def _fine_scan_peak(self, cp):
line, _ = self.graph.new_series(plotid=1)
c = cp.dac
w = self.fwindow / 2.0
steps = self._calc_step_values(c - w, c + w, self.fstep_dac)
self._scan_dac(steps)
# get last scan
xs = line.index.get_data()
ys = line.value.get_data()
try:
center = calculate_peak_center(xs, ys)
# if not isinstance(center, str):
[lx, cx, hx], [ly, cy, hy], mx, my = center
self.graph.add_vertical_rule(cx, plotid=1)
self.info('new peak center. {} nominal={} dx={}'.format(
cp.isotope, cp.dac, cx))
cp.dac += cx
self._redraw()
except PeakCenterError as e:
self.warning(e)
def _calculate_peak_center(self, x, y):
try:
result = calculate_peak_center(x, y,
min_peak_height=self.min_peak_height)
return result
except PeakCenterError, e:
self.warning('Failed to find a valid peak. {}'.format(e))
def _calculate_peak_center(self, x, y):
result = calculate_peak_center(x, y,
min_peak_height=self.min_peak_height)
if result is not None:
if isinstance(result, str):
self.warning(result)
else:
return result
def _calculate_peak_center(self, x, y):
result = calculate_peak_center(x,
y,
min_peak_height=self.min_peak_height)
if result is not None:
if isinstance(result, str):
self.warning(result)
else:
return result
def _calculate_peak_center(self, x, y):
# from pychron.core.time_series.time_series import smooth
# graph = self.graph
# self._series_factory(graph)
# smooth_y = smooth(y)
# graph.set_data(x, series=self._markup_idx-1)
# graph.set_data(smooth_y, series=self._markup_idx-1, axis=1)
try:
result = calculate_peak_center(x, y,
min_peak_height=self.min_peak_height,
percent=self.percent)
return result
except PeakCenterError, e:
self.warning('Failed to find a valid peak. {}'.format(e))
def _calculate_peak_center(self, x, y, update_plot):
if self.use_interpolation:
f = interpolate.interp1d(x, y, kind=self.interpolation_kind)
x = linspace(x.min(), x.max(), 500)
y = f(x)
if update_plot:
self.graph.new_series(x, y, line_width=1)
self.graph.redraw()
if self.n_peaks > 1:
self.warning('peak deconvolution disabled')
# def res(p, y, x):
# yfit = None
# n = p.shape[0] / 3
# for h, m, s in p.reshape(n, 3):
# yi = h * norm.pdf(x, m, s)
# if yfit is None:
# yfit = yi
# else:
# yfit += yi
# err = y - yfit
# return err
#
# mm = x[y.argmax()]
# counter = range(self.n_peaks)
# p = [(1, mm, 1) for _ in counter]
# plsq = leastsq(res, p, args=(y, x))
#
# centers = plsq[0]
# for i in counter:
# c = centers[1 + 3 * i]
# self.graph.add_vertical_rule(c, color='blue')
#
# return c[1 + 3 * (self.select_peak - 1)]
try:
result = calculate_peak_center(x, y,
min_peak_height=self.min_peak_height,
percent=self.percent)
return result
except PeakCenterError, e:
self.warning('Failed to find a valid peak. {}'.format(e))
def _calculate_peak_center(self, x, y):
if self.use_interpolation:
f = interpolate.interp1d(x, y)
x = linspace(x[0], x[-1], 1000)
y = f(x)
self.graph.new_series(x, y, line_style='dash')
if self.n_peaks > 1:
def res(p, y, x):
yfit = None
n = p.shape[0] / 3
for h, m, s in p.reshape(n, 3):
yi = h * norm.pdf(x, m, s)
if yfit is None:
yfit = yi
else:
yfit += yi
err = y - yfit
return err
mm = x[y.argmax()]
counter = range(self.n_peaks)
p = [(1, mm, 1) for _ in counter]
plsq = leastsq(res, p, args=(y, x))
centers = plsq[0]
for i in counter:
c = centers[1 + 3 * i]
self.graph.add_vertical_rule(c, color='blue')
return c[1 + 3 * (self.select_peak - 1)]
try:
result = calculate_peak_center(x, y,
min_peak_height=self.min_peak_height,
percent=self.percent)
return result
except PeakCenterError, e:
self.warning('Failed to find a valid peak. {}'.format(e))
def _fine_scan_peak(self, cp):
line, _ = self.graph.new_series(plotid=1)
c = cp.dac
w = self.fwindow / 2.0
steps = self._calc_step_values(c - w, c + w, self.fstep_dac)
self._scan_dac(steps)
#get last scan
xs = line.index.get_data()
ys = line.value.get_data()
center = calculate_peak_center(xs, ys)
if not isinstance(center, str):
[lx, cx, hx], [ly, cy, hy], mx, my = center
self.graph.add_vertical_rule(cx, plotid=1)
self.info('new peak center. {} nominal={} dx={}'.format(cp.isotope, cp.dac, cx))
cp.dac += cx
self._redraw()
else:
self.warning(center)
