break up preamble and specializations so there are no duplicate includes

python/gtsam/preamble/base.h

@@ -0,0 +1,16 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `PYBIND11_MAKE_OPAQUE` will mark the type as "opaque" for the pybind11
+ * automatic STL binding, such that the raw objects can be accessed in Python.
+ * Without this they will be automatically converted to a Python object, and all
+ * mutations on Python side will not be reflected on C++.
+ */
+
+PYBIND11_MAKE_OPAQUE(std::vector<gtsam::IndexPair>);
+
+PYBIND11_MAKE_OPAQUE(std::vector<gtsam::Matrix>);  // JacobianVector

python/gtsam/preamble/geometry.h

@@ -0,0 +1,21 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `PYBIND11_MAKE_OPAQUE` will mark the type as "opaque" for the pybind11
+ * automatic STL binding, such that the raw objects can be accessed in Python.
+ * Without this they will be automatically converted to a Python object, and all
+ * mutations on Python side will not be reflected on C++.
+ */
+
+PYBIND11_MAKE_OPAQUE(
+    std::vector<gtsam::Point2, Eigen::aligned_allocator<gtsam::Point2>>);
+PYBIND11_MAKE_OPAQUE(gtsam::Point3Pairs);
+PYBIND11_MAKE_OPAQUE(gtsam::Pose3Pairs);
+PYBIND11_MAKE_OPAQUE(std::vector<gtsam::Pose3>);
+PYBIND11_MAKE_OPAQUE(
+    gtsam::CameraSet<gtsam::PinholeCamera<gtsam::Cal3Bundler>>);
+PYBIND11_MAKE_OPAQUE(gtsam::CameraSet<gtsam::PinholeCamera<gtsam::Cal3_S2>>);

python/gtsam/preamble/gtsam.h

@@ -0,0 +1,17 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `PYBIND11_MAKE_OPAQUE` will mark the type as "opaque" for the pybind11
+ * automatic STL binding, such that the raw objects can be accessed in Python.
+ * Without this they will be automatically converted to a Python object, and all
+ * mutations on Python side will not be reflected on C++.
+ */
+#ifdef GTSAM_ALLOCATOR_TBB
+PYBIND11_MAKE_OPAQUE(std::vector<gtsam::Key, tbb::tbb_allocator<gtsam::Key>>);
+#else
+PYBIND11_MAKE_OPAQUE(std::vector<gtsam::Key>);
+#endif

python/gtsam/preamble/linear.h

@@ -0,0 +1,12 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `PYBIND11_MAKE_OPAQUE` will mark the type as "opaque" for the pybind11
+ * automatic STL binding, such that the raw objects can be accessed in Python.
+ * Without this they will be automatically converted to a Python object, and all
+ * mutations on Python side will not be reflected on C++.
+ */

python/gtsam/preamble/navigation.h

@@ -0,0 +1,18 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `PYBIND11_MAKE_OPAQUE` will mark the type as "opaque" for the pybind11
+ * automatic STL binding, such that the raw objects can be accessed in Python.
+ * Without this they will be automatically converted to a Python object, and all
+ * mutations on Python side will not be reflected on C++.
+ */
+
+// TODO(fan): This is to fix the Argument-dependent lookup (ADL) of std::pair.
+// We should find a way to NOT do this.
+namespace std {
+using gtsam::operator<<;
+}

python/gtsam/preamble/nonlinear.h

@@ -0,0 +1,12 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `PYBIND11_MAKE_OPAQUE` will mark the type as "opaque" for the pybind11
+ * automatic STL binding, such that the raw objects can be accessed in Python.
+ * Without this they will be automatically converted to a Python object, and all
+ * mutations on Python side will not be reflected on C++.
+ */

python/gtsam/preamble/sam.h

@@ -0,0 +1,12 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `PYBIND11_MAKE_OPAQUE` will mark the type as "opaque" for the pybind11
+ * automatic STL binding, such that the raw objects can be accessed in Python.
+ * Without this they will be automatically converted to a Python object, and all
+ * mutations on Python side will not be reflected on C++.
+ */

python/gtsam/preamble/sfm.h

@@ -0,0 +1,12 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `PYBIND11_MAKE_OPAQUE` will mark the type as "opaque" for the pybind11
+ * automatic STL binding, such that the raw objects can be accessed in Python.
+ * Without this they will be automatically converted to a Python object, and all
+ * mutations on Python side will not be reflected on C++.
+ */

python/gtsam/preamble/slam.h

@@ -0,0 +1,17 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `PYBIND11_MAKE_OPAQUE` will mark the type as "opaque" for the pybind11
+ * automatic STL binding, such that the raw objects can be accessed in Python.
+ * Without this they will be automatically converted to a Python object, and all
+ * mutations on Python side will not be reflected on C++.
+ */
+
+PYBIND11_MAKE_OPAQUE(
+    std::vector<boost::shared_ptr<gtsam::BetweenFactor<gtsam::Pose3> > >);
+PYBIND11_MAKE_OPAQUE(
+    std::vector<boost::shared_ptr<gtsam::BetweenFactor<gtsam::Pose2> > >);

python/gtsam/preamble/symbolic.h

@@ -0,0 +1,12 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `PYBIND11_MAKE_OPAQUE` will mark the type as "opaque" for the pybind11
+ * automatic STL binding, such that the raw objects can be accessed in Python.
+ * Without this they will be automatically converted to a Python object, and all
+ * mutations on Python side will not be reflected on C++.
+ */

python/gtsam/specializations/base.h

@@ -0,0 +1,17 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `py::bind_vector` and similar machinery gives the std container a Python-like
+ * interface, but without the `<pybind11/stl.h>` copying mechanism. Combined
+ * with `PYBIND11_MAKE_OPAQUE` this allows the types to be modified with Python,
+ * and saves one copy operation.
+ */
+
+py::bind_map<gtsam::IndexPairSetMap>(m_, "IndexPairSetMap");
+py::bind_vector<gtsam::IndexPairVector>(m_, "IndexPairVector");
+
+py::bind_vector<std::vector<gtsam::Matrix> >(m_, "JacobianVector");

python/gtsam/specializations/geometry.h

@@ -0,0 +1,23 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `py::bind_vector` and similar machinery gives the std container a Python-like
+ * interface, but without the `<pybind11/stl.h>` copying mechanism. Combined
+ * with `PYBIND11_MAKE_OPAQUE` this allows the types to be modified with Python,
+ * and saves one copy operation.
+ */
+
+py::bind_vector<
+    std::vector<gtsam::Point2, Eigen::aligned_allocator<gtsam::Point2>>>(
+    m_, "Point2Vector");
+py::bind_vector<std::vector<gtsam::Point3Pair>>(m_, "Point3Pairs");
+py::bind_vector<std::vector<gtsam::Pose3Pair>>(m_, "Pose3Pairs");
+py::bind_vector<std::vector<gtsam::Pose3>>(m_, "Pose3Vector");
+py::bind_vector<gtsam::CameraSet<gtsam::PinholeCamera<gtsam::Cal3_S2>>>(
+    m_, "CameraSetCal3_S2");
+py::bind_vector<gtsam::CameraSet<gtsam::PinholeCamera<gtsam::Cal3Bundler>>>(
+    m_, "CameraSetCal3Bundler");

python/gtsam/specializations/gtsam.h

@@ -0,0 +1,20 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `py::bind_vector` and similar machinery gives the std container a Python-like
+ * interface, but without the `<pybind11/stl.h>` copying mechanism. Combined
+ * with `PYBIND11_MAKE_OPAQUE` this allows the types to be modified with Python,
+ * and saves one copy operation.
+ */
+
+#ifdef GTSAM_ALLOCATOR_TBB
+py::bind_vector<std::vector<gtsam::Key, tbb::tbb_allocator<gtsam::Key> > >(m_, "KeyVector");
+py::implicitly_convertible<py::list, std::vector<gtsam::Key, tbb::tbb_allocator<gtsam::Key> > >();
+#else
+py::bind_vector<std::vector<gtsam::Key> >(m_, "KeyVector");
+py::implicitly_convertible<py::list, std::vector<gtsam::Key> >();
+#endif

python/gtsam/specializations/linear.h

@@ -0,0 +1,12 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `py::bind_vector` and similar machinery gives the std container a Python-like
+ * interface, but without the `<pybind11/stl.h>` copying mechanism. Combined
+ * with `PYBIND11_MAKE_OPAQUE` this allows the types to be modified with Python,
+ * and saves one copy operation.
+ */

python/gtsam/specializations/navigation.h

@@ -0,0 +1,12 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `py::bind_vector` and similar machinery gives the std container a Python-like
+ * interface, but without the `<pybind11/stl.h>` copying mechanism. Combined
+ * with `PYBIND11_MAKE_OPAQUE` this allows the types to be modified with Python,
+ * and saves one copy operation.
+ */

python/gtsam/specializations/nonlinear.h

@@ -0,0 +1,12 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `py::bind_vector` and similar machinery gives the std container a Python-like
+ * interface, but without the `<pybind11/stl.h>` copying mechanism. Combined
+ * with `PYBIND11_MAKE_OPAQUE` this allows the types to be modified with Python,
+ * and saves one copy operation.
+ */

python/gtsam/specializations/sam.h

@@ -0,0 +1,12 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `py::bind_vector` and similar machinery gives the std container a Python-like
+ * interface, but without the `<pybind11/stl.h>` copying mechanism. Combined
+ * with `PYBIND11_MAKE_OPAQUE` this allows the types to be modified with Python,
+ * and saves one copy operation.
+ */

python/gtsam/specializations/sfm.h

@@ -0,0 +1,16 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `py::bind_vector` and similar machinery gives the std container a Python-like
+ * interface, but without the `<pybind11/stl.h>` copying mechanism. Combined
+ * with `PYBIND11_MAKE_OPAQUE` this allows the types to be modified with Python,
+ * and saves one copy operation.
+ */
+
+py::bind_vector<std::vector<gtsam::BinaryMeasurement<gtsam::Unit3> > >(
+    m_, "BinaryMeasurementsUnit3");
+py::bind_map<gtsam::KeyPairDoubleMap>(m_, "KeyPairDoubleMap");

python/gtsam/specializations/slam.h

@@ -0,0 +1,19 @@
+/* Please refer to:
+ * https://pybind11.readthedocs.io/en/stable/advanced/cast/stl.html
+ * These are required to save one copy operation on Python calls.
+ *
+ * NOTES
+ * =================
+ *
+ * `py::bind_vector` and similar machinery gives the std container a Python-like
+ * interface, but without the `<pybind11/stl.h>` copying mechanism. Combined
+ * with `PYBIND11_MAKE_OPAQUE` this allows the types to be modified with Python,
+ * and saves one copy operation.
+ */
+
+py::bind_vector<
+    std::vector<boost::shared_ptr<gtsam::BetweenFactor<gtsam::Pose3> > > >(
+    m_, "BetweenFactorPose3s");
+py::bind_vector<
+    std::vector<boost::shared_ptr<gtsam::BetweenFactor<gtsam::Pose2> > > >(
+    m_, "BetweenFactorPose2s");