def test_sync(self):
# Test casting non-uniformly-sampled data to a evenly-sampled TimeSeries.
# Begin by defining sampling intervals of random half-normally distributed length
times = np.cumsum(np.abs(np.random.normal(loc=4., scale=6., size=100)))
# take sample values as though the value was increasing as a cube of sample time
samples = times**3
# Use cubic interpolation to resample to uniform interval
cubes = core.TimeSeries(times=times, values=samples, columns=('cubic',))
resamp = processing.sync(0.1, cubes, interp='cubic', fillval='extrapolate')
# Check that the sync function is returning a new time series object
self.assertTrue(isinstance(resamp, core.TimeSeries))
# Test that all returned sample times are uniformly spaced
# We need to use np.isclose because of floating point arithematic problems instead of ==0.1
# Since the actual diff returns 0.09999999999999964
self.assertTrue(np.all(np.isclose(np.diff(resamp.times), 0.1)))
# Check that we're within a margin of error on the interpolation
err_margin = 1e-3 # Maximum percent error allowed
err_percs = np.abs(resamp.times**3 - resamp.values.T) / (resamp.times**3)
self.assertTrue(np.all(err_percs < err_margin))
# Make a second timeseries of square-law increasing samples
times2 = np.cumsum(np.abs(np.random.normal(loc=2., scale=1., size=200)))
samples2 = times2**2
squares = core.TimeSeries(times=times2, values=samples2, columns=('square',))
# Use cubic interpolation again, this time on both timeseries
resamp2 = processing.sync(0.1, [squares, cubes], interp='cubic', fillval='extrapolate')
# Check that the new TS has both squares and cubes as keys and attribs
self.assertTrue(hasattr(resamp2, 'cubic'))
self.assertTrue(hasattr(resamp2, 'square'))
# Check that both timeseries are fully contained in the resampled TS
self.assertTrue(cubes.times.min() >= resamp2.times.min())
self.assertTrue(cubes.times.max() <= resamp2.times.max())
self.assertTrue(squares.times.min() >= resamp2.times.min())
self.assertTrue(squares.times.max() <= resamp2.times.max())
# Check that all interpolated values are within the margin of error against the known func
sq_errperc = np.abs(resamp2.times**2 - resamp2.square) / resamp2.times**2
cu_errperc = np.abs(resamp2.times**3 - resamp2.cubic) / resamp2.times**3
self.assertTrue(np.all(sq_errperc < err_margin) & np.all(cu_errperc < err_margin))
# Now check the numpy array behavior of sync.
# Try running sync on the cubic times and values only.
resamp = processing.sync(0.1, times=times, values=samples, interp='cubic',
fillval='extrapolate')
# Do all the tests we did for the instance created using TimeSeries objects
self.assertTrue(isinstance(resamp, core.TimeSeries))
self.assertTrue(np.all(np.isclose(np.diff(resamp.times), 0.1)))
err_margin = 1e-3 # Maximum percent error allowed
err_percs = np.abs(resamp.times**3 - resamp.values.T) / (resamp.times**3)
self.assertTrue(np.all(err_percs < err_margin))
# Try the multiple-arrays case in which we pass two times and two values
resamp2 = processing.sync(0.1, times=(times, times2), values=(samples, samples2),
interp='cubic', fillval='extrapolate')
self.assertTrue(times.min() >= resamp2.times.min())
self.assertTrue(times.max() <= resamp2.times.max())
self.assertTrue(times2.min() >= resamp2.times.min())
self.assertTrue(times2.max() <= resamp2.times.max())
def bin_spikes(spikes, binsize, interval_indices=False):
"""
Wrapper for bincount2D which is intended to take in a TimeSeries object of spike times
and cluster identities and spit out spike counts in bins of a specified width binsize, also in
another TimeSeries object. Can either return a TS object with each row labeled with the
corresponding interval or the value of the left edge of the bin.
:param spikes: Spike times and cluster identities of sorted spikes
:type spikes: TimeSeries object with \'clusters\' column and timestamps
:param binsize: Width of the non-overlapping bins in which to bin spikes
:type binsize: float
:param interval_indices: Whether to use intervals as the time stamps for binned spikes, rather
than the left edge value of the bins, defaults to False
:type interval_indices: bool, optional
:return: Object with 2D array of shape T x N, for T timesteps and N clusters, and the
associated time stamps.
:rtype: TimeSeries object
"""
if type(spikes) is not core.TimeSeries:
raise TypeError('Input spikes need to be in TimeSeries object format')
if not hasattr(spikes, 'clusters'):
raise AttributeError(
'Input spikes need to have a clusters attribute. Make sure you set '
'columns=(\'clusters\',)) when constructing spikes.')
rates, tbins, clusters = bincount2D(spikes.times, spikes.clusters, binsize)
if interval_indices:
intervals = pd.interval_range(tbins[0],
tbins[-1],
freq=binsize,
closed='left')
return core.TimeSeries(times=intervals,
values=rates.T[:-1],
columns=clusters)
else:
return core.TimeSeries(times=tbins, values=rates.T, columns=clusters)
def sync(dt,
times=None,
values=None,
timeseries=None,
offsets=None,
interp='zero',
fillval=np.nan):
"""
Function for resampling a single or multiple time series to a single, evenly-spaced, delta t
between observations. Uses interpolation to find values.
Can be used on raw numpy arrays of timestamps and values using the 'times' and 'values' kwargs
and/or on brainbox.core.TimeSeries objects passed to the 'timeseries' kwarg. If passing both
TimeSeries objects and numpy arrays, the offsets passed should be for the TS objects first and
then the numpy arrays.
Uses scipy's interpolation library to perform interpolation.
See scipy.interp1d for more information regarding interp and fillval parameters.
:param dt: Separation of points which the output timeseries will be sampled at
:type dt: float
:param timeseries: A group of time series to perform alignment or a single time series.
Must have time stamps.
:type timeseries: tuple of TimeSeries objects, or a single TimeSeries object.
:param times: time stamps for the observations in 'values']
:type times: np.ndarray or list of np.ndarrays
:param values: observations corresponding to the timestamps in 'times'
:type values: np.ndarray or list of np.ndarrays
:param offsets: tuple of offsets for time stamps of each time series. Offsets for passed
TimeSeries objects first, then offsets for passed numpy arrays. defaults to None
:type offsets: tuple of floats, optional
:param interp: Type of interpolation to use. Refer to scipy.interpolate.interp1d for possible
values, defaults to np.nan
:type interp: str
:param fillval: Fill values to use when interpolating outside of range of data. See interp1d
for possible values, defaults to np.nan
:return: TimeSeries object with each row representing synchronized values of all
input TimeSeries. Will carry column names from input time series if all of them have column
names.
"""
#########################################
# Checks on inputs and input processing #
#########################################
# Initialize a list to contain times/values pairs if no TS objs are passed
if timeseries is None:
timeseries = []
# If a single time series is passed for resampling, wrap it in an iterable
elif isinstance(timeseries, core.TimeSeries):
timeseries = [timeseries]
# Yell at the user if they try to pass stuff to timeseries that isn't a TimeSeries object
elif not all([isinstance(ts, core.TimeSeries) for ts in timeseries]):
raise TypeError(
'All elements of \'timeseries\' argument must be brainbox.core.TimeSeries '
'objects. Please uses \'times\' and \'values\' for np.ndarray args.'
)
# Check that if something is passed to times or values, there is a corresponding equal-length
# argument for the other element.
if (times is not None) or (values is not None):
if len(times) != len(values):
raise ValueError(
'\'times\' and \'values\' must have the same number of elements.'
)
if type(times[0]) is np.ndarray:
if not all([t.shape == v.shape for t, v in zip(times, values)]):
raise ValueError(
'All arrays in \'times\' must match the shape of the'
' corresponding entry in \'values\'.')
# If all checks are passed, convert all times and values args into TimeSeries objects
timeseries.extend(
[core.TimeSeries(t, v) for t, v in zip(times, values)])
else:
# If times and values are only numpy arrays and lists of arrays, pair them and add
timeseries.append(core.TimeSeries(times, values))
# Adjust each timeseries by the associated offset if necessary then load into a list
if offsets is not None:
tstamps = [ts.times + os for ts, os in zip(timeseries, offsets)]
else:
tstamps = [ts.times for ts in timeseries]
# If all input timeseries have column names, put them together for the output TS
if all([ts.columns is not None for ts in timeseries]):
colnames = []
for ts in timeseries:
colnames.extend(ts.columns)
else:
colnames = None
#################
# Main function #
#################
# Get the min and max values for all timeseries combined after offsetting
tbounds = np.array([(np.amin(ts), np.amax(ts)) for ts in tstamps])
if not np.all(np.isfinite(tbounds)):
# If there is a np.inf or np.nan in the time stamps for any of the timeseries this will
# break any further code so we check for all finite values and throw an informative error.
raise ValueError('NaN or inf encountered in passed timeseries.\
Please either drop or fill these values.')
tmin, tmax = np.amin(tbounds[:, 0]), np.amax(tbounds[:, 1])
if fillval == 'extrapolate':
# If extrapolation is enabled we can ensure we have a full coverage of the data by
# extending the t max to be an whole integer multiple of dt above tmin.
# The 0.01% fudge factor is to account for floating point arithmetic errors.
newt = np.arange(tmin, tmax + 1.0001 * (dt - (tmax - tmin) % dt), dt)
else:
newt = np.arange(tmin, tmax, dt)
tsinterps = [
interpolate.interp1d(ts.times,
ts.values,
kind=interp,
fill_value=fillval,
axis=0) for ts in timeseries
]
syncd = core.TimeSeries(newt,
np.hstack([tsi(newt) for tsi in tsinterps]),
columns=colnames)
return syncd
