Gabriele Cosmo
179 lines
10 KiB
Plaintext
179 lines
10 KiB
Plaintext
stim_pixe_tomography advanced example
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The stim_pixe_tomography advanced example is developed to simulate three dimensional STIM or
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PIXE tomography experiments. The simulation results are written in a binary file and can be easily accessed using the
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provided scripts.
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Publications:
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[1] Li Z, Incerti S, Beasley D, Shen H, Wang S, Seznec H, et al. Accuracy of three-dimensional proton imaging of an
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inertial confinement fusion target assessed by Geant4 simulation. Nucl Instrum Methods Phys Res B. 2023;
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536:38-44. https://doi.org/10.1016/j.nimb.2022.12.026.
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[2] Michelet C, Li Z, Jalenques H, Incerti S, Barberet P, Devs G, et al. A Geant4 simulation of X-ray emission
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for three-dimensional proton imaging of microscopic samples. Phys Med. 2022;94:85-93. https://doi.org/10.1016/j.ejmp.2021.12.002.
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[3] Michelet C, Li Z, Yang W, Incerti S, Desbarats P, Giovannelli J-F, et al. A Geant4 simulation for
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three-dimensional proton imaging of microscopic samples. Phys Med. 2019;65:172-80. https://doi.org/10.1016/j.ejmp.2019.08.022.
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Contact:
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michelet@lp2ib.in2p3.fr (Claire Michelet)
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zhuxin.li@outlook.com (Zhuxin Li)
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More information and a detailed UserGuide are available: http://geant4.in2p3.fr (Documentation section)
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1 - GEOMETRY DEFINITION
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Three phantoms are available, users can build up new phantoms or choose the following
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three phantoms by setting the "phantom_type":
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1) A simple cube (see publication [2-3]), phantom_type = 1
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The absorber is a box made of a given material.
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2) Upper part of Caenorhabditis elegans (C.elegans) worm (see publication [2-3]) , phantom_type = 2
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C.elegans phantom is composed of 6 ellipsoids. The size and shape of ellipsoids are based on the
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nanotoxicology studies carried-out at LP2I Bordeaux laboratory .
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3) Inertial confinement fusion (ICF) target (see publication [1]), phantom_type = 3
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ICF target is sphere shell, made of Ge-doped glow discharge polymer (GDP)
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2 - PHYSICS LIST
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Physics lists are based on modular design. Several modules are instantiated:
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1) Transportation
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2) EM physics
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3) Decay physics
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4) Hadron physics, optional
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EM physics builders can be local or from G4 kernel physics_lists subdirectory.
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- "emlivermore" default low-energy EM physics using Livermore data
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- "local" local physics builders, options are explicit in PhysListEmStandard
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- "emstandard_opt0" recommended standard EM physics for LHC
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- "emstandard_opt1" best CPU performance standard physics for LHC
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- "emstandard_opt2" similar fast simulation
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- "emstandard_opt3" best standard EM options - analog to "local" above
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- "emstandard_opt4" best current advanced EM options standard + lowenergy
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- "emstandardWVI" standard EM physics and WentzelVI multiple scattering
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- "emstandardSS" standard EM physics and single scattering model
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- "emstandardGS" standard EM physics and Goudsmit-Saunderson multiple scatt.
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- "empenelope" low-energy EM physics implementing Penelope models
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- "emlowenergy" low-energy EM physics implementing experimental
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Decay and StepMax processes are added to each list.
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Optional components can be added:
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- "elastic" elastic scattering of hadrons
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- "binary" QBBC configuration of hadron inelastic models
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- "binary_ion" Binary ion inelastic models
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Physics lists and options can be (re)set with UI commands.
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3 - HOW TO RUN
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To run a PIXE tomography simulation in 'batch' mode using a pixe3d.mac file:
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./stim_pixe_tomography -p pixe3d.mac
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or if you want to specify the number of threads:
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./stim_pixe_tomography -p pixe3d.mac N
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N is the number of threads
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An example of pixe3d.mac is provided.
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It is designed for the PIXE-T simulation of the cube phantom of 40 um.
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It is defined for 10 projections 1 slice 20 pixels. 1000000 protons are used for each beam.
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To run a STIM tomography simulation:
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./stim_pixe_tomography -s pixe3d_stim.mac
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or if you want to specify the number of threads:
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./stim_pixe_tomography -s pixe3d_stim.mac N
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N is the number of threads
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An example of pixe3d_stim.mac (arbitrarily name, you may rename it pixe3d.mac if you wish) is provided.
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It is designed for the STIM-T simulation of the cube phantom of 40 um.
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It is defined for 10 projections 1 slice 20 pixels. 100 protons are used for each beam.
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4 - VISUALISATION
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To visualize the phantoms, run:
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./stim_pixe_tomography
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5 - OUTPUT FILES
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If a PIXE tomography simulation is made, two files are going to be generated:
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1) GammaAtCreation.dat, which keeps the info of secondary photons at creation
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2) GammaAtExit.dat, which keeps the info of secondary photons at exit of the phantom
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If a STIM tomography simulation is made, ProtonAtExit.dat is generated, in which the info of primary protons is kept
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6 - LIST OF MACROS AND SCRIPTS
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Once you build the example, the following macros and script will be copied to your build directory:
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pixe3d.mac: an example macro to run a PIXE-T simulation for cube of 40 um
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pixe3d_stim.mac: an example macro to run a STIM-T simulation for cube of 40 um
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pixe3d_initial.mac: it contains the information of physics processes
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init_vis.mac and vis.mac: for the visualization
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GPSPointLoop.C: it generates a macro file to run the simulation by reading pixe3d_initial.mac
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In the Scripts folder, you will find other scripts for different uses.
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To obtain the reconstruction data:
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BinToStd_ProtonAtExit.C: it reads the STIM-T simulation results and generates the data file for STIM-T reconstruction using selection with particle momentum.
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BinToStd_GammaAtCreation.C: it reads the PIXE-T simulation results for X-rays at creation and generates the data file for PIXE-T reconstruction using selection with particle momentum.
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BinToStd_GammaAtExit.C: it reads the PIXE-T simulation results for X-rays at exit and generates the data file for PIXE-T reconstruction using selection with particle momentum.
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BinToStd_proton_position.C: it reads the STIM-T simulation results and generates the data file for STIM-T reconstruction using selection with particle position and momentum
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BinToStd_gamma_position.C: it reads the PIXE-T simulation results for X-rays and generates the data file for PIXE-T reconstruction using selection with particle position and momentum
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To locate the interruption if an interruption of simulation occurs:
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LocateInterruption_ProtonAtExit.C: in case of interruption, it locates the projection position of interruption for STIM-T simulation.
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LocateInterruption_GammaAtExit.C: in case of interruption, it locates the projection position of interruption for PIXE-T simulation.
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To obtain the reconstruction data in case of an interruption of simulation:***
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Concatenate_BinToStd_ProtonAtExit.C: in case of one interruption, it reads STIM-T simulation results and generates the data file for STIM-T reconstruction.
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Concatenate_BinToStd_GammaAtCreation.C: in case of one interruption, it reads PIXE-T simulation results for X-rays at creation and generates the data file for PIXE-T reconstruction.
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Concatenate_BinToStd_GammaAtExit.C: in case of one interruption, it reads PIXE-T simulation results for X-rays at exit and generates the data file for PIXE-T reconstruction.
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To visualize the spectrum:
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Spectrum_proton.C: it visualizes the spectrum of protons and plots a histogram by reading simulation result ProtonAtExit.dat.
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Spectrum_gamma.C: it visualizes the spectrum of X-rays and plots a histogram by reading simulation result GammaAtCreation.dat or GammaAtExit.dat.
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TomoSpectrum_HIST_proton.C: it visualizes the spectrum of protons and plots a histogram by reading StimEvent data. It also writes the spectrum data in a txt file.
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TomoSpectrum.C: it visualizes the spectrum of X-rays and plots a graph by reading PixeEvent data. It also writes the spectrum data in a txt file.
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TomoSpectrum_HIST.C: it visualizes the spectrum of X-rays and plots a histogram by reading PixeEvent data. It also writes the spectrum data in a txt file.
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Scripts for specific use:
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Extract_Projection.C: it extracts 50 projections from a PixeEvent data file for tomographic reconstruction, which contains 100 projections. In fact, it extracts the projection 0, 2, 4, 6, 898 from projections 0-99. It eventually generates a new file with new index number of projections 0-49.
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Check_PixeEventFile.C: it checks if the index of projections of a PixeEvent data file for tomographic reconstruction is correct. For example, if the user extract 50 projections from a data file composed 100 projections, it is necessary to make sure in the new data file, the index of projection starts from 0 and ends at 49.
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Extract_Slice.C: it extracts a certain number of slice(s) from a PixeEvent data file for tomographic reconstruction. Users need to specify the first and the last slice to be extracted. Note that when writing a new data file, the index of slices will be initiated from 0.
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Concatenate_BinToStd_GammaAtCreation_fabricate.C: if users make a PIXE-T simulation on a symmetrical object with only one projection, this script can be used to fabricate the other 99 projection data for X-rays at creation with same energy.
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Concatenate_BinToStd_GammaAtExit_fabricate.C: if users make a PIXE-T simulation on a symmetrical object with only one projection, this script can be used to fabricate the other 99 projection data for X-rays at exit with same energy
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Scripts to generate voxelized phantoms:***
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In order to compare the reconstructed tomographic images with original
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phantoms, it may be necessary to use a voxelized phantom.
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generate_voxelized_sphere_phantom.py: it generates a voxelized phantom of an inertial confinement fusion target.
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generate_voxelized_worm_phantom.py: it generates a voxelized phantom of the upper part of C. elegans.
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More information can be found in the UserGuide.
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