def initialize_module(self):
""" Set up FSL environment variables according to current
configuration.
"""
if self.study_config.use_fsl is False:
# Configuration is explicitely asking not to use FSL
return
if self.study_config.use_fsl is Undefined:
# If use_fsl is not defined, FSL configuration will
# be done if possible but there will be no error if it cannot be
# done.
force_configuration = False
else:
# If use_fsl is True configuration must be valid otherwise
# an EnvironmentError is raised
force_configuration = True
# Get the fsl.sh path from the study configuration elements
fsl_config_file = self.study_config.fsl_config
# If the fsl.sh path has been defined
if fsl_config_file is not Undefined and \
os.path.exists(fsl_config_file):
# Parse the fsl environment
envfsl = environment(fsl_config_file)
if "FSLDIR" not in envfsl and "FSLDIR" not in os.environ:
# assume the fsl.sh script is in $FSLDIR/etc/fslconf/fsl.sh
envfsl["FSLDIR"] = os.path.dirname(os.path.dirname(
os.path.dirname(fsl_config_file)))
if envfsl.get("FSLDIR", "") != os.environ.get("FSLDIR", ""):
# Set the fsl environment
for envname, envval in six.iteritems(envfsl):
if envname in os.environ:
if envname.startswith("FSL"):
os.environ[envname] = envval
else:
os.environ[envname] += ":" + envval
else:
os.environ[envname] = envval
# No error detected in configuration, set use_fsl to
# True
self.study_config.use_fsl = True
else:
# Error in configuration, do not let use_fsl = Undefined
self.study_config.use_fsl = False
if force_configuration:
raise EnvironmentError(
"No valid FSL configuration file specified. "
"It is impossible to configure FSL.")
def initialize_module(self):
""" Set up Freesurfer environment variables according to current
configuration.
"""
if self.study_config.use_freesurfer is False:
# Configuration is explicitely asking not to use FreeSurfer
return
if self.study_config.use_freesurfer is Undefined:
# If use_freesurfer is not defined, FreeSurfer configuration will
# be done if possible but there will be no error if it cannot be
# done.
force_configuration = False
else:
# If use_freesurfer is True configuration must be valid otherwise
# an EnvironmentError is raised
force_configuration = True
# Get the 'SetUpFreeSurfer.sh' path from the study configuration
# elements
fs_config_file = self.study_config.freesurfer_config
# If the 'SetUpFreeSurfer.sh' path has been defined
if fs_config_file is not Undefined:
if os.path.exists(fs_config_file):
# Parse the fs environment: check if the 'FREESURFER_HOME'
# environment varibale is already set and use it to configure
# freesurfer
fs_home = os.environ.get("FREESURFER_HOME", None)
env = {}
if fs_home is not None:
env["FREESURFER_HOME"] = fs_home
envfs = environment(fs_config_file, env)
# Set the fs environment
for envname, envval in six.iteritems(envfs):
if envname in os.environ:
if envname.startswith(("FS", "FREESURFER")):
os.environ[envname] = envval
else:
os.environ[envname] += ":" + envval
else:
os.environ[envname] = envval
# No error detected in configuration, set use_freesurfer to
# True
self.study_config.use_freesurfer = True
else:
#Error in configuration, do not let use_freesurfer = Undefined
self.study_config.use_freesurfer = False
if force_configuration:
raise EnvironmentError(
"FreeSurfer configuration file (%s) does not exist. "
"It is impossible to configure FreeSurfer." % \
fs_config_file)
else:
# Error in configuration, do not let use_freesurfer = Undefined
self.study_config.use_freesurfer = False
if force_configuration:
raise EnvironmentError(
"No FreeSurfer configuration file specified. "
"It is impossible to configure FreeSurfer.")
def initialize_module(self):
""" Set up Freesurfer environment variables according to current
configuration.
"""
if self.study_config.use_freesurfer is False:
# Configuration is explicitely asking not to use FreeSurfer
return
if self.study_config.use_freesurfer is Undefined:
# If use_freesurfer is not defined, FreeSurfer configuration will
# be done if possible but there will be no error if it cannot be
# done.
force_configuration = False
else:
# If use_freesurfer is True configuration must be valid otherwise
# an EnvironmentError is raised
force_configuration = True
# Get the 'SetUpFreeSurfer.sh' path from the study configuration
# elements
fs_config_file = self.study_config.freesurfer_config
# If the 'SetUpFreeSurfer.sh' path has been defined
if fs_config_file is not Undefined:
if os.path.exists(fs_config_file):
# Parse the fs environment: check if the 'FREESURFER_HOME'
# environment varibale is already set and use it to configure
# freesurfer
fs_home = os.environ.get("FREESURFER_HOME", None)
env = {}
if fs_home is not None:
env["FREESURFER_HOME"] = fs_home
envfs = environment(fs_config_file, env)
# Set the fs environment
for envname, envval in envfs.iteritems():
if envname in os.environ:
if envname.startswith(("FS", "FREESURFER")):
os.environ[envname] = envval
else:
os.environ[envname] += ":" + envval
else:
os.environ[envname] = envval
# No error detected in configuration, set use_freesurfer to
# True
self.study_config.use_freesurfer = True
else:
#Error in configuration, do not let use_freesurfer = Undefined
self.study_config.use_freesurfer = False
if force_configuration:
raise EnvironmentError(
"FreeSurfer configuration file (%s) does not exist. "
"It is impossible to configure FreeSurfer." % \
fs_config_file)
else:
# Error in configuration, do not let use_freesurfer = Undefined
self.study_config.use_freesurfer = False
if force_configuration:
raise EnvironmentError(
"No FreeSurfer configuration file specified. "
"It is impossible to configure FreeSurfer.")
