inflammation-analysis.py

#!/usr/bin/env python3
"""Software for managing and analysing patients' inflammation data in our imaginary hospital."""

import argparse

from inflammation import models, views, serializers


def main(args):
    """The MVC Controller of the patient inflammation data system.

    The Controller is responsible for:
    - selecting the necessary models and views for the current task
    - passing data between models and views
    """
    infiles = args.infiles
    if not isinstance(infiles, list):
        infiles = [args.infiles]

    for filename in infiles:
        if args.file_type == 'cvs':
            inflammation_data = models.load_csv(filename)
        elif args.file_type == 'json':
            inflammation_data = serializers.PatientJSONSerializer.load(filename)

        if args.view == 'visualize':
            view_data = {
                'average': models.daily_mean(inflammation_data),
                'max': models.daily_max(inflammation_data),
                'min': models.daily_min(inflammation_data),
            }

            views.visualize(view_data)

        elif args.view == 'record' and args.file_type == 'cvs':
            patient_data = inflammation_data[args.patient]
            observations = [models.Observation(day, value) for day, value in enumerate(patient_data)]
            patient = models.Patient('UNKNOWN', observations)

            views.display_patient_record(patient)

        elif args.view == 'record' and args.file_type == 'json':
            for patient in inflammation_data:
                #print(patient.name)
                views.display_patient_record(patient)


if __name__ == "__main__":

    parser = argparse.ArgumentParser(
        description='A basic patient inflammation data management system')

    parser.add_argument(
        '--infiles',
        nargs='+',
        help='Input containing inflammation series for each patient')

    parser.add_argument(
        '--file_type',
        default='cvs',
        choices=['cvs', 'json'],
        help='The file type to load')

    parser.add_argument(
        '--view',
        default='visualize',
        choices=['visualize', 'record'],
        help='Which view should be used?')

    parser.add_argument(
        '--patient',
        type=int,
        default=0,
        help='Which patient should be displayed?')

    args = parser.parse_args()

    main(args)