Consolidate dose actor

.github/workflows/main.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-12, windows-latest]
+        os: [ubuntu-latest, macos-13, windows-latest]
         python-version: [3.9, '3.10', '3.11', '3.12']
 
     env:
@@ -33,7 +33,7 @@ jobs:
         if [[ ${{ matrix.os }} == "ubuntu-latest" ]]; then
           export GIT_SSL_NO_VERIFY=1
           git submodule update --init --recursive
-        elif [[ ${{ matrix.os }} == "macos-12" ]]; then
+        elif [[ ${{ matrix.os }} == "macos-13" ]]; then
           export GIT_SSL_NO_VERIFY=1
           git submodule update --init --recursive
         else
@@ -53,7 +53,7 @@ jobs:
             varOS=`cat /etc/os-release | grep "VERSION=" | grep -oP '(?<=\").*?(?=\")'`
             varOS=($varOS)
             echo "release=${varOS[0]}" >> $GITHUB_OUTPUT
-        elif [[ ${{ matrix.os }} == "macos-12" ]]; then
+        elif [[ ${{ matrix.os }} == "macos-13" ]]; then
             varOS=`sw_vers | grep "ProductVersion:"`
             varOS="${varOS#*:}"
             echo "release=${varOS:1}" >> $GITHUB_OUTPUT
@@ -103,18 +103,18 @@ jobs:
               mv dist_opengate/* dist/
           fi
     - uses: conda-incubator/setup-miniconda@v3
-      if: (matrix.os == 'macos-12') || (matrix.os == 'windows-latest')
+      if: (matrix.os == 'macos-13') || (matrix.os == 'windows-latest')
       with:
           miniconda-version: "latest"
           auto-update-conda: true
           activate-environment: opengate_core
           python-version: ${{ matrix.python-version }}
     - name: Set up Homebrew
-      if: matrix.os == 'macos-12'
+      if: matrix.os == 'macos-13'
       id: set-up-homebrew
       uses: Homebrew/actions/setup-homebrew@master
     - name: Create opengate_core Wheel Mac
-      if: matrix.os == 'macos-12'
+      if: matrix.os == 'macos-13'
       shell: bash -l {0}
       run: |
           brew install python@3.12 || true
@@ -191,7 +191,7 @@ jobs:
           delocate-listdeps --all fixed_wheels/*.whl
           mv fixed_wheels dist
           cd dist
-          find . -name '*whl' -exec bash -c ' mv $0 ${0/macosx_12_0/macosx_10_9}' {} \;
+          find . -name '*whl' -exec bash -c ' mv $0 ${0/macosx_13_0/macosx_10_9}' {} \;
           cd ../..
           mv core/dist .
     - name: Create opengate_core Wheel Windows
@@ -299,7 +299,7 @@ jobs:
 #    env:
 #      GEANT4_VERSION: 'v11.2.1'
 #      ITK_VERSION: 'v5.2.1'
-#    runs-on: macos-12
+#    runs-on: macos-13
 #    steps:
 #    - name: Checkout github repo
 #      uses: actions/checkout@v4
@@ -348,7 +348,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-12, windows-latest]
+        os: [ubuntu-latest, macos-13, windows-latest]
         python-version: [3.9, '3.10', '3.11', '3.12']
     steps:
     - uses: actions/download-artifact@v4
@@ -377,7 +377,7 @@ jobs:
             export OSNAME="manylinux"
             export PLATFORM="x86_"
             pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
-          elif [[ ${{ matrix.os }} == "macos-12" ]]; then
+          elif [[ ${{ matrix.os }} == "macos-13" ]]; then
             export OSNAME="macosx"
             export PLATFORM="x86_"
             which python
@@ -397,10 +397,6 @@ jobs:
           if [[ ${{ matrix.os }} == "ubuntu-latest" ]]; then
               path=`opengate_library_path.py -p site_packages`
               export LD_LIBRARY_PATH="${path}/opengate_core.libs":${LD_LIBRARY_PATH}
-              path=`opengate_library_path.py -p libG4processes`
-              export LD_PRELOAD=${path}:${LD_PRELOAD}
-              path=`opengate_library_path.py -p libG4geometry`
-              export LD_PRELOAD=${path}:${LD_PRELOAD}
           fi
           if [[ ${{ matrix.os }} == "windows-latest" ]]; then
               path=`opengate_library_path.py -p site_packages`

.gitignore

@@ -3,6 +3,7 @@ __pycache__
 .DS_Store
 *.jpeg
 *.save
+*.pyi
 
 /.idea/
 .idea
@@ -163,3 +164,5 @@ singles.root
 opengate/tests/src/geant4_out.txt
 failing_tests.txt
 opengate/tests/output_dashboard
+
+nohup.out

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
     -   id: black
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v19.1.0
+    rev: v19.1.1
     hooks:
     -   id: clang-format
 ci:

README.md

@@ -11,7 +11,7 @@ See the [User Guide](https://opengate-python.readthedocs.io/en/latest/user_guide
 
 ### How to install (short version)
 
-*Compatible with Python 3.9, 3.10, 3.11, 3.12. On Windows multithreading, Qt visualization and the "spawn new subprocess" are not (yet) available.*
+*Compatible with Python 3.9, 3.10, 3.11, 3.12. On Windows multithreading and Qt visualization are not (yet) available.*
 
 First, create an environment (not mandatory but highly advised)
 
@@ -23,7 +23,7 @@ source opengate_env/bin/activate
 or you can use the conda environment.
 
 ```
-conda create --name opengate_env python=3.9
+conda create --name opengate_env python=3.12
 conda activate opengate_env
 ```
 
@@ -33,6 +33,8 @@ pip install --upgrade pip
 pip install --pre opengate
 ```
 
+*Warning* while it is still beta, the `--pre` option is needed.
+
 If you already installed the packages and want to upgrade to the latest version:
 
 ```
@@ -44,19 +46,24 @@ Once installed, you can run all tests:
 opengate_tests
 ````
 
-**WARNING** The first time you run this command, the geant4 data and the test data will be downloaded. If the download fails (on some systems), try to add the following command before running opengate_tests:
+**WARNING (1)** The first time you run this command, the geant4 data and the test data will be downloaded. If the download fails (on some systems), try to add the following command before running opengate_tests:
 ````
 export GIT_SSL_NO_VERIFY=1
 ````
 
 All tests are in the folder [here](https://github.com/OpenGATE/opengate/tree/master/opengate/tests/src). The test data (binary files) are stored, for technical reasons, in this git: https://gitlab.in2p3.fr/opengamgate/gam_tests_data (which is stored as a git submodule).
 
-**WARNING** Some tests (e.g. test034) needs [gaga-phsp](https://github.com/dsarrut/gaga-phsp) which needs [pytorch](https://pytorch.org/) that cannot really be automatically installed by the previous pip install (at least we don't know how to do). So, in order to run those tests, you will have to install both PyTorch and gaga-phsp first with
+**WARNING (2)** Some tests (e.g. test034) needs [gaga-phsp](https://github.com/dsarrut/gaga-phsp) which needs [pytorch](https://pytorch.org/) that cannot really be automatically installed by the previous pip install (at least we don't know how to do). So, in order to run those tests, you will have to install both PyTorch and gaga-phsp first with
 ````
 pip install torch
 pip install gaga-phsp
 ````
 
+**WARNING (3)** With some linux systems (not all), you may encounter an error similar to “cannot allocate memory in static TLS block”. In that case, you must add a specific path to the linker as follows:
+````
+export LD_PRELOAD=<path to libG4processes>:<path to libG4geometry>:${LD_PRELOAD}
+````
+
 The documentation is here: https://opengate-python.readthedocs.io/en/latest/user_guide.html
 
 The test history can be visualized here: https://opengate.github.io/opengate_tests_results/

VERSION

@@ -1 +1 @@
-10.0beta08
+10.0beta09

core/CMakeLists.txt

@@ -14,6 +14,9 @@ project(opengate_core)
 
 set(CMAKE_CXX_STANDARD 17)
 
+# Enable Position Independent Code for all targets (-fPIC)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
 # Need Geant4
 find_package(Geant4 REQUIRED OPTIONAL_COMPONENTS qt)
 include(${Geant4_USE_FILE})
@@ -103,13 +106,8 @@ if (WIN32)
     endif ()
 endif ()
 
-# correct one on OSX
-#target_link_libraries(opengate_core PRIVATE pybind11::module ${Geant4_LIBRARIES} Threads::Threads ${ITK_LIBRARIES})
-
 # additional utilities
 target_include_directories(opengate_core PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/external/)
 
 #set(CMAKE_VERBOSE_MAKEFILE on)
 target_link_libraries(opengate_core PRIVATE pybind11::module ${Geant4_LIBRARIES} Threads::Threads ${ITK_LIBRARIES} fmt::fmt-header-only)
-
-# Do not not add ${PYTHON_LIBRARIES}) here (seg fault)

core/opengate_core/__init__.py

@@ -41,37 +41,23 @@ def get_libG4_path(lib):
         "site-packages" in pathCurrentFile
     ):  # opengate_core is installed using wheel (for "pip install -e .", the paths are different)
         reloadPython = False
-        if (
-            "LD_LIBRARY_PATH" not in os.environ
-            or os.path.join(get_site_packages_dir(), "opengate_core.libs")
-            not in os.environ["LD_LIBRARY_PATH"]
-        ):
-            reloadPython = True
+        # if (
+        #    "LD_LIBRARY_PATH" not in os.environ
+        #    or os.path.join(get_site_packages_dir(), "opengate_core.libs")
+        #    not in os.environ["LD_LIBRARY_PATH"]
+        # ):
+        #    reloadPython = True
 
-        if (
-            "LD_PRELOAD" not in os.environ
-            or get_libG4_path("processes") not in os.environ["LD_PRELOAD"]
-            or get_libG4_path("geometry") not in os.environ["LD_PRELOAD"]
-        ):
-            reloadPython = True
-
-        if reloadPython:
-            print(
-                "opengate_core is not detected. Be sure to execute these lines before to run python:"
-            )
-            print(
-                "export LD_LIBRARY_PATH="
-                + os.path.join(get_site_packages_dir(), "opengate_core.libs")
-                + ":${LD_LIBRARY_PATH}"
-            )
-            print(
-                "export LD_PRELOAD="
-                + get_libG4_path("processes")
-                + ":"
-                + get_libG4_path("geometry")
-                + ":${LD_PRELOAD}"
-            )
-            sys.exit(-1)
+        # if reloadPython:
+        #    print(
+        #        "opengate_core is not detected. Be sure to execute these lines before to run python:"
+        #    )
+        #    print(
+        #        "export LD_LIBRARY_PATH="
+        #        + os.path.join(get_site_packages_dir(), "opengate_core.libs")
+        #        + ":${LD_LIBRARY_PATH}"
+        #    )
+        #    sys.exit(-1)
 elif sys.platform == "win32":
     print(os.path.dirname(pathCurrentFile))
     os.add_dll_directory(os.path.dirname(pathCurrentFile))

core/opengate_core/g4DataSetup.py

@@ -9,19 +9,19 @@
 
 # Data for Geant4
 # Geant4 11.2.1
-data_packages = [
-    "https://cern.ch/geant4-data/datasets/G4NDL.4.7.tar.gz",
-    "https://cern.ch/geant4-data/datasets/G4EMLOW.8.5.tar.gz",
-    "https://cern.ch/geant4-data/datasets/G4PhotonEvaporation.5.7.tar.gz",
-    "https://cern.ch/geant4-data/datasets/G4RadioactiveDecay.5.6.tar.gz",
-    "https://cern.ch/geant4-data/datasets/G4PARTICLEXS.4.0.tar.gz",
-    "https://cern.ch/geant4-data/datasets/G4PII.1.3.tar.gz",
-    "https://cern.ch/geant4-data/datasets/G4RealSurface.2.2.tar.gz",
-    "https://cern.ch/geant4-data/datasets/G4SAIDDATA.2.0.tar.gz",
-    "https://cern.ch/geant4-data/datasets/G4ABLA.3.3.tar.gz",
-    "https://cern.ch/geant4-data/datasets/G4INCL.1.2.tar.gz",
-    "https://cern.ch/geant4-data/datasets/G4ENSDFSTATE.2.3.tar.gz",
-]
+data_packages = {
+    "G4NEUTRONHPDATA": "https://cern.ch/geant4-data/datasets/G4NDL.4.7.tar.gz",
+    "G4LEDATA": "https://cern.ch/geant4-data/datasets/G4EMLOW.8.5.tar.gz",
+    "G4LEVELGAMMADATA": "https://cern.ch/geant4-data/datasets/G4PhotonEvaporation.5.7.tar.gz",
+    "G4RADIOACTIVEDATA": "https://cern.ch/geant4-data/datasets/G4RadioactiveDecay.5.6.tar.gz",
+    "G4PARTICLEXSDATA": "https://cern.ch/geant4-data/datasets/G4PARTICLEXS.4.0.tar.gz",
+    "G4PIIDATA": "https://cern.ch/geant4-data/datasets/G4PII.1.3.tar.gz",
+    "G4REALSURFACEDATA": "https://cern.ch/geant4-data/datasets/G4RealSurface.2.2.tar.gz",
+    "G4SAIDXSDATA": "https://cern.ch/geant4-data/datasets/G4SAIDDATA.2.0.tar.gz",
+    "G4ABLADATA": "https://cern.ch/geant4-data/datasets/G4ABLA.3.3.tar.gz",
+    "G4INCLDATA": "https://cern.ch/geant4-data/datasets/G4INCL.1.2.tar.gz",
+    "G4ENSDFSTATEDATA": "https://cern.ch/geant4-data/datasets/G4ENSDFSTATE.2.3.tar.gz",
+}
 
 
 def check_g4_data():
@@ -38,12 +38,12 @@ def check_g4_data():
         return
     else:
         # Check if the G4 data folder is up to date
-        consistent = check_consistency_g4_data_folders()
-        if consistent is False:
+        missing_g4_Data = get_missing_g4_data()
+        if len(missing_g4_Data) != 0:
             print("\nI will download a fresh G4 dataset for you.")
             print("This will take a moment.")
-            download_g4_data()
-            if check_consistency_g4_data_folders() is True:
+            download_g4_data(missing_g4_Data)
+            if len(get_missing_g4_data()) == 0:
                 print("\nGeant4 data has been set up successfully.")
             else:
                 print("There is (still) a problem with the Geant4 data.")
@@ -79,12 +79,22 @@ def download_with_resume(url, out, retries=5, delay=10):
 
 
 # Download Geant4 data:
-def download_g4_data():
+def download_g4_data(missing_g4_Data=None):
     data_location = get_g4_data_folder()
     data_location.mkdir(parents=True, exist_ok=True)
     folder_names_from_tar = set()
-    for i, package in enumerate(data_packages):
-        print(f"\nDownloading {i + 1}/{len(data_packages)} {package}")
+
+    if missing_g4_Data is None:
+        data_packages_needed = list(data_packages.values())
+    else:
+        data_packages_needed = [
+            package
+            for g4_data, package in data_packages.items()
+            if g4_data in missing_g4_Data
+        ]
+
+    for i, package in enumerate(data_packages_needed):
+        print(f"\nDownloading {i + 1}/{len(data_packages_needed)} {package}")
 
         # download the archive (with resume if the connexion failed)
         package_archive = package.split("/")[-1]
@@ -128,7 +138,7 @@ def check_for_non_required_files_folders():
         print("\n" + 10 * "*")
 
 
-def check_consistency_g4_data_folders() -> bool:
+def get_missing_g4_data() -> list:
     dataLocation = get_g4_data_folder()
     required_paths = set(get_g4_data_paths().values())
     existing_paths = set([(dataLocation / f) for f in dataLocation.iterdir()])
@@ -137,9 +147,13 @@ def check_consistency_g4_data_folders() -> bool:
         print("\nSome Geant4 data folder seem to be missing, namely:")
         for p in missing_paths:
             print(str(p))
-        return False
+        return [
+            g4_data
+            for g4_data, folder in get_g4_data_paths().items()
+            if folder in missing_paths
+        ]
     else:
-        return True
+        return []
 
 
 # Return Geant4 data folder: