Software/Geant4/Tutorials/Basic/Monoenergetic Photon Pencil Beam - Revision history

SimonJolly at 17:48, 5 October 2016

2016-10-05T17:48:50Z

← Older revision		Revision as of 17:48, 5 October 2016
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	<pre>		<pre>
	[username@plus1 PhotonPBFolder]$ source /unix/pbt/software/~~dev/bin~~/pbt~~-dev~~.sh		[username@plus1 PhotonPBFolder]$ source /unix/pbt/software/scripts/pbt.sh
	</pre>		</pre>

SimonJolly at 17:59, 1 April 2016

2016-04-01T17:59:49Z

← Older revision		Revision as of 17:59, 1 April 2016
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	== ~~Introduction~~ ==		== Monoenergetic Photon Pencil Beam ==

	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.		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.

SimonJolly at 19:01, 31 March 2016

2016-03-31T19:01:50Z

← Older revision		Revision as of 19:01, 31 March 2016
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	Photons are in green, electrons are in red.		Photons are in green, electrons are in red.

	== ~~Run~~ the ~~tutorial~~ ==		== Running the Tutorial ==

			All the source files for the tutorial can be found in http://www.hep.ucl.ac.uk/pbt/wikiData/code/PhotonPB/.

	=== Connect to the HEP cluster and create folder PhotonPBFolder in your area ===		=== Connect to the HEP cluster and create folder PhotonPBFolder in your area ===

SimonJolly: Undo revision 74 by SimonJolly (talk)

2016-03-31T18:50:21Z

Undo revision 74 by SimonJolly (talk)

← Older revision		Revision as of 18:50, 31 March 2016
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	== Files ==		== Files ==

	[[/Photon Pencil Beam Files\|List of files for Mononenergetic Photon Pencil Beam simulation]].		[[Software/Geant4/Tutorials/Basic/Photon Pencil Beam Files\|List of files for Mononenergetic Photon Pencil Beam simulation]].

SimonJolly at 18:49, 31 March 2016

2016-03-31T18:49:49Z

← Older revision		Revision as of 18:49, 31 March 2016
Line 484:		Line 484:
	== Files ==		== Files ==

	[[~~Software/Geant4/Tutorials/Basic~~/Photon Pencil Beam Files\|List of files for Mononenergetic Photon Pencil Beam simulation]].		[[/Photon Pencil Beam Files\|List of files for Mononenergetic Photon Pencil Beam simulation]].

SimonJolly at 17:19, 31 March 2016

2016-03-31T17:19:07Z

← Older revision		Revision as of 17:19, 31 March 2016
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	There is an option to chose among several <code>EM</code> physics lists.		There is an option to chose among several <code>EM</code> physics lists.

	~~http~~:~~//www~~.~~hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/g4_00_6000e.png~~		[[File:PhotonPB_g4_00_6000e.gif\|475px]]

	The image shows the water box divided into slices using class <code>G4PVReplica</code>.		The image shows the water box divided into slices using class <code>G4PVReplica</code>.
Line 192:		Line 192:

	The histogram inside Gamma.root shows the energy deposition in water box:		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		[[File:PhotonPB_Edep_PhotonB1.png]]

	To exit the ROOT terminal type		To exit the ROOT terminal type
Line 230:		Line 230:
	This is the result:		This is the result:

	~~http~~:~~//www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/DoseDeposition1~~.png		[[File:PhotoPB_DoseDeposition1.png]]

	You can also plot the file <code>PlotDose.txt</code> using MATLAB.		You can also plot the file <code>PlotDose.txt</code> using MATLAB.
Line 252:		Line 252:
	This plot will be created with added axis labels and a legend:		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		[[File:PhotonPB_matlab0photon.png]]

	=== Run with different settings ===		=== Run with different settings ===
Line 468:		Line 468:
	In addition to the text files the code will create two .prim files, <code>g4_00.prim</code> and <code>g4_01.prim</code>. Both files contain detector geometry and particle interactions. While running the <code>gamma.mac</code> you will be asked to open g4_00.prim in DAWN. In the opened window press OK. This will create your first visualisation:		In addition to the text files the code will create two .prim files, <code>g4_00.prim</code> and <code>g4_01.prim</code>. Both files contain detector geometry and particle interactions. While running the <code>gamma.mac</code> 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~~		[[File:PhotonPB_g4_00_6000e.gif\|475px]]

	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:		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:
Line 478:		Line 478:
	In the DAWN display change the polar and azimuthal angles to 0 and 90 degrees, then press OK. This will create the image:		In the DAWN display change the polar and azimuthal angles to 0 and 90 degrees, then press OK. This will create the image:

	~~http~~:~~//www~~.~~hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/g4_01_6000e.eps~~		[[File:PhotonPB_g4_01_6000e.gif\|493px]]

	The color in the images indicates the type of the particle. Photons are in green, electrons are in red and positrons are in cyan.		The color in the images indicates the type of the particle. Photons are in green, electrons are in red and positrons are in cyan.
Line 484:		Line 484:
	== Files ==		== Files ==

	[[List of ~~monoenergetic photon pencil beam~~ files ~~with brief description~~]]		[[Software/Geant4/Tutorials/Basic/Photon Pencil Beam Files\|List of files for Mononenergetic Photon Pencil Beam simulation]].

SimonJolly: Created page with "== Introduction == 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 o..."

2016-03-31T16:32:55Z

Created page with "== Introduction == 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 o..."

New page

== Introduction ==

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.

The slices are created using class <code>G4PVReplica</code>. The energy and dose are scored using classes <code>G4UserSteppingAction</code> and <code>G4UserRunAction</code>.
Photons are generated using <code>G4ParticleGun</code> class.
There is an option to chose among several <code>EM</code> physics lists.

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/g4_00_6000e.png

The image shows the water box divided into slices using class <code>G4PVReplica</code>.
Photons are in green, electrons are in red.

== Run the tutorial ==

=== Connect to the HEP cluster and create folder PhotonPBFolder in your area ===

<pre>
ssh -X username@plus1.hep.ucl.ac.uk

username@plus1.hep.ucl.ac.uk's password: type your password here

[username@plus1 ~]$ mkdir PhotonPBFolder

[username@plus1 ~]$ cd PhotonPBFolder
</pre>

=== Setup your environment ===

<pre>
[username@plus1 PhotonPBFolder]$ source /unix/pbt/software/dev/bin/pbt-dev.sh
</pre>

=== Copy the code to your working directory and rename it ===

<pre>
[username@plus1 PhotonPBFolder]$ cp -r /unix/pbt/tutorials/basic/PhotonPB .

[username@plus1 PhotonPBFolder]$ mv PhotonPB PhotonPB_source
</pre>

=== Inside /home/username/PhotonPBFolder/ create a directory ===

<pre>
[username@plus1 PhotonPBFolder]$ mkdir PhotonPB_build
</pre>

=== Compile the code with cmake and make ===

<pre>
[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 <code>gamma.mac</code> ===

<pre>
[username@plus1 PhotonPB_build]$ ./photonPB gamma.mac
</pre>

== Analysing the Data ==

The macro produces root file <code>Gamma.root</code> with a histogram showing the energy deposition in water box along the beam line.
It also produces text files: <code>DoseFile.txt</code> with energy and dose deposited in each slice and <code>PlotDose.txt</code> with dose deposited in each slice.

=== Text files ===

This is output from <code>DoseFile.txt</code> with physics process <code>emstandard_opt0</code> and incident photon energy of '''20 MeV'''.
Use your favorite editor <code>pico</code>, <code>vi</code>, <code>emacs</code> etc. to open text files.
For example, use editor pico:

<pre>
[username@plus1 PhotonPB_build]$ pico DoseFile.txt
</pre>

<pre>
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 <code>PlotDose.txt</code>.
These values can be analyzed with MATLAB and ROOT.

<pre>
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>

=== Root file ===

Open <code>Gamma.root</code> file in the following way:

<pre>
[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>
.q
</pre>

You can plot the dose deposition along the depth of the absorber (<code>PlotDose.txt</code>) using script <code>PlotSimulation.C</code> from folder <code>PhotonPB_source</code>.
Copy this script to your current <code>PhotonPB_build</code> directory:

<pre>
[username@plus1 PhotonPB_build]$ cp /home/username/PhotonPBFolder/PhotonPB_source/PlotSimulation.C .
</pre>

Then run the script:

<pre>
[username@plus1 PhotonPB_build]$ root -l

root [1] .x PlotSimulation.C

</pre>

This will create <code>Simulation.root</code> file.
Open the root file:

<pre>
[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 <code>PlotDose.txt</code> using MATLAB.
This software is installed on the UCL HEP Linux 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 <code>PlotDose.txt</code> 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>
scp username@plus1.hep.ucl.ac.uk:/home/username/PhotonPBFolder/PhotonPB_build/PlotDose.txt .
</pre>

The file <code>PlotDose.txt</code> 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

=== Run with different settings ===

You can change the physics process, incident photon energy, phantom material, number of slices etc. by
modifying the macro <code>gamma.mac</code>. Open the macro with editor pico:

<pre>
[username@plus1 PhotonPB_build]$ pico gamma.mac
</pre>

This is the content of the macro:

<pre>
# 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 <code>emstandard_opt0</code>.
This package is used in high energy experiments.
In <code>gamma.mac</code> change

<pre>
/photonPB/phys/addPhysics emstandard_opt0
</pre>

to

<pre>
/photonPB/phys/addPhysics emlivermore
</pre>

The process <code>emlivermore</code> 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 <code>gamma.mac</code> you can change the value of 20 MeV:

<pre>
/gun/energy 20 MeV
</pre>

to, for example, 1.25 MeV:

<pre>
/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 <code>/PhotonPB_source/src/PrimaryGeneratorAction.cc</code>.
This is part of the <code>PrimaryGeneratorAction.cc</code>:

<pre>
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>
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>
/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 <code>gamma.mac</code> change:

<pre>
/photonPB/det/setMat Water
</pre>

to:

<pre>
/photonPB/det/setMat Lead
</pre>

==== Change the type of incident particle ====

In <code>gamma.mac</code> change the photon

<pre>
/gun/particle gamma
</pre>

to electron

<pre>
/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 <code>DetectorConstruction.hh</code> in <code>/PhotonPB_source/include/</code>.

In <code>DetectorConstruction.hh</code> set <code>MaxLayer</code> to a value which is bigger then the number of your slices.
The default number is <code>MaxLayer=50</code>.
For example, if you want your box to be divided to 60 slices you need to set the value of <code>MaxLayer</code> to, for example, 65 then in <code>gamma.mac</code> you need to change the number of slices:

<pre>
/photonPB/det/sliceNumber 60
</pre>

Every time you modify files in directory <code>PhotonPB_source</code> you need to compile your code.
In directory <code>PhotonPB_build</code> do:

<pre>
make
</pre>

then run the macro

<pre>
[username@plus1 PhotonPB_build]$ ./photonPB gamma.mac
</pre>

=== Visualisation ===

If you want to use visualisation, in macro <code>gamma.mac</code> uncomment the line <code>/control/execute visualisation.mac</code>.
This will run macro <code>visualisation.mac</code> with a specific visualisation setup.
In this example, we use <code>DAWN</code> 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 <code>/control/execute visualisation.mac</code> and run the <code>gamma.mac</code> macro:

<pre>
[username@plus1 PhotonPB_build]$ ./photonPB gamma.mac
</pre>

In addition to the text files the code will create two .prim files, <code>g4_00.prim</code> and <code>g4_01.prim</code>. Both files contain detector geometry and particle interactions. While running the <code>gamma.mac</code> 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:

<pre>
[username@plus1 PhotonPB_build]$ dawn g4_01.prim
</pre>

In the DAWN display change the polar and azimuthal angles to 0 and 90 degrees, then press OK. This will create the image:

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

The color in the images indicates the type of the particle. Photons are in green, electrons are in red and positrons are in cyan.

== Files ==

[[List of monoenergetic photon pencil beam files with brief description]]