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Re-enabled computing marginals of a set of variables (Inference::Marginal(...))

release/4.3a0
Richard Roberts 2010-10-10 00:51:57 +00:00
parent 5be0bf6e28
commit 84d6b5be6a
11 changed files with 286 additions and 211 deletions
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406
.cproject
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@ -21,7 +21,7 @@
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@ -322,6 +322,14 @@
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@ -348,7 +356,6 @@
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@ -356,7 +363,6 @@
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@ -404,7 +410,6 @@
</target>
<target name="testSymbolicBayesNet.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
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@ -412,7 +417,6 @@
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@ -420,7 +424,6 @@
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@ -436,20 +439,11 @@
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<buildCommand>make</buildCommand>
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<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
@ -484,6 +478,7 @@
</target>
<target name="testGraph.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
<buildTarget>testGraph.run</buildTarget>
<stopOnError>true</stopOnError>
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@ -579,6 +574,7 @@
</target>
<target name="testInference.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
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@ -586,6 +582,7 @@
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<buildCommand>make</buildCommand>
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@ -593,6 +590,7 @@
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<target name="testGaussianFactor.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
<buildTarget>testGaussianFactor.run</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -600,6 +598,7 @@
</target>
<target name="testJunctionTree.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
<buildTarget>testJunctionTree.run</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -607,6 +606,7 @@
</target>
<target name="testSymbolicBayesNet.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
<buildTarget>testSymbolicBayesNet.run</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -614,6 +614,7 @@
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<target name="testSymbolicFactorGraph.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
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@ -811,6 +812,14 @@
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<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
@ -909,7 +918,6 @@
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<buildCommand>make</buildCommand>
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@ -1245,6 +1253,7 @@
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@ -1284,6 +1293,7 @@
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@ -1291,6 +1301,7 @@
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<buildCommand>make</buildCommand>
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@ -1338,6 +1349,7 @@
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@ -1359,86 +1371,6 @@
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<buildCommand>make</buildCommand>
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@ -1535,6 +1467,86 @@
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<runAllBuilders>true</runAllBuilders>
</target>
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<runAllBuilders>true</runAllBuilders>
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<buildArguments>-j2</buildArguments>
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<buildCommand>make</buildCommand>
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<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
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<runAllBuilders>true</runAllBuilders>
</target>
<target name="linear/tests/testGaussianJunctionTree" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
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</target>
<target name="check" path="build" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
@ -1889,6 +1901,14 @@
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="testGaussianFactor.run" path="linear/tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>testGaussianFactor.run</buildTarget>
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<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
@ -1915,7 +1935,6 @@
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<target name="tests/testBayesTree.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
<buildTarget>tests/testBayesTree.run</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -1923,7 +1942,6 @@
</target>
<target name="testBinaryBayesNet.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
<buildTarget>testBinaryBayesNet.run</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -1971,7 +1989,6 @@
</target>
<target name="testSymbolicBayesNet.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildArguments/>
<buildTarget>testSymbolicBayesNet.run</buildTarget>
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@ -1979,7 +1996,6 @@
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<target name="tests/testSymbolicFactor.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
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@ -1987,7 +2003,6 @@
</target>
<target name="testSymbolicFactorGraph.run" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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@ -2003,20 +2018,11 @@
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<target name="tests/testBayesTree" path="inference" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildArguments/>
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<buildArguments>-j2</buildArguments>
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<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
@ -2051,6 +2057,7 @@
</target>
<target name="testGraph.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
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<stopOnError>true</stopOnError>
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@ -2146,6 +2153,7 @@
</target>
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@ -2153,6 +2161,7 @@
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<target name="testGaussianBayesNet.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<stopOnError>true</stopOnError>
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@ -2160,6 +2169,7 @@
</target>
<target name="testGaussianFactor.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
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<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -2167,6 +2177,7 @@
</target>
<target name="testJunctionTree.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
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<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -2174,6 +2185,7 @@
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<target name="testSymbolicBayesNet.run" path="tests" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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@ -2181,6 +2193,7 @@
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@ -2378,6 +2391,14 @@
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@ -2476,7 +2497,6 @@
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@ -2812,6 +2832,7 @@
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<buildTarget>testSimulated2DOriented.run</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -2851,6 +2872,7 @@
</target>
<target name="testSimulated2D.run" path="slam" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
<buildTarget>testSimulated2D.run</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -2858,6 +2880,7 @@
</target>
<target name="testSimulated3D.run" path="slam" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
<buildTarget>testSimulated3D.run</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -2905,6 +2928,7 @@
</target>
<target name="tests/testGaussianISAM2" path="build/slam" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments/>
<buildTarget>tests/testGaussianISAM2</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>false</useDefaultCommand>
@ -2926,86 +2950,6 @@
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="install" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>install</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="clean" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>clean</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="check" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>check</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="all" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>all</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="dist" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>dist</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="inference/tests/testEliminationTree" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>inference/tests/testEliminationTree</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="slam/tests/testGaussianISAM2" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>slam/tests/testGaussianISAM2</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="inference/tests/testVariableIndex" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>inference/tests/testVariableIndex</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="inference/tests/testJunctionTree" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>inference/tests/testJunctionTree</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="linear/tests/testGaussianJunctionTree" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>linear/tests/testGaussianJunctionTree</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="testRot3.run" path="geometry" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
@ -3102,6 +3046,86 @@
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="install" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>install</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="clean" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>clean</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="check" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>check</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="all" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>all</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="dist" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>dist</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="inference/tests/testEliminationTree" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>inference/tests/testEliminationTree</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="slam/tests/testGaussianISAM2" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>slam/tests/testGaussianISAM2</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="inference/tests/testVariableIndex" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>inference/tests/testVariableIndex</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="inference/tests/testJunctionTree" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>inference/tests/testJunctionTree</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="linear/tests/testGaussianJunctionTree" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>
<buildTarget>linear/tests/testGaussianJunctionTree</buildTarget>
<stopOnError>true</stopOnError>
<useDefaultCommand>true</useDefaultCommand>
<runAllBuilders>true</runAllBuilders>
</target>
<target name="check" path="build" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
<buildCommand>make</buildCommand>
<buildArguments>-j2</buildArguments>

2
.project
View File

@ -23,7 +23,7 @@
</dictionary>
<dictionary>
<key>org.eclipse.cdt.make.core.buildArguments</key>
<value>-j2</value>
<value></value>
</dictionary>
<dictionary>
<key>org.eclipse.cdt.make.core.buildCommand</key>

8
inference/BayesNet.h
View File

@ -102,8 +102,14 @@ namespace gtsam {
/** SLOW O(n) random access to Conditional by key */
sharedConditional operator[](varid_t key) const;
/** return last node in ordering */
sharedConditional& front() { return conditionals_.front(); }
/** return last node in ordering */
boost::shared_ptr<const Conditional> front() const { return conditionals_.front(); }
/** return last node in ordering */
inline sharedConditional& back() { return conditionals_.back(); }
sharedConditional& back() { return conditionals_.back(); }
/** return last node in ordering */
boost::shared_ptr<const Conditional> back() const { return conditionals_.back(); }

35
inference/inference-inl.h
View File

@ -276,6 +276,41 @@ Inference::EliminateOne(FactorGraph& factorGraph, typename FactorGraph::variable
}
}
/* ************************************************************************* */
template<class FactorGraph, class VarContainer>
typename FactorGraph::bayesnet_type::shared_ptr Inference::Marginal(const FactorGraph& factorGraph, const VarContainer& variables) {
// Compute a COLAMD permutation with the marginal variables constrained to the end
typename FactorGraph::variableindex_type varIndex(factorGraph);
Permutation::shared_ptr permutation(Inference::PermutationCOLAMD(varIndex, variables));
Permutation::shared_ptr permutationInverse(permutation->inverse());
// Copy and permute the factors
varIndex.permute(*permutation);
FactorGraph eliminationGraph; eliminationGraph.reserve(factorGraph.size());
BOOST_FOREACH(const typename FactorGraph::sharedFactor& factor, factorGraph) {
typename FactorGraph::sharedFactor permFactor(new typename FactorGraph::factor_type(*factor));
permFactor->permuteWithInverse(*permutationInverse);
eliminationGraph.push_back(permFactor);
}
// Eliminate all variables
typename FactorGraph::bayesnet_type::shared_ptr bn(Inference::Eliminate(eliminationGraph, varIndex));
// The last conditionals in the eliminated BayesNet contain the marginal for
// the variables we want.
typename FactorGraph::bayesnet_type::shared_ptr marginal(new typename FactorGraph::bayesnet_type());
typename FactorGraph::bayesnet_type::const_reverse_iterator conditional = bn->rbegin();
for(varid_t j=0; j<variables.size(); ++j, ++conditional) {
marginal->push_front(*conditional);
assert(std::find(variables.begin(), variables.end(), (*permutation)[(*conditional)->key()]) != variables.end());
}
// Undo the permutation
marginal->permuteWithInverse(*permutation);
return marginal;
}
/* ************************************************************************* */
template<class VariableIndexType, typename ConstraintContainer>
Permutation::shared_ptr Inference::PermutationCOLAMD(const VariableIndexType& variableIndex, const ConstraintContainer& constrainLast) {

11
inference/inference.h
View File

@ -85,6 +85,17 @@ class Conditional;
static boost::shared_ptr<Conditional>
EliminateOneSymbolic(FactorGraph<Factor>& factorGraph, VariableIndex<>& variableIndex, varid_t var);
/**
* Eliminate all variables except the specified ones. Internally this
* permutes these variables to the end of the ordering, eliminates all
* other variables, and then undoes the permutation. This is
* inefficient if multiple marginals are needed - in that case use the
* BayesTree which supports efficiently computing marginals for multiple
* variables.
*/
template<class FactorGraph, class VarContainer>
static typename FactorGraph::bayesnet_type::shared_ptr Marginal(const FactorGraph& factorGraph, const VarContainer& variables);
/**
* Compute a permutation (variable ordering) using colamd
*/

2
myconfigure
View File

@ -1,4 +1,4 @@
../configure --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CPP="/opt/local/bin/cpp-mp-4.5" CC="/opt/local/bin/gcc-mp-4.5" CXX="/usr/local/bin/gfilt" CXXFLAGS="-fno-inline -g -Wall -D_GLIBCXX_DEBUG" CFLAGS="-fno-inline -g -Wall -D_GLIBCXX_DEBUG" LDFLAGS="-fno-inline -g -Wall" --disable-static --enable-blas --enable-lapack --disable-fast-install
../configure --prefix=$HOME/borg --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CPP="/opt/local/bin/cpp-mp-4.5" CC="/opt/local/bin/gcc-mp-4.5" CXX="/usr/local/bin/gfilt" CPPFLAGS="-fno-inline -g -Wall -D_GLIBCXX_DEBUG" LDFLAGS="-fno-inline -g -Wall" --disable-static --enable-blas --enable-lapack --disable-fast-install
#../configure --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CPP="/opt/local/bin/cpp-mp-4.5" CC="/opt/local/bin/gcc-mp-4.5" CXX="/usr/local/bin/gfilt" CXXFLAGS="-fno-inline -g -Wall -D_GLIBCXX_DEBUG -DNDEBUG" CFLAGS="-fno-inline -g -Wall -D_GLIBCXX_DEBUG -DNDEBUG" LDFLAGS="-fno-inline -g -Wall" --disable-static --enable-blas --enable-lapack --disable-fast-install
#cd build && ../configure --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CXXFLAGS="-fno-inline -g -DNDEBUG -O3" CFLAGS="-fno-inline -g -DNDEBUG -O3" LDFLAGS="-fno-inline -g -DNDEBUG -O3" --disable-static --enable-blas --enable-lapack
#cd build && ../configure --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CXXFLAGS="-DNDEBUG -O3" CFLAGS="-g -DNDEBUG -O3" LDFLAGS="-DNDEBUG -O3" --disable-static --enable-blas --enable-lapack

2
myconfigure.profiling
View File

@ -1,3 +1,3 @@
#../configure --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CXXFLAGS="-fno-inline -g -DNDEBUG -O3" CFLAGS="-fno-inline -g -DNDEBUG -O3" LDFLAGS="-fno-inline -g -DNDEBUG -O3" --disable-static --enable-blas --enable-lapack
#../configure --disable-fast-install --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CXXFLAGS="-fno-inline -g -D_GLIBCXX_DEBUG -DNDEBUG" CFLAGS="-fno-inline -g -D_GLIBCXX_DEBUG -DNDEBUG" LDFLAGS="-fno-inline -g " --disable-static --enable-blas --enable-lapack
../configure --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CXXFLAGS="-g -DNDEBUG -O3" CFLAGS="-g -DNDEBUG -O3" LDFLAGS="-g -DNDEBUG -O3" --disable-static --enable-blas --enable-lapack
../configure --prefix=$HOME/borg --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CPPFLAGS="-g -DNDEBUG -O3" LDFLAGS="-g -DNDEBUG -O3" --disable-static --enable-blas --enable-lapack

2
myconfigure.timing
View File

@ -1,2 +1,2 @@
../configure --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CPP="/opt/local/bin/cpp-mp-4.5" CC="/opt/local/bin/gcc-mp-4.5" CXX="/opt/local/bin/g++-mp-4.5" CPPFLAGS="-DENABLE_TIMING -DNDEBUG -O3" LDFLAGS="-DNDEBUG -O3" --disable-static --enable-blas --enable-lapack
../configure --prefix=$HOME/borg --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CPP="/opt/local/bin/cpp-mp-4.5" CC="/opt/local/bin/gcc-mp-4.5" CXX="/opt/local/bin/g++-mp-4.5" CPPFLAGS="-DENABLE_TIMING -DNDEBUG -O3" LDFLAGS="-DNDEBUG -O3" --disable-static --enable-blas --enable-lapack
#../configure --prefix=$HOME/borg-simplelinear --with-toolbox=$HOME/toolbox/ --with-boost=/opt/local/include/ CPP="/opt/local/bin/cpp-mp-4.5" CC="/opt/local/bin/gcc-mp-4.5" CXX="/opt/local/bin/g++-mp-4.5" CXXFLAGS="-DNDEBUG -g" CFLAGS="-DNDEBUG -g" LDFLAGS="-DNDEBUG -g" --disable-static --enable-blas --enable-lapack

4
slam/smallExample.cpp
View File

@ -171,8 +171,8 @@ namespace example {
tau(0) = 1.0;
// define nodes and specify in reverse topological sort (i.e. parents last)
GaussianConditional::shared_ptr Px_y(new GaussianConditional(_x_, d1, R11,
_y_, S12, tau)), Py(new GaussianConditional(_y_, d2, R22, tau));
GaussianConditional::shared_ptr Px_y(new GaussianConditional(_x_, d1, R11, _y_, S12, tau));
GaussianConditional::shared_ptr Py(new GaussianConditional(_y_, d2, R22, tau));
GaussianBayesNet cbn;
cbn.push_back(Px_y);
cbn.push_back(Py);

2
tests/Makefile.am
View File

@ -12,7 +12,7 @@ check_PROGRAMS =
check_PROGRAMS += testGaussianBayesNet testGaussianFactor testGaussianFactorGraph
check_PROGRAMS += testGaussianISAM
check_PROGRAMS += testGraph
#check_PROGRAMS += testInference
check_PROGRAMS += testInference
#check_PROGRAMS += testIterative
check_PROGRAMS += testGaussianJunctionTree
check_PROGRAMS += testNonlinearEquality testNonlinearFactor testNonlinearFactorGraph

23
tests/testInference.cpp
View File

@ -23,15 +23,17 @@ using namespace example;
/* ************************************************************************* */
TEST(GaussianFactorGraph, createSmoother)
{
GaussianFactorGraph fg2 = createSmoother(3);
GaussianFactorGraph fg2;
Ordering ordering;
boost::tie(fg2,ordering) = createSmoother(3);
LONGS_EQUAL(5,fg2.size());
// eliminate
Ordering ordering;
GaussianBayesNet bayesNet = fg2.eliminate(ordering);
FactorGraph<GaussianFactor> p_x3 = marginalize<GaussianFactor,GaussianConditional>(bayesNet, Ordering("x3"));
FactorGraph<GaussianFactor> p_x1 = marginalize<GaussianFactor,GaussianConditional>(bayesNet, Ordering("x1"));
CHECK(assert_equal(p_x1,p_x3)); // should be the same because of symmetry
list<varid_t> x3var; x3var.push_back(ordering["x3"]);
list<varid_t> x1var; x1var.push_back(ordering["x1"]);
GaussianBayesNet p_x3 = *Inference::Marginal(fg2, x3var);
GaussianBayesNet p_x1 = *Inference::Marginal(fg2, x1var);
CHECK(assert_equal(*p_x1.back(),*p_x3.front())); // should be the same because of symmetry
}
/* ************************************************************************* */
@ -39,14 +41,11 @@ TEST( Inference, marginals )
{
// create and marginalize a small Bayes net on "x"
GaussianBayesNet cbn = createSmallGaussianBayesNet();
Ordering keys("x");
FactorGraph<GaussianFactor> fg = marginalize<GaussianFactor, GaussianConditional>(cbn,keys);
// turn into Bayes net to test easily
BayesNet<GaussianConditional> actual = eliminate<GaussianFactor,GaussianConditional>(fg,keys);
list<varid_t> xvar; xvar.push_back(0);
GaussianBayesNet actual = *Inference::Marginal(GaussianFactorGraph(cbn), xvar);
// expected is just scalar Gaussian on x
GaussianBayesNet expected = scalarGaussian("x", 4, sqrt(2));
GaussianBayesNet expected = scalarGaussian(0, 4, sqrt(2));
CHECK(assert_equal(expected,actual));
}