[Insight-developers] Problem again in NRRDIO
Michel Audette
michel.audette at kitware.com
Wed Mar 24 17:33:30 EDT 2010
Hi Daniel,
Awesome. I will commit this new mangle.pl to ITK. Gordon, okay to commit it
to NrrdIO?
Michel
On Wed, Mar 24, 2010 at 5:27 PM, Daniel Blezek <Blezek.Daniel at mayo.edu>wrote:
> Great! this fixed it. Thanks for the help.
>
> -dan
>
>
>
> On 3/24/10 3:45 PM, "Michel Audette" <michel.audette at kitware.com> wrote:
>
> Daniel,
>
> please give this one a try...
>
> Best wishes,
>
> Michel
>
> On Wed, Mar 24, 2010 at 4:42 PM, Michel Audette <
> michel.audette at kitware.com> wrote:
>
> Think that I found it.
>
> Needs a t, b and r at least in the perl script...
>
> t _nrrdSprintCH
> ...
> b _nrrdSanity.8527
> ...
> r _nrrdGzErrMsg
>
> Michel
>
>
> On Tue, Mar 23, 2010 at 6:55 PM, Daniel Blezek <Blezek.Daniel at mayo.edu>
> wrote:
>
> Ok, dumped itk header in NrrdIO. Here are the remaining naked teem symbols
> (or at least some of them).
>
> revelation:Insight-macosx blezek$ make -C Utilities/NrrdIO/ clean && make
> -C Utilities/NrrdIO/
> <snip>
> [100%] Built target ITKNrrdIO
> revelation:Insight-macosx blezek$ date
> Tue Mar 23 16:53:30 CDT 2010
> revelation:Insight-macosx blezek$ ls -ltr bin/libITKNrrdIO.a
> -rw-r--r-- 1 blezek staff 321600 Mar 23 16:52 bin/libITKNrrdIO.a
> revelation:Insight-macosx blezek$ nm bin/libITKNrrdIO.a | grep -v itk |
> grep nrrd
> 00001bd0 t __nrrdSprintCH
> 00001980 t __nrrdSprintDB
> 000019c0 t __nrrdSprintFL
> 00001ad0 t __nrrdSprintIN
> 00001a50 t __nrrdSprintLL
> 00001b50 t __nrrdSprintSH
> 00001b90 t __nrrdSprintUC
> 00001a90 t __nrrdSprintUI
> 00001a10 t __nrrdSprintUL
> 00001b10 t __nrrdSprintUS
> 00003c88 b __nrrdSanity.6421
> 000004e0 t __nrrdGzCheckHeader
> 00000130 t __nrrdGzDestroy
> 00001e40 s __nrrdGzErrMsg
> revelation:Insight-macosx blezek$ nm bin/libITKNrrdIO.a | grep -v itk |
> grep air
> 00000fac b __airSanity.5193
> revelation:Insight-macosx blezek$ nm bin/libITKNrrdIO.a | grep -v itk |
> grep biff
> bin/libITKNrrdIO.a(biffbiff.o):
> bin/libITKNrrdIO.a(biffmsg.o):
> revelation:Insight-macosx blezek$ nm bin/libITKNrrdIO.a | grep -v itk |
> grep bmsg
> 00001594 b __bmsg
> 00001598 b __bmsgArr
> 00001590 b __bmsgNum
> revelation:Insight-macosx blezek$
>
>
>
> On 3/23/10 3:38 PM, "Michel Audette" <michel.audette at kitware.com <
> http://michel.audette@kitware.com> > wrote:
>
> Hi Daniel,
>
> I have another file for you. I meant to send it before to you, but
> mistakenly only sent it to Gordon.
>
> Please try the enclosed.
>
> Michel
>
> On Tue, Mar 23, 2010 at 5:00 PM, Michel Audette <
> michel.audette at kitware.com <http://michel.audette@kitware.com> > wrote:
>
> With both lines modified in the manner suggested by Gordon,
> if (m/ [TBDRS] /) {
> s|.* [TBDRS] (.*)|$1|g;
> the outcome is a little different.
>
> michel at michel-desktop:~/tools/Insight_ALL/generatedNrrdIO$ diff
> itk_NrrdIO_mangle.h itk_NrrdIO_mangleOld.h
> 89d88
> < #define airDisableDio itk_airDisableDio
> 109d107
> < #define airStrtokQuoting itk_airStrtokQuoting
> 153d150
> < #define _biffMsgNoop itk__biffMsgNoop
> 353,357d349
> < #define nrrdStateDisableContent itk_nrrdStateDisableContent
> < #define nrrdStateGrayscaleImage3D itk_nrrdStateGrayscaleImage3D
> < #define nrrdStateKeyValuePairsPropagate
> itk_nrrdStateKeyValuePairsPropagate
> < #define nrrdStateKeyValueReturnInternalPointers
> itk_nrrdStateKeyValueReturnInternalPointers
> < #define nrrdStateKindNoop itk_nrrdStateKindNoop
> 359d350
> < #define nrrdStateVerboseIO itk_nrrdStateVerboseIO
>
> Try that?
>
> Michel
>
>
> On Tue, Mar 23, 2010 at 4:56 PM, Michel Audette <
> michel.audette at kitware.com <http://michel.audette@kitware.com> > wrote:
>
> Hi Gordon,
>
> only the line substitution that you suggested was implemented in the
> mangle.pl <http://mangle.pl> <http://mangle.pl> . Had you intende to
> apply the same change to the if line just above. I didn't notice until now.
>
> Michel
>
>
> On Tue, Mar 23, 2010 at 5:53 PM, Daniel Blezek <Blezek.Daniel at mayo.edu <
> http://Blezek.Daniel@mayo.edu> > wrote:
>
> Ok, at least one symbol made it through unscathed.
>
> ld: duplicate symbol _airStrtokQuoting in
> /Users/blezek/Source/Insight-macosx/bin/libITKNrrdIO.a(string.o) and
> ../bin/libteem.a(string.o)
>
> Here are the non-itk procteced symbols:
>
> nm /Users/blezek/Source/Insight-macosx/bin/libITKNrrdIO.a | grep -v itk >
> Tmp.txt
>
> + some editing.
>
>
>
> On 3/23/10 2:33 PM, "Michel Audette" <michel.audette at kitware.com <
> http://michel.audette@kitware.com> <http://michel.audette@kitware.com> >
> wrote:
>
> Hi Daniel,
>
> here it is...
>
> Michel
>
> On Tue, Mar 23, 2010 at 4:29 PM, Gordon L. Kindlmann <glk at uchicago.edu <
> http://glk@uchicago.edu> <http://glk@uchicago.edu> > wrote:
> Hi,
>
> so can you try changing in mangle.pl <http://mangle.pl> <http://mangle.pl>
> <http://mangle.pl>
>
> s|.* [TDRS] (.*)|$1|g;
>
> to
>
> s|.* [TBDRS] (.*)|$1|g;
>
> and send the resulting itk_NrrdIO_mangle.h to Daniel so he can see if it
> fixes the problem?
>
> Gordon
>
>
>
> On Mar 23, 2010, at 3:25 PM, Michel Audette wrote:
>
> defaultsNrrd.o:
> 0000000000000010 D nrrdDefaultCenter
> 0000000000000018 D nrrdDefaultSpacing
> 0000000000000004 D nrrdDefaultWriteBareText
> 0000000000000008 D nrrdDefaultWriteCharsPerLine
> 0000000000000000 D nrrdDefaultWriteEncodingType
> 000000000000000c D nrrdDefaultWriteValsPerLine
> 0000000000000020 D nrrdStateAlwaysSetContent
> 0000000000000008 B nrrdStateDisableContent
> 000000000000000c B nrrdStateGrayscaleImage3D
> 0000000000000004 B nrrdStateKeyValuePairsPropagate
> 0000000000000010 B nrrdStateKeyValueReturnInternalPointers
> 0000000000000014 B nrrdStateKindNoop
> 0000000000000028 D nrrdStateUnknownContent
> 0000000000000000 B nrrdStateVerboseIO
>
> We can talk on the phone if you prefer... Let me know.
>
> Cheers,
>
> Michel
>
> On Tue, Mar 23, 2010 at 4:23 PM, Gordon L. Kindlmann <glk at uchicago.edu <
> http://glk@uchicago.edu> <http://glk@uchicago.edu> > wrote:
> Hello,
>
> Ok, so the question is, *how* is nrrdStateGrayscaleImage3D listed? there
> is probably some cryptic single letter code that identifies the type of
> symbol. mangle.pl <http://mangle.pl> <http://mangle.pl> <
> http://mangle.pl> is using these letter codes to distinguish between
> symbols that the NrrdIO library is actually supplying, versus merely using,
> and the problem is that nrrdStateGrayscaleImage3D is actually being
> supplied, but is not being recorded as such in the output of mangle.pl <
> http://mangle.pl> <http://mangle.pl> <http://mangle.pl> . Line 66 of
> mangle.pl <http://mangle.pl> <http://mangle.pl> <http://mangle.pl> is
> where this decision is made; so it may need tweaking.
>
>
>
>
> Gordon
>
>
> On Mar 23, 2010, at 3:18 PM, Michel Audette wrote:
>
> Hi Gordon,
>
> According to this procedure, _nrrdStateGrayscaleImage3D fails to appear,
> although nrrdStateGrayscaleImage3D is listed in the result of nm.
>
> What next?
>
> Michel
>
> On Tue, Mar 23, 2010 at 2:07 PM, Gordon L. Kindlmann <glk at uchicago.edu <
> http://glk@uchicago.edu> <http://glk@uchicago.edu> > wrote:
> Hello,
>
> Shoot- sorry about this; I was just thinking the NrrdIO update was
> finished!
>
> There indeed probably aren't any tests for checking compiling applications
> against both Teem (containing the air, biff, and nrrd libraries that these
> symbols are coming from) and ITK (containing NrrdIO, the fraction of Teem
> required for Nrrd file IO). Aren't Slicer builds doing this? Are there
> analogous tests for, say, compiling applications against non-ITK zlib and
> ITK name-mangled zlib, which can be copied from?
>
> I can tell that these names are for the global variables that exist in
> NrrdIO. These are probably not getting correctly picked up from the list of
> symbols in the NrrdIO library, which mangle.pl <http://mangle.pl> <
> http://mangle.pl> <http://mangle.pl> does by using "nm".
>
> Michel, can go through the NrrdIO process on whatever platform you used
> last, and at the point of running mangle.pl <http://mangle.pl> <
> http://mangle.pl> <http://mangle.pl> , can you run "nm" manually and grep
> for, say, _nrrdStateGrayscaleImage3D, and see how that symbol is identified?
> Line 66 of mangle.pl <http://mangle.pl> <http://mangle.pl> <
> http://mangle.pl> apparently is missing this.
>
>
>
>
> Gordon
>
>
> On Mar 23, 2010, at 12:33 PM, Daniel Blezek wrote:
>
> Hi,
>
> We link both against NRRD and ITK in our applications. At the end of
> February, the mangled ITK names were changed from what I fixed. Clearly,
> this is not tested properly, because today I updated ITK and re-built:
>
> 34>ITKNrrdIO.lib(string.obj) : error LNK2005: _airStrtokQuoting already
> defined in teem.lib(string.obj)
> 34>ITKNrrdIO.lib(defaultsNrrd.obj) : error LNK2005: _nrrdStateVerboseIO
> already defined in teem.lib(defaultsNrrd.obj)
> 34>ITKNrrdIO.lib(defaultsNrrd.obj) : error LNK2005:
> _nrrdStateKeyValuePairsPropagate already defined in
> teem.lib(defaultsNrrd.obj)
> 34>ITKNrrdIO.lib(defaultsNrrd.obj) : error LNK2005:
> _nrrdStateDisableContent already defined in teem.lib(defaultsNrrd.obj)
> 34>ITKNrrdIO.lib(defaultsNrrd.obj) : error LNK2005:
> _nrrdStateGrayscaleImage3D already defined in teem.lib(defaultsNrrd.obj)
> 34>ITKNrrdIO.lib(defaultsNrrd.obj) : error LNK2005:
> _nrrdStateKeyValueReturnInternalPointers already defined in
> teem.lib(defaultsNrrd.obj)
> 34>ITKNrrdIO.lib(defaultsNrrd.obj) : error LNK2005: _nrrdStateKindNoop
> already defined in teem.lib(defaultsNrrd.obj)
> 34>ITKNrrdIO.lib(biffmsg.obj) : error LNK2005: __biffMsgNoop already
> defined in teem.lib(biffmsg.obj)
> 34>ITKNrrdIO.lib(dio.obj) : error LNK2005: _airDisableDio already defined
> in teem.lib(dio.obj)
>
> Could “Michel” (according to CVS) please have a closer look at this? I had
> tweaked this once before, and my changes were blown away by the (broken)
> mangle.pl <http://mangle.pl> <http://mangle.pl> <http://mangle.pl>
> script.
>
>
>
>
> I’ll go back through and manually add the names if necessary.
>
> Cheers,
> -dan
>
> --
> *Daniel Blezek, PhD
> *Medical Imaging Informatics Innovation Center
>
> P 127 or (77) 8 8886
> T 507 538 8886
> E blezek.daniel at mayo.edu
>
> Mayo Clinic
> 200 First St. S.W.
> Harwick SL-44
> Rochester, MN 55905
> mayoclinic.org
>
>
--
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.
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