def _get_head(self):
"""Wraps EEGFile._get_head to modify the channel information"""
# Retreive data
head = super(MontageFile, self)._get_head()
chan = head.chan
# Check montage labels
labels = [c.label for c in chan]
labels_lower = [l.lower() for l in labels]
new_chan = []
self.indices = []
for label in self.montage:
# Montage could use different case from file
elec1, elec2 = label.lower().split('-')
elec1 = labels[labels_lower.index(elec1)]
elec2 = labels[labels_lower.index(elec2)]
# Create chan dict for new chan
cnew = chan[labels.index(elec1)]
label = elec1 + '-' + elec2
new_chan.append(cnew._replace(label=label))
# These are used in _get_blocks
self.indices.append((label, elec1, elec2))
#
descr = [(c.label, 'i2', c.nsblock) for c in new_chan]
self._block_descriptor = BlockDescriptor(descr)
return head._replace(chan=new_chan, nchan=len(new_chan))
def __init__(self, tstart, tend, samples, labels=None, name='samples'):
"""Create a SampleFile interface to the data in samples
tstart : start time of file
tend : end time of file
samples : list of arrays of samples
labels : names of channels
"""
# Establish the number of channels
nchan = len(samples)
# Invent labels if necessary
if labels is None:
labels = ['Chan {0}'.format(n) for n in range(1, nchan + 1)]
# Enforce equal sample rates
nsamples = len(samples[0])
if not all((len(x) == nsamples) for x in samples):
raise EEGUnequalSamplesError("samples must be of equal length")
# Check number of labels
if len(labels) != nchan:
msg = "Expected {0} labels found {1}"
raise ValueError(msg.format(nchan, len(labels)))
# Determine block size
samplenos = [len(x) for x in samples]
secsdur = self.as_seconds(tend, tstart)
nblocks = _optimal_nblocks(secsdur, samplenos)
# Determine the number of seconds in a block as an integer
secsblock = secsdur / nblocks
if secsblock == int(secsblock):
secsblock = int(secsblock)
# Create channel header structures
chan = []
kwargs = {'calib':1, 'offset':0, 'dim':'uV'}
for lab, sam in zip(labels, samples):
nsblock = len(sam) // nblocks
chan.append(Chan(label=lab, nsblock=nsblock, **kwargs))
# Create main header structure
head = Head(tstart=tstart, secsblock=secsblock, chan=chan,
nchan=len(chan), nblocks=nblocks)
# Store what's needed for later
self.__samples = samples
self._head = head
self.name = name
# Used in _get_blocks
descr = [(c.label, 'i2', c.nsblock) for c in chan]
self._block_descriptor = BlockDescriptor(descr)
# Initialise
super(SampleFile, self).__init__(self)
def _read_head(self):
"""Read the main file header"""
# Actually read the file:
self._seek(0)
wg1_head = self._fromfile(_head_descr)[0]
# Extract channels
nchan = int(wg1_head["nchan"])
raw_chan = wg1_head["wg1_chan"][:nchan]
def as_chan(c):
return Chan(
label=c["label"].strip(), dim="uV", calib=1e-3 * c["calib"], offset=0, nsblock=_wg1_nsblock, finfo=c
)
head = Head(
pat_id="",
rec_id=split(self.name)[1],
tstart=self._wg1_datetime(wg1_head["wg1_daynum"], wg1_head["wg1_msnum"]),
nblocks=-1,
secsblock=_wg1_nsblock * 1e-6 * int(wg1_head["wg1_dtusec"]),
nchan=int(wg1_head["nchan"]),
chan=[as_chan(c) for c in raw_chan],
fmt="wg1",
finfo=wg1_head,
)
# How the block will be represented in memory
descr = [(c.label, "i2", c.nsblock) for c in head.chan]
self._block_descr = BlockDescriptor(descr)
# How the block appears on disk
self._headlen = _wg1_headlen
nchan = head.nchan
ntotal, nbegin = wg1_head["wg1_ntotal"], wg1_head["wg1_nbegin"]
self._blocklen = ntotal * _wg1_nsblock
pad1 = _wg1_nsblock * nbegin - 4 * nchan
pad2 = _wg1_nsblock * (ntotal - nbegin - nchan)
pad1 = pad1 or ""
pad2 = pad2 or ""
self._block_descr_raw = HeadDescriptor(
[
("chan", HeadDescriptor([("offset", "i2"), ("pad", "u2")]), nchan),
("pad1", "S" + str(pad1)),
("bytes", str(_wg1_nsblock) + "u1", nchan),
("pad2", "S" + str(pad2)),
],
nbytes=ntotal * _wg1_nsblock,
)
return head
class ChanMapFile(EEGFile):
"""ChanMapFile class
"""
def __init__(self, infile, chanmap=None):
"""Store the chanmap and initialise"""
self._chanmap = chanmap
super(ChanMapFile, self).__init__(infile)
def _setup_chanmap(self, channames, chanmap):
"""Returns a new chanmap based on the source chan info"""
# If not provided fill the identity map here
if chanmap is None:
chanmap = zip(channames, channames)
return chanmap
def _get_head(self):
"""Override EEGFile._get_head to modify channels"""
# Read original header
head = super(ChanMapFile, self)._get_head()
chan = head.chan
# Finalise the chanmap based on the source channel list
channames = [c.label for c in chan]
self._chanmap = self._setup_chanmap(channames, self._chanmap)
# Create new channel data
chan_d = dict((c.label, c) for c in chan)
new_chan = []
for c_old, c_new in self._chanmap:
new_chan.append(chan_d[c_old]._replace(label=c_new))
# Prepare data blocks
descr = [(c.label, 'i2', c.nsblock) for c in new_chan]
self._block_descriptor = BlockDescriptor(descr)
# Return head with modified information
return head._replace(chan=new_chan, nchan=len(new_chan))
def _get_blocks(self, n1, n2):
"""Override EEGFile._get_blocks to modify channels"""
# Read original blocks
old_blocks = super(ChanMapFile, self)._get_blocks(n1, n2)
# Map into the new block
new_blocks = self._block_descriptor.new(len(old_blocks))
for c_old, c_new in self._chanmap:
new_blocks[c_new] = old_blocks[c_old]
return new_blocks
class MontageFile(EEGFile):
def __init__(self, infile, montage, *args, **kwargs):
"""Set montage and initialise EEGFile object"""
if not montage in MONTAGES:
msg = "Unrecognised montage: '{0}'".format(montage)
raise UnrecognisedMontageError(msg)
self.montage = MONTAGES[montage]
EEGFile.__init__(self, infile, *args, **kwargs)
def _get_head(self):
"""Wraps EEGFile._get_head to modify the channel information"""
# Retreive data
head = super(MontageFile, self)._get_head()
chan = head.chan
# Check montage labels
labels = [c.label for c in chan]
labels_lower = [l.lower() for l in labels]
new_chan = []
self.indices = []
for label in self.montage:
# Montage could use different case from file
elec1, elec2 = label.lower().split('-')
elec1 = labels[labels_lower.index(elec1)]
elec2 = labels[labels_lower.index(elec2)]
# Create chan dict for new chan
cnew = chan[labels.index(elec1)]
label = elec1 + '-' + elec2
new_chan.append(cnew._replace(label=label))
# These are used in _get_blocks
self.indices.append((label, elec1, elec2))
#
descr = [(c.label, 'i2', c.nsblock) for c in new_chan]
self._block_descriptor = BlockDescriptor(descr)
return head._replace(chan=new_chan, nchan=len(new_chan))
def _get_blocks(self, n1, n2):
"""Wraps EEGFile._get_blocks to change the montage of the data"""
block = EEGFile._get_blocks(self, n1, n2)
new_block = self._block_descriptor.new(len(block))
for label, elec1, elec2 in self.indices:
new_block[label] = block[elec2] - block[elec1]
return new_block
def _get_head(self):
"""Override EEGFile._get_head to modify channels"""
# Read original header
head = super(ChanMapFile, self)._get_head()
chan = head.chan
# Finalise the chanmap based on the source channel list
channames = [c.label for c in chan]
self._chanmap = self._setup_chanmap(channames, self._chanmap)
# Create new channel data
chan_d = dict((c.label, c) for c in chan)
new_chan = []
for c_old, c_new in self._chanmap:
new_chan.append(chan_d[c_old]._replace(label=c_new))
# Prepare data blocks
descr = [(c.label, 'i2', c.nsblock) for c in new_chan]
self._block_descriptor = BlockDescriptor(descr)
# Return head with modified information
return head._replace(chan=new_chan, nchan=len(new_chan))
class Wg1File(IOFile):
"""Specialised for reading WG1 files"""
# String for use when opening the file
_binary = "b"
def _read_head(self):
"""Read the main file header"""
# Actually read the file:
self._seek(0)
wg1_head = self._fromfile(_head_descr)[0]
# Extract channels
nchan = int(wg1_head["nchan"])
raw_chan = wg1_head["wg1_chan"][:nchan]
def as_chan(c):
return Chan(
label=c["label"].strip(), dim="uV", calib=1e-3 * c["calib"], offset=0, nsblock=_wg1_nsblock, finfo=c
)
head = Head(
pat_id="",
rec_id=split(self.name)[1],
tstart=self._wg1_datetime(wg1_head["wg1_daynum"], wg1_head["wg1_msnum"]),
nblocks=-1,
secsblock=_wg1_nsblock * 1e-6 * int(wg1_head["wg1_dtusec"]),
nchan=int(wg1_head["nchan"]),
chan=[as_chan(c) for c in raw_chan],
fmt="wg1",
finfo=wg1_head,
)
# How the block will be represented in memory
descr = [(c.label, "i2", c.nsblock) for c in head.chan]
self._block_descr = BlockDescriptor(descr)
# How the block appears on disk
self._headlen = _wg1_headlen
nchan = head.nchan
ntotal, nbegin = wg1_head["wg1_ntotal"], wg1_head["wg1_nbegin"]
self._blocklen = ntotal * _wg1_nsblock
pad1 = _wg1_nsblock * nbegin - 4 * nchan
pad2 = _wg1_nsblock * (ntotal - nbegin - nchan)
pad1 = pad1 or ""
pad2 = pad2 or ""
self._block_descr_raw = HeadDescriptor(
[
("chan", HeadDescriptor([("offset", "i2"), ("pad", "u2")]), nchan),
("pad1", "S" + str(pad1)),
("bytes", str(_wg1_nsblock) + "u1", nchan),
("pad2", "S" + str(pad2)),
],
nbytes=ntotal * _wg1_nsblock,
)
return head
# ReadBlock reads in and converts one block of EEG data
# at a time.
def _read_block(self, n):
"""Read in one datablock"""
# Read raw block
self._seek(self._headlen + n * self._blocklen)
block_raw = self._fromfile(self._block_descr_raw)
# Check against magic end value:
if block_raw["chan"]["pad"][0][0] == _wg1_end:
self.nblocks = n
raise EOFError
# Convert to standard block type
chan = self.get_chan()
sigs = block_raw["bytes"][0]
block = self._block_descr.new(1)
for n, c in enumerate(chan):
label = c.label
index = c.finfo["wg1_index"]
sig = sigs[n]
offset = block_raw["chan"]["offset"][0, n]
diff = _wg1_conv[sig].cumsum()
block[label] = diff - offset
# import pdb; pdb.set_trace()
return block
def _read_blocks(self, n1, n2):
blocks = []
for n in range(n1, n2):
try:
blocks.append(self._read_block(n))
except EOFError:
if not blocks:
raise
else:
break
return self._block_descr.concatenate(blocks)
def _wg1_datetime(self, daynum, millisecond):
"""Convert two numbers in wg1 file to datetime"""
day = daynum - 0x250000 - 15755 - 1
timestamp = day * 86400 + millisecond / 1000.0
return datetime.fromtimestamp(timestamp)