Merge pull request #422 from axelrannou/carm_contrib

C-arm contrib

.github/workflows/main.yml

@@ -394,6 +394,7 @@ jobs:
           fi
           pip install SimpleITK
           pip install gaga_phsp==0.7.2
+          pip install spekpy
           pip install dist/opengate_core-*-${PYTHONFOLDER}-${OSNAME}*_${PLATFORM}64.whl
           pip install dist/opengate-*.whl
           export GIT_SSL_NO_VERIFY=1

core/CMakeLists.txt

@@ -24,7 +24,7 @@ if (Geant4_multithreaded_FOUND)
 ENDIF ()
 find_package(Threads REQUIRED)
 
-#GDML
+# GDML
 IF (Geant4_gdml_FOUND)
     message(STATUS "OPENGATE - Geant4 is compiled with GDML")
     add_definitions(-DUSE_GDML=1)

core/opengate_core/opengate_lib/GateAcceptanceAngleTesterManager.cpp

@@ -19,7 +19,7 @@ GateAcceptanceAngleTesterManager::GateAcceptanceAngleTesterManager() {
 }
 
 void GateAcceptanceAngleTesterManager::Initialize(py::dict puser_info,
-                                                  bool is_iso) {
+                                                  bool is_valid_type) {
   fAcceptanceAngleVolumeNames = DictGetVecStr(puser_info, "volumes");
   fEnabledFlag = !fAcceptanceAngleVolumeNames.empty();
   if (!fEnabledFlag)
@@ -39,10 +39,11 @@ void GateAcceptanceAngleTesterManager::Initialize(py::dict puser_info,
     Fatal(oss.str());
   }
 
-  // Cannot use SkipEvent with non iso source
-  if (!is_iso && fPolicy == AASkipEvent) {
+  // Cannot use SkipEvent with not a valid type of source
+  if (!is_valid_type && fPolicy == AASkipEvent) {
     std::ostringstream oss;
-    oss << "Cannot use 'SkipEvent' mode without 'iso' direction type";
+    oss << "Cannot use 'SkipEvent' mode without 'iso' or 'histogram' direction "
+           "type";
     Fatal(oss.str());
   }
 }

core/opengate_core/opengate_lib/GateGenericSource.cpp

@@ -30,6 +30,8 @@ GateGenericSource::GateGenericSource() : GateVSource() {
   fEffectiveEventTime = -1;
   fEffectiveEventTime = -1;
   fDirectionRelativeToAttachedVolume = false;
+  fUserParticleLifeTime = -1;
+  fBackToBackMode = false;
 }
 
 GateGenericSource::~GateGenericSource() {
@@ -90,7 +92,6 @@ void GateGenericSource::InitializeUserInfo(py::dict &user_info) {
   fCurrentSkippedEvents = 0;
   fTotalSkippedEvents = 0;
   fEffectiveEventTime = -1;
-
   fDirectionRelativeToAttachedVolume =
       DictGetBool(user_info, "direction_relative_to_attached_volume");
 }
@@ -162,14 +163,13 @@ double GateGenericSource::PrepareNextTime(double current_simulation_time) {
 }
 
 void GateGenericSource::PrepareNextRun() {
-  // The following compute the global transformation from
+  // The following function computes the global transformation from
   // the local volume (mother) to the world
   GateVSource::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);
 
@@ -180,17 +180,23 @@ void GateGenericSource::PrepareNextRun() {
   pos->SetPosRot1(r1);
   pos->SetPosRot2(r2);
 
+  // For the direction, the orientation may or may not be
+  // relative to the volume according to user option
   auto *ang = fSPS->GetAngDist();
-
+  ang->fDirectionRelativeToAttachedVolume = fDirectionRelativeToAttachedVolume;
+  ang->fGlobalRotation = l.fGlobalRotation;
+  ang->fGlobalTranslation = l.fGlobalTranslation;
   if (fangType == "momentum" && fDirectionRelativeToAttachedVolume) {
     auto new_d = rotation * fInitializeMomentum;
     ang->SetParticleMomentumDirection(new_d);
+    ang->fDirectionRelativeToAttachedVolume = false;
   }
   if (fangType == "focused" && fDirectionRelativeToAttachedVolume) {
     auto vec_f = fInitiliazeFocusPoint - fInitTranslation;
     auto rot_f = rotation * vec_f;
     auto new_f = rot_f + l.fGlobalTranslation;
     ang->SetFocusPoint(new_f);
+    ang->fDirectionRelativeToAttachedVolume = false;
   }
 }
 
@@ -443,10 +449,11 @@ void GateGenericSource::InitializeDirection(py::dict puser_info) {
   // set the angle acceptance volume if needed
   auto d = py::dict(puser_info["direction"]);
   auto dd = py::dict(d["acceptance_angle"]);
-  auto is_iso = ang->GetDistType() == "iso";
+  auto is_valid_type =
+      ang->GetDistType() == "iso" || ang->GetDistType() == "user";
   auto &l = fThreadLocalDataAA.Get();
   l.fAAManager = new GateAcceptanceAngleTesterManager;
-  l.fAAManager->Initialize(dd, is_iso);
+  l.fAAManager->Initialize(dd, is_valid_type);
   fSPS->SetAAManager(l.fAAManager);
 }
 

core/opengate_core/opengate_lib/GateSPSAngDistribution.cpp

@@ -0,0 +1,19 @@
+/* --------------------------------------------------
+   Copyright (C): OpenGate Collaboration
+   This software is distributed under the terms
+   of the GNU Lesser General  Public Licence (LGPL)
+   See LICENSE.md for further details
+   -------------------------------------------------- */
+
+#include "GateSPSAngDistribution.h"
+#include "GateHelpers.h"
+
+G4ThreeVector GateSPSAngDistribution::VGenerateOne() {
+  // return GenerateOne();
+  auto direction = GenerateOne();
+  if (fDirectionRelativeToAttachedVolume) {
+    direction = direction / direction.mag();
+    direction = fGlobalRotation * direction;
+  }
+  return direction;
+}

core/opengate_core/opengate_lib/GateSPSAngDistribution.h

@@ -0,0 +1,30 @@
+/* --------------------------------------------------
+   Copyright (C): OpenGATE Collaboration
+   This software is distributed under the terms
+   of the GNU Lesser General  Public Licence (LGPL)
+   See LICENSE.md for further details
+   -------------------------------------------------- */
+
+#ifndef GateSPSAngDistribution_h
+#define GateSPSAngDistribution_h
+
+#include "G4ParticleDefinition.hh"
+#include "G4SPSAngDistribution.hh"
+
+class GateSPSAngDistribution : public G4SPSAngDistribution {
+
+public:
+  virtual ~GateSPSAngDistribution() = default;
+
+  // Cannot inherit from GenerateOne, so we consider VGenerateOne instead
+  virtual G4ThreeVector VGenerateOne();
+
+  // Store the global orientation that may be applied to the direction
+  // in the GenerateOne function.
+  // (Must be updated each run)
+  bool fDirectionRelativeToAttachedVolume;
+  G4ThreeVector fGlobalTranslation;
+  G4RotationMatrix fGlobalRotation;
+};
+
+#endif // GateSPSAngDistribution_h

core/opengate_core/opengate_lib/GateSingleParticleSource.cpp

@@ -10,13 +10,12 @@
 #include "G4PrimaryVertex.hh"
 #include "G4RunManager.hh"
 #include "GateHelpers.h"
-
 #include "GateRandomMultiGauss.h"
 
 GateSingleParticleSource::GateSingleParticleSource(
     std::string /*mother_volume*/) {
   fPositionGenerator = new GateSPSPosDistribution();
-  fDirectionGenerator = new G4SPSAngDistribution();
+  fDirectionGenerator = new GateSPSAngDistribution();
   fEnergyGenerator = new GateSPSEneDistribution();
 
   // needed
@@ -64,7 +63,8 @@ GateSingleParticleSource::GenerateDirectionWithAA(const G4ThreeVector &position,
   fAAManager->StartAcceptLoop();
   while (!accept_angle) {
     // direction
-    direction = fDirectionGenerator->GenerateOne();
+    direction = fDirectionGenerator->VGenerateOne();
+
     // accept ?
     accept_angle = fAAManager->TestIfAccept(position, direction);
     if (!accept_angle && fAAManager->GetPolicy() ==

core/opengate_core/opengate_lib/GateSingleParticleSource.h

@@ -10,16 +10,15 @@
 
 #include "G4AffineTransform.hh"
 #include "G4ParticleDefinition.hh"
-#include "G4SPSAngDistribution.hh"
 #include "G4VPrimaryGenerator.hh"
 #include "GateAcceptanceAngleTester.h"
 #include "GateAcceptanceAngleTesterManager.h"
 #include "GateHelpers.h"
+#include "GateRandomMultiGauss.h"
+#include "GateSPSAngDistribution.h"
 #include "GateSPSEneDistribution.h"
 #include "GateSPSPosDistribution.h"
 
-#include "GateRandomMultiGauss.h"
-
 /*
     Single Particle Source generator.
     We need to re-implement the one from G4 in order to
@@ -37,7 +36,7 @@ class GateSingleParticleSource : public G4VPrimaryGenerator {
 
   GateSPSPosDistribution *GetPosDist() { return fPositionGenerator; }
 
-  G4SPSAngDistribution *GetAngDist() { return fDirectionGenerator; }
+  GateSPSAngDistribution *GetAngDist() { return fDirectionGenerator; }
 
   GateSPSEneDistribution *GetEneDist() { return fEnergyGenerator; }
 
@@ -62,7 +61,7 @@ class GateSingleParticleSource : public G4VPrimaryGenerator {
   double fCharge;
   double fMass;
   GateSPSPosDistribution *fPositionGenerator;
-  G4SPSAngDistribution *fDirectionGenerator;
+  GateSPSAngDistribution *fDirectionGenerator;
   GateSPSEneDistribution *fEnergyGenerator;
   G4SPSRandomGenerator *fBiasRndm;
   bool fAccolinearityFlag;