Merge remote-tracking branch 'origin/master' into safir_updates

UCL · Sep 4, 2024 · b98ce8a · b98ce8a
2 parents 46e1b98 + 5d12267
commit b98ce8a
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diff --git a/.appveyor.yml b/.appveyor.yml
@@ -14,7 +14,6 @@ version: '{build}'
 os:
   - Visual Studio 2022
   - Visual Studio 2019
-  - Visual Studio 2015
 
 platform:
   - x64

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,8 @@
+# change to Apache 2.0 license
+47d1aa5f302c5b6b579de176535e01aa97d1ff27
+# run clang-tidy --modernize-use-override
+8af125617a113724f52d26e991bfc6c36abb952f
+# manual fixes in stir_experimental and clang-tidy modernize-use-override
+c5a1c6bc29d3f24d8fdb5c198946ec9580947257
+# stir_maintenance run pre-commit
+88f4ce70929a41c745fc39030e90c87bfaf046b7
diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -70,7 +70,7 @@ jobs:
           compiler: gcc
           compiler_version: 12
           cuda_version: "0"
-          BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=14"
+          BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=20"
           BUILD_TYPE: "RelWithDebInfo"
           parallelproj: "ON"
           ROOT: "OFF"
@@ -79,14 +79,14 @@ jobs:
           compiler: gcc
           compiler_version: 12
           cuda_version: "12.1.0"
-          BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=14"
+          BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17"
           BUILD_TYPE: "Release"
           parallelproj: "ON"
           ROOT: "OFF"
           ITK: "ON"
         - os: macOS-latest
           compiler: gcc
-          compiler_version: 11
+          # compiler_version: 11
           cuda_version: "0"
           BUILD_FLAGS: "-DSTIR_OPENMP=OFF"
           parallelproj: "OFF"
@@ -162,9 +162,6 @@ jobs:
             CXX=${CXX}-${{ matrix.compiler_version }}            
           fi
           if test 'XX${{ matrix.os }}' = 'XXmacOS-latest'; then
-            # need to force XCode version for the moment due to a linker bug
-            # see https://github.com/UCL/STIR/issues/1103
-            echo DEVELOPER_DIR="/Applications/Xcode_14.1.app/Contents/Developer" >> $GITHUB_ENV
             if test 'XX${{ matrix.compiler }}' = 'XXclang'; then
               brew install llvm@${{ matrix.compiler_version }}
               if test XX${HOMEBREW_PREFIX} = XX; then
@@ -211,7 +208,7 @@ jobs:
                 sudo apt install libinsighttoolkit5-dev
               fi
               # free up some disk space
-              sudo apt clean
+              apt autoremove --purge && sudo apt clean
               PYTHON_EXECUTABLE=$(which python3)
               ;;
             (macOS*)
@@ -255,12 +252,15 @@ jobs:
              cmake .. -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} ${extra_args}
              cmake --build . --target install --config Release
              cd ../..
+             rm -rf parallelproj
           fi
 
           # Install ROOT (warning: currently only valid on Ubuntu)
           if test "${{matrix.ROOT}}XX" == "ONXX"; then
-             wget https://root.cern/download/root_v6.24.02.Linux-ubuntu20-x86_64-gcc9.3.tar.gz
-             tar -xzvf root_v6.24.02.Linux-ubuntu20-x86_64-gcc9.3.tar.gz
+             ROOT_file=root_v6.28.12.Linux-ubuntu20-x86_64-gcc9.4.tar.gz
+             wget https://root.cern/download/"$ROOT_file"
+             tar -xzvf "$ROOT_file"
+             rm "$ROOT_file"
              source root/bin/thisroot.sh
           fi
 
@@ -330,6 +330,12 @@ jobs:
           source ${GITHUB_WORKSPACE}/my-env/bin/activate
           cmake --build . -j 2 --config ${BUILD_TYPE}} --target install
 
+    # Enable tmate debugging of manually-triggered workflows if the input option was provided
+    - name: Setup tmate session if triggered
+      uses: mxschmitt/action-tmate@v3
+      timeout-minutes: 15
+      if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled == 'true' }}
+
     - name: ctest
       shell: bash
       env:
@@ -344,7 +350,10 @@ jobs:
           fi
           # don't run all of them in Debug mode as it takes too long
           if test ${BUILD_TYPE} = Debug; then
-              EXCLUDE_Debug="test_data_processor_projectors|test_export_array|test_ArcCorrection"
+              # Also excluding test_PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin
+              # as it is a bit slow. Moreover it fails on MacOS (Debug)
+              # https://github.com/UCL/STIR/pull/1418#issuecomment-2109518132
+              EXCLUDE_Debug="test_data_processor_projectors|test_export_array|test_ArcCorrection|test_PoissonLogLikelihoodWithLinearModelForMeanAndListModeWithProjMatrixByBin"
               EXCLUDE="${EXCLUDE_Debug}${EXCLUDE:+"|"}${EXCLUDE}"
           fi
           # prepend -E
@@ -354,47 +363,20 @@ jobs:
           # execute tests
           ctest --output-on-failure -C ${BUILD_TYPE} ${EXCLUDE}
 
-    - name: recon_test_pack
-      shell: bash
-      env:
-          BUILD_FLAGS: ${{ matrix.BUILD_FLAGS }}
-          BUILD_TYPE: ${{ matrix.BUILD_TYPE }}
-      run: |
-          set -ex;
-          PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH
-          cd ${GITHUB_WORKSPACE}/recon_test_pack
-          ./run_tests.sh --nointbp
-          # don't run all of them in Debug mode as it takes too long
-          if test ${BUILD_TYPE} != Debug; then
-            ./run_test_simulate_and_recon.sh
-            ./run_test_listmode_recon.sh
-            ./run_test_simulate_and_recon_with_motion.sh
-            ./run_scatter_tests.sh
-            ./run_test_zoom_image.sh
-            ./run_ML_norm_tests.sh
-            if test "${{matrix.ROOT}}XX" == "ONXX"; then ./run_root_GATE.sh; fi
-            ./run_tests_modelling.sh
-            cd ${GITHUB_WORKSPACE}/recon_test_pack/SPECT
-            ./run_SPECT_tests.sh
-          fi
-
-    - name: Upload log files for debugging
-      uses: actions/upload-artifact@v3
+    - name: Upload ctest log files for debugging
+      uses: actions/upload-artifact@v4
       if: failure()
       with:
-        name: recon_test_pack_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
-        path: ${{ github.workspace }}/recon_test_pack/**/*.log
-          ${{ github.workspace }}/recon_test_pack/**/my_*v
-          ${{ github.workspace }}/recon_test_pack/**/my_*s
+        name: ctest_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
+        path: |
+          ${{ github.workspace }}/build/**/*.log
+          ${{ github.workspace }}/build/**/*.hv
+          ${{ github.workspace }}/build/**/*.v
+          ${{ github.workspace }}/build/**/*.hs
+          ${{ github.workspace }}/build/**/*.s
         retention-days: 7
 
-    # Enable tmate debugging of manually-triggered workflows if the input option was provided
-    - name: Setup tmate session if triggered
-      uses: mxschmitt/action-tmate@v3
-      timeout-minutes: 15
-      if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled == 'true' }}
-
-    - name: examples
+    - name: C++ examples with STIR_LOCAL
       shell: bash
       run: |
           set -ex;
@@ -416,14 +398,70 @@ jobs:
           ${EXE_LOC}/demo4_obj_fun demo4_obj_fun.par
           ${EXE_LOC}/demo5_line_search demo5_line_search.par
 
+    - name: remove build
+      shell: bash
+         # remove to create some disk space
+      run: |
+          set -x
+          cd ${GITHUB_WORKSPACE}
+          df -h .
+          rm -rf ./build
+          df -h .
+
+    - name: C++ examples with installed STIR
+      shell: bash
+      run: |
+          set -ex;
           # build and run C++/using_installed_STIR
+          PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH
           cd ${GITHUB_WORKSPACE}/examples/C++/using_installed_STIR
           cmake -S . -B build/  -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
           cmake --build build/ --config Release  --target install
           # run demo
           demo_create_image
           # just check if its output makes sense
           list_image_info test.hv
+          rm -rf build
+
+    - name: recon_test_pack
+      shell: bash
+      env:
+          BUILD_FLAGS: ${{ matrix.BUILD_FLAGS }}
+          BUILD_TYPE: ${{ matrix.BUILD_TYPE }}
+      run: |
+          set -ex;
+          PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH
+          cd ${GITHUB_WORKSPACE}/recon_test_pack
+          ./run_tests.sh --nointbp
+          # don't run all of them in Debug mode as it takes too long
+          if test ${BUILD_TYPE} != Debug; then
+            ./run_test_simulate_and_recon.sh
+            ./run_test_listmode_recon.sh
+            ./run_test_simulate_and_recon_with_motion.sh
+            ./run_scatter_tests.sh
+            ./run_test_zoom_image.sh
+            ./run_ML_norm_tests.sh
+            if test "${{matrix.ROOT}}XX" == "ONXX"; then ./run_root_GATE.sh; fi
+            ./run_tests_modelling.sh
+            cd ${GITHUB_WORKSPACE}/recon_test_pack/SPECT
+            ./run_SPECT_tests.sh
+          fi
+
+    - name: Upload recon_test_pack log files for debugging
+      uses: actions/upload-artifact@v4
+      if: failure()
+      with:
+        name: recon_test_pack_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
+        path: |
+          ${{ github.workspace }}/recon_test_pack/**/*.log
+          ${{ github.workspace }}/recon_test_pack/**/my_*v
+          ${{ github.workspace }}/recon_test_pack/**/my_*s
+        retention-days: 7
+
+    - name: remove recon_test_pack
+      shell: bash
+      run: |
+          rm -rf ${GITHUB_WORKSPACE}/recon_test_pack
 
     - name: Python
       shell: bash

diff --git a/.github/workflows/pre-commit-check.yml b/.github/workflows/pre-commit-check.yml
@@ -8,6 +8,9 @@ jobs:
     name: pre-commit
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-    - run: sudo apt-get install -yqq clang-format
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+          activate-environment: pre-commit-env
+          environment-file: pre-commit-environment.yml
+          auto-activate-base: false
     - uses: pre-commit/action@v3.0.0
diff --git a/.gitignore b/.gitignore
@@ -57,6 +57,7 @@ install_manifest.txt
 ~$*
 *~
 *.bak
+\#*#
 
 # Ignore Visual Studio User-specific files
 *.suo

diff --git a/.mailmap b/.mailmap
@@ -37,6 +37,7 @@ Matthias Ehrhardt <m.ehrhardt@bath.ac.uk> <m.ehrhardt@bath.ac.uk>
 Matthias Ehrhardt <m.ehrhardt@bath.ac.uk> <m.j.ehrhardt@damtp.cam.ac.uk>
 Nikos Efthimiou <nikos.efthimiou@gmail.com> <nikos.efthimiou@gmail.com>
 Nikos Efthimiou <nikos.efthimiou@gmail.com> <NikEfth@users.noreply.github.com>
+Nikos Efthimiou <nikos.efthimiou@gmail.com> <n.efthymiou@hull.ac.uk>
 Ottavia Bertolli <ottavia.bertolli.13@ucl.ac.uk>
 Palak Wadhwa <pwadhwa351@gmail.com> <38861704+pwadhwa351@users.noreply.github.com>
 Palak Wadhwa <pwadhwa351@gmail.com> <medpwad@leeds.ac.uk>
@@ -67,3 +68,5 @@ Sam D Porter <92305641+samdporter@users.noreply.github.com>
 Sam D Porter <92305641+samdporter@users.noreply.github.com>  <porter.samd@gmail.com>
 Matthew Strugari <matthew.strugari@dal.ca>
 Matthew Strugari <matthew.strugari@dal.ca> <56315593+mastergari@users.noreply.github.com>
+Imraj Singh <imraj.singh.20@ucl.ac.uk>
+Imraj Singh <imraj.singh.20@ucl.ac.uk> <72553490+Imraj-Singh@users.noreply.github.com>
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,4 +3,4 @@ repos:
     rev: '62302476'
     hooks:
     -   id: clang-format
-        files: \.(c|cc|cxx|cpp|h|hpp|hxx|inl|txx)$
+        files: \.(c|cc|cxx|cpp|cu|h|hpp|hxx|inl|txx)$
diff --git a/CITATION.cff b/CITATION.cff
@@ -32,31 +32,31 @@ authors:
     - family-names: Jehl
       given-names:  Markus
       affiliation:  Positrigo
+    - family-names: Borgeaud
+      given-names:  Tim
+      affiliation:  Hammersmith Imanet Ltd
     - family-names: Strugari
       given-names:  Matthew
       affiliation:  Dalhousie University (Canada)
     - family-names: Khateri
       given-names:  Parisa
       affiliation:  ETH Zuerich
-    - family-names: Beisel
-      given-names:  Tobias
     - family-names: Wadhwa
       given-names:  Palak
       affiliation:  University of Leeds (UK)
-    - family-names: Borgeaud
-      given-names:  Tim
-      affiliation:  Hammersmith Imanet Ltd
+    - family-names: Beisel
+      given-names:  Tobias
     - family-names: Emond
       given-names:  Elise
       affiliation:  University College London
-    - family-names: Jacobson
-      given-names:  Matthew
     - family-names: Gillman
       given-names:  Ashley
       orcid:        'https://orcid.org/0000-0001-9130-1092'
       affiliation:  >-
         Commonwealth Scientific and Industrial Research
         Organisation, and University of Queensland
+    - family-names: Jacobson
+      given-names:  Matthew
     - family-names: Zverovich
       given-names:  Alexey
       affiliation:  Brunel University (UK)
@@ -81,23 +81,21 @@ authors:
     - family-names: Brusaferri
       given-names:  Ludovica
       affiliation:  University College London
-    - family-names: Pasca
-      given-names:  Edoardo
-      affiliation:  UK Research & Innovation
-      orcid:        'https://orcid.org/0000-0001-6957-2160'
     - family-names: Thomas
       given-names:  Benjamin
       orcid:        'https://orcid.org/0000-0002-9784-1177'
       affiliation:  University College London
+    - family-names: Pasca
+      given-names:  Edoardo
+      affiliation:  UK Research & Innovation
+      orcid:        'https://orcid.org/0000-0001-6957-2160'
     - family-names: Aguiar
       given-names:  Pablo
     - family-names: Niknejad
       given-names:  Tahereh
     - family-names: Sadki
       given-names:  Mustapha
       affiliation:  Brunel University (UK)
-    - family-names: Schmidtlein
-      given-names:  C Ross
     - family-names: Kerrouche
       given-names:  Nacer
       affiliation:  Hammersmith Imanet Ltd
@@ -110,13 +108,22 @@ authors:
     - family-names: Ehrhardt
       given-names:  Matthias J.
       orcid:        'https://orcid.org/0000-0001-8523-353X'
-    - family-names: Valente
-      given-names:  Patrick
-      affiliation:  Brunel University (UK)
+    - family-names: Singh
+      given-names:  Imraj
+      orcid:        'https://orcid.org/0000-0003-2186-0977'
+      affiliation:  University College London (UK)
+    - family-names: Schmidtlein
+      given-names:  C Ross
     - family-names: Ovtchinnikov
       given-names:  Evgueni
       orcid:        'https://orcid.org/0000-0002-9359-6514'
       affiliation:  UK Research & Innovation
+    - family-names: Valente
+      given-names:  Patrick
+      affiliation:  Brunel University (UK)
+    - family-names: Jurjew
+      given-names:  Nicole
+      affiliation:  University College London
     - family-names: Schramm
       given-names:  Georg
       affiliation:  Katholieke Universiteit Leuven (Belgium)
@@ -127,9 +134,6 @@ authors:
     - family-names: Belluzzo
       given-names:  Damiano
       affiliation:  Hospedale San Raffaele Milano (Italy)
-    - family-names: Jurjew
-      given-names:  Nicole
-      affiliation:  University College London
     - family-names: Ching
       given-names:  Daniel
     - family-names: Hague
@@ -178,10 +182,14 @@ authors:
 identifiers:
     - type: doi
       value: 10.1088/0031-9155/57/4/867
+    - type: doi
+      value: 10.3389/fnume.2023.1134774
     - type: doi
       value: 10.1186/s40658-019-0248-9
     - type: doi
       value: 10.3390/jimaging8060172
+    - type: doi
+      value: 10.1088/1361-6560/aaf9b9
     - type: doi
       value: 10.1109/NSSMIC.2018.8824341
     - type: doi