Wrapper update

matlab/README.md

@@ -8,6 +8,8 @@ The interface to the toolbox is generated automatically by the wrap tool which d
 The tool generates matlab proxy objects together with all the native functions for wrapping and unwrapping scalar and non scalar types and objects.
 The interface generated by the wrap tool also redirects the standard output stream (cout) to matlab's console.
 
+For instructions on updating the version of the [wrap library](https://github.com/borglab/wrap) included in GTSAM to the latest version, please refer to the [wrap README](https://github.com/borglab/wrap/blob/master/README.md#git-subtree-and-contributing)
+
 ## Ubuntu
 
 If you have a newer Ubuntu system (later than 10.04), you must make a small modification to your MATLAB installation, due to MATLAB being distributed with an old version of the C++ standard library. Delete or rename all files starting with `libstdc++` in your MATLAB installation directory, in paths:

python/README.md

@@ -4,6 +4,8 @@
 
 This is the Python wrapper around the GTSAM C++ library. We use our custom [wrap library](https://github.com/borglab/wrap) to generate the bindings to the underlying C++ code.
 
+For instructions on updating the version of the [wrap library](https://github.com/borglab/wrap) included in GTSAM to the latest version, please refer to the [wrap README](https://github.com/borglab/wrap/blob/master/README.md#git-subtree-and-contributing)
+
 ## Requirements
 
 - If you want to build the GTSAM python library for a specific python version (eg 3.6),

python/gtsam/gtsam.tpl

@@ -13,6 +13,7 @@
 #include <pybind11/eigen.h>
 #include <pybind11/stl_bind.h>
 #include <pybind11/pybind11.h>
+#include <pybind11/iostream.h>
 #include "gtsam/config.h"
 #include "gtsam/base/serialization.h"
 #include "gtsam/nonlinear/utilities.h"  // for RedirectCout.

python/gtsam_unstable/gtsam_unstable.tpl

@@ -13,6 +13,7 @@
 #include <pybind11/eigen.h>
 #include <pybind11/stl_bind.h>
 #include <pybind11/pybind11.h>
+#include <pybind11/iostream.h>
 #include "gtsam/base/serialization.h"
 #include "gtsam/nonlinear/utilities.h"  // for RedirectCout.
 

wrap/DOCS.md

@@ -98,6 +98,7 @@ The python wrapper supports keyword arguments for functions/methods. Hence, the
 - Virtual inheritance
     - Specify fully-qualified base classes, i.e. `virtual class Derived : ns::Base {` where `ns` is the namespace.
     - Mark with `virtual` keyword, e.g. `virtual class Base {`, and also `virtual class Derived : ns::Base {`.
+    - Base classes can be templated, e.g. `virtual class Dog: ns::Animal<Pet> {};`. This is useful when you want to inherit from specialized classes.
     - Forward declarations must also be marked virtual, e.g. `virtual class ns::Base;` and
       also `virtual class ns::Derived;`.
     - Pure virtual (abstract) classes should list no constructors in the interface file.

wrap/cmake/GtwrapUtils.cmake

@@ -103,3 +103,37 @@ macro(gtwrap_get_python_version)
   configure_python_variables()
 
 endmacro()
+
+# Concatenate multiple wrapper interface headers into one.
+# The concatenation will be (re)performed if and only if any interface files
+# change.
+#
+# Arguments:
+# ~~~
+# destination: The concatenated master interface header file will be placed here.
+# inputs (optional): All the input interface header files
+function(combine_interface_headers
+         destination
+         #inputs
+         )
+  # check if any interface headers changed
+  foreach(INTERFACE_FILE ${ARGN})
+    if(NOT EXISTS ${destination} OR
+      ${INTERFACE_FILE} IS_NEWER_THAN ${destination})
+      set(UPDATE_INTERFACE TRUE)
+    endif()
+    # trigger cmake on file change
+    set_property(DIRECTORY
+                 APPEND
+                 PROPERTY CMAKE_CONFIGURE_DEPENDS ${INTERFACE_FILE})
+  endforeach()
+  # if so, then update the overall interface file
+  if (UPDATE_INTERFACE)
+    file(WRITE ${destination} "")
+    # append additional interface headers to end of gtdynamics.i
+    foreach(INTERFACE_FILE ${ARGN})
+      file(READ ${INTERFACE_FILE} interface_contents)
+      file(APPEND ${destination} "${interface_contents}")
+    endforeach()
+  endif()
+endfunction()

wrap/gtwrap/interface_parser/classes.py

@@ -279,7 +279,7 @@ def __init__(self,
                 elif isinstance(m, Operator):
                     self.operators.append(m)
 
-    _parent = COLON + Typename.rule("parent_class")
+    _parent = COLON + (TemplatedType.rule ^ Typename.rule)("parent_class")
     rule = (
         Optional(Template.rule("template"))  #
         + Optional(VIRTUAL("is_virtual"))  #
@@ -319,11 +319,16 @@ def __init__(
         self.is_virtual = is_virtual
         self.name = name
         if parent_class:
+            # If it is in an iterable, extract the parent class.
             if isinstance(parent_class, Iterable):
-                self.parent_class = parent_class[0]
-            else:
-                self.parent_class = parent_class
+                parent_class = parent_class[0]
 
+            # If the base class is a TemplatedType,
+            # we want the instantiated Typename
+            if isinstance(parent_class, TemplatedType):
+                parent_class = parent_class.typename
+
+            self.parent_class = parent_class
         else:
             self.parent_class = ''
 

wrap/gtwrap/pybind_wrapper.py

@@ -125,6 +125,11 @@ def _wrap_method(self, method, cpp_class, prefix, suffix, method_suffix=""):
                ))
 
         if method.name == 'print':
+            # Redirect stdout - see pybind docs for why this is a good idea:
+            # https://pybind11.readthedocs.io/en/stable/advanced/pycpp/utilities.html#capturing-standard-output-from-ostream
+            ret = ret.replace('self->', 'py::scoped_ostream_redirect output; self->')
+
+            # __repr__() uses print's implementation:
             type_list = method.args.to_cpp(self.use_boost)
             if len(type_list) > 0 and type_list[0].strip() == 'string':
                 ret += '''{prefix}.def("__repr__",

wrap/tests/expected/matlab/inheritance_wrapper.cpp

@@ -50,6 +50,8 @@ typedef std::set<boost::shared_ptr<MyTemplatePoint2>*> Collector_MyTemplatePoint
 static Collector_MyTemplatePoint2 collector_MyTemplatePoint2;
 typedef std::set<boost::shared_ptr<MyTemplateMatrix>*> Collector_MyTemplateMatrix;
 static Collector_MyTemplateMatrix collector_MyTemplateMatrix;
+typedef std::set<boost::shared_ptr<ForwardKinematicsFactor>*> Collector_ForwardKinematicsFactor;
+static Collector_ForwardKinematicsFactor collector_ForwardKinematicsFactor;
 
 void _deleteAllObjects()
 {
@@ -141,6 +143,12 @@ void _deleteAllObjects()
     collector_MyTemplateMatrix.erase(iter++);
     anyDeleted = true;
   } }
+  { for(Collector_ForwardKinematicsFactor::iterator iter = collector_ForwardKinematicsFactor.begin();
+      iter != collector_ForwardKinematicsFactor.end(); ) {
+    delete *iter;
+    collector_ForwardKinematicsFactor.erase(iter++);
+    anyDeleted = true;
+  } }
   if(anyDeleted)
     cout <<
       "WARNING:  Wrap modules with variables in the workspace have been reloaded due to\n"
@@ -156,6 +164,7 @@ void _inheritance_RTTIRegister() {
     types.insert(std::make_pair(typeid(MyBase).name(), "MyBase"));
     types.insert(std::make_pair(typeid(MyTemplatePoint2).name(), "MyTemplatePoint2"));
     types.insert(std::make_pair(typeid(MyTemplateMatrix).name(), "MyTemplateMatrix"));
+    types.insert(std::make_pair(typeid(ForwardKinematicsFactor).name(), "ForwardKinematicsFactor"));
 
     mxArray *registry = mexGetVariable("global", "gtsamwrap_rttiRegistry");
     if(!registry)
@@ -555,6 +564,40 @@ void MyTemplateMatrix_Level_34(int nargout, mxArray *out[], int nargin, const mx
   out[0] = wrap_shared_ptr(boost::make_shared<MyTemplate<Matrix>>(MyTemplate<gtsam::Matrix>::Level(K)),"MyTemplateMatrix", false);
 }
 
+void Test_set_container_35(int nargout, mxArray *out[], int nargin, const mxArray *in[])
+{
+  checkArguments("set_container",nargout,nargin-1,1);
+  auto obj = unwrap_shared_ptr<Test>(in[0], "ptr_Test");
+  boost::shared_ptr<std::vector<testing::Test>> container = unwrap_shared_ptr< std::vector<testing::Test> >(in[1], "ptr_stdvectorTest");
+  obj->set_container(*container);
+}
+
+void ForwardKinematicsFactor_collectorInsertAndMakeBase_35(int nargout, mxArray *out[], int nargin, const mxArray *in[])
+{
+  mexAtExit(&_deleteAllObjects);
+  typedef boost::shared_ptr<ForwardKinematicsFactor> Shared;
+
+  Shared *self = *reinterpret_cast<Shared**> (mxGetData(in[0]));
+  collector_ForwardKinematicsFactor.insert(self);
+
+  typedef boost::shared_ptr<gtsam::BetweenFactor<gtsam::Pose3>> SharedBase;
+  out[0] = mxCreateNumericMatrix(1, 1, mxUINT32OR64_CLASS, mxREAL);
+  *reinterpret_cast<SharedBase**>(mxGetData(out[0])) = new SharedBase(*self);
+}
+
+void ForwardKinematicsFactor_deconstructor_37(int nargout, mxArray *out[], int nargin, const mxArray *in[])
+{
+  typedef boost::shared_ptr<ForwardKinematicsFactor> Shared;
+  checkArguments("delete_ForwardKinematicsFactor",nargout,nargin,1);
+  Shared *self = *reinterpret_cast<Shared**>(mxGetData(in[0]));
+  Collector_ForwardKinematicsFactor::iterator item;
+  item = collector_ForwardKinematicsFactor.find(self);
+  if(item != collector_ForwardKinematicsFactor.end()) {
+    delete self;
+    collector_ForwardKinematicsFactor.erase(item);
+  }
+}
+
 
 void mexFunction(int nargout, mxArray *out[], int nargin, const mxArray *in[])
 {
@@ -672,6 +715,15 @@ void mexFunction(int nargout, mxArray *out[], int nargin, const mxArray *in[])
     case 34:
       MyTemplateMatrix_Level_34(nargout, out, nargin-1, in+1);
       break;
+    case 35:
+      Test_set_container_35(nargout, out, nargin-1, in+1);
+      break;
+    case 36:
+      ForwardKinematicsFactor_collectorInsertAndMakeBase_35(nargout, out, nargin-1, in+1);
+      break;
+    case 37:
+      ForwardKinematicsFactor_deconstructor_37(nargout, out, nargin-1, in+1);
+      break;
     }
   } catch(const std::exception& e) {
     mexErrMsgTxt(("Exception from gtsam:\n" + std::string(e.what()) + "\n").c_str());

wrap/tests/expected/matlab/namespaces_wrapper.cpp

@@ -55,6 +55,8 @@ typedef std::set<boost::shared_ptr<MyTemplatePoint2>*> Collector_MyTemplatePoint
 static Collector_MyTemplatePoint2 collector_MyTemplatePoint2;
 typedef std::set<boost::shared_ptr<MyTemplateMatrix>*> Collector_MyTemplateMatrix;
 static Collector_MyTemplateMatrix collector_MyTemplateMatrix;
+typedef std::set<boost::shared_ptr<ForwardKinematicsFactor>*> Collector_ForwardKinematicsFactor;
+static Collector_ForwardKinematicsFactor collector_ForwardKinematicsFactor;
 typedef std::set<boost::shared_ptr<ns1::ClassA>*> Collector_ns1ClassA;
 static Collector_ns1ClassA collector_ns1ClassA;
 typedef std::set<boost::shared_ptr<ns1::ClassB>*> Collector_ns1ClassB;
@@ -158,6 +160,12 @@ void _deleteAllObjects()
     collector_MyTemplateMatrix.erase(iter++);
     anyDeleted = true;
   } }
+  { for(Collector_ForwardKinematicsFactor::iterator iter = collector_ForwardKinematicsFactor.begin();
+      iter != collector_ForwardKinematicsFactor.end(); ) {
+    delete *iter;
+    collector_ForwardKinematicsFactor.erase(iter++);
+    anyDeleted = true;
+  } }
   { for(Collector_ns1ClassA::iterator iter = collector_ns1ClassA.begin();
       iter != collector_ns1ClassA.end(); ) {
     delete *iter;
@@ -209,6 +217,7 @@ void _namespaces_RTTIRegister() {
     types.insert(std::make_pair(typeid(MyBase).name(), "MyBase"));
     types.insert(std::make_pair(typeid(MyTemplatePoint2).name(), "MyTemplatePoint2"));
     types.insert(std::make_pair(typeid(MyTemplateMatrix).name(), "MyTemplateMatrix"));
+    types.insert(std::make_pair(typeid(ForwardKinematicsFactor).name(), "ForwardKinematicsFactor"));
 
     mxArray *registry = mexGetVariable("global", "gtsamwrap_rttiRegistry");
     if(!registry)

wrap/tests/expected/matlab/special_cases_wrapper.cpp

@@ -58,6 +58,8 @@ typedef std::set<boost::shared_ptr<MyTemplatePoint2>*> Collector_MyTemplatePoint
 static Collector_MyTemplatePoint2 collector_MyTemplatePoint2;
 typedef std::set<boost::shared_ptr<MyTemplateMatrix>*> Collector_MyTemplateMatrix;
 static Collector_MyTemplateMatrix collector_MyTemplateMatrix;
+typedef std::set<boost::shared_ptr<ForwardKinematicsFactor>*> Collector_ForwardKinematicsFactor;
+static Collector_ForwardKinematicsFactor collector_ForwardKinematicsFactor;
 typedef std::set<boost::shared_ptr<ns1::ClassA>*> Collector_ns1ClassA;
 static Collector_ns1ClassA collector_ns1ClassA;
 typedef std::set<boost::shared_ptr<ns1::ClassB>*> Collector_ns1ClassB;
@@ -169,6 +171,12 @@ void _deleteAllObjects()
     collector_MyTemplateMatrix.erase(iter++);
     anyDeleted = true;
   } }
+  { for(Collector_ForwardKinematicsFactor::iterator iter = collector_ForwardKinematicsFactor.begin();
+      iter != collector_ForwardKinematicsFactor.end(); ) {
+    delete *iter;
+    collector_ForwardKinematicsFactor.erase(iter++);
+    anyDeleted = true;
+  } }
   { for(Collector_ns1ClassA::iterator iter = collector_ns1ClassA.begin();
       iter != collector_ns1ClassA.end(); ) {
     delete *iter;
@@ -244,6 +252,7 @@ void _special_cases_RTTIRegister() {
     types.insert(std::make_pair(typeid(MyBase).name(), "MyBase"));
     types.insert(std::make_pair(typeid(MyTemplatePoint2).name(), "MyTemplatePoint2"));
     types.insert(std::make_pair(typeid(MyTemplateMatrix).name(), "MyTemplateMatrix"));
+    types.insert(std::make_pair(typeid(ForwardKinematicsFactor).name(), "ForwardKinematicsFactor"));
 
     mxArray *registry = mexGetVariable("global", "gtsamwrap_rttiRegistry");
     if(!registry)

wrap/tests/expected/python/class_pybind.cpp

@@ -55,7 +55,7 @@ PYBIND11_MODULE(class_py, m_) {
         .def("create_ptrs",[](Test* self){return self->create_ptrs();})
         .def("create_MixedPtrs",[](Test* self){return self->create_MixedPtrs();})
         .def("return_ptrs",[](Test* self, std::shared_ptr<Test> p1, std::shared_ptr<Test> p2){return self->return_ptrs(p1, p2);}, py::arg("p1"), py::arg("p2"))
-        .def("print_",[](Test* self){ self->print();})
+        .def("print_",[](Test* self){ py::scoped_ostream_redirect output; self->print();})
         .def("__repr__",
                     [](const Test &a) {
                         gtsam::RedirectCout redirect;

wrap/tests/expected/python/inheritance_pybind.cpp

@@ -54,6 +54,8 @@ PYBIND11_MODULE(inheritance_py, m_) {
         .def("return_ptrs",[](MyTemplate<gtsam::Matrix>* self, const std::shared_ptr<gtsam::Matrix> p1, const std::shared_ptr<gtsam::Matrix> p2){return self->return_ptrs(p1, p2);}, py::arg("p1"), py::arg("p2"))
         .def_static("Level",[](const gtsam::Matrix& K){return MyTemplate<gtsam::Matrix>::Level(K);}, py::arg("K"));
 
+    py::class_<ForwardKinematicsFactor, gtsam::BetweenFactor<gtsam::Pose3>, std::shared_ptr<ForwardKinematicsFactor>>(m_, "ForwardKinematicsFactor");
+
 
 #include "python/specializations.h"
 

wrap/tests/fixtures/inheritance.i

@@ -22,3 +22,6 @@ virtual class MyTemplate : MyBase {
 
   static This Level(const T& K);
 };
+
+
+virtual class ForwardKinematicsFactor : gtsam::BetweenFactor<gtsam::Pose3> {};

wrap/tests/test_interface_parser.py

@@ -388,6 +388,15 @@ def test_class_inheritance(self):
                          ret.parent_class.namespaces)
         self.assertTrue(ret.is_virtual)
 
+        ret = Class.rule.parseString(
+            "class ForwardKinematicsFactor : gtsam::BetweenFactor<gtsam::Pose3> {};"
+        )[0]
+        self.assertEqual("ForwardKinematicsFactor", ret.name)
+        self.assertEqual("BetweenFactor", ret.parent_class.name)
+        self.assertEqual(["gtsam"], ret.parent_class.namespaces)
+        self.assertEqual("Pose3", ret.parent_class.instantiations[0].name)
+        self.assertEqual(["gtsam"], ret.parent_class.instantiations[0].namespaces)
+
     def test_include(self):
         """Test for include statements."""
         include = Include.rule.parseString(