def _calculate_factor(self, z):
fluorescence = FluorescenceFactor(self._config_filepath,
self._characteristic_model,
self._bremsstrahlung_model)
energy_keV = self._measurement.options.beam.energy_eV / 1000.0
fluorescence.setIncidentEnergy_keV(energy_keV)
toa_deg = self._measurement.detector.takeoffangle_deg
fluorescence.setTakeoffAngle_deg(toa_deg)
elements = []
material = self._measurement.unknown_body.material
for atomicnumber, wf in material.composition.iteritems():
elements.append(Element(atomicnumber, weightFraction=wf))
region = SampleRegion(elements)
fluorescence.setSpecimenBulk(region)
elements = []
material = self._measurement.get_standards()[z].material
for atomicnumber, wf in material.composition.iteritems():
elements.append(Element(atomicnumber, weightFraction=wf))
region = SampleRegion(elements)
fluorescence.setStandardBulk(region)
transitions = self._measurement.get_transitions()
transition = [t for t in transitions if t.z == z][0]
element = ep.symbol(transition.z)
if hasattr(transition, '__iter__'):
line = transition.name
else:
line = transition.siegbahn_nogreek
return fluorescence.getFactor(element, line)
def add_kratio(self, transition, val, unc=0.0, standard=None):
"""
Adds a k-ratio to this measurement.
:arg transition: transition or set of transition for this k-ratio
:type transition: :class:`.Transition` or :class:`.transitionset`
:arg val: k-ratio value
:type val: :class:`float`
:arg unc: uncertainty on the k-ratio value (default: 0.0)
:type unc: :class:`float`
:arg standard: geometry of the standard. Although standard are usually
bulk sample, it may occur that the standard geometry is not a
substrate. Specifying a geometry also allows to define exact
simulation parameters for the standard.
If ``None``, a substrate geometry is created. The standard is
assumed to be a pure (100% of the element in the specified
transition)
:type standard: instance of :class:`._Geometry`
:raise: :exc:`ValueError` if a k-ratio or rule is already defined for
the atomic number of the specified transition
"""
z = transition.z
if z in self._transitions:
raise ValueError, 'A k-ratio is already defined for element: %s' % ep.symbol(
z)
if z in self._rules:
raise ValueError, 'A rule is already defined for element: %s' % ep.symbol(
z)
if val < 0.0:
raise ValueError, 'k-ratio value must be greater than 0.0'
if unc < 0.0:
raise ValueError, 'k-ratio uncertainty must be greater than 0.0'
if standard is None:
standard = Substrate(pure(z))
self._transitions[z] = transition
self._kratios[z] = (val, unc)
self._standards[z] = standard
def selectionSymbol(self):
selection = self.selection()
if self.isMultipleSelection():
return frozenset(map(ep.symbol, selection))
else:
if selection is None:
return None
else:
return ep.symbol(selection)
def add_kratio(self, transition, val, unc=0.0, standard=None):
"""
Adds a k-ratio to this measurement.
:arg transition: transition or set of transition for this k-ratio
:type transition: :class:`.Transition` or :class:`.transitionset`
:arg val: k-ratio value
:type val: :class:`float`
:arg unc: uncertainty on the k-ratio value (default: 0.0)
:type unc: :class:`float`
:arg standard: geometry of the standard. Although standard are usually
bulk sample, it may occur that the standard geometry is not a
substrate. Specifying a geometry also allows to define exact
simulation parameters for the standard.
If ``None``, a substrate geometry is created. The standard is
assumed to be a pure (100% of the element in the specified
transition)
:type standard: instance of :class:`._Geometry`
:raise: :exc:`ValueError` if a k-ratio or rule is already defined for
the atomic number of the specified transition
"""
z = transition.z
if z in self._transitions:
raise ValueError, 'A k-ratio is already defined for element: %s' % ep.symbol(z)
if z in self._rules:
raise ValueError, 'A rule is already defined for element: %s' % ep.symbol(z)
if val < 0.0:
raise ValueError, 'k-ratio value must be greater than 0.0'
if unc < 0.0:
raise ValueError, 'k-ratio uncertainty must be greater than 0.0'
if standard is None:
standard = Substrate(pure(z))
self._transitions[z] = transition
self._kratios[z] = (val, unc)
self._standards[z] = standard
def _setup_region_material(region, material):
region.removeAllElements()
for z, fraction in material.composition.items():
region.addElement(ep.symbol(z), weightFraction=fraction)
region.update() # Calculate number of elements, mean atomic number
region.User_Density = True
region.Rho = material.density_kg_m3 / 1000.0 # g/cm3
region.Name = material.name
def add_rule(self, rule):
"""
Adds a rule to this measurement.
:arg rule: rule object
"""
z = rule.z
if z in self._rules:
raise ValueError, 'A rule is already defined for element: %s' % ep.symbol(z)
if z in self._transitions:
raise ValueError, 'A k-ratio is already defined for element: %s' % ep.symbol(z)
# Ensure that there is only one ElementByDifference rule
diff_rules = any(map(lambda rule: isinstance(rule, ElementByDifferenceRule),
self._rules.values()))
if diff_rules and isinstance(rule, ElementByDifferenceRule):
raise ValueError, 'A ElementByDifferenceRule was already added'
self._rules[z] = rule
def add_rule(self, rule):
"""
Adds a rule to this measurement.
:arg rule: rule object
"""
z = rule.z
if z in self._rules:
raise ValueError, 'A rule is already defined for element: %s' % ep.symbol(
z)
if z in self._transitions:
raise ValueError, 'A k-ratio is already defined for element: %s' % ep.symbol(
z)
# Ensure that there is only one ElementByDifference rule
diff_rules = any(
map(lambda rule: isinstance(rule, ElementByDifferenceRule),
self._rules.values()))
if diff_rules and isinstance(rule, ElementByDifferenceRule):
raise ValueError, 'A ElementByDifferenceRule was already added'
self._rules[z] = rule
def _group(z, siegbahn, iupac, include_satellite=False):
transitions = []
for ssiegbahn in _SIEGBAHNS:
if ssiegbahn.startswith(siegbahn):
transitions.append(Transition(z, siegbahn=ssiegbahn))
transitions = filter(methodcaller('exists'), transitions)
if not include_satellite:
transitions = filter(methodcaller('is_diagram_line'), transitions)
if not transitions:
raise ValueError('No transition for %s %s' % (ep.symbol(z), iupac))
return transitionset(z, siegbahn, iupac, list(transitions))
def _group(z, siegbahn, iupac, include_satellite=False):
transitions = []
for ssiegbahn in _SIEGBAHNS:
if ssiegbahn.startswith(siegbahn):
transitions.append(Transition(z, siegbahn=ssiegbahn))
transitions = filter(methodcaller('exists'), transitions)
if not include_satellite:
transitions = filter(methodcaller('is_diagram_line'), transitions)
if not transitions:
raise ValueError('No transition for %s %s' % (ep.symbol(z), iupac))
return transitionset(z, siegbahn, iupac, list(transitions))
def _shell(z, dest, include_satellite=False):
subshell = Subshell(z, dest)
siegbahn = subshell.siegbahn
iupac = subshell.iupac
transitions = []
for src, ddest, satellite in _SUBSHELLS:
if ddest != dest: continue
if satellite != 0 and not include_satellite: continue
transitions.append(Transition(z, src, dest))
transitions = filter(methodcaller('exists'), transitions)
if not transitions:
raise ValueError('No transition for %s %s' % (ep.symbol(z), iupac))
return transitionset(z, siegbahn, iupac, list(transitions))
def _shell(z, dest, include_satellite=False):
subshell = Subshell(z, dest)
siegbahn = subshell.siegbahn
iupac = subshell.iupac
transitions = []
for src, ddest, satellite in _SUBSHELLS:
if ddest != dest: continue
if satellite != 0 and not include_satellite: continue
transitions.append(Transition(z, src, dest))
transitions = filter(methodcaller('exists'), transitions)
if not transitions:
raise ValueError('No transition for %s %s' % (ep.symbol(z), iupac))
return transitionset(z, siegbahn, iupac, list(transitions))
def _import_photon_intensity(self, options, name, detector, path):
wxrresult = CharacteristicIntensity(path)
factor = self._get_normalization_factor(options, detector)
# Retrieve intensities
intensities = {}
for z, line in wxrresult.getAtomicNumberLines():
data = wxrresult.intensities[z][line]
transition = from_string("%s %s" % (symbol(z), line))
gnf = list(map(mul, data[WXRGENERATED], [factor] * 2))
enf = list(map(mul, data[WXREMITTED], [factor] * 2))
intensities[PhotonKey(transition, False, PhotonKey.P)] = gnf
intensities[PhotonKey(transition, True, PhotonKey.P)] = enf
return PhotonIntensityResult(intensities)
def __init__(self, atomic_number, parent=None):
QPushButton.__init__(self, parent)
self.setFixedSize(40, 40)
self._atomic_number = atomic_number
self._symbol = ep.symbol(atomic_number)
self.setText(self._symbol)
font = self.font()
font.setWeight(QFont.Bold)
self.setFont(font)
self.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.MinimumExpanding)
self.setDefault(False)
self.setAutoDefault(False)
def generate_name(composition):
"""
Generates a name from the composition.
The name is generated on the basis of a classical chemical formula.
:arg composition: composition in weight fraction.
The composition is specified by a dictionary.
The key are atomic numbers and the values weight fractions.
No wildcard are accepted.
:type composition: :class:`dict`
"""
composition = Material.calculate_composition(composition)
composition_atomic = Material.calculate_composition_atomic(composition)
symbols = []
fractions = []
for z in sorted(composition_atomic.keys(), reverse=True):
symbols.append(ep.symbol(z))
fractions.append(int(composition_atomic[z] * 100.0))
# Find gcd of the fractions
smallest_gcd = 100
if len(fractions) >= 2:
gcds = []
for a, b in combinations(fractions, 2):
gcds.append(gcd(a, b))
smallest_gcd = min(gcds)
if smallest_gcd == 0.0:
smallest_gcd = 100.0
# Write formula
name = ''
for symbol, fraction in zip(symbols, fractions):
fraction /= smallest_gcd
if fraction == 0:
continue
elif fraction == 1:
name += "%s" % symbol
else:
name += '%s%i' % (symbol, fraction)
return name
def _extract(data, absorption):
distributions = {}
for z in data:
for xrayline in data[z]:
transition = from_string(symbol(z) + " " + xrayline)
dist = np.array(data[z][xrayline]).T
# Convert z values in meters
dist[:, 0] *= -1e-9
# WinXRay starts from the bottom to the top
# The order must be reversed
dist = dist[::-1]
key = PhotonKey(transition, absorption, PhotonKey.P)
distributions[key] = dist
return distributions
def __init__(self, z, index=None, orbital=None, iupac=None, siegbahn=None):
"""
Creates an atomic subshell::
s = SubShell(29, 1) # K
s = SubShell(29, siegbahn='K')
:arg z: atomic number (from 1 to 99 inclusively)
:arg index: index of the subshell between 1 (K) and 30 (outer)
:arg orbital: orbital of the subshell (e.g. ``1s1/2``)
:arg iupac: IUPAC symbol of the subshell
:arg siegbahn: Siegbahn symbol of the subshell
If more than one argument is given, only the first one is used to create
the subshell.
"""
self._z = z
self._symbol = ep.symbol(z)
if index is not None:
if index < 1 or index > 30:
raise ValueError("Id (%s) must be between [1, 30]." % index)
elif orbital is not None:
try:
index = _ORBITALS.index(orbital.lower()) + 1
except ValueError:
raise ValueError("Unknown orbital (%s). Possible orbitals: %s" % \
(orbital, _ORBITALS))
elif iupac is not None:
try:
index = _IUPACS.index(iupac.upper()) + 1
except ValueError:
raise ValueError("Unknown IUPAC (%s). Possible IUPAC: %s" % \
(iupac, _IUPACS))
elif siegbahn is not None:
try:
index = _SIEGBAHNS.index(siegbahn.upper()) + 1
except ValueError:
raise ValueError("Unknown Siegbahn (%s). Possible Siegbahn: %s" % \
(siegbahn, _SIEGBAHNS))
else:
raise ValueError("You must specify an index, orbital, IUPAC or Siegbahn")
self._index = index
self._orbtial = _ORBITALS[index - 1]
self._iupac = _IUPACS[index - 1]
self._siegbahn = _SIEGBAHNS[index - 1]
self._family = self._iupac[0].upper() if index != 30 else None
try:
self._ionization_energy_eV = subshell_data.energy_eV(z, index)
except ValueError:
self._ionization_energy_eV = float('inf')
self._exists = subshell_data.exists(z, index)
try:
self._width_eV = subshell_data.width_eV(z, index)
except ValueError:
self._width_eV = 0.0
def testsymbol(self):
self.assertEqual('H', ep.symbol(1))
self.assertEqual('Uuo', ep.symbol(118))
def testsymbol(self):
self.assertEqual('Al', ep.symbol(13))
def testsymbol(self):
self.assertEqual('H', ep.symbol(1))
self.assertEqual('Uuo', ep.symbol(118))
def _export_geometry_substrate(self, options, geometry, outputdir, *args):
material = geometry.body.material
composition = sorted(material.composition.items(), key=itemgetter(0))
density_g_cm3 = material.density_kg_m3 / 1000.0
filepath = os.path.join(outputdir, options.name + '.MAT')
with open(filepath, 'wb') as fp:
# Header
# DELPHI: s:=6;Blockwrite(Matfile,Typ,6,f);Inc(Sum,f);
# 1st Byte: Type = 2 (homogenous bulk)
# 2nd Byte: NC = <nr. of elements> (amount of occurring formulae (compounds or elements))
# 3rd Byte: NZ = <nr. of elements>
# 4th Byte: NP = 0 (nr. of layers)
# 5th Byte: CU = 2 (1=at%, 2=wt%)
# 6th Byte: MU = 1 (not important for bulk; this is the unit for the layer thickness)
fp.write(struct.pack('b', 2))
fp.write(struct.pack('b', len(composition)))
fp.write(struct.pack('b', len(composition)))
fp.write(struct.pack('b', 0))
fp.write(struct.pack('b', 2))
fp.write(struct.pack('b', 1))
# Write length of element and element
# DELPHI:
# for i:=1 to Nc do begin
# l:=1+Length(Comp[i]);Inc(s,l);
# Blockwrite(Matfile,Comp[i,0],l,f);Inc(Sum,f);
# end;
for z, _wf in composition:
symbol = ep.symbol(z).upper()
fp.write(
struct.pack('b', len(symbol)) + symbol.encode('ascii'))
# Write molar mass
# DELPHI: l:=4*Nc;Inc(s,l);Blockwrite(Matfile,AC[1],l,f);Inc(Sum,f);
for z, _wf in composition:
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
# Write atomic number
# DELPHI: Inc(s,NZ);Blockwrite(Matfile,Z[1],NZ,f);Inc(Sum,f);
for z, _wf in composition:
fp.write(struct.pack('b', z))
# Write molar mass
# DELPHI:
# l:=4*Nc+4;
# for i:=0 to NZ do begin
# Inc(s,l);BlockWrite(Matfile,GZ[i],l,f);Inc(Sum,f);
# end;
fp.write(b'\x00\x00\x00\x00') # Skip 4 bytes
for z, _wf in composition:
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
for i, item in enumerate(composition):
z = item[0]
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
fp.write(b'\x00\x00\x00\x00' * i) # Skip 4 bytes
fp.write(struct.pack('f', 1.0 / mass))
fp.write(b'\x00\x00\x00\x00' *
(len(composition) - i - 1)) # Skip 4 bytes
# DELPHI: Inc(s,l);BlockWrite(Matfile,GM,l,f);Inc(Sum,f);
gs = [
wf / (ep.atomic_mass_kg_mol(z) * 1000.0)
for z, wf in composition
]
g0 = 1.0 / sum(gs)
fp.write(struct.pack('f', g0))
for g in gs:
fp.write(struct.pack('f', g))
# DELPHI:
# for i:=0 to NP do begin
# Inc(s,l);BlockWrite(Matfile,GS[i],l,f);Inc(Sum,f);
# end;
fp.write(b'\x00\x00\x00\x00' * (len(composition) + 1))
# DELPHI:
# l:=4*NP+4;Inc(s,l);Blockwrite(Matfile,ML[0],l,f);Inc(Sum,f);
fp.write(b'\x00\x00\x00\x00')
# DELPHI: Inc(s,l);Blockwrite(Matfile,rho[0],l,f);Inc(Sum,f);
fp.write(struct.pack('f', density_g_cm3))
# DELPHI:
# l:=NC+1;
# for i:=0 to NP do begin
# Inc(s,l);BlockWrite(Matfile,PC[i],l,f);Inc(Sum,f);
# end;
fp.write(struct.pack('b', len(composition)))
fp.write(b'\x00' * len(composition))
# DELPHI: Inc(s,l);BlockWrite(Matfile,PM,l,f);Inc(Sum,f);
fp.write(struct.pack('b', len(composition)))
for i in range(len(composition)):
fp.write(struct.pack('b', i + 1))
return filepath
def testsymbol(self):
self.assertEqual('Al', ep.symbol(13))
def _export_geometry_substrate(self, options, geometry, outputdir, *args):
material = geometry.body.material
composition = sorted(material.composition.items(), key=itemgetter(0))
density_g_cm3 = material.density_kg_m3 / 1000.0
filepath = os.path.join(outputdir, options.name + '.MAT')
with open(filepath, 'wb') as fp:
# Header
# DELPHI: s:=6;Blockwrite(Matfile,Typ,6,f);Inc(Sum,f);
# 1st Byte: Type = 2 (homogenous bulk)
# 2nd Byte: NC = <nr. of elements> (amount of occurring formulae (compounds or elements))
# 3rd Byte: NZ = <nr. of elements>
# 4th Byte: NP = 0 (nr. of layers)
# 5th Byte: CU = 2 (1=at%, 2=wt%)
# 6th Byte: MU = 1 (not important for bulk; this is the unit for the layer thickness)
fp.write(struct.pack('b', 2))
fp.write(struct.pack('b', len(composition)))
fp.write(struct.pack('b', len(composition)))
fp.write(struct.pack('b', 0))
fp.write(struct.pack('b', 2))
fp.write(struct.pack('b', 1))
# Write length of element and element
# DELPHI:
# for i:=1 to Nc do begin
# l:=1+Length(Comp[i]);Inc(s,l);
# Blockwrite(Matfile,Comp[i,0],l,f);Inc(Sum,f);
# end;
for z, _wf in composition:
symbol = ep.symbol(z).upper()
fp.write(struct.pack('b', len(symbol)) + symbol.encode('ascii'))
# Write molar mass
# DELPHI: l:=4*Nc;Inc(s,l);Blockwrite(Matfile,AC[1],l,f);Inc(Sum,f);
for z, _wf in composition:
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
# Write atomic number
# DELPHI: Inc(s,NZ);Blockwrite(Matfile,Z[1],NZ,f);Inc(Sum,f);
for z, _wf in composition:
fp.write(struct.pack('b', z))
# Write molar mass
# DELPHI:
# l:=4*Nc+4;
# for i:=0 to NZ do begin
# Inc(s,l);BlockWrite(Matfile,GZ[i],l,f);Inc(Sum,f);
# end;
fp.write(b'\x00\x00\x00\x00') # Skip 4 bytes
for z, _wf in composition:
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
for i, item in enumerate(composition):
z = item[0]
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
fp.write(b'\x00\x00\x00\x00' * i) # Skip 4 bytes
fp.write(struct.pack('f', 1.0 / mass))
fp.write(b'\x00\x00\x00\x00' * (len(composition) - i - 1)) # Skip 4 bytes
# DELPHI: Inc(s,l);BlockWrite(Matfile,GM,l,f);Inc(Sum,f);
gs = [wf / (ep.atomic_mass_kg_mol(z) * 1000.0) for z, wf in composition]
g0 = 1.0 / sum(gs)
fp.write(struct.pack('f', g0))
for g in gs:
fp.write(struct.pack('f', g))
# DELPHI:
# for i:=0 to NP do begin
# Inc(s,l);BlockWrite(Matfile,GS[i],l,f);Inc(Sum,f);
# end;
fp.write(b'\x00\x00\x00\x00' * (len(composition) + 1))
# DELPHI:
# l:=4*NP+4;Inc(s,l);Blockwrite(Matfile,ML[0],l,f);Inc(Sum,f);
fp.write(b'\x00\x00\x00\x00')
# DELPHI: Inc(s,l);Blockwrite(Matfile,rho[0],l,f);Inc(Sum,f);
fp.write(struct.pack('f', density_g_cm3))
# DELPHI:
# l:=NC+1;
# for i:=0 to NP do begin
# Inc(s,l);BlockWrite(Matfile,PC[i],l,f);Inc(Sum,f);
# end;
fp.write(struct.pack('b', len(composition)))
fp.write(b'\x00' * len(composition))
# DELPHI: Inc(s,l);BlockWrite(Matfile,PM,l,f);Inc(Sum,f);
fp.write(struct.pack('b', len(composition)))
for i in range(len(composition)):
fp.write(struct.pack('b', i + 1))
return filepath
def __init__(self, z, siegbahn, iupac):
self._z = z
self._symbol = ep.symbol(z)
self._siegbahn = siegbahn
self._iupac = iupac
def __init__(self, z, index=None, orbital=None, iupac=None, siegbahn=None):
"""
Creates an atomic subshell::
s = SubShell(29, 1) # K
s = SubShell(29, siegbahn='K')
:arg z: atomic number (from 1 to 99 inclusively)
:arg index: index of the subshell between 1 (K) and 30 (outer)
:arg orbital: orbital of the subshell (e.g. ``1s1/2``)
:arg iupac: IUPAC symbol of the subshell
:arg siegbahn: Siegbahn symbol of the subshell
If more than one argument is given, only the first one is used to create
the subshell.
"""
self._z = z
self._symbol = ep.symbol(z)
if index is not None:
if index < 1 or index > 30:
raise ValueError("Id (%s) must be between [1, 30]." % index)
elif orbital is not None:
try:
index = _ORBITALS.index(orbital.lower()) + 1
except ValueError:
raise ValueError("Unknown orbital (%s). Possible orbitals: %s" % \
(orbital, _ORBITALS))
elif iupac is not None:
try:
index = _IUPACS.index(iupac.upper()) + 1
except ValueError:
raise ValueError("Unknown IUPAC (%s). Possible IUPAC: %s" % \
(iupac, _IUPACS))
elif siegbahn is not None:
try:
index = _SIEGBAHNS.index(siegbahn.upper()) + 1
except ValueError:
raise ValueError("Unknown Siegbahn (%s). Possible Siegbahn: %s" % \
(siegbahn, _SIEGBAHNS))
else:
raise ValueError(
"You must specify an index, orbital, IUPAC or Siegbahn")
self._index = index
self._orbtial = _ORBITALS[index - 1]
self._iupac = _IUPACS[index - 1]
self._siegbahn = _SIEGBAHNS[index - 1]
self._family = self._iupac[0].upper() if index != 30 else None
try:
self._ionization_energy_eV = subshell_data.energy_eV(z, index)
except ValueError:
self._ionization_energy_eV = float('inf')
self._exists = subshell_data.exists(z, index)
try:
self._width_eV = subshell_data.width_eV(z, index)
except ValueError:
self._width_eV = 0.0
def __init__(self, z, siegbahn, iupac):
self._z = z
self._symbol = ep.symbol(z)
self._siegbahn = siegbahn
self._iupac = iupac
