class TestUBCalculationWithYouStrategy():
"""Testing the math only here.
"""
def setUp(self):
self.tempdir = tempfile.mkdtemp()
geometry = SixCircle() # pass through
hardware = Mock()
names = 'm', 'd', 'n', 'e', 'c', 'p'
hardware.get_axes_names.return_value = names
self.tmpdir = tempfile.mkdtemp()
print self.tmpdir
self.ubcalc = UBCalculation(hardware,
geometry,
UBCalculationJSONPersister(self.tmpdir),
YouUbCalcStrategy())
def testAgainstI16Results(self):
self.ubcalc.start_new('cubcalc')
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', None)
self.ubcalc.add_reflection(0, 0, 1, REF1b, EN1, '001', None)
matrixeq_(self.ubcalc.UB, UB1)
def test_save_and_restore_empty_ubcalc_with_one_already_started(self):
NAME = 'test_save_and_restore_empty_ubcalc_with_one_already_started'
self.ubcalc.start_new(NAME)
self.ubcalc.start_new(NAME)
def test_save_and_restore_empty_ubcalc(self):
NAME = 'test_save_and_restore_empty_ubcalc'
self.ubcalc.start_new(NAME)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
eq_(self.ubcalc.name, NAME)
def test_save_and_restore_ubcalc_with_lattice(self):
NAME = 'test_save_and_restore_ubcalc_with_lattice'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
eq_(self.ubcalc._state.crystal.getLattice(), ('latt', 1, 1, 1, 90, 90, 90))
def test_save_and_restore_ubcalc_with_reflections(self):
NAME = 'test_save_and_restore_ubcalc_with_reflections'
self.ubcalc.start_new(NAME)
now = datetime.datetime.now()
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', now)
self.ubcalc.add_reflection(0, 0, 1, REF1b, EN1, '001', now)
self.ubcalc.add_reflection(0, 0, 1.5, REF1b, EN1, '001_5', now)
ref1 = self.ubcalc.get_reflection(1)
ref2 = self.ubcalc.get_reflection(2)
ref3 = self.ubcalc.get_reflection(3)
eq_(self.ubcalc.get_reflection(1), ref1)
eq_(self.ubcalc.get_reflection(2), ref2)
eq_(self.ubcalc.get_reflection(3), ref3)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
eq_(self.ubcalc.get_reflection(1), ref1)
eq_(self.ubcalc.get_reflection(2), ref2)
eq_(self.ubcalc.get_reflection(3), ref3)
def test_save_and_restore_ubcalc_with_UB_from_two_ref(self):
NAME = 'test_save_and_restore_ubcalc_with_UB_from_two_ref'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', None)
self.ubcalc.add_reflection(0, 0, 1, REF1b, EN1, '001', None)
matrixeq_(self.ubcalc.UB, UB1)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, UB1)
def test_save_and_restore_ubcalc_with_UB_from_one_ref(self):
NAME = 'test_save_and_restore_ubcalc_with_UB_from_one_ref'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', None)
self.ubcalc.calculate_UB_from_primary_only()
matrixeq_(self.ubcalc.UB, UB1, places=2)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, UB1, places=2)
def test_save_and_restore_ubcalc_with_manual_ub(self):
NAME = 'test_save_and_restore_ubcalc_with_manual_ub'
UB = matrix([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
self.ubcalc.start_new(NAME)
self.ubcalc.set_UB_manually(UB)
matrixeq_(self.ubcalc.UB, UB)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, UB)
def test_save_and_restore_ubcalc_with_manual_u(self):
NAME = 'test_save_and_restore_ubcalc_with_manual_u'
U = matrix([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.set_U_manually(U)
matrixeq_(self.ubcalc.UB, U * 2 * pi)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, U * 2 * pi)
class TestUBCalculationWithYouStrategy():
"""Testing the math only here.
"""
def setup_method(self):
self.tempdir = tempfile.mkdtemp()
geometry = SixCircle() # pass through
hardware = Mock()
names = 'm', 'd', 'n', 'e', 'c', 'p'
hardware.get_axes_names.return_value = names
self.tmpdir = tempfile.mkdtemp()
print self.tmpdir
settings.hardware = hardware
settings.geometry = geometry
self.ubcalc = UBCalculation(
UBCalculationJSONPersister(self.tmpdir, UBCalcStateEncoder),
YouUbCalcStrategy())
def testAgainstI16Results(self):
self.ubcalc.start_new('cubcalc')
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', None)
self.ubcalc.add_reflection(0, 0, 1, REF1b, EN1, '001', None)
matrixeq_(self.ubcalc.UB, UB1)
def test_save_and_restore_empty_ubcalc_with_one_already_started(self):
NAME = 'test_save_and_restore_empty_ubcalc_with_one_already_started'
self.ubcalc.start_new(NAME)
self.ubcalc.start_new(NAME)
def test_save_and_restore_empty_ubcalc(self):
NAME = 'test_save_and_restore_empty_ubcalc'
self.ubcalc.start_new(NAME)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
eq_(self.ubcalc.name, NAME)
def test_save_and_restore_ubcalc_with_lattice(self):
NAME = 'test_save_and_restore_ubcalc_with_lattice'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
eq_(self.ubcalc._state.crystal.getLattice(),
('latt', 1, 1, 1, 90, 90, 90))
def test_save_and_restore_ubcalc_with_reflections(self):
NAME = 'test_save_and_restore_ubcalc_with_reflections'
self.ubcalc.start_new(NAME)
now = datetime.datetime.now()
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', now)
self.ubcalc.add_reflection(0, 0, 1, REF1b, EN1, '001', now)
self.ubcalc.add_reflection(0, 0, 1.5, REF1b, EN1, '001_5', now)
ref1 = self.ubcalc.get_reflection(1)
ref2 = self.ubcalc.get_reflection(2)
ref3 = self.ubcalc.get_reflection(3)
eq_(self.ubcalc.get_reflection(1), ref1)
eq_(self.ubcalc.get_reflection(2), ref2)
eq_(self.ubcalc.get_reflection(3), ref3)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
eq_(self.ubcalc.get_reflection(1), ref1)
eq_(self.ubcalc.get_reflection(2), ref2)
eq_(self.ubcalc.get_reflection(3), ref3)
def test_save_and_restore_ubcalc_with_UB_from_two_ref(self):
NAME = 'test_save_and_restore_ubcalc_with_UB_from_two_ref'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', None)
self.ubcalc.add_reflection(0, 0, 1, REF1b, EN1, '001', None)
matrixeq_(self.ubcalc.UB, UB1)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, UB1)
def test_save_and_restore_ubcalc_with_UB_from_one_ref(self):
NAME = 'test_save_and_restore_ubcalc_with_UB_from_one_ref'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', None)
self.ubcalc.calculate_UB_from_primary_only()
matrixeq_(self.ubcalc.UB, UB1, places=2)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, UB1, places=2)
def test_save_and_restore_ubcalc_with_manual_ub(self):
NAME = 'test_save_and_restore_ubcalc_with_manual_ub'
UB = matrix([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
self.ubcalc.start_new(NAME)
self.ubcalc.set_UB_manually(UB)
matrixeq_(self.ubcalc.UB, UB)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, UB)
def test_save_and_restore_ubcalc_with_manual_u(self):
NAME = 'test_save_and_restore_ubcalc_with_manual_u'
U = matrix([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.set_U_manually(U)
matrixeq_(self.ubcalc.UB, U * 2 * pi)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, U * 2 * pi)
def test_calc_hkl_offset(self):
NAME = 'test_calc_hkl_offset'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.set_U_manually(x_rotation(0))
hkloff_110 = self.ubcalc.calc_hkl_offset(0, 0, sqrt(2), 90. * TORAD,
-45 * TORAD)
hkloff_m101 = self.ubcalc.calc_hkl_offset(0, 0, sqrt(2), 45. * TORAD,
90 * TORAD)
alpha = atan2(2, 1)
hkloff_102 = self.ubcalc.calc_hkl_offset(sqrt(5), 0, 0, alpha,
90 * TORAD)
matrixeq_(matrix('1 1 0'), matrix(hkloff_110))
matrixeq_(matrix('-1 0 1'), matrix(hkloff_m101))
matrixeq_(matrix('1 0 2'), matrix(hkloff_102))
def test_calc_offset_for_hkl(self):
NAME = 'test_calc_offset_for_hkl'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.set_U_manually(x_rotation(0))
for hklref, hkloff, pol_ref, az_ref, sc_ref in [
([0, 0, 1], [1, 1, 0], 90 * TORAD, -45 * TORAD, sqrt(2)),
([0, 0, 1], [-1, 0, 1], 45 * TORAD, 90 * TORAD, sqrt(2)),
([1, 0, 0], [1, 0, 2], atan2(2, 1), 90 * TORAD, sqrt(5)),
]:
pol, az, sc = self.ubcalc.calc_offset_for_hkl(hkloff, hklref)
matrixeq_(matrix([[pol_ref, az_ref, sc_ref]]),
matrix([[pol, az, sc]]))
class TestUBCalculationWithYouStrategy():
"""Testing the math only here.
"""
def setup_method(self):
self.tempdir = tempfile.mkdtemp()
geometry = SixCircle() # pass through
hardware = Mock()
names = 'm', 'd', 'n', 'e', 'c', 'p'
hardware.get_axes_names.return_value = names
self.tmpdir = tempfile.mkdtemp()
print self.tmpdir
self.ubcalc = UBCalculation(hardware,
geometry,
UBCalculationJSONPersister(self.tmpdir),
YouUbCalcStrategy())
def testAgainstI16Results(self):
self.ubcalc.start_new('cubcalc')
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', None)
self.ubcalc.add_reflection(0, 0, 1, REF1b, EN1, '001', None)
matrixeq_(self.ubcalc.UB, UB1)
def test_save_and_restore_empty_ubcalc_with_one_already_started(self):
NAME = 'test_save_and_restore_empty_ubcalc_with_one_already_started'
self.ubcalc.start_new(NAME)
self.ubcalc.start_new(NAME)
def test_save_and_restore_empty_ubcalc(self):
NAME = 'test_save_and_restore_empty_ubcalc'
self.ubcalc.start_new(NAME)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
eq_(self.ubcalc.name, NAME)
def test_save_and_restore_ubcalc_with_lattice(self):
NAME = 'test_save_and_restore_ubcalc_with_lattice'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
eq_(self.ubcalc._state.crystal.getLattice(), ('latt', 1, 1, 1, 90, 90, 90))
def test_save_and_restore_ubcalc_with_reflections(self):
NAME = 'test_save_and_restore_ubcalc_with_reflections'
self.ubcalc.start_new(NAME)
now = datetime.datetime.now()
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', now)
self.ubcalc.add_reflection(0, 0, 1, REF1b, EN1, '001', now)
self.ubcalc.add_reflection(0, 0, 1.5, REF1b, EN1, '001_5', now)
ref1 = self.ubcalc.get_reflection(1)
ref2 = self.ubcalc.get_reflection(2)
ref3 = self.ubcalc.get_reflection(3)
eq_(self.ubcalc.get_reflection(1), ref1)
eq_(self.ubcalc.get_reflection(2), ref2)
eq_(self.ubcalc.get_reflection(3), ref3)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
eq_(self.ubcalc.get_reflection(1), ref1)
eq_(self.ubcalc.get_reflection(2), ref2)
eq_(self.ubcalc.get_reflection(3), ref3)
def test_save_and_restore_ubcalc_with_UB_from_two_ref(self):
NAME = 'test_save_and_restore_ubcalc_with_UB_from_two_ref'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', None)
self.ubcalc.add_reflection(0, 0, 1, REF1b, EN1, '001', None)
matrixeq_(self.ubcalc.UB, UB1)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, UB1)
def test_save_and_restore_ubcalc_with_UB_from_one_ref(self):
NAME = 'test_save_and_restore_ubcalc_with_UB_from_one_ref'
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.add_reflection(1, 0, 0, REF1a, EN1, '100', None)
self.ubcalc.calculate_UB_from_primary_only()
matrixeq_(self.ubcalc.UB, UB1, places=2)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, UB1, places=2)
def test_save_and_restore_ubcalc_with_manual_ub(self):
NAME = 'test_save_and_restore_ubcalc_with_manual_ub'
UB = matrix([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
self.ubcalc.start_new(NAME)
self.ubcalc.set_UB_manually(UB)
matrixeq_(self.ubcalc.UB, UB)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, UB)
def test_save_and_restore_ubcalc_with_manual_u(self):
NAME = 'test_save_and_restore_ubcalc_with_manual_u'
U = matrix([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
self.ubcalc.start_new(NAME)
self.ubcalc.set_lattice('latt', 1, 1, 1, 90, 90, 90)
self.ubcalc.set_U_manually(U)
matrixeq_(self.ubcalc.UB, U * 2 * pi)
self.ubcalc.start_new(NAME + '2')
self.ubcalc.load(NAME)
matrixeq_(self.ubcalc.UB, U * 2 * pi)
