WIP: ITK initial conversion 20171210

.circleci/config.yml

@@ -36,7 +36,7 @@ jobs:
             sudo apt-get install -y  rsync ninja-build ccache
             sudo pip install --upgrade pip
             sudo pip install scikit-ci-addons
-            ci_addons circle/install_cmake.py 3.7.2
+            ci_addons circle/install_cmake.py 3.8.2
       - run:
           name: CCache initialization
           command: |

CMake/ITKModuleAPI.cmake

@@ -1,5 +1,3 @@
-
-
 #-----------------------------------------------------------------------------
 # Private helper macros.
 
@@ -19,6 +17,13 @@ macro(_itk_module_use_recurse mod)
   endif()
 endmacro()
 
+# _itk_module_config_recurse(<namespace> <module>)
+#
+# Internal macro to recursively load module information into the supplied
+# namespace, this is called from itk_module_config. It should be noted that
+# _${ns}_${mod}_USED must be cleared if this macro is to work correctly on
+# subsequent invocations. The macro will load the module files using the
+# itk_module_load, making all of its variables available in the local scope.
 macro(_itk_module_config_recurse ns mod)
   if(NOT _${ns}_${mod}_USED)
     set(_${ns}_${mod}_USED 1)

CMake/ITKModuleRemote.cmake

@@ -126,6 +126,7 @@ function(itk_fetch_module _name _description)
   option(Module_${_name} "${_description}" OFF)
   mark_as_advanced(Module_${_name})
 
+
   # Fetch_$_remote_module} is deprecated. To maintain backward compatibility:
   if(Fetch_${_name})
     message(WARNING "Fetch_${_name} is deprecated, please use Module_${_name} to download and enable the remote module.")
@@ -136,6 +137,7 @@ function(itk_fetch_module _name _description)
     itk_download_attempt_check(Module_${_name})
     include(CMakeParseArguments)
     cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" ${ARGN})
+    find_package(Git)
     if(NOT GIT_EXECUTABLE)
       message(FATAL_ERROR "error: could not find git for clone of ${_name}")
     endif()

CMake/itkApple.cmake

@@ -0,0 +1,19 @@
+# Objective-C++ compile flags.
+# CMake has no equivalent of CMAKE_CXX_FLAGS for Objective-C++ (bug #4756)
+# so we provide this in case the user needs to specify flags specifically
+# for Objective-C++ source files.  For example, to build with garbage
+# collection support, the -fobjc-gc flag would be used.
+set(ITK_OBJCXX_FLAGS_DEFAULT "")
+set(ITK_REQUIRED_OBJCXX_FLAGS ${ITK_OBJCXX_FLAGS_DEFAULT} CACHE STRING "Extra flags for Objective-C++ compilation")
+mark_as_advanced(ITK_REQUIRED_OBJCXX_FLAGS)
+
+mark_as_advanced(
+  CMAKE_OSX_ARCHITECTURES
+  CMAKE_OSX_DEPLOYMENT_TARGET
+  CMAKE_OSX_SYSROOT)
+
+# OSX SDK 10.6 is the standard SDK for Python
+if (CMAKE_OSX_DEPLOYMENT_TARGET AND
+    CMAKE_OSX_DEPLOYMENT_TARGET VERSION_LESS "10.6")
+  message(FATAL_ERROR "Minimum OS X deployment target is 10.6, please update CMAKE_OSX_DEPLOYMENT_TARGET.")
+endif ()

CMake/itkCompilerChecks.cmake

@@ -0,0 +1,45 @@
+# Minimum compiler version check: GCC >= 4.8
+if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND
+    CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.8)
+  message(FATAL_ERROR "GCC 4.8 or later is required.")
+endif ()
+
+# Minimum compiler version check: LLVM Clang >= 3.3
+if (CMAKE_CXX_COMPILER_ID STREQUAL "Clang" AND
+    CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.3)
+  message(FATAL_ERROR "LLVM Clang 3.3 or later is required.")
+endif ()
+
+# Minimum compiler version check: Apple Clang >= 5.0 (Xcode 5.0)
+if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang" AND
+    CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
+  message(FATAL_ERROR "Apple Clang 5.0 or later is required.")
+endif ()
+
+# Minimum compiler version check: Microsoft C/C++ >= 18.0 (aka VS 2013 aka VS 12.0)
+if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC" AND
+    CMAKE_CXX_COMPILER_VERSION VERSION_LESS 18.0)
+  message(FATAL_ERROR "Microsoft Visual Studio 2013 or later is required.")
+endif ()
+
+# Minimum compiler version check: Intel C++ (ICC) >= 14
+if (CMAKE_CXX_COMPILER_ID STREQUAL "Intel" AND
+    CMAKE_CXX_COMPILER_VERSION VERSION_LESS 14.0)
+  message(FATAL_ERROR "Intel C++ (ICC) 14.0 or later is required.")
+endif ()
+
+# Make sure we have C++11 enabled.
+if(NOT ITK_IGNORE_CMAKE_CXX11_CHECKS)
+  # Needed to make sure libraries and executables not built by the
+  # itkModuleMacros still have the C++11 compiler flags enabled
+  # Wrap this in an escape hatch for unknown compilers
+  if(NOT CMAKE_CXX_STANDARD)
+    set(CMAKE_CXX_STANDARD 11) # Supported values are ``11``, ``14``, and ``17``.
+  endif()
+  if(NOT CMAKE_CXX_STANDARD_REQUIRED)
+    set(CMAKE_CXX_STANDARD_REQUIRED ON)
+  endif()
+  if(NOT CMAKE_CXX_EXTENSIONS)
+    set(CMAKE_CXX_EXTENSIONS OFF)
+  endif()
+endif()

CMake/itkSupportMacros.cmake

@@ -0,0 +1,30 @@
+macro (itk_set_with_default var value)
+  if (NOT ${var})
+    set(${var} "${value}")
+  endif ()
+endmacro ()
+
+# Bridge an old, deprecated, setting to a new replacement setting.
+#
+# Use this function when a user-visible flag is being renamed or otherwise
+# replaced. If the old value is set, it will be given as the default value,
+# otherwise the given default value will be used. This returned value should
+# then be used in the ``set(CACHE)`` or ``option()`` call for the new value.
+#
+# If the old value is set, it will warn that it is deprecated for the new name.
+#
+# If replacing the setting ``OLD_SETTING`` with ``NEW_SETTING``, its usage
+# would look like:
+#
+#   itk_deprecated_setting(default_setting NEW_SETTING OLD_SETTING "default value")
+#   set(NEW_SETTING "${default_setting}"
+#     CACHE STRING "Documentation for the setting.")
+function (itk_deprecated_setting output_default new old intended_default)
+  set(default "${intended_default}")
+  if (DEFINED "${old}")
+    message(WARNING "The '${old}' variable is deprecated for '${new}'.")
+    set(default "${${old}}")
+  endif ()
+
+  set("${output_default}" "${default}" PARENT_SCOPE)
+endfunction ()

CMake/itkTargetLinkLibrariesWithDynamicLookup.cmake

@@ -57,8 +57,12 @@ add_library(foo SHARED \"foo.c\")
 extern int bar(void);
 int foo(void) {return bar()+1;}
 ")
-    # ITK requires CMake >= 2.8.12. Before that, on APPLE, no flag should be passed.
-    set( _rpath_arg  "-DCMAKE_MACOSX_RPATH='${CMAKE_MACOSX_RPATH}'" )
+    # APPLE: the CMAKE_MACOSX_RPATH flag should be passed.
+    if(APPLE)
+      set( _rpath_arg  "-DCMAKE_MACOSX_RPATH='${CMAKE_MACOSX_RPATH}'" )
+    else()
+      set( _rpath_arg )
+    endif()
 
     try_compile(${VARIABLE}
       "${test_project_dir}"

CMake/itkVersion.cmake

@@ -0,0 +1,4 @@
+# ITK version number components.
+set(ITK_VERSION_MAJOR "5")
+set(ITK_VERSION_MINOR "0")
+set(ITK_VERSION_PATCH "0")

CMakeLists.txt

@@ -1,20 +1,23 @@
-cmake_minimum_required(VERSION 2.8.12 FATAL_ERROR)
-
-foreach(p
-    CMP0025 # CMake 3.0
-    CMP0028
-    CMP0042 # CMake 3.0
-    CMP0054 # CMake 3.1
-    CMP0056 # CMake 3.2
-    CMP0058 # CMake 3.3
-    CMP0063 # CMake 3.3.2
-    )
-  if(POLICY ${p})
-    cmake_policy(SET ${p} NEW)
-  endif()
-endforeach()
+cmake_minimum_required(VERSION 3.8.2 FATAL_ERROR)
+if(CMAKE_CXX_STANDARD EQUAL "98" )
+   MESSAGE(FATAL_ERROR "CMAKE_CXX_STANDARD:STRING=98 is not supported in ITK version 5 and greater.")
+endif()
 
 project(ITK NONE)
+
+set(ITK_CMAKE_DIR "${ITK_SOURCE_DIR}/CMake")
+set(CMAKE_MODULE_PATH ${ITK_CMAKE_DIR} ${CMAKE_MODULE_PATH})
+
+if (APPLE)
+  include(itkApple)
+endif ()
+
+include(itkCompilerChecks)
+include(itkVersion)
+set(ITK_VERSION
+    "${ITK_MAJOR_VERSION}.${ITK_MINOR_VERSION}.${ITK_BUILD_VERSION}")
+include(itkSupportMacros)
+
 # Configure CMake variables that will be used in the module macros
 # ITK_USE_FILE is used when a remote module includes an example directory
 # that can be configured as an independent project.
@@ -79,8 +82,6 @@ endif()
 include(CTest)
 mark_as_advanced(CLEAR BUILD_TESTING)
 
-set(ITK_CMAKE_DIR ${ITK_SOURCE_DIR}/CMake)
-set(CMAKE_MODULE_PATH ${ITK_CMAKE_DIR} ${CMAKE_MODULE_PATH})
 include(ITKDownloadSetup)
 include(PreventInSourceBuilds)
 include(PreventInBuildInstalls)
@@ -93,10 +94,6 @@ include(itkCheckSourceTree)
 set(main_project_name ${_ITKModuleMacros_DEFAULT_LABEL})
 
 #-----------------------------------------------------------------------------
-# ITK version number.
-set(ITK_VERSION_MAJOR "5")
-set(ITK_VERSION_MINOR "0")
-set(ITK_VERSION_PATCH "0")
 configure_file(CMake/ITKConfigVersion.cmake.in ITKConfigVersion.cmake @ONLY)
 
 if(NOT ITK_INSTALL_RUNTIME_DIR)

Examples/DataRepresentation/Mesh/Mesh2.cxx

@@ -315,7 +315,7 @@ int main(int, char *[])
     {
     MeshType::CellType * cellptr = cellIterator.Value();
     LineType * line = dynamic_cast<LineType *>( cellptr );
-    if(line == ITK_NULLPTR)
+    if(line == nullptr)
       {
       continue;
       }

Examples/DataRepresentation/Mesh/MeshCellVisitor2.cxx

@@ -120,7 +120,7 @@ class CustomVertexVisitor
 class CustomLineVisitor
 {
 public:
-  CustomLineVisitor():m_Mesh( 0 ) {}
+  CustomLineVisitor():m_Mesh( nullptr ) {}
   virtual ~CustomLineVisitor() {}
 
   void SetMesh( MeshType * mesh ) { m_Mesh = mesh; }

Examples/Filtering/CompositeFilterExample.cxx

@@ -122,10 +122,10 @@ class CompositeExampleImageFilter :
   typedef RescaleIntensityImageFilter< ImageType, ImageType >  RescalerType;
 //  Software Guide : EndCodeSnippet
 
-  virtual void GenerateData() ITK_OVERRIDE;
+  void GenerateData() override;
 
   /** Display */
-  void PrintSelf( std::ostream& os, Indent indent ) const ITK_OVERRIDE;
+  void PrintSelf( std::ostream& os, Indent indent ) const override;
 
 private:
   ITK_DISALLOW_COPY_AND_ASSIGN(CompositeExampleImageFilter);

Examples/Filtering/DigitallyReconstructedRadiograph1.cxx

@@ -75,8 +75,8 @@ void usage()
 
 int main( int argc, char *argv[] )
 {
-  char *input_name = ITK_NULLPTR;
-  char *output_name = ITK_NULLPTR;
+  char *input_name = nullptr;
+  char *output_name = nullptr;
 
   bool ok;
   bool verbose = false;
@@ -232,7 +232,7 @@ int main( int argc, char *argv[] )
     if (ok == false)
       {
 
-      if (input_name == ITK_NULLPTR)
+      if (input_name == nullptr)
         {
         input_name = argv[1];
         argc--;

Examples/Filtering/OtsuMultipleThresholdImageFilter.cxx

@@ -39,7 +39,7 @@
 #include "itkNumericTraits.h"
 
 #include <iomanip>
-#include <stdio.h>
+#include <cstdio>
 
 int main( int argc, char * argv[] )
 {

Examples/Filtering/ScaleSpaceGenerator2D.cxx

@@ -29,7 +29,7 @@
 #include "itkImageFileWriter.h"
 #include "itkLaplacianRecursiveGaussianImageFilter.h"
 
-#include <stdio.h>
+#include <cstdio>
 #include <iomanip>
 
 int main( int argc, char * argv[] )

Examples/IO/XML/DOMFindDemo.cxx

@@ -68,7 +68,7 @@ int main( int argc, char* argv[] )
       {
       std::cout << "query = \"" << query << "\"" << std::endl;
       itk::DOMNode::Pointer dom2 = dom1->Find( query );
-      if ( (itk::DOMNode*)dom2 == 0 )
+      if ( (itk::DOMNode*)dom2 == nullptr )
         {
         std::cout << "invalid query!" << std::endl;
         }

Examples/IO/XML/itkParticleSwarmOptimizerDOMReader.cxx

@@ -31,7 +31,7 @@ ParticleSwarmOptimizerDOMReader::GenerateData( const DOMNodeType* inputdom, cons
   LoggerType* logger = this->GetLogger();
 
   OutputType* output = this->GetOutput();
-  if ( output == ITK_NULLPTR )
+  if ( output == nullptr )
     {
     logger->Info( "creating the output PSO object ...\n" );
     OutputType::Pointer object = OutputType::New();

Examples/IO/XML/itkParticleSwarmOptimizerDOMReader.h

@@ -57,7 +57,7 @@ class ParticleSwarmOptimizerDOMReader : public DOMReader<ParticleSwarmOptimizer>
    * This function is called automatically when update functions are performed.
    * It should fill the contents of the output object by pulling information from the intermediate DOM object.
    */
-  virtual void GenerateData( const DOMNodeType* inputdom, const void* ) ITK_OVERRIDE;
+  void GenerateData( const DOMNodeType* inputdom, const void* ) override;
 
 private:
   ITK_DISALLOW_COPY_AND_ASSIGN(ParticleSwarmOptimizerDOMReader);

Examples/IO/XML/itkParticleSwarmOptimizerDOMWriter.h

@@ -57,7 +57,7 @@ class ParticleSwarmOptimizerDOMWriter : public DOMWriter<ParticleSwarmOptimizer>
    * This function is called automatically when update functions are performed.
    * It should fill the contents of the intermediate DOM object by pulling information from the input object.
    */
-  virtual void GenerateData( DOMNodeType* outputdom, const void* ) const ITK_OVERRIDE;
+  void GenerateData( DOMNodeType* outputdom, const void* ) const override;
 
 private:
   ITK_DISALLOW_COPY_AND_ASSIGN(ParticleSwarmOptimizerDOMWriter);

Examples/IO/XML/itkParticleSwarmOptimizerSAXReader.cxx

@@ -49,10 +49,10 @@ void ParticleSwarmOptimizerSAXReader::StartElement( const char* name, const char
     }
   else if ( itksys::SystemTools::Strucmp( name, "bound" ) == 0 && this->ContextIs( "/optimizer" ) )
     {
-    std::vector<double>* bound = 0;
+    std::vector<double>* bound = nullptr;
 
     const char* id = this->GetAttribute( atts, "id" );
-    if ( id == 0 )
+    if ( id == nullptr )
       {
       itkExceptionMacro( "Bound ID is missing!\n" );
       }
@@ -156,7 +156,7 @@ int ParticleSwarmOptimizerSAXReader::ReadFile()
       throw e;
       }
 
-    if ( this->m_OutputObject == 0 )
+    if ( this->m_OutputObject == nullptr )
       {
       itkExceptionMacro( "Object to be read is null!\n" );
       }
@@ -178,7 +178,7 @@ int ParticleSwarmOptimizerSAXReader::ReadFile()
 void ParticleSwarmOptimizerSAXReader::ProcessOptimizerAttributes( const char** atts, ParticleSwarmOptimizer* opt )
 {
   // go over all the attribute-value pairs
-  for ( size_t i = 0; atts[i] != 0; i += 2 )
+  for ( size_t i = 0; atts[i] != nullptr; i += 2 )
     {
     if ( itksys::SystemTools::Strucmp( atts[i], "NumberOfParticles" ) == 0 )
       {
@@ -236,7 +236,7 @@ void ParticleSwarmOptimizerSAXReader::ProcessOptimizerAttributes( const char** a
 void ParticleSwarmOptimizerSAXReader::ProcessBoundAttributes( const char** atts, std::vector<double>& bound )
 {
   // go over all the attribute-value pairs
-  for ( size_t i = 0; atts[i] != 0; i += 2 )
+  for ( size_t i = 0; atts[i] != nullptr; i += 2 )
     {
     if ( itksys::SystemTools::Strucmp( atts[i], "value" ) == 0 )
       {
@@ -260,14 +260,14 @@ void ParticleSwarmOptimizerSAXReader::ProcessBoundAttributes( const char** atts,
 const char* ParticleSwarmOptimizerSAXReader::GetAttribute( const char** atts, const char* key )
 {
   // go over all the attribute-value pairs
-  for ( size_t i = 0; atts[i] != 0; i += 2 )
+  for ( size_t i = 0; atts[i] != nullptr; i += 2 )
     {
     if ( itksys::SystemTools::Strucmp( atts[i], key ) == 0 )
       {
       return atts[i+1];
       }
     }
-  return 0;
+  return nullptr;
 }
 
 /** Check the current tags to see whether it matches a user input. */