This is a personal note for learning Monte Carlo software GATE. The official document is here. I found that the official document is somehow outdated, and some parts are not very clear (e.g. the visualization in 'Getting Started' section). This personal note is a complementary of official document. For some basic and detailed description, you still need to refer to the official document.
In the Getting Started section, it is not clear how to visualize the geometry. Here is how to do it.
First you need to open a window:
/vis/open OGL
Then you should run
/vis/drawVolume
to enable showing object. The default view angle is not good. It is recommended to change it to a different angle, for example:
/vis/viewer/set/viewpointThetaPhi 45 45
GATE does not automatically update visualization. You need to type
/gate/geometry/rebuild
to let it update your geometry. In my test, it is not needed to type /gate/run/initialize to let it show the geometry, though this command is necessary for running the complete simulation.
There are two ways to zoom in or zoom out the view. The first way is to zoom based on current view. For example,
/vis/viewer/zoom 2
will zoom in by a factor of 2. If the number is smaller than 1, it will zoom out with the given factor.
Another method is to zoom based on default view. The syntax is
/vis/viewer/zoomTo 2
This will zoom in based on the default view. You can take relative path and absolute path as an analogy. Without doubt, the following command will set zoom to default.
/vis/viewer/zoomTo 1
The command to translate viewer window is pan and panTo. For example
/vis/viewer/pan 0.5 0
/vis/viewer/panTo 20 -40 mm
In my test, if unit is not specified, the default unit seems to be meter. Correct me if this is wrong.
To render a volume (e.g. phantom) in solid style instead of wire frame style, the following command can be used:
/gate/my_phantom/vis/forceSolid
To display the particles' trajectory, the following commands can be used:
/vis/viewer/flush
/tracking/storeTrajectory 1
/vis/scene/add/trajectories
/vis/scene/endOfEventAction accumulate
To keep the visualization window after running the simulation, execute GATE with --qt option. In addition, you need to reduce the number of particles for visualization purpose.
System is a key-concept of GATE which provides a template of a predefined geometry to simulate a scanner. The document is here.
In section Step 1: Defining a scanner geometry of Getting Started part, it says that volumes should be attached to a sensitive detector in order to save the hits, and gives the following example:
# D E F I N E A S E N S I T I V E D E T E C T O R
/gate/box2/attachCrystalSD vglue 1cm
where the argument vglue 1cm is very confusing. I checked the email archive, and found that vglue 1cm seems to be a typo. In other words, there should be no vglue 1cm. The correct command should be
/gate/box2/attachCrystalSD
The discussion in email archive is based on old version GATE v6.1, but I think it is still applicable to current version (v9.2).
GATE recommends "physics list builder" mechanism starting from Version 7.0. A short (and old) introduction is here. For X-ray imaging application, I think the best option is emstandard_opt3? This is how to add the physics list in GATE:
/gate/physics/addPhysicsList emstandard_opt3
The document says the list of production threshold can be displayed with the command:
/gate/physics/displayCuts
However, in my test, it does not display anything. Why? In addition, it says this command should be used after the initialization. Again, I found other examples use this command before initialization.
This part seems to be very complicated ...
There is a command gps in GATE, which is not described. According to GEANT4 document, gps should mean General Particle Source. In addition, some commands related to gps are deprecated, for example,
/gate/source/twogamma/gps/centre 0 0 0 cm
is shown to be deprecated, where twogamma is the source name defined by users. It seems that it should be replaced with
/gate/source/twogamma/gps/pos/centre 0 0 0 cm
which is shown (in Qt window) that it has the same effect as
/gate/source/twogamma/gps/position 0 0 0 cm
(Pretty confusing!) So I recommend checking the message in Qt window, which can be opened with command
Gate --qt