def test_record_data_matrix(self, sampler_args):
mesh, poslist, fn_hdf5, roi = sampler_args
S = simnibs_gpc.gPCSampler(mesh, poslist, fn_hdf5, roi)
rand_vars1 = [.1, .2]
potential1 = np.random.rand(100)
E1 = np.random.rand(100, 3)
S.record_data_matrix(potential1, 'potential', 'data')
S.record_data_matrix(rand_vars1, 'random_vars', 'data')
S.record_data_matrix(E1, 'E', 'data')
rand_vars2 = [.2, .4]
potential2 = np.random.rand(100)
E2 = np.random.rand(100, 3)
S.record_data_matrix(potential2, 'potential', 'data')
S.record_data_matrix(rand_vars2, 'random_vars', 'data')
S.record_data_matrix(E2, 'E', 'data')
with h5py.File(fn_hdf5) as f:
assert np.allclose(f['data/random_vars'][0, :], rand_vars1)
assert np.allclose(f['data/random_vars'][1, :], rand_vars2)
assert np.allclose(f['data/potential'][0, :], potential1)
assert np.allclose(f['data/potential'][1, :], potential2)
assert np.allclose(f['data/E'][0, ...], E1)
assert np.allclose(f['data/E'][1, ...], E2)
def test_run_N_random_simulations(self, sampler_args):
mesh, poslist, fn_hdf5, roi = sampler_args
S = simnibs_gpc.gPCSampler(mesh, poslist, fn_hdf5, roi)
S.run_simulation = Mock()
S.run_N_random_simulations(1000)
for c in S.run_simulation.call_args_list:
assert c[0][0][0] <= .4
assert c[0][0][0] >= .3
def test_update_poslist(self, sampler_args):
mesh, poslist, fn_hdf5, roi = sampler_args
S = simnibs_gpc.gPCSampler(mesh, poslist, fn_hdf5, roi)
random_vars = [0.35]
poslist = S._update_poslist(random_vars)
assert np.isclose(poslist.cond[2].value, 0.35)
assert np.isclose(poslist.cond[3].value, 1)
assert np.isclose(poslist.cond[4].value, 10)
def test_set_up_sampler(self, sampler_args):
mesh, poslist, fn_hdf5, roi = sampler_args
S = simnibs_gpc.gPCSampler(mesh, poslist, fn_hdf5, roi)
assert np.all(S.mesh_roi.elm.tag1 == 3)
S.create_hdf5()
with h5py.File(fn_hdf5) as f:
assert f['mesh']
assert f['mesh_roi']
assert f['cond']
assert np.all(f['roi'][()] == 3)
S2 = simnibs_gpc.gPCSampler.load_hdf5(fn_hdf5)
assert S2.mesh.nodes.nr == mesh.nodes.nr
assert S2.mesh.elm.nr == mesh.elm.nr
assert S2.roi == roi
for i, c in enumerate(S2.poslist.cond):
assert c.name == poslist.cond[i].name
assert c.value == poslist.cond[i].value
assert c.distribution_type == poslist.cond[i].distribution_type
assert c.distribution_parameters == poslist.cond[i].distribution_parameters
def test_calc_E(self, sampler_args):
mesh, poslist, fn_hdf5, roi = sampler_args
S = simnibs_gpc.gPCSampler(mesh, poslist, fn_hdf5, roi)
v = mesh_io.NodeData(mesh.nodes.node_coord[:, 0], mesh=mesh)
E = S._calc_E(v, None)
assert np.allclose(E, [-1e3, 0, 0])