def test_surf_fs_asc(self):
s = surf.generate_sphere(5) * 100
_, fn = tempfile.mkstemp('surf', 'test')
surf_fs_asc.write(fn, s, overwrite=True)
t = surf_fs_asc.read(fn)
os.remove(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_fs_asc.sphere_reg_leftrightmapping(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_fs_asc.hemi_pairs_reposition(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):
s = surf.generate_sphere(5) * 100
_, fn = tempfile.mkstemp('surf', 'test')
surf_fs_asc.write(fn, s, overwrite=True)
t = surf_fs_asc.read(fn)
os.remove(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_fs_asc.sphere_reg_leftrightmapping(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_fs_asc.hemi_pairs_reposition(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 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)
