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                        Geant4 - human_phantom example 
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                                 README
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Authors: S. Guatelli (susanna@uow.edu.au), University of Wollongong, Australia,  M. G. Pia (pia@ge.infn.it),
         INFN Genova, Italy and F. Ambroglini (filippo.ambroglini@pg.infn.it), INFN Perugia, Italy.

This example is currently maintained by S. Guatelli, University of Wollongong, Australia 
and L. Pandola, LNGS, INFN, Italy.

The example is based on code developed by G. Guerrieri, University of 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.

Note: Currently the ORNL phantom is under review.

-----> 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.
If using ORNL phantom model with no GDML set-up a segmentation
fault will be otained when running the simulation.

*** 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: charged particles, gamma, geantino
Physics list: electromagnetic processes are modelled.
The threshold of production of secondary particles is set to 1 * mm.

-----> Primary particles

The G4 General Particle Source is used to generate primary radiation field.
Macro primary.mac contains the definition of the primary radiation field.   

-----> 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.

Currently for ORNL model the energy deposition is calculated in the head only.

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
To activate the analysis, the application must be built with the option
WITH_ANALYSIS_USE=ON :
make -DCMAKE_INSTALL_PREFIX=/path/to/geant4-installation -DWITH_ANALYSIS_USE=ON /path/to/human_phantom/

**** SEQUENTIAL MODE *************
output file: g4humanphantom.root containing
an ntuple with the Energy Deposit in each Body Part.
macro.C is provided to print the content of the ntuple in a ROOT
interactive analysis session.

**** MULTITHREAD MODE
output files:
human_phantom.root_t0
..
..
human_phantom.root_t#

where # is the number of threads

type: source MergeFiles to merge the output of each thread in a single one
called human_phantom.root
macro.C is provided to print the content of the ntuple in a ROOT
interactive analysis session.

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

default.mac is executed by default in the simulation, with visualisation
batch.mac: macro to run in batch mode ( with no visualisation)
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 - THIS NEEDS GDML INSTALLED
adultORNLMale.mac: example to define a ORNL male human phantom - THIS NEEDS GDML INSTALLED
adultMIXFemale.mac : example of MIRD human female phantom with 
	             parameterised breast

-----> How to build the example 

If the user wants to run the example importing geometries via GDML, 
he/she needs to have built the persistency/gdml module by having
set the -DGEANT4_USE_GDML=ON flag during the CMAKE configuration step, 
as well as the -DXERCESC_ROOT_DIR=<path_to_xercesc> flag pointing to 
the path where the XercesC XML parser package is installed in your system.

- By default GDML is not configured to be used in the example. If the user wishes
to use GDML, he/she has to build the example with the following command:
cmake -DCMAKE_INSTALL_PREFIX=/path/to/geant4-installation -DWITH_GDML_USE=ON /path/to/human_phantom/

- if using GDML, the directory gdmlData must be copied in the directory where 
the simulation will be launched.

- Compile and link to generate the executable (in your CMAKE build directory):
 	      % make

- Execute the application:
 	      % ./phantom
	 
- Default macro: default.mac (MIRD, Female model) 

- Visualization macros: vrmlVis.mac, dawnVis.mac, openGLVis.mac

- Run simulation in batch mode: batch.mac

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