Digitizer projection actor splitter

core/opengate_core/opengate_lib/digitizer/GateDigitizerProjectionActor.cpp

@@ -51,18 +51,20 @@ void GateDigitizerProjectionActor::EnableSquaredImage(const bool b) {
   // FIXME check if weight exists ?
 }
 
-// Called when the simulation starts
+// Resolve the input collections once. Their contents change for each event,
+// but the collection objects and their attribute schema are simulation-wide.
 void GateDigitizerProjectionActor::StartSimulationAction() {
-  // Get the input hits collection
   auto *hcm = GateDigiCollectionManager::GetInstance();
+  fInputDigiCollections.clear();
   for (const auto &name : fInputDigiCollectionNames) {
     auto *hc = hcm->GetDigiCollection(name);
     fInputDigiCollections.push_back(hc);
     CheckRequiredAttribute(hc, "PostPosition");
   }
 }
 
-void GateDigitizerProjectionActor::BeginOfRunActionMasterThread(int run_id) {
+void GateDigitizerProjectionActor::BeginOfRunActionMasterThread(
+    int /*run_id*/) {
   // Set the image to the correct position/orientation
   AttachImageToVolume<ImageType>(fImage, fPhysicalVolumeName, G4ThreeVector(),
                                  fDetectorOrientationMatrix);
@@ -153,7 +155,7 @@ void GateDigitizerProjectionActor::BeginOfRunAction(const G4Run *run) {
 void GateDigitizerProjectionActor::EndOfEventAction(const G4Event * /*event*/) {
   const auto run = G4RunManager::GetRunManager()->GetCurrentRun()->GetRunID();
   for (size_t channel = 0; channel < fInputDigiCollections.size(); channel++) {
-    const auto slice = channel + run * fInputDigiCollections.size();
+    const auto slice = channel;
     ProcessSlice(slice, channel);
   }
 }
@@ -233,11 +235,10 @@ void GateDigitizerProjectionActor::ScoreSquaredValue(
 }
 
 GateDigitizerProjectionActor::ImageType::RegionType
-GateDigitizerProjectionActor::GetRunRegion(const int run_id) const {
+GateDigitizerProjectionActor::GetRunRegion(const int /*run_id*/) const {
   auto region = fImage->GetLargestPossibleRegion();
   auto index = region.GetIndex();
   auto size = region.GetSize();
-  index[2] += run_id * fInputDigiCollections.size();
   size[2] = fInputDigiCollections.size();
   region.SetIndex(index);
   region.SetSize(size);

core/opengate_core/opengate_lib/digitizer/pyGateDigitizerProjectionActor.cpp

@@ -9,12 +9,32 @@
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
+class PyDigitizerProjectionActor : public GateDigitizerProjectionActor {
+public:
+  // Inherit the constructors
+  using GateDigitizerProjectionActor::GateDigitizerProjectionActor;
+
+  void BeginOfRunActionMasterThread(int run_id) override {
+    PYBIND11_OVERLOAD(void, GateDigitizerProjectionActor,
+                      BeginOfRunActionMasterThread, run_id);
+  }
+
+  int EndOfRunActionMasterThread(int run_id) override {
+    PYBIND11_OVERLOAD(int, GateDigitizerProjectionActor,
+                      EndOfRunActionMasterThread, run_id);
+  }
+};
+
 void init_GateDigitizerProjectionActor(py::module &m) {
 
-  py::class_<GateDigitizerProjectionActor,
+  py::class_<GateDigitizerProjectionActor, PyDigitizerProjectionActor,
              std::unique_ptr<GateDigitizerProjectionActor, py::nodelete>,
              GateVActor>(m, "GateDigitizerProjectionActor")
       .def(py::init<py::dict &>())
+      .def("BeginOfRunActionMasterThread",
+           &GateDigitizerProjectionActor::BeginOfRunActionMasterThread)
+      .def("EndOfRunActionMasterThread",
+           &GateDigitizerProjectionActor::EndOfRunActionMasterThread)
       .def_readwrite("fImage", &GateDigitizerProjectionActor::fImage)
       .def_readwrite("fSquaredImage",
                      &GateDigitizerProjectionActor::fSquaredImage)

docs/source/user_guide/user_guide_chemistry.rst

@@ -536,7 +536,7 @@ This combines the main pieces in one small script:
     source.position.translation = [0, 0, 0]
     source.direction.type = "momentum"
     source.direction.momentum = [0, 0, 1]
-    source.n = 1
+    source.number_of_primaries = 1
 
     chem_actor = sim.add_actor("ChemicalCountingActor", "chem_actor")
     chem_actor.attached_to = target

docs/source/user_guide/user_guide_dynamic_parametrisations.rst

@@ -171,7 +171,7 @@ Example:
    source.image = "activity_0.mhd"
    source.direction.type = "iso"
    source.energy.mono = 1 * MeV
-   source.n = [2000, 2000, 2000]
+   source.number_of_primaries = [2000, 2000, 2000]
 
    source.add_dynamic_parametrisation(
        image=[

docs/source/user_guide/user_guide_how_to_convert_example_1.rst

@@ -209,7 +209,7 @@ GATE 10
     source.position.translation = [1060 * mm, 0 * mm, 0 * mm]
     source.direction.type = "focused"
     source.direction.focus_point = [1000 * mm, 0 * mm, 0 * mm]
-    source.n = 720000 / sim.number_of_threads
+    source.number_of_primaries = 720000
     source.visualization.count = 2000
     source.visualization.color = "red"
     source.visualization.size = 5

docs/source/user_guide/user_guide_multijobs.rst

@@ -7,7 +7,7 @@ their output again. This is useful in two main situations:
 - local execution on a workstation, where several jobs can run in parallel on
   the same machine
 - server execution, where the split jobs are submitted to a scheduler such as
-  Slurm or HTCondor
+  Slurm, HTCondor or PBS.
 
 This section focuses on the current user-facing workflow in GATE 10.
 
@@ -186,8 +186,8 @@ Server-based execution
 Server-based multi-job execution is intended to be file-based:
 
 1. prepare a campaign folder containing ``simulation.json`` and the required
-   input files, probably locally
-2. transfer the campaign folder to the server
+   input files, probably locally. To create the ```simulation.json`` file, you can use ``sim.to_json_file()`` in your script instead of ``sim.run(...)``.
+2. transfer the campaign folder to the server. Be aware of the paths used in the .json file for material database or other input files. They should be valid on the server.
 3. split the simulation on the server
 4. submit the child jobs through a scheduler
 5. inspect job status
@@ -246,6 +246,9 @@ As a convenience, the command also looks for a default file named
 ``jobs_backend_options.json`` inside the campaign folder when no
 ``--backend-options-json`` or ``--backend`` argument is provided.
 
+You can find examples you can adapt in the ``contrib/cluster`` folder for slurm and pbs backends.
+The backend options are usually site-specific and should be adapted to the target server.
+
 
 .. Example: Slurm
 .. ~~~~~~~~~~~~~~

docs/source/user_guide/user_guide_optical_photons.rst

@@ -16,7 +16,7 @@ Optical photon polarization is not yet implemented. A random polarization is the
     source.particle = 'opticalphoton'
     source.position.type = 'point'
     source.position.translation = [0, 0, 0]
-    source.n = 100
+    source.number_of_primaries = 100
     source.energy.mono = 1.9*eV
     source.mother = 'world
     source.direction.type = "iso"

docs/source/user_guide/user_guide_reference_sources_common_params.rst

@@ -11,13 +11,13 @@ a source description to the simulation, you do:
 .. code:: python
 
    source1 = sim.add_source('GenericSource', 'source1')
-   source1.n = 100
+   source1.number_of_primaries = 100
 
    source2 = sim.add_source('VoxelSource', 'source2')
    source2.activity = 10 * g4_units.Bq
 
 There are several source types, each one with different parameter. In
-this example, ``source1.n`` indicates that this source will generate 100
+this example, ``source1.number_of_primaries`` indicates that this source will generate 100
 Events. The second source manages the time and will generate 10 Events
 per second, so according to the simulation run timing, a different
 number of Events will be generated.
@@ -59,11 +59,11 @@ A minimal working example would be:
 .. code:: python
 
    source = sim.add_source("GenericSource", "mySource")
-   source.n = [10000, 150000, 36]
+   source.number_of_primaries = [10000, 150000, 36]
 
    sim.run_timing_intervals = [[0, 1 * sec], [2 * sec, 2.5 * sec], [4 * sec, 5 * sec]]
 
-Please note that sim.run_timing_intervals must have the same length as source.n.
+Please note that ``sim.run_timing_intervals`` must have the same length as ``source.number_of_primaries``.
 By default, all particles of a given run will be emitted at a timestamp equal to the minimum time of the corresponding timing interval.
 
 Coordinate system

docs/source/user_guide/user_guide_reference_sources_generic_source.rst

@@ -34,7 +34,7 @@ All parameters are stored into a dict-like structure (a Box). Particle
 can be ‘gamma’, ‘e+’, ‘e-’, ‘proton’ (all Geant4 names). The number of
 particles that will be generated by the source can be described by an
 activity ``source.activity = 10 * MBq`` or by a number of particle
-``source.n = 100``.
+``source.number_of_primaries = 100``.
 
 The positions from where the particles will be generated are defined by a
 shape (‘box’, ‘sphere’, ‘point’, ‘disc’), defined by several parameters

docs/source/user_guide/user_guide_reference_sources_ion_pencil_beam_source.rst

@@ -41,7 +41,7 @@ a 120 MeV/n carbon ion beam.
    source.energy.mono = 1440 * MeV
    source.particle = "ion 6 12"  # carbon
    source.position.translation = [100 * mm, 0 * mm, 0 * cm]
-   source.n = 20000
+   source.number_of_primaries = 20000
    source.direction.partPhSp_x = [
        2.3335754 * mm,
        2.3335754 * mrad,

docs/source/user_guide/user_guide_reference_sources_treatment_plan_pencil_beam_source.rst

@@ -85,7 +85,7 @@ simulation:
        # tps
        n_sim = 80000  # particles to simulate per beam
        tps = sim.add_source("TreatmentPlanPBSource", "TPSource")
-       tps.n = n_sim
+       tps.number_of_primaries = n_sim
        tps.beam_model = beamline
        tps.plan_path = ref_path / "TreatmentPlan2Spots.txt"
        tps.beam_nr = 1

docs/source/user_guide/user_guide_sources.rst

@@ -49,7 +49,7 @@ Alternatively, you can specify the fixed number of primary particles to be gener
 
 .. code-block:: python
 
-    source1.n = 100
+    source1.number_of_primaries = 100
 
 Note, however, that certain functionality regarding simulations with multiple runs is currently not supported when sources specify the fixed number of particles as above.
 

opengate/actors/biasingactors.py

@@ -418,11 +418,20 @@ class ScatterSplittingFreeFlightActor(
             False,
             {"doc": "Print debug information during the stepping action of the actor."},
         ),
+        "particles": (
+            [
+                "gamma",
+            ],
+            {
+                "doc": "For scatter splitting free flight, only gamma is supported",
+                "override": True,
+                "read_only": True,
+            },
+        ),
     }
 
     # Do NOT work with GammaGeneralProc
     processes = ["compt", "phot", "conv", "Rayl"]
-    particles = ["gamma"]
 
     user_output_config = {
         "info": {