diff --git a/.travis.yml b/.travis.yml
index 1686428b280793636cf5c541a8861c9382b4543f..80eb02fe4056453cbf255c088725c411ff96fd89 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,4 +1,5 @@
-sudo: false
+sudo: required
+dist: trusty
language: cpp
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 81e9fb94c800d4b0debfb979b96eb16563deefc9..952f2264934e1a1d386877ea3e171755b02c2471 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -32,7 +32,7 @@ find_package( Boost )
include_directories( ${Boost_INCLUDE_DIRS} )
# ---------------------------------------------------------------------
-# Build Elastix
+# Build SuperElastix
# For now we just enable all modules
include( elxModules )
elxmodule_enable( elxModuleCore )
@@ -42,13 +42,13 @@ 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} )
+option( SUPERELASTIX_BUILD_TESTING "Enable building tests." ${ELASTIX_BUILD_TESTING_DEFAULT} )
if( ${ELASTIX_BUILD_TESTING} )
enable_testing()
add_subdirectory( Testing )
@@ -57,9 +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 )
diff --git a/SuperBuild/CMakeLists.txt b/SuperBuild/CMakeLists.txt
index 74fd55b13d4956db07142de67ea63e6a829d1e9e..a7f864fe4db147bc65799dc2777c978aa0631b7e 100644
--- a/SuperBuild/CMakeLists.txt
+++ b/SuperBuild/CMakeLists.txt
@@ -1,7 +1,7 @@
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}" )
@@ -51,7 +51,7 @@ 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 )
endif()
@@ -83,7 +83,17 @@ 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 )
diff --git a/SuperBuild/Elastix.cmake b/SuperBuild/Elastix.cmake
deleted file mode 100644
index c96535d2f1b330007672ab584168b1ac6e51d0f3..0000000000000000000000000000000000000000
--- a/SuperBuild/Elastix.cmake
+++ /dev/null
@@ -1,18 +0,0 @@
-set( proj Elastix )
-
-ExternalProject_Add( ${proj}
- DOWNLOAD_COMMAND ""
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/..
- 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=${ELASTIX_BUILD_DASHBOARD}
- -DITK_DIR:PATH=${ITK_DIR}
- -DBOOST_ROOT:PATH=${BOOST_ROOT}
- -DGTEST_ROOT:PATH=${GTEST_ROOT}
- DEPENDS ${ELASTIX_DEPENDENCIES}
- INSTALL_COMMAND ""
-)
diff --git a/SuperBuild/ExternalElastix.cmake b/SuperBuild/ExternalElastix.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..f99860c9de6e3a144909a695553ef200055ec313
--- /dev/null
+++ b/SuperBuild/ExternalElastix.cmake
@@ -0,0 +1,102 @@
+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} )
diff --git a/SuperBuild/SuperElastix.cmake b/SuperBuild/SuperElastix.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..38c6ed2feb058a1b8cb09851e208f1a348071696
--- /dev/null
+++ b/SuperBuild/SuperElastix.cmake
@@ -0,0 +1,19 @@
+set( proj SuperElastix )
+
+ExternalProject_Add( ${proj}
+ DOWNLOAD_COMMAND ""
+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/..
+ BINARY_DIR ${proj}-build
+ CMAKE_ARGS
+ --no-warn-unused-cli
+ -DSUPERELASTIX_BUILD_EXAMPLES:BOOL=${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 ""
+)