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General improvements for GM handling #1

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General improvements for GM handling #1

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328f6d2
Allow saving GMs in OpenGM format
fgrsnau Mar 29, 2018
baaf6a2
Adjust PairwiseFactorContainer to match LP_MP
fgrsnau Apr 10, 2018
22ce444
Get rid of MrfHasTripletFactors trait
fgrsnau Apr 17, 2018
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150 changes: 99 additions & 51 deletions include/hdf5_routines.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -164,71 +164,119 @@ namespace LP_MP {
}
*/

template<typename MRF_CONSTRUCTOR>
bool ParseGM(const std::string filename, MRF_CONSTRUCTOR& mrf)
{
typedef double ValueType;
typedef size_t IndexType;
typedef size_t LabelType;
typedef opengm::Adder OperatorType;
typedef opengm::Minimizer AccumulatorType;
typedef opengm::DiscreteSpace<IndexType, LabelType> SpaceType;
namespace opengm_mrf_types {
typedef double ValueType;
typedef size_t IndexType;
typedef size_t LabelType;
typedef opengm::Adder OperatorType;
typedef opengm::Minimizer AccumulatorType;
typedef opengm::DiscreteSpace<IndexType, LabelType> SpaceType;

// Set functions for graphical model
typedef opengm::meta::TypeListGenerator<
opengm::ExplicitFunction<ValueType, IndexType, LabelType>,
opengm::PottsFunction<ValueType, IndexType, LabelType>,
opengm::PottsNFunction<ValueType, IndexType, LabelType>,
opengm::PottsGFunction<ValueType, IndexType, LabelType>,
opengm::TruncatedSquaredDifferenceFunction<ValueType, IndexType, LabelType>,
opengm::TruncatedAbsoluteDifferenceFunction<ValueType, IndexType, LabelType>
>::type FunctionTypeList;
typedef opengm::meta::TypeListGenerator<
opengm::ExplicitFunction<ValueType, IndexType, LabelType>,
opengm::PottsFunction<ValueType, IndexType, LabelType>,
opengm::PottsNFunction<ValueType, IndexType, LabelType>,
opengm::PottsGFunction<ValueType, IndexType, LabelType>,
opengm::TruncatedSquaredDifferenceFunction<ValueType, IndexType, LabelType>,
opengm::TruncatedAbsoluteDifferenceFunction<ValueType, IndexType, LabelType>
>::type FunctionTypeList;

typedef opengm::GraphicalModel<
ValueType,
OperatorType,
FunctionTypeList,
SpaceType
> GmType;
}

typedef opengm::GraphicalModel<
ValueType,
OperatorType,
FunctionTypeList,
SpaceType
> GmType;

template<typename MRF_CONSTRUCTOR>
bool ParseGM(const std::string filename, MRF_CONSTRUCTOR& mrf)
{
using namespace opengm_mrf_types;

GmType gm;
opengm::hdf5::load(gm, filename,"gm");
GmType gm;
::opengm::hdf5::load(gm, filename, "gm");

for(INDEX f=0; f<gm.numberOfFactors(); ++f){
for(INDEX f=0; f<gm.numberOfFactors(); ++f){

if(gm[f].numberOfVariables()==0){
// ignore for now
}
else if(gm[f].numberOfVariables()==1){
const INDEX i = gm.variableOfFactor(f,0);
std::vector<REAL> unaryCost(gm[f].numberOfLabels(0));
for(INDEX l=0; l<gm[f].numberOfLabels(0); ++l){
unaryCost[l] = gm[f](std::array<INDEX,1>({l}).begin());
if(gm[f].numberOfVariables()==0){
// ignore for now
}
else if(gm[f].numberOfVariables()==1){
const INDEX i = gm.variableOfFactor(f,0);
std::vector<REAL> unaryCost(gm[f].numberOfLabels(0));
for(INDEX l=0; l<gm[f].numberOfLabels(0); ++l){
unaryCost[l] = gm[f](std::array<INDEX,1>({l}).begin());
}
mrf.AddUnaryFactor(i,unaryCost);
}
mrf.AddUnaryFactor(i,unaryCost);
}
else if(gm[f].numberOfVariables()==2){
const INDEX i = gm.variableOfFactor(f,0);
const INDEX j = gm.variableOfFactor(f,1);
matrix<REAL> pairwiseCost(gm[f].numberOfLabels(0), gm[f].numberOfLabels(1));//gm[f].size());
for(INDEX l1=0; l1<gm[f].numberOfLabels(0); ++l1){
for(INDEX l2=0; l2<gm[f].numberOfLabels(1); ++l2){
pairwiseCost(l1, l2) = gm[f](std::array<INDEX,2>({l1,l2}).begin());
else if(gm[f].numberOfVariables()==2){
const INDEX i = gm.variableOfFactor(f,0);
const INDEX j = gm.variableOfFactor(f,1);
matrix<REAL> pairwiseCost(gm[f].numberOfLabels(0), gm[f].numberOfLabels(1));//gm[f].size());
for(INDEX l1=0; l1<gm[f].numberOfLabels(0); ++l1){
for(INDEX l2=0; l2<gm[f].numberOfLabels(1); ++l2){
pairwiseCost(l1, l2) = gm[f](std::array<INDEX,2>({l1,l2}).begin());
}
}
mrf.AddPairwiseFactor(i,j,pairwiseCost);
}
else{
std::cout << "Factors of order higher than 2 are so far not supported !" <<std::endl;
return 1;
}
mrf.AddPairwiseFactor(i,j,pairwiseCost);
}
else{
std::cout << "Factors of order higher than 2 are so far not supported !" <<std::endl;
return 1;
}

return true;
}

template<typename MRF_CONSTRUCTOR>
bool WriteGM(const std::string filename, MRF_CONSTRUCTOR& mrf)
{
using namespace opengm_mrf_types;
GmType gm;

// TODO: Handle constant term (future commit...).

for (INDEX i = 0; i < mrf.GetNumberOfVariables(); ++i) {
INDEX gm_i = gm.addVariable(mrf.GetNumberOfLabels(i)); assert(gm_i == i);
std::array<IndexType, 1> variables { i };
std::array<IndexType, 1> space { mrf.GetNumberOfLabels(i) };
opengm::ExplicitFunction<ValueType, IndexType, LabelType> f(space.begin(), space.end());
for (INDEX j = 0; j < mrf.GetNumberOfLabels(i); ++j)
f(j) = mrf.GetUnaryFactor(i)->GetFactor()->operator[](j);
gm.addFactor(gm.addFunction(f), variables.begin(), variables.end());
}

return true;
for (INDEX i = 0; i < mrf.GetNumberOfPairwiseFactors(); ++i) {
auto variables = mrf.GetPairwiseVariables(i);
std::array<IndexType, 2> space {
mrf.GetNumberOfLabels(variables[0]),
mrf.GetNumberOfLabels(variables[1]) };
opengm::ExplicitFunction<ValueType, IndexType, LabelType> f(space.begin(), space.begin() + 2);
for (INDEX j = 0; j < mrf.GetNumberOfLabels(variables[0]); ++j)
for (INDEX k = 0; k < mrf.GetNumberOfLabels(variables[1]); ++k)
f(j, k) = mrf.GetPairwiseFactor(i)->GetFactor()->operator()(j, k);
gm.addFactor(gm.addFunction(f), variables.begin(), variables.end());
}

if constexpr (mrf.arity() >= 3) {
for (INDEX i = 0; i < mrf.GetNumberOfTripletFactors(); ++i) {
auto variables = mrf.GetTripletIndices(i);
std::array<IndexType, 3> space {
mrf.GetNumberOfLabels(variables[0]),
mrf.GetNumberOfLabels(variables[1]),
mrf.GetNumberOfLabels(variables[2]) };
opengm::ExplicitFunction<ValueType, IndexType, LabelType> f(space.begin(), space.begin() + 2);
for (INDEX j = 0; j < mrf.GetNumberOfLabels(variables[0]); ++j)
for (INDEX k = 0; k < mrf.GetNumberOfLabels(variables[1]); ++k)
for (INDEX l = 0; l < mrf.GetNumberOfLabels(variables[2]); ++l)
f(j, k, l) = mrf.GetPairwiseFactor(i)->GetFactor()->operator()(j, k, l);
gm.addFactor(gm.addFunction(f), variables.begin(), variables.end());
}
}

opengm::hdf5::save(gm, filename, "gm");
}

template<typename MRF_CONSTRUCTOR>
Expand Down
14 changes: 11 additions & 3 deletions include/mrf_problem_construction.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -70,16 +70,16 @@ public:
}
unaryFactor_[node_number] = u;
}
template<typename COST>
PairwiseFactorContainer* AddPairwiseFactor(INDEX var1, INDEX var2, const COST& cost)
template<typename... ARGS>
PairwiseFactorContainer* AddPairwiseFactor(INDEX var1, INDEX var2, ARGS... args)
{
//if(var1 > var2) std::swap(var1,var2);
assert(var1<var2);
assert(!HasPairwiseFactor(var1,var2));
//assert(cost.size() == GetNumberOfLabels(var1) * GetNumberOfLabels(var2));
//assert(pairwiseMap_.find(std::make_tuple(var1,var2)) == pairwiseMap_.end());
//PairwiseFactorContainer* p = new PairwiseFactorContainer(PairwiseFactor(cost), cost);
auto* p = new PairwiseFactorContainer(GetNumberOfLabels(var1), GetNumberOfLabels(var2), cost);
auto* p = new PairwiseFactorContainer(GetNumberOfLabels(var1), GetNumberOfLabels(var2), args...);
lp_->AddFactor(p);
ConstructPairwiseFactor(*(p->GetFactor()), var1, var2);
pairwiseFactor_.push_back(p);
Expand Down Expand Up @@ -348,6 +348,10 @@ public:
return std::move(trees);
}

constexpr INDEX arity() {
return 2;
}

protected:
std::vector<UnaryFactorContainer*> unaryFactor_;
std::vector<PairwiseFactorContainer*> pairwiseFactor_;
Expand Down Expand Up @@ -719,6 +723,10 @@ public:
return no_triplets_added;
}

constexpr INDEX arity() {
return 3;
}


protected:
std::vector<TripletFactorContainer*> tripletFactor_;
Expand Down