Monoenergetic photon pencil beam

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== Introduction ==
+
== <span style="color:#000080"> Introduction </span> ==
-
This example shows the dose distribution in water along the incident photon 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 voxels. At each voxel the dose contribution from the pencil beams is summed up and yields the total dose along the beam axis.  
+
This example shows the dose distribution in water along the incident photon 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.  
-
== Setting up the environment ==
+
The slices are created using class '''G4PVReplica'''. The energy and dose are scored using classes '''G4UserSteppingAction''' and '''G4UserRunAction'''. Photons are generated using '''G4ParticleGun''' class. There is an option to chose among several '''EM''' physics lists.
-
; Connect to plus1 cluster and create folder PhotonPencilBeam in your area
+
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/g4_00_6000e.png
-
<blockquote>
+
The image shows the water box divided into slices using class '''G4PVReplica'''. Photons are in green, electrons are in red.  
-
<span style="color:#800000"> ssh username@plus1.hep.ucl.ac.uk </span> <br/>
+
-
<span style="color:#800000"> cd /home/username/ </span> <br/>
+
-
<span style="color:#800000"> mkdir PhotonPencilBeam </span> <br/>
+
-
<span style="color:#800000"> cd PhotonPencilBeam </span>
+
-
</blockquote>
+
-
; Setup GEANT4 environment
+
== <span style="color:#000080"> How to run the tutorial </span> ==
-
<blockquote>
+
; Connect to the HEP cluster and create folder PhotonPBFolder in your area
-
<span style="color:#800000"> source GEANT4 script </span>
+
-
</blockquote>
+
-
== How to get the code ==
+
<pre style="color: #800000; background-color: #dcdcdc">
 +
ssh -X username@plus1.hep.ucl.ac.uk
-
; Copy the code to your area
+
username@plus1.hep.ucl.ac.uk's password: type your password here
 +
 +
[username@plus1 ~]$ mkdir PhotonPBFolder
-
<blockquote>
+
[username@plus1 ~]$ cd PhotonPBFolder 
-
<span style="color:#800000"> cp -r /vasileva/BasicExamples/PhotonPencilBeam_source /username/PhotonPencilBeam/ </span>
+
</pre>
-
</blockquote>
+
-
* How to run the code
+
; Setup your environment
-
; Inside /username/PhotonPencilBeam/ create directory
+
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPBFolder]$ source /unix/pbt/software/dev/bin/pbt-dev.sh 
 +
</pre>
-
<blockquote>
+
; Copy the code to your working directory and rename it
-
<span style="color:#800000"> mkdir PhotonPencilBeam_build </span>
+
-
</blockquote>
+
-
; Change to this directory and run cmake and make to build the PhotonPencilBeam tutorial
+
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPBFolder]$ cp -r /unix/pbt/tutorials/basic/PhotonPB .
 +
 
 +
[username@plus1 PhotonPBFolder]$ mv PhotonPB PhotonPB_source
 +
</pre>
-
<blockquote>
+
; Inside /home/username/PhotonPBFolder/ create a directory
-
<span style="color:#800000"> cd PhotonPencilBeam_build </span> <br/>
+
-
<span style="color:#800000"> cmake -DGeant4_DIR=/unix/pbt/Software/..../ /username/PhotonPencilBeam_source/ </span> <br/>
+
-
<span style="color:#800000"> make </span>
+
-
</blockquote>
+
-
== How to analyze data ==
+
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPBFolder]$ mkdir PhotonPB_build 
 +
</pre>
 +
 
 +
; To compile the code enter this directory and run cmake and make
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPBFolder]$ cd PhotonPB_build
 +
 
 +
[username@plus1 PhotonPB_build]$ cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/PhotonPBFolder/PhotonPB_source
 +
 
 +
[username@plus1 PhotonPB_build]$ make 
 +
</pre>
 +
 
 +
; Run macro gamma.mac
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPB_build]$ ./photonPB gamma.mac
 +
</pre>
 +
 +
== <span style="color:#000080"> How to analyze data </span> ==
 +
 
 +
The macro produces root file '''Gamma.root''' with a histogram showing the energy deposition in
 +
water box along the beam line. It also produces text files: '''DoseFile.txt''' with
 +
energy and dose deposited in each slice and '''PlotDose.txt''' with dose deposited in each slice.
 +
 
 +
=== <span style="color:#000080"> Text files </span> ===
 +
 
 +
This is output from '''DoseFile.txt''' with physics process '''emstandard_opt0''' and incident photon energy of '''20 MeV'''. Use your favorite editor '''pico''', '''vi''', '''emacs''' etc. to open text files. For example, use editor pico:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPB_build]$ pico DoseFile.txt
 +
</pre>
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
Layers : x[mm] Edep      Edep/Ebeam[%] Dose       Dose/MaxDose[%]
 +
layer 1: 5 119.065 MeV 0.0992211 9.53818e-11 Gy 15.1483
 +
layer 2: 10 206.505 MeV 0.172088 1.65429e-10 Gy 26.2731
 +
layer 3: 15 259.584 MeV 0.21632         2.07949e-10 Gy 33.026
 +
layer 4: 20 311.898 MeV 0.259915 2.49858e-10 Gy 39.6819
 +
layer 5: 25 395.255 MeV 0.329379 3.16634e-10 Gy 50.2871
 +
layer 6: 30 439.052 MeV 0.365876 3.51719e-10 Gy 55.8592
 +
layer 7: 35 503.311 MeV 0.419426 4.03197e-10 Gy 64.0348
 +
layer 8: 40 573.742 MeV 0.478118 4.59618e-10 Gy 72.9954
 +
layer 9: 45 624.707 MeV 0.520589 5.00446e-10 Gy 79.4796
 +
layer 10: 50 678.383 MeV 0.565319 5.43445e-10 Gy 86.3086
 +
layer 11: 55 694.602 MeV 0.578835 5.56437e-10 Gy 88.3721
 +
layer 12: 60 710.771 MeV 0.592309 5.6939e-10 Gy 90.4292
 +
layer 13: 65 744.826 MeV 0.620689 5.96672e-10 Gy 94.762
 +
layer 14: 70 742.436 MeV 0.618697 5.94757e-10 Gy 94.4579
 +
layer 15: 75 771.713 MeV 0.643094 6.1821e-10 Gy 98.1827
 +
layer 16: 80 767.22 MeV 0.63935         6.14611e-10 Gy 97.611
 +
layer 17: 85 775.608 MeV 0.64634         6.21331e-10 Gy 98.6783
 +
layer 18: 90 762.779 MeV 0.635649 6.11053e-10 Gy 97.046
 +
layer 19: 95 785.997 MeV 0.654997 6.29653e-10 Gy 100
 +
layer 20: 100 735.186 MeV 0.612655 5.88949e-10 Gy 93.5355
 +
layer 21: 105 761.414 MeV 0.634512 6.0996e-10 Gy 96.8724
 +
layer 22: 110 721.836 MeV 0.60153         5.78254e-10 Gy 91.837
 +
layer 23: 115 730.726 MeV 0.608939 5.85376e-10 Gy 92.9681
 +
layer 24: 120 728.394 MeV 0.606995 5.83508e-10 Gy 92.6714
 +
layer 25: 125 744.904 MeV 0.620753 5.96734e-10 Gy 94.7719
 +
layer 26: 130 731.53 MeV 0.609608 5.8602e-10 Gy 93.0703
 +
layer 27: 135 702.85 MeV 0.585709 5.63045e-10 Gy 89.4215
 +
layer 28: 140 671.716 MeV 0.559763 5.38104e-10 Gy 85.4604
 +
layer 29: 145 676.297 MeV 0.56358         5.41773e-10 Gy 86.0432
 +
layer 30: 150 653.849 MeV 0.544875 5.23791e-10 Gy 83.1873
 +
layer 31: 155 674.152 MeV 0.561793 5.40055e-10 Gy 85.7703
 +
layer 32: 160 687.008 MeV 0.572507 5.50354e-10 Gy 87.406
 +
layer 33: 165 706.2 MeV 0.5885         5.65729e-10 Gy 89.8478
 +
layer 34: 170 700.841 MeV 0.584034 5.61435e-10 Gy 89.1659
 +
layer 35: 175 686.009 MeV 0.571674 5.49553e-10 Gy 87.2788
 +
layer 36: 180 658.891 MeV 0.549076 5.2783e-10 Gy 83.8287
 +
layer 37: 185 644.999 MeV 0.537499 5.16701e-10 Gy 82.0613
 +
layer 38: 190 655.81 MeV 0.546508 5.25362e-10 Gy 83.4367
 +
layer 39: 195 645.691 MeV 0.538075 5.17255e-10 Gy 82.1493
 +
layer 40: 200 0 eV         0         0 Gy         0
 +
 
 +
 
 +
The run consists of 6000 gamma of 20 MeV through 20 cm  of Water (density: 1 g/cm3 )
 +
divided into 40 slices.
 +
 
 +
Edep is the deposited energy in every slice.
 +
Total incident energy(Ebeam)= 120 GeV
 +
Total energy deposit= 24.8344 GeV
 +
Dose is the deposited dose in every slice.
 +
MaxDose is the highest dose value from all slices.
 +
</pre>
 +
 
 +
This is '''PlotDose.txt'''. These values can be analyzed with MATLAB and ROOT .
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc"> 
 +
5 15.1483
 +
10 26.2731
 +
15 33.026
 +
20 39.6819
 +
25 50.2871
 +
30 55.8592
 +
35 64.0348
 +
40 72.9954
 +
45 79.4796
 +
50 86.3086
 +
55 88.3721
 +
60 90.4292
 +
65 94.762
 +
70 94.4579
 +
75 98.1827
 +
80 97.611
 +
85 98.6783
 +
90 97.046
 +
95 100
 +
100 93.5355
 +
105 96.8724
 +
110 91.837
 +
115 92.9681
 +
120 92.6714
 +
125 94.7719
 +
130 93.0703
 +
135 89.4215
 +
140 85.4604
 +
145 86.0432
 +
150 83.1873
 +
155 85.7703
 +
160 87.406
 +
165 89.8478
 +
170 89.1659
 +
175 87.2788
 +
180 83.8287
 +
185 82.0613
 +
190 83.4367
 +
195 82.1493
 +
200 0
 +
</pre>
 +
 
 +
=== <span style="color:#000080"> Root file </span> ===
 +
 
 +
Open '''Gamma.root''' file in the following way:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPB_build]$ root -l Gamma.root
 +
 
 +
root [1] new TBrowser
 +
 
 +
Select ROOT files and Gamma.root
 +
</pre>
 +
 
 +
The histogram inside Gamma.root shows the energy deposition in water box:
 +
 +
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/Edep_PhotonB1.png
 +
 
 +
To exit the ROOT terminal type
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
.q
 +
</pre>
 +
 
 +
You can plot the dose deposition along the depth of the absorber ('''PlotDose.txt''') using script '''PlotSimulation.C''' from folder '''PhotonPB_source'''. Copy this script to your current '''PhotonPB_build''' directory:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPB_build]$ cp /home/username/PhotonPBFolder/PhotonPB_source/PlotSimulation.C .
 +
</pre> 
 +
 
 +
Then run the script:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPB_build]$ root -l
 +
 
 +
root [1] .x PlotSimulation.C
 +
 
 +
</pre>
 +
 
 +
This will create '''Simulation.root''' file. Open the root file:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPB_build]$ root -l Simulation.root
 +
 
 +
root [1] new TBrowser
 +
 
 +
Select ROOT files and Gamma.root
 +
</pre>
 +
 +
This is the result:
 +
 
 +
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/DoseDeposition1.png 
 +
 
 +
You can also plot the file '''PlotDose.txt''' using MATLAB. This software is installed on the plus1 cluster but using it via ssh is not recommended because it is slow. If you have MATLAB installed on your computer you can import the '''PlotDose.txt''' file and plot it. You can also use the MATLAB installed on the computers at the Science Library.
 +
Before proceeding with MATLAB you need to copy the text files from the cluster to your computer. In the terminal at your computer write:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
scp username@plus1.hep.ucl.ac.uk:/home/username/PhotonPBFolder/PhotonPB_build/PlotDose.txt .
 +
</pre>
 +
 
 +
The file '''PlotDose.txt''' will be copied in your current directory. 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:
 +
 
 +
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/matlab0photon.png
 +
 
 +
=== <span style="color:#000080"> Run with different settings </span> ===
 +
 
 +
You can change the physics process, incident photon energy, phantom material, number of slices etc. by
 +
modifying the macro gamma.mac. Open the macro with editor pico:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPB_build]$ pico gamma.mac
 +
</pre> 
 +
 
 +
This is the content of the macro:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
# gamma.mac
 +
#
 +
/control/verbose 2
 +
/run/verbose 2
 +
/tracking/verbose 0
 +
/run/particle/verbose 1
 +
/run/particle/dumpList
 +
#
 +
# set geometry and material
 +
/photonPB/det/setMat Water
 +
#/photonPB/det/setMat Lead
 +
/photonPB/det/setSizeX  20 cm
 +
/photonPB/det/setSizeYZ 20 cm
 +
/photonPB/det/setSliceSizeYZ 20 cm
 +
/photonPB/det/sliceNumber 40
 +
#
 +
# set physics process
 +
/photonPB/phys/addPhysics emstandard_opt0
 +
#/photonPB/phys/addPhysics emlivermore
 +
#/photonPB/phys/addPhysics empenelope
 +
#
 +
# production tresholds (range cut off-
 +
# not bigger than 10% of slice thickness)
 +
/photonPB/phys/setCuts 1 mm
 +
#/photonPB/phys/setGCut 1 um
 +
#/photonPB/phys/setECut 1 um
 +
#/photonPB/phys/setPCut 1 um
 +
#
 +
# initialize
 +
/run/initialize
 +
#
 +
# visualisation
 +
#/control/execute visualisation.mac
 +
 
 +
# particle gun properties (type of
 +
#particle and energy)
 +
/gun/particle gamma
 +
#/gun/particle e-
 +
/gun/energy 20 MeV
 +
#
 +
# beam size
 +
#/photonPB/gun/rndm 3 mm
 +
#
 +
# step limit (not bigger than 5% of
 +
# slice thickness)
 +
/photonPB/stepMax 0.5 mm
 +
#
 +
/photonPB/event/printModulo 50
 +
#
 +
# output root file
 +
/analysis/setFileName Gamma
 +
#
 +
# number of events
 +
/run/beamOn 6000
 +
</pre>
 +
 
 +
'''Change the physics process'''
 +
 
 +
The default physics process is '''emstandard_opt0'''. This package is used in high energy experiments. In gamma.mac change
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
/photonPB/phys/addPhysics emstandard_opt0
 +
</pre>
 +
 
 +
to
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
/photonPB/phys/addPhysics emlivermore
 +
</pre>
 +
 
 +
The process '''emlivermore''' is used in low energy physics experiments.
 +
 
 +
'''Change the incident particle energy'''
 +
 
 +
The default energy is 20 MeV. The typical therapeutic beam energy used in radiotherapy is in the interval 0.3 to 20 MeV. In gamma.mac you can change the value of 20 MeV
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
/gun/energy 20 MeV
 +
</pre>
 +
 
 +
to, for example, 1.25 MeV
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
/gun/energy 1.25 MeV
 +
</pre>
 +
 
 +
This is the energy of the photon beams from cobalt-60 therapy machines.
 +
 
 +
Keep in mind that the primary particle generation is done at /PhotonPB_source/src/PrimaryGeneratorAction.cc.
 +
This is part of the PrimaryGeneratorAction.cc:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
fParticleGun  = new G4ParticleGun(1);
 +
G4ParticleDefinition* particle = G4ParticleTable::GetParticleTable()->FindParticle("proton");
 +
fParticleGun->SetParticleDefinition(particle);
 +
fParticleGun->SetParticleEnergy(160*MeV); 
 +
fParticleGun->SetParticleMomentumDirection(G4ThreeVector(1.,0.,0.));
 +
   
 +
...
 +
 
 +
G4double x0 = -0.5*(fDetector->GetAbsorSizeX());
 +
G4double y0 = 0.*cm, z0 = 0.*cm;
 +
 
 +
...
 +
 
 +
fParticleGun->SetParticlePosition(G4ThreeVector(x0,y0,z0));
 +
</pre>
 +
 
 +
The line
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
fParticleGun  = new G4ParticleGun(1);
 +
</pre>
 +
 
 +
means that only one particle is generated, incident from (x0,y0,z0). The default number of
 +
events is set to 6000. Therefore, 6000 particles are incident to the water box.
 +
 
 +
'''Change the diameter of the beam'''
 +
 
 +
You can set the diameter of the beam with the command:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
/photonPB/gun/rndm 3 mm
 +
</pre>
 +
 
 +
'''Change the material'''
 +
 
 +
In this example we compute the energy deposition of photons in water box. However,
 +
there is an option to change the box material from water to lead.
 +
 
 +
In gamma.mac change
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
/photonPB/det/setMat Water
 +
</pre>
 +
 
 +
to
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
/photonPB/det/setMat Lead
 +
</pre>
 +
 
 +
'''Change the type of incident particle'''
 +
 
 +
In gamma.mac change the photon
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
/gun/particle gamma
 +
</pre>
 +
 
 +
to electron
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
/gun/particle e-
 +
</pre>
 +
 
 +
'''Change the number of slices'''
 +
 
 +
You can change the number of slices. The default number is 40. Keep in mind that
 +
if you want to have bigger number of slices you need to modify the file DetectorConstruction.hh in
 +
/PhotonPB_source/include/.
 +
 
 +
In DetectorConstruction.hh set MaxLayer to a value which is bigger then the number of your slices. The default number is MaxLayer=50. For example, if you want your box to be divided to 60 slices you need to set the value of MaxLayer to ,for example, 65 then in gamma.mac you need to change the number of slices:
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
/photonPB/det/sliceNumber 60
 +
</pre>
 +
 
 +
Every time you modify files in directory PhotonPB_source you need to compile your code. In directory PhotonPB_build do
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
make
 +
</pre>
 +
 
 +
then run the macro
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPB_build]$ ./photonPB gamma.mac
 +
</pre>
 +
 
 +
=== <span style="color:#000080"> Visualisation </span> ===
 +
 
 +
If you want to use visualisation, in macro '''gamma.mac''' uncomment the line '''/control/execute visualisation.mac'''. This will run macro '''visualisation.mac''' with a specific visualisation setup.
 +
In this example, we use '''DAWN''' event display. Before running the visualisation look at the [http://geant4.slac.stanford.edu/Presentations/vis/G4DAWNTutorial/G4DAWNTutorial.html DAWN tutorial].
 +
 
 +
To run the visualisation, uncomment line '''/control/execute visualisation.mac''' and run the 
 +
gamma.mac macro
 +
 
 +
<pre style="color: #800000; background-color: #dcdcdc">
 +
[username@plus1 PhotonPB_build]$ ./photonPB gamma.mac
 +
</pre>
 +
 
 +
In addition to the text files the code will create two .prim files, '''g4_00.prim''' and '''g4_01.prim'''. Both files contain detector geometry and particle interactions. While running the gamma.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/PhotonPB/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:
 +
 
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<pre style="color: #800000; background-color: #dcdcdc">
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[username@plus1 PhotonPB_build]$ dawn g4_01.prim
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</pre>
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In the DAWN display change the polar and azimuthal angles to 0 and 90 degrees, then press OK.  This will create the image:
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http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/g4_01_6000e.eps
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The color in the images indicates the type of the particle. Photons are in green, electrons are in red and positrons are in cyan.
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== <span style="color:#000080"> Files </span> ==
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[[List of monoenergetic photon pencil beam files with brief description]]

Latest revision as of 13:31, 10 September 2014

Retrieved from "https://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/index.php/Monoenergetic_photon_pencil_beam"
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