def test_store_load_complete_region_mapping(tmph5factory, connectivity_factory, surface_factory, region_mapping_factory):
connectivity = connectivity_factory(2)
surface = surface_factory(5)
region_mapping = region_mapping_factory(surface, connectivity)
with ConnectivityH5(tmph5factory('Connectivity_{}.h5'.format(connectivity.gid))) as conn_h5:
conn_h5.store(connectivity)
conn_stored = Connectivity()
conn_h5.load_into(conn_stored)
with SurfaceH5(tmph5factory('Surface_{}.h5'.format(surface.gid))) as surf_h5:
surf_h5.store(surface)
surf_stored = Surface()
surf_h5.load_into(surf_stored)
with RegionMappingH5(tmph5factory('RegionMapping_{}.h5'.format(region_mapping.gid))) as rm_h5:
rm_h5.store(region_mapping)
rm_stored = RegionMapping()
rm_h5.load_into(rm_stored)
# load_into will not load dependent datatypes. connectivity and surface are undefined
with pytest.raises(TraitAttributeError):
rm_stored.connectivity
with pytest.raises(TraitAttributeError):
rm_stored.surface
rm_stored.connectivity = conn_stored
rm_stored.surface = surf_stored
assert rm_stored.connectivity is not None
assert rm_stored.surface is not None
def test_store_load_region_mapping(tmph5factory, region_mapping_factory):
region_mapping = region_mapping_factory()
rm_h5 = RegionMappingH5(tmph5factory())
rm_h5.store(region_mapping)
rm_h5.close()
rm_stored = RegionMapping()
with pytest.raises(TraitAttributeError):
rm_stored.array_data
rm_h5.load_into(rm_stored) # loads connectivity/surface as None inside rm_stored
assert rm_stored.array_data.shape == (5,)
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