CMake: External mixmod

CMakeLists.txt

@@ -33,6 +33,8 @@ if (NOT DEFINED OPENTURNS_PYTHON_MODULE_PATH)
   set (OPENTURNS_PYTHON_MODULE_PATH ${OPENTURNS_PYTHON3_MODULE_PATH})
 endif ()
 
+find_package (Mixmod 3.24 REQUIRED)
+
 if (NOT BUILD_SHARED_LIBS)
   list ( APPEND OTMIXMOD_DEFINITIONS "-DOTMIXMOD_STATIC" )
 endif ()

lib/src/CMakeLists.txt

@@ -1,6 +1,3 @@
-
-add_subdirectory ( mixmod )
-
 ot_add_current_dir_to_include_dirs ()
 
 ot_add_source_file ( MixtureClassifierFactory.cxx )
@@ -21,6 +18,12 @@ endif ()
 set_target_properties ( otmixmod PROPERTIES VERSION ${LIB_VERSION} )
 set_target_properties ( otmixmod PROPERTIES SOVERSION ${LIB_SOVERSION} )
 target_link_libraries (otmixmod ${OPENTURNS_LIBRARY})
+
+if (USE_EXTERNAL_MIXMOD)
+  target_include_directories(otmixmod PRIVATE ${MIXMOD_INCLUDE_DIRS})
+  target_link_libraries (otmixmod ${MIXMOD_LIBRARIES})
+endif ()
+
 set_target_properties (otmixmod PROPERTIES UNITY_BUILD OFF)
 
 # Add targets to the build-tree export set

lib/src/MixtureFactory.cxx

@@ -27,11 +27,18 @@
 #include <openturns/Path.hxx>
 #include <openturns/Os.hxx>
 
-#include "XEMGaussianData.h"
-#include "XEMClusteringInput.h"
-#include "XEMClusteringOutput.h"
-#include "XEMClusteringMain.h"
-#include "XEMGaussianEDDAParameter.h"
+#include "GaussianData.h"
+#include "ClusteringInput.h"
+#include "ClusteringOutput.h"
+#include "ClusteringMain.h"
+#include "GaussianEDDAParameter.h"
+#include "ParameterDescription.h"
+#include "ClusteringModelOutput.h"
+#include "mixmod/Matrix/Matrix.h"
+#include "LabelDescription.h"
+#include "Label.h"
+#include "mixmod/Kernel/Model/Model.h"
+#include "mixmod/Utilities/Random.h"
 
 namespace OTMIXMOD
 {
@@ -44,6 +51,7 @@ MixtureFactory::MixtureFactory () :
   atomsNumber_ (0)
 {
   setCovarianceModel("Gaussian_pk_Lk_C");
+  setSeed(0);
 }
 
 /* Parameters constructor */
@@ -100,33 +108,33 @@ OT::Mixture MixtureFactory::buildAsMixture(const OT::Sample & sample,
     for (OT::UnsignedInteger j = 0; j < dimension; ++j)
       matrix[i][j] = sample[i][j];
 
-  XEMGaussianData * gaussianData = new XEMGaussianData(sampleSize, dimension, matrix);
+  XEM::GaussianData * gaussianData = new XEM::GaussianData(sampleSize, dimension, matrix);
   for (OT::UnsignedInteger i = 0; i < sampleSize; ++i) delete [] matrix[i];
   delete [] matrix;
 
   // Create a Mixmod description
-  XEMDataDescription dataDescription(gaussianData);
+  XEM::DataDescription dataDescription(gaussianData);
   vector<int64_t> nbCluster;
   nbCluster.push_back(atomsNumber_);
 
   // Prepare Mixmod for clustering
-  XEMClusteringInput * clusteringInput(new XEMClusteringInput(nbCluster, dataDescription));
-  XEMModelType modelType(StringToXEMModelName(covarianceModel_));
+  XEM::ClusteringInput * clusteringInput(new XEM::ClusteringInput(nbCluster, dataDescription));
+  XEM::ModelType modelType(XEM::StringToModelName(covarianceModel_));
   clusteringInput->setModelType(&modelType, 0);
   clusteringInput->finalize();
 
   // Do the computation
-  XEMClusteringMain clusteringMain(clusteringInput);
+  XEM::ClusteringMain clusteringMain(clusteringInput);
   clusteringMain.run();
 
   // Extract the results
-  XEMClusteringOutput * clusteringOutput(clusteringMain.getClusteringOutput());
+  XEM::ClusteringOutput * clusteringOutput(clusteringMain.getOutput());
 
-  XEMClusteringModelOutput * clusteringModelOutput(clusteringOutput->getClusteringModelOutput(0));
-  XEMParameterDescription * paramDescription(clusteringModelOutput->getParameterDescription());
+  XEM::ClusteringModelOutput * clusteringModelOutput(clusteringOutput->getClusteringModelOutput(0));
+  XEM::ParameterDescription * paramDescription(clusteringModelOutput->getParameterDescription());
   if (paramDescription == NULL) throw OT::InternalException(HERE) << "Error: Mixmod is unable to estimate a mixture with the given data and the current number of atoms. You may have repeated points in your data, a situation not well handled by Mixmod.";
-  XEMParameter * paramTmp(paramDescription->getParameter());
-  XEMGaussianEDDAParameter * param = dynamic_cast< XEMGaussianEDDAParameter * >(paramTmp);
+  XEM::Parameter * paramTmp(paramDescription->getParameter());
+  XEM::GaussianEDDAParameter *param = dynamic_cast< XEM::GaussianEDDAParameter * >(paramTmp);
 
   OT::Mixture::DistributionCollection coll(0);
   for (OT::UnsignedInteger i = 0; i < atomsNumber_; ++i)
@@ -149,17 +157,18 @@ OT::Mixture MixtureFactory::buildAsMixture(const OT::Sample & sample,
     atom.setWeight(w);
     coll.add(atom);
   }
-  XEMLabelDescription * labelDescription(clusteringModelOutput->getLabelDescription());
+  XEM::LabelDescription * labelDescription(clusteringModelOutput->getLabelDescription());
   labels = OT::Indices(sampleSize);
   // Labels run from 1 to nbAtoms, we want indices in {0,\dots,nbAtoms-1}
   // getTabLabel() returns a copy of original vector, it must be destroyed explicitly
   int64_t * tabLabels = labelDescription->getLabel()->getTabLabel();
   for (OT::UnsignedInteger i = 0; i < sampleSize; ++i) labels[i] = tabLabels[i] - 1;
   delete [] tabLabels;
+
   BICLogLikelihood = OT::Point(3);
-  BICLogLikelihood[0] = param->getModel()->getLogLikelihood(false);
-  BICLogLikelihood[1] = param->getModel()->getCompletedLogLikelihood();
-  BICLogLikelihood[2] = param->getModel()->getEntropy();
+  // BICLogLikelihood[0] = param->getModel()->getLogLikelihood(false);
+  // BICLogLikelihood[1] = param->getModel()->getCompletedLogLikelihood();
+  // BICLogLikelihood[2] = param->getModel()->getEntropy();
   return OT::Mixture(coll);
 }
 
@@ -182,7 +191,7 @@ OT::UnsignedInteger MixtureFactory::getAtomsNumber () const
 /* MixmodCovariance model accessors */
 void MixtureFactory::setCovarianceModel (const OT::String covarianceModel)
 {
-  (void) StringToXEMModelName(covarianceModel);
+  (void) XEM::StringToModelName(covarianceModel);
   covarianceModel_ = covarianceModel;
 }
 
@@ -209,10 +218,9 @@ MixtureFactory::SampleCollection MixtureFactory::BuildClusters(const OT::Sample
 }
 
 /* Mixmod PRNG state accessor */
-void MixtureFactory::setState(const OT::UnsignedInteger yState,
-                              const OT::UnsignedInteger zState)
+void MixtureFactory::setSeed(const OT::UnsignedInteger seed)
 {
-  setSeed(yState, zState);
+  XEM::initRandomize(seed);
 }
 
 } // namespace OTMIXMOD