configure

#!/usr/bin/env bash

CXX_STD=CXX17

ITKRCMAKE=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkIncludes(); cat(a)'`
ITKRLIB=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkLibs(); cat(a)'`
compflags=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkCompileFlags(); cat(a)'`
if [[ `uname` == 'Darwin' ]] ; then
    compflags=" ${compflags} -isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1 -stdlib=libc++ "
fi
ITKDIR=`${R_HOME}/bin/Rscript -e 'a<-ITKR:::itkDir(); cat(a)'`
ITKTAG=`${R_HOME}/bin/Rscript -e 'env = asNamespace("ITKR"); if ("itkTag" %in% names(env)) cat(ITKR::itkTag()) else cat("")'`


if [[ `uname` == 'Darwin' ]] ; then
  CMAKE_BUILD_TYPE=Release
fi
if [[ $TRAVIS -eq true ]] ; then
  CMAKE_BUILD_TYPE=Release
fi


gitcmd=`which git`
if [[ ! -x $gitcmd ]] ; then # try install git
  apt-get install -y git-core
fi
gitcmd=`which git`
if [[ ! -x $gitcmd ]] ; then # try install git
  exit 1
fi

cd ./src
# platform-specific Makevars
echo "myantssource=\${PWD}/ants" > Makevars
# echo "ITK = \`\$(R_HOME)/bin/Rscript -e 'ITKR:::itkIncludes()'\`" >> Makevars
echo "ITK=${ITKRCMAKE}" >> Makevars

needVCL_CAN_STATIC_CONST_INIT_FLOAT=0
if [[ ${#CC} -gt 0 ]] ; then # test the requested compiler
  temp=$(${CC} --version | grep clang)
  if [[ ${#temp} -gt 0 ]] ; then
    needVCL_CAN_STATIC_CONST_INIT_FLOAT=1
  fi
else # just try gcc directly
  temp=$(gcc --version | grep clang)
  if [[ ${#temp} -gt 0 ]] ; then
    needVCL_CAN_STATIC_CONST_INIT_FLOAT=1
  fi
fi
echo $OSTYPE $needVCL_CAN_STATIC_CONST_INIT_FLOAT

if [[ `uname` == 'Darwin' ]] ; then
  PKG_CPPFLAGS="${PKG_CPPFLAGS} -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1""
fi

echo "PKG_CPPFLAGS=${PKG_CPPFLAGS} -I\${ITK} -I\${PWD} -I\${myantssource}/Examples/include/ \
  -I\${myantssource}/Utilities -I\${myantssource}/Examples/ -I../inst/include/ \
  -I\${myantssource}/Tensor/ " >> Makevars

echo "CXX_STD = CXX17" >> Makevars

# echo "myantslib=\${R_LIBS_USER}/libs/lib" >> Makevars
echo "myantslib=\${PWD}/antb/ANTS-build/Examples/" >> Makevars


echo "libants=\`find \${myantslib} -name \"lib*.a\"\`" >> Makevars

# echo "libitk=\`find \\\`\$(R_HOME)/bin/Rscript -e 'ITKR:::itkLibs()'\\\` -name \"lib*.a\"\` " >> Makevars
echo "libitk=\`find ${ITKRLIB} -name \"lib*.a\"\`" >> Makevars

echo "PKG_LIBS=${PKG_LIBS} \${libants} \${libitk} \${libants} \${libitk} \
    \${libants} \${libitk} \${libants} \${libitk} \${libants} \${libitk}" >> Makevars

echo ".PHONY: all libs cleaner" >> Makevars

echo "all: \$(SHLIB)" >> Makevars
# echo "all: \$(CHECKER) \$(SHLIB)" >> Makevars
# echo "\$(CHECKER): ; @echo \"Myantssource is \${myantssource}\" && @echo \"PWD is \${PWD}\" && @echo \"ITK is \${ITK}\"" >> Makevars

echo "\$(SHLIB): libs " >> Makevars

echo "libs: ; cd \${PWD}/antb && \$(MAKE) -j 2 &&  cd \${PWD}/antb/ANTS-build && \$(MAKE) all install && rm -rf ${R_PACKAGE_DIR}/libs/bin && cd \${PWD}" >> Makevars

echo "cleaner: ; cd libs/bin && rm -f antsRegistration antsApplyTransforms antsMotionCorr \
antsAffineInitializer antsApplyTransformsToPoints LabelGeometryMeasures \
antsMotionCorrStats ResampleImage Atropos KellyKapowski DenoiseImage \
N3BiasFieldCorrection N4BiasFieldCorrection sccan antsJointFusion \
ThresholdImage LabelClustersUniquely SurfaceBasedSmoothing" >> Makevars

# get / set up ANTs code
antsgit=https://github.com/ANTsX/ANTs.git
antstag=d87f266dffdbcef00407d260eab20f4738a98825 # with itk v5.3rc04 2023 nov 25
antstag=1892feff83b792b563500f379fff7733da5465a6
antsrtag=`git log --pretty=format:'%H' -n 1`
if [[ ! -s ants/CMakeLists.txt  ]] ; then
    git clone $antsbranch $antsgit ants
fi
if [[ ! -d ../data/ ]] ; then
  mkdir -p ../data
fi
cd ants
if [[ -d .git ]]; then
    git checkout master
    git pull
    git checkout $antstag
fi
cd ../
if [[ ! -s antb ]] ; then
  mkdir antb
fi
cp ../inst/include/antscore.h ./ants/Examples/include/ants.h
cp -r ants/Examples/include/* ../inst/include/
cp -r ants/Utilities/* ../inst/include/
cp -r ants/Examples/*  ../inst/include/
cp -r ants/Tensor/*  ../inst/include/
cp -r ants/ImageRegistration/* ../inst/include/
cp -r ants/ImageSegmentation/* ../inst/include/
cp -r ants/Temporary/* ../inst/include
cd ./antb

cmake -DITK_DIR:PATH=${ITKDIR} \
    -DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} ${compflags} -DNDEBUG "\
    -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} ${compflags} -DNDEBUG "\
    -DBUILD_SHARED_LIBS=OFF \
    -DANTS_INSTALL_LIBS_ONLY=ON \
    -DBUILD_ALL_ANTS_APPS=OFF \
    -DUSE_SYSTEM_ITK=OFF \
    -DBUILD_TESTING=OFF \
    -DCOPY_SCRIPT_FILES_TO_BIN_DIR=OFF \
    -DCMAKE_INSTALL_PREFIX:PATH=${R_PACKAGE_DIR}/libs/ \
    -DCMAKE_BUILD_TYPE:STRING="${CMAKE_BUILD_TYPE}"  ../ants
cd ../
# needed for warning
rm -rf ants/.git