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Merge pull request #655 from OpenGATE/kochebina-patch-7
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Update digitizer_and_detector_modeling.rst
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kochebina authored Dec 8, 2023
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Expand Up @@ -829,6 +829,9 @@ TransferEfficiency: the transfer efficiencies of the light photons in each cryst

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).

It is possible also take into account the crosstalk of the scintillation light between neighboring crystals. The percentage of energy that is given to the neighboring crystals is determined by the user. To insert a crosstalk module for corners and for egdes, please use *setXtalkEdgesFraction* and *setXtalkCornersFraction*.


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%

In the case of a *cylindricalPET* system, the construction of the crystal geometry is truncated for clarity (the truncation is denoted by ...). The *digitizer* command lines are::
Expand Down Expand Up @@ -858,13 +861,17 @@ In the case of a *cylindricalPET* system, the construction of the crystal geomet
/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/LSOlayer/SinglesDigitizer/Singles/intrinsicResolution/setXtalkEdgesFraction 0.1
/gate/digitizerMgr/LSOlayer/SinglesDigitizer/Singles/intrinsicResolution/setXtalkCornersFraction 0.05

/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
/gate/digitizerMgr/LSOlayer/SinglesDigitizer/Singles/intrinsicResolution/setXtalkEdgesFraction 0.15
/gate/digitizerMgr/LSOlayer/SinglesDigitizer/Singles/intrinsicResolution/setXtalkCornersFraction 0.1

Note: A complete example of a phoswich module can be in the PET benchmark.
Expand All @@ -881,55 +888,32 @@ To set multiple quantum efficiencies using files (*fileName1*, *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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



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

The crosstalk module simulates the optical and/or electronic crosstalk of the scintillation light between neighboring crystals. Thus, if the input pulse arrives in a crystal array, this module creates pulses around it (in the edge and corner neighbor crystals). The percentage of energy that is given to the neighboring crystals is determined by the user. To insert a crosstalk module that distributes 10% of input pulse energy to the adjacent crystals and 5% to the corner crystals, the following commands can be used::

/gate/digitizer/Singles/insert crosstalk
/gate/digitizer/Singles/crosstalk/chooseCrosstalkVolume crystal
/gate/digitizer/Singles/crosstalk/setEdgesFraction 0.1
/gate/digitizer/Singles/crosstalk/setCornersFraction 0.05
/gate/digitizerMgr/crystal/SinglesDigitizer/Singles/insert crosstalk
/gate/digitizerMgr/crystal/SinglesDigitizer/Singles/crosstalk/setEdgesFraction 0.1
/gate/digitizerMgr/crystal/SinglesDigitizer/Singles/crosstalk/setCornersFraction 0.05

In this example, a pulse is created in each neighbor of the crystal that received the initial pulse. These secondary pulses have 10% (5% for each corner crystals) of the initial energy of the pulse.

**BEWARE:** this module works only for a chosen volume that is an array repeater!!!


Spatial blurring in sinogrmas
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

In PET analysis, coincidence events provide the lines of response (LOR) needed for the image reconstruction. Only the two crystal numbers are transferred by the simulation. The determination of these crystal numbers is based on the crystal in which the highest energy has been deposited. Without additional spatial blurring of the crystal, simulation results will always have a better spatial resolution than experimental measurements. This module is only available for the *ecat* system. The spatial blurring is based on a 2D Gaussian function::

# E C A T 7
/gate/output/sinogram/enable
/gate/output/sinogram/RadialBins Your_Sinogram_Radial_Bin_Number
/gate/output/sinogram/setTangCrystalBlurring Your_Value_1 mm
/gate/output/sinogram/setAxialCrystalBlurring Your_Value_2 mm
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.**


.. _digitizer_multiple_processor_chains-label:
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