def test_some_to_many(self, dummy_signal):
scope = MetricScope.SOME_TO_MANY
assert scope.name == "SOME_TO_MANY"
assert scope.value == "some_to_many"
sig_shape = dummy_signal.axes_manager.signal_shape
expt = dummy_signal.data.reshape((-1, ) + sig_shape)
sim = expt[:3]
dims = (expt.ndim, sim.ndim)
assert dims == (3, 3)
# Expansion of dimensions works
ncc_metric = _SIMILARITY_METRICS["ncc"]
ncc = ncc_metric(expt, sim)
assert ncc.shape == (9, 3)
assert np.allclose(np.diagonal(ncc), 1)
def dot_product(a, b):
norm_a = np.linalg.norm(a, axis=(1, 2))[:, np.newaxis, np.newaxis]
norm_b = np.linalg.norm(b, axis=(1, 2))[:, np.newaxis, np.newaxis]
return np.tensordot(a / norm_a, b / norm_b, axes=([1, 2], [2, 1]))
metric = make_similarity_metric(metric_func=dot_product, scope=scope)
assert metric._EXPT_SIM_NDIM_TO_SCOPE[dims] == scope
assert metric._SCOPE_TO_EXPT_SIM_NDIM[scope] == dims
ndp = metric(expt, sim)
assert ndp.shape == (9, 3)
assert np.allclose(np.sum(ndp), 19.92476)
def test_some_to_one(self, dummy_signal):
scope = MetricScope.SOME_TO_ONE
assert scope.name == "SOME_TO_ONE"
assert scope.value == "some_to_one"
sig_shape = dummy_signal.axes_manager.signal_shape
expt = dummy_signal.data.reshape((-1, ) + sig_shape)
sim = expt[0]
dims = (expt.ndim, sim.ndim)
assert dims == (3, 2)
# Expansion of dimensions works
ndp_metric = _SIMILARITY_METRICS["ndp"]
ndp = ndp_metric(expt, sim)
assert ndp.shape == (9, )
assert np.allclose(ndp[0], 1)
def dot_product(a, b):
norm_a = np.linalg.norm(a, axis=(1, 2))[:, np.newaxis, np.newaxis]
norm_b = np.linalg.norm(b)
return np.tensordot(a / norm_a, b / norm_b, axes=([1, 2], [1, 0]))
metric = make_similarity_metric(metric_func=dot_product, scope=scope)
assert metric._EXPT_SIM_NDIM_TO_SCOPE[dims] == scope
assert metric._SCOPE_TO_EXPT_SIM_NDIM[scope] == dims
ndp = metric(expt, sim)
assert ndp.shape == (9, )
assert np.allclose(np.sum(ndp), 6.9578266)
def test_negative_metric(self, get_single_phase_xmap):
def negative_sad(p, t): # pragma: no cover
return -np.sum(np.abs(p - t), axis=(2, 3))
metric = make_similarity_metric(negative_sad, greater_is_better=False)
map_shape = (5, 6)
rot_per_point = 5
scores_prop = "scores"
sim_idx_prop = "simulation_indices"
xmap1 = get_single_phase_xmap(map_shape, rot_per_point,
[scores_prop, sim_idx_prop], "a", 0)
xmap2 = get_single_phase_xmap(map_shape, rot_per_point,
[scores_prop, sim_idx_prop], "b", 1)
xmap2[0, 3].prop[scores_prop] = 0
desired_phase_id = np.zeros(np.prod(map_shape))
desired_phase_id[3] = 1
merged_xmap = merge_crystal_maps(
crystal_maps=[xmap1, xmap2],
metric=metric,
)
assert np.allclose(merged_xmap.phase_id, desired_phase_id)
def test_make_similarity_metric(self, flat, returned_class):
assert (type(
make_similarity_metric(
lambda expt, sim: np.zeros((2, 4)) if flat else np.zeros(
(2, 2, 2)),
flat=flat,
scope=MetricScope.MANY_TO_MANY,
)) is returned_class)
def test_too_small_scoped_inputs(self):
metric = make_similarity_metric(
lambda expt, sim: np.zeros((2, 2, 2)),
scope=MetricScope.MANY_TO_MANY,
)
assert (metric._is_compatible(
np.zeros((2, 2)).ndim,
np.zeros((2, 2)).ndim) is False)
def test_not_supported_inputs(self):
metric = make_similarity_metric(
lambda expt, sim: 1.0,
scope=MetricScope.MANY_TO_MANY,
make_compatible_to_lower_scopes=True,
)
assert (metric._is_compatible(
np.zeros((2, 2, 2, 2, 2)).ndim,
np.zeros((4, 2, 2)).ndim) is False)
def test_some_to_one_flat(self, dummy_signal):
scope_in = MetricScope.SOME_TO_ONE
metric = make_similarity_metric(metric_func=_zncc_einsum,
scope=scope_in,
flat=True)
scope_out = metric.scope
assert metric.flat
assert scope_out.name == "MANY_TO_ONE"
def test_similarity_metric_representation(self):
metrics = [
make_similarity_metric(
metric_func=lambda expt, sim: np.zeros((2, 2, 2)),
scope=MetricScope.MANY_TO_MANY,
),
make_similarity_metric(
metric_func=lambda expt, sim: np.zeros((2, 2, 2)),
scope=MetricScope.ONE_TO_MANY,
flat=True,
),
_SIMILARITY_METRICS["ncc"],
_SIMILARITY_METRICS["ndp"],
]
desired_repr = [
"SimilarityMetric <lambda>, scope: many_to_many",
"FlatSimilarityMetric <lambda>, scope: one_to_many",
"SimilarityMetric _zncc_einsum, scope: many_to_many",
"SimilarityMetric _ndp_einsum, scope: many_to_many",
]
for i in range(len(desired_repr)):
assert repr(metrics[i]) == desired_repr[i]
def test_flat_metric(self):
expt = np.array(
[
[[[1, 2], [3, 4]], [[5, 6], [7, 8]]],
[[[9, 8], [1, 7]], [[5, 2], [2, 7]]],
],
np.int8,
)
sim = np.array([[[5, 3], [2, 7]], [[9, 8], [1, 7]]], np.int8)
euclidean_metric = make_similarity_metric(
lambda expt, sim: cdist(expt, sim, metric="euclidean"),
greater_is_better=False,
flat=True,
scope=MetricScope.MANY_TO_MANY,
make_compatible_to_lower_scopes=True,
)
assert (euclidean_metric._is_compatible(expt.ndim, sim.ndim) is True
and pytest.approx(euclidean_metric(expt, sim)[2, 1]) == 0)
def test_too_large_scoped_inputs(self):
metric = make_similarity_metric(lambda expt, sim: 1.0,
scope=MetricScope.ONE_TO_ONE)
assert (metric._is_compatible(
np.zeros((2, 2, 2, 2)).ndim,
np.zeros((4, 2, 2)).ndim) is False)
class TestPatternMatching:
zncc_flat_metric = make_similarity_metric(
lambda p, t: cdist(p, t, metric="correlation"),
greater_is_better=False,
flat=True,
)
dummy_metric = make_similarity_metric(lambda p, t: 1.0)
def test_not_recognized_metric(self):
with pytest.raises(ValueError):
_pattern_match(np.zeros((2, 2)),
np.zeros((2, 2)),
metric="not_recognized")
def test_mismatching_signal_shapes(self):
self.dummy_metric.scope = MetricScope.MANY_TO_MANY
with pytest.raises(OSError):
_pattern_match(np.zeros((2, 2)),
np.zeros((3, 3)),
metric=self.dummy_metric)
def test_metric_not_compatible_with_data(self):
self.dummy_metric.scope = MetricScope.ONE_TO_MANY
with pytest.raises(OSError):
_pattern_match(
np.zeros((2, 2, 2, 2)),
np.zeros((2, 2)),
metric=self.dummy_metric,
)
@pytest.mark.parametrize("n_slices", [1, 2])
def test_pattern_match_compute_true(self, n_slices):
# Four patterns
p = np.array(
[
[[[1, 2], [3, 4]], [[5, 6], [7, 8]]],
[[[9, 8], [1, 7]], [[5, 2], [2, 7]]],
],
np.int8,
)
# Five templates
t = np.array(
[
[[5, 3], [2, 7]],
[[9, 8], [1, 7]],
[[10, 2], [5, 3]],
[[8, 4], [6, 12]],
[[43, 0], [5, 3]],
],
np.int8,
)
t_da = da.from_array(t)
mr = _pattern_match(p, t_da, n_slices=n_slices, keep_n=1)
assert mr[0][2] == 1 # Template index in t of perfect match
assert np.allclose(mr[1][2], 1.0) # ZNCC of perfect match
def test_pattern_match_compute_false(self):
p = np.arange(16).reshape((2, 2, 2, 2))
t = np.arange(8).reshape((2, 2, 2))
mr = _pattern_match(p, t, compute=False)
assert len(mr) == 2
assert isinstance(mr[0], da.Array) and isinstance(mr[1], da.Array)
def test_pattern_match_slices_compute_false(self):
p = np.arange(16).reshape((2, 2, 2, 2))
t = np.arange(8).reshape((2, 2, 2))
with pytest.raises(NotImplementedError):
_pattern_match(p, t, n_slices=2, compute=False)
def test_pattern_match_one_to_one(self):
p = np.random.random(3 * 3).reshape((3, 3))
mr = _pattern_match(p, p)
assert mr[0][0] == 0
def test_pattern_match_phase_name(self):
"""Ensure that the `phase_name` accepts different types."""
exp = nickel_ebsd_small().data
sim = exp.reshape((-1, ) + exp.shape[-2:])
sim_idx1, scores1 = _pattern_match(exp, sim, n_slices=2)
sim_idx2, scores2 = _pattern_match(exp,
sim,
phase_name="a",
n_slices=2)
sim_idx3, scores3 = _pattern_match(exp, sim, phase_name="", n_slices=2)
assert np.allclose(sim_idx1[0], [0, 3, 6, 4, 7, 1, 8, 5, 2])
assert np.allclose(sim_idx2[0], [0, 3, 6, 4, 7, 1, 8, 5, 2])
assert np.allclose(sim_idx3[0], [0, 3, 6, 4, 7, 1, 8, 5, 2])
def test_passing_results_from_get_patterns(self):
s = nickel_ebsd_small()
print(s)
s.remove_static_background()
s.remove_dynamic_background()
mp = nickel_ebsd_master_pattern_small(projection="lambert")
r = Rotation([
[0.9522, -0.0151, -0.2883, 0.1001], # Left grain
[0.9534, 0.0465, -0.2187, -0.2026], # Right grain
[0.8876, -0.2312, 0.3364, -0.2131], # 50th best match
])
detector = EBSDDetector(
shape=s.axes_manager.signal_shape[::-1],
pc=[0.421, 0.7794, 0.5049],
convention="tsl",
sample_tilt=70,
)
sim = mp.get_patterns(rotations=r, detector=detector, energy=20)
xmap = s.match_patterns(sim, keep_n=1)
scores = xmap.scores.reshape(xmap.size, )
sim_idx = xmap.simulation_indices.reshape(xmap.size, )
assert np.allclose(
scores,
[0.197, 0.188, 0.207, 0.198, 0.186, 0.225, 0.191, 0.191, 0.206],
atol=1e-3,
)
assert np.allclose(sim_idx, [0, 1, 1, 0, 1, 1, 0, 1, 1])