[Gate-users] GateApplicationMgr.cc Error
Siti Salasiah MusNMey
ctsalasiah1950 at gmail.com
Mon Mar 11 01:51:28 CET 2013
Hi,
Please help me considering my simulation problem. I define my mac file with
the following simulation:
##################################
# EXPERIMENT
#
/gate/application/setTimeSlice 60.0 s
/gate/application/setTimeStart 0 s
/gate/application/setTimeStop 60.0 s
/gate/application/startDAQ
After running for a week, I have this error
*/home/gate/Progs/Gate/gate_v6.2/source/general/src/GateApplicationMgr.cc
(l.220): Error in GateApplicationMgr::GetTimeSlice, run=2. *The same
problem happens when I simulate before for 1800 s after running for two
weeks. Is it because of memory or what? It has been a month but I cant get
correct GATE simulation. Please help me.
Siti
List of initialized processes:
[Core-0] Initialization of geometry
[Physic-1]
[Physic-1] ----------------------------------------------------------
[Physic-1] Ionization potential
[Physic-1] - worldDefaultAir defaut value: I = 85.7031 eV
[Physic-1] - Air defaut value: I = 85.6694 eV
[Physic-1] - Vacuum defaut value: I = 19.2 eV
[Physic-1] - BGO defaut value: I = 473.785 eV
[Physic-1] - Tungsten defaut value: I = 727 eV
[Physic-1] - Lung defaut value: I = 69.7265 eV
[Physic-1] - Body defaut value: I = 69.0157 eV
[Physic-1] - SpineBone defaut value: I = 85.2598 eV
[Physic-1] - RibBone defaut value: I = 102.82 eV
[Physic-1] ----------------------------------------------------------
[Core-0] Initialization of physics
[Physic-2] GatePhysicsList::ConstructProcess
[Physic-3] mLoadState = 1
[Physic-3] mListOfStepLimiter.size = 0
[Core-0] Initialization of actors
Nof Higher level 2
GATE object: 'digitizer/Coincidences'
Is enabled? Yes
Coincidence window: 1.000e+01 ns
Coincidence window jitter: 0.000e+00 ps
Coincidence offset: 0.000e+00 ps
Coincidence offset jitter: 0.000e+00 ps
Min sector diff.: 2
Input: 'Singles'
Output: 'Coincidences'
GATE object: 'digitizer/delay'
Is enabled? Yes
Coincidence window: 1.000e+01 ns
Coincidence window jitter: 0.000e+00 ps
Coincidence offset: 5.000e+02 ns
Coincidence offset jitter: 0.000e+00 ps
Min sector diff.: 2
Input: 'Singles'
Output: 'delay'
in GateCoincidencePulseProcessorChain call new GateCoincidenceDigiMaker
GATE object: 'digitizer/finalCoinc'
Is enabled? Yes
Nb of elements: 0
Attached to: 'digitizer'
Output: 'finalCoinc'
Output module: 'sinogram'
>> Job: build a set of 2D sinograms from a
PET simulation
>> Is enabled ? Yes
>> Number of crystals per crystal ring: 0
>> Number of crystal rings: 0
>> Number of radial sinogram bins: 0
>> Filled ? No
>> Attached to system: systems/ecat
>> Input data: finalCoinc
Output module: 'ecat7'
>> Job: write a set of 2D sinograms into an Ecat7 output
file
>> Is enabled ? Yes
>> File name: NCATSinogramEcat.S
>> Attached to system: systems/ecat
Range Translator
Range 0 : imageValue in [ 0.000e+00 , 0.000e+00 ] ---> activity (Bq)
0.000e+00
Range 1 : imageValue in [ 2.000e+00 , 2.000e+00 ] ---> activity (Bq)
8.000e+03
Range 2 : imageValue in [ 4.000e+00 , 4.000e+00 ] ---> activity (Bq)
2.400e+03
Range 3 : imageValue in [ 6.000e+01 , 6.000e+01 ] ---> activity (Bq)
6.000e+04
Range 4 : imageValue in [ 7.500e+01 , 7.500e+01 ] ---> activity (Bq)
8.400e+04
GateSourceVoxelImageReader::ReadFile : fileName: ncat_header_act.h33
Header read from 'ncat_header_act.h33'
Data file name 'Section1_act.i33'
Nb of planes: 21
Nb of pixels per plane: 64 64
Pixel size: 6.250e+00 6.250e+00
Slice thickness: 6.250e+00
Matrix size: 4.000e+02 4.000e+02
Data type: UNSIGNED INTEGER
Data byte order: LITTLEENDIAN
**** Error: Volume does not exist ****
Ignoring confine condition
Source ---------------> voxel_NCAT
ID : 0
type : backtoback
startTime (s) : 0.000e+00
time (s) : 0.000e+00
forcedUnstable : 1
forcedLifetime (s) : 9.502e+03
verboseLevel : 0
-----------------------
Voxel reader ----------> number of voxels : 44735
total activity (Bq) : 8.224e+08
position (mm) : 0.000e+00 0.000e+00 0.000e+00
voxel size (mm) : 6.250e+00 6.250e+00 6.250e+00
Source --------------> voxel_NCAT
ID : 0
type : backtoback
activity (Bq) : 0.000e+00
startTime (s) : 0.000e+00
time (s) : 0.000e+00
forcedUnstable : 1
forcedHalfLife (s) : 6.586e+03
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 manager
Source ---------------> voxel_NCAT
ID : 0
type : backtoback
startTime (s) : 0.000e+00
time (s) : 0.000e+00
forcedUnstable : 1
forcedLifetime (s) : 9.502e+03
verboseLevel : 0
-----------------------
GateSourceMgr::ListSources: List of the sources in the source manager
Source ---------------> voxel_NCAT
ID : 0
type : backtoback
startTime (s) : 0.000e+00
time (s) : 0.000e+00
forcedUnstable : 1
forcedLifetime (s) : 9.502e+03
verboseLevel : 0
-----------------------
[Acquisition-0]
[Acquisition-0] ============= Source initialization =============
[Acquisition-0]
[Acquisition-0] ============= Acquisition starts! =============
[Acquisition-0] Simulation start time = 0 sec
[Acquisition-0] Simulation end time = 60 sec
[Acquisition-0] Simulation will have = 1 run(s)
----- HepJamesRandom engine status -----
Initial seed = 669708517
u[] = 0.313493 0.22101 0.720638 0.288275 0.209104 0.961876 0.0185378
0.767277 0.570899 0.11677 0.585697 0.361668 0.499346 0.969958 0.659357
0.470614 0.232287 0.851241 0.27455 0.788571 0.407255 0.205312 0.558045
0.841456 0.443543 0.0437512 0.20597 0.975022 0.180286 0.842097 0.240617
0.115375 0.0104213 0.86239 0.254429 0.284886 0.114014 0.250714 0.477909
0.527364 0.887455 0.402326 0.5341 0.418133 0.107406 0.124517 0.302133
0.489961 0.8011 0.598657 0.398494 0.285134 0.133646 0.956609 0.548981
0.0394724 0.830412 0.922722 0.527004 0.588913 0.129604 0.169863 0.043967
0.0808861 0.801898 0.583084 0.269808 0.84379 0.235689 0.208139 0.683603
0.275 0.411587 0.134052 0.253045 0.356203 0.629278 0.233236 0.444437
0.502942 0.77252 0.00816381 0.210178 0.938382 0.894515 0.511199 0.913346
0.907528 0.240269 0.448999 0.814368 0.13479 0.692496 0.707161 0.983838
0.703152 0.403158
c = 0.652903, cd = 0.456233, cm = 1
i97 = 93, u[i97] = 0.707161
j97 = 29, u[j97] = 0.842097
----------------------------------------
>> entering [GateToSinogram::RecordBeginOfAcquisition]
Acquisition start time: 0.000e+00
Number of frames: 1
Total number of crystals per crystal rings: 576
Number of crystal rings: 32
Number of radial sinogram bins: 288
Number of azimuthal sinogram bins: 288
Crystal location blurring in tangential direction: 1.800e+00 mm
Crystal location blurring in axial direction: 1.800e+00 mm
Prompt coincidences are recorded in data = 0
Delayed coincidences (if simulated) are recorded in data = 1
True scattered coincidences (eventID1 = eventID2) are recorded in data
= 4
>> leaving [GateToSinogram::RecordBeginOfAcquisition]
>> entering [GateSinoToEcat7::RecordBeginOfAcquisition]
Number of crystal rings: 32
crystal axial pitch: 4.850e+00 mm
crystal transverse pitch: 4.494e+00 mm
ECAT7 file NCATSinogramEcat.S created
>> leaving [GateSinoToEcat7::RecordBeginOfAcquisition]
[Acquisition-0]
[Acquisition-0] Slice 0 from 0 to 60 s [slice=60 s], final stop at 60 s.
RayleighScattering: for gamma SubType= 11
Lambda tables from 1.000e+02 eV to 1.000e+01 TeV in 200 bins,
spline: 1
===== EM models for the G4Region DefaultRegionForTheWorld ======
PenRayleigh : Emin= 0.000e+00 eV Emax= 1.000e+02 GeV
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
PhotoElectric: for gamma SubType= 12
===== EM models for the G4Region DefaultRegionForTheWorld ======
PhotoElectric : Emin= 0.000e+00 eV Emax= 1.000e+01 TeV
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 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
annihil: for e+ SubType= 5
===== EM models for the G4Region DefaultRegionForTheWorld ======
eplus2gg : Emin= 0.000e+00 eV Emax= 1.000e+01 TeV
>> entering [GateToSinogram::RecordBeginOfRun]
Frame ID = 1
>> leaving [GateToSinogram::RecordBeginOfRun]
>> entering [GateSinoToEcat7::RecordBeginOfRun]
Frame ID: 1
Gate ID: 1
Bed position: 0
Prompt coincidences are recorded with data = 0
Delayed coincidences (if simulated) are recorded with data = 1
True scattered coincidences are recorded with data = 4
>> leaving [GateSinoToEcat7::RecordBeginOfRun]
WARNING: Scene "refresh" not found.
/vis/scene/list to see scenes.
>> entering [GateToSinogram::RecordEndOfRun]
Number of prompt coincidences for all ring combinations 2889636
Number of true coincidences for all ring combinations 513257
Number of scattered coincidences for all ring combinations 8
Number of random coincidences for all ring combinations 2376379
Number of delayed coincidences for all ring combinations 2273250
sinograms 1,1,1,0,0 written to the raw file NCATSinogram_1.ima
sinograms 1,1,1,1,0 written to the raw file NCATSinogram_1_del.ima
sinograms 1,1,1,4,0 written to the raw file NCATSinogram_1_sct.ima
>> leaving [GateToSinogram::RecordEndOfRun]
>> entering [GateSinoToEcat7::RecordEndOfRun]
Frame ID: 1
Gate ID: 1
Data ID: 0
Bed ID: 0
Number of sinogram radial elements: 288
Number of sinogram azimutal elements: 144
Maximum ring difference: 22
Span factor: 9
==> Number of segments 5
Segment 0 is for ring difference -4 to 4
and goes from slice 0 to slice 62
Segment 1 is for ring difference 5 to 13
and goes from slice 5 to slice 57
Segment -1 is for ring difference -13 to -5
and goes from slice 5 to slice 57
Segment 2 is for ring difference 14 to 22
and goes from slice 14 to slice 48
Segment -2 is for ring difference -22 to -14
and goes from slice 14 to slice 48
Frame start time: 0 msec
Frame duration: 60000 msec
Number of prompts in ECAT sinogram 2613153
Number of delayeds in ECAT sinogram 2064498
Number of net trues in ECAT sinogram 548655
Maximum bin content: 8
Frame ID: 1
Gate ID: 1
Data ID: 1
Bed ID: 0
Number of sinogram radial elements: 288
Number of sinogram azimutal elements: 144
Maximum ring difference: 22
Span factor: 9
==> Number of segments 5
Segment 0 is for ring difference -4 to 4
and goes from slice 0 to slice 62
Segment 1 is for ring difference 5 to 13
and goes from slice 5 to slice 57
Segment -1 is for ring difference -13 to -5
and goes from slice 5 to slice 57
Segment 2 is for ring difference 14 to 22
and goes from slice 14 to slice 48
Segment -2 is for ring difference -22 to -14
and goes from slice 14 to slice 48
Frame start time: 0 msec
Frame duration: 60000 msec
Number of prompts in ECAT sinogram 2613153
Number of delayeds in ECAT sinogram 2064498
Number of net trues in ECAT sinogram 548655
Maximum bin content: 6
Frame ID: 1
Gate ID: 1
Data ID: 4
Bed ID: 0
Number of sinogram radial elements: 288
Number of sinogram azimutal elements: 144
Maximum ring difference: 22
Span factor: 9
==> Number of segments 5
Segment 0 is for ring difference -4 to 4
and goes from slice 0 to slice 62
Segment 1 is for ring difference 5 to 13
and goes from slice 5 to slice 57
Segment -1 is for ring difference -13 to -5
and goes from slice 5 to slice 57
Segment 2 is for ring difference 14 to 22
and goes from slice 14 to slice 48
Segment -2 is for ring difference -22 to -14
and goes from slice 14 to slice 48
Frame start time: 0 msec
Frame duration: 60000 msec
Number of prompts in ECAT sinogram 2613153
Number of delayeds in ECAT sinogram 2064498
Number of net trues in ECAT sinogram 548655
Maximum bin content: 1
>> leaving [GateSinoToEcat7::RecordEndOfRun]
ERROR: G4VisCommandsViewerUpdate::SetNewValue: no current viewer.
[Acquisition-0]
[Acquisition-0] Slice 1 from 60 to 60 s [slice=5.2865e-322 s], final stop
at 60 s.
>> entering [GateToSinogram::RecordBeginOfRun]
Frame ID = 2
>> leaving [GateToSinogram::RecordBeginOfRun]
>> entering [GateSinoToEcat7::RecordBeginOfRun]
Frame ID: 2
Gate ID: 1
Bed position: 0
Prompt coincidences are recorded with data = 0
Delayed coincidences (if simulated) are recorded with data = 1
True scattered coincidences are recorded with data = 4
>> leaving [GateSinoToEcat7::RecordBeginOfRun]
WARNING: Scene "refresh" not found.
/vis/scene/list to see scenes.
>> entering [GateToSinogram::RecordEndOfRun]
Number of prompt coincidences for all ring combinations 2893393
Number of true coincidences for all ring combinations 514122
Number of scattered coincidences for all ring combinations 15
Number of random coincidences for all ring combinations 4755650
Number of delayed coincidences for all ring combinations 2276450
sinograms 2,1,1,0,0 written to the raw file NCATSinogram_2.ima
sinograms 2,1,1,1,0 written to the raw file NCATSinogram_2_del.ima
sinograms 2,1,1,4,0 written to the raw file NCATSinogram_2_sct.ima
>> leaving [GateToSinogram::RecordEndOfRun]
>> entering [GateSinoToEcat7::RecordEndOfRun]
Frame ID: 2
Gate ID: 1
Data ID: 0
Bed ID: 0
Number of sinogram radial elements: 288
Number of sinogram azimutal elements: 144
Maximum ring difference: 22
Span factor: 9
==> Number of segments 5
Segment 0 is for ring difference -4 to 4
and goes from slice 0 to slice 62
Segment 1 is for ring difference 5 to 13
and goes from slice 5 to slice 57
Segment -1 is for ring difference -13 to -5
and goes from slice 5 to slice 57
Segment 2 is for ring difference 14 to 22
and goes from slice 14 to slice 48
Segment -2 is for ring difference -22 to -14
and goes from slice 14 to slice 48
Frame start time: 60000 msec
Frame duration: 60000 msec
Number of prompts in ECAT sinogram 2617690
Number of delayeds in ECAT sinogram 2067230
Number of net trues in ECAT sinogram 550460
Maximum bin content: 7
Frame ID: 2
Gate ID: 1
Data ID: 1
Bed ID: 0
Number of sinogram radial elements: 288
Number of sinogram azimutal elements: 144
Maximum ring difference: 22
Span factor: 9
==> Number of segments 5
Segment 0 is for ring difference -4 to 4
and goes from slice 0 to slice 62
Segment 1 is for ring difference 5 to 13
and goes from slice 5 to slice 57
Segment -1 is for ring difference -13 to -5
and goes from slice 5 to slice 57
Segment 2 is for ring difference 14 to 22
and goes from slice 14 to slice 48
Segment -2 is for ring difference -22 to -14
and goes from slice 14 to slice 48
Frame start time: 60000 msec
Frame duration: 60000 msec
Number of prompts in ECAT sinogram 2617690
Number of delayeds in ECAT sinogram 2067230
Number of net trues in ECAT sinogram 550460
Maximum bin content: 5
Frame ID: 2
Gate ID: 1
Data ID: 4
Bed ID: 0
Number of sinogram radial elements: 288
Number of sinogram azimutal elements: 144
Maximum ring difference: 22
Span factor: 9
==> Number of segments 5
Segment 0 is for ring difference -4 to 4
and goes from slice 0 to slice 62
Segment 1 is for ring difference 5 to 13
and goes from slice 5 to slice 57
Segment -1 is for ring difference -13 to -5
and goes from slice 5 to slice 57
Segment 2 is for ring difference 14 to 22
and goes from slice 14 to slice 48
Segment -2 is for ring difference -22 to -14
and goes from slice 14 to slice 48
Frame start time: 60000 msec
Frame duration: 60000 msec
Number of prompts in ECAT sinogram 2617690
Number of delayeds in ECAT sinogram 2067230
Number of net trues in ECAT sinogram 550460
Maximum bin content: 1
>> leaving [GateSinoToEcat7::RecordEndOfRun]
ERROR: G4VisCommandsViewerUpdate::SetNewValue: no current viewer.
[Acquisition-0]
[Acquisition-0] Slice 2 from 60 to 7.01573e-322 s [slice=1.14623e-321 s],
final stop at 60 s.
>> entering [GateToSinogram::RecordBeginOfRun]
Frame ID = 3
>> leaving [GateToSinogram::RecordBeginOfRun]
>> entering [GateSinoToEcat7::RecordBeginOfRun]
Frame ID: 3
Gate ID: 1
Bed position: 0
Prompt coincidences are recorded with data = 0
Delayed coincidences (if simulated) are recorded with data = 1
True scattered coincidences are recorded with data = 4
>> leaving [GateSinoToEcat7::RecordBeginOfRun]
WARNING: Scene "refresh" not found.
/vis/scene/list to see scenes.
*/home/gate/Progs/Gate/gate_v6.2/source/general/src/GateApplicationMgr.cc
(l.220): Error in GateApplicationMgr::GetTimeSlice, run=2*
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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