Merge branch 'develop'

.travis.yml

@@ -6,10 +6,10 @@ compiler:
 before_install:
   - sudo add-apt-repository ppa:zarquon42/precise-backports -y
   - sudo apt-get update -qq
-  - sudo apt-get install -y cmake libboost1.55-dev libboost1.55 libeigen3-dev libhdf5-serial-dev libvtk6-dev libinsighttoolkit4-dev
+  - sudo apt-get install -y cmake libboost1.55-dev libboost1.55 libeigen3-dev libvtk6-dev libinsighttoolkit4-dev
 
 script:
   - mkdir -p build
   - cd build
-  - cmake -DCMAKE_BUILD_TYPE:STRING=Release ../
+  - cmake -DCMAKE_BUILD_TYPE:STRING=Release -DON_TRAVIS=True ../
   - make -j2

CMakeLists.txt

@@ -57,7 +57,7 @@ set(INSTALL_LIB_DIR lib CACHE PATH "Installation directory for libraries")
 set(INSTALL_BIN_DIR bin CACHE PATH "Installation directory for executables")
 set(INSTALL_INCLUDE_DIR include CACHE PATH
   "Installation directory for header files")
-set(INSTALL_DOC_DIR share/doc/statismo CACHE PATH 
+set(INSTALL_DOC_DIR share/doc/statismo CACHE PATH
   "Installation directory for documentation")
 
 if(WIN32 AND NOT CYGWIN)
@@ -116,8 +116,6 @@ include_directories( ${Boost_INCLUDE_DIRS} )
 link_directories( ${Boost_LIBRARY_DIRS} )
 add_definitions( -DBOOST_THREAD_VERSION=3 -DBOOST_FILESYSTEM_VERSION=3 )
 
-find_package( HDF5  COMPONENTS C CXX)
-include_directories( ${HDF5_INCLUDE_DIRS} )
 
 if(WIN32)
   # On Windows, we can only build static libraries, as the dynamic libraries would be
@@ -127,22 +125,29 @@ if(WIN32)
   set(statismo_LIB_TYPE STATIC)
 endif()
 
-foreach( _library ${HDF5_LIBRARIES} )
-  get_filename_component( _tempDir${_library} ${_library} PATH )
-  list( APPEND HDF5_LIBRARY_DIR ${_tempDir${_library}} )
-endforeach()
-
 option( ITK_SUPPORT "Build ITK Support" ON )
 
 if( ${ITK_SUPPORT} MATCHES "ON" )
-  find_package( ITK REQUIRED )
+  find_package( ITK REQUIRED PATHS ${INSTALL_DEPENDENCIES_DIR})
   include( ${ITK_USE_FILE} )
 endif()
 
+# We rely on the hdf5 libraries that are shipped with ITK, as this will reduce version conflicts.
+set(ITK_VERSION ${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR})
+find_path(ITK_INCLUDE_WITH_HDF5 NAMES itkhdf5/hdf5.h PATHS ${ITK_INCLUDE_DIRS} )
+set(ITK_HDF5_DIR ${ITK_INCLUDE_WITH_HDF5}/itkhdf5)
+set(HDF5_INCLUDE_DIRS ${ITK_HDF5_DIR} ${ITK_HDF5_DIR}/cpp)
+set(HDF5_LIBRARIES ${ITKHDF5_LIBRARIES})
+
+
+set(HDF5_LIBRARY_DIR ${INSTALL_DEPENDENCIES_DIR}/lib)
+include_directories( ${HDF5_INCLUDE_DIRS} )
+
+
 option( VTK_SUPPORT "Build VTK Support" ON )
 
 if( ${VTK_SUPPORT} MATCHES "ON" )
-  find_package( VTK REQUIRED )
+  find_package( VTK REQUIRED PATHS ${INSTALL_DEPENDENCIES_DIR})
   include( ${VTK_USE_FILE} )
 endif()
 
@@ -152,6 +157,13 @@ option( BUILD_EXAMPLES "Build examples" ON )
 option( BUILD_WRAPPING "Build Python Wrappers (experimental)" OFF )
 mark_as_advanced(BUILD_WRAPPING)
 
+#make sure the executables have access to the dll's created by the superbuild on windows to make them runnable even without installing & adding the isntall path to the cmd PATH
+if( NOT INSTALL_DEPENDENCIES_DIR )
+  set( TESTS_WORKING_DIR "." CACHE INTERNAL "")
+else()
+  set( TEST_WORKING_DIR "${INSTALL_DEPENDENCIES_DIR}/bin" CACHE INTERNAL "")
+endif()
+
 add_subdirectory( modules )
 add_subdirectory( doc )
 # -------------------------------------------------------------

doc/IJ/statismo_ij.tex

@@ -411,10 +411,8 @@ \subsection{Representers} \label{sec:representers}
 form.  The discretization and normalization step are specific to the
 type of object that are modeled.  A \code{Representer} class in
 \Statismo needs to provide the methods
-\code{Representer::DatasetToSample},
 \code{Representer::SampleToSampleVector} and
-\code{Representer::SampleVectorToSample}.  The first method takes care
-of the discretization and normalization, the second method is used to
+\code{Representer::SampleVectorToSample}.  The first method is used to
 convert a dataset to its vectorial representation.  The last method is
 used to convert the vectorial representation back to an object of the
 modeled type. Figure~\ref{fig:statismo-flow} illustrates this concept.
@@ -594,13 +592,13 @@ \subsection{Using statistical models as  a prior}
 \code{DrawSample} method:
 \begin{verbatim}
 vtkPolyData* dataset = someAlgorithm();
-VectorType coeffs = model->ComputeCoefficientsForDataset(dataset);
+VectorType coeffs = model->ComputeCoefficients(dataset);
 vtkPolyData* projection = model->DrawSample(coeffs);
 \end{verbatim}
 Often, an algorithm is regularized by penalizing unlikely solutions. For this purpose, \Statismo 
 provides a method to compute a (log) probability of a given dataset. 
 \begin{verbatim}
-float logProbability = model->ComputeLogProbabilityForDataset(aDataset);
+float logProbability = model->ComputeLogProbability(aDataset);
 \end{verbatim}
 
 \subsection{Cross validation}
@@ -635,7 +633,7 @@ \subsection{Cross validation}
     {
         vtkPolyData* testSample = (*it)->GetAsNewSample();
         vtkPolyData* projection = model->DrawSample(
-                                         model->ComputeCoefficientsForDataset(dataset));
+                                         model->ComputeCoefficients(dataset));
         /// here we could for example compute the approximation error between the 
         /// projection and the test sample - omitted
 

modules/ITK/CMakeLists.txt

@@ -6,6 +6,7 @@ if(MSVC11) #i.e. Visual Studio 2012
   add_definitions( -D BOOST_NO_0X_HDR_INITIALIZER_LIST )
 endif()
 
+include( ${ITK_USE_FILE} )
 
 include_directories( BEFORE
   ${CMAKE_CURRENT_SOURCE_DIR}/include

modules/ITK/cli/statismo-build-deformation-model.cxx

@@ -38,6 +38,7 @@
 #include <itkImageFileReader.h>
 #include <itkPCAModelBuilder.h>
 #include <itkStandardImageRepresenter.h>
+#include <itkStatismoIO.h>
 #include <itkStatisticalModel.h>
 
 #include "utils/statismo-build-models-utils.h"
@@ -47,6 +48,7 @@ using namespace std;
 
 struct programOptions {
     bool bDisplayHelp;
+    bool bComputeScores;
     string strDataListFile;
     string strOutputFileName;
     float fNoiseVariance;
@@ -143,26 +145,22 @@ void buildAndSaveDeformationModel(programOptions opt) {
 
     typedef itk::ImageFileReader<ImageType> ImageReaderType;
     typedef vector<typename ImageReaderType::Pointer> ImageReaderList;
-    ImageReaderList images;
-    images.reserve(fileNames.size());
 
+    if (fileNames.size() == 0) {
+        itkGenericExceptionMacro( << "No Data was loaded and thus the model can't be built.");
+    }
+    bool firstPass = true;
     for (StringList::const_iterator it = fileNames.begin(); it != fileNames.end(); ++it) {
+
         typename ImageReaderType::Pointer reader = ImageReaderType::New();
+
         reader->SetFileName(it->c_str());
         reader->Update();
-        //itk::PCAModelBuilder is not a Filter in the ITK world, so the pipeline would not get executed if its main method is called. So the pipeline before calling itk::PCAModelBuilder must be executed by the means of calls to Update() (at least for last elements needed by itk::PCAModelBuilder).
-        images.push_back(reader);
-    }
-
-    if (images.size() == 0) {
-        itkGenericExceptionMacro( << "No Data was loaded and thus the model can't be built.");
-    }
-    typename  ImageReaderType::Pointer referenceReader = *images.begin();
-    representer->SetReference(referenceReader->GetOutput());
-    dataManager->SetRepresenter(representer);
-
-    for (typename ImageReaderList::const_iterator it = images.begin(); it != images.end(); ++it) {
-        typename ImageReaderType::Pointer reader = *it;
+        if ( firstPass ) {
+            representer->SetReference(reader->GetOutput());
+            dataManager->SetRepresenter(representer);
+            firstPass = false;
+        }
         dataManager->AddDataset(reader->GetOutput(), reader->GetFileName().c_str());
     }
 
@@ -171,8 +169,8 @@ void buildAndSaveDeformationModel(programOptions opt) {
 
     typedef itk::PCAModelBuilder<ImageType> ModelBuilderType;
     typename ModelBuilderType::Pointer pcaModelBuilder = ModelBuilderType::New();
-    model = pcaModelBuilder->BuildNewModel(dataManager->GetData(), opt.fNoiseVariance);
-    model->Save(opt.strOutputFileName.c_str());
+    model = pcaModelBuilder->BuildNewModel(dataManager->GetData(), opt.fNoiseVariance, opt.bComputeScores);
+    itk::StatismoIO<ImageType>::SaveStatisticalModel(model, opt.strOutputFileName.c_str());
 }
 
 po::options_description initializeProgramOptions(programOptions& poParameters) {
@@ -185,10 +183,11 @@ po::options_description initializeProgramOptions(programOptions& poParameters) {
     po::options_description optAdditional("Optional options");
     optAdditional.add_options()
     ("noise,n", po::value<float>(&poParameters.fNoiseVariance)->default_value(0), "Noise variance of the PPCA model")
+    ("scores,s", po::value<bool>(&poParameters.bComputeScores)->default_value(true), "Compute scores (default true)")
     ("help,h", po::bool_switch(&poParameters.bDisplayHelp), "Display this help message")
     ;
 
     po::options_description optAllOptions;
     optAllOptions.add(optMandatory).add(optAdditional);
     return optAllOptions;
-}
+}

modules/ITK/cli/statismo-build-gp-model.cxx

@@ -42,6 +42,7 @@
 #include <itkMeshFileReader.h>
 #include <itkStandardImageRepresenter.h>
 #include <itkStandardMeshRepresenter.h>
+#include <itkStatismoIO.h>
 #include <itkStatisticalModel.h>
 
 //Add new kernels in this file (and document their usage in the statismo-build-gp-model.md file)
@@ -204,7 +205,8 @@ void buildAndSaveModel(programOptions opt) {
 
     if(opt.strOptionalModelPath != "") {
         try {
-            pRawStatisticalModel.reset(RawModelType::Load(pRepresenter.GetPointer(), opt.strOptionalModelPath.c_str()));
+            pRawStatisticalModel.reset(statismo::IO<DataType>::LoadStatisticalModel(pRepresenter.GetPointer(),
+                                                                                    opt.strOptionalModelPath.c_str()));
             pStatModelKernel.reset(new statismo::StatisticalModelKernel<DataType>(pRawStatisticalModel.get()));
             pModelBuildingKernel.reset(new statismo::SumKernel<PointType>(pStatModelKernel.get(), pScaledKernel.get()));
         } catch (statismo::StatisticalModelException& s) {
@@ -218,22 +220,17 @@ void buildAndSaveModel(programOptions opt) {
         pReferenceReader->Update();
         pRepresenter->SetReference(pReferenceReader->GetOutput());
         pMean = pRepresenter->IdentitySample();
-
     }
 
-
-
-
     typedef itk::LowRankGPModelBuilder<DataType> ModelBuilderType;
     typename ModelBuilderType::Pointer gpModelBuilder = ModelBuilderType::New();
     gpModelBuilder->SetRepresenter(pRepresenter);
 
-
     typedef itk::StatisticalModel<DataType> StatisticalModelType;
     typename StatisticalModelType::Pointer pModel;
     pModel = gpModelBuilder->BuildNewModel(pMean, *pModelBuildingKernel.get(), opt.iNrOfBasisFunctions);
 
-    pModel->Save(opt.strOutputFileName.c_str());
+    itk::StatismoIO<DataType>::SaveStatisticalModel(pModel, opt.strOutputFileName.c_str());
 }
 
 string getAvailableKernelsStr() {
@@ -276,4 +273,4 @@ po::options_description initializeProgramOptions(programOptions& poParameters) {
     po::options_description optAllOptions;
     optAllOptions.add(optMandatory).add(optAdditional);
     return optAllOptions;
-}
+}

modules/ITK/cli/statismo-build-shape-model.cxx

@@ -44,6 +44,7 @@
 #include <itkPCAModelBuilder.h>
 #include <itkRigid3DTransform.h>
 #include <itkStandardMeshRepresenter.h>
+#include <itkStatismoIO.h>
 #include <itkStatisticalModel.h>
 #include <itkTransformMeshFilter.h>
 
@@ -212,7 +213,7 @@ void buildAndSaveShapeModel(programOptions opt) {
     typedef itk::PCAModelBuilder<MeshType> PCAModelBuilder;
     PCAModelBuilder::Pointer pcaModelBuilder = PCAModelBuilder::New();
     model = pcaModelBuilder->BuildNewModel(dataManager->GetData(), opt.fNoiseVariance);
-    model->Save(opt.strOutputFileName.c_str());
+    itk::StatismoIO<MeshType>::SaveStatisticalModel(model, opt.strOutputFileName.c_str());
 }
 
 po::options_description initializeProgramOptions(programOptions& poParameters) {
@@ -232,4 +233,4 @@ po::options_description initializeProgramOptions(programOptions& poParameters) {
     po::options_description optAllOptions;
     optAllOptions.add(optMandatory).add(optAdditional);
     return optAllOptions;
-}
+}

modules/ITK/cli/statismo-fit-image.cxx

@@ -43,6 +43,7 @@
 #include <itkNormalizedCorrelationImageToImageMetric.h>
 #include <itkRigid2DTransform.h>
 #include <itkStandardImageRepresenter.h>
+#include <itkStatismoIO.h>
 #include <itkStatisticalModel.h>
 #if (ITK_VERSION_MAJOR >= 4 && ITK_VERSION_MINOR >= 6)
 #include <itkTransformToDisplacementFieldFilter.h>
@@ -223,7 +224,7 @@ void fitImage(programOptions opt, ConsoleOutputSilencer* pCOSilencer) {
 
     typedef itk::StatisticalModel<VectorImageType> StatisticalModelType;
     typename StatisticalModelType::Pointer pModel = StatisticalModelType::New();
-    pModel->Load(pRepresenter, opt.strInputModelFileName.c_str());
+    pModel = itk::StatismoIO<VectorImageType>::LoadStatisticalModel(pRepresenter, opt.strInputModelFileName.c_str());
 
     typedef itk::Transform<double, Dimensions, Dimensions> TransformType;
     typename TransformType::Pointer pTransform;

modules/ITK/cli/statismo-fit-surface.cxx

@@ -44,6 +44,7 @@
 #include <itkPointsLocator.h>
 #include <itkReducedVarianceModelBuilder.h>
 #include <itkStandardMeshRepresenter.h>
+#include <itkStatismoIO.h>
 #include <itkStatisticalModel.h>
 #include <itkStatisticalShapeModelTransform.h>
 #include <itkVersorRigid3DTransform.h>
@@ -224,7 +225,8 @@ void fitMesh(programOptions opt, ConsoleOutputSilencer* pCOSilencer) {
     typedef itk::StandardMeshRepresenter<float, Dimensions> RepresenterType;
     RepresenterType::Pointer pRepresenter = RepresenterType::New();
     StatisticalModelType::Pointer pModel = StatisticalModelType::New();
-    pModel->Load(pRepresenter.GetPointer(), opt.strInputModelFileName.c_str());
+    pModel = itk::StatismoIO<DataType>::LoadStatisticalModel(pRepresenter.GetPointer(),
+                                                             opt.strInputModelFileName.c_str());
 
     StatisticalModelType::Pointer pConstrainedModel;
     typedef itk::StatisticalShapeModelTransform<DataType, double, Dimensions> StatisticalModelTransformType;

modules/ITK/cli/statismo-posterior.cxx

@@ -40,6 +40,7 @@
 #include <itkPointsLocator.h>
 #include <itkStandardImageRepresenter.h>
 #include <itkStandardMeshRepresenter.h>
+#include <itkStatismoIO.h>
 #include <itkStatisticalModel.h>
 #include <itkVersorRigid3DTransform.h>
 
@@ -172,7 +173,8 @@ void buildPosteriorShapeModel(programOptions& opt) {
     typedef itk::StandardMeshRepresenter<float, Dimensionality3D> RepresenterType;
     RepresenterType::Pointer pRepresenter = RepresenterType::New();
     StatisticalModelType::Pointer pModel = StatisticalModelType::New();
-    pModel->Load(pRepresenter.GetPointer(), opt.strInputModelFileName.c_str());
+    pModel = itk::StatismoIO<DataType>::LoadStatisticalModel(pRepresenter.GetPointer(),
+                                                             opt.strInputModelFileName.c_str());
 
     StatisticalModelType::Pointer pConstrainedModel;
     if (opt.strInputMeshFileName == "") {
@@ -187,7 +189,7 @@ void buildPosteriorShapeModel(programOptions& opt) {
         pConstrainedModel = buildPosteriorShapeModel<DataType, StatisticalModelType>(pModel, pMeshInCorrespondence, opt.dVariance);
     }
 
-    pConstrainedModel->Save(opt.strOutputModelFileName.c_str());
+    itk::StatismoIO<DataType>::SaveStatisticalModel(pConstrainedModel, opt.strOutputModelFileName.c_str());
 }
 
 template<unsigned Dimensionality>
@@ -198,12 +200,13 @@ void buildPosteriorDeformationModel(programOptions& opt) {
     typedef itk::StandardImageRepresenter<VectorPixelType, Dimensionality> RepresenterType;
     typename RepresenterType::Pointer pRepresenter = RepresenterType::New();
     typename StatisticalModelType::Pointer pModel = StatisticalModelType::New();
-    pModel->Load(pRepresenter.GetPointer(), opt.strInputModelFileName.c_str());
+    pModel = itk::StatismoIO<DataType>::LoadStatisticalModel(pRepresenter.GetPointer(),
+                                                             opt.strInputModelFileName.c_str());
 
     typename StatisticalModelType::Pointer pConstrainedModel;
     pConstrainedModel = buildPosteriorDeformationModel<DataType, StatisticalModelType>(pModel, opt.strInputFixedLandmarksFileName, opt.strInputMovingLandmarksFileName, opt.dVariance);
 
-    pConstrainedModel->Save(opt.strOutputModelFileName.c_str());
+    itk::StatismoIO<DataType>::SaveStatisticalModel(pConstrainedModel, opt.strOutputModelFileName.c_str());
 }
 
 
@@ -237,4 +240,4 @@ po::options_description initializeProgramOptions(programOptions& poParameters) {
     po::options_description optAllOptions;
     optAllOptions.add(optMandatory).add(optMesh).add(optLandmarks).add(optAdditional);
     return optAllOptions;
-}
+}