[807] | 1 | qYY$Id: README,v 1.13 2007/06/06 19:11:20 pia Exp $ |
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| 2 | ------------------------------------------------------------------- |
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| 3 | |
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| 4 | ========================================================= |
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| 5 | Geant4 - human_phantom example |
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| 6 | ========================================================= |
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| 7 | |
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| 8 | README |
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| 9 | ----------------------- |
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| 10 | |
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| 11 | Authors: S. Guatelli (guatelli@ge.infn.it) and M. G. Pia (pia@ge.infn.it), |
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| 12 | INFN Genova, Italy. |
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| 13 | |
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| 14 | ------> Introduction |
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| 15 | |
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| 16 | The human_phantom example models anthropomorphic phantoms for |
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| 17 | Geant4 simulations. |
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| 18 | Two models are available: MIRD [1] and ORNL [2] (Male and Female for each approach). |
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| 19 | |
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| 20 | [1] W.S. Snyder, et al, "MIRD Pamphlet No. 5 Revised, Estimates of |
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| 21 | absorbed fractions for monoenergetic photon sources uniformly distributed |
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| 22 | in various organs of a heterogeneous phantom", |
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| 23 | J. Nucl. Med. Suppl., no. 3, pp. 5-52, 1969. |
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| 24 | |
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| 25 | [2] M. Cristy and K. F. Eckerman, "Specific absorbed fractions of energy |
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| 26 | at various ages from internal photon sources", ORNL/TM-8381/VI, Apr. 1987. |
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| 27 | |
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| 28 | The example is based on code developed by the undergraduate student |
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| 29 | G. Guerrieri. |
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| 30 | Note: this is a preliminary beta-version of the code; an improved |
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| 31 | version will be distributed in the next Geant4 public release, compliant |
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| 32 | with the design in a forthcoming publication, and subject to a design |
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| 33 | and code review. |
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| 34 | |
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| 35 | NOTE: At the moment this advanced example is executed correctly with geantino |
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| 36 | particles as primary particles; it is not executed correctly with other primary particle types. |
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| 37 | This is due to an internal Geant4 bug concerning ellipsoids. |
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| 38 | For details look at the Geant4 Bug Report #914. This problem is taken under |
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| 39 | care by the Geant4 Collaboration. |
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| 40 | |
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| 41 | -----> Geometry |
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| 42 | |
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| 43 | The process of building a phantom is handled through the Builder |
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| 44 | design pattern. |
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| 45 | The creation of coherent models of the human phantom is handled through |
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| 46 | an Abstract Factory design pattern. |
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| 47 | |
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| 48 | The organs of the MIRD phantom are implemented in hard-code; the organs of |
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| 49 | the ORNL phantom are handled through GDML (Geometry Description Markup Language, www.cern.ch/gdml). The materials of the MIRD model are defined in the |
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| 50 | class G4HumanPhantomMaterial. The materials of the ORNL model are defined in |
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| 51 | the GDML files. |
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| 52 | |
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| 53 | *** Parameterized breast *** |
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| 54 | MIRD Female model: a breast is analytical and derives from the MIRD |
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| 55 | anthropomorphic phantom; the other breast derives from the model [3] and |
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| 56 | it is voxelised. |
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| 57 | |
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| 58 | [3] D.R. Dance and R. A. Hunt, "Voxel breast phantom to represent breasts |
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| 59 | of different sizes and glandularities for use with a Monte Carlo simulation |
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| 60 | program", Report RMTPC 02/1005. |
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| 61 | |
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| 62 | -----> Physics |
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| 63 | |
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| 64 | Particles: e-, e+, photon, geantino |
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| 65 | Physics list: electromagnetic processes are active for photons, e- and e+ |
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| 66 | The threshold of production of secondary particles is set to 0.1 * mm. |
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| 67 | |
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| 68 | -----> Primary particles |
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| 69 | |
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| 70 | The primary particles are geantino. |
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| 71 | UI commands: |
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| 72 | |
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| 73 | /gun/energy energy : to change the energy of primary particles |
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| 74 | /gun/particle particle_type : to change the type of primary particle |
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| 75 | /gun/setBeam beamAlongX : generate a primary particle beam along the X axis |
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| 76 | /gun/setBeam beamAlongY : generate a primary particle beam along the Y axis |
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| 77 | /gun/setBeam beamAlongZ : generate a primary particle beam along the Y axis |
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| 78 | /gun/setBeam isotropicFlux : generate a primary particle with random direction, |
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| 79 | from a random point. |
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| 80 | |
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| 81 | -----> Energy deposit |
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| 82 | |
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| 83 | The energy deposit is calculated in the organs of the phantom. |
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| 84 | At the end of the execution of the simulation the summary of the total energy deposit in |
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| 85 | each organ is print out. |
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| 86 | The user can set the sensitivity of each organ interactively through the UI command: |
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| 87 | /bodypart/addBodyPart organName yes |
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| 88 | (see adultFemale.mac as example) |
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| 89 | |
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| 90 | If the sensitivity is not set ( /bodypart/addBodyPart organName no ), |
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| 91 | the energy deposit is not calculated in the specific organ. |
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| 92 | |
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| 93 | The energy deposit is calculated in each voxel of the parameterised breast. |
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| 94 | |
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| 95 | -----> Analysis |
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| 96 | |
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| 97 | output file: g4humanphantom.hbk containing |
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| 98 | 1D histogram id=10: Particle Path Distribution (cm) |
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| 99 | 2D histogram id=20: Particle Projection XY (cm, cm) |
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| 100 | 2D histogram id=30: Particle Projection YZ (cm, cm) |
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| 101 | 2D histogram id=40: Particle Projection ZX (cm, cm) |
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| 102 | 2D histogram id=50: Energy Deposit (MeV, y axis) in Body Part (x axis) |
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| 103 | 2D histogram id=100: Edep(MeV) in the parameterized breast, x= slice, y= sector |
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| 104 | |
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| 105 | ----> Macro files: example of different human phantoms |
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| 106 | |
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| 107 | default.mac is executed by default in the simulation |
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| 108 | adultMIRDFemale.mac: example to define a MIRD female human phantom |
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| 109 | adultMIRDMale.mac: example to define a MIRD male human phantom |
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| 110 | adultHead.mac: example how to define one piece of the anatomy |
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| 111 | adultORNLFemale.mac: example to define a ORNL female human phantom |
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| 112 | adultORNLMale.mac: example to define a ORNL male human phantom |
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| 113 | adultMIXFemale.mac : example of MIRD human female phantom with |
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| 114 | parameterised breast |
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| 115 | |
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| 116 | -----> Setup |
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| 117 | |
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| 118 | Example enviroment with the compiler gcc-3.2.3, on the Linux platform |
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| 119 | |
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| 120 | A standard Geant4 example GNUmakefile is provided. |
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| 121 | |
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| 122 | The following environment variables need to be set: |
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| 123 | G4LEDATA : points to low energy data base |
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| 124 | set G4ANALYSIS_USE equal to 1 to activate the analysis |
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| 125 | |
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| 126 | - Install the GDML package with Geant4 extensions and Xerces |
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| 127 | . |
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| 128 | See: http://cern.ch/gdml. |
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| 129 | |
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| 130 | - Set the environment variable GDML_BASE to point to the area where |
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| 131 | GDML is installed. |
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| 132 | |
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| 133 | - Set the environment variable XERCESCROOT to point to the area where |
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| 134 | Xerces is installed. |
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| 135 | |
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| 136 | - Add to the LD_LIBRARY_PATH the $XERCESCROOT/lib |
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| 137 | |
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| 138 | - IMPORTANT!!!! Customize the '*.gdml' schema file in the directories |
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| 139 | gdmlData/Female and gdmlData/Male, specifying in the top line the |
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| 140 | right path where to retrieve the main GDML schema file. |
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| 141 | |
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| 142 | - Analysis set-up: AIDA 3.2.1, PI 1.3.3 |
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| 143 | Users can download the analysis tools from: |
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| 144 | http://aida.freehep.org/ |
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| 145 | http://www.cern.ch/PI |
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| 146 | |
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| 147 | - Compile and link to generate an executable: |
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| 148 | % gmake |
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| 149 | |
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| 150 | - Execute the application: |
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| 151 | % phantom |
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| 152 | |
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| 153 | - Default macro: adultFemale.mac (MIRD, Female model) |
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| 154 | - Other macros: adultMale.mac (MIRD, Male model) |
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| 155 | adultORNLFemale.mac (ORNL, Female model) |
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| 156 | adultORNLMale.mac (ORNL, Male model) |
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| 157 | - Visualization macros: vrmlVis.mac, dawnVis.mac, openGLVis.mac, noVis.mac |
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| 158 | - Run particles: run.mac |
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| 159 | |
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| 160 | --------------------------------------------------------------------------- |
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