[Insight-developers] itk 3.18's nrrd io on windows vs 2008 pro

Mon May 3 08:12:32 EDT 2010

Sorry for the slow response.

No, I haven't changed anything in the automatic regeneration of NrrdIO  
from Teem.

The kind of error here is probably from the header being the wrong  
length in the original Teem source; but that's odd; all the Teem  
sources should have identical boilerplate headers.

Gordon

On Apr 27, 2010, at 10:20 AM, Michel Audette wrote:

> Hi Gordon,
>
> has anything changed in the pre-GNUmakefile? Perhaps I didn''t catch  
> it before, but running it seems to reproduced the last two commented  
> lines in sane.c, which prevents make -f sample-GNUmakefile from  
> running successfully. If I take out those two lines (appearing in  
> bold), the make -f sample-GNUmakefile runs successfully.
>
>  2. Altered source versions must be plainly marked as such, and must
>     not be misrepresented as being the original software.
>
>  3. This notice may not be removed or altered from any source  
> distribution.
> */
>  3. This notice may not be removed or altered from any source  
> distribution.
> */
>
> In any event, I've committed sane.c, with c-style comments, to teem.  
> I will commit this sane.c to ITK.
>
> Let me know if there is anything else.
>
> Best wishes,
>
> Michel
>
> On Mon, Apr 26, 2010 at 4:11 PM, Michel Audette <michel.audette at kitware.com 
> > wrote:
> > I'll do it now. Gordon, please report back if there is a problem.
> >
> > Michel
> >
> > On Mon, Apr 26, 2010 at 12:48 PM, Luis Ibanez <luis.ibanez at kitware.com 
> > wrote:
> >>
> >> Hi Gordon,
> >>
> >> Thanks for pointing this out.
> >>
> >>            The answer is "No"      :-/
> >>
> >> We only committed the change to the file
> >>
> >>            Utilities/NrrdIO/sane.c
> >>
> >> in the ITK CVS HEAD and the ITK 3.18 branch.
> >>
> >>
> >> You are right in that we should propagate this to Teem,
> >> and then repeat the cycle for generating the NrrdIO code.
> >>
> >>
> >>         Michel:  Would you like to do this ?
> >>
> >> Otherwise, it looks like a good challenge for one
> >> of the recent volunteers for the Adopt-A-Bug 2.0
> >> program...
> >>
> >>
> >>     Please let me know,
> >>
> >>
> >>          Thanks
> >>
> >>
> >>                Luis
> >>
> >>
> >> --------------------------------------------------------
> >> On Mon, Apr 26, 2010 at 10:03 AM, Gordon L. Kindlmann <glk at uchicago.edu 
> >
> >> wrote:
> >>>
> >>> Hi,
> >>>
> >>> Not to be a debbie downer, but are these also in sync with Teem,  
> so that
> >>> the regenerated NrrdIO has the same fixes?
> >>>
> >>> If not, this might be a good occasion for me to make sure  
> someone else can
> >>> go through and process the instructions that we created, but I  
> won't be able
> >>> to get to that for a few weeks.
> >>>
> >>> Gordon
> >>>
> >>> On Apr 26, 2010, at 8:03 AM, Michel Audette wrote:
> >>>
> >>>> Glad that it's been sorted out. I'm starting to have nightmares  
> about
> >>>> NrrdIO. :-P
> >>>>
> >>>> Cheers,
> >>>>
> >>>> Michel
> >>>>
> >>>>
> >>>> On Sun, Apr 25, 2010 at 2:32 PM, Luis Ibanez <luis.ibanez at kitware.com 
> >
> >>>> wrote:
> >>>>>
> >>>>> Steve, Michel,
> >>>>>
> >>>>> Thanks for your help on tracking this problem.
> >>>>>
> >>>>> We have now committed patches to both
> >>>>>
> >>>>> the ITK CVS head
> >>>>>
> >>>>>
> >>>>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Utilities/NrrdIO/sane.c?root=Insight&r1=1.21&r2=1.22&sortby=date
> >>>>>
> >>>>> and the 3.18 branch.
> >>>>>
> >>>>>
> >>>>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Utilities/NrrdIO/sane.c?r1=1.21&r2=1.21.2.1&pathrev=ITK-3-18&sortby=date&root=Insight
> >>>>>
> >>>>>
> >>>>> Details are available at:
> >>>>>
> >>>>> http://public.kitware.com/Bug/view.php?id=10609
> >>>>>
> >>>>>
> >>>>> This should take care of the problem.
> >>>>>
> >>>>>
> >>>>>
> >>>>>     Thanks
> >>>>>
> >>>>>
> >>>>>             Luis
> >>>>>
> >>>>>
> >>>>> --------------------------------------------------
> >>>>> On Thu, Apr 22, 2010 at 11:43 AM, Luis Ibanez <luis.ibanez at kitware.com 
> >
> >>>>> wrote:
> >>>>>>
> >>>>>> Steve,
> >>>>>>
> >>>>>> Thanks for passing this along.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> Gordon, Michel,
> >>>>>>
> >>>>>> It looks like there are still some quirks with  NrrdIO.
> >>>>>>
> >>>>>> Could you please advise  ?
> >>>>>>
> >>>>>>
> >>>>>>     Thanks
> >>>>>>
> >>>>>>
> >>>>>>            Luis
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>  
> --------------------------------------------------------------------------------
> >>>>>> On Thu, Apr 22, 2010 at 11:27 AM, Steve Pieper <pieper at bwh.harvard.edu 
> >
> >>>>>> wrote:
> >>>>>>>
> >>>>>>> [Luis, I'm cc'ing you since this may be an issue for itk- 
> developers
> >>>>>>> and
> >>>>>>> I'm not on that list].
> >>>>>>>
> >>>>>>> Hi -
> >>>>>>>
> >>>>>>> When I try to use the version of nrrdio in ITK 3.18 on  
> windows I get a
> >>>>>>> problem inside airSanity().  The same file loads fine on  
> linux.
> >>>>>>>
> >>>>>>>>
> >>>>>>>> (GUI) 112 % ../../lib/Slicer3/Plugins/Debug/Add.exe
> >>>>>>>> c:/data/liverdata/LabelMap-Liver.nrrd
> >>>>>>>> c:/data/liverdata/LabelMap-Liver.nrrd
> >>>>>>>> c:/tmp/out.nrrd
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> C:\pieper\bwh\slicer3\fresh\Slicer3-build\lib 
> \Slicer3\Plugins\Debug\Add.exe:
> >>>>>>>> exception caught !
> >>>>>>>>
> >>>>>>>> itk::ExceptionObject (00D9DB20)
> >>>>>>>> Location: "void __thiscall
> >>>>>>>> itk::NrrdImageIO::ReadImageInformation(void)"
> >>>>>>>> File: ..\..\..\Insight\Code\IO\itkNrrdImageIO.cxx
> >>>>>>>> Line: 264
> >>>>>>>> Description: itk::ERROR: NrrdImageIO(0A638638):  
> ReadImageInformation:
> >>>>>>>> Error reading c:/data/liverdata/LabelMap-Liver.nrrd:
> >>>>>>>> [nrrd] nrrdLoad: trouble reading
> >>>>>>>> "c:/data/liverdata/LabelMap-Liver.nrrd"
> >>>>>>>> [nrrd] nrrdRead: trouble
> >>>>>>>> [nrrd] _nrrdRead: sanity check FAILED: have to fix and re- 
> compile
> >>>>>>>> [nrrd] nrrdSanity: airSanity() failed:  
> airFPClass(AIR_QNAN,AIR_SNAN)
> >>>>>>>> wrong
> >>>>>>>
> >>>>>>>
> >>>>>>> Also, my non-ITK teem (1.11) build works fine on this  
> platform and
> >>>>>>> compiler.
> >>>>>>>
> >>>>>>> I believe the issue is this checkin:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> http://public.kitware.com/cgi-bin/viewcvs.cgi/Utilities/NrrdIO/sane.c?root=Insight&r1=1.20&r2=1.21
> >>>>>>>
> >>>>>>>
> >>>>>>> I don't know the history of this check, but I think the  
> logic should
> >>>>>>> be:
> >>>>>>>
> >>>>>>> #if !defined(__APPLE__) || !defined(_MSC_VER) || _MSC_VER <  
> 1400 /*
> >>>>>>> Apple
> >>>>>>> and VS2005 convert SNAN to QNAN */
> >>>>>>>        && airFP_SNAN == airFPClass_f(AIR_SNAN)
> >>>>>>> #endif
> >>>>>>>
> >>>>>>> I.e. exclude the check for apple and mscv < 1400 compilers,  
> but
> >>>>>>> include
> >>>>>>> it for everything else.
> >>>>>>>
> >>>>>>> perhaps clearer would be:
> >>>>>>>
> >>>>>>> #if defined(__APPLE__) || (defined(_MSC_VER) && _MSC_VER <  
> 1400) /*
> >>>>>>> Apple
> >>>>>>> and VS2005 convert SNAN to QNAN so don't include check*/
> >>>>>>>       // do nothing
> >>>>>>> #else
> >>>>>>>        && airFP_SNAN == airFPClass_f(AIR_SNAN)
> >>>>>>> #endif
> >>>>>>>
> >>>>>>>
> >>>>>>> This is critical for us, since we can't use ITK 3.18 until  
> this issue
> >>>>>>> is
> >>>>>>> fixed.
> >>>>>>>
> >>>>>>> -Steve
> >>>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Michel Audette, Ph.D.
> >>>> R & D Engineer,
> >>>> Kitware Inc.,
> >>>> Chapel Hill, N.C.
> >>>>
> >>>
> >>
> >>
> >
> >
> >
> > --
> > Michel Audette, Ph.D.
> > R & D Engineer,
> > Kitware Inc.,
> > Chapel Hill, N.C.
> >
>
>
>
> -- 
> Michel Audette, Ph.D.
> R & D Engineer,
> Kitware Inc.,
> Chapel Hill, N.C.
>
>