def validate(self, qstring, pos):
text = str(qstring)
if text == '-':
return (self.Valid, pos)
try:
# this test is needed even if pyflakes complains!
float(text)
return (self.Invalid, pos)
except:
pass
if text.endswith(' '):
return (self.Invalid, pos)
if Elements.isValidFormula(text):
return (self.Valid, pos)
elif Elements.isValidMaterial(text):
return (self.Valid, pos)
else:
return (self.Invalid, pos)
def _checkDensityThickness(self, text, row):
try:
currentDensity = float(str(self.text(row, 3)))
except:
currentDensity = 0.0
try:
currentThickness = float(str(self.text(row, 4)))
except:
currentThickness = 0.0
defaultDensity = -1.0
defaultThickness = -0.1
#check if default density is there
if Elements.isValidFormula(text):
#check if single element
if text in Elements.Element.keys():
defaultDensity = Elements.Element[text]['density']
else:
elts = [ w for w in re.split('[0-9]', text) if w != '']
nbs = [ int(w) for w in re.split('[a-zA-Z]', text) if w != '']
if len(elts) == 1 and len(nbs) == 1:
defaultDensity = Elements.Element[elts[0]]['density']
elif Elements.isValidMaterial(text):
key = Elements.getMaterialKey(text)
if key is not None:
if 'Density' in Elements.Material[key]:
defaultDensity = Elements.Material[key]['Density']
if 'Thickness' in Elements.Material[key]:
defaultThickness = Elements.Material[key]['Thickness']
if defaultDensity >= 0.0:
self.setText(row, 3, "%g" % defaultDensity)
elif currentDensity <= 0:
# should not be better to raise an exception if the
# entered density or thickness were negative?
self.setText(row, 3, "%g" % 1.0)
if defaultThickness >= 0.0:
self.setText(row, 4, "%g" % defaultThickness)
elif currentThickness <= 0.0:
# should not be better to raise an exception if the
# entered density or thickness were negative?
self.setText(row, 4, "%g" % 0.1)
def processFitResult(self,
config=None,
fitresult=None,
elementsfrommatrix=False,
fluorates=None,
addinfo=False):
# I should check if fit was successful ...
if fitresult is None:
fitresult = self.fitresult
else:
self.fitresult = fitresult
if config is None:
config = self.config
else:
self.config = config
if 'usemultilayersecondary' not in self.config:
self.config['usemultilayersecondary'] = 0
if 'usexrfmc' not in self.config:
self.config['usexrfmc'] = 0
secondary = self.config['usemultilayersecondary']
xrfmcSecondary = self.config['usexrfmc']
if secondary and xrfmcSecondary:
txt = "Only one of built-in secondary and Monte Carlo correction can be used"
raise ValueError(txt)
# get attenuators and matrix from fit
attenuators = []
beamfilters = []
funnyfilters = []
matrix = None
detectoratt = None
multilayer = None
for attenuator in fitresult['result']['config']['attenuators'].keys():
if not fitresult['result']['config']['attenuators'][attenuator][0]:
continue
if attenuator.upper() == "MATRIX":
matrix = fitresult['result']['config']['attenuators'][
attenuator][1:4]
alphain = fitresult['result']['config']['attenuators'][
attenuator][4]
alphaout = fitresult['result']['config']['attenuators'][
attenuator][5]
elif attenuator.upper()[:-1] == "BEAMFILTER":
beamfilters.append(fitresult['result']['config']['attenuators']\
[attenuator][1:])
elif attenuator.upper() == "DETECTOR":
detectoratt = fitresult['result']['config']['attenuators'][
attenuator][1:]
else:
if len(fitresult['result']['config']['attenuators'][attenuator]
[1:]) == 4:
fitresult['result']['config']['attenuators'][
attenuator].append(1.0)
if abs(fitresult['result']['config']['attenuators'][attenuator]
[4] - 1.0) > 1.0e-10:
#funny attenuator
funnyfilters.append(fitresult['result']['config']['attenuators']\
[attenuator][1:])
else:
attenuators.append(fitresult['result']['config']['attenuators']\
[attenuator][1:])
if matrix is None:
raise ValueError("Invalid or undefined sample matrix")
if matrix[0].upper() == "MULTILAYER":
layerlist = fitresult['result']['config']['multilayer'].keys()
layerlist.sort()
for layer in layerlist:
if fitresult['result']['config']['multilayer'][layer][0]:
if multilayer is None:
multilayer = []
multilayer.append(
fitresult['result']['config']['multilayer'][layer][1:])
if not Elements.isValidMaterial(multilayer[-1][0]):
raise ValueError("Material %s is not defined" %
multilayer[-1][0])
else:
layerlist = ["Layer0"]
multilayer = [matrix]
if not Elements.isValidMaterial(matrix[0]):
raise ValueError("Material %s is not defined" % matrix[0])
if xrfmcSecondary and (len(layerlist) > 1):
txt = "Multilayer Monte Carlo correction not implemented yet"
raise ValueError(txt)
energyList = fitresult['result']['config']['fit']['energy']
if energyList is None:
raise ValueError("Invalid energy")
if type(energyList) != type([]):
energyList = [energyList]
flagList = [1]
weightList = [1.0]
else:
flagList = fitresult['result']['config']['fit']['energyflag']
weightList = fitresult['result']['config']['fit']['energyweight']
finalEnergy = []
finalWeight = []
finalFlag = []
for idx in range(len(energyList)):
if flagList[idx]:
energy = energyList[idx]
if energy is None:
raise ValueError(\
"Energy %d isn't a valid energy" % idx)
if energy <= 0.001:
raise ValueError(\
"Energy %d with value %f isn't a valid energy" %\
(idx, energy))
if weightList[idx] is None:
raise ValueError(\
"Weight %d isn't a valid weight" % idx)
if weightList[idx] < 0.0:
raise ValueError(\
"Weight %d with value %f isn't a valid weight" %\
(idx, weightList[idx]))
finalEnergy.append(energy)
finalWeight.append(weightList[idx])
finalFlag.append(1)
totalWeight = sum(weightList)
if totalWeight == 0.0:
raise ValueError("Sum of energy weights is 0.0")
weightList = [x / totalWeight for x in finalWeight]
energyList = finalEnergy
flagList = finalFlag
# get elements list from fit, not from matrix
groupsList = fitresult['result']['groups'] * 1
if type(groupsList) != type([]):
groupsList = [groupsList]
todelete = []
for i in range(len(groupsList)):
ele = groupsList[i].split()[0]
if len(ele) > 2:
todelete.append(i)
if len(todelete):
todelete.reverse()
for i in todelete:
del groupsList[i]
elements = []
newelements = []
for group in groupsList:
splitted = group.split()
ele = splitted[0]
newelements.append(
[Elements.getz(splitted[0]), splitted[0], splitted[1]])
if len(elements):
if elements[-1] != ele:
elements.append(ele)
else:
elements.append(ele)
newelements.sort()
elements.sort()
if not config['useattenuators']:
attenuators = None
funnyfilters = None
#import time
#t0=time.time()
if elementsfrommatrix:
newelementsList = []
for ilayer in range(len(multilayer)):
pseudomatrix = multilayer[ilayer]
eleDict = Elements.getMaterialMassFractions([pseudomatrix[0]],
[1.0])
if eleDict == {}:
raise ValueError(\
"Invalid layer material %s" % pseudomatrix[0])
keys = eleDict.keys()
for ele in keys:
for group in newelements:
if ele == group[1]:
if not group in newelementsList:
newelementsList.append(group)
newelementsList.sort()
fluo0 = Elements.getMultilayerFluorescence(
multilayer,
energyList,
layerList=None,
weightList=weightList,
flagList=weightList,
fulloutput=1,
beamfilters=beamfilters * 1,
attenuators=attenuators * 1,
elementsList=newelementsList * 1,
alphain=alphain,
alphaout=alphaout,
cascade=True,
detector=detectoratt,
funnyfilters=funnyfilters * 1,
forcepresent=0,
secondary=secondary)
fluototal = fluo0[0]
fluolist = fluo0[1:]
else:
if matrix[0].upper() != "MULTILAYER":
multilayer = [matrix * 1]
if fluorates is None:
fluo0 = Elements.getMultilayerFluorescence(
multilayer,
energyList,
layerList=None,
weightList=weightList,
flagList=flagList,
fulloutput=1,
beamfilters=beamfilters * 1,
attenuators=attenuators * 1,
elementsList=newelements * 1,
alphain=alphain,
alphaout=alphaout,
cascade=True,
detector=detectoratt,
funnyfilters=funnyfilters * 1,
forcepresent=1,
secondary=secondary)
else:
fluo0 = fluorates
fluototal = fluo0[0]
fluolist = fluo0[1:]
#I'll need total fluo element by element at some point
#print "getMatrixFluorescence elapsed = ",time.time()-t0
if config['usematrix']:
present = []
referenceLayerDict = {}
materialComposition = []
for ilayer in range(len(multilayer)):
pseudomatrix = multilayer[ilayer] * 1
#get elemental composition from matrix
materialComposition.append(
Elements.getMaterialMassFractions([pseudomatrix[0]],
[1.0]))
keys = materialComposition[-1].keys()
materialElements = [[Elements.getz(x), x] for x in keys]
materialElements.sort()
for z, key in materialElements:
for ele in elements:
if key == ele:
present.append(key)
if not (ele in referenceLayerDict):
referenceLayerDict[ele] = []
referenceLayerDict[ele].append(ilayer)
if len(present) == 0:
text = "Matrix must contain at least one fitted element\n"
text += "in order to estimate flux and efficiency from it."
raise ValueError(text)
referenceElement = config['reference'].replace(' ', "")
if len(referenceElement) and (referenceElement.upper() != 'AUTO'):
if Elements.isValidFormula(referenceElement):
if len(referenceElement) == 2:
referenceElement = referenceElement.upper()[0] +\
referenceElement.lower()[1]
elif len(referenceElement) == 1:
referenceElement = referenceElement.upper()[0]
if not (referenceElement in elements):
text = "Element %s not among fitted elements" % referenceElement
raise ValueError(text)
elif not (referenceElement in present):
text = "Element %s not among matrix elements" % referenceElement
raise ValueError(text)
referenceLayers = referenceLayerDict[referenceElement]
else:
text = "Element %s not a valid element" % referenceElement
raise ValueError(text)
elif len(present) == 1:
referenceElement = present[0]
referenceLayers = referenceLayerDict[referenceElement]
else:
# how to choose? Best fitted, largest fit area or
# greater concentration? or better to give a weight to
# the different shells, energies , ...?
referenceElement = present[0]
fom = self._figureOfMerit(present[0], fluototal, fitresult)
for key in present:
#if materialComposition[key] > materialComposition[referenceElement]:
# referenceElement = key
newfom = self._figureOfMerit(key, fluototal, fitresult)
if newfom > fom:
fom = newfom
referenceElement = key
referenceLayers = referenceLayerDict[referenceElement]
referenceTransitions = None
for group in groupsList:
item = group.split()
element = item[0]
if element == referenceElement:
transitions = item[1] + " xrays"
if referenceTransitions is None:
referenceTransitions = transitions
referenceGroup = group
elif (referenceTransitions[0] == transitions[0]) and\
(referenceTransitions[0] == 'L'):
# this prevents selecting L1 and selects L3 although
# given the appropriate area, L2 can be a safer choice.
referenceGroup = group
referenceTransitions = transitions
elif referenceTransitions is not None:
break
theoretical = 0.0
for ilayer in referenceLayers:
if elementsfrommatrix:
theoretical += fluolist[ilayer][referenceElement]['rates'][referenceTransitions] * \
fluolist[ilayer][referenceElement]['mass fraction']
else:
theoretical += materialComposition[ilayer][referenceElement] * \
fluolist[ilayer][referenceElement]['rates'][referenceTransitions]
if theoretical <= 0.0:
raise ValueError(\
"Theoretical rate is almost 0.0 Impossible to determine flux")
else:
if (config['distance'] > 0.0) and (config['area'] > 0.0):
#solidangle = config['area']/(4.0 * numpy.pi * pow(config['distance'],2))
radius2 = config['area'] / numpy.pi
solidangle = 0.5 * (
1.0 -
(config['distance'] /
numpy.sqrt(pow(config['distance'], 2) + radius2)))
else:
solidangle = 1.0
flux = fitresult['result'][referenceGroup]['fitarea'] / (
theoretical * solidangle)
else:
referenceElement = None
referenceTransitions = None
#solidangle = config['area']/(4.0 * numpy.pi * pow(config['distance'],2))
radius2 = config['area'] / numpy.pi
solidangle = 0.5 * (
1.0 - (config['distance'] /
numpy.sqrt(pow(config['distance'], 2) + radius2)))
flux = config['flux'] * config['time']
#print "OBTAINED FLUX * SOLID ANGLE= ",flux * solidangle
#print "flux * time = ",flux
#print "actual solid angle = ",0.5 * (1.0 - (config['distance']/sqrt(pow(config['distance'],2)+ config['area']/pi)))
#print "solid angle factor= ",solidangle
#ele = 'Pb'
#rays = "L xrays"
#print "theoretical = ",fluototal[ele]['rates'][rays]
#print "expected = ",flux * solidangle * fluototal[ele]['rates'][rays]
#for ilayer in range(len(multilayer)):
# print "ilayer = ",ilayer, "theoretical = ",fluolist[ilayer][ele]['rates'][rays]
# print "ilayer = ",ilayer, "expected = ",flux * solidangle * fluolist[ilayer][ele]['rates'][rays]
ddict = {}
ddict['groups'] = groupsList
ddict['elements'] = elements
ddict['mass fraction'] = {}
if 'mmolarflag' in config:
if config['mmolarflag']:
ddict['mmolar'] = {}
else:
config['mmolarflag'] = 0
ddict['area'] = {}
ddict['fitarea'] = {}
ddict['sigmaarea'] = {}
fluo = fluototal
for group in groupsList:
item = group.split()
element = item[0]
transitions = item[1] + " xrays"
if element in fluo.keys():
if transitions in fluo[element]:
#this SHOULD be with concentration one
theoretical = fluo[element]['rates'][transitions] * 1.0
expected = theoretical * flux * solidangle
concentration = fitresult['result'][group][
'fitarea'] / expected
else:
theoretical = 0.0
concentration = 0.0
else:
theoretical = 0.0
concentration = 0.0
#ddict['area'][group] = theoretical * flux * solidangle * concentration
ddict['fitarea'][group] = fitresult['result'][group]['fitarea']
ddict['sigmaarea'][group] = fitresult['result'][group]['sigmaarea']
if elementsfrommatrix:
if element in fluo.keys():
ddict['mass fraction'][
group] = 1.0 * fluo[element]['mass fraction']
else:
ddict['mass fraction'][group] = 0.0
ddict['area'][group] = theoretical * flux * solidangle *\
ddict['mass fraction'][group]
else:
ddict['mass fraction'][group] = concentration
ddict['area'][group] = theoretical * flux * solidangle
if config['mmolarflag']:
#mM = (mass_fraction * density)/atomic_weight
ddict['mmolar'] [group]= 1000000. *\
(multilayer[0][1] * ddict['mass fraction'][group])/Elements.Element[element]['mass']
#I have the globals/average values now I calculate layer per layer
#if necessary
ddict['layerlist'] = []
if matrix[0].upper() == "MULTILAYER":
ilayer = 0
for layer in layerlist:
if fitresult['result']['config']['multilayer'][layer][0]:
ddict['layerlist'].append(layer)
ddict[layer] = {}
dict2 = ddict[layer]
dict2['groups'] = groupsList
dict2['elements'] = elements
dict2['mass fraction'] = {}
if config['mmolarflag']:
dict2['mmolar'] = {}
dict2['area'] = {}
dict2['fitarea'] = {}
fluo = fluolist[ilayer]
for group in groupsList:
item = group.split()
element = item[0]
transitions = item[1] + " xrays"
if element in fluo.keys():
if transitions in fluo[element]:
theoretical = fluo[element]['rates'][
transitions] * 1
expected = theoretical * flux * solidangle
if expected > 0.0:
concentration = fitresult['result'][group][
'fitarea'] / expected
else:
concentration = -1
else:
theoretical = 0.0
concentration = 0.0
else:
theoretical = 0.0
concentration = 0.0
dict2['fitarea'][
group] = 1 * fitresult['result'][group]['fitarea']
if elementsfrommatrix:
if element in fluo.keys():
dict2['mass fraction'][
group] = 1 * fluo[element]['mass fraction']
else:
dict2['mass fraction'][group] = 0.0
#I calculate matrix in optimized form,
#so I have to multiply by the mass fraction
dict2['area'][group] = theoretical * flux * solidangle *\
dict2['mass fraction'][group]
else:
dict2['mass fraction'][group] = concentration
dict2['area'][
group] = theoretical * flux * solidangle
if config['mmolarflag']:
#mM = (mass_fraction * density)/atomic_weight
dict2['mmolar'][group] = 1000000. *\
(multilayer[ilayer][1] * dict2['mass fraction'][group]) /\
Elements.Element[element]['mass']
#if group == "Pb L":
# print "layer", ilayer,'area ', dict2['area'][group]
# print "layer", ilayer,'mass fraction =', dict2['mass fraction'][group]
ilayer += 1
if elementsfrommatrix:
for group in groupsList:
ddict['area'][group] = 0.0
for layer in ddict['layerlist']:
if group in ddict[layer]['area'].keys():
ddict['area'][group] += ddict[layer]['area'][group]
if xrfmcSecondary and (not elementsfrommatrix):
xrfmcCorrections = None
if 'xrfmc' in fitresult:
xrfmcCorrections = fitresult['xrfmc'].get('corrections', None)
if xrfmcCorrections is None:
if 'xrfmc' in fitresult['result']:
xrfmcCorrections = fitresult['result']['xrfmc'].get(
'corrections', None)
if xrfmcCorrections is None:
# try to see if they were in the configuration
if 'xrfmc' in fitresult['result']['config']:
xrfmcCorrections = fitresult['result']['config'][
'xrfmc'].get('corrections', None)
if xrfmcCorrections is None:
# calculate the corrections
xrfmcCorrections = XRFMCHelper.getXRFMCCorrectionFactors(
fitresult['result']['config'])
if referenceElement is not None:
referenceLines = referenceTransitions.split()[0]
referenceCorrection = xrfmcCorrections[referenceElement][referenceLines]\
['correction_factor'][-1]
xrfmcCorrections[referenceElement][referenceLines]\
['correction_factor'][-1] = 1.0
for group in groupsList:
item = group.split()
element = item[0]
lines = item[1]
if element in xrfmcCorrections:
if element != referenceElement:
if lines != referenceLines:
xrfmcCorrections[element][lines][
'correction_factor'][
-1] *= referenceCorrection
# now we have to apply the corrections
for group in groupsList:
item = group.split()
element = item[0]
lines = item[1]
if element in xrfmcCorrections:
correction = xrfmcCorrections[element][
item[1]]['correction_factor'][-1]
ddict['mass fraction'][group] /= correction
if addinfo:
addInfo = {}
addInfo['ReferenceElement'] = referenceElement
addInfo['ReferenceTransitions'] = referenceTransitions
addInfo['SolidAngle'] = solidangle
if config['time'] > 0.0:
addInfo['Time'] = config['time']
else:
addInfo['Time'] = 1.0
addInfo['Flux'] = flux / addInfo['Time']
addInfo['I0'] = flux
addInfo['DetectorDistance'] = config['distance']
addInfo['DetectorArea'] = config['area']
return ddict, addInfo
else:
return ddict