Example for Windows file operation using Python

windows_file_operation.py

import os
import glob
import errno
import pandas as pd
import subprocess as sp

si = sp.STARTUPINFO()
si.dwFlags |= sp.STARTF_USESHOWWINDOW


def mkdir_p(path):
    try:
        os.makedirs(path)
    except OSError as exc:  # Python >2.5
        if exc.errno == errno.EEXIST and os.path.isdir(path):
            pass
        else:
            raise


cwd = os.getcwd()
data_dir = os.path.abspath(os.path.join(cwd, os.pardir, 'data'))
dest_dir = os.path.abspath(
    os.path.join(cwd, os.pardir, 'data_clean', 'data'))

dest_dir_dti = os.path.join(dest_dir, 'dti')

mkdir_p(dest_dir_dti)
subj_info = pd.read_csv(os.path.join(cwd, 'SubInfo.csv'))
NC_IDs = subj_info[subj_info.Group == 'NC']['Scan_ID']

subj_folder_names = next(os.walk(data_dir))[1]  # find all folders


for sfn in subj_folder_names:
    print(sfn)
    scan_n = int(float(sfn.split(' ')[0]))
    sn = sfn.split(' ')[1]
    raw_path = os.path.join(data_dir, sfn, sn + '_DICOM')
    if scan_n in NC_IDs:
        dest_dir_fun = os.path.join(dest_dir_dti, 'NC', 'DTI')
        dest_dir_t1 = os.path.join(dest_dir_dti, 'NC', 'T1Img')
    else:
        dest_dir_fun = os.path.join(dest_dir_dti, 'SCZ', 'DTI')
        dest_dir_t1 = os.path.join(dest_dir_dti, 'SCZ', 'T1Img')
    sub_id = subj_info[subj_info.Scan_ID == scan_n]['Sub_ID'].values[0]
    mkdir_p(dest_dir_fun)
    mkdir_p(dest_dir_t1)

    fun_path = os.path.join(dest_dir_fun, sub_id)
    t1_path = os.path.join(dest_dir_t1, sub_id)
    mkdir_p(fun_path)
    fun_files = glob.iglob(os.path.join(raw_path, 'x*DTI32*10??.*'))
    for file_ in fun_files:
        sp.call(['xcopy', file_, fun_path, '/Y'],
                startupinfo=si)

    mkdir_p(t1_path)
    t1_files = glob.iglob(os.path.join(raw_path, '*DAX*10??.nii.gz'))
    for file_ in t1_files:
        sp.call(['xcopy', file_, t1_path, '/Y'],
                startupinfo=si)