def __init__(self, datapdf):
'''d=data.read(datapdf)'''
self.datapdf=datapdf
self.hdr=header.read(datapdf)
self.ext = 'pymdat'
self.filename = datapdf
self.total_chans=self.hdr.header_data.total_chans[0]
#self.pnts_in_file=self.hdr.epoch_data[0].pts_in_epoch[0]*self.hdr.header_data.input_epochs
#print 'pnts in file ', self.pnts_in_file
self.format=self.hdr.header_data.data_format[0]
self.fid=open(datapdf, "r")
print 'fidtell', self.fid.tell()
if self.format == 1:
self.dataprecision='h';
self.time_slice_size = 2 * self.total_chans;
if self.format == 2:
self.dataprecision='i';
self.time_slice_size = 4 * self.total_chans;
if self.format == 3:
self.dataprecision='f';
self.time_slice_size = 4 * self.total_chans;
if self.format == 4:
self.dataprecision='d';
self.time_slice_size = 8 * self.total_chans;
print 'time_slice_size ',self.time_slice_size
print 'precision ', self.dataprecision
self.pnts_in_file = self.hdr.header_offset / self.time_slice_size
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 run():
stage = os.environ['STAGE']
#path = stage+'/data/'
x=os.walk(stage+'/data/')
datapaths = x.next()[1]
listofscans = []
dirofscans = {}
for i in datapaths:
x=os.walk(stage+'/data/'+i)
dirs = x.next()[1]
if size(dirs) > 0:
for ii in dirs:
xx = os.walk(stage+'/data/'+i+'/'+ii)
scan = xx.next()[1]
#print 'scans',scan
if size(scan) > 0:
for iii in scan:
xx = os.walk(stage+'/data/'+i+'/'+ii+'/'+iii) #added 090324 to fix bug
session = xx.next()[1]
#print 'scan',iii,'sessions',session
for iiii in session: #added 090324 to fix bug
#print iiii
#if size(session) > 0: #removed 090324 to fix bug
xx = os.walk(stage+'/data/'+i+'/'+ii+'/'+iii+'/'+iiii) #added 090324 to fix bug
run = xx.next()[1]
#print 'run',run
if size(run) > 0:
data = xx.next()
#print 'data',data
if size(data[2]) > 0:
for d in data[2]:
#try and read
#print data[0]+'/'+d
try:
h = header.read(data[0]+'/'+d)
if h.header_offset[0] > 0:
dirofscans[iii] = data[0]+'/'+d
#print 'dirofscans',dirofscans
except IOError:
pass
except MemoryError:
pass
except OverflowError:
pass
except AttributeError:
print 'Attribute Error in dbscan'
except IndexError:
pass
#dirofscans[iii] = data[0]+data[2][0]
#listofscans.extend(iii)
#listofids.extend(dirs)
uscans = unique(listofscans)
return dirofscans
def __init__(self, datapdf, epoch, starttime, endtime):
'''
give epoch number and start and end times and returns sample indexes.
starttime and endtime in seconds.
'''
h=header.read(datapdf)
h.header_data.total_epochs[0]
self.epochlength=h.epoch_data[0].pts_in_epoch[0]
self.startind=round(starttime/h.header_data.sample_period[0]+(h.epoch_data[0].pts_in_epoch[0]*(epoch-1)))
self.endind=round(endtime/h.header_data.sample_period[0]+(h.epoch_data[0].pts_in_epoch[0]*(epoch-1)))
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):
'''d=data.read(datapdf)'''
try:
self.datapdf=datapdf
self.hdr=header.read(datapdf)
self.ext = 'pymdat'
self.filepath = datapdf
pathlist = self.filepath.split('/')
self.filename = pathlist.pop()
self.run = pathlist.pop()
self.session = pathlist.pop()
self.scan = pathlist.pop()
self.pid = pathlist.pop()
self.filedir = self.filepath.replace(self.filepath.split('/')[-1],'')
self.total_chans=self.hdr.header_data.total_chans[0]
self.format=self.hdr.header_data.data_format[0]
self.fid=open(datapdf, "r")
#print 'fidtell', self.fid.tell()
except IndexError:
print 'probably not a 4D MEG file'
pass
if self.format == 1:
self.dataprecision='h';
self.time_slice_size = 2 * self.total_chans;
if self.format == 2:
self.dataprecision='i';
self.time_slice_size = 4 * self.total_chans;
if self.format == 3:
self.dataprecision='f';
self.time_slice_size = 4 * self.total_chans;
if self.format == 4:
self.dataprecision='d';
self.time_slice_size = 8 * self.total_chans;
print 'time_slice_size ',self.time_slice_size
print 'precision ', self.dataprecision
self.pnts_in_file = self.hdr.header_offset / self.time_slice_size
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
