CrystalMap#

class orix.crystal_map.CrystalMap(rotations: Rotation, phase_id: Optional[ndarray] = None, x: Optional[ndarray] = None, y: Optional[ndarray] = None, z: Optional[ndarray] = None, phase_list: Optional[PhaseList] = None, prop: Optional[dict] = None, scan_unit: Optional[str] = 'px', is_in_data: Optional[ndarray] = None)[source]#

Bases: object

Crystallographic map of orientations, crystal phases and key properties associated with every spatial coordinate in a 1D or 2D.

Parameters:
rotations

Rotation in each 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

Phase ID of each pixel. IDs equal to -1 are considered not indexed. If not given, all points are considered to belong to one phase with ID 0.

x

Map x coordinate of each data point. If not given, 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

Map y coordinate of each data point. If not given, the map is assumed to be 1D, and it is set to None.

z

Map z coordinate of each data point. If not given, the map is assumed to be 2D or 1D, and it is set to None.

Deprecated since version 0.10.1: Will be removed in 0.11.0. Support for 3D crystal maps is minimal and brittle, and it was therefore decided to remove it altogether. If you rely on this functionality, please report it in an issue at https://github.com/pyxem/orix/issues.

phase_list

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 not given, a phase list with as many phases as there are unique phase IDs in phase_id is created.

prop

Dictionary of properties of each data point.

scan_unit

Length unit of the data. Default is "px".

is_in_data

Array of booleans signifying whether a point is in the data.

Notes

Data is stored as 1D arrays and reshaped when necessary.

Examples

Constructing a crystal map from scratch, with two rows and three columns and containing Austenite and Ferrite orientations

>>> from diffpy.structure import Atom, Lattice, Structure
>>> from orix.crystal_map import create_coordinate_arrays, CrystalMap, PhaseList
>>> from orix.quaternion import Rotation
>>> coords, n = create_coordinate_arrays(shape=(2, 3))
>>> 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)
...     )
... ]
>>> xmap = CrystalMap(
...     rotations=Rotation.from_axes_angles([0, 0, 1], np.linspace(0, np.pi, n)),
...     phase_id=np.array([0, 0, 1, 1, 0, 1]),
...     x=coords["x"],
...     y=coords["y"],
...     phase_list=PhaseList(space_groups=[225, 229], structures=structures),
...     prop={"score": np.random.random(n)},
...     scan_unit="nm",
... )
>>> xmap
Phase  Orientations       Name  Space group  Point group  Proper point group       Color
    0     3 (50.0%)  austenite        Fm-3m         m-3m                 432    tab:blue
    1     3 (50.0%)    ferrite        Im-3m         m-3m                 432  tab:orange
Properties: score
Scan unit: nm

Data in a crystal map can be selected in multiple ways. Let’s demonstrate this on a dual phase dataset available in the data module

>>> from orix import data
>>> xmap = data.sdss_ferrite_austenite()
>>> xmap
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
>>> xmap.shape
(100, 117)

Selecting based on coordinates, passing ranges (slices), integers or both

>>> xmap2 = xmap[20:40, 50:60]
>>> xmap2
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
>>> xmap2.shape
(20, 10)
>>> xmap2 = xmap[20:40, 3]
>>> xmap2
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
>>> xmap2.shape
(20, 1)

Note that 1-dimensions are NOT removed

>>> xmap2 = xmap[10, 10]
>>> xmap2
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
>>> xmap2.shape
(1, 1)

Select by phase name(s)

>>> xmap2 = xmap["austenite"]
>>> xmap2
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
>>> xmap2.shape
(100, 117)
>>> xmap["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

Select by indexed and not indexed data

>>> xmap["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
>>> xmap["not_indexed"]
No data.

Select with a boolean array (possibly chained)

>>> xmap[xmap.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
>>> xmap[(xmap.iq > np.mean(xmap.iq)) & (xmap.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

Attributes

CrystalMap.all_indexed

Return whether all points in data are indexed.

CrystalMap.dx

Return the x coordinate step size.

CrystalMap.dy

Return the y coordinate step size.

CrystalMap.dz

[Deprecated] Return the z coordiante step size.

CrystalMap.id

Return the ID of points in data.

CrystalMap.is_indexed

Return whether points in data are indexed.

CrystalMap.ndim

Return the number of data dimensions of points in data.

CrystalMap.orientations

Return orientations (rotations respecting symmetry), in data.

CrystalMap.phase_id

Return or set the phase IDs of points in data.

CrystalMap.phases

Return or set the list of phases.

CrystalMap.phases_in_data

Return the list of phases in data.

CrystalMap.prop

Return the data properties in each data point.

CrystalMap.rotations

Return the rotations in the data.

CrystalMap.rotations_per_point

Return the number of rotations per data point in data.

CrystalMap.rotations_shape

Return the shape of rotations.

CrystalMap.shape

Return the shape of points in data.

CrystalMap.size

Return the total number of points in data.

CrystalMap.x

Return the x coordinates of points in data.

CrystalMap.y

Return the y coordinates of points in data.

CrystalMap.z

[Deprecated] Return the z coordinates of points in data.

Methods

CrystalMap.deepcopy()

Return a deep copy using copy.deepcopy() function.

CrystalMap.empty([shape, step_sizes])

Return a crystal map of a given shape and step sizes with identity rotations.

CrystalMap.get_map_data(item[, decimals, ...])

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.

CrystalMap.plot([value, overlay, scalebar, ...])

Plot a 2D map with any crystallographic map property as map values.

Examples using CrystalMap#