[gate-users] Re: gate-users Digest, Vol 19, Issue 6

elbitar at clermont.in2p3.fr elbitar at clermont.in2p3.fr
Wed Oct 12 14:38:37 CEST 2005 

Quoting gate-users-request at lphe1pet1.epfl.ch:
I am not sure that doing "file size = xpixel X ypixel X numslices X numbytes per
pixel" will fix the problem.
There is a bad allocation somewhere. Try to access to the data within the
hofmann phantom and print them to the standard output.

Regards
ziad
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> Today's Topics:
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>    1. Re: range.dat (Mutanga Theodore)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
I>
Date: Wed, 12 Oct 2005 11:39:19 +0200 (MET DST)
> From: "Mutanga Theodore" <muathe02 at student.umu.se>
> Subject: Re: [gate-users] range.dat
> To: "GATE feedback and helpline for Users"
> 	<gate-users at lphe1pet1.epfl.ch>
> Message-ID: <33009.130.239.99.15.1129109959.squirrel at 130.239.99.15>
> Content-Type: text/plain;charset=iso-8859-1
>
> Greetings
> thanks for replying.
> I had found out that the medcon program was not able to manipulate my data
> well I don't know why. I have managed to verify what data I have and now
> there is another conversion which which seems to be right ie :
>
> file size = xpixel X ypixel X numslices X numbytes per pixel
>
> I have done this and checked the data to be unsigned integer but using
> Gate I still get the second arror that I mentioned above.  ie :
>
> >> 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 this error too while using the hofmann phantom and the voxelized
> phantom example.
>
> Regards
>
> Theo
>
> > 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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> >> >>
> >> >>
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> End of gate-users Digest, Vol 19, Issue 6
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