WMGM

#!/usr/bin/env python
#
# This script is initiated by daemon_SOFTWEB_2files.py, which communicates with the data submission on NiftyWeb.
# WMGM is run without an extension.
#
# Three inputs are provided to NiftyWeb. Two are NIfTI files: an initial scan (image1) and a re-scan without
# repositioning (image2). The third input is a PDF containing protocol information. In addition, 4 parameters are
# provided (field strength, coil type, sequence, and data type). Each NiftyWeb submission is assigned an ID when it is
# added to the queue for processing.
#
# Dependency:
# - SCT's Python
#
# USAGE (normal launch through the daemon):
#   ${SCT_DIR}/python/bin/python PATH_TO_DAEMON/daemon_SOFTWEB_2files.py WMGM <ID> <IMAGE1> <IMAGE2>
#
# USAGE (for debugging):
#   ${SCT_DIR}/python/bin/python WMGM <ID> <IMAGE1> <IMAGE2>
#
# WMGM extracts the two NIfTI files, and calls process_data.py to process and analyze the data. WMGM then waits for
# these results files to be returned:
#   ID_WMGM.txt: text file containing metric results
#   ID_WMGM.zip: folder containing text file with results as well as cord and gray matter segmentations
#
# Once the results files have been generated, they are returned to the user by the daemon.
#
# Authors: Stephanie Alley, Julien Cohen-Adad


import os, sys, subprocess, time, argparse
# get path of running script
path_script = os.path.dirname(os.path.abspath(os.path.basename(__file__)))
# append path to allow import
sys.path.append(path_script)
import process_data


def get_parameters():
    parser = argparse.ArgumentParser(description='Extract the two NIfTI images and submission ID, and use them to call '
                                                 'process_data.py.')
    parser.add_argument('num', help='NiftyWeb ID')
    parser.add_argument('image_1', help='Initial scan')
    parser.add_argument('image_2', help='Re-scan')
    parser.add_argument('pdf', help='File name of pdf protocol.')
    parser.add_argument('-field', help='Field strength [T]', required=False)
    parser.add_argument('-coil', help='Type of coil', required=False)
    parser.add_argument('-sequence', help='Type of sequence', required=False)
    parser.add_argument('-data', help='Name of dataset', required=False)
    args = parser.parse_args()
    return args


def main():
    # get arguments
    num = args.num
    image_1 = os.path.basename(args.image_1)
    image_2 = os.path.basename(args.image_2)
    dir_data = os.path.abspath(os.path.dirname(args.image_1))

    # Send email notification of request
    #mail = 'mutt -s "Request received for {}"jcohen@polymtl.ca,f.carrasco@ucl.ac.uk < /dev/null'.format(num)
    # subprocess.check_call(mail, shell=True)
    
    os.chdir(dir_data)
    # Initiate processing script
    #process_data.main([image_1, image_2], None, None, num=num, create_txt_output=True)
    subprocess.call(["/home/niftyweb_sct/sct/python/bin/python", "/home/niftyweb_sct/gm_challenge/process_data.py", "-i", image_1, image_2, "-n", num, "-o","{}_WMGM".format(num)])
    #sys.exit(0)

    # Check for output files to return to user
    final_txt = os.path.join(dir_data + '/' + num + '_WMGM.txt')
    final_zip = os.path.join(dir_data + '/' + num + '_WMGM.zip')
    if (os.path.isfile(final_txt)) and (os.path.isfile(final_zip)):
        sys.exit(0)
    else:
        sys.exit(1)

#    done = 0
#    while(done == 0):
#        if (os.path.isfile(final_txt)) and (os.path.isfile(final_zip)):
#            done = 1
#        else:
#            time.sleep(60)


if __name__ == "__main__":
    args = get_parameters()
    main()