Monoenergetic proton pencil beam

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Contents

Introduction

This example shows the dose distribution in water along the incident proton beam. The beam hits the water cube surface and deposits a dose under the surface of the water. The volume of the water cube is divided into slices perpendicular to the incident beam. At each slice the deposited dose and energy is computed.

The slices are created using class G4PVReplica. The energy and the dose are scored using classes G4UserSteppingAction and G4UserRunAction. Alternatively, the energy and the dose are scored using class G4ScoringManager by defining two scoring meshes in longitudinal and lateral direction of the beam. More information about the scoring meshes can be found here. The protons are generated using G4ParticleGun class. There is an option to chose among several EM and the QGSP_BIC_EMY physics lists.

g4_00_6000e.png

The image shows the water box divided into slices using class G4PVReplica. Protons are in blue, photons are in green.

How to run the tutorial

Connect to the HEP cluster and create folder ProtonPBFolder in your area
ssh -X username@plus1.hep.ucl.ac.uk 

username@plus1.hep.ucl.ac.uk's password: type your password here
 
[username@plus1 ~]$ mkdir ProtonPBFolder 

[username@plus1 ~]$ cd ProtonPBFolder  
Setup your environment
[username@plus1 ProtonPBFolder]$ source /unix/pbt/software/dev/bin/pbt-dev.sh  
Copy the code to your working directory and rename it
[username@plus1 ProtonPBFolder]$ cp -r /unix/pbt/tutorials/basic/ProtonPB .
  
[username@plus1 ProtonPBFolder]$ mv ProtonPB ProtonPB_source
Inside /home/username/ProtonPBFolder/ create a directory
[username@plus1 ProtonPBFolder]$ mkdir ProtonPB_build  
To compile the code enter this directory and run cmake and make
[username@plus1 ProtonPBFolder]$ cd ProtonPB_build 

[username@plus1 ProtonPB_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/ProtonPBFolder/ProtonPB_source 

[username@plus1 ProtonPB_build]$ make  
Run macro proton.mac
[username@plus1 ProtonPB_build]$ ./protonPB proton.mac

How to analyze data

The macro produces a root file Proton.root with two histograms. The first histogram shows the energy deposition in water box along the beam line, the second histogram shows zoomed energy deposition around the peak. The macro also produces several text files.

  • The data in files DoseFile.txt and PlotDose.txt was created using classes G4UserSteppingAction and G4UserRunAction. The file DoseFile.txt contains energy and dose deposition for every layer. The file PlotDose.txt contains only depth vs dose for each layer. These text files can be analyzed with MATLAB or ROOT.
  • The files DoseLongitudinalMesh.txt, EnergyLongitudinalMesh.txt, DoseLateralMesh.txt and EnergyLateralMesh.txt contain information about the dose and energy deposition in voxels in longitudinal and lateral direction of the beam. The data was created using class G4ScoringManager and commands /score/ in proton.mac. These text files can be analyzed with MATLAB or ROOT.
  • The two ways to record data should give similar result.

Text files

This is output from DoseFile.txt with physics process QGSP_BIC_EMY and incident proton energy of 62 MeV. Use your favorite editor pico, vi, emacs etc to open text files. For example, open this text file with editor pico:

[username@plus1 ProtonPB_build]$ pico DoseFile.txt
 Layers :	x[mm]  	Edep 	    Edep/Ebeam[%]  Dose        Dose/MaxDose[%]
 layer 1: 	0.8	5.17382 GeV	1.39081	6.47608e-07 Gy	17.3315	
 layer 2: 	1.6	5.24175 GeV	1.40907	6.5611e-07 Gy	17.5591	
 layer 3: 	2.4	5.29862 GeV	1.42436	6.63229e-07 Gy	17.7496	
 layer 4: 	3.2	5.41481 GeV	1.45559	6.77772e-07 Gy	18.1388	
 layer 5: 	4	5.43787 GeV	1.46179	6.80658e-07 Gy	18.216	
 layer 6: 	4.8	5.52101 GeV	1.48414	6.91065e-07 Gy	18.4946	
 layer 7: 	5.6	5.64633 GeV	1.51783	7.06751e-07 Gy	18.9144	
 layer 8: 	6.4	5.63969 GeV	1.51605	7.0592e-07 Gy	18.8921	
 layer 9: 	7.2	5.71744 GeV	1.53695	7.15652e-07 Gy	19.1526	
 layer 10: 	8	5.78086 GeV	1.55399	7.2359e-07 Gy	19.365	
 layer 11: 	8.8	5.94371 GeV	1.59777	7.43975e-07 Gy	19.9106	
 layer 12: 	9.6	6.02518 GeV	1.61967	7.54172e-07 Gy	20.1835	
 layer 13: 	10.4	6.10292 GeV	1.64057	7.63903e-07 Gy	20.4439	
 layer 14: 	11.2	6.18071 GeV	1.66148	7.7364e-07 Gy	20.7045	
 layer 15: 	12	6.2621 GeV	1.68336	7.83827e-07 Gy	20.9771	
 layer 16: 	12.8	6.37762 GeV	1.71441	7.98286e-07 Gy	21.3641	
 layer 17: 	13.6	6.52458 GeV	1.75392	8.16682e-07 Gy	21.8564	
 layer 18: 	14.4	6.67805 GeV	1.79517	8.35892e-07 Gy	22.3705	
 layer 19: 	15.2	6.86252 GeV	1.84476	8.58982e-07 Gy	22.9884	
 layer 20: 	16	6.95226 GeV	1.86889	8.70215e-07 Gy	23.289	
 layer 21: 	16.8	7.11679 GeV	1.91312	8.90809e-07 Gy	23.8402	
 layer 22: 	17.6	7.15125 GeV	1.92238	8.95122e-07 Gy	23.9556	
 layer 23: 	18.4	7.43274 GeV	1.99805	9.30356e-07 Gy	24.8986	
 layer 24: 	19.2	7.58811 GeV	2.03981	9.49804e-07 Gy	25.419	
 layer 25: 	20	7.8156 GeV	2.10097	9.78279e-07 Gy	26.1811	
 layer 26: 	20.8	7.94754 GeV	2.13643	9.94794e-07 Gy	26.6231	
 layer 27: 	21.6	8.35363 GeV	2.2456	1.04562e-06 Gy	27.9834	
 layer 28: 	22.4	8.44564 GeV	2.27033	1.05714e-06 Gy	28.2917	
 layer 29: 	23.2	8.74817 GeV	2.35166	1.09501e-06 Gy	29.3051	
 layer 30: 	24	9.08194 GeV	2.44138	1.13679e-06 Gy	30.4232	
 layer 31: 	24.8	9.50886 GeV	2.55615	1.19022e-06 Gy	31.8533	
 layer 32: 	25.6	9.93302 GeV	2.67017	1.24332e-06 Gy	33.2741	
 layer 33: 	26.4	10.5627 GeV	2.83943	1.32213e-06 Gy	35.3834	
 layer 34: 	27.2	11.1563 GeV	2.99902	1.39644e-06 Gy	37.3721	
 layer 35: 	28	12.0025 GeV	3.22647	1.50235e-06 Gy	40.2065	
 layer 36: 	28.8	13.1124 GeV	3.52485	1.64128e-06 Gy	43.9247	
 layer 37: 	29.6	14.5158 GeV	3.90209	1.81694e-06 Gy	48.6257	
 layer 38: 	30.4	16.8932 GeV	4.54119	2.11452e-06 Gy	56.5898	
 layer 39: 	31.2	20.9827 GeV	5.64051	2.62641e-06 Gy	70.289	
 layer 40: 	32	29.8521 GeV	8.02475	3.73658e-06 Gy	100	
 layer 41: 	32.8	14.922 GeV	4.0113	1.86779e-06 Gy	49.9866	
 layer 42: 	33.6	330.005 MeV	0.088711     4.13067e-08 Gy  1.10547	
 layer 43: 	34.4	2.92265 MeV	0.000785658  3.65828e-10 Gy  0.00979044	
 layer 44: 	35.2	864.413 keV	0.000232369  1.08199e-10 Gy  0.00289566	
 layer 45: 	36	673.958 keV	0.000181172  8.43594e-11 Gy  0.00225766	
 layer 46: 	36.8	1.18851 MeV	0.000319491  1.48765e-10 Gy  0.00398132	
 layer 47: 	37.6	3.81319 MeV	0.00102505   4.77297e-10 Gy  0.0127736	
 layer 48: 	38.4	4.58219 MeV	0.00123177   5.73552e-10 Gy  0.0153496	
 layer 49: 	39.2	7.29449 MeV	0.00196088   9.13052e-10 Gy  0.0244355	
 layer 50: 	40	0 eV 	0	0 Gy	0	


 The run consists of 6000 proton of 62 MeV through 4 cm  of Water (density: 1 g/cm3 ) 
 divided into 50 slices.

 Edep is the deposited energy in every slice.
 Total incident energy(Ebeam)= 372 GeV
 Total energy deposit= 367.368 GeV
 Dose is the deposited dose in every slice.
 MaxDose is the highest dose value from all slices.

The corresponding PlotDose.txt is:

0.8	17.3315	
1.6	17.5591	
2.4	17.7496	
3.2	18.1388	
4	18.216	
4.8	18.4946	
5.6	18.9144	
6.4	18.8921	
7.2	19.1526	
8	19.365	
8.8	19.9106	
9.6	20.1835	
10.4	20.4439	
11.2	20.7045	
12	20.9771	
12.8	21.3641	
13.6	21.8564	
14.4	22.3705	
15.2	22.9884	
16	23.289	
16.8	23.8402	
17.6	23.9556	
18.4	24.8986	
19.2	25.419	
20	26.1811	
20.8	26.6231	
21.6	27.9834	
22.4	28.2917	
23.2	29.3051	
24	30.4232	
24.8	31.8533	
25.6	33.2741	
26.4	35.3834	
27.2	37.3721	
28	40.2065	
28.8	43.9247	
29.6	48.6257	
30.4	56.5898	
31.2	70.289	
32	100	
32.8	49.9866	
33.6	1.10547	
34.4	0.00979044	
35.2	0.00289566	
36	0.00225766	
36.8	0.00398132	
37.6	0.0127736	
38.4	0.0153496	
39.2	0.0244355	
40	0		

DoseLongitudinalMesh.txt and EnergyLongitudinalMesh.txt contain information about the dose and energy deposition in 50 voxels along the beam.

DoseLateralMesh.txt and EnergyLateralMesh.txt contain information about the dose and energy deposition in 50 voxels in direction perpendicular to the beam at its peak location along the beam.

Root file

Open Proton.root file in the following way:

[username@plus1 ProtonPB_build]$ root -l Proton.root

root [1] new TBrowser

Select ROOT Files and Proton.root

This is the energy deposition along the beam in the absorber:

BraggPeak_PB1.png

This is the energy deposition along the beam in the absorber, zoomed around the peak:

BraggPeak_PBzoom1.png

You can close your ROOT session by typing

.q

Folder RootScripts contains several ROOT scripts which plot dose deposition in data and simulation. You can use script PlotSimulation.C to plot the dose deposition along the absorber. This script uses PlotDose.txt. Copy the script to your current ProtonPB_build directory:

cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotSimulation.C .

Then run the script in the following way:

[username@plus1 ProtonPB_build]$ root -l 

root [1] .x PlotSimulation.C

This will create Simulation.root file with the following plot:

Simulation1.png

You can also plot the file PlotDose.txt using MATLAB. Similarly to the previous example first copy the text file to your computer. In the terminal at your computer write:

scp username@plus1.hep.ucl.ac.uk:/home/username/ProtonPBFolder/ProtonPB_build/PlotDose.txt .

Then, open MATLAB and follow the procedure:

  • Import the file: Chose 'HOME' tab and 'Import Data'.
  • In the 'Import Data' window select the 'PlotDose.txt' file choosing the right path.
  • In the opened window select the data points in the 'IMPORT' tab. If you like, you can change the name of the variables. For example, 'x' instead of 'VarName1' and 'Dose' instead of 'VarName2'. Then, press 'Import Selection'/'Import Data'.
  • Close the Import Window and in the Command Window type plot(x,Dose). Press Enter.

This plot will be created with added axis labels and a legend:

matlab1proton.png

You can also plot the data in DoseLongitudinalMesh.txt and DoseLateralMesh.txt which were created using commands /score/ in the macro proton.mac. The file DoseLongitudinalMesh.txt will be used later to compare with data from the Clatterbridge Cancer Center. Now, use script PlotLateralDoseMesh.C to plot the lateral dose distribution. Before running the script substitude the commas in DoseLateralMesh.txt with spaces. Remove also the header in the text file. Then, save the text file as DoseLateralMesh_Mod.txt.

[username@plus1 ProtonPB_build]$ cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotLateralDoseMesh.C .

[username@plus1 ProtonPB_build]$ root -l 

root [1] .x PlotLateralDoseMesh.C

This will create LateralDose_Mesh.root file with the following plot:

SimulationLateralMesh.png

Run with different settings

You can change the physics process, incident proton energy and number of slices etc. by modifying the macro proton.mac. Open the macro with editor pico:

[username@plus1 ProtonPB_build]$ pico proton.mac

This is the content of the macro:

# proton.mac
#
/control/verbose 2
/run/verbose 2
/tracking/verbose 0
/run/particle/verbose 1
/run/particle/dumpList
#
# set geometry 
/protonPB/det/setSizeX  4 cm
/protonPB/det/setSizeYZ 4 cm
/protonPB/det/setSliceSizeYZ 4 cm
/protonPB/det/sliceNumber 50 
#
# define longitudinal scoring mesh
# along the beam
/score/create/boxMesh waterMeshlongitudinal
/score/mesh/boxSize 2. 2. 2. cm
/score/mesh/nBin 50 1 1
/score/mesh/translate/xyz 0. 0. 0. cm
/score/quantity/energyDeposit energyDeposit 
/score/quantity/doseDeposit doseDeposit
/score/close
#
# define lateral scoring mesh
# centered at the Bragg peak
/score/create/boxMesh waterMeshlateral
/score/mesh/boxSize 0.1 2. 2. cm
/score/mesh/nBin 1 1 50
/score/mesh/translate/xyz 1.2 0. 0. cm
/score/quantity/energyDeposit energyDeposit 
/score/quantity/doseDeposit doseDeposit
/score/close
#
# set physics process
/protonPB/phys/addPhysics QGSP_BIC_EMY
#/protonPB/phys/addPhysics emlivermore
#/protonPB/phys/addPhysics empenelope
#
# production tresholds (recommended range 
#cut off not bigger than 10% of slice thickness)
/protonPB/phys/setCuts 0.2 mm
#/protonPB/phys/setGCut 1 um
#/protonPB/phys/setECut 1 um
#/protonPB/phys/setPCut 1 um
#
# initialize
/run/initialize
#
# visualisation
#/control/execute visualisation.mac
#
/gun/particle proton
# particle energy used in Clatterbridge Centre  
/gun/energy 62 MeV
#
# beam size
#/photonPB/gun/rndm 3 mm
#
# step limit (recommended not bigger than 5% of 
# slice thickness)
/protonPB/stepMax 0.1 mm
#
/protonPB/event/printModulo 50
#
# output file
/analysis/setFileName Proton
#
# histogram 
/analysis/h1/set 2 50 25 35 mm
# number of events
/run/beamOn 6000
#
# drawing projections
#/score/drawProjection waterMeshlongitudinal doseDeposit
#/score/drawProjection waterMeshlateral doseDeposit
#
# dump scores to a file
/score/dumpQuantityToFile waterMeshlongitudinal doseDeposit DoseLongitudinalMesh.txt
/score/dumpQuantityToFile waterMeshlongitudinal energyDeposit EnergyLongitudinalMesh.txt
/score/dumpQuantityToFile waterMeshlateral doseDeposit DoseLateralMesh.txt
/score/dumpQuantityToFile waterMeshlateral energyDeposit EnergyLateralMesh.txt

Change dimensions of the water box

The default size is 4x4x4 cm. You can change the dimensions by modifying the lines

/protonPB/det/setSizeX  4 cm
/protonPB/det/setSizeYZ 4 cm 

Change the physics process

The default physics process is QGSP_BIC_EMY. This is a physics list recommended for proton therapy. You can check what will be the dose deposition if you change the physics list. In proton.mac change

/photonPB/phys/addPhysics QGSP_BIC_EMY

to

/photonPB/phys/addPhysics emlivermore

Change the incident proton energy

The default energy is 62 MeV. This is one of the energies used in radiotherapy. In proton.mac you can change the value of 62 MeV

/gun/energy 62 MeV

to, for example, 50 MeV

/gun/energy 50 MeV

Change the diameter of the beam

You can set the diameter of the beam with the command:

/protonPB/gun/rndm 3 mm

Change the number of slices

You can change the number of slices. The default number is 50. Keep in mind that if you want to increase the number of slices you need to modify the file DetectorConstruction.hh in /ProtonPB_source/include/.

In DetectorConstruction.hh set MaxLayer to value bigger than the number of your slices. The default value is MaxLayer=60. For example, if you want to have 55 slices you do not need to modify MaxLayer. Then, only in proton.mac change the number of slices

/protonPB/det/sliceNumber 55 

Modify the mesh

You can change the size of the mesh (longitudinal and lateral) and the number of voxels by modifying their corresponding lines

/score/mesh/boxSize 2. 2. 2. cm
/score/mesh/nBin 30 1 1

After modifications in proton.mac

After modifying the macro proton.mac you can run it

[username@plus1 ProtonPB_build]$ ./protonPB proton.mac

If you modify files in directory ProtonPB_source (for example you change the value of MaxLayer) you need to comppile the code. In directory PhotonPB_build do

[username@plus1 ProtonPB_build]$ make 

then run the macro proton.mac.

Visualisation

If you want to use visualisation, in macro proton.mac uncomment the line /control/execute visualisation.mac. This will run macro visualisation.mac with a specific visualisation setup. If you uncomment the lines /score/drawProjection waterMeshlongitudinal doseDeposit and /score/drawProjection waterMeshlateral doseDeposit you will draw the dose projections. In this example, we use DAWN event display. Before running the visualisation look at this DAWN tutorial.

To run the visualisation, first uncomment lines /control/execute visualisation.mac and /score/drawProjection waterMeshlongitudinal doseDeposit. Then, run the proton.mac

[username@plus1 ProtonPB_build]$ ./protonPB proton.mac

In addition to the text files the code will create two .prim files, g4_00.prim and g4_01.prim. The first file contains detector geometry and particle interactions. The second file contains dose projections. While running the proton.mac you will be asked to open g4_00.prim in DAWN. In the opened window press OK. This will create your first visualisation:

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/g4_00_6000e.eps

The second file g4_01.prim will not open automatically. It will be created after the running is finished. Open the file in the following way:

[username@plus1 ProtonPB_build]$ dawn g4_01.prim

In the opened window press OK and this will create the image:

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/g4_02_6000e.eps

You can modify the .prim files in DAWN. For example, in the DAWN display change the polar and azimuthal angles. 1) (polar angle, azimuthal angle) = (0,90) will create this image

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/g4_01_6000e.eps

2) (polar angle, azimuthal angle) = (90,0) will create this image

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/g4_04_6000e.eps

Now, in proton.mac macro uncomment /score/drawProjection waterMeshlateral doseDeposit and comment /score/drawProjection waterMeshlongitudinal doseDeposit. Run proton.mac with the new settings. The image with the lateral dose projections will look like that:

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/g4_03_6000e.eps

Data from The Clatterbridge Cancer Centre

This is data from the Clatterbridge Cancer Center. The first column represents the values in mm in depth, the second column represents the normalized values of deposited dose and normalized at the peak. You can use script PlotData.C from folderRootScripts to plot the data. Copy files ClatterbridgeData.txt and PlotData.C to your current ProtonPB_build directory and run the script:

[username@plus1 ProtonPB_build]$ cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotData.C .

[username@plus1 ProtonPB_build]$ cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/ClatterbridgeData.txt .

[username@plus1 ProtonPB_build]$ root -l 

root [1] .x PlotData.C

This will create ClatterbridgeData.root file with the following plot:

Clatterbridge.png

Comparison between data and simulation

The scripts PlotDataAndSim.C and PlotDataAndSimMesh.C in folder RootScripts compare data with simulation. You can use script PlotDataAndSim.C to compare data (ClatterbridgeData.txt) and simulation (PlotDose.txt). Both text files must be in the folder where you run the script.

[username@plus1 ProtonPB_build]$ cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotDataAndSim.C .

[username@plus1 ProtonPB_build]$ root -l 

root [1] .x PlotDataAndSim.C

This will create BraggPeakComparison.root file with the following plot:

DataSimulation.png

You can also compare data (ClatterbridgeData.txt) with simulation done with scoring mesh (DoseLongitudinalMesh.txt). This can be done with script PlotDataAndSimMesh.C. This script works only if before running it you substitude the commas in DoseLongitudinalMesh.txt with spaces. Remove also the header in the text file. Save the new text file as DoseLongitudinalMesh_Mod.txt.

[username@plus1 ProtonPB_build]$ cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotDataAndSimMesh.C .

[username@plus1 ProtonPB_build]$ root -l 

root [1] .x PlotDataAndSimMesh.C

This creates BraggPeakComparison_Mesh.root file with the following plot:

DataSimulationMesh.png

Files

List of monoenergetic proton pencil beam files with brief description

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