def _set_h5_signal(self, h5):
# ----------------------------
self._h5 = h5
if h5.clock:
self.clock = Clock(h5.clock.uri, h5.clock.times, units=h5.clock.units)
elif h5.rate:
self.clock = UniformClock(None, h5.rate, units=h5.clock.units)
def _set_h5_signal(self, h5):
#----------------------------
self._h5 = h5
if h5.clock:
self.clock = Clock(h5.clock.uri,
h5.clock.times,
units=h5.clock.units)
elif h5.rate:
self.clock = UniformClock(None, h5.rate, units=h5.clock.units)
class HDF5Signal(BSMLSignal):
#============================
"""
A :class:`~biosignalml.Signal` in a HDF5 Recording.
:param uri: The signal's URI.
:param units: The physical units of the signal's data.
:param kwds: Other :class:`~biosignalml.Signal` attributes to set.
"""
def __init__(self, uri, units, **kwds):
#--------------------------------------
BSMLSignal.__init__(self, uri, units, **kwds)
self._h5 = None
def __len__(self):
#-----------------
"""
Get the number of data points in a signal.
"""
return len(self._h5) if self._h5 is not None else 0
def _set_h5_signal(self, h5):
#----------------------------
self._h5 = h5
if h5.clock:
self.clock = Clock(h5.clock.uri,
h5.clock.times,
units=h5.clock.units)
elif h5.rate:
self.clock = UniformClock(None, h5.rate, units=h5.clock.units)
@classmethod
def create_from_H5Signal(cls, index, signal):
#--------------------------------------------
"""
Create a new signal from a signal dataset in a
BioSignalML HDF5 file.
"""
self = cls(signal.uri,
signal.units,
rate=signal.rate,
clock=signal.clock)
self._set_h5_signal(signal)
return self
def read(self,
interval=None,
segment=None,
maxduration=None,
maxpoints=None):
#-----------------------------------------------------------------------------
"""
Read data from a signal.
:param interval: The portion of the signal to read.
:type interval: :class:`~biosignaml.time.Interval`
:param segment: A 2-tuple with start and finishing data indices, with the end
point not included in the returned range.
:param maxduration: The maximum duration, in seconds, of a single returned segment.
:param maxpoints: The maximum length, in samples, of a single returned segment.
:return: An `iterator` returning :class:`~biosignalml.data.DataSegment` segments
of the signal data.
If both ``maxduration`` and ``maxpoints`` are given their minimum value is used.
"""
if interval is not None and segment is not None:
raise ValueError(
"'interval' and 'segment' cannot both be specified")
if maxduration:
pts = int(self.rate * maxduration + 0.5)
if maxpoints: maxpoints = min(maxpoints, pts)
else: maxpoints = pts
if maxpoints is None or not (0 < maxpoints <= BSMLSignal.MAXPOINTS):
maxpoints = BSMLSignal.MAXPOINTS
# We need to be consistent as to what an interval is....
# Use model.Interval ??
if interval is not None:
segment = (self.clock.index(interval.start),
self.clock.index(interval.end))
if segment is None:
startpos = 0
length = len(self)
else:
if segment[0] <= segment[1]: seg = segment
else: seg = (segment[1], segment[0])
##startpos = max(0, int(math.floor(seg[0])))
startpos = max(0, seg[0])
length = min(len(self), seg[1] + 1) - startpos
while length > 0:
if maxpoints > length: maxpoints = length
data = self._h5[startpos:startpos + maxpoints]
if isinstance(self.clock, UniformClock):
yield DataSegment(self.clock[startpos],
UniformTimeSeries(data, self.clock.rate))
else:
yield DataSegment(
0,
TimeSeries(data,
self.clock[startpos:startpos + maxpoints]))
startpos += len(data)
length -= len(data)
def initialise(self, **kwds):
#----------------------------
"""
Set signal attributes once the HDF5 file of its recording is opened.
Creates a signal dataset in the HDF5 file if it doesn't exist.
"""
if self.recording._h5 is not None:
rec_h5 = self.recording._h5
h5 = rec_h5.get_signal(self.uri)
if h5 is None and kwds.pop('create', False):
if self.clock:
rec_h5.create_clock(self.clock.uri)
kwds['clock'] = self.clock.uri
kwds['rate'] = getattr(self, 'rate', None)
h5 = rec_h5.create_signal(self.uri, self.units, **kwds)
if h5 is not None: self._set_h5_signal(h5)
def append(self, timeseries):
#----------------------------
'''
Append data to a signal.
:param timeseries: The data points (and times) to append.
:type timeseries: :class:`~biosignalml.data.TimeSeries`
'''
if self.clock and not isinstance(self.clock, UniformClock):
self.recording._h5.extend_clock(self.clock.uri,
timeseries.time.times)
self.recording._h5.extend_signal(self.uri, timeseries.data)
def extend(self, points):
#------------------------
'''
Append data points to a signal.
:param points: The data points to append.
:type points: :class:`numpy.ndarray` or an iterable.
'''
self.recording._h5.extend_signal(self.uri, points)
class HDF5Signal(BSMLSignal):
# ============================
"""
A :class:`~biosignalml.Signal` in a HDF5 Recording.
:param uri: The signal's URI.
:param units: The physical units of the signal's data.
:param kwds: Other :class:`~biosignalml.Signal` attributes to set.
"""
def __init__(self, uri, units, **kwds):
# --------------------------------------
BSMLSignal.__init__(self, uri, units, **kwds)
self._h5 = None
def __len__(self):
# -----------------
"""
Get the number of data points in a signal.
"""
return len(self._h5) if self._h5 is not None else 0
def _set_h5_signal(self, h5):
# ----------------------------
self._h5 = h5
if h5.clock:
self.clock = Clock(h5.clock.uri, h5.clock.times, units=h5.clock.units)
elif h5.rate:
self.clock = UniformClock(None, h5.rate, units=h5.clock.units)
@classmethod
def create_from_H5Signal(cls, index, signal):
# --------------------------------------------
"""
Create a new signal from a signal dataset in a
BioSignalML HDF5 file.
"""
self = cls(signal.uri, signal.units, rate=signal.rate, clock=signal.clock)
self._set_h5_signal(signal)
return self
def read(self, interval=None, segment=None, maxduration=None, maxpoints=None):
# -----------------------------------------------------------------------------
"""
Read data from a signal.
:param interval: The portion of the signal to read.
:type interval: :class:`~biosignaml.time.Interval`
:param segment: A 2-tuple with start and finishing data indices, with the end
point not included in the returned range.
:param maxduration: The maximum duration, in seconds, of a single returned segment.
:param maxpoints: The maximum length, in samples, of a single returned segment.
:return: An `iterator` returning :class:`~biosignalml.data.DataSegment` segments
of the signal data.
If both ``maxduration`` and ``maxpoints`` are given their minimum value is used.
"""
if interval is not None and segment is not None:
raise ValueError("'interval' and 'segment' cannot both be specified")
if maxduration:
pts = int(self.rate * maxduration + 0.5)
if maxpoints:
maxpoints = min(maxpoints, pts)
else:
maxpoints = pts
if maxpoints is None or not (0 < maxpoints <= BSMLSignal.MAXPOINTS):
maxpoints = BSMLSignal.MAXPOINTS
# We need to be consistent as to what an interval is....
# Use model.Interval ??
if interval is not None:
segment = (self.clock.index(interval.start), self.clock.index(interval.end))
if segment is None:
startpos = 0
length = len(self)
else:
if segment[0] <= segment[1]:
seg = segment
else:
seg = (segment[1], segment[0])
##startpos = max(0, int(math.floor(seg[0])))
startpos = max(0, seg[0])
length = min(len(self), seg[1] + 1) - startpos
while length > 0:
if maxpoints > length:
maxpoints = length
data = self._h5[startpos : startpos + maxpoints]
if isinstance(self.clock, UniformClock):
yield DataSegment(self.clock[startpos], UniformTimeSeries(data, self.clock.rate))
else:
yield DataSegment(0, TimeSeries(data, self.clock[startpos : startpos + maxpoints]))
startpos += len(data)
length -= len(data)
def initialise(self, **kwds):
# ----------------------------
"""
Set signal attributes once the HDF5 file of its recording is opened.
Creates a signal dataset in the HDF5 file if it doesn't exist.
"""
if self.recording._h5 is not None:
rec_h5 = self.recording._h5
h5 = rec_h5.get_signal(self.uri)
if h5 is None and kwds.pop("create", False):
if self.clock:
rec_h5.create_clock(self.clock.uri)
kwds["clock"] = self.clock.uri
kwds["rate"] = getattr(self, "rate", None)
h5 = rec_h5.create_signal(self.uri, self.units, **kwds)
if h5 is not None:
self._set_h5_signal(h5)
def append(self, timeseries):
# ----------------------------
"""
Append data to a signal.
:param timeseries: The data points (and times) to append.
:type timeseries: :class:`~biosignalml.data.TimeSeries`
"""
if self.clock and not isinstance(self.clock, UniformClock):
self.recording._h5.extend_clock(self.clock.uri, timeseries.time.times)
self.recording._h5.extend_signal(self.uri, timeseries.data)
def extend(self, points):
# ------------------------
"""
Append data points to a signal.
:param points: The data points to append.
:type points: :class:`numpy.ndarray` or an iterable.
"""
self.recording._h5.extend_signal(self.uri, points)
