/usr/share/pyshared/PyMca/XRayTubeEbel.py is in pymca 4.5.0-4.
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# Copyright (C) 2004-2011 European Synchrotron Radiation Facility
#
# This file is part of the PyMCA X-ray Fluorescence Toolkit developed at
# the ESRF by the Beamline Instrumentation Software Support (BLISS) group.
#
# This toolkit is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# PyMCA is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# PyMCA; if not, write to the Free Software Foundation, Inc., 59 Temple Place,
# Suite 330, Boston, MA 02111-1307, USA.
#
# PyMCA follows the dual licensing model of Trolltech's Qt and Riverbank's PyQt
# and cannot be used as a free plugin for a non-free program.
#
# Please contact the ESRF industrial unit (industry@esrf.fr) if this license
# is a problem for you.
#############################################################################*/
import Elements
import numpy.oldnumeric as Numeric
DEBUG = 0
def continuumEbel(target, e0, e = None, window = None,
alphae = None, alphax = None,
transmission = None, targetthickness = None,
filterlist=None):
"""
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.
def continuum(target, e, e0, window = None, mode=None)
target = Tuple [Symbol, density, thickness]
e0 = Tube Voltage in kV
e = Energy of interest
window = Tube window [Formula, density, thickness]
filterlist = Additional filters [[Formula, density, thickness], ...]
"""
if type(target) == type([]):
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 = Numeric.arange(e0 * 1.0)[1:]
elif type(e) == type([]):
energy = Numeric.array(e).astype(Numeric.Float)
elif type(e) == Numeric.ArrayType:
energy = Numeric.array(e).astype(Numeric.Float)
else:
energy = Numeric.array([e]).astype(Numeric.Float)
if alphae is None:alphae = 75.0
if alphax is None:alphax = 15.0
if transmission is None:transmission = False
sinalphae = Numeric.sin(Numeric.pi * alphae/180.)
sinalphax = Numeric.sin(Numeric.pi * alphax/180.)
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 / Numeric.sqrt(z)
logz = Numeric.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 * Numeric.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 = Numeric.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 = Numeric.array(Elements.getMaterialMassAttenuationCoefficients(element,
1.0,
energy)['photo'])
if not transmission:
rhelp = tau * 2.0 * rhoz * sinfactor
if len(Numeric.nonzero(rhelp) <= 0.0):
result = Numeric.zeros(Numeric.shape(rhelp), Numeric.Float)
for i in range(len(rhelp)):
if rhelp[i] > 0.0:
result [i] = const * z * pow(u0[i] - 1.0, x) * \
(1.0 - Numeric.exp(-rhelp[i])) / rhelp[i]
else:
result = const * z * pow(u0 - 1.0, x) * \
(1.0 - Numeric.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 = 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 = 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(Numeric.nonzero(rhelp) <= 0.0):
result = Numeric.zeros(Numeric.shape(rhelp), Numeric.Float)
for i in range(len(rhelp)):
if rhelp[i] > 0.0:
result [i] = const * z * pow(u0[i] - 1.0, x) * \
(Numeric.exp(-tau[i] *(ttarget-2.0*rhoz[i])/sinalphax)-Numeric.exp(-tau[i]*ttarget/sinalphax)) / rhelp[i]
else:
result = const * z * pow(u0 - 1.0, x) * \
(Numeric.exp(-tau *(ttarget-2.0*rhoz)/sinalphax)-Numeric.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 = 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 = result * w
return result
def characteristicEbel(target, e0, window = None,
alphae = None, alphax = None,
transmission = None, targetthickness = None,
filterlist=None):
"""
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.
def continuum(target, e, e0, window = None, mode=None)
target = Tuple [Symbol, density, thickness]
e0 = Tube Voltage in kV
e = Energy of interest
window = Tube window [Formula, density, thickness]
"""
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 = Numeric.sin(Numeric.pi * alphae/180.)
sinalphax = Numeric.sin(Numeric.pi * alphax/180.)
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(peaklist, 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 = Numeric.log(u0)
#stopping factor
oneovers = (Numeric.sqrt(u0) * logu0 + 2 * (1.0 - Numeric.sqrt(u0)))
oneovers = oneovers / (u0 * logu0 + 1.0 - u0)
oneovers = 1.0 + 16.05 * Numeric.sqrt(0.0135*z/energy) * oneovers
oneovers = (zk*bk/z) * (u0 * logu0 + 1.0 - u0) * oneovers
#backscattering factor
r = 1.0 - 0.0081517 * z + 3.613e-05 * z * z +\
0.009583 * z * Numeric.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 / Numeric.sqrt(z)
logz = Numeric.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 * Numeric.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 = Numeric.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 - Numeric.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] = (Numeric.exp(-tau[i] *(ttarget-2.0*rhoz)/sinalphax)-Numeric.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
def generateLists(target, e0, window = None,
alphae = None, alphax = None,
transmission = None, targetthickness=None,
filterlist=None):
e0w = 1.0 * e0
x1min = 1.4
step1 = 0.2
#x1min = 8.0
#step1 = 0.15
x2min = min(e0-2*step1, 20.0)
#step2 = 0.3
if x2min < 20:
step2 = step1
else:
step2 = 0.5
x3min = e0w
x1 = Numeric.arange(x1min, x2min+step1, step1)
x2 = Numeric.arange(x2min+step1, x3min, step2)
#get K shell characteristic lines and intensities
fllines = characteristicEbel(target, e0, window,
alphae=alphae, alphax=alphax,
transmission = transmission,
targetthickness=targetthickness,
filterlist=filterlist)
energy = Numeric.ones(len(x1) + len(x2)).astype(Numeric.Float)
energy[0:len(x1)] = energy[0:len(x1)] * x1
energy[len(x1):(len(x1)+len(x2))] = energy[len(x1):(len(x1)+len(x2))] * x2
#energy[(len(x1)+len(x2)):] = energy[(len(x1)+len(x2)):] * x3
#print "len(energy) = ",len(energy)
energyweight = continuumEbel(target, e0, energy, window,
alphae=alphae, alphax=alphax,
transmission = transmission,
targetthickness=targetthickness,
filterlist=filterlist)
energyweight[0:len(x1)] *= step1
energyweight[len(x1):(len(x1)+len(x2))] *= step2
energyweight[len(x1)] *= (energy[len(x1)] - energy[len(x1) - 1])/step2
finalenergy = Numeric.zeros(len(fllines)+len(energyweight), Numeric.Float)
finalweight = Numeric.zeros(len(fllines)+len(energyweight), Numeric.Float)
scatterflag = Numeric.zeros(len(fllines)+len(energyweight))
finalenergy[len(fllines):] = energy[0:]
finalweight[len(fllines):] = energyweight[0:]/1.0e7
for i in range(len(fllines)):
finalenergy[i] = fllines[i][0]
finalweight[i] = fllines[i][1]/1.0e7
scatterflag[i] = 1
return finalenergy, finalweight, scatterflag
if __name__ == "__main__":
import sys
import getopt
options = ''
longoptions = ['target=', 'voltage=', 'wele=', 'window=', 'wthickness=','anglee=', 'anglex=',
'cfg=', 'deltae=', 'transmission=','tthickness=']
opts, args = getopt.getopt(
sys.argv[1:],
options,
longoptions)
target = 'Ag'
voltage = 40
wele = 'Be'
wthickness = 0.0125
anglee = 70
anglex = 50
cfgfile = None
transmission = None
ttarget = None
filterlist = None
for opt,arg in opts:
if opt in ('--target'):
target = arg
elif opt in ('--tthickness'):
ttarget = float(arg)
if opt in ('--cfg'):
cfgfile = arg
if opt in ('--voltage'):
voltage = float(arg)
if opt in ('--wthickness'):
wthickness = float(arg)
if opt in ('--wele','window'):
wele = arg
if opt in ('--transmission'):
transmission=int(arg)
if opt in ('--anglee', '--alphae'):
anglee=float(arg)
if opt in ('--anglex', '--alphax'):
anglex=float(arg)
try:
e = Numeric.arange(voltage*10+1)[1:]/10
y= continuumEbel(target, voltage, e,
[wele, Elements.Element[wele]['density'], wthickness],
alphae=anglee, alphax=anglex,
transmission=transmission,
targetthickness=ttarget,
filterlist=filterlist)
fllines = characteristicEbel(target, voltage,
[wele, Elements.Element[wele]['density'], wthickness],
alphae=anglee, alphax=anglex,
transmission=transmission,
targetthickness=ttarget,
filterlist=filterlist)
fsum = 0.0
for l in fllines:
print("%s %.4f %.3e" % (l[2],l[0],l[1]))
fsum += l[1]
energy, weight, scatter = generateLists(target, voltage,
[wele, Elements.Element[wele]['density'], wthickness],
alphae=anglee, alphax=anglex,
transmission=transmission, targetthickness=ttarget,
filterlist=filterlist)
f = open("Tube_%s_%.1f_%s_%.5f_ae%.1f_ax%.1f.txt" % (target,voltage,wele,wthickness,anglee,anglex),"w+")
text = "energyweight="
for i in range(len(energy)):
if i == 0:
text +=" %f" % weight[i]
else:
text +=", %f" % weight[i]
text +="\n"
f.write(text)
text = "energy="
for i in range(len(energy)):
if i == 0:
text +=" %f" % energy[i]
else:
text +=", %f" % energy[i]
text +="\n"
f.write(text)
text = "energyflag="
for i in range(len(energy)):
if i == 0:
text +=" %f" % 1
else:
text +=", %f" % 1
text +="\n"
f.write(text)
text = "energyscatter="
for i in range(len(energy)):
if i == 0:
text +=" %f" % scatter[i]
else:
text +=", %f" % scatter[i]
text +="\n"
f.write(text)
f.close()
except:
print("Usage:")
print("options = ",longoptions)
sys.exit(0)
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