merge_ROI_demo_and_test.py

import argparse

import pandas as pd

from spare_scores import spare_test


def merge_and_test(
    roi_file,
    demographic_file,
    model_path,
    key_var,
    output_file,
    spare_column_name,
    verbose,
    logs_file,
):

    # Read the input CSV files into pandas DataFrames
    df_roi = pd.read_csv(roi_file)
    df_demographic = pd.read_csv(demographic_file)

    # Merge the DataFrames based on the desired column
    if not key_var:
        key_var = df_roi.columns[0]
    merged_df = pd.merge(df_roi, df_demographic, on=key_var)

    # Call the spare_test function from the spare_scores package
    result = spare_test(
        merged_df,
        model_path,
        key_var,
        output_file,
        spare_column_name,
        verbose,
        logs_file,
    )

    return result


if __name__ == "__main__":
    # Example usage:
    # python merge_ROI_demo_and_test.py -i spare_scores/data/example_data_ROIs.csv \
    #                                   -d spare_scores/data/example_data_demographics.csv \
    #                                   -m spare_scores/mdl/mdl_SPARE_AD_hMUSE_single.pkl.gz \
    #                                   -kv ID \
    #                                   -o zzz_output.csv \
    #                                   -l zzz_logs.txt \
    #                                   -sv SPARE_score
    # # Create an ArgumentParser object
    parser = argparse.ArgumentParser(description="Spare Scores Analysis")

    # Define the command-line arguments
    parser.add_argument("-i", "--input", required=True, help="Input ROI CSV file")
    parser.add_argument(
        "-d", "--demographic", required=True, help="Input demographic CSV file"
    )
    parser.add_argument("-m", "--model", required=True, help="Model for spare_train")
    parser.add_argument(
        "-kv",
        "--key_var",
        required=False,
        default="",
        help="The key variable of the dataset.",
    )
    parser.add_argument(
        "-o", "--output", required=False, default="", help="Output CSV file"
    )
    parser.add_argument(
        "-l", "--logs", required=False, default="", help="Output logs file"
    )
    parser.add_argument(
        "-sv",
        "--spare_var",
        required=False,
        default="SPARE_score",
        help="Column for calculated spare score",
    )
    parser.add_argument(
        "-v", "--verbose", required=False, default=1, help="Type of logging messages."
    )

    # Parse the command-line arguments
    args = parser.parse_args()

    # Call the merge_and_test function with the provided arguments
    merge_and_test(
        args.input,
        args.demographic,
        args.model,
        args.key_var,
        args.output,
        args.spare_var,
        args.verbose,
        args.logs,
    )