def moveFileToDest(local_path, destination):
import os, shutil
from printMessage import printMessage
if destination[0] != '/':
destination = os.path.abspath(os.path.join(workingDir, destination))
printMessage('Moving output file from temporary directory to user specified location')
shutil.move(local_path, destination)
def delTempDir(temp_dir, verbose):
import shutil
from printMessage import printMessage
if verbose:
printMessage("Deleting temporary directory " + temp_dir)
shutil.rmtree(temp_dir)
def getHeaderInfo(image_path, header_item, verbose):
import os, subprocess, sys
from printMessage import printMessage
command = 'mrinfo ' + image_path + ' -' + header_item
if verbose:
printMessage('Command: \'' + command + '\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None, shell=True)
result = proc.stdout.read()
result = result.rstrip()
if verbose:
printMessage ('Result: ' + result)
return result
def getHeaderInfo(image_path, header_item):
import app, os, subprocess, sys
from printMessage import printMessage
command = 'mrinfo ' + image_path + ' -' + header_item
if app.verbosity > 1:
printMessage('Command: \'' + command + '\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None, shell=True)
result = proc.stdout.read()
result = result.rstrip()
if app.verbosity > 1:
printMessage ('Result: ' + result)
return result
def initialise(n):
import os, random, string, sys
from printMessage import printMessage
from readMRtrixConfSetting import readMRtrixConfSetting
global cleanup, mrtrixQuiet, numArgs, tempDir, verbosity, workingDir
#if not numArgs:
# sys.stderr.write('Must set numArgs value before calling initialise()\n')
# exit(1)
numArgs = n
workingDir = os.getcwd()
for option in sys.argv[numArgs+1:]:
if '-verbose'.startswith(option):
verbosity = 2
mrtrixQuiet = ''
elif '-quiet'.startswith(option):
verbosity = 0
mrtrixQuiet = '-quiet'
elif '-nocleanup'.startswith(option):
cleanup = False
else:
sys.stderr.write('Unknown option: ' + option + '\n')
exit(1)
# Create the temporary directory
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
def terminate():
import os, shutil
from printMessage import printMessage
printMessage('Changing back to original directory (' + workingDir + ')')
os.chdir(workingDir)
if cleanup:
printMessage('Deleting temporary directory ' + tempDir)
shutil.rmtree(tempDir)
else:
printMessage('Contents of temporary directory kept, location: ' + tempDir)
def delTempDir(temp_dir, verbose):
import shutil
from printMessage import printMessage
if verbose:
printMessage('Deleting temporary directory ' + temp_dir)
shutil.rmtree(temp_dir)
def gotoTempDir():
import os
from printMessage import printMessage
if verbosity:
printMessage('Changing to temporary directory (' + tempDir + ')')
os.chdir(tempDir)