Merge branch 'develop' into coincidenceSorter

.github/workflows/main.yml

@@ -18,9 +18,12 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
         options: [none, rtk, torch, optic]
+        exclude:
+          - os: macos-latest
+            options: torch
 
     env:
-      ROOT_VERSION: 'v6-26-08'
+      ROOT_VERSION: 'v6-32-02'
       GEANT4_VERSION: 'v11.2.1'
       ITK_VERSION: 'v5.3.0'
       ROOT_DIR: $(HOME)/software/root
@@ -38,8 +41,8 @@ jobs:
       uses: actions/cache@v3
       with:
         path: ~/software
-        key: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-build4
-        restore-keys: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-build4
+        key: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-build1
+        restore-keys: ${{ matrix.os }}-geant4-${{ env.GEANT4_VERSION }}-root-${{ env.ROOT_VERSION }}-build1
     - name: Install dependencies
       run: |
         if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
@@ -129,8 +132,8 @@ jobs:
               wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.10.1%2Bcpu.zip
               unzip libtorch-cxx11-abi-shared-with-deps-1.10.1+cpu.zip
             elif [ "${{ matrix.os }}" == 'macos-latest' ]; then
-              wget https://download.pytorch.org/libtorch/cpu/libtorch-macos-1.10.1.zip
-              unzip libtorch-macos-1.10.1.zip
+              wget https://download.pytorch.org/libtorch/cpu/libtorch-macos-arm64-2.2.0.zip
+              unzip libtorch-macos-arm64-2.2.0.zip
             fi
           fi
           if [ "${{ matrix.options }}" == 'rtk' ]; then

docs/digitizer_and_detector_modeling.rst

@@ -225,7 +225,7 @@ Five types of distribution are available in GATE, namely:
 *  Gaussian distributions, defined by a mean value and a standard deviation. 
 *  Exponential distributions, defined by its power. 
 *  Manual distributions, defined by a discrete set of points specified in the GATE macro file. The data are linearly interpolated to define the function in a continuous range. 
-*  File distribution, acting as the manual distribution, but where the points are defined in a separate ASCII file, whose name is given as a parameter. This method is appropriate for large numbers of points and allows to describe any distribution in a totally generic way.
+*  File distribution, acting as the manual distribution, but where the points are defined in a separate ASCII file, whose name is given as a parameter. This method is appropriate for large numbers of points and allows to describe any distribution in a totally generic way. Now, GATE supports reading 2D distributions from ASCII files where values are organized in matrices.
 
 A distribution is declared by specifying its name then by creating a new instance, with its type name::
 
@@ -297,7 +297,8 @@ The possible type name available corresponds to the five distributions described
    +----------------+--------------------------------------------------------------------------------+
    | read           | do read the file (should be called after specifying all the other parameters)  | 
    +----------------+--------------------------------------------------------------------------------+
-
+   | ReadMatrix2d   | do read a data file that organizes its contents in a 2D matrix format          | 
+   +----------------+--------------------------------------------------------------------------------+ 
 
 Singles Digitizers
 -------------------
@@ -518,11 +519,53 @@ In case if the position obtained after applying a Gaussian blurring exceeds the
 BEWARE: This relocation procedure is validated only for the first group level of crystals.
 
 **Example**::
- 
+
    /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/insert   spatialResolution
    /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/spatialResolution/fwhm 1.0 mm
    /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/spatialResolution/confineInsideOfSmallestElement true 
-   
+
+**Configuring Spatial Resolution with 1D and 2D Distributions**::
+
+This approach is particularly essential  for  monolithic crystal detectors, where factors like edge effects and interaction positions significantly  may influence spatial  resolution.
+Here is an example of how to configure this in a macro file:
+
+**Example for 2D distribution**::
+
+
+  /gate/distributions/name    my_distrib2D
+  /gate/distributions/insert   File
+  /gate/distributions/my_distrib2D/setFileName    Lut(X,Y).txt
+  /gate/distributions/my_distrib2D/readMatrix2d
+  /gate/digitizerMgr/crystalUnit/SinglesDigitizer/Singles/insert spatialResolution
+  /gate/digitizerMgr/crystalUnit/SinglesDigitizer/Singles/spatialResolution/fwhmXdistrib2D my_distrib2D
+**Example for 1D distribution**::
+
+  /gate/distributions/name   my_distrib1D
+  /gate/distributions/insert  File
+  /gate/distributions/my_distrib1D/setFileName  macros/LutY.txt
+  /gate/distributions/my_distrib1D/read
+  /gate/digitizerMgr/crystalUnit/SinglesDigitizer/Singles/insert spatialResolution
+  /gate/digitizerMgr/crystalUnit/SinglesDigitizer/Singles/spatialResolution/fwhmYdistrib my_distrib1D
+
+
+
+
+
+These commands allow for more precise control over the spatial resolution by using predefined distributions for the X and Y axes.
+
+BEWARE : The file for 2D Distribution  should be structured such that:
+
+-The first line contains the x values.
+
+-Each subsequent line begins with a y value followed by the standard deviation (stddev) values corresponding to each x value and y value pair.
+
+**Example**::
+
+-29.50 -28.50 -27.50 
+-29.50 9.62 13.66 10.22
+-28.50 11.38 11.18 10.23
+-27.50 12.82 10.43 9.70
+
 Energy Framing
 ^^^^^^^^^^^^^^
 *Previously Thresholder and Upholder*
@@ -1111,7 +1154,7 @@ Then, the rejection can be set to the whole event or only to those pulses within
 
 Example::
 
-	/gate/digitizerMgr/absorber/SinglesDigitizer/Singles/insert                        multipleRejection
+    /gate/digitizerMgr/absorber/SinglesDigitizer/Singles/insert                        multipleRejection
    /gate/digitizerMgr/absorber/SinglesDigitizer/Singles/multipleRejection/setMultipleDefinition volumeID
    /gate/digitizerMgr/absorber/SinglesDigitizer/Singles/multipleRejection/setEventRejection 1
 
@@ -1368,20 +1411,32 @@ The dead time for coincidences works in the same way as that acting on the *sing
 
 Coincidence buffers
 ~~~~~~~~~~~~~~~~~~~
+It simulates the operation of a detector by modeling coincidences, transfer speed limits, and data loss due to buffer capacity overflows. It manages a memory buffer for coincidence events, allowing for the modeling of data loss due to buffer overflow. It uses a read frequency and allows defining the buffer size and read mode, influencing how events are processed. There are two buffer operation modes. Mode 1 empties the entire buffer at each read clock tick, while Mode 0 reads events one by one.
+
+Example::
+
+/gate/digitizerMgr/CoincidenceDigitizer/finalCoinc/insert buffer
+/gate/digitizerMgr/CoincidenceDigitizer/finalCoinc/buffer/setBufferSize 64 B
+/gate/digitizerMgr/CoincidenceDigitizer/finalCoinc/buffer/setReadFrequency 10 MHz
+/gate/digitizerMgr/CoincidenceDigitizer/finalCoinc/buffer/setMode 1
+
 
 For a coincidence sorter user can chose a presort buffer with a following command: 
 
    /gate/digitizer/Coincidences/setPresortBufferSize 256 
 
+
 A presort buffer contains singles that have not yet been checked for coincidence with the already open coincidence windows. The default value is 256, the minimum value is 32. For more details, check https://iopscience.iop.org/article/10.1088/0031-9155/61/18/N522
 
 
 Multiple coincidence removal
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-If the multiple coincidences are kept and not splitted into pairs (ie. if any of the **keepXXX** multiple coincidence policy is used), the multicoincidences could participate to dataflow occupancy, but could not be written to the disk. Unless otherwise specified, any multicoincidence is then cleared from data just before the disk writing. If needed, this clearing could be performed at any former coincidence processing step, by inserting the **multipleKiller** module at the required level. This module has no parameter and just kill the multicoincidence events. Multiple coincidences split into many pairs are not affected by this module and cannot be distinguished from the normal "simple" coincidences. To insert a multipleKiller, one has to use the syntax::
+If the multiple coincidences are kept and not split into pairs (i.e., if any of the **keepXXX** multiple coincidence policies are used), the multicoincidences could contribute to dataflow occupancy but cannot be written to the disk. Unless otherwise specified, any multicoincidence is then cleared from data just before the disk writing. If needed, this clearing could be performed at any earlier coincidence processing step by inserting the **multipleKiller** module at the required level. This module has no parameters and simply removes the multicoincidence events. Multiple coincidences split into many pairs are not affected by this module and cannot be distinguished from normal "simple" coincidences. To insert a multipleKiller, use the syntax::
+
+
+/gate/digitizerMgr/CoincidenceDigitizer/finalCoinc/insert multiplesKiller
 
-   /gate/digitizer/myCoincChain/insert multipleKiller
 
 Example of a digitizer setting
 ------------------------------
@@ -1486,6 +1541,7 @@ Example::
    87 /gate/digitizer/finalCoinc/buffer/setBufferSize 32 B 
    88 /gate/digitizer/finalCoinc/buffer/setReadFrequency 14.45 MHz  
    89 /gate/digitizer/finalCoinc/buffer/setMode 0 
+   
 
 Lines 1 to 15: The branch named "Singles" contains the result of applying the adder, readout, blurring, and threshold (50 keV) modules.
 

source/digits_hits/include/GateDistributionFile.hh

@@ -32,7 +32,8 @@ class GateDistributionFile : public GateVDistributionArray
     inline G4int GetColumnX() const {return m_column_for_X;}
     inline G4int GetColumnY() const {return m_column_for_Y;}
 
-    void Read();
+     void Read();
+     void ReadMatrix2d();
 
     virtual void DescribeMyself(size_t indent);
   private:
@@ -41,6 +42,11 @@ class GateDistributionFile : public GateVDistributionArray
     G4int m_column_for_X;
     G4int m_column_for_Y;
     GateDistributionFileMessenger* m_messenger;
+    std::map<std::pair<double, double>, double> stddevMap;
+
+    std::vector<double> xValues;
+        std::vector<double> yValues;
+
 };
 
 

source/digits_hits/include/GateDistributionFileMessenger.hh

@@ -33,6 +33,7 @@ class GateDistributionFileMessenger: public GateDistributionArrayMessenger
     G4UIcmdWithAnInteger      *setColXCmd;
     G4UIcmdWithAnInteger      *setColYCmd;
     G4UIcmdWithoutParameter   *readCmd;
+    G4UIcmdWithoutParameter   *read2DCmd;
     G4UIcmdWithoutParameter   *autoXCmd;
 };
 

source/digits_hits/include/GateDistributionMessenger.hh

@@ -30,6 +30,7 @@ class GateDistributionMessenger: public GateNamedObjectMessenger
     void SetNewValue(G4UIcommand* aCommand, G4String aString);
     void SetUnitX(const G4String& unitX);
     void SetUnitY(const G4String& unitY);
+
     inline G4String UnitCategoryX() const {return m_unitX.empty()?"":G4UIcommand::CategoryOf(m_unitX);}
     inline G4String UnitCategoryY() const {return m_unitY.empty()?"":G4UIcommand::CategoryOf(m_unitY);}
 
@@ -41,8 +42,10 @@ class GateDistributionMessenger: public GateNamedObjectMessenger
     G4UIcmdWithoutParameter        *getMaxY_Cmd ;
     G4UIcmdWithoutParameter        *getRandom_Cmd ;
     G4UIcmdWithADoubleAndUnit      *getValueCmd ;
+
     G4String	    	    	   m_unitX;
     G4String	    	    	   m_unitY;
+
 };
 
 #endif

source/digits_hits/include/GateSpatialResolution.hh

@@ -31,7 +31,10 @@ See LICENSE.md for further details
 #include "G4TouchableHistoryHandle.hh"
 #include "GateSinglesDigitizer.hh"
 
+class GateVDistribution;
+
 class GateSpatialResolution : public GateVDigitizerModule
+
 {
 public:
 
@@ -40,9 +43,15 @@ public:
 
   void Digitize() override;
 
+
+
   //! These functions return the resolution in use.
     G4double GetFWHM()   	       { return m_fwhm; }
-    G4double GetFWHMx()   	       { return m_fwhmX; }
+    GateVDistribution* GetFWHMxdistrib()    { return m_fwhmXdistrib; }
+    GateVDistribution* GetFWHMydistrib()    { return m_fwhmYdistrib; }
+    GateVDistribution* GetFWHMxydistrib2D()    { return m_fwhmXYdistrib2D; }
+
+    G4double GetFWHMx()            { return m_fwhmX; }
     G4double GetFWHMy()   	       { return m_fwhmY; }
     G4double GetFWHMz()   	       { return m_fwhmZ; }
 
@@ -51,11 +60,14 @@ public:
       If you want a resolution of 10%, SetSpresolution(0.1)
     */
     void SetFWHM(G4double val)   { m_fwhm = val;  }
+    void SetFWHMxdistrib(GateVDistribution* dist)  { m_fwhmXdistrib= dist; }
+    void SetFWHMydistrib(GateVDistribution* dist)  { m_fwhmYdistrib = dist; }
+    void SetFWHMxydistrib2D(GateVDistribution* dist)  { m_fwhmXYdistrib2D= dist; }
+
     void SetFWHMx(G4double val)   { m_fwhmX = val;  }
     void SetFWHMy(G4double val)   { m_fwhmY = val;  }
     void SetFWHMz(G4double val)   { m_fwhmZ = val;  }
-
-
+    void SetSpatialResolutionParameters();
     inline void ConfineInsideOfSmallestElement(const G4bool& value) { m_IsConfined = value; };
     inline G4bool IsConfinedInsideOfSmallestElement() const  	      	{ return m_IsConfined; }
 
@@ -64,17 +76,23 @@ public:
 
     void UpdateVolumeID();
 
-
     //! Implementation of the pure virtual method declared by the base class GateClockDependent
     //! print-out the attributes specific of the blurring
     void DescribeMyself(size_t );
 
 protected:
     G4double m_fwhm;
 
+
     G4double m_fwhmX;
+
     G4double m_fwhmY;
     G4double m_fwhmZ;
+
+    GateVDistribution*  m_fwhmXdistrib;
+    GateVDistribution* m_fwhmYdistrib;
+    GateVDistribution*  m_fwhmXYdistrib2D;
+
     G4bool m_IsConfined;
     G4Navigator* m_Navigator;
     G4TouchableHistoryHandle m_Touchable;
@@ -83,16 +101,15 @@ protected:
 
 private:
 
-    G4int m_systemDepth;
-
-  GateDigi* m_outputDigi;
+   G4int m_systemDepth;
 
+  GateDigi* m_outputDigi;;
   GateSpatialResolutionMessenger *m_Messenger;
 
   GateDigiCollection*  m_OutputDigiCollection;
 
   GateSinglesDigitizer *m_digitizer;
-
+  G4bool   m_IsFirstEntrance;
   G4VoxelLimits limits;
   G4double Xmin, Xmax, Ymin, Ymax, Zmin, Zmax;
   G4AffineTransform at;

source/digits_hits/include/GateSpatialResolutionMessenger.hh

@@ -27,7 +27,6 @@ See LICENSE.md for further details
 #include "GateClockDependentMessenger.hh"
 class GateSpatialResolution;
 class G4UIcmdWithAString;
-
 class GateSpatialResolutionMessenger : public GateClockDependentMessenger
 {
 public:
@@ -41,10 +40,13 @@ public:
 private:
   GateSpatialResolution* m_SpatialResolution;
 
-  G4UIcmdWithADouble*  	spresolutionCmd;
-  G4UIcmdWithADouble*   spresolutionXCmd;
-  G4UIcmdWithADouble*   spresolutionYCmd;
-  G4UIcmdWithADouble*   spresolutionZCmd;
+  G4UIcmdWithADoubleAndUnit*  	spresolutionCmd;
+  G4UIcmdWithADoubleAndUnit*   spresolutionXCmd;
+  G4UIcmdWithADoubleAndUnit*   spresolutionYCmd;
+  G4UIcmdWithADoubleAndUnit*   spresolutionZCmd;
+  G4UIcmdWithAString   *spresolutionXdistribCmd;// Command declaration for 1D X-resolution distribution
+  G4UIcmdWithAString   *spresolutionYdistribCmd;// Command declaration for 1D Y-resolution distribution
+  G4UIcmdWithAString   *spresolutionXYdistrib2DCmd; // Command declaration for 2D XY-resolution distribution
   G4UIcmdWithABool* 	confineCmd;
 
 

source/digits_hits/include/GateToTree.hh

@@ -65,6 +65,10 @@ public:
   static void SetOutputIDName(G4int id_system, const char * anOutputIDName, size_t depth);
   G4bool getHitsEnabled() const;
   void setHitsEnabled(G4bool mHitsEnabled);
+
+  G4bool getHitsCommonOutputEnabled() const;
+  void setHitsCommonOutputEnabled(G4bool mHitsCommonOutputEnabled);
+
   void addCollection(const std::string &str); //called by messenger
   //OK GND 2022
   void setCCenabled(G4bool mCCenabled){m_cc_enabled=mCCenabled;};
@@ -135,6 +139,7 @@ private:
   std::vector<std::string> m_listOfSinglesCollection;
   std::vector<std::string> m_listOfCoincidencesCollection;
   G4bool m_hits_enabled;
+  G4bool m_hitsCommonOutput_enabled;
   G4String m_uselessFileName; //only for GiveNameOfFile which return a reference..
 
   G4bool m_opticalData_enabled = false;

source/digits_hits/include/GateToTreeMessenger.hh

@@ -41,6 +41,10 @@ private:
   G4UIcmdWithoutParameter *m_enableHitsOutput;
   G4UIcmdWithoutParameter *m_disableHitsOutput;
 
+  G4UIcmdWithoutParameter *m_enableHitsCommonOutput;
+  G4UIcmdWithoutParameter *m_disableHitsCommonOutput;
+
+
   G4UIcmdWithoutParameter *m_enableOpticalDataOutput;
   G4UIcmdWithoutParameter *m_disableOpticalDataOutput;
 

source/digits_hits/include/GateVDistribution.hh

@@ -41,6 +41,8 @@ class GateVDistribution : public GateNamedObject
     virtual G4double MaxX() const=0;
     virtual G4double MaxY() const=0;
     virtual G4double Value(G4double x) const=0;
+    virtual G4double Value2D(G4double  x, G4double y) const;
+
     // Returns a random number following the current distribution
     // should be optimised according to each distrbution type
     virtual G4double ShootRandom() const=0;