test_points_alignment.py

# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.

import unittest

import numpy as np
import torch
from common_testing import TestCaseMixin, get_tests_dir
from pytorch3d.ops import points_alignment
from pytorch3d.structures.pointclouds import Pointclouds
from pytorch3d.transforms import rotation_conversions


def _apply_pcl_transformation(X, R, T, s=None):
    """
    Apply a batch of similarity/rigid transformations, parametrized with
    rotation `R`, translation `T` and scale `s`, to an input batch of
    point clouds `X`.
    """
    if isinstance(X, Pointclouds):
        num_points = X.num_points_per_cloud()
        X_t = X.points_padded()
    else:
        X_t = X

    if s is not None:
        X_t = s[:, None, None] * X_t

    X_t = torch.bmm(X_t, R) + T[:, None, :]

    if isinstance(X, Pointclouds):
        X_list = [x[:n_p] for x, n_p in zip(X_t, num_points)]
        X_t = Pointclouds(X_list)

    return X_t


class TestICP(TestCaseMixin, unittest.TestCase):
    def setUp(self) -> None:
        super().setUp()
        torch.manual_seed(42)
        np.random.seed(42)
        trimesh_results_path = get_tests_dir() / "data/icp_data.pth"
        self.trimesh_results = torch.load(trimesh_results_path)

    @staticmethod
    def iterative_closest_point(
        batch_size=10,
        n_points_X=100,
        n_points_Y=100,
        dim=3,
        use_pointclouds=False,
        estimate_scale=False,
    ):

        device = torch.device("cuda:0")

        # initialize a ground truth point cloud
        X, Y = [
            TestCorrespondingPointsAlignment.init_point_cloud(
                batch_size=batch_size,
                n_points=n_points,
                dim=dim,
                device=device,
                use_pointclouds=use_pointclouds,
                random_pcl_size=True,
                fix_seed=i,
            )
            for i, n_points in enumerate((n_points_X, n_points_Y))
        ]

        torch.cuda.synchronize()

        def run_iterative_closest_point():
            points_alignment.iterative_closest_point(
                X,
                Y,
                estimate_scale=estimate_scale,
                allow_reflection=False,
                verbose=False,
                max_iterations=100,
                relative_rmse_thr=1e-4,
            )
            torch.cuda.synchronize()

        return run_iterative_closest_point

    def test_init_transformation(self, batch_size=10):
        """
        First runs a full ICP on a random problem. Then takes a given point
        in the history of ICP iteration transformations, initializes
        a second run of ICP with this transformation and checks whether
        both runs ended with the same solution.
        """

        device = torch.device("cuda:0")

        for dim in (2, 3, 11):
            for n_points_X in (30, 100):
                for n_points_Y in (30, 100):
                    # initialize ground truth point clouds
                    X, Y = [
                        TestCorrespondingPointsAlignment.init_point_cloud(
                            batch_size=batch_size,
                            n_points=n_points,
                            dim=dim,
                            device=device,
                            use_pointclouds=False,
                            random_pcl_size=True,
                        )
                        for n_points in (n_points_X, n_points_Y)
                    ]

                    # run full icp
                    (
                        converged,
                        _,
                        Xt,
                        (R, T, s),
                        t_hist,
                    ) = points_alignment.iterative_closest_point(
                        X,
                        Y,
                        estimate_scale=False,
                        allow_reflection=False,
                        verbose=False,
                        max_iterations=100,
                    )

                    # start from the solution after the third
                    # iteration of the previous ICP
                    t_init = t_hist[min(2, len(t_hist) - 1)]

                    # rerun the ICP
                    (
                        converged_init,
                        _,
                        Xt_init,
                        (R_init, T_init, s_init),
                        t_hist_init,
                    ) = points_alignment.iterative_closest_point(
                        X,
                        Y,
                        init_transform=t_init,
                        estimate_scale=False,
                        allow_reflection=False,
                        verbose=False,
                        max_iterations=100,
                    )

                    # compare transformations and obtained clouds
                    # check that both sets of transforms are the same
                    atol = 3e-5
                    self.assertClose(R_init, R, atol=atol)
                    self.assertClose(T_init, T, atol=atol)
                    self.assertClose(s_init, s, atol=atol)
                    self.assertClose(Xt_init, Xt, atol=atol)

    def test_heterogeneous_inputs(self, batch_size=10):
        """
        Tests whether we get the same result when running ICP on
        a set of randomly-sized Pointclouds and on their padded versions.
        """

        device = torch.device("cuda:0")

        for estimate_scale in (True, False):
            for max_n_points in (10, 30, 100):
                # initialize ground truth point clouds
                X_pcl, Y_pcl = [
                    TestCorrespondingPointsAlignment.init_point_cloud(
                        batch_size=batch_size,
                        n_points=max_n_points,
                        dim=3,
                        device=device,
                        use_pointclouds=True,
                        random_pcl_size=True,
                    )
                    for _ in range(2)
                ]

                # get the padded versions and their num of points
                X_padded = X_pcl.points_padded()
                Y_padded = Y_pcl.points_padded()
                n_points_X = X_pcl.num_points_per_cloud()
                n_points_Y = Y_pcl.num_points_per_cloud()

                # run icp with Pointlouds inputs
                (
                    _,
                    _,
                    Xt_pcl,
                    (R_pcl, T_pcl, s_pcl),
                    _,
                ) = points_alignment.iterative_closest_point(
                    X_pcl,
                    Y_pcl,
                    estimate_scale=estimate_scale,
                    allow_reflection=False,
                    verbose=False,
                    max_iterations=100,
                )
                Xt_pcl = Xt_pcl.points_padded()

                # run icp with tensor inputs on each element
                # of the batch separately
                icp_results = [
                    points_alignment.iterative_closest_point(
                        X_[None, :n_X, :],
                        Y_[None, :n_Y, :],
                        estimate_scale=estimate_scale,
                        allow_reflection=False,
                        verbose=False,
                        max_iterations=100,
                    )
                    for X_, Y_, n_X, n_Y in zip(
                        X_padded, Y_padded, n_points_X, n_points_Y
                    )
                ]

                # parse out the transformation results
                R, T, s = [
                    torch.cat([x.RTs[i] for x in icp_results], dim=0) for i in range(3)
                ]

                # check that both sets of transforms are the same
                atol = 1e-5
                self.assertClose(R_pcl, R, atol=atol)
                self.assertClose(T_pcl, T, atol=atol)
                self.assertClose(s_pcl, s, atol=atol)

                # compare the transformed point clouds
                for pcli in range(batch_size):
                    nX = n_points_X[pcli]
                    Xt_ = icp_results[pcli].Xt[0, :nX]
                    Xt_pcl_ = Xt_pcl[pcli][:nX]
                    self.assertClose(Xt_pcl_, Xt_, atol=atol)

    def test_compare_with_trimesh(self):
        """
        Compares the outputs of `iterative_closest_point` with the results
        of `trimesh.registration.icp` from the `trimesh` python package:
        https://github.com/mikedh/trimesh

        We have run `trimesh.registration.icp` on several random problems
        with different point cloud sizes. The results of trimesh, together with
        the randomly generated input clouds are loaded in the constructor of
        this class and this test compares the loaded results to our runs.
        """
        for n_points_X in (10, 20, 50, 100):
            for n_points_Y in (10, 20, 50, 100):
                self._compare_with_trimesh(n_points_X=n_points_X, n_points_Y=n_points_Y)

    def _compare_with_trimesh(
        self, n_points_X=100, n_points_Y=100, estimate_scale=False
    ):
        """
        Executes a single test for `iterative_closest_point` for a
        specific setting of the inputs / outputs. Compares the result with
        the result of the trimesh package on the same input data.
        """

        device = torch.device("cuda:0")

        # load the trimesh results and the initial point clouds for icp
        key = (int(n_points_X), int(n_points_Y), int(estimate_scale))
        X, Y, R_trimesh, T_trimesh, s_trimesh = [
            x.to(device) for x in self.trimesh_results[key]
        ]

        # run the icp algorithm
        (
            converged,
            _,
            _,
            (R_ours, T_ours, s_ours),
            _,
        ) = points_alignment.iterative_closest_point(
            X,
            Y,
            estimate_scale=estimate_scale,
            allow_reflection=False,
            verbose=False,
            max_iterations=100,
        )

        # check that we have the same transformation
        # and that the icp converged
        atol = 1e-5
        self.assertClose(R_ours, R_trimesh, atol=atol)
        self.assertClose(T_ours, T_trimesh, atol=atol)
        self.assertClose(s_ours, s_trimesh, atol=atol)
        self.assertTrue(converged)


class TestCorrespondingPointsAlignment(TestCaseMixin, unittest.TestCase):
    def setUp(self) -> None:
        super().setUp()
        torch.manual_seed(42)
        np.random.seed(42)

    @staticmethod
    def random_rotation(batch_size, dim, device=None):
        """
        Generates a batch of random `dim`-dimensional rotation matrices.
        """
        if dim == 3:
            R = rotation_conversions.random_rotations(batch_size, device=device)
        else:
            # generate random rotation matrices with orthogonalization of
            # random normal square matrices, followed by a transformation
            # that ensures determinant(R)==1
            H = torch.randn(batch_size, dim, dim, dtype=torch.float32, device=device)
            U, _, V = torch.svd(H)
            E = torch.eye(dim, dtype=torch.float32, device=device)[None].repeat(
                batch_size, 1, 1
            )
            E[:, -1, -1] = torch.det(torch.bmm(U, V.transpose(2, 1)))
            R = torch.bmm(torch.bmm(U, E), V.transpose(2, 1))
            assert torch.allclose(torch.det(R), R.new_ones(batch_size), atol=1e-4)

        return R

    @staticmethod
    def init_point_cloud(
        batch_size=10,
        n_points=1000,
        dim=3,
        device=None,
        use_pointclouds=False,
        random_pcl_size=True,
        fix_seed=None,
    ):
        """
        Generate a batch of normally distributed point clouds.
        """

        if fix_seed is not None:
            # make sure we always generate the same pointcloud
            seed = torch.random.get_rng_state()
            torch.manual_seed(fix_seed)

        if use_pointclouds:
            assert dim == 3, "Pointclouds support only 3-dim points."
            # generate a `batch_size` point clouds with number of points
            # between 4 and `n_points`
            if random_pcl_size:
                n_points_per_batch = torch.randint(
                    low=4,
                    high=n_points,
                    size=(batch_size,),
                    device=device,
                    dtype=torch.int64,
                )
                X_list = [
                    torch.randn(int(n_pt), dim, device=device, dtype=torch.float32)
                    for n_pt in n_points_per_batch
                ]
                X = Pointclouds(X_list)
            else:
                X = torch.randn(
                    batch_size, n_points, dim, device=device, dtype=torch.float32
                )
                X = Pointclouds(list(X))
        else:
            X = torch.randn(
                batch_size, n_points, dim, device=device, dtype=torch.float32
            )

        if fix_seed:
            torch.random.set_rng_state(seed)

        return X

    @staticmethod
    def generate_pcl_transformation(
        batch_size=10, scale=False, reflect=False, dim=3, device=None
    ):
        """
        Generate a batch of random rigid/similarity transformations.
        """
        R = TestCorrespondingPointsAlignment.random_rotation(
            batch_size, dim, device=device
        )
        T = torch.randn(batch_size, dim, dtype=torch.float32, device=device)
        if scale:
            s = torch.rand(batch_size, dtype=torch.float32, device=device) + 0.1
        else:
            s = torch.ones(batch_size, dtype=torch.float32, device=device)

        return R, T, s

    @staticmethod
    def generate_random_reflection(batch_size=10, dim=3, device=None):
        """
        Generate a batch of reflection matrices of shape (batch_size, dim, dim),
        where M_i is an identity matrix with one random entry on the
        diagonal equal to -1.
        """
        # randomly select one of the dimensions to reflect for each
        # element in the batch
        dim_to_reflect = torch.randint(
            low=0, high=dim, size=(batch_size,), device=device, dtype=torch.int64
        )

        # convert dim_to_reflect to a batch of reflection matrices M
        M = torch.diag_embed(
            (
                dim_to_reflect[:, None]
                != torch.arange(dim, device=device, dtype=torch.float32)
            ).float()
            * 2
            - 1,
            dim1=1,
            dim2=2,
        )

        return M

    @staticmethod
    def corresponding_points_alignment(
        batch_size=10,
        n_points=100,
        dim=3,
        use_pointclouds=False,
        estimate_scale=False,
        allow_reflection=False,
        reflect=False,
        random_weights=False,
    ):

        device = torch.device("cuda:0")

        # initialize a ground truth point cloud
        X = TestCorrespondingPointsAlignment.init_point_cloud(
            batch_size=batch_size,
            n_points=n_points,
            dim=dim,
            device=device,
            use_pointclouds=use_pointclouds,
            random_pcl_size=True,
        )

        # generate the true transformation
        R, T, s = TestCorrespondingPointsAlignment.generate_pcl_transformation(
            batch_size=batch_size,
            scale=estimate_scale,
            reflect=reflect,
            dim=dim,
            device=device,
        )

        # apply the generated transformation to the generated
        # point cloud X
        X_t = _apply_pcl_transformation(X, R, T, s=s)

        weights = None
        if random_weights:
            template = X.points_padded() if use_pointclouds else X
            weights = torch.rand_like(template[:, :, 0])
            weights = weights / weights.sum(dim=1, keepdim=True)
            # zero out some weights as zero weights are a common use case
            # this guarantees there are no zero weight
            weights *= (weights * template.size()[1] > 0.3).to(weights)
            if use_pointclouds:  # convert to List[Tensor]
                weights = [
                    w[:npts] for w, npts in zip(weights, X.num_points_per_cloud())
                ]

        torch.cuda.synchronize()

        def run_corresponding_points_alignment():
            points_alignment.corresponding_points_alignment(
                X,
                X_t,
                weights,
                allow_reflection=allow_reflection,
                estimate_scale=estimate_scale,
            )
            torch.cuda.synchronize()

        return run_corresponding_points_alignment

    def test_corresponding_points_alignment(self, batch_size=10):
        """
        Tests whether we can estimate a rigid/similarity motion between
        a randomly initialized point cloud and its randomly transformed version.

        The tests are done for all possible combinations
        of the following boolean flags:
            - estimate_scale ... Estimate also a scaling component of
                                 the transformation.
            - reflect ... The ground truth orthonormal part of the generated
                         transformation is a reflection (det==-1).
            - allow_reflection ... If True, the orthonormal matrix of the
                                  estimated transformation is allowed to be
                                  a reflection (det==-1).
            - use_pointclouds ... If True, passes the Pointclouds objects
                                  to corresponding_points_alignment.
        """
        self.skipTest("Temporarily disabled pending investigation")
        # run this for several different point cloud sizes
        for n_points in (100, 3, 2, 1):
            # run this for several different dimensionalities
            for dim in range(2, 10):
                # switches whether we should use the Pointclouds inputs
                use_point_clouds_cases = (
                    (True, False) if dim == 3 and n_points > 3 else (False,)
                )
                for random_weights in (False, True):
                    for use_pointclouds in use_point_clouds_cases:
                        for estimate_scale in (False, True):
                            for reflect in (False, True):
                                for allow_reflection in (False, True):
                                    self._test_single_corresponding_points_alignment(
                                        batch_size=10,
                                        n_points=n_points,
                                        dim=dim,
                                        use_pointclouds=use_pointclouds,
                                        estimate_scale=estimate_scale,
                                        reflect=reflect,
                                        allow_reflection=allow_reflection,
                                        random_weights=random_weights,
                                    )

    def _test_single_corresponding_points_alignment(
        self,
        batch_size=10,
        n_points=100,
        dim=3,
        use_pointclouds=False,
        estimate_scale=False,
        reflect=False,
        allow_reflection=False,
        random_weights=False,
    ):
        """
        Executes a single test for `corresponding_points_alignment` for a
        specific setting of the inputs / outputs.
        """

        device = torch.device("cuda:0")

        # initialize the a ground truth point cloud
        X = TestCorrespondingPointsAlignment.init_point_cloud(
            batch_size=batch_size,
            n_points=n_points,
            dim=dim,
            device=device,
            use_pointclouds=use_pointclouds,
            random_pcl_size=True,
        )

        # generate the true transformation
        R, T, s = TestCorrespondingPointsAlignment.generate_pcl_transformation(
            batch_size=batch_size,
            scale=estimate_scale,
            reflect=reflect,
            dim=dim,
            device=device,
        )

        if reflect:
            # generate random reflection M and apply to the rotations
            M = TestCorrespondingPointsAlignment.generate_random_reflection(
                batch_size=batch_size, dim=dim, device=device
            )
            R = torch.bmm(M, R)

        weights = None
        if random_weights:
            template = X.points_padded() if use_pointclouds else X
            weights = torch.rand_like(template[:, :, 0])
            weights = weights / weights.sum(dim=1, keepdim=True)
            # zero out some weights as zero weights are a common use case
            # this guarantees there are no zero weight
            weights *= (weights * template.size()[1] > 0.3).to(weights)
            if use_pointclouds:  # convert to List[Tensor]
                weights = [
                    w[:npts] for w, npts in zip(weights, X.num_points_per_cloud())
                ]

        # apply the generated transformation to the generated
        # point cloud X
        X_t = _apply_pcl_transformation(X, R, T, s=s)

        # run the CorrespondingPointsAlignment algorithm
        R_est, T_est, s_est = points_alignment.corresponding_points_alignment(
            X,
            X_t,
            weights,
            allow_reflection=allow_reflection,
            estimate_scale=estimate_scale,
        )

        assert_error_message = (
            f"Corresponding_points_alignment assertion failure for "
            f"n_points={n_points}, "
            f"dim={dim}, "
            f"use_pointclouds={use_pointclouds}, "
            f"estimate_scale={estimate_scale}, "
            f"reflect={reflect}, "
            f"allow_reflection={allow_reflection},"
            f"random_weights={random_weights}."
        )

        # if we test the weighted case, check that weights help with noise
        if random_weights and not use_pointclouds and n_points >= (dim + 10):
            # add noise to 20% points with smallest weight
            X_noisy = X_t.clone()
            _, mink_idx = torch.topk(-weights, int(n_points * 0.2), dim=1)
            mink_idx = mink_idx[:, :, None].expand(-1, -1, X_t.shape[-1])
            X_noisy.scatter_add_(
                1, mink_idx, 0.3 * torch.randn_like(mink_idx, dtype=X_t.dtype)
            )

            def align_and_get_mse(weights_):
                R_n, T_n, s_n = points_alignment.corresponding_points_alignment(
                    X_noisy,
                    X_t,
                    weights_,
                    allow_reflection=allow_reflection,
                    estimate_scale=estimate_scale,
                )

                X_t_est = _apply_pcl_transformation(X_noisy, R_n, T_n, s=s_n)

                return (((X_t_est - X_t) * weights[..., None]) ** 2).sum(
                    dim=(1, 2)
                ) / weights.sum(dim=-1)

            # check that using weights leads to lower weighted_MSE(X_noisy, X_t)
            self.assertTrue(
                torch.all(align_and_get_mse(weights) <= align_and_get_mse(None))
            )

        if reflect and not allow_reflection:
            # check that all rotations have det=1
            self._assert_all_close(
                torch.det(R_est), R_est.new_ones(batch_size), assert_error_message
            )

        else:
            # mask out inputs with too few non-degenerate points for assertions
            w = (
                torch.ones_like(R_est[:, 0, 0])
                if weights is None or n_points >= dim + 10
                else (weights > 0.0).all(dim=1).to(R_est)
            )
            # check that the estimated tranformation is the same
            # as the ground truth
            if n_points >= (dim + 1):
                # the checks on transforms apply only when
                # the problem setup is unambiguous
                msg = assert_error_message
                self._assert_all_close(R_est, R, msg, w[:, None, None], atol=1e-5)
                self._assert_all_close(T_est, T, msg, w[:, None])
                self._assert_all_close(s_est, s, msg, w)

                # check that the orthonormal part of the
                # transformation has a correct determinant (+1/-1)
                desired_det = R_est.new_ones(batch_size)
                if reflect:
                    desired_det *= -1.0
                self._assert_all_close(torch.det(R_est), desired_det, msg, w)

            # check that the transformed point cloud
            # X matches X_t
            X_t_est = _apply_pcl_transformation(X, R_est, T_est, s=s_est)
            self._assert_all_close(
                X_t, X_t_est, assert_error_message, w[:, None, None], atol=1e-5
            )

    def _assert_all_close(self, a_, b_, err_message, weights=None, atol=1e-6):
        if isinstance(a_, Pointclouds):
            a_ = a_.points_packed()
        if isinstance(b_, Pointclouds):
            b_ = b_.points_packed()
        if weights is None:
            self.assertClose(a_, b_, atol=atol, msg=err_message)
        else:
            self.assertClose(a_ * weights, b_ * weights, atol=atol, msg=err_message)