def testAddorient(self):
with pytest.raises(TypeError):
self.ub.addorient(1)
with pytest.raises(TypeError):
self.ub.addorient(1, 2)
with pytest.raises(TypeError):
self.ub.addorient(1, 2, 'blarghh')
# start new ubcalc
self.ub.newub('testing_addorient')
orientlist = self.ub.ubcalc._state.orientlist # for convenience
hkl1 = [1.1, 1.2, 1.3]
hkl2 = [2.1, 2.2, 2.3]
orient1 = [1.4, 1.5, 1.6]
orient2 = [2.4, 2.5, 2.6]
#
self.ub.addorient(hkl1, orient1)
result = orientlist.getOrientation(1)
trans_orient1 = self.t_matrix.I * matrix([orient1]).T
eq_(result[0], hkl1)
mneq_(matrix([result[1]]), trans_orient1.T)
eq_(result[2], None)
self.ub.addorient(hkl2, orient2, 'atag')
result = orientlist.getOrientation(2)
trans_orient2 = self.t_matrix.I * matrix([orient2]).T
eq_(result[0], hkl2)
mneq_(matrix([result[1]]), trans_orient2.T)
eq_(result[2], 'atag')
def testSetub(self):
self.ub.newub('testsetub_custom')
self.ub.setlat('NaCl', 1.1)
zrot = xyz_rotation([0, 0 , 1], 30. * TORAD)
self.ub.setu(zrot.tolist())
mneq_(self.ub.ubcalc.UB, self.conv.transform(self.zrot) * self.ub.ubcalc._state.crystal.B)
def testOrientub(self):
with pytest.raises(TypeError):
self.ub.orientub(1) # wrong input
# no ubcalc started:
with pytest.raises(DiffcalcException):
self.ub.orientub()
self.ub.newub('testorientub')
# not enough orientations:
with pytest.raises(DiffcalcException):
self.ub.orientub()
self.ub.newub('testorientub')
s = scenarios.sessions(settings.Pos)[1]
self.ub.setlat(s.name, *s.lattice)
r1 = s.ref1
orient1 = self.t_matrix * matrix('1; 0; 0')
self.ub.addorient((r1.h, r1.k, r1.l), orient1.T.tolist()[0], r1.tag)
r2 = s.ref2
orient2 = self.t_matrix * matrix('0; -1; 0')
self.ub.addorient((r2.h, r2.k, r2.l), orient2.T.tolist()[0], r2.tag)
self.ub.orientub()
mneq_(self.ub.ubcalc.UB,
matrix(s.umatrix) * matrix(s.bmatrix),
4,
note="wrong UB matrix after calculating U")
def testAddorientInteractively(self):
prepareRawInput([])
# start new ubcalc
self.ub.newub('testing_addorient')
orientlist = self.ub.ubcalc._state.orientlist # for convenience
hkl1 = [1.1, 1.2, 1.3]
hkl2 = [2.1, 2.2, 2.3]
orient1 = [1.4, 1.5, 1.6]
orient2 = [2.4, 2.5, 2.6]
#
prepareRawInput(['1.1', '1.2', '1.3', '1.4', '1.5', '1.6', ''])
self.ub.addorient()
result = orientlist.getOrientation(1)
trans_orient1 = self.t_matrix.I * matrix([orient1]).T
eq_(result[0], hkl1)
mneq_(matrix([result[1]]), trans_orient1.T)
eq_(result[2], None)
prepareRawInput(['2.1', '2.2', '2.3', '2.4', '2.5', '2.6', 'atag'])
self.ub.addorient()
result = orientlist.getOrientation(2)
trans_orient2 = self.t_matrix.I * matrix([orient2]).T
eq_(result[0], hkl2)
mneq_(matrix([result[1]]), trans_orient2.T)
eq_(result[2], 'atag')
def testSetub(self):
self.ub.newub('testsetub_custom')
self.ub.setlat('NaCl', 1.1)
zrot = xyz_rotation([0, 0, 1], self.t_hand * 30. * TORAD)
self.ub.setu(zrot.tolist())
mneq_(self.ub.ubcalc.UB, self.xrot * self.ub.ubcalc._state.crystal.B)
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 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")
def testRefineub(self):
self.ub.newub('testing_refineub')
self.ub.setlat('xtal', 1, 1, 1, 90, 90, 90)
self.ub.setmiscut(0)
prepareRawInput(['y', 'y'])
self.ub.refineub([1, 1, 0], [0, 60, 0, 30, 0, 0])
getLattice = self.ub.ubcalc._state.crystal.getLattice
eq_(('xtal', sqrt(2.), sqrt(2.), 1, 90, 90, 90), getLattice())
mneq_(self.ub.ubcalc.U, self._refineub_matrix,
4, note="wrong U matrix after refinement")
def testRefineubInteractively(self):
self.ub.newub('testing_refineubinteractive')
self.ub.setlat('xtal', 1, 1, 1, 90, 90, 90)
self.ub.setmiscut(0)
prepareRawInput(['1', '1', '', 'n', '0', '60', '0', '30', '0', '0', 'y', 'y'])
self.ub.refineub()
getLattice = self.ub.ubcalc._state.crystal.getLattice
eq_(('xtal', sqrt(2.), sqrt(2.), 1, 90, 90, 90), getLattice())
mneq_(self.ub.ubcalc.U, self._refineub_matrix,
4, note="wrong U matrix after refinement")
def test__orientation_phase():
_orient()
you.ub()
you.checkub()
you.showref()
U = matrix('1 0 0; 0 1 0; 0 0 1')
UB = U * 2 * pi
mneq_(you.ubcalc.U, U)
mneq_(you.ubcalc.UB, UB)
def test_orientation_phase(self):
self._orient()
ub()
checkub()
showref()
U = matrix('1 0 0; 0 1 0; 0 0 1')
UB = U * 2 * pi
mneq_(dc.ub._ubcalc.U, U)
mneq_(dc.ub._ubcalc.UB, UB)
def test__orientation_phase():
_orient()
you.ub()
you.checkub()
you.showref()
U = matrix('1 0 0; 0 1 0; 0 0 1')
UB = U * 2 * pi
mneq_(you.ubcalc.U, U)
mneq_(you.ubcalc.UB, UB)
def test_orientation_phase():
# assumes reflections added were ideal (with no mis-mount)
dc.ub()
dc.checkub()
dc.showref()
U = matrix('1 0 0; 0 1 0; 0 0 1')
UB = U * 2 * pi
mneq_(dc._ub.ubcalc.U, U)
mneq_(dc._ub.ubcalc.UB, UB)
def testRefineubInteractivelyWithHKL(self):
self.ub.newub('testing_refineubinteractivehkl')
self.ub.setlat('xtal', 1, 1, 1, 90, 90, 90)
self.ub.setmiscut(0)
self.hardware.position = [0, 60, 0, 30, 0, 0]
prepareRawInput(['y', 'y', 'y'])
self.ub.refineub([1, 1, 0])
getLattice = self.ub.ubcalc._state.crystal.getLattice
eq_(('xtal', sqrt(2.), sqrt(2.), 1, 90, 90, 90), getLattice())
mneq_(self.ub.ubcalc.U, self._refineub_matrix,
4, note="wrong U matrix after refinement")
def testGetBMatrix(self):
# Check the calculated B Matrix
for sess in scenarios.sessions():
if sess.bmatrix is None:
continue
cut = CrystalUnderTest('tc', *sess.lattice)
desired = matrix(sess.bmatrix)
print desired.tolist()
answer = cut.B
print answer.tolist()
note = "Incorrect B matrix calculation for scenario " + sess.name
mneq_(answer, desired, 4, note=note)
def testGetBMatrix(self):
# Check the calculated B Matrix
for sess in scenarios.sessions():
if sess.bmatrix is None:
continue
cut = CrystalUnderTest('tc', *sess.lattice)
desired = matrix(sess.bmatrix)
print desired.tolist()
answer = cut.B
print answer.tolist()
note = "Incorrect B matrix calculation for scenario " + sess.name
mneq_(answer, desired, 4, note=note)
def test_hkl_to_angles(self):
s = self.sess
c = self.calc
## setup session info
self.dc.newub(s.name)
self.dc.setlat(s.name, *s.lattice)
r = s.ref1
self.dc.addref([r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
r = s.ref2
self.dc.addref([r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.dc.calcub()
# check the ubcalculation is okay before continuing
# (useful to check for typos !)
mneq_(self.dc.ubcalc.UB,
matrix(s.umatrix) * matrix(s.bmatrix),
4,
note="wrong UB matrix after calculating U")
## setup calculation info
self.dc.hklmode(c.modeNumber)
# Set fixed parameters
if c.alpha != None:
self.dc.setpar('alpha', c.alpha)
if c.gamma != None:
self.dc.setpar('gamma', c.alpha)
# Test each hkl/position pair
for idx in range(len(c.hklList)):
(h, k, l) = c.hklList[idx]
expectedangles = \
self.geometry.internal_position_to_physical_angles(c.posList[idx])
(angles, params) = self.dc.hkl_to_angles(h, k, l, c.energy)
expectedAnglesStr = ("%f " * len(expectedangles)) % expectedangles
anglesString = ("%f " * len(angles)) % angles
namesString = (("%s " * len(self.hardware.get_axes_names())) %
self.hardware.get_axes_names())
note = ("wrong position calcualted for TestScenario=%s, "
"AngleTestScenario=%s, hkl=%f %f %f:\n"
" { %s }\n"
" expected pos=%s\n returned pos=%s " %
(s.name, c.tag, h, k, l, namesString, expectedAnglesStr,
anglesString))
mneq_(matrix([list(expectedangles)]),
matrix([list(angles)]),
2,
note=note)
del params
def test_angles_to_hkl(self):
self.assertRaises(DiffcalcException, self.d.angles_to_hkl,
(1, 2, 3, 4, 5, 6)) # no energy has been set yet
self.d._hardware.energy = 10
self.assertRaises(DiffcalcException, self.d.angles_to_hkl,
(1, 2, 3, 4, 5, 6)) # no ub calculated yet
s = self.sess
c = self.calc
# setup session info
self.d.ub.newub(s.name)
self.d.ub.setlat(s.name, *s.lattice)
r = s.ref1
self.d.ub.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
r = s.ref2
self.d.ub.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.d.ub.calcub()
# check the ubcalculation is okay before continuing
# (useful to check for typos!)
mneq_(self.d._ubcalc.UB,
matrix(s.umatrix) * matrix(s.bmatrix), 4,
note="wrong UB matrix after calculating U")
# Test each hkl/position pair
for idx in range(len(c.hklList)):
hkl = c.hklList[idx]
pos = c.posList[idx]
# 1) specifying energy explicitely
((h, k, l), params) = self.d.angles_to_hkl(pos.totuple(), c.energy)
msg = ("wrong hkl calc for TestScenario=%s, AngleTestScenario"
"=%s, pos=%s):\n expected hkl=%f %f %f\n returned hkl="
"%f %f %f "
% (s.name, c.tag, str(pos), hkl[0], hkl[1], hkl[2], h, k, l)
)
self.assert_((abs(h - hkl[0]) < .001) & (abs(k - hkl[1]) < .001)
& (abs(l - hkl[2]) < .001), msg)
# 2) specifying energy via hardware
self.d._hardware.energy = c.energy
msg = ("wrong hkl calcualted for TestScenario=%s, "
"AngleTestScenario=%s, pos=%s):\n expected hkl=%f %f %f\n"
" returned hkl=%f %f %f " %
(s.name, c.tag, str(pos), hkl[0], hkl[1], hkl[2], h, k, l))
((h, k, l), params) = self.d.angles_to_hkl(pos.totuple())
self.assert_((abs(h - hkl[0]) < .001) & (abs(k - hkl[1]) < .001) &
(abs(l - hkl[2]) < .001), msg)
del params
def test_hkl_to_angles(self):
s = self.sess
c = self.calc
## setup session info
self.dc.newub(s.name)
self.dc.setlat(s.name, *s.lattice)
r = s.ref1
self.dc.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
r = s.ref2
self.dc.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.dc.calcub()
# check the ubcalculation is okay before continuing
# (useful to check for typos !)
mneq_(self.dc.ubcalc.UB,
matrix(s.umatrix) * matrix(s.bmatrix), 4,
note="wrong UB matrix after calculating U")
## setup calculation info
self.dc.hklmode(c.modeNumber)
# Set fixed parameters
if c.alpha != None:
self.dc.setpar('alpha', c.alpha)
if c.gamma != None:
self.dc.setpar('gamma', c.alpha)
# Test each hkl/position pair
for idx in range(len(c.hklList)):
(h, k, l) = c.hklList[idx]
expectedangles = \
self.geometry.internal_position_to_physical_angles(c.posList[idx])
(angles, params) = self.dc.hkl_to_angles(h, k, l, c.energy)
expectedAnglesStr = ("%f " * len(expectedangles)) % expectedangles
anglesString = ("%f " * len(angles)) % angles
namesString = (("%s " * len(self.hardware.get_axes_names()))
% self.hardware.get_axes_names())
note = ("wrong position calcualted for TestScenario=%s, "
"AngleTestScenario=%s, hkl=%f %f %f:\n"
" { %s }\n"
" expected pos=%s\n returned pos=%s "
% (s.name, c.tag, h, k, l, namesString, expectedAnglesStr,
anglesString))
mneq_(matrix([list(expectedangles)]), matrix([list(angles)]), 2,
note=note)
del params
def testRefineubInteractivelyWithPosition(self):
self.ub.newub('testing_refineubinteractivepos')
self.ub.setlat('xtal', 1, 1, 1, 90, 90, 90)
self.ub.setmiscut(0)
self.hardware.position = [0, 60, 0, 30, 0, 0]
prepareRawInput(['1', '1', '', 'y', 'y', 'y'])
self.ub.refineub()
getLattice = self.ub.ubcalc._state.crystal.getLattice
eq_(('xtal', sqrt(2.), sqrt(2.), 1, 90, 90, 90), getLattice())
mneq_(
self.ub.ubcalc.U,
matrix(
'0.70711 0.70711 0.00000; -0.70711 0.70711 0.00000; 0.00000 0.00000 1.00000'
),
4,
note="wrong U matrix after refinement")
def test_angles_to_hkl(self):
with pytest.raises(DiffcalcException):
self.dc.angles_to_hkl((1, 2, 3, 4, 5, 6)) # no energy set
settings.hardware.energy = 10
with pytest.raises(DiffcalcException):
self.dc.angles_to_hkl((1, 2, 3, 4, 5, 6)) # no ub calculated
s = self.sess
c = self.calc
# setup session info
self.dc.newub(s.name)
self.dc.setlat(s.name, *s.lattice)
r = s.ref1
self.dc.addref([r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
r = s.ref2
self.dc.addref([r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.dc.calcub()
# check the ubcalculation is okay before continuing
# (useful to check for typos!)
mneq_(self.dc.ubcalc.UB,
matrix(s.umatrix) * matrix(s.bmatrix),
4,
note="wrong UB matrix after calculating U")
# Test each hkl/position pair
for idx in range(len(c.hklList)):
hkl = c.hklList[idx]
pos = c.posList[idx]
# 1) specifying energy explicitely
((h, k, l),
params) = self.dc.angles_to_hkl(pos.totuple(), c.energy)
msg = ("wrong hkl calc for TestScenario=%s, AngleTestScenario"
"=%s, pos=%s):\n expected hkl=%f %f %f\n returned hkl="
"%f %f %f " %
(s.name, c.tag, str(pos), hkl[0], hkl[1], hkl[2], h, k, l))
assert [h, k, l] == pytest.approx(hkl, abs=.001)
# self.assert_((abs(h - hkl[0]) < .001) & (abs(k - hkl[1]) < .001)
# & (abs(l - hkl[2]) < .001), msg)
# 2) specifying energy via hardware
settings.hardware.energy = c.energy
msg = ("wrong hkl calcualted for TestScenario=%s, "
"AngleTestScenario=%s, pos=%s):\n expected hkl=%f %f %f\n"
" returned hkl=%f %f %f " %
(s.name, c.tag, str(pos), hkl[0], hkl[1], hkl[2], h, k, l))
((h, k, l), params) = self.dc.angles_to_hkl(pos.totuple())
assert [h, k, l] == pytest.approx(hkl, abs=.001)
del params
def testSimWithHklAndSixc(self):
dummyAxes = createDummyAxes(
['alpha', 'delta', 'gamma', 'omega', 'chi', 'phi'])
dummySixcScannableGroup = ScannableGroup('sixcgrp', dummyAxes)
sixcdevice = DiffractometerScannableGroup(
'SixCircleGammaOnArmGeometry', self.dc, dummySixcScannableGroup)
hkldevice = Hkl('hkl', sixcdevice, self.dc)
with pytest.raises(TypeError):
sim()
with pytest.raises(TypeError):
sim(hkldevice)
with pytest.raises(TypeError):
sim(hkldevice, 1, 2, 3)
with pytest.raises(TypeError):
sim('not a proper scannable', 1)
with pytest.raises(TypeError):
sim(hkldevice, (1, 2, 'not a number'))
with pytest.raises(TypeError):
sim(hkldevice, 1)
with pytest.raises(ValueError):
sim(hkldevice, (1, 2, 3, 4))
s = self.sess
c = self.calc
# setup session info
self.dc.newub(s.name)
self.dc.setlat(s.name, *s.lattice)
r = s.ref1
self.dc.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
r = s.ref2
self.dc.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.dc.calcub()
# check the ubcalculation is okay before continuing
# (useful to check for typos!)
mneq_(self.dc.ubcalc.UB,
(matrix(s.umatrix) * (matrix(s.bmatrix))),
4, note="wrong UB matrix after calculating U")
self.hardware.energy = c.energy
# Test each hkl/position pair
for idx in range(len(c.hklList)):
hkl = c.hklList[idx]
pos = c.posList[idx].totuple()
sim(sixcdevice, pos)
sim(hkldevice, hkl)
def testEditOrientInteractively(self):
hkl1 = [1.1, 1.2, 1.3]
hkl2 = [1.1, 1.2, 3.1]
orient1 = [1.4, 1.5, 1.6]
orient2 = [2.4, 1.5, 2.6]
orient2s = ['2.4', '', '2.6']
self.ub.newub('testing_editorient')
self.ub.addorient(hkl1, orient1, 'tag1')
prepareRawInput(['1.1', '', '3.1'] + orient2s + ['y', 'newtag',])
self.ub.editorient(1)
orientlist = self.ub.ubcalc._state.orientlist
result = orientlist.getOrientation(1)
trans_orient2 = self.conv.transform(matrix([orient2]).T)
eq_(result[0], hkl2)
mneq_(matrix([result[1]]), trans_orient2.T)
eq_(result[-2], 'newtag')
def testSimWithHklAndSixc(self):
dummyAxes = createDummyAxes(
['alpha', 'delta', 'gamma', 'omega', 'chi', 'phi'])
dummySixcScannableGroup = ScannableGroup('sixcgrp', dummyAxes)
sixcdevice = DiffractometerScannableGroup(
'SixCircleGammaOnArmGeometry', self.dc, dummySixcScannableGroup)
hkldevice = Hkl('hkl', sixcdevice, self.dc)
with pytest.raises(TypeError):
sim()
with pytest.raises(TypeError):
sim(hkldevice)
with pytest.raises(TypeError):
sim(hkldevice, 1, 2, 3)
with pytest.raises(TypeError):
sim('not a proper scannable', 1)
with pytest.raises(TypeError):
sim(hkldevice, (1, 2, 'not a number'))
with pytest.raises(TypeError):
sim(hkldevice, 1)
with pytest.raises(ValueError):
sim(hkldevice, (1, 2, 3, 4))
s = self.sess
c = self.calc
# setup session info
self.dc.newub(s.name)
self.dc.setlat(s.name, *s.lattice)
r = s.ref1
self.dc.addref([r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
r = s.ref2
self.dc.addref([r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.dc.calcub()
# check the ubcalculation is okay before continuing
# (useful to check for typos!)
mneq_(self.dc.ubcalc.UB, (matrix(s.umatrix) * (matrix(s.bmatrix))),
4,
note="wrong UB matrix after calculating U")
self.hardware.energy = c.energy
# Test each hkl/position pair
for idx in range(len(c.hklList)):
hkl = c.hklList[idx]
pos = c.posList[idx].totuple()
sim(sixcdevice, pos)
sim(hkldevice, hkl)
def testCalcub(self):
self.assertRaises(TypeError, self.ubcommands.calcub, 1) # wrong input
# no ubcalc started:
self.assertRaises(DiffcalcException, self.ubcommands.calcub)
self.ubcommands.newub('testcalcub')
# not enougth reflections:
self.assertRaises(DiffcalcException, self.ubcommands.calcub)
s = scenarios.sessions()[0]
self.ubcommands.setlat(s.name, *s.lattice)
r = s.ref1
self.ubcommands.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
r = s.ref2
self.ubcommands.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.ubcommands.calcub()
mneq_(self.ubcalc.UB, matrix(s.umatrix) * matrix(s.bmatrix),
4, note="wrong UB matrix after calculating U")
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")
def testOrientation(self):
self.dc.newub('cubic')
self.dc.setlat('cubic', 1, 1, 1)
self.en(39842 / 1)
self.dc.sigtau(0, 0)
self.sixc([0, 90, 0, 45, 45, 0])
self.dc.addref([1, 0, 1])
self.sixc([0, 90, 0, 45, 45, 90])
self.dc.addref([0, 1, 1])
self.dc.checkub()
res = self.dc.ubcalc.U
des = matrix([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
mneq_(res, des, 4)
# print "***"
# self.dc.dc()
print "***"
self.dc.showref()
print "***"
self.dc.hklmode()
print "***"
def testOrientation(self):
self.dc.newub('cubic')
self.dc.setlat('cubic', 1, 1, 1)
self.en(39842 / 1)
self.dc.sigtau(0, 0)
self.sixc([0, 90, 0, 45, 45, 0])
self.dc.addref([1, 0, 1])
self.sixc([0, 90, 0, 45, 45, 90])
self.dc.addref([0, 1, 1])
self.dc.checkub()
res = self.dc.ubcalc.U
des = matrix([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
mneq_(res, des, 4)
# print "***"
# self.dc.dc()
print "***"
self.dc.showref()
print "***"
self.dc.hklmode()
print "***"
def testAnglesToHkl(self):
mockUbcalc = createMockUbcalc(
matrix(self.sess.umatrix) * matrix(self.sess.bmatrix))
self.ac = VliegHklCalculator(mockUbcalc,
createMockDiffractometerGeometry(),
createMockHardwareMonitor())
self.ac.raiseExceptionsIfAnglesDoNotMapBackToHkl = True
# Check the two given reflections
(hklactual1, params) = self.ac.anglesToHkl(self.sess.ref1.pos,
self.sess.ref1.wavelength)
del params
(hklactual2, params) = self.ac.anglesToHkl(self.sess.ref2.pos,
self.sess.ref2.wavelength)
mneq_(matrix([hklactual1]), matrix([self.sess.ref1calchkl]), 3)
mneq_(matrix([hklactual2]), matrix([self.sess.ref2calchkl]), 3)
# ... znd in each calculation through the hkl/posiiont pairs
if self.calc:
for hkl, pos, param in zip(self.calc.hklList,
self.calc.posList,
self.calc.paramList):
(hkl_actual, params) = self.ac.anglesToHkl(pos,
self.calc.wavelength)
note = ("wrong hkl calcualted for scenario.name=%s, "
"calculation.tag=%s\n expected hkl=(%f,%f,%f)\n"
"calculated hkl=(%f,%f,%f)" %
(self.sess.name, self.calc.tag, hkl[0], hkl[1], hkl[2],
hkl_actual[0], hkl_actual[1], hkl_actual[2]))
mneq_(matrix([hkl_actual]), matrix([hkl]), 3, note=note)
print "***anglesToHkl***"
print "*** ", str(hkl), " ***"
print params
print param
def testAnglesToHkl(self):
mockUbcalc = createMockUbcalc(
matrix(self.sess.umatrix) * matrix(self.sess.bmatrix))
self.ac = VliegHklCalculator(mockUbcalc,
createMockDiffractometerGeometry(),
createMockHardwareMonitor())
self.ac.raiseExceptionsIfAnglesDoNotMapBackToHkl = True
# Check the two given reflections
(hklactual1, params) = self.ac.anglesToHkl(self.sess.ref1.pos,
self.sess.ref1.wavelength)
del params
(hklactual2, params) = self.ac.anglesToHkl(self.sess.ref2.pos,
self.sess.ref2.wavelength)
mneq_(matrix([hklactual1]), matrix([self.sess.ref1calchkl]), 3)
mneq_(matrix([hklactual2]), matrix([self.sess.ref2calchkl]), 3)
# ... znd in each calculation through the hkl/posiiont pairs
if self.calc:
for hkl, pos, param in zip(self.calc.hklList, self.calc.posList,
self.calc.paramList):
(hkl_actual,
params) = self.ac.anglesToHkl(pos, self.calc.wavelength)
note = ("wrong hkl calcualted for scenario.name=%s, "
"calculation.tag=%s\n expected hkl=(%f,%f,%f)\n"
"calculated hkl=(%f,%f,%f)" %
(self.sess.name, self.calc.tag, hkl[0], hkl[1], hkl[2],
hkl_actual[0], hkl_actual[1], hkl_actual[2]))
mneq_(matrix([hkl_actual]), matrix([hkl]), 3, note=note)
print "***anglesToHkl***"
print "*** ", str(hkl), " ***"
print params
print param
def testCalcub(self):
with pytest.raises(TypeError):
self.ub.calcub(1) # wrong input
# no ubcalc started:
with pytest.raises(DiffcalcException):
self.ub.calcub()
self.ub.newub('testcalcub')
# not enough reflections:
with pytest.raises(DiffcalcException):
self.ub.calcub()
s = scenarios.sessions(settings.Pos)[0]
self.ub.setlat(s.name, *s.lattice)
r = s.ref1
self.ub.addref([r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
r = s.ref2
self.ub.addref([r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.ub.calcub()
mneq_(self.ub.ubcalc.UB,
matrix(s.umatrix) * matrix(s.bmatrix),
4,
note="wrong UB matrix after calculating U")
def testFitub(self):
self.ub.newub('testfitub')
for s in scenarios.sessions(settings.Pos)[-3:]:
a, b, c, alpha, beta, gamma = s.lattice
self.ub.clearref()
for r in s.reflist:
self.ub.addref(
[r.h, r.k, r.l], r.pos.totuple(), r.energy, r.tag)
self.ub.setlat(s.name, s.system, *s.lattice)
self.ub.calcub(s.ref1.tag, s.ref2.tag)
init_latt = (1.06 * a, 1.07 * b, 0.94 * c,
1.05 * alpha, 1.06 * beta, 0.95 * gamma)
self.ub.setlat(s.name, s.system, *init_latt)
self.ub.addmiscut(3., [0.2, 0.8, 0.1])
prepareRawInput(['y', 'y'])
self.ub.fitub(*tuple(r.tag for r in s.reflist))
assert self.ub.ubcalc._state.crystal._system == s.system
mneq_(matrix((self.ub.ubcalc._state.crystal.getLattice()[1:])), matrix(s.lattice),
2, note="wrong lattice after fitting UB")
mneq_(self.ub.ubcalc.U, matrix(s.umatrix),
3, note="wrong U matrix after fitting UB")
def testMiscut(self):
self.ub.newub('testsetmiscut')
self.ub.ubcalc._state.reference._set_n_phi_configured(matrix('0; 0; 1'))
self.ub.setlat('cube', 1, 1, 1, 90, 90, 90)
beam_axis = self.conv.transform(matrix('0; 1; 0'), True).T.tolist()[0]
beam_maxis = self.conv.transform(matrix('0; -1; 0'), True).T.tolist()[0]
self.ub.setmiscut(self.t_hand * 30, beam_axis)
mneq_(self.ub.ubcalc._state.reference.n_hkl, matrix('-0.5000000; 0.00000; 0.8660254'))
self.ub.addmiscut(self.t_hand * 15, beam_axis)
mneq_(self.ub.ubcalc._state.reference.n_hkl, matrix('-0.7071068; 0.00000; 0.7071068'))
self.ub.addmiscut(self.t_hand * 45, beam_maxis)
mneq_(self.ub.ubcalc._state.reference.n_hkl, matrix('0.0; 0.0; 1.0'))
def testMiscut(self):
self.ub.newub('testsetmiscut')
self.ub.setlat('cube', 1, 1, 1, 90, 90, 90)
beam_axis = (self.t_matrix * matrix('0; 1; 0')).T.tolist()[0]
beam_maxis = (self.t_matrix * matrix('0; -1; 0')).T.tolist()[0]
self.ub.setmiscut(self.t_hand * 30, beam_axis)
mneq_(self.ub.ubcalc._state.reference.n_hkl,
matrix('-0.5000000; 0.00000; 0.8660254'))
self.ub.addmiscut(self.t_hand * 15, beam_axis)
mneq_(self.ub.ubcalc._state.reference.n_hkl,
matrix('-0.7071068; 0.00000; 0.7071068'))
self.ub.addmiscut(self.t_hand * 45, beam_maxis)
mneq_(self.ub.ubcalc._state.reference.n_hkl, matrix('0.0; 0.0; 1.0'))
def testOrientub(self):
with pytest.raises(DiffcalcException):
self.ub.orientub(1) # wrong input
# no ubcalc started:
with pytest.raises(DiffcalcException):
self.ub.orientub()
self.ub.newub('testorientub')
# not enough orientations:
with pytest.raises(DiffcalcException):
self.ub.orientub()
s = scenarios.sessions(settings.Pos)[1]
self.ub.setlat(s.name, *s.lattice)
r1 = s.ref1
orient1 = self.conv.transform(matrix('1; 0; 0'), True)
tag1 = 'or'+r1.tag
self.ub.addorient(
(r1.h, r1.k, r1.l), orient1.T.tolist()[0], tag1)
r2 = s.ref2
orient2 = self.conv.transform(matrix('0; -1; 0'), True)
tag2 = 'or'+r2.tag
self.ub.addorient(
(r2.h, r2.k, r2.l), orient2.T.tolist()[0], tag2)
self.ub.orientub()
mneq_(self.ub.ubcalc.UB, matrix(s.umatrix) * matrix(s.bmatrix),
4, note="wrong UB matrix after calculating U")
self.ub.orientub(tag1, tag2)
mneq_(self.ub.ubcalc.UB, matrix(s.umatrix) * matrix(s.bmatrix),
4, note="wrong UB matrix after calculating U")
self.ub.addref(
[r1.h, r1.k, r1.l], r1.pos.totuple(), r1.energy, r1.tag)
self.ub.orientub(r1.tag, tag2)
mneq_(self.ub.ubcalc.UB, matrix(s.umatrix) * matrix(s.bmatrix),
4, note="wrong UB matrix after calculating U")
self.ub.addref(
[r2.h, r2.k, r2.l], r2.pos.totuple(), r2.energy, r2.tag)
self.ub.orientub(tag1, r2.tag)
mneq_(self.ub.ubcalc.UB, matrix(s.umatrix) * matrix(s.bmatrix),
4, note="wrong UB matrix after calculating U")
def testCalcUB(self):
UB = matrix([[2 * pi, 0, 0], [0, 2 * pi, 0], [0, 0, 2 * pi]])
mneq_(self.scc.UB, UB)
def testInternalPositionToPhysicalAngles(self):
pos = VliegPosition(1, 2, 3, 4, 5, 6)
result = self.geometry.internal_position_to_physical_angles(pos)
mneq_(matrix([pos.totuple()]), matrix([result]), 4)
def testCalcUB(self):
UB = matrix([[2 * pi, 0, 0], [0, 2 * pi, 0], [0, 0, 2 * pi]])
mneq_(self.scc.UB, UB)
def testInternalPositionToPhysicalAngles(self):
pos = VliegPosition(1, 2, 3, 4, 5, 6)
result = self.geometry.internal_position_to_physical_angles(pos)
mneq_(matrix([pos.totuple()]), matrix([result]), 4)