def initialize_module(self):
'''Load configured FOMs and create FOM completion data in
self.study_config.modules_data
'''
if self.study_config.use_fom is False:
return
soma_app = Application('capsul', plugin_modules=['soma.fom'])
if 'soma.fom' not in soma_app.loaded_plugin_modules:
# WARNING: this is unsafe, may erase configured things, and
# probably not thread-safe.
soma_app.initialize()
self.study_config.modules_data.foms = {}
self.study_config.modules_data.all_foms = SortedDictionary()
self.study_config.modules_data.fom_atp = {'all': {}}
self.study_config.modules_data.fom_pta = {'all': {}}
foms = (('input', self.study_config.input_fom),
('output', self.study_config.output_fom),
('shared', self.study_config.shared_fom))
for fom_type, fom_filename in foms:
if fom_filename != "":
fom, atp, pta = self.load_fom(fom_filename)
self.study_config.modules_data.foms[fom_type] = fom
self.study_config.modules_data.fom_atp[fom_type] = atp
self.study_config.modules_data.fom_pta[fom_type] = pta
self.study_config.use_fom = True
self.update_module()
def __init__(self):
super(Study, self).__init__()
HasTraits.__init__(self)
# Find foms available
foms = Application().fom_manager.find_foms()
foms.insert(0, ' ')
self.add_trait('input_directory', Directory)
# self.add_trait('input_directory',Directory('/nfs/neurospin/cati/cati_shared'))
self.add_trait('input_fom', Enum(foms))
self.add_trait('output_directory', Directory)
self.add_trait('output_fom', Enum(foms))
self.add_trait('shared_directory', Directory)
self.add_trait('spm_directory', Directory)
self.add_trait('format_image', Str)
self.add_trait('format_mesh', Str)
self.add_trait(
'process',
Enum(
' ',
'morphologist.process.morphologist_simplified.SimplifiedMorphologist',
'morphologist.process.morphologist.Morphologist',
'morpho.morphologist.morphologist',
'morphologist.process.customized.morphologist.CustomMorphologist'
))
# self.process_specific=None
self.compteur_run_process = {}
self.runs = collections.OrderedDict()
def load_fom(self, schema):
soma_app = Application('capsul', plugin_modules=['soma.fom'])
if 'soma.fom' not in soma_app.loaded_plugin_modules:
# WARNING: this is unsafe, may erase configured things, and
# probably not thread-safe.
soma_app.initialize()
fom = soma_app.fom_manager.load_foms(schema)
self.study_config.modules_data.all_foms[schema] = fom
# Create FOM completion data in self.study_config.modules_data
formats = tuple(getattr(self.study_config, key) \
for key in self.study_config.user_traits() \
if key.endswith('_format') \
and getattr(self.study_config, key) is not Undefined)
directories = {}
directories['spm'] = self.study_config.spm_directory
directories['shared'] = self.study_config.shared_directory
directories['input'] = self.study_config.input_directory
directories['output'] = self.study_config.output_directory
atp = AttributesToPaths(fom,
selection={},
directories=directories,
preferred_formats=set((formats)))
self.study_config.modules_data.fom_atp['all'][schema] = atp
pta = PathToAttributes(fom, selection={})
self.study_config.modules_data.fom_pta['all'][schema] = pta
return fom, atp, pta
def reset_foms(capsul_engine, environment):
soma_app = Application('capsul', plugin_modules=['soma.fom'])
if 'soma.fom' not in soma_app.loaded_plugin_modules:
# WARNING: this is unsafe, may erase configured things, and
# probably not thread-safe.
soma_app.initialize()
soma_app.fom_manager.clear_cache()
update_fom(capsul_engine, environment)
def initialize_module(self):
'''Load configured FOMs and create FOM completion data in
self.study_config.modules_data
'''
if self.study_config.use_fom is False:
return
soma_app = Application('capsul', plugin_modules=['soma.fom'])
if 'soma.fom' not in soma_app.loaded_plugin_modules:
# WARNING: this is unsafe, may erase configured things, and
# probably not thread-safe.
soma_app.initialize()
self.study_config.modules_data.foms = {}
foms = (('input', self.study_config.input_fom),
('output', self.study_config.output_fom),
('shared', self.study_config.shared_fom))
for fom_type, fom_filename in foms:
if fom_filename != "":
fom = soma_app.fom_manager.load_foms(fom_filename)
self.study_config.modules_data.foms[fom_type] = fom
# Create FOM completion data in self.study_config.modules_data
formats = tuple(getattr(self.study_config, key) \
for key in self.study_config.user_traits() \
if key.endswith('_format') \
and getattr(self.study_config, key) is not Undefined)
directories = {}
directories['spm'] = self.study_config.spm_directory
directories['shared'] = self.study_config.shared_directory
directories['input'] = self.study_config.input_directory
directories['output'] = self.study_config.output_directory
self.study_config.modules_data.fom_atp = {}
self.study_config.modules_data.fom_pta = {}
for fom_type, fom \
in six.iteritems(self.study_config.modules_data.foms):
atp = AttributesToPaths(
fom,
selection={},
directories=directories,
prefered_formats=set((formats)))
self.study_config.modules_data.fom_atp[fom_type] = atp
pta = PathToAttributes(fom, selection={})
self.study_config.modules_data.fom_pta[fom_type] = pta
self.study_config.use_fom = True
def load_fom(capsul_engine, schema, config, session, environment='global'):
#print('=== load fom', schema, '===')
#import time
#t0 = time.time()
soma_app = Application('capsul', plugin_modules=['soma.fom'])
if 'soma.fom' not in soma_app.loaded_plugin_modules:
# WARNING: this is unsafe, may erase configured things, and
# probably not thread-safe.
soma_app.initialize()
old_fom_path = soma_app.fom_path
if config.fom_path:
soma_app.fom_path = [six.ensure_str(p) for p in config.fom_path
if p not in soma_app.fom_path] \
+ soma_app.fom_path
else:
soma_app.fom_path = list(soma_app.fom_path)
fom = soma_app.fom_manager.load_foms(schema)
soma_app.fom_path = old_fom_path
store = capsul_engine._modules_data['fom']
store['all_foms'][schema] = fom
# Create FOM completion data
fields = config._dbs.get_fields_names(config._collection)
formats = tuple(getattr(config, key) \
for key in fields \
if key.endswith('_format') \
and getattr(config, key) is not None)
directories = {}
spm = session.config('spm', environment)
if spm:
directories['spm'] = spm.directory
axon = session.config('axon', environment)
if axon:
directories['shared'] = axon.shared_directory
directories['input'] = config.input_directory
directories['output'] = config.output_directory
atp = AttributesToPaths(fom,
selection={},
directories=directories,
preferred_formats=set((formats)))
store['fom_atp']['all'][schema] = atp
pta = PathToAttributes(fom, selection={})
store['fom_pta']['all'][schema] = pta
#print(' load fom done:', time.time() - t0, 's')
return fom, atp, pta
def update_module(self):
if not self.study_config.use_fom:
return
modules_data = self.study_config.modules_data
if self.study_config.auto_fom \
and len(modules_data.all_foms) <= 3:
soma_app = Application('capsul', plugin_modules=['soma.fom'])
for schema in soma_app.fom_manager.find_foms():
if schema not in modules_data.all_foms:
modules_data.all_foms[schema] = None # not loaded yet.
foms = (('input', self.study_config.input_fom),
('output', self.study_config.output_fom),
('shared', self.study_config.shared_fom))
for fom_type, fom_filename in foms:
if fom_filename != "":
fom = self.study_config.modules_data.all_foms.get(fom_filename)
if fom is None:
fom, atp, pta = self.load_fom(fom_filename)
else:
atp = self.study_config.modules_data.fom_atp['all'] \
[fom_filename]
pta = self.study_config.modules_data.fom_pta['all'] \
[fom_filename]
self.study_config.modules_data.foms[fom_type] = fom
self.study_config.modules_data.fom_atp[fom_type] = atp
self.study_config.modules_data.fom_pta[fom_type] = pta
# update directories
directories = {}
directories['spm'] = self.study_config.spm_directory
directories['shared'] = self.study_config.shared_directory
directories['input'] = self.study_config.input_directory
directories['output'] = self.study_config.output_directory
for atp in modules_data.fom_atp['all'].values():
atp.directories = directories
import os
import glob
from morphologist.core.analysis import SharedPipelineAnalysis
from morphologist.core.subject import Subject
from capsul.process import get_process_instance
from capsul.process.process_with_fom import ProcessWithFom
# the following 4 lines are a hack to add /tmp to the FOM search path
# before it is used by StudyConfig
from soma.application import Application
soma_app = Application('capsul', plugin_modules=['soma.fom'])
soma_app.initialize()
soma_app.fom_manager.paths.append('/tmp')
fom_content = '''{
"fom_name": "mock_fom",
"formats": {
"NIFTI": "nii",
"NIFTI gz": "nii.gz"
},
"format_lists": {
"images": ["NIFTI gz", "NIFTI"]
},
"shared_patterns": {
"subject": "<group>-<subject>"
},
"processes": {
def update_fom(capsul_engine, environment='global', param=None, value=None):
'''Load configured FOMs and create FOM completion data
'''
#print('***update_fom ***')
with capsul_engine.settings as session:
config = session.config('fom', environment)
if config is None:
return
soma_app = Application('capsul', plugin_modules=['soma.fom'])
if 'soma.fom' not in soma_app.loaded_plugin_modules:
# WARNING: this is unsafe, may erase configured things, and
# probably not thread-safe.
soma_app.initialize()
if config.fom_path:
fom_path = [p for p in config.fom_path
if p not in soma_app.fom_path] \
+ soma_app.fom_path
else:
fom_path = list(soma_app.fom_path)
soma_app.fom_manager.paths = fom_path
soma_app.fom_manager.fom_files()
store = capsul_engine._modules_data['fom']
if config.auto_fom \
and len(store['all_foms']) <= 3:
for schema in soma_app.fom_manager.fom_files():
if schema not in store['all_foms']:
store['all_foms'][schema] = None # not loaded yet.
foms = (('input', config.input_fom), ('output', config.output_fom),
('shared', config.shared_fom))
for fom_type, fom_filename in foms:
if fom_filename not in ("", None, traits.Undefined):
fom = store['all_foms'].get(fom_filename)
if fom is None:
fom, atp, pta = load_fom(capsul_engine, fom_filename,
config, session, environment)
else:
atp = store['fom_atp']['all'][fom_filename]
pta = store['fom_pta']['all'][fom_filename]
store['foms'][fom_type] = fom
store['fom_atp'][fom_type] = atp
store['fom_pta'][fom_type] = pta
# update directories
directories = {}
spm = session.config('spm', environment)
if spm:
directories['spm'] = spm.directory
axon = session.config('axon', environment)
if axon:
directories['shared'] = axon.shared_directory
directories['input'] = config.input_directory
directories['output'] = config.output_directory
for atp in store['fom_atp']['all'].values():
atp.directories = directories
# backward compatibility for StudyConfig
capsul_engine.study_config.modules_data.foms = store['foms']
capsul_engine.study_config.modules_data.all_foms = store['all_foms']
capsul_engine.study_config.modules_data.fom_atp = store['fom_atp']
capsul_engine.study_config.modules_data.fom_pta = store['fom_pta']
