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