def save_movement(allmove, datadir):
allmove = np.asarray(allmove).squeeze()
dims = ("x", "y", "z")
cols = ["trans_%s" % x for x in dims] + ["rot_%s" % x for x in dims] + ["displacement"]
movedf = pandas.DataFrame(allmove, columns=cols)
movedf.to_excel(os.path.join(datadir, "movement.xls"))
np.save(os.path.join(datadir, "movement.npy"), allmove)
regressors = []
for tmpf, tmp in zip(cols, allmove.T):
outf = os.path.join(datadir, tmpf)
tmp.tofile(outf, sep="\n", format="2.5%f")
regressors.append(outf)
xfm.plot_movement(allmove, datadir)
return regressors
def save_movement(allmove, datadir):
allmove = np.asarray(allmove).squeeze()
dims = ('x','y','z')
cols = ['trans_%s'%x for x in dims] + ['rot_%s'%x for x in dims] +\
['displacement']
movedf = pandas.DataFrame(allmove, columns=cols)
movedf.to_excel(os.path.join(datadir, 'movement.xls'))
np.save( os.path.join(datadir, 'movement.npy'), allmove)
regressors = []
for tmpf, tmp in zip(cols, allmove.T):
outf = os.path.join(datadir, tmpf)
tmp.tofile(outf, sep='\n', format='2.5%f')
regressors.append(outf)
xfm.plot_movement(allmove, datadir)
return regressors
allmoved = [target]
for movin in allf[1:3]:
tmpaff = reg.affine_register_cc(target, movin)
if tmpaff is None:
continue
displacement, translate, angles = xfm.params_from_ants(tmpaff)
allmove.append([translate.tolist() + angles + [displacement]])
moved = reg.apply_affine(movin, tmpaff)
allmoved.append(moved)
## merge aligned into 4D
merged_fname = os.path.join(datadir, 'aligned_4d.nii.gz')
try:
merged_img = ni.concat_images(allmoved)
merged_img.to_filename(merged_fname)
except:
cmd = 'fslmerge -t %s '%(merged_fname)
cmd = cmd + ' '.join([x for x in allmoved])
os.system(cmd)
allmove = np.asarray(allmove).squeeze()
dims = ('x','y','z')
cols = ['trans_%s'%x for x in dims] + ['rot_%s'%x for x in dims] +\
['displacement']
movedf = pandas.DataFrame(allmove, columns=cols)
movedf.to_excel(os.path.join(datadir, 'movement.xls'))
np.save( os.path.join(datadir, 'movement.npy'), allmove)
## create subplots
xfm.plot_movement(allmove, datadir)
