def _get_tracking(self, channel, conversion):
if channel is not None:
eva = Event()
ttls = self._kwe['event_types']['TTL']['events'][
'time_samples'].value
event_channels = self._kwe['event_types']['TTL']['events'][
'user_data']['event_channels'].value
event_id = self._kwe['event_types']['TTL']['events']['user_data'][
'eventID'].value
eva.times = (ttls[(event_channels == channel) & (event_id == 1)] /
self._attrs['kwe']['sample_rate']) * pq.s
eva.name = 'TrackingTTL'
posdata = self._kwe['event_types']['Binary_messages']['events'][
'user_data']['Data'].value
node_id = self._kwe['event_types']['Binary_messages']['events'][
'user_data']['nodeID'].value
time_samples = self._kwe['event_types']['Binary_messages']['events'][
'time_samples'].value
sigs = []
for node in self._nodes['OSC Port']:
irsig = IrregularlySampledSignal(
signal=posdata[node_id == int(node['NodeId'])] * conversion *
pq.m,
times=(time_samples[node_id == int(node['NodeId'])] /
self._attrs['kwe']['sample_rate']) * pq.s,
name=node['address'])
sigs += [irsig]
if channel is not None:
return eva, sigs
else:
return sigs
def read_segment(self, import_neuroshare_segment = True,
lazy=False, cascade=True):
"""
Arguments:
import_neuroshare_segment: import neuroshare segment as SpikeTrain with associated waveforms or not imported at all.
"""
seg = Segment( file_origin = os.path.basename(self.filename), )
if sys.platform.startswith('win'):
neuroshare = ctypes.windll.LoadLibrary(self.dllname)
elif sys.platform.startswith('linux'):
neuroshare = ctypes.cdll.LoadLibrary(self.dllname)
neuroshare = DllWithError(neuroshare)
#elif sys.platform.startswith('darwin'):
# API version
info = ns_LIBRARYINFO()
neuroshare.ns_GetLibraryInfo(ctypes.byref(info) , ctypes.sizeof(info))
seg.annotate(neuroshare_version = str(info.dwAPIVersionMaj)+'.'+str(info.dwAPIVersionMin))
if not cascade:
return seg
# open file
hFile = ctypes.c_uint32(0)
neuroshare.ns_OpenFile(ctypes.c_char_p(self.filename) ,ctypes.byref(hFile))
fileinfo = ns_FILEINFO()
neuroshare.ns_GetFileInfo(hFile, ctypes.byref(fileinfo) , ctypes.sizeof(fileinfo))
# read all entities
for dwEntityID in range(fileinfo.dwEntityCount):
entityInfo = ns_ENTITYINFO()
neuroshare.ns_GetEntityInfo( hFile, dwEntityID, ctypes.byref(entityInfo), ctypes.sizeof(entityInfo))
# EVENT
if entity_types[entityInfo.dwEntityType] == 'ns_ENTITY_EVENT':
pEventInfo = ns_EVENTINFO()
neuroshare.ns_GetEventInfo ( hFile, dwEntityID, ctypes.byref(pEventInfo), ctypes.sizeof(pEventInfo))
if pEventInfo.dwEventType == 0: #TEXT
pData = ctypes.create_string_buffer(pEventInfo.dwMaxDataLength)
elif pEventInfo.dwEventType == 1:#CVS
pData = ctypes.create_string_buffer(pEventInfo.dwMaxDataLength)
elif pEventInfo.dwEventType == 2:# 8bit
pData = ctypes.c_byte(0)
elif pEventInfo.dwEventType == 3:# 16bit
pData = ctypes.c_int16(0)
elif pEventInfo.dwEventType == 4:# 32bit
pData = ctypes.c_int32(0)
pdTimeStamp = ctypes.c_double(0.)
pdwDataRetSize = ctypes.c_uint32(0)
ea = Event(name = str(entityInfo.szEntityLabel),)
if not lazy:
times = [ ]
labels = [ ]
for dwIndex in range(entityInfo.dwItemCount ):
neuroshare.ns_GetEventData ( hFile, dwEntityID, dwIndex,
ctypes.byref(pdTimeStamp), ctypes.byref(pData),
ctypes.sizeof(pData), ctypes.byref(pdwDataRetSize) )
times.append(pdTimeStamp.value)
labels.append(str(pData.value))
ea.times = times*pq.s
ea.labels = np.array(labels, dtype ='S')
else :
ea.lazy_shape = entityInfo.dwItemCount
seg.eventarrays.append(ea)
# analog
if entity_types[entityInfo.dwEntityType] == 'ns_ENTITY_ANALOG':
pAnalogInfo = ns_ANALOGINFO()
neuroshare.ns_GetAnalogInfo( hFile, dwEntityID,ctypes.byref(pAnalogInfo),ctypes.sizeof(pAnalogInfo) )
dwIndexCount = entityInfo.dwItemCount
if lazy:
signal = [ ]*pq.Quantity(1, pAnalogInfo.szUnits)
else:
pdwContCount = ctypes.c_uint32(0)
pData = np.zeros( (entityInfo.dwItemCount,), dtype = 'float64')
total_read = 0
while total_read< entityInfo.dwItemCount:
dwStartIndex = ctypes.c_uint32(total_read)
dwStopIndex = ctypes.c_uint32(entityInfo.dwItemCount - total_read)
neuroshare.ns_GetAnalogData( hFile, dwEntityID, dwStartIndex,
dwStopIndex, ctypes.byref( pdwContCount) , pData[total_read:].ctypes.data_as(ctypes.POINTER(ctypes.c_double)))
total_read += pdwContCount.value
signal = pq.Quantity(pData, units=pAnalogInfo.szUnits, copy = False)
#t_start
dwIndex = 0
pdTime = ctypes.c_double(0)
neuroshare.ns_GetTimeByIndex( hFile, dwEntityID, dwIndex, ctypes.byref(pdTime))
anaSig = AnalogSignal(signal,
sampling_rate = pAnalogInfo.dSampleRate*pq.Hz,
t_start = pdTime.value * pq.s,
name = str(entityInfo.szEntityLabel),
)
anaSig.annotate( probe_info = str(pAnalogInfo.szProbeInfo))
if lazy:
anaSig.lazy_shape = entityInfo.dwItemCount
seg.analogsignals.append( anaSig )
#segment
if entity_types[entityInfo.dwEntityType] == 'ns_ENTITY_SEGMENT' and import_neuroshare_segment:
pdwSegmentInfo = ns_SEGMENTINFO()
if not str(entityInfo.szEntityLabel).startswith('spks'):
continue
neuroshare.ns_GetSegmentInfo( hFile, dwEntityID,
ctypes.byref(pdwSegmentInfo), ctypes.sizeof(pdwSegmentInfo) )
nsource = pdwSegmentInfo.dwSourceCount
pszMsgBuffer = ctypes.create_string_buffer(" "*256)
neuroshare.ns_GetLastErrorMsg(ctypes.byref(pszMsgBuffer), 256)
for dwSourceID in range(pdwSegmentInfo.dwSourceCount) :
pSourceInfo = ns_SEGSOURCEINFO()
neuroshare.ns_GetSegmentSourceInfo( hFile, dwEntityID, dwSourceID,
ctypes.byref(pSourceInfo), ctypes.sizeof(pSourceInfo) )
if lazy:
sptr = SpikeTrain(times, name = str(entityInfo.szEntityLabel), t_stop = 0.*pq.s)
sptr.lazy_shape = entityInfo.dwItemCount
else:
pdTimeStamp = ctypes.c_double(0.)
dwDataBufferSize = pdwSegmentInfo.dwMaxSampleCount*pdwSegmentInfo.dwSourceCount
pData = np.zeros( (dwDataBufferSize), dtype = 'float64')
pdwSampleCount = ctypes.c_uint32(0)
pdwUnitID= ctypes.c_uint32(0)
nsample = int(dwDataBufferSize)
times = np.empty( (entityInfo.dwItemCount), dtype = 'f')
waveforms = np.empty( (entityInfo.dwItemCount, nsource, nsample), dtype = 'f')
for dwIndex in range(entityInfo.dwItemCount ):
neuroshare.ns_GetSegmentData ( hFile, dwEntityID, dwIndex,
ctypes.byref(pdTimeStamp), pData.ctypes.data_as(ctypes.POINTER(ctypes.c_double)),
dwDataBufferSize * 8, ctypes.byref(pdwSampleCount),
ctypes.byref(pdwUnitID ) )
times[dwIndex] = pdTimeStamp.value
waveforms[dwIndex, :,:] = pData[:nsample*nsource].reshape(nsample ,nsource).transpose()
sptr = SpikeTrain(times = pq.Quantity(times, units = 's', copy = False),
t_stop = times.max(),
waveforms = pq.Quantity(waveforms, units = str(pdwSegmentInfo.szUnits), copy = False ),
left_sweep = nsample/2./float(pdwSegmentInfo.dSampleRate)*pq.s,
sampling_rate = float(pdwSegmentInfo.dSampleRate)*pq.Hz,
name = str(entityInfo.szEntityLabel),
)
seg.spiketrains.append(sptr)
# neuralevent
if entity_types[entityInfo.dwEntityType] == 'ns_ENTITY_NEURALEVENT':
pNeuralInfo = ns_NEURALINFO()
neuroshare.ns_GetNeuralInfo ( hFile, dwEntityID,
ctypes.byref(pNeuralInfo), ctypes.sizeof(pNeuralInfo))
if lazy:
times = [ ]*pq.s
t_stop = 0*pq.s
else:
pData = np.zeros( (entityInfo.dwItemCount,), dtype = 'float64')
dwStartIndex = 0
dwIndexCount = entityInfo.dwItemCount
neuroshare.ns_GetNeuralData( hFile, dwEntityID, dwStartIndex,
dwIndexCount, pData.ctypes.data_as(ctypes.POINTER(ctypes.c_double)))
times = pData*pq.s
t_stop = times.max()
sptr = SpikeTrain(times, t_stop =t_stop,
name = str(entityInfo.szEntityLabel),)
if lazy:
sptr.lazy_shape = entityInfo.dwItemCount
seg.spiketrains.append(sptr)
# close
neuroshare.ns_CloseFile(hFile)
seg.create_many_to_one_relationship()
return seg
def read_segment(self,
import_neuroshare_segment=True,
lazy=False,
cascade=True):
"""
Arguments:
import_neuroshare_segment: import neuroshare segment as SpikeTrain with associated waveforms or not imported at all.
"""
seg = Segment(file_origin=os.path.basename(self.filename), )
if sys.platform.startswith('win'):
neuroshare = ctypes.windll.LoadLibrary(self.dllname)
elif sys.platform.startswith('linux'):
neuroshare = ctypes.cdll.LoadLibrary(self.dllname)
neuroshare = DllWithError(neuroshare)
#elif sys.platform.startswith('darwin'):
# API version
info = ns_LIBRARYINFO()
neuroshare.ns_GetLibraryInfo(ctypes.byref(info), ctypes.sizeof(info))
seg.annotate(neuroshare_version=str(info.dwAPIVersionMaj) + '.' +
str(info.dwAPIVersionMin))
if not cascade:
return seg
# open file
hFile = ctypes.c_uint32(0)
neuroshare.ns_OpenFile(ctypes.c_char_p(self.filename),
ctypes.byref(hFile))
fileinfo = ns_FILEINFO()
neuroshare.ns_GetFileInfo(hFile, ctypes.byref(fileinfo),
ctypes.sizeof(fileinfo))
# read all entities
for dwEntityID in range(fileinfo.dwEntityCount):
entityInfo = ns_ENTITYINFO()
neuroshare.ns_GetEntityInfo(hFile, dwEntityID,
ctypes.byref(entityInfo),
ctypes.sizeof(entityInfo))
# EVENT
if entity_types[entityInfo.dwEntityType] == 'ns_ENTITY_EVENT':
pEventInfo = ns_EVENTINFO()
neuroshare.ns_GetEventInfo(hFile, dwEntityID,
ctypes.byref(pEventInfo),
ctypes.sizeof(pEventInfo))
if pEventInfo.dwEventType == 0: #TEXT
pData = ctypes.create_string_buffer(
pEventInfo.dwMaxDataLength)
elif pEventInfo.dwEventType == 1: #CVS
pData = ctypes.create_string_buffer(
pEventInfo.dwMaxDataLength)
elif pEventInfo.dwEventType == 2: # 8bit
pData = ctypes.c_byte(0)
elif pEventInfo.dwEventType == 3: # 16bit
pData = ctypes.c_int16(0)
elif pEventInfo.dwEventType == 4: # 32bit
pData = ctypes.c_int32(0)
pdTimeStamp = ctypes.c_double(0.)
pdwDataRetSize = ctypes.c_uint32(0)
ea = Event(name=str(entityInfo.szEntityLabel), )
if not lazy:
times = []
labels = []
for dwIndex in range(entityInfo.dwItemCount):
neuroshare.ns_GetEventData(
hFile, dwEntityID, dwIndex,
ctypes.byref(pdTimeStamp), ctypes.byref(pData),
ctypes.sizeof(pData), ctypes.byref(pdwDataRetSize))
times.append(pdTimeStamp.value)
labels.append(str(pData.value))
ea.times = times * pq.s
ea.labels = np.array(labels, dtype='S')
else:
ea.lazy_shape = entityInfo.dwItemCount
seg.eventarrays.append(ea)
# analog
if entity_types[entityInfo.dwEntityType] == 'ns_ENTITY_ANALOG':
pAnalogInfo = ns_ANALOGINFO()
neuroshare.ns_GetAnalogInfo(hFile, dwEntityID,
ctypes.byref(pAnalogInfo),
ctypes.sizeof(pAnalogInfo))
dwIndexCount = entityInfo.dwItemCount
if lazy:
signal = [] * pq.Quantity(1, pAnalogInfo.szUnits)
else:
pdwContCount = ctypes.c_uint32(0)
pData = np.zeros((entityInfo.dwItemCount, ),
dtype='float64')
total_read = 0
while total_read < entityInfo.dwItemCount:
dwStartIndex = ctypes.c_uint32(total_read)
dwStopIndex = ctypes.c_uint32(entityInfo.dwItemCount -
total_read)
neuroshare.ns_GetAnalogData(
hFile, dwEntityID, dwStartIndex, dwStopIndex,
ctypes.byref(pdwContCount),
pData[total_read:].ctypes.data_as(
ctypes.POINTER(ctypes.c_double)))
total_read += pdwContCount.value
signal = pq.Quantity(pData,
units=pAnalogInfo.szUnits,
copy=False)
#t_start
dwIndex = 0
pdTime = ctypes.c_double(0)
neuroshare.ns_GetTimeByIndex(hFile, dwEntityID, dwIndex,
ctypes.byref(pdTime))
anaSig = AnalogSignal(
signal,
sampling_rate=pAnalogInfo.dSampleRate * pq.Hz,
t_start=pdTime.value * pq.s,
name=str(entityInfo.szEntityLabel),
)
anaSig.annotate(probe_info=str(pAnalogInfo.szProbeInfo))
if lazy:
anaSig.lazy_shape = entityInfo.dwItemCount
seg.analogsignals.append(anaSig)
#segment
if entity_types[
entityInfo.
dwEntityType] == 'ns_ENTITY_SEGMENT' and import_neuroshare_segment:
pdwSegmentInfo = ns_SEGMENTINFO()
if not str(entityInfo.szEntityLabel).startswith('spks'):
continue
neuroshare.ns_GetSegmentInfo(hFile, dwEntityID,
ctypes.byref(pdwSegmentInfo),
ctypes.sizeof(pdwSegmentInfo))
nsource = pdwSegmentInfo.dwSourceCount
pszMsgBuffer = ctypes.create_string_buffer(" " * 256)
neuroshare.ns_GetLastErrorMsg(ctypes.byref(pszMsgBuffer), 256)
for dwSourceID in range(pdwSegmentInfo.dwSourceCount):
pSourceInfo = ns_SEGSOURCEINFO()
neuroshare.ns_GetSegmentSourceInfo(
hFile, dwEntityID, dwSourceID,
ctypes.byref(pSourceInfo), ctypes.sizeof(pSourceInfo))
if lazy:
sptr = SpikeTrain(times,
name=str(entityInfo.szEntityLabel),
t_stop=0. * pq.s)
sptr.lazy_shape = entityInfo.dwItemCount
else:
pdTimeStamp = ctypes.c_double(0.)
dwDataBufferSize = pdwSegmentInfo.dwMaxSampleCount * pdwSegmentInfo.dwSourceCount
pData = np.zeros((dwDataBufferSize), dtype='float64')
pdwSampleCount = ctypes.c_uint32(0)
pdwUnitID = ctypes.c_uint32(0)
nsample = int(dwDataBufferSize)
times = np.empty((entityInfo.dwItemCount), dtype='f')
waveforms = np.empty(
(entityInfo.dwItemCount, nsource, nsample), dtype='f')
for dwIndex in range(entityInfo.dwItemCount):
neuroshare.ns_GetSegmentData(
hFile, dwEntityID, dwIndex,
ctypes.byref(pdTimeStamp),
pData.ctypes.data_as(
ctypes.POINTER(ctypes.c_double)),
dwDataBufferSize * 8, ctypes.byref(pdwSampleCount),
ctypes.byref(pdwUnitID))
times[dwIndex] = pdTimeStamp.value
waveforms[
dwIndex, :, :] = pData[:nsample * nsource].reshape(
nsample, nsource).transpose()
sptr = SpikeTrain(
times=pq.Quantity(times, units='s', copy=False),
t_stop=times.max(),
waveforms=pq.Quantity(waveforms,
units=str(
pdwSegmentInfo.szUnits),
copy=False),
left_sweep=nsample / 2. /
float(pdwSegmentInfo.dSampleRate) * pq.s,
sampling_rate=float(pdwSegmentInfo.dSampleRate) *
pq.Hz,
name=str(entityInfo.szEntityLabel),
)
seg.spiketrains.append(sptr)
# neuralevent
if entity_types[
entityInfo.dwEntityType] == 'ns_ENTITY_NEURALEVENT':
pNeuralInfo = ns_NEURALINFO()
neuroshare.ns_GetNeuralInfo(hFile, dwEntityID,
ctypes.byref(pNeuralInfo),
ctypes.sizeof(pNeuralInfo))
if lazy:
times = [] * pq.s
t_stop = 0 * pq.s
else:
pData = np.zeros((entityInfo.dwItemCount, ),
dtype='float64')
dwStartIndex = 0
dwIndexCount = entityInfo.dwItemCount
neuroshare.ns_GetNeuralData(
hFile, dwEntityID, dwStartIndex, dwIndexCount,
pData.ctypes.data_as(ctypes.POINTER(ctypes.c_double)))
times = pData * pq.s
t_stop = times.max()
sptr = SpikeTrain(
times,
t_stop=t_stop,
name=str(entityInfo.szEntityLabel),
)
if lazy:
sptr.lazy_shape = entityInfo.dwItemCount
seg.spiketrains.append(sptr)
# close
neuroshare.ns_CloseFile(hFile)
seg.create_many_to_one_relationship()
return seg