DOC: beautified code by Uncrustify

Modules/CommandLine/src/selxCommandLine.cxx

 /*=========================================================================
  *
- *  Copyright Leiden University Medical Center, Erasmus University Medical 
+ *  Copyright Leiden University Medical Center, Erasmus University Medical
  *  Center and contributors
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
@@ -42,141 +42,142 @@ namespace po = boost::program_options;
 using namespace std;
 using namespace selx;
 
-template<class T>
-ostream& operator<<(ostream& os, const vector<T>& v)
+template< class T >
+ostream &
+operator<<( ostream & os, const vector< T > & v )
 {
-  copy(v.begin(), v.end(), ostream_iterator<T>(os, " "));
+  copy( v.begin(), v.end(), ostream_iterator< T >( os, " " ) );
   return os;
 }
 
 
-
-
-int main(int ac, char* av[])
+int
+main( int ac, char * av[] )
 {
-  try {
-   
-
+  try
+  {
     typedef vector< string > split_vector_type;
 
-    SuperElastixFilter<DefaultComponents>::Pointer superElastixFilter = SuperElastixFilter<DefaultComponents>::New();
-    
+    SuperElastixFilter< DefaultComponents >::Pointer superElastixFilter = SuperElastixFilter< DefaultComponents >::New();
 
-    fs::path configurationPath;
-    vector<string> inputPairs;
-    vector<string> outputPairs;
+    fs::path         configurationPath;
+    vector< string > inputPairs;
+    vector< string > outputPairs;
 
     // Store the reader so that they will not be destroyed before the pipeline is executed.
-    vector<AnyFileReader::Pointer> fileReaders;
+    vector< AnyFileReader::Pointer > fileReaders;
     // Store the writers for the update call
     //vector<ImageWriter2DType::Pointer> fileWriters;
-    vector<AnyFileWriter::Pointer> fileWriters;
+    vector< AnyFileWriter::Pointer > fileWriters;
 
-    po::options_description desc("Allowed options");
+    po::options_description desc( "Allowed options" );
     desc.add_options()
-      ("help", "produce help message")
-      ("conf", po::value<fs::path>(&configurationPath)->required(), "Configuration file")
-      ("in", po::value<vector<string>>(&inputPairs)->multitoken(), "Input data: images, labels, meshes, etc. Usage <name>=<path>")
-      ("out", po::value<vector<string>>(&outputPairs)->multitoken(), "Output data: images, labels, meshes, etc. Usage <name>=<path>")
-      ("graphout", po::value<fs::path>(), "Output Graphviz dot file")
-      ;
+      ( "help", "produce help message" )
+      ( "conf", po::value< fs::path >( &configurationPath )->required(), "Configuration file" )
+      ( "in", po::value< vector< string >>( &inputPairs )->multitoken(), "Input data: images, labels, meshes, etc. Usage <name>=<path>" )
+      ( "out", po::value< vector< string >>( &outputPairs )->multitoken(), "Output data: images, labels, meshes, etc. Usage <name>=<path>" )
+      ( "graphout", po::value< fs::path >(), "Output Graphviz dot file" )
+    ;
 
     po::variables_map vm;
-    po::store(po::parse_command_line(ac, av, desc), vm);
-    po::notify(vm);
+    po::store( po::parse_command_line( ac, av, desc ), vm );
+    po::notify( vm );
 
-    if (vm.count("help")) {
+    if( vm.count( "help" ) )
+    {
       cout << desc << "\n";
       return 0;
     }
 
     Blueprint::Pointer blueprint;
-    if (configurationPath.extension() == ".xml")
+    if( configurationPath.extension() == ".xml" )
     {
       // TODO: open file here and pass a stream to the ConfigurationReader
-      blueprint = ConfigurationReader::FromXML(configurationPath.string());
+      blueprint = ConfigurationReader::FromXML( configurationPath.string() );
     }
-    else if (configurationPath.extension() == ".json")
+    else if( configurationPath.extension() == ".json" )
     {
       // TODO: open file here and pass a stream to the ConfigurationReader
-      blueprint = ConfigurationReader::FromJson(configurationPath.string());
+      blueprint = ConfigurationReader::FromJson( configurationPath.string() );
     }
-    else {
-      throw invalid_argument("Configuration file requires extension .xml or .json");
+    else
+    {
+      throw invalid_argument( "Configuration file requires extension .xml or .json" );
     }
 
-    if (vm.count("graphout"))
+    if( vm.count( "graphout" ) )
     {
-      blueprint->WriteBlueprint(vm["graphout"].as<fs::path>().string());
+      blueprint->WriteBlueprint( vm[ "graphout" ].as< fs::path >().string() );
     }
 
-    superElastixFilter->SetBlueprint(blueprint);
+    superElastixFilter->SetBlueprint( blueprint );
 
-    if (vm.count("in")) {
+    if( vm.count( "in" ) )
+    {
       cout << "Number of input data: " << inputPairs.size() << "\n";
       int index = 0;
-      for (const auto & inputPair : inputPairs)
+      for( const auto & inputPair : inputPairs )
       {
         split_vector_type nameAndPath;
-        boost::split(nameAndPath, inputPair, boost::is_any_of("="));  // NameAndPath == { "name","path" }
-        const string & name = nameAndPath[0];
-        const string & path = nameAndPath[1];
+        boost::split( nameAndPath, inputPair, boost::is_any_of( "=" ) );  // NameAndPath == { "name","path" }
+        const string & name = nameAndPath[ 0 ];
+        const string & path = nameAndPath[ 1 ];
 
         cout << " " << index << " " << name << " : " << path << "\n";
         ++index;
 
-        // since we do not know which reader type we should instantiate for input "name", 
+        // since we do not know which reader type we should instantiate for input "name",
         // we ask SuperElastix for a reader that matches the type of the source component "name"
 
-        AnyFileReader::Pointer reader = superElastixFilter->GetInputFileReader(name);        
-        reader->SetFileName(path);
-        superElastixFilter->SetInput(name, reader->GetOutput());
-        fileReaders.push_back(reader);
+        AnyFileReader::Pointer reader = superElastixFilter->GetInputFileReader( name );
+        reader->SetFileName( path );
+        superElastixFilter->SetInput( name, reader->GetOutput() );
+        fileReaders.push_back( reader );
       }
     }
 
-    if (vm.count("out")) {
+    if( vm.count( "out" ) )
+    {
       cout << "Number of output data: " << outputPairs.size() << "\n";
       int index = 0;
-      for (const auto & outputPair : outputPairs)
+      for( const auto & outputPair : outputPairs )
       {
         split_vector_type nameAndPath;
-        boost::split(nameAndPath, outputPair, boost::is_any_of("="));  // NameAndPath == { "name","path" }
-        const string & name = nameAndPath[0];
-        const string & path = nameAndPath[1];
+        boost::split( nameAndPath, outputPair, boost::is_any_of( "=" ) );  // NameAndPath == { "name","path" }
+        const string & name = nameAndPath[ 0 ];
+        const string & path = nameAndPath[ 1 ];
 
         cout << " " << index << " " << name << " : " << path << "\n";
         ++index;
 
-        // since we do not know which writer type we should instantiate for output "name", 
+        // since we do not know which writer type we should instantiate for output "name",
         // we ask SuperElastix for a writer that matches the type of the sink component "name"
-        AnyFileWriter::Pointer writer = superElastixFilter->GetOutputFileWriter(name);
-        
+        AnyFileWriter::Pointer writer = superElastixFilter->GetOutputFileWriter( name );
+
         //ImageWriter2DType::Pointer writer = ImageWriter2DType::New();
-        writer->SetFileName(path);
+        writer->SetFileName( path );
         //writer->SetInput(superElastixFilter->GetOutput<Image2DType>(name));
-        writer->SetInput(superElastixFilter->GetOutput(name));
-        fileWriters.push_back(writer);
+        writer->SetInput( superElastixFilter->GetOutput( name ) );
+        fileWriters.push_back( writer );
       }
     }
-    
+
     /* Execute SuperElastix by updating the writers */
 
-    for (auto & writer : fileWriters)
+    for( auto & writer : fileWriters )
     {
       writer->Update();
     }
-
-
   }
-  catch (exception& e) {
+  catch( exception & e )
+  {
     cerr << "error: " << e.what() << "\n";
     return 1;
   }
-  catch (...) {
+  catch( ... )
+  {
     cerr << "Exception of unknown type!\n";
   }
 
-
   return 0;
-}
\ No newline at end of file
+}

Modules/Components/Controller/include/selxRegistrationController.h

 /*=========================================================================
  *
- *  Copyright Leiden University Medical Center, Erasmus University Medical 
+ *  Copyright Leiden University Medical Center, Erasmus University Medical
  *  Center and contributors
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
@@ -27,48 +27,51 @@
 
 namespace selx
 {
-  template<bool dummy = true>
-  class RegistrationControllerComponent :
-    public SuperElastixComponent <
-    Accepting< RunRegistrationInterface, ReconnectTransformInterface, AfterRegistrationInterface >,
-    Providing < RegistrationControllerStartInterface >
-    >
-  {
-    // RegistrationControllerComponent is a work-around for broken itk-pipelines.
-    // Both the elastix and itkv4 require to connect their transforms *after* execution of the registration.
-    // This controller explicitly performs these steps
-    // TODO: see if signals-and-slots paradigm is appropriate here.
-
-
-  public:
-    selxNewMacro(RegistrationControllerComponent, ComponentBase);
-
-    //itkStaticConstMacro(Dimensionality, unsigned int, Dimensionality);
-
-    RegistrationControllerComponent();
-    virtual ~RegistrationControllerComponent();
-
-    
-	// Accepting Interfaces:
-    virtual int Set(RunRegistrationInterface*) override;
-	  virtual int Set(ReconnectTransformInterface*) override;
-    virtual int Set(AfterRegistrationInterface*) override;
-
-	// Providing Interfaces:
-    virtual void RegistrationControllerStart(void) override;
-
-    virtual bool MeetsCriterion(const ComponentBase::CriterionType &criterion) override;
-    static const char * GetDescription() { return "RegistrationController Component"; };
-  private:
-	  std::set<RunRegistrationInterface*> m_RunRegistrationInterfaces;
-    std::set<ReconnectTransformInterface*> m_ReconnectTransformInterfaces;
-    std::set<AfterRegistrationInterface*> m_AfterRegistrationInterfaces;
-
-    protected:
-  };
+template< bool dummy = true >
+class RegistrationControllerComponent :
+  public SuperElastixComponent<
+  Accepting< RunRegistrationInterface, ReconnectTransformInterface, AfterRegistrationInterface >,
+  Providing< RegistrationControllerStartInterface >
+  >
+{
+  // RegistrationControllerComponent is a work-around for broken itk-pipelines.
+  // Both the elastix and itkv4 require to connect their transforms *after* execution of the registration.
+  // This controller explicitly performs these steps
+  // TODO: see if signals-and-slots paradigm is appropriate here.
+
+public:
+
+  selxNewMacro( RegistrationControllerComponent, ComponentBase );
+
+  //itkStaticConstMacro(Dimensionality, unsigned int, Dimensionality);
+
+  RegistrationControllerComponent();
+  virtual ~RegistrationControllerComponent();
+
+  // Accepting Interfaces:
+  virtual int Set( RunRegistrationInterface * ) override;
+
+  virtual int Set( ReconnectTransformInterface * ) override;
+
+  virtual int Set( AfterRegistrationInterface * ) override;
+
+  // Providing Interfaces:
+  virtual void RegistrationControllerStart( void ) override;
+
+  virtual bool MeetsCriterion( const ComponentBase::CriterionType & criterion ) override;
+
+  static const char * GetDescription() { return "RegistrationController Component"; }
+
+private:
+
+  std::set< RunRegistrationInterface * >    m_RunRegistrationInterfaces;
+  std::set< ReconnectTransformInterface * > m_ReconnectTransformInterfaces;
+  std::set< AfterRegistrationInterface * >  m_AfterRegistrationInterfaces;
 
+protected:
+};
 } //end namespace selx
 #ifndef ITK_MANUAL_INSTANTIATION
 #include "selxRegistrationController.hxx"
 #endif
-#endif // #define selxRegistrationController_h
\ No newline at end of file
+#endif // #define selxRegistrationController_h

Modules/Components/Controller/include/selxRegistrationController.hxx

 /*=========================================================================
  *
- *  Copyright Leiden University Medical Center, Erasmus University Medical 
+ *  Copyright Leiden University Medical Center, Erasmus University Medical
  *  Center and contributors
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
@@ -21,71 +21,81 @@
 
 namespace selx
 {
-  template<bool dummy>
-  RegistrationControllerComponent< dummy>::RegistrationControllerComponent()
-  {
-  }
+template< bool dummy >
+RegistrationControllerComponent< dummy >::RegistrationControllerComponent()
+{
+}
 
-  template<bool dummy>
-  RegistrationControllerComponent< dummy>::~RegistrationControllerComponent()
-  {
-  }
 
-  template<bool dummy>
-  int RegistrationControllerComponent< dummy>::Set(RunRegistrationInterface* other)
-  {
-    this->m_RunRegistrationInterfaces.insert(other);
-    return 0;
-  }
+template< bool dummy >
+RegistrationControllerComponent< dummy >::~RegistrationControllerComponent()
+{
+}
 
-  template<bool dummy>
-  int RegistrationControllerComponent< dummy>::Set(ReconnectTransformInterface* other)
-  {
-    this->m_ReconnectTransformInterfaces.insert(other);
-    return 0;
-  }
 
-  template<bool dummy>
-  int RegistrationControllerComponent< dummy>::Set(AfterRegistrationInterface* other)
+template< bool dummy >
+int
+RegistrationControllerComponent< dummy >::Set( RunRegistrationInterface * other )
+{
+  this->m_RunRegistrationInterfaces.insert( other );
+  return 0;
+}
+
+
+template< bool dummy >
+int
+RegistrationControllerComponent< dummy >::Set( ReconnectTransformInterface * other )
+{
+  this->m_ReconnectTransformInterfaces.insert( other );
+  return 0;
+}
+
+
+template< bool dummy >
+int
+RegistrationControllerComponent< dummy >::Set( AfterRegistrationInterface * other )
+{
+  this->m_AfterRegistrationInterfaces.insert( other );
+  return 0;
+}
+
+
+template< bool dummy >
+void
+RegistrationControllerComponent< dummy >::RegistrationControllerStart()
+{
+  for( auto && runRegistrationInterface : this->m_RunRegistrationInterfaces )
   {
-    this->m_AfterRegistrationInterfaces.insert(other);
-    return 0;
+    runRegistrationInterface->RunRegistration();
   }
-
-  template<bool dummy>
-  void RegistrationControllerComponent< dummy>::RegistrationControllerStart()
+  for( auto && reconnectTransformInterface : this->m_ReconnectTransformInterfaces )
   {
-    for (auto && runRegistrationInterface : this->m_RunRegistrationInterfaces)
-    {
-      runRegistrationInterface->RunRegistration();
-    }
-    for (auto && reconnectTransformInterface : this->m_ReconnectTransformInterfaces)
-    {
-      reconnectTransformInterface->ReconnectTransform();
-    }
-    //for (auto && afterRegistrationInterface : this->m_AfterRegistrationInterfaces)
-    //{
-    //  afterRegistrationInterface->AfterRegistration();
-    //}
+    reconnectTransformInterface->ReconnectTransform();
   }
+  //for (auto && afterRegistrationInterface : this->m_AfterRegistrationInterfaces)
+  //{
+  //  afterRegistrationInterface->AfterRegistration();
+  //}
+}
+
 
-  template<bool dummy>
-  bool RegistrationControllerComponent< dummy>::MeetsCriterion(const ComponentBase::CriterionType &criterion)
+template< bool dummy >
+bool
+RegistrationControllerComponent< dummy >::MeetsCriterion( const ComponentBase::CriterionType & criterion )
+{
+  bool hasUndefinedCriteria( false );
+  bool meetsCriteria( false );
+  if( criterion.first == "ComponentProperty" )
   {
-    bool hasUndefinedCriteria(false);
-    bool meetsCriteria(false);
-    if (criterion.first == "ComponentProperty")
+    meetsCriteria = true;
+    for( auto const & criterionValue : criterion.second )  // auto&& preferred?
     {
-      meetsCriteria = true;
-      for (auto const & criterionValue : criterion.second) // auto&& preferred?
+      if( criterionValue != "SomeProperty" )   // e.g. "GradientDescent", "SupportsSparseSamples
       {
-        if (criterionValue != "SomeProperty")  // e.g. "GradientDescent", "SupportsSparseSamples
-        {
-          meetsCriteria = false;
-        }
+        meetsCriteria = false;
       }
-    }    
-    return meetsCriteria;
+    }
   }
-
+  return meetsCriteria;
+}
 } //end namespace selx

Modules/Components/Controller/src/selxRegistrationController.cxx

 /*=========================================================================
  *
- *  Copyright Leiden University Medical Center, Erasmus University Medical 
+ *  Copyright Leiden University Medical Center, Erasmus University Medical
  *  Center and contributors
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");

Modules/Components/Elastix/include/selxElastixComponent.h

 /*=========================================================================
  *
- *  Copyright Leiden University Medical Center, Erasmus University Medical 
+ *  Copyright Leiden University Medical Center, Erasmus University Medical
  *  Center and contributors
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
@@ -32,165 +32,179 @@
 #include "selxMacro.h"
 namespace selx
 {
-  template <int Dimensionality, class TPixel>
-  class ElastixComponent : 
-    public SuperElastixComponent<
-      Accepting< 
-        itkImageFixedInterface<Dimensionality, TPixel>,
-        itkImageMovingInterface<Dimensionality, TPixel>
-      >,
-      Providing< 
-        itkImageInterface<Dimensionality, TPixel>, 
-        RunRegistrationInterface
-      >
-    >
-  {
-  public:
-    selxNewMacro(ElastixComponent, ComponentBase);
-
-    //itkStaticConstMacro(Dimensionality, unsigned int, Dimensionality);
-
-    ElastixComponent();
-    virtual ~ElastixComponent();
-    
-    typedef typename ComponentBase::CriterionType CriterionType;
-    typedef TPixel PixelType;
-
-    // the in and output image type of the component are chosen to be the same 
-    typedef itk::Image<PixelType, Dimensionality> ConnectionImageType;
-
-    // fixed and moving image types are all the same, these aliases can be used to be explicit. 
-    typedef itk::Image<PixelType, Dimensionality> FixedImageType;
-    typedef itk::Image<PixelType, Dimensionality> MovingImageType;
-
-    typedef typename ConnectionImageType::Pointer ItkImagePointer;
-
-    typedef elastix::ElastixFilter< FixedImageType, MovingImageType > ElastixFilterType;
-    typedef elastix::ParameterObject elxParameterObjectType;
-    typedef elxParameterObjectType::Pointer elxParameterObjectPointer;
-    
-    typedef elastix::TransformixFilter<FixedImageType> TransformixFilterType;
-
-
-    typedef itk::ResampleImageFilter<MovingImageType, ConnectionImageType> ResampleFilterType;
-
-    virtual int Set(itkImageFixedInterface<Dimensionality, TPixel>*) override;
-    virtual int Set(itkImageMovingInterface<Dimensionality, TPixel>*) override;
-    
-    virtual ItkImagePointer GetItkImage() override;
-    virtual void RunRegistration() override;
-
-    virtual bool MeetsCriterion(const CriterionType &criterion) override;
-    static const char * GetDescription() { return "Elastix Component"; };
-  private:
-    typename ElastixFilterType::Pointer m_elastixFilter;
-    typename TransformixFilterType::Pointer m_transformixFilter;
-    //selxParameterObjectPointer m_ParameterObject;
-
-    ItkImagePointer m_OutputImage;
-  protected:
-    /* The following struct returns the string name of computation type */
-    /* default implementation */
-
-    static inline const std::string GetTypeNameString()
-    {
-      itkGenericExceptionMacro(<< "Unknown ScalarType" << typeid(TPixel).name());
-      // TODO: provide the user instructions how to enable the compilation of the component with the required template types (if desired)
-      // We might define an exception object that can communicate various error messages: for simple user, for developer user, etc
-    }
-
-    static inline const std::string GetPixelTypeNameString()
-    {
-      itkGenericExceptionMacro(<< "Unknown PixelType" << typeid(TPixel).name());
-      // TODO: provide the user instructions how to enable the compilation of the component with the required template types (if desired)
-      // We might define an exception object that can communicate various error messages: for simple user, for developer user, etc
-    }
-
-  };
-
-  // unfortunately partial specialization of member functions is not allowed, without partially specializing the entire class.
-
-  /*
-  template <int Dimensionality>
-  class ElastixComponent < Dimensionality, double >
-  {
-    static inline const std::string GetPixelTypeNameString();
-  };
+template< int Dimensionality, class TPixel >
+class ElastixComponent :
+  public SuperElastixComponent<
+  Accepting<
+  itkImageFixedInterface< Dimensionality, TPixel >,
+  itkImageMovingInterface< Dimensionality, TPixel >
+  >,
+  Providing<
+  itkImageInterface< Dimensionality, TPixel >,
+  RunRegistrationInterface
+  >
+  >
+{
+public:
 
-  template <int Dimensionality>
-  inline const std::string
-    ElastixComponent<Dimensionality, double>
-    ::GetPixelTypeNameString()
-  {
-    return std::string("double");
-  }
-  */
+  selxNewMacro( ElastixComponent, ComponentBase );
 
-  template <>
-  inline const std::string
-    ElastixComponent<2, float