def test_memory_storage():
"""test methods specific to memory storage"""
sf = ScalarField(UnitGrid([1]))
s1 = MemoryStorage()
s1.start_writing(sf)
sf.data = 0
s1.append(sf, 0)
sf.data = 2
s1.append(sf, 1)
s2 = MemoryStorage()
s2.start_writing(sf)
sf.data = 1
s2.append(sf, 0)
sf.data = 3
s2.append(sf, 1)
# test from_fields
s3 = MemoryStorage.from_fields(s1.times, [s1[0], s1[1]])
assert s3.times == s1.times
np.testing.assert_allclose(s3.data, s1.data)
# test from_collection
s3 = MemoryStorage.from_collection([s1, s2])
assert s3.times == s1.times
np.testing.assert_allclose(np.ravel(s3.data), np.arange(4))
def test_storage_copy(tmp_path):
"""test the copy function of StorageBase"""
grid = UnitGrid([2])
field = ScalarField(grid)
storage_classes = {"None": None, "MemoryStorage": MemoryStorage}
if module_available("h5py"):
file_path = tmp_path / "test_storage_apply.hdf5"
storage_classes["FileStorage"] = functools.partial(
FileStorage, file_path)
s1 = MemoryStorage()
s1.start_writing(field, info={"b": 2})
field.data = np.array([0, 1])
s1.append(field, 0)
field.data = np.array([1, 2])
s1.append(field, 1)
s1.end_writing()
for name, storage_cls in storage_classes.items():
out = None if storage_cls is None else storage_cls()
s2 = s1.copy(out=out)
assert storage_cls is None or s2 is out
assert len(s2) == 2
np.testing.assert_allclose(s2.times, s1.times)
assert s2[0] == s1[0], name
assert s2[1] == s1[1], name
# test empty storage
s1 = MemoryStorage()
s2 = s1.copy()
assert len(s2) == 0
def test_storage_write(tmp_path):
"""test simple memory storage"""
dim = 5
grid = UnitGrid([dim])
field = ScalarField(grid)
storage_classes = {"MemoryStorage": MemoryStorage}
if module_available("h5py"):
file_path = tmp_path / "test_storage_write.hdf5"
storage_classes["FileStorage"] = functools.partial(
FileStorage, file_path)
for name, storage_cls in storage_classes.items():
storage = storage_cls(info={"a": 1})
storage.start_writing(field, info={"b": 2})
field.data = np.arange(dim)
storage.append(field, 0)
field.data = np.arange(dim)
storage.append(field, 1)
storage.end_writing()
assert not storage.has_collection
np.testing.assert_allclose(storage.times, np.arange(2))
for f in storage:
np.testing.assert_array_equal(f.data, np.arange(dim))
for i in range(2):
np.testing.assert_array_equal(storage[i].data, np.arange(dim))
assert {"a": 1, "b": 2}.items() <= storage.info.items()
storage = storage_cls()
storage.clear()
for i in range(3):
storage.start_writing(field)
field.data = np.arange(dim) + i
storage.append(field, i)
storage.end_writing()
np.testing.assert_allclose(storage.times,
np.arange(3),
err_msg="storage class: " + name)
def test_storing_extract_range(tmp_path):
"""test methods specific to FieldCollections in memory storage"""
sf = ScalarField(UnitGrid([1]))
storage_classes = {"MemoryStorage": MemoryStorage}
if module_available("h5py"):
file_path = tmp_path / "test_storage_write.hdf5"
storage_classes["FileStorage"] = functools.partial(
FileStorage, file_path)
for storage_cls in storage_classes.values():
# store some data
s1 = storage_cls()
s1.start_writing(sf)
sf.data = np.array([0])
s1.append(sf, 0)
sf.data = np.array([2])
s1.append(sf, 1)
s1.end_writing()
np.testing.assert_equal(s1[0].data, 0)
np.testing.assert_equal(s1[1].data, 2)
np.testing.assert_equal(s1[-1].data, 2)
np.testing.assert_equal(s1[-2].data, 0)
with pytest.raises(IndexError):
s1[2]
with pytest.raises(IndexError):
s1[-3]
# test extraction
s2 = s1.extract_time_range()
assert s2.times == list(s1.times)
np.testing.assert_allclose(s2.data, s1.data)
s3 = s1.extract_time_range(0.5)
assert s3.times == s1.times[:1]
np.testing.assert_allclose(s3.data, s1.data[:1])
s4 = s1.extract_time_range((0.5, 1.5))
assert s4.times == s1.times[1:]
np.testing.assert_allclose(s4.data, s1.data[1:])
def test_kymograph_single(tmp_path):
"""test making kymographs for single fields"""
# create some storage
field = ScalarField(UnitGrid(8))
with get_memory_storage(field) as storage:
for i in range(8):
field.data = i
storage.append(field, i)
# create single kymograph
path = tmp_path / "test1.png"
plotting.plot_kymograph(storage,
colorbar=True,
transpose=True,
filename=path)
assert path.stat().st_size > 0
# create multiple kymographs
path = tmp_path / "test2.png"
plotting.plot_kymographs(storage, filename=path)
assert path.stat().st_size > 0