def test_surf_fs_asc(self, temp_fn):
s = surf.generate_sphere(5) * 100
surf_fs_asc.write(temp_fn, s, overwrite=True)
t = surf_fs_asc.read(temp_fn)
assert_array_almost_equal(s.vertices, t.vertices)
assert_array_almost_equal(s.vertices, t.vertices)
theta = np.asarray([0, 0., 180.])
r = s.rotate(theta, unit='deg')
l2r = surf.get_sphere_left_right_mapping(s, r)
l2r_expected = [0, 1, 2, 6, 5, 4, 3, 11, 10, 9, 8, 7, 15, 14, 13, 12,
16, 19, 18, 17, 21, 20, 23, 22, 26, 25, 24]
assert_array_equal(l2r, np.asarray(l2r_expected))
sides_facing = 'apism'
for side_facing in sides_facing:
l, r = surf.reposition_hemisphere_pairs(s + 10., t + (-10.),
side_facing)
m = surf.merge(l, r)
# not sure at the moment why medial rotation
# messes up - but leave for now
eps = 666 if side_facing == 'm' else .001
assert_true((abs(m.center_of_mass) < eps).all())
def test_surf_fs_asc(self, temp_fn):
s = surf.generate_sphere(5) * 100
surf_fs_asc.write(temp_fn, s, overwrite=True)
t = surf_fs_asc.read(temp_fn)
assert_array_almost_equal(s.vertices, t.vertices)
assert_array_almost_equal(s.vertices, t.vertices)
theta = np.asarray([0, 0., 180.])
r = s.rotate(theta, unit='deg')
l2r = surf.get_sphere_left_right_mapping(s, r)
l2r_expected = [
0, 1, 2, 6, 5, 4, 3, 11, 10, 9, 8, 7, 15, 14, 13, 12, 16, 19, 18,
17, 21, 20, 23, 22, 26, 25, 24
]
assert_array_equal(l2r, np.asarray(l2r_expected))
sides_facing = 'apism'
for side_facing in sides_facing:
l, r = surf.reposition_hemisphere_pairs(s + 10., t + (-10.),
side_facing)
m = surf.merge(l, r)
# not sure at the moment why medial rotation
# messes up - but leave for now
eps = 666 if side_facing == 'm' else .001
assert_true((abs(m.center_of_mass) < eps).all())
def run_makespec_bothhemis(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
icolds, hemis = _get_hemis_icolds(config)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
for icold in icolds:
specs = []
for hemi in hemis:
#surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
specs.append(afni_suma_spec.read(specpathfn))
specs = afni_suma_spec.hemi_pairs_add_views(specs,
'inflated',
refdir,
overwrite=overwrite)
specs = afni_suma_spec.hemi_pairs_add_views(specs,
'sphere.reg',
refdir,
overwrite=overwrite)
spec_both = afni_suma_spec.combine_left_right(specs)
# generate spec files for both hemispheres
hemiboth = 'b'
specfn = afni_suma_spec.canonical_filename(icold, hemiboth,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
spec_both.write(specpathfn, overwrite=overwrite)
# merge left and right into one surface
# and generate the spec files as well
hemimerged = 'm'
specfn = afni_suma_spec.canonical_filename(icold, hemimerged,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
if config['overwrite'] or not os.path.exists(specpathfn):
spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(
spec_both)
spec_merged.write(specpathfn, overwrite=overwrite)
full_path = lambda x: os.path.join(refdir, x)
for fn_out, fns_in in surfs_to_join.iteritems():
surfs_in = [surf_fs_asc.read(full_path(fn)) for fn in fns_in]
surf_merged = surf.merge(*surfs_in)
if config['overwrite'] or not os.path.exists(
full_path(fn_out)):
surf_fs_asc.write(surf_merged,
full_path(fn_out),
overwrite=overwrite)
print "Merged surfaces written to %s" % fn_out
def run_makespec_bothhemis(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
icolds, hemis = _get_hemis_icolds(config)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
for icold in icolds:
specs = []
for hemi in hemis:
#surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
specs.append(afni_suma_spec.read(specpathfn))
specs = afni_suma_spec.hemi_pairs_add_views(specs,
'inflated', refdir, overwrite=overwrite)
specs = afni_suma_spec.hemi_pairs_add_views(specs,
'sphere.reg', refdir, overwrite=overwrite)
spec_both = afni_suma_spec.combine_left_right(specs)
# generate spec files for both hemispheres
hemiboth = 'b'
specfn = afni_suma_spec.canonical_filename(icold, hemiboth, config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
spec_both.write(specpathfn, overwrite=overwrite)
# merge left and right into one surface
# and generate the spec files as well
hemimerged = 'm'
specfn = afni_suma_spec.canonical_filename(icold, hemimerged, config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
if config['overwrite'] or not os.path.exists(specpathfn):
spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(spec_both)
spec_merged.write(specpathfn, overwrite=overwrite)
full_path = lambda x:os.path.join(refdir, x)
for fn_out, fns_in in surfs_to_join.iteritems():
surfs_in = [surf_fs_asc.read(full_path(fn)) for fn in fns_in]
surf_merged = surf.merge(*surfs_in)
if config['overwrite'] or not os.path.exists(full_path(fn_out)):
surf_fs_asc.write(surf_merged, full_path(fn_out),
overwrite=overwrite)
print "Merged surfaces written to %s" % fn_out
def read(fn):
'''General read function for surfaces
For now only supports ascii (as used in AFNI's SUMA), Caret
and freesurfer formats
'''
if fn.endswith('.asc'):
from mvpa2.support.nibabel import surf_fs_asc
return surf_fs_asc.read(fn)
elif fn.endswith('.coord'):
from mvpa2.support.nibabel import surf_caret
return surf_caret.read(fn)
else:
import nibabel.freesurfer.io as fsio
coords, faces = fsio.read_geometry(fn)
return Surface(coords, faces)
def average_fs_asc_surfs(fn1, fn2, fnout):
'''averages two surfaces'''
surf1 = surf_fs_asc.read(fn1)
surf2 = surf_fs_asc.read(fn2)
surfavg = surf1 * .5 + surf2 * .5
surf_fs_asc.write(surfavg, fnout, overwrite=True)
def average_fs_asc_surfs(fn1, fn2, fnout):
'''averages two surfaces'''
surf1 = surf_fs_asc.read(fn1)
surf2 = surf_fs_asc.read(fn2)
surfavg = surf1 * .5 + surf2 * .5
surf_fs_asc.write(surfavg, fnout, overwrite=True)
