PhaseList#

class orix.crystal_map.PhaseList(phases: Union[Phase, List[Phase], Dict[Phase], None] = None, names: Union[str, List[str], None] = None, space_groups: Union[int, SpaceGroup, List[Union[int, SpaceGroup]], None] = None, point_groups: Union[str, int, Symmetry, List[Union[str, int, Symmetry]], None] = None, colors: Union[str, List[str], None] = None, ids: Union[int, List[int], np.ndarray, None] = None, structures: Union[Structure, List[Structure], None] = None)[source]#

Bases: object

A list of phases in a crystallographic map.

Each phase in the list must have a unique phase id and name.

Parameters:

phases: A list or dict of phases or a single phase. The other arguments are ignored if this is passed.
names: Phase names. Overwrites the names in the structure objects.
space_groups: Space groups.
point_groups: Point groups.
colors: Phase colors.
ids: Phase IDs.
structures: Unit cells with atoms and a lattice of each phase. If not given, a default diffpy.structure.Structure is created for each phase.

Examples

>>> from diffpy.structure import Atom, Lattice, Structure
>>> from orix.crystal_map import Phase, PhaseList
>>> pl = PhaseList(
...     names=["al", "cu"],
...     space_groups=[225] * 2,
...     structures=[
...         Structure(
...             atoms=[Atom("al", [0] * 3)],
...             lattice=Lattice(0.405, 0.405, 0.405, 90, 90, 90)
...         ),
...         Structure(
...             atoms=[Atom("cu", [0] * 3)],
...             lattice=Lattice(0.361, 0.361, 0.361, 90, 90, 90)
...         ),
...     ]
... )
>>> pl
Id  Name  Space group  Point group  Proper point group       Color
 0    al        Fm-3m         m-3m                 432    tab:blue
 1    cu        Fm-3m         m-3m                 432  tab:orange
>>> pl["al"].structure
[al   0.000000 0.000000 0.000000 1.0000]

A phase list can be indexed in multiple ways:

Return a phase if only one phase matches the key

>>> pl[0]  # Index with a single phase id
<name: al. space group: Fm-3m. point group: m-3m. proper point group: 432. color: tab:blue>
>>> pl["cu"]  # Index with a phase name
<name: cu. space group: Fm-3m. point group: m-3m. proper point group: 432. color: tab:orange>
>>> pl[:1]
<name: al. space group: Fm-3m. point group: m-3m. proper point group: 432. color: tab:blue>

Return a phase list

>>> pl[0:]  # Index with slices
Id  Name  Space group  Point group  Proper point group       Color
 0    al        Fm-3m         m-3m                 432    tab:blue
 1    cu        Fm-3m         m-3m                 432  tab:orange
>>> pl["al", "cu"]  # Index with a tuple of phase names
Id  Name  Space group  Point group  Proper point group       Color
 0    al        Fm-3m         m-3m                 432    tab:blue
 1    cu        Fm-3m         m-3m                 432  tab:orange
>>> pl[0, 1]  # Index with a tuple of phase phase_ids
Id  Name  Space group  Point group  Proper point group       Color
 0    al        Fm-3m         m-3m                 432    tab:blue
 1    cu        Fm-3m         m-3m                 432  tab:orange
>>> pl[[0, 1]]  # Index with a list of phase_ids
Id  Name  Space group  Point group  Proper point group       Color
 0    al        Fm-3m         m-3m                 432    tab:blue
 1    cu        Fm-3m         m-3m                 432  tab:orange

Attributes

`PhaseList.colors`	Return the phases' colors.
`PhaseList.colors_rgb`	Return the phases' RGB color values.
`PhaseList.ids`	Return the unique phase IDs in the list of phases.
`PhaseList.names`	Return the phases' names.
`PhaseList.point_groups`	Return the phases' point groups.
`PhaseList.size`	Return the number of phases in the list.
`PhaseList.space_groups`	Return the phases' space groups.
`PhaseList.structures`	Return the phases' structures.

Methods

`PhaseList.add`(value)	Add phases to the end of a phase list in-place, incrementing the phase IDs.
`PhaseList.add_not_indexed`()	Add a dummy phase to assign to not indexed data points.
`PhaseList.deepcopy`()	Return a deep copy using `copy.deepcopy()` function.
`PhaseList.id_from_name`(name)	Return the phase ID from a phase name or raise an error if the phase is not in the list.
`PhaseList.sort_by_id`()	Sort the list according to phase ID in-place.