def test_rotate_tsl2bruker(self, r_tsl2bruker):
s_tilt = 70
d_tilt = 10
r_tsl_matrix = detector2sample(sample_tilt=s_tilt, detector_tilt=d_tilt)
r_tsl = Rotation.from_matrix(r_tsl_matrix)
r_bruker_matrix = detector2sample(
sample_tilt=s_tilt, detector_tilt=d_tilt, convention="bruker"
)
r_bruker = Rotation.from_matrix(r_bruker_matrix)
assert np.allclose((~r_tsl2bruker * r_tsl).data, r_bruker.data)
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])
def test_get_item(
self,
nickel_ebsd_simulation_generator,
nav_idx,
desired_shape,
desired_pc,
desired_rotation,
):
"""Desired PC and rotation values from __getitem__()."""
simgen = nickel_ebsd_simulation_generator
simgen.navigation_shape = (5, 5)
simgen.detector.pc[nav_idx] = desired_pc
r = Rotation.from_euler(desired_rotation)
simgen.rotations[nav_idx] = r
simgen2 = simgen[nav_idx]
assert simgen2.navigation_shape == desired_shape
assert np.allclose(simgen2.detector.pc, desired_pc)
assert np.allclose(simgen2.rotations.data, r.data)
new_pc = [
0.5,
] * 3
simgen2.detector.pc[0] = new_pc
assert not np.allclose(simgen[nav_idx].detector.pc,
simgen2.detector.pc)
def to_crystal_map(self):
"""
Exports an indexation result with multiple results per navigation position to
crystal map with one result per pixel
Returns
-------
orix.CrystalMap
"""
_s = self.data.map(_get_best_match,inplace=False)
""" Gets properties """
phase_id = _s.isig[0].data.flatten()
alpha = _s.isig[1].data.flatten()
beta = _s.isig[2].data.flatten()
gamma = _s.isig[3].data.flatten()
score = _s.isig[4].data.flatten()
""" Gets navigation placements """
xy = np.indices(_s.data.shape[:2])
x = xy[1].flatten()
y = xy[0].flatten()
""" Tidies up so we can put these things into CrystalMap """
euler = np.vstack((alpha,beta,gamma)).T
rotations = Rotation.from_euler(euler,convention="bunge", direction="crystal2lab")
properties = {"score":score}
return CrystalMap(
rotations=rotations,
phase_id=phase_id,
x=x,
y=y,
prop=properties)
def test_detector_azimuthal(self):
"""Test that setting an azimuthal angle of a detector results in
different patterns.
"""
det1 = self.detector
# Looking from the detector toward the sample, the left part of
# the detector is closer to the sample than the right part
det2 = det1.deepcopy()
det2.azimuthal = 10
# Looking from the detector toward the sample, the right part of
# the detector is closer to the sample than the left part
det3 = det1.deepcopy()
det3.azimuthal = -10
mp = nickel_ebsd_master_pattern_small(projection="lambert")
r = Rotation.identity()
kwargs = dict(rotations=r, energy=20, compute=True, dtype_out=np.uint8)
sim1 = mp.get_patterns(detector=det1, **kwargs)
sim2 = mp.get_patterns(detector=det2, **kwargs)
sim3 = mp.get_patterns(detector=det3, **kwargs)
assert not np.allclose(sim1.data, sim2.data)
assert np.allclose(sim2.data.mean(), 43.56, atol=1e-2)
assert np.allclose(sim3.data.mean(), 43.39, atol=1e-2)
def test_get_patterns_navigation_shape_raises(self):
mp = nickel_ebsd_master_pattern_small(projection="lambert")
r = Rotation(np.random.uniform(low=0, high=1, size=(1, 2, 3, 4)))
detector = kp.detectors.EBSDDetector(shape=(60, 60))
with pytest.raises(ValueError,
match="`rotations` can only have one or two "):
_ = mp.get_patterns(rotations=r, detector=detector, energy=20)
def rotate(self, axis=None, angle=0):
"""Convenience function for rotating this vector.
Shapes of 'axis' and 'angle' must be compatible with shape of this
vector for broadcasting.
Parameters
----------
axis : Vector3d or array_like, optional
The axis of rotation. Defaults to the z-vector.
angle : array_like, optional
The angle of rotation, in radians.
Returns
-------
Vector3d
A new vector with entries rotated.
Examples
--------
>>> from math import pi
>>> v = Vector3d((0, 1, 0))
>>> axis = Vector3d((0, 0, 1))
>>> angles = [0, pi/4, pi/2, 3*pi/4, pi]
>>> v.rotate(axis=axis, angle=angles)
"""
# Import here to avoid circular import
from orix.quaternion import Rotation
from orix.vector.neo_euler import AxAngle
axis = Vector3d.zvector() if axis is None else axis
angle = 0 if angle is None else angle
q = Rotation.from_neo_euler(AxAngle.from_axes_angles(axis, angle))
return q * self
def test_get_orientation_similarity_map(self):
s = nickel_ebsd_small()
s_dict1 = EBSD(s.data.reshape(-1, 60, 60))
s_dict2 = EBSD(s.data.reshape(-1, 60, 60))
n_patterns = s_dict1.axes_manager.navigation_size
s_dict1._xmap = CrystalMap(Rotation(np.zeros((n_patterns, 4))))
s_dict2._xmap = CrystalMap(Rotation(np.zeros((n_patterns, 4))))
s_dict1.xmap.phases[0].name = "a"
s_dict2.xmap.phases[0].name = "b"
sd = StaticPatternMatching([s_dict1, s_dict2])
res = sd(s, keep_n=1, get_orientation_similarity_map=True)
xmap1, _ = res
assert np.allclose(xmap1.scores, 1)
assert np.all(["osm" in xmap.prop for xmap in res])
def test_orientation_similarity_map(self):
xmap = CrystalMap(
rotations=Rotation(np.zeros((100, 4))),
prop={"simulation_indices": np.tile(np.arange(5), (100, 1))},
x=np.tile(np.arange(10), 10),
y=np.tile(np.arange(10), 10),
)
assert np.allclose(orientation_similarity_map(xmap), np.ones((10, 10)))
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_get_patterns_dtype(self):
r = Rotation.identity()
mp = nickel_ebsd_master_pattern_small(projection="lambert")
dtype_out = np.dtype("float64")
pattern = mp.get_patterns(rotations=r,
detector=self.detector,
energy=20,
dtype_out=dtype_out)
assert pattern.data.dtype == dtype_out
def test_n_best_too_great(self):
xmap = CrystalMap(
rotations=Rotation(np.zeros((100, 4))),
prop={"simulation_indices": np.ones((100, 5))},
x=np.tile(np.arange(10), 10),
y=np.tile(np.arange(10), 10),
)
with pytest.raises(ValueError,
match="n_best 6 cannot be greater than"):
orientation_similarity_map(xmap, n_best=6)
def compute_refine_orientation_projection_center_results(
results: list,
detector,
xmap: CrystalMap,
master_pattern,
):
"""Compute the results from
:meth:`~kikuchipy.signals.EBSD.refine_orientation_projection_center`
and return the :class:`~orix.crystal_map.CrystalMap` and
:class:`~kikuchipy.detectors.EBSDDetector`.
Parameters
----------
results
Results returned from `refine_orientation_projection_center()`,
which is a list of :class:`~dask.delayed.Delayed`.
detector : ~kikuchipy.detectors.EBSDDetector
Detector passed to `refine_orientation_projection_center()` to
obtain `results`.
xmap
Crystal map passed to `refine_orientation_projection_center()`
to obtain `results`.
master_pattern : ~kikuchipy.signals.EBSDMasterPattern
Master pattern passed to
`refine_orientation_projection_center()` to obtain `results`.
Returns
-------
xmap_refined : :class:`~orix.crystal_map.CrystalMap`
Crystal map with refined orientations and scores.
new_detector : :class:`~kikuchipy.detectors.EBSDDetector`
EBSD detector with refined projection center parameters.
"""
n_patterns = len(results)
nav_shape = xmap.shape
with ProgressBar():
print(
f"Refining {n_patterns} orientation(s) and projection center(s):",
file=sys.stdout,
)
computed_results = dask.compute(*results)
computed_results = np.array(computed_results)
# (n, score, phi1, Phi, phi2, PCx, PCy, PCz)
xmap_refined = CrystalMap(
rotations=Rotation.from_euler(computed_results[:, 1:4]),
phase_id=np.zeros(n_patterns),
x=xmap.x,
y=xmap.y,
phase_list=PhaseList(phases=master_pattern.phase),
prop=dict(scores=computed_results[:, 0]),
scan_unit=xmap.scan_unit,
)
new_detector = detector.deepcopy()
new_detector.pc = computed_results[:, 4:].reshape(nav_shape + (3, ))
return xmap_refined, new_detector
def test_signal_varying_dimensions(self, dummy_signal, slices,
desired_xmap_shape):
s = dummy_signal.inav[slices]
sig_shape = dummy_signal.axes_manager.signal_shape
s_dict1 = EBSD(dummy_signal.data.reshape((-1, ) + sig_shape))
n_sim = s_dict1.axes_manager.navigation_size
s_dict1._xmap = CrystalMap(Rotation(np.zeros((n_sim, 4))))
sd = StaticPatternMatching(s_dict1)
res = sd(s)
assert res.shape == desired_xmap_shape
def to_crystal_map(self):
"""Obtain a crystallographic map specifying the best matching phase and
orientation at each probe position with corresponding metrics.
Raises
-------
ValueError("Currently under development")
"""
raise ValueError("Currently under development")
_s = self.map(
crystal_from_vector_matching, inplace=False)
""" Gets phase, the easy bit """
phase_id = _s.isig[0].data.flatten()
""" Deals with the properties, hard coded as of v0.13 """
# need to invert an array of dicts into a dict of arrays
def _map_to_get_property(prop):
return d[prop]
# assume same properties at every point of the signal
key_list = []
for key in _s.inav[0,0].isig[2]:
key_list.append(key)
properties = {}
for key in key_list:
_key_signal = _s.isig[2].map(_map_to_get_property,prop=key,inplace=False)
properties[key] = _key_signal
""" Deal with the rotations """
def _map_for_alpha_beta_gamma(ix):
return z[ix]
alpha = _s.isig[1].map(_map_for_alpha_beta_gamma,ix=0,inplace=False)
beta = _s.isig[1].map(_map_for_alpha_beta_gamma,ix=1,inplace=False)
gamma = _s.isig[1].map(_map_for_alpha_beta_gamma,ix=2,inplace=False)
euler = np.vstack((alpha,beta,gamma)).T
rotations = Rotation.from_euler(euler,convention="bunge", direction="crystal2lab")
""" Gets navigation placements """
xy = np.indices(_s.data.shape[:2])
x = xy[1].flatten()
y = xy[0].flatten()
return CrystalMap(
rotations=rotations,
phase_id=phase_id,
x=x,
y=y,
prop=properties)
def test_from_n_best(self):
sim_idx_prop = "simulated_indices"
xmap = CrystalMap(
rotations=Rotation(np.zeros((100, 4))),
prop={sim_idx_prop: np.ones((100, 5))},
x=np.tile(np.arange(10), 10),
y=np.tile(np.arange(10), 10),
)
osm = orientation_similarity_map(xmap,
simulation_indices_prop=sim_idx_prop,
from_n_best=2)
assert osm.shape == (10, 10, 4)
def test_keep_n(self, n_rot_in, n_rot_out, keep_n):
s = nickel_ebsd_small()
s_dict = EBSD(np.random.random((n_rot_in, 60, 60)).astype(np.float32))
s_dict._xmap = CrystalMap(Rotation(np.zeros((n_rot_in, 4))))
sd = StaticPatternMatching(s_dict)
xmap = sd(s)
assert xmap.rotations_per_point == n_rot_out
xmap2 = sd(s, keep_n=keep_n)
assert xmap2.rotations_per_point == keep_n
def test_n_slices_input(self, dummy_signal):
sig_shape = dummy_signal.axes_manager.signal_shape
n_px = np.prod(sig_shape)
n_sim = 13500 + 1
rand_data = (np.random.randint(
0, 255,
n_sim * n_px).reshape((n_sim, ) + sig_shape).astype(np.uint8))
s_dict1 = EBSD(rand_data)
s_dict1._xmap = CrystalMap(Rotation(np.zeros((n_sim, 4))))
sd = StaticPatternMatching(s_dict1)
with replace_stdin(io.StringIO("y")):
res = sd(dummy_signal, n_slices=1)
assert isinstance(res, CrystalMap)
with replace_stdin(io.StringIO("n")):
res = sd(dummy_signal, n_slices=1)
assert res is None
def test_simulated_patterns_xmap_detector(self):
mp = nickel_ebsd_master_pattern_small(projection="lambert")
r = Rotation.from_euler([[0, 0, 0], [0, np.pi / 2, 0]])
detector = EBSDDetector(
shape=(60, 60),
pc=[0.5, 0.5, 0.5],
sample_tilt=70,
convention="tsl",
)
s = mp.get_patterns(rotations=r, detector=detector, energy=20)
assert np.allclose(s.xmap.rotations.to_euler(), r.to_euler())
assert s.xmap.phases.names == [mp.phase.name]
assert s.xmap.phases[0].point_group.name == mp.phase.point_group.name
assert s.detector.shape == detector.shape
assert np.allclose(s.detector.pc, detector.pc)
assert s.detector.sample_tilt == detector.sample_tilt
async def preview_dictionary(req: DictionaryIndexingIn):
if req.ebsd_info.uid not in kp_signals:
raise HTTPException(status_code=404, detail="Patterns not found")
s = kp_signals[req.ebsd_info.uid]
detector = kp.detectors.EBSDDetector(
shape=s.axes_manager.signal_shape[::-1],
pc=req.detector.pc,
sample_tilt=req.detector.sample_tilt,
convention=req.detector.pc_convention,
tilt=req.detector.camera_tilt,
)
res = PreviewDictionary(patterns=[])
if req.preview_angles:
euler = np.array(req.preview_angles)
else:
euler = np.array([0.0, 0.0, 0.0])
for mp_req in req.masterpatterns:
mp = kp.load(
mp_req.filepath,
projection=mp_req.projection,
hemisphere="both",
energy=mp_req.energy,
)
sim = mp.get_patterns(
rotations=Rotation.from_euler(np.deg2rad(euler)),
detector=detector,
energy=mp_req.energy,
compute=True,
)
svg_string = io.StringIO()
plt.figure()
plt.imshow(sim.data[0], cmap="gray")
plt.title(
f"{mp.phase.name.capitalize()}\n($\phi_1, \Phi, \phi_2)$ = {np.array_str(euler, precision=1)}"
)
plt.axis("off")
plt.savefig(svg_string,
format="svg",
bbox_inches="tight",
transparent=True)
svg_string.seek(0)
res.patterns.append(svg_string.getvalue())
return res
def test_get_patterns_chunk(self):
r = Rotation.from_euler(((0, 0, 0), (1, 1, 1), (2, 2, 2)))
dc = _get_direction_cosines(self.detector)
mpn = np.empty((1001, 1001))
mps = mpn
npx = 1001
npy = npx
out = _get_patterns_chunk(
rotations_array=r.data,
dc=dc,
master_north=mpn,
master_south=mps,
npx=npx,
npy=npy,
scale=(npx - 1) / 2,
rescale=False,
)
assert out.shape == r.shape + dc.shape
def compute_refine_orientation_results(results: list, xmap: CrystalMap,
master_pattern):
"""Compute the results from
:meth:`~kikuchipy.signals.EBSD.refine_orientation` and return the
:class:`~orix.crystal_map.CrystalMap`.
Parameters
----------
results
Results returned from `refine_orientation()`, which is a list of
:class:`~dask.delayed.Delayed`.
xmap
Crystal map passed to `refine_orientation()` to obtain
`results`.
master_pattern : ~kikuchipy.signals.EBSDMasterPattern
Master pattern passed to `refine_orientation()` to obtain
`results`.
Returns
-------
refined_xmap : :class:`~orix.crystal_map.CrystalMap`
Crystal map with refined orientations and scores.
"""
n_patterns = len(results)
with ProgressBar():
print(f"Refining {n_patterns} orientation(s):", file=sys.stdout)
computed_results = dask.compute(*results)
# (n, score, phi1, Phi, phi2)
computed_results = np.array(computed_results)
xmap_refined = CrystalMap(
rotations=Rotation.from_euler(computed_results[:, 1:]),
phase_id=np.zeros(n_patterns),
x=xmap.x,
y=xmap.y,
phase_list=PhaseList(phases=master_pattern.phase),
prop=dict(scores=computed_results[:, 0]),
scan_unit=xmap.scan_unit,
)
return xmap_refined
def test_project_patterns_from_master_pattern(self):
"""Make sure the Numba function is covered."""
r = Rotation.from_euler(((0, 0, 0), (1, 1, 1), (2, 2, 2)))
dc = _get_direction_cosines_for_single_pc_from_detector(self.detector)
npx = npy = 101
mpn = mps = np.zeros((npy, npx))
patterns = _project_patterns_from_master_pattern.py_func(
rotations=r.data,
direction_cosines=dc,
master_north=mpn,
master_south=mps,
npx=npx,
npy=npy,
scale=float((npx - 1) / 2),
dtype_out=mpn.dtype,
rescale=False,
# Aren't used
out_min=1,
out_max=2,
)
assert patterns.shape == r.shape + dc.shape[:-1]
def test_return_merged_crystal_map(self, return_merged_xmap,
desired_n_xmaps_out):
s = nickel_ebsd_small()
s_dict1 = EBSD(s.data.reshape(-1, 60, 60))
s_dict2 = s_dict1.deepcopy()
n_patterns = s_dict1.axes_manager.navigation_size
s_dict1._xmap = CrystalMap(Rotation(np.zeros((n_patterns, 4))))
s_dict2._xmap = s_dict1.xmap.deepcopy()
s_dict1.xmap.phases[0].name = "a"
s_dict2.xmap.phases[0].name = "b"
sd = StaticPatternMatching([s_dict1, s_dict2])
res1 = sd(s, return_merged_crystal_map=return_merged_xmap)
assert len(res1) == desired_n_xmaps_out
sd.dictionaries.pop(-1)
res2 = sd(s, return_merged_crystal_map=True)
assert isinstance(res2, CrystalMap)
res3 = sd(s)
assert isinstance(res3, CrystalMap)
def test_get_patterns(self):
# Ni Test
EMSOFT_EBSD_FILE = os.path.join(
DIR_PATH, "../../data/emsoft_ebsd/EBSD_TEST_Ni.h5")
emsoft_key = load(EMSOFT_EBSD_FILE)
emsoft_key = emsoft_key.data[0]
angles = np.array((120, 45, 60))
r = Rotation.from_euler(np.radians(angles))
kp_mp = nickel_ebsd_master_pattern_small(projection="lambert",
hemisphere="both")
kp_pattern = kp_mp.get_patterns(rotations=r,
detector=self.detector,
energy=20,
dtype_out=np.uint8)
kp_pat = kp_pattern.data[0].compute()
ncc1 = ncc(kp_pat, emsoft_key)
ndp1 = ndp(kp_pat, emsoft_key)
assert ncc1 >= 0.935
assert ndp1 >= 0.935
detector_shape = self.detector.shape
r2 = Rotation.from_euler(((0, 0, 0), (1, 1, 1), (2, 2, 2)))
mp_a = EBSDMasterPattern(np.zeros((2, 10, 11, 11)))
print(mp_a.axes_manager)
mp_a.axes_manager[0].name = "hemisphere"
mp_a.axes_manager[1].name = "energy"
mp_a.projection = "lambert"
mp_a.phase = Phase("Ni", 225)
out_a = mp_a.get_patterns(r2, self.detector, 5)
assert isinstance(out_a, LazyEBSD)
desired_data_shape = (3, ) + detector_shape[::-1]
assert out_a.axes_manager.shape == desired_data_shape
mp_b = EBSDMasterPattern(np.zeros((10, 11, 11)))
mp_b.axes_manager[0].name = "energy"
mp_b.projection = "lambert"
mp_b.phase = Phase("Ni", 225)
out_b = mp_b.get_patterns(r2, self.detector, 5)
assert isinstance(out_b, LazyEBSD)
assert out_b.axes_manager.shape == desired_data_shape
mp_c = EBSDMasterPattern(np.zeros((11, 11)))
mp_c.projection = "lambert"
mp_c.phase = Phase("Ni", 225)
out_c = mp_c.get_patterns(r2, self.detector, 5)
out_c_2 = mp_c.get_patterns(r2, self.detector, 5, compute=True)
assert isinstance(out_c, LazyEBSD)
assert isinstance(out_c_2, EBSD)
assert out_c.axes_manager.shape == desired_data_shape
mp_c2 = EBSDMasterPattern(np.zeros((11, 11)))
mp_c2.projection = "lambert"
mp_c2.phase = Phase("!Ni", 220)
with pytest.raises(AttributeError):
mp_c2.get_patterns(r2, self.detector, 5)
mp_d = EBSDMasterPattern(np.zeros((2, 11, 11)))
with pytest.raises(NotImplementedError):
mp_d.get_patterns(r2, self.detector, 5)
mp_e = EBSDMasterPattern(np.zeros((10, 11, 11)))
mp_e.axes_manager[0].name = "energy"
mp_e.projection = "lambert"
mp_e.phase = Phase("!Ni", 220)
with pytest.raises(AttributeError):
mp_e.get_patterns(r2, self.detector, 5)
# More than one Projection center is currently not supported so
# it should fail
d2 = EBSDDetector(
shape=(10, 10),
px_size=50,
pc=((0, 0, 15000), (0, 0, 15000)),
convention="emsoft4",
tilt=0,
sample_tilt=70,
)
with pytest.raises(NotImplementedError):
mp_c.get_patterns(r2, d2, 5)
def _get_patterns_chunk(
rotations_array: np.ndarray,
dc: Vector3d,
master_north: np.ndarray,
master_south: np.ndarray,
npx: int,
npy: int,
scale: Union[int, float],
rescale: bool,
dtype_out: Optional[type] = np.float32,
) -> np.ndarray:
"""Get the EBSD patterns on the detector for each rotation in the
chunk. Each pattern is found by a bi-quadratic interpolation of the
master pattern as described in EMsoft.
Parameters
----------
rotations_array
Array of rotations of shape (..., 4) for a given chunk in
quaternions.
dc
Direction cosines unit vector between detector and sample.
master_north
Northern hemisphere of the master pattern.
master_south
Southern hemisphere of the master pattern.
npx
Number of pixels in the x-direction on the master pattern.
npy
Number of pixels in the y-direction on the master pattern.
scale
Factor to scale up from square Lambert projection to the master
pattern.
rescale
Whether to call rescale_intensities() or not.
dtype_out
Data type of the returned patterns, by default np.float32.
Returns
-------
numpy.ndarray
3D or 4D array with simulated patterns.
"""
rotations = Rotation(rotations_array)
rotations_shape = rotations_array.shape[:-1]
simulated = np.empty(shape=rotations_shape + dc.shape, dtype=dtype_out)
for i in np.ndindex(rotations_shape):
rotated_dc = rotations[i] * dc
(
nii,
nij,
niip,
nijp,
di,
dj,
dim,
djm,
) = _get_lambert_interpolation_parameters(
rotated_direction_cosines=rotated_dc, npx=npx, npy=npy, scale=scale,
)
pattern = np.where(
rotated_dc.z >= 0,
(
master_north[nii, nij] * dim * djm
+ master_north[niip, nij] * di * djm
+ master_north[nii, nijp] * dim * dj
+ master_north[niip, nijp] * di * dj
),
(
master_south[nii, nij] * dim * djm
+ master_south[niip, nij] * di * djm
+ master_south[nii, nijp] * dim * dj
+ master_south[niip, nijp] * di * dj
),
)
if rescale:
pattern = rescale_intensity(pattern, dtype_out=dtype_out)
simulated[i] = pattern
return simulated
def file_reader(
filename: str,
scan_size: Union[None, int, Tuple[int, ...]] = None,
lazy: bool = False,
**kwargs,
) -> List[dict]:
"""Read dynamically simulated electron backscatter diffraction
patterns from EMsoft's format produced by their EMEBSD.f90 program.
Parameters
----------
filename
Full file path of the HDF file.
scan_size
Scan size in number of patterns in width and height.
lazy
Open the data lazily without actually reading the data from disk
until requested. Allows opening datasets larger than available
memory. Default is False.
kwargs :
Keyword arguments passed to h5py.File.
Returns
-------
signal_dict_list: list of dicts
Data, axes, metadata and original metadata.
"""
mode = kwargs.pop("mode", "r")
f = File(filename, mode=mode, **kwargs)
_check_file_format(f)
# Read original metadata
omd = hdf5group2dict(f["/"],
data_dset_names=["EBSDPatterns"],
recursive=True)
# Set metadata and original metadata dictionaries
md = _get_metadata(omd)
md.update({
"Signal": {
"signal_type": "EBSD",
"record_by": "image"
},
"General": {
"title": f.filename.split("/")[-1].split(".")[0],
"original_filename": f.filename.split("/")[-1],
},
})
scan = {"metadata": md, "original_metadata": omd}
# Read patterns
dataset = f["EMData/EBSD/EBSDPatterns"]
if lazy:
chunks = "auto" if dataset.chunks is None else dataset.chunks
patterns = da.from_array(dataset, chunks=chunks)
else:
patterns = np.asanyarray(dataset)
# Reshape data if desired
sy = omd["NMLparameters"]["EBSDNameList"]["numsy"]
sx = omd["NMLparameters"]["EBSDNameList"]["numsx"]
if scan_size is not None:
if isinstance(scan_size, int):
new_shape = (scan_size, sy, sx)
else:
new_shape = scan_size + (sy, sx)
patterns = patterns.reshape(new_shape)
scan["data"] = patterns
# Set navigation and signal axes
pixel_size = omd["NMLparameters"]["EBSDNameList"]["delta"]
ndim = patterns.ndim
units = ["px", "um", "um"]
names = ["x", "dy", "dx"]
scales = np.array([1, pixel_size, pixel_size])
if ndim == 4:
units = ["px"] + units
names = ["y"] + names
scales = np.append([1], scales)
scan["axes"] = [{
"size": patterns.shape[i],
"index_in_array": i,
"name": names[i],
"scale": scales[i],
"offset": 0,
"units": units[i],
} for i in range(patterns.ndim)]
# Get crystal map
phase = _crystaldata2phase(hdf5group2dict(f["CrystalData"]))
xtal_fname = f["EMData/EBSD/xtalname"][()][0].decode().split("/")[-1]
phase.name, _ = os.path.splitext(xtal_fname)
scan["xmap"] = CrystalMap(
rotations=Rotation.from_euler(f["EMData/EBSD/EulerAngles"][()]),
phase_list=PhaseList(phase),
)
if not lazy:
f.close()
return [scan]
def test_results_dict_to_crystal_map(test_library_phases_multi, test_lib_gen):
"""Test getting a :class:`orix.crystal_map.CrystalMap` from returns
from :func:`index_dataset_with_template_rotation`.
"""
# Map and signal shapes
nav_shape = (2, 3)
sig_shape = (80, 80)
test_set = np.zeros(nav_shape + sig_shape)
# Diffraction conditions
diff_lib = test_lib_gen.get_diffraction_library(
test_library_phases_multi,
calibration=0.015,
reciprocal_radius=1.18,
half_shape=tuple(np.array(sig_shape) // 2),
with_direct_beam=False,
)
# Simulate multi-phase results
phase_id = np.zeros(nav_shape, dtype=int)
phase_id[:, [0, 2]] = 1
phase_names = list(diff_lib.keys())
# Simulate patterns
sim_kwargs = dict(size=sig_shape[0], sigma=4)
for idx in np.ndindex(*nav_shape):
i = phase_id[idx]
j = int(idx[1] / 2)
test_pattern = diff_lib[phase_names[i]]["simulations"][j].\
get_diffraction_pattern(**sim_kwargs)
test_set[idx] = test_pattern
# Perform template matching
n_best = 3
results, phase_dict = index_dataset_with_template_rotation(
Signal2D(test_set),
diff_lib,
phases=phase_names,
n_best=n_best,
)
# Extract various results once
phase_id = results["phase_index"].reshape((-1, n_best))
ori = np.deg2rad(results["orientation"].reshape((-1, n_best, 3)))
# Property names in `results`
prop_names = ["correlation", "mirrored_template", "template_index"]
# Only get the bast match when multiple phases match best to some
# patterns
xmap = results_dict_to_crystal_map(results,
phase_dict,
diffraction_library=diff_lib)
assert np.allclose(xmap.phase_id, phase_id[:, 0])
assert xmap.rotations_per_point == 1
assert xmap.phases.names == phase_names
assert (xmap.phases.structures[0].lattice.abcABG() ==
test_library_phases_multi.structures[0].lattice.abcABG())
# Raise warning when a property is not present as expected
del results[prop_names[0]]
with pytest.warns(UserWarning,
match=f"Property '{prop_names[0]}' was expected"):
xmap2 = results_dict_to_crystal_map(results,
phase_dict,
diffraction_library=diff_lib)
assert list(xmap2.prop.keys()) == prop_names[1:]
# Raise error when trying to access a best match which isn't
# available
with pytest.raises(ValueError, match="`index` cannot be higher than 2"):
_ = results_dict_to_crystal_map(results, phase_dict, index=3)
# Get second best match
i = 1
xmap3 = results_dict_to_crystal_map(results, phase_dict, index=i)
assert xmap3.rotations_per_point == 1
assert np.allclose(xmap3.phase_id, phase_id[:, i])
assert np.allclose(xmap3.rotations.data,
Rotation.from_euler(ori[:, i]).data)
assert np.allclose(xmap3.prop[prop_names[1]],
results[prop_names[1]][:, :, i].flatten())
# Make map single-phase and get all matches per point
results["phase_index"][..., 0] = 0
xmap4 = results_dict_to_crystal_map(results, phase_dict)
assert np.all(xmap4.phase_id == 0)
assert xmap4.phases.names[0] == phase_names[0]
assert xmap4.rotations_per_point == 3
# Get only best match even though map is single-phase
i = 0
xmap5 = results_dict_to_crystal_map(results, phase_dict, index=i)
assert xmap5.rotations_per_point == 1
assert np.allclose(xmap5.rotations.data,
Rotation.from_euler(ori[:, i]).data)
assert np.allclose(xmap5.prop[prop_names[1]],
results[prop_names[1]][:, :, i].flatten())
def test_get_patterns_navigation_shape(self, nav_shape):
mp = nickel_ebsd_master_pattern_small(projection="lambert")
r = Rotation(np.random.uniform(low=0, high=1, size=nav_shape + (4, )))
detector = EBSDDetector(shape=(60, 60))
sim = mp.get_patterns(rotations=r, detector=detector, energy=20)
assert sim.axes_manager.navigation_shape[::-1] == nav_shape
def test_get_patterns(self):
emsoft_key = load(EMSOFT_EBSD_FILE)
emsoft_key = emsoft_key.data[0]
r = Rotation.from_euler(np.radians([120, 45, 60]))
mp1 = nickel_ebsd_master_pattern_small(projection="lambert",
hemisphere="both")
kp_pattern = mp1.get_patterns(rotations=r,
detector=self.detector,
energy=20,
dtype_out=emsoft_key.dtype)
kp_pat = kp_pattern.data[0].compute()
assert kp_pat.dtype == emsoft_key.dtype
ncc = NormalizedCrossCorrelationMetric(1, 1)
ncc1 = ncc(kp_pat, emsoft_key)
assert ncc1 >= 0.935
ndp = NormalizedDotProductMetric(1, 1)
ndp1 = ndp(kp_pat, emsoft_key)
assert ndp1 >= 0.935
detector_shape = self.detector.shape
r2 = Rotation.from_euler(((0, 0, 0), (1, 1, 1), (2, 2, 2)))
mp2 = kp.signals.EBSDMasterPattern(np.zeros((2, 10, 11, 11)))
mp2.axes_manager[0].name = "hemisphere"
mp2.axes_manager[1].name = "energy"
mp2.projection = "lambert"
mp2.phase = Phase("Ni", 225)
out2 = mp2.get_patterns(r2, self.detector, 5)
assert isinstance(out2, kp.signals.LazyEBSD)
desired_data_shape = (3, ) + detector_shape[::-1]
assert out2.axes_manager.shape == desired_data_shape
mp3 = kp.signals.EBSDMasterPattern(np.zeros((10, 11, 11)))
mp3.axes_manager[0].name = "energy"
mp3.projection = "lambert"
mp3.phase = Phase("Ni", 225)
out3 = mp3.get_patterns(r2, self.detector, 5)
assert isinstance(out3, kp.signals.LazyEBSD)
assert out3.axes_manager.shape == desired_data_shape
mp4 = kp.signals.EBSDMasterPattern(np.zeros((11, 11)))
mp4.projection = "lambert"
mp4.phase = Phase("Ni", 225)
out41 = mp4.get_patterns(r2, self.detector, 5)
out42 = mp4.get_patterns(r2, self.detector, 5, compute=True)
assert isinstance(out41, kp.signals.LazyEBSD)
assert isinstance(out42, kp.signals.EBSD)
assert out41.axes_manager.shape == desired_data_shape
mp5 = kp.signals.EBSDMasterPattern(np.zeros((11, 11)))
mp5.projection = "lambert"
mp5.phase = Phase("!Ni", 220)
with pytest.raises(AttributeError):
_ = mp5.get_patterns(r2, self.detector, 5)
mp6 = kp.signals.EBSDMasterPattern(np.zeros((2, 11, 11)))
with pytest.raises(AttributeError,
match="Master pattern `phase` attribute"):
_ = mp6.get_patterns(r2, self.detector, 5)
mp7 = kp.signals.EBSDMasterPattern(np.zeros((10, 11, 11)))
mp7.axes_manager[0].name = "energy"
mp7.projection = "lambert"
mp7.phase = Phase("!Ni", 220)
with pytest.raises(AttributeError,
match="For point groups without inversion"):
_ = mp7.get_patterns(r2, self.detector, 5)
# More than one PC is currently not supported so should fail
d2 = kp.detectors.EBSDDetector(
shape=(10, 10),
px_size=50,
pc=((0, 0, 15000), (0, 0, 15000)),
convention="emsoft4",
sample_tilt=70,
)
with pytest.raises(NotImplementedError):
_ = mp4.get_patterns(r2, d2, 5)