Merge branch 'develop' into develop

arifoley · Aug 22, 2017 · 5142cbf · 5142cbf
2 parents c308142 + 34b51e2
commit 5142cbf
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Showing 17 changed files with 671 additions and 809 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -234,7 +234,7 @@ ENDIF()
 #=========================================================
 # Add the executable, and link it to the Geant4/ROOT/CLHEP/ITK libraries
 IF(GATE_USE_GPU AND CUDA_FOUND)
-  SET(CUDA_NVCC_FLAGS "-gencode arch=compute_20,code=sm_20;-gencode arch=compute_21,code=sm_21;-gencode arch=compute_30,code=sm_30;-gencode arch=compute_32,code=sm_32;-gencode arch=compute_35,code=sm_35;-gencode arch=compute_37,code=sm_37;-gencode arch=compute_50,code=sm_50;-gencode arch=compute_52,code=sm_52;-gencode arch=compute_53,code=sm_53;-gencode arch=compute_60,code=sm_60;-gencode arch=compute_61,code=sm_61;-use_fast_math;-w;--ptxas-options=-v")
+  SET(CUDA_NVCC_FLAGS "-gencode arch=compute_20,code=sm_20;-gencode arch=compute_20,code=sm_21;-gencode arch=compute_30,code=sm_30;-gencode arch=compute_32,code=sm_32;-gencode arch=compute_35,code=sm_35;-gencode arch=compute_37,code=sm_37;-gencode arch=compute_50,code=sm_50;-gencode arch=compute_52,code=sm_52;-gencode arch=compute_53,code=sm_53;-gencode arch=compute_60,code=sm_60;-gencode arch=compute_61,code=sm_61;-use_fast_math;-w;--ptxas-options=-v")
   CUDA_ADD_EXECUTABLE(Gate Gate.cc ${sources} ${sourcesGPU} ${headers})
 ELSE(GATE_USE_GPU AND CUDA_FOUND)
   ADD_EXECUTABLE(Gate Gate.cc ${sources} ${headers})

diff --git a/cluster_tools/jobsplitter/src/GateMacfileParser.cc b/cluster_tools/jobsplitter/src/GateMacfileParser.cc
@@ -226,7 +226,7 @@ void GateMacfileParser::InsertAliases()
 	nAliases = (G4int)(listOfAliases.size());
 	for (G4int i=1;i<nAliases;i+=2)
 	{
-		if (macline.contains("{"+listOfAliases[i]+"}"))
+		while (macline.contains("{"+aliases[i]+"}"))
 		{
 			insert=listOfAliases[i-1];
 			G4int position=macline.find("{"+listOfAliases[i]+"}",0);

diff --git a/source/digits_hits/include/GateDoseActor.hh b/source/digits_hits/include/GateDoseActor.hh
@@ -1,22 +1,22 @@
 /*----------------------
-   Copyright (C): OpenGATE Collaboration
+  Copyright (C): OpenGATE Collaboration
 
-This software is distributed under the terms
-of the GNU Lesser General  Public Licence (LGPL)
-See GATE/LICENSE.txt for further details
-----------------------*/
+  This software is distributed under the terms
+  of the GNU Lesser General  Public Licence (LGPL)
+  See GATE/LICENSE.txt for further details
+  ----------------------*/
 
 
 /*!
   \class  GateDoseActor
   \author thibault.frisson@creatis.insa-lyon.fr
-          laurent.guigues@creatis.insa-lyon.fr
-          david.sarrut@creatis.insa-lyon.fr
+  laurent.guigues@creatis.insa-lyon.fr
+  david.sarrut@creatis.insa-lyon.fr
   \date	March 2011
 
-	  - DoseToWater option added by Loïc Grevillot
-	  - Dose calculation in inhomogeneous volume added by Thomas Deschler (thomas.deschler@iphc.cnrs.fr)
- */
+  - DoseToWater option added by Loïc Grevillot
+  - Dose calculation in inhomogeneous volume added by Thomas Deschler (thomas.deschler@iphc.cnrs.fr)
+*/
 
 
 #ifndef GATEDOSEACTOR_HH
@@ -30,12 +30,13 @@ See GATE/LICENSE.txt for further details
 #include "GateDoseActorMessenger.hh"
 #include "GateImageWithStatistic.hh"
 #include "GateVoxelizedMass.hh"
+#include "GateRegionDoseStat.hh"
 
 class G4EmCalculator;
 
 class GateDoseActor : public GateVImageActor
 {
- public:
+public:
 
   //-----------------------------------------------------------------------------
   // Actor name
@@ -67,6 +68,11 @@ class GateDoseActor : public GateVImageActor
   void VolumeFilter(G4String b) { mVolumeFilter = b; }
   void MaterialFilter(G4String b) { mMaterialFilter = b; }
 
+  void SetDoseByRegionsInputFilename(std::string f);
+  void SetDoseByRegionsOutputFilename(std::string f);
+
+  void SetOutputScalingFactor(double s);
+
   virtual void BeginOfRunAction(const G4Run*r);
   virtual void BeginOfEventAction(const G4Event * event);
 
@@ -104,13 +110,17 @@ protected:
   bool mIsDoseNormalisationEnabled;
   bool mIsDoseToWaterNormalisationEnabled;
   bool mDose2WaterWarningFlag;
+  bool mDoseByRegionsFlag;
 
   GateImageWithStatistic mEdepImage;
   GateImageWithStatistic mDoseImage;
   GateImageWithStatistic mDoseToWaterImage;
   GateImageInt mNumberOfHitsImage;
   GateImageInt mLastHitEventImage;
   GateImageDouble mMassImage;
+  GateImageFloat mDoseByRegionsLabelImage;
+  std::map<int, GateRegionDoseStat> mMapOfRegionStat;
+  double mScalingFactor;
 
   G4String mEdepFilename;
   G4String mDoseFilename;
@@ -119,6 +129,8 @@ protected:
   G4String mDoseAlgorithmType;
   G4String mImportMassImage;
   G4String mExportMassImage;
+  G4String mDoseByRegionsInputFilename;
+  G4String mDoseByRegionsOutputFilename;
 
   G4String mVolumeFilter;
   G4String mMaterialFilter;

diff --git a/source/digits_hits/include/GateDoseActorMessenger.hh b/source/digits_hits/include/GateDoseActorMessenger.hh
@@ -1,23 +1,27 @@
 /*----------------------
-   Copyright (C): OpenGATE Collaboration
+  Copyright (C): OpenGATE Collaboration
 
-This software is distributed under the terms
-of the GNU Lesser General  Public Licence (LGPL)
-See GATE/LICENSE.txt for further details
-----------------------*/
+  This software is distributed under the terms
+  of the GNU Lesser General  Public Licence (LGPL)
+  See GATE/LICENSE.txt for further details
+  ----------------------*/
 
 /*
   \class  GateDoseActorMessenger
   \author thibault.frisson@creatis.insa-lyon.fr
-          laurent.guigues@creatis.insa-lyon.fr
-          david.sarrut@creatis.insa-lyon.fr
+  laurent.guigues@creatis.insa-lyon.fr
+  david.sarrut@creatis.insa-lyon.fr
 */
 
 #ifndef GATEDOSEACTORMESSENGER_HH
 #define GATEDOSEACTORMESSENGER_HH
 
+// g4
 #include "G4UIcmdWithABool.hh"
 #include "G4UIcmdWithAString.hh"
+#include "G4UIcmdWithADouble.hh"
+
+// gate
 #include "GateImageActorMessenger.hh"
 
 class GateDoseActor;
@@ -52,6 +56,11 @@ protected:
 
   G4UIcmdWithAString * pVolumeFilterCmd;
   G4UIcmdWithAString * pMaterialFilterCmd;
+
+  G4UIcmdWithAString * pDoseRegionInputCmd;
+  G4UIcmdWithAString * pDoseRegionOutputCmd;
+
+  G4UIcmdWithADouble * pScaleOutputCmd;
 };
 
 #endif /* end #define GATEDOSEACTORMESSENGER_HH*/
diff --git a/source/digits_hits/include/GateRegionDoseStat.hh b/source/digits_hits/include/GateRegionDoseStat.hh
@@ -0,0 +1,40 @@
+/*----------------------
+  Copyright (C): OpenGATE Collaboration
+
+  This software is distributed under the terms
+  of the GNU Lesser General  Public Licence (LGPL)
+  See GATE/LICENSE.txt for further details
+  ----------------------*/
+
+#ifndef GATEREGIONDOSESTAT_HH
+#define GATEREGIONDOSESTAT_HH
+
+#include "GateMiscFunctions.hh"
+#include "GateImage.hh"
+
+//-----------------------------------------------------------------------------
+class GateRegionDoseStat {
+
+public:
+
+  GateRegionDoseStat();
+  std::string ToString();
+  void Update(long event_id, double edep, double density);
+
+  static void ComputeRegionVolumes(GateImageFloat & image,
+                                   std::map<int, GateRegionDoseStat> & mMapOfRegionStat);
+
+  double sum_edep;
+  double sum_squared_edep;
+  double sum_temp_edep;
+  double sum_dose;
+  double sum_squared_dose;
+  double sum_temp_dose;
+  double volume;
+  long last_event_id;
+  long nb_hits;
+  long nb_event_hits;
+};
+//-----------------------------------------------------------------------------
+
+#endif /* end #define GATEREGIONDOSESTAT_HH */