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ChangeLog

v3.x.x

  • Udated Versions:
    • CIL: 4f6e3cfb0648d08071974eba35c1369a892d4924

v3.8.0

  • Removed ACE as no longer needed by Gadgetron
  • Updated Versions:
    • SIRF: 3.8.0
    • STIR: 6.2.0
    • parallelproj: 1.9.1 (contains a fix for truncation of the TOF kernel)
    • CIL: v24.1.0
    • Armadillo: 12.8.4 (as per latest Gadgetron, see #923)
    • pet-rd-tools: 2.0.2
  • docker image updates:
    • fix CUDA toolkit on GPU image
    • use CMake 3.29.6
  • VM updates:
    • use CMake 3.29.6

v3.7.0

  • Adds CCPi-Regularisation-Toolkit as prerequisite for CIL and reinstate unit tests
  • Docker:
    • Handle BUILD_CIL correctly and not install CIL from conda if BUILD_CIL=ON
  • CMake:
    • only pass through OpenMP*LIBRARY variables if set, and add OpenMP_iomp_LIBRARY to the list (for Intel compiler) #879
  • Updated Versions:
    • SIRF: v3.7.0
    • CIL: ccf17f393ba911d13b74f2327779dde030098fe6 # 28 May 2024
    • CCPi-Regularisation-Toolkit: v24.0.1
    • STIR: v6.1.0

v3.6.0

  • build the STIR native Python interface by default (STIR_BUILD_SWIG_PYTHON=ON). You can still switch this off.
  • docker image updates:
    • uses docker-stacks
    • CPU: ubuntu:22.04
    • GPU: nvidia/cuda:11.7.1-cudnn8-runtime-ubuntu22.04
    • Important: Docker tags have now changed, see docker/README.md for a table. Changes w.r.t. previous versions are listed below (note that -gpu versions of all tags exist as well, e.g. latest-gpu etc).
      • The latest tag now includes the jupyter server etc, so the service tag should no longer be used (and corresponding images on DockerHub will not be updated).
      • The new edge tag corresponds to master branch of the SIRF-SuperBuild. Note that this will include the "normal" versions of all packages.
      • The devel tag (for DEVEL_BUILD=ON with master versions of SIRF, STIR etc) is no longer pushed to DockerHub, and therefore will not be updated.
    • Docker images are now pushed to DockerHub and GHCR
    • added requirements.yml
    • revert to conda but with libmamba solver
  • updated versions:
    • SIRF: v3.6.0
    • STIR: v6.0.0
    • parallelproj: v1.7.3
    • Gadgetron: 6202fb7352a14fb82817b57a97d928c988eb0f4b (version of Oct 13, 2023)
    • ISMRMRD: v1.13.7
    • NiftyReg: a328efb3a2f8ea4b47cf0f7b581d983a570a1ffd (version of 8 Mar, 2024, fixing find omp.h problems on MacOS)
    • siemens_to_ismrmrd: v1.2.11
    • CIL: db5a2a6cd3bddfbbf53e65f0549ac206096e5b44 (version of Feb 13, 2024)
    • CCPi-Regularisation-Toolkit: 71f8d304d804b54d378f0ed05539f01aaaf13758 (version of Dec 3. 2023)
    • ROOT: v6-28-12
    • nlohmann/json: 3.11.3
  • CMake changes
    • pass through OpenMP_CXX_INCLUDE_DIR and OpenMP_C_INCLUDE_DIR to dependent projects. For instance, on MacOS the compiler might not find omp.h unless these variables are set.
  • VM changes
    • UPDATE.sh (and hence update_VM.sh) has extra developer options to set the DEVEL_BUILD=ON (-D) and skip the build (-S).
  • Drop Travis

v3.5.0

  • Temporarily disable CCPi-Regularisation due to #832
  • CMake/building:
    • default DISABLE_MATLAB to ON as SIRF Matlab support is out-of-date and enabling it could generate conflicts with Python shared libraries.
  • docker image updates
    • introduce REMOVE_BUILD_FILES variable. If set to 1 (which is the default), most build files will be removed in the docker image.
    • introduce RUN_CTEST variable. If set to 1 (which is the default), the CTests will be run while building the image.
    • remove obsolete copying of gadgetron.xml
    • Installing requirements for SIRF-Exercises uses its environment.yml or requirements.txt depending on settings.
  • Build Gadgetron master. Requires new Ubuntu packages: libdcmtk-dev, libpugixml-dev, libgflags-dev, libssl-dev, libcurl4-openssl-dev, pkg-config, golang, libboost-coroutine-dev, libboost-context-dev, libboost-random-dev.
  • Added SuperBuild project dependencies for Gadgetron: range-v3, RocksDB, Date, mrd-storage-server
  • updated versions:
    • Gadgetron: 42f11bf14b77b16f1ca5bcfbfa435d5ee8cb22a6 (master)
    • RocksDB: 6.26.0
    • range-v3: 0.12.0
    • siemens_to_ismrmrd: 8bb8b08f53ce73c2de9ba5f47f1532f96292d92b
    • ISMRMRD: v1.13.2
    • SIRF: v3.5.0
    • CIL: v23.1.0
    • CCPi-Regularisation: v22.0.0
    • TomoPhantom: v2.0.0

v3.4.0

  • Removed CIL-ASTRA as it has been merged into CIL code base.
  • docker images updates
    • Ubuntu: 22.04
    • added dependencies to python-opencv , pytest, pytest-cov and coverage
    • added requirements.yml and requirements-service.yml to handle dependencies for conda python
    • updates to use mamba
    • use jupyterlab as opposed to notebook in the "service" images
    • CMake: v3.25.1
  • VM updates
    • Ubuntu: 22.04
    • update configuration and documentation to use jupyterlab as opposed to the notebook server
    • CMake: 3.21.3
    • fixes documentation
    • use the VMSVGA graphics controller
    • use environment variables in Vagrantfile for easier building
  • jupyterhub updates:
    • Ubuntu: 22.04 and nvidia/cuda:11.7.1-cudnn8-runtime-ubuntu22.04
    • added requirements.yml for jupyterhub
  • updated versions:
    • SIRF: v3.4.0
    • CIL: a6062410028c9872c5b355be40b96ed1497fed2a > 22.1.0
    • GTest: 1.12.1
    • glog: 0.6.0
    • parallelproj: v1.2.13
    • STIR: rel_5.1.0
    • Boost: 1.78.0

v3.3.1

  • VM:
    • "update_VM.sh -s" (i.e. "UPDATE.sh -s") no longer runs configure_gnome.sh. If you have a very old VM, run it manually instead.
    • Updates to run using docker scripts
    • installs custom pip and all python prerequisites with pip
    • Bugfix in finding cython and python in UPDATE.sh
    • general refresh of scripts etc
    • move zero_fill.sh from first_run.sh and move it to a new clean_before_VM_export.sh script, which also removes build files to make the exported VM smaller.
  • docker and VM:
    • install uuid-dev such that we're prepared for installing ROOT
    • no longer force numpy<=1.20
  • CMake:
    • FindCython allows hints

v3.3.0

  • known problems:
    • VM and jupyterhub scripts need merging various fixes
  • gemeric *.cmake fixes:
    • update to the ASTRA build script
    • fix/add minimum versions for various packages
    • improve finding GTest
  • Windows
    • Boost build add regex and random
    • install env_sirf.PS1 and .bat files (similar to the existing .sh and .csh files)
  • docker:
    • fix problems with CUDA repo keys
    • minor fixes to scripts for use elsewhere (including preparation for more recent Ubuntu)
  • VM:
    • set BUILD_CIL=ON
  • add CITATION.cff (and remove .zenodo.json)
  • added numba as dependency in docker files
  • updated versions:
    • SIRF: 3.3.0
    • STIR: 5.0.2
    • parallelproj: v0.8
    • CCPi Regularisation: v21.0.0
    • CIL: v21.4.1 (CIL devel build to commit hash ef66083de231492f9571f5512b33068f6950e877 )

v3.2.0

  • Moved the VM scripts etc to this repo
  • CMake: removed USE_SYSTEM_siemens_to_ismrmrd
  • CMake: added required versions for STIR, NIFTYREG, ISMRMRD.
  • Drop Python 2 support
  • CMake minimum required version is set to 3.16.2, as it supports Boost 1.72
  • VirtualBox VM is created from the SIRF-SuperBuild repository
  • Docker images install CIL via conda, so setting BUILD_CIL=OFF in the docker build
  • Added jupyterhub Dockerfile and documentation to build the jupyterhub image used in training on top of SIRF docker images and jupyter datascience-notebook image with GPU access.
  • Adds Boost random for ISMRMRD 1.5.0 #636
  • moved the VM repository to the VirtualBox subdirectory
  • fix usage of proj_EXTRA_CMAKE_ARGS facility (it was broken for all projects except ITK) #616
  • Boost: fix cases where the wrong version of boost could be found #627
  • GTest: if USE_SYSTEM_GTest=OFF, attempt to force finding our version, otherwise, pass GTest_DIR or GTEST_ROOT on to dependent projects.
  • add the CERN ROOT library (if USE_ROOT=ON, but defaults to OFF), which can be used by STIR to read GATE ROOT files.
  • updated versions:
    • CMake: 3.16.2
    • ISMRMRD: 1.7.0 if siemens_to_ismrmrd is built, 1.4.2.1 otherwise
    • siemens_to_ismrmrd: 6d0ab3d3d0c8ade5c0526db1c6af9825008425ad > 1.2.2 with bug-fix for boost/foreach.hpp
    • ITK: 5.2.1 However, we now build a smaller set of modules, most (but not all) of IO, and Filtering. See SuperBuild/External_ITK.cmake)
    • NiftyReg: 99d584e2b8ea0bffe7e65e40c8dc818751782d92 ) (fixes gcc-9 OpenMP problems)
    • CIL: v21.4.0
    • GTest: 1.11.0
    • Boost: 1.72.0
    • JSON: 3.10.4
    • ACE: 6.5.9
    • parallelproj: v0.8

v3.1.1

  • added external project astra-python-wrapper to allow updates of ASTRA without conflicts #605
  • fix docker/entrypoint for case where a user has a GID that already exists in the Docker image #606

v3.1.0

  • docker:
    • configure nbstripout in SIRF-Exercises for sirf-service
    • major change w.r.t. users and permissions. We now build as user jovyan (by default) and still switch to sirfuser for running the container. This avoids having to reset permissions of many files, and therefore speeds-up container start-up.
    • introduced SIRF_SB_URL, SIRF_SB_TAG and NUM_PARALLEL_BUILDS. They default to the values used before (i.e. resp. the main SIRF-SuperBuild repo, master and 2).
    • add dependencies that are available only from conda-forge (for CIL)
    • improved documentation
  • allow specifying HDF5_URL and HDF5_TAG like for other projects
  • updated versions:
    • SIRF: 3.1.0
    • CIL: 21.2.0
    • CIL-ASTRA: 21.2.0
  • disable built of NiftyPET by default as our current setup requires Python2 for which we dropped support
  • Continuous Integration testing:
    • Removed all Travis runs except those that run docker

v3.0.0

  • use BUILD_CIL=ON for all Docker builds
  • Docker build moved to Python3 only.
  • Environment files with name env_sirf.sh (and csh) are created. Symbolic links or copies with the previous name env_ccppetmr.sh (and csh) depending on the version of CMake available are made.
  • Fix some issues with finding Python #472
  • Handling dependent projects:
    • Sets USE_ITK=ON by default.
    • Disabled building of Module_ITKReview by default
    • Updates for CIL 20.11+ which has a different python module structure. CCPi-FrameworkPlugins has been also removed.
    • CIL repository has been transferred to the TomographicImaging organisation; reflect changes in CIL repositories
    • Patch Gadgetron include file hoNDFFT.h to remove spurious ".."
    • Add Gadgetron as a dependency of SIRF if BUILD_Gadgetron is ON.
    • Enabled HDF5 support for STIR by default (build C++ libraries for HDF5)
    • Add option BUILD_TESTING_JSON (default OFF)
  • Updated versions:
    • JSON: 3.9.1
    • SWIG: 4.0.2
    • STIR: 4.1.1
    • SIRF: 3.0.0
    • CIL: 21.1.0
    • CCPi-Regularisation toolkit: 20.09
  • Continuous Integration testing:
    • Add GitHub actions and removed most Travis runs
    • Switched Travis ctest from --verbose to --output-on-failure and added travis_wait of 20 minutes to keep it from timing-out if some tests take longer than 10.

v2.2.0

  • Updated to reflect change from CCPPETMR to CCPSyneRBI.
  • Made ${proj}_SOURCE_DIR a cached variables such that the user can point to an existing directory.
  • Added support for passing CMAKE args to projects from the SuperBuild call.
  • Use macros to drastically simplify (and reduce size of) the External*.cmake files.
  • Pass HDF5_ROOT through to projects if it's defined and USE_SYSTEM_HDF5=ON
  • Added checking whether default SWIG executable exists.
  • Corrected logic around building SIRF and Registration.
  • Added JSON as external package.
  • Added option to build ITK with static libraries.
  • Added option to skip ITK path length checks.
  • Added option to compile Armadillo without HDF5 support.
  • Added options to disable STIR JSON support.
  • Added option to disable CUDA.
  • Added option to disable Gadgetron checkouts.
  • Added option to disable Python or MATLAB support.
  • Sorted out Nifty PET capitalisation.
  • Unified OpenMP control.
  • Updated versions:
    • STIR: rel_4.0.2
    • CIL: 20.04
    • SIRF: 2.2.0

v2.1.0

  • Switch NiftyReg remote from rijobro to KCL-BMEIS (following the acceptance of one of our PRs to their code).
  • Azure:
    • Added NVIDIA GPU support
    • Now using Terraform HCL v0.12
  • Added CCPi CIL support and various packages for that
  • Added preliminary install option for NiftyPET
  • Added CUDA and OpenMP support for some packages
  • Improved documentation for docker
  • Updated various versions
    • NiftyReg: 1.5.68
    • ISMRMRD: v1.4.1
    • STIR: stir_rel_4_00_alpha
    • SIRF: v2.1.0
    • PET RD Tools: v1.1.0
    • Armadillo: 9.800.2
  • petmr-rd-tools -> pet-rd-tools fixes

v2.0.0

  • Added CMake Variable Gadgetron_USE_MKL to allow Gadgetron build with MKL if available
  • Added build of NiftyReg and ACE (optional)
  • Added tests for various packages, not just SIRF (CMake variables BUILD_TESTING_*)
  • Updated various versions
    • ISMRMRD: v1.4.0
    • Gadgetron: b6191ea
    • Boost: 1.65.1 (linux) 1.68.0 (OSX)
    • STIR to version of 9 Apr 2019
    • SIRF v2.0.0. If NiftyReg is built (or provided), SIRF will be built with registration capabilities.
  • docker images updates
    • Ubuntu: 18.04
    • :service images with Jupyter and SIRF-Exercises
  • addition of Azure scripts
  • require CMake: 3.10.0
  • changed some CMake variable names:
    • BUILD_GADGETRON -> BUILD_Gadgetron
    • BUILD_GADGETRON_NATIVE_MATLAB_SUPPORT -> Gadgetron_BUILD_MATLAB_SUPPORT
    • BUILD_STIR_WITH_OPENMP -> STIR_ENABLE_OPENMP
    • BUILD_STIR_EXECUTABLES -> STIR_BUILD_EXECUTABLES
    • BUILD_STIR_SWIG_PYTHON -> STIR_BUILD_SWIG_PYTHON
  • petmr-rd-tools -> pet-rd-tools

v1.1.0

  • Added PYTHON_DEST_DIR variable, which allows the user to select the install destination of the SIRF python modules. PYTHON_DEST_DIR is a cached variable which can be updated on the GUI. If PYTHON_DEST_DIR is not set, we will install in ${CMAKE_INSTALL_PREFIX}/python. Likewise for MATLAB_DEST_DIR.
  • Export GADGETRON_HOME environment variable (necessary for recent versions of Gadgetron)
  • Updates to Docker builds
  • On OSX, use the system boost by default to avoid run-time problems with boost dynamic libraries
  • Build STIR with OPENMP

v1.0.0

  • optionally build siemens_to_ismrmrd
  • optionally build petmr_rd_tools
  • major restructuring of SuperBuild build directory
  • User can specify the location of the sources via the variable SOURCES_ROOT_DIR
  • Updated dependency versions (STIR)
  • Defaults to USE_SYSTEM_BOOST=ON on Windows and MacOSX #63, see here

New in Release 0.9.1

  • build specific versions of dependencies (ISMRMRD, Gadgetron, STIR, SIRF)
  • run tests via CTest