def test_initializeSession(self):
""" test general_utils.initializeSession() """
# loop over the different scan environments
for scanEnv in ['GE', 'Philips', 'Siemens']:
print('testing environment: ' + scanEnv)
# set paths based on current test environment
if scanEnv == 'GE':
envDir = paths['GE_dir']
funcDir = paths['GE_funcDir']
elif scanEnv == 'Philips':
envDir = paths['Philips_dir']
funcDir = paths['Philips_funcDir']
elif scanEnv == 'Siemens':
envDir = paths['Siemens_dir']
funcDir = paths['Siemens_funcDir']
# update config file to match local paths
configFile = join(envDir, 'scannerConfig.yaml')
helper_tools.replace_scannerConfig_sessionDir(configFile, funcDir)
general_utils.initializeSession(pynealScannerDir=envDir)
# remove local paths from config file
helper_tools.cleanConfigFile(configFile)
print('Passed!')
def test_initializeSession(self):
""" test general_utils.initializeSession() """
# loop over the different scan environments
for scanEnv in ['GE', 'Philips', 'Siemens']:
print('testing environment: ' + scanEnv)
# set paths based on current test environment
if scanEnv == 'GE':
envDir = paths['GE_dir']
funcDir = paths['GE_funcDir']
elif scanEnv == 'Philips':
envDir = paths['Philips_dir']
funcDir = paths['Philips_funcDir']
elif scanEnv == 'Siemens':
envDir = paths['Siemens_dir']
funcDir = paths['Siemens_funcDir']
# update config file to match local paths
configFile = join(envDir, 'scannerConfig.yaml')
helper_tools.replace_scannerConfig_baseDir(configFile, funcDir)
general_utils.initializeSession(pynealScannerDir=envDir)
# remove local paths from config file
helper_tools.cleanConfigFile(configFile)
print('Passed!')
def test_getSeries_Siemens(self):
""" test getSeries.getSeries_Siemens """
envDir = paths['Siemens_dir']
funcDir = paths['Siemens_funcDir']
# update config file to match local paths
configFile = join(envDir, 'scannerConfig.yaml')
helper_tools.replace_scannerConfig_baseDir(configFile, funcDir)
# run initializeSettings to get the scannerDirs object
scannerSettings, scannerDirs = general_utils.initializeSession(
pynealScannerDir=envDir)
### run getSeries_Siemens
import pyneal_scanner.getSeries as getSeries
# module expects user to input 2 things: desired series, and output prefix.
# We have to mock the input for automatic testing, but can only mock one
# input (at least as far as I can figure out). So, by hardcoding the input
# to '000013', we will get series 000013 and build a nifti named
# '000013_000013.nii.gz' saved in pyneal/pyneal_scanner/data. Delete this file
# at end of test
seriesNum = '000013'
getSeries.input = lambda x: seriesNum
getSeries.getSeries_Siemens(scannerDirs)
# return the module input to the normal __builtin__ input function
getSeries.input = input
# ensure output file created, then delete
outputFile = join(paths['pynealScannerDir'], 'data',
'{}_{}.nii.gz'.format(seriesNum, seriesNum))
assert os.path.exists(outputFile)
os.remove(outputFile)
# remove local paths from the config file
helper_tools.cleanConfigFile(configFile)