How to generate system response matrix from Gate simulation#

Luo Jinghong, Fang Han

Sept 19, 2024

30 min ~ 1 hour

How to open Gate v9.4#

Note

Following contents are based on using UB OnDemand

You can apply for a node when click on “Quick Launch General-Computer Desktop”, and then you will have a 24 hours node; Then you can import these codes line by line:

module load gcc/11.2.0 geant4/11.2.1 geant4-data/11.2 
export GEANT4_DATA_DIR=${EBROOTGEANT4MINDATA} 
module load gcc/11.2.0 openmpi/4.1.1 gate/9.4 geant4-data/11.2

after that you should go to the top folder of your .mac file,and then use code as follow:

Gate --qt Yourfilename.mac

then it will start to run.

How to change root file into PDF/npz/hdf5#

Tip

You should use Jupyter Lab/Notebook Advanced Options.

  1. Cilck on “Jupyter Lab/Notebook Advanced Options”

  2. Put gcc/11.2.0  openmpi/4.1.1 root/6.26.10 matplotlib/3.5.2 in Extra Modules To Load with Jupyter

  3. Set QoS as general-compute

  4. Take a look at my code decribed in change_root_to_pdf. I recommand all use .npz, because if you want to use hdf5, you should import h5py which will cause more trouble.

How to reconstruct by digital picture#

  1. open pyrecon file;

  2. put your .npz or .hdf5 file into data file;

  3. use test_projection_nonmpi.py to generate projection;

  4. use test_recon_nonmpi.py to generate reconstruction picture;

  5. In pyrecon/data file, there is not only hotrod_phantom, but also a file 2p-source-gen.ipynb to generate digital picture(that code can change the position and size of a point)

  6. you can use read_projection_npz and read_recon_npz to see the picture result

How to reconstruct by MC simulation#

You can simply change the shape and number of your source and then run the .mac file. Then you can use “change_root_to_projection” in Jupyter notebook to get your projection file.

Tricks of using Gate to build your machine#

  1. http://opengatecollaboration.org/ is the most useful one, and then you find the documentation to get start.

  2. after v9.3 the digitizer code has a big change

  3. only the repeater code applied in the crystal can you get different crystalID

  4. rotate would happen in the axis of your object. For example, if you want to rotate the machine head, please rotate the world.

Tricks of using root#

After import:

module load gcc/11.2.0 geant4/11.2.1 geant4-data/11.2 
export GEANT4_DATA_DIR=${EBROOTGEANT4MINDATA} 
module load gcc/11.2.0 openmpi/4.1.1 gate/9.4 geant4-data/11.2

Your should do

"root Yourfilename.root" to open your root file.

For me, use root command

  • .ls to see the file in my root file,

  • command Singles->Print() to see the list of “Singles”

  • command Singles->Draw("Your target name") to draw the histogram

  • Singles->GetEntries() to get the number of the events

Tip

More code about root is here https://root.cern/learn/ (it is really a big task!!!)

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