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#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2015 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__doc__= "Generate specfile from EPL97 total cross sections in keV and barn"
import os
import sys
import EPDL97Parser as EPDLParser
Elements = EPDLParser.Elements
AVOGADRO_NUMBER = EPDLParser.AVOGADRO_NUMBER
import numpy
log = numpy.log
exp = numpy.exp
getTotalCoherentCrossSection = EPDLParser.getTotalCoherentCrossSection
getTotalIncoherentCrossSection = EPDLParser.getTotalIncoherentCrossSection
getTotalPhotoelectricCrossSection = EPDLParser.getTotalPhotoelectricCrossSection
getTotalPairCrossSection = EPDLParser.getTotalPairCrossSection
getTotalTripletCrossSection = EPDLParser.getTotalTripletCrossSection
def getHeader(filename):
text = '#F %s\n' % filename
text += '#U00 This file is a direct conversion to specfile format of \n'
text += '#U01 the original EPDL97 total cross sections contained in the\n'
text += '#U02 EPDL97.DAT from the library.\n'
text += '#U03 EPDL97 itself can be found at:\n'
text += '#U04 http://www-nds.iaea.org/epdl97/libsall.htm\n'
text += '\n'
return text
if __name__ == "__main__":
if len(sys.argv) < 3:
print("Usage:")
print("python EPDLGenerateTotalCrossSections SPEC_output_filename barns_flag")
sys.exit(0)
fname = sys.argv[1]
if os.path.exists(fname):
os.remove(fname)
if int(sys.argv[2]):
BARNS = True
else:
BARNS = False
print("BARNS = %s" % BARNS)
outfile = open(fname, 'wb')
outfile.write(getHeader(fname))
for i in range(1, 101):
print("i = %d element = %s" % (i, Elements[i-1]))
#coherent
energy_cohe, value_cohe, mode_cohe = getTotalCoherentCrossSection(i,
getmode=True)
#incoherent
energy_incohe, value_incohe, mode_incohe = getTotalIncoherentCrossSection(i,
getmode=True)
#photoelectric
energy_photo, value_photo, mode_photo = getTotalPhotoelectricCrossSection(i,
getmode=True)
#check to see the energies:
#for j in range(10):
# print energy_cohe[j], energy_incohe[j], energy_photo[j]
#to select an appropriate energy grid as close as possible to the original
#while keeping in mind the PyMca goals, I use the coherent energy grid till
#the non-zero first value of the photoelectric cross section. At that point,
#I use the photoelectric energy grid.
energy = numpy.concatenate((energy_cohe[energy_cohe<energy_photo[0]],
energy_photo))
#now perform a log-log interpolation when needed
#lin-lin interpolation:
#
# y0 (x1-x) + y1 (x-x0)
# y = -------------------------
# x1 - x0
#
#log-log interpolation:
#
# log(y0) * log(x1/x) + log(y1) * log(x/x0)
# log(y) = ------------------------------------------
# log (x1/x0)
#
cohe = numpy.zeros(len(energy), numpy.float64)
incohe = numpy.zeros(len(energy), numpy.float64)
photo = numpy.zeros(len(energy), numpy.float64)
total = numpy.zeros(len(energy), numpy.float64)
#coherent needs to interpolate
indices = numpy.nonzero(energy_cohe<energy_photo[0])
cohe[indices] = value_cohe[indices]
for n in range(len(indices),len(energy)):
x = energy[n]
j1 = len(indices)
while energy_cohe[j1] < x:
j1 += 1
j0 = j1 - 1
x0 = energy_cohe[j0]
x1 = energy_cohe[j1]
y0 = value_cohe[j0]
y1 = value_cohe[j1]
cohe[n] = exp((log(y0) * log(x1/x) + log(y1) * log(x/x0))/log(x1/x0))
#compton needs to interpolate everything
for n in range(len(energy)):
x = energy[n]
j1 = 0
while energy_incohe[j1] < x:
j1 += 1
j0 = j1 - 1
x0 = energy_incohe[j0]
x1 = energy_incohe[j1]
y0 = value_incohe[j0]
y1 = value_incohe[j1]
incohe[n] = exp((log(y0) * log(x1/x) + log(y1) * log(x/x0))/log(x1/x0))
#photoelectric does not need to interpolate anything
photo[energy>=energy_photo[0]] = value_photo[:]
#convert to keV and cut at 500 keV
energy *= 1000.
indices = numpy.nonzero(energy<=500.)
energy = energy[indices]
photo = photo[indices]
cohe = cohe[indices]
incohe = incohe[indices]
#I cut at 500 keV, I do not need to take the pair production
total = photo + cohe + incohe
#now I am ready to write a Specfile
ele = Elements[i-1]
text = '#S %d %s\n' % (i, ele)
text += '#N 5\n'
labels = '#L PhotonEnergy[keV]'
labels += ' Rayleigh(coherent)[barn/atom]'
labels += ' Compton(incoherent)[barn/atom]'
labels += ' CoherentPlusIncoherent[barn/atom]'
labels += ' Photoelectric[barn/atom]'
labels += ' TotalCrossSection[barn/atom]\n'
if not BARNS:
labels = labels.replace("barn/atom", "cm2/g")
factor = (1.0E-24*AVOGADRO_NUMBER)/EPDLParser.getAtomicWeights()[i-1]
else:
factor = 1.0
text += labels
if 0:
fformat = "%g %g %g %g %g %g\n"
else:
fformat = "%.6E %.6E %.6E %.6E %.6E %.6E\n"
outfile.write(text)
for n in range(len(energy)):
line = fformat % (energy[n],
cohe[n] * factor,
incohe[n] * factor,
(cohe[n]+incohe[n]) * factor,
photo[n] * factor,
total[n] * factor)
outfile.write(line)
outfile.write('\n')
outfile.close()
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