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Merge remote-tracking branch 'origin/fix/Bayestree_in_out' into feature/iSAM2_refactor 

# Conflicts:
#	gtsam/inference/BayesTree-inst.h
#	gtsam/nonlinear/ISAM2.cpp
release/4.3a0
Frank Dellaert 2019-06-03 15:32:56 -04:00
parent 18553feb03 a30855181a
commit d385c1e698
13 changed files with 248 additions and 170 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

18
.travis.sh
View File

@ -22,19 +22,8 @@ function build_and_test ()
sudo update-alternatives --set gcc /usr/bin/gcc-$GCC_VERSION sudo update-alternatives --set gcc /usr/bin/gcc-$GCC_VERSION
fi fi
# gcc is too slow and we have a time limit in Travis CI: selective builds.
if [ "$BUILD_EXAMPLES" == "1" ]; then
GTSAM_BUILD_EXAMPLES_ALWAYS=ON
else
GTSAM_BUILD_EXAMPLES_ALWAYS=OFF
fi
if [ "$RUN_TESTS" == "1" ]; then
GTSAM_BUILD_TESTS=ON
else
GTSAM_BUILD_TESTS=OFF
fi
cmake $SOURCE_DIR \ cmake $SOURCE_DIR \
-DGTSAM_BUILD_UNSTABLE=$GTSAM_BUILD_UNSTABLE \
-DGTSAM_BUILD_EXAMPLES_ALWAYS=$GTSAM_BUILD_EXAMPLES_ALWAYS \ -DGTSAM_BUILD_EXAMPLES_ALWAYS=$GTSAM_BUILD_EXAMPLES_ALWAYS \
-DGTSAM_BUILD_TESTS=$GTSAM_BUILD_TESTS -DGTSAM_BUILD_TESTS=$GTSAM_BUILD_TESTS
@ -42,10 +31,13 @@ function build_and_test ()
make -j2 make -j2
# Run tests: # Run tests:
if [ "$RUN_TESTS" == "1" ]; then if [ "$GTSAM_BUILD_TESTS" == "ON" ]; then
make check make check
fi fi
# Print ccache stats
ccache -s
cd $SOURCE_DIR cd $SOURCE_DIR
} }

25
.travis.yml
View File

@ -16,8 +16,12 @@ addons:
- libpython-dev python-numpy - libpython-dev python-numpy
- libboost-all-dev - libboost-all-dev
before_install: # before_install:
- if [ "$TRAVIS_OS_NAME" == "osx" ]; then brew update ; fi # - if [ "$TRAVIS_OS_NAME" == "osx" ]; then brew update ; fi
install:
- if [ "$TRAVIS_OS_NAME" == "osx" ]; then HOMEBREW_NO_AUTO_UPDATE=1 brew install ccache ; fi
- if [ "$TRAVIS_OS_NAME" == "osx" ]; then export PATH="/usr/local/opt/ccache/libexec:$PATH" ; fi
script: script:
- bash .travis.sh - bash .travis.sh
@ -27,23 +31,24 @@ env:
- MAKEFLAGS="-j 2" - MAKEFLAGS="-j 2"
- CCACHE_SLOPPINESS=pch_defines,time_macros - CCACHE_SLOPPINESS=pch_defines,time_macros
# gcc is too slow and we have a time limit in Travis CI: selective builds.
matrix: matrix:
include: include:
- compiler: gcc - compiler: gcc
os: linux os: linux
env: BUILD_EXAMPLES=1 env: GTSAM_BUILD_UNSTABLE=ON GTSAM_BUILD_EXAMPLES_ALWAYS=ON GTSAM_BUILD_TESTS=OFF
- compiler: gcc - compiler: gcc
os: linux os: linux
env: RUN_TESTS=1 env: GTSAM_BUILD_UNSTABLE=OFF GTSAM_BUILD_EXAMPLES_ALWAYS=OFF GTSAM_BUILD_TESTS=ON # gcc too slow for all tests
- compiler: gcc - compiler: gcc
os: linux os: linux
env: BUILD_EXAMPLES=1 GCC_VERSION="8" env: GTSAM_BUILD_UNSTABLE=ON GTSAM_BUILD_EXAMPLES_ALWAYS=ON GTSAM_BUILD_TESTS=OFF GCC_VERSION="8"
- compiler: clang - compiler: clang
os: linux os: linux
env: BUILD_EXAMPLES=1 env: GTSAM_BUILD_UNSTABLE=ON GTSAM_BUILD_EXAMPLES_ALWAYS=ON GTSAM_BUILD_TESTS=OFF
- compiler: gcc # - compiler: gcc
os: osx # os: osx
env: BUILD_EXAMPLES=1 # env: GTSAM_BUILD_UNSTABLE=ON GTSAM_BUILD_EXAMPLES_ALWAYS=ON GTSAM_BUILD_TESTS=OFF
- compiler: clang - compiler: clang
os: osx os: osx
env: RUN_TESTS=1 env: GTSAM_BUILD_UNSTABLE=ON GTSAM_BUILD_EXAMPLES_ALWAYS=OFF GTSAM_BUILD_TESTS=ON

29
CMakeLists.txt
View File

@ -314,6 +314,29 @@ else()
set(GTSAM_EIGEN_INCLUDE_FOR_BUILD "${CMAKE_SOURCE_DIR}/gtsam/3rdparty/Eigen/") set(GTSAM_EIGEN_INCLUDE_FOR_BUILD "${CMAKE_SOURCE_DIR}/gtsam/3rdparty/Eigen/")
endif() endif()
# Detect Eigen version:
set(EIGEN_VER_H "${GTSAM_EIGEN_INCLUDE_FOR_BUILD}/Eigen/src/Core/util/Macros.h")
if (EXISTS ${EIGEN_VER_H})
file(READ "${EIGEN_VER_H}" STR_EIGEN_VERSION)
# Extract the Eigen version from the Macros.h file, lines "#define EIGEN_WORLD_VERSION XX", etc...
string(REGEX MATCH "EIGEN_WORLD_VERSION[ ]+[0-9]+" GTSAM_EIGEN_VERSION_WORLD "${STR_EIGEN_VERSION}")
string(REGEX MATCH "[0-9]+" GTSAM_EIGEN_VERSION_WORLD "${GTSAM_EIGEN_VERSION_WORLD}")
string(REGEX MATCH "EIGEN_MAJOR_VERSION[ ]+[0-9]+" GTSAM_EIGEN_VERSION_MAJOR "${STR_EIGEN_VERSION}")
string(REGEX MATCH "[0-9]+" GTSAM_EIGEN_VERSION_MAJOR "${GTSAM_EIGEN_VERSION_MAJOR}")
string(REGEX MATCH "EIGEN_MINOR_VERSION[ ]+[0-9]+" GTSAM_EIGEN_VERSION_MINOR "${STR_EIGEN_VERSION}")
string(REGEX MATCH "[0-9]+" GTSAM_EIGEN_VERSION_MINOR "${GTSAM_EIGEN_VERSION_MINOR}")
set(GTSAM_EIGEN_VERSION "${GTSAM_EIGEN_VERSION_WORLD}.${GTSAM_EIGEN_VERSION_MAJOR}.${GTSAM_EIGEN_VERSION_MINOR}")
message(STATUS "Found Eigen version: ${GTSAM_EIGEN_VERSION}")
else()
message(WARNING "Cannot determine Eigen version, missing file: `${EIGEN_VER_H}`")
endif ()
if (MSVC) if (MSVC)
if (BUILD_SHARED_LIBS) if (BUILD_SHARED_LIBS)
# mute eigen static assert to avoid errors in shared lib # mute eigen static assert to avoid errors in shared lib
@ -499,11 +522,7 @@ if(NOT MSVC AND NOT XCODE_VERSION)
message(STATUS " C compilation flags : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${cmake_build_type_toupper}}") message(STATUS " C compilation flags : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${cmake_build_type_toupper}}")
message(STATUS " C++ compilation flags : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${cmake_build_type_toupper}}") message(STATUS " C++ compilation flags : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${cmake_build_type_toupper}}")
endif() endif()
if(GTSAM_USE_SYSTEM_EIGEN) message(STATUS " Use System Eigen : ${GTSAM_USE_SYSTEM_EIGEN} (Using version: ${GTSAM_EIGEN_VERSION})")
message(STATUS " Use System Eigen : Yes")
else()
message(STATUS " Use System Eigen : No")
endif()
if(GTSAM_USE_TBB) if(GTSAM_USE_TBB)
message(STATUS " Use Intel TBB : Yes") message(STATUS " Use Intel TBB : Yes")
elseif(TBB_FOUND) elseif(TBB_FOUND)

11
doc/trustregion.bib
View File

@ -8,7 +8,6 @@
%% Saved with string encoding Unicode (UTF-8) %% Saved with string encoding Unicode (UTF-8)
@webpage{Hauser06lecture, @webpage{Hauser06lecture,
Author = {Raphael Hauser}, Author = {Raphael Hauser},
Date-Added = {2011-10-10 15:21:22 +0000}, Date-Added = {2011-10-10 15:21:22 +0000},
@ -16,11 +15,5 @@
Title = {Lecture Notes on Unconstrained Optimization}, Title = {Lecture Notes on Unconstrained Optimization},
Url = {http://www.numerical.rl.ac.uk/nimg/oupartc/lectures/raphael/}, Url = {http://www.numerical.rl.ac.uk/nimg/oupartc/lectures/raphael/},
Year = {2006}, Year = {2006},
Bdsk-Url-1 = {http://www.numerical.rl.ac.uk/nimg/oupartc/lectures/raphael/}, howpublished = {\href{http://www.numerical.rl.ac.uk/nimg/oupartc/lectures/raphael/}{link}},
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71
doc/trustregion.lyx
View File

@ -1,10 +1,11 @@
#LyX 2.0 created this file. For more info see http://www.lyx.org/ #LyX 2.1 created this file. For more info see http://www.lyx.org/
\lyxformat 413 \lyxformat 474
\begin_document \begin_document
\begin_header \begin_header
\textclass article \textclass article
\begin_preamble \begin_preamble
\usepackage{amssymb} \usepackage{url}
\usepackage{hyperref}
\end_preamble \end_preamble
\use_default_options true \use_default_options true
\maintain_unincluded_children false \maintain_unincluded_children false
@ -15,13 +16,13 @@
\font_roman default \font_roman default
\font_sans default \font_sans default
\font_typewriter default \font_typewriter default
\font_math auto
\font_default_family default \font_default_family default
\use_non_tex_fonts false \use_non_tex_fonts false
\font_sc false \font_sc false
\font_osf false \font_osf false
\font_sf_scale 100 \font_sf_scale 100
\font_tt_scale 100 \font_tt_scale 100
\graphics default \graphics default
\default_output_format default \default_output_format default
\output_sync 0 \output_sync 0
@ -32,15 +33,24 @@
\use_hyperref false \use_hyperref false
\papersize default \papersize default
\use_geometry false \use_geometry false
\use_amsmath 1 \use_package amsmath 1
\use_esint 1 \use_package amssymb 2
\use_mhchem 1 \use_package cancel 1
\use_mathdots 1 \use_package esint 1
\use_package mathdots 1
\use_package mathtools 1
\use_package mhchem 1
\use_package stackrel 0
\use_package stmaryrd 1
\use_package undertilde 1
\cite_engine basic \cite_engine basic
\cite_engine_type default
\biblio_style plain
\use_bibtopic false \use_bibtopic false
\use_indices false \use_indices false
\paperorientation portrait \paperorientation portrait
\suppress_date false \suppress_date false
\justification true
\use_refstyle 1 \use_refstyle 1
\index Index \index Index
\shortcut idx \shortcut idx
@ -231,7 +241,7 @@ key "Hauser06lecture"
\end_inset \end_inset
(in our /net/hp223/borg/Literature folder). .
\end_layout \end_layout
\begin_layout Standard \begin_layout Standard
@ -465,22 +475,39 @@ where
\end_inset \end_inset
. .
A typical update rule [ A typical update rule, as per Lec.
\color blue 7-1.2 of
see where this came from in paper \begin_inset CommandInset citation
\color inherit LatexCommand cite
] is key "Hauser06lecture"
\end_inset
is:
\begin_inset Formula \begin_inset Formula
\[ \[
\Delta\leftarrow\begin{cases} \Delta_{k+1}\leftarrow\begin{cases}
\max\left(\Delta,3\norm{\delta x_{d}}\right)\text{,} & \rho>0.75\\ \Delta_{k}/4 & \rho<0.25\\
\Delta & 0.75>\rho>0.25\\ \min\left(2\Delta_{k},\Delta_{max}\right)\text{,} & \rho>0.75\\
\Delta/2 & 0.25>\rho \Delta_{k} & 0.75>\rho>0.25
\end{cases} \end{cases}
\] \]
\end_inset \end_inset
where
\begin_inset Formula $\Delta_{k}\triangleq\norm{\delta x_{d}}$
\end_inset
.
Note that the rule is designed to ensure that
\begin_inset Formula $\Delta_{k}$
\end_inset
never exceeds the maximum trust region size
\begin_inset Formula $\Delta_{max}.$
\end_inset
\end_layout \end_layout
@ -593,9 +620,9 @@ To find the intersection of the line between
\begin{align*} \begin{align*}
\Delta & =\norm{\left(1-\tau\right)\delta x_{u}+\tau\delta x_{n}}\\ \Delta & =\norm{\left(1-\tau\right)\delta x_{u}+\tau\delta x_{n}}\\
\Delta^{2} & =\left(1-\tau\right)^{2}\delta x_{u}^{\t}\delta x_{u}+2\tau\left(1-\tau\right)\delta x_{u}^{\t}\delta x_{n}+\tau^{2}\delta x_{n}^{\t}\delta x_{n}\\ \Delta^{2} & =\left(1-\tau\right)^{2}\delta x_{u}^{\t}\delta x_{u}+2\tau\left(1-\tau\right)\delta x_{u}^{\t}\delta x_{n}+\tau^{2}\delta x_{n}^{\t}\delta x_{n}\\
0 & =uu-2\tau uu+\tau^{2}uu+2\tau un-2\tau^{2}un+\tau^{2}nn-\Delta^{2}\\ 0 & =\delta x_{u}^{\t}\delta x_{u}-2\tau\delta x_{u}^{\t}\delta x_{u}+\tau^{2}\delta x_{u}^{\t}\delta x_{u}+2\tau\delta x_{u}^{\t}\delta x_{n}-2\tau^{2}\delta x_{u}^{\t}\delta x_{n}+\tau^{2}\delta x_{n}^{\t}\delta x_{n}-\Delta^{2}\\
0 & =\left(uu-2un+nn\right)\tau^{2}+\left(2un-2uu\right)\tau-\Delta^{2}+uu\\ 0 & =\left(\delta x_{u}^{\t}\delta x_{u}-2\delta x_{u}^{\t}\delta x_{n}+\delta x_{n}^{\t}\delta x_{n}\right)\tau^{2}+\left(2\delta x_{u}^{\t}\delta x_{n}-2\delta x_{u}^{\t}\delta x_{u}\right)\tau-\Delta^{2}+\delta x_{u}^{\t}\delta x_{u}\\
\tau & =\frac{-\left(2un-2uu\right)\pm\sqrt{\left(2un-2uu\right)^{2}-4\left(uu-2un+nn\right)\left(uu-\Delta^{2}\right)}}{2\left(uu-un+nn\right)} \tau & =\frac{-\left(2\delta x_{u}^{\t}\delta x_{n}-2\delta x_{u}^{\t}\delta x_{u}\right)\pm\sqrt{\left(2\delta x_{u}^{\t}\delta x_{n}-2\delta x_{u}^{\t}\delta x_{u}\right)^{2}-4\left(\delta x_{u}^{\t}\delta x_{u}-2\delta x_{u}^{\t}\delta x_{n}+\delta x_{n}^{\t}\delta x_{n}\right)\left(\delta x_{u}^{\t}\delta x_{u}-\Delta^{2}\right)}}{2\left(\delta x_{u}^{\t}\delta x_{u}-\delta x_{u}^{\t}\delta x_{n}+\delta x_{n}^{\t}\delta x_{n}\right)}
\end{align*} \end{align*}
\end_inset \end_inset
@ -641,7 +668,7 @@ Thus, mathematically, we can write the dogleg update
\begin_inset Formula \begin_inset Formula
\[ \[
\delta x_{d}^{\left(k\right)}=\begin{cases} \delta x_{d}^{\left(k\right)}=\begin{cases}
-\frac{\Delta}{\norm{g^{\left(k\right)}}}g^{\left(k\right)}\text{,} & \Delta<\norm{\delta x_{u}^{\left(k\right)}}\\ -\frac{\Delta}{\norm{\delta x_{u}^{\left(k\right)}}}\delta x_{u}^{\left(k\right)}\text{,} & \Delta<\norm{\delta x_{u}^{\left(k\right)}}\\
\left(1-\tau^{\left(k\right)}\right)\delta x_{u}^{\left(k\right)}+\tau^{\left(k\right)}\delta x_{n}^{\left(k\right)}\text{,} & \norm{\delta x_{u}^{\left(k\right)}}<\Delta<\norm{\delta x_{n}^{\left(k\right)}}\\ \left(1-\tau^{\left(k\right)}\right)\delta x_{u}^{\left(k\right)}+\tau^{\left(k\right)}\delta x_{n}^{\left(k\right)}\text{,} & \norm{\delta x_{u}^{\left(k\right)}}<\Delta<\norm{\delta x_{n}^{\left(k\right)}}\\
\delta x_{n}^{\left(k\right)}\text{,} & \norm{\delta x_{n}^{\left(k\right)}}<\Delta \delta x_{n}^{\left(k\right)}\text{,} & \norm{\delta x_{n}^{\left(k\right)}}<\Delta
\end{cases} \end{cases}

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13
gtsam/base/Vector.h
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@ -63,6 +63,19 @@ GTSAM_MAKE_VECTOR_DEFS(12);
typedef Eigen::VectorBlock<Vector> SubVector; typedef Eigen::VectorBlock<Vector> SubVector;
typedef Eigen::VectorBlock<const Vector> ConstSubVector; typedef Eigen::VectorBlock<const Vector> ConstSubVector;
/**
* Ensure we are not including a different version of Eigen in user code than
* while compiling gtsam, since it can lead to hard-to-understand runtime
* crashes.
*/
#if defined(GTSAM_EIGEN_VERSION_WORLD)
static_assert(
GTSAM_EIGEN_VERSION_WORLD==EIGEN_WORLD_VERSION &&
GTSAM_EIGEN_VERSION_MAJOR==EIGEN_MAJOR_VERSION &&
GTSAM_EIGEN_VERSION_MINOR==EIGEN_MINOR_VERSION,
"Error: GTSAM was built against a different version of Eigen");
#endif
/** /**
* print without optional string, must specify cout yourself * print without optional string, must specify cout yourself
*/ */

6
gtsam/config.h.in
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@ -52,6 +52,12 @@
// Whether Eigen with MKL will use OpenMP (if OpenMP was found, Eigen uses MKL, and GTSAM_WITH_EIGEN_MKL_OPENMP is enabled in CMake) // Whether Eigen with MKL will use OpenMP (if OpenMP was found, Eigen uses MKL, and GTSAM_WITH_EIGEN_MKL_OPENMP is enabled in CMake)
#cmakedefine GTSAM_USE_EIGEN_MKL_OPENMP #cmakedefine GTSAM_USE_EIGEN_MKL_OPENMP
// Eigen library version (needed to avoid mixing versions, which often leads
// to segfaults)
#cmakedefine GTSAM_EIGEN_VERSION_WORLD @GTSAM_EIGEN_VERSION_WORLD@
#cmakedefine GTSAM_EIGEN_VERSION_MAJOR @GTSAM_EIGEN_VERSION_MAJOR@
#cmakedefine GTSAM_EIGEN_VERSION_MINOR @GTSAM_EIGEN_VERSION_MINOR@
// The default allocator to use // The default allocator to use
#cmakedefine GTSAM_ALLOCATOR_BOOSTPOOL #cmakedefine GTSAM_ALLOCATOR_BOOSTPOOL
#cmakedefine GTSAM_ALLOCATOR_TBB #cmakedefine GTSAM_ALLOCATOR_TBB

91
gtsam/inference/BayesTree-inst.h
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@ -36,19 +36,20 @@ namespace gtsam {
/* ************************************************************************* */ /* ************************************************************************* */
template<class CLIQUE> template<class CLIQUE>
BayesTreeCliqueData BayesTree<CLIQUE>::getCliqueData() const { BayesTreeCliqueData BayesTree<CLIQUE>::getCliqueData() const {
BayesTreeCliqueData data; BayesTreeCliqueData stats;
for(const sharedClique& root: roots_) for (const sharedClique& root : roots_) getCliqueData(root, &stats);
getCliqueData(data, root); return stats;
return data;
} }
/* ************************************************************************* */ /* ************************************************************************* */
template<class CLIQUE> template <class CLIQUE>
void BayesTree<CLIQUE>::getCliqueData(BayesTreeCliqueData& data, sharedClique clique) const { void BayesTree<CLIQUE>::getCliqueData(sharedClique clique,
data.conditionalSizes.push_back(clique->conditional()->nrFrontals()); BayesTreeCliqueData* stats) const {
data.separatorSizes.push_back(clique->conditional()->nrParents()); const auto conditional = clique->conditional();
for(sharedClique c: clique->children) { stats->conditionalSizes.push_back(conditional->nrFrontals());
getCliqueData(data, c); stats->separatorSizes.push_back(conditional->nrParents());
for (sharedClique c : clique->children) {
getCliqueData(c, stats);
} }
} }
@ -133,34 +134,26 @@ namespace gtsam {
} }
/* ************************************************************************* */ /* ************************************************************************* */
// TODO: Clean up
namespace { namespace {
template<class FACTOR, class CLIQUE> template <class FACTOR, class CLIQUE>
int _pushClique(FactorGraph<FACTOR>& fg, const boost::shared_ptr<CLIQUE>& clique) {
fg.push_back(clique->conditional_);
return 0;
}
template<class FACTOR, class CLIQUE>
struct _pushCliqueFunctor { struct _pushCliqueFunctor {
_pushCliqueFunctor(FactorGraph<FACTOR>& graph_) : graph(graph_) {} _pushCliqueFunctor(FactorGraph<FACTOR>* graph_) : graph(graph_) {}
FactorGraph<FACTOR>& graph; FactorGraph<FACTOR>* graph;
int operator()(const boost::shared_ptr<CLIQUE>& clique, int dummy) { int operator()(const boost::shared_ptr<CLIQUE>& clique, int dummy) {
graph.push_back(clique->conditional_); graph->push_back(clique->conditional_);
return 0; return 0;
} }
}; };
} } // namespace
/* ************************************************************************* */ /* ************************************************************************* */
template<class CLIQUE> template <class CLIQUE>
void BayesTree<CLIQUE>::addFactorsToGraph(FactorGraph<FactorType>& graph) const void BayesTree<CLIQUE>::addFactorsToGraph(
{ FactorGraph<FactorType>* graph) const {
// Traverse the BayesTree and add all conditionals to this graph // Traverse the BayesTree and add all conditionals to this graph
int data = 0; // Unused int data = 0; // Unused
_pushCliqueFunctor<FactorType,CLIQUE> functor(graph); _pushCliqueFunctor<FactorType, CLIQUE> functor(graph);
treeTraversal::DepthFirstForest(*this, data, functor); // FIXME: sort of works? treeTraversal::DepthFirstForest(*this, data, functor);
// treeTraversal::DepthFirstForest(*this, data, boost::bind(&_pushClique<FactorType,CLIQUE>, boost::ref(graph), _1));
} }
/* ************************************************************************* */ /* ************************************************************************* */
@ -434,51 +427,51 @@ namespace gtsam {
} }
/* ************************************************************************* */ /* ************************************************************************* */
template<class CLIQUE> template <class CLIQUE>
void BayesTree<CLIQUE>::removePath(sharedClique clique, BayesNetType& bn, Cliques& orphans) void BayesTree<CLIQUE>::removePath(sharedClique clique, BayesNetType* bn,
{ Cliques* orphans) {
// base case is NULL, if so we do nothing and return empties above // base case is NULL, if so we do nothing and return empties above
if (clique) { if (clique) {
// remove the clique from orphans in case it has been added earlier // remove the clique from orphans in case it has been added earlier
orphans.remove(clique); orphans->remove(clique);
// remove me // remove me
this->removeClique(clique); this->removeClique(clique);
// remove path above me // remove path above me
this->removePath(typename Clique::shared_ptr(clique->parent_.lock()), bn, orphans); this->removePath(typename Clique::shared_ptr(clique->parent_.lock()), bn,
orphans);
// add children to list of orphans (splice also removed them from clique->children_) // add children to list of orphans (splice also removed them from
orphans.insert(orphans.begin(), clique->children.begin(), clique->children.end()); // clique->children_)
orphans->insert(orphans->begin(), clique->children.begin(),
clique->children.end());
clique->children.clear(); clique->children.clear();
bn.push_back(clique->conditional_); bn->push_back(clique->conditional_);
} }
} }
/* ************************************************************************* */ /* *************************************************************************
template<class CLIQUE> */
void BayesTree<CLIQUE>::removeTop(const KeyVector& keys, BayesNetType& bn, Cliques& orphans) template <class CLIQUE>
{ void BayesTree<CLIQUE>::removeTop(const KeyVector& keys, BayesNetType* bn,
Cliques* orphans) {
gttic(removetop); gttic(removetop);
// process each key of the new factor // process each key of the new factor
for(const Key& j: keys) for (const Key& j : keys) {
{
// get the clique // get the clique
// TODO: Nodes will be searched again in removeClique // TODO(frank): Nodes will be searched again in removeClique
typename Nodes::const_iterator node = nodes_.find(j); typename Nodes::const_iterator node = nodes_.find(j);
if(node != nodes_.end()) { if (node != nodes_.end()) {
// remove path from clique to root // remove path from clique to root
this->removePath(node->second, bn, orphans); this->removePath(node->second, bn, orphans);
} }
} }
// Delete cachedShortcuts for each orphan subtree // Delete cachedShortcuts for each orphan subtree
//TODO: Consider Improving // TODO(frank): Consider Improving
for(sharedClique& orphan: orphans) for (sharedClique& orphan : *orphans) orphan->deleteCachedShortcuts();
orphan->deleteCachedShortcuts();
} }
/* ************************************************************************* */ /* ************************************************************************* */

27
gtsam/inference/BayesTree.h
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@ -208,13 +208,13 @@ namespace gtsam {
* Remove path from clique to root and return that path as factors * Remove path from clique to root and return that path as factors
* plus a list of orphaned subtree roots. Used in removeTop below. * plus a list of orphaned subtree roots. Used in removeTop below.
*/ */
void removePath(sharedClique clique, BayesNetType& bn, Cliques& orphans); void removePath(sharedClique clique, BayesNetType* bn, Cliques* orphans);
/** /**
* Given a list of indices, turn "contaminated" part of the tree back into a factor graph. * Given a list of indices, turn "contaminated" part of the tree back into a factor graph.
* Factors and orphans are added to the in/out arguments. * Factors and orphans are added to the in/out arguments.
*/ */
void removeTop(const KeyVector& keys, BayesNetType& bn, Cliques& orphans); void removeTop(const KeyVector& keys, BayesNetType* bn, Cliques* orphans);
/** /**
* Remove the requested subtree. */ * Remove the requested subtree. */
@ -229,7 +229,7 @@ namespace gtsam {
void addClique(const sharedClique& clique, const sharedClique& parent_clique = sharedClique()); void addClique(const sharedClique& clique, const sharedClique& parent_clique = sharedClique());
/** Add all cliques in this BayesTree to the specified factor graph */ /** Add all cliques in this BayesTree to the specified factor graph */
void addFactorsToGraph(FactorGraph<FactorType>& graph) const; void addFactorsToGraph(FactorGraph<FactorType>* graph) const;
protected: protected:
@ -238,7 +238,7 @@ namespace gtsam {
int parentnum = 0) const; int parentnum = 0) const;
/** Gather data on a single clique */ /** Gather data on a single clique */
void getCliqueData(BayesTreeCliqueData& stats, sharedClique clique) const; void getCliqueData(sharedClique clique, BayesTreeCliqueData* stats) const;
/** remove a clique: warning, can result in a forest */ /** remove a clique: warning, can result in a forest */
void removeClique(sharedClique clique); void removeClique(sharedClique clique);
@ -249,6 +249,25 @@ namespace gtsam {
// Friend JunctionTree because it directly fills roots and nodes index. // Friend JunctionTree because it directly fills roots and nodes index.
template<class BAYESRTEE, class GRAPH> friend class EliminatableClusterTree; template<class BAYESRTEE, class GRAPH> friend class EliminatableClusterTree;
#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V4
public:
/// @name Deprecated
/// @{
void removePath(sharedClique clique, BayesNetType& bn, Cliques& orphans) {
removePath(clique, &bn, &orphans);
}
void removeTop(const KeyVector& keys, BayesNetType& bn, Cliques& orphans) {
removeTop(keys, &bn, &orphans);
}
void getCliqueData(BayesTreeCliqueData& stats, sharedClique clique) const {
getCliqueData(clique, &stats);
}
void addFactorsToGraph(FactorGraph<FactorType>& graph) const{
addFactorsToGraph(& graph);
}
/// @}
#endif
private: private:
/** Serialization function */ /** Serialization function */
friend class boost::serialization::access; friend class boost::serialization::access;

2
gtsam/inference/FactorGraph.h
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@ -270,7 +270,7 @@ class FactorGraph {
typename std::enable_if< typename std::enable_if<
std::is_base_of<This, typename CLIQUE::FactorGraphType>::value>::type std::is_base_of<This, typename CLIQUE::FactorGraphType>::value>::type
push_back(const BayesTree<CLIQUE>& bayesTree) { push_back(const BayesTree<CLIQUE>& bayesTree) {
bayesTree.addFactorsToGraph(*this); bayesTree.addFactorsToGraph(this);
} }
/** /**

10
gtsam/inference/ISAM-inst.h
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@ -24,14 +24,14 @@ namespace gtsam {
/* ************************************************************************* */ /* ************************************************************************* */
template<class BAYESTREE> template<class BAYESTREE>
void ISAM<BAYESTREE>::update_internal(const FactorGraphType& newFactors, void ISAM<BAYESTREE>::updateInternal(const FactorGraphType& newFactors,
Cliques& orphans, const Eliminate& function) { Cliques* orphans, const Eliminate& function) {
// Remove the contaminated part of the Bayes tree // Remove the contaminated part of the Bayes tree
BayesNetType bn; BayesNetType bn;
const KeySet newFactorKeys = newFactors.keys(); const KeySet newFactorKeys = newFactors.keys();
if (!this->empty()) { if (!this->empty()) {
KeyVector keyVector(newFactorKeys.begin(), newFactorKeys.end()); KeyVector keyVector(newFactorKeys.begin(), newFactorKeys.end());
this->removeTop(keyVector, bn, orphans); this->removeTop(keyVector, &bn, orphans);
} }
// Add the removed top and the new factors // Add the removed top and the new factors
@ -40,7 +40,7 @@ void ISAM<BAYESTREE>::update_internal(const FactorGraphType& newFactors,
factors += newFactors; factors += newFactors;
// Add the orphaned subtrees // Add the orphaned subtrees
for (const sharedClique& orphan : orphans) for (const sharedClique& orphan : *orphans)
factors += boost::make_shared<BayesTreeOrphanWrapper<Clique> >(orphan); factors += boost::make_shared<BayesTreeOrphanWrapper<Clique> >(orphan);
// Get an ordering where the new keys are eliminated last // Get an ordering where the new keys are eliminated last
@ -62,7 +62,7 @@ template<class BAYESTREE>
void ISAM<BAYESTREE>::update(const FactorGraphType& newFactors, void ISAM<BAYESTREE>::update(const FactorGraphType& newFactors,
const Eliminate& function) { const Eliminate& function) {
Cliques orphans; Cliques orphans;
this->update_internal(newFactors, orphans, function); this->updateInternal(newFactors, &orphans, function);
} }
} }

43
gtsam/inference/ISAM.h
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@ -22,16 +22,14 @@
namespace gtsam { namespace gtsam {
/** /**
* A Bayes tree with an update methods that implements the iSAM algorithm. * A Bayes tree with an update methods that implements the iSAM algorithm.
* Given a set of new factors, it re-eliminates the invalidated part of the tree. * Given a set of new factors, it re-eliminates the invalidated part of the
* \nosubgrouping * tree. \nosubgrouping
*/ */
template<class BAYESTREE> template <class BAYESTREE>
class ISAM: public BAYESTREE class ISAM : public BAYESTREE {
{
public: public:
typedef BAYESTREE Base; typedef BAYESTREE Base;
typedef typename Base::BayesNetType BayesNetType; typedef typename Base::BayesNetType BayesNetType;
typedef typename Base::FactorGraphType FactorGraphType; typedef typename Base::FactorGraphType FactorGraphType;
@ -40,12 +38,10 @@ namespace gtsam {
typedef typename Base::Cliques Cliques; typedef typename Base::Cliques Cliques;
private: private:
typedef typename Base::Eliminate Eliminate; typedef typename Base::Eliminate Eliminate;
typedef typename Base::EliminationTraitsType EliminationTraitsType; typedef typename Base::EliminationTraitsType EliminationTraitsType;
public: public:
/// @name Standard Constructors /// @name Standard Constructors
/// @{ /// @{
@ -53,25 +49,40 @@ namespace gtsam {
ISAM() {} ISAM() {}
/** Copy constructor */ /** Copy constructor */
ISAM(const Base& bayesTree) : Base(bayesTree) {} explicit ISAM(const Base& bayesTree) : Base(bayesTree) {}
/// @} /// @}
/// @name Advanced Interface Interface /// @name Advanced Interface Interface
/// @{ /// @{
/** /**
* update the Bayes tree with a set of new factors, typically derived from measurements * update the Bayes tree with a set of new factors, typically derived from
* measurements
* @param newFactors is a factor graph that contains the new factors * @param newFactors is a factor graph that contains the new factors
* @param function an elimination routine * @param function an elimination routine
*/ */
void update(const FactorGraphType& newFactors, const Eliminate& function = EliminationTraitsType::DefaultEliminate); void update(
const FactorGraphType& newFactors,
const Eliminate& function = EliminationTraitsType::DefaultEliminate);
/** update_internal provides access to list of orphans for drawing purposes */ /** updateInternal provides access to list of orphans for drawing purposes
void update_internal(const FactorGraphType& newFactors, Cliques& orphans, */
void updateInternal(
const FactorGraphType& newFactors, Cliques* orphans,
const Eliminate& function = EliminationTraitsType::DefaultEliminate); const Eliminate& function = EliminationTraitsType::DefaultEliminate);
/// @} /// @}
}; #ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V4
/// @name Deprecated
/// @{
void update_internal(
const FactorGraphType& newFactors, Cliques& orphans,
const Eliminate& function = EliminationTraitsType::DefaultEliminate) {
updateInternal(newFactors, &orphans, function);
}
/// @}
#endif
};
}/// namespace gtsam } // namespace gtsam