def __init__(self,
symbol,
xray_energy=None,
energy_min=1.5,
overlap_energy=None):
self.symbol = symbol
self.xray_energy = xray_energy
self.mu = 1.0
self.edges = ['K']
self.fyields = {}
if xray_energy is not None:
self.mu = mu_elam(symbol, 1000 * xray_energy, kind='photo')
self.edges = []
for ename, xedge in xray_edges(self.symbol).items():
if ename.lower() in ('k', 'l1', 'l2', 'l3', 'm5'):
edge_kev = 0.001 * xedge.energy
if (edge_kev < xray_energy and edge_kev > energy_min):
self.edges.append(ename)
self.fyields[ename] = xedge.fyield
# currently, we consider only one edge per element
if 'K' in self.edges:
self.edges = ['K']
if 'L3' in self.edges:
tmp = []
for ename in self.edges:
if ename.lower().startswith('l'):
tmp.append(ename)
self.edges = tmp
# apply CK corrections to fluorescent yields
if 'L3' in self.edges:
nlines = 1.0
ck13 = ck_probability(symbol, 'L1', 'L3')
ck12 = ck_probability(symbol, 'L1', 'L2')
ck23 = ck_probability(symbol, 'L2', 'L3')
fy3 = self.fyields['L3']
fy2 = self.fyields.get('L2', 0)
fy1 = self.fyields.get('L1', 0)
if 'L2' in self.edges:
nlines = 2.0
fy3 = fy3 + fy2 * ck23
fy2 = fy2 * (1 - ck23)
if 'L1' in self.edges:
nlines = 3.0
fy3 = fy3 + fy1 * (ck13 + ck12 * ck23)
fy2 = fy2 + fy1 * ck12
fy1 = fy1 * (1 - ck12 - ck13 - ck12 * ck23)
self.fyields['L1'] = fy1
self.fyields['L2'] = fy2
self.fyields['L3'] = fy3 / nlines
self.fyields['L2'] = fy2 / nlines
self.fyields['L1'] = fy1 / nlines
# look up X-ray lines, keep track of very close lines
# so that they can be consolidate
# slightly confusing (and working with XrayLine energies in ev)
self.lines = {}
self.all_lines = {}
energy0 = None
for ename in self.edges:
for key, xline in xray_lines(symbol, ename).items():
self.all_lines[key] = xline
if xline.intensity > 0.002:
self.lines[key] = xline
if energy0 is None:
energy0 = xline.energy
if overlap_energy is None:
if xray_energy is None: xray_energy = 10.0
if energy0 is not None: xray_energy = energy0
# note: at this point xray_energy is in keV
overlap_energy = 5.0 * (2 + np.sqrt(5 + xray_energy))
# collect lines from the same initial level that are close in energy
nlines = len(self.lines)
combos = [[] for k in range(nlines)]
comboe = [-1 for k in range(nlines)]
combol = [None for k in range(nlines)]
for key, xline in self.lines.items():
assigned = False
for i, en in enumerate(comboe):
if (abs(0.001 * xline.energy - en) < overlap_energy
and xline.initial_level == combol[i]):
combos[i].append(key)
assigned = True
break
if not assigned:
for k in range(nlines):
if comboe[k] < 0:
break
combol[k] = xline.initial_level
comboe[k] = xline.energy
combos[k].append(key)
# consolidate overlapping X-ray lines
for comps in combos:
if len(comps) > 0:
key = comps[0]
l0 = self.lines.pop(key)
ilevel = l0.initial_level
iweight = l0.intensity
flevel = [l0.final_level]
en = [l0.energy]
wt = [l0.intensity]
for other in comps[1:]:
lx = self.lines.pop(other)
if lx.intensity > iweight:
iweight = lx.intensity
ilevel = lx.initial_level
flevel.append(lx.final_level)
en.append(lx.energy)
wt.append(lx.intensity)
wt = np.array(wt)
en = np.array(en)
flevel = ', '.join(flevel)
if len(comps) > 1:
newkey = key.replace('1', '').replace('2',
'').replace('3', '')
newkey = newkey.replace('4',
'').replace('5',
'').replace(',', '')
if newkey not in self.lines:
key = newkey
self.lines[key] = XrayLine(energy=(en * wt).sum() / wt.sum(),
intensity=wt.sum(),
initial_level=ilevel,
final_level=flevel)
def test_ck_probability():
assert_allclose(ck_probability('W', 'L1', 'L3'), 0.3, rtol=0.01)