runPossum.py

#!/usr/bin/env python
#Code to generate a full shell of diffusion-weighted, eddy distorted images using FSL's possum, along with data that can be used to
#establish a ground truth.
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function

# Handle arguments (before imports so --help can be fast)
def str2bool(v):
    #Function allows boolean arguments to take a wider variety of inputs
    if v.lower() in ('yes', 'true', 't', 'y', '1'):
        return True
    elif v.lower() in ('no', 'false', 'f', 'n', '0'):
        return False
    else:
        raise argparse.ArgumentTypeError('Boolean value expected.')

import argparse
parser = argparse.ArgumentParser(description="Run the simulations.")
parser.add_argument("simulation_dir",help="Path to the simulation directory (output_dir of generateFileStructure.py)")
parser.add_argument("num_images",help='Number of volumes.',type=int)
parser.add_argument("--simulate_artefact_free",help='Run simulation on datasets without eddy-current and motion artefacts. Default=True.',type=str2bool, nargs='?',const=True,default=True)
parser.add_argument("--simulate_distorted",help='Run simulation datasets with eddy-current and motion artefacts. Default=False',type=str2bool, nargs='?',const=True,default=False)
parser.add_argument("--num_processors",help='Number of processors to split each simulation over. Default=1',type=int,default=1)
args=parser.parse_args()

import os
from subprocess import call
import os.path

#Assign args
simDirCluster = os.path.abspath(args.simulation_dir)
numImages = args.num_images
normalImages = args.simulate_artefact_free
motionAndEddyImages = args.simulate_distorted
processors = args.num_processors 

def saveImage(simDir,saveImageDir,fileName):
    call(["mv", simDir + "/image_abs.nii.gz", os.path.join(saveImageDir,fileName)])

def saveNoiseyImage(simDir,saveImageDir,fileName):
    call(["mv", simDir + "/imageNoise_abs.nii.gz", os.path.join(saveImageDir,fileName)])


resultsDir = simDirCluster+"/Results"
resultsNoiseDir = simDirCluster+"/ResultsNoise"

for direction in range(numImages):
    if normalImages == True:
        simDirClusterDirection = simDirCluster+"/Direction"+str(direction)
    if motionAndEddyImages == True:
        simDirClusterDirectionMotionAndEddy = simDirCluster+"/DirectionMotionAndEddy"+str(direction)

    #Run possum
    if normalImages == True:
        if os.path.isfile(simDirClusterDirection + '/image_abs.nii.gz') == False:
            call(["possumX", simDirClusterDirection,"-n",str(processors),"-t","20"])
    if motionAndEddyImages == True:
        if os.path.isfile(simDirClusterDirectionMotionAndEddy + '/image_abs.nii.gz') == False:
            call(["possumX", simDirClusterDirectionMotionAndEddy,"-n",str(processors),"-t","20"])