/usr/share/pyshared/neo/io/spike2io.py is in python-neo 0.3.3-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 | # -*- coding: utf-8 -*-
"""
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
"""
import os
import sys
import numpy as np
import quantities as pq
from neo.io.baseio import BaseIO
from neo.core import Segment, AnalogSignal, SpikeTrain, EventArray
from neo.io.tools import create_many_to_one_relationship
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 : [ ('take_ideal_sampling_rate' , { 'value' : False })] }
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 ,
take_ideal_sampling_rate = False,
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, take_ideal_sampling_rate, lazy = lazy)
#~ print 'nb sigs', len(anaSigs) , ' sizes : ',
for anaSig in anaSigs :
addannotations(anaSig, channelHeader)
anaSig.name = str(anaSig.annotations['title'])
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)
if ea is not None:
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, np.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, np.dtype(channelHeaderDesciption1))
if channelHeader.kind in [1, 6]:
dt = [('scale' , 'f4'),
('offset' , 'f4'),
('unit' , 'S6'),]
channelHeader += HeaderReader(fid, np.dtype(dt))
if header.system_id < 6:
channelHeader += HeaderReader(fid, np.dtype([ ('divide' , 'i4')]) )#i8
else :
channelHeader +=HeaderReader(fid, np.dtype([ ('interleave' , 'i4')]) )#i8
if channelHeader.kind in [7, 9]:
dt = [('min' , 'f4'),
('max' , 'f4'),
('unit' , 'S6'),]
channelHeader += HeaderReader(fid, np.dtype(dt))
if header.system_id < 6:
channelHeader += HeaderReader(fid, np.dtype([ ('divide' , 'i4')]))#i8
else :
channelHeader += HeaderReader(fid, np.dtype([ ('interleave' , 'i4')]) )#i8
if channelHeader.kind in [4]:
dt = [('init_low' , 'u1'),
('next_low' , 'u1'),]
channelHeader += HeaderReader(fid, np.dtype(dt))
channelHeader.type = dict_kind[channelHeader.kind]
#~ print i, channelHeader
channelHeaders.append(channelHeader)
header.channelHeaders = channelHeaders
fid.close()
return header
def readOneChannelContinuous(self , fid, channel_num, header, take_ideal_sampling_rate, 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 take_ideal_sampling_rate:
sampling_rate = channelHeader.ideal_rate*pq.Hz
else:
if header.system_id in [1,2,3,4,5]: # Before version 5
#~ print channel_num, channelHeader.divide, header.us_per_time, header.time_per_adc
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, np.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, np.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 = pq.Quantity(np.empty( bs , dtype = 'f4'), units=unit)
anaSig = AnalogSignal(signal,
sampling_rate=sampling_rate,
t_start=(starttimes[b] *
header.us_per_time *
header.dtime_base * pq.s),
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, np.dtype(blockHeaderDesciption))
# read data
sig = np.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
fmt = [('tick' , 'i4') ]
elif channelHeader.kind in [5]:
# Marker data
fmt = [('tick' , 'i4') , ('marker' , 'i4') ]
elif channelHeader.kind in [6]:
# AdcMark data
fmt = [('tick' , 'i4') , ('marker' , 'i4') , ('adc' , 'S%d' %channelHeader.n_extra )]
elif channelHeader.kind in [7]:
# RealMark data
fmt = [('tick' , 'i4') , ('marker' , 'i4') , ('real' , 'S%d' %channelHeader.n_extra )]
elif channelHeader.kind in [8]:
# TextMark data
fmt = [('tick' , 'i4') , ('marker' , 'i4') , ('label' , 'S%d'%channelHeader.n_extra)]
dt = np.dtype(fmt)
## Step 2 : first read for allocating mem
fid.seek(channelHeader.firstblock)
totalitems = 0
for _ in range(channelHeader.blocks) :
blockHeader = HeaderReader(fid, np.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 = np.zeros( totalitems , dtype = dt)
## Step 3 : read
fid.seek(channelHeader.firstblock)
pos = 0
for _ in range(channelHeader.blocks) :
blockHeader = HeaderReader(fid, np.dtype(blockHeaderDesciption))
# read all events in block
trigs = np.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('S32')
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 = np.fromstring(alltrigs['adc'].tostring() , dtype = 'i2')
waveforms = waveforms.astype('f4') *channelHeader.scale/ 6553.6 + channelHeader.offset
elif channelHeader.kind == 7 :
waveforms = np.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 = np.zeros( (1) , dtype = dtype)[0]
super(HeaderReader, self).__setattr__('dtype', dtype)
super(HeaderReader, self).__setattr__('array', array)
def __setattr__(self, name , val):
if name in self.dtype.names :
self.array[name] = val
else :
super(HeaderReader, self).__setattr__(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]
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)
s += '{}: {}\n'.format(name, getattr(self, 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 = np.dtype(newdtype)
newHeader = HeaderReader(None , newdtype )
newHeader.array = np.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' ,
}
|