Merge branch 'master' into update_gaga_garf

.github/workflows/main.yml

@@ -17,10 +17,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-11, windows-latest]
         python-version: [3.8, 3.9, '3.10', '3.11']
         exclude:
-          - os: macos-latest
+          - os: macos-11
             python-version: '3.11'
 
     env:
@@ -36,7 +36,7 @@ jobs:
         if [[ ${{ matrix.os }} == "ubuntu-latest" ]]; then
           export GIT_SSL_NO_VERIFY=1
           git submodule update --init --recursive
-        elif [[ ${{ matrix.os }} == "macos-latest" ]]; then
+        elif [[ ${{ matrix.os }} == "macos-11" ]]; then
           export GIT_SSL_NO_VERIFY=1
           git submodule update --init --recursive
         else
@@ -56,7 +56,7 @@ jobs:
             varOS=`cat /etc/os-release | grep "VERSION=" | grep -oP '(?<=\").*?(?=\")'`
             varOS=($varOS)
             echo "release=${varOS[0]}" >> $GITHUB_OUTPUT
-        elif [[ ${{ matrix.os }} == "macos-latest" ]]; then
+        elif [[ ${{ matrix.os }} == "macos-11" ]]; then
             varOS=`sw_vers | grep "ProductVersion:"`
             varOS="${varOS#*:}"
             echo "release=${varOS:1}" >> $GITHUB_OUTPUT
@@ -106,21 +106,21 @@ jobs:
               mv dist_opengate/* dist/
           fi
     - uses: conda-incubator/setup-miniconda@v2
-      if: (matrix.os == 'macos-latest') || (matrix.os == 'windows-latest')
+      if: (matrix.os == 'macos-11') || (matrix.os == 'windows-latest')
       with:
           auto-update-conda: true
           activate-environment: opengate_core
           python-version: ${{ matrix.python-version }}
     - name: Set up Homebrew
-      if: matrix.os == 'macos-latest'
+      if: matrix.os == 'macos-11'
       id: set-up-homebrew
       uses: Homebrew/actions/setup-homebrew@master
     - name: Create opengate_core Wheel Mac
-      if: matrix.os == 'macos-latest'
+      if: matrix.os == 'macos-11'
       shell: bash -l {0}
       run: |
           brew update
-          rm -rf /usr/local/bin/python3.11-config /usr/local/bin/2to3-3.11 /usr/local/bin/idle3.11 /usr/local/bin/pydoc3.11 /usr/local/bin/python3.11
+          rm -rf /usr/local/bin/python3.1*-config /usr/local/bin/2to3-3.1* /usr/local/bin/idle3.1* /usr/local/bin/pydoc3.1* /usr/local/bin/python3.1*
           rm -rf /usr/local/bin/python3-config /usr/local/bin/2to3 /usr/local/bin/idle3 /usr/local/bin/pydoc3 /usr/local/bin/python3
           brew install --force --verbose --overwrite \
                        ccache \

.pre-commit-config.yaml

@@ -5,11 +5,11 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 23.12.0
     hooks:
     -   id: black
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v17.0.5
+    rev: v17.0.6
     hooks:
     -   id: clang-format
 ci:

core/opengate_core/opengate_lib/GateGANSource.cpp

@@ -88,7 +88,20 @@ void GateGANSource::PrepareNextRun() {
   // (no need to update th fSPS pos in GateGenericSource)
   // GateVSource::PrepareNextRun();
   // FIXME remove this function ?
-  GateGenericSource::PrepareNextRun();
+  // GateGenericSource::PrepareNextRun();
+  GateVSource::PrepareNextRun();
+  // This global transformation is given to the SPS that will
+  // generate particles in the correct coordinate system
+  auto &l = fThreadLocalData.Get();
+  auto *pos = fSPS->GetPosDist();
+  pos->SetCentreCoords(l.fGlobalTranslation);
+
+  // orientation according to mother volume
+  auto rotation = l.fGlobalRotation;
+  G4ThreeVector r1(rotation(0, 0), rotation(1, 0), rotation(2, 0));
+  G4ThreeVector r2(rotation(0, 1), rotation(1, 1), rotation(2, 1));
+  pos->SetPosRot1(r1);
+  pos->SetPosRot2(r2);
 }
 
 void GateGANSource::SetGeneratorFunction(ParticleGeneratorType &f) {

core/opengate_core/opengate_lib/GateGenericSource.cpp

@@ -13,18 +13,19 @@
 #include <G4UnitsTable.hh>
 
 GateGenericSource::GateGenericSource() : GateVSource() {
-  fNumberOfGeneratedEvents = 0;
+  /*fNumberOfGeneratedEvents = 0;
   fMaxN = 0;
   fActivity = 0;
+  fHalfLife = -1;
+  fLambda = -1;
+  */
   fInitGenericIon = false;
   fA = 0;
   fZ = 0;
   fE = 0;
   fInitConfine = false;
   fWeight = -1;
   fWeightSigma = -1;
-  fHalfLife = -1;
-  fDecayConstant = -1;
   fTotalSkippedEvents = 0;
   fCurrentSkippedEvents = 0;
   fTotalZeroEvents = 0;
@@ -34,6 +35,7 @@ GateGenericSource::GateGenericSource() : GateVSource() {
   fParticleDefinition = nullptr;
   fEffectiveEventTime = -1;
   fEffectiveEventTime = -1;
+  fforceRotation = false;
 }
 
 GateGenericSource::~GateGenericSource() {
@@ -75,18 +77,20 @@ void GateGenericSource::InitializeUserInfo(py::dict &user_info) {
   CreateSPS();
 
   // get user info about activity or nb of events
+  /*
   fMaxN = DictGetInt(user_info, "n");
   fActivity = DictGetDouble(user_info, "activity");
   fInitialActivity = fActivity;
 
   // half life ?
   fHalfLife = DictGetDouble(user_info, "half_life");
-  fDecayConstant = log(2) / fHalfLife;
-  fUserParticleLifeTime = DictGetDouble(user_info, "user_particle_life_time");
+  fLambda = log(2) / fHalfLife;
+  */
 
   // weight
   fWeight = DictGetDouble(user_info, "weight");
   fWeightSigma = DictGetDouble(user_info, "weight_sigma");
+  fUserParticleLifeTime = DictGetDouble(user_info, "user_particle_life_time");
 
   // get the user info for the particle
   InitializeParticle(user_info);
@@ -103,14 +107,14 @@ void GateGenericSource::InitializeUserInfo(py::dict &user_info) {
   fCurrentSkippedEvents = 0;
   fTotalSkippedEvents = 0;
   fEffectiveEventTime = -1;
+
+  fforceRotation = DictGetDouble(user_info, "force_rotation");
 }
 
 void GateGenericSource::UpdateActivity(double time) {
   if (!fTAC_Times.empty())
     return UpdateActivityWithTAC(time);
-  if (fHalfLife <= 0)
-    return;
-  fActivity = fInitialActivity * exp(-fDecayConstant * (time - fStartTime));
+  GateVSource::UpdateActivity(time);
 }
 
 void GateGenericSource::UpdateActivityWithTAC(double time) {
@@ -159,14 +163,15 @@ double GateGenericSource::PrepareNextTime(double current_simulation_time) {
       return -1;
 
     // get next time according to current fActivity
-    double next_time =
-        fEffectiveEventTime - log(G4UniformRand()) * (1.0 / fActivity);
+    double next_time = CalcNextTime(fEffectiveEventTime);
     if (next_time >= fEndTime)
       return -1;
     return next_time;
   }
 
   // check according to t MaxN
+  // std::cout<<fNumberOfGeneratedEvents<<std::endl;
+
   if (fNumberOfGeneratedEvents + cse >= fMaxN) {
     return -1;
   }
@@ -180,15 +185,30 @@ void GateGenericSource::PrepareNextRun() {
   // This global transformation is given to the SPS that will
   // generate particles in the correct coordinate system
   auto &l = fThreadLocalData.Get();
+  // auto user_info_pos = py::dict(puser_info["position"]);
+  // auto pos_init = DictGetG4ThreeVector(user_info_pos, "translation");
   auto *pos = fSPS->GetPosDist();
   pos->SetCentreCoords(l.fGlobalTranslation);
 
   // orientation according to mother volume
   auto rotation = l.fGlobalRotation;
-  G4ThreeVector r1(rotation(0, 0), rotation(0, 1), rotation(0, 2));
-  G4ThreeVector r2(rotation(1, 0), rotation(1, 1), rotation(1, 2));
+  G4ThreeVector r1(rotation(0, 0), rotation(1, 0), rotation(2, 0));
+  G4ThreeVector r2(rotation(0, 1), rotation(1, 1), rotation(2, 1));
   pos->SetPosRot1(r1);
   pos->SetPosRot2(r2);
+
+  auto *ang = fSPS->GetAngDist();
+
+  if (fangType == "momentum" && fforceRotation) {
+    auto new_d = rotation * fInitializeMomentum;
+    ang->SetParticleMomentumDirection(new_d);
+  }
+  if (fangType == "focused" && fforceRotation) {
+    auto vec_f = fInitiliazeFocusPoint - fInitTranslation;
+    auto rot_f = rotation * vec_f;
+    auto new_f = rot_f + l.fGlobalTranslation;
+    ang->SetFocusPoint(new_f);
+  }
 }
 
 void GateGenericSource::UpdateEffectiveEventTime(
@@ -226,7 +246,6 @@ void GateGenericSource::GeneratePrimaries(G4Event *event,
   // (acceptance angle is included)
   fSPS->SetParticleTime(current_simulation_time);
   fSPS->GeneratePrimaryVertex(event);
-
   // update the time according to skipped events
   fEffectiveEventTime = current_simulation_time;
   auto &l = fThreadLocalDataAA.Get();
@@ -300,6 +319,7 @@ void GateGenericSource::InitializePosition(py::dict puser_info) {
   std::vector<std::string> l = {"sphere", "point", "box", "disc", "cylinder"};
   CheckIsIn(pos_type, l);
   auto translation = DictGetG4ThreeVector(user_info, "translation");
+  fInitTranslation = translation;
   if (pos_type == "point") {
     pos->SetPosDisType("Point");
   }
@@ -365,6 +385,7 @@ void GateGenericSource::InitializeDirection(py::dict puser_info) {
   auto user_info = py::dict(puser_info["direction"]);
   auto *ang = fSPS->GetAngDist();
   auto ang_type = DictGetStr(user_info, "type");
+  fangType = ang_type;
   std::vector<std::string> ll = {"iso", "momentum", "focused",
                                  "beam2d"}; // FIXME check on py side ?
   CheckIsIn(ang_type, ll);
@@ -382,11 +403,13 @@ void GateGenericSource::InitializeDirection(py::dict puser_info) {
   if (ang_type == "momentum") {
     ang->SetAngDistType("planar"); // FIXME really ??
     auto d = DictGetG4ThreeVector(user_info, "momentum");
+    fInitializeMomentum = d;
     ang->SetParticleMomentumDirection(d);
   }
   if (ang_type == "focused") {
     ang->SetAngDistType("focused");
     auto f = DictGetG4ThreeVector(user_info, "focus_point");
+    fInitiliazeFocusPoint = f;
     ang->SetFocusPoint(f);
   }
   if (ang_type == "beam2d") {

core/opengate_core/opengate_lib/GateGenericSource.h

@@ -34,7 +34,7 @@ class GateGenericSource : public GateVSource {
 
   /// Current number of simulated events in this source
   /// (do not include skipped events)
-  unsigned long fNumberOfGeneratedEvents;
+  // unsigned long fNumberOfGeneratedEvents;
 
   /// Count the number of skipped events
   /// (e.g. Acceptance Angle or in GANSource)
@@ -51,16 +51,22 @@ class GateGenericSource : public GateVSource {
               const std::vector<double> &activities);
 
 protected:
-  unsigned long fMaxN;
-  // We cannot not use a std::unique_ptr
-  // (or maybe by controlling the deletion during the CleanWorkerThread ?)
+  // unsigned long fMaxN;
+  //  We cannot not use a std::unique_ptr
+  //  (or maybe by controlling the deletion during the CleanWorkerThread ?)
   GateSingleParticleSource *fSPS;
-
+  /*
   double fActivity;
   double fInitialActivity;
   double fHalfLife;
-  double fDecayConstant;
+  double fLambda;
+  */
+
   G4ParticleDefinition *fParticleDefinition;
+  G4ThreeVector fInitializeMomentum;
+  G4ThreeVector fInitiliazeFocusPoint;
+  G4ThreeVector fInitTranslation;
+  G4String fangType;
   double fEffectiveEventTime;
   double fUserParticleLifeTime;
 
@@ -78,6 +84,10 @@ class GateGenericSource : public GateVSource {
   double fWeight;
   double fWeightSigma;
 
+  // Force the rotation of momentum and focal point to follow rotation of the
+  // source, eg: needed for motion actor
+  bool fforceRotation;
+
   // angular acceptance management
   struct threadLocalT {
     GateAcceptanceAngleTesterManager *fAAManager;
@@ -106,7 +116,7 @@ class GateGenericSource : public GateVSource {
 
   virtual void InitializeEnergy(py::dict user_info);
 
-  virtual void UpdateActivity(double time);
+  virtual void UpdateActivity(double time) override;
 
   void UpdateEffectiveEventTime(double current_simulation_time,
                                 unsigned long skipped_particle);

core/opengate_core/opengate_lib/GateMotionVolumeActor.cpp

@@ -63,7 +63,7 @@ void GateMotionVolumeActor::MoveGeometry(int run_id) {
   rot->set(r.rep3x3());
 
   // close the geometry manager
-  gm->CloseGeometry(false, false, pv);
+  gm->CloseGeometry(true, false, pv);
   // G4RunManager::GetRunManager()->GeometryHasBeenModified(true);
 }