Merge branch 'develop' into ELASTIX-24-Component-Interface-Handshake

.gitmodules

-[submodule "Testing/GoogleTest"]
-	path = Testing/GoogleTest
-	url = https://github.com/kaspermarstal/GoogleTest
-	tag = release-1.7.0

.travis.yml

-sudo: false
+sudo: required
+dist: trusty
 
 language: cpp
 
@@ -26,8 +27,8 @@ before_script:
 
 script:
   - cmake ../SuperElastix/SuperBuild
-  - make --jobs=2 | grep -v '^--' | grep -v '^Installing'
+  - make --jobs=2 | grep -v '^--' | grep -v '^Installing' | grep -v '^common'
 
-after_sucess:
+after_success:
   - cd Elastix-build
   - ctest

CMake/elxComponent.cmake

-macro( ElastixComponent COMPONENT )
-  ElastixModuleCheckName( ${COMPONENT} )
-  set( ELASTIX_COMPONENT_{$COMPONENT}_DEFINED TRUE )
-endmacro()
-
-macro( ElastixComponentCheckName COMPONENT )
-  if( NOT "${_name}" MATCHES "^[a-zA-Z][a-zA-Z0-9]*$" )
-    message( FATAL_ERROR "Invalid component name: ${COMPONENT}" )
-  endif()
-endmacro()
\ No newline at end of file

CMake/elxModules.cmake

@@ -6,7 +6,7 @@ macro( _elxmodule_check_name MODULE )
     message( FATAL_ERROR "Invalid module name: ${MODULE}" )
   endif()
 
-  list( FIND ELXMODULE_ALL "${MODULE}" MODULE_FOUND )
+  list( FIND ELASTIX_MODULES "${MODULE}" MODULE_FOUND )
   if( ${MODULE_FOUND} EQUAL -1 )
     message( FATAL_ERROR "Module not found: ${MODULE}")
   endif()
@@ -16,7 +16,7 @@ macro( _elxmodule_enable MODULE )
   _elxmodule_check_name( ${MODULE} )
 
   if( NOT ${MODULE}_ENABLED )
-    set( USE_${MODULE} ON )
+    set( ELASTIX_USE_${MODULE} ON )
 
     include( ${${MODULE}_FILE} )
 
@@ -24,14 +24,9 @@ macro( _elxmodule_enable MODULE )
       include_directories( ${${MODULE}_INCLUDE_DIRS} )
     endif()
 
-    add_subdirectory( ${${MODULE}_SOURCE_DIR} )
-
     if( ${MODULE}_LIBRARIES )
       link_directories( ${${MODULE}_LIBRARY_DIRS} )
-
-      list( APPEND ELASTIX_LIBRARIES
-        ${${MODULE}_LIBRARIES}
-      )
+      list( APPEND ELASTIX_LIBRARIES ${${MODULE}_LIBRARIES} )
     endif()
 
     # TODO: Add recursive dependency walk
@@ -43,30 +38,32 @@ macro( _elxmodule_disable MODULE )
 endmacro()
 
 macro( _elxmodules_initialize )
-  set( ELXMODULE_ALL )
+  set( ELASTIX_LIBRARIES )
+  set( ELASTIX_MODULES )
 
-  file( GLOB MODULE_FILES RELATIVE "${CMAKE_SOURCE_DIR}"
+  file( GLOB_RECURSE MODULE_FILES RELATIVE "${CMAKE_SOURCE_DIR}"
      "${CMAKE_SOURCE_DIR}/Modules/*/elxModule*.cmake"
   )
 
   message( STATUS "Found the following elastix modules:")
   foreach( MODULE_FILE ${MODULE_FILES})
-    get_filename_component( MODULE_PATH ${MODULE_FILE} PATH )
-    get_filename_component( MODULE ${MODULE_FILE} NAME_WE )
-    message( STATUS "  ${MODULE}" )
+    get_filename_component( MODULE_NAME ${MODULE_FILE} NAME_WE )
+    get_filename_component( ${MODULE_NAME}_PATH ${MODULE_FILE} PATH )
+    
+    message( STATUS "  ${MODULE_NAME}" )
 
-    option( "USE_${MODULE}" OFF )
-    set( "${MODULE}_FILE" ${CMAKE_SOURCE_DIR}/${MODULE_FILE} )
-    set( "${MODULE}_ENABLED" OFF )
+    option( "ELASTIX_USE_${MODULE_NAME}" OFF )
+    set( "${MODULE_NAME}_FILE" ${CMAKE_SOURCE_DIR}/${MODULE_FILE} )
+    set( "${MODULE_NAME}_ENABLED" OFF )
 
-    set( ${MODULE}_SOURCE_DIR ${CMAKE_SOURCE_DIR}/${MODULE_PATH} )
-    set( ${MODULE}_BINARY_DIR ${CMAKE_BINARY_DIR}/${MODULE_PATH} )
+    set( ${MODULE_NAME}_SOURCE_DIR ${CMAKE_SOURCE_DIR}/${${MODULE_NAME}_PATH} )
+    set( ${MODULE_NAME}_BINARY_DIR ${CMAKE_BINARY_DIR}/${${MODULE_NAME}_PATH} )
 
-    set( ${MODULE}_INCLUDE_DIRS )
-    set( ${MODULE}_LIBRARY_DIRS )
-    set( ${MODULE}_LIBRARIES )
+    set( ${MODULE_NAME}_INCLUDE_DIRS )
+    set( ${MODULE_NAME}_LIBRARY_DIRS )
+    set( ${MODULE_NAME}_LIBRARIES )
 
-    list(APPEND ELXMODULE_ALL ${MODULE} )
+    list(APPEND ELASTIX_MODULES ${MODULE_NAME} )
   endforeach()
 endmacro()
 
@@ -79,9 +76,3 @@ macro( elxmodule_enable MODULE )
   _elxmodule_enable( ${MODULE} )
 endmacro()
 
-macro( elxmodule_compile MODULE )
-  project( "${MODULE}" )
-  add_library( ${MODULE} STATIC "${${MODULE}_SOURCE_FILES}" )
-  target_link_libraries( ${MODULE} ${ELASTIX_LIBRARIES} )
-  list( APPEND ${MODULE}_LIBRARIES ${MODULE} )
-endmacro()

CMake/elxWinConfig.cmake

 # Visual Studio complains if paths are too long
+string( LENGTH "${CMAKE_CURRENT_SOURCE_DIR}" n )
+if( n GREATER 50 )
+message(
+  FATAL_ERROR
+    "Source code directory path length is too long for MSVC (${n} > 50)."
+    "Please move the source code directory to a directory with a shorter path."
+  )
+endif()
 
-if( MSVC )
-  string( LENGTH "${CMAKE_CURRENT_SOURCE_DIR}" n )
-  if( n GREATER 50 )
-  message(
-    FATAL_ERROR
-      "Source code directory path length is too long for MSVC (${n} > 50)."
-      "Please move the source code directory to a directory with a shorter path."
-    )
-  endif()
-
-  string( LENGTH "${CMAKE_CURRENT_BINARY_DIR}" n )
-  if( n GREATER 50 )
-  message(
-    FATAL_ERROR
-      "Build directory path length is too long for MSVC (${n} > 50)."
-      "Please move the build directory to a directory with a shorter path."
-    )
-  endif()
-
-  set( CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /bigobj" )
-  set( CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} /bigobj" )
-  set( CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} /bigobj" )
+string( LENGTH "${CMAKE_CURRENT_BINARY_DIR}" n )
+if( n GREATER 50 )
+message(
+  FATAL_ERROR
+    "Build directory path length is too long for MSVC (${n} > 50)."
+    "Please move the build directory to a directory with a shorter path."
+  )
 endif()
\ No newline at end of file

CMake/elxWinConfigGoogleTest.cmake

-# GoogleTest needs static linking
-
-include( elxCompilerFlags.cmake )
-foreach( CompilerFlag ${CompilerFlags} )
-  string( REPLACE "/MD" "/MT" ${CompilerFlag} "${${CompilerFlag}}" )
-endforeach()

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required( VERSION 2.8 )
 
 # Explicitly add INCREMENTAL linking option to command lines.
 # http://www.cmake.org/pipermail/cmake/2010-February/035174.html
-set( MSVC_INCREMENTAL_DEFAULT ON )
+#set( MSVC_INCREMENTAL_DEFAULT ON )
 
 # ---------------------------------------------------------------------
 project( Elastix )
@@ -13,13 +13,10 @@ set( CMAKE_RUNTIME_OUTPUT_DIRECTORY
 )
 
 # Include SuperElastix CMake scripts
-set( CMAKE_MODULE_PATH
-  "${CMAKE_CURRENT_SOURCE_DIR}/CMake" 
-  ${CMAKE_MODULE_PATH}
-)
+list( APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/CMake" )
 
-if( ${CMAKE_CXX_COMPILER_ID} STREQUAL "MSVC" )
-  include( elxWinConfig.cmake )
+if( ${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC )
+  include( elxWinConfig )
 endif()
 
 # ---------------------------------------------------------------------
@@ -31,14 +28,13 @@ include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/elxITKRequiredModules.cmake" )
 
 # ---------------------------------------------------------------------
 # Boost Graph Library
-find_package( Boost REQUIRED graph )
+find_package( Boost )
 include_directories( ${Boost_INCLUDE_DIRS} )
 
 # ---------------------------------------------------------------------
-# Build Elastix
-
+# Build SuperElastix
 # For now we just enable all modules
-include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/elxModules.cmake" )
+include( elxModules )
 elxmodule_enable( elxModuleCore )
 
 # ---------------------------------------------------------------------
@@ -46,14 +42,14 @@ elxmodule_enable( elxModuleCore )
 
 # Testing requires CMake version 2.8.11 to download test data
 if( CMAKE_VERSION VERSION_LESS 2.8.11 )
-  set( ELASTIX_BUILD_TESTING_DEFAULT OFF )
+  set( SUPERELASTIX_BUILD_TESTING_DEFAULT OFF )
   message( STATUS "ELASTIX_BUILD_TESTING is set to OFF because CMake version is less than 2.8.11" )
 else()
-  set( ELASTIX BUILD_TESTING_DEFAULT ON )
+  set( SUPERELASTIX_BUILD_TESTING_DEFAULT ON )
 endif()
 
-option( ELASTIX_BUILD_TESTING "Enable building tests." ${ELASTIX_BUILD_TESTING_DEFAULT} )
-if( ${ELASTIX_BUILD_TESTING} )
+option( SUPERELASTIX_BUILD_TESTING "Enable building tests." ${SUPERELASTIX_BUILD_TESTING_DEFAULT} )
+if( ${SUPERELASTIX_BUILD_TESTING} )
   enable_testing()
   add_subdirectory( Testing )
 endif()
@@ -61,9 +57,9 @@ endif()
 # ---------------------------------------------------------------------
 # Build Documentation
 
-mark_as_advanced( ELASTIX_BUILD_DOXYGEN )
-option( ELASTIX_BUILD_DOXYGEN "Enable building Doxygen documentation." OFF )
+mark_as_advanced( SUPERELASTIX_BUILD_DOXYGEN )
+option( SUPERELASTIX_BUILD_DOXYGEN "Enable building Doxygen documentation." OFF )
 
-mark_as_advanced( ELASTIX_BUILD_READTHEDOCS )
-option( ELASTIX_BUILD_READTHEDOCS "Enable building readthedocs.org documentation." OFF )
+mark_as_advanced( SUPERELASTIX_BUILD_READTHEDOCS )
+option( SUPERELASTIX_BUILD_READTHEDOCS "Enable building readthedocs.org documentation." OFF )
 

Modules/Core/Blueprints/include/elxBlueprint.h

 #ifndef __Blueprint_h
 #define __Blueprint_h
 
+#include "boost/graph/graph_traits.hpp"
+#include "boost/graph/directed_graph.hpp"
+
 #include "itkObjectFactory.h"
 #include "itkDataObject.h"
 
 #include "elxMacro.h"
-#include "elxComponentDescriptor.h"
-
-#include "boost/graph/graph_traits.hpp"
-#include "boost/graph/directed_graph.hpp"
 
 namespace elx {
 
-template< class TComponentDescriptor >
 class Blueprint : public itk::DataObject
 {
 public:
 
   elxNewMacro( Blueprint, itk::DataObject );
 
-  typedef TComponentDescriptor                                                ComponentDescriptorType;
-  typedef typename TComponentDescriptor::ComponentNameType                    ComponentNameType;
+  typedef std::string                                                ParameterKeyType;
+  typedef std::vector< std::string >                                 ParameterValueType;
+  typedef std::map< ParameterKeyType, ParameterValueType >           ParameterMapType;
+
+  // Component parameter map that sits on a node in the graph 
+  // and holds component configuration settings
+  struct ComponentPropertyType { 
+    ParameterMapType parameterMap;
+  };
+
+  // Component parameter map that sits on an edge in the graph 
+  // and holds component configuration settings
+  struct ConnectionPropertyType { 
+    ParameterMapType parameterMap;
+  };
   
   typedef boost::adjacency_list< boost::vecS,      
                                  boost::vecS,      
                                  boost::directedS,
-                                 ComponentDescriptorType >                    GraphType;
-
-  typedef typename boost::graph_traits< GraphType >::vertex_descriptor        ComponentType;
-  typedef typename boost::graph_traits< GraphType >::vertex_iterator          ComponentIterator, ComponentIteratorEnd;
-
-  typedef boost::vertex_index_t                                               ComponentIndexType;
-  typedef typename boost::property_map< GraphType, ComponentIndexType >::type ComponentIndexMapType;
-
-  typedef typename boost::graph_traits< GraphType >::edge_descriptor          ConnectionDescriptorType;
-  typedef typename boost::graph_traits< GraphType >::edge_iterator            ConnectionIterator, ConnectionIteratorEnd;
-
-  typedef typename boost::graph_traits< GraphType >::in_edge_iterator         InputIterator, InputIteratorEnd;
-  typedef typename boost::graph_traits< GraphType >::out_edge_iterator        OutputIterator, OutputIteratorEnd;
-
-  int TestFunction( void );
-  bool AddComponent( ComponentDescriptorType component );
-  bool SetComponent( ComponentIndexType componentIndex, ComponentDescriptorType component );
-  ComponentDescriptorType GetComponent( ComponentIndexType componentIndex );
-  bool RemoveComponent( ComponentDescriptorType component );
-
-  bool SetConnection( ComponentIndexType upstream, ComponentIndexType downstream );
-  ConnectionDescriptorType GetConnection( ConnectionDescriptorType Connection );
-  bool RemoveConnection( ConnectionDescriptorType connection );
-
-  void PrintGraph( void );
+                                 ComponentPropertyType,
+                                 ConnectionPropertyType >             GraphType;
+
+  typedef boost::graph_traits< GraphType >::vertex_descriptor         ComponentIndexType;
+  typedef boost::graph_traits< GraphType >::vertex_iterator           ComponentIteratorType;
+  typedef std::pair< ComponentIteratorType, ComponentIteratorType >   ComponentIteratorPairType;
+
+  typedef boost::graph_traits< GraphType >::edge_descriptor           ConnectionIndexType;
+  typedef boost::graph_traits< GraphType >::edge_iterator             ConnectionIteratorType;
+  typedef std::pair< ConnectionIteratorType, ConnectionIteratorType > ConnectionIteratorPairType;
+
+  typedef boost::graph_traits< GraphType >::in_edge_iterator          InputIteratorType;
+  typedef std::pair< InputIteratorType, InputIteratorType >           InputIteratorPairType;
+
+  typedef boost::graph_traits< GraphType >::out_edge_iterator         OutputIteratorType;
+  typedef std::pair< OutputIteratorType, OutputIteratorType >         OutputIteratorPairType;
+
+  // Interface for managing components
+  ComponentIndexType AddComponent( void );
+  ComponentIndexType AddComponent( ParameterMapType parameterMap );
+  ParameterMapType GetComponent( ComponentIndexType index );
+  void SetComponent( ComponentIndexType, ParameterMapType parameterMap );
+
+  // TODO: Let user delete component. Before we do this, we need a proper way of 
+  // checking that a vertex exist. Otherwise a call to GetComponent() on 
+  // a deleted vertex will result in segfault. It is not really a in issue
+  // _before_ release since typically we (the developers) will use blueprint 
+  // interface procedurally.
+  // void DeleteComponent( ComponentIndexType );
+
+  ComponentIteratorPairType GetComponentIterator( void ) {
+    return boost::vertices( this->m_Graph );
+  }
+
+  // Interface for managing connections between components in which we 
+  // deliberately avoid using connection indexes, but instead force
+  // the user to think in terms of components (which is conceptually simpler)
+  bool AddConnection( ComponentIndexType upstream, ComponentIndexType downstream );
+  bool AddConnection( ComponentIndexType upstream, ComponentIndexType downstream, ParameterMapType parameterMap );
+  ParameterMapType GetConnection( ComponentIndexType upstream, ComponentIndexType downstream );
+  bool SetConnection(  ComponentIndexType upstream, ComponentIndexType downstream, ParameterMapType parameterMap );
+  bool DeleteConnection( ComponentIndexType upstream, ComponentIndexType downstream );
+  bool ConnectionExists( ComponentIndexType upstream, ComponentIndexType downstream );
+
+  // Returns iterator for all connections in the graph
+  ConnectionIteratorPairType GetConnectionIterator( void ) {
+    return boost::edges(this->m_Graph);
+  }
+
+  // Returns the outgoing connections from a component in the graph,
+  // i.e. all components that reads data from given component
+  OutputIteratorPairType GetOutputIterator( const ComponentIndexType index ) {
+    return boost::out_edges( index, this->m_Graph );
+  }
+
+  void WriteBlueprint( const std::string filename );
 
 private:
+  
+  ConnectionIndexType GetConnectionIndex( ComponentIndexType upsteam, ComponentIndexType downstream );
 
   GraphType m_Graph;
 

Modules/Core/Blueprints/include/elxComponentDescriptor.h

-#ifndef __ComponentDescriptor_h
-#define __ComponentDescriptor_h
-
-#include "elxMacro.h"
-#include "itkObjectFactory.h"
-#include "itkDataObject.h"
-
-namespace elx {
-
-class ComponentDescriptor : public itk::DataObject
-{
-public:
-
-  elxNewMacro( ComponentDescriptor, itk::DataObject );
-
-  // Identifier to find component in the component database
-  typedef std::string ComponentNameType;
-
-  ComponentDescriptor( void ) { this->SetComponentName( ComponentNameType() ); }
-  ComponentDescriptor( const ComponentNameType componentName );
-
-  // TODO: Setter should validate ComponentName exists in ComponentDatabase
-  itkSetMacro( ComponentName, ComponentNameType ); 
-  itkGetMacro( ComponentName, ComponentNameType );
-
-private:
-
-  ComponentNameType m_ComponentName;
-
-};
-
-}
-
-#endif // __ComponentDescriptor_h

Modules/Core/Blueprints/src/elxBlueprint.cxx

-#ifndef __Blueprint_hxx
-#define __Blueprint_hxx
+#ifndef __Blueprint_cxx
+#define __Blueprint_cxx
 
-#include <boost/graph/graphviz.hpp>
+#include "boost/graph/graphviz.hpp"
 
 #include "elxBlueprint.h"
 
 namespace elx {
 
-/*
-Blueprint< ComponentDescriptor >::ComponentDescriptorType
-Blueprint< ComponentDescriptor >
-::AddComponent( ComponentDescriptorType component )
+Blueprint::ComponentIndexType
+Blueprint
+::AddComponent( void )
 {
-  // TODO: Check that the component is in the ComponentDatabase
   this->Modified();
-  return this->m_Graph->add_vertex( component );
+
+  ComponentIndexType index = boost::add_vertex( this->m_Graph );
+
+  // Return component index so component can retrieved at a later time
+  return index;
 }
 
-bool
-Blueprint< ComponentDescriptor >
-::SetComponent( ComponentDescriptorType component )
+Blueprint::ComponentIndexType
+Blueprint
+::AddComponent( ParameterMapType parameterMap )
+{
+  this->Modified();
+
+  ComponentIndexType index = boost::add_vertex( this->m_Graph );
+  this->m_Graph[index].parameterMap = parameterMap;
+
+  // Return component index so component can retrieved at a later time
+  return index;
+}
+
+Blueprint::ParameterMapType
+Blueprint
+::GetComponent( ComponentIndexType index )
 {
   this->Modified();
-  return this->m_Graph->remove_vertex( connection );
+
+  return this->m_Graph[ index ].parameterMap;
+}
+
+void
+Blueprint
+::SetComponent( ComponentIndexType index, ParameterMapType parameterMap )
+{
+  this->Modified();
+  this->m_Graph[ index ].parameterMap = parameterMap;
 }
 
+// TODO: See explanation in elxBlueprint.h
+// void
+// Blueprint
+// ::DeleteComponent( const ComponentIndexType index )
+// {
+//   this->Modified();
+//
+//   clear_vertex( index, this->m_Graph );
+//   remove_vertex( index, this->m_Graph );
+// }
+
 bool
-Blueprint< ComponentDescriptor >
-::RemoveComponent( ComponentDescriptorType component )
+Blueprint
+::AddConnection( ComponentIndexType upstream, ComponentIndexType downstream )
 {
   this->Modified();
-  return this->m_Graph->remove_vertex( connection );
+
+  if( this->ConnectionExists( upstream, downstream) ) {
+    return false;
+  }
+  
+  // Adds directed connection from upstream component to downstream component
+  return boost::add_edge( upstream, downstream, this->m_Graph ).second;
 }
 
 bool
-Blueprint< ComponentDescriptor >
-::AddConnection( ComponentDescriptorType upsteam, ComponentDescriptorType downstream )
+Blueprint
+::AddConnection( ComponentIndexType upstream, ComponentIndexType downstream, ParameterMapType parameterMap )
+{
+  this->Modified();
+
+  if( !this->ConnectionExists( upstream, downstream ) ) {
+    ConnectionIndexType index = boost::add_edge( upstream, downstream, this->m_Graph ).first;
+    this->m_Graph[ index ].parameterMap = parameterMap;
+    return true;
+  }
+
+  // If the connection does not exist don't do anything because previous settings 
+  // will be overwritten.  If the user do want to overwrite current settings, 
+  // she should use SetConnection() instead where the intent is explicit.  
+  return false;
+}
+
+Blueprint::ParameterMapType
+Blueprint
+::GetConnection( ComponentIndexType upstream, ComponentIndexType downstream )
 {
   this->Modified();
-  return this->m_Graph->add_edge( upstream, downstream );
+
+  return this->m_Graph[ this->GetConnectionIndex( upstream, downstream ) ].parameterMap;
 }
 
-ConnectionDescriptorType
-Blueprint< ComponentDescriptor >
-::GetConnection( ConnectionDescriptorType Connection )
+bool
+Blueprint
+::SetConnection( ComponentIndexType upstream, ComponentIndexType downstream, ParameterMapType parameterMap )
 {
   this->Modified();
+
+  if( !this->ConnectionExists( upstream, downstream ) ) {
+    return this->AddConnection( upstream, downstream, parameterMap );
+  } else {
+    this->m_Graph[ this->GetConnectionIndex( upstream, downstream ) ].parameterMap = parameterMap;
+    return true;
+  }
 }
 
-void 
-Blueprint< ComponentDescriptor >
-::RemoveConnection( ConnectionType connection )
+bool
+Blueprint
+::DeleteConnection( ComponentIndexType upstream, ComponentIndexType downstream )
 {
   this->Modified();
-  this->m_Graph->remove_edge( connection );
+
+  if( this->ConnectionExists( upstream, downstream ) ) {
+    this->m_Graph.remove_edge( this->GetConnectionIndex( upstream, downstream ) );
+  }
+  
+  return !this->ConnectionExists( upstream, downstream );
 }
 
-void 
-Blueprint< ComponentDescriptor >
-::PrintGraph( void )
+bool
+Blueprint
+::ConnectionExists( ComponentIndexType upstream, ComponentIndexType downstream )
 {
-  // TODO: Link to graphviz library
-  // boost::write_graphviz(std::cout, this->m_Graph);
-  std::cout << "Printed graph" << std::endl;
+  return boost::edge( upstream, downstream, this->m_Graph).second;
 }
-*/
 
-template<>
-int
-Blueprint< ComponentDescriptor >
-::TestFunction( void )
-{ return 0; }
+Blueprint::ConnectionIndexType
+Blueprint
+::GetConnectionIndex( ComponentIndexType upstream, ComponentIndexType downstream )
+{
+  // This function is part of the internal API and should fail hard if we use it incorrectly
+  if( !this->ConnectionExists( upstream, downstream ) ) {
+    itkExceptionMacro( "Blueprint does not contain connection from component " << upstream << " to " << downstream );
+  }
+  
+  return boost::edge( upstream, downstream, this->m_Graph).first;
+}
+
+void 
+Blueprint
+::WriteBlueprint( const std::string filename ) 
+{
+  std::ofstream dotfile( filename.c_str() );
+  boost::write_graphviz( dotfile, this->m_Graph );
+}
 
 } // namespace elx 
 
-#endif // __Blueprint_hxx
\ No newline at end of file
+#endif // __Blueprint_cxx

Modules/Core/Blueprints/src/elxComponentDescriptor.cxx

-#ifndef __ComponentDescriptor_cxx
-#define __ComponentDescriptor_cxx
-
-#include "elxComponentDescriptor.h"
-
-// TODO: Need enum for component name?
-
-namespace elx {
-
-ComponentDescriptor
-::ComponentDescriptor( const ComponentNameType componentName )
-{
-  this->SetComponentName( componentName );
-}
-
-} // namespace elx
-
-#endif // __ComponentDescriptor_cxx
\ No newline at end of file

Modules/Core/CMakeLists.txt

-elxmodule_compile( ${MODULE} )

Modules/Core/elxModuleCore.cmake

+set( MODULE elxModuleCore )
+
+# Export include files
 set( ${MODULE}_INCLUDE_DIRS
-  ${CMAKE_SOURCE_DIR}/${MODULE_PATH}/Common/include
-  ${CMAKE_SOURCE_DIR}/${MODULE_PATH}/Blueprints/include
+  ${${MODULE}_SOURCE_DIR}/Common/include
+  ${${MODULE}_SOURCE_DIR}/Blueprints/include
+)
+
+# Export libraries
+set( ${MODULE}_LIBRARIES 
+  ${MODULE}
 )
 
+# Module source files
 set( ${MODULE}_SOURCE_FILES
-  ${CMAKE_SOURCE_DIR}/${MODULE_PATH}/Blueprints/src/elxComponentDescriptor.cxx
-  ${CMAKE_SOURCE_DIR}/${MODULE_PATH}/Blueprints/src/elxBlueprint.cxx
+  ${${MODULE}_SOURCE_DIR}/Blueprints/src/elxBlueprint.cxx
 )
 
-set( ${MODULE}_LIBRARIES 
-  elxModuleCore
-)
\ No newline at end of file
+# Compile library
+
+add_library( ${MODULE} STATIC "${${MODULE}_SOURCE_FILES}" )
+target_link_libraries( ${MODULE} ${ELASTIX_LIBRARIES} )

SuperBuild/CMakeLists.txt

 cmake_minimum_required( VERSION 2.8 )
 
 # ---------------------------------------------------------------------
-project( ElastixSuperBuild )
+project( SuperElastixSuperBuild )
 
 find_package( Git REQUIRED )
 
@@ -25,24 +25,24 @@ endif()
 
 # Build examples by default
 # Examples will be build as an external project to verify the installation of elastix
-option( ELASTIX_BUILD_EXAMPLES "Enable building examples." ON )
+option( SUPERELASTIX_BUILD_EXAMPLES "Enable building examples." ON )
 
 # Build tests by default
-option( ELASTIX_BUILD_TESTING "Enable building tests." ON )
-if( ELASTIX_BUILD_TESTING )
-  option( ELASTIX_BUILD_BENCHMARKING "Enable building benchmarks." ON )
-  option( ELASTIX_BUILD_DASHBOARD "Enable building benchmarks." ON )
+option( SUPERELASTIX_BUILD_TESTING "Enable building tests." ON )
+if( SUPERELASTIX_BUILD_TESTING )
+  option( SUPERELASTIX_BUILD_BENCHMARKING "Enable building benchmarks." ON )
+  option( SUPERELASTIX_BUILD_DASHBOARD "Enable building benchmarks." ON )
 endif()
 
 # Do not build dashboard by default
-option( ELASTIX_BUILD_DASHBOARD "Enable building dashboard." OFF )
+option( SUPERELASTIX_BUILD_DASHBOARD "Enable building dashboard." OFF )
 
 
 # ---------------------------------------------------------------------
 # Build ITK
 
 set( ITK_VERSION_MAJOR "4" )
-set( ITK_VERSION_MINOR "7" )
+set( ITK_VERSION_MINOR "8" )
 set( ITK_VERSION_PATCH "1" )
 set( ITK_VERSION_STRING "${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR}.${ITK_VERSION_PATCH}" )
 
@@ -51,10 +51,9 @@ option( USE_SYSTEM_ITK "Use an installed version of ITK" OFF )
 
 if( USE_SYSTEM_ITK )
   find_package( ITK ${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR} REQUIRED )
-  include( "${CMAKE_CURRENT_SOURCE_DIR}/../CMake/elxRequiredITKModules.cmake" )
+  include( elxRequiredITKModules )
 else()
   include( ExternalITK )
-  list( APPEND ELASTIX_DEPENDENCIES ITK )
 endif()
 
 # ---------------------------------------------------------------------
@@ -66,13 +65,35 @@ if( USE_SYSTEM_BOOST )
   find_package( BOOST REQUIRED graph )
 else()
   include( ExternalBoost )
-  list( APPEND ELASTIX_DEPENDENCIES BOOST )
 endif()
 
+# ---------------------------------------------------------------------
+# Build GoogleTest
+
+option( USE_SYSTEM_GOOGLETEST "Use a pre-compiled version of GoogleTest. " OFF ) 
+mark_as_advanced(USE_SYSTEM_GOOGLETEST) 
+if ( SUPERELASTIX_BUILD_TESTING ) 
+  if ( USE_SYSTEM_GOOGLETEST ) 
+    find_package( GTest REQUIRED ) 
+  else() 
+    include( ExternalGoogleTest ) 
+  endif() 
+endif() 
+
 # ---------------------------------------------------------------------
 # Build Elastix
 
-include( Elastix )
+# TODO: Add USE_SYSTEM_ELASTICLEGACY option
+mark_as_advanced( SUPERELASTIX_BUILD_ELASTIX )
+option( SUPERELASTIX_BUILD_ELASTIX ON )
+if( SUPERELASTIX_BUILD_ELASTIX )
+  include( ExternalElastix )
+endif()
+
+# ---------------------------------------------------------------------
+# Build SuperElastix
+
+include( SuperElastix )
 
 
 

SuperBuild/ExternalBoost.cmake

-set( PROJECT BOOST )
+set( proj BOOST )
 
 # Note: It IS important to download different files on different OS's:
 # on Unix-like systems, we need the file persmissions (only available in the .tar.gz),
@@ -19,7 +19,7 @@ else()
   endif()
 endif()
 
-set( BOOST_BUILD_DIR "${CMAKE_INSTALL_PREFIX}/${PROJECT}-build/" )
+set( BOOST_BUILD_DIR "${CMAKE_INSTALL_PREFIX}/${proj}-build/" )
 
 ExternalProject_Add( BOOST
   BUILD_IN_SOURCE 1
@@ -27,13 +27,10 @@ ExternalProject_Add( BOOST
   URL_MD5 ${BOOST_MD5}
   UPDATE_COMMAND ""
   CONFIGURE_COMMAND ${BOOST_CONFIGURE_COMMAND} 
-    --prefix=${BOOST_BUILD_DIR}/lib
-  BUILD_COMMAND ${BOOST_BUILD_COMMAND} install 
-    --prefix=${BOOST_BUILD_DIR}
-    --with-graph
-    --variant=release
-    --jobs=4
+  BUILD_COMMAND ""
   INSTALL_COMMAND ""
 )
 
-set( BOOST_ROOT ${BOOST_BUILD_DIR} )
+set( BOOST_ROOT "${CMAKE_INSTALL_PREFIX}/${proj}-prefix/src/BOOST" )
+
+list( APPEND ELASTIX_DEPENDENCIES ${proj} )

SuperBuild/ExternalElastix.cmake

+set( proj Elastix )
+
+set( ELASTIX_REPOSITORY git://github.com/mstaring/elastix.git )
+set( ELASTIX_TAG 6eb6fc7e0d86bafdfdffb1b8bbd125f2a56a486e )
+
+ExternalProject_Add( ${proj} 
+  GIT_REPOSITORY ${ELASTIX_REPOSITORY}
+  GIT_TAG ${ELASTIX_TAG}
+  UPDATE_COMMAND ""
+  SOURCE_DIR ${proj}
+  BINARY_DIR ${proj}-build
+  CMAKE_GENERATOR ${gen}
+  CMAKE_ARGS
+  --no-warn-unused-cli
+  -DELASTIX_BUILD_TESTING:BOOL=OFF
+  -DELASTIX_BUILD_EXECUTABLE:BOOL=OFF
+  -DELASTIX_BUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+  -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
+  -DITK_DIR:PATH=${ITK_DIR}
+  # Elastix components configuration
+  -DUSE_AdaptiveStochasticGradientDescent:BOOL=ON                                           
+  -DUSE_AdvancedAffineTransformElastix:BOOL=ON
+  -DUSE_AdvancedBSplineTransform:BOOL=ON                                           
+  -DUSE_AdvancedKappaStatisticMetric:BOOL=ON                                           
+  -DUSE_AdvancedMattesMutualInformationMetric:BOOL=ON                                           
+  -DUSE_AdvancedMeanSquaresMetric:BOOL=ON                                           
+  -DUSE_AdvancedNormalizedCorrelationMetric:BOOL=ON                                           
+  -DUSE_AffineDTITransformElastix:BOOL=ON                                           
+  -DUSE_BSplineInterpolator:BOOL=ON                                           
+  -DUSE_BSplineInterpolatorFloat:BOOL=ON                                           
+  -DUSE_BSplineResampleInterpolator:BOOL=ON                                           
+  -DUSE_BSplineResampleInterpolatorFloat:BOOL=ON                                           
+  -DUSE_BSplineStackTransform:BOOL=ON                                           
+  -DUSE_BSplineTransformWithDiffusion:BOOL=ON                                           
+  -DUSE_CMAEvolutionStrategy:BOOL=ON                                           
+  -DUSE_CUDAResampler:BOOL=OFF                                          
+  -DUSE_ConjugateGradient:BOOL=ON                                           
+  -DUSE_ConjugateGradientFRPR:BOOL=ON                                           
+  -DUSE_CorrespondingPointsEuclideanDistanceMetric:BOOL=ON
+  -DUSE_DeformationFieldTransform:BOOL=ON                                           
+  -DUSE_DisplacementMagnitudePenalty:BOOL=ON                                           
+  -DUSE_DistancePreservingRigidityPenalty:BOOL=ON                                           
+  -DUSE_EulerTransformElastix:BOOL=ON                                           
+  -DUSE_FiniteDifferenceGradientDescent:BOOL=ON                                           
+  -DUSE_FixedGenericPyramid:BOOL=ON                                           
+  -DUSE_FixedRecursivePyramid:BOOL=ON                                           
+  -DUSE_FixedShrinkingPyramid:BOOL=ON                                           
+  -DUSE_FixedSmoothingPyramid:BOOL=ON                                           
+  -DUSE_FullSampler:BOOL=ON                                           
+  -DUSE_FullSearch:BOOL=ON                                           
+  -DUSE_GradientDifferenceMetric:BOOL=ON                                           
+  -DUSE_GridSampler:BOOL=ON                                           
+  -DUSE_KNNGraphAlphaMutualInformationMetric:BOOL=OFF                                         
+  -DUSE_LinearInterpolator:BOOL=ON                                           
+  -DUSE_LinearResampleInterpolator:BOOL=ON                                           
+  -DUSE_MissingStructurePenalty:BOOL=ON
+  -DUSE_MovingRecursivePyramid:BOOL=ON                                           
+  -DUSE_MovingShrinkingPyramid:BOOL=ON                                           
+  -DUSE_MovingSmoothingPyramid:BOOL=ON                                           
+  -DUSE_MultiBSplineTransformWithNormal:BOOL=ON                                           
+  -DUSE_MultiInputRandomCoordinateSampler:BOOL=ON                                           
+  -DUSE_MultiMetricMultiResolutionRegistration:BOOL=ON                                           
+  -DUSE_MultiResolutionRegistration:BOOL=ON                                           
+  -DUSE_MultiResolutionRegistrationWithFeatures:BOOL=ON                                           
+  -DUSE_MutualInformationHistogramMetric:BOOL=ON                                           
+  -DUSE_MyStandardResampler:BOOL=ON                                           
+  -DUSE_NearestNeighborInterpolator:BOOL=ON                                           
+  -DUSE_NearestNeighborResampleInterpolator:BOOL=ON                                           
+  -DUSE_NormalizedGradientCorrelationMetric:BOOL=ON                                           
+  -DUSE_NormalizedMutualInformationMetric:BOOL=ON                                           
+  -DUSE_PatternIntensityMetric:BOOL=ON                                           
+  -DUSE_PolydataDummyPenalty:BOOL=ON                                           
+  -DUSE_Powell:BOOL=ON
+  -DUSE_QuasiNewtonLBFGS:BOOL=ON                                           
+  -DUSE_RSGDEachParameterApart:BOOL=ON                                           
+  -DUSE_RandomCoordinateSampler:BOOL=ON                                           
+  -DUSE_RandomSampler:BOOL=ON                                           
+  -DUSE_RandomSamplerSparseMask:BOOL=ON                                           
+  -DUSE_RayCastInterpolator:BOOL=ON                                           
+  -DUSE_RayCastResampleInterpolator:BOOL=ON                                           
+  -DUSE_ReducedDimensionBSplineInterpolator:BOOL=ON                                           
+  -DUSE_ReducedDimensionBSplineResampleInterpolator:BOOL=ON                                           
+  -DUSE_RegularStepGradientDescent:BOOL=ON                                           
+  -DUSE_SimilarityTransformElastix:BOOL=ON                                           
+  -DUSE_Simplex:BOOL=ON                                           
+  -DUSE_SimultaneousPerturbation:BOOL=ON                                           
+  -DUSE_SplineKernelTransform:BOOL=ON                                           
+  -DUSE_StandardGradientDescent:BOOL=ON                                           
+  -DUSE_StatisticalShapePenalty:BOOL=ON                                           
+  -DUSE_TransformBendingEnergyPenanalty:BOOL=ON
+  -DUSE_TransformRigidityPenalty:BOOL=ON                                           
+  -DUSE_TranslationTransformElastix:BOOL=ON                                           
+  -DUSE_VarianceOverLastDimensionMetric:BOOL=ON                                           
+  -DUSE_ViolaWellsMutualInformationMetric:BOOL=ON                                           
+  -DUSE_WeightedCombinationTransformElastix:BOOL=ON
+  DEPENDS ITK
+)
+
+ExternalProject_Get_Property( Elastix binary_dir )
+set( ELASTIX_USE_FILE "${binary_dir}/src/UseElastix.cmake" )
+
+list( APPEND ELASTIX_DEPENDENCIES ${proj} )

SuperBuild/ExternalGoogleTest.cmake

+set( proj GoogleTest )
+
+set( GTEST_TARGET_VERSION 1.7.0 )
+set( GTEST_DOWNLOAD_SOURCE_HASH "2d6ec8ccdf5c46b05ba54a9fd1d130d7" )
+
+set( GTEST_binary_dir ${CMAKE_CURRENT_BINARY_DIR}/${proj}-prefix/src/${proj}-build )
+set( GTEST_source_dir ${CMAKE_CURRENT_BINARY_DIR}/${proj}-prefix/src/${proj} )
+set( GTEST_install_dir ${CMAKE_CURRENT_BINARY_DIR}/${proj} )
+
+set( ${proj}_ARCHIVE_OUTPUT_DIRECTORY "<BINARY_DIR>/lib" )
+if( MSVC )
+  set( ${proj}_ARCHIVE_OUTPUT_DIRECTORY "<BINARY_DIR>/lib/$<CONFIGURATION>" )
+endif()
+
+set( MSVS_ARGS )
+if(MSVC_VERSION EQUAL 1700)
+  set(MSVS_ARGS ${MSVS_ARGS} -D CMAKE_CXX_FLAGS=-DGTEST_HAS_TR1_TUPLE=0 ${CMAKE_CXX_FLAGS})
+endif()
+
+if( MSVC)
+  set( MSVS_ARGS ${MSVS_ARGS} -D gtest_force_shared_crt:BOOL=ON )
+endif()
+
+ExternalProject_Add(${proj}
+  URL http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${GTEST_DOWNLOAD_SOURCE_HASH}&name=swig-${GTEST_TARGET_VERSION}.zip
+  URL_MD5 ${GTEST_DOWNLOAD_SOURCE_HASH}
+  INSTALL_DIR ${GTEST_install_dir}
+  CMAKE_GENERATOR ${gen}
+  CMAKE_ARGS
+    --no-warn-unused-cli
+    ${MSVS_ARGS}
+    -D BUILD_SHARED_LIBS:BOOL=OFF
+    -D CMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=<BINARY_DIR>/lib
+  INSTALL_COMMAND
+      ${CMAKE_COMMAND} -E copy_directory ${${proj}_ARCHIVE_OUTPUT_DIRECTORY} <INSTALL_DIR>/lib
+    COMMAND
+      ${CMAKE_COMMAND} -E copy_directory <SOURCE_DIR>/include <INSTALL_DIR>/include
+)
+
+set( GTEST_ROOT ${GTEST_install_dir} )
+list( APPEND ELASTIX_DEPENDENCIES ${proj} )
+

SuperBuild/ExternalITK.cmake

-set( PROJECT ITK )
+set( proj ITK )
 set( ITK_REPOSITORY https://github.com/InsightSoftwareConsortium/ITK.git )
 set( ITK_TAG "v${ITK_VERSION_STRING}")
 
-ExternalProject_Add( ${PROJECT}
+ExternalProject_Add( ${proj}
   GIT_REPOSITORY ${ITK_REPOSITORY}
   GIT_TAG ${ITK_TAG}
   UPDATE_COMMAND ""
-  SOURCE_DIR ${PROJECT}
-  BINARY_DIR ${PROJECT}-build
+  SOURCE_DIR ${proj}
+  BINARY_DIR ${proj}-build
   CMAKE_ARGS
     --no-warn-unused-cli
     -DBUILD_EXAMPLES:BOOL=OFF
     -DBUILD_TESTING:BOOL=OFF
     -DITK_BUILD_DEFAULT_MODULES:BOOL=ON
     -DModule_ITKReview:BOOL=ON
-    -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
     -DCMAKE_SKIP_RPATH:BOOL=ON
     -DITK_LEGACY_REMOVE:BOOL=ON
     -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
 )
 
-ExternalProject_Get_Property( ITK install_dir )
+ExternalProject_Get_Property( ${proj} install_dir )
 set( ITK_DIR "${install_dir}/lib/cmake/ITK-${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR}" )
+
+list( APPEND ELASTIX_DEPENDENCIES ${proj} )

SuperBuild/Elastix.cmake → SuperBuild/SuperElastix.cmake

-set( proj Elastix )
+set( proj SuperElastix )
 
 ExternalProject_Add( ${proj}
   DOWNLOAD_COMMAND ""
@@ -6,12 +6,14 @@ ExternalProject_Add( ${proj}
   BINARY_DIR ${proj}-build
   CMAKE_ARGS
     --no-warn-unused-cli
-    -DELASTIX_BUILD_EXAMPLES:BOOL=${ELASTIX_BUILD_EXAMPLES}
-    -DELASTIX_BUILD_TESTING:BOOL=${ELASTIX_BUILD_TESTING}
-    -DELASTIX_BUILD_BENCHMARKING:BOOL=${ELASTIX_BUILD_BENCHMARKING}
-    -DELASTIX_BUILD_DASHBOARD:BOOL=${ELASTIX_BUILD_DASHBOARD}
+    -DSUPERELASTIX_BUILD_EXAMPLES:BOOL=${SUPERELASTIX_BUILD_EXAMPLES}
+    -DSUPERELASTIX_BUILD_TESTING:BOOL=${SUPERELASTIX_BUILD_TESTING}
+    -DSUPERELASTIX_BUILD_BENCHMARKING:BOOL=${SUPERELASTIX_BUILD_BENCHMARKING}
+    -DSUPERELASTIX_BUILD_DASHBOARD:BOOL=${SUPERELASTIX_BUILD_DASHBOARD}
     -DITK_DIR:PATH=${ITK_DIR}
     -DBOOST_ROOT:PATH=${BOOST_ROOT}
+    -DGTEST_ROOT:PATH=${GTEST_ROOT}
+    -DELASTIX_USE_FILE:PATH=${ELASTIX_USE_FILE}
   DEPENDS ${ELASTIX_DEPENDENCIES}
   INSTALL_COMMAND ""
 )

Testing/CMakeLists.txt

@@ -30,50 +30,23 @@ endforeach()
 ExternalData_Add_Target( ElastixData )
 
 # ---------------------------------------------------------------------
-# Add GoogleTest
+# Find GoogleTest library
 
-find_package( Git )
-if( NOT EXISTS "${CMAKE_SOURCE_DIR}/Testing/GoogleTest/.git" AND GIT_EXECUTABLE )
-  execute_process( 
-  	COMMAND ${GIT_EXECUTABLE} submodule update --init
-    WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
-    OUTPUT_QUIET
-  )
-endif()
-
-if( NOT EXISTS ${CMAKE_SOURCE_DIR}/Testing/GoogleTest/.git )
-  message( 
-  	FATAL_ERROR "Could not find GoogleTest submodule. Please run 
-  	git submodule update --init in the source directory to compile tests."
-  )
-endif()
-
-if( ${CMAKE_CXX_COMPILER_ID} STREQUAL "MSVC" )
-  include( elxWinConfigGoogleTest.cmake )
-endif()
-
-add_subdirectory( GoogleTest )
-
-include_directories(
-  ${gtest_SOURCE_DIR}/include
-)
+find_package( GTest REQUIRED )
+include_directories( ${GTEST_INCLUDE_DIRS} )
 
 set( TEST_LIBRARIES
-  gtest_main
+  ${GTEST_BOTH_LIBRARIES}
 )
 
 # ---------------------------------------------------------------------
 # Build test suite
 
+set( CTEST_CONFIGURATION_TYPE Debug )
+
 # Unit tests
 add_subdirectory( Unit )
 
-# Benchmarks
-option( ELASTIX_BUILD_BENCHMARKING "Enable building benchmarks." OFF )
-if( ${ELASTIX_BUILD_BENCHMARKING} )
-	add_subdirectory( Benchmark )
-endif()
-
 # ---------------------------------------------------------------------
 # Configure dashboard
 mark_as_advanced( ELASTIX_BUILD_DASHBOARD )