def _increase_layers(self, b):
self.w_layers.disabled = False
self.do_fit_button.disabled = False
self.to_code_button.disabled = False
self.save_model_button.disabled = False
self.load_model_button.disabled = False
how_many = self.w_layers.value - (len(self.model.structure) - 2)
loc = self._location.value
for i in range(how_many):
slab = Slab(0, 0, 3)
slab.thick.bounds = (0, 2 * slab.thick.value)
slab.sld.real.bounds = (0, 2 * slab.sld.real.value)
slab.sld.imag.bounds = (0, 2 * slab.sld.imag.value)
slab.rough.bounds = (0, 2 * slab.rough.value)
slab_view = SlabView(slab)
self.model.structure.insert(loc, slab)
self.structure_view.slab_views.insert(loc, slab_view)
slab_view.observe(self._on_slab_params_modified)
rename_params(self.model.structure)
self._varying_layers = False
# set the number of varying parameters
self.num_varying = len(self.model.parameters.varying_parameters())
self.view_redraw = time.time()
def test_materialsld(self):
p = MaterialSLD("SiO2", density=2.2, name="silica")
sldc = complex(p)
assert_allclose(sldc.real, 3.4752690258246504)
assert_allclose(sldc.imag, 1.0508799522721932e-05)
assert p.probe == "neutron"
# is X-ray SLD correct?
p.wavelength = 1.54
p.probe = "x-ray"
sldc = complex(p)
assert_allclose(sldc.real, 18.864796064009866)
assert_allclose(sldc.imag, 0.2436013463223236)
assert len(p.parameters) == 1
assert p.formula == "SiO2"
# the density value should change the SLD
p.probe = "neutron"
p.density.value = 4.4
sldc = complex(p)
assert_allclose(sldc.real, 3.4752690258246504 * 2)
assert_allclose(sldc.imag, 1.0508799522721932e-05 * 2)
# should be able to make a Slab from MaterialSLD
slab = p(10, 3)
assert isinstance(slab, Slab)
slab = Slab(10, p, 3)
assert isinstance(slab, Slab)
# make a full structure and check that the reflectivity calc works
air = SLD(0)
sio2 = MaterialSLD("SiO2", density=2.2)
si = MaterialSLD("Si", density=2.33)
s = air | sio2(10, 3) | si(0, 3)
s.reflectivity(np.linspace(0.005, 0.3, 100))
p = s.parameters
assert len(list(flatten(p))) == 5 + 4 + 4
def __init__(self):
# attributes for the graph
# for the graph
self.qmin = 0.005
self.qmax = 0.5
self.qpnt = 1000
self.fig = None
self.ax_data = None
self.ax_residual = None
self.ax_sld = None
# gridspecs specify how the plots are laid out. Gridspec1 is when the
# residuals plot is displayed. Gridspec2 is when it's not visible
self._gridspec1 = gridspec.GridSpec(2,
2,
height_ratios=[5, 1],
width_ratios=[1, 1],
hspace=0.01)
self._gridspec2 = gridspec.GridSpec(1, 2)
self.theoretical_plot = None
self.theoretical_plot_sld = None
# attributes for a user dataset
self.dataset = None
self.objective = None
self._curvefitter = None
self.data_plot = None
self.residuals_plot = None
self.data_plot_sld = None
self.dataset_name = widgets.Text(description="dataset:")
self.dataset_name.disabled = True
self.chisqr = widgets.FloatText(description="chi-squared:")
self.chisqr.disabled = True
# fronting
slab0 = Slab(0, 0, 0)
slab1 = Slab(25, 3.47, 3)
slab2 = Slab(0, 2.07, 3)
structure = slab0 | slab1 | slab2
rename_params(structure)
self.model = ReflectModel(structure)
structure = slab0 | slab1 | slab2
self.model = ReflectModel(structure)
# give some default parameter limits
self.model.scale.bounds = (0.1, 2)
self.model.bkg.bounds = (1e-8, 2e-5)
self.model.dq.bounds = (0, 20)
for slab in self.model.structure:
slab.thick.bounds = (0, 2 * slab.thick.value)
slab.sld.real.bounds = (0, 2 * slab.sld.real.value)
slab.sld.imag.bounds = (0, 2 * slab.sld.imag.value)
slab.rough.bounds = (0, 2 * slab.rough.value)
# the main GUI widget
self.display_box = widgets.VBox()
self.tab = widgets.Tab()
self.tab.set_title(0, "Model")
self.tab.set_title(1, "Limits")
self.tab.set_title(2, "Options")
self.tab.observe(self._on_tab_changed, names="selected_index")
# an output area for messages.
self.output = widgets.Output()
# options tab
self.plot_type = widgets.Dropdown(
options=["lin", "logY", "YX4", "YX2"],
value="lin",
description="Plot Type:",
disabled=False,
)
self.plot_type.observe(self._on_plot_type_changed, names="value")
self.use_weights = widgets.RadioButtons(
options=["Yes", "No"],
value="Yes",
description="use dataset weights?",
style={"description_width": "initial"},
)
self.use_weights.observe(self._on_use_weights_changed, names="value")
self.transform = Transform("lin")
self.display_residuals = widgets.Checkbox(
value=False, description="Display residuals")
self.display_residuals.observe(self._on_display_residuals_changed,
names="value")
self.model_view = None
self.set_model(self.model)
def test_materialsld(self):
p = MaterialSLD("SiO2", density=2.2, name="silica")
sldc = complex(p)
assert_allclose(sldc.real, 3.4752690258246504)
assert_allclose(sldc.imag, 1.0508799522721932e-05)
assert p.probe == "neutron"
# is X-ray SLD correct?
p.wavelength = 1.54
p.probe = "x-ray"
sldc = complex(p)
assert_allclose(sldc.real, 18.864796064009866)
assert_allclose(sldc.imag, 0.2436013463223236)
assert len(p.parameters) == 1
assert p.formula == "SiO2"
# the density value should change the SLD
p.probe = "neutron"
p.density.value = 4.4
sldc = complex(p)
assert_allclose(sldc.real, 3.4752690258246504 * 2)
assert_allclose(sldc.imag, 1.0508799522721932e-05 * 2)
# should be able to make a Slab from MaterialSLD
slab = p(10, 3)
assert isinstance(slab, Slab)
slab = Slab(10, p, 3)
assert isinstance(slab, Slab)
# make a full structure and check that the reflectivity calc works
air = SLD(0)
sio2 = MaterialSLD("SiO2", density=2.2)
si = MaterialSLD("Si", density=2.33)
s = air | sio2(10, 3) | si(0, 3)
s.reflectivity(np.linspace(0.005, 0.3, 100))
p = s.parameters
assert len(list(flatten(p))) == 5 + 4 + 4
# check that energy dispersive calculation works
au = MaterialSLD("Au",
density=19.33,
name="Gold",
probe="x-ray",
wavelength=1.54)
si = SLD(20.1)
s = air | au(100, 3) | si(0, 3)
slabs = s.slabs(wavelength=0.5)
assert_allclose(s.wavelength, 0.5)
au_sld = complex(slabs[1, 1], slabs[1, 2])
au_check = MaterialSLD("Au",
density=19.33,
name="Gold",
probe="x-ray",
wavelength=0.5)
assert_allclose(au_sld, complex(au_check))
# check that the Scatterer.complex method works as intended
assert_allclose(au.complex(0.5), complex(au_check))