Monoenergetic photon pencil beam
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== <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 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'''. Photons are generated using '''G4ParticleGun''' class. There is an option to chose among several '''EM''' 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 '''G4PVReplica'''. Photons are in green, electrons are in red. == <span style="color:#000080"> How to run the tutorial </span> == ; Connect to the HEP cluster and create folder PhotonPBFolder in your area <pre style="color: #800000; background-color: #dcdcdc"> 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 style="color: #800000; background-color: #dcdcdc"> [username@plus1 PhotonPBFolder]$ source /unix/pbt/software/dev/bin/pbt-dev.sh </pre> ; Copy the code to your working directory and rename it <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> ; Inside /home/username/PhotonPBFolder/ create a directory <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: === <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: <pre style="color: #800000; background-color: #dcdcdc"> [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. == <span style="color:#000080"> Files </span> == [[List of monoenergetic photon pencil beam files with brief description]]
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