def test_surface_face_normal(self, do_deterioriate_surface):
vec1 = np.random.normal(size=(3,))
vec2 = np.random.normal(size=(3,))
vec_normal = -np.cross(vec1, vec2)
plane = generate_plane((0, 0, 0), vec1, vec2, 10, 10)
if do_deterioriate_surface:
plane = SurfingSurfaceTests.deterioriate_surface(plane)
plane_face_normals = plane.face_normals
has_non_nan = False
for f_n in plane_face_normals:
if np.any(np.isnan(f_n)):
continue
assert_vector_direction_almost_equal(f_n, vec_normal, decimal=0)
assert_almost_equal(f_n, surf.normalized(
plane.nanmean_face_normal), decimal=0)
has_non_nan = True
if not has_non_nan:
assert False, "Test should include faces with non-NaN normals"
def test_average_node_edge_length(self):
for side in xrange(1, 5):
s_flat = surf.generate_plane((0, 0, 0), (0, 0, 1), (0, 1, 0), 6, 6)
rnd_xyz = 0 * np.random.normal(size=s_flat.vertices.shape)
s = surf.Surface(s_flat.vertices + rnd_xyz, s_flat.faces)
nvertices = s.nvertices
sd = np.zeros((nvertices,))
c = np.zeros((nvertices,))
def d(src, trg, vertices=s.vertices):
s = vertices[src, :]
t = vertices[trg, :]
delta = s - t
print s, t, delta
return np.sum(delta ** 2) ** .5
for i_face in s.faces:
for i in xrange(3):
src = i_face[i]
trg = i_face[(i + 1) % 3]
sd[src] += d(src, trg)
sd[trg] += d(src, trg)
c[src] += 1
c[trg] += 1
print i, src, trg, d(src, trg)
assert_array_almost_equal(sd / c, s.average_node_edge_length)
def test_volsurf_projections(self):
white = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1), 10, 10)
pial = white + np.asarray([[1, 0, 0]])
above = pial + np.asarray([[3, 0, 0]])
vg = volgeom.VolGeom((10, 10, 10), np.eye(4))
vs = volsurf.VolSurfMaximalMapping(vg, white, pial)
dx = pial.vertices - white.vertices
for s, w in ((white, 0), (pial, 1), (above, 4)):
xyz = s.vertices
ws = vs.surf_project_weights(True, xyz)
delta = vs.surf_unproject_weights_nodewise(ws) - xyz
assert_array_equal(delta, np.zeros((100, 3)))
assert_true(np.all(w == ws))
vs = volsurf.VolSurfMaximalMapping(vg, white, pial, nsteps=2)
n2vs = vs.get_node2voxels_mapping()
assert_equal(n2vs, dict((i, {i: 0.0, i + 100: 1.0}) for i in xrange(100)))
nd = 17
ds_mm_expected = np.sum((above.vertices - pial.vertices[nd, :]) ** 2, 1) ** 0.5
ds_mm = vs.coordinates_to_grey_distance_mm(nd, above.vertices)
assert_array_almost_equal(ds_mm_expected, ds_mm)
ds_mm_nodewise = vs.coordinates_to_grey_distance_mm(True, above.vertices)
assert_array_equal(ds_mm_nodewise, np.ones((100,)) * 3)
def test_volsurf_projections(self):
white = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1), 10, 10)
pial = white + np.asarray([[1, 0, 0]])
above = pial + np.asarray([[3, 0, 0]])
vg = volgeom.VolGeom((10, 10, 10), np.eye(4))
vs = volsurf.VolSurfMaximalMapping(vg, white, pial)
dx = pial.vertices - white.vertices
for s, w in ((white, 0), (pial, 1), (above, 4)):
xyz = s.vertices
ws = vs.surf_project_weights(True, xyz)
delta = vs.surf_unproject_weights_nodewise(ws) - xyz
assert_array_equal(delta, np.zeros((100, 3)))
assert_true(np.all(w == ws))
vs = volsurf.VolSurfMaximalMapping(vg, white, pial, nsteps=2)
n2vs = vs.get_node2voxels_mapping()
assert_equal(n2vs, dict((i, {
i: 0.,
i + 100: 1.
}) for i in xrange(100)))
nd = 17
ds_mm_expected = np.sum((above.vertices - pial.vertices[nd, :])**2,
1)**.5
ds_mm = vs.coordinates_to_grey_distance_mm(nd, above.vertices)
assert_array_almost_equal(ds_mm_expected, ds_mm)
ds_mm_nodewise = vs.coordinates_to_grey_distance_mm(
True, above.vertices)
assert_array_equal(ds_mm_nodewise, np.ones((100, )) * 3)
def test_surface_minimal_lowres_voxel_selection(self, fn):
vol_shape = (4, 10, 10, 1)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
# make surfaces that are far away from all voxels
# in the volume
sphere_density = 10
radius = 10
outer = surf.generate_plane((0, 0, 4), (0, .4, 0),
(0, 0, .4), 14, 14)
inner = outer + 2
source = surf.generate_plane((0, 0, 4), (0, .8, 0),
(0, 0, .8), 7, 7) + 1
for i, nvm in enumerate(('minimal', 'minimal_lowres')):
qe = disc_surface_queryengine(radius, vg, inner,
outer, source,
node_voxel_mapping=nvm)
voxsel = qe.voxsel
if i == 0:
voxsel0 = voxsel
else:
assert_equal(voxsel.keys(), voxsel0.keys())
for k in voxsel.keys():
p = voxsel[k]
q = voxsel0[k]
# require at least 60% agreement
delta = set.symmetric_difference(set(p), set(q))
assert_true(len(delta) < .8 * (len(p) + len(q)))
if externals.exists('h5py'):
from mvpa2.base.hdf5 import h5save, h5load
h5save(fn, voxsel)
voxsel_copy = h5load(fn)
assert_equal(voxsel.keys(), voxsel_copy.keys())
for id in qe.ids:
assert_array_equal(voxsel.get(id),
voxsel_copy.get(id))
def test_surface_minimal_lowres_voxel_selection(self, fn):
vol_shape = (4, 10, 10, 1)
vol_affine = np.identity(4)
vg = volgeom.VolGeom(vol_shape, vol_affine)
# make surfaces that are far away from all voxels
# in the volume
sphere_density = 10
radius = 10
outer = surf.generate_plane((0, 0, 4), (0, .4, 0), (0, 0, .4), 14, 14)
inner = outer + 2
source = surf.generate_plane((0, 0, 4), (0, .8, 0),
(0, 0, .8), 7, 7) + 1
for i, nvm in enumerate(('minimal', 'minimal_lowres')):
qe = disc_surface_queryengine(radius,
vg,
inner,
outer,
source,
node_voxel_mapping=nvm)
voxsel = qe.voxsel
if i == 0:
voxsel0 = voxsel
else:
assert_equal(voxsel.keys(), voxsel0.keys())
for k in voxsel.keys():
p = voxsel[k]
q = voxsel0[k]
# require at least 60% agreement
delta = set.symmetric_difference(set(p), set(q))
assert_true(len(delta) < .8 * (len(p) + len(q)))
if externals.exists('h5py'):
from mvpa2.base.hdf5 import h5save, h5load
h5save(fn, voxsel)
voxsel_copy = h5load(fn)
assert_equal(voxsel.keys(), voxsel_copy.keys())
for id in qe.ids:
assert_array_equal(voxsel.get(id), voxsel_copy.get(id))
def test_surface_flatten(self, dim):
def unit_vec3(dim, scale):
v = [0, 0, 0]
v[dim] = float(scale)
return tuple(v)
origin = (0, 0, 0)
plane_size = 10
scale = 1.
vec1 = unit_vec3(dim, scale=scale)
vec2 = unit_vec3((dim + 1) % 3, scale=scale)
plane = generate_plane(origin, vec1, vec2, plane_size, plane_size)
noise_level = .05
nan_vertices_ratio = .05
# add some noise to spatial coordinates
vertices = plane.vertices
noise = np.random.uniform(size=vertices.shape,
low=-.5,
high=.5) * noise_level * scale
vertices_noisy = vertices + noise
# make some vertices NaN (as might be the case for flat surfaces)
nan_count_float = plane.nvertices * nan_vertices_ratio
nan_count = np.ceil(nan_count_float).astype(np.int)
nan_vertices = np.random.random_integers(plane.nvertices,
size=(nan_count,)) - 1
vertices_noisy[nan_vertices, dim] = np.nan
plane_noisy = Surface(vertices_noisy, plane.faces)
# compute normals
f_normal = plane_noisy.face_normals
# find average normal
non_nan_f_normal = np.logical_not(np.any(np.isnan(f_normal), axis=1))
f_normal_avg = np.mean(f_normal[non_nan_f_normal], axis=0)
# test average normal
assert_array_almost_equal(plane.nanmean_face_normal, f_normal_avg,
decimal=2)
# the output has only x and y coordinates; with z-coordinates set
# to zero, the coordinates must be at similar pairwise distances
max_deformation = .1
x, y = flat_surface2xy(plane_noisy, max_deformation)
n_vertices = plane.nvertices
z = np.zeros((n_vertices,))
flat_xyz = np.asarray((x, y, z))
# nodes are rotated must have same pairwise distance as
# the original surface
max_difference = 3 * noise_level
SurfingSurfaceTests.assert_coordinates_almost_equal_modulo_rotation(
flat_xyz.T, plane.vertices, max_difference)
def test_surf_ring_queryengine(self):
s = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1), 4, 5)
# add second layer
s2 = surf.merge(s, (s + (.01, 0, 0)))
ds = Dataset(samples=np.arange(20)[np.newaxis],
fa=dict(node_indices=np.arange(39, 0, -2)))
# add more features (with shared node indices)
ds3 = hstack((ds, ds, ds))
radius = 2.5
inner_radius = 1.0
# Makes sure it raises error if inner_radius is >= radius
assert_raises(ValueError,
lambda: queryengine.SurfaceRingQueryEngine(surface=s2,
inner_radius=2.5,
radius=radius))
distance_metrics = ('euclidean', 'dijkstra', 'euclidean', 'dijkstra')
for distance_metric, include_center in zip(distance_metrics, [True, False]*2):
qe = queryengine.SurfaceRingQueryEngine(surface=s2, radius=radius,
inner_radius=inner_radius, distance_metric=distance_metric,
include_center=include_center)
# untrained qe should give errors
assert_raises(ValueError, lambda: qe.ids)
assert_raises(ValueError, lambda: qe.query_byid(0))
# node index out of bounds should give error
ds_ = ds.copy()
ds_.fa.node_indices[0] = 100
assert_raises(ValueError, lambda: qe.train(ds_))
# lack of node indices should give error
ds_.fa.pop('node_indices')
assert_raises(ValueError, lambda: qe.train(ds_))
# train the qe
qe.train(ds3)
for node in np.arange(-1, s2.nvertices + 1):
if node < 0 or node >= s2.nvertices:
assert_raises(KeyError, lambda: qe.query_byid(node))
continue
feature_ids = np.asarray(qe.query_byid(node))
# node indices relative to ds
base_ids = feature_ids[feature_ids < 20]
# should have multiples of 20
assert_equal(set(feature_ids),
set((base_ids[np.newaxis].T + \
[0, 20, 40]).ravel()))
node_indices = s2.circlearound_n2d(node,
radius, distance_metric or 'dijkstra')
fa_indices = [fa_index for fa_index, inode in
enumerate(ds3.fa.node_indices)
if inode in node_indices and node_indices[inode] > inner_radius]
if include_center and node in ds3.fa.node_indices:
fa_indices += np.where(ds3.fa.node_indices == node)[0].tolist()
assert_equal(set(feature_ids), set(fa_indices))
def test_surf_pairs(self):
o, x, y = map(np.asarray, [(0, 0, 0), (0, 1, 0), (1, 0, 0)])
d = np.asarray((0, 0, .1))
n = 10
s1 = surf.generate_plane(o, x, y, n, n)
s2 = surf.generate_plane(o + d, x, y, n, n)
s = surf.merge(s1, s2)
# try for small surface
eps = .0000001
pw = s.pairwise_near_nodes(.5)
for i in xrange(n ** 2):
d = pw.pop((i, i + 100))
assert_array_almost_equal(d, .1)
assert_true(len(pw) == 0)
pw = s.pairwise_near_nodes(.5)
for i in xrange(n ** 2):
d = pw.pop((i, i + 100))
assert_array_almost_equal(d, .1)
assert_true(len(pw) == 0)
# bigger one
pw = s.pairwise_near_nodes(1.4)
for i in xrange(n ** 2):
p, q = i // n, i % n
offsets = sum(([] if q == 0 else [-1],
[] if q == n - 1 else [+1],
[] if p == 0 else [-n],
[] if p == n - 1 else [n],
[0]), [])
for offset in offsets:
ii = i + offset + n ** 2
d = pw.pop((i, ii))
assert_true((d < .5) ^ (offset > 0))
assert_true(len(pw) == 0)
def test_surf_border(self):
s = surf.generate_sphere(3)
assert_array_equal(s.nodes_on_border(), [False] * 11)
s = surf.generate_plane((0, 0, 0), (0, 1, 0), (1, 0, 0), 10, 10)
b = s.nodes_on_border()
v = s.vertices
vb = reduce(np.logical_or, [v[:, 0] == 0, v[:, 1] == 0,
v[:, 0] == 9, v[:, 1] == 9])
assert_array_equal(b, vb)
assert_true(s.nodes_on_border(0))
def test_flat_surface_plotting(self):
side = 10
step = 1 / float(side)
plane = surf.generate_plane((0, 0, 0), (step, 0, 0), (0, step, 0),
side, side)
# generate data with simple gradient
data = plane.vertices[:, 0] - plane.vertices[:, 1]
data = (data - np.min(data)) / (np.max(data) - np.min(data))
color_map = None
img_side = 50
fsp = FlatSurfacePlotter(plane,
min_nsteps=img_side,
color_map=color_map)
img_arr = fsp(data)
# verify shape
##assert_equal(img_arr.shape,(img_side,img_side,4))
# get colors
cmap = plt.get_cmap(color_map)
expected_img_arr = cmap(data)
# map vertex coordinates to indices in img_arr
# (using nearest neighbor interpolation)
xs = (plane.vertices[:, 0] * img_side).astype(np.int)
ys = (plane.vertices[:, 1] * img_side).astype(np.int)
# allocate space for rgb values
img_rgb = np.zeros((plane.nvertices, 3))
expected_img_rgb = np.zeros((plane.nvertices, 3))
# store expected and found RGB values
for i, (x, y) in enumerate(zip(*(xs, ys))):
img_rgb[i] = img_arr[y, x, :3]
expected_img_rgb[i] = expected_img_arr[i, :3]
# RGB values should match
c = np.corrcoef(img_rgb.T, expected_img_rgb.T)[:3, 3:6]
assert (np.all(np.diag(c) > .9))
def test_flat_surface_plotting(self):
side = 10
step = 1 / float(side)
plane = surf.generate_plane((0, 0, 0), (step, 0, 0), (0, step, 0),
side, side)
# generate data with simple gradient
data = plane.vertices[:, 0] - plane.vertices[:, 1]
data = (data - np.min(data)) / (np.max(data) - np.min(data))
color_map = None
img_side = 50
fsp = FlatSurfacePlotter(plane, min_nsteps=img_side,
color_map=color_map)
img_arr = fsp(data)
# verify shape
##assert_equal(img_arr.shape,(img_side,img_side,4))
# get colors
cmap = plt.get_cmap(color_map)
expected_img_arr = cmap(data)
# map vertex coordinates to indices in img_arr
# (using nearest neighbor interpolation)
xs = (plane.vertices[:, 0] * img_side).astype(np.int)
ys = (plane.vertices[:, 1] * img_side).astype(np.int)
# allocate space for rgb values
img_rgb = np.zeros((plane.nvertices, 3))
expected_img_rgb = np.zeros((plane.nvertices, 3))
# store expected and found RGB values
for i, (x, y) in enumerate(zip(*(xs, ys))):
img_rgb[i] = img_arr[y, x, :3]
expected_img_rgb[i] = expected_img_arr[i, :3]
# RGB values should match
c = np.corrcoef(img_rgb.T, expected_img_rgb.T)[:3, 3:6]
assert (np.all(np.diag(c) > .9))
def test_surfing_nodes_on_border_paths_surface_with_hole(self):
s = surf.generate_plane((0, 0, 0), (0, 0, 1), (0, 1, 0), 6, 6)
faces_to_remove = [1, 3, 7, 8, 3, 12, 13, 14, 22]
faces_to_keep = np.setdiff1d(np.arange(s.nfaces), faces_to_remove)
faces_to_add = [(0, 3, 10), (0, 4, 7), (0, 6, 4)]
faces_hole = np.vstack((s.faces[faces_to_keep], faces_to_add))
s_hole = surf.Surface(s.vertices, faces_hole)
pths = s_hole.nodes_on_border_paths()
expected_pths = [[1, 6, 4, 7, 0],
[3, 4, 9, 8, 2],
[11, 17, 23, 29, 35,
34, 33, 32, 31, 30,
24, 18, 12, 6, 7,
13, 19, 14, 9, 10,
5]]
def as_sorted_sets(xs):
return sorted(map(set, xs), key=min)
assert_equal(as_sorted_sets(pths),
as_sorted_sets(expected_pths), )
def test_surf_queryengine(self, qefn):
s = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1), 4, 5)
# add scond layer
s2 = surf.merge(s, (s + (.01, 0, 0)))
ds = Dataset(samples=np.arange(20)[np.newaxis],
fa=dict(node_indices=np.arange(39, 0, -2)))
# add more features (with shared node indices)
ds3 = hstack((ds, ds, ds))
radius = 2.5
# Note: sweepargs it not used to avoid re-generating the same
# surface and dataset multiple times.
for distance_metric in ('euclidean', 'dijkstra', '<illegal>', None):
builder = lambda: queryengine.SurfaceQueryEngine(s2, radius,
distance_metric)
if distance_metric in ('<illegal>', None):
assert_raises(ValueError, builder)
continue
qe = builder()
# test i/o and ensure that the untrained instance is not trained
if externals.exists('h5py'):
fd, qefn = tempfile.mkstemp('qe.hdf5', 'test'); os.close(fd)
h5save(qefn, qe)
qe = h5load(qefn)
os.remove(qefn)
# untrained qe should give errors
assert_raises(ValueError, lambda:qe.ids)
assert_raises(ValueError, lambda:qe.query_byid(0))
# node index out of bounds should give error
ds_ = ds.copy()
ds_.fa.node_indices[0] = 100
assert_raises(ValueError, lambda: qe.train(ds_))
# lack of node indices should give error
ds_.fa.pop('node_indices')
assert_raises(ValueError, lambda: qe.train(ds_))
# train the qe
qe.train(ds3)
# test i/o and ensure that the loaded instance is trained
if externals.exists('h5py'):
h5save(qefn, qe)
qe = h5load(qefn)
for node in np.arange(-1, s2.nvertices + 1):
if node < 0 or node >= s2.nvertices:
assert_raises(KeyError, lambda: qe.query_byid(node))
continue
feature_ids = np.asarray(qe.query_byid(node))
# node indices relative to ds
base_ids = feature_ids[feature_ids < 20]
# should have multiples of 20
assert_equal(set(feature_ids),
set((base_ids[np.newaxis].T + \
[0, 20, 40]).ravel()))
node_indices = list(s2.circlearound_n2d(node,
radius, distance_metric or 'dijkstra'))
fa_indices = [fa_index for fa_index, node in
enumerate(ds3.fa.node_indices)
if node in node_indices]
assert_equal(set(feature_ids), set(fa_indices))
# smoke tests
assert_true('SurfaceQueryEngine' in '%s' % qe)
assert_true('SurfaceQueryEngine' in '%r' % qe)
def test_surf(self, temp_fn):
"""Some simple testing with surfaces
"""
s = surf.generate_sphere(10)
assert_true(s.nvertices == 102)
assert_true(s.nfaces == 200)
v = s.vertices
f = s.faces
assert_true(v.shape == (102, 3))
assert_true(f.shape == (200, 3))
# another surface
t = s * 10 + 2
assert_true(t.same_topology(s))
assert_array_equal(f, t.faces)
assert_array_equal(v * 10 + 2, t.vertices)
# allow updating, but should not affect original array
# CHECKME: maybe we want to throw an exception instead
assert_true((v * 10 + 2 == t.vertices).all().all())
assert_true((s.vertices * 10 + 2 == t.vertices).all().all())
# a few checks on vertices and nodes
v_check = {40:(0.86511144 , -0.28109175, -0.41541501),
10:(0.08706015, -0.26794358, -0.95949297)}
f_check = {10:(7, 8, 1), 40:(30, 31, 21)}
vf_checks = [(v_check, lambda x:x.vertices),
(f_check, lambda x:x.faces)]
eps = .0001
for cmap, f in vf_checks:
for k, v in cmap.iteritems():
surfval = f(s)[k, :]
assert_true((abs(surfval - v) < eps).all())
# make sure same topology fails with different topology
u = surf.generate_cube()
assert_false(u.same_topology(s))
# check that neighbours are computed correctly
# even if we nuke the topology afterwards
for _ in [0, 1]:
nbrs = s.neighbors
n_check = [(0, 96, 0.284629),
(40, 39, 0.56218349),
(100, 99, 0.1741202)]
for i, j, k in n_check:
assert_true(abs(nbrs[i][j] - k) < eps)
def assign_zero(x):
x.faces[:, :] = 0
return None
assert_raises((ValueError, RuntimeError), assign_zero, s)
# see if mapping to high res works
h = surf.generate_sphere(40)
low2high = s.map_to_high_resolution_surf(h, .1)
partmap = {7: 141, 8: 144, 9: 148, 10: 153, 11: 157, 12: 281}
for k, v in partmap.iteritems():
assert_true(low2high[k] == v)
# ensure that slow implementation gives same results as fast one
low2high_slow = s.map_to_high_resolution_surf(h, .1)
for k, v in low2high.iteritems():
assert_true(low2high_slow[k] == v)
# should fail if epsilon is too small
assert_raises(ValueError,
lambda x:x.map_to_high_resolution_surf(h, .01), s)
n2f = s.node2faces
for i in xrange(s.nvertices):
nf = [10] if i < 2 else [5, 6] # number of faces expected
assert_true(len(n2f[i]) in nf)
# test dijkstra distances
ds2 = s.dijkstra_distance(2)
some_ds = {0: 3.613173280799, 1: 0.2846296765, 2: 0.,
52: 1.87458018, 53: 2.0487004817, 54: 2.222820777,
99: 3.32854360, 100: 3.328543604, 101: 3.3285436042}
eps = np.finfo('f').eps
for k, v in some_ds.iteritems():
assert_true(abs(v - ds2[k]) < eps)
# test I/O (through ascii files)
surf.write(temp_fn, s, overwrite=True)
s2 = surf.read(temp_fn)
# test i/o and ensure that the loaded instance is trained
if externals.exists('h5py'):
h5save(temp_fn, s2)
s2 = h5load(temp_fn)
assert_array_almost_equal(s.vertices, s2.vertices, 4)
assert_array_almost_equal(s.faces, s2.faces, 4)
# test plane (new feature end of August 2012)
s3 = surf.generate_plane((0, 0, 0), (2, 0, 0), (0, 1, 0), 10, 20)
assert_equal(s3.nvertices, 200)
assert_equal(s3.nfaces, 342)
assert_array_almost_equal(s3.vertices[-1, :], np.array([18., 19, 0.]))
assert_array_almost_equal(s3.faces[-1, :], np.array([199, 198, 179]))
# test bar
p, q = (0, 0, 0), (100, 0, 0)
s4 = surf.generate_bar(p, q, 10, 12)
assert_equal(s4.nvertices, 26)
assert_equal(s4.nfaces, 48)
def test_afni_suma_spec(self, temp_dir):
# XXX this function generates quite a few temporary files,
# which are removed at the end.
# the decorator @with_tempfile seems unsuitable as it only
# supports a single temporary file
# make temporary directory
os.mkdir(temp_dir)
# generate surfaces
inflated_surf = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1),
10, 10)
white_surf = inflated_surf + 1.
# helper function
_tmp = lambda x:pathjoin(temp_dir, x)
# filenames for surfaces and spec file
inflated_fn = _tmp('_lh_inflated.asc')
white_fn = _tmp('_lh_white.asc')
spec_fn = _tmp('lh.spec')
spec_dir = os.path.split(spec_fn)[0]
# generate SUMA-like spec dictionary
white = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=white_fn,
Anatomical='Y',
LocalCurvatureParent='SAME',
LocalDomainParent='SAME',
SurfaceState='smoothwm')
inflated = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=inflated_fn,
Anatomical='N',
LocalCurvatureParent=white_fn,
LocalDomainParent=white_fn,
SurfaceState='inflated')
# make SurfaceSpec object
spec = afni_suma_spec.SurfaceSpec([white], directory=spec_dir)
spec.add_surface(inflated)
# test __str__ and __repr__
assert_true('SurfaceSpec instance with 2 surfaces'
', 2 states ' in '%s' % spec)
assert_true(('%r' % spec).startswith('SurfaceSpec'))
# test finding surfaces
inflated_ = spec.find_surface_from_state('inflated')
assert_equal([(1, inflated)], inflated_)
empty = spec.find_surface_from_state('unknown')
assert_equal(empty, [])
# test .same_states
minimal = afni_suma_spec.SurfaceSpec([dict(SurfaceState=s)
for s in ('smoothwm', 'inflated')])
assert_true(spec.same_states(minimal))
assert_false(spec.same_states(afni_suma_spec.SurfaceSpec(dict())))
# test 'smart' surface file matching
assert_equal(spec.get_surface_file('smo'), white_fn)
assert_equal(spec.get_surface_file('inflated'), inflated_fn)
assert_equal(spec.get_surface_file('this should be None'), None)
# test i/o
spec.write(spec_fn)
spec_ = afni_suma_spec.from_any(spec_fn)
# prepare for another (right-hemisphere) spec file
lh_spec = spec
rh_spec_fn = spec_fn.replace('lh', 'rh')
rh_inflated_fn = _tmp(os.path.split(inflated_fn)[1].replace('_lh',
'_rh'))
rh_white_fn = _tmp(os.path.split(white_fn)[1].replace('_lh',
'_rh'))
rh_spec_fn = _tmp('rh.spec')
rh_white = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=rh_white_fn,
Anatomical='Y',
LocalCurvatureParent='SAME',
LocalDomainParent='SAME',
SurfaceState='smoothwm')
rh_inflated = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=rh_inflated_fn,
Anatomical='N',
LocalCurvatureParent=rh_white_fn,
LocalDomainParent=rh_white_fn,
SurfaceState='inflated')
rh_spec = afni_suma_spec.SurfaceSpec([rh_white], directory=spec_dir)
rh_spec.add_surface(rh_inflated)
# write files
all_temp_fns = [spec_fn, rh_spec_fn]
for fn, s in [(rh_inflated_fn, inflated_surf),
(rh_white_fn, white_surf),
(inflated_fn, inflated_surf),
(white_fn, white_surf)]:
surf.write(fn, s)
all_temp_fns.append(fn)
# test adding views
added_specs = afni_suma_spec.hemi_pairs_add_views((lh_spec, rh_spec),
'inflated', '.asc')
for hemi, added_spec in zip(('l', 'r'), added_specs):
states = ['smoothwm', 'inflated'] + ['CoM%sinflated' % i
for i in 'msiap']
assert_equal(states, [s['SurfaceState']
for s in added_specs[0].surfaces])
all_temp_fns.extend([s['SurfaceName']
for s in added_spec.surfaces])
# test combining specs (bh=both hemispheres)
bh_spec = afni_suma_spec.combine_left_right(added_specs)
# test merging specs (mh=merged hemispheres)
mh_spec, mh_surfs = afni_suma_spec.merge_left_right(bh_spec)
assert_equal([s['SurfaceState'] for s in mh_spec.surfaces],
['smoothwm'] + ['CoM%sinflated' % i for i in 'msiap'])
def test_voxel_selection(self):
"""Compare surface and volume based searchlight"""
"""
Tests to see whether results are identical for surface-based
searchlight (just one plane; Euclidean distnace) and volume-based
searchlight.
Note that the current value is a float; if it were int, it would
specify the number of voxels in each searchlight"""
radius = 10.0
"""Define input filenames"""
epi_fn = pathjoin(pymvpa_dataroot, "bold.nii.gz")
maskfn = pathjoin(pymvpa_dataroot, "mask.nii.gz")
"""
Use the EPI datafile to define a surface.
The surface has as many nodes as there are voxels
and is parallel to the volume 'slice'
"""
vg = volgeom.from_any(maskfn, mask_volume=True)
aff = vg.affine
nx, ny, nz = vg.shape[:3]
"""Plane goes in x and y direction, so we take these vectors
from the affine transformation matrix of the volume"""
plane = surf.generate_plane(aff[:3, 3], aff[:3, 0], aff[:3, 1], nx, ny)
"""
Simulate pial and white matter as just above and below
the central plane
"""
normal_vec = aff[:3, 2]
outer = plane + normal_vec
inner = plane + -normal_vec
"""
Combine volume and surface information
"""
vsm = volsurf.VolSurfMaximalMapping(vg, outer, inner)
"""
Run voxel selection with specified radius (in mm), using
Euclidean distance measure
"""
surf_voxsel = surf_voxel_selection.voxel_selection(vsm, radius, distance_metric="e")
"""Define the measure"""
# run_slow=True would give an actual cross-validation with meaningful
# accuracies. Because this is a unit-test only the number of voxels
# in each searchlight is tested.
run_slow = False
if run_slow:
meas = CrossValidation(GNB(), OddEvenPartitioner(), errorfx=lambda p, t: np.mean(p == t))
postproc = mean_sample
else:
meas = _Voxel_Count_Measure()
postproc = lambda x: x
"""
Surface analysis: define the query engine, cross validation,
and searchlight
"""
surf_qe = SurfaceVerticesQueryEngine(surf_voxsel)
surf_sl = Searchlight(meas, queryengine=surf_qe, postproc=postproc)
"""
new (Sep 2012): also test 'simple' queryengine wrapper function
"""
surf_qe2 = disc_surface_queryengine(
radius, maskfn, inner, outer, plane, volume_mask=True, distance_metric="euclidean"
)
surf_sl2 = Searchlight(meas, queryengine=surf_qe2, postproc=postproc)
"""
Same for the volume analysis
"""
element_sizes = tuple(map(abs, (aff[0, 0], aff[1, 1], aff[2, 2])))
sph = Sphere(radius, element_sizes=element_sizes)
kwa = {"voxel_indices": sph}
vol_qe = IndexQueryEngine(**kwa)
vol_sl = Searchlight(meas, queryengine=vol_qe, postproc=postproc)
"""The following steps are similar to start_easy.py"""
attr = SampleAttributes(pathjoin(pymvpa_dataroot, "attributes_literal.txt"))
mask = surf_voxsel.get_mask()
dataset = fmri_dataset(
samples=pathjoin(pymvpa_dataroot, "bold.nii.gz"), targets=attr.targets, chunks=attr.chunks, mask=mask
)
if run_slow:
# do chunkswise linear detrending on dataset
poly_detrend(dataset, polyord=1, chunks_attr="chunks")
# zscore dataset relative to baseline ('rest') mean
zscore(dataset, chunks_attr="chunks", param_est=("targets", ["rest"]))
# select class face and house for this demo analysis
# would work with full datasets (just a little slower)
dataset = dataset[np.array([l in ["face", "house"] for l in dataset.sa.targets], dtype="bool")]
"""Apply searchlight to datasets"""
surf_dset = surf_sl(dataset)
surf_dset2 = surf_sl2(dataset)
vol_dset = vol_sl(dataset)
surf_data = surf_dset.samples
surf_data2 = surf_dset2.samples
vol_data = vol_dset.samples
assert_array_equal(surf_data, surf_data2)
assert_array_equal(surf_data, vol_data)
def test_flat_surface_plotting_exception_wrong_size(self):
s = surf.generate_plane((0, 0, 0), (0, 0, 1), (0, 1, 0), 6, 6)
for offset in (-1, 0, 1):
nfeatures = s.nvertices + offset
ds = AttrDataset(samples=np.random.normal(size=(1, nfeatures)))
def test_voxel_selection(self):
'''Compare surface and volume based searchlight'''
'''
Tests to see whether results are identical for surface-based
searchlight (just one plane; Euclidean distnace) and volume-based
searchlight.
Note that the current value is a float; if it were int, it would
specify the number of voxels in each searchlight'''
radius = 10.
'''Define input filenames'''
epi_fn = os.path.join(pymvpa_dataroot, 'bold.nii.gz')
maskfn = os.path.join(pymvpa_dataroot, 'mask.nii.gz')
'''
Use the EPI datafile to define a surface.
The surface has as many nodes as there are voxels
and is parallel to the volume 'slice'
'''
vg = volgeom.from_any(maskfn, mask_volume=True)
aff = vg.affine
nx, ny, nz = vg.shape[:3]
'''Plane goes in x and y direction, so we take these vectors
from the affine transformation matrix of the volume'''
plane = surf.generate_plane(aff[:3, 3], aff[:3, 0], aff[:3, 1], nx, ny)
'''
Simulate pial and white matter as just above and below
the central plane
'''
normal_vec = aff[:3, 2]
outer = plane + normal_vec
inner = plane + -normal_vec
'''
Combine volume and surface information
'''
vsm = volsurf.VolSurfMaximalMapping(vg, outer, inner)
'''
Run voxel selection with specified radius (in mm), using
Euclidean distance measure
'''
surf_voxsel = surf_voxel_selection.voxel_selection(vsm,
radius,
distance_metric='e')
'''Define the measure'''
# run_slow=True would give an actual cross-validation with meaningful
# accuracies. Because this is a unit-test only the number of voxels
# in each searchlight is tested.
run_slow = False
if run_slow:
meas = CrossValidation(GNB(),
OddEvenPartitioner(),
errorfx=lambda p, t: np.mean(p == t))
postproc = mean_sample
else:
meas = _Voxel_Count_Measure()
postproc = lambda x: x
'''
Surface analysis: define the query engine, cross validation,
and searchlight
'''
surf_qe = SurfaceVerticesQueryEngine(surf_voxsel)
surf_sl = Searchlight(meas, queryengine=surf_qe, postproc=postproc)
'''
new (Sep 2012): also test 'simple' queryengine wrapper function
'''
surf_qe2 = disc_surface_queryengine(radius,
maskfn,
inner,
outer,
plane,
volume_mask=True,
distance_metric='euclidean')
surf_sl2 = Searchlight(meas, queryengine=surf_qe2, postproc=postproc)
'''
Same for the volume analysis
'''
element_sizes = tuple(map(abs, (aff[0, 0], aff[1, 1], aff[2, 2])))
sph = Sphere(radius, element_sizes=element_sizes)
kwa = {'voxel_indices': sph}
vol_qe = IndexQueryEngine(**kwa)
vol_sl = Searchlight(meas, queryengine=vol_qe, postproc=postproc)
'''The following steps are similar to start_easy.py'''
attr = SampleAttributes(
os.path.join(pymvpa_dataroot, 'attributes_literal.txt'))
mask = surf_voxsel.get_mask()
dataset = fmri_dataset(samples=os.path.join(pymvpa_dataroot,
'bold.nii.gz'),
targets=attr.targets,
chunks=attr.chunks,
mask=mask)
if run_slow:
# do chunkswise linear detrending on dataset
poly_detrend(dataset, polyord=1, chunks_attr='chunks')
# zscore dataset relative to baseline ('rest') mean
zscore(dataset,
chunks_attr='chunks',
param_est=('targets', ['rest']))
# select class face and house for this demo analysis
# would work with full datasets (just a little slower)
dataset = dataset[np.array(
[l in ['face', 'house'] for l in dataset.sa.targets],
dtype='bool')]
'''Apply searchlight to datasets'''
surf_dset = surf_sl(dataset)
surf_dset2 = surf_sl2(dataset)
vol_dset = vol_sl(dataset)
surf_data = surf_dset.samples
surf_data2 = surf_dset2.samples
vol_data = vol_dset.samples
assert_array_equal(surf_data, surf_data2)
assert_array_equal(surf_data, vol_data)
def test_afni_suma_spec(self, temp_dir):
# XXX this function generates quite a few temporary files,
# which are removed at the end.
# the decorator @with_tempfile seems unsuitable as it only
# supports a single temporary file
# make temporary directory
os.mkdir(temp_dir)
# generate surfaces
inflated_surf = surf.generate_plane((0, 0, 0), (0, 1, 0), (0, 0, 1),
10, 10)
white_surf = inflated_surf + 1.
# helper function
_tmp = lambda x: os.path.join(temp_dir, x)
# filenames for surfaces and spec file
inflated_fn = _tmp('_lh_inflated.asc')
white_fn = _tmp('_lh_white.asc')
spec_fn = _tmp('lh.spec')
spec_dir = os.path.split(spec_fn)[0]
# generate SUMA-like spec dictionary
white = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=white_fn,
Anatomical='Y',
LocalCurvatureParent='SAME',
LocalDomainParent='SAME',
SurfaceState='smoothwm')
inflated = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=inflated_fn,
Anatomical='N',
LocalCurvatureParent=white_fn,
LocalDomainParent=white_fn,
SurfaceState='inflated')
# make SurfaceSpec object
spec = afni_suma_spec.SurfaceSpec([white], directory=spec_dir)
spec.add_surface(inflated)
# test __str__ and __repr__
assert_true('SurfaceSpec instance with 2 surfaces'
', 2 states ' in '%s' % spec)
assert_true(('%r' % spec).startswith('SurfaceSpec'))
# test finding surfaces
inflated_ = spec.find_surface_from_state('inflated')
assert_equal([(1, inflated)], inflated_)
empty = spec.find_surface_from_state('unknown')
assert_equal(empty, [])
# test .same_states
minimal = afni_suma_spec.SurfaceSpec(
[dict(SurfaceState=s) for s in ('smoothwm', 'inflated')])
assert_true(spec.same_states(minimal))
assert_false(spec.same_states(afni_suma_spec.SurfaceSpec(dict())))
# test 'smart' surface file matching
assert_equal(spec.get_surface_file('smo'), white_fn)
assert_equal(spec.get_surface_file('inflated'), inflated_fn)
assert_equal(spec.get_surface_file('this should be None'), None)
# test i/o
spec.write(spec_fn)
spec_ = afni_suma_spec.from_any(spec_fn)
# prepare for another (right-hemisphere) spec file
lh_spec = spec
rh_spec_fn = spec_fn.replace('lh', 'rh')
rh_inflated_fn = _tmp(
os.path.split(inflated_fn)[1].replace('_lh', '_rh'))
rh_white_fn = _tmp(os.path.split(white_fn)[1].replace('_lh', '_rh'))
rh_spec_fn = _tmp('rh.spec')
rh_white = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=rh_white_fn,
Anatomical='Y',
LocalCurvatureParent='SAME',
LocalDomainParent='SAME',
SurfaceState='smoothwm')
rh_inflated = dict(SurfaceFormat='ASCII',
EmbedDimension='3',
SurfaceType='FreeSurfer',
SurfaceName=rh_inflated_fn,
Anatomical='N',
LocalCurvatureParent=rh_white_fn,
LocalDomainParent=rh_white_fn,
SurfaceState='inflated')
rh_spec = afni_suma_spec.SurfaceSpec([rh_white], directory=spec_dir)
rh_spec.add_surface(rh_inflated)
# write files
all_temp_fns = [spec_fn, rh_spec_fn]
for fn, s in [(rh_inflated_fn, inflated_surf),
(rh_white_fn, white_surf), (inflated_fn, inflated_surf),
(white_fn, white_surf)]:
surf.write(fn, s)
all_temp_fns.append(fn)
# test adding views
added_specs = afni_suma_spec.hemi_pairs_add_views((lh_spec, rh_spec),
'inflated', '.asc')
for hemi, added_spec in zip(('l', 'r'), added_specs):
states = ['smoothwm', 'inflated'
] + ['CoM%sinflated' % i for i in 'msiap']
assert_equal(states,
[s['SurfaceState'] for s in added_specs[0].surfaces])
all_temp_fns.extend(
[s['SurfaceName'] for s in added_spec.surfaces])
# test combining specs (bh=both hemispheres)
bh_spec = afni_suma_spec.combine_left_right(added_specs)
# test merging specs (mh=merged hemispheres)
mh_spec, mh_surfs = afni_suma_spec.merge_left_right(bh_spec)
assert_equal([s['SurfaceState'] for s in mh_spec.surfaces],
['smoothwm'] + ['CoM%sinflated' % i for i in 'msiap'])