def test_Philips_DirStructure(self):
""" test Philips_utils.Philips_DirStucture """
# update config file to match local paths
configFile = join(paths['Philips_dir'], 'scannerConfig.yaml')
helper_tools.replace_scannerConfig_baseDir(configFile, paths['Philips_funcDir'])
# create instance of ScannerSettings class from general_utils
scannerSettings = general_utils.ScannerSettings(paths['Philips_dir'])
# create instance of Philips_DirStructure for testing
scannerDirs = Philips_utils.Philips_DirStructure(scannerSettings)
### Run through Philips_DirStructure class methods
scannerDirs.print_currentSeries()
assert scannerDirs.get_seriesDirs() == ['0001']
### Test the waitForSeriesDir function by creating a fake dir
# threading.timer object to create a new dir after a few sec
fakeNewSeries = join(paths['Philips_funcDir'], '0TEST')
t = threading.Timer(1.0, helper_tools.createFakeSeriesDir, [fakeNewSeries])
t.start()
scannerDirs.waitForSeriesDir()
# assuming it didn't crash, cancel the timer function and delete new dir
t.cancel()
shutil.rmtree(fakeNewSeries)
# remove local paths from the config file
helper_tools.cleanConfigFile(configFile)
def test_Siemens_DirStructure(self):
# update config file to match local paths
configFile = join(paths['Siemens_dir'], 'scannerConfig.yaml')
helper_tools.replace_scannerConfig_baseDir(configFile, paths['Siemens_funcDir'])
# create instace of ScannerSettings class from general_utils
scannerSettings = general_utils.ScannerSettings(paths['Siemens_dir'])
# create instance of Philips_DirStructure for testing
scannerDirs = Siemens_utils.Siemens_DirStructure(scannerSettings)
## Run through the Siemens_DirStructure class methods
scannerDirs.print_currentSeries()
assert scannerDirs.getUniqueSeries() == set(['000013'])
## Test waitForNewSeries function by simulating new series data
# threading.timer object to copy in new data after a few sec
newSeriesNum = 999
t = threading.Timer(1.0, fakeNewSiemensSeries, [newSeriesNum])
t.start()
scannerDirs.waitForNewSeries()
# assuming that didn't crash, stop the timer object and remove new file
t.cancel()
removeFakeSiemensSeries(newSeriesNum)
# remove local paths from the config file
helper_tools.cleanConfigFile(configFile)
def test_Siemens_DirStructure(self):
# update config file to match local paths
configFile = join(paths['Siemens_dir'], 'scannerConfig.yaml')
helper_tools.replace_scannerConfig_baseDir(configFile,
paths['Siemens_funcDir'])
# create instace of ScannerSettings class from general_utils
scannerSettings = general_utils.ScannerSettings(paths['Siemens_dir'])
# create instance of Philips_DirStructure for testing
scannerDirs = Siemens_utils.Siemens_DirStructure(scannerSettings)
## Run through the Siemens_DirStructure class methods
scannerDirs.print_currentSeries()
assert scannerDirs.getUniqueSeries() == set(['000013'])
## Test waitForNewSeries function by simulating new series data
# threading.timer object to copy in new data after a few sec
newSeriesNum = 999
t = threading.Timer(1.0, fakeNewSiemensSeries, [newSeriesNum])
t.start()
scannerDirs.waitForNewSeries()
# assuming that didn't crash, stop the timer object and remove new file
t.cancel()
removeFakeSiemensSeries(newSeriesNum)
# remove local paths from the config file
helper_tools.cleanConfigFile(configFile)
def test_Philips_DirStructure(self):
""" test Philips_utils.Philips_DirStucture """
# update config file to match local paths
configFile = join(paths['Philips_dir'], 'scannerConfig.yaml')
helper_tools.replace_scannerConfig_baseDir(configFile,
paths['Philips_funcDir'])
# create instance of ScannerSettings class from general_utils
scannerSettings = general_utils.ScannerSettings(paths['Philips_dir'])
# create instance of Philips_DirStructure for testing
scannerDirs = Philips_utils.Philips_DirStructure(scannerSettings)
### Run through Philips_DirStructure class methods
scannerDirs.print_currentSeries()
assert scannerDirs.get_seriesDirs() == ['0001']
### Test the waitForSeriesDir function by creating a fake dir
# threading.timer object to create a new dir after a few sec
fakeNewSeries = join(paths['Philips_funcDir'], '0TEST')
t = threading.Timer(1.0, helper_tools.createFakeSeriesDir,
[fakeNewSeries])
t.start()
scannerDirs.waitForSeriesDir()
# assuming it didn't crash, cancel the timer function and delete new dir
t.cancel()
shutil.rmtree(fakeNewSeries)
# remove local paths from the config file
helper_tools.cleanConfigFile(configFile)
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_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_ScannerSettings(self):
""" test general_utils.ScannerSettings class
Test methods in ScannerSettings class against sample data from each
scanner make
"""
# 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)
# run through all functions in ScannerSettings class
scanSettings = general_utils.ScannerSettings(envDir)
scanSettings.print_allSettings()
scanSettings.get_scannerMake()
scanSettings.get_scannerBaseDir()
scanSettings.get_pynealSocketHost()
scanSettings.get_pynealSocketPort()
scanSettings.get_allSettings()
# 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)
def test_GE_DirStructure(self):
""" test GE_utils.GE_DirStructure """
# update config file to match local paths
configFile = join(paths['GE_dir'], 'scannerConfig.yaml')
helper_tools.replace_scannerConfig_baseDir(configFile,
paths['GE_funcDir'])
# create instance of ScannerSettings class from general_utils
scannerSettings = general_utils.ScannerSettings(paths['GE_dir'])
# create instance of GE_DirStructure for testing
scannerDirs = GE_utils.GE_DirStructure(scannerSettings)
### Run through the GE_DirStructure class methods
scannerDirs.print_currentSeries()
# confirm paths match test directories
assert scannerDirs.get_seriesDirs() == ['s1925']
assert scannerDirs.get_pDir() == 'p1'
assert scannerDirs.get_eDir() == 'e123'
assert scannerDirs.get_sessionDir() == join(paths['GE_dir'], 'p1/e123')
### Test the waitForSeriesDir function by creating a fake dir
# threading.timer object to create a new directory after a few sec
fakeNewSeries = join(paths['GE_funcDir'], 'p1/e123/sTEST')
t = threading.Timer(1.0, helper_tools.createFakeSeriesDir,
[fakeNewSeries])
t.start()
scannerDirs.waitForSeriesDir()
# assuming it didn't crash, cancel the timer function and delete new dir
t.cancel()
shutil.rmtree(fakeNewSeries)
# remove local paths from config file
helper_tools.cleanConfigFile(configFile)
def test_ScannerSettings(self):
""" test general_utils.ScannerSettings class
Test methods in ScannerSettings class against sample data from each
scanner make
"""
# 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)
# run through all functions in ScannerSettings class
scanSettings = general_utils.ScannerSettings(envDir)
scanSettings.print_allSettings()
scanSettings.get_scannerMake()
scanSettings.get_scannerBaseDir()
scanSettings.get_pynealSocketHost()
scanSettings.get_pynealSocketPort()
scanSettings.get_allSettings()
# remove local paths from config file
helper_tools.cleanConfigFile(configFile)
print('Passed!')