def importFile(self, filename):
if not os.path.exists(filename):
qt.QMessageBox.critical(self, "ERROR opening file",
"File %s not found" % filename)
return 1
Elements.Material.read(filename)
error = 0
for material in list(Elements.Material.keys()):
keys = list(Elements.Material[material].keys())
compoundList = []
if "CompoundList" in keys:
compoundList = Elements.Material[material]["CompoundList"]
if "CompoundFraction" in keys:
compoundFraction = Elements.Material[material][
"CompoundFraction"]
if (compoundList == []) or (compoundFraction == []):
#no message?
error = 1
del Elements.Material[material]
continue
#I should try to calculate the attenuation at one energy ...
try:
Elements.getMaterialMassAttenuationCoefficients(
compoundList, compoundFraction, energy=10.0)
except:
#no message?
error = 1
del Elements.Material[material]
continue
return error
def _massAttenuationSlot(self, ddict):
try:
compoundList = ddict['CompoundList']
fractionList = ddict['CompoundFraction']
energy = numpy.arange(1, 100, 0.1)
data = Elements.getMaterialMassAttenuationCoefficients(
compoundList, fractionList, energy)
addButton = False
if (self.graph is None) and SCANWINDOW:
self.graphDialog = qt.QDialog(self)
self.graphDialog.mainLayout = qt.QVBoxLayout(self.graphDialog)
self.graphDialog.mainLayout.setMargin(0)
self.graphDialog.mainLayout.setSpacing(0)
self.graph = ScanWindow.ScanWindow(self.graphDialog)
self.graphDialog.mainLayout.addWidget(self.graph)
self.graph._togglePointsSignal()
self.graph.graph.crossPicker.setEnabled(False)
addButton = True
elif self.graph is None:
self.graphDialog = Plot1DMatplotlib.Plot1DMatplotlibDialog()
self.graph = self.graphDialog.plot1DWindow
addButton = True
if addButton:
self._addGraphDialogButton()
self.graph.setTitle(ddict['Comment'])
legend = 'Coherent'
self.graph.newCurve(energy,
numpy.array(data[legend.lower()]),
legend=legend,
xlabel='Energy (keV)',
ylabel='Mass Att. (cm2/g)',
replace=True)
for legend in ['Compton', 'Photo', 'Total']:
self.graph.newCurve(energy,
numpy.array(data[legend.lower()]),
legend=legend,
xlabel='Energy (keV)',
ylabel='Mass Att. (cm2/g)',
replace=False)
self.graph.setActiveCurve(legend + ' ' + 'Mass Att. (cm2/g)')
self.graph.setTitle(ddict['Comment'])
if self.graphDialog is not None:
self.graphDialog.exec_()
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Error %s" % sys.exc_info()[0])
msg.exec_()
def continuumEbel(target,
e0,
e=None,
window=None,
alphae=None,
alphax=None,
transmission=None,
targetthickness=None,
filterlist=None):
"""
Calculation of X-ray Tube continuum emission spectrum
Parameters:
-----------
target : list [Symbol, density (g/cm2), thickness(cm)] or atomic ymbol
If set to atomic symbol, the program sets density and thickness of 0.1 cm
e0 : float
Tube Voltage in kV
e : float or array of floats
Energy of interest. If not given, the program will generate an array of energies
from 1 to the given tube voltage minus 1 kV in keV.
window : list
Tube window [Formula, density, thickness]
alphae : float
Angle, in degrees, between electron beam and tube target. Normal incidence is 90.
alphax : float
Angle, in degrees, of X-ray exit beam. Normal exit is 90.
transmission : Boolean, default is False
If True the X-ray come out of the tube target by the side opposite to the one
receiving the exciting electron beam.
targetthickness : Target thickness in cm
Only considered in transmission case. If not given, the program uses as target
thickness the maximal penetration depth of the incident electron beam.
filterlist : [list]
Additional filters [[Formula, density, thickness], ...]
Return:
-------
result : Array
Spectral flux density.
Flux of photons at the given energies in photons/sr/mA/keV/s
Reference:
H. Ebel, X-Ray Spectrometry 28 (1999) 255-266
Tube voltage from 5 to 50 kV
Electron incident angle from 50 to 90 deg.
X-Ray take off angle from 90 to 5 deg.
"""
if type(target) in [type([]), type(list())]:
element = target[0]
density = target[1]
thickness = target[2]
else:
element = target
density = Elements.Element[element]['density']
thickness = 0.1
if e is None:
energy = numpy.arange(e0 * 1.0)[1:]
elif type(e) == type([]):
energy = numpy.array(e, dtype=numpy.float)
elif type(e) == numpy.ndarray:
energy = numpy.array(e, dtype=numpy.float)
else:
energy = numpy.array([e], dtype=numpy.float)
if alphae is None:
alphae = 75.0
if alphax is None:
alphax = 15.0
if transmission is None:
transmission = False
sinalphae = math.sin(math.radians(alphae))
sinalphax = math.sin(math.radians(alphax))
sinfactor = sinalphae / sinalphax
z = Elements.getz(element)
const = 1.35e+09
x = 1.109 - 0.00435 * z + 0.00175 * e0
# calculate intermediate constants from formulae (4) in Ebel's paper
# eta in Ebel's paper
m = 0.1382 - 0.9211 / math.sqrt(z)
logz = math.log(z)
eta = 0.1904 - 0.2236 * logz + 0.1292 * pow(logz, 2) - \
0.0149 * pow(logz, 3)
eta = eta * pow(e0, m)
# dephmax? in Ebel's paper
p3 = 0.787e-05 * math.sqrt(0.0135 * z) * pow(e0, 1.5) + \
0.735e-06 * pow(e0, 2)
rhozmax = (Elements.Element[element]['mass'] / z) * p3
# print "max depth = ",2 * rhozmax
# and finally we get rhoz
u0 = e0 / energy
logu0 = numpy.log(u0)
p1 = logu0 * (0.49269 - 1.09870 * eta + 0.78557 * pow(eta, 2))
p2 = 0.70256 - 1.09865 * eta + 1.00460 * pow(eta, 2) + logu0
rhoz = rhozmax * (p1 / p2)
# the term dealing with the photoelectric absorption of the Bremsstrahlung
tau = numpy.array(
Elements.getMaterialMassAttenuationCoefficients(element, 1.0,
energy)['photo'])
if not transmission:
rhelp = tau * 2.0 * rhoz * sinfactor
if len(numpy.nonzero(rhelp <= 0.0)[0]):
result = numpy.zeros(rhelp.shape, numpy.float)
for i in range(len(rhelp)):
if rhelp[i] > 0.0:
result[i] = const * z * pow(u0[i] - 1.0, x) * \
(1.0 - numpy.exp(-rhelp[i])) / rhelp[i]
else:
result = const * z * pow(u0 - 1.0, x) * \
(1.0 - numpy.exp(-rhelp)) / rhelp
# the term dealing with absorption in tube's window
if window is not None:
if window[2] != 0:
w = Elements.getMaterialTransmission(
window[0],
1.0,
energy,
density=window[1],
thickness=window[2],
listoutput=False)['transmission']
result *= w
if filterlist is not None:
w = 1
for fwindow in filterlist:
if fwindow[2] == 0:
continue
w *= Elements.getMaterialTransmission(
fwindow[0],
1.0,
energy,
density=fwindow[1],
thickness=fwindow[2],
listoutput=False)['transmission']
result *= w
return result
# transmission case
if targetthickness is None:
#d = Elements.Element[target]['density']
d = density
ttarget = 2 * rhozmax
print(
"WARNING target thickness assumed equal to maximum depth of %f cm"
% (ttarget / d))
else:
#ttarget = targetthickness * Elements.Element[target]['density']
ttarget = targetthickness * density
# generationdepth = min(ttarget, 2 * rhozmax)
rhelp = tau * 2.0 * rhoz * sinfactor
if len(numpy.nonzero(rhelp <= 0.0)[0]):
result = numpy.zeros(rhelp.shape, numpy.float)
for i in range(len(rhelp)):
if rhelp[i] > 0.0:
result[i] = const * z * pow(u0[i] - 1.0, x) * \
(numpy.exp(-tau[i] *(ttarget - 2.0 * rhoz[i]) / sinalphax) - \
numpy.exp(-tau[i] * ttarget / sinalphax)) / rhelp[i]
else:
result = const * z * pow(u0 - 1.0, x) * \
(numpy.exp(-tau *(ttarget - 2.0 * rhoz) / sinalphax) - \
numpy.exp(-tau * ttarget / sinalphax)) / rhelp
# the term dealing with absorption in tube's window
if window is not None:
if window[2] != 0.0:
w = Elements.getMaterialTransmission(
window[0],
1.0,
energy,
density=window[1],
thickness=window[2] / sinalphax,
listoutput=False)['transmission']
result *= w
if filterlist is not None:
for fwindow in filterlist:
if fwindow[2] == 0:
continue
w = Elements.getMaterialTransmission(
fwindow[0],
1.0,
energy,
density=fwindow[1],
thickness=fwindow[2],
listoutput=False)['transmission']
result *= w
return result
def characteristicEbel(target,
e0,
window=None,
alphae=None,
alphax=None,
transmission=None,
targetthickness=None,
filterlist=None):
"""
Calculation of target characteritic lines and intensities
Parameters:
-----------
target : list [Symbol, density (g/cm2), thickness(cm)] or atomic ymbol
If set to atomic symbol, the program sets density and thickness of 0.1 cm
e0 : float
Tube Voltage in kV
e : float
Energy of interest
window : list
Tube window [Formula, density, thickness]
alphae : float
Angle, in degrees, between electron beam and tube target. Normal incidence is 90.
alphax : float
Angle, in degrees, of X-ray exit beam. Normal exit is 90.
transmission : Boolean, default is False
If True the X-ray come out of the tube target by the side opposite to the one
receiving the exciting electron beam.
targetthickness : Target thickness in cm
Only considered in transmission case. If not given, the program uses as target
thickness the maximal penetration depth of the incident electron beam.
filterlist : [list]
Additional filters [[Formula, density, thickness], ...]
Result: list
Characteristic lines and intensities in the form
[[energy0, intensity0, name0], [energy1, intensity1, name1], ...]
Energies in keV
Intensities in photons/sr/mA/keV/s
"""
if type(target) == type([]):
element = target[0]
density = target[1]
thickness = target[2]
if targetthickness is None:
targetthickness = target[2]
else:
element = target
density = Elements.Element[element]['density']
thickness = 0.1
if alphae is None:
alphae = 75.0
if alphax is None:
alphax = 15.0
if transmission is None:
transmission = False
sinalphae = math.sin(math.radians(alphae))
sinalphax = math.sin(math.radians(alphax))
sinfactor = sinalphae / sinalphax
z = Elements.getz(element)
const = 6.0e+13
# K Shell
energy = Elements.Element[element]['binding']['K']
# get the energy of the characteristic lines
lines = Elements._getUnfilteredElementDict(element,
None,
photoweights=True)
if 0:
# L shell lines will have to be entered directly by the user
# L shell
lpeaks = []
for label in lines['L xrays']:
lpeaks.append([
lines[label]['energy'], lines[label]['rate'],
element + ' ' + label
])
lfluo = Elements._filterPeaks(lpeaks,
ethreshold=0.020,
ithreshold=0.001,
nthreshold=6,
absoluteithreshold=False,
keeptotalrate=True)
lfluo.sort()
peaklist = []
rays = 'K xrays'
if rays in lines.keys():
#K shell
for label in lines[rays]:
peaklist.append([
lines[label]['energy'], lines[label]['rate'],
element + ' ' + label
])
fl = Elements._filterPeaks(peaklist,
ethreshold=0.020,
ithreshold=0.001,
nthreshold=4,
absoluteithreshold=False,
keeptotalrate=True)
fl.sort()
if (energy > 0) and (e0 > energy):
zk = 2.0
bk = 0.35
else:
for i in range(len(fl)):
fl[i][1] = 0.00
return fl
u0 = e0 / energy
logu0 = numpy.log(u0)
# stopping factor
oneovers = (numpy.sqrt(u0) * logu0 + 2 * (1.0 - numpy.sqrt(u0)))
oneovers /= u0 * logu0 + 1.0 - u0
oneovers = 1.0 + 16.05 * numpy.sqrt(0.0135 * z / energy) * oneovers
oneovers *= (zk * bk / z) * (u0 * logu0 + 1.0 - u0)
# backscattering factor
r = 1.0 - 0.0081517 * z + 3.613e-05 * z * z +\
0.009583 * z * numpy.exp(-u0) + 0.001141 * e0
# Absorption correction
# calculate intermediate constants from formulae (4) in Ebel's paper
# eta in Ebel's paper
m = 0.1382 - 0.9211 / numpy.sqrt(z)
logz = numpy.log(z)
eta = 0.1904 - 0.2236 * logz + 0.1292 * pow(logz, 2) - 0.0149 * pow(
logz, 3)
eta = eta * pow(e0, m)
# depmax? in Ebel's paper
p3 = 0.787e-05 * numpy.sqrt(0.0135 * z) * pow(e0, 1.5) + \
0.735e-06 * pow(e0, 2)
rhozmax = (Elements.Element[element]['mass'] / z) * p3
# and finally we get rhoz
p1 = logu0 * (0.49269 - 1.09870 * eta + 0.78557 * pow(eta, 2))
p2 = 0.70256 - 1.09865 * eta + 1.00460 * pow(eta, 2) + logu0
rhoz = rhozmax * (p1 / p2)
# the term dealing with the photoelectric absorption
energylist = []
for i in range(len(fl)):
energylist.append(fl[i][0])
tau = numpy.array(
Elements.getMaterialMassAttenuationCoefficients(
element, 1.0, energylist)['photo'])
if not transmission:
rhelp = tau * 2.0 * rhoz * sinfactor
w = None
if window is not None:
if window[2] != 0.0:
w = Elements.getMaterialTransmission(
window[0],
1.0,
energylist,
density=window[1],
thickness=window[2],
listoutput=False)['transmission']
if filterlist is not None:
for fwindow in filterlist:
if fwindow[2] == 0:
continue
if w is None:
w = Elements.getMaterialTransmission(
fwindow[0],
1.0,
energylist,
density=fwindow[1],
thickness=fwindow[2],
listoutput=False)['transmission']
else:
w *= Elements.getMaterialTransmission(
fwindow[0],
1.0,
energylist,
density=fwindow[1],
thickness=fwindow[2],
listoutput=False)['transmission']
for i in range(len(fl)):
if rhelp[i] > 0.0:
rhelp[i] = (1.0 - numpy.exp(-rhelp[i])) / rhelp[i]
else:
rhelp[i] = 0.0
intensity = const * oneovers * r * Elements.getomegak(
element) * rhelp[i]
#the term dealing with absorption in tube's window
if w is not None:
intensity = intensity * w[i]
fl[i][1] = intensity * fl[i][1]
return fl
#transmission case
if targetthickness is None:
d = density
ttarget = 2 * rhozmax
print(
"WARNING target thickness assumed equal to maximum depth of %f cm"
% (ttarget / d))
else:
ttarget = targetthickness * density
#generationdepth = min(ttarget, 2 * rhozmax)
rhelp = tau * 2.0 * rhoz * sinfactor
w = None
if (window is not None) or (filterlist is not None):
if window is not None:
if window[2] != 0.0:
w = Elements.getMaterialTransmission(
window[0],
1.0,
energylist,
density=window[1],
thickness=window[2] / sinalphax,
listoutput=False)['transmission']
if filterlist is not None:
for fwindow in filterlist:
if w is None:
w = Elements.getMaterialTransmission(
fwindow[0],
1.0,
energylist,
density=fwindow[1],
thickness=fwindow[2],
listoutput=False)['transmission']
else:
w *= Elements.getMaterialTransmission(
fwindow[0],
1.0,
energylist,
density=fwindow[1],
thickness=fwindow[2],
listoutput=False)['transmission']
for i in range(len(fl)):
if rhelp[i] > 0.0:
rhelp[i] = (
numpy.exp(-tau[i] * (ttarget - 2.0 * rhoz) / sinalphax) -
numpy.exp(-tau[i] * ttarget / sinalphax)) / rhelp[i]
else:
rhelp[i] = 0.0
intensity = const * oneovers * r * Elements.getomegak(
element) * rhelp[i]
if w is not None:
intensity = intensity * w[i]
fl[i][1] = intensity * fl[i][1]
return fl
