High-precision dosimetry
From UCL HEP PBT Wiki
m |
m |
||
| Line 1: | Line 1: | ||
== <span style="color:#000080"> Introduction </span> == | == <span style="color:#000080"> Introduction </span> == | ||
| - | This tutorial is based on the [http://geant4-dna.org/ Geant4-DNA project] tutorials. We chose to show | + | This tutorial is based on the [http://geant4-dna.org/ Geant4-DNA project] tutorials. We chose to show three of the examples: |
| - | * <span style="color:#ff0000"> dnaphysics </span>: This example | + | * <span style="color:#ff0000"> dnaphysics </span>: This example simulates track structures in 100-micron side cube made of liquid water. The physics processes are defined using class '''G4EmDNAPhysics'''. [http://geant4-dna.in2p3.fr/styled-3/styled-8/index.html Here] you can find more information about the different physics process that are used to build class '''G4EmDNAPhysics''' . [http://geant4-dna.in2p3.fr/styled-3/styled-9/index.html Here] you can find how to build your own '''G4EmDNAPhysics''' class. Simulated is a an electron beam using class '''G4ParticleGun'''. The beam is shot from the center of the cube. The output of this tutorial is a root ntuple with type of particle, type of physics process, energy deposit, energy loss and step length for every simulation step. |
| - | * <span style="color:#ff0000"> dnageometry </span>: This example simulates | + | * <span style="color:#ff0000"> dnageometry </span>: This example simulates track structures of different charged particles within a simplified geometrical model of the DNA molecule in a cell nucleus. [http://www.chemguide.co.uk/organicprops/aminoacids/dna1.html Here] you can read more about the DNA structure. Simulated are 6109 DNA pairs with the following structures: double helix, nucleosome, chromatine fibres, chromatine fibre loops and chromosome territories. Proton beam is simulated using class '''G4ParticleGun'''. The physics processes are defined using class '''G4EmDNAPhysics'''. The output is a root ntuple with type of particle, type of physics process, energy deposit and step length for every simulation step. |
| - | * <span style="color:#ff0000"> microbeam </span>: This example simulates the cellular irradiation beam line installed on the [http://www.cenbg.in2p3.fr/-AIFIRA-Home-?lang=en AIFIRA] electrostatic accelerator facility located at [http://www.cenbg.in2p3.fr/ CENBG], Bordeaux-Gradignan, France. This | + | * <span style="color:#ff0000"> microbeam </span>: This example simulates the cellular irradiation beam line installed on the [http://www.cenbg.in2p3.fr/-AIFIRA-Home-?lang=en AIFIRA] electrostatic accelerator facility located at [http://www.cenbg.in2p3.fr/ CENBG], Bordeaux-Gradignan, France. This accelerator is mainly used to investigate the effects of low dose irradiation on living cells. A realistic cell phantom is obtained from confocal microscopy and from ion beam anlysis techniques. Alpha particles of 3 MeV are incident on this phantom. The output among other things is the dose deposited in the cell cytoplasm and in the cell nucleus. |
| - | == <span style="color:#000080"> | + | == <span style="color:#000080"> How to run the tutorial </span> == |
; Connect to the HEP cluster | ; Connect to the HEP cluster | ||
| Line 25: | Line 25: | ||
[username@plus1 ~]$ source /unix/pbt/software/dev/bin/pbt-dev.sh | [username@plus1 ~]$ source /unix/pbt/software/dev/bin/pbt-dev.sh | ||
</pre> | </pre> | ||
| - | |||
| - | |||
; Copy the code to your working directory | ; Copy the code to your working directory | ||
| Line 36: | Line 34: | ||
</pre> | </pre> | ||
| - | |||
| - | |||
* <span style="color:#ff0000"> dnaphysics </span>: | * <span style="color:#ff0000"> dnaphysics </span>: | ||
| Line 112: | Line 108: | ||
== <span style="color:#000080"> How to analyze data </span> == | == <span style="color:#000080"> How to analyze data </span> == | ||
| - | === <span style="color:# | + | === <span style="color:#ff0000"> dnaphysics </span> === |
| + | |||
| + | This is a [http://geant4advancedexampleswg.wikispaces.com/DNAPhysics link] to the official dnaphysics tutorial explanation notes. We recommend to read it before proceeding with this tutorial. | ||
==== <span style="color:#000080"> Root file </span> ==== | ==== <span style="color:#000080"> Root file </span> ==== | ||
| - | The macro dna.mac produces two root files '''dna_t0.root''' and '''dna_t1.root''' with ntuples containing | + | The macro dna.mac produces two root files '''dna_t0.root''' and '''dna_t1.root''' with ntuples containing the following information for every step: |
* type of particle | * type of particle | ||
* type of physics process | * type of physics process | ||
| - | * x, y and z coordinates of the step | + | * x, y and z coordinates of the beginning of the step |
| - | * total energy deposit [eV] | + | * total energy deposit alo[eV] |
* step length [nm] | * step length [nm] | ||
| - | * kinetic energy difference along the step[eV] | + | * kinetic energy difference along the step [eV] |
| + | |||
| + | You can open the first root file and see the different ntuples: | ||
| + | |||
| + | <pre style="color: #800000; background-color: #dcdcdc"> | ||
| + | [username@plus1 dnaphysics_build]$ root -l dna_t0.root | ||
| + | |||
| + | root [1] new TBrowser | ||
| + | |||
| + | Select ROOT Files, dna_t0.root and Folder dna | ||
| + | |||
| + | Click on the different leafs | ||
| + | </pre> | ||
You can analyze the root files using '''plot.C''' macro. | You can analyze the root files using '''plot.C''' macro. | ||
| Line 133: | Line 143: | ||
</pre> | </pre> | ||
| - | The macro produces two plots. The first plot shows the distribution of the different physics plrocesses | + | The macro produces two plots. The first plot shows the distribution of the different physics plrocesses. The second plot shows the trajectory of the incident particle. [http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnaphysics/flags.txt Here] you can find the codes for '''flagParticle''' and '''flagProcess'''. The root macro produces the following plots: |
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnaphysics/plot.png | http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnaphysics/plot.png | ||
| - | ==== <span style="color:#000080"> | + | ==== <span style="color:#000080"> Run with different settings </span> ==== |
You can change the type and the energy of the incident particle by modifying the macro dna.mac. Open the macro with editor pico: | You can change the type and the energy of the incident particle by modifying the macro dna.mac. Open the macro with editor pico: | ||
| Line 166: | Line 176: | ||
==== <span style="color:#000080"> Visualisation </span> ==== | ==== <span style="color:#000080"> Visualisation </span> ==== | ||
| + | |||
| + | There is an option to run dna.mac with visualisation (in dna.mac uncomment line /control/execute vis.mac). However, runing with visualisation is very slow and it is not recommended. | ||
| + | |||
| + | === <span style="color:#ff0000"> dnageometry </span> === | ||
| + | |||
| + | This is a [http://geant4advancedexampleswg.wikispaces.com/DNAGeometry link] to the official dnageometry tutorial explanation notes. | ||
| + | |||
| + | ==== <span style="color:#000080"> Root file </span> ==== | ||
| + | |||
| + | The macro dnageometry.mac produces a root file '''dnageometry.root''' with ntuples. The ntuples contain information for those geant4 steps for which the deposited energy in the DNA backbone is different from zero: | ||
| + | |||
| + | * type of particle | ||
| + | * type of physics process | ||
| + | * the two DNA strands | ||
| + | * x, y and z coordinates of the post step [nm] | ||
| + | * total energy deposit alo[eV] | ||
| + | * step length [nm] | ||
| + | |||
| + | You can analyze the root files using '''plot.C''' macro. First, copy this macro to your directory, then run the root | ||
| + | macro. | ||
| + | |||
| + | <pre style="color: #800000; background-color: #dcdcdc"> | ||
| + | [username@plus1 dnaphysics_build]$ cp /home/username/DNAProject/dnageometry/plot.C . | ||
| + | |||
| + | [username@plus1 dnaphysics_build]$ root -l | ||
| + | |||
| + | root [1] .x plot.C | ||
| + | </pre> | ||
| + | |||
| + | The macro produces a plot that shows the position of the two DNA strands in two colors. The spheres represent the amino bases. The plot shows only the DNA pairs with deposited energy (see the ntuple deffinition in SteppingAction.cc). | ||
| + | |||
| + | http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/dnageometry/plot.png | ||
| + | |||
| + | You can modify root macro '''plot.C''' and plot the other ntuples. | ||
| + | |||
| + | === <span style="color:#ff0000"> microbeam </span> === | ||
| + | |||
| + | This is a [http://geant4advancedexampleswg.wikispaces.com/MicrobeamExample link] to the official microbeam tutorial explanation notes. | ||
| + | |||
| + | ==== <span style="color:#000080"> Root file </span> ==== | ||
| + | |||
| + | The macro microbeam.mac produces root files '''microbeam_t0.root''' and '''microbeam_t1.root''' with ntuples grouped in five folders. | ||
| + | |||
| + | You can analyze the root ntuples using the '''plot.C''' macro. | ||
| + | |||
| + | <pre style="color: #800000; background-color: #dcdcdc"> | ||
| + | [username@plus1 dnaphysics_build]$ root -l | ||
| + | |||
| + | root [1] .x plot.C | ||
| + | </pre> | ||
| + | |||
| + | http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/DNAProject/microbeam/plot.png | ||
| + | |||
| + | == <span style="color:#000080"> Files </span> == | ||
| + | |||
| + | [[List of high-precision dosimetry files with brief description]] | ||
