Merge #210 from harripj/transpose_feature

Add transpose method to all 3D classes

CHANGELOG.rst

@@ -21,6 +21,7 @@ Added
   Rodrigues fundamental zone, without having to set it up via Matplotlib.
 - Method Object3d.get_random_sample(), inherited by all 3D objects, returning a new
   flattened instance with elements drawn randomly from the original instance.
+- Add transpose method to all 3D classes to transpose navigation dimensions.
 - Reading of a crystal map from orientation data in Bruker's HDF5 file format.
 
 2021-05-23 - version 0.6.0

doc/reference.rst

@@ -288,6 +288,7 @@ Orientation
     get_distance_matrix
     scatter
     set_symmetry
+    transpose
 .. autoclass:: orix.quaternion.Orientation
     :show-inheritance:
     :members:
@@ -300,6 +301,7 @@ Misorientation
     distance
     equivalent
     set_symmetry
+    transpose
 .. autoclass:: orix.quaternion.Misorientation
     :show-inheritance:
     :members:
@@ -342,6 +344,7 @@ Rotation
     random_vonmises
     to_euler
     to_matrix
+    transpose
     unique
 .. autoclass:: orix.quaternion.Rotation
     :show-inheritance:
@@ -438,6 +441,7 @@ Miller
     rotate
     scatter
     symmetrise
+    transpose
     unique
 .. autoclass:: orix.vector.Miller
     :members:
@@ -485,6 +489,7 @@ Vector3d
     rotate
     scatter
     to_polar
+    transpose
     xvector
     yvector
     zvector

orix/base/__init__.py

@@ -54,9 +54,7 @@ def __init__(self, this, data):
 
 
 class Object3d:
-    """Base class for 3d objects.
-
-    """
+    """Base class for 3d objects."""
 
     dim = None
     """int : The number of dimensions for this object."""
@@ -206,6 +204,43 @@ def reshape(self, *shape):
         obj._data = self._data.reshape(*shape, -1)
         return obj
 
+    def transpose(self, *axes):
+        """Returns a new object containing the same data transposed.
+
+        If ndim is originally 2, then order may be undefined.
+        In this case the first two dimensions will be transposed.
+
+        Parameters
+        ----------
+        axes : int, optional
+            The transposed axes order. Only navigation axes need to be defined.
+            May be undefined if self only contains two navigation dimensions.
+
+        Returns
+        -------
+        obj :
+            A transposed instance of the object.
+
+        """
+        # 1d object should not be transposed
+        if len(self.shape) == 1:
+            return self
+
+        # allow 2d object to be transposed without specifying axes
+        if not len(axes):
+            if len(self.shape) != 2:
+                raise ValueError("Axes must be defined for more than two dimensions.")
+            else:
+                # swap first two axes
+                axes = (1, 0)
+
+        if len(axes) != len(self.shape):
+            raise ValueError(
+                f"Number of axes is ill-defined: {tuple(axes)} does not fit with {self.shape}."
+            )
+
+        return self.__class__(self.data.transpose(*axes, -1))
+
     def get_plot_data(self):
         return self
 

orix/quaternion/orientation.py

@@ -228,6 +228,28 @@ def distance(self, verbose=False, split_size=100):
         distance = _distance(self, verbose, split_size)
         return distance.reshape(self.shape + self.shape)
 
+    def transpose(self, *axes):
+        """Returns a new Misorientation containing the same data transposed.
+
+        If ndim is originally 2, then order may be undefined.
+        In this case the first two dimensions will be transposed.
+
+        Parameters
+        ----------
+        axes: int, optional
+            The transposed axes order. Only navigation axes need to be defined.
+            May be undefined if self only contains two navigation dimensions.
+
+        Returns
+        -------
+        Misorientation
+            The transposed Misorientation.
+
+        """
+        mori = super().transpose(*axes)
+        mori._symmetry = self._symmetry
+        return mori
+
     def __repr__(self):
         """String representation."""
         cls = self.__class__.__name__

orix/tests/test_miller.py

@@ -306,6 +306,31 @@ def test_various_shapes(self):
         assert np.allclose(m6.hkl, v.reshape(shape2 + (3,)))
         assert m1._compatible_with(m6)  # Phase carries over
 
+    def test_transpose(self):
+        # test 2d
+        shape = (11, 5)
+        v = np.random.randint(-5, 5, shape + (3,))
+
+        m1 = Miller(hkl=v, phase=TETRAGONAL_PHASE)
+        m2 = m1.transpose()
+
+        assert m1.shape == m2.shape[::-1]
+        assert m1.phase == m2.phase
+
+        # test 2d
+        shape = (11, 5, 4)
+        v = np.random.randint(-5, 5, shape + (3,))
+
+        m1 = Miller(hkl=v, phase=TETRAGONAL_PHASE)
+        m2 = m1.transpose(0, 2, 1)
+
+        assert m2.shape == (11, 4, 5)
+        assert m1.phase == m2.phase
+
+        m2 = m1.transpose(1, 0, 2)
+        assert m2.shape == (5, 11, 4)
+        assert m1.phase == m2.phase
+
 
 class TestMillerBravais:
     def test_uvw2UVTW(self):

orix/tests/test_orientation.py

@@ -112,7 +112,7 @@ def test_getitem(orientation, symmetry):
 
 @pytest.mark.parametrize("Gl", [C4, C2])
 def test_equivalent(Gl):
-    """ Tests that the property Misorientation.equivalent runs without error,
+    """Tests that the property Misorientation.equivalent runs without error,
     use grain_exchange=True as this falls back to grain_exchange=False when
     Gl!=Gr:
 
@@ -149,6 +149,31 @@ def test_sub_orientation_and_other():
         _ = m - 3
 
 
+def test_transpose_2d():
+    o1 = Orientation.random_vonmises((11, 3))
+    o2 = o1.transpose()
+
+    assert o1.shape == o2.shape[::-1]
+
+
+@pytest.mark.parametrize(
+    "shape, expected_shape, axes",
+    [((11, 3, 5), (11, 5, 3), (0, 2, 1)), ((11, 3, 5), (3, 5, 11), (1, 2, 0))],
+)
+def test_transpose_3d(shape, expected_shape, axes):
+    o1 = Orientation.random_vonmises(shape)
+    o2 = o1.transpose(*axes)
+
+    assert o2.shape == tuple(expected_shape)
+
+
+def test_transpose_symmetry():
+    o1 = Orientation.random_vonmises((11, 3)).set_symmetry(Oh)
+    o2 = o1.transpose()
+
+    assert o1.symmetry == o2.symmetry
+
+
 class TestOrientationInitialization:
     def test_from_euler_symmetry(self):
         euler = np.deg2rad([90, 45, 90])

orix/tests/test_vector3d.py

@@ -27,17 +27,29 @@
 vectors = [
     (1, 0, 0),
     (0, 0, 1),
-    ((0.5, 0.5, 0.5), (-1, 0, 0),),
-    [[[-0.707, 0.707, 1], [2, 2, 2]], [[0.1, -0.3, 0.2], [-5, -6, -7]],],
+    (
+        (0.5, 0.5, 0.5),
+        (-1, 0, 0),
+    ),
+    [
+        [[-0.707, 0.707, 1], [2, 2, 2]],
+        [[0.1, -0.3, 0.2], [-5, -6, -7]],
+    ],
     np.random.rand(3),
 ]
 
 singles = [
     (1, -1, 1),
     (-5, -5, -6),
-    [[9, 9, 9], [0.001, 0.0001, 0.00001],],
+    [
+        [9, 9, 9],
+        [0.001, 0.0001, 0.00001],
+    ],
     np.array(
-        [[[0.5, 0.25, 0.125], [-0.125, 0.25, 0.5]], [[1, 2, 4], [1, -0.3333, 0.1667]],]
+        [
+            [[0.5, 0.25, 0.125], [-0.125, 0.25, 0.5]],
+            [[1, 2, 4], [1, -0.3333, 0.1667]],
+        ]
     ),
 ]
 
@@ -141,8 +153,16 @@ def test_mul(vector, other, expected):
         ),
         ([4, 8, 12], Scalar([4]), [1, 2, 3]),
         ([0.5, 1.0, 1.5], 0.5, [1, 2, 3]),
-        ([1, 2, 3], [-1, 2], [[-1, -2, -3], [1 / 2, 1, 3 / 2]],),
-        ([1, 2, 3], np.array([-1, 1]), [[-1, -2, -3], [1, 2, 3]],),
+        (
+            [1, 2, 3],
+            [-1, 2],
+            [[-1, -2, -3], [1 / 2, 1, 3 / 2]],
+        ),
+        (
+            [1, 2, 3],
+            np.array([-1, 1]),
+            [[-1, -2, -3], [1, 2, 3]],
+        ),
         pytest.param([1, 2, 3], "dracula", None, marks=pytest.mark.xfail),
     ],
     indirect=["vector"],
@@ -202,7 +222,12 @@ def test_polar(azimuth, polar, radial, expected):
 
 
 @pytest.mark.parametrize(
-    "shape", [(1,), (2, 2), (5, 4, 3),],
+    "shape",
+    [
+        (1,),
+        (2, 2),
+        (5, 4, 3),
+    ],
 )
 def test_zero(shape):
     v = Vector3d.zero(shape)
@@ -229,7 +254,10 @@ def test_mul_array(vector):
 
 @pytest.mark.parametrize(
     "vector, x, y, z",
-    [([1, 2, 3], 1, 2, 3), ([[0, 2, 3], [2, 2, 3]], [0, 2], [2, 2], [3, 3]),],
+    [
+        ([1, 2, 3], 1, 2, 3),
+        ([[0, 2, 3], [2, 2, 3]], [0, 2], [2, 2], [3, 3]),
+    ],
     indirect=["vector"],
 )
 def test_xyz(vector, x, y, z):
@@ -302,7 +330,12 @@ def test_assign_z(vector, data, expected):
 
 
 @pytest.mark.parametrize(
-    "vector", [[(1, 0, 0)], [(0.5, 0.5, 1.25), (-1, -1, -1)],], indirect=["vector"],
+    "vector",
+    [
+        [(1, 0, 0)],
+        [(0.5, 0.5, 1.25), (-1, -1, -1)],
+    ],
+    indirect=["vector"],
 )
 def test_perpendicular(vector: Vector3d):
     assert np.allclose(vector.dot(vector.perpendicular).data, 0)
@@ -316,6 +349,75 @@ def test_mean_xyz():
     np.allclose(t.mean().data, 1)
 
 
+def test_transpose_1d():
+    v1 = Vector3d(np.random.rand(7, 3))
+    v2 = v1.transpose()
+
+    assert np.allclose(v1.data, v2.data)
+
+
+@pytest.mark.parametrize(
+    "shape, expected_shape",
+    [
+        ([6, 4, 3], [4, 6, 3]),
+        ([11, 5, 3], [5, 11, 3]),
+    ],
+)
+def test_transpose_2d_data_shape(shape, expected_shape):
+    v1 = Vector3d(np.random.rand(*shape))
+    v2 = v1.transpose()
+
+    assert v2.data.shape == tuple(expected_shape)
+
+
+def test_transpose_3d_no_axes():
+    v1 = Vector3d(np.random.rand(5, 4, 2, 3))
+    with pytest.raises(ValueError, match="Axes must be defined for more than"):
+        _ = v1.transpose()
+
+
+def test_transpose_3d_wrong_number_of_axes():
+    v1 = Vector3d(np.random.rand(5, 4, 2, 3))
+    with pytest.raises(ValueError, match="Number of axes is ill-defined"):
+        _ = v1.transpose(0, 2)
+
+
+@pytest.mark.parametrize(
+    "shape, expected_shape",
+    [
+        ([6, 4], [4, 6]),
+        ([11, 5], [5, 11]),
+    ],
+)
+def test_transpose_2d_shape(shape, expected_shape):
+    v1 = Vector3d(np.random.rand(*shape, 3))
+    v2 = v1.transpose()
+
+    assert v2.shape == tuple(expected_shape)
+
+
+@pytest.mark.parametrize(
+    "shape, expected_shape, axes",
+    [([6, 4, 5, 3], [4, 5, 6, 3], [1, 2, 0]), ([6, 4, 5, 3], [5, 4, 6, 3], [2, 1, 0])],
+)
+def test_transpose_3d_data_shape(shape, expected_shape, axes):
+    v1 = Vector3d(np.random.rand(*shape))
+    v2 = v1.transpose(*axes)
+
+    assert v2.data.shape == tuple(expected_shape)
+
+
+@pytest.mark.parametrize(
+    "shape, expected_shape, axes",
+    [([6, 4, 5], [4, 5, 6], [1, 2, 0]), ([6, 4, 5], [5, 4, 6], [2, 1, 0])],
+)
+def test_transpose_3d_shape(shape, expected_shape, axes):
+    v1 = Vector3d(np.random.rand(*shape, 3))
+    v2 = v1.transpose(*axes)
+
+    assert v2.shape == tuple(expected_shape)
+
+
 @pytest.mark.xfail(strict=True, reason=ValueError)
 def test_zero_perpendicular():
     t = Vector3d(np.asarray([0, 0, 0]))