def test_plot_add_background_windows():
s = EDS_TEM_Spectrum().isig[5.0:8.0]
s.plot()
bw = s.estimate_background_windows()
s._add_background_windows_markers(bw)
# Add integration windows
iw = s.estimate_integration_windows(windows_width=2.0, xray_lines=['Fe_Ka'])
s._add_vertical_lines_groups(iw, linestyle='--')
def test_plot_xray_lines():
# It should be the same image as with previous test (test_plot_eds_lines)
a = EDS_TEM_Spectrum()
s = stack([a, a * 5])
s.plot()
s._plot_xray_lines(xray_lines=True)
s.axes_manager.navigation_axes[0].index = 1
return s._plot.signal_plot.figure
def test_plot_eds_lines_not_in_range(caplog):
s = EDS_TEM_Spectrum().isig[5.0:8.0]
s.plot()
with caplog.at_level(logging.WARNING):
s._plot_xray_lines(xray_lines=['Pt_Ka'])
assert "Pt_Ka is not in the data energy range." in caplog.text
def test_strings_from_py2():
s = EDS_TEM_Spectrum()
assert s.metadata.Sample.elements.dtype.char == "U"
def test_comparison_quantification():
kfactors = [1.450226, 5.075602] # For Fe Ka and Pt La
s = EDS_TEM_Spectrum()
s.add_elements(['Cu']) # to get good estimation of the background
m = s.create_model(True)
m.set_signal_range(5.5, 10.0) # to get good fit
m.fit()
intensities_m = m.get_lines_intensity(['Fe_Ka', "Pt_La"])
quant_model = s.quantification(intensities_m,
method='CL',
factors=kfactors)
# Background substracted EDS quantification
s2 = EDS_TEM_Spectrum()
s2.add_lines()
bw = s2.estimate_background_windows(line_width=[5.0, 2.0])
intensities = s2.get_lines_intensity(background_windows=bw)
atomic_percent = s2.quantification(intensities,
method='CL',
factors=kfactors)
np.testing.assert_allclose([q.data for q in quant_model],
[q.data for q in atomic_percent],
rtol=0.5E-1)
def test_strings_from_py2():
s = EDS_TEM_Spectrum()
assert isinstance(s.metadata.Sample.elements, list)
def test_plot_eds_markers_no_energy():
s = EDS_TEM_Spectrum()
del s.metadata.Acquisition_instrument.TEM.beam_energy
s.plot(True)
def test_plot_eds_markers_close():
s = EDS_TEM_Spectrum()
s.plot(True)
return s
def test_plot_eds_lines():
a = EDS_TEM_Spectrum()
s = stack([a, a * 5])
s.plot(True)
s.axes_manager.navigation_axes[0].index = 1
return s._plot.signal_plot.figure
def test_close_figure_with_plotted_marker(self):
s = EDS_TEM_Spectrum()
s.plot(True)
s._plot.close()
self._assert_figure_state_after_close(s._plot.signal_plot)
def test_strings_from_py2():
s = EDS_TEM_Spectrum()
nt.assert_equal(s.metadata.Sample.elements.dtype.char, "U")
def test_plot_eds_lines_background():
s = EDS_TEM_Spectrum().isig[5.0:8.0]
s.plot()
bw = s.estimate_background_windows()
s._plot_xray_lines(background_windows=bw)
def test_close_figure_with_plotted_marker():
s = EDS_TEM_Spectrum()
s.plot(True)
s._plot.close()
check_closing_plot(s)
