Building SIRF and CIL with conda

These are instructions to build SIRF, CIL and all prerequisites using conda for dependencies. It is recommended to do this if you use conda for your normal python development. The instructions are for a Linux system although minor variations should work on other systems.

First, install miniconda.

Then follow these steps:

mkdir ~/devel
cd ~/devel
git clone https://github.com/SyneRBI/SIRF-SuperBuild
mkdir buildVM
cd buildVM

conda create --name cilsirfbuild python=3 numpy cxx-compiler cmake scipy python-wget cython six pillow nose h5py matplotlib numpy boost libitk-devel libitk nlohmann_json libparallelproj -c conda-forge

conda activate cilsirfbuild

cmake -S ../SIRF-SuperBuild/ -B . -DUSE_SYSTEM_ACE=OFF -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_ITK=ON -DUSE_SYSTEM_parallelproj=ON -DUSE_SYSTEM_HDF5=ON -DUSE_ITK=ON -DCMAKE_INSTALL_PREFIX=../install

make

This will download, build, & install all CIL & SIRF dependencies in ~/devel/install.

To run SIRF+CIL you need to create a shell script like the following and source it:

# activate conda environment
conda activate cilsirfbuild
# source the SIRF environment file
source ~/devel/install/bin/env_sirf.sh
# add CONDA_PREFIX/lib to LD_LIBRARY_PATH (probably not necessary)
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH