configure

#!/usr/bin/env bash

CXX_STD=CXX17
JTHREADS=4
if [[ `uname` == 'Darwin' ]] ; then
  CMAKE_BUILD_TYPE=Release
fi
if [[ $TRAVIS -eq true ]] ; then
  CMAKE_BUILD_TYPE=Release
  JTHREADS=2
fi
cd ./src
itkgit=https://github.com/InsightSoftwareConsortium/ITK
itktag=20edc269b1d9bf9ff27a34db40a438b1b3044f3c # April 28, 2025
# if there is a directory but no git,
# remove it
if [[ -d itks ]]; then
	if [[ ! -d itks/.git ]]; then
		rm -rf itks/
	fi
fi
git_exe=`${R_HOME}/bin/Rscript -e "x=Sys.which('git'); cat(x)"`
if [ -z "${git_exe}" ]; then
    ${R_HOME}/bin/Rscript -e 'if (!requireNamespace("git2r")) install.packages("git2r")'
    str='if (!requireNamespace("git2r")) { install.packages("git2r") }'
    str="${str}; repo = git2r::clone(\""
    str="${str}${itkgit}"
    str="${str}\", local_path = \"./itks\")"
    if [ -n "${itktag}" ]; then
        str="${str}; git2r::checkout(repo, branch = \""
        str="${str}${itktag}"
        str="${str}\");"
    fi
	${R_HOME}/bin/Rscript -e "${str}"
	cd itks
else
	# if no directory, clone it
	if [[ ! -d itks ]]; then
	    git clone $itkgit itks
	fi
	cd itks
	if [[ -d .git ]]; then
	    git checkout master;
	    git checkout $itktag
	fi
fi
rm -rf .git


cd ../
if [[ ! -d ../data/ ]] ; then
  mkdir -p ../data
fi
echo "Dependency;GitTag" > ../data/softwareVersions.csv
echo "ITK;${itktag}" >> ../data/softwareVersions.csv
echo "ITKURL;${itkgit}" >> ../data/softwareVersions.csv
mkdir -p itkb
cd itkb
compcflags=" -fPIC -O2 -Wno-c++11-long-long "
compcxxflags=" ${compcflags} "
osx_sysroot=""
if [[ `uname` == 'Darwin' ]] ; then
    osx_sysroot=$(xcrun --sdk macosx --show-sdk-path)
fi
cmaker=`${R_HOME}/bin/Rscript -e "x=Sys.which('cmake'); cat(x)"`
if [[ -z "${cmaker}" ]]; then
	res=`${R_HOME}/bin/Rscript -e "cat(('cmaker' %in% installed.packages())*1)"`
	if [[ $res -eq 0 ]];
		then
	    git clone https://github.com/stnava/cmaker ;
	    R CMD INSTALL cmaker ;
	    rm -rf cmaker ;
	fi
    cmaker=`${R_HOME}/bin/Rscript -e "x=cmaker::cmake()"`
else
	cmaker="cmake"
fi

${cmaker} \
    -DCMAKE_BUILD_TYPE:STRING="${CMAKE_BUILD_TYPE}" \
    -DCMAKE_CXX_STANDARD="17"\
    -DCMAKE_CXX_STANDARD_REQUIRED="YES"\
    -DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} ${compcflags} -DNDEBUG  "\
    -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} ${compcxxflags} -DNDEBUG  "\
    -DCMAKE_OSX_SYSROOT="${osx_sysroot}"\
    -DITK_USE_GIT_PROTOCOL:BOOL=OFF \
    -DBUILD_SHARED_LIBS=OFF \
    -DBUILD_TESTING:BOOL=OFF \
    -DBUILD_EXAMPLES:BOOL=OFF \
    -DCMAKE_INSTALL_PREFIX:PATH="${R_PACKAGE_DIR}"/libs/  \
    -DITK_LEGACY_REMOVE:BOOL=OFF  \
    -DITK_FUTURE_LEGACY_REMOVE:BOOL=OFF \
    -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF \
    -DModule_AdaptiveDenoising:BOOL=ON \
    -DModule_GenericLabelInterpolator:BOOL=ON \
    -DKWSYS_USE_MD5:BOOL=ON \
    -DITK_WRAPPING:BOOL=OFF \
    -DModule_MGHIO:BOOL=ON \
    -DModule_ITKDeprecated:BOOL=OFF \
    -DModule_ITKReview:BOOL=ON \
    -DModule_ITKVtkGlue:BOOL=OFF \
    -D ITKGroup_Core=ON \
    -D Module_ITKReview=ON \
    -D ITKGroup_Filtering=ON \
    -D ITKGroup_IO=ON \
    -D ITKGroup_Numerics=ON \
    -D ITKGroup_Registration=ON \
    -D ITKGroup_Segmentation=ON ../itks/
cd ../
    # -DModule_ITKDCMTK:BOOL=ON \