def setUp(self):
"""To test the kramers_kronig_analysis we will generate 3
EELSSpectrum instances. First a model energy loss function(ELF),
in our case following the Drude bulk plasmon peak. Second, we
simulate the inelastic scattering to generate a model scattering
distribution (SPC). Finally, we use a lorentzian peak with
integral equal to 1 to simulate a ZLP.
"""
# Parameters
i0 = 1.
t = signals.Signal(np.arange(10, 70, 10).reshape((2, 3))) # thickness
t.axes_manager.set_signal_dimension(0)
scale = 0.02
# Create an 3x2x2048 spectrum with Drude plasmon
s = EELSSpectrum(np.zeros((2, 3, 2 * 2048)))
s.set_microscope_parameters(beam_energy=300.0,
convergence_angle=5,
collection_angle=10.0)
s.axes_manager.signal_axes[0].scale = scale
k = eels_constant(s, i0, t)
vpm = VolumePlasmonDrude()
m = create_model(s, auto_background=False)
m.append(vpm)
vpm.intensity.map['values'][:] = 1
vpm.plasmon_energy.map['values'] = np.array([[8., 18.4, 15.8],
[16.6, 4.3, 3.7]])
vpm.fwhm.map['values'] = np.array([[2.3, 4.8, 0.53], [3.7, 0.3, 0.3]])
vpm.intensity.map['is_set'][:] = True
vpm.plasmon_energy.map['is_set'][:] = True
vpm.fwhm.map['is_set'][:] = True
s.data = (m.as_signal() * k).data
# Create ZLP
z = s.deepcopy()
z.axes_manager.signal_axes[0].scale = scale
z.axes_manager.signal_axes[0].offset = -10
zlp = Lorentzian()
zlp.A.value = i0
zlp.gamma.value = 0.2
zlp.centre.value = 0.0
z.data[:] = zlp.function(z.axes_manager[-1].axis).reshape((1, 1, -1))
z.data *= scale
self.s = s
self.thickness = t
self.k = k
self.zlp = z
def test_eels():
s = EELSSpectrum(([0, 1]))
s0 = s.deepcopy()
s.axes_manager[0].convert_to_non_uniform_axis()
with pytest.raises(NotImplementedError):
s.align_zero_loss_peak()
with pytest.raises(NotImplementedError):
s.create_model(ll=s)
with pytest.raises(NotImplementedError):
s.fourier_log_deconvolution(0)
with pytest.raises(NotImplementedError):
s.fourier_ratio_deconvolution(s)
with pytest.raises(NotImplementedError):
s.fourier_ratio_deconvolution(s0)
with pytest.raises(NotImplementedError):
s0.fourier_ratio_deconvolution(s)
with pytest.raises(NotImplementedError):
s.richardson_lucy_deconvolution(s)
with pytest.raises(NotImplementedError):
s.kramers_kronig_analysis()
m = s.create_model()
g = EELSCLEdge('N_K')
with pytest.raises(NotImplementedError):
m.append(g)
