@@ Line 3: / Line 3: @@
 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 '''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.
-== <span style="color:#000080"> Setting up the environment </span> ==
+http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/g4_00_6000e.png
-; Connect to HEP cluster and create folder ProtonPBFolder in your area
+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> ==
+; Connect to the HEP cluster and create folder ProtonPBFolder in your area
 <pre style="color: #800000; background-color: #dcdcdc">
 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>
@@ Line 24: / Line 26: @@
 <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>
-== <span style="color:#000080"> How to get the code </span> ==
 ; Copy the code to your working directory and rename it
 <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>
-== <span style="color:#000080"> How to run the code </span> ==
 ; Inside /home/username/ProtonPBFolder/ create a directory
 <pre style="color: #800000; background-color: #dcdcdc">
-mkdir ProtonPB_build
+[username@plus1 ProtonPBFolder]$ mkdir ProtonPB_build
 </pre>
@@ Line 48: / Line 46: @@
 <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>
-; Run macro proton.mac. The macro generates 6000 events.
+; Run macro proton.mac
 <pre style="color: #800000; background-color: #dcdcdc">
-./protonPB proton.mac
+[username@plus1 ProtonPB_build]$ ./protonPB proton.mac
 </pre>
@@ Line 76: / Line 74: @@
 <pre style="color: #800000; background-color: #dcdcdc">
-pico DoseFile.txt
+[username@plus1 ProtonPB_build]$ pico DoseFile.txt
 </pre>
@@ Line 133: / Line 131: @@
-  The run consists of 6000 proton of 62 MeV through 4 cm  of Water (density: 1 g/cm3 ) divided into 50 slices.
+  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.
@@ Line 206: / Line 205: @@
 <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
@@ Line 237: / Line 236: @@
 <pre style="color: #800000; background-color: #dcdcdc">
-root -l
+[username@plus1 ProtonPB_build]$ root -l
-.x PlotSimulation.C
+root [1] .x PlotSimulation.C
 </pre>
@@ Line 245: / Line 244: @@
 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/ProtonPBFolder/ProtonPB_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 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.
@@ Line 250: / Line 266: @@
 <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>
@@ Line 261: / Line 277: @@
 http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/ProtonPB/SimulationLateralMesh.png
-=== <span style="color:#000080"> Changes in 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
@@ Line 267: / Line 283: @@
 <pre style="color: #800000; background-color: #dcdcdc">
-pico proton.mac
+[username@plus1 ProtonPB_build]$ pico proton.mac
 </pre>
@@ Line 428: / Line 444: @@
 <pre style="color: #800000; background-color: #dcdcdc">
-./protonPB proton.mac
+[username@plus1 ProtonPB_build]$ ./protonPB proton.mac
 </pre>
@@ Line 434: / Line 450: @@
 <pre style="color: #800000; background-color: #dcdcdc">
-make
+[username@plus1 ProtonPB_build]$ make
 </pre>
@@ Line 441: / Line 457: @@
 === <span style="color:#000080"> Visualisation </span> ===
-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 settup.
+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 the '''DAWN''' event display. Before running the visualisation
+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 [http://geant4.slac.stanford.edu/Presentations/vis/G4DAWNTutorial/G4DAWNTutorial.html DAWN tutorial].
-have a look at this [http://geant4.slac.stanford.edu/Presentations/vis/G4DAWNTutorial/G4DAWNTutorial.html DAWN tutorial].
 To run the visualisation, first uncomment lines '''/control/execute visualisation.mac''' and '''/score/drawProjection waterMeshlongitudinal doseDeposit'''. Then, run the proton.mac
 <pre style="color: #800000; background-color: #dcdcdc">
-./protonPB proton.mac
+[username@plus1 ProtonPB_build]$ ./protonPB proton.mac
 </pre>
-In addition to the text files it will create two .prim files, g4_00.prim and g4_01.prim. The first one with geometry and particle interactions and the second with dose projections. While running the proton.mac it will ask you 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, '''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. Open it 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:
 <pre style="color: #800000; background-color: #dcdcdc">
-dawn g4_01.prim
+[username@plus1 ProtonPB_build]$ dawn g4_01.prim
 </pre>
@@ Line 465: / Line 480: @@
 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, change the polar and azimuthal angles: (polar angle, azimuthal angle) = (0,90) will create this image
+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
-(polar angle, azimuthal angle) = (90,0) will create this image
+) (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 the proton.mac with the new settings. The file with the lateral dose projections will look like that:
+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
@@ Line 482: / Line 497: @@
 <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>
@@ Line 501: / Line 516: @@
 <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>
@@ Line 517: / Line 532: @@
 <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>

Monoenergetic proton pencil beam

From UCL HEP PBT Wiki

Latest revision as of 13:36, 10 September 2014

Views

Personal tools

Navigation

Search

Toolbox