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reduce atol/rtol on tests
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@jonwright
jonwright committed Mar 28, 2024
1 parent a2828df commit a482dff
Showing 1 changed file with 90 additions and 54 deletions.
144 changes: 90 additions & 54 deletions test/test_orix.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,16 +19,16 @@ class TestOrixPhase(unittest.TestCase):

def test_no_spacegroup(self):
# set up hexagonal B matrix without a spacegroup
hex_ucell_array = np.array([3, 3, 4, 90., 90., 120.])
hex_ucell = unitcell(hex_ucell_array, symmetry='P')
hex_ucell_array = np.array([3, 3, 4, 90.0, 90.0, 120.0])
hex_ucell = unitcell(hex_ucell_array, symmetry="P")

# should fail because we didn't pass a spacegroup for the symmetry
with self.assertRaises(AttributeError):
phase = hex_ucell.orix_phase

def test_with_spacegroup(self):
# set up hexagonal B matrix with a spacegroup
hex_ucell_array = np.array([3, 3, 4, 90., 90., 120.])
hex_ucell_array = np.array([3, 3, 4, 90.0, 90.0, 120.0])
hex_ucell = unitcell(hex_ucell_array, symmetry=194)

# we should have an orix phase object
Expand All @@ -41,16 +41,16 @@ class TestGetOrixOrien(unittest.TestCase):

def test_no_spacegroup(self):
# set up hexagonal B matrix without a spacegroup
hex_ucell_array = np.array([3, 3, 4.1, 90., 90., 120.])
hex_ucell_array = np.array([3, 3, 4.1, 90.0, 90.0, 120.0])
hex_ucell = unitcell(hex_ucell_array, symmetry=194)

B = hex_ucell.B

# set up reference unit cell
ref_hex_ucell_array = np.array([3, 3, 4.0, 90., 90., 120.])
ref_hex_ucell = unitcell(ref_hex_ucell_array, symmetry='P')
ref_hex_ucell_array = np.array([3, 3, 4.0, 90.0, 90.0, 120.0])
ref_hex_ucell = unitcell(ref_hex_ucell_array, symmetry="P")

U = np.squeeze(R.from_euler('zyx', [-90, 0, -90], degrees=True).as_matrix())
U = np.squeeze(R.from_euler("zyx", [-90, 0, -90], degrees=True).as_matrix())

UB = np.dot(U, B)

Expand All @@ -60,13 +60,13 @@ def test_no_spacegroup(self):

def test_hexagonal(self):
# set up hexagonal B matrix
hex_ucell_array = np.array([3, 3, 4.1, 90., 90., 120.])
hex_ucell_array = np.array([3, 3, 4.1, 90.0, 90.0, 120.0])
hex_ucell = unitcell(hex_ucell_array, symmetry=194)

B = hex_ucell.B

# set up reference unit cell
ref_hex_ucell_array = np.array([3, 3, 4.0, 90., 90., 120.])
ref_hex_ucell_array = np.array([3, 3, 4.0, 90.0, 90.0, 120.0])
ref_hex_ucell = unitcell(ref_hex_ucell_array, symmetry=194)

# set up U matrix
Expand All @@ -76,7 +76,7 @@ def test_hexagonal(self):
# b* to point in +X lab
# c* to point in +Y lab

U = np.squeeze(R.from_euler('zyx', [-90, 0, -90], degrees=True).as_matrix())
U = np.squeeze(R.from_euler("zyx", [-90, 0, -90], degrees=True).as_matrix())

UB = np.dot(U, B)

Expand All @@ -86,27 +86,29 @@ def test_hexagonal(self):
# a* should be pointing in lab Z

# get direction of (100) normal in cartesian lab frame as Numpy array
ra_direc_lab = np.array((~orix_orien * Miller(hkl=(1, 0, 0), phase=orix_phase)).xyz).T
ra_direc_lab = np.array(
(~orix_orien * Miller(hkl=(1, 0, 0), phase=orix_phase)).xyz
).T
lab_z = np.array([0, 0, 1])

ra_direc_lab_unit = ra_direc_lab / np.linalg.norm(ra_direc_lab)

self.assertTrue(np.allclose(ra_direc_lab_unit, lab_z))

def test_hexagonal_many(self):
print("")
# print("")
# set up hexagonal B matrix
hex_ucell_array = np.array([3, 3, 4.0, 90., 90., 120.])
hex_ucell_array = np.array([3, 3, 4.0, 90.0, 90.0, 120.0])
hex_ucell = unitcell(hex_ucell_array, symmetry=194)

B = hex_ucell.B

# set up reference unit cell
ref_hex_ucell_array = np.array([3, 3, 4.0, 90., 90., 120.])
ref_hex_ucell_array = np.array([3, 3, 4.0, 90.0, 90.0, 120.0])
ref_hex_ucell = unitcell(ref_hex_ucell_array, symmetry=194)

# many random orientations
Us = R.random(100000).as_matrix()
Us = R.random(1000).as_matrix()

UBs = np.dot(Us, B)

Expand All @@ -124,20 +126,53 @@ def test_hexagonal_many(self):
# work out a* directions in lab frame using Orix
astar_lab_orix = np.array((~orix_orien).outer(astar_miller).xyz).T[0]

# are they close within 5%?
self.assertTrue(np.allclose(astar_lab_id11, astar_lab_orix, rtol=0.05, atol=0))
# are they essentially the same:
self.assertTrue(np.allclose(astar_lab_id11, astar_lab_orix))

def test_one_equals_many(self):
"""
Check that the orientation we get back with one orientation is the same
as for an array (the code path is different)
"""
Umats = [m.as_matrix() for m in R.random(10)]
for uc in (
[3, 3, 3, 90, 90, 90], # cubic
[3, 3, 4, 90, 90, 120], # hexagonal
[3, 3, 3, 65, 65, 65], # trigonal PROBLEM CASE!!! which number/setting?
[3, 3, 4, 90, 90, 90], # tetragonal
[3, 4, 5, 90, 90, 90], # orthorhombic
[3, 4, 5, 95, 90, 90], # monoclinic a
[3, 4, 5, 90, 95, 90], # monoclinic b
[3, 4, 5, 90, 90, 95], # monoclinic c
[3, 4, 5, 91, 92, 93], # triclinic
):
for sgno in (
2, # P-1,
10, # P2/m
123, # P4/mmm
162, # R-3m
191, # P6/mm
221, # Pm3m
):
cell = unitcell(uc, sgno)
UBs = [m.dot(cell.B) for m in Umats]
# convert one at a time:
o1 = [cell.get_orix_orien(m).to_matrix() for m in UBs]
# convert as an array:
o2 = [m.to_matrix() for m in cell.get_orix_orien(UBs)]
self.assertTrue(np.allclose(o1, o2))


class TestIPFCol(unittest.TestCase):
def test_cubic(self):
# set up B matrix
cubic_ucell_array = np.array([3., 3., 3., 90., 90., 90.])
cubic_ucell_array = np.array([3.0, 3.0, 3.0, 90.0, 90.0, 90.0])
cubic_ucell = unitcell(cubic_ucell_array, symmetry="F")

B = cubic_ucell.B

# set up reference unit cell
ref_cubic_ucell_array = np.array([3, 3, 3, 90., 90., 90.])
ref_cubic_ucell_array = np.array([3, 3, 3, 90.0, 90.0, 90.0])
ref_cubic_ucell = unitcell(ref_cubic_ucell_array, symmetry=225)

# set up U matrix
Expand All @@ -147,35 +182,30 @@ def test_cubic(self):
# b* to point in +X lab
# c* to point in +Y lab

U = np.squeeze(R.from_euler('zyx', [-90, 0, -90], degrees=True).as_matrix())
U = np.squeeze(R.from_euler("zyx", [-90, 0, -90], degrees=True).as_matrix())

UB = np.dot(U, B)

# each of the 100, 010, 001, etc directions should have red colours (cubic symmetry)

axes = np.array([
[1., 0, 0],
[0, 1, 0],
[0, 0, 1],
[-1, 0, 0],
[0, -1, 0],
[0, 0, -1]
])
axes = np.array(
[[1.0, 0, 0], [0, 1, 0], [0, 0, 1], [-1, 0, 0], [0, -1, 0], [0, 0, -1]]
)

red = np.array([[1., 0., 0.]])
red = np.array([[1.0, 0.0, 0.0]])

for axis in axes:
rgb = ref_cubic_ucell.get_ipf_colour(UBs=UB, axis=axis)
self.assertTrue(np.allclose(rgb, red))

def test_cubic_110(self):
cubic_ucell_array = np.array([3., 3., 3., 90., 90., 90.])
cubic_ucell_array = np.array([3.0, 3.0, 3.0, 90.0, 90.0, 90.0])
cubic_ucell = unitcell(cubic_ucell_array, symmetry="F")

B = cubic_ucell.B

# set up reference unit cell
ref_cubic_ucell_array = np.array([3, 3, 3, 90., 90., 90.])
ref_cubic_ucell_array = np.array([3, 3, 3, 90.0, 90.0, 90.0])
ref_cubic_ucell = unitcell(ref_cubic_ucell_array, symmetry=225)

# set up U matrix
Expand All @@ -185,57 +215,60 @@ def test_cubic_110(self):
# rotate 45 degrees in Z
# should mean 0.5 e1 + 0.5 e2 + 0.0 e3

U = np.squeeze(R.from_euler('z', [44], degrees=True).as_matrix())
U = np.squeeze(R.from_euler("z", [45.0], degrees=True).as_matrix())

UB = np.dot(U, B)

# 110 should be pointing along X
# so in an IPF-X plot, the colour should be green

rgb = ref_cubic_ucell.get_ipf_colour(UBs=UB, axis=np.array([1, 0, 0]))
green = np.array([0., 1., 0.])

self.assertTrue(np.allclose(rgb, green, atol=0.05))
green = np.array([0.0, 1.0, 0.0])
self.assertTrue(np.allclose(rgb, green, atol=0.01))

def test_cubic_111(self):
# set up B matrix
cubic_ucell_array = np.array([3., 3., 3., 90., 90., 90.])
cubic_ucell_array = np.array([3.0, 3.0, 3.0, 90.0, 90.0, 90.0])
cubic_ucell = unitcell(cubic_ucell_array, symmetry="F")

B = cubic_ucell.B

# set up reference unit cell
ref_cubic_ucell_array = np.array([3, 3, 3, 90., 90., 90.])
ref_cubic_ucell_array = np.array([3, 3, 3, 90.0, 90.0, 90.0])
ref_cubic_ucell = unitcell(ref_cubic_ucell_array, symmetry=225)

# set up U matrix

# we want:
# some (111) normal to point along X
# rotate 45 degrees in Z
# should mean 0.5 e1 + 0.5 e2 + 0.0 e3

U = np.squeeze(R.from_euler('zy', [45, 45], degrees=True).as_matrix())

# You need 111 along an axis, so the angle between 111 and the 110 axis is:
cosangle = (
np.dot((1, 1, 1), (1, 1, 0))
/ np.linalg.norm((1, 1, 1))
/ np.linalg.norm((1, 1, 0))
)
angle = np.degrees(np.arccos(cosangle))
U = R.from_euler("ZYZ", (0, angle, -45), degrees=True).as_matrix()
UB = np.dot(U, B)

# 111 should be pointing along X
# 111 should be pointing along X : check this
g111 = UB.dot((1, 1, 1))
self.assertTrue(np.allclose((1, 0, 0), g111 / np.linalg.norm(g111)))
# so in an IPF-X plot, the colour should be blue-ish

rgb = ref_cubic_ucell.get_ipf_colour(UBs=UB, axis=np.array([1, 0, 0]))
blue = np.array([0., 0., 1.])

self.assertTrue(np.allclose(rgb, blue, atol=0.3))
blue = np.array([0.0, 0.0, 1.0])
self.assertTrue(np.allclose(rgb, blue, atol=0.01))

def test_hexagonal(self):
# set up hexagonal B matrix
hex_ucell_array = np.array([3, 3, 4, 90., 90., 120.])
hex_ucell_array = np.array([3, 3, 4, 90.0, 90.0, 120.0])
hex_ucell = unitcell(hex_ucell_array, symmetry="P")

B = hex_ucell.B

# set up reference unit cell
ref_hex_ucell_array = np.array([3, 3, 4.0, 90., 90., 120.])
ref_hex_ucell_array = np.array([3, 3, 4.0, 90.0, 90.0, 120.0])
ref_hex_ucell = unitcell(ref_hex_ucell_array, symmetry=194)

# set up U matrix
Expand All @@ -245,7 +278,7 @@ def test_hexagonal(self):
# b* to point in +X lab
# c* to point in +Y lab

U = np.squeeze(R.from_euler('zyx', [-90, 0, -90], degrees=True).as_matrix())
U = np.squeeze(R.from_euler("zyx", [-90, 0, -90], degrees=True).as_matrix())

UB = np.dot(U, B)

Expand All @@ -255,14 +288,17 @@ def test_hexagonal(self):
# on TSL, (10-10) is blue

rgb = ref_hex_ucell.get_ipf_colour(UBs=UB, axis=np.array([0, 0, 1]))
blue = np.array([0., 0., 1.])

self.assertTrue(np.allclose(rgb, blue, atol=0.3))
blue = np.array([0.0, 0.0, 1.0])
self.assertTrue(np.allclose(rgb, blue, atol=0.01))

# on an IPF-Y, c* should be parallel to Y
# c* is (0001) normal

rgb = ref_hex_ucell.get_ipf_colour(UBs=UB, axis=np.array([0, 1, 0]))
red = np.array([1., 0., 0.])
red = np.array([1.0, 0.0, 0.0])

self.assertTrue(np.allclose(rgb, red, atol=0.01))


self.assertTrue(np.allclose(rgb, red, atol=0.3))
if __name__ == "__main__":
unittest.main()

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