Merge remote-tracking branch 'origin/develop' into fix/logging_lambda

.travis.yml

@@ -14,7 +14,8 @@ addons:
     - clang-9
     - build-essential pkg-config
     - cmake
-    - libpython-dev python-numpy
+    - python3-dev libpython-dev
+    - python3-numpy
     - libboost-all-dev
 
 # before_install:

cython/gtsam/tests/test_FrobeniusFactor.py

@@ -0,0 +1,56 @@
+"""
+GTSAM Copyright 2010-2019, Georgia Tech Research Corporation,
+Atlanta, Georgia 30332-0415
+All Rights Reserved
+
+See LICENSE for the license information
+
+FrobeniusFactor unit tests.
+Author: Frank Dellaert
+"""
+# pylint: disable=no-name-in-module, import-error, invalid-name
+import unittest
+
+import numpy as np
+from gtsam import (Rot3, SO3, SO4, FrobeniusBetweenFactorSO4, FrobeniusFactorSO4,
+                   FrobeniusWormholeFactor, SOn)
+
+id = SO4()
+v1 = np.array([0, 0, 0, 0.1, 0, 0])
+Q1 = SO4.Expmap(v1)
+v2 = np.array([0, 0, 0, 0.01, 0.02, 0.03])
+Q2 = SO4.Expmap(v2)
+
+
+class TestFrobeniusFactorSO4(unittest.TestCase):
+    """Test FrobeniusFactor factors."""
+
+    def test_frobenius_factor(self):
+        """Test creation of a factor that calculates the Frobenius norm."""
+        factor = FrobeniusFactorSO4(1, 2)
+        actual = factor.evaluateError(Q1, Q2)
+        expected = (Q2.matrix()-Q1.matrix()).transpose().reshape((16,))
+        np.testing.assert_array_equal(actual, expected)
+
+    def test_frobenius_between_factor(self):
+        """Test creation of a Frobenius BetweenFactor."""
+        factor = FrobeniusBetweenFactorSO4(1, 2, Q1.between(Q2))
+        actual = factor.evaluateError(Q1, Q2)
+        expected = np.zeros((16,))
+        np.testing.assert_array_almost_equal(actual, expected)
+
+    def test_frobenius_wormhole_factor(self):
+        """Test creation of a factor that calculates Shonan error."""
+        R1 = SO3.Expmap(v1[3:])
+        R2 = SO3.Expmap(v2[3:])
+        factor = FrobeniusWormholeFactor(1, 2, Rot3(R1.between(R2).matrix()), p=4)
+        I4 = SOn(4)
+        Q1 = I4.retract(v1)
+        Q2 = I4.retract(v2)
+        actual = factor.evaluateError(Q1, Q2)
+        expected = np.zeros((12,))
+        np.testing.assert_array_almost_equal(actual, expected, decimal=4)
+
+
+if __name__ == "__main__":
+    unittest.main()

cython/gtsam/tests/test_logging_optimizer.py

@@ -4,6 +4,12 @@ Author: Jing Wu and Frank Dellaert
 """
 # pylint: disable=invalid-name
 
+import sys
+if sys.version_info.major >= 3:
+    from io import StringIO
+else:
+    from cStringIO import StringIO
+
 import unittest
 from datetime import datetime
 
@@ -37,11 +43,19 @@ class TestOptimizeComet(GtsamTestCase):
         self.optimizer = gtsam.GaussNewtonOptimizer(
             graph, initial, self.params)
 
+        # setup output capture
+        self.capturedOutput = StringIO()
+        sys.stdout = self.capturedOutput
+
+    def tearDown(self):
+        """Reset print capture."""
+        sys.stdout = sys.__stdout__
+
     def test_simple_printing(self):
         """Test with a simple hook."""
 
         # Provide a hook that just prints
-        def hook(_, error: float):
+        def hook(_, error):
             print(error)
 
         # Only thing we require from optimizer is an iterate method
@@ -65,7 +79,7 @@ class TestOptimizeComet(GtsamTestCase):
                        + str(time.hour)+":"+str(time.minute)+":"+str(time.second))
 
         # I want to do some comet thing here
-        def hook(optimizer, error: float):
+        def hook(optimizer, error):
             comet.log_metric("Karcher error",
                              error, optimizer.iterations())
 

cython/gtsam/utils/logging_optimizer.py

@@ -4,15 +4,11 @@ Author: Jing Wu and Frank Dellaert
 """
 # pylint: disable=invalid-name
 
-from typing import TypeVar
-
 from gtsam import NonlinearOptimizer, NonlinearOptimizerParams
 import gtsam
 
-T = TypeVar('T')
 
-
-def optimize(optimizer: T, check_convergence, hook):
+def optimize(optimizer, check_convergence, hook):
     """ Given an optimizer and a convergence check, iterate until convergence.
         After each iteration, hook(optimizer, error) is called.
         After the function, use values and errors to get the result.
@@ -36,8 +32,8 @@ def optimize(optimizer: T, check_convergence, hook):
         current_error = new_error
 
 
-def gtsam_optimize(optimizer: NonlinearOptimizer,
-                   params: NonlinearOptimizerParams,
+def gtsam_optimize(optimizer,
+                   params,
                    hook):
     """ Given an optimizer and params, iterate until convergence.
         After each iteration, hook(optimizer) is called.

cython/requirements.txt

@@ -1,3 +1,3 @@
 Cython>=0.25.2
 backports_abc>=0.5
-numpy>=1.12.0
+numpy>=1.11.0

gtsam.h

@@ -281,7 +281,7 @@ virtual class Value {
 };
 
 #include <gtsam/base/GenericValue.h>
-template<T = {Vector, gtsam::Point2, gtsam::Point3, gtsam::Rot2, gtsam::Rot3, gtsam::Pose2, gtsam::Pose3, gtsam::StereoPoint2, gtsam::Cal3_S2, gtsam::CalibratedCamera, gtsam::SimpleCamera, gtsam::imuBias::ConstantBias}>
+template<T = {Vector, Matrix, gtsam::Point2, gtsam::Point3, gtsam::Rot2, gtsam::Rot3, gtsam::Pose2, gtsam::Pose3, gtsam::StereoPoint2, gtsam::Cal3_S2, gtsam::Cal3DS2, gtsam::Cal3Bundler, gtsam::EssentialMatrix, gtsam::CalibratedCamera, gtsam::SimpleCamera, gtsam::imuBias::ConstantBias}>
 virtual class GenericValue : gtsam::Value {
   void serializable() const;
 };
@@ -598,6 +598,7 @@ class SOn {
   // Standard Constructors
   SOn(size_t n);
   static gtsam::SOn FromMatrix(Matrix R);
+  static gtsam::SOn Lift(size_t n, Matrix R);
 
   // Testable
   void print(string s) const;
@@ -2835,6 +2836,34 @@ virtual class KarcherMeanFactor : gtsam::NonlinearFactor {
   KarcherMeanFactor(const gtsam::KeyVector& keys);
 };
 
+#include <gtsam/slam/FrobeniusFactor.h>
+gtsam::noiseModel::Isotropic* ConvertPose3NoiseModel(
+    gtsam::noiseModel::Base* model, size_t d);
+
+template<T = {gtsam::SO3, gtsam::SO4}>
+virtual class FrobeniusFactor : gtsam::NoiseModelFactor {
+  FrobeniusFactor(size_t key1, size_t key2);
+  FrobeniusFactor(size_t key1, size_t key2, gtsam::noiseModel::Base* model);
+
+  Vector evaluateError(const T& R1, const T& R2);
+};
+
+template<T = {gtsam::SO3, gtsam::SO4}>
+virtual class FrobeniusBetweenFactor : gtsam::NoiseModelFactor {
+  FrobeniusBetweenFactor(size_t key1, size_t key2, const T& R12);
+  FrobeniusBetweenFactor(size_t key1, size_t key2, const T& R12, gtsam::noiseModel::Base* model);
+
+  Vector evaluateError(const T& R1, const T& R2);
+};
+
+virtual class FrobeniusWormholeFactor : gtsam::NoiseModelFactor {
+  FrobeniusWormholeFactor(size_t key1, size_t key2, const gtsam::Rot3& R12,
+                          size_t p);
+  FrobeniusWormholeFactor(size_t key1, size_t key2, const gtsam::Rot3& R12,
+                          size_t p, gtsam::noiseModel::Base* model);
+  Vector evaluateError(const gtsam::SOn& Q1, const gtsam::SOn& Q2);
+};
+
 //*************************************************************************
 // Navigation
 //*************************************************************************
@@ -2955,6 +2984,7 @@ class PreintegratedImuMeasurements {
   gtsam::Rot3 deltaRij() const;
   Vector deltaPij() const;
   Vector deltaVij() const;
+  gtsam::imuBias::ConstantBias biasHat() const;
   Vector biasHatVector() const;
   gtsam::NavState predict(const gtsam::NavState& state_i,
       const gtsam::imuBias::ConstantBias& bias) const;
@@ -3016,6 +3046,7 @@ class PreintegratedCombinedMeasurements {
   gtsam::Rot3 deltaRij() const;
   Vector deltaPij() const;
   Vector deltaVij() const;
+  gtsam::imuBias::ConstantBias biasHat() const;
   Vector biasHatVector() const;
   gtsam::NavState predict(const gtsam::NavState& state_i,
       const gtsam::imuBias::ConstantBias& bias) const;

gtsam/3rdparty/CMakeLists.txt

@@ -17,7 +17,7 @@ if(NOT GTSAM_USE_SYSTEM_EIGEN)
 	endforeach(eigen_dir)
 
 	if(GTSAM_WITH_EIGEN_UNSUPPORTED)
-		message("-- Installing Eigen Unsupported modules")
+		message(STATUS "Installing Eigen Unsupported modules")
 		# do the same for the unsupported eigen folder
 		file(GLOB_RECURSE  unsupported_eigen_headers "${CMAKE_CURRENT_SOURCE_DIR}/Eigen/unsupported/Eigen/*.h")
 

gtsam/base/GenericValue.h

@@ -181,7 +181,7 @@ public:
   // Alignment, see https://eigen.tuxfamily.org/dox/group__TopicStructHavingEigenMembers.html
   enum { NeedsToAlign = (sizeof(T) % 16) == 0 };
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
 };
 
 /// use this macro instead of BOOST_CLASS_EXPORT for GenericValues

gtsam/base/Manifold.h

@@ -214,7 +214,7 @@ public:
   enum { NeedsToAlign = (sizeof(M1) % 16) == 0 || (sizeof(M2) % 16) == 0
   };
 public:
-	EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
+	GTSAM_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
 };
 
 // Define any direct product group to be a model of the multiplicative Group concept

gtsam/base/make_shared.h

@@ -0,0 +1,67 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2020, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file make_shared.h
+ * @brief make_shared trampoline function to ensure proper alignment
+ * @author Fan Jiang
+ */
+
+#pragma once
+
+#include <gtsam/base/types.h>
+
+#include <Eigen/Core>
+
+#include <boost/make_shared.hpp>
+
+#include <type_traits>
+
+namespace gtsam {
+  /// An shorthand alias for accessing the ::type inside std::enable_if that can be used in a template directly
+  template<bool B, class T = void>
+  using enable_if_t = typename std::enable_if<B, T>::type;
+}
+
+namespace gtsam {
+
+  /**
+   * Add our own `make_shared` as a layer of wrapping on `boost::make_shared`
+   * This solves the problem with the stock `make_shared` that custom alignment is not respected, causing SEGFAULTs
+   * at runtime, which is notoriously hard to debug.
+   *
+   * Explanation
+   * ===============
+   * The template `needs_eigen_aligned_allocator<T>::value` will evaluate to `std::true_type` if the type alias
+   * `_eigen_aligned_allocator_trait = void` is present in a class, which is automatically added by the
+   * `GTSAM_MAKE_ALIGNED_OPERATOR_NEW` macro.
+   *
+   * This function declaration will only be taken when the above condition is true, so if some object does not need to
+   * be aligned, `gtsam::make_shared` will fall back to the next definition, which is a simple wrapper for
+   * `boost::make_shared`.
+   *
+   * @tparam T The type of object being constructed
+   * @tparam Args Type of the arguments of the constructor
+   * @param args Arguments of the constructor
+   * @return The object created as a boost::shared_ptr<T>
+   */
+  template<typename T, typename ... Args>
+  gtsam::enable_if_t<needs_eigen_aligned_allocator<T>::value, boost::shared_ptr<T>> make_shared(Args &&... args) {
+    return boost::allocate_shared<T>(Eigen::aligned_allocator<T>(), std::forward<Args>(args)...);
+  }
+
+  /// Fall back to the boost version if no need for alignment
+  template<typename T, typename ... Args>
+  gtsam::enable_if_t<!needs_eigen_aligned_allocator<T>::value, boost::shared_ptr<T>> make_shared(Args &&... args) {
+    return boost::make_shared<T>(std::forward<Args>(args)...);
+  }
+
+}

gtsam/base/serialization.h

@@ -42,123 +42,218 @@
 
 namespace gtsam {
 
-// Serialization directly to strings in compressed format
-template<class T>
-std::string serialize(const T& input) {
-  std::ostringstream out_archive_stream;
+/** @name Standard serialization
+ *  Serialization in default compressed format
+ */
+///@{
+/// serializes to a stream
+template <class T>
+void serializeToStream(const T& input, std::ostream& out_archive_stream) {
   boost::archive::text_oarchive out_archive(out_archive_stream);
   out_archive << input;
-  return out_archive_stream.str();
 }
 
-template<class T>
-void deserialize(const std::string& serialized, T& output) {
-  std::istringstream in_archive_stream(serialized);
+/// deserializes from a stream
+template <class T>
+void deserializeFromStream(std::istream& in_archive_stream, T& output) {
   boost::archive::text_iarchive in_archive(in_archive_stream);
   in_archive >> output;
 }
 
-template<class T>
+/// serializes to a string
+template <class T>
+std::string serializeToString(const T& input) {
+  std::ostringstream out_archive_stream;
+  serializeToStream(input, out_archive_stream);
+  return out_archive_stream.str();
+}
+
+/// deserializes from a string
+template <class T>
+void deserializeFromString(const std::string& serialized, T& output) {
+  std::istringstream in_archive_stream(serialized);
+  deserializeFromStream(in_archive_stream, output);
+}
+
+/// serializes to a file
+template <class T>
 bool serializeToFile(const T& input, const std::string& filename) {
   std::ofstream out_archive_stream(filename.c_str());
-  if (!out_archive_stream.is_open())
-    return false;
-  boost::archive::text_oarchive out_archive(out_archive_stream);
-  out_archive << input;
+  if (!out_archive_stream.is_open()) return false;
+  serializeToStream(input, out_archive_stream);
   out_archive_stream.close();
   return true;
 }
 
-template<class T>
+/// deserializes from a file
+template <class T>
 bool deserializeFromFile(const std::string& filename, T& output) {
   std::ifstream in_archive_stream(filename.c_str());
-  if (!in_archive_stream.is_open())
-    return false;
-  boost::archive::text_iarchive in_archive(in_archive_stream);
-  in_archive >> output;
+  if (!in_archive_stream.is_open()) return false;
+  deserializeFromStream(in_archive_stream, output);
   in_archive_stream.close();
   return true;
 }
 
-// Serialization to XML format with named structures
-template<class T>
-std::string serializeXML(const T& input, const std::string& name="data") {
-  std::ostringstream out_archive_stream;
-  // braces to flush out_archive as it goes out of scope before taking str()
-  // fixes crash with boost 1.66-1.68
-  // see https://github.com/boostorg/serialization/issues/82
-  {
-    boost::archive::xml_oarchive out_archive(out_archive_stream);
-    out_archive << boost::serialization::make_nvp(name.c_str(), input);
-  }
-  return out_archive_stream.str();
+/// serializes to a string
+template <class T>
+std::string serialize(const T& input) {
+  return serializeToString(input);
 }
 
-template<class T>
-void deserializeXML(const std::string& serialized, T& output, const std::string& name="data") {
-  std::istringstream in_archive_stream(serialized);
+/// deserializes from a string
+template <class T>
+void deserialize(const std::string& serialized, T& output) {
+  deserializeFromString(serialized, output);
+}
+///@}
+
+/** @name XML Serialization
+ *  Serialization to XML format with named structures
+ */
+///@{
+/// serializes to a stream in XML
+template <class T>
+void serializeToXMLStream(const T& input, std::ostream& out_archive_stream,
+                  const std::string& name = "data") {
+  boost::archive::xml_oarchive out_archive(out_archive_stream);
+  out_archive << boost::serialization::make_nvp(name.c_str(), input);
+}
+
+/// deserializes from a stream in XML
+template <class T>
+void deserializeFromXMLStream(std::istream& in_archive_stream, T& output,
+                    const std::string& name = "data") {
   boost::archive::xml_iarchive in_archive(in_archive_stream);
   in_archive >> boost::serialization::make_nvp(name.c_str(), output);
 }
 
-template<class T>
-bool serializeToXMLFile(const T& input, const std::string& filename, const std::string& name="data") {
-  std::ofstream out_archive_stream(filename.c_str());
-  if (!out_archive_stream.is_open())
-    return false;
-  boost::archive::xml_oarchive out_archive(out_archive_stream);
-  out_archive << boost::serialization::make_nvp(name.c_str(), input);;
-  out_archive_stream.close();
-  return true;
-}
-
-template<class T>
-bool deserializeFromXMLFile(const std::string& filename, T& output, const std::string& name="data") {
-  std::ifstream in_archive_stream(filename.c_str());
-  if (!in_archive_stream.is_open())
-    return false;
-  boost::archive::xml_iarchive in_archive(in_archive_stream);
-  in_archive >> boost::serialization::make_nvp(name.c_str(), output);
-  in_archive_stream.close();
-  return true;
-}
-
-// Serialization to binary format with named structures
-template<class T>
-std::string serializeBinary(const T& input, const std::string& name="data") {
+/// serializes to a string in XML
+template <class T>
+std::string serializeToXMLString(const T& input,
+                         const std::string& name = "data") {
   std::ostringstream out_archive_stream;
-  boost::archive::binary_oarchive out_archive(out_archive_stream);
-  out_archive << boost::serialization::make_nvp(name.c_str(), input);
+  serializeToXMLStream(input, out_archive_stream, name);
   return out_archive_stream.str();
 }
 
-template<class T>
-void deserializeBinary(const std::string& serialized, T& output, const std::string& name="data") {
+/// deserializes from a string in XML
+template <class T>
+void deserializeFromXMLString(const std::string& serialized, T& output,
+                    const std::string& name = "data") {
   std::istringstream in_archive_stream(serialized);
-  boost::archive::binary_iarchive in_archive(in_archive_stream);
-  in_archive >> boost::serialization::make_nvp(name.c_str(), output);
+  deserializeFromXMLStream(in_archive_stream, output, name);
 }
 
-template<class T>
-bool serializeToBinaryFile(const T& input, const std::string& filename, const std::string& name="data") {
+/// serializes to an XML file
+template <class T>
+bool serializeToXMLFile(const T& input, const std::string& filename,
+                        const std::string& name = "data") {
   std::ofstream out_archive_stream(filename.c_str());
-  if (!out_archive_stream.is_open())
-    return false;
-  boost::archive::binary_oarchive out_archive(out_archive_stream);
-  out_archive << boost::serialization::make_nvp(name.c_str(), input);
+  if (!out_archive_stream.is_open()) return false;
+  serializeToXMLStream(input, out_archive_stream, name);
   out_archive_stream.close();
   return true;
 }
 
-template<class T>
-bool deserializeFromBinaryFile(const std::string& filename, T& output, const std::string& name="data") {
+/// deserializes from an XML file
+template <class T>
+bool deserializeFromXMLFile(const std::string& filename, T& output,
+                            const std::string& name = "data") {
   std::ifstream in_archive_stream(filename.c_str());
-  if (!in_archive_stream.is_open())
-    return false;
-  boost::archive::binary_iarchive in_archive(in_archive_stream);
-  in_archive >> boost::serialization::make_nvp(name.c_str(), output);
+  if (!in_archive_stream.is_open()) return false;
+  deserializeFromXMLStream(in_archive_stream, output, name);
   in_archive_stream.close();
   return true;
 }
 
-} // \namespace gtsam
+/// serializes to a string in XML
+template <class T>
+std::string serializeXML(const T& input,
+                         const std::string& name = "data") {
+  return serializeToXMLString(input, name);
+}
+
+/// deserializes from a string in XML
+template <class T>
+void deserializeXML(const std::string& serialized, T& output,
+                    const std::string& name = "data") {
+  deserializeFromXMLString(serialized, output, name);
+}
+///@}
+
+/** @name Binary Serialization
+ *  Serialization to binary format with named structures
+ */
+///@{
+/// serializes to a stream in binary
+template <class T>
+void serializeToBinaryStream(const T& input, std::ostream& out_archive_stream,
+                     const std::string& name = "data") {
+  boost::archive::binary_oarchive out_archive(out_archive_stream);
+  out_archive << boost::serialization::make_nvp(name.c_str(), input);
+}
+
+/// deserializes from a stream in binary
+template <class T>
+void deserializeFromBinaryStream(std::istream& in_archive_stream, T& output,
+                       const std::string& name = "data") {
+  boost::archive::binary_iarchive in_archive(in_archive_stream);
+  in_archive >> boost::serialization::make_nvp(name.c_str(), output);
+}
+
+/// serializes to a string in binary
+template <class T>
+std::string serializeToBinaryString(const T& input,
+                            const std::string& name = "data") {
+  std::ostringstream out_archive_stream;
+  serializeToBinaryStream(input, out_archive_stream, name);
+  return out_archive_stream.str();
+}
+
+/// deserializes from a string in binary
+template <class T>
+void deserializeFromBinaryString(const std::string& serialized, T& output,
+                       const std::string& name = "data") {
+  std::istringstream in_archive_stream(serialized);
+  deserializeFromBinaryStream(in_archive_stream, output, name);
+}
+
+/// serializes to a binary file
+template <class T>
+bool serializeToBinaryFile(const T& input, const std::string& filename,
+                           const std::string& name = "data") {
+  std::ofstream out_archive_stream(filename.c_str());
+  if (!out_archive_stream.is_open()) return false;
+  serializeToBinaryStream(input, out_archive_stream, name);
+  out_archive_stream.close();
+  return true;
+}
+
+/// deserializes from a binary file
+template <class T>
+bool deserializeFromBinaryFile(const std::string& filename, T& output,
+                               const std::string& name = "data") {
+  std::ifstream in_archive_stream(filename.c_str());
+  if (!in_archive_stream.is_open()) return false;
+  deserializeFromBinaryStream(in_archive_stream, output, name);
+  in_archive_stream.close();
+  return true;
+}
+
+/// serializes to a string in binary
+template <class T>
+std::string serializeBinary(const T& input,
+                            const std::string& name = "data") {
+  return serializeToBinaryString(input, name);
+}
+
+/// deserializes from a string in binary
+template <class T>
+void deserializeBinary(const std::string& serialized, T& output,
+                       const std::string& name = "data") {
+  deserializeFromBinaryString(serialized, output, name);
+}
+///@}
+
+}  // namespace gtsam

gtsam/base/serializationTestHelpers.h

@@ -26,6 +26,7 @@
 #include <gtsam/base/serialization.h>
 
 #include <boost/serialization/serialization.hpp>
+#include <boost/filesystem.hpp>
 
 
 // whether to print the serialized text to stdout
@@ -40,22 +41,37 @@ T create() {
   return T();
 }
 
+// Creates or empties a folder in the build folder and returns the relative path
+boost::filesystem::path resetFilesystem(
+    boost::filesystem::path folder = "actual") {
+  boost::filesystem::remove_all(folder);
+  boost::filesystem::create_directory(folder);
+  return folder;
+}
+
 // Templated round-trip serialization
 template<class T>
 void roundtrip(const T& input, T& output) {
-  // Serialize
   std::string serialized = serialize(input);
   if (verbose) std::cout << serialized << std::endl << std::endl;
-
   deserialize(serialized, output);
 }
 
-// This version requires equality operator
+// Templated round-trip serialization using a file
+template<class T>
+void roundtripFile(const T& input, T& output) {
+  boost::filesystem::path path = resetFilesystem()/"graph.dat";
+  serializeToFile(input, path.string());
+  deserializeFromFile(path.string(), output);
+}
+
+// This version requires equality operator and uses string and file round-trips
 template<class T>
 bool equality(const T& input = T()) {
-  T output = create<T>();
+  T output = create<T>(), outputf = create<T>();
   roundtrip<T>(input,output);
-  return input==output;
+  roundtripFile<T>(input,outputf);
+  return (input==output) && (input==outputf);
 }
 
 // This version requires Testable
@@ -77,20 +93,26 @@ bool equalsDereferenced(const T& input) {
 // Templated round-trip serialization using XML
 template<class T>
 void roundtripXML(const T& input, T& output) {
-  // Serialize
   std::string serialized = serializeXML<T>(input);
   if (verbose) std::cout << serialized << std::endl << std::endl;
-
-  // De-serialize
   deserializeXML(serialized, output);
 }
 
+// Templated round-trip serialization using XML File
+template<class T>
+void roundtripXMLFile(const T& input, T& output) {
+  boost::filesystem::path path = resetFilesystem()/"graph.xml";
+  serializeToXMLFile(input, path.string());
+  deserializeFromXMLFile(path.string(), output);
+}
+
 // This version requires equality operator
 template<class T>
 bool equalityXML(const T& input = T()) {
-  T output = create<T>();
+  T output = create<T>(), outputf = create<T>();
   roundtripXML<T>(input,output);
-  return input==output;
+  roundtripXMLFile<T>(input,outputf);
+  return (input==output) && (input==outputf);
 }
 
 // This version requires Testable
@@ -112,20 +134,26 @@ bool equalsDereferencedXML(const T& input = T()) {
 // Templated round-trip serialization using XML
 template<class T>
 void roundtripBinary(const T& input, T& output) {
-  // Serialize
   std::string serialized = serializeBinary<T>(input);
   if (verbose) std::cout << serialized << std::endl << std::endl;
-
-  // De-serialize
   deserializeBinary(serialized, output);
 }
 
+// Templated round-trip serialization using Binary file
+template<class T>
+void roundtripBinaryFile(const T& input, T& output) {
+  boost::filesystem::path path = resetFilesystem()/"graph.bin";
+  serializeToBinaryFile(input, path.string());
+  deserializeFromBinaryFile(path.string(), output);
+}
+
 // This version requires equality operator
 template<class T>
 bool equalityBinary(const T& input = T()) {
-  T output = create<T>();
+  T output = create<T>(), outputf = create<T>();
   roundtripBinary<T>(input,output);
-  return input==output;
+  roundtripBinaryFile<T>(input,outputf);
+  return (input==output) && (input==outputf);
 }
 
 // This version requires Testable

gtsam/base/types.h

@@ -28,6 +28,7 @@
 #include <cstdint>
 
 #include <exception>
+#include <string>
 
 #ifdef GTSAM_USE_TBB
 #include <tbb/scalable_allocator.h>
@@ -54,7 +55,7 @@
 namespace gtsam {
 
   /// Function to demangle type name of variable, e.g. demangle(typeid(x).name())
-  std::string demangle(const char* name);
+  std::string GTSAM_EXPORT demangle(const char* name);
 
   /// Integer nonlinear key type
   typedef std::uint64_t Key;
@@ -230,3 +231,50 @@ namespace std {
 #ifdef ERROR
 #undef ERROR
 #endif
+
+namespace gtsam {
+
+  /// Convenience void_t as we assume C++11, it will not conflict the std one in C++17 as this is in `gtsam::`
+  template<typename ...> using void_t = void;
+
+  /**
+   * A SFINAE trait to mark classes that need special alignment.
+   *
+   * This is required to make boost::make_shared and etc respect alignment, which is essential for the Python
+   * wrappers to work properly.
+   *
+   * Explanation
+   * =============
+   * When a GTSAM type is not declared with the type alias `_eigen_aligned_allocator_trait = void`, the first template
+   * will be taken so `needs_eigen_aligned_allocator` will be resolved to `std::false_type`.
+   *
+   * Otherwise, it will resolve to the second template, which will be resolved to `std::true_type`.
+   *
+   * Please refer to `gtsam/base/make_shared.h` for an example.
+   */
+  template<typename, typename = void_t<>>
+  struct needs_eigen_aligned_allocator : std::false_type {
+  };
+  template<typename T>
+  struct needs_eigen_aligned_allocator<T, void_t<typename T::_eigen_aligned_allocator_trait>> : std::true_type {
+  };
+
+}
+
+/**
+ * This marks a GTSAM object to require alignment. With this macro an object will automatically be allocated in aligned
+ * memory when one uses `gtsam::make_shared`. It reduces future misalignment problems that is hard to debug.
+ * See https://eigen.tuxfamily.org/dox/group__DenseMatrixManipulation__Alignement.html for detailed explanation.
+ */
+#define GTSAM_MAKE_ALIGNED_OPERATOR_NEW \
+  EIGEN_MAKE_ALIGNED_OPERATOR_NEW \
+  using _eigen_aligned_allocator_trait = void;
+
+/**
+ * This marks a GTSAM object to require alignment. With this macro an object will automatically be allocated in aligned
+ * memory when one uses `gtsam::make_shared`. It reduces future misalignment problems that is hard to debug.
+ * See https://eigen.tuxfamily.org/dox/group__DenseMatrixManipulation__Alignement.html for detailed explanation.
+ */
+#define GTSAM_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign) \
+  EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign) \
+  using _eigen_aligned_allocator_trait = void;

gtsam/geometry/BearingRange.h

@@ -162,7 +162,7 @@ private:
     NeedsToAlign = (sizeof(B) % 16) == 0 || (sizeof(R) % 16) == 0
   };
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
 };
 
 // Declare this to be both Testable and a Manifold

gtsam/geometry/CameraSet.h

@@ -319,7 +319,7 @@ private:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 template<class CAMERA>

gtsam/geometry/EssentialMatrix.h

@@ -212,7 +212,7 @@ class EssentialMatrix {
   /// @}
 
  public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 template<>

gtsam/geometry/PinholeCamera.h

@@ -325,7 +325,7 @@ private:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 // manifold traits

gtsam/geometry/PinholePose.h

@@ -222,7 +222,7 @@ private:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 // end of class PinholeBaseK
 
@@ -425,7 +425,7 @@ private:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 // end of class PinholePose
 

gtsam/geometry/Pose2.h

@@ -317,7 +317,7 @@ public:
 
 public:
   // Align for Point2, which is either derived from, or is typedef, of Vector2
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 }; // Pose2
 
 /** specialization for pose2 wedge function (generic template in Lie.h) */

gtsam/geometry/Pose3.h

@@ -355,7 +355,7 @@ public:
 #ifdef GTSAM_USE_QUATERNIONS
   // Align if we are using Quaternions
   public:
-    EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+    GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 #endif
 };
 // Pose3 class

gtsam/geometry/Rot3.h

@@ -544,7 +544,7 @@ namespace gtsam {
 #ifdef GTSAM_USE_QUATERNIONS
   // only align if quaternion, Matrix3 has no alignment requirements
   public:
-    EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+    GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 #endif
   };
 

gtsam/geometry/SOn.h

@@ -20,8 +20,8 @@
 
 #include <gtsam/base/Lie.h>
 #include <gtsam/base/Manifold.h>
+#include <gtsam/base/make_shared.h>
 #include <gtsam/dllexport.h>
-
 #include <Eigen/Core>
 
 #include <iostream> // TODO(frank): how to avoid?
@@ -54,7 +54,7 @@ class SO : public LieGroup<SO<N>, internal::DimensionSO(N)> {
   using VectorN2 = Eigen::Matrix<double, internal::NSquaredSO(N), 1>;
   using MatrixDD = Eigen::Matrix<double, dimension, dimension>;
 
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW_IF(true)
 
  protected:
   MatrixNN matrix_;  ///< Rotation matrix
@@ -292,6 +292,10 @@ class SO : public LieGroup<SO<N>, internal::DimensionSO(N)> {
                    boost::none) const;
   /// @}
 
+  template <class Archive>
+  friend void save(Archive&, SO&, const unsigned int);
+  template <class Archive>
+  friend void load(Archive&, SO&, const unsigned int);
   template <class Archive>
   friend void serialize(Archive&, SO&, const unsigned int);
   friend class boost::serialization::access;
@@ -329,6 +333,16 @@ template <>
 SOn LieGroup<SOn, Eigen::Dynamic>::between(const SOn& g, DynamicJacobian H1,
                                            DynamicJacobian H2) const;
 
+/** Serialization function */
+template<class Archive>
+void serialize(
+  Archive& ar, SOn& Q,
+  const unsigned int file_version
+) {
+  Matrix& M = Q.matrix_;
+  ar& M;
+}
+
 /*
  * Define the traits. internal::LieGroup provides both Lie group and Testable
  */

gtsam/geometry/Unit3.h

@@ -214,7 +214,7 @@ private:
   /// @}
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 // Define GTSAM traits

gtsam/geometry/triangulation.h

@@ -215,7 +215,7 @@ struct CameraProjectionMatrix {
 private:
   const Matrix3 K_;
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 /**

gtsam/navigation/AttitudeFactor.h

@@ -139,7 +139,7 @@ private:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 /// traits
@@ -219,7 +219,7 @@ private:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 /// traits

gtsam/navigation/CombinedImuFactor.h

@@ -100,7 +100,7 @@ private:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 
@@ -210,7 +210,7 @@ public:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 /**
@@ -332,7 +332,7 @@ private:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 // class CombinedImuFactor
 

gtsam/navigation/ImuBias.h

@@ -171,7 +171,7 @@ private:
 
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
   /// @}
 
 }; // ConstantBias class

gtsam/navigation/PreintegratedRotation.h

@@ -69,7 +69,7 @@ struct GTSAM_EXPORT PreintegratedRotationParams {
 #ifdef GTSAM_USE_QUATERNIONS
   // Align if we are using Quaternions
 public:
-	EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+	GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 #endif
 };
 
@@ -182,7 +182,7 @@ class GTSAM_EXPORT PreintegratedRotation {
 #ifdef GTSAM_USE_QUATERNIONS
   // Align if we are using Quaternions
   public:
-	  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+	  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 #endif
 };
 

gtsam/navigation/PreintegrationBase.h

@@ -214,7 +214,7 @@ class GTSAM_EXPORT PreintegrationBase {
 #endif
 
  public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 }  /// namespace gtsam

gtsam/navigation/PreintegrationParams.h

@@ -84,7 +84,7 @@ protected:
 #ifdef GTSAM_USE_QUATERNIONS
   // Align if we are using Quaternions
 public:
-	EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+	GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 #endif
 };
 

gtsam/navigation/TangentPreintegration.h

@@ -141,7 +141,7 @@ private:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 } /// namespace gtsam

gtsam/nonlinear/ExpressionFactor.h

@@ -209,7 +209,7 @@ private:
  // Alignment, see https://eigen.tuxfamily.org/dox/group__TopicStructHavingEigenMembers.html
  enum { NeedsToAlign = (sizeof(T) % 16) == 0 };
   public:
-	  EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
+	  GTSAM_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
 };
 // ExpressionFactor
 

gtsam/nonlinear/NonlinearEquality.h

@@ -175,7 +175,7 @@ public:
 
   /// @}
 
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 
 private:
 
@@ -265,7 +265,7 @@ public:
     traits<X>::Print(value_, "Value");
   }
 
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 
 private:
 
@@ -331,7 +331,7 @@ public:
     return traits<X>::Local(x1,x2);
   }
 
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 
 private:
 

gtsam/nonlinear/PriorFactor.h

@@ -114,7 +114,7 @@ namespace gtsam {
 	// Alignment, see https://eigen.tuxfamily.org/dox/group__TopicStructHavingEigenMembers.html
 	enum { NeedsToAlign = (sizeof(T) % 16) == 0 };
   public:
-	EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
+	GTSAM_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
   };
 
 } /// namespace gtsam

gtsam/nonlinear/internal/ExecutionTrace.h

@@ -169,6 +169,12 @@ class ExecutionTrace {
       content.ptr->reverseAD2(dTdA, jacobians);
   }
 
+  ~ExecutionTrace() {
+    if (kind == Function) {
+      content.ptr->~CallRecord<Dim>();
+    }
+  }
+
   /// Define type so we can apply it as a meta-function
   typedef ExecutionTrace<T> type;
 };

gtsam/nonlinear/internal/ExpressionNode.h

@@ -150,7 +150,7 @@ public:
     return constant_;
   }
 
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 //-----------------------------------------------------------------------------

gtsam/nonlinear/tests/testExecutionTrace.cpp

@@ -16,6 +16,7 @@
  * @brief unit tests for Expression internals
  */
 
+#include <gtsam/nonlinear/internal/CallRecord.h>
 #include <gtsam/nonlinear/internal/ExecutionTrace.h>
 #include <gtsam/geometry/Point2.h>
 

gtsam/sfm/TranslationFactor.h

@@ -0,0 +1,84 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010-2020, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+#pragma once
+
+/**
+ * @file TranslationFactor.h
+ * @author Frank Dellaert
+ * @date March 2020
+ * @brief Binary factor for a relative translation direction measurement.
+ */
+
+#include <gtsam/geometry/Point3.h>
+#include <gtsam/geometry/Unit3.h>
+#include <gtsam/linear/NoiseModel.h>
+#include <gtsam/nonlinear/NonlinearFactor.h>
+
+namespace gtsam {
+
+/**
+ * Binary factor for a relative translation direction measurement
+ * w_aZb. The measurement equation is
+ *    w_aZb = Unit3(Tb - Ta)
+ * i.e., w_aZb is the translation direction from frame A to B, in world
+ * coordinates. Although Unit3 instances live on a manifold, following
+ * Wilson14eccv_1DSfM.pdf error we compute the *chordal distance* in the
+ * ambient world coordinate frame:
+ *    normalized(Tb - Ta) - w_aZb.point3()
+ *
+ * @addtogroup SFM
+ */
+class TranslationFactor : public NoiseModelFactor2<Point3, Point3> {
+ private:
+  typedef NoiseModelFactor2<Point3, Point3> Base;
+  Point3 measured_w_aZb_;
+
+ public:
+  /// default constructor
+  TranslationFactor() {}
+
+  TranslationFactor(Key a, Key b, const Unit3& w_aZb,
+                    const SharedNoiseModel& noiseModel)
+      : Base(noiseModel, a, b), measured_w_aZb_(w_aZb.point3()) {}
+
+  /**
+   * @brief Caclulate error: (norm(Tb - Ta) - measurement)
+   * where Tb and Ta are Point3 translations and measurement is
+   * the Unit3 translation direction from a to b.
+   * 
+   * @param Ta translation for key a
+   * @param Tb translation for key b
+   * @param H1 optional jacobian in Ta
+   * @param H2 optional jacobian in Tb
+   * @return * Vector
+   */
+  Vector evaluateError(
+      const Point3& Ta, const Point3& Tb,
+      boost::optional<Matrix&> H1 = boost::none,
+      boost::optional<Matrix&> H2 = boost::none) const override {
+    const Point3 dir = Tb - Ta;
+    Matrix33 H_predicted_dir;
+    const Point3 predicted = normalize(dir, H1 || H2 ? &H_predicted_dir : nullptr);
+    if (H1) *H1 = -H_predicted_dir;
+    if (H2) *H2 = H_predicted_dir;
+    return predicted - measured_w_aZb_;
+  }
+
+ private:
+  friend class boost::serialization::access;
+  template <class ARCHIVE>
+  void serialize(ARCHIVE& ar, const unsigned int /*version*/) {
+    ar& boost::serialization::make_nvp(
+        "Base", boost::serialization::base_object<Base>(*this));
+  }
+};  // \ TranslationFactor
+}  // namespace gtsam

gtsam/sfm/TranslationRecovery.cpp

@@ -0,0 +1,103 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010-2020, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file TranslationRecovery.h
+ * @author Frank Dellaert
+ * @date March 2020
+ * @brief test recovering translations when rotations are given.
+ */
+
+#include <gtsam/sfm/TranslationRecovery.h>
+
+#include <gtsam/geometry/Point3.h>
+#include <gtsam/geometry/Pose3.h>
+#include <gtsam/geometry/Unit3.h>
+#include <gtsam/linear/NoiseModel.h>
+#include <gtsam/nonlinear/LevenbergMarquardtOptimizer.h>
+#include <gtsam/nonlinear/NonlinearFactor.h>
+#include <gtsam/nonlinear/NonlinearFactorGraph.h>
+#include <gtsam/nonlinear/Values.h>
+#include <gtsam/sfm/TranslationFactor.h>
+#include <gtsam/slam/PriorFactor.h>
+
+using namespace gtsam;
+using namespace std;
+
+NonlinearFactorGraph TranslationRecovery::buildGraph() const {
+  auto noiseModel = noiseModel::Isotropic::Sigma(3, 0.01);
+  NonlinearFactorGraph graph;
+
+  // Add all relative translation edges
+  for (auto edge : relativeTranslations_) {
+    Key a, b;
+    tie(a, b) = edge.first;
+    const Unit3 w_aZb = edge.second;
+    graph.emplace_shared<TranslationFactor>(a, b, w_aZb, noiseModel);
+  }
+
+  return graph;
+}
+
+void TranslationRecovery::addPrior(const double scale,
+                                   NonlinearFactorGraph* graph) const {
+  auto noiseModel = noiseModel::Isotropic::Sigma(3, 0.01);
+  auto edge = relativeTranslations_.begin();
+  Key a, b;
+  tie(a, b) = edge->first;
+  const Unit3 w_aZb = edge->second;
+  graph->emplace_shared<PriorFactor<Point3> >(a, Point3(0, 0, 0), noiseModel);
+  graph->emplace_shared<PriorFactor<Point3> >(b, scale * w_aZb.point3(),
+                                              noiseModel);
+}
+
+Values TranslationRecovery::initalizeRandomly() const {
+  // Create a lambda expression that checks whether value exists and randomly
+  // initializes if not.
+  Values initial;
+  auto insert = [&initial](Key j) {
+    if (!initial.exists(j)) {
+      initial.insert<Point3>(j, Vector3::Random());
+    }
+  };
+
+  // Loop over measurements and add a random translation
+  for (auto edge : relativeTranslations_) {
+    Key a, b;
+    tie(a, b) = edge.first;
+    insert(a);
+    insert(b);
+  }
+  return initial;
+}
+
+Values TranslationRecovery::run(const double scale) const {
+  auto graph = buildGraph();
+  addPrior(scale, &graph);
+  const Values initial = initalizeRandomly();
+  LevenbergMarquardtOptimizer lm(graph, initial, params_);
+  Values result = lm.optimize();
+  return result;
+}
+
+TranslationRecovery::TranslationEdges TranslationRecovery::SimulateMeasurements(
+    const Values& poses, const vector<KeyPair>& edges) {
+  TranslationEdges relativeTranslations;
+  for (auto edge : edges) {
+    Key a, b;
+    tie(a, b) = edge;
+    const Pose3 wTa = poses.at<Pose3>(a), wTb = poses.at<Pose3>(b);
+    const Point3 Ta = wTa.translation(), Tb = wTb.translation();
+    const Unit3 w_aZb(Tb - Ta);
+    relativeTranslations[edge] = w_aZb;
+  }
+  return relativeTranslations;
+}

gtsam/sfm/TranslationRecovery.h

@@ -0,0 +1,114 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010-2020, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file TranslationRecovery.h
+ * @author Frank Dellaert
+ * @date March 2020
+ * @brief test recovering translations when rotations are given.
+ */
+
+#include <gtsam/geometry/Unit3.h>
+#include <gtsam/nonlinear/LevenbergMarquardtOptimizer.h>
+#include <gtsam/nonlinear/Values.h>
+
+#include <map>
+#include <utility>
+
+namespace gtsam {
+
+// Set up an optimization problem for the unknown translations Ti in the world
+// coordinate frame, given the known camera attitudes wRi with respect to the
+// world frame, and a set of (noisy) translation directions of type Unit3,
+// w_aZb. The measurement equation is
+//    w_aZb = Unit3(Tb - Ta)   (1)
+// i.e., w_aZb is the translation direction from frame A to B, in world
+// coordinates. Although Unit3 instances live on a manifold, following
+// Wilson14eccv_1DSfM.pdf error we compute the *chordal distance* in the
+// ambient world coordinate frame.
+//
+// It is clear that we cannot recover the scale, nor the absolute position,
+// so the gauge freedom in this case is 3 + 1 = 4. We fix these by taking fixing
+// the translations Ta and Tb associated with the first measurement w_aZb,
+// clamping them to their initial values as given to this method. If no initial
+// values are given, we use the origin for Tb and set Tb to make (1) come
+// through, i.e.,
+//    Tb = s * wRa * Point3(w_aZb)     (2)
+// where s is an arbitrary scale that can be supplied, default 1.0. Hence, two
+// versions are supplied below corresponding to whether we have initial values
+// or not.
+class TranslationRecovery {
+ public:
+  using KeyPair = std::pair<Key, Key>;
+  using TranslationEdges = std::map<KeyPair, Unit3>;
+
+ private:
+  TranslationEdges relativeTranslations_;
+  LevenbergMarquardtParams params_;
+
+ public:
+  /**
+   * @brief Construct a new Translation Recovery object
+   *
+   * @param relativeTranslations the relative translations, in world coordinate
+   * frames, indexed in a map by a pair of Pose keys.
+   * @param lmParams (optional) gtsam::LavenbergMarquardtParams that can be
+   * used to modify the parameters for the LM optimizer. By default, uses the
+   * default LM parameters. 
+   */
+  TranslationRecovery(const TranslationEdges& relativeTranslations,
+                      const LevenbergMarquardtParams& lmParams = LevenbergMarquardtParams())
+      : relativeTranslations_(relativeTranslations), params_(lmParams) {
+    params_.setVerbosityLM("Summary");
+  }
+
+  /**
+   * @brief Build the factor graph to do the optimization.
+   *
+   * @return NonlinearFactorGraph
+   */
+  NonlinearFactorGraph buildGraph() const;
+
+  /**
+   * @brief Add priors on ednpoints of first measurement edge.
+   *
+   * @param scale scale for first relative translation which fixes gauge.
+   * @param graph factor graph to which prior is added.
+   */
+  void addPrior(const double scale, NonlinearFactorGraph* graph) const;
+
+  /**
+   * @brief Create random initial translations.
+   *
+   * @return Values
+   */
+  Values initalizeRandomly() const;
+
+  /**
+   * @brief Build and optimize factor graph.
+   *
+   * @param scale scale for first relative translation which fixes gauge.
+   * @return Values
+   */
+  Values run(const double scale = 1.0) const;
+
+  /**
+   * @brief Simulate translation direction measurements
+   *
+   * @param poses SE(3) ground truth poses stored as Values
+   * @param edges pairs (a,b) for which a measurement w_aZb will be generated.
+   * @return TranslationEdges map from a KeyPair to the simulated Unit3
+   * translation direction measurement between the cameras in KeyPair.
+   */
+  static TranslationEdges SimulateMeasurements(
+      const Values& poses, const std::vector<KeyPair>& edges);
+};
+}  // namespace gtsam

gtsam/sfm/tests/testTranslationFactor.cpp

@@ -0,0 +1,108 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010-2020, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ *  @file  testTranslationFactor.cpp
+ *  @brief Unit tests for TranslationFactor Class
+ *  @author Frank dellaert
+ *  @date March 2020
+ */
+
+#include <gtsam/base/numericalDerivative.h>
+#include <gtsam/geometry/Point3.h>
+#include <gtsam/sfm/TranslationFactor.h>
+
+#include <CppUnitLite/TestHarness.h>
+
+using namespace std;
+using namespace gtsam;
+
+// Create a noise model for the chordal error
+static SharedNoiseModel model(noiseModel::Isotropic::Sigma(3, 0.05));
+
+// Keys are deliberately *not* in sorted order to test that case.
+static const Key kKey1(2), kKey2(1);
+static const Unit3 kMeasured(1, 0, 0);
+
+/* ************************************************************************* */
+TEST(TranslationFactor, Constructor) {
+  TranslationFactor factor(kKey1, kKey2, kMeasured, model);
+}
+
+/* ************************************************************************* */
+TEST(TranslationFactor, ZeroError) {
+  // Create a factor
+  TranslationFactor factor(kKey1, kKey2, kMeasured, model);
+
+  // Set the linearization
+  Point3 T1(1, 0, 0), T2(2, 0, 0);
+
+  // Use the factor to calculate the error
+  Vector actualError(factor.evaluateError(T1, T2));
+
+  // Verify we get the expected error
+  Vector expected = (Vector3() << 0, 0, 0).finished();
+  EXPECT(assert_equal(expected, actualError, 1e-9));
+
+
+}
+
+/* ************************************************************************* */
+TEST(TranslationFactor, NonZeroError) {
+  // create a factor
+  TranslationFactor factor(kKey1, kKey2, kMeasured, model);
+
+  // set the linearization
+  Point3 T1(0, 1, 1), T2(0, 2, 2);
+
+  // use the factor to calculate the error
+  Vector actualError(factor.evaluateError(T1, T2));
+
+  // verify we get the expected error
+  Vector expected = (Vector3() << -1, 1/sqrt(2), 1/sqrt(2)).finished();
+  EXPECT(assert_equal(expected, actualError, 1e-9));
+}
+
+/* ************************************************************************* */
+Vector factorError(const Point3& T1, const Point3& T2,
+                   const TranslationFactor& factor) {
+  return factor.evaluateError(T1, T2);
+}
+
+TEST(TranslationFactor, Jacobian) {
+  // Create a factor
+  TranslationFactor factor(kKey1, kKey2, kMeasured, model);
+
+  // Set the linearization
+  Point3 T1(1, 0, 0), T2(2, 0, 0);
+
+  // Use the factor to calculate the Jacobians
+  Matrix H1Actual, H2Actual;
+  factor.evaluateError(T1, T2, H1Actual, H2Actual);
+
+  // Use numerical derivatives to calculate the Jacobians
+  Matrix H1Expected, H2Expected;
+  H1Expected = numericalDerivative11<Vector, Point3>(
+      boost::bind(&factorError, _1, T2, factor), T1);
+  H2Expected = numericalDerivative11<Vector, Point3>(
+      boost::bind(&factorError, T1, _1, factor), T2);
+
+  // Verify the Jacobians are correct
+  EXPECT(assert_equal(H1Expected, H1Actual, 1e-9));
+  EXPECT(assert_equal(H2Expected, H2Actual, 1e-9));
+}
+
+/* ************************************************************************* */
+int main() {
+  TestResult tr;
+  return TestRegistry::runAllTests(tr);
+}
+/* ************************************************************************* */

gtsam/slam/BetweenFactor.h

@@ -126,7 +126,7 @@ namespace gtsam {
 	  // Alignment, see https://eigen.tuxfamily.org/dox/group__TopicStructHavingEigenMembers.html
 	  enum { NeedsToAlign = (sizeof(VALUE) % 16) == 0 };
     public:
-      EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
+      GTSAM_MAKE_ALIGNED_OPERATOR_NEW_IF(NeedsToAlign)
   }; // \class BetweenFactor
 
   /// traits

gtsam/slam/EssentialMatrixConstraint.h

@@ -105,7 +105,7 @@ private:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 // \class EssentialMatrixConstraint
 

gtsam/slam/EssentialMatrixFactor.h

@@ -81,7 +81,7 @@ public:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 /**
@@ -201,7 +201,7 @@ public:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 // EssentialMatrixFactor2
 
@@ -286,7 +286,7 @@ public:
   }
 
 public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 // EssentialMatrixFactor3
 

gtsam/slam/FrobeniusFactor.cpp

@@ -0,0 +1,117 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010-2019, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file   FrobeniusFactor.cpp
+ * @date   March 2019
+ * @author Frank Dellaert
+ * @brief  Various factors that minimize some Frobenius norm
+ */
+
+#include <gtsam/slam/FrobeniusFactor.h>
+
+#include <gtsam/base/timing.h>
+#include <gtsam/nonlinear/GaussNewtonOptimizer.h>
+#include <gtsam/nonlinear/NonlinearFactorGraph.h>
+
+#include <cmath>
+#include <iostream>
+#include <vector>
+
+using namespace std;
+
+namespace gtsam {
+
+//******************************************************************************
+boost::shared_ptr<noiseModel::Isotropic> ConvertPose3NoiseModel(
+    const SharedNoiseModel& model, size_t d, bool defaultToUnit) {
+  double sigma = 1.0;
+  if (model != nullptr) {
+    if (model->dim() != 6) {
+      if (!defaultToUnit)
+        throw std::runtime_error("Can only convert Pose3 noise models");
+    } else {
+      auto sigmas = model->sigmas().head(3).eval();
+      if (sigmas(1) != sigmas(0) || sigmas(2) != sigmas(0)) {
+        if (!defaultToUnit)
+          throw std::runtime_error("Can only convert isotropic rotation noise");
+      } else {
+        sigma = sigmas(0);
+      }
+    }
+  }
+  return noiseModel::Isotropic::Sigma(d, sigma);
+}
+
+//******************************************************************************
+FrobeniusWormholeFactor::FrobeniusWormholeFactor(Key j1, Key j2, const Rot3& R12,
+                                                 size_t p,
+                                                 const SharedNoiseModel& model)
+    : NoiseModelFactor2<SOn, SOn>(ConvertPose3NoiseModel(model, p * 3), j1, j2),
+      M_(R12.matrix()),               // 3*3 in all cases
+      p_(p),                          // 4 for SO(4)
+      pp_(p * p),                     // 16 for SO(4)
+      dimension_(SOn::Dimension(p)),  // 6 for SO(4)
+      G_(pp_, dimension_)             // 16*6 for SO(4)
+{
+  // Calculate G matrix of vectorized generators
+  Matrix Z = Matrix::Zero(p, p);
+  for (size_t j = 0; j < dimension_; j++) {
+    const auto X = SOn::Hat(Eigen::VectorXd::Unit(dimension_, j));
+    G_.col(j) = Eigen::Map<const Matrix>(X.data(), pp_, 1);
+  }
+  assert(noiseModel()->dim() == 3 * p_);
+}
+
+//******************************************************************************
+Vector FrobeniusWormholeFactor::evaluateError(
+    const SOn& Q1, const SOn& Q2, boost::optional<Matrix&> H1,
+    boost::optional<Matrix&> H2) const {
+  gttic(FrobeniusWormholeFactorP_evaluateError);
+
+  const Matrix& M1 = Q1.matrix();
+  const Matrix& M2 = Q2.matrix();
+  assert(M1.rows() == p_ && M2.rows() == p_);
+
+  const size_t dim = 3 * p_;  // Stiefel manifold dimension
+  Vector fQ2(dim), hQ1(dim);
+
+  // Vectorize and extract only d leftmost columns, i.e. vec(M2*P)
+  fQ2 << Eigen::Map<const Matrix>(M2.data(), dim, 1);
+
+  // Vectorize M1*P*R12
+  const Matrix Q1PR12 = M1.leftCols<3>() * M_;
+  hQ1 << Eigen::Map<const Matrix>(Q1PR12.data(), dim, 1);
+
+  // If asked, calculate Jacobian as (M \otimes M1) * G
+  if (H1) {
+    const size_t p2 = 2 * p_;
+    Matrix RPxQ = Matrix::Zero(dim, pp_);
+    RPxQ.block(0, 0, p_, dim) << M1 * M_(0, 0), M1 * M_(1, 0), M1 * M_(2, 0);
+    RPxQ.block(p_, 0, p_, dim) << M1 * M_(0, 1), M1 * M_(1, 1), M1 * M_(2, 1);
+    RPxQ.block(p2, 0, p_, dim) << M1 * M_(0, 2), M1 * M_(1, 2), M1 * M_(2, 2);
+    *H1 = -RPxQ * G_;
+  }
+  if (H2) {
+    const size_t p2 = 2 * p_;
+    Matrix PxQ = Matrix::Zero(dim, pp_);
+    PxQ.block(0, 0, p_, p_) = M2;
+    PxQ.block(p_, p_, p_, p_) = M2;
+    PxQ.block(p2, p2, p_, p_) = M2;
+    *H2 = PxQ * G_;
+  }
+
+  return fQ2 - hQ1;
+}
+
+//******************************************************************************
+
+}  // namespace gtsam

gtsam/slam/FrobeniusFactor.h

@@ -0,0 +1,145 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010-2019, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file   FrobeniusFactor.h
+ * @date   March 2019
+ * @author Frank Dellaert
+ * @brief  Various factors that minimize some Frobenius norm
+ */
+
+#pragma once
+
+#include <gtsam/geometry/Rot3.h>
+#include <gtsam/geometry/SOn.h>
+#include <gtsam/nonlinear/NonlinearFactor.h>
+
+namespace gtsam {
+
+/**
+ * When creating (any) FrobeniusFactor we convert a 6-dimensional Pose3
+ * BetweenFactor noise model into an 9 or 16-dimensional isotropic noise
+ * model used to weight the Frobenius norm.  If the noise model passed is
+ * null we return a Dim-dimensional isotropic noise model with sigma=1.0. If
+ * not, we we check if the 3-dimensional noise model on rotations is
+ * isotropic. If it is, we extend to 'Dim' dimensions, otherwise we throw an
+ * error. If defaultToUnit == false throws an exception on unexepcted input.
+ */
+  GTSAM_EXPORT boost::shared_ptr<noiseModel::Isotropic> ConvertPose3NoiseModel(
+    const SharedNoiseModel& model, size_t d, bool defaultToUnit = true);
+
+/**
+ * FrobeniusPrior calculates the Frobenius norm between a given matrix and an
+ * element of SO(3) or SO(4).
+ */
+template <class Rot>
+class FrobeniusPrior : public NoiseModelFactor1<Rot> {
+  enum { Dim = Rot::VectorN2::RowsAtCompileTime };
+  using MatrixNN = typename Rot::MatrixNN;
+  Eigen::Matrix<double, Dim, 1> vecM_;  ///< vectorized matrix to approximate
+
+ public:
+  /// Constructor
+  FrobeniusPrior(Key j, const MatrixNN& M,
+                 const SharedNoiseModel& model = nullptr)
+      : NoiseModelFactor1<Rot>(ConvertPose3NoiseModel(model, Dim), j) {
+    vecM_ << Eigen::Map<const Matrix>(M.data(), Dim, 1);
+  }
+
+  /// Error is just Frobenius norm between Rot element and vectorized matrix M.
+  Vector evaluateError(const Rot& R,
+                       boost::optional<Matrix&> H = boost::none) const {
+    return R.vec(H) - vecM_;  // Jacobian is computed only when needed.
+  }
+};
+
+/**
+ * FrobeniusFactor calculates the Frobenius norm between rotation matrices.
+ * The template argument can be any fixed-size SO<N>.
+ */
+template <class Rot>
+class FrobeniusFactor : public NoiseModelFactor2<Rot, Rot> {
+  enum { Dim = Rot::VectorN2::RowsAtCompileTime };
+
+ public:
+  /// Constructor
+  FrobeniusFactor(Key j1, Key j2, const SharedNoiseModel& model = nullptr)
+      : NoiseModelFactor2<Rot, Rot>(ConvertPose3NoiseModel(model, Dim), j1,
+                                    j2) {}
+
+  /// Error is just Frobenius norm between rotation matrices.
+  Vector evaluateError(const Rot& R1, const Rot& R2,
+                       boost::optional<Matrix&> H1 = boost::none,
+                       boost::optional<Matrix&> H2 = boost::none) const {
+    Vector error = R2.vec(H2) - R1.vec(H1);
+    if (H1) *H1 = -*H1;
+    return error;
+  }
+};
+
+/**
+ * FrobeniusBetweenFactor is a BetweenFactor that evaluates the Frobenius norm
+ * of the rotation error between measured and predicted (rather than the
+ * Logmap of the error). This factor is only defined for fixed-dimension types,
+ * and in fact only SO3 and SO4 really work, as we need SO<N>::AdjointMap.
+ */
+template <class Rot>
+class FrobeniusBetweenFactor : public NoiseModelFactor2<Rot, Rot> {
+  Rot R12_;  ///< measured rotation between R1 and R2
+  Eigen::Matrix<double, Rot::dimension, Rot::dimension>
+      R2hat_H_R1_;  ///< fixed derivative of R2hat wrpt R1
+  enum { Dim = Rot::VectorN2::RowsAtCompileTime };
+
+ public:
+  /// Constructor
+  FrobeniusBetweenFactor(Key j1, Key j2, const Rot& R12,
+                         const SharedNoiseModel& model = nullptr)
+      : NoiseModelFactor2<Rot, Rot>(
+            ConvertPose3NoiseModel(model, Dim), j1, j2),
+        R12_(R12),
+        R2hat_H_R1_(R12.inverse().AdjointMap()) {}
+
+  /// Error is Frobenius norm between R1*R12 and R2.
+  Vector evaluateError(const Rot& R1, const Rot& R2,
+                       boost::optional<Matrix&> H1 = boost::none,
+                       boost::optional<Matrix&> H2 = boost::none) const {
+    const Rot R2hat = R1.compose(R12_);
+    Eigen::Matrix<double, Dim, Rot::dimension> vec_H_R2hat;
+    Vector error = R2.vec(H2) - R2hat.vec(H1 ? &vec_H_R2hat : nullptr);
+    if (H1) *H1 = -vec_H_R2hat * R2hat_H_R1_;
+    return error;
+  }
+};
+
+/**
+ * FrobeniusWormholeFactor is a BetweenFactor that moves in SO(p), but will
+ * land on the SO(3) sub-manifold of SO(p) at the global minimum. It projects
+ * the SO(p) matrices down to a Stiefel manifold of p*d matrices.
+ * TODO(frank): template on D=2 or 3
+ */
+class GTSAM_EXPORT FrobeniusWormholeFactor : public NoiseModelFactor2<SOn, SOn> {
+  Matrix M_;                   ///< measured rotation between R1 and R2
+  size_t p_, pp_, dimension_;  ///< dimensionality constants
+  Matrix G_;                   ///< matrix of vectorized generators
+
+ public:
+  /// Constructor. Note we convert to 3*p-dimensional noise model.
+  FrobeniusWormholeFactor(Key j1, Key j2, const Rot3& R12, size_t p = 4,
+                          const SharedNoiseModel& model = nullptr);
+
+  /// Error is Frobenius norm between Q1*P*R12 and Q2*P, where P=[I_3x3;0]
+  /// projects down from SO(p) to the Stiefel manifold of px3 matrices.
+  Vector evaluateError(const SOn& Q1, const SOn& Q2,
+                       boost::optional<Matrix&> H1 = boost::none,
+                       boost::optional<Matrix&> H2 = boost::none) const;
+};
+
+}  // namespace gtsam

gtsam/slam/ProjectionFactor.h

@@ -189,7 +189,7 @@ namespace gtsam {
     }
 
   public:
-    EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+    GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 
   /// traits

gtsam/slam/RotateFactor.h

@@ -113,7 +113,7 @@ public:
     return error;
   }
 
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 };
 }  // namespace gtsam
 

gtsam/slam/SmartFactorBase.h

@@ -81,7 +81,7 @@ protected:
   mutable FBlocks Fs;
 
  public:
-  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+  GTSAM_MAKE_ALIGNED_OPERATOR_NEW
 
   /// shorthand for a smart pointer to a factor
   typedef boost::shared_ptr<This> shared_ptr;

gtsam/slam/tests/testFrobeniusFactor.cpp

@@ -0,0 +1,244 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010-2019, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * testFrobeniusFactor.cpp
+ *
+ * @file   testFrobeniusFactor.cpp
+ * @date   March 2019
+ * @author Frank Dellaert
+ * @brief  Check evaluateError for various Frobenius norm
+ */
+
+#include <gtsam/base/lieProxies.h>
+#include <gtsam/base/testLie.h>
+#include <gtsam/geometry/Rot3.h>
+#include <gtsam/geometry/SO3.h>
+#include <gtsam/geometry/SO4.h>
+#include <gtsam/nonlinear/GaussNewtonOptimizer.h>
+#include <gtsam/nonlinear/NonlinearFactorGraph.h>
+#include <gtsam/nonlinear/factorTesting.h>
+#include <gtsam/slam/FrobeniusFactor.h>
+
+#include <CppUnitLite/TestHarness.h>
+
+using namespace std;
+using namespace gtsam;
+
+//******************************************************************************
+namespace so3 {
+SO3 id;
+Vector3 v1 = (Vector(3) << 0.1, 0, 0).finished();
+SO3 R1 = SO3::Expmap(v1);
+Vector3 v2 = (Vector(3) << 0.01, 0.02, 0.03).finished();
+SO3 R2 = SO3::Expmap(v2);
+SO3 R12 = R1.between(R2);
+}  // namespace so3
+
+/* ************************************************************************* */
+TEST(FrobeniusPriorSO3, evaluateError) {
+  using namespace ::so3;
+  auto factor = FrobeniusPrior<SO3>(1, R2.matrix());
+  Vector actual = factor.evaluateError(R1);
+  Vector expected = R1.vec() - R2.vec();
+  EXPECT(assert_equal(expected, actual, 1e-9));
+
+  Values values;
+  values.insert(1, R1);
+  EXPECT_CORRECT_FACTOR_JACOBIANS(factor, values, 1e-7, 1e-5);
+}
+
+/* ************************************************************************* */
+TEST(FrobeniusPriorSO3, ClosestTo) {
+  // Example top-left of SO(4) matrix not quite on SO(3) manifold
+  Matrix3 M;
+  M << 0.79067393, 0.6051136, -0.0930814,   //
+      0.4155925, -0.64214347, -0.64324489,  //
+      -0.44948549, 0.47046326, -0.75917576;
+
+  SO3 expected = SO3::ClosestTo(M);
+
+  // manifold optimization gets same result as SVD solution in ClosestTo
+  NonlinearFactorGraph graph;
+  graph.emplace_shared<FrobeniusPrior<SO3> >(1, M);
+
+  Values initial;
+  initial.insert(1, SO3(I_3x3));
+  auto result = GaussNewtonOptimizer(graph, initial).optimize();
+  EXPECT_DOUBLES_EQUAL(0.0, graph.error(result), 1e-6);
+  EXPECT(assert_equal(expected, result.at<SO3>(1), 1e-6));
+}
+
+/* ************************************************************************* */
+TEST(FrobeniusPriorSO3, ChordalL2mean) {
+  // See Hartley13ijcv:
+  // Cost function C(R) = \sum FrobeniusPrior(R,R_i)
+  // Closed form solution = ClosestTo(C_e), where
+  // C_e = \sum R_i !!!!
+
+  // We will test by computing mean of R1=exp(v1) R1^T=exp(-v1):
+  using namespace ::so3;
+  SO3 expected;  // identity
+  Matrix3 M = R1.matrix() + R1.matrix().transpose();
+  EXPECT(assert_equal(expected, SO3::ClosestTo(M), 1e-6));
+  EXPECT(assert_equal(expected, SO3::ChordalMean({R1, R1.inverse()}), 1e-6));
+
+  // manifold optimization gets same result as ChordalMean
+  NonlinearFactorGraph graph;
+  graph.emplace_shared<FrobeniusPrior<SO3> >(1, R1.matrix());
+  graph.emplace_shared<FrobeniusPrior<SO3> >(1, R1.matrix().transpose());
+
+  Values initial;
+  initial.insert<SO3>(1, R1.inverse());
+  auto result = GaussNewtonOptimizer(graph, initial).optimize();
+  EXPECT_DOUBLES_EQUAL(0.0, graph.error(result), 0.1);  // Why so loose?
+  EXPECT(assert_equal(expected, result.at<SO3>(1), 1e-5));
+}
+
+/* ************************************************************************* */
+TEST(FrobeniusFactorSO3, evaluateError) {
+  using namespace ::so3;
+  auto factor = FrobeniusFactor<SO3>(1, 2);
+  Vector actual = factor.evaluateError(R1, R2);
+  Vector expected = R2.vec() - R1.vec();
+  EXPECT(assert_equal(expected, actual, 1e-9));
+
+  Values values;
+  values.insert(1, R1);
+  values.insert(2, R2);
+  EXPECT_CORRECT_FACTOR_JACOBIANS(factor, values, 1e-7, 1e-5);
+}
+
+/* ************************************************************************* */
+// Commented out as SO(n) not yet supported (and might never be)
+// TEST(FrobeniusBetweenFactorSOn, evaluateError) {
+//   using namespace ::so3;
+//   auto factor =
+//       FrobeniusBetweenFactor<SOn>(1, 2, SOn::FromMatrix(R12.matrix()));
+//   Vector actual = factor.evaluateError(SOn::FromMatrix(R1.matrix()),
+//                                        SOn::FromMatrix(R2.matrix()));
+//   Vector expected = Vector9::Zero();
+//   EXPECT(assert_equal(expected, actual, 1e-9));
+
+//   Values values;
+//   values.insert(1, R1);
+//   values.insert(2, R2);
+//   EXPECT_CORRECT_FACTOR_JACOBIANS(factor, values, 1e-7, 1e-5);
+// }
+
+/* ************************************************************************* */
+TEST(FrobeniusBetweenFactorSO3, evaluateError) {
+  using namespace ::so3;
+  auto factor = FrobeniusBetweenFactor<SO3>(1, 2, R12);
+  Vector actual = factor.evaluateError(R1, R2);
+  Vector expected = Vector9::Zero();
+  EXPECT(assert_equal(expected, actual, 1e-9));
+
+  Values values;
+  values.insert(1, R1);
+  values.insert(2, R2);
+  EXPECT_CORRECT_FACTOR_JACOBIANS(factor, values, 1e-7, 1e-5);
+}
+
+//******************************************************************************
+namespace so4 {
+SO4 id;
+Vector6 v1 = (Vector(6) << 0.1, 0, 0, 0, 0, 0).finished();
+SO4 Q1 = SO4::Expmap(v1);
+Vector6 v2 = (Vector(6) << 0.01, 0.02, 0.03, 0.04, 0.05, 0.06).finished();
+SO4 Q2 = SO4::Expmap(v2);
+}  // namespace so4
+
+/* ************************************************************************* */
+TEST(FrobeniusFactorSO4, evaluateError) {
+  using namespace ::so4;
+  auto factor = FrobeniusFactor<SO4>(1, 2, noiseModel::Unit::Create(6));
+  Vector actual = factor.evaluateError(Q1, Q2);
+  Vector expected = Q2.vec() - Q1.vec();
+  EXPECT(assert_equal(expected, actual, 1e-9));
+
+  Values values;
+  values.insert(1, Q1);
+  values.insert(2, Q2);
+  EXPECT_CORRECT_FACTOR_JACOBIANS(factor, values, 1e-7, 1e-5);
+}
+
+/* ************************************************************************* */
+TEST(FrobeniusBetweenFactorSO4, evaluateError) {
+  using namespace ::so4;
+  Matrix4 M{I_4x4};
+  M.topLeftCorner<3, 3>() = ::so3::R12.matrix();
+  auto factor = FrobeniusBetweenFactor<SO4>(1, 2, Q1.between(Q2));
+  Matrix H1, H2;
+  Vector actual = factor.evaluateError(Q1, Q2, H1, H2);
+  Vector expected = SO4::VectorN2::Zero();
+  EXPECT(assert_equal(expected, actual, 1e-9));
+
+  Values values;
+  values.insert(1, Q1);
+  values.insert(2, Q2);
+  EXPECT_CORRECT_FACTOR_JACOBIANS(factor, values, 1e-7, 1e-5);
+}
+
+//******************************************************************************
+namespace submanifold {
+SO4 id;
+Vector6 v1 = (Vector(6) << 0, 0, 0, 0.1, 0, 0).finished();
+SO3 R1 = SO3::Expmap(v1.tail<3>());
+SO4 Q1 = SO4::Expmap(v1);
+Vector6 v2 = (Vector(6) << 0, 0, 0, 0.01, 0.02, 0.03).finished();
+SO3 R2 = SO3::Expmap(v2.tail<3>());
+SO4 Q2 = SO4::Expmap(v2);
+SO3 R12 = R1.between(R2);
+}  // namespace submanifold
+
+/* ************************************************************************* */
+TEST(FrobeniusWormholeFactor, evaluateError) {
+  auto model = noiseModel::Isotropic::Sigma(6, 1.2);  // dimension = 6 not 16
+  for (const size_t p : {5, 4, 3}) {
+    Matrix M = Matrix::Identity(p, p);
+    M.topLeftCorner(3, 3) = submanifold::R1.matrix();
+    SOn Q1(M);
+    M.topLeftCorner(3, 3) = submanifold::R2.matrix();
+    SOn Q2(M);
+    auto factor =
+        FrobeniusWormholeFactor(1, 2, Rot3(::so3::R12.matrix()), p, model);
+    Matrix H1, H2;
+    factor.evaluateError(Q1, Q2, H1, H2);
+
+    // Test derivatives
+    Values values;
+    values.insert(1, Q1);
+    values.insert(2, Q2);
+    EXPECT_CORRECT_FACTOR_JACOBIANS(factor, values, 1e-7, 1e-5);
+  }
+}
+
+/* ************************************************************************* */
+TEST(FrobeniusWormholeFactor, equivalenceToSO3) {
+  using namespace ::submanifold;
+  auto R12 = ::so3::R12.retract(Vector3(0.1, 0.2, -0.1));
+  auto model = noiseModel::Isotropic::Sigma(6, 1.2);  // wrong dimension
+  auto factor3 = FrobeniusBetweenFactor<SO3>(1, 2, R12, model);
+  auto factor4 = FrobeniusWormholeFactor(1, 2, Rot3(R12.matrix()), 4, model);
+  const Matrix3 E3(factor3.evaluateError(R1, R2).data());
+  const Matrix43 E4(
+      factor4.evaluateError(SOn(Q1.matrix()), SOn(Q2.matrix())).data());
+  EXPECT(assert_equal((Matrix)E4.topLeftCorner<3, 3>(), E3, 1e-9));
+  EXPECT(assert_equal((Matrix)E4.row(3), Matrix13::Zero(), 1e-9));
+}
+
+/* ************************************************************************* */
+int main() {
+  TestResult tr;
+  return TestRegistry::runAllTests(tr);
+}
+/* ************************************************************************* */

gtsam_extra.cmake.in

@@ -9,5 +9,6 @@ set (GTSAM_USE_TBB @GTSAM_USE_TBB@)
 set (GTSAM_DEFAULT_ALLOCATOR @GTSAM_DEFAULT_ALLOCATOR@)
 
 if("@GTSAM_INSTALL_CYTHON_TOOLBOX@")
+  list(APPEND GTSAM_CYTHON_INSTALL_PATH "@GTSAM_CYTHON_INSTALL_PATH@")
   list(APPEND GTSAM_EIGENCY_INSTALL_PATH "@GTSAM_EIGENCY_INSTALL_PATH@")
 endif()

gtsam_unstable/slam/PoseToPointFactor.h

@@ -0,0 +1,90 @@
+/**
+ *  @file   PoseToPointFactor.hpp
+ *  @brief  This factor can be used to track a 3D landmark over time by
+ *providing local measurements of its location.
+ *  @author David Wisth
+ **/
+#pragma once
+
+#include <gtsam/geometry/Point3.h>
+#include <gtsam/geometry/Pose3.h>
+#include <gtsam/nonlinear/NonlinearFactor.h>
+#include <ostream>
+
+namespace gtsam {
+
+/**
+ * A class for a measurement between a pose and a point.
+ * @addtogroup SLAM
+ */
+class PoseToPointFactor : public NoiseModelFactor2<Pose3, Point3> {
+ private:
+  typedef PoseToPointFactor This;
+  typedef NoiseModelFactor2<Pose3, Point3> Base;
+
+  Point3 measured_; /** the point measurement in local coordinates */
+
+ public:
+  // shorthand for a smart pointer to a factor
+  typedef boost::shared_ptr<PoseToPointFactor> shared_ptr;
+
+  /** default constructor - only use for serialization */
+  PoseToPointFactor() {}
+
+  /** Constructor */
+  PoseToPointFactor(Key key1, Key key2, const Point3& measured,
+                    const SharedNoiseModel& model)
+      : Base(model, key1, key2), measured_(measured) {}
+
+  virtual ~PoseToPointFactor() {}
+
+  /** implement functions needed for Testable */
+
+  /** print */
+  virtual void print(const std::string& s, const KeyFormatter& keyFormatter =
+                                               DefaultKeyFormatter) const {
+    std::cout << s << "PoseToPointFactor(" << keyFormatter(this->key1()) << ","
+              << keyFormatter(this->key2()) << ")\n"
+              << "  measured: " << measured_.transpose() << std::endl;
+    this->noiseModel_->print("  noise model: ");
+  }
+
+  /** equals */
+  virtual bool equals(const NonlinearFactor& expected,
+                      double tol = 1e-9) const {
+    const This* e = dynamic_cast<const This*>(&expected);
+    return e != nullptr && Base::equals(*e, tol) &&
+           traits<Point3>::Equals(this->measured_, e->measured_, tol);
+  }
+
+  /** implement functions needed to derive from Factor */
+
+  /** vector of errors
+   * @brief Error = wTwi.inverse()*wPwp - measured_
+   * @param wTwi The pose of the sensor in world coordinates
+   * @param wPwp The estimated point location in world coordinates
+   *
+   * Note: measured_ and the error are in local coordiantes.
+   */
+  Vector evaluateError(const Pose3& wTwi, const Point3& wPwp,
+                       boost::optional<Matrix&> H1 = boost::none,
+                       boost::optional<Matrix&> H2 = boost::none) const {
+    return wTwi.transformTo(wPwp, H1, H2) - measured_;
+  }
+
+  /** return the measured */
+  const Point3& measured() const { return measured_; }
+
+ private:
+  /** Serialization function */
+  friend class boost::serialization::access;
+  template <class ARCHIVE>
+  void serialize(ARCHIVE& ar, const unsigned int /*version*/) {
+    ar& boost::serialization::make_nvp(
+        "NoiseModelFactor2", boost::serialization::base_object<Base>(*this));
+    ar& BOOST_SERIALIZATION_NVP(measured_);
+  }
+
+};  // \class PoseToPointFactor
+
+}  // namespace gtsam

gtsam_unstable/slam/tests/testPoseToPointFactor.h

@@ -0,0 +1,86 @@
+/**
+ * @file   testPoseToPointFactor.cpp
+ * @brief
+ * @author David Wisth
+ * @date   June 20, 2020
+ */
+
+#include <CppUnitLite/TestHarness.h>
+#include <gtsam/base/numericalDerivative.h>
+#include <gtsam_unstable/slam/PoseToPointFactor.h>
+
+using namespace gtsam;
+using namespace gtsam::noiseModel;
+
+/// Verify zero error when there is no noise
+TEST(PoseToPointFactor, errorNoiseless) {
+  Pose3 pose = Pose3::identity();
+  Point3 point(1.0, 2.0, 3.0);
+  Point3 noise(0.0, 0.0, 0.0);
+  Point3 measured = t + noise;
+
+  Key pose_key(1);
+  Key point_key(2);
+  PoseToPointFactor factor(pose_key, point_key, measured,
+                           Isotropic::Sigma(3, 0.05));
+  Vector expectedError = Vector3(0.0, 0.0, 0.0);
+  Vector actualError = factor.evaluateError(pose, point);
+  EXPECT(assert_equal(expectedError, actualError, 1E-5));
+}
+
+/// Verify expected error in test scenario
+TEST(PoseToPointFactor, errorNoise) {
+  Pose3 pose = Pose3::identity();
+  Point3 point(1.0, 2.0, 3.0);
+  Point3 noise(-1.0, 0.5, 0.3);
+  Point3 measured = t + noise;
+
+  Key pose_key(1);
+  Key point_key(2);
+  PoseToPointFactor factor(pose_key, point_key, measured,
+                           Isotropic::Sigma(3, 0.05));
+  Vector expectedError = noise;
+  Vector actualError = factor.evaluateError(pose, point);
+  EXPECT(assert_equal(expectedError, actualError, 1E-5));
+}
+
+/// Check Jacobians are correct
+TEST(PoseToPointFactor, jacobian) {
+  // Measurement
+  gtsam::Point3 l_meas = gtsam::Point3(1, 2, 3);
+
+  // Linearisation point
+  gtsam::Point3 p_t = gtsam::Point3(-5, 12, 2);
+  gtsam::Rot3 p_R = gtsam::Rot3::RzRyRx(1.5 * M_PI, -0.3 * M_PI, 0.4 * M_PI);
+  Pose3 p(p_R, p_t);
+
+  gtsam::Point3 l = gtsam::Point3(3, 0, 5);
+
+  // Factor
+  Key pose_key(1);
+  Key point_key(2);
+  SharedGaussian noise = noiseModel::Diagonal::Sigmas(Vector3(0.1, 0.1, 0.1));
+  PoseToPointFactor factor(pose_key, point_key, l_meas, noise);
+
+  // Calculate numerical derivatives
+  auto f = boost::bind(&PoseToPointFactor::evaluateError, factor, _1, _2,
+                       boost::none, boost::none);
+  Matrix numerical_H1 = numericalDerivative21<Vector, Pose3, Point3>(f, p, l);
+  Matrix numerical_H2 = numericalDerivative22<Vector, Pose3, Point3>(f, p, l);
+
+  // Use the factor to calculate the derivative
+  Matrix actual_H1;
+  Matrix actual_H2;
+  factor.evaluateError(p, l, actual_H1, actual_H2);
+
+  // Verify we get the expected error
+  EXPECT_TRUE(assert_equal(numerical_H1, actual_H1, 1e-8));
+  EXPECT_TRUE(assert_equal(numerical_H2, actual_H2, 1e-8));
+}
+
+/* ************************************************************************* */
+int main() {
+  TestResult tr;
+  return TestRegistry::runAllTests(tr);
+}
+/* ************************************************************************* */

tests/testTranslationRecovery.cpp

@@ -0,0 +1,87 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010-2020, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file testTranslationRecovery.cpp
+ * @author Frank Dellaert
+ * @date March 2020
+ * @brief test recovering translations when rotations are given.
+ */
+
+#include <gtsam/sfm/TranslationRecovery.h>
+
+#include <CppUnitLite/TestHarness.h>
+#include <gtsam/slam/dataset.h>
+
+using namespace std;
+using namespace gtsam;
+
+/* ************************************************************************* */
+// We read the BAL file, which has 3 cameras in it, with poses. We then assume
+// the rotations are correct, but translations have to be estimated from
+// translation directions only. Since we have 3 cameras, A, B, and C, we can at
+// most create three relative measurements, let's call them w_aZb, w_aZc, and
+// bZc. These will be of type Unit3. We then call `recoverTranslations` which
+// sets up an optimization problem for the three unknown translations.
+TEST(TranslationRecovery, BAL) {
+  const string filename = findExampleDataFile("dubrovnik-3-7-pre");
+  SfmData db;
+  bool success = readBAL(filename, db);
+  if (!success) throw runtime_error("Could not access file!");
+
+  // Get camera poses, as Values
+  size_t j = 0;
+  Values poses;
+  for (auto camera : db.cameras) {
+    poses.insert(j++, camera.pose());
+  }
+
+  // Simulate measurements
+  const auto relativeTranslations = TranslationRecovery::SimulateMeasurements(
+      poses, {{0, 1}, {0, 2}, {1, 2}});
+
+  // Check
+  const Pose3 wTa = poses.at<Pose3>(0), wTb = poses.at<Pose3>(1),
+              wTc = poses.at<Pose3>(2);
+  const Point3 Ta = wTa.translation(), Tb = wTb.translation(),
+               Tc = wTc.translation();
+  const Rot3 aRw = wTa.rotation().inverse();
+  const Unit3 w_aZb = relativeTranslations.at({0, 1});
+  EXPECT(assert_equal(Unit3(Tb - Ta), w_aZb));
+  const Unit3 w_aZc = relativeTranslations.at({0, 2});
+  EXPECT(assert_equal(Unit3(Tc - Ta), w_aZc));
+
+  TranslationRecovery algorithm(relativeTranslations);
+  const auto graph = algorithm.buildGraph();
+  EXPECT_LONGS_EQUAL(3, graph.size());
+
+  // Translation recovery, version 1
+  const double scale = 2.0;
+  const auto result = algorithm.run(scale);
+
+  // Check result for first two translations, determined by prior
+  EXPECT(assert_equal(Point3(0, 0, 0), result.at<Point3>(0)));
+  EXPECT(assert_equal(Point3(2 * w_aZb.point3()), result.at<Point3>(1)));
+
+  // Check that the third translations is correct
+  Point3 expected = (Tc - Ta) * (scale / (Tb - Ta).norm());
+  EXPECT(assert_equal(expected, result.at<Point3>(2), 1e-4));
+
+  // TODO(frank): how to get stats back?
+  // EXPECT_DOUBLES_EQUAL(0.0199833, actualError, 1e-5);
+}
+
+/* ************************************************************************* */
+int main() {
+  TestResult tr;
+  return TestRegistry::runAllTests(tr);
+}
+/* ************************************************************************* */

timing/timeFrobeniusFactor.cpp

@@ -0,0 +1,110 @@
+/* ----------------------------------------------------------------------------
+
+ * GTSAM Copyright 2010, Georgia Tech Research Corporation,
+ * Atlanta, Georgia 30332-0415
+ * All Rights Reserved
+ * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+ * See LICENSE for the license information
+
+ * -------------------------------------------------------------------------- */
+
+/**
+ * @file    timeFrobeniusFactor.cpp
+ * @brief   time FrobeniusFactor with BAL file
+ * @author  Frank Dellaert
+ * @date    June 6, 2015
+ */
+
+#include <gtsam/base/timing.h>
+#include <gtsam/geometry/Pose3.h>
+#include <gtsam/geometry/SO4.h>
+#include <gtsam/linear/NoiseModel.h>
+#include <gtsam/linear/PCGSolver.h>
+#include <gtsam/linear/SubgraphPreconditioner.h>
+#include <gtsam/nonlinear/LevenbergMarquardtOptimizer.h>
+#include <gtsam/nonlinear/NonlinearEquality.h>
+#include <gtsam/nonlinear/NonlinearFactorGraph.h>
+#include <gtsam/nonlinear/Values.h>
+#include <gtsam/slam/PriorFactor.h>
+#include <gtsam/slam/dataset.h>
+#include <gtsam/slam/FrobeniusFactor.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+using namespace std;
+using namespace gtsam;
+
+static SharedNoiseModel gNoiseModel = noiseModel::Unit::Create(2);
+
+int main(int argc, char* argv[]) {
+  // primitive argument parsing:
+  if (argc > 3) {
+    throw runtime_error("Usage: timeFrobeniusFactor [g2oFile]");
+  }
+
+  string g2oFile;
+  try {
+    if (argc > 1)
+      g2oFile = argv[argc - 1];
+    else
+      g2oFile =
+          "/Users/dellaert/git/2019c-notes-shonanrotationaveraging/matlabCode/"
+          "datasets/randomTorus3D.g2o";
+    // g2oFile = findExampleDataFile("sphere_smallnoise.graph");
+  } catch (const exception& e) {
+    cerr << e.what() << '\n';
+    exit(1);
+  }
+
+  // Read G2O file
+  const auto factors = parse3DFactors(g2oFile);
+  const auto poses = parse3DPoses(g2oFile);
+
+  // Build graph
+  NonlinearFactorGraph graph;
+  // graph.add(NonlinearEquality<SO4>(0, SO4()));
+  auto priorModel = noiseModel::Isotropic::Sigma(6, 10000);
+  graph.add(PriorFactor<SO4>(0, SO4(), priorModel));
+  for (const auto& factor : factors) {
+    const auto& keys = factor->keys();
+    const auto& Tij = factor->measured();
+    const auto& model = factor->noiseModel();
+    graph.emplace_shared<FrobeniusWormholeFactor>(
+        keys[0], keys[1], SO3(Tij.rotation().matrix()), model);
+  }
+
+  boost::mt19937 rng(42);
+
+  // Set parameters to be similar to ceres
+  LevenbergMarquardtParams params;
+  LevenbergMarquardtParams::SetCeresDefaults(&params);
+  params.setLinearSolverType("MULTIFRONTAL_QR");
+  // params.setVerbosityLM("SUMMARY");
+  // params.linearSolverType = LevenbergMarquardtParams::Iterative;
+  // auto pcg = boost::make_shared<PCGSolverParameters>();
+  // pcg->preconditioner_ =
+  // boost::make_shared<SubgraphPreconditionerParameters>();
+  // boost::make_shared<BlockJacobiPreconditionerParameters>();
+  // params.iterativeParams = pcg;
+
+  // Optimize
+  for (size_t i = 0; i < 100; i++) {
+    gttic_(optimize);
+    Values initial;
+    initial.insert(0, SO4());
+    for (size_t j = 1; j < poses.size(); j++) {
+      initial.insert(j, SO4::Random(rng));
+    }
+    LevenbergMarquardtOptimizer lm(graph, initial, params);
+    Values result = lm.optimize();
+    cout << "cost = " << graph.error(result) << endl;
+  }
+
+  tictoc_finishedIteration_();
+  tictoc_print_();
+
+  return 0;
+}

wrap/Module.cpp

@@ -350,7 +350,10 @@ void Module::emit_cython_pxd(FileWriter& pxdFile) const {
                  "        T* get()\n"
                  "        long use_count() const\n"
                  "        T& operator*()\n\n"
-                 "    cdef shared_ptr[T] dynamic_pointer_cast[T,U](const shared_ptr[U]& r)\n"
+                 "    cdef shared_ptr[T] dynamic_pointer_cast[T,U](const shared_ptr[U]& r)\n\n";
+
+  // gtsam alignment-friendly shared_ptr
+  pxdFile.oss << "cdef extern from \"gtsam/base/make_shared.h\" namespace \"gtsam\":\n"
                  "    cdef shared_ptr[T] make_shared[T](const T& r)\n\n";
 
   for(const TypedefPair& types: typedefs)

wrap/tests/expected-cython/geometry.pxd

@@ -16,6 +16,8 @@ cdef extern from "boost/shared_ptr.hpp" namespace "boost":
         T& operator*()
 
     cdef shared_ptr[T] dynamic_pointer_cast[T,U](const shared_ptr[U]& r)
+
+cdef extern from "gtsam/base/make_shared.h" namespace "gtsam":
     cdef shared_ptr[T] make_shared[T](const T& r)
 
 cdef extern from "gtsam/geometry/Point2.h" namespace "gtsam":