def materialSignal(self, txt):
txt = str(txt)
if Elements.isValidFormula(txt):
if DEBUG:
print("validFormula")
elementDict = Elements.getMaterialMassFractions([txt], [1.0])
elif Elements.isValidMaterial(txt):
if DEBUG:
print("ValidMaterial")
elementDict = Elements.getMaterialMassFractions([txt], [1.0])
else:
if DEBUG:
print("to be defined")
msg=qt.QMessageBox.information(self,
"Invalid Material %s" % txt,
"The material %s is not a valid Formula " \
"nor a valid Material.\n" \
"Please use the material editor to define materials" % txt)
self.materialWidget.setEditText(self._lastMaterial)
if self.materialEditor.isHidden():
self.materialEditor.show()
return
# We have to update the possible elements
elements = list(elementDict.keys())
self.updateElementsWidget(elements)
def _referenceLineSlot(self, ddict):
if ddict['event'] == "returnPressed":
current = str(self.referenceLine.text())
current = current.replace(' ', '')
if (current == '') or (current.upper() == 'AUTO'):
pass
elif len(current) == 2:
current = current.upper()[0] + current.lower()[1]
elif len(current) == 1:
current = current.upper()[0]
else:
self.referenceLine.setText('Auto')
msg = qt.QMessageBox(self.referenceLine)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Element %s" % current)
msg.exec_()
self.referenceLine.setFocus()
return
if (current == '') or (current.upper() == 'AUTO'):
self.referenceLine.setText('Auto')
self._mySignal()
elif not Elements.isValidFormula(current):
self.referenceLine.setText('Auto')
msg = qt.QMessageBox(self.referenceLine)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Element %s" % current)
msg.exec_()
self.referenceLine.setFocus()
else:
self.referenceLine.setText(current)
self._mySignal()
def _referenceLineSlot(self, ddict):
if ddict['event'] == "returnPressed":
current = str(self.referenceLine.text())
current = current.replace(' ', '')
if (current == '') or (current.upper() == 'AUTO'):
pass
elif len(current) == 2:
current = current.upper()[0] + current.lower()[1]
elif len(current) == 1:
current = current.upper()[0]
else:
self.referenceLine.setText('Auto')
msg = qt.QMessageBox(self.referenceLine)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Element %s" % current)
msg.exec_()
self.referenceLine.setFocus()
return
if (current == '') or (current.upper() == 'AUTO'):
self.referenceLine.setText('Auto')
self._mySignal()
elif not Elements.isValidFormula(current):
self.referenceLine.setText('Auto')
msg = qt.QMessageBox(self.referenceLine)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Element %s" % current)
msg.exec_()
self.referenceLine.setFocus()
else:
self.referenceLine.setText(current)
self._mySignal()
def setParameters(self, ddict=None):
if ddict is None:
ddict = {}
key = "material"
if key in ddict:
material = ddict['material']
if Elements.isValidMaterial(material):
self.materialWidget.setEditText(material)
self.materialSignal(material)
else:
raise ValueError("Invalid Material %s" % material)
key = "element"
if key in ddict:
ele = ddict[key]
for i in range(self.elementWidget.count()):
if str(self.elementWidget.itemText(i)).split("(")[0] == ele:
self.elementWidget.setCurrentIndex(i)
self.elementSignal(ele)
key = "edge"
if key in ddict:
shellList = ["K", "L1", "L2", "L3", "M1", "M2", "M3", "M4", "M5"]
idx = shellList.index(ddict[key])
else:
idx = 0
self.edgeWidget.setCurrentIndex(idx)
self.edgeSignal(idx)
key = "energy"
if key in ddict:
energy = ddict[key]
self.energyWidget.setText("%.2f" % energy)
def setParameters(self, ddict=None):
if ddict is None:
ddict = {}
key = "material"
if key in ddict:
material = ddict['material']
if Elements.isValidMaterial(material):
self.materialWidget.setEditText(material)
self.materialSignal(material)
else:
raise ValueError("Invalid Material %s" % material)
key = "element"
if key in ddict:
ele = ddict[key]
for i in range(self.elementWidget.count()):
if str(self.elementWidget.itemText(i)).split("(")[0] == ele:
self.elementWidget.setCurrentIndex(i)
self.elementSignal(ele)
key = "edge"
if key in ddict:
shellList = ["K", "L1", "L2", "L3", "M1", "M2", "M3", "M4", "M5"]
idx = shellList.index(ddict[key])
else:
idx = 0
self.edgeWidget.setCurrentIndex(idx)
self.edgeSignal(idx)
key = "energy"
if key in ddict:
energy = ddict[key]
self.energyWidget.setText("%.2f" % energy)
def FindXrays(elsym, energy=60.0, minenergy=1.0, maxenergy=35.0, minrate=0.00010):
xr=['K', 'L', 'M']
# chosenxr=[]
# chosenxren=[]
foundpeaks=[]
allpeaksdictlist=[]
eltr_quantels=[]
for ele in elsym:
ElDict={}
PyMEl._updateElementDict(ele, ElDict, energy=energy, minenergy=minenergy, minrate=minrate)
xray_en_rate=[[x, ElDict[tr]['energy'], ElDict[tr]['rate']] for x in xr for tr in ElDict['%s xrays' %x] if ElDict[tr]['energy']<maxenergy]
xraytypes=set([xer[0] for xer in xray_en_rate])
totyieldlist=[]
eltrlist=[]
for xt in xraytypes:
totyield=numpy.float32([v for k, v in PyMEl.Element[ele].iteritems() if k.startswith('omega'+xt.lower())]).sum()
totyieldlist+=[totyield]
en_rate=[[xer[1], xer[2]] for xer in xray_en_rate if xer[0]==xt]
en_rate=numpy.float32(en_rate)
enofmaxrate=en_rate[numpy.argmax(en_rate[:, 1]), 0]
eltrlist+=[' '.join((ele, xt))]
dt={}
dt['el']=ele
dt['tr']=xt
dt['eltr']=' '.join((ele, xt))
dt['repen']=enofmaxrate
dt['totyield']=totyield
allpeaksdictlist+=[dt]
# if len(xraytypes)>1:
# tempstr=' and '.join(list(xraytypes))
# print 'XRF ANALYSIS PROBLEM: ', tempstr, ' transitions can be fit but only one will be chosen for', ele
if len(xraytypes)==0:
print 'XRF ANALYSIS PROBLEM: no valid transitions could be found for ', ele
foundpeaks+=[False]
else:
foundpeaks+=[True]
eltr_quantels+=[eltrlist[numpy.argmax(numpy.float32(totyieldlist))]]
# xray_en_rate=sorted(xray_en_rate, key=operator.itemgetter(2), reverse=True)
# print xray_en_rate
# chosenxr+=[' '.join((ele, xray_en_rate[0][0]))]
# chosenxren+=[xray_en_rate[0][1]]
# return chosenxr, chosenxren, foundpeaks
return allpeaksdictlist, eltr_quantels, foundpeaks
def __init__(self, parent=None, name="Elements Info"):
qt.QWidget.__init__(self, parent)
self.setWindowTitle(name)
layout = qt.QVBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
self.energyValue = None
self.splitter = qt.QSplitter(self)
layout.addWidget(self.splitter)
self.splitter.setOrientation(qt.Qt.Horizontal)
self.table = QPeriodicTable(self.splitter)
self.html = ElementHtml.ElementHtml()
self.infoWidget = None
self.table.setMinimumSize(500, 400)
self.table.sigElementClicked.connect(self.elementClicked)
self.lastElement = None
Elements.registerUpdate(self._updateCallback)
def __init__(self, parent=None, name="Elements Info"):
qt.QWidget.__init__(self, parent)
self.setWindowTitle(name)
layout = qt.QVBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
self.energyValue = None
self.splitter = qt.QSplitter(self)
layout.addWidget(self.splitter)
self.splitter.setOrientation(qt.Qt.Horizontal)
self.table = QPeriodicTable(self.splitter)
self.html = ElementHtml.ElementHtml()
self.infoWidget = None
self.table.setMinimumSize(500,
400)
self.table.sigElementClicked.connect(self.elementClicked)
self.lastElement = None
Elements.registerUpdate(self._updateCallback)
def materialSignal(self, txt):
txt = str(txt)
if Elements.isValidFormula(txt):
_logger.debug("validFormula")
elementDict = Elements.getMaterialMassFractions([txt], [1.0])
elif Elements.isValidMaterial(txt):
_logger.debug("ValidMaterial")
elementDict = Elements.getMaterialMassFractions([txt], [1.0])
else:
_logger.debug("Material to be defined")
msg=qt.QMessageBox.information(self,
"Invalid Material %s" % txt,
"The material %s is not a valid Formula " \
"nor a valid Material.\n" \
"Please use the material editor to define materials" % txt)
self.materialWidget.setEditText(self._lastMaterial)
if self.materialEditor.isHidden():
self.materialEditor.show()
return
# We have to update the possible elements
elements = list(elementDict.keys())
self.updateElementsWidget(elements)
def _energySlot(self):
string = str(self.energy.text())
if len(string):
try:
value = float(string)
except:
msg=qt.QMessageBox(self.energy)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Float")
msg.exec_()
self.energy.setFocus()
return
if self.energyValue is not None:
if value != self.energyValue:
self.energyValue = value
Elements.updateDict(energy=value)
else:
self.energyValue = value
Elements.updateDict(energy=value)
self.energy.setPaletteBackgroundColor(qt.QColor('white'))
self.infoWidget.setFocus()
else:
self.energyValue = None
self.energy.setText("")
def _energySlot(self):
string = str(self.energy.text())
if len(string):
try:
value = float(string)
except:
msg = qt.QMessageBox(self.energy)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Float")
msg.exec_()
self.energy.setFocus()
return
if self.energyValue is not None:
if value != self.energyValue:
self.energyValue = value
Elements.updateDict(energy=value)
else:
self.energyValue = value
Elements.updateDict(energy=value)
self.energy.setPaletteBackgroundColor(qt.QColor('white'))
self.infoWidget.setFocus()
else:
self.energyValue = None
self.energy.setText("")
def _mySlot(self, ddict):
if ddict['event'] == "returnPressed":
current = str(self.currentText())
current = current.replace(' ', '')
if (current == '') or (current.upper() == 'AUTO'):
pass
elif len(current) == 2:
current = current.upper()[0] + current.lower()[1]
elif len(current) == 1:
current = current.upper()[0]
else:
msg = qt.QMessageBox(self._lineEdit)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Element %s" % current)
msg.exec_()
self._lineEdit.setFocus()
if not Elements.isValidFormula(current):
msg = qt.QMessageBox(self._lineEdit)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Element %s" % current)
msg.exec_()
self._lineEdit.setFocus()
else:
self.setCurrentText(current)
def _mySlot(self, ddict):
if ddict['event'] == "returnPressed":
current = str(self.currentText())
current = current.replace(' ', '')
if (current == '') or (current.upper() == 'AUTO'):
pass
elif len(current) == 2:
current = current.upper()[0] + current.lower()[1]
elif len(current) == 1:
current = current.upper()[0]
else:
msg = qt.QMessageBox(self._lineEdit)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Element %s" % current)
msg.exec_()
self._lineEdit.setFocus()
if not Elements.isValidFormula(current):
msg = qt.QMessageBox(self._lineEdit)
msg.setIcon(qt.QMessageBox.Critical)
msg.setText("Invalid Element %s" % current)
msg.exec_()
self._lineEdit.setFocus()
else:
self.setCurrentText(current)
def correctNormalizedSpectrum(self, energy0, spectrum):
"""
"""
element = self._configuration['XAS']['element']
material = self._configuration['XAS'].get('material', element)
edge = self._configuration['XAS']['edge']
alphaIn, alphaOut = self._configuration['XAS']['angles']
edgeEnergy = Elements.Element[element]['binding'][edge]
userEdgeEnergy = self._configuration['XAS'].get('energy', edgeEnergy)
energy = numpy.array(energy0, dtype=numpy.float64)
#PyMca data ar in keV but XAS data are usually in eV
if 0.5 * (energy[0] + energy[-1]) / edgeEnergy > 100:
# if the user did not do stupid things most likely
# the energy was given in eV
energy *= 0.001
if userEdgeEnergy / edgeEnergy > 100:
userEdgeEnergy *= 0.001
# forget about multilayers for the time being
# Elements.getMaterialMassFractions(materialList, massFractionsList)
massFractions = Elements.getMaterialMassFractions([material], [1.0])
# calculate the total mass attenuation coefficients at the given energies
# exciting the given element shell and not exciting it
EPDL = Elements.PyMcaEPDL97
totalCrossSection = 0.0
totalCrossSectionBackground = 0.0
for ele in massFractions.keys():
# make sure EPDL97 respects the Elements energies
if EPDL.EPDL97_DICT[ele]['original']:
EPDL.setElementBindingEnergies(
ele, Elements.Element[ele]['binding'])
if ele == element:
# make sure we respect the user energy
if abs(userEdgeEnergy - edgeEnergy) > 0.01:
newBinding = Elements.Element[ele]['binding']
newBinding[edge] = userEdgeEnergy
try:
EPDL.setElementBindingEnergies(ele, newBinding)
crossSections = EPDL.getElementCrossSections(
ele, energy)
EPDL.setElementBindingEnergies(
ele, Elements.Element[ele]['binding'])
except:
EPDL.setElementBindingEnergies(
ele, Elements.Element[ele]['binding'])
raise
else:
crossSections = EPDL.getElementCrossSections(ele, energy)
else:
crossSections = EPDL.getElementCrossSections(ele, energy)
total = numpy.array(crossSections['total'])
tmpFloat = massFractions[ele] * total
totalCrossSection += tmpFloat
if ele != element:
totalCrossSectionBackground += tmpFloat
else:
edgeCrossSections = numpy.array(crossSections[edge])
muSampleJump = massFractions[ele] * edgeCrossSections
totalCrossSectionBackground += massFractions[ele] *\
(total - edgeCrossSections)
# calculate the mass attenuation coefficient of the sample at the fluorescent energy
# assume we are detecting the main fluorescence line of the element shell
if edge == 'K':
rays = Elements.Element[element]["Ka xrays"]
elif edge[0] == 'L':
rays = Elements.Element[element][edge + " xrays"]
elif edge[0] == 'M':
rays = []
for transition in Elements.Element[element]['M xrays']:
if transition.startswith(edge):
rays.append(transition)
lineList = []
for label in rays:
ene = Elements.Element[element][label]['energy']
rate = Elements.Element[element][label]['rate']
lineList.append([ene, rate, label])
# whithin 50 eV lines considered the same
lineList = Elements._filterPeaks(lineList, ethreshold=0.050)
# now take the returned line with the highest intensity
fluoLine = lineList[0]
for line in lineList:
if line[1] > fluoLine[1]:
fluoLine = line
# and calculate the sample total mass attenuation
muTotalFluorescence = 0.0
for ele in massFractions.keys():
crossSections = EPDL.getElementCrossSections(ele, fluoLine[0])
muTotalFluorescence += massFractions[ele] * crossSections['total'][
0]
#define some convenience variables
sinIn = numpy.sin(numpy.deg2rad(alphaIn))
sinOut = numpy.sin(numpy.deg2rad(alphaOut))
g = sinIn / sinOut
if 1:
# thick sample
idx = numpy.where(muSampleJump > 0.0)[0][0]
muSampleJump[0:idx] = muSampleJump[idx]
ALPHA = g * (muTotalFluorescence / muSampleJump
) + totalCrossSectionBackground / muSampleJump
return (spectrum * ALPHA) / (1 + ALPHA - spectrum)
elif 1:
# all samples (to be tested)
d = thickness * density
idx = numpy.where(muSampleJump > 0.0)[0][0]
muSampleJump[0:idx] = muSampleJump[idx]
ALPHA = g * (muTotalFluorescence / muSampleJump
) + totalCrossSectionBackground / muSampleJump
thickTarget0 = (spectrum * ALPHA) / (1 + ALPHA - spectrum)
# Iterate to find the solution
x = spectrum
t = (ALPHA + 1) * d * muSampleJump / sinIn
if t.max() < 0.001:
A = 1 - t
else:
A = numpy.exp(-t)
t = (ALPHA * d * muSampleJump / sinIn)
if t.max() < 0.001:
B = 1.0 - t
else:
B = numpy.exp(-t)
delta = 10.0
i = 0
while (delta > 1.0e-5) and (i < 30):
old = x
x = thickTarget0 * (1.0 - A) / \
(1.0 - B * numpy.exp(- x * d * muSampleJump/sinIn))
delta = numpy.abs(x - old).max()
i += 1
return x
else:
thickness = 1.0
density = 1.0e-6
# FORMULA Booth and Bridges
ALPHA = g * muTotalFluorescence + totalCrossSection
tmpFloat0 = density * thickness * ALPHA / sinIn
tmpFloat1 = numpy.exp(-tmpFloat0)
BETA = (muSampleJump * tmpFloat0) * tmpFloat1
GAMMA = 1.0 - tmpFloat1
b = GAMMA * (ALPHA - muSampleJump * spectrum + BETA)
discriminant = b * b + 4 * ALPHA * BETA * GAMMA * (spectrum - 1.0)
return 1 + (-b + numpy.sqrt(discriminant)) / (2 * BETA)
def gethtml(self, element=None):
if element is None: element = self.element
if element is None: return ""
ele = element
#text="<center><b><font color=red size=5>Summary</font></b></center>"
text = ""
if ele not in Elements.Element.keys():
text += "<br><b><font color=blue size=4>Unknown Element</font></b>"
return text
symbol = Elements.getsymbol(Elements.getz(ele))
omegak = Elements.Element[ele]['omegak']
omegal = [
Elements.Element[ele]['omegal1'], Elements.Element[ele]['omegal2'],
Elements.Element[ele]['omegal3']
]
omegam = [
Elements.Element[ele]['omegam1'], Elements.Element[ele]['omegam2'],
Elements.Element[ele]['omegam3'], Elements.Element[ele]['omegam4'],
Elements.Element[ele]['omegam5']
]
#text+="<center>
text += "<br><b><font color=blue size=4>Element Info</font></b>"
#text+="</center>"
if 0:
text += "<br><b><font size=3>Name = %s</font></b>" % Elements.Element[
ele]['name']
text += "<br><b><font size=3>Symbol = %s</font></b>" % symbol
text += "<br><b><font size=3>At. Number = %d</font></b>" % Elements.Element[
ele]['Z']
text += "<br><b><font size=3>At. Weight = %.5f</font></b>" % Elements.Element[
ele]['mass']
text += "<br><b><font size=3>Density = %.5f</font></b>" % Elements.Element[
ele]['density']
else:
hcolor = 'white'
finalcolor = 'white'
text += "<nobr><table>"
#symbol
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>Symbol</font></b>"
text += "</td>"
text += '<td align="center" bgcolor="%s">' % finalcolor
text += "<b><font size=3>=</font></b>"
text += "</td>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%s </font></b>" % symbol
text += "</td>"
#Z
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>At. Number</font></b>"
text += "</td>"
text += '<td align="center" bgcolor="%s">' % finalcolor
text += "<b><font size=3>=</font></b>"
text += "</td>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%d </font></b>" % Elements.Element[ele][
'Z']
text += "</td>"
#name
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>Name</font></b>"
text += "</td>"
text += '<td align="center" bgcolor="%s">' % finalcolor
text += "<b><font size=3>=</font></b>"
text += "</td>"
text += '<td align="left" bgcolor="%s">' % finalcolor
name = Elements.Element[ele]['name'][0].upper(
) + Elements.Element[ele]['name'][1:]
text += "<b><font size=3>%s </font></b>" % name
text += "</td>"
#mass
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>At. Weight</font></b>"
text += "</td>"
text += '<td align="center" bgcolor="%s">' % finalcolor
text += "<b><font size=3>=</font></b>"
text += "</td>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.5f </font></b>" % Elements.Element[ele][
'mass']
text += "</td>"
#density
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>Density</font></b>"
text += "</td>"
text += '<td align="center" bgcolor="%s">' % finalcolor
text += "<b><font size=3>=</font></b>"
text += "</td>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.5f g/cm3</font></b>" % Elements.Element[
ele]['density']
text += "</td>"
text += "</tr>"
text += "</table>"
# Shell (round) propierties
hcolor = 'white'
finalcolor = 'white'
if Elements.Element[ele]['Z'] > 2:
text += "<br><b><font color=blue size=4>Fluorescence Yields (Rounded)</font></b>"
text += "<nobr><table><tr>"
text += '<td align="left" bgcolor="%s"><b>' % hcolor
text += 'Shell'
text += "</b></td>"
text += '<td align="right" bgcolor="%s"><b>' % hcolor
text += 'Yield'
text += "</b></td>"
text += "</tr>"
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%s </font></b>" % "K"
text += "</td>"
text += '<td align="right" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.3f </font></b>" % round(omegak, 3)
text += "</td>"
for i in range(len(omegal)):
if omegal[i] > 0.0:
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>L%d </font></b>" % (i + 1)
text += "</td>"
text += '<td align="right" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.3f </font></b>" % round(
omegal[i], 3)
text += "</td>"
for i in range(len(omegam)):
if omegam[i] > 0.0:
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>M%d </font></b>" % (i + 1)
text += "</td>"
text += '<td align="right" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.3f </font></b>" % round(
omegam[i], 3)
text += "</td>"
text += "</tr>"
text += "</table>"
# Shell propierties
hcolor = 'white'
finalcolor = 'white'
if Elements.Element[ele]['Z'] > 2:
text += "<br><b><font color=blue size=4>Fluorescence Yields</font></b>"
text += "<nobr><table><tr>"
text += '<td align="left" bgcolor="%s"><b>' % hcolor
text += 'Shell'
text += "</b></td>"
text += '<td align="right" bgcolor="%s"><b>' % hcolor
text += 'Yield'
text += "</b></td>"
text += "</tr>"
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%s </font></b>" % "K"
text += "</td>"
text += '<td align="right" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.3e </font></b>" % omegak
text += "</td>"
for i in range(len(omegal)):
if omegal[i] > 0.0:
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>L%d </font></b>" % (i + 1)
text += "</td>"
text += '<td align="right" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.3e </font></b>" % omegal[i]
text += "</td>"
for i in range(len(omegam)):
if omegam[i] > 0.0:
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>M%d </font></b>" % (i + 1)
text += "</td>"
text += '<td align="right" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.3e </font></b>" % omegam[i]
text += "</td>"
text += "</tr>"
text += "</table>"
hcolor = 'white'
finalcolor = 'white'
f = ['f12', 'f13', 'f23']
ck = []
doit = 0
for item in f:
value = Elements.Element[ele]['CosterKronig']['L'][item]
if value > 0: doit = 1
ck.append(value)
if doit:
text += "<br><b><font color=blue size=4>L-Shell Coster-Kronig</font></b>"
text += "<nobr><table><tr>"
for item in f:
text += '<td align="left" bgcolor="%s"><b>' % hcolor
text += item
text += "</b></td>"
text += "</tr>"
text += "<tr>"
for i in range(len(f)):
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.3f </font></b>" % ck[i]
text += "</td>"
text += "</tr>"
text += "</table>"
#M shell
fs = [['f12', 'f13', 'f14', 'f15'], ['f23', 'f24', 'f25'],
['f34', 'f35'], ['f45']]
doit = 0
for f in fs:
for item in f:
value = Elements.Element[ele]['CosterKronig']['M'][item]
if value > 0: doit = 1
if doit:
text += "<br><b><font color=blue size=4>M-Shell Coster-Kronig</font></b>"
text += "<nobr><table>"
for f in fs:
text += "<tr>"
for item in f:
text += '<td align="left" bgcolor="%s"><b>' % hcolor
text += item
text += "</b></td>"
text += "</tr>"
text += "<tr>"
for item in f:
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.3f </font></b>" % Elements.Element[
ele]['CosterKronig']['M'][item]
text += "</td>"
text += "</tr>"
text += "</table>"
hcolor = 'white'
finalcolor = 'white'
for rays in Elements.Element[ele]['rays']:
if rays == "Ka xrays": continue
if rays == "Kb xrays": continue
#text+="<center>"
text += "<br><b><font color=blue size=4>%s Emission Energies</font></b>" % rays[
0:-1]
#text+="</center>"
if 0:
for transition in Elements.Element[ele][rays]:
text += "<br><b><font size=3>%s energy = %.5f rate = %.5f</font></b>" % (
transition,
Elements.Element[ele][transition]['energy'],
Elements.Element[ele][transition]['rate'])
else:
text += "<nobr><table><tr>"
text += '<td align="left" bgcolor="%s"><b>' % hcolor
text += 'Line'
text += "</b></td>"
text += '<td align="right" bgcolor="%s"><b>' % hcolor
text += 'Energy (keV)'
text += "</b></td>"
text += '<td align="right" bgcolor="%s"><b>' % hcolor
text += 'Rate'
text += "</b></td>"
text += "</tr>"
for transition in Elements.Element[ele][rays]:
transitiontext = transition.replace('*', '')
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%s </font></b>" % transitiontext
text += "</td>"
text += '<td align="right" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.5f</font></b>" % Elements.Element[
ele][transition]['energy']
text += "</td>"
text += '<td align="right" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.5f </font></b>" % Elements.Element[
ele][transition]['rate']
text += "</td>"
text += "</tr>"
text += "</table>"
hcolor = 'white'
finalcolor = 'white'
#text+="<center>"
text += "<br><b><font color=blue size=4>%s Binding Energies</font></b>" % "Electron"
#text+="</center>"
text += "<nobr><table><tr>"
text += '<td align="left" bgcolor="%s"><b>' % hcolor
text += 'Shell'
text += "</b></td>"
text += '<td align="right" bgcolor="%s"><b>' % hcolor
text += 'Energy (keV)'
text += "</b></td>"
text += "</tr>"
for shell in Elements.ElementShells:
if Elements.Element[ele]['binding'][shell] > 0.0:
text += "<tr>"
text += '<td align="left" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%s </font></b>" % shell
text += "</td>"
text += '<td align="right" bgcolor="%s">' % finalcolor
text += "<b><font size=3>%.5f </font></b>" % Elements.Element[
ele]['binding'][shell]
text += "</td>"
text += "</tr>"
text += "</table>"
return text
def plot(data,
labels=None,
cfg=None,
xrange=None,
yrange=None,
normtochan=None,
savename='plot.png'):
data = np.array(data) #expected dimensions: [N, channels]
if len(data.shape) == 1:
data = np.reshape((1, data.shape[0]))
elif len(data.shape) >= 3:
print("Error: expected data dimensions: [N, channels]; ", data.shape)
return
if cfg is not None: # we're looking for the energy calibration values...
from PyMca5.PyMca import ConfigDict
config = ConfigDict.ConfigDict()
config.read(cfg)
cfg = [
config['detector']['zero'], config['detector']['gain'],
config['fit']['energy'][0]
] #zero, gain, E_Rayleigh
names = []
peaks = list(config['peaks'].keys())
for peak in peaks:
for linetype in config['peaks'][peak]:
names.append(peak + ' ' + str(linetype))
plt.figure(figsize=(20, 15))
for j in range(0, data.shape[0]):
spe = data[j, :]
if labels is None:
lbl = 'spectrum ' + str(j)
else:
lbl = labels[j]
if normtochan is not None:
spe = spe[:] / spe[normtochan]
if cfg is None:
zero = 0.
gain = 1.
xtitle = "Channel Number"
else:
zero = cfg[0]
gain = cfg[1]
xtitle = "Energy [keV]"
# plot the spectrum, Ylog, X-axis converted to Energy (keV) if PyMca cfg provided
if xrange is None:
xrange = (zero, (spe.shape[0] - 1) * gain + zero)
plt.plot(np.linspace(0, spe.shape[0] - 1, num=spe.shape[0]) * gain +
zero,
spe,
label=lbl,
linestyle='-')
ax = plt.gca()
handles, labels = ax.get_legend_handles_labels()
plt.yscale('log')
plt.xlim(xrange)
if yrange is not None:
plt.ylim(yrange)
plt.legend(handles, labels, loc='best')
ax.set_xlabel(xtitle, fontsize=16)
ax.set_ylabel("Intensity [counts]", fontsize=16)
ax.tick_params(axis='both', which='major', labelsize=14)
ax.tick_params(axis='x', which='minor', bottom=True)
# add peak annotation if names and cfg provided
if cfg is not None:
# x axis of plot is in Energy (keV)
# determine peak energy values (Rayl energy = cfg[2])
from PyMca5.PyMcaPhysics.xrf import Elements
for n in names:
if n != 'Rayl' and n != 'Compt':
if n.split(" ")[1][0] == 'K':
energy = Elements.getxrayenergy(
n.split(" ")[0],
n.split(" ")[1] + 'L3') #Ka1
elif n.split(" ")[1][0] == 'L':
energy = Elements.getxrayenergy(
n.split(" ")[0],
n.split(" ")[1] + '3M5') #La1
elif n.split(" ")[1][0] == 'M':
energy = Elements.getxrayenergy(
n.split(" ")[0],
n.split(" ")[1] + '5N7') #Ma1
elif n == 'Rayl':
energy = cfg[2]
else:
energy = None
# if energy not None, plot label at this energy value
if energy is not None:
idx = max(np.where(handles[0].get_xdata() <= energy)[-1])
yval = 10**(
np.log10(max([hand.get_ydata()[idx]
for hand in handles])) * 1.025)
# plot the text label X% above this value
plt.text(energy,
yval,
n,
horizontalalignment='center',
fontsize=14)
plt.show()
plt.savefig(savename) #, bbox_inches='tight', pad_inches=0)
plt.close()
def h5_plot(h5file,
channel='channel00',
label=None,
xrange=None,
normtochan=None,
yrange=None):
# read the h5 file, formatted according to the XMI format
# If fit was performed, also read in the PyMCA config file to figure out detector calibration
h5file = np.array(h5file)
plt.figure(figsize=(20, 15))
for j in range(0, h5file.size):
if h5file.size == 1:
savename = str(h5file).split('.')[0] + '.png'
h5 = str(h5file)
else:
savename = str(h5file[0]).split('.')[0] + '-' + str(
h5file[-1]).split('.')[0].split('/')[-1] + '.png'
h5 = str(h5file[j])
fileid = str(h5.split('.')[0].split('/')[-1])
if channel == 'all':
chnl = ['channel00', 'channel02']
for i in range(0, 2):
spe, names, cfg = gplot_rh5(h5, chnl[i])
if normtochan is not None:
spe = spe[:] / spe[normtochan]
if cfg is None:
zero = 0.
gain = 1.
xtitle = "Channel Number"
else:
zero = cfg[0]
gain = cfg[1]
xtitle = "Energy [keV]"
# plot the spectrum, Ylog, X-axis converted to Energy (keV) if PyMca cfg provided
plt.plot(
np.linspace(0, spe.shape[0] - 1, num=spe.shape[0]) * gain +
zero,
spe,
label=fileid + '_' + str(chnl[i]),
linestyle='-')
else:
spe, names, cfg = gplot_rh5(h5, channel)
if normtochan is not None:
spe = spe[:] / spe[normtochan]
if cfg is None:
zero = 0.
gain = 1.
xtitle = "Channel Number"
else:
zero = cfg[0]
gain = cfg[1]
xtitle = "Energy [keV]"
# plot the spectrum, Ylog, X-axis converted to Energy (keV) if PyMca cfg provided
if xrange is None:
xrange = (zero, (spe.shape[0] - 1) * gain + zero)
plt.plot(
np.linspace(0, spe.shape[0] - 1, num=spe.shape[0]) * gain +
zero,
spe,
label=fileid + '_' + str(channel),
linestyle='-')
ax = plt.gca()
handles, labels = ax.get_legend_handles_labels()
plt.yscale('log')
plt.xlim(xrange)
if yrange is not None:
plt.ylim(yrange)
plt.legend(handles, labels, loc='best')
ax.set_xlabel(xtitle, fontsize=16)
ax.set_ylabel("Intensity [counts]", fontsize=16)
ax.tick_params(axis='both', which='major', labelsize=14)
ax.tick_params(axis='x', which='minor', bottom=True)
# add peak annotation if names and cfg provided
if cfg is not None and names is not None:
# x axis of plot is in Energy (keV)
# determine peak energy values (Rayl energy = cfg[2])
from PyMca5.PyMcaPhysics.xrf import Elements
for n in names:
if n != 'Rayl' and n != 'Compt':
if n.split(" ")[1][0] == 'K':
energy = Elements.getxrayenergy(
n.split(" ")[0],
n.split(" ")[1] + 'L3') #Ka1
elif n.split(" ")[1][0] == 'L':
energy = Elements.getxrayenergy(
n.split(" ")[0],
n.split(" ")[1] + '3M5') #La1
elif n.split(" ")[1][0] == 'M':
energy = Elements.getxrayenergy(
n.split(" ")[0],
n.split(" ")[1] + '5N7') #Ma1
elif n == 'Rayl':
energy = cfg[2]
else:
energy = None
# if energy not None, plot label at this energy value
if energy is not None:
idx = max(np.where(handles[0].get_xdata() <= energy)[-1])
yval = 10**(
np.log10(max([hand.get_ydata()[idx]
for hand in handles])) * 1.025)
# plot the text label X% above this value
plt.text(energy,
yval,
n,
horizontalalignment='center',
fontsize=14)
#TODO: Increase fontsizes, add minor tickmarks on x-axis
plt.show()
plt.savefig(savename) #, bbox_inches='tight', pad_inches=0)
plt.close()
def FindXrays(elsym,
energy=60.0,
minenergy=1.0,
maxenergy=35.0,
minrate=0.00010):
xr = ['K', 'L', 'M']
# chosenxr=[]
# chosenxren=[]
foundpeaks = []
allpeaksdictlist = []
eltr_quantels = []
for ele in elsym:
ElDict = {}
PyMEl._updateElementDict(ele,
ElDict,
energy=energy,
minenergy=minenergy,
minrate=minrate)
xray_en_rate = [[x, ElDict[tr]['energy'], ElDict[tr]['rate']]
for x in xr for tr in ElDict['%s xrays' % x]
if ElDict[tr]['energy'] < maxenergy]
xraytypes = set([xer[0] for xer in xray_en_rate])
totyieldlist = []
eltrlist = []
for xt in xraytypes:
totyield = numpy.float32([
v for k, v in PyMEl.Element[ele].iteritems()
if k.startswith('omega' + xt.lower())
]).sum()
totyieldlist += [totyield]
en_rate = [[xer[1], xer[2]] for xer in xray_en_rate
if xer[0] == xt]
en_rate = numpy.float32(en_rate)
enofmaxrate = en_rate[numpy.argmax(en_rate[:, 1]), 0]
eltrlist += [' '.join((ele, xt))]
dt = {}
dt['el'] = ele
dt['tr'] = xt
dt['eltr'] = ' '.join((ele, xt))
dt['repen'] = enofmaxrate
dt['totyield'] = totyield
allpeaksdictlist += [dt]
# if len(xraytypes)>1:
# tempstr=' and '.join(list(xraytypes))
# print 'XRF ANALYSIS PROBLEM: ', tempstr, ' transitions can be fit but only one will be chosen for', ele
if len(xraytypes) == 0:
print 'XRF ANALYSIS PROBLEM: no valid transitions could be found for ', ele
foundpeaks += [False]
else:
foundpeaks += [True]
eltr_quantels += [
eltrlist[numpy.argmax(numpy.float32(totyieldlist))]
]
# xray_en_rate=sorted(xray_en_rate, key=operator.itemgetter(2), reverse=True)
# print xray_en_rate
# chosenxr+=[' '.join((ele, xray_en_rate[0][0]))]
# chosenxren+=[xray_en_rate[0][1]]
# return chosenxr, chosenxren, foundpeaks
return allpeaksdictlist, eltr_quantels, foundpeaks
def correctNormalizedSpectrum(self, energy0, spectrum):
"""
"""
element = self._configuration['XAS']['element']
material = self._configuration['XAS'].get('material', element)
edge = self._configuration['XAS']['edge']
alphaIn, alphaOut = self._configuration['XAS']['angles']
edgeEnergy = Elements.Element[element]['binding'][edge]
userEdgeEnergy = self._configuration['XAS'].get('energy', edgeEnergy)
energy = numpy.array(energy0, dtype=numpy.float)
#PyMca data ar in keV but XAS data are usually in eV
if 0.5 * (energy[0] + energy[-1])/edgeEnergy > 100:
# if the user did not do stupid things most likely
# the energy was given in eV
energy *= 0.001
if userEdgeEnergy/edgeEnergy > 100:
userEdgeEnergy *= 0.001
# forget about multilayers for the time being
# Elements.getMaterialMassFractions(materialList, massFractionsList)
massFractions = Elements.getMaterialMassFractions([material], [1.0])
# calculate the total mass attenuation coefficients at the given energies
# exciting the given element shell and not exciting it
EPDL = Elements.PyMcaEPDL97
totalCrossSection = 0.0
totalCrossSectionBackground = 0.0
for ele in massFractions.keys():
# make sure EPDL97 respects the Elements energies
if EPDL.EPDL97_DICT[ele]['original']:
EPDL.setElementBindingEnergies(ele,
Elements.Element[ele]['binding'])
if ele == element:
# make sure we respect the user energy
if abs(userEdgeEnergy-edgeEnergy) > 0.01:
newBinding = Elements.Element[ele]['binding']
newBinding[edge] = userEdgeEnergy
try:
EPDL.setElementBindingEnergies(ele, newBinding)
crossSections = EPDL.getElementCrossSections(ele, energy)
EPDL.setElementBindingEnergies(ele,
Elements.Element[ele]['binding'])
except:
EPDL.setElementBindingEnergies(ele,
Elements.Element[ele]['binding'])
raise
else:
crossSections = EPDL.getElementCrossSections(ele, energy)
else:
crossSections = EPDL.getElementCrossSections(ele, energy)
total = numpy.array(crossSections['total'])
tmpFloat = massFractions[ele] * total
totalCrossSection += tmpFloat
if ele != element:
totalCrossSectionBackground += tmpFloat
else:
edgeCrossSections = numpy.array(crossSections[edge])
muSampleJump = massFractions[ele] * edgeCrossSections
totalCrossSectionBackground += massFractions[ele] *\
(total - edgeCrossSections)
# calculate the mass attenuation coefficient of the sample at the fluorescent energy
# assume we are detecting the main fluorescence line of the element shell
if edge == 'K':
rays = Elements.Element[element]["Ka xrays"]
elif edge[0] == 'L':
rays = Elements.Element[element][edge + " xrays"]
elif edge[0] == 'M':
rays = []
for transition in Elements.Element[element]['M xrays']:
if transition.startswith(edge):
rays.append(transition)
lineList = []
for label in rays:
ene = Elements.Element[element][label]['energy']
rate = Elements.Element[element][label]['rate']
lineList.append([ene, rate, label])
# whithin 50 eV lines considered the same
lineList = Elements._filterPeaks(lineList, ethreshold=0.050)
# now take the returned line with the highest intensity
fluoLine = lineList[0]
for line in lineList:
if line[1] > fluoLine[1]:
fluoLine = line
# and calculate the sample total mass attenuation
muTotalFluorescence = 0.0
for ele in massFractions.keys():
crossSections = EPDL.getElementCrossSections(ele, fluoLine[0])
muTotalFluorescence += massFractions[ele] * crossSections['total'][0]
#define some convenience variables
sinIn = numpy.sin(numpy.deg2rad(alphaIn))
sinOut= numpy.sin(numpy.deg2rad(alphaOut))
g = sinIn / sinOut
if 1:
# thick sample
idx = numpy.where(muSampleJump > 0.0)[0][0]
muSampleJump[0:idx] = muSampleJump[idx]
ALPHA = g * (muTotalFluorescence/muSampleJump) + totalCrossSectionBackground/muSampleJump
return (spectrum * ALPHA)/(1 + ALPHA - spectrum)
elif 1:
# all samples (to be tested)
d = thickness * density
idx = numpy.where(muSampleJump > 0.0)[0][0]
muSampleJump[0:idx] = muSampleJump[idx]
ALPHA = g * (muTotalFluorescence/muSampleJump) + totalCrossSectionBackground/muSampleJump
thickTarget0 = (spectrum * ALPHA)/(1 + ALPHA - spectrum)
# Iterate to find the solution
x = spectrum
t = (ALPHA + 1) * d * muSampleJump/sinIn
if t.max() < 0.001:
A = 1 - t
else:
A = numpy.exp(-t)
t = (ALPHA * d * muSampleJump/sinIn)
if t.max() < 0.001:
B = 1.0 - t
else:
B = numpy.exp(-t)
delta = 10.0
i = 0
while (delta > 1.0e-5) and (i < 30):
old = x
x = thickTarget0 * (1.0 - A) / \
(1.0 - B * numpy.exp(- x * d * muSampleJump/sinIn))
delta = numpy.abs(x - old).max()
i += 1
return x
else:
thickness = 1.0
density = 1.0e-6
# FORMULA Booth and Bridges
ALPHA = g * muTotalFluorescence + totalCrossSection
tmpFloat0 = density * thickness * ALPHA / sinIn
tmpFloat1 = numpy.exp(-tmpFloat0)
BETA = (muSampleJump * tmpFloat0) * tmpFloat1
GAMMA = 1.0 - tmpFloat1
b = GAMMA * ( ALPHA - muSampleJump * spectrum + BETA)
discriminant = b*b + 4 * ALPHA * BETA * GAMMA * (spectrum - 1.0)
return 1 + (-b + numpy.sqrt(discriminant))/(2 * BETA)
