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GAMOS 5.0.0 User`s Guide

1. HActivationUA_inWindowEk IME 900 sec Sc46 0 0 ACTIVI Y 1795 27 decay Chapter 23 Shielding application SHActivationUA_inWindowF TIME 900 sec V46 0 0 ACTIVITY 3 5688296e 20 It contains first a line with the number of events per second as calculated from the two following numbers the number of events simulated and the time that correspond to these events The following line print the periods when the beam is on or off Then come a set of lines for each time when you requested the activity to be calculated Each of these lines gives the time value the isotope chain name the activity the lifetime of the last isotope in the chain the number of atoms of the same type than the last isotope in the chain created in the job and the number of atoms that would be present at the time requested Two warnings are due here the first is that only chains with two decays are con sidered currently the second is that GEANT4 does not create metastable isotopes in an interaction so that the activit of these isotopes will not be taken into ac count Print channel by channel cross sections You may print the hadronic cross sections with the user action gamos userAction SHPrintPHPChannelXSUA If the physics model selected is neutron_hp or particle_hp it will also print the channel by channel cross sections and if required the particle yields as read from the database This user action invokes the GEANT4 internal methods to g
2. gamos setParam GmGeometryFromText FileName test geom gamos geometry GmGeometryFromText gamos physicsList GnMCNPDummyPhysics gamos generator GnMCNPDummyGenerator run initialize run beamOn 10 In this example the geometry is read from a text file so that the first line sets the name of the file where the geometry is described and the second line sets that the geometry will be read from a text file In fact the geometry is not important as GAMOS will not do any tracking but it will take the positions from the MCNP ptrac file See the section on geometry for more details 231 Chapter 25 Extracting detailed information from a MCNP run The next line sets a dummy physics This is all you need as particles will not suffer any interaction but GAMOS will take the interactions as read from the MCNP ptrac file See the section on physics for more details Similary you do not need to set any generator of primary particles source in MCNP notation as GAMOS will use the particles as they are read from the MCNP file See the section on source for more details Once you have written the above commands in a file called for example test in you just have to execute in your shell script mcnpGamos test in A file named ptrac will be read and GEANT4 tracks and steps will be created form the information therein You may change the name of this file by adding a command line at the beginning of the file gamos setParam GmMCNPG
3. GmProcessFilter accepts a step if the 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 de fined 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 AcceptTrack method GmCreatorProcessFilter accepts a track if the process that created the track is in the list given as extra parameters It does not implement the AcceptTrack method GmInteractionFilter accepts a step if the process that defined it is an interaction i e if itis of one of the G4ProcessType s fElectromagnetic fOptical fHadronic fPhotolepton_hadron fDecay fGeneral or fParameterisation It does not imple ment the AcceptTrack method GmMaterialFilter accepts a step if the material that it is in the initial step point 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 returns a value equal to the second parameter It does not implement the Ac ceptTrack method 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 volum
4. Region a G4Region object 139 Chapter 12 Filters 140 LogicalVolumeChildren a G4Logical Volume object or any of the G4Logical Volume children of it PhysicalVolumeChildren a G4VPhysicalVolume object or any of the G4V Physical Volume children of it Physical Volume ReplicatedChildren please read the discussion about Physical Vol umeReplicated RegionChildren a G4VTouchable object or any of the G4VTouchable children of it TouchableChildren a G4Region object or any of the G4Region children of it The name of these filters is constructed combining the geometry condition and the volume type e g GmInPhysicalVolumeFilter GmTraverseTouchableFilter GmEn dRegionFilter 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 EndParallelLogicalVolumeFilter EndParallelPhysicalVolumeFilter EndParallelPhysicalVolumeReplicatedFilter EndParallelRegionFilter EnterParallelLogicalVolumeFilter EnterParallelPhysical VolumeFilter EnterParallelPhysical VolumeReplicated Filter EnterParallelRegionFilter ExitParallelLogicalVolumeFilter ExitParallelPhysical Vo
5. e Score value float e Square of score value float This value is needed instead of the error for properly 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_SCORER NAME FileName FILE NAME 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_LNAME The user must define the histogram name number of bins and axis minimum and maximum giving them as arguments of the gamos scoring printer com mand 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 happen that the first index is not 1 If this is the case a num ber positive or negative 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 sec ond four to the second one Then
6. gamos scoring printByEvent PRINTER_NAME FALSE The error in the scored quantity per voxel is also calculated by default using the following formula sqrt SumV2 nEvents SumV SumV nEvents 1 nEvents where nEvents is the total number of events in the run SumV is the sum of the scored quantity value times its weight i e the scored quantity itself and SumV2 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 squaring 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 uses 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 in creasing 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 I
7. gamos setParam GmV Gener Dist Position VolumesAndSurfaces OnlyVolume 1 Position in a Geant4 volume surface gamos generator position Dist SOURCE_NAME GmGenerDistPosition InG4Surfaces 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 This distribution can only be used if the volumes are G4Box G4Orb G4Sphere G4Tubs or G4Cons Position in a user defined volume surface gamos generator positionDist SOURCE_NAME GmGenerDistPositionInUser Surfaces POS_X POS_Y POS_Z ANG_X 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 param eters 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 different 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 ar
8. For the case of PET and Compton camera 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 two 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 ef ficient 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 CC gamos setParam PET EvtClass ComptonStudyHistos 1 which by default takes a value of 0 The histograms count the proportion of times that the algorithm used selected correctly 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 pre cision you may reach Chapter 17 Detector applications 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 particle comes from the annihilation of a positron that is a primary particle or if a radiactive 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 ga
9. SOLID Crystal2 BOX 5 5 5 VOLU_ASSEMBLY CrystalSet 3 Crystal RMO 0 0 0 Crystal RM1 0 0 20 Crystal2 RM0 0 20 10 PLACE_ASSEMBLY CrystalSet 1 expHall ROO 100 0 0 29 Chapter 3 Geometry 30 Rotation matrix A rotation matrix is interpreted as the rotation that should be applied to the object in the reference system of its mother It can be defined in three ways a By giving the three rotation angles around the X Y and Z axis in this order of rotations b By giving the polar and azimuthal angles of the X Y and Z axis after the rotation is applied 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 Y axis e Angle of rotation around global Z axis Example ROTM RO 0 0 0 b ROTM Name Polar angle for axis X Azimuthal angle for axis X Polar angle for axis Y Azimuthal angle for axis Y Polar angle for axis Z 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 geometry While these pieces could be built by adding several volum
10. gamos setParam RT GeneratorPhaseSpace 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 following user actions RTExtralnfoProviderCrossings fills a bit if the track has crossed the correspond ing region before reaching the phase space RTExtralnfoProviderInteractions fills a bit if the track has intereacted in the cor responding region before reaching the phase space RTExtralnfoProviderOrigin fills a bit if the track has been created in the corre sponding region before reaching the phase space 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
11. 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 geometry by including a second file for GmGeometryFromText with the command gamos set Param 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 associate 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 geometry 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 copying 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
12. Chapter 25 Extracting detailed information from a MCNP run gamos scoring assignClassifier2Scorer energyNC fluxSurfl1ScorerN As its name says GnMCNPPSSurfaceFlux scores the flux that is the number of particles that reach the surface multiplied by their weights divided by the sur face area and by the angle between the particle and the surface normal The area of each surface is read from a file whose name is given by the parameter gamos setParam GmMCNPPSSurfaceFlux SurfaceAreaFileName FILENAME The default file name is surfaceArea dat This file contains a list of two words lines with the surface name and the surface area for example for two spherical sur faces of radius 1 and 2 cm surface_11 4 3 1416 10 10 surface_12 4 3 1416 20 20 One thing to note is that the angle between the particle and the surface normal in the ptrac file is given in degrees as an integer This restricts its precision and for this reason you may find small differences between the result of the F1 tally in the MCNP job and the GmMCNPPSSurfaceFlux scorer in GAMOS If you want to do a F2 tally you use the same commands as for a F1 tally but you avoid the division by the angle and the area with two parameters gamos setParam SCORER_NAME DivideByAngle 0 gamos setParam SCORER_NAME DivideByArea 0 F4 tally The F4 tally or track length estimate of cell flux is equivalent to the GAMOS scorer GmG4PSCellFlux For example if you want to do a F4 tal
13. cumulated number 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 anal ysePS 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 ubs 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
14. 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 DLTRANSAXIAL N_BINS 1 In 3 dimensional PET acquisition the maximum ring difference is another fundamental 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 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 Chapter 18 PET application PET histograms positrons These histograms are related to the original positron and the two secondary gam mas created at its annihilation They are produced if the user action PETHis tosPositron 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
15. Detector effects horae ebe cuts oeies e Seclta wade ce aces svat oboe Bes Ge cg oe sivas lated eet 82 Energy TeSOM Iti ONL nnaspan iesirea subset paea A A Eaa ER 83 Time TESOL ON sasmata E 83 Detector measuring time esssessssseressesssresssressesesresessessesessesesseseeseseesereese 84 Detector dead time ccccccccccccccccccsssseesessecsssesssesscesessesesececessssesseseseseeeesss 84 Minimum hit energy s ss sesssssssssssssesisissesssessestentinsissesstnnseniesieseennesnesnente 85 Identifying each sensitive detector COPY ss sssssserisrsssississessesieriesressessessesne 85 Storing and retrieving Nits sensere asii a aa eed 86 VTISE KOI a afe i OEA ENEE EE EEEE E EEE 86 Storing reconstructed Nits si cssisse sissdessvesiatvsevesidaeestsvieae se seeeesiesh veces 87 Hits histogram siii ea E aa a ae E 88 8 SCOTING E E T E 91 Creating a SCOTen miaire iosa ortida a iia cust win orao EEEE Bre a E 91 Scorer classes rar e A E a a a E E a a r a aas 92 Scoring in voxelised phantomS s ssssseesssiserississessssssesiesiesrisnrsressseee 96 1i Enei nk le ee e EER RET E A E T E T E ER 96 Seter printers iire eenei eE oe E gea i E EE EEEE T Eia 97 EET E AE E A E E E E EES 98 Multiplying Dy datas cc icc Secoatets tocccusattesenesbatucseseus Aat svcbosdunescbpessebeosobeterteans 98 Multiplying by distributio ssns srenrosiddsseia nri s 99 Convergence testno anniina eneee aAa a E a La A aaia 99 Point detector Scorer ees rrn r a EE
16. 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 GmFutureWith ChildrenFilter Future filters only act on steps so if you use them for example together with a GmTrackDataHistosUA they will always return true i e they will have no effect Chapter 12 Filters In the case of scorers the use of future filters has to take into account the fact that scorers 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 so lution 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 vol ume s where you want to score 143 Chapter 12 Filters 144 Chapter 13 Classifiers Introduction A classifier is a class that contains a method that receives a G4Step or a G4Track and return
17. It creates intervals as a function of spherical radius with the parameters given at score definition NSLICES_R MIN_R MAX_R and calculates the volume of each spherical shell so that dose can be computed Three extra parameters may be given CENTRE_X CENTRE_Y CENTRE_Z if the you do not want the sphere to be centred at the origin of coordinates 0 0 0 e GmPSCylindricalRZDoseDeposit This scorer is designed to compute the dose deposit and assign a different index to each interval in cylindrical coordinates in 2D radius and Z despite no cylindircal division is defined in the geometry It creates intervals as a function of the cylindrical radius and the Z coordinate with the parameters given at score definition NSLICES_R MIN_R MAX_R NSLICES_Z MIN_Z MAX_Z and calculates the volume of each cylindrical section so that dose can be computed Three extra parameters may be given CENTRE_X CENTRE_Y CENTRE_Z if you do not want the cylinder to be centred at the origin of coordinates 0 0 0 and another three ZAXIS_X ZAXIS_Y ZAXIS_Z if the you do not want the cylinder axis to be along the Z global axis 0 0 1 The index of the scorer is build as NSLICES_R indexZ indexR GmPSCylindricalRPhiDoseDeposit This scorer is designed to compute the dose deposit and assign a different index to each interval in cylindrical coordinates in 2D radius and phi angle despite no cylindircal division is defined in the geometry It creates intervals as a function o
18. Radius BREPTORUS Boundary REPresented torus e Origin X e Origin Y e Origin Z e Axis X e Axis Y e Axis Z Direction X 23 Chapter 3 Geometry 24 e Direction Y e Direction Z e Length e Minimum radius e Maximum radius BREPPCONE Boundary REPresented polycone e Phi starting angle e Delta size 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 Delta size 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 2X e Point 2 Y Point 2Z e Point 3 X Point 3 Y Point 3 Z If there are four points e Point 4X e Point 4 Y Chapter 3 Geometry 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
19. 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 sec ondary 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 sec tion 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 score 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 infor mation 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 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 ex tracts the data at the end of the current track step from the G4Track object equal to the current track sta
20. The parameter file ir_soe_userparameters conf has the following contents m_iterations 100000 m_bins_z 100 ee zPositionl 95 0 zPosition2 1055 0 m_bins_x 100 as m_xmin 5 0 m_xmax 540 7 m_bins_y 100 m_ymin o 0 m_ymax 50s of m_sourceEnergy DataFileName EventSetSize 511 0 0 ail aa es CCs_Machiel CC_img out_Gamma511_A110FE 1000 0 0 tom tom tom sigma percentage m_maxNumberOfEvents UseEnergyResolutionFactorFWHM UseSpatialDeltaxX 0 0 UseSpatialDeltaY 0 0 UseSpatialDeltaZ 0 0 UseDopplerEffectSigmaTheta 0 0 Each line should contain three fields 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 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 191 Chapter 21 Image reconstruction utilities 192 Output Files The output files are e data_beginstate_xy dat This file contains a list for all events with the initial positions 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 con
21. 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 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 76 Chapter 6 User Actions Geant4 user actions are the way the user can interact with a job at the begin ning 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 command User actions can be associated to filters or classifiers as explained below Several functionalities are already implemented in GAMOS as user actions like histograms event classifiers and you may use them as examples for creating your own one All user actions are instantiated
22. cc cesses cetesssesescseseesescsseeseeceees 134 Example of Analysing text output files 0 0 cece ceceseeeseseseeeteeeeees 136 12 FIETS ceiccclssdcvacdcccccuvesdetecsevensesseesavcsesaseca counceuscacsd caubecusesedcacsveduvecdsedcecsaudeseuschocssecedeves 137 TAErO AUCH ON narenn a eA E ERE E E EE dutise rieile wise leneissoce ts 137 Simple ETS fo srono eea cede atte ante Sean AEAEE sete atues E SeSe A Tei 137 Volume filters r em e a a n e a a a ies 139 dW i 69 8 Groen a OP 141 Applying filters to a user action cccccc cece sssssseesenssssesescseseesescssseseecees 141 Checking filters at a user action oo cece eeeseseeeeesssesescsesesesescseeeseeeees 142 Filtering steps in the future cece ceeseseeseenssesescsesesesescsseeseecses 142 13 ClASSIf CTS in csccccccessicsacevesess sccse css coucodneadsvucousescevsensosdteesnesecsonsdoestevenesess deve s S 145 1K amp 0y hE KELO 9 eee tN Px ee RPO a A 145 Setting indices toclassifi rS esea a erau Eear Ia A SA Aa 146 Classifiying on secondary data ss sssssesssessessessersississtestessesssntinsesnessnesteseeeee 147 T4 Distrib Uti ONS 20iseshsiscosseciveccsvecuscescadeicdecccceuiedessSelonsecevccsssedcecossescecceiveseesSesessavebeivesees 149 AOR UCH ON sik ahi hte biel ie in ies Me i ae Seed 149 Creating a distribution 0 00 cseecseesesssseeseessesescsesesesescsseeseecses 149 Assigning a GAMOS data jvvitscs seveccsssests aistersevetiat aveveaidenteesvieaevisrernestest vars 149 Re
23. cceececesseeeeseseseteeceeeeeeeeees 44 Non uniform magnetic fields cesses cesssssesesceeeescsseenecssees 45 Ass GONNETALOE 3s ces EEEE E AE E EEEE usa seGeegeose E E A 47 Using GAMOS generatore eaei ranea aaee Ene Eanan aa TEA A EEE E RE aaia 47 Introduchon sesen r Siow a a E 47 ParticleSOurces iee ae a N a e a EAE E ESES 47 PISCE HOS enee ee r E TE e cusseen Sache Ake 48 Reading your generator particles from a text file cce ccc eee 55 Reading your generator particles from a binary file ccs 56 Event generator changing energy and material cccccsseeeceeteeeeeeees 56 Event generator histograms isien apetaren airaa aans 57 Biasing generator distributions ssssssesississessssssestestessississtsntesiesiesresnesnesnenee 58 Building your generator With C s sssssissesssessesiessirsississtsssesinsieseesensnesnenee 58 Using TOMS oeei et eea p a ea a ieii 58 5 A th Ae e EE E E A E E A E EE 61 GAMOS electromagnetic physics lists ccc ce ceteesesteteseeeeteseseseeeeeeeenes 61 Basic electromagnetic PHYSICS list 0 0 cece esesteteteseeceeesesestaneneeees 61 GAMOS electromagnetic extended physics list ccccccsessesteteeeees 62 Standard electromagnetic physics list options ccccceeeseeteeeeees 63 Multiple scattering Models esses seneseeescsesesesescssensseeesees 63 Bremsstrahlung angular distributions ccccsesecsesetesee cerns eeeeees 64 GAMOS hadrontherapy physics li
24. e dielectric_LUT e firsov e x_ray e Polish value e Sigma alpha value 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 e First physical volume name e Second physical volume name e Optical surface name You can create a logical skin surface with the tag LOGICAL_SKIN SURFACE e Material 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 polarization using the parameter see chapter on Generator gamos setParam SOURCE_NAME Polarization POLARIZ_X POLARIZ_Y POLARIZ_Z Chapter 5 Physics 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 indices for each material and for each energy This can be done by using the com mand you may use one command per material gamos geometry set
25. inheriting 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 accu mulating 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 in voking 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 Serves to define the logic you want to apply to give a different number to each detector unit for example to each individual crystal virtual void CalculateAndSetPosition GmHit hit G4Step aStep 0 Serves to define the way you want to define the position of the hit centre of the crystal barycentre of energy depositions Hits If you have activated any of the GAMOS sensitive detectors each time a track deposits 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
26. mm Distance of closest approach between vertex and the line joining the points where the gammas enter the sensitive detectors DCA orig from Gamma en tering SD mm Z position of vertex of gamma if it reaches the sensitive detector Orig Pos Z if Gamma reaches SD mm 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 N original gammas are gammas that are primary particles or that are directly created by the annihilation of positron that is a primary particle 175 Chapter 18 PET application 176 Chapter 19 SPECT application Before reading this chapter we recommend you to read the chapter on Detector that contains the utilities that are common to all detector 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 characteristics 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
27. sidered to belong to the same block if their division by a number given by the parameter gamos set Param SD GmRecHitBuilder ByBlock 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 GmRecHitBuilderByBlock NAncestors VALUE GmRecHitBuilder1to1 Two hits are never merged so that a reconstructed hit is built 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 S D recHitBuilder RHITBUILDER_NAME where RHITBUILDER_NAME is one of the classes described above Chapter 7 Sensitive Detector and Hits Detector effects There are a number of detector effects which can be simulated with a few user commands It is important to note that these effects are applied to the recon structed hits as these hits are meant to simulated the digitizationt reconstruction process that happens in the detector If for any reason you want to see a detec tor effect on the hits you should use the GmRecHitBuilder1tol reconstructed hit builder 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 mor
28. unless you want to study some special behaviour The secondary particles should be stopped before being tracked because if not they will be counted as particle exiting the shield layers You can do it with the command gamos userAction GmKillAtStackingActionUA GmSecondaryFilter SHNthValueLayeruA should be accompanied by a filter and a classifier The filter should be on the particles exiting the slab volume for example gamos filter exitShieldLayerF GmExitLogicalVolumeFilter shield The classifier should classify the particles by the copy number of the slab there fore it should be of the type GmClassifierBy1 Ancestor gamos classifier copyNoC GmClassifierBy1Ancestor 0 Activation studies 222 The user action SHActivationUA serves to make activation studies It counts the number of all radioactive isotopes produced in a job and calculates their activity at any given time as given by the user You can find an example of its use in MY_GAMOS_DIR tutorials S Hielding Tutorial exercise4 exercise4a The first thing you should do is to define the rate of particles generated You may use for example the time generator distribution gamos generator timeDist GmGenerDistTimeConstantChange TIME_INTERVAL To define when you want the activity to be calculated you can use the parameter gamos set Param USER_ACTION_NAME Times TIME_1 TIME_2 TIME_3 You may also define the periods when the source of particles is on or off You can thi
29. 0 0001 User 0 Real 0 Sys 0 6 le 05 User 0 Real 0 Sys 0 01 0 001 User 0 53 Real 0 37 Sys 0 02 1 00 01 User 12 42 Real 13 58 Sys 0 29 T User 5 98 Real 6 42 Sys 0 16 diss User 7 78 Real 8 8 Sys 0 22 User 0 Real 0 Sys 0 5 0 0001 User 0 Real 0 Sys 0 6 le 05 User 0 Real 0 Sys 0 001 0 01 User 1 29 Real 1 49 Sys 0 02 01 0 1 User 0 63 Real 0 58 Sys 0 01 aha User 27 95 Real 29 7 Sys 0 48 gamma 1 10 User 0 38 Real 0 36 Sys 0 ooo 00 0 10 Ss oO fo rFoOoOoOOoO o 10 o 10 a oO NOOO OG Q o 3 3 D en which can be obtained with the commands gamos classifier ClassifierByParticleAndKinE GmCompoundClassifier GmClassifierBy Particle GmClassifierByKineticEnergy gamos userAction GmTimeStudyUA ClassifierByParticleAndKinE The time in each category is the time counted at each step Exactly it is the count ing from the beginning to the end of the method G4SteppingManager Stepping To do this without modifying the Geant4 class the class GmTimeStudyMgr inher its from G4VStepping Verbose and it is set as the stepping verbose class substitut ing the class G4SteppingVerbose 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
30. 11 Analysis extracting data 121 Chapter 11 Analysis extracting data e AccumulateEnergyLost e AccumulatedEnergyDeposited GmSecondaryTrackDataHistosUA TrackID Initial PrimMinusSecoKineticEnergy FinalPrimMinusSecoKineticEnergy SecoDividedInitialPrimKineticEnergy SecoKineticEnergy PrimSecoAngleChange InitialPrimKineticEnergy FinalPrimKineticEnergy GmSecondaryTrackDataTextFileuA EventID TrackID Initial PrimMinusSecoKineticEnergy FinalPrimMinusSecoKineticEnergy SecoDividedInitialPrimKineticEnergy SecoKineticEnergy PrimSecoAngleChange InitialPrimKineticEnergy FinalPrimKineticEnergy GmSecondaryTrackDataBinFileUuA TrackID Initial PrimMinusSecoKineticEnergy FinalPrimMinusSecoKineticEnergy SecoDividedInitialPrimKineticEnergy SecoKineticEnergy PrimSecoAngleChange Initial PrimKineticEnergy FinalPrimKineticEnergy 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 By default the TTree is created with the GmDataTTree name and saved in the Gm Dat aTTree root file The following command can be used to modify both both TFile and TTree names gamos setParam DATA_USER_NAME TreeFileName NEW_NAME Four categories of GAMOS data can be saved in the TTree Event data Track data Secondary Track data and
31. 1x1 50 50 50 50 0 NVoxelZ 1 1Z RTPSPDoseHistos Dose Profile Z 3x3 49 51 49 51 0 NVoxelZ 1 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 This 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 ITAEFAheader ps 20001 IAEAheader ps 20002 IAEAheader Then you just have to run the executable sumPS INP
32. 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 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 22 244 25 18 7 3 Chapter 22 Radiotherapy application 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 10 3 3 1 0 4 2 1 0 5 3 1 0 6 4 10 0 29 G4_W Material GROSS LEAVE FOCUS P zous Crocs Leave Start Port M Reference Plane i 2_ SAP PLANE Gefinitton io 2 TOP plana re T J i i i a f LL itereaves Gaps r Wk 7 fy r i i fg ___fe A a DEORE ZJSOCENTRE 7 20 Ad w a C L ra rere Figure 22 1 Cross leaves representation 199 Chapter 22 Radiotherapy application 200 E a Git Fone Figure 22 2 Inline leaves representation for endleaf type ROUND If we change the END_LEAF_TYPE for STRAIGHT type the variable RDIM rep resents 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 Chapter 22 Radiotherapy application 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 e
33. 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 Chapter 3 Geometry e Axis of division e Number of divisions e Division width e Offset not mandatory Example REPL crystal Block X 10 5 cm 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 visuali sation 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 posi tions of all the logical volumes VOLU_ASSEMBLY e Volume name 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 e 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
34. Boolean solids The three types of Geant4 boolean solids are supported union subtraction and intersection 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 operation 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 Instead of SOLID HALL BOX 5000 5000 20000 25 Chapter 3 Geometry 26 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 place ment a parameterised one a division a replica and an assembly Single placement PLACE Volume name Copy number Parent volume name Name of rotation matrix X position Y position Z
35. 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 reconstructed 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 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 compcam DumpCartesian TRUE 185 Chapter 20 Compton camera application 186 Chapter 21 Image reconstruction utilities Several utilities are provided for helping the user to process projection data and reconstruct PET images These utilities are installed along with the rest of GAMOS code and their source code included in the GAMOSINSTALL analysis NuclMed PET directory 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
36. 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 verbosity 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 overflow e 2 Prints number of entries mean with error RMS with error underflow and overflow 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 Histograms 1D The first word is HISTO1D then the following info is dumped his_name number_of_bins Xaxis_minimum Xaxis_maximum bin_contents ynumber_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 o
37. Chapter 27 Appendix B Extending GAMOS functionality with 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 GmPhysicsFactory and G4VUserPhysicsList for a geome try plug in GmVerbosityFactory and GmVerbosityMegr for a verbosity plug in etc 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 e G4VUserDetectorConstruction geometry G4VUserPhysicsList physics list e G4VUserPrimaryGeneratorAction primary generator e GmVG
38. GmCountTracksUA EachNEvent TIMES USED 1 PARAMETER GmGeometryFromText FileName TIMES USED 1 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 237 Chapter 26 Appendix A GAMOS_SEARCH_PATH contains the list of directories where GAMOS will look for your file The directories are 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 configuration 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 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
39. GmG4PSTermination This scores the number of tracks that are terminated in a given cell per event A particle weight is not applied by default e From data e GmG4PSData This score uses a GAMOS data as quantity to score See section on GAMOS data All scorers that must divide by the volume to obtain the relevant quantity use by default the cubic volume of the physical volume in which the particle is being propagated If you want to use instead the total volume of all copies of the logical volume with the same name as the volume the particle is in you have to set the parameter gamos setParam SCORER_NAME IntegrateVolumes 1 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 material 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 nevertheless 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
40. 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 coinci dences 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 Then you just have to run the executable 187 Chapter 21 Image reconstruction utilities sumProjdata INPUT_FILE_LIST OUTPUT_FILE where INPUT_FILE_LIST 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 185 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
41. Parallel SGOMEetri S c isasincieteanittetiense Sitesi eure 35 Building simple geometries ccc cece ceeseseesesesseescsesesesescssensneeeeeees 36 Building a simple geometry with one material 0 0 0 0 cece eens 36 Building your geometry with C code s ssssssssssssississessessesisiesseseessessesee 36 Reading DICOM files ioc vscscccc sevencsstbseenscutgssveslsssacsdst Aeaaeai i nE is Bih 36 Converting a DICOM file to a simulation file cccccceseeseeteteeeees 37 DPICOM file fOrmiatsssc eina aaa herevih tis eee eo a R 37 Reading a DICOM file in a GAMOS job cece sececcsete nese ceeeeeeeeees 38 Reading DICOM Structures ccccceeeesesssseeseeseeescsesesesescsseesneeesees 39 Partial phantom Geometries cee sseseseeseesseescseseseseecesseseecssees 40 Simple phantom geometries cc cesses seteeseescseeseesceeseseeeeeees 40 Setting off visualization of phantom geometries ccccceesceeseeeees 41 MOVemenits seiessce che incckecs Bh tila site eee haces edits CO ee hb eee 41 Movement description from a file ccceseseescecseststeteseececesesesnaeneeeees 42 Geometry Utes cascscct set ccasieee aeaa enra Ee EIo ateseSvesonsistesssstbasrbverae teed 43 Commands to print geometrical Objects cccccecseetetesceeesesesteneseeeees 43 CHP TSS ws eka te aed r ales ses ech dapesiaiont E E a Aeetiads 43 Magnetic and electric fields insisnnsssiniansi ianiai 44 Uniform magnetic and electric fields
42. RefractionIndex 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 ener gies 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 Zhigiang Chen Kejun Kang Implement X ray refraction effect in Geant4 for phase contrast imaging IEEE Nuclear Science Symposium Conference Record 2009 1082 3654 Coulomb scattering You may activate Coulomb scattering for electrons and positrons by suing the command gamos physics addPhysics CoulombScattering Atomic deexcitation processes The atomic deexcitation i e the production of characteristic X rays and Auger electrons when the atoms are excited after an ionisation or photo electric process is activated by default if one of the two GAMOS electromagnetic physics list is selected To deactivate it you can use the parameter gamos set Param 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 Atomic
43. 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 122 Chapter 11 Analysis extracting data 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 selected GAMOS data is stored in a std vector apart from Event data that cor respond 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 given event step and secon
44. 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 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 GmDigitiz erFactory After this you select it with the command gamos SD 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 imple ment the two methods virtual std vector lt GmRecHit gt ReconstructDigits const std vector lt GmDigit gt amp 0 virtual void CleanRecHits in the case of GmVRecHitBuilderFromDigits or virtual std vector lt GmRecHit gt Re
45. a bias when a particle 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 smallest 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 addFilter2 Scorer 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 by 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 di
46. 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 vol ume 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 par 80 Chapter 7 Sensitive Detector and Hits ticle or if it is a gamma created in an original positron annihilation or by a radioactive decay of the primary isotope e std vector lt GmEDepo gt theEDepos The list of energy depositions A GmEDepo contains the energy and position of each step e G4String theSDType The type of sensitive detector Hits digitization and reconstruction Hits digitization The conversion of the hits into digital signals is very dependent on the detec tor Therefore GAMOS just provides a general class GmV Digitizer
47. a volume defined in your geometry Alternatively you may use a virtual volume you create for the accasion in a sim ilar way as it is doen at buildPartial_userVolume in In this case you have to add a command gamos geometry DICOM intersect WithUserVolume 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 4dcm files The start is the same list of materials number of voxels and phantom dimensions as if it were the original 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 indi cating the X index 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 GmReadPhantomPartialG4Geometry Simple phantom geometries The user may build simple regular phantom geometries without the need of writ ing a DICOM file by using gamos geometry GmSimplePhantomGeometry The number of voxels is def
48. apas08 html sect G4MatrDb NISTCmp 14 http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplica tionDeveloper html Detector geomSolids html 15 http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplica tionDeveloper html ch04s04 html sect Hits G4Multi 16 http Aoww 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 improve ments 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 Projec tions 2nd ed Herman G T Springer ISBN 978 1 85233 617 2 2009 21 The Radon Transform Theory and Implementation Toft P Ph D thesis Department of Mathematical Modelling Technical University of Denmark 326 pages http petertoft dk PhD 1996 251 Bibliography 252 22 AMIDE Amides a Medical Imaging Data Examiner http amide 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 An
49. 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 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 Detector histograms distance between two gammas Notes 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 his tograms about these two gammas are provided for further information They are produced if the user action DetHistosGammaDist is activated with the command gamos userAction DetHistosGammaDist The name of all these histograms starts with NHGammaDist and all are written in the file NHGammaDist root csv txt The histograms are the following Angle between the direction of the two gammas when they are created angle between gammas at vertex deg Angle between the direction of the two gammas when they enter the sensitive detector angle between gammas at entering SD deg Distance of closest approach between vertex and the line joining the vertex points of the two gammas DCA orig from Gamma vertex
50. 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 characters 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 SUF or SUFFIX followed by a list of pairs word position numbers and word characters 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 ea
51. between the reconstructed hit sets using the position of the hit identified as corre sponding to the first interaction and the interactions For example for the num ber of reconstructed hits variable the following 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 M
52. bigger it will assign an index INT_MAX 2432 In both cases a warning will be printed If you do not want to allow this behaviour but you want that the job is stopped if the datais out of limits you have to set the parameter gamos setParam DISTRIBUTION_NAME AllowOutOfLimits 0 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 logarithmicaly 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 logarithmically in the output f x f x_S exp Chapter 14 Distributions 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 GmNumericDistributionLogLog Interpolates logarithmicaly in the input and logarithmicaly in the output f x f x_S exp log x log x_S K 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 file GmNumericDistributionLower Takes the value corresponding to the closest smaller value f x f x_S GmNumericDistributi
53. calculated Field X projection Field Y projection Material Parent volume name 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 and 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 Geometrical module definition and variables list The MLC module description has to start with the two words words have to be separated by blank spaces and follow the order described here but there is no constraint on the number of lines they may occupy 195 Chapter 22 Radiotherapy application 196 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 plac
54. changed the dimensions of the vol umes 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 xylimits dat 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 RITVZRLimitsUA 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 210 To use a phantom geometry you can use the GAMOS utilities to read phantom geometries in EGS or GEANT4 formats o
55. class scores the number of secondary particles generated in the volume A particle weight is not applied by default The user can choose if the scoring is done 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 tech nique 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 95 Chapter 8 Scoring 96 e GmG4PSPopulation This scores the number of tracks within in a given cell per event A particle weight is not applied by default
56. 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 203 Chapter 22 Radiotherapy application 204 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 When 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 phaseS pace root csv For each of the following particle types a different set of histograms are produced containing 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 proton will be produce if the following parameter is set gamos setParam RT PhaseSpaceHistos Hadrons TRUE A full set of histograms is produc
57. erro in a score does not always guarantee that it has converged to a good result This may be specially true when there are con tributions 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 be haviour 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 code and are inspired in the MCNFP 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 scores 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_v
58. face at pDz or alternatively if your trapezoid is a simpler one you can use the parameters e Length along z e Length along y e Length along x at the wider side e Length along x at the narrower side SPHERE sphere e Inner radius e Outer radius e Starting phi angle of the segment e Delta size phi angle of the segment e Starting theta angle of the segment e Delta size theta 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 SPhi gt 2P1 e Delta size phi angle of the segment POLYCONE polycone e Phi starting angle e Delta size phi angle Number of z planes or Number of rz points For each z plane e Position of z plane 19 Chapter 3 Geometry 20 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 look ing 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 3 751 3 75 2 32 or equivalently SOLID polyc POLYCONE 0 360 4 2 3 3 5 0 75 3 3 5 1 3 3 75 23 375 POLYHEDRA polyhedra e Phi starting angle e Delta size phi angle Number of sides Number of z pla
59. 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 setParam GmReadPhantomGeometry VoxelName VOXEL_NAME It is also possible to displace the phantom from its 0 0 0 position in the mother volume 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 ANGLE_Z Reading DICOM structures A DICOM structure is used to define the voxels that belong to a given volume for example an organ like brain lungs thyroid etc or the tumor or also a treat ment volume In a Z plane a contour is drawn to define the area that belong to the structure which includes all the voxels that are totally or partially inside the structure this operation is repeated in a set of contiguous Z planes to define the full set of voxels belonging to the structure The format to define a D
60. 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 43 Chapter 3 Geometry We list here the available methods with an explanation of their functionality 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 logi cal 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 tol 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 G4VPhysicalVolume pv size_t leafDepth std ostream amp out G4cout Dumps a physical volume with its
61. 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 root csv The following histograms are defined 167 Chapter 17 Detector applications 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 inter actions 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 pho toelectric interaction happened Diff pos when PhotoElec mm Difference in direction from the gamma entering SD to the point where a pho toelectric 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
62. 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 develope ment Therefore if you do not have this software in your installation youd should download the following packages e g Chapter 2 Getting started libexxtools dev libx11 dev libxmu dev libxi dev libxft dev libxpm dev libxext dev freeglut dev dpkg dev Tips for installation in Fedora Core If you are using the Fedora Core Linux distribution you have to select the soft ware development tools at your installation If you do not have this software in your installation youd should download the following packages gcc c libX11 devel libXmu devel libXi devel libSM devel libICE devel freeglut dev this package has some dependency problems so you should se lect the option skip broken libXft devevl libXpm devel Downloading the files separately and installing afterwards If you have poor connection it may be better to download the GAMOS installa tion files one by one first and then running the installation process You have to download the following files e GAMOS 5 0 0 tgz e geant4 9 6 p02 gamos tar gz e geant4 9 6 p02 gamos data tar gz e root_v5 34 10 source tar gz Put all the files in a directory and then type installGamos sh MY_INSTALLATION_DIR MY_DOWNLOAD_DIR where MY_INSTALLATION_DIR is the directory where you want to install GAMO
63. in any of your classes even in several of them There are four classes of parameters numbers string list of numbers list of strings To change the value of a parameter of any of the four types in your input file you have to use the command gamos setParam 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 247 Chapter 27 Appendix B Extending GAMOS functionality with C utilities if it is anumber 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 vdefault 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 GmVSimuEventClas sifier that will return the cla
64. 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 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 Chapter 17 Detector applications 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 tar get 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 h
65. 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 de tector and one hit from the Absorber detector Combining the information of these hits both the positions and the deposited energies Compton cones can 189 Chapter 21 Image reconstruction utilities 190 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 detector corresponding to the two back to back gamma particles caused 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 random 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 matrix 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 itera tion for each event a new position on the corresponding Compton cone or LOR is calculated The new position is accepted according
66. 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 structure struct SPECTOutput char name 8 float xVtx yVtx zVtx x1 yl z21 x2 y2 z2 ener class 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 created by the annihilation of positron that is a primary particle 179 Chapter 19 SPECT application 180 Chapter 20 Compton camera application Before reading this chapter we recommend you to read the chapter on Detector that contains the utilities that are common to all detector applications The Compton camera application is a new addition to the GAMOS framework The application has been developed for researchers investigating the potential of Compton cameras i
67. it GAMOS has been tested in over ten Linux and MacOS distributions and com pilers and in Windows XP and Windows 7 with Visual Studio 2010 Each new release is tested with over sixty tests in at least three different operating systems You can download GAMOS from http fismed ciemat es GAMOS GAMOS depends on Geant4 and on ROOT 5 To download and install every thing you can follow the instruction in the Code download area Installing in Linux and Mac OS As explained in the web page you need to get first the installation scripts and uncompress them in the scripts directory you may do it automatically by down loading 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 The directory name has to be an absolute path i e starting with HOME is OK because it means home This command will download the GAMOS code as well as Geant4 and 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 usr local lib or usr lib check for the following libraries libXmu so libXt so libXext so libX11 so 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 continue witho
68. 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 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 Initia
69. jobs have independent random numbers it may happen that the numbers chosen happen to give some correlation To avoid this GAMOS provides a set of initial random number seeds that are independent They have been produced by running contiguous sets of 1E10 random numbers and storing the final random numbers or in other words Chapter 26 Appendix A running random numbers and storing them each 1E10 The command to use this utility is gamos random restoreSeeds SEED_SET_NUMBER N_RANDOM_NUMBERS where SEED_SET NUMBER the first number correspond to the file name where the seed is stored by default data initialS eeds initialSeeds 1e 10 SEED_SET NUMBER it can be from 0 to 999 N_RANDOM_NUMBERS is the number of times a random seed is sampled before starting the simulation GAMOS provides 1000 random seed files separated by 1e 10 random numbers using the JamesRandom engine You may build your own set but you have to follow some rules All files should be put in the same directory whose name is given by the pa rameter gamos setParam GmRunManager SeedFileDir DIR_NAME The directory will be looked for in the current directory orin the data directory or you may use an absolute path starting by The file names should be initialSeeds NNUMBERS SEED_SET NUMBER where NNUMBERS is the number of random numbers thrown for each file You have to set this number with the parameter by default it is 1 e 10 gamos setParam GmRunManag
70. limits including tools to automatically optimise them e VarianceReduction implementation of several variance reduction techniques e 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 scorin E manag 8 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 e GamosData e Management data management and base data classes e Data data Users data users e GamosAnalysis utilities that can help the advanced user to analyse results e GamosReadDICOM code to read in DICOM files containing patient data e GamosUtilsUA user action utilities tracking verbosity control track count ing process counting time study e GamosUltils general C utilities e GamosApplication GAMOS run manager and the main program 249 Chapter 27 Appendix B Extending GAMOS functionality with C utilities 250 e PET example of PET simulation PETGeometry example to simulate the most common PET devices by defin ing 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 read ing phase space files Each package
71. moment was not 141 Chapter 12 Filters 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 pa rameters gamos set Param 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 section 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 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 fa
72. 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 with 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 GmClassifierBy1 Ancestor 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 corre sponding 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 intermediate 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 likel
73. 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 provide 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 Simulations 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 her project with out having to code in C and with a minimal knowledge of Geant4 and at the same time let an advanced 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 detail your simulation controlling the verbosity making histograms about many variables scoring different quantities etc as we
74. 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 value for later use in any tag P e parameter name e parameter value 31 Chapter 3 Geometry 32 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 Arithmetic Expressions For any value you want to define in a tag you can use the most common mathe matical 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
75. param eter 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 assignClassifier2 Scorer 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 name 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 tutorial The following classifiers are currently implemented in GAMOS GmPSClassifierBy1Ancestor It assigns a different index to different copy num bers of a volume It has an extra parameter that sets the level of the ancestor if it is N 0 it will use the co
76. point transversal length minimum distance from an step position to the line built from the initial shower point and the shower direction From the above two definitions several shower variables are calculated e Maximum longitudinal length maximum of the step point longitudinal lengths Maximum transversal length maximum of the step point transversal lengths e Average longitudinal length average of the step point longitudinal lengths weighted with the energy deposits e 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 approx imately uniformly distributed along the step As it would be too CPU tiem con suming 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 PreStepPoint and PostStep Point 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 written with the following histograms the second name is the type of histogram for histogram limits setting see s
77. 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 parameterisa tion may be added at user request PLACE_PARAM Volume name Copy number Parent volume name Parameterisation type Name of rotation matrix Number of copies Step separation between copies Offset 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 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 Chapter 3 Geometry For this bidimensional parameterisations you have to provide two copy numbers two steps and optionally two offsets For the general case SQUARE t
78. register it to GAMOS you have to create it with a line like myAnaMgr gt CreateHisto1 D HNAM NBINS MAXBIN MINBIN HIS_NUMBER myAnaMgr gt CreateHisto D HNAM NBINSX MAXBINX MINBINX NBINSY MAXBINY MINBINY HIS_NUMBER myAnaMgr gt CreateHistoProfile1D HNAM NBINS MAXBIN MINBIN HIS_NUMBER myAnaMgr gt CreateHistoProfile D HNAM NBINSX MAXBINX MINBINX NBINSY MAXBINY MINBINY HIS_NUMBER The last argument is the histogram number that can be later used to retrieve 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 GmAnalysis Mgr for a histogram by its number or its name myAnaMegr 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
79. 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 set Param CC EvtClass PhotopeakEPrecMax VALUE Only hits whose relative time difference is less than the value given by the pa rameter gamos set 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 nec essary 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 detector it Compton scatters and undergoes Photoelectric absorp tion This event can be reconstructed if the 1st hit ie the Compton scattering in teraction is correctly identified 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 respectively with the parameters gamos set Param CC EvtClass ComptonRecHitDistScat DIST gamos setParam CC EvtCl
80. 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 at the method mentioned above which does not take into account the initialisation and termination times of each track event and run 157 Chapter 15 Utility user actions Changing the weight using a distribution The command gamos userAction GmChangeWeightUA changes the weight at each step or track following a GAMOS 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 cre ates 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 gamos userAction GmCopyWeightToSecondaryUA Stop run after a certain CPU time 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 gamos userAction GmStopRunAfterTimeUA The time is limited with the paremeter gamos set Param USER_ACTION_NAME 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 Visualising only a set of events This ut
81. 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 The whole algorithm is repeated selecting as first the other hit of the pair of recon structed 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
82. the equivalent doses H Hp 0 15 can be obtained In this chapter we describe first the theoretical basis of the method Then we ex plain how it is implemented in GAMOS how to select the different available op tions 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 j1 the probability that at a source or neutron gamma interaction the the particle produced or scattered goes into the Chapter 8 Scoring solid angle dQ about the direction u where u cos 6 if R is the distance to the detector from the source or interaction point RR Et ajds pl je odk Ja Figure 8 1 yields the probability that the particle reaches the detector point with no further collisions where px f Ej gt Pd SOe y Figure 8 2 is the attenuation of a beam of monoenergetic particles passing through a mate rial medium where s is measured along the direction from the source or interac tion point to the detector and s is the macroscopic total cross section at s If dA is an element of area normal to the l
83. the par ticle is in The InitialLocalPos data for a Step object calculates the transformation in the volume the track step has just traversed while for a Track object 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 Chapter 11 Analysis extracting data transformation in the volume the track step has just traversed but using the po sition 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 If you want to get the vertex position for a step for a track is obtained as InitialPos you may use the data Vertex this data are useful for StackData data users as the initial or final positions are not calculated at stacking action Another set of data RandomPos select randomly a point in the line joining the PreStepPoint and PostStepPoint 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 FinalPosP
84. 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 tar get 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 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 tha
85. 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 detec tor without any further interaction The first probability is based on a precalcu lated table of angle probabilities 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 free paths that the neutron or gamma would have to traverse along the path to reach the point detector A similar cal culation 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 ref erence system of the parent particle i e probability equal to 0 5 Summing up these probabilities for a number of events usuallly several orders of magnitude less than with conventional methods one can get the flux and the energy spec trum at the point detector and with these magnitude
86. three histogram will be filled the compound index will be split in the two indices as defined with the NShift of the GmCom poundClassifier 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 Other scorer printers are provided for specific applications See corresponding sections in this guide Classifiers See section on Filters Multiplying by data 98 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 mul tiplied by the value of that the GAMOS data has in that step To do it you have to use the parameter gamos setParam SCORER_NAME MultiplyByData DATA_NAME where DATA_NAME is the name of the data you want to use Chapter 8 Scoring Multiplying by distribution 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 multiplied 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 Convergence testing The fact of having a small relative
87. to do scoring or filtering in a volume you have to use this notation Physics No physics is needed as there is no tracking Therefore we recommend you to use GmMCNPDummyPhysics as in the first example This physics simply defines all the particles that you may need and no physics When from the MCNP ptrac file one step is read that has suffered a collision GAMOS creates a dummy pro cess with the name corresponding to the process type The names are taken from the GEANT4 terminology Here you can see the names of the processes for each particle together with the MT type you find in MCNP e Neutrons e Elastic NeutronElastic MT 2 e Capture nCapture MT 102 e Fission there are several channels e NeutronFission MT 18 e NeutronFission_f MT 19 e NeutronFission_n f MT 20 e NeutronFission_2nf MT 21 Inelastic there are several channels NeutronInelastic_2n MT 16 NeutronInelastic_3n MT 17 NeutronInelastic_n a MT 22 NeutronInelastic_n p MT 28 NeutronInelastic_n d MT 32 NeutronInelastic_n t MT 33 NeutronInelastic_3nf MT 38 NeutronInelastic_n 1st MT 51 NeutronInelastic_n 2nd MT 52 NeutronInelastic_n 3rd MT 53 NeutronInelastic_n Xth MT 50 X NeutronInelastic_n _continuum MT 91 NeutronInelastic_p MT 103 NeutronInelastic_d MT 104 NeutronInelastic_t MT 105 NeutronInelastic_3He MT 106 NeutronInelastic_a MT 107 e Photons gammas Compton scattering co
88. to the density value of the voxel corresponding to the new position compared to the density at the old po sition 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 res olution 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 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 SOE_ImageRecon PE for PET data SOE_ImageRecon Compton for Compton data SOE_ImageRecon PETGauss for PET data using a Gauss distribution for guessir SOE_ImageRecon seed lt seedNumber gt selecting specific seed SOE_ImageRecon xtraIterI
89. 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 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 position Dist SOURCE_NAME GmGenerDistPosi tionDiscGaussian SIGMA POS_X POS_Y POS_Z DIRX DIR_Y DIR_Z The position is distributed in a disc in the XY plane with the radius in a gaus sian 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 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 randomly in the voxels of a phantom gamos generator position Dist SOURCE_NAME GmGenerDist Position VoxelPhantomMaterials MATERIALI1 MATERIAL2 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
90. 0 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 e verb verbosity it sets the RTVerbosity 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 simulati
91. 04 Reading phase spaces siesssieveicssssseveiesdaevestaossses tideresesiannevtessnacsteonats 205 Adding extra information to a phase Space cccecccseseseseeseeneeceees 206 Reusing a particle at a phase space without filling the phase space file Optimisation of a linac simulation ee ceesee ee seeseseseeeeeseseeseeeees 208 Cutts Optimisation sissie inireseta eiaeiiai dieen 208 Electromagnetic parameters optimisation ssesssssssrersissessseseeseete 208 Particle spitting sses a sp raes 208 Killing particles at big X Y nnisisiiiissnisisspsii siisii 210 Scoring dose in phantom e esessesssesserisssississessssinsisstesresnesnenrinnesnesssentestenet 210 Saving scores and score errors in text file tees cetesesteteeneees 211 Saving scores and scores squared in binary file ccc 211 Saving scores in histograms cccceees esses eesessesesesesesesescseeeseecees 212 Analysis Utilities iee aan ieta e ayen e aara E R A aE 213 Summing phase space files csecvsisssesevesisesees disevesessanheevierseacseviersiats 213 Making histograms out of a phase space file cececececeeseeteteseees 214 Merging sqdose files c cece ec cseeeceessseeseesssesesesesesesescsseeseeceses 215 Merging Sddose files ccc cesses ssessseeseessesesesesesesescsseeseecees 215 Making histograms out of a sqdose file ccsccseseeteteeeetesesteteeneees 215 Automatic determination of production cuts for an accelerato
92. 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 j144 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 o T To run ImageJ 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 expression S HOME ImageJ jre bin java Xmx512m jar HOME ImageJ ij jar ijpath 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 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
93. 4RunManager FileName FILE_NAME Geometry 232 GEANT4 needs a geometry to run but this can be anyone as it will not be used for tracking Nevertheless if you want to set some condition on a given cell vol ume you have to previously define it And if you want for example to get a F4 tally cell scorer you have to set the right cubic volume of the cell An important difference of GEANT4 with respect to MCNP is that geometry parts are defined as volumes box cube cone trapezoid and placed one with re spect to the other There is no concept of surface so you cannot define any but we have added a trick to be able to du surface tallies see section on tallies A simple example of a geometry implementing a unique volume named cell_11 of cubic volume 20 cm3 is the following VOLU world BOX 1000 1000 1000 G4_AIR MATE mate_11 111 VOLU cell_11 BOX 20 cm 1 cm 1 cm mate_11 ROTM RM0000 PLACE cell _11 1 world RM0000 You can define the explanation of the geometry text file format in the chapter about Geometry in this guide but we will go though this example line by line for better understanding The first line defines a world volume what is mandatory in GEANT4 This vol ume is simply one that is not placed anywhere but others are placed inside it The second line defines a material Materials are also not used but you may like to define one with the name you like for example for applying some condition in it In th
94. AES E Ea e iEn N EENEN 100 Theoretical pasisin m a r a a os E 100 GAMOS implementation s sssssssssseessessesssesiesessteseessesnentinnesresssenteseesee 102 Variance reduction techniques cccccccscessseesesssssesescseeesesceeeeecses 105 9 Variance reduction techniques ceccrsrsreressssssssssssssssssscscessesesessesseseeseseseeees 109 Introd chon REPPIN SD a OT PPR Oe 109 Timportanice Sampling sssini catacscoesesvacdectsevascucsevescouessesosesuasivvee seats 109 Geometrical biasing i tescieietsetiseeectiit crt teenie telasvenniadivta iae 109 General process splitting arisini satie ap eea aR a ia 110 Particle splitting techniques for radiotherapy sssssssssssssssessessesssseeseesee 110 Production of deexcitation secondary particles cccccccseseseceenee cess 110 10 Histogramming scscecesscssssssecessssssesesesessnssseesoeseessesssecesesseseseoesesenseseseoeseees 111 Histogram formats sheeran un oia ia a ao iaa ate 111 Histograms in CSV formatines aaea aa aaria aaie 111 Changing histogram minimum maximum and number of bins 111 Output fil s names nissene nr iee ea e eia i e ea SEEE tives 112 Analysing your histograms with ROOT s sssssssssssisssssessssssesrersessesssssreseenee 112 Printing the histograms in graphics files snsssssssssossosessessseseesesee 113 Comparing histograms in two fileS sssssssssssesssesssssessssrirsissesssestestesee 113 Creating your OWN his
95. Action which initializes the data to 0 the End OfEventAction 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 Accumu lated these data users implement a UserSteppingAction method which accumu lates 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 Note the data of type Initial is printed or used to fill an histogram at the end of track event or run with the aim of having together all the information relevant to an object This behaviour can be changed so that this data is print at the start with the parameter gamos setParam DATA_USER_NAME UseAtlInitial 1 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 GmTrackDataHistosUuA GmSecondaryTrackDataHistosuA GmStackDataHistosUA GmEventDataHistosuA GmRunDataHistosuA 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 possible if a 2 dimensional histogram is required the names of the two data have to be separated by vs
96. Chapter 3 Geometry 12 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 Material made of one element MATE e Name Z eA 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 Proportions by weight fractions MIXT_BY_WEIGHT This tag is equivalent to the MIXT tag Proportions by number of atoms MIXT_BY_NATOMS e Proportions by volume MIXT_BY_VOLUME The first two tags can be used to build material mixtures out of elements or ma terials but the last tag can only be applied with material components elements do not have density Example Chapter 3 Geometry MIXT Fiber Lead 9 29 2 Lead 0 9778 Polystyrene 0 0222 MIXT_BY_NATOMS CO2 1 8182E 3 2 Cl O2 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
97. Cuts cccececeseseseceeeeeeeeees 74 Apply cuts for all processes 0 0 ceeseesessssseseessesescsesesesescssenseeesnees 74 LOETI E aa EE e EEA EE E A A E A E AEE tate 74 Automatic optimisation Of CUtS s se ssesssetssstesttssstestttssttrtitsstenteesteenterstesnteentes 75 Range rejection esii ssa e aa e a E a a EA RNET 76 Building your physics list with C code sssssssssssssssssississesssesississseseessessesee 76 ROTA A COONS E EEA A E E AIE ERE AETA EE 77 Addins aftenens na oeae Erea eea Teea ael ane rea Ea aee aaa 77 Adding classifier eirese psi tnei e iain ait noha n NE EER 77 TO ET aO aE ae 1i a EAEI RA EA A E AE AN 77 Creating your GAMOS user action cccescccsesesessensteseeeesescsesesesescseseseeceeees 78 7 Sensitive Detector and Hits ccssccesccssrcesssscsccesscescecccesssececcesceceseececcecceceeeees 79 Sensitive detectors n a Sede sdacesaesvesiocteonadcedestiedes a e AEEA iR 79 Attaching a sensitive detector to a Volume sss ssissssssesiesisssissssesseeee 79 Building your sensitive detector with C code ccc 80 PALES N A TNA E OEE EAE A POR EEE EREE E 80 Hits digitization and reconstruction esssssessesssesissississssstesieseesreseessessente 81 FLIES Gi git ZatlON sessen sonin ee aves cesses Dalvie Se Tae stances 81 Hits and digits reconstruction ss ssssssessssisssississesstsssesiesiessessssressenee 81 Examples of reconstructed hit builders cece ceeesesesneeneeeees 82
98. Deexcitation 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 inde pendently for the secondary particles generated by ionisation and photo electric effect The parameters to do it for ionisation are By default production of characteristic X rays by fluorescence and Auger elec trons 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 affected by the same cuts than the production of bremmstrahlung gammas and ionisation 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 69 Chapter 5 Physics Decay process You can activate the decay process for all particles for which it is applicable with the user command gamos physics add Physics decay Radioactive decay process Each time an ion is created by a GAMOS comman
99. E 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 gamos setParam SCORER_NAME Surfaces SUREACE_1 SURFACE_2 These surfaces depend on the volume solid Box e X YZ plane at positive X e X YZ plane at positive X e Y XZ plane at positive Y e Y XZ plane at positive Y e Z XY plane at positive Z e Z XY plane at positive Z 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 com posed of the points of same phi that limit the tube volume e TOP the top surface e BOTTOM the bottom surface Sphere e INNER inner radius surface Chapter 8 Scoring e OUTER outer radius surface e THETA if the full theta 180 degrees is not defined it is the two surfaces composed of the points of same theta that limit the sphere volume e PHI if the full phi 360 degrees is not defined it is the two surfaces com posed of the points of same phi that limit the sphere volume GmPSSurfaceFlux This is a surface based scorer The quantity is the flux i e the number of tracks that reach the surface divided by the area and the co sine of the angle between the track and the surface normal GmG4PSPassageCellCurrent P
100. E ProductMaxAZ VALUE Print yields of production of secondary particles from charged particles traversing a thich material 226 The user action gamos userAction SHPrintPHPChannelThick YieldUA prints the average yield of secondary particles produced when a charged particle traverses a thick yield of a material as it loses energy from a maximum until a minimum energy value It will show you the yield for each hadronic channel independently As this user action invokes the GEANT4 internal methods there is no need to simulate an event Nevertheless to profit from the GAMOS utilities you should set up an input file similar to other GAMOS input files You can see an example on the use of this utility at MY_GAMOS_DIR tutorials S Hielding Tutorial exercise5 exerciseof in This example print the thick yield of a proton in several materials using the parti cle_hp GEANT4 package for several energies in several materials The first thing it does is to replace the geometry GmGeometryFromText by GmGeometryUseMate rials This geometry class will generate a world for each of the materials given by the parameter gamos set Param GmGeometryUseMaterials Materials MATE_1 MATE_2 Notes Chapter 23 Shielding application If any of the materials is not aGEANT4 one you will need a geometry file where the material is defined The name of this file is given with the parameter gamos setParam GmGeometry UseMaterials FileName FILE_NAME The SHPrint
101. ELEC_FIELD_X ELEC_FIELD_Y ELEC_FIELD_Z where MAG_FIELD_X MAG_FIELD_Y MAG_FIELD_Z are the magnetic field val ues along the three axesand ELEC_FIELD_X ELEC_FIELD_Y ELEC_FIELD_Z are the electric field values along the three axes Remember 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 VOL UME_ 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 Non uniform magnetic fields If you need other types of fields different than uniform use the MagFieldManager utility This is an utility that allows to define arbitrary magnetic fields and control their tracking precision paramters and also calculates the magnetic fields for different structures circular coil solenoid and stores them in a file for later used To use if you have to set the GAMOS parameter gamos setParam MagneticFieldModelManager On 1 You can find all the relevant documentation in the file GAMOS 5 0 0 source Mag FieldManager doc user_manual_bfield_manager pdf In GAMO it is already installed so you may skip the installation instructions 1 This f
102. Effect Ct prodcuts root percentage and look at the last lines of output those that contain the word FINAL like the following ones PARTICLE e FINAL 17 19 PARTICLE e FINAL 72 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 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 infor mation per track reaching the target and therefo
103. 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 will be illustrated in the following lines The first step is to define a class inheriting from G4tgrLineProcessor see for exam ple 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 pass ing 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 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 tiret id 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 GmGeomTextDetectorBuilder ReadDetector to set as line processor the one you have created and to trigger the
104. G4_OCTANE G4_PARAFFIN G4_N PENTANE G4_PHOTO_EMULSION G4_PLASTIC_SC_VINYLTOLUENE G4_PLUTONIUM_DIOXID G4_POLYACRYLONITRIL G4_POLYCARBONATE G4_POLYCHLOROSTYRENE G4_POLYETHYLENE G4_MYLAR G4_PLEXIGLASS G4_POLYOXYMETHYLENE G4_POLYPROPYLENE G4_POLYSTYRENE G4_TEFLON E r GQaaqaqaa E Gl La ro ae Ba 15 Chapter 3 Geometry G4_POLYTRIFLUOROCHLOROETHYLENE 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_NATURAL G4_RUBBER_NEOPRE G4_SILICON_DIOXID G4_SILVER_BROMIDE G4_SILVER_CHLORIDE G4_SILVER_HALIDES 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 G4_TISSUE_SOFT_ICRP G4_TISSUE_SOFT_ICRU 4 G4_TISSUE METHANE G4_TISSUE PROPANE G4_
105. 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 is not set it is STP i e 273 15 kelvin The default unit of tempera ture 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 Example MATE_PRESSURE G4_WATER 1 5xbar 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 vol ume corresponds to the name of one of these predefined materials they all start 13 Chapter 3 Geometry 14 with G4_ The Geant4 materials have the mean excitation energy set explic itly 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 defi
106. 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 dis card 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 ramplak 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 Inter file 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 re
107. GAMOS 5 0 0 User s Guide GAMOS Collaboration GAMOS 5 0 0 User s Guide by GAMOS Collaboration Published February 23 2013 Table of Contents T DO UC O80 nedene nases ieod esee naes deed seoed ese esae airea 1 About this d cuMm nt sesia e E E En E EEIE 1 Introduction to GAMOS siiret eeg ehren e eE Senda EEE SEE EO ATE 1 Structure Of GAMOS isseiieesnsrener ressec eiseressen orr erans e sheera rein 1 The plug in CONCEP ti wees wad inann ne A a ah 2 Zs Getting Started cccecdcecccasseccasnivonasessstonesduaessacustonnseescosetvas sansnsnsvousvesssosusdennsnsdensedwasee 3 Getting the code and installing it sisesinnesiihirie eoii isinna 3 Installing in Linux and Mac OS cee cesessesecsssesescsceeneeceseesneeesenees 3 Installing in WindOWS cccsccscsseeseesesesesceesesescesesssesnenesescecesesesnseneseseans 5 Running an example in Linux or Mac OS s sssssssssssssesissessesssssiesissressesresnsssenees 5 Running an example in Wind OWS uc cece esessseeseseseesescsceseseecsssssnessseeenes 6 Compiling GAMO vis csc Siec dete nel N botven E E Meee tere geet aces 8 Compiling your new Code i aree ar a Ea a anta 8 3 GOOMELTY A 11 Building your geometry with a text file 0 0 eee eseses cesses ceenseeeeeees 11 Description of geometry text file format ccccceeseetetes cece esteteteneeeees 11 Dumping your Geant4 geometry in text file format 33 Adding new tags to your input text file oo cece eeeseseeeeeeeeneees 34
108. 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 param eter gamos set Param GmTrackingVerboseUA VerboseLevel VALUE 161 Chapter 16 Managing the verbosity Dumping the standard output and error in log files 162 By default the standard output what is printed by G4cout or std cout is saved in a file called gamos log while the standard error what is printer by G4cerr or std cerr is saved in a 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 interactions before the photoelectric one and then i
109. ICOM files Converting a DICOM file to a simulation file GAM6OS is able to read the patient data resulting from a CT scan in DICOM for mat The first step is to change the DICOM format into a format readable by GAMOS converting the Hounsfield nubmers into material and density informa tion To do this you can use the utility at analysis DICOM which is based from the Geant4 example examples extended medical DICOM We describe here the pro cedure you have to follow The first step is to write a file named Data dat This file has the following informa tion Aline with the compression value e 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 e The number of materials you want to use e A line for each material describing its name and the upper bound of the den sity interval The materials should be described in increasing order of density The voxels with a density between 0 and the first upper bound will be as signed 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 material 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 e
110. ICOM strucutre in a GAMOS phantom is the follow ing after the description of the material indices and the material densities there should be an index for each of the voxels setting the structure it belongs to If the voxel dose not belong to any structure a 1 should be written If the phan tom file is in EGS format the numbers are contiguous while if it is in GEANT4 format the numbers are separated by a blank space If a voxel belongs to several structures the structure index contains the list of structure indices in the form IN DEX_1 INDEX_2 100 INDEX_3 100 100 In case more than 100 indices are needed the multiplication number may be changed with the parameter gamos setParam GmReadPhantomGeometrywithPS NShift VALUE In the case of the EGS format by default the number of digits used to store the index is two so if more than one structure is assigned to a voxel it is needed to increase this number by changing the parameter GmReadPhantomEGSwithPSGeometry PVNumberOfDigits VALUE After all the voxel indices there should be a list of two column lines to give a number and a name to each structure in the phantom for example 0 head_tumor 1 heart 2 lungs To use the phantom structure it is needed to select a different geometry depend ing on the format gamos geometry GmReadPhantomEGSwithPSGeometry or gamos geometry GmReadPhantomG4withPSGeometry 39 Chapter 3 Geometry 40 Filtering on DICOM structures It is
111. IST 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 gamma compt PROC_LIST gamma conv PROC_LIST gamma phot This list may not be printed unless you set the parameter gamos setParam USER_ACTION_NAME PrintPartList 1 153 Chapter 15 Utility user actions e At the end of run how many times a process determined the step for each particle type 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_COUN
112. ISTO_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 histol NBins 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 The name of the histogram file for each of the GAMOS histogram classes is ex plained in the corresponding section of this guide As these classes are user ac tions to this file name it is added the name of the filters and classifier as ex plained 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
113. 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 density 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 e 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 e m_cd 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 corresp
114. MF Detector 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 detectors 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 command to associate several scorers to the same detector To each of the defined scorers you can add a filter to select for which track con ditions 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 section 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 vol umes with different copy number This is m
115. MOS electromagnetic extended physics list This physics list can be selected with the command gamos physicsList GnEMExtendedPhysics It creates all GEANT4 particles using the constructors G4BosonConstructor G4LeptonConstructor G4MesonConstructor G4BaryonConstructor G4lIonConstructor G4ShortLivedConstructor For these particles the physics implemented is the following see GEANT4 Physics Reference manual for a detailed explanation of the physics options e 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 pit pi kaon kaon G4hMultipleScattering G4hIonisation with SetStepFunc tion 0 2 50 um G4hBremsstrahlung and G4hPairProduction The minimum energy for the validity of G4hBremsstrahlung is set to 10 keV instead of the default value 1 GeV Other charged particlesG4hMultipleScattering and G4hlonisation This physics lists inherits from GmEMPhysics so that the command gamos GmEMPhysics replacePhysics can be used to change the physics models of the electromagnetic particles Standard electromagnetic physics list options Geant4 offers several options of standard
116. MomPhi InitialMomTheta FinalMomX FinalMomY FinalMomZ FinalMomMag FinalMomPerp FinalMomPhi FinalMomTheta VertexMomxX VertexMomY VertexMomZ VertexMomMag VertexMomPerp VertexMomPhi VertexMomTheta MomChangexX MomChangeY MomChangeZ MomChangeMag MomChangePerp MomChangePhi MomChangeTheta 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 InitialKineticEnergy FinalKineticEnergy KineticEnergyChange Initial TotalEnergy FinalTotalEnergy InitialDEDX This is not exactly the energy lost divided by the path length as one may think from its name but the dE dX i e the fraction of energy lost per distance travelled as calcualted by the GEANT4 utilities with the final kinetic energy in the volume material the PreStepPoint or track vertex is in FinalDEDX Similar as above Plus some data of type Accumulated e AccumulateEnergyLost e AccumulatedEnergyDeposited e AccumulatedDose This is the energy deposited divided by the volume mass Chapter 11 Analysis extracting data AccumulatedKerma This is the sum of energies of the charged secondary parti cles produced by non charged particles divided by the volume mass InitialGammaEquivalentDose Calculates the equivalent dose multiplying the volume flux step length divided by cubic volue by flux to equivalent dose conversion fac
117. NShift is de fined 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 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 indices to classifiers In most classifiers by default the indices are built automatically as the objects of classification 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 process names and INDEX_ii are the new indices In the case of classifier Chapter 13 Classifiers GmClassifierByParticleProcess 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 number following the maximum index defined with the user command The exceptions are the classifiers GmClassifierBy1Ancestor and GmClassifierByAncestors for
118. N_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 be ing 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 char acters that will be used when writing a binary file The string 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 FinalPosX FinalPosyY Each data has as a property the histogram number of bins that for all is 100 the minimum and maximum In case it is a composed data i e using mathemat ical expressions the minimum and maximum will be calculated with the same formula used for the data If you want to avoid this calculation the following parameter must be set gamos set Param GmV Data ComposeHistoLimits 0 These values can be changed as for any histogram see section on Histograms Data users 116
119. 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 his togram file equal to the file that was created when producing the phase space file will be created 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 EMax maximum limit of the energy histograms e RMax maximum limit of the position histograms Chapter 22 Radiotherapy application NBins number of bins of histograms verb verbosity it sets the RTVerbosity 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 utility serves to merge dose files in the format sqdose corresponding to dif ferent jobs with the same setup and getting the average dose of them To use it you have to write a file containing the li
120. PHPChannelThickYieldUA user action accumulates the yield of sec ondary particle from an initial energy down to a minimum energy These energies are set with the parametes gamos setParam USER_ACTION_NAME minE VALUE gamos setParam USER_ACTION_NAME maxE VALUE To calculate the average yields in a fast way it does not simulate N particles but just computes them from the channel cross sections The number of intermediate energy that it will use for these calculations is given by the parameter take into account that more stepts means bigger precision but longer running time gamos setParam USER_ACTION_NAME nStepsE VALUE If you want that the steps are taken logarithmically you can set the parameter gamos setParam USER_ACTION_NAME logE 1 1 The fit is done using ROOT utilities so you must install GAMOS with ROOT to get this result 227 Chapter 23 Shielding application 228 Chapter 24 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 parti cle 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
121. S and MY_DOWNLOAD_DIR is the directory where you copied the installation files Both directory names have to be absolute paths i e starting with HOME is OK because it means home Copying GAMOS to a different place If you have GAMOS installed at a given directory in a given computer and you want to copy it to another directory or to another computer you can skip the downloading phase and go directly to the compilation you should not try to use the original GAMOS distribution unless you are sure that the new computer Chapter 2 Getting started has exactly the same operative system and the directory is the same as in the old computer To reinstall without downloading use the command reInstallGamos sh MY_INSTALLATION_DIR where MY_INSTALLATION_DIR is the directory where you have copied GAMOS The directory name has to be an absolute path i e starting with HOME is OK because it means home Installing in Windows The first thing to do to install in Windows is selecting a directory which we will call MY_INSTALLATION_DIR and which can be for example c gamos Before installing GAMOS you have to install ROOT Get the executable file from the GAMOS web page and install it GAMOS has to know automatically where ROOT is so be careful not to use the Standard installation but the Custom one and change the default directory to the directory MY_INSTALLATION_DIR external root 5 34 10 root To install GAMOS you hav
122. SSSS Classification of Gamma Interactions in SD S GC nEvents 1000000 GC n gamma in SD 516170 25 8085 GC n PE 321588 62 30273 GC PE 0 COMP 157614 49 011157 GC PE 1 COMP 111304 34 610744 GC PE gt 1 COMP 52670 16 378099 GC n COMP i 222590 343 12339 GC 1 COMP 159193 71 518487 GC gt 1 COMP 63397 28 481513 GC nGamma_COMP event 0 585931 e nEvents total number of events e n gamma in SD number of original gammas reaching one sensitive detector e n PE number of original gammas with photoelectric interaction in SD e 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 e n COMP number of original gammas with Compton interactions in SD e 1 COMP number of original gammas with only one Compton interaction in SD percentage relates to n COMP e gt 1 COMP number of original gammas with more than one Compton inter actions in SD percentage relates to n COMP e nCOMP event number of Compton interactions
123. ST_Eye Lens ICRU 44 IST_Ferrous Sulfate Standard Fricke NIST_Gafchromic Sensor IST_Lung Tissue ICRU 44 IST_Muscle Skeletal ICRU 44 IST_Ovary ICRU 44 IST_Photographic Emulsion Kodak Type AA IST_Polyethylene Terephthalate Mylar IST_Polymethyl Methacrylate NIST_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 Chapter 3 Geometry The meaning and order of the solid parameters is the same as in the correspond ing Geant4 solid constructor All the Geant4 CSG and specific solids are imple mented 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 J BOX box 17 Chapter 3 Geometry 18 X Half length Y Half length Z Half length TUBE tube Inner radius Outer radius Half length in z TUBS tube section Inner radius Outer radius Half length in z Starting phi angle Delta size phi angle of the segment CONE cone Inner radius at fDz Outer radius at fDz Inner radius at fDz Outer radius at fDz 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 phi angle of the segment Delta size phi angle of the
124. S_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_DIMENSIONS are the solid dimensions By default the volume is placed 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 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 ro tating 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 Chapter 4 Generator The direction is taken as the line that goes from the position to the point 0 0 0 Position in a point pointing towards a box GmGener DistPositionDirectionInVolumeSurface POINT_X POINT_Y POINT_Y TOUCHABLE_NAME_1 TOUCHABLE NAME 2 All particles are generated at a fixed point pointing towards a random point of the touchables which must be of tyep G4Box As this distribution is of position and direction types at the same time you have to use the two commands gamos generator positionDist gamos generator directionDist You can see editing the file GamosCore GamosGenerator src GmGener Dist PositionDirectionInVolum
125. T 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 e If the second parameter is fixed the energies used are only those listed For example 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 e 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 probabil ity in the histogram bin In this case if the difference between data points is not constant 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 quarters between 1 and 2 MeV you can write the following file 0 5 0 25 1 5 0 75 e 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 behaviour has to be different than for the histogram case above
126. T 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 The 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 This user action may be combined with filters and classifiers Shower shape studies 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 action 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 wil
127. TITANIUM_DIOXIDE G4 OLUENE G4_TRICHLOROETHYLENE G4_TRIETHYL_PHOSPHATE G4_TUNGSTEN_HEXAFLUORIDE G4_URANIUM_DICARBIDE G4_URANIUM_MONOCARBIDE G4_URANIUM_OXIDE 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 3 wwe Other materials common in medical physics are also predefined in the files MY_GAMOS_DIR data NIST_materials txt and MY_GAMOS_DIR data PET_materials txt The full list is the following BaF2 Bal2 BGO CdTe 16 Cdwo4 CAE CeBr CeC1 GST GaAs 3 3 Gd202S GSO HgI2 LaBr Lacl LiF 3 3 Li2B407 LSO LYSO LuAG LuAP LuYAP Lul3 Nal PbWO SEIZ YAG 4 YAPNIST_A1203 IST_Barite IST_BasSo4 NIST_CaoO IST_Concrete IST_PMMA IST PVC IST_Adipose Tissu ICRU 44 IST_Blood Whole ICRU 44 IST_Bone Cortical ICRU 44 IST_Brain Grey White Matter ICRU 44 NIST_Breast Tissue ICRU 44 IST_Cadmium Telluride IST_15 mmol L 1 Ceric Ammonium Sulfate Solution IST_Concrete Ordinary IST_Concrete Barite TYPE BA I
128. ToOther Order ORDER This algorithm cannot be used for SPECT detectors Det1stHitByComptonCone 163 Chapter 17 Detector applications 164 The idea of this algorithm is to profit from the fixed relationship between the initial and final energy and the deviation anble in Compton interactions It se lects a pair of reconstructed hits and between the two chooses one as corre sponding 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 interaction 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 detec tor before any other interaction 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
129. UT_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 OUTPUT_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 IAE 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 IAE PARTICLES 224635 NPART_TOT 450072 NPARTORIG_TOT 10000000 RATIO 0 044927 0 000101455 RATIO_TOT 0 0450072 Opening phase space contained in ps 20002 IAFAheader of type IAE PARTICLES 224813 NPART_TOT 674885 NPARTORIG_TOT 15000000 213 Lea 1Y RTPSPDoseHistos Dose Profile Y_merged 0 NVoxelX 1 0 NVoxelyY ae 1 il 1 6 9 0 NVoxelZ 1 0 NVoxelZ 1 0 NVoxelZ 1 49 Chapter 22 Radiotherapy application 214 RATIO 0 0449626 0 000101501 RATIO_TOT 0 0449923 x x x N Particles 674885 x x N Photons 673804 x x N Electrons 1057 x x x x N Positrons 24 x x N Original 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 ac
130. UrbanMscModel96 Step limit type is set to UseDistanceToBoundary e positron e ionisation process G4elonisation using G4MollerBhabhaModel e bremsstrahlung process G4eBremsstrahlung using model G4SeltzerBergerModel below 1 GeV and G4eBremsstrahlungRelModel above e multiple scattering process G4VMultipleScattering using model G4UrbanMscModel96 61 Chapter 5 Physics 62 e opticalphoton e scintillation this process is activated for all particles except short lived ones Process class is G4Scintillation with yield factor 1 the option to track secondaries before the primary track ends is activated by default It may be changed with the paremeter gamos setParam GmPhysicsOpticalPhoton TrackSecondariesFirst 0 e optical absorption G4OpAbsorption e optical rayleigh G4OpRayleigh e optical boundary process G4OpBoundaryProcess with unified model The default physics models can be overridden by choosing among the three cat egories that Geant4 proposes for electromagnetic interactions standard low en ergy or Penelope models This can be done with the command gamos GmPhysics replacePhysics PHY SICS_MODEL_NAME where PHYSICS_MODEL_NAME is one of the names in the list below The de fault options those explained above are underlined The following physics models are available e gammas gamma lowener low energy based on Livermore Evaluated Particle Data Li brary gamma standard standard electromagnetic
131. With DataFileName only the third field is important the second field should be an integer that is ignored by the code The EventSetSize 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 i e all events are kept in memory Iterations The number of iterations is set in the parameter file ir_soe_userparameters conf m_iterations 100000 ee Geometry The geometry parameters are set in 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 5 0 m_bins_y 100 m_ymin 5 0 m_ymax SO fF 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 UseSpatialDeltay 0 0 mm UseSpatialDeltaZ 0 0 rm UseDopplerEffectSigmaTheta 0 0 sigma The UseEnergyResolutionFactorFWHM parameter sets the Gaussian variation in Energy used to recover for resolution loss due to energy resolution The UseSpa
132. _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 238 If you want to run several jobs with the same configuration but different random seeds each you can use the GEANT4 random number management or do it the GAMOS way GAMOS offers two ways to set the initial random seed or to restore it from a file Both options are explained below Setting the initial random number seeds GAMOS offers a single command with which you can give a different initial ran dom seed to your job so that the results are statisticaly independent gamos random setSeeds INITIAL_SEED N_LRANDOM_NUMBERS where two numbers are given to better guarantee the independence of the results INITIAL_SEED is the initial random seed and N_RANDOM_NUMBERS 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 Restoring the initial random number seeds Although the previous method should guarantee that two
133. _CYCLOHEXANE G4_1 2 DICHLOROBENZENE G4_DICHLORODIETHYL_ETHER G4_1 2 DICHLOROETHANE G4_DIETHYL_ETH G4_N N DIMETHYL_FORMAMIDE G4_DIMETHYL_SU I G4_ETHANE G4_ETHYL_ ALCOHOL G4_ETHYL_ CELLULOSE G4_ETHYLENE G4_EYE_LENS_ICRP Chapter 3 Geometry 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 13I1 G4_GADOLINIUM_OXYSULFID G4_GALLIUM_ARSENIDE G4_ _PHOTO_EMULSION G4_Pyrex_Glass G4 ASS_LEAD G4 AASS_PLATE G4 UCOSE G4 G4 G4 G4 G4 Gl ies GUE K Q oy Z J HOH AAAAAAATA re mm tu Pp 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_TETRABORATE G4_LUNG_ICRP G4_M3_WAX G4_MAGNESIUM_CARBONAT G4_MAGNESIUM_FLUORIDE G4_MAGNESIUM_OXIDE G4_MAGNESIUM_TETRABORATE G4_MERCURIC_IODIDE G4_METHANE G4_METHANOL G4_MIX_D_WAX G4_MS20_TISSUE G4_MUSCLE_SKELETAL_ICRP G4_MUSCLE_STRIATED_ICRU G4_MUSCLE_WITH_SUCROSE G4_MUSCLE_WITHOUT_SUCROS G4_NAPHTHALENE G4_NITROBENZENE G4_NITROUS_OXID G4_NYLON 8062 G4_NYLON 6 6 G4_NYLON 6 10 G4_NYLON 11_RILSAN
134. a radioactive decay chain 158 16 Managing the VerboSity ccssssssssssssssssssesssssssssescesesssssssessssasssnsssessesessenseees 159 GAMOS verbosity Managels ccccccc cess ssesesseeesesseeseeesesescsseseecses 159 Controlling GAMOS verbosity by eVeMt cece ceccssseseseceeeeeeees 160 Using a GAMOS verbosity manager in your COdE cee ecceeeeeeeteteteeeeees 160 Creating your OWN verbosity Manager 0 ees esse esteseseeeeseseseeeeeees 161 Controlling the Geant4 verbosity by event and track eee 161 Dumping the standard output and error in log files cece 161 17 Detector applications ccsessssssssscssssesscseseessesessecesssssssesessssststsesessenessesesesssees 163 Identifying Compton interactions 0 0 ces eeseseeeeneeseseseseeseescsseseeeeees 163 Compton studies histograms c ccsccesccsesnesesseseseeceteneseseeeesesssneneneneees 164 Histograms of data about the interactions and the reconstructed hits 165 Classification of good and bad identification histograms as a function of variablen enen n ae cite Beet eee aa a a 166 Histograms of gammas at sensitive detectorS se ssssersssssserttssseestesss erte 167 Automatic determination of production cuts for a detector 168 Automatic determination of user limits for a detector cccccceeeesseeeeees 169 18 PET application cucaccessscscsessscuescesssenonswsonensbonessessesten sousieossdensvsnsonseseedendesssstonscouesvon 171 PELT geometry o
135. 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 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 Rus sian 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 inter action 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 probabil ities 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 setParam GmPDS MinimumWeightForSplitting MIN_VALUE which
136. ack those numbers when reading your file To write this header the following parameter 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 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 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 setParam 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 gamo
137. 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 volume of the parallel geometry in case the track navigates in it else a touchable 35 Chapter 3 Geometry of the mass geometry Nevertheless the G4VPhysical Volume 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 Geant4 can navigate in the parallel geometries but the materials are not taken into account This means that a track never interacts on a parallel geometry vol ume If you want that particles interact in the parallel volumes you have to set the parameter gamos setParam GmPhysicsParallel LayeredMaterial 1 Building simple geometries There are several examples of geometries for common medical devices for exam ple the ones you find in the PET directory and the one to build simple voxelised phantoms They have been d
138. 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 setMaxT OF USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE NAME MAX_TOF e gamos physics userLimits setMinE Kin 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 setMinE KinByRange USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE_NAME MIN_RANGE Once a user 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 Part
139. ading values from a file c cece cesses seeseseesessssesescsesesesescssseseecees 149 Numeric distributions asena a aa o E a a a a 150 String distribuon aie a e EE AE R Ea Et 151 String data distribution sssessssesssissessesssssiesissteseessesnerinnesnesssenteseenee 151 Geometrical biasing distribution cccccccseces cesses eesescstaneneneees 151 Ratio OfF Gist DU tons ea aa eaa aAa E E A a a A a ae aa 151 15 Utility user actionss ccscsssssssssseseececcsssssssesssssssesessssssssscsecesssesesessesseseessseseeees 153 Counting the number of tracks and events cccsesessetesceneesesesteteseeeenenens 153 Courting th processes c ic ccccciiccistceesetccetcvsesMsetaesectsetascucsevescsnessosovssuasivtee sodas 153 Shower shape Studies vex cieiessvseceisnsteeiieatese diia aS e 154 Killing all tracks 22 2 vivckusles thet die a a a a R 156 Table of tracks and Step n r iieiea otpasti iaeei ani eha 156 Material budget studies cece cee cesses csessseesessssesescsssesesescsseeseecees 156 Detailed report of where CPU time is spent c cccccssecescenetesesesteteseeeenenens 157 Changing the weight using a distribution cceccesseseeseteseseseeeeeeeees 157 Copying the weight to the secondary particles cccccsseseseeeeeteeeeees 158 Stop run after a certain CPU Meerse boiie a 158 Visualising only a Set Of events oo cece ceeseseetessseescsesesesescseeeseeeeees 158 Setting the correlation between the gammas of
140. al void UserStepping Action const G4Step aStep e GmUuserStackingAction e virtual G4ClassificationOfNewTrack ClassifyNewTrack const G4Track aTrack G4ClassificationOfNew Track 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 GmUserAction Factory 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 energy 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 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 e
141. al volume 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 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 33 Chapter 3 Geometry The name of the output file can be set by setting the parameter before the user action gamos set Param GmGeomText DumperUA OutputName
142. alDir Phi InitialDirTheta FinalDirX FinalDirY FinalDirZ FinalDirPerp FinalDirPhi FinalDirTheta InitialLocalDirX InitialLocalDirY InitialLocalDirZ InitialLocalDirPerp InitialLocalDirPhi InitialLocalDirTheta FinalLocalDirX FinalLocalDirY FinalLocalDirZ FinalLocalDirPerp FinalLocalDirPhi FinalLocalDirTheta FinalLocalInPreDirX FinalLocalInPreDirY FinalLocalInPreDirZ FinalLocalInPreDirPerp FinalLocalInPreDirPhi FinalLocalInPreDirTheta VertexDirX VertexDirY VertexDirZ VertexDirMag VertexDirPerp VertexDirPhi VertexDirTheta DirChangeX DirChangeY DirChangeZ DirChangeMag DirChangePerp DirChangePhi DirChangeTheta Chapter 11 Analysis extracting data AngleChange This data represents the angle between the initial and the final directions 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 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 127 Chapter 11 Analysis extracting data 125 InitialMomPerp Initial
143. 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 GnPDSCreateAngleTablesuA 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 The histogram will only be saved for the secondary particle type defined with the parameter gamos set Param USER_ACTION_NAME SecondaryParticleName NAME The histogram file name is by default angleDeviation but it can be changed by the parameter gamos setParam USER_ACTION_NAME HistoFileName NAME To create the tables for different materials and tables you may use the genera tor GmGeneratorChangeEnergyAndMaterials see section on Event generator chang ing 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 Chapter 8 Scoring hadd MERGED_FILE root FILE1 root FILE2 root The file created in this way should be passed to the point detector scorer gamos setParam GmPDS AngleDeviationFileName FILE_LNAME 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
144. ally 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 41 Chapter 3 Geometry 42 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 num ber_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 com mand gamos userAction GmMovementEventAction If you forget it the above commands will not exist and you will get a Geant4 exception 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 move ments 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 lin
145. alues 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 param eter 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 e 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 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 211 Chapter 22 Radiotherapy application 212 e Array of dose values Gy cm 3 n_x n_y n_z valu
146. alues 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 This value can be changed with the parameter gamos setParam GmConvergenceTester Rmin VALUE VOV follows 1 std sqrt N 99 Chapter 8 Scoring e VOV is monotonically decrease e FOM distribution is RANDOM e SLOPE is large enough Finalyy it prints the evolution of several variables i e the cahnge of these vari ables 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 e var e sd e r e vov shift reff e r2int Point detector scorer 100 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 pri mary particles source In
147. alues are separated by commas and string values are surrounded by double quotes 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 HEADER 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 GmStepDataTextFileuA GmGammaFilter will produce a file named GmStepDataTextFileuUA_GmGammaFilter out whose name can be changed with the command gamos setParam GmStepDataTextFileUA_GmGammaFilter FileName NEW_FILE_ NAME to produce a file named NEW_FILE_NAME out Binary files These data users i e GmStepDataBinFileUA GmTrackDataBinFileUA GmSecondaryTrackDataBinFileuA GmStackDataBinFileUA GmEventDataBinFileuUA GmRunDataBinFileUA 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 Gamo
148. am in the same way independently on how the hits are pro duced 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 resolu tion 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 GmKillAIUA File format The file to be written can be a text file or a binary file The format depends on the value of the parameter gamos setParam SD GmHitsWriteUA BinFile TRUE FALSE The text file contains a line for each hit with the follo
149. ame 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 de creased 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 generator distribution in the Plugin tutorial you may ask for help in the GAMOS Discussion Forum if you do not feel confident on doing it An example of this can be using GmGenerDistPositionDiscGaussian instead of GmGenerDistPo sitionDisc 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 i
150. amed recHits root with the follow ing 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 Chapter 7 Sensitive Detector and Hits e Position theta THETA hit deg e Position R3 sqrt X X Y Y Z Z R3 hit mm Notes 1 You may see the PET application for an illustration of this 2 This is the time considered when you call the method GetTime You may also invoke explicitly GetTimeMin or GetTimeMax 3 The time smeared is theTimeMin 89 Chapter 7 Sensitive Detector and Hits 90 Chapter 8 Scoring Creating a scorer Geant4 provides several classes to score different quantities in the selected vol umes 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 multifunc tional detector 15 and associate it with a list of logical volumes with the user command gamos scoring create
151. ameters 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 an gles 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 phantom with enough precision you may reuse the particles several times by setting the parameter gamos setParam RT Generator PhaseSpace MaxNReuse N 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 particles 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 setParam RTGeneratorPhaseSpace MaxNRecycle N which must take a value bigger than 1 If no reusing is explicitly s
152. amos generator energyDist SOURCE_NAME GmGenerDistEnergyConstantIsoto peDecay 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 iso topes 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 distribution 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 49 Chapter 4 Generator 50 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 dis tribution of mean MEAN and sigma SIGMA Energy probabilities from file gamos generator energyDist _SOURCE_NAME GmGenerDistEnergyFromFile FILE_NAME CALCULATION_TYPE UNI
153. anaged by the scorer classifier Gm ScorerClassifierBy1Ancestor 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 toa printer built from a 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 91 Chapter 8 Scoring gamos scoring useTrackWeight SCORER_NAME FALSE The quantities scored are given per event by default If you want the score with out dividing by the number of events use the command
154. ant the cylinder axis to be along the Z global axis 0 0 1 The index of the scorer is build as NSLICES_Z indexPHI indexZ e 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 into 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 GmPSSurfaceFlux This is a surface based scorer The quantity is the flux i e the number of tracks that reach the surface divided by the area and the co sine of the angle between the track and the surface normal Instead of the flux the user may choose not to divide by the area by setting the parameter gamos setParam SCORER_NAME DivideByArea 0 And also not to divide by the cosine of the angle between the track direction and the surface normal by setting the parameter gamos set Param SCORER_NAME DivideByAngle 0 It serves to score the flux 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_NAM
155. ant to use ions you have to define a physics list that creates the physics for them This means that you cannot use for example GmEM Physics 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 dumpList or see Appendix This distribution can not be used for single particle sources For understanding the notation to identify touchables in GAMOS see Identi fying touchables section Other volume types may be added at user request For understanding the notation to identify touchables in GAMOS see Identi fying touchables section 8 Other volume types may be added at user request 59 Chapter 4 Generator 60 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 lists Basic electromagnetic physics list The GAMOS basic electromagnetic physics list defines electromagnetic particles photons electrons positrons and optical photons To use this physics list you have to use the command gamos physicsList GmEMPhysics This physics list insta
156. ant value of the Gaussian distri bution 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 cre ated To assign the data the following parameter must be used gamos setParam DISTRIBUTION_NAME Data DATA_1_NAME GmPolynomialDistribution It can serve to define any polynomial distribution f x a_0 a_1 x a_2 pow x 2 The parameters a_i are given as ex tra parameterswhen the distribution is created The number of extra param eters defines the order of the polynomial POLYNOMIAL_ORDER NUM BER_OF_PARAMETERS 1 To assign the data the following parameter must be used gamos setParam DISTRIBUTION_NAME Data DATA_1_NAME The other numeric distributions are general ones they read the input output relationship from a file so that any distribution shape can be defined The dis tribution 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 out put values corresponding to these two input values The difference between the distributions described below lies in the way this interpolation is done GAMOS will check if the data value is inside the interval defined by the mini mum and maximum of the distribution If it is smaller it will assign an index 0 if it is
157. apsed 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 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 happen You may option
158. are CHIPS FTF_BIC FTFP_BERT_EMV FTFP_BERT_EMX FTFP_BERT FTFP_BERT_TRV G4PhysListFactory e LBE LHEP_EMV e LHEP e OBBC QGS_BIC QGSC_BERT QGSC_CHIPS QGSP_BERT_CHIPS QGSP_BERT_EMV e QGSP_BERT_EMX e QGSP_BERT e QGSP_BERT_HP QGSP_BERT_NOLEP e QGSP_BERT_TRV e QGSP_BIC_EMY e QGSP_BIC e QGSP_BIC_HP QGSP_BIC_NHP e QGSP_BIC_PHP e QGSP_FTFP_BERT e QGSP e QGSP_INCL_ABLA e QGSP_INCLXX e QGSP_QEL e Shielding There is a couple of physics lists that use the new particle_hp GEANT4 package which simulated charged particle inelastic interactions using evaluated particle data bases Please go to the web page http telemaco ciemat es GAMOS particle_hp for details on using this package The physics list GmQGSP_BIC_PHP uses the same phsysics as GmQGSP_BIC_HP but uses particle_hp for proton inelastic interactions The physics list GmQGSP_BIC_NHP uses the same phsysics as GmQGSP_BIC_HP but uses particle_hp for all neutron interactions 65 Chapter 5 Physics Optical photons 66 You may add the physics of optical photons to any physics list including the command 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 th
159. 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 RT PhaseSpaceUA 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 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 Chapter 26 Appendix A 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 direc tory tutorials RTTytorial exercise2 Identi
160. 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 pa rameter 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 first 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 cm43 n_x n_y n_z v
161. ash 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 should be in a subdirectory called src For the declaration files you have a greater 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 consistent 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 GamosX XX directories We take as example the file GamosCore GamosGeometry GN Umakefile name GamosGeometry G4TARGET name G4EXLIB true PHONY all all lib plugin include GAMOSINSTALL config binmake gmk include GAMOSINSTALL config general gmk EXTRALIBS l1GamosBase_Base l1GamosUtils l1GamosUserActionMgr Chapter 2 Getting started 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 mandatory G4TARGET name G4EXLIB true Then you define w
162. ass ComptonRecHitDistAbs DIST 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 en ergy of the 1st hits identified through the algorithms described in the Identifying Compton Interactions section of the PET chapter By default the algorithm used 183 Chapter 20 Compton camera application is the one which identifies the 1st hit as the one with biggest energy however other algorithms may be selected with the parameter gamos setParam CC EvtClass 1stHitAlgorithm ALGORITHM You may select a different algorigthm for the first and second hit classified by time with the paremeters gamos set Param CC EvtClass 1stHitAlgorithmFirst ALGORITHM gamos set Param CC EvtClass 1stHitAlgorithmSecond 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 identifi cation 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
163. assage current is a volume based scorer The current is defined by the number of tracks that pass through the volume GmG4PSCellFlux Cell flux is a volume based flux scorer The cell flux is de fined by a track length L of the particle inside a volume divided 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 This scorer is also called GmPSVolumeFlux 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 scorers GmPSSurfaceFlux and 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 se lect among these three options you can add an extra parameter when defining the scorer that can be In Out or InOut Other scorers e GmG4PSMinkinEAtGeneration This scorer records the minimum kinetic en ergy 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 quantity GmG4PSNofSecondary This
164. 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 GmGenerDistPosition InVoxelsFromFile 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 53 Chapter 4 Generator 54 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 gamos generator directionDist SOURCE_NAME GmGenerDistDirectionRandom 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
165. 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 GetLogical Volumes const G4String amp name bool ex ists 1 Gets the list of logical volumes with the given name std vector lt G4V Physical Volume gt GetPhysicalVolumes const G4String amp name bool exists 1 Gets the list of physical volumes with the given name 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 and electric fields 44 Uniform magnetic and electric fields To set a uniform magnetic field you can use the command gamos field setMagField FIELD_X FIELD_Y FIELD_Z where FIELD_X FIELD_Y FIELD_Z are the field values along the three axes To set a uniform magnetic field you can use the command gamos field setElecField FIELD_X FIELD_Y FIELD_Z where FIELD_X FIELD_Y FIELD_Z are the field values along the three axes To set a uniform electromagnetic field you can use the command Notes Chapter 3 Geometry gamos field setEMField MAG_FIELD_X MAG_FIELD_Y MAG_FIELD_Z
166. aves 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 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 65 197 Chapter 22 Radiotherapy application 195 22 244 25 2 78 2 22 24 25 6 2 78 2 22 244 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 22 244 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 24 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
167. ax MAX_VALUE 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 limits of the N intervals with the parameter gamos setParam DetCClassifEnergy IntervalLimits VALUE_1 VALUE_2 VALUE_N 1 Chapter 17 Detector applications The same set of histograms can done for the maximum minimum or average reconstructed 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 Classification Variables VAR1 VAR2 VARN where the variables can be EnergyMin EnergyMax EnergyAverage XPosMin YPosMin 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 SSSSS
168. 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 Crystal 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 neighbour ing scatterer detectors SCATCRYS_MATE Scatterer detector material 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_NAME which contains the parameters used to define Compton camera geom
169. ay 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 RT PhaseSpaceuA 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 probably 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 neverthe less eliminate this check and store all particles by setting the parameter gamos setParam RT PhaseSpaceUA NotStoreBackwards FALSE You can limit the number of particles stored in
170. 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 learn 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 terminal 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 e GmGammaFilter accepts a track if the particle is a gamma e GmElectronFilter accepts a track if the particle is an electron e GmPositronFilter accepts a track if the particle is a positron 137 Chapter 12 Filters 138 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
171. 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 which by default takes a value of 100 Each time a geantino reaches the detector its weight will be checked If it is be tween the minimum and maximum the splitting number will be calculated mak ing a logarithmic 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 detector geantino log10 energy vs log10 weight to determine which are the min imum and maximum weight and splitting number that best match your applica tion Chapter 8 Scoring Notes 1 A geantino is a pseudoparticle that has only transportation but no physical process 107 Chapter 8 Scoring 105 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 introduc ing a bias in the result The usual criteria t
172. 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 ion isation 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 values are very big it means that ou are not creating electrons or gam mas 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 setCut 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 sens
173. cesses You may observe that the behaviour of the two commands is indeed quite dif ferent While the GEANT4 electromagnetic process implements a mechanism to make use fo the production cuts the hadronic processes do not Therefore the first command is executed at each process not creating the corresponding sec ondary particles if their range is small On the other side the second command is implemented as a user stacking action so that the tracks are created but killed before they are started to be tracked User limits 74 The user limits is a mechanism that Geant4 offers to limit the tracking of a parti cle There are five types of user limits e Limit the step size e Limit the track length e Limit the time of flight e Stop the particle when the kinetic energy is below a limit and deposit its en ergy 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 physics userLimits setUserLimits USER_LIMITS_NAME LOGICAL_VOLUME_NAME PARTICLE_NAME MAX_STEP MAX_TRK LENGTH MAX_TOF MIN_KIN_E MIN_RANGE Chapter 5 Physics 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
174. ch 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 135 Chapter 11 Analysis extracting data 136 e Sor 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 Finally 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 WY YH WH wa We have three files that we have run with different
175. ch they are given in the user command plus the name of the classifier all separated by underscore characters For example if you typed gamos userAction GmTrackHistosuA GmGamma Filter GmPrimaryFilter GmClassifier ByParticle 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 77 Chapter 6 User Actions 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 78 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 GmUserTrackingAction 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 virtu
176. 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 RTExtraInfoProviderOrigin INDEX REGION 0 DefaultRegionForTheWorld RTExtraInfoProviderOrigin INDEX REGION 1 targetReg Chapter 22 Radiotherapy application ExtraInfoProviderOrigin INDEX REGION 2 collimatorReg ExtraInfoProviderOrigin INDEX REGION 3 filterReg ExtraInfoProviderOrigin INDEX REGION 4 monitorReg 5 6 ExtraInfoProviderOrigin INDEX REGION shieldingReg ExtraInfoProviderOrigin INDEX REGION jawsReg J I DyN 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 RTExtralnfoProvide
177. 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 GmGenerDistDirectionGaussian The primary particles will be generated close a line where the two perpen dicular 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 distribu tions 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 energy 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 PO
178. constructHits 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 one at the end of each event to convert the digits or hits into reconstructed hits and the second one at the beginning 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 81 Chapter 7 Sensitive Detector and Hits 82 gamos SD 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 weighted sum of the hit positions weighted by the energy of each hit 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 all the energy depositions of the particle shower produced by the elec tron foll
179. construction to a projection data file named MY_PROJDATA_ALL hv using a Butterworth filter of order 6 and cutoff 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 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 www fftw org Chapter 21 Image reconstruction utilities Visualization tools Currently GAMOS does not include any utility to visualize the reconstructed im ages or projection data instead of it we recommend the installation of one of the following free programs to visualize or analyze images AMIDE and Image AMIDE 22 isa free tool for viewing analyzing and registering volumetric medi cal 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
180. count the correlations when the errors of several files are summed If you do not want it to be printed you have to set the parameter gamos set Param PRINTER_NAME PrintSumV2 1 ScorerName SUM ALL Sum of all scores REL Relative error Unit name An example is the following MultiFunctionalDet fluxDet PrimitiveScorer fluxScorer Number of entries 2 index 1 0 0422424 REL 0 02251 cm 2 sumV2 108 251 index 2 0 010207 REL 0 0710814 cm 2 sumV2 53 6754 fluxScorer SUM ALL 0 0524494 REL 0 00119606 cm 2 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 text file the same information than the GmP SPrinterG4cout printer The name of the file is PRINTER NAME out It can be changed with the parameter gamos setParam PRINTER NAME_SCORER NAME FileName FILE NAME GmPSPrinterBinFile Prints in a binary file almost the same information than the GmPSPrinterG4cout printer The format of the data is the following 97 Chapter 8 Scoring 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 e Index name char 20
181. cs Bremsstrahlung angular distributions The Geant4 low energy electromagnetic model of bremsstrahlung offers three different angular distributions namely Tsai 2BN and 2BS see Geant4 Physics Reference Manual for an explanation of the difference between the three models If you are using any of the three GAMOS physics lists above you may select among one of the three with the following parameter gamos setParam GmPhysicsElectron Bremsstrahlung Angular Distribution MODEL where MODEL can be tsai which is the default model 2bn or 2bs You should nevertheless take into account that the 2bn distribution has an in trinsic kinematical limit of 1 MeV so you should not set the upper energy limit to a higher value if you want to use it In the latest Geant4 release it is also possible to change the bremsstrahlung an gular distributions for standard processes To do it use the same parameter as above In this case the model is applied for all energies GAMOS hadrontherapy physics list The GAMOS hadrontherapy physics list is based on the hadron therapy Geant4 advanced example 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 replacePhysics PHY SICS_LIST where PHYSICS_LIST can be
182. ction 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 G4Boxx worldBox G4Box x 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 GmUserXXX lt Action instead of G4UserXXXAction Then we have to add the following lines in module cc DEFINE_GAMOS_USER_ACTION ExNO02RunAction DEFINE_GAMOS_USER_ACTION ExN02Event Action 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 construc tion 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 245
183. d 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 add Physics radioactiveDecay This command has to be used after the run initialize command and activates automatically this process for all ions Cerenkov process You can activate the Cerenkov processes for all charged particles with the user command gamos physics add Physics cerenkov Several parameters can be set before this command to control the Cerenkov pro cess gamos setParam GmPhysicsCerenkov MaxNumPhotonsPerStep VALUE limits the step size by specifying a maximum average number of Cerenkov pho tons created during the step The default value is 0 i e no limit gamos set Param GmPhysicsCerenkov TrackSecondariesFirst 1 serves to avoid blowing up the memory by the thousands of photons that may be created 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 MaxBetaChange VALUE sets the maximum allowed change in beta v c in perCent The default value is 0 i e no limit Coulomb scattering Coulomb scattering is an alternative to multipl
184. d by this ratio SHGetHadronicChannelXSUA G4_Fe 10 MeV NeutronInelastic CHANNEL_ALL Fe54 n 2n Fe56 2 2974 XS micro 0 00094994 SHGetHadronicChannelXSUA G4_Fe 10 MeV NeutronInelastic CHANNEL_ALL Fe54 n a Cr51 4 2974 XS micro 0 00189988 SHGetHadronicChannelXSUA G4_Fe 10 MeV NeutronInelastic CHANNEL_ALL Fe54 n a Cr53 12 2974 XS micro 0 00569964 Finally if you set the parameter gamos setParam USER_ACTION_NAME Particle Yield 1 it will print the particle yield ie the number of times a particle is produced for each collision with a target nucleus As you can see in this example the data may be printed for several materials and several energies in a sinble job But to do this you have to follow some rules The geometry should be GmGeometryUseMaterials see Geometry chapter The generator should be GmGeneratorChangeEnergyAndMaterial see Generator chapter And you have to define a primary particle source with a particle of the type you want to study You should delete the hadronic elastic process unless you are interested in stydying it And if you are studying charged particle collisions also the elec tromagnetic processes gamos physics removeProcessesByType Electromagnetic gamos physics removeProcessesByName hadElastic In case you do not want to take into account the gammas you can set the param eter gamos setParam USER_ACTION_NAME NotGammas 1 In case you want to take into account only ions you can
185. d input for image reconstruction algorithms By default GAMOS generates 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 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_LANGULAR 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
186. dFilter2Scorer 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 distributed 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 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 histograms 219 Chapter 22 Radiotherapy application 220 Chapter 23 Shielding application The shielding application contains a set of utilities that may be useful for shield ing calculations Studying penetration You may get the Nth value layer i e the layer width to get reduction of 1 N in the number of original particles of any particle in any material with the user action gamos userAction SHNthValueLayer uA To use it you may follow the example in MY_GAMOS_DIR tutorials Shielding Tutorial exercise1 exercise1a As you can see there a beam of particles should be set along the Z direction into a geometry made of a slabs stacked along Z which are very wide in X and Y dime
187. dary 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 GmNumericDataFilter if the data is of numeric type int or float and GmString DataFilter 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 minimum and maximum value of the data For example gamos filter dataF GmNumericDataFilter InitialKineticEnergy 0 0 3 GmStringDataFilter In this case after the filter name you have to give the list of accepted 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 Classifiers To use it you have to use the command to define a classiifier using the classifier named GmClassifierByNumericData if the data is of numeric type int or float and GmClassifierByString Data if the data is of string type and passing the following arguments e Data is integer or float In this case after the classifier name you have to give the number of intervals the minimum data limit and the maximum data limit For example to define 20 energy intervals between 0 and 10 gamos classifier dataC GmClassifierByData InitialKineticEner
188. do not forget to use the command run initialize after setting the cuts if you want that your change Chapter 5 Physics is effective The Geant4 command run particle dumpCut Values 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 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 cuts setLowEdge ENERGY ENERGY_UNIT Production cuts by region A region in Geant4 is a set of G4LogicalVolume 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 command gamos geometry createRegion REGION_NAME LOGICAL_VOLUME_NAME Do not forget that in Geant4 when a logical volume belongs to a region automat ically all its daughters belong to the same region unless there is another region e
189. dreyev Arkadiusz Sitek Anna Celler IEEE Nuclear Science Symposium Conference Record 2009
190. e 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 InitialSolid FinalSolid InitialLogical Volume FinalLogical Volume Initial Physical Volume FinalPhysical Volume InitialTouchable FinalTouchable InitialRegion FinalRegion InitialMaterial FinalMaterial InitialSolidType FinalSolidType InitialPVCopyNumber FinalPVCopyNumber 129 Chapter 11 Analysis extracting data 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 InitialNuclearInterLength FinalNuclearInterLength InitialElectronDensity 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 avail able for Step FinalProcess Name of process that defined the point PostStepPoint Only avail able for Step CreatorProcess Name of process that created the particle track Not available for Event nor Run ParticlePDGEncoding Par
191. e AcceptTrack method returns always false ex cept 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 The types of volume are the following ones LogicalVolume a G4Logical Volume object PhysicalVolume a G4VPhysical Volume object The volume name and copy num ber 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 repli cated physical volumes i e divisions replicas and parameterisations there is a unique PhysicalVolume pointer while the different copies are managed in ternally 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 Volume Replicated 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 v0lA 1 see section on Identifying touchables
192. e TOTAL_XS macro 2 91782e 07 cm 1 TOTAL_XS micro 0 000343635 barn SHGetHadronicChannelXSUA G4_Fe 10 MeV nFission TOTAL_XS macro 0 cm 1 TOTAL_XS micro 0 barn Then it prints the number of times each reaction channel happens in the job For a reaction channel it is understood each combination of target nucleus plus sec ondaries The description of the channel is printed by enumerating the list of particles together with the number of times they appear at the end it is printed the count number of the channel The target nucleus is easily identified as it starts with a character SHGetHadronicChannelXSUA G4_Fe 10 MeV NeutronInelastic CHANNEL gamma 2 alpha 1 Fe54 1 Cr51 0 0 1 3 SHGetHadronicChannelXSUA G4_Fe 10 MeV NeutronInelastic CHANNEL gamma 4 alpha 1 Fe54 1 Cr51 0 0 1 1 SHGetHadronicChannelXSUA G4_Fe 10 MeV NeutronInelastic CHANNEL gamma 1 alpha 1 Fe56 1 Cr51 0 0 1 3 224 Chapter 23 Shielding application After all the channels are printed they are merged putting together those that have the same particles without taking into account the gammas The channel name is printed in a compact form with the target nucleus first the projectile particle the list of non ion particles and the list of ions usually only one For each channel it is printed the number of times it happens divided by the number of times a collision with the target nucleus happens and the total process micro scopic cross section multiple
193. e are focused to a point UN FOCUSED 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 inter leave 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 ori entation if the endleaf is curved this 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 Nu
194. e complicated energy resolution can be implemented corresponding to a more realistic calorimeter resolution Apart from the constant term described above energy independent sigma E K which may be due to calibration errors non uniformities and non linearities in photomultipliers proportional counters ADC s etc two other terms can be de fined 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 fluctuations in the energy loss and multiple scattering during the shower devel opment 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 energy 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 sDTYPE VALUE where SDTYPE is the type of the sensitive detector If you have an energy function that is different you may implement it by creat ing a new reconstructed hit builder class inheriting from GmVRecHitBuilder and overwrite the method virtual void SmearRecHitsEnergy Time resolution The time of the hits can also be smeared for each detector type with a gaussian given by the valu
195. e interpreted ro tating 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 Adding an extra volume If you have defined a distribution of type GmGenerDistPositionInG4Volumes GmGenerDistPositionInUserVolumes GmGenerDistPositionInG4Surfaces or GmGenerDistPositionInUserSurfaces you can add more volumes with the following user command gamos generator GmPosition VolumesAndSurfaces 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 positionDist SOURCE_NAME GmGenerDistPositionLineSteps 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 start ing at the initial position and in steps given by STEP Position in a square Chapter 4 Generator gamos generator positionDist _SOURCE_NAME GmGenerDistPositionSquare HALF_WIDTH POS_X POS_Y POS_Z DIR_X DIR_Y DIR_Z The positi
196. e 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 setParam 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 set Param GmPhysicsOpticalPhoton YieldFactor FACTOR To define the optical properties of the medium you must create a G4MaterialPropertiesTable which is linked to the G4Material in question without it no optical photon will be created 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 G4MaterialProperties 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 prop erties 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
197. e of the parameter gamos setParam SD TimeResol SDTY PE VALUE If you have a time resolution function that is different you may implement it by creating a new reconstructed hit builder class inheriting from GmVRecHitBuilder and overwrite the method 83 Chapter 7 Sensitive Detector and Hits 84 virtual void SmearRecHitsTime 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 parameter 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 are produced in one event the hit with smallest time trig gers so that all hits of all events with a time later than this hit time and shorter than this hit time measuring time are considered together This is the default behaviour Several independent triggers are defined it may be that each detector volume is associated to a trigger or that detectors that have a common ancestor in the geometry hiera
198. e 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 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 e Oif itis 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 e 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 orig inal 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 175 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 histograms starts with SPECTEvtClass and all are written in the file spect root csv The f
199. e recommend that you use the user limit gamos physics userLimits set MinE 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 getting the best values Killing particles The two user actions GmKillAtStackinguA and GmkillAtSteppingUA 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 con sume a non negligible amount of CPU time Therefore a simple recommendation is to check that you deactivate all the user actions you do not n
200. e scattering where the particles are transported colliding with an atom per step instead of averaging multiple collisions It is therefore a precise but slow process This process can be activated with the user command gamos physics addPhysics CoulombScattering You also have to remember to delete the multiple scattering process gamos physics removeProcessByName msc Nuclear processes of electromagnetic particles You can activate the nuclear process of gammas electrons or positrons with one of the following user commands gamos physics addPhysics gammaNuclear 70 Chapter 5 Physics gamos physics addPhysics electronNuclear gamos physics addPhysics positronNuclear Replacing process models Replacing a set process models Whatever physics list you have chosen you can replace part of the electromag netic models of one of more particles by one of the three models standard low energy or Penelope with the command gamos physics replacePhysics MODELS_1 MODELS_2 where MODELS_i may be gamma standard gamma lowener gamma penelope electron standard electron lowener electron penelope positron standard positron penelope there are no positron low energy models in Geant4 Replacing one process model Another command allows to replace only one model of one process also inde pendent of the physics list you have set gamos physics replaceProcessModel PARTICLE_NAME PROCESS_NAME MODEL_NAME The following set o
201. e 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 cre ated another N 1 gammas are created at the same position with weight 1 N Chapter 22 Radiotherapy application 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 us ing 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 possi bility of reaching the patient There are two splitting techniques implemented in GAMOS Uniform bremsstrahlung splitting This technique is the simplest one When a gamma suffers a bremsstrahlung in teraction 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 addPhysics electron lowener UBS gamos GmPhy
202. e standard_opt3 G4EmStandardPhysics_option3 e LowE_Livermore G4EmLivermorePhysics e LowE_Penelope G4EmPenelopePhysics e local_ion_ion_inelastic LocallonlIonInelasticPhysics 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 64 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 Chapter 5 Physics gamos physicsList QGSP As you can see looking at this 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 All the GEANT4 physics list that can be found in the directory source physics_lists These
203. e 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 and 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 terminal 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 Mag magnitude 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 avail able only for Step and Track There are other data that calculate the local position i e the global position transformed into the local frame of the volume
204. e to download the GAMOS 5 0 0 zip file copy it to your MY_INSTALLATION_DIR and uncompress it If your windows system does not have an unzip software and you do not have one you may download a free one from http 7zip com After it is decompressed you just have to open the file MY_INSTALLATION_DIR GAMOS 5 0 0 GAMOSGULexe The first time it is opened it will configure GAMOS and create a GAMOSGULini file To run GAMOS you just have to select your input file clicking on the Open Input File and run it clicking on the Run button All the output files will be written in the same directory where the input file is Checking your windows installation As explained above it is mandatory that the directory structure is correct so that the GAMOS executable cna find all the dynamic libraries You should check that ROOT has been installed in the directory MY_DIRECTORY external root 5 34 10 root while GAMOS has been installed at MY_DIRECTORY GAMOS 5 0 0 GAMOSGULexe where MY_DIRECTORY is the directory you chose for GAMOS If the directory structure is OK the first time you execute GAMOSGULexe it does not find any file named GAMOSGULini and then a command prompt window a black window pops up This windows should stay for about 1 minute or more and you should see a list of messages telling you that the GAMOS libraries are being processed If the black window disappears quickly is that the library pro cessing is giving some error message In this case you pr
205. e two widths are printed in a format similar to the following ae HNthValueLayerUA_exitShieldLayerF_copyNoC gamma G4_Pb 1 MeV UCTION FROM FIT 2 reached at depth 10 8174 0 00725647 mm HNthValueLayerUA_exitShieldLayerF_copyNoC gamma G4_Pb 1 MeV S D S EDUCTION FROM SCORES 2 reached at depth 12 0863 mm S D oe oe oe oe HNthValueLayerUA_exitShieldLayerF_copyNoC gamma G4_Pb 1 MeV UCTION FROM FIT 10 reached at depth 35 9345 0 0241055 mm SHNthValueLayerUA_exitShieldLayerF_copyNoC gamma G4_Pb 1 MeV EDUCTION FROM SCORES 10 reached at depth 36 864 mm oe oe Woe DW oe WD ae DW oe From looking in detail to the example in you can find some important features that you must follow e The stacked slab solid must be a box and must be placed with a parameteri sation along the Z axis SHNthValueLayerUA will look for a parameterised vol 221 Chapter 23 Shielding application ume and from it it will extract the layer width as the Z box length If not found you have to define this layer width with the parameter gamos setParam USER_ACTION_NAME LayerWdith VALUE Also the material name to be printed in the final report will be extracted from the parameterised volume If not found you have to define this material name the parameter gamos setParam USER_ACTION_NAME MaterialName NAME The generator direction distribution should be along the Z axis
206. e with the following parameters 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 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 occur ring 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 Chapter 3 Geometry 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 1005 1 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 Commands to print geometrical objects The command gamos geometry print VolumeTree VERBOSE_LEVEL serves to print the hierarchical tree of ge
207. eSurface 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 GmGenerDistTimeConstant 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 GmGen erDistTimeFactory 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 fro
208. eV 1 Position distributions Position at a point gamos generator position Dist SOURCE_NAME GmGenerDistPositionPoint POS_X POS_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 position Dist SOURCE_NAME GmGenerDistPosition InG4Volumes 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 setParam GmV Gener Dist Position VolumesAndSurfaces OnlyVolume 1 gamos generator position Dist SOURCE_NAME GmGen erDistPositionInG4VolumesGeneral 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 v
209. ection on Using a common histogram class Total energy Total Energy E Maximum longitudinal length Maximum R transv Pos Maximum transversal length Maximum R transv Pos Average longitudinal length Maximum R transv Pos Average transversal length Maximum R transv Pos Shower direction theta angle Shower direction theta Angle Shower direction phi angle Shower direction phi Angle The sum of energy deposits inside a certain transversal distance a radius is cal culated 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 155 Chapter 15 Utility user actions 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 radius E Killing all tracks The action gamos userAction GmKillAtStackingActionuA serves to kill all particles at the stacking action G4ClassificationOfNew Track 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 GmElectronFilter will only kill electrons If you want to apply the killing at steppin
210. ed 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 The user can choose not to produce any of these histograms by setting the follow ing 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 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 his tograms of position gamos setParam RT PhaseSpaceHistos HisRMax MAX that takes by default a value of 100 histograms of angle gamos setParam RT PhaseSpaceH
211. ed 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 code you will have to follow the instructions in this section GAMOS uses the GNU make tool to manage the compilation and generation of executables 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 different 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 directory GamosCore GamosApplication it will also create the gamos executable You may need to type the Linux command reh
212. eed when you are making a big production of events Using variance reduction techniques 230 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 25 Extracting detailed information from a MCNP run Introduction While MCNP is a well recognised Monte Carlo simulation tool specially in the field of nuclear physics users find often that it behaves as a black box i e it offers a set of tables with the results but it is very difficult to understand any detail of the simulation that led to those results For example questions like how much is the contribution to a tally from primary or secondary neutrons how many elastic collisions suffers in average a neutron in a given volume which is the energy or angle spectrum of the gammas produced at each of the reaction channels etc On the other side GAMOS offers many tools to get with a few lines in the input script a big detail of any aspect of the simulation The present tools joins the best of the two worlds by giving the possibility of using the GAMOS tools in a MCNP job The mechanism to do this is to run first a MCNP job dumping the track information in a file by using the ptrac option and then run a GAMOS job that just reads the ptrac file A first example To run GAMOS you have to prepare an input script This input script doe
213. electromagnetic physics which are used extensively in the Geant4 examples Those options are named G4EmStandardPhysics G4EmStandardPhysics_option1 G4EmStandardPhysics_option2 G4EmStandardPhysics_option3 and G4EmStandardPhysics_option4 See http www geant4 org geant4 collaboration working_groups electromagnetic physlist shtml for the documentation on these options To use these options can be done selecting the physics list gamos physicsList GnEMStandardPhysics By default the first option is selected to change it the following command has to be used gamos EMStandard Physics replacePhysics OPTION where OPTION may be emstandard_opt0 emstandard_opt1 emstandard_opt2 or em standard_opt3 default Multiple scattering models If you use any of the three GAMOS physics list described above you may use any of the multiple scattering models available in the current version of Geant4 This may be done with the following parameter gamos set Param GmMultipleScattering Model PARTICLE_NAME MODEL where PARTICLE_NAME can be Electron Positron or Hadron and MODEL canbe Urban90 Urban92 Urban93 Urban95 Urban96 WentzelVI or GoudsmitSaun derson see the GEANT4 User s Guide for an explanation of each model The de fault model for all particles is Urban96 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 63 Chapter 5 Physi
214. enerDistPosition primary particles position distribution e GmVGenerDistDirection primary particles direction distribution e GmVGenerDistEnergy primary particles energy distribution e GmVGenerDistTime primary particles time distribution e GmVUserXXXAction user action XXX can be Run Event Tracking Stepping or Stacking e G4VSensitiveDetector sensitive detector e GmVDigitizer hits digitizer e GmVRecHitBuilder reconstructed hits builder e GmvVPrimitiveScorer scorer e GmVPSPrinter scorer printer e GmVkFilter filter e GmVClassifier classifier e GmVVerbosityMer verbosity 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 con tain the necessary methods that you have to implement for each plug in type 2 Include the SEAL module definition include PluginManager ModuleDef h 246 Chapter 27 Appendix B Extending GAMOS functionality with C utilities DEFINE_SEAL MODULE Then you have to include the relevant 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 ob
215. er 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 toa printer built from a 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 F1 and F2 tallies As mentioned above there is no concept of surface in GEANT4 therefore we have created some trick to do scoring in a similar ways to the F1 tally surface current and the F2 tally surface flux To do surface scoring you have to use the scorer GnMCNPPSSurfaceFlux and you have to define the list of surfaces with a parameter like in the example gamos scoring createMFDetector fluxDet gamos setParam fluxSurfl1ScorerN SurfaceNames surface_11 If you want to do the scoring only for neutrons you have to add the filter gamos scoring addFilter2Scorer GmNeutronFilter fluxSurf11ScorerN If you want to have a different score for each energy interval in six isolethargical bins from 1 E 11 to 1 E1 MeV you can add the following classifier gamos classifier energy NC GmClassifierBy NumericData log10 InitialKineticEnergy 6 111 235
216. er RandomSeedsInFile NUMBER 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 Any of the engines available in CLHEP can be chosen i e DRand48Engine Du alRand Hurd160Engine Hurd288Engine HepJamesRandom MTwistEngine NonRan domEngine 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 possible 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 are many ways of sending many jobs together in a machine Here we pro pose 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 com
217. ers You may repeat this command to associate several scorers to the same detector GAMOS offers many more types of scorers than MCNP in the sections below we will explain the equivalence between the MCNP scorers and the GAMOS ones To each of the defined scorers you can add a filter to select for which track con ditions 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 section on Filters for a description of the available filters and how to create your own one For example if you want that the scoring is only done for neutrons you will use the filter GmNeutronFilter By default a different count is scored for each of the copies of the selected vol umes with different copy number This is managed by the scorer classifier Gm ScorerClassifierBy1Ancestor 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 classifi
218. es 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 RT PSPDoseHistos gamos scoring addPrinter2Scorer RTPSPDoseHistos DoseScorer The name of the histogram file if by default dose_PRINTER_NAME but it may be chanted with the paramter gamos setParam PRINTER_NAME FileName VALUE 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 Dose in X direction Dose Profile X_merged Dose in Y direction Dose Profile Y_merged Dose in Z direction Dose Profile Z_merged Dose in XY direction Dose XY_merged Dose in XZ direction Dose XZ_merged Dose in YZ direction Dose YZ_merged 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 volu
219. es 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 cal culations to create the volumes and place them The current implementation has two modules defined JAWS and MLC multileaf collimators See section on Ra dioTherapy for a detailed description of these modules Chapter 3 Geometry 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 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 param eter 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 e Volume name 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
220. esigned to be used for describing different devices by simply changing the configuration data For more details please see the cor responding sections of this manual Building 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 GmGeometry UseMaterials 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 Shielding Tutorial exercised Building your geometry with C code 36 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 the section Creating your plug in using the GmGeometryFactory or see the example examples NO2 Chapter 3 Geometry Reading D
221. esressessteresessesssesresteee 230 Limiting the number of user actions ssssessssssssiesissteseessessenrersessesssestestesee 230 Using variance reduction techniques se sssssestsssserttsssserttessterttsntentessseen te 230 25 Extracting detailed information from a MCNP run sessesessesesseseesercesesceseeses 231 IMtHOMUCHON respe rare ri aia E AEE nia E EERE NEE 231 ATIPSE OKA POs oi eeta e a E aa e i eae E a eaa 231 Geometry miiie ni a EAE a E A a EA A ER S EN 232 1AA e E EA E E E E E 233 Source primary generator seniecsnnoiiiks iaia s 234 Extracting imformationa saipa a a aa anaE AE A A a 234 Tallying SCONE Jets cis cl e e n dodccunstestesetlatacDenthcapdoSshevissstsbevsetheswSbebectch 234 Fland Fz tallies ieena huia aten a an a isa 235 EA ta ye costs nocesireestectc wea en athe TE cab asiresu E tee ealtt ta elvan cide uted ttle ested 236 vii vill 26 Appendix A serioses rerit E E a RE E E E A ES EEEE SEEE 237 Using parameters onteni iert a uan a AEN a UE RERAN 237 Checking the usage of parameters c cccccessesces cs eeneteeseeeetescsteneneneees 237 Managing the input data files cee ceeseseeeersnssesescsesesesescsseeseecees 237 Random number seeds oreesa aA a aaa 238 Setting the initial random number seeds ccceccesssssesesecseeteeeeees 238 Restoring the initial random number seeds ccscccesceceseseeneteneees 238 Changing the random engine ss sssssesssssssiesisstestessesse
222. est additions specially 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 248 Chapter 27 Appendix B Extending GAMOS functionality with C utilities 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 e GamosBase e Base parameter manager analysis manager CSV histograms and other ba sic functionalities Filters filters e Classifiers classifiers e GamosGeometry geometry related utilities and support for text detector de scription e GamosMovement support for displacements rotations or general movements of volumes during a job e GamosSD classes for sensitive detectors hits and digitization e GamosGenerator utilities to support single particle and isotope source gener ators as well as different initial particle distributions e GamosPhysics 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
223. et 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 205 Chapter 22 Radiotherapy application 206 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 RTGeneratorPhaseSpace MirrorWhenReuse 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 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 parameter gamos setParam RT Generator PhaseSpace NEventsSkip N You can produce the same histograms that were produced when writing the phase space file by setting the following parameter
224. et the cross sections so there is no need to simulate an event Nevertheless to profit from the GAMOS utilities you should set up an input file similar to other GAMOS input files You can see an example on the use of this utility at MY_GAMOS_DIR tutorials S Hielding Tutorial exercise5 exercise5a in This example prints the cross section of neutrons as given by the neutron_hp or particle_hp GEANT4 package for several energies in several materials The first thing it does is to replace the geometry GmGeometryFromText by GmGeome tryUseMaterials This geometry class will generate a world for each of the materi als given by the parameter gamos set Param GmGeometryUseMaterials Materials MATE_1 MATE_2 If any of the materials is not aGEANT4 one you will need a geometry file where the material is defined The name of this file is given with the parameter gamos setParam GmGeometry UseMaterials FileName FILE_NAME The SHPrintPHPChannelXSUA user action can print the cross sections for several energies The energies to be printed are controlled by defining a minimum and a maximum energy and the number of energy steps gamos setParam USER_ACTION_NAME minE VALUE gamos setParam USER_ACTION_NAME maxE VALUE gamos setParam USER_ACTION_NAME nStepsE VALUE If you want that the steps are taken logarithmically you can set the parameter gamos setParam USER_ACTION_NAME logE 1 If the model defined for the inelastic or neutron capture processes bel
225. etry gamos setParam GmGeometryFromText FileName FILE_LNAME A few example files are included of simple Compton camera systems with suffix geom in the Compton camera tutorial for example CCGeometryRingEx1 geom Chapter 20 Compton camera application 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 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 userAction 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 recon structed 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 parameter gamos setParam 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
226. ext file as described in the following subsection 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 setParam GmGeometryFromText FileName MY_FILENAME 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 restrictions 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 ex plaining 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 eZ eN eA Example ISOT C135 17 18 35 Element made of one unique isotope ELEM e Name e Symbol Z eA Example ELEM Hydrogen H 1 1 11
227. extracting data G4Particle Type Subtype 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_Bs0 meson Bs anti_D0 meson D anti_kaon0 meson kaon eta meson eta eta_prime meson eta_prime kaon meson kaon kaon meson kaon kaon0O 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_ct 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 132 Chapter 11 Analysis extracting data G4Particle Type Subtype sigma_cO baryon sigma_c xi baryon xi xi0 baryon xi xi_ct baryon xi_c xi_c0 baryon xi_c geantino geantino geantino chargedgeantino geantino geantino Secondary tracks These are data that give information about the secondary particles o
228. f particles process and model can be used gamma phot standard gamma phot lowener gamma phot penelope gamma compt standard gamma compt lowener gamma compt penelope gamma conv standard gamma conv lowener gamma conv penelope gamma Rayl lowener gamma Ray penelope electron eloni standard electron eloni lowener electron eloni penelope electron eBrem standard electron eBrem lowener electron msc Urban90 electron msc Urban92 electron msc Urban93 electron msc Urban95 electron msc Urban96 electron msc WentzelVI electron msc GoudsmitSounderson positron eloni penelope 71 Chapter 5 Physics positron eloni standard positron eloni lowener positron eBrem penelope positron eBrem standard positron eBrem lowener positron annihil lowener positron annihil penelope positron msc Urban90 positron msc Urban92 positron msc Urban93 positron msc Urban95 positron msc Urban96 positron msc WentzelVI positron msc GoudsmitSounderson Removing a process from a physics list 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 user Action GmCountProcessesUA which will give yo a list of the pr
229. f 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 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 struct PetOutput char name 8 float xVtx yVtx zVtx x1 yl 21 x2 y2 22 173 Chapter 18 PET application 174 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 DumpEventList Mode 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 fol lowing parameter gamos setParam PET EvtClass DumpProjData 1 Projection data or sinogram is a common way to organize PET events and represents the standar
230. f the cylindrical radius and the phi angle with the parameters given at score definition NSLICES_R MIN_R MAX_R NSLICES_PHI MIN_PHI MAX_PHI and calculates the volume of each cylindrical section so that dose can be computed Tow more parameters are mandatory to define the dimension in Z MIN_Z MAX_Z Three extra parameters are optional CENTRE_X CENTRE_Y CENTRE_Z if you do not want the cylinder to be centred at the origin of coordinates 0 0 0 and another three ZAXIS_X ZAXIS_Y ZAXIS_Z if the you do not want the cylinder axis to be along the Z global axis 0 0 1 The index of the scorer is build as NSLICES_R indexPHI indexR GmPSCylindricalZPhiDoseDeposit This scorer is designed to compute the dose deposit and assign a different index to each interval in cylindrical coordinates in 2D radius and phi angle despite no cylindircal division is defined in the geometry It creates intervals as a function of the cylindrical radius and the phi angle with the parameters given at score definition NSLICES_Z MIN_Z MAX_Z NSLICES_PHI MIN_PHI MAX_PHI and calculates the volume of each cylindrical section so that dose can be computed Tow more parameters are mandatory to define the dimension in Z MIN_Z MAX_Z Three extra parameters are optional CENTRE_X 93 Chapter 8 Scoring 94 CENTRE_Y CENTRE_Z if you do not want the cylinder to be centred at the origin of coordinates 0 0 0 and another three ZAXIS_X ZAXIS_Y ZAXIS_Z if the you do not w
231. fied 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 GammaEnergy will be taken and the event will receive a subclassification type of 2 gt 1 Random coincidence It is checked that the hit is built only from tracks from the same original gamma Scattered The event is classified as scattered if any of the original gamma has suffered an interaction in the list of volumes defined by the parameter gamos setParam DetCountScatteringUuA VolumeNames VOLUME_1 VOLUME_2 177 Chapter 19 SPECT application 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 DetCountScatteringuA 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 LineDistIoVtx DISTANCE where DISTANCE has a default value of 10 mm Gamma traversed collimator it checks if the original gamma or on
232. 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 volume 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 classi
233. fix 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 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 202 f ANA er oe ee Chapter 22 Radiotherapy application 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 have 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 e 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 m
234. 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 second 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 By default the classifier will act on the G4Track but it may act on the G4Step if the following parameter is set gamos set Param GmPDS ClassifierOnTrack 0 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 rel ative flux error error div
235. from GmVerbosityMer and fill it as follows e In the include file i e the one with suffix h of this class define an object of type GmVerbosity as extern extern GmVerbosity MyVerb e In the method void SetFilterLevel int fl call the same method of your GmVer bosity object MyVerb SetFilterLevel fl In the method void GetFilterLevel int fl call the same method of your GmVer bosity object MyVerb GetFilterLevel fl Finally you have to transform your class into a plug in DEF INE_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 user Action GmTracking VerboseuA You have to define the minimum and maximum events for which you want the verbosity on and you can also set it ON only each N events gamos setParam GmTrackingVerboseUA EventMin VALUE gamos setParam GmTrackingVerboseUA EventMax VALUE gamos setParam 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 GmTracking VerboseuUA TrackMin VALUE gamos setParam GmTrackingVerboseUA TrackMax VALUE gamos setParam
236. fying touchables As explained in several points through this guide you can use the concept of touchable 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 G4VSolid A solid is a geometrical object that has a shape and specific values for each of the shape dimensions G4LogicalVolume A logical volume contains the volume s full properties It in cludes the geometrical properties of the solid and adds physical character istics the material of the volume whether it contains any sensitive detector elements the magnetic field etc G4V Physical Volume A physical volume is a volume placed already in another volume that is a volume with position and rotation matrix G4VTouchable A touchable is each copy of a volume To understand the differ ence with a physical volume we put an example If you place 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 in dividual touchable whenever you like When you need it you can ask GAMOS to create a GmTouc
237. g action probably because you want to apply some step filter you can use the user actions gamos userAction GmkillAtSteppingActionuA Table of tracks and steps You may get a table of the number of tracks and steps by instantiating the user action gamos userAction GmCountTracksAndStepsUA 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 GmClassifierByParticle will produce a table similar to this one COUNT_TRACKS_AND_STEPS GmClassifierByParticle COUNT_TRACKS gamma 100 5 COUNT_TRACKS e 8 5 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 Material budget studies 156 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 Chapter 15 Uti
238. gical 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 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 GmORfFilter returns true if one of the filters returns true GmxXORFilter returns true if one and only one of the filters returns true 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 GmHistoryAllFilter returns true if all the filters in all previous steps and the beginning 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 returns true if the condition is fulfilled by any step or track of the ancestors of the current track GmHistoryAncestorsAllFilter 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 curre
239. gy 20 0 10 GAMOS will check if the data value is inside the interval defined by the min imum and maximum If it is smaller it will assign an index 0 if it is bigger it will assign an index INT_MAX 2432 In both cases a warning will be printed If you do not want to allow this behaviour but you want that the job is stopped if the datais out of limits you have to set the parameter gamos setParam CLASSIFIER_NAME AllowOutOfLimits 0 Data is string In this case no argument is needed after the classifier name For example 123 Chapter 11 Analysis extracting data 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 124 There are over one hundred types of data currently available in GAMOS We list her
240. hTimeMax VAL 57 Chapter 4 Generator gamos setParam gener hTimeNbins VAL 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 pri mary generator distribution multiplying each resulting value by a probability of occurrence To do this you ahve first to define a numeric distribution see section on Distributions where you assing the probabilities 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 corre sponds 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 sam ple 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 distribu tion 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 GENERA TOR_DIST_TYPE is one of the generator distribution variables listed above and BIAS_DIST_NAME is the n
241. hable which will have the same characteristics as the corre sponding 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 Exists GmGeometryUtils GetInstance gt GetTouchables touch_name it 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 true There is a limitation on the use of touchables they cannot be used for assembly volumes 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 vol ume physical volume touchable particle or material so that GAMOS finds the corresponding Geant4 object In case you want to apply your command to several 241 Chapter 26 Appendix A volumes with similar names you can use an asterisk t
242. 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 pack age 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 Pho ton Transport Workshop Proceedings Issy les Moulineaux France 5 7 November 2001 AEN NEA 7 http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplica tionDeveloper html ch02s02 html 8 http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplica tionDeveloper html ch04 html sect Geom Navig 9 http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplica tionDeveloper html ch02s06 html 10 http geant4 web cern ch geant4 User Documentation UsersGuides PhysicsRef erenceManual html ch02s05 html 11 http geant4 web cern ch geant4 UserDocumentation UsersGuides PhysicsRef erenceManual html PhysicsReferenceManual html 12 http vww 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 UserDocumentation UsersGuides ForApplica tionDeveloper html
243. hat would mean any char acter For example if you have the volumes named CRYSTAL_BGO_1 CRYS TAL_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 S D assocS D2Log Vol GmSDSimple Calor CRYSTAL_BGO_ will associate a sensitive detector to the two volumes CRYSTAL _ BGO_1 and CRYSTAL_BGO_2 and gamos S D assocSD2Log Vol GmSDSimple Calor CRYSTAL_ 1 will associate a sensitive detector to the two volumes CRYSTAL _BGO_1 and CRYSTAL_LUYAP_ 1 Using particle names 242 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 do this after instantiating the GAMOS electromagnetic physics list you will get the 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 GenericlIon He3 alpha anti_neutron anti_nu_e anti_nu_mu anti_nu_tau anti_proton chargedgeantino deuteron eta eta_prime gamma geantino mut mu neutron nu_e nu_mu nu_tau opticalphoton pit pi pil proton taut tau triton These are the names that should be used in the commands that need a parti cle name If you wa
244. hat 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 that 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 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 li braries 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 possibili
245. he polarization using the parameter gamos setParam SOURCE_NAME Polarization POLARIZ_X POLARIZ_Y POLARIZ_Z 47 Chapter 4 Generator 48 Isotope source GAMOS implements an isotope generator that simulates the activity of different isotopes 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 data isotopes dat part of which we reproduce here ISOTOPE Na22 2150535 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 SOTOPE 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 primary 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 i
246. he file or bigger than the maximum value an excep tion 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 149 Chapter 14 Distributions gamos setParam DISTRIBUTION_NAME HistoName HISTO_LNAME 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 his togram 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 interpolated using the low est 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 150 A numeric distribution is a distribution where the input and output values are numbers There are several classes of numeric distributions e GmGaussianDistribution The sigma and const
247. he 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 paramerisation type you have to provide two number of copies one for each axis 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 navigation 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 Number of copies in Y Number of copies in Z Step separation between cop
248. he 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 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 LineDistIoVtx DISTANCE where DISTANCE has a default value of 10 mm The ClassifyPET method returns an integer with several digits containing the event classification 172 Chapter 18 PET application 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 histograms sta
249. hi FinalPosTheta InitialLocalPosX InitialLocalPosY InitialLocalPosZ InitialLocalPosMag InitialLocalPosPerp InitialLocalPosPhi InitialLocalPosTheta FinalLocalPosX FinalLocalPosY FinalLocalPosZ FinalLocalPosMag FinalLocalPosPerp FinalLocalPosPhi FinalLocalPosTheta FinalLocalInPrePosX FinalLocalInPrePosY FinalLocalInPrePosZ FinalLocalInPrePosMag FinalLocalInPrePosPerp FinalLocalInPrePosPhi FinalLocalInPrePosTheta 125 Chapter 11 Analysis extracting data 126 RandomPosX RandomPosY RandomPosZ RandomPosMag RandomPosPerp RandomPosPhi RandomPosTheta VertexPosX VertexPosY VertexPosZ VertexPosMag VertexPosPerp VertexPosPhi VertexPosTheta PosChangeX PosChangeY PosChangeZ PosChangeMag PosChangePerp PosChangePhi PosChangeTheta The Pos positions are calculated in the global reference frame the LocalPos are calculated in the reference frame of the volume the step or track is in 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 An other 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 Initi
250. hics 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 and followed by gif If you want another format different than gif you may edit the printAlLC 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 histograms 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 arguments 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 histograms the histogram of the f
251. his event and the accumulated number of tracks in all events ae oe oe VENT 0 NTRACKS 4 TOTAL NTRACKS 4 EVENT 1000 NTRACKS 6 TOTAL NTRACKS 4663 VENT 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 print ing with the parameters gamos set Param USER_ACTION_NAME EachNEvent NEV gamos set Param USER_ACTION_NAME FirstEvent NEV These parameters have a default value of 10 and 0 respectively 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 To activate this utility use the command gamos userAction GmCountProcessesUA It 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_L
252. his 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 parameters 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 6 PARAMETERS NOT USED DEFINED IN SCRIPT BUT OT USED BY C CODE SSS AYBE YOU HAVE MISPELLED THEM PARAMETER GmGeometryText FileNam Other lists are available at user request to get a more detailed information You may get them anywhere in your simulation by using the command gamos base printParametersUsage 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 S5555 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 3 5 5 NUMBER OF TIMES EACH PARAMETER IS USED IN C CODE PARAMETER
253. 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 following two parameters gamos setParam PET EvtClass 511EPrecMin ENERGY_MIN gamos setParam PET EvtClass 511EPrecMax ENERGY_MAX 171 Chapter 18 PET application 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 algo rithm 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
254. i_c0O omeca_c0O anti_omega_c0 baryon All baryons ion ions GenericlIon alpha He3 deuteron triton ALL All particles 243 Chapter 26 Appendix A 244 Chapter 27 Appendix B Extending GAMOS functionality with 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 examples NO2 you can see the official Geant4 example novice NO2 trans formed into a GAMOS example We will use it to illustrate the procedure to fol low The first thing to do is to substitute the Geant4 GNUmakefile by a GAMOS GNU makefile 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 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 correspond ing 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 ExN02PrimaryGeneratorA
255. icle names A last command serves to print the active user limits for each volume and each particle gamos physics userLimits print Automatic optimisation of cuts The production cuts and user limits are powerful methods to tune your simu lation 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 usu ally a long and difficult task We have developed in GAMOS a method to help the user to obtain the optimal value of the production cuts and user limits for her his application in a single 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 process and 75 Chapter 5 Physics particle type In the case of production cuts this information is stored at parti cle 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 y
256. ics list GmPSEMPhysics has to be selected gamos physicsList GnPSEMPhysics Then the deexcitation splitting processes for gammas and electrons has to be se lected gamos GmPhysics addPhysics electron lowener Deex Split gamos GmPhysics addPhysics gamma lowener DeexSplit Before this several parameters can be selected namely The regions for which deexcitation is active gamos setParam GmPhysicsElectronDeexSplit Deexcitation REGION_1 RE GION_2 gamos setParam GmPhysicsGammaDeexSplit Deexcitation REGION_1 REGION 2 remember that you can use to name several regions e g only mean all regions The number of splittings times secondary particle production method will be invoked 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 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 Separated Value For the ROOT format we refer you to the ROOT doc umentation 5 The
257. ided by value number of particles contributing to the flux and then for later 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 de tector 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 contribut ing to the flux If the dose equivalent magnitudes are required they come at the end in a line starting also with the filter names classifier name particle type de tector 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 SCORE IN POINT DETECTOR FOR set ALL NeutronInelastic gamma PD1 ALL at 480 ALL NeutronInelastic gamma PD1 ALL ENERGY 0 01 FLUX 0 REL 0 N 6 Fwei2 0 Fwei3 0 Fw ALL NeutronInelastic gamma PD1 ALL ENERGY 0 015 FLUX 0 REL 0 N 0 Fwei2 0 Fwei3 0 Fv 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 104 Chapter 8 Scoring 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 ga
258. ies in X Step separation between copies in Y Step separation between copies in Z Following the rules of G4RegularNavigation the voxels must completely fill the mother volume therefore a container volume of appropiate dimensions 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 27 Chapter 3 Geometry 28 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 automati cally calculated the division width so that the number of divisions will be automatically cal culated 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 e Number of divisions e Division width e Offset not mandatory Example DIV_WIDTH mybox mother
259. 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 example FinalKineticEnergy vs InitialKineticEnergy will fill a 2D histogram FinalKineticEnergy prof InitialKineticEnergy will fill a 1D profile histogram FinalKineticEnergy vs InitialKineticEnergy prof InitialPositionZ will fill a 2D pro file 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 117 Chapter 11 Analysis extracting data 118 gamos userAction GmStepDataHistosUA GmGammaFilter will produce a file named GmStepDataHistosUA_GmGammaFilter root whose name can be changed with the command gamos set Param GmStepDataHistosUA_GmGammaFilter FileName NEW_FILE_ NAME to produce a file named NEW_FILE_NAME root Text files These data users i e GmStepDataTextFileuA GmTrackDataTextFileuA GmSecondaryTrackDataTextFileuA GmStackDataTextFileUA GmEventDataTextFileuA GmRunDataTextFileUA dump the data values into text files A line is written for each call to the data user object ie each G4Step G4Track The text file is indeed a CSV Comma Separated Value file this means that v
260. ification 184 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 histograms starts with CCEvtClass and all are written in the file comptoncam era root The following histograms are written Chapter 20 Compton camera application Classification index of event Compton camera classification This index is the one described in the precedent section The scatterer addback energy for the classified events The absorber addback energy for the classified events Number of reconstructed hits in the scatterer detector Number of reconstructed hits in absorber detector 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 output file should contain only data for single single Compton imaging events 2 reconstructed hits or those events which contain the multiple reconstructed hits through the parameter gamos setParam
261. ility is designed for the case when you want to visualise only a few events but not the rest e g because the interesting event happens after many others and storing them all occupies a log of space in the visualization file To do this you have to select the user action gamos userAction GmVisStoreTrajUA You can set the list of events that you want to visualise with the parameter gamos setParam USER_ACTION_NAME EventLis EVENT_1 EVENT_2 And starting by one event in the list you can select how many events are to be visualised with the parameter gamos set Param USER_ACTION_NAME NEvents NEVENTS Setting the correlation between the gammas of a radioactive decay chain 158 The user action gamos userAction GmRadDecayGammaAngleCorrelationUA is a prototype class to allow the user to set the correlation between the gammas produced in a decay chain As of now it onl sets the correlations for the two gammas of energies 1 1732 and 1 3325 MeV of the decay chain of the Cobalt 60 radioisotope and the correlation is a random one If you are interested in this feature please contact the GAMOS team 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 lev els Silent 1 no output is printed on
262. ime ns e posXYZ Position_X Position_Y Position_Z mm e N SimHits Number of simulated hits The binary file contains the same information in the following format e Energy MeV float e Minimum time ns unsigned long long 87 Chapter 7 Sensitive Detector and Hits Maximum time ns unsigned long long Position X mm float Position Y mm float Position Z mm float Number of hits unsigned int Hits histograms There are two user actions that provide a number of hits histograms GmHitsHis tosUA provides statistics about simulated hits while GmRecHitsHistosUA pro vides statistics about reconstructed hits 88 The class GmHitsHistosUA produces a file named hits root with the following his tograms Number of 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 The class GmRecHitsHistosUA produces a file n
263. ime 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 Chapter 7 Sensitive Detector and Hits The dead time affects by default all detectors in a block This means that if a detec tor is dead it is assumed that all detectors that are placed in the same ancestor 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 set Param SD DeadTimeDUListByBlock NAncestors SDTY PE N_ANCESTORS which as just mention takes a default value equal to the value of the parameter SD DetUnitID NAncestors SDTYPE Take into account that the number of ances tors include the detector itself so that you can tell GAMOS to consider dead only the crystal itself by setting this parameter to 1 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 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 para
264. in concept To provide the user with a big flexibility in choosing different simulation com ponents 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 components 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 anew 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 viewing 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 correspond ing section which is the command to select it and how to transform a new user component into a GAMOS plug in For the implementation of plug in s GAMOS has chosen the CERN package ROOT Chapter 2 Getting started This chapter explains the practical details to obtain the GAMOS code compile and run it Getting the code and installing
265. ine 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 j 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 pigs 2 D pluje 27F 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 depends 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 infinity The technique is still valid and unbiased but convergence is slower and often impractical To avoid this singularity a fictitious sphere of radius RO sur rounding 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 101 Chapter 8 Scoring 102 _ Plp l eTR oy Th eTO DIR lt ang gth 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 sc
266. ined 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 parameter Chapter 3 Geometry gamos setParam GmSimplePhantomGeometry PhantomDims MIN_X MAX_X MIN_Y MAX Y MIN ZMAX Z Then you can divide the phantom in different regions along the Z axis with the parameter 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 MATE RIAL 2 gamos setParam GmSimplePhantomGeometry MaterialDensities DENSITY _1 DEN SITY _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 phan tom container Instead you may use the following parameters gamos set Param GmReadPhantomGeometry Phantom VisOff TRUE gamos setParam GmReadPhantomGeometry PhantomContainer VisOff TRUE Movements 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 el
267. ing the position along the positive or negative X axis you may use this algorithm which classifies the reconstructed hits in order of increasing ab solute value of X position 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 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 corre sponding 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 reconstructed 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 Det1stHitByDistance
268. 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 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 Compton 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 165 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 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
269. ion in Y mm A line with the minimum and maximum extension in Z mm e A number of lines containing the nVoxelX nVoxelY nVoxelZ material indices one per voxel e A number of lines containing 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 geom etry 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 pa rameter gamos set Param GmReadPhantomGeometry FileName MY_FILENAME In a phantom file the voxels of the same material may have a different density By default GAMOS uses the density for each voxel from the DICOM file instead of the original one of the material But to avoid creating too many materials what willl increase the memory GAMOS groups densities in intervals creating a new material for each co
270. irst 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 graphics 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 before gif If you want another format different than gif you may edit the compareAll C file and change the histogram name 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 113 Chapter 10 Histogramming Creating your own histogram Notes 114 When you write your histogram in C you just have to take care of creating and filling it The class GmAnalysisMer 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 pass ing 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 E To create your histogram and
271. 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 ge ometry files Example include mygeom2 txt Combining C and ASCII 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 Con struct method build the geometry from a set of ASCII files Chapter 3 Geometry G4tgbVolumeMgrx volmgr G4tgbVolumeMgr GetInstance volmgr gt AddTextFile mifilel txt volmgr gt AddTextFile mifile2 txt G4vPhysicalVolumex 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 geometry retrieving them by name To retrieve the pointer of a material GmGeometryUtils x 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 logic
272. is example we have defined a simple material named mate_11 of atomic number 1 atomic mass 1 and density 1 The third line defines a volume cell in MCNP terminology that is a box The only important thing is the name you give to it and its cubic volume therefore we recommend you to define always a box with one dimension equal to the cu bic volume and the other two equal to 1 cm One important thing to mark here GEANT4 default unit is mm not cm for this reason we have explicitly multiplied the box dimensions by cm Once you have defined a volume you have to place it into another one To do this you need to define the relative rotation matrix and the relative position As rotation matrix we have defined the unity rotation of 0 around X 0 around Y and 0 around Z As you can see for placing a volume you have to define first the volume name the volume copy as you may place several copies of the same volume and the name of the parent volume then the name of the rotation matrix and finally the three relative position coordinates If you need to define more volumes you can simply copy this one as many times as you like changing the name Chapter 25 Extracting detailed information from a MCNP run Note that the name of the volume is cell_N You may indeed call the volume as you like but when GAMOS read a step from the ptrac file and finds that the cell ID is N it will assume that the particle is in a volume called cell_N So if you want
273. istogram 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 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 getProdCuts
274. istos HisAngMax MAX Chapter 22 Radiotherapy application that takes by default a value of 180 and histograms of energy gamos set Param 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 RI Generator PhaseSpace You can change the filename by default test with the parameter gamos setParam RTGeneratorPhaseSpace FileName MY_FILENAME The particles in the phase space can be translated or rotated by using the param eters 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 then the momentum 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 par
275. it to the number of materials 10 isotopes 50 and products 200 They may be changed by the parameters gamos set Param USER_ACTION_NAME MaterialIndexMax VALUE gamos set Param USER_ACTION_NAME IsotopeIndexMax VALUE gamos setParam USER_ACTION_NAME ProductIndexMax VALUE Counting hadronic cross sections Although the previous user action may be used to get the inelastic cross sections channel by channel it only serves for the neutron_hp and particle_hp physics and only for those cases where the database contains channel by channel cross sec tions i e not for those where only total cross sections and particle yields are given only data in the F02 directory The user action SHGetHadronicChannelXSUA serves to get the inelastic or neutron capture cross sections per reaction in any case as it simulates a number of events and counts how often each reaction happens It also serves to print the average particle yields of the inelastic collisions You can see an example on the use of this utility at MY_GAMOS_DIR tutorials S HieldingTutorial exercise5 exercise5b in The user action first prints the total cross section of the hadronic processed defined in a line showing the material the primary particle energy the process name the total and the microscopic cross sections SHGetHadronicChannelXSUA G4_Fe 10 MeV NeutronInelastic TOTAL_XS macro 0 00119941 cm 1 TOTAL_XS micro 1 41256 barn SHGetHadronicChannelXSUA G4_Fe 10 MeV nCaptur
276. itive 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 study checking if the particles created by ionisa tion 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 en ergy becomes small see section on User limits It is likely logic that if you put a production cut to kill particles of small range you kill the particles when their 229 Chapter 24 Optimising the CPU time of your application energy becomes small so that they will not travel more than that range value For efficiency reasons w
277. ity 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 activate 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 160 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 ver bosity level is set you have to write this verbosity with the value of the level in parenthesis For example if you write one new generator position distribution and you want that a
278. ject 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 directories Remember in any case that you cannot have two defini tions of DEFINE_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 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 a new 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
279. l not be included in the shower If this behaviour does not provide you with the expected results you may consider using the filter GmAncestorsFilter see section of Filters 154 Chapter 15 Utility user actions As we just mentioned each 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 At the end of each event the showers are analysed and several variables are cal culated 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
280. l 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 for 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 e Event the value summed up of all the tracks of the event e Run the value summed up of all the events of the run 115 Chapter 11 Analysis extracting data 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 accumu lated 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 setParam USER_ACTIO
281. lding simple PET ring detectors with text geometry files by just defining the following parameters e P NCRYSTALS_transaxial VALUE Number of crystals per block in the transax ial direction P NCRYSTALS_axial VALUE Number of crystals per block in the axial direc tion P NBLOCKS VALUE Number of blocks of crystals per ring P NRINGS VALUE Number of rings of blocks P CRYS_transaxial VALUE Crystal size trans axial P CRYS_axial VALUE Crystal size axial P CRYS_radial VALUE Crystal size radial e P DIAMETER VALUE Detector ring diameter e PS CRYS_MATE VALUE Name of crystal material e P WORLD_Z VALUE 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 geometry 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 isa GAMOS user action so you can activate it with the command gamos userAction PETEventClassifierUA First it counts
282. length pDz Polar angle of the line joining the centres of the faces at pDz 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 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 Chapter 3 Geometry e Origin Y e Origin Z e Axis X e Axis Y e Axis Z e Direction X e Direction Y e Direction Z e Radius e Length BREPCYLINDER Boundary REPresented cylinder e Origin X e Origin Y e 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
283. lity user actions perpendicular to the geantino direction and computing the material budget for each of them The user action GmMaterialBudgetuA 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 6 TIMING RESULTS for timer GmTimeStudyUA_ClassifierByParticleAndKinE mTimeStudyUA_GmClassifierByParticle_GmClassifierByKineticEnergy 0 0001 0 001 User 0 Real 0 Sys 0 01 0 001 0 01 User 0 07 Real 0 16 Sys 0 0 01 0 1 User 1 3 Real 1 48 Sys 0 04 0 1 1 User 74 66 Real 78 74 Sys 1 17 5
284. lizable 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 not be used they may be used in the next event if more energy is added to them and they are inside the time window gamos setParam SD Hit MinimumEnergy SDTY PE VALUE To simulate Constant Fraction Discriminator CFD thresholds you may also set a minimum energy and a behaviour to treat this threshold First to set the param eter gamos setParam SD RecHit MinimumEnergy S DTYPE VALUE Then you have to select among the two possible behaviours gamos setParam SD RecHit MinimumEnergyBehaviour sDTYPE BEHAV_TYPE where BEHAV_TYPE can be Deletelf1Small if one of the hits in the reconstructed hit has smaller energy than the threshold all reconstructed hits are deleted e AcceptIf1Big if one of the hits in the reconstructed hits has bigger energy than the threshold all reconstructed hits are accepted else all are deleted Remember that there is no default behaviour so if no behaviour is selected the minimum energy threshold is not taken into account Identifying each sensitive detector copy To identify each detector unit individually you have to give a different detector unit ID
285. ll as other tools to help you in optimising 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 5 0 0 directory you can find several directories The directories tmp lib and bin 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 proba bly 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 in stallation you run the example examples test test in tutorials you can find nine step by step tutorials Primer Histogram and Scorers PET SPECT Compton Camera Radiotherapy and Shielding Gamma spectrometry plug in s They include several exercises with increasing difficulty and the exer cise outputs as well as the exercise solutions are provided We recommend you 1 Chapter 1 Introduction to follow one or several of these tutorials to become acquainted with GAMOS The Primer may be a good place to start as it starts with a few basic examples and shows how to visualize geometries and histograms e analysis some utilities that may serve you to analyse your output e data directory where GAMOS algorithms look for data files after current di rectory The plug
286. lse 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 142 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 another 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
287. lumeFilter ExitParallelPhysical VolumeReplicatedFilter ExitParallelRegionFilter InParallelLogical VolumeFilter InParallelPhysicalVolumeFilter InParallelPhysical VolumeReplicated Filter InParallelRegionFilter StartParallelLogicalVolumeFilter StartParallelPhysical VolumeFilter StartParallelPhysical VolumeReplicated Filter StartParallelRegionFilter TraverseParallelLogical VolumeFilter TraverseParallelPhysicalVolumeFilter TraverseParallelPhysicalVolumeReplicated Filter e 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 because 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 im plemented namely GmInMassLogical VolumeFilter GmInMassPhysical VolumeFilter GmInMass Physical VolumeReplicatedFilter and GmInMassRegionFilter When you use for example GmExitLogical VolumeFilter 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 Chapter 12 Filters 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 GmDifferentLo
288. ly for neutrons in cell 21 you can do it with the following commands gamos scoring createMFDetector fluxDet cell_21 gamos scoring addScorer2MFD fluxVol22ScorerN GmG4PSCellFlux fluxDet gamos scoring addFilter2Scorer GmNeutronFilter flux Vol22ScorerN If you want to have a different score for each energy interval in six isolethargical bins from 1 E 11 to 1 E1 MeV you can add the following classifier gamos classifier energy NC GmClassifierBy NumericData log10 InitialKineticEnergy 6 111 gamos scoring assignClassifier2Scorer energyNC fluxVol22ScorerN 236 Chapter 26 Appendix A Using parameters As you can see through this guide many algorithms in GAMOS use parame ters 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 de pending 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 t
289. ly 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 messages 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 GmBaseVerbosity controls the verbosity of the base classes filters classifiers input output management GmGeomVerbosity controls the verbosity of the geometry classes GmGenerVerbosity controls the verbosity of the GAMOS generator GmPhysics Verbosity controls the verbosity of the physics classes GmSDvVerbosity controls the verbosity of the sensitive detectors hits digits and reconstructed hits GmUAVerbosity controls the verbosity of the classes for user action manage ment GmScoringVerbosity controls the verbosity of the scoring classes GmReadDICOMVerbosity controls the verbosity of the classes to read DICOM files GmDataVerbosity controls the ve
290. m the name of the class itself Reading your generator particles from a text file 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 e EventID e Particle e Posx 55 Chapter 4 Generator e Posy e PosZ e MomxX e MomY e MomZ e Time Weight The lines will be read one by one and all the particles that have the same event ID will 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 com mand gamos set Param 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 InitialMomyY Initial MomZ InitialTime InitialWeight Reading your generator particles from a binary file 56 You can also define your event primary particles with a binary file with the fol lowing 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 com
291. mand 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 InitialMomyY Initial MomZ InitialTime InitialWeight Chapter 4 Generator Event generator changing energy and material As you can find in some of the tutorial exercises this generator serves to scan dif ferent energies and different materials and obtain for example the cross sections at each point the activation or whatever quantity you want To select it you have to use the command gamos generator GmGeneratorChangeEnergyAndMaterial The first thing to choose is the energies To do it a minimum a maximum energy have to be defined as well as a number of steps gamos set Param GmGeneratorChangeEnergyAndMaterial minE VALUE gamos set Param GmGeneratorChangeEnergyAndMaterial maxE VALUE gamos setParam 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 Yo
292. mand line ENERGY 1 SEED 2 NEV 3 NJOBS 4 239 Chapter 26 Appendix A 240 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 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 Ys s n 1 2 test SUFFIX else if 1 gamos generator addSingleParticleSource printf s s s Ys n 1 2 3 ENERC else print 0 Y exercise2b in gt new_inputfile inn You can observe that each of the variables that
293. mber of different types of leaf cross profiles n_leaves_cross_profiles For each cross profile the following data has to be defined e Leave type It will be a LEAF or BLOCK but this options is not implemented yet so it must be LEAF Number of 2 dimensional points taht define the cross profile n_leaves_cross_points Chapter 22 Radiotherapy application 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 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 corre sponding 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 Interle
294. mbination material name density interval The width of the interval can be selected with the parameter gamos set Param GmReadPhantomGeometry Phantom DensityStep DENSITY_INTERVAL which by default takes a value of 0 1 g cm3 If you want to use the original material density for all voxels of a given material disregarding the density values from the DICOM file you have to set to false the parameter gamos set Param GmReadPhantomGeometry RecalculateMaterialDensities 0 The navigation 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 navigation with 1 dimensional optimization that occupies similar memory as RegularNavigation but is very slow gamos set Param GmReadPhantomGeometry Phantom RegularStructureID 0 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 Chapter 3 Geometry GAMOS is also able to read the EGSnrc DOSXYZnrc format for DICOM
295. me 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 Histogram type it must be 1X 1Y 1Z 2XY 2XZ or 2YZ Histogram name e Minimum voxel in X e Maximum voxel in X e Minimum voxel in Y e Maximum voxel in Y e Minimum voxel in Z e Maximum voxel in Z Chapter 22 Radiotherapy application 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 expressions 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 NVoxel 1Z RTPSPDoseHistos Dose Profile Z_merged 0 NVoxelX 1 0 NVoxel Y profiles at several depths 1Y RTPSPDoseHistos Dose Profile Y 1 400 cm 50 50 0 NVoxelY 1 6 1Y RTPSPDoseHistos Dose Profile Y 10 000 cm 50 50 0 NVoxelyY 1 4 PDDs merging voxels 1Z RTPSPDoseHistos Dose Profile Z
296. 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 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 calcu lated position at each event you may write G4cout lt lt GenerVerb debugVerb lt lt MyPositionGeneratorDistribution position lt lt position lt lt G4endl uw 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 Chapter 16 Managing the verbosity from GmAnaVerbosity you use AnaVerb And the name of the level in C code is the same as the one in the input command file adding Verb e g for warning you use warningVerb Creating your own verbosity manager You can create your own verbosity manager for the code you use taking as exam ple one of the GAMOS verbosity managers for example the class GmGenerVer bostityMgr in the package GamosCore GamosGenerator First create a class inheriting
297. 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 ClassifyNew Track methods will only be invoked if the AccepTrack method of every filter re turns true and UserSteppingAction method will only be invoked if the AccepStep method of every filter returns true In the case of filters 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 ob tain 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 follow ing command 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
298. milar to the following one IAI GmCutsEnergy2RangeUA MATERIAL G4_AIR PART gamma 73 Chapter 5 Physics 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 0 1 MeV RANGE CUT 131 938 GmCut sEnergy2RangeUA ATERIAL 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 produc tion 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 ionisation bremsstrahlung and to electron positron production by muons but they may be applied to any electromagnetic process by using the command gamos physics applyCutsForAllEMP rocesses If you want to apply it to all processes you have then to use the command gamos physics applyCutsForAllPro
299. mma interaction 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 choice 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 identify 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 ina 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 grou
300. mos set Param GmPDS ControlHistograms 0 The histograms are written in a file named pds but this name can be changed with the parameter gamos setParam GmPDS HistosFileName VALUE All histograms start with the 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 interaction 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 follow ing e log10 energy MeV log10 of track kinetic energy times the weight e log10 energy no weighted MeV log10 of track kinetic energy e log10 energy weighted by Hstar log10 of track kinetic energy times the weight a
301. mpt MT 1 e Rayleigh scattering rayl MT 2 e Photoelectric effect phot MT 3 233 Chapter 25 Extracting detailed information from a MCNP run e e e pair conversion conv MT 4 e Electrons e Protons e Elastic ProtonElastic MT 1 e Elastic ProtonInelastic MT 2 If the step has a MT type different that those above the code will throw an excep tion and will stop Source primary generator As for the physics no source is needed Therefore we recommend you to use GmMCNPDummyGenerator as in the first example Extracting information GAMOS offers a big amount of possibilities to extract detailed information at any moment of the simulation We recommend you to have a look at the chapter about Analysis extracting data to understand how this is done Tallying scoring 234 Tallies are called scorers in GEANT4 terminology In the chapter about Scoring you may find all the details about how to do scoring in GAMOS Nevertheless we will summarize them here marking the differences with MCNP tallying Scoring is always done in GEANT4 in a volume This means that to define a scorer you have first to define the list of volumes where you will score and only particles in one of this volume will be added to the scorer see later about surface scoring Therefore the first thing you should do to use GAMOS scoring is to cre ate a multifunctional detector 15 and associate it with a list of logical volumes with
302. ms 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 initialize Geant4 and to run N events In this case your input file may look like this one 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 elec tron 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 de pends on the current state The main state change is triggered by the run initialize command which changes the state from G4State_PreInit to G4State_Idle You may get a full list of the available commands at any moment with the command con trol manual Running an example in Windows To run in Wind
303. n 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 infor mation 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 GnMinRangeLimitsStudyUA 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 amp tee ou Chapter 22 Radiotherapy application and look at the last lines of output those that contain the word FINAL 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 gamma cut and the electron cut like in the following example gamos filter ProdCutFilter GnMinRangeCutOutsideVoxelFilter 10 mm 1 mm gamos scoring ad
304. n be done with GAMOS using the impor tance sampling and assigning different distributions with different data For ex ample 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 You may also consider the special distribution GmGeometrical BiasingDistribution see chapter on Distributions that calculates the weight as the division of the weights of the entering and exiting volumes General process splitting Several particle splitting techniques are available to increase the efficiency of ra diotherapy accelerators simulations See the chapter on Radiotherapy Particle splitting techniques for radiotherapy Several particle splitting techniques are available to increase the efficiency of ra diotherapy accelerators simulations See the chapter on Radiotherapy Production of deexcitation secondary particles 110 As the production of secondary particles by deexcitation processes i e charac teristic 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 deexcitation secondary particles is going to be produced GAMOS in vokes 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 phys
305. n 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 appli cation The example contains a utility to build a Compton camera which is com posed of either rings of detectors or a stack of parallel detectors through the user defined geometrical parameters Information relevant to Compton camera applications is accessed using the Compton camera event classifier Many of the utilities for Compton camera detectors are related to the sensitive detectors 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 Photoelectric absorption is the ideal gamma ray interaction It is neces sary to define the sensitive detectors as either a scatterer or absorber using the parameter gamos SD assocSD2LogVol GmSDSimple Scatterer DETECTOR_LOGICAL_ NAME gamos SD assocSD2LogVol GmSDSimple Absorber DETECTOR_LOGICAL_ NAME The Compton camera directory contains a utility to build a Compton camera sys tem in either i a dual ring configuration or as ii a stack of detectors Altho
306. n 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 scorer Unit SCORER_NAME UNIT_NAME UNIT_VALUE Scorer classes 92 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 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 e 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 fr
307. nd Hstar value e log10 weight log10 of track weight e 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 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 prop agation 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 105 Chapter 8 Scoring 106 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 l0g10 of geantino ki netic energy versus geantino weight to determine which are the minimum weight and Russian roulette factor that best match your application Kill contributions too far from detector A more efficient technique consists on not taking into
308. ndleaf 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 201 Chapter 22 Radiotherapy application f Leave type 2 defined te the reference plane Z_TOP Leave type 1 __Leave typed m Leave type 4 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 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 suf
309. nes 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 look ing 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 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 e 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 Chapter 3 Geometry 21 Chapter 3 Geometry 22 Half z length TWISTEDTRAP trapezoid twisted along one axis Twisted angle Half x length at y pDy Half x length at y pDy Half y length pDy1 Half z
310. nfo additional output files for intermediate iterat SOE_ImageRecon averageStatesOut additional output each 100 iterations before SOE_ImageRecon readDensityMatrix read density matrix density_matrix img SOE_ImageRecon readCurrentState read current state file currentstat SOE_ImageRecon help for this help output Chapter 21 Image reconstruction utilities Input files In the directory in which you run the code you need the following input files ir_soe_userparameters conf CC_img out parameters file data file with any kind of name as given in the parameters file In the data file every line should contain the following Hitl1 Z mm Hitl1 Y mm Hit1 X mm Hitl Energy keV Hit2 Z mm Hit2 Y mm Hit In the case of Compton camera data Hit1 corresponds to the hit in the Scatter detector 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
311. nition 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 the 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 5527 G4_CADMIUM_TELLURIDE G4_CADMIUM_TUNGSTATE G4_CALCIUM_CARBONATE G4_CALCIUM_OXIDE G4_CALCIUM_SULFATE G4_CALCIUM_TUNGSTATE G4_CARBON_DIOXIDE Cc G4_CALCIUM_FLUORIDE o S G4_CARBON_TETRACHLORIDE G4_CELLULOSE_CELLOPHANE G4_CELLULOSE_BUTYRATE G4_CELLULOSE_NITRATE G4_CERIC_SULFATE G4_CESIUM_FLUORIDE G4_CESIUM_IODIDE G4_CHLOROBENZENE G4_CHLOROFORM G4_CONCRETE G4
312. nneni a n net Gogh vin badsdareecded ee Golesi nbacsdatn eth 171 PET event classification ccccccccccesscceccssesssecesesseesescsessseceesscesessesesseeeessesesesess 171 PET histograms event classification cccc cesses eesesssesescseesesescseeseeeeees 173 PET output for reconstruction ccccc cess ssesessesessssseescesesesescseseeecees 173 List mode binary file ccc cece e E 173 Projection data file sis c ics net asset aistionit evident an a 174 PET histograms POSItrON c cccccecesee esse eseeseseeseesesesssesescsesesesescssenseeesses 175 Detector histograms distance between twO ZaMMAS ceeeseseseeeneees 175 19 SPECT ap plication sciscseevssascessesececcsessncerussvsevcsenicossseosonse senstenssdereaedosensesnrenstdvesense 177 SPECT event classification cccccccccceccssssssccessseesesceesssesesessceeessesssseesessesseeeess 177 SPECT histograms event classification ccccceseeessssssesescsenesesescseeeeeeees 178 SPECT output for reconstruction cccc eee cseseseeeessssesescseeseescsseeseecees 179 20 Compton camera application seseseessssessesesseseesesseseeseseesceeeseerereeseeeeseeeeseeeeseesee 181 Compton cariera ZCOMEITY sin uiii rasina i e AE E a 181 Compton camera Event Classification ss sssssessessissteseessesserersessesssesteseesee 183 Compton camera histograms event classification ssssssessssessesseesees1ee 184 Compton camera output for reconstruction cece ce
313. nning 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 215 Chapter 22 Radiotherapy application 216 TPSPDoseHistos nvoxel 21 112 150 PSPDoseHistos dim 1 1 1 PSPDoseHistos translation 0 0 4 PSPDoseHistos rotation 1 0 0 0 a 0 0 0 1 MINIMUM DOSE 2 352e 15 MAXIMUM DOSE 4 76001e 13 AAT BRD TPSPDoseHistos AVERAGE ERROR 20 0 0139839 TPSPDoseHistos AVERAGE ERROR 50 0 0111726 TPSPDoseHistos AVERAGE ERROR 90 0 00996564 zZ lI nnn saving histograms in file EVENTS IN SOURCE 2 5e 08 dose_analyseSqdose 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 argument descriptions below Then the total number of voxels to be read and the information from the class RTPSPDoseHistos number of voxels in X Y and Z voxel dimensions in X Y and Z translation and rotation applied to phantom when dose file was written and the statistics i e minimum and max imum voxel dose and average dose error in 20 50 and 9
314. nsions SHNthValueLayeruA counts the number of particles that exit each slab and at the end of run prints these numbers divided by the total number of events in a format similar to the following one 66 SHNthValueLayerUA_NSTEPS shield 0 0 96763 66 SHNthValueLayerUA_NSTEPS shield 1 0 92561 66 SHNthValueLayerUA_NSTEPS shield 2 0 88194 SHNthValueLayerUA_NSTEPS shield 3 0 83882 66 SHNthValueLayerUA_NSTEPS shield 4 0 79542 At the end it makes a exponential fit to the histogram of the number of particles exiting the slabs as a function of the penetration and the result is printed in a format similar to the following FCN 6713 22 FROM MIGRAD STATUS CONVERGED 51 CALLS 52 TOTAL EDM 6 48994e 08 STRATEGY 1 ERROR MATRIX ACCURATE EXT PARAMETER STEP FIRST O NAME VALUE ERROR SIZE DERIVATIVE 1 Constant 1 16833e 01 1 02026e 03 2 99800e 05 4 71215e 01 2 Slope 6 40772e 02 4 29841e 05 1 26302e 06 5 92494e 00 SHNthValueLayerUA_exitShieldLayerF_copyNoC gamma G4_Pb 1 MeV FIT chi2 6713 22 nDoF 162 From the fitted function it calculates the width corresponding to each of the re duction factors in the list given by the parameter gamos setParam USER_ACTION_NAME Reductions VALUE_1 VALUE_2 This width is also calculated interpolating with a lin log interpolation in the list of values of number of particles exiting each slab Th
315. nt 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 pi0 eta eta_prime kaont kaon kaon0O kaonoOL kaonOS a0 x al a2 k x k1l k2 k_star x kO_star k2_star k3_star anti_k anti_k0O x 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 pi pi2 rho rho3 gt e charmMeson Mesons that contain a charm quark D D D0 anit_D0 Ds Ds J psi bottomMeson Mesons that contain a bottom quark B B BO anti_B0 Bs0 anti_Bs0 meson All mesons lightBaryon Baryons that only contain up and down quarks proton anti_proton neutron anti_neutron N x anti _ N x Chapter 26 Appendix A delta anti_delta x 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 anti_sigma x xi anti_xi omega omega3 charmBaryon Baryons that contain a charm quark lambda_c anti_lambda_c sigma_c0O anti_sigma_c0O sigma_c anti_sigma_c sigma_c anti_sigma_ct xi_ct anti_xi_ct xi_cO anti_x
316. nt track GmAncestorsFilter behaves similarly as the GmHistoryOrAncestorsFilter but it does not check if a previous step has passed the filter GmOnAllSecondariesFilter makes the list of filters act of the secondary tracks created in the step or in the whole track returns true if all secondary tracks created accept all the filters GmOn1SecondaryFilter makes the list of filters act of the secondary tracks cre ated in the step or in the whole track returns true if any of the secondary tracks created accept all the filters GmOnSecondaryFilter this filter is designed to work with GmSecondaryTrack Data users The filter will be applied not the current step or track but to the secondary tracks created GmlnverseFilter 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 circunstances i e each begin of track each track step and each end of track An example can be a user action that is using a accumulating data see section onGAMOS data at PreUserTrackingAction the variable for example energy de posited is initialized to 0 at SteppingAction the new energy deposit is added and at PostUserTrackingAction 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
317. ntiates the most common processes for gammas electrons and positrons and also for optical photons For gammas and electrons uses the low energy based on Livermore data models while for positrons uses the stan dard models no low wnergy models exists The detail of the processes and models used plus the options of the models for which the defaults values are changed is the following see Geant4 documentation for a better understanding of the physics of each process and model e gamma e photo electric process G4PhotoElectricEffect using model G4LivermorePhotoElectricModel below 1 GeV and G4PEEffectFluoModel above e Compton scattering process G4ComptonScattering using model G4LivermoreComptonModel below 1 GeV and G4KleinNishinaCompton above e Gamma conversion process _G4GammaConversion using model G4LivermoreGammaConversionModel above 1 GeV and G4BetheHeitlerModel above e Rayleigh scattering process G4RayleighScattering using model G4LivermoreRayleighModel below 1 GeV and none above e electron e ionisation process G4elonisation using G4LivermorelonisationModel with G4UniversalFluctuation below 1 GeV and G4MollerBhabhaModel above The RoverRange and the finalRangeRequested of the step function are set to 0 2 and 0 1 mm e bremsstrahlung process G4eBremsstrahlung using GmLivermore BremsstrahlungModel below 1 GeV and G4eBremsstrahlungRelModel above e multiple scattering process G4VMultipleScattering using model G4
318. 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 setParam GmPDS InteractionAngleManager MinimumNumberOfEntries VALUE Point detector volume The detector where the flux will be scored has to be a real volume in your geome try 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 setParam GmPDS EnergyBinsFileName FILE_LNAME 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 namely the ambient 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 gammas gamos setParam GmPDS PrintHstar 1 gamos se
319. nviromental 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 given density and then to a material type The relation between CT number and density is more or less linear 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 distribution contains the assignment of material densities to mate rials 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 g4dcm e A line with the number of materials e A line for each material with its index and name the same name of materials that you constru ct as G4Material s e A line with the number of voxels in X Y and Z e A line with the minimum and maximum extension in X mm 37 Chapter 3 Geometry 38 e Aline with the minimum and maximum extens
320. o measure the gain of a variance reduc tion 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 estimat ing the properties of a particular distribution 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 ex ample 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 survive
321. obably are not able to read the messages fast enough before the windows disappears so you should try to process the libraries in other way e Open a command prompt window In windows XP e Type c or the disk unit where the GAMOS directories lie e Type cd MY_DIRECTORY where MY_DIRECTORY is the directory where GAMOSGULexe lies Type cd config e Type genmap win bat gt genmap log e Open the genmap log for example with more genmap log or send this file to the GAMOS developers if you need help Chapter 2 Getting started Running an example in Linux or Mac OS 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 MY_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 histogra
322. ocess 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 removeProcessesByParticleAndName PARTICLE_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 Op tical Hadronic Photolepton_hadron Decay General Parameterisation UserDefined or NotDefined Production cuts 72 Several physics processes namely bremsstrahlung ionisation from all charged particles and e e pair production from muons have very high cross sections at low energies It is therefore necessary to implement a production cut so that all particles below it are not generated but their energy is accounted as energy de posited 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 setCut value unit set the cuts for all process to the desired value But
323. od 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 de positing 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 GmProdCutsStudyUA RTCutsStudyFilter It will produce a table with the number of tracks that would be killed by the range rejection and would not reach the target the tracks themselves or any of their children As for the production cuts they are printed by region by particle and by creator process type To get a closer inside on this technique several plots are produced one per each region each particle and each creator process repre senting the logarithm of the difference safety range vs the logarithm of the range To distinguish the cases where the range is bigger than the safety no range rejec tion 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
324. oduced 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 tables We will describe the steps you should follow to do this and illustrate them with an example Chapter 11 Analysis extracting data 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 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
325. 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 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 itis nota useful Compton imaging event 1 if it is a coincident event but not fully absorbed 2 if it is a fully absorbed coincident event and 3 if it is a fully absorbed Compton imaging event with a single interaction in the scatter detec tor 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 multiples are carried out then the number of absorbed events in creases by the number of useable multiple events which can now be used for imaging e 10 1 if the search for 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 Compton camera histograms event class
326. ollowing histograms are written Classification index of event SPECT classification This index is the one de scribed in the precedent section e Number of 511 keV reconstructed 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 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 Chapter 19 SPECT application e 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 e 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
327. olumes which can be quite slow if the volume dimensions are small Position in a user defined volume gamos generator positionDist SOURCE_NAME GmGenerDistPositionInUser Volumes POS_X POS_Y POS_Z ANG_X 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 or der 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 different position you have to add three optional extra parameters POS_X POS Y POS 2 51 Chapter 4 Generator 52 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 ro tating 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
328. om 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 eval uate 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 di vided by the mass of the cell The mass is calculated from the density and vol ume of the cell taken from the methods of G4VSolid and G4LogicalVolume 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 The following scorers serve to calculate the deposited dose in a volume divid ing it virtually in smaller pieces This means that the energy deposited is not divided by the volume the track is in but by the division volume as defined by the scorer As you may find other type of use for these scorers you can choose also to divided by the total volume defined with the scorer by setting the parameter gamos setParam SCORER_NAME UseTotal Volume 1 e GmPSSphericalDoseDeposit This scorer is designed to compute the dose de posit and assign a different index to each spherical radius interval despite no spherical division is defined in the geometry
329. ometry volumes starting 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 tens controls the information about physical vol umes e gt 1 Prints physical volume name copy number and parent volume name 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 ma terial name global position and rotation and local position and rotation The command gamos geometry printMaterials VERBOSE_LEVEL Print the list of all materials TheVERBOSE_LEVEL controls the amount of infor mation given each level print also the information from previous level It is a one digit number e gt 1 Prints elements and isotopes of each material e gt 2 Prints density effect data C utilities There is a set of geometry utilities that are meant to help the user that is writing some C code to
330. on 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 parti cle 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 Chapter 22 Radiotherapy application ancestors We know then that if we set in any of the regions where each of the an cestor 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 tar get 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 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
331. on is randomly distributed in a 2D square in the XY plane of half width HALF_WIDTH at position 0 0 0 If you want it placed at a differ ent position you have to add three optional extra parameters POS_X POS_Y POS_Z By default the square 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 DIR_X DIR_Y DIR_Z Those are the director cosines of the Z axis of the square the axis perpendicular to the 2D surface Position in a rectangle gamos generator positionDist SOURCE_NAME GmGenerDistPosition Rectangle HALF _WIDTH_X HALF 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 half widths HALF_WIDTH_X in X and HALF_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 position Dist 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 RA DIUS at position 0 0
332. onUpper Takes the value corresponding to the closest big ger value f x f x_B String distributions A string distribution is a distribution where the input values are strings e g par ticle 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 distri butions two columns where the first column is a list of names and the second column the values that correspond to each name String data distribution The GmStringDistribution is a general string distribution It takes the value from the data associated to it which has to be of type string see chapter on Analysis Geometrical biasing distribution The GmGeometricalBiasing Distribution is a special distribution that serves to do ge ometrical 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 PreStep Point else it returns 1 The file is supposed to contain in the first colummn the list of volume names and in the second the list of weights Two data has to be assigned to it what can be done with the parameters gamos setParam DISTRIBUTION_NAME DataPre DATA_NAME gamos setParam DISTRIBUTION_NAME DataPost DATA_NAME These data should be one of the volume data FinalLogicalVolume and InitialLog icalVolume FinalPhysicalVol
333. onding to each bin Le 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 e 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 Chapter 22 Radiotherapy application The Radiotherapy application contains some utilities for the simulation of a teletherapy linear accelerator and dose calculations in the patient Many 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 multileaf 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 parame ters of its projection in into a plane The following parameters have to be provided MODULE JAWS Module name Module type giving the direction 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 of the position where the centre of the volume would be if the field were 0 no rotation Z position of the plane where the projections are
334. one cannot use the bin centres and calculate the bin limits but the bin limits have to be explicitly 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 probability 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 e 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 Chapter 4 Generator 0 0 25 1 0 75 10 0 e Isolethargical gamos generator energyDist SOURCE_NAME GmGenerDistEnergylsolethargi cal ENERGY_MIN ENERGY_MAX The energy will be sampled following a distribution that is flat in the loga rithm of the energy The third argument serves to define which is the unit of the energies in the file If not provided it will be taken as M
335. ong to the neutron_hp or particle_hp GEANT4 packages you will also get the cross sections channel by channel unless you set the parameter gamos set Param USER_ACTION_NAME OnlyTotalXS 1 The channel cross sections may be printed as a fraction of the total cross section if you set the parameter gamos setParam USER_ACTION_NAME NormaliseToTotalXS 1 It is possible to discard products with high atomic number and mass but setting the maximum isotope number atomic number 1000 atomic mass for exam 223 Chapter 23 Shielding application ple discard all isotopes higher than alphas by setting this number to 2004 This number is set with the parameter gamos setParam USER_ACTION_NAME ProductMaxAZ VALUE Also the particle yields can be printed the mean number of particles of a given type produced in a reaction channel and the particle yield multiplied by the channel cross sections i e the particle cross section of production of the given particle if you select the parameter gamos setParam USER_ACTION_NAME Particle Yields 1 The SHPrintPHPChannelXSUA user action writes also a set of histograms with the cross sections as a function of energy channel by channel for each isotope in each material The set of energies is the one selected with the minE maxE and nStepsE parameters If it is requested to print the particle yields it will also Each of the histogram needs to have a well identified internal number This puts a lim
336. or hv v Its functionality is similar to the Proj DataMgr class see Projection data file section using the following arguments a axial field of view in millimeters by default 100 0 e d diameter of the transaxial field of view in millimeters by default 300 0 e m maximum ring difference by default 1 number of planes e n name of the output file without extension e o output format 0 for GAMOS ad hoc format by default extension hv v compatible with GAMOS analytic image reconstructor or 1 for STIR projection data extension hs s e p number of axial planes by default 40 e r number of tangential bins by default 81 e t theta number of angular views by default 80 v verbosity by default 0 silent 3 debug e 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 maxi mum 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
337. orer is selected as other GAMOS scorers although as ex plained 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 gam mas 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 in 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 what may be enough in your case To do this you can run a job that writes in a ROOT file the probability of emis sion angle for
338. ormat 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 Managing the input data files 45 Chapter 3 Geometry 46 Chapter 4 Generator GAMOS offers several primary generators the general one which allows you to select 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 Alternatively 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 dis tributions that the user may combine to his her will The user can select to gen erate 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 manage
339. ou 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 ioniza tion and bremsstrahlung processes this method allows to extend the production cuts to other processes To do this we provide the abovementioned numbers and plots separately for each process 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 meth
340. owing a photoelectric interaction The merging of this is always 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 its position is recalculated There are two ways to calculate the reconstructed hit position e By default it is defined as the barycentre i e the average of all the hits position weighted by their energy If the following parameter is set gamos setParam SD RecHit PosAtBarycentre SDTY PE 0 the reconstructed hit position will be taken as that of the hit with highest en ergy The reconstructed hit builders implemented are GmRecHitBuilderByDistance Two hits are merged if they are separated by a dis tance closer than the parameter gamos setParam SD GmRecHitBuilder ByDistance HitsDistInRecHit that by default takes a value of 10 mm GmkRecHitBuilderByBlock 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 grand parent_volume_copy_number and therefore two detector unit IDs are con
341. ows we recommmend you to use the Graphical User Interface that you can find at MY_INSTALLATION_DIR GAMOS 5 0 0 GAMOSGULexe Chapter 2 Getting started ES WinGAMOS BEE ftracking verbose 1 fgamos setParam GmGeometryFromText FileName exercise0 geom fgamos geometry GmGeometryFromText fgamos physicsList GmEM Physics fgamos generator GmGenerator frun initialize fgamos generatorfaddSingleParticleSource source gamma 10 MeV fcontrolfexecute examples visVRML2FILE in frunfbeamOn 10 Figure 2 1 GAMOS Graphical User Interface The first you should do is open an input file and then run it Or alternatively you may create a new one The list of buttons of this GUI is the following Vag e Open File Open an existing input file gt Dd _ Run run GAMOS with the input file in the screen it is saved before run Open Log open the log file of a GAMOS run gamos log in the same direc tory that the current intput file A Open Error Log open the error log file of aGAMOS run gamos_error log in the same directory that the current intput file Ld New File create a new input file U A Save File save current input file using current name L ra Save File As save current input file changing name m Select Font select the font for input and log files 2 Help open the pdf file of GAMOS User s Guide Chapter 2 Getting started KEI Exit exit GUI Compiling GAMOS If you installed GAMOS as explain
342. parameters gamos setParam 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 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 134 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 parameters 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 pr
343. ping 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 Energy of second gamma interaction e DetCompton Algo Interaction Energy 3rd Energy of third and higher gamma interactions e DetCompton Algo Interaction Energy Ist others Energy of first gamma interac tion minus energy of other interaction e DetCompton Algo Interaction Energy 2nd others Energy of second gamma in teraction 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 interac tion vs energy of other interaction e DetCompton Algo Interaction Energy 2nd others Energy of second gamma in teraction vs energy of other interaction e DetCompton Algo Interaction Energy 3rd others Energy of third and higher gamma interactions vs energy of other interaction 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 position 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 165 Chapter 17 Detector applications 166 gamos setParam DetComptonStudyHi
344. position 0 0 0 and random direction Chapter 4 Generator Distributions Time distributions Constant time gamos generator timeDist SOURCE_NAME GmGenerDistTimeConstant 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 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 Decay time gamos generator timeDist SOURCE_NAME GmGenerDistTimeDecay ACTIVITY LIFETIME The primary particles will be generated with a time following a typical decay distribution 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 Energy distributions Constant energy gamos generator energyDist SOURCE_NAME GmGenerDistEnergyConstant EN ERGY All the primary particles will be generated with energy given by the parameter ENERGY Constant decay energy g
345. 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 see 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 moment 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 DetCountScatteringuUA VolumeNames VOLUME_1 VOLUME_2 and this interaction is of one of the process types defined by t
346. possible 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 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 ReuseAtZPlane MirrorWhenReuse 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 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 Optimisation of a linac simulation 208 To optimise your simulation in GEANT4 you may tune the physics parameters production cuts special cuts multiple scattering options as well as try some reduction 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 th
347. possible to filter when a track or a track step En ter Exit Start Stop In Traverse a DICOM structure by using the corresponding filter GmEnterPhantomStructureFilter GmExitPhantomStruc tureFilter GmStartPhantomStructureFilter GmStopPhantomStructureFilter GmInPhantomStructureFilter GmTraversePhantomStructureFilter These filters must receive an argument the list of names of phantom structures for example gamos filter InBrainF GmInPhantomStructureFilter brain 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 intersecting 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 input 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 GmReadPhantomG4Geometry 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
348. processes photo electric uses G4PEEffectFluoModel Compton scattering uses G4KleinNishinaCompton gamma conversion uses G4BetheHeitlerModel No Rayleigh scattering y gamma penelope processes a la Penelope 6 Below 1 GeV photo electric uses G4PenelopePhotoElectricModel Compton scattering uses G4PenelopeComptonModel gamma conversion uses G4PenelopeGammaConversionModel above 1 GeV the standard models are used Rayleigh scattering uses G4PenelopeRayleighModel e electrons electron lowener low energy based on Livermore Evaluated Particle Data Li brary electron standard standard electromagnetic processes Ionisation uses G4MollerBhabhaModel bremsstralung uses G4SeltzerBergerModel below 1 GeV and G4eBremsstrahlungRelModel above multiple scattering uses G4UrbanMscModel96 electron penelope processes a la Penelope Below 1 GeV ionisation uses G4PenelopelonisationModel and bremsstrahlung usesG4PenelopelonisationModel and bremsstrahlung above 1 GeV the standard models are used Multiple scattering uses G4UrbanMscModel96 e positrons positron standard standard electromagnetic processes positron penelope processes a la Penelope 6 positron penelope processes a la Penelope For details on the physics implemented in each of these physics proceses and models please read the Geant4 physics manual 10 This physics list also switches on the atomic deexcitation see section below Chapter 5 Physics GA
349. produce a different index despite the process be ing called the same for both particles GmClassifierByCreatorProcess It assigns a different index to different track cre ator 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 GmClassifier By SecondariesList It builds a list of the secondary particle names in alphabetical order without repeating names and assigns a different index to each list GmClassifierBySecondariesListExclude It builds a list of the secondary particle names in alphabetical order without repeating names and assigns a different index to each list When the classifier is defined you can add as parameter a list of particles and they will be excluded from the list GmClassifierByHadronicReaction It builds the name of the hadronic reaction and assigns a different index to each reaction name The name is built taking into account the target nucleus the projectile and the emitted particles with outh taking into account the gammas except in the case of neutron capture Examples of reaction names are Be9 n p Li9 Fe56 p pn Fe55 Pb208 a p T1211 GmCompoundClassifier This classifier receives a list of classifiers and builds an index as Classifier_1 NShift Classifier_2 NShift NShift Where
350. pter 11 Analysis extracting data 120 FinalPosX FinalPosY FinalPosZ FinalMomx FinalMomyY FinalMomZ AccumulatedEnergyLost AccumulatedEnergyDeposited GmStepDataTextFileUuA EventID TrackID Particle FinalPosX FinalPosY FinalPosZ FinalMomxX FinalMomY FinalMomZ AccumulateEnergyLost AccumulateEnergyDeposited GmStepDataBinFileUA EventID TrackID Particle FinalPosX FinalPosY FinalPosZ FinalMomX FinalMomY FinalMomZ AccumulateEnergyLost AccumulateEnergyDeposited GmTrackDataHistosUA FinalPosX FinalPosY FinalPosZ FinalMomx FinalMomY FinalMomZ AccumulatedEnergyLost Accumulated EnergyDeposited GmTrackDataTextFileUA EventID TrackID Particle FinalPosX FinalPosY FinalPosZ FinalMomX FinalMomY FinalMomZ AccumulateEnergyLost AccumulateEnergyDeposited GmTrackDataBinFileUA EventID TrackID Particle FinalPosX FinalPosY FinalPosZ FinalMomX 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 GmRunDataBinFileUuA e RunID Chapter
351. py numbers of the volume itself if it is N gt 0 it will look for the copy numbers of the N th ancestor GmPSClassifierByAncestors It assigns a different index to different copy num bers of the sensitive volume It has two extra parameters that set the number of ancestor 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 1 145 Chapter 13 Setting 146 Classifiers GmClassifier ByLogical Volume It assigns a different index to different logical vol umes GmClassifierByPhysicalVolume It assigns a different index to different physical volumes GmClassifier By Physical VolumeReplicated See discussion about Physical Volume Replicated filters GmClassifierByRegion It assigns a different index to different regions GmClassifierByMaterial It assigns a different index to different volume materi als GmClassifier ByKineticEnergy 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
352. r SIMUMIAION a a EAEE AAA ae AREON 216 Automatic determination of production cuts for a dose in a phantom similati Oisans eiernes ee Er aa a N iaee E eS 217 Automatic determination of user limits for an accelerator simulation 218 Automatic determination for a dose in phantom simulation 219 23 Shielding application csocorsscececsrssssecesssssssesessssssssscsessesseseseseesseseeescesesees 221 Studying penetrati onie psani aeiae tai ete SE A 221 Acivahon studies eieaa rerea eE ATAOE AEA 222 Print channel by channel cross sections ss sesssssserstsssserstsssserttssseertesssees te 223 Counting hadronic cross sections ss se sessesrssrtttsetersttsssertttsstertessntentesstten tt 224 Make histograms of secondary particles from the neutron_hp or particle hp databas ss sninu cancun a ea 225 Print yields of production of secondary particles from charged particles traversing a thich material ss sssssssssessesssssisesseesesssesssnrensisnrsssenteseenee 226 24 Optimising the CPU time of your application ssessesseesssssosseseeosessessesscoseesee 229 Knowing where the time is spent s ss ssssssssesrssrsttssterstissserttnsstertesntentesseen te 229 Produc nonton RAA E E E E N 229 Killing particles of small energy se ss ssssssessssssssiesisstessssnsssenrinsessessseseeseesne 229 Killinepartid Snein a ra a E tbe S E EE sence 230 Optimising the particle generation sss ssessssssssierisst
353. r also in stantiates 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 exception After this command you have to add one or several particle sources there is no default 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 repeatedly 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 EN ERGY 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 If you are using optical photons as primary generator particles you may set t
354. r build simple phantoms with a few user commands 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 createMF Detector DoseDet patient gamos scoring addScorer2MFD DoseScorer GnG4PSDoseDeposit 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 the correct number of events when 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 Chapter 22 Radiotherapy application 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
355. r the pri mary 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 sec ondary kinetic energies SecoDividedInitialPrimKineticEnergy Fraction of kinetic energy of primary at PreStepPoint taken by a secondary particle SecoKineticEnergy Secondary particle kinetic energy InitialPrimSecoAngle Angle between secondary particle and Primary particle at PreStepPoint FinalPrimSecoAngle Angle between secondary particle and Primary particle at PostStepPoint InitialPrimKineticEnergy Primary particle PreStepPoint kinetic energy when a secondary particle is emitted FinalPrimKineticEnergy Primary particle PostStepPoint kinetic energy when a secondary 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 Initial Weight initial track weight Not available for Event nor Run FinalWeight final track weight Not a
356. rZOrigin stores the Z position of the origin of the track RTExtralnfoProviderZLast stores the Z position of the last interaction before reaching the phase space RTExtralnfoProviderZLastNoMaterial stores the Z position of the last interaction before reaching the phase space but you may define a list of materials that will not be taken into account by default this list is G4_AIR but it can be changed with the parameter gamos setParam RTExtraInfoProviderZLastNoMaterial Materials MATERIAL_1 MATERIAL 2 At the end of the job each of these extra information user actions fills a file ex plainning the information contained in each float By default this file is called RTExtralInfoProvider summ but the user may change the name of it with the pa rameter gamos setParam RTExtralnfoProviderFloat FileName FILE_NAME If you have written a phase space file in a 32 bit machine and try to read it ina 64 bit one you will not be able to recover the numbers properly You may avoid it with the parameterr gamos setParam IAEArecord ExtraLong Size 32 Similarly if you wrote the file in a 64 bit machine and try to read it in a 32 bit one Filtering and classifying on extra information It is possible to define a filter and a classifier see sections on Filters and Classifiers based on the long extra information The filter name is RTEILongFilter When it is defined it must receive as extra ar gument the list of extra info values that are accep
357. rameter gamos setParam GmGeometry UseMaterials FileName FILE_NAME The SHPlotPHPDBSpectraUA gt user action can make histograms with several en ergies at the same job The energies used in the histograms are defined by giving a minimum and a maximum energy and the number of energy steps gamos setParam USER_ACTION_NAME minE VALUE gamos setParam USER_ACTION_NAME maxE VALUE gamos setParam USER_ACTION_NAME nStepsE VALUE If you want that the steps are taken logarithmically you can set the parameter gamos set Param USER_ACTION_NAME logE 1 To make the histograms the energy and theta variables are sampled as GEANT4 would do it after reading the database The number of times the distributions are sampled is set with the parameter gamos set Param USER_ACTION_NAME NEvents VALUE Each of the histogram needs to have a well identified internal number This puts a limit to the number of materials 10 isotopes 50 and products 200 They may be changed by the parameters gamos set Param USER_ACTION_NAME MaterialIndexMax VALUE gamos setParam USER_ACTION_NAME IsotopeIndexMax VALUE gamos set Param USER_ACTION_NAME ProductIndexMax VALUE It is possible to discard products with high atomic number and mass but setting the maximum isotope number atomic number 1000 atomic mass for exam ple discard all isotopes higher than alphas by setting this number to 2004 This number is set with the parameter gamos setParam USER_ACTION_NAM
358. 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 TS M Events PRE 1 ALL 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 Chapter 12 Filters Introduction A filter is a class that receives a G4Step or a G4Track and accepts it or not depend ing 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 corre sponding to the G4Step If the AcceptTrack method is not implemented by a filter the
359. rbosity of the GAMOS data GmDistributionVerbosity controls the verbosity of the GAMOS distributions GmAnalysisVerbosity controls the verbosity of the analysis classes GmUtilsUAVerbosity controls the verbosity of the utility user actions DetVerbosity controls the verbosity of the Detector packages the base classes for PET SPECT and Compton Camera applications PETVerbosity controls the verbosity of the classes in the PET package If set if sets automatically the DetVerbosity SPECTVerbosity controls the verbosity of the classes in the SPECT package If set if sets automatically the DetVerbosity CCVerbosity controls the verbosity of the classes in the Compton Camera If set if sets automatically the DetVerbosity RTVerbosity controls the verbosity of the classes in the RadioTherapy package ShieldingVerbosity controls the verbosity of the classes in the RadioTherapy package 159 Chapter 16 Managing the verbosity You can set the verbosity of each of the GAMOS verbosity types with a simple command on your command input file for example 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 verbos
360. rchy are associated to the same trigger By default the trigger detector units are the same units explained in the section on Identifying each sensitive detector copy But you may change this behaviour by changing how many ancestors levels are used with the following parameter gamos setParam SD Trigger NAncestors S DTYPE VALUE This may serve you for example to define a unique global trigger by setting the number of ancestors equal to the maximum number of volumes in the geo metrical 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 measuringTime e Backwards Hits are accumulated if they have a time after 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 mea suring time in the case that you set the type of measuring to Interval the dead time starts also at the end of the measuring time but in this case it is the current triggering time plus 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 t
361. re 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 169 Chapter 17 Detector applications 170 To use this utility in 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 amp tee ot and look at the last lines of output those that contain the word FINAL like the following ones PARTICLE e FINAL 17 19 PARTICLE e FINAL 72 34185 PARTICLE gamma FINAL 72 34184 Chapter 18 PET application Before reading this chapter we recommend you to read the chapter on Detector that contains the utilities that are common to all detector applications The PET application contains two directories The first one PetGeometry con tains an utility to build a simple PET ring detector by just defining a few parame ters 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 source Detector PET GeometryData contains several examples of bui
362. reading of the file z 7 construct g4 geometry GmGeomTextLineProcessors tlproc new GmGeomTextLineProcessor G4tgrFileReaderx tfr G4tgrFileReader GetInstance tfr gt SetLineProcessor tlproc tfr gt ReadFiles fess ss s gt find 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 tgrVoltop 34 Chapter 3 Geometry 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 Inform G4tgbVolumeMgr to use your detector builder instead of the default one G4tgbVolumeMgrx volmgr G4tgbVolumeMgr GetInstance volmgr gt SetDetectorBuilder gtb A al Trigger the detector construction G4vPhysicalVolumex physiWorld
363. ribution 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 DISTRI BUTION_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 variable 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 column 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 order 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 value in t
364. rts 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 de scribed in the precedent section Number of 511 keV reconstructed 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 The energy of the 511 keV reconstructed hits PET RecHit energy keV The energy of the 511 keV reconstructed hits that are rejected because there are more than two PETEvtClass Extra PET RecHit energy keV Distance of closest approach between vertex and the line joining the two 511 keV reconstructed hits DCA PET dist line vertex mm 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 Phi coordinate if distance of closest approach between vertex and the line join ing the two 511 keV reconstructed hits DCA PET dist line vertex PHI mm Radial position in the XY plane of the primary positrons e position X Y mm 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 o
365. s 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 functional ity 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 and scorers together with classifiers is a powerful means to obtain very detailed information on the simulation through simple user com mands 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 control their behaviour To use these classifiers they have to be declared first with the following command gamos classifier CLASSIFIER NAME CLASSIFIER_CLASS PARAMETER_1 PARAMETER _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 pa rameters that the classifier needs Those classifiers that do not need any
366. s by listing the period durations starting at time 0 and for each one set if the source is on 1 or off 0 gamos setParam USER_ACTION_NAME Periods PERIOD_1 1 PERIOD_2 0 PERIOD_3 1 PERIOD_4 0 If the period pattern is complicated you may define them in a file name contain ing a line per period with the duration followed by 1 or 0 The periods file name is set with the parameters gamos set Param USER_ACTION_NAME PeriodsFileName FILE_NAME If no period is defined it will be assumed that the source is on all time Similarly if the sum of all the period durations is smaller than the time when you want the activity to be calculated it will be assumed that the during that time difference the source is on The output will be similar to the following one Z55555 SHActivationUA_inWindowEF BER_OF_EVENTS_PER_SECOND 6 25001le 12 le 0 Y 920809 7 dece U 55 55 SHActivationUA_inWindowF PERIODS 300 1 600 HActivationUA_inWindowEk IME 300 sec Sc43 0 0 ACTIVI 0 0 S H SHActivationUA_inWindowF IME 300 sec Sc44 ACTIVI SHActivationUA_inWindowF IME 300 sec V46 0 0 ACTIVI 55 5 SHActivationUA_inWindowF TIME 300 sec TOTAL ACTIVI Y 2189774 6 dec Y 2 2500023e 08 Y 0 HActivationUA_inWindowE IME 900 sec Sc43 0 0 ACTIVI Y 907243 47 dec ae oe oe NNN HActivationUA_inWindowE IME 900 sec Sc44 0 0 ACTIVI Y 2157807 2 dec
367. s its weight will be incremented by 1 SPLIT_VALUE You may activate the importance sampling for a list of particles with the com mand gamos physics V R importanceSampling NAME DISTRIBUTION_NAME PARTICLE_NAME_1 PARTICLE_NAME_2 where the NAME you give to the importance sampling will be later 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 parameters 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 parameter gamos setParam IMPORTANCE_SAMPLING_NAME SplitAtSeveralSteps Finally you may add one of more filters so that particles have to pass them before being split gamos setParam IMPORTANCE_SAMPLING_NAME Filters FILTER_1 FILTER_2 109 Chapter 9 Variance reduction techniques Geometrical biasing Many types of geometrical biasing ca
368. s not contain datacards as in a MCNP one but line commands This means that each line read will traslate into a command that is executed by GAMOS There is no restriction on the length of variables nor the number of columns of a line and very few about the order of these commands GEANT4 is a state machine what means that the list of available commands depends on the state it is in The main states are those that may be called pre initialization and post initialization In practical terms this only means that some commands have to be placed before the run initialize command and some after and for some others the order does not matter The last commands is the one that starts the run i e the creation and further transportation of particles This command is run beamOn NEV where NEV is the number of histories events in GEANT4 terminology that will be run The behaviour of many GAMOS algorithms may be changed by parameters you will see through these examples many commands starting with gamos setParam You always have to remember that a line command setting the value of a parameter has always to appear before the line command that is going to use it else the algorithm will use the default value of the parameter In any GEANT4 job it is mandatory to define the geometry physics and source primary generator in GEANT4 terminology The other mandatory commands are run initialize and run beamOn Then a minimal script could be the following
369. s sDTYPE VALUE The divisions start at the negative wall of the box that is selected as sensitive volume that is the offsets are the half lenghts of the box You may change these offsets with the parameter gamos setParam SD VirtSegmBox Offset SDTYPE OFFSET_X OFSET_Y OFFSET_Z If the offsets are not set thay are calculated at each track step as it may happen that different volumes are assigned to the same sensitive detector type If 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 SDTY PE TRUE 79 Chapter 7 Sensitive Detector and Hits To attach aGAMOS sensitive detector to a logical volume in your geometry you have to use the command gamos SD assocSD2LogVol 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 sensitive detectors so that you can later apply different properties to them e g different energy resolutions The LOGICAL_VOLUME_NAME is the name of the G4LogicalVolume in your geometry that you want to make sensitive You may repeat 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
370. s userAction GmStepDataBinFileuUA 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 Cout These data users i e GmStepDataCoutuA GmTrackDataCoutuA GmSec ondaryTrackDataCoutuA GmStackDataCoutuA GmEventDataCoutuA GmRun DataCoutUA dump the data values into the standard output they may be helpful to debug an application together 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 Sep arated 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 set Param 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 119 Cha
371. sCore 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 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 num ber 3 40282e 38 and as a double the number 1 79769e 308 You should check Chapter 11 Analysis extracting data that you read b
372. 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 length 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 Chapter 3 Geometry TRAP generic trapezoid Half length along the z axis pDz Polar angle of the line joining the centres of the faces at pDz e 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 e 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 e Angle with respect to the y axis from the centre of the side at y pDy2 to the centre at y pDy2 of the
373. set the parameter gamos setParam USER_ACTION_NAME Onlylons 1 Make histograms of secondary particles from the neutron_hp or particle_hp databases The user action gamos userAction SHPlotPHPDBSpectrauA serves to print the energy and theta angle spectra of secondary particles as read from the nuclear databases This means that the energy and theta angle are taken directly from the database without applying thermal or Lorentz boost corrections As this user action invokes the GEANT4 internal methods there is no need to simulate an event Nevertheless to profit from the GAMOS utilities you should set up an input file similar to other GAMOS input files You can see an example on the use of this utility at MY_GAMOS_DIR tutorials S HieldingTutorial exercise5 exercise5c in This example plots the energy and angle spectra from all the secondary particles that would be created at the collison of neutrons as given by the neutron_hp or particle_hp GEANT4 package for several energies in several materials The 225 Chapter 23 Shielding application first thing it does is to replace the geometry GmGeometryFromText by GmGeome tryUseMaterials This geometry class will generate a world for each of the materi als given by the parameter gamos set Param GmGeometryUseMaterials Materials MATE_1 MATE_2 If any of the materials is not aGEANT4 one you will need a geometry file where the material is defined The name of this file is given with the pa
374. 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 209 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 extends 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 auto matic definition of limits You may simply
375. 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 Analysing your histograms with ROOT 112 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 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 Chapter 10 Histogramming 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 ROOTUtilities 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 grap
376. sics 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 wider than the phantom To apply it you should select the following physics list gamos physics GmEMPS Physics and the physics options gamos GmPhysics addPhysics 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
377. sses 185 21 Image reconstruction utilitieS essessessesseeseessessesscoscoseeseessossosncoreosessesseoscoseesee 187 List mode to projection data Im2pd ss sss1ssrsssrrtssssrstsssserttssssesttssntestesssees te 187 Summing projection data files sumProjdata c cccccetesestetescststeesesteteseeeenenens 187 Analytic image reconstruction ssrb_fbp s ssssssessssessisssessesseerisissesssssseseeee 188 VisualizaHorn tools en meae E e eaa ASEET base EN eE A hoe hese es 188 Stochastic Image Ensemble method sn sssssssssesrtssserstssssettssstenttssneentesssern te 189 TALEO UI CHO ss a ae a a aud Aa a e A aa 189 Getting Started ssssnineu kienean oaia 190 Program Parameters and Flags ss ssessessississeeseessessesrirsessessseseeseeeee 192 PTIALY SIS oera e eee EEE E a E T E E 194 vi 22 Radiotherapy application ccccsserecsrsrersresssssssssessssssssscsssssesesessesseseesssesseees 195 Geometrical MOMUIES ccecessessccessssscssesssccccesssesscssusescescessesesensussssessususess 195 JAWS module tcc sccssdscccgcacadeeceesccetucecosdeacedcatae becgudbadonatsntsestessosdeacauecataedecds 195 ME Crm Od tiles semte steel tase ohn Gree ie hie T EE A na 195 Using phase spaces caite isi t diate ina ae Ran EEE E a aR EA EEEE A REA AR 202 Writing phase Spates ien piesei enke eras PSE Ea Ao oaa Ea a tka e 202 Phas space text Mle si senmano wah Seas a E 203 Phase space histOgrams ccccccce eimi a eiii 2
378. ssification 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 GmClassifierByIn teraction to classify it based on the type and number of interactions The method Classify of this class returns an integer with the meaning 100 100 Number of LowEnPhotoElec interactions 100 Number of LowEnCompton interactions Num ber 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 lat
379. st c cesses sess nsseseseseesesescsseesneeesees 64 Other PHYSics lists resini pi sR aa re eaaa E EAE A E RARR En 64 Optical Photons s cuic catenin anishecs devil ah EE NAS 65 Using optical photons as primary generator cece cceeesteteeeeees 68 X tay refractions stnran SA aE aea e eea eaeoe SETE EYEE Oa aeska aeei NA 68 Cotllomb scattering aneen eher no iii oa o aaa 69 Atomic deexcitation Processes ccccccseeseesssssseeseessesescssesesescssenseecssees 69 Decay PLOCeSS iavisicssstensicdceadriemiattrmnin Siero utndadieme entation 69 Radioactive Aecay PLrOcess isian noesa ere E E EE E E EREE EEEn 70 Cerenkov processing e a a e a E aE 70 Coulomb Scattering srie i eaei e E r a E NEEE isa Eei eiat 70 Nuclear processes of electromagnetic Particles s sssssessssstsrtsrsssrtetsttsrterstes 70 Replacing process MOdelS cccccccce ees sseseseesessssseseesssesescsesesesescsseeseesesenes 71 Replacing a set process models ccsccccsesteteseeeesesesteneteseeceeesesesneneneeees 71 Replacing one process MOCel cccccceesesteteseecesescsnsteeseececesssesneeneeeees 71 Removing a process from a physics list c cccscsccsssseseseeseseseeneeseseeneeseeenes 72 PHOGU CEO CUES es cco ieena r a a a cates dosu eee e a 72 Production cuts by TeGioN c s e essissseseeiat evesniteteeiesteemeis sores nee 73 Energy cuts to range cuts CONVELFSION ccececesessteteseseeeseseseseseseeeeees 73 Minimum and maximum production
380. st 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 con tain 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 dif ferent 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 con tain 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 Making histograms out of a sqdose file You can make histograms out of dose information contained in a sqdose file by ru
381. stosUA AlgorithmVariables VARI VAR2 VARN where the variables can be Energy XPos YPos ZPos XYPos XZPos YZPos or XYZPos At the same time that the histograms about gamma interaction data they are filled also histograms about the reconstructed hits that are associated to each in teraction 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 histograms 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 en ergy bins for different position variables The histograms are about the distance
382. stributed in a different manner than the total dose introduc ing 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 RTP SPDoseHistos 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 histograms 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 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 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 whe
383. t you may use the parameter gamos setParam SOURCE_NAME MaxBiasIterations VALUE Building your generator with C 58 You can build your generator by writing your C class inheriting from G4VUserPrimaryGeneratorAction see example in 9 After that you have to transform it into a GAMOS plug in To learn how to do this see the instructions in the section Creating your plug in using the GmGener atorFactory or see the example examples N02 Chapter 4 Generator Using ions Notes 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 it self 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 parti cle 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 w
384. t 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 RT CutsStudyFilter 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 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 FINAL like the following ones PARTICLE e FINAL 17 19 PARTICLE e FINAL 72 34185 PARTICLE gamma FINAL 72 34184 217 Chapter 22 Radiotherapy application 218 Automatic determination of production cuts for a dose in a phantom simulation The use of production cuts in a dose computation may introduce
385. t may leave several hits in dif ferent detector elements GAMOS offers several algorithms to identify which of the hits corresponds to the first gamma interaction so that the line to the origin of the positron annihilation can be properly reconstructed This is specially use ful 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 likely the one that is based on the energy of the hits The following algorithms are currently available DetistHitByEnergy Classifies the reconstructed hits in order of decreasing en ergy and selects the first one as the one corresponding to the 1st Compton inter action A parameter can be used to select instead the second third highest energy hit gamos setParam Det1stHitByEnergy Order ORDER DetistHitByXYPos 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 increasing 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 Det1stHitByX Y Pos Order ORDER DetistHitByX Pos If the detector is a block and the gamma travels preferential lly increas
386. tParam 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 103 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 detector By default the filter will act on the G4Track but it may act on the G4Step if the following parameter is set gamos set Param GmPDS FiltersOnTrack 0 Scoring per category The scoring of flux and equivalent dose can be split
387. tains a list for all events with the final posi tions 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 posi tions 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 the 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 distribu tion on the entire LOR where the sigma corresponds to 16 of the LOR length and the 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 Chapter 21 Image reconstruction utilities Input Data The input parameters are set in the parameter file ir_soe_userparameters conf DataFileName 0 CCS_Machiel CC_img out_Gamma511_2 EventSetSize 0
388. ted gamos filter MY FILTER RTEILongFilter VALUE_1 VALUE_2 The classifier is named RTClassifierByEILong It will read the names of the indices of the extra long information from a file named RTExtraInfoProvider summ The name of this file can be changed with the parameter gamos set Param CLASSIFIER_NAME FileName VALUE 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 207 Chapter 22 Radiotherapy application of reusing 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 set Param RTReuseAtZPlane N Reuse 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
389. tensesresssenteseesee 239 Sending several jobs in the same machine 0 0 0 cece cenetesesesteeseeeeenens 239 Identifying touchabl si ns sirier sia sioni eiaa iiaa 241 Using asterisks to get volume particle and material names 05 241 Using particl names 1 2 c cccetcn iE a Ea atten dives RE 242 27 Appendix B Extending GAMOS functionality with C utilities 245 Converting a Geant4 example into a GAMOS example ccccceeee 245 Creating your pli g inh scciccccec seseucstesseenctuscesvsessatagstsesestacusseuesensnssosoedvadsoveee sedan 246 Using a parameter in your C code wees cesesseeesenssesesceeseesesseseeeees 247 Event classification by interaction tyPes cccccccssessetetesceneesesesneeseseenenees 248 Strictire OF GAM OS aE E a ctssbescouethests eis a anat 248 Bibliography eran seese teresa iae aere aaaeeeaeo asie eron SEEE EAE Taone SeS San eiT 251 Chapter 1 Introduction About this document This manual refers to GAMOS version 5 0 0 It is written in DocBook and it is maintained at the following address http fismed ciemat es GAMOS GAMOS_doc GAMOS 5 0 0 GamosUsersGuide_V5 0 0 pdf We will use through this manual many terms common to the Monte Carlo simu lation 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
390. the list of energies that you will use to assign the different properties to the table MATEPT_ADD_ENERGIES e Material properties table name 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 Chapter 5 Physics 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 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 e Surface finish type It can be e polishedfrontpainted e polishedbackpainted e ground e groundfrontpainted groundbackpainted e polishedlumirrorair polishedlumirrorglue e polishedair polishedteflonair polishedtioair polishedtyvekair e polishedvm2000air e polishedvm2000glue e etchedlumirrorair e etchedlumirrorglue e etchedair e etchedteflonair e etchedtioair e etchedtyvekair e etchedvm2000air e etchedvm2000glue 67 Chapter 5 Physics 68 e groundlumirrorair e groundlumirrorglue e groundair e groundteflonair e groundtioair e groundtyvekair e groundvm2000air e groundvm2000glue Surface type It can be e dielectric_metal e dielectric_dielectric
391. 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 GmKineticEnergyFilter accepts a track if its kinetic energy is between the two values given as extra parameters including the two values For steps it con siders 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 en ergy 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 values given by the two extra parameters including the two values It does not implement the AcceptTrack method GmInitialRangeFilter accepts a track if its range at creation is between the two values given as extra parameters including the two values GmkRangeFilter accepts a track if the range is between the values given b
392. 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 You may use as LOGICAL_VOLUME_NAME s an asterisk meaning that all volumes will be included Something important to take into account is that this list of volumes will only include those found in the geometry This means that if you want to do a cell tally F4 in a given cell you have to define a GAMOS volume equivalent to it in your geometry see the simple example above and if you are using a surface tally F1 or F2 you have to be sure that all the cells that traverse a track before reaching the surface are defined as GAMOS volumes Remember as explained in the section about geometry that volume names should be called cell_N where N is the number of the MCNP cell After selecting the volumes to score it is necessary to define a scorer 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 Chapter 25 Extracting detailed information from a MCNP run multifunctional detectors created above and SCORER_PARAMETERS are the optional parameters a scorer may need see section on Scorers for the description of the scor
393. tialDeltaX SpatialDeltaY and SpatialDeltaZ parameters set the Uni formly distributed variation in x y and z coordinates of the detector hits used to recover for resolution loss due to spatial resolution 193 Chapter 21 Image reconstruction utilities 194 The UseDopplerEffectSigmaTheta parameter sets the Gaussian distributed varia tion 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 xtralIterInfo additional output files for intermediate it SOE_ImageRecon averageStatesOut additional output each 100 iterations bef SOE_ImageRecon readDensityMatrix read density matrix in_density_matrix i 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
394. ticle code following the Particle Data Group number ing 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 Type Subtype gamma gamma photon e lepton e e lepton e proton baryon nucleon neutron baryon nucleon 130 Chapter 11 Analysis extracting data G4Particle Type Subtype 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 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_Bs0 meson Bs anti_DO 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 131 Chapter 11 Analysis
395. to each copy of your sensitive detectors each G4VTouchable in Geant4 terminology GAMOS does this automatically for you If you use the GmSDSim ple 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 85 Chapter 7 Sensitive Detector and Hits You can change the number of ancestor volumes to build the detector unit ID with the parameter gamos setParam SD DetUnitID NAncestors SsDTYPE VALUE 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 The ID is made multiplying the copy number of each ancestor by a fixed value NShift to the power of the ancestor level minus 1 ID copyNo_1 copyNo_2 NShift copyNo_3 pow NShift 2 You can change the value of the NShift that multiplies each ancestor copy number using the parameter gamos setParam SD DetUnitID NShift SsDTYPE VALUE that takes a default value of 100 Storing and retrieving hits 86 GAMOS provides you with the option of storing in a file the hits produced dur ing a run and reading them back in another run Creating hits from track in the sensitive detector or reading them from a file will produce the same in memory representation therefore you can apply any of the above described effects and produce any histogr
396. togram ccccc eee cseseseesenesesescsesesesesesseeseecees 113 11 Analysis extracting data sisisi seneese eeii eier saes 115 Introduction GAMOS data ccccccccccsessecessssesssssssssseseessceeessessseesesesseeeeess 115 Data tiSers se en E e a EE e E N A N 116 Behaviour as a function of information object ccccecceeeeteteseees 116 Behaviour as a function of output format ssssesssssssestsssserteesseesteese 117 Selection of data list for a data user c ccccccesececcsseesseceesseeseeesesseeeeees 119 Saving GAMOS data in a ROOT TTree s ssssssssssssestssssertttssserttssstesteese 122 Filter from Calta serio 2008 cis Boss tra view Sethe WSL ea eee a 123 Classifier Dy atta s ic0ceetleccearecssccovatescedevtatacten ei e ee o E aE 123 Primitive scorer from data asss erse nee a ES AR 124 Listof available datane o nase ae ae E E A EER A E a tat 124 JOSTE n10 a KEE REE EEE S AEE E AEE OS te Ss A AAEE 124 DireCt On ie ea A A E a EE ANE a be E 126 MO TE a abt a a EAE EENE EE AEE E E E ASTA 127 ENCES E E ET A EEE E E 128 Gedmetrical Objects misrin e a arar E Ai 129 Mat rial Varialll 6S scicsecesctsesoesds a tsccduenes ae n a S No 129 Particle arid process riip aasa a ea ae Rie ea E RE aE etaa 130 Secondary HACKS so cogieron iE o nE g EEEE 133 Others ian eih reo E EE dest RE N a a a a es 133 Output filenames sisaning doc ccusettepenculatdedetesandcvctevinsscobesstsheocsbeties 134 Merging results from different jobs
397. tor read from an input file These factors are by default the ICRU report 57 and they are read from the file MY_GAMOS_DIR data Flux2Dose gamma ICRU57 lis You may change the input file with the paremeter gamos setParam GmDatalInitialGammaEquivalentDose Flux2DoseFileName NEW_FILE_ NAME You may select to calculate the personale equivalent dose AccumulatedKerma You may select the magnitude to use H 10 default Hp 10 0 Hp 10 15 HAp 10 30 Hp 10 45 Hp 10 60 Hp 10 75 with the parameter gamos setParam GmDataInitialGammaEquivalent Dose EquivDoseType TY PE where TYPE may be Hstar Hp0 Hp15 Hp30 Hp45 Hp60 H75 FinalGammaEquivalentDose Similar as above InitialNeutronEquivalentDose Calculates the equivalent dose multiplying the volume flux step length divided by cubic volue by flux to equivalent dose conversion factor read from an input file These factors are by default the ICRU report 57 and they are read from the file MY_GAMOS_DIR data Flux2Dose neutron ICRU57 lis You may select the magnitude to use H 10 default Hp 10 0 Hp 10 15 Hp 10 30 Hp 10 45 Hp 10 60 Hp 10 75 with the parameter gamos set Param GmDatalInitial NeutronEquivalentDose EquivDoseType TY PE where TYPE may be Hstar Hp0 Hp15 Hp30 Hp45 Hp60 H75 FinalNeutronEquivalentDose Similar as above Geometrical objects These are string data that extract the name of different geometrical objects and also the type of solids Box Tubs Polycon
398. ts 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 isotope 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 distri bution 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 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
399. tus For the data of type Initial the data is ex tracted from the vertex information of the G4Track object For the data of type Accumulated these data users implement a UserSteppingAction method which Chapter 11 Analysis extracting data accumulates the data at each track step and a PreUserTrackingAction which initializes the data to 0 the PostUserTrackingAction uses the accumulated data instead of extracting the data from the G4Track object The SecondaryTrack data users implement a UserSteppingAction method which extracts the data at each track step from the G4Track object of all secondary tracks created in the step When setting filters or classifiers to one of these data users you have to remember that they are applied by default to the primary tracks if you want to applied them to the secondary tracks you have to explic itly do it see sections on Filters and Classifiers The Stack data users implement a ClassifyNewTrack method which extracts the data when the tracks are taken from the stack 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 data users implement a UserSteppingAction method which accumulates the data at each track step and a BeginOfEvent
400. ty of typing make at the top most directory to trigger the compilation of all the di rectories 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 here 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 Chapter 2 Getting started Notes 10 You only have to change the line starting by SUBDIRS to list the name of your subdirectories 1 2 You may type for example locate libXmu so to know where they are in they are not in the mentioned directories 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 installed ie MY_INSTALLATION_DIR GAMOS 5 0 0 For the external packages the set of libraries is fixed and defined in the con figuration files 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 t
401. u 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 setParam GmGeneratorChangeEnergyAndMaterial VolumesToChange VOLUME_1 VOLUME_2 Event generator histograms These are histograms of event generator particles that may serve to check that you have actually generated what you 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 particle 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
402. ugh 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 ax ial direction so that a full body system can be simulated The following parameters are used 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 181 Chapter 20 Compton camera application 182 NABSCRYSTALS_axial Number of crystals in each block axial 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 de tectors parallel to each other The stack is produced through the
403. ume and InitialPhysicalVolume FinalTouchable and Ini tialTouchable etc But this is not enforced so that you may find another use for this distribution If your geometry is complicated it may happen that at some place there is a fron tier between two volumes with too different weights so that if a track traverses this frontier it gets a too high index To avoid this you may set a maximum value of the index with the parameter gamos setParam DISTRIBUTION_NAME Max Value VALUE Another trick to give more flexibility to your biasing is to avoid that a tracks receives a weight given by this distribution several times Ratio of distributions You may define a distribution whose value is defined as the raio of two distribu tion values The distribution class is named GmDistributionRatio The two distri butions has to be defined with the parameters gamos setParam DISTRIBUTION_NAME DistributionPre DISTRIBUTION gamos setParam DISTRIBUTION_NAME DistributionPost DISTRIBUTION 151 Chapter 14 Distributions 152 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 t
404. ut them In case of positive answer GAMOS will be installed without OpenGLxX 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 histograms ROOT has some extra checks for libraries namely libXpm so libXft so and libXi so so you also have to install them After all the code is compiled follow the instructions on how to run an example If the installation fails you can find the cause of it in the file install log at the directory where you tried to do the installation Look for the first occurrence of the characters error with a blank space first as several class name have these characters It is likely that the error is due to the fact that you are using a ROOT version not compatible with your system If this is the case try to find a new version number at the ROOT web page htt root cern ch and change it at the file installGamosBaseDefs sh that you will find at the scripts directory Use an older version if you think your operative system is old and a new version if you think it is old If you still are not able to install successfully GAMOS please open a report at the GAMOS Users Forum https groups google com forum forum gamos_users and attach the install log file compress it first Tips for installation
405. vailable 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 133 Chapter 11 Analysis extracting data NofSecondaries number of secondary tracks produced Only available for Step and Track SumSecoKineticEnergy sum of the kinetic energies of all secondary particles produced Only available for Step and Track InitialTime initial global time FinalTime final global time InitialLocalTime initial local time FinalLocalTime initial local time InitialProperTime initial proper time FinalProperTime final proper time 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 setParam FILE_NAME FileName NEW_FILE_NAME If you are running a job and you want to identify all your output 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
406. verflow 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 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 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 81 111 Chapter 10 Histogramming 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 H
407. which all values should be given Classifiying on secondary data As mentioned above the classifiers take the data to be classified from a G4Step ora G4Track But when a classifier is used by GmSecondaryTrackHistosUA see chapter on Analysis it may be useful that the classification is based on the data of the secondary particles created in the step To get this behaviour it should be used the paramter gamos set Param CLASSIFIER_NAME OnSecondary 1 147 Chapter 13 Classifiers 145 Chapter 14 Distributions Introduction The GAMOS distribution classes represent one dimensional functions which assing an output value for 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 e To bias a primary generator distribution In this case the output values repre sent 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 de fined 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 ByDist
408. wing information e Event ID e Sensitive detector type Chapter 7 Sensitive Detector and Hits e Detector unit ID Energy MeV e Minimum time ns e 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 One line per track with track ID The binary file contains the same information in the following format e Event ID float e 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 e Detector unit ID unsigned long long e Energy MeV float e Minimum time ns unsigned long long e Maximum time ns unsigned long long Position X mm float Position Y mm float Position Z mm float e Number of original tracks unsigned int One line per original track with track ID unsigned int e Number of tracks unsigned int One line per track with track ID unsigned int Storing reconstructed hits It is also possible to store the reconstructed hits by instantiating the user action gamos userAction GmRecHitsWriteUA The parameter gamos setParam SD GmRecHitsWriteUA BinFile 0 1 serves to select between binary default or text format The text file contains a line for each hit with the following information e Gamos RecHit energy Energy MeV e time_min Minimum time ns e time_max Maximum t
409. with the same user command gamos userAction USER_ACTION_NAME Adding a filter One or several filters can be added 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 action 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 PreUser TrackingAction and PostUserTrackingAction for tracking actions and ClassifyNew Track 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 GmTrackDataHistosuA 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 filters in the order whi
410. xplained in the sub chapter Identifying each sensitive detector copy GmSDSimpleExactPos It is similar to GnSDSimple but the hits position is the centroid of the energy depositions of the different tracks that produced it weighted by their energy GmSDOpticalPhoton This class inherits from GmSDSimple but only produces hits if the process that defined the step is OpAbsorption 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 SDTYPE NDIV_X NDIV_Y NDIV_Z where SDTYPE is the type of the sensitive detector Widths of the voxels in X Y and Z gamos setParam SD VirtSegmBox Width sDTYPE 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 MaxNVoxel
411. xplicitly 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 the cuts for gamma electrons and positrons the cut for positron is optional if not set it will take the one for electrons 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 instruc tions 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 si
412. y has no sense to calcualte the flux entering and exiting voxels Please contact the GAMOS team if ou think you need this feature Chapter 8 Scoring Filter classes See section on Filters Scorer printers 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 men tioned above several printers can be associated to the same scorer To associate a printer to an scorer you can use the command mentioned above gamos scoring addPrinter2 Scorer 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 MultiFunctionalDet Detector name PrimitiveScorer Scorer name Number of entries Number of scores For each per score one line with index IndexName Score value REL Relative score error er ror value sumV2 Square of score values This last value is needed instead of the error for properly taking into ac
413. y 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 GmPositionXFilter accepts a track if the final X position is between the values given by the two extra parameters GmPositionPreX Filter accepts a track if the initial X position is between the val ues given by the two extra parameters GmPositionY Filter accepts a track if the final Y position is between the values given by the two extra parameters GmPositionPreY Filter accepts a track if the initial Y position is between the val ues given by the two extra parameters GmPositionZFilter accepts a track if the final Z position is between the values given by the two extra parameters GmPositionPreZFilter accepts a track if the initial Z position is between the val ues given by the two extra parameters GmDirectionPhiFilter accepts a track if the final phi direction is between the values given by the two extra parameters GmDirectionPrePhiFilter accepts a track if the initial phi direction is between the values given by the two extra parameters GmDirectionThetaFilter accepts a track if the final phi direction is between the values given by the two extra parameters Chapter 12 Filters GmDirectionPreThetaFilter accepts a track if the initial phi direction is between the values given by the two extra parameters

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