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#
# Copyright (C) 2013 V. Armando Sole - ESRF
#
# 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.
#
__license__ = "MIT"
__author__ = "V.A. Sole - ESRF Data Analysis"
import sys
import os
import xml.etree.ElementTree as ElementTree
DEBUG = 0
def getXMSOFileFluorescenceInformation(xmsoFile):
f = ElementTree.parse(xmsoFile)
ddict = {}
root = f.getroot()
transitions = ['K', 'Ka', 'Kb', 'L', 'L1', 'L2', 'L3', 'M']
for i in root.iter('fluorescence_line_counts'):
if DEBUG:
print(i.attrib)
for key in ['symbol', 'total_counts']:
print(key, '= ', i.get(key))
element = i.get('symbol')
ddict[element] = {}
#ddict[element]['z'] = i.get('atomic_number')
for key in transitions:
ddict[element][key] = { 'total':0.0,
'counts': [],
'correction_factor':[]}
for a in i.iter('fluorescence_line'):
if DEBUG:
print(a.attrib)
for key in ['type', 'total_counts']:
print(key, '= ', a.get(key))
line = a.get('type')
ddict[element][line] = {}
#ddict[element][line]['total'] = float(a.get('total_counts'))
ddict[element][line]['counts'] = []
ddict[element][line]['total']=0
transitionsAffected = []
for key in transitions:
if line.startswith(key):
transitionsAffected.append(key)
elif line.startswith('KL') and (key == 'Ka'):
transitionsAffected.append(key)
elif line.startswith('K') and (key == 'Kb'):
if not line.startswith('KL'):
transitionsAffected.append(key)
cumulator = 0
for b in a.iter('counts'):
if DEBUG:
print(b.attrib)
value = float(b.text)
ddict[element][line]['counts'].append(value)
cumulator += value
ddict[element][line]['total'] = cumulator
single = ddict[element][line]['counts'][0]
multiple = 0.0
ddict[element][line]['correction_factor'] = []
excitationCounter = 0
for value in ddict[element][line]['counts']:
multiple += value
ddict[element][line]['correction_factor'].append(\
multiple/single)
for key in transitionsAffected:
nValues = len(ddict[element][line]['counts'])
while(len(ddict[element][key]['counts']) < nValues):
ddict[element][key]['counts'].append(0.0)
ddict[element][key]['counts'][excitationCounter] += value
excitationCounter += 1
ddict[element][key]['correction_factor'] = []
for key in transitions:
multiple = 0.0
if len(ddict[element][key]['counts']) == 0:
nValues = len(ddict[element][line]['counts'])
ddict[element][key]['counts'] = [0.0] * nValues
ddict[element][key]['correction_factor'] = [1.0] * nValues
else:
single = ddict[element][key]['counts'][0]
for value in ddict[element][key]['counts']:
multiple += value
ddict[element][key]['correction_factor'].append(\
multiple/single)
ddict[element][key]['total'] = multiple
return ddict
def test(xmsoFile='t.xmso'):
ddict = getXMSOFileFluorescenceInformation(xmsoFile)
for element in ddict:
for line in ddict[element]:
if line == "z":
#atomic number
continue
if 1 or DEBUG or line in ['K', 'Ka', 'Kb', 'L', 'L1', 'L2', 'L3', 'M']:
correction1 = ddict[element][line]['correction_factor'][1]
correctionn = ddict[element][line]['correction_factor'][-1]
print("Element %s Line %s Correction 2 = %f Correction n = %f" %\
(element, line,correction1, correctionn))
if __name__ == "__main__":
if len(sys.argv) < 2:
if os.path.exists('t.xmso'):
test()
else:
print("Usage:")
print("python XMSOParser.py xmso_file")
sys.exit(0)
else:
test(sys.argv[1])
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