import torch import scipy.spatial if torch.cuda.is_available(): import knn_cuda def knn(x, y, k, batch_x=None, batch_y=None): """Finds for each element in `y` the `k` nearest points in `x`. Args: x (Tensor): D-dimensional point features. y (Tensor): D-dimensional point features. k (int): The number of neighbors. batch_x (LongTensor, optional): Vector that maps each point to its example identifier. If :obj:`None`, all points belong to the same example. If not :obj:`None`, points in the same example need to have contiguous memory layout and :obj:`batch` needs to be ascending. (default: :obj:`None`) batch_y (LongTensor, optional): See `batch_x` (default: :obj:`None`) :rtype: :class:`LongTensor` Examples:: >>> x = torch.Tensor([[-1, -1], [-1, 1], [1, -1], [1, 1]]) >>> batch_x = torch.tensor([0, 0, 0, 0]) >>> y = torch.Tensor([[-1, 0], [1, 0]]) >>> batch_x = torch.tensor([0, 0]) >>> assign_index = knn(x, y, 2, batch_x, batch_y) """ if batch_x is None: batch_x = x.new_zeros(x.size(0), dtype=torch.long) if batch_y is None: batch_y = y.new_zeros(y.size(0), dtype=torch.long) x = x.view(-1, 1) if x.dim() == 1 else x y = y.view(-1, 1) if y.dim() == 1 else y assert x.dim() == 2 and batch_x.dim() == 1 assert y.dim() == 2 and batch_y.dim() == 1 assert x.size(1) == y.size(1) assert x.size(0) == batch_x.size(0) assert y.size(0) == batch_y.size(0) if x.is_cuda: assign_index = knn_cuda.knn(x, y, k, batch_x, batch_y) return assign_index # Rescale x and y. min_xy = min(x.min().item(), y.min().item()) x, y = x - min_xy, y - min_xy max_xy = max(x.max().item(), y.max().item()) x, y, = x / max_xy, y / max_xy # Concat batch/features to ensure no cross-links between examples exist. x = torch.cat([x, 2 * x.size(1) * batch_x.view(-1, 1).to(x.dtype)], dim=-1) y = torch.cat([y, 2 * y.size(1) * batch_y.view(-1, 1).to(y.dtype)], dim=-1) tree = scipy.spatial.cKDTree(x) dist, col = tree.query(y, k=k, distance_upper_bound=x.size(1)) dist, col = torch.tensor(dist), torch.tensor(col) row = torch.arange(col.size(0)).view(-1, 1).repeat(1, k) mask = 1 - torch.isinf(dist).view(-1) row, col = row.view(-1)[mask], col.view(-1)[mask] return torch.stack([row, col], dim=0) def knn_graph(x, k, batch=None, loop=False): """Finds for each element in `x` the `k` nearest points. Args: x (Tensor): D-dimensional point features. k (int): The number of neighbors. batch (LongTensor, optional): Vector that maps each point to its example identifier. If :obj:`None`, all points belong to the same example. If not :obj:`None`, points in the same example need to have contiguous memory layout and :obj:`batch` needs to be ascending. (default: :obj:`None`) loop (bool, optional): If :obj:`True`, the graph will contain self-loops. (default: :obj:`False`) :rtype: :class:`LongTensor` Examples:: >>> x = torch.Tensor([[-1, -1], [-1, 1], [1, -1], [1, 1]]) >>> batch = torch.tensor([0, 0, 0, 0]) >>> edge_index = knn_graph(x, k=2, batch=batch, loop=False) """ edge_index = knn(x, x, k if loop else k + 1, batch, batch) if not loop: row, col = edge_index mask = row != col row, col = row[mask], col[mask] edge_index = torch.stack([row, col], dim=0) return edge_index