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Update digitizer_and_detector_modeling.rst #649

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85 changes: 26 additions & 59 deletions docs/digitizer_and_detector_modeling.rst
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Expand Up @@ -809,22 +809,11 @@ Thus, the output of *Singles_crystal2* should be used in the following analysis

/gate/digitizerMgr/CoincidenceSorter/Coincidences/setInputCollection Singles_crystal2








Modules to be addapted (NOT YET INCLUDED IN GATE NEW DIGITIZER)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Blurring: Intrinsic resolution blurring with crystals of different compositions
Intrinsic resolution
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
*(Previously blurring with crystals of different compositions, now includes GateLightYield, GateTransferEfficiency, and GateQuantumEfficiency)*



This blurring pulse-processor simulates a local Gaussian blurring of the energy spectrum (different for different crystals) based on the following model:
This resolution simulates a Gaussian blurring of the energy spectrum based on the following model:

:math:`R=\sqrt{{2.35}^2\cdot\frac{1+\bar{\nu}}{{\bar{N}}_{ph}\cdot \bar{\epsilon} \cdot \bar{p}} +{R_i}^2}`

Expand All @@ -834,7 +823,11 @@ where :math:`N_{ph}=LY\cdot E` and :math:`LY`, :math:`\bar p` and :math:`\bar \e

If the intrinsic resolutions, :math:`( R_i )`, of the individual crystals are not defined, then they are set to one.

To use this *digitizer* module properly, several modules must be set first. These digitizer modules are **GateLightYield**, **GateTransferEfficiency**, and **GateQuantumEfficiency**. The light yield pulse-processor simulates the crystal light yield. Each crystal must be given the correct light yield. This module converts the *pulse* energy into the number of scintillation photons emitted, :math:`N_{ph}`. The transfer efficiency pulse-processor simulates the transfer efficiencies of the light photons in each crystal. This digitizer reduces the "pulse" energy (by reducing the number of scintillation photons) by a transfer efficiency coefficient which must be a number between 0 and 1. The quantum efficiency pulse-processor simulates the quantum efficiency for each channel of a photo-detector, which can be a Photo Multiplier Tube (PMT) or an Avalanche Photo Diode (APD).
LightYield: It converts the *digi* energy into the number of scintillation photons emitted, :math:`N_{ph}`.

TransferEfficiency: the transfer efficiencies of the light photons in each crystal. It reduces the "pulse" energy (by reducing the number of scintillation photons) by a transfer efficiency coefficient which must be a number between 0 and 1.

QuantumEfficiency: simulates the quantum efficiency for each channel of a photo-detector, which can be a Photo Multiplier Tube (PMT) or an Avalanche Photo Diode (APD).

The command lines are illustrated using an example of a phoswich module made of two layers of different crystals. One crystal has a light yield of 27000 photons per MeV (LSO crystal), a transfer efficiency of 28%, and an intrinsic resolution of 8.8%. The other crystal has a light yield of 8500 photons per MeV (LuYAP crystal), a transfer efficiency of 24% and an intrinsic resolution of 5.3%

Expand All @@ -858,33 +851,21 @@ In the case of a *cylindricalPET* system, the construction of the crystal geomet
# In this example the phoswich module is represented by the *crystal* volume and is made of two different material layers.
# To apply the resolution blurring of equation , the parameters discussed above must be defined for each layer
#(i.e. Light Yield, Transfer, Intrinsic Resolution, and the Quantum Efficiency).
# DEFINE TRANSFER EFFICIENCY FOR EACH LAYER
/gate/digitizer/Singles/insert transferEfficiency
/gate/digitizer/Singles/transferEfficiency/chooseNewVolume LSOlayer
/gate/digitizer/Singles/transferEfficiency/LSOlayer/setTECoef 0.28
/gate/digitizer/Singles/transferEfficiency/chooseNewVolume LuYAPlayer
/gate/digitizer/Singles/transferEfficiency/LuYAPlayer/setTECoef 0.24

# DEFINE LIGHT YIELD FOR EACH LAYER
/gate/digitizer/Singles/insert lightYield
/gate/digitizer/Singles/lightYield/chooseNewVolume LSOlayer
/gate/digitizer/Singles/lightYield/LSOlayer/setLightOutput 27000
/gate/digitizer/Singles/lightYield/chooseNewVolume LuYAPlayer
/gate/digitizer/Singles/lightYield/LuYAPlayer/setLightOutput 8500

# DEFINE INTRINSIC RESOLUTION FOR EACH LAYER
/gate/digitizer/Singles/insert intrinsicResolutionBlurring
/gate/digitizer/Singles/intrinsicResolutionBlurring/ chooseNewVolume LSOlayer
/gate/digitizer/Singles/intrinsicResolutionBlurring/ LSOlayer/setIntrinsicResolution 0.088
/gate/digitizer/Singles/intrinsicResolutionBlurring/ LSOlayer/setEnergyOfReference 511 keV
/gate/digitizer/Singles/intrinsicResolutionBlurring/ chooseNewVolume LuYAPlayer
/gate/digitizer/Singles/intrinsicResolutionBlurring/ LuYAPlayer/setIntrinsicResolution 0.053
/gate/digitizer/Singles/intrinsicResolutionBlurring/ LuYAPlayer/setEnergyOfReference 511 keV
# DEFINE INTRINSIC RESOLUTION
/gate/digitizerMgr/LSOlayer/SinglesDigitizer/Singles/insert intrinsicResolution
/gate/digitizerMgr/LSOlayer/SinglesDigitizer/Singles/intrinsicResolution/setIntrinsicResolution 0.088
/gate/digitizerMgr/LSOlayer/SinglesDigitizer/Singles/intrinsicResolution/setEnergyOfReference 511 keV
/gate/digitizerMgr/LSOlayer/SinglesDigitizer/Singles/intrinsicResolution/setTECoef 0.28
/gate/digitizerMgr/LSOlayer/SinglesDigitizer/Singles/intrinsicResolution/setLightOutput 27000
/gate/digitizerMgr/LSOlayer/SinglesDigitizer/Singles/intrinsicResolution/setUniqueQE 0.1

/gate/digitizerMgr/LuYAPlayer/SinglesDigitizer/Singles/insert intrinsicResolution
/gate/digitizerMgr/LuYAPlayer/SinglesDigitizer/Singles/intrinsicResolution/setIntrinsicResolution 0.088
/gate/digitizerMgr/LuYAPlayer/SinglesDigitizer/Singles/intrinsicResolution/setEnergyOfReference 511 keV
/gate/digitizerMgr/LuYAPlayer/SinglesDigitizer/Singles/intrinsicResolution/setTECoef 0.24
/gate/digitizerMgr/LuYAPlayer/SinglesDigitizer/Singles/intrinsicResolution/setLightOutput 8500
/gate/digitizerMgr/LuYAPlayer/SinglesDigitizer/Singles/intrinsicResolution/setUniqueQE 0.1

# DEFINE QUANTUM EFFICIENCY OF THE PHOTODETECTOR
/gate/digitizer/Singles/insert quantumEfficiency
/gate/digitizer/Singles/quantumEfficiency/chooseQEVolume crystal
/gate/digitizer/Singles/quantumEfficiency/setUniqueQE 0.1

Note: A complete example of a phoswich module can be in the PET benchmark.

Expand All @@ -895,29 +876,15 @@ 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/digitizer/Singles/quantumEfficiency/chooseQEVolume crystal
/gate/digitizer/Singles/quantumEfficiency/useFileDataForQE fileName1
/gate/digitizer/Singles/quantumEfficiency/useFileDataForQE fileName2
/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*.

**Important note**

After the introduction of the lightYield (LY), transferEfficiency :math:`(\bar{p})` and quantumEfficiency} :math:`(\bar{\epsilon})` modules, the energy variable of a *pulse* is not in energy unit (MeV) but in number of photoelectrons :math:`N_{pe}`.

:math:`N_{phe}={N}_{ph} \cdot \bar{\epsilon} \cdot \bar{p} = LY \cdot E \cdot \bar{\epsilon} \cdot \bar{p}`

In order to correctly apply a threshold on a phoswhich module, the threshold should be based on this number and not on the real energy. In this situation, to apply a threshold at this step of the digitizer chain, the threshold should be applied as explained in :ref:`thresholder_upholder-label`. In this case, the GATE program knows that these modules have been used, and will apply threshold based upon the number :math:`N_{pe}` rather than energy. The threshold set with this sigmoidal function in energy unit by the user is translated into number :math:`N_{pe}` with the lower light yield of the phoswish module. To retrieve the energy it is necessary to apply a calibration module.

Calibration
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The Calibration module of the pulse-processor models a calibration between :math:`N_{phe}` and :math:`Energy`. This is useful when using the class(es) GateLightYield, GateTransferEfficiency, and GateQuantumEfficiency. In addition, a user specified calibration factor can be used. To set a calibration factor on the energy, use the following commands::
Modules to be addapted (NOT YET INCLUDED IN GATE NEW DIGITIZER)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

/gate/digitizer/Singles/insert calibration
/gate/digitizer/Singles/setCalibration VALUE

If the calibration digitizer is used without any value, it will correct the energy as a function of values used in GateLightYield, GateTransferEfficiency, and GateQuantumEfficiency.

Crosstalk
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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