[Gate-users] GATE cannot find interfile data from header

[Tristan Glatard]

Hi Marc,

Modifying the header files works, but it makes the image unreadable by 
other programs (e.g. xmedcon) that assume that the data is referred 
relatively to the header.
This should be fixed in GATE I think. No show-stopper of course.

Cheers,
Tristan

On 08/30/2012 03:09 PM, Marc Chamberland wrote:
> Hi Tristan!
>
> I took a look at the source code of the Interfile reader in Gate, and 
> yes, you do need to include the sub-directory in the Interfile header.
>
> If you look at the Time Activity Curve example included with Gate, 
> you'll see that they include the sub-directory in the "name of data 
> file" in the Interfile header.
>
> I don't know if this qualifies as a bug or not, but I'd suggest you 
> just work around it by modifying your header files (or moving them to 
> your execution directory).
>
> Marc
>
>
>
> __________________________
>
> Marc Chamberland, MSc
> PhD candidate
> Department of Physics
> Carleton University
> Ottawa (ON)
>
>
> Le 2012-08-30 à 8:58 AM, Tristan Glatard 
> <tristan.glatard at creatis.insa-lyon.fr 
> <mailto:tristan.glatard at creatis.insa-lyon.fr>>
>  a écrit :
>
>> Hi,
>>
>> We have a macro involving a source in interfile format, stored in a 
>> subdirectory called "data":
>>> [glatard at kingkong gate.sh-2294696198382639]$ grep phantom 
>>> mac/adapted-mainMacro.mac  | grep -v \#
>>> /gate/hof_brain/interfileReader/readFile data/brain_phantom.h33
>>> /gate/source/voxel_brain/interfileReader/readFile data/brain_phantom.h33
>> The header of this interfile references the data relatively to the 
>> header path, i.e. without the subdirectory:
>>> [glatard at kingkong gate.sh-2294696198382639]$ grep phantom 
>>> data/brain_phantom.h33
>>> !name of data file := brain_phantom.i33
>>> [glatard at kingkong gate.sh-2294696198382639]$ ls data | grep phantom
>>> brain_phantom.h33
>>> brain_phantom.i33
>> GATE cannot find the data file:
>>> [glatard at kingkong gate.sh-2294696198382639]$ ./Gate 
>>> mac/adapted-mainMacro.mac 1>/dev/null
>>>    [G4-cerr]
>>>    [G4-cerr] Error: Could not open header file 'brain_phantom.i33'!
>>>    [G4-cerr] ERROR - G4Box()::G4Box(): hof_brain_solid
>>>    [G4-cerr]         Dimensions too small ! - 0, 0, 0
>>>    [G4-cerr]
>>>    [G4-cerr] *** G4Exception : InvalidSetup
>>>    [G4-cerr]       issued by : G4Box::G4Box()
>>>    [G4-cerr] Invalid dimensions. Too small.
>>>    [G4-cerr] *** Fatal Exception *** core dump ***
>>>    [G4-cerr]
>>>    [G4-cerr] *** G4Exception: Aborting execution ***
>>> Aborted
>> It works if we add the subdirectory to the data file name in the 
>> interfile header:
>>> [glatard at kingkong gate.sh-2294696198382639]$ grep phantom 
>>> data/brain_phantom.h33
>>> !name of data file := data/brain_phantom.i33
>>> [glatard at kingkong gate.sh-2294696198382639]$ ./Gate 
>>> mac/adapted-mainMacro.mac 1>/dev/null
>>> [glatard at kingkong gate.sh-2294696198382639]$ echo $?
>>> 0
>>
>> Is it a bug in the interfile reader of GATE, or should we adjust 
>> interfile headers according to their location?
>>
>> Thanks in advance, cheers,
>> Tristan
>>
>> -- 
>> Tristan Glatard
>> CNRS researcher, CREATIS
>> http://www.creatis.insa-lyon.fr/~glatard 
>> <http://www.creatis.insa-lyon.fr/%7Eglatard>
>> Tél : +33 (0) 4 72 43 75 47
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>


-- 
Tristan Glatard
CNRS researcher, CREATIS
http://www.creatis.insa-lyon.fr/~glatard
Tél : +33 (0) 4 72 43 75 47