def updateGraph(self, ddict):
self.__lastDict = ddict
edgeEnergy = ddict['edge_energy']
preRegions = ddict['pre_edge']['regions']
postRegions = ddict['post_edge']['regions']
event = ddict.get('event', None)
if event == "AutoEdgeEnergyClicked":
try:
# recalculate edge energy following region limits
xmin = edgeEnergy + preRegions[0][0]
xmax = edgeEnergy + postRegions[0][1]
idx = numpy.nonzero((self.energy >= xmin) &\
(self.energy <= xmax))[0]
x = numpy.take(self.energy, idx)
y = numpy.take(self.spectrum, idx)
edgeEnergy = XASNormalization.estimateXANESEdge(y,
energy=x,
full=False)
self.parametersWidget.setEdgeEnergy(edgeEnergy,
emin=self.energy.min(),
emax=self.energy.max())
self.__lastDict['edge_energy'] = edgeEnergy
except:
pass
parameters = {}
parameters['pre_edge_order'] = ddict['pre_edge']['polynomial']
parameters['post_edge_order'] = ddict['post_edge']['polynomial']
algorithm = 'polynomial'
self.updateMarkers(edgeEnergy,
preRegions,
postRegions,
edge_auto=ddict['auto_edge'])
try:
normalizationResult = XASNormalization.XASNormalization(
self.spectrum,
self.energy,
edge=edgeEnergy,
pre_edge_regions=preRegions,
post_edge_regions=postRegions,
algorithm=algorithm,
algorithm_parameters=parameters)
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setWindowTitle("Normalization Error")
msg.setText("An error has occured while normalizing the data")
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec_()
return
nEnergy, nSpectrum, usedEdge, jump = normalizationResult[0:4]
preEdgeFunction, preEdgeParameters = normalizationResult[4:6]
postEdgeFunction, postEdgeParameters = normalizationResult[6:8]
idx = self.energy > (usedEdge + preRegions[0][0])
x = self.energy[idx]
yPre = preEdgeFunction(preEdgeParameters, x)
yPost = postEdgeFunction(postEdgeParameters, x)
self.graph.addCurve(x, yPre, legend="Pre-edge Polynomial")
self.graph.addCurve(x, yPost + yPre, legend="Post-edge Polynomial")
def __init__(self, parent, spectrum, energy=None):
qt.QWidget.__init__(self, parent)
self.setWindowTitle("XAS Normalization Configuration Window")
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(2)
if energy is None:
self.energy = range(len(spectrum))
else:
self.energy = energy
self.spectrum = spectrum
self.parametersWidget = XASNormalizationParametersWidget(self)
self.graph = PlotWindow.PlotWindow(self, backend=backend,
plugins=False, newplot=False)
self.__lastDict = {}
self.graph.sigPlotSignal.connect(self._handleGraphSignal)
self.graph.addCurve(self.energy,
spectrum, legend="Spectrum", replace=True)
self.mainLayout.addWidget(self.parametersWidget)
self.mainLayout.addWidget(self.graph)
# initialize variables
edgeEnergy, sortedX, sortedY, xPrime, yPrime =\
XASNormalization.estimateXANESEdge(spectrum, energy=self.energy, full=True)
self._xPrime = xPrime
self._yPrime = yPrime
self.parametersWidget.setEdgeEnergy(edgeEnergy,
emin=self.energy.min(),
emax=self.energy.max())
self.getParameters = self.parametersWidget.getParameters
self.setParameters = self.parametersWidget.setParameters
self.parametersWidget.sigXASNormalizationParametersSignal.connect( \
self.updateGraph)
self.updateGraph(self.getParameters())
def __init__(self, parent, spectrum, energy=None):
qt.QWidget.__init__(self, parent)
self.setWindowTitle("XAS Normalization Configuration Window")
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(2)
if energy is None:
self.energy = numpy.arange(len(spectrum)).astype(numpy.float64)
else:
self.energy = energy
self.spectrum = numpy.array(spectrum, dtype=numpy.float64, copy=False)
self.parametersWidget = XASNormalizationParametersWidget(self)
self.graph = PlotWindow.PlotWindow(self, backend=backend,
plugins=False, newplot=False)
self.__lastDict = {}
self.graph.sigPlotSignal.connect(self._handleGraphSignal)
self.graph.addCurve(self.energy,
spectrum, legend="Spectrum", replace=True)
self.mainLayout.addWidget(self.parametersWidget)
self.mainLayout.addWidget(self.graph)
# initialize variables
edgeEnergy, sortedX, sortedY, xPrime, yPrime =\
XASNormalization.estimateXANESEdge(spectrum, energy=self.energy, full=True)
self._xPrime = xPrime
self._yPrime = yPrime
self.parametersWidget.setEdgeEnergy(edgeEnergy,
emin=self.energy.min(),
emax=self.energy.max())
self.getParameters = self.parametersWidget.getParameters
self.setParameters = self.parametersWidget.setParameters
self.parametersWidget.sigXASNormalizationParametersSignal.connect( \
self.updateGraph)
self.updateGraph(self.getParameters())
def setData(self, spectrum, energy=None):
self.spectrum = spectrum
if energy is None:
self.energy = range(len(spectrum))
else:
self.energy = energy
self.graph.clearMarkers()
self.graph.clearCurves()
self.graph.addCurve(self.energy, self.spectrum, legend="Spectrum")
edgeEnergy = XASNormalization.estimateXANESEdge(self.spectrum,
energy=self.energy,
full=False)
self.parametersWidget.setEdgeEnergy(edgeEnergy,
emin=self.energy.min(),
emax=self.energy.max())
self.updateGraph(self.getParameters())
def __init__(self, parent, spectrum, energy=None):
qt.QWidget.__init__(self, parent)
self.setWindowTitle("XAS Normalization Configuration Window")
self.mainLayout = qt.QVBoxLayout(self)
self.mainLayout.setContentsMargins(0, 0, 0, 0)
self.mainLayout.setSpacing(2)
if energy is None:
self.energy = range(len(spectrum))
else:
self.energy = energy
self.spectrum = spectrum
self.parametersWidget = XASNormalizationParametersWidget(self)
self.graph = PlotWindow(self,
position=False,
aspectRatio=False,
colormap=False,
yInverted=False,
roi=False,
mask=False,
fit=False)
# next two lines deprecated with silx 0.8.0
# self.graph.zoomModeAction.setVisible(False)
# self.graph.panModeAction.setVisible(False)
toolbar = self.graph.getInteractiveModeToolBar()
toolbar.getZoomModeAction().setVisible(False)
toolbar.getPanModeAction().setVisible(False)
self.__lastDict = {}
self.graph.sigPlotSignal.connect(self._handleGraphSignal)
self.graph.addCurve(self.energy, spectrum, legend="Spectrum")
self.graph.setActiveCurve("Spectrum")
self.mainLayout.addWidget(self.parametersWidget)
self.mainLayout.addWidget(self.graph)
# initialize variables
edgeEnergy, sortedX, sortedY, xPrime, yPrime =\
XASNormalization.estimateXANESEdge(spectrum, energy=self.energy, full=True)
self._xPrime = xPrime
self._yPrime = yPrime
self.parametersWidget.setEdgeEnergy(edgeEnergy,
emin=self.energy.min(),
emax=self.energy.max())
self.getParameters = self.parametersWidget.getParameters
self.setParameters = self.parametersWidget.setParameters
self.parametersWidget.sigXASNormalizationParametersSignal.connect( \
self.updateGraph)
self.updateGraph(self.getParameters())
def setData(self, spectrum, energy=None):
self.spectrum = spectrum
if energy is None:
self.energy = range(len(spectrum))
else:
self.energy = energy
self.graph.clearMarkers()
self.graph.addCurve(self.energy,
self.spectrum,
legend="Spectrum",
replot=True,
replace=True)
edgeEnergy = XASNormalization.estimateXANESEdge(self.spectrum,
energy=self.energy,
full=False)
self.parametersWidget.setEdgeEnergy(edgeEnergy,
emin=self.energy.min(),
emax=self.energy.max())
self.updateGraph(self.getParameters())
def updateGraph(self, ddict):
self.__lastDict = ddict
edgeEnergy = ddict['edge_energy']
preRegions = ddict['pre_edge']['regions']
postRegions = ddict['post_edge']['regions']
event = ddict.get('event', None)
if event == "AutoEdgeEnergyClicked":
try:
# recalculate edge energy following region limits
xmin = edgeEnergy + preRegions[0][0]
xmax = edgeEnergy + postRegions[0][1]
idx = numpy.nonzero((self.energy >= xmin) &\
(self.energy <= xmax))[0]
x = numpy.take(self.energy, idx)
y = numpy.take(self.spectrum, idx)
edgeEnergy = XASNormalization.estimateXANESEdge(y,
energy=x,
full=False)
self.parametersWidget.setEdgeEnergy(edgeEnergy,
emin=self.energy.min(),
emax=self.energy.max())
self.__lastDict['edge_energy'] = edgeEnergy
except:
pass
parameters = {}
parameters['pre_edge_order'] = ddict['pre_edge']['polynomial']
parameters['post_edge_order'] = ddict['post_edge']['polynomial']
algorithm = 'polynomial'
self.updateMarkers(edgeEnergy,
preRegions,
postRegions,
edge_auto=ddict['auto_edge'])
try:
normalizationResult = XASNormalization.XASNormalization(self.spectrum,
self.energy,
edge=edgeEnergy,
pre_edge_regions=preRegions,
post_edge_regions=postRegions,
algorithm=algorithm,
algorithm_parameters=parameters)
except:
msg = qt.QMessageBox(self)
msg.setIcon(qt.QMessageBox.Critical)
msg.setWindowTitle("Normalization Error")
msg.setText("An error has occured while normalizing the data")
msg.setInformativeText(str(sys.exc_info()[1]))
msg.setDetailedText(traceback.format_exc())
msg.exec_()
return
nEnergy, nSpectrum, usedEdge, jump = normalizationResult[0:4]
preEdgeFunction, preEdgeParameters = normalizationResult[4:6]
postEdgeFunction, postEdgeParameters = normalizationResult[6:8]
idx = self.energy > (usedEdge + preRegions[0][0])
x = self.energy[idx]
yPre = preEdgeFunction(preEdgeParameters, x)
yPost = postEdgeFunction(postEdgeParameters, x)
self.graph.addCurve(x,
yPre,
legend="Pre-edge Polynomial",
replace=False)
self.graph.addCurve(x,
yPost+yPre,
legend="Post-edge Polynomial",
replace=False,
replot=True)
