Merge pull request #1108 from borglab/fix/headers

Header discipline in base

.github/scripts/unix.sh

@@ -96,7 +96,11 @@ function build ()
   configure
 
   if [ "$(uname)" == "Linux" ]; then
-    make -j$(nproc)
+    if (($(nproc) > 2)); then
+      make -j$(nproc)
+    else
+      make -j2
+    fi
   elif [ "$(uname)" == "Darwin" ]; then
     make -j$(sysctl -n hw.physicalcpu)
   fi
@@ -114,7 +118,11 @@ function test ()
 
   # Actual testing
   if [ "$(uname)" == "Linux" ]; then
-    make -j$(nproc) check
+    if (($(nproc) > 2)); then
+      make -j$(nproc) check
+    else
+      make -j2 check
+    fi
   elif [ "$(uname)" == "Darwin" ]; then
     make -j$(sysctl -n hw.physicalcpu) check
   fi

examples/SFMExampleExpressions_bal.cpp

@@ -26,10 +26,12 @@
 #include <gtsam/nonlinear/ExpressionFactorGraph.h>
 
 // Header order is close to far
-#include <gtsam/inference/Symbol.h>
-#include <gtsam/nonlinear/LevenbergMarquardtOptimizer.h>
 #include <gtsam/sfm/SfmData.h>  // for loading BAL datasets !
 #include <gtsam/slam/dataset.h>
+#include <gtsam/nonlinear/LevenbergMarquardtOptimizer.h>
+#include <gtsam/inference/Symbol.h>
+
+#include <boost/format.hpp>
 #include <vector>
 
 using namespace std;

examples/SFMExample_bal.cpp

@@ -16,12 +16,14 @@
  */
 
 // For an explanation of headers, see SFMExample.cpp
-#include <gtsam/inference/Symbol.h>
+#include <gtsam/sfm/SfmData.h> // for loading BAL datasets !
+#include <gtsam/slam/GeneralSFMFactor.h>
+#include <gtsam/slam/dataset.h>
 #include <gtsam/nonlinear/NonlinearFactorGraph.h>
 #include <gtsam/nonlinear/LevenbergMarquardtOptimizer.h>
-#include <gtsam/slam/GeneralSFMFactor.h>
-#include <gtsam/sfm/SfmData.h> // for loading BAL datasets !
-#include <gtsam/slam/dataset.h>
+#include <gtsam/inference/Symbol.h>
+
+#include <boost/format.hpp>
 #include <vector>
 
 using namespace std;

examples/SFMExample_bal_COLAMD_METIS.cpp

@@ -17,16 +17,16 @@
  */
 
 // For an explanation of headers, see SFMExample.cpp
-#include <gtsam/inference/Symbol.h>
-#include <gtsam/inference/Ordering.h>
-#include <gtsam/nonlinear/NonlinearFactorGraph.h>
-#include <gtsam/nonlinear/LevenbergMarquardtOptimizer.h>
 #include <gtsam/slam/GeneralSFMFactor.h>
 #include <gtsam/sfm/SfmData.h>  // for loading BAL datasets !
 #include <gtsam/slam/dataset.h>
-
+#include <gtsam/nonlinear/NonlinearFactorGraph.h>
+#include <gtsam/nonlinear/LevenbergMarquardtOptimizer.h>
+#include <gtsam/inference/Symbol.h>
+#include <gtsam/inference/Ordering.h>
 #include <gtsam/base/timing.h>
 
+#include <boost/format.hpp>
 #include <vector>
 
 using namespace std;

gtsam/base/Matrix.cpp

@@ -25,6 +25,7 @@
 
 #include <boost/tuple/tuple.hpp>
 #include <boost/tokenizer.hpp>
+#include <boost/format.hpp>
 
 #include <cstdarg>
 #include <cstring>

gtsam/base/Matrix.h

@@ -26,12 +26,9 @@
 
 #include <gtsam/base/OptionalJacobian.h>
 #include <gtsam/base/Vector.h>
-#include <gtsam/config.h>
-
-#include <boost/format.hpp>
-#include <functional>
 #include <boost/tuple/tuple.hpp>
-#include <boost/math/special_functions/fpclassify.hpp>
+
+#include <vector>
 
 /**
  * Matrix is a typedef in the gtsam namespace
@@ -523,82 +520,4 @@ GTSAM_EXPORT Matrix LLt(const Matrix& A);
 GTSAM_EXPORT Matrix RtR(const Matrix& A);
 
 GTSAM_EXPORT Vector columnNormSquare(const Matrix &A);
-} // namespace gtsam
-
-#include <boost/serialization/nvp.hpp>
-#include <boost/serialization/array.hpp>
-#include <boost/serialization/split_free.hpp>
-
-namespace boost {
-  namespace serialization {
-
-    /**
-     * Ref. https://stackoverflow.com/questions/18382457/eigen-and-boostserialize/22903063#22903063
-     * 
-     * Eigen supports calling resize() on both static and dynamic matrices.
-     * This allows for a uniform API, with resize having no effect if the static matrix
-     * is already the correct size.
-     * https://eigen.tuxfamily.org/dox/group__TutorialMatrixClass.html#TutorialMatrixSizesResizing
-     * 
-     * We use all the Matrix template parameters to ensure wide compatibility.
-     * 
-     * eigen_typekit in ROS uses the same code
-     * http://docs.ros.org/lunar/api/eigen_typekit/html/eigen__mqueue_8cpp_source.html
-     */
-
-    // split version - sends sizes ahead
-    template<class Archive,
-             typename Scalar_,
-             int Rows_,
-             int Cols_,
-             int Ops_,
-             int MaxRows_,
-             int MaxCols_>
-    void save(Archive & ar,
-              const Eigen::Matrix<Scalar_, Rows_, Cols_, Ops_, MaxRows_, MaxCols_> & m,
-              const unsigned int /*version*/) {
-      const size_t rows = m.rows(), cols = m.cols();
-      ar << BOOST_SERIALIZATION_NVP(rows);
-      ar << BOOST_SERIALIZATION_NVP(cols);
-      ar << make_nvp("data", make_array(m.data(), m.size()));
-    }
-
-    template<class Archive,
-             typename Scalar_,
-             int Rows_,
-             int Cols_,
-             int Ops_,
-             int MaxRows_,
-             int MaxCols_>
-    void load(Archive & ar,
-              Eigen::Matrix<Scalar_, Rows_, Cols_, Ops_, MaxRows_, MaxCols_> & m,
-              const unsigned int /*version*/) {
-      size_t rows, cols;
-      ar >> BOOST_SERIALIZATION_NVP(rows);
-      ar >> BOOST_SERIALIZATION_NVP(cols);
-      m.resize(rows, cols);
-      ar >> make_nvp("data", make_array(m.data(), m.size()));
-    }
-
-    // templated version of BOOST_SERIALIZATION_SPLIT_FREE(Eigen::Matrix);
-    template<class Archive,
-             typename Scalar_,
-             int Rows_,
-             int Cols_,
-             int Ops_,
-             int MaxRows_,
-             int MaxCols_>
-    void serialize(Archive & ar,
-              Eigen::Matrix<Scalar_, Rows_, Cols_, Ops_, MaxRows_, MaxCols_> & m,
-              const unsigned int version) {
-      split_free(ar, m, version);
-    }
-
-    // specialized to Matrix for MATLAB wrapper
-    template <class Archive>
-    void serialize(Archive& ar, gtsam::Matrix& m, const unsigned int version) {
-      split_free(ar, m, version);
-    }
-
-  } // namespace serialization
-} // namespace boost
+}  // namespace gtsam

gtsam/base/MatrixSerialization.h

@@ -0,0 +1,89 @@
+/* ----------------------------------------------------------------------------
+
+ * 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    MatrixSerialization.h
+ * @brief   Serialization for matrices
+ * @author  Frank Dellaert
+ * @date    February 2022
+ */
+
+// \callgraph
+
+#pragma once
+
+#include <gtsam/base/Matrix.h>
+
+#include <boost/serialization/array.hpp>
+#include <boost/serialization/nvp.hpp>
+#include <boost/serialization/split_free.hpp>
+
+namespace boost {
+namespace serialization {
+
+/**
+ * Ref.
+ * https://stackoverflow.com/questions/18382457/eigen-and-boostserialize/22903063#22903063
+ *
+ * Eigen supports calling resize() on both static and dynamic matrices.
+ * This allows for a uniform API, with resize having no effect if the static
+ * matrix is already the correct size.
+ * https://eigen.tuxfamily.org/dox/group__TutorialMatrixClass.html#TutorialMatrixSizesResizing
+ *
+ * We use all the Matrix template parameters to ensure wide compatibility.
+ *
+ * eigen_typekit in ROS uses the same code
+ * http://docs.ros.org/lunar/api/eigen_typekit/html/eigen__mqueue_8cpp_source.html
+ */
+
+// split version - sends sizes ahead
+template <class Archive, typename Scalar_, int Rows_, int Cols_, int Ops_,
+          int MaxRows_, int MaxCols_>
+void save(
+    Archive& ar,
+    const Eigen::Matrix<Scalar_, Rows_, Cols_, Ops_, MaxRows_, MaxCols_>& m,
+    const unsigned int /*version*/) {
+  const size_t rows = m.rows(), cols = m.cols();
+  ar << BOOST_SERIALIZATION_NVP(rows);
+  ar << BOOST_SERIALIZATION_NVP(cols);
+  ar << make_nvp("data", make_array(m.data(), m.size()));
+}
+
+template <class Archive, typename Scalar_, int Rows_, int Cols_, int Ops_,
+          int MaxRows_, int MaxCols_>
+void load(Archive& ar,
+          Eigen::Matrix<Scalar_, Rows_, Cols_, Ops_, MaxRows_, MaxCols_>& m,
+          const unsigned int /*version*/) {
+  size_t rows, cols;
+  ar >> BOOST_SERIALIZATION_NVP(rows);
+  ar >> BOOST_SERIALIZATION_NVP(cols);
+  m.resize(rows, cols);
+  ar >> make_nvp("data", make_array(m.data(), m.size()));
+}
+
+// templated version of BOOST_SERIALIZATION_SPLIT_FREE(Eigen::Matrix);
+template <class Archive, typename Scalar_, int Rows_, int Cols_, int Ops_,
+          int MaxRows_, int MaxCols_>
+void serialize(
+    Archive& ar,
+    Eigen::Matrix<Scalar_, Rows_, Cols_, Ops_, MaxRows_, MaxCols_>& m,
+    const unsigned int version) {
+  split_free(ar, m, version);
+}
+
+// specialized to Matrix for MATLAB wrapper
+template <class Archive>
+void serialize(Archive& ar, gtsam::Matrix& m, const unsigned int version) {
+  split_free(ar, m, version);
+}
+
+}  // namespace serialization
+}  // namespace boost

gtsam/base/Value.h

@@ -21,6 +21,7 @@
 #include <gtsam/config.h>      // Configuration from CMake
 
 #include <gtsam/base/Vector.h>
+#include <boost/serialization/nvp.hpp>
 #include <boost/serialization/assume_abstract.hpp>
 #include <memory>
 

gtsam/base/Vector.h

@@ -264,46 +264,4 @@ GTSAM_EXPORT Vector concatVectors(const std::list<Vector>& vs);
  * concatenate Vectors
  */
 GTSAM_EXPORT Vector concatVectors(size_t nrVectors, ...);
-} // namespace gtsam
-
-#include <boost/serialization/nvp.hpp>
-#include <boost/serialization/array.hpp>
-#include <boost/serialization/split_free.hpp>
-
-namespace boost {
-  namespace serialization {
-
-    // split version - copies into an STL vector for serialization
-    template<class Archive>
-    void save(Archive & ar, const gtsam::Vector & v, unsigned int /*version*/) {
-      const size_t size = v.size();
-      ar << BOOST_SERIALIZATION_NVP(size);
-      ar << make_nvp("data", make_array(v.data(), v.size()));
-    }
-
-    template<class Archive>
-    void load(Archive & ar, gtsam::Vector & v, unsigned int /*version*/) {
-      size_t size;
-      ar >> BOOST_SERIALIZATION_NVP(size);
-      v.resize(size);
-      ar >> make_nvp("data", make_array(v.data(), v.size()));
-    }
-
-    // split version - copies into an STL vector for serialization
-    template<class Archive, int D>
-    void save(Archive & ar, const Eigen::Matrix<double,D,1> & v, unsigned int /*version*/) {
-      ar << make_nvp("data", make_array(v.data(), v.RowsAtCompileTime));
-    }
-
-    template<class Archive, int D>
-    void load(Archive & ar, Eigen::Matrix<double,D,1> & v, unsigned int /*version*/) {
-      ar >> make_nvp("data", make_array(v.data(), v.RowsAtCompileTime));
-    }
-
-  } // namespace serialization
-} // namespace boost
-
-BOOST_SERIALIZATION_SPLIT_FREE(gtsam::Vector)
-BOOST_SERIALIZATION_SPLIT_FREE(gtsam::Vector2)
-BOOST_SERIALIZATION_SPLIT_FREE(gtsam::Vector3)
-BOOST_SERIALIZATION_SPLIT_FREE(gtsam::Vector6)
+}  // namespace gtsam

gtsam/base/VectorSerialization.h

@@ -0,0 +1,65 @@
+/* ----------------------------------------------------------------------------
+
+ * 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    VectorSerialization.h
+ * @brief   serialization for Vectors
+ * @author  Frank Dellaert
+ * @date    February 2022
+ */
+
+#pragma once
+
+#include <gtsam/base/Vector.h>
+
+#include <boost/serialization/array.hpp>
+#include <boost/serialization/nvp.hpp>
+#include <boost/serialization/split_free.hpp>
+
+namespace boost {
+namespace serialization {
+
+// split version - copies into an STL vector for serialization
+template <class Archive>
+void save(Archive& ar, const gtsam::Vector& v, unsigned int /*version*/) {
+  const size_t size = v.size();
+  ar << BOOST_SERIALIZATION_NVP(size);
+  ar << make_nvp("data", make_array(v.data(), v.size()));
+}
+
+template <class Archive>
+void load(Archive& ar, gtsam::Vector& v, unsigned int /*version*/) {
+  size_t size;
+  ar >> BOOST_SERIALIZATION_NVP(size);
+  v.resize(size);
+  ar >> make_nvp("data", make_array(v.data(), v.size()));
+}
+
+// split version - copies into an STL vector for serialization
+template <class Archive, int D>
+void save(Archive& ar, const Eigen::Matrix<double, D, 1>& v,
+          unsigned int /*version*/) {
+  ar << make_nvp("data", make_array(v.data(), v.RowsAtCompileTime));
+}
+
+template <class Archive, int D>
+void load(Archive& ar, Eigen::Matrix<double, D, 1>& v,
+          unsigned int /*version*/) {
+  ar >> make_nvp("data", make_array(v.data(), v.RowsAtCompileTime));
+}
+
+}  // namespace serialization
+}  // namespace boost
+
+BOOST_SERIALIZATION_SPLIT_FREE(gtsam::Vector)
+BOOST_SERIALIZATION_SPLIT_FREE(gtsam::Vector2)
+BOOST_SERIALIZATION_SPLIT_FREE(gtsam::Vector3)
+BOOST_SERIALIZATION_SPLIT_FREE(gtsam::Vector6)

gtsam/base/VerticalBlockMatrix.h

@@ -18,6 +18,7 @@
 #pragma once
 
 #include <gtsam/base/Matrix.h>
+#include <gtsam/base/MatrixSerialization.h>
 #include <gtsam/base/FastVector.h>
 
 namespace gtsam {

gtsam/base/base.i

@@ -82,6 +82,7 @@ class IndexPairSetMap {
 };
 
 #include <gtsam/base/Matrix.h>
+#include <gtsam/base/MatrixSerialization.h>
 bool linear_independent(Matrix A, Matrix B, double tol);
 
 #include <gtsam/base/Value.h>

gtsam/base/cholesky.h

@@ -18,7 +18,6 @@
 #pragma once
 
 #include <gtsam/base/Matrix.h>
-#include <boost/shared_ptr.hpp>
 
 namespace gtsam {
 

gtsam/base/tests/testSerializationBase.cpp

@@ -19,6 +19,7 @@
 #include <gtsam/inference/Key.h>
 
 #include <gtsam/base/Matrix.h>
+#include <gtsam/base/MatrixSerialization.h>
 #include <gtsam/base/Vector.h>
 #include <gtsam/base/FastList.h>
 #include <gtsam/base/FastMap.h>

gtsam/geometry/BearingRange.h

@@ -22,6 +22,7 @@
 #include <gtsam/base/Testable.h>
 #include <gtsam/base/OptionalJacobian.h>
 #include <boost/concept/assert.hpp>
+#include <boost/serialization/nvp.hpp>
 #include <iostream>
 
 namespace gtsam {

gtsam/geometry/Cal3DS2.h

@@ -21,6 +21,7 @@
 #pragma once
 
 #include <gtsam/geometry/Cal3DS2_Base.h>
+#include <boost/shared_ptr.hpp>
 
 namespace gtsam {
 

gtsam/geometry/Cal3DS2_Base.h

@@ -21,6 +21,7 @@
 
 #include <gtsam/geometry/Cal3.h>
 #include <gtsam/geometry/Point2.h>
+#include <boost/shared_ptr.hpp>
 
 namespace gtsam {
 

gtsam/geometry/Cal3Fisheye.h

@@ -22,6 +22,8 @@
 #include <gtsam/geometry/Cal3.h>
 #include <gtsam/geometry/Point2.h>
 
+#include <boost/shared_ptr.hpp>
+
 #include <string>
 
 namespace gtsam {

gtsam/geometry/Point3.cpp

@@ -17,6 +17,7 @@
 #include <gtsam/geometry/Point3.h>
 #include <cmath>
 #include <iostream>
+#include <vector>
 
 using namespace std;
 

gtsam/geometry/SOn.h

@@ -24,6 +24,8 @@
 #include <gtsam/dllexport.h>
 #include <Eigen/Core>
 
+#include <boost/serialization/nvp.hpp>
+
 #include <iostream> // TODO(frank): how to avoid?
 #include <string>
 #include <type_traits>

gtsam/geometry/Unit3.h

@@ -23,11 +23,12 @@
 #include <gtsam/geometry/Point2.h>
 #include <gtsam/geometry/Point3.h>
 #include <gtsam/base/Manifold.h>
+#include <gtsam/base/Vector.h>
+#include <gtsam/base/VectorSerialization.h>
 #include <gtsam/base/Matrix.h>
 #include <gtsam/dllexport.h>
 
 #include <boost/optional.hpp>
-#include <boost/serialization/nvp.hpp>
 
 #include <random>
 #include <string>

gtsam/linear/GaussianDensity.cpp

@@ -17,42 +17,41 @@
  */
 
 #include <gtsam/linear/GaussianDensity.h>
+#include <boost/format.hpp>
+#include <string>
 
-using namespace std;
+using std::cout;
+using std::endl;
+using std::string;
 
 namespace gtsam {
 
-  /* ************************************************************************* */
-  GaussianDensity GaussianDensity::FromMeanAndStddev(Key key,
-                                                     const Vector& mean,
-                                                     double sigma) {
-    return GaussianDensity(key, mean,
-                           Matrix::Identity(mean.size(), mean.size()),
-                           noiseModel::Isotropic::Sigma(mean.size(), sigma));
-  }
+/* ************************************************************************* */
+GaussianDensity GaussianDensity::FromMeanAndStddev(Key key, const Vector& mean,
+                                                   double sigma) {
+  return GaussianDensity(key, mean, Matrix::Identity(mean.size(), mean.size()),
+                         noiseModel::Isotropic::Sigma(mean.size(), sigma));
+}
 
-  /* ************************************************************************* */
-  void GaussianDensity::print(const string &s, const KeyFormatter& formatter) const
-  {
-    cout << s << ": density on ";
-    for(const_iterator it = beginFrontals(); it != endFrontals(); ++it)
-      cout << (boost::format("[%1%]")%(formatter(*it))).str() << " ";
-    cout << endl;
-    gtsam::print(mean(), "mean: ");
-    gtsam::print(covariance(), "covariance: ");
-    if(model_)
-      model_->print("Noise model: ");
-  }
+/* ************************************************************************* */
+void GaussianDensity::print(const string& s,
+                            const KeyFormatter& formatter) const {
+  cout << s << ": density on ";
+  for (const_iterator it = beginFrontals(); it != endFrontals(); ++it)
+    cout << (boost::format("[%1%]") % (formatter(*it))).str() << " ";
+  cout << endl;
+  gtsam::print(mean(), "mean: ");
+  gtsam::print(covariance(), "covariance: ");
+  if (model_) model_->print("Noise model: ");
+}
 
-  /* ************************************************************************* */
-  Vector GaussianDensity::mean() const {
-    VectorValues soln = this->solve(VectorValues());
-    return soln[firstFrontalKey()];
-  }
+/* ************************************************************************* */
+Vector GaussianDensity::mean() const {
+  VectorValues soln = this->solve(VectorValues());
+  return soln[firstFrontalKey()];
+}
 
-  /* ************************************************************************* */
-  Matrix GaussianDensity::covariance() const {
-    return information().inverse();
-  }
+/* ************************************************************************* */
+Matrix GaussianDensity::covariance() const { return information().inverse(); }
 
-} // gtsam
+}  // namespace gtsam

gtsam/linear/LossFunctions.cpp

@@ -19,6 +19,7 @@
 #include <gtsam/linear/LossFunctions.h>
 
 #include <iostream>
+#include <vector>
 
 using namespace std;
 

gtsam_unstable/nonlinear/LinearizedFactor.cpp

@@ -16,6 +16,7 @@
  */
 
 #include <gtsam_unstable/nonlinear/LinearizedFactor.h>
+#include <boost/format.hpp>
 #include <iostream>
 
 namespace gtsam {

gtsam_unstable/slam/tests/testSerialization.cpp

@@ -7,9 +7,6 @@
  * @author Alex Cunningham
  */
 
-#include <CppUnitLite/TestHarness.h>
-#include <iostream>
-
 #include <gtsam_unstable/slam/serialization.h>
 
 #include <gtsam/geometry/Pose2.h>
@@ -18,12 +15,16 @@
 #include <gtsam/slam/BetweenFactor.h>
 #include <gtsam/sam/BearingRangeFactor.h>
 
-#include <stdlib.h>
-#include <fstream>
-#include <sstream>
+#include <CppUnitLite/TestHarness.h>
+
 #include <boost/assign/std/vector.hpp>
 #include <boost/filesystem.hpp>
 
+#include <iostream>
+#include <cstdlib>
+#include <fstream>
+#include <sstream>
+
 using namespace std;
 using namespace gtsam;
 using namespace boost::assign;