[gate-users] range.dat

[ziad bitar]

Good morning Theodore!
First i suggest that you verify the type of your data,
whether it's in "unsigned integer" or in "float".
Second, I suggest that you go to the source code
"GateGeometryVoxelIneterfileReader.cc" and find out
whether there is anydeclaration of a table of unsigned
integer or float.
I supposed that your data can't be read within Gate
cause Gate for the moment can read only "unsigned
integer data".
Verify your data type and its size.
I've had the same problems few days ago and it comes
from what i said above.
 > Error: the number of pixels that were read from
> the data file (1787386)
> > is inferior to the number computed from its header
> file (3574773)!
This message means that your dats has not the same
type of the data read by Gate by default!You can
clearly notice that the number of pixles computed
within the intefile header id the double of the one
read from data file.
Keep me up to date!
Good Luck
ziad
--- Mutanga Theodore <muathe02 at student.umu.se> wrote:

> Here is yet another error :
>   ...
> nx ny nz: 512 512 47
> dx dy dz: 9.766e-01 9.766e-01 3.348e+00
> terminate called after throwing an instance of
> 'std::bad_alloc'
>   what():  St9bad_alloc
> Abort
> 
> 
> I get that even from using the example for voxelized
> phantom source en
> GATE examples.
> 
> Please someone help on this error message
> 
> Regards
> 
> Theo
> 
> > Greetings
> >
> > Please disregard the first message I found out
> that there were extra ( ^M
> > )added to each line in the header file of the
> interfile header, when I
> > took all of them away I no longer had the message
> I posted earlier.
> > But after that , the GATE interfile reader
> complains thus
> >
> > Error: the number of pixels that were read from
> the data file (1787386)
> > is inferior to the number computed from its header
> file (3574773)!
> >
> > This is GATE 2.2.0 as stated on the website and
> the version of Xmedcon  is
> >
> > conversion program := (X)MedCon
> >
> > program author := Erik Nolf
> >
> > program version := 0.9.8.6
> >
> > program date := 2005:07:31
> >
> > I look forward to hearing from anyone with
> simillar experiences.
> >
> > Cheers
> >
> > Theo
> >
> >> Greetings and thanks for the answer to the post
> for yesterday. I had
> >> figured out how to avoid the negative values
> using medcon.
> >
> >>
> >> Now I have my voxel phantom as unsigned integer
> in interfile format
> >> converted using xmedcon but still i get the error
> message below and gate
> >> aborts :
> >>
> >>
> >> /gate/nema_vox_phant/interfileReader/readFile
> m001-nema.h33
> >> 'nrecognised type name 'unsigned integer
> >>  Header read from       'm001-nema.h33'
> >> 'Data file name         'm001-nema.i33
> >>  Nb of planes:           47
> >>  Nb of pixels per plane: 313 243
> >>  Pixel size:             9.766e-01 9.766e-01
> >>  Slice thickness:        3.348e+00
> >>  Matrix size:            3.057e+02 2.373e+02
> >>  Data type:
> >>
> >>
> >> '!ror: Could not open header file 'm001-nema.i33
> >> /gate/nema_vox_phant/placement/setTranslation  0.
> 0. 0. mm
> >> /gate/nema_vox_phant/placement/setRotationAxis 1
> 0 0
> >> /gate/nema_vox_phant/placement/setRotationAngle 0
> deg
> >> /gate/nema_vox_phant/attachVoxelPhantomSD
> >> PreInit>
> >> PreInit> /gate/physics/gamma/selectRayleigh
> lowenergy
> >> /gate/physics/gamma/selectRayleigh lowenergy
> >> PreInit> /gate/physics/gamma/selectPhotoelectric
> standard
> >> /gate/physics/gamma/selectPhotoelectric standard
> >> PreInit> /gate/physics/gamma/selectCompton
> standard
> >> /gate/physics/gamma/selectCompton standard
> >> PreInit> /gate/physics/setElectronCut 1. m
> >> /gate/physics/setElectronCut 1. m
> >> PreInit> /gate/physics/setXRayCut 1. GeV
> >> /gate/physics/setXRayCut 1. GeV
> >> PreInit> /gate/physics/setDeltaRayCut 1. GeV
> >> /gate/physics/setDeltaRayCut 1. GeV
> >> PreInit>
> >> PreInit> /gate/geometry/enableAutoUpdate
> >> /gate/geometry/enableAutoUpdate
> >> ERROR - G4Box()::G4Box(): nema_vox_phant_S
> >>         Dimensions too small ! - 0, 0, 0
> >>
> >> *** G4Exception : InvalidSetup
> >>       issued by : G4Box::G4Box()
> >> Invalid dimensions. Too small.
> >> *** Fatal Exception *** core dump ***
> >>
> >> *** G4Exception: Aborting execution ***
> >> Abort
> >>
>
********************************************************************
> >>
> >> Is there something wrong with my voxel phantom
> datatype ?
> >>
> >> Cheers
> >>
> >> theo
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>> Dear Theodore,
> >>>
> >>> The thing to do is to use unsigned integers for
> your voxelized phantom
> >>> values.
> >>>
> >>> example:
> >>>  5  ==  [nr of intervals to be defined]
> >>>   0      0       Air        false 0.0  0.0  0.0 
> 0.2    == [range from]
> >>> [to] [material] [visualisation boolean]
> [%Red][%Green][%Blue][%Alpha]
> >>>   6      6       Lung       false 1.0  0.0  0.0 
> 0.2
> >>>   6      16      Breast     flase 0.0  1.0  0.0 
> 0.2
> >>>   16     36      Plastic    true  0.0  0.0  1.0 
> 0.2
> >>>   36     200     Air        false 0.0  0.0  0.0 
> 0.2
> >>>
> >>> Cheers
> >>>
> >>> Roel
> >>> _______________________________________________
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> >>> gate-users at lphe1pet1.epfl.ch
> >>>
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >>>
> >>
> >>
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> >>
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> >>
> >
> >
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> >
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> 
> 
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