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

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