[Insight-developers] [slicer-devel] Fwd: Re: itk 3.18's nrrd io on windows vs 2008 pro
Gordon L. Kindlmann
glk at uchicago.edu
Fri Apr 23 12:20:49 EDT 2010
FYI, I'd be surprised if there's anything about this file which is
triggering the error. The sanity checks in airSanity() should be
called prior to any data reading.
Gordon
On Apr 23, 2010, at 10:28 AM, Michel Audette wrote:
> Hi Steve,
>
> Luis and I believe that the tests that we had previously did not
> account for Nan pixels within the data, and I just generated a small
> synthetic image that has it. I am about to test it on Windows.
>
> I will also try your data as well.
>
> Best wishes,
>
> Michel
>
> On Fri, Apr 23, 2010 at 8:11 AM, Steve Pieper
> <pieper at bwh.harvard.edu> wrote:
>> Hi Michel -
>>
>> Any nrrd file should be the same - here's one that is failing for me:
>>
>> http://dl.dropbox.com/u/1686930/file.nrrd
>>
>> -Steve
>> On Apr/23/10 9:58 AM, Michel Audette wrote:
>>>
>>> Hi Steve,
>>>
>>> I'm using Visual Studio 2008. I would like to try to replicate the
>>> problem. Whom can I contact to get that liver file?
>>>
>>> Cheers,
>>>
>>> Michel
>>>
>>>
>>> On Fri, Apr 23, 2010 at 6:45 AM, Steve Pieper
>>> <pieper at bwh.harvard.edu
>>> <mailto:pieper at bwh.harvard.edu>> wrote:
>>>
>>> Hi Michel -
>>>
>>> This really isn't a slicer issue - it's in pure ITK code.
>>>
>>> Do you have a visual studio 2008 build of ITK where you can see
>>> if
>>> you get the same behavior?
>>>
>>> -Steve
>>>
>>>
>>> On Apr/23/10 9:38 AM, Michel Audette wrote:
>>>
>>> Hi Steve,
>>>
>>> do you have a link for superbuild instructions for Slicer on
>>> Windows?
>>>
>>> I have a feeling that it will simplify this endeavour to
>>> proceed
>>> this way...
>>>
>>> Cheers,
>>>
>>> Michel
>>>
>>> On Thu, Apr 22, 2010 at 3:06 PM, Steve Pieper
>>> <pieper at bwh.harvard.edu <mailto:pieper at bwh.harvard.edu>
>>> <mailto:pieper at bwh.harvard.edu
>>> <mailto:pieper at bwh.harvard.edu>>>
>>> wrote:
>>>
>>> FYI - upgrading to ITK 3.18 seems to have caused some
>>> issues
>>> on windows
>>> (can't read .nrrd files). We're investigating and it
>>> should
>>> be fixable.
>>>
>>> If you notice any other issues please speak up...
>>>
>>> -Steve
>>>
>>> -------- Original Message --------
>>> Subject: Re: itk 3.18's nrrd io on windows vs
>>> 2008 pro
>>> Date: Thu, 22 Apr 2010 11:43:03 -0400
>>> From: Luis Ibanez <luis.ibanez at kitware.com
>>> <mailto:luis.ibanez at kitware.com>
>>> <mailto:luis.ibanez at kitware.com <mailto:luis.ibanez at kitware.com
>>> >>>
>>> To: Steve Pieper <pieper at bwh.harvard.edu
>>> <mailto:pieper at bwh.harvard.edu>
>>> <mailto:pieper at bwh.harvard.edu
>>> <mailto:pieper at bwh.harvard.edu>>>
>>> CC: Teem Users <teem-users at lists.sourceforge.net
>>> <mailto:teem-users at lists.sourceforge.net>
>>> <mailto:teem-users at lists.sourceforge.net
>>> <mailto:teem-users at lists.sourceforge.net>>>, "Stephen R.
>>> Aylward"
>>> <Stephen.Aylward at kitware.com
>>> <mailto:Stephen.Aylward at kitware.com>
>>> <mailto:Stephen.Aylward at kitware.com
>>> <mailto:Stephen.Aylward at kitware.com>>>,
>>> "Gordon L. Kindlmann" <glk at uchicago.edu
>>> <mailto:glk at uchicago.edu> <mailto:glk at uchicago.edu
>>> <mailto:glk at uchicago.edu>>>,
>>>
>>> Michel Audette <michel.audette at kitware.com
>>> <mailto:michel.audette at kitware.com>
>>> <mailto:michel.audette at kitware.com
>>> <mailto:michel.audette at kitware.com>>>, Insight Developers
>>> <Insight-developers at itk.org <mailto:Insight-developers at itk.org
>>> >
>>> <mailto:Insight-developers at itk.org
>>> <mailto:Insight-developers at itk.org>>>
>>>
>>>
>>>
>>>
>>>
>>> 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 <mailto:pieper at bwh.harvard.edu>
>>> <mailto:pieper at bwh.harvard.edu
>>> <mailto:pieper at bwh.harvard.edu>>
>>> <mailto:pieper at bwh.harvard.edu
>>> <mailto:pieper at bwh.harvard.edu>
>>> <mailto:pieper at bwh.harvard.edu
>>> <mailto: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
>>>
>>> <http://public.kitware.com/cgi-bin/viewcvs.cgi/Utilities/NrrdIO/sane.c?root=Insight&r1=1.20&r2=1.21
>>> >
>>>
>>> <http://public.kitware.com/cgi-bin/viewcvs.cgi/Utilities/NrrdIO/sane.c?root=Insight&r1=1.20&r2=1.21
>>>
>>> <http://public.kitware.com/cgi-bin/viewcvs.cgi/Utilities/NrrdIO/sane.c?root=Insight&r1=1.20&r2=1.21
>>> >>
>>>
>>>
>>> <http://public.kitware.com/cgi-bin/viewcvs.cgi/Utilities/NrrdIO/sane.c?root=Insight&r1=1.20&r2=1.21
>>>
>>> <http://public.kitware.com/cgi-bin/viewcvs.cgi/Utilities/NrrdIO/sane.c?root=Insight&r1=1.20&r2=1.21
>>> >
>>>
>>> <http://public.kitware.com/cgi-bin/viewcvs.cgi/Utilities/NrrdIO/sane.c?root=Insight&r1=1.20&r2=1.21
>>>
>>> <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
>>>
>>>
>>> _______________________________________________
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>>>
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>>>
>>>
>>>
>>> --
>>> 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.
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