Fix EBSD orientation refinement on Windows

CHANGELOG.rst

@@ -12,6 +12,19 @@ best to adhere to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 Contributors to each release are listed in alphabetical order by first name. List
 entries are sorted in descending chronological order.
 
+0.5.7 (2022-01-10)
+==================
+
+Contributors
+------------
+- Håkon Wiik Ånes
+
+Fixed
+-----
+- EBSD orientation refinement on Windows producing garbage results due to unpredictable
+  behaviour in Numba function which converts Euler triplet to quaternion.
+  (`#495 <https://github.com/pyxem/kikuchipy/pull/495>`_)
+
 0.5.6 (2022-01-02)
 ==================
 

kikuchipy/_rotation/__init__.py

@@ -57,16 +57,15 @@ def _rotation_from_euler(alpha: float, beta: float, gamma: float) -> np.ndarray:
     This function is optimized with Numba, so care must be taken with
     array shapes and data types.
     """
-    sigma = 0.5 * np.add(alpha, gamma)
-    delta = 0.5 * np.subtract(alpha, gamma)
-    c = np.cos(beta / 2)
-    s = np.sin(beta / 2)
-
-    rotation = np.zeros(4)
-    rotation[0] = c * np.cos(sigma)
-    rotation[1] = -s * np.cos(delta)
-    rotation[2] = -s * np.sin(delta)
-    rotation[3] = -c * np.sin(sigma)
+    sigma = 0.5 * (alpha + gamma)
+    delta = 0.5 * (alpha - gamma)
+    c = np.cos(0.5 * beta)
+    s = np.sin(0.5 * beta)
+
+    rotation = np.array(
+        (c * np.cos(sigma), -s * np.cos(delta), -s * np.sin(delta), -c * np.sin(sigma)),
+        dtype=np.float64,
+    )
 
     if rotation[0] < 0:
         rotation = -rotation

kikuchipy/conftest.py

@@ -479,6 +479,57 @@ def oxford_binary_file(tmpdir, request):
     yield f
 
 
+@pytest.fixture
+def nickel_ebsd_small_di_xmap():
+    """Yield an :class:`~orix.crystal_map.CrystalMap` from dictionary
+    indexing of the :func:`kikuchipy.data.nickel_ebsd_small` data set.
+
+    Dictionary indexing was performed with the following script:
+
+    .. code-block:: python
+
+        import kikuchipy as kp
+        from orix.sampling import get_sample_fundamental
+
+
+        s = kp.data.nickel_ebsd_small()
+        s.remove_static_background()
+        s.remove_dynamic_background()
+
+        mp = kp.data.nickel_ebsd_master_pattern_small(energy=20, projection="lambert")
+        rot = get_sample_fundamental(resolution=1.4, point_group=mp.phase.point_group)
+        detector = kp.detectors.EBSDDetector(
+            shape=s.axes_manager.signal_shape[::-1],
+            sample_tilt=70,
+            pc=(0.421, 0.7794, 0.5049),
+            convention="tsl"
+        )
+        sim_dict = mp.get_patterns(rotations=rot, detector=detector, energy=20)
+        xmap = s.dictionary_indexing(dictionary=sim_dict, keep_n=1)
+    """
+    coords, _ = create_coordinate_arrays(shape=(3, 3), step_sizes=(1.5, 1.5))
+    # fmt: off
+    grain1 = (0.9542, -0.0183, -0.2806,  0.1018)
+    grain2 = (0.9542,  0.0608, -0.2295, -0.1818)
+    xmap = CrystalMap(
+        rotations=Rotation((
+            grain1, grain2, grain2,
+            grain1, grain2, grain2,
+            grain1, grain2, grain2
+        )),
+        x=coords["x"],
+        y=coords["y"],
+        prop=dict(scores=np.array((
+            0.4364652,  0.3772456,  0.4140171,
+            0.4537009,  0.37445727, 0.43675864,
+            0.42391658, 0.38740265, 0.41931134
+        ))),
+        phase_list=PhaseList(Phase("ni", 225, "m-3m")),
+    )
+    # fmt: on
+    yield xmap
+
+
 # ---------------------- pytest doctest-modules ---------------------- #
 
 

kikuchipy/indexing/_refinement/_refinement.py

@@ -751,7 +751,7 @@ def compute_refine_orientation_results(
     refined_xmap
         Crystal map with refined orientations and scores.
     """
-    n_patterns = np.prod(results.shape[:-1])
+    n_patterns = int(np.prod(results.shape[:-1]))
     with ProgressBar():
         print(f"Refining {n_patterns} orientation(s):", file=sys.stdout)
         time_start = time()
@@ -798,7 +798,7 @@ def compute_refine_projection_center_results(
     new_detector : :class:`~kikuchipy.detectors.EBSDDetector`
         EBSD detector with refined projection center parameters.
     """
-    n_patterns = np.prod(results.shape[:-1])
+    n_patterns = int(np.prod(results.shape[:-1]))
     nav_shape = xmap.shape
     with ProgressBar():
         print(f"Refining {n_patterns} projection center(s):", file=sys.stdout)
@@ -847,7 +847,7 @@ def compute_refine_orientation_projection_center_results(
     new_detector : :class:`~kikuchipy.detectors.EBSDDetector`
         EBSD detector with refined projection center parameters.
     """
-    n_patterns = np.prod(results.shape[:-1])
+    n_patterns = int(np.prod(results.shape[:-1]))
     nav_shape = xmap.shape
     with ProgressBar():
         print(

kikuchipy/release.py

@@ -35,4 +35,4 @@
 name = "kikuchipy"
 platforms = ["Linux", "MacOS X", "Windows"]
 status = "Development"
-version = "0.5.6"
+version = "0.5.7"

kikuchipy/signals/tests/test_ebsd.py

@@ -1646,6 +1646,29 @@ def test_refine_orientation_chunking(
         )
         assert dask_array.chunksize == chunksize
 
+    def test_refine_orientation_nickel_ebsd_small(
+        self, nickel_ebsd_small_di_xmap, detector
+    ):
+        xmap = nickel_ebsd_small_di_xmap
+
+        s = kp.data.nickel_ebsd_small()
+        s.remove_static_background()
+        s.remove_dynamic_background()
+
+        energy = 20
+        xmap_ref = s.refine_orientation(
+            xmap=xmap,
+            detector=detector,
+            master_pattern=kp.data.nickel_ebsd_master_pattern_small(
+                energy=energy,
+                projection="lambert",
+                hemisphere="north",
+            ),
+            energy=energy,
+        )
+
+        assert np.all(xmap_ref.scores > xmap.scores)
+
     # ------------------- Refine projection centers ------------------ #
 
     @pytest.mark.parametrize(