[Gate-users] problem with voxelez the phantom and the source
mariam zoubair
zoubair-mariam at hotmail.fr
Tue Mar 5 17:21:43 CET 2013
Dear Gate users
I try to follow all the steps to run CT scanner, I have an image of 512 x 512 pixels. I'm voxelez the phantom and the source (position = -256, -256, 0) but I have not seen any interaction and I have this message.
Can you help me
Thank you
/tracking/storeTrajectory 1Attributes available for modeling and filtering with "/vis/modeling/trajectories/create/drawByAttribute" and "/vis/filtering/trajectories/create/attributeFilter" commands:G4Trajectory: Charge (Ch): unit: e+ (G4double) Track ID (ID): G4int Initial kinetic energy (IKE): G4BestUnit (G4double) Initial momentum magnitude (IMag): G4BestUnit (G4double) Initial momentum (IMom): G4BestUnit (G4ThreeVector) No. of points (NTP): G4int
PDG Encoding (PDG): G4int Parent ID (PID): G4int Particle Name (PN): G4StringG4TrajectoryPoint: Position (Pos): G4BestUnit (G4ThreeVector)WARNING: Trajectory storing has been requested. This action may be reversed with "/tracking/storeTrajectory 0".WARNING: The vis manager will keep up to 100 events. This may use a lot of memory. It may be changed with, e.g., "/vis/scene/endOfEventAction accumulate 10". CREATED THE COMMAND /gate/systems/cylindricalPET/addAnewRsector Call VoxelParameterized::InsertReader Range Translator Range 0 : imageValue in [ 0.000e+00 , 1.500e+03 ] ---> material Air, visibility 1, coulour (0.000e+00,1.000e+00,0.000e+00,2.000e-01) Range 1 : imageValue in [ 1.501e+03 , 2.250e+03 ] ---> material Water, visibility 1, coulour (1.000e+00,0.000e+00,0.000e+00,2.000e-01) Range 2 : imageValue in [ 2.251e+03 , 2.750e+03 ] ---> material Air, visibility 1, coulour (0.000e+00,1.000e+00,0.000e+00,2.000e-01) Range 3 : imageValue in [ 2.751e+03 , 3.848e+03 ] ---> material RibBone, visibility 1, coulour (0.000e+00,0.000e+00,1.000e+00,2.000e-01)', assuming default BIGENDIAN'LITTLEENDIAN
'nrecognised type name 'unsigned integer Header read from 'CT-IM00120_uint16.h33''Data file name 'm001-IM00120.i33 Nb of planes: 1 Nb of pixels per plane: 512 512 Pixel size: 4.590e-01 4.590e-01 Slice thickness: 2.179e+00 Matrix size: 2.350e+02 2.350e+02 Data type: Data byte order: BIGENDIAN
'!ror: Could not open header file 'm001-IM00120.i33 <!> *** WARNING *** <!> Unknown process: PositronAnnihilationStd <!> *** WARNING *** <!> Unknown process: MultipleScattering <!> *** WARNING *** <!> Unknown process: MultipleScattering
List of Enabled processes:
=== Process: PhotoElectric ===Particle: gamma * Model(s): - StandardModel
=== Process: Compton ===Particle: gamma * Model(s): - StandardModel
=== Process: Bremsstrahlung ===Particle: e+ * Model(s): - StandardModelParticle: e- * Model(s): - StandardModel
=== Process: ElectronIonisation ===Particle: e+ * Model(s): - StandardModelParticle: e- * Model(s): - StandardModel
List of initialized processes:
[Core-0] Initialization of geometryG4PhysicalVolumeModel::Validate(): A volume of the same name and copy number ("world_phys", copy 0) still exists and is being used. But it is not the same volume you originally specified in /vis/scene/add/.[Core-0] Initialization of physics[Core-0] Initialization of actors
GATE object: 'systems/cylindricalPET'
Components:
GATE object: 'systems/cylindricalPET/base'Attached to volume: cylindricalPETNb of children: 1
GATE object: 'systems/cylindricalPET/rsector' Attached to volume: head Nb of children: 1
GATE object: 'systems/cylindricalPET/module' Attached to volume: --- Nb of children: 1
GATE object: 'systems/cylindricalPET/submodule' Attached to volume: block Nb of children: 1
GATE object: 'systems/cylindricalPET/crystal' Attached to volume: crystal Nb of children: 4
GATE object: 'systems/cylindricalPET/layer0' Attached to volume: LYSO Nb of children: 0
GATE object: 'systems/cylindricalPET/layer1' Attached to volume: LSO Nb of children: 0
GATE object: 'systems/cylindricalPET/layer2' Attached to volume: --- Nb of children: 0
GATE object: 'systems/cylindricalPET/layer3' Attached to volume: --- Nb of children: 0geometrical design type: 1ring diameter: -1.750e+01 cm rsector axial pitch: 0.000e+00 fm rsector azimuthal pitch: -4.500e+01 degreersector tangential size: 2.000e+00 cm rsector axial size: 2.530e+01 cm module axial size: 2.530e+01 cm module tangential size: 2.000e+00 cm module axial pitch: 0.000e+00 fm module tangential pitch: 0.000e+00 fm submodule axial size: 1.900e+00 cm submodule tangential size: 2.000e+00 cm submodule axial pitch: 1.950e+00 cm submodule tangential pitch: 0.000e+00 fm crystal radial size: 2.200e+00 mm crystal axial size: 2.200e+00 mm crystal tangential size: 2.000e+00 cm crystal axial pitch: 2.400e+00 mm crystal tangential pitch: 0.000e+00 fm layer0 radial size: 2.200e+00 mm in layer0 interaction length: 1.100e+00 mm layer1 radial size: 2.200e+00 mm in layer1 interaction length: 1.100e+00 mm Axial nb of rsectors: 1Azimuthal nb of rsectors: 8Axial nb of modules: 1Tangential nb of modules: 1Axial nb of submodules: 13Tangential nb of submodules: 1Axial nb of crystals: 8Tangential nb of crystals: 1Radial nb of layers: 2 Range Translator Range 0 : imageValue in [ 0.000e+00 , 1.500e+03 ] ---> activity (Bq) 0.000e+00 Range 1 : imageValue in [ 1.501e+03 , 2.250e+03 ] ---> activity (Bq) 1.000e+01 Range 2 : imageValue in [ 2.251e+03 , 2.750e+03 ] ---> activity (Bq) 2.000e+01 Range 3 : imageValue in [ 2.751e+03 , 3.848e+03 ] ---> activity (Bq) 3.000e+01GateSourceVoxelImageReader::ReadFile : fileName: CT-IM00120_uint16.h33', assuming default BIGENDIAN'LITTLEENDIAN
'nrecognised type name 'unsigned integer Header read from 'CT-IM00120_uint16.h33''Data file name 'm001-IM00120.i33 Nb of planes: 1 Nb of pixels per plane: 512 512 Pixel size: 4.590e-01 4.590e-01 Slice thickness: 2.179e+00 Matrix size: 2.350e+02 2.350e+02 Data type: Data byte order: BIGENDIAN
'!ror: Could not open header file 'm001-IM00120.i33 **** Error: Volume does not exist **** Ignoring confine conditionSource ---------------> voxel_brain ID : 0 type : backtoback startTime (s) : 0.000e+00 time (s) : 0.000e+00 forcedUnstable : 0 verboseLevel : 0----------------------- Voxel reader ----------> number of voxels : 0 total activity (Bq) : 0.000e+00 position (mm) : 0.000e+00 0.000e+00 0.000e+00 voxel size (mm) : 1.000e+00 1.000e+00 1.000e+00Source --------------> voxel_brain ID : 0 type : backtoback activity (Bq) : 0.000e+00 startTime (s) : 0.000e+00 time (s) : 0.000e+00 forcedUnstable : 0 forcedHalfLife (s) : -6.931e-01 verboseLevel : 0 relative to vol : World----------------------
GPS info ----------------> particle : gamma SourcePosType : Point Shape : NULL halfx,halfy,halfz (mm) : 0.000e+00 0.000e+00 0.000e+00 Radius (mm) : 0.000e+00 CentreCoords (mm) : 0.000e+00 0.000e+00 0.000e+00 EnergyDisType : Mono AngleDisType : iso MinTheta, MaxTheta (deg) : 0.000e+00 1.800e+02 MinPhi, MaxPhi (deg) : 0.000e+00 3.600e+02 --------------------------
GateSourceMgr::ListSources: List of the sources in the source managerSource ---------------> voxel_brain ID : 0 type : backtoback startTime (s) : 0.000e+00 time (s) : 0.000e+00 forcedUnstable : 0
verboseLevel : 0----------------------- ***** COMMAND NOT FOUND </gate/output/root/setRootdelayFlag 1> *****
***** Batch is interrupted!! *****[Acquisition-0] [Acquisition-0] ============= Source initialization =============[Acquisition-0] [Acquisition-0] ============= Acquisition starts! =============[Acquisition-0] Simulation start time = 0 sec[Acquisition-0] Simulation end time = 2.5 sec[Acquisition-0] Simulation will have = 1 run(s)[Acquisition-0] [Acquisition-0] Slice 0 from 0 to 2.5 s [slice=2.5 s], final stop at 2.5 s.
PhotoElectric: for gamma SubType= 12 ===== EM models for the G4Region DefaultRegionForTheWorld ====== PhotoElectric : Emin= 0.000e+00 eV Emax= 1.000e+01 TeV
Compton: for gamma SubType= 13 Lambda tables from 1.000e+02 eV to 1.000e+01 TeV in 77 bins, spline: 1 ===== EM models for the G4Region DefaultRegionForTheWorld ====== Klein-Nishina : Emin= 0.000e+00 eV Emax= 1.000e+01 TeV
Bremsstrahlung: for e- SubType= 3 dE/dx and range tables from 1.000e+02 eV to 1.000e+01 TeV in 77 bins Lambda tables from threshold to 1.000e+01 TeV in 77 bins, spline: 1 LPM flag: 1 for E > 1.000e+00 GeV ===== EM models for the G4Region DefaultRegionForTheWorld ====== eBremSB : Emin= 0.000e+00 eV Emax= 1.000e+00 GeV AngularGenUrban eBremLPM : Emin= 1.000e+00 GeV Emax= 1.000e+01 TeV AngularGenUrban
ElectronIonisation: for e- SubType= 2 dE/dx and range tables from 1.000e+02 eV to 1.000e+01 TeV in 77 bins Lambda tables from threshold to 1.000e+01 TeV in 77 bins, spline: 1 finalRange(mm)= 1.000e+00, dRoverRange= 2.000e-01, integral: 1, fluct: 1, linLossLimit= 1.000e-02 ===== EM models for the G4Region DefaultRegionForTheWorld ====== MollerBhabha : Emin= 0.000e+00 eV Emax= 1.000e+01 TeV
Bremsstrahlung: for e+ SubType= 3 dE/dx and range tables from 1.000e+02 eV to 1.000e+01 TeV in 77 bins Lambda tables from threshold to 1.000e+01 TeV in 77 bins, spline: 1 LPM flag: 1 for E > 1.000e+00 GeV ===== EM models for the G4Region DefaultRegionForTheWorld ====== eBremSB : Emin= 0.000e+00 eV Emax= 1.000e+00 GeV AngularGenUrban eBremLPM : Emin= 1.000e+00 GeV Emax= 1.000e+01 TeV AngularGenUrban
ElectronIonisation: for e+ SubType= 2 dE/dx and range tables from 1.000e+02 eV to 1.000e+01 TeV in 77 bins Lambda tables from threshold to 1.000e+01 TeV in 77 bins, spline: 1 finalRange(mm)= 1.000e+00, dRoverRange= 2.000e-01, integral: 1, fluct: 1, linLossLimit= 1.000e-02 ===== EM models for the G4Region DefaultRegionForTheWorld ====== MollerBhabha : Emin= 0.000e+00 eV Emax= 1.000e+01 TeV1 event has been kept for refreshing and/or reviewing. User simulation time (sec) := 4.900e-01 Real simulation time (sec) := 2.860e+00 System simulation time (sec) := 6.000e-02[Core-0] End of macro hrrt.macGateOutputMgr deleting...Graphics systems deleted.Visualization Manager deleting...WARNING - Attempt to delete the physical volume store while geometry closed !WARNING - Attempt to delete the logical volume store while geometry closed !WARNING - Attempt to delete the solid store while geometry closed !WARNING - Attempt to delete the region store while geometry closed !
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