def __init__(self, uri, **kwds): #------------------------------- from biosignalml.data.time import RelativeTimeLine ## Otherwise circular import... super(Recording, self).__init__(uri, **kwds) self.timeline = RelativeTimeLine(str(uri) + '/timeline') self._resources = OrderedDict()
class Recording(AbstractObject):
#===============================
"""
An abstract BioSignalML Recording.
:param uri: The URI of the recording.
:param kwds: Recording attributes, specified as keywords.
"""
metaclass = BSML.Recording #: :attr:`.BSML.Recording`
attributes = [ 'dataset', 'source', 'format', 'comment', 'investigation',
'starttime', 'duration', 'timeline', 'generatedBy'
] #: Generic attributes of a Recording.
mapping = { 'format': PropertyMap(DCT.format),
'dataset': PropertyMap(BSML.dataset),
'source': PropertyMap(DCT.source, functional=False),
'investigation': PropertyMap(DCT.subject),
'investigator': PropertyMap(DCT.creator),
'starttime': PropertyMap(DCT.created, XSD.dateTime,
utils.datetime_to_isoformat,
utils.isoformat_to_datetime),
'duration': PropertyMap(DCT.extent, XSD.dayTimeDuration,
utils.seconds_to_isoduration,
utils.isoduration_to_seconds),
## 'digest': PropertyMap(BSML.digest),
'timeline': PropertyMap(TL.timeline,
to_rdf=PropertyMap.get_uri,
from_rdf=_get_timeline, subelement=True),
'generatedBy': PropertyMap(PROV.wasGeneratedBy, to_rdf=PropertyMap.get_uri,
subelement=True),
}
SignalClass = Signal #: The class of :class:`~.signal.Signal`\s in the Recording
EventClass = Event #: The class of :class:`~.event.Event`\s in the Recording
def __init__(self, uri, **kwds):
#-------------------------------
from biosignalml.data.time import RelativeTimeLine ## Otherwise circular import...
super(Recording, self).__init__(uri, **kwds)
self.timeline = RelativeTimeLine(str(uri) + '/timeline')
self._resources = OrderedDict()
def resources(self, cls):
#-------------------------
"""
The recording's resources of a given class, as a list.
"""
return [ r for r in self._resources.values() if isinstance(r, cls) ]
def add_resource(self, resource):
#--------------------------------
"""Associate a resource with a Recording."""
self._resources[str(resource.uri)] = resource
return resource
def remove_resource(self, uri):
#------------------------------
"""Remove a resource from a Recording."""
return self._resources.pop(str(uri), None)
def get_resource(self, uri):
#---------------------------
"""
Get a resource associated with the Recording.
:param uri: The resource's URI.
"""
return self._resources.get(str(uri))
def __len__(self):
#-----------------
return len(self.signals())
def signals(self):
#-----------------
"""
The recording's signals as a list.
"""
return self.resources(Signal)
def get_signal(self, uri):
#-------------------------
"""
Retrieve a :class:`~.signal.Signal` from a Recording.
:param uri: The URI of the signal.
:return: A signal in the recording.
"""
signal = self.get_resource(uri)
if not isinstance(signal, self.SignalClass):
raise KeyError, str(uri)
return signal
def add_signal(self, signal):
#----------------------------
"""
Add a :class:`~.signal.Signal` to a Recording.
:param signal: The signal to add to the recording.
"""
sig_uri = str(signal.uri)
try:
self.get_signal(sig_uri)
raise Exception, "Signal '%s' already in recording" % sig_uri
except KeyError:
pass
if signal.recording is not None: ## Set from RDF mapping...
if isinstance(signal.recording, Recording): rec_uri = signal.recording.uri
else: rec_uri = signal.recording
if str(rec_uri) != str(self.uri):
raise Exception, "Adding to '%s', but signal '%s' is in '%s'" % (self.uri, sig_uri, rec_uri)
signal.recording = self
self.add_resource(signal)
return signal
def new_signal(self, uri, units, id=None, **kwds):
#-------------------------------------------------
"""
Create a new Signal and add it to the Recording.
:param uri: The URI for the signal.
:param units: The units signal data values are in.
:return: A Signal of type :attr:`SignalClass`.
"""
if uri is None and id is None:
raise Exception, "Signal must have 'uri' or 'id' specified"
if uri is None:
uri = str(self.uri) + '/signal/%s' % str(id)
try:
self.get_signal(uri)
raise Exception, "Signal '%s' already in recording" % uri
except KeyError:
pass
signal = self.SignalClass(uri, units, **kwds)
signal.recording = self
self.add_resource(signal)
return signal
def events(self):
#-----------------
"""
The recording's events as a list.
"""
return self.resources(Event)
def get_event(self, uri):
#------------------------
"""
Retrieve an :class:`~.event.Event` from a Recording.
:param uri: The URI of the event.
:return: An event in the recording.
"""
event = self.get_resource(uri)
if event is None:
event = Event.create_from_graph(uri, self.graph) ## graphstore ??
if self.uri != event.recording.uri:
raise KeyError, "Event <%s> doesn't refer to recording" % uri
self.add_event(event)
elif not isinstance(event, self.EventClass):
raise KeyError, "<%s> isn't an Event" % uri
return event
def add_event(self, event):
#--------------------------
"""
Add an :class:`~.event.Event` to a Recording.
:param event: The event to add to the recording.
"""
event.recording = self
self.add_resource(event)
return event
def new_event(self, uri, etype, at, duration=None, end=None, **kwds):
#--------------------------------------------------------------------
"""
Create a new Event and add it to the Recording.
:return: An Event of type :attr:`EventClass`.
"""
return self.add_event(self.EventClass(uri, etype, self.interval(at, duration, end), **kwds))
def instant(self, when):
#----------------------
"""
Create an :class:`.Instant` on the recording's timeline.
"""
return self.timeline.instant(when)
def interval(self, start, duration=None, end=None):
#--------------------------------------------------
"""
Create an :class:`.Interval` on the recording's timeline.
"""
return self.timeline.interval(start, duration, end=end)
## Or create urn:uuid URIs ??
def new_segment(self, uri, at, duration=None, end=None, **kwds): ## Of a Recording
#---------------------------------------------------------------
"""
Create a new :class:`~.segment.Segment` of a Recording.
:param uri: The URI of the Segment.
:param float at: When the segment starts.
:param float duration: The duration of the Segment. Optional.
:param float duration: When the Segment ends. Optional.
:param kwds: Optional additional attributes for the Segment.
"""
return self.add_resource(Segment(uri, self, self.interval(at, duration, end), **kwds))
def save_metadata_to_graph(self, graph):
#---------------------------------------
"""
Add a Recording's metadata to a RDF graph.
:param graph: A RDF graph.
:type graph: :class:`~biosignalml.rdf.Graph`
"""
super(Recording, self).save_metadata_to_graph(graph)
for resource in self._resources.values():
resource.save_metadata_to_graph(graph)
@classmethod
def create_from_graph(cls, uri, graph, signals=True, **kwds):
#------------------------------------------------------------
"""
Create a new instance of a Recording, setting attributes from RDF triples in a graph.
:param uri: The URI for the Recording.
:param graph: A RDF graph.
:type graph: :class:`~biosignalml.rdf.Graph`
:type signals: Set False to not load the Recording's Signals.
:rtype: :class:`Recording`
"""
self = super(Recording, cls).create_from_graph(uri, graph, **kwds)
if signals:
for r in graph.query("select ?s where { ?s a <%s> . ?s <%s> <%s> } order by ?s"
% (BSML.Signal, BSML.recording, self.uri)):
self.add_signal(self.SignalClass.create_from_graph(str(r['s']), graph, units=None))
# Do we load events? There may be a lot of them...
return self
class Recording(AbstractObject):
#===============================
"""
An abstract BioSignalML Recording.
:param uri: The URI of the recording.
:param kwds: Recording attributes, specified as keywords.
"""
metaclass = BSML.Recording #: :attr:`.BSML.Recording`
attributes = [
'dataset', 'source', 'format', 'comment', 'investigation', 'starttime',
'duration', 'timeline', 'generatedBy'
] #: Generic attributes of a Recording.
mapping = {
'format':
PropertyMap(DCT.format),
'dataset':
PropertyMap(BSML.dataset),
'source':
PropertyMap(DCT.source, functional=False),
'investigation':
PropertyMap(DCT.subject),
'investigator':
PropertyMap(DCT.creator),
'starttime':
PropertyMap(DCT.created, XSD.dateTime, utils.datetime_to_isoformat,
utils.isoformat_to_datetime),
'duration':
PropertyMap(DCT.extent, XSD.dayTimeDuration,
utils.seconds_to_isoduration,
utils.isoduration_to_seconds),
## 'digest': PropertyMap(BSML.digest),
'timeline':
PropertyMap(TL.timeline,
to_rdf=PropertyMap.get_uri,
from_rdf=_get_timeline,
subelement=True),
'generatedBy':
PropertyMap(PROV.wasGeneratedBy,
to_rdf=PropertyMap.get_uri,
subelement=True),
}
SignalClass = Signal #: The class of :class:`~.signal.Signal`\s in the Recording
EventClass = Event #: The class of :class:`~.event.Event`\s in the Recording
def __init__(self, uri, **kwds):
#-------------------------------
from biosignalml.data.time import RelativeTimeLine ## Otherwise circular import...
super(Recording, self).__init__(uri, **kwds)
self.timeline = RelativeTimeLine(str(uri) + '/timeline')
self._resources = OrderedDict()
def resources(self, cls):
#-------------------------
"""
The recording's resources of a given class, as a list.
"""
return [r for r in self._resources.values() if isinstance(r, cls)]
def add_resource(self, resource):
#--------------------------------
"""Associate a resource with a Recording."""
self._resources[str(resource.uri)] = resource
return resource
def remove_resource(self, uri):
#------------------------------
"""Remove a resource from a Recording."""
return self._resources.pop(str(uri), None)
def get_resource(self, uri):
#---------------------------
"""
Get a resource associated with the Recording.
:param uri: The resource's URI.
"""
return self._resources.get(str(uri))
def __len__(self):
#-----------------
return len(self.signals())
def signals(self):
#-----------------
"""
The recording's signals as a list.
"""
return self.resources(Signal)
def get_signal(self, uri):
#-------------------------
"""
Retrieve a :class:`~.signal.Signal` from a Recording.
:param uri: The URI of the signal.
:return: A signal in the recording.
"""
signal = self.get_resource(uri)
if not isinstance(signal, self.SignalClass):
raise KeyError, str(uri)
return signal
def add_signal(self, signal):
#----------------------------
"""
Add a :class:`~.signal.Signal` to a Recording.
:param signal: The signal to add to the recording.
"""
sig_uri = str(signal.uri)
try:
self.get_signal(sig_uri)
raise Exception, "Signal '%s' already in recording" % sig_uri
except KeyError:
pass
if signal.recording is not None: ## Set from RDF mapping...
if isinstance(signal.recording, Recording):
rec_uri = signal.recording.uri
else:
rec_uri = signal.recording
if str(rec_uri) != str(self.uri):
raise Exception, "Adding to '%s', but signal '%s' is in '%s'" % (
self.uri, sig_uri, rec_uri)
signal.recording = self
self.add_resource(signal)
return signal
def new_signal(self, uri, units, id=None, **kwds):
#-------------------------------------------------
"""
Create a new Signal and add it to the Recording.
:param uri: The URI for the signal.
:param units: The units signal data values are in.
:return: A Signal of type :attr:`SignalClass`.
"""
if uri is None and id is None:
raise Exception, "Signal must have 'uri' or 'id' specified"
if uri is None:
uri = str(self.uri) + '/signal/%s' % str(id)
try:
self.get_signal(uri)
raise Exception, "Signal '%s' already in recording" % uri
except KeyError:
pass
signal = self.SignalClass(uri, units, **kwds)
signal.recording = self
self.add_resource(signal)
return signal
def events(self):
#-----------------
"""
The recording's events as a list.
"""
return self.resources(Event)
def get_event(self, uri):
#------------------------
"""
Retrieve an :class:`~.event.Event` from a Recording.
:param uri: The URI of the event.
:return: An event in the recording.
"""
event = self.get_resource(uri)
if event is None:
event = Event.create_from_graph(uri, self.graph) ## graphstore ??
if self.uri != event.recording.uri:
raise KeyError, "Event <%s> doesn't refer to recording" % uri
self.add_event(event)
elif not isinstance(event, self.EventClass):
raise KeyError, "<%s> isn't an Event" % uri
return event
def add_event(self, event):
#--------------------------
"""
Add an :class:`~.event.Event` to a Recording.
:param event: The event to add to the recording.
"""
event.recording = self
self.add_resource(event)
return event
def new_event(self, uri, etype, at, duration=None, end=None, **kwds):
#--------------------------------------------------------------------
"""
Create a new Event and add it to the Recording.
:return: An Event of type :attr:`EventClass`.
"""
return self.add_event(
self.EventClass(uri, etype, self.interval(at, duration, end),
**kwds))
def instant(self, when):
#----------------------
"""
Create an :class:`.Instant` on the recording's timeline.
"""
return self.timeline.instant(when)
def interval(self, start, duration=None, end=None):
#--------------------------------------------------
"""
Create an :class:`.Interval` on the recording's timeline.
"""
return self.timeline.interval(start, duration, end=end)
## Or create urn:uuid URIs ??
def new_segment(self,
uri,
at,
duration=None,
end=None,
**kwds): ## Of a Recording
#---------------------------------------------------------------
"""
Create a new :class:`~.segment.Segment` of a Recording.
:param uri: The URI of the Segment.
:param float at: When the segment starts.
:param float duration: The duration of the Segment. Optional.
:param float duration: When the Segment ends. Optional.
:param kwds: Optional additional attributes for the Segment.
"""
return self.add_resource(
Segment(uri, self, self.interval(at, duration, end), **kwds))
def save_metadata_to_graph(self, graph):
#---------------------------------------
"""
Add a Recording's metadata to a RDF graph.
:param graph: A RDF graph.
:type graph: :class:`~biosignalml.rdf.Graph`
"""
super(Recording, self).save_metadata_to_graph(graph)
for resource in self._resources.values():
resource.save_metadata_to_graph(graph)
@classmethod
def create_from_graph(cls, uri, graph, signals=True, **kwds):
#------------------------------------------------------------
"""
Create a new instance of a Recording, setting attributes from RDF triples in a graph.
:param uri: The URI for the Recording.
:param graph: A RDF graph.
:type graph: :class:`~biosignalml.rdf.Graph`
:type signals: Set False to not load the Recording's Signals.
:rtype: :class:`Recording`
"""
self = super(Recording, cls).create_from_graph(uri, graph, **kwds)
if signals:
for r in graph.query(
"select ?s where { ?s a <%s> . ?s <%s> <%s> } order by ?s"
% (BSML.Signal, BSML.recording, self.uri)):
self.add_signal(
self.SignalClass.create_from_graph(str(r['s']),
graph,
units=None))
# Do we load events? There may be a lot of them...
return self
def __init__(self, uri, **kwds):
#-------------------------------
from biosignalml.data.time import RelativeTimeLine ## Otherwise circular import...
super(Recording, self).__init__(uri, **kwds)
self.timeline = RelativeTimeLine(str(uri) + '/timeline')
self._resources = OrderedDict()
def _get_timeline(tl): # Stops a circular import
#--------------------
from biosignalml.data.time import RelativeTimeLine
return RelativeTimeLine(tl)