feat: add batch knn for kdtrees and docs (#65)

* feat: add batch knn for kdtrees and docs

* fix: update batch nns func name

src/python/kdtree.cpp

@@ -16,11 +16,22 @@ using namespace small_gicp;
 
 void define_kdtree(py::module& m) {
   // KdTree
-  py::class_<KdTree<PointCloud>, std::shared_ptr<KdTree<PointCloud>>>(m, "KdTree", "KdTree")  //
+  py::class_<KdTree<PointCloud>, std::shared_ptr<KdTree<PointCloud>>>(m, "KdTree")  //
     .def(
       py::init([](const PointCloud::ConstPtr& points, int num_threads) { return std::make_shared<KdTree<PointCloud>>(points, KdTreeBuilderOMP(num_threads)); }),
       py::arg("points"),
-      py::arg("num_threads") = 1)
+      py::arg("num_threads") = 1,
+      R"""(
+         Construct a KdTree from a point cloud.
+
+         Parameters
+         ----------
+         points : PointCloud
+             The input point cloud.
+         num_threads : int, optional
+             The number of threads to use for KdTree construction. Default is 1.
+       )""")
+
     .def(
       "nearest_neighbor_search",
       [](const KdTree<PointCloud>& kdtree, const Eigen::Vector3d& pt) {
@@ -30,7 +41,23 @@ void define_kdtree(py::module& m) {
         return std::make_tuple(found, k_index, k_sq_dist);
       },
       py::arg("pt"),
-      "Search the nearest neighbor. Returns a tuple of found flag, index, and squared distance.")
+      R"""(
+         Find the nearest neighbor to a given point.
+
+         Parameters
+         ----------
+         pt : NDArray, shape (3,)
+             The input point.
+
+         Returns
+         -------
+         found : int
+             Whether a neighbor was found (1 if found, 0 if not).
+         k_index : int
+             The index of the nearest neighbor in the point cloud.
+         k_sq_dist : float
+             The squared distance to the nearest neighbor.
+       )""")
     .def(
       "knn_search",
       [](const KdTree<PointCloud>& kdtree, const Eigen::Vector3d& pt, int k) {
@@ -41,5 +68,86 @@ void define_kdtree(py::module& m) {
       },
       py::arg("pt"),
       py::arg("k"),
-      "Search the k-nearest neighbors. Returns a pair of indices and squared distances.");
+      R"""(
-}
+       Find the k nearest neighbors to a given point.
+
+       Parameters
+       ----------
+       pt : NDArray, shape (3,)
+           The input point.
+       k : int
+           The number of nearest neighbors to search for.
+
+       Returns
+       -------
+       k_indices : NDArray, shape (k,)
+           The indices of the k nearest neighbors in the point cloud.
+       k_sq_dists : NDArray, shape (k,)
+           The squared distances to the k nearest neighbors.
+     )""")
+    .def(
+      "batch_nearest_neighbor_search",
+      [](const KdTree<PointCloud>& kdtree, const Eigen::MatrixXd& pts) {
+        std::vector<size_t> k_indices(pts.rows(), -1);
+        std::vector<double> k_sq_dists(pts.rows(), std::numeric_limits<double>::max());
+        for (int i = 0; i < pts.rows(); ++i) {
+          const size_t found = traits::nearest_neighbor_search(kdtree, Eigen::Vector4d(pts(i, 0), pts(i, 1), pts(i, 2), 1.0), &k_indices[i], &k_sq_dists[i]);
+          if (!found) {
+            k_indices[i] = -1;
+            k_sq_dists[i] = std::numeric_limits<double>::max();
+          }
+        }
+        return std::make_pair(k_indices, k_sq_dists);
+      },
+      py::arg("pts"),
+      R"""(
+       Find the nearest neighbors for a batch of points.
+
+       Parameters
+       ----------
+       pts : NDArray, shape (n, 3)
+           The input points.
+
+       Returns
+       -------
+       k_indices : NDArray, shape (n,)
+           The indices of the nearest neighbors for each input point.
+       k_sq_dists : NDArray, shape (n,)
+           The squared distances to the nearest neighbors for each input point.
+     )""")
+    .def(
+      "batch_knn_search",
+      [](const KdTree<PointCloud>& kdtree, const Eigen::MatrixXd& pts, int k) {
+        std::vector<std::vector<size_t>> k_indices(pts.rows(), std::vector<size_t>(k, -1));
+        std::vector<std::vector<double>> k_sq_dists(pts.rows(), std::vector<double>(k, std::numeric_limits<double>::max()));
+        for (int i = 0; i < pts.rows(); ++i) {
+          const size_t found = traits::knn_search(kdtree, Eigen::Vector4d(pts(i, 0), pts(i, 1), pts(i, 2), 1.0), k, k_indices[i].data(), k_sq_dists[i].data());
+          if (found < k) {
+            for (size_t j = found; j < k; ++j) {
+              k_indices[i][j] = -1;
+              k_sq_dists[i][j] = std::numeric_limits<double>::max();
+            }
+          }
+        }
+        return std::make_pair(k_indices, k_sq_dists);
+      },
+      py::arg("pts"),
+      py::arg("k"),
+      R"""(
+       Find the k nearest neighbors for a batch of points.
+
+       Parameters
+       ----------
+       pts : NDArray, shape (n, 3)
+           The input points.
+       k : int
+           The number of nearest neighbors to search for.
+
+       Returns
+       -------
+       k_indices : list of NDArray, shape (n,)
+           The list of indices of the k nearest neighbors for each input point.
+       k_sq_dists : list of NDArray, shape (n,)
+           The list of squared distances to the k nearest neighbors for each input point.
+     )""");
+}