Added Kmeans pybind11 interface (#341)

Signed-off-by: Alejandro Hernández <[email protected]>

Co-authored-by: Louise Poubel <[email protected]>

src/python/CMakeLists.txt

@@ -94,7 +94,6 @@ if (PYTHONLIBS_FOUND)
       Frustum_TEST
       GaussMarkovProcess_TEST
       Inertial_TEST
-      Kmeans_TEST
       MassMatrix3_TEST
       Material_TEST
       Matrix4_TEST

src/python_pybind11/CMakeLists.txt

@@ -17,6 +17,7 @@ if (${pybind11_FOUND})
     src/Angle.cc
     src/Color.cc
     src/Helpers.cc
+    src/Kmeans.cc
     src/Rand.cc
     src/RollingMean.cc
     src/SemanticVersion.cc
@@ -78,6 +79,7 @@ if (${pybind11_FOUND})
       Color_TEST
       Filter_TEST
       Helpers_TEST
+      Kmeans_TEST
       Line2_TEST
       Line3_TEST
       Matrix3_TEST

src/python_pybind11/src/Kmeans.cc

@@ -0,0 +1,60 @@
+/*
+ * Copyright (C) 2021 Open Source Robotics Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+*/
+#include <string>
+#include <vector>
+
+#include "Kmeans.hh"
+#include <ignition/math/Kmeans.hh>
+#include <pybind11/stl.h>
+
+namespace ignition
+{
+namespace math
+{
+namespace python
+{
+void defineMathKmeans(py::module &m, const std::string &typestr)
+{
+  using Class = ignition::math::Kmeans;
+  std::string pyclass_name = typestr;
+  py::class_<Class>(m,
+                    pyclass_name.c_str(),
+                    py::buffer_protocol(),
+                    py::dynamic_attr())
+  .def(py::init<const std::vector<ignition::math::Vector3d>&>())
+  .def("observations",
+       py::overload_cast<const std::vector<ignition::math::Vector3d>&>
+        (&Class::Observations),
+        "Set the observations to cluster.")
+  .def("observations",
+       py::overload_cast<>(&Class::Observations, py::const_),
+       "Get the observations to cluster.")
+  .def("append_observations",
+       &Class::AppendObservations,
+       "Add observations to the cluster.")
+  .def("cluster",
+       [](Class &self, int k) {
+         std::vector<ignition::math::Vector3<double>> centroids;
+         std::vector<unsigned int> labels;
+         bool result = self.Cluster(k, centroids, labels);
+         return std::make_tuple(result, centroids, labels);
+       },
+       "Executes the k-means algorithm.");
+}
+}  // namespace python
+}  // namespace math
+}  // namespace ignition

src/python_pybind11/src/Kmeans.hh

@@ -0,0 +1,42 @@
+/*
+ * Copyright (C) 2021 Open Source Robotics Foundation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+*/
+
+#ifndef IGNITION_MATH_PYTHON__KMEANS_HH_
+#define IGNITION_MATH_PYTHON__KMEANS_HH_
+
+#include <pybind11/pybind11.h>
+#include <string>
+
+namespace py = pybind11;
+
+namespace ignition
+{
+namespace math
+{
+namespace python
+{
+/// Define a pybind11 wrapper for an ignition::math::Kmeans
+/**
+ * \param[in] module a pybind11 module to add the definition to
+ * \param[in] typestr name of the type used by Python
+ */
+void defineMathKmeans(py::module &m, const std::string &typestr);
+}  // namespace python
+}  // namespace math
+}  // namespace ignition
+
+#endif  // IGNITION_MATH_PYTHON__KMEANS_HH_

src/python_pybind11/src/_ignition_math_pybind11.cc

@@ -18,6 +18,7 @@
 #include "Color.hh"
 #include "Filter.hh"
 #include "Helpers.hh"
+#include "Kmeans.hh"
 #include "Line2.hh"
 #include "Line3.hh"
 #include "Matrix3.hh"
@@ -47,6 +48,8 @@ PYBIND11_MODULE(math, m)
 
   ignition::math::python::defineMathHelpers(m);
 
+  ignition::math::python::defineMathKmeans(m, "Kmeans");
+
   ignition::math::python::defineMathMovingWindowFilter<int>(
     m, "MovingWindowFilteri");
   ignition::math::python::defineMathMovingWindowFilter<double>(

src/python/Kmeans_TEST.py → src/python_pybind11/test/Kmeans_TEST.py

@@ -15,7 +15,6 @@
 import unittest
 from ignition.math import Kmeans
 from ignition.math import Vector3d
-from ignition.math import vector_vector3d
 
 
 class TestKmeans(unittest.TestCase):
@@ -128,13 +127,13 @@ def test_kmeans_append(self):
 
         kmeans.append_observations(obs2)
 
-        obs_copy = vector_vector3d(kmeans.observations())
+        obs_copy = kmeans.observations()
 
-        for i in range(obs_copy.size()):
+        for i in range(len(obs_copy)):
             self.assertEqual(obs_total[i], obs_copy[i])
 
         # Append an empty vector.
-        emptyVector = vector_vector3d()
+        emptyVector = []
         self.assertFalse(kmeans.append_observations(emptyVector))