qYY$Id: README,v 1.13 2007/06/06 19:11:20 pia Exp $
-------------------------------------------------------------------

     =========================================================
                        Geant4 - human_phantom example 
     =========================================================

                                 README
                          -----------------------

Authors: S. Guatelli (guatelli@ge.infn.it) and M. G. Pia (pia@ge.infn.it),
         INFN Genova, Italy.

------> Introduction

The human_phantom example models anthropomorphic phantoms for
Geant4 simulations.
Two models are available: MIRD [1] and ORNL [2] (Male and Female for each approach).

[1] W.S. Snyder, et al, "MIRD Pamphlet No. 5 Revised, Estimates of 
absorbed fractions for monoenergetic photon sources uniformly distributed 
in various organs of a heterogeneous phantom",
J. Nucl. Med. Suppl., no. 3, pp. 5-52, 1969.

[2] M. Cristy and K. F. Eckerman, "Specific absorbed fractions of energy 
at various ages from internal photon sources", ORNL/TM-8381/VI, Apr. 1987.
 
The example is based on code developed by the undergraduate student
G. Guerrieri.
Note: this is a preliminary beta-version of the code; an improved 
version will be distributed in the next Geant4 public release, compliant
with the design in a forthcoming publication, and subject to a design 
and code review.

NOTE: At the moment this advanced example is executed correctly with geantino 
particles as primary particles; it is not executed correctly with other primary particle types. 
This is due to an internal Geant4 bug concerning ellipsoids.
For details look at the Geant4 Bug Report #914. This problem is taken under 
care by the Geant4 Collaboration.
 
-----> Geometry 

The process of building a phantom is handled through the Builder 
design pattern.
The creation of coherent models of the human phantom is handled through 
an Abstract Factory design pattern.

The organs of the MIRD phantom are implemented in hard-code; the organs of 
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
class G4HumanPhantomMaterial. The materials of the ORNL model are defined in 
the GDML files.

*** Parameterized breast ***
MIRD Female model: a breast is analytical and derives from the MIRD 
anthropomorphic phantom; the other breast derives from the model [3] and 
it is voxelised.

[3] D.R. Dance and R. A. Hunt, "Voxel breast phantom to represent breasts 
of different sizes and glandularities for use with a Monte Carlo simulation 
program", Report RMTPC 02/1005.

-----> Physics

Particles: e-, e+, photon, geantino
Physics list: electromagnetic processes are active for photons, e- and e+
The threshold of production of secondary particles is set to 0.1 * mm.

-----> Primary particles

The primary particles are geantino.
UI commands:

/gun/energy energy : to change the energy of primary particles
/gun/particle particle_type : to change the type of primary particle
/gun/setBeam beamAlongX : generate a primary particle beam along the X axis
/gun/setBeam beamAlongY : generate a primary particle beam along the Y axis
/gun/setBeam beamAlongZ : generate a primary particle beam along the Y axis
/gun/setBeam isotropicFlux : generate a primary particle with random direction,
                             from a random point.   

-----> Energy deposit

The energy deposit is calculated in the organs of the phantom.
At the end of the execution of the simulation  the summary of the total energy deposit in 
each organ is print out.
The user can set the sensitivity of each organ interactively through the UI command:
/bodypart/addBodyPart organName yes
(see adultFemale.mac as example)

If the sensitivity is not set ( /bodypart/addBodyPart organName no ), 
the energy deposit is not calculated in the specific organ.

The energy deposit is calculated in each voxel of the parameterised breast.

-----> Analysis

output file: g4humanphantom.hbk containing
1D histogram id=10:     Particle Path Distribution (cm)
2D histogram id=20:     Particle Projection XY (cm, cm)
2D histogram id=30:     Particle Projection YZ (cm, cm)
2D histogram id=40:     Particle Projection ZX (cm, cm)
2D histogram id=50:     Energy Deposit (MeV, y axis) in Body Part (x axis)
2D histogram id=100:    Edep(MeV) in the parameterized breast, x= slice, y= sector

----> Macro files: example of different human phantoms

default.mac is executed by default in the simulation
adultMIRDFemale.mac: example to define a MIRD female human phantom
adultMIRDMale.mac: example to define a MIRD male human phantom
adultHead.mac: example how to define one piece of the anatomy
adultORNLFemale.mac: example to define a ORNL female human phantom
adultORNLMale.mac: example to define a ORNL male human phantom
adultMIXFemale.mac : example of MIRD human female phantom with 
	             parameterised breast

-----> Setup

Example enviroment with the compiler gcc-3.2.3, on the Linux platform                              

A standard Geant4 example GNUmakefile is provided.                     

The following environment variables need to be set:
G4LEDATA : points to low energy data base
set G4ANALYSIS_USE equal to 1 to activate the analysis

- Install the GDML package with Geant4 extensions and Xerces
.
  See: http://cern.ch/gdml.

- Set the environment variable GDML_BASE to point to the area where
  GDML is installed.
  
- Set the environment variable XERCESCROOT to point to the area where
  Xerces is installed.

- Add to the LD_LIBRARY_PATH the $XERCESCROOT/lib

- IMPORTANT!!!! Customize the '*.gdml' schema file in the directories
gdmlData/Female and gdmlData/Male, specifying in the top line the
  right path where to retrieve the main GDML schema file.

- Analysis set-up:  AIDA 3.2.1, PI 1.3.3                            
                    Users can download the analysis tools from:  
                    http://aida.freehep.org/
                    http://www.cern.ch/PI      

- Compile and link to generate an executable:
 	      % gmake
 		
- Execute the application:
 	      % phantom
	 
- Default macro: adultFemale.mac (MIRD, Female model) 
- Other macros:  adultMale.mac (MIRD, Male model)
                 adultORNLFemale.mac (ORNL, Female model)
                 adultORNLMale.mac (ORNL, Male model)
- Visualization macros: vrmlVis.mac, dawnVis.mac, openGLVis.mac, noVis.mac
- Run particles: run.mac

---------------------------------------------------------------------------
