NiftyReg (#59)

* NiftyReg added to the superbuild

* updated NiftyReg tag

* added one compilation of NiftyReg to travis

.travis.yml

@@ -15,6 +15,14 @@ language: cpp
 # so try to keep this concise to avoid need to update
 matrix:
  include:
+ - os: linux
+   python: 3
+   # +boost -itk +fftw3 +hdf5 -ace
+   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_ITK=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DUSE_SYSTEM_ACE=OFF -DUSE_NiftyReg=ON" CC=gcc-5 CXX=g++-5 PYMVER=3
+ - os: linux
+   python: 2.7
+   # +boost -itk +fftw3 +hdf5 -ace
+   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_ITK=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DUSE_SYSTEM_ACE=OFF -DUSE_NiftyReg=ON" CC=gcc-5 CXX=g++-5 PYMVER=3
  - os: linux
    python: 3
    # +boost -itk +fftw3 +hdf5 -ace

SuperBuild.cmake

@@ -112,15 +112,18 @@ option(USE_SYSTEM_Armadillo "Build using an external version of Armadillo" OFF)
 option(USE_SYSTEM_SWIG "Build using an external version of SWIG" OFF)
 #option(USE_SYSTEM_Gadgetron "Build using an external version of Gadgetron" OFF)
 option(USE_SYSTEM_SIRF "Build using an external version of SIRF" OFF)
+option(USE_SYSTEM_NiftyReg "Build using an external version of NiftyReg" OFF)
 option(USE_SYSTEM_GTest "Build using an external version of GTest" OFF)
 option(USE_SYSTEM_ACE "Build using an external version of ACE" ON)
+
 if (APPLE)
   set (build_STIR_OPENMP_default OFF)
 else()
   set (build_STIR_OPENMP_default ON)
 endif()  
 option(BUILD_STIR_WITH_OPENMP "Build STIR with OpenMP acceleration" ${build_STIR_OPENMP_default})
 
+
 if (WIN32)
   set(build_Gadgetron_default OFF)
 else()

SuperBuild/External_NiftyReg.cmake

@@ -0,0 +1,88 @@
+#========================================================================
+# Author: Richard Brown
+# Author: Benjamin A Thomas
+# Author: Kris Thielemans
+# Copyright 2017 University College London
+# Copyright 2017 STFC
+#
+# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+#=========================================================================
+
+#This needs to be unique globally
+set(proj NiftyReg)
+
+# Set dependency list
+set(${proj}_DEPENDENCIES "")
+
+# Include dependent projects if any
+ExternalProject_Include_Dependencies(${proj} DEPENDS_VAR ${proj}_DEPENDENCIES)
+
+# Set external name (same as internal for now)
+set(externalProjName ${proj})
+
+if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalProjName}}" ) )
+  message(STATUS "${__indent}Adding project ${proj}")
+
+  ### --- Project specific additions here
+  set(${proj}_Install_Dir ${SUPERBUILD_INSTALL_DIR})
+
+  #message(STATUS "HDF5_ROOT in External_SIRF: " ${HDF5_ROOT})
+  set(CMAKE_LIBRARY_PATH ${CMAKE_LIBRARY_PATH} ${SUPERBUILD_INSTALL_DIR})
+  set(CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH} ${SUPERBUILD_INSTALL_DIR})
+
+  set(${proj}_SOURCE_DIR "${SOURCE_ROOT_DIR}/${proj}" )
+  set(${proj}_BINARY_DIR "${SUPERBUILD_WORK_DIR}/builds/${proj}/build" )
+  set(${proj}_DOWNLOAD_DIR "${SUPERBUILD_WORK_DIR}/downloads/${proj}" )
+  set(${proj}_STAMP_DIR "${SUPERBUILD_WORK_DIR}/builds/${proj}/stamp" )
+  set(${proj}_TMP_DIR "${SUPERBUILD_WORK_DIR}/builds/${proj}/tmp" )
+
+  ExternalProject_Add(${proj}
+    ${${proj}_EP_ARGS}
+    GIT_REPOSITORY ${${proj}_URL}
+    GIT_TAG ${${proj}_TAG}
+    SOURCE_DIR ${${proj}_SOURCE_DIR}
+    BINARY_DIR ${${proj}_BINARY_DIR}
+    DOWNLOAD_DIR ${${proj}_DOWNLOAD_DIR}
+    STAMP_DIR ${${proj}_STAMP_DIR}
+    TMP_DIR ${${proj}_TMP_DIR}
+
+    CMAKE_ARGS
+        -DCMAKE_PREFIX_PATH=${SUPERBUILD_INSTALL_DIR}
+        -DCMAKE_LIBRARY_PATH=${SUPERBUILD_INSTALL_DIR}/lib
+        -DCMAKE_INCLUDE_PATH=${SUPERBUILD_INSTALL_DIR}
+        -DCMAKE_INSTALL_PREFIX=${${proj}_Install_Dir}
+	    INSTALL_DIR ${${proj}_Install_Dir}
+    DEPENDS
+        ${${proj}_DEPENDENCIES}
+  )
+
+    set(${proj}_ROOT        ${${proj}_SOURCE_DIR})
+    set(${proj}_INCLUDE_DIR ${${proj}_SOURCE_DIR})
+
+   else()
+      if(${USE_SYSTEM_${externalProjName}})
+        find_package(${proj} ${${externalProjName}_REQUIRED_VERSION} REQUIRED)
+        message("USING the system ${externalProjName}, set ${externalProjName}_DIR=${${externalProjName}_DIR}")
+    endif()
+    ExternalProject_Add_Empty(${proj} DEPENDS "${${proj}_DEPENDENCIES}")
+  endif()
+
+  mark_as_superbuild(
+    VARS
+      ${externalProjName}_DIR:PATH
+    LABELS
+      "FIND_PACKAGE"
+  )

SuperBuild/External_SIRF.cmake

@@ -23,7 +23,11 @@
 set(proj SIRF)
 
 # Set dependency list
-set(${proj}_DEPENDENCIES "STIR;Boost;HDF5;ISMRMRD;FFTW3;SWIG")
+if (${USE_NiftyReg})
+  set(${proj}_DEPENDENCIES "STIR;Boost;HDF5;ISMRMRD;FFTW3;SWIG;NiftyReg")
+else()
+  set(${proj}_DEPENDENCIES "STIR;Boost;HDF5;ISMRMRD;FFTW3;SWIG")
+endif()
 
 message(STATUS "Matlab_ROOT_DIR=" ${Matlab_ROOT_DIR})
 message(STATUS "STIR_DIR=" ${STIR_DIR})

version_config.cmake

@@ -81,6 +81,10 @@ set(glog_TAG v035)
 set(ITK_URL https://itk.org/ITK.git)
 set(ITK_TAG v4.13.0)
 
+## NiftyReg
+set(NiftyReg_URL https://git.code.sf.net/p/niftyreg/git )
+set(NiftyReg_TAG 4e4525b84223c182b988afaa85e32ac027774c42 )
+
 option (DEVEL_BUILD "Developer Build" OFF)
 mark_as_advanced(DEVEL_BUILD)