///\file "medical/dna/cellularPhantom/.README.txt"
///\brief Example cellularPhantom README page


/*! \page ExamplecellularPhantom Example cellularPhantom

\authors P. Barberet, S. Incerti, N. H. Tran, L. Morelli
LP2i, IN2P3 / CNRS / Bordeaux University, 33175 Gradignan, France
E-mail: barberet@lp2ib.in2p3.fr or incerti@lp2ib.in2p3.fr

If you use this code, please cite the following publication:
Monte-Carlo dosimetry on a realistic cell monolayer geometry exposed to alpha-particle,
P. Barberet, F. Vianna, M. Karamitros, T. Brun, N. Gordillo, P. Moretto, S. Incerti, H. Seznec,
Phys. Med. Biol. 57 (2012) 2189-2207
https://doi.org/10.1088/0031-9155/57/8/2189

\section cellularPhantom_s1 INTRODUCTION.

The cellularPhantom example shows how to simulate the irradiation of a 3D voxel
phantom containing biological cells, created from a confocal microscopy 24-bit RGB image.

The original image was created thanks to:
- H. De Oliveira, T. Désigaux, N. Dusserre, ART BioPrint, France
- F. Paris, C. Niaudet, Inserm, France

These developments were carried out as part of the "Flash'Atlantic" project
(2023-2024) funded by CNRS-MITI, France, and Inserm, France.

Two phantom files phantom.dat (low resolution) and phantomHR.dat (high resolution)
are provided in the phantoms directory.

They were created using the ImageJ phantom.ijm macro located in the ImageJ directory.
See the phantoms/Documentation.pdf file for more information

The low resolution file is used for visualization in the macro vis.mac.
It contains the following lines:

54300   20230   17320   16750
=> total number of voxels, number of red, green and blue voxels

734.0507        734.0507        90.6372 microns
=> whole X, Y and Z size of the phantom, with unit

2.8674  2.8674  2.0142  microns
=> size of a single voxel, with unit

And the list of individual voxels, with the format: X, Y and Z positions, type
(type is 1 for R, 2 for G, 3 for B):
232.2582        31.5412         0.0000          2
235.1256        31.5412         0.0000          2
...

The low resolution and high resolution files can be used by the run.mac macro.

\section cellularPhantom_s2 GEOMETRY SET-UP

The geometry is a 1-mm side cube ("World") made of air, with a thickness of 100 um,
containing a liquid water medium ("Medium") of side 900 um and thickness 95 um,
containing itself the phantom ("Phantom").

The World and Medium dimensions can be changed by UI command.

\section cellularPhantom_s3 SET-UP

Make sure $G4LEDATA points to the low energy electromagnetic data files.

\section cellularPhantom_s4 HOW TO RUN THE EXAMPLE

In interactive mode, run:
\verbatim
./cellularPhantom
this will show the phantom in 3D (requires memory).
\endverbatim

In batch, the macro run.mac can be used:
\verbatim
./cellularPhantom run.mac
\endverbatim

In this macro, the user can select:
- the number of threads (MT mode)
- the phantom file name
- the World and Medium dimensions
- the Medium material
- the phantom voxel density
- the position (shift in X or Y or Z) of the phantom in the Medium
- the production cuts outside and inside in the phantom
- the incident particles (using GPS)

\section cellularPhantom_s5 PHYSICS

The PhysicsList class uses Geant4 option4 electromagnetic physics.

It also contains other physics lists including Geant4-DNA option2,
which is commented by default.

\section cellularPhantom_s6 SIMULATION OUTPUT AND RESULT ANALYSIS

The output results consists in a phantom.root file, containing three ntuples,
corresponding to the 3 types of voxels (red, green and blue) of the original image.

The ROOT macro plot.C can be run to extract and display:
- the cellular phantom
- the absorbed energy distribution in the 3 types of voxels
- the absorbed energy 2D map for the 3 types of voxels
- the absorbed dose 2D map for the 3 types of voxels

Simply do, after the simulation:
\verbatim
root plot.C
\endverbatim

In addition, the following quantities are displayed:
- total number of voxels in phantom
- total number of RED voxels in phantom
- total number of GREEN voxels in phantom
- total number of BLUE voxels in phantom
- total absorbed energy in RED voxels (MeV)
- total absorbed energy in GREEN voxels (MeV)
- total absorbed energy in BLUE voxels (MeV)
- total absorbed dose in RED voxels (Gy)
- total absorbed dose in GREEN voxels (Gy)
- total absorbed dose in BLUE voxels (Gy)

Results are stored in the results.root file.

*/
