478 Other Diseases Of Upper Respiratory Tract
- 480-488 Pneumonia And Influenza
- 490-496 Chronic Obstructive Pulmonary Disease And Allied Conditions
- 500-508 Pneumoconioses And Other Lung Diseases Due To External Agents
- 510-519 Other Diseases Of Respiratory System
- E8859 Accidental fall on same level from slipping tripping or stumbling
The python files can be found under the folder Python_Files, with the main files being Sorter.py and iSorter.py.
Sorter.py is a file for parsing an individual patient file while iSorter.py parses multiple patient files in batches.
- Python 2.7 or 3.6
Project is: Completed
All remaining issues have been resolved. Possible implementation of a dashboard or analysis algorithm is in progress.
