def main(template, subjectsdir, thresh = 0, run_eta = False):
tdat = ni.load(template).get_data().squeeze()
_, tname = os.path.split(template)
tname = tname.split('.')[0]
subfiles = get_subjects_files(subjectsdir)
allresults = []
for sf in subfiles:
pth, nme = os.path.split(sf)
nme = nme.split('.')[0]
tmpdat = ni.load(sf).get_data().squeeze()
if not tmpdat.shape == tdat.shape:
raise IndexError('shape mismatch: '+\
'template:%s, data: %s'%(tdat.shape,
tmpdat.shape))
mask = tmpdat > 0
maskd_template = tdat.copy()
maskd_template[tdat <=thresh] = 0
maskd_template[tdat > thresh] = 1
gof = matching.calc_gof(tmpdat, maskd_template, mask)
res = [nme, gof]
print res
if run_eta:
eta = matching.calc_eta(tmpdat[mask], tdat[mask])
res.append(eta)
allresults.append(res)
columns = ['name', 'gof']
if run_eta:
columns.append('eta')
df = pandas.DataFrame(allresults, columns = columns)
outf = os.path.join(subjectsdir, 'matching_%s_data.xls'%(tname))
df.to_excel(outf)
print 'wrote %s'%(outf)
for i in range(t):
for j in metrics:
level_tuples.append((str(i),j))
row_index = pandas.MultiIndex.from_tuples(level_tuples,
names=['Component', 'Metric']) #Level1 and Level2 names
#Create empty dataframe to hold metric scores
matchframe = pandas.DataFrame(index=row_index, columns=template_map.values())
#Calculate matching metrics of all components with template networks
for cmpnt in range(t): #Loop over all components in 4d ICA file
icavol = icadat[:,:,:,cmpnt]
for net in template_map.keys(): #Loop over all networks in 4d template
tempvol = tempdat[:,:,:,(net - 1)]
tempname = template_map[net]
gof = matching.calc_gof(icavol, #Calc goodness of fit (Greicius 2004)
tempvol,
maskdat)
(eta, (pear_r, pear_p)) = matching.calc_eta(icavol, #Calc Cohen's eta
tempvol,
getr=True)
matchframe.ix[str(cmpnt),'gof'][tempname] = gof
matchframe.ix[str(cmpnt),'eta'][tempname] = eta
matchframe.ix[str(cmpnt),'pear_r'][tempname] = pear_r
matchframe.ix[str(cmpnt),'pear_p'][tempname] = pear_p
saveout = os.path.join(outdir, outfile)
matchframe.to_csv(saveout, header=True, index=True) #Save to file