def test_uniform_detrended_periodicity():
topography = Topography(np.array([[0, 1, 0], [0, 0, 0]]),
physical_sizes=(4., 3.),
periodic=True)
assert topography.detrend("center").is_periodic
assert not topography.detrend("height").is_periodic
assert not topography.detrend("curvature").is_periodic
def test_fill_undefined_data_parallel(comm):
np.random.seed(comm.rank)
local_data = np.random.uniform(size=(3, 1))
local_data[local_data > 0.9] = np.nan
if comm.rank == 0: # make sure we always have undefined data
local_data[0, 0] = np.nan
topography = Topography(local_data, (1., 1.),
info=dict(test=1),
communicator=comm,
decomposition="subdomain",
nb_grid_pts=(3, comm.size),
subdomain_locations=(0, comm.rank))
filled_topography = topography.fill_undefined_data(fill_value=-np.infty)
assert topography.has_undefined_data
assert not filled_topography.has_undefined_data
mask = np.ma.getmask(topography.heights())
nmask = np.logical_not(mask)
reduction = Reduction(comm)
assert reduction.all(filled_topography[nmask] == topography[nmask])
assert reduction.all(filled_topography[mask] == -np.infty)
assert not filled_topography.has_undefined_data
def test_translate(comm_self):
topography = Topography(np.array([[0, 1, 0], [0, 0, 0]]),
physical_sizes=(4., 3.))
assert (topography.translate(offset=(1,
0)).heights() == np.array([[0, 0, 0],
[0, 1, 0]
])).all()
assert (topography.translate(offset=(2,
0)).heights() == np.array([[0, 1, 0],
[0, 0, 0]
])).all()
assert (topography.translate(offset=(0,
-1)).heights() == np.array([[1, 0, 0],
[0, 0, 0]
])).all()
def test_fill_undefined_data(periodic):
topography = Topography(
np.array([[1, np.nan, 4.], [3, 4, 5]]),
(1., 1.),
info=dict(test=1),
periodic=periodic,
)
assert topography.has_undefined_data
filled_topography = topography.fill_undefined_data(fill_value=-np.infty)
mask = np.ma.getmask(topography.heights())
nmask = np.logical_not(mask)
assert (filled_topography[nmask] == topography[nmask]).all()
assert (filled_topography[mask] == -np.infty).all()
assert not filled_topography.has_undefined_data
assert filled_topography.physical_sizes == topography.physical_sizes
assert filled_topography.is_periodic == topography.is_periodic
assert filled_topography.info["test"] == 1
def test_to_matrix():
y = np.arange(10).reshape((1, -1))
x = np.arange(5).reshape((-1, 1))
arr = -2 * y + 0 * x
t = Topography(arr, (5, 10), unit='nm')
# Check that we can export downstream the pipeline
with tempfile.TemporaryDirectory() as d:
t.to_matrix(f"{d}/topo.txt")
t.detrend('center').to_matrix(f'{d}/topo.txt')
t2 = read_matrix(f'{d}/topo.txt')
np.testing.assert_allclose(t.detrend('center').heights(), t2.heights())
def test_passing_of_docstring():
from SurfaceTopography.Uniform.PowerSpectrum import power_spectrum_from_profile
topography = Topography(np.array([[0, 1, 0], [0, 0, 0]]),
physical_sizes=(4., 3.),
periodic=True)
assert topography.power_spectrum_from_profile.__doc__ == power_spectrum_from_profile.__doc__