[Insight-developers] [slicer-devel] Fwd: Re: itk 3.18's nrrd io on windows vs 2008 pro
Michel Audette
michel.audette at kitware.com
Fri Apr 23 11:28:17 EDT 2010
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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>>
>>
>> --
>> 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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