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_phase2dict_spacegroup(self):
"""Space group is written to dict as an int or "None"."""
sg100 = 100
phase = Phase(space_group=sg100)
phase_dict1 = phase2dict(phase)
assert phase_dict1["space_group"] == sg100
sg200 = GetSpaceGroup(200)
phase.space_group = sg200
phase_dict2 = phase2dict(phase)
assert phase_dict2["space_group"] == sg200.number
phase.space_group = None
phase_dict3 = phase2dict(phase)
assert phase_dict3["space_group"] == "None"
def test_symmetrise(self):
assert np.allclose(
ReciprocalLatticePoint(phase=Phase(space_group=225), hkl=[1, 1, 1])
.symmetrise()
.hkl.data,
np.array(
[
[1, 1, 1],
[-1, 1, 1],
[-1, -1, 1],
[1, -1, 1],
[1, -1, -1],
[1, 1, -1],
[-1, 1, -1],
[-1, -1, -1],
]
),
)
rlp2, multiplicity = ReciprocalLatticePoint(
phase=Phase(space_group=186), hkl=[2, 2, 0]
).symmetrise(return_multiplicity=True)
assert multiplicity == 12
assert np.allclose(
rlp2.hkl.data,
[
[2, 2, 0],
[-2, 0, 0],
[0, -2, 0],
[-2, -2, 0],
[2, 0, 0],
[0, 2, 0],
[-2, 2, 0],
[0, -2, 0],
[2, 0, 0],
[2, -2, 0],
[0, 2, 0],
[-2, 0, 0],
],
)
rlp3 = ReciprocalLatticePoint(
phase=Phase(space_group=186), hkl=[2, 2, 0]
).symmetrise(antipodal=False)
assert np.allclose(
rlp3.hkl.data,
[[2, 2, 0], [-2, 0, 0], [0, -2, 0], [-2, -2, 0], [2, 0, 0], [0, 2, 0]],
)
def nickel_phase():
return Phase(
name="nickel",
space_group=225,
structure=Structure(
lattice=Lattice(3.5236, 3.5236, 3.5236, 90, 90, 90),
atoms=[Atom(xyz=[0, 0, 0], atype="Ni", Uisoequiv=0.006332)],
),
)
def __init__(self, *args, **kwargs):
"""Create an :class:`~kikuchipy.signals.EBSDMasterPattern`
object from a :class:`hyperspy.signals.Signal2D` or a
:class:`numpy.ndarray`.
"""
Signal2D.__init__(self, *args, **kwargs)
self.phase = kwargs.pop("phase", Phase())
self.projection = kwargs.pop("projection", None)
self.hemisphere = kwargs.pop("hemisphere", None)
def test_allowed_b_centering(self):
"""B centering will never fire since no diffpy.structure space group has
'B' first in the name.
"""
phase = Phase(space_group=15)
phase.space_group.short_name = "B"
rlp = ReciprocalLatticePoint(
phase=phase, hkl=[[1, 2, 2], [1, 1, -1], [1, 1, 2]]
)
assert np.allclose(rlp.allowed, [False, True, False])
def test_dict2phase_spacegroup(self):
"""Space group number int or None is properly parsed from a dict.
"""
phase1 = Phase(space_group=200)
phase_dict = phase2dict(phase1)
phase2 = dict2phase(phase_dict)
assert phase1.space_group.number == phase2.space_group.number
phase_dict.pop("space_group")
phase3 = dict2phase(phase_dict)
assert phase3.space_group is None
def __init__(self, *args, **kwargs):
"""Create an :class:`~kikuchipy.signals.EBSDMasterPattern`
instance from a :class:`hyperspy.signals.Signal2D` or a
:class:`numpy.ndarray`. See the docstring of
:class:`hyperspy.signal.BaseSignal` for optional input
parameters.
"""
Signal2D.__init__(self, *args, **kwargs)
self.phase = kwargs.pop("phase", Phase())
self.projection = kwargs.pop("projection", None)
self.hemisphere = kwargs.pop("hemisphere", None)
def ferrite_phase():
return Phase(
name="ferrite",
space_group=229,
structure=Structure(
lattice=Lattice(2.8665, 2.8665, 2.8665, 90, 90, 90),
atoms=[
Atom(xyz=[0, 0, 0], atype="Fe", Uisoequiv=0.006332),
Atom(xyz=[0.5, 0.5, 0.5], atype="Fe", Uisoequiv=0.006332),
],
),
)
def test_init_no_metadata(self):
s = EBSDMasterPattern(
np.zeros((2, 10, 11, 11)),
projection="lambert",
hemisphere="both",
phase=Phase("a"),
)
assert isinstance(s.phase, Phase)
assert s.phase.name == "a"
assert s.projection == "lambert"
assert s.hemisphere == "both"
def silicon_carbide_phase():
"""Silicon Carbide 4H polytype (hexagonal, space group 186)."""
return Phase(
space_group=186,
structure=Structure(
lattice=Lattice(3.073, 3.073, 10.053, 90, 90, 120),
atoms=[
Atom(atype="Si", xyz=[0, 0, 0]),
Atom(atype="Si", xyz=[0.33, 0.667, 0.25]),
Atom(atype="C", xyz=[0, 0, 0.188]),
Atom(atype="C", xyz=[0.333, 0.667, 0.438]),
],
),
)
def test_extra_phases(self, crystal_map, tmp_path, extra_phase_names):
crystal_map.phases.add_not_indexed()
for i, name in enumerate(extra_phase_names):
crystal_map.phases.add(Phase(name=name))
crystal_map[i].phase_id = crystal_map.phases.id_from_name(name)
fname = tmp_path / "test_extra_phases.ang"
save(fname, crystal_map)
xmap_reload = load(fname)
crystal_map.phases[0].name = "phase1"
assert np.allclose(xmap_reload.phase_id - 1, crystal_map.phase_id)
pl = crystal_map.phases
del pl[-1]
assert xmap_reload.phases.names == pl.names
def __init__(
self,
detector: EBSDDetector,
phase: Phase,
rotations: Rotation,
):
"""A generator storing necessary parameters to simulate
geometrical EBSD patterns.
Parameters
----------
detector
Detector describing the detector-sample geometry.
phase
A phase container with a crystal structure and a space and
point group describing the allowed symmetry operations.
rotations
Unit cell rotations to simulate patterns for. The
navigation shape of the resulting simulation is determined
from the rotations' shape, with a maximum dimension of 2.
Examples
--------
>>> from orix.crystal_map import Phase
>>> from orix.quaternion import Rotation
>>> from kikuchipy.detectors import EBSDDetector
>>> from kikuchipy.generators import EBSDSimulationGenerator
>>> det = EBSDDetector(
... shape=(60, 60), sample_tilt=70, pc=[0.5,] * 3
... )
>>> p = Phase(name="ni", space_group=225)
>>> p.structure.lattice.setLatPar(3.52, 3.52, 3.52, 90, 90, 90)
>>> simgen = EBSDSimulationGenerator(
... detector=det,
... phase=p,
... rotations=Rotation.from_euler([90, 45, 90])
... )
>>> simgen
EBSDSimulationGenerator (1,)
EBSDDetector (60, 60), px_size 1 um, binning 1, tilt 0, pc
(0.5, 0.5, 0.5)
<name: . space group: None. point group: None. proper point
group: None. color: tab:blue>
Rotation (1,)
"""
self.detector = detector.deepcopy()
self.phase = phase.deepcopy()
self.rotations = deepcopy(rotations)
def dict2phase(dictionary):
"""Get a :class:`~orix.crystal_map.phase_list.Phase` object from a
dictionary.
Parameters
----------
dictionary : dict
Dictionary with phase information.
Returns
-------
Phase
"""
dictionary = copy.deepcopy(dictionary)
structure = dict2structure(dictionary["structure"])
structure.title = dictionary["name"]
# TODO: Remove this check in v0.6.0, since space_group was introduced in v0.4.0
try:
space_group = dictionary["space_group"] # Either "None" or int
except KeyError: # v0.3.0
space_group = "None"
if space_group == "None":
space_group = None
else:
space_group = int(space_group)
# TODO: Remove this check in v0.6.0, since name change was introduced in v0.4.0
try:
point_group = dictionary["point_group"]
except KeyError: # v0.3.0
point_group = dictionary["symmetry"]
if point_group == "None":
point_group = None
return Phase(
name=dictionary["name"],
space_group=space_group,
point_group=point_group,
structure=structure,
color=dictionary["color"],
)
def _get_single_phase_xmap(
nav_shape,
rotations_per_point=5,
prop_names=["scores", "simulation_indices"],
name="a",
phase_id=0,
):
d, map_size = _get_spatial_array_dicts(nav_shape)
rot_idx = np.random.choice(np.arange(rotations.size),
map_size * rotations_per_point)
data_shape = (map_size, )
if rotations_per_point > 1:
data_shape += (rotations_per_point, )
d["rotations"] = rotations[rot_idx].reshape(*data_shape)
d["phase_id"] = np.ones(map_size) * phase_id
d["phase_list"] = PhaseList(Phase(name=name))
# Scores and simulation indices
d["prop"] = {
prop_names[0]: np.ones(data_shape, dtype=np.float32),
prop_names[1]: np.arange(np.prod(data_shape)).reshape(data_shape),
}
return CrystalMap(**d)
def _crystaldata2phase(dictionary: dict) -> Phase:
"""Return a :class:`~orix.crystal_map.Phase` object from a
dictionary with EMsoft CrystalData group content.
Parameters
----------
dictionary
Dictionary with phase information.
Returns
-------
Phase
"""
# TODO: Move this to orix.io.plugins.emsoft_h5ebsd as part of v0.6
# Get list of atoms
n_atoms = dictionary["Natomtypes"]
atom_data = dictionary["AtomData"]
atom_types = dictionary["Atomtypes"]
if n_atoms == 1:
atom_types = (atom_types, ) # Make iterable
atoms = []
for i in range(n_atoms):
# TODO: Convert atom type integer to element name, like Ni for 26
atoms.append(
Atom(
atype=atom_types[i],
xyz=atom_data[:3, i],
occupancy=atom_data[3, i],
Uisoequiv=atom_data[4, i] / (8 * np.pi**2) * 1e2, # Å^-2
))
# TODO: Use space group setting
return Phase(
space_group=int(dictionary["SpaceGroupNumber"]),
structure=Structure(
lattice=Lattice(*dictionary["LatticeParameters"].T), atoms=atoms),
)
def test_check_master_pattern_and_get_data(self):
axes = [
dict(name="hemisphere", size=2, scale=1),
dict(name="energy", size=5, offset=16, scale=1),
dict(name="dy", size=5, scale=1),
dict(name="dx", size=5, scale=1),
]
mp_data = np.random.rand(2, 5, 5, 5).astype(np.float64)
mp = kp.signals.EBSDMasterPattern(
mp_data,
axes=axes,
projection="lambert",
hemisphere="both",
phase=Phase("ni", 225),
)
(
mpn,
mps,
npx,
npy,
scale,
) = kp.indexing._refinement._refinement._check_master_pattern_and_get_data(
master_pattern=mp,
energy=20,
)
assert npx == mp_data.shape[3]
assert npy == mp_data.shape[2]
assert scale == (mp_data.shape[3] - 1) / 2
# Master patterns are rescaled
assert mpn.dtype == np.float32
assert not np.allclose(mpn, mp_data[0, -1])
assert not np.allclose(mps, mp_data[1, -1])
assert np.min(mpn) >= -1
assert np.max(mpn) <= 1
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)
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)
class EBSDMasterPattern(CommonImage, Signal2D):
"""Simulated Electron Backscatter Diffraction (EBSD) master pattern.
This class extends HyperSpy's Signal2D class for EBSD master
patterns. Methods inherited from HyperSpy can be found in the
HyperSpy user guide. See the docstring of
:class:`hyperspy.signal.BaseSignal` for a list of additional
attributes.
Attributes
----------
projection : str
Which projection the pattern is in, "stereographic" or
"lambert".
hemisphere : str
Which hemisphere the data contains: "north", "south" or "both".
phase : orix.crystal_map.phase_list.Phase
Phase describing the crystal structure used in the master
pattern simulation.
"""
_signal_type = "EBSDMasterPattern"
_alias_signal_types = ["ebsd_master_pattern", "master_pattern"]
_lazy = False
phase = Phase()
projection = None
hemisphere = None
def __init__(self, *args, **kwargs):
"""Create an :class:`~kikuchipy.signals.EBSDMasterPattern`
object from a :class:`hyperspy.signals.Signal2D` or a
:class:`numpy.ndarray`.
"""
Signal2D.__init__(self, *args, **kwargs)
self.phase = kwargs.pop("phase", Phase())
self.projection = kwargs.pop("projection", None)
self.hemisphere = kwargs.pop("hemisphere", None)
def get_patterns(
self,
rotations: Rotation,
detector: EBSDDetector,
energy: Union[int, float],
dtype_out: type = np.float32,
compute: bool = False,
**kwargs,
) -> Union[EBSD, LazyEBSD]:
"""Return a dictionary of EBSD patterns projected onto a
detector from a master pattern in the square Lambert
projection :cite:`callahan2013dynamical`, for a set of crystal
rotations relative to the EDAX TSL sample reference frame (RD,
TD, ND) and a fixed detector-sample geometry.
Parameters
----------
rotations
Set of crystal rotations to get patterns from. The shape of
this object, a maximum of two dimensions, determines the
navigation shape of the output signal.
detector
EBSD detector describing the detector dimensions and the
detector-sample geometry with a single, fixed
projection/pattern center.
energy
Acceleration voltage, in kV, used to simulate the desired
master pattern to create a dictionary from.
dtype_out
Data type of the returned patterns, by default np.float32.
compute
Whether to return a lazy result, by default False. For more
information see :func:`~dask.array.Array.compute`.
kwargs
Keyword arguments passed to
:func:`~kikuchipy.signals.util.get_chunking` to control the
number of chunks the dictionary creation and the output data
array is split into. Only `chunk_shape`, `chunk_bytes` and
`dtype_out` (to `dtype`) are passed on.
Returns
-------
EBSD or LazyEBSD
Signal with navigation and signal shape equal to the
rotation object's and detector shape, respectively.
Notes
-----
If the master pattern phase has a non-centrosymmetric point
group, both the northern and southern hemispheres must be
provided. For more details regarding the reference frame visit
the reference frame user guide at:
https://kikuchipy.org/en/latest/reference_frames.html.
"""
if self.projection != "lambert":
raise NotImplementedError(
"Master pattern must be in the square Lambert projection"
)
if len(detector.pc) > 1:
raise NotImplementedError(
"Detector must have exactly one projection center"
)
# Get suitable chunks when iterating over the rotations. The
# signal axes are not chunked.
nav_shape = rotations.shape
nav_dim = len(nav_shape)
if nav_dim > 2:
raise ValueError(
"The rotations object can only have one or two dimensions, but "
f"an object with {nav_dim} was passed"
)
data_shape = nav_shape + detector.shape
chunks = get_chunking(
data_shape=data_shape,
nav_dim=nav_dim,
sig_dim=len(detector.shape),
chunk_shape=kwargs.pop("chunk_shape", None),
chunk_bytes=kwargs.pop("chunk_bytes", None),
dtype=dtype_out,
)
# Get the master pattern arrays created by a desired energy
north_slice = ()
if "energy" in [i.name for i in self.axes_manager.navigation_axes]:
energies = self.axes_manager["energy"].axis
north_slice += ((np.abs(energies - energy)).argmin(),)
south_slice = north_slice
if self.hemisphere == "both":
north_slice = (0,) + north_slice
south_slice = (1,) + south_slice
elif not self.phase.point_group.contains_inversion:
raise AttributeError(
"For crystals of point groups without inversion symmetry, like "
f"the current {self.phase.point_group.name}, both hemispheres "
"must be present in the master pattern signal"
)
master_north = self.data[north_slice]
master_south = self.data[south_slice]
# Whether to rescale pattern intensities after projection
rescale = False
if dtype_out != np.float32:
rescale = True
# Get direction cosines for each detector pixel relative to the
# source point
dc = _get_direction_cosines(detector)
# Get dask array from rotations
r_da = da.from_array(rotations.data, chunks=chunks[:nav_dim] + (-1,))
# Which axes to drop and add when iterating over the rotations
# dask array to produce the EBSD signal array, i.e. drop the
# (4,)-shape quaternion axis and add detector shape axes, e.g.
# (60, 60)
if nav_dim == 1:
drop_axis = 1
new_axis = (1, 2)
else: # nav_dim == 2
drop_axis = 2
new_axis = (2, 3)
# Project simulated patterns onto detector
npx, npy = self.axes_manager.signal_shape
scale = (npx - 1) / 2
simulated = r_da.map_blocks(
_get_patterns_chunk,
dc=dc,
master_north=master_north,
master_south=master_south,
npx=npx,
npy=npy,
scale=scale,
rescale=rescale,
dtype_out=dtype_out,
drop_axis=drop_axis,
new_axis=new_axis,
chunks=chunks,
dtype=dtype_out,
)
# Add crystal map and detector to keyword arguments
kwargs = dict(
xmap=CrystalMap(
phase_list=PhaseList(self.phase), rotations=rotations,
),
detector=detector,
)
# Specify navigation and signal axes for signal initialization
names = ["y", "x", "dy", "dx"]
scales = np.ones(4)
ndim = simulated.ndim
if ndim == 3:
names = names[1:]
scales = scales[1:]
axes = [
dict(
size=data_shape[i],
index_in_array=i,
name=names[i],
scale=scales[i],
offset=0.0,
units="px",
)
for i in range(ndim)
]
if compute:
with ProgressBar():
print(
f"Creating a dictionary of {nav_shape} simulated patterns:",
file=sys.stdout,
)
patterns = simulated.compute()
out = EBSD(patterns, axes=axes, **kwargs)
else:
out = LazyEBSD(simulated, axes=axes, **kwargs)
return out
def nickel_phase(nickel_structure):
"""A orix.crystal_map.Phase with a Nickel crystal structure and
symmetry operations.
"""
return Phase(name="ni", structure=nickel_structure, space_group=225)
class TestCrystallographicComputations:
@pytest.mark.parametrize(
"hkl, desired_uvw",
[
([1, 1, 1], np.array([]).reshape((0, 3))),
([[1, 1, 1], [2, 2, 2]], np.array([]).reshape((0, 3))),
([[1, 1, 1], [1, 1, -1]], [[-1, 1, 0], [1, -1, 0]]),
],
)
def test_get_uvw_from_hkl(self, hkl, desired_uvw):
"""Desired uvw from the cross product of hkl."""
assert np.allclose(_get_uvw_from_hkl(hkl), desired_uvw)
@pytest.mark.parametrize(
("hkl, desired_family_keys, desired_family_values, desired_indices, "
"reduce"),
[
([1, 1, 1], [[1, 1, 1]], [1, 1, 1], [0], False),
([1, 1, 1], [[1, 1, 1]], [1, 1, 1], [0], True),
(
[[1, 1, 1], [2, 0, 0]],
[[1, 1, 1], [2, 0, 0]],
[[[1, 1, 1]], [[2, 0, 0]]],
[[0], [1]],
False,
),
(
ReciprocalLatticePoint(phase=Phase(space_group=225),
hkl=[1, 1, 1]).symmetrise().hkl.data,
[1, 1, 1],
[[
[1, 1, 1],
[-1, 1, 1],
[-1, -1, 1],
[1, -1, 1],
[1, -1, -1],
[1, 1, -1],
[-1, 1, -1],
[-1, -1, -1],
]],
[np.arange(8)],
False,
),
(
ReciprocalLatticePoint(phase=Phase(space_group=225),
hkl=[[1, 1, 1], [2, 0, 0]
]).symmetrise().hkl.data,
[[1, 1, 1], [2, 0, 0]],
[
[
[1, 1, 1],
[-1, 1, 1],
[-1, -1, 1],
[1, -1, 1],
[1, -1, -1],
[1, 1, -1],
[-1, 1, -1],
[-1, -1, -1],
],
[
[2, 0, 0],
[0, 2, 0],
[-2, 0, 0],
[0, -2, 0],
[0, 0, 2],
[0, 0, -2],
],
],
[np.arange(8).tolist(),
np.arange(8, 14).tolist()],
False,
),
(
ReciprocalLatticePoint(phase=Phase(space_group=225),
hkl=[[1, 1, 1], [2, 2, 2]
]).symmetrise().hkl.data,
[1, 1, 1],
[[
[1, 1, 1],
[-1, 1, 1],
[-1, -1, 1],
[1, -1, 1],
[1, -1, -1],
[1, 1, -1],
[-1, 1, -1],
[-1, -1, -1],
[2, 2, 2],
[-2, 2, 2],
[-2, -2, 2],
[2, -2, 2],
[2, -2, -2],
[2, 2, -2],
[-2, 2, -2],
[-2, -2, -2],
]],
[np.arange(16)],
True,
),
],
)
def test_get_hkl_family(self, hkl, desired_family_keys,
desired_family_values, desired_indices, reduce):
"""Desired sets of families and indices."""
families, families_idx = _get_hkl_family(hkl, reduce=reduce)
for i, (k, v) in enumerate(families.items()):
assert np.allclose(k, desired_family_keys[i])
assert np.allclose(v, desired_family_values[i])
assert np.allclose(families_idx[k], desired_indices[i])
@pytest.mark.parametrize(
"highest_hkl, color_cycle, desired_hkl_colors",
[
([1, 1, 1], ["C0", "C1"], [[1, 1, 1], [0.12, 0.47, 0.71]]),
(
[2, 2, 2],
["g", "b"],
[
[[1, 1, 1], [0, 0.5, 0]],
[[2, 0, 0], [0, 0, 1]],
[[2, 2, 0], [0, 0.5, 0]],
[[2, 2, 2], [0, 0.5, 0]],
],
),
(
[2, 2, 2],
None,
[
[[1, 1, 1], [1, 0, 0]],
[[2, 0, 0], [1, 1, 0]],
[[2, 2, 0], [0, 1, 0]],
[[2, 2, 2], [1, 0, 0]],
],
),
],
)
def test_get_colors_for_allowed_bands(self, nickel_phase, highest_hkl,
color_cycle, desired_hkl_colors):
"""Desired colors for bands."""
hkl_colors = _get_colors_for_allowed_bands(phase=nickel_phase,
highest_hkl=highest_hkl,
color_cycle=color_cycle)
assert np.allclose(hkl_colors, desired_hkl_colors, atol=1e-2)
def test_get_colors_for_allowed_bands_999(self, nickel_phase):
"""Not passing `highest_hkl` works fine."""
hkl_colors = _get_colors_for_allowed_bands(phase=nickel_phase)
assert np.shape(hkl_colors) == (69, 2, 3)
def test_get_allowed_without_space_group_raises(self):
phase = Phase(point_group="432")
rlp = ReciprocalLatticePoint(phase=phase, hkl=[1, 1, 1])
with pytest.raises(ValueError, match=f"The phase {phase} must have a"):
_ = rlp.allowed
def test_init_without_point_group_raises(self):
phase = Phase()
with pytest.raises(ValueError, match=f"The phase {phase} must have a"):
_ = ReciprocalLatticePoint(phase=phase, hkl=[1, 1, 1])
class EBSDMasterPattern(CommonImage, Signal2D):
"""Simulated Electron Backscatter Diffraction (EBSD) master pattern.
This class extends HyperSpy's Signal2D class for EBSD master
patterns. Methods inherited from HyperSpy can be found in the
HyperSpy user guide. See the docstring of
:class:`hyperspy.signal.BaseSignal` for a list of additional
attributes.
Attributes
----------
projection : str
Which projection the pattern is in, "stereographic" or
"lambert".
hemisphere : str
Which hemisphere the data contains: "north", "south" or "both".
phase : orix.crystal_map.phase_list.Phase
Phase describing the crystal structure used in the master
pattern simulation.
"""
_signal_type = "EBSDMasterPattern"
_alias_signal_types = ["ebsd_master_pattern", "master_pattern"]
_lazy = False
# ---------------------- Custom properties ----------------------- #
phase = Phase()
projection = None
hemisphere = None
def __init__(self, *args, **kwargs):
"""Create an :class:`~kikuchipy.signals.EBSDMasterPattern`
instance from a :class:`hyperspy.signals.Signal2D` or a
:class:`numpy.ndarray`. See the docstring of
:class:`hyperspy.signal.BaseSignal` for optional input
parameters.
"""
Signal2D.__init__(self, *args, **kwargs)
self.phase = kwargs.pop("phase", Phase())
self.projection = kwargs.pop("projection", None)
self.hemisphere = kwargs.pop("hemisphere", None)
def get_patterns(
self,
rotations: Rotation,
detector: EBSDDetector,
energy: Union[int, float],
dtype_out: Union[type, np.dtype] = np.float32,
compute: bool = False,
**kwargs,
) -> Union[EBSD, LazyEBSD]:
"""Return a dictionary of EBSD patterns projected onto a
detector from a master pattern in the square Lambert
projection :cite:`callahan2013dynamical`, for a set of crystal
rotations relative to the EDAX TSL sample reference frame (RD,
TD, ND) and a fixed detector-sample geometry.
Parameters
----------
rotations
Crystal rotations to get patterns from. The shape of this
instance, a maximum of two dimensions, determines the
navigation shape of the output signal.
detector
EBSD detector describing the detector dimensions and the
detector-sample geometry with a single, fixed
projection/pattern center.
energy
Acceleration voltage, in kV, used to simulate the desired
master pattern to create a dictionary from. If only a single
energy is present in the signal, this will be returned no
matter its energy.
dtype_out
Data type of the returned patterns, by default np.float32.
compute
Whether to return a lazy result, by default False. For more
information see :func:`~dask.array.Array.compute`.
kwargs
Keyword arguments passed to
:func:`~kikuchipy.signals.util.get_chunking` to control the
number of chunks the dictionary creation and the output data
array is split into. Only `chunk_shape`, `chunk_bytes` and
`dtype_out` (to `dtype`) are passed on.
Returns
-------
EBSD or LazyEBSD
Signal with navigation and signal shape equal to the
rotation instance and detector shape, respectively.
Notes
-----
If the master pattern phase has a non-centrosymmetric point
group, both the northern and southern hemispheres must be
provided. For more details regarding the reference frame visit
the reference frame user guide.
"""
self._is_suitable_for_projection(raise_if_not=True)
if len(detector.pc) > 1:
raise NotImplementedError(
"Detector must have exactly one projection center")
# Get suitable chunks when iterating over the rotations. Signal
# axes are not chunked.
nav_shape = rotations.shape
nav_dim = len(nav_shape)
if nav_dim > 2:
raise ValueError(
"`rotations` can only have one or two dimensions, but an instance with "
f"{nav_dim} dimensions was passed")
data_shape = nav_shape + detector.shape
chunks = get_chunking(
data_shape=data_shape,
nav_dim=nav_dim,
sig_dim=len(detector.shape),
chunk_shape=kwargs.pop("chunk_shape", None),
chunk_bytes=kwargs.pop("chunk_bytes", None),
dtype=dtype_out,
)
# Whether to rescale pattern intensities after projection
if dtype_out != self.data.dtype:
rescale = True
if isinstance(dtype_out, np.dtype):
dtype_out = dtype_out.type
out_min, out_max = dtype_range[dtype_out]
else:
rescale = False
# Cannot be None due to Numba, so they are set to something
# here. Values aren't used unless `rescale` is True.
out_min, out_max = 1, 2
# Get direction cosines for each detector pixel relative to the
# source point
direction_cosines = _get_direction_cosines_for_single_pc_from_detector(
detector)
# Get dask array from rotations
rot_da = da.from_array(rotations.data,
chunks=chunks[:nav_dim] + (-1, ))
# Which axes to drop and add when iterating over the rotations
# dask array to produce the EBSD signal array, i.e. drop the
# (4,)-shape quaternion axis and add detector shape axes, e.g.
# (60, 60)
if nav_dim == 1:
drop_axis = 1
new_axis = (1, 2)
else: # nav_dim == 2
drop_axis = 2
new_axis = (2, 3)
master_north, master_south = self._get_master_pattern_arrays_from_energy(
energy)
# Project simulated patterns onto detector
npx, npy = self.axes_manager.signal_shape
scale = (npx - 1) / 2
# TODO: Use dask.delayed instead?
simulated = rot_da.map_blocks(
_project_patterns_from_master_pattern,
direction_cosines=direction_cosines,
master_north=master_north,
master_south=master_south,
npx=int(npx),
npy=int(npy),
scale=float(scale),
dtype_out=dtype_out,
rescale=rescale,
out_min=out_min,
out_max=out_max,
drop_axis=drop_axis,
new_axis=new_axis,
chunks=chunks,
dtype=dtype_out,
)
# Add crystal map and detector to keyword arguments
kwargs = dict(
xmap=CrystalMap(phase_list=PhaseList(self.phase),
rotations=rotations),
detector=detector,
)
# Specify navigation and signal axes for signal initialization
names = ["y", "x", "dy", "dx"]
scales = np.ones(4)
ndim = simulated.ndim
if ndim == 3:
names = names[1:]
scales = scales[1:]
axes = [
dict(
size=data_shape[i],
index_in_array=i,
name=names[i],
scale=scales[i],
offset=0.0,
units="px",
) for i in range(ndim)
]
if compute:
patterns = np.zeros(shape=simulated.shape, dtype=simulated.dtype)
with ProgressBar():
print(
f"Creating a dictionary of {nav_shape} simulated patterns:",
file=sys.stdout,
)
simulated.store(patterns, compute=True)
out = EBSD(patterns, axes=axes, **kwargs)
else:
out = LazyEBSD(simulated, axes=axes, **kwargs)
gc.collect()
return out
# ------ Methods overwritten from hyperspy.signals.Signal2D ------ #
def deepcopy(self):
new = super().deepcopy()
new.phase = self.phase.deepcopy()
new.projection = copy.deepcopy(self.projection)
new.hemisphere = copy.deepcopy(self.hemisphere)
return new
# ------------------------ Private methods ----------------------- #
def _get_master_pattern_arrays_from_energy(
self, energy: Union[int, float]) -> Tuple[np.ndarray, np.ndarray]:
"""Return northern and southern master patterns created with a
single, given energy.
Parameters
----------
energy
Acceleration voltage in kV. If only a single energy is
present in the signal, this will be returned no matter its
energy.
Returns
-------
master_north, master_south
Northern and southern hemispheres of master pattern.
"""
if "energy" in [i.name for i in self.axes_manager.navigation_axes]:
master_patterns = self.inav[float(energy)].data
else: # Assume a single energy
master_patterns = self.data
if self.hemisphere == "both":
master_north, master_south = master_patterns
else:
master_north = master_south = master_patterns
return master_north, master_south
def _is_suitable_for_projection(self, raise_if_not: bool = False):
"""Check whether the master pattern is suitable for projection
onto an EBSD detector and return a bool or raise an error
message if desired.
"""
suitable = True
error = None
if self.projection != "lambert":
error = NotImplementedError(
"Master pattern must be in the square Lambert projection")
suitable = False
pg = self.phase.point_group
if pg is None:
error = AttributeError(
"Master pattern `phase` attribute must have a valid point group"
)
suitable = False
elif self.hemisphere != "both" and not pg.contains_inversion:
error = AttributeError(
"For point groups without inversion symmetry, like the current "
f"{pg.name}, both hemispheres must be present in the master pattern "
"signal")
suitable = False
if not suitable and raise_if_not:
raise error
else:
return suitable
def file_reader(filename, refined=False, **kwargs):
"""Return a :class:`~orix.crystal_map.crystal_map.CrystalMap` object
from a file in EMsoft's dictionary indexing dot product file format.
Parameters
----------
filename : str
Path and file name.
refined : bool, optional
Whether to return refined orientations (default is False).
kwargs
Keyword arguments passed to :func:`h5py.File`.
Returns
-------
CrystalMap
"""
mode = kwargs.pop("mode", "r")
f = File(filename, mode=mode, **kwargs)
# Get groups for convenience
ebsd_group = f["Scan 1/EBSD"]
data_group = ebsd_group["Data"]
header_group = ebsd_group["Header"]
phase_group = header_group["Phase/1"]
# Get map shape and step sizes
ny = header_group["nRows"][:][0]
nx = header_group["nColumns"][:][0]
step_y = header_group["Step Y"][:][0]
map_size = ny * nx
# Some of the data needed to create a CrystalMap object
phase_name, point_group, structure = _get_phase(phase_group)
data_dict = {
# Get map coordinates ("Y Position" data set is not correct in EMsoft as of
# 2020-04, see:
# https://github.com/EMsoft-org/EMsoft/blob/7762e1961508fe3e71d4702620764ceb98a78b9e/Source/EMsoftHDFLib/EMh5ebsd.f90#L1093)
"x":
data_group["X Position"][:],
# y = data_group["Y Position"][:]
"y":
np.sort(np.tile(np.arange(ny) * step_y, nx)),
# Get phase IDs
"phase_id":
data_group["Phase"][:],
# Get phase name, point group and structure (lattice)
"phase_list":
PhaseList(
Phase(name=phase_name,
point_group=point_group,
structure=structure)),
"scan_unit":
"um",
}
# Get rotations
if refined:
euler = data_group["RefinedEulerAngles"][:] # Radians
else: # Get n top matches for each pixel
top_match_idx = data_group["TopMatchIndices"][:][:map_size] - 1
dictionary_size = data_group["FZcnt"][:][0]
# Degrees
dictionary_euler = data_group[
"DictionaryEulerAngles"][:][:dictionary_size]
dictionary_euler = np.deg2rad(dictionary_euler)
euler = dictionary_euler[top_match_idx, :]
data_dict["rotations"] = Rotation.from_euler(euler)
# Get number of top matches kept per data point
n_top_matches = f["NMLparameters/EBSDIndexingNameListType/nnk"][:][0]
data_dict["prop"] = _get_properties(
data_group=data_group,
n_top_matches=n_top_matches,
map_size=map_size,
)
f.close()
return CrystalMap(**data_dict)
def test_allowed(self, space_group, hkl, centering, desired_allowed):
rlp = ReciprocalLatticePoint(phase=Phase(space_group=space_group), hkl=hkl)
assert rlp.phase.space_group.short_name[0] == centering
assert np.allclose(rlp.allowed, desired_allowed)
import numpy as np
from orix.crystal_map import Phase
import pytest
from diffsims.structure_factor import (
find_asymmetric_positions,
get_kinematical_structure_factor,
get_doyleturner_structure_factor,
get_refraction_corrected_wavelength,
)
# Debye-Waller factor in Å^-2: Biosequiv = 8 * np.pi ** 2 * Uisoequiv
nickel = Phase(
space_group=225,
structure=Structure(
lattice=Lattice(3.5236, 3.5236, 3.5236, 90, 90, 90),
atoms=[Atom(xyz=[0, 0, 0], atype="Ni", Uisoequiv=0.006332)],
),
)
ferrite = Phase(
space_group=229,
structure=Structure(
lattice=Lattice(2.8665, 2.8665, 2.8665, 90, 90, 90),
atoms=[
Atom(xyz=[0, 0, 0], atype="Fe", Uisoequiv=0.006332),
Atom(xyz=[0.5, 0.5, 0.5], atype="Fe", Uisoequiv=0.006332),
],
),
)
sic4h = Phase(
space_group=186,
