def test_joint_pdf_gradients_dense(): # Compare the analytical and numerical (finite differences) gradient of # the joint distribution (i.e. derivatives of each histogram cell) w.r.t. # the transform parameters. Since the histograms are discrete partitions # of the image intensities, the finite difference approximation is # normally not very close to the analytical derivatives. Other sources of # error are the interpolation used when transforming the images and the # boundary intensities introduced when interpolating outside of the image # (i.e. some "zeros" are introduced at the boundary which affect the # numerical derivatives but is not taken into account by the analytical # derivatives). Thus, we need to relax the verification. Instead of # looking for the analytical and numerical gradients to be very close to # each other, we will verify that they approximately point in the same # direction by testing if the angle they form is close to zero. h = 1e-4 # Make sure dictionary entries are processed in the same order regardless # of the platform. Otherwise any random numbers drawn within the loop # would make the test non-deterministic even if we fix the seed before # the loop. Right now, this test does not draw any samples, but we still # sort the entries to prevent future related failures. for ttype in sorted(factors): dim = ttype[1] if dim == 2: nslices = 1 transform_method = vf.transform_2d_affine else: nslices = 45 transform_method = vf.transform_3d_affine transform = regtransforms[ttype] factor = factors[ttype] theta = transform.get_identity_parameters() static, moving, static_g2w, moving_g2w, smask, mmask, M = \ setup_random_transform(transform, factor, nslices, 5.0) parzen_hist = ParzenJointHistogram(32) parzen_hist.setup(static, moving, smask, mmask) # Compute the gradient at theta with the implementation under test M = transform.param_to_matrix(theta) shape = np.array(static.shape, dtype=np.int32) moved = transform_method(moving.astype(np.float32), shape, M) moved = np.array(moved) parzen_hist.update_pdfs_dense(static.astype(np.float64), moved.astype(np.float64)) # Get the joint distribution evaluated at theta J0 = np.copy(parzen_hist.joint) grid_to_space = np.eye(dim + 1) spacing = np.ones(dim, dtype=np.float64) mgrad, inside = vf.gradient(moving.astype(np.float32), moving_g2w, spacing, shape, grid_to_space) id = transform.get_identity_parameters() parzen_hist.update_gradient_dense(id, transform, static.astype(np.float64), moved.astype(np.float64), grid_to_space, mgrad, smask, mmask) actual = np.copy(parzen_hist.joint_grad) # Now we have the gradient of the joint distribution w.r.t. the # transform parameters # Compute the gradient using finite-diferences n = transform.get_number_of_parameters() expected = np.empty_like(actual) for i in range(n): dtheta = theta.copy() dtheta[i] += h # Update the joint distribution with the transformed moving image M = transform.param_to_matrix(dtheta) shape = np.array(static.shape, dtype=np.int32) moved = transform_method(moving.astype(np.float32), shape, M) moved = np.array(moved) parzen_hist.update_pdfs_dense(static.astype(np.float64), moved.astype(np.float64)) J1 = np.copy(parzen_hist.joint) expected[..., i] = (J1 - J0) / h # Dot product and norms of gradients of each joint histogram cell # i.e. the derivatives of each cell w.r.t. all parameters P = (expected * actual).sum(2) enorms = np.sqrt((expected**2).sum(2)) anorms = np.sqrt((actual**2).sum(2)) prodnorms = enorms * anorms # Cosine of angle between the expected and actual gradients. # Exclude very small gradients P[prodnorms > 1e-6] /= (prodnorms[prodnorms > 1e-6]) P[prodnorms <= 1e-6] = 0 # Verify that a large proportion of the gradients point almost in # the same direction. Disregard very small gradients mean_cosine = P[P != 0].mean() std_cosine = P[P != 0].std() assert (mean_cosine > 0.9) assert (std_cosine < 0.25)
def test_parzen_densities(): # Test the computation of the joint intensity distribution # using a dense and a sparse set of values seed = 1246592 nbins = 32 nr = 30 nc = 35 ns = 20 nvals = 50 for dim in [2, 3]: if dim == 2: shape = (nr, nc) static, moving = create_random_image_pair(shape, nvals, seed) else: shape = (ns, nr, nc) static, moving = create_random_image_pair(shape, nvals, seed) # Initialize parzen_hist = ParzenJointHistogram(nbins) parzen_hist.setup(static, moving) # Get distributions computed by dense sampling parzen_hist.update_pdfs_dense(static, moving) actual_joint_dense = parzen_hist.joint actual_mmarginal_dense = parzen_hist.mmarginal actual_smarginal_dense = parzen_hist.smarginal # Get distributions computed by sparse sampling sval = static.reshape(-1) mval = moving.reshape(-1) parzen_hist.update_pdfs_sparse(sval, mval) actual_joint_sparse = parzen_hist.joint actual_mmarginal_sparse = parzen_hist.mmarginal actual_smarginal_sparse = parzen_hist.smarginal # Compute the expected joint distribution with dense sampling expected_joint_dense = np.zeros(shape=(nbins, nbins)) for index in ndindex(shape): sv = parzen_hist.bin_normalize_static(static[index]) mv = parzen_hist.bin_normalize_moving(moving[index]) sbin = parzen_hist.bin_index(sv) # The spline is centered at mv, will evaluate for all row spline_arg = np.array([i - mv for i in range(nbins)]) contribution = cubic_spline(spline_arg) expected_joint_dense[sbin, :] += contribution # Compute the expected joint distribution with sparse sampling expected_joint_sparse = np.zeros(shape=(nbins, nbins)) for index in range(sval.shape[0]): sv = parzen_hist.bin_normalize_static(sval[index]) mv = parzen_hist.bin_normalize_moving(mval[index]) sbin = parzen_hist.bin_index(sv) # The spline is centered at mv, will evaluate for all row spline_arg = np.array([i - mv for i in range(nbins)]) contribution = cubic_spline(spline_arg) expected_joint_sparse[sbin, :] += contribution # Verify joint distributions expected_joint_dense /= expected_joint_dense.sum() expected_joint_sparse /= expected_joint_sparse.sum() assert_array_almost_equal(actual_joint_dense, expected_joint_dense) assert_array_almost_equal(actual_joint_sparse, expected_joint_sparse) # Verify moving marginals expected_mmarginal_dense = expected_joint_dense.sum(0) expected_mmarginal_dense /= expected_mmarginal_dense.sum() expected_mmarginal_sparse = expected_joint_sparse.sum(0) expected_mmarginal_sparse /= expected_mmarginal_sparse.sum() assert_array_almost_equal(actual_mmarginal_dense, expected_mmarginal_dense) assert_array_almost_equal(actual_mmarginal_sparse, expected_mmarginal_sparse) # Verify static marginals expected_smarginal_dense = expected_joint_dense.sum(1) expected_smarginal_dense /= expected_smarginal_dense.sum() expected_smarginal_sparse = expected_joint_sparse.sum(1) expected_smarginal_sparse /= expected_smarginal_sparse.sum() assert_array_almost_equal(actual_smarginal_dense, expected_smarginal_dense) assert_array_almost_equal(actual_smarginal_sparse, expected_smarginal_sparse)
def test_parzen_densities(): # Test the computation of the joint intensity distribution # using a dense and a sparse set of values seed = 1246592 nbins = 32 nr = 30 nc = 35 ns = 20 nvals = 50 for dim in [2, 3]: if dim == 2: shape = (nr, nc) static, moving = create_random_image_pair(shape, nvals, seed) else: shape = (ns, nr, nc) static, moving = create_random_image_pair(shape, nvals, seed) # Initialize parzen_hist = ParzenJointHistogram(nbins) parzen_hist.setup(static, moving) # Get distributions computed by dense sampling parzen_hist.update_pdfs_dense(static, moving) actual_joint_dense = parzen_hist.joint actual_mmarginal_dense = parzen_hist.mmarginal actual_smarginal_dense = parzen_hist.smarginal # Get distributions computed by sparse sampling sval = static.reshape(-1) mval = moving.reshape(-1) parzen_hist.update_pdfs_sparse(sval, mval) actual_joint_sparse = parzen_hist.joint actual_mmarginal_sparse = parzen_hist.mmarginal actual_smarginal_sparse = parzen_hist.smarginal # Compute the expected joint distribution with dense sampling expected_joint_dense = np.zeros(shape=(nbins, nbins)) for index in ndindex(shape): sv = parzen_hist.bin_normalize_static(static[index]) mv = parzen_hist.bin_normalize_moving(moving[index]) sbin = parzen_hist.bin_index(sv) # The spline is centered at mv, will evaluate for all row spline_arg = np.array([i - mv for i in range(nbins)]) contribution = cubic_spline(spline_arg) expected_joint_dense[sbin, :] += contribution # Compute the expected joint distribution with sparse sampling expected_joint_sparse = np.zeros(shape=(nbins, nbins)) for index in range(sval.shape[0]): sv = parzen_hist.bin_normalize_static(sval[index]) mv = parzen_hist.bin_normalize_moving(mval[index]) sbin = parzen_hist.bin_index(sv) # The spline is centered at mv, will evaluate for all row spline_arg = np.array([i - mv for i in range(nbins)]) contribution = cubic_spline(spline_arg) expected_joint_sparse[sbin, :] += contribution # Verify joint distributions expected_joint_dense /= expected_joint_dense.sum() expected_joint_sparse /= expected_joint_sparse.sum() assert_array_almost_equal(actual_joint_dense, expected_joint_dense) assert_array_almost_equal(actual_joint_sparse, expected_joint_sparse) # Verify moving marginals expected_mmarginal_dense = expected_joint_dense.sum(0) expected_mmarginal_dense /= expected_mmarginal_dense.sum() expected_mmarginal_sparse = expected_joint_sparse.sum(0) expected_mmarginal_sparse /= expected_mmarginal_sparse.sum() assert_array_almost_equal(actual_mmarginal_dense, expected_mmarginal_dense) assert_array_almost_equal(actual_mmarginal_sparse, expected_mmarginal_sparse) # Verify static marginals expected_smarginal_dense = expected_joint_dense.sum(1) expected_smarginal_dense /= expected_smarginal_dense.sum() expected_smarginal_sparse = expected_joint_sparse.sum(1) expected_smarginal_sparse /= expected_smarginal_sparse.sum() assert_array_almost_equal(actual_smarginal_dense, expected_smarginal_dense) assert_array_almost_equal(actual_smarginal_sparse, expected_smarginal_sparse)
def test_joint_pdf_gradients_dense(): # Compare the analytical and numerical (finite differences) gradient of the # joint distribution (i.e. derivatives of each histogram cell) w.r.t. the # transform parameters. Since the histograms are discrete partitions of the # image intensities, the finite difference approximation is normally not # very close to the analytical derivatives. Other sources of error are the # interpolation used when transforming the images and the boundary intensities # introduced when interpolating outside of the image (i.e. some "zeros" are # introduced at the boundary which affect the numerical derivatives but is # not taken into account by the analytical derivatives). Thus, we need to # relax the verification. Instead of looking for the analytical and # numerical gradients to be very close to each other, we will verify that # they approximately point in the same direction by testing if the angle # they form is close to zero. h = 1e-4 # Make sure dictionary entries are processed in the same order regardless of # the platform. Otherwise any random numbers drawn within the loop would make # the test non-deterministic even if we fix the seed before the loop. # Right now, this test does not draw any samples, but we still sort the entries # to prevent future related failures. for ttype in sorted(factors): dim = ttype[1] if dim == 2: nslices = 1 transform_method = vf.transform_2d_affine else: nslices = 45 transform_method = vf.transform_3d_affine transform = regtransforms[ttype] factor = factors[ttype] theta = transform.get_identity_parameters() static, moving, static_g2w, moving_g2w, smask, mmask, M = \ setup_random_transform(transform, factor, nslices, 5.0) parzen_hist = ParzenJointHistogram(32) parzen_hist.setup(static, moving, smask, mmask) # Compute the gradient at theta with the implementation under test M = transform.param_to_matrix(theta) shape = np.array(static.shape, dtype=np.int32) moved = transform_method(moving.astype(np.float32), shape, M) moved = np.array(moved) parzen_hist.update_pdfs_dense(static.astype(np.float64), moved.astype(np.float64)) # Get the joint distribution evaluated at theta J0 = np.copy(parzen_hist.joint) grid_to_space = np.eye(dim + 1) spacing = np.ones(dim, dtype=np.float64) mgrad, inside = vf.gradient(moving.astype(np.float32), moving_g2w, spacing, shape, grid_to_space) id = transform.get_identity_parameters() parzen_hist.update_gradient_dense(id, transform, static.astype(np.float64), moved.astype(np.float64), grid_to_space, mgrad, smask, mmask) actual = np.copy(parzen_hist.joint_grad) # Now we have the gradient of the joint distribution w.r.t. the # transform parameters # Compute the gradient using finite-diferences n = transform.get_number_of_parameters() expected = np.empty_like(actual) for i in range(n): dtheta = theta.copy() dtheta[i] += h # Update the joint distribution with the transformed moving image M = transform.param_to_matrix(dtheta) shape = np.array(static.shape, dtype=np.int32) moved = transform_method(moving.astype(np.float32), shape, M) moved = np.array(moved) parzen_hist.update_pdfs_dense(static.astype(np.float64), moved.astype(np.float64)) J1 = np.copy(parzen_hist.joint) expected[..., i] = (J1 - J0) / h # Dot product and norms of gradients of each joint histogram cell # i.e. the derivatives of each cell w.r.t. all parameters P = (expected * actual).sum(2) enorms = np.sqrt((expected ** 2).sum(2)) anorms = np.sqrt((actual ** 2).sum(2)) prodnorms = enorms * anorms # Cosine of angle between the expected and actual gradients. # Exclude very small gradients P[prodnorms > 1e-6] /= (prodnorms[prodnorms > 1e-6]) P[prodnorms <= 1e-6] = 0 # Verify that a large proportion of the gradients point almost in # the same direction. Disregard very small gradients mean_cosine = P[P != 0].mean() std_cosine = P[P != 0].std() assert(mean_cosine > 0.9) assert(std_cosine < 0.25)
fetch_syn_data() _, nib_syn_b0 = read_syn_data() moving = np.array(nib_syn_b0.get_data()) moving_grid2world = nib_syn_b0.affine static = ((static.astype(np.float64) - static.min()) / (static.max() - static.min())) moving = ((moving.astype(np.float64) - moving.min()) / (moving.max() - moving.min())) static = np.array(static).astype(np.float64) moving = np.array(moving).astype(np.float64) from dipy.align.imaffine import AffineMap dim = len(static.shape) starting_affine = np.eye(dim + 1) affine_map = AffineMap(starting_affine, static.shape, static_grid2world, moving.shape, moving_grid2world) static_values = static moving_values = affine_map.transform(moving) from dipy.align.parzenhist import ParzenJointHistogram nbins = 32 histogram = ParzenJointHistogram(nbins) histogram.update_pdfs_dense(static_values, moving_values) np.save('sl_aff_par_cpdf_joint', histogram.joint) np.save('sl_aff_par_cpdf_smarg', histogram.smarginal) np.save('sl_aff_par_cpdf_mmarg', histogram.mmarginal)