# -*- coding: utf-8 -*-
'''
FreeSurfer configuration module
Classes
=======
:class:`FreeSurferConfig`
-------------------------
'''
# System import
from __future__ import absolute_import
import os
import six
# Trait import
from traits.api import File, Bool, Undefined, Directory
# Capsul import
from capsul.study_config.study_config import StudyConfigModule
from capsul.engine import CapsulEngine
[docs]
class FreeSurferConfig(StudyConfigModule):
""" Class to set up freesurfer configuration.
Parse the 'SetUpFreeSurfer.sh' file and update dynamically the system
environment.
"""
def __init__(self, study_config, configuration):
""" Initilaize the FreeSurferConfig class.
Parameters
----------
study_config: StudyConfig object
the study configuration we want to update in order to deal with
freesurfer functions.
"""
super(FreeSurferConfig, self).__init__(study_config, configuration)
self.study_config.add_trait("freesurfer_config", File(
Undefined,
desc="Path to 'FreeSurferEnv.sh'", groups=['freesurfer']))
self.study_config.add_trait('freesurfer_subjectsdir', Directory(
Undefined,
desc='FreeSurfer subjects data directory', groups=['freesurfer']))
self.study_config.add_trait("use_freesurfer", Bool(
False,
desc="If True, FreeSurfer configuration is set up on startup",
groups=['freesurfer']))
[docs]
def initialize_module(self):
""" Set up FSL environment variables according to current
configuration.
"""
if 'capsul.engine.module.freesurfer' \
not in self.study_config.engine._loaded_modules:
self.study_config.engine.load_module(
'capsul.engine.module.freesurfer')
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()
[docs]
def initialize_callbacks(self):
self.study_config.on_trait_change(
self.sync_to_engine,
['freesurfer_config', 'freesurfer_subjectsdir'])
# WARNING ref to self in callback
self.study_config.engine.settings.module_notifiers[
'capsul.engine.module.freesurfer'] = [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 'FreeSurferConfig' in self.study_config.modules \
and 'capsul.engine.module.freesurfer' \
in self.study_config.engine._loaded_modules:
with self.study_config.engine.settings as session:
cif = self.study_config.engine.settings.config_id_field
params = {
'freesurfer_config': 'setup',
'freesurfer_subjectsdir': 'subjects_dir',
}
config = session.config('freesurfer', 'global')
if config is None:
values = {cif: 'freesurfer'}
for param, ceparam in six.iteritems(params):
val = getattr(self.study_config, param)
if val is Undefined:
val = None
values[ceparam] = val
session.new_config('freesurfer', 'global', values)
else:
for param, ceparam in six.iteritems(params):
val = getattr(self.study_config, param)
if val is Undefined:
val = None
setattr(config, ceparam, val)
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 'FreeSurferConfig' in self.study_config.modules \
and 'capsul.engine.module.freesurfer' \
in self.study_config.engine._loaded_modules:
with self.study_config.engine.settings as session:
config = session.config('freesurfer', 'global')
if config:
params = {
'freesurfer_config': 'setup',
'freesurfer_subjectsdir': 'subjects_dir',
}
for param, ceparam in six.iteritems(params):
val = getattr(config, ceparam)
if val in (None, ''):
val = Undefined
setattr(self.study_config, param, val)
if self.study_config.freesurfer_config:
self.study_config.use_freesurfer = True
else:
self.study_config.use_freesurfer = False
finally:
del self._syncing
