Merge pull request #61 from pc494/tidy-up-streographic

Tidy up streographic code + StructureLibrary changes

diffsims/libraries/structure_library.py

@@ -17,6 +17,7 @@
 # along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
 
 import diffsims as ds
+from diffsims.generators.rotation_list_generators import get_grid_streographic
 
 
 class StructureLibrary():
@@ -54,3 +55,51 @@ def __init__(self,
         self.struct_lib = dict()
         for ident, struct, ori in zip(identifiers, structures, orientations):
             self.struct_lib[ident] = (struct, ori)
+
+    @classmethod
+    def from_orientation_lists(cls,identifiers,structures,orientations):
+        """
+        Creates a structure library from "manual" orientation lists
+
+        Parameters
+        ----------
+        identifiers : list of strings/ints
+            A list of phase identifiers referring to different atomic structures.
+        structures : list of diffpy.structure.Structure objects.
+            A list of diffpy.structure.Structure objects describing the atomic
+            structure associated with each phase in the library.
+        orientations : list of lists of tuples
+            A list over identifiers of lists of euler angles (as tuples) in the rzxz
+            convention and in degrees.
+        Returns
+        -------
+        StructureLibrary
+        """
+        return cls(identifiers,structures,orientations)
+
+    @classmethod
+    def from_crystal_systems(cls,identifiers,structures,systems,resolution,equal='angle'):
+        """
+        Creates a structure library from crystal system derived orientation lists
+
+        Parameters
+        ----------
+        identifiers : list of strings/ints
+            A list of phase identifiers referring to different atomic structures.
+        structures : list of diffpy.structure.Structure objects.
+            A list of diffpy.structure.Structure objects describing the atomic
+            structure associated with each phase in the library.
+        systems : list
+            A list over indentifiers of crystal systems
+        resolution : float
+            resolution in degrees
+        equal : str
+            Default is 'angle'
+        Returns
+        -------
+        StructureLibrary
+        """
+        orientations = []
+        for system in systems:
+            orientations.append(get_grid_streographic(system,resolution,equal))
+        return cls(identifiers,structures,orientations)

diffsims/tests/test_library/test_structure_library.py

@@ -21,20 +21,24 @@
 
 from diffsims.libraries.structure_library import StructureLibrary
 
-
-def test_constructor():
+def test_from_orientations_method():
     identifiers = ['a', 'b']
-    # Arbitrary values for tracking
     structures = [1, 2]
     orientations = [3, 4]
-    library = StructureLibrary(identifiers, structures, orientations)
-
+    library = StructureLibrary.from_orientation_lists(identifiers,structures,orientations)
     np.testing.assert_equal(library.identifiers, identifiers)
     np.testing.assert_equal(library.structures, structures)
     np.testing.assert_equal(library.orientations, orientations)
     np.testing.assert_equal(library.struct_lib['a'], (1, 3))
     np.testing.assert_equal(library.struct_lib['b'], (2, 4))
 
+def test_from_systems_methods():
+    identifiers = ['a', 'b']
+    structures = [1, 2]
+    systems = ['cubic', 'hexagonal']
+    library = StructureLibrary.from_crystal_systems(identifiers,structures,systems,resolution=2,equal='angle')
+    assert len(library.struct_lib['a'][1]) < len(library.struct_lib['b'][1]) #cubic is less area the hexagonal
+
 
 @pytest.mark.parametrize('identifiers, structures, orientations', [
     (['a'], [1, 2], [3, 4]),

diffsims/tests/test_utils/test_sim_utils.py

@@ -23,39 +23,7 @@
 from diffsims.utils.sim_utils import get_electron_wavelength, \
     get_interaction_constant, get_unique_families, get_kinematical_intensities, \
     get_vectorized_list_for_atomic_scattering_factors, get_points_in_sphere, \
-    simulate_kinematic_scattering, is_lattice_hexagonal, uvtw_to_uvw, \
-    rotation_list_stereographic
-
-
-def create_lattice_structure(a, b, c, alpha, beta, gamma):
-    lattice = diffpy.structure.lattice.Lattice(a, b, c, alpha, beta, gamma)
-    atom = diffpy.structure.atom.Atom(atype='Si', xyz=[0, 0, 0], lattice=lattice)
-    return diffpy.structure.Structure(atoms=[atom], lattice=lattice)
-
-
-def create_structure_cubic():
-    return create_lattice_structure(1, 1, 1, 90, 90, 90)
-
-
-def create_structure_hexagonal():
-    return create_lattice_structure(1, 1, 1, 90, 90, 120)
-
-
-def create_structure_orthorombic():
-    return create_lattice_structure(1, 2, 3, 90, 90, 90)
-
-
-def create_structure_tetragonal():
-    return create_lattice_structure(1, 1, 2, 90, 90, 90)
-
-
-def create_structure_trigonal():
-    return create_lattice_structure(1, 1, 1, 100, 100, 100)
-
-
-def create_structure_monoclinic():
-    return create_lattice_structure(1, 2, 3, 90, 100, 90)
-
+    simulate_kinematic_scattering, is_lattice_hexagonal, uvtw_to_uvw
 
 @pytest.mark.parametrize('accelerating_voltage, wavelength', [
     (100, 0.0370143659),
@@ -143,65 +111,3 @@ def test_kinematic_simulator_invalid_illumination():
 def test_uvtw_to_uvw(uvtw, uvw):
     val = uvtw_to_uvw(uvtw)
     np.testing.assert_almost_equal(val, uvw)
-
-
-# Three corners of the rotation lists, for comparison
-structure_cubic_rotations = [
-    [0, 0, 0],
-    [90, 45, 0],
-    [135, 54.73561032, 0]
-]
-
-structure_hexagonal_rotations = [
-    [0, 0, 0],
-    [90, 90, 0],
-    [120, 90, 0]
-]
-
-structure_orthogonal_rotations = [
-    [0, 0, 0],
-    [90, 90, 0],
-    [180, 90, 0]
-]
-
-structure_tetragonal_rotations = [
-    [0, 0, 0],
-    [90, 90, 0],
-    [135, 90, 0]
-]
-
-structure_trigonal_rotations = [
-    [0, 0, 0],
-    [-28.64458044, 75.45951959, 0],
-    [38.93477108, 90, 0]
-]
-
-structure_monoclinic_rotations = [
-    [0, 0, 0],
-    [0, 90, 0],
-    [180, 90, 0]
-]
-
-
-@pytest.mark.parametrize('structure, corner_a, corner_b, corner_c, rotation_list', [
-    (create_structure_cubic(), (0, 0, 1), (1, 0, 1), (1, 1, 1), structure_cubic_rotations),
-    (create_structure_hexagonal(), (0, 0, 0, 1), (1, 0, -1, 0), (1, 1, -2, 0), structure_hexagonal_rotations),
-    (create_structure_orthorombic(), (0, 0, 1), (1, 0, 0), (0, 1, 0), structure_orthogonal_rotations),
-    (create_structure_tetragonal(), (0, 0, 1), (1, 0, 0), (1, 1, 0), structure_tetragonal_rotations),
-    (create_structure_trigonal(), (0, 0, 0, 1), (0, -1, 1, 0), (1, -1, 0, 0), structure_trigonal_rotations),
-    (create_structure_monoclinic(), (0, 0, 1), (0, 1, 0), (0, -1, 0), structure_monoclinic_rotations),
-])
-def test_rotation_list_stereographic(structure, corner_a, corner_b, corner_c, rotation_list):
-    val = rotation_list_stereographic(structure, corner_a, corner_b, corner_c, [0], np.deg2rad(10))
-    for expected in rotation_list:
-        assert any((np.allclose(expected, actual) for actual in val))
-
-
-@pytest.mark.xfail(raises=ValueError)
-@pytest.mark.parametrize('structure, corner_a, corner_b, corner_c, inplane_rotations, resolution, rotation_list', [
-    (create_structure_cubic(), (0, 0, 1), (0, 0, 1), (1, 1, 1), [0], np.deg2rad(10), structure_cubic_rotations),
-    (create_structure_cubic(), (0, 0, 1), (1, 0, 1), (0, 0, 1), [0], np.deg2rad(10), structure_cubic_rotations)
-])
-def test_rotation_list_stereographic_raises_invalid_corners(
-        structure, corner_a, corner_b, corner_c, inplane_rotations, resolution, rotation_list):
-    rotation_list_stereographic(structure, corner_a, corner_b, corner_c, inplane_rotations, resolution)