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GAMOS 4.0.0 User`s Guide

1. Automatic determination of production cuts for a dose in a phantom simulation The use of production cuts in a dose computation may introduce a bias when a par ticle is killed and then its energy is deposited locally and it has enough energy to reach the next phantom voxel or enough energy to create a particle that reaches the next phantom voxel this happens mainly for electrons creating gammas which have a much higher range To calculate automatically the best production cut that is the one that gives the small est CPU while biasing the dose computation a minimal amount GAMOS uses an inverse reasoning For a given set of cuts for electron and gamma it does not apply them but tags the particles that would have been killed by them It also tags the voxel in which the particle is produced and then it computes all the dose deposited by the tagged particle or any of its children in a voxel that is not the same as the tagged voxel To use this utility in GAMOS you just have to associate to your dose scorer a filter of type GmProdCutOutsideVoxelFilter passing to it as arguments the gamma cut and the electron cut like in the following example gamos scoring addFilter2Scorer ProdCutFilter GmProdCutOutsideVoxelFilter PDDscorerPC10 1 10 mm 1 mm You should add another scorer without filter to get the total dose After running your job with as many scorer filter combinations as you like you can look at the total dose deposited b
2. SUF or SUFFIX followed by a list of pairs word position numbers and word char acters If there are several lines in a file satisfying the prefix and suffix conditions you may set that only one line or a few of them are processed by using the word L or LINE followed by the list of numbers corresponding to the time order the line appears For example PRE 1 Events 2 PET L 1 will only process the first line found Then you have to define which are the words in the line that are going to be processed by using the word W or WORD followed by the list of numbers of the words in the lines For example PRE 1 Events 2 PET L1 W34 will process the third and fourth words of the lines selected After you have to define the kind of treatment to be done to the words by using the word T or TREATMENT followed by the treatment type For example PRE 1 Events 2 PET L1 W34 T PT The treatment type can be one of the following ones e P or PRINT print the words found at each line of each file each one in a line e PT or PRINT_TOGETHER print the words found at each line of each file putting in one line the words extracted from each file i e all the words found corresponding to the same instruction line together Chapter 11 Analysis extracting data e S or SUM print the sum of the values of the words found in any line of any file e Mor MEAN print the mean of the values of the words found in any line of any file Final
3. electron penelope processes a la Penelope 6 e positrons e positron standard standard electromagnetic processes no low energy e positron penelope processes a la Penelope 6 To tell your job to use one of the possible combinations of physics models just de scribed you have first to select the GAMOS electromagnetic physics list using the command gamos physicsList GmEM Physics and then you can select one of the physics models for each particle with the command gamos GmPhysics addPhysics PHYSICS_MODEL_NAME where PHYSICS_MODEL_NAME is one of the above names If you do not select anyone for a given particle the first one in each list is taken as default For details on the physics implemented in each of these physics models please read the Geant4 physics manual 10 This physics list also sets on the atomic deexcitation see section below 59 Chapter 5 Physics Multiple scattering model There are several multiple scattering models available in the current version of Geant4 If you have selected the GAMOS physics list you may select a different one for different particles with the following parameter gamos setParam GmMultipleScattering Model PARTICLE_NAME MODEL where PARTICLE NAME can be Electron Positron or Hadron and MODEL can be Urban90 Urban92 Urban93 WentzelVI or GoudsmitSaunderson see the GEANT4 User s Guide for an explanation of each model The default model for all particles i
4. Chapter 2 Getting started This chapter explains the practical details to obtain the GAMOS code compile and run it Getting the code and installing it GAMOS has been tested in over ten Linux and MacOS distributions and compilers Each new release is tested with over sixty tests in three different operating systems You can download GAMOS from http fismed ciemat es GAMOS GAMOS depends on Geant4 and also on CLHEP 4 and optionally ROOT 5 To download and install everything you can follow the instruction in the Code down load area As explained there you need to get first the installation scripts and un compress them in the scripts directory you may do it automatically by downloading the scripts installation utility from the web page After that you just need to type the command installGamos sh MY_INSTALLATION_DIR where MY_INSTALLATION_DIR is the directory where you want to install GAMOS This command will download the GAMOS code as well as CLHEP Geant4 and op tionally ROOT packages and will compile them all Be sure that you have installed in your system the X11 libraries in the directory usr X11R6 lib or usrflocal lib or usr lib check for the following libraries libXmu so libXt so libXext so libX11 s0 libICE so as well as the OpenGL libraries check for the following libraries libGL so libGLU so If the OpenGL libraries are not found GAMOS will ask you if you want to con tinue without them
5. To use this utility in GAMOS it is only needed to add this command in your script gamos userAction GmProdCutsStudyuA RTCutsStudyFilter or that will use as target condition that a track reaches a plane perpendicualr to the Z axis defined with the parameters gamos setParam RTCutsStudyFilter PlaneZ ZPOS gamos setParam RTCutsStudyFilter PlaneXDim XDIM gamos setParam RTCutsStudyFilter PlaneY Dim YDIM This command will produce at the end of run a table and a histogram file with the needed information The table will contain the minimum range that can be applied for each region particle process not to lose any track reaching the target and it will look like this PRODUCTION CUTS STUDY RESULTS GmProdCutsStudyUA REGION DefaultRegionForTheWorld PARTICLE Chapter 22 Radiotherapy application gamma PROCESS ALL MIN RANGE 353161 38 GmProdCutsStudyUA REGION DefaultRegionForTheWorld PARTICLE gamma PROCESS eBrem MIN RANGE 353161 38 To get the cuts values for not losing a given percentage of particles in the target plane you can execute the ROOT script that can be found at GamosCore GamosPhysics GamosCuts getProdCutsEffect C root b p q x getProdCutsEffect Ct prodcuts root percentage and look at the last lines of output those that contain the word FINAU like the following ones PARTICLE e FINAL 17 19 PARTICLE e FINAL 72 34185 PARTICLE gamma FINAL 72 34184
6. Material made of one element MATE e Name Z oA e Density Example MATE Iron 26 55 85 7 87 Material made of a mixture of elements or materials MIXT e Name e Density Number of components One line per material or element with e material name e proportion of material in the mixture The components can be either all elements or all materials but both types cannot appear in the same mixture There are three mixture tags depending of the way the proportions are defined e Proportions by weight fractions MIXT_BY_WEIGHT This tag is equivalent to the MIXT tag e Proportions by number of atoms MIXT_BY_NATOMS Chapter 3 Geometry e Proportions by volume MIXT_BY_VOLUME The first two tags can be used to build material mixtures out of elements or materials but the last tag can only be applied with material components elements do not have density Example MIXT Fiber Lead 9 29 2 Lead 0 9778 Polystyrene 0 0222 MIXT_BY_NATOMS CO2 1 8182E 3 2 Cl O 2 MIXT_BY_VOLUME H CO2 1 214E 03 1 8182E 3 2 2 Hydrogen 0 5 CO2 0 5 Material properties MATE_MEE e Material name e Mean excitation energy Example MATE_MEE G4_WATER 10 eV MATE STATE e Material name e State Undefined Solid Liquid Gas If material is not set it is Undefined Example MATE_STATE G4_WATER Solid MATE TEMPERATURE e Material name e Temperature If temperature i
7. where name is SPECT xVtx yVtx zVtx are the coordinates of the event vertex x1 y1 z1 are the coordinates of the reconstructed hit x2 y2 z2 are the coordinates of the collimator centre ener is the hit energy and class is the SPECT classification The same data that is written to the file can be written in the standard output if the parameter gamos setParam SPECT DumpToCout TRUE is set to true The positions in the standard output not in the file will be written in cylindrical coordinates by default If you want them in cartesian coordinates you should set to true the parameter gamos setParam SPECT DumpCartesian TRUE 1 original gammas are gammas that are primary particles or that are directly cre ated by the annihilation of positron that is a primary particle 169 Chapter 19 SPECT application 170 Chapter 20 Compton camera application The Compton camera application is a new addition to the GAMOS framework The application has been developed for researchers investigating the potential of Comp ton cameras in nuclear medicine but can be used for a wide variety of fields outside of medicine The Compton camera example has a structure very similar to the SPECT applica tion The example contains a utility to build a Compton camera which is composed of either rings of detectors or a stack of parallel detectors through the user defined geometrical parameters Information relevant to Compton camera applications i
8. 2 Butterworth e 3 Shepp Logan e a Alpha parameter for generalized Hamming window by default 1 ramplak filter e b Order for Butterworth window by default 4 c Cutoff frequency relative to Nyquist freq bin_size 2 by default 0 75 e n Name of the output image file MY_NAME without extension The pro gram will write a MY_NAME img data file and two associated header text files MY_NAME hv and MY NAME hdr The hv file has a STIR like Interfile format 24 whereas the hdr file uses Interfile 3 3 conventions it is done to make possible opening the image by different programs see Visualization tools section e h Help printing arguments list v Verbosity by default 0 for silent 3 for debugging The following example will apply a SSRB FBP2D reconstruction to a projection data file named MY_PROJDATA_ALL hv using a Butterworth filter of order 6 and cut off frequency 0 5 Nyquist units image and pixel sizes take values from the projection data tangential bins ssrb_fbp MY_PROJDATA_ALL f 2 b 6 c 0 5 n MY_IMAGE Chapter 21 Image reconstruction utilities To use this utility you have to install the FFTW library at the path where the vari able FFTW_BASE_DIR points type echo FFTW_BASE_DIR You can download this library at http Avww fftw org Visualization tools Currently GAMOS does not include any utility to visualize the reconstructed images or projection data instead of it
9. Example PLACE_PARAM mytube 1 subworld2 LINEAR_X RMO 5 20 0 PLACE_PARAM mytube 1 subworld1 LINEAR RMO 5 20 0 1 1 1 50 0 0 PLACE_PARAM mybox 0 mother CIRCLE_XY RMO 30 6 deg 90 deg 15 cm PLACE_PARAM mybox 1 subworld2 SQUARE_XZ RM0 5 5 20 20 PLACE_PARAM mybox 1 subworld1 SQUARE RMO 5 8 20 10 0 1 1 0 1 0 Be aware that putting offset 0 means that the first copy is placed at 0 0 0 This may be not what you want if for example you are filling a box with an square of small boxes using an square parameterisation offset 0 will mean that all the copies are placed in the positive positive quarter of the mother box Phantom parameterisation This is a special case of parameterisation that serves to create a three dimensional grid of equal voxels The parameterisation is instantiated as a G4PhantomParameterisation so that the G4RegularNavigation algorithm is used for optimal efficiency in the navi gation The format of this parameterisation is the following Volume name Copy number Parent volume name Parameterisation type Name of rotation matrix Number of copies in X e Number of copies in Y e Number of copies in Z e Step separation between copies in X e Step separation between copies in Y e Step separation between copies in Z Chapter 3 Geometry Following the rules of G4RegularNavigation the voxels must completely fill the mother volume therefore a container volume of appropiate dimensio
10. Table of tracks and steps 146 You may get a table of the number of tracks and steps by instantiating the user action gamos userAction GmCountTracksAndStepsuUA It will produce a table with the number of tracks and steps in the whole run You may get more details by using it with filters and classifiers For example the command gamos userAction GmCountTracksAndStepsUA GmClassifier By Particle will produce a table similar to this one COUNT_TRACKS_AND_STEPS GmClassifierByParticle COUNT_TRACKS gamma 100 5 COUNT_TRACKS e 8 COUNT_TRACKS e 1 5 COUNT_TRACKS ALL 109 COUNT_NSTEPS gamma 399 5 COUNT_NSTEPS e 29 5 COUNT_NSTEPS e 4 COU STEPS ALL 432 Chapter 15 Utility user actions Material budget studies The action gamos userAction GmMaterialBudgetuA serves to make an study of the material budget of your geometry We compute the material budget of a geometry along a line by integrating the radiation length of each volume traversed multiplied by the length of the line segment in that volume This user action may be useful for checking your geometry The usual way to use this user action is to send parallel geantinos the Geant4 particle that does not interact only traverses the geometry starting in a plane perpendicular to the geantino direction and computing the material budget for each of them The user action GmMaterialBudg
11. The user can choose not to produce any of these histograms by setting the following parameter gamos setParam RT PhaseSpaceUA Histos FALSE The name of the histogram file can be controlled with the parameter gamos setParam RT PhaseSpaceHistos FileName MY_FILENAME 197 Chapter 22 Radiotherapy application 195 that by default is phaseSpace Several parameters serve to control the number of histogram bins gamos setParam RT PhaseSpaceHistos Nbins NBINS that takes by default a value of 100 and the maximum absolute value for histograms of position gamos setParam RT PhaseSpaceHistos HisRMax MAX that takes by default a value of 100 histograms of angle gamos setParam RT PhaseSpaceHistos HisAngMax MAX that takes by default a value of 180 and histograms of energy gamos setParam RT PhaseSpaceHistos HisEMax MAX that takes by default a value of 10 MeV Reading phase spaces To use the generated phase space you have to define as your primary generator gamos generator RTGenerator PhaseSpace You can change the filename by default test with the parameter gamos setParam RT Generator PhaseSpace FileName MY_FILENAME The particles in the phase space can be translated or rotated by using the parameters gamos setParam RTGeneratorPhaseSpace InitialDisplacement POS_X POS_Y POS_Z gamos setParam RTGeneratorPhaseSpace InitialRotAngles ANG_X ANG_Y ANG_Z the position of the particles is first changed by the initial displacement th
12. This physics list can be selected with the command gamos physicsList HadronTherapyPhysics The default physics options are those include in the GEANT4 physics lists G4EmStandardPhysics_option3 G4DecayPhysics and G4RadioactiveDecayPhysics This default physics can be changed with the command HT Physics addPhysics PHYSICS_LIST where PHYSICS_LIST can be e standard_opt3 G4EmStandardPhysics_option3 e LowE_Livermore G4EmLivermorePhysics e LowE_Penelope G4EmPenelopePhysics e local_ion_ion_inelastic LocallonIonInelasticPhysics e QGSP_BIC_EMY QGSP_BIC_EMY This list has several commands to select cuts HT Physics setCuts VALUE UNIT set the cuts for all volumes and particles HT Physics setGCut VALUE UNIT set the cuts for gammas for all volumes HT Physics setECut VALUE UNIT set the cuts for electrons for all volumes HT Physics setPCut VALUE UNIT set the cuts for positrons for all volumes Other physics lists You can use easily in GAMOS any of the Geant4 physics lists 12 All you have to do to use a Geant4 physics list is to add in the file GAMOS_DIR source GamosCore Gamos Physics GamosOtherPhysicsList src module cc or in any other in GAMOS code or created by you see Appendix on Creating your plug in two lines like these ones include QGSP hh DEFINE _GAMOS_PHYSICS QGSP Compile it and then you can use it in your command file with the line gamos physicsList QGSP As you can see looking at this
13. gamos setParam GmPDS AngleDeviationFileName FILE_NAME Chapter 8 Scoring the default name is angleDeviation neutron root for neutrons and angleDeviation gamma root for gammas When this file is read it will be checked if the number of events in each histograms is big enough else the histogram will not be used You may control the minimum number of events in the histogram with the parameter gamos set Param GmPDS InteractionAngleManager MinimumNumberOfEntries VALUE Point detector volume The detector where the flux will be scored has to be a real volume in your geometry It should be an small volume as small as you want although you may decide to make it the size of the real detector in your experiment It is important to take into account that despite the flux is calculated as the probability that tracks reach the detector if a track actually reaches it it will also be counted The name of the detector volume is given with the parameter gamos setParam GmPDS DetectorName VOLUME_NAME If you want to score the flux in several points you may place the detector volume at several places Energy and dose equivalent bins The flux will be scored in different energy bins These energy bins should be defined in a file whose name is gamos set Param GmPDS EnergyBinsFileName FILE_NAME The format of this file is a set of one column lines with the energy values There are several dose equivalent magnitudes that can be calculated name
14. 12 J http www slac stanford edu comp physics geant4 slac_physics_lists G4_Physics_Lists html http geant4 web cern ch geant4 physics_lists 13 http geant4 web cern ch geant4 User Documentation UsersGuides ForApplication Developer html apas08 html sect G4MatrDb NISTCmp 14 http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplication Developer html Detector geomSolids html 15 http geant4 web cern ch geant4 User Documentation UsersGuides ForApplication Developer html ch04s04 html sect Hits G4Multi 16 http oww irs inms nrc ca BEAM beamhome html 17 http howw nds iaea org phsp phsp htmlx 18 Kawrakow I Rogers D W O Walters B R B Large efficiency improvements in BEAMnrc using directional bremsstrahlung splitting Medical physics 31 10 2883 98 2004 19 http stir sourceforge net main htm 20 Treatment of axial data in three dimensional PET Daube Witherspoon M E Muehllehner G J Nucl Med vol 28 pp 1717 24 1987 21 Fundamentals of Computerized Tomography Image Reconstruction from Projections 2nd ed Herman G T Springer ISBN 978 1 85233 617 2 2009 233 Bibliography 21 The Radon Transform Theory and Implementation Toft P Ph D thesis Depart ment of Mathematical Modelling Technical University of Denmark 326 pages http petertoft dk PhD 1996 22 AMIDE Amide s a Medical Imaging Data Examiner y http amide
15. 2 78 2 22 24 25 6 2 78 2 22 24 25 7 2 78 2 1 22 24 25 8 2 78 2 75 8 1 2 78 2 75 8 1 1 2 75 8 1 2 75 8 4 5 75 8 1 6 5 75 8 1 2 78 2 75 8 6 2 78 2 75 8 7 2 78 2 1 75 8 8 2 78 2 22 24 25 0 05 2 78 2 20 24 25 0 05 2 78 2 0 65 22 24 0 05 2 78 2 0 65 20 24 0 05 2 78 2 20 24 0 05 6 2 78 2 20 24 0 05 7 2 78 2 1 20 24 0 05 8 2 78 2 2 2 78 2 1 2 78 2 1 2 2 2 78 2 2 3 LEAF 32 N Leaves Cross Points and type 2 1 2 Z and C coordinate 1 1 2 2 2 78 2 20 24 6 2 2 78 2 20 24 6 1 2 78 2 1 20 24 6 2 78 2 20 24 2 78 2 22 24 2 78 2 0 65 20 24 25 2 78 2 0 65 22 244 25 2 78 2 75 8 8 2 78 2 75 8 7 2 78 2 1 75 8 6 2 78 2 75 8 1 2 78 2 75 8 1 6 5 75 8 4 5 75 8 1 2 75 8 1 1 2 75 8 1 2 78 2 22 24 25 8 2 78 2 22 24 25 7 2 78 2 1 22 24 25 6 2 78 2 22 24 25 0 05 2 78 2 20 24 25 0 05 2 78 2 0 65 22 24 0 05 2 78 2 0 65 20 24 0 05 2 78 2 Chapter 22 Radiotherapy application 8 2 78 2 7 2 78 2 1 6 2 78 2 2 2 78 2 1 2 78 2 1 2 2 2 78 2 2 3 LEAF 15 N Leaves Cross Points and type 2 5 0 3 Z and C coordinate 1 5 0 3 1 18 7 3 20 24 18 7 3 22 24 18 7 3 0 65 20 24 25 18 7 3 0 65 22 24 25 18 7 3 75 8 1 18 7 3 75 8 1 18 7 3 75 8 1 5 0 3 75 8 5 0 3 75 8 5 0 3 1 5 0 3 1 5 0 3 2 5 0 3 7 Total Leave Number 1 1 0 1 Leave_type Left and Right at isocenter 3 1 0 2 2 1 0 3 3 1 0 4 2 1 0 5 3 1 0 6 4 10 0 29 G4_W Mater
16. G4_WATER PART gamma ENERGY CUT 0 1 MeV RANGE CUT 334 152 GmCut sEnergy2RangeUA ATERIAL G4_WATER PART e ENERGY CUT 0 1 MeV RANGE CUT 0 134781 GmCut sEnergy2RangeUA IATERIAL G4 WATER PART e ENERGY CUT 0 1 MeV RANGE CUT 0 137686 Minimum and maximum production cuts GEANT4 has internal limits in the minimum and maximum energy of a production cuts These values are by default 990 eV and 100 TeV You may change these values with the command gamos physics prodCutsEnergyLimits MIN_ENERGY MAX_ENERGY Apply cuts for all processes By default the production cuts are only applied to ionisatio bremsstrahlung and electron positron production by muons but they may be applied to any process by using the command gamos physics applyCutsForAllProcesses User limits 64 The user limits is a mechanism that Geant4 offers to limit the tracking of a particle There are five types of user limits e Limit the step size e Limit the track length Chapter 5 Physics e Limit the time of flight e Stop the particle when the kinetic energy is below a limit and deposit its energy locally e Stop the particle when the expected range is below a limit and deposit its energy locally In GAMOS a user can set the user limits through simple user commands and user limits can be set independently for different particle types in the same or different logical volumes The set of commands to set user limits are e gamos physi
17. If the event is classified as a PET one it is dumped in a binary file given by the name gamos setParam pet FileName MY_FILENAME that takes the name pet out by default The variables written are given by the structure 163 Chapter 18 PET application 164 struct PetOutput char name 8 float xVtx yVtx zVtx x1 yl z21 x2 y2 22 where name is PET xVtx yVtx zVtx are the coordinates of the event vertex x1 y1 z1 are the coordinates of the first reconstructed hit x2 y2 z2 are the coordinates of the second vertex The same data that is written to the file can be written in the standard output if the parameter gamos setParam PET EvtClass DumpEventListMode TRUE is set to true The positions in the standard output not in the file will be written in cylindrical coordinates by default If you want them in cartesian coordinates you should set to true the parameter gamos setParam pet DumpCartesian TRUE Projection data file PET events can also be stored as projection data sinograms by selecting the follow ing parameter gamos setParam PET EvtClass DumpProjData 1 Projection data or sinogram is a common way to organize PET events and represents the standard input for image reconstruction algorithms By default GAMOS gener ates a file compatible with its own image reconstructor see Image reconstruction utilities section data are written in pairs including a header text file hv and a binary data file v
18. ImageJ jre bin java Xmx512m jar HOME ImageJ ij jar ijpath S HOME ImageJ eval run NucMed Open open MY_IMAGE hv Stochastic Image Ensemble method Introduction About this Document This manual refers to the SOE_ImageRecon program version 0 0 0 of February 2012 Complaints or questions about installation compilation and use of this program can be sent to lt mkolstein ifae es gt Introduction to SOE The SOE Stochastic Origin Ensemble method is based on the article Stochastic Image Reconstruction Method for Compton Camera by Andriy Andreyev Arkadiusz Sitek 179 Chapter 21 Image reconstruction utilities 180 and Anna Celler published in IEEE Nuclear Science Symposium Conference Record 2009 21 The SOE algorithm works on data files that contain coincidences of two hits The exact format of these files is described in the Getting Started section The data can be from a Compton Camera detector or from a PET detector In the case of Compton Camera data one hit should be from the Scatter detector and one hit from the Absorber detector Combining the information of these hits both the positions and the deposited energies Compton cones can be constructed The original gamma source for an event lies somewhere on the corresponding Compton cone In the case of PET data the two hits should be on opposing sides of the PET detec tor corresponding to the two back to back gamma particles cau
19. Running SOE SOE is installed in GAMOS at the directory analysis Detector SOE The SOE algorithm works on data files that contain coincidences of two hits The exact format of these files is described below in the section called Input files The data can be either from a Compton camera detector or from a PET detector To run the code for Compton Camera data type SOE_ImageRecon Compton or for PET data SOE_ImageRecon PET The complete list of possible flags is SOE_ImageRecon SOE_ImageRecon Chapter 21 Image reconstruction utilities SOE_ImageRecon PE for PET data SOE_ImageRecon Compton for Compton data SOE_ImageRecon PETGauss for PET data using a Gauss distribution for guessing f SOE_ImageRecon seed lt seedNumber gt selecting specific seed SOE_ImageRecon xtraIterInfo additional output files for intermediate iteratior SOE_ImageRecon averageStatesOut additional output each 100 iterations before fi SOE_ImageRecon readDensityMatrix read density matrix density_matrix img at ir SOE_ImageRecon readCurrentState read current state file currentstate dat at i SOE_ImageRecon help for this help output Input files In the directory in which you run the code you need the following input files ir_soe_userparameters conf parameters file CC_img out data file with any kind of name as given in the parameters file In the data file
20. every line should contain the following Hitl1 Z mm Hitl1 Y mm Hit1 X mm Hitl Energy keV Hit2 Z mm Hit2 Y mm Hit2 x In the case of Compton camera data Hit1 corresponds to the hit in the Scatter de tector and Hit2 corresponds to the hit in the Absorber In the case of PET data the hits correspond to the two back to back hits in opposite regions of the detector Note 1 Note that the order of the coordinates in the files is Z Y X Energy Note 2 The geometry used in the SOE algorithm is as follows The z axis is the axis that separates the Scatter detector from the Absorber detector The front of the Scatter detector is located at z 0 mm The gamma source must be at a location with a negative value for the z coordinate The Absorber detector is at positive z with respect to the Scatter detector The parameter file ir_soe_userparameters conf has the following contents m_iterations 100000 m_bins_z 100 zPositionl 95 0 zPosition2 105 0 m_bins_x 100 m_xmin 5 0 m_xmax 540 ff m_bins_y 100 Lf m_ymin 5 0 m_ymax 570 fF m_sourceEnergy 511 DataFileName 0 ey ae EventSetSize 0 m_maxNumberOfEvents 1000 UseEnergyResolutionFactorFWHM 0 0 percentage UseSpatialDeltax 0 0 mm UseSpatialDeltay 0 0 mm UseSpatialDeltaZ 0 0 mm UseDopplerEffectSigmaTheta 0 0 sigma CCs_Machiel CC_img out_Gamma511_A110FF Each line should contain three fields e
21. is not defined it is the two surfaces composed of the points of same theta that limit the sphere volume PHI if the full phi 360 degrees is not defined it is the two surfaces composed of the points of same phi that limit the sphere volume The current may be divided by the area of the surface being traversed if the following parameter is set to 1 gamos setParam SCORER_NAME DivideByArea 1 The current may be divided by the cosine of the angle between the track direction and the surface normal gamos setParam SCORER_NAME DivideByAnegle 1 GmPSSurfaceFlux This scorer is similar to GmPSSurfaceCurrent but flux is calcu lated instead of current that is the current is always divided by area and angle GmG4PSFlatSurfaceCurrent Flat surface current is a surface based scorer The present implementation is limited to scoring only at the Z surface of a G4Box solid The quantity is defined by the number of tracks that reach the surface The user must choose a direction of the particle to be scored as extra argument in gamos scoring addScorer2MFD The choices are In Out or InOut Here In scores incoming particles to the volume while Out scores only outgoing particles from the volume InOut scores both directions The current is normalized for a unit area if an extra second parameter is set to TRUE GmG4PSCylinderSurfaceCurrent Cylinder surface current is a surface based scorer and similar to the GmG4PSFlatSurfaceCurrent The only di
22. lt lt MyPositionGeneratorDistribution created lt lt G4endl This message will only be printed if the generator verbosity is set to info or a level above debug or test If you want for example that your distribution prints a message with the calculated position at each event you may write G4cout lt lt GenerVerb debugVerb lt lt MyPositionGeneratorDistribution position lt lt position lt lt G4endl m This message will only be printed if the generator verbosity is set to debug or a level above test As you may have deduced the rules for using each of the GAMOS verbosity man agers are that the name of the verbosity is the same as the name of the verbosity manager simplified no Gm at the beginning and Verb instead of Verbosity e g from GmAnaVerbosity you use AnaVerb And the name of the level in C code is the Chapter 16 Managing the verbosity same as the one in the input command file adding Verb e g for warning you use warning Verb Creating your own verbosity manager You can create your own verbosity manager for the code you use taking as example one of the GAMOS verbosity managers for example the class GmGenerVerbostityMgr in the package GamosCore GamosGenerator First create a class inheriting from GmVerbosityMegr and fill it as follows e In the include file i e the one with suffix hh of this class define an object of type GmvVerbosity as extern extern GmVerbosity MyVer
23. not mandatory Example REPL crystal Block X 10 5 xcm Remember that different to the divisions where the solid type and dimensions are calculated automatically be Geant4 in the case of replicas the volume name used must be the name of a previously defined volume This solid is not really used for navigation but should have the correct type and dimensions for visualisation Assembly volumes Assembly volumes are sets of logical volumes that are combined together so that they act as if there were in a real mother but without creation of the mother To define assembly volumes you have to define the relative rotations and positions of all the logical volumes VOLU_ASSEMBLY e Volume name e Number of logical volumes e Axis of division e Number of divisions e Division width e Offset not mandatory One line per logical volume with e Logical volume name e Rotation matrix name e position X position Y position Z Then to place the assembly volume you can use PLACE_ASSEMBLY e Volume name Chapter 3 Geometry Copy number e Parent volume name e Name of rotation matrix e X position e Y position e Z position Example SOLID Crystal BOX 10 10 10 SOLID Crystal2 BOX 5 5 5 VOLU_ASSEMBLY CrystalSet 3 Crystal RMO 0 0 0 Crystal RM1 0 0 20 Crystal2 RMO 0 20 10 PLACE_ASSEMBLY CrystalSet 1 expHall ROO 100 0 0 Rotation matrix A rotation matrix is interpreted as the rotation tha
24. process and particle type In the case of production cuts this information is stored at particle creation In the case of user limits this information is stored at each step for parents only the steps before the creation of the interesting track At the end of run you can can get for each region process particle a list of all the ranges or energies of all the particles created Then you can easily know if you apply a cut how many particles are below it This is valid if you are only interested in counting how many particles you lose For other cases another approach should be used For example if you want to check how your dose distribution changes you can build a set of filters each one with a set of cut values These filters do not really cut the particles but only serve to tag a particle if it would have been killed by the set of cuts in the filter Therefore for each track that contributes to your results GAMOS can check if it or any of its ancestors would have been killed by each of these sets of cut values If you build your results N times in a job each one using only those tracks that pass one filter you can compare each result to see how it changes with each set of cuts Although as mentioned above the production cuts are only necessary for ionization and bremsstrahlung processes this method allows to extend the production cuts to other processes To do this we provide the abovementioned numbers and plots sepa rately for each p
25. that simulates the activity of different iso topes that decay in one or several photons electrons or positrons First a file is read with the description of the isotope decays in a format as the one that can be found at MY_GAMOS_DIR src GamosCore GamosGenerator test isotopes dat part of which we reproduce here ISOTOPE Na22 215 5 0 905 e 1275 0 0 9995 gamma ISOTOPE F18 249 8 0 967 et For each isotope there must be a first line starting by ISOTOPE and followed by the isotope name Then there is a line for each of the possible isotope decays with three columns describing the decay particle energy the probability of the decay and the particle type This file contains the most common isotopes in medical physics If you want to use another isotope you can add it following the format described above If you selected this generator each event will be generated with one of several pri mary particles in the decay list of each of the selected isotopes The presence of each decay particle will occur following its corresponding probability To choose an isotope as particle source you have to use the command gamos generator addIsotopeSource SOURCE_NAME ISOTOPE_NAME ACTIVITY SOURCE_NAME is the name of this source that you have to use if you want later to change its time energy position or direction distribution ISOTOPE_NAME is one of the isotopes read from the input file ACTIVITY is the activity you want to set for that is
26. 32 bit integer so be careful that the index is not too big bigger than 2 Filters are plug in s so that a user can create her his own filter and select it with a user command To learn how to do this see the instructions in the section Creating your plug in using the GmClassifierFactory Setting indices to classifiers In most classifiers by default the indices are built automatically as the objects of clas sification appear and they start with 0 and grow one by one You may want to change this behaviour it may be specially useful if you are using importance sampling To do it you should use the command gamos classifier setIndices VALUE_1 INDEX_1 VALUE_2 INDEX_2 where VALUE_ii are the names of the objects of classifications logical volumes pro cess names and INDEX_ii are the new indices In the case of classifier GmClassi fierByParticleProcess you need two values for each index particle name and process name You should be careful to list all the values that may appear in the classifier If not GAMOS will automatically assign an index to the new values starting with the num ber following the maximum index defined with the user command The exceptions are the classifiers GmClassifierBy1Ancestor and GmClassifierByAncestors for which all values should be given 138 Chapter 14 Distributions Introduction The GAMOS distribution classes represent one dimensional functions which assing an output value for
27. 34185 PARTICLE gamma FINAL 72 34184 Automatic determination of user limits for a detector The method used in GAMOS to determine the minimum range user limits is similar to the one used to determine the best production cuts The main difference is that when a track reaches the target we do not have to look at the range it had when 159 Chapter 17 Detector applications 160 created but at the range it had in every step This is because even if we want the minimum step the track may have crossed several regions and the smallest range may not correspond to the last step What we do nevertheless is to consider only the last step when there are a set of contiguous steps in the same region Also for the ancestor tracks we have to store the information of each step starting of course with the one when the track that reached the target or its n th ancestor if we are looking at the n 1 th ancestor was created The same warning as for the production cuts should be mentioned here but in this case it is more than a mere warning when a track reaches the target we accumulate one track information of the last step in each region for each of the ancestor tracks Therefore it is very likely that there are more than one track information per track reaching the target and therefore there will be overcounting of the number of tracks killed by a cut As for the production cuts you should keep an eye on this To use this utility i
28. Detector and Hits These two methods will be called automatically The first one at the end of each event to convert the hits in digits and the second one at the beginning of each event to clear the digits of the previous event You can then convert your digitizer into a GAMOS plug in To learn how to do this see the instructions in the section Creating your plug in using the GmDigitizerFactory After this you select it with the command gamos digitizer MY_DIGITIZER Hits and digits reconstruction The digital signals are usually treated so that they become reconstructed hits which contain sensible variables like energy time This conversion is also very dependent on the detector and therefore GAMOS just provides a general class GmVRecHitBuilderFromDigits There is also another class GmVRecHitBuilderFromHits which serves in case the user wants to transform the hits into reconstructed hits directly The user may inherit her his own reconstructed hit builder from it and implement the two methods virtual std vector lt GmRecHit gt ReconstructDigits const std vector lt GmDigitx gt amp 0 virtual void CleanRecHits in the case of GmVRecHitBuilderFromDigits or virtual std vector lt GmRecHit gt ReconstructHits const std vector lt GmHit gt amp 0 virtual void CleanRecHits in the case of GmV RecHitBuilderFromHits These two methods will be called automatically The first on
29. GmReadPhantomGeometry VoxelName VOXEL_NAME It is also possible to displace the phantom from its 0 0 0 position in the mother vol ume To do it you have to set the parameter gamos setParam GmReadPhantomGeometry InitialDisplacement DISP_X DISP_Y DISP_Z And to rotate it around the X axis then Y axis and finally Z axis around the phantom centre you can use the parameter gamos setParam GmReadPhantomGeometry InitialRotAngles ANGLE_X ANGLE_Y AN GLE_Z Partial phantom geometries The DICOM files always describe a parallelepiped geometry including air around the real patient animal or phantom It may be that you have a CT DICOM file that you want to simulated inside a PET scanner or a radiotherapy accelerator and it does not fit becuase this air overlaps with the machine In this case you may use a part of your g4dcm file taking the parallelepipedal DICOM geometry and in tersecting it with some volume to create a new file The volume can be one in the Geant4 volume or a virtual one you create To do this you can follow the example in analysis DICOM buildPartialDICOM You have to run a GAMOS job with an in put file similar to the one in that directory buildPartial_G4Volume in The physics and primary generator can be anyone but for the geometry you have to use GmReadPhan tomG4Geometry to read your g4dcm file Then you have to add a command gamos geometry DICOM intersect WithG4 Volume VOLUME_NAME where VOLUME_NAME is the name of a
30. GmSDSimple but the hits position is the cen troid of the energy depositions of the different tracks that produced it weighted by their energy e GmSDOpticalPhoton This class inherits from GmSDSimple but only produces hits if the process that defined the step is OpAbsorption e GmSDSimple This class separates in different hits not only those energy deposi tions in different detector units but also if they differ by more than the measuring time see below If no measuring time is set it takes a value given by the parameter gamos set Param GmSDSeparateByTime MinimalMeasuringTime SDTY PE VALUE which has a default value of 100 nanoseconds In fact the grouping of times is done using the logic of the triggering see below For example if a trigger hap pens at time t the energy depositions willbe separated by times intervals t N measuringTime This sensitive detector type is meant for particle with radioactive decay where in the same event you may have very different times Each hit with big times will be kept in memory until an event happens with times close to it so that the hits of the event may be merged with it To avoid keeping hits whose time will never be reached by any event in the simulation a maximum job time is calculated in the following way 100 event times are sampled and with them the average time per event is calculated this time is multiplied by the number of event s to be processed in the job and to avoid
31. L 1 W 3 T M M Good PET Events PRE 1 ALL L 2 W 3 T PT M Mean Random coincidences PET Events And if you run the command analysOutput anaout lis Then you may get a result like this Events 2596 Good PET Events 92 6667 Mean Random coincidences PET Events 769 765 763 129 Chapter 11 Analysis extracting data 130 Chapter 12 Filters Introduction A filter is a class that receives a G4Step or a G4Track and accepts it or not depending on some given criteria AGAMOS filter has therefore two main methods e AcceptStep const G4Step receives a G4Step pointer and decides to return true or false e AcceptTrack const G4Track receives a G4Track pointer and decides to return true or false A filter may implement the two methods or only one of them If the AcceptStep method is not implemented by a filter the AcceptStep method from the base class is invoked and it calls the AcceptTrack method passing to it the G4Track correspond ing to the G4Step If the AcceptTrack method is not implemented by a filter the method from the base class returns true Filters can act on user actions or scorers If one or several filters are set to act on a user action the PreUserTrackingAction PostUserTrackingAction and ClassifyNewTrack methods will only be invoked if the AccepTrack method of every filter returns true and UserSteppingAction method will only be invoked if the AccepStep method of every filter returns true In the case of f
32. Maximum transversal length Maximum R transv Pos e Average longitudinal length Maximum R transv Pos 145 Chapter 15 Utility user actions e Average transversal length Maximum R transv Pos e Shower direction theta angle Shower direction theta Angle e Shower direction phi angle Shower direction phi Angle The sum of energy deposits inside a certain transversal distance a radius is calcu lated and an histogram is filled By default the list of radii is 0 1 0 3 0 5 1 5 mm and infinite DBL_MAX You may change this list with the parameter gamos setParam USER_ACTION_NAME Radii RADIUS_1 RADIUS_2 With these variables two sets of histograms are filled e Energy inside radius Energy inside radius E e Energy inside radius divided by total shower energy Relative energy inside ra dius E Killing all tracks The action gamos userAction GmKillAtStackingActionuA serves to kill all particles at the stacking action G4ClassificationOfNewTrack method i e before they start being tracked You may use it in combination with one or several filters to kill only the particles that are accepted by them For example gamos userAction GmKillAtStackingActionUA GmEletronFilter will only kill electrons If you want to apply the killing at stepping action probably because you want to apply some step filter you can use the user actions gamos userAction GmKillAtSteppingActionuA
33. Notes 58 Geant4 uses any kind of ion whether in its ground stante or in an excited state Ions are named with the element symbol followed by the atomic mass number and the excitation energy between brackets e g Fe56 0 0 Na22 0 0 Co57 136 5 note that the ground state is named as 0 0 There two ways two use ions as primary particles in GAMOS generator The first one is defining an isotope source as described above In this case the isotope itself willnot be created but only its decay products as defined in the isotopes lis file In this way you have a direct access to the position direction energy or time distributions of these particles what may increase your simulation efficiency The alternative way is to define a single particle source and use an ion name as particle Geant4 will create this ion and will use its readioactive decay utitlity to decay it and follow the decay chain until stable ions are produced Do not forget that if you want to use ions you have to define a physics list that creates the physics for them This means that you cannot use for example GmEMPhysics but you may use GmExtendedEMPhysics or any other physics where this physics is created 1 For a list of the names of the available particles use the Geant4 command run particle dumpList or see Appendix The available units in Geant4 are becquerel and curie For a list of the names of the available particles use the Geant4 command run particle dum
34. POS_Y POS_Z By default the square is not rotated If you want it rotated you have to add three optional extra param eters and always add the three positions even if they are 0 0 0 DIR_X DIR_Y DIR_Z Those are the director cosines of the Z axis of the square the axis perpen dicular to the 2D surface Position in a rectangle 51 Chapter 4 Generator 52 gamos generator position Dist SOURCE_NAME GmGenerDistPositionRectangle WIDTH_X WIDTH_Y POS_X POS_Y POS_Z DIR_X DIR_Y DIR_Z The position is randomly distributed in a 2D rectangle in the XY plane of widths WIDTH_X in X and WIDTH_Y in Y at position 0 0 0 If you want it placed at a different position you have to add three optional extra parameters POS_X POS_Y POS_Z By default the rectangle is not rotated If you want it rotated you have to add three optional extra parameters and always add the three positions even if they are 0 0 0 Those are the director cosines of the Z axis of the rectangle the axis perpendicular to the 2D surface Position in a disc gamos generator positionDist SOURCE_NAME GmGenerDistPositionDisc RADIUS POS_X POS_Y POS_Z DIR_X DIR_Y DIR_Z The position is randomly distributed in a disc in the XY plane of radius RADIUS at position 0 0 0 If you want it placed at a different position you have to add three optional extra parameters POS_X POS_Y POS_Z By default the cylinder is not rotated If you want it rotated you have to add t
35. PRINTER_NAME out It can be changed with the parameter gamos setParam PRINTER_NAME FileName FILE_NAME GmPSPrinterBinFile Prints in a text file almost the same information than the GmP SPrinterG4cout printer The format of the data is the following e Detector name char 30 e Scorer name char 20 e Unit name char 10 e Unit value float e Number of entries unsigned int For each classifier index Index name char 20 e Score value float e Square of score value float This value is needed instead of the error for prop erly taking into account the correlations when the errors of several files are summed The name of the file is PRINTER_NAME out It can be changed with the parameter gamos setParam PRINTER_NAME FileName FILE_LNAME 93 Chapter 8 Scoring e GmPSPrinterHistos Prints scoring dat in histograms The name of the file is PRINTER_NAME root It can be changed with the parameter gamos setParam PRINTER_NAME FileName FILE_NAME The user must define the histogram name number of bins and axis minimum and maximum giving them as arguments of the gamos scoring printer command this means that the class GmPSPrinterHistos cannot be used directly The scoring data corresponding to index IDX will be used to set the content of the histogram bin IDX It should be noted that the first histogram bin is number 1 while it may hap pen that the first index is not 1 If this is the case a number positive or negat
36. Param CC EvtClass CoincidenceTime COINCIDENCE_TIME will be taken into account to make a Compton imaging event it is assumed that one of the two started the trigger and the other must be in the coincidence time open at that moment To utilise events in which multiple interactions occur within a detector it is necessary to identify the appropriate interactions to reconstruct The most simple example is if a gamma ray Compton scatters in the scatterer detector and then in the absorber de tector it Compton scatters and undergoes Photoelectric absorption This event can be reconstructed if the 1st hit ie the Compton scattering interaction is correctly identi fied in the absorber detector It is possible to recover these hits when one of several Compton interactions have occurred by examining those that are close You may set the distance to examine multiple hits within the scatterer and absorber detectors re spectively with the parameters gamos set Param CC EvtClass ComptonRecHitDistScat DIST gamos setParam CC EvtClass ComptonRecHitDistAbs DIST 173 Chapter 20 Compton camera application DIST takes by default a value of 0 what means that no identification of multiple Compton hits will be done If DIST is gt 0 you may select the position and energy of the 1st hits identified through the algorithms described in the Identifying Compton Interactions section of the PET chapter By default the algorithm used is the one which identifies th
37. The name of these filters is constructed combining the geometry condition and the volume type e g GmInPhysical VolumeFilter GmTraverseTouchableFilter GmEndRegion Filter GmTraverseLogical VolumeChildrenFilter GmExitRegionChildrenFilter There is a special case when parallel worlds are used the scorers see the parallel world volumes but the user actions do not This means that you cannot use the above filters on a parallel world volume if you are using the filter for a user action while you can if you use it for a scorer If you want to do it you have to use the special parallel filters namely e EndParallelLogicalVolumeFilter e EndParallelPhysicalVolumeFilter e EndParallelPhysicalVolumeReplicatedFilter e EndParallelRegionFilter 133 Chapter 12 Filters EnterParallelLogicalVolumeFilter EnterParallelPhysical VolumeFilter EnterParallelPhysical VolumeReplicated Filter EnterParallelRegionFilter ExitParallelLogicalVolumeFilter ExitParallelPhysical VolumeFilter ExitParallelPhysical VolumeReplicatedFilter ExitParallelRegionFilter InParallelLogical VolumeFilter InParallelPhysicalVolumeFilter InParallelPhysical VolumeReplicated Filter InParallelRegionFilter StartParallelLogicalVolumeFilter StartParallelPhysical VolumeFilter StartParallelPhysical VolumeReplicated Filter StartParallelRegionFilter TraverseParallelLogicalVolumeFilter TraverseParallelPhysicalVolumeFilter TraverseParallelPhysicalVolumeReplicated
38. The types of volume are the following ones LogicalVolume a G4Logical Volume object PhysicalVolume a G4VPhysicalVolume object The volume name and copy number are set separated with a character e g volA 1 see section on Identifying touchables Physical Volume Replicated for optimisation reasons the PhysicalVolume filters use the pointers to the physical volumes to find them But in the case of replicated physi cal volumes i e divisions replicas and parameterisations there is a unique Phys icalVolume pointer while the different copies are managed internally by Geant4 Therefore you cannot select only a few of the copies of a physical volume with the above filters For these cases you should use the Physical VolumeReplicated filters Touchable a G4VTouchable object The volume name and copy number are set separated with a character the ancestors are separated by a character e g volB 3 volA 1 see section on Identifying touchables Region a G4Region object Logical VolumeChildren a G4Logical Volume object or any of the G4Logical Volume chil dren of it PhysicalVolumeChildren a G4VPhysicalVolume object or any of the G4V Physical Volume children of it PhysicalVolumeReplicatedChildren please read the discussion about Physical Volume Replicated RegionChildren a G4VTouchable object or any of the G4VTouchable children of it TouchableChildren a G4Region object or any of the G4Region children of it
39. The whole algorithm is repeated selecting as first the other hit of the pair of reconstructed hits and then making other pairs of hits with the rest of hits in the set By looking at all the minimal distances stored it selects as good combination the one with the smallest distance For PET detectors when the algorithms is applied to the second set of hits the position of the first set is used instead of looking at the position of all hits in the other side of the detector These algorithms act only on those event that have been accepted by the PET SPECT ComptonCamera classifier To use them the first step is to merge the reconstructed hits that are supposed to correspond to the interaction of the same gamma into a single one This is done by setting the distance between hits to be merged with the parameter substitute PET by SPECT or ComptonCamera gamos setParam PET EvtClass ComptonRecHitDist DISTANCE which by default takes a value of 0 By default the position of the set of hits is the one of the hit with highest energy i e the DetlstHitByEnergy algorithm is used Other algorithms may be selected instead with the parameter gamos setParam PET EvtClass 1stHitAlgorithm ALGORITHM where ALGORITHM is one of those enumerated above For the case of PET events it is possible to use a different algorithm for the first and second set of hits what may be specially useful if the Compton cone algorithm is used but also in other cases To do it t
40. There are two extra parameters that are FALSE by default and can be set TRUE or FALSE to multiply by the kinetic energy and to divide by the velocity If the energy track flux is required then you should set them to TRUE FALSE Alternatively to measure the flux per unit velocity then you should set them to FALSE TRUE Finally to measure the flux energy per unit velocity then you should set them to TRUE TRUE GmG4PSPassageTrackLength The passage track length is the same as the track length in GmG4PSTrackLength except that only tracks which pass through the volume are taken into account This means that newly generated or stopped tracks inside the cell are excluded from the calculation A particle weight is not applied by default e Deposited energy scorers Chapter 8 Scoring GmG4PSEnergyDeposit This scorer stores a sum of particles energy deposits at each step in the cell GmG4PSDoseDeposit In some cases dose is a more convenient way to evaluate the effect of energy deposit in a cell than simple deposited energy The dose deposit is defined by the sum of energy deposits at each step in a cell divided by the mass of the cell The mass is calculated from the density and volume of the cell taken from the methods of G4VSolid and G4LogicalVolume GmPSSphericalDoseDeposit This is a _ special case of emphasis GmG4PSDoseDeposit where the scoring volume is virtually divided in concentric spherical shells so that one score is given for eac
41. You may also consider the special distribution GmGeometricalBiasingDistribution see chapter on Distributions that calculates the weight as the division of the weights of the entering and exiting volumes Production of deexcitation secondary particles As the production of secondary particles by deexcitation processes i e characteristic X rays and auger electrons is often quite a rare process it is possible to increment the statistics of these particles by using a variance reduction technique Each time a deex citation secondary particles is going to be produced GAMOS invokes the production method N times instead of 1 and reduces the weight of any produced particles by 1 N To use this technique the following procedure should be followed First the physics list GmPSEMPhysics has to be selected gamos physicsList GnPSEMPhysics Then the deexcitation splitting processes for gammas and electrons has to be selected gamos GmPhysics addPhysics electron lowener Deex Split gamos GmPhysics addPhysics gamma lowener Deex Split Before this several parameters can be selected namely The regions for which deexcitation is active gamos setParam GmPhysicsElectronDeexSplit Deexcitation REGION_1 REGION _2 gamos setParam GmPhysicsGammaDeexSplit Deexcitation REGION_1 REGION_2 remember that you can use to name several regions e g only mean all re gions The number of splittings times secondary particle productio
42. a volume A in 5 places and a volume B in 12 places you will have 5 12 physical volumes each one with a distinct position and rotation matrix But you will have 5 X 12 60 individual copies that is 60 touchables To save memory the G4VTouchable are instantiated in Geant4 only when a track traverses the corresponding volume in space and they are immediately deleted when the track leaves In GAMOS you have the possibility of accessing any individual touchable whenever you like When you need it you can ask GAMOS to create a GmTouchable which will have the same characteristics as the corresponding G4VTouchable that would be created when a track reaches it To identify the touchable you want to use you have to use the following notation For example the name CRYSTAL identifies all individual crystals of your detector that have name CRYSTAL while BLOCK 2 CRYSTAL 1 refers only to the crystal s with copy number 1 in block s with copy number 2 RING 3 BLOCK CRYSTAL 1 refers to all the crystal s with copy number 1 in all the block s whatever copy number they have in the ring s that have copy number 3 If you are writing some new C code for GAMOS you can have easy access to the list of touchables with a given name with the line GmGeometryUtils GetInstance gt GetTouchables touch_name itExists If the touchables do not exist in your geometry you will get a warning in case itExists is false and an exception if itExists is tru
43. add a file that we called src module cc where all the plug in s are created The first line of this file after the corresponding includes must be DEFINE_SEAL_ MODULE For the detector construction it is only needed to add a line plus the corresponding include files DEFINE_GAMOS_GEOMETRY ExN02DetectorConstruction For the physics in a similar way we add DEFINE_GAMOS_PHYSICS ExN02PhysicsList The primary generator requires some more changes As you can see ExN02PrimaryGeneratorAction constructor receives as argument the detector construction class so that it can then ask it for the dimensions of the world This is not needed in GAMOS because all volumes are available in any class through the singleton class GmGeometryUtils Therefore we have deleted the detector construction argument in the constructor and then we have substituted the line G4double position 0 5 myDetector gt GetWorldFullLength by this one G4Box x worldBox G4Box GmGeometryUtils GetInstance gt Get LogicalVolumes World 0 gt GetSolid G4double position 0 5 worldBox gt GetXHalfLength After this in the src module cc a line has to be included DEFINE_GAMOS_GENERATOR ExN02PrimaryGeneratorAction For the user actions we have first to transform then into GAMOS user actions what requires simply to edit the hh classes and make them inherit from GmUserXXXAction instead of G4UserXXXAction Then we have to add the foll
44. atest a E a aea 44 A GONCLALON sisceccicccincsscccansecdevssscosesconvesecescssevsccseaseseseaasesssesdassessdeseseevecenbesededcesosesssdasseessssteos 45 Using GAMOS generator sssri iinis ieii ii iier i eii eeii 45 Ea R616 NETOA 6 ARETE EEE Rol nt E AAA E A ENE A EE 45 Particle SOUrCES eon n a e E o e Eaa E ee ees 45 TDIStHID ULLOIS aeut A E aaa e OE EE E NRA 47 Reading your generator particles from a text file ccccccesseeesteesteeeeseseateneeees 54 Reading your generator particles from a binary file ccccsessesescseeseesteteeeees 55 Event generator changing energy and material 0 0 0 0 cccceseseeessseseseseeeeeeeeees 55 Event generator histograms cccccccsecceeecseseseesesssseeseessesesesssesesesesesesescesend 56 Biasing generator distributions cece eee ceeeeseeceesseseseseseseseseseseseecenees 57 Building your generator With C wees cssseseeserssseseseseeseesceeeeecenees 57 WSIS MONS recite aaieses tices lanes aaraa aan eana a Eea Aaa a a eaa raa a a A AARS 57 5 PHYSIS aea e cased NEE E E R RES 59 GAMOS electromagnetic physics list cece cs eetsteteseecesesesnensneseeceeesesesnanenesees 59 Multiple scattering model cece ceeeeseesenensesesessesesescseseseeceeees 59 Bremsstrahlung angular distribution 00 0 0 ccs ceeeeseeseseeeeseseseeeeeeeens 60 GAMOS electromagnetic extended physics list ccccccceeseeesteesceeeesesesneneeees 60 GAMOS hadrontherapy physics list 0 0 0 eee ceesese
45. background at the same time as they will have to share the CPU and memory wasting your computer resources or even saturating your memory A smarter approach would be to type four times a sendjobs command running jobs in foreground sh sendjobs 6 1111 10000 10 amp sh sendjobs 6 2111 10000 10 amp sh sendjobs 6 3111 10000 10 amp sh sendjobs 6 4111 10000 10 amp The full sendjobs file can be found in your GAMOS distribution under the directory tutorials RT Tytorial exercise2 Identifying touchables 222 As explained in several points through this guide you can use the concept of touch able available in GAMOS We will explain first in a few lines the concept of touchable in Geant4 and GAMOS In Geant4 there are several geometrical objects 7 e G4VSolid A solid is a geometrical object that has a shape and specific values for each of the shape dimensions e G4LogicalVolume A logical volume contains the volume s full properties It in cludes the geometrical properties of the solid and adds physical characteristics the material of the volume whether it contains any sensitive detector elements the magnetic field etc Chapter 26 Appendix A G4V Physical Volume A physical volume is a volume placed already in another vol ume that is a volume with position and rotation matrix G4VTouchable A touchable is each copy of a volume To understand the difference with a physical volume we put an example If you place
46. be saved in the TTree Event data Track data Secondary Track data and Step data GAMOS users can s elect one list of data for each one of the four categories If data with no meaning for a given category are included in the correspondent list e g adding trackID data to the Event data list an exception will be returned By default the four data lists are empty and nothi ng is saved in the TTree unless otherwise specified The four data lists are selected as follows gamos setParam DATA_USER_NAME EventDataList EVENT_DATA_1 EVENT_DATA_2 gamos setParam DATA_USER_NAME TrackDataList TRACK DATA_1 TRACK_DATA_2 gamos setParam DATA_USER_NAME SecondaryTrackDataList SECO_DATA_1 SECO_DATA_2 gamos setParam DATA_USER_NAME StepDataList STEP_DATA_1 STEP_DATA_2 DATA_USER_NAME is the name of the user action i e the word GmDataTreeUA plus the name of filters and classifier The TTree is filled at the end of each GAMOS event and contains a number of entries equal to the number of simulated events Each of the selected GAMOS data is stored in an independent TBranch inside the TTree Data are saved as integers doubles or strings For each TTree entry each of the se lected GAMOS data is stored in a std vector apart from Event data that correspond to single values The size of a std vector varies in accordance with the corresponding category track data vectors contain a number of elements equal to the number of tracks for a giv
47. by default 81 t theta number of angular views by default 80 v verbosity by default 0 silent 3 debug x maximum number of coincidences to process by default 1 no limit For example the following line describes how to convert a list mode file pet out in projection data file MY_PROJDATA covering a 100 mm axial and 250 mm transaxial field of view using 48 axial planes rings 160 angular views and 151 tangential bins Output projection data is written in STIR format with a maximum ring difference of 12 im2pd pet out a 100 0 d 250 0 p 48 t 160 r 151 m 12 n MY_PROJDATA o 1 Summing projection data files sumProjdata Merging output files is necessary after simulating different jobs under the same setup This is straightforward when dealing with list mode PET files that can be concatenated with a command like cat in Linux but projection data files must be summed position by position every position of each file contains the coincidences stored by the same PET line of response this can be done thanks to the utility sumProjdata To use it you have to write a file containing the list of projection data file without extension it searches for files hs s or hv v one per line for example projdata_000 projdata_001 projdata_002 177 Chapter 21 Image reconstruction utilities Then you just have to run the executable sumProjdata INPUT_FILE_LIST OUTPUT_FILE where INPUT_FILE_LIS
48. by default the minimal energy is 0 Check PET line distance a line joining the position of the two reconstructed hits is built and the distance of closest approach DCA to the origin of the positron is calculated the events are classified as near of far if the DCA is smaller or bigger than the parameter gamos setParam PET EvtClass LineDistToVtx DISTANCE Chapter 18 PET application where DISTANCE has a default value of 10 mm The ClassifyPET method returns an integer with several digits containing the event classification e Oif itis not PET 1 if it is PET and PET line is close to the event vertex 2 if it is PET and PET line is far from event vertex e 10 1 if the search for 511 keV reconstructed hits found more than 2 e 100 1 if the event is a random coincidence event e 1000 1 if the event is a scattered event At the end of the run a table is printed with the number of events in each of the combinations of the sub classification types PET histograms event classification These histograms are related to the event classification explained above They are produced if the event classification user action is selected The name of all these his tograms starts with PETEvtClass and all are written in the file pet root csv The following histograms are written Classification index of event PET classification This index is the one described in the precedent section e Number of 511 keV reconstructed
49. cut you use is very small it will be converted to this energy value The default value in Geant4 is 990 eV You may change this value with the Geant4 user command Production cuts by region A region in Geant4 is a set of G4Logical Volume s that share common properties You can define a region in the text file where you defined your geometry by using the tag REGION REGION_NAME LOGICAL _VOLUME_NAME s where REGION_NAME is the name that identifies the region and LOGICAL_VOLUME_NAME s is the list of G4LogicalVolume s that belong to the region For example REGION myRegion Crystal Wall Alternatively you can define a new region in your user script through a user com mand gamos geometry createRegion REGION_NAME LOGICAL_VOLUME_NAME Do not forget that in Geant4 when a logical volume belongs to a region automatically all its daughters belong to the same region unless there is another region explicitly defined for some of the daughters Also do not forget that regions in Geant4 have to be set in a hierarchical way if you place a volume A in the world and inside it you place a volume B you cannot create a new region for B unless you have explicitly created a region for A Once you have defined a region you may set a cut for the particles that traverse that region with the tag CUTS REGION_NAME gamma_CUT e _CUT e _CUT where REGION_NAME is the name of a previously defined region gamma_CUT e _CUT e _CUT are t
50. done Adding an extra volume If you have defined a distribution of type GmGenerDistPositionInG4Volumes GmGenerDistPositionInUser Volumes GmGenerDistPositionInG4Surfaces or GmGener DistPositionInUserSurfaces you can add more volumes with the following user command gamos generator GmPosition VolumesAnd Surfaces addVolumeOrSurface SOURCE_NAME LV_NAME1 LV_NAME2 for the Geant4 volumes or gamos generator GmPosition VolumesAndSurfaces addVolumeOrSurface SOURCE_NAME POS_X POS_Y POS_Z ANG_X ANG_Y ANG_Z SOLID_TYPE SOLID_DIMENSIONS for the user defined volumes The primary particles will be distributed equally in the volumes proportionally to their volume or surface Position in steps along a line gamos generator position Dist SOURCE_NAME GmGenerDistPositionLine Steps POS_X POS_Y POS_Z DIR_X DIR_Y DIR_Z STEP The position is distributed uniformly along a line starting at position POS_X POS_Y POS_Z and with direction given by the three director cosines DIR_X DIR_Y DIR_Z Each event is generated in a different point along the line starting at the initial position and in steps given by STEP Position in a square gamos generator positionDist SOURCE_NAME GmGenerDistPositionSquare WIDTH POS_X POS_Y POS_Z DIR_X DIR_Y DIR_Z The position is randomly distributed in a 2D square in the XY plane of width WIDTH at position 0 0 0 If you want it placed at a different position you have to add three optional extra parameters POS_X
51. each input variable of the a given variable In other words they represent one dimensional functions y f x In fact the correspondence between x and y values is read from a file so that any arbitrary function shape can be easily defined There are currently three users of GAMOS distributions We briefly decribe them here and give further details in the corresponding section To bias a primary generator distribution In this case the output values represent the probabilities of occurrence of the variables e g position coordinate X direction angle theta energy time To define the weights in importance sampling A GAMOS data should be defined so that the input values are those of the data at each track step To define the index corresponding to each value for the classifier GmClassifier By Distribution A GAMOS data should be defined so that the input values are those of the data at each track or track step Creating a distribution A distribution has to be created with the command gamos distribution DISTRIBUTION_NAME DISTRIBUTION_CLASS where DISTRIBUTION_NAME is the name you give to the distribution which will be used to assign it to an object and to define its parameters and DISTRIBUTION_CLASS is the class name see below for the list available distribution classes Assigning a GAMOS data Except in the use of a GAMOS distribution is for primary generator biasing you have to assign a GAMOS data This data is the va
52. file all the physics list in the GEANT4 source code are already included and therefore can be selected with a user command There is also in GAMOS a GmDummyPhysicsList that defines all the particles but only the process G4Transportation 61 Chapter 5 Physics All the GEANT4 physics list that can be found in the directory source physics_lists These are CHIPS FTF_BIC FTFP_BERT FTFP_BERT_EMV FTFP_BERT_EMX FTFP_BERT_TRV e LBE LHEP LHEP_EMV QBBC e QGS_BIC e QGSC_BERT e QGSC_CHIPS QGSP e QGSP_BERT QGSP_BERT_CHIPS QGSP_BERT_EMV e QGSP_BERT_EMX QGSP_BERT_HP QGSP_BERT_NOLEP QGSP_BERT_TRV e QGSP_BIC e QGSP_BIC_EMY QGSP_BIC_HP QGSP_FTFP_BERT e QGSP_INCL_ABLA QGSP_QEL There is an extra physics list that for the simulation of neutron below 20 MeV uses the neutron XS physics a faster neutron HP physics GnQGSP_BIC_HPXS Building your physics list with C code To build your physics list first write it in the usual Geant4 way that is inheriting from G4VUserPhysicsList see example in 10 After that you have to transform it into a plug in To learn how to do this see the instructions in the section above Replacing process models Whatever physics list you have chosen you can replace part of the electromagnetic models of one of more particles by one of the three models standard low energy or Penelope with the command 62 Chapter 5 Physics gamos physics replacePro
53. file is read back specially useful if the file is read in a different computer system than the one where it was written or by another program than GAMOS a check line is read This check line consists on first an L or B character depending on whether the computer system uses little endian or big endian second the integer 1234567890 is written occupying four bytes third the float 3 40282e 38 is written occupying four bytes last the double 1 79769e 308 is written occupying eight bytes Optionally four other headers can be written after the first check line If any header is being written before then four integer numbers are always written whose values are 0 or 1 depending if the corresponding header is written The first optional header serves to check that your software system is able to read the file which you may have written using another system It writes first a char equal to L or B depending if the system uses little endian or big endian convention Then it writes as an int the nubmer 1234567890 as a float the number 3 40282e 38 and as a double the number 1 79769e 308 You should check that you read back those numbers when reading your file To write this header the following parame ter has to be used gamos setParam FILE_NAME WriteHeaderCheck 1 The second optional header contains the names and order of the data to be written the first word is an integer with the number of data then for each data it is written an integer with
54. filter names classifier name and particle type There is an histogram about the particle interaction e interaction log Energy MeV Kinetic energy of neutrons gamma at each step initial position A set histograms are about the distance to each detector so they also have the detector name and copy interaction dist to detector mm Distance from each neutron interaction or origin to the detector interaction dist to detector mm weighted by Hstar Distance from each neutron inter action or origin to the detector weighted by Hstar interaction dist to detector mm vs weight Distance from each neutron interaction or origin to the detector versus weight when detector is reached The rest of histograms are for each detector copy and score type The variables are calculated when the geantino or neutron gamma reaches the detector so they have the name At detector and they also have the score type There is a set for the geantinos and another set for the neutron gamma particles They are the following log10 energy MeV log10 of track kinetic energy times the weight log10 energy no weighted MeV log10 of track kinetic energy log10 energy weighted by Hstar log10 of track kinetic energy times the weight and Hstar value log10 weight log10 of track weight log10 weight weighted by Hstar log10 of track weight times the weight and Hstar value e log10 energy vs log10 weight log10 of track kinetic energy versus
55. following list anti_nu_e chargedgeantino e e gamma geantino nu_e opticalphoton If you use the GAMOS hadronic physics list you will get the following list GenericIon He3 alpha anti_neutron anti_nu_e anti_nu_mu anti_nu_tau anti_proton chargedgeantino deuteron eta eta_prime gamma geantino mu mu neutron nu_e nu_mu nu_tau opticalphoton pit pi piO proton taut tau triton These are the names that should be used in the commands that need a particle name If you want to use hadrons GAMOS also provides the possibility of grouping them so that with a single name you can identify the whole group The groups defined are the following e lightMeson Mesons that only contain up and down quarks pit pi piO eta eta_prime kaont kaon kaon0O kaonOL kaonOS a0O al a2 k k1l k2 ku star x kO_star k2_star k3_star anti_k anti_k0O anti_k1l anti_k2 anti_k_star anti_k2_star x anti_k3_star bl f0 f1 2 2_prime x hl eta eta2 phi phi3 pits pi2 rho rho3 x e charmMeson Mesons that contain a charm quark D D DO anit_DO Dst Ds J psi e bottomMeson Mesons that contain a bottom quark B B BO anti_BO Bs0O anti_Bs0O e meson All mesons e lightBaryon Baryons that only contain up and down quarks proton anti_proton neutron anti_neutron N x anti_N x del
56. gamma cut and the electron cut like in the following example gamos filter ProdCutFilter GmMinRangeCutOutside VoxelFilter 10 mm 1 mm gamos scoring addFilter2Scorer ProdCutFilter DoseScorerPC10 1 After running your job with as many scorer filter combinations as desired you can look at the total dose deposited and compare it with the dose with very small cuts It may happen that the dose with certain cuts despite being a small number is dis tributed in a different manner than with very small cuts introducing some bias that you consider not acceptable To check in detail the dose produced with a certain fil ter you can add a scorer printer of type RTPSPDoseHistos that will produce several histograms of the dose PDD X amp Y profiles dose dose volume gamos scoring addPrinter2Scorer RTPSPDoseHistos DoseScorerPC10 1 The name of the printer will be passed to the name of the file containing the his tograms amp tee out Chapter 23 DICOM utilities This is an utility that allows to define arbitrary magnetic fields and control their track ing precision paramters and also calculates the magnetic fields for different structures circular coil solenoid and stores them in a file for later used You can find all the relevant documentation in the file GAMOS 3 0 0 source Mag FieldManager doc user_manual_bfield_manager pdf In GAMO it is already installed so you may skip the installation instructions 213 Chapter 23
57. geometry To activate this utility you just have to use the command gamos geometry copyParallelToMassGeom VOL_NAME_1 VOL_NAME_2 VOL_NAME_N DISP_X DISP_Y DISP_Z where VOL_NAME_1 VOL_NAME 2 VOL_NAME_N is the list of volumes in a parallel geometry that will be copied and DISP_X DISP_Y DISP_Z are the values of the displacement vector The user should check that the copy of the parallel geometry volumes in the mass ge ometry are inside the user defined world volume and also that they do not overlap with any of the preexisting mass geometry volumes GAMOS will check that these two conditions are satisfied but only a warning message will be sent We also recom mend taht the copy is placed far from the rest of the mass geometry volumes If this is not done it may happen taht some particles navigating in the mass geometry will enter the copy what is a non physical situation Alternatively the user can take care of killing the particles that approach the copy for example by using the user action GmkillAtSteppingActionUA with the corresponding filters Building simple geometries There are several examples of geometries for common medical devices for example the ones you find in the PET directory and the one to build simple voxelised phan toms They have been designed to be used for describing different devices by simply changing the configuration data For more details please see the corresponding sec tions of this manual Bu
58. have to be sure to have the plugin option in the GNUmakefile as explained in the section Compiling your new code Using a parameter in your C code We describe in this section how to create and use a new parameter if you are creating anew C class GAMOS provides an utility that allows you to change the value of a parameter in the input file together with the line commands and use it in any of your classes even in several of them There are four classes of parameters numbers string list of numbers list of strings 229 Chapter 27 Appendix B C utilities To change the value of a parameter of any of the four types in your input file you have to use the command gamos set Param MY_PARAM_NAME MY_PARAM_VALUE s Then you can use this parameter in your class with a line like this G4double value GmParameterMgr GetInstance gt GetNumericValue MY_PARAM NAME DEFAULT_VALUE if it is a number or G4String value GmParameterMgr GetInstance gt Get StringValue MY_PARAM_NAME DEFAULT_VALUE if it is a string or std vector lt G4double gt vdefault std vector lt G4double gt values GmParameterMgr GetInstance gt Get VNumericValue MY_PARAM_NAME vdefault if it is a list of numbers or std vector lt G4String gt vdefault std vector lt G4String gt values GmParameterMgr GetInstance gt Get VStringValue MY_PARAM_NAME vde
59. her project without having to code in C and with a minimal knowledge of Geant4 and at the same time let an ad vanced user add new functionalities and easily integrate it with the rest of GAMOS functionality We have also tried to provide you with several tools that help you understand in de tail your simulation controlling the verbosity making histograms about many vari ables scoring different quantities etc as well as other tools to help you in optimis ing your simulation GAMOS is composed of a core software that covers the main functionality of a Geant4 simulation and a set of applications for specific domains Structure of GAMOS If you loook into GAMOS 3 0 0 directory you can find several directories The direc tories tmp lib bin and module are internal directories created at GAMOS compilation The other directories are the following source this is the directory where the GAMOS C code lies You will probably not have to care about this unless you are an advanced user and need to develop new code examples some first examples We recommend you that after the GAMOS installa tion you run the example examples test test in Chapter 1 Introduction e tutorials you can find four step by step tutorials Histogram and Scorers PET Radio therapy and plug in s They include several exercises with increasing difficulty and the exercise outputs as well as the exercise solutions are provided We recommend you to follow
60. hits Nhits Number of hits compatible in time Nhits good Kinetic energy Energy keV Width maximum separation between energy deposits Width R3 mm Width Z Width Z mm Width phi Width phi deg Number of energy deposits N E depos Maximum difference in time between energy deposits Time span ns Maximum distance between a hit and the rest Distance between hits mm Position X X hit mm Position Y Y hit mm Position Z Z hit mm Position R2 sqrt X X Y Y R2 hit mm Position phi PHI hit deg Position theta THETA hit deg Position R3 sqrt X X Y Y Z Z R3 hit mm Notes Chapter 7 Sensitive Detector and Hits The class GmRecHitsHistosUA produces a file named recHits root with the following histograms Number of hits N rec hits Kinetic energy Energy keV Width maximum separation between hits Width R3 mm Width Z Width Z mm Width phi Width phi deg Number of simulated simulated hits N sim hits Maximum difference in time between simulated hits Time span ns Maximum distance between a hit and the rest Distance between hits mm Position X X hit mm Position Y Y hit mm Position Z Z hit mm Position R2 sqrt X X Y Y R2 hit mm Position phi PHI hit deg Position theta THETA hit deg Position R3 sqrt X X Y Y Z Z R3 hit mm You may see the PET application for an il
61. hits before cleaning if there are more than two and searching for Compton hits i e hits produced merging two crystals see above N 511 recHits initial e The energy of the 511 keV reconstructed hits PET RecHit energy keV e The energy of the 511 keV reconstructed hits that are rejected because there are more than two PETEvtClass Extra PET RecHit energy keV e Distance of closest approach between vertex and the line joining the two 511 keV reconstructed hits _DCA PET dist line vertex mm e Z coordinate if distance of closest approach between vertex and the line joining the two 511 keV reconstructed hits DCA PET dist line vertex Z mm e Phi coordinate if distance of closest approach between vertex and the line joining the two 511 keV reconstructed hits DCA PET dist line vertex PHI mm e Radial position in the XY plane of the primary positrons e position X Y mm e Radial position in the XY plane of the primary positrons only for those events that are good PET events e position X Y _PET Events mm There are also a histogram of the DCA and the reconstructed hit energies for each of the sixteen subclassification types combinations of the 4 subindices and also for the all the events that are far from vertex all the events where there were more than two hits all the events with random coincidences and all the scttered events PET output for reconstruction List mode binary file
62. in X Y and Z translation and rotation applied to phantom when dose file was written and the statistics i e minimum and maximum voxel dose and aver age dose error in 20 50 and 90 highest dose voxels You will also get a file named dose_analyseSqdose root that contains the same his tograms that you get when you run the job to write the dose file using the scorer printer RTPSPDoseHistos Several arguments can be supplied to the executable in the standard Unix format e f phase space file name in this case do not use the file name alone as first argument as before e NRead number of particles to be read from the phase space file e fOut output file name e fHistos name of file with list of histograms e DoseMin minimum limit of dose histograms e DoseMax maximum limit of the dose histograms e cont type of the STL container that will be used to store the doses and dose errors It can be MAP or map that uses a std map it is the default one the one used by the Geant4 scorers It can also be VECTOR or vector that uses a std vector it occupies about ten times less than the std map The std map container occupies a big amount of space about 500 Mb for 10 million voxels so we recommend you that you use std vector if your phantom is big e NVoxels total number of voxels in phantom argument needed if sqdose file is of type FILLED 209 Chapter 22 Radiotherapy application 210 e verb verbosity it sets the RT Verb
63. in the name marks the event type the histogram refers to e ALL every event No PE events where no photoelectric interaction occurred Only PE events where only photoelectric interaction occurred PE 1 Compt events where one photoelectric interaction plus only one Comp ton interaction occurred PE gt 1 Compt events where one photoelectric interaction plus more than one Compton interaction occurred Automatic determination of production cuts for a detector 158 The method used in GAMOS to determine the best production cuts is based on what we can call an inverse reasoning We count each particle that reaches the sensitive detector and we calculate first the range of the particle in the region where it is cre ated Then we can know that if we put a range cut in that region smaller than the calculated range that particle would not reach our target plane We also compute the range of the mother particle in the region where it was created and the same consec utively for all the ancestors We know then that if we set in any of the regions where each of the ancestor particles are created a cut smaller than the corresponding range Chapter 17 Detector applications we would stop the chain of particles and therefore we would have no particle in the target plane After running a good number of tracks we can know for each particle type and for each region which is the biggest range we can put if we do not want to
64. interpolated using the lowest and second lowest bins Similarly for values between the maximum and the highest bin centre The type of the file will be automatically determined from the file name if it ends by csv it will be taken as a CSV format histogram file if it ends by root it will be taken as a ROOT format histogram file else it will be taken as a text file If you do not want to follow this convention then you have to set the file type explicitly by using the parameters gamos setParam DISTRIBUTION_NAME FileNameCSV FILE_NAME gamos setParam DISTRIBUTION_NAME FileNameROOT FILE_NAME Numeric distributions 140 A numeric distribution is a distribution where the input and output values are num bers There are several classes of numeric distributions GmGaussianDistribution The sigma and constant value of the Gaussian distribution has to be given as two extra parameters when the distribution is created By default the Gaussian distribution is centred at 0 if you want to centre it at other value you have to give a third parameter when the distribution is created GmPolynomialDistribution It can serve to define any polynomial distribution f x aO a1 x a_2 pow x 2 The parameters a_i are given as extra parame terswhen the distribution is created The number of extra parameters defines the order of the polynomial POLYNOMIAL_ORDER NUMBER_OF_PARAMETERS The other numeric distributions are general ones they read the in
65. leave_type e Opening distance of positive leave when leave is projected on the isocenter plane open_leave_a_at_isocenter e Opening distance of negative leave when leave is projected on the isocenter plane open_leave_a_at_isocenter Finally the material of the leaves have to be defined material Module MLC example On the next lines we include a simplified geometrical description that you can use as example to build your own On the figure 1 and 2 we can see the corresponding representation dimensions MODULE MLC MLC Realistic_CASE myMLC_x world Module_name and Mother_volume_name FOCUSED x STRAIGHT Type Orientation End_leave_type 5 2 5 Z_focus Cross Leave Focus 100 200 Z_ref Z_isocenter 297 024 80 Leaf_length Endleaf_length Endleaf_radius 75 8 8 1 25 Interleaves Gap Z_gap relative to Z_ref 18 7 2 3 2 78 2 50 1 25 2 Cross Leave Start Point 5 N Leaves Cross Profiles LEAF 14 N Leaves Cross Points and type 2 5 0 3 Z and C coordinate 1 5 0 3 1 5 0 3 75 8 5 1 3 75 8 5 0 3 75 8 1 5 0 3 75 8 1 18 7 3 22 244 25 0 05 18 7 3 20 24 25 0 05 18 7 3 0 65 22 24 0 05 18 7 3 0 65 20 24 0 05 18 7 3 1 18 7 3 1 5 0 3 2 5 0 3 189 Chapter 22 Radiotherapy application 190 LEAF 32 N Leaves Cross Points and type 2 2 3 Z and C coordinate 1 2 3 2 2 78 2 6 2 78 2 6 1 2 78 2 1 6 2 2 78 2 20 24 2 78 2 22 24 2 78 2 0 65 20 24 25 2 78 2 0 65 22 24 25
66. lose any particle Indeed we may allow to lose a small amount of particles if this speeds up our simulation To know easily which is the biggest cut you can use to lose less than a given percentage of particles GAMOS provides a set of plots one per each particle type and per each region and a simple script to get automatically the cut values One warning is due here as mentioned above when a track reaches the target its range fills a histogram but also the range of all the ancestors of this track It may happen then that when you set a certain cut and the abovementioned script gives you how many tracks would be killed more than one killed track correspond to the same track reaching the target i e with a cut you kill the track that reaches the target and the parent track Therefore you might have an overcounting of the number of tracks killed by a cut To avoid this the total number of tracks the last lines of output is not computed as the sum of tracks in the region This number uses a histogram that contains only one entry per track reaching the target the one corresponding to the track with the smallest range If you want to set a different cut for each region and are worried for this double counting you may have a look at the histogram named trackInfos per Track in target that plots per each track reaching the target how many track informations are kept in the histograms Another useful histogram for this case may be the 2D histogram
67. momentum direction will be changed sign while when it is an uneven time it will not be changed If it is Y the same but mirroring in Y And if it XY the second time a particle is used the X values will be changed sign the third time the Y values will be changed sign the fourth time both X and Y values will be changed sign the fifth time it will be no change and the cycles restarts When reading a phase space file you may skip the first N events by using the param eter gamos setParam RT GeneratorPhaseSpace NEventsSkip N You can produce the same histograms that were produced when writing the phase space file by setting the following parameter gamos setParam RT Generator PhaseSpace Histos TRUE Adding extra information to a phase space The IAEA format allows to store two long integers and two floats in the phase space file as extra information In GAMOS we have extended this functionality by putting the 32 32 bits of the two integers in a continuous stream that the user can divide in groups of bits of the desired length to store several informations The user can even add more sets of 32 bits by changing the the following line at source RadioTherapy include iaeaRecord hh define NUM_EXTRA_LONG 2 and recompiling cd source RadioTherapy make To store some information in this format the user has to instantiate one of the follow ing user actions RTExtralnfoProviderCrossings fills a bit if the track has crossed the correspo
68. more than two and searching for Compton hits i e hits produced merging two crystals see above N 511 recHits initial The energy of the 511 keV reconstructed hits RecHit energy keV Distance of closest approach between vertex and the line joining the two 511 keV reconstructed hits DCA SPECT dist line vertex mm Distance of closest approach between vertex and the line joining the two 511 keV reconstructed hits in Z axis DCA SPECT dist line vertex Z mm Distance of closest approach between vertex and the line joining the two 511 keV reconstructed hits in R phi plane DCA SPECT dist line vertex RPHI mm There are also a histogram of the DCA and the reconstructed hit energies for each of the sixteen subclassification types combinations of the 4 subindices and also for the all the events that are far from vertex all the events where there were more than two hits all the events with random coincidences and all the scttered events SPECT output for reconstruction Notes If the event is classified as a SPECT one it may be dumped in a binary file if the following parameter is set to 1 gamos setParam SPECT DumpEvent MY_FILENAME The file name is given by the parameter gamos setParam SPECT FileName MY_FILENAME that takes the name spect out by default The variables written are given by the struc ture struct SPECTOutput char name 8 float xVtx yVtx zVtx x1 yl z1 x2 y2 z2 ener class
69. of the utilities can also be useful in the simulation of brachytherapy treatments Geometrical modules Two geometrical modules are defined related to Radiotherapy JAWS and MLC mul tileaf collimators They can be defined in the usual geometry text file see chapter on Geometry with the format described below JAWS module This module serves to describe the jaws of a radiotherapy accelerator The jaws are described by their dimensions and its rotation is calculated with the parameters of its projection in into a plane The following parameters have to be provided MODULE JAWS Module name parent volume name Module type giving the direciton of the jaws It has to be X or Y X half dimension Y half dimension Z half dimension Z position of the focus Z position of the plane where the projections are calculated Z position of the field Field X projection Field Y projection Material MLC module Introduction A MLC Multi Leave Collimator is a collimator system composed of a set of pairs of leaves a few millimeters thick that serves to conform a hole in the field of view of an irradiation treatment beam These systems are used to shape irregulars volumes or to generate intensity modulate beams This module can describe a high variety of MLC models whether focused to a point in the Z axis or to an off axis point Any shape of leave profile can be described by enumerating the list of 2 dimensional points that describe it a
70. one corresponding to the 1st Compton interaction A parameter can be used to select instead the second third highest energy hit gamos setParam Det1stHitByXPos Order ORDER DetistHitByXYZPos Even if the detector has somoe symmetry it may happen that the best variable is the 3D position i e the spherical radius You may then use this algorithm which classifies the reconstructed hits in order of increasing 3D position i e sqrt x x y y z z and selects the first one as the one corresponding to the 1st Compton interaction A parameter can be used to select instead the second third highest energy hit gamos setParam Det1stHitByXYZPos Order ORDER DetistHitByDistanceToOther This algorithm is a generalization of the two above it calculate the minimun distance from each reconstructed hit to any of the recon structed hit that belongs to the other sets a PET event has two sets corresponding to the two gammas from positron annihilation and classifies the reconstructed hits in order of increasing value of this minimum distance It then the first one as the one corresponding to the 1st Compton interaction A parameter can be used to select instead the second third highest energy hit gamos setParam Det1stHitByDistanceToOther Order ORDER 153 Chapter 17 Detector applications 154 This algorithm cannot be used for SPECT detectors Det1stHitByComptonCone The idea of this algorithm is to profit from the fixed rela
71. pDy2 Angle with respect to the y axis from the centre of the side TWISTEDTRD twisted trapezoid with the x and y dimensions varying along z Half x length at the surface positioned at pDz Half x length at the surface positioned at pDz Half y length at the surface positioned at pDz Half y length at the surface positioned at pDz Half z length pDz Twisted angle TWISTEDTUBS tube section twisted along its axis Twisted angle Inner radius at end cap Outer radius at end cap Half z length Phi angle of a segment BREPBOX Boundary REPresented box Point 1 X Point 1 Y Point 1 Z Point 2 X Point 2 Y Point 2 Z Point 8 X Point 8 Y Point 8 Z BREPCYLINDER Boundary REPresented cylinder Origin X Origin Y Origin Z Axis X Axis Y Axis Z Direction X 21 Chapter 3 Geometry e Direction Y e Direction Z e Radius e Length BREPCYLINDER Boundary REPresented cylinder e Origin X e Origin Y Origin Z e Axis X e Axis Y e Axis Z e Direction X e Direction Y e Direction Z e Length e Small radius e Large radius BREPSPHERE Boundary REPresented sphere Origin X Origin Y Origin Z e Xhat X e Xhat Y e Xhat Z ZHat X ZHat Y ZHat Z Radius BREPTORUS Boundary REPresented torus e Origin X e Origin Y e Origin Z e Axis X e Axis Y e Axis Z e Direction X Direction Y Direction Z e Length 22 Chapter 3 Geometry e Minimum radius e Maximum radius BREPPCONE Boundary R
72. plane in Z and the later starting of the next simulation from this set of particles This technique can save a lot of time in cases several calculations share some accelerator parts and in the case where the accelerator simulation is very slow compared to the dose calculation Writing phase spaces The writing of phase space can be done automatically in GAMOS by selecting the user action gamos userAction RTPhaseSpaceuA When a particle crosses any of the planes defined by the parameter gamos setParam RTPhaseSpaceUA ZStops Z_1 Z_2 Z_3 its information is stored in a file whose named is given by the parameter gamos setParam RTPhaseSpaceUA FileName MY_FILENAME plus a suffix AEAphsp The default value of this parameter is test If there are several Z planes the Z value of each plane will be added to the name with a _ in front so 195 Chapter 22 Radiotherapy application 196 that each phase space will go to a different file If there is only one Z defined the Z value may be written in the file name if the following parameter is set gamos setParam RTPhaseSpaceUA ZStopInFileName TRUE If the plane crossed is the one with maximum Z the particle may be stopped if the following parameter is set gamos setParam RT PhaseSpaceUA KillAfterLastZStop TRUE The format of the phase space files is the one defined by the IAEA 17 generated using the official C files from IAEA First there is a header file that will ha
73. printer class by using the command gamos printer see section on Scorer printers below and SCORER_NAME is one of the scorers defined above If no printer is attached to a scorer it will use the printer type GmG4PSPrinterG4cout The scoring is done by default taking into account the track weight except for the scorers when it is explicitly mentioned see scorers description If you do not want to take weights into account you can switch them off with the command gamos scoring use TrackWeight SCORER_NAME FALSE 87 Chapter 8 Scoring The quantities scored are given per event by default If you want the score without dividing by the number of events use the command gamos scoring printByEvent PRINTER_NAME FALSE The error in the scored quantity per voxel is also calculated by default using the following formula sqrt SumW2 nEvents SumW SumW nEvents 1 nEvents where nEvents is the total number of events in the run SumW is the sum of the scored quantity value times its weight i e the scored quantity itself and SumW2 is the sum of squares of scored quantity value times its weight When the scoring is done per event this sum of squares is done summing first all the values times its weight belonging to all the particles of the same event and then squar ing this quantity In this way the correlations between particles of the same event is properly taken into account If the scoring is not by event the error calculation us
74. properties table name e Logical volume name e Optical surface name Using optical photons as primary generator If you are using optical photons as primary generator particles you may set the po larization using the parameter see chapter on Generator gamos set Param SOURCE_NAME Polarization POLARIZ_X POLARIZ_Y POLARIZ_Z X ray refraction GAMOS offers the novelty of an X ray refraction process which implements a Snell s law refraction and is based on the GEANT4 refraction process for optical photons You may instantiate it with the command gamos physics add Physics xray refraction always after the run initialize command Is it also necessary to set the refraction in dices for each material and for each energy This can be done by using the command you may use one command per material gamos geometry setRefractionIndex MATERIAL NAME ENERGY_1 REFRACTION_INDEX_1 ENERGY_2 REFRACTION_INDEX 2 the value for a given energy of a given material will be interpolated among these set of values It is important that you give a refraction index for all possible energies in your problem if not you will get a warning that the error is out of range If you use this code you should quote the following reference in your results Zhentian Wang Zhifeng Huang Li Zhang Zhiqiang Chen Kejun Kang Implement X ray re fraction effect in Geant4 for phase contrast imaging IEEE Nuclear Science Symposium Con ference Record 2009 1082 3654
75. returns true Chapter 12 Filters GmANDFilter returns true if every filter returns true GmParentFilter apply a filter to the parent track instead of the current track GmHistoryFilter returns true if all the filters in one of the previous steps or the beginning of track have returned true i e it does not check again the current step if it was accepted in a previous one or begin of track GmbHistoryAllFilter returns true if all the filters in all previous steps and the begin ning of track have returned true i e it does not check again the current step if it was rejected in a previous one or begin of track GmHistoryOrAncestorsFilter behaves similarly as the GmHistoryFilter but also re turns true if the condition is fulfilled by any step or track of the ancestors of the current track GmHistoryOrAncestorsAllFilter behaves similarly as the GmHistoryAllFilter but also returns false if the condition is not fulfilled by any step or track of the ancestors of the current track GmAncestorsFilter behaves similarly as the GmHistoryOrAncestorsFilter but it does not check if a previous step has passed the filter GmOnSecondaryFilter makes the list of filters act of the secondary tracks created in the step returns true if one of the secondary tracks created accepts all the filters It does not implement the AcceptTrack method GmOnAllSecondariesFilter makes the list of filters act of the secondary tracks cre ated in the step return
76. secondary gammas energy 1 022 MeV positron energy at annihilation total gamma energy vs e energy keV This is the energy deposited locally at annihilation PET histograms distance between two gammas These histograms are related to the distance between the line joining two gammas originated at the positron annihilation and the vertex position at the moment of the gamma creation and when they hit the sensitive detector Also other histograms about these two gammas are provided for further information They are produced if the user action PETHistosGammaDist is activated with the command gamos userAction PETHistosGammaDist The name of all these histograms starts with PETGammaDist and all are written in the file pet root csv The histograms are the following e Angle between the direction of the two gammas when they are created angle between gammas at vertex deg e Angle between the direction of the two gammas when they enter the sensitive detector angle between gammas at entering SD deg e Distance of closest approach between vertex and the line joining the vertices of the two gammas DCA orig from Gamma vertex mm 165 Chapter 18 PET application Notes 166 e Distance of closest approach between vertex and the line joining the points where the gammas enter the sensitive detectors DCA orig from Gamma entering SD mm e Z position of vertex of gamma if it reaches the sensitive dete
77. separated by a colon and their order in this variable reflects the order in which they will be searched This variable is set up when you configure GAMOS and takes a default value of iMY_GAMOS_DIR data You may change this value at your will but remember not to reset the GAMOS con figuration after that because it will reset it to its original value gamos setParam PARAMETER_NAME PARAMETER_VALUE S There are four types of parameters in GAMOS e One number e A list of numbers One string e A list of strings The above command can be used for any kind of parameters and GAMOS will detect which of the four types it is by analysing the parameter values There may be though some peculiar cases where this automatic identification may fail For example if you want to set a parameter for a list of volume names like VOL_A1 VOL_B1 VOL_C1 and you use a parameter to set its value equal to the three like gamos setParam PARAMETER_NAME 1 GAMOS will mistakenly think that is a parameter of type number number For this cases it is possible to use a command specific for each of the four types gamos setParamN PARAMETER_NAME NUMBER gamos setParamLN PARAMETER_NAME NUMBER_1 NUMBER _2 gamos setParamS PARAMETER_NAME STRING gamos setParamLS PARAMETER_NAME STRING_1 STRING_2 Random number seeds 220 If you want to run several jobs with the same configuration but different random seeds each you can use the GEANT4 random number mana
78. sourceforge net 23 ImageJ Processing and Analysis in Java http rsbweb nih gov ij 24 http www med harvard edu JPNM ij plugins Interfile html 21 Stochastic Image Reconstruction Method for Compton Camera Andriy Andreyev Arkadiusz Sitek Anna Celler IEEE Nuclear Science Symposium Conference Record 2009 234
79. step of a track may initiate a new shower but if you want to include all the steps of the same track and their children in a unique shower you have to set the parameter gamos set Param USER_ACTION_NAME IncludeOtherStepsOfFirstTrack TRUE where USER_ACTION_NAME is GmShowerShapeUA plus the filters and classifier name see section on User action names At the end of each event the showers are analysed and several variables are calcu lated for each of them Total energy sum of the deposited energies of all steps belonging to the shower Shower direction two options are provided to define the shower direction The first one default is to take the direction of the particle that initiated the shower this is the direction of th PreStepPoint of the first track step The second option is to calculate a shower average direction formed joining the point where the track is initiated and an average shower point This average point is calculating as the sum of all the shower step points weighted with the energy deposited at each step To use this second definition instead of the first one you have to set the parameter gamos setParam USER_ACTION_NAME ShowerDirection Shower Step point longitudinal length distance from an step position to the initial shower point along the shower direction Step point transversal length minimum distance from an step position to the line built from the initial shower point and the shower di
80. target or its n th ancestor if we are looking at the n 1 th ancestor was created The same warning as for the production cuts should be mentioned here but in this case it is more than a mere warning when a track reaches the target we accumulate one track information of the last step in each region for each of the ancestor tracks Therefore it is very likely that there are more than one track information per track reaching the target and therefore there will be overcounting of the number of tracks killed by a cut As for the production cuts you should keep an eye on this To use this utility in GAMOS it is only needed to add the command in your script gamos userAction GnMinRangeLimitsStudyuUA RTCutsStudyFilter what will produce at the end of run a table and a histogram file with the needed information root b p q x getMinRangeCutsEffect Ct prodcuts root percentage and look at the last lines of output those that contain the word FINAU like the following ones PARTICLE e FINAL 17 19 PARTICLE e FINAL 72 34185 PARTICLE gamma FINAL 72 34184 Automatic determination for a dose in phantom simulation The method used in GAMOS to determine the minimum range user limits is similar to the one used to determine the best production cut To use this utility in GAMOS you just have to associate to your dose scorer a filter of type GmProdCutOutsideVoxelFilter passing to it as arguments the
81. the beginning of a run e At the end of a run e When a secondary track is created this case is used for relating the variables of an initial track and the secondary tracks it creates Each of the GAMOS data does not have to implement the methods to return a value in all cases as in some cases it has no meaning Examples can be the position for a run the final energy for a secondary track which has not been started to be tracked or the track ID for an event If a data is used when the case has no meaning it will return an exception For many types of data one can make a distinction between the Initial and the Final values This again has a different meaning depending on when it is called Track step Initial refers to the data at PreStepPoint i e at the first point of the step Final refers to the data at PostStepPoint i e at the second point of the step Track Initial refers to the data at vertex Final refers to the data at the current point Event Initial refers to the data of the first particle in the event Final has no meaning Run Initial has no meaning Final has no meaning Secondary tracks Initial refers to the data when the particle is created not being tracked yet Final has no meaning The data of these type have in their name the word Initial or Final Other data are of type Change because they return the data at the Final point minus the data at the Initial point Of course these data can only have sense fo
82. the first field is the name of the parameter e the second field is the value except in the case of DataFileName where the value is a dummy 181 Chapter 21 Image reconstruction utilities 182 e the third field is a dummy string except in the case of DataFileName where it gives the name of the input file It should NOT contain any blanks empty spaces Output Files The output files are e data_beginstate_xy dat This file contains a list for all events with the initial posi tions assigned to each cone Each position represents a guess of the real location of the gamma source It has the following format xposition yposition zposition e g 260 788 142 073 97 8255 0 722199 18 968 96 3066 2 74312 43 1098 95 7843 data_endstate_xy dat This file contains a list for all events with the final positions associated with each cone after lt N gt iterations Each position represents a guess of the real location of the gamma source In the perfect case all positions in the list would be identical to the real position of the gamma source It has the following format xposition yposition zposition e g 0 44799 0 412472 100 032 0 491477 0 46389 100 056 0 459591 0 449933 99 9168 e density_matrix hdr This is a header file for the AMIDE program e density_matrix img This is the binary image file for the AMIDE program Program Parameters and Flags PET or Compton camera In order to run on PET data run th
83. the model is applied for all energies GAMOS electromagnetic extended physics list 60 This physics list can be selected with the command gamos physicsList GnEMExtended Physics It creates all GEANT4 particles using the constructors G4BosonConstructor G4LeptonConstructor G4MesonConstructor G4BaryonConstructor G4lonConstructor G4ShortLivedConstructor For these particles the physics implemented is the following see GEANT4 Physics Reference manual for a detailed explanation of the physics options mu mu G4MuMultipleScattering with G4WentzelVIModel G4Mulonisation with SetStepFunction 0 2 50 um G4MuBremsstrahlung G4MuPairProduction and G4CoulombScattering alpha He3 G4hMultipleScattering G4ionlonisation with SetStepFunction 0 2 50 um and G4NuclearStopping Genericlon G4hMultipleScattering G4ionlonisation with model G4lonParametrisedLossModel and SetStepFunction 0 1 10 um m and G4NuclearStopping Chapter 5 Physics pit pi kaon kaon G4hMultipleScattering G4hIonisation with SetStepFunction 0 2 50 um G4hBremsstrahlung and G4hPairProduction e Other charged particlesG4hMultipleScattering and G4hIonisation This physics lists inherits from GmEMPhysics so that the command gamos GmEMPhysics addPhysics can be used to change the physics models of the electromagnetic particles GAMOS hadrontherapy physics list The GAMOS hadrontherapy physics list is based on the hadron therapy Geant4 ad vanced example
84. trackInfo Region vs trackInfo Region that plots all the region number of all the pairs of track informations that correspond to the same track reaching the target you can get a list of which region number corresponds to which region at the end of the standard output file To use this utility in GAMOS it is only needed to add this command in your script gamos userAction GmProdCutsStudyUA DetCutsStudyFilter that will use as target condition that a track enters a sensitive detector This command will produce at the end of run a table and a histogram file with the needed information The table will contain the minimum range that can be applied for each region particle process not to lose any track reaching the target and it will look like this PRODUCTION CUTS STUDY RESULTS GmProdCutsStudyUA REGION DefaultRegionForTheWorld PARTICLE gamma PROCESS ALL MIN RANGE 353161 38 GmProdCutsStudyUA REGION DefaultRegionForTheWorld PARTICLE gamma PROCESS eBrem MIN RANGE 353161 38 To get the cuts values for not losing a given percentage of particles in the target plane you can execute the ROOT script that can be found at GamosCore GamosPhysics Cuts getProdCutsEffect C root b p q x getProdCutsEffect Ct prodcuts root percentage and look at the last lines of output those that contain the word FINAU like the following ones PARTICLE e FINAL 17 19 PARTICLE e FINAL 72
85. volume defined in your geometry Alternatively you may use a virtual volume you create for the accasion in a similar way as it is doen at buildPartial_userVolume in In this case you have to add a com mand gamos geometry DICOM intersectWithUserVolume POS_X POS_Y POS_Z ANG_X ANG_Y ANG_Z SOLID_TYPE SOLID_PARAM_1 SOLID_PARAM_2 where POS_X POS_Y POS_Z is the position of the centre of the volume ANG_X ANG_Y ANG_Z are the angles of rotation around X Y and Z axis and then it comes the solid type and paramter with the same format as the one used to define a solid in the geometry text file format The file format is slightly different than that of the g4dcm files The start is the same list of materials number of voxels and phantom dimensions as if it were the origi nal parallelepiped Then it comes the information about which voxels are used and which not for each Z slice and for each Y slice there is a line indicating the X index 39 Chapter 3 Geometry of the first voxel used and that of the last voxel used 1 1 if no voxel is used in that X row The rest of the file is also similar the list of voxel material indices and the list of voxel densities To read this file the geometry to be used is gamos geometry GmReadPhantomG4Geometry Simple phantom geometries The user may build simple regular phantom geometries without the need of writing a DICOM file by using gamos geometry GmSimplePhantomGeometry The numbe
86. we recommend the installation of one of the follow ing free programs to visualize or analyze images AMIDE and ImageJ AMIDE 22 is a free tool for viewing analyzing and registering volumetric medical imaging data sets It has been written on top of GTK and runs on any system that supports this toolkit including Linux Both hv and hdr image header files can be opened by AMIDE using the option File gt Import File guess AMIDE also is also recommended to visualize STIR images ImageJ 23 is an image processing tool written in Java which allows it to run on Linux Mac OS X and Windows ImageJ and its Java source code are freely available and in the public domain To open hv images the program needs a plug in to read Interfile formats next it is described how to install its version 1 44 bundled with 32 bit Java with the Interfile decoder plug in in Linux Installing ImageJ cd HOME wget http rsb info nih gov ij download linux ij144 x86 tar gz gunzip i 3144 x86 tar gz tar xvf ij3144 x86 tar Installing plug in jar file to read Interfile images cd ImageJ plugins wget http www med harvard edu JPNM ij plugins download Interfile_TP jar Odie To run Image execute the run script Images with extension hv can be opened by the NucMed Open command in menu Plugins gt NucMed alternatively the user can open it MY_IMAGE hv from the command line using the following expres sion S HOME
87. 11_RILSAN G4_OCTANE G4_PARAFFIN G4_N PENTANE G4_PHOTO_EMULSION G4_PLASTIC_SC_VINYLTOLUENE G4_PLUTONIUM_DIOXID G4_POLYACRYLONITRIL G4_POLYCARBONATE G4_POLYCHLOROSTYRENE 12 ed 7 Gl G4_POLYETHYLENE G4_MYLAR G4_PLEXIGLASS G4_POLYOXYMETHYLENE G4_POLYPROPYLENE G4_POLYSTYRENE G4_TEFLON G4_POLYTRIFLUOROCHLOROETHYL G4_POLYVINYL_ACETATE G4_POLYVINYL_ALCOHOL G4_POLYVINYL_BUTYRAL G4_POLYVINYL_CHLORIDE G4_POLYVINYLIDENE_CHLORIDE G4_POLYVINYLIDENE_FLUORIDE G4_POLYVINYL_PYRROLIDONE G4_POTASSIUM_IODIDE G4_POTASSIUM_OXIDE G4_PROPANE G4_1PROPANE G4_N PROPYL_ALCOHOL G4_PYRIDINE G4_RUBBER_BUTYL G4_RUBBER_NATURAI G4_RUBBER_NEOPRE G4_SILICON_DIOXI G4_SILVER_BROMID G4_SILVER_CHLORI G4_SILVER_HALIDE G4_SILVER_IODIDE G4_SKIN_ICRP G4_SODIUM_CARBONATE G4_SODIUM_IODIDE G4_SODIUM_MONOXIDE G4_SODIUM_NITRATE G4_STILBENE G4_SUCROSE G4_TERPHENYL G4_TESTES_ICRP G4_TETRACHLOROETHYLENE G4_THALLIUM_CHLORIDE C FI1U G4_TISSUE_SOFT_ICRP G4_TISSUE_SOFT_ICRU 4 G4_TISSUE METHANE G4_TISSUE PROPANE G4_TITANIUM_DIOXIDE G4 OLUENE G4_TRICHLOR
88. 3 Real 0 37 Sys 0 02 e 0 001 0 01 User 12 42 Real 13 58 Sys 0 29 e 0 01 0 1 User 5 98 Real 6 42 Sys 0 16 e 0 1 1 User 7 78 Real 8 8 Sys 0 22 e 1 10 User 0 Real 0 Sys 0 e 1e 05 0 0001 User 0 Real 0 Sys 0 e le 06 le 05 User 0 Real 0 Sys 0 gamma 0 001 0 01 User 1 29 Real 1 49 Sys 0 02 gamma 0 01 0 1 User 0 63 Real 0 58 Sys 0 01 gamma 0 1 1 User 27 95 Real 29 7 Sys 0 48 gamma 1 10 User 0 38 Real 0 36 Sys 0 which can be obtained with the commands gamos classifier ClassifierByParticleAndKinE GmCompoundClassifier GmClassifier ByPar ticle GmClassifier ByKineticEnergy 147 Chapter 15 Utility user actions gamos userAction GmTimeStudyUA ClassifierByParticleAndKinE The time in each category is the time counted at each step Exactly it is the counting from the beginning to the end of the method G4SteppingManager Stepping To do this without modifying the Geant4 class the class GmTimeStudyMegr inherits from G4VStepping Verbose and it is set as the stepping verbose class substituting the class G4Stepping Verbose class that is the one that controls the verbosity of the command tracking verbose This means that this command will have no effect and if you want to use it you should do with the parameter gamos setParam GmTimeStudyUA G4VerboseLevel VERB You may observe that the time summed over all the categories is smaller than the run time given by the command run verbose 1 This is because the time is only the time spent
89. 8 Automatic determination of production cuts for an accelerator SU lath On merei a e a e eae Dabo den id Boca ees eet 210 Automatic determination of production cuts for a dose in a phantom Sit ati Onn anani scars sec acces hoer TN EN OIT 211 Automatic determination of user limits for an accelerator simulation 211 Automatic determination for a dose in phantom simulation 212 23 DICOM Utilities ise scscccaesisssscoacacdsscsvessacccesvecaesuccercecssssescdascecuessvecdevecasvesdevessdsevtenseseeaves 213 24 Magnetic field Manager cccsscssecessrssecsccsssssecesssssssesessssssssscssssssesesesesseseesseeesees 215 25 Optimising the CPU time of your application e ssesseessesseseessesreeseeseeseossosseseeosees 217 Knowing where the time is spent c ccc cece ceeseseecesesesesesseseseseeseseecees 217 PPO UU CEL OME CULES ses E A aed E AEE S ETE shttbeaouebleouneel cote 217 Killing particles of small energy sssrssiosidisssesoianni eissii haa 217 Kalling particless sis cthitse visistscccssietiscvesceutssesthvistevadelaaatuehdetescvesterasatsciptevateccapdoasten 218 Optimising the particle generation c ccc cesses ceseeseeseseeseeeseeeseecees 218 Limiting the number of User actions c ccc eee eeeseeeecenseseeteseeseeseseeeseeeeee 218 Using variance reduction techniques ccccccseccescseseeteeseecesesssteneeseecenesesnsnanenees 218 26 APPendix A erer re eae aeea E EEEn a ae esa aen AE EE EE Seo S
90. ACKS 4663 EVENT 2000 NTRACKS 4 TOTAL NTRACKS 9440 oe oe oe ae oe oe Its main use is to inform the user of the progress of the job in interactive running To activate this utility use the command gamos userAction GmCountTracksUA The user can control the interval of events as well as the first event to start printing with the parameters gamos setParam USER_ACTION_NAME EachNEvent NEV 10 gamos setParam USER_ACTION_NAME FirstEvent NEV 0 where USER_ACTION_NAME is GmCountTracksuA plus the filters and classifier name see section on User action names This utility distinguishes for the ionisation and bremsstrahlung processes those cases when a secondary particle is emitted and those when the step is limited to assure a correct energy loss and multiple scattering but no secondary particle is emitted it adds _NoSeco at the end of the process name Counting the processes This utility prints four tables e At the beginning of run all the active processes for each particle type PROC_LIST e Transportation PROC_LIST e annihil PROC_LIST e eBrem PROC_LIST e eBrem_NoSeco PROC_LIST e eloni PROC_LIST e eloni_NoSeco PROC_LIST e msc PROC_LIST e Transportation PROC_LIST e eBrem PROC_LIST eBrem_NoSeco PROC_LIST e eloni PROC_LIST e eloni_NoSeco PROC_LIST e msc PROC_LIST gamma Rayl PROC_LIST gamma Transportation PROC_LIST gamm
91. ADER The second word is the number of words and then the data names To select this option the following parameter has to be used gamos setParam FILE_NAME WriteHeaderData 1 The name of the text file is given by the name of the data user plus the filters and classifiers plus i e out It can be changed with the parameter gamos setParam DATA_USER_NAME FileName NEW_FILE_NAME For example gamos userAction GmStepDataTextFileuUA GmGammaFilter will produce a file named GmStepDataTextFileuA_GmGammaFilter out whose name can be changed with the command gamos setParam GmStepDataTextFile UA_GmGammaFilter FileName NEW_FILE NAME to produce a file named NEW_FILE_NAME out Binary files These data users i e GmStepDataBinFileUA GmTrackDataBinFileUuA GmEventDataBinFileuA GmRunDataBinFileuA GmSecondaryTrackDataBinFileUA dump the data values into binary files Data of integer type are written as int occupying four bytes Data of double type are written as float for space savings occupying four bytes NOTE in case you want to write all your data as double you just have to replace float by double in the four WriteBin methods in the file GamosCore GamosData Data src GmV Data cc and recompile GAMOS Data of string type are written as a list of char each string data has a default number of characters that can be overridden with the parameter gamos setParam DATA_NAME NumberOfChars NCHARS To allow checking the format when the
92. Atomic deexcitation processes 70 The atomic deexcitation i e the production of characteristic X rays and Auger elec trons when the atoms are excited after an ionisation or photo electric process is ac tivated by default if one of the two GAMOS electromagnetic physics list is selected To deactivate it you can use the parameter gamos setParam GmEMPhysicsList AtomicDeexcitation 0 The default behaviour activates atomic deexcitation only for the default GEANT4 region DefaultRegionForTheWorld which is created for volumes not associated to any region see section on Production cuts by region To activate it for list of regions you can use the parameter gamos setParam AtomicDeexcitation Regions REGION_1 REGION_2 You may also want to change the production cuts that is the minimum value of the energy of the characterisic X rays or Auger electrons This can be done independently for the secondary particles generated by ionisation and photo electric effect The pa rameters to do it for ionisation are Chapter 5 Physics By default production of characteristic X rays by fluorescence and Auger electrons is on whil PIXE is off You can also select which process to activate with the parameters gamos setParam AtomicDeexcitation Fluorescence 1 gamos setParam AtomicDeexcitation Auger 1 gamos setParam AtomicDeexcitation PIXE 1 It is important to note that the production of secondary gammas or electrons is af fected by the same
93. DICOM utilities 214 Chapter 24 Magnetic field manager This is an utility that allows to define arbitrary magnetic fields and control their track ing precision paramters and also calculates the magnetic fields for different structures circular coil solenoid and stores them in a file for later used You can find all the relevant documentation in the file GAMOS 3 0 0 source Mag FieldManager doc user_manual_bfield_manager pdf In GAMO it is already installed so you may skip the installation instructions 215 Chapter 24 Magnetic field manager 216 Chapter 25 Optimising the CPU time of your application We recommend you to spend some time in optimising the CPU time spent by your application as you may save a big amount of CPU time with not too much effort Knowing where the time is spent Before starting your optimisation it may be very useful to understand wher the time is spent For example if most of the time is spent tracking some typr of particle some volumes or particles created by some process To get a report of where the time is spent GAMOS provides the user action GmTimeStudyUA that you can combine with one or more classifiers to get a detailed report Production cuts The production cuts are the minimum energy of the electrons produced by ionisation and of gammas produced by bremsstrahlung and also of the positrons produced by pair production process of muons if you are using these particles If the cut val
94. Discussion Forum if you do not feel confident on doing it An example of this can be using Gm GenerDist PositionDiscGaussian instead of GmGenerDistPositionDisc and biasing with a Gaussian distribution the PosPerp variable The word bias may be misleading as indeed the result is not biased Thanks to the multiplication of the particle s weight by 1 X mentioned above the result will not change within statistical fluctuations if you are using some variable that takes into account weights This is not the case for example if you are using sensitive detectors and hits so we do not recommend its use for those applications It may happen that the distribution has some bins with very low probabilities so that the search for a valid value can be too long In this case you will get a warning so that you may reconsider if your biasing is indeed gaining CPU or not The default value for the number of loops in searching for a bias value is 10000 if you want to change it you may use the parameter gamos setParam SOURCE_NAME MaxBiasIterations VALUE Building your generator with C You can build your generator by writing your C class inheriting from G4VUserPrimaryGeneratorAction see example in 9 After that you have to transform it intoa GAMOS plug in To learn how to do this see the instructions in the section Creating your plug in using the GmGeneratorFactory or see the example examples N02 57 Chapter 4 Generator Using ions
95. E 1 COMP 111304 34 610744 GC PE gt 1 COMP 52670 16 378099 GC n COMP z 222590 i 43 12339 GC 1 COMP 159193 71 518487 GC gt 1 COMP 63397 28 481513 GC nGamma_COMP event 0 585931 nEvents total number of events n gamma in SD number of original gammas reaching one sensitive detector n PE number of original gammas with photoelectric interaction in SD PE 0 COMP number of original gammas with photoelectric interaction and no Compton interactions in SD percentage relates to n PE PE 1 COMP number of original gammas with photoelectric interaction and one Compton interaction in SD percentage relates to n PE PE gt 1 COMP number of original gammas with photoelectric interaction and more than one Compton interaction in SD percentage relates to n PE n COMP number of original gammas with Compton interactions in SD 157 Chapter 17 Detector applications e 1 COMP number of original gammas with only one Compton interaction in SD percentage relates to n COMP gt 1 COMP number of original gammas with more than one Compton interactions in SD percentage relates to n COMP nCOMP event number of Compton interactions in SD per original gamma This class also makes several histograms all of them have the words Gamma At SD included in their names And all are written to the file gammaSD r
96. E EEA ERE E ioa 141 Geometrical biasing distribution sss sressssissrissstssrsesststeesstsrtersressteestes 141 vi 15 Utility user actions ccssscscsssssesesescssssseecesssssesesesssssnsesessssssssscsessasssesesssssesesseseesees 143 Counting the number of tracks and events ccccccsceseescesesceteteneseeeesesesnsnenenees 143 Courting th processes iiscs sc iijccdtelescacsssbieesdciovan secgaeneubseueseseussstadevadesvvansestessioess 143 Shower shape studies nsescsesiecsisnisiii diede huaai Sa dees clare 144 KillipgalltrackSi ise inaapi aa a A RAE a 146 Table of tracks and Ste issii iseseisana tee derea Spe Eae Eeoa saasaa b Ea esas sr ia 146 Material budget Studies cece sense ae i a E E 146 Detailed report of where CPU time is spent s sss sssssssssrtsesstsrtsrstessterstessteestesstees 147 Changing the weight using a distribution cesseseeeeeereeseseseneeeeeee 148 Copying the weight to the secondary particles cccccccsesseteteeecesesestsneenees 148 Stop run after a certain CPU time sses Seeon E EE S E 148 16 Managing the VerbOSity csssesssssscececssssssesesssssssesssssssnsescssesssscseesssseseeseseesees 149 GAMOS verbosity Managers cccccccs sec eee cesses cssseseesssssseesesesseeseseeeeseece 149 Controlling GAMOS verbosity by eVeMt ccccccccceesestetetescetesesesneneneeeans 150 Using a GAMOS verbosity manager in your COC cececceseeseeteteeetetesestenenenees 150 Creating your OWN verb
97. E VALUE The divisions start at the negative wall of the box that is selected as sensitive vol ume that is the offsets are the half lenghts of the box You may change these offsets with the parameter gamos setParam SD VirtSegmBox Offset S DT Y PE OFFSET_X OFSET_Y OFFSET_Z If the offsets are not set thay are calcualted at each track step as it may happen that different volumes are assigned to the same sensitive detector type If the all the volumes assigned to a sensitive detector type have the same solid dimensions we recommend you that the offsets are only calculated once what can be done with the parameter gamos setParam SD VirtSegmBox OffsetOnce Ss DTY PE TRUE The detector unit ID is built from the volume IDs of the ancestor volumes see section on Identifying each sensitive detector copy The number of ancestors and the NShift used to buld the ID number are controlled by the parameters gamos setParam SD VirtSegmBox NAncestor VALUE gamos setParam SD VirtSegmBox NShift VALUE which by default take a value of 2 and 100 respectively To attach aGAMOS sensitive detector to a logical volume in your geometry you have to use the command gamos S D assocSD2Log Vol SD_CLASS SD_TYPE LOGICAL_VOLUME_NAME The SD_CLASS has to be one of the sensitive detector types described above or any other that you create The SD_TYPE serves to differentiate your different sen sitive detectors so that you can later apply different properties to
98. E _NAME_1 PROCESS_NAME_1 PARTICLE NAME_2 PROCESS_NAME 2 Alternatively you may select all process of a given type gamos physics removeProcessesByType PROCESS_TYPE_1 PROCESS_TYPE_2 where the types are those defined by GEANT4 Transportation Electromagnetic Opti cal Hadronic Photolepton_hadron Decay General Parameterisation UserDefined or Not Defined Chapter 6 User Actions Geant4 user actions are the way the user can interact with a job at the beginning end of each run beginning end of each event beginning end of each track or at each step The user can write a class inheriting from one of the Geant4 user action abstract classes and Geant4 will take care of calling the user code The GAMOS user actions classes provide all the functionality of the Geant4 classes and also allow the user to define several user actions of the same type in the same job and to define a class that inherits from several user action types at the same time Moreover as they are plug in s the user can activate them by means of a user com mand User actions can be associated to filters or classifiers as explained below Several functionalities are already implemented in GAMOS as user actions like his tograms event classifiers and you may use them as examples for creating your own one All user actions are instantiated with the same user command gamos userAction USER_ACTION_NAME Adding a filter One or several filters can be a
99. EPresented polycone e Phi starting angle e Total phi angle e Number of z planes e Starting value of z For each z plane e Position of z plane e Tangent distance to inner surface e Tangent distance to outer surface BREPPOLYHEDRA Boundary REPresented polyhedra e Phi starting angle e Total phi angle e Number of sides e Number of z planes e Starting value of z For each z plane e Position of z plane e Tangent distance to inner surface e Tangent distance to outer surface TESSELATED Boundary REPresented polyhedra e Number of facets For each facet e Number of points must be 3 or 4 e Point 1X e Point 1 Y e Point 1Z e Point 2 X e Point 2 Y e Point 2 Z Point 3 X Point 3 Y e Point 3 Z If there are four points e Point 4X e Point 4 Y 23 Chapter 3 Geometry 24 e Point 4Z e Type of facet vertex 0 ABSOULUTE 1 RELATIVE EXTRUDED Boundary REPresented polyhedra e Number of polygon vertices For each vertex of the outlined polygon defined in clock wise order e X e Y Number of Z sections For each Z section defined by z position in increasing order e Half length in Z e Offset X e Offset Y e Scale Boolean solids The three types of Geant4 boolean solids are supported union subtraction and inter section The same tag should be used as for normal solids but putting as solid type the type of boolean operation The parameters are Solid name Solid boolean operat
100. Filter TraverseParallelRegionFilter And it also means that you cannot use the above filters to act on a mass world whose position coincides with the one of a parallel world in the case of scorers be cause the scorer filter will see the parallel world volume instead of the mass one If you need to filter on mass volumes for a scorer a few volume filters are imple mented namely GmInMassLogical VolumeFilter GmInMassPhysical VolumeFilter GmIn MassPhysical VolumeReplicatedFilter and GmInMassRegionFilter When you use for example GmExitLogicalVolumeFilter the step is accepted when it exits the selected volume without looking if the next volume it is entering is another copy of the selected volume If what you want is that the steps are only accepted when they exit the selected volume and enter a different one you may use the a filter that checks that if the PreStepPoint and the PostStepPoint are in different logical volumes e GmDifferentLogical VolumeFilter Although you may use the inverse of this filter to check if the two volumes are the same GAMOS provides explicitly this filter e GmSameLogicalVolumeFilter Filters of filters 134 There are another set of filters that receive as parameter one or several filters and act on them The list of composed filters in the current GAMOS version is the following e GmORFilter returns true if one of the filters returns true e GmXORFilter returns true if one and only one of the filters
101. For example if you typed gamos userAction GmTrackHistosuA GmGammaFilter GmPrimaryFilter GmClassifier By Particle 73 Chapter 6 User Actions the name of the user action will be GmTrackHisto sUA_GmGammaFilter_GmPrimaryFilter_GmClassifierByParticle Unless explicitly mentioned in this guide this name will be the name of the histogram or data file in case the user action is writing a file plus the corresponding file suffix unless the file name is changed with a parameter It is also the name that has to be used for any parameter corresponding to the user action Creating your GAMOS user action 74 If you need a new user action you have to create a class inheriting from one or several of the GAMOS user actions GmUserRunAction GmUserEventAction GmUser TrackingAction GmUserSteppingAction GmUserStackingAction Then you implement the same methods as for the Geant4 user actions e GmUserRunAction e virtual void BeginOfRunAction const G4Run aRun e virtual void EndOfRunAction const G4Run aRun e GmUserEventAction e virtual void BeginOfEventAction const G4Event anEvent e virtual void EndOfEventAction const G4Event anEvent e GmUuserTrackingAction e virtual void PreUserTrackingAction const G4Track aTrack e virtual void PostUserTrackingAction const G4Track aTrack e GmUuserSteppingAction e virtual void UserStepping Action const G4Step aStep e GmUuserStackingAction e virtual G4ClassificationOfNew
102. G4PSData This score uses a GAMOS data as quantity to score See section on GAMOS data Scoring in voxelised phantoms When you are navigating in a voxelised pantom geometry and you are using the regular navigation you have the option of skipping voxel frontiers when the ma terial does not change see section on Reading DICOM files In this case the scorer GmG4PSDoseDeposit will automatically distribute in the voxels traversed the dose corresponding to the energy deposited along each step A correction is neverthe less needed when the particle travels it loses energy and therefore it is not right to distribute the dose proportionally to the length traversed inside each voxel The needed corrections to the multiple scattering and energy loss when the particle loses energy are done in an iterative way the increase of multiple scattering increases the path length what increases the energ losty what makes the multiple scattering even bigger what increases the path length and therefore the energy lost By default the number of iterations is two but you may change it with the parameter gamos setParam GmEnergySplitter NIterations NITER Other scorers need the same corrections namely GmG4PSEnergyDeposit GmG4PSEnergyLost GmG4PSKerma and GmG4PSTrackLength In this case the index used is the copy number of the voxels traversed what means that the classifier index is not used at all You may nevertheless force the use of the classifier index wit
103. GAMOS 4 0 0 User s Guide GAMOS Collaboration GAMOS 4 0 0 User s Guide by GAMOS Collaboration Published July 6 2012 Table of Contents Ds LivtrO biLa aTa a ALEEA E AAE ETE E EERIE HESA EESE N EEA ETEEN A 1 About this AOCument esc tesoscesessd chev ciess exadedustecbene debe reveadt a E E a vests 1 Introduction to GA MOS ieee e ies oie e ee Modes E A E E S eases sto oe 1 Structure Of GAMOS isie icc ccecscccccssecsscessssecescssesssececesscsescsscssseceeusscesesssessseseeessseeesens 1 The plug in concepts win Aon TR ah alent ta elie 2 Zs Getting Started 5 cc cccdc cconsoescssssvonssesnsbenessuaedsocuctonnsasccoseswarnensdenodouseedscoousdenbsesdgedeswasnsnsvssoess 3 Getting the code and installing it cesses ceenseescsesesesescssseseecesessnesssenens 3 Tips for installation in Ubuntu occ ceseesesescsesesesescssseseecesessneseenees 3 Tips for installation in Fedora Core cccceeseecesssssesescsenesesescssseseecesessneseevens 4 Rimming AN EXAM Plea se oes cess cvevea gs sseseecestetelsesetstcdssnevuseventesversvivessadorecviotelacansedevdeces 4 Compiling GAMO sisip pe peee ake aTi eetarea E ae EOE ESEE E Ee EE Ee 5 Compiling yout New COde cciciccescesteessissssssesusateessesensteovsesenetscvereeranessevnnteees 5 3 GOOMELTY AETA A ETA 9 Building your geometry with a text file ssssssssssssssessessssssestestesresressesnsenieseeseeseess 9 Description of geometry text file format s sessesssssssesttsrserstt
104. HOL G4_ETHYL_ CELLULOSE G4_ETHYLENE G4_EYE_LENS_ICRP G4_FERRIC_OXIDE G4_FERROBORIDE G4_FERROUS_OXIDE G4_FERROUS_SULFATE G4_FREON 12 G4_FREON 12B2 G4_FREON 13 G4_FREON 13B1 G4_FREON 1311 G4_GADOLINIUM_OXYSULFIDE G4_GALLIUM_ARSENIDE G4_GEL_PHOTO_EMULSION G4_Pyrex_Glass G4_GLASS_LEAD G4_GLASS_PLATE G4_GLUCOSE G4_GLUTAMINE G4_GLYCEROL G4_GUANINE G4_GYPSUM G4_N HEPTANE G4_N HEXANE G4_KAPTON G4_LANTHANUM_OXYBROMIDE G4_LANTHANUM_OXYSULFIDE G4_LEAD_OXIDE G4_LITHIUM_AMIDE G4_LITHIUM_CARBONATE G4_LITHIUM_FLUORID G4_LITHIUM_HYDRIDE G4_LITHIUM_IODIDE G4_LITHIUM_OXIDE G4_LITHIUM_TETRABORA G4_LUNG_ICRP G4_M3_WAX G4 AGNES IUM_CARBONA G4 AGNES IUM_FLUORIDE G4 AGNES IUM_OXIDE G4_MAGNESIUM_TETRABORATE G4 ERCURIC_IODIDE G4 ETHANE G4 ETHANOL G4_MIX_D_WAX G4 S20 TISSUE G4_MUSCLE_SKELETAL_ICRP G4_MUSCLE_STRIATED_ICRU G4 USCLE_WITH_SUCROSE G4_MUSCLE_WITHOUT_SUCROS G4 APHTHALENE E f E B T it 13 Chapter 3 Geometry G4 ITROBENZENE G4_NITROUS_OXID G4_NYLON 8062 G4_NYLON 6 6 G4_NYLON 6 10 G4_NYLON
105. ICOM format into a format readable by GAMOS con verting the Hounsfield nubmers into material and density information To do this you can use the utility at analysis DICOM which is based from the Geant4 exam ple examples extended medical DICOM We describe here the procedure you have to follow The first step is to write a file named Data dat This file has the following information A line with the compression value A line with the number of files A line for each file name to these names it will be added the suffix dcm to read the DICOM files in their original format The number of materials you want to use A line for each material describing its name and the upper bound of the density interval The materials should be described in increasing order of density The vox els with a density between 0 and the first upper bound will be assigned to the first material those with a density between the first upper bound and the second upper bound will be assigned to the second material etc Each dcm corresponds to a Z slice For each file a g4dcm will be written with the ma terial density information The Z slices may be merged at runtime to form a unique patient volume in this case the different slices have to be contiguous in Z if you set the enviromental variable DICOM_MERGE_ZSLICES to 1 The DICOM images pixel values represent CT Hounsfield numbers related to the electronic density and they should be converted first to a g
106. In case of positive answer GAMOS will be installed without OpenGLx visualisation but still with VRML visualisation If the X11 libraries are not found GAMOS will ask you if you want to continue without them In case of positive answer GAMOS will be installed without OpenGLX visualisation but still with VRML visualisation and without ROOT ROOT has some extra checks for li braries like libXpm so If you cannot install some of these libraries you may decide to install GAMOS without ROOT If you do not want to install ROOT you may set the enviromental variable GAMOS_NO_ROOT to 1 before typing the installation command After all the code is compiled follow the instructions on how to run an example Tips for installation in Ubuntu If you are using the Ubuntu Linux distribution you have to take into account that the default installation does not include the software for C developement There fore if you do not have this software in your installation youd should download the following packages e g libcxxtools dev e libx11 dev e libxmu dev e libxi dev e libxft dev e libxpm dev e libxext dev freeglut dev Chapter 2 Getting started e dpkg dev Tips for installation in Fedora Core If you are using the Fedora Core Linux distribution you have to select the software development tools at your installation If you do not have this software in your in stallation youd should download the following packages e gcc ct
107. LogicalVolume gt crystal_logic geomUtils gt GetLogicalVolumes crystal exists true To retrieve the physical volumes GmGeometryUtils geomUtils GmGeometryUtils GetInstance std vector lt G4VPhysicalVolumex gt crystal_phys geomUtils gt GetPhysicalVolumes crystal exists true You can find an example in the Geant4 examples directory xamples extended persistency P03 src ExTGDetectorConstructionWithCpp cc Dumping your Geant4 geometry in text file format If you have already a Geant4 geometry written with C code or any other method you can get a geometry text file by simply adding a line in your code G4tgbGeometryDumper GetInstance gt DumpGeometry theFileName This line should be executed once your geometry has been built for example in a BeginOfRunAction method or at the end of the Construct method in your detector constructor class You can do this in GAMOS by simply adding in your command file the user action named GmGeomTextDumperUA gamos userAction GmGeomTextDumperUA The name of the output file can be set by setting the parameter before the user action gamos set Param GmGeomTextDumperAction OutputName FILE_NAME Adding new tags to your input text file You may want to add new tags to your text file and give them any meaning you like For example you may use your text file to define your G4Region s and assigning different production cuts to each region as it wi
108. Managing the input data files Chapter 4 Generator GAMOS offers several primary generators the general one which allows you to se lect among many particles and generator distributions one that reads the primary particles from a text file and anothre one that reads them from a binary file Alterna tively you may create your generator in the standard Geant4 way by writing your C class inheriting from G4VUserPrimaryGeneratorAction Using GAMOS generator Introduction The GAMOS generator provides several time energy position and direction distri butions that the user may combine to his her will The user can select to generate as primary particles one or several single particles together with one or several isotopes and set any of the available time energy position or direction distributions for each one of the single particles or isotopes We describe below the commands to select the single particles the commands to select the isotopes and then the commands for selecting the time energy position and direction distributions The first command you have to use is the one that tells GAMOS that you want to use the GAMOS generator gamos generator GmGenerator This command apart from instantiating the GAMOS generator manager also instan tiates the messenger Therefore if you forget to write this command first the other generator commands described below will not exist and Geant4 will throw an excep tion After this comma
109. NPHOT limits the step size by specifying a maximum average number of Cerenkov photons created during the step The default value is 0 i e no limit gamos setParam GmPhysicsCerenkov MaxBetaChange 1 limits the maximum change of beta velocity velocity of light gamos setParam GmPhysicsCerenkov TrackSecondariesFirst 1 serves to avoid blowing up the memory by the thousands of photons that may be cre ated at one step by tracking the secondary photons at the moment they are created this means that the primary particle is stopped and later it is restarted gamos setParam GmPhysicsCerenkov MaxNumPhotons NPHOT 71 Chapter 5 Physics sets the maximum allowed change in beta v c in perCent The default value is 0 i e no limit Removing a process from a physics list 72 Several commands can be used to remove a process that is instantiated by a physics list without having to modify the C code and recompile The process to be removed can be selected by name gamos physics removeProcessesByName PROCESS_NAME_1 PROCESS_NAME_2 To find the name that GEANT4 gives to a process you may use the user action gamos userAction GmCountProcessesUA which will give yo a list of the process names attached to each particle in your physics list If you do not want to select all the processes give a given name but only if they are attached to a particle you can use the command gamos physics removeP rocessesByParticleAndName PARTICL
110. NSIONS are the solid dimensions By default the volume is placed at position 0 0 0 If you want it placed at a dif ferent position you have to add three optional extra parameters POS_X POS_Y POS_Z By default the volume is not rotated If you want it rotated you have to add three optional extra parameters and always add the three positions even if they are 0 0 0 ANG_X ANG_Y ANG_Z Those angles are interpreted as rotating the vol ume first around the X axis then around the Y axis and finally around the Z axis around the 0 0 0 point after the displacement is done The direction is taken as the line that goes from the position to the point 0 0 0 As this distribution is of position and direction types at the same time you have to use the two commands gamos generator positionDist 53 Chapter 4 Generator gamos generator directionDist You can see editing the file GamosCore GamosGenerator src GmGenerDistPositionDirectionInVolumeSurface cc that internally the method GenerateDirection knows the position by interrogating the source Creating your own distribution If you want to use a time energy position or direction distribution that is not foreseen in GAMOS you can easily create your own one Let s see as example the creation of a time distribution randomly distributed between two values You have to create your class inheriting from the class GmVGenerDistTime see for example the class GmGenerDist
111. Nevertheless the user can also select an output file compatible with the STIR package 23 a Open Source software for use in tomographic imaging In this case data files are also written in pairs a header text file hs and a binary data file s but following the STIR Interfile format The type of output format 0 for GAMOS ad hoc or 1 for STIR Interfile is controlled by the OutFormat parameter gamos setParam PET ProjData OutFormat OUT_TYPE In order to generate the sinograms the user must specify the dimensions of image axial and transaxial field of view FOV These values are given in milimetres by gamos setParam PET ProjData DistAxial D_AXIAL gamos setParam PET ProjData DiameterTranFOV D_TRANSAXIAL In addition projection data are discretized in axial tangential and angular dimen sions The user must indicate the number of axial planes N_PLANES by default 40 tangential bins N_BINS by default 81 and angular views N_ANGULAR by default 80 using these parameters gamos setParam PET ProjData Nplanes N_PLANES gamos setParam PET ProjData Nbin N_BINS gamos setParam PET ProjData Nang Views N_LANGULAR Note that once axial FOV is fixed the plane width is given by D_AXIAL N_PLANES 1 which represents the double of the slice thickness in the reconstructed image by default In the same way the image transaxial pixel size will have a value of D_TRANSAXIAL N_BINS 1 In 3 dimensional PET acquisition the maximum ring dif
112. OETHYLENE G4_TRIETHYL_ PHOSPHATE G4_TUNGSTEN_HEXAFLUORIDE G4_URANIUM_DICARBIDE G4_URANIUM_MONOCARBIDE 14 G4_URANIUM_OXID G4_UREA G4_VALINE G4_VITON G4_WATER G4_WATER_VAPOR G4_XYLENE G4_GRAPHITE G4_1H2 G4_1N2 G4_102 G4_lAr G4_1Kr G4_1Xe G4_PbWO4 G4_Galactic i Other materials co in the files mmon in medical physics MY_GAMOS_DIR data NIST_materials txt MY_GAMOS_DIR data PI ET materials txt The full list is the following BaF2 Bal2 BGO CdTe Cdwo4 CZT CeBr3 CeC13 CsI GaAs Gd202S GSO HgI2 LaBr3 Lacl3 LiF Li2B407 LSO LYSO LuAG LuAP LuYAP LUTS Nal PbwWo4 SrI2 YAG YAPNIST_A1203 NIST_Barite IST_15 mmol NIST_Concrete IST_Concrete IST_BaSo4 NIST_Cao IST_Concrete IST_PMMA IST_PVC NIST_Adipose Tissu ICRU 44 IST_Blood Whole ICRU 44 NIST_Bone Cortical ICRU 44 NIST_Brain Grey White Matter ICRU 44 IST_Breast Tissue ICRU 44 IST_Cadmium Telluride L 1 Ceric Ammonium Sulfate Solution Ordinary Barite TYPI BA KJ are Chapter 3 Geometry also predefined and 15 Chapter 3 Geometry 16 IST_Eye Lens ICRU 44 IST_Ferrous Sulfate Standard Fricke IST_Gafchromic Sensor IST_Lung Tissue ICRU 44 IST_Muscle Skeletal ICRU 44 IST_Ovary ICRU 44 IST_Ph
113. REGION 3 filterReg 4 5 6 ExtraInfoProviderOrigin INDEX REGION monitorReg ExtraInfoProviderOrigin INDEX REGION shieldingReg ExtraInfoProviderOrigin INDEX REGION jawsReg DANDWDWDD DD The float extra information providers fill one of the two available words in the order they have been defined The user can add more float words by changing the the following line at source RadioTherapy include iaeaRecord hh define NUM_EXTRA_FLOAT 2 and recompile the GAMOS code after that To store some information as float the user has to instantiate one of the following user actions e RTExtralnfoProviderZOrigin stores the Z position of the origin of the track e RTExtralnfoProviderZLast stores the Z position of the last interaction before reach ing the phase space At the end of the job each of these extra information user actions fills a file explain ning the information contained in each float By default this file is called RTExtraIn foProvider summ but the user may change the name of it with the parameter gamos setParam RTExtralnfoProviderFloat FileName FILE_LNAME If you have written a phase space file in a 32 bit machine and try to read it in a 64 bit one you will not be able to recover the numbers properly You may avoid it with the parameterr gamos setParam IAEArecord ExtraLongSize 32 Similarly if you wrote the file in a 64 bit machine and try to read it in a 32
114. RTVZRLimitsUA UseRussianRoulette TRUE The value of the Russian rouleet threshold is set with the parameter gamos setParam RT VZRLimits UA RussianRoulette Value VALUE which by default takes a value of 100 Scoring dose in phantom To use a phantom geometry you can use the GAMOS utilities to read phantom ge ometries in EGS or GEANT4 formats or build simple phantoms with a few user com mands The scoring of the dose in the phantom volumes can be done using the scorer GmG4PSDoseDeposit and selecting as detector the voxels that are named patient For example you can use the following commands gamos scoring createMFDetector DoseDet patient gamos scoring addScorer2MFD DoseScorer GmG4PSDoseDeposit DoseDet This is all you need to get on the standard output the dose by event deposited in each voxel When you use a phase space as input the number of events is not the number of events run in your job what would equal be the number of particles in the phase space multiplied by the number of times each particles is reused but GAMOS uses as number of events the original number of events that were used to generate the phase space In fact GAMOS gets the ratio of particles written in the phase space per original event transported through the accelerator and multiplies this ratio by the number of phase space particles used This allows to get the best approximation to 203 Chapter 22 Radiotherapy application 204 the correct number of events whe
115. SDTY PE VALUE where SDTYPE is the type of the sensitive detector Time resolution The time of the hits can also be smeared for each detector type with a gaussian given by the value of the parameter gamos setParam SD TimeResol SDTY PE VALUE If you have a resolution function that is different you may implement it by creating a new sensitive detector class inheriting from GmVSD or GmSDSimple if you don t want to change the logic to define the detector unit IDs and overwrite the methods virtual G4double SmearEnergy G4double energy G4double enerResol virtual G4double SmearTimeMin G4double time G4double timeResol Detector measuring time A detector has a finite time resolution so that it is not able to distinguish hits that come from different events when their time is close You can define the value of the measuring time for each detector type with the pa rameter gamos setParam SD MeasuringTime SDTYPE VALUE where SDTYPE is the type of the sensitive detector that takes a default value of 0 ns GAMOS offers several treatments of the masuring time so that the user can choose the one that best fits the detector under study To select the treatment type you have to use the parameter gamos setParam SD MeasuringType SDTYPE VALUE The following measurement types are currently available e Trigger When hits is produced in one event the hit with smallest time triggers so that all hits of all events with a time late
116. SOURCE_NAME GmGenerDistPositionInUser Volumes POS_X POS_Y POS_Z ANGX ANG Y ANG Z SOLID_TYPE SOLID_DIMENSIONS The particles are randomly distributed inside a volume defined by the user it does not need to be a real volume in the geometry The user must provide the definition of the volume as extra parameters SOLID_TYPE can be Orb Sphere Ellipsoid Tubs Box SOLID_DIMENSIONS are the solid dimensions For the order and meaning of the solid dimensions please look at the corresponding Geant4 solid By default the volume is placed at position 0 0 0 If you want it placed at a dif ferent position you have to add three optional extra parameters POS_X POS_Y POS_Z By default the volume is not rotated If you want it rotated you have to add three optional extra parameters and always add the three positions even if they are 0 0 0 ANG_X ANG_Y ANG_Z Those angles are interpreted rotating the volume first around the X axis then around the Y axis and finally around the Z axis around the 0 0 0 point after the displacement is done By default the positions are distributed in the volumes selected without taking care if they contain other volumes inside If you want to consider only the space that is not filled by daughter volumes you have to add the parameter gamos setParam GmVGenerDist Position VolumesAndSurfaces OnlyVolume 1 Position in a Geant4 volume surface gamos generator positionDist SOURCE_NAME GmGenerDistPositionInG4Sur
117. T is the name of the file containing the list of files to add and OUTPUT_FILE is the name of the output file that will contain the sum of all the files Two files will be generated the header OUTPUT_FILE hs or hv and the binary data OUTPUT_FILE s or v Analytic image reconstruction ssrb_fbp 175 This program applies a SSRB FBP2D 20 method to reconstruct PET images First a Single Slice rebinning algorithm SSRB converts 3 dimensional projection data in a set of 2 dimensional sinograms one per each axial image slice next a Filtered Back Projection image reconstruction algorithm that makes use of the Radon transform 21 is performed in each slice As input data the program requires the name of the GAMOS projection data file without extension hv v These files can be generated by GAMOS see PET output for reconstruction section or converted from list mode files using the Im2pd utility The command line options are the following m SSRB Maximum ring difference by default n_planes 1 The user can discard too axially tilted lines of response by selecting a lower value e r SSRB Normalization by default 1 yes 0 no e i Image size number of X and Y pixels by default number of sinogram bins e x Transaxial pixel size by default sinogram bin size e f Type of apodization window for filtering 21 low frequency pass e 1 Generalized Hamming value by default it includes Hann window and ram plak
118. TimeConstant virtual G4double GenerateTime const GmParticleSource source that will return the time value for each event If you want the user to be able to input some parameters of your class from the command line like the minimum and maximum time you have to implement the method virtual void SetParams const std vector lt G4String gt amp params This method will be called automatically passing the extra parameters in the com mand line selecting your distribution Last you have to transform your distribution into a plug in To learn how to do this see the instructions in the section Creating your plug in using the GmGenerDistTime Factory or see the plug in tutorial Then you can choose that any of the particle sources use your new distribution in any GAMOS job by adding the command line gamos generator directionDist SOURCE_NAME MyTimeDist where MyTimeDist is the name you chose when defining your plug in which could be different from the name of the class itself Reading your generator particles from a text file 54 You can also define your event primary particles with a text file The format of the input file is the following Each line corresponds to a primary particle with the following variables EventID Particle e PosX e PosY e PosZ e MomX e MomY e MomZ e Time Chapter 4 Generator e Weight The lines will be read one by one and all the particles that have the same event ID wi
119. Track ClassifyNewTrack const G4Track aTrack G4ClassificationOfNewTrack oldClassificationx e virtual void NewStage e virtual void PrepareNewEvent Finally you have to transform your class into a plug in To learn how to do this see the instructions in the section Creating your plug in using the GmUserActionFactory or see the PlugIn tutorial If you define twice the same user action in your command file you will get a warning message but it will be executed twice Chapter 7 Sensitive Detector and Hits Sensitive detectors Attaching a sensitive detector to a volume The sensitive detector class in Geant4 has the task of creating hits deposits of en ergy each time a track traverses a sensitive volume and loses some energy You can write your own sensitive detector class inheriting from G4VSensitiveDetector that produces your own hits and attach it to any volume in your geometry However GAMOS provides some utilities to make this easier and without the need of C programming or a detailed knowledge of how the sensitive detector and hits work in Geant4 GAMOS provides several predefined sensitive detectors that you can find in GamosCore GamosSD e GmSDSimple It is a general purpose class that produces hits with the position at the centre of the detector The identification of each detector unit is done as explained in the sub chapter Identifying each sensitive detector copy e GmSDSimpleExactPos It is similar to
120. VoxelZ 1 1Z RTPSPDoseHistos Dose Profile Zmerged 0 NVoxelX 1 0 NVoxelY 1 0 NVoxelZ 1 Y profiles at several depths pP P 1Y RTPSPDoseHistos Dose Profile Y 1 400 cm 50 50 0 NVoxelY 1 6 6 1Y RTPSPDoseHistos Dose Profile Y 10 000 cm 50 50 0 NVoxelY 1 49 49 PDDs merging voxels 1Z RTPSPDoseHistos Dose Profile Z 1x1 50 50 50 50 0 NVoxelZ 1 1Z RTPSPDoseHistos Dose Profile Z 3x3 49 51 49 51 0 NVoxelz 1 pP P It is also possible to produce in a simple way a full set of 2 dimensional plots covering a whole phantom in any of the three dimensions To do one must use the following parameter gamos setParam RTPSPDoseHistos AllHistos2D 2DIM_2 2DIM_2 The 2DIM_i values can be XY XZ or YZ you can use one of several of these three in your command To visualise them in a simple way you may use the printAll C see Appendix ROOT utility to convert all the histograms in graphics files Analysis utilities This is a set of utilities that may serve in the analysis of phase space and dose files for example to sum phase space or dose files from different jobs to get basic information of the file contents to fill histograms out of the files or to compare files from two jobs All these utilities are under the directory analysis They are compiled by default with the rest of GAMOS code and after that they are available as executables as mentioned in the following subsections Summing phase space files Thi
121. VoxelsFromFile FILE_NAME POS_X POS_Y POS_Z DIRX DIR_Y DIR_Z The voxels are read from a file with a format similar to the Geant4 DICOM files the main difference being that there are no materials the first line contains the number of voxels in X Y and Z the second one the lower and upper limits in X then in Y and then in Z then for each voxel it comes a number representing the relative probability to contain the position By adding three extra parameters you may displace the phantom By adding three more you may rotate it the parameters correspond to the new direction of the Z axis after the rotation Direction distributions Random distribution Chapter 4 Generator gamos generator directionDist SOURCE_NAME GmGenerDistDirectionRand The primary particles will be generated in a random distribution so that each solid angle receives the same number of particles Constant distribution gamos generator directionDist SOURCE_NAME GmGenerDistDirectionConst The primary particles will be generated all in the same direction given by the extra parameters DIR_X DIR_Y DIR_Z Cone distribution gamos generator directionDist SOURCE_NAME GmGenerDistDirectionCone The primary particles will be generated in a random distribution around a cone given by the extra parameters DIR_X DIR_Y DIR_Z OPENING_ANGLE so that each solid angle receives the same number of particles Gaussian along an axis gamos generator directionDist SOURCE_NAME GmGenerDis
122. X Y and Z directions e g n_x n_y n_z Chapter 22 Radiotherapy application e Array of voxel boundaries cm in the X direction n_x 1 values e Array of voxel boundaries cm in the Y direction n_y 1 values e Array of voxel boundaries cm in the Z direction n_z 1 values e Array of dose values Gy cm 3 n_x n_y n_z values e Array of dose squared values Gy cm 3 2 n_x n_y n_z values To optimise the disk space and the memory needed to read the file back it is possible to only store the dose and dose squares of those voxels that are filled This can be done by setting the parameter gamos setParam GmSqdose FileType FILLED The default value of this parameter is ALL Saving scores in histograms If you want to store the scores in the phantom in an histogram file you can use the scorer printer RTPSPDoseHistos gamos scoring addPrinter2Scorer RTPSPDoseHistos DoseScorer The number of bins in the histograms will be equal to the number of voxels in the phantom nVoxel and the histogram limits are the nVoxel 2 to nVoxel 2 The name of all these histograms start with RTPSPDoseHistos and they are all dumped into the file dose root csv The following histograms are produced by default e Dose in X direction Dose Profile X_merged e Dose in Y direction Dose Profile Y_merged e Dose in Z direction Dose Profile Z_merged e Dose in XY direction Dose XY_merged e Dose in XZ direction Dose XZ_merged e Do
123. _Y POS_Z All primary particles are generated at the same position If no extra argument is given the point is 0 0 0 Position in a Geant4 volume gamos generator positionDist SOURCE_NAME GmGenerDistPositionInG4Volumes LV_NAME1 LV_NAME2 The position is distributed randomly inside one or several volumes of the Geant4 geometry The user must add as extra parameters the list of volume names The volumes can be logical volumes physical volumes or touchables This distribution can only be used if the volumes are G4Box G4Orb G4Sphere G4Ellipsoid G4Tubs G4Cons or G4Polycone If you want to use it for any other volume shape you have to use the distribution By default the positions are distributed in the volumes selected without taking care if they contain other volumes inside If you want to consider only the space that is not filled by daughter volumes you have to add the parameter gamos set Param GmVGenerDist Position VolumesAndSurfaces OnlyVolume 1 gamos generator position Dist SOURCE_NAME GmGener Dist Position InG4VolumesGeneral LV_NAME1 LV_NAME2 This distributions works with any solid shape including boolean solids but it is in general quite slower than the previous one it creates a random position in the whole world volume and then looks if it is in one of the selected volumes which can be quite slow if the volume dimensions are small Position in a user defined volume gamos generator positionDist
124. a compt PROC_LIST gamma conv PROC_LIST gamma phot e At the end of run how many times a process determined the step for each particle type 143 Chapter 15 Utility user actions PROC_COUNT e Transportation 1870 PROC_COUNT e annihil 728 PROC_COUNT e eBrem 86 PROC_COUNT e eBrem_NoSeco 5 PROC_COUNT e elIoni 861 PROC_COUNT e elIoni_NoSeco 864 PROC_COUNT e msc 5531 PROC_COUNT e ALL 9945 PROC_COUNT e Transportation 1977 PROC_COUNT e eBrem 142 PROC_COUNT eBrem_NoSeco 10 PROC_COUNT e eloni 1736 PROC_COUNT e elIoni_NoSeco 9812 PROC_COUNT e msc 25744 PROC_COUNT e ALL 39421 PROC_COUNT gamma Rayl 4 PROC_COUNT gamma Transportation 4657 PROC_COUNT gamma compt 53 PROC_COUNT gamma phot 125 PROC_COUNT gamma ALL 4839 e At the end of run how many times a process was the creator of a particle for each particle type PROC_CREATOR_COUNT e Primary 1000 PROC_CREATOR_COUNT e Primary 1000 PROC_CREATOR_COUNT e compt 53 PROC_CREATOR_COUNT e eloni 2597 PROC_CREATOR_COUNT e phot 125 PROC_CREATOR_COUNT gamma annihil 1456 PROC_CREATOR_COUNT gamma eBrem 228 e At the end of run how many particles of each type were created PART_LIST e 1000 PART_LIST e 1485 PART_LIST gamma 2285 To activate this utility use the command gamos userAction GmCountProcessesUA T
125. a secondary particle SecoKineticEnergy Secondary particle kinetic energy PrimSecoAngleChange Angle between secondary particle and Primary particle at PreStepPoint InitialPrimKineticEnergy Primary particle PreStepPoint kinetic energy when a sec ondary particle is emitted FinalPrimKineticEnergy Primary particle PostStepPoint kinetic energy when a sec ondary particle is emitted Others These are miscellaneous data TrackID ID of track It is of integer type Only available for Step Track and Secondary Track ParentTrackID ID of parent track It is of integer type Only available for Step Track and Secondary Track EventID ID of event It is of integer type Only available for Step Track and Event RunID ID of run It is of integer type Not available for Secondary Track StepNumber number of step It is of integer type Only available for Step and Track InitialWeight initial track weight Not available for Event nor Run FinalWeight final track weight Not available for Secondary Track nor Event nor Run AccumulatedLength Accumulated step length Not available for Secondary Track TrackLength step length for Step and track length for Track Gives same result than AccumulatedLength but is faster NofSecondaries number of secondary tracks produced Only available for Step and Track SumSecoKineticEnergy sum of the kinetic energies of all secondary particles pro duced Only available for Step and Track Ini
126. addPrinter2Scorer PRINTER_NAME SCORER_NAME The name of the printer is the name of the printer class see list below If you want to change the printer name or you want to add some parameters to a printer you can use the command gamos scoring printer PRINTER_NAME PRINTER_CLASS PARAMETERS where PRINTER_NAME is the new name you want to give to the printer and PRINTER_CLASS is the name of the printer class see list below The general use scorer printers currently in GAMOS are the following e GmPSPrinterG4cout Prints in the standard output the summary of scoring in the following format MultiFunctionalDet MFD_NAME PrimitiveScorer SCORER_NAME Number of entries 5 index 0 2 6625344e 18 REL 0 031622777 Gy index 1 8 661742le 17 REL 0 011622713 Gy index 2 2 1034987e 17 REL 0 021166675 Gy index 6 5 9651155e 17 REL 0 01418326 Gy index 7 8 2850179e 17 REL 0 013747866 Gy SCORER_NAME SUM ALL 2 683331le 13 7 9512158e 15 Gy where MFD_NAME is the name of multifunctional detector and SCORER_NAME is the name of the scorer The columns after index have the following meaning Index scorer value scorer error relative i e error value unit name At the end it is printer the sum of all scores with error non relative GmPSPrinterTextFile Prints in a binary file the same information than the GmP SPrinterG4cout printer The name of the file is
127. al in question All the properties can be managed in the geometry text file using tags similar to those of the geometry text file utility For details on the meaning of these paramters please refer to the Geant4 documentation We describe here these tags with the parameters that should accompany them To define a new G4Material Properties Table you have to use the tag MATE_PROPERTIES_TABLE e Table name Then you can add different properties to the table There are two kinds of proper ties those that are defined by a single number called constant properties in Geant4 notation and those that are defined by a list of numbers one associated to an energy To define a constant property the following tag must be used MATEPT_ADD_CONST_PROPERTY e Material properties table name e Property name e Property value To define non constant properties you have to define first the list of energies that you will use to assign the different properties to the table MATEPT_ADD_ENERGIES e Material properties table name 67 Chapter 5 Physics 68 e Energy 1 e Energy 2 e Energy N Then to define a property MATEPT_ADD_PROPERTY e Material properties table name e Property name e Value 1 e Value 2 e Value N The material properties table can be attached to a material with the tag use it several times to attach it to several materials MATEPT_ATTACH_TO_MATERIAL e Material properties table name e Material name You can
128. al size Z direction SCATDIST Distance in Z from centre of first scatterer detector to world origin SCATSEP Separation distance in Z between the centres of neighbouring scatterer detectors SCATCRYS_MATE Scatterer detector material e Absorber layers NABSLAYERS Number of absorber detector layers NABSCRYSTALS_X Number of crystals in each layer X direction NABSCRYSTALS_Y Number of crystals in each layer Y direction NABSCRYSTALS_Z Number of crystals in each layer Z direction ABSCRYS_X Crystal size X direction ABSCRYS_Y Crystal size Y direction ABSCRYS_Z Crystal size Z direction ABSDIST Distance in Z from centre of first absorber detector to world origin ABSSEP Separation distance in Z between the centres of neighbouring absorber detectors ABSCRYS_MATE Absorber detector material To use this utility the user must choose to read the geometry from a text file gamos geometry GmGeometryFromText The user must also provide the FILE_LNAME which contains the parameters used to define Compton camera geometry gamos set Param GmGeometryFromText FileName FILE_NAME Chapter 20 Compton camera application A few example files are included of simple Compton camera systems with suffix geom in the Compton camera tutorial for example CCGeometryRingEx1 geom Within this text file the user must then choose whether to read the Ring or Stack geometry text file by typing include CCGeometryRing geom for a ring geometry or
129. also add a prefix or suffix with the above commands to all of them as all the input and output of these classes is controlled in GAMOS through a common base class Merging results from different jobs When running an application you may get a table of the different types of results It is usual that you run different jobs with the same setup to accumulate statistics or with different setups to study the dependency of your results with some pa rameters In the analysis directory of your GAMOS distribution there are specific utilities for specific outputs for example RTPhaseSpace sumPS RTDose sumSqdose RTDose sum3ddose Shielding sumScores Shielding sumPDS NuclMed PET sumProjdata they are described in the corresponding section of this manual In this section we will describe an utility to analyse the output tables produced from various runs extract sum or compare results and also how to merge and analyse the output files of good events If you have run one or several jobs and produced a table with the statistics of good events we describe here an utility that allows to process these results and present them in a more convenient way This utiltiy analyses the files containing the output tables and allows you to extract the desired numbers out of them and present them together in a single table with the possibility to add the numbers from different ta bles We will describe the steps you should follow to do this and illustrate them with an e
130. ameters e Name of the volume to be moved Type of movement It can be Time or NEvents see above Interval of events or time between movements e Ofsset number of events before movement starts 41 Chapter 3 Geometry e Number of times movement is done Number of movements that are describe in the following lines The offset and number of intervals is optional as above For each movement a line has to be written with the following parameters e Displacement value e Displacement axis X e Displacement axis Y e Displacement axis Z e Rotation value e Rotation axis X e Rotation axis Y e Rotation axis Z The above format can be repeated as many times as desired for the same volume or other The following example file describes two movements a first simple one occurring five times each ten events that displaces the volume mybox 50 mm along the X axis and rotates it 10 degrees around the Y axis and a double movement occurring 2 times each ten events starting form the event 50 that displaces the same volume 50 mm along the Y axis and 100 mm along the Z axis and rotates it 2 deg around the Z axis mybox NEvents 10051 50 mm 1 0 0 10 deg 0 1 0 mybox NEvents 10 50 2 2 50 mm 0 1 0 2 deg 0 0 1 100 mm 0 0 1 O deg 0 0 0 Geometry utilities 42 Commands to print geometry objects The command gamos geometry print VolumeTree VERBOSE_LEVEL serves to print the hierarchical tree of geometry volumes starting
131. amos Physics e PhysicsList example of electromagnetic physics list supporting standard low energy and Penelope classes and example of hadronic physics list meant for hadrontherapy e OtherPhysicsLists other examples of electromagnetic and hadronic physics lists e Cuts management of production cuts and user limits including tools to auto matically optimise them e VarianceReduction implementation of several variance reduction techniques GamosUserActionMgr user action management to allow several user actions of the same type selectable by user commands GamosScoring scoring manager and messenger and examples of scoring plug in classes scorers filters and printers e Management scoring manager and messenger and base class for scorer and scorer printers e Scorers scorers e Printers scorer printers e PointDector point detector scoring 231 Chapter 27 Appendix B C utilities 232 e GamosData e Management data management and base data classes e Data data e Users data users GamosAnalysis utilities that can help the advanced user to analyse results GamosReadDICOM code to read in DICOM files containing patient data GamosUtilsUA user action utilities tracking verbosity control track counting process counting time study GamosUtils general C utilities GamosApplication GAMOS run manager and the main program e PET example of PET simulation e PETGeometry example to simulate t
132. an a ar a S EEES 71 Removing a process from a physics list s ssssssssesssssissesssesiesissressesresnesseseeseeses 72 6 User ACHONS wssccssssccsscecisctecisssevsncssessctssosvsescescousencssessbessanssvenssdeuesedcacsevecscsseveadeauesessecssebees 73 Adding a filter scott id ot nt A e a Galan E win tin wt ates 73 Addmsaclassifier 2 iis 20 csc x peesi a p aE E E GEA 73 Us racton Nane in eE E EE E E E E AR EE E NA 73 Creating your GAMOS user action s s ssessesseserierietesierertesereseenestenesnenesnesessessssesse 74 7 Sensitive Detector and Hits essessoesoesoesoeseorsorsoesoescesooreorsoesoesoessoreoreoesoessoreorsoesoeeoesee 75 Sensitive detectors mena ee 75 Attaching a sensitive detector to a VOlUMe ss ssessesssssississtssessesseeseeseeses 75 Building your sensitive detector with C code s ssssssssesssissessesseesesreese 76 FICS ET NEE E E A R N TE AE E TEETE Ce 77 POtTECTOMCEECIS 2s 5 Sisson Be rain n E E A E A NN Sods E A 77 Energy resolution rosipa iseenesesse ean ane epar Nea aE EA E a E an 77 Bianan koI aT a RAAPA E EEE N E S NTEN Mio 78 Detector MeAaSUTING tM sissi innos sses kere e ASE oaea i Ee ni 78 Detector dead time cccccccccccccccccscessscecsssecsscesessssceeesscessssecsseceesssesssssesssseesesass 79 Minimum hit energy icsisccvsccsisscnescsseseussess weeaateasisesauecesnsesseceseessbaneee ene dnates 80 Hits digitization and reconstruction ccccc eee sees eetessesesessseseseseseeee
133. aram GmGeometryFromText FileName MY_FILENAME 2 and then telling GAMOS to use the constructor of geometry from text file gamos geometry GmGeometryFromText Description of geometry text file format The description of the geometry is based on tags A tag is a word that appears at the first one in a line and sets what the line means There are no constraints on the order of the tags in the file except some logical restric tions e g a volume cannot be positioned or given attributes if it has not been defined e g no PLACE VIS COLOUR CHECK_OVERLAPS tags before VOLU tag We will explain in this section the tags used to describe the geometry also explaining the meaning of each of the words that follow the tag and an example of each tag Tags can be given with any combination of upper case and lower case letters Each tag has a fixed number of arguments known by the parser therefore you may write all arguments in a line or in several lines at your will Isotope ISOT e Name Z eN eA Example ISOT C135 17 18 35 Element made of one unique isotope ELEM e Name Symbol eZ Chapter 3 Geometry 10 oA Example ELEM Hydrogen H 1 1 Element composed of several isotopes ELEM_FROM_ISOT e Name e Symbol Number of components One line per isotope with e isotope name e fraction of number of atoms per volume Example ELEM_FROM_ISOT Chlorine Cl 2 C135 0 4 C136 0 6
134. arn how to do this see the instructions in the section Creating your plug in using the GmFilterFactory or the Histograms and scorers tutorial Simple filters The list of available filters can be obtained by typing SealPluginDump on your termi nal window and look for the list of classes after Category GmFilterFactory they all contain the word Filter The list of simple filters in the current GAMOS version is the following 131 Chapter 12 Filters 132 GmGammaFilter accepts a track if the particle is a gamma GmElectronFilter accepts a track if the particle is an electron GmPositronFilter accepts a track if the particle is a positron GmElectronOrPositronFilter accepts a track if the particle is an electron or positron GmEMParticleFilter accepts a track if the particle is of electromagnetic type gamma electron or positron GmProtonFilter accepts a track if the particle is a proton GmNeutronFilter accepts a track if the particle is a neutron GmParticleFilter accepts a track if the particle is in the list of particles given as extra parameters see the list of particle names in the section Using particle names GmChargedFilter accepts a track if the particle is charged GmNeutralFilter accepts a track if the particle is neutral GmPrimaryFilter accepts a track if it is a primary it does not come from another track GmSecondaryFilter accepts a track if it is a secondary it comes from another track GmKineticE
135. at the method mentioned above which does not take into account the initialisation and termination times of each track event and run Changing the weight using a distribution The user action GmChangeWeightUA changes the weight at each step or track follow ing aGAMOS distribution You have to set the distribtution with the parameter gamos setParam USER_ACTION_NAME Distribution DIST_NAME Copying the weight to the secondary particles Geant4 usually copies the weight of a track to the secondary tracks that it creates But in the process is RadioactiveDecay this does not work Therefore if you are using readioactive decay and need this feature you have to activate the user action GmCopyWeightToSecondaryUA Stop run after a certain CPU time 145 There may be some times when you want to limit the CPU time so that the job stops even if all the events demanded have not run To do it you can use the user action GmCopyStopRunAfterTimeUA The time is limited with the paremeter GmStopRunAfterTimeUA Time TIME In fact the time is only checked after each event so you may find that the time it actually stops is bigger than what you demanded Chapter 16 Managing the verbosity GAMOS verbosity managers While GAMOS is running you can control the amount of information you get on the screen and in the log files with the GAMOS verbosity management There are six levels of verbosity each level includes the verbosity of the previous level
136. ateEnergyLost AccumulateEnergyDeposited GmStepDataBinFileUA EventID TrackID Particle FinalPosX FinalPosY FinalPosZ FinalMomX FinalMomY FinalMomZ AccumulateEnergyLost AccumulateEnergyDeposited GmTrackDataHistosUA FinalPosX FinalPosY FinalPosZ FinalMomxX FinalMomyY FinalMomZ Accumulated EnergyLost AccumulatedEnergyDeposited GmTrackDataTextFileUA EventID TrackID Particle FinalPosX FinalPosY e FinalPosZ e FinalMomxX e FinalMomY e FinalMomZ e AccumulateEnergyLost e AccumulateEnergyDeposited GmTrackDataBinFileUA EventID TrackID Particle FinalPosX FinalPosY FinalPosZ FinalMomxX FinalMomY FinalMomZ AccumulateEnergyLost AccumulateEnergyDeposited GmEventDataHistosuA e AccumulateEnergyLost e AccumulatedEnergyDeposited GmEventDataTextFileUA e EventID e AccumulateEnergyLost e AccumulatedEnergyDeposited GmEventDataBinFileUA e EventID e AccumulateEnergyLost e AccumulatedEnergyDeposited GmRunDataHistosuA e AccumulateEnergyLost e AccumulatedEnergyDeposited GmRunDataTextFileuA e RunID e AccumulateEnergyLost e AccumulatedEnergyDeposited GmRunDataBinFileUA e RunID e AccumulateEnergyLost Chapter 11 Analysis extracting data 115 Chapter 11 Analysis extracting data e AccumulatedEnergyDeposited GmSecondaryTrackDataHistosUA TrackID Initial PrimMinusSecoKineticEnergy FinalPrimMinusSecoKineticEnergy SecoDividedInitialPrimKineticEner
137. ater used to set the parameters As the number of particle duplications will be set by the classifier index you may want to set a different index than the default of the classifier See section on Classifiers to learn how to do this Several options can be controlled with GAMOS parameters First you may decide to deactivate the splitting leaving only Russian roulette or viceversa with the param eters gamos setParam IMPORTANCE_SAMPLING_NAME ApplySplitting 0 gamos setParam IMPORTANCE_SAMPLING_NAME ApplyRussianRoulette 0 If you do not want that a particle already split is split again you may control how many times a particle is split with the parameter gamos setParam IMPORTANCE_SAMPLING_NAME MaxSplitTimes VALUE You may also set that the same particle is not split several times by setting the pa rameter gamos setParam IMPORTANCE_SAMPLING_NAME SplitAtSeveralSteps Finally you may add one of more filters so that particles have to pass them before being split 103 Chapter 9 Variance reduction techniques gamos setParam IMPORTANCE_SAMPLING_NAME Filters FILTER_1 FILTER_2 Geometrical biasing Many types of geometrical biasing can be done with GAMOS using the importance sampling and assigning different distributions with different data For example you may use adifferent weight for each physical volume logical volume or touchable or you can divide your space in bins along X Y or Z or combinations of these variables
138. aviour you have to use the user action gamos userAction GnNoUseG4RadDecayTimeUA This user action will not only keep the time sampled with the activity set in the time distribution but will also treat the time of secondary products in case there a decay chain If an ion A decays to a secondary ion B it will happen at the time set by the time distribution if ion B decays it will calculate the activity that it has at the this time This activity will be proportional to the activity of ion A at time 0 the activity set by the distribution parameter corrected by the time the activity diminishes proportionally to exp time lifetime_A and multiplied by the inverse of lifetime_B Activity_B t Activity_A t 0 exp t lifetime_A lifetime_B 47 Chapter 4 Generator 48 If a third or consecutive decay happens it will also calculate the corresponding activities with have a more complicated formula If the lifetimes are big it may happen that the activities of become very small giving precision problems For this reason the minimum activity is set to 1 E 30 seconds so that if an smaller ac tivity results form the calculation it it set to 0 i e the decay does not happen This parameter can be overloaded with the parameter gamos setParam USER_ACTION_NAME MinimumActivity gt Energy distributions Constant energy gamos generator energy Dist SOURCE_NAME GmGenerDistEnergyConstant ENERGY All the primary particles will be genera
139. b e In the method void SetFilterLevel int fl call the same method of your GmVerbosity object MyVerb SetFilterLevel fl e In the method void GetFilterLevel int fl call the same method of your GmVerbosity object MyVerb GetFilterLevel fl Finally you have to transform your class into a plug in DEFINE_GAMOS_VERBOSITY MyVerbosityMgr Controlling the Geant4 verbosity by event and track If you want to print the detailed step information provided by Geant4 for a given interval of events or tracks but you do not want that it is printed for all you can use the user action gamos userAction GmTracking VerboseUA You have to define the minimum and maximum events for which you want the ver bosity on and you can also set it ON only each N events gamos setParam GmTrackingVerboseUA EventMin VALUE gamos setParam GmTrackingVerboseUA EventMax VALUE gamos set Param GmTrackingVerboseUA EventStep VALUE If these parameters are not set the verbosity will be ON for all events You can also define for which tracks interval in the selected events the verbosity will be ON and set it ON only each N tracks gamos setParam GmTrackingVerboseUA TrackMin VALUE gamos setParam GmTrackingVerboseUA TrackMax VALUE gamos setParam GmTrackingVerboseUA TrackStep VALUE If these parameters are not set the verbosity will be ON for all tracks Finally you may select the Geant4 verbosity level by default 1 with the parameter gam
140. bably not a physical plane in the geometry particle steps will start before the plane and end after the plane Therefore the position and energy are rescaled as if the particle would have stopped at the Z plane by a simple linear interpolation By default particles that travel towards the negative Z direction are not stored as it is assumed that the original directio was towards positive Z and therefore this particles or their ancestors should already have been stored You may nevertheless eliminate this check and store all particles by setting the parameter gamos setParam RT PhaseSpaceUA NotStoreBackwards FALSE Chapter 22 Radiotherapy application You can limit the number of particles stored in each phase space what may be useful when you are filling several phase spaces in a job and do not want that the first phase spaces end occupying too much disk space To do this you have to set the parameter gamos setParam RT PhaseSpaceUA MaxNTracksRecorded NTRACKS Phase space text file You can also write the phase space in a simple text format The following variables will be written for each track that reaches the phase space plane particle_code kinetic_energy MeV x cm y cm z cm direction_x direction_y direction_z weight extra_information_word_1 extra_information_word_2 extra_information_word_n The name of the file is set with the parameter gamos setParam RT PhaseSpaceUA TextFileName FILE_NAME Phase space histograms Whe
141. be rejected if the number of hits found is bigger than the value given by the parameter gamos setParam SPECT EvtClass RejectIfNRecHits VALUE The ClassifySPECT method returns an integer with several digits containing the event classification 0 if it is not SPECT 1 if it is SPECT and SPECT line is close to the event vertex 2 if it is SPECT and SPECT line is far from event vertex e 10 1 if the search for 511 keV reconstructed hits found more than 2 100 1 if the event is a random coincidence event 1000 1 if the event is a scattered event 10000 1 if there are several collimators and the collimator traversed by the original gamma is the wrong one i e not the one closest to the hit e 20000 1 if the original gamma did not traverse a collimator At the end of the run a table is printed with the number of events in each of the combinations of the sub classification types You may SPECT histograms event classification 165 These histograms are related to the event classification explained above They are produced if the event classification user action is selected The name of all these his tograms starts with SPECTEvtClass and all are written in the file spect root csv The following histograms are written e Classification index of event SPECT classification This index is the one de scribed in the precedent section Chapter 19 SPECT application Number of 511 keV reconstructed hits before cleaning if there are
142. bit one Reusing a particle at a phase space without filling the phase space file It is commmon in radiotherapy treatment simulations that in a first job a phase space file is created and in a second job the particles therein are read and reused several times to calculate the dose in the patient GAMOS provides the possibility of reusing Chapter 22 Radiotherapy application particles in a phase space file without having to divide the jobs in two To use this utility the user has to instantiate the user action gamos userAction RT ReuseAtZPlaneuA and then use the command gamos RT ReuseAtZPlane and before the user has to define the z value of the plane where particles will be replicated with the parameter gamos setParam RT ReuseAtZPlane ZReusePlane Z_POS and the number of times particles will be reused indeed the particles is copied NREUSE 1 times gamos setParam RTReuseAtZPlane NReuse NREUSE The user may independently create the phase space file or not at the smae Z position or at others An important thing to take into account is that the particle is copied from the position of the PreStepPoint A possbile option would be to extrapolate it to the Z plane and copied it at that position but if the extrapolation is done with a straight line it would not take into account the straggling of charged particles Optimisation of a linac simulation To optimise your simulation in GEANT4 you may tune the physics parameters pro
143. bject calculates the transformation in the volume where the track was initiated The FinalLocalPos data for a Step object calculate the transformation in the volume the track step is going to enter the same as for a Track object You may be interested in getting the transformation in the volume the track step has just traversed but using the position and the end of the step In this case you can use another set of data called LocalInPre For a Track object these data use the current position of the track but the volume where the track was initiated The histogram limits for X Y and Z are 1000 mm to 1000 mm for Mag and Perp are 0 to 1000 mm for Phi are 0 to 360 deg and for Theta are 0 to 180 deg The position data are InitialPosX InitialPosY InitialPosZ InitialPosMag InitialPosPerp InitialPosPhi InitialPosTheta FinalPosX FinalPosY FinalPosZ FinalPosMag FinalPosPerp FinalPosPhi FinalPosTheta PosChangeX PosChangeY PosChangeZ PosChangeMag PosChangePerp PosChangePhi PosChangeTheta InitialLocalPosX InitialLocalPosY InitialLocalPosZ InitialLocalPosMag InitialLocalPosPerp InitialLocalPosPhi 119 Chapter 11 Analysis extracting data InitialLocalPosTheta FinalLocalPosX FinalLocalPosY FinalLocalPosZ FinalLocalPosMag FinalLocalPosPerp FinalLocalPosPhi FinalLocalPosTheta FinalLocalInPrePosX FinalLocalInPrePosY FinalLocalInPrePosZ FinalLocalInPrePosMag FinalLocalInPrePosPerp FinalLocalInPrePosPhi FinalLoca
144. bs 10x10 6 ORIGINAL HISTORIES 2000000 N PARTICLES 5 13303e 07 PER ORIG_HIST 25 6651 0 0184982 N GAMMAS 5 11882e 07 PER ORIG_HIST 25 5941 0 0184479 N ELECTRONS 137257 PER ORIG_HIST 0 0686285 0 000191492 N POSITRONS 4839 PER ORIG_HIST 0 0024195 3 48235e 05 Reading PHSP track 0 Reading PHSP track 51000000 saving histograms in file phaseSpace root The output contains the total number of original histories and after the number of particles gammas electrons and positrons in the phase space file and these numbers divided by the number of original histories with the error Also an histogram file equal to the file that was created when producing the phase space file will be created 207 Chapter 22 Radiotherapy application 208 Several arguments can be supplied to the executable in the standard Unix format f phase space file name in this case do not use the file name alone as first argument as before NRead number of particles to be read from the phase space file fOut output file name EMax maximum limit of the energy histograms e RMax maximum limit of the position histograms NBins number of bins of histograms verb verbosity it sets the RT Verbosity Default is warning that will print the above lines debug that will print each particle read form the phase space file help prints the set of arguments Merging sqdose files This util
145. ccccceeeseseseesssseseesesesseseseseeeeeeces 101 9 Variance reduction techniques scsssrscecesrsrssecesssssssesesssssessscsssssssscsesssssesessesseeees 103 Introd chon rs eneee a a EENE Rasen hoon So eet ose bi DG N occ ics ook 103 Importance Sam pling sesssccsccscasssecsseneseneseasesecaassateedecscahscsessaveucooascetdsschstiveeasedgusneaees 103 Geometrical biasing i ecieieiscelntenintia tea den aa S debt aeeecietes 104 Production of deexcitation secondary particles cccccccsscseescesessseensenees 104 Particle splitting techniques for radiotherapy cccccceccescesesteteeeeesesesesneenees 104 10 Histo gramming sccscsssssessssesssseesssesseseesseseesssecsssscssesseseeseseesessesessssesessesesesesees 105 FAIStO Sram formats oren Meenen ostene RAE menee IAEE aa a a EER Ea eaa Se aE LEA aaee 105 Histograms CSV formatasesssieroreo iiine n e a a 105 Changing histogram minimum maximum and number of bins 004 106 Output files NaMe siS issir a eaa ar e aa TEAR neinei i 106 Analysing your histograms With ROOT s ssesssssssssessissessesssesisiesresensnesnenrensees 107 Printing the histograms in graphics files ccc eeeseeeesessseseseeeneeeees 107 Comparing histograms in two files ec eeeecenseseesesereeeseseeeseecee 107 Creating your own histogram ccccce cece cess csseeseesessseesesseseseseseseseecee 108 11 Analysis extracting data seeseessssseseeseeesesseseesscoreeseeseessessessc
146. cessModels MODELS_1 MODELS_2 where MODEL _i may be gamma standard gamma lowener gamma penelope electron standard electron lowener electron penelope Production cuts Several physics processes namely bremsstrahlung ionisation and e e pair produc tion from muons have very high cross sections at low energies It is therefore neces sary to implement a production cut so that all particles below it are not generated but their energy is accounted as energy deposited Geant4 uses production cuts in range instead of in energy as used previously by GEANT3 and most Monte Carlo codes A cut of for example 1 mm for photons means that no photon will be produced if the expected range in the current material is less than 1 mm If you use the GAMOS electromagnetic physics list the default production cut value is 0 1 mm for all processes in all materials The Geant4 command run particle setCut value unit set the cuts for all process to the desired value But do not forget to use the command run initialize after setting the cuts if you want that your change is ef fective The Geant4 command run particle dumpCutValues dumps the list of materials and for each one the list of cuts for each particle in GAMOS it is printed by default One word of caution is due here internally Geant4 converts the cuts for range in each material to cuts for energy and uses these for their computations There is a low energy limit so that if the range
147. core the data values These three usages are explained in the corresponding sections The behaviour of each of the data users depends on one side on the type of informa tion object they manage and on the other side on the type of output provided Behaviour as a function of information object The behaviour of each of the data users for each of the information objects is the following e The Track step data users implement a UserSteppingAction method which extracts the data at each track step from the G4Step object e The Track data users implement a PostUserTrackingAction method which extracts the data at the end of the current track step from the G4Track object equal to the current track status For the data of type Initial the data is extracted from the vertex information of the G4Track object For the data of type Accumulated these data users implement a UserSteppingAction method which accumulates the data at each track step and a PreUserTrackingAction which initializes the data to 0 the Chapter 11 Analysis extracting data PostUserTrackingAction uses the accumulated data instead of extracting the data from the G4Track object The Event data users implement a EndOfEventAction method which extracts the data at the end of the event from the G4Event object For the data of type Initial the data is extracted from the information of the first primary particle of the first primary vertex For the data of type Accumulated these
148. create an optical surface with the tag OPTICAL SURFACE e Name Boundary process model It can be e UNIFIED e GLISUR e LUT e Boundary process model It can be e UNIFIED e GLISUR e LUT Surface finish type It can be e polishedfrontpainted e polishedbackpainted e ground e groundfrontpainted e groundbackpainted e polishedlumirrorair polishedlumirrorglue e polishedair polishedteflonair polishedtioair polishedtyvekair polishedvm2000air polishedvm2000glue etchedlumirrorair etchedlumirrorglue etchedair etchedteflonair etchedtioair etchedtyvekair etchedvm2000air etchedvm2000glue groundlumirrorair groundlumirrorglue groundair groundteflonair groundtioair groundtyvekair groundvm2000air groundvm2000glue Surface type It can be dielectric_metal dielectric_dielectric dielectric_LUT firsov x_ray Polish value Sigma alpha value Chapter 5 Physics The material properties table can be attached to a optical surface with the tag use it several times to attach it to several optical surfaces MATEPT_ATTACH_TO_OPTICAL SURFACE e Material properties table name e Optical surface name You can create a logical border surface with the tag LOGICAL_BORDER SURFACE e Material properties table name First physical volume name e Second physical volume name 69 Chapter 5 Physics e Optical surface name You can create a logical skin surface with the tag LOGICAL_SKIN SURFACE e Material
149. cs userLimits setUserLimits USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE _ NAME MAX_STEP MAX_ TRK LENGTH MAX_TOF MIN_KIN_E MIN_RANGE where USER_LIMITS_NAME is the name of the user limits every user limits must have a name so that new logical volumes and particles can be added with user commands later MAX_STEP MAX_TRK_LENGTH MAX_TOF MIN_KIN_E and MIN_RANGE are the values of the five user limit types described above If you want to set only one user limit type you can use one of the following commands e gamos physics userLimits setMaxStep USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE_NAME MAX_STEP e gamos physics userLimits setMaxTrkLen USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE_NAME MAX_TRK_LENGTH e gamos physics userLimits setMaxTOF USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE_NAME MAX_TOF e gamos physics userLimits setMinEKin USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE_NAME MIN_KIN_E e gamos physics userLimits setMinRange USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE_NAME MIN_RANGE There is another command in GAMOS that serves to set the minimum range user limit using a distance value but internally it is applied as a minimum kinetic energy limit This permits to use range values but avoids the lengthy process of converting the kinetic energy at each step into range For this you can use the command e gamos physics userLimits setMinEKinByRange USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE_NAME MIN_RANGE Once a user
150. ctor Orig Pos Z if Gamma reaches SD mm e R position of vertex of gamma if it reaches the sensitive detector Orig Pos R if Gamma reaches SD mm 1 Indeed the exact mass of the electron is always used 2 original gammas are gammas that are primary particles or that are directly cre ated by the annihilation of positron that is a primary particle Chapter 19 SPECT application Before reading this chapter we recommend you to read the chapter on nuclear medicine that contains the utilities that are common to all nuclear medicine applications The SPECT example is quite similar to the PET one we will describe here the main characteristics that differentiate it and refer to the PET example for those characteris tics they share Many of the utilities for SPECT detectors are related to the sensitive detectors that they contain so please read the Sensitive Detectors chapter if you have not done it yet SPECT event classification The class SPECTEventClassifierUA in the directory SPECT classifies the events as SPECT by looking at the reconstructed hits It is a GAMOS user action so you can activate it with the command gamos userAction SPECTEventClassifieruA The first thing you have to define is the original gamma energy what you can do with the parameter gamos setParam SPECT EvtClass GammaEnergy ENERGY Another thing you have to define is where is your collimator You can define it by giving the collimator volum
151. cuts than the production of bremmstrahlung gammas and ion isation electrons This means that if these cuts are high those particles will not be produced although the atomic deexcitation processes will be active the energy of the secondary particles will be added to the energy deposited We remind you that the production cuts are set by range in GEANT4 but you can find the range to energy threshold conversion for each matrial at the beginning of your job Decay process You can activate the decay process for all particles for which it is applicable with the user command gamos physics addPhysics decay Radioactive decay process Each time an ion is created by a GAMOS command to use is as primary particle to create a filter to select it the radioactive decay process is activated for it You can avoid this by using the parameter gamos setParam Physics RadioactiveDecay 0 But if the ion is created by Geant4 and you want to activate the radioactive decay process to have to use command gamos physics addPhysics radioactiveDecay This command has to be used after the run initialize command and activates auto matically this process for all ions Cerenkov process You can activate the Cerenkov processes for all charged particles with the user com mand gamos physics addPhysics cerenkov Several parameters can be set before this command to control the Cerenkov process gamos setParam GmPhysicsCerenkov MaxNumPhotonsPerStep
152. d to define the RING system e Scatterer Ring e NSCATRINGS Number of rings of blocks e NSCATBLOCKS Number of blocks of crystals per ring e NSCATCRYSTALS_transaxial Number of crystals in each block transaxial NSCATCRYSTALS_axial Number of crystals in each block axial e SCATCRYS_transaxial Crystal size transaxial e SCATCRYS_axial Crystal size axial e SCATDIAMETER Detector ring diameter e SCATCRYS_MATE Scatterer detector material e Absorber Ring e NABSRINGS Number of rings of blocks e NABSBLOCKS Number of blocks of crystals per ring e NABSCRYSTALS_transaxial Number of crystals in each block transaxial e NABSCRYSTALS_axial Number of crystals in each block axial 171 Chapter 20 Compton camera application 172 ABSCRYS_transaxial Crystal size transaxial ABSCRYS_axial Crystal size axial ABSDIAMETER Detector ring diameter ABSCRYS_MATE Absorber detector material ii The stack system is composed of a number of scatterer and absorber detectors parallel to each other The stack is produced through the axial z direction and is defined using the following parameters e Scatterer layers NSCATLAYERS Number of scatterer detector layers NSCATCRYSTALS_X Number of crystals in each layer X direction NSCATCRYSTALS_Y Number of crystals in each layer Y direction NSCATCRYSTALS_Z Number of crystals in each layer Z direction SCATCRYS_X Crystal size X direction SCATCRYS_Y Crystal size Y direction SCATCRYS_Z Cryst
153. data users i e GmStepDataCoutuA GmTrackDataCoutuA GmEvent DataCoutuA GmRunDataCoutuA GmSecondaryTrackDataCoutuA dump the data values into the standard output they may be helpful to debug an application to gether with the command tracking verbose 1 Similarly to the text file data users a line is written for each call to the data user object i e each G4Step G4Track The text file is indeed a CSV Comma Separated Value file this means that values are separated by commas and string values are surrounded by double quotes Selection of data list for a data user Each data user has a default list of data that we will enumerate below This list can be changed with the parameter gamos setParam DATA_USER_NAME DataList DATA_1 DATA_2 For example if we use gamos userAction GmStepDataBinFileuUA GmGammaFilter the data list may be changed with the parameter gamos setParam GmStepDataBinFileUA_GmGammaFilter DataList TrackID FinalPosX sqrt 2 FinalPosX FinalPosY InitialKineticEnergy Default data list for each data user The default data list of each of the fifteen data users are GmStepDataHistosuA e FinalPosX e FinalPosY e FinalPosZ e FinalMomxX e FinalMomY e FinalMomZ e AccumulatedEnergyLost 113 Chapter 11 Analysis extracting data 114 AccumulatedEnergyDeposited GmStepDataTextFileUuA EventID TrackID Particle FinalPosX FinalPosY FinalPosZ FinalMomX FinalMomY FinalMomZ Accumul
154. data users implement a UserSteppingAction method which accumulates the data at each track step and a BeginOfEventAction which initializes the data to 0 the EndOfEventAction uses the accumulated data instead of extracting the data from the G4Event object The Run data users implement a EndOfRunAction method which extracts the data at the end of the run from the G4Run object For the data of type Accumulated these data users implement a UserSteppingAction method which accumulates the data at each track step and a BeginOfRunAction which initializes the data to 0 the EndOfRunAction uses the accumulated data instead of extracting the data from the G4Run object Behaviour as a function of output format The behaviour of each of the data users for each of the output type provided is the following Histograms the histogram data users i e GmStepDataHistosUA GmTrackDataHis tosuA GmEventDataHistosuA GmRunDataHistosuA GmSecondaryTrackDataHisto sUA fill histograms with the data values By default 1 dimensional histograms are filled but if several data are used at the same type other histogram types are pos sible if a 2 dimensional histogram is required the names of the two data have to be separated by vs if a 1 dimensional profile histogram is required the names of the two data have to be separated by prof if a 2 dimensional profile histogram is required the names of the three data have to be separated by vs and prof For exa
155. dded to a user action by simply adding their names in the user command where an action is selected See section on Filters to get a list of the available filters in GAMOS and how to add parameters to a filter If the filter you are using is a step filter and your user action is a stepping user ac tion the method SteppingAction will only be called if all the filters accept the step If the filter you are using is a track filter it affects the callings to the PreUserTrackingAc tion and PostUserTrackingAction for tracking actions and ClassifyNewTrack for stacking actions For example gamos userAction GmTrackDataHistosuA GmGammaFilter will only produce histograms for tracks whose particle is a gamma Adding a classifier One classifier can be added to a user action by simply adding their names in the user command where an action is selected See section on Classifiers to get a list of the available classifiers in GAMOS and how to add parameters to a classifier It is up to the concrete user action to use the classifiers or not See examples in this User s Guide For example gamos userAction GmTrackDataHistosuUA GmClassifierByParticle will produce a different set of histograms for each particle type User action name The name of the user action is the name of the class itself plus the name of the fil ters in the order which they are given in the user command plus the name of the classifier all separated by underscore characters
156. de and are inspired in the MCNP tests The tests are based in the analysis of the sum of scores at the end of each event The following variables are printed about the sum of scors EFFICIENCY Proportion of events that have a non zero value MEAN Average value VAR variance of values SD standard deviation e R The estimated relative erro SD MEAN sqrt number of values SHIFT Shift in the midpoint of the confidence interval to a higher value SUM Xi MEAN Xi MEAN Xi MEAN N Number_of_non_zero_values MEAN MEAN MEAN 2 VAR N e VOV Variance of variance SUM Xi MEAN Xi MEAN Xi MEAN Xi MEAN N Number_of_non_zero_values MEAN MEAN MEAN MEAN VAR VAR 1 N e FOM Figure of merit 1 R R CPU_time_of_last_event e THE LARGEST VALUE and where in which event it happened To get a feeling of how big are the fluctuations the same variables i e mean variance R shift and FOM are printed again but adding to the values a new one equal to the largest value so that this value is counted twice And also the ratio of thies affected to the original ones Then the results of eight convergence tests are shown MEAN distribution is RANDOM r follows 1 std sqrt N r is monotonically decrease r is less than 0 1 r 0 0153184 VOV follows 1 std sqrt N VOV is monotonically decrease FOM distribution is RANDOM SLOPE is large enough Finalyy it prints the evolution of several variables i e t
157. duction cuts special cuts multiple scattering options as well as try some reduc tion variance techniques Cuts optimisation Please read the sections on automatic optimisation of production cuts and user limits for accelerator and dose calculation simulations Electromagnetic parameters optimisation There are many parameters that control the speed of the electromagnetic physics vs its precision Please see the web page http fismed ciemat es GAMOS RToptim to get a list of the best electromagnetic physics parameters that can optimise your simulation Particle splitting Particle splitting is a non biased variance reduction technique that may reduce the CPU time of your accelerator simulation by a big factor It basically consists on splitting the secondary particles in radiotherapy mainly gammas generated by bremsstrahlung N times so that each time a bremsstrahlung gamma is created another N 1 gammas are created at the same position with weight 1 N re sampling the energy and or angle distribution As most of the particles that reach a patient in a radiotherapy accelerator are bremsstrahlung gammas by using this technique we can spare the time simulating the original electron usually even close to 50 and we can the time tracking gammas that have small possibility of reaching the patient There are two splitting techniques implemented in GAMOS 201 Chapter 22 Radiotherapy application 202 Uniform bremsstrahlung spli
158. e e GmNumericDistributionLower Takes the value corresponding to the closest smaller value f x f x_S e GmNumericDistributionUpper Takes the value corresponding to the closest bigger value f x f x_B String distributions A string distribution is a distribution where the input values are strings e g parti cle names process names volume names and the output valeus are numbers The values must be defined in a text file similar to the one for numeric distributions two columns where the first column is a list of names and the second column the values that correspond to each name If you are using a string distribution for example to assign a value to each particle you should list in your file all particle names If a name is not found an exception will be thrown If you do not that this exception is thrown but only a warning and that the value returned is 1 you have to set the parameter gamos setParam GmvV String Distribution GetString ValueFromIndex 1 Geometrical biasing distribution Thi GmGeometricalBiasing Distribution is a special distribution that serves to do geo metrical biasing For each track step it checks if the step is at a volume boundary and if so it calculates the output value as the division between the value at the end and the value at the beginning of the step the PostStepPoint and PreStepPoint else it re turns 1 The file is supposed to contain in the first colummn the list of volume na
159. e There is a limitation on the use of touchables they cannot be used for assembly vol umes as Geant4 creates internally the physical volumes Using asterisks to get volume particle and material names In many commands described in this guide you give the name of a logical volume physical volume touchable particle or material so that GAMOS finds the corre sponding Geant4 object In case you want to apply your command to several vol umes with similar names you can use an asterisk that would mean any character For example if you have the volumes named CRYSTAL_BGO_1 CRYSTAL_BGO_2 CRYSTAL_LUYAP_1 and CRYSTAL_LUYAP_2 gamos S D assocS D2Log Vol GmSDSimple Calor CRYSTAL will associate a sensitive detector to the four volumes while gamos SD assocSD2LogVol GmSDSimple Calor CRYSTAL_BGO_ will associate a sensitive detector to the two volumes CRYSTAL _BGO_1 and CRYS TAL BGO _2 and gamos S D assocS D2Log Vol GmSDSimple Calor CRYSTAL_ 1 will associate a sensitive detector to the two volumes CRYSTAL _BGO_1 and CRYS TAL_LUYAP_ 1 Using particle names Each particle type in Geant4 is identified by a unique name No particle is created by Geant4 unless the user code does it explicitly At any time in your command file you can ask for a list of created particles with the command run particle dumpList If you 223 Chapter 26 Appendix A do this after instantiating the GAMOS electromagnetic physics list you will get the
160. e 1st hit as the one with biggest energy however other algorithms may be selected with the parameter gamos set Param CC EvtClass 1stHitAlgorithm ALGORITHM If two reconstructed hits have a summed energy which is calculated to lie within the photopeak gates the event is classified as a good Compton imaging event Then sub classification is carried out More than two reconstructed hits These events are maximum when no identification of 1st hit multiple interactions is carried out Random coincidence It is checked that each of the two reconstructed hits is built only from tracks from the same original gamma and that the hits come from the same event Scattered The event is classified as scattered outside the detector volumes if the gamma has suffered an interaction in the list of volumes defined by the parameter gamos setParam DetCountScatteringUA VolumeNames VOLUME_1 VOLUME_2 and this interaction is of one of the process types defined by the parameter gamos setParam DetCountScatteringUA ProcessNames PROCESS_1 PROCESS_2 by default Compton are Rayleigh interactions are counted and it has lost in the volumes more energy than the parameter gamos set Param DetCountScatteringUA EnergyMin ENER _MIN by default the minimal energy is 0 The ClassifyCC method returns an integer with several digits containing the event classification e Oif it is not a useful Compton imaging event 1 if it is a coincident event but not fu
161. e Ee e SE EE ENAS 219 Usine parameter Ssenari Ee E EE a R E R A 219 Checking the usage of parameters 0 ceceesesesneeseeceesesesneeneseens 219 Managing the input data files cece cece censeseeceseseseseeseseseseseseseecens 219 Random number Seed cccccccccccssssccescsssessecesssseecessecescesesssscesesseeseseesssseceeesseesessees 220 Changing the random engine c ccc eee ceeeseecensessenesenseseseseeseseecees 220 Sending several jobs in the same machine eee ee se sseeeeteneeeseseeeeeeees 221 Identifying t chables sers esane ea Na estoy 222 Using asterisks to get volume particle and material names cccceee 223 Using particle names siiis atinsa eaa a a en Eees bites 223 27 Appendix B C utilities e eesesossoseveesossoroseroecoreoreoorsovooeeserereoreoresorerroneeersersorssreeeres 227 Converting a Geant4 example into a GAMOS example s ssssssssississsessssesreesees 227 Creatine your plugi sessione iri a denies oe wee a S 228 Using a parameter in your C code ssssssssssssesisstessisrissesssesieriestessnsnesnenrensees 229 Event classification by interaction tyPes ccccccsccssseesessesescstsneesescesessstenanenees 230 Structure Of GA MOS amp aeeoe dicts cc cucnes lous Siac sce cite ovebe booth A ar A sesso 231 viii Bibliography Chapter 1 Introduction About this document This manual refers to GAMOS version 3 0 0 It is written in DocBook and it is main tain
162. e Geant4 file source materials src G4NistMaterialBuilder cc The full list is the following G4_A 150_TISSUE G4_ACETONE G4_ACETYLENE G4_ADENINE G4_ADIPOSE_TISSUE_ICRP G4_AIR G4_ALANINE G4_ALUMINUM_OXIDE G4_AMBER G4_AMMONIA G4_ANILINE G4_ANTHRACENE G4_B 100_BONE G4_BAKELITE G4_BARIUM_FLUORIDE G4_BARIUM_SULFATE G4_BENZENE G4_BERYLLIUM_OXIDE G4_BGO G4_BLOOD_ICRP G4_BONE_COMPACT_ICRU G4_BONE_CORTICAL_ICRP G4_BORON_CARBIDE G4_BORON_OXIDE G4_BRAIN_ICRP G4_BUTANE G4_N BUTYL_ALCOHOL G4_C 552 G4_CADMIUM_TELLURIDE G4_CADMIUM_TUNGSTATE G4_CALCIUM_CARBONATE G4_CALCIUM_FLUORIDE G4_CALCIUM_OXIDE G4_CALCIUM_SULFATE G4_CALCIUM_TUNGSTATE G4_CARBON_DIOXIDE G4_CARBON_TETRACHLORIDE G4_CELLULOSE_CELLOPHANE G4_CELLULOSE_BUTYRATE G4_CELLULOSE_NITRATE G4_CERIC_SULFATE Chapter 3 Geometry G4 G4 ESIUM_FLUORIDE ESIUM_IODID G4_CHLOROBENZEN G4_CHLOROFORM G4_CONCRETE G4_CYCLOHEXANE G4_1 2 DICHLOROBENZENE G4_DICHLORODIETHYL_ETHER G4_1 2 DICHLOROETHANE G4_DIET H G4_N N DIMETHYL FORMAMIDE E i sat Be ae Ze CI e uC G4_DI G4_ETHANE G4_ETHYL ALCO
163. e angle between the initial and the final direc tions i e acos InitialDir FinalDir In contrast the DirChangeXXX are calculated substraction the final minus the initial direction what gives a 3 dimensional vector from which the X Y Z Mag magnitudes are obtained Energy The energy data are a miscellaneous set of data that extract some information about energy They have in common that the histogram limits are 0 MeV to 1 MeV They are the following e InitialKineticEnergy e FinalKineticEnergy e KineticEnergyChange e InitialTotalEnergy e FinalTotalEnergy 121 Chapter 11 Analysis extracting data 122 Plus some data of type Accumulated e AccumulateEnergyLost e AccumulatedEnergyDeposited e AccumulatedDose This is the energy deposited divided by the volume mass e AccumulatedKerma This is the sum of energies of the charged secondary particles produced by non charged particles divided by the volume mass Geometrical objects These are string data that extract the name of different geometrical objects and also the type of solids Box Tubs Polycone All of them have 25 characters when written in a binary file There is also an integer data for the copy number of physical volumes They are the following Initial Solid FinalSolid InitialLogical Volume FinalLogical Volume Initial Physical Volume FinalPhysical Volume Initial Touchable FinalTouchable InitialRegion FinalRegion InitialMater
164. e at the end of each event to convert the digits or hits into reconstructed hits and the second one at the begin ning of each event to clear the reconstructed hits of the previous event You can then convert your reconstructed hit builder into a GAMOS plug in To learn how to do this see the instructions in the section Creating your plug in using the GmRecHitBuilderFactory After this you select it with the command gamos recHitBuilder MY_RECHITBUILDER Examples of reconstructed hit builders If you do not need to simulate in detail the electronics of your detectore you may use one of the simple reconstructed hit builders implemented in GAMOS which serve to merge hits that are close to each other The energy of the reconstructed hit is the sum of the hit energies while the position is the position of the biggest enrgy hit The position can be set as the weighted sum of the hit positions weighted by the energy of each hit if the following parameter is set gamos setParam SD RecHit PosAtBarycentre 1 This can be useful for example for recovering the total energy of a photon when it has suffered a Compton scattering near the photoelectric interaction the user has always the freedom to choose how near the other hits are or for clustering together 81 Chapter 7 Sensitive Detector and Hits all the energy depositions of the particle shower produced by the electron following a photoelectric interaction The merging of this is al
165. e detector Detector effects Energy resolution If you use one of the GAMOS sensitive detectors or you inherit your own one from GmVSD you can smear automatically the energy of the hits for each detector type with a gaussian given by the value of the parameter gamos setParam SD EnergyResol sDTYPE VALUE where SDTYPE is the type of the sensitive detector A more complicated energy resolution can be implemented corresponding to a more realistic calorimeter resolution Apart from the constant term described above en ergy independent that may be due to calibration errors non uniformities and non linearities in photomultipliers proportional counters ADC s etc two other terms can be defined 77 Chapter 7 Sensitive Detector and Hits 78 The first one is a term where the relative gaussian error is inversely proportional to the square root of the energy a term that can be attributed to the statistical fluctua tions in the energy loss and multiple scattering during the shower development sigma E K sqrt E where K can be set with the parameter gamos setParam SD EnergyResolFluct sDTYPE VALUE where SDTYPE is the type of the sensitive detector In the second term the relative gaussian error is inversely proportional to the en ergy and it can be attributed to instrumental effects being rather energy independent noise pedestal sigma E K E where K can be set with the parameter gamos setParam SD EnergyResolInstr
166. e for later use in any tag oP e parameter name e parameter value You can then use the parameter as parameter_name Example P InnerR 12 VOLU yoke TUBS Iron 3 InnerR 820 1270 Units Any value in a tag has a default unit that depends on the dimension of the value automatically known by the parser The default units are the following length mm angle degrees density g cm3 atomic mass g mole temperature kelvin pressure atmosphere The user can override the default value of a unit by indicating the unit of each value This can be done adding at the end of the value the unit name see CLHEP file Units SystemOfUnits h preceded by a character e g 3 mm 1 4 rad 31 Chapter 3 Geometry Arithmetic Expressions For any value you want to define in a tag you can use the most common mathematical expressions instead of directly writing the figures e g 3 sin 8 2 3 5 3 4 7 log 3 You can also use parameters and units in the expressions e g 7 2 RADIUS mm X_LENGTH 1 5 cm If you use a regular expression remember that there can only be a unit in the whole expression and it must be at the end The regular expressions used include their meaning is evident sin cos tan asin acos atan atan2 sinh cosh tanh sqrt exp log log10 pow Including other files You can nest several files by using the include directive anywhere in your geometry
167. e many ways of sending many jobs together in a machine Here we propose a simple but flexible script that may facilitate this task This script is written in the Unix command language bash and it just needs the utility awk a data extraction and reporting tool which is available on any Unix or MacOS operative system The example has four input parameters that the user has to give energy random seed number of events number of jobs The four parameters will be converted to internal variables set the variables read from the command line ENERGY 1 SEED 2 NEV 3 NJOBS 4 Then the loop to the number of jobs is started start the loop of jobs nj 0 while test nj lt SNJOBS do A different suffix for each job is created which will be added to the new name of the input file as well as to the output file name defined inside the input file set the suffix of the output files SUFFIX 1 2 3 nj echo SUFFIX SUFFIX The input file is copied into a new one so that you can keep a track of the different files that are run copy the input file into a new one so that you can keep a track of the different files that are run new_inputfile exercise2 SUFFIX log_inputfile zz _ new_inputtfile echo The new input file new_inputfile The awk tool is used to substitute the scrip input variables in the GAMOS input file substitute in the input file the variables from the command line 221 Chapt
168. e name gamos setParam SPECT EvtClass Collimator Volume VOLUME_NAME Then the user action counts how many reconstructed hits have this energy within a precision given by the two parameters gamos setParam SPECT EvtClass EPrecMin ENERGY_MIN gamos setParam SPECT EvtClass EPrecMax ENERGY_MAX where ENERGY_MIN is the minimum energy that by default takes a value of 0 7 GammaEnergy and ENERGY_MAX is the maximum energy that by default takes a value of 1 3 GammaEnergy To recover hits when one of several Compton interactions have occurred you may switch the merging of hits that are close into one You may set the distance to merge hits with the parameter gamos setParam SPECT EvtClass ComptonRecHitDist DIST DIST takes by default a value of 0 what means that no Compton hits merging will be done If you want hits merging you may select as position of the combined hits the one of the biggest energy or the second biggest or the n th biggest where the order is given by the parameter gamos setParam SPECT EvtClass SelectPosOrder ORDER ORDER takes by default a value of 1 that is the position is that of the hit with biggest energy If one good hit is finally found the event is classified as a good SPECT event Then the sub classification code enters in the game More than one hit If more than one hit is found the one that is closer to the Gam maEnergy will be taken and the event will receive a subclassification type of 2 gt 1 Rand
169. e parameter gamos setParam SCORER_NAME MultiplyByData DATA_NAME where DATA_NAME is the name of the data you want to use Multiplying by distribution 94 You can multiply the quantity you are scoring by a GAMOS distribution see section on GAMOS distributions so that before scoring the quantity value it will be multi plied by the value of that the GAMOS distribution has in that step To do it you have to use the parameter gamos setParam SCORER_NAME MultiplyByDistribution DISTRIBUTION_NAME where DISTRIBUTION_NAME is the name of a distribution you have previously created Chapter 8 Scoring Convergence testing The fact of having a small relative erro in a score does not always guarantee that it has converged to a good result This may be specially true when there are contributions of very different weights to the scorer and the high weight scores have not been properly sampling with your statistics If you suspect of a wrong behaviour you can activate the convergence test with the parameter as these tests consume some CPU time and memorey bu default they are deactivated gamos setParam SCORER_NAME ConvergenceTester CONVERGENCE_NAME where SCORER_NAME is the name of the scorer and CONVERGENCE_NAME is the name you want to give to the convergence tester which will be used in the report If you are using a point detector scorer you should substitute SCORER_NAME by GmPDS The convergence tests are taken from the Geant4 co
170. e process name that defined it is in the list given as extra parameters It does not implement the AcceptTrack method GmParticleProcessFilter accepts a track if the particle and the process that defined the step are in the list given as extra parameters The parameters must be provided as a list of pairs particle name process name It does not implement the Accept Track method GmCreatorProcessFilter accepts a track if the process that defined it is in the list given as extra parameters It does not implement the AcceptTrack method GmFilterFromClassifier accepts a track if the classifier given as first parameter re turns a value equal to the second parameter It does not implement the AcceptTrack method Chapter 12 Filters Volume filters These are a set of filters that accept tracks under one of the following conditions In particle is in a volume Enter particle is entering a volume AcceptTrack method returns always false Exit particle is exiting a volume AcceptTrack method returns always false except in the case where one of the selected volumes is the world and track is exiting it Traverse particle traverses a volume it does neither enter nor exits it Start particle is starting in a volume AcceptTrack method may only return true if it is the first step End particle is ending in a volume AcceptTrack method may only return true if the track is ending The volume names are given as extra parameters to the filter
171. e program with either one of the following flags SOE_ImageRecon PET or SOE_ImageRecon PETGauss With the PET flag the possible locations are taking uniformly from the entire LOR With the PETGauss flag the possible locations are taking from a Gauss distribution on the entire LOR where the sigma corresponds to 16 of the LOR length and the Chapter 21 Image reconstruction utilities mean is in the middle of the LOR Note this actually only makes sense in the case of a single source located at the centre of the PET detector and is mainly meant for testing purposes Input Data The input parameters are set in the parameter file ir_soe_userparameters conf DataFileName 0 CCS_Machiel CC_img out_Gamma511_A11 EventSetSize 0 With DataFileName only the third field is important the second field should be an integer that is ignored by the code The LEventSetSize parameters sets the size of the number of events that are main tained in memory at the same time The remaining number of events are stored on disk What is lost in time because of the I O is won in time and memory capacity because of smaller data set handling For data sets smaller than a few million events it should be set to 0 ie all events are kept in memory Iterations The number of iterations is set in the parameter file ir_soe_userparameters conf m_iterations 100000 Geometry The geometry parameters are set in
172. e section on Identifying Compton interactions If two hits are found it will be checked that their relative time difference is less than the value given by the parameter gamos setParam PET EvtClass CoincidenceTime COINCIDENCE_TIME which by default takes a value almost infinite it is assumed that one of the two started the trigger and the other must be in the coincidence time opened at that mo ment If two 511 keV hits are finally found the event is classified as a good PET event Then the sub classification code enters in the game e More than two 511 keV hits If more than two hits are found the two that are closer to 511 keV will be taken and the event will receive a subclassification type of 3 gt 2 e Random coincidence It is checked that each of the two 511 keV hits is built only from tracks from the same original gamma and that the two hits come from the same event e Scattered The event is classified as scattered if any of the 511 keV gammas has suffered an interaction in the list of volumes defined by the parameter gamos setParam DetCountScattering UA VolumeNames VOLUME_1 VOLUME _2 and this interaction is of one of the process types defined by the parameter gamos setParam DetCountScatteringUA ProcessNames PROCESS_1 PROCESS_2 by default Compton are Rayleigh interactions are counted and it has lost in the volumes more energy than the parameter gamos setParam DetCountScatteringUuA EnergyMin ENER_MIN
173. ed at the following address http fismed ciemat es GAMOS GAMOS_doc GAMOS 3 0 0 GamosUsersGuide_V3 0 0 pdf We will use through this manual many terms common to the Monte Carlo simula tion terminology and specifically to the Geant4 1 terminology If you are new to it please read before for example the Geant4 documentation 2 We have tried though to make this manual self consistent and we hope that unless you need a deep knowledge of the Geant4 software you will not need to refer to any further documentation If you find that some of the instructions given here do not give the expected result please use the GAMOS bug report system http telemaco ciemat es bugzilla and detail the problem the GAMOS version and providing as much information as possible We will also warmly welcome any kind of comment or suggestion you would like to send us about this guide or about the GAMOS functionalities or user interface If you have some questions about something you do not understand or want to ask for some new functionality in GAMOS please use the GAMOS Discussion Forum http groups google com group gamos_users Introduction to GAMOS The acronym GAMOS stands for Geant4 based Architecture for Medicine Oriented Sim ulations It is therefore a Monte Carlo simulation software and it is based on the Geant4 toolkit 1 The objective of GAMOS is to provide a software framework that serves the unexperienced user to simulate his
174. efore gif If you want another format different than gif you may edit the compareAll C file and change the histogram name 107 Chapter 10 Histogramming You may also run the file without opening a ROOT session by typing beware the inverted slashes root b p q x compareAll C MYFILE root Creating your own histogram Notes 108 When you write your histogram in C you just have to take care of creating and filling it The class GmAnalysisMgr will take care of automatically writing it in the file format you chose To use GmAnalysisMer you have to instantiate it in your histogram class passing to it the name of your file you may use the same name for several of your histogram classes or different ones GmAnalysisMgr myAnaMgr GmAnalysisMgr GetInstance MY_FILE_NAME There are four types of histograms currently supported by GAMOS 1 dimensional 2 dimensional profile 1 dimensional and profile 2 dimensional To create your his togram and register it to GAMOS you have to create it with a line like myAnaMegr gt CreateHistolD HNAM NBINS MAXBIN MINBIN HIS_NUMBER myAnaMgr gt CreateHisto2D HNAM NBINSX MAXBINX MINBINX NBINSY MAXBINY MINBINY HIS_NUMBER myAnaMgr gt CreateHistoProfilel DDHNAM NBINS MAXBIN MINBIN HIS_NUMBER myAnaMegr gt CreateHistoProfile2D HNAM NBINSX MAXBINX MINBINX NBINSY MAXBINY MINBINY HIS_NUMBER The last argument is the histogram number that can be later used to r
175. em anywhere in your simulation by using the command gamos base printParameters Usage LEVEL If LEVEL takes a value gt 0 you will get the same list as above If LEVEL takes a value gt 1 you will get a list of parameters that are using the default value you may then check if this list contains one of the parameters whose value you thought you have changed This list looks similar to this one 6 PARAMETERS USING DEFAULT VALUE DEFINED IN C CODE BUT VALUE NOT DEFINED IN SCRIPT PARAMETER Generator Isotope FileName PARAMETER GmCountTracksUA FirstEvent If LEVEL takes a value gt 2 you will get a list of how many times each parameter have been used This list looks similar to this one NUMBER OF TIMES EACH PARAMETER IS USED IN C CODE PARAMETER GmCountTracksUA EachNEvent TIMES USED 1 PARAMETER GmGeometryFromText FileName TIMES USED 1 219 Chapter 26 Appendix A Managing the input data files To run an example you will probably need some input data like for example the file describing the geometry the list of isotopes etc You can set the name of your file in your script but you do not need to tell the path where to look for it An environmental variable called GAMOS_SEARCH_PATH con tains the list of directories where GAMOS will look for your file The directories are
176. en event step and secondary track data vectors equal to the number of steps for the same event Filter from data It is possible to use any GAMOS data to filter on its value see chapter on Filters To use it you have to use the command to define a filter using the filter named GmNu mericDataFilter if the data is of numeric type int or float and GmStringDataFilter if the data is of string type and passing the following arguments GmNumericDataFilter In this case after the filter name you have to give the the mini mum and maximum value of the data For example gamos ffilter dataF GmNumericDataFilter InitialKineticEnergy 0 0 3 GmStringDataFilter In this case after the filter name you have to give the list of ac cepted values For example gamos filter dataF GmStringDataFilter InitialLogical Volume detector world Classifier by data It is possible to use any GAMOS data to classify on its value see chapter on Classi fiers To use it you have to use the command to define a classiifier using the clas sifier named GmClassifierByNumericData if the data is of numeric type int or float and GmClassifierByStringData if the data is of string type and passing the following arguments 117 Chapter 11 Analysis extracting data Data is integer or float In this case after the classifier name you have to give the min imum data limit the maximum data limit and the step or interval For example to define 0 5 MeV energy interva
177. en the mo mentum vector is rotated around the X axis by ANG_X around the Y axis by ANG_Y and around the Z axis by ANG_Z and finally the position vector is rotated around the X axis by ANG_X around the Y axis by ANG_Y and around the Z axis by ANG_Z An alternative way to provide the initial rotation and displacement is by setting the transformation The transformations are set with the parameter gamos setParam RTGeneratorPhaseSpace Transformations TYPE_1 VAL1_1 VAL2_1 VAL3_1 TYPE_2 VAL1_2 VAL2 2 VAL3 2 Several transformations can be set at the same type with this parameter and they will be executed in the order provided For each transformation four parameters have to be supplied transformation type first value second value third value Three types of transformation are supported Displacement D the three values are the displacement in X Y and Z Rotations around XYZ RXYZ the three values are the angles of rotation around the X Y and Z axis always executed in this order Rotation around accelerator axis RTPS the three values correspond to the angles of rotation in theta phi and around the accelerator axis itself in other words a rotation around the Z axis is done with angle VAL3 then a rotation around Y with angle VAL1 and finally a rotation around Z with anlge VAL2 If the number of phase space particles is not enough to calculate the dose in the phan tom with enough precision you may reuse the partic
178. er gamos setParam SD Minimum1HitEnergy SDTYPE VALUE and all the hits with energy value sum of all the energy depositions of all tracks contributing to it less than VALUE will not be considered If you want to do it at the level of reconstructed hits you have firsr to set the param eter gamos setParam SD RecHit MinimumEnergy SDTYPE VALUE Then you have to select among four different possible behaviours to delete the hits that form the reconstructed hit hits are not really deleted but they are not taken into account to form the reconstructed hit gamos setParam SD RecHit MinimumEnergyBehaviour sdtypeSDTY PE BEHAV_TYPE where BEHAV_TYPE can be e DeleteSmall if a hit has small energy it is not considered e Deletelf1Small if one of the hits in the reconstructed hits has small energy all are deleted e AcceptIf1Big if one of the hits in the reconstructed hits does not have small energy all are accepted e AcceptAll all hits are accepted i e minimum hit energy is not taken into account Hits digitization and reconstruction 80 Hits digitization The conversion of the hits into digital signals is very dependent on the detector Therefore GAMOS just provides a general class GmVDigitizer The user may inherit her his own digitizer from it and implement the two methods virtual std vector lt GmDigit gt DigitizeHits const std vector lt GmHit gt amp virtual void CleanDigits Chapter 7 Sensitive
179. er statistical processing sum of flux values squared and to the third and fourth power After all energies comes a line with the total sum of flux in all energies which has the filter names classifier name particle type detector name and copy score type the words FLUX_TOTAL particle followed by the total flux value and relative error and the total number of particles contributing to the flux If the dose equivalent magni tudes are required they come at the end in a line starting also with the filter names classifier name particle type detector name and copy and score type followed by the magnitude name Hstar Hp 10 0 Hp 10 15 An example output is the following A P SCORE IN POINT DETECTOR FOR set ALL NeutronInelastic gamma PD1 ALL at 4800 0 0 ALL NeutronInelastic gamma PD1 ALL ENERGY 0 01 FLUX 0 REL 0 N 6 Fwei2 0 Fwei3 0 Fwei4 ALL NeutronInelastic gamma PD1 ALL ENERGY 0 015 FLUX 0 REL 0 N 0 Fwei2 0 Fwei3 0 Fwei4 ALL NeutronInelastic gamma PD1 ALL FLUX_TOTAL particle 1 33272e 13 REL 0 97118 N 12 ALL NeutronInelastic gamma PD1 ALL Hstar 1 49381e 13 pSv particle Control Histograms There are several optional histograms that may help you in better understanding the behaviour of your point detector scoring By default they are created but you can switch them off with the parameter gamos setParam GmPDS ControlHistograms 0 100 Chapter 8 Scoring All histograms start with the
180. er 26 Appendix A awk v ENERGY ENERGY v SEED SEED v NEV NEV v nj nj v SUFFIX SUFFIX if 1 run beamOn printf s s n 1 NEV else if 1 gamos random setSeeds printf s s s n 1 SEED SEED n j else if 2 RTPhaseSpaceUA FileName printf s s s n 1 2 test SUFFIX else if 1 gamos generator addSingleParticleSource printf s s s Ys n 1 2 63 ENERGY else print 0 F exercise2b in gt new_inputfile inn You can observe that each of the variables that are going to be used by awk have to be passed with the v option The awk will loop through the lines in the input file and will make the substitutions For example the line else if 2 RTPhaseSpaceUA FileName printf s s s n 1 2 test SUFFIX means that it looks for a line whose second word is RTPhaseSpaceUA FileName and then substitutes this line by three words three s the first two are left intact and the third one is substituted by the value of the SUFFIX preceded by test Finally the job is sent in background You may run it in foreground what means that you have to wait until a job finish to start the next one run job in background gamos new_inputfile inn 2 gt amp 1 tee log_inputfile amp run job in foreground gamos new_inputtfile inn 2 gt amp 1 tee log_inputfile If for example you want to run 40 jobs in your 4 core machine you should not run them all in
181. er of ancestors include the detector itself so that you can tell GAMOS to consider dead only the crystal itself by setting this parameter to 1 The parameter gamos setParam SD DeadTimeDUListByBlock NShift N_SHIFT controls the number that each multiplied by each ancestor level which should be bigger than the number of volume copies see section on Identifying each sensitive detector copy A warning is due here the hits that belong to the same block are identified by the detector unit ID so if you are using a bigger number of ancestors you should take care that the hit detector unit ID takes into account a number of ancestors as least as big as the number used here see section on Hits 79 Chapter 7 Sensitive Detector and Hits You also have the option to define your detector as paralizable default or non paralizable by setting the parameter gamos setParam SD DeadTimeParalizable sDTYPE TRUE FALSE In a non paralizable detector an event happening during the dead time since the previous event is simply lost while in a paralizable detector an event happening during the dead time since the previous one will not just be missed but will restart the dead time Minimum hit energy You may set a threshold to the minimum hit energy so that hits with smaller energy will be deleted This can be done at the lvevel of hits or at the level or reconstructed hits If you want to do it at the level of hits you have to use the paramet
182. er of reconstructed hits in absorber detector e Sum energy for the classified events Compton camera output for reconstruction To write data to a file the following parameter must be set to 1 gamos set Param CC EvtClass DumpEvent 1 If the event is classified as a Compton imaging one it is dumped in a file given by the name gamos setParam compcam FileName MY_FILENAME You can select the file format to be a binary file or a text file by setting to 1 or 0 the parameter gamos setParam compcam BinFile 1 0 that takes the name compcam out by default It is necessary to define whether the out put file should contain only data for single single Compton imaging events 2 recon structed hits or those events which contain the multiple reconstructed hits through the parameter gamos setParam CC EvtClass DumpSingles TRUE FALSE gamos setParam CC EvtClass DumpMultiples TRUE FALSE where TRUE writes the data to the file compcam out The variables written are given by the structure struct CCOutput char name 9 float xl yl zl el x2 y2 22 e2 where name is COMPCAM x1 y1 z1 e1 are the coordinates and energy of the recon structed hit in the scatterer detector and x2 y2 z2 e2 are the coordinates and energy of the reconstructed hit in the absorber detector The same data that is written to the file can be written in the standard output if the parameter gamos setParam compcam DumpToCout TRUE is set to true The pos
183. erbosity e 0 Prints number of entries mean RMS underflow and overflow e 1 Prints number of entries mean with error RMS with error underflow and over flow lt e 2 Prints number of entries mean with error RMS with error underflow and over flow lt Also number of bins axis lower and upper edges Histograms in CSV format The CSV Comma Separated Value format is a simple text file where the values are separated by commas The utility of this format is that it can be easily read by any analysis package Excel Origin Matlab and converted to its own format The information written in GAMOS is the following e Histograms 1D The first word is HISTO1D then the following info is dumped his_name number_of_bins Xaxis_minimum Xaxis_maximum bin_contents number_of_entries mean RMS The bin_contents is the list of entries in each bin It has indeed number_of_binsX 2 numbers as the first one is the underflow entries below axis_minimum and the last one is the overflow entries above axis maximum Histograms 2D The first word is HISTO2D then the following info is dumped his_name number_of_binsX Xaxis_minimum Xaxis_maximum number_of_binsY Yaxis_minimum Yaxis_maximum bin_contents number_of_entries smean RMS The bin_contents is the bi dimensional list of entries in each bin It has indeed number_of_binsX 2 number_of_binsY 2 numbers as the first row column is the underflow entries below axis_minimum and the
184. error by a safety number set by the parameter gamos set Param GmSDSeparateByTime BigTimeFactor SDTYPE VALUE which has a default value of 1000 hits with time higher than this number will be deleted You may decide to always keep all hits by setting the parameter gamos set Param GmSDSeparateByTime DiscardBigTime SDTYPE 0 There are other classes that serve to make a virtual segmentation when you have a big sensitive volume that you want to segment in different pieces although you have not segmented it in your geometry The only class currently implemented is e GmSDVirtSegmBox It divides a box into voxels of equal size in X Y and Z Several parameters control its use Number of divisions in X Y and Z gamos setParam SD VirtSegmBox NDiv SDTY PE NDIV_X NDIV_Y NDIV_Z 75 Chapter 7 Sensitive Detector and Hits 76 where SDTYPE is the type of the sensitive detector Widths of the voxels in X Y and Z gamos setParam SD VirtSegmBox Width sDTY PE WIDTH_X WIDRH_Y WIDTH_Z It must be taken into account that the product NDIV WIDTH has to be equal to the total length of the mother box in each of the three coordinates If this is not the case when a step happens near the positive border it will be assinged a division number bigger that NDIV and an exception will be thrown For efficiency a maximum number of voxels in each direction is allowed you may change it with the parameter gamos setParam SD VirtSegmBox MaxN Voxels SDTYP
185. es the same formula but the sum of squares is not done summing the contribution of the particles of the same event but squaring each contribution individually Calculating the errors makes it necessary to store the square of the weights increasing substantially the memory usage and CPU time If you want to deactivate this option for a scorer use the command gamos scoring scoreErrors SCORER_NAME FALSE SCORER_NAME is one of the scorers defined above As mentioned above the errors that are calculated taking into account the number of events You have to be careful then if you set to off the option of scoring by event and keep on the option of calculating the errors In the default GAMOS scorer printers the errors are printed are relative i e the error divided by the value so no caution is necessary but be careful if you define a printer yourself Each scorer has a default unit see section below but it can be overridden with the command gamos scoring scorerUnit SCORER_NAME UNIT_NAME UNIT_VALUE Scorer classes 85 All the available scorers in Geant4 are also available in GAMOS The classes have been slightly changed to provide the extra functionality The scorers can be classified in the following types e Track length scorers e GmG4PSTrackLength The track length is defined by the sum of step lengths of the particles inside the cell i e the volume where the scoring happens A particle weight is not applied by default
186. esenesseseseseseseseseseeeseeceeeed 61 Other physics ists pirenen ssai aeee a Aesan AE a E ETER E ar ES 61 Building your physics list with C code s sssssssssssssssessessssssesiesressesresnesnsseesesses 62 Replacing process models sesssssssssssssessessiestsssessestestinsessesssnstenieseessesnesnesnereeneenes 62 Producton ctts a eain a Bk aie Rech dete Oli ol Beste ois wel EN 63 Production cuts by region oo cece cee cesses seeseseesessseesesssesesescsseeseecsnee 63 Energy cuts to range cuts CONVELSION ceesescsseseeeseneneteteteseesesesesesesesesees 64 Minimum and maximum production cuts cceccessseesesessneesescteeeeeeeees 64 Apply cuts forall processes is csirsierrassansssdiserercpaecctanteadieceniasen se dienes 64 User limits pacien aee siete elo in eins iibhn Baie einen 64 Automatic optimisation Of CUtS ccccccecsseseseesesssceteeseseecesesssesnsnesesceeesesesnaeneeees 65 Range rejection oymi oo EA E EE E nck betes cesta sticscaue esas eis aeseotad 66 Optical PhotoNSsn sessir aaa a eoe Aaa Aeae saa ES E T na S 67 Using optical photons as primary generator ss ssessiesiesiessissessesseeriereeses 70 Xray refrac oshere panee eia re aa AR a NEEE E eh oat a eanan 70 Atomic deexcitation processes ss es esissiesesseesrestestirissesstsstesiestessesresntsneereeneenes 70 DQCAY IE R RE E AEA casbiy Valens dip evensshana Teets reyes 71 Radioactive decay Process ipsia i a r 71 Cerenkov processies a aa
187. etUA computes the material budget along each track and writes in the file matbud root csv the following histograms 1D Profile histogram of material budget in position X Position X 1D Profile histogram of material budget in position Y Position Y 1D Profile histogram of material budget in position Z Position Z 2D Profile histogram of material budget in positions X and Y Position XY 2D Profile histogram of material budget in positions X and Z Position XZ 2D Profile histogram of material budget in positions Y and Z Position YZ Detailed report of where CPU time is spent You may get a detailed report of where the CPU time is spent by instantiating the user action gamos userAction GmTimeStudyUA CLASSIFIER_1 CLASSIFIER_2 By selecting different classifiers you can get a report of the time spent by each particle in each logical volume in each energy bin etc see section on Classifiers The table will have a format similar to the following one o o 6 6 TIMING RESULTS for timer GmTimeStudyUA_ClassifierByParticleAndKinE o GmTimeStudyUA_GmClassifierByParticle_GmClassifierByKineticEnergy e 0 0001 0 001 User 0 Real 0 Sys 0 01 e 0 001 0 01 User 0 07 Real 0 16 Sys 0 e 0 01 0 1 User 1 3 Real 1 48 Sys 0 04 e 0 1 1 User 74 66 Real 78 74 Sys 1 17 e 1e 05 0 0001 User 0 Real 0 Sys 0 e le 06 le 05 User 0 Real 0 Sys 0 e 0 0001 0 001 User 0 5
188. etrieve this histogram from any method in any class If you don t set it GAMOS will assign it automatically starting from 1 Once a histogram is registered you can get a pointer to it by asking GmAnalysisMgr for a histogram by its number or its name myAnaMer gt GetHistol HIS_NUMBER gt Fill value myAnaMegr gt GetHisto2 HIS_NUMBER gt Fill value myAnaMegr gt GetHistoProfilel HIS_NUMBER gt Fill value myAnaMegr gt GetHistoProfile2 HIS_NUMBER gt Fill value or similarly if you want to retrieve it by the histogram name 1 A profile histogram sets the value of a bin as the average of all entries in that bin and the error as the RMS of these entries Chapter 11 Analysis extracting data Introduction GAMOS data There is a big variety of data that can be extracted out of a simulation position energy lost event ID particle name angle between primary and secondary We have transformed each of these data into a plug in so that it can be used iwth a user command to fill an histogram be dumped into a text or binary file filter on an interval of its values make a clssification as a function of the data value intervals or use them for importance sampling A GAMOS data plug in may return a different value depending on when it is called The following options are possible e At each track step e At the beginning of a track e At the end of a track e At the beginning of a event e At the end of a event e At
189. ety range vs the logarithm of the range To distinguish the cases where the range is bigger than the safety no range rejection those cases are plotted in the bins 15 to 5 while the cases where the range is smaller than the safety occupy the bins 5 to 5 if there is a case not likely for a radiotherapy simulation where the log10 fabs safety range is smaller than 5 of course before the 10 substraction it is set to 5 and if is bigger than 5 it is set to 5 Optical photons You may add the physics of optical photons to any physics list including the com mand gamos physics addPhysics opticalPhoton This will activate the scintillation process for all the particles and the G4OpAbsorption G4OpRayleigh and G4OpBoundaryProcess processes for optical photons To avoid blowing up the memory by the thousands of optical photons that may be created at one step by default the secondary optical photons are tracked at the moment they are created this means that the primary particle is stopped and later it is restarted You may deactivate this option with the parameter gamos set Param GmPhysicsOpticalPhoton TrackSecondariesFirst 0 The yield factor i e the number of optical photons created per MeV is set by default to 1 you may change it with the parameter gamos setParam GmPhysicsOpticalPhoton YieldFactor FACTOR To define the optical properties of the medium you must create a G4MaterialPropertiesTable which is linked to the G4Materi
190. f the hit Hits If you have activated any of the GAMOS sensitive detectors each time a track de posits some energy in any copy of the selected logical volume you can indeed select several volumes by repeating the command a GmHit will be created If the energy deposition happens in the same volume copy a real one or a virtual one in case of a virtually segmented sensitive detector than a previous one in the same event a new hit is not created but the existing hit is updated adding to it the new energy deposition The GmHit stores the following variables long int theDetUnitID Identification of the touchable G4int theEventID Event number G4double theEnergy Total energy G4double theTimeMin Minimum time of energy depositions G4double theTimeMax Maximum time of energy depositions G4ThreeVector thePosition Position it is defined in the Sensitive detector class it can be the centre of gravity of the energy depositions the centre of the volume std set lt G4int gt theTrackIDs The list of track numbers std set lt G4int gt theOriginalTrackIDs The list of original track numbers a track is called original if it is a gamma electron or positron and it is a primary particle or if it is a gamma created in an original positron annihilation std vector lt GmEDepo gt theEDepos The list of energy depositions A GmEDepo contains the energy and position of each step G4String theSDType The type of sensitiv
191. faces LV_NAME1 LV_NAME2 The position is distributed randomly in the surface of one or several volumes of the Geant4 geometry The user must add a number of extra parameters with the list of volume names The volumes can be physical volumes or touchables Chapter 4 Generator This distribution can only be used if the volumes are G4Box G4Orb G4Sphere G4Tubs or G4Cons 8 Position in a user defined volume surface gamos generator positionDist SOURCE_NAME GmGenerDistPositionInUser Surfaces POS_X POS_Y POS_Z ANGX ANG Y ANG Z SOLID_TYPE SOLID_DIMENSIONS The particles are randomly distributed in a volume surface of a volume defined by the user The user must provide the definition of the volume as extra parameters SOLID_TYPE can be Box Orb Sphere Tubs Cons SOLID_DIMENSIONS are the solid dimensions For the order and meaning of the solid dimensions please look at the corresponding Geant4 solid By default the volume is placed at position 0 0 0 If you want it placed at a dif ferent position you have to add three optional extra parameters POS_X POS_Y POS_Z By default the volume is not rotated If you want it rotated you have to add three optional extra parameters and always add the three positions even if they are 0 0 0 ANG_X ANG_Y ANG_Z Those angles are interpreted rotating the volume first around the X axis then around the Y axis and finally around the Z axis around the 0 0 0 point after the displacement is
192. fault if it is a list of strings Event classification by interaction types There is a utility in GAMOS that helps you in counting and classifying the tracks by the type of interactions they have suffered You just have to create at each step a new GmTrajPoint and at the end of track pass this list to a GmVSimuEventClassifier that will return the classification You can see an example at GamosCore GamosAnalysis src GmHistosGammaAtSD cc that we explain here in detail This class counts the type of interaction of the photons in the sensitive detectors of your geometry The first thing it does at the PreUserTrackingAction is checking if the current track is an original gamma To do this it gets the help of the GmCheckOriginalGamma class that classifies the gammas as e 0 not an original gamma e 1 itis a primary particle created at the beginning of the event e 2 is is created at the annihilation of the positron it is assumed that the positron is a primary particle At each step the UserSteppingAction method checks that it is inside a volume declared as sensitive detector In this case it adds a new GmTrajPoint for this track with all the information of the track at this moment plus it adds at the beginning another point with the vertex information At the end of track if it is an original gamma it asks the class GmClassifierByInterac tion to classify it based on the type and number of interactions The me
193. ference is another funda mental parameter which limits the axial distance between the two planes rings of a detected PET coincidence It is used to discard lines of response which are too axially tilted since these events can deteriorate the image quality with some reconstruction Chapter 18 PET application methods By default value 1 all axial planes are included the number of planes which defines the maximum ring difference can be changed with gamos setParam PET ProjData MaxRingDiff MY_MRD The projection data file name without extension is given by gamos setParam PET ProjData Filename MY_PROJDATA_FILE that takes the name default_sino3D by default PET histograms positrons These histograms are related to the original positron and the two secondary gammas created at its annihilation They are produced if the user action PETHistosPositron is activated with the command gamos userAction PETHistosPositron The name of all these histograms starts with PETPositron and all are written in the file pet root csv The histograms are the following Positron energy at creation e initial energy keV Positron range e range mm Positron energy at annihilation e energy at annihilation keV Positron energy at creation vs range e initial energy keV vs range mm Positron energy at annihilation vs secondary gammas energy e e gammas vs e energy keV Positron energy at annihilation vs sum of
194. fference is that the surface is defined at the inner surface of a G4Tubs solid GmG4PSSphereSurfaceCurrent Sphere surface current is a surface based scorer and similar to the GmG4PSFlatSurfaceCurrent The only difference is that the sur face is defined at the inner surface of a G4Sphere solid GmG4PSPassageCellCurrent Passage current is a volume based scorer The cur rent is defined by the number of tracks that pass through the volume GmG4PSFlatSurfaceFlux Flat surface flux is a surface based flux scorer The sur face flux is defined by the number of tracks that reach the surface The expression of surface flux is given by the sum of W cos t A where W t and A represent particle weight injection angle of particle with respect to the surface normal and area of the surface The user must enter one of the particle directions as in GmG4PSFlatSurfaceCurrent GmG4PSCylinderSurfaceFlux Cylinder surface flux is a surface based flux scorer and similar to the GmG4PSFlatSurfaceFlux The only difference is that the surface is defined at the inner surface of a G4Tubs solid GmG4PSSphereSurfaceFlux Sphere surface flux is a surface based flux scorer and similar to the GmG4PSFlatSurfaceFlux The only difference is that the surface is defined at the inner surface of a G4Sphere solid Chapter 8 Scoring e GmG4PSCellFlux Cell flux is a volume based flux scorer The cell flux is defined by a track length L of the particle inside a volume div
195. files Example include mygeom2 txt Combining C and ASCIl files If you want to define part of your geometry with C and another part with ASCII files you should follow these instructions Write a C class inheriting from G4VuserDetectorConstruction and in the Construct method build the geometry from a set of ASCII files G4tgbVolumeMgrx volmgr G4tgbVolumeMgr GetInstance volmgr gt AddTextFile mifilel txt volmgr gt AddTextFile mifile2 txt G4vPhysicalVolume physiSubWorld volmgr gt ReadAndConstructDetector You can then use the returned G4VPhysical Volume as the world volume or get its logical volume and place it inside any other logical volume You can also use the materials and volumes of the ASCII geometry in your C ge ometry retrieving them by name To retrieve the pointer of a material GmGeometryUtils geomUtils GmGeometryUtils GetInstance one volume G4LogicalVolumex world_logic geomUtils gt GetLogicalVolumes world true 0 several volumes with same name std vector lt G4LogicalVolume gt crystal_logic geomUtils gt GetLogicalVolumes crystal exists true To retrieve a logical volume GmGeometryUtils geomUtils GmGeometryUtils GetInstance 32 Chapter 3 Geometry one volume G4LogicalVolumex world_logic geomUtils gt GetLogicalVolumes world true 0 several volumes with same name std vector lt G4
196. free paths that the neutron or gamma would have to traverse along the path to reach the point detector A similar calculation is done for each neutron or gamma initial step except that the angle probability it is based on is simplified as a constant distribution in the local reference system of the parent particle i e probability equal to 0 5 Summing up these probabilities for a number of events usuallly several or ders of magnitude less than with conventional methods one can get the flux and the energy spectrum at the point detector and with these magnitude the equivalent doses H Hp 0 15 can be obtained In this chapter we describe first the theoretical basis of the method Then we explain how it is implemented in GAMOS how to select the different available options and which are the possible outputs tables or histograms In the third part we describe the several variance reduction techniques that can be used to readuce the CPU time and give some recommendations on how to use the output table and histograms to help in determining the best variance reduction techniques for a given problem Theoretical basis The point detector scorer calculates the fulx at a point based on the probability that particles reach it Suppose we call p j the probability that at a source or neu tron gamma interaction the the particle produced or scattered goes into the solid angle dQ about the direction u where u cos if R is the dista
197. from the world volume TheVERBOSE_LEVEL controls the amount of information given each level print also the information from previous level It is a two digit number each of the two controls a different verbosity The second digit the one of the units controls the information about solids and materials e gt 1 Prints logical volume name e gt 2 Prints solid name material name cubic volume and volume mass e gt 3 Prints solid parameters and visualisation attributes The first digit the one of the tenths controls the information about physical volumes e gt 1 Prints physical volume name copy number and parent volume name Chapter 3 Geometry e gt 2 Print physical volume position and rotation e gt 3 Print replica or parameterisation data if the physical volume is of this type The command gamos geometry print Touchables Print the list of all touchables and for each one touchable name solid type material name global position and rotation and local position and rotation C utilities There is a set of geometry utilities that are meant to help the user that is writing some C code to for example debug the geometry get a touchable or a volume by name etc They are all in the GmGeometryUtils class which is a singleton To use them in your C code you can do it like in the following example GmGeometryUtils GetInstance gt DumpG4LVList We list here the available methods with an explanation of their functio
198. g data cannot be used to fill an histogram It is possible to use at the same time several data to fill 2D 1D profile or 2D profile histograms To do it the data has to be separated by vs if it is for a 2D histogram prof if it is for a 1D profile histogram and both vs and prof if it is for a 2D profile histogram See section on Data users for examples on this Data can also be used in mathematical expressions for example log10 InitialKineticEnergy sqrt 2 FinalPositionX FinalPositionY Each data has as a property the histogram number of bins that for all is 100 the minimum and maximum These values can be changed as for any histogram see section on Histograms Data users 110 The data users are user actions that use the data to fill histograms or to dump them in text or binary files or dump them in the screen There is one user action for each of the five types of information objects step track event run and secondary tracks and one user action for each of the four actions making in total twenty user actions There is also a user action to dump data in a ROOT Tree its behaviour is explained in a dedicated section below We will describe in this section the available data users and how they behave with the different data types mentioned above The data can also be used to filter on an interval of values in classifiers to give a different classification index in different user defined intervals and in scorers to s
199. gement or do it the GAMOS way GAMOS offers a single command with which you can give a different initial random seed to your job so that the results are statisticaly independent gamos random setSeeds SEED_1 SEED_2 where two numbers are given to better guarantee the independence of the results SEED_1 is the initial random seed and SEED_2 is the number of times a random seed is sampled before starting the simulation You may use different or equal numbers for these two and use continuous numbers e g 1001 1002 1003 if you want Changing the random engine The random engine the algorithm that gets the random numbers may be changed with the command gamos random setEngine ENGINE_NAME Chapter 26 Appendix A Any of the engines available in CLHEP can be chosen i e DRand48Engine DualRand Hurd160Engine Hurd288Engine HepJamesRandom MTwistEngine NonRandomEngine RandEngine RanecuEngine Ranlux64Engine RanluxEngine RanshiEngine TripleRand Sending several jobs in the same machine It may often happen that you have a multi core machine and you want to run several jobs at the same time on it to accumulate statistics The approach that is explained here is to send the same job several times with different random seeds Another pos sible approach which will be available in future GAMOS releases is to use multi threading what will spare the initialisation time and reduce the memory by sharing it among the different jobs There ar
200. getting the best values Killing particles The two user actions GmkillAtStackinguA and GmkKillAtSteppinguA combined with the filtering mechanism can help you to kill those particles that you know are not affecting your result by a sensible amount For example you may kill the neutrinos produced in a radioactive decay or the electrons in an application where you are scoring neutrons Optimising the particle generation GAMOS provides a wide variety of primary generator distributions with which to simulate in detail the primary particles that correspond to your application But you may consider that some particles will not reach your detector or will reach it with a very small probability and modify your distributions so that those particles are never produced Another alternative is to use a biasing distribution see section on Biasing generator distributions Limiting the number of user actions Some of the user actions for example those that fill lots of histograms may consume anon negligible amount of CPU time Therefore a simple recommendation is to check that you deactivate all the user actions you do not need when you are making a big production of events Using variance reduction techniques 218 Several variance reduction techniques are provided by GAMOS to optimise the CPU time for specific applications See the section on Variance reduction techniques or the corresponding application Chapter 26 Appendix A Using parame
201. gy SecoKineticEnergy PrimSecoAngleChange InitialPrimKineticEnergy FinalPrimKineticEnergy GmSecondaryTrackDataTextFileuA EventID TrackID Initial PrimMinusSecoKineticEnergy FinalPrimMinusSecoKineticEnergy SecoDividedInitialPrimKineticEnergy SecoKineticEnergy PrimSecoAngleChange InitialPrimKineticEnergy FinalPrimKineticEnergy GmSecondaryTrackDataBinFileuA TrackID Initial PrimMinusSecoKineticEnergy FinalPrimMinusSecoKineticEnergy SecoDividedInitialPrimKineticEnergy SecoKineticEnergy PrimSecoAngleChange InitialPrimKineticEnergy FinalPrimKineticEnergy If you use for example GmTrackDataTextFileUA and select a data list that contains Initial and Final data they will be written at the end of the track so that they can be written in the order you set If you want a different behaviour you may use the parameter gamos setParam DATA_USER_NAME UseAtlInitial 1 Saving GAMOS data in a ROOT TTree The GmDataTTreeUA data user sorts GAMOS data in a ROOT TTree structure and save the new TTree in a ROOT TFile The GmDataTTreeUA is invoked with the usual command gamos user Action GmDataTTreeUA 116 Chapter 11 Analysis extracting data By default the TTree is created with the GmDataTTree name and saved in the GmDat aTTree root file The following command can be used to modify both both TFile and TTree names gamos setParam GmDataT TreeUA TreeFileName NEW_NAME Four categories of GAMOS data can
202. gyFromFile FILE_NAME CALCULATION_TYPE UNIT This distribution permits to use an arbitrary energy distribution The energies and probabilities are read from the file named FILENAME This file contains a list of lines with two words each ENERGY PROBABILITY The energies are given in MeV the default Geant4 unit if no unit is provided This data can be interpreted in four different ways Chapter 4 Generator e If the second parameter is fixed the energies used are only those listed For ex ample if you want a quarter of your primary particles with energy 0 5 MeV and three quarters with energy 1 MeV you can write the following file 0 5 0 5 1 0 5 If the second parameter is histogram the default value if the second argument is not provided the data read will be interpreted as that of a constant bin his togram the energies are the values of the centre of each histogram bin and the energies will be randomly distributed with the corresponding probability in the histogram bin In this case if the difference between data points is not con stant an exception will be thrown For example if you want a quarter of your primary particles uniformly distributed between 0 and 1 MeV and three quar ters between 1 and 2 MeV you can write the following file 0 5 0 25 1 5 0 75 If the second parameter is interpolate the data read will be interpreted as that of an histogram with constant or non constant bin As the bins may be not equal the behavi
203. h The user should give several extra parameters when defining the score to set the number of shells minimum and maximum radius Optionally three more parameters can be defined to set the sphere centre if not set the centre will be 0 0 0 GmPSCylindricalDoseDeposit This is a _ special case of emphasis GmG4PSDoseDeposit where the scoring volume is virtually divided in concentric cylindrical shells and each one in phi slices so that one score is given for each slice in each shell The user should give several extra parameters when defining the score to set the number of shells minimum and maximum radius and the number of phi slices minimum and maximum phi Optionally three more parameters can be defined to set the sphere centre if not set the centre will be 0 0 0 And three more optional parameters can be given to define the clinder axis which if not set will be 0 0 1 GmG4PSKerma This scorer stores a sum of particles kerma each step in the cell that is the energies of the charged secondary particles produced by non charged particles divided by the mass of the cell Current and flux scorers There are two different definitions of a particles flow for a given geometry One is a current and the other is a flux In our scorers the current is simply defined as the number of particle s with the particle s weight passing through a certain surface or volume while the flux takes the particle s injection angle to the geometry i
204. h along y at the surface positioned at dz Half length along z axis PARA parallelepiped Half length in x Half length in y Half length in z Angle formed by the y axis and by the plane joining the centre of the faces G4Parallel to the z x plane at dy and dy Polar angle of the line joining the centres of the faces at dz and dz in z Azimuthal angle of the line joining the centres of the faces at dz and dz in z TRAP generic trapezoid Half length along the z axis pDz Polar angle of the line joining the centres of the faces at pDz Azimuthal angle of the line joining the centre of the face at pDzto the centre of the face at pDz Half length along y of the face at pDz pDy1 Half length along x of the side at y pDy1 of the face at pDz Half length along x of the side at y pDy1 of the face at pDz Angle with respect to the y axis from the centre of the side at y pDy1 to the centre at y pDy1 of the face at pDz Half length along y of the face at pDz pDy2 Half length along x of the side at y pDy2 of the face at pDz Half length along x of the side at y pDy2 of the face at pDz Angle with respect to the y axis from the centre of the side at y pDy 2 to the centre at y pDy2 of the face at pDz or alternatively if your trapezoid is a simpler one you can use the parameters 17 Chapter 3 Geometry 18 e Length along z e Length along y e Length along x at the wider side e Length along x at the narr
205. h the parameter gamos scoring printer SCORER_NAME UseClassifierIndex 1 but you have to be conscient that if you do so the score will not be distributed in the voxels traversed even if the classifier is GmClassifierBy1Ancestor Other scorers are also affected by the feature of skipping voxel boundaries GmG4PSNofSecondary the score is done at the last voxel traversed while using the default classifier GmClassifierBy1Ancestor would assign it to the one corresponding to the origin of the step that is the first voxel GmG4PSNofCollision the same as GmG4PSNofSecondary GmG4PSNofStep a score is assigned to each one of the voxels traversed GmG4PSTrackCounter for the first step it is always that the track exited for inter mediate voxels it is always that the track entered and exited for the last voxel it is always that the track entered The flux and current scorers are not corrected as it likely has no sense to calcualte the flux entering and exiting voxels Please contact the GAMOS team if ou think you need this feature Filter classes See section on Filters Scorer printers 92 A scorer printers serves to select the format of the output of a scorer These classes are unique to GAMOS as Geant4 does not provide this functionality As mentioned above several printers can be associated to the same scorer Chapter 8 Scoring To associate a printer to an scorer you can use the command mentioned above gamos scoring
206. he cahnge of these variables when more events are added The variables are printed each N 16 events where N is the total number of events The variables printed are the following e mean 95 Chapter 8 Scoring e var e sd er e vov shift reff e r2int Point detector scorer 96 The point detector scorer covers the problems where the quantity to be calculated is the flux or the dose of neutral particles neutrons or gammas in a very small detector small with respect to the setup dimensions situated far from the primary particles source In this kind of problems the fraction of particles that reach the detector is very reduced and threfore if one wants to calculate the flux or dose by conventional methods the statistics needed would be prohibitive The technique implemented in GAMOS is similar to the F5 tally implemented in MCNP It is based on the following idea normal tracks are propagated and for each neutron or gamma interaction is calculated the probability that it would be deviated in the direction of the point detector instead of the real direction towards which it is deviated and the probability that it reaches the point detector without any further interaction The first probability is based on a precalculated table of angle probabili ties for each interaction type each material and each energy multiplied by the solid angle covered by the point detector The second probability is based of the number of mean
207. he cuts for gamma electrons and positrons the cut for positron is optional if not set it will take the one for electrons 63 Chapter 5 Physics Alternatively you can set the cuts in your user script through a user command gamos physics setCuts REGION_NAME gamma_CuT e _CUT e _CUT Energy cuts to range cuts conversion If you want to know the traslation from an energy cut value to a range cut value for a given particle in a given material you can do with the following instructions First you have to instantiate the user action gamos userAction GmCutsEnergy2RangeuA and then you can use the command gamos physics ECuts2RangeCuts MATERIAL_NAME CUT_VALUE PARTICLE_NAME You may use in the material name an if you want to name several materials at the same time For the particle name only the following names have a meaning gamma e e e This will produce a table with the conversion for each material and particle similar to the following one GmCut sEnergy2RangeUA ATERIAL G4_AIR PART gamma ENERGY CUT 0 1 MeV RANGE CUT 286588 GmCut sEnergy2RangeUA IATERIAL G4_AIR PART e ENERGY CUT 0 1 MeV RANGE CUT 129 155 GmCut sEnergy2RangeUA IATERIAL G4_AIR PART e ENERGY CUT MeV RANGE CUT 131 938 GmCut sEnergy2RangeUA ATERIAL
208. he eloni_NoSeco and eBrem_NoSeco refer to the cases when ionisation or bremsstrahlung processes limit the step but no secondary particle is produced The reason for this limitation is to guarantee that the step are not too big so that physics precision may be spoiled You may have a look for example at http fismed ciemat es GAMOS RToptim ParameterHelp html for a description of the Geant4 electromagnetic physics parameters Shower shape studies 144 GAMOS offers an utility to help in doing shower shape studies To use is it is enough to active the user action gamos userAction GmShowerShapeuA Each time a new track step satisfies the conditions of the filters associated to this ac tion a new shower is started and the user action accumulates all the energy deposits of all the children created from this track step This means taht each track step that passes the filter initiates a new shower unless the track is a children of a track which has already initiated a shower But you should not forget the logic of the user actions and filters the user action GmShowerShapeUA will only be invoked for the steps that pass the associated filters i e if one of the children track steps does not pass the filter it will not be included in the shower If this behaviour does not provide you with the Chapter 15 Utility user actions expected results you may consider using the filter GmAncestorsFilter see section of Filters As we just mentioned each
209. he most common PET devices by defining its properties in a few lines text file e PETAnalysis PET event classifier and PET histograms e RadioTherapy example of radiotherapy simulation including writing and reading phase space files Each package has the following subdirectories e src the source code e include the header files You do not need to follow this file distribution if you want to create a new package but we recommend you to do so Bibliography 1 http howw cern ch geant4 2 http geant4 web cern ch geant4 support userdocuments shtml 3 http seal cern ch 4 http proj clhep web cern ch proj clhep 5 http root cern ch 6 Penelope A Code System for Monte Carlo Simulation of Electron and Photon Transport Workshop Proceedings Issy les Moulineaux France 5 7 November 2001 AEN NEA 7 http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplication Developer html ch02s02 himl 8 http geant4 web cern ch geant4 User Documentation UsersGuides ForApplication Developer html ch04 html sect Geom Navig 9 http geant4 web cern ch geant4 User Documentation UsersGuides ForApplication Developer html ch02s06 himl 10 http geant4 web cern ch geant4 User Documentation UsersGuides PhysicsReferenceManual html ch02s05 html 11 http geant4 web cern ch geant4 UserDocumentation UsersGuides PhysicsReferenceManual html P hysicsReferenceManual html
210. hey will always return true i e they will have no effect In the case of scorers the use of future filters has to take into account the fact that scor ers are only invoked when a step happens in the detector volume that has attached the scorer This could create a problem if the FILTER_FUTURE implies a geometrical condition like for example if steps happens in a given volume In this case the scorer will not be invoked and this filter will never be checked The solution for this is that you attach a detector to the volume of the FILTER_FUTURE and then add in the FILTER_PAST filter asking for steps to be only in the volume s where you want to score Chapter 13 Classifiers Introduction A classifier is a class that contains a method that receives a G4Step or a G4Track and re turns a different index an integer depending on some given criteria In other words it classifies the step or track and returns the index of its classification These classes are unique to GAMOS as Geant4 does not provide this functionality Classifiers can act on user actions or scorers If one or several classifiers are set to act on a user action it is up to the concrete user action to determine which use it makes of them or to ignore them The most common use of classifiers by user actions is to produce a different histogram or table for each classification index For details on classifiers acting on scorers see the section on Scorers The use of user actions a
211. histograms are filled DetCompton Classif NRecHit INTERVAL_LOWER_EDGE INTERVAL_UPPER_ EDGE Dist RecHitSet Associated Interaction Distance between a reconstructed hit set and the interaction to which it is associated DetCompton Classif NRecHit INTERVAL_LOWER_EDGE INTERVAL_UPPER_EDGE Dist RecHitSet 1st Interaction Distance between a reconstructed hit set and the first interaction DetCompton Classif NRecHit INTERVAL_LOWER_EDGE INTERVAL_UPPER_EDGE Dist RecHitSet 1st Interaction Wrong assoc Distance between a reconstructed hit set and the first interaction only for those sets with wrong association other hit is closest to the first interaction than the one identifed by the algorithm DetCompton Classif NRecHit INTERVAL_LOWER_EDGE INTERVAL_UPPER_EDGE Dist RecHitSet 1st Interaction Good assoc Distance between a reconstructed hit set and the first interaction only for those sets with good association These four histograms are filled for each interval of the variable being INTERVAL_LOWER_EDGE the lower edge of each interval and INTERVAL_UPPER_EDGE the upper edge of each interval The intervals are set by the parameters gamos setParam DetCClassifEnergy Min MIN_VALUE gamos setParam DetCClassifEnergy Max MAX_VALUE Chapter 17 Detector applications gamos setParam DetCClassifEnergy Step STEP_VALUE The intervals will be built between MIN VALUE and MAX VALUE each STEP_VALUE Alternatively you can define the N 1 l
212. hould be in a subdirectory called src For the declaration files you have a greater 5 Chapter 2 Getting started freedom the Geant4 way is that they have the suffix hh and lie in a subdirectory called include but you can do it your own way and after that you have to be consis tent in the GNUmakefile as explained below You then have to build a GNUmakefile that will steer the compilation and the buidling of the libray and the plug in s when you type the command make For building it you may follow the examples in the GamosCore GamosXXX directories We take as example the file GamosCore GamosGeometry GNUmakefile name GamosGeometry G4TARGET name G4EXLIB true PHONY all all lib plugin include GAMOSINSTALL config binmake gmk include GAMOSINSTALL config general gmk EXTRALIBS lGamosBase_Base l1GamosUtils l1GamosUserActionMgr Let s go one by one through the lines In the first one you define the name of your library name GamosGeometry The following two lines are used internally by the GAMOS scripts and are manda tory G4TARGET name G4EXLIB true Then you define what you want to do when you type make PHONY all all lib plugin There are several possibilities lib Compile and build the library plugin Build the plug in Use it if and only if you are creating a new plug in plugin_check Check that you are linking with all the libraries tha
213. hree optional extra parameters and always add the three positions even if they are 0 0 0 DIR_X DIR_Y DIR_Z Those are the director cosines of the Z axis of the cylinder the axis perpendicular to the 2D surface Position in a disc with gaussian distribution gamos generator positionDist SOURCE_NAME GmGenerDistPositionDiscGaussian SIGMA POS_X POS_Y POS_Z DIR_X DIR_Y DIR_Z The position is distributed in a disc in the XY plane with the radius in a gaussian distribution of sigma SIGMA and random in phi at position 0 0 0 If you want it placed at a different position you have to add three optional extra parameters POS_X POS_Y POS_Z By default the cylinder is not rotated If you want it rotated you have to add three optional extra parameters and always add the three posi tions even if they are 0 0 0 DIR_X DIR_Y DIR_Z Those are the director cosines of the Z axis of the cylinder the axis perpendicular to the 2D surface Position randomly in the voxels of a phantom gamos generator position Dist SOURCE_NAME GmGenerDist Position VoxelPhantomMaterials MATERIAL1 MATERIAL 2 The position is randomly distributed in the voxels of a phantom with material equal to one of the materials in the list of parameters There must be at least one volume defined by a parameterisation of type G4PhantomParameterisation Position in the voxels of a phantom file gamos generator position Dist SOURCE_NAME GmGener Dist Position In
214. ial 191 Chapter 22 Radiotherapy application cal mi Io pig a ld 0 Cee L ra min Figure 22 1 Cross leaves representation 192 Chapter 22 Radiotherapy application E a Git Fiaa Figure 22 2 Inline leaves representation for endleaf type ROUND If we change the END_LEAF_TYPE for STRAIGHT type the variable RDIM repre sents a new value named END_LEAF_FOCUS If we set it to 10 mm the leaf profile changes as it is described in the figure 3 193 Chapter 22 Radiotherapy application 194 O21 End Laawe Focus _ Z_min Z_TOP Z_TOP Z_GAP A ate aperture bo the isocenire Figure 22 3 Inline leaves representation for endleaf type STRAIGHT The example uses four leaf cross profiles types the data written are relative to the Z ref Z_TOP plane In the figure 4 we can see a representation of each profile referred to the Z_TOP plane and the result after the corresponding projection in the final geometry representation Chapter 22 Radiotherapy application Leave type 2 defined te the reference plane Z_TOP o RIRE re Leave type 7 a ___Leave type 3 m Leave type 4 mn a Figure 22 4 Cross leaves types representation relative to the Z_TOP plane for four leaf cross profiles and its representation in the final geometry Using phase spaces A very common utility in teletherapy simulation is the writing of a phase space i e the set of particles that reach a certain
215. ial FinalMaterial InitialSolidType FinalSolidType InitialPVCopyNumber FinalPVCopyNumber Material variables These are numeric data that are related to the material They are the following InitialDensity FinalDensity InitialPressure FinalPressure Initial Temperature FinalTemperature InitialRadLength FinalRadLength InitialNuclearIntLength Chapter 11 Analysis extracting data e FinalNuclearIntLength e InitialEletronDensity e FinalElectronDensity Particle and process These are string data that extract the name of the particle and the processes and also data about the particle properties They are only available for Step Track and Secondary Track All of them have 25 characters when written in a binary file They are the following Particle InitialProcess Name of process that defined the point PreStepPoint Only available for Step FinalProcess Name of process that defined the point PostStepPoint Only available for Step CreatorProcess Name of process that created the particle track Not available for Event nor Run ParticlePDGEncoding Particle code following the Particle Data Group numbering ParticleCharge ParticleMass ParticleLifetime ParticleWidth ParticleStable 1 if stable 0 if unstable ParticleType ParticleSubType The particles types and subtypes are listed below Table 11 1 GEANT4 particle types and subtypes G4Particle Ty
216. ided by the volume V of this cell The track length is calculated by a sum of the step lengths in the volume The expression for cell flux is given by the sum of W L V where W is a particle weight and is multiplied by the track length at each step GmG4PSPassageCellFlux Passage cell flux is a volume based scorer similar to G4PSCellFlux The only difference is that tracks which pass through a cell are taken into account It means that tracks generated or stopped inside the volume are excluded from the calculation In Out behaviour For the following scorers GmG4PSCylinderSurfaceCurrent GmG4PSCylinderSurfaceFlux GmG4PSFlatSurfaceCurrent GmG4PSFlatSurfaceFlux GmG4PSSphereSurfaceCurrent GmG4PSSphereSurfaceFlux GmG4PSTrackCounter you can make the scoring only for tracks that are entering only for tracks that are exiting or both for tracks that are entering or exiting default behaviour To select among these three options you can add an extra parameter when defining the scorer that can be In Out or InOut Other scorers GmG4PSMinkinEAtGeneration This scorer records the minimum kinetic energy of secondary particles at their production point in the volume in an event This primitive scorer does not integrate the quantity but records the minimum quan tity GmG4PSNofSecondary This class scores the number of secondary particles gen erated in the volume A particle weight is not applied by default The user can choose if the scoring is do
217. ider than the phantom To apply it you should select the following physics list gamos physics GmEMPS Physics and the physics options gamos GmPhysics add Physics electron lowener ZBS gamos GmPhysics addPhysics positron standard ZBS remember that there is no low energy physics for positrons The splitting number should be set with the parameter gamos setParam GmParticleSplittingProcess NSplit NSPLIT This bremsstrahlung splitting technique is more efficient than the uniform bremsstrahlung splitting because only a few gammas that are not aimed to the region of interest are tracked but it has the inconvenient that tracks with different weights 1 N and 1 reach the patient spoiling the efficiency gain To take profit of the definition of a region of interest while keeping the same weight for all the particles that reach the phantom a third splitting technique has been developed that is described below Chapter 22 Radiotherapy application Killing particles at big X Y This utility serves to kill the particles that would probably not reach your detector because they have too big X and Y positions it is assumed that that your detector is described along Z and that your initial particles move in this direction in the positive sense It makes a list of the volumes that are placed directly on the world volume and computes the minimum and maximum extension in X and Y using the method G4VSolid GetExtent This rectangular area extend
218. if the numbers refer to plane or rz points by looking at the number of parameters provided and comparing it with the number expected Example SOLID polyh POLYHEDRA 20 180 3 4 1900 32 1800 30 1800 0 1900 0 or equivalently SOLID polyh POLYHEDRA 20 180 3 2 1800 0 30 1900 0 32 ELLIPTICALTUBE elliptical tube e Half length X 19 Chapter 3 Geometry 20 e Half length Y e Half length Z ELLIPSOID ellipsoid e Semiaxis in X e Semiaxis in Y e Semiaxis in Z e Lower cut plane level z e Upper cut plane level z ELLIPTICALCONE elliptical cone e Semiaxis in X e Semiaxis in Y e Height of elliptical cone e Upper cut plane level HYPE hyperbolic profile e Inner radius e Outer radius e Inner stereo angle e Outer stereo angle e Half length in Z TET tetrahedron e Anchor point e Point 2 e Point 3 Point 4 e Flag indicating degeneracy of points TWISTEDBOxX box twisted along one axis e Twist angle e Half x length e Half y length e Half z length TWISTEDTRAP trapezoid twisted along one axis e Twisted angle e Half x length at y pDy e Half x length at y pDy e Half y length pDy1 e Half z length pDz e Polar angle of the line joining the centres of the faces at pDz Chapter 3 Geometry Half y length at pDz pDy2 Half x length at pDz y pDy1 Half x length at pDz y pDy1 Half y length at pDz Half x length at pDz y pDy2 Half x length at pDz y
219. ilding a simple geometry with one material This geometry can serve for example when you want to get the cross section of a set of materials so you do not really need to define any geometry but just a fake one containing the materials you need so that you can use the Geant4 utilities to get the cross sections To use this you have to set the geometry to gamos geometry GmGeometryUseMaterials The file name where you can define the materials unless you want to use the Geant4 predefined ones can be set with the parameter gamos setParam GmGeometry UseMaterials FileName FILE_NAME Then you have to set a list of maeterials with the parameter gamos setParam GmGeometryUseMaterials Materials MATE_1 MATE_2 The geometry to be built will be a list of volumes on with each material You can see an example on the use of this utility at tutorials ShieldingTutorial exercise5 Building your geometry with C code You can build your geometry by writing your C class inheriting from G4VUserDetectorConstruction see example in 7 After that you have to transform it into a GAMOS plug in To learn how to do this see the instructions in 36 Chapter 3 Geometry the section Creating your plug in using the GmGeometryFactory or see the example examples NO2 Reading DICOM files Converting a DICOM file to a simulation file GAMOS is able to read the patient data resulting from a CT scan in DICOM format The first step is to change the D
220. ilities for each resulting value of the generator distribution These probabilities are normalized so that the highest is assigned a value of 1 If the generator variable takes a value to which it corresponds a probability value X that is less than 1 then Russian rouletter is played with a survival probability of X if the value is not accepted a new value is sample from the generator distribution if it is accepted the weight of the particle that is going to use this generator distribution is multiplied by 1 X Several generator distribution variables can be biased namely PosX PosY PosZ PosPerp PosR PosPhi PosTheta DirTheta DirPhi Energy Time To bias a distribution you have to use the command gamos generator addBiasDistribution SOURCE_NAME GENERATOR_DIST_TYPE BIAS_DIST_NAME where SOURCE_NAME is the name of a source declared previously GENERATOR_DIST_TYPE is one of the generator distribution variables listed above and BIAS_DIST_NAME is the name of the distribution you have previously created see section on Distributions A word of caution is due here if you use low probabilities the Russian roulette will often fail and then the efficiency of your simulation may be sensibly decreased In this case you may think on using a generator distribution that includes the bias in an efficient way or create a new one there is an example on creating a new genera tor distribution in the Plugin tutorial you may ask for help in the GAMOS
221. ilters applied to scorers they only act if the scorer is called i e if the step happens in the selected volume For details on filters acting on scorers see the section on Scorers The use of user actions and scorers together with filters is a powerful means to obtain very detailed information on the simulation through simple user commands See the tutorial on Histograms and scorers for examples on this Several filters need some extra parameters see list of filters below that control their behaviour To use these filters they have to be declared first with the following com mand gamos filter FILTER_NAME FILTER_CLASS PARAMETER_1 PARAMETER 2 where FILTER_NAME is the new name you want to give to a filter to attach it to a user action of a scorer FILTER_CLASS is the name of the filter class and PARAMETER_1 PARAMETER 2 are the values of the parameters that the filter needs Those filters that do not need any parameter can be assigned directly to a user action or a scorer without giving them a new name the name will be the one of the filter class To attach one or more filters to a user action you put them after the user action name in the command line that selects it gamos userAction USER_ACTION FILTER_NAME or you can use filters to act on a scorer with the command gamos scoring addFilter2Scorer FILTER_NAME SCORER_NAME Filter are plug in s so that a user can create her his own filter and select it with a user command To le
222. imeConstant TIME All the primary particles will be generated at time 0 If you want to set it at a different time you can add the extra parameter TIME e Time changing at constant interval gamos generator timeDist SOURCE_NAME GmGenerDistTimeConstantChange TIME_INTERVAL TIME_OFFSET The time will increase for each event with a constant value The interval is defined as an extra parameter If desired a second parameter can be added to set the offset the time of the first event if the offset is not set it is set to 0 e Decay time gamos generator timeDist SOURCE_NAME GmGenerDistTimeDecay ACTIVITY LIFETIME The primary particles will be generated with a time following a typical decay dis tribution with the activity of the particle source To be concrete the time is sampled with a Poisson distribution that is obtained as follows rnd_poiss 1 0 activity second log RandFlat shoot the activity is given by the parameter ACTIVITY If the second parameter is set is is not mandatory the activity is scaled witht the lifetime chosen If the particle of the source is an ion it uses its lifetime unless set by the above parameter A warning is due here if a particle is an ion and suffers radioactive decay Geant4 selects a time corresponding to the ion and changes the time of this ion and of the secondary particles to this time This means that it will not use the time set by this time distribution To avoid this beh
223. imits of the N intervals with the parameter gamos setParam DetCClassifEnergy IntervalLimits VALUE_1 VALUE_2 VALUE_N 1 The same set of histograms can done for the maximum minimum or average recon structed hit energy and minimum position X Y Z XY sqrt X X Y Y XZ YZ XYZ To fill these histograms the following parameter should be used gamos setParam DetComptonStudyHistosUA ClassificationVariables VAR1 VAR2 VARN where the variables can be EnergyMin EnergyMax EnergyAverage XPosMin YPos Min ZPosMin XYPosMin XZPosMin YZPosMin or XYZPosMin Another variable but in this case it is always filled is the variable ALL which indeed is not a variable and it makes no classification but fill all reconstructed hit in a unique set of histograms The classes that manage this histograms are plug ins so that other variables could easily be created Histograms of gammas at sensitive detectors We describe here the GmHistosGammaAtSD an utility that prints information about the interaction of original gammas in the sensitive detector It is a user action and therefore it can be activated with the command gamos userAction GmHistosGammaAtSD At the end of run a table like the following one is printed SSSSSSSSS Classification of Gamma Interactions in SD S GC nEvents 1000000 SSGC n gamma in SD 516170 25 8085 GC n PE gt 321588 62 30273 GC PE 0 COMP 157614 49 011157 GC P
224. in the voxels is done using the Geant4 algorithm G4RegularNavigation that is the optimal one for regular geometries see 8 The user may select if when a track navigates through contiguous voxels with the same material the frontier between them will be skipped or not with the parameter gamos setParam GmReadPhantomGeometry Phantom SkipEqualMaterials VALUE that by default takes a value of 1 For testing purposes other navigation algorithms may be selected namely voxel nav igation with 1 dimensional optimization that occupies similar memory as Regular Navigation but is very slow gamos set Param GmReadPhantomGeometry Phantom RegularStructureID 0 Chapter 3 Geometry or 3 dimensional optimization that occupies a lot of memory but it is almost as fast as G4RegularNavigation when no equal materials skipping is used gamos setParam GmReadPhantomGeometry Phantom OptimAxis kUndefined GAMO is also able to read the EGSnrce DOSXYZnrc format for DICOM files Simply use gamos geometry GmReadPhantomEGSGeometry and the rest of parameters are the same as for the Geant4 DICOM files By default every phantom is placed in the world volume If you want to place it into another physical volume you can set the parameter gamos setParam GmReadPhantomGeometry MotherName PHYSVOL_NAME By default the name of the voxels is phantom and this is the name that you should use in you commands You may change it with the parameter gamos set Param
225. inal Histories 1 5e 07 For each phase space files after the name of the file comes a line with the file statistics number of particles accumulated number of particles of all files accumulated num ber of original histories ratio particles original histories ratio error accumulated ratio particles original histories And at the end the statistics on the total number of particles in total photons electron and positrons and the total number of original histories in all summed files Making histograms out of a phase space file You can make histograms out of the particles contained in a phase space file by running gamos with the input script that you can file in RadioTherapy analysis phaseSpace analysePS rt analysePS in If you edit it and change the name of the input phase space file at gamos setParam RTGeneratorPhaseSpace FileName and run gamos rt analysePS in You will get a file named phaseSpace root that contains the same histograms that you get when you run the job to write the phase space file see section on Phase space histograms Alternatively you can directly analyse a phase space file with the executable analy sePS You just have to type in your shell analysePS FILE_NAME where FILE_NAME is the name of the phase space header file the one that ends with AEAheader you may indeed omit the suffix AEAheader if you want When running you will see on the screen something similar to this READING FILE ps u
226. include CCGeometryStack geom or a stack geometry Note that different user parameters are required to define a stack and ring geometry Compton camera Event Classification The class CCEventClassifierUA classifies the events as useful events for Compton imaging by looking at the reconstructed hits It is a GAMOS user action and can be activated with the command gamos user Action CCEventClassifierUA It is currently possible to output data for single single type Compton imaging events where there is one reconstructed scatterer detector hit and one reconstructed absorber detector hit The event classifier counts how many of these single single reconstructed hits have deposited the total incident gamma ray energy within a precision given by the pa rameter gamos set Param CC EvtClass PhotopeakEPrec GATE The total gamma ray energy is set with the parameter gamos setParam CC EvtClass GammaEnergy ENERGY which by default takes a value of 141 keV where the minimum energy will be 1 GATE photopeak energy that by default takes a value of 0 9 photopeak energy and the maximum energy will be 1 GATE photopeak energy that by default takes a value of 1 1 photopeak energy You can set independently the minimum and maximum interval values with gamos setParam CC EvtClass PhotopeakEPrecMin VALUE gamos setParam CC EvtClass PhotopeakEPrecMax VALUE Only hits whose relative time difference is less than the value given by the parameter gamos set
227. ind top G4tgrVolume G4tgrVolumeMgr tgrVolmgr G4tgrVolumeMgr GetInstance const G4tgrVolumex tgrVoltop tgrVolmgr gt GetTopVolume return tgrVoltop You should also define another method virtual G4VPhysicalVolumex GmGeomTextDetectorBuilder ConstructDetector const G4tgrVolume x tgrVoltop You should first call the default detector builder to build the Geant4 geometry using the standard tags defined through this chapter G4vPhysicalVolumex topPV G4tgbDetectorBuilder ConstructDetector tgrVoltop After that you can add your code that will process your new tags Create regions GmRegionCutsMgr GetInstance gt BuildRegions Finally in your detector construction class inheriting from G4V UserDetectorConstruction you have to set up your detector builder Construct your detector builder GmGeomTextDetectorBuilder gtb new GmGeomTextDetectorBuilder Chapter 3 Geometry Inform G4tgbVolumeMgr to use your detector builder instead of the default one G4tgbVolumeMgrx volmgr G4tgbVolumeMgr GetInstance volmgr gt SetDetectorBuilder gtb Trigger the detector construction G4vPhysicalVolumex physiWorld volmgr gt ReadAndConstructDetector return physiWorld You can find an example in the Geant4 examples directory xamples extended persistency P03 src ExTGDetectorConstructionWithCuts cc Parallel geometries You can define a parallel geome
228. ined scorers you can add a filter to select for which track conditions the scoring will be done gamos scoring addFilter2Scorer FILTER_NAME CLASS SCORER_NAME FILTER_NAME CLASS is the name of a GmVFilter class or the name you gave to a filter built from a filter class by using the command gamos filter see section on Filters and SCORER_NAME is one of the scorers defined above You may repeat this command to associate several filters to the same scorer See sec tion on Filters for a description of the available filters and how to create your own one By default a different count is scored for each of the copies of the selected volumes with different copy number This is managed by the scorer classifier GmScorerClassi fierBy1Ancestor The user can attach different classifiers to the different scorers so that the counts are done in different ways gamos scoring assignClassifier2Scorer CLASSIFIER_NAME CLASS SCORER_NAME CLASSIFIER_NAME CLASS is the name of a GmVClassifier class or the name you gave to a classifier built from a classifier class by using the command gamos classifier see section on Classifiers and SCORER_NAME is one of the scorers defined above Finally you may select the format of the scoring results by associating one of the available scorer printers for each scorer gamos scoring addPrinter2Scorer PRINTER_NAME SCORER_NAME PRINTER_NAME is the name of a GmVPSPrinter class or the name you gave to a printer built from a
229. ion UNION SUBTRACTION INTERSECTION First component solid name Second component solid name Name of relative rotation matrix Relative X position Relative Y position Relative Z position Example SOLID myunion UNION solidl solid2 RM30 11 8 12 5 0 Volumes There are two ways to define a logical volume You can build if from a previously declared solid associating a material to it VOLU e Volume name e Solid name e Material name Example VOLU HALL HALL Air or you can skip the definition of the solid and in one unique line define the solid and the material valid also for boolean solids You should then use the same format as for the SOLID tag but adding as last word the material name Example Chapter 3 Geometry Instead of SOLID HALL BOX 5000 5000 20000 VOLU HALL HALL Air use VOLU HALL BOX 5000 5000 20000 Air Placement of a volume All the possible ways to place a volume in Geant4 are supported a single placement a parameterised one a division a replica and an assembly Single placement PLACE e Volume name e Copy number e Parent volume name e Name of rotation matrix e X position e Y position e Z position Example VOLU yoke TUBS Iron 3 620 820 1270 PLACE yoke 1 expHall R00 0 0 0 0 370 Parameterisation The parameterisations supported are the placement of several copies of a volume along a line in a circle and in a bidimensional grid other types of parame
230. is length varies and it is defined at the Z of the reference plane If the endleaf is straight so i e it has a circular shape the length also varies and it is defined at the Z value which when the arc is extrapolated to the Z line passing by the focus it intersects it at the Z of the reference plane leaf_length If the leafend is round it is the leafend radius If the leafend is straight it is Z position where the projection of the leafend interesect the Z line passing by the focus endleaf_radius endleaf_focus Z distance of the plane where the interleave separation are defined and z_ref z_gap Separation of leaves in the cross plane defined in the projection onto the z_gap plane interleaves_gap Separation of projection of first leave on the z_gap plane and on the reference plane cross_start_point Number of different types of leaf cross profiles n_leaves_cross_profiles For each cross profile the following data has to be defined Chapter 22 Radiotherapy application e Leave type It will be a LEAF or BLOCK but this options is not implemented yet so it must be LEAF e Number of 2 dimensional points taht define the cross profile n_leaves_cross_points e For each point the Z and cross coordinates must be defined Z_coordinate cross_coordinate Number of leave pairs total_leaves_number For each leave pair the following data has to be defined e Leave type number 1 2 3 following the order of leave types defined
231. issesssesiesenstessnsnesnenrennees 177 Summing projection data files sumProjdata ss sssnnssnssssnssrsssnsrtsessesstersresnteestesneeee 177 Analytic image reconstruction ssrb_fbp ccsccccsesseceeststeteseecesesestaneneseecesescsnananenees 178 Visualization tOOlS sicscchasisehsvecessissaceviebizens a a ab ov spots feted svbecs a shee 179 Stochastic Image Ensemble method cccccccesceseseeseneeseecescscenaneneseecesesesnenanenees 179 EO GUC TOM PARAE AE E A dion cues AA tite dence EAA 179 Getting Started aa fesse n Ea a olden ed alae REN R donne 180 Program Parameters and Flags esses sesssseesesesseeseseneeeeeces 182 Analysis yeso nio e ities shes E Gis Oe EE a E E EEO 184 22 Radiotherapy application ccsccsossssrscecscssssesecesssssssecessssssssscssssessscsesssssesesssseesees 187 Geometrical Modules icine Oi hon So hii la Red oie Beach 187 JAWS module occ sccssaecscgsacsdeeceescsetucesokdesceicatan decgedsadeusasacsestesset desceuicntandedgeasigees 187 MECmod les serene aa a a Be Beco a ith tires oes EN RAR les aks ieee 187 Using phase spaces ai sictesisihdiudeshiadivescustenstedebiattovebistigdasebetiecsetddsenssceptevabeetip tones 195 Writing phase SPaces cscscsesetesssosesassepsovetoosessescossusbecssessvaseusstepsevebecsevaen cnet 195 Phas space text file wc thrash eretar n E E tase 197 Phase space histOgrams ccccccscecsesee cesses eee a aaa aE ES 197 Reading phase spaces ss essscivecssssgeusiesseec
232. itialMomZ InitialTime Initial Weight Event generator changing energy and material As you can find in some of the tutorial exercises this generator serves to scan different energies and different materials and obtain for example the cross sections at each point the activation or whatever quantity you want 55 Chapter 4 Generator To select it you have to use the command gamos generator GmGeneratorChangeEnergyAndMaterial The first thing to choose is the energies To do ita minimum a maximum energy have to be defined as well as a number of steps gamos setParam GmGeneratorChangeEnergyAndMaterial minE VALUE gamos set Param GmGeneratorChangeEnergyAndMaterial maxE VALUE gamos set Param GmGeneratorChangeEnergyAndMaterial nstepsE VALUE Then it must be selected if the steps are done linearly or logarithmically default gamos set Param GmGeneratorChangeEnergyAndMaterial logE 1 0 The materials used will be those found from the geometry constructed You may define a dummy geometry as it will not be used anyhow For each material at a time a world made of one single volume of the material will be used You may nevertheless select only a subgroup of the materials in the geometry with the parameter gamos set Param GmGeneratorChangeEnergyAndMaterial VolumesToChange VOLUME_1 VOLUME_2 Event generator histograms 56 These are histograms of event generator particles that may serve to check that you have actually generated what yo
233. itions in the standard output not in the file will be written in cylindrical coordinates by default If you want them in cartesian coordinates you should set to true the parameter gamos setParam compcam DumpCartesian TRUE 175 Chapter 20 Compton camera application 176 Chapter 21 Image reconstruction utilities Several utilities are provided for helping the user to process projection data and re construct PET images These utilities are installed along with the rest of GAMOS code and their source code included in the GAMOSINSTALL analysis NuclMed PET di rectory They are available as executables as mentioned in the following subsections List mode to projection data m2pd This program is devised to convert previously stored PET list mode output files out in projection data hs s or hv v Its functionality is similar to the ProjDataMgr class see Projection data file section using the following arguments a axial field of view in millimeters by default 100 0 d diameter of the transaxial field of view in millimeters by default 300 0 m maximum ring difference by default 1 number of planes n name of the output file without extension o output format 0 for GAMOS ad hoc format by default extension hv v com patible with GAMOS analytic image reconstructor or 1 for STIR projection data extension hs s p number of axial planes by default 40 r number of tangential bins
234. itron annihilation can be properly reconstructed This is specially useful for detectors that have 3D identification capabilities like solid state or liquid xenon detectors For those without these capabilities the only algorithm of choice is likelA y the one that is based on the energy of the hits The following algorithms are currently available Det1stHitByEnergy Classifies the reconstructed hits in order of decreasing energy and selects the first one as the one corresponding to the 1st Compton interaction A parameter can be used to select instead the second third highest energy hit gamos setParam Det1stHitByEnergy Order ORDER Det1stHitByXY Pos If the detector has cylindrical symmetry and the gamma travels preferentiallly increasing the position in the XY plane i e the cylinder radius you may use this algorithm which classifies the reconstructed hits in order of increas ing position in the XY plane i e sqrt x x y y and selects the first one as the one corresponding to the 1st Compton interaction A parameter can be used to select instead the second third highest energy hit gamos setParam Det1stHitByXY Pos Order ORDER DetistHitByXPos If the detector is a block and the gamma travels preferentiallly increasing the position along the positive or negative X axis you may use this algo rithm which classifies the reconstructed hits in order of increasing absolute value of X position and selects the first one as the
235. ity serves to merge dose files in the format sqdose corresponding to different jobs with the same setup and getting the average dose of them To use it you have to write a file containing the list of header phase space files one file per line for example sqddose water 20000 out sqdose water 20001 out sqdose water 20002 out Then you just have to run the executable mergeSqdose INPUT_FILE_LIST_NAME OUTPUT_FILE_NAME where INPUT_FILE_LIST_NAME is the name of the file containing the list of files to merge and OUTPUT_FILE_NAME is the name of the output file that will contain the merging of all the files When merging files it will be checked that they correspond to the same phantom by checking the number of voxels and voxel limits Merging 3ddose files This utility serves to merge dose files in the format 3ddose corresponding to different jobs with the same setup and getting the average dose of them To use it you have to write a file containing the list of header phase space files one file per line for example 3ddose water 20000 out 3ddose water 20001 out 3ddose water 20002 out Then you just have to run the executable merge3ddose INPUT_FILE_LIST_NAME OUTPUT_FILE_NAME where INPUT_FILE_LIST_NAME is the name of the file containing the list of files to merge and OUTPUT_FILE_NAME is the name of the output file that will contain the merging of all the files When merging files it will be checked that they correspond to the same pha
236. ivate the user action gamos userAction GmGamosVerboseByEventuA Then you have to set the event intervals with the command gamos verbosity byEvent VERB_CLASS VERB_LEVEL FIRST_EVENT LAST_EVENT where VERB_CLASS is one of the verbosity name in the previous section VERB_LEVEL can be any of the six values described in the previous section and FIRST_EVENT LAST_EVENT are the first and last event affected by the verbosity level You may use as many times as desired this command so that any number of event intervals may be defined for any of the GAMOS verbosities The use of this command overwrite the command gamos verbosity so that all the events not included in an interval including the LAST_EVENT have verbosity silent Using a GAMOS verbosity manager in your code 150 If you write some new code for example a new generator distribution you may use one of the GAMOS verbosity managers following the instructions below Each of the GAMOS verbosity managers instantiates an object of the type GmVer bosity If you want that your code is only printed when the corresponding verbosity level is set you have to write this verbosity with the value of the level in parenthe sis For example if you write one new generator position distribution and you want that a message is printed when somebody chooses it in the input file you can write a message like the following one in the constructor of your class G4cout lt lt GenerVerb infoVerb
237. ive can be added to the index by defining an offset as a parameter gamos setParam PRINTER_NAME OffsetX OFFSET If and only if you are using a GmCompoundClassifier built from two classifiers you may want to produce a 2 dimensional histogram In this case you should give eight instead of four parameters to the gamos scoring printer command the first four should correspond to the data of the first classifier and the second four to the second one Then three histogram will be filled the compound index will be split in the two indices as defined with the NShift of the GmCompoundClassifier then an histogram will be filled for the first index another for the second one and a 2 dimensional histogram combining the two indices A second offset may be defined for the second index gamos setParam PRINTER_NAME OffsetY OFFSET The three above scorer printers may also print the sum of squared scores which will be useful to sum up scores from different jobs To do it you have to set the parameter gamos setParam PRINTER_NAME PrintSumW2 1 Other scorer printers are provided for specific applications See corresponding sec tions in this guide Classifiers See section on Filters Multiplying by data You can multiply the quantity you are scoring by any of the GAMOS data see section on GAMOS data so that before scoring the quantity value it will be multiplied by the value of that the GAMOS data has in that step To do it you have to use th
238. iven density and then to a material type The relation between CT number and density is more or less lin ear The file CT2Density dat contains the calibration curve to convert CT Hounsfield number to phy sical density The example Data dat provided with the GAMOS distri bution contains the assignment of material densities to materials as recommended by the International Commission on Radiation Units and measurements ICRU report 46 In the class DicomDetectorConstruction it is defined a density interval G4double densityDiff 0 1 This means that the voxels of each material will be grouped in density intervals of 0 1 g cm3 and a new material will be created for each group of voxels After filling your data files you just have to run the executable buildG4Dicom DICOM file format The DICOM files are converted to a simple text format You may create your own file with the following format see e g 1 4dcm 37 Chapter 3 Geometry 38 A line with the number of materials A line for each material with its index and name the same name of materials that you constru ct as G4Material s A line with the number of voxels in X Y and Z A line with the minimum and maximum extension in X mm A line with the minimum and maximum extension in Y mm A line with the minimum and maximum extension in Z mm A number of lines containing the nVoxelX nVoxelY nVoxelZ material indices one per voxel e A number of lines contai
239. l Volumes const G4String amp name bool exists 1 Gets the list of logical volumes with the given name std vector lt G4V Physical Volume gt GetPhysical Volumes const G4String amp name bool ex ists 1 Gets the list of physical volumes with the given name 43 Chapter 3 Geometry e std vector lt GmTouchable gt GetTouchables const G4String amp name bool exists 1 Gets the list of touchables with the given name std set lt G4String gt GetAllSDTypes Gets all distinct sensitive detector types Magnetic field Notes 44 You can set a uniform magnetic field with the command gamos magneticField setField FIELD_X FIELD_Y FIELD_Z where FIELD_X FIELD_Y FIELD_Z are the field values along the three axes Remem ber than in Geant4 internal units 1 Tesla is equal to 0 001 therefore if you do not use any unit it will be understood as 1 that is 1000 Teslas Local magnetic field You can set a uniform magnetic field uniquely to a list of volumes To do it use the command gamos magneticField setLocalField FIELD_X FIELD_Y FIELD_Z VOLUME_1 VOLUME 2 VOLUME_N where FIELD_X FIELD_Y FIELD_Z are the field values along the three axes And VOLUME_1 VOLUME_2 VOLUME_N are the list of volumes to which the mag netic field is attached 1 This format is in the official Geant4 release since geant4 9 1 2 The default path to look for this file is defined by the variable GAMOS_SEARCH_PATH For details see section on
240. lInPrePosTheta Momentum The momentum data are very similar to the position data so that all what was said for position data is also valid for them The main different is the histogram limits which are for X Y and Z are 0 to 1 MeV for Mag and Perp are 0 to 1 MeV for Phi are 0 to 360 deg and for Theta are 0 to 180 deg The momentum data are InitialMomx InitialMomY InitialMomZ InitialMomMag InitialMomPerp InitialMomPhi InitialMomTheta FinalMomx FinalMomY FinalMomZ FinalMomMag FinalMomPerp FinalMomPhi FinalMomTheta MomChangexX MomChangeY MomChangeZ MomChangeMag MomChangePerp MomChangePhi 120 Chapter 11 Analysis extracting data e MomChangeTheta Direction The direction data are very similar to the position data so that all what was said for position data is also valid for them The main different is the histogram limits which are for X Y and Z are 1 MeV to 1 MeV for Mag and Perp are 0 MeV to 1 MeV for Phi are 0 deg to 360 deg and for Theta are 0 MeV to 180 deg Another difference is that the InitialDirMag and FinalDirMag do not exists because their value would always be one The direction data are InitialDirX InitialDirY InitialDirZ InitialDirPerp InitialDirPhi InitialDirTheta FinalDirX FinalDirY FinalDirZ FinalDirPerp FinalDirPhi FinalDirTheta DirChangeX DirChangeY DirChangeZ DirChangeMag DirChangePerp DirChangePhi DirChangeTheta AngleChange This data represents th
241. lapsed the time will be checked after each event therefore the time interval will only be approximated You also have to choose how much you want to move it and the axis the axis of displacement or the axis around which happens the rotation You have then to set the interval of events or time between movements After you can define an offset so that the first interval does not start at 0 Finally you can choose that your movement is done forever i e until the number of events in the run are exhausted or it is only done N times Chapter 3 Geometry The commands to tell GAMOS to make a movement are gamos movement moveEachTime if you want that the movement happens after a certain interval of time and gamos movement moveEachN Events if you want that the movement happens after a certain number of events In both cases the command has to be followed by these arguments MOVEMENT_TYPE VOLUME_NAME VALUE AXIS_X AXIS_Y AXIS_Z TIME_INTERVAL NEVENT_INTERVAL where MOVEMENT_TYPE can be displace or rotate where the first word has to be either displace or rotate VOLUME_NAME must be one of the Geant4 volumes of your geometry VALUE is the amount by which you want to displace or rotate default Geant4 units are assumed i e mm and rad you can change them in the usual way e g cm deg AXIS_X AXIS_Y AXIS_Z are the three coordinates of the axes TIME_INTERVAL NEVENTS_INTERAVL is the interval after which the movements will happe
242. last row column is the overflow entries above axis maximum Histograms profile 1D The first word is HISTO_PROFILE1D the rest is the same as the histograms 1D Histograms profile 2D The first word is HISTO_PROFILE2D the rest is the same as the histograms 2D 105 Chapter 10 Histogramming You can see an example of 1D histogram here 1D example 10 0 1000 0 3 3 1 3 5 6 12 15 16 2 66 0 460 2 353 81 Changing histogram minimum maximum and number of bins You may change minimum maximum and number of bins of any histogram with the following user commands 1D or 1D profile histograms gamos analysis histolINBins HISTO_NAME VALUE gamos analysis histolMin HISTO_LNAME VALUE gamos analysis histolMax HISTO_NAME VALUE 2D or 2D profile histograms gamos analysis histo2NBinsX HISTO_NAME VALUE gamos analysis histo2MinX HISTO_NAME VALUE gamos analysis histo2MaxX HISTO_NAME VALUE gamos analysis histo2N Bins Y HISTO_NAME VALUE gamos analysis histo2MinY HISTO_NAME VALUE gamos analysis histo2MaxY HISTO_NAME VALUE HISTO_NAME may contain asterisks to include several histograms at the same time For example gamos analysis histo1NBins Energy 300 will set to 300 the number of bins of all histograms ending with Energy The name of each histogram is documented in this guide If you are not sure about an histogram name you may run the job with limited statistics and open the file Output files name 106 The na
243. led also histograms about the reconstructed hits that are associated to each interaction are filled so the first hit is the one closest to the first interaction etc The only difference is that insted of the word Interaction in their name they have the word RecHit The classes that manage this histograms are plug ins so that other variables could easily be created Classification of good and bad identification histograms as a function of variable It may happen that different algorithms to identify the first gamma interaction may be optimal for different types of reconstructed hit set For example for sets with only two hits the Compton cone algorithm may be optimal while for sets with more hits it may give worse resutls or the minimal position algorithm may be optimal when hits have small energy but if there is one with high energy and therefore high deviation angle it may give worse resutls To help you in doing this optimization several his tograms about the number of good and bad first gamma interaction identification can be done for different variables e g for different number of reconstructed hits in the set for different maximum hit energy bins for different position variables The his tograms are about the distance between the reconstructed hit sets using the position of the hit identified as corresponding to the first interaction and the interactions For example for the number of reconstructed hits variable the following
244. les several times by setting the parameter gamos setParam RT Generator PhaseSpace MaxNReuse N Chapter 22 Radiotherapy application to a value bigger than 1 In fact if this parameter is not explicitly set to 1 GAMOS calculates it automatically by dividing the number of events asked for by the number of events in the input phase space Alternatively you may recycle the full phase space several times i e when all parti cles in the phase space are read the file is closed and restarted again The number of times a phase space is recycled is controlled by the parameter gamos set Param RT GeneratorPhaseSpace MaxNRecycle N which must take a value bigger than 1 If no reusing is explicitly set the number of reuses will be automatically calculated as mentioned above and the number of recyclings will be set to 1 so that no recycling is done Caution should be taken when recycling phase spaces as the error correlations due to the reusing of the same particles is not taken account Therefore you should first consider reusing instead of recycling If you think your phase space has X Y symmetry you may reduce the correlations due to reusing the same particle several times by mirroring your particles each time they are reused by setting the parameter gamos setParam RT Generator PhaseSpace Mirror WhenReuse OPT where OPT can be X or Y or XY If it is X it means that when a particle is used an even time the X original value of position and
245. limit is set you may apply it to a new pair of logical volume and particle type with the following command e gamos physics userLimits addLVAnd Particle USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE _NAME for the list of particle names in GAMOS see section Particle names A last command serves to print the active user limits for each volume and each par ticle gamos physics userLimits print Automatic optimisation of cuts The production cuts and user limits are powerful methods to tune your simulation so that you can save a lot of CPU time by not tracking the particles that are not going to contribute to your results Nevertheless the tuning of cuts is usually a long and difficult task We have developed in GAMOS a method to help the user to obtain the 65 Chapter 5 Physics 66 optimal value of the production cuts and user limits for her his application in a sin gle job We describe here the basic idea of the method and then in the corresponding sections the details of its implementation for different cases To use this utility you have to define in a clear way which are the results you don t want to change when cuts change for example e Number of particles reaching a region e Dose distribution e Number energy spatial distribution of hits e Shower shape in a volume For each track that contributes to your result GAMOS stores all its history for the track itself and each of its ancestors stores energy range region
246. ll be illustrated in the following lines The first step is to define a class inheriting from G4tgrLineProcessor see for example GamosCore GamosGeometry include GmGeomTextLineProcessor hh You should then define a method virtual G4bool GmGeomTextLineProcessor ProcessLine const std vector lt G4String gt amp wl This is the method that will be invoked each time a line in your file is read passing to it the line as a vector of strings In this method you should first call the default line processor to process the standard tags defined through this chapter 33 Chapter 3 Geometry 34 G4bool iret G4tgrLineProcessor ProcessLine wl iret will be set to 1 if the tag is found else you should process the tag yourself For example if iret parameter number if wl0 REGION GmRegionCutsMgr GetInstance gt AddRegionData wl iret 1 The second step is to define a class inheriting from G4tgbDetectorBuilder see GamosCore GamosGeometry include GmGeomText Detector Builder hh You should then define a method virtual const G4tgrVolume x GmGeomTextDetectorBuilder ReadDetector to set as line processor the one you have created and to trigger the reading of the file construct g4 geometry GmGeomTextLineProcessorx tlproc new GmGeomTextLineProcessor G4tgrFileReader tfr G4tgrFileReader GetInstance tfr gt SetLineProcessor tlproc tfr gt ReadFiles f
247. ll be simulated together in an event To select this generator you have to use the command gamos generator GmGeneratorFromTextFile By default the file to be read is called generator txt you can see an example at MY_GAMOS_DIR data generator txt You can change its name with the command gamos setParam GmGeneratorFromTextFile FileName MY_FILENAME To change the search path please read the section Managing the input data files A file of this type may be created with the user action GmTrackDataTextFileUA using the following list of data EventID Particle InitialPosX InitialPosY InitialPosZ InitialMomX InitialMomY InitialMomZ InitialTime Initial Weight Reading your generator particles from a binary file You can also define your event primary particles with a binary file with the following data per particle EventID Particle e PosX e PosY e PosZ e MomX e MomY e MomZ e Time Weight To select this generator you have to use the command gamos generator GmGeneratorFromBinFile By default the file to be read is called generator bin You can change its name with the command gamos setParam GmGeneratorFromBinFile FileName MY_FILENAME To change the search path please read the section Managing the input data files A file of this type may be created with the user action GmTrackDataBinFileUA using the following list of data EventID Particle InitialPosX InitialPosY InitialPosZ InitialMomX InitialMomY In
248. lly absorbed 2 if it is a fully absorbed coincident event and 3 if it is a fully ab sorbed Compton imaging event with a single interaction in the scatter detector and in the absorber detector The imaging events are equal to the absorbed events ie if no multiples examination is carried out the absorbed events are the singles If mul tiples are carried out then the number of absorbed events increases by the number of useable multiple events which can now be used for imaging 10 1 if the search for reconstructed hits found more than 2 100 1 if the event is a random coincidence event 1000 1 if the event is a scattered event At the end of the run a table is printed with the number of events in each of the combinations of the sub classification types Compton camera histograms event classification 174 These histograms are related to the event classification explained above They are produced if the event classification user action is selected The name of all these his tograms starts with CCEvtClass and all are written in the file comptoncamera root The following histograms are written e Classification index of event Compton camera classification This index is the one described in the precedent section Chapter 20 Compton camera application e The scatterer addback energy for the classified events e The absorber addback energy for the classified events e Number of reconstructed hits in the scatterer detector e Numb
249. ls between 0 and 10 gamos classifier dataC GmClassifier ByData InitialKineticEnergy 0 10 0 5 If the data value is outside the limits you have given a warning will be thrown This warning can be an exception if you set the parameter gamos setParam CLASSIFIER_NAME AllowOutOfLimits 0 Data is string In this case no argument is needed after the classifier name For exam ple gamos classifier dataC GmClassifierByData InitialLogical Volume If you want to assign different indices than 0 to N you may use the command gamos classifier setIndices VALUE_1 INDEX_1 VALUE_2 INDEX_2 See section on Setting indices to classifiers for further details on this feature Primitive scorer from data It is possible to use any GAMOS data if its type is interger of float to build an scorer on its value see chapter on Scorers To use it you have to use the command to define a scorer using the scorer named GmG4PSData and passing to it the data name and the minimum and maximum value of the data For example gamos scoring createMF Detector contDet container gamos scoring addScorer2MFD dataScorer GmG4PSData contDet InitialKineticEnergy List of available data 118 There are over one hundred types of data currently available in GAMOS We list here them all mentioning for each one if it is of type double default not needed to be indicated int of string if it is of type Accumulated Initial Final or Change is in the data name the minimum a
250. lustration of this This is the time considered when you call the method GetTime You may also invoke explicitly GetTimeMin or GetTimeMax The time smeared is theTimeMin 85 Chapter 7 Sensitive Detector and Hits 86 Chapter 8 Scoring Creating a scorer Geant4 provides several classes to score different quantities in the selected volumes GAMOS provides all the Geant4 functionality through user commands and also some extra functionality that we describe in this section The first thing you should do to use GAMOS scoring is to create a multifunctional detector 15 and associate it with a list of logical volumes with the user command gamos scoring createMFDetector MFD_NAME LOGICAL_VOLUME_NAME s where MFD_NAME is the detector name that will be used later and LOGICAL_VOLUME_NAME s is a list of logical volumes that you associate to this detector Then you should add to the detector one of the GAMOS scorers or your own ones with the user command gamos scoring addScorer2MFD SCORER_NAME SCORER_CLASS MFD_NAME SCORER_PARAMETERS SCORER_NAME is a name you give to the scorer to be used later SCORER_CLASS is one of the available scorer classes MFD_NAME is one of the multifunctional detec tors created above and SCORER_PARAMETERS are the optional parameters a scorer may need see below for the description of the scorers You may repeat this com mand to associate several scorers to the same detector To each of the def
251. ly the am bient dose and the personal dose at several angles 0 15 30 45 60 76 To select them you have to set the following parameters not a different one for neutrons and gam mas gamos setParam GmPDS PrintHstar 1 gamos setParam GmPDS PrintHp0 1 gamos setParam GmPDS PrintHp15 1 gamos setParam GmPDS PrintHp30 1 gamos setParam GmPDS PrintHp45 1 gamos setParam GmPDS PrintHp60 1 gamos setParam GmPDS PrintHp75 1 For each magnitude you have to define the conversion factor for each energy bin These are defined in a file whose name is given by the parameter gamos setParam GmPDS Flux2DoseFileName FILE_NAME This file must contain in each line the energy and the conversion factors in pSv cm2 for the magnitudes H 10 H_pslab 10 0 H_pslab 10 15 H_pslab 10 30 H_pslab 10 45 H_pslab 10 60 H_pslab 10 75 The default name of this file is Flux2Dose neutron ICRU57 lis for neutrons and Flux2Dose gamma ICRU5 lis for gammas These two files contain the conversion factor given by the ICRU57 report and can be found in the data directory of the GAMOS release By default these files will also be used to read the list of energy bins to be used for the flux results 99 Chapter 8 Scoring Scoring with filters As for any user action you may add one or more filters so that only track steps that pass them will be scored The filter is applied to the neutron or gamma that creates the geantino not to the geantino that reaches the detecto
252. ly you may write a message that will be printed together with the results that may serve you to identify the output For example PRE 1 Events 2 PET L 1 W 3 4 T PT M PET_EVENTS Example of Analysing text output files As an example of this utility we will analyse three PET output files and extract some information from the table of PET events classification Let s take an output file with a table similar to this one Events PET 862 8 62 Good PET ALL 93 0 93 1 PET 2 recHits close to vtx 0 0 2 PET 2 recHits far from vtx 93 0 93 11 PET 3 gt 2 recHit close to vtx 0 0 12 PET 3 gt 2 recHit far from vtx 0 0 Random Coincidences ALL 769 7 69 101 PET 2 recHits close to vtx 0 0 102 PET 2 recHits far from vtx 769 7 69 111 PET 3 gt 2 recHit close to vtx 0 0 112 PET 3 gt 2 recHit far from vtx 0 0 Ya SY WH We have three files that we have run with different random seeds and we want to extract the following information e Sum of total number of PET events in the three files e Mean number of good PET events in each of the three files e List of numbers of random coincidences PET events in each of the three files The file to obtain these results that we name anaout is may look like this FILE_TXT out exercise3c 1 FILE_TXT out exercise3c 2 FILE_TXT out exercise3c 3 PRE 1 Events 2 PET W 4 T S M Events PRE 1 ALL
253. mPhysicsFactory and G4VUserPhysicsList for a geometry plug in GmVerbosityFactory and GmVerbosityMgr for a verbosity plug in etc 228 To write a new plug in of any type follow these steps 1 Create your class or use one of the existing Geant4 classes This class should inherit from the corresponding Geant4 or GAMOS class G4VUserDetectorConstruction geometry G4VUserPhysicsList physics list G4VUserPrimaryGeneratorAction primary generator GmVGenerDistPosition primary particles position distribution GmVGenerDistDirection primary particles direction distribution GmVGenerDistEnergy primary particles energy distribution GmVGenerDistTime primary particles time distribution GmVUserxXXAction user action XXX can be Run Event Tracking Step ping or Stacking G4VSensitiveDetector sensitive detector GmV Digitizer hits digitizer GmVRecHitBuilder reconstructed hits builder GmVPrimitiveScorer scorer GmVPSPrinter scorer printer GmVkFilter filter GmvVClassifier classifier GmVVerbosityMer verbosity Chapter 27 Appendix B C utilities If you are creating a new class you can use as example one of the classes at directory examples PlugInTemplates that are nearly empty classes that contain the necessary methods that you have to implement for each plug in type Include the SEAL module definition include PluginManager ModuleDef h N DEFINE_SEAL MODULE Then you have to include the releva
254. me for each index value If a classifier does not implement this method the one in the base class returns the index number converted to a string This method is used by user actions and scorers to add the index number to the name of the histograms tables or scores Classifiers are plug in s so that a user an create her his own classifier and select it with a user command To learn how to do this see the instructions in the section Creating your plug in using the GmClassifierFactory or the Histograms and scorers tu torial The following classifiers are currently implemented in GAMOS e GmPSClassifierBy1Ancestor It assigns a different index to different copy numbers of a volume It has an extra parameter that sets the level of the ancestor if it is N 0 it will use the copy numbers of the volume itself if it is N gt 0 it will look for the copy numbers of the N th ancestor e GmPSClassifierByAncestors It assigns a different index to different copy numbers of the sensitive volume It has two extra parameters that set the number of ancestor 137 Chapter 13 Classifiers levels NAncestor and the maximum number of copies in a level NShift The index is built as a sum of NShift copyNumber_of_Nancestor from N 0 to N NAncestor 1 GmClassifierByLogical Volume It assigns a different index to different logical vol umes GmClassifierByPhysical Volume It assigns a different index to different physical vol umes GmClassifie
255. me of the histogram file for each of the GAMOS histogram classes is explained in the corresponding section of this guide As these classes are user actions to this file name it is added the name of the filters and classifier as explained in the section on Using a common histogram class Also there it is explained how to change the name with the parameter gamos setParam FILE_NAME FileName NEW_FILE_NAME If you are running a job and you want to identify all your histogram files with a characteristic prefix or suffix for example to differentiate them from the files from another job you may do it by defining the parameters gamos setParam GmAnalysisMgr FileNamePrefix PREFIX The name PREFIX will be added at the beggining of all histogram names gamos setParam GmAnalysisMgr FileNameSuffix SUFFIX The name SUFFIX will be added at the end of all histogram names before the file type root or csv In the case of other output files or input like the text or binary files with several kinds of data that are explained in different sections of this guide you can also add a prefix or suffix with the above commands to all of them as all the input and output of these classes is controlled in GAMOS through a common base class Chapter 10 Histogramming Analysing your histograms with ROOT You may open a ROOT file by typing in the command line root and then open a browser by typing in the ROOT prompt new TBrowser This will open a window where
256. mes and in the second the list of weights Two data has to be assinged to it what can be done with the parameter gamos setParam DISTRIBUTION_NAME Data DATA_1_NAME DATA_2_NAME These data should be one of the volume data FinalLogical Volume and InitialLogical Vol ume FinalPhysical Volume and InitialPhysical Volume FinalTouchable and InitialTouchable etc But this is not enforced so that you may find another use for this distribution To avoid that the biasing value becomes too high for example if a track traverses several times the border between two volumes with very different weights you can avoid that a weight is repeated twice by settting the parameter gamos setParam DISTRIBUTION_NAME NoRepeat Weight 1 Alternatively you can set a maximum value of the weight with the parameter gamos setParam DISTRIBUTION_NAME MaxValue VALUE 141 Chapter 14 Distributions 142 Chapter 15 Utility user actions These are a miscellaneous set of user actions that add some functionality As for any user action filters can be assigned to them to select for which type of tracks they will be activated and in some cases classifiers may be used to classify the output tables Counting the number of tracks and events This utility prints a line every N events with the event number the number of tracks in this event and the accumulated number of tracks in all events ae oe oe EVENT 0 NTRACKS 4 TOTAL NTRACKS 4 EVENT 1000 NTRACKS 6 TOTAL NTR
257. mple FinalKineticEnergy vs InitialKineticEnergy will filla 2D histogram FinalKineticEnergy prof InitialKineticEnergy will fill a 1D profile histogram FinalKineticEnergy vs InitialKineticEnergy prof InitialPositionZ will fill a 2D profile histogram The name of the histogram file is given by the name of the data user plus the filters and classifiers plus the histogram type i e root or csv It can be changed with the parameter gamos setParam DATA_USER_NAME FileName NEW_FILE_NAME For example gamos userAction GmStepDataHistosUA GmGammaFilter will produce a file named GmStepDataHistosUA_GmGammaFilter root whose name can be changed with the command gamos setParam GmStepDataHistosUA_GmGammaFilter FileName NEW_FILE NAME to produce a file named NEW_FILE_NAME root Text files These data users i e GmStepDataTextFileUA GmTrackDataTextFileuA GmEventDataTextFileUuA GmRunDataTextFileUA GmSecondaryTrackDataTextFileUA dump the data values into text files A line is written for each call to the data user object i e each G4Step G4Track The text file is indeed a CSV Comma Separated Value file this means that values are separated by commas and string values are surrounded by double quotes 111 Chapter 11 Analysis extracting data 112 Optionally a header line can be written containing the names and order of the data to be written With the aim of clearly distinguishing it the first word of the header is always HE
258. n You may optionally use two extra parameters OFFSET 0 if not set to change the value for the first movement and NUMBER_OF_INTERVALS infinite by default to set the number of times the movement will happen If you want several movements in your run you can use these commands as many times as you want Then after each event GAMOS will check which of the movements must be done If you want for example to move the same volume with different types of movements one after the other you can use the number_of_intervals and offset arguments to do it The movements are managed in GAMOS by a user event action called GmMove mentEventAction that checks at the beginning of event if the movement must be done Therefore you cannot forget to activate this action with the GAMOS command gamos userAction GmMovementEventAction If you forget it the above commands will not exist and you will get a Geant4 excep tion There is an example of GAMOS movements that you can run in the directory MY_GAMOS_DIR examples test Just run gamos testMovement in and you will see an OpenGL view of a moving box Movement description from a file You may implement any kind of movement in GAMOS by describing the movements in a file To do it you just have to use the command gamos movement moveFromFile FILE_LNAME after instantiating the user action GmMovementEventAction This file must have the following format A first line with the following par
259. n onUser action names Checking filters at a user action The default behaviour of a user action is that their filters are invoked one after the other and all of them have to return OK before the user action method is invoked For efficiency reasons if a filter is not passed the other filters will not even be asked This behaviour may represent a problem in some cases For example if you implement two history filters and the first one is not accepted for a step the second one will not 135 Chapter 12 Filters be invoked but history filters need to be invoked at each step because they have to check if any of the steps in a track history passed the filter To prevent these cases there is the option of not applying the filters in a given circunstance by setting the parameters gamos setParam USER_ACTION_NAME CheckAllFiltersAtStepping false gamos setParam USER_ACTION_NAME CheckAllFiltersAtPreTracking false gamos setParam USER_ACTION_NAME CheckAllFiltersAtPostTracking false gamos setParam USER_ACTION_NAME CheckAllFiltersAtStacking false where USER_ACTION_NAME is the name of the user action where you want this to take effect which includes the name of the filters and classifiers see section onUser action names Filtering steps in the future 136 It is possible to filter an step with a future condition For example you may want to score the energy of the steps that are in a volume only if the track in a future step reaches anothe
260. n GAMOS it is only needed to add the command in your script gamos userAction GnMinRangeLimitsStudyUA DetCutsStudyFilter what will produce at the end of run a table and a histogram file with the needed information root b p q x getMinRangeCutsEffect Ct prodcuts root percentage and look at the last lines of output those that contain the word FINAU like the following ones PARTICLE e FINAL 17 19 PARTICLE e FINAL 72 34185 PARTICLE gamma FINAL 72 34184 amp tee out Chapter 18 PET application Before reading this chapter we recommend you to read the chapter on nuclear medicine that contains the utilities that are common to all nuclear medicine applications The PET application contains two directories The first one PetGeometry contains an utility to build a simple PET ring detector by just defining a few parameters The second one contains the PET event classifier the Compton identification algorithms and a few histogram classes Many of the utilities for PET detectors are related to the sensitive detectors that they contain so please read the Sensitive Detectors chapter if you have not done it yet PET geometry The directory PET GeometryData contains several examples of building simple PET ring detectors with text geometry files by just defining the following parameters e P NCRYSTAL_transaxial Number of crystals per block in the transaxial direction e P NCRYSTAL_a
261. n a phase space is generated a set of histograms are produced to give you some information about the particles in the phase space The name of all these histograms start with PhaseSpace and they are all dumped into the file phaseSpace root csv For each of the following particle types a different set of histograms are produced con taining the particle type in the histogram name gamma e e plus a set of histograms for all particles named ALL Also histograms for neutron and pro ton will be produce if the following parameter is set gamos setParam RT PhaseSpaceHistos Hadrons TRUE A full set of histograms is produced for each Z plane with the Z value on its name The following histograms are produced Position X cm X at Zstop Position Y cm Y at Zstop Position X and Y cm XY at Zstop Radial position in the XY plane cm R at Zstop Theta angle of direction degrees Direction Theta at Zstop Phi angle of direction degrees Direction Phi at Zstop Energy MeV Energy at Zstop X direction cosine Vx at Zstop Y direction cosine Vy at Zstop Z direction cosine Vz at Zstop Radial position in the XY plane cm vs theta angle of direction degrees R vs Direction Theta at Zstop Radial position in the XY plane cm vs energy MeV R vs Energy at Zstop Theta angle of direction degrees vs energy MeV Direction Theta vs Energy at Zstop
262. n method will be in voked per step for the ionisation and the photo electric processes gamos setParam GmDeexSplitLivermorelonisationModel NSplit N_SPLIT gamos setParam GmDeexSplitLivermorePhotoElectricModel NSplit N_SPLIT which by default take a value of 1 no splitting The production cuts for the characteristic X rays and Auger electrons produced see section on Deexcitation processes above Particle splitting techniques for radiotherapy Several particle splitting techniques are available to increase the efficiency of radio therapy accelerators simulations See the chapter on Radiotherapy 104 Chapter 10 Histogramming Histogram formats GAMOS supports several data analysis formats The format is selected at run time by the user so that the same C code can be used to write any format In this GAMOS version there are two formats implemented ROOT and CSV Comma Sep arated Value For the ROOT format we refer you to the ROOT documentation 5 The CSV format is explained below You can choose which format to use with the command gamos analysis fileFormat FORMAT where FORMAT can be ROOT root CSV csv You can also use several formats at the same file using the command gamos analysis addFileFormat FORMAT Whatever format you choose you can also get a print out in the screen of the main parameters of each histogram using the command gamos analysis printHisto VERBOSITY_LEVEL where VERBOSITY_LEVEL is the level of v
263. n the cases where it is explicitly mentioned that there is a unique parameter for both particles Creating angle deviation probability densities The first thing you should do before running your point detector scoring job is to create a file that contains the probability density functions of the emission angles for each energy process and material Else GAMOS will assume flat probabilities for all angles waht may be enough in your case To do this you can run a job that writes in a ROOT file the probability of emission angle for all the materials that constitute your setup You may follow the example found in tutorials ShieldingTutorial exercise3 exercise3 angle gg in that we explain here The class that makes the work is called GmPDSCreateAngleTablesUA but remember that the parameters have to go before the class that uses them so you should add this line at the end of your script gamos userAction GmPDSCreateAngleTablesuA To create the tables for different materials and tables you may use the generator Gm GeneratorChangeEnergyAndMaterials see section on Event generator changing energy and material If you have in your setup several particles that produce neutrons or gammas you should repeat the process with different primary particle types Then you may add all histograms in a file by using the ROOT command hadd MERGED_FILE root FILE1 root FILE2 root The file created in this way should be passed to the point detector scorer
264. n the phase space is not used fully or when particles are reused it is indeed not the exact number if for example you use only the 10 first particles in the phase space the number of events that generated those 10 particles may be bigger or smaller than the number of events that generated the following 10 particles due to statistical fluctuations If you are using the option of skipping voxel frontiers when the material does not change see section on Reading DICOM files you may take into account the possibility of tuning the distributions of dose deposited in the voxels traversed by one step see section on Scoring in voxelised phantoms Saving scores and score errors in text file You can also store the dose in each voxel in a file what allows to calculate the average dose calculated with several jobs see dose analysis section The first file is a text file where it is written the dose and dose error in each voxel To obtain it you just have to add the scorer printer GmPSPrinter3ddose to your scorer for example gamos scoring addPrinter2Scorer GmPSPrinter3ddose DoseScorer The output file is named by default 3ddose out You may change it with the parameter gamos setParam PRINTERNAME_SCORERNAME FileName MY_FILENAME wherePRINTERNAME is the name of the printer by default GmPSPrinter3ddose and SCORERNAME is the name you have given to the scorer The format is the same as the one 3ddose format used in DOSXYZnrc except that the fir
265. nality void DumpSummary std ostream amp out G4cout Dumps a summary of the ge ometry i e number of solids logical volumes physical volumes touchables and materials void DumpG4LVList std ostream amp out G4cout Dumps list of logical volumes void DumpG4LVTree std ostream amp out G4cout Dumps the hierarchy of logical volumes void DumpG4PVLVTree std ostream amp out G4cout Dumps in the following order 1 a logical volume with details 2 list of physical volumes that are daughters of this logical volume with details 3 list of logical volumes daughters of this logical volume and for each go to 1 void DumpMaterialList std ostream amp out G4cout Dumps list of materials void DumpSolid G4VSolid sol size_t leafDepth std ostream amp out G4cout Dumps a solid with its attributes void DumpLV G4LogicalVolume lv size_t leafDepth std ostream amp out G4cout Dumps a logical volume with its attributes void DumpPV G4VPhysical Volume pv size_t leafDepth std ostream amp out G4cout Dumps a physical volume with its attributes G4LogicalVolume GetTopLV Gets a pointer to the logical volume on top of the geometry hierarchy G4V Physical Volume GetTopPV Gets a pointer to the physical volume on top of the geometry hierarchy G4Material GetMaterial const G4String amp name bool exists 1 Gets the material with the given name std vector lt G4Logical Volume gt GetLogica
266. nce to the detector from the source or interaction point Chapter 8 Scoring 1 WS Et ada piu ode Jo Figure 8 1 yields the probability that the particle reaches the detector point with no further col lisions where rae edo Sht Figure 8 2 is the attenuation of a beam of monoenergetic particles passing through a material medium where s is measured along the direction from the source or interaction point to the detector and X s is the macroscopic total cross section at s If dA is an element of area normal to the line of flight to the detector dQ dA R2 As the flux is the number of particles passing through a unit area normal to the line of flight direction we can write the flux as s 2 D plp oe R Figure 8 3 If there is azimuthal geometry then p u p u 2 7 and we can finally write pS is 2 D pluje 2rR Figure 8 4 The attenaution term exp A is calculated summing up the number of interaction lengths from the source or interaction point until the detector this calculation de pends on the neutron gamma energy and the materials traversed and it is computed in GAMOS through the use of geantino The R2 term in the denominator causes a singularity when a source or interaction event occurs near the detector point R approaches zero and the flux approaches in finity The technique is still valid and unbiased but convergence is slower and often impractical To avoid this singularity a ficti
267. nd followed by gif If you want another format different than gif you may edit the printAll C file and change the histogram name You may also run the file without opening a ROOT session by typing root b p q x printAll C MYFILE root Comparing histograms in two files This utilitiy serves to compare the histograms of two files that contain the smae his tograms for example to compare the results of two jobs you have run with different options To do the comparison open a ROOT session and then type the command x compareAll C MYFILE1 root MYFILE2 root There are two optional extra argu ments that can be given after the file names separated by a comma e A boolean 0 or 1 to indicate if the histograms are compared normalising one to the other or not e A boolean 0 or 1 to indicate if the Y axis is in logarithmic scale or not For each histogram two graphics file will be written the first one contains the his tograms the histogram of the first file on the top left quadrant the histogram fo the second file on the top right one and in the lower half the histogram of the first file in red and superimposed the histogram of the second file in blue in the second graph ics file there is the division of the histogram of the first file and that of the second file The first file name is built with the name of the histogram preceded by his and followed by gif The second file name is the same as the first plus _div b
268. nd maximum values if an histogram is filled with it and if it is not available for Step Track Event Run or Secondary track For each data we explain how its value is obtained for each of these five cases if the value is not evident i e the behaviour of FinalKineticEnergy should be evident for what we have explained above if called for a Step or a Track We may also get a list of available data for a GAMOS release by typing in your ter minal window after GAMOS has been configured SealPluginDump grep GmData For a better description of the available data we have classified them in several groups Position The position is a 3 dimensional vector so the following data can be obtained from it e X projection on X axis e Y projection on Y axis e Z projection on Z axis e Mag magnitude Chapter 11 Analysis extracting data e Perp perpendicular projection i e sqrt X X Y Y e Phi phi angle in degrees e Theta theta angle in degrees All these data can be of type Initial Final or Change The Initial data are available for all information objects except Run while the Final and Change data are available only for Step and Track There are other data that calcualte the local position that is the global position transformed into the local frame of the volume the particle is in The InitialLocalPos data for a Step object calculate the transformation in the volume the track step has just traversed while for a Track o
269. nd scorers together with classifiers is a powerful means to obtain very detailed information on the simulation through simple user commands See the tutorial in section Histograms and scorers for more details on this Several classifiers need some extra parameters see list of classifiers below that con trol their behaviour To use these classifiers they have to be declared first with the following command gamos classifier CLASSIFIER_NAME CLASSIFIER_CLASS PARAMETER_1 PARAM ETER_2 where CLASSIFIER_NAME is the new name you want to give to a classifier to attach it to a user action or to a scorer CLASSIFIER_CLASS is the name of the classifier class and PARAMETER_1 PARAMETER _ 2 are the values of the parameters that the classifier needs Those classifiers that do not need any parameter can be assigned directly to a user action or a scorer without giving them a new name the name will be the one of the classifier class To attach one classifier to a user action you put its name after the user action name in the command line that selects it gamos userAction USER_ACTION CLASSIFIER_NAME or you can use a classifier to act on a scorer with the command gamos scoring assignClassifier2Scorer CLASSIFIER_NAME SCORER_NAME If you want to use more than one classifier for a user action or a scorer you have to use the classifer GmCompoundClassifier see below Each classifier has a method GetIndexName G4int index that returns a different na
270. nd two endleaves type are supported rounded or straight focused to a point in the z axis The endleave straight implicates a circular shape as in the Siemens PRIMUS MLC Each leave cross profile is described by its projection onto a reference plane The endleave position is described by its projection at the isocenter plane 187 Chapter 22 Radiotherapy application 185 Geometrical module definition and variables list The MLC module description has to start with the two words words have to be sep arated by blank spaces and follow the order described here but there is no constraint on the number of lines they may occupy MODULE MLC Then the following parameters have to be filled Module name Mother volume name The type of MLC has to be FOCUSED what means that all leaves profiles in the cross place are focused to a point UNFO CUSED will be supported in future releases Orientation of the leaves i e the axis of movement can be x y X or Y End leaf type must be ROUND or STRAIGHT Z position of the focus z_focus Transversal position X or Y depends on the orientation of the focus cross_focus Z position of the plane onto which the leaves are projected to describe the interleave gaps z_ref Z position of the isocentre which is used to calculate the profile in the inline plane z_isocentre Leave half dimension in the inline plane X or Y direction depending on the orien tation if the endleaf is curved th
271. nd you have to add one or several particle sources there is no de fault primary particle source therefore if you do not choose one GAMOS will throw an exception You may combine several particle sources in each event by repeat edly using the commands described below Each type of particle source has default distributions of time energy position and direction that you may change with the commands described below An important point not to forget is that when you define a particle source you have to give it a name This name serves to distinguish it when you want later to change its time energy position or direction distribution Particle sources Single particle source To add a single particle source you have to use the command gamos generator addSingleParticleSource SOURCE_NAME PARTICLE NAME ENERGY SOURCE_NAME is the name of this source that you have to use if you want later to change its time energy position or direction distribution PARTICLE_NAME can be any of the Geant4 particles ENERGY is the initial energy of the particle If you don t change any property the particle will be generated at time 0 position 0 0 0 and random direction 45 Chapter 4 Generator 46 If you are using optical photons as primary generator particles you may set the po larization using the parameter gamos setParam SOURCE_NAME Polarization POLARIZ_X POLARIZ_Y POLARIZ_Z Isotope source GAMOS implements an isotope generator
272. nding region before reaching the phase space RTExtralnfoProviderInteractions fills a bit if the track has intereacted in the corre sponding region before reaching the phase space RTExtralnfoProviderOrigin fills a bit if the track has been created in the correspond ing region before reaching the phase space 199 Chapter 22 Radiotherapy application 200 The user may select how many bits each information must occupy by using the GAMOS parameter gamos setParam EXTRA_INFO_NAME NBits NBITS where EXTRA_INFO_NAME is the name of the extra information class see above GAMOS will check that the index to be filled by a class is not bigger than the number of bits reserved for it And it will also check that the total number of bits is not bigger than the available quantity 32 NUM_EXTRA_LONG The order of declaration of the extra information user actions sets the order of bits occupancy At the end of the job each of these extra information uer actions fills a file explainning the information contained in each bit By default this file is called RTExtraInfoProvider summ but the user may change the name of it with the parameter gamos setParam RTExtralnfoProviderLong FileName FILE_NAME An example of a file is the following one ExtraInfoProviderOrigin INDEX REGION ExtraInfoProviderOrigin INDEX REGION targetReg ExtraInfoProviderOrigin INDEX REGION collimatorReg 0 DefaultRegionForTheWorld 1 2 ExtraInfoProviderOrigin INDEX
273. nds on the value of the parameter gamos setParam SD GmHitsWriteUA BinFile TRUE FALSE The text file contains a line for each hit with the following information Event ID Sensitive detector type Detector unit ID Energy MeV Minimum time ns Maximum time ns Position X mm Position Y mm Position Z mm e Number of original tracks One line per original track with track ID e Number of tracks 83 Chapter 7 Sensitive Detector and Hits One line per track with track ID The binary file contains the same information in the following format Event ID float Sensitive detector type char 10 only first 10 characters are stored if type has less than 10 characters blank spaces will be added at the end Detector unit ID unsigned long long Energy MeV float Minimum time ns unsigned long long Maximum time ns unsigned long long Position X mm float Position Y mm float Position Z mm float Number of original tracks unsigned int One line per original track with track ID unsigned int Number of tracks unsigned int One line per track with track ID unsigned int Hits histograms There are two user actions that provide a number of hits histograms GmHitsHistosUA provides statistics about simulated hits while GmRecHitsHistosUA provides statistics about reconstructed hits 84 The class GmHitsHistosUA produces a file named hits root with the following his tograms Number of
274. ne for all types of particles default or only for a set of particles by naming them as extra parameters GmG4PSNofStep This class scores the number of steps in the cell A particle weight is not applied by default If an extra parameter is set to TRUE those steps with step length zero will not be taken into account GmG4PSCellCharge This class scores the total charge of particles which have stopped or have been created in the volume i e the tracks that enter count as 1 and the tracks that exit count as 1 GmG4PSTrackCounter This class scores the number of tracks in a cell For Event Biasing Scoring for event biasing is a very specific use case whereby particle weights and fluxes through importance cells are required The goals of the scoring technique are to e appraise particle quantities related to special regions or surfaces e be applicable to all cells physical volumes or replicas of a given geometry e be customizable A number of scorers have been created for this specific application e GmG4PSNofCollision This scorer records the number of collisions that occur within a scored volume cell e GmG4PSPopulation This scores the number of tracks within in a given cell per event A particle weight is not applied by default e GmG4PSTermination This scores the number of tracks that are terminated in a given cell per event A particle weight is not applied by default From data 91 Chapter 8 Scoring e Gm
275. nergyFilter accepts a track if its kinetic energy is between the two values given as extra parameters including the two values For steps it considers the energy at the beginning that is the G4PreStepPoint energy GmPostKineticEnergyFilter accepts a track if its kinetic energy is between the two values given as extra parameters including the two values For steps it considers the energy at the end that is the G4PostStepPoint energy GmVertexKineticEnergyFilter accepts a track if its vertex kinetic energy the energy at creation is between the two values given as extra parameters including the two values GmbDepositedEnergyFilter accepts a track if the deposited energy is between the val ues given by the two extra parameters including the two values It does not im plement the AcceptTrack method GmInitialRangeFilter accepts a track if its range at creation is between the two val ues given as extra parameters including the two values GmkRangeFilter accepts a track if the range is between the values given by the two extra parameters including the two values GmStepNumberFilter accepts a track if the step number is between the values given by the two extra parameters It does not implement the AcceptTrack method GmNumberOfSecondaries accepts a track if the number of secondaries created is between the values given by the two extra parameters It does not implement the AcceptTrack method GmProcessFilter accepts a track if th
276. ng them from a file will produce the same in memory representa tion therefore you can apply any of the above described effects and produce any histogram in the same way independently on how the hits are produced This can serve you for example for doing a study on how much your results change with different energy resolutions you produce the hits with zero resolution and store them and in another run you can read applying a certain energy resolution this way you spare the time to recreate them what usually is several orders of magnitude slower than reading them To use this utility you just have to activate the user action gamos userAction GmHitsWriteUA The name of the file can be controlled with the parameter gamos setParam hits FileName MY_FILENAME If this parameter is not found the name will be hits out You can read back the hits by activating the user action gamos userAction GmHitsReadUA The name of the file can be controlled with the parameter gamos setParam hits FileName MY_FILENAME If this parameter is not found the name will be hits out As commented above you can use all the other options in your script and just read the hits instead of generating them But probably you do not want that new hits are created when you are reading them from a file in this case you should also activate the user action gamos userAction GmKillAllUA File format The file to be written can be a text file or a binary file The format depe
277. ning the nVoxelX nVoxelY nVoxelZ material densities one per voxel The same information is also used to fill a file in binary format that contains the same information as the text format Its name ends in g4dcmb instead of g4dcm Reading a DICOM file in a GAMOS job To read the file produced by the DICOM utility you should define as your geometry the class gamos geometry GmReadPhantomG4Geometry if you use the Geant4 text format or gamos geometry GmReadPhantomG4BinGeometry if you use the Geant4 binary format You should have then a file where your phantom is described whose name is set with the parameter gamos set Param GmReadPhantomGeometry Phantom FileName MY_FILENAME and another file where you describe the rest of your geometry at least the world volume where the phantom is placed The name of this file is set with the parameter gamos set Param GmReadPhantomGeometry FileName MY_FILENAME In a phantom file the voxels of the same material may have a different density GAMOS allows you to group densities in intervals You have to set true the parame ter gamos setParam GmReadPhantomGeometry RecalculateMaterialDensities 1 and choose the interval width with the parameter gamos setParam GmReadPhantomGeometry Phantom DensityStep DENSITY_INTERVAL so that that the voxels of each material will be grouped in density intervals of DEN SITY_INTERVAL and a new material will be created for each group of voxels The navigation
278. nitialize Geant4 and to run N events In this case your input file may look like this one Chapter 2 Getting started gamos setParam GmGeometryFromText FileName test geom gamos geometry GmGeometryFromText gamos physicsList GmEMPhysics gamos generator GmGenerator gamos generator addSingleParticleSource MY_SOURCE e 1 MeV run initialize run beamOn 10 This will create a simple geometry the one described in the file test geom lying in the current directory or in the MY_GAMOS_DIR data directory set the physics as the low energy electromagnetic Geant4 physics and run 10 events with an electron of 1 MeV as primary particle You can then add any of the command described in this document or any Geant4 command or any command you created yourself Beware that Geant4 is a state machine and the list of available commands depends on the current state The main state change is triggered by the run initialize command which changes the state from G4State_Prelnit to G4State_Idle You may get a full list of the available commands at any moment with the command control manual Compiling GAMOS If you installed GAMOS as explained in the previous section the compilation will be done automatically Then you may run your application in GAMOS by writing your user commands without any need of compiling ever more and therefore you do not need to read this section Only if you want to extend the GAMOS functionality by providing new c
279. ns should be defined as mother volume see the example below Example VOLU phantom_container BOX 50 100 100 G4_WATER VOLU phantom BOX 10 10 10 G4_WATER PLACE_PARAM phantom 1 phantom_container PHANTOM 5 10 10 20 20 20 Division There are several ways to define a division in Geant4 by giving the number of divisions so that the width of each division will be automatically calculated the division width so that the number of divisions will be automatically calculated to fill as much of the mother as possible both the number of divisions and the division width this is especially designed for the case where the copies do not fully fill the mother To each of these types correspond a different tag DIV_WIDTH e Volume name e Parent volume name e Material name e Axis of division e Division width e Offset not mandatory DIV_NDIV e Volume name e Parent volume name e Material name e Axis of division e Number of divisions e Offset not mandatory DIV_NDIV_WIDTH Volume name Parent volume name Material name Axis of division Number of divisions Division width Offset not mandatory 27 Chapter 3 Geometry 28 Example DIV_WIDTH mybox mother AIR Z 10 DIV_NDIV_WIDTH mytube mother copper PHI 12 10 deg Replica To define a replica the following tag must be used REPL e Volume name e Parent volume name e Axis of division e Number of divisions e Division width e Offset
280. nt factory and define your plug in include GmCore GmFactories include GmXxxFactory hh DEFINE_SEAL_PLUGIN GmXxxFactory MY_CLASS MY_PLUGIN_NAME Alternatively if you do not mind that the plug in name has the same name as your class you can use a short notation instead of DEFINE_SEAL_PLUGIN DEFINE_XXX MY_CLASS where XXX is the type of object you are defining the name of the factory without Factory e g from GmGenerDistEnergyFactory the Gm substituted by GAMOS and the separation of words with For example GAMOS_GEOMETRY GAMOS_USER_ACTION GAMOS_GENER_DIST_POSITION beware the capitals You can add these lines in your class or create a new file with these lines only see as example the files called module cc in almost all the GAMOS code direc tories Remember in any case that you cannot have two definitions of DE FINE_SEAL_ MODULE in the same directory Once this is done you can select your geometry with the command gamos xxx MY_PLUGIN_NAME For example if you have written DEFINE_SEAL_PLUGIN GmGeometryFactory MyGeometry MyGeom you can then use ies gamos geometry MyGeom to select your geometry Or if you have written DEFINE_GAMOS_GEOMETRY MyGeometry you can tell your job to select your geometry with the command gamos geometry MyGeometry NOTE If you are creating a plug in in a new directory you have created you
281. nto account dividing the area of the surface that is traversed and the cosine of the angle between the track direction and the surface normal The current and flux are usually defined at a surface but volume current and volume flux are also provided e GmPSSurfaceCurrent This is a surface based scorer The quantity is defined by the number of tracks that reach the surface It serves to score the current in the surfaces of a box tube or sphere The user can choose the direction of the particle to be scored with the parameter gamos setParam SCORER_NAME Direction DIRECTION The choices are In Out or InOut In scores incoming particles to the volume while Out scores only outgoing particles from the volume InOut scores both directions The user should also define the list of volume surfaces in which the scoring will be done These surfaces depend on the volume solid Box e X YZ plane at positive X e X YZ plane at positive X Y XZ plane at positive Y Y XZ plane at positive Y Z XY plane at positive Z Z XY plane at positive Z 89 Chapter 8 Scoring 90 Tube e INNER inner radius surface e OUTER outer radius surface PHI if the full phi 360 degrees is not defined it is the two surfaces composed of the points of same phi that limit the tube volume TOP the top surface BOTTOM the bottom surface Sphere e INNER inner radius surface e OUTER outer radius surface e THETA if the full theta 180 degrees
282. ntom by checking the number of voxels and voxel limits Chapter 22 Radiotherapy application Making histograms out of a sqdose file You can make histograms out of dose information contained in a sqdose file by run ning analyseSqdose SQDOSE_FILE_NAME When running you will see on the screen something similar to this READING FILE sqdose ubs 10x10 6 out GmSqdoseHeader Read NEvent 2 5e 08 GmSqdoseHeader Read NVoxels 21 112 150 GmSqdose Read type 1 USING std map to store doses Number of voxels 352800 RTPSPDoseHistos nvoxel 21 112 150 RTPSPDoseHistos dim 1 1 1 RTPSPDoseHistos translation 0 0 4 R TPSPDoseHistos rotation 1 0 0 0 T 0 0 0 1 MINIMUM DOSE 2 352e 15 MAXIMUM DOSE 4 76001le 13 TPSPDoseHistos AVERAGE ERROR 20 0 0139839 TPSPDoseHistos AVERAGE ERROR 50 0 0111726 TPSPDoseHistos AVERAGE ERROR 90 0 00996564 ZI oyy saving histograms in file EVENTS IN SOURCE 2 5e 08 dose_analysesSqdose root First it is printer the sqdose file header information number of events original events run and number of voxels in X Y and Z Then the type of the sqdose see above Then the STL container that will be used to store the doses and dose errors see ar gument descriptions below Then the total number of voxels to be read and the in formation from the class RTPSPDoseHistos number of voxels in X Y and Z voxel dimensions
283. ode you will have to follow the instructions in this section GAMOS uses the GNU make tool to manage the compilation and generation of ex ecutables It uses a set of configuration files based on the Geant4 ones Therefore if you are familiar to Geant4 you will find no difficulty in compiling GAMOS After untarring the installation file you will have a directory called MY_GAMOS_DIR substitute it by whatever name you used This is the directory where the GAMOS code is the rest are the external libraries used by GAMOS and the configuration utilities Before compiling you have to define a few variables mainly the location of the dif ferent external packages All this is done by sourcing the file source MY_GAMOS_DIR config confgamos sh or source MY_GAMOS_DIR config confgamos csh To compile any directory of GAMOS and all the directories below you just have to go to that directory and type make This will compile all the cc files found in the src directory build the library and the plug in s and in the case of the direc tory GamosCore GamosApplication it will also create the gamos executable You may need to type the Linux command rehash to refresh your environmental variables in case there was no executable file before starting the compilation Compiling your new code If you have created a new directory with your C code you have to compile it following the Geant4 way The implementation files should have the suffix cc and s
284. oice is correct The following histograms are filled N gamma interactions Number of original gamma interactions in one event e N rec hits Number of reconstructed hits in one event N gamma interactions N rec hits Number of original gamma interactions minus number of reconstructed hits in one event Histograms of data about the interactions and the reconstructed hits Another set of histograms may help to evaluate if the energy is a good criteria to iden tify the reconstructed hit that corresponds to the first gamma interaction The energy lost at each first interaction of an original gamma is plotted and also the energy of the second one the third one To avoid reserving space for an unlimited number of interactions the third and later interactions are grouped in a unique histogram You may change the interaction number to start this grouping with the parameter gamos setParam DetCAlgoEnergy HistoGroupingNumber NUMBER Also histograms of the difference between the first interaction and each of the other ones the second and each of the other ones etc are done And two dimensional histograms of the energy of the first vs the rest the second vs the rest etc The name of the histograms are assuming the grouping number is three e DetCompton Algo Interaction Energy Energy of gamma interactions e DetCompton Algo Interaction Energy 1st Energy of first gamma interaction e DetCompton Algo Interaction Energy 2nd Ene
285. ollowing two pa rameters 161 Chapter 18 PET application 162 gamos setParam PET EvtClass 511EPrecMin ENERGY_MIN gamos setParam PET EvtClass 511EPrecMax ENERGY_MAX where ENERGY_MIN is the minimum energy that by default takes a value of 0 7 511 keV and ENERGY_MAX is the maximum energy that by default takes a value of 1 3 511 keV To recover hits when one of several Compton interactions have occurred you may switch the merging of hits that are close into a single one You may set the distance to merge hits with the parameter gamos setParam PET EvtClass ComptonRecHitDist DIST DIST takes by default a value of 0 what means that no Compton hits merging will be done The merging of hits first identifies the hit with biggest energy and merges with it those hits that are closer than the given distance The same algorithm is repeated with the hits not associated until no hit is left If hits merging is chosen you may choose among several algorithms to try to identify the hit that corresponds to the first gamma interaction and this will be the position of the whole set See section Identifying Compton interactions to learn how to do it If no algorithm is selectedm the position will be the one of biggest energy or second biggest or n th biggest where the order is given by the parameter gamos setParam PET1stHitByEnergy Order ORDER ORDER takes by default a value of 1 that is the position is that of the hit with biggest energy se
286. om coincidence It is checked that the hit is built only from tracks from the same original gamma 167 Chapter 19 SPECT application Scattered The event is classified as scattered if any of the original gamma has suf fered an interaction in the list of volumes defined by the parameter gamos setParam DetCountScatteringUA VolumeNames VOLUME_1 VOLUME_2 and this interaction is of one of the process types defined by the parameter gamos setParam DetCountScatteringUA ProcessNames PROCESS_1 PROCESS_2 by default Compton are Rayleigh interactions are counted and it has lost in the volumes more energy than the parameter gamos setParam DetCountScatteringUuA EnergyMin ENER _MIN by default the minimal energy is 0 Check SPECT line distance a line joining the position of the hit with the centre of the collimator volume is built and the distance of closest approach DCA to the origin of the positron is calculated the events are classified as near of far if the DCA is smaller or bigger than the parameter gamos setParam SPECT EvtClass LineDistToVtx DISTANCE where DISTANCE has a default value of 10 mm Gamma traversed collimator it checks if the original gamma or one of them if there are several that left the hits traversed the volume s defined as collimator with the parameter gamos setParam SPECT EvtClass Collimator Volume VOLUME_1 VOLUME_2 where DISTANCE has a default value of 10 mm The event will
287. on eta meson eta eta_prime meson eta_prime kaon meson kaon kaon meson kaon kaon0 meson kaon kaon0L meson kaon kaon0S meson kaon anti_lambda baryon lambda anti_lambda_c baryon lambda_c anti_omega baryon omega anti_omega_c0 baryon omega_c anti_sigma baryon sigma anti_sigma baryon sigma anti_sigma0 baryon sigma anti_sigma_c baryon sigma_c anti_sigma_c baryon sigma_c anti_sigma_c0 baryon sigma_c anti_xi baryon xi anti_xi0 baryon xi anti_xi_c baryon xi_c anti_xi_c0 baryon xi_c lambda baryon lambda lambda_c baryon lambda_c omega baryon omega omega_c0 baryon omega_c opticalphoton opticalphoton photon sigmat baryon sigma sigma baryon sigma sigma0 baryon sigma sigma_c baryon sigma_c sigma_ct baryon sigma_c sigma_cO baryon sigma_c xi baryon xi xi0 baryon xi xi_ct baryon xi_c 125 Chapter 11 Analysis extracting data 126 G4Particle Type Subtype xi_cO baryon xi_c geantino geantino geantino chargedgeantino geantino geantino Secondary tracks These are data that give information about the secondary particles or the primary particle when secondary particles are created They are only available for Secondary Track They are the following PrimParticle Primary particle name FinalPrimMinusSecoKineticEnergy Primary particle PostStepPoint minus secondary kinetic energies SecoDividedInitialPrimKineticEnergy Fraction of kinetic energy of primary at PreStepPoint taken by
288. oncoseesesseossoseeseeoressesses 109 Introduction GAMOS ata secs ics cess esse he E a E 109 TJ atATUIS CTS sasdactsthoectaccceceatilosost nl otha we teattecus ENEA A AE AE E E A 110 Behaviour as a function of information Object cccccsccescteeesteteeeeens 110 Behaviour as a function of output format cccccceesetesesceteesesteteneeeens 111 Selection of data list for a data USEF cccccccccsecescessecescecssceeseceseecsseesaeceseens 113 Saving GAMOS data in a ROOT TTree eee ee eseeeeeensneseseseeeeeces 116 Filtertrom dataene on Ey e ree vateser deh ea E aANT Naa Cea bese Ackactecest sen 117 Classifier by data 2 ticsainonn uihesiideiiin ES a Ea AE E RSE Eaa Balas 117 Primitive scorer from ata cc ccccccceccccssseccccsscssscccsesscssessesssseceesscesessesssseesees 118 Listofayaila l dat onnea a aa eevee E ES 118 RES ae a EEEE E E E E E EET 118 MOO mentum e oats ce SSN ete ae A ai a E te Bie 120 DITCCHON itis cre seid BACs ehose a ight Bech E O tel feoreetsgheltshet en 121 IBTCEB Yo A E A E TE A E 121 Geometrical Objects ss rsiun mesire ikoon ra E E SE 122 Material va ables initiis a A E a aaa aane 122 Particle and ProcESSssss nenaon anaa arei AISEA a 123 Secondary TACKS ss iorsin pone R nean nE E eR EARTE EE AE ARET EAEE 126 ESS OE E N AT AEE EAE A S A E E EEA 126 Output file names nrero e T bh at sanding ei iii ch wa vlaiees 127 Merging results from different jobs ccccccseesessseensteseseecescseeneneneseeeesese
289. one or several of these tutorials to become acquainted with GAMOS e analysis some utilities that may serve you to analyse your output The plug in concept To provide the user with a big flexibility in choosing different simulation components geometry physics user actions histograms and combining them to his her will in a simple way GAMOS is based on the plug in concept This means that the main program runs without predefined components and the user tells it which compo nents are being loaded at run time without needing to recompile by simply listing them in a text input file This mechanism also lets the user define a new component that was not foreseen by GAMOS and easily tell GAMOS to use it together with any other of his her own components or GAMOS components A common example to better understand the plug in concept is the plug in s that are installed on your computer when you open some Internet page with your web browser Your web browser can use these plug in s to get an extra functionality view ing videos animated figures without your having to recompile it and even if the web browser designers had never before heard of the new plug in For each of the simulation component types we will describe in the corresponding section which is the command to select it and how to transform a new user compo nent into a GAMOS plug in For the implementation of plug in s GAMOS has chosen the CERN library SEAL 3
290. oot csv The fol lowing histograms are defined Event Type 100 i e no Rayleigh counting Event Type Number of photoelectric interactions per original gamma N PhotoElec Number of Compton interactions per original gamma N Compton Number of Rayleigh interactions per original gamma N Rayleigh Number of photoelectric interactions vs Number of Compton Rayleigh interac tions per original gamma N PhotoElec vs Compton Rayleigh Energy of gamma upon entering SD Energy at entering SD keV Energy lost in the photoelectric interactions Energy lost PhotoElec keV Difference in position from the gamma entering SD to the point where a photoelec tric interaction happened Diff pos when PhotoElec mm Difference in direction from the gamma entering SD to the point where a photo electric interaction happened Diff dir when PhotoElec mm Difference in kinetic energy from the gamma entering SD to the point where a photoelectric interaction happened Diff energy when PhotoElec mm Energy lost in the Compton interactions Energy lost Compton keV Angle variation in the Compton interactions Angle variation Compton mrad Energy lost in the Rayleigh interactions must be 0 Energy lost Rayleigh eV Angle variation in the Rayleigh interactions Angle variation Rayleigh mrad All these histograms are repeated for the different types of events a prefix
291. os setParam GmTrackingVerboseUA VerboseLevel VALUE 151 Chapter 16 Managing the verbosity Dumping the standard output and error in log files 152 By default the standard output what is printed by G4cout or std cout is saved ina file called gamos log while the standard error what is printer by G4cerr or std cerr is saved ina file called gamos_error log The user may change the name of the output file with the command gamos log setCoutFile FILE_NAME and the name of the error file can be changed with the command gamos log setCerrFile FILE_NAME To avoid filling any log file the following user command must be used gamos log writeFiles FALSE Chapter 17 Detector applications There are three detector applications in GAMOS two related to Nuclear Medicine i e PET SPECT and another one that while also used in Nuclear Medicine it has also an extensive use in other fields Compton camera We describe in this chapter the utilities that are common to all detector applications while we leave those that are specific to each of the in the corresponding chapter Identifying Compton interactions It is frequent that a gamma that enters a detector suffers one or more Compton in teractions before the photoelectric one and then it may leave several hits in different detector elements GAMOS offers several algorithms to identify which of the hits cor responds to the first gamma interaction so that the line to the origin of the pos
292. osity Default is warning that will print the above lines debug that will print each particle read form the phase space file e help prints the set of arguments Automatic determination of production cuts for an accelerator simulation The method used in GAMOS to determine the best production cuts is based on what we can call an inverse reasoning We count each particle that reaches a given Z plane corresponding to the phantom surface and we calculate first the range of the particle in the region where it is created Then we can know that if we put a range cut in that region smaller than the calculated range that particle would not reach our target plane We also compute the range of the mother particle in the region where it was created and the same consecutively for all the ancestors We know then that if we set in any of the regions where each of the ancestor particles are created a cut smaller than the corresponding range we would stop the chain of particles and therefore we would have no particle in the target plane After running a good number of tracks we can know for each particle type and for each region which is the biggest range we can put if we do not want to lose any particle Indeed we may allow to lose a small amount of particles if this speeds up our simulation To know easily which is the biggest cut you can use to lose less than a given percentage of particles GAMOS provides a set of plots one per each particle type and
293. osity Manager c cc eee eeteesteeeteneeeseseeeeeeee 151 Controlling the Geant4 verbosity by event and track cccsessesesceseeseetetenees 151 Dumping the standard output and error in log files 0 0 0 cscs cetesesteteenees 151 17 Detector applications cccssssssssscscesseseececesssesesessensssesssssssstscsesessssseseesssseseeseseeeees 153 Identifying Compton interactions c ccs cesses tenssseeesensseseseseeseseece 153 Compton studies histogram c ccccscceesesesseescecesesesesnenesescenesesesneneneeens 154 Histograms of data about the interactions and the reconstructed hits 155 Classification of good and bad identification histograms as a function of yarale e ea hii iee aha a seeded ceclinaly awed Bown a dae et eet ee 156 Histograms of gammas at sensitive AetectOrs cccceececcescsesteneeseseetesesesneenees 157 Automatic determination of production cuts for a detector cece 158 Automatic determination of user limits for a detector cccccsccsecesseesseeeseeees 159 18 PET application iiien eeii ier as ee Ai EEA E AE EE 161 PET ge MEtry iin ner oa tenir sa ee hardata Nar aO TE T oleae eerie mittee ees 161 PET event classification cccccccccccssscsescsecessecesssseesessessscesessecesesscssscessesseceesesssessees 161 PET histograms event classification ss ssessesssesissssesisressesseesieriestesensnesnenrennees 163 PET output for recOnstructiONn ccccceccce eee cesses csesesee
294. otographic Emulsion Kodak Type AA IST_Polyethylene Terephthalate Mylar IST_Polymethyl Methacrylate IST_Polytetrafluoroethylene Teflon IST_Radiochromic Dye Film Nylon Base IST_Testis ICRU 44 IST_Tissue Soft ICRU 44 Solids SOLID e solid name e solid type name List of solid parameters The meaning and order of the solid parameters is the same as in the corresponding Geant4 solid constructor All the Geant4 CSG and specific solids are implemented The list of solid types and the corresponding parameters is the following for better understanding of the solid parameters meaning we refer to the Geant4 user s manual 7 BOX box e X Half length e Y Half length e Z Half length TUBE tube e Inner radius e Outer radius e Half length in z TUBS tube section e Inner radius e Outer radius Half length in z e Starting phi angle e Delta angle of the segment CONE cone e Inner radius at fDz e Inner radius at fDz e Outer radius at fDz e Outer radius at fDz Chapter 3 Geometry Half length in z fDz CONS cone section Inner radius at fDz Inner radius at fDz Outer radius at fDz Outer radius at fDz Half length in z fDz Starting angle of the segment Delta angle of the segment TRD trapezoid Half length along x at the surface positioned at dz Half length along x at the surface positioned at dz Half length along y at the surface positioned at dz Half lengt
295. otope You may choose several isotopes by repeatedly writing this command This command triggers the reading of the file named isotopes dat if it has not been read yet You may change the name of this file with the command gamos setParam Generator Isotope FileName MY_FILENAME To learn how to change the directory list where GAMOS looks for this file please read the section Managing the input data files If you don t change any property the particle will be generated with a time distribu tion of type decay see below energy distribution of type constant isotope decay see below position at 0 0 0 and random direction Double back to back particle source This is a special source that generates two identical particles back to back i e with the same position energy and time but opposite directions To select it you have to use the command gamos generator addDoubleBackToBackParticleSource SOURCE_NAME PARTICLE NAME ENERGY Chapter 4 Generator SOURCE_NAME is the name of this source that you have to use if you want later to change its time energy position or direction distribution PARTICLE_NAME can be any of the Geant4 particles ENERGY is the initial energy of the particle If you don t change any property the particle will be generated at time 0 position 0 0 0 and random direction Distributions Time distributions e Constant time gamos generator timeDist SOURCE_NAME GmGenerDistT
296. our has to be different than for the histogram case above one cannot use the bin centres and calculate the bin limits but the bin limits have to be ex plicitly provided In other words the energies given will be the limits of the bins and the probability read together with an energy is the probability between the energy and the next energy We recommend then that the last energy has proba bility 0 For example if you want a quarter of your primary particles uniformly distributed between 0 and 1 MeV and three quarters between 1 and 2 MeV you can write the following file 0 0 25 1 0 75 2 0 If the second parameter is interpolate_log the data read will be interpreted as that of an histogram with constant or non constant bin The behaviour is the same as for the interpolate case but the energies are used logarithmically i e the energy will be constantly distributed inside an energy bin taking the logarithm of the energies For example if you want a quarter of your primary particles logarithmically uniformly distributed between 0 and 1 MeV and three quarters between 1 and 10 MeV you can write the following file 0 0 25 1 0 75 10 0 The third argument serves to define which is the unit of the energies in the file If not provided it will be taken as MeV 1 Position distributions e Position at a point 49 Chapter 4 Generator 50 gamos generator positionDist SOURCE_NAME GmGenerDistPositionPoint POS_X POS
297. ower side SPHERE sphere e Inner radius e Outer radius e Starting angle of the segment e Delta angle of the segment e Theta starting angle of the segment e Theta delta angle of the segment ORB full solid sphere e Outer radius TORUS torus e Inside radius e Outside radius e Swept radius of torus e Starting Phi angle fSPhit fDPhi lt 2PI fSPhi gt 2P1 e Delta angle of the segment POLYCONE polycone e Phi starting angle e Total phi angle Number of z planes or Number of rz points For each z plane e Position of z plane e Tangent distance to inner surface e Tangent distance to outer surface For each rz corner e R coordinate of these corners e Z coordinate of these corners The software will know which if the numbers refer to plane or rz points by looking at the number of parameters provided and comparing it with the number expected Example SOLID polyc POLYCONE 0 360 6 3 2 3 5 2 3 5 0 75 3 75 1 3 75 2 Chapter 3 Geometry 32 or equivalently SOLID polyc POLYCONE 0 360 4 233 5 0 75 33 5 1 3 3 75 2 3 3 75 POLYHEDRA polyhedra e Phi starting angle e Total phi angle e Number of sides Number of z planes or Number of rz points For each z plane e Position of z plane e Tangent distance to inner surface e Tangent distance to outer surface For each rz corner e R coordinate of these corners e Z coordinate of these corners The software will know which
298. owing lines in module cc DEFINE_GAMOS_USER_ACTION ExNO02RunAction DEFINE_GAMOS_USER_ACTION ExN02EventAction DEFINE_GAMOS_USER_ACTION ExN02SteppingAction It is not needed to conver the sensitive detector into a plug in that could be called in the user command file because it is explicitly called in the detector construction class Indeed if you want to do it you should delete the lines that instantiate it there and then you can write DEFINE_GAMOS_SENSDET ExN02TrackerSD 227 Chapter 27 Appendix B C utilities The main class exampleNO2 cc is not needed any more We use the GAMOS main and a user command file that we may exampleNO2_GAMOS in with the user commands that select the example components like the following one gamos geometry ExNO2DetectorConstruction gamos physicshList ExNO2PhysicsList gamos generator ExNO2PrimaryGeneratorAction gamos userAction ExNO2RunAction gamos userAction ExNO2EventAction gamos userAction ExNO2SteppingAction run initialize run beamOn 10 You can then run gamos exampleNO2_GAMOS in and you will get the same results as if you run the original Geant4 example Creating your plug in There are several factories in GAMOS that take care of the different plug in types To transform your class into a plug in you have to follow the instructions in this section using the relevant factory and class as indicated in the relevant section of this guide e g G
299. pList or see Appendix This distribution can not be used for single particle sources For understanding the notation to identify touchables in GAMOS see Identifying touchables section Other volume types may be added at user request For understanding the notation to identify touchables in GAMOS see Identifying touchables section 8 Other volume types may be added at user request Chapter 5 Physics You can use the GAMOS physics list use one of the Geant4 physics lists or write your own one following the standard Geant4 way i e by writing your C class inheriting from G4VUserPhysicsList GAMOS electromagnetic physics list The GAMOS electromagnetic physics list defines electromagnetic particles photons electrons positrons and optical photons This physics list lets the user choose among the standard low energy or Penelope models The following physics models are available e gammas e gamma lowener low energy Evaluated Particle Data Library e gamma standard standard electromagnetic processes no low energy gamma penelope processes a la Penelope 6 e electrons electron lowener low energy Evaluated Particle Data Library The bremsstrahlung angular cross section can be selected among tsai 2bn or 2bs see GEANT4 Physics Reference Manual with the parameter gamos set Param GmPhysicsElectronLowEner AngularGenerator GENERATOR_NAME e electron standard standard electromagnetic processes no low energy
300. pe Subtype gamma gamma photon e lepton e e lepton e proton baryon nucleon neutron baryon nucleon deuteron nucleus static triton nucleus static He3 nucleus static alpha nucleus static Genericlon nucleus generic mu lepton mu mu lepton mu tau lepton tau tau lepton tau nu_e lepton e 123 Chapter 11 Analysis extracting data G4Particle Type Subtype nu_mu lepton mu nu_tau lepton tau anti_nu_e lepton e anti_nu_mu lepton mu anti_nu_tau lepton tau anti_neutron baryon nucleon anti_proton baryon nucleon pit meson pi pi meson pi pid meson pi B meson B B meson B BO meson B Bs0 meson Bs D meson D D meson D DO meson D Ds meson Ds Ds meson Ds J psi meson J psi anti_BO meson B anti_Bs0O meson Bs anti_D0 meson D anti_kaon0 meson kaon eta meson eta eta_prime meson eta_prime kaon meson kaon kaon meson kaon kaon0 meson kaon kaon0L meson kaon kaon0S meson kaon B meson B B meson B BO meson B Bs0 meson Bs D meson D D meson D DO meson D Ds meson Ds Ds meson Ds 124 Chapter 11 Analysis extracting data G4Particle Type Subtype J psi meson J psi anti_BO meson B anti_Bs0 meson Bs anti_DO meson D anti_kaon0 meson ka
301. per each region and a simple script to get automatically the cut values One warning is due here as mentioned above when a track reaches the target its range fills a histogram but also the range of all the ancestors of this track It may happen then that when you set a certain cut and the abovementioned script gives you how many tracks would be killed more than one killed track correspond to the same track reaching the target i e with a cut you kill the track that reaches the target and the parent track Therefore you might have an overcounting of the number of tracks killed by a cut To avoid this the total number of tracks the last lines of output is not computed as the sum of tracks in the region This number uses a histogram that contains only one entry per track reaching the target the one corresponding to the track with the smallest range If you want to set a different cut for each region and are worried for this double counting you may have a look at the histogram named trackInfos per Track in target that plots per each track reaching the target how many track informations are kept in the histograms Another useful histogram for this case may be the 2D histogram trackInfo Region vs trackInfo Region that plots all the region number of all the pairs of track informations that correspond to the same track reaching the target you can get a list of which region number corresponds to which region at the end of the standard output file
302. put output re lationship from a file so that any distribution shape can be defined The distribu tion finds among the list of read input values after ordering them the two that are closest i e one bigger and one smaller then it interpolates the two output values corresponding to these two input values The difference between the distributions described below lies in the way this interpolation is done e GmNumericDistributionLinLin Interpolates linearly in the input and linearly in the output f x f x_S x x_S x_B x_S f x_B f x_S where x_S and x_B are the closest smaller and bigger values of x read from the file e GmNumericDistributionLogLin Interpolates logarigthmicaly in the input and lin early in the output f x f x_S log x log x_S log x_B log x_S f x_B f x_S where x_S and x_B are the closest smaller and bigger values of x read from the file e GmNumericDistributionLinLog Interpolates linearly in the input and logarithmi cally in the output f x f x_S exp x x_S x_B x_S log f x_B log f x_S where x_S and x_B are the closest smaller and bigger values of x read from the file e GmNumericDistributionLogLog Interpolates logarigthmicaly in the input and logarithmicaly in the output f x f x_S exp Chapter 14 Distributions log x log x_S log x_B log x_S log f x_B log f x_S where x_S and x_B are the closest smaller and bigger values of x read from the fil
303. r Scoring per category The scoring of flux and equivalent dose can be split following different criteria The first possibility is to score separately the contributions from the real particles that reach the point detector and the indirect contributions calculated with the geantinos The first one will have in the score name the word Neutron or Gamma while the sec ond one will have the word Geantino To activate this option the following parameter should be used gamos setParam GmPDS ScoreSeparatelyTrueAndGeantino 1 The second possibility is use a classifier and get a different score for each classifier index You can add a classifier to GmPDSUAas you do for any other user action Output format At the end of the run the results are written in the standard output or in a file given by the parameter gamos setParam GmPDS ResultsFileName FILE_NAME The following table is written for each score or neutrons or gammas one per point detector copy one per category as describe above First a line with the filter names classifier name particle type detector name and copy score type named ALL if it is not a sub category the detector position and the number of events in the job Then follows a line for each energy with the filter names classifier name particle type detector name and copy score type energy value flux value relative flux error er ror divided by value number of particles contributing to the flux and then for lat
304. r By Physical VolumeReplicated See discussion about Physical VolumeRepli cated filters GmClassifierByRegion It assigns a different index to different regions GmClassifierByKineticEnergy The user must define a minimum a maximum and a width of the energy intervals It creates kinetic energy at PreStepPoint intervals with these values and assigns a different index to different intervals GmClassifierByProcess It assigns a different index to different process names that define the G4Step GmClassifierByParticleProcess It assigns a different index to different particle process name pairs that define the G4Step This means that the ionisation for electrons and positrons will produce a different index despite the process being called the same for both particles GmClassifierByCreatorProcess It assigns a different index to different track creator process names GmClassifierBy Particle It assigns a different index to different particle types GmClassifierByPrimaryParticle It assigns a different index following the particle type for the primary that originated the current particle or the particle itself if it is a primary GmCompoundClassifier This classifier receives a list of classifiers and builds an in dex as Classifier_1 NShift Classifier_2 NShift NShift Where NShift is defined by the parameter gamos setParam GmCompoundClassifier NShift NSHIFT that by default takes a value of 100 Be aware that the classifier index is stored as a
305. r Step and Track The data of these type have in their name the word Change Still other data are of type Accumulated because they return the data accumulated along the steps The data of these type have in their name the word Accumulated Their behaviour depends on when they are called e Track step the value of the step itself e Track the value summed up of all the step of the track Event the value summed up of all the tracks of the event 109 Chapter 11 Analysis extracting data e Run the value summed up of all the events of the run e Secondary tracks it has no meaning Be aware of the behaviour of the filters when you use data of type Accumulated with a user action If an step does not pass a filter the data will not be accumulated and when the value is printed at the end of the track event or run it may give a wrong result You may want to use the option to switch off the filters at stepping with the parameter gamos set Param USER_ACTION_NAME ApplyFiltersToStepping false See section on Filters for more details on this option Another source of classification of data is their C type double int or string The behaviour of double and integer data is very similar the main difference being that in a binary file they are written in different format and occupy a different number of bytes Each string data has a variable that defines the number of characters that will be used when writing a binary file The strin
306. r of voxels is defined with the parameter gamos setParam GmSimplePhantomGeometry NVoxels NVOXEL_X NVOXEL_Y NVOXEL_Z The minimum and maximum extensions in the three axes are defined with the pa rameter gamos setParam GmSimplePhantomGeometry PhantomDims MIN_X MAX_X MIN_Y MAX_Y MIN_Z MAX_Z Then you can divide the phantom in different regions along the Z axis with the pa rameter gamos setParam GmSimplePhantomGeometry MaterialZ Voxels NZ_1 NZ_2 where NZ_iis the number of voxels along Z of the i region Then you can assign the material and material densities of each Z region with the parameters gamos setParam GmSimplePhantomGeometry MaterialNames MATERIAL_1 MATERIAL 2 gamos setParam GmSimplePhantomGeometry Material Densities DENSITY _1 DENSITY _2 Setting off visualization of phantom geometries As the phantom geometry is not built with the text file format the tag VIS that serves to set off the visualization cannot be used for the phantom and the phantom container Instead you may use the following parameters gamos setParam GmReadPhantomGeometry Phantom VisOff TRUE gamos setParam GmReadPhantomGeometry PhantomContainer VisOff TRUE Movements 40 Thanks to the functionality of Geant4 it is possible to displace or rotate a volume during a run To do this in GAMOS you have first to select the volume you want to move and if you want to move it after a certain number of events or after a certain time is e
307. r than this hit time and shorter than this hit time measuring time are considered together This is the default behaviour If your detector is a PET or Compton camera it is likely that it waits for a time at least as long as the measuring time to start the coincidence sorting But it may Chapter 7 Sensitive Detector and Hits happen that this time is even bigger that the measuring time If you think you should simulate this effect you can do it by adding an extra parameter gamos setParam SD Trigger CoincidenceDelayTime SDTYPE VALUE Several independent triggers are defined it may be that each detector volume is associated a trigger or that detectors that have a common ancestor in the geometry hierarchy are associated the same trigger By default the trigger detetor units are the same units defined as explained in the section on Identifying each sensitive de tector copy But you may change this behaviour by changing how many ancestors levels are used with the following parameter gamos setParam SD Trigger NAncestors sDTY PE VALUE This may serve you for example to define a unique global trigger but setting the number of ancestors equal to the maximum number of volumes in the geometrical hierarchy of the detectors e Interval The triggers happen at a constant interval Starting at time 0 the hits are merged if their time are between N measuringTime and N 1 measuring Time e Backwards Hits are accumulated if they have a time afte
308. r the event time minus the measuring time The event time is computed as the time of creation of the first particle in the event Detector dead time A detector takes a finite time to transform an energy deposit into an electronic signal and during that time it is dead and cannot account for any other energy deposition The dead time is considered to start after the hit time plus the measuring time in the case that you set the tpe of measuring to Interval the dead time starts also at the end of the measuring but in this case it is the current triggering time plsu hte measuring time GAMOS holds a list of the dead sensitive detectors i e those that have produced a hit in a time prior than the current time minus the dead time You can define the value of the dead time for each detector type with the parameter gamos setParam SD DeadTime SDTYPE VALUE that takes a default value of 0 ns The dead time affects by default all detectors in a block This means that if a detector is dead it considers that all detectors that are placed in the same mother are also dead the usual behaviour for example in a PET or SPECT detector where all crystals in a block share the readout You may change the number of ancestors that become dead by setting the paramter gamos setParam SD DeadTimeDUListByBlock NAncestors NLANCESTORS which as just mention takes a default equal to the value of the parameter SD DetUnitID NAncestors Take into account that the numb
309. r volume This feature needs a special mechanism as the steps cannot be saved until knowing if a future step will fulfill the second consition and when this happens the steps to be saved have been deleted Geant4 only saves one step at a time To use this mechanism a GmFutureFilter has to be defined giving as arguments two filters first the one that should fulfill the steps to be used for scoring for saving their information filling histograms and second the one that shuld fulfill the steps that trigger the use of the first steps gamos filter myFutureFilter GmFutureFilter FILTER_PAST FILTER_FUTURE If a future filter is used with a user action it must be the only filter If you want to add more normal filter together with the future filter you should combine them with GmANDFilter and put them as FILTER_PAST of the future filter GmFutureFilter only acts in one track this means that the steps to be used as well as the future steps belong to the same track If you want to set a condition in the future also to the children tracks of the steps to be used e g score the energy of the steps that are in a volume only if the track or any of the secondary tracks created at this step or any future step of this track including the children of these secondary tracks reach another given volume you have to use GmFutureWithChildrenFilter Future filters only act on steps so if you use them for example together with a Gm TrackDataHistosUA t
310. re include GAMOSINSTALL config architecture gmk SUBDIRS GamosUtils GamosBase GamosUserActionMgr GamosData GamosAnalysis GamosGeometry GamosMovement GamosPhysics GamosGenerator GamosSD GamosUtilsUA GamosReadDICOM GamosScoring GamosApplication include GAMOSINSTALL config globlib gmk You only have to change the line starting by SUBDIRS to list the name of your subdirectories 1 You may type for example locate libXmu so to know where they are in they are not in the mentioned directories 2 By MY_GAMOS_DIR we mean the installation directory you have chosen i e MY_INSTALLATION_DIR plus the directory where the GAMOS version is in stalled ite MY_INSTALLATION_DIR GAMOS 3 0 0 3 For the external packages the set of libraries is fixed and defined in the configu ration files Chapter 2 Getting started Chapter 3 Geometry You can describe your detector in three different ways by defining your setup in a text file by using one of the geometry examples provided or in the standard Geant4 way by writing your C class inheriting from G4VUserDetectorConstruction Building your geometry with a text file You can define your geometry in a simple text file as described in the following sub section You can also use as example the one at MY_GAMOS_DIR data test geom Once your file is ready you have to tell GAMOS to use your geometry definition first telling the name of your file with the command gamos setP
311. rection From the above two definitions several shower variables are calculated Maximum longitudinal length maximum of the step point longitudinal lengths Maximum transversal length maximum of the step point transversal lengths Average longitudinal length average of the step point longitudinal lengths weighted with the energy deposits Average transversal length average of the step point transversal lengths weighted with the energy deposits The deposition of energy in the step is actually done in small quantities approxi mately uniformly distributed along the step As it would be too CPU tiem consuming to simulate eacho of these interactions we just consider a deposition point making a linear interpolation between the two steps edges in other words we use as energy deposit point the average of the pre and post step points If you want to use instead the PreStepPoint or PostStepPoint you have to use the parameter gamos setParam USER_ACTION_NAME StepPointToUse TYPE where TYPE can be Pre Post or Linear the default choice Other algorithms may be implemented in the future at user request With the above mentioned histograms variables a file named shower root csv is writ ten with the following histograms the second name is the type of histogram for his togram limits setting see section on Using a common histogram class e Total energy Total Energy E e Maximum longitudinal length Maximum R transv Pos e
312. rgy of second gamma interaction e DetCompton Algo Interaction Energy 3rd Energy of third and higher gamma inter actions e DetCompton Algo Interaction Energy 1st others Energy of first gamma interaction minus energy of other interaction e DetCompton Algo Interaction Energy 2nd others Energy of second gamma interac tion minus energy of other interaction e DetCompton Algo Interaction Energy 3rd others Energy of third and higher gamma interactions minus energy of other interaction e DetCompton Algo Interaction Energy 1st others Energy of first gamma interaction vs energy of other interaction e DetCompton Algo Interaction Energy 2nd others Energy of second gamma interac tion vs energy of other interaction e DetCompton Algo Interaction Energy 3rd others Energy of third and higher gamma interactions vs energy of other interaction 155 Chapter 17 Detector applications 156 By default all these histograms have 100 bins betwen 0 and 1 The same set of histograms can done for the position instead of energy Several posi tion variables can be selected X Y Z XY sqrt X X Y Y XZ YZ XYZ To fill these histograms the following parameter should be used gamos setParam DetComptonStudyHistosUA Algorithm Variables VAR1 VAR2 VARN where the variables can be Energy XPos YPos ZPos XY Pos XZPos YZPos or XYZ Pos At the same time that the histograms about gamma interaction data they are fil
313. riable of the distribution i e it will be used to extract the input value for each track or track step To assign a data the following parameter should be used gamos setParam DISTRIBUTION_NAME Data DATA_NAME Reading values from a file Many of the distributions described below need to read the data from a file The parameter gamos setParam DISTRIBUTION_NAME FileName FILE_NAME defines the name of the file that contains the distribution data This file is a two col umn set of values where the first column gives the input values x and the second the output values y After being read the input values are ordered in increasing or der To calculate the output value corresponding to an input value each distribution uses its own algorithm see below If the input value is smaller than the minimum 139 Chapter 14 Distributions value in the file or bigger than the maximum value an exception will be thrown as the value cannot be calculated It is also possible to read the data from a histogram in ROOT or CSV format In this case an extra parameter has to be provided to set the name of the histogram gamos setParam DISTRIBUTION_NAME HistoName HISTO_NAME The input values are taken as the centres of the histogram bins The minimum and maximum values read are extended to the lower and upper edge of the histogram axis i e minux and plus half a bin If the input value is between this minimum and the lowest bin centre the output is
314. rocess so that the cuts can be automatically set in an easy way If you want to apply the same cuts to all processes you can use the GAMOS command gamos GMphysics applyCutsToAllProcesses that will instantiate an object of type G4EmProcessOptions and invoke the method SetApplyCuts true In the PET and Radiotherapy applications chapters you can see the details of how to apply this technique in these fields Range rejection The range rejection technique consists on killing a particle at creation and deposit ing all its energy locally if it is not going to leave the current volume To do this in practical terms the particle is killed if the range is smaller than the distance to the volume boundary although it would have a chance to exit the volume this chance is considered negligible You can analyze which would be the effect of applying this technique by using the same user action as for the production cuts e g gamos userAction GmProdCutsStudyuUA RTCutsStudyFilter It will produce a table with the number of tracks that would be killed by the range re jection and would not reach the target the tracks themselves or any of their children Chapter 5 Physics As for the production cuts they are printed by region by particle and by creator pro cess type To get a closer inside on this technique several plots are produced one per each region each particle and each creator process representing the logarithm of the difference saf
315. s Silent 1 no output is printed only when there is an exception and the job stops you will get the details of why it happened Error 0 only error messages are printed Warning 1 only error and warning messages are printed Info 2 you get some detailed information of what is happening Mainly mes sages at each run and each event Debug 3 you get a quite detailed information of what is happening Mainly messages at each track and each step Test 4 this level is only meant for testing your code the first time you write it On top of this the verbosity in GAMOS is classified in different types so that you can set different verbosity options for different parts of the code The list of parts of the code that have its independent verbosity in the current GAMOS version is the following GmBase controls the verbosity of the base classes filters classifiers input output management GmGeometry controls the verbosity of the geometry classes GmGeneration controls the verbosity of the GAMOS generator GmPhysics controls the verbosity of the physics classes GmSD controls the verbosity of the sensitive detectors hits digits and recon structed hits GmUA controls the verbosity of the classes for user action management GmScoring controls the verbosity of the scoring classes GmReadDICOM controls the verbosity of the classes to read DICOM files GmData controls the verbosity of the GAMOS data GmAnal
316. s Urban93 If your problem is in the micrometer or nanometer range this model may give incorrect results and we recommend you to use the GoudsmitSaunderson one Bremsstrahlung angular distribution The Geant4 low energy electromagnetic model of bremsstrahlung offers three differ ent angular distributions namely Tsai 2BN and 2BS see Geant4 Physics Reference Manual for an explanation of the difference between the three models If you have selected the low energy extension in the GAMOS physics list you may select among one of the three with the following parameter gamos setParam GmPhysicsElectron Bremsstrahlung Angular Distribution MODEL where MODEL canbe tsai which is the default model 2bn or 2bs The recom mended behaviour is that below 1 keV and above 1 MeV the distribution is always tsai while for the energies in between it can be changed If you want to override this limits you may do it with the parameters gamos set Param GmPhysicsElectron Bremsstrahlung EnergyToForceTsaiMin ENERGY gamos setParam GmPhysicsElectron Bremsstrahlung EnergyToForceTsaiMax ENERGY You should nevertheless take into account that the 2bn distribution has an intrinsic kinematical limit of 1 MeV so you should not set the upper limit to a higher value if you want to use it In the latest Geant4 release it is also possible to change the bremsstrahlung angular distributions for standard processes To do it use the same parameter as above In this case
317. s ac cessed using the Compton camera event classifier Many of the utilities for Compton camera detectors are related to the sensitive detec tors that they contain so please read the Sensitive Detectors chapter if you have not done so yet Compton camera geometry No standard geometry for Compton cameras exists and as such it is impossible to provide the user with a single standard geometry file to model all systems A typical Compton camera is defined using scatterer detectors where Compton scattering is the ideal interaction of incident gamma rays and absorber detectors where Photo electric absorption is the ideal gamma ray interaction It is necessary to define the sensitive detectors as either a scatterer or absorber using the parameter gamos SD assocSD2LogVol GmSDSimple Scatterer DETECTOR_LOGICAL_ NAME gamos S D assocSD2LogVol GmSDSimple Absorber DETECTOR_LOGICAL_ NAME The Compton camera directory contains a utility to build a Compton camera system in either i a dual ring configuration or as ii a stack of detectors Although it is expected that these two examples will cover most users needs it is still possible for the user to define their system via the GAMOS geometry text file input i The ring system is composed of an inner ring of scatterer detectors and outer ring of absorber detectors The rings can be replicated along the axial direction so that a full body system can be simulated The following parameters are use
318. s from the minimum Z value of this volume until the minimum Z value of the next volume so that all tracks that are outside it will be killed This utility is activated by selecting the user action gamos userAction RTZRLimitsAutouA You may argue that too many particles or too few are killed with this automatic definition of limits You may simply changed the dimensions of the volumes placed at world adding container volumes made of air will not change your physics or you can define the limits your self by selecting the user action gamos userAction RTZRLimitsuA Then you have to write a file named rtzrlimits lis with the list of values you want to use The format of that file should be the following a set of lines with three numbers representing the Z value of the plane and then the X and Y limits The planes will be extended in Z until the previously defined Z for the minimum Z defined the world negative Z limit will be used If you want to change the name of the limits file you can do it with the command remember to define a parameter always before selecting the user action gamos setParam RTZRLimitsUA FileName MY_FILENAME The user has also the option that particles rejected are not killed but Russian Roulette is played with them and only if they are rejected they are killed If they are accepted their weight will be increased by the corresponding value To use this option the following parameter must be set gamos setParam
319. s not set it is STP i e 273 15 kelvin The default unit of temperature is kelvin Example MATE_TEMPERATURE G4_WATER 293 15 kelvin 20 oC MATE PRESSURE e Material name e Pressure If pressure is not set it is STP i e 1 atmosphere The default unit of temperature is atmosphere 11 Chapter 3 Geometry 12 Example MATE_PRESSURE G4_WATER 1 5x bar Geant4 internal database of materials and elements Geant4 provides a list of predefined materials whose compositions correspond to the NIST definition 13 Among them you can find all single elementary materials from Z 1 Hydrogen to Z 98 Californium You can use those materials when building a volume without the need to redefine them on your ASCII text file It is just enough that the material name you assign to a volume corresponds to the name of one of these predefined materials they all start with G4_ The Geant4 materi als have the mean excitation energy set explicitly instead of allowing an automatic calculation from its components You may override those materials if you want by redefining them in your ASCII file Also Geant4 provides the definition of all elements from Z 1 Hydrogen to Z 107 Bohrium Their names are the usual symbol in the periodic table of elements no G4_ These elements take into account the isotope composition you can find the details of the NIST materials composition in th
320. s true if all secondary tracks created accept all the filters It does not implement the AcceptTrack method GmlInverseFilter returns the opposite that the filter it receives as only parameter Applying filters to a user action It may happen that you do not want that a filter is applied to a user action in all cir cunstances i e each begin of track each track step and each end of track An exam ple can be a user action that is using a accumulating data see section onGAMOS data at PreUserTrackingAction the variable for example energy deposited is ini tialized to 0 at SteppingAction the new energy deposit is added and at PostUser TrackingAction the variable is printed but if you use in this case a filter that checks that the track is in a certain volume it may happen that the PreUserTrackingAction is not invoked because the track at that moment was not in the volume and then the variable will be wrong To prevent these cases there is the option of not applying the filters in a given circunstance by setting the parameters gamos setParam USER_ACTION_NAME ApplyFiltersToStepping false gamos setParam USER_ACTION_NAME ApplyFiltersToPreTracking false gamos setParam USER_ACTION_NAME ApplyFiltersToPostTracking false gamos setParam USER_ACTION_NAME ApplyFiltersToStacking false where USER_ACTION_NAME is the name of the user action where you want the filter to take effect which includes the name of the filters and classifiers see sectio
321. s utility serves to sum phase space files corresponding to different jobs with the same setup To use it you have to write a file containing the list of header phase space files one file per line for example ps 20000 IAEAheader ps 20001 IAEAheader ps 20002 IAEAheader Then you just have to run the executable sumPS INPUT_FILE_LIST_NAME OUTPUT_FILE_NAME where INPUT_FILE_LIST_NAME is the name of the file containing the list of files to add and OUTPUT_FILE_NAME is the name of the output file that will contain the sum of all the files two files indeed as usual for IAEA phase space files OUT PUT_FILE_NAME IAEAheader and OUTPUT_FILE_NAME IAEAphsp When running you will see on the screen something similar to this Opening phase space contained in ps 20000 1TAEAheader of type IAEA 206 Chapter 22 Radiotherapy application PARTICLES 225437 NPART_TOT 225437 NPARTORIG_TOT 5000000 RATIO 0 0450874 0 000101661 RATIO_TOT 0 0450874 Opening phase space contained in ps 20001 1TAEAheader of type IAEA PARTICLES 224635 NPART_TOT 450072 NPARTORIG_TOT 10000000 RATIO 0 044927 0 000101455 RATIO_TOT 0 0450072 Opening phase space contained in ps 20002 1TAEAheader of type IAEA PARTICLES 224813 NPART_TOT 674885 NPARTORIG_TOT 15000000 RATIO 0 0449626 0 000101501 RATIO_TOT 0 0449923 x x x x N Particles 674885 x x N Photons 673804 x x x N Electrons 1057 x x x x N Positrons 24 x x x N Orig
322. sceeees 80 Hits GigitiZatlOn 5 isie sien ad a a nants bated aes 80 Hits and digits reconstruction c cece sseseseeserenssesesesssesesescseseseecesees 81 Examples of reconstructed hit builders cccceceeeeseeeetesceneneseseeneeseenens 81 Identifying each sensitive detector COPY seccseccseseseseeseseeesssesnstesesceeesesesnsnenesees 82 Storing and retrieving Nitss ipime apee E EE Eea A aE 82 Fil f rmats ienes naa a Lovech e a a 83 Hits histo Sram sis sinaoso aie eaa EER AEE a AEE TEE E a Aea 84 8 SCOTING aaa a a A i EE 87 Creating a SCOTET siisi iioii iaia a ahere aeae usta caste i raa aa aire Ea TET 87 SCOrEEClAS SESE eE e Tosca e e e er a e a ee e ee AE e Riestoee 88 Scoring in voxelised phantomS ss ssssseessesssesissississeesiesiestessissesnesneeseeneeses 92 Bilter Classes E RE E E es ETE T O R ASTE EE 92 Sc rer Printers naia Soa EE SeT a EE Ged e EEA 92 Classifiers in sainia a a a ee aa i e an a e ee a 94 Multiplying Dy d tass tersine Seccsenetispenscbeharvedeussssenshatdvesssbsavabbeoaboetasvapas sndeze 94 Multiplying by distribution cee cesses sesseseesenesesesenssesesessnseseecssen 94 Convergence testing mirisi aean a aa eA aa E a a a 94 Point detector Score eenen n A Ea Ea aS EE E a IR OE ES 96 Theoretical pasisi Seniat a a a e aE E Ee eae a SE TERCIER ged 96 GAMOS implementation ssssssssessisseessstessestestissessesstssiesiesressesnesnesneenieneenes 98 Variance reduction techniqueS cccc
323. se in YZ direction Dose YZ_merged e Dose of each voxel Dose Integrated dose of each voxel i e all the voxels that have dose equal or greater that a given bin fill that bin Dose volume The word merged refers to the fact that this histograms count the dose in one direction or two integrating the dose in all the voxels in the ohter two or one direction If you want to obtain other histograms out of the dose in the voxels you may list what you want in a file in the following way first give the name of your file with the parameter gamos setParam RTPSPDoseHistos HistosFileName FILE_NAME In this file you have to fill a line for each histogram you want with the following information e Histogram type it must be 1X 1Y 1Z 2XY 2XZ or 2YZ e Histogram name e Minimum voxel in X e Maximum voxel in X e Minimum voxel in Y e Maximum voxel in Y 205 Chapter 22 Radiotherapy application e Minimum voxel in Z e Maximum voxel in Z For the minimum and maximum voxel value you may use the total number of voxels by writing one of the words NVoxelX NVoxelY or NVoxelZ Also arithmetic expres sions are comment starting the line with are allowed One example file can be the following for a phantom with number of voxels 101 101 100 recovering the 1D merged histograms 1X RTPSPDoseHistos Dose Profile X_merged 0 NVoxelX 1 0 NVoxelY 1 0 NVoxelZ 1 1Y RTPSPDoseHistos Dose Profile Y_merged 0 NVoxelX 1 0 NVoxelY 1 0 N
324. sed by an electron positron annihilation Combining the position information of these hits a Line of Response LOR can be reconstructed The original gamma source for an event lies somewhere on the LOR Both for Compton camera data as for PET data the SOE algorithm starts with a ran dom ensemble of states This means that at initialization for each event a random position on the corresponding Compton cone or LOR is assigned A 3D density ma trix is defined where the solution space is divided in voxels and the density per voxel depends on the number of initial event positions in that voxel Subsequently the SOE algorithm performs a number of iterations At each iteration for each event a new position on the corresponding Compton cone or LOR is cal culated The new position is accepted according to the density value of the voxel corresponding to the new position compared to the density at the old position The density matrix is updated accordingly The iterations are repeated until the algorithm has converged By switching on particular parameters as explained later the Resolution Recovery method can be used This method tries to recover for possible deviations in the hit positions the hit energies and the Compton cone angle due to the spatial resolution the energy resolution and the Doppler broadening effect By randomly smearing these variables for each event the method tries to find their optimum values Getting Started
325. sesnanenees 127 Example of Analysing text output files 0 0 0 0 cece censeeeneseneneneeces 129 TZ Falters sa enian a n a Ra Ne ee E aoa eE EEIE 131 TAtrO Gu ctlOny e Oe ele ees riod Solin Bee ee 131 Simple filters ss sseses esse ses overs e E R Mideast AA EEN EE R R 131 VO LITO TAILOTS ea ota chasing aree eSa ERA au ade cdasVa obese abe cbavatevedecen suudestesvesde lesan Stes 132 Filters OL filters ninr na ra Maes eee shes ows lb bien oc bbe dewalt sede eae 134 Applying filters to a user Actionissa toisiaan taarna 135 Checking filters at a user ACHO sssini iatan 135 Filtering steps in the future cee cece ceeesseesesseesessseseseseeseseecee 136 13 CLASSIIEIS iini isesend E a EE i E sedebsactocedsshases 137 TPO GUC HOD rites a eek Aes BS esse a r a a e EE ar e aa 137 Setting indices to ClaSSifiers cccesesceseeceseeseseeteseeeeeneseseeescsceaneneseecesesssnsanenees 138 14 Distributions ick ccsscadecs caciisssscesessccassvace cau cessnvaedecdeVecascssdetecwsccussascessetesdasesceiacsessetcocseceies 139 JERAR OTG hE KEE ON ESAE A TETA AE ad nadie a anced ded E A TETT 139 Creating aidistrib tion s is isetare eae L stievcaassssiesssassvedouesestsedgute chee 139 Assigning a GAMOS dataiis rerep iereti ss ere a E E eE iedit 139 Reading values from a file ccccccccce cee cise ceeseseecesseseesessseesesessseseseseneseseeeees 139 Numeric distributions essa a a a i ao TEE 140 String distributions assii arla area aaar raa E Aa roa Aea ET A
326. sity unless the real source location is given in which case this is used e m_c3 Y profile plot Shows the density along the Y axis with X x_max and Z z_max the x and z coordinates of the voxel with maximum density unless the real source location is given in which case this is used Chapter 21 Image reconstruction utilities m_c4 Z profile plot Shows the density along the Z axis with X x_max and Y y_max the x and y coordinates of the voxel with maximum density unless the real source location is given in which case this is used m_c5 R profile plot The density as a function of the radius is calculated The ra dius is taken from the voxel with the maximum density unless the real source location is given in which case this is used The bin contents in this histogram are normalised with the 3D volume corresponding to each bin I e for R 0 bin1 the volume is 4 3 pi R_bin142 for R bin1 bin2 the volume is 4 3 pi R_bin2 2 R_bin1 2 m_c6 Accumulative R plot The same as m_c5 but without normalising with the corresponding volume of the solution space This way it can be clearly seen how many events reach the center bin and how many events are outside it 185 Chapter 21 Image reconstruction utilities 186 Chapter 22 Radiotherapy application The Radiotherapy example contains some utilities for the simulation of a teletherapy linear accelerator and dose calculations in the patient Many
327. smaller if the point is farther from the detector what is not always the case as it may be that a point closer to the detector traverses denser materials Indeed the contributions are not eliminated but to avoid biasing Russian roulette is played The maximum distance is set with the parameter gamos setParam GmPDS MaximumDistance DISTANCE which by default takes a value of 1000 mm The Russian roulette factor is given by the parameter gamos setParam GmPDS MaximumDistanceRRFactor VALUE which by default takes a value of 100 To activate this technique you have to set the parameter gamos setParam GmPDS UseVRMaximumDistance 1 You may use the control histograms specially the histogram Neutron PD N interac tion dist to detector mm vs weight to determine which are the maximum distance and Russian roulette factor that best match your application Split particles of big weight The idea of this technique is to sample more those cases which bigger probabilities It may be very useful also to eliminate the seldomly occurring big weight contributions that will make your error big The user defines a minimum and maximum weight for the particles to be split gamos set Param GmPDS MinimumWeightForSplitting MIN_VALUE which by default takes a value of 1 E 30 gamos setParam GmPDS MaximumWeightForSplitting MAX_VALUE which by default takes a value of 1 E 5 and the maximum splitting number gamos setParam GmPDS MaximumSplitting MAX_SPLIT
328. sssssseesesesseeseseeeseseecee 163 histimiode binary files 0 j v ccventeisn dh Aveslge we cediaiee EA weed A aS 163 Projectiondata tile esigere ae apa Near ae Aaa aara 164 PET histograms positrons ssis iiia araser o eines i ienee Geoana ioner I raain 165 PET histograms distance between twO gaMmAas ss ssssissesssesiesisstessessessesrersees 165 19 SPECT application csscsssssssesssceseeseececesssssesesssssssesessssssssscssssstscsesssssesesseseesees 167 SPECT event classification nesine en e e a a E ERAS 167 SPECT histograms event classification s ssssssssesssessisrissesssesisrtestessesnesnenreesees 168 SPECT output for reconstruction sssesesesssserttssstesttesststeesttsrteesttsnteestesnteentesnteet 169 20 Compton camera application sseessessessesseoreeseesessessroseeseeoressessesseoseeseeseesrossesseseeosees 171 Compton camera geometry cecccceccscesecsseecsesesessteeessesesesseecseseseseseessesssesseeeeeeeaees 171 Compton camera Event Classification sss sessssssertssstseteesrtrterstterterstesnteestesneees 173 Compton camera histograms event classification s ssssssssssesseiseessssereeeeeee 174 Compton camera output for reconstruction sses sessesissessissiesieresstessessesresrersees 175 21 Image reconstruction utilitieS eseessssesseesreeseesessesssoseeseeoressessesseoseoseeseesrossosseseeosees 177 List mode to projection data Im2pd sessesssssssssssesisssessisr
329. ssterstessserttesees 9 Dumping your Geant4 geometry in text file format cc cece 33 Adding new tags to your input text file cece seeneeseeceeeeceeens 33 Parallel geometries nisipate seia aa napeto a aia 35 Building simple SeOmetries sinnis 36 Building a simple geometry with one material ccs seseseseseseeeeeeeeeeee 36 Building your geometry With C code oo ee eeseseesenessesereseneseseseeseeeceeee 36 Reading DICOM Ailes kranten best steucctedtdeet con Sselicecaileletiseiiivotttatiretbaties 37 Converting a DICOM file to a simulation file ccccecceeeeeteeseeteteseeens 37 DICOM file format sssi a a a BoM eats ode ea aa 37 Reading a DICOM file in a GAMOS jOb ssssensesssssssessesssssissesssessessesnseseesesses 38 Partial phantom geometries ssssssssesssssssssestestiesessisssesiesieseessessenesseeneereeses 39 Simple phantom geometries ss sssssessssssessestetissesstsstesiesiestesresnesnesneeseeneeses 40 Setting off visualization of phantom geometries ss ss ssesssissessrseeseereese 40 MO VeMme nits ssai o a a e a 40 Movement description from a file ssn sssssssssstssssesstssstesttsnteesttsnteentesstersensss 41 Geometry utiliti ssy sisses sa on a a Di RE a 42 Commands to print geometry objects sesssssssessssstssssesttssteesttsteestessteestesse 42 Cr ruhesh Aaaa TE Oaa e ees S ES Ee SEENT 43 Masnetic field inung en e a r E a E E e Moths ooh tind 44 Local magnetic field iiipin aeaa
330. st line contains the number of events e Number of voxels in the X Y and Z directions e g n_x n_y n_z e Array of voxel boundaries cm in the X direction n_x 1 values e Array of voxel boundaries cm in the Y direction n_y 1 values e Array of voxel boundaries cm in the Z direction n_z 1 values e Array of dose values Gy cm 3 n_x n_y n_z values e Array of dose relative error values n_x n_y n_z values Saving scores and scores squared in binary file The second available file is a binary file where it is written the dose and dose squared in each voxel The binary format allows for a faster writing and reading and the fact of writing the dose squared instead of the error serves to calculate in a proper way the error correlations when the doses from several jobs are added To obtain it you just have to add the scorer printer GmPSPrinterSqdose to your scorer for example gamos scoring addPrinter2Scorer GmPSPrinterSqdose DoseScorer The output file is named by default sqdose out You may change it with the parameter gamos setParam PRINTERNAME_SCORERNAME FileName MY_FILENAME wherePRINTERNAME is the name of the printer by default GmPSPrinterSqdose and SCORERNAME is the name you have given to the scorer All variables are of type float and the format is the following Number of events original number of events used to generate a phase space file is phase space file is used as primary generator e Number of voxels in the
331. study checking if the particles created by ionisation or bremsstrahlung are taking a big proportion of the time by adding the command gamos userAction GmTimeStudyUA GmClassifierByCreator Process If your application is a nuclear medicine detector or a radiotherapy tratment we recommend you to read the sections of autmatic optimisation of production cuts which may help you in getting the best cut values By default the production cuts only affect ionisation and bremsstrahlung but you may force that they are also used in all processes by using the command gamos physics applyCutsForAllProcesses 1 Killing particles of small energy An alternative or complementary approach ot the optimisation of production cuts is the optimisation of the user limits that kill the particles when their energy becomes small see section on User limits It is likely logic that if you put a production cut to 217 Chapter 25 Optimising the CPU time of your application kill particles of small range you kill the particles when their energy becomes small so that they will not travel more than that range value For efficiency reasons we recommend that you use the user limit gamos physics userLimits setMinE KinBy Range USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE_NAME MIN_RANGE If your application is a nuclear medicine detector or a radiotherapy tratment we recommend you to read the sections of autmatic optimisation of user limits which may help you in
332. t e libX11 devel e libXmu devel e libXi devel e libSM devel e libICE devel e freeglut dev this package has some dependency problems so you should select the option skip broken e libXft devevl e libXpm devel Running an example If you have done a standard installation you will have your code compiled and ready to run Before running any example you have to set some configuration variables mainly where you have installed GAMOS and the depending libraries This is all done in the file MyY_GAMOS_DIR config confgamos sh or MY_GAMOS_DIR config confgamos csh Therefore before running you have to source this file source MY_GAMOS_DIR config confgamos sh or source MY_GAMOS_DIR config confgamos csh depending on your shell flavour Remember to type this command every time you start a new session to run GAMOS To run your application inside GAMOS you do not have to write a main program as GAMOS provides a unique main that serves to run any application When you run the GAMOS main it will load and call the components you want geometry physics generator hits building histograms by simply defining them in the input command file Therefore to run your application simply type gamos MY_INPUT_FILE where MY_INPUT_FILE is a typical Geant4 macro file that includes Geant4 and GAMOS commands The minimum set of commands that you need are those to select a geometry a physics list and a generator to i
333. t additional output each 100 iterations before SOE_ImageRecon readDensityMatrix read density matrix in_density_matrix img SOE_ImageRecon readCurrentStat read current state file currentstate dat SOE_ImageRecon help for this help output The seed flag sets the seed for the SOE algorithm This way a SOE run can be repeated with exactly the same random numbers With the extralterInfo and the averageStatesOut flags there will be additional output for debugging purposes With the readDensityMatrix and readCurrentState flags the densitymatrix img and currentstate dat of the format as the standard output file data_endstate dat are read in at initialisation for debugging purposes With the help flag the list of all flags is printed to screen Analysis In the root directory there are various ROOT programs that can be used for the analysis One of the most important ones is SOE_img3D C This ROOT program visualises the output of a SOE 3D image reconstruction At start up will ask the user whether the real location of the gamma source is known If it is not just type 0 If it is type 1 and subsequently give the x y and z coordinates of the source location Each plot is drawn in its own separate canvas e m_cl 3dcontour plot Shows a 3D contour plot e m_c2 X profile plot Shows the density along the X axis with Y y_max and Z z_max the y and z coordinates of the voxel with maximum den
334. t for each hit If you want any of these reconstructed hit builders to be active you can select one of them with the command gamos recHitBuilder RHITBUILDER_NAME where RHITBUILDER_NAME is one of the classes described above Identifying each sensitive detector copy 82 To identify each detector unit individually you have to give a different detector unit ID to each copy of your sensitive detectors each G4VTouchable in Geant4 terminol ogy GAMOS does this automatically for you If you use the GmSDSimple class it will give each SD copy a detector unit ID that will be the copy number of physical volume 100 copy number of parent physical volume 100 100 copy number of grandparent physical volume You can change the number of ancestor volumes to build the detector unit ID with the parameter gamos setParam SD DetUnitID NAncestors that takes a default value of 3 These ancestors include the detector itself i e if set to 1 it is only the detector without looking at the geometry hierarchy You can also change the value of the shift that multiplies each ancestor copy num ber using the parameter gamos set Param SD DetUnitID NShift that takes a default value of 100 Chapter 7 Sensitive Detector and Hits Storing and retrieving hits GAMOS provides you with the option of storing in a file the hits produced during a run and reading them back in another run Creating hits from track in the sensitive detector or readi
335. t should be applied to the object in the reference system of its mother It can be defined in three ways e a By giving the three rotation angles around the X Y and Z axis in this order of rotations e b By giving the polar and azimuthal angles of the X Y and Z axis after the rotation is applied e c By giving the nine matrix elements of the rotation matrix XX XY XZ YX YY YZ ZX ZY ZZ The tag for the three cases is the same The parser will know which case is meant by the number of parameters a ROTM e Name e Angle of rotation around global X axis e Angle of rotation around global X axis e Angle of rotation around global X axis Example ROTM RO 0 0 0 b ROTM e Name e Polar angle for axis X e Azimuthal angle for axis X e Polar angle for axis Y e Azimuthal angle for axis Y e Polar angle for axis Z 29 Chapter 3 Geometry 30 e Azimuthal angle for axis Z Example ROTM RO 90 0 90 90 0 0 c ROTM e Name e 9 parameters defining the rotation matrix Example ROTM RO 1 0 0 0 1 0 0 0 1 Module A module is a new concept that simplifies the description of difficult pieces of a ge ometry While these pieces could be built by adding several volumes and placing them in the correct position it is sometimes much easier to give a few parameters that describe them and GAMOS will take care of making all the calculations to create the volumes and place them The current implementation has
336. t will be needed This check is not mandatory but if you do not do it and you are missing some library when you run you will get an error message bin Build the executable You will probably never need this as GAMOS is based on dynamic loading and plug in s so that there is only one GAMOS executable which is built at installation The following two lines are needed for configuration include GAMOSINSTALL config binmake gmk include GAMOSINSTALL config general gmk Notes Chapter 2 Getting started If you edit the file general gmk you will see that it is just including a different file for each package Therefore instead of using it you may include all or only a subset of them if you do not need them all Finally you define the GAMOS libraries that will be linked to yours i e the libraries of each of the files that you have included in your code EXTRALIBS l1GamosBase lGamosUtils l1GamosFactories l1GamosUserActionMgr If you have doubts about which GAMOS libraries to include you may include them all by including include GAMOSINSTALL config gamos_libraries gmk If you have built several levels of directories you may want to have the possibility of typing make at the top most directory to trigger the compilation of all the directories To do this you just have to add a GNUmakefile at the top level directory similar to the one at GAMOSINSTALL source GamosCore GNUmakefile that we reproduce he
337. tDirectionGaussian The primary particles will be generated close a line where the two perpendicular directions are sampled with a Gaussian distribution The parameters are DIR_X DIR_Y DIR_Z SIGMA_Y SIGMA_Z The direction is first selected along the X axis the Y and Z are them samples with two Gaussian distributions centered at 0 and with widths given by SIGMA_Y SIGMA_Z and them the direction is rotated with the angles given by DIR_X DIR_Y DIR_Z Position and direction distributions It is also possible to create distributions where several of the four variables time en ergy position and direction are generated at the same time so that they are related You have nevertheless to keep in mind that the order of calling will be time position energy and direction distributions In case you need a different order for example if the position is determined by the value of the direction you can calculate both the direction and the position in the GeneratePosition method return only the position and keep the direction in a class data so that it can be returned in the GenerateDirection method e Position in volume surface pointing towards centre GmGener DistPositionDirectionIn VolumeSurface SOLID_TYPE SOLID_DIMENSIONS POS_X POS_Y POS_Z ANG_X ANG_Y ANG_Z The position is distributed in the surface of a volume defined by the user The user must provide the definition of the volume as extra parameters SOLID_TYPE can be of type Box SOLID_DIME
338. ta anti_delta x e strangeBaryon Baryons that contain a strange quark lambda anti_lambda sigma0 anti_sigma0 sigmat anti_sigmat sigma anti_sigma xi0 anto_xi0 xi anti_xi omega anti_omega lambda x anti_lambda x sigma x anti_sigma x xi anti_xi omega omega3 x e charmBaryon Baryons that contain a charm quark lambda_c anti_lambda_ct sigma_cO anti_sigma_c0O sigma_c anti_sigma_ct sigma_c anti_sigma_ct xi_ct anti_xi_ct xi_cO anti_xi_c0O omeca_c0O anti_omega_c0 e baryon All baryons 224 Chapter 26 Appendix A e ion ions GenericlIon alpha He3 deuteron triton e ALL All particles 225 Chapter 26 Appendix A 226 Chapter 27 Appendix B C utilities Converting a Geant4 example into a GAMOS example Converting a Geant4 example into a GAMOS examples usually requires only adding a few lines to transform the different simulation components into plug in s In ex amples NO2 you can see the official Geant4 example novice NO2 transformed into a GAMOS example We will use it to illustrate the procedure to follow The first thing to do is to substitute the Geant4 GNUmakefile by a GAMOS GNUmake file You can use the file in this example for any other example you want to transform just substitute the line name exampleNO2 by the name of your example indeed you can use any name you want it will be automatically detected by GAMOS Then you have to
339. ted with energy given by the parameter ENERGY Constant decay energy gamos generator energyDist SOURCE_NAME GmGenerDistEnergyConstantlsotope Decay All the primary particles will be generated with energy given by the energy of the isotope decay selected by the isotope source as read from the file isotopes dat Random flat energy gamos generator energyDist _SOURCE_NAME GmGenerDistEnergyRandomFlat MIN_ENERGY MAX_ENERGY The primary particles will be generated with an energy given by a random distri bution between the minimum and maximum energy Beta decay energy gamos generator energyDist SOURCE_NAME GmGenerDistEnergyBetaDecay The energy will be sampled following the energy distribution of the decay of the isotope The energy distribution will be read from a file called EnergyDist source_particle_name BetaMinus dat or EnergyDist source_particle_name BetaPlus dat The data is taken from the http fe lbl gov toi html goto LBNL LUND Table of Radioactive Isotopes then Nuclide search and save the table Beta Spectrum There are several examples at MY_GAMOS_DIR data EnergyDist XXX dat Gaussian gamos generator energyDist SOURCE_NAME GmGenerDistEnergyGaussian MEAN SIGMA Primary particles will be generated with an energy given by the gaussian distribu tion of mean MEAN and sigma SIGMA Energy probabilities from file gamos generator energy Dist SOURCE_NAME GmGenerDistEner
340. terisation may be added at user request PLACE_PARAM Volume name Copy number Parent volume name Parameterisation type e Name of rotation matrix e Number of copies e Step separation between copies e Offset e Extra arguments optional depend on parameterisation type There are three types of linear parameterisations along the three axis X Y Z types LINEAR_X LINEAR_Y LINEAR_Z and a general one type LINEAR for which you 25 Chapter 3 Geometry 26 have to add as extra arguments the axis direction DIR_X DIR_Y DIR_Z The offset for linear parameterisations represents the distance from the centre of the first copy to the point 0 0 0 along the line In the case of circle parameterisation the circle is around the Z axis by default If you want a circle around another axis you can provide as extra arguments the axis and optionally the position of the first copy There are three types of square parameterisation in the planes XY XZ YZ types SQUARE_XY SQUARE_XZ SQUARE_YZ and a general one type SQUARE For this bidimensional parameterisations you have to provide two copy numbers two steps and optionally two offsets For the general case SQUARE the offset is not needed but you have to add as extra arguments the two axis that do not have to be orthogonal and optionally the position of the first copy In the case of this parameri sation type you have to provide two number of copies one for each axis
341. ters As you can see through this guide many algorithms in GAMOS use parameters to let the user change their behaviour All the parameters in GAMOS have a default value and the user may change it in the user command file with the command Checking the usage of parameters Many of the GAMOS classes or your own classes have a different behaviour depend ing on the value of some parameters You can see many example of this throughout this guide You have to remember always to set a parameter before you invoke any code that may use it we recommend you to set all the parameters at the beginning of your command file The parameters are read usually in the class constructors therefore if you set a parameter after the class has been constructed it will take no effect and the default value will be used To guarantee that you have done it this way you will get at the end of aGAMOS job the information on the usage of parameters You will always get a list of the parame ters that have not been used in the code This is probably an indication that you have mistyped a parameter name This list appears at the end of your output and looks similar to this one S S PARAMETERS NOT USED DEFINED IN SCRIPT BUT OT USED BY C CODE 53 AYBE YOU HAVE MISPELLED THEM PARAMETER GmGeometryText FileNam Other lists are available at user request to get a more detailed information You may get th
342. the number of characters of the data name the data name itself with this number of characters the number of characters of the data C type and finally the C type itself with this number of characters which can be int float or char To write this header the following parameter has to be used gamos setParam FILE_NAME WriteHeaderData 1 The third optional header is a float containing the number of events used in the job see for example the section on Radiotherapy phase space reading or using files as Chapter 11 Analysis extracting data generator for the exact meaning of the number of events in these cases To write this header the following parameter has to be used gamos setParam FILE_NAME WriteHeaderNEvents 1 The fourth optional header is an integer containing the number of calls to the data user object To write this header the following parameter has to be used gamos set Param FILE_NAME WriteHeaderNCalls 1 The name of the binary file is given by the name of the data user plus the filters and classifiers plus i e out It can be changed with the parameter gamos setParam DATA_USER_NAME FileName NEW_FILE_NAME For example gamos userAction GmStepDataBinFileuA GmGammaFilter will produce a file named GmStepDataBinFileUA_GmGammaFilter out whose name can be changed with the command gamos setParam GmStepDataBinFileUA_GmGammaFilter FileName NEW_FILE NAME to produce a file named NEW_FILE_NAME out e Cout These
343. the parameter file ir_soe_userparameters conf m_bins_z 100 zPositionl 95 0 zPosition2 105 0 m_bins_x 100 m_xmin 5 0 m_xmax 5a 77 m_bins_y 100 m_ymin 540 77 m_ymax 5 0 m_sourceEnergy 511 These parameters set the number of bins and the Field Of View FOV of the image solution space Resolution Recovery The resolution recovery parameters are set in the parameter file ir_soe_userparameters conf UseEnergyResolutionFactorFWHM 0 0 percentage UseSpatialDeltax 0 0 mm UseSpatialDeltaYy 0 0 mm UseSpatialDeltaZ 0 0 rm 183 Chapter 21 Image reconstruction utilities 184 UseDopplerEffectSigmaTheta 0 0 sigma The UseEnergyResolutionFactorFWHM parameter sets the Gaussian variation in En ergy used to recover for resolution loss due to energy resolution The UseSpatialDeltaX SpatialDeltaY and SpatialDeltaZ parameters set the Uniformly distributed variation in x y and z coordinates of the detector hits used to recover for resolution loss due to spatial resolution The UseDopplerEffectSigmaTheta parameter sets the Gaussian distributed variation in the Compton angle used to recover for resolution loss due to Doppler broadening Special running flags Flags to run with the code SOE_ImageRecon seed lt seedNumber gt selecting specific seed SOE_ImageRecon xtraIterInfo additional output files for intermediate iter SOE_ImageRecon averageStatesOu
344. them e g dif ferent energy resolutions The LOGICAL_VOLUME_NAME is the name of the G4LogicalVolume in your geometry that you want to make sensitive You may re peat this command with different logical volumes Building your sensitive detector with C code To build a new sensitive detector you can do it the usual Geant4 way that is in heriting from G4VSensitiveDetector see example in 10 After that you have to transform it into a plug in To learn how to do this see the instructions in the section Creating your plug in using the GmSensDetFactory You may also choose to inherit your sensitive detector from the GAMOS class GmVSD so that you can profit easily from its extra functionality Namely it will take care of applying the energy and time resolutions by detector type accumulating the energy of different energy depositions if they happen in the same detector unit taking into account the measuring time and the dead time and invoking the digitization and reconstruction of hits at the end of the event There are at least two methods that you have to define in your class virtual long int GetDetUnitID G4Stepx aStep Chapter 7 Sensitive Detector and Hits Serves to define the logic you want to apply to give a different number to each detec tor unit for example to each individual crystal virtual void CalculateAndSetPosition GmHit hit G4Step x aStep 0 Serves to define the way you want to define the position o
345. thod Classify of this class returns an integer with the meaning 100 100 Number of LowEnPhotoElec 230 Chapter 27 Appendix B C utilities interactions 100 Number of LowEnCompton interactions Number of LowEnRayleigh interactions See PET section for more details on the concrete class GmHistosGammaAtSD Structure of GAMOS Although the origin of GAMOS is the medical physics field the latest additions spe cially the many utilities to extract detail information of many types make it likely that you can profit from GAMOS to do your simulation in other field of physics as already several people are doing Although you will not need to know anything about the C code unless you want to develop new code for GAMOS we explain here how the GAMOS source code is organized in the subsystems each one subdivided in the packages e GamosCore core software covering main Geant4 functionality Gamos Base e Base parameter manager analysis manager CSV histograms and other basic functionalities Filters filters e Classifiers classifiers GamosGeometry geometry related utilities and support for text detector descrip tion GamosMovement support for displacements rotations or general movements of volumes during a job GamosSD classes for sensitive detectors hits and digitization GamosGenerator utilities to support single particle and isotope source generators as well as different initial particle distributions G
346. tialTime initial global time FinalTime final global time Chapter 11 Analysis extracting data e InitialLocalTime initial local time e FinalLocalTime initial local time e InitialProperTime initial proper time e FinalProperTime final proper time e TimeChange Global time change Only available for Step Output file names Each user action has a default name for the output file it produces histogram text or binary file as it is explained in the corresponding section of this guide As these classes are user actions they can be used with filters and classifiers and in this cases to the default file name it is added the name of the filters and classifier This default file name can be changed with the parameter gamos set Param FILE_NAME FileName NEW_FILE_NAME If you are running a job and you want to identify all your output files with a charac teristic prefix or suffix for example to differentiate them from the files from another job you may do it by defining the parameters gamos set Param GmAnalysisMgr FileNamePrefix PREFIX the name PREFIX will be added at the beggining of all output file names gamos setParam GmAnalysisMgr FileNameSuffix SUFFIX the name SUFFIX will be added at the end of all output file names before the file type root or csv In the case of other output files or input like the text or binary files with several kinds of data that are explained in different sections of this guide you can
347. tionship between the initial and final energy and the deviation anble in Compton interactions It selects a pair of reconstructed hits and between the two chooses one as corresponding to the first interaction Assuming that the gamma suffered the first interaction with energy equal to the electron mass for SPECT detectors you may change this value with the parameter gamos setParam DetRecHitCone InitialHitEnergy ENERGY It then calculates the deviation angle using the initial energy and final energy initial hit energy Using the line joining the two reconstructed hits and this angle it can build the cone of possible directions of the gamma before the first interac tion If the hit selected as first is indeed the one corresponding to the first gamma interaction this cone points ideally to the origin of the gamma as the origin of the gamma cannot be determined in a real detector it is assumed that there is another gamma from the positron annihilation with the same direction and opposite sense and that if has left a hit in the opposite side of the detector before any other inter action As it cannot be known which of the hits in the other side of the detector corresponds to the first interaction the algorithm computes the distance from the cone surface to each of these reconstructed hits only those that do not belong to the hit set being analysed are considered the hit with smallest distance is selected and this minimal distance is stored
348. tious sphere of radius RO surrounding the detector point is defined which we call the exclusion sphere If we can assume that the flux is uniformly distributed inside this sphere then it can be demonstrated that the average flux in the sphere is 97 Chapter 8 Scoring 98 i pla 1 e Fo DIR iF a _ Zr ROD Figure 8 5 The exclusion sphere radius has a default value of 1 mm which can be changed with the parameter gamos setParam GmPDS ExclusionRadius RADIUS GAMOS implementation The point detector scorer is selected as other GAMOS scorers although as explained below it does not really behave as the other scorers To activate you have to select the user action gamos userAction GmPDSUA But before this command you have to set the parameters that drive the behaviour of the point detector scoring You may first decide if you want to score the flux for neutrons gammas or for both with the two parameters gamos setParam GmPDS ScoreNeutrons 1 0 gamos setParam GmPDS ScoreGammas 1 0 There are several parameters that you may change distinctly for neutrons or gammas or that you may want to set the same value for both All the parameters start with GmPDS and then they are followed by neutron or gamma if the second word is not one of these two then the parameter serves for both We will then omit this word in the explanation of the parameters in this section but remember you can always add it except i
349. track weight Variance reduction techniques There are three variance reduction techniques available that will provide a better efficiency i e less CPU time for the same error Kill contributions of low weight The first technique consist on not taking into account the contributions of low weight It works checking the weight of the geantinos at each step of their propagation each time they change volume and playing Russian roulette with them if their way is smaller than the value given by the parameter gamos setParam GmPDS UseMinimumGeantinoWeight MIN_WEIGHT which by default takes a value of 1 E 30 The Russian roulette factor is given by the parameter gamos setParam GmPDS MinimumGeantinoWeightRRFactor VALUE which by default takes a value of 100 To activate this technique you have to set the parameter gamos setParam GmPDS UseV RMinimumGeantinoWeight 1 You may use the control histograms specially the histogram log10 of geantino kinetic energy versus geantino weight to determine which are the minimum weight and Rus sian roulette factor that best match your application 101 Chapter 8 Scoring Notes 102 Kill contributions too far from detector A more efficient technique consists on not taking into account the contributions of interactions or sources that are too far from the detector without the need to send a geantino to calculate the probability to reach it But this technique assumes that the probability is
350. tribution while using a different sampling than the distribution of interest It may help you saving CPU time if you choose to sample more times when the contribution to the distribution is bigger An example can be a case when you want to estimate the dose of particles that reach a volume and you sample more particles when the distance to reach that volume is smaller you may do this by duplicating a particle N times of courser reducing its weight 1 N when the particle comes closer to the volume calculating N as an inverse of the distance to the volume In GAMOS you may do importance sampling using many different criteria any of the GAMOS data can be used as the importance sampling process uses a GAMOS distribution taking the output value of the distribution as the splitting value that corresponds to each input value If the splitting value SPLIT_VALUE is bigger than 1 it will duplicate the current particle SPLIT_VALUE 1 times producing SPLIT_VALUE equal particles with a weight reduced by 1 SPLIT_VALUE If the splitting value is smaller than 1 Russian roulette will be played with the particle with a surviving probability SPLIT_VALUE if it survives its weight will be incremented by 1 SPLIT_VALUE You may activate the importance sampling for a list of particles with the command gamos physics V R AmportanceSampling NAME DISTRIBUTION_NAME PARTICLE_NAME_1 PARTICLE_NAME_2 where the NAME you give to the importance sampling will be l
351. try by including a second file for GmGeometryFrom Text with the command gamos setParam GmGeometryFromText FileNameParallel FILE_NAME FILE_NUMB ER where FILE_NAME is the name of a file similar to the one that describe your mass geometry you can indeed interchange them FILE_NUMBER is the number you as sociate to the parallel geometry as you may have several parallel geometries at the same time The only difference between a parallel geometry file and a mass geome try file is that in the case of parallel geometry the volume at the top of the hierarchy world volume should not appear in the file as Geant4 creates it automatically copy ing the mass world volume This means that you should place your geometry in the same world as the volumes of the mass geometry The parallel geometry will not be seen by Geant4 unless a process is instatntiated to take care of it To do it you can create a G4ParallelWorldScoringProcess with the following command gamos physics addParallelProcess When it is a parallel geometry volume boundary the one that limits the step the process that defined the step will be called parallelWorldProcess_N where N is the number you gave to the parallel geometry that is acting The G4ParallelWorldScoringProcess process takes care of changing the touchable so that it points to the parallel geometry therefore if an scorer acts on a step the G4PreStepPoint and G4PostStetPoint will return a touchable corresponding to a
352. tting This technique is the simplest one When a gamma suffers a bremsstrahlung interac tion the resulting gamma is split N times producing N equal particles each of weight 1 N To apply it you should select the following physics list gamos physics GmEMPS Physics and the physics options gamos GmPhysics add Physics electron lowener UBS gamos GmPhysics addPhysics positron standard UBS remember that there is no low energy physics for positrons The splitting number should be set with the parameter gamos setParam GmParticleSplittingProcess NSplit NSPLIT that by default takes a value of 10 Another parameter controls how many times a particles will be split Z plane directional bremsstrahlung splitting In this technique the user must define first a plane perpendicular to the Z axis at a given Z position and limit its dimensions in X and Y This can be done with the parameters gamos setParam GmPSZPlaneDirChecker ZPos ZPOS gamos setParam GmPSZPlaneDirChecker XDim XDIM gamos setParam GmPSZPlaneDirChecker YDim XDIM When a bremmstrahlung interaction occurs it will be checked if the direction of each of the split gamma points towards the user defined square If it does the gamma is kept if it does not Russian roulette is played with a probability 1 N so that if the gamma survives its weight will be set back to 1 It is recommended that the square is placed close to the phantom upper plane and has dimensions a few centimeteres w
353. two modules defined JAWS and MLC multileaf collimators See section on RadioTherapy for a detailed description of these modules Visibility VIS e Volume name e ON or TRUE OFF or FALSE Example VIS yoke OFF By default the visibility of all volumes is set to ON Colour and transparency To define the colour of a volume gt COLOUR COLOR e Volume name e Red colour proportion e Green colour proportion Blue colour proportion e Transparency The four parameters can take a value between 0 and 1 The transparency parameter is not mandatory Example COLOUR NDC_chamber 0 2 0 4 0 1 By default the three colour proportions will be set to 1 Check overlaps Geant4 offers the possibility to check if a volume overlaps with other volumes By default it is not set but you can activate it with the commands gt CHECK_OVERLAPS Chapter 3 Geometry e Volume name e ON or TRUE OFF or FALSE Example CHECK_OVERLAPS NDC_chamber 0 2 0 4 0 1 By default the three colour proportions will be set to 1 Use of in names In the case of the VIS COLOUR MATE_MEE MATE_PRESSURE MATE_TEMPERATURE MATE_STATE and CHECK_OVERLAPS tags you may use to define the volume or material name This will be replaced by any name For example Crys means all the volume names starting by Crys means all volume names Use of parameters You can also define a parameter to set a valu
354. u meant The names of all these histograms start with GmGenerHistosUA and they are all dumped into the file gener root csv The following histograms are produced Kinetic energy of primary particles KinEnergy X position Position X Y position Position Y Z position Position Z Theta angle Angle theta Phi angle Angle phi Difference between consecutive event times taken as time of the first primary par ticle Time between source decays ns The user can control the minimum maximum and number of steps of these his tograms with the following parameters gamos setParam gener hEMin VAL gamos setParam gener hEMax VAL gamos setParam gener hENbins VAL gamos setParam gener hPosMin VAL gamos setParam gener hPosMax VAL gamos setParam gener hPosNbins VAL gamos setParam gener hAngleMin VAL gamos setParam gener hAngleMax VAL gamos setParam gener hAngleNbins VAL gamos setParam gener hTimeMin VAL gamos setParam gener hTimeMax VAL gamos setParam gener hTimeNbins VAL Chapter 4 Generator To activate this user action use the command gamos userAction GmGenerHistosuA Biasing generator distributions If you are using the GAMOS generator GmGenerator it is possible to bias a primary generator distribution multiplying each resulting value by a probability of occur rence To do this you ahve first to define a numeric distribution see section on Distri butions where you assing the probab
355. ues are very big it means that ou are not creating electrons or gammas of high energ but instead you count all their energy as energ deposited at the last step position so you should check that your value is not too high On the other side the number of these particles produces grows exponentially as ou diminish these cuts so you should check that your value is not too low The cut is given in Genat4 as a distance value meaning that ou are not creating an electron or gamma if in average it is not going to travel a distance longer thatn the cut value A rule of thumb may be that you set a cut value of the order of 1 10 of the resolution you have so that your results are not affected much of course if you want to have a very high precision the effect of the cut should be reduced even further The default cut value in GAMOS is 0 1 mm You may change it with the Geant4 command run particle setCuts VALUE mm You should also take into account the possibilit of using different cut for different parts of your geometry regions For example a bigger cut in regions where you do not measure anything and a lower cut in your sensitive regions or a big cut if the particles created in a region are far from you detectors so that they have a very small probability of reaching them To set cuts per region see section production cuts by region To understand if the changing of cuts may have an important effect in your CPU time you may do first a time
356. ve the same name but with the suffix AEAheader It is generated by the IAEA code and you can find the description of it at 17 The variables stored for each particle are the following X coordinate cm Y coordinate cm X direction cosine Y direction cosine Kinetic energy MeV Particle statistical weight Type of the particle 1 gamma 2 electron 3 positron 4 neutron 5 proton Z direction cosine particle charge Is new history Extra integers 0 1 or 2 values Extra floats 0 1 or 2 values The Z value may optionally be stored if the following parameter is set gamos setParam RT PhaseSpaceUA StoreZ TRUE The header file may be written each N events so that if the job ends abnormally the first N events may be recovered in the phase space The number of events ellapsed between header writing is controlled with the parameter gamos setParam RT PhaseSpaceUA NEventsToSave TRUE FALSE By default this parameter takes a value of 1 and no header is saved until the end of the run It is also possible to limit the number of particles in a file This can be useful if you want to store a phase space at different Z values and you do not want too many particles at the smallest Z planes To do this you can set the parameter gamos setParam RTPhaseSpaceUA MaxNTracksInFile NTRACKS The number of tracks stored in each file will be stopped at NTRACKS but it may continue in other files As the Z plane is pro
357. vestsonseatigenesegstevieenteasesvstaraees Sisese 198 Adding extra information to a phase Space e ssessesssssiesessiisressesserrersees 199 Reusing a particle at a phase space without filling the phase space file 200 Optimisation of a linac simulation ce eee ee ceeeseeeseneseseeseeseseecees 201 CUES optimisation 3 3 05 ctesdecssoctshanbascs seutsaarotessaszesnenesssosbanis sOesaasstelesaveesasuagarsese 201 Electromagnetic parameters Optimisation cccccccseseeseseeceteesesteteeeeens 201 Particle splitting eteerinen taparar EaR LA are a ADE ar aena 201 Killing particles at big X Y rssparsuiiarpni hiasan Sites 202 Scoring dose in ph ntoM ssis ihian pior raat eiiiai eR ESAE aE aiioa 203 Saving scores and score errors in text file s ssssssssssssssstsstsesstsrtsrstessteesee gt 204 Saving scores and scores squared in binary file ccccccecseseeseeteteeeens 204 Saving scores in histograms c ccc cece cesses cesseseeseseeeeeseseneeeeeees 205 Analysis Utmltes sox sive ena e raie SN AEE terse sees des S ESE SEO 206 Summing phase space filesini ipni ais i arean ape tanara 206 Making histograms out of a phase space fil cccccccseeesesseteesesteteeseens 207 Merging Sqdose filesini irere s aria austen atrial cttbves estes 208 Merging S3ddose files cece eee ceeeeeecesseseesssssseeseseseseseseneseseecees 208 Making histograms out of a sqdose file ccccsceteesteeetescetesesesteeneeeens 20
358. volume of the parallel geometry in case the track navigates in it else a touchable of the mass geometry Nevertheless the G4VPhysicalVolume is not cahnged and it will always point to the mass geometry volumes In this way the user can access at the same time the volume of the parallel geometry and the volume of the mass geometry see an example in the Histograms and scorers tutorial The user must be aware that is the scorer mechanism that makes these changes therefore the user actions will not see the parallel geometry Please ask for this functionality in case you think you need it Simulating materials and interactions in parallel geometries In any case Geant4 can navigate in the parallel geometries but the materials are never taken into account This means that a track never interacts on a parallel geome try volume We have developed in GAMOS an utility that allows to have interactions in both geometries at the same time that is to have real overlapping geometries This maybe useful for example to simulate the real geometry of brachytherapy seeds or ionisation chambers inside a phantom This utility is based on making a copy of the parallel geometry in the mass geometry When a particle is going to enter the parallel 35 Chapter 3 Geometry geometry volume its position is shifted to the border of its copy in the mass geome try and when a particle exits the parallel volume copy its position is shifted back to the border of the parallel
359. ways started by the hit that has bigger energy in each detector type only hits in the same detector type are merged Then the hits are looked one by one to check if they are close Each time a hit is added the centre is recalculated The reconstructed hit builders implemented are e GmRecHitBuilderByDistance Two hits are merged if they are separated by a distance closer than the parameter gamos setParam SD GmRecHitBuilder ByDistance HitsDistInRecHit that by default takes a value of 10 mm e GmRecHitBuilderByBlock Two hits are merged if they are in sensitive detectors that belong to the same block i e a volume whose parent volume is the same To check if two hits belong to the same block the detector unit ID i e the iden tification of the touchable where the hits is located is used Usually the detec tor unit ID is built from the volume copy numbers of the volume ancestors e g volume_copy_number 100 parent_volume_copy_number 100 100 grandpar ent_volume_copy_number and therefore two detector unit IDs are considered to belong to the same block if their division by a number given by the parameter gamos setParam SD GmRecHitBuilderByBlock NShift VALUE gives the same results This parameter takes a default value of 100 The number of ancestors to be used is given by the parameter gamos setParam SD GmRecHitBuilder ByBlock NAncestors VALUE e GmRecHitBuilder1to1 Two hits are never merged so that a reconstructed hit is buil
360. which by default takes a value of 100 Each time a geantino reaches the detector its weight will be checked If it is between the minimum and maximum the splitting number will be calculated making a log arithmic interpolation using 0 at the minimum weight and the maximum splitting number at the maximum weight If this number nSplit is bigger than one nSplit 1 particles will be created at the position direction energy and time of the neutron or gamma that created the geantino To activate this technique you have to set the parameter gamos setParam GmPDS UseVRSplitting 1 You may use the control histograms specially the histogram SCORE_NAME At de tector geantino log10 energy vs log10 weight to determine which are the minimum and maximum weight and splitting number that best match your application 1 A geantino is a pseudoparticle that has only transportation but no physical pro cess Chapter 9 Variance reduction techniques Introduction Variance reduction are the techniques that allow to get the same precision of the estimates of a Monte Carlo simulation reducing the CPU time without introducing a bias in the result The usual criteria to measure the gain of a variance reduction is the efficiency defined as the CPU time divided by the square of the error or the variable of interest Importance sampling Importance sampling is a variance reduction techniques that consists in estimating the properties of a particular dis
361. wo different parameters should be set gamos setParam PET EvtClass 1stHitAlgorithmFirst ALGORITHM gamos setParam PET EvtClass 1stHitAlgorithmSecond ALGORITHM Compton studies histograms Several histograms can be filled to help you in determining which is the most efficient algorithm to identify the hit corresponding to the first gamma interaction To produce them you have to set the parameter substitute PET by SPECT or ComptonCamera gamos setParam PET EvtClass ComptonStudyHistos 1 which by default takes a value of 0 Chapter 17 Detector applications The histograms count the proportion of times that the algorithm used selected cor rectly the hit closest to the first gamma interaction and how are the hits are from the gamma interactions what can serve you to have an estimate of the precision you may reach The logic of this class is the following the interactions of the orignial gammas are stored we understand by an original gamma the one that is created as primary par ticle comes from the annihilation of a positron that is a primary particle or if a radi active ion was the primary particle the gamma originated by the ion decay or by the annihilation of the positron that was created by the ion decay Each gamma interac tion is associated to the closest reconstructed hit If the first interaction identificaion algorithm chooses as first hit the one that is associated to the first gamma interaction it is considered that the ch
362. xample The first thing you should do is to write a file that describe what you want to do with the output files In the first section of this file you should list the names of the files to be used For each file there should be a line containing two words the first must be 127 Chapter 11 Analysis extracting data 125 FILE_TXT and the second the file name For example if you have run three jobs with three different energy resolution values you may put in your file FILE_TXT out pet 5 FILE_TXT out pet 10 FILE_TXT out pet 15 After this you should describe the actions to be taken Several actions can be done for each one you have to write a line in which you describe which lines are going to be processed which words in these lines and which action is done print value sum values from different files In this action line you should first describe the criteria to identify which lines in each file are to be processed This can be done by setting which words in the line are going to be looked for Instead of setting the full word one can set the starting characters prefix or the ending characters suffix To set the list of prefixes you add the words PRE or PREFIX followed by a list of pairs word position numbers and word char acters For example PRE 1 Events 2 PET will look for the lines in which the first word starts by Events and the second word starts by PET In a similar way it can be done with the suffixes
363. xial Number of crystals per block in the axial direction e P NBLOCKS Number of blocks of crystals per ring e P NRINGS Number of rings of blocks e CRYS_transaxial Crystal size trans axial e CRYS_axial Crystal size axial CRYS_radial Crystal size radial P DIAMETER Detector ring diameter PS CRYS_MATE Name of crystal material P WORLD_Z World Z dimension the X and Y are calculated as slightly bigger than the detector There are several examples of simplified commercial PET detectors in the files with suffix geom in that directory To use this utility you just have to choose as your geom etry the GmGeometryFromText one gamos geometry GmGeometryFromText NOTE This module is just thought for simple PET geometries If you want to do more complicated geometries we recommend you to describe them with a text file see section Building your geometry with a text file PET event classification The class PETEventClassifierUA in the directory NuclearMedicine PET classifies the events as PET by looking at the reconstructed hits It is a GAMOS user action so you can activate it with the command gamos userAction PET EventClassifierUA First it counts how many reconstructed hits have 511 keV within a precision given by the parameter gamos setParam PET EvtClass 511EPrec ENERGY_FRACTION That is the energies accepted will be those between 511 1 ENERGY_FRACTION and 511 1 ENERGY_FRACTION Alternatively you may use the f
364. y each scorer and compare it with the total dose It may happen that the dose lost with certain cuts despite being a small proportion of the total dose is distributed in a different manner than the total dose introducing some bias in some region that you consider not acceptable To check in detail the dose produced with a certain filter you can add a scorer printer of type RTPSPDoseHistos that will produce several histograms of the dose PDD X amp Y profiles dose dose volume gamos scoring addPrinter2Scorer RTPSPDoseHistos DoseScorerPC10 1 The name of the printer will be passed to the name of the file containing the his tograms Automatic determination of user limits for an accelerator simulation The method used in GAMOS to determine the minimum range user limits is similar to the one used to determine the best production cuts The main difference is that when a track reaches the target we do not have to look at the range it had when 211 Chapter 22 Radiotherapy application 212 created but at the range it had in every step This is because even if we want the minimum step the track may have crossed several regions and the smallest range may not correspond to the last step What we do nevertheless is only consider the last step when there are a set of contiguous steps in the same region Also for the ancestor tracks we have to store the information of each step starting of course with the one when the track that reached the
365. you can see at the left a sub window with tje set of folders Under the folder titled PROOF Sessions you can see a folder with the name of the directory you are in By clicking on it you may navigate on your folders and open your ROOT file By double clicking on your ROOT file when it appears in the right sub window you will see the list of your histograms If you do double click in an histogram ROOT will visualise it Alternatively you may directly open your file when you start a ROOT session by typing root MYFILE root Then by double clicking in ROOT Files you will see your file and you can open your histograms as below You may get more instructions on using ROOT in the web page http root cern ch We provide a few utilities to help you in analysing ROOT files They can be found in the directory analysis ROOT Utilities Printing the histograms in graphics files For a faster visualisation of the histograms in a ROOT file you may print each of the histogram in a graphics file of type gif Open a ROOT session and then type the command x printAll C MYFILE root There are two optional extra arguments that can be given after the file name separated by a comma e A boolean 0 or 1 to indicate if the Y axis is in logarithmic scale or not e An string in between quotes indicating the type of histogram represention lego cont For each histogram a graphics file will be written with the name of the histogram preceded by his a
366. ysis controls the verbosity of the analysis classes GmuUA controls the verbosity of the utility user actions NM controls the verbosity of the Nuclear Medicine packages the base classes for PET SPECT and Compton Camera applications PET controls the verbosity of the classes in the PET package If set if sets automat ically the NMVerbosity SPECT controls the verbosity of the classes in the SPECT package If set if sets automatically the NMVerbosity CC controls the verbosity of the classes in the Compton Camera If set if sets au tomatically the NMVerbosity RT controls the verbosity of the classes in the RadioTherapy package SH controls the verbosity of the classes in the RadioTherapy package You can set the verbosity of each of the GAMOS verbosity types with a simple com mand on your command input file for example 149 Chapter 16 Managing the verbosity gamos verbosity VERB_CLASS VERB_LEVEL where VERB_CLASS is one of the verbosity name in the list above and VERB_LEVEL can be any of the six values described above in non capital letters Instead of the names you may use the numbers that appear besides them By default the values of all GAMOS verbosities are warning Controlling GAMOS verbosity by event You may control the verbosity of each of the GAMOS verbosity managers event by event that is activate it for a certain interval of events and deactivate for another interval To do this you have first to act

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