move_completed_subjects.py

"""
Small script that moves the final results of the subjects
For safekeeping and backup reasons.
"""

import click
import shutil
import os
import pandas as pd
import numpy as np


@click.command(
    help="Move the results folder to create a backup on the desired folder ."
)
@click.option("--pip_csv", type=click.STRING, help="csv with the completed pipeline")
@click.option(
    "--out_dir",
    type=click.STRING,
    help="Directory where we will store the results. Each subject would have a subdirectory",
)
@click.argument("ind_dir")
def move_completed_subjects(ind_dir, pip_csv, out_dir):
    df_pipeline = pd.read_csv(pip_csv)
    for row in df_pipeline.itertuples():
        subID = row.id
        type_dir = row.CENTER

        if type_dir != "LONDON":
            continue
        # if type_dir != "CLINIC": continue
        subj_dir_id = f"{ind_dir}/{type_dir}_Post/{subID}"

        # store only subjects that have been processed
        if row.toTVB:
            out_dir_subj = f"{out_dir}/{type_dir}_{subID}"

            # create subject if it does not exist
            if not os.path.exists(f"{out_dir_subj}/results/"):
                os.makedirs(f"{out_dir_subj}/results/")

            # copy connectivity.zip, weights, tracts, z_matrix and zr_matrix
            shutil.copy2(
                f"{subj_dir_id}/results/Connectivity.zip", f"{out_dir_subj}/results/"
            )
            shutil.copy2(
                f"{subj_dir_id}/results/{subID}_SC_distances.txt",
                f"{out_dir_subj}/results/{type_dir}_{subID}_SC_distances.txt",
            )
            shutil.copy2(
                f"{subj_dir_id}/results/{subID}_SC_weights.txt",
                f"{out_dir_subj}/results/{type_dir}_{subID}_SC_weights.txt",
            )
            shutil.copy2(
                f"{subj_dir_id}/fmri_proc_dti/r_matrix.csv", f"{out_dir_subj}/results/"
            )
            shutil.copy2(
                f"{subj_dir_id}/fmri_proc_dti/zr_matrix.csv", f"{out_dir_subj}/results/"
            )
            shutil.copy2(
                f"{subj_dir_id}/fmri_proc_dti/corrlabel_ts.txt",
                f"{out_dir_subj}/results/",
            )


if __name__ == "__main__":
    # those parameters have to be entered from outside
    move_completed_subjects()