| Geant4 Cross Reference |
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