def element(elem=None):
edges = atomic = lines = {}
if elem is not None:
atomic = {
'n': xraydb.atomic_number(elem),
'mass': xraydb.atomic_mass(elem),
'density': xraydb.atomic_density(elem)
}
_edges = xraydb.xray_edges(elem)
_lines = xraydb.xray_lines(elem)
lines = OrderedDict()
for k in sorted(_lines.keys()):
en, inten, init, final = _lines[k] # XrayLine
lines[k] = XrayLine(energy=f'{en:.1f}',
intensity=f'{inten:.5f}',
initial_level=init,
final_level=final)
edges = OrderedDict()
for k in sorted(_edges.keys()):
en, fy, jump = _edges[k] # XrayEdge
edges[k] = XrayEdge(energy=f'{en:.1f}',
fyield=f'{fy:.5f}',
jump_ratio=f'{jump:.3f}')
return render_template('elements.html',
edges=edges,
elem=elem,
atomic=atomic,
lines=lines,
materials_dict=materials_dict)
def look_edges_db(element, edge='all'):
'''
uses xray_edges to return energies,fyield and jump ratio
takes element, specific lines and group of lines
'''
try:
edges = xray_edges(element)
except:
raise ValueError(
'cant find element {}, please try Co, Xe or F'.format(element))
string = str()
string = 'edges for {}: \n'.format(element)
string = string + 'edge \t | energy \t | fyield \t | jump ratio\n'
if edge == 'all':
for n in edges.keys():
string = string + str(n) + '\t | ' + str(
edges[n][0]) + ' eV' + '\t | ' + str(
edges[n][1]) + '\t | ' + str(edges[n][2]) + '\n'
else:
edge = edge.upper()
try:
for n in edges.keys():
if n.startswith(edge):
string = string + str(n) + '\t | ' + str(
edges[n][0]) + ' eV' + '\t | ' + str(
edges[n][1]) + '\t | ' + str(edges[n][2]) + '\n'
except:
raise ValueError('cant find edge')
return string
def test_edge_energies():
from xraydb.xray import _edge_energies
assert xray_edge(30, 'K') == xray_edge('Zn', 'K')
for edge in ('k', 'l3', 'l2'):
for iz in range(1, 98):
_edge = xray_edge(iz, edge)
if _edge is not None:
en = _edge.energy
assert _edge_energies[edge][iz] < en + 0.5
assert _edge_energies[edge][iz] > en - 0.5
assert_allclose(xray_edge('Zn', 'K', energy_only=True), 9660, rtol=0.01)
sr_edges = xray_edges('Sr')
assert_allclose(sr_edges['K'].energy, 16105.0, rtol=0.001)
assert_allclose(sr_edges['L1'].energy, 2216.0, rtol=0.001)
assert_allclose(sr_edges['L2'].energy, 2007.0, rtol=0.001)
assert_allclose(sr_edges['L3'].energy, 1940.0, rtol=0.001)
assert_allclose(sr_edges['M1'].energy, 358.7, rtol=0.001)
assert_allclose(sr_edges['M2'].energy, 280.3, rtol=0.001)
assert_allclose(sr_edges['M3'].energy, 270.0, rtol=0.001)
assert_allclose(sr_edges['M4'].energy, 136.0, rtol=0.001)
assert_allclose(sr_edges['M5'].energy, 134.2, rtol=0.001)
assert_allclose(sr_edges['N1'].energy, 38.9, rtol=0.001)
assert_allclose(sr_edges['N2'].energy, 21.6, rtol=0.001)
assert_allclose(sr_edges['N3'].energy, 20.1, rtol=0.001)
assert_allclose(sr_edges['K'].fyield, 0.664652, rtol=0.001)
assert_allclose(sr_edges['L1'].fyield, 0.0051, rtol=0.001)
assert_allclose(sr_edges['L2'].fyield, 0.024, rtol=0.001)
assert_allclose(sr_edges['L3'].fyield, 0.026, rtol=0.001)
assert_allclose(sr_edges['M1'].fyield, 5.95e-05, rtol=0.001)
assert_allclose(sr_edges['M2'].fyield, 3.7e-05, rtol=0.001)
assert_allclose(sr_edges['M3'].fyield, 0.000105, rtol=0.001)
assert_allclose(sr_edges['M4'].fyield, 0.0027, rtol=0.001)
assert_allclose(sr_edges['M5'].fyield, 0.0, rtol=0.001)
assert_allclose(sr_edges['N1'].fyield, 1.2e-05, rtol=0.001)
assert_allclose(sr_edges['N2'].fyield, 0.013, rtol=0.001)
assert_allclose(sr_edges['N3'].fyield, 0.013, rtol=0.001)
assert_allclose(sr_edges['K'].jump_ratio, 6.888, rtol=0.01)
assert_allclose(sr_edges['L1'].jump_ratio, 1.1415, rtol=0.01)
assert_allclose(sr_edges['L2'].jump_ratio, 1.4, rtol=0.01)
assert_allclose(sr_edges['L3'].jump_ratio, 3.982, rtol=0.01)
assert_allclose(sr_edges['M1'].jump_ratio, 1.04, rtol=0.01)
assert_allclose(sr_edges['M2'].jump_ratio, 1.058, rtol=0.01)
assert_allclose(sr_edges['M3'].jump_ratio, 1.12491, rtol=0.01)
assert_allclose(sr_edges['M4'].jump_ratio, 1.139, rtol=0.01)
assert_allclose(sr_edges['M5'].jump_ratio, 1.808, rtol=0.01)
assert_allclose(sr_edges['N1'].jump_ratio, 1.0, rtol=0.01)
assert_allclose(sr_edges['N2'].jump_ratio, 1.0, rtol=0.01)
assert_allclose(sr_edges['N3'].jump_ratio, 1.0, rtol=0.01)
def darwinwidth(elem=None):
edges = atomic = lines = {}
if elem is not None:
edges= xraydb.xray_edges(elem)
atomic= {'n': xraydb.atomic_number(elem),
'mass': xraydb.atomic_mass(elem),
'density': xraydb.atomic_density(elem)}
lines= xraydb.xray_lines(elem)
return render_template('darwinwidth.html', edges=edges, elem=elem,
atomic=atomic, lines=lines, materials_dict=materials_dict)
def element(elem=None):
edges = atomic = lines = {}
if elem is not None:
atomic= {'n': xraydb.atomic_number(elem),
'mass': xraydb.atomic_mass(elem),
'density': xraydb.atomic_density(elem)}
_edges= xraydb.xray_edges(elem)
_lines= xraydb.xray_lines(elem)
lines = OrderedDict()
for k in sorted(_lines.keys()):
lines[k] = _lines[k]
edges = OrderedDict()
for k in sorted(_edges.keys()):
edges[k] = _edges[k]
return render_template('elements.html', edges=edges, elem=elem,
atomic=atomic, lines=lines, materials_dict=materials_dict)
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)