def __init__(self, uri, dataset=None, **kwds):
#---------------------------------------------
newfile = kwds.pop('create', False)
if uri is None and (newfile or dataset is None):
raise TypeError("No URI given for HDF5 recording")
if uri is not None:
BSMLRecording.__init__(self, uri, dataset, **kwds)
if dataset:
if newfile:
self._h5 = H5Recording.create(uri, str(dataset), **kwds)
self.graph = RecordingGraph(uri, rec_class=HDF5Recording)
else:
self._h5 = H5Recording.open(dataset, **kwds)
if uri is None:
BSMLRecording.__init__(self, self._h5.uri, dataset, **kwds)
elif str(uri) != str(self._h5.uri):
raise TypeError("Wrong URI in HDF5 recording")
self._load_metadata()
for n, s in enumerate(self._h5.signals()):
signal = HDF5Signal.create_from_H5Signal(n, s)
signal.add_metadata(self.graph)
signal.clock.add_metadata(
self.graph) ## We need to cache clocks in recording...
self.add_signal(signal)
else:
self._h5 = None
def __init__(self, uri, dataset=None, **kwds):
# ---------------------------------------------
newfile = kwds.pop("create", False)
if uri is None and (newfile or dataset is None):
raise TypeError("No URI given for HDF5 recording")
if uri is not None:
BSMLRecording.__init__(self, uri, dataset, **kwds)
if dataset:
if newfile:
self._h5 = H5Recording.create(uri, str(dataset), **kwds)
self.graph = RecordingGraph(uri, rec_class=HDF5Recording)
else:
self._h5 = H5Recording.open(dataset, **kwds)
if uri is None:
BSMLRecording.__init__(self, self._h5.uri, dataset, **kwds)
elif str(uri) != str(self._h5.uri):
raise TypeError("Wrong URI in HDF5 recording")
self._load_metadata()
for n, s in enumerate(self._h5.signals()):
signal = HDF5Signal.create_from_H5Signal(n, s)
signal.add_metadata(self.graph)
signal.clock.add_metadata(self.graph) ## We need to cache clocks in recording...
self.add_signal(signal)
else:
self._h5 = None
def _load_metadata(self):
# ------------------------
"""
Set metadata attributes of the recording from its associated
BioSignalML HDF5 file.
"""
string, format = self._h5.get_metadata()
if string:
self.graph = RecordingGraph.create_from_string(self.uri, string, format=format, rec_class=HDF5Recording)
self.add_metadata(self.graph)
else:
raise TypeError("No metadata in BioSignalML file")
def _load_metadata(self):
#------------------------
"""
Set metadata attributes of the recording from its associated
BioSignalML HDF5 file.
"""
string, format = self._h5.get_metadata()
if string:
self.graph = RecordingGraph.create_from_string(
self.uri, string, format=format, rec_class=HDF5Recording)
self.add_metadata(self.graph)
else:
raise TypeError("No metadata in BioSignalML file")
class HDF5Recording(BSMLRecording):
#==================================
"""
A HDF5 :class:`~biosignalml.Recording`.
:param uri: The recording's URI.
:param dataset: The file path or URI of the BioSignalML HDF5 file for the recording.
:param kwds: :class:`~biosignalml.Recording` attributes to set.
"""
MIMETYPE = MIMETYPES.HDF5 #: The mimetype for BioSignalML HDF5 files
EXTENSIONS = ['h5', 'hdf',
'hdf5'] #: File extensions to try when opening a file
SignalClass = HDF5Signal #: The class of Signals HDF5Recording
def __init__(self, uri, dataset=None, **kwds):
#---------------------------------------------
newfile = kwds.pop('create', False)
if uri is None and (newfile or dataset is None):
raise TypeError("No URI given for HDF5 recording")
if uri is not None:
BSMLRecording.__init__(self, uri, dataset, **kwds)
if dataset:
if newfile:
self._h5 = H5Recording.create(uri, str(dataset), **kwds)
self.graph = RecordingGraph(uri, rec_class=HDF5Recording)
else:
self._h5 = H5Recording.open(dataset, **kwds)
if uri is None:
BSMLRecording.__init__(self, self._h5.uri, dataset, **kwds)
elif str(uri) != str(self._h5.uri):
raise TypeError("Wrong URI in HDF5 recording")
self._load_metadata()
for n, s in enumerate(self._h5.signals()):
signal = HDF5Signal.create_from_H5Signal(n, s)
signal.add_metadata(self.graph)
signal.clock.add_metadata(
self.graph) ## We need to cache clocks in recording...
self.add_signal(signal)
else:
self._h5 = None
@classmethod
def open(cls, dataset, **kwds):
#------------------------------
"""
Open a BioSignalML HDF5 file to obtain a HDF5 Recording.
:param dataset: The file path or URI of the BioSignalML HDF5 file.
:param kwds: Other :class:`~biosignalml.Recording` attributes to set.
"""
return cls(None, dataset, **kwds)
@classmethod
def create(cls, uri, dataset, **kwds):
#-------------------------------------
"""
Create a new recording and its BioSignalML HDF5 file.
:param uri: The recording's URI.
:param dataset: The file path or URI of the BioSignalML HDF5 file.
:param kwds: Other :class:`~biosignalml.Recording` attributes to set.
"""
return cls(uri, dataset, create=True, **kwds)
### self.dataset = dataset ### Only set dataset in metadata when storing into a repository??
def close(self, prefixes=None):
#------------------------------
""" Close a recording`. """
if self._h5:
self._save_metadata(prefixes=prefixes)
self._h5.close()
self._h5 = None
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 physical units of the signal's data.
:rtype: :class:`HDF5Signal`
:param kwds: Other :class:`~biosignalml.Signal` attributes to set.
"""
sig = BSMLRecording.new_signal(self, uri, units, id=id, **kwds)
if self._h5:
if sig.clock:
self._h5.create_clock(sig.clock.uri,
sig.clock.units,
times=sig.clock.times)
kwds['clock'] = sig.clock.uri
sig._h5 = self._h5.create_signal(sig.uri, units, **kwds)
return sig
def _save_metadata(self, format=rdf.Format.TURTLE, prefixes=None):
#-----------------------------------------------------------------
"""
Save all metadata associated with the recording in its
BioSignalML HDF5 file.
:param format: The :class:`~biosignalml.rdf.Format` in which to serialise RDF.
:param prefixes: An optional dictionary of namespace abbreviations and URIs.
"""
self.save_metadata_to_graph(self.graph)
self._h5.store_metadata(
self.graph.serialise(format=format,
prefixes=prefixes,
base=self.uri), rdf.Format.mimetype(format))
def _load_metadata(self):
#------------------------
"""
Set metadata attributes of the recording from its associated
BioSignalML HDF5 file.
"""
string, format = self._h5.get_metadata()
if string:
self.graph = RecordingGraph.create_from_string(
self.uri, string, format=format, rec_class=HDF5Recording)
self.add_metadata(self.graph)
else:
raise TypeError("No metadata in BioSignalML file")
def initialise(self, **kwds):
#----------------------------
"""
Set recording and associated signal attributes
once the recording's dataset is known.
"""
if self.dataset is not None and kwds.pop('open_dataset', True):
dataset = str(self.dataset)
creating = kwds.pop('create', False)
try:
self._h5 = H5Recording.open(dataset, **kwds)
except IOError:
if not creating: raise
H5Recording.create(self.uri, dataset, **kwds)
self._h5 = H5Recording.open(dataset, **kwds)
if kwds.pop('create_signals', False): kwds['create'] = True
for s in self.signals():
HDF5Signal.initialise_class(s, **kwds)
def get_recording(self, uri, graph_uri=None, **kwds):
# ----------------------------------------------------
rgraph = RecordingGraph.create_from_store(self, uri, rec_class=self.RecordingClass)
return rgraph.get_recording(repository=self, **kwds)
def get_recording(self, uri, graph_uri=None, **kwds):
#----------------------------------------------------
rgraph = RecordingGraph.create_from_store(
self, uri, rec_class=self.RecordingClass)
return rgraph.get_recording(repository=self, **kwds)
class HDF5Recording(BSMLRecording):
# ==================================
"""
A HDF5 :class:`~biosignalml.Recording`.
:param uri: The recording's URI.
:param dataset: The file path or URI of the BioSignalML HDF5 file for the recording.
:param kwds: :class:`~biosignalml.Recording` attributes to set.
"""
MIMETYPE = MIMETYPES.HDF5 #: The mimetype for BioSignalML HDF5 files
EXTENSIONS = ["h5", "hdf", "hdf5"] #: File extensions to try when opening a file
SignalClass = HDF5Signal #: The class of Signals HDF5Recording
def __init__(self, uri, dataset=None, **kwds):
# ---------------------------------------------
newfile = kwds.pop("create", False)
if uri is None and (newfile or dataset is None):
raise TypeError("No URI given for HDF5 recording")
if uri is not None:
BSMLRecording.__init__(self, uri, dataset, **kwds)
if dataset:
if newfile:
self._h5 = H5Recording.create(uri, str(dataset), **kwds)
self.graph = RecordingGraph(uri, rec_class=HDF5Recording)
else:
self._h5 = H5Recording.open(dataset, **kwds)
if uri is None:
BSMLRecording.__init__(self, self._h5.uri, dataset, **kwds)
elif str(uri) != str(self._h5.uri):
raise TypeError("Wrong URI in HDF5 recording")
self._load_metadata()
for n, s in enumerate(self._h5.signals()):
signal = HDF5Signal.create_from_H5Signal(n, s)
signal.add_metadata(self.graph)
signal.clock.add_metadata(self.graph) ## We need to cache clocks in recording...
self.add_signal(signal)
else:
self._h5 = None
@classmethod
def open(cls, dataset, **kwds):
# ------------------------------
"""
Open a BioSignalML HDF5 file to obtain a HDF5 Recording.
:param dataset: The file path or URI of the BioSignalML HDF5 file.
:param kwds: Other :class:`~biosignalml.Recording` attributes to set.
"""
return cls(None, dataset, **kwds)
@classmethod
def create(cls, uri, dataset, **kwds):
# -------------------------------------
"""
Create a new recording and its BioSignalML HDF5 file.
:param uri: The recording's URI.
:param dataset: The file path or URI of the BioSignalML HDF5 file.
:param kwds: Other :class:`~biosignalml.Recording` attributes to set.
"""
return cls(uri, dataset, create=True, **kwds)
### self.dataset = dataset ### Only set dataset in metadata when storing into a repository??
def close(self, prefixes=None):
# ------------------------------
""" Close a recording`. """
if self._h5:
self._save_metadata(prefixes=prefixes)
self._h5.close()
self._h5 = None
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 physical units of the signal's data.
:rtype: :class:`HDF5Signal`
:param kwds: Other :class:`~biosignalml.Signal` attributes to set.
"""
sig = BSMLRecording.new_signal(self, uri, units, id=id, **kwds)
if self._h5:
if sig.clock:
self._h5.create_clock(sig.clock.uri, sig.clock.units, times=sig.clock.times)
kwds["clock"] = sig.clock.uri
sig._h5 = self._h5.create_signal(sig.uri, units, **kwds)
return sig
def _save_metadata(self, format=rdf.Format.TURTLE, prefixes=None):
# -----------------------------------------------------------------
"""
Save all metadata associated with the recording in its
BioSignalML HDF5 file.
:param format: The :class:`~biosignalml.rdf.Format` in which to serialise RDF.
:param prefixes: An optional dictionary of namespace abbreviations and URIs.
"""
self.save_metadata_to_graph(self.graph)
self._h5.store_metadata(
self.graph.serialise(format=format, prefixes=prefixes, base=self.uri), rdf.Format.mimetype(format)
)
def _load_metadata(self):
# ------------------------
"""
Set metadata attributes of the recording from its associated
BioSignalML HDF5 file.
"""
string, format = self._h5.get_metadata()
if string:
self.graph = RecordingGraph.create_from_string(self.uri, string, format=format, rec_class=HDF5Recording)
self.add_metadata(self.graph)
else:
raise TypeError("No metadata in BioSignalML file")
def initialise(self, **kwds):
# ----------------------------
"""
Set recording and associated signal attributes
once the recording's dataset is known.
"""
if self.dataset is not None and kwds.pop("open_dataset", True):
dataset = str(self.dataset)
creating = kwds.pop("create", False)
try:
self._h5 = H5Recording.open(dataset, **kwds)
except IOError:
if not creating:
raise
H5Recording.create(self.uri, dataset, **kwds)
self._h5 = H5Recording.open(dataset, **kwds)
if kwds.pop("create_signals", False):
kwds["create"] = True
for s in self.signals():
HDF5Signal.initialise_class(s, **kwds)
