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Geant4/examples/advanced/stim_pixe_tomography/README

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Differences between /examples/advanced/stim_pixe_tomography/README (Version 11.3.0) and /examples/advanced/stim_pixe_tomography/README (Version 10.3.p3)


  1 stim_pixe_tomography advanced example             
  2                                                   
  3 The stim_pixe_tomography advanced example is d    
  4 PIXE tomography experiments. The simulation re    
  5 provided scripts.                                 
  6                                                   
  7  Publications:                                    
  8                                                   
  9     [1] Li Z, Incerti S, Beasley D, Shen H, Wa    
 10     inertial confinement fusion target assesse    
 11     536:38-44. https://doi.org/10.1016/j.nimb.    
 12                                                   
 13     [2] Michelet C, Li Z, Jalenques H, Incerti    
 14     for three-dimensional proton imaging of mi    
 15                                                   
 16     [3] Michelet C, Li Z, Yang W, Incerti S, D    
 17     three-dimensional proton imaging of micros    
 18                                                   
 19  Contact:                                         
 20                                                   
 21     michelet@lp2ib.in2p3.fr      (Claire Miche    
 22                                                   
 23     zhuxin.li@outlook.com        (Zhuxin Li)      
 24                                                   
 25                                                   
 26 More information and a detailed UserGuide are     
 27                                                   
 28  1 - GEOMETRY DEFINITION                          
 29                                                   
 30   Three phantoms are available, users can buil    
 31   three phantoms by setting the "phantom_type"    
 32                                                   
 33     1) A simple cube (see publication [2-3]),     
 34                                                   
 35     The absorber is a box made of a given mate    
 36                                                   
 37     2) Upper part of Caenorhabditis elegans (C    
 38                                                   
 39     C.elegans phantom is composed of  6 ellips    
 40     nanotoxicology studies carried-out at LP2I    
 41                                                   
 42     3) Inertial confinement fusion (ICF) targe    
 43                                                   
 44     ICF target is sphere shell, made of Ge-dop    
 45                                                   
 46                                                   
 47 2 - PHYSICS LIST                                  
 48                                                   
 49   Physics lists are based on modular design. S    
 50                                                   
 51     1) Transportation                             
 52     2) EM physics                                 
 53     3) Decay physics                              
 54     4) Hadron physics, optional                   
 55                                                   
 56  EM physics builders can be local or from G4 k    
 57                                                   
 58      - "emlivermore"             default low-e    
 59      - "local"                   local physics    
 60      - "emstandard_opt0"         recommended s    
 61      - "emstandard_opt1"         best CPU perf    
 62      - "emstandard_opt2"         similar fast     
 63      - "emstandard_opt3"         best standard    
 64      - "emstandard_opt4"         best current     
 65      - "emstandardWVI"           standard EM p    
 66      - "emstandardSS"            standard EM p    
 67      - "emstandardGS"            standard EM p    
 68      - "empenelope"              low-energy EM    
 69      - "emlowenergy"             low-energy EM    
 70                                                   
 71   Decay and StepMax processes are added to eac    
 72                                                   
 73   Optional components can be added:               
 74                                                   
 75      - "elastic"       elastic scattering of h    
 76      - "binary"        QBBC configuration of h    
 77      - "binary_ion"    Binary ion inelastic mo    
 78                                                   
 79   Physics lists and options can be (re)set wit    
 80                                                   
 81                                                   
 82 3 - HOW TO RUN                                    
 83                                                   
 84  To run a PIXE tomography simulation in 'batch    
 85                                                   
 86     ./stim_pixe_tomography -p pixe3d.mac          
 87                                                   
 88  or if you want to specify the number of threa    
 89                                                   
 90     ./stim_pixe_tomography -p pixe3d.mac N        
 91                                                   
 92     N is the number of threads                    
 93                                                   
 94   An example of pixe3d.mac is provided.           
 95   It is designed for the PIXE-T simulation of     
 96   It is defined for 10 projections  1 slice  2    
 97                                                   
 98                                                   
 99  To run a STIM tomography simulation:             
100                                                   
101       ./stim_pixe_tomography -s pixe3d_stim.ma    
102                                                   
103   or if you want to specify the number of thre    
104                                                   
105     ./stim_pixe_tomography -s pixe3d_stim.mac     
106                                                   
107     N is the number of threads                    
108                                                   
109  An example of pixe3d_stim.mac (arbitrarily na    
110  It is designed for the STIM-T simulation of t    
111  It is defined for 10 projections  1 slice  20    
112                                                   
113 4 - VISUALISATION                                 
114 To visualize the phantoms, run:                   
115                                                   
116     ./stim_pixe_tomography                        
117                                                   
118 5 - OUTPUT FILES                                  
119                                                   
120  If a PIXE tomography simulation is made, two     
121                                                   
122     1) GammaAtCreation.dat, which keeps the in    
123     2) GammaAtExit.dat, which keeps the info o    
124                                                   
125  If a STIM tomography simulation is made, Prot    
126                                                   
127                                                   
128 6 - LIST OF MACROS AND SCRIPTS                    
129                                                   
130 Once you build the example, the following macr    
131                                                   
132         pixe3d.mac: an example macro to run a     
133         pixe3d_stim.mac: an example macro to r    
134         pixe3d_initial.mac: it contains the in    
135         init_vis.mac and vis.mac: for the visu    
136         GPSPointLoop.C: it generates a macro f    
137                                                   
138 In the Scripts folder, you will find other scr    
139                                                   
140 To obtain the reconstruction data:                
141                                                   
142         BinToStd_ProtonAtExit.C: it reads the     
143         BinToStd_GammaAtCreation.C: it reads t    
144         BinToStd_GammaAtExit.C: it reads the P    
145         BinToStd_proton_position.C: it reads t    
146         BinToStd_gamma_position.C: it reads th    
147                                                   
148 To locate the interruption if an interruption     
149                                                   
150         LocateInterruption_ProtonAtExit.C: in     
151         LocateInterruption_GammaAtExit.C: in c    
152 To obtain the reconstruction data in case of a    
153                                                   
154         Concatenate_BinToStd_ProtonAtExit.C: i    
155         Concatenate_BinToStd_GammaAtCreation.C    
156         Concatenate_BinToStd_GammaAtExit.C: in    
157 To visualize the spectrum:                        
158                                                   
159         Spectrum_proton.C: it visualizes the s    
160         Spectrum_gamma.C: it visualizes the sp    
161         TomoSpectrum_HIST_proton.C: it visuali    
162         TomoSpectrum.C: it visualizes the spec    
163         TomoSpectrum_HIST.C: it visualizes the    
164 Scripts for specific use:                         
165                                                   
166         Extract_Projection.C: it extracts 50 p    
167         Check_PixeEventFile.C: it checks if th    
168         Extract_Slice.C: it extracts a certain    
169         Concatenate_BinToStd_GammaAtCreation_f    
170         Concatenate_BinToStd_GammaAtExit_fabri    
171 Scripts to generate voxelized phantoms:***        
172                                                   
173 In order to compare the reconstructed tomograp    
174 phantoms, it may be necessary to use a voxeliz    
175                                                   
176         generate_voxelized_sphere_phantom.py:     
177         generate_voxelized_worm_phantom.py: it    
178 More information can be found in the UserGuide