super-build.sh

#!/usr/bin/env bash

export NUM_THREADS=4
export ITK_VERSION=v5.1.2
export VTK_VERSION=v9.0.1
export PROJECT_DIR="$(pwd)"
export SUPERBUILD_DIR=${PROJECT_DIR}/super-build
export ITK_SOURCE_DIR=${SUPERBUILD_DIR}/itk-${ITK_VERSION}
export VTK_SOURCE_DIR=${SUPERBUILD_DIR}/vtk-${VTK_VERSION}
export ITK_BUILD_DIR=${ITK_SOURCE_DIR}-build
export VTK_BUILD_DIR=${VTK_SOURCE_DIR}-build


if ! test -d ${SUPERBUILD_DIR}; then mkdir ${SUPERBUILD_DIR}; fi
cd ${SUPERBUILD_DIR}

# submodule update
git submodule init && git submodule update

# miniconda install
set +e
export MINICONDA_MAC=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
export MINICONDA_LINUX=https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
if [[ "$OSTYPE" == "linux-gnu" ]]; then
  curl $MINICONDA_LINUX -C - -o miniconda_install.sh
  if [ $? -ne 0 ]; then
      curl $MINICONDA_LINUX -o miniconda_install.sh
  fi
elif [[ "$OSTYPE" == "darwin"* ]]; then
  curl $MINICONDA_MAC -C - -o miniconda_install.sh
  if [ $? -ne 0 ]; then
      curl $MINICONDA_MAC -o miniconda_install.sh
  fi
fi
set -e

! bash miniconda_install.sh -b -f -p "${SUPERBUILD_DIR}/miniconda/"

# Activate the new environment
PATH=${SUPERBUILD_DIR}"/miniconda/bin":$PATH

# install python modules
! bash ${PROJECT_DIR}/install_modules.sh

! conda install cryptography

cd ${PROJECT_DIR}/externals/TCIAExplorer
! python3 setup.py install
cd -

if ! test -e ${VTK_SOURCE_DIR}/CMakeLists.txt; then rm -fr $VTK_SOURCE_DIR; fi
if ! test -d ${VTK_SOURCE_DIR}; then git clone --branch ${VTK_VERSION} https://gitlab.kitware.com/vtk/vtk.git ${VTK_SOURCE_DIR}; fi
if ! test -d ${VTK_BUILD_DIR}; then mkdir ${VTK_BUILD_DIR}; fi
cd ${VTK_BUILD_DIR}
cmake ${VTK_SOURCE_DIR} -DCMAKE_BUILD_TYPE=Release -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF 
make --jobs=${NUM_THREADS} --keep-going
cd -

if ! test -e ${ITK_SOURCE_DIR}/CMakeLists.txt; then rm -fr $ITK_SOURCE_DIR; fi
if ! test -d ${ITK_SOURCE_DIR}; then git clone --branch ${ITK_VERSION} https://github.com/InsightSoftwareConsortium/ITK.git ${ITK_SOURCE_DIR}; fi
if ! test -d ${ITK_BUILD_DIR}; then mkdir ${ITK_BUILD_DIR}; fi
cd ${ITK_BUILD_DIR}
cmake ${ITK_SOURCE_DIR} -DCMAKE_BUILD_TYPE=Release -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF -DModule_ITKReview=ON -DModule_LesionSizingToolkit=ON
make --jobs=${NUM_THREADS} --keep-going
cd -

if ! test -d build; then mkdir build; fi
cd build
cmake ${PROJECT_DIR} -DITK_DIR=${ITK_BUILD_DIR} && make
cd ${PROJECT_DIR}