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 REQUIRED)
+
 if (NOT BUILD_SHARED_LIBS)
   list ( APPEND OTMIXMOD_DEFINITIONS "-DOTMIXMOD_STATIC" )
 endif ()

ChangeLog

@@ -1,3 +1,8 @@
+= 0.16 release (in-progress)
+
+- Depend on mixmod library (https://github.com/mixmod)
+- Removed MixtureClassifierFactory
+
 = 0.15 release (2023-11-15)
 
  * Maintenance release

cmake/FindMixmod.cmake

@@ -0,0 +1,87 @@
+# - Find Mixmod
+# Classification with Mixture Modelling
+# available at https://github.com/mixmod
+#
+# The module defines the following variables:
+#  MIXMOD_FOUND - the system has LibSVM
+#  MIXMOD_INCLUDE_DIR - where to find svm.h
+#  MIXMOD_INCLUDE_DIRS - libsvm includes
+#  MIXMOD_LIBRARY - where to find the LibSVM library
+#  MIXMOD_LIBRARIES - aditional libraries
+#  MIXMOD_MAJOR_VERSION - major version
+#  MIXMOD_MINOR_VERSION - minor version
+#  MIXMOD_VERSION_STRING - version (ex. 2.9.0)
+#  MIXMOD_ROOT_DIR - root dir (ex. /usr/local)
+
+#=============================================================================
+# Copyright 2010-2023, Julien Schueller
+# All rights reserved.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met: 
+# 
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer. 
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution. 
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+# The views and conclusions contained in the software and documentation are those
+# of the authors and should not be interpreted as representing official policies, 
+# either expressed or implied, of the FreeBSD Project.
+#=============================================================================
+
+# set MIXMOD_INCLUDE_DIR
+find_path (MIXMOD_INCLUDE_DIR
+  NAMES
+    mixmod.h
+)
+
+
+# set MIXMOD_INCLUDE_DIRS
+set (MIXMOD_INCLUDE_DIRS ${MIXMOD_INCLUDE_DIR})
+
+# set MIXMOD_LIBRARY
+find_library (MIXMOD_LIBRARY
+  NAMES
+    mixmod
+  DOC
+    "Mixmod library location"
+)
+
+# set MIXMOD_LIBRARIES
+set (MIXMOD_LIBRARIES ${MIXMOD_LIBRARY})
+
+
+
+# try to guess root dir from include dir
+if (MIXMOD_INCLUDE_DIR)
+  string (REGEX REPLACE "(.*)/include.*" "\\1" MIXMOD_ROOT_DIR ${MIXMOD_INCLUDE_DIR})
+# try to guess root dir from library dir
+elseif (MIXMOD_LIBRARY)
+  string (REGEX REPLACE "(.*)/lib[/|32|64].*" "\\1" MIXMOD_ROOT_DIR ${MIXMOD_LIBRARY})
+endif ()
+
+
+# handle REQUIRED and QUIET options
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (Mixmod REQUIRED_VARS MIXMOD_LIBRARY MIXMOD_INCLUDE_DIR)
+
+mark_as_advanced (
+  MIXMOD_LIBRARY
+  MIXMOD_LIBRARIES
+  MIXMOD_INCLUDE_DIR
+  MIXMOD_INCLUDE_DIRS
+  MIXMOD_ROOT_DIR
+)

lib/src/CMakeLists.txt

@@ -1,12 +1,7 @@
-
-add_subdirectory ( mixmod )
-
 ot_add_current_dir_to_include_dirs ()
 
-ot_add_source_file ( MixtureClassifierFactory.cxx )
 ot_add_source_file ( MixtureFactory.cxx )
 
-ot_install_header_file ( MixtureClassifierFactory.hxx )
 ot_install_header_file ( MixtureFactory.hxx )
 
 include_directories ( ${INTERNAL_INCLUDE_DIRS} )
@@ -21,6 +16,10 @@ endif ()
 set_target_properties ( otmixmod PROPERTIES VERSION ${LIB_VERSION} )
 set_target_properties ( otmixmod PROPERTIES SOVERSION ${LIB_SOVERSION} )
 target_link_libraries (otmixmod ${OPENTURNS_LIBRARY})
+
+target_include_directories(otmixmod PRIVATE ${MIXMOD_INCLUDE_DIRS})
+target_link_libraries (otmixmod ${MIXMOD_LIBRARIES})
+
 set_target_properties (otmixmod PROPERTIES UNITY_BUILD OFF)
 
 # Add targets to the build-tree export set

lib/src/MixtureFactory.cxx

@@ -27,11 +27,17 @@
 #include <openturns/Path.hxx>
 #include <openturns/Os.hxx>
 
-#include "XEMGaussianData.h"
-#include "XEMClusteringInput.h"
-#include "XEMClusteringOutput.h"
-#include "XEMClusteringMain.h"
-#include "XEMGaussianEDDAParameter.h"
+#include <mixmod/Clustering/ClusteringInput.h>
+#include <mixmod/Clustering/ClusteringOutput.h>
+#include <mixmod/Clustering/ClusteringMain.h>
+#include <mixmod/Clustering/ClusteringModelOutput.h>
+#include <mixmod/Kernel/IO/GaussianData.h>
+#include <mixmod/Kernel/Parameter/GaussianEDDAParameter.h>
+#include <mixmod/Kernel/IO/ParameterDescription.h>
+#include <mixmod/Kernel/IO/LabelDescription.h>
+#include <mixmod/Kernel/IO/Label.h>
+#include <mixmod/Kernel/Model/Model.h>
+#include <mixmod/Matrix/Matrix.h>
 
 namespace OTMIXMOD
 {
@@ -100,33 +106,33 @@ 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);
-  clusteringMain.run();
+  XEM::ClusteringMain clusteringMain(clusteringInput);
+  clusteringMain.run(seed_);
 
   // 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 +155,15 @@ 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 = {clusteringModelOutput->getLikelihood()};
   return OT::Mixture(coll);
 }
 
@@ -182,7 +186,7 @@ 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 +213,9 @@ 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::SignedInteger seed)
 {
-  setSeed(yState, zState);
+  seed_ = seed;
 }
 
 } // namespace OTMIXMOD