def test_spline_smoke(self):
# smoke test to make Spline at least gives us something
a = Spline(100, [2], [0.5], zgrad=False, microslab_max_thickness=1)
s = self.left | a | self.right | self.solvent
b = a.slabs(s)
assert_equal(b[:, 2], 0)
# microslabs are assessed in the middle of the slab
assert_equal(b[0, 1], a(0.5 * b[0, 0], s))
# with the ends turned off the profile should be a straight line
assert_equal(a(50, s), 2.0)
# construct a structure
a = Spline(
100,
[2.0, 3.0, 4.0],
[0.25] * 3,
zgrad=False,
microslab_max_thickness=1,
)
# s.solvent = None
s = self.left | a | self.right | self.solvent
# calculate an SLD profile
s.sld_profile()
# ask for the parameters
for p in flatten(s.parameters):
assert_(isinstance(p, Parameter))
# s.solvent is not None
s.solvent = self.solvent
# calculate an SLD profile
s.sld_profile()
def test_slab_addition(self):
# The slabs method for the main Structure component constructs
# the overall slabs by concatenating Component slabs. This checks that
# the slab concatenation is correct.
si = SLD(2.07)
sio2 = SLD(3.47)
polymer = SLD(1.5)
d2o = SLD(6.36)
d2o_layer = d2o(0, 3)
polymer_layer = polymer(20, 3)
a = Spline(400, [4, 5.9], [0.2, .4], zgrad=True)
film = si | sio2(10, 3) | polymer_layer | a | d2o_layer
film.sld_profile()
structure = si(0, 0)
for i in range(200):
p = SLD(i)(i, i)
structure |= p
structure |= d2o(0, 3)
slabs = structure.slabs()
assert_equal(slabs[1:-1, 0], np.arange(200))
assert_equal(slabs[1:-1, 1], np.arange(200))
assert_equal(slabs[1:-1, 3], np.arange(200))
assert_equal(slabs[-1, 1], 6.36)
assert_equal(slabs[0, 1], 2.07)
assert_equal(len(slabs), 202)
def test_add_spline_save(qtbot, tmpdir):
# test if we can add a spline to a model and save an experiment
myapp, model = mysetup(qtbot)
# get index of theoretical dataset --> structure --> slab1
data_object_node = model.data_object_node("theoretical")
model_node = data_object_node.child(1)
assert isinstance(model_node, ReflectModelNode)
structs = model_node.structures
for struct in structs:
assert isinstance(struct, Structure)
structure_node = model_node.child(4)
assert isinstance(structure_node, StructureNode)
# selection_model = myapp.ui.treeView.selectionModel()
# slab_node = structure_node.child(1)
# selection_model.select(slab_node.index,
# QtCore.QItemSelectionModel.Select)
# add a Spline after the slab
component = Spline(50, [-1.0, -1.0], [0.33, 0.33], name="spline")
structure_node.insert_component(1, component)
save_and_reload_experiment(myapp, tmpdir)
def test_spline_solvation(self):
a = Spline(100, [2], [0.5], zgrad=False, microslab_max_thickness=1)
front = SLD(0.1)
air = SLD(0.0)
s = front | self.left | a | self.right | self.solvent
# assign a solvent
s.solvent = air
self.left.vfsolv.value = 0.5
self.right.vfsolv.value = 0.5
assert_equal(s.slabs()[1, 1], 0.75)
assert_equal(s.slabs()[-2, 1], 1.25)
assert_almost_equal(a(0, s), 0.75)
assert_almost_equal(a(100, s), 1.25)
# remove solvent, should be solvated by backing medium
s.solvent = None
assert_equal(s.slabs()[1, 1], 5.75)
assert_equal(s.slabs()[-2, 1], 6.25)
assert_almost_equal(a(0, s), 5.75)
assert_almost_equal(a(100, s), 6.25)
# reverse structure, should be solvated by fronting medium
s.reverse_structure = True
assert_equal(s.slabs()[1, 1], 1.3)
assert_equal(s.slabs()[-2, 1], 0.8)
# note that a(0, s) end becomes the end when the structure is reversed
assert_almost_equal(a(0, s), 0.8)
assert_almost_equal(a(100, s), 1.3)
def test_spline_no_knots(self):
# try and make Spline with no knots
a = Spline(100, [], [], zgrad=False, microslab_max_thickness=1)
s = self.left | a | self.right | self.solvent
b = a.slabs(s)
assert_equal(b[:, 2], 0)
# microslabs are assessed in the middle of the slab
assert_equal(b[0, 1], a(0.5 * b[0, 0], s))
# with the ends turned off the profile should be a straight line
assert_equal(a(50, s), 2.0)
q = np.linspace(0.01, 0.5, 1001)
s.reflectivity(q)
def test_left_right_influence(self):
# make sure that if the left and right components change, so does the
# spline
a = Spline(100, [2], [0.5], zgrad=False, microslab_max_thickness=1)
s = self.left | a | self.right | self.solvent
# change the SLD of the left component, spline should respond
self.left.sld.real.value = 2.0
assert_almost_equal(a(0, s), 2)
# check that the spline responds if it's a vfsolv that changes
self.left.vfsolv.value = 0.5
assert_almost_equal(
Structure.overall_sld(self.left.slabs(), self.solvent)[0, 1], 6.0)
assert_almost_equal(a(0, s), 6.0)
# check that the right side responds.
self.right.sld.real.value = 5.0
assert_almost_equal(a(100, s), 5.0)
# the spline should respond if the knot SLD's are changed
a.vs[0].value = 3.0
assert_almost_equal(a(50, s), 3.0)
# spline responds if the interval knot spacing is changed
a.dz[0].value = 0.9
assert_almost_equal(a(90, s), 3.0)
def test_spline_repeat(self):
# can't have two splines in a row.
a = Spline(100, [2], [0.5], zgrad=False, microslab_max_thickness=1)
s = self.left | a | a | self.right | self.solvent
from pytest import raises
with raises(ValueError):
s.slabs()
def test_spine_interfaces(self):
a = Spline(100, [2, 3], [0.3, 0.3],
zgrad=False,
microslab_max_thickness=1)
s = self.left | a | self.right | self.solvent
# this is a check to ensure that:
# 1) _micro_slabs is being called by Structure.slabs()
# 2) _micro_slabs works correctly when a Spline is being used.
# Spline.interfaces should be `None`, which should expanded from
# that default in _micro_slabs to `[Erf] * len(Structure.slabs())`.
s[-1].interfaces = Linear()
s._micro_slabs()
assert_equal(len(s._micro_slabs()), len(s.slabs()))
# should be able to set all the interfaces in Spline to Linear.
a.interfaces = Linear()
a.interfaces = [Linear()]
def test_repr(self):
# make sure that if the left and right components change, so does the
# spline
a = Spline(100, [2, 3, 4], [0.1, 0.2, 0.3],
zgrad=False,
microslab_max_thickness=1)
s = self.left | a | self.right | self.solvent
# should be able to repr the whole lot
q = repr(s)
r = eval(q)
assert_equal(r.slabs(), s.slabs())
def test_pickle(self):
a = Spline(100, [2, 3], [0.3, 0.3],
zgrad=False,
microslab_max_thickness=1)
s = self.left | a | self.right | self.solvent
# cause the spline to be evaluated
s.sld_profile()
assert a._Spline__cached_interpolator["interp"] is not None
pkl = pickle.dumps(s)
r = pickle.loads(pkl)
assert isinstance(r, Structure)
def component(self):
# return a SplineComponent
dz = []
vs = []
extent = self.extent.value()
for i in range(self.knots.rowCount()):
dz.append(float(self.knots.item(i, 0).text()))
vs.append(float(self.knots.item(i, 1).text()))
return Spline(extent,
vs,
dz,
name='spline',
microslab_max_thickness=1.0)
def test_add_spline_save(qtbot, tmpdir):
# test if we can add a spline to a model and save an experiment
myapp, model = mysetup(qtbot)
# get index of theoretical dataset --> structure --> slab1
data_object_node = model.data_object_node('theoretical')
model_node = data_object_node.child(1)
structure_node = model_node.child(3)
# selection_model = myapp.ui.treeView.selectionModel()
# slab_node = structure_node.child(1)
# selection_model.select(slab_node.index,
# QtCore.QItemSelectionModel.Select)
# add a Spline after the slab
component = Spline(50, [-1., -1.], [0.33, 0.33], name='spline')
structure_node.insert_component(1, component)
save_and_reload_experiment(myapp, tmpdir)
def make_model(names, bs, thicks, roughs, fig_i, data, show=False, mcmc=False):
extent = sum(
thicks[:, 0]) # (float or Parameter) – Total extent of spline region
vs = array(
bs
)[:,
0] #(Sequence of float/Parameter) – the real part of the SLD values of each of the knots.
dz = cum_sum(
array(thicks[:, 0])
) #(Sequence of float/Parameter) – the lateral offset between successive knots.
print(dz)
name = "number of nots " + str(len(names)) #(str) – Name of component
component = Spline(extent, vs, dz, name)
front = SLD(0)
front = front(0, 0)
back = SLD(0)
back = back(0, 0)
structure = front | component | back
model = ReflectModel(structure, bkg=3e-6, dq=5.0)
objective = Objective(model, data, transform=Transform('logY'))
fitter = CurveFitter(objective)
fitter.fit('differential_evolution')
return structure, fitter, objective, fig_i + 1