Monoenergetic proton pencil beam - Revision history

IlinaMediaWiki at 13:36, 10 September 2014

2014-09-10T13:36:46Z

← Older revision		Revision as of 13:36, 10 September 2014
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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	scp username@plus1.hep.ucl.ac.uk:/home/username/~~PhotonPBFolder~~/~~PhotonPB_build~~/PlotDose.txt .	+	scp username@plus1.hep.ucl.ac.uk:/home/username/ProtonPBFolder/ProtonPB_build/PlotDose.txt .
	</pre>		</pre>

IlinaMediaWiki at 13:33, 10 September 2014

2014-09-10T13:33:03Z

← Older revision		Revision as of 13:33, 10 September 2014
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	* Close the Import Window and in the Command Window type plot(x,Dose). Press Enter.		* Close the Import Window and in the Command Window type plot(x,Dose). Press Enter.

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

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

IlinaMediaWiki at 11:41, 10 September 2014

2014-09-10T11:41:23Z

← Older revision		Revision as of 11:41, 10 September 2014
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	http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/Simulation1.png		http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/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:
		+
		+	<pre style="color: #800000; background-color: #dcdcdc">
		+	scp username@plus1.hep.ucl.ac.uk:/home/username/PhotonPBFolder/PhotonPB_build/PlotDose.txt .
		+	</pre>
		+
		+	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:
		+

	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.		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.

IlinaMediaWiki at 18:57, 3 September 2014

2014-09-03T18:57:27Z

← Older revision		Revision as of 18:57, 3 September 2014
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	http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/g4_00_6000e.png		http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/g4_00_6000e.png

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

	== <span style="color:#000080"> How to run the tutorial </span> ==		== <span style="color:#000080"> How to run the tutorial </span> ==

IlinaMediaWiki at 10:03, 1 September 2014

2014-09-01T10:03:35Z

← Older revision		Revision as of 10:03, 1 September 2014
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	http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/SimulationLateralMesh.png		http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/SimulationLateralMesh.png

-	=== <span style="color:#000080"> ~~Changes in macro proton.mac~~ </span> ===	+	=== <span style="color:#000080"> Run with different settings </span> ===

	You can change the physics process, incident proton energy and number of slices etc. by		You can change the physics process, incident proton energy and number of slices etc. by

IlinaMediaWiki at 15:40, 31 August 2014

2014-08-31T15:40:00Z

← Older revision		Revision as of 15:40, 31 August 2014
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	</pre>		</pre>

-	; Run macro proton.mac~~. The macro generates 6000 events.~~	+	; Run macro proton.mac

	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">

IlinaMediaWiki at 15:23, 31 August 2014

2014-08-31T15:23:56Z

← Older revision		Revision as of 15:23, 31 August 2014
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	The image shows the water box divided into slices using class '''G4PVReplica'''.		The image shows the water box divided into slices using class '''G4PVReplica'''.

-	== <span style="color:#000080"> ~~Setting up~~ the ~~environment~~ </span> ==	+	== <span style="color:#000080"> How to run the tutorial </span> ==

	; Connect to the HEP cluster and create folder ProtonPBFolder in your area		; Connect to the HEP cluster and create folder ProtonPBFolder in your area
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	[username@plus1 ProtonPBFolder]$ source /unix/pbt/software/dev/bin/pbt-dev.sh		[username@plus1 ProtonPBFolder]$ source /unix/pbt/software/dev/bin/pbt-dev.sh
	</pre>		</pre>
-
-	~~== <span style="color:#000080"> How to get the code </span> ==~~

	; Copy the code to your working directory and rename it		; Copy the code to your working directory and rename it
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	[username@plus1 ProtonPBFolder]$ mv ProtonPB ProtonPB_source		[username@plus1 ProtonPBFolder]$ mv ProtonPB ProtonPB_source
	</pre>		</pre>
-
-	~~== <span style="color:#000080"> How to run the code </span> ==~~

	; Inside /home/username/ProtonPBFolder/ create a directory		; Inside /home/username/ProtonPBFolder/ create a directory

IlinaMediaWiki at 14:30, 31 August 2014

2014-08-31T14:30:44Z

← Older revision		Revision as of 14:30, 31 August 2014
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	== <span style="color:#000080"> Setting up the environment </span> ==		== <span style="color:#000080"> Setting up the environment </span> ==

-	; Connect to HEP cluster and create folder ProtonPBFolder in your area	+	; Connect to the HEP cluster and create folder ProtonPBFolder in your area

	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">

IlinaMediaWiki at 14:04, 31 August 2014

2014-08-31T14:04:40Z

← Older revision		Revision as of 14:04, 31 August 2014
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	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.		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 dose are scored using classes '''G4UserSteppingAction''' and '''G4UserRunAction'''. Alternatively, the energy and dose are scored using class '''G4ScoringManager''' by defining two scoring meshes in ~~logitudinal~~ and lateral direction of the beam. More information about scoring meshes can be found [https://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ch04s08.html here]. ~~Protons~~ are generated using '''G4ParticleGun''' class. There is an option to chose among several '''EM''' and the '''QGSP_BIC_EMY''' physics lists.	+	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 [https://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ch04s08.html here]. The protons are generated using '''G4ParticleGun''' class. There is an option to chose among several '''EM''' and the '''QGSP_BIC_EMY''' physics lists.

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

IlinaMediaWiki at 13:47, 31 August 2014

2014-08-31T13:47:58Z

← Older revision		Revision as of 13:47, 31 August 2014
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	ssh -X username@plus1.hep.ucl.ac.uk		ssh -X username@plus1.hep.ucl.ac.uk

-	password: type your password here	+	username@plus1.hep.ucl.ac.uk's password: type your password here
-		+
-	~~cd /home/username/~~	+

-	mkdir ProtonPBFolder	+	[username@plus1 ~]$ mkdir ProtonPBFolder

-	cd ProtonPBFolder	+	[username@plus1 ~]$ cd ProtonPBFolder
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	source /unix/pbt/software/dev/bin/pbt-dev.sh	+	[username@plus1 ProtonPBFolder]$ source /unix/pbt/software/dev/bin/pbt-dev.sh
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	cp -r /unix/pbt/tutorials/basic/ProtonPB .	+	[username@plus1 ProtonPBFolder]$ cp -r /unix/pbt/tutorials/basic/ProtonPB .

-	mv ProtonPB ProtonPB_source	+	[username@plus1 ProtonPBFolder]$ mv ProtonPB ProtonPB_source
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	mkdir ProtonPB_build	+	[username@plus1 ProtonPBFolder]$ mkdir ProtonPB_build
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	cd ProtonPB_build	+	[username@plus1 ProtonPBFolder]$ cd ProtonPB_build

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

-	make	+	[username@plus1 ProtonPB_build]$ make
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	./protonPB proton.mac	+	[username@plus1 ProtonPB_build]$ ./protonPB proton.mac
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	pico DoseFile.txt	+	[username@plus1 ProtonPB_build]$ pico DoseFile.txt
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	root -l Proton.root	+	[username@plus1 ProtonPB_build]$ root -l Proton.root

-	new TBrowser	+	root [1] new TBrowser

	Select ROOT Files and Proton.root		Select ROOT Files and Proton.root
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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	root -l	+	[username@plus1 ProtonPB_build]$ root -l

-	.x PlotSimulation.C	+	root [1] .x PlotSimulation.C
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotLateralDoseMesh.C .	+	[username@plus1 ProtonPB_build]$ cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotLateralDoseMesh.C .

-	root -l	+	[username@plus1 ProtonPB_build]$ root -l

-	.x PlotLateralDoseMesh.C	+	root [1] .x PlotLateralDoseMesh.C
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	pico proton.mac	+	[username@plus1 ProtonPB_build]$ pico proton.mac
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	./protonPB proton.mac	+	[username@plus1 ProtonPB_build]$ ./protonPB proton.mac
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	make	+	[username@plus1 ProtonPB_build]$ make
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	./protonPB proton.mac	+	[username@plus1 ProtonPB_build]$ ./protonPB proton.mac
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	dawn g4_01.prim	+	[username@plus1 ProtonPB_build]$ dawn g4_01.prim
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotData.C .	+	[username@plus1 ProtonPB_build]$ cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotData.C .

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

-	root -l	+	[username@plus1 ProtonPB_build]$ root -l

-	.x PlotData.C	+	root [1] .x PlotData.C
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotDataAndSim.C .	+	[username@plus1 ProtonPB_build]$ cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotDataAndSim.C .

-	root -l	+	[username@plus1 ProtonPB_build]$ root -l

-	.x PlotDataAndSim.C	+	root [1] .x PlotDataAndSim.C
	</pre>		</pre>

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	<pre style="color: #800000; background-color: #dcdcdc">		<pre style="color: #800000; background-color: #dcdcdc">
-	cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotDataAndSimMesh.C .	+	[username@plus1 ProtonPB_build]$ cp /home/username/ProtonPBFolder/ProtonPB_source/RootScripts/PlotDataAndSimMesh.C .

-	root -l	+	[username@plus1 ProtonPB_build]$ root -l

-	.x PlotDataAndSimMesh.C	+	root [1] .x PlotDataAndSimMesh.C
	</pre>		</pre>