def read_brik(brikname):
h = afni_header_read(brikname)
hn = h['HISTORY_NOTE']
tfdim = hn.find('tfdim:')
if tfdim < 0:
printerror("Brik %s doesn't contain TF data." % brikname)
sys.exit(1)
tfdim = hn[tfdim:]
title = hn.find('tftitle:')
if title < 0:
tftitle = brikname
else:
tftitle = hn[title + 9:].split('\n')[0]
dim = h['DATASET_DIMENSIONS']
isstat = hn.find('3dWilcoxon') >= 0 or hn.find('3dMannWhitney') >= 0
# Format is 'tfdim: start end srate lo hi'
# Also return xdim and ydim.
s = tfdim.split()
return [tftitle, float(s[1]), float(s[2]), float(s[3]), float(s[4]),
float(s[5]), int(dim[0]), int(dim[1]), isstat]
if s[0] == 'c_ras':
c_ras = list(map(float, s[1:]))
break
if c_ras is None:
raise
except:
print("Reading", name)
print("Can't find c_ras origin offset!")
sys.exit(1)
c_ras = np.array(c_ras) * .001 # mm to m
# Read the AFNI header, get the tags.
pathname = op.expanduser(brikname)
h = afni_header_read(pathname)
if not h.get('TAGSET_NUM'):
print("{} has no tags!".format(pathname))
sys.exit(1)
ntags, pertag = h['TAGSET_NUM']
f = h['TAGSET_FLOATS']
lab = h['TAGSET_LABELS']
d = {}
for i in range(ntags):
tl = f[i * pertag : (i+1) * pertag] # get this tag's coordinate list
x = np.array(tl[0:3]) * .001 # convert from mm to m
x = np.array((-x[0], -x[1], x[2])) # convert from RAI to LPI (aka ras)
d[lab[i]] = x - c_ras # shift to ras origin
# AFNI tag name to MNE tag ident
# If the argument is a .ds directory, get the corresponding .hc or .hdm file.
s = filename.split('.')
ext = s[-1]
if ext == 'ds' or ext == 'ds/':
base = s[0].split('/')[-1]
if type == HDM:
msg("using default.hdm\n")
filename += '/' + 'default.hdm'
elif type == HC:
msg("using %s.hc\n" % base)
filename += '/' + base + '.hc'
# If it's a BRIK, read the header, otherwise just open the file.
if type == BRIK:
h = afni_header_read(filename)
if not h.has_key('TAGSET_NUM'):
printerror("%s has no tags!" % filename)
sys.exit(1)
else:
x = open(filename)
def get_coord(f):
l = f.next()
return float(l.split()[2])
# HC
def coord(f):
x = get_coord(f)
y = get_coord(f)
z = get_coord(f)
