Merge branch 'develop' into IRnewOption

CMakeLists.txt

@@ -318,7 +318,6 @@ MESSAGE("- Coincidence digitizer modules (combining of several Coincidence Sorte
 MESSAGE("- Compton Camera digitizer modules and output")
 MESSAGE("- Output: Sinogram, Ecat7, LMF")
 MESSAGE("- ARF may work not properly yet")
-MESSAGE("- Digitizer Modules to be added soon: Buffer, intrinsicResolutionBlurring, lightYield, transferEfficiency, quantumEfficiency, crosstalk, calibration")
 MESSAGE("We apologize for this inconvenience and kindly ask for your patience.")
 MESSAGE("This functionalities will be added during 2023.")
 MESSAGE("Meanwhile, please, use Gate 9.2")

docs/digitizer_and_detector_modeling.rst

@@ -875,12 +875,28 @@ With the previous commands, the same quantum efficiency will be applied to all t
 
 To set multiple quantum efficiencies using files (*fileName1*, *fileName2*, ... for each of the different modules), the following commands can be used::
 
-   /gate/digitizer/Singles/insert quantumEfficiency 
+   /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/insert quantumEfficiency 
    /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/intrinsicResolution/useFileDataForQE fileName1 
    /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/intrinsicResolution/useFileDataForQE fileName2  
 
 If the *crystal* volume is a daughter of a *module* volume which is an array of 8 x 8 crystals, the file *fileName1* will contain 64 values of quantum efficiency. If several files are given (in this example two files), the program will choose randomly between theses files for each *module*.
 
+
+Memory buffers and bandwidth
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To mimic the effect of limited transfer rate, a module models the data loss due to an overflow of a memory buffer, read periodically, following a given reading frequency. This module uses two parameters, the reading frequency :math:`\nu ` and the memory depth :math:`D` . Moreover, two reading methods can be modelled, that is, in an event per event basis (an event is read at each reading clock tick), or in a full buffer reading basic (at each reading clock tick, the whole buffer is emptied out). In the first reading method, the data rate is then limited to :math:`\nu` , while in the second method, the data rate is limited to :math:`D\cdot\nu`. When the size limit is reached, any new pulse is rejected, until the next reading clock tick arrival which frees a part of the buffer. In such a case, a non null buffer depth allows to manage a local rise of the input data flow. To specify a buffer, read at 10 MHz, with a buffer depth of 64 events, in a mode where the whole buffer is read in one clock tick, one can use::
+
+   /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/insert buffer 
+   /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/buffer/setBufferSize 64 B 
+   /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/buffer/setReadFrequency 10 MHz 
+   /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/buffer/setMode 1 
+
+The size of the buffer represents the number of elements, 64 Singles in this example, that the user can store in a buffer. To read the buffer in an event by event basis, one should replace the last line by **setMode = 0.**
+
+
+
+
 Modules to be addapted (NOT YET INCLUDED IN GATE NEW DIGITIZER)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -915,20 +931,6 @@ In PET analysis, coincidence events provide the lines of response (LOR) needed f
 
 
 
-Memory buffers and bandwidth
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-To mimic the effect of limited transfer rate, a module models the data loss due to an overflow of a memory buffer, read periodically, following a given reading frequency. This module uses two parameters, the reading frequency :math:`\nu ` and the memory depth :math:`D` . Moreover, two reading methods can be modelled, that is, in an event per event basis (an event is read at each reading clock tick), or in a full buffer reading basic (at each reading clock tick, the whole buffer is emptied out). In the first reading method, the data rate is then limited to :math:`\nu` , while in the second method, the data rate is limited to :math:`D\cdot\nu`. When the size limit is reached, any new pulse is rejected, until the next reading clock tick arrival which frees a part of the buffer. In such a case, a non null buffer depth allows to manage a local rise of the input data flow. To specify a buffer, read at 10 MHz, with a buffer depth of 64 events, in a mode where the whole buffer is read in one clock tick, one can use::
-
-   /gate/digitizer/Your_Single_chain/insert buffer 
-   /gate/digitizer/Your_Single_chain/buffer/setBufferSize 64 B 
-   /gate/digitizer/Your_Single_chain/buffer/setReadFrequency 10 MHz 
-   /gate/digitizer/Your_Single_chain/buffer/setMode 1 
-
-The chain *Your_Single_chain* can be the default chain *Singles* or any of single chain that the user has defined. The size of the buffer represents the number of elements, 64 Singles in this example, that the user can store in a buffer. To read the buffer in an event by event basis, one should replace the last line by **setMode = 0.**
-
-
-
 
 .. _digitizer_multiple_processor_chains-label:
 

source/digits_hits/include/GateCrosstalk.hh

@@ -6,91 +6,80 @@ of the GNU Lesser General  Public Licence (LGPL)
 See LICENSE.md for further details
 ----------------------*/
 
+// OK GND 2022
 
+/*! \class  GateCrosstalk
+    \brief  Digitizer Module for simulating an optical and/or an electronic Crosstalk
+    - GateCrosstalk - by [email protected] (dec 2002)
+
+    - Digitizer Module for simulating an optical and/or an electronic Crosstalk
+    of the scintillation light between the neighbor crystals:
+    if the input Digi arrives in a crystal array, Digis around
+    it are created (in the edge and corner neighbor crystals).
+    ATTENTION: this module functions only for a chosen volume which is an array repeater !!!
+
+	5/12/23 - added to GND by [email protected] but MAYBE NOT PROPERLY TESTED !!!!
+
+      \sa GateVDigitizerModule
+*/
 #ifndef GateCrosstalk_h
 #define GateCrosstalk_h 1
 
+#include "GateVDigitizerModule.hh"
+#include "GateDigi.hh"
+#include "GateClockDependent.hh"
+#include "GateCrystalSD.hh"
+
 #include "globals.hh"
-#include <iostream>
-#include <vector>
 
-#include "GateVPulseProcessor.hh"
+#include "GateCrosstalkMessenger.hh"
+#include "GateSinglesDigitizer.hh"
 
-class GateCrosstalkMessenger;
 class GateArrayParamsFinder;
-class GateOutputVolumeID;
 
-/*! \class  GateCrosstalk
-    \brief  Pulse-processor for simulating an optical and/or an electronic crosstalk
-    - GateCrosstalk - by [email protected] (dec 2002)
+class GateCrosstalk : public GateVDigitizerModule
+{
+public:
+	//! This function allows to retrieve the current instance of the GateCrosstalk singleton
+	/*!
+	   If the GateCrosstalk already exists, GetInstance only returns a pointer to this singleton.
+	   If this singleton does not exist yet, GetInstance creates it by calling the private
+	   GateCrosstalk constructor
+	*/
+	static GateCrosstalk* GetInstance(GateSinglesDigitizer* itsChain,
+			const G4String& itsName,
+			G4double itsEdgesFraction, G4double itsCornersFraction);
 
-    - Pulse-processor for simulating an optical and/or an electronic crosstalk
-    of the scintillation light between the neighbor crystals:
-    if the input pulse arrives in a crystal array, pulses around
-    it are created (in the edge and corner neighbor crystals).
-    ATTENTION: this module functions only for a chosen volume which is an array repeater !!!
 
+  GateCrosstalk(GateSinglesDigitizer *digitizer, G4String name, G4double itsEdgesFraction, G4double itsCornersFraction);
+  ~GateCrosstalk();
+
+  void Digitize() override;
 
-      \sa GateVPulseProcessor
-*/
-class GateCrosstalk : public GateVPulseProcessor
-{
-  public:
-    //! This function allows to retrieve the current instance of the GateCrosstalk singleton
-    /*!
-        If the GateCrosstalk already exists, GetInstance only returns a pointer to this singleton.
-        If this singleton does not exist yet, GetInstance creates it by calling the private
-        GateCrosstalk constructor
-    */
-    static GateCrosstalk* GetInstance(GatePulseProcessorChain* itsChain,
-				      const G4String& itsName,
-				      G4double itsEdgesFraction, G4double itsCornersFraction);
-
-        //! Public Destructor
-    virtual ~GateCrosstalk() ;
-
-  private:
-    //!< Private constructor which Constructs a new crosstalk module attached to a GateDigitizer:
-    //! this function should only be called from GetInstance()
-    GateCrosstalk(GatePulseProcessorChain* itsChain,
-				      const G4String& itsName,
-				      G4double itsEdgesFraction, G4double itsCornersFraction) ;
-
-  public:
-
-
-    void CheckVolumeName(G4String val);
-
-     //! \name getters and setters
-    //@{
-    //! This function returns the fraction of the part of energy which goes in the edge crystals.
-    G4double GetEdgesFraction()                { return m_edgesCrosstalkFraction; }
-
-    //! This function sets the fraction of the part of energy which goes in the edge crystals.
-    void SetEdgesFraction (G4double val)       { m_edgesCrosstalkFraction = val;  }
-
-    //! This function returns the fraction of the part of energy which goes in the corner crystals.
-    G4double GetCornersFraction()              { return m_cornersCrosstalkFraction; }
-
-    //! This function sets the fraction of the part of energy which goes in the corner crystals.
-    void SetCornersFraction (G4double val)     { m_cornersCrosstalkFraction = val;  }
-
-    //! Return the rest crosstalk per cent
-    G4double GetXTPerCent() { return m_XtalkpCent; };
-    //@}
-
-    //! Implementation of the pure virtual method declared by the base class GateDigitizerComponent
-    //! print-out the attributes specific of the crosstalk
-    virtual void DescribeMyself(size_t indent);
-
-  protected:
-    //! Implementation of the pure virtual method declared by the base class GateVPulseProcessor
-    //! This methods processes one input-pulse
-    //! It is is called by ProcessPulseList() for each of the input pulses
-    //! The result of the pulse-processing is incorporated into the output pulse-list
-    void ProcessOnePulse(const GatePulse* inputPulse,GatePulseList& outputPulseList);
-
-  private:
+
+  void CheckVolumeName(G4String val);
+
+  //! \name getters and setters
+  //@{
+  //! This function returns the fraction of the part of energy which goes in the edge crystals.
+  G4double GetEdgesFraction()                { return m_edgesCrosstalkFraction; }
+
+  //! This function sets the fraction of the part of energy which goes in the edge crystals.
+  void SetEdgesFraction (G4double val)       { m_edgesCrosstalkFraction = val;  }
+
+  //! This function returns the fraction of the part of energy which goes in the corner crystals.
+  G4double GetCornersFraction()              { return m_cornersCrosstalkFraction; }
+
+  //! This function sets the fraction of the part of energy which goes in the corner crystals.
+  void SetCornersFraction (G4double val)     { m_cornersCrosstalkFraction = val;  }
+
+  //! Return the rest Crosstalk per cent
+  G4double GetXTPerCent() { return m_XtalkpCent; };
+  //@}
+
+  void DescribeMyself(size_t );
+
+private:
 //     //! Find the different parameters of the array of detection :
 //     //! The numbers of rows in x, y and z
 //     //! The position in this matrix of the hit
@@ -102,34 +91,54 @@ class GateCrosstalk : public GateVPulseProcessor
 //     //! Get the ArrayRepeater from an VObjectReapeater (if it isn't an ArrayRepeater return 0)
 //     GateArrayRepeater* GetArrayRepeater(GateVGlobalPlacement* aRepeater);
 
-//     //! Find the different parameters of the input Pulse :
+//     //! Find the different parameters of the input Digi :
 //     //! e.g. the position in this array of the hit
-//     void FindInputPulseParams(const GateVolumeID* m_volumeID);
+//     void FindInputDigiParams(const GateVolumeID* m_volumeID);
 
-    //! Create a new VolumeID for the volume of in the matrix with position \i,\j,\k
-    GateVolumeID CreateVolumeID(const GateVolumeID* m_volumeID, G4int i, G4int j, G4int k);
+   //! Create a new VolumeID for the volume of in the matrix with position \i,\j,\k
+   GateVolumeID CreateVolumeID(const GateVolumeID* m_volumeID, G4int i, G4int j, G4int k);
 
-    //! Create a new OutputVolumeID for the volume of in the matrix with position \i,\j,\k
-    GateOutputVolumeID CreateOutputVolumeID(const GateVolumeID m_volumeID);
+   //! Create a new OutputVolumeID for the volume of in the matrix with position \i,\j,\k
+   GateOutputVolumeID CreateOutputVolumeID(const GateVolumeID m_volumeID);
 
-    //! Create a new Pulse of an energy of \val * ENERGY of \pulse in the volume in position \i,\j,\k
-    GatePulse* CreatePulse(G4double val, const GatePulse* pulse, G4int i, G4int j, G4int k);
+   //! Create a new Digi of an energy of \val * ENERGY of \Digi in the volume in position \i,\j,\k
+   GateDigi* CreateDigi(G4double val, const GateDigi* Digi, G4int i, G4int j, G4int k);
 
-  private:
-    //! Static pointer to the GateCrosstalk singleton
-    static GateCrosstalk* theGateCrosstalk;
 
-    G4double m_XtalkpCent;                                         //!< Actual crosstalk per cent of energy
-    G4double m_edgesCrosstalkFraction, m_cornersCrosstalkFraction; //!< Coefficient which connects energy to the resolution
-    GateCrosstalkMessenger *m_messenger;                           //!< Messenger
-    G4String m_volume;                                             //!< Name of the crosstalk volume
-    G4int m_testVolume;                                            //!< Equal to 1 if m_volume is a valid volume name, else 0
+protected:
+   G4double m_XtalkpCent;                                         //!< Actual Crosstalk per cent of energy
+   G4double m_edgesCrosstalkFraction, m_cornersCrosstalkFraction; //!< Coefficient which connects energy to the resolution
+   GateCrosstalkMessenger *m_messenger;                           //!< Messenger
+   G4String m_volume;                                             //!< Name of the Crosstalk volume
+   G4int m_testVolume;                                            //!< Equal to 1 if m_volume is a valid volume name, else 0
 
-    GateArrayParamsFinder* ArrayFinder;
-    size_t m_nbX, m_nbY, m_nbZ;                                    //!< Parameters of the matrix of detection
-    size_t m_i, m_j, m_k;                                          //!< position \i,\j,\k in the matrix
-    size_t m_depth;                                                //!< Depth of the selected volume in the Inserter
-};
+   GateArrayParamsFinder* ArrayFinder;
+   size_t m_nbX, m_nbY, m_nbZ;                                    //!< Parameters of the matrix of detection
+   size_t m_i, m_j, m_k;                                          //!< position \i,\j,\k in the matrix
+   size_t m_depth;
+
+private:
+
+  //! Static pointer to the GateCrosstalk singleton
+  static GateCrosstalk* theGateCrosstalk;
+
+  GateDigi* m_outputDigi;
+
+  GateCrosstalkMessenger *m_Messenger;
+
+  GateDigiCollection*  m_OutputDigiCollection;
+
+  GateSinglesDigitizer *m_digitizer;
 
 
+};
+
 #endif
+
+
+
+
+
+
+
+

source/digits_hits/include/GateCrosstalkMessenger.hh

@@ -6,34 +6,59 @@ of the GNU Lesser General  Public Licence (LGPL)
 See LICENSE.md for further details
 ----------------------*/
 
+// OK GND 2022
+/*This class is not used by GATE !
+  The purpose of this class is to help to create new users digitizer module(DM).
+  Please, check GateCrosstalk.cc for more detals
+  */
+
+
+/*! \class  GateCrosstalkMessenger
+    \brief  Messenger for the GateCrosstalk
+
+    - GateCrosstalk - by [email protected]
+
+    \sa GateCrosstalk, GateCrosstalkMessenger
+*/
+
 
 #ifndef GateCrosstalkMessenger_h
 #define GateCrosstalkMessenger_h 1
 
-#include "GatePulseProcessorMessenger.hh"
-#include <vector>
-#include "G4UIdirectory.hh"
+#include "G4UImessenger.hh"
+#include "globals.hh"
+
+#include "GateClockDependentMessenger.hh"
+class GateCrosstalk;
 
 class G4UIcmdWithAString;
 class G4UIcmdWithADouble;
 
-class GateCrosstalk;
-
-class GateCrosstalkMessenger: public GatePulseProcessorMessenger
+class GateCrosstalkMessenger : public GateClockDependentMessenger
 {
-  public:
-    GateCrosstalkMessenger(GateCrosstalk* itsCrosstalk);
-    virtual ~GateCrosstalkMessenger();
+public:
+
+  GateCrosstalkMessenger(GateCrosstalk*);
+  ~GateCrosstalkMessenger();
+
+  void SetNewValue(G4UIcommand*, G4String);
 
-    inline void SetNewValue(G4UIcommand* aCommand, G4String aString);
+
+private:
+  GateCrosstalk* m_Crosstalk;
+
+  G4UIcmdWithADouble   *edgesFractionCmd;
+  G4UIcmdWithADouble   *cornersFractionCmd;
 
-    inline GateCrosstalk* GetCrosstalk()
-      { return (GateCrosstalk*) GetPulseProcessor(); }
 
-  private:
-    G4UIcmdWithAString   *newVolCmd;
-    G4UIcmdWithADouble   *edgesFractionCmd;
-    G4UIcmdWithADouble   *cornersFractionCmd;
 };
 
 #endif
+
+
+
+
+
+
+
+

source/digits_hits/include/GateIntrinsicResolution.hh

@@ -51,6 +51,9 @@ public:
   void SetEref(const G4double& value ){ m_Eref=value;} ;
   void SetLightOutput(const G4double& value ){ m_LY=value;} ;
   void SetTransferEff(const G4double& value ){ m_TE=value;} ;
+  void SetEdgesFraction (G4double val)       { m_edgesCrosstalkFraction = val;  }
+  void SetCornersFraction (G4double val)     { m_cornersCrosstalkFraction = val;  }
+
 
   //! Allow to use file(s) as lookout table for quantum efficiency
   void UseFile(G4String aFile);
@@ -72,6 +75,7 @@ protected:
   G4double   m_LY; //Light Yield
   G4double   m_TE; //Transfer efficiency
   G4double   m_QE; //Quantum efficiency
+  G4double m_XtalkpCent;
   G4bool isFirstEvent;
 
   G4double m_variance;
@@ -97,6 +101,8 @@ protected:
   G4double** m_table;     //!< Lookout table for the quantum efficiency of all channels
   G4String m_volumeName;  //!< Name of the module
   G4int m_testVolume;     //!< equal to 1 if the volume name is valid, 0 else
+  G4double m_edgesCrosstalkFraction, m_cornersCrosstalkFraction; //!< Coefficient which connects energy to the resolution
+
 
 private:
   GateDigi* m_outputDigi;