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 TestUBCalculationWithSixCircleGammaOnArm(unittest.TestCase): def setUp(self): self.geometry = SixCircleGammaOnArmGeometry() self.ubcalc = UBCalculation( ("a", "d", "g", "o", "c", "p"), self.geometry, UbCalculationNonPersister(), VliegUbCalcStrategy() ) self.time = datetime.now() ### State ### def testNewCalculation(self): self.ubcalc.start_new("testcalc") self.assertEqual(self.ubcalc.name, "testcalc", "Name not set by newCalcualtion") @raises(DiffcalcException) def testNewCalculationHasNoU(self): self.ubcalc.start_new("testcalc") print self.ubcalc.U @raises(DiffcalcException) def testNewCalculationHasNoUB(self): self.ubcalc.start_new("testcalc") print self.ubcalc.UB ### Lattice ### def testSetLattice(self): # Not much to test, just make sure no exceptions self.ubcalc.start_new("testcalc") self.ubcalc.set_lattice("testlattice", 4.0004, 4.0004, 2.27, 90, 90, 90) ### Calculations ### def testset_U_manually(self): # Test the calculations with U=I U = [[1, 0, 0], [0, 1, 0], [0, 0, 1]] for sess in scenarios.sessions(): self.setUp() self.ubcalc.start_new("testcalc") self.ubcalc.set_lattice(sess.name, *sess.lattice) self.ubcalc.set_U_manually(U) # Check the U matrix mneq_(self.ubcalc.U, matrix(U), 4, note="wrong U after manually setting U") # Check the UB matrix if sess.bmatrix is None: continue print "U: ", U print "actual ub: ", self.ubcalc.UB.tolist() print " desired b: ", sess.bmatrix mneq_(self.ubcalc.UB, matrix(sess.bmatrix), 4, note="wrong UB after manually setting U") @raises(DiffcalcException) def testGetUMatrix(self): self.ubcalc.start_new("testcalc") print self.ubcalc.U @raises(DiffcalcException) def testGetUBMatrix(self): self.ubcalc.start_new("testcalc") print self.ubcalc.UB def testCalculateU(self): for sess in scenarios.sessions(): self.setUp() self.ubcalc.start_new("testcalc") # Skip this test case unless it contains a umatrix if sess.umatrix is None: continue self.ubcalc.set_lattice(sess.name, *sess.lattice) ref1 = sess.ref1 ref2 = sess.ref2 t = sess.time self.ubcalc.add_reflection(ref1.h, ref1.k, ref1.l, ref1.pos, ref1.energy, ref1.tag, t) self.ubcalc.add_reflection(ref2.h, ref2.k, ref2.l, ref2.pos, ref2.energy, ref2.tag, t) self.ubcalc.calculate_UB() returned = self.ubcalc.U.tolist() print "*Required:" print sess.umatrix print "*Returned:" print returned mneq_(self.ubcalc.U, matrix(sess.umatrix), 4, note="wrong U calulated for sess.name=" + sess.name) def test__str__(self): sess = scenarios.sessions()[0] print "***" print self.ubcalc.__str__() print "***" self.ubcalc.start_new("test") print self.ubcalc.__str__() print "***" self.ubcalc.set_lattice(sess.name, *sess.lattice) print self.ubcalc.__str__() print "***" ref1 = sess.ref1 ref2 = sess.ref2 t = sess.time self.ubcalc.add_reflection(ref1.h, ref1.k, ref1.l, ref1.pos, ref1.energy, ref1.tag, t) self.ubcalc.add_reflection(ref2.h, ref2.k, ref2.l, ref2.pos, ref2.energy, ref2.tag, t) print self.ubcalc.__str__() print "***" self.ubcalc.calculate_UB() print self.ubcalc.__str__()
class TestUBCalculationWithSixCircleGammaOnArm(object): def setup_method(self): self.geometry = SixCircleGammaOnArmGeometry() mock_hardware = Mock() mock_hardware.get_axes_names.return_value = ('a', 'd', 'g', 'o', 'c', 'p') self.ubcalc = UBCalculation( mock_hardware, self.geometry, UbCalculationNonPersister(), VliegUbCalcStrategy()) self.time = datetime.now() ### State ### def testNewCalculation(self): self.ubcalc.start_new('testcalc') assert self.ubcalc.name, 'testcalc' == "Name not set by newCalcualtion" @raises(DiffcalcException) def testNewCalculationHasNoU(self): self.ubcalc.start_new('testcalc') print self.ubcalc.U @raises(DiffcalcException) def testNewCalculationHasNoUB(self): self.ubcalc.start_new('testcalc') print self.ubcalc.UB ### Lattice ### def testSetLattice(self): # Not much to test, just make sure no exceptions self.ubcalc.start_new('testcalc') self.ubcalc.set_lattice('testlattice', 4.0004, 4.0004, 2.27, 90, 90, 90) ### Calculations ### def testset_U_manually(self): # Test the calculations with U=I U = [[1, 0, 0], [0, 1, 0], [0, 0, 1]] for sess in scenarios.sessions(): self.setup_method() self.ubcalc.start_new('testcalc') self.ubcalc.set_lattice(sess.name, *sess.lattice) self.ubcalc.set_U_manually(U) # Check the U matrix mneq_(self.ubcalc.U, matrix(U), 4, note="wrong U after manually setting U") # Check the UB matrix if sess.bmatrix is None: continue print "U: ", U print "actual ub: ", self.ubcalc.UB.tolist() print " desired b: ", sess.bmatrix mneq_(self.ubcalc.UB, matrix(sess.bmatrix), 4, note="wrong UB after manually setting U") @raises(DiffcalcException) def testGetUMatrix(self): self.ubcalc.start_new('testcalc') print self.ubcalc.U @raises(DiffcalcException) def testGetUBMatrix(self): self.ubcalc.start_new('testcalc') print self.ubcalc.UB def testCalculateU(self): for sess in scenarios.sessions(): self.setup_method() self.ubcalc.start_new('testcalc') # Skip this test case unless it contains a umatrix if sess.umatrix is None: continue self.ubcalc.set_lattice(sess.name, *sess.lattice) ref1 = sess.ref1 ref2 = sess.ref2 t = sess.time self.ubcalc.add_reflection( ref1.h, ref1.k, ref1.l, ref1.pos, ref1.energy, ref1.tag, t) self.ubcalc.add_reflection( ref2.h, ref2.k, ref2.l, ref2.pos, ref2.energy, ref2.tag, t) self.ubcalc.calculate_UB() returned = self.ubcalc.U.tolist() print "*Required:" print sess.umatrix print "*Returned:" print returned mneq_(self.ubcalc.U, matrix(sess.umatrix), 4, note="wrong U calulated for sess.name=" + sess.name) def test__str__(self): sess = scenarios.sessions()[0] print "***" print self.ubcalc.__str__() print "***" self.ubcalc.start_new('test') print self.ubcalc.__str__() print "***" self.ubcalc.set_lattice(sess.name, *sess.lattice) print self.ubcalc.__str__() print "***" ref1 = sess.ref1 ref2 = sess.ref2 t = sess.time self.ubcalc.add_reflection( ref1.h, ref1.k, ref1.l, ref1.pos, ref1.energy, ref1.tag, t) self.ubcalc.add_reflection( ref2.h, ref2.k, ref2.l, ref2.pos, ref2.energy, ref2.tag, t) print self.ubcalc.__str__() print "***" self.ubcalc.calculate_UB() print self.ubcalc.__str__()
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 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)