.circleci/config.yml

@@ -35,8 +35,7 @@ jobs:
           command: |
             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
+            sudo pip install cmake==3.7.2 scikit-ci-addons
       - run:
           name: CCache initialization
           command: |

CMake/ITKExternalData.cmake

@@ -37,9 +37,6 @@ if(NOT ITK_FORBID_DOWNLOADS)
     # Data published on Girder
     "https://data.kitware.com:443/api/v1/file/hashsum/%(algo)/%(hash)/download"
 
-    # Data published on MIDAS
-    "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=%(hash)&algorithm=%(algo)"
-
     # Data published by developers using git-gerrit-push.
     "https://itk.org/files/ExternalData/%(algo)/%(hash)"
 

CMake/ITKModuleMacros.cmake

@@ -331,12 +331,22 @@ macro(itk_module_test)
 endmacro()
 
 macro(itk_module_examples)
-  cmake_dependent_option(Module_${itk-module}_BUILD_EXAMPLES "Build the examples" OFF "BUILD_EXAMPLES" OFF)
+  set(_build_examples_default OFF)
+  if(BUILD_EXAMPLES OR ITK_BUILD_EXAMPLES)
+    set(_build_examples_default ON)
+  endif()
+  set(Module_${itk-module}_BUILD_EXAMPLES ${_build_examples_default} CACHE BOOL "Build the examples for Module_${itk-module}")
   if(Module_${itk-module}_BUILD_EXAMPLES)
     if(ITK_SOURCE_DIR)
       # If configuration is done from within ITK,
       # point to internal ITKConfig.cmake
       set(ITK_DIR ${ITK_BINARY_DIR}/CMakeTmp)
+    else()
+      # Ensure that executables get added to the current build tree instead of
+      # ITK's build tree when building as an external module.
+      if(CMAKE_RUNTIME_OUTPUT_DIRECTORY STREQUAL "${ITK_DIR}/bin")
+        set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
+      endif()
     endif()
     # Adds example subdirectory
     add_subdirectory( examples )

CMake/ITKModuleRemote.cmake

@@ -46,10 +46,11 @@ endfunction()
 # desired revision and only performs a fetch and checkout if needed.
 function(_git_update git_executable git_repository git_tag module_dir)
   execute_process(
-    COMMAND "${git_executable}" rev-parse --verify ${git_tag}
+    COMMAND "${git_executable}" rev-parse --verify "${git_tag}"
     WORKING_DIRECTORY "${module_dir}"
     RESULT_VARIABLE error_code
     OUTPUT_VARIABLE tag_hash
+    OUTPUT_STRIP_TRAILING_WHITESPACE
     )
   if(error_code)
     message(FATAL_ERROR "Failed to get the hash for tag '${module_dir}'")
@@ -59,6 +60,7 @@ function(_git_update git_executable git_repository git_tag module_dir)
     WORKING_DIRECTORY "${module_dir}"
     RESULT_VARIABLE error_code
     OUTPUT_VARIABLE head_hash
+    OUTPUT_STRIP_TRAILING_WHITESPACE
     )
   if(error_code)
     message(FATAL_ERROR "Failed to get the hash for ${git_repository} HEAD")

CMake/itkExternal_FFTW.cmake

@@ -82,15 +82,15 @@ else()
     endif()
 
     set(_fftw_target_version 3.3.4)
-    set(_fftw_url_md5 "2edab8c06b24feeb3b82bbb3ebf3e7b3")
-    set(_fftw_url "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${_fftw_url_md5}&name=fftw-${_fftw_target_version}.tar.gz")
+    set(_fftw_url_hash "1ee2c7bec3657f6846e63c6dfa71410563830d2b951966bf0123bd8f4f2f5d6b50f13b76d9a7b0eae70e44856f829ca6ceb3d080bb01649d1572c9f3f68e8eb1")
+    set(_fftw_url "https://data.kitware.com/api/v1/file/hashsum/sha512/${_fftw_url_hash}/download")
 
     if(ITK_USE_FFTWF)
       itk_download_attempt_check(FFTW)
       ExternalProject_add(fftwf
         PREFIX fftwf
         URL "${_fftw_url}"
-        URL_MD5 "${_fftw_url_md5}"
+        URL_HASH SHA512="${_fftw_url_hash}"
         DOWNLOAD_NAME "fftw-${_fftw_target_version}.tar.gz"
         CONFIGURE_COMMAND
           env
@@ -118,7 +118,7 @@ else()
       ExternalProject_add(fftwd
         PREFIX fftwd
         URL "${_fftw_url}"
-        URL_MD5 "${_fftw_url_md5}"
+        URL_HASH SHA512="${_fftw_url_hash}"
         DOWNLOAD_NAME "fftw-${_fftw_target_version}.tar.gz"
         CONFIGURE_COMMAND
           env

CMakeLists.txt

@@ -4,6 +4,7 @@ foreach(p
     CMP0025 # CMake 3.0
     CMP0028
     CMP0042 # CMake 3.0
+    CMP0048
     CMP0054 # CMake 3.1
     CMP0056 # CMake 3.2
     CMP0058 # CMake 3.3
@@ -14,7 +15,22 @@ foreach(p
   endif()
 endforeach()
 
-project(ITK NONE)
+include(${CMAKE_CURRENT_SOURCE_DIR}/CMake/ITKInitializeBuildType.cmake)
+
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/CMake ${CMAKE_MODULE_PATH})
+
+# ITK version number components.
+set(ITK_VERSION_MAJOR "4")
+set(ITK_VERSION_MINOR "13")
+set(ITK_VERSION_PATCH "1")
+set(ITK_VERSION
+    "${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR}.${ITK_VERSION_PATCH}")
+project(ITK
+  VERSION ${ITK_VERSION}
+  LANGUAGES CXX C)
+
+set(ITK_CMAKE_DIR "${ITK_SOURCE_DIR}/CMake")
+
 # 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.
@@ -197,6 +213,11 @@ set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} ${ITK_REQUIRED_LINK_
 if(NOT CMAKE_POSITION_INDEPENDENT_CODE)
   set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 endif()
+# Because GoogleTest sets CMAKE_DEBUG_POSTFIX CMake CACHE variable to "d" when it is
+# built in debug, we preemptively set it to an empty string to avoid having a postfix
+# added to the ITK library names.
+set(CMAKE_DEBUG_POSTFIX "" CACHE STRING "Generate debug library name with a postfix.")
+mark_as_advanced(CMAKE_DEBUG_POSTFIX)
 
 # Setup build locations.
 if(NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)

Examples/IO/test/Baseline/DicomSliceReadPythonOutputBaseline.png.sha512

-01b8f1331be6b3f5239509c90e0aeb1a815f40de4bcd2f9cae4a69afbdc011f8311fbfc119e8ee144f7bce333bda7acf2c205ef801f3a3c2eaf718bb5267d359

Modules/Core/Common/CMakeLists.txt

@@ -14,7 +14,7 @@ set(ITK_USE_PTHREADS 0)
 set(ITK_HP_PTHREADS 0)
 if(CMAKE_USE_WIN32_THREADS_INIT)
   set(ITK_USE_WIN32_THREADS 1)
-elseif(CMAKE_USE_PTHREADS_INIT AND NOT EMSCRIPTEN)
+elseif(CMAKE_USE_PTHREADS_INIT)
   set(ITK_USE_PTHREADS 1)
 elseif(CMAKE_HP_PTHREADS_INIT)
   set(ITK_HP_PTHREADS 1)

Modules/Core/Common/include/itkBSplineInterpolationWeightFunction.hxx

@@ -116,7 +116,10 @@ void BSplineInterpolationWeightFunction< TCoordRep, VSpaceDimension,
   // Find the starting index of the support region
   for ( j = 0; j < SpaceDimension; j++ )
     {
-    startIndex[j] = Math::Floor< IndexValueType >(index[j] - static_cast< double >( SplineOrder - 1 ) / 2.0);
+    // Note that the expression passed to Math::Floor is adapted to work around
+    // a compiler bug which caused endless compilations (apparently), by
+    // Visual C++ 2015 Update 3, on 64-bit builds of Release configurations.
+    startIndex[j] = Math::Floor< IndexValueType >(index[j] + 0.5 - SplineOrder/2.0);
     }
 
   // Compute the weights

Modules/Core/Common/include/itkMemoryUsageObserver.h

@@ -79,7 +79,7 @@ protected:
 };
 #endif // defined(WIN32) || defined(_WIN32)
 
-#ifdef linux
+#ifdef __linux__
 class ITKCommon_EXPORT LinuxMemoryUsageObserver:public MemoryUsageObserverBase
 {
 public:
@@ -87,7 +87,7 @@ public:
   virtual ~LinuxMemoryUsageObserver();
   virtual MemoryLoadType GetMemoryUsage();
 };
-#endif // linux
+#endif // __linux__
 
 #if defined( __APPLE__ )
 class ITKCommon_EXPORT MacOSXMemoryUsageObserver:public MemoryUsageObserverBase
@@ -143,7 +143,7 @@ public:
 class ITKCommon_EXPORT MemoryUsageObserver:
 #if defined( WIN32 ) || defined( _WIN32 )
   public WindowsMemoryUsageObserver
-#elif defined( linux )
+#elif defined( __linux__ )
   public LinuxMemoryUsageObserver
 #elif defined( __SUNPRO_CC ) || defined ( __sun__ )
   public SunSolarisMemoryUsageObserver

Modules/Core/Common/src/itkMemoryUsageObserver.cxx

@@ -42,7 +42,7 @@
 #include <stdlib.h>
 #endif
 
-#ifdef linux
+#ifdef __linux__
 #include <fstream>
 #include <unistd.h>
 #endif
@@ -270,7 +270,7 @@ WindowsMemoryUsageObserver::GetMemoryUsage()
 
 #endif // WIN32
 
-#if defined(linux)
+#if defined(__linux__)
 
 /**         ----         Linux Memory Usage Observer       ----       */
 

Modules/Core/Common/src/itkThreadPoolPosix.cxx

@@ -47,8 +47,6 @@ ThreadPool
 
   itksys::SystemInformation mySys;
   mySys.RunCPUCheck();
-  mySys.RunOSCheck();
-  mySys.RunMemoryCheck();
   int result = mySys.GetNumberOfPhysicalCPU(); // Avoid using hyperthreading cores.
   if( result == -1 )
     {

Modules/Core/Common/test/itkBSplineInterpolationWeightFunctionTest.cxx

@@ -18,6 +18,13 @@
 
 #include "itkBSplineInterpolationWeightFunction.h"
 
+// Test template instantiation for TCoordRep = float and VSplineOrder = 1.
+// Note that this particular template instantiation would take forever to
+// compile on VS2015 Update 3 64-bit Release when using ITK 4.13, but
+// itkBSplineInterpolationWeightFunction.hxx can now handle this Visual C++
+// compiler bug.
+template class itk::BSplineInterpolationWeightFunction<float, 2U, 1U>;
+
 /*
  * This test exercises methods in the
  * BSplineInterpolationWeightFunction class.

Modules/Core/Common/wrapping/itkSimpleDataObjectDecorator.wrap

@@ -2,19 +2,19 @@ itk_wrap_class("itk::SimpleDataObjectDecorator" POINTER)
   itk_wrap_template("${ITKM_D}"   "${ITKT_D}")
   itk_wrap_template("${ITKM_F}"   "${ITKT_F}")
   itk_wrap_template("${ITKM_UL}"  "${ITKT_UL}")
+  itk_wrap_template("${ITKM_ULL}"  "${ITKT_ULL}")
   itk_wrap_template("${ITKM_US}"  "${ITKT_US}")
   itk_wrap_template("${ITKM_UC}"  "${ITKT_UC}")
   itk_wrap_template("${ITKM_SL}"  "${ITKT_SL}")
+  itk_wrap_template("${ITKM_SLL}"  "${ITKT_SLL}")
   itk_wrap_template("${ITKM_SS}"  "${ITKT_SS}")
   itk_wrap_template("${ITKM_SC}"  "${ITKT_SC}")
   itk_wrap_template("${ITKM_B}"   "${ITKT_B}")
   itk_wrap_template("${ITKM_AD}"  "${ITKT_AD}")
   itk_wrap_template("${ITKM_AF}"  "${ITKT_AF}")
-  if(WIN32 AND ITK_USE_64BITS_IDS)
+  # For ImageToHistogramFilter
   itk_wrap_template("${ITKM_AULL}"  "${ITKT_AULL}")
-  else()
   itk_wrap_template("${ITKM_AUL}"  "${ITKT_AUL}")
-  endif()
   # non scalar types
   foreach(t ${WRAP_ITK_VECTOR})
     foreach(d ${ITK_WRAP_VECTOR_COMPONENTS})

Modules/Core/Common/wrapping/vnl_c_vector.wrap

@@ -9,11 +9,13 @@ itk_wrap_class("vnl_c_vector" EXPLICIT_SPECIALIZATION)
   itk_wrap_template("${ITKM_F}" "${ITKT_F}")
   itk_wrap_template("${ITKM_SI}" "${ITKT_SI}")
   itk_wrap_template("${ITKM_SL}" "${ITKT_SL}")
+  itk_wrap_template("${ITKM_SLL}" "${ITKT_SLL}")
   itk_wrap_template("${ITKM_LD}" "${ITKT_LD}")
   itk_wrap_template("${ITKM_SC}" "${ITKT_SC}")
   itk_wrap_template("${ITKM_UC}" "un${ITKT_SC}")
   itk_wrap_template("${ITKM_UI}" "un${ITKT_SI}")
   itk_wrap_template("${ITKM_UL}" "un${ITKT_SL}")
+  itk_wrap_template("${ITKM_ULL}" "un${ITKT_SLL}")
   foreach(t ${WRAP_ITK_COMPLEX_REAL})
     itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
   endforeach()

Modules/Core/Common/wrapping/vnl_matrix.wrap

@@ -10,11 +10,13 @@ itk_wrap_class("vnl_matrix" EXPLICIT_SPECIALIZATION)
   itk_wrap_template("${ITKM_F}" "${ITKT_F}")
   itk_wrap_template("${ITKM_SI}" "${ITKT_SI}")
   itk_wrap_template("${ITKM_SL}" "${ITKT_SL}")
+  itk_wrap_template("${ITKM_SLL}" "${ITKT_SLL}")
   itk_wrap_template("${ITKM_LD}" "${ITKT_LD}")
   itk_wrap_template("${ITKM_SC}" "${ITKT_SC}")
   itk_wrap_template("${ITKM_UC}" "un${ITKT_SC}")
   itk_wrap_template("${ITKM_UI}" "un${ITKT_SI}")
   itk_wrap_template("${ITKM_UL}" "un${ITKT_SL}")
+  itk_wrap_template("${ITKM_ULL}" "un${ITKT_SLL}")
   itk_wrap_template("${ITKM_SS}" "${ITKT_SS}")
   itk_wrap_template("${ITKM_US}" "${ITKT_US}")
   foreach(t ${WRAP_ITK_COMPLEX_REAL})

Modules/Core/Common/wrapping/vnl_vector.wrap

@@ -6,7 +6,7 @@ itk_wrap_include("vnl/vnl_matrix.h")
 itk_wrap_include("vnl/vnl_vector.h")
 
 itk_wrap_class("vnl_vector" EXPLICIT_SPECIALIZATION)
-  UNIQUE(vector_types "D;F;SI;SL;LD;SC;UC;US;UI;UL;${ITKM_IT};${ITKM_OT};${WRAP_ITK_SCALAR}")
+  UNIQUE(vector_types "D;F;SI;SL;SLL;LD;SC;UC;US;UI;UL;ULL;${ITKM_IT};${ITKM_OT};${WRAP_ITK_SCALAR}")
   foreach(t ${vector_types})
     itk_wrap_template("${ITKM_${t}}"  "${ITKT_${t}}")
   endforeach()

Modules/Core/Common/wrapping/vnl_vector_ref.wrap

@@ -4,7 +4,7 @@ set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
 itk_wrap_include("vnl/vnl_vector_ref.h")
 
 itk_wrap_class("vnl_vector_ref" EXPLICIT_SPECIALIZATION)
-  UNIQUE(vector_types "D;F;SI;SL;LD;SC;UC;US;UI;UL;${WRAP_ITK_SCALAR}")
+  UNIQUE(vector_types "D;F;SI;SL;SLL;LD;SC;UC;US;UI;UL;ULL;${WRAP_ITK_SCALAR}")
   foreach(t ${vector_types})
     itk_wrap_template("${ITKM_${t}}"  "${ITKT_${t}}")
   endforeach()

Modules/Core/Transform/include/itkEuler3DTransform.hxx

@@ -134,7 +134,7 @@ Euler3DTransform<TParametersValueType>
   // array, we ignore the returned data and add the additional
   // information to the updated array.
   Superclass::GetFixedParameters();
-  this->m_FixedParameters[3] = this-> m_ComputeZYX;
+  this->m_FixedParameters[3] = this->m_ComputeZYX ? 1.0 : 0.0;
   return this->m_FixedParameters;
 }
 
@@ -155,7 +155,7 @@ Euler3DTransform<TParametersValueType>
   if( parameters.Size() == 4 )
     {
     this->m_FixedParameters[3] = parameters[3];
-    this->SetComputeZYX(this->m_FixedParameters[3]);
+    this->SetComputeZYX(this->m_FixedParameters[3] != 0.0);
     }
 }
 

Modules/Core/Transform/wrapping/itkBSplineBaseTransform.wrap

 itk_wrap_class("itk::BSplineBaseTransform" POINTER)
   foreach(d ${ITK_WRAP_IMAGE_DIMS})
-    itk_wrap_template("${ITKM_D}${d}${d}" "${ITKT_D},${d},${d}")
+    itk_wrap_template("${ITKM_D}${d}3" "${ITKT_D},${d},3")
   endforeach()
 itk_end_wrap_class()