Pytorch batch procrustes implementation

batch_procrustes_pytorch.py

import numpy as np
import torch

def compute_similarity_transform(S1, S2):
    '''
    Computes a similarity transform (sR, t) that takes
    a set of 3D points S1 (3 x N) closest to a set of 3D points S2,
    where R is an 3x3 rotation matrix, t 3x1 translation, s scale.
    i.e. solves the orthogonal Procrutes problem.
    '''
    transposed = False
    if S1.shape[0] != 3 and S1.shape[0] != 2:
        S1 = S1.T
        S2 = S2.T
        transposed = True
    assert(S2.shape[1] == S1.shape[1])

    # 1. Remove mean.
    mu1 = S1.mean(axis=1, keepdims=True)
    mu2 = S2.mean(axis=1, keepdims=True)
    X1 = S1 - mu1
    X2 = S2 - mu2

    # 2. Compute variance of X1 used for scale.
    var1 = np.sum(X1**2)

    # 3. The outer product of X1 and X2.
    K = X1.dot(X2.T)

    # 4. Solution that Maximizes trace(R'K) is R=U*V', where U, V are
    # singular vectors of K.
    U, s, Vh = np.linalg.svd(K)
    V = Vh.T
    # Construct Z that fixes the orientation of R to get det(R)=1.
    Z = np.eye(U.shape[0])
    Z[-1, -1] *= np.sign(np.linalg.det(U.dot(V.T)))
    # Construct R.
    R = V.dot(Z.dot(U.T))

    # 5. Recover scale.
    scale = np.trace(R.dot(K)) / var1

    # 6. Recover translation.
    t = mu2 - scale*(R.dot(mu1))

    # 7. Error:
    S1_hat = scale*R.dot(S1) + t

    if transposed:
        S1_hat = S1_hat.T

    return S1_hat


def compute_similarity_transform_torch(S1, S2):
    '''
    Computes a similarity transform (sR, t) that takes
    a set of 3D points S1 (3 x N) closest to a set of 3D points S2,
    where R is an 3x3 rotation matrix, t 3x1 translation, s scale.
    i.e. solves the orthogonal Procrutes problem.
    '''
    transposed = False
    if S1.shape[0] != 3 and S1.shape[0] != 2:
        S1 = S1.T
        S2 = S2.T
        transposed = True
    assert (S2.shape[1] == S1.shape[1])

    # 1. Remove mean.
    mu1 = S1.mean(axis=1, keepdims=True)
    mu2 = S2.mean(axis=1, keepdims=True)
    X1 = S1 - mu1
    X2 = S2 - mu2

    # print('X1', X1.shape)

    # 2. Compute variance of X1 used for scale.
    var1 = torch.sum(X1 ** 2)

    # print('var', var1.shape)

    # 3. The outer product of X1 and X2.
    K = X1.mm(X2.T)

    # 4. Solution that Maximizes trace(R'K) is R=U*V', where U, V are
    # singular vectors of K.
    U, s, V = torch.svd(K)
    # V = Vh.T
    # Construct Z that fixes the orientation of R to get det(R)=1.
    Z = torch.eye(U.shape[0], device=S1.device)
    Z[-1, -1] *= torch.sign(torch.det(U @ V.T))
    # Construct R.
    R = V.mm(Z.mm(U.T))

    # print('R', X1.shape)

    # 5. Recover scale.
    scale = torch.trace(R.mm(K)) / var1
    # print(R.shape, mu1.shape)
    # 6. Recover translation.
    t = mu2 - scale * (R.mm(mu1))
    # print(t.shape)

    # 7. Error:
    S1_hat = scale * R.mm(S1) + t

    if transposed:
        S1_hat = S1_hat.T

    return S1_hat


def batch_compute_similarity_transform_torch(S1, S2):
    '''
    Computes a similarity transform (sR, t) that takes
    a set of 3D points S1 (3 x N) closest to a set of 3D points S2,
    where R is an 3x3 rotation matrix, t 3x1 translation, s scale.
    i.e. solves the orthogonal Procrutes problem.
    '''
    transposed = False
    if S1.shape[0] != 3 and S1.shape[0] != 2:
        S1 = S1.permute(0,2,1)
        S2 = S2.permute(0,2,1)
        transposed = True
    assert(S2.shape[1] == S1.shape[1])

    # 1. Remove mean.
    mu1 = S1.mean(axis=-1, keepdims=True)
    mu2 = S2.mean(axis=-1, keepdims=True)

    X1 = S1 - mu1
    X2 = S2 - mu2

    # 2. Compute variance of X1 used for scale.
    var1 = torch.sum(X1**2, dim=1).sum(dim=1)

    # 3. The outer product of X1 and X2.
    K = X1.bmm(X2.permute(0,2,1))

    # 4. Solution that Maximizes trace(R'K) is R=U*V', where U, V are
    # singular vectors of K.
    U, s, V = torch.svd(K)

    # Construct Z that fixes the orientation of R to get det(R)=1.
    Z = torch.eye(U.shape[1], device=S1.device).unsqueeze(0)
    Z = Z.repeat(U.shape[0],1,1)
    Z[:,-1, -1] *= torch.sign(torch.det(U.bmm(V.permute(0,2,1))))

    # Construct R.
    R = V.bmm(Z.bmm(U.permute(0,2,1)))

    # 5. Recover scale.
    scale = torch.cat([torch.trace(x).unsqueeze(0) for x in R.bmm(K)]) / var1

    # 6. Recover translation.
    t = mu2 - (scale.unsqueeze(-1).unsqueeze(-1) * (R.bmm(mu1)))

    # 7. Error:
    S1_hat = scale.unsqueeze(-1).unsqueeze(-1) * R.bmm(S1) + t

    if transposed:
        S1_hat = S1_hat.permute(0,2,1)

    return S1_hat

why restrict to 3?

There is an issue with batch_compute_similarity_transform_torch.
The check for the shapes of S1 and S2 should be done for the 1st dimension, and not 0th, i.e. it should be "if S1.shape[1] != 3 and S1.shape[1] != 2:". But then again, there would be a problem if the number of 2D/3D points happens to be 2 or 3, in which case the tensors wouldn't get permuted. This check should probably be removed altogether and the required dimensions should just be explained in the docstring.

@dusangrujicic does this solve it? https://github.com/brando90/ultimate-anatome/blob/7d23ca83bac7201a91c5515145269d2288f7bbb6/anatome/similarity.py#L518