Bump CIL

CHANGES.md

@@ -2,15 +2,16 @@
 
 ## v3.9.0
 - VM: set the matplotlib backend to tkagg
-- Updated versions (when building the packages):
-  - CIL: 4f6e3cfb0648d08071974eba35c1369a892d4924
+- Updated Versions:
+  - CIL: v25.0.0
   - STIR: 6.3.0
   - SIRF: 3.9.0
   - ITK: 5.4.4
   - parallelproj: 1.10.2
   - boost: 1.88.0
 - CMake:
   - Use [new `FindPython` module](https://cmake.org/cmake/help/latest/module/FindPython.html). You might need to help it find the correct Python path, e.g. by setting `Python_ROOT_DIR`.
+  - Use `IPP_ROOT` instead of `IPP_LIBRARY` (for `BUILD_CIL`)
   - Suppress compilation warnings for Gadgetron for future compatibility (as Gadgetron converts them to errors)
   - Support the `Gadgetron_EXTRA_CMAKE_ARGS` option
 

README.md

@@ -355,13 +355,18 @@ Notice that other packages may look for a blas implementation issuing CMake's [`
 
 ### Building CCPi CIL
 
-It is possible to build the [CCPi Core Imaging Library CIL](https://www.ccpi.ac.uk/CIL) as part of the SuperBuild. The functionality of `CIL` can be expanded by plugins. Currently available: [`CCPi-Regularisation`](https://github.com/vais-ral/CCPi-Regularisation-Toolkit), [`TomoPhantom`](https://github.com/dkazanc/TomoPhantom) [ASTRA-toolbox](https://github.com/astra-toolbox/astra-toolbox) and [`TIGRE`](https://github.com/CERN/TIGRE)).
+The [CCPi Core Imaging Library (CIL)](https://www.ccpi.ac.uk/CIL) is included in the SuperBuild. The functionality of `CIL` can be expanded by plugins. Currently included by default are:
 
-There is one mandatory flag and 2 optional:
+<!-- TODO: mention BUILD_ASTRA etc CMake flags, and check that they remove from requirements.yml -->
 
-- `BUILD_CIL=ON`, will build `CIL` and all the following plugins: `CCPi-Regularisation` and `TomoPhantom`; default `OFF`
-- Optional `IPP_LIBRARY=<location of IPP shared libraries>` and `IPP_INCLUDE=<location of IPP includes>` if you want to build CIL with [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.dnfk5r) support for optimised [FBP/FDK](https://github.com/TomographicImaging/CIL#dependency) .
-- Optional `BUILD_ASTRA=ON`, if you want to use CIL for CT reconstruction with the ASTRA-toolbox engine. Default `OFF`
+- [`CCPi-Regularisation`](https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit)
+- [`TomoPhantom`](https://github.com/dkazanc/TomoPhantom)
+- [IPP](https://www.intel.com/content/www/us/en/developer/tools/oneapi/ipp.html#gs.dnfk5r) support for optimised [FBP/FDK](https://github.com/TomographicImaging/CIL#dependency)
+- (requires CUDA) [ASTRA-toolbox](https://github.com/astra-toolbox/astra-toolbox) for CT reconstruction
+
+Optional dependencies include:
+
+- (requires CUDA) [`TIGRE`](https://github.com/CERN/TIGRE)
 
 ### Passing CMake arguments to specific projects
 

SuperBuild.cmake

@@ -311,7 +311,9 @@ if ("${PYTHON_STRATEGY}" STREQUAL "CONDA")
   set (BUILD_CIL OFF)
 endif()
 if (BUILD_CIL)
-  list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES CIL CCPi-Regularisation-Toolkit TomoPhantom)
+  list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES CIL CCPi-Regularisation-Toolkit)
+  # TODO: once TomoPhantom adds numpy>=2 support:
+  # list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES CIL CCPi-Regularisation-Toolkit TomoPhantom)
 endif()
 if (BUILD_ASTRA)
   list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES astra-python-wrapper)

SuperBuild/External_CIL.cmake

@@ -42,13 +42,8 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   # Sets ${proj}_URL_MODIFIED and ${proj}_TAG_MODIFIED
   SetGitTagAndRepo("${proj}")
 
-  # Pass IPP_INCLUDE And IPP_LIBRARY if they exist
-
-  if (IPP_LIBRARY)
-    set(DIPP_LIBRARY "-DIPP_LIBRARY:STRING=${IPP_LIBRARY}")
-  endif()
-  if (IPP_INCLUDE)
-    set(DIPP_INCLUDE "-DIPP_INCLUDE:STRING=${IPP_INCLUDE}")
+  if (IPP_ROOT)
+    set(DIPP_ROOT "-Ccmake.define.IPP_ROOT=${IPP_ROOT}")
   endif()
 
   # conda build should never get here
@@ -73,17 +68,9 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
       # external projects
       PATCH_COMMAND ${Python_EXECUTABLE} ${CMAKE_SOURCE_DIR}/patches/cil-patch.py ${${proj}_SOURCE_DIR}/Wrappers/Python/cil/utilities/dataexample.py
       UPDATE_COMMAND ""
-      CONFIGURE_COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${${proj}_TAG}
-        ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" -S ${${proj}_SOURCE_DIR}
-          -DCMAKE_INSTALL_PREFIX:PATH=${${proj}_INSTALL_DIR}
-          -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
-          ${PYTHONLIBS_CMAKE_ARGS}
-          -DPYTHON_DEST_DIR:PATH=${PYTHON_DEST}
-          -DCIL_VERSION:STRING=${${proj}_TAG}
-          ${DIPP_INCLUDE}
-          ${DIPP_LIBRARY}
-      BUILD_COMMAND ${CMAKE_COMMAND} --build . --config ${_config}
-      INSTALL_COMMAND ${CMAKE_COMMAND} --build . --config ${_config}  --target install
+      CONFIGURE_COMMAND ""
+      BUILD_COMMAND ""
+      INSTALL_COMMAND ${CMAKE_COMMAND} -E env ${Python_EXECUTABLE} -m pip install ${${proj}_SOURCE_DIR} ${DIPP_ROOT} -Ccmake.build-type=${config} -Ccmake.args="-G ${CMAKE_GENERATOR}"
         && ${CMAKE_COMMAND} -E copy_directory ${${proj}_SOURCE_DIR}/Wrappers/Python/data ${SUPERBUILD_INSTALL_DIR}/share/cil/
       DEPENDS ${${proj}_DEPENDENCIES}
     )

docker/docker-compose.gpu.yml

@@ -27,6 +27,7 @@ services:
     BASE_CONTAINER: synerbi/jupyter:scipy-gpu
     BUILD_GPU: 1
     Gadgetron_USE_CUDA: "ON"
+    BUILD_CIL: "ON"
  sirf:
   deploy: {resources: {reservations: {devices: [{driver: nvidia, count: all, capabilities: [gpu]}]}}}
   image: synerbi/sirf:latest-gpu
@@ -35,4 +36,5 @@ services:
     BASE_CONTAINER: synerbi/jupyter:scipy-gpu
     BUILD_GPU: 1
     Gadgetron_USE_CUDA: "ON"
+    BUILD_CIL: "ON"
    cache_from: [synerbi/jupyter:sirf-build-gpu]

docker/requirements.yml

@@ -32,9 +32,9 @@ dependencies:
   - cil-data >=21.3.0 # cil
   - ipp >=2021.10     # cil
   - tqdm              # cil
-  - numba             # cil 
-  # - tigre          # cil (GPU)
-  # - astra-toolbox  # cil (GPU)
+  - numba             # cil
+  ## - tigre          # cil (GPU) # TODO: remove second # prefix once tigre is build for numpy>=2
+  # - astra-toolbox 2 cuda* # cil (GPU)
   - pip:
     - git+https://github.com/ismrmrd/ismrmrd-python-tools.git@master#egg=ismrmrd-python-tools
     # TODO: labextension @jupyter-widgets/jupyterlab-manager (jupyterlab_widgets ipywidgets ipympl)

version_config.cmake

@@ -143,7 +143,7 @@ set(DEFAULT_STIR_TAG rel_6.3.0)
 
 ## SIRF
 set(DEFAULT_SIRF_URL https://github.com/SyneRBI/SIRF)
-set(DEFAULT_SIRF_TAG v3.9.0)
+set(DEFAULT_SIRF_TAG "0ba22c9b5d8b6c2f008e0b1e1846c059703a88c3") # 2025-11-03
 
 ## pet-rd-tools
 set(DEFAULT_pet_rd_tools_URL https://github.com/UCL/pet-rd-tools)
@@ -161,9 +161,8 @@ set(DEFAULT_JSON_URL https://github.com/nlohmann/json)
 set(DEFAULT_JSON_TAG v3.11.3)
 
 # CCPi CIL
-# minimum supported version of CIL supported is > 22.1.0 or from commit a6062410028c9872c5b355be40b96ed1497fed2a
 set(DEFAULT_CIL_URL https://github.com/TomographicImaging/CIL)
-set(DEFAULT_CIL_TAG 4f6e3cfb0648d08071974eba35c1369a892d4924) # 23/08/24
+set(DEFAULT_CIL_TAG "numpy-2")
 
 set(DEFAULT_CCPi-Regularisation-Toolkit_URL https://github.com/TomographicImaging/CCPi-Regularisation-Toolkit)
 set(DEFAULT_CCPi-Regularisation-Toolkit_TAG "v24.0.1")