[gate-users] Re: gate-users Digest, Vol 16, Issue 26
Christian Wietholt
cwietholt at nhri.org.tw
Wed Aug 3 03:16:55 CEST 2005
Dear Sebastien,
I am sorry for the very late reply, but there were some deadlines coming up, and I also wanted to make sure that everything is in order with my installation. I have the software recompiled, and made sure that I have the correct versions of LMF, GEANT, GATE, ROOT and CLHEP installed. Currently, I am still using the 1.2.0 version of gate, and I compiled everything using gcc 3.4. I am running the latest Debian stable. Today I will try Fedora Core 3. I also put my macro into the framework that you provided in your examples that were supplied with GATE.
I hope I understood your question correctly: I ran my simulation with 0mm and 10mm spblurring, nothing else changed. After each simulation, I moved the ouput files into a different directory, just to make sure that there are no conflicts. I opened the gateSingles.dat file in openoffice.org and computed the stdev, var, and averages of columns 4, 5, 6, 15, 16, 17. I found no differences between 0mm and 10mm spblurring.
I am looking forward to reading from you and would greatly appreciate any help you can provide.
Best Regards,
Christian
gate-users at lphe1pet1.epfl.ch schrieb am 25.07.05 14:22:03:
>
>
> Send gate-users mailing list submissions to
> gate-users at lphe1pet1.epfl.ch
>
> To subscribe or unsubscribe via the World Wide Web, visit
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>
> Please use the GATE's site webmaster e-mail to reach the person
> managing the list.
>
>
> Today's Topics:
>
> 1. Re: gate-users Digest, Vol 16, Issue 25 (Christian Wietholt)
> 2. Re: Re: gate-users Digest, Vol 16, Issue 25 (Sebastien JAN)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 25 Jul 2005 19:01:34 +0800
> From: Christian Wietholt <cwietholt at nhri.org.tw>
> Subject: [gate-users] Re: gate-users Digest, Vol 16, Issue 25
> To: gate-users at lphe1pet1.epfl.ch
> Message-ID: <200507251901.34310.cwietholt at nhri.org.tw>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Sebastien,
>
> Thank you so much for your reply and offering your help. I still could not
> figure out how to get the digitizer blurring to work. I am already wondering
> if the digitizer blurring is enabled in the interfile output function, or
> wether I will have to use the singles.dat file and the supplied C programs to
> generate the correct projection images.
>
> Please find attached to this email my most current version of the macro file.
>
> Thanks again,
>
> Christian
>
>
>
> On Monday 25 July 2005 18:02, gate-users-request at lphe1pet1.epfl.ch wrote:
> > Send gate-users mailing list submissions to
> > gate-users at lphe1pet1.epfl.ch
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >
> > Please use the GATE's site webmaster e-mail to reach the person
> > managing the list.
> >
> >
> > Today's Topics:
> >
> > 1. Re: SPblurring (Sebastien JAN)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 25 Jul 2005 11:39:55 +0200
> > From: Sebastien JAN <jan at shfj.cea.fr>
> > Subject: Re: [gate-users] SPblurring
> > To: GATE feedback and helpline for Users
> > <gate-users at lphe1pet1.epfl.ch>
> > Message-ID: <42E4B36B.3080306 at shfj.cea.fr>
> > Content-Type: text/plain; charset=iso-8859-1; format=flowed
> >
> > Hi ,
> >
> > Can you send me your macro please ?
> >
> > seb
> >
> > Christian Wietholt a écrit:
> > > Dear Gate Users,
> > >
> > > After I submitted my question about SPblurring, I realized that
> > > I should first initialize and then set up the detector. I did so, and
> > > the Gate ouput on the command shell was completely different,
> > > but still no detector spatial blurr in the projection images. What
> > > am I doing wrong? Anybody has a suggestion what I could try
> > > next?
> > >
> > > Christian
> > > _______________________________________________
> > > gate-users mailing list
> > > gate-users at lphe1pet1.epfl.ch
> > > http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >
> > ------------------------------
> >
> > _______________________________________________
> > gate-users mailing list
> > gate-users at lphe1pet1.epfl.ch
> > http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >
> > End of gate-users Digest, Vol 16, Issue 25
> > ******************************************
> -------------- next part --------------
> #############################################
> # V I S U A L I S A T I O N
> /control/execute visu.mac
>
> /tracking/storeTrajectory 1
> /gate/geometry/enableAutoUpdate
>
> #############################################
> # V E R B O S I T Y
> /gate/output/verbose 2
>
> #############################################
> # W O R L D
> # Define the world dimensions
> /gate/world/geometry/setXLength 1000 mm
> /gate/world/geometry/setYLength 1000 mm
> /gate/world/geometry/setZLength 1000 mm
>
> #############################################
> # S C A N N E R H E A D
> # Create a new box representing the main
> # head-volume SPECThead is the name of the
> # predefined SPECT system Create the SPECT
> # system, which will yield an Interfile output
> # of projection data
> /gate/world/daughters/name SPECThead
> /gate/world/daughters/insert box
>
> # Define the dimensions of the main volume
> /gate/SPECThead/geometry/setXLength 300. mm
> /gate/SPECThead/geometry/setYLength 300. mm
> /gate/SPECThead/geometry/setZLength 300. mm
>
> # Define the position of the main volume
> # Move the head 9 cm away from the Z axis,
> # which is the rotation axis and the
> # replication axis
> /gate/SPECThead/placement/setTranslation 200. 0. 0. mm
>
> # Set the material associated with the main volume
> /gate/SPECThead/setMaterial Air
> /gate/SPECThead/attachPhantomSD
>
> # Define the rotation speed of the head
> # Define the orbiting around the Z axis
> /gate/SPECThead/moves/insert orbiting
> /gate/SPECThead/orbiting/setSpeed 0.5625 deg/s
> /gate/SPECThead/orbiting/setPoint1 0. 0. 0. mm
> /gate/SPECThead/orbiting/setPoint2 0. 0. 1. mm
>
> # Define some visualisation options
> /gate/SPECThead/vis/forceWireframe
>
> # Shielding
> # Create the shielding volume
> /gate/SPECThead/daughters/name shielding
> /gate/SPECThead/daughters/insert box
>
> # Define the dimensions of the shielding volume
> /gate/shielding/geometry/setXLength 300. mm
> /gate/shielding/geometry/setYLength 300. mm
> /gate/shielding/geometry/setZLength 300. mm
>
> # Define the position of the shielding volume
> /gate/shielding/placement/setTranslation 0. 0. 0. mm
>
> # Set the material corresponding to the
> # shielding volume
> /gate/shielding/setMaterial Lead
>
> # Define some visualisation options
> /gate/shielding/vis/setColor red
> /gate/shielding/vis/forceWireframe
>
> # Attach phantom SD to record Compton
> # interactions in the shielding volume
> # Needed to discriminate between scattered
> # and unscattered photons
> /gate/shielding/attachPhantomSD
>
>
> #############################################
> # C O L L I M A T O R
> # Create a full volume defining the shape
> # of the collimator
> /gate/SPECThead/daughters/name collimator
> /gate/SPECThead/daughters/insert box
>
> /gate/collimator/geometry/setXLength 20. mm
> /gate/collimator/geometry/setYLength 300. mm
> /gate/collimator/geometry/setZLength 300. mm
>
> /gate/collimator/setMaterial Lead
> /gate/collimator/placement/setTranslation -140. 0. 0. mm
>
> /gate/collimator/vis/forceWireframe
> /gate/collimator/vis/setColor red
>
> # Attach PhantomSD to record Compton
> # interactions in the collimator volume
> /gate/collimator/attachPhantomSD
>
> #############################################
> # P I N H O L E
> # Insert the pinhole in the collimator
> /gate/collimator/daughters/name hole
> /gate/collimator/daughters/insert cylinder
> /gate/hole/geometry/setHeight 20. mm
> /gate/hole/geometry/setRmax 2.5 mm
> /gate/hole/placement/alignToX
> /gate/hole/setMaterial Air
> /gate/hole/vis/forceSolid
>
> /gate/collimator/daughters/name cone1
> /gate/collimator/daughters/insert cone
> #/gate/cone1/geometry/setHeight 7.5 mm
> /gate/cone1/geometry/setHeight 9 mm
> /gate/cone1/geometry/setRmax1 10. mm
> /gate/cone1/geometry/setRmax2 2.5 mm
> #/gate/cone1/placement/setTranslation -6.25 0 0 mm
> /gate/cone1/placement/setTranslation -5.5 0 0 mm
> /gate/cone1/placement/alignToX
> /gate/cone1/setMaterial Air
> /gate/cone1/vis/forceSolid
>
> /gate/collimator/daughters/name cone2
> /gate/collimator/daughters/insert cone
> #/gate/cone2/geometry/setHeight 7.5 mm
> /gate/cone2/geometry/setHeight 9 mm
> /gate/cone2/geometry/setRmax1 2.5 mm
> /gate/cone2/geometry/setRmax2 10. mm
> #/gate/cone2/placement/setTranslation 6.25 0 0 mm
> /gate/cone2/placement/setTranslation 5.5 0 0 mm
> /gate/cone2/placement/alignToX
> /gate/cone2/setMaterial Air
> /gate/cone2/vis/forceSolid
>
> ############################################
> # C A M H E A D A I R
> # insert air behind the collimator
> /gate/SPECThead/daughters/name aircomp
> /gate/SPECThead/daughters/insert box
> /gate/aircomp/geometry/setXLength 170 mm
> /gate/aircomp/geometry/setYLength 260 mm
> /gate/aircomp/geometry/setZLength 260 mm
> /gate/aircomp/placement/setTranslation -45 0 0 mm
> /gate/aircomp/vis/forceWireframe
>
> ############################################
> # C R Y S T A L
> # Create the crystal volume
> /gate/SPECThead/daughters/name crystal
> /gate/SPECThead/daughters/insert box
>
> # Define the dimensions of the crystal volume
> /gate/crystal/geometry/setXLength 6. mm
> /gate/crystal/geometry/setYLength 260. mm
> /gate/crystal/geometry/setZLength 260. mm
>
> # Define the position of the crystal volume
> /gate/crystal/placement/setTranslation 43. 0. 0. mm
>
> # Set the material associated with the crystal
> # volume
> /gate/crystal/setMaterial NaI
>
> # Define some visualisation options
> /gate/crystal/vis/setColor yellow
>
> ###########################################
> # B A C K - C O M P A R T M E N T
> # Create the back-compartment volume
> /gate/SPECThead/daughters/name compartment
> /gate/SPECThead/daughters/insert box
>
> # Define the dimensions of the back-compartment volume
> /gate/compartment/geometry/setXLength 30. mm
> /gate/compartment/geometry/setYLength 260. mm
> /gate/compartment/geometry/setZLength 260. mm
>
> # Define the position of the back-compartment volume
> /gate/compartment/placement/setTranslation 61. 0. 0. mm
>
> # Set the material of the back-compartment volume
> /gate/compartment/setMaterial Glass
>
> # Define some visualisation options
> /gate/compartment/vis/setColor grey
>
> # Attach PhantomSD to record Compton
> # interactions in the back-compartment volume
> /gate/compartment/attachPhantomSD
>
>
> #############################################
> # P H A N T O M
> # Create the phantom volume
> /gate/world/daughters/name Phantom
> /gate/world/daughters/insert cylinder
>
> # Define the dimensions of the phantom
> # volume
> /gate/Phantom/geometry/setRmax 0.5 mm
> /gate/Phantom/geometry/setRmin 0. mm
> /gate/Phantom/geometry/setHeight 0.5 mm
> /gate/Phantom/placement/setTranslation 0 0 0 mm
>
> # Set the material corresponding to the
> # phantom volume
> /gate/Phantom/setMaterial Water
>
> # Define some visualisation options
> /gate/Phantom/vis/setColor blue
> /gate/Phantom/vis/forceWireframe
>
> # Attach PhantomSD to record Compton
> # interactions in the phantom volume
> /gate/Phantom/attachPhantomSD
>
>
> #############################################
> # M O V I N G S O U R C E
> # Add an extra object for source confinement
> /gate/Phantom/daughters/name movsource
> /gate/Phantom/daughters/insert cylinder
>
> # Define the dimensions of the source volume
> /gate/movsource/geometry/setRmax 0.5 mm
> /gate/movsource/geometry/setRmin 0. mm
> /gate/movsource/geometry/setHeight 0.5 mm
>
> # Set the material corresponding to the
> # phantom volume
> /gate/movsource/setMaterial Water
>
> # Define some visualisation options
> /gate/movsource/vis/setColor magenta
> /gate/movsource/attachPhantomSD
>
> /control/execute timing.mac
>
> #################################
> # SENSITIVE DETECTORS
> # GATE provides two sensitive detectors,
> # which have two different functions
> # Using them properly is very important
> # for getting accurate results
>
> ###########################################
> # Crystal SD
> # The crystal SD makes it possible to
> # record hits in a sensitive volume
> # (e.g.,. in a scintillation crystal)
> # It must be attached to any volume for
> # which hit-data must be obtained
> # For recording hits in the NaI volume
> # only, the name of which is crystal,
> # this volume is attached to the crystal SD
> /gate/crystal/attachCrystalSD
>
> #############################################
> # Phantom SD
> # The phantom SD makes it possible to record
> # Compton events in the volumes within the
> # field of view. This can provide information
> # for result analysis to discriminate between
> # scattered and unscattered photons. It must
> # be attached to each and every volume for
> # whom Compton interactions have to be recorded
> /gate/Phantom/attachPhantomSD
>
> #############################################
> # S Y S T E M
> # The system acts as an interpretor between
> # the GATE geometry and data outputs for
> # reconstruction in our case, the Interfile
> # writer. A system must know which components
> # of the geometry are parts of the scanner,
> # and what their role are. For the moment,
> # there is only a system SPECThead, which
> # was built when the SPECThead volume was
> # inserted.
>
> # The SPECThead system is made of three
> # levels: base (for the head), crystal (for
> # the crystal and crystal matrix) and pixel
> # (for individual crystals for pixellated
> # gamma camera) For now, only the base of
> # the system is attached to a volume: the
> # volume SPECThead. For the system to get
> # information about your crystal, the level
> # crystal must be attached to the volume that
> # has been defined for the scintillating
> # crystal (crystal)
> /gate/systems/SPECThead/crystal/attach crystal
> # Look at the system
> /gate/systems/SPECThead/describe
>
> #############################################
> # P H Y S I C S
> # Select the processes to consider
> /gate/physics/gamma/selectRayleigh lowenergy
> /gate/physics/gamma/selectPhotoelectric lowenergy
> /gate/physics/gamma/selectCompton lowenergy
> /gate/physics/gamma/selectGammaConversion inactive
> /gate/physics/gamma/listProcesses
>
> # Set some cuts to speed up the simulation
> # X-rays are tracked until their energy fell
> # under 20 keV
> /gate/physics/setXRayCut 20. keV
> # Cut in order not to follow the secondary
> # electrons
> /gate/physics/setElectronCut 1. km
> /gate/physics/setDeltaRayCut 1. GeV
>
>
> # Physics initialization
> /run/initialize
>
> #############################################
> # D I G I T I Z E R
> # The digitizer tracks what happens in the
> # detection system and in the electronics
> # Build a digitizer that first computes the
> # centroid of interactions
>
> /gate/digitizer/Singles/insert adder
>
> /gate/digitizer/Singles/insert blurring
> /gate/digitizer/Singles/blurring/setResolution 0.15
> /gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV
>
> /gate/digitizer/Singles/insert spblurring
> /gate/digitizer/Singles/spblurring/setSpresolution 0.0 mm
> /gate/digitizer/Singles/spblurring/verbose 1
>
> /gate/digitizer/Singles/insert thresholder
> /gate/digitizer/Singles/thresholder/setThreshold 20. keV
>
> /gate/digitizer/Singles/insert upholder
> /gate/digitizer/Singles/upholder/setUphold 190. keV
>
> #############################################
> # S O U R C E
> # Setting up the source
> /gate/source/addSource SourceConfinement
>
> # Define the shape of the source
> /gate/source/SourceConfinement/gps/type Volume
> /gate/source/SourceConfinement/gps/shape Cylinder
>
> # Define the dimensions of the source
> /gate/source/SourceConfinement/gps/radius 0.5 mm
> /gate/source/SourceConfinement/gps/halfz 0.25 mm
>
> # Define the placement of the source
> /gate/source/SourceConfinement/gps/centre 0. 0. 0. mm
>
> # Define the source as a gamma source
> /gate/source/SourceConfinement/gps/particle gamma
>
> # Define the gamma energy
> #/gate/source/SourceConfinement/gps/energytype Mono
> /gate/source/SourceConfinement/gps/energy 140. keV
>
> # Set the activity of the source
> /gate/source/SourceConfinement/setActivity 500000. Bq
>
> # Define a confinement
> # the activity cannot move with time so the attenuating
> # medium is moved and the activity is forced to be in the
> # attenuating medium
> /gate/source/SourceConfinement/gps/confine movsource_P
>
> # Define the emission direction (4 str)
> /gate/source/SourceConfinement/gps/angtype iso
> /gate/source/SourceConfinement/gps/mintheta 0. deg
> /gate/source/SourceConfinement/gps/maxtheta 180. deg
> /gate/source/SourceConfinement/gps/minphi 0. deg
> /gate/source/SourceConfinement/gps/maxphi 360. deg
>
> #############################################
> # R A N D O M
> # Change the root of the random module to run different simulations
> /gate/output/root/setSaveRndmFlag 1
>
> #############################################
> # O U T P U T
> # Select the options of the data output
> # As there are several modules, settings have
> # to be defined for each module, especially in
> # SPECT, where there are a lots of hits for
> # only a few counts, so it's better to limit
> # the amount of data produced Here the
> # SingleDigi output can be used if you have
> # your own program to process the data
>
> /gate/output/root/setFileName pinholeSPECT
> /gate/output/root/setRootSinglesAdderFlag 1
> /gate/output/root/setRootSinglesBlurringFlag 1
> /gate/output/root/setRootSinglesSpblurringFlag 1
> /gate/output/root/setRootSinglesThresholderFlag 1
> /gate/output/root/setRootSinglesUpholderFlag 1
>
> #/gate/output/root/setRootHitFlag 0
> #/gate/output/root/setRootSinglesFlag 0
> #/gate/output/root/setRootCoincidencesFlag 0
> #/gate/output/root/setRootNtupleFlag 0
>
> #/gate/output/ascii/disable
> /gate/output/ascii/setOutFileSinglesAdderFlag 0
> /gate/output/ascii/setOutFileSinglesSpblurringFlag 0
> /gate/output/ascii/setOutFileSinglesBlurringFlag 0
> /gate/output/ascii/setOutFileSinglesThresholderFlag 0
> /gate/output/ascii/setOutFileSinglesUpholderFlag 0
>
> #############################################
> # P R O J E C T I O N
> # Makes a set of projections from the crystal
> # hits Define the binning the projection module
> # to be used
> /gate/output/projection/pixelSizeX 2.03125 mm
> /gate/output/projection/pixelSizeY 2.03125 mm
> /gate/output/projection/pixelNumberX 128
> /gate/output/projection/pixelNumberY 128
>
> # Specify the projection plane (XY, YZ or ZX)
> /gate/output/projection/projectionPlane YZ
>
> #############################################
> # E X P E R I M E N T
> # Define the parameters of the experiment
> # (start time, stop time and time slice)
> # The number of projections depends on the
> # number of time slice, the rotation speed of
> # the system and the number of heads
> /gate/application/setTimeSlice 10. s
> /gate/application/setTimeStart 0. s
> /gate/application/setTimeStop 10. s
>
> #############################################
> # V E R B O S I T Y
> /control/verbose 0
> /grdm/verbose 0
> /run/verbose 0
> /event/verbose 0
> /tracking/verbose 0
> /gate/application/verbose 0
> /gate/generator/verbose 0
> /gate/stacking/verbose 0
> /gate/event/verbose 0
> /gate/source/verbose 0
> /gate/output/projection/verbose 0
> /gate/output/verbose 0
>
> # LET'S RUN THE SIMULATION!
> /gate/application/startDAQ
> -------------- next part --------------
> /control/verbose 1
> /control/saveHistory
> /run/verbose 2
> /event/verbose 1
> /tracking/verbose 1
>
> /gate/timing/setTime 0. s
> /gate/application/setTimeSlice 1. s
>
> #/control/execute mucam.mac
> #/control/execute startGammas.mac
> #/control/execute startTwoSources.mac
>
>
> -------------- next part --------------
> # Show how the geometry moves with time
> /gate/timing/setTime 0. s
> /gate/timing/setTime 20. s
> /gate/timing/setTime 40. s
> /gate/timing/setTime 60. s
> /gate/timing/setTime 80. s
> /gate/timing/setTime 100. s
> /gate/timing/setTime 120. s
> /gate/timing/setTime 140. s
> /gate/timing/setTime 160. s
> /gate/timing/setTime 180. s
> /gate/timing/setTime 200. s
> /gate/timing/setTime 220. s
> /gate/timing/setTime 240. s
> /gate/timing/setTime 260. s
> /gate/timing/setTime 270. s
> /gate/timing/setTime 280. s
> /gate/timing/setTime 300. s
> /gate/timing/setTime 320. s
> /gate/timing/setTime 340. s
> /gate/timing/setTime 360. s
> /gate/timing/setTime 380. s
> /gate/timing/setTime 400. s
> /gate/timing/setTime 420. s
> /gate/timing/setTime 440. s
> /gate/timing/setTime 460. s
> /gate/timing/setTime 480. s
> /gate/timing/setTime 500. s
> /gate/timing/setTime 520. s
> /gate/timing/setTime 540. s
> /gate/timing/setTime 560. s
> /gate/timing/setTime 580. s
> /gate/timing/setTime 600. s
> /gate/timing/setTime 620. s
> /gate/timing/setTime 640. s
> -------------- next part --------------
> # V I S U A L I S A T I O N
> /vis/open OGLSX
> /vis/viewer/reset
> /vis/drawView 60 60
> /vis/viewer/zoom 2
> /vis/viewer/set/style surface
> /vis/drawVolume
> /vis/scene/endOfEventAction accumulate
> /vis/viewer/update
> /vis/verbose 2
>
> ------------------------------
>
> Message: 2
> Date: Mon, 25 Jul 2005 13:56:50 +0200
> From: Sebastien JAN <jan at shfj.cea.fr>
> Subject: Re: [gate-users] Re: gate-users Digest, Vol 16, Issue 25
> To: GATE feedback and helpline for Users
> <gate-users at lphe1pet1.epfl.ch>
> Message-ID: <42E4D382.8050105 at shfj.cea.fr>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi Christian,
>
> Could you check the distributions (with root or ASCII output) of
> globalPosX ; globalPosY ; globalPosZ for the 2 following configurations:
>
> 1/ /gate/digitizer/Singles/spblurring/setSpresolution 0.0
> 2/ /gate/digitizer/Singles/spblurring/setSpresolution 10.0
>
> let me know if you find some differences in your output according to the
> spatial blurring
>
> seb
>
>
>
> Christian Wietholt a écrit:
> > Hi Sebastien,
> >
> > Thank you so much for your reply and offering your help. I still could not
> > figure out how to get the digitizer blurring to work. I am already wondering
> > if the digitizer blurring is enabled in the interfile output function, or
> > wether I will have to use the singles.dat file and the supplied C programs to
> > generate the correct projection images.
> >
> > Please find attached to this email my most current version of the macro file.
> >
> > Thanks again,
> >
> > Christian
> >
> >
> >
> > On Monday 25 July 2005 18:02, gate-users-request at lphe1pet1.epfl.ch wrote:
> >
> >>Send gate-users mailing list submissions to
> >> gate-users at lphe1pet1.epfl.ch
> >>
> >>To subscribe or unsubscribe via the World Wide Web, visit
> >> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >>
> >>Please use the GATE's site webmaster e-mail to reach the person
> >>managing the list.
> >>
> >>
> >>Today's Topics:
> >>
> >> 1. Re: SPblurring (Sebastien JAN)
> >>
> >>
> >>----------------------------------------------------------------------
> >>
> >>Message: 1
> >>Date: Mon, 25 Jul 2005 11:39:55 +0200
> >>From: Sebastien JAN <jan at shfj.cea.fr>
> >>Subject: Re: [gate-users] SPblurring
> >>To: GATE feedback and helpline for Users
> >> <gate-users at lphe1pet1.epfl.ch>
> >>Message-ID: <42E4B36B.3080306 at shfj.cea.fr>
> >>Content-Type: text/plain; charset=iso-8859-1; format=flowed
> >>
> >>Hi ,
> >>
> >>Can you send me your macro please ?
> >>
> >>seb
> >>
> >>Christian Wietholt a écrit:
> >>
> >>>Dear Gate Users,
> >>>
> >>>After I submitted my question about SPblurring, I realized that
> >>>I should first initialize and then set up the detector. I did so, and
> >>>the Gate ouput on the command shell was completely different,
> >>>but still no detector spatial blurr in the projection images. What
> >>>am I doing wrong? Anybody has a suggestion what I could try
> >>>next?
> >>>
> >>>Christian
> >>>_______________________________________________
> >>>gate-users mailing list
> >>>gate-users at lphe1pet1.epfl.ch
> >>>http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >>
> >>------------------------------
> >>
> >>_______________________________________________
> >>gate-users mailing list
> >>gate-users at lphe1pet1.epfl.ch
> >>http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >>
> >>End of gate-users Digest, Vol 16, Issue 25
> >>*****************************************
> >
> > *
> >
> >
> > ------------------------------------------------------------------------
> >
> > #############################################
> > # V I S U A L I S A T I O N
> > /control/execute visu.mac
> >
> > /tracking/storeTrajectory 1
> > /gate/geometry/enableAutoUpdate
> >
> > #############################################
> > # V E R B O S I T Y
> > /gate/output/verbose 2
> >
> > #############################################
> > # W O R L D
> > # Define the world dimensions
> > /gate/world/geometry/setXLength 1000 mm
> > /gate/world/geometry/setYLength 1000 mm
> > /gate/world/geometry/setZLength 1000 mm
> >
> > #############################################
> > # S C A N N E R H E A D
> > # Create a new box representing the main
> > # head-volume SPECThead is the name of the
> > # predefined SPECT system Create the SPECT
> > # system, which will yield an Interfile output
> > # of projection data
> > /gate/world/daughters/name SPECThead
> > /gate/world/daughters/insert box
> >
> > # Define the dimensions of the main volume
> > /gate/SPECThead/geometry/setXLength 300. mm
> > /gate/SPECThead/geometry/setYLength 300. mm
> > /gate/SPECThead/geometry/setZLength 300. mm
> >
> > # Define the position of the main volume
> > # Move the head 9 cm away from the Z axis,
> > # which is the rotation axis and the
> > # replication axis
> > /gate/SPECThead/placement/setTranslation 200. 0. 0. mm
> >
> > # Set the material associated with the main volume
> > /gate/SPECThead/setMaterial Air
> > /gate/SPECThead/attachPhantomSD
> >
> > # Define the rotation speed of the head
> > # Define the orbiting around the Z axis
> > /gate/SPECThead/moves/insert orbiting
> > /gate/SPECThead/orbiting/setSpeed 0.5625 deg/s
> > /gate/SPECThead/orbiting/setPoint1 0. 0. 0. mm
> > /gate/SPECThead/orbiting/setPoint2 0. 0. 1. mm
> >
> > # Define some visualisation options
> > /gate/SPECThead/vis/forceWireframe
> >
> > # Shielding
> > # Create the shielding volume
> > /gate/SPECThead/daughters/name shielding
> > /gate/SPECThead/daughters/insert box
> >
> > # Define the dimensions of the shielding volume
> > /gate/shielding/geometry/setXLength 300. mm
> > /gate/shielding/geometry/setYLength 300. mm
> > /gate/shielding/geometry/setZLength 300. mm
> >
> > # Define the position of the shielding volume
> > /gate/shielding/placement/setTranslation 0. 0. 0. mm
> >
> > # Set the material corresponding to the
> > # shielding volume
> > /gate/shielding/setMaterial Lead
> >
> > # Define some visualisation options
> > /gate/shielding/vis/setColor red
> > /gate/shielding/vis/forceWireframe
> >
> > # Attach phantom SD to record Compton
> > # interactions in the shielding volume
> > # Needed to discriminate between scattered
> > # and unscattered photons
> > /gate/shielding/attachPhantomSD
> >
> >
> > #############################################
> > # C O L L I M A T O R
> > # Create a full volume defining the shape
> > # of the collimator
> > /gate/SPECThead/daughters/name collimator
> > /gate/SPECThead/daughters/insert box
> >
> > /gate/collimator/geometry/setXLength 20. mm
> > /gate/collimator/geometry/setYLength 300. mm
> > /gate/collimator/geometry/setZLength 300. mm
> >
> > /gate/collimator/setMaterial Lead
> > /gate/collimator/placement/setTranslation -140. 0. 0. mm
> >
> > /gate/collimator/vis/forceWireframe
> > /gate/collimator/vis/setColor red
> >
> > # Attach PhantomSD to record Compton
> > # interactions in the collimator volume
> > /gate/collimator/attachPhantomSD
> >
> > #############################################
> > # P I N H O L E
> > # Insert the pinhole in the collimator
> > /gate/collimator/daughters/name hole
> > /gate/collimator/daughters/insert cylinder
> > /gate/hole/geometry/setHeight 20. mm
> > /gate/hole/geometry/setRmax 2.5 mm
> > /gate/hole/placement/alignToX
> > /gate/hole/setMaterial Air
> > /gate/hole/vis/forceSolid
> >
> > /gate/collimator/daughters/name cone1
> > /gate/collimator/daughters/insert cone
> > #/gate/cone1/geometry/setHeight 7.5 mm
> > /gate/cone1/geometry/setHeight 9 mm
> > /gate/cone1/geometry/setRmax1 10. mm
> > /gate/cone1/geometry/setRmax2 2.5 mm
> > #/gate/cone1/placement/setTranslation -6.25 0 0 mm
> > /gate/cone1/placement/setTranslation -5.5 0 0 mm
> > /gate/cone1/placement/alignToX
> > /gate/cone1/setMaterial Air
> > /gate/cone1/vis/forceSolid
> >
> > /gate/collimator/daughters/name cone2
> > /gate/collimator/daughters/insert cone
> > #/gate/cone2/geometry/setHeight 7.5 mm
> > /gate/cone2/geometry/setHeight 9 mm
> > /gate/cone2/geometry/setRmax1 2.5 mm
> > /gate/cone2/geometry/setRmax2 10. mm
> > #/gate/cone2/placement/setTranslation 6.25 0 0 mm
> > /gate/cone2/placement/setTranslation 5.5 0 0 mm
> > /gate/cone2/placement/alignToX
> > /gate/cone2/setMaterial Air
> > /gate/cone2/vis/forceSolid
> >
> > ############################################
> > # C A M H E A D A I R
> > # insert air behind the collimator
> > /gate/SPECThead/daughters/name aircomp
> > /gate/SPECThead/daughters/insert box
> > /gate/aircomp/geometry/setXLength 170 mm
> > /gate/aircomp/geometry/setYLength 260 mm
> > /gate/aircomp/geometry/setZLength 260 mm
> > /gate/aircomp/placement/setTranslation -45 0 0 mm
> > /gate/aircomp/vis/forceWireframe
> >
> > ############################################
> > # C R Y S T A L
> > # Create the crystal volume
> > /gate/SPECThead/daughters/name crystal
> > /gate/SPECThead/daughters/insert box
> >
> > # Define the dimensions of the crystal volume
> > /gate/crystal/geometry/setXLength 6. mm
> > /gate/crystal/geometry/setYLength 260. mm
> > /gate/crystal/geometry/setZLength 260. mm
> >
> > # Define the position of the crystal volume
> > /gate/crystal/placement/setTranslation 43. 0. 0. mm
> >
> > # Set the material associated with the crystal
> > # volume
> > /gate/crystal/setMaterial NaI
> >
> > # Define some visualisation options
> > /gate/crystal/vis/setColor yellow
> >
> > ###########################################
> > # B A C K - C O M P A R T M E N T
> > # Create the back-compartment volume
> > /gate/SPECThead/daughters/name compartment
> > /gate/SPECThead/daughters/insert box
> >
> > # Define the dimensions of the back-compartment volume
> > /gate/compartment/geometry/setXLength 30. mm
> > /gate/compartment/geometry/setYLength 260. mm
> > /gate/compartment/geometry/setZLength 260. mm
> >
> > # Define the position of the back-compartment volume
> > /gate/compartment/placement/setTranslation 61. 0. 0. mm
> >
> > # Set the material of the back-compartment volume
> > /gate/compartment/setMaterial Glass
> >
> > # Define some visualisation options
> > /gate/compartment/vis/setColor grey
> >
> > # Attach PhantomSD to record Compton
> > # interactions in the back-compartment volume
> > /gate/compartment/attachPhantomSD
> >
> >
> > #############################################
> > # P H A N T O M
> > # Create the phantom volume
> > /gate/world/daughters/name Phantom
> > /gate/world/daughters/insert cylinder
> >
> > # Define the dimensions of the phantom
> > # volume
> > /gate/Phantom/geometry/setRmax 0.5 mm
> > /gate/Phantom/geometry/setRmin 0. mm
> > /gate/Phantom/geometry/setHeight 0.5 mm
> > /gate/Phantom/placement/setTranslation 0 0 0 mm
> >
> > # Set the material corresponding to the
> > # phantom volume
> > /gate/Phantom/setMaterial Water
> >
> > # Define some visualisation options
> > /gate/Phantom/vis/setColor blue
> > /gate/Phantom/vis/forceWireframe
> >
> > # Attach PhantomSD to record Compton
> > # interactions in the phantom volume
> > /gate/Phantom/attachPhantomSD
> >
> >
> > #############################################
> > # M O V I N G S O U R C E
> > # Add an extra object for source confinement
> > /gate/Phantom/daughters/name movsource
> > /gate/Phantom/daughters/insert cylinder
> >
> > # Define the dimensions of the source volume
> > /gate/movsource/geometry/setRmax 0.5 mm
> > /gate/movsource/geometry/setRmin 0. mm
> > /gate/movsource/geometry/setHeight 0.5 mm
> >
> > # Set the material corresponding to the
> > # phantom volume
> > /gate/movsource/setMaterial Water
> >
> > # Define some visualisation options
> > /gate/movsource/vis/setColor magenta
> > /gate/movsource/attachPhantomSD
> >
> > /control/execute timing.mac
> >
> > #################################
> > # SENSITIVE DETECTORS
> > # GATE provides two sensitive detectors,
> > # which have two different functions
> > # Using them properly is very important
> > # for getting accurate results
> >
> > ###########################################
> > # Crystal SD
> > # The crystal SD makes it possible to
> > # record hits in a sensitive volume
> > # (e.g.,. in a scintillation crystal)
> > # It must be attached to any volume for
> > # which hit-data must be obtained
> > # For recording hits in the NaI volume
> > # only, the name of which is crystal,
> > # this volume is attached to the crystal SD
> > /gate/crystal/attachCrystalSD
> >
> > #############################################
> > # Phantom SD
> > # The phantom SD makes it possible to record
> > # Compton events in the volumes within the
> > # field of view. This can provide information
> > # for result analysis to discriminate between
> > # scattered and unscattered photons. It must
> > # be attached to each and every volume for
> > # whom Compton interactions have to be recorded
> > /gate/Phantom/attachPhantomSD
> >
> > #############################################
> > # S Y S T E M
> > # The system acts as an interpretor between
> > # the GATE geometry and data outputs for
> > # reconstruction in our case, the Interfile
> > # writer. A system must know which components
> > # of the geometry are parts of the scanner,
> > # and what their role are. For the moment,
> > # there is only a system SPECThead, which
> > # was built when the SPECThead volume was
> > # inserted.
> >
> > # The SPECThead system is made of three
> > # levels: base (for the head), crystal (for
> > # the crystal and crystal matrix) and pixel
> > # (for individual crystals for pixellated
> > # gamma camera) For now, only the base of
> > # the system is attached to a volume: the
> > # volume SPECThead. For the system to get
> > # information about your crystal, the level
> > # crystal must be attached to the volume that
> > # has been defined for the scintillating
> > # crystal (crystal)
> > /gate/systems/SPECThead/crystal/attach crystal
> > # Look at the system
> > /gate/systems/SPECThead/describe
> >
> > #############################################
> > # P H Y S I C S
> > # Select the processes to consider
> > /gate/physics/gamma/selectRayleigh lowenergy
> > /gate/physics/gamma/selectPhotoelectric lowenergy
> > /gate/physics/gamma/selectCompton lowenergy
> > /gate/physics/gamma/selectGammaConversion inactive
> > /gate/physics/gamma/listProcesses
> >
> > # Set some cuts to speed up the simulation
> > # X-rays are tracked until their energy fell
> > # under 20 keV
> > /gate/physics/setXRayCut 20. keV
> > # Cut in order not to follow the secondary
> > # electrons
> > /gate/physics/setElectronCut 1. km
> > /gate/physics/setDeltaRayCut 1. GeV
> >
> >
> > # Physics initialization
> > /run/initialize
> >
> > #############################################
> > # D I G I T I Z E R
> > # The digitizer tracks what happens in the
> > # detection system and in the electronics
> > # Build a digitizer that first computes the
> > # centroid of interactions
> >
> > /gate/digitizer/Singles/insert adder
> >
> > /gate/digitizer/Singles/insert blurring
> > /gate/digitizer/Singles/blurring/setResolution 0.15
> > /gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV
> >
> > /gate/digitizer/Singles/insert spblurring
> > /gate/digitizer/Singles/spblurring/setSpresolution 0.0 mm
> > /gate/digitizer/Singles/spblurring/verbose 1
> >
> > /gate/digitizer/Singles/insert thresholder
> > /gate/digitizer/Singles/thresholder/setThreshold 20. keV
> >
> > /gate/digitizer/Singles/insert upholder
> > /gate/digitizer/Singles/upholder/setUphold 190. keV
> >
> > #############################################
> > # S O U R C E
> > # Setting up the source
> > /gate/source/addSource SourceConfinement
> >
> > # Define the shape of the source
> > /gate/source/SourceConfinement/gps/type Volume
> > /gate/source/SourceConfinement/gps/shape Cylinder
> >
> > # Define the dimensions of the source
> > /gate/source/SourceConfinement/gps/radius 0.5 mm
> > /gate/source/SourceConfinement/gps/halfz 0.25 mm
> >
> > # Define the placement of the source
> > /gate/source/SourceConfinement/gps/centre 0. 0. 0. mm
> >
> > # Define the source as a gamma source
> > /gate/source/SourceConfinement/gps/particle gamma
> >
> > # Define the gamma energy
> > #/gate/source/SourceConfinement/gps/energytype Mono
> > /gate/source/SourceConfinement/gps/energy 140. keV
> >
> > # Set the activity of the source
> > /gate/source/SourceConfinement/setActivity 500000. Bq
> >
> > # Define a confinement
> > # the activity cannot move with time so the attenuating
> > # medium is moved and the activity is forced to be in the
> > # attenuating medium
> > /gate/source/SourceConfinement/gps/confine movsource_P
> >
> > # Define the emission direction (4 str)
> > /gate/source/SourceConfinement/gps/angtype iso
> > /gate/source/SourceConfinement/gps/mintheta 0. deg
> > /gate/source/SourceConfinement/gps/maxtheta 180. deg
> > /gate/source/SourceConfinement/gps/minphi 0. deg
> > /gate/source/SourceConfinement/gps/maxphi 360. deg
> >
> > #############################################
> > # R A N D O M
> > # Change the root of the random module to run different simulations
> > /gate/output/root/setSaveRndmFlag 1
> >
> > #############################################
> > # O U T P U T
> > # Select the options of the data output
> > # As there are several modules, settings have
> > # to be defined for each module, especially in
> > # SPECT, where there are a lots of hits for
> > # only a few counts, so it's better to limit
> > # the amount of data produced Here the
> > # SingleDigi output can be used if you have
> > # your own program to process the data
> >
> > /gate/output/root/setFileName pinholeSPECT
> > /gate/output/root/setRootSinglesAdderFlag 1
> > /gate/output/root/setRootSinglesBlurringFlag 1
> > /gate/output/root/setRootSinglesSpblurringFlag 1
> > /gate/output/root/setRootSinglesThresholderFlag 1
> > /gate/output/root/setRootSinglesUpholderFlag 1
> >
> > #/gate/output/root/setRootHitFlag 0
> > #/gate/output/root/setRootSinglesFlag 0
> > #/gate/output/root/setRootCoincidencesFlag 0
> > #/gate/output/root/setRootNtupleFlag 0
> >
> > #/gate/output/ascii/disable
> > /gate/output/ascii/setOutFileSinglesAdderFlag 0
> > /gate/output/ascii/setOutFileSinglesSpblurringFlag 0
> > /gate/output/ascii/setOutFileSinglesBlurringFlag 0
> > /gate/output/ascii/setOutFileSinglesThresholderFlag 0
> > /gate/output/ascii/setOutFileSinglesUpholderFlag 0
> >
> > #############################################
> > # P R O J E C T I O N
> > # Makes a set of projections from the crystal
> > # hits Define the binning the projection module
> > # to be used
> > /gate/output/projection/pixelSizeX 2.03125 mm
> > /gate/output/projection/pixelSizeY 2.03125 mm
> > /gate/output/projection/pixelNumberX 128
> > /gate/output/projection/pixelNumberY 128
> >
> > # Specify the projection plane (XY, YZ or ZX)
> > /gate/output/projection/projectionPlane YZ
> >
> > #############################################
> > # E X P E R I M E N T
> > # Define the parameters of the experiment
> > # (start time, stop time and time slice)
> > # The number of projections depends on the
> > # number of time slice, the rotation speed of
> > # the system and the number of heads
> > /gate/application/setTimeSlice 10. s
> > /gate/application/setTimeStart 0. s
> > /gate/application/setTimeStop 10. s
> >
> > #############################################
> > # V E R B O S I T Y
> > /control/verbose 0
> > /grdm/verbose 0
> > /run/verbose 0
> > /event/verbose 0
> > /tracking/verbose 0
> > /gate/application/verbose 0
> > /gate/generator/verbose 0
> > /gate/stacking/verbose 0
> > /gate/event/verbose 0
> > /gate/source/verbose 0
> > /gate/output/projection/verbose 0
> > /gate/output/verbose 0
> >
> > # LET'S RUN THE SIMULATION!
> > /gate/application/startDAQ
> >
> >
> > ------------------------------------------------------------------------
> >
> > /control/verbose 1
> > /control/saveHistory
> > /run/verbose 2
> > /event/verbose 1
> > /tracking/verbose 1
> >
> > /gate/timing/setTime 0. s
> > /gate/application/setTimeSlice 1. s
> >
> > #/control/execute mucam.mac
> > #/control/execute startGammas.mac
> > #/control/execute startTwoSources.mac
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > # Show how the geometry moves with time
> > /gate/timing/setTime 0. s
> > /gate/timing/setTime 20. s
> > /gate/timing/setTime 40. s
> > /gate/timing/setTime 60. s
> > /gate/timing/setTime 80. s
> > /gate/timing/setTime 100. s
> > /gate/timing/setTime 120. s
> > /gate/timing/setTime 140. s
> > /gate/timing/setTime 160. s
> > /gate/timing/setTime 180. s
> > /gate/timing/setTime 200. s
> > /gate/timing/setTime 220. s
> > /gate/timing/setTime 240. s
> > /gate/timing/setTime 260. s
> > /gate/timing/setTime 270. s
> > /gate/timing/setTime 280. s
> > /gate/timing/setTime 300. s
> > /gate/timing/setTime 320. s
> > /gate/timing/setTime 340. s
> > /gate/timing/setTime 360. s
> > /gate/timing/setTime 380. s
> > /gate/timing/setTime 400. s
> > /gate/timing/setTime 420. s
> > /gate/timing/setTime 440. s
> > /gate/timing/setTime 460. s
> > /gate/timing/setTime 480. s
> > /gate/timing/setTime 500. s
> > /gate/timing/setTime 520. s
> > /gate/timing/setTime 540. s
> > /gate/timing/setTime 560. s
> > /gate/timing/setTime 580. s
> > /gate/timing/setTime 600. s
> > /gate/timing/setTime 620. s
> > /gate/timing/setTime 640. s
> >
> >
> > ------------------------------------------------------------------------
> >
> > # V I S U A L I S A T I O N
> > /vis/open OGLSX
> > /vis/viewer/reset
> > /vis/drawView 60 60
> > /vis/viewer/zoom 2
> > /vis/viewer/set/style surface
> > /vis/drawVolume
> > /vis/scene/endOfEventAction accumulate
> > /vis/viewer/update
> > /vis/verbose 2
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gate-users mailing list
> > gate-users at lphe1pet1.epfl.ch
> > http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
>
>
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>
> End of gate-users Digest, Vol 16, Issue 26
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