def deserialize_simulator(simulator_gid, storage_path):
simulator_in_path = h5.path_for(storage_path, SimulatorH5,
simulator_gid)
simulator_in = SimulatorAdapterModel()
with SimulatorH5(simulator_in_path) as simulator_in_h5:
simulator_in_h5.load_into(simulator_in)
simulator_in.connectivity = simulator_in_h5.connectivity.load()
simulator_in.stimulus = simulator_in_h5.stimulus.load()
simulator_in.history_gid = simulator_in_h5.simulation_state.load()
if isinstance(simulator_in.monitors[0], Projection):
# TODO: simplify this part
with SimulatorH5(simulator_in_path) as simulator_in_h5:
monitor_h5_path = simulator_in_h5.get_reference_path(
simulator_in.monitors[0].gid)
monitor_h5_class = h5_factory.monitor_h5_factory(
type(simulator_in.monitors[0]))
with monitor_h5_class(monitor_h5_path) as monitor_h5:
sensors_gid = monitor_h5.sensors.load()
region_mapping_gid = monitor_h5.region_mapping.load()
sensors = ABCAdapter.load_traited_by_gid(sensors_gid)
if isinstance(simulator_in.monitors[0], EEG):
sensors = SensorsEEG.build_sensors_subclass(sensors)
elif isinstance(simulator_in.monitors[0], MEG):
sensors = SensorsMEG.build_sensors_subclass(sensors)
elif isinstance(simulator_in.monitors[0], iEEG):
sensors = SensorsInternal.build_sensors_subclass(sensors)
simulator_in.monitors[0].sensors = sensors
region_mapping = ABCAdapter.load_traited_by_gid(region_mapping_gid)
simulator_in.monitors[0].region_mapping = region_mapping
if simulator_in.surface:
cortex_path = h5.path_for(storage_path, CortexH5,
simulator_in.surface.gid)
with CortexH5(cortex_path) as cortex_h5:
simulator_in.surface.local_connectivity = cortex_h5.local_connectivity.load(
)
simulator_in.surface.region_mapping_data = cortex_h5.region_mapping_data.load(
)
rm_index = dao.get_datatype_by_gid(
simulator_in.surface.region_mapping_data.hex)
simulator_in.surface.surface_gid = uuid.UUID(
rm_index.surface_gid)
return simulator_in
def transactional_setup_method(self):
"""
Sets up the environment for running the tests;
creates a test user, a test project, a connectivity and a list of BCT adapters;
imports a CFF data-set
"""
self.test_user = TestFactory.create_user("BCT_User")
self.test_project = TestFactory.create_project(self.test_user,
"BCT-Project")
# Make sure Connectivity is in DB
zip_path = os.path.join(os.path.dirname(tvb_data.__file__),
'connectivity', 'connectivity_66.zip')
conn_index = TestFactory.import_zip_connectivity(
self.test_user, self.test_project, zip_path)
self.connectivity = ABCAdapter.load_traited_by_gid(conn_index.gid)
# make weights matrix symmetric, or else some BCT algorithms will run infinitely:
w = self.connectivity.weights
self.connectivity.weights = w + w.T - numpy.diag(w.diagonal())
algorithms = dao.get_generic_entity(Algorithm,
'Brain Connectivity Toolbox',
'group_description')
assert algorithms is not None
assert len(algorithms) > 5
self.bct_adapters = []
for algo in algorithms:
self.bct_adapters.append(ABCAdapter.build_adapter(algo))
def deserialize_simulator(simulator_gid, storage_path):
simulator_in_path = h5.path_for(storage_path, SimulatorH5,
simulator_gid)
simulator_in = SimulatorAdapterModel()
with SimulatorH5(simulator_in_path) as simulator_in_h5:
simulator_in_h5.load_into(simulator_in)
simulator_in.connectivity = simulator_in_h5.connectivity.load()
simulator_in.stimulus = simulator_in_h5.stimulus.load()
simulator_in.history_gid = simulator_in_h5.simulation_state.load()
for monitor in simulator_in.monitors:
if isinstance(monitor, Projection):
with SimulatorH5(simulator_in_path) as simulator_in_h5:
monitor_h5_path = simulator_in_h5.get_reference_path(
monitor.gid)
monitor_h5_class = h5_factory.monitor_h5_factory(type(monitor))
with monitor_h5_class(monitor_h5_path) as monitor_h5:
sensors_gid = monitor_h5.sensors.load()
projection_gid = monitor_h5.projection.load()
region_mapping_gid = monitor_h5.region_mapping.load()
sensors_index = ABCAdapter.load_entity_by_gid(sensors_gid.hex)
projection_index = ABCAdapter.load_entity_by_gid(
projection_gid.hex)
sensors_class = monitor.projection_class().sensors.field_type
sensors = h5.load_from_index(sensors_index,
dt_class=sensors_class)
projection_class = monitor.projection_class()
projection = h5.load_from_index(projection_index,
dt_class=projection_class)
region_mapping = ABCAdapter.load_traited_by_gid(
region_mapping_gid)
monitor.sensors = sensors
monitor.projection = projection
monitor.region_mapping = region_mapping
if simulator_in.surface:
cortex_path = h5.path_for(storage_path, CortexH5,
simulator_in.surface.gid)
with CortexH5(cortex_path) as cortex_h5:
simulator_in.surface.local_connectivity = cortex_h5.local_connectivity.load(
)
simulator_in.surface.region_mapping_data = cortex_h5.region_mapping_data.load(
)
rm_index = dao.get_datatype_by_gid(
simulator_in.surface.region_mapping_data.hex)
simulator_in.surface.surface_gid = uuid.UUID(
rm_index.fk_surface_gid)
return simulator_in