def test_merging_refined_maps(self):
ny, nx = (3, 3)
nav_size = ny * nx
r = Rotation.from_euler(np.ones((nav_size, 3)))
x = np.tile(np.arange(ny), nx)
y = np.repeat(np.arange(nx), ny)
# Simulation indices
n_sim_indices = 10
sim_indices1 = np.random.randint(low=0,
high=1000,
size=n_sim_indices *
nav_size).reshape(
(nav_size, n_sim_indices))
sim_indices2 = np.random.randint(low=0,
high=1000,
size=n_sim_indices *
nav_size).reshape(
(nav_size, n_sim_indices))
# Scores
scores1 = np.ones(nav_size)
scores1[0] = 3
scores2 = 2 * np.ones(nav_size)
xmap1 = CrystalMap(
rotations=r,
phase_id=np.ones(nav_size) * 0,
phase_list=PhaseList(Phase(name="a")),
x=x,
y=y,
prop={
"simulation_indices": sim_indices1,
"scores": scores1
},
)
xmap2 = CrystalMap(
rotations=r,
phase_id=np.ones(nav_size),
phase_list=PhaseList(Phase(name="b")),
x=x,
y=y,
prop={
"simulation_indices": sim_indices2,
"scores": scores2
},
)
xmap_merged = merge_crystal_maps(crystal_maps=[xmap1, xmap2])
assert "simulation_indices" not in xmap_merged.prop.keys()
assert "merged_simulation_indices" not in xmap_merged.prop.keys()
with pytest.raises(ValueError, match="Cannot merge maps with more"):
_ = merge_crystal_maps(
crystal_maps=[xmap1, xmap2],
simulation_indices_prop="simulation_indices",
)
def test_warning_merge_maps_with_same_phase(self, get_single_phase_xmap,
phase_names,
desired_phase_names):
n_phases = len(phase_names)
scores_prop = "scores"
sim_idx_prop = "simulated_indices"
map_shape = (5, 6)
rot_per_point = 5
xmaps = []
xmap_args = (map_shape, rot_per_point, [scores_prop, sim_idx_prop])
phase_ids = np.arange(n_phases)
for i in range(n_phases):
xmap = get_single_phase_xmap(*xmap_args, phase_names[i],
phase_ids[i])
# All maps have at least one point with the best score
xmap[i, i].scores += i + 1
xmaps.append(xmap)
with pytest.warns(
UserWarning,
match=f"There are duplicates of phase {phase_names[0]}"):
merged_xmap = merge_crystal_maps(
crystal_maps=xmaps,
scores_prop=scores_prop,
simulation_indices_prop=sim_idx_prop,
)
assert all(
[name in merged_xmap.phases.names for name in desired_phase_names])
def test_property_names(self, get_single_phase_xmap, scores_prop,
sim_idx_prop):
"""Passing scores and simulation indices property names returns
expected properties in merged map.
"""
map_shape = (5, 6)
rot_per_point = 50
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[3, 3].prop[scores_prop] = 2
merged_xmap = merge_crystal_maps(
crystal_maps=[xmap1, xmap2],
greater_is_better=True,
scores_prop=scores_prop,
simulation_indices_prop=sim_idx_prop,
)
assert scores_prop in merged_xmap.prop.keys()
assert sim_idx_prop in merged_xmap.prop.keys()
desired_merged_shapes = (np.prod(map_shape), rot_per_point * 2)
assert merged_xmap.prop[
f"merged_{scores_prop}"].shape == desired_merged_shapes
assert merged_xmap.prop[
f"merged_{sim_idx_prop}"].shape == desired_merged_shapes
def test_merging_maps_different_number_of_scores_raises(
self, get_single_phase_xmap):
nav_shape = (2, 3)
xmap1 = get_single_phase_xmap(nav_shape, 3, name="a")
xmap2 = get_single_phase_xmap(nav_shape, 4, name="b")
xmap2[0, 1].scores = 2.0 # Both maps in both merged maps
crystal_maps = [xmap1, xmap2]
with pytest.raises(ValueError, match="All crystal maps must have the"):
_ = merge_crystal_maps(crystal_maps)
def test_mean_n_best_varying_scores(self, get_single_phase_xmap):
"""Ensure various combinations of scores per point and how many
of these are evaulated to find the best match return expected
results.
"""
nav_shape = (2, 3)
rot_per_point = 3
xmap1 = get_single_phase_xmap(nav_shape, rot_per_point, name="a")
xmap2 = get_single_phase_xmap(nav_shape, rot_per_point, name="b")
idx = (0, 0)
xmap1[idx].scores = [1, 2, 2.1]
xmap2[idx].scores = [1, 1.9, 3]
xmap2[0, 1].scores = 2.0 # Both maps in both merged maps
crystal_maps = [xmap1, xmap2]
merged_xmap1 = merge_crystal_maps(crystal_maps, mean_n_best=2)
merged_xmap2 = merge_crystal_maps(crystal_maps, mean_n_best=3)
assert np.allclose(merged_xmap1.phase_id, [0, 1, 0, 0, 0, 0])
assert np.allclose(merged_xmap2.phase_id, [1, 1, 0, 0, 0, 0])
def test_lower_is_better(self, get_single_phase_xmap):
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],
greater_is_better=False,
simulation_indices_prop=sim_idx_prop,
)
assert np.allclose(merged_xmap.phase_id, desired_phase_id)
def test_mean_n_best(
self,
get_single_phase_xmap,
nav_shape,
rot_per_point,
mean_n_best,
desired_merged_scores,
desired_merged_sim_idx,
):
"""Ensure that the merge sorted scores and simulation index
properties in the merged map has the correct values and shape.
"""
prop_names = ["scores", "simulation_indices"]
n_phases = np.shape(desired_merged_scores)[-1] // rot_per_point
xmaps = []
for i in range(n_phases):
xmap = get_single_phase_xmap(nav_shape,
rot_per_point,
name=str(i),
prop_names=prop_names)
xmap[i].scores += i
xmaps.append(xmap)
# The simulation indices should be the same in all maps
all_sim_idx = np.dstack([xmap.simulation_indices for xmap in xmaps])
assert np.sum(np.diff(all_sim_idx)) == 0
merged_xmap = merge_crystal_maps(
crystal_maps=xmaps,
mean_n_best=mean_n_best,
simulation_indices_prop=prop_names[1],
)
assert merged_xmap.phases.size == n_phases
assert np.allclose(merged_xmap.merged_scores, desired_merged_scores)
assert np.allclose(merged_xmap.merged_simulation_indices,
desired_merged_sim_idx)
def test_merging_maps_different_shapes_raises(self, get_single_phase_xmap):
xmap1 = get_single_phase_xmap((4, 3))
xmap2 = get_single_phase_xmap((3, 4))
with pytest.raises(ValueError, match="All crystal maps must have the"):
_ = merge_crystal_maps([xmap1, xmap2])
def test_merge_crystal_maps_1d(self, map_shape, rot_per_point, phase_names,
get_single_phase_xmap):
"""Crystal maps with a 1D navigation shape can be merged
successfully and yields an expected output.
"""
n_phases = len(phase_names)
scores_prop, sim_idx_prop = "scores", "sim_idx"
map_size = np.sum(map_shape)
data_shape = (map_size, )
if rot_per_point > 1:
data_shape += (rot_per_point, )
desired_phase_ids = np.zeros(map_size)
desired_scores = np.ones(data_shape)
desired_idx = np.arange(np.prod(data_shape)).reshape(data_shape)
xmaps = []
xmap_kwargs = dict(
nav_shape=map_shape,
rotations_per_point=rot_per_point,
prop_names=[scores_prop, sim_idx_prop],
step_sizes=(1, ),
)
phase_ids = np.arange(n_phases)
for i in range(n_phases):
xmap = get_single_phase_xmap(name=phase_names[i],
phase_id=phase_ids[i],
**xmap_kwargs)
# All maps have at least one point with the best score
xmap[i].prop[scores_prop] += i + 1
xmaps.append(xmap)
desired_phase_ids[i] = i
desired_scores[i] = xmap[i].prop[scores_prop]
desired_idx[i] = xmap[i].prop[sim_idx_prop]
if i == 0:
desired_rot = xmap.rotations.data
else:
desired_rot[i] = xmap[i].rotations.data
merged_xmap = merge_crystal_maps(
crystal_maps=xmaps,
scores_prop=scores_prop,
simulation_indices_prop=sim_idx_prop,
)
assert merged_xmap.shape == xmaps[0].shape
assert merged_xmap.size == xmaps[0].size
for v1, v2 in zip(merged_xmap._coordinates.values(),
xmaps[0]._coordinates.values()):
if v1 is None:
assert v1 is v2
else:
np.allclose(v1, v2)
assert np.allclose(merged_xmap.phase_id, desired_phase_ids)
assert np.allclose(merged_xmap.prop[scores_prop], desired_scores)
assert np.allclose(merged_xmap.prop[sim_idx_prop], desired_idx)
assert np.allclose(merged_xmap.rotations.data, desired_rot)
desired_merged_shapes = (map_size, rot_per_point * n_phases)
assert merged_xmap.prop[
f"merged_{scores_prop}"].shape == desired_merged_shapes
assert merged_xmap.prop[
f"merged_{sim_idx_prop}"].shape == desired_merged_shapes
def test_merge_crystal_maps_2d(
self,
get_single_phase_xmap,
map_shape,
rot_per_point,
phase_names,
mean_n_best,
):
"""Crystal maps with a 2D navigation shape can be merged
successfully and yields an expected output.
"""
n_phases = len(phase_names)
scores_prop, sim_idx_prop = "scores", "sim_idx"
map_size = np.prod(map_shape)
data_shape = (map_size, )
if rot_per_point > 1:
data_shape += (rot_per_point, )
desired_phase_ids = np.zeros(map_size)
desired_scores = np.ones(data_shape)
desired_idx = np.arange(np.prod(data_shape)).reshape(data_shape)
xmaps = []
xmap_args = (map_shape, rot_per_point, [scores_prop, sim_idx_prop])
phase_ids = np.arange(n_phases)
ny, nx = map_shape
for i in range(n_phases):
xmap = get_single_phase_xmap(*xmap_args, phase_names[i],
phase_ids[i])
# All maps have at least one point with the best score along
# the map diagonal
idx = (i, i)
xmap[idx].prop[scores_prop] += i + 1
xmaps.append(xmap)
j = i * (1 + nx)
desired_phase_ids[j] = i
desired_scores[j] = xmap[idx].prop[scores_prop]
desired_idx[j] = xmap[idx].prop[sim_idx_prop]
if i == 0:
desired_rot = xmap.rotations.data
else:
desired_rot[j] = xmap[idx].rotations.data
merged_xmap = merge_crystal_maps(
crystal_maps=xmaps,
mean_n_best=mean_n_best,
scores_prop=scores_prop,
simulation_indices_prop=sim_idx_prop,
)
assert merged_xmap.shape == xmaps[0].shape
assert merged_xmap.size == xmaps[0].size
for v1, v2 in zip(merged_xmap._coordinates.values(),
xmaps[0]._coordinates.values()):
if v1 is None:
assert v1 is v2
else:
np.allclose(v1, v2)
assert np.allclose(merged_xmap.phase_id, desired_phase_ids)
assert np.allclose(merged_xmap.prop[scores_prop], desired_scores)
assert np.allclose(merged_xmap.prop[sim_idx_prop], desired_idx)
assert np.allclose(merged_xmap.rotations.data, desired_rot)
desired_merged_shapes = (map_size, rot_per_point * n_phases)
assert merged_xmap.prop[
f"merged_{scores_prop}"].shape == desired_merged_shapes
assert merged_xmap.prop[
f"merged_{sim_idx_prop}"].shape == desired_merged_shapes
