inflammation-analysis.py

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

import argparse
import os

from inflammation import models, views
from inflammation.compute_data import analyse_data_from_data_source
from inflammation.file_data_class import CSVDataSource, JSONDataSource


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]

    if args.full_data_analysis:
        _, extension = os.path.splitext(infiles[0])
        if extension == '.json':
            data_source = JSONDataSource(os.path.dirname(infiles[0]))
        elif extension == '.csv':
            data_source = CSVDataSource(os.path.dirname(infiles[0]))
        else:
            raise ValueError(f"Unsupported file format: {extension}")
        daily_standard_deviation = analyse_data_from_data_source(data_source)
        graph_data = {"standard deviation by day": daily_standard_deviation}
        views.visualize(graph_data)
        return

    for filename in infiles:
        inflammation_data = models.load_csv(filename)

        view_data = {'average': models.daily_mean(inflammation_data), 'max': models.daily_max(inflammation_data), 'min': models.daily_min(inflammation_data), **(models.s_dev(inflammation_data))}

        views.visualize(view_data)


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="A basic patient inflammation data management system"
    )

    parser.add_argument(
        "infiles",
        nargs="+",
        help="Input CSV(s) containing inflammation series for each patient",
    )

    parser.add_argument(
        "--full-data-analysis", action="store_true", dest="full_data_analysis"
    )

    args = parser.parse_args()

    main(args)