def update(self):
if self._y is None:
return
pars = self.getParameters()
#smoothed data
y = numpy.ravel(numpy.array(self._y)).astype(numpy.float)
ysmooth = SpecfitFuns.SavitskyGolay(y, pars['stripfilterwidth'])
f = [0.25, 0.5, 0.25]
ysmooth[1:-1] = numpy.convolve(ysmooth, f, mode=0)
ysmooth[0] = 0.5 * (ysmooth[0] + ysmooth[1])
ysmooth[-1] = 0.5 * (ysmooth[-1] + ysmooth[-2])
#loop for anchors
x = self._x
niter = pars['stripiterations']
anchorslist = []
if pars['stripanchorsflag']:
if pars['stripanchorslist'] is not None:
ravelled = x
for channel in pars['stripanchorslist']:
if channel <= ravelled[0]: continue
index = numpy.nonzero(ravelled >= channel)[0]
if len(index):
index = min(index)
if index > 0:
anchorslist.append(index)
if niter > 1000:
stripBackground = SpecfitFuns.subac(ysmooth, pars['stripconstant'],
niter, pars['stripwidth'],
anchorslist)
#final smoothing
stripBackground = SpecfitFuns.subac(stripBackground,
pars['stripconstant'], 500, 1,
anchorslist)
elif niter > 0:
stripBackground = SpecfitFuns.subac(ysmooth, pars['stripconstant'],
niter, pars['stripwidth'],
anchorslist)
else:
stripBackground = 0.0 * ysmooth + ysmooth.min()
if len(anchorslist) == 0:
anchorslist = [0, len(ysmooth) - 1]
anchorslist.sort()
snipBackground = 0.0 * ysmooth
lastAnchor = 0
width = pars['snipwidth']
for anchor in anchorslist:
if (anchor > lastAnchor) and (anchor < len(ysmooth)):
snipBackground[lastAnchor:anchor] =\
SpecfitFuns.snip1d(ysmooth[lastAnchor:anchor], width, 0)
lastAnchor = anchor
if lastAnchor < len(ysmooth):
snipBackground[lastAnchor:] =\
SpecfitFuns.snip1d(ysmooth[lastAnchor:], width, 0)
self.graphWidget.addCurve(x, y, \
legend='Input Data',\
replace=True,
replot=False)
self.graphWidget.addCurve(x, stripBackground,\
legend='Strip Background',\
replot=False)
self.graphWidget.addCurve(x, snipBackground,\
legend='SNIP Background',
replot=True)
def _getStripBackground(self, x=None, y=None):
#this makes the assumption x are equally spaced
#and I should build a spline if that is not the case
#but I do not want to put a dependency on SciPy
if y is not None:
ywork = y
else:
ywork = self._y
if x is not None:
xwork = x
else:
xwork = self._x
n=len(xwork)
#loop for anchors
anchorslist = []
if self._fitConfiguration['fit']['stripanchorsflag']:
if self._fitConfiguration['fit']['stripanchorslist'] is not None:
oldShape = xwork.shape
ravelled = xwork
ravelled.shape = -1
for channel in self._fitConfiguration['fit']['stripanchorslist']:
if channel <= ravelled[0]:continue
index = numpy.nonzero(ravelled >= channel)
if len(index):
index = min(index)
if index > 0:
anchorslist.append(index)
ravelled.shape = oldShape
#work with smoothed data
ysmooth = self._getSmooth(xwork, ywork)
#SNIP algorithm
if self._fitConfiguration['fit']['stripalgorithm'] in ["SNIP", 1]:
if DEBUG:
print("CALCULATING SNIP")
if len(anchorslist) == 0:
anchorslist = [0, len(ysmooth)-1]
anchorslist.sort()
result = 0.0 * ysmooth
lastAnchor = 0
width = self._fitConfiguration['fit']['snipwidth']
for anchor in anchorslist:
if (anchor > lastAnchor) and (anchor < len(ysmooth)):
result[lastAnchor:anchor] =\
SpecfitFuns.snip1d(ysmooth[lastAnchor:anchor], width, 0)
lastAnchor = anchor
if lastAnchor < len(ysmooth):
result[lastAnchor:] =\
SpecfitFuns.snip1d(ysmooth[lastAnchor:], width, 0)
return result
#strip background
niter = self._fitConfiguration['fit']['stripiterations']
if niter > 0:
if DEBUG:
print("CALCULATING STRIP")
print("iterations = ", niter)
print("constant = ",
self._fitConfiguration['fit']['stripconstant'])
print("width = ",
self._fitConfiguration['fit']['stripwidth'])
print("anchors = ", anchorslist)
result=SpecfitFuns.subac(ysmooth,
self._fitConfiguration['fit']['stripconstant'],
niter,
self._fitConfiguration['fit']['stripwidth'],
anchorslist)
if niter > 1000:
#make sure to get something smooth
result = SpecfitFuns.subac(result,
self._fitConfiguration['fit']['stripconstant'],
500,1,
anchorslist)
else:
#make sure to get something smooth but with less than
#500 iterations
result = SpecfitFuns.subac(result,
self._fitConfiguration['fit']['stripconstant'],
int(self._fitConfiguration['fit']['stripwidth']*2),
1,
anchorslist)
else:
if DEBUG:
print("NO STRIP, NO SNIP")
result = numpy.zeros(ysmooth.shape, numpy.float) + min(ysmooth)
return result