def test_agreement_surface_volume(self):
'''test agreement between volume-based and surface-based
searchlights when using euclidean measure'''
# import runner
def sum_ds(ds):
return np.sum(ds)
radius = 3
# make a small dataset with a mask
sh = (10, 10, 10)
msk = np.zeros(sh)
for i in xrange(0, sh[0], 2):
msk[i, :, :] = 1
vg = volgeom.VolGeom(sh, np.identity(4), mask=msk)
# make an image
nt = 6
img = vg.get_masked_nifti_image(6)
ds = fmri_dataset(img, mask=msk)
# run the searchlight
sl = sphere_searchlight(sum_ds, radius=radius)
m = sl(ds)
# now use surface-based searchlight
v = volsurf.from_volume(ds)
source_surf = v.intermediate_surface
node_msk = np.logical_not(np.isnan(source_surf.vertices[:, 0]))
# check that the mask matches with what we used earlier
assert_array_equal(msk.ravel() + 0., node_msk.ravel() + 0.)
source_surf_nodes = np.nonzero(node_msk)[0]
sel = surf_voxel_selection.voxel_selection(
v,
float(radius),
source_surf=source_surf,
source_surf_nodes=source_surf_nodes,
distance_metric='euclidean')
qe = queryengine.SurfaceVerticesQueryEngine(sel)
sl = Searchlight(sum_ds, queryengine=qe)
r = sl(ds)
# check whether they give the same results
assert_array_equal(r.samples, m.samples)
def test_agreement_surface_volume(self):
'''test agreement between volume-based and surface-based
searchlights when using euclidean measure'''
#import runner
def sum_ds(ds):
return np.sum(ds)
radius = 3
# make a small dataset with a mask
sh = (10, 10, 10)
msk = np.zeros(sh)
for i in xrange(0, sh[0], 2):
msk[i, :, :] = 1
vg = volgeom.VolGeom(sh, np.identity(4), mask=msk)
# make an image
nt = 6
img = vg.get_masked_nifti_image(6)
ds = fmri_dataset(img, mask=msk)
# run the searchlight
sl = sphere_searchlight(sum_ds, radius=radius)
m = sl(ds)
# now use surface-based searchlight
v = volsurf.from_volume(ds)
source_surf = v.intermediate_surface
node_msk = np.logical_not(np.isnan(source_surf.vertices[:, 0]))
# check that the mask matches with what we used earlier
assert_array_equal(msk.ravel() + 0., node_msk.ravel() + 0.)
source_surf_nodes = np.nonzero(node_msk)[0]
sel = surf_voxel_selection.voxel_selection(v, float(radius),
source_surf=source_surf,
source_surf_nodes=source_surf_nodes,
distance_metric='euclidean')
qe = queryengine.SurfaceVerticesQueryEngine(sel)
sl = Searchlight(sum_ds, queryengine=qe)
r = sl(ds)
# check whether they give the same results
assert_array_equal(r.samples, m.samples)
def test_volsurf_surf_from_volume(self):
aff = np.eye(4)
aff[0, 0] = aff[1, 1] = aff[2, 2] = 3
sh = (40, 40, 40)
vg = volgeom.VolGeom(sh, aff)
p = volsurf.from_volume(vg).intermediate_surface
q = volsurf.VolumeBasedSurface(vg)
centers = [0, 10, 10000, (-1, -1, -1), (5, 5, 5)]
radii = [0, 10, 20, 100]
for center in centers:
for radius in radii:
x = p.circlearound_n2d(center, radius)
y = q.circlearound_n2d(center, radius)
assert_equal(x, y)
def test_volsurf_surf_from_volume(self):
aff = np.eye(4)
aff[0, 0] = aff[1, 1] = aff[2, 2] = 3
sh = (40, 40, 40)
vg = volgeom.VolGeom(sh, aff)
p = volsurf.from_volume(vg).intermediate_surface
q = volsurf.VolumeBasedSurface(vg)
centers = [0, 10, 10000, (-1, -1, -1), (5, 5, 5)]
radii = [0, 10, 20, 100]
for center in centers:
for radius in radii:
x = p.circlearound_n2d(center, radius)
y = q.circlearound_n2d(center, radius)
assert_equal(x, y)
