Olga for 878

.github/workflows/main.yml

@@ -297,6 +297,26 @@ jobs:
       uses: actions/checkout@v6
     - uses: ./.github/workflows/actions_tests
 
+  test_wheel_castor:
+    runs-on: ubuntu-24.04
+    needs: [build_opengate_wheel, build_opengate_core_wheel_pr]
+    strategy:
+      fail-fast: false
+    steps:
+    - name: Checkout github repo
+      uses: actions/checkout@v4
+    - uses: actions/download-artifact@v4
+      with:
+        pattern: dist-*
+        merge-multiple: true
+        path: dist/
+    - name: Run tests
+      shell: bash {0}
+      run: |
+            mv dist/opengate_core-*-cp312-cp312-manylinux*_x86_64.whl $GITHUB_WORKSPACE/.github/workflows/
+            mv dist/opengate-*.whl $GITHUB_WORKSPACE/.github/workflows/
+            docker run --rm -v $GITHUB_WORKSPACE:/home tbaudier/opengate_castor_ci /home/opengate/tests/src/external/castor/run_test_opengate_castor.sh
+
   publish_test:
     runs-on: ubuntu-24.04
     if: ${{ (always()) && (github.ref == 'refs/heads/master') }}

opengate/bin/opengate_tests.py

@@ -205,6 +205,8 @@ def get_files_to_run():
         "test094a_spect_simu_prim",  # to compute the reference data
         "test094b_spect_simu_scatter",  # to compute the reference data
         "test094c_build_sinogram",  # to compute the reference data
+        "test096_pet_castor_ref.py",  # test for castor compatibility
+        "test096_pet_castor_coinc.py",  # test for castor compatibility
     ]
     path_tests_src = Path(path_tests_src)
     all_file_paths = []

opengate/contrib/pet/ge_signa.py

@@ -0,0 +1,233 @@
+import pathlib
+from opengate.utility import g4_units
+from opengate.geometry.utility import get_grid_repetition, get_circular_repetition
+from opengate.actors.coincidences import *
+
+# colors
+red = [1, 0, 0, 1]
+blue = [0, 0, 1, 1]
+green = [0, 1, 0, 1]
+yellow = [0.9, 0.9, 0.3, 1]
+gray = [0.5, 0.5, 0.5, 1]
+white = [1, 1, 1, 0.8]
+transparent = [1, 1, 1, 0]
+
+
+def create_LYSO_material(sim):
+    g_cm3 = g4_units.g_cm3
+    sim.volume_manager.material_database.add_material_weights(
+        "LYSO", ["Lu", "Y", "Si", "O"], [0.7299, 0.0279, 0.0628, 0.1794], 7.21 * g_cm3    
+    )
+
+
+def add_pet(sim, name="pet"):
+    """
+    Geometry of a PET/MR SIGNA GE
+    """
+
+    # unit
+    mm = g4_units.mm
+
+    create_LYSO_material(sim)
+
+     # ring volume
+    pet = sim.add_volume("Tubs", "pet")
+    pet.rmax = 350 * mm
+    pet.rmin = 290 * mm
+    pet.dz = 135 * mm
+    pet.color = gray
+    pet.material = "G4_AIR"
+
+    # module
+    module = sim.add_volume("Box", "module")
+    module.mother = pet.name
+    module.size = [64.5 * mm, 25 * mm, 250.4  * mm]
+    translations_ring, rotations_ring = get_circular_repetition(
+        28, [0 * mm, 324.3 * mm, 0 ], start_angle_deg=190, axis=[0, 0, 1]
+    )
+    module.translation = translations_ring
+    module.rotation = rotations_ring
+    module.material = "G4_AIR"
+    module.color = white
+
+
+    # unit
+    unit = sim.add_volume("Box", "unit")
+    unit.mother = module.name
+    unit.size =  [ module.size[0] , module.size[1] , 47.84 * mm ]
+    unit.material = "G4_AIR"
+    unit.translation = get_grid_repetition([1, 1, 5], [0, 0 * mm, 50.64 * mm])
+    unit.color = blue
+
+
+    # block
+    block = sim.add_volume("Box", "block")
+    block.mother = unit.name
+    block.size =  [ 15.9 * mm , module.size[1] , 47.84 * mm ]
+    block.material = "G4_AIR"
+    block.translation = get_grid_repetition([4, 1, 1], [16.2 * mm, 0 * mm, 0 * mm])
+    block.color = red
+
+    # optical
+    optical = sim.add_volume("Box", "optical")
+    optical.mother = block.name
+    optical.size =  [ 15.9 * mm , module.size[1] , 15.9 * mm ]
+    optical.material = "G4_AIR"
+    optical.translation = get_grid_repetition([1, 1, 3], [0, 0 , 15.97 * mm])
+    optical.color = yellow
+
+    # Crystal
+    crystal = sim.add_volume("Box", "crystal")
+    crystal.mother = optical.name
+    crystal.size = [3.95 * mm, module.size[1], 5.3 * mm]
+    crystal.material = "LYSO"
+    #crystal.translation = get_grid_repetition([1, 1, 1], [0 * mm ,0 * mm, 0 * mm])
+    crystal.color = green
+
+    n_crystal = len(crystal.translation)
+    n_optical= len(optical.translation)
+    n_block = len(block.translation)
+    n_unit = len(unit.translation) 
+    n_module = len(module.translation)
+
+    print(f"Number of crystals : {n_crystal}")
+    print(f"Number of opticals     : {n_optical}")
+    print(f"Number of blocks   : {n_block}")
+    print(f"Number of units   : {n_unit}")
+    print(f"Number of modules  : {n_module}")
+    return pet
+
+
+def add_digitizer(
+        sim, pet_name, output_filename, hits_name="Hits", singles_name="Singles"
+):
+
+    print( output_filename)
+    # unit
+    mm = g4_units.mm
+    keV = g4_units.keV
+    ps = g4_units.ps
+
+
+    # get crystal volume
+    crystal = sim.volume_manager.volumes["crystal"]
+    unit = sim.volume_manager.volumes["unit"]
+
+    # hits collection
+    hc = sim.add_actor("DigitizerHitsCollectionActor", hits_name)
+    hc.attached_to = crystal.name
+    hc.authorize_repeated_volumes = True
+    #hc.output_filename = output_filename
+    hc.attributes = [
+        "EventID",
+        "PreStepUniqueVolumeIDAsInt",
+        "PostPositionLocal",
+        "PostPosition",
+        "TotalEnergyDeposit",
+        "PreStepUniqueVolumeID",
+        "GlobalTime",
+    ]
+
+    # ADDER
+    sc_adder = sim.add_actor("DigitizerAdderActor", f"Singles_{crystal.name}_adder")
+    sc_adder.attached_to = hc.attached_to
+    sc_adder.authorize_repeated_volumes = True
+    sc_adder.input_digi_collection = hc.name
+    sc_adder.discretize_volume = crystal.name
+    sc_adder.policy = "EnergyWeightedCentroidPosition"
+    #sc_adder.output =  output_filename
+
+    # READOUT 
+    sc_ro = sim.add_actor("DigitizerReadoutActor",  f"Singles_{crystal.name}_readout")
+    sc_ro.authorize_repeated_volumes = True
+    sc_ro.attached_to = sc_adder.attached_to
+    sc_ro.input_digi_collection = sc_adder.name
+    sc_ro.group_volume = unit.name
+    sc_ro.discretize_volume = crystal.name
+    sc_ro.policy = "EnergyWinnerPosition"
+    #sc_ro.output_filename =  output_filename
+
+    # SPATIAL BLURRING
+    sc_sp_blur = sim.add_actor("DigitizerSpatialBlurringActor", f"Singles_{crystal.name}_sp_blur")
+    sc_sp_blur.attached_to = sc_ro.attached_to
+    sc_sp_blur.authorize_repeated_volumes = True
+    sc_sp_blur.input_digi_collection = sc_ro.name
+    sc_sp_blur.keep_in_solid_limits = False
+    sc_sp_blur.use_truncated_Gaussian = True
+    sc_sp_blur.blur_attribute = "PostPosition"
+    sc_sp_blur.blur_fwhm = [1*mm, 1*mm, 1*mm]
+    #sc_sp_blur.output_filename =  output_filename
+
+    # EFFICIENCY
+    sc_efficiency = sim.add_actor("DigitizerEfficiencyActor",f"Singles_{crystal.name}_efficiency")
+    sc_efficiency.attached_to = sc_sp_blur.attached_to
+    sc_efficiency.authorize_repeated_volumes = True  
+    sc_efficiency.input_digi_collection = sc_sp_blur.name
+    sc_efficiency.efficiency = 0.93
+    #sc_eff.output_filename =  output_filename
+
+    # ENERGY BLURRING
+    sc_energy_blur = sim.add_actor("DigitizerBlurringActor", f"Singles_{crystal.name}_energy_blur")
+    sc_energy_blur.attached_to = sc_efficiency.attached_to
+    sc_energy_blur.authorize_repeated_volumes = True
+    sc_energy_blur.input_digi_collection = sc_efficiency.name
+    sc_energy_blur.blur_attribute = "TotalEnergyDeposit"
+    sc_energy_blur.blur_method = "InverseSquare" 
+    sc_energy_blur.blur_resolution = 0.12
+    sc_energy_blur.blur_reference_value = 511 * keV
+    #sc_ebergy_blur.output_filename =  output_filename
+
+    # TIME BLURRING
+    sc_time_blur = sim.add_actor("DigitizerBlurringActor", f"Singles_{crystal.name}_time_blur")
+    sc_time_blur.input_digi_collection = sc_energy_blur.name
+    sc_time_blur.attached_to = sc_energy_blur.attached_to
+    sc_time_blur.authorize_repeated_volumes = True     
+    sc_time_blur.blur_attribute = "GlobalTime"
+    sc_time_blur.blur_method = "Gaussian"
+    sc_time_blur.blur_fwhm = 270 * ps
+    #sc_time_blur.output_filename =  output_filename
+
+
+    # ENERGY WINDOW 
+    sc_energy_window = sim.add_actor("DigitizerEnergyWindowsActor",f"{singles_name}" )
+    sc_energy_window.attached_to = sc_time_blur.attached_to
+    sc_energy_window.authorize_repeated_volumes = True     
+    sc_energy_window.input_digi_collection = sc_time_blur.name
+    sc_energy_window.channels = [
+        {"name": f"{singles_name}", "min": 425 * keV, "max": 650 * keV}]
+    sc_energy_window.output_filename =  output_filename
+
+    return sc_energy_window
+
+## Sorter: 4.57 takeAllGoods minsecDiff 3
+
+def add_coincidences_sorter(
+        singles_tree
+):
+
+    mm = g4_units.mm
+    ns = g4_units.ns
+
+    time_window = 4.57 * ns
+    policy = "takeAllGoods"
+    min_trans_dist = 26 * mm
+    transaxial_plane = "xy"
+    max_axial_dist =  300 * mm
+
+
+    # apply coincidences sorter
+    # (chunk size can be much larger, keep a low value to check it is ok)
+    coincidences = coincidences_sorter(
+        singles_tree,
+        time_window,
+        policy,
+        min_trans_dist,
+        transaxial_plane,
+        max_axial_dist,
+        chunk_size=1000000,
+    )
+
+
+
+
+    return coincidences

opengate/tests/src/external/castor/Dockerfile_opengate_castor

@@ -0,0 +1,44 @@
+#Docker for opengate_core
+#systemctl start docker
+#login: docker login
+#build: docker build -t tbaudier/opengate_castor_ci -f Dockerfile_opengate_castor.
+#push: docker push tbaudier/opengate_castor_ci
+#run: docker run --rm -v $(Pipeline.Workspace):/home tbaudier/opengate_castor_ci /home/.github/workflows/run_test_opengate_castor.sh
+#interactive: docker run -ti --rm -v $PWD:/home quay.io/pypa/manylinux_2_34_x86_64 /bin/bash
+
+FROM quay.io/pypa/manylinux_2_34_x86_64
+MAINTAINER Thomas Baudier <thomas.baudier@creatis.insa-lyon.fr>
+#Install packages
+RUN     yum install -y gcc wget git expat-devel fftw-devel qt6-qtbase-devel freeglut-devel libXmu-devel xerces-c-devel libXpm-devel libXft-devel xrootd-devel openssl-devel libuuid-devel \
+
+#Create folder
+    &&  mkdir -p /software/cmake /software/root/src /software/root/bin /software/castor/src /software/castor/bin /software/wheelhouse \
+
+#Install cmake
+    &&  cd /software/cmake \
+    &&  wget https://github.com/Kitware/CMake/releases/download/v3.31.8/cmake-3.31.8-linux-x86_64.tar.gz \
+    &&  tar xzvf cmake-3.31.8-linux-x86_64.tar.gz \
+    &&  rm -rf cmake-3.31.8-linux-x86_64.tar.gz \
+    &&  mv cmake-3.31.8-linux-x86_64 cmake \
+    &&  export PATH=/software/cmake/cmake/bin/:${PATH} \
+
+#Compile root
+    &&  cd /software/root \
+    &&  git clone --branch v6-36-06 https://github.com/root-project/root.git --depth 1 src \
+    &&  cd bin \
+    &&  . /opt/rh/gcc-toolset-14/enable \
+    &&  cmake -Dxrootd=OFF ../src \
+    &&  make -j10 \
+    &&  source /software/root/bin/bin/thisroot.sh \
+
+#Compile castor
+    &&  cd /software/castor \
+    &&  git clone -b feature/gatev10_converter https://gitlab.com/castor-collaboration/castor.git --depth 1 src \
+    &&  cd bin \
+    &&  cmake -DCMAKE_CXX_FLAGS=-std=c++17 -DCASToR_BUILD_GATE_UTILITIES=ON ../src \
+    &&  make -j10 \
+    &&  export PATH=/software/castor/bin/:$PATH
+
+# docker commit <container_name>
+# docker tag <image_id> tbaudier/opengate_castor_ci:1.0.0
+

opengate/tests/src/external/castor/run_test_opengate_castor.sh

@@ -0,0 +1,19 @@
+#! /bin/bash
+
+#Instal opengate wheels
+cd /home/.github/workflows
+/opt/python/cp312-cp312/bin/pip install opengate_core-*.whl
+/opt/python/cp312-cp312/bin/pip install opengate-*.whl
+cd /opt/_internal/cpython-3.12.12/lib/python3.12/site-packages/opengate/tests/src/external/castor
+/opt/python/cp312-cp312/bin/python test096_pet_castor.py
+/opt/python/cp312-cp312/bin/python test096_pet_castor_ref.py
+/opt/python/cp312-cp312/bin/python test096_pet_castor_coinc.py
+cd /opt/_internal/cpython-3.12.12/lib/python3.12/site-packages/opengate/tests/output/test096_pet_castor_interface
+
+#Convert Gate root output to Castor
+export PATH=/software/castor/bin/:$PATH
+castor-GATERootToCastor -vb 2 -i coincidences.root -o test_gatev10 -js castor_config.json -s "PET_GATEv10_TEST" -t -geo
+
+#Reonstruction with castor
+castor-recon -vb 2 -df test_gatev10_df.Cdh -fout reco_test_gatev10 -oit -1 -it 10:1 -dim 128,128,40 -vox 3,3,3 -th 0 -fov-out 98. -slice-out 2
+