[gate-users] range.dat
Mutanga Theodore
muathe02 at student.umu.se
Wed Oct 12 11:39:19 CEST 2005
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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