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_mapico(config, env):
'''run MapIcosehedron to convert surfaces to standard topology'''
sumadir = config['sumadir']
firstcmd = 'cd "%s" || exit 1' % sumadir
cmds = []
icolds, hemis = _get_hemis_icolds(config)
sid = config['sid'] # subject id
ext = '.asc' # input is always ascii
for icold in icolds:
icoprefix = config['mi_icopat'] % icold
spherefns = []
for hemi in hemis:
if not config['overwrite']:
# the last file that is generated by MapIcosahedron
lastsurffn = '%s/%s%sh.sphere.reg%s' % (
sumadir, config['mi_icopat'] % icold, hemi, ext)
spherefns.append(lastsurffn)
if os.path.exists(lastsurffn):
print(
"Seems MapIcosahedron was already run for %sh with ld=%d"
% (hemi, icold))
continue
cmd = (
'MapIcosahedron -overwrite -spec %s_%sh.spec -ld %d -fix_cut_surfaces -prefix %s'
% (sid, hemi, icold, icoprefix))
cmds.append(cmd)
if cmds:
cmd = '%s;%s' % (firstcmd, ';'.join(cmds))
utils.run_cmds(cmd, env)
cmds = []
if len(spherefns) == 2 and 'l' in hemis and 'r' in hemis:
spheres = map(surf.read, spherefns)
mapfn = (config['mi_icopat'] % icold) + config['hemimappingsuffix']
mappathfn = os.path.join(sumadir, mapfn)
if config['overwrite'] or not os.path.exists(mappathfn):
eps = .001
print "Computing bijection between nodes (ico=%d) - this may take a while" % icold
bijection = surf.get_sphere_left_right_mapping(
spheres[0], spheres[1], eps)
with open(mappathfn, 'w') as f:
f.write('\n'.join(map(str, bijection)))
print "Written bijection to %s" % mappathfn
def run_mapico(config, env):
"""run MapIcosehedron to convert surfaces to standard topology"""
sumadir = config["sumadir"]
firstcmd = 'cd "%s" || exit 1' % sumadir
cmds = []
icolds, hemis = _get_hemis_icolds(config)
sid = config["sid"] # subject id
ext = ".asc" # input is always ascii
for icold in icolds:
icoprefix = config["mi_icopat"] % icold
spherefns = []
for hemi in hemis:
if not config["overwrite"]:
# the last file that is generated by MapIcosahedron
lastsurffn = "%s/%s%sh.sphere.reg%s" % (sumadir, config["mi_icopat"] % icold, hemi, ext)
spherefns.append(lastsurffn)
if os.path.exists(lastsurffn):
print ("Seems MapIcosahedron was already run for %sh with ld=%d" % (hemi, icold))
continue
cmd = "MapIcosahedron -overwrite -spec %s_%sh.spec -ld %d -fix_cut_surfaces -prefix %s" % (
sid,
hemi,
icold,
icoprefix,
)
cmds.append(cmd)
if cmds:
cmd = "%s;%s" % (firstcmd, ";".join(cmds))
utils.run_cmds(cmd, env)
cmds = []
if len(spherefns) == 2 and "l" in hemis and "r" in hemis:
spheres = map(surf.read, spherefns)
mapfn = (config["mi_icopat"] % icold) + config["hemimappingsuffix"]
mappathfn = pathjoin(sumadir, mapfn)
if config["overwrite"] or not os.path.exists(mappathfn):
eps = 0.001
print "Computing bijection between nodes (ico=%d) - this may take a while" % icold
bijection = surf.get_sphere_left_right_mapping(spheres[0], spheres[1], eps)
with open(mappathfn, "w") as f:
f.write("\n".join(map(str, bijection)))
print "Written bijection to %s" % mappathfn
