def updateGraph(self, ddict):
width = ddict['width']
roi_min = ddict['roi_min']
roi_max = ddict['roi_max']
smoothing = ddict['smoothing']
if self.__image:
if self.xMarkers == []:
xMin, xMax = self.graph.getX1AxisLimits()
yMin, yMax = self.graph.getY1AxisLimits()
xMean = 0.5 * (xMin + xMax)
yMean = 0.5 * (yMin + yMax)
self.xMarkers.append(self.graph.insertX1Marker(roi_min[1], yMean, label='C Min'))
self.xMarkers.append(self.graph.insertX1Marker(roi_max[1], yMean, label='C Max'))
self.yMarkers.append(self.graph.insertY1Marker(xMean, roi_min[0], label='R Min'))
self.yMarkers.append(self.graph.insertY1Marker(xMean, roi_max[0], label='R Max'))
else:
self.graph.markersdict[self.xMarkers[0]]['marker'].setXValue(roi_min[1])
self.graph.markersdict[self.xMarkers[1]]['marker'].setXValue(roi_max[1])
self.graph.markersdict[self.yMarkers[0]]['marker'].setYValue(roi_min[0])
self.graph.markersdict[self.yMarkers[1]]['marker'].setYValue(roi_max[0])
self.background = SNIPModule.getImageBackground(self.image, width,
roi_min=roi_min,
roi_max=roi_max,
smoothing=smoothing)
difference = self.image-self.background
self.graphWidget.setImageData(difference)
if OBJECT3D:
if self.o3dScene is None:
self.o3dScene = Object3DScene.Object3DScene()
self.o3dScene.show()
if 0:
imageData =(self.image * 1).astype(numpy.float32)
backgroundData = (self.background * 1).astype(numpy.float32)
self.o3dScene.mesh(imageData, z=imageData * 1, legend='Data', update_scene=True)
self.o3dScene.mesh(backgroundData, z=backgroundData , legend='Background', update_scene=True)
else:
self.o3dScene.mesh(difference, z=difference, legend='Data-Background')
self.o3dScene.show()
else:
self.background = SNIPModule.getSpectrumBackground(self.spectrum, width,
roi_min=roi_min,
roi_max=roi_max,
smoothing=smoothing)
if self.__smooth:
legend0 = "Smoothed Spectrum"
else:
legend0 = "Background"
self.graph.newCurve(self.xValues,
self.background, legend0, replace=False)
#Force information update
legend = self.graph.getActiveCurve(just_legend=True)
if legend.startswith(legend0[0:5]):
self.graph.setActiveCurve(legend)
def updateGraph(self, ddict):
width = ddict['width']
roi_min = ddict['roi_min']
roi_max = ddict['roi_max']
smoothing = ddict['smoothing']
if self.__image:
if self.xMarkers == []:
xMin, xMax = self.graph.getGraphXLimits()
yMin, yMax = self.graph.getGraphYLimits()
xMean = 0.5 * (xMin + xMax)
yMean = 0.5 * (yMin + yMax)
self.xMarkers.append(
self.graph.insertXMarker(roi_min[1],
legend='C Min',
text='C Min'))
self.xMarkers.append(
self.graph.insertXMarker(roi_max[1],
legend='C Max',
text='C Max'))
self.yMarkers.append(
self.graph.insertYMarker(roi_min[0],
legend='R Min',
text='R Min'))
self.yMarkers.append(
self.graph.insertYMarker(roi_max[0],
legend='R Max',
text='R Max'))
else:
self.graph.insertXMarker(roi_min[1],
legend='C Min',
text='C Min')
self.graph.insertXMarker(roi_max[1],
legend='C Max',
text='C Max')
self.graph.insertYMarker(roi_min[0],
legend='R Min',
text='R Min')
self.graph.insertYMarker(roi_max[0],
legend='R Max',
text='R Max')
self.background = SNIPModule.getImageBackground(
self.image,
width,
roi_min=roi_min,
roi_max=roi_max,
smoothing=smoothing)
difference = self.image - self.background
self.graphWidget.setImageData(difference)
if OBJECT3D:
if self.o3dScene is None:
self.o3dScene = Object3DScene.Object3DScene()
self.o3dScene.show()
if 0:
imageData = (self.image * 1).astype(numpy.float32)
backgroundData = (self.background * 1).astype(
numpy.float32)
self.o3dScene.mesh(imageData,
z=imageData * 1,
legend='Data',
update_scene=True)
self.o3dScene.mesh(backgroundData,
z=backgroundData,
legend='Background',
update_scene=True)
else:
self.o3dScene.mesh(difference,
z=difference,
legend='Data-Background')
self.o3dScene.show()
else:
self.background = SNIPModule.getSpectrumBackground(
self.spectrum,
width,
roi_min=roi_min,
roi_max=roi_max,
smoothing=smoothing)
if self.__smooth:
legend0 = "Smoothed Spectrum"
else:
legend0 = "Background"
self.graph.addCurve(self.xValues,
self.background,
legend0,
replace=False)
#Force information update
legend = self.graph.getActiveCurve(just_legend=True)
if legend.startswith(legend0[0:5]):
self.graph.setActiveCurve(legend)
def findPeaks(self, x, y, thr, derivative):
"""
Input
-----
x,y : ndarrays
Arrays contain curve intformation
thr : float
Threshold in percent of normalized maximum
derivative : bool
The derivative of a curve is being fitted
Finds most prominent feature contained in y
and tries to estimate starting parameters for a
Gaussian least squares fit (LSF). Recommends values
used to fit the Gaussian.
Return
------
xpeak, ypeak, fwhm : float
Estimated values for x-position, amplitude
and width of the Gaussian
fwhmIdx : ndarray
Indices determine the range on which the LSF
is performed
"""
# Use SNIP algorithm for background substraction &
# seek method for peak detection
sffuns = SF.SpecfitFunctions()
if derivative:
# Avoid BG substraction & normalization if
# fitting the derivate of a curve
ybg = y
ynorm = y/(abs(y.max())+abs(y.min()))
else:
ybg = y-snip.getSnip1DBackground(y, len(y)//thr) # USER INPUT!!!
# Normalize background substracted data to
# standardize the yscaling of seek method
#ynorm = (ybg - ybg.min())/(ybg.max()-ybg.min())
ynorm = self.normalize(ybg)
# Replace by max()?
try:
# Calculate array with all peak indices
peakIdx = numpy.asarray(sffuns.seek(ybg, yscaling=1000.), dtype=int)
# Extract highest peak
sortIdx = y[peakIdx].argsort()[-1]
except IndexError:
if DEBUG == 1:
print('No peaks found..')
return None
except SystemError:
if DEBUG == 1:
print('Peak search failed. Continue with y maximum')
peakIdx = [ybg.argmax()]
sortIdx = 0
xpeak = float(x[peakIdx][sortIdx])
ypeak = float(y[peakIdx][sortIdx])
ypeak_norm = float(ynorm[peakIdx][sortIdx])
ypeak_bg = float(ybg[peakIdx][sortIdx])
# Estimate FWHM
fwhmIdx = numpy.nonzero(ynorm >= thr*ypeak_norm)[0]
#fwhmIdx = numpy.nonzero(ybg >= thr*ypeak_bg)[0]
# Underestimates FWHM
x0, x1 = x[fwhmIdx].min(), x[fwhmIdx].max()
fwhm = x1 - x0
return xpeak, ypeak, fwhm, fwhmIdx
def fitAlignment(image, params):
idx0 = params.get('idx0', 0)
axis = params.get('axis', -1) # Axis defines direction of curves
snipWidth = params.get('snipWidth', None)
peakSearch = params.get('peakSearch', False)
#
# Determine which axis defines curves
# Make shure to convert image to float!!!
#
if axis < 0:
# If axis not specified..
rows, cols = image.shape
# ..align along smaller axis
if rows < cols:
axis = 0
else:
axis = 1
if axis == 0:
nCurves, nPoints = image.shape
curves = numpy.float64(image)
elif axis == 1:
nPoints, nCurves = image.shape
curves = numpy.float64(image.T)
else:
raise ValueError('Alignment instance -- Axis must be either -1, 0 or 1')
#
# Image preprocessing: Snip background
#
imRows, imCols = image.shape
if snipWidth is None:
snipWidth = max(imRows, imCols)//10
specfitObj = SF.SpecfitFunctions()
background = numpy.zeros(shape=curves.shape,
dtype=numpy.float64)
for idx, curve in enumerate(curves):
background[idx] = SNIP.getSnip1DBackground(curve, snipWidth)
subtracted = curves-background
normResult = Normalization.zeroToOne(image=subtracted,
params={})
normalized = normResult['image']
#
# Loop through curves: Find peak (max..), Estimate fit params, Perform Gaussian fit
#
fitList = nCurves * [float('NaN')]
if DEBUG >= 1:
print('Alignment.fitAlignment -- fitting..')
for idx, y in enumerate(subtracted):
#
# Peak search
#
if peakSearch:
try:
# Calculate array with all peak indices
peakIdx = numpy.asarray(specfitObj.seek(y, yscaling=100.),
dtype=int)
# Extract highest feature
maxIdx = y[peakIdx].argsort()[-1]
except IndexError:
if DEBUG >= 1:
print('Alignment.fitAlignment -- No peaks found..')
return None
except SystemError:
if DEBUG >= 1:
print('Alignment.fitAlignment -- Peak search failed. Continue with y maximum')
peakIdx = [y.argmax()]
maxIdx = 0
else:
peakIdx = [y.argmax()]
maxIdx = 0
height = float(y[peakIdx][maxIdx]) + curves[idx].min()
pos = float(peakIdx[maxIdx])
#
# Estimate FWHM
#
fwhmIdx = numpy.nonzero(y >= .5*normalized[idx])[0]
# Underestimates FWHM, since carried out on normalized image
fwhm = float(fwhmIdx.max()-fwhmIdx.min())
#
# Peak fit: Uses actual data
#
#xrange = numpy.arange(0, len(y), dtype=y.dtype) # Full range
mask = numpy.nonzero(y >= .1*normalized[idx])[0]
ydata = curves[idx,mask]
#ydata -= ydata.min()
try:
fitp, chisq, sigma = LSF(gaussianModel,
numpy.asarray([height, pos, fwhm]),
xdata=mask,
ydata=(ydata-ydata.min()))
if DEBUG >= 1:
print('\tCurve %d -- fitp: %s' % (idx, str(fitp)))
print('\tCurve %d -- chisq: %s' % (idx, str(chisq)))
print('\tCurve %d -- sigma: %s' % (idx, str(sigma)))
except numpy.linalg.linalg.LinAlgError:
fitp, chisq, sigma = [None, None, None],\
float('Nan'),\
float('Nan')
if DEBUG >= 1:
print('\tCurve %d -- Fit failed!' % idx)
fitList[idx] = fitp # ftip is 3-tuple..
posIdx = 1 # ..2nd argument of fitp is peak position
shift0 = fitList[idx0][posIdx]
shiftList = [shift0-fit[posIdx] for fit in fitList]
#ddict = {
# 'op': 'fitAlignment',
# 'shiftList': shiftList
#}
#return ddict
return shiftList
