def test_droplettracklist_plotting():
"""test plotting droplet tracks"""
t1 = DropletTrack()
ds = [DiffuseDroplet([0, 1], 10, 0.5)] * 2
t2 = DropletTrack(droplets=ds, times=[0, 10])
DropletTrackList([t1, t2]).plot()
DropletTrackList([t1, t2]).plot_positions()
def test_droplettrack_plotting():
"""test writing and reading droplet tracks"""
ds = [DiffuseDroplet([0, 1], 10, 0.5)] * 2
t = DropletTrack(droplets=ds, times=[0, 10])
t.plot("radius")
t.plot("volume")
t.plot_positions()
t.plot_positions(grid=UnitGrid([5, 5], periodic=True))
def test_emulsion_processing():
"""test identifying emulsions in phase fields"""
grid = UnitGrid([32, 32], periodic=True)
e1 = Emulsion(
[
DiffuseDroplet(position=[5, 6], radius=9, interface_width=1),
DiffuseDroplet(position=[20, 19], radius=8, interface_width=1),
],
grid=grid,
)
field = e1.get_phasefield()
e2 = image_analysis.locate_droplets(field, refine=True)
np.testing.assert_allclose(
structured_to_unstructured(e1.data),
structured_to_unstructured(e2.data),
rtol=0.02,
)
def test_localization_threshold():
"""tests different localization thresholds"""
pos = np.random.random(2) * 16
radius = np.random.uniform(2, 5)
width = np.random.uniform(1, 2)
d1 = DiffuseDroplet(pos, radius, interface_width=width)
grid = UnitGrid((16, 16), periodic=False)
field = d1.get_phase_field(grid)
for threshold in [0.25, 0.75, "auto"]:
emulsion = image_analysis.locate_droplets(
field, threshold=threshold, refine=True
)
assert len(emulsion) == 1
d2 = emulsion[0]
np.testing.assert_almost_equal(d1.position, d2.position)
assert d1.radius == pytest.approx(d2.radius, rel=1e-4)
assert d1.interface_width == pytest.approx(d2.interface_width)
def test_localization_spherical():
"""tests simple droplets localization in spherical grid"""
radius = np.random.uniform(2, 3)
width = np.random.uniform(0.5, 1.5)
d1 = DiffuseDroplet((0, 0, 0), radius, interface_width=width)
grid_radius = 6 + 2 * np.random.random()
grid = SphericalSymGrid(grid_radius, 16)
field = d1.get_phase_field(grid)
emulsion = image_analysis.locate_droplets(field, refine=True)
assert len(emulsion) == 1
d2 = emulsion[0]
np.testing.assert_almost_equal(d1.position, d2.position, decimal=5)
assert d1.radius == pytest.approx(d2.radius, rel=1e-5)
assert d1.interface_width == pytest.approx(d2.interface_width, rel=1e-5)
emulsion = image_analysis.locate_droplets(ScalarField(grid))
assert len(emulsion) == 0
def test_droplettracklist_io(tmp_path):
"""test writing and reading droplet tracks"""
path = tmp_path / "test_droplettracklist_io.hdf5"
t1 = DropletTrack()
ds = [DiffuseDroplet([0, 1], 10, 0.5)] * 2
t2 = DropletTrack(droplets=ds, times=[0, 10])
tl_out = DropletTrackList([t1, t2])
tl_out.to_file(path)
tl_in = DropletTrackList.from_file(path)
assert tl_in == tl_out
def test_droplettracklist():
"""test droplet tracks"""
t1 = DropletTrack()
ds = [DiffuseDroplet([0, 1], 10, 0.5)] * 2
t2 = DropletTrack(droplets=ds, times=[0, 10])
tl = DropletTrackList([t1, t2])
assert len(tl) == 2
assert tl[0] == t1
assert tl[1] == t2
tl.remove_short_tracks()
assert len(tl) == 1
def test_localization_cylindrical(periodic):
"""tests simple droplets localization in cylindrical grid"""
pos = (0, 0, np.random.uniform(-4, 4))
radius = np.random.uniform(2, 3)
width = np.random.uniform(0.5, 1.5)
d1 = DiffuseDroplet(pos, radius, interface_width=width)
grid_radius = 6 + 2 * np.random.random()
bounds_z = np.random.uniform(1, 2, size=2) * np.array([-4, 4])
grid = CylindricalSymGrid(grid_radius, bounds_z, (16, 32), periodic_z=periodic)
field = d1.get_phase_field(grid)
emulsion = image_analysis.locate_droplets(field, refine=True)
assert len(emulsion) == 1
d2 = emulsion[0]
np.testing.assert_almost_equal(d1.position, d2.position, decimal=5)
assert d1.radius == pytest.approx(d2.radius, rel=1e-5)
assert d1.interface_width == pytest.approx(d2.interface_width)
emulsion = image_analysis.locate_droplets(ScalarField(grid))
assert len(emulsion) == 0
def test_droplettrack_io(tmp_path):
"""test writing and reading droplet tracks"""
path = tmp_path / "test_droplettrack_io.hdf5"
t1 = DropletTrack()
ds = [DiffuseDroplet([0, 1], 10, 0.5)] * 2
t2 = DropletTrack(droplets=ds, times=[0, 10])
for t_out in [t1, t2]:
t_out.to_file(path)
t_in = DropletTrack.from_file(path)
assert t_in == t_out
assert t_in.times == t_out.times
assert t_in.droplets == t_out.droplets
def test_localization_sym_unit(size, periodic):
"""tests simple droplets localization in 2d"""
pos = np.random.random(2) * size
radius = np.random.uniform(2, 5)
width = np.random.uniform(1, 2)
d1 = DiffuseDroplet(pos, radius, interface_width=width)
grid = UnitGrid((size, size), periodic=periodic)
field = d1.get_phase_field(grid)
emulsion = image_analysis.locate_droplets(field, refine=True)
assert len(emulsion) == 1
d2 = emulsion[0]
np.testing.assert_almost_equal(d1.position, d2.position)
assert d1.radius == pytest.approx(d2.radius, rel=1e-4)
assert d1.interface_width == pytest.approx(d2.interface_width)
emulsion = image_analysis.locate_droplets(field, minimal_radius=size)
assert len(emulsion) == 0
emulsion = image_analysis.locate_droplets(ScalarField(grid))
assert len(emulsion) == 0
def test_localization_sym_rect(periodic):
"""tests simple droplets localization in 2d with a rectangular grid"""
size = 16
pos = np.random.uniform(-4, 4, size=2)
radius = np.random.uniform(2, 5)
width = np.random.uniform(0.5, 1.5)
d1 = DiffuseDroplet(pos, radius, interface_width=width)
a = np.random.random(2) - size / 2
b = np.random.random(2) + size / 2
grid = CartesianGrid(np.c_[a, b], 3 * size, periodic=periodic)
field = d1.get_phase_field(grid)
emulsion = image_analysis.locate_droplets(field, refine=True)
assert len(emulsion) == 1
d2 = emulsion[0]
np.testing.assert_almost_equal(d1.position, d2.position)
assert d1.radius == pytest.approx(d2.radius, rel=1e-5)
assert d1.interface_width == pytest.approx(d2.interface_width)
emulsion = image_analysis.locate_droplets(ScalarField(grid))
assert len(emulsion) == 0