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 write(fn, s, overwrite=True):
'''General write function for surfaces
For now only supports ascii (as used in AFNI's SUMA)
'''
if fn.endswith('.asc'):
from mvpa2.support.nibabel import surf_fs_asc
surf_fs_asc.write(fn, s, overwrite=overwrite)
else:
raise ValueError("Not implemented (based on extension): %r" % fn)
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 hemi_pairs_add_views(spec_both, state, directory=None, overwrite=False):
'''adds views for medial, superior, inferior, anterior, posterior viewing
of two surfaces together. Also generates these surfaces'''
spec_left, spec_right = spec_both[0], spec_both[1]
ext = '.asc'
if directory is None:
directory = os.path.curdir
if not spec_left.same_states(spec_right):
raise ValueError('Incompatible states for left and right')
#views = collections.OrderedDict(m='medial', s='superior', i='inferior', a='anterior', p='posterior')
# for compatibility use a normal dict
if state == 'inflated':
views = dict(m='medial',
s='superior',
i='inferior',
a='anterior',
p='posterior')
viewkeys = ['m', 's', 'i', 'a', 'p']
else:
views = dict(m='medial')
viewkeys = 'm'
spec_both = [spec_left, spec_right]
spec_both_new = map(copy.deepcopy, spec_both)
for view in viewkeys:
longname = views[view]
oldfns = []
newfns = []
for i, spec in enumerate(spec_both):
idxdef = spec.find_surface_from_state(state)
if len(idxdef) != 1:
raise ValueError('Not unique surface with state %s' % state)
surfidx, surfdef = idxdef[0]
# take whichever is there (in order of preference)
# shame that python has no builtin foldr
surfnamelabels = ['SurfaceName', 'FreeSurferSurface']
for surfnamelabel in surfnamelabels:
surfname = surfdef.get(surfnamelabel)
if not surfname is None:
break
#surfname = utils.foldr(surfdef.get, None, surfnamelabels)
fn = os.path.join(directory, surfname)
if not os.path.exists(fn):
raise ValueError("File not found: %s" % fn)
if not surfname.endswith(ext):
error('Expected extension %s for %s' % (ext, fn))
oldfns.append(fn) # store old name
shortfn = surfname[:-(len(ext))]
newsurfname = '%s%s%s%s' % (shortfn, _COMPREFIX, longname, ext)
newfn = os.path.join(directory, newsurfname)
newsurfdef = copy.deepcopy(surfdef)
# ensure no naming cnoflicts
for surfnamelabel in surfnamelabels:
if surfnamelabel in newsurfdef:
newsurfdef.pop(surfnamelabel)
newsurfdef['SurfaceName'] = newsurfname
newsurfdef['SurfaceState'] = '%s%s%s' % (_COMPREFIX, view, state)
spec_both_new[i].add_surface(newsurfdef)
newfns.append(newfn)
if all(map(os.path.exists, newfns)) and not overwrite:
print "Output already exist for %s" % longname
else:
surf_left, surf_right = map(surf_fs_asc.read, oldfns)
surf_both_moved = surf_fs_asc.hemi_pairs_reposition(
surf_left, surf_right, view)
for fn, surf in zip(newfns, surf_both_moved):
surf_fs_asc.write(surf, fn, overwrite)
print "Written %s" % fn
return tuple(spec_both_new)
def hemi_pairs_add_views(spec_both, state, directory=None, overwrite=False):
'''adds views for medial, superior, inferior, anterior, posterior viewing
of two surfaces together. Also generates these surfaces'''
spec_left, spec_right = spec_both[0], spec_both[1]
ext = '.asc'
if directory is None:
directory = os.path.curdir
if not spec_left.same_states(spec_right):
raise ValueError('Incompatible states for left and right')
#views = collections.OrderedDict(m='medial', s='superior', i='inferior', a='anterior', p='posterior')
# for compatibility use a normal dict
if state == 'inflated':
views = dict(m='medial', s='superior', i='inferior', a='anterior', p='posterior')
viewkeys = ['m', 's', 'i', 'a', 'p']
else:
views = dict(m='medial')
viewkeys = 'm'
spec_both = [spec_left, spec_right]
spec_both_new = map(copy.deepcopy, spec_both)
for view in viewkeys:
longname = views[view]
oldfns = []
newfns = []
for i, spec in enumerate(spec_both):
idxdef = spec.find_surface_from_state(state)
if len(idxdef) != 1:
raise ValueError('Not unique surface with state %s' % state)
surfidx, surfdef = idxdef[0]
# take whichever is there (in order of preference)
# shame that python has no builtin foldr
surfnamelabels = ['SurfaceName', 'FreeSurferSurface']
for surfnamelabel in surfnamelabels:
surfname = surfdef.get(surfnamelabel)
if not surfname is None:
break
#surfname = utils.foldr(surfdef.get, None, surfnamelabels)
fn = os.path.join(directory, surfname)
if not os.path.exists(fn):
raise ValueError("File not found: %s" % fn)
if not surfname.endswith(ext):
error('Expected extension %s for %s' % (ext, fn))
oldfns.append(fn) # store old name
shortfn = surfname[:-(len(ext))]
newsurfname = '%s%s%s%s' % (shortfn, _COMPREFIX, longname, ext)
newfn = os.path.join(directory, newsurfname)
newsurfdef = copy.deepcopy(surfdef)
# ensure no naming cnoflicts
for surfnamelabel in surfnamelabels:
if surfnamelabel in newsurfdef:
newsurfdef.pop(surfnamelabel)
newsurfdef['SurfaceName'] = newsurfname
newsurfdef['SurfaceState'] = '%s%s%s' % (_COMPREFIX, view, state)
spec_both_new[i].add_surface(newsurfdef)
newfns.append(newfn)
if all(map(os.path.exists, newfns)) and not overwrite:
print "Output already exist for %s" % longname
else:
surf_left, surf_right = map(surf_fs_asc.read, oldfns)
surf_both_moved = surf_fs_asc.hemi_pairs_reposition(surf_left,
surf_right,
view)
for fn, surf in zip(newfns, surf_both_moved):
surf_fs_asc.write(surf, fn, overwrite)
print "Written %s" % fn
return tuple(spec_both_new)
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)