def __init__(self, datapdf):
if os.path.isfile(datapdf)==True:
print 'reading pdf header', os.path.abspath(datapdf)
self.hdr=header.read(datapdf);
if os.path.isfile(os.path.dirname(datapdf)+'/config')==True:
print 'found config file in same dir. Reading config'
self.cfg=config.read(os.path.dirname(datapdf)+'/config');
if os.path.isfile(os.path.dirname(datapdf)+'/hs_file')==True:
print 'found headshape file in same dir. Reading headshape'
self.hs=headshape.read(os.path.dirname(datapdf)+'/hs_file');
##conf=config.read('file')
##h=header.read('file')
##
##
## os.path.dirname(pdf)
##
##
##j=[];
##
##for i in range(0, len(h.channel_ref_data)):
## j.append(h.channel_ref_data[i].chan_label)
##
##
##dd={}
## for x in range(0, len(j)):
## dd[j[x]]=int(ind[x])
def __init__(self, datapdf, index):
'''returns sensor locations from an index provided
sensors.locationsbyindex(datapdf, ch.channelindexcfg)'''
#--20090707--danc--read config directly to keep from infinite looping
#pdfinstance=pdf.read(datapdf)
if os.path.isfile(os.path.dirname(datapdf)+'/config')==True:
#print 'found config file in same dir. Reading config'
cfg=config.read(os.path.dirname(datapdf)+'/config');
self.chlpos = array([]);self.chupos=array([])
self.chldir = array([]);self.chudir=array([])
self.chname = array([])
#--20090817--danc--flipped lower and upper position and direction, as I had it wrong before now.
for i in index:
self.chupos = append(self.chupos,cfg.channel_data[i].device_data.loop_data[1].position)
self.chlpos = append(self.chlpos,cfg.channel_data[i].device_data.loop_data[0].position)
self.chudir = append(self.chudir,cfg.channel_data[i].device_data.loop_data[1].direction)
self.chldir = append(self.chldir,cfg.channel_data[i].device_data.loop_data[0].direction)
self.chname = append(self.chname,cfg.channel_data[i].name)
self.chupos=self.chupos.reshape(size(self.chupos)/3,3)
self.chlpos=self.chlpos.reshape(size(self.chlpos)/3,3)
self.chudir=self.chudir.reshape(size(self.chudir)/3,3)
self.chldir=self.chldir.reshape(size(self.chldir)/3,3)
def getdata(self, start, end, chindex=None):#chanindex):
from meg import functions
'''d.getdata(0, d.pnts_in_file, chindex=[1,2])
or
chind=ch.channelindexhdr[ch.channelsortedlabels == 'A63']
d.getdata(0, d.pnts_in_file, chindex=chind)'''
self.fid.seek(start*self.time_slice_size, os.SEEK_SET)
self.fid_start_pos = self.fid.tell()
data_block = fread(self.fid, self.total_chans*(end-start), self.dataprecision, self.dataprecision, 1);
self.fid_end_pos = self.fid.tell()
data_blockreshape=(data_block.reshape([ (end-start),self.total_chans]))
if self.format == 1:
print 'WARNING, bug in scalefactor order here. NEED TO FIX'
print 'short format, multiplying units_per_bit from cfg'
if os.path.isfile(os.path.dirname(self.datapdf)+'/config')==True:
print 'found config file in same dir. Reading config'
self.cfg=config.read(os.path.dirname(self.datapdf)+'/config');
cfgchlist = []
for t in range(0, self.cfg.data_total_chans):
cfgchlist.append(self.cfg.channel_data[t].chan_no)
self.scalefact = []
for c in range(0, self.hdr.header_data.total_chans):
scalefact = self.cfg.channel_data[cfgchlist.index(self.hdr.channel_ref_data[c].chan_no)].units_per_bit
self.scalefact = append(self.scalefact, scalefact)
data_blockreshape = data_blockreshape*scalefact
else:
print "can't read config from same directory"
if chindex!=None:
self.data_block = data_blockreshape[:,chindex]
self.scalefact = 1
else:
try:
self.data_block = data_blockreshape[:,self.channels.indexlist]
except AttributeError:
print 'no channels specified'
print "try something like... obj.setchannels('meg')"
print "or something like... obj.data.getdata(0,p.data.pnts_in_file, chindex=obj.data.channels.channelsind)"
return
self.fid.close
self.numofepochs = self.hdr.header_data.total_epochs[0] #self.pnts_in_file/self.time_slice_size
#lasttimepnt = (self.pnts_in_file / self.numofepochs)/\
#(1/self.hdr.header_data.sample_period)
#self.wintime = arange(0,lasttimepnt,self.hdr.header_data.sample_period)[:-1]
lasttimepnt = self.hdr.header_data.sample_period * self.pnts_in_file
self.wintime = arange(0,lasttimepnt,self.hdr.header_data.sample_period)
self.epoch_size = self.pnts_in_file / self.numofepochs
self.eventtime = self.wintime[0:self.epoch_size] - self.hdr.event_data[0].start_lat
self.numofchannels = size(self.data_block,1)
self.srate = 1/self.hdr.header_data.sample_period[0]
self.frames = self.data_block.shape[0] / self.numofepochs
print 'DATA DEBUG', shape(self.data_block)
def __init__(self, datapdf):
if os.path.isfile(datapdf)==True:
print('reading pdf', os.path.abspath(datapdf))
self.data = data.read(datapdf)
print('reading pdf header', os.path.abspath(datapdf))
self.hdr=header.read(datapdf); #reading withing data module
if os.path.isfile(os.path.dirname(datapdf)+'/config')==True:
print('found config file in same dir. Reading config')
self.cfg=config.read(os.path.dirname(datapdf)+'/config');
if os.path.isfile(os.path.dirname(datapdf)+'/hs_file')==True:
print('found headshape file in same dir. Reading headshape')
self.hs=headshape.read(os.path.dirname(datapdf)+'/hs_file');
#self.results = self.__class__
else: print('no file found')
def __init__(self, datapdf, type=None, labels=None):
'''Returns the channelindex for TYPE channels
type = type of channel (meg | eeg | ref | trig | ext | derived | utility | shorted)'''
'''sortedindtype----is the index to channels of type. use for extracting those meg channels
ex.
fn = '/path/to/file'
ch = channel.index(fn, 'meg') #return meg channels
'''
self.datapdf = datapdf
self.type = type
if os.path.isfile(datapdf)==True:
self.hdr=header.read(datapdf);
if os.path.isfile(os.path.dirname(datapdf)+'/config')==True:
self.cfg=config.read(os.path.dirname(datapdf)+'/config');
if os.path.isfile(os.path.dirname(datapdf)+'/hs_file')==True:
headshape.read
self.hs=headshape.read(os.path.dirname(datapdf)+'/hs_file');
else:
print 'no headshape file'
if type != None:
self.labellist, self.indexlist = self.getchindexfromtype(type)
if labels != None:
self.indexlist, self.labellist = self.getchindexfromlabelsinhdr(labels)
if type == 'derived':
self.indexlist, self.labellist = self.getchindexfromchannuminhdr('derived')
try:
self.chanlocs = self.locs2D(self.labellist)
except:
print 'something wrong with new chanloc method'
try:
if self.device_types.__contains__(1): #has meg channel data
print 'Data contains MEG channels. Making 2D chanlocs map'
self.chanlocs = self.locs2D(self.labellist)#, self.indexlist)
except AttributeError:
pass
self.reverseindex = []; sortedindex = sort(self.indexlist)
for i in sortedindex: #reverse index
self.reverseindex.append(self.indexlist.index(i))
def __init__(self, datapdf, type):
'''Returns the channelindex for TYPE channels
type = type of channel (meg | eeg | ref | trig | ext | derived | utility | shorted)'''
'''sortedindtype----is the index to channels of type. use for extracting those meg channels
ex.
fn = '/path/to/file'
ch = channel.index(fn[0], 'meg') #return meg channels
'''
self.datapdf = datapdf
self.type = type
if os.path.isfile(datapdf)==True:
self.hdr=header.read(datapdf);
if os.path.isfile(os.path.dirname(datapdf)+'/config')==True:
self.cfg=config.read(os.path.dirname(datapdf)+'/config');
if os.path.isfile(os.path.dirname(datapdf)+'/hs_file')==True:
headshape.read
self.hs=headshape.read(os.path.dirname(datapdf)+'/hs_file');
else:
print 'no headshape file'
cind=[];
chlabellist=[]#=empty
chnumber=zeros([len(self.hdr.channel_ref_data)], dtype=int) #channel label, number and index array
chindex=zeros([len(self.hdr.channel_ref_data)], dtype=int) #channel label, number and index array
cfgchname=[]
cfgchtype=zeros([len(self.cfg.channel_data)], dtype=int) #channel label, number and index array
cfgchannumber=zeros([len(self.cfg.channel_data)], dtype=int) #channel label, number and index array
for i in range(0, len(self.hdr.channel_ref_data)):
cind.append(self.hdr.channel_ref_data[i].chan_label)
chlabellist.append(self.hdr.channel_ref_data[i].chan_label)
chnumber[i]=(self.hdr.channel_ref_data[i].chan_no)
chindex[i]=(self.hdr.channel_ref_data[i].index)
chlabel=array(chlabellist)
self.chlabel=chlabel
self.chnumber=chnumber
self.chindex=chindex
for i in range(0, len(self.cfg.channel_data)):
cfgchname.append(self.cfg.channel_data[i].name)
cfgchtype[i]=(self.cfg.channel_data[i].type)
cfgchannumber[i]=(self.cfg.channel_data[i].chan_no)
cfgchname=array(cfgchname)
self.cfgchname=cfgchname
self.cfgchtype=cfgchtype
self.cfgchannumber=cfgchannumber
def indexsorted(sortedch, chlisttoindex):
chlist=list(chlisttoindex)
sortind=[];
for i in sortedch:
sortind.append(chlist.index(i))
return sortind
'''sort channels and return indexing array'''
self.unsortedch=chlabel;
if type == 'derived':
print 'cant sort derived channels'
return
self.sortedch=array(sorted(self.unsortedch))
self.sortedind=array(indexsorted(self.sortedch, self.chlabel))
self.sortedcharray=array(chlabel[self.sortedind])
'''EXTRACT CHANNELS'''
if type == 'meg':
device_data=[1]
elif type == 'ref':
device_data=[3]
elif type == 'eeg':
device_data=[2]
elif type == 'ext':
device_data=[4]
elif type == 'trig':
device_data=[5]
elif type == 'util':
device_data=[6]
elif type == 'derived':
device_data=[7]
elif type == 'shorted':
device_data=[8]
elif type == 'all':
device_data=unique(cfgchtype)
else:
print 'unknown channel type', type
device_data=[1000]
dd = device_data
self.chanbool=cfgchtype[chnumber-1]==dd #cfgchtype[chnumber-1] returns boolean to unsorted channel of type
self.unsortedlabeltype=self.unsortedch[self.cfgchtype[self.chnumber-1]==dd] #unsorted of only device type
self.sortedlabeltype=array(sorted(self.unsortedlabeltype)) #sorted labels
self.sortedindtype=array(indexsorted(self.sortedlabeltype, self.chlabel)) #sorted index of certain type
self.channelsind=self.chindex[self.chanbool]
self.channelsname=self.chlabel[self.chanbool]
self.allfromconfig=cfgchname[cfgchtype[cfgchannumber<1000-1]==dd] #get all channels from config less than number value=1000 (excludes weird types)
'''return index to config'''
try:
self.ind2cfg=array(indexsorted(self.sortedlabeltype, self.cfgchname))
except ValueError:
print 'names in config don\'t match header. no sort'
return
#--20090928--danc--fixing bug from previous channel locs method which picked up unsorted channel labels and used that to index sorted coordinates, which produced wrong results.
chfound=[] #empty array
cfglabels = []
import readline
if type == 'meg': #build meg channel 2d locations
#chaninfo = read_array(os.path.dirname(__file__)+'/configs/megchannels.cfg')
chaninfo = loadtxt(os.path.dirname(__file__)+'/configs/megchannels.cfg')
for l in chaninfo[0]:
#print l
cfglabels.append('A'+str(int(l)))
chanlocs248 = chaninfo[1:4]
for ch in cfglabels:
chfound.append(ch in self.sortedlabeltype)
if ch in self.sortedlabeltype:
pass
else:
print 'Chanloc Maker Warning:',ch, 'not found'
self.chfound=array(chfound);
self.chanlocs=chanlocs248[:,self.chfound];
self.channelindexhdr=self.sortedindtype
self.channelindexcfg=self.ind2cfg
self.channelsortedlabels=self.sortedlabeltype
self.channeltype = type
del self.channelsind,self.chanbool,self.unsortedlabeltype,self.unsortedch
del self.cfgchannumber,self.cfgchname,self.cfgchtype,self.cfg,self.allfromconfig
del self.channelsname,self.chindex,self.chlabel,self.chnumber
del self.hdr,self.sortedcharray,self.sortedlabeltype,self.ind2cfg
