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