def strip_bg(x, y0, width, niter):
"""Extract and return the strip bg from y0.
Use anchors coordinates in CONFIG["AnchorsList"] if flag
CONFIG["AnchorsFlag"] is True. Convert anchors from x coordinate
to array index prior to passing it to silx.math.fit.filters.strip
:param x: Abscissa array
:param x: Ordinate array (data values at x positions)
:param width: strip width
:param niter: strip niter
"""
global _BG_STRIP_OLDY
global _BG_STRIP_OLDPARS
global _BG_STRIP_OLDBG
global _BG_SMOOTH_OLDWIDTH
global _BG_SMOOTH_OLDFLAG
global _BG_OLD_ANCHORS
global _BG_OLD_ANCHORS_FLAG
parameters_changed =\
_BG_STRIP_OLDPARS != [width, niter] or\
_BG_SMOOTH_OLDWIDTH != CONFIG["SmoothingWidth"] or\
_BG_SMOOTH_OLDFLAG != CONFIG["SmoothingFlag"] or\
_BG_OLD_ANCHORS_FLAG != CONFIG["AnchorsFlag"] or\
_BG_OLD_ANCHORS != CONFIG["AnchorsList"]
# same parameters
if not parameters_changed:
# same data
if numpy.array_equal(_BG_STRIP_OLDY, y0):
# same result
return _BG_STRIP_OLDBG
_BG_STRIP_OLDY = y0
_BG_STRIP_OLDPARS = [width, niter]
_BG_SMOOTH_OLDWIDTH = CONFIG["SmoothingWidth"]
_BG_SMOOTH_OLDFLAG = CONFIG["SmoothingFlag"]
_BG_OLD_ANCHORS = CONFIG["AnchorsList"]
_BG_OLD_ANCHORS_FLAG = CONFIG["AnchorsFlag"]
y1 = savitsky_golay(
y0, CONFIG["SmoothingWidth"]) if CONFIG["SmoothingFlag"] else y0
anchors_indices = _convert_anchors_to_indices(x)
background = strip(y1,
w=width,
niterations=niter,
factor=CONFIG["StripThresholdFactor"],
anchors=anchors_indices)
_BG_STRIP_OLDBG = background
return background
def snip_bg(x, y0, width):
"""Compute the snip bg for y0"""
global _BG_SNIP_OLDY
global _BG_SNIP_OLDWIDTH
global _BG_SNIP_OLDBG
global _BG_SMOOTH_OLDWIDTH
global _BG_SMOOTH_OLDFLAG
global _BG_OLD_ANCHORS
global _BG_OLD_ANCHORS_FLAG
parameters_changed =\
_BG_SNIP_OLDWIDTH != width or\
_BG_SMOOTH_OLDWIDTH != CONFIG["SmoothingWidth"] or\
_BG_SMOOTH_OLDFLAG != CONFIG["SmoothingFlag"] or\
_BG_OLD_ANCHORS_FLAG != CONFIG["AnchorsFlag"] or\
_BG_OLD_ANCHORS != CONFIG["AnchorsList"]
# same parameters
if not parameters_changed:
# same data
if numpy.sum(_BG_SNIP_OLDY == y0) == len(y0):
# same result
return _BG_SNIP_OLDBG
_BG_SNIP_OLDY = y0
_BG_SNIP_OLDWIDTH = width
_BG_SMOOTH_OLDWIDTH = CONFIG["SmoothingWidth"]
_BG_SMOOTH_OLDFLAG = CONFIG["SmoothingFlag"]
_BG_OLD_ANCHORS = CONFIG["AnchorsList"]
_BG_OLD_ANCHORS_FLAG = CONFIG["AnchorsFlag"]
y1 = savitsky_golay(
y0, CONFIG["SmoothingWidth"]) if CONFIG["SmoothingFlag"] else y0
anchors_indices = _convert_anchors_to_indices(x)
if anchors_indices is None or not len(anchors_indices):
anchors_indices = [0, len(y1) - 1]
background = numpy.zeros_like(y1)
previous_anchor = 0
for anchor_index in anchors_indices:
if (anchor_index > previous_anchor) and (anchor_index < len(y1)):
background[previous_anchor:anchor_index] =\
snip1d(y1[previous_anchor:anchor_index],
width)
previous_anchor = anchor_index
if previous_anchor < len(y1):
background[previous_anchor:] = snip1d(y1[previous_anchor:], width)
_BG_SNIP_OLDBG = background
return background
def snip_bg(x, y0, width):
"""Compute the snip bg for y0"""
global _BG_SNIP_OLDY
global _BG_SNIP_OLDWIDTH
global _BG_SNIP_OLDBG
global _BG_SMOOTH_OLDWIDTH
global _BG_SMOOTH_OLDFLAG
global _BG_OLD_ANCHORS
global _BG_OLD_ANCHORS_FLAG
parameters_changed =\
_BG_SNIP_OLDWIDTH != width or\
_BG_SMOOTH_OLDWIDTH != CONFIG["SmoothingWidth"] or\
_BG_SMOOTH_OLDFLAG != CONFIG["SmoothingFlag"] or\
_BG_OLD_ANCHORS_FLAG != CONFIG["AnchorsFlag"] or\
_BG_OLD_ANCHORS != CONFIG["AnchorsList"]
# same parameters
if not parameters_changed:
# same data
if numpy.sum(_BG_SNIP_OLDY == y0) == len(y0):
# same result
return _BG_SNIP_OLDBG
_BG_SNIP_OLDY = y0
_BG_SNIP_OLDWIDTH = width
_BG_SMOOTH_OLDWIDTH = CONFIG["SmoothingWidth"]
_BG_SMOOTH_OLDFLAG = CONFIG["SmoothingFlag"]
_BG_OLD_ANCHORS = CONFIG["AnchorsList"]
_BG_OLD_ANCHORS_FLAG = CONFIG["AnchorsFlag"]
y1 = savitsky_golay(y0, CONFIG["SmoothingWidth"]) if CONFIG["SmoothingFlag"] else y0
anchors_indices = _convert_anchors_to_indices(x)
if anchors_indices is None or not len(anchors_indices):
anchors_indices = [0, len(y1) - 1]
background = numpy.zeros_like(y1)
previous_anchor = 0
for anchor_index in anchors_indices:
if (anchor_index > previous_anchor) and (anchor_index < len(y1)):
background[previous_anchor:anchor_index] =\
snip1d(y1[previous_anchor:anchor_index],
width)
previous_anchor = anchor_index
if previous_anchor < len(y1):
background[previous_anchor:] = snip1d(y1[previous_anchor:],
width)
_BG_SNIP_OLDBG = background
return background
def strip_bg(x, y0, width, niter):
"""Extract and return the strip bg from y0.
Use anchors coordinates in CONFIG["AnchorsList"] if flag
CONFIG["AnchorsFlag"] is True. Convert anchors from x coordinate
to array index prior to passing it to silx.math.fit.filters.strip
:param x: Abscissa array
:param x: Ordinate array (data values at x positions)
:param width: strip width
:param niter: strip niter
"""
global _BG_STRIP_OLDY
global _BG_STRIP_OLDPARS
global _BG_STRIP_OLDBG
global _BG_SMOOTH_OLDWIDTH
global _BG_SMOOTH_OLDFLAG
global _BG_OLD_ANCHORS
global _BG_OLD_ANCHORS_FLAG
parameters_changed =\
_BG_STRIP_OLDPARS != [width, niter] or\
_BG_SMOOTH_OLDWIDTH != CONFIG["SmoothingWidth"] or\
_BG_SMOOTH_OLDFLAG != CONFIG["SmoothingFlag"] or\
_BG_OLD_ANCHORS_FLAG != CONFIG["AnchorsFlag"] or\
_BG_OLD_ANCHORS != CONFIG["AnchorsList"]
# same parameters
if not parameters_changed:
# same data
if numpy.sum(_BG_STRIP_OLDY == y0) == len(y0):
# same result
return _BG_STRIP_OLDBG
_BG_STRIP_OLDY = y0
_BG_STRIP_OLDPARS = [width, niter]
_BG_SMOOTH_OLDWIDTH = CONFIG["SmoothingWidth"]
_BG_SMOOTH_OLDFLAG = CONFIG["SmoothingFlag"]
_BG_OLD_ANCHORS = CONFIG["AnchorsList"]
_BG_OLD_ANCHORS_FLAG = CONFIG["AnchorsFlag"]
y1 = savitsky_golay(y0, CONFIG["SmoothingWidth"]) if CONFIG["SmoothingFlag"] else y0
anchors_indices = _convert_anchors_to_indices(x)
background = strip(y1,
w=width,
niterations=niter,
factor=CONFIG["StripThresholdFactor"],
anchors=anchors_indices)
_BG_STRIP_OLDBG = background
return background
def testSavitskyGolay(self):
npts = 25
for y in [self.y1, self.y2, self.y3]:
smoothed_y = filters.savitsky_golay(y, npoints=npts)
# we added +-5% of random noise. The difference must be much lower
# than 5%.
diff = abs(sum(smoothed_y) - sum(y)) / sum(y)
self.assertLess(diff, 0.05,
"Difference between data with 5%% noise and " +
"smoothed data is > 5%% (%f %%)" % (diff * 100))
# Try various smoothing levels
npts += 25
def testSavitskyGolay(self):
npts = 25
for y in [self.y1, self.y2, self.y3]:
smoothed_y = filters.savitsky_golay(y, npoints=npts)
# we added +-5% of random noise. The difference must be much lower
# than 5%.
diff = abs(sum(smoothed_y) - sum(y)) / sum(y)
self.assertLess(
diff, 0.05, "Difference between data with 5%% noise and " +
"smoothed data is > 5%% (%f %%)" % (diff * 100))
# Try various smoothing levels
npts += 25
def _update(self, resetzoom=False):
"""Compute strip and snip backgrounds, update the curves
"""
if self._y is None:
return
pars = self.getParameters()
# smoothed data
y = numpy.ravel(numpy.array(self._y)).astype(numpy.float64)
if pars["SmoothingFlag"]:
ysmooth = filters.savitsky_golay(y, pars['SmoothingWidth'])
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])
else:
ysmooth = y
# loop for anchors
x = self._x
niter = pars['StripIterations']
anchors_indices = []
if pars['AnchorsFlag'] and pars['AnchorsList'] is not None:
ravelled = x
for channel in pars['AnchorsList']:
if channel <= ravelled[0]:
continue
index = numpy.nonzero(ravelled >= channel)[0]
if len(index):
index = min(index)
if index > 0:
anchors_indices.append(index)
stripBackground = filters.strip(ysmooth,
w=pars['StripWidth'],
niterations=niter,
factor=pars['StripThreshold'],
anchors=anchors_indices)
if niter >= 1000:
# final smoothing
stripBackground = filters.strip(stripBackground,
w=1,
niterations=50*pars['StripWidth'],
factor=pars['StripThreshold'],
anchors=anchors_indices)
if len(anchors_indices) == 0:
anchors_indices = [0, len(ysmooth)-1]
anchors_indices.sort()
snipBackground = 0.0 * ysmooth
lastAnchor = 0
for anchor in anchors_indices:
if (anchor > lastAnchor) and (anchor < len(ysmooth)):
snipBackground[lastAnchor:anchor] =\
filters.snip1d(ysmooth[lastAnchor:anchor],
pars['SnipWidth'])
lastAnchor = anchor
if lastAnchor < len(ysmooth):
snipBackground[lastAnchor:] =\
filters.snip1d(ysmooth[lastAnchor:],
pars['SnipWidth'])
self.graphWidget.addCurve(x, y,
legend='Input Data',
replace=True,
resetzoom=resetzoom)
self.graphWidget.addCurve(x, stripBackground,
legend='Strip Background',
resetzoom=False)
self.graphWidget.addCurve(x, snipBackground,
legend='SNIP Background',
resetzoom=False)
if self._xmin is not None and self._xmax is not None:
self.graphWidget.getXAxis().setLimits(self._xmin, self._xmax)
def _update(self, resetzoom=False):
"""Compute strip and snip backgrounds, update the curves
"""
if self._y is None:
return
pars = self.getParameters()
# smoothed data
y = numpy.ravel(numpy.array(self._y)).astype(numpy.float)
if pars["SmoothingFlag"]:
ysmooth = filters.savitsky_golay(y, pars['SmoothingWidth'])
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])
else:
ysmooth = y
# loop for anchors
x = self._x
niter = pars['StripIterations']
anchors_indices = []
if pars['AnchorsFlag'] and pars['AnchorsList'] is not None:
ravelled = x
for channel in pars['AnchorsList']:
if channel <= ravelled[0]:
continue
index = numpy.nonzero(ravelled >= channel)[0]
if len(index):
index = min(index)
if index > 0:
anchors_indices.append(index)
stripBackground = filters.strip(ysmooth,
w=pars['StripWidth'],
niterations=niter,
factor=pars['StripThreshold'],
anchors=anchors_indices)
if niter >= 1000:
# final smoothing
stripBackground = filters.strip(stripBackground,
w=1,
niterations=50*pars['StripWidth'],
factor=pars['StripThreshold'],
anchors=anchors_indices)
if len(anchors_indices) == 0:
anchors_indices = [0, len(ysmooth)-1]
anchors_indices.sort()
snipBackground = 0.0 * ysmooth
lastAnchor = 0
for anchor in anchors_indices:
if (anchor > lastAnchor) and (anchor < len(ysmooth)):
snipBackground[lastAnchor:anchor] =\
filters.snip1d(ysmooth[lastAnchor:anchor],
pars['SnipWidth'])
lastAnchor = anchor
if lastAnchor < len(ysmooth):
snipBackground[lastAnchor:] =\
filters.snip1d(ysmooth[lastAnchor:],
pars['SnipWidth'])
self.graphWidget.addCurve(x, y,
legend='Input Data',
replace=True,
resetzoom=resetzoom)
self.graphWidget.addCurve(x, stripBackground,
legend='Strip Background',
resetzoom=False)
self.graphWidget.addCurve(x, snipBackground,
legend='SNIP Background',
resetzoom=False)
if self._xmin is not None and self._xmax is not None:
self.graphWidget.getXAxis().setLimits(self._xmin, self._xmax)
