main_cluster_batch_AI_data_preparation.py

""" 
@author: Joao Periquito 
iBEAt Analysis MAIN CLUSTER Scrpit
2022
Download XNAT dataset -> Name Standardization ->    Execute MDR   -> Custom Moddeling (T1, T2...) ->     Biomarker extraction   -> Google Drive Upload
  pipelines.xnat.py   -> pipelines.rename.py  -> pipelines.mdr.py ->      pipelines.mapping.py    -> pipelines.export_ROI_stats -> scripts.upload.py

TO RUN THE SCRIPT YOU USE: python main_cluster.py --num n (WHERE n is an integer with the value of the XNAT dataset)
"""
import argparse
from scripts.project_prepare_pre_Dixon_AI import single_subject
import utilities.XNAT_credentials as XNAT_cred
import os

if __name__ == '__main__':

    #XNAT Credentials
    username, password = XNAT_cred.main()

    path = "//mnt//fastdata//" + username + "//<insert project name>" #CLUSTER PATH TO SAVE DATA, ADD YOUR LOCAL PATH IF YOU WANT TO RUN IT LOCALLY

    if not os.path.exists(path):
        os.mkdir(path)

    parser = argparse.ArgumentParser()
    parser.add_argument('--num',
                        dest='num',
                        help='Define the XNAT dataset',
                        type=int)

    args = parser.parse_args()

    #SELECT YOUR DATASET
    #dataset = [site, study, dataset]
    dataset = [6,1,args.num]

    ################################################# EXAMPLE DATASET SELECTION #############################################################
    #DATASET CODE FOR LEEDS
    #  (FIRST NUMBER)                 (SECOND NUMBER)                                 (THIRD NUMBER - INNPUT from --num when you run the main script: python main_cluster.py --num n)
    #  2: BEAt-DKD-WP4-Bordeaux    (selected) BEAt-DKD-WP4-Leeds                 (selected) BEAt-DKD-WP4-Leeds -> (selected) Leeds_Patients
    #  3: BEAt-DKD-WP4-Exeter       ->0: Leeds_Patients                            0: Leeds_Patient_4128001
    #  4: BEAt-DKD-WP4-Turku          1: Leeds_volunteer_repeatability_study       1: Leeds_Patient_4128002
    #  5: BEAt-DKD-WP4-Bari           2: Leeds_Phantom_scans                       2: Leeds_Patient_4128004
    #->6: BEAt-DKD-WP4-Leeds          3: Leeds_RAVE_Reconstructions                       ..........
    #  7: BEAt-DKD-WP4-Sheffield      4: Leeds_setup_scans                      ->14: Leeds_Patient_4128015
    #########################################################################################################################################
    offset = 0
    
    ID_num      = str(args.num + offset)
    if len(ID_num) == 1:
        ID_num = '00' + ID_num
    
    if len(ID_num) == 2:
        ID_num = '0' + ID_num
        
    subject_ID = ID_num

    single_subject(username, password, path, dataset,subject_ID=subject_ID)