ENH: Add Active Registration Model metrics

Components/Metrics/ActiveRegistrationModel/CMakeLists.txt

@@ -0,0 +1,29 @@
+ADD_ELXCOMPONENT(ActiveRegistrationModelShapeMetric OFF
+  elxActiveRegistrationModelShapeMetric.cxx
+  elxActiveRegistrationModelShapeMetric.h
+  elxActiveRegistrationModelShapeMetric.hxx
+  itkActiveRegistrationModelShapeMetric.h
+  itkActiveRegistrationModelShapeMetric.hxx
+)
+
+ADD_ELXCOMPONENT(ActiveRegistrationModelIntensityMetric OFF
+  elxActiveRegistrationModelIntensityMetric.h
+  elxActiveRegistrationModelIntensityMetric.hxx
+  elxActiveRegistrationModelIntensityMetric.cxx
+  itkActiveRegistrationModelIntensityMetric.h
+  itkActiveRegistrationModelIntensityMetric.hxx
+)
+
+# Eigen3, statismo and hdf5 include directories and Eigen3 and hdf5 libraries are transitively included via
+# the statismo_core target
+if(${USE_ActiveRegistrationModelShapeMetric} OR ${USE_ActiveRegistrationModelIntensityMetric})
+  add_subdirectory(Statismo)
+endif()
+
+if(${USE_ActiveRegistrationModelShapeMetric})
+  target_link_libraries(ActiveRegistrationModelShapeMetric statismo_core ${Boost_LIBRARIES} ITKInternalEigen3::Eigen)
+endif()
+
+if(${USE_ActiveRegistrationModelIntensityMetric})
+  target_link_libraries(ActiveRegistrationModelIntensityMetric statismo_core ${Boost_LIBRARIES} ITKInternalEigen3::Eigen)
+endif()

Components/Metrics/ActiveRegistrationModel/Statismo/CMakeLists.txt

@@ -0,0 +1,2 @@
+add_subdirectory(core)
+add_subdirectory(ITK)

Components/Metrics/ActiveRegistrationModel/Statismo/ITK/CMakeLists.txt

@@ -0,0 +1,7 @@
+if(MSVC11) #i.e. Visual Studio 2012
+  # Fix for VS2012 that has _VARIADIC_MAX set to 5. Don't set too high because it increases compiler memory usage / compile-time.
+  add_definitions(-D_VARIADIC_MAX=10 )
+  # Fix for another VS2012 problem: not all TR1 options are automatically detected, therefore we force them here.
+  add_definitions(-D BOOST_HAS_TR1)
+  add_definitions(-D BOOST_NO_0X_HDR_INITIALIZER_LIST)
+endif()

Components/Metrics/ActiveRegistrationModel/Statismo/ITK/include/itkConditionalModelBuilder.h

@@ -0,0 +1,116 @@
+/*
+ * This file is part of the statismo library.
+ *
+ * Author: Marcel Luethi ([email protected])
+ *
+ * Copyright (c) 2011 University of Basel
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ *
+ * 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.
+ *
+ * Neither the name of the project's author nor the names of its
+ * contributors may be used to endorse or promote products derived from
+ * this software without specific prior written permission.
+ *
+ * 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
+ * HOLDER 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.
+ *
+ */
+
+
+#ifndef ITKMODELBUILDER_H_
+#define ITKMODELBUILDER_H_
+
+#include <itkObject.h>
+#include <itkObjectFactory.h>
+
+#include "itkDataManager.h"
+#include "itkStatisticalModel.h"
+#include "ConditionalModelBuilder.h"
+#include "statismoITKConfig.h"
+
+namespace itk {
+
+/**
+ * \brief ITK Wrapper for the statismo::PCAModelBuilder class.
+ * \see statismo::PCAModelBuilder for detailed documentation.
+ */
+template <class Representer>
+class ConditionalModelBuilder : public Object {
+  public:
+
+    typedef ConditionalModelBuilder            Self;
+    typedef Object	Superclass;
+    typedef SmartPointer<Self>                Pointer;
+    typedef SmartPointer<const Self>          ConstPointer;
+
+    itkNewMacro( Self );
+    itkTypeMacro( ConditionalModelBuilder, Object );
+
+
+    typedef statismo::ConditionalModelBuilder<Representer> ImplType;
+    typedef statismo::DataManager<Representer> DataManagerType;
+    typedef typename DataManagerType::SampleDataStructureListType SampleDataStructureListType;
+
+    ConditionalModelBuilder() : m_impl(ImplType::Create()) {}
+
+    virtual ~ConditionalModelBuilder() {
+        if (m_impl) {
+            delete m_impl;
+            m_impl = 0;
+        }
+    }
+
+    template <class F>
+    typename boost::result_of<F()>::type callstatismoImpl(F f) const {
+        try {
+            return f();
+        } catch (statismo::StatisticalModelException& s) {
+            itkExceptionMacro(<< s.what());
+        }
+    }
+
+
+    typename StatisticalModel<Representer>::Pointer
+    BuildNewModel(SampleDataStructureListType SampleDataStructureList,
+                  const typename statismo::ConditionalModelBuilder<Representer>::SurrogateTypeVectorType& surrogateTypes,
+                  const typename statismo::ConditionalModelBuilder<Representer>::CondVariableValueVectorType& conditioningInfo,
+                  float noiseVariance,
+                  double modelVarianceRetained
+                 ) {
+        statismo::StatisticalModel<Representer>* model_statismo = callstatismoImpl(boost::bind(&ImplType::BuildNewModel, this->m_impl, SampleDataStructureList, surrogateTypes, conditioningInfo, noiseVariance, modelVarianceRetained));
+        typename StatisticalModel<Representer>::Pointer model_itk = StatisticalModel<Representer>::New();
+        model_itk->SetstatismoImplObj(model_statismo);
+        return model_itk;
+    }
+
+
+  private:
+    ConditionalModelBuilder(const ConditionalModelBuilder& orig);
+    ConditionalModelBuilder& operator=(const ConditionalModelBuilder& rhs);
+
+    ImplType* m_impl;
+};
+
+
+}
+
+#endif /* ITKMODELBUILDER_H_ */

Components/Metrics/ActiveRegistrationModel/Statismo/ITK/include/itkDataManager.h

@@ -0,0 +1,146 @@
+/*
+ * This file is part of the statismo library.
+ *
+ * Author: Marcel Luethi ([email protected])
+ *
+ * Copyright (c) 2011 University of Basel
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ *
+ * 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.
+ *
+ * Neither the name of the project's author nor the names of its
+ * contributors may be used to endorse or promote products derived from
+ * this software without specific prior written permission.
+ *
+ * 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
+ * HOLDER 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.
+ *
+ */
+
+
+#ifndef ITK_DATAMANAGER_H_
+#define ITK_DATAMANAGER_H_
+
+#include <boost/bind.hpp>
+#include <boost/utility/result_of.hpp>
+
+#include <itkObject.h>
+#include <itkObjectFactory.h>
+
+#include "DataManager.h"
+#include "statismoITKConfig.h"
+
+namespace itk {
+
+
+/**
+ * \brief ITK Wrapper for the statismo::DataManager class.
+ * \see statismo::DataManager for detailed documentation.
+ */
+template <class T>
+class DataManager : public Object {
+  public:
+
+
+    typedef DataManager            Self;
+    typedef Object	Superclass;
+    typedef SmartPointer<Self>                Pointer;
+    typedef SmartPointer<const Self>          ConstPointer;
+
+    itkNewMacro( Self );
+    itkTypeMacro( DataManager, Object );
+
+
+    typedef statismo::DataManager<T> ImplType;
+    typedef typename statismo::DataManager<T>::DataItemType     DataItemType;
+    typedef typename statismo::DataManager<T>::DataItemListType DataItemListType;
+    typedef statismo::Representer<T> RepresenterType;
+
+    template <class F>
+    typename boost::result_of<F()>::type callstatismoImpl(F f) const {
+        if (m_impl == 0) {
+            itkExceptionMacro(<< "Model not properly initialized. Maybe you forgot to call SetRepresenter");
+        }
+        try {
+            return f();
+        } catch (statismo::StatisticalModelException& s) {
+            itkExceptionMacro(<< s.what());
+        }
+    }
+
+
+    DataManager() : m_impl(0) {}
+
+    virtual ~DataManager() {
+        if (m_impl) {
+            delete m_impl;
+            m_impl = 0;
+        }
+    }
+
+    ImplType* GetstatismoImplObj() const {
+        return m_impl;
+    }
+
+
+    void SetstatismoImplObj(ImplType* impl) {
+        if (m_impl) {
+            delete m_impl;
+        }
+        m_impl = impl;
+    }
+
+    void SetRepresenter(const RepresenterType* representer) {
+        SetstatismoImplObj(ImplType::Create(representer));
+    }
+
+    void AddDataset(typename RepresenterType::DatasetType* ds, const char* filename) {
+        callstatismoImpl(boost::bind(&ImplType::AddDataset, this->m_impl, ds, filename));
+    }
+
+    void Load(const char* filename) {
+        try {
+            SetstatismoImplObj(ImplType::Load(filename));
+        } catch (statismo::StatisticalModelException& s) {
+            itkExceptionMacro(<< s.what());
+        }
+    }
+
+    void Save(const char* filename) {
+        callstatismoImpl(boost::bind(&ImplType::Save, this->m_impl, filename));
+    }
+
+    typename statismo::DataManager<T>::DataItemListType GetData() const {
+        return callstatismoImpl(boost::bind(&ImplType::GetData, this->m_impl));
+    }
+
+
+  private:
+    DataManager(const DataManager& orig);
+    DataManager& operator=(const DataManager& rhs);
+
+    ImplType* m_impl;
+};
+
+
+}
+
+#endif /* ITK_DATAMANAGER_H_ */