Merge branch 'ELASTIX-1-setup-development-infrastructure' into develop

CMake/elxWinConfig.cmake

 # Visual Studio complains if paths are too long
 
-string( LENGTH "${CMAKE_CURRENT_SOURCE_DIR}" n )
-if( n GREATER 50 )
-message(
-  FATAL_ERROR
-  "ITK source code directory path length is too long (${n} > 50)."
-  "Please move the ITK source code directory to a directory with a shorter path."
-  )
-endif()
+if( MSVC )
+  string( LENGTH "${CMAKE_CURRENT_SOURCE_DIR}" n )
+  if( n GREATER 50 )
+  message(
+    FATAL_ERROR
+    "ITK source code directory path length is too long for MSVC (${n} > 50)."
+    )
+  endif()
+
+  string( LENGTH "${CMAKE_CURRENT_BINARY_DIR}" n )
+  if( n GREATER 50 )
+  message(
+    FATAL_ERROR
+    "ITK build directory path length is too long for MSVC (${n} > 50)."
+    )
+  endif()
 
-string( LENGTH "${CMAKE_CURRENT_BINARY_DIR}" n )
-if( n GREATER 50 )
-message(
-  FATAL_ERROR
-  "ITK build directory path length is too long (${n} > 50)."
-  "Please set the ITK build directory to a directory with a shorter path."
-  )
+  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" )
 endif()

CMakeLists.txt

 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 )
+
+# ---------------------------------------------------------------------
+project( Elastix )
+
 # Include SuperElastix CMake scripts
-list( APPEND CMAKE_MODULE_PATH 
-  "${CMAKE_CURRENT_SOURCE_DIR}/CMake"
+list( APPEND CMAKE_MODULE_PATH
+  "${CMAKE_CURRENT_SOURCE_DIR}/CMake" 
 )
 
-if( CMAKE_HOST_WIN32 )
+if( ${CMAKE_CXX_COMPILER_ID} STREQUAL "MSVC" )
   include( elxWinConfig.cmake )
 endif()
 
-#---------------------------------------------------------------------
-project( Elastix )
-
-#---------------------------------------------------------------------
+# ---------------------------------------------------------------------
 # ITK
 
 find_package( ITK REQUIRED )
-set( ITK_NO_IO_FACTORY_REGISTER_MANAGER 1 )
 include( ${ITK_USE_FILE} )
 include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/elxITKRequiredModules.cmake" )
 
-#---------------------------------------------------------------------
+# ---------------------------------------------------------------------
 # Build Elastix
 
-#---------------------------------------------------------------------
-# Testing
+set( ELASTIX_COMMON_INCLUDE_DIRECTORIES
+  ${CMAKE_SOURCE_DIR}/Modules/Core/Common/include
+)
 
-# Build tests by default
-option( ELASTIX_BUILD_TESTING "Enable building tests." ON )
+set( ELASTIX_CORE_INCLUDE_DIRECTORIES
+  ${CMAKE_SOURCE_DIR}/Modules/Core/Blueprints/include
+)
+
+set( ELASTIX_INCLUDE_DIRECTORIES
+  ${ELASTIX_COMMON_INCLUDE_DIRECTORIES}
+  ${ELASTIX_CORE_INCLUDE_DIRECTORIES}
+)
+
+include_directories( ${ELASTIX_INCLUDE_DIRECTORIES} )
+add_subdirectory( Modules )
 
-# ExternalData module requires newer CMake versions
+# ---------------------------------------------------------------------
+# Testing
+
+# Testing requires CMake version 2.8.11 to download test data
 if( CMAKE_VERSION VERSION_LESS 2.8.11 )
-  set( ELASTIX_BUILD_TESTING OFF FORCE )
-  message( STATUS "ELASTIX_BUILD_TESTING was set to OFF because CMake version is less than 2.8.11")
+  set( ELASTIX_BUILD_TESTING_DEFAULT OFF )
+  message( STATUS "ELASTIX_BUILD_TESTING is set to OFF by default because CMake version is less than 2.8.11" )
+else()
+  set( ELASTIX BUILD_TESTING_DEFAULT ON )
 endif()
 
+option( ELASTIX_BUILD_TESTING "Enable building tests." ${ELASTIX_BUILD_TESTING_DEFAULT} )
+
 if( ELASTIX_BUILD_TESTING )
   enable_testing()
   add_subdirectory( Testing )
 endif()
 
-#---------------------------------------------------------------------
+# ---------------------------------------------------------------------
 # Build Documentation
 
 mark_as_advanced( ELASTIX_BUILD_DOXYGEN )

Modules/CMakeLists.txt

+add_subdirectory(
+  Core
+)
\ No newline at end of file

Modules/Core/CMakeLists.txt

+add_subdirectory(
+  Common
+  Blueprints
+)
\ No newline at end of file

Modules/Core/Common/CMakeLists.txt

+include_directories( include )
\ No newline at end of file

Modules/Core/Common/include/elxMacro.h

+#ifndef __elxMacro_h
+#define __elxMacro_h
+
+/**
+ * Register class with the object factory and provide 
+ * associated RTTI (Run-Time Type Information)
+ */
+#define elxNewMacro( className, superClassName )        \
+  typedef className                       Self;         \
+  typedef itk::SmartPointer< Self >       Pointer;      \
+  typedef itk::SmartPointer< const Self > ConstPointer; \
+  itkNewMacro( Self );                                  \
+  itkTypeMacro( Self, superClassName );                 \
+
+#endif // __elxMacro_h
\ No newline at end of file

Testing/CMakeLists.txt

@@ -30,7 +30,7 @@ endforeach()
 ExternalData_Add_Target( ElastixData )
 
 # ---------------------------------------------------------------------
-# Setup GoogleTest
+# Add GoogleTest
 
 find_package( Git )
 if( NOT EXISTS "${CMAKE_SOURCE_DIR}/Testing/GoogleTest/.git" AND GIT_EXECUTABLE )
@@ -70,7 +70,6 @@ add_subdirectory( Unit )
 
 # Benchmarks
 option( ELASTIX_BUILD_BENCHMARKING "Enable building benchmarks." OFF )
-
 if( ${ELASTIX_BUILD_BENCHMARKING} )
 	add_subdirectory( Benchmark )
 endif()

Testing/Dashboard/CMakeLists.txt

@@ -8,24 +8,23 @@ mark_as_advanced( ELASTIX_DASHBOARD_BINARY_DIR )
 set( ELASTIX_DASHBOARD_BINARY_DIR "${CMAKE_BINARY_DIR}/Testing/Dashboard" )
 
 mark_as_advanced( ELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE )
-set( ELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE "elxLogstashForwarder.crt" )
+set( ELASTIX_DASHBOARD_LOGSTASH_CERTIFICATE "elxLogstash.crt" )
 
 mark_as_advanced( ELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY )
-set( ELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY "elxLogstashForwarder.key" )
+set( ELASTIX_DASHBOARD_LOGSTASH_RSA_PRIVATE_KEY "elxLogstash.key" )
 
 mark_as_advanced( ELASTIX_DASHBOARD_VOLUME )
-set( ELASTIX_DASHBOARD_VOLUME "${ELASTIX_DASHBOARD_BINARY_DIR}/Data" )
-
 if( NOT EXISTS "${ELASTIX_DASHBOARD_VOLUME}" )
   message( STATUS
-    "ELASTIX_DASHBOARD_VOLUME points to the default ${CMAKE_BINARY_DIR}/Testing/Dashboard/Data path in your build directory. In production you should point this variable to a safe directory outside the build tree."
+    "ELASTIX_DASHBOARD_VOLUME points to the folder ${CMAKE_BINARY_DIR}/Testing/Dashboard/Data in your build directory. In production you should point this variable to a safe directory outside the build tree."
   )
-
+  
+  set( ELASTIX_DASHBOARD_VOLUME "${ELASTIX_DASHBOARD_BINARY_DIR}/Data" )
   file( MAKE_DIRECTORY "${ELASTIX_DASHBOARD_VOLUME}" )
 endif()
 
 # Test/Benchmark results will be forwarded to this IP. You will probably
-# have change this in order to  match docker settings on your own machine. 
+# have change this in order to match docker settings on your own machine. 
 mark_as_advanced( ELASTIX_DASHBOARD_IP )
 set( ELASTIX_DASHBOARD_IP "192.168.59.103" )
 

Testing/Unit/CMakeLists.txt

@@ -24,19 +24,24 @@ if( NOT EXISTS ${ELASTIX_UNITTEST_OUTPUT_DATA_DIR} )
   )
 endif()
 
+# ---------------------------------------------------------------------
+# Build test data manager
 configure_file(
   ${CMAKE_CURRENT_SOURCE_DIR}/elxDataDirectories.h.in
-  ${CMAKE_CURRENT_SOURCE_DIR}/elxDataDirectories.h
+  ${CMAKE_CURRENT_BINARY_DIR}/elxDataDirectories.h
   ESCAPE_QUOTES
 )
 
-# Build tests
+include_directories( ${CMAKE_CURRENT_BINARY_DIR} )
+
 add_library( DataManager elxDataManager.cxx )
 
 list( APPEND TEST_LIBRARIES 
   DataManager
 )
 
+# ---------------------------------------------------------------------
+# Build tests
 foreach( ElastixUnitTestFilename ${ElastixUnitTestFilenames} )
   # Build tests executables
   string( REPLACE ".cxx" "" ElastixUnitTest ${ElastixUnitTestFilename} )

Testing/Unit/elxDataDirectories.h

-#ifndef __elxTestDataDirectories_h
-#define __elxTestDataDirectories_h
-
-#define ELASTIX_UNITTEST_INPUT_DATA_DIR "/Users/kasper/Development/build/SuperElastix/Elastix-build/Testing/Unit/Data/Input"
-#define ELASTIX_UNITTEST_OUTPUT_DATA_DIR "/Users/kasper/Development/build/SuperElastix/Elastix-build/Testing/Unit/Data/Output"
-#define ELASTIX_UNITTEST_BASELINE_DATA_DIR "/Users/kasper/Development/build/SuperElastix/Elastix-build/Testing/Unit/Data/Baseline"
-
-#endif // __elxTestDataDirectories_h

Testing/Unit/elxDataDirectories.h.in

-#ifndef __elxTestDataDirectories_h
-#define __elxTestDataDirectories_h
+#ifndef __elxDataDirectories_h
+#define __elxDataDirectories_h
 
 #define ELASTIX_UNITTEST_INPUT_DATA_DIR "@ELASTIX_UNITTEST_INPUT_DATA_DIR@"
 #define ELASTIX_UNITTEST_OUTPUT_DATA_DIR "@ELASTIX_UNITTEST_OUTPUT_DATA_DIR@"

Testing/Unit/elxDataManager.cxx

 #ifndef __DataManager_cxx
 #define __DataManager_cxx
 
+#include <itkSimpleDataObjectDecorator.h>
 #include "elxDataManager.h"
 
-std::string
+const std::string
 DataManager
-::GetInput( const std::string filename ) const 
+::GetInputFullPath( const std::string filename ) const 
 {
-  const std::string path = this->GetInputDirectory() + this->GetPathSeparator() + filename;
+  const std::string path = this->GetInputDirectory() + this->GetFolderSeparator() + filename;
   return path;
 }
 
-std::string
+const std::string
 DataManager
-::GetOutput( const std::string filename ) const
+::GetOutputFullPath( const std::string filename ) const
 {
-  const std::string path = this->GetOutputDirectory() + this->GetPathSeparator() + filename;
+  const std::string path = this->GetOutputDirectory() + this->GetFolderSeparator() + filename;
   return path;
 }
 
-std::string
+const std::string
 DataManager
-::GetBaseline( const std::string filename ) const
+::GetBaselineFullPath( const std::string filename ) const
 {
-  const std::string path = this->GetBaselineDirectory() + this->GetPathSeparator() + filename;
+  const std::string path = this->GetBaselineDirectory() + this->GetFolderSeparator() + filename;
   return path;
 }
 

Testing/Unit/elxDataManager.h

@@ -2,16 +2,19 @@
 #define __DataManager_h
 
 #include <string>
+#include <itkSimpleDataObjectDecorator.h>
 
-#include "itkMacro.h"
-#include "itkProcessObject.h"
-
+#include "elxMacro.h"
+#include "itkObjectFactory.h"
+#include "itkLightObject.h"
 #include "elxDataDirectories.h"
 
-class DataManager
+class DataManager : public itk::LightObject
 {
 public:
 
+  elxNewMacro( DataManager, itk::LightObject );
+
   DataManager()
   {
     this->m_InputDirectory = ELASTIX_UNITTEST_INPUT_DATA_DIR;
@@ -20,16 +23,25 @@ public:
   }
 
   std::string GetInputDirectory( void ) const { return this->m_InputDirectory; };
-  std::string GetOutputDirectory( void ) const { return this->m_InputDirectory; };
-  std::string GetBaselineDirectory( void ) const { return this->m_InputDirectory; };
+  std::string GetOutputDirectory( void ) const { return this->m_OutputDirectory; };
+  std::string GetBaselineDirectory( void ) const { return this->m_BaselineDirectory; };
+
+  const std::string GetInputFullPath( const std::string filename ) const;
+  const std::string GetOutputFullPath( const std::string filename ) const;
+  const std::string GetBaselineFullPath( const std::string filename ) const;
 
-  std::string GetInput( const std::string filename ) const;
-  std::string GetOutput( const std::string filename ) const;
-  std::string GetBaseline( const std::string filename ) const;
+  std::string GetFolderSeparator() const
+  {
+#ifdef _WIN32
+    return "\\";
+#else
+    return "/";
+#endif
+  } 
 
   std::string GetPathSeparator () const
   {
-#ifdef WIN32
+#ifdef _WIN32
     return ";";
 #else
     return ":";

Testing/Unit/itkRegistration.cxx

@@ -3,27 +3,84 @@
 #include "elxDataManager.h"
 #include "gtest/gtest.h"
 
+#include "itkImageRegistrationMethod.h"
+#include "itkTranslationTransform.h"
+#include "itkMeanSquaresImageToImageMetric.h"
+#include "itkLinearInterpolateImageFunction.h"
+#include "itkRegularStepGradientDescentOptimizer.h"
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkResampleImageFilter.h"
+#include "itkCastImageFilter.h"
+
 class itkRegistration : public ::testing::Test {
 public:
   virtual void SetUp()
   {
-    DataManager dataManager;
-    typedef itk::ImageFileReader< ImageType > ReaderType;
+    // TODO: Loading images here result in segfault
+  }
 
-    ReaderType::Pointer reader = ReaderType::New();
-    reader->SetFileName( dataManager.GetInput( "BrainProtonDensitySliceR10X13Y17.png" ) );
-    inputImage = reader->GetOutput();
+  typedef itk::Image< unsigned short, 2 > ImageType;
 
-    reader->SetFileName( dataManager.GetBaseline( "BrainProtonDensitySlice.png" ) );
-    baselineImage = reader->GetOutput();
-  }
+  typedef itk::ImageFileReader< ImageType > FixedImageReaderType;
+  typedef itk::ImageFileReader< ImageType > MovingImageReaderType;
+
+  FixedImageReaderType::Pointer fixedImageReader;
+  MovingImageReaderType::Pointer movingImageReader;
 
-  typedef itk::Image< unsigned int, 2 > ImageType;
-  ImageType::Pointer inputImage;
-  ImageType::Pointer baselineImage;
 };
 
-TEST_F( itkRegistration, Affine2D )
-{
-  ASSERT_TRUE( true );
+TEST_F( itkRegistration, ImageRegistration3 )
+{ 
+
+  typedef itk::TranslationTransform< double, ImageType::ImageDimension > TransformType;
+  typedef itk::RegularStepGradientDescentOptimizer                       OptimizerType;
+  typedef itk::LinearInterpolateImageFunction< ImageType, double >       InterpolatorType;
+  typedef itk::ImageRegistrationMethod< ImageType, ImageType >           RegistrationType;
+
+
+  typedef itk::MeanSquaresImageToImageMetric< ImageType, ImageType > MetricType;
+
+  TransformType::Pointer      transform     = TransformType::New();
+  OptimizerType::Pointer      optimizer     = OptimizerType::New();
+  InterpolatorType::Pointer   interpolator  = InterpolatorType::New();
+  RegistrationType::Pointer   registration  = RegistrationType::New();
+
+  MetricType::Pointer         metric        = MetricType::New();
+  registration->SetMetric( metric  );
+  registration->SetOptimizer(     optimizer     );
+  registration->SetTransform(     transform     );
+  registration->SetInterpolator(  interpolator  );
+
+  FixedImageReaderType::Pointer fixedImageReader = FixedImageReaderType::New();
+  MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();
+
+  DataManager::Pointer dataManager = DataManager::New();
+
+  fixedImageReader->SetFileName( dataManager->GetInputFullPath( "BrainProtonDensitySlice.png" ) );
+  movingImageReader->SetFileName( dataManager->GetInputFullPath( "BrainProtonDensitySliceR10X13Y17.png" ) );
+
+  registration->SetFixedImage(    fixedImageReader->GetOutput()    );
+  registration->SetMovingImage(   movingImageReader->GetOutput()   );
+
+  fixedImageReader->Update(); // This is needed to make the BufferedRegion valid.
+  registration->SetFixedImageRegion( fixedImageReader->GetOutput()->GetBufferedRegion() );
+
+  typedef RegistrationType::ParametersType ParametersType;
+  ParametersType initialParameters( transform->GetNumberOfParameters() );
+
+  initialParameters[0] = 0.0;  // Initial offset in mm along X
+  initialParameters[1] = 0.0;  // Initial offset in mm along Y
+
+  registration->SetInitialTransformParameters( initialParameters );
+
+  optimizer->SetMaximumStepLength( 4.00 );  
+  optimizer->SetMinimumStepLength( 0.01 );
+  optimizer->SetNumberOfIterations( 200 );
+
+  optimizer->MaximizeOff();
+
+  EXPECT_NO_THROW( registration->Update() );
+  RecordProperty( "MetricValue", optimizer->GetValue() );
 }
+