Merge branch 'master' into Array

.appveyor.yml

@@ -3,6 +3,7 @@ shallow_clone: true
 skip_commits:
   files:
     - .github/**/*
+    - 'CITATION.cff'
     - '**/*.md'
     - '**/*.html'
     - '**/*.htm'
@@ -31,15 +32,30 @@ build_script:
   # find boost on Appveyor. Version depends on VM
   - for /D %%d in (C:\Libraries\boost_*) do set BOOST_ROOT=%%d
   - echo Using Boost %BOOST_ROOT%
+  # find miniconda
+  - for /D %%d in (C:\Miniconda*-x64) do set MINICONDA=%%d
+  - echo Using Miniconda %MINICONDA%
+  - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%MINICONDA%\\Library\\bin;%PATH%"
+  # install parallelproj and Python stuff
+  - conda install -c conda-forge  -yq libparallelproj swig numpy pytest
+  - CALL conda.bat activate base
+  - python --version
   - mkdir build
   - mkdir install
   - cd build
-  - cmake.exe .. -DCMAKE_INSTALL_PREFIX="C:\projects\stir\install" -DCMAKE_BUILD_TYPE=%CONFIGURATION%  -DCMAKE_CONFIGURATION_TYPES=%CONFIGURATION% -DSTIR_OPENMP:BOOL=ON -DBUILD_DOCUMENTATION:BOOL=OFF
+  - cmake.exe .. -A x64 -DCMAKE_INSTALL_PREFIX="C:\projects\stir\install" -DCMAKE_BUILD_TYPE=%CONFIGURATION%  -DCMAKE_CONFIGURATION_TYPES=%CONFIGURATION% -DSTIR_OPENMP:BOOL=ON -DBUILD_DOCUMENTATION:BOOL=OFF -DBUILD_SWIG_PYTHON:BOOL=ON -DPython_EXECUTABLE="%MINICONDA%\\python.exe"
   - cmake.exe --build . --config %CONFIGURATION%
   - cmake.exe --build . --target install --config %CONFIGURATION%
+  - conda deactivate
 
 test_script:
   - cd C:\projects\stir\build
+  - CALL conda.bat activate base
+  - python --version
   - ctest --output-on-failure  -C %CONFIGURATION%
   - cd ..\recon_test_pack
   - run_tests --nointbp "C:\projects\stir\install\bin\"
+  - cd ..\src
+  - "set PYTHONPATH=C:\\projects\\stir\\install\\python"
+  - python -m pytest .
+  - conda deactivate

.clang-format

@@ -25,13 +25,12 @@ BraceWrapping:
   SplitEmptyFunction: false
   SplitEmptyRecord: true
   SplitEmptyNamespace: true
-  # non-standard GNU
-  SplitEmptyFunction: false
 ColumnLimit:     130
 IndentPPDirectives: AfterHash
 PointerAlignment: Left
 SortIncludes:    false
 SortUsingDeclarations: false
 SpaceBeforeParens: ControlStatements
+PackConstructorInitializers: Never
 Standard:        Cpp11
 ...

.gitattributes

@@ -12,6 +12,8 @@
 *.v     -text -diff
 *.s     -text -diff
 *.scn     -text -diff
+*.l     -text -diff
+*.root  -text -diff
 *.gz     -text -diff
 *.nii     -text -diff
 *.sh    eol=lf

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,22 @@
+<!-- Fill in most of this text, and delete what is not appropriate.
+Please read and adhere to the [contribution guidelines](https://github.com/UCL/STIR/blob/master/CONTRIBUTING.md).
+Did you sign the STIR Contribution License Agreement?
+-->
+
+## Changes in this pull request
+
+
+## Testing performed
+
+
+## Related issues
+<!-- Use keywords such as "fixes", "closes", see https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue -->
+
+
+## Checklist before requesting a review
+<!--Put an x between the [] when completed. Delete a line if not applicable. -->
+  - [] I have performed a self-review of my code
+  - [] I have added docstrings/doxygen in line with the guidance in the developer guide
+  - [] I have implemented unit tests that cover any new or modified functionality (if applicable)
+  - [] The code builds and runs on my machine
+  - [] `documentation/release_XXX.md` has been updated with any functionality change (if applicable)

.github/workflows/GHA_increase_disk_space.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+df -h
+# locations from the internet, e.g. https://github.com/easimon/maximize-build-space
+# saves about 2GB
+if [ -d /usr/share/dotnet ]; then
+    echo removing dotnet
+    sudo rm -rf /usr/share/dotnet
+fi
+# saves about 10 GB
+if [ -d "$AGENT_TOOLSDIRECTORY" ]; then
+    echo removing agent_tools
+    sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+fi
+# saves about 10 GB
+if [ -d /usr/local/lib/android ]; then
+    echo removing android files
+    sudo rm -rf /usr/local/lib/android
+fi
+if [ -d /opt/ghc ]; then
+    echo removing android files
+    sudo rm -rf /opt/ghc
+fi
+df -h

.github/workflows/build-test.yml

@@ -2,18 +2,24 @@ name: Build and ctest and recon_test_pack CI
 
 on:
   push:
-    branches: [ master ]
+    branches: 
+      - master
+      - tof_sino_UCL
     paths-ignore:
       - '.appveyor.yml'
+      - 'CITATION.cff'
       - '**/*.md'
       - '**/*.html'
       - '**/*.htm'
       - '**/*.tex'
 
   pull_request:
-    branches: [ master ]
+    branches:
+      - master
+      - tof_sino_UCL
     paths-ignore:
       - '.appveyor.yml'
+      - 'CITATION.cff'
       - '**/*.md'
       - '**/*.html'
       - '**/*.htm'
@@ -114,6 +120,18 @@ jobs:
       with:
         submodules: recursive
 
+    - name: disk space
+      shell: bash
+      run: |
+          case ${{matrix.os}} in
+            (ubuntu* | macOS*)
+              sudo .github/workflows/GHA_increase_disk_space.sh
+              ;;
+            (windows*)
+              # no idea what to do here
+              ;;
+           esac
+
     - name: set_compiler_variables
       shell: bash
       run: |
@@ -264,7 +282,7 @@ jobs:
           EXTRA_BUILD_FLAGS="-DBUILD_SWIG_PYTHON=ON -DPYTHON_EXECUTABLE=`which python`"
           EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} -DCMAKE_BUILD_TYPE=${BUILD_TYPE}"
           EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDOWNLOAD_ZENODO_TEST_DATA=ON"
-          EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDISABLE_STIR_LOCAL=OFF -DSTIR_LOCAL=${GITHUB_WORKSPACE}/examples/C++/src"
+          EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDISABLE_STIR_LOCAL=OFF -DSTIR_LOCAL=${GITHUB_WORKSPACE}/examples/C++/using_STIR_LOCAL"
           echo "cmake flags $BUILD_FLAGS $EXTRA_BUILD_FLAGS"          
           mkdir build
           cd build
@@ -296,7 +314,7 @@ jobs:
           cd ${GITHUB_WORKSPACE}/build
           # don't run all of them in Debug mode as it takes too long
           if test ${BUILD_TYPE} = Debug; then
-              EXCLUDE="-E test_data_processor_projectors|test_export_array|test_ArcCorrection|test_blocks_on_cylindrical_projectors"
+              EXCLUDE="-E test_data_processor_projectors|test_export_array|test_ArcCorrection"
           fi
           ctest --output-on-failure -C ${BUILD_TYPE} ${EXCLUDE}
 
@@ -318,7 +336,7 @@ jobs:
             ./run_scatter_tests.sh
             ./run_test_zoom_image.sh
             ./run_ML_norm_tests.sh
-            if [[ $BUILD_FLAGS == *"DDISABLE_CERN_ROOT=0"* ]]; then ./run_root_GATE.sh; fi
+            if test "${{matrix.ROOT}}XX" == "ONXX"; then ./run_root_GATE.sh; fi
             ./run_tests_modelling.sh
             cd ${GITHUB_WORKSPACE}/recon_test_pack/SPECT
             ./run_SPECT_tests.sh
@@ -329,14 +347,17 @@ jobs:
       if: failure()
       with:
         name: recon_test_pack_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
-        path: ${{ github.workspace }}/recon_test_pack/**/*.log
+        path: |
+          ${{ github.workspace }}/recon_test_pack/**/*.log
+          ${{ github.workspace }}/recon_test_pack/**/my_*v
+          ${{ github.workspace }}/recon_test_pack/**/my_*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' && github.event.inputs.debug_enabled }}
+      if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled == 'true' }}
 
     - name: examples
       shell: bash
@@ -348,8 +369,8 @@ jobs:
           ./run_simulation.sh 1> /dev/null
 
           # Run the Demo executables
-          EXE_LOC=${GITHUB_WORKSPACE}/build/src/examples/C++
-          cd ${GITHUB_WORKSPACE}/examples/C++/src
+          EXE_LOC=${GITHUB_WORKSPACE}/build/src/examples/C++/using_STIR_LOCAL
+          cd ${GITHUB_WORKSPACE}/examples/C++/using_STIR_LOCAL
 
           generate_image generate_image.par
           forward_project sino.hs image.hv  small.hs
@@ -360,6 +381,15 @@ jobs:
           ${EXE_LOC}/demo4_obj_fun demo4_obj_fun.par
           ${EXE_LOC}/demo5_line_search demo5_line_search.par
 
+          # build and run C++/using_installed_STIR
+          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
+
     - name: Python
       shell: bash
       run: |

.github/workflows/cffconvert.yml

@@ -0,0 +1,19 @@
+name: cffconvert
+
+on:
+  push:
+    paths:
+      - CITATION.cff
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@v2
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/cffconvert-github-action@2.0.0
+        with:
+          args: "--validate"

.gitignore

@@ -94,6 +94,6 @@ install/
 examples/ROOT_files/ROOT_STIR_consistency/Gate_macros/main_GATE_macro_test*.mac
 examples/ROOT_files/ROOT_STIR_consistency/pretest_output/root_data_test*.root
 examples/ROOT_files/ROOT_STIR_consistency/pretest_output/root_header_test*.hroot
-examples/ROOT_files/ROOT_STIR_consistency/pretest_output/root_header_test*_lor_pos.txt
+examples/ROOT_files/ROOT_STIR_consistency/*voxel_data_*.*
 examples/ROOT_files/ROOT_STIR_consistency/pretest_output/stir_image*.*
 

.mailmap

@@ -45,8 +45,10 @@ Palak Wadhwa <pwadhwa351@gmail.com> <umdde@leeds.ac.uk>
 Rebecca Gillen <rebecca.gillen.18@ucl.ac.uk> <43674917+RebeccaGillen@users.noreply.github.com>
 Richard Brown <richard.brown@ucl.ac.uk> <33289025+rijobro@users.noreply.github.com>
 Richard Brown <richard.brown@ucl.ac.uk>  <richard.brown@ucl.ac.uk>
-Robert Twyman <robbietuk@gmail.com> <robbietuk@gmail.com>
-Robert Twyman <robbietuk@gmail.com> <robert.twyman.18@ucl.ac.uk>
+Robert Twyman Skelly <robbietuk@gmail.com> <robbietuk@gmail.com>
+Robert Twyman Skelly <robbietuk@gmail.com> <robert.twyman.18@ucl.ac.uk>
+Robert Twyman Skelly <robbietuk@gmail.com> <robert@prescientimaging.com>
+Robert Twyman Skelly <robbietuk@gmail.com> <117300855+Robert-PrescientImaging@users.noreply.github.com>
 Yu-jung Tsai <yu-jung.tsai.14@ucl.ac.uk> <yu-jung.tsai.14@ucl.ac.uk>
 Gemma Fardell <gemma.fardell@stfc.ac.uk> <gemma.fardell@stfc.ac.uk>
 Gemma Fardell <gemma.fardell@stfc.ac.uk> <47746591+gfardell@users.noreply.github.com>
@@ -62,5 +64,6 @@ Nicole Jurjew <nicole.jurjew.20@ucl.ac.uk>
 Tahereh Niknejad <tahereh.niknejad@tecnico.ulisboa.pt>
 Tahereh Niknejad <tahereh.niknejad@tecnico.ulisboa.pt> <tahereh@Taherehs-MacBook-Pro.local>
 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>