Gate9.4.2

.github/workflows/main.yml

@@ -23,9 +23,9 @@ jobs:
             options: torch
 
     env:
-      ROOT_VERSION: 'v6-32-02'
+      ROOT_VERSION: 'v6-32-04'
       ITK_VERSION: 'v5.4.2'
-      GEANT4_VERSION: 'v11.3.0'
+      GEANT4_VERSION: 'v11.4.0'
       ROOT_DIR: $(HOME)/software/root
       GEANT4_DIR: $(HOME)/software/geant4
 
@@ -41,8 +41,8 @@ jobs:
       uses: actions/cache@v3
       with:
         path: ~/software
-        key: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-build1
-        restore-keys: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-build1
+        key: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-qt6-build0
+        restore-keys: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-qt6-build0
     - name: Install dependencies
       run: |
         if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
@@ -56,32 +56,51 @@ jobs:
                                   libxpm-dev \
                                   libxft-dev \
                                   libxext-dev \
-                                  qtbase5-dev \
-                                  qt5-qmake \
+                                  qt6-base-dev \
+                                  qt6-base-dev-tools \
+                                  qt6-tools-dev \
+                                  qt6-tools-dev-tools \
                                   git \
                                   cmake \
                                   libssl-dev \
                                   python3.8-dev \
                                   ccache \
                                   libfftw3-dev
           gcc -v
-        elif [ "${{ matrix.os }}" == "macos-latest" ]; then
+        elif [ "${{ matrix.os }}" == "macos-latest" ]; then          
+          brew update || true
           brew install python@3.12 || true
-          brew link --overwrite python@3.12
+
+          brew link --overwrite --force python@3.12
           #brew update
-          brew cleanup
-          brew config
+          #brew cleanup
+          #brew config
           #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-config /usr/local/bin/2to3 /usr/local/bin/idle3 /usr/local/bin/pydoc3 /usr/local/bin/python3
-          brew install --force --verbose --overwrite --debug qt5 \
+          brew install --force --verbose --overwrite --debug qt \
                                                              ccache \
                                                              tbb \
                                                              xrootd \
                                                              fftw
-          brew link qt5 --force && sudo ln -s /usr/local/opt/qt/mkspecs /usr/local/mkspecs && sudo ln -s /usr/local/opt/qt/plugins /usr/local/plugins
-          export PATH=/usr/local/opt/qt/bin:$PATH
-          export LDFLAGS="-L/usr/local/opt/qt/lib -L/usr/local/opt/llvm/lib"
-          export CPPFLAGS="-I/usr/local/opt/qt/include -I/usr/local/opt/llvm/include -fopenmp"
+          #brew link qt --force && sudo ln -s /usr/local/opt/qt/mkspecs /usr/local/mkspecs && sudo ln -s /usr/local/opt/qt/plugins /usr/local/plugins
+          brew cleanup
+          #export PATH=/usr/local/opt/qt/bin:$PATH
+          #export LDFLAGS="-L/usr/local/opt/qt/lib -L/usr/local/opt/llvm/lib"
+          #export CPPFLAGS="-I/usr/local/opt/qt/include -I/usr/local/opt/llvm/include -fopenmp"
+
+          export Qt6_DIR="$(brew --prefix qt)/lib/cmake/Qt6"
+          export CMAKE_PREFIX_PATH="$(brew --prefix qt):$CMAKE_PREFIX_PATH"
+          export Qt6_DIR="$(brew --prefix qt)/lib/cmake/Qt6"
+
+          QT_PREFIX="$(brew --prefix qt)"
+
+          LLVM_PREFIX="$(brew --prefix llvm || true)"
+          export LDFLAGS="-L$QT_PREFIX/lib ${LLVM_PREFIX:+-L$LLVM_PREFIX/lib}"
+          export CPPFLAGS="-I$QT_PREFIX/include ${LLVM_PREFIX:+-I$LLVM_PREFIX/include}"
+
+          cmake --version
+          which cmake
+
         fi
         cd $HOME/
         mkdir -p software option_dependencies
@@ -92,16 +111,39 @@ jobs:
           cd $HOME/software
           mkdir root
           cd root
-          mkdir src bin install
+          mkdir -p src bin install
           git clone  --branch $ROOT_VERSION https://github.com/root-project/root.git --depth 1 src
+          rm -rf bin
+          mkdir -p bin
           cd bin
           cmake ../src -DCMAKE_CXX_STANDARD=17 \
                        -Dpython=OFF \
                        -Dpyroot=OFF \
                        -Dclad=OFF \
                        -Dxrootd=OFF \
+                       -Dinterpreter=OFF \
+                       -Dvdt=OFF \
+                       -Dbuiltin_vdt=OFF \
+                       -Dqt6=OFF \
+                       -Dqt5=OFF \
+                       -Dbuiltin_cling=OFF \
+                       -Dcxxmodules=OFF \
+                       -Droot7=OFF \
+                       -Dcling=OFF \
+                       -Dllvm=OFF \
+                       -Dwebgui=OFF \
+                       -Dx11=OFF \
+                       -Droofit=OFF \
+                       -Dtmva=OFF \
+                       -DCMAKE_PREFIX_PATH="$CMAKE_PREFIX_PATH" \
                        -DCMAKE_INSTALL_PREFIX=$HOME/software/root/install
-          make -j4 install
+          #grep -i vdt CMakeCache.txt || true
+          make -j4 install VERBOSE=1
+          #echo "===== VDT CONFIGURE STDOUT ====="
+          #cat /Users/runner/software/root/bin/VDT-prefix/src/VDT-stamp/VDT-configure-out.log || true
+          #echo "===== VDT CONFIGURE STDERR ====="
+          #cat /Users/runner/software/root/bin/VDT-prefix/src/VDT-stamp/VDT-configure-err.log || true
+          #exit 1
           cd ..
           rm -rf bin src
         fi
@@ -116,8 +158,10 @@ jobs:
           cd bin
           cmake -DGEANT4_INSTALL_DATA=ON \
                 -DGEANT4_BUILD_MULTITHREADED=OFF \
+                -DGEANT4_USE_QT=ON \
                 -DGEANT4_INSTALL_DATADIR=$HOME/software/geant4/data \
                 -DCMAKE_INSTALL_PREFIX=$HOME/software/geant4/install \
+                -DQt6_DIR="$Qt6_DIR" \
                 ../src
           make -j4 install
           cd ..

CMakeLists.txt

@@ -98,8 +98,8 @@ STRING(REGEX REPLACE "(.*)[.](.*)[.](.*)" "\\3" G4VERSION_PATCH ${Geant4_VERSION
 #MESSAGE(${G4VERSION_MAJOR})
 #MESSAGE(${G4VERSION_MINOR})
 #MESSAGE(${G4VERSION_PATCH})
-IF(NOT ${G4VERSION_MAJOR}.${G4VERSION_MINOR} EQUAL 11.3)
-  MESSAGE("Warning! This GATE version is not validated for Geant4 ${G4VERSION_MAJOR}.${G4VERSION_MINOR} distribution. Please use Geant4 11.3 distribution instead.")
+IF(NOT ${G4VERSION_MAJOR}.${G4VERSION_MINOR} EQUAL 11.4.0)
+  MESSAGE("Warning! This GATE version is not validated for Geant4 ${G4VERSION_MAJOR}.${G4VERSION_MINOR} distribution. Please use Geant4 11.4.0 distribution instead.")
 ENDIF()
 
 #=========================================================
@@ -312,13 +312,13 @@ MESSAGE("Your current Geant4 version is ${Geant4_VERSION}")
 
 #=========================================================
 # Display message about this version
-MESSAGE("IMPORTANT! This version of GATE (9.4.1) has still some traces of passage for new digitizer.")
+MESSAGE("IMPORTANT! This version of GATE (9.4.2) has still some traces of passage for new digitizer.")
 MESSAGE("Please, be aware that some of functionalities are NOT YET re-implemented: ")
 MESSAGE("- Output: Sinogram, Ecat7, LMF")
 MESSAGE("- ARF may work not properly yet")
 MESSAGE("We apologize for this inconvenience and kindly ask for your patience.")
 MESSAGE("This functionalities will be added during 2025.")
-MESSAGE("Meanwhile, please, use Gate 9.4")
+MESSAGE("Meanwhile, please, use Gate 9.2")
 
 
 

Gate.cc

@@ -158,7 +158,7 @@ void welcome()
 {
   GateMessage("Core", 0, G4endl);
   GateMessage("Core", 0, "*******************************************************" << G4endl);
-  GateMessage("Core", 0, " GATE version 9.4.1 (2025)" << G4endl);
+  GateMessage("Core", 0, " GATE version 9.4.2 (2026)" << G4endl);
   GateMessage("Core", 0, " Copyright : OpenGATE Collaboration" << G4endl);
   GateMessage("Core", 0, " Reference : Phys. Med. Biol. 49(19) 4543-4561     2004 " << G4endl);
   GateMessage("Core", 0, " Reference : Phys. Med. Biol. 56(4)  881-901       2011 " << G4endl);
@@ -256,7 +256,7 @@ int main( int argc, char* argv[] )
           break;
         case 'v':
           ss << G4VERSION_MAJOR << "." << G4VERSION_MINOR << "." << G4VERSION_PATCH;
-          std::cout << "Gate version is 9.4.1; Geant4 version is " << ss.str() << std::endl;
+          std::cout << "Gate version is 9.4.2; Geant4 version is " << ss.str() << std::endl;
           exit(0);
           break;
         case 'a':

cluster_tools/jobsplitter/src/GateMacfileParser.cc

@@ -107,8 +107,7 @@ G4int GateMacfileParser::GenerateResolvedMacros(G4String directory)
 		i_str<<j;
 		GenerateResolvedMacro(dir+macNameDir+i_str.str()+".mac",j,splitfile); 
 		splitfile<<endl;  
-
-		if(j%(nSplits/10)==0)
+		if(nSplits>=10 && j%(nSplits/10)==0)
 			cout<<100*j/nSplits<<"% "<<flush;
 	}
 	if (filenames[ROOT]==1)
@@ -202,8 +201,11 @@ G4int GateMacfileParser::GenerateResolvedMacro(G4String outputName,G4int splitNu
 		// Actor check
 		G4cout << "Number of enabled actors: " << listOfEnabledActorName.size() << endl;
 		// Check if no output nor actor
+
+
 		if (enabledOutput+listOfEnabledActorName.size()==0) G4cerr << "***** Warning: No output module nor actor are enabled !" << endl;
 		// Check if all aliases from the command line are used
+
 		bool flag=true;
 		nAliases = (G4int)listOfUsedAliases.size();
 		for (G4int i=1;i<nAliases;i+=2) flag&=listOfUsedAliases[i];
@@ -214,7 +216,9 @@ G4int GateMacfileParser::GenerateResolvedMacro(G4String outputName,G4int splitNu
 				if(!listOfUsedAliases[i]) G4cout<<" "<<listOfAliases[i]<<G4endl;
 			return 1; 
 		}
+
 	}
+
 	macfile.close();
 	outputMacfile.close();
 	return 0;
@@ -546,7 +550,6 @@ void GateMacfileParser::DealWithTimeCommands(ofstream& output,G4int splitNumber,
 		// so all output should be defined
 		if(splitNumber==1) CheckOutputPrint();
 		CheckOutput(output,splitfile,splitNumber);
-
 		// ==============================================================================================================
 		// This part is here to check the presence of time commands and to deal with fu*** default
 		// values permitted ... And default values always give very nice part of code, hummmmm.

readme.md

@@ -15,7 +15,7 @@ More details : http://www.opengatecollaboration.org
 
 Documentation : https://opengate.readthedocs.io
 
-* The stable version is tag 9.4.1: https://github.com/OpenGATE/Gate/tree/v9.4.1 with Geant4 11.3.0
+* The stable version is tag 9.4.2: https://github.com/OpenGATE/Gate/tree/v9.4.2 with Geant4 11.4.0
 * The current development version is branch 'develop' (default): http://github.com/OpenGATE/Gate/tree/develop
 * [Benchmarks](https://github.com/OpenGATE/GateBenchmarks)
 * [Examples](https://github.com/OpenGATE/GateContrib)

source/digits_hits/src/GateClustering.cc

@@ -121,11 +121,11 @@ void GateClustering::Digitize()
 		          G4cout << Gateendl;
 		      }
 
-		      GateDigi* m_outputDigi = new GateDigi(*inputDigi);
-		          m_outputDigi->SetEnergyFin(-1);
-		          m_outputDigi->SetEnergyIniTrack(-1);
-		          std::vector<double> dist;
-		          std::vector<int> index4ClustSameVol;
+		      m_outputDigi = new GateDigi(*inputDigi);
+		      m_outputDigi->SetEnergyFin(-1);
+		      m_outputDigi->SetEnergyIniTrack(-1);
+		      std::vector<double> dist;
+		      std::vector<int> index4ClustSameVol;
 
 		          if(OutputDigiCollectionVector->empty()){
 		        	  m_OutputDigiCollection->insert(m_outputDigi);

source/digits_hits/src/GateDoIModels.cc

@@ -117,7 +117,7 @@ void GateDoIModels::Digitize()
 		   	   return;
 		   	}
 
-		   GateDigi* m_outputDigi = new GateDigi(*inputDigi);
+		   m_outputDigi = new GateDigi(*inputDigi);
 
 		   if (flgCorrectAxis==1)
 		   {

source/digits_hits/src/GateEnergyFraming.cc

@@ -93,7 +93,7 @@ void GateEnergyFraming::Digitize()
 		  {
 	  	      G4double energy = 0;
 		      inputDigi=(*IDC)[i];
-		      GateDigi* m_outputDigi = new GateDigi(*inputDigi);
+		      m_outputDigi = new GateDigi(*inputDigi);
 
 		      if( m_EnergyFramingLaw != 0 ){
 

source/digits_hits/src/GateTimeDelay.cc

@@ -76,7 +76,7 @@ void GateTimeDelay::Digitize()
 	  {
 		  inputDigi=(*IDC)[i];
 
-		  GateDigi* m_outputDigi = new GateDigi(*inputDigi);
+		  m_outputDigi = new GateDigi(*inputDigi);
 
 		  m_outputDigi->SetTime(inputDigi->GetTime()+ m_TimeDelay);
 

source/externals/itk-mhd/CMakeLists.txt

@@ -1,5 +1,5 @@
 PROJECT(testmhd)
-CMAKE_MINIMUM_REQUIRED (VERSION 2.4)
+CMAKE_MINIMUM_REQUIRED (VERSION 3.6)
 IF(COMMAND CMAKE_POLICY)
   CMAKE_POLICY(SET CMP0003 NEW)
 ENDIF(COMMAND CMAKE_POLICY)