/usr/share/pyshared/neo/io/spike2io.py is in python-neo 0.2.0-1.
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"""
Classe for reading data in CED spike2 files (.smr).
This code is based on:
- sonpy, written by Antonio Gonzalez <Antonio.Gonzalez@cantab.net>
Disponible here ::
http://www.neuro.ki.se/broberger/
and sonpy come from :
- SON Library 2.0 for MATLAB, written by Malcolm Lidierth at
King's College London. See http://www.kcl.ac.uk/depsta/biomedical/cfnr/lidierth.html
This IO support old (<v6) and new files (>v7) of spike2
Depend on:
Supported : Read
Author: sgarcia
"""
from .baseio import BaseIO
from ..core import *
from .tools import create_many_to_one_relationship
import numpy as np
from numpy import dtype, zeros, fromstring, empty
import quantities as pq
import os, sys
PY3K = (sys.version_info[0] == 3)
class Spike2IO(BaseIO):
"""
Class for reading data from CED spike2.
Usage:
>>> from neo import io
>>> r = io.Spike2IO( filename = 'File_spike2_1.smr')
>>> seg = r.read_segment(lazy = False, cascade = True,)
>>> print seg.analogsignals
>>> print seg.spiketrains
>>> print seg.eventarrays
"""
is_readable = True
is_writable = False
supported_objects = [ Segment , AnalogSignal , EventArray, SpikeTrain]
readable_objects = [Segment]
writeable_objects = [ ]
has_header = False
is_streameable = False
read_params = { Segment : [ ], }
write_params = None
name = 'Spike 2 CED'
extensions = [ 'smr' ]
mode = 'file'
def __init__(self , filename = None) :
"""
This class read a smr file.
Arguments:
filename : the filename
"""
BaseIO.__init__(self)
self.filename = filename
def read_segment(self ,
lazy = False,
cascade = True,
):
"""
Arguments:
"""
header = self.read_header(filename = self.filename)
#~ print header
fid = open(self.filename, 'rb')
seg = Segment(
file_origin = os.path.basename(self.filename),
ced_version = str(header.system_id),
)
if not cascade:
return seg
def addannotations(ob, channelHeader):
ob.annotate(title = channelHeader.title)
ob.annotate(physical_channel_index = channelHeader.phy_chan)
ob.annotate(comment = channelHeader.comment)
for i in range(header.channels) :
channelHeader = header.channelHeaders[i]
#~ print 'channel' , i , 'kind' , channelHeader.kind
if channelHeader.kind !=0:
#~ print '####'
#~ print 'channel' , i, 'kind' , channelHeader.kind , channelHeader.type , channelHeader.phy_chan
#~ print channelHeader
pass
if channelHeader.kind in [1, 9]:
#~ print 'analogChanel'
anaSigs = self.readOneChannelContinuous( fid, i, header ,lazy = lazy)
#~ print 'nb sigs', len(anaSigs) , ' sizes : ',
for anaSig in anaSigs :
addannotations(anaSig, channelHeader)
seg.analogsignals.append( anaSig )
#~ print sig.signal.size,
#~ print ''
elif channelHeader.kind in [2, 3, 4, 5, 8] :
ea = self.readOneChannelEventOrSpike( fid, i, header , lazy = lazy)
addannotations(ea, channelHeader)
seg.eventarrays.append(ea)
elif channelHeader.kind in [6,7] :
sptr = self.readOneChannelEventOrSpike( fid, i, header, lazy = lazy )
if sptr is not None:
addannotations(sptr, channelHeader)
seg.spiketrains.append(sptr)
fid.close()
create_many_to_one_relationship(seg)
return seg
def read_header(self , filename = ''):
fid = open(filename, 'rb')
header = HeaderReader(fid, dtype(headerDescription))
#~ print 'chan_size' , header.chan_size
if header.system_id < 6:
header.dtime_base = 1e-6
header.datetime_detail = 0
header.datetime_year = 0
channelHeaders = [ ]
for i in range(header.channels):
# read global channel header
fid.seek(512 + 140*i) # TODO verifier i ou i-1
channelHeader = HeaderReader(fid, dtype(channelHeaderDesciption1))
if channelHeader.kind in [1, 6]:
dt = [('scale' , 'f4'),
('offset' , 'f4'),
('unit' , 'S6'),]
channelHeader += HeaderReader(fid, dtype(dt))
if header.system_id < 6:
channelHeader += HeaderReader(fid, dtype([ ('divide' , 'i4')]) )#i8
else :
channelHeader +=HeaderReader(fid, dtype([ ('interleave' , 'i4')]) )#i8
if channelHeader.kind in [7, 9]:
dt = [('min' , 'f4'),
('max' , 'f4'),
('unit' , 'S6'),]
channelHeader += HeaderReader(fid, dtype(dt))
if header.system_id < 6:
channelHeader += HeaderReader(fid, dtype([ ('divide' , 'i4')]))#i8
else :
channelHeader += HeaderReader(fid, dtype([ ('interleave' , 'i4')]) )#i8
if channelHeader.kind in [4]:
dt = [('init_low' , 'u1'),
('next_low' , 'u1'),]
channelHeader += HeaderReader(fid, dtype(dt))
channelHeader.type = dict_kind[channelHeader.kind]
channelHeaders.append(channelHeader)
header.channelHeaders = channelHeaders
fid.close()
return header
def readOneChannelContinuous(self , fid, channel_num, header ,lazy = True):
# read AnalogSignal
channelHeader = header.channelHeaders[channel_num]
# data type
if channelHeader.kind == 1:
dt = np.dtype('i2')
elif channelHeader.kind == 9:
dt = np.dtype('f4')
# sample rate
if header.system_id in [1,2,3,4,5]: # Before version 5
sample_interval = (channelHeader.divide*header.us_per_time*header.time_per_adc)*1e-6
else :
sample_interval = (channelHeader.l_chan_dvd*header.us_per_time*header.dtime_base)
sampling_rate = (1./sample_interval)*pq.Hz
# read blocks header to preallocate memory by jumping block to block
fid.seek(channelHeader.firstblock)
blocksize = [ 0 ]
starttimes = [ ]
for b in range(channelHeader.blocks) :
blockHeader = HeaderReader(fid, dtype(blockHeaderDesciption))
if len(blocksize) > len(starttimes):
starttimes.append(blockHeader.start_time)
blocksize[-1] += blockHeader.items
if blockHeader.succ_block > 0 :
# this is ugly but CED do not garanty continuity in AnalogSignal
fid.seek(blockHeader.succ_block)
nextBlockHeader = HeaderReader(fid, dtype(blockHeaderDesciption))
sample_interval = (blockHeader.end_time-blockHeader.start_time)/(blockHeader.items-1)
interval_with_next = nextBlockHeader.start_time - blockHeader.end_time
if interval_with_next > sample_interval:
blocksize.append(0)
fid.seek(blockHeader.succ_block)
anaSigs = [ ]
if channelHeader.unit in unit_convert:
unit = pq.Quantity(1, unit_convert[channelHeader.unit] )
else:
#print channelHeader.unit
try:
unit = pq.Quantity(1, channelHeader.unit )
except:
unit = pq.Quantity(1, '')
for b,bs in enumerate(blocksize ):
if lazy:
signal = [ ]*unit
else:
signal = empty( bs , dtype = 'f4') * unit
anaSig = AnalogSignal(signal ,
sampling_rate = sampling_rate,
t_start = starttimes[b]*header.us_per_time * header.dtime_base * pq.s,
)
anaSig.annotate(channel_index = channel_num)
anaSigs.append( anaSig )
if lazy:
for s, anaSig in enumerate(anaSigs):
anaSig.lazy_shape = blocksize[s]
else:
# read data by jumping block to block
fid.seek(channelHeader.firstblock)
pos = 0
numblock = 0
for b in range(channelHeader.blocks) :
blockHeader = HeaderReader(fid, dtype(blockHeaderDesciption))
# read data
sig = fromstring( fid.read(blockHeader.items*dt.itemsize) , dtype = dt)
anaSigs[numblock][pos:pos+sig.size] = sig.astype('f4')*unit
pos += sig.size
if pos >= blocksize[numblock] :
numblock += 1
pos = 0
# jump to next block
if blockHeader.succ_block > 0 :
fid.seek(blockHeader.succ_block)
# convert for int16
if dt.kind == 'i' :
for anaSig in anaSigs :
anaSig *= channelHeader.scale/ 6553.6
anaSig += channelHeader.offset*unit
return anaSigs
def readOneChannelEventOrSpike(self , fid, channel_num, header ,lazy = True):
# return SPikeTrain or EventArray
channelHeader = header.channelHeaders[channel_num]
if channelHeader.firstblock <0: return
if channelHeader.kind not in [2, 3, 4 , 5 , 6 ,7, 8]: return
## Step 1 : type of blocks
if channelHeader.kind in [2, 3, 4]:
# Event data
format = [('tick' , 'i4') ]
elif channelHeader.kind in [5]:
# Marker data
format = [('tick' , 'i4') , ('marker' , 'i4') ]
elif channelHeader.kind in [6]:
# AdcMark data
format = [('tick' , 'i4') , ('marker' , 'i4') , ('adc' , 'S%d' %channelHeader.n_extra )]
elif channelHeader.kind in [7]:
# RealMark data
format = [('tick' , 'i4') , ('marker' , 'i4') , ('real' , 'S%d' %channelHeader.n_extra )]
elif channelHeader.kind in [8]:
# TextMark data
format = [('tick' , 'i4') , ('marker' , 'i4') , ('label' , 'S%d'%channelHeader.n_extra)]
dt = dtype(format)
## Step 2 : first read for allocating mem
fid.seek(channelHeader.firstblock)
totalitems = 0
for b in range(channelHeader.blocks) :
blockHeader = HeaderReader(fid, dtype(blockHeaderDesciption))
totalitems += blockHeader.items
if blockHeader.succ_block > 0 :
fid.seek(blockHeader.succ_block)
#~ print 'totalitems' , totalitems
if lazy :
if channelHeader.kind in [2, 3, 4 , 5 , 8]:
ea = EventArray( )
ea.annotate(channel_index = channel_num)
ea.lazy_shape = totalitems
return ea
elif channelHeader.kind in [6 ,7]:
sptr = SpikeTrain([ ]*pq.s, t_stop=1e99) # correct value for t_stop to be put in later
sptr.annotate(channel_index = channel_num)
sptr.lazy_shape = totalitems
return sptr
else:
alltrigs = zeros( totalitems , dtype = dt)
## Step 3 : read
fid.seek(channelHeader.firstblock)
pos = 0
for b in range(channelHeader.blocks) :
blockHeader = HeaderReader(fid, dtype(blockHeaderDesciption))
# read all events in block
trigs = fromstring( fid.read( blockHeader.items*dt.itemsize) , dtype = dt)
alltrigs[pos:pos+trigs.size] = trigs
pos += trigs.size
if blockHeader.succ_block > 0 :
fid.seek(blockHeader.succ_block)
## Step 3 convert in neo standard class : eventarrays or spiketrains
alltimes = alltrigs['tick'].astype('f')*header.us_per_time * header.dtime_base*pq.s
if channelHeader.kind in [2, 3, 4 , 5 , 8]:
#events
ea = EventArray( )
ea.annotate(channel_index = channel_num)
ea.times = alltimes
if channelHeader.kind >= 5:
# Spike2 marker is closer to label sens of neo
ea.labels = alltrigs['marker'].astype('S')
if channelHeader.kind == 8:
ea.annotate(extra_labels = alltrigs['label'])
return ea
elif channelHeader.kind in [6 ,7]:
# spiketrains
# waveforms
if channelHeader.kind == 6 :
waveforms = fromstring(alltrigs['adc'].tostring() , dtype = 'i2')
waveforms = waveforms.astype('f4') *channelHeader.scale/ 6553.6 + channelHeader.offset
elif channelHeader.kind == 7 :
waveforms = fromstring(alltrigs['real'].tostring() , dtype = 'f4')
if header.system_id>=6 and channelHeader.interleave>1:
waveforms = waveforms.reshape((alltimes.size,-1,channelHeader.interleave))
waveforms = waveforms.swapaxes(1,2)
else:
waveforms = waveforms.reshape(( alltimes.size,1, -1))
if header.system_id in [1,2,3,4,5]:
sample_interval = (channelHeader.divide*header.us_per_time*header.time_per_adc)*1e-6
else :
sample_interval = (channelHeader.l_chan_dvd*header.us_per_time*header.dtime_base)
if channelHeader.unit in unit_convert:
unit = pq.Quantity(1, unit_convert[channelHeader.unit] )
else:
#print channelHeader.unit
try:
unit = pq.Quantity(1, channelHeader.unit )
except:
unit = pq.Quantity(1, '')
if len(alltimes) > 0:
t_stop = alltimes.max() # can get better value from associated AnalogSignal(s) ?
else:
t_stop = 0.0
sptr = SpikeTrain(alltimes,
waveforms = waveforms*unit,
sampling_rate = (1./sample_interval)*pq.Hz,
t_stop = t_stop
)
sptr.annotate(channel_index = channel_num)
return sptr
class HeaderReader(object):
def __init__(self , fid , dtype):
if fid is not None :
array = np.fromstring( fid.read(dtype.itemsize) , dtype)[0]
else :
array = zeros( (1) , dtype = dtype)[0]
object.__setattr__(self, 'dtype' , dtype)
object.__setattr__(self, 'array' , array)
def __setattr__(self, name , val):
if name in self.dtype.names :
self.array[name] = val
else :
object.__setattr__(self, name , val)
def __getattr__(self , name):
#~ print name
if name in self.dtype.names :
if self.dtype[name].kind == 'S':
if PY3K:
l = np.fromstring(self.array[name].decode('iso-8859-1')[0], 'u1')
else:
l = np.fromstring(self.array[name][0], 'u1')
return self.array[name][1:l+1]
else:
return self.array[name]
else :
object.__getattr__(self, name )
def names(self):
return self.array.dtype.names
def __repr__(self):
s = 'HEADER'
for name in self.dtype.names :
#~ if self.dtype[name].kind != 'S' :
s += name + self.__getattr__(name)
return s
def __add__(self, header2):
# print 'add' , self.dtype, header2.dtype
newdtype = [ ]
for name in self.dtype.names :
newdtype.append( (name , self.dtype[name].str) )
for name in header2.dtype.names :
newdtype.append( (name , header2.dtype[name].str) )
newdtype = dtype(newdtype)
newHeader = HeaderReader(None , newdtype )
newHeader.array = fromstring( self.array.tostring()+header2.array.tostring() , newdtype)[0]
return newHeader
# headers structures :
headerDescription = [
( 'system_id', 'i2' ),
( 'copyright', 'S10' ),
( 'creator', 'S8' ),
( 'us_per_time', 'i2' ),
( 'time_per_adc', 'i2' ),
( 'filestate', 'i2' ),
( 'first_data', 'i4' ),#i8
( 'channels', 'i2' ),
( 'chan_size', 'i2' ),
( 'extra_data', 'i2' ),
( 'buffersize', 'i2' ),
( 'os_format', 'i2' ),
( 'max_ftime', 'i4' ),#i8
( 'dtime_base', 'f8' ),
( 'datetime_detail', 'u1' ),
( 'datetime_year', 'i2' ),
( 'pad', 'S52' ),
( 'comment1', 'S80' ),
( 'comment2', 'S80' ),
( 'comment3', 'S80' ),
( 'comment4', 'S80' ),
( 'comment5', 'S80' ),
]
channelHeaderDesciption1 = [
('del_size','i2'),
('next_del_block','i4'),#i8
('firstblock','i4'),#i8
('lastblock','i4'),#i8
('blocks','i2'),
('n_extra','i2'),
('pre_trig','i2'),
('free0','i2'),
('py_sz','i2'),
('max_data','i2'),
('comment','S72'),
('max_chan_time','i4'),#i8
('l_chan_dvd','i4'),#i8
('phy_chan','i2'),
('title','S10'),
('ideal_rate','f4'),
('kind','u1'),
('unused1','i1'),
]
dict_kind = {
0 : 'empty',
1: 'Adc',
2: 'EventFall',
3: 'EventRise',
4: 'EventBoth',
5: 'Marker',
6: 'AdcMark',
7: 'RealMark',
8: 'TextMark',
9: 'RealWave',
}
blockHeaderDesciption =[
('pred_block','i4'),#i8
('succ_block','i4'),#i8
('start_time','i4'),#i8
('end_time','i4'),#i8
('channel_num','i2'),
('items','i2'),
]
unit_convert = {
'Volts' : 'V' ,
}
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