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46 changes: 22 additions & 24 deletions docs/how_to_run_gate.rst
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Expand Up @@ -150,7 +150,6 @@ and the following output (or something similar) will appear on the screen::
[Core-0] -h, --help print the help
[Core-0] -v, --version print the version
[Core-0] -a, --param set alias. format is '[alias1,value1] [alias2,value2] ...'
[Core-0] --d use the DigiMode
[Core-0] --qt use the Qt visualization mode

Running GATE in Qt mode
Expand Down Expand Up @@ -204,18 +203,18 @@ For instance, suppose we want to parameterize the lower and upper level energy d
and the length of coincidence window. Here is the corresponding macro command lines::

# D I G I T I Z E R
1 /gate/digitizer/Singles/insert adder
2 /gate/digitizer/Singles/insert readout
3 /gate/digitizer/Singles/readout/setDepth 1
4 /gate/digitizer/Singles/insert blurring
5 /gate/digitizer/Singles/blurring/setResolution 0.26
6 /gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
7 /gate/digitizer/Singles/insert thresholder
8 /gate/digitizer/Singles/thresholder/setThreshold {lld} keV
9 /gate/digitizer/Singles/insert upholder
10 /gate/digitizer/Singles/upholder/setUphold {uld} keV
1 /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/insert adder
2 /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/insert readout
3 /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/readout/setDepth 1
4 /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/insert blurring
5 /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/blurring/setResolution 0.26
6 /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/blurring/setEnergyOfReference 511. keV
7 /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/insert thresholder
8 /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/thresholder/setThreshold {lld} keV
9 /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/insert upholder
10 /gate/digitizerMgr/crystal/SinglesDigitizer/Singles/upholder/setUphold {uld} keV
# C O I N C I D E N C E S O R T E R
11 /gate/digitizer/Coincidences/setWindow {CoincWindow} ns
11 /gate/digitizerMgr/crystal/CoincidencesDigitizer/Coincidences/setWindow {CoincWindow} ns

Lines 8, 10, and 11 define aliases for the lower level discriminator,
the upper level discriminator, and the length of the coincidence window, respectively.
Expand All @@ -233,29 +232,28 @@ It is worth emphasizing the following points about aliases:
* Aliases are case sensitive, so **[lld,350]** is not the same as **[LLD,350]**.
* All aliases in your macro file(s) must be defined when you run Gate. If some are undefined the simulation will fail.

How to launch *DigiGate*
How to launch *DigiGate* or *OFFLINE DIGITIZER*
------------------------

GATE offers an operating mode dedicated to digitizer optimization, known as *DigiGate* (see :ref:`digitizer_and_readout_parameters-label`). *DigiGate* works by re-reading a previously generated ROOT hit-file.
GATE offers an operating mode dedicated to digitizer optimization, known as *DigiGate* or *OFFLINE DIGITIZER* (see :ref:`digitizer_and_readout_parameters-label`). *DigiGate* works by re-reading a previously generated ROOT hit or singles file.

The use of **DigiGate** consists of two steps.

* In the first step, the simulation runs according to **MacroTest.mac**. This macro file should save the **Hits** data in the root output file with the name **gate.root** (which is the default name).
* In the second step, the digitizer modifications are made in **MacroTest.mac** (like a new module for the energy resolution, or a different dead-time...), and then the analysis is repeated by using the **gate.root** file as an input file for the program **DigiGate**. This is achieved by launching **Gate** with a '-d' option::
* In the first step, the simulation runs according to **MacroTest.mac**. This macro file should save the **Hits** or **Singles** data in the root output file with the name a **your_gate_output.root**::

Gate < MacroTest.mac
> Gate MacroTest.mac

-> a root output file is produced with *Hits* information.
* In the second step, the digitizer modifications are made in **MacroTest.mac** (like a new module for the energy resolution, or a different dead-time...) if needed, and then the analysis is repeated by using the **your_gate_output.root** file as an input file. This is achieved by launching **Gate** with '-d-fromHits' or '-d-fromSingles' options and the name of a file to take as input::

-> the digitizer of MacroTest.mac is changed along with the name of the root output file::
Gate MacroTest.mac -d_fromHits your_gate_output.root (to get Hits -> Singles -> Coincidences)

or::

Gate MacroTest.mac -d_fromSingles your_gate_output.root (to get Singles -> Coincidences)

Gate --d < MacroTest.mac

-> a new root output file is produced which incorporates the changes due to a different digitizer without having to repeat the particle generation and
-> a new root output file **your_gate_output_digi.root** is produced which incorporates the changes due to a different digitizer without having to repeat the particle generation and
its propagation.
user can use the following GATE command to read the hit file replaced the name **gate.root**::

/gate/hitreader/setFileName FileName

How to separate the phantom and detector tracking - Phase space approach
------------------------------------------------------------------------
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