Several small generic bug fixes and one typo fix in GatePositroniumSource settings

docs/source_and_particle_management.rst

@@ -822,7 +822,7 @@ Required commands
 ``/gate/source/NAME/setPositroniumLifetimes t1 t2 ... tn unit``
    Lifetime of each component. The last token is a Geant4 time unit such as ``ns``.
 
-``/gate/source/NAME/setPromptPhotonProbabilites p1 p2 ... pn``
+``/gate/source/NAME/setPromptPhotonProbabilities p1 p2 ... pn``
    Probability of prompt-gamma emission for each component. Values are restricted to the ``[0, 1]`` range by the messenger.
 
 ``/gate/source/NAME/setPromptPhotonEnergies e1 e2 ... en unit``
@@ -855,7 +855,7 @@ Optional commands
 
 .. note::
 
-   The current implementation requires both ``setPromptPhotonProbabilites`` and ``setPromptPhotonEnergies`` even when the prompt-gamma probability is zero for all components. A common convention is to set the corresponding energies to ``0``.
+   The current implementation requires both ``setPromptPhotonProbabilities`` and ``setPromptPhotonEnergies`` even when the prompt-gamma probability is zero for all components. A common convention is to set the corresponding energies to ``0``.
 
 Event timing and generated vertices
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -958,7 +958,7 @@ The example below defines a two-component source with explicit 2-gamma and 3-gam
    /gate/source/psSource/setPositroniumLifetimes 0.125 142.0 ns
    /gate/source/psSource/setDecayKinds k2Gamma k3Gamma
    /gate/source/psSource/setPositronInteractions kParaPs kOrthoPs
-   /gate/source/psSource/setPromptPhotonProbabilites 1.0 1.0
+   /gate/source/psSource/setPromptPhotonProbabilities 1.0 1.0
    /gate/source/psSource/setPromptPhotonEnergies 1.274 1.274 MeV
    /gate/source/psSource/setElectronCaptureProbabilities 0.0 0.0
    /gate/source/psSource/setMeanPositronRange 0.2 0.2 mm

source/digits_hits/src/GateDigitizerInitializationModule.cc

@@ -135,14 +135,15 @@ void GateDigitizerInitializationModule::Digitize()
 
     		  //-------------------------------------------------
 
+    		    // An empty volume name only means that the output module in use did not
+    		    // fill it, so it is replaced by the "NULL" placeholder. It tells nothing
+    		    // about the source of the event, hence sourceID is left untouched.
     		    if ((*inHC)[i]->GetComptonVolumeName().empty()) {
     		      Digi->SetComptonVolumeName( "NULL" );
-    		      Digi->SetSourceID( -1 );
     		    }
 
     		    if ((*inHC)[i]->GetRayleighVolumeName().empty()) {
     		      Digi->SetRayleighVolumeName( "NULL" );
-    		      Digi->SetSourceID( -1 );
     		    }
 
     		/* //  if (nVerboseLevel>1)

source/digits_hits/src/GateHit.cc

@@ -27,6 +27,7 @@ GateHit::GateHit()
   m_PDGEncoding(0),
   m_trackID(0),
   m_parentID(0),
+  m_sourceID(-1),
   m_systemID(-1),
   m_sourceEnergy(-1),
   m_sourcePDG(0),

source/digits_hits/src/GateHitConvertor.cc

@@ -179,14 +179,15 @@ void GateHitConvertor::ProcessOneHit(const GateHit* hit,GatePulseList* pulseList
 
 
 
+  // An empty volume name only means that the output module in use did not fill it,
+  // so it is replaced by the "NULL" placeholder. It tells nothing about the source
+  // of the event, hence sourceID is left untouched.
   if (hit->GetComptonVolumeName().empty()) {
     pulse->SetComptonVolumeName( "NULL" );
-    pulse->SetSourceID( -1 );
   }
 
   if (hit->GetRayleighVolumeName().empty()) {
     pulse->SetRayleighVolumeName( "NULL" );
-    pulse->SetSourceID( -1 );
   }
 
   if (nVerboseLevel>1)

source/digits_hits/src/GateMultiPhotonAnalysis.cc

@@ -226,6 +226,20 @@ void RunDigitizersIfNeeded() {
   }
 }
 
+//! Runs the digitizer chain when the enclosing scope is left, whichever path is taken.
+//! GateAnalysis calls the digitizer outside of its "no trajectory container" branch, so
+//! whether Singles and Coincidences are produced for an event does not depend on the
+//! analysis being able to process that event. The guard gives the same guarantee here,
+//! where the event is abandoned in more than one place.
+class ScopedDigitizerRunner {
+ public:
+  ScopedDigitizerRunner() = default;
+  ~ScopedDigitizerRunner() { RunDigitizersIfNeeded(); }
+
+  ScopedDigitizerRunner(const ScopedDigitizerRunner &) = delete;
+  ScopedDigitizerRunner &operator=(const ScopedDigitizerRunner &) = delete;
+};
+
 }  // namespace
 
 GateMultiPhotonAnalysis::GateMultiPhotonAnalysis(const G4String &name, GateOutputMgr *outputMgr, DigiMode digiMode)
@@ -312,6 +326,18 @@ void GateMultiPhotonAnalysis::RecordEndOfEvent(const G4Event *event) {
     return;
   }
 
+  // From here on the event is digitized whatever happens to the analysis itself.
+  ScopedDigitizerRunner digitizerRunner;
+
+  // An event without any primary vertex carries no track, hence no hit and no trajectory
+  // container. GateSourceMgr stops generating vertices once the time limit of the run is
+  // reached, so the last event of every run looks exactly like this. There is nothing to
+  // analyse and nothing anomalous about it, so it is skipped quietly instead of being
+  // reported as a missing trajectory container.
+  if (event->GetNumberOfPrimaryVertex() == 0) {
+    return;
+  }
+
   std::vector<GateHitsCollection *> CHC_vector = GetOutputMgr()->GetHitCollections();
   GatePhantomHitsCollection *PHC = GetOutputMgr()->GetPhantomHitCollection();
 
@@ -375,8 +401,6 @@ void GateMultiPhotonAnalysis::RecordEndOfEvent(const G4Event *event) {
         m_trajectoryNavigator);
     ProcessTimeline(&timeline, m_trajectoryNavigator, context, legacyPhotonIDPolicy);
   }
-
-  RunDigitizersIfNeeded();
 }
 
 void GateMultiPhotonAnalysis::RecordStepWithVolume(const GateVVolume *, const G4Step *) {

source/digits_hits/src/GateToRoot.cc

@@ -628,9 +628,17 @@ void GateToRoot::RecordEndOfAcquisition() {
 
        // m_hfile = m_treeHit->GetCurrentFile();
 
-    	// Get file only for the 1st tree as it is the same file for all trees
-    	m_hfile = m_treesHit[0]->GetCurrentFile();
+    	// Get file only for the 1st tree as it is the same file for all trees.
+    	// The vector may be empty here: RecordEndOfRun() drops the trees (it saves the
+    	// current file beforehand) and a setup without any sensitive detector never fills
+    	// it. In both cases m_hfile already points to the file to be written.
+    	if (!m_treesHit.empty() && m_treesHit[0])
+    		m_hfile = m_treesHit[0]->GetCurrentFile();
 
+        if (!m_hfile) {
+            G4cerr << "GateToRoot::RecordEndOfAcquisition(): no ROOT file to write !\n";
+            return;
+        }
 
         if (nVerboseLevel > 0)
             G4cout << "GateToRoot: ROOT: files writing...\n";
@@ -686,6 +694,12 @@ void GateToRoot::RecordEndOfRun(const G4Run *) {
 
     nbPrimaries -= 1.; // Number of primaries increase too much at each end of run !
 
+    // ROOT may have switched to another file while the run was written (files are split
+    // above 1.9 GBytes), so remember where the trees actually live before dropping them -
+    // RecordEndOfAcquisition() has no tree left to ask.
+    if (!m_treesHit.empty() && m_treesHit[0])
+        m_hfile = m_treesHit[0]->GetCurrentFile();
+
     m_hitBuffers.clear();
     m_treesHit.clear();
 }

source/physics/include/GatePositroniumSourceMessenger.hh

@@ -49,7 +49,7 @@ class GatePositroniumSourceMessenger: public GateVSourceMessenger
 
   std::unique_ptr<G4UIcmdWithAString> upCmdSetPositroniumFractions;
   std::unique_ptr<G4UIcmdWithAString> upCmdSetPositroniumLifetimes;
-  std::unique_ptr<G4UIcmdWithAString> upCmdSetPromptPhotonProbabilites;
+  std::unique_ptr<G4UIcmdWithAString> upCmdSetPromptPhotonProbabilities;
   std::unique_ptr<G4UIcmdWithAString> upCmdSetPromptPhotonEnergies;
   std::unique_ptr<G4UIcmdWithAString> upCmdSetElectronCaptureProbabilities;
   std::unique_ptr<G4UIcmdWithAString> upCmdSetDecayKinds;

source/physics/src/GatePositroniumDecayParamsGenerator.cc

@@ -122,7 +122,7 @@ void GatePositroniumDecayParamsGenerator::validatePositroniumDecayParams(const P
     GateError(
         "GatePositroniumDecayParamsGenerator::generatePositroniumDecayParams: "
         "number of provided parameters in Fractions, PromptGamma, Lifetimes, "
-        "Gamma Energies, Electron Capture Probabilites are not the same");
+        "Gamma Energies, Electron Capture Probabilities are not the same");
   }
   if (params.fPositronInteractions.empty())
     GateWarning("PositroniumSource: setPositronInteractions was not called. "

source/physics/src/GatePositroniumSourceMessenger.cc

@@ -79,7 +79,7 @@ void GatePositroniumSourceMessenger::InitCommands()
  upCmdSetPositroniumLifetimes.reset(GetStringCmd( "setPositroniumLifetimes", "\"t1, t2, t3 .., tn t_unit\" - where ti corresponds to lifetime constants and t_unit is one of the Geant4 time units e.g. ns" ) );
  upCmdSetDecayKinds.reset(GetStringCmd( "setDecayKinds", "\"k1, k2, k3 .., kn\" - where ki is k2Gamma or k3Gamma" ) );
  upCmdSetPositronInteractions.reset(GetStringCmd( "setPositronInteractions", "\"k1, k2, k3 .., kn\" - where ki is kParaPs, kDirect or kOrthoPs, of a given element in vector of components. Used to properly recalculate intensities of the components from the theory" ) );
- upCmdSetPromptPhotonProbabilites.reset(GetStringCmd( "setPromptPhotonProbabilites", "\"f1, f2, f3 .., fn\" - where fi in [0.0, 1.0] " ) );
+ upCmdSetPromptPhotonProbabilities.reset(GetStringCmd( "setPromptPhotonProbabilities", "\"f1, f2, f3 .., fn\" - where fi in [0.0, 1.0] " ) );
  upCmdSetPromptPhotonEnergies.reset(GetStringCmd( "setPromptPhotonEnergies", "\"e1, e2, e3 .., en e_unit\" - where ei are energies and e_unit is one of the Geant4 energy units e.g. MeV" ) );
  upCmdSetMeanPositronRange.reset(GetStringCmd( "setMeanPositronRange", "\"r1, r2, r3 .., rn r_unit\" - where ri are mean positron range and r_unit is one of the Geant 4 distance units e.g. mm " ) );
  upCmdSetElectronCaptureProbabilities.reset(GetStringCmd( "setElectronCaptureProbabilities", "\"f1, f2, f3 .., fn\" - where fi in [0.0, 1.0] " ) );
@@ -123,7 +123,7 @@ void GatePositroniumSourceMessenger::SetNewValue(G4UIcommand *command, G4String
   } else if (command == upCmdSetPositroniumLifetimes.get()) {
     auto lifetimes = parseListOfParamsWithUnit(new_value);
     fParamGenerator.SetPositroniumLifetimes(lifetimes);
-  } else if (command == upCmdSetPromptPhotonProbabilites.get()) {
+  } else if (command == upCmdSetPromptPhotonProbabilities.get()) {
     std::vector<float> promptPhotonProb;
     std::stringstream ss(new_value);
     float prob;