def test_write_sonata_append(st_cls, write_fnc):
# Check that we can append spikes data to an existing sonata file. Currently it only works if /spikes/<pop_name>
# does not already exists, since append to an h5 can be prohibitive. iI the future may want ot implement.
tmpfile = tempfile.NamedTemporaryFile(suffix='.h5')
with h5py.File(tmpfile.name, 'w') as h5:
h5.create_group('/spikes/V1')
st = create_st_buffer(st_cls)
st.add_spikes(population='V2',
node_ids=0,
timestamps=np.linspace(0, 1.0, 100))
write_fnc(tmpfile.name, st, mode='a', sort_order=sort_order.by_id)
with h5py.File(tmpfile.name) as h5:
assert (check_magic(h5))
assert (get_version(h5) is not None)
assert ('/spikes/V1' in h5)
assert ('/spikes/V2' in h5)
assert (len(h5['/spikes/V2/node_ids']) == 100)
assert (len(h5['/spikes/V2/timestamps']) == 100)
# Throw error if same pop_name alrady exists
tmpfile2 = tempfile.NamedTemporaryFile(suffix='.h5')
with h5py.File(tmpfile2.name, 'w') as h5:
h5.create_group('/spikes/V2')
with pytest.raises(ValueError):
write_fnc(tmpfile2.name, st, mode='a', sort_order=sort_order.by_id)
def test_write_sonata(st_cls, write_fnc):
st = create_st_buffer(st_cls)
st.add_spikes(population='V1',
node_ids=0,
timestamps=np.linspace(0, 1.0, 100))
st.add_spikes(population='V1',
node_ids=2,
timestamps=np.linspace(2.0, 1.0, 10))
st.add_spike(population='V1', node_id=1, timestamp=3.0)
st.add_spikes(population='V2',
node_ids=[3, 3, 3],
timestamps=[0.25, 0.5, 0.75])
tmpfile = tempfile.NamedTemporaryFile(suffix='.h5')
write_fnc(tmpfile.name, st)
with h5py.File(tmpfile.name) as h5:
assert (check_magic(h5))
assert (get_version(h5) is not None)
assert ('/spikes/V1' in h5)
node_ids = h5['/spikes/V1/node_ids'][()]
assert (len(node_ids) == 111)
assert (set(np.unique(node_ids)) == {0, 1, 2})
assert (len(h5['/spikes/V1/timestamps'][()]) == 111)
assert ('/spikes/V2' in h5)
assert (np.all(h5['/spikes/V2/node_ids'][()] == [3, 3, 3]))
# WARNING: Not all adaptor guarentee order of spikes
assert (np.allclose(np.sort(h5['/spikes/V2/timestamps'][()]),
[0.25, 0.50, 0.75]))
def test_write_sonata(st_cls, write_fnc):
st = create_st_buffer_mpi(st_cls)
st.add_spikes(population='V1',
node_ids=MPI_rank,
timestamps=[MPI_rank] * 5)
st.add_spike(population='V2', node_id=MPI_size, timestamp=float(MPI_rank))
st.add_spikes(population='R{}'.format(MPI_rank),
node_ids=0,
timestamps=[0.1, 0.2, 0.3, 0.4])
tmp_h5 = tmpfile()
write_fnc(tmp_h5, st)
if MPI_rank == 0:
# Warnings: some systems creates lock even for reading an hdf5 file
with h5py.File(tmp_h5, 'r') as h5:
assert (check_magic(h5))
assert (get_version(h5) is not None)
assert (set(h5['/spikes'].keys()) >=
{'R{}'.format(r)
for r in range(MPI_size)} | {'V1', 'V2'})
assert (set(h5['/spikes/V1']['node_ids'][()]) == {
i
for i in range(MPI_size)
})
assert (set(h5['/spikes/V2']['timestamps'][()]) == {
float(i)
for i in range(MPI_size)
})
for r in range(MPI_size):
grp = h5['/spikes/R{}'.format(r)]
assert (np.all(grp['node_ids'][()] == [0, 0, 0, 0]))
assert (np.allclose(grp['timestamps'][()],
[0.1, 0.2, 0.3, 0.4]))
def test_write_sonata_empty(st_cls, write_fnc):
st = create_st_buffer_mpi(st_cls)
tmp_h5 = tmpfile()
write_fnc(tmp_h5, st)
if MPI_rank == 0:
with h5py.File(tmp_h5, 'r') as h5:
assert(check_magic(h5))
assert(get_version(h5) is not None)
assert('/spikes' in h5)
def test_write_sonata_empty(st_cls, write_fnc):
# Important use case, a valid simulation may run for a long time but not produce any spikes, make sure it doesn't
# fail trying to write any empty set of spike-trains to h5
st = create_st_buffer(st_cls)
tmpfile = tempfile.NamedTemporaryFile(suffix='.h5')
write_fnc(tmpfile.name, st)
with h5py.File(tmpfile.name) as h5:
assert (check_magic(h5))
assert (get_version(h5) is not None)
assert ('/spikes' in h5)
assert (len(h5['/spikes']) == 0)
def test_write_sonata_byid(st_cls, write_fnc):
# Check we can sort by node_ids
st = create_st_buffer(st_cls)
st.add_spikes(population='V1', node_ids=[2, 4, 2, 1, 3, 3, 6, 0], timestamps=[0.1]*8)
tmpfile = tempfile.NamedTemporaryFile(suffix='.h5')
write_fnc(tmpfile.name, st, sort_order=sort_order.by_id)
with h5py.File(tmpfile.name, 'r') as h5:
assert(check_magic(h5))
assert(get_version(h5) is not None)
assert(h5['/spikes/V1'].attrs['sorting'] == 'by_id')
assert(np.all(h5['/spikes/V1/node_ids'][()] == [0, 1, 2, 2, 3, 3, 4, 6]))
assert(np.all(h5['/spikes/V1/timestamps'][()] == [0.1]*8))
def test_write_sonata_bytime(st_cls, write_fnc):
# Check we can sort by timestamps
st = create_st_buffer(st_cls)
st.add_spikes(population='V1', node_ids=0, timestamps=[0.5, 0.3, 0.1, 0.2, 0.4])
tmpfile = tempfile.NamedTemporaryFile(suffix='.h5')
write_fnc(tmpfile.name, st, sort_order=sort_order.by_time)
with h5py.File(tmpfile.name, 'r') as h5:
assert(check_magic(h5))
assert(get_version(h5) is not None)
assert(h5['/spikes/V1'].attrs['sorting'] == 'by_time')
assert(np.all(h5['/spikes/V1/node_ids'][()] == [0, 0, 0, 0, 0]))
assert(np.all(h5['/spikes/V1/timestamps'][()] == [0.1, 0.2, 0.3, 0.4, 0.5]))
def test_write_sonata_byid(st_cls, write_fnc):
st = create_st_buffer_mpi(st_cls)
st.add_spikes(population='V1', node_ids=[MPI_size + MPI_rank, MPI_rank], timestamps=[0.5, 1.0])
tmp_h5 = tmpfile()
write_fnc(tmp_h5, st, sort_order=sort_order.by_id)
if MPI_rank == 0:
with h5py.File(tmp_h5, 'r') as h5:
assert(check_magic(h5))
assert(get_version(h5) is not None)
assert(np.all(h5['/spikes/V1']['node_ids'][()] == list(range(MPI_size*2))))
assert(len(h5['/spikes/V1']['timestamps'][()]) == MPI_size * 2)
def test_write_sonata_bytime(st_cls, write_fnc):
st = create_st_buffer_mpi(st_cls)
st.add_spikes(population='V1', node_ids=[MPI_rank, MPI_rank],
timestamps=np.array([MPI_rank/10.0, (MPI_size + MPI_rank)/10.0], dtype=float))
tmp_h5 = tmpfile()
write_fnc(tmp_h5, st, sort_order=sort_order.by_time)
if MPI_rank == 0:
with h5py.File(tmp_h5, 'r') as h5:
assert(check_magic(h5))
assert(get_version(h5) is not None)
assert(len(h5['/spikes/V1']['node_ids'][()]) == MPI_size*2)
assert(np.all(np.diff(h5['/spikes/V1']['timestamps'][()]) > 0))
def _check_edges(h5, n_edges):
assert(check_magic(h5))
assert(get_version(h5))
assert(len(h5['/edges/a_to_b/source_node_id']) == n_edges)
assert(h5['/edges/a_to_b/source_node_id'].attrs['node_population'] == 'a')
assert(len(h5['/edges/a_to_b/target_node_id']) == n_edges)
assert(h5['/edges/a_to_b/target_node_id'].attrs['node_population'] == 'b')
assert(len(h5['/edges/a_to_b/edge_type_id']) == n_edges)
assert(len(h5['/edges/a_to_b/edge_group_id']) == n_edges)
assert(len(h5['/edges/a_to_b/edge_group_index']) == n_edges)
for i in range(n_edges):
grp_id = h5['/edges/a_to_b/edge_group_id'][i]
grp_indx = h5['/edges/a_to_b/edge_group_index'][i]
assert (h5['/edges/a_to_b/source_node_id'][i] == h5['/edges/a_to_b'][str(grp_id)]['src_id'][grp_indx])
assert (h5['/edges/a_to_b/target_node_id'][i] == h5['/edges/a_to_b'][str(grp_id)]['trg_id'][grp_indx])
assert (h5['/edges/a_to_b/edge_type_id'][i] == h5['/edges/a_to_b'][str(grp_id)]['et_id'][grp_indx])