Merge #405 from hakonanes/fix-404

Change rounding from 12 to 10 decimals when finding unique vectors and rotations

CHANGELOG.rst

@@ -7,6 +7,19 @@ All notable changes to the ``orix`` project are documented in this file.
 The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`_, and
 this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
+2022-10-25 - version 0.10.2
+===========================
+
+Fixed
+-----
+- ``Miller.symmetrise(unique=True)`` return the correct number of symmetrically
+  equivalent but unique vectors, by rounding to 10 instead of 12 decimals prior to
+  finding the unique vectors with NumPy.
+
+Changed
+-------
+- Unique rotations and vectors are now found by rounding to 10 instead of 12 decimals.
+
 2022-10-03 - version 0.10.1
 ===========================
 

orix/__init__.py

@@ -1,5 +1,5 @@
 __name__ = "orix"
-__version__ = "0.10.1"
+__version__ = "0.10.2"
 __author__ = "orix developers"
 __author_email__ = "[email protected]"
 __description__ = "orix is an open-source Python library for handling crystal orientation mapping data."

orix/base/__init__.py

@@ -192,7 +192,7 @@ def unique(
             The indices of the (flattened) data in the unique array if
             ``return_inverse=True``.
         """
-        data = self.flatten()._data.round(12)
+        data = self.flatten()._data.round(10)
         data = data[~np.all(np.isclose(data, 0), axis=1)]  # Remove zeros
         _, idx, inv = np.unique(data, axis=0, return_index=True, return_inverse=True)
         obj = self.__class__(data[np.sort(idx), : self.dim])
@@ -284,7 +284,7 @@ def transpose(self, *axes: Optional[int]) -> Object3d:
                 + f"{tuple(axes)} does not fit with {self.shape}."
             )
 
-        return self.__class__(self.data.transpose(*axes, -1))
+        return self.__class__(self.data.transpose(*axes + (-1,)))
 
     def get_random_sample(
         self, size: Optional[int] = 1, replace: bool = False, shuffle: bool = False

orix/quaternion/rotation.py

@@ -193,7 +193,7 @@ def unique(
                     rotation.improper,
                 ],
                 axis=-1,
-            ).round(12)
+            ).round(10)
         _, idx, inv = np.unique(abcd, axis=0, return_index=True, return_inverse=True)
         idx_argsort = np.argsort(idx)
         idx_sort = idx[idx_argsort]
@@ -513,7 +513,10 @@ def to_euler(self, **kwargs) -> np.ndarray:
     @classmethod
     @deprecated_argument("convention", "0.9", "1.0", "direction")
     def from_euler(
-        cls, euler: np.ndarray, direction: str = "lab2crystal", **kwargs
+        cls,
+        euler: Union[np.ndarray, list, tuple],
+        direction: str = "lab2crystal",
+        **kwargs,
     ) -> Rotation:
         """Create a rotation from an array of Euler angles in radians.
 
@@ -623,7 +626,7 @@ def to_matrix(self) -> np.ndarray:
         return om
 
     @classmethod
-    def from_matrix(cls, matrix: np.ndarray) -> Rotation:
+    def from_matrix(cls, matrix: Union[np.ndarray, list, tuple]) -> Rotation:
         """Return rotations from the orientation matrices
         :cite:`rowenhorst2015consistent`.
 

orix/tests/test_miller.py

@@ -32,6 +32,10 @@
 TETRAGONAL_PHASE = Phase(
     point_group="4", structure=Structure(lattice=TETRAGONAL_LATTICE)
 )
+HEXAGONAL_PHASE = Phase(
+    point_group="6/mmm",
+    structure=Structure(lattice=Lattice(3.073, 3.073, 10.053, 90, 90, 120)),
+)
 CUBIC_PHASE = Phase(point_group="m-3m")
 
 
@@ -206,6 +210,24 @@ def test_symmetrise(self):
         )
         assert np.allclose(mult2, [6, 12, 8])
 
+        # Test from https://github.com/pyxem/orix/issues/404
+        m3 = Miller(UVTW=[1, -1, 0, 0], phase=HEXAGONAL_PHASE)
+        assert np.allclose(m3.multiplicity, 6)
+        # fmt: off
+        assert np.allclose(
+            m3.symmetrise(unique=True).data,
+            [
+                [ 4.6095, -2.6613, 0],
+                [ 0     ,  5.3226, 0],
+                [-4.6095, -2.6613, 0],
+                [-4.6095,  2.6613, 0],
+                [ 0     , -5.3226, 0],
+                [ 4.6095,  2.6613, 0],
+            ],
+            atol=1e-4,
+        )
+        # fmt: on
+
     def test_unique(self):
         # From the "Crystal geometry" notebook
         diamond = Phase(space_group=227)

orix/vector/miller.py

@@ -773,7 +773,7 @@ def unique(
             operations = self.phase.point_group
             n_v = v.size
             v2 = operations.outer(v).flatten().reshape(*(n_v, operations.size))
-            data = v2.data.round(12)
+            data = v2.data.round(10)
             data_sorted = np.zeros_like(data)
             for i in range(n_v):
                 a = data[i]

orix/vector/vector3d.py

@@ -480,7 +480,7 @@ def angle_with(self, other: Vector3d) -> np.ndarray:
         angles
             The angle between the vectors, in radians.
         """
-        cosines = np.round(self.dot(other) / self.norm / other.norm, 12)
+        cosines = np.round(self.dot(other) / self.norm / other.norm, 10)
         return np.arccos(cosines)
 
     def rotate(