NiftyPET version 2

.github/workflows/build-test.yml

@@ -37,6 +37,7 @@ jobs:
         - os: ubuntu-latest
           compiler: gcc
           compiler_version: 9
+          cuda_version: "0"
           BUILD_FLAGS: "-DSTIR_OPENMP=ON"
           BUILD_TYPE: "Release"
           parallelproj: "ON"
@@ -45,6 +46,7 @@ jobs:
         - os: ubuntu-latest
           compiler: clang
           #compiler_version:
+          cuda_version: "0"
           BUILD_FLAGS: "-DSTIR_OPENMP=ON"
           BUILD_TYPE: "Release"
           parallelproj: "ON"
@@ -54,6 +56,7 @@ jobs:
         - os: ubuntu-latest
           compiler: gcc
           compiler_version: 10
+          cuda_version: "0"
           BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17"
           BUILD_TYPE: "Debug"
           parallelproj: "OFF"
@@ -62,14 +65,25 @@ jobs:
         - os: ubuntu-latest
           compiler: gcc
           compiler_version: 12
+          cuda_version: "0"
           BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=14"
           BUILD_TYPE: "RelWithDebInfo"
           parallelproj: "ON"
           ROOT: "OFF"
           ITK: "ON"
+        - os: ubuntu-latest
+          compiler: gcc
+          compiler_version: 12
+          cuda_version: "12.1.0"
+          BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=14"
+          BUILD_TYPE: "Release"
+          parallelproj: "ON"
+          ROOT: "OFF"
+          ITK: "ON"
         - os: macOS-latest
           compiler: gcc
           compiler_version: 11
+          cuda_version: "0"
           BUILD_FLAGS: "-DSTIR_OPENMP=OFF"
           parallelproj: "OFF"
           BUILD_TYPE: "Debug"
@@ -88,7 +102,7 @@ jobs:
       # let's run all of them, as opposed to aborting when one fails
       fail-fast: false
 
-    name: ${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
+    name: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
 
     steps:
     - name: disk space
@@ -152,6 +166,13 @@ jobs:
           echo CC="$CC" >> $GITHUB_ENV
           echo CXX="$CXX" >> $GITHUB_ENV
 
+    - if: matrix.cuda_version != '0'
+      uses: Jimver/[email protected]
+      id: cuda-toolkit
+      with:
+          cuda: ${{ matrix.cuda_version }}
+          linux-local-args: '["--toolkit"]'
+
     - name: install_dependencies
       shell: bash
       run: |
@@ -212,10 +233,22 @@ jobs:
              git clone --depth 1 --branch v1.3.7 https://github.com/gschramm/parallelproj
              mkdir parallelproj/build
              cd parallelproj/build
-             cmake .. -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} -DSKIP_CUDA_LIB:BOOL=ON
+             if test "${{matrix.cuda_version}}" == "0"; then
+               extra_args="-DSKIP_CUDA_LIB:BOOL=ON"
+             fi
+             cmake .. -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} ${extra_args}
              cmake --build . --target install --config Release
              cd ../..
           fi
+          # Install NiftyPET
+          if test ! "${{matrix.cuda_version}}" == "0"; then
+             export PATHTOOLS=${GITHUB_WORKSPACE}/NiftyPET_tools
+             export HMUDIR=${GITHUB_WORKSPACE}/mmr_hardwareumaps
+             python -m pip install "nipet>=2"
+             niftypet_cmake_prefix=$(python -c "from niftypet.nipet import cmake_prefix; print(cmake_prefix)")
+             find /home/runner/work/STIR/STIR/my-env/ -name prjb.h
+             echo NiftyPET_DIR="$niftypet_cmake_prefix" >> $GITHUB_ENV
+          fi
 
           # Install ROOT (warning: currently only valid on Ubuntu)
           if test "${{matrix.ROOT}}XX" == "ONXX"; then
@@ -243,7 +276,7 @@ jobs:
     - name: ccache
       uses: hendrikmuhs/ccache-action@v1
       with:
-        key: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.compiler_version }}-${{ matrix.BUILD_TYPE }}
+        key: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}
         max-size: "2G"
 
     - name: configure
@@ -265,6 +298,7 @@ jobs:
           echo CMAKE_INSTALL_PREFIX="$CMAKE_INSTALL_PREFIX" >> $GITHUB_ENV
           EXTRA_BUILD_FLAGS="-DBUILD_SWIG_PYTHON=ON -DPYTHON_EXECUTABLE=`which python`"
           EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} -DCMAKE_BUILD_TYPE=${BUILD_TYPE}"
+          EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DNiftyPETnipet_DIR=${NiftyPET_DIR}"
           EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDOWNLOAD_ZENODO_TEST_DATA=ON"
           EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDISABLE_STIR_LOCAL=OFF -DSTIR_LOCAL=${GITHUB_WORKSPACE}/examples/C++/src"
           echo "cmake flags $BUILD_FLAGS $EXTRA_BUILD_FLAGS"          
@@ -288,8 +322,9 @@ jobs:
       run: |
           cd ${GITHUB_WORKSPACE}/build;
           source ${GITHUB_WORKSPACE}/my-env/bin/activate
-          cmake --build . -j 2 --config ${BUILD_TYPE}} --target install
-
+          cmake --build . -j 2 --config ${BUILD_TYPE}} --target install || true
+          #debug
+          make VERBOSE=ON
     - name: ctest
       shell: bash
       env:
@@ -300,6 +335,10 @@ jobs:
           if test ${BUILD_TYPE} = Debug; then
               EXCLUDE="-E test_data_processor_projectors|test_export_array|test_ArcCorrection|test_blocks_on_cylindrical_projectors"
           fi
+          if test ${{matrix.cuda_version}} != "0"; then
+              # No CUDA drivers on GitHub Actions
+              EXCLUDE="${EXCLUDE}|parallelproj|NiftyPET|test_blocks_on_cylindrical_projectors"
+          fi
           ctest --output-on-failure -C ${BUILD_TYPE} ${EXCLUDE}
 
     - name: recon_test_pack

CMakeLists.txt

@@ -5,11 +5,7 @@
 # See STIR/LICENSE.txt for details
 
 # cmake file for building STIR. See the STIR User's Guide and http://www.cmake.org.
-if (CMAKE_HOST_WIN32)
-  cmake_minimum_required(VERSION 3.12.0)
-else()
-  cmake_minimum_required(VERSION 3.1.0)
-endif()
+cmake_minimum_required(VERSION 3.14.0)
 
 # enable ccache https://ccache.samba.org/
 find_program(CCACHE_PROGRAM ccache)
@@ -183,8 +179,8 @@ endif()
 
 if(NOT DISABLE_NiftyPET_PROJECTOR)
   if (CUDAToolkit_FOUND)
-    find_package(NiftyPET)
-    if (NiftyPET_FOUND)
+    find_package(NiftyPETnipet COMPONENTS mmr_auxe mmr_lmproc petprj CONFIG)
+    if (NiftyPETnipet_FOUND)
       set(STIR_WITH_NiftyPET_PROJECTOR ON)
     endif()
   endif()

examples/C++/src/CMakeLists.txt

@@ -5,7 +5,7 @@ set(dir examples)
 set(dir_EXE_SOURCES ${dir}_EXE_SOURCES)
 
 set(${dir_EXE_SOURCES}
-	demo1 demo2 demo3 demo4_obj_fun demo5_line_search
+	demo1.cxx demo2.cxx demo3.cxx demo4_obj_fun.cxx demo5_line_search.cxx
 )
 
 

src/listmode_buildblock/CMakeLists.txt

@@ -58,3 +58,7 @@ endif()
 include(stir_lib_target)
 
 target_link_libraries(listmode_buildblock PUBLIC data_buildblock )
+
+if (STIR_WITH_NiftyPET_PROJECTOR)
+   target_link_libraries(listmode_buildblock PRIVATE NiftyPET::mmr_auxe NiftyPET::mmr_lmproc NiftyPET::petprj)
+endif()

src/listmode_utilities/CMakeLists.txt

@@ -35,8 +35,8 @@ if (HAVE_ECAT)
 endif()
 
 if (STIR_WITH_NiftyPET_PROJECTOR)
-  list(APPEND ${dir_EXE_SOURCES} conv_NiftyPET_stir)
-  list(APPEND ${dir_EXE_SOURCES} lm_to_projdata_NiftyPET)
+  list(APPEND ${dir_EXE_SOURCES} conv_NiftyPET_stir.cxx)
+  list(APPEND ${dir_EXE_SOURCES} lm_to_projdata_NiftyPET.cxx)
 endif()
 
 

src/recon_buildblock/CMakeLists.txt

@@ -143,10 +143,7 @@ endif()
 target_link_libraries(recon_buildblock PUBLIC modelling_buildblock display numerics_buildblock listmode_buildblock data_buildblock buildblock spatial_transformation_buildblock )
 
 if (STIR_WITH_NiftyPET_PROJECTOR)
-	target_link_libraries(recon_buildblock PUBLIC NiftyPET::petprj)
-	target_link_libraries(recon_buildblock PUBLIC NiftyPET::mmr_auxe)
-	target_link_libraries(recon_buildblock PUBLIC NiftyPET::mmr_lmproc)
-	target_link_libraries(recon_buildblock PUBLIC CUDA::cudart)
+   target_link_libraries(recon_buildblock PRIVATE NiftyPET::mmr_auxe NiftyPET::mmr_lmproc NiftyPET::petprj)
 endif()
 
 if (STIR_WITH_Parallelproj_PROJECTOR)

src/recon_buildblock/NiftyPET_projector/NiftyPETHelper.cxx

@@ -83,7 +83,7 @@ shared_ptr<Cnst> get_cnst(const Scanner &scanner, const bool cuda_verbose, const
     shared_ptr<Cnst> cnt_sptr = MAKE_SHARED<Cnst>();
 
     cnt_sptr->DEVID = cuda_device; // device (GPU) ID.  allows choosing the device on which to perform calculations
-    cnt_sptr->VERBOSE = cuda_verbose;
+    cnt_sptr->LOG = cuda_verbose;
 
     if (scanner.get_type() == Scanner::Siemens_mMR) {
         if (!(span==0 || span==1 || span==11))
@@ -123,8 +123,10 @@ shared_ptr<Cnst> get_cnst(const Scanner &scanner, const bool cuda_verbose, const
         cnt_sptr->MRD = mxRD; // maximum ring difference
 
         cnt_sptr->ALPHA = aLPHA; //angle subtended by a crystal
+#if 0 // NiftyPET v1 or so. Now this is hardwored as R_RING in sct.h
         float R = 32.8f; // ring radius
         cnt_sptr->RE = R + 0.67f; // effective ring radius accounting for the depth of interaction
+#endif
         cnt_sptr->AXR = SZ_RING; //axial crystal dim
 
         cnt_sptr->COSUPSMX = 0.725f; //cosine of max allowed scatter angle

src/test/NiftyPET_projector/CMakeLists.txt

@@ -14,10 +14,10 @@ set(dir_INVOLVED_TEST_EXE_SOURCES ${dir}_INVOLVED_TEST_EXE_SOURCES)
 set(dir_SIMPLE_TEST_EXE_SOURCES_NO_REGISTRIES ${dir}_SIMPLE_TEST_EXE_SOURCES_NO_REGISTRIES)
 
 set(${dir_INVOLVED_TEST_EXE_SOURCES}
-	test_ProjectorNiftyPET_adjoint
+	test_ProjectorNiftyPET_adjoint.cxx
 )
 
 ADD_TEST(test_ProjectorNiftyPET_adjoint
    ${CMAKE_CURRENT_BINARY_DIR}/test_ProjectorNiftyPET_adjoint 3)
 
-include(stir_test_exe_targets)
+include(stir_test_exe_targets)