def test_add_to_phaselist_raises(self):
"""Trying to add a Phase with a name already in the PhaseList
raises a ValueError.
"""
pl = PhaseList(names=["a"])
with pytest.raises(ValueError, match="'a' is already in the phase list"):
pl.add(Phase("a"))
def test_init_empty_phaselist(self, empty_input):
pl = PhaseList(empty_input)
assert repr(pl) == "No phases."
pl.add(Phase("al", point_group="m-3m"))
assert repr(pl) == (
"Id Name Space group Point group Proper point group Color\n"
" 0 al None m-3m 432 tab:blue")
def test_add_phase_in_empty_phaselist(self):
"""Add Phase to empty PhaseList."""
sg_no = 10
name = "a"
pl = PhaseList()
pl.add(Phase(name, space_group=sg_no))
assert pl.ids == [0]
assert pl.names == [name]
assert pl.space_groups == [GetSpaceGroup(sg_no)]
assert pl.structures == [Structure()]
def test_make_not_indexed(self):
phase_names = ["a", "b", "c"]
phase_colors = ["r", "g", "b"]
pl = PhaseList(names=phase_names, colors=phase_colors, ids=[-1, 0, 1])
assert pl.names == phase_names
assert pl.colors == phase_colors
pl.add_not_indexed()
phase_names[0] = "not_indexed"
phase_colors[0] = "w"
assert pl.names == phase_names
assert pl.colors == phase_colors
def test_init_with_single_structure(self):
structure = Structure()
names = ["a", "b"]
pl = PhaseList(names=names, structures=structure)
assert pl.names == names
assert pl.structures == [structure] * 2
def test_get_phaselist_size(self, n_names):
phase_names_pool = "abcd"
phase_names = [phase_names_pool[i] for i in range(n_names)]
pl = PhaseList(names=phase_names)
assert pl.size == n_names
def test_init_with_too_many_phases(
self, crystal_map_input, phase_names, phase_ids, desired_phase_names
):
"""More phases than phase IDs."""
phase_list = PhaseList(names=phase_names, ids=phase_ids)
xmap = CrystalMap(phase_list=phase_list, **crystal_map_input)
assert xmap.phases.names == desired_phase_names
def test_init_phaselist_from_phase(self):
p = Phase(name="austenite", point_group="432", color="C2")
pl = PhaseList(p)
assert pl.names == [p.name]
assert pl.point_groups == [p.point_group]
assert pl.space_groups == [p.space_group]
assert pl.colors == [p.color]
assert pl.colors_rgb == [p.color_rgb]
def test_add_list_phases_to_phaselist(self):
"""Add a list of Phase objects to PhaseList, also ensuring that
unique colors are given.
"""
names = ["a", "b"]
sg_no = [10, 20]
colors = ["tab:blue", "tab:orange"]
pl = PhaseList(names=names, space_groups=sg_no)
assert pl.colors == colors
new_names = ["c", "d"]
new_sg_no = [30, 40]
pl.add([Phase(name=n, space_group=i) for n, i in zip(new_names, new_sg_no)])
assert pl.names == names + new_names
assert pl.space_groups == (
[GetSpaceGroup(i) for i in sg_no] + [GetSpaceGroup(i) for i in new_sg_no]
)
assert pl.colors == colors + ["tab:green", "tab:red"]
def test_add_phaselist_to_phaselist(self):
"""Add a PhaseList to a PhaseList, also ensuring that new IDs are
given.
"""
names = ["a", "b"]
sg_no = [10, 20]
pl1 = PhaseList(names=names, space_groups=sg_no)
assert pl1.ids == [0, 1]
names2 = ["c", "d"]
sg_no2 = [30, 40]
ids = [4, 5]
pl2 = PhaseList(names=names2, space_groups=sg_no2, ids=ids)
pl1.add(pl2)
assert pl1.names == names + names2
assert pl1.space_groups == ([GetSpaceGroup(i) for i in sg_no] +
[GetSpaceGroup(i) for i in sg_no2])
assert pl1.ids == [0, 1, 2, 3]
def test_get_phaselist_ids(self, n_names, phase_ids, desired_names,
desired_phase_ids):
phase_names_pool = "abc"
phase_names = [phase_names_pool[i] for i in range(n_names)]
pl = PhaseList(names=phase_names, ids=phase_ids)
assert pl.names == desired_names
assert pl.ids == desired_phase_ids
def test_init_set_to_nones(self):
phase_ids = [1, 2]
pl = PhaseList(ids=phase_ids)
assert pl.ids == phase_ids
assert pl.names == [""] * 2
assert pl.point_groups == [None] * 2
assert pl.space_groups == [None] * 2
assert pl.colors == ["tab:blue", "tab:orange"]
assert pl.structures == [Structure()] * 2
def test_orientations_symmetry(self, point_group, rotation, expected_orientation):
r = Rotation(rotation)
cm = CrystalMap(rotations=r, phase_id=np.array([0]))
cm.phases = PhaseList(Phase("a", point_group=point_group))
o = cm.orientations
assert np.allclose(
o.data, Orientation(r).set_symmetry(point_group).data, atol=1e-3
)
assert np.allclose(o.data, expected_orientation, atol=1e-3)
def phase_list(request):
names, space_groups, point_group_names, colors, lattices, atoms = request.param
# Apparently diffpy.structure don't allow iteration over a list of lattices
structures = [Structure(lattice=lattices[i], atoms=a) for i, a in enumerate(atoms)]
return PhaseList(
names=names,
space_groups=space_groups,
point_groups=point_group_names,
colors=colors,
structures=structures,
)
def phases_in_data(self):
"""List of phases in data.
Needed because it can be useful to have phases not in data but in
`self.phases`.
"""
unique_ids = np.unique(self.phase_id)
phase_list = self.phases[np.intersect1d(unique_ids, self.phases.ids)]
if isinstance(phase_list, Phase): # One phase in data
# Get phase ID so it carries over to the new `PhaseList` object
phase = phase_list # Since it's actually a single phase
phase_id = self.phases.id_from_name(phase.name)
return PhaseList(phases=phase, ids=phase_id)
else: # Multiple phases in data
return phase_list
def test_init_phaselist_from_phases(self, phase_collection):
p1 = Phase(name="austenite", point_group=432, color=None)
p2 = Phase(name="ferrite", point_group="432", color="C1")
if phase_collection == "dict":
phases = {1: p1, 2: p2}
else: # phase_collection == "list":
phases = [p1, p2]
pl = PhaseList(phases)
assert pl.names == [p.name for p in [p1, p2]]
assert pl.point_groups == [p.point_group for p in [p1, p2]]
assert pl.space_groups == [p.space_group for p in [p1, p2]]
assert pl.colors == [p.color for p in [p1, p2]]
assert pl.colors_rgb == [p.color_rgb for p in [p1, p2]]
def test_init_with_phase_list(self, crystal_map_input):
point_groups = [C2, C3, C4]
phase_list = PhaseList(point_groups=point_groups)
cm = CrystalMap(phase_list=phase_list, **crystal_map_input)
n_point_groups = len(point_groups)
n_phase_ids = len(cm.phases.ids)
n_different = n_point_groups - n_phase_ids
if n_different < 0:
point_groups += [None] * abs(n_different)
assert [
cm.phases.point_groups[i] == point_groups[i] for i in range(n_phase_ids)
]
unique_phase_ids = list(np.unique(crystal_map_input["phase_id"]).astype(int))
assert cm.phases.ids == unique_phase_ids
def test_iterate_phaselist(self):
names = ["al", "ni", "sigma"]
point_groups = [3, 432, "m-3m"]
colors = ["g", "b", "r"]
structures = [
Structure(),
Structure(lattice=Lattice(1, 2, 3, 90, 90, 90)),
Structure(),
]
pl = PhaseList(
names=names, point_groups=point_groups, colors=colors, structures=structures
)
for i, ((phase_id, phase), n, s, c, structure) in enumerate(
zip(pl, names, point_groups, colors, structures)
):
assert phase_id == i
assert phase.name == n
assert phase.point_group.name == str(s)
assert phase.color == c
assert phase.structure == structure
def test_init_phaselist_from_strings(
self,
names,
space_groups,
point_groups,
colors,
phase_ids,
desired_names,
desired_space_groups,
desired_point_groups,
desired_colors,
desired_phase_ids,
):
pl = PhaseList(
names=names,
space_groups=space_groups,
point_groups=point_groups,
colors=colors,
ids=phase_ids,
)
actual_point_group_names = []
actual_space_group_names = []
for _, p in pl:
if p.point_group is None:
actual_point_group_names.append(None)
else:
actual_point_group_names.append(p.point_group.name)
if p.space_group is None:
actual_space_group_names.append(None)
else:
actual_space_group_names.append(p.space_group.short_name)
assert pl.names == desired_names
assert actual_space_group_names == desired_space_groups
assert actual_point_group_names == desired_point_groups
assert pl.colors == desired_colors
assert pl.ids == desired_phase_ids
def test_phase_legend(self, crystal_map, phase_names, phase_colors,
legend_properties):
cm = crystal_map
cm[0, 0].phase_id = 1
cm.phases = PhaseList(names=phase_names,
point_groups=[3, 3],
colors=phase_colors)
fig = plt.figure()
ax = fig.add_subplot(projection=PLOT_MAP)
_ = ax.plot_map(cm, legend_properties=legend_properties)
legend = ax.legend_
assert legend._fontsize == 11.0
assert [i._text for i in legend.texts] == phase_names
frame_alpha = legend_properties.pop("framealpha", 0.6)
assert legend.get_frame().get_alpha() == frame_alpha
for k, v in legend_properties.items():
assert legend.__getattribute__(k) == v
plt.close("all")
def test_get_phaselist_colors_rgb(self):
pl = PhaseList(names=["a", "b", "c"], colors=["r", "g", (0, 0, 1)])
assert pl.colors == ["r", "g", "b"]
assert np.allclose(pl.colors_rgb, [(1.0, 0.0, 0.0), [0, 0.5, 0], (0, 0, 1)])
class CrystalMap:
"""Crystallographic map of rotations, crystal phases and key
properties associated with every spatial coordinate in a 1D, 2D or 3D
space.
All properties are stored as 1D arrays, and reshaped when necessary.
"""
def __init__(
self,
rotations,
phase_id=None,
x=None,
y=None,
z=None,
phase_list=None,
prop=None,
scan_unit=None,
is_in_data=None,
):
"""
Parameters
----------
rotations : orix.quaternion.rotation.Rotation
Rotation of each data point. Must be passed with all spatial
dimensions in the first array axis (flattened). May contain
multiple rotations per point, included in the second array
axes. Crystal map data size is set equal to the first array
axis' size.
phase_id : numpy.ndarray, optional
Phase ID of each pixel. IDs equal to -1 are considered not
indexed. If None is passed (default), all points are
considered to belong to one phase with ID 0.
x : numpy.ndarray, optional
Map x coordinate of each data point. If None is passed,
the map is assumed to be 1D, and it is set to an array of
increasing integers from 0 to the length of the `phase_id`
array.
y : numpy.ndarray, optional
Map y coordinate of each data point. If None is passed,
the map is assumed to be 1D, and it is set to None.
z : numpy.ndarray, optional
Map z coordinate of each data point. If None is passed, the
map is assumed to be 2D or 1D, and it is set to None.
phase_list : PhaseList, optional
A list of phases in the data with their with names,
space groups, point groups, and structures. The order in which
the phases appear in the list is important, as it is this, and
not the phases' IDs, that is used to link the phases to the
input `phase_id` if the IDs aren't exactly the same as in
`phase_id`. If None (default), a phase list with as many
phases as there are unique phase IDs in `phase_id` is created.
prop : dict of numpy.ndarray, optional
Dictionary of properties of each data point.
scan_unit : str, optional
Length unit of the data. If None (default), "px" is used.
is_in_data : np.ndarray, optional
Array of booleans signifying whether a point is in the data.
Examples
--------
>>> from diffpy.structure import Atom, Lattice, Structure
>>> import numpy as np
>>> from orix.crystal_map import CrystalMap
>>> from orix.quaternion.rotation import Rotation
>>> euler1, euler2, euler3, x, y, iq, dp, phase_id = np.loadtxt(
... "/some/file.ang", unpack=True)
>>> euler_angles = np.column_stack((euler1, euler2, euler3))
>>> rotations = Rotation.from_euler(euler_angles)
>>> properties = {"iq": iq, "dp": dp}
>>> structures = [
... Structure(
... title="austenite",
... atoms=[Atom("fe", [0] * 3)],
... lattice=Lattice(0.360, 0.360, 0.360, 90, 90, 90)
... ),
... Structure(
... title="ferrite",
... atoms=[Atom("fe", [0] * 3)],
... lattice=Lattice(0.287, 0.287, 0.287, 90, 90, 90)
... )
... ]
>>> pl = PhaseList(space_groups=[225, 229], structures=structures)
>>> cm = CrystalMap(
... rotations=rotations,
... phase_id=phase_id,
... x=x,
... y=y,
... phase_list=pl,
... prop=properties,
... )
"""
# Set rotations
if not isinstance(rotations, Rotation):
raise ValueError(
f"rotations must be of type {Rotation}, not {type(rotations)}."
)
self._rotations = rotations
# Set data size
data_size = rotations.shape[0]
# Set phase IDs
if phase_id is None: # Assume single phase data
phase_id = np.zeros(data_size)
phase_id = phase_id.astype(int)
self._phase_id = phase_id
# Set data point IDs
point_id = np.arange(data_size)
self._id = point_id
# Set spatial coordinates
if x is None and y is None and z is None:
x = np.arange(data_size)
self._x = x
self._y = y
self._z = z
# Create phase list
# Sorted in ascending order
unique_phase_ids = np.unique(phase_id)
include_not_indexed = False
if unique_phase_ids[0] == -1:
include_not_indexed = True
unique_phase_ids = unique_phase_ids[1:]
# Also sorted in ascending order
if phase_list is None:
self.phases = PhaseList(ids=unique_phase_ids)
else:
phase_list = copy.deepcopy(phase_list)
phase_ids = phase_list.ids
n_different = len(phase_ids) - len(unique_phase_ids)
if n_different > 0:
# Remove superfluous phases by removing the phases whose
# ID is not in the ID array, in descending list order
for i in phase_ids[::-1]:
if i not in unique_phase_ids:
del phase_list[i]
n_different -= 1
if n_different == 0:
break
elif n_different < 0:
# Create new phase list adding the missing phases with
# default initial values
phase_list = PhaseList(
names=phase_list.names,
space_groups=phase_list.space_groups,
point_groups=phase_list.point_groups,
colors=phase_list.colors,
structures=phase_list.structures,
ids=unique_phase_ids,
)
# Ensure phase list IDs correspond to IDs in phase_id array
new_ids = list(unique_phase_ids.astype(int))
phase_list._dict = dict(zip(new_ids, phase_list._dict.values()))
self.phases = phase_list
# Set whether measurements are indexed
is_indexed = np.ones(data_size, dtype=bool)
is_indexed[np.where(phase_id == -1)] = False
# Add "not_indexed" to phase list and ensure not indexed points
# have correct phase ID
if include_not_indexed:
self.phases.add_not_indexed()
self._phase_id[~is_indexed] = -1
# Set array with True for points in data
if is_in_data is None:
is_in_data = np.ones(data_size, dtype=bool)
self.is_in_data = is_in_data
# Set scan unit
if scan_unit is None:
scan_unit = "px"
self.scan_unit = scan_unit
# Set properties
if prop is None:
prop = {}
self._prop = CrystalMapProperties(prop, id=point_id)
# Set original data shape (needed if data shape changes in
# __getitem__())
self._original_shape = self._data_shape_from_coordinates()
@property
def id(self):
"""ID of points in data."""
return self._id[self.is_in_data]
@property
def size(self):
"""Total number of points in data."""
return np.count_nonzero(self.is_in_data)
@property
def shape(self):
"""Shape of points in data."""
return self._data_shape_from_coordinates()
@property
def ndim(self):
"""Number of data dimensions of points in data."""
return len(self.shape)
@property
def x(self):
"""X coordinates of points in data."""
if self._x is None or len(np.unique(self._x)) == 1:
return None
else:
return self._x[self.is_in_data]
@property
def y(self):
"""Y coordinates of points in data."""
if self._y is None or len(np.unique(self._y)) == 1:
return None
else:
return self._y[self.is_in_data]
@property
def z(self):
"""Z coordinates of points in data."""
if self._z is None or len(np.unique(self._z)) == 1:
return None
else:
return self._z[self.is_in_data]
@property
def dx(self):
return self._step_size_from_coordinates(self._x)
@property
def dy(self):
return self._step_size_from_coordinates(self._y)
@property
def dz(self):
return self._step_size_from_coordinates(self._z)
@property
def phase_id(self):
"""Phase IDs of points in data."""
return self._phase_id[self.is_in_data]
@phase_id.setter
def phase_id(self, value):
"""Set phase ID of points in data by passing an int to `value`."""
self._phase_id[self.is_in_data] = value
if value == -1 and "not_indexed" not in self.phases.names:
self.phases.add_not_indexed()
@property
def phases_in_data(self):
"""List of phases in data.
Needed because it can be useful to have phases not in data but in
`self.phases`.
"""
unique_ids = np.unique(self.phase_id)
phase_list = self.phases[np.intersect1d(unique_ids, self.phases.ids)]
if isinstance(phase_list, Phase): # One phase in data
# Get phase ID so it carries over to the new `PhaseList` object
phase = phase_list # Since it's actually a single phase
phase_id = self.phases.id_from_name(phase.name)
return PhaseList(phases=phase, ids=phase_id)
else: # Multiple phases in data
return phase_list
@property
def rotations(self):
"""Rotations in data."""
return self._rotations[self.is_in_data]
@property
def rotations_per_point(self):
"""Number of rotations per data point in data."""
return self.rotations.size // self.is_indexed.size
@property
def rotations_shape(self):
"""Shape of rotation object.
Map shape and possible multiple rotations per point are accounted
for. 1-dimensions are squeezed out.
"""
return tuple(i for i in self.shape + (self.rotations_per_point,) if i != 1)
@property
def orientations(self):
"""Rotations, respecting symmetry, in data."""
# TODO: Consider whether orientations should be calculated upon
# loading since computing orientations are slow (should benefit
# from dask!)
phases = self.phases_in_data
if phases.size == 1:
# Extract top matching rotations per point, if more than one
if self.rotations_per_point > 1:
rotations = self.rotations[:, 0]
else:
rotations = self.rotations
return Orientation(rotations).set_symmetry(phases[:].point_group)
else:
raise ValueError(
f"Data has the phases {phases.names}, however, you are executing a "
"command that only permits one phase."
)
@property
def is_indexed(self):
"""Whether points in data are indexed."""
return self.phase_id != -1
@property
def all_indexed(self):
"""Whether all points in data are indexed."""
return np.count_nonzero(self.is_indexed) == self.is_indexed.size
@property
def prop(self):
""":class:`~orix.crystal_map.CrystalMapProperties` dictionary with
data properties in each data point.
"""
self._prop.is_in_data = self.is_in_data
self._prop.id = self.id
return self._prop
@property
def _coordinates(self):
"""Dictionary of coordinates of points in data."""
# TODO: Make this "dynamic"/dependable when enabling specimen
# reference frame
return {"z": self.z, "y": self.y, "x": self.x}
@property
def _step_sizes(self):
"""Dictionary of step sizes of dimensions in data."""
# TODO: Make this "dynamic"/dependable when enabling specimen
# reference frame
return {"z": self.dz, "y": self.dy, "x": self.dx}
@property
def _coordinate_axes(self):
"""Dictionary of which data axis corresponds to which cartesian
coordinate.
"""
present_coordinates = [k for k, v in self._coordinates.items() if v is not None]
return {i: coord for i, coord in zip(range(self.ndim), present_coordinates)}
def __getattr__(self, item):
"""Get an attribute in the `prop` dictionary directly from the
CrystalMap object.
Called when the default attribute access fails with an
AttributeError.
"""
if item in self.__getattribute__("_prop"):
# Calls CrystalMapProperties.__getitem__()
return self.prop[item]
else:
return object.__getattribute__(self, item)
def __setattr__(self, name, value):
"""Set a class instance attribute."""
if hasattr(self, "_prop") and name in self._prop:
# Calls CrystalMapProperties.__setitem__()
self.prop[name] = value
else:
return object.__setattr__(self, name, value)
def __getitem__(self, key):
"""Get a masked copy of the CrystalMap object.
Parameters
----------
key : str, slice, tuple, int or boolean numpy.ndarray
If ``str``, it must be a valid phase or "not_indexed" or
"indexed". If ``slice`` or ``tuple``, it must be within the
map shape. If ``int``, it must be a valid ``self.id``. If
boolean array, it must be of map shape.
Examples
--------
A CrystalMap object can be indexed in multiple ways...
>>> cm
Phase Orientations Name Space group Point group Proper point group Color
1 5657 (48.4%) austenite None 432 432 tab:blue
2 6043 (51.6%) ferrite None 432 432 tab:orange
Properties: iq, dp
Scan unit: um
>>> cm.shape
(100, 117)
... by slicing with slices, integers, or both
>>> cm2 = cm[20:40, 50:60]
>>> cm2
Phase Orientations Name Space group Point group Proper point group Color
1 148 (74.0%) austenite None 432 432 tab:blue
2 52 (26.0%) ferrite None 432 432 tab:orange
Properties: iq, dp
Scan unit: um
>>> cm2.shape
(20, 10)
>>> cm2 = cm[20:40, 3]
>>> cm2
Phase Orientations Name Space group Point group Proper point group Color
1 16 (80.0%) austenite None 432 432 tab:blue
2 4 (20.0%) ferrite None 432 432 tab:orange
Properties: iq, dp
Scan unit: um
>>> cm2.shape
(20, 3)
Note that 1-dimensions are NOT removed
>>> cm2 = cm[10, 10]
>>> cm2
Phase Orientations Name Space group Point group Proper point group Color
2 1 (100.0%) ferrite None 432 432 tab:orange
Properties: iq, dp
Scan unit: um
>>> cm.shape
(1, 1)
... by phase name(s)
>>> cm2 = cm["austenite"]
Phase Orientations Name Space group Point group Proper point group Color
1 5657 (100.0%) austenite None 432 432 tab:blue
Properties: iq, dp
Scan unit: um
>>> cm2.shape
(100, 117)
>>> cm["austenite", "ferrite"]
Phase Orientations Name Space group Point group Proper point group Color
1 5657 (48.4%) austenite None 432 432 tab:blue
2 6043 (51.6%) ferrite None 432 432 tab:orange
Properties: iq, dp
Scan unit: um
... by "indexed" and "not_indexed"
>>> cm["indexed"]
Phase Orientations Name Space group Point group Proper point group Color
1 5657 (48.4%) austenite None 432 432 tab:blue
2 6043 (51.6%) ferrite None 432 432 tab:orange
Properties: iq, dp
Scan unit: um
>>> cm["not_indexed"]
No data.
... or by boolean arrays ((chained) conditional(s))
>>> cm[cm.dp > 0.81]
Phase Orientations Name Space group Point group Proper point group Color
1 4092 (44.8%) austenite None 432 432 tab:blue
2 5035 (55.2%) ferrite None 432 432 tab:orange
Properties: iq, dp
Scan unit: um
>>> cm[(cm.iq > np.mean(cm.iq)) & (cm.phase_id == 1)]
Phase Orientations Name Space group Point group Proper point group Color
1 1890 (100.0%) austenite None 432 432 tab:blue
Properties: iq, dp
Scan unit: um
"""
# TODO: Crop new map to the extremal spatial values (e.g. if all values in first
# or last row/column are masked out by the key), i.e. not just mask the values
# Initiate a mask to be added to the returned copy of the
# CrystalMap object, to ensure that only the unmasked values are
# in the data of the copy (True in `is_in_data`). First, no points
# are in the data, but are added if they satisfy the condition in
# the input key.
is_in_data = np.zeros(self.size, dtype=bool)
# The original object might already have set some points to not be
# in the data. If so, `is_in_data` is used to update the original
# `is_in_data`. Since `new_is_in_data` is not initiated for all
# key types, we declare it here and check for it later.
new_is_in_data = None
# Override mask values
if isinstance(key, str) or (isinstance(key, tuple) and isinstance(key[0], str)):
# From phase string(s)
if not isinstance(key, tuple): # Make single string iterable
key = (key,)
for k in key:
for phase_id, phase in self.phases:
if k == phase.name:
is_in_data[self.phase_id == phase_id] = True
elif k.lower() == "indexed":
# Add all indexed phases to data
is_in_data[self.phase_id != -1] = True
elif isinstance(key, np.ndarray) and key.dtype == np.bool_:
# From boolean numpy array
is_in_data = key
elif isinstance(key, (slice, int)) or (
isinstance(key, tuple)
and any([(isinstance(i, slice) or isinstance(i, int)) for i in key])
):
# From slice(s) or int
if isinstance(key, (slice, int)):
key = (key,)
slices = [slice(None, None, None)] * self.ndim
for i, k in enumerate(key):
slices[i] = k
new_is_in_data = np.zeros(self._original_shape, dtype=bool) # > 1D
new_is_in_data[tuple(slices)] = True
# Note that although all points within slice(s) was sought,
# points within the slice(s) which are already removed from
# the data are still kept out by this boolean multiplication
new_is_in_data = new_is_in_data.flatten() * self.is_in_data
# Insert the mask into a mask with the full map shape, if not done
# already
if new_is_in_data is None:
new_is_in_data = np.zeros_like(self.is_in_data, dtype=bool) # 1D
new_is_in_data[self.id] = is_in_data
# Return a copy with all attributes shallow except for the mask
new_map = copy.copy(self)
new_map.is_in_data = new_is_in_data
return new_map
def __repr__(self):
"""Print a nice representation of the data."""
if self.size == 0:
return "No data."
phases = self.phases_in_data
phase_ids = self.phase_id
# Ensure attributes set to None are treated OK
names = ["None" if not name else name for name in phases.names]
sg_names = ["None" if not i else i.short_name for i in phases.space_groups]
pg_names = ["None" if not i else i.name for i in phases.point_groups]
ppg_names = [
"None" if not i else i.proper_subgroup.name for i in phases.point_groups
]
# Determine column widths
unique_phases = np.unique(phase_ids)
p_sizes = [np.where(phase_ids == i)[0].size for i in unique_phases]
id_len = 5
ori_len = max(max([len(str(p_size)) for p_size in p_sizes]) + 9, 12)
name_len = max(max([len(n) for n in names]), 4)
sg_len = max(max([len(i) for i in sg_names]), 11)
pg_len = max(max([len(i) for i in pg_names]), 11)
ppg_len = max(max([len(i) for i in ppg_names]), 18)
col_len = max(max([len(i) for i in phases.colors]), 5)
# Column alignment
align = ">" # right ">" or left "<"
# Header (note the two-space spacing)
representation = (
"{:{align}{width}} ".format("Phase", width=id_len, align=align)
+ "{:{align}{width}} ".format("Orientations", width=ori_len, align=align)
+ "{:{align}{width}} ".format("Name", width=name_len, align=align)
+ "{:{align}{width}} ".format("Space group", width=sg_len, align=align)
+ "{:{align}{width}} ".format("Point group", width=pg_len, align=align)
+ "{:{align}{width}} ".format(
"Proper point group", width=ppg_len, align=align
)
+ "{:{align}{width}}\n".format("Color", width=col_len, align=align)
)
# Overview of data for each phase
for i, phase_id in enumerate(unique_phases.astype(int)):
p_size = np.where(phase_ids == phase_id)[0].size
p_fraction = 100 * p_size / self.size
ori_str = f"{p_size} ({p_fraction:.1f}%)"
representation += (
f"{phase_id:{align}{id_len}} "
+ f"{ori_str:{align}{ori_len}} "
+ f"{names[i]:{align}{name_len}} "
+ f"{sg_names[i]:{align}{sg_len}} "
+ f"{pg_names[i]:{align}{pg_len}} "
+ f"{ppg_names[i]:{align}{ppg_len}} "
+ f"{phases.colors[i]:{align}{col_len}}\n"
)
# Properties and spatial coordinates
props = []
for k in self.prop.keys():
props.append(k)
representation += "Properties: " + ", ".join(props) + "\n"
# Scan unit
representation += f"Scan unit: {self.scan_unit}"
return representation
def get_map_data(self, item, decimals=3, fill_value=None):
"""Return an array of a class instance attribute, with values
equal to ``False`` in ``self.is_in_data`` set to `fill_value`, of
map data shape.
If `item` is "orientations"/"rotations" and there are multiple
rotations per point, only the first rotation is used. Rotations
are returned as Euler angles.
Parameters
----------
item : str or numpy.ndarray
Name of the class instance attribute or a numpy.ndarray.
decimals : int, optional
How many decimals to round data point values to (default is
3).
fill_value : None, optional
Value to fill points not in the data with. If None
(default), np.nan is used.
Returns
-------
output_array : numpy.ndarray
Array of the class instance attribute with points not in data
set to `fill_value`, of float data type.
"""
# TODO: Consider an `axes` argument along which to get map data
# if > 2D
# Get full map shape
map_shape = self._original_shape
# Declare array of correct shape, accounting for RGB
# TODO: Better account for `item.shape`, e.g. quaternions
# (item.shape[-1] == 4) in a more general way than here (not more
# if/else)!
map_size = np.prod(map_shape)
if isinstance(item, np.ndarray):
array = np.empty(map_size, dtype=item.dtype)
if item.shape[-1] == 3: # Assume RGB
map_shape += (3,)
array = np.column_stack((array,) * 3)
elif item in ["orientations", "rotations"]: # Definitely RGB
array = np.empty(map_size, dtype=np.float64)
map_shape += (3,)
array = np.column_stack((array,) * 3)
else:
array = np.empty(map_size, dtype=np.float64)
# Enter non-masked values into array
if isinstance(item, np.ndarray):
# TODO: Account for 2D map with more than one value per point
array[self.is_in_data] = item
elif item in ["orientations", "rotations"]:
if item == "rotations":
# Use only the top matching rotation per point
if self.rotations_per_point > 1:
rotations = self.rotations[:, 0]
else:
rotations = self.rotations
array[self.is_in_data] = rotations.to_euler()
else: # item == "orientations"
# Fill in orientations per phase
# TODO: Consider whether orientations should be calculated
# upon loading
for i, phase in self.phases_in_data:
phase_mask = (self._phase_id == i) * self.is_in_data
phase_mask_in_data = self.phase_id == i
array[phase_mask] = self[phase_mask_in_data].orientations.to_euler()
else: # String
data = self.__getattr__(item)
if data is None:
raise ValueError(f"{item} is {data}.")
else:
# TODO: Account for 2D map with more than one value per point
array[self.is_in_data] = data
array = array.astype(data.dtype)
# Slice and reshape array
slices = self._data_slices_from_coordinates()
reshaped_array = array.reshape(map_shape)
sliced_array = reshaped_array[slices]
# Reshape and slice mask with points not in data
if array.shape[-1] == 3: # RGB
not_in_data = np.dstack((~self.is_in_data,) * 3)
else: # Scalar
not_in_data = ~self.is_in_data
not_in_data = not_in_data.reshape(map_shape)[slices]
# Fill points not in data with the fill value
if not_in_data.any():
if fill_value is None or fill_value is np.nan:
sliced_array = sliced_array.astype(np.float64)
sliced_array[not_in_data] = fill_value
# Round values
if np.issubdtype(array.dtype, np.bool_):
output_array = sliced_array
else:
output_array = np.round(sliced_array, decimals=decimals)
return output_array
def deepcopy(self):
"""Return a deep copy using :func:`copy.deepcopy` function."""
return copy.deepcopy(self)
@staticmethod
def _step_size_from_coordinates(coordinates):
"""Return step size in input `coordinates` array.
Parameters
----------
coordinates : numpy.ndarray
Linear coordinate array.
Returns
-------
step_size : float
Step size in `coordinates` array.
"""
unique_sorted = np.sort(np.unique(coordinates))
step_size = 0
if unique_sorted.size != 1:
step_size = unique_sorted[1] - unique_sorted[0]
return step_size
def _data_slices_from_coordinates(self):
"""Return a tuple of slices defining the current data extent in
all directions.
Returns
-------
slices : tuple of slices
Data slice in each existing dimension, in (z, y, x) order.
"""
slices = []
# Loop over dimension coordinates and step sizes
for coordinates, step in zip(
self._coordinates.values(), self._step_sizes.values()
):
if coordinates is not None:
c_min, c_max = np.min(coordinates), np.max(coordinates)
i_min = int(np.around(c_min / step))
i_max = int(np.around((c_max / step) + 1))
slices.append(slice(i_min, i_max))
return tuple(slices)
def _data_shape_from_coordinates(self):
"""Return data shape based upon coordinate arrays.
Returns
-------
data_shape : tuple of ints
Shape of data in all existing dimensions, in (z, y, x) order.
"""
data_shape = []
for dim_slice in self._data_slices_from_coordinates():
data_shape.append(dim_slice.stop - dim_slice.start)
return tuple(data_shape)
def test_init_with_single_point_group(self, crystal_map_input):
point_group = O
phase_list = PhaseList(point_groups=point_group)
cm = CrystalMap(phase_list=phase_list, **crystal_map_input)
assert np.allclose(cm.phases.point_groups[0].data, point_group.data)
def test_get_item_not_indexed(self, phase_slice):
ids = np.arange(-1, 9) # [-1, 0, 1, 2, ...]
pl = PhaseList(ids=ids) # [-1, 0, 1, 2, ...]
pl.add_not_indexed() # [-1, 0, 1, 2, ...]
assert np.allclose(pl[phase_slice].ids, ids[phase_slice])
def __init__(
self,
rotations,
phase_id=None,
x=None,
y=None,
z=None,
phase_list=None,
prop=None,
scan_unit=None,
is_in_data=None,
):
"""
Parameters
----------
rotations : orix.quaternion.rotation.Rotation
Rotation of each data point. Must be passed with all spatial
dimensions in the first array axis (flattened). May contain
multiple rotations per point, included in the second array
axes. Crystal map data size is set equal to the first array
axis' size.
phase_id : numpy.ndarray, optional
Phase ID of each pixel. IDs equal to -1 are considered not
indexed. If None is passed (default), all points are
considered to belong to one phase with ID 0.
x : numpy.ndarray, optional
Map x coordinate of each data point. If None is passed,
the map is assumed to be 1D, and it is set to an array of
increasing integers from 0 to the length of the `phase_id`
array.
y : numpy.ndarray, optional
Map y coordinate of each data point. If None is passed,
the map is assumed to be 1D, and it is set to None.
z : numpy.ndarray, optional
Map z coordinate of each data point. If None is passed, the
map is assumed to be 2D or 1D, and it is set to None.
phase_list : PhaseList, optional
A list of phases in the data with their with names,
space groups, point groups, and structures. The order in which
the phases appear in the list is important, as it is this, and
not the phases' IDs, that is used to link the phases to the
input `phase_id` if the IDs aren't exactly the same as in
`phase_id`. If None (default), a phase list with as many
phases as there are unique phase IDs in `phase_id` is created.
prop : dict of numpy.ndarray, optional
Dictionary of properties of each data point.
scan_unit : str, optional
Length unit of the data. If None (default), "px" is used.
is_in_data : np.ndarray, optional
Array of booleans signifying whether a point is in the data.
Examples
--------
>>> from diffpy.structure import Atom, Lattice, Structure
>>> import numpy as np
>>> from orix.crystal_map import CrystalMap
>>> from orix.quaternion.rotation import Rotation
>>> euler1, euler2, euler3, x, y, iq, dp, phase_id = np.loadtxt(
... "/some/file.ang", unpack=True)
>>> euler_angles = np.column_stack((euler1, euler2, euler3))
>>> rotations = Rotation.from_euler(euler_angles)
>>> properties = {"iq": iq, "dp": dp}
>>> structures = [
... Structure(
... title="austenite",
... atoms=[Atom("fe", [0] * 3)],
... lattice=Lattice(0.360, 0.360, 0.360, 90, 90, 90)
... ),
... Structure(
... title="ferrite",
... atoms=[Atom("fe", [0] * 3)],
... lattice=Lattice(0.287, 0.287, 0.287, 90, 90, 90)
... )
... ]
>>> pl = PhaseList(space_groups=[225, 229], structures=structures)
>>> cm = CrystalMap(
... rotations=rotations,
... phase_id=phase_id,
... x=x,
... y=y,
... phase_list=pl,
... prop=properties,
... )
"""
# Set rotations
if not isinstance(rotations, Rotation):
raise ValueError(
f"rotations must be of type {Rotation}, not {type(rotations)}."
)
self._rotations = rotations
# Set data size
data_size = rotations.shape[0]
# Set phase IDs
if phase_id is None: # Assume single phase data
phase_id = np.zeros(data_size)
phase_id = phase_id.astype(int)
self._phase_id = phase_id
# Set data point IDs
point_id = np.arange(data_size)
self._id = point_id
# Set spatial coordinates
if x is None and y is None and z is None:
x = np.arange(data_size)
self._x = x
self._y = y
self._z = z
# Create phase list
# Sorted in ascending order
unique_phase_ids = np.unique(phase_id)
include_not_indexed = False
if unique_phase_ids[0] == -1:
include_not_indexed = True
unique_phase_ids = unique_phase_ids[1:]
# Also sorted in ascending order
if phase_list is None:
self.phases = PhaseList(ids=unique_phase_ids)
else:
phase_list = copy.deepcopy(phase_list)
phase_ids = phase_list.ids
n_different = len(phase_ids) - len(unique_phase_ids)
if n_different > 0:
# Remove superfluous phases by removing the phases whose
# ID is not in the ID array, in descending list order
for i in phase_ids[::-1]:
if i not in unique_phase_ids:
del phase_list[i]
n_different -= 1
if n_different == 0:
break
elif n_different < 0:
# Create new phase list adding the missing phases with
# default initial values
phase_list = PhaseList(
names=phase_list.names,
space_groups=phase_list.space_groups,
point_groups=phase_list.point_groups,
colors=phase_list.colors,
structures=phase_list.structures,
ids=unique_phase_ids,
)
# Ensure phase list IDs correspond to IDs in phase_id array
new_ids = list(unique_phase_ids.astype(int))
phase_list._dict = dict(zip(new_ids, phase_list._dict.values()))
self.phases = phase_list
# Set whether measurements are indexed
is_indexed = np.ones(data_size, dtype=bool)
is_indexed[np.where(phase_id == -1)] = False
# Add "not_indexed" to phase list and ensure not indexed points
# have correct phase ID
if include_not_indexed:
self.phases.add_not_indexed()
self._phase_id[~is_indexed] = -1
# Set array with True for points in data
if is_in_data is None:
is_in_data = np.ones(data_size, dtype=bool)
self.is_in_data = is_in_data
# Set scan unit
if scan_unit is None:
scan_unit = "px"
self.scan_unit = scan_unit
# Set properties
if prop is None:
prop = {}
self._prop = CrystalMapProperties(prop, id=point_id)
# Set original data shape (needed if data shape changes in
# __getitem__())
self._original_shape = self._data_shape_from_coordinates()