def test_scofield_limits(self):
"""Check Scofield parametrisation refuses to extrapolate"""
with self.assertRaises(ValueError):
get_cross_sections_scofield(0.5, elements=['H'])
with self.assertRaises(ValueError):
get_cross_sections_scofield((10, 11, 0.5), elements=['H'])
with self.assertRaises(ValueError):
get_cross_sections_scofield(1600, elements=['H'])
with self.assertRaises(ValueError):
get_cross_sections_scofield((10, 11, 1600, 12), elements=['H'])
def test_scofield_ref(self):
"""Check Scofield parametrisation: spot-check vs tables"""
for el, orb, occ, energy, value in self.ref_values:
cs = get_cross_sections_scofield(energy, elements=[el])
# Check error is below 1 percent; small error is due to
# fitting, not implementation in this part of code!
self.assertAlmostEqual(cs[el][orb] * occ,
value, delta=(value * 0.01))
def run(elements, emin=1, emax=10, size=None, output=None, fontsize=10):
energies = np.linspace(emin, emax, 200)
cross_sections = get_cross_sections_scofield(energies, elements)
if size is None:
fig = plt.figure()
else:
size_inches = [float(x) / 2.54 for x in size]
fig = plt.figure(figsize=size_inches)
ax = fig.add_subplot(1, 1, 1)
colors = cycle(('C0', 'C1', 'C2', 'C3', 'C4'))
markers = cycle(('o', '^', 'D', 'x', '*'))
for element in elements:
color, marker = next(colors), next(markers)
linestyles = cycle((['-', '--', ':', '-.']))
if 'warning' in cross_sections[element]:
logging.warning(" {0}: {1}".format(
element, cross_sections[element]['warning']))
for orbital in 'spdf':
if (orbital in cross_sections[element]
and cross_sections[element][orbital] is not None):
ax.plot(energies,
cross_sections[element][orbital],
color=color,
linestyle=next(linestyles),
marker=marker,
markevery=40,
label='{0}-{1}'.format(element, orbital),
markersize=5)
ax.tick_params(labelsize=(fontsize - 2))
ax.set_xlabel('Photon energy / keV', fontsize=fontsize)
ax.set_ylabel(r'Photoionization cross-section / barns electron$^{-1}$',
fontsize=fontsize)
ax.set_yscale('log')
ax.legend(loc='lower right', fontsize=fontsize)
fig.subplots_adjust(right=0.98, top=0.98)
if output is None:
plt.show()
else:
fig.savefig(output)