def _prepare_simulator_from_view_model(self, view_model):
simulator = Simulator()
simulator.gid = view_model.gid
conn = self.load_traited_by_gid(view_model.connectivity)
simulator.connectivity = conn
simulator.conduction_speed = view_model.conduction_speed
simulator.coupling = view_model.coupling
rm_surface = None
if view_model.surface:
simulator.surface = Cortex()
rm_index = self.load_entity_by_gid(
view_model.surface.region_mapping_data.hex)
rm = h5.load_from_index(rm_index)
rm_surface_index = self.load_entity_by_gid(rm_index.fk_surface_gid)
rm_surface = h5.load_from_index(rm_surface_index, CorticalSurface)
rm.surface = rm_surface
rm.connectivity = conn
simulator.surface.region_mapping_data = rm
if simulator.surface.local_connectivity:
lc = self.load_traited_by_gid(
view_model.surface.local_connectivity)
assert lc.surface.gid == rm_index.fk_surface_gid
lc.surface = rm_surface
simulator.surface.local_connectivity = lc
if view_model.stimulus:
stimulus_index = self.load_entity_by_gid(view_model.stimulus.hex)
stimulus = h5.load_from_index(stimulus_index)
simulator.stimulus = stimulus
if isinstance(stimulus, StimuliSurface):
simulator.stimulus.surface = rm_surface
else:
simulator.stimulus.connectivity = simulator.connectivity
simulator.model = view_model.model
simulator.integrator = view_model.integrator
simulator.initial_conditions = view_model.initial_conditions
simulator.monitors = view_model.monitors
simulator.simulation_length = view_model.simulation_length
# TODO: why not load history here?
# if view_model.history:
# history_index = dao.get_datatype_by_gid(view_model.history.hex)
# history = h5.load_from_index(history_index)
# assert isinstance(history, SimulationHistory)
# history.fill_into(self.algorithm)
return simulator
def deserialize_simulator(simulator_gid, storage_path):
simulator_in_path = h5.path_for(storage_path, SimulatorH5,
simulator_gid)
simulator_in = Simulator()
with SimulatorH5(simulator_in_path) as simulator_in_h5:
simulator_in_h5.load_into(simulator_in)
connectivity_gid = simulator_in_h5.connectivity.load()
stimulus_gid = simulator_in_h5.stimulus.load()
simulation_state_gid = simulator_in_h5.simulation_state.load()
conn_index = dao.get_datatype_by_gid(connectivity_gid.hex)
conn = h5.load_from_index(conn_index)
simulator_in.connectivity = conn
if simulator_in.surface:
cortex_path = h5.path_for(storage_path, CortexH5,
simulator_in.surface.gid)
with CortexH5(cortex_path) as cortex_h5:
local_conn_gid = cortex_h5.local_connectivity.load()
region_mapping_gid = cortex_h5.region_mapping_data.load()
region_mapping_index = dao.get_datatype_by_gid(
region_mapping_gid.hex)
region_mapping_path = h5.path_for_stored_index(
region_mapping_index)
region_mapping = RegionMapping()
with RegionMappingH5(region_mapping_path) as region_mapping_h5:
region_mapping_h5.load_into(region_mapping)
region_mapping.gid = region_mapping_h5.gid.load()
surf_gid = region_mapping_h5.surface.load()
surf_index = dao.get_datatype_by_gid(surf_gid.hex)
surf_h5 = h5.h5_file_for_index(surf_index)
surf = CorticalSurface()
surf_h5.load_into(surf)
surf_h5.close()
region_mapping.surface = surf
simulator_in.surface.region_mapping_data = region_mapping
if local_conn_gid:
local_conn_index = dao.get_datatype_by_gid(local_conn_gid.hex)
local_conn = h5.load_from_index(local_conn_index)
simulator_in.surface.local_connectivity = local_conn
if stimulus_gid:
stimulus_index = dao.get_datatype_by_gid(stimulus_gid.hex)
stimulus = h5.load_from_index(stimulus_index)
simulator_in.stimulus = stimulus
return simulator_in, simulation_state_gid