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 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 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)
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)
