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