def setup_recordingchannels(self):
params = {'testarg2': 'yes', 'testarg3': True}
self.rchan1 = RecordingChannel(index=10,
coordinate=[1.1, 1.5, 1.7] * pq.mm,
name='test',
description='tester 1',
file_origin='test.file',
testarg1=1,
**params)
self.rchan2 = RecordingChannel(index=100,
coordinate=[11., 15., 17.] * pq.mm,
name='test',
description='tester 2',
file_origin='test.file',
testarg1=1,
**params)
self.rchan1.annotate(testarg1=1.1, testarg0=[1, 2, 3])
self.rchan2.annotate(testarg11=1.1, testarg10=[1, 2, 3])
self.rchan1.analogsignals = self.sig1
self.rchan2.analogsignals = self.sig2
self.rchan1.irregularlysampledsignals = self.irsig1
self.rchan2.irregularlysampledsignals = self.irsig2
create_many_to_one_relationship(self.rchan1)
create_many_to_one_relationship(self.rchan2)
def read_segment(self, lazy=False, cascade=True):
data, metadata = self._read_file_contents()
annotations = dict(
(k, metadata.get(k, 'unknown'))
for k in ("label", "variable", "first_id", "last_id"))
seg = Segment(**annotations)
if cascade:
if metadata['variable'] == 'spikes':
for i in range(metadata['first_index'],
metadata['last_index']):
spiketrain = self._extract_spikes(data, metadata, i, lazy)
if spiketrain is not None:
seg.spiketrains.append(spiketrain)
seg.annotate(
dt=metadata['dt']
) # store dt for SpikeTrains only, as can be retrieved from sampling_period for AnalogSignal
else:
for i in range(metadata['first_index'],
metadata['last_index']):
# probably slow. Replace with numpy-based version from 0.1
signal = self._extract_signal(data, metadata, i, lazy)
if signal is not None:
seg.analogsignals.append(signal)
create_many_to_one_relationship(seg)
return seg
def setup_units(self):
params = {'testarg2': 'yes', 'testarg3': True}
self.unit1 = Unit(name='test',
description='tester 1',
file_origin='test.file',
channels_indexes=[1],
testarg1=1,
**params)
self.unit2 = Unit(name='test',
description='tester 2',
file_origin='test.file',
channels_indexes=[2],
testarg1=1,
**params)
self.unit1.annotate(testarg1=1.1, testarg0=[1, 2, 3])
self.unit2.annotate(testarg11=1.1, testarg10=[1, 2, 3])
self.unit1.spiketrains = self.train1
self.unit2.spiketrains = self.train2
self.unit1.spikes = self.spike1
self.unit2.spikes = self.spike2
create_many_to_one_relationship(self.unit1)
create_many_to_one_relationship(self.unit2)
def setup_units(self):
params = {'testarg2': 'yes', 'testarg3': True}
self.unit1 = Unit(name='test', description='tester 1',
file_origin='test.file',
channel_indexes=np.array([1]),
testarg1=1, **params)
self.unit2 = Unit(name='test', description='tester 2',
file_origin='test.file',
channel_indexes=np.array([2]),
testarg1=1, **params)
self.unit1.annotate(testarg1=1.1, testarg0=[1, 2, 3])
self.unit2.annotate(testarg11=1.1, testarg10=[1, 2, 3])
self.unit1train = [self.train1[0], self.train2[1]]
self.unit2train = [self.train1[1], self.train2[0]]
self.unit1.spiketrains = self.unit1train
self.unit2.spiketrains = self.unit2train
self.unit1spike = [self.spike1[0], self.spike2[1]]
self.unit2spike = [self.spike1[1], self.spike2[0]]
self.unit1.spikes = self.unit1spike
self.unit2.spikes = self.unit2spike
create_many_to_one_relationship(self.unit1)
create_many_to_one_relationship(self.unit2)
def read_segment(self,
lazy = False,
cascade = True,
group = 0,
series = 0):
seg = Segment( name = 'test')
if cascade:
tree = getbyroute(self.pul.tree,[0,group,series])
for sw,sweep in enumerate(tree['children']):
if sw == 0:
starttime = pq.Quantity(float(sweep['contents'].swTimer),'s')
for ch,channel in enumerate(sweep['children']):
sig = self.read_analogsignal(group=group,
series=series,
sweep=sw,
channel = ch)
annotations = sweep['contents'].__dict__.keys()
annotations.remove('readlist')
for a in annotations:
d = {a:str(sweep['contents'].__dict__[a])}
sig.annotate(**d)
sig.t_start = pq.Quantity(float(sig.annotations['swTimer']),'s') - starttime
seg.analogsignals.append(sig)
annotations = tree['contents'].__dict__.keys()
annotations.remove('readlist')
for a in annotations:
d = {a:str(tree['contents'].__dict__[a])}
seg.annotate(**d)
create_many_to_one_relationship(seg)
return seg
def proc_dam(filename):
'''Load an dam file that has already been processed by the official matlab
file converter. That matlab data is saved to an m-file, which is then
converted to a numpy '.npz' file. This numpy file is the file actually
loaded. This function converts it to a neo block and returns the block.
This block can be compared to the block produced by BrainwareDamIO to
make sure BrainwareDamIO is working properly
block = proc_dam(filename)
filename: The file name of the numpy file to load. It should end with
'*_dam_py?.npz'. This will be converted to a neo 'file_origin' property
with the value '*.dam', so the filename to compare should fit that pattern.
'py?' should be 'py2' for the python 2 version of the numpy file or 'py3'
for the python 3 version of the numpy file.
example: filename = 'file1_dam_py2.npz'
dam file name = 'file1.dam'
'''
with np.load(filename) as damobj:
damfile = damobj.items()[0][1].flatten()
filename = os.path.basename(filename[:-12]+'.dam')
signals = [res.flatten() for res in damfile['signal']]
stimIndexes = [int(res[0, 0].tolist()) for res in damfile['stimIndex']]
timestamps = [res[0, 0] for res in damfile['timestamp']]
block = Block(file_origin=filename)
rcg = RecordingChannelGroup(file_origin=filename)
chan = RecordingChannel(file_origin=filename, index=0, name='Chan1')
rcg.channel_indexes = np.array([1])
rcg.channel_names = np.array(['Chan1'], dtype='S')
block.recordingchannelgroups.append(rcg)
rcg.recordingchannels.append(chan)
params = [res['params'][0, 0].flatten() for res in damfile['stim']]
values = [res['values'][0, 0].flatten() for res in damfile['stim']]
params = [[res1[0] for res1 in res] for res in params]
values = [[res1 for res1 in res] for res in values]
stims = [dict(zip(param, value)) for param, value in zip(params, values)]
fulldam = zip(stimIndexes, timestamps, signals, stims)
for stimIndex, timestamp, signal, stim in fulldam:
sig = AnalogSignal(signal=signal*pq.mV,
t_start=timestamp*pq.d,
file_origin=filename,
sampling_period=1.*pq.s)
segment = Segment(file_origin=filename,
index=stimIndex,
**stim)
segment.analogsignals = [sig]
block.segments.append(segment)
create_many_to_one_relationship(block)
return block
def read_block(self, lazy=False, cascade=True, **kargs):
'''
Reads a block from the simple spike data file "fname" generated
with BrainWare
'''
# there are no keyargs implemented to so far. If someone tries to pass
# them they are expecting them to do something or making a mistake,
# neither of which should pass silently
if kargs:
raise NotImplementedError('This method does not have any '
'argument implemented yet')
self._fsrc = None
self.__lazy = lazy
self._blk = Block(file_origin=self._filename)
block = self._blk
# if we aren't doing cascade, don't load anything
if not cascade:
return block
# create the objects to store other objects
rcg = RecordingChannelGroup(file_origin=self._filename)
rcg.channel_indexes = np.array([], dtype=np.int)
rcg.channel_names = np.array([], dtype='S')
self.__unit = Unit(file_origin=self._filename)
# load objects into their containers
block.recordingchannelgroups.append(rcg)
rcg.units.append(self.__unit)
# initialize values
self.__t_stop = None
self.__params = None
self.__seg = None
self.__spiketimes = None
# open the file
with open(self._path, 'rb') as self._fsrc:
res = True
# while the file is not done keep reading segments
while res:
res = self.__read_id()
create_many_to_one_relationship(block)
# cleanup attributes
self._fsrc = None
self.__lazy = False
self._blk = None
self.__t_stop = None
self.__params = None
self.__seg = None
self.__spiketimes = None
return block
def _read_entity(self, path="/", cascade=True, lazy=False):
"""
Wrapper for base io "reader" functions.
"""
ob = self.get(path, cascade, lazy)
if cascade and cascade != 'lazy':
create_many_to_one_relationship(ob)
return ob
def read_block(self, lazy=False, cascade=True, **kargs):
'''
Reads a block from the simple spike data file "fname" generated
with BrainWare
'''
# there are no keyargs implemented to so far. If someone tries to pass
# them they are expecting them to do something or making a mistake,
# neither of which should pass silently
if kargs:
raise NotImplementedError('This method does not have any '
'argument implemented yet')
self._fsrc = None
self.__lazy = lazy
self._blk = Block(file_origin=self._filename)
block = self._blk
# if we aren't doing cascade, don't load anything
if not cascade:
return block
# create the objects to store other objects
rcg = RecordingChannelGroup(file_origin=self._filename)
self.__unit = Unit(file_origin=self._filename)
# load objects into their containers
block.recordingchannelgroups.append(rcg)
rcg.units.append(self.__unit)
# initialize values
self.__t_stop = None
self.__params = None
self.__seg = None
self.__spiketimes = None
# open the file
with open(self._path, 'rb') as self._fsrc:
res = True
# while the file is not done keep reading segments
while res:
res = self.__read_id()
create_many_to_one_relationship(block)
# cleanup attributes
self._fsrc = None
self.__lazy = False
self._blk = None
self.__t_stop = None
self.__params = None
self.__seg = None
self.__spiketimes = None
return block
def proc_dam(filename):
'''Load an dam file that has already been processed by the official matlab
file converter. That matlab data is saved to an m-file, which is then
converted to a numpy '.npz' file. This numpy file is the file actually
loaded. This function converts it to a neo block and returns the block.
This block can be compared to the block produced by BrainwareDamIO to
make sure BrainwareDamIO is working properly
block = proc_dam(filename)
filename: The file name of the numpy file to load. It should end with
'*_dam_py?.npz'. This will be converted to a neo 'file_origin' property
with the value '*.dam', so the filename to compare should fit that pattern.
'py?' should be 'py2' for the python 2 version of the numpy file or 'py3'
for the python 3 version of the numpy file.
example: filename = 'file1_dam_py2.npz'
dam file name = 'file1.dam'
'''
with np.load(filename) as damobj:
damfile = damobj.items()[0][1].flatten()
filename = os.path.basename(filename[:-12] + '.dam')
signals = [res.flatten() for res in damfile['signal']]
stimIndexes = [int(res[0, 0].tolist()) for res in damfile['stimIndex']]
timestamps = [res[0, 0] for res in damfile['timestamp']]
block = Block(file_origin=filename)
rcg = RecordingChannelGroup(file_origin=filename)
chan = RecordingChannel(file_origin=filename, index=0, name='Chan1')
rcg.channel_indexes = np.array([1])
rcg.channel_names = np.array(['Chan1'], dtype='S')
block.recordingchannelgroups.append(rcg)
rcg.recordingchannels.append(chan)
params = [res['params'][0, 0].flatten() for res in damfile['stim']]
values = [res['values'][0, 0].flatten() for res in damfile['stim']]
params = [[res1[0] for res1 in res] for res in params]
values = [[res1 for res1 in res] for res in values]
stims = [dict(zip(param, value)) for param, value in zip(params, values)]
fulldam = zip(stimIndexes, timestamps, signals, stims)
for stimIndex, timestamp, signal, stim in fulldam:
sig = AnalogSignal(signal=signal * pq.mV,
t_start=timestamp * pq.d,
file_origin=filename,
sampling_period=1. * pq.s)
segment = Segment(file_origin=filename, index=stimIndex, **stim)
segment.analogsignals = [sig]
block.segments.append(segment)
create_many_to_one_relationship(block)
return block
def proc_src(filename):
'''Load an src file that has already been processed by the official matlab
file converter. That matlab data is saved to an m-file, which is then
converted to a numpy '.npz' file. This numpy file is the file actually
loaded. This function converts it to a neo block and returns the block.
This block can be compared to the block produced by BrainwareSrcIO to
make sure BrainwareSrcIO is working properly
block = proc_src(filename)
filename: The file name of the numpy file to load. It should end with
'*_src_py?.npz'. This will be converted to a neo 'file_origin' property
with the value '*.src', so the filename to compare should fit that pattern.
'py?' should be 'py2' for the python 2 version of the numpy file or 'py3'
for the python 3 version of the numpy file.
example: filename = 'file1_src_py2.npz'
src file name = 'file1.src'
'''
with np.load(filename) as srcobj:
srcfile = srcobj.items()[0][1]
filename = os.path.basename(filename[:-12]+'.src')
block = Block(file_origin=filename)
NChannels = srcfile['NChannels'][0, 0][0, 0]
side = str(srcfile['side'][0, 0][0])
ADperiod = srcfile['ADperiod'][0, 0][0, 0]
comm_seg = proc_src_comments(srcfile, filename)
block.segments.append(comm_seg)
rcg = proc_src_units(srcfile, filename)
chan_nums = np.arange(NChannels, dtype='int')
chan_names = []
for i in chan_nums:
name = 'Chan'+str(i)
chan_names.append(name)
chan = RecordingChannel(file_origin='filename',
name=name,
index=i)
rcg.recordingchannels.append(chan)
rcg.channel_indexes = chan_nums
rcg.channel_names = np.array(chan_names, dtype='string_')
block.recordingchannelgroups.append(rcg)
for rep in srcfile['sets'][0, 0].flatten():
proc_src_condition(rep, filename, ADperiod, side, block)
create_many_to_one_relationship(block)
return block
def test_block_list_units(self):
blk = Block(name='a block')
blk.recordingchannelgroups = [self.rcg1, self.rcg2]
create_many_to_one_relationship(blk)
#assert_neo_object_is_compliant(blk)
unitres1 = [unit.name for unit in blk.recordingchannelgroups[0].units]
unitres2 = [unit.name for unit in blk.recordingchannelgroups[1].units]
unitres = [unit.name for unit in blk.list_units]
self.assertEqual(self.unitnames1, unitres1)
self.assertEqual(self.unitnames2, unitres2)
self.assertEqual(self.unitnames, unitres)
def proc_src(filename):
'''Load an src file that has already been processed by the official matlab
file converter. That matlab data is saved to an m-file, which is then
converted to a numpy '.npz' file. This numpy file is the file actually
loaded. This function converts it to a neo block and returns the block.
This block can be compared to the block produced by BrainwareSrcIO to
make sure BrainwareSrcIO is working properly
block = proc_src(filename)
filename: The file name of the numpy file to load. It should end with
'*_src_py?.npz'. This will be converted to a neo 'file_origin' property
with the value '*.src', so the filename to compare should fit that pattern.
'py?' should be 'py2' for the python 2 version of the numpy file or 'py3'
for the python 3 version of the numpy file.
example: filename = 'file1_src_py2.npz'
src file name = 'file1.src'
'''
with np.load(filename) as srcobj:
srcfile = srcobj.items()[0][1]
filename = os.path.basename(filename[:-12] + '.src')
block = Block(file_origin=filename)
NChannels = srcfile['NChannels'][0, 0][0, 0]
side = str(srcfile['side'][0, 0][0])
ADperiod = srcfile['ADperiod'][0, 0][0, 0]
comm_seg = proc_src_comments(srcfile, filename)
block.segments.append(comm_seg)
rcg = proc_src_units(srcfile, filename)
chan_nums = np.arange(NChannels, dtype='int')
chan_names = []
for i in chan_nums:
name = 'Chan' + str(i)
chan_names.append(name)
chan = RecordingChannel(file_origin='filename', name=name, index=i)
rcg.recordingchannels.append(chan)
rcg.channel_indexes = chan_nums
rcg.channel_names = np.array(chan_names, dtype='string_')
block.recordingchannelgroups.append(rcg)
for rep in srcfile['sets'][0, 0].flatten():
proc_src_condition(rep, filename, ADperiod, side, block)
create_many_to_one_relationship(block)
return block
def read_block(self, lazy=False, cascade=True, **kargs):
'''
Reads a block from the raw data file "fname" generated
with BrainWare
'''
# there are no keyargs implemented to so far. If someone tries to pass
# them they are expecting them to do something or making a mistake,
# neither of which should pass silently
if kargs:
raise NotImplementedError('This method does not have any '
'argument implemented yet')
self._fsrc = None
block = Block(file_origin=self._filename)
# if we aren't doing cascade, don't load anything
if not cascade:
return block
# create the objects to store other objects
rcg = RecordingChannelGroup(file_origin=self._filename)
rchan = RecordingChannel(file_origin=self._filename,
index=1,
name='Chan1')
# load objects into their containers
rcg.recordingchannels.append(rchan)
block.recordingchannelgroups.append(rcg)
rcg.channel_indexes = np.array([1])
rcg.channel_names = np.array(['Chan1'], dtype='S')
# open the file
with open(self._path, 'rb') as fobject:
# while the file is not done keep reading segments
while True:
seg = self._read_segment(fobject, lazy)
# if there are no more Segments, stop
if not seg:
break
# store the segment and signals
block.segments.append(seg)
rchan.analogsignals.append(seg.analogsignals[0])
# remove the file object
self._fsrc = None
create_many_to_one_relationship(block)
return block
def read_block(self, lazy=False, cascade=True, **kargs):
'''
Reads a block from the raw data file "fname" generated
with BrainWare
'''
# there are no keyargs implemented to so far. If someone tries to pass
# them they are expecting them to do something or making a mistake,
# neither of which should pass silently
if kargs:
raise NotImplementedError('This method does not have any '
'argument implemented yet')
self._fsrc = None
block = Block(file_origin=self._filename)
# if we aren't doing cascade, don't load anything
if not cascade:
return block
# create the objects to store other objects
rcg = RecordingChannelGroup(file_origin=self._filename)
rchan = RecordingChannel(file_origin=self._filename,
index=1, name='Chan1')
# load objects into their containers
rcg.recordingchannels.append(rchan)
block.recordingchannelgroups.append(rcg)
rcg.channel_indexes = np.array([1])
rcg.channel_names = np.array(['Chan1'], dtype='S')
# open the file
with open(self._path, 'rb') as fobject:
# while the file is not done keep reading segments
while True:
seg = self._read_segment(fobject, lazy)
# if there are no more Segments, stop
if not seg:
break
# store the segment and signals
block.segments.append(seg)
rchan.analogsignals.append(seg.analogsignals[0])
# remove the file object
self._fsrc = None
create_many_to_one_relationship(block)
return block
def read_segment(self,
lazy = False,
cascade = True,
group = 0,
series = 0):
seg = Segment( name = 'test')
if cascade:
tree = getbyroute(self.pul.tree,[0,group,series])
for sw,sweep in enumerate(tree['children']):
if sw == 0:
starttime = pq.Quantity(float(sweep['contents'].swTimer),'s')
for ch,channel in enumerate(sweep['children']):
sig = self.read_analogsignal(group=group,
series=series,
sweep=sw,
channel = ch)
annotations = sweep['contents'].__dict__.keys()
annotations.remove('readlist')
for a in annotations:
d = {a:str(sweep['contents'].__dict__[a])}
sig.annotate(**d)
sig.t_start = pq.Quantity(float(sig.annotations['swTimer']),'s') - starttime
seg.analogsignals.append(sig)
annotations = tree['contents'].__dict__.keys()
annotations.remove('readlist')
for a in annotations:
d = {a:str(tree['contents'].__dict__[a])}
seg.annotate(**d)
create_many_to_one_relationship(seg)
### add protocols to signals
for sig_index,sig in enumerate(seg.analogsignals):
pgf_index = sig.annotations['pgf_index']
st_rec = self.pgf.tree['children'][pgf_index]['contents']
chnls = [ch for ch in self.pgf.tree['children'][pgf_index]['children']]
for ch_index, chnl in enumerate(chnls):
ep_start = sig.t_start
for se_epoch_index, se_epoch in enumerate(chnl['children']):
se_rec = se_epoch['contents']
se_duration = pq.Quantity(float(se_rec.seDuration),'s')
if not(int(se_rec.seVoltageSource)):
se_voltage = pq.Quantity(float(se_rec.seVoltage),'V')
else:
se_voltage = pq.Quantity(float(chnl['contents'].chHolding),'V')
epoch = neo.Epoch(ep_start,se_duration,'protocol_epoch',value=se_voltage,channel_index=ch_index)
fully_annototate(chnl,epoch)
epoch.annotations['sig_index'] = sig_index
ep_start = ep_start + se_duration
seg.epochs.append(epoch)
return seg
def read_block(self,
lazy = False,
cascade = True,
group = 0):
blo = Block(name = 'test')
if cascade:
tree = getbyroute(self.pul.tree,[0,group])
for i,child in enumerate(tree['children']):
blo.segments.append(self.read_segment(group=group,series = i))
annotations = tree['contents'].__dict__.keys()
annotations.remove('readlist')
for a in annotations:
d = {a:str(tree['contents'].__dict__[a])}
blo.annotate(**d)
create_many_to_one_relationship(blo)
return blo
def test__construct_subsegment_by_unit(self):
nb_seg = 3
nb_unit = 7
unit_with_sig = np.array([0, 2, 5])
signal_types = ['Vm', 'Conductances']
sig_len = 100
#recordingchannelgroups
rcgs = [RecordingChannelGroup(name='Vm',
channel_indexes=unit_with_sig),
RecordingChannelGroup(name='Conductance',
channel_indexes=unit_with_sig)]
# Unit
all_unit = []
for u in range(nb_unit):
un = Unit(name='Unit #%d' % u, channel_indexes=np.array([u]))
assert_neo_object_is_compliant(un)
all_unit.append(un)
blk = Block()
blk.recordingchannelgroups = rcgs
for s in range(nb_seg):
seg = Segment(name='Simulation %s' % s)
for j in range(nb_unit):
st = SpikeTrain([1, 2, 3], units='ms',
t_start=0., t_stop=10)
st.unit = all_unit[j]
for t in signal_types:
anasigarr = AnalogSignalArray(np.zeros((sig_len,
len(unit_with_sig))),
units='nA',
sampling_rate=1000.*pq.Hz,
channel_indexes=unit_with_sig)
seg.analogsignalarrays.append(anasigarr)
create_many_to_one_relationship(blk)
for unit in all_unit:
assert_neo_object_is_compliant(unit)
for rcg in rcgs:
assert_neo_object_is_compliant(rcg)
assert_neo_object_is_compliant(blk)
# what you want
newseg = seg.construct_subsegment_by_unit(all_unit[:4])
assert_neo_object_is_compliant(newseg)
def read(self, lazy=False, cascade=True, **kargs):
if Block in self.readable_objects:
if (hasattr(self, 'read_all_blocks') and
callable(getattr(self, 'read_all_blocks'))):
return self.read_all_blocks(lazy=lazy, cascade=cascade,
**kargs)
return [self.read_block(lazy=lazy, cascade=cascade, **kargs)]
elif Segment in self.readable_objects:
bl = Block(name='One segment only')
if not cascade:
return bl
seg = self.read_segment(lazy=lazy, cascade=cascade, **kargs)
bl.segments.append(seg)
create_many_to_one_relationship(bl)
return [bl]
else:
raise NotImplementedError
def generate_from_supported_objects( supported_objects ):
#~ create_many_to_one_relationship
if Block in supported_objects:
higher = generate_one_simple_block(supported_objects= supported_objects)
# Chris we do not create RC and RCG if it is not in supported_objects
# there is a test in generate_one_simple_block so I removed
#finalize_block(higher)
elif Segment in supported_objects:
higher = generate_one_simple_segment(supported_objects= supported_objects)
else:
#TODO
return None
create_many_to_one_relationship(higher)
return higher
def generate_from_supported_objects(supported_objects):
#~ create_many_to_one_relationship
objects = supported_objects
if Block in objects:
higher = generate_one_simple_block(supported_objects=objects)
# Chris we do not create RC and RCG if it is not in objects
# there is a test in generate_one_simple_block so I removed
#finalize_block(higher)
elif Segment in objects:
higher = generate_one_simple_segment(supported_objects=objects)
else:
#TODO
return None
create_many_to_one_relationship(higher)
return higher
def test_block_list_recordingchannel(self):
blk = Block(name='a block')
blk.recordingchannelgroups = [self.rcg1, self.rcg2]
create_many_to_one_relationship(blk)
#assert_neo_object_is_compliant(blk)
chanres1 = [
chan.name
for chan in blk.recordingchannelgroups[0].recordingchannels
]
chanres2 = [
chan.name
for chan in blk.recordingchannelgroups[1].recordingchannels
]
chanres = [chan.name for chan in blk.list_recordingchannels]
self.assertEqual(self.channames1, chanres1)
self.assertEqual(self.channames2, chanres2)
self.assertEqual(self.channames, chanres)
def read_block(
self,
cascade=True,
lazy=False,
):
"""
Arguments:
"""
d = scipy.io.loadmat(self.filename,
struct_as_record=False,
squeeze_me=True)
assert 'block' in d, 'no block in' + self.filename
bl_struct = d['block']
bl = self.create_ob_from_struct(bl_struct,
'Block',
cascade=cascade,
lazy=lazy)
create_many_to_one_relationship(bl)
return bl
def read_segment(self,
lazy = False,
cascade = True,
delimiter = '\t',
t_start = 0.*pq.s,
unit = pq.s,
):
"""
Arguments:
delimiter : columns delimiter in file '\t' or one space or two space or ',' or ';'
t_start : time start of all spiketrain 0 by default
unit : unit of spike times, can be a str or directly a Quantities
"""
unit = pq.Quantity(1, unit)
seg = Segment(file_origin = os.path.basename(self.filename))
if not cascade:
return seg
f = open(self.filename, 'Ur')
for i,line in enumerate(f) :
alldata = line[:-1].split(delimiter)
if alldata[-1] == '': alldata = alldata[:-1]
if alldata[0] == '': alldata = alldata[1:]
if lazy:
spike_times = [ ]
t_stop = t_start
else:
spike_times = np.array(alldata).astype('f')
t_stop = spike_times.max()*unit
sptr = SpikeTrain(spike_times*unit, t_start=t_start, t_stop=t_stop)
if lazy:
sptr.lazy_shape = len(alldata)
sptr.annotate(channel_index = i)
seg.spiketrains.append(sptr)
f.close()
create_many_to_one_relationship(seg)
return seg
def setup_segments(self):
params = {'testarg2': 'yes', 'testarg3': True}
self.segment1 = Segment(name='test', description='tester 1',
file_origin='test.file',
testarg1=1, **params)
self.segment2 = Segment(name='test', description='tester 2',
file_origin='test.file',
testarg1=1, **params)
self.segment1.annotate(testarg1=1.1, testarg0=[1, 2, 3])
self.segment2.annotate(testarg11=1.1, testarg10=[1, 2, 3])
self.segment1.analogsignals = self.sig1
self.segment2.analogsignals = self.sig2
self.segment1.analogsignalarrays = self.sigarr1
self.segment2.analogsignalarrays = self.sigarr2
self.segment1.epochs = self.epoch1
self.segment2.epochs = self.epoch2
self.segment1.epocharrays = self.epocharr1
self.segment2.epocharrays = self.epocharr2
self.segment1.events = self.event1
self.segment2.events = self.event2
self.segment1.eventarrays = self.eventarr1
self.segment2.eventarrays = self.eventarr2
self.segment1.irregularlysampledsignals = self.irsig1
self.segment2.irregularlysampledsignals = self.irsig2
self.segment1.spikes = self.spike1
self.segment2.spikes = self.spike2
self.segment1.spiketrains = self.train1
self.segment2.spiketrains = self.train2
create_many_to_one_relationship(self.segment1)
create_many_to_one_relationship(self.segment2)
def setup_recordingchannelgroups(self):
params = {'testarg2': 'yes', 'testarg3': True}
self.rcg1 = RecordingChannelGroup(name='test',
description='tester 1',
file_origin='test.file',
testarg1=1,
**params)
self.rcg2 = RecordingChannelGroup(name='test',
description='tester 2',
file_origin='test.file',
testarg1=1,
**params)
self.rcg1.annotate(testarg1=1.1, testarg0=[1, 2, 3])
self.rcg2.annotate(testarg11=1.1, testarg10=[1, 2, 3])
self.rcg1.units = self.units1
self.rcg2.units = self.units2
self.rcg1.recordingchannels = self.rchan1
self.rcg2.recordingchannels = self.rchan2
self.rcg1.analogsignalarrays = self.sigarr1
self.rcg2.analogsignalarrays = self.sigarr2
create_many_to_one_relationship(self.rcg1)
create_many_to_one_relationship(self.rcg2)
def read_block(
self,
lazy=False,
cascade=True,
):
"""
"""
tree = ElementTree.parse(self.filename)
root = tree.getroot()
acq = root.find('acquisitionSystem')
nbits = int(acq.find('nBits').text)
nbchannel = int(acq.find('nChannels').text)
sampling_rate = float(acq.find('samplingRate').text) * pq.Hz
voltage_range = float(acq.find('voltageRange').text)
#offset = int(acq.find('offset').text)
amplification = float(acq.find('amplification').text)
bl = Block(
file_origin=os.path.basename(self.filename).replace('.xml', ''))
if cascade:
seg = Segment()
bl.segments.append(seg)
# RC and RCG
rc_list = []
for i, xml_rcg in enumerate(
root.find('anatomicalDescription').find(
'channelGroups').findall('group')):
rcg = RecordingChannelGroup(name='Group {}'.format(i))
bl.recordingchannelgroups.append(rcg)
for xml_rc in xml_rcg:
rc = RecordingChannel(index=int(xml_rc.text))
rc_list.append(rc)
rcg.recordingchannels.append(rc)
rc.recordingchannelgroups.append(rcg)
rcg.channel_indexes = np.array(
[rc.index for rc in rcg.recordingchannels], dtype=int)
rcg.channel_names = np.array([
'Channel{}'.format(rc.index)
for rc in rcg.recordingchannels
],
dtype='S')
# AnalogSignals
reader = RawBinarySignalIO(
filename=self.filename.replace('.xml', '.dat'))
seg2 = reader.read_segment(
cascade=True,
lazy=lazy,
sampling_rate=sampling_rate,
t_start=0. * pq.s,
unit=pq.V,
nbchannel=nbchannel,
bytesoffset=0,
dtype=np.int16 if nbits <= 16 else np.int32,
rangemin=-voltage_range / 2.,
rangemax=voltage_range / 2.,
)
for s, sig in enumerate(seg2.analogsignals):
if not lazy:
sig /= amplification
sig.segment = seg
seg.analogsignals.append(sig)
rc_list[s].analogsignals.append(sig)
create_many_to_one_relationship(bl)
return bl
def read_segment(
self,
lazy=False,
cascade=True,
delimiter='\t',
usecols=None,
skiprows=0,
timecolumn=None,
sampling_rate=1. * pq.Hz,
t_start=0. * pq.s,
unit=pq.V,
method='genfromtxt',
):
"""
Arguments:
delimiter : columns delimiter in file '\t' or one space or two space or ',' or ';'
usecols : if None take all columns otherwise a list for selected columns
skiprows : skip n first lines in case they contains header informations
timecolumn : None or a valid int that point the time vector
samplerate : the samplerate of signals if timecolumn is not None this is not take in account
t_start : time of the first sample
unit : unit of AnalogSignal can be a str or directly a Quantities
method : 'genfromtxt' or 'csv' or 'homemade'
in case of bugs you can try one of this methods
'genfromtxt' use numpy.genfromtxt
'csv' use cvs module
'homemade' use a intuitive more robust but slow method
"""
seg = Segment(file_origin=os.path.basename(self.filename))
if not cascade:
return seg
if type(sampling_rate) == float or type(sampling_rate) == int:
# if not quantitities Hz by default
sampling_rate = sampling_rate * pq.Hz
if type(t_start) == float or type(t_start) == int:
# if not quantitities s by default
t_start = t_start * pq.s
unit = pq.Quantity(1, unit)
#loadtxt
if method == 'genfromtxt':
sig = np.genfromtxt(self.filename,
delimiter=delimiter,
usecols=usecols,
skiprows=skiprows,
dtype='f')
if len(sig.shape) == 1:
sig = sig[:, np.newaxis]
elif method == 'csv':
tab = [
l for l in csv.reader(file(self.filename, 'rU'),
delimiter=delimiter)
]
tab = tab[skiprows:]
sig = np.array(tab, dtype='f')
elif method == 'homemade':
fid = open(self.filename, 'rU')
for l in range(skiprows):
fid.readline()
tab = []
for line in fid.readlines():
line = line.replace('\r', '')
line = line.replace('\n', '')
l = line.split(delimiter)
while '' in l:
l.remove('')
tab.append(l)
sig = np.array(tab, dtype='f')
if timecolumn is not None:
sampling_rate = 1. / np.mean(np.diff(sig[:, timecolumn])) * pq.Hz
t_start = sig[0, timecolumn] * pq.s
for i in range(sig.shape[1]):
if timecolumn == i: continue
if usecols is not None and i not in usecols: continue
if lazy:
signal = [] * unit
else:
signal = sig[:, i] * unit
anaSig = AnalogSignal(signal,
sampling_rate=sampling_rate,
t_start=t_start,
channel_index=i,
name='Column %d' % i)
if lazy:
anaSig.lazy_shape = sig.shape
seg.analogsignals.append(anaSig)
create_many_to_one_relationship(seg)
return seg
def read_segment(
self,
# the 2 first keyword arguments are imposed by neo.io API
lazy=False,
cascade=True,
# all following arguments are decied by this IO and are free
segment_duration=15.,
num_analogsignal=4,
num_spiketrain_by_channel=3,
):
"""
Return a fake Segment.
The self.filename does not matter.
In this IO read by default a Segment.
This is just a example to be adapted to each ClassIO.
In this case these 3 paramters are taken in account because this function
return a generated segment with fake AnalogSignal and fake SpikeTrain.
Parameters:
segment_duration :is the size in secend of the segment.
num_analogsignal : number of AnalogSignal in this segment
num_spiketrain : number of SpikeTrain in this segment
"""
sampling_rate = 10000. #Hz
t_start = -1.
#time vector for generated signal
timevect = np.arange(t_start, t_start + segment_duration,
1. / sampling_rate)
# create an empty segment
seg = Segment(name='it is a seg from exampleio')
if cascade:
# read nested analosignal
for i in range(num_analogsignal):
ana = self.read_analogsignal(lazy=lazy,
cascade=cascade,
channel_index=i,
segment_duration=segment_duration,
t_start=t_start)
seg.analogsignals += [ana]
# read nested spiketrain
for i in range(num_analogsignal):
for _ in range(num_spiketrain_by_channel):
sptr = self.read_spiketrain(
lazy=lazy,
cascade=cascade,
segment_duration=segment_duration,
t_start=t_start,
channel_index=i)
seg.spiketrains += [sptr]
# create an EventArray that mimic triggers.
# note that ExampleIO do not allow to acess directly to EventArray
# for that you need read_segment(cascade = True)
eva = EventArray()
if lazy:
# in lazy case no data are readed
# eva is empty
pass
else:
# otherwise it really contain data
n = 1000
# neo.io support quantities my vector use second for unit
eva.times = timevect[(np.random.rand(n) *
timevect.size).astype('i')] * pq.s
# all duration are the same
eva.durations = np.ones(n) * 500 * pq.ms
# label
l = []
for i in range(n):
if np.random.rand() > .6: l.append('TriggerA')
else: l.append('TriggerB')
eva.labels = np.array(l)
seg.eventarrays += [eva]
create_many_to_one_relationship(seg)
return seg
def read_segment(self, cascade = True, lazy = False,):
"""
Arguments:
"""
f = struct_file(self.filename, 'rb')
#Name
f.seek(64,0)
surname = f.read(22)
while surname[-1] == ' ' :
if len(surname) == 0 :break
surname = surname[:-1]
firstname = f.read(20)
while firstname[-1] == ' ' :
if len(firstname) == 0 :break
firstname = firstname[:-1]
#Date
f.seek(128,0)
day, month, year, hour, minute, sec = f.read_f('bbbbbb')
rec_datetime = datetime.datetime(year+1900 , month , day, hour, minute, sec)
f.seek(138,0)
Data_Start_Offset , Num_Chan , Multiplexer , Rate_Min , Bytes = f.read_f('IHHHH')
#~ print Num_Chan, Bytes
#header version
f.seek(175,0)
header_version, = f.read_f('b')
assert header_version == 4
seg = Segment( name = firstname+' '+surname,
file_origin = os.path.basename(self.filename),
)
seg.annotate(surname = surname)
seg.annotate(firstname = firstname)
seg.annotate(rec_datetime = rec_datetime)
if not cascade:
return seg
# area
f.seek(176,0)
zone_names = ['ORDER', 'LABCOD', 'NOTE', 'FLAGS', 'TRONCA', 'IMPED_B', 'IMPED_E', 'MONTAGE',
'COMPRESS', 'AVERAGE', 'HISTORY', 'DVIDEO', 'EVENT A', 'EVENT B', 'TRIGGER']
zones = { }
for zname in zone_names:
zname2, pos, length = f.read_f('8sII')
zones[zname] = zname2, pos, length
#~ print zname2, pos, length
# reading raw data
if not lazy:
f.seek(Data_Start_Offset,0)
rawdata = np.fromstring(f.read() , dtype = 'u'+str(Bytes))
rawdata = rawdata.reshape(( rawdata.size/Num_Chan , Num_Chan))
# Reading Code Info
zname2, pos, length = zones['ORDER']
f.seek(pos,0)
code = np.fromfile(f, dtype='u2', count=Num_Chan)
units = {-1: pq.nano*pq.V, 0:pq.uV, 1:pq.mV, 2:1, 100: pq.percent, 101:pq.dimensionless, 102:pq.dimensionless}
for c in range(Num_Chan):
zname2, pos, length = zones['LABCOD']
f.seek(pos+code[c]*128+2,0)
label = f.read(6).strip("\x00")
ground = f.read(6).strip("\x00")
logical_min , logical_max, logical_ground, physical_min, physical_max = f.read_f('iiiii')
k, = f.read_f('h')
if k in units.keys() :
unit = units[k]
else :
unit = pq.uV
f.seek(8,1)
sampling_rate, = f.read_f('H') * pq.Hz
sampling_rate *= Rate_Min
if lazy:
signal = [ ]*unit
else:
factor = float(physical_max - physical_min) / float(logical_max-logical_min+1)
signal = ( rawdata[:,c].astype('f') - logical_ground )* factor*unit
anaSig = AnalogSignal(signal, sampling_rate=sampling_rate,
name=label, channel_index=c)
if lazy:
anaSig.lazy_shape = None
anaSig.annotate(ground = ground)
seg.analogsignals.append( anaSig )
sampling_rate = np.mean([ anaSig.sampling_rate for anaSig in seg.analogsignals ])*pq.Hz
# Read trigger and notes
for zname, label_dtype in [ ('TRIGGER', 'u2'), ('NOTE', 'S40') ]:
zname2, pos, length = zones[zname]
f.seek(pos,0)
triggers = np.fromstring(f.read(length) , dtype = [('pos','u4'), ('label', label_dtype)] , )
ea = EventArray(name =zname[0]+zname[1:].lower())
if not lazy:
keep = (triggers['pos']>=triggers['pos'][0]) & (triggers['pos']<rawdata.shape[0]) & (triggers['pos']!=0)
triggers = triggers[keep]
ea.labels = triggers['label'].astype('S')
ea.times = (triggers['pos']/sampling_rate).rescale('s')
else:
ea.lazy_shape = triggers.size
seg.eventarrays.append(ea)
# Read Event A and B
# Not so well tested
for zname in ['EVENT A', 'EVENT B']:
zname2, pos, length = zones[zname]
f.seek(pos,0)
epochs = np.fromstring(f.read(length) ,
dtype = [('label','u4'),('start','u4'),('stop','u4'),] )
ep = EpochArray(name =zname[0]+zname[1:].lower())
if not lazy:
keep = (epochs['start']>0) & (epochs['start']<rawdata.shape[0]) & (epochs['stop']<rawdata.shape[0])
epochs = epochs[keep]
ep.labels = epochs['label'].astype('S')
ep.times = (epochs['start']/sampling_rate).rescale('s')
ep.durations = ((epochs['stop'] - epochs['start'])/sampling_rate).rescale('s')
else:
ep.lazy_shape = triggers.size
seg.epocharrays.append(ep)
create_many_to_one_relationship(seg)
return seg
def read_block(self,
lazy=False,
cascade=True,
n_starts=None,
n_stops=None,
channel_list=None):
"""Reads the file and returns contents as a Block.
The Block contains one Segment for each entry in zip(n_starts,
n_stops). If these parameters are not specified, the default is
to store all data in one Segment.
The Block also contains one RecordingChannelGroup for all channels.
n_starts: list or array of starting times of each Segment in
samples from the beginning of the file.
n_stops: similar, stopping times of each Segment
channel_list: list of channel numbers to get. The neural data channels
are 1 - 128. The analog inputs are 129 - 144. The default
is to acquire all channels.
Returns: Block object containing the data.
"""
# Create block
block = Block(file_origin=self.filename)
if not cascade:
return block
self.loader = Loader(self.filename)
self.loader.load_file()
self.header = self.loader.header
# If channels not specified, get all
if channel_list is None:
channel_list = self.loader.get_neural_channel_numbers()
# If not specified, load all as one Segment
if n_starts is None:
n_starts = [0]
n_stops = [self.loader.header.n_samples]
#~ # Add channel hierarchy
#~ rcg = RecordingChannelGroup(name='allchannels',
#~ description='group of all channels', file_origin=self.filename)
#~ block.recordingchannelgroups.append(rcg)
#~ self.channel_number_to_recording_channel = {}
#~ # Add each channel at a time to hierarchy
#~ for ch in channel_list:
#~ ch_object = RecordingChannel(name='channel%d' % ch,
#~ file_origin=self.filename, index=ch)
#~ rcg.channel_indexes.append(ch_object.index)
#~ rcg.channel_names.append(ch_object.name)
#~ rcg.recordingchannels.append(ch_object)
#~ self.channel_number_to_recording_channel[ch] = ch_object
# Iterate through n_starts and n_stops and add one Segment
# per each.
for n, (t1, t2) in enumerate(zip(n_starts, n_stops)):
# Create segment and add metadata
seg = self.read_segment(n_start=t1,
n_stop=t2,
chlist=channel_list,
lazy=lazy,
cascade=cascade)
seg.name = 'Segment %d' % n
seg.index = n
t1sec = t1 / self.loader.header.f_samp
t2sec = t2 / self.loader.header.f_samp
seg.description = 'Segment %d from %f to %f' % (n, t1sec, t2sec)
# Link to block
block.segments.append(seg)
# Create hardware view, and bijectivity
tools.populate_RecordingChannel(block)
tools.create_many_to_one_relationship(block)
return block
def proc_f32(filename):
'''Load an f32 file that has already been processed by the official matlab
file converter. That matlab data is saved to an m-file, which is then
converted to a numpy '.npz' file. This numpy file is the file actually
loaded. This function converts it to a neo block and returns the block.
This block can be compared to the block produced by BrainwareF32IO to
make sure BrainwareF32IO is working properly
block = proc_f32(filename)
filename: The file name of the numpy file to load. It should end with
'*_f32_py?.npz'. This will be converted to a neo 'file_origin' property
with the value '*.f32', so the filename to compare should fit that pattern.
'py?' should be 'py2' for the python 2 version of the numpy file or 'py3'
for the python 3 version of the numpy file.
example: filename = 'file1_f32_py2.npz'
f32 file name = 'file1.f32'
'''
filenameorig = os.path.basename(filename[:-12] + '.f32')
# create the objects to store other objects
block = Block(file_origin=filenameorig)
rcg = RecordingChannelGroup(file_origin=filenameorig)
rcg.channel_indexes = np.array([], dtype=np.int)
rcg.channel_names = np.array([], dtype='S')
unit = Unit(file_origin=filenameorig)
# load objects into their containers
block.recordingchannelgroups.append(rcg)
rcg.units.append(unit)
try:
with np.load(filename) as f32obj:
f32file = f32obj.items()[0][1].flatten()
except IOError as exc:
if 'as a pickle' in exc.message:
create_many_to_one_relationship(block)
return block
else:
raise
sweeplengths = [res[0, 0].tolist() for res in f32file['sweeplength']]
stims = [res.flatten().tolist() for res in f32file['stim']]
sweeps = [res['spikes'].flatten() for res in f32file['sweep'] if res.size]
fullf32 = zip(sweeplengths, stims, sweeps)
for sweeplength, stim, sweep in fullf32:
for trainpts in sweep:
if trainpts.size:
trainpts = trainpts.flatten().astype('float32')
else:
trainpts = []
paramnames = ['Param%s' % i for i in range(len(stim))]
params = dict(zip(paramnames, stim))
train = SpikeTrain(trainpts,
units=pq.ms,
t_start=0,
t_stop=sweeplength,
file_origin=filenameorig)
segment = Segment(file_origin=filenameorig, **params)
segment.spiketrains = [train]
unit.spiketrains.append(train)
block.segments.append(segment)
create_many_to_one_relationship(block)
return block
def read_block(self, lazy=False, cascade=True,
n_starts=None, n_stops=None, channel_list=None):
"""Reads the file and returns contents as a Block.
The Block contains one Segment for each entry in zip(n_starts,
n_stops). If these parameters are not specified, the default is
to store all data in one Segment.
The Block also contains one RecordingChannelGroup for all channels.
n_starts: list or array of starting times of each Segment in
samples from the beginning of the file.
n_stops: similar, stopping times of each Segment
channel_list: list of channel numbers to get. The neural data channels
are 1 - 128. The analog inputs are 129 - 144. The default
is to acquire all channels.
Returns: Block object containing the data.
"""
# Create block
block = Block(file_origin=self.filename)
if not cascade:
return block
self.loader = Loader(self.filename)
self.loader.load_file()
self.header = self.loader.header
# If channels not specified, get all
if channel_list is None:
channel_list = self.loader.get_neural_channel_numbers()
# If not specified, load all as one Segment
if n_starts is None:
n_starts = [0]
n_stops = [self.loader.header.n_samples]
#~ # Add channel hierarchy
#~ rcg = RecordingChannelGroup(name='allchannels',
#~ description='group of all channels', file_origin=self.filename)
#~ block.recordingchannelgroups.append(rcg)
#~ self.channel_number_to_recording_channel = {}
#~ # Add each channel at a time to hierarchy
#~ for ch in channel_list:
#~ ch_object = RecordingChannel(name='channel%d' % ch,
#~ file_origin=self.filename, index=ch)
#~ rcg.channel_indexes.append(ch_object.index)
#~ rcg.channel_names.append(ch_object.name)
#~ rcg.recordingchannels.append(ch_object)
#~ self.channel_number_to_recording_channel[ch] = ch_object
# Iterate through n_starts and n_stops and add one Segment
# per each.
for n, (t1, t2) in enumerate(zip(n_starts, n_stops)):
# Create segment and add metadata
seg = self.read_segment(n_start=t1, n_stop=t2, chlist=channel_list,
lazy=lazy, cascade=cascade)
seg.name = 'Segment %d' % n
seg.index = n
t1sec = t1 / self.loader.header.f_samp
t2sec = t2 / self.loader.header.f_samp
seg.description = 'Segment %d from %f to %f' % (n, t1sec, t2sec)
# Link to block
block.segments.append(seg)
# Create hardware view, and bijectivity
tools.populate_RecordingChannel(block)
tools.create_many_to_one_relationship(block)
return block
def read_block(self, lazy=False, cascade=True, waveform=False):
"""Returns a Block containing spike information.
There is no obvious way to infer the segment boundaries from
raw spike times, so for now all spike times are returned in one
big segment. The way around this would be to specify the segment
boundaries, and then change this code to put the spikes in the right
segments.
"""
# Create block and segment to hold all the data
block = Block()
# Search data directory for KlustaKwik files.
# If nothing found, return empty block
self._fetfiles = self._fp.read_filenames("fet")
self._clufiles = self._fp.read_filenames("clu")
if len(self._fetfiles) == 0 or not cascade:
return block
# Create segments to hold all of the data
segs = {}
for rec_name, rec_offset in self.split_table:
seg = Segment(name=(rec_name), index=int(rec_name), file_origin=self.filename)
block.segments.append(seg)
segs[rec_name] = seg
# Load spike times from each group and store in a dict, keyed
# by group number
self.spiketrains = dict()
for group in sorted(self._fetfiles.keys()):
# Load spike times
fetfile = self._fetfiles[group]
spks, features = self._load_spike_times(fetfile)
# Load cluster ids or generate
if group in self._clufiles:
clufile = self._clufiles[group]
uids = self._load_unit_id(clufile)
else:
# unclustered data, assume all zeros
uids = np.zeros(spks.shape, dtype=np.int32)
# error check
if len(spks) != len(uids):
raise ValueError("lengths of fet and clu files are different")
# Create a recording channel group
rcg = RecordingChannelGroup(name=group)
block.recordingchannelgroups.append(rcg)
# Create Unit for each cluster
unique_unit_ids = np.unique(uids)
for unit_id in sorted(unique_unit_ids):
if unit_id > 1:
# Initialize the unit
u = Unit(name=("unit %d from group %d" % (unit_id, group)), index=unit_id, group=group)
offset = 0
for rec_name, rec_offset in self.split_table:
idx = (spks > offset) & (spks <= (offset + rec_offset))
# print str(offset) + ' : ' + str(rec_offset)
tmp_spks = spks[idx] - offset
offset += rec_offset
tmp_uids = uids[idx]
if len(tmp_spks) > 0:
tmp_t_stop = tmp_spks.max() / self.sampling_rate
else:
tmp_t_stop = 0
# Initialize a new SpikeTrain for the spikes from this unit
if lazy:
st = SpikeTrain(
times=[],
units="sec",
t_start=0.0,
t_stop=tmp_t_stop,
name=("unit %d from group %d" % (unit_id, group)),
)
st.lazy_shape = len(tmp_spks[tmp_uids == unit_id])
else:
st = SpikeTrain(
times=tmp_spks[tmp_uids == unit_id] / self.sampling_rate,
units="sec",
t_start=0.0,
t_stop=tmp_t_stop,
name=("unit %d from group %d" % (unit_id, group)),
)
st.annotations["cluster"] = unit_id
st.annotations["group"] = group
# put features in
if waveform:
st.waveforms = features
# .spk.n (spike waveforms)
# .upsk.n (unfiltered spike waveforms)
# Link
u.spiketrains.append(st)
# TODO add u to block!!!
tmp_seg = segs[rec_name]
tmp_seg.spiketrains.append(st)
rcg.units.append(u)
print block.recordingchannelgroups
create_many_to_one_relationship(block)
return block
def test1(self):
"""Write data to binary file, then read it back in and verify"""
# delete temporary file before trying to write to it
if os.path.exists(self.fn):
os.remove(self.fn)
block = neo.Block()
full_range = 234 * pq.mV
# Create segment1 with analogsignals
segment1 = neo.Segment()
sig1 = neo.AnalogSignal([3, 4, 5],
units='mV',
channel_index=3,
sampling_rate=30000. * pq.Hz)
sig2 = neo.AnalogSignal([6, -4, -5],
units='mV',
channel_index=4,
sampling_rate=30000. * pq.Hz)
segment1.analogsignals.append(sig1)
segment1.analogsignals.append(sig2)
# Create segment2 with analogsignals
segment2 = neo.Segment()
sig3 = neo.AnalogSignal([-3, -4, -5],
units='mV',
channel_index=3,
sampling_rate=30000. * pq.Hz)
sig4 = neo.AnalogSignal([-6, 4, 5],
units='mV',
channel_index=4,
sampling_rate=30000. * pq.Hz)
segment2.analogsignals.append(sig3)
segment2.analogsignals.append(sig4)
# Link segments to block
block.segments.append(segment1)
block.segments.append(segment2)
# Create hardware view, and bijectivity
#tools.populate_RecordingChannel(block)
#print "problem happening"
#print block.recordingchannelgroups[0].recordingchannels
#chan = block.recordingchannelgroups[0].recordingchannels[0]
#print chan.analogsignals
#tools.create_many_to_one_relationship(block)
#print "here: "
#print block.segments[0].analogsignals[0].recordingchannel
# Chris I prefer that:
#tools.finalize_block(block)
tools.populate_RecordingChannel(block)
tools.create_many_to_one_relationship(block)
# Check that blackrockio is correctly extracting channel indexes
self.assertEqual(
neo.io.blackrockio.channel_indexes_in_segment(segment1), [3, 4])
self.assertEqual(
neo.io.blackrockio.channel_indexes_in_segment(segment2), [3, 4])
# Create writer. Write block, then read back in.
bio = neo.io.BlackrockIO(filename=self.fn, full_range=full_range)
bio.write_block(block)
fi = file(self.fn)
# Text header
self.assertEqual(fi.read(16), 'NEURALSG30 kS/s\x00')
self.assertEqual(fi.read(8), '\x00\x00\x00\x00\x00\x00\x00\x00')
# Integers: period, channel count, channel index1, channel index2
self.assertEqual(struct.unpack('<4I', fi.read(16)), (1, 2, 3, 4))
# What should the signals be after conversion?
conv = float(full_range) / 2**16
sigs = np.array(
[np.concatenate((sig1, sig3)),
np.concatenate((sig2, sig4))])
sigs_converted = np.rint(sigs / conv).astype(np.int)
# Check that each time point is the same
for time_slc in sigs_converted.transpose():
written_data = struct.unpack('<2h', fi.read(4))
self.assertEqual(list(time_slc), list(written_data))
# Check that we read to the end
currentpos = fi.tell()
fi.seek(0, 2)
truelen = fi.tell()
self.assertEqual(currentpos, truelen)
fi.close()
def test1(self):
"""Write data to binary file, then read it back in and verify"""
# delete temporary file before trying to write to it
if os.path.exists(self.fn):
os.remove(self.fn)
block = neo.Block()
full_range = 234 * pq.mV
# Create segment1 with analogsignals
segment1 = neo.Segment()
sig1 = neo.AnalogSignal([3,4,5], units='mV', channel_index=3,
sampling_rate=30000.*pq.Hz)
sig2 = neo.AnalogSignal([6,-4,-5], units='mV', channel_index=4,
sampling_rate=30000.*pq.Hz)
segment1.analogsignals.append(sig1)
segment1.analogsignals.append(sig2)
# Create segment2 with analogsignals
segment2 = neo.Segment()
sig3 = neo.AnalogSignal([-3,-4,-5], units='mV', channel_index=3,
sampling_rate=30000.*pq.Hz)
sig4 = neo.AnalogSignal([-6,4,5], units='mV', channel_index=4,
sampling_rate=30000.*pq.Hz)
segment2.analogsignals.append(sig3)
segment2.analogsignals.append(sig4)
# Link segments to block
block.segments.append(segment1)
block.segments.append(segment2)
# Create hardware view, and bijectivity
#tools.populate_RecordingChannel(block)
#print "problem happening"
#print block.recordingchannelgroups[0].recordingchannels
#print block.recordingchannelgroups[0].recordingchannels[0].analogsignals
#tools.create_many_to_one_relationship(block)
#print "here: "
#print block.segments[0].analogsignals[0].recordingchannel
# Chris I prefer that:
#tools.finalize_block(block)
tools.populate_RecordingChannel(block)
tools.create_many_to_one_relationship(block)
# Check that blackrockio is correctly extracting channel indexes
self.assertEqual(neo.io.blackrockio.channel_indexes_in_segment(
segment1), [3,4])
self.assertEqual(neo.io.blackrockio.channel_indexes_in_segment(
segment2), [3,4])
# Create writer. Write block, then read back in.
bio = neo.io.BlackrockIO(filename=self.fn, full_range=full_range)
bio.write_block(block)
fi = file(self.fn)
# Text header
self.assertEqual(fi.read(16), 'NEURALSG30 kS/s\x00')
self.assertEqual(fi.read(8), '\x00\x00\x00\x00\x00\x00\x00\x00')
# Integers: period, channel count, channel index1, channel index2
self.assertEqual(struct.unpack('<4I', fi.read(16)), (1,2,3,4))
# What should the signals be after conversion?
conv = float(full_range) / 2**16
sigs = np.array(\
[np.concatenate((sig1,sig3)), np.concatenate((sig2, sig4))])
sigs_converted = np.rint(sigs / conv).astype(np.int)
# Check that each time point is the same
for time_slc in sigs_converted.transpose():
written_data = struct.unpack('<2h', fi.read(4))
self.assertEqual(list(time_slc), list(written_data))
# Check that we read to the end
currentpos = fi.tell()
fi.seek(0, 2)
truelen = fi.tell()
self.assertEqual(currentpos, truelen)
fi.close()
def read_segment(self,
# the 2 first keyword arguments are imposed by neo.io API
lazy = False,
cascade = True,
# all following arguments are decided by this IO and are free
t_start = 0.,
segment_duration = 0.,
):
"""
Return a Segment containing all analog and spike channels, as well as
all trigger events.
Parameters:
segment_duration :is the size in secend of the segment.
num_analogsignal : number of AnalogSignal in this segment
num_spiketrain : number of SpikeTrain in this segment
"""
#if no segment duration is given, use the complete file
if segment_duration == 0. :
segment_duration=float(self.metadata["TimeSpan"])
#if the segment duration is bigger than file, use the complete file
if segment_duration >=float(self.metadata["TimeSpan"]):
segment_duration=float(self.metadata["TimeSpan"])
#if the time sum of start point and segment duration is bigger than
#the file time span, cap it at the end
if segment_duration+t_start>float(self.metadata["TimeSpan"]):
segment_duration = float(self.metadata["TimeSpan"])-t_start
# create an empty segment
seg = Segment( name = "segment from the NeuroshareapiIO")
if cascade:
# read nested analosignal
if self.metadata["num_analogs"] == 0:
print ("no analog signals in this file!")
else:
#run through the number of analog channels found at the __init__ function
for i in range(self.metadata["num_analogs"]):
#create an analog signal object for each channel found
ana = self.read_analogsignal( lazy = lazy , cascade = cascade ,
channel_index = self.metadata["elecChanId"][i],
segment_duration = segment_duration, t_start=t_start)
#add analog signal read to segment object
seg.analogsignals += [ ana ]
# read triggers (in this case without any duration)
for i in range(self.metadata["num_trigs"]):
#create event object for each trigger/bit found
eva = self.read_eventarray(lazy = lazy ,
cascade = cascade,
channel_index = self.metadata["triggersId"][i],
segment_duration = segment_duration,
t_start = t_start,)
#add event object to segment
seg.eventarrays += [eva]
#read epochs (digital events with duration)
for i in range(self.metadata["num_digiEpochs"]):
#create event object for each trigger/bit found
epa = self.read_epocharray(lazy = lazy,
cascade = cascade,
channel_index = self.metadata["digiEpochId"][i],
segment_duration = segment_duration,
t_start = t_start,)
#add event object to segment
seg.epocharrays += [epa]
# read nested spiketrain
#run through all spike channels found
for i in range(self.metadata["num_spkChans"]):
#create spike object
sptr = self.read_spiketrain(lazy = lazy, cascade = cascade,
channel_index = self.metadata["spkChanId"][i],
segment_duration = segment_duration,
t_start = t_start)
#add the spike object to segment
seg.spiketrains += [sptr]
create_many_to_one_relationship(seg)
return seg
def test3():
"""
With no db : just a file
"""
url = 'sqlite://'
dbinfo = open_db(url,
object_number_in_cache = 3000,
use_global_session = False,
compress = None,
)
session = dbinfo.Session()
#~ bl = neo.AxonIO(filename = 'File_axon_1.abf').read()
#~ print bl.segments
#~ bl2 = OEBase.from_neo(bl, generic_classes, cascade = True)
from neo.test.io.generate_datasets import generate_one_simple_block
from neo.io.tools import create_many_to_one_relationship, populate_RecordingChannel
bl = generate_one_simple_block(supported_objects = [neo.Segment, neo.AnalogSignal, ])
create_many_to_one_relationship(bl)
populate_RecordingChannel(bl)
bl2 = OEBase.from_neo(bl, dbinfo.mapped_classes, cascade = True)
session.add(bl2)
session.commit()
print bl2
treedescription1 = TreeDescription(
dbinfo = dbinfo,
table_children = {
'Block' : ['Segment' ],
'Segment' : [ 'AnalogSignal'],
},
columns_to_show = { },
table_on_top = 'Block',
#~ table_order = None,
)
treedescription2 = TreeDescription(
dbinfo = dbinfo,
table_children = {
'Block' : ['RecordingChannelGroup' ],
'RecordingChannelGroup' : [ 'RecordingChannel', ],
'RecordingChannel' : [ 'AnalogSignal'],
},
columns_to_show = { },
table_on_top = 'Block',
#~ table_order = None,
)
app = QApplication([ ])
from OpenElectrophy.gui.contextmenu import context_menu
w1 = QtSqlTreeView(session = session, treedescription = treedescription1, context_menu = context_menu)
w2 = QtSqlTreeView(session = session, treedescription = treedescription2, context_menu = context_menu)
w1.show()
w2.show()
sys.exit(app.exec_())
def read_segment(self,
lazy = False,
cascade = True,
load_spike_waveform = True,
):
"""
"""
fid = open(self.filename, 'rb')
globalHeader = HeaderReader(fid , GlobalHeader ).read_f(offset = 0)
# metadatas
seg = Segment()
seg.rec_datetime = datetime.datetime( globalHeader['Year'] , globalHeader['Month'] , globalHeader['Day'] ,
globalHeader['Hour'] , globalHeader['Minute'] , globalHeader['Second'] )
seg.file_origin = os.path.basename(self.filename)
seg.annotate(plexon_version = globalHeader['Version'])
if not cascade:
return seg
## Step 1 : read headers
# dsp channels header = sipkes and waveforms
dspChannelHeaders = { }
maxunit=0
maxchan = 0
for _ in range(globalHeader['NumDSPChannels']):
# channel is 1 based
channelHeader = HeaderReader(fid , ChannelHeader ).read_f(offset = None)
channelHeader['Template'] = np.array(channelHeader['Template']).reshape((5,64))
channelHeader['Boxes'] = np.array(channelHeader['Boxes']).reshape((5,2,4))
dspChannelHeaders[channelHeader['Channel']]=channelHeader
maxunit = max(channelHeader['NUnits'],maxunit)
maxchan = max(channelHeader['Channel'],maxchan)
# event channel header
eventHeaders = { }
for _ in range(globalHeader['NumEventChannels']):
eventHeader = HeaderReader(fid , EventHeader ).read_f(offset = None)
eventHeaders[eventHeader['Channel']] = eventHeader
# slow channel header = signal
slowChannelHeaders = { }
for _ in range(globalHeader['NumSlowChannels']):
slowChannelHeader = HeaderReader(fid , SlowChannelHeader ).read_f(offset = None)
slowChannelHeaders[slowChannelHeader['Channel']] = slowChannelHeader
## Step 2 : a first loop for counting size
# signal
nb_samples = np.zeros(len(slowChannelHeaders))
sample_positions = np.zeros(len(slowChannelHeaders))
t_starts = np.zeros(len(slowChannelHeaders), dtype = 'f')
#spiketimes and waveform
nb_spikes = np.zeros((maxchan+1, maxunit+1) ,dtype='i')
wf_sizes = np.zeros((maxchan+1, maxunit+1, 2) ,dtype='i')
# eventarrays
nb_events = { }
#maxstrsizeperchannel = { }
for chan, h in iteritems(eventHeaders):
nb_events[chan] = 0
#maxstrsizeperchannel[chan] = 0
start = fid.tell()
while fid.tell() !=-1 :
# read block header
dataBlockHeader = HeaderReader(fid , DataBlockHeader ).read_f(offset = None)
if dataBlockHeader is None : break
chan = dataBlockHeader['Channel']
unit = dataBlockHeader['Unit']
n1,n2 = dataBlockHeader['NumberOfWaveforms'] , dataBlockHeader['NumberOfWordsInWaveform']
time = (dataBlockHeader['UpperByteOf5ByteTimestamp']*2.**32 +
dataBlockHeader['TimeStamp'])
if dataBlockHeader['Type'] == 1:
nb_spikes[chan,unit] +=1
wf_sizes[chan,unit,:] = [n1,n2]
fid.seek(n1*n2*2,1)
elif dataBlockHeader['Type'] ==4:
#event
nb_events[chan] += 1
elif dataBlockHeader['Type'] == 5:
#continuous signal
fid.seek(n2*2, 1)
if n2> 0:
nb_samples[chan] += n2
if nb_samples[chan] ==0:
t_starts[chan] = time
## Step 3: allocating memory and 2 loop for reading if not lazy
if not lazy:
# allocating mem for signal
sigarrays = { }
for chan, h in iteritems(slowChannelHeaders):
sigarrays[chan] = np.zeros(nb_samples[chan])
# allocating mem for SpikeTrain
stimearrays = np.zeros((maxchan+1, maxunit+1) ,dtype=object)
swfarrays = np.zeros((maxchan+1, maxunit+1) ,dtype=object)
for (chan, unit), _ in np.ndenumerate(nb_spikes):
stimearrays[chan,unit] = np.zeros(nb_spikes[chan,unit], dtype = 'f')
if load_spike_waveform:
n1,n2 = wf_sizes[chan, unit,:]
swfarrays[chan, unit] = np.zeros( (nb_spikes[chan, unit], n1, n2 ) , dtype = 'f4' )
pos_spikes = np.zeros(nb_spikes.shape, dtype = 'i')
# allocating mem for event
eventpositions = { }
evarrays = { }
for chan, nb in iteritems(nb_events):
evarrays[chan] = np.zeros(nb, dtype = 'f' )
eventpositions[chan]=0
fid.seek(start)
while fid.tell() !=-1 :
dataBlockHeader = HeaderReader(fid , DataBlockHeader ).read_f(offset = None)
if dataBlockHeader is None : break
chan = dataBlockHeader['Channel']
n1,n2 = dataBlockHeader['NumberOfWaveforms'] , dataBlockHeader['NumberOfWordsInWaveform']
time = dataBlockHeader['UpperByteOf5ByteTimestamp']*2.**32 + dataBlockHeader['TimeStamp']
time/= globalHeader['ADFrequency']
if n2 <0: break
if dataBlockHeader['Type'] == 1:
#spike
unit = dataBlockHeader['Unit']
pos = pos_spikes[chan,unit]
stimearrays[chan, unit][pos] = time
if load_spike_waveform and n1*n2 != 0 :
swfarrays[chan,unit][pos,:,:] = np.fromstring( fid.read(n1*n2*2) , dtype = 'i2').reshape(n1,n2).astype('f4')
else:
fid.seek(n1*n2*2,1)
pos_spikes[chan,unit] +=1
elif dataBlockHeader['Type'] == 4:
# event
pos = eventpositions[chan]
evarrays[chan][pos] = time
eventpositions[chan]+= 1
elif dataBlockHeader['Type'] == 5:
#signal
data = np.fromstring( fid.read(n2*2) , dtype = 'i2').astype('f4')
sigarrays[chan][sample_positions[chan] : sample_positions[chan]+data.size] = data
sample_positions[chan] += data.size
## Step 3: create neo object
for chan, h in iteritems(eventHeaders):
if lazy:
times = [ ]
else:
times = evarrays[chan]
ea = EventArray(times*pq.s,
channel_name= eventHeaders[chan]['Name'],
channel_index = chan)
if lazy:
ea.lazy_shape = nb_events[chan]
seg.eventarrays.append(ea)
for chan, h in iteritems(slowChannelHeaders):
if lazy:
signal = [ ]
else:
if globalHeader['Version'] ==100 or globalHeader['Version'] ==101 :
gain = 5000./(2048*slowChannelHeaders[chan]['Gain']*1000.)
elif globalHeader['Version'] ==102 :
gain = 5000./(2048*slowChannelHeaders[chan]['Gain']*slowChannelHeaders[chan]['PreampGain'])
elif globalHeader['Version'] >= 103:
gain = globalHeader['SlowMaxMagnitudeMV']/(.5*(2**globalHeader['BitsPerSpikeSample'])*\
slowChannelHeaders[chan]['Gain']*slowChannelHeaders[chan]['PreampGain'])
signal = sigarrays[chan]*gain
anasig = AnalogSignal(signal*pq.V,
sampling_rate = float(slowChannelHeaders[chan]['ADFreq'])*pq.Hz,
t_start = t_starts[chan]*pq.s,
channel_index = slowChannelHeaders[chan]['Channel'],
channel_name = slowChannelHeaders[chan]['Name'],
)
if lazy:
anasig.lazy_shape = nb_samples[chan]
seg.analogsignals.append(anasig)
for (chan, unit), value in np.ndenumerate(nb_spikes):
if nb_spikes[chan, unit] == 0: continue
if lazy:
times = [ ]
waveforms = None
t_stop = 0
else:
times = stimearrays[chan,unit]
t_stop = times.max()
if load_spike_waveform:
if globalHeader['Version'] <103:
gain = 3000./(2048*dspChannelHeaders[chan]['Gain']*1000.)
elif globalHeader['Version'] >=103 and globalHeader['Version'] <105:
gain = globalHeader['SpikeMaxMagnitudeMV']/(.5*2.**(globalHeader['BitsPerSpikeSample'])*1000.)
elif globalHeader['Version'] >105:
gain = globalHeader['SpikeMaxMagnitudeMV']/(.5*2.**(globalHeader['BitsPerSpikeSample'])*globalHeader['SpikePreAmpGain'])
waveforms = swfarrays[chan, unit] * gain * pq.V
else:
waveforms = None
sptr = SpikeTrain(times,
units='s', t_stop=t_stop*pq.s,
waveforms = waveforms,
)
sptr.annotate(unit_name = dspChannelHeaders[chan]['Name'])
sptr.annotate(channel_index = chan)
if lazy:
sptr.lazy_shape = nb_spikes[chan,unit]
seg.spiketrains.append(sptr)
create_many_to_one_relationship(seg)
return seg
def read_segment(self, lazy=False, cascade=True):
seg = Segment(file_origin=os.path.basename(self.filename), )
if not cascade:
return seg
fid = open(self.filename, 'rb')
headertext = fid.read(2048)
if PY3K:
headertext = headertext.decode('ascii')
header = {}
for line in headertext.split('\r\n'):
if '=' not in line: continue
#print '#' , line , '#'
key, val = line.split('=')
if key in [
'NC', 'NR', 'NBH', 'NBA', 'NBD', 'ADCMAX', 'NP', 'NZ',
'ADCMAX'
]:
val = int(val)
elif key in [
'AD',
'DT',
]:
val = val.replace(',', '.')
val = float(val)
header[key] = val
if not lazy:
data = np.memmap(
self.filename,
np.dtype('i2'),
'r',
#shape = (header['NC'], header['NP']) ,
shape=(
header['NP'] / header['NC'],
header['NC'],
),
offset=header['NBH'])
for c in range(header['NC']):
YCF = float(header['YCF%d' % c].replace(',', '.'))
YAG = float(header['YAG%d' % c].replace(',', '.'))
YZ = float(header['YZ%d' % c].replace(',', '.'))
ADCMAX = header['ADCMAX']
AD = header['AD']
DT = header['DT']
if 'TU' in header:
if header['TU'] == 'ms':
DT *= .001
unit = header['YU%d' % c]
try:
unit = pq.Quantity(1., unit)
except:
unit = pq.Quantity(1., '')
if lazy:
signal = [] * unit
else:
signal = (data[:, header['YO%d' % c]].astype('f4') -
YZ) * AD / (YCF * YAG * (ADCMAX + 1)) * unit
ana = AnalogSignal(signal,
sampling_rate=pq.Hz / DT,
t_start=0. * pq.s,
name=header['YN%d' % c],
channel_index=c)
if lazy:
ana.lazy_shape = header['NP'] / header['NC']
seg.analogsignals.append(ana)
create_many_to_one_relationship(seg)
return seg
def read_segment(self, lazy=False, cascade=True):
## Read header file (vhdr)
header = readBrainSoup(self.filename)
assert header['Common Infos'][
'DataFormat'] == 'BINARY', NotImplementedError
assert header['Common Infos'][
'DataOrientation'] == 'MULTIPLEXED', NotImplementedError
nb_channel = int(header['Common Infos']['NumberOfChannels'])
sampling_rate = 1.e6 / float(
header['Common Infos']['SamplingInterval']) * pq.Hz
fmt = header['Binary Infos']['BinaryFormat']
fmts = {
'INT_16': np.int16,
'IEEE_FLOAT_32': np.float32,
}
assert fmt in fmts, NotImplementedError
dt = fmts[fmt]
seg = Segment(file_origin=os.path.basename(self.filename), )
if not cascade: return seg
# read binary
if not lazy:
binary_file = os.path.splitext(self.filename)[0] + '.eeg'
sigs = np.memmap(
binary_file,
dt,
'r',
).astype('f')
n = int(sigs.size / nb_channel)
sigs = sigs[:n * nb_channel]
sigs = sigs.reshape(n, nb_channel)
for c in range(nb_channel):
name, ref, res, units = header['Channel Infos']['Ch%d' %
(c +
1, )].split(',')
units = pq.Quantity(1, units.replace('µ', 'u'))
if lazy:
signal = [] * units
else:
signal = sigs[:, c] * units
anasig = AnalogSignal(
signal=signal,
channel_index=c,
name=name,
sampling_rate=sampling_rate,
)
if lazy:
anasig.lazy_shape = -1
seg.analogsignals.append(anasig)
# read marker
marker_file = os.path.splitext(self.filename)[0] + '.vmrk'
all_info = readBrainSoup(marker_file)['Marker Infos']
all_types = []
times = []
labels = []
for i in range(len(all_info)):
type_, label, pos, size, channel = all_info['Mk%d' %
(i +
1, )].split(',')[:5]
all_types.append(type_)
times.append(float(pos) / sampling_rate.magnitude)
labels.append(label)
all_types = np.array(all_types)
times = np.array(times) * pq.s
labels = np.array(labels, dtype='S')
for type_ in np.unique(all_types):
ind = type_ == all_types
if lazy:
ea = EventArray(name=str(type_))
ea.lazy_shape = -1
else:
ea = EventArray(
times=times[ind],
labels=labels[ind],
name=str(type_),
)
seg.eventarrays.append(ea)
create_many_to_one_relationship(seg)
return seg
def read_block(
self,
lazy=False,
cascade=True,
):
bl = Block(file_origin=os.path.basename(self.filename), )
if not cascade:
return bl
fid = open(self.filename, 'rb')
headertext = fid.read(1024)
if PY3K:
headertext = headertext.decode('ascii')
header = {}
for line in headertext.split('\r\n'):
if '=' not in line: continue
#print '#' , line , '#'
key, val = line.split('=')
if key in [
'NC',
'NR',
'NBH',
'NBA',
'NBD',
'ADCMAX',
'NP',
'NZ',
]:
val = int(val)
elif key in [
'AD',
'DT',
]:
val = val.replace(',', '.')
val = float(val)
header[key] = val
#print header
SECTORSIZE = 512
# loop for record number
for i in range(header['NR']):
#print 'record ',i
offset = 1024 + i * (SECTORSIZE * header['NBD'] + 1024)
# read analysis zone
analysisHeader = HeaderReader(
fid, AnalysisDescription).read_f(offset=offset)
#print analysisHeader
# read data
NP = (SECTORSIZE * header['NBD']) / 2
NP = NP - NP % header['NC']
NP = NP / header['NC']
if not lazy:
data = np.memmap(
self.filename,
np.dtype('i2'),
'r',
#shape = (header['NC'], header['NP']) ,
shape=(
NP,
header['NC'],
),
offset=offset + header['NBA'] * SECTORSIZE)
# create a segment
seg = Segment()
bl.segments.append(seg)
for c in range(header['NC']):
unit = header['YU%d' % c]
try:
unit = pq.Quantity(1., unit)
except:
unit = pq.Quantity(1., '')
if lazy:
signal = [] * unit
else:
YG = float(header['YG%d' % c].replace(',', '.'))
ADCMAX = header['ADCMAX']
VMax = analysisHeader['VMax'][c]
signal = data[:, header['YO%d' % c]].astype(
'f4') * VMax / ADCMAX / YG * unit
anaSig = AnalogSignal(
signal,
sampling_rate=pq.Hz / analysisHeader['SamplingInterval'],
t_start=analysisHeader['TimeRecorded'] * pq.s,
name=header['YN%d' % c],
channel_index=c)
if lazy:
anaSig.lazy_shape = NP
seg.analogsignals.append(anaSig)
fid.close()
create_many_to_one_relationship(bl)
return bl
def read_segment(
self,
lazy=False,
cascade=True,
):
fid = open(self.filename, 'rb')
globalHeader = HeaderReader(fid, GlobalHeader).read_f(offset=0)
#~ print globalHeader
#~ print 'version' , globalHeader['version']
seg = Segment()
seg.file_origin = os.path.basename(self.filename)
seg.annotate(neuroexplorer_version=globalHeader['version'])
seg.annotate(comment=globalHeader['comment'])
if not cascade:
return seg
offset = 544
for i in range(globalHeader['nvar']):
entityHeader = HeaderReader(
fid, EntityHeader).read_f(offset=offset + i * 208)
entityHeader['name'] = entityHeader['name'].replace('\x00', '')
#print 'i',i, entityHeader['type']
if entityHeader['type'] == 0:
# neuron
if lazy:
spike_times = [] * pq.s
else:
spike_times = np.memmap(
self.filename,
np.dtype('i4'),
'r',
shape=(entityHeader['n']),
offset=entityHeader['offset'],
)
spike_times = spike_times.astype(
'f8') / globalHeader['freq'] * pq.s
sptr = SpikeTrain(
times=spike_times,
t_start=globalHeader['tbeg'] / globalHeader['freq'] * pq.s,
t_stop=globalHeader['tend'] / globalHeader['freq'] * pq.s,
name=entityHeader['name'],
)
if lazy:
sptr.lazy_shape = entityHeader['n']
sptr.annotate(channel_index=entityHeader['WireNumber'])
seg.spiketrains.append(sptr)
if entityHeader['type'] == 1:
# event
if lazy:
event_times = [] * pq.s
else:
event_times = np.memmap(
self.filename,
np.dtype('i4'),
'r',
shape=(entityHeader['n']),
offset=entityHeader['offset'],
)
event_times = event_times.astype(
'f8') / globalHeader['freq'] * pq.s
labels = np.array([''] * event_times.size, dtype='S')
evar = EventArray(times=event_times,
labels=labels,
channel_name=entityHeader['name'])
if lazy:
evar.lazy_shape = entityHeader['n']
seg.eventarrays.append(evar)
if entityHeader['type'] == 2:
# interval
if lazy:
start_times = [] * pq.s
stop_times = [] * pq.s
else:
start_times = np.memmap(
self.filename,
np.dtype('i4'),
'r',
shape=(entityHeader['n']),
offset=entityHeader['offset'],
)
start_times = start_times.astype(
'f8') / globalHeader['freq'] * pq.s
stop_times = np.memmap(
self.filename,
np.dtype('i4'),
'r',
shape=(entityHeader['n']),
offset=entityHeader['offset'] + entityHeader['n'] * 4,
)
stop_times = stop_times.astype(
'f') / globalHeader['freq'] * pq.s
epar = EpochArray(times=start_times,
durations=stop_times - start_times,
labels=np.array([''] * start_times.size,
dtype='S'),
channel_name=entityHeader['name'])
if lazy:
epar.lazy_shape = entityHeader['n']
seg.epocharrays.append(epar)
if entityHeader['type'] == 3:
# spiketrain and wavefoms
if lazy:
spike_times = [] * pq.s
waveforms = None
else:
spike_times = np.memmap(
self.filename,
np.dtype('i4'),
'r',
shape=(entityHeader['n']),
offset=entityHeader['offset'],
)
spike_times = spike_times.astype(
'f8') / globalHeader['freq'] * pq.s
waveforms = np.memmap(
self.filename,
np.dtype('i2'),
'r',
shape=(entityHeader['n'], 1,
entityHeader['NPointsWave']),
offset=entityHeader['offset'] + entityHeader['n'] * 4,
)
waveforms = (waveforms.astype('f') * entityHeader['ADtoMV']
+ entityHeader['MVOffset']) * pq.mV
t_stop = globalHeader['tend'] / globalHeader['freq'] * pq.s
if spike_times.size > 0:
t_stop = max(t_stop, max(spike_times))
sptr = SpikeTrain(
times=spike_times,
t_start=globalHeader['tbeg'] / globalHeader['freq'] * pq.s,
#~ t_stop = max(globalHeader['tend']/globalHeader['freq']*pq.s,max(spike_times)),
t_stop=t_stop,
name=entityHeader['name'],
waveforms=waveforms,
sampling_rate=entityHeader['WFrequency'] * pq.Hz,
left_sweep=0 * pq.ms,
)
if lazy:
sptr.lazy_shape = entityHeader['n']
sptr.annotate(channel_index=entityHeader['WireNumber'])
seg.spiketrains.append(sptr)
if entityHeader['type'] == 4:
# popvectors
pass
if entityHeader['type'] == 5:
# analog
timestamps = np.memmap(
self.filename,
np.dtype('i4'),
'r',
shape=(entityHeader['n']),
offset=entityHeader['offset'],
)
timestamps = timestamps.astype('f8') / globalHeader['freq']
fragmentStarts = np.memmap(
self.filename,
np.dtype('i4'),
'r',
shape=(entityHeader['n']),
offset=entityHeader['offset'],
)
fragmentStarts = fragmentStarts.astype(
'f8') / globalHeader['freq']
t_start = timestamps[0] - fragmentStarts[0] / float(
entityHeader['WFrequency'])
del timestamps, fragmentStarts
if lazy:
signal = [] * pq.mV
else:
signal = np.memmap(
self.filename,
np.dtype('i2'),
'r',
shape=(entityHeader['NPointsWave']),
offset=entityHeader['offset'],
)
signal = signal.astype('f')
signal *= entityHeader['ADtoMV']
signal += entityHeader['MVOffset']
signal = signal * pq.mV
anaSig = AnalogSignal(
signal=signal,
t_start=t_start * pq.s,
sampling_rate=entityHeader['WFrequency'] * pq.Hz,
name=entityHeader['name'],
channel_index=entityHeader['WireNumber'])
if lazy:
anaSig.lazy_shape = entityHeader['NPointsWave']
seg.analogsignals.append(anaSig)
if entityHeader['type'] == 6:
# markers : TO TEST
if lazy:
times = [] * pq.s
labels = np.array([], dtype='S')
markertype = None
else:
times = np.memmap(
self.filename,
np.dtype('i4'),
'r',
shape=(entityHeader['n']),
offset=entityHeader['offset'],
)
times = times.astype('f8') / globalHeader['freq'] * pq.s
fid.seek(entityHeader['offset'] + entityHeader['n'] * 4)
markertype = fid.read(64).replace('\x00', '')
labels = np.memmap(
self.filename,
np.dtype('S' + str(entityHeader['MarkerLength'])),
'r',
shape=(entityHeader['n']),
offset=entityHeader['offset'] + entityHeader['n'] * 4 +
64)
ea = EventArray(times=times,
labels=labels.view(np.ndarray),
name=entityHeader['name'],
channel_index=entityHeader['WireNumber'],
marker_type=markertype)
if lazy:
ea.lazy_shape = entityHeader['n']
seg.eventarrays.append(ea)
create_many_to_one_relationship(seg)
return seg
def proc_f32(filename):
'''Load an f32 file that has already been processed by the official matlab
file converter. That matlab data is saved to an m-file, which is then
converted to a numpy '.npz' file. This numpy file is the file actually
loaded. This function converts it to a neo block and returns the block.
This block can be compared to the block produced by BrainwareF32IO to
make sure BrainwareF32IO is working properly
block = proc_f32(filename)
filename: The file name of the numpy file to load. It should end with
'*_f32_py?.npz'. This will be converted to a neo 'file_origin' property
with the value '*.f32', so the filename to compare should fit that pattern.
'py?' should be 'py2' for the python 2 version of the numpy file or 'py3'
for the python 3 version of the numpy file.
example: filename = 'file1_f32_py2.npz'
f32 file name = 'file1.f32'
'''
filenameorig = os.path.basename(filename[:-12]+'.f32')
# create the objects to store other objects
block = Block(file_origin=filenameorig)
rcg = RecordingChannelGroup(file_origin=filenameorig)
rcg.channel_indexes = np.array([], dtype=np.int)
rcg.channel_names = np.array([], dtype='S')
unit = Unit(file_origin=filenameorig)
# load objects into their containers
block.recordingchannelgroups.append(rcg)
rcg.units.append(unit)
try:
with np.load(filename) as f32obj:
f32file = f32obj.items()[0][1].flatten()
except IOError as exc:
if 'as a pickle' in exc.message:
create_many_to_one_relationship(block)
return block
else:
raise
sweeplengths = [res[0, 0].tolist() for res in f32file['sweeplength']]
stims = [res.flatten().tolist() for res in f32file['stim']]
sweeps = [res['spikes'].flatten() for res in f32file['sweep'] if res.size]
fullf32 = zip(sweeplengths, stims, sweeps)
for sweeplength, stim, sweep in fullf32:
for trainpts in sweep:
if trainpts.size:
trainpts = trainpts.flatten().astype('float32')
else:
trainpts = []
paramnames = ['Param%s' % i for i in range(len(stim))]
params = dict(zip(paramnames, stim))
train = SpikeTrain(trainpts, units=pq.ms,
t_start=0, t_stop=sweeplength,
file_origin=filenameorig)
segment = Segment(file_origin=filenameorig, **params)
segment.spiketrains = [train]
unit.spiketrains.append(train)
block.segments.append(segment)
create_many_to_one_relationship(block)
return block
