# -*- coding: utf-8 -*-
'''
FSL configuration module
Classes
=======
:class:`FSLConfig`
------------------
'''
from __future__ import absolute_import
from traits.api import File, Bool, Undefined, String
from capsul.study_config.study_config import StudyConfigModule
from capsul.engine import CapsulEngine
from capsul.subprocess.fsl import check_fsl_configuration
import os.path as osp
[docs]class FSLConfig(StudyConfigModule):
'''
`FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki>`_ configuration module
'''
def __init__(self, study_config, configuration):
super(FSLConfig, self).__init__(study_config, configuration)
self.study_config.add_trait('fsl_config', File(
Undefined,
output=False,
desc='Parameter to specify the fsl.sh path', groups=['fsl']))
self.study_config.add_trait('fsl_prefix', String(Undefined,
desc='Prefix to add to FSL commands', groups=['fsl']))
self.study_config.add_trait('use_fsl', Bool(
Undefined,
output=False,
desc='Parameter to tell that we need to configure FSL',
groups=['fsl']))
def __del__(self):
try:
self.study_config.engine.settings.module_notifiers.get(
'capsul.engine.module.fsl', []).remove(self.sync_from_engine)
except (ValueError, ReferenceError):
pass
[docs] def initialize_module(self):
""" Set up FSL environment variables according to current
configuration.
"""
if 'capsul.engine.module.fsl' \
not in self.study_config.engine._loaded_modules:
self.study_config.engine.load_module('capsul.engine.module.fsl')
if type(self.study_config.engine) is not CapsulEngine:
# engine is a proxy, thus we are initialized from a real
# CapsulEngine, which holds the reference values
self.sync_from_engine()
else:
self.sync_to_engine()
# this test aims to raise an exception in case of incorrect setting,
# complying to capsul 2.x behavior.
if self.study_config.use_fsl is True:
check_fsl_configuration(self.study_config)
[docs] def initialize_callbacks(self):
self.study_config.on_trait_change(
self.sync_to_engine, '[fsl_config, fsl_prefix, use_fsl]')
# WARNING ref to self in callback
self.study_config.engine.settings.module_notifiers[
'capsul.engine.module.fsl'] = [self.sync_from_engine]
def sync_to_engine(self, param=None, value=None):
if getattr(self, '_syncing', False):
# manage recursive calls
return
self._syncing = True
try:
if 'FSLConfig' in self.study_config.modules \
and 'capsul.engine.module.fsl' \
in self.study_config.engine._loaded_modules:
with self.study_config.engine.settings as session:
cif = self.study_config.engine.settings.config_id_field
config = session.config('fsl', 'global')
fsl_conf = self.study_config.fsl_config
if fsl_conf is Undefined:
fsl_conf = None
fsl_dir = None
else:
fsl_dir = osp.dirname(fsl_conf)
if fsl_dir.endswith('/etc/fslconf'):
fsl_dir = osp.dirname(osp.dirname(fsl_dir))
elif fsl_dir.endswith('/etc'):
fsl_dir = osp.dirname(fsl_dir)
if config is None:
session.new_config(
'fsl', 'global',
{'directory': fsl_dir,
'config': fsl_conf,
'prefix': self.study_config.fsl_prefix
if self.study_config.fsl_prefix
is not Undefined
else None,
cif: 'fsl'})
else:
tparam = {'fsl_config': 'config',
'fsl_prefix': 'prefix'}
if param is not None:
if param not in ('use_fsl', ):
params = [param]
else:
params = []
else:
params = ['fsl_config', 'fsl_prefix']
defaults = {'prefix': None, 'config': None}
for p in params:
val = getattr(self.study_config, p)
ceparam = tparam[p]
if val is Undefined:
val = defaults.get(ceparam, None)
setattr(config, ceparam, val)
if 'fsl_config' in params:
config.directory = fsl_dir
del config
del session
finally:
del self._syncing
def sync_from_engine(self, param=None, value=None):
if getattr(self, '_syncing', False):
# manage recursive calls
return
self._syncing = True
try:
if 'FSLConfig' in self.study_config.modules \
and 'capsul.engine.module.fsl' \
in self.study_config.engine._loaded_modules:
with self.study_config.engine.settings as session:
config = session.config('fsl', 'global')
if config:
directory = config.directory \
if config.directory not in (None, '') \
else Undefined
self.study_config.fsl_config = config.config \
if config.config is not None else Undefined
self.study_config.fsl_prefix = config.prefix \
if config.prefix is not None else Undefined
if self.study_config.fsl_config not in (
'', None, Undefined)\
or self.study_config.fsl_prefix not in (
'', None, Undefined):
self.study_config.use_fsl = True
else:
self.study_config.use_fsl = False
except ReferenceError:
pass
finally:
del self._syncing
