class AlignTime:
def __init__(self, filter=True, filt_ord=4, filt_cut=5, datetime=False):
"""
Method for aligning time-stamps of different time series data
Parameters
----------
filter : {bool, array_like}, optional
Filter the input data. Either bool for both data series, or an array_like of bools if only one series of
data should be filtered.
filt_ord : {int, array_like}, optional
Filter order for the filtering process. Either a single int for both data series, or an array_like of 2
ints, with orders for the first and second time series. Default is 4. Ignored if filter is False.
filt_cut : {float, array_like}, optional
Low-pass filter cutoffs for the filtering process. Either a signal float for both data series, or an
array_like of 2 floats, with orders for the first and second time series. Default is 5Hz. Ignored if filter
is False.
datetime : bool, optional
Whether or not datetime units are provided for the the time. Default is False, in which case seconds
are expected
"""
# assign values as appropriate
if isinstance(filter, (tuple, list, ndarray)):
self._filt1, self._filt2 = filter
else:
self._filt1, self._filt2 = filter, filter
if isinstance(filt_ord, (tuple, list, ndarray)):
self._ord1, self._ord2 = filt_ord
else:
self._ord1, self._ord2 = filt_ord, filt_ord
if isinstance(filt_cut, (tuple, list, ndarray)):
self._cut1, self._cut2 = filt_cut
else:
self._cut1, self._cut2 = filt_cut, filt_cut
self.datetime = datetime
# line for plotting the aligned signals
self.line = None
def fit(self,
time1,
data1,
time2,
data2,
dt1=None,
dt2=None,
xlim1=None,
xlim2=None,
xnear1=None,
xnear2=None):
"""
Align the two time series
Parameters
----------
time1 : numpy.ndarray
(N1, ) array of time-stamps for the first series of data. Will be resampled to match the sampling rate of
the second data series if necessary during the alignment process.
data1 : numpy.ndarray
(N1, M1) array of the first series of data
time2 : numpy.ndarray
(N2, ) array of time-stamps for the second series of data. Does not have to be the same sampling rate as
the first series of data. The first series of data will be resampled to match that of the second series
data2 : numpy.ndarray
(N2, M2) array of the second series of data
dt1 : {None, float}, optional
Sampling time for the first series time stamps, if necessary. Default is None, which will be ignored and
the mean difference in time-stamps for the first 100 samples of the provided time stamps will be used.
dt2 : {None, float}, optional
Sampling time for the second series time stamps, if necessary. Default is None, which will be ignored and
the mean difference in time-stamps for the first 100 samples of the provided time stamps will be used.
xlim1 : array_like, optional
X-limits for plotting series 1 data. Useful if you know approximately where the events to time sync are
located in the series 1 data.
xlim2 : array_like, optional
X-limits for plotting series 2 data. Useful if you now approximately where the events to time sync are
located in the series 2 data.
xnear1 : float, optional
X-value where to search near in the first signal. Will be marked on the graph with a vertical line.
xnear2 : float, optional
X-value where to search near in the second signal. Will be marked on the graph with a vertical line.
Returns
-------
dt_1_2 : float
The time difference between series 2 and series 1, calculated by subtracting the aligned time 2 - time 1
Attributes
----------
t1_0 : float
Aligned time int time1 detected by the convolution of the two signals in th regions chosen.
t2_0 : float
Aligned time in time2 detected by the convolution of the two signals in the regions chosen.
"""
# assign the times
self._t1 = time1
self._t2 = time2
# assign the raw data
self._rx1 = data1
self._rx2 = data2
# compute the sampling times
if dt1 is None:
if self.datetime:
self._dt1 = mean(diff(self._t1[:100])) / timedelta64(1, 's')
else:
self._dt1 = mean(diff(self._t1[:100]))
else:
self._dt1 = dt1
if dt2 is None:
if self.datetime:
self._dt2 = mean(diff(self._t2[:100])) / timedelta64(1, 's')
else:
self._dt2 = mean(diff(self._t2[:100]))
else:
self._dt2 = dt2
# filter the data
if self._filt1:
fc1 = butter(self._ord1, 2 * self._cut1 * self._dt1, btype='low')
self._x1 = filtfilt(fc1[0], fc1[1], self._rx1)
else:
self._x1 = self._rx1
if self._filt2:
fc2 = butter(self._ord2, 2 * self._cut2 * self._dt2, btype='low')
self._x2 = filtfilt(fc2[0], fc2[1], self._rx2)
else:
self._x2 = self._rx2
# plot the data
self._f, (self._ax1, self._ax2) = plt.subplots(2, figsize=(20, 10))
if self._filt1:
self._ax1.plot(self._t1,
self._rx1,
color='C0',
linewidth=1.5,
label='Raw',
alpha=0.7)
if self._filt2:
self._ax2.plot(self._t2,
self._rx2,
color='C0',
linewidth=1.5,
label='Raw',
alpha=0.7)
self._ax1.plot(self._t1,
self._x1,
color='C1',
linewidth=2,
label='Filtered')
self._ax2.plot(self._t2,
self._x2,
color='C1',
linewidth=2,
label='Filtered')
if xlim1 is not None:
self._ax1.set_xlim(xlim1)
if xlim2 is not None:
self._ax2.set_xlim(xlim2)
if xnear1 is not None:
self._ax1.axvline(xnear1, color='k', linewidth=3, alpha=0.5)
if xnear2 is not None:
self._ax2.axvline(xnear2, color='k', linewidth=3, alpha=0.5)
self._ax1.legend(loc='best')
self._ax2.legend(loc='best')
# create the cursor and span selectors for the first axis
self._ax1.set_title('Navigate and select the region to check: '
) # let user know what they are doing
self._cursor1 = Cursor(self._ax1,
color='C0',
useblit=True,
linewidth=1)
self._span1 = SpanSelector(self._ax1,
self._on_select1,
'horizontal',
useblit=True,
rectprops=dict(alpha=0.5, facecolor='red'),
button=1,
span_stays=True)
self._ax2.set_title('Navigate and select region to match: ')
self._cursor2 = Cursor(self._ax2,
color='C0',
useblit=True,
linewidth=1)
self._span2 = SpanSelector(self._ax2,
self._on_select2,
'horizontal',
useblit=True,
rectprops=dict(alpha=0.5, facecolor='red'),
button=1,
span_stays=True)
self._cursor2.set_active(False)
self._span2.set_visible(False)
self._f.tight_layout()
plt.show(block=True)
return self.t_diff
def _on_select1(self, xmin, xmax):
self._ax1.set_title(None)
if self.datetime:
t1 = date2num(self._t1)
else:
t1 = self._t1
start, stop = searchsorted(t1, (xmin, xmax))
f = interp1d(t1[start - 10:stop + 10],
self._x1[start - 10:stop + 10],
kind='cubic')
if self.datetime:
self._ta = drange(self._t1[start], self._t1[stop],
to_timedelta(self._dt2, unit='s'))
else:
self._t1 = arange(self._t1[start], self._t1[stop], self._dt2)
self._a = f(self._ta)
self._cursor2.set_active(True)
self._span2.set_visible(True)
def _on_select2(self, xmin, xmax):
self._ax2.set_title(None)
if self.datetime:
t2 = date2num(self._t2)
else:
t2 = self._t2
start, stop = searchsorted(t2, (xmin, xmax))
self._b = zeros(self._a.shape)
self._tb = t2[stop - self._a.size:stop]
self._b[-(stop - start):] = self._x2[start:stop]
A = fftpack.fft(self._a)
B = fftpack.fft(self._b)
Ar = -A.conjugate()
self._ind_shift = argmax(nabs(fftpack.ifft(
Ar * B))) # convolve the arrays and find the peak
self.t1_0 = self._ta[0] # find the time value in the first signal
self.t2_0 = self._tb[
self._ind_shift] # find the time value in the second signal
t_pl = self._ta + (self.t2_0 - self.t1_0)
x_pl = self._a
if self.line is not None:
self.line.set_data([], [])
self.line, = self._ax2.plot(t_pl, x_pl, color='C2', label='Aligned')
if self.datetime:
self.t1_0 = to_datetime(num2date(self.t1_0)).tz_localize(None)
self.t2_0 = to_datetime(num2date(self.t2_0)).tz_localize(None)
# time difference between the signals
self.t_diff = self.t2_0 - self.t1_0
run.save_result("peakODX", pOptX[0])
run.save_result("widthX", widthX)
run.save_result("tempX", tempX)
run.save_result("centerX", centerX)
run.save_result("peakODZ", pOptZ[0])
run.save_result("widthZ", widthZ)
run.save_result("tempZ", tempZ)
run.save_result("centerZ", centerZ)
run.save_result("avgWidth", avgWidth)
run.save_result("avgPeakOD", avgPeakOD)
run.save_result("avgTemp", avgTemp)
# Set Center event
cursor = Cursor(ax, useblit=True, color='white', linewidth=1)
cursor.set_active(False)
def set_center(event):
if event.key in ['C', 'c'] and not cursor.active:
cursor.set_active(True)
elif event.key in ['C', 'c'] and cursor.active:
cursor.set_active(False)
center = (int(event.xdata), int(event.ydata))
print(center)
with h5py.File('current_roi.h5', 'w') as f:
if 'center' not in f:
f.attrs.create('center', center)
else:
f.attrs['center'] = center
