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)