From pablo.hernandez.cerdan at outlook.com Sat Jan 2 09:04:29 2016 From: pablo.hernandez.cerdan at outlook.com (=?iso-8859-1?B?UGFibG8gSGVybuFuZGV6?=) Date: Sat, 2 Jan 2016 15:04:29 +0100 Subject: [ITK-dev] Integrating header-only boost::Compute for faster itkGPU development. Message-ID: https://github.com/boostorg/compute It is like cuda::Thrust library, functional oriented, but using opencl and header-only. It implements quite a lot of STL algorithms to run in GPU's. It requires c++11, and will be officially available in next boost release (1.61) I mention this, because I was creating a home-brewed itkGPU filters, and it is painful to hand-write opencl code for every basic operation out there. I can of course use it by my own, but I thought it could be helpful to boost:: the GPU developing in ITK. I have no conflict of interests with this particular library, but wanted to share it and hear what you think. Also any comment about the road map involving GPU in ITK would be interesting. Regards, Pablo -------------- next part -------------- An HTML attachment was scrubbed... URL: From Victor.Poughon at cnes.fr Mon Jan 4 08:30:43 2016 From: Victor.Poughon at cnes.fr (Poughon Victor) Date: Mon, 4 Jan 2016 13:30:43 +0000 Subject: [ITK-dev] itkStaticAssert warnings with clang Message-ID: <3E55146A6A81B44A9CB69CAB65908CEA0D95E1F2@TW-MBX-P01.cnesnet.ad.cnes.fr> Hi all, I think there is an issue in itkStaticAssert causing a large number of warnings (199) when building with clang 3.5.0. Here is a clean dashboard build of the current master branch showing the warnings: https://open.cdash.org/viewBuildError.php?type=1&buildid=4174833 This was previously discussed on OTB's mailing list: https://groups.google.com/forum/#!searchin/otb-developers/itkStaticAssert/otb-developers/X8Bfvzh8g-A/T9basCNfCAAJ They are caused by __attribute__(error(str)) being used, which is a GCC specific attribute. I will quote my colleague Luc Hermitte: > clang defines GCC macros (__GNUC__ & all). > The #if should also test for !defined(__clang__). When building with this version of clang: clang version 3.5.0 (tags/RELEASE_350/final) Target: x86_64-redhat-linux-gnu Thread model: posix Happy 2016, Victor Poughon From dzenanz at gmail.com Mon Jan 4 11:23:56 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 4 Jan 2016 11:23:56 -0500 Subject: [ITK-dev] itkStaticAssert warnings with clang In-Reply-To: <3E55146A6A81B44A9CB69CAB65908CEA0D95E1F2@TW-MBX-P01.cnesnet.ad.cnes.fr> References: <3E55146A6A81B44A9CB69CAB65908CEA0D95E1F2@TW-MBX-P01.cnesnet.ad.cnes.fr> Message-ID: Hi Victor, this is an excellent opportunity for you to contribute to ITK the patch which fixes the described issue. Add Matt McCormick as one of the reviewers. Regards, D?enan On Mon, Jan 4, 2016 at 8:30 AM, Poughon Victor wrote: > Hi all, > > I think there is an issue in itkStaticAssert causing a large number of > warnings (199) when building with clang 3.5.0. Here is a clean dashboard > build of the current master branch showing the warnings: > https://open.cdash.org/viewBuildError.php?type=1&buildid=4174833 > > This was previously discussed on OTB's mailing list: > > https://groups.google.com/forum/#!searchin/otb-developers/itkStaticAssert/otb-developers/X8Bfvzh8g-A/T9basCNfCAAJ > > They are caused by __attribute__(error(str)) being used, which is a GCC > specific attribute. I will quote my colleague Luc Hermitte: > > > clang defines GCC macros (__GNUC__ & all). > > The #if should also test for !defined(__clang__). > > When building with this version of clang: > clang version 3.5.0 (tags/RELEASE_350/final) > Target: x86_64-redhat-linux-gnu > Thread model: posix > > Happy 2016, > > Victor Poughon > > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sean at rogue-research.com Mon Jan 4 16:17:44 2016 From: sean at rogue-research.com (Sean McBride) Date: Mon, 4 Jan 2016 16:17:44 -0500 Subject: [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: Message-ID: <20160104211744.1213332491@mail.rogue-research.com> On Tue, 22 Dec 2015 18:57:04 -0500, Matt McCormick said: >On behalf of the Insight Toolkit community, we are proud to announce >that ITK 4.9 release candidate 3 has been tagged and is available for >testing! Please take this opportunity to test the new features in the >release candidate. > >* Third Party Library Updates > * GDCM updated to the latest upstream If I understand ITK's git history correctly, ThirdParty/GDCM was last updated 2015-09-22: According to this: GDCM 2.6.1 was released 2015-11-02 and 2.6.2 on 2015-12-23. Try as I may, I don't see an easy way to determine which version of GDCM ITK actually includes... how does one determine this? Thanks, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From Victor.Poughon at cnes.fr Tue Jan 5 05:09:33 2016 From: Victor.Poughon at cnes.fr (Poughon Victor) Date: Tue, 5 Jan 2016 10:09:33 +0000 Subject: [ITK-dev] itkStaticAssert warnings with clang In-Reply-To: References: <3E55146A6A81B44A9CB69CAB65908CEA0D95E1F2@TW-MBX-P01.cnesnet.ad.cnes.fr>, Message-ID: <3E55146A6A81B44A9CB69CAB65908CEA0D95EF80@TW-MBX-P01.cnesnet.ad.cnes.fr> Hello, I made a patch for this issue, but I'm having trouble with gerrit-push over http (I'm behind a firewall and proxy): $ git gerrit-push Fetching gerrit master Pushing to gerrit remote: Unauthorized fatal: Authentication failed for 'http://vpoughon at review.source.kitware.com/p/ITK/' Not sure why it's not working, I followed instructions from the wiki. Maybe it's related to the issue my colleague was having: http://permalink.gmane.org/gmane.comp.lib.itk.devel/3159 So here is a format-patch. Thanks, Victor Poughon ________________________________ De : D?enan Zuki? [dzenanz at gmail.com] Envoy? : lundi 4 janvier 2016 17:23 ? : Poughon Victor Cc : insight-developers at itk.org Objet : Re: [ITK-dev] itkStaticAssert warnings with clang Hi Victor, this is an excellent opportunity for you to contribute to ITK the patch which fixes the described issue. Add Matt McCormick as one of the reviewers. Regards, D?enan On Mon, Jan 4, 2016 at 8:30 AM, Poughon Victor > wrote: Hi all, I think there is an issue in itkStaticAssert causing a large number of warnings (199) when building with clang 3.5.0. Here is a clean dashboard build of the current master branch showing the warnings: https://open.cdash.org/viewBuildError.php?type=1&buildid=4174833 This was previously discussed on OTB's mailing list: https://groups.google.com/forum/#!searchin/otb-developers/itkStaticAssert/otb-developers/X8Bfvzh8g-A/T9basCNfCAAJ They are caused by __attribute__(error(str)) being used, which is a GCC specific attribute. I will quote my colleague Luc Hermitte: > clang defines GCC macros (__GNUC__ & all). > The #if should also test for !defined(__clang__). When building with this version of clang: clang version 3.5.0 (tags/RELEASE_350/final) Target: x86_64-redhat-linux-gnu Thread model: posix Happy 2016, Victor Poughon _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 0001-COMP-fix-itkStaticAssert-warnings-with-clang.patch Type: text/x-patch Size: 1260 bytes Desc: 0001-COMP-fix-itkStaticAssert-warnings-with-clang.patch URL: From dzenanz at gmail.com Tue Jan 5 09:48:23 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 5 Jan 2016 09:48:23 -0500 Subject: [ITK-dev] itkStaticAssert warnings with clang In-Reply-To: <3E55146A6A81B44A9CB69CAB65908CEA0D95EF80@TW-MBX-P01.cnesnet.ad.cnes.fr> References: <3E55146A6A81B44A9CB69CAB65908CEA0D95E1F2@TW-MBX-P01.cnesnet.ad.cnes.fr> <3E55146A6A81B44A9CB69CAB65908CEA0D95EF80@TW-MBX-P01.cnesnet.ad.cnes.fr> Message-ID: I submitted the patch to code review: http://review.source.kitware.com/#/c/20624/ Thanks Victor On Tue, Jan 5, 2016 at 5:09 AM, Poughon Victor wrote: > Hello, > > I made a patch for this issue, but I'm having trouble with gerrit-push > over http (I'm behind a firewall and proxy): > > $ git gerrit-push > Fetching gerrit master > Pushing to gerrit > remote: Unauthorized > fatal: Authentication failed for ' > http://vpoughon at review.source.kitware.com/p/ITK/' > > Not sure why it's not working, I followed instructions from the wiki. > Maybe it's related to the issue my colleague was having: > http://permalink.gmane.org/gmane.comp.lib.itk.devel/3159 > > So here is a format-patch. > > Thanks, > > Victor Poughon > ------------------------------ > *De :* D?enan Zuki? [dzenanz at gmail.com] > *Envoy? :* lundi 4 janvier 2016 17:23 > *? :* Poughon Victor > *Cc :* insight-developers at itk.org > *Objet :* Re: [ITK-dev] itkStaticAssert warnings with clang > > Hi Victor, > > this is an excellent opportunity for you to contribute > to ITK the patch which fixes the > described issue. Add Matt McCormick as one of the reviewers. > > Regards, > D?enan > > On Mon, Jan 4, 2016 at 8:30 AM, Poughon Victor > wrote: > >> Hi all, >> >> I think there is an issue in itkStaticAssert causing a large number of >> warnings (199) when building with clang 3.5.0. Here is a clean dashboard >> build of the current master branch showing the warnings: >> https://open.cdash.org/viewBuildError.php?type=1&buildid=4174833 >> >> This was previously discussed on OTB's mailing list: >> >> https://groups.google.com/forum/#!searchin/otb-developers/itkStaticAssert/otb-developers/X8Bfvzh8g-A/T9basCNfCAAJ >> >> They are caused by __attribute__(error(str)) being used, which is a GCC >> specific attribute. I will quote my colleague Luc Hermitte: >> >> > clang defines GCC macros (__GNUC__ & all). >> > The #if should also test for !defined(__clang__). >> >> When building with this version of clang: >> clang version 3.5.0 (tags/RELEASE_350/final) >> Target: x86_64-redhat-linux-gnu >> Thread model: posix >> >> Happy 2016, >> >> Victor Poughon >> >> >> >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hobbsk at ohio.edu Tue Jan 5 11:04:54 2016 From: hobbsk at ohio.edu (Kevin H. Hobbs) Date: Tue, 5 Jan 2016 11:04:54 -0500 Subject: [ITK-dev] Retire expected builds Message-ID: <568BE9A6.4020303@ohio.edu> I'm moving to a new job, and will no longer be able to maintain my nightly builds (even in their neglected state.) Please expect the expected builds from bubbles, murron, and k450e to dissapear. -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 173 bytes Desc: OpenPGP digital signature URL: From matt.mccormick at kitware.com Tue Jan 5 14:54:47 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jan 2016 14:54:47 -0500 Subject: [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: <20160104211744.1213332491@mail.rogue-research.com> References: <20160104211744.1213332491@mail.rogue-research.com> Message-ID: Hi Sean, On Mon, Jan 4, 2016 at 4:17 PM, Sean McBride wrote: > On Tue, 22 Dec 2015 18:57:04 -0500, Matt McCormick said: > >>On behalf of the Insight Toolkit community, we are proud to announce >>that ITK 4.9 release candidate 3 has been tagged and is available for >>testing! Please take this opportunity to test the new features in the >>release candidate. >> >>* Third Party Library Updates >> * GDCM updated to the latest upstream > > If I understand ITK's git history correctly, ThirdParty/GDCM was last updated 2015-09-22: > > > According to this: > > > GDCM 2.6.1 was released 2015-11-02 and 2.6.2 on 2015-12-23. > > Try as I may, I don't see an easy way to determine which version of GDCM ITK actually includes... how does one determine this? The upstream commits should have the author "GDCM Upstream". So, cd ~/src/ITK git log --author="GDCM Upstream" This shows that this release note item is an error -- the last time GDCM was updated was 2015-04-29, which was included for ITK 4.8. I have corrected the release notes. To update GDCM, run the Modules/ThirdParty/GDCM/UpdateFromUpstream.sh script. Since GDCM 2.6 has been released, we should switch from GDCM "master" to GDCM "release" before doing the update. This can be changed here: https://github.com/InsightSoftwareConsortium/ITK/blob/af6b2c82ba794ada4d487c5bbd83f2bd1ed39e2f/Modules/ThirdParty/GDCM/UpdateFromUpstream.sh#L6 Thanks, Matt From sean at rogue-research.com Tue Jan 5 16:22:22 2016 From: sean at rogue-research.com (Sean McBride) Date: Tue, 5 Jan 2016 16:22:22 -0500 Subject: [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: <20160104211744.1213332491@mail.rogue-research.com> Message-ID: <20160105212222.570045939@mail.rogue-research.com> On Tue, 5 Jan 2016 14:54:47 -0500, Matt McCormick said: >To update GDCM, run the > > Modules/ThirdParty/GDCM/UpdateFromUpstream.sh I've just tried, but it looks like no one has tried this from OS X before... :) It seems that OS X's sed, dirname, and basename do not accept '--version', and so I hit the 'die' at line 67. If I change it to 'echo' and let it proceed, I get: Command "sed" not found Command "dirname" not found Command "basename" not found sed: 1: "/GDCM 20[0-9][0-9]-[0-9 ...": extra characters at the end of p command Modules/ThirdParty/GDCM/../../../Utilities/Maintenance/UpdateThirdPartyFromUpstream.sh: line 125: upstream-${thirdparty_module_name,,}: bad substitution I guess it's one of those subtle GNU vs BSD differences tripping things up... I didn't debug further though, I think the author of this script could find the issue faster than me. :) Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From matt.mccormick at kitware.com Tue Jan 5 22:01:50 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jan 2016 22:01:50 -0500 Subject: [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: <20160105212222.570045939@mail.rogue-research.com> References: <20160104211744.1213332491@mail.rogue-research.com> <20160105212222.570045939@mail.rogue-research.com> Message-ID: On Tue, Jan 5, 2016 at 4:22 PM, Sean McBride wrote: > On Tue, 5 Jan 2016 14:54:47 -0500, Matt McCormick said: > >>To update GDCM, run the >> >> Modules/ThirdParty/GDCM/UpdateFromUpstream.sh > > I've just tried, but it looks like no one has tried this from OS X before... :) > > It seems that OS X's sed, dirname, and basename do not accept '--version', and so I hit the 'die' at line 67. If I change it to 'echo' and let it proceed, I get: > > Command "sed" not found > Command "dirname" not found > Command "basename" not found > sed: 1: "/GDCM 20[0-9][0-9]-[0-9 ...": extra characters at the end of p command > Modules/ThirdParty/GDCM/../../../Utilities/Maintenance/UpdateThirdPartyFromUpstream.sh: line 125: upstream-${thirdparty_module_name,,}: bad substitution > > I guess it's one of those subtle GNU vs BSD differences tripping things up... I didn't debug further though, I think the author of this script could find the issue faster than me. :) Thanks for giving it a whirl. It is worth another try after this patch is merged: http://review.source.kitware.com/#/c/20400/ Thanks, Matt From matt.mccormick at kitware.com Tue Jan 5 22:46:37 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jan 2016 22:46:37 -0500 Subject: [ITK-dev] Integrating header-only boost::Compute for faster itkGPU development. In-Reply-To: References: Message-ID: Hi Pablo, To make it easier to develop ITK-GPU filters with boost::Compute, an ITK Module should be created. See the Modules in ITK/Modules/ThirdParty/ as examples. Documentation on how to create a Module can now be found in the ITK Software Guide: http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch9.html#x50-1430009 If an Insight Journal article is submitted, the module can be merged into ITK as a Remote Module, and it can be dependency for modules that want to use boost::Compute in ITK. Other similar libraries that have been discussed include Cuda: http://www.insight-journal.org/browse/publication/802 https://code.google.com/p/cuda-insight-toolkit/ https://github.com/SimonRit/RTK/tree/1defcbdfe0bdcac6d0786f62ed8530e1b39204f9/code and ArrayFire: http://arrayfire.com/ And similar Modules could be created for these. Each has its own advantages in terms of platform support and programability. It is recommended to reuse as much of the existing ITK OpenCL GPU infrastructure as possible or to use a similar design. To drive ITK-GPU computing forward in general, we need more software quality dashboard submissions. Instructions on how to set up a Nightly dashboard submission can be found here: http://www.itk.org/Wiki/ITK/Git/Dashboard Thanks, Matt On Sat, Jan 2, 2016 at 9:04 AM, Pablo Hern?ndez wrote: > https://github.com/boostorg/compute > It is like cuda::Thrust library, functional oriented, but using opencl and > header-only. It implements quite a lot of STL algorithms to run in GPU's. It > requires c++11, and will be officially available in next boost release > (1.61) > I mention this, because I was creating a home-brewed itkGPU filters, and it > is painful to hand-write opencl code for every basic operation out there. I > can of course use it by my own, but I thought it could be helpful to boost:: > the GPU developing in ITK. > I have no conflict of interests with this particular library, but wanted to > share it and hear what you think. Also any comment about the road map > involving GPU in ITK would be interesting. > > Regards, > Pablo > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > From pablo.hernandez.cerdan at outlook.com Wed Jan 6 04:27:24 2016 From: pablo.hernandez.cerdan at outlook.com (=?iso-8859-1?B?UGFibG8gSGVybuFuZGV6?=) Date: Wed, 6 Jan 2016 10:27:24 +0100 Subject: [ITK-dev] Integrating header-only boost::Compute for faster itkGPU development. In-Reply-To: References: , Message-ID: Thanks a lot Matt, I will have a look at those sources. Pablo > Date: Tue, 5 Jan 2016 22:46:37 -0500 > Subject: Re: [ITK-dev] Integrating header-only boost::Compute for faster itkGPU development. > From: matt.mccormick at kitware.com > To: pablo.hernandez.cerdan at outlook.com > CC: insight-developers at itk.org > > Hi Pablo, > > To make it easier to develop ITK-GPU filters with boost::Compute, an > ITK Module should be created. See the Modules in > ITK/Modules/ThirdParty/ as examples. Documentation on how to create a > Module can now be found in the ITK Software Guide: > > http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch9.html#x50-1430009 > > If an Insight Journal article is submitted, the module can be merged > into ITK as a Remote Module, and it can be dependency for modules that > want to use boost::Compute in ITK. > > > Other similar libraries that have been discussed include Cuda: > > http://www.insight-journal.org/browse/publication/802 > https://code.google.com/p/cuda-insight-toolkit/ > https://github.com/SimonRit/RTK/tree/1defcbdfe0bdcac6d0786f62ed8530e1b39204f9/code > > and ArrayFire: > > http://arrayfire.com/ > > And similar Modules could be created for these. Each has its own > advantages in terms of platform support and programability. It is > recommended to reuse as much of the existing ITK OpenCL GPU > infrastructure as possible or to use a similar design. > > > To drive ITK-GPU computing forward in general, we need more software > quality dashboard submissions. Instructions on how to set up a Nightly > dashboard submission can be found here: > > http://www.itk.org/Wiki/ITK/Git/Dashboard > > Thanks, > Matt > > > On Sat, Jan 2, 2016 at 9:04 AM, Pablo Hern?ndez > wrote: > > https://github.com/boostorg/compute > > It is like cuda::Thrust library, functional oriented, but using opencl and > > header-only. It implements quite a lot of STL algorithms to run in GPU's. It > > requires c++11, and will be officially available in next boost release > > (1.61) > > I mention this, because I was creating a home-brewed itkGPU filters, and it > > is painful to hand-write opencl code for every basic operation out there. I > > can of course use it by my own, but I thought it could be helpful to boost:: > > the GPU developing in ITK. > > I have no conflict of interests with this particular library, but wanted to > > share it and hear what you think. Also any comment about the road map > > involving GPU in ITK would be interesting. > > > > Regards, > > Pablo > > > > > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sean at rogue-research.com Thu Jan 7 12:42:37 2016 From: sean at rogue-research.com (Sean McBride) Date: Thu, 7 Jan 2016 12:42:37 -0500 Subject: [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: <20160104211744.1213332491@mail.rogue-research.com> <20160105212222.570045939@mail.rogue-research.com> Message-ID: <20160107174237.459545705@mail.rogue-research.com> On Tue, 5 Jan 2016 22:01:50 -0500, Matt McCormick said: >> It seems that OS X's sed, dirname, and basename do not accept '-- >version', and so I hit the 'die' at line 67. If I change it to 'echo' >and let it proceed, I get: >> >> Command "sed" not found >> Command "dirname" not found >> Command "basename" not found >> sed: 1: "/GDCM 20[0-9][0-9]-[0-9 ...": extra characters at the end of >p command >> Modules/ThirdParty/GDCM/../../../Utilities/Maintenance/ >UpdateThirdPartyFromUpstream.sh: line 125: upstream-$ >{thirdparty_module_name,,}: bad substitution >> >> I guess it's one of those subtle GNU vs BSD differences tripping >things up... I didn't debug further though, I think the author of this >script could find the issue faster than me. :) > >Thanks for giving it a whirl. It is worth another try after this patch >is merged: > > http://review.source.kitware.com/#/c/20400/ Matt, Sorry I wasn't more clear... the '--version' thing is trivial and I bypassed it already (though that patch is great!), the problem is the last line of output: sed: 1: "/GDCM 20[0-9][0-9]-[0-9 ...": extra characters at the end of p command Modules/ThirdParty/GDCM/../../../Utilities/Maintenance/UpdateThirdPartyFromUpstream.sh: line 125: upstream-${thirdparty_module_name,,}: bad substitution This is the real problem. It's what I was referring to wrt 'subtle GNU vs BSD differences'. Commands like 'sed' don't behave exactly the same on GNU vs BSD. Or that's my guess anyway... for all I know, the script doesn't work on linux either... Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From bill.hoffman at kitware.com Fri Jan 8 11:14:39 2016 From: bill.hoffman at kitware.com (Bill Hoffman) Date: Fri, 8 Jan 2016 11:14:39 -0500 Subject: [ITK-dev] speed up windows ITK IDE builds Message-ID: <568FE06F.5030200@kitware.com> I setup a dashboard for VS 2015 with this generator: set(CTEST_CMAKE_GENERATOR "Visual Studio 14 Win64") build time was 2h 33m. I then added this to the CTest script: set(ENV{CFLAGS} /MP) set(ENV{CXXFLAGS} /MP) Now the build time is 1h 20m. Not as good as the ninja build of 54m, but a much better time. It might be a good idea to add this to other VS IDE builds on the dashboard. For reference you can see the blog I wrote three years ago: http://www.kitware.com/blog/home/post/434 -Bill From sean at rogue-research.com Fri Jan 8 14:00:55 2016 From: sean at rogue-research.com (Sean McBride) Date: Fri, 8 Jan 2016 14:00:55 -0500 Subject: [ITK-dev] Proposal: file reader API additions to eliminate need for guessing pair file paths Message-ID: <20160108190055.2126428888@mail.rogue-research.com> Hi all, Some (annoying) file formats like Analyze and PhilipsREC come in pairs: one metadata file and one data file, ex: .hdr & .img and .par & .rec. The reader classes currently take the path to one of the files and then auto-guess/construct the other path. Of course this works most of the time, but is fragile for a few reasons: - the file name parsing code assumes ASCII. - the code has to guess the case of the pair file. ex, if you provide foo.HDR, it has to guess either .img or .IMG, and this may succeed or fail depending if the file system is case sensitive or not. To say nothing of users maybe having mixed case names like "foo.imG". - OSes these days often sandbox access to the file system and this guessing around of paths can cause sandbox violations (which could be merely warnings or errors depending on OS). I'd like to propose new API for such file readers, specifically that clients can pass the path to *both* files. Then no fragile is guessing is needed. We wouldn't need to change existing API, merely add new ones. But before starting, I'd like to know if this would be accepted... Thanks, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From hans-johnson at uiowa.edu Fri Jan 8 14:10:00 2016 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Fri, 8 Jan 2016 19:10:00 +0000 Subject: [ITK-dev] Proposal: file reader API additions to eliminate need for guessing pair file paths In-Reply-To: <20160108190055.2126428888@mail.rogue-research.com> References: <20160108190055.2126428888@mail.rogue-research.com> Message-ID: Sean, I think that an API to provided overloading to SetFilename() would be nice. SetFilename(std::string myfilename) ?. Of course keep the old name. { NewIOStreamObjectExtractorThingy * nios = NewIOStreamMultiFileObject(); nios.SetHeaderInformation( myfilename ); SetFilename( NewIOStreamObjectExtractorThingyBaseClass * nios); } NewIOStreamObjectExtractorThingy * nios = NewIOStreamMultiFileObject(); nios.SetHeaderInformation(?my.hdr?); nios.SetDataStream(?my.img?); SetFilename( NewIOStreamObjectExtractorThingyBaseClass * nios) ? To support new IO mechanism flexibility. =========== I?m trying to think of an interface that would support interfacing with databases or URL?s. Hans On 1/8/16, 1:00 PM, "Insight-developers on behalf of Sean McBride" wrote: >Hi all, > >Some (annoying) file formats like Analyze and PhilipsREC come in pairs: one metadata file and one data file, ex: .hdr & .img and .par & .rec. > >The reader classes currently take the path to one of the files and then auto-guess/construct the other path. Of course this works most of the time, but is fragile for a few reasons: > > - the file name parsing code assumes ASCII. > - the code has to guess the case of the pair file. ex, if you provide foo.HDR, it has to guess either .img or .IMG, and this may succeed or fail depending if the file system is case sensitive or not. To say nothing of users maybe having mixed case names like "foo.imG". > - OSes these days often sandbox access to the file system and this guessing around of paths can cause sandbox violations (which could be merely warnings or errors depending on OS). > >I'd like to propose new API for such file readers, specifically that clients can pass the path to *both* files. Then no fragile is guessing is needed. We wouldn't need to change existing API, merely add new ones. > >But before starting, I'd like to know if this would be accepted... > >Thanks, > >-- >____________________________________________________________ >Sean McBride, B. Eng sean at rogue-research.com >Rogue Research www.rogue-research.com >Mac Software Developer Montr?al, Qu?bec, Canada > > >_______________________________________________ >Powered by www.kitware.com > >Visit other Kitware open-source projects at >http://www.kitware.com/opensource/opensource.html > >Kitware offers ITK Training Courses, for more information visit: >http://kitware.com/products/protraining.php > >Please keep messages on-topic and check the ITK FAQ at: >http://www.itk.org/Wiki/ITK_FAQ > >Follow this link to subscribe/unsubscribe: >http://public.kitware.com/mailman/listinfo/insight-developers ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ From isaiah.norton at gmail.com Wed Jan 13 18:47:32 2016 From: isaiah.norton at gmail.com (Isaiah Norton) Date: Wed, 13 Jan 2016 18:47:32 -0500 Subject: [ITK-dev] [slicer-devel] build error in simpleitk In-Reply-To: <89eefd6f837d4081a7b84a375052afe8@PHSX10HT5.partners.org> References: <89eefd6f837d4081a7b84a375052afe8@PHSX10HT5.partners.org> Message-ID: (cc: insight-devel) We are also seeing this issue, and several SimpleITK dashboards are failing with the same error for the OS X 10.9 (since bumping to ITK 4.9) and 10.10 (since yesterday) dashboards: https://open.cdash.org/buildSummary.php?buildid=4188623 It looks like this is essentially caused by SimpleITK being compiled with `-std=c++11`, whereas ITK (and VXL) are not. So, there is a mismatch between the configured definition of `VCL_CONSTEXPR` and the ` VCL_STATIC_CONST_INIT_*` macros. For reference, VCL_CONSTEXPR was introduced here: http://review.source.kitware.com/#/c/20386/ A proposed patch [1] is attached. Best, Isaiah [1] https://github.com/ihnorton/ITK/commit/0f748d8c86ffb2369c3a343c0db5ca87b067843e On Mon, Jan 11, 2016 at 11:21 AM, Steve Pieper wrote: > Hi - > > This morning with Xcode 7.2 on mac 10.11.2 I get the build errors pasted > below. This was in a fresh build directory. With SimpleITK turned off the > build completes and everything works as expected. > > I found an old issue with similar errors [1] but nothing lately. > > -Steve > > [1] https://issues.itk.org/jira/browse/ITK-2976 > > > > > In file included from > /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_c_vector.h:26: > > */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:388:41: > **error: **declaration of constexpr static data member* > > * 'zero' requires an initializer* > > static VNL_EXPORT VCL_CONSTEXPR float zero > VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); > > * ^* > > */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:390:41: > **error: **declaration of constexpr static data member* > > * 'one' requires an initializer* > > static VNL_EXPORT VCL_CONSTEXPR float one > VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); > > * ^* > > */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:392:41: > **error: **declaration of constexpr static data member* > > * 'maxval' requires an initializer* > > static VNL_EXPORT VCL_CONSTEXPR float maxval > VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); > > * ^* > > */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:411:42: > **error: **declaration of constexpr static data member* > > * 'zero' requires an initializer* > > static VNL_EXPORT VCL_CONSTEXPR double zero > VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); > > * ^* > > */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:413:42: > **error: **declaration of constexpr static data member* > > * 'one' requires an initializer* > > static VNL_EXPORT VCL_CONSTEXPR double one > VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); > > * ^* > > */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:415:42: > **error: **declaration of constexpr static data member* > > * 'maxval' requires an initializer* > > static VNL_EXPORT VCL_CONSTEXPR double maxval > VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); > > * ^* > > */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:434:47: > **error: **declaration of constexpr static data member* > > * 'zero' requires an initializer* > > static VNL_EXPORT VCL_CONSTEXPR long double zero > VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); > > * ^* > > */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:436:47: > **error: **declaration of constexpr static data member* > > * 'one' requires an initializer* > > static VNL_EXPORT VCL_CONSTEXPR long double one > VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); > > * ^* > > */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:438:47: > **error: **declaration of constexpr static data member* > > * 'maxval' requires an initializer* > > static VNL_EXPORT VCL_CONSTEXPR long double maxval > VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); > > * ^* > > 9 errors generated. > > make[8]: *** > [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/sitkExplicitITKComposeImageFilter.cxx.o] > Error 1 > > make[7]: *** [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/all] > Error 2 > > make[6]: *** [all] Error 2 > > make[5]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2 > > make[4]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 > > make[3]: *** [all] Error 2 > > make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2 > > make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 > > make: *** [all] Error 2 > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with > unsubscribe as the subject > > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 0001-COMP-fix-build-with-std-c-11-when-ITK-VXL-initially-.patch Type: application/octet-stream Size: 3416 bytes Desc: not available URL: From brad at lowekamp.net Wed Jan 13 19:38:23 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Wed, 13 Jan 2016 19:38:23 -0500 Subject: [ITK-dev] [slicer-devel] build error in simpleitk In-Reply-To: References: <89eefd6f837d4081a7b84a375052afe8@PHSX10HT5.partners.org> Message-ID: <66CED681-3509-46AB-BD82-4F88750CCCD9@mail.nih.gov> Hello, The patch looks pretty good. Thank you for contributing. Can you please submit the patch to ITK Gerrit for review? http://www.itk.org/Wiki/ITK/Git/Develop Thanks Brad > On Jan 13, 2016, at 6:47 PM, Isaiah Norton wrote: > > (cc: insight-devel) > > We are also seeing this issue, and several SimpleITK dashboards are failing with the same error for the OS X 10.9 (since bumping to ITK 4.9) and 10.10 (since yesterday) dashboards: > https://open.cdash.org/buildSummary.php?buildid=4188623 > > It looks like this is essentially caused by SimpleITK being compiled with `-std=c++11`, whereas ITK (and VXL) are not. So, there is a mismatch between the configured definition of `VCL_CONSTEXPR` and the `VCL_STATIC_CONST_INIT_*` macros. > > For reference, VCL_CONSTEXPR was introduced here: > http://review.source.kitware.com/#/c/20386/ > > A proposed patch [1] is attached. > > Best, > Isaiah > > [1] https://github.com/ihnorton/ITK/commit/0f748d8c86ffb2369c3a343c0db5ca87b067843e > > > >> On Mon, Jan 11, 2016 at 11:21 AM, Steve Pieper wrote: >> Hi - >> >> This morning with Xcode 7.2 on mac 10.11.2 I get the build errors pasted below. This was in a fresh build directory. With SimpleITK turned off the build completes and everything works as expected. >> >> I found an old issue with similar errors [1] but nothing lately. >> >> -Steve >> >> [1] https://issues.itk.org/jira/browse/ITK-2976 >> >> >> >> >> >> >> In file included from /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_c_vector.h:26: >> >> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:388:41: error: declaration of constexpr static data member >> >> 'zero' requires an initializer >> >> static VNL_EXPORT VCL_CONSTEXPR float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); >> >> ^ >> >> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:390:41: error: declaration of constexpr static data member >> >> 'one' requires an initializer >> >> static VNL_EXPORT VCL_CONSTEXPR float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); >> >> ^ >> >> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:392:41: error: declaration of constexpr static data member >> >> 'maxval' requires an initializer >> >> static VNL_EXPORT VCL_CONSTEXPR float maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); >> >> ^ >> >> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:411:42: error: declaration of constexpr static data member >> >> 'zero' requires an initializer >> >> static VNL_EXPORT VCL_CONSTEXPR double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); >> >> ^ >> >> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:413:42: error: declaration of constexpr static data member >> >> 'one' requires an initializer >> >> static VNL_EXPORT VCL_CONSTEXPR double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); >> >> ^ >> >> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:415:42: error: declaration of constexpr static data member >> >> 'maxval' requires an initializer >> >> static VNL_EXPORT VCL_CONSTEXPR double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); >> >> ^ >> >> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:434:47: error: declaration of constexpr static data member >> >> 'zero' requires an initializer >> >> static VNL_EXPORT VCL_CONSTEXPR long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); >> >> ^ >> >> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:436:47: error: declaration of constexpr static data member >> >> 'one' requires an initializer >> >> static VNL_EXPORT VCL_CONSTEXPR long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); >> >> ^ >> >> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:438:47: error: declaration of constexpr static data member >> >> 'maxval' requires an initializer >> >> static VNL_EXPORT VCL_CONSTEXPR long double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); >> >> ^ >> >> 9 errors generated. >> >> make[8]: *** [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/sitkExplicitITKComposeImageFilter.cxx.o] Error 1 >> >> make[7]: *** [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/all] Error 2 >> >> make[6]: *** [all] Error 2 >> >> make[5]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2 >> >> make[4]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 >> >> make[3]: *** [all] Error 2 >> >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2 >> >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 >> >> make: *** [all] Error 2 >> >> >> _______________________________________________ >> slicer-devel mailing list >> slicer-devel at bwh.harvard.edu >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >> To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with unsubscribe as the subject >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. > > <0001-COMP-fix-build-with-std-c-11-when-ITK-VXL-initially-.patch> > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with unsubscribe as the subject > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hans-johnson at uiowa.edu Wed Jan 13 20:16:42 2016 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Thu, 14 Jan 2016 01:16:42 +0000 Subject: [ITK-dev] [slicer-devel] build error in simpleitk In-Reply-To: <66CED681-3509-46AB-BD82-4F88750CCCD9@mail.nih.gov> References: <89eefd6f837d4081a7b84a375052afe8@PHSX10HT5.partners.org> <66CED681-3509-46AB-BD82-4F88750CCCD9@mail.nih.gov> Message-ID: I?m making a patch for this. I?ve noticed this today as well. mkdir XX; cd XX; cmake -DCMAKE_CXX_STANDARD:STRING=11 ../ITK; make ?j23 Before this patch, there was a build failure. After this patch it is now building. I made modifications to more closely match upstream VXL. Gerrit- review at : http://review.source.kitware.com/#/c/20658/ Hans From: Insight-developers > on behalf of Bradley Lowekamp > Date: Wednesday, January 13, 2016 at 6:38 PM To: Isaiah Norton > Cc: SPL Slicer Devel >, Insight Developers > Subject: Re: [ITK-dev] [slicer-devel] build error in simpleitk Hello, The patch looks pretty good. Thank you for contributing. Can you please submit the patch to ITK Gerrit for review? http://www.itk.org/Wiki/ITK/Git/Develop Thanks Brad On Jan 13, 2016, at 6:47 PM, Isaiah Norton > wrote: (cc: insight-devel) We are also seeing this issue, and several SimpleITK dashboards are failing with the same error for the OS X 10.9 (since bumping to ITK 4.9) and 10.10 (since yesterday) dashboards: https://open.cdash.org/buildSummary.php?buildid=4188623 It looks like this is essentially caused by SimpleITK being compiled with `-std=c++11`, whereas ITK (and VXL) are not. So, there is a mismatch between the configured definition of `VCL_CONSTEXPR` and the `VCL_STATIC_CONST_INIT_*` macros. For reference, VCL_CONSTEXPR was introduced here: http://review.source.kitware.com/#/c/20386/ A proposed patch [1] is attached. Best, Isaiah [1] https://github.com/ihnorton/ITK/commit/0f748d8c86ffb2369c3a343c0db5ca87b067843e On Mon, Jan 11, 2016 at 11:21 AM, Steve Pieper > wrote: Hi - This morning with Xcode 7.2 on mac 10.11.2 I get the build errors pasted below. This was in a fresh build directory. With SimpleITK turned off the build completes and everything works as expected. I found an old issue with similar errors [1] but nothing lately. -Steve [1] https://issues.itk.org/jira/browse/ITK-2976 In file included from /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_c_vector.h:26: /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:388:41: error: declaration of constexpr static data member 'zero' requires an initializer static VNL_EXPORT VCL_CONSTEXPR float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:390:41: error: declaration of constexpr static data member 'one' requires an initializer static VNL_EXPORT VCL_CONSTEXPR float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:392:41: error: declaration of constexpr static data member 'maxval' requires an initializer static VNL_EXPORT VCL_CONSTEXPR float maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:411:42: error: declaration of constexpr static data member 'zero' requires an initializer static VNL_EXPORT VCL_CONSTEXPR double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:413:42: error: declaration of constexpr static data member 'one' requires an initializer static VNL_EXPORT VCL_CONSTEXPR double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:415:42: error: declaration of constexpr static data member 'maxval' requires an initializer static VNL_EXPORT VCL_CONSTEXPR double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:434:47: error: declaration of constexpr static data member 'zero' requires an initializer static VNL_EXPORT VCL_CONSTEXPR long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:436:47: error: declaration of constexpr static data member 'one' requires an initializer static VNL_EXPORT VCL_CONSTEXPR long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:438:47: error: declaration of constexpr static data member 'maxval' requires an initializer static VNL_EXPORT VCL_CONSTEXPR long double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); ^ 9 errors generated. make[8]: *** [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/sitkExplicitITKComposeImageFilter.cxx.o] Error 1 make[7]: *** [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/all] Error 2 make[6]: *** [all] Error 2 make[5]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2 make[4]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 make[3]: *** [all] Error 2 make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2 make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 make: *** [all] Error 2 _______________________________________________ slicer-devel mailing list slicer-devel at bwh.harvard.edu http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. <0001-COMP-fix-build-with-std-c-11-when-ITK-VXL-initially-.patch> _______________________________________________ slicer-devel mailing list slicer-devel at bwh.harvard.edu http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From isaiah.norton at gmail.com Wed Jan 13 20:59:19 2016 From: isaiah.norton at gmail.com (Isaiah Norton) Date: Wed, 13 Jan 2016 20:59:19 -0500 Subject: [ITK-dev] [slicer-devel] build error in simpleitk In-Reply-To: References: <89eefd6f837d4081a7b84a375052afe8@PHSX10HT5.partners.org> <66CED681-3509-46AB-BD82-4F88750CCCD9@mail.nih.gov> Message-ID: Brad, Hans: great, thanks! (as an aside: I would be happy to submit patches directly in the future, but it's not really clear why the Gerrit <-> GitHub KWRobot application asks for R/W on all GitHub repositories I have access to... It would be great if this could be reduced to the minimal necessary privileges for authentication) Isaiah On Wed, Jan 13, 2016 at 8:16 PM, Johnson, Hans J wrote: > I?m making a patch for this. > > I?ve noticed this today as well. > > mkdir XX; > cd XX; > cmake -DCMAKE_CXX_STANDARD:STRING=11 ../ITK; > make ?j23 > > Before this patch, there was a build failure. > After this patch it is now building. > > I made modifications to more closely match upstream VXL. > > Gerrit- review at : http://review.source.kitware.com/#/c/20658/ > > Hans > > From: Insight-developers on behalf > of Bradley Lowekamp > Date: Wednesday, January 13, 2016 at 6:38 PM > To: Isaiah Norton > Cc: SPL Slicer Devel , Insight Developers < > insight-developers at itk.org> > Subject: Re: [ITK-dev] [slicer-devel] build error in simpleitk > > Hello, > > The patch looks pretty good. Thank you for contributing. > > Can you please submit the patch to ITK Gerrit for review? > > http://www.itk.org/Wiki/ITK/Git/Develop > > Thanks > Brad > > On Jan 13, 2016, at 6:47 PM, Isaiah Norton > wrote: > > (cc: insight-devel) > > We are also seeing this issue, and several SimpleITK dashboards are > failing with the same error for the OS X 10.9 (since bumping to ITK 4.9) > and 10.10 (since yesterday) dashboards: > https://open.cdash.org/buildSummary.php?buildid=4188623 > > It looks like this is essentially caused by SimpleITK being compiled with > `-std=c++11`, whereas ITK (and VXL) are not. So, there is a mismatch > between the configured definition of `VCL_CONSTEXPR` and the ` > VCL_STATIC_CONST_INIT_*` macros. > > For reference, VCL_CONSTEXPR was introduced here: > http://review.source.kitware.com/#/c/20386/ > > A proposed patch [1] is attached. > > Best, > Isaiah > > [1] > https://github.com/ihnorton/ITK/commit/0f748d8c86ffb2369c3a343c0db5ca87b067843e > > > > On Mon, Jan 11, 2016 at 11:21 AM, Steve Pieper wrote: > >> Hi - >> >> This morning with Xcode 7.2 on mac 10.11.2 I get the build errors pasted >> below. This was in a fresh build directory. With SimpleITK turned off the >> build completes and everything works as expected. >> >> I found an old issue with similar errors [1] but nothing lately. >> >> -Steve >> >> [1] https://issues.itk.org/jira/browse/ITK-2976 >> >> >> >> >> In file included from >> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_c_vector.h:26: >> >> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:388:41: >> **error: **declaration of constexpr static data member* >> >> * 'zero' requires an initializer* >> >> static VNL_EXPORT VCL_CONSTEXPR float zero >> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); >> >> * ^* >> >> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:390:41: >> **error: **declaration of constexpr static data member* >> >> * 'one' requires an initializer* >> >> static VNL_EXPORT VCL_CONSTEXPR float one >> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); >> >> * ^* >> >> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:392:41: >> **error: **declaration of constexpr static data member* >> >> * 'maxval' requires an initializer* >> >> static VNL_EXPORT VCL_CONSTEXPR float maxval >> VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); >> >> * ^* >> >> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:411:42: >> **error: **declaration of constexpr static data member* >> >> * 'zero' requires an initializer* >> >> static VNL_EXPORT VCL_CONSTEXPR double zero >> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); >> >> * ^* >> >> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:413:42: >> **error: **declaration of constexpr static data member* >> >> * 'one' requires an initializer* >> >> static VNL_EXPORT VCL_CONSTEXPR double one >> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); >> >> * ^* >> >> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:415:42: >> **error: **declaration of constexpr static data member* >> >> * 'maxval' requires an initializer* >> >> static VNL_EXPORT VCL_CONSTEXPR double maxval >> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); >> >> * ^* >> >> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:434:47: >> **error: **declaration of constexpr static data member* >> >> * 'zero' requires an initializer* >> >> static VNL_EXPORT VCL_CONSTEXPR long double zero >> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); >> >> * ^* >> >> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:436:47: >> **error: **declaration of constexpr static data member* >> >> * 'one' requires an initializer* >> >> static VNL_EXPORT VCL_CONSTEXPR long double one >> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); >> >> * ^* >> >> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:438:47: >> **error: **declaration of constexpr static data member* >> >> * 'maxval' requires an initializer* >> >> static VNL_EXPORT VCL_CONSTEXPR long double maxval >> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); >> >> * ^* >> >> 9 errors generated. >> >> make[8]: *** >> [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/sitkExplicitITKComposeImageFilter.cxx.o] >> Error 1 >> >> make[7]: *** [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/all] >> Error 2 >> >> make[6]: *** [all] Error 2 >> >> make[5]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error >> 2 >> >> make[4]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 >> >> make[3]: *** [all] Error 2 >> >> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error >> 2 >> >> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 >> >> make: *** [all] Error 2 >> >> _______________________________________________ >> slicer-devel mailing list >> slicer-devel at bwh.harvard.edu >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >> To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with >> unsubscribe as the subject >> >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > <0001-COMP-fix-build-with-std-c-11-when-ITK-VXL-initially-.patch> > > _______________________________________________ > slicer-devel mailing list > slicer-devel at bwh.harvard.edu > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel > To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with > unsubscribe as the subject > > http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > ------------------------------ > Notice: This UI Health Care e-mail (including attachments) is covered by > the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is > confidential and may be legally privileged. If you are not the intended > recipient, you are hereby notified that any retention, dissemination, > distribution, or copying of this communication is strictly prohibited. > Please reply to the sender that you have received the message in error, > then delete it. Thank you. > ------------------------------ > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hans-johnson at uiowa.edu Wed Jan 13 21:01:47 2016 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Thu, 14 Jan 2016 02:01:47 +0000 Subject: [ITK-dev] [slicer-devel] build error in simpleitk In-Reply-To: References: <89eefd6f837d4081a7b84a375052afe8@PHSX10HT5.partners.org> <66CED681-3509-46AB-BD82-4F88750CCCD9@mail.nih.gov> Message-ID: <83D6B469-0DE4-476D-9B35-0EE5D0A46646@uiowa.edu> Isaiah, There is no need for R/W. I don?t think you have configured your ITK development evnironment correctly. Are you running ?SetupForDevelopment.sh? script? Hans From: Isaiah Norton > Date: Wednesday, January 13, 2016 at 7:59 PM To: Hans Johnson > Cc: Bradley Lowekamp >, SPL Slicer Devel >, Insight Developers > Subject: Re: [ITK-dev] [slicer-devel] build error in simpleitk Brad, Hans: great, thanks! (as an aside: I would be happy to submit patches directly in the future, but it's not really clear why the Gerrit <-> GitHub KWRobot application asks for R/W on all GitHub repositories I have access to... It would be great if this could be reduced to the minimal necessary privileges for authentication) Isaiah On Wed, Jan 13, 2016 at 8:16 PM, Johnson, Hans J > wrote: I?m making a patch for this. I?ve noticed this today as well. mkdir XX; cd XX; cmake -DCMAKE_CXX_STANDARD:STRING=11 ../ITK; make ?j23 Before this patch, there was a build failure. After this patch it is now building. I made modifications to more closely match upstream VXL. Gerrit- review at : http://review.source.kitware.com/#/c/20658/ Hans From: Insight-developers > on behalf of Bradley Lowekamp > Date: Wednesday, January 13, 2016 at 6:38 PM To: Isaiah Norton > Cc: SPL Slicer Devel >, Insight Developers > Subject: Re: [ITK-dev] [slicer-devel] build error in simpleitk Hello, The patch looks pretty good. Thank you for contributing. Can you please submit the patch to ITK Gerrit for review? http://www.itk.org/Wiki/ITK/Git/Develop Thanks Brad On Jan 13, 2016, at 6:47 PM, Isaiah Norton > wrote: (cc: insight-devel) We are also seeing this issue, and several SimpleITK dashboards are failing with the same error for the OS X 10.9 (since bumping to ITK 4.9) and 10.10 (since yesterday) dashboards: https://open.cdash.org/buildSummary.php?buildid=4188623 It looks like this is essentially caused by SimpleITK being compiled with `-std=c++11`, whereas ITK (and VXL) are not. So, there is a mismatch between the configured definition of `VCL_CONSTEXPR` and the `VCL_STATIC_CONST_INIT_*` macros. For reference, VCL_CONSTEXPR was introduced here: http://review.source.kitware.com/#/c/20386/ A proposed patch [1] is attached. Best, Isaiah [1] https://github.com/ihnorton/ITK/commit/0f748d8c86ffb2369c3a343c0db5ca87b067843e On Mon, Jan 11, 2016 at 11:21 AM, Steve Pieper > wrote: Hi - This morning with Xcode 7.2 on mac 10.11.2 I get the build errors pasted below. This was in a fresh build directory. With SimpleITK turned off the build completes and everything works as expected. I found an old issue with similar errors [1] but nothing lately. -Steve [1] https://issues.itk.org/jira/browse/ITK-2976 In file included from /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_c_vector.h:26: /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:388:41: error: declaration of constexpr static data member 'zero' requires an initializer static VNL_EXPORT VCL_CONSTEXPR float zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:390:41: error: declaration of constexpr static data member 'one' requires an initializer static VNL_EXPORT VCL_CONSTEXPR float one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:392:41: error: declaration of constexpr static data member 'maxval' requires an initializer static VNL_EXPORT VCL_CONSTEXPR float maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:411:42: error: declaration of constexpr static data member 'zero' requires an initializer static VNL_EXPORT VCL_CONSTEXPR double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:413:42: error: declaration of constexpr static data member 'one' requires an initializer static VNL_EXPORT VCL_CONSTEXPR double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:415:42: error: declaration of constexpr static data member 'maxval' requires an initializer static VNL_EXPORT VCL_CONSTEXPR double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:434:47: error: declaration of constexpr static data member 'zero' requires an initializer static VNL_EXPORT VCL_CONSTEXPR long double zero VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:436:47: error: declaration of constexpr static data member 'one' requires an initializer static VNL_EXPORT VCL_CONSTEXPR long double one VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); ^ /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:438:47: error: declaration of constexpr static data member 'maxval' requires an initializer static VNL_EXPORT VCL_CONSTEXPR long double maxval VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); ^ 9 errors generated. make[8]: *** [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/sitkExplicitITKComposeImageFilter.cxx.o] Error 1 make[7]: *** [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/all] Error 2 make[6]: *** [all] Error 2 make[5]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2 make[4]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 make[3]: *** [all] Error 2 make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2 make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 make: *** [all] Error 2 _______________________________________________ slicer-devel mailing list slicer-devel at bwh.harvard.edu http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. <0001-COMP-fix-build-with-std-c-11-when-ITK-VXL-initially-.patch> _______________________________________________ slicer-devel mailing list slicer-devel at bwh.harvard.edu http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From isaiah.norton at gmail.com Wed Jan 13 22:02:08 2016 From: isaiah.norton at gmail.com (Isaiah Norton) Date: Wed, 13 Jan 2016 22:02:08 -0500 Subject: [ITK-dev] [slicer-devel] build error in simpleitk In-Reply-To: <83D6B469-0DE4-476D-9B35-0EE5D0A46646@uiowa.edu> References: <89eefd6f837d4081a7b84a375052afe8@PHSX10HT5.partners.org> <66CED681-3509-46AB-BD82-4F88750CCCD9@mail.nih.gov> <83D6B469-0DE4-476D-9B35-0EE5D0A46646@uiowa.edu> Message-ID: This is during authentication to Gerrit; the application asks for repo-level access: https://gist.github.com/ihnorton/76642485ff40eac0aa46 Which GitHub describes as: > This is one of the most expansive configurations you can permit, so accept it with caution! https://help.github.com/articles/connecting-with-third-party-applications/#repositories It's not really clear why KWRobot requires this level of access, given the other OAuth scopes available: https://developer.github.com/v3/oauth/#scopes Some clarification would be useful (I've read http://www.itk.org/Wiki/ITK/Git/Account, and looked around elsewhere, but didn't find any prior discussion). Isaiah On Wed, Jan 13, 2016 at 9:01 PM, Johnson, Hans J wrote: > Isaiah, > > There is no need for R/W. I don?t think you have configured your ITK > development evnironment correctly. Are you running > ?SetupForDevelopment.sh? script? > > Hans > > From: Isaiah Norton > Date: Wednesday, January 13, 2016 at 7:59 PM > To: Hans Johnson > Cc: Bradley Lowekamp , SPL Slicer Devel < > slicer-devel at bwh.harvard.edu>, Insight Developers < > insight-developers at itk.org> > > Subject: Re: [ITK-dev] [slicer-devel] build error in simpleitk > > Brad, Hans: great, thanks! > > (as an aside: I would be happy to submit patches directly in the future, > but it's not really clear why the Gerrit <-> GitHub KWRobot application > asks for R/W on all GitHub repositories I have access to... It would be > great if this could be reduced to the minimal necessary privileges for > authentication) > > Isaiah > > On Wed, Jan 13, 2016 at 8:16 PM, Johnson, Hans J > wrote: > >> I?m making a patch for this. >> >> I?ve noticed this today as well. >> >> mkdir XX; >> cd XX; >> cmake -DCMAKE_CXX_STANDARD:STRING=11 ../ITK; >> make ?j23 >> >> Before this patch, there was a build failure. >> After this patch it is now building. >> >> I made modifications to more closely match upstream VXL. >> >> Gerrit- review at : http://review.source.kitware.com/#/c/20658/ >> >> Hans >> >> From: Insight-developers on behalf >> of Bradley Lowekamp >> Date: Wednesday, January 13, 2016 at 6:38 PM >> To: Isaiah Norton >> Cc: SPL Slicer Devel , Insight Developers < >> insight-developers at itk.org> >> Subject: Re: [ITK-dev] [slicer-devel] build error in simpleitk >> >> Hello, >> >> The patch looks pretty good. Thank you for contributing. >> >> Can you please submit the patch to ITK Gerrit for review? >> >> http://www.itk.org/Wiki/ITK/Git/Develop >> >> Thanks >> Brad >> >> On Jan 13, 2016, at 6:47 PM, Isaiah Norton >> wrote: >> >> (cc: insight-devel) >> >> We are also seeing this issue, and several SimpleITK dashboards are >> failing with the same error for the OS X 10.9 (since bumping to ITK 4.9) >> and 10.10 (since yesterday) dashboards: >> https://open.cdash.org/buildSummary.php?buildid=4188623 >> >> It looks like this is essentially caused by SimpleITK being compiled with >> `-std=c++11`, whereas ITK (and VXL) are not. So, there is a mismatch >> between the configured definition of `VCL_CONSTEXPR` and the ` >> VCL_STATIC_CONST_INIT_*` macros. >> >> For reference, VCL_CONSTEXPR was introduced here: >> http://review.source.kitware.com/#/c/20386/ >> >> A proposed patch [1] is attached. >> >> Best, >> Isaiah >> >> [1] >> https://github.com/ihnorton/ITK/commit/0f748d8c86ffb2369c3a343c0db5ca87b067843e >> >> >> >> On Mon, Jan 11, 2016 at 11:21 AM, Steve Pieper >> wrote: >> >>> Hi - >>> >>> This morning with Xcode 7.2 on mac 10.11.2 I get the build errors pasted >>> below. This was in a fresh build directory. With SimpleITK turned off the >>> build completes and everything works as expected. >>> >>> I found an old issue with similar errors [1] but nothing lately. >>> >>> -Steve >>> >>> [1] https://issues.itk.org/jira/browse/ITK-2976 >>> >>> >>> >>> >>> In file included from >>> /Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_c_vector.h:26: >>> >>> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:388:41: >>> **error: **declaration of constexpr static data member* >>> >>> * 'zero' requires an initializer* >>> >>> static VNL_EXPORT VCL_CONSTEXPR float zero >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0F); >>> >>> * ^* >>> >>> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:390:41: >>> **error: **declaration of constexpr static data member* >>> >>> * 'one' requires an initializer* >>> >>> static VNL_EXPORT VCL_CONSTEXPR float one >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0F); >>> >>> * ^* >>> >>> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:392:41: >>> **error: **declaration of constexpr static data member* >>> >>> * 'maxval' requires an initializer* >>> >>> static VNL_EXPORT VCL_CONSTEXPR float maxval >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(3.40282346638528860e+38F); >>> >>> * ^* >>> >>> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:411:42: >>> **error: **declaration of constexpr static data member* >>> >>> * 'zero' requires an initializer* >>> >>> static VNL_EXPORT VCL_CONSTEXPR double zero >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); >>> >>> * ^* >>> >>> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:413:42: >>> **error: **declaration of constexpr static data member* >>> >>> * 'one' requires an initializer* >>> >>> static VNL_EXPORT VCL_CONSTEXPR double one >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); >>> >>> * ^* >>> >>> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:415:42: >>> **error: **declaration of constexpr static data member* >>> >>> * 'maxval' requires an initializer* >>> >>> static VNL_EXPORT VCL_CONSTEXPR double maxval >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); >>> >>> * ^* >>> >>> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:434:47: >>> **error: **declaration of constexpr static data member* >>> >>> * 'zero' requires an initializer* >>> >>> static VNL_EXPORT VCL_CONSTEXPR long double zero >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(0.0); >>> >>> * ^* >>> >>> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:436:47: >>> **error: **declaration of constexpr static data member* >>> >>> * 'one' requires an initializer* >>> >>> static VNL_EXPORT VCL_CONSTEXPR long double one >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.0); >>> >>> * ^* >>> >>> */Users/pieper/slicer4/latest/Slicer-superbuild/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_numeric_traits.h:438:47: >>> **error: **declaration of constexpr static data member* >>> >>> * 'maxval' requires an initializer* >>> >>> static VNL_EXPORT VCL_CONSTEXPR long double maxval >>> VCL_STATIC_CONST_INIT_FLOAT_DECL(1.7976931348623157E+308); >>> >>> * ^* >>> >>> 9 errors generated. >>> >>> make[8]: *** >>> [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/sitkExplicitITKComposeImageFilter.cxx.o] >>> Error 1 >>> >>> make[7]: *** [Code/Explicit/src/CMakeFiles/SimpleITKExplicit.dir/all] >>> Error 2 >>> >>> make[6]: *** [all] Error 2 >>> >>> make[5]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] >>> Error 2 >>> >>> make[4]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 >>> >>> make[3]: *** [all] Error 2 >>> >>> make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] >>> Error 2 >>> >>> make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2 >>> >>> make: *** [all] Error 2 >>> >>> _______________________________________________ >>> slicer-devel mailing list >>> slicer-devel at bwh.harvard.edu >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >>> To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with >>> unsubscribe as the subject >>> >>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> <0001-COMP-fix-build-with-std-c-11-when-ITK-VXL-initially-.patch> >> >> _______________________________________________ >> slicer-devel mailing list >> slicer-devel at bwh.harvard.edu >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel >> To unsubscribe: send email to slicer-devel-request at bwh.harvard.edu with >> unsubscribe as the subject >> >> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> ------------------------------ >> Notice: This UI Health Care e-mail (including attachments) is covered by >> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is >> confidential and may be legally privileged. If you are not the intended >> recipient, you are hereby notified that any retention, dissemination, >> distribution, or copying of this communication is strictly prohibited. >> Please reply to the sender that you have received the message in error, >> then delete it. Thank you. >> ------------------------------ >> > > > > ------------------------------ > Notice: This UI Health Care e-mail (including attachments) is covered by > the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is > confidential and may be legally privileged. If you are not the intended > recipient, you are hereby notified that any retention, dissemination, > distribution, or copying of this communication is strictly prohibited. > Please reply to the sender that you have received the message in error, > then delete it. Thank you. > ------------------------------ > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Jan 13 22:12:06 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 13 Jan 2016 22:12:06 -0500 Subject: [ITK-dev] [slicer-devel] build error in simpleitk In-Reply-To: References: <89eefd6f837d4081a7b84a375052afe8@PHSX10HT5.partners.org> <66CED681-3509-46AB-BD82-4F88750CCCD9@mail.nih.gov> <83D6B469-0DE4-476D-9B35-0EE5D0A46646@uiowa.edu> Message-ID: Hi Isaiah, On Wed, Jan 13, 2016 at 10:02 PM, Isaiah Norton wrote: > This is during authentication to Gerrit; the application asks for repo-level > access: > https://gist.github.com/ihnorton/76642485ff40eac0aa46 > > Which GitHub describes as: >> This is one of the most expansive configurations you can permit, so accept >> it with caution! > > https://help.github.com/articles/connecting-with-third-party-applications/#repositories > > It's not really clear why KWRobot requires this level of access, given the > other OAuth scopes available: > https://developer.github.com/v3/oauth/#scopes Yes, we are looking into ways to better limit the scope. > Some clarification would be useful (I've read > http://www.itk.org/Wiki/ITK/Git/Account, and looked around elsewhere, but > didn't find any prior discussion). I made a note on the wiki. None of your repositories will be modified. Thanks, Matt From brad at lowekamp.net Sat Jan 16 12:13:28 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Sat, 16 Jan 2016 12:13:28 -0500 Subject: [ITK-dev] Itk release branch demons registration Message-ID: <694F0867-74B1-4867-B74C-3763ADB057FF@mail.nih.gov> Hello, I updated SimpleITK From brad at lowekamp.net Sat Jan 16 12:18:05 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Sat, 16 Jan 2016 12:18:05 -0500 Subject: [ITK-dev] Itk release branch demons registration In-Reply-To: <694F0867-74B1-4867-B74C-3763ADB057FF@mail.nih.gov> References: <694F0867-74B1-4867-B74C-3763ADB057FF@mail.nih.gov> Message-ID: I just updated SimpleITK to the release branch yesterday and there are some changes in the result of the demons registration. I'm not going to get a chance to look at it until Monday. The only change potentially related I know of is the rounding related numeric traits, but that does not seem likely to me. Any ideas why the Demons Registration would have changed fro rc3? > On Jan 16, 2016, at 12:13 PM, Bradley Lowekamp wrote: > > Hello, > > I updated SimpleITK > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Sat Jan 16 12:57:35 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sat, 16 Jan 2016 12:57:35 -0500 Subject: [ITK-dev] Itk release branch demons registration In-Reply-To: References: <694F0867-74B1-4867-B74C-3763ADB057FF@mail.nih.gov> Message-ID: Hi, Nothing comes to mind. Here is the log for v4.9rc03..release: Bill Hoffman (3): COMP: fix 64 bit build warnings with windows auto-export on. COMP: work around for VS 2015 optimizer bug causing test failures. COMP: work around for VS 2015 optimizer bug causing test failures. Bradley Lowekamp (1): BUG: Fix precision with accumulation and scaling in AdaptiveHistogram Davis Vigneault (1): COMP: Include itkMacro.h in itkTestingMacros.h Hans Johnson (2): COMP: BSD command lines do not have --version COMP: Respect CMAKE_CXX_STANDARD during config Hyun Jae Kang (12): COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 BUG: Fixed the runtime crash of itkTimeProbeTest2 BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's tests on OSX 10.6 COMP: Fixed the data conversion warning messages of itkResourceProbe BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1 BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 BUG: Fixed the runtime crash of vnl_test_numeric_traits BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 Isaiah Norton (1): COMP: fix build with -std=c++11 when ITK/VXL initially configured without Matthew McCormick (6): BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper. COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5. DOC: Update the location of the GNUPlot Software Guide scripts. DOC: Update the Software Guide repo location in Examples/README.txt. COMP: Add export specification for itk::ResourceProbe. COMP: Require NO_MODULE with DCMTK find_package. Michka Popoff (2): ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7 COMP: Re-enable review module for python 3 and older VTK's Sean McBride (1): DOC: Update some woefully out-of-date GDCM comments, and typos Seun Odutola (1): BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions HTH, Matt On Sat, Jan 16, 2016 at 12:18 PM, Bradley Lowekamp wrote: > I just updated SimpleITK to the release branch yesterday and there are some changes in the result of the demons registration. I'm not going to get a chance to look at it until Monday. The only change potentially related I know of is the rounding related numeric traits, but that does not seem likely to me. > > Any ideas why the Demons Registration would have changed fro rc3? > >> On Jan 16, 2016, at 12:13 PM, Bradley Lowekamp wrote: >> >> Hello, >> >> I updated SimpleITK >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers From brad at lowekamp.net Sat Jan 16 14:58:42 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Sat, 16 Jan 2016 14:58:42 -0500 Subject: [ITK-dev] Itk release branch demons registration In-Reply-To: References: <694F0867-74B1-4867-B74C-3763ADB057FF@mail.nih.gov> Message-ID: <48C7905E-F141-42E9-AF23-45079365F771@lowekamp.net> Thanks. I'll run a git bisect tonight to try to figure it out. > On Jan 16, 2016, at 12:57 PM, Matt McCormick wrote: > > Hi, > > Nothing comes to mind. > > Here is the log for v4.9rc03..release: > > Bill Hoffman (3): > COMP: fix 64 bit build warnings with windows auto-export on. > COMP: work around for VS 2015 optimizer bug causing test failures. > COMP: work around for VS 2015 optimizer bug causing test failures. > > Bradley Lowekamp (1): > BUG: Fix precision with accumulation and scaling in AdaptiveHistogram > > Davis Vigneault (1): > COMP: Include itkMacro.h in itkTestingMacros.h > > Hans Johnson (2): > COMP: BSD command lines do not have --version > COMP: Respect CMAKE_CXX_STANDARD during config > > Hyun Jae Kang (12): > COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 > BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 > BUG: Fixed the runtime crash of itkTimeProbeTest2 > BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 > BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 > BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's > tests on OSX 10.6 > COMP: Fixed the data conversion warning messages of itkResourceProbe > BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 > BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1 > BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 > BUG: Fixed the runtime crash of vnl_test_numeric_traits > BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 > > Isaiah Norton (1): > COMP: fix build with -std=c++11 when ITK/VXL initially configured without > > Matthew McCormick (6): > BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper. > COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5. > DOC: Update the location of the GNUPlot Software Guide scripts. > DOC: Update the Software Guide repo location in Examples/README.txt. > COMP: Add export specification for itk::ResourceProbe. > COMP: Require NO_MODULE with DCMTK find_package. > > Michka Popoff (2): > ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7 > COMP: Re-enable review module for python 3 and older VTK's > > Sean McBride (1): > DOC: Update some woefully out-of-date GDCM comments, and typos > > Seun Odutola (1): > BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions > > HTH, > Matt > >> On Sat, Jan 16, 2016 at 12:18 PM, Bradley Lowekamp wrote: >> I just updated SimpleITK to the release branch yesterday and there are some changes in the result of the demons registration. I'm not going to get a chance to look at it until Monday. The only change potentially related I know of is the rounding related numeric traits, but that does not seem likely to me. >> >> Any ideas why the Demons Registration would have changed fro rc3? >> >>> On Jan 16, 2016, at 12:13 PM, Bradley Lowekamp wrote: >>> >>> Hello, >>> >>> I updated SimpleITK >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-developers >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers From andinet.enqu at kitware.com Sun Jan 17 08:10:04 2016 From: andinet.enqu at kitware.com (Andinet Enquobahrie) Date: Sun, 17 Jan 2016 08:10:04 -0500 Subject: [ITK-dev] ANN: Kitware is hiring Image Guided Intervention Applications Research and Development Engineers in the Medical Computing Group Message-ID: Apologies for duplicate postings. =================== Hi folks, We are looking to hire image guided intervention applications research and development engineers in our Medical Computing group. If you are a talented medical image analysis and visualization expert with image guided intervention software applications development experience, please consider applying. For the full posting see: http://tinyurl.com/zxlpyyj JOB DESCRIPTION =============== Kitware is actively seeking talented individuals to contribute to the creation and development of image guided intervention software applications. The candidate will participate in research projects focused on building intelligent virtual surgical planning and guidance applications for a variety of clinical procedures including orthopedic, neurological and abdominal surgeries and other types of interventions such as needle biopsy. We aim to develop advanced algorithms to process pre-operative images, to localize surgical instruments and register pre-operative images with intraoperative images to guide surgeons and interventional radiologists for better clinical outcomes. Our efforts build upon our extensive C++ software libraries as well as our expertise in a variety of synergistic disciplines including machine learning, pattern recognition, medical image analysis, visualization, informatics, and computer vision. In these projects, the employee will collaborate with world-renowned researchers and talented engineers in industry, academia, and at government agencies. Qualifications *Masters or PhD in computer science, biomedical engineering, or a related field that has emphasis in medical image analysis and visualization *Concrete experience implementing image guided intervention applications using open-source libraries such as ITK, VTK, 3D Slicer and Qt. *Experience implementing biomedical analysis solutions such as: image registration, segmentation, volume rendering, statistical computing, visualization, etc. *Strong C++ programming skills *Excellent communication and writing skills =============== For other job openings at Kitware, please check http://jobs.kitware.com/opportunities.html -- Andinet Enquobahrie, Ph.D., MBA Assistant Director of Medical Computing Kitware, Inc. http://www.kitware.com (919) 969-6990 x311 -------------- next part -------------- An HTML attachment was scrubbed... URL: From brad at lowekamp.net Sun Jan 17 18:13:44 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Sun, 17 Jan 2016 18:13:44 -0500 Subject: [ITK-dev] [ITK] Itk release branch demons registration In-Reply-To: <48C7905E-F141-42E9-AF23-45079365F771@lowekamp.net> References: <694F0867-74B1-4867-B74C-3763ADB057FF@mail.nih.gov> <48C7905E-F141-42E9-AF23-45079365F771@lowekamp.net> Message-ID: <63AE857C-91FE-4B80-B31B-921A6CDAD2C6@lowekamp.net> Just to follow up my git bisect narrowed the change down to this: commit 0fd462a3226e84bdce77b68830903b3888dab244 Author: Hyun Jae Kang Date: Thu Dec 31 10:56:25 2015 -0500 BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 - Fixed the runtime crash of the following ITKStatisticsTestDriver's tests on OSX 10.6 ( clang 3.0 ) by modifying the itkHistogram's Initialize function to handle a data value out of range of a specific data type with type-casting operator. - itkSampleToHistogramFilterTest3 (ILLEGAL) - itkSampleToHistogramFilterTest7 (ILLEGAL) - These crash were reported at the following page: https://open.cdash.org/viewTest.php?onlyfailed&buildid=4170483 Change-Id: I2063912edee79422d88125ffd5f7513c31a9e98c diff --git a/Modules/Numerics/Statistics/include/itkHistogram.hxx b/Modules/Numerics/Statistics/include/itkHistogram.hxx index 380b8d0..d11d788 100644 --- a/Modules/Numerics/Statistics/include/itkHistogram.hxx +++ b/Modules/Numerics/Statistics/include/itkHistogram.hxx @@ -248,8 +248,8 @@ Histogram< TMeasurement, TFrequencyContainer > { if ( size[i] > 0 ) { - interval = static_cast( upperBound[i] - lowerBound[i] ) - / static_cast< MeasurementType >( size[i] ); + interval = (static_cast( upperBound[i] ) - static_cast(lowerBound[i] )) + / static_cast< float >( size[i] ); Here is the failing example [1], which uses the HistogramMatching filter. I am not sure why float was choose at the type here. Are results being truncated now? When there was temporary double computation going on? It needs more investigation, as it?s changing the results of some filters? not sure how significant yet. Brad [1] https://github.com/SimpleITK/SimpleITK/blob/master/Examples/DemonsRegistration1.py#L41 > On Jan 16, 2016, at 2:58 PM, Bradley Lowekamp wrote: > > Thanks. I'll run a git bisect tonight to try to figure it out. > >> On Jan 16, 2016, at 12:57 PM, Matt McCormick wrote: >> >> Hi, >> >> Nothing comes to mind. >> >> Here is the log for v4.9rc03..release: >> >> Bill Hoffman (3): >> COMP: fix 64 bit build warnings with windows auto-export on. >> COMP: work around for VS 2015 optimizer bug causing test failures. >> COMP: work around for VS 2015 optimizer bug causing test failures. >> >> Bradley Lowekamp (1): >> BUG: Fix precision with accumulation and scaling in AdaptiveHistogram >> >> Davis Vigneault (1): >> COMP: Include itkMacro.h in itkTestingMacros.h >> >> Hans Johnson (2): >> COMP: BSD command lines do not have --version >> COMP: Respect CMAKE_CXX_STANDARD during config >> >> Hyun Jae Kang (12): >> COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 >> BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 >> BUG: Fixed the runtime crash of itkTimeProbeTest2 >> BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 >> BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 >> BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's >> tests on OSX 10.6 >> COMP: Fixed the data conversion warning messages of itkResourceProbe >> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 >> BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1 >> BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 >> BUG: Fixed the runtime crash of vnl_test_numeric_traits >> BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 >> >> Isaiah Norton (1): >> COMP: fix build with -std=c++11 when ITK/VXL initially configured without >> >> Matthew McCormick (6): >> BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper. >> COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5. >> DOC: Update the location of the GNUPlot Software Guide scripts. >> DOC: Update the Software Guide repo location in Examples/README.txt. >> COMP: Add export specification for itk::ResourceProbe. >> COMP: Require NO_MODULE with DCMTK find_package. >> >> Michka Popoff (2): >> ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7 >> COMP: Re-enable review module for python 3 and older VTK's >> >> Sean McBride (1): >> DOC: Update some woefully out-of-date GDCM comments, and typos >> >> Seun Odutola (1): >> BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions >> >> HTH, >> Matt >> >>> On Sat, Jan 16, 2016 at 12:18 PM, Bradley Lowekamp wrote: >>> I just updated SimpleITK to the release branch yesterday and there are some changes in the result of the demons registration. I'm not going to get a chance to look at it until Monday. The only change potentially related I know of is the rounding related numeric traits, but that does not seem likely to me. >>> >>> Any ideas why the Demons Registration would have changed fro rc3? >>> >>>> On Jan 16, 2016, at 12:13 PM, Bradley Lowekamp wrote: >>>> >>>> Hello, >>>> >>>> I updated SimpleITK >>>> _______________________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-developers >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From hyunjae.kang at kitware.com Mon Jan 18 12:20:48 2016 From: hyunjae.kang at kitware.com (Hyun Jae Kang) Date: Mon, 18 Jan 2016 12:20:48 -0500 Subject: [ITK-dev] [ITK] Itk release branch demons registration Message-ID: Hi Bradley, Thank you for your comments on the code. The lines you mentioned in itkHistogram.hxx generated the run-time crash on Mac OSX 10.6 with clang compiler (3.0). When I found this error, I checked the data type of the local variable ( float interval ) and I put "float" in the lines to avoid the run-time error. This is why I chose "float" as the data type of data-casting. If I did something wrong, please let me know. I will fix it. Thanks, Hyun Jae On Mon, Jan 18, 2016 at 12:00 PM, wrote: > Send Insight-developers mailing list submissions to > insight-developers at itk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/insight-developers > or, via email, send a message with subject or body 'help' to > insight-developers-request at itk.org > > You can reach the person managing the list at > insight-developers-owner at itk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Insight-developers digest..." > > > Today's Topics: > > 1. Re: [ITK] Itk release branch demons registration > (Bradley Lowekamp) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 17 Jan 2016 18:13:44 -0500 > From: Bradley Lowekamp > To: Bradley Lowekamp > Cc: ITK > Subject: Re: [ITK-dev] [ITK] Itk release branch demons registration > Message-ID: <63AE857C-91FE-4B80-B31B-921A6CDAD2C6 at lowekamp.net> > Content-Type: text/plain; charset="utf-8" > > Just to follow up my git bisect narrowed the change down to this: > commit 0fd462a3226e84bdce77b68830903b3888dab244 > Author: Hyun Jae Kang > Date: Thu Dec 31 10:56:25 2015 -0500 > > BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX > 10.6 > > - Fixed the runtime crash of the following ITKStatisticsTestDriver's > tests on > OSX 10.6 ( clang 3.0 ) by modifying the itkHistogram's Initialize > function > to handle a data value out of range of a specific data type with > type-casting operator. > > - itkSampleToHistogramFilterTest3 (ILLEGAL) > - itkSampleToHistogramFilterTest7 (ILLEGAL) > > - These crash were reported at the following page: > https://open.cdash.org/viewTest.php?onlyfailed&buildid=4170483 > > Change-Id: I2063912edee79422d88125ffd5f7513c31a9e98c > > diff --git a/Modules/Numerics/Statistics/include/itkHistogram.hxx > b/Modules/Numerics/Statistics/include/itkHistogram.hxx > index 380b8d0..d11d788 100644 > --- a/Modules/Numerics/Statistics/include/itkHistogram.hxx > +++ b/Modules/Numerics/Statistics/include/itkHistogram.hxx > @@ -248,8 +248,8 @@ Histogram< TMeasurement, TFrequencyContainer > > { > if ( size[i] > 0 ) > { > - interval = static_cast( upperBound[i] - lowerBound[i] ) > - / static_cast< MeasurementType >( size[i] ); > + interval = (static_cast( upperBound[i] ) - > static_cast(lowerBound[i] )) > + / static_cast< float >( size[i] ); > > > Here is the failing example [1], which uses the HistogramMatching filter. > > I am not sure why float was choose at the type here. Are results being > truncated now? When there was temporary double computation going on? > > It needs more investigation, as it?s changing the results of some > filters? not sure how significant yet. > > Brad > > > > > [1] > https://github.com/SimpleITK/SimpleITK/blob/master/Examples/DemonsRegistration1.py#L41 > > On Jan 16, 2016, at 2:58 PM, Bradley Lowekamp wrote: > > > > Thanks. I'll run a git bisect tonight to try to figure it out. > > > >> On Jan 16, 2016, at 12:57 PM, Matt McCormick < > matt.mccormick at kitware.com> wrote: > >> > >> Hi, > >> > >> Nothing comes to mind. > >> > >> Here is the log for v4.9rc03..release: > >> > >> Bill Hoffman (3): > >> COMP: fix 64 bit build warnings with windows auto-export on. > >> COMP: work around for VS 2015 optimizer bug causing test failures. > >> COMP: work around for VS 2015 optimizer bug causing test failures. > >> > >> Bradley Lowekamp (1): > >> BUG: Fix precision with accumulation and scaling in > AdaptiveHistogram > >> > >> Davis Vigneault (1): > >> COMP: Include itkMacro.h in itkTestingMacros.h > >> > >> Hans Johnson (2): > >> COMP: BSD command lines do not have --version > >> COMP: Respect CMAKE_CXX_STANDARD during config > >> > >> Hyun Jae Kang (12): > >> COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 > >> BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 > >> BUG: Fixed the runtime crash of itkTimeProbeTest2 > >> BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 > >> BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 > >> BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's > >> tests on OSX 10.6 > >> COMP: Fixed the data conversion warning messages of itkResourceProbe > >> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on > OSX 10.6 > >> BUG: Fixed the runtime crash of > itkBinaryShapeOpeningImageFilterTest1 > >> BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 > >> BUG: Fixed the runtime crash of vnl_test_numeric_traits > >> BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 > >> > >> Isaiah Norton (1): > >> COMP: fix build with -std=c++11 when ITK/VXL initially configured > without > >> > >> Matthew McCormick (6): > >> BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper. > >> COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5. > >> DOC: Update the location of the GNUPlot Software Guide scripts. > >> DOC: Update the Software Guide repo location in Examples/README.txt. > >> COMP: Add export specification for itk::ResourceProbe. > >> COMP: Require NO_MODULE with DCMTK find_package. > >> > >> Michka Popoff (2): > >> ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7 > >> COMP: Re-enable review module for python 3 and older VTK's > >> > >> Sean McBride (1): > >> DOC: Update some woefully out-of-date GDCM comments, and typos > >> > >> Seun Odutola (1): > >> BUG: Improved itkAnalyzeImageIO to handle case insensitive > extensions > >> > >> HTH, > >> Matt > >> > >>> On Sat, Jan 16, 2016 at 12:18 PM, Bradley Lowekamp > wrote: > >>> I just updated SimpleITK to the release branch yesterday and there are > some changes in the result of the demons registration. I'm not going to get > a chance to look at it until Monday. The only change potentially related I > know of is the rounding related numeric traits, but that does not seem > likely to me. > >>> > >>> Any ideas why the Demons Registration would have changed fro rc3? > >>> > >>>> On Jan 16, 2016, at 12:13 PM, Bradley Lowekamp > wrote: > >>>> > >>>> Hello, > >>>> > >>>> I updated SimpleITK > >>>> _______________________________________________ > >>>> Powered by www.kitware.com > >>>> > >>>> Visit other Kitware open-source projects at > >>>> http://www.kitware.com/opensource/opensource.html > >>>> > >>>> Kitware offers ITK Training Courses, for more information visit: > >>>> http://kitware.com/products/protraining.php > >>>> > >>>> Please keep messages on-topic and check the ITK FAQ at: > >>>> http://www.itk.org/Wiki/ITK_FAQ > >>>> > >>>> Follow this link to subscribe/unsubscribe: > >>>> http://public.kitware.com/mailman/listinfo/insight-developers > >>> _______________________________________________ > >>> Powered by www.kitware.com > >>> > >>> Visit other Kitware open-source projects at > >>> http://www.kitware.com/opensource/opensource.html > >>> > >>> Kitware offers ITK Training Courses, for more information visit: > >>> http://kitware.com/products/protraining.php > >>> > >>> Please keep messages on-topic and check the ITK FAQ at: > >>> http://www.itk.org/Wiki/ITK_FAQ > >>> > >>> Follow this link to subscribe/unsubscribe: > >>> http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-developers/attachments/20160117/188815c1/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Insight-developers mailing list > Insight-developers at itk.org > http://public.kitware.com/mailman/listinfo/insight-developers > > > ------------------------------ > > End of Insight-developers Digest, Vol 141, Issue 10 > *************************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Jan 19 09:09:54 2016 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 19 Jan 2016 09:09:54 -0500 Subject: [ITK-dev] [ITK] Itk release branch demons registration In-Reply-To: References: Message-ID: <48C8C5A2-BBA5-4806-B212-38B8CB6C126E@mail.nih.gov> Hello Hyun, From you description, I don?t understand what was the cause of the crass nor how this fixed the problem. Why was it the wrong type? Brad > On Jan 18, 2016, at 12:20 PM, Hyun Jae Kang wrote: > > Hi Bradley, > > Thank you for your comments on the code. The lines you mentioned in itkHistogram.hxx generated the run-time crash on Mac OSX 10.6 with clang compiler (3.0). > > When I found this error, I checked the data type of the local variable ( float interval ) and I put "float" in the lines to avoid the run-time error. > > This is why I chose "float" as the data type of data-casting. > > If I did something wrong, please let me know. I will fix it. > > Thanks, > > Hyun Jae > > > On Mon, Jan 18, 2016 at 12:00 PM, > wrote: > Send Insight-developers mailing list submissions to > insight-developers at itk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/insight-developers > or, via email, send a message with subject or body 'help' to > insight-developers-request at itk.org > > You can reach the person managing the list at > insight-developers-owner at itk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Insight-developers digest..." > > > Today's Topics: > > 1. Re: [ITK] Itk release branch demons registration > (Bradley Lowekamp) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 17 Jan 2016 18:13:44 -0500 > From: Bradley Lowekamp > > To: Bradley Lowekamp > > Cc: ITK > > Subject: Re: [ITK-dev] [ITK] Itk release branch demons registration > Message-ID: <63AE857C-91FE-4B80-B31B-921A6CDAD2C6 at lowekamp.net > > Content-Type: text/plain; charset="utf-8" > > Just to follow up my git bisect narrowed the change down to this: > commit 0fd462a3226e84bdce77b68830903b3888dab244 > Author: Hyun Jae Kang > > Date: Thu Dec 31 10:56:25 2015 -0500 > > BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 > > - Fixed the runtime crash of the following ITKStatisticsTestDriver's tests on > OSX 10.6 ( clang 3.0 ) by modifying the itkHistogram's Initialize function > to handle a data value out of range of a specific data type with > type-casting operator. > > - itkSampleToHistogramFilterTest3 (ILLEGAL) > - itkSampleToHistogramFilterTest7 (ILLEGAL) > > - These crash were reported at the following page: > https://open.cdash.org/viewTest.php?onlyfailed&buildid=4170483 > > Change-Id: I2063912edee79422d88125ffd5f7513c31a9e98c > > diff --git a/Modules/Numerics/Statistics/include/itkHistogram.hxx b/Modules/Numerics/Statistics/include/itkHistogram.hxx > index 380b8d0..d11d788 100644 > --- a/Modules/Numerics/Statistics/include/itkHistogram.hxx > +++ b/Modules/Numerics/Statistics/include/itkHistogram.hxx > @@ -248,8 +248,8 @@ Histogram< TMeasurement, TFrequencyContainer > > { > if ( size[i] > 0 ) > { > - interval = static_cast( upperBound[i] - lowerBound[i] ) > - / static_cast< MeasurementType >( size[i] ); > + interval = (static_cast( upperBound[i] ) - static_cast(lowerBound[i] )) > + / static_cast< float >( size[i] ); > > > Here is the failing example [1], which uses the HistogramMatching filter. > > I am not sure why float was choose at the type here. Are results being truncated now? When there was temporary double computation going on? > > It needs more investigation, as it?s changing the results of some filters? not sure how significant yet. > > Brad > > > > > [1] https://github.com/SimpleITK/SimpleITK/blob/master/Examples/DemonsRegistration1.py#L41 > > On Jan 16, 2016, at 2:58 PM, Bradley Lowekamp > wrote: > > > > Thanks. I'll run a git bisect tonight to try to figure it out. > > > >> On Jan 16, 2016, at 12:57 PM, Matt McCormick > wrote: > >> > >> Hi, > >> > >> Nothing comes to mind. > >> > >> Here is the log for v4.9rc03..release: > >> > >> Bill Hoffman (3): > >> COMP: fix 64 bit build warnings with windows auto-export on. > >> COMP: work around for VS 2015 optimizer bug causing test failures. > >> COMP: work around for VS 2015 optimizer bug causing test failures. > >> > >> Bradley Lowekamp (1): > >> BUG: Fix precision with accumulation and scaling in AdaptiveHistogram > >> > >> Davis Vigneault (1): > >> COMP: Include itkMacro.h in itkTestingMacros.h > >> > >> Hans Johnson (2): > >> COMP: BSD command lines do not have --version > >> COMP: Respect CMAKE_CXX_STANDARD during config > >> > >> Hyun Jae Kang (12): > >> COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 > >> BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 > >> BUG: Fixed the runtime crash of itkTimeProbeTest2 > >> BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 > >> BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 > >> BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's > >> tests on OSX 10.6 > >> COMP: Fixed the data conversion warning messages of itkResourceProbe > >> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 > >> BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1 > >> BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 > >> BUG: Fixed the runtime crash of vnl_test_numeric_traits > >> BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 > >> > >> Isaiah Norton (1): > >> COMP: fix build with -std=c++11 when ITK/VXL initially configured without > >> > >> Matthew McCormick (6): > >> BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper. > >> COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5. > >> DOC: Update the location of the GNUPlot Software Guide scripts. > >> DOC: Update the Software Guide repo location in Examples/README.txt. > >> COMP: Add export specification for itk::ResourceProbe. > >> COMP: Require NO_MODULE with DCMTK find_package. > >> > >> Michka Popoff (2): > >> ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7 > >> COMP: Re-enable review module for python 3 and older VTK's > >> > >> Sean McBride (1): > >> DOC: Update some woefully out-of-date GDCM comments, and typos > >> > >> Seun Odutola (1): > >> BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions > >> > >> HTH, > >> Matt > >> > >>> On Sat, Jan 16, 2016 at 12:18 PM, Bradley Lowekamp > wrote: > >>> I just updated SimpleITK to the release branch yesterday and there are some changes in the result of the demons registration. I'm not going to get a chance to look at it until Monday. The only change potentially related I know of is the rounding related numeric traits, but that does not seem likely to me. > >>> > >>> Any ideas why the Demons Registration would have changed fro rc3? > >>> > >>>> On Jan 16, 2016, at 12:13 PM, Bradley Lowekamp > wrote: > >>>> > >>>> Hello, > >>>> > >>>> I updated SimpleITK > >>>> _______________________________________________ > >>>> Powered by www.kitware.com > >>>> > >>>> Visit other Kitware open-source projects at > >>>> http://www.kitware.com/opensource/opensource.html > >>>> > >>>> Kitware offers ITK Training Courses, for more information visit: > >>>> http://kitware.com/products/protraining.php > >>>> > >>>> Please keep messages on-topic and check the ITK FAQ at: > >>>> http://www.itk.org/Wiki/ITK_FAQ > >>>> > >>>> Follow this link to subscribe/unsubscribe: > >>>> http://public.kitware.com/mailman/listinfo/insight-developers > >>> _______________________________________________ > >>> Powered by www.kitware.com > >>> > >>> Visit other Kitware open-source projects at > >>> http://www.kitware.com/opensource/opensource.html > >>> > >>> Kitware offers ITK Training Courses, for more information visit: > >>> http://kitware.com/products/protraining.php > >>> > >>> Please keep messages on-topic and check the ITK FAQ at: > >>> http://www.itk.org/Wiki/ITK_FAQ > >>> > >>> Follow this link to subscribe/unsubscribe: > >>> http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Insight-developers mailing list > Insight-developers at itk.org > http://public.kitware.com/mailman/listinfo/insight-developers > > > ------------------------------ > > End of Insight-developers Digest, Vol 141, Issue 10 > *************************************************** > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Jan 19 11:02:00 2016 From: blowekamp at mail.nih.gov (Bradly Lowekamp) Date: Tue, 19 Jan 2016 11:02:00 -0500 Subject: [ITK-dev] [ITK] Itk release branch demons registration In-Reply-To: <48C8C5A2-BBA5-4806-B212-38B8CB6C126E@mail.nih.gov> References: <48C8C5A2-BBA5-4806-B212-38B8CB6C126E@mail.nih.gov> Message-ID: Hello, Just to follow up. Your code seems to correct a long long time bug. That has had a work around [1] for at least one usage. The truncation of the ?size? variable to the MeasurementType, can easily result in a divide by zero when the number of bins is NumericTraints::max() + 1. It may need to be noted in the release notes, that histogram calculations may change due to this correction, which can change the bounds of histograms. Good job tracking down the problem. Brad [1] https://github.com/InsightSoftwareConsortium/ITK/commit/4011c5d85e77387f59cadc0b12b79fdaa3251339 > On Jan 19, 2016, at 9:09 AM, Bradley Lowekamp wrote: > > Hello Hyun, > > From you description, I don?t understand what was the cause of the crass nor how this fixed the problem. Why was it the wrong type? > > > Brad > > >> On Jan 18, 2016, at 12:20 PM, Hyun Jae Kang > wrote: >> >> Hi Bradley, >> >> Thank you for your comments on the code. The lines you mentioned in itkHistogram.hxx generated the run-time crash on Mac OSX 10.6 with clang compiler (3.0). >> >> When I found this error, I checked the data type of the local variable ( float interval ) and I put "float" in the lines to avoid the run-time error. >> >> This is why I chose "float" as the data type of data-casting. >> >> If I did something wrong, please let me know. I will fix it. >> >> Thanks, >> >> Hyun Jae >> >> >> On Mon, Jan 18, 2016 at 12:00 PM, > wrote: >> Send Insight-developers mailing list submissions to >> insight-developers at itk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/mailman/listinfo/insight-developers >> or, via email, send a message with subject or body 'help' to >> insight-developers-request at itk.org >> >> You can reach the person managing the list at >> insight-developers-owner at itk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Insight-developers digest..." >> >> >> Today's Topics: >> >> 1. Re: [ITK] Itk release branch demons registration >> (Bradley Lowekamp) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 17 Jan 2016 18:13:44 -0500 >> From: Bradley Lowekamp > >> To: Bradley Lowekamp > >> Cc: ITK > >> Subject: Re: [ITK-dev] [ITK] Itk release branch demons registration >> Message-ID: <63AE857C-91FE-4B80-B31B-921A6CDAD2C6 at lowekamp.net > >> Content-Type: text/plain; charset="utf-8" >> >> Just to follow up my git bisect narrowed the change down to this: >> commit 0fd462a3226e84bdce77b68830903b3888dab244 >> Author: Hyun Jae Kang > >> Date: Thu Dec 31 10:56:25 2015 -0500 >> >> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 >> >> - Fixed the runtime crash of the following ITKStatisticsTestDriver's tests on >> OSX 10.6 ( clang 3.0 ) by modifying the itkHistogram's Initialize function >> to handle a data value out of range of a specific data type with >> type-casting operator. >> >> - itkSampleToHistogramFilterTest3 (ILLEGAL) >> - itkSampleToHistogramFilterTest7 (ILLEGAL) >> >> - These crash were reported at the following page: >> https://open.cdash.org/viewTest.php?onlyfailed&buildid=4170483 >> >> Change-Id: I2063912edee79422d88125ffd5f7513c31a9e98c >> >> diff --git a/Modules/Numerics/Statistics/include/itkHistogram.hxx b/Modules/Numerics/Statistics/include/itkHistogram.hxx >> index 380b8d0..d11d788 100644 >> --- a/Modules/Numerics/Statistics/include/itkHistogram.hxx >> +++ b/Modules/Numerics/Statistics/include/itkHistogram.hxx >> @@ -248,8 +248,8 @@ Histogram< TMeasurement, TFrequencyContainer > >> { >> if ( size[i] > 0 ) >> { >> - interval = static_cast( upperBound[i] - lowerBound[i] ) >> - / static_cast< MeasurementType >( size[i] ); >> + interval = (static_cast( upperBound[i] ) - static_cast(lowerBound[i] )) >> + / static_cast< float >( size[i] ); >> >> >> Here is the failing example [1], which uses the HistogramMatching filter. >> >> I am not sure why float was choose at the type here. Are results being truncated now? When there was temporary double computation going on? >> >> It needs more investigation, as it?s changing the results of some filters? not sure how significant yet. >> >> Brad >> >> >> >> >> [1] https://github.com/SimpleITK/SimpleITK/blob/master/Examples/DemonsRegistration1.py#L41 >> > On Jan 16, 2016, at 2:58 PM, Bradley Lowekamp > wrote: >> > >> > Thanks. I'll run a git bisect tonight to try to figure it out. >> > >> >> On Jan 16, 2016, at 12:57 PM, Matt McCormick > wrote: >> >> >> >> Hi, >> >> >> >> Nothing comes to mind. >> >> >> >> Here is the log for v4.9rc03..release: >> >> >> >> Bill Hoffman (3): >> >> COMP: fix 64 bit build warnings with windows auto-export on. >> >> COMP: work around for VS 2015 optimizer bug causing test failures. >> >> COMP: work around for VS 2015 optimizer bug causing test failures. >> >> >> >> Bradley Lowekamp (1): >> >> BUG: Fix precision with accumulation and scaling in AdaptiveHistogram >> >> >> >> Davis Vigneault (1): >> >> COMP: Include itkMacro.h in itkTestingMacros.h >> >> >> >> Hans Johnson (2): >> >> COMP: BSD command lines do not have --version >> >> COMP: Respect CMAKE_CXX_STANDARD during config >> >> >> >> Hyun Jae Kang (12): >> >> COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 >> >> BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 >> >> BUG: Fixed the runtime crash of itkTimeProbeTest2 >> >> BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 >> >> BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 >> >> BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's >> >> tests on OSX 10.6 >> >> COMP: Fixed the data conversion warning messages of itkResourceProbe >> >> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 >> >> BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1 >> >> BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 >> >> BUG: Fixed the runtime crash of vnl_test_numeric_traits >> >> BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 >> >> >> >> Isaiah Norton (1): >> >> COMP: fix build with -std=c++11 when ITK/VXL initially configured without >> >> >> >> Matthew McCormick (6): >> >> BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper. >> >> COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5. >> >> DOC: Update the location of the GNUPlot Software Guide scripts. >> >> DOC: Update the Software Guide repo location in Examples/README.txt. >> >> COMP: Add export specification for itk::ResourceProbe. >> >> COMP: Require NO_MODULE with DCMTK find_package. >> >> >> >> Michka Popoff (2): >> >> ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7 >> >> COMP: Re-enable review module for python 3 and older VTK's >> >> >> >> Sean McBride (1): >> >> DOC: Update some woefully out-of-date GDCM comments, and typos >> >> >> >> Seun Odutola (1): >> >> BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions >> >> >> >> HTH, >> >> Matt >> >> >> >>> On Sat, Jan 16, 2016 at 12:18 PM, Bradley Lowekamp > wrote: >> >>> I just updated SimpleITK to the release branch yesterday and there are some changes in the result of the demons registration. I'm not going to get a chance to look at it until Monday. The only change potentially related I know of is the rounding related numeric traits, but that does not seem likely to me. >> >>> >> >>> Any ideas why the Demons Registration would have changed fro rc3? >> >>> >> >>>> On Jan 16, 2016, at 12:13 PM, Bradley Lowekamp > wrote: >> >>>> >> >>>> Hello, >> >>>> >> >>>> I updated SimpleITK >> >>>> _______________________________________________ >> >>>> Powered by www.kitware.com >> >>>> >> >>>> Visit other Kitware open-source projects at >> >>>> http://www.kitware.com/opensource/opensource.html >> >>>> >> >>>> Kitware offers ITK Training Courses, for more information visit: >> >>>> http://kitware.com/products/protraining.php >> >>>> >> >>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>> http://www.itk.org/Wiki/ITK_FAQ >> >>>> >> >>>> Follow this link to subscribe/unsubscribe: >> >>>> http://public.kitware.com/mailman/listinfo/insight-developers >> >>> _______________________________________________ >> >>> Powered by www.kitware.com >> >>> >> >>> Visit other Kitware open-source projects at >> >>> http://www.kitware.com/opensource/opensource.html >> >>> >> >>> Kitware offers ITK Training Courses, for more information visit: >> >>> http://kitware.com/products/protraining.php >> >>> >> >>> Please keep messages on-topic and check the ITK FAQ at: >> >>> http://www.itk.org/Wiki/ITK_FAQ >> >>> >> >>> Follow this link to subscribe/unsubscribe: >> >>> http://public.kitware.com/mailman/listinfo/insight-developers >> > _______________________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-developers >> > _______________________________________________ >> > Community mailing list >> > Community at itk.org >> > http://public.kitware.com/mailman/listinfo/community >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Insight-developers mailing list >> Insight-developers at itk.org >> http://public.kitware.com/mailman/listinfo/insight-developers >> >> >> ------------------------------ >> >> End of Insight-developers Digest, Vol 141, Issue 10 >> *************************************************** >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Jan 19 13:15:01 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 19 Jan 2016 13:15:01 -0500 Subject: [ITK-dev] [ITK] Itk release branch demons registration In-Reply-To: References: <48C8C5A2-BBA5-4806-B212-38B8CB6C126E@mail.nih.gov> Message-ID: Hi Brad and Hyun Jae, Thank you for looking into this and discussing it on the mailing list! I have added a note to the release notes. Thanks, Matt On Tue, Jan 19, 2016 at 11:02 AM, Bradly Lowekamp wrote: > Hello, > > Just to follow up. > > Your code seems to correct a long long time bug. That has had a work around > [1] for at least one usage. > > The truncation of the ?size? variable to the MeasurementType, can easily > result in a divide by zero when the number of bins is > NumericTraints::max() + 1. > > It may need to be noted in the release notes, that histogram calculations > may change due to this correction, which can change the bounds of > histograms. > > Good job tracking down the problem. > > Brad > > > [1] > https://github.com/InsightSoftwareConsortium/ITK/commit/4011c5d85e77387f59cadc0b12b79fdaa3251339 > > On Jan 19, 2016, at 9:09 AM, Bradley Lowekamp > wrote: > > Hello Hyun, > > From you description, I don?t understand what was the cause of the crass nor > how this fixed the problem. Why was it the wrong type? > > > Brad > > > On Jan 18, 2016, at 12:20 PM, Hyun Jae Kang > wrote: > > Hi Bradley, > > Thank you for your comments on the code. The lines you mentioned in > itkHistogram.hxx generated the run-time crash on Mac OSX 10.6 with clang > compiler (3.0). > > When I found this error, I checked the data type of the local variable ( > float interval ) and I put "float" in the lines to avoid the run-time error. > > This is why I chose "float" as the data type of data-casting. > > If I did something wrong, please let me know. I will fix it. > > Thanks, > > Hyun Jae > > > On Mon, Jan 18, 2016 at 12:00 PM, > wrote: >> >> Send Insight-developers mailing list submissions to >> insight-developers at itk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/mailman/listinfo/insight-developers >> or, via email, send a message with subject or body 'help' to >> insight-developers-request at itk.org >> >> You can reach the person managing the list at >> insight-developers-owner at itk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Insight-developers digest..." >> >> >> Today's Topics: >> >> 1. Re: [ITK] Itk release branch demons registration >> (Bradley Lowekamp) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 17 Jan 2016 18:13:44 -0500 >> From: Bradley Lowekamp >> To: Bradley Lowekamp >> Cc: ITK >> Subject: Re: [ITK-dev] [ITK] Itk release branch demons registration >> Message-ID: <63AE857C-91FE-4B80-B31B-921A6CDAD2C6 at lowekamp.net> >> Content-Type: text/plain; charset="utf-8" >> >> Just to follow up my git bisect narrowed the change down to this: >> commit 0fd462a3226e84bdce77b68830903b3888dab244 >> Author: Hyun Jae Kang >> Date: Thu Dec 31 10:56:25 2015 -0500 >> >> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX >> 10.6 >> >> - Fixed the runtime crash of the following ITKStatisticsTestDriver's >> tests on >> OSX 10.6 ( clang 3.0 ) by modifying the itkHistogram's Initialize >> function >> to handle a data value out of range of a specific data type with >> type-casting operator. >> >> - itkSampleToHistogramFilterTest3 (ILLEGAL) >> - itkSampleToHistogramFilterTest7 (ILLEGAL) >> >> - These crash were reported at the following page: >> https://open.cdash.org/viewTest.php?onlyfailed&buildid=4170483 >> >> Change-Id: I2063912edee79422d88125ffd5f7513c31a9e98c >> >> diff --git a/Modules/Numerics/Statistics/include/itkHistogram.hxx >> b/Modules/Numerics/Statistics/include/itkHistogram.hxx >> index 380b8d0..d11d788 100644 >> --- a/Modules/Numerics/Statistics/include/itkHistogram.hxx >> +++ b/Modules/Numerics/Statistics/include/itkHistogram.hxx >> @@ -248,8 +248,8 @@ Histogram< TMeasurement, TFrequencyContainer > >> { >> if ( size[i] > 0 ) >> { >> - interval = static_cast( upperBound[i] - lowerBound[i] ) >> - / static_cast< MeasurementType >( size[i] ); >> + interval = (static_cast( upperBound[i] ) - >> static_cast(lowerBound[i] )) >> + / static_cast< float >( size[i] ); >> >> >> Here is the failing example [1], which uses the HistogramMatching filter. >> >> I am not sure why float was choose at the type here. Are results being >> truncated now? When there was temporary double computation going on? >> >> It needs more investigation, as it?s changing the results of some >> filters? not sure how significant yet. >> >> Brad >> >> >> >> >> [1] >> https://github.com/SimpleITK/SimpleITK/blob/master/Examples/DemonsRegistration1.py#L41 >> > On Jan 16, 2016, at 2:58 PM, Bradley Lowekamp wrote: >> > >> > Thanks. I'll run a git bisect tonight to try to figure it out. >> > >> >> On Jan 16, 2016, at 12:57 PM, Matt McCormick >> >> wrote: >> >> >> >> Hi, >> >> >> >> Nothing comes to mind. >> >> >> >> Here is the log for v4.9rc03..release: >> >> >> >> Bill Hoffman (3): >> >> COMP: fix 64 bit build warnings with windows auto-export on. >> >> COMP: work around for VS 2015 optimizer bug causing test failures. >> >> COMP: work around for VS 2015 optimizer bug causing test failures. >> >> >> >> Bradley Lowekamp (1): >> >> BUG: Fix precision with accumulation and scaling in >> >> AdaptiveHistogram >> >> >> >> Davis Vigneault (1): >> >> COMP: Include itkMacro.h in itkTestingMacros.h >> >> >> >> Hans Johnson (2): >> >> COMP: BSD command lines do not have --version >> >> COMP: Respect CMAKE_CXX_STANDARD during config >> >> >> >> Hyun Jae Kang (12): >> >> COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 >> >> BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 >> >> BUG: Fixed the runtime crash of itkTimeProbeTest2 >> >> BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 >> >> BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 >> >> BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's >> >> tests on OSX 10.6 >> >> COMP: Fixed the data conversion warning messages of >> >> itkResourceProbe >> >> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on >> >> OSX 10.6 >> >> BUG: Fixed the runtime crash of >> >> itkBinaryShapeOpeningImageFilterTest1 >> >> BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 >> >> BUG: Fixed the runtime crash of vnl_test_numeric_traits >> >> BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 >> >> >> >> Isaiah Norton (1): >> >> COMP: fix build with -std=c++11 when ITK/VXL initially configured >> >> without >> >> >> >> Matthew McCormick (6): >> >> BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper. >> >> COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5. >> >> DOC: Update the location of the GNUPlot Software Guide scripts. >> >> DOC: Update the Software Guide repo location in >> >> Examples/README.txt. >> >> COMP: Add export specification for itk::ResourceProbe. >> >> COMP: Require NO_MODULE with DCMTK find_package. >> >> >> >> Michka Popoff (2): >> >> ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7 >> >> COMP: Re-enable review module for python 3 and older VTK's >> >> >> >> Sean McBride (1): >> >> DOC: Update some woefully out-of-date GDCM comments, and typos >> >> >> >> Seun Odutola (1): >> >> BUG: Improved itkAnalyzeImageIO to handle case insensitive >> >> extensions >> >> >> >> HTH, >> >> Matt >> >> >> >>> On Sat, Jan 16, 2016 at 12:18 PM, Bradley Lowekamp >> >>> wrote: >> >>> I just updated SimpleITK to the release branch yesterday and there are >> >>> some changes in the result of the demons registration. I'm not going to get >> >>> a chance to look at it until Monday. The only change potentially related I >> >>> know of is the rounding related numeric traits, but that does not seem >> >>> likely to me. >> >>> >> >>> Any ideas why the Demons Registration would have changed fro rc3? >> >>> >> >>>> On Jan 16, 2016, at 12:13 PM, Bradley Lowekamp >> >>>> wrote: >> >>>> >> >>>> Hello, >> >>>> >> >>>> I updated SimpleITK >> >>>> _______________________________________________ >> >>>> Powered by www.kitware.com >> >>>> >> >>>> Visit other Kitware open-source projects at >> >>>> http://www.kitware.com/opensource/opensource.html >> >>>> >> >>>> Kitware offers ITK Training Courses, for more information visit: >> >>>> http://kitware.com/products/protraining.php >> >>>> >> >>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>> http://www.itk.org/Wiki/ITK_FAQ >> >>>> >> >>>> Follow this link to subscribe/unsubscribe: >> >>>> http://public.kitware.com/mailman/listinfo/insight-developers >> >>> _______________________________________________ >> >>> Powered by www.kitware.com >> >>> >> >>> Visit other Kitware open-source projects at >> >>> http://www.kitware.com/opensource/opensource.html >> >>> >> >>> Kitware offers ITK Training Courses, for more information visit: >> >>> http://kitware.com/products/protraining.php >> >>> >> >>> Please keep messages on-topic and check the ITK FAQ at: >> >>> http://www.itk.org/Wiki/ITK_FAQ >> >>> >> >>> Follow this link to subscribe/unsubscribe: >> >>> http://public.kitware.com/mailman/listinfo/insight-developers >> > _______________________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-developers >> > _______________________________________________ >> > Community mailing list >> > Community at itk.org >> > http://public.kitware.com/mailman/listinfo/community >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Insight-developers mailing list >> Insight-developers at itk.org >> http://public.kitware.com/mailman/listinfo/insight-developers >> >> >> ------------------------------ >> >> End of Insight-developers Digest, Vol 141, Issue 10 >> *************************************************** > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > From hyunjae.kang at kitware.com Tue Jan 19 13:20:02 2016 From: hyunjae.kang at kitware.com (Hyun Jae Kang) Date: Tue, 19 Jan 2016 13:20:02 -0500 Subject: [ITK-dev] [ITK] Itk release branch demons registration In-Reply-To: References: <48C8C5A2-BBA5-4806-B212-38B8CB6C126E@mail.nih.gov> Message-ID: Hi Bradly, Thank you for your comments. And, I am sorry about lack of my previous explanation. I would like to share my observation about that part. I made debug messages to figure out why the run-time crash was happened on the previous code as the following: ------------------------------------------------------- 2310: upperBound[i] ::2147483647 2310: lowerBound[i] ::-2147483648 2310: size[i] ::36 2310: MAX (signed int).::2147483647 1/1 Test #2310: itkSampleToHistogramFilterTest3 ...***Exception: Illegal 0.45 sec ------------------------------------------------------- ---------------- if ( size[i] > 0 ) { - interval = static_cast( upperBound[i] - lowerBound[i] ) - / static_cast< MeasurementType >( size[i] ); + interval = (static_cast( upperBound[i] ) - static_cast(lowerBound[i] )) + / static_cast< float >( size[i] ); --------------- >From the above debug messages and the previous code (see the above code snippet), the value of the numerator exceeded the max value of the assigned data type (signed int). And, the Clang compiler (3.0) generated a run-time crash on the case. If you have any question or comment, please let me know. Thanks, Hyun Jae On Tue, Jan 19, 2016 at 11:02 AM, Bradly Lowekamp wrote: > Hello, > > Just to follow up. > > Your code seems to correct a long long time bug. That has had a work > around [1] for at least one usage. > > The truncation of the ?size? variable to the MeasurementType, can easily > result in a divide by zero when the number of bins is > NumericTraints::max() + 1. > > It may need to be noted in the release notes, that histogram calculations > may change due to this correction, which can change the bounds of > histograms. > > Good job tracking down the problem. > > Brad > > > [1] > https://github.com/InsightSoftwareConsortium/ITK/commit/4011c5d85e77387f59cadc0b12b79fdaa3251339 > > On Jan 19, 2016, at 9:09 AM, Bradley Lowekamp > wrote: > > Hello Hyun, > > From you description, I don?t understand what was the cause of the crass > nor how this fixed the problem. Why was it the wrong type? > > > Brad > > > On Jan 18, 2016, at 12:20 PM, Hyun Jae Kang > wrote: > > Hi Bradley, > > Thank you for your comments on the code. The lines you mentioned in itkHistogram.hxx > generated the run-time crash on Mac OSX 10.6 with clang compiler (3.0). > > When I found this error, I checked the data type of the local variable ( > float interval ) and I put "float" in the lines to avoid the run-time > error. > > This is why I chose "float" as the data type of data-casting. > > If I did something wrong, please let me know. I will fix it. > > Thanks, > > Hyun Jae > > > On Mon, Jan 18, 2016 at 12:00 PM, > wrote: > >> Send Insight-developers mailing list submissions to >> insight-developers at itk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/mailman/listinfo/insight-developers >> or, via email, send a message with subject or body 'help' to >> insight-developers-request at itk.org >> >> You can reach the person managing the list at >> insight-developers-owner at itk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Insight-developers digest..." >> >> >> Today's Topics: >> >> 1. Re: [ITK] Itk release branch demons registration >> (Bradley Lowekamp) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 17 Jan 2016 18:13:44 -0500 >> From: Bradley Lowekamp >> To: Bradley Lowekamp >> Cc: ITK >> Subject: Re: [ITK-dev] [ITK] Itk release branch demons registration >> Message-ID: <63AE857C-91FE-4B80-B31B-921A6CDAD2C6 at lowekamp.net> >> Content-Type: text/plain; charset="utf-8" >> >> Just to follow up my git bisect narrowed the change down to this: >> commit 0fd462a3226e84bdce77b68830903b3888dab244 >> Author: Hyun Jae Kang >> Date: Thu Dec 31 10:56:25 2015 -0500 >> >> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX >> 10.6 >> >> - Fixed the runtime crash of the following ITKStatisticsTestDriver's >> tests on >> OSX 10.6 ( clang 3.0 ) by modifying the itkHistogram's Initialize >> function >> to handle a data value out of range of a specific data type with >> type-casting operator. >> >> - itkSampleToHistogramFilterTest3 (ILLEGAL) >> - itkSampleToHistogramFilterTest7 (ILLEGAL) >> >> - These crash were reported at the following page: >> https://open.cdash.org/viewTest.php?onlyfailed&buildid=4170483 >> >> Change-Id: I2063912edee79422d88125ffd5f7513c31a9e98c >> >> diff --git a/Modules/Numerics/Statistics/include/itkHistogram.hxx >> b/Modules/Numerics/Statistics/include/itkHistogram.hxx >> index 380b8d0..d11d788 100644 >> --- a/Modules/Numerics/Statistics/include/itkHistogram.hxx >> +++ b/Modules/Numerics/Statistics/include/itkHistogram.hxx >> @@ -248,8 +248,8 @@ Histogram< TMeasurement, TFrequencyContainer > >> { >> if ( size[i] > 0 ) >> { >> - interval = static_cast( upperBound[i] - lowerBound[i] ) >> - / static_cast< MeasurementType >( size[i] ); >> + interval = (static_cast( upperBound[i] ) - >> static_cast(lowerBound[i] )) >> + / static_cast< float >( size[i] ); >> >> >> Here is the failing example [1], which uses the HistogramMatching filter. >> >> I am not sure why float was choose at the type here. Are results being >> truncated now? When there was temporary double computation going on? >> >> It needs more investigation, as it?s changing the results of some >> filters? not sure how significant yet. >> >> Brad >> >> >> >> >> [1] >> https://github.com/SimpleITK/SimpleITK/blob/master/Examples/DemonsRegistration1.py#L41 >> > On Jan 16, 2016, at 2:58 PM, Bradley Lowekamp >> wrote: >> > >> > Thanks. I'll run a git bisect tonight to try to figure it out. >> > >> >> On Jan 16, 2016, at 12:57 PM, Matt McCormick < >> matt.mccormick at kitware.com> wrote: >> >> >> >> Hi, >> >> >> >> Nothing comes to mind. >> >> >> >> Here is the log for v4.9rc03..release: >> >> >> >> Bill Hoffman (3): >> >> COMP: fix 64 bit build warnings with windows auto-export on. >> >> COMP: work around for VS 2015 optimizer bug causing test failures. >> >> COMP: work around for VS 2015 optimizer bug causing test failures. >> >> >> >> Bradley Lowekamp (1): >> >> BUG: Fix precision with accumulation and scaling in >> AdaptiveHistogram >> >> >> >> Davis Vigneault (1): >> >> COMP: Include itkMacro.h in itkTestingMacros.h >> >> >> >> Hans Johnson (2): >> >> COMP: BSD command lines do not have --version >> >> COMP: Respect CMAKE_CXX_STANDARD during config >> >> >> >> Hyun Jae Kang (12): >> >> COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 >> >> BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 >> >> BUG: Fixed the runtime crash of itkTimeProbeTest2 >> >> BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 >> >> BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 >> >> BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's >> >> tests on OSX 10.6 >> >> COMP: Fixed the data conversion warning messages of >> itkResourceProbe >> >> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on >> OSX 10.6 >> >> BUG: Fixed the runtime crash of >> itkBinaryShapeOpeningImageFilterTest1 >> >> BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 >> >> BUG: Fixed the runtime crash of vnl_test_numeric_traits >> >> BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 >> >> >> >> Isaiah Norton (1): >> >> COMP: fix build with -std=c++11 when ITK/VXL initially configured >> without >> >> >> >> Matthew McCormick (6): >> >> BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper. >> >> COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5. >> >> DOC: Update the location of the GNUPlot Software Guide scripts. >> >> DOC: Update the Software Guide repo location in >> Examples/README.txt. >> >> COMP: Add export specification for itk::ResourceProbe. >> >> COMP: Require NO_MODULE with DCMTK find_package. >> >> >> >> Michka Popoff (2): >> >> ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7 >> >> COMP: Re-enable review module for python 3 and older VTK's >> >> >> >> Sean McBride (1): >> >> DOC: Update some woefully out-of-date GDCM comments, and typos >> >> >> >> Seun Odutola (1): >> >> BUG: Improved itkAnalyzeImageIO to handle case insensitive >> extensions >> >> >> >> HTH, >> >> Matt >> >> >> >>> On Sat, Jan 16, 2016 at 12:18 PM, Bradley Lowekamp >> wrote: >> >>> I just updated SimpleITK to the release branch yesterday and there >> are some changes in the result of the demons registration. I'm not going to >> get a chance to look at it until Monday. The only change potentially >> related I know of is the rounding related numeric traits, but that does not >> seem likely to me. >> >>> >> >>> Any ideas why the Demons Registration would have changed fro rc3? >> >>> >> >>>> On Jan 16, 2016, at 12:13 PM, Bradley Lowekamp >> wrote: >> >>>> >> >>>> Hello, >> >>>> >> >>>> I updated SimpleITK >> >>>> _______________________________________________ >> >>>> Powered by www.kitware.com >> >>>> >> >>>> Visit other Kitware open-source projects at >> >>>> http://www.kitware.com/opensource/opensource.html >> >>>> >> >>>> Kitware offers ITK Training Courses, for more information visit: >> >>>> http://kitware.com/products/protraining.php >> >>>> >> >>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>> http://www.itk.org/Wiki/ITK_FAQ >> >>>> >> >>>> Follow this link to subscribe/unsubscribe: >> >>>> http://public.kitware.com/mailman/listinfo/insight-developers >> >>> _______________________________________________ >> >>> Powered by www.kitware.com >> >>> >> >>> Visit other Kitware open-source projects at >> >>> http://www.kitware.com/opensource/opensource.html >> >>> >> >>> Kitware offers ITK Training Courses, for more information visit: >> >>> http://kitware.com/products/protraining.php >> >>> >> >>> Please keep messages on-topic and check the ITK FAQ at: >> >>> http://www.itk.org/Wiki/ITK_FAQ >> >>> >> >>> Follow this link to subscribe/unsubscribe: >> >>> http://public.kitware.com/mailman/listinfo/insight-developers >> > _______________________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-developers >> > _______________________________________________ >> > Community mailing list >> > Community at itk.org >> > http://public.kitware.com/mailman/listinfo/community >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://public.kitware.com/pipermail/insight-developers/attachments/20160117/188815c1/attachment-0001.html >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> Insight-developers mailing list >> Insight-developers at itk.org >> http://public.kitware.com/mailman/listinfo/insight-developers >> >> >> ------------------------------ >> >> End of Insight-developers Digest, Vol 141, Issue 10 >> *************************************************** >> > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Jan 19 13:52:37 2016 From: blowekamp at mail.nih.gov (Bradly Lowekamp) Date: Tue, 19 Jan 2016 13:52:37 -0500 Subject: [ITK-dev] [ITK] Itk release branch demons registration In-Reply-To: References: <48C8C5A2-BBA5-4806-B212-38B8CB6C126E@mail.nih.gov> Message-ID: <0F56A94B-84F0-4EC5-A6D3-E5985BE7C634@mail.nih.gov> Hello, Sounds like you addressed a separate issue of ?undefined behavior of signed integer overflow? [1], in additional to the ?floating point division by zero? and ?conversion truncation? I mentioned. Amazing one line of computation can contain so many bugs :) Brad [1] http://stackoverflow.com/questions/16188263/is-signed-integer-overflow-still-undefined-behavior-in-c > On Jan 19, 2016, at 1:20 PM, Hyun Jae Kang wrote: > > Hi Bradly, > > Thank you for your comments. And, I am sorry about lack of my previous explanation. > > I would like to share my observation about that part. > I made debug messages to figure out why the run-time crash was happened on the previous code as the following: > > ------------------------------------------------------- > 2310: upperBound[i] ::2147483647 > 2310: lowerBound[i] ::-2147483648 > 2310: size[i] ::36 > 2310: MAX (signed int).::2147483647 > > 1/1 Test #2310: itkSampleToHistogramFilterTest3 ...***Exception: Illegal 0.45 sec > ------------------------------------------------------- > > ---------------- > if ( size[i] > 0 ) > { > - interval = static_cast( upperBound[i] - lowerBound[i] ) > - / static_cast< MeasurementType >( size[i] ); > + interval = (static_cast( upperBound[i] ) - static_cast(lowerBound[i] )) > + / static_cast< float >( size[i] ); > --------------- > > From the above debug messages and the previous code (see the above code snippet), the value of the numerator exceeded the max value of the assigned data type (signed int). And, the Clang compiler (3.0) generated a run-time crash on the case. > > > If you have any question or comment, please let me know. > > Thanks, > > Hyun Jae > > > > On Tue, Jan 19, 2016 at 11:02 AM, Bradly Lowekamp > wrote: > Hello, > > Just to follow up. > > Your code seems to correct a long long time bug. That has had a work around [1] for at least one usage. > > The truncation of the ?size? variable to the MeasurementType, can easily result in a divide by zero when the number of bins is NumericTraints::max() + 1. > > It may need to be noted in the release notes, that histogram calculations may change due to this correction, which can change the bounds of histograms. > > Good job tracking down the problem. > > Brad > > > [1] https://github.com/InsightSoftwareConsortium/ITK/commit/4011c5d85e77387f59cadc0b12b79fdaa3251339 > >> On Jan 19, 2016, at 9:09 AM, Bradley Lowekamp > wrote: >> >> Hello Hyun, >> >> From you description, I don?t understand what was the cause of the crass nor how this fixed the problem. Why was it the wrong type? >> >> >> Brad >> >> >>> On Jan 18, 2016, at 12:20 PM, Hyun Jae Kang > wrote: >>> >>> Hi Bradley, >>> >>> Thank you for your comments on the code. The lines you mentioned in itkHistogram.hxx generated the run-time crash on Mac OSX 10.6 with clang compiler (3.0). >>> >>> When I found this error, I checked the data type of the local variable ( float interval ) and I put "float" in the lines to avoid the run-time error. >>> >>> This is why I chose "float" as the data type of data-casting. >>> >>> If I did something wrong, please let me know. I will fix it. >>> >>> Thanks, >>> >>> Hyun Jae >>> >>> >>> On Mon, Jan 18, 2016 at 12:00 PM, > wrote: >>> Send Insight-developers mailing list submissions to >>> insight-developers at itk.org >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> http://public.kitware.com/mailman/listinfo/insight-developers >>> or, via email, send a message with subject or body 'help' to >>> insight-developers-request at itk.org >>> >>> You can reach the person managing the list at >>> insight-developers-owner at itk.org >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of Insight-developers digest..." >>> >>> >>> Today's Topics: >>> >>> 1. Re: [ITK] Itk release branch demons registration >>> (Bradley Lowekamp) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Sun, 17 Jan 2016 18:13:44 -0500 >>> From: Bradley Lowekamp > >>> To: Bradley Lowekamp > >>> Cc: ITK > >>> Subject: Re: [ITK-dev] [ITK] Itk release branch demons registration >>> Message-ID: <63AE857C-91FE-4B80-B31B-921A6CDAD2C6 at lowekamp.net > >>> Content-Type: text/plain; charset="utf-8" >>> >>> Just to follow up my git bisect narrowed the change down to this: >>> commit 0fd462a3226e84bdce77b68830903b3888dab244 >>> Author: Hyun Jae Kang > >>> Date: Thu Dec 31 10:56:25 2015 -0500 >>> >>> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 >>> >>> - Fixed the runtime crash of the following ITKStatisticsTestDriver's tests on >>> OSX 10.6 ( clang 3.0 ) by modifying the itkHistogram's Initialize function >>> to handle a data value out of range of a specific data type with >>> type-casting operator. >>> >>> - itkSampleToHistogramFilterTest3 (ILLEGAL) >>> - itkSampleToHistogramFilterTest7 (ILLEGAL) >>> >>> - These crash were reported at the following page: >>> https://open.cdash.org/viewTest.php?onlyfailed&buildid=4170483 >>> >>> Change-Id: I2063912edee79422d88125ffd5f7513c31a9e98c >>> >>> diff --git a/Modules/Numerics/Statistics/include/itkHistogram.hxx b/Modules/Numerics/Statistics/include/itkHistogram.hxx >>> index 380b8d0..d11d788 100644 >>> --- a/Modules/Numerics/Statistics/include/itkHistogram.hxx >>> +++ b/Modules/Numerics/Statistics/include/itkHistogram.hxx >>> @@ -248,8 +248,8 @@ Histogram< TMeasurement, TFrequencyContainer > >>> { >>> if ( size[i] > 0 ) >>> { >>> - interval = static_cast( upperBound[i] - lowerBound[i] ) >>> - / static_cast< MeasurementType >( size[i] ); >>> + interval = (static_cast( upperBound[i] ) - static_cast(lowerBound[i] )) >>> + / static_cast< float >( size[i] ); >>> >>> >>> Here is the failing example [1], which uses the HistogramMatching filter. >>> >>> I am not sure why float was choose at the type here. Are results being truncated now? When there was temporary double computation going on? >>> >>> It needs more investigation, as it?s changing the results of some filters? not sure how significant yet. >>> >>> Brad >>> >>> >>> >>> >>> [1] https://github.com/SimpleITK/SimpleITK/blob/master/Examples/DemonsRegistration1.py#L41 >>> > On Jan 16, 2016, at 2:58 PM, Bradley Lowekamp > wrote: >>> > >>> > Thanks. I'll run a git bisect tonight to try to figure it out. >>> > >>> >> On Jan 16, 2016, at 12:57 PM, Matt McCormick > wrote: >>> >> >>> >> Hi, >>> >> >>> >> Nothing comes to mind. >>> >> >>> >> Here is the log for v4.9rc03..release: >>> >> >>> >> Bill Hoffman (3): >>> >> COMP: fix 64 bit build warnings with windows auto-export on. >>> >> COMP: work around for VS 2015 optimizer bug causing test failures. >>> >> COMP: work around for VS 2015 optimizer bug causing test failures. >>> >> >>> >> Bradley Lowekamp (1): >>> >> BUG: Fix precision with accumulation and scaling in AdaptiveHistogram >>> >> >>> >> Davis Vigneault (1): >>> >> COMP: Include itkMacro.h in itkTestingMacros.h >>> >> >>> >> Hans Johnson (2): >>> >> COMP: BSD command lines do not have --version >>> >> COMP: Respect CMAKE_CXX_STANDARD during config >>> >> >>> >> Hyun Jae Kang (12): >>> >> COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 >>> >> BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 >>> >> BUG: Fixed the runtime crash of itkTimeProbeTest2 >>> >> BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 >>> >> BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 >>> >> BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's >>> >> tests on OSX 10.6 >>> >> COMP: Fixed the data conversion warning messages of itkResourceProbe >>> >> BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 >>> >> BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1 >>> >> BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 >>> >> BUG: Fixed the runtime crash of vnl_test_numeric_traits >>> >> BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 >>> >> >>> >> Isaiah Norton (1): >>> >> COMP: fix build with -std=c++11 when ITK/VXL initially configured without >>> >> >>> >> Matthew McCormick (6): >>> >> BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper. >>> >> COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5. >>> >> DOC: Update the location of the GNUPlot Software Guide scripts. >>> >> DOC: Update the Software Guide repo location in Examples/README.txt. >>> >> COMP: Add export specification for itk::ResourceProbe. >>> >> COMP: Require NO_MODULE with DCMTK find_package. >>> >> >>> >> Michka Popoff (2): >>> >> ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7 >>> >> COMP: Re-enable review module for python 3 and older VTK's >>> >> >>> >> Sean McBride (1): >>> >> DOC: Update some woefully out-of-date GDCM comments, and typos >>> >> >>> >> Seun Odutola (1): >>> >> BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions >>> >> >>> >> HTH, >>> >> Matt >>> >> >>> >>> On Sat, Jan 16, 2016 at 12:18 PM, Bradley Lowekamp > wrote: >>> >>> I just updated SimpleITK to the release branch yesterday and there are some changes in the result of the demons registration. I'm not going to get a chance to look at it until Monday. The only change potentially related I know of is the rounding related numeric traits, but that does not seem likely to me. >>> >>> >>> >>> Any ideas why the Demons Registration would have changed fro rc3? >>> >>> >>> >>>> On Jan 16, 2016, at 12:13 PM, Bradley Lowekamp > wrote: >>> >>>> >>> >>>> Hello, >>> >>>> >>> >>>> I updated SimpleITK >>> >>>> _______________________________________________ >>> >>>> Powered by www.kitware.com >>> >>>> >>> >>>> Visit other Kitware open-source projects at >>> >>>> http://www.kitware.com/opensource/opensource.html >>> >>>> >>> >>>> Kitware offers ITK Training Courses, for more information visit: >>> >>>> http://kitware.com/products/protraining.php >>> >>>> >>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>> >>>> http://www.itk.org/Wiki/ITK_FAQ >>> >>>> >>> >>>> Follow this link to subscribe/unsubscribe: >>> >>>> http://public.kitware.com/mailman/listinfo/insight-developers >>> >>> _______________________________________________ >>> >>> Powered by www.kitware.com >>> >>> >>> >>> Visit other Kitware open-source projects at >>> >>> http://www.kitware.com/opensource/opensource.html >>> >>> >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> >>> http://kitware.com/products/protraining.php >>> >>> >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> >>> >>> Follow this link to subscribe/unsubscribe: >>> >>> http://public.kitware.com/mailman/listinfo/insight-developers >>> > _______________________________________________ >>> > Powered by www.kitware.com >>> > >>> > Visit other Kitware open-source projects at >>> > http://www.kitware.com/opensource/opensource.html >>> > >>> > Kitware offers ITK Training Courses, for more information visit: >>> > http://kitware.com/products/protraining.php >>> > >>> > Please keep messages on-topic and check the ITK FAQ at: >>> > http://www.itk.org/Wiki/ITK_FAQ >>> > >>> > Follow this link to subscribe/unsubscribe: >>> > http://public.kitware.com/mailman/listinfo/insight-developers >>> > _______________________________________________ >>> > Community mailing list >>> > Community at itk.org >>> > http://public.kitware.com/mailman/listinfo/community >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: > >>> >>> ------------------------------ >>> >>> Subject: Digest Footer >>> >>> _______________________________________________ >>> Insight-developers mailing list >>> Insight-developers at itk.org >>> http://public.kitware.com/mailman/listinfo/insight-developers >>> >>> >>> ------------------------------ >>> >>> End of Insight-developers Digest, Vol 141, Issue 10 >>> *************************************************** >>> >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-developers >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Jan 19 15:19:38 2016 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 19 Jan 2016 15:19:38 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro Message-ID: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> Hello, My release builds for SimpleITK are having significant problems with the change done here [1] to the itkStaticConstMacro. My builds on Redhat 5, with gcc 5.1, are filling my disk with errors along the following: /scratch/dashboards/SimpleITK-RH5-i686-pkg/SimpleITK-build/ITK-prefix/include/ITK-4.9/itkImageToImageFilter.h: In instantiation of ?const unsigned int itk::ImageToImageFilter, itk::Image >::OutputImageDimension?: /scratch/dashboards/SimpleITK-RH5-i686-pkg/SimpleITK-build/ITK-prefix/include/ITK-4.9/itkImageToImageFilter.h:267: instantiated from ?itk::ImageToImageFilter, itk::Image >? /scratch/dashboards/SimpleITK-RH5-i686-pkg/SimpleITK/Code/Explicit/include/sitkExplicitITKImageToImageFilter.h:259: instantiated from here /scratch/dashboards/SimpleITK-RH5-i686-pkg/SimpleITK-build/ITK-prefix/include/ITK-4.9/itkImageToImageFilter.h:267: error: explicit instantiation of ?itk::ImageToImageFilter, itk::Image >::OutputImageDimension? but no definition available Reverting the change enables SimpleITK explicit instantiation to work with this compiler. I?ll look into alternatives... Brad [1] https://github.com/InsightSoftwareConsortium/ITK/commit/a5aeef59cbbcb3cb136adbe9d450155ede4c8cac -------------- next part -------------- An HTML attachment was scrubbed... URL: From luc.hermitte at c-s.fr Wed Jan 20 04:39:05 2016 From: luc.hermitte at c-s.fr (Luc Hermitte) Date: Wed, 20 Jan 2016 10:39:05 +0100 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: <569F4BE4.4030607@c-s.fr> References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> Message-ID: <569F55B9.5090606@c-s.fr> Le 20/01/2016 09:57, Luc Hermitte a ?crit : > Hello, > > Le 19/01/2016 21:19, Bradley Lowekamp a ?crit : >> Hello, >> >> My release builds for SimpleITK are having significant problems with the >> change done here [1] to the itkStaticConstMacro. >> >> My builds on Redhat 5, with gcc 5.1, are filling my disk with errors >> along the following: >> [...] > [...] >> I?ll look into alternatives... > > Can you isolate the error on a simple test case that reproduce the issue? I've tried the file attached on https://ideone.com/SGlJ1i but it seems valid with GCC 5.1. However, in C++11, constexpr is required. And my g++ 4.8.2, and clang++ as well, tell me: || g++ -std=c++03 -Werror -Wall -pedantic extern-templ.cpp -o extern-templ extern-templ.cpp|19 col 24| error: ISO C++ 1998 forbids the use of 'extern' on explicit instantiations [-Werror=pedantic] || extern template struct Bar, Foo >; What differs in SimpleITK source code? --Luc -------------- next part -------------- #include #if 0 # define CONSTEXPR constexpr #else # define CONSTEXPR #endif template struct Foo { typedef T Type; static const CONSTEXPR std::size_t k_Dim = sizeof(T); }; template struct Bar { static const CONSTEXPR std::size_t k_IDim = I::k_Dim; static const CONSTEXPR std::size_t k_ODim = O::k_Dim; }; // declare extern template struct Bar, Foo >; // ----< end of .h // define in one TU template struct Bar, Foo >; // use, in another TU int main () { typedef Bar, Foo > Type; std::cout << Type::k_IDim << " -- " << Type::k_ODim << "\n"; } From luc.hermitte at c-s.fr Wed Jan 20 03:57:08 2016 From: luc.hermitte at c-s.fr (Luc Hermitte) Date: Wed, 20 Jan 2016 09:57:08 +0100 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> Message-ID: <569F4BE4.4030607@c-s.fr> Hello, Le 19/01/2016 21:19, Bradley Lowekamp a ?crit : > Hello, > > My release builds for SimpleITK are having significant problems with the > change done here [1] to the itkStaticConstMacro. > > My builds on Redhat 5, with gcc 5.1, are filling my disk with errors > along the following: > > /scratch/dashboards/SimpleITK-RH5-i686-pkg/SimpleITK-build/ITK-prefix/include/ITK-4.9/itkImageToImageFilter.h: > In instantiation of ?const unsigned int > itk::ImageToImageFilter, itk::Image 2u> >::OutputImageDimension?: > /scratch/dashboards/SimpleITK-RH5-i686-pkg/SimpleITK-build/ITK-prefix/include/ITK-4.9/itkImageToImageFilter.h:267: > instantiated from ?itk::ImageToImageFilter 2u>, itk::Image >? > /scratch/dashboards/SimpleITK-RH5-i686-pkg/SimpleITK/Code/Explicit/include/sitkExplicitITKImageToImageFilter.h:259: > instantiated from here > /scratch/dashboards/SimpleITK-RH5-i686-pkg/SimpleITK-build/ITK-prefix/include/ITK-4.9/itkImageToImageFilter.h:267: > error: explicit instantiation of > ?itk::ImageToImageFilter, itk::Image 2u> >::OutputImageDimension? but no definition available If I remember correctly, I had similar issues in the past. All the time, the issues were not on the macro side, but on how it was used. Sometimes a constant was redefined/masked for no valid reason, sometimes "typename" weren't issued. anonymous enums are no longer the right way to proceed. > Reverting the change enables SimpleITK explicit instantiation to work > with this compiler. > > I?ll look into alternatives... Can you isolate the error on a simple test case that reproduce the issue? --Luc > > Brad > > [1] https://github.com/InsightSoftwareConsortium/ITK/commit/a5aeef59cbbcb3cb136adbe9d450155ede4c8cac > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > From blowekamp at mail.nih.gov Wed Jan 20 10:00:19 2016 From: blowekamp at mail.nih.gov (Bradly Lowekamp) Date: Wed, 20 Jan 2016 10:00:19 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: <569F55B9.5090606@c-s.fr> References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> Message-ID: Hello Luc, Thanks for looking into this. This bug is related to the older GCC 4.1 compiler that is found standard with Redhat 5 and Fedora 5 and used for distributions such as Anaconda?s Python. I apologize for the incorrect version before. Here is some ITK code to reproduce the error: http://review.source.kitware.com/#/c/20674/ Thank you for exploring a minimal test case. Your code does compile and run OK with GCC 4.1. As a work around for SimpleITK I have disabled the SimpleITK Explicit library for now [1], this is not an optimal solution, and we should try to get explicit instantiation working again with GCC 4.1 Brad https://github.com/SimpleITK/SimpleITK/compare/next#diff-af3b638bc2a3e6c650974192a53c7291 > On Jan 20, 2016, at 4:39 AM, Luc Hermitte wrote: > > Le 20/01/2016 09:57, Luc Hermitte a ?crit : >> Hello, >> >> Le 19/01/2016 21:19, Bradley Lowekamp a ?crit : >>> Hello, >>> >>> My release builds for SimpleITK are having significant problems with the >>> change done here [1] to the itkStaticConstMacro. >>> >>> My builds on Redhat 5, with gcc 5.1, are filling my disk with errors >>> along the following: >>> [...] >> [...] > >>> I?ll look into alternatives... >> >> Can you isolate the error on a simple test case that reproduce the issue? > > I've tried the file attached on https://ideone.com/SGlJ1i but it seems > valid with GCC 5.1. > > However, in C++11, constexpr is required. And my g++ 4.8.2, and clang++ > as well, tell me: > > || g++ -std=c++03 -Werror -Wall -pedantic extern-templ.cpp -o > extern-templ > extern-templ.cpp|19 col 24| error: ISO C++ 1998 forbids the use of > 'extern' on explicit instantiations [-Werror=pedantic] > || extern template struct Bar, Foo >; > > > What differs in SimpleITK source code? > > > --Luc > From blowekamp at mail.nih.gov Thu Jan 21 14:27:22 2016 From: blowekamp at mail.nih.gov (Bradly Lowekamp) Date: Thu, 21 Jan 2016 14:27:22 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> Message-ID: <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> Just to re-iterate the importance of maintain full support for GCC 4.1 with the ability is instantiate ITK templates, here is the new Python PEP 513[1], which suggests using CentOS with gcc 4.1 Also note my working around for disabling SimpleITK?s explicit template instantiation, did not work [2] yet. Brad [1] https://www.python.org/dev/peps/pep-0513/ [2] https://open.cdash.org/index.php?project=SimpleITK > On Jan 20, 2016, at 10:00 AM, Bradly Lowekamp wrote: > > Hello Luc, > > Thanks for looking into this. > > This bug is related to the older GCC 4.1 compiler that is found standard with Redhat 5 and Fedora 5 and used for distributions such as Anaconda?s Python. I apologize for the incorrect version before. > > Here is some ITK code to reproduce the error: > http://review.source.kitware.com/#/c/20674/ > > Thank you for exploring a minimal test case. Your code does compile and run OK with GCC 4.1. > > As a work around for SimpleITK I have disabled the SimpleITK Explicit library for now [1], this is not an optimal solution, and we should try to get explicit instantiation working again with GCC 4.1 > > Brad > > > https://github.com/SimpleITK/SimpleITK/compare/next#diff-af3b638bc2a3e6c650974192a53c7291 > > >> On Jan 20, 2016, at 4:39 AM, Luc Hermitte wrote: >> >> Le 20/01/2016 09:57, Luc Hermitte a ?crit : >>> Hello, >>> >>> Le 19/01/2016 21:19, Bradley Lowekamp a ?crit : >>>> Hello, >>>> >>>> My release builds for SimpleITK are having significant problems with the >>>> change done here [1] to the itkStaticConstMacro. >>>> >>>> My builds on Redhat 5, with gcc 5.1, are filling my disk with errors >>>> along the following: >>>> [...] >>> [...] >> >>>> I?ll look into alternatives... >>> >>> Can you isolate the error on a simple test case that reproduce the issue? >> >> I've tried the file attached on https://ideone.com/SGlJ1i but it seems >> valid with GCC 5.1. >> >> However, in C++11, constexpr is required. And my g++ 4.8.2, and clang++ >> as well, tell me: >> >> || g++ -std=c++03 -Werror -Wall -pedantic extern-templ.cpp -o >> extern-templ >> extern-templ.cpp|19 col 24| error: ISO C++ 1998 forbids the use of >> 'extern' on explicit instantiations [-Werror=pedantic] >> || extern template struct Bar, Foo >; >> >> >> What differs in SimpleITK source code? >> >> >> --Luc >> > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From sean at rogue-research.com Thu Jan 21 14:28:54 2016 From: sean at rogue-research.com (Sean McBride) Date: Thu, 21 Jan 2016 14:28:54 -0500 Subject: [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: <20160104211744.1213332491@mail.rogue-research.com> Message-ID: <20160121192854.4986335@mail.rogue-research.com> On Tue, 5 Jan 2016 14:54:47 -0500, Matt McCormick said: >To update GDCM, run the > > Modules/ThirdParty/GDCM/UpdateFromUpstream.sh > >script. > > >Since GDCM 2.6 has been released, we should switch from GDCM "master" >to GDCM "release" before doing the update. Even more conservatively, I'll start from the "release-2-4" branch. So now the update script works on OS X, I've run it successfully and did: git merge -X subtree=Modules/ThirdParty/GDCM/src/gdcm upstream-gdcm as it instructs. This leaves one file conflicted: Modules/ThirdParty/GDCM/src/gdcm/Utilities/socketxx/socket++/CMakeLists.txt Due to the change in git SHA 70306386. What is the correct way to deal with that? Thanks, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From matt.mccormick at kitware.com Thu Jan 21 14:41:42 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 21 Jan 2016 14:41:42 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> Message-ID: Hi, PEP 513 proposes using GCC 4.8.2 in a CentOS 5 Docker image. This was discussed here: http://kitware.com/blog/home/post/986 Our planned compiler support does not explicitly mention GCC 4.1, but it says GCC 4.2 should be phased out this year: http://www.itk.org/Wiki/ITK_Release_4/Modern_C%2B%2B Matt On Thu, Jan 21, 2016 at 2:27 PM, Bradly Lowekamp wrote: > Just to re-iterate the importance of maintain full support for GCC 4.1 with > the ability is instantiate ITK templates, here is the new Python PEP 513[1], > which suggests using CentOS with gcc 4.1 > > Also note my working around for disabling SimpleITK?s explicit template > instantiation, did not work [2] yet. > > Brad > > > [1] https://www.python.org/dev/peps/pep-0513/ > [2] https://open.cdash.org/index.php?project=SimpleITK > > On Jan 20, 2016, at 10:00 AM, Bradly Lowekamp > wrote: > > Hello Luc, > > Thanks for looking into this. > > This bug is related to the older GCC 4.1 compiler that is found standard > with Redhat 5 and Fedora 5 and used for distributions such as Anaconda?s > Python. I apologize for the incorrect version before. > > Here is some ITK code to reproduce the error: > http://review.source.kitware.com/#/c/20674/ > > Thank you for exploring a minimal test case. Your code does compile and run > OK with GCC 4.1. > > As a work around for SimpleITK I have disabled the SimpleITK Explicit > library for now [1], this is not an optimal solution, and we should try to > get explicit instantiation working again with GCC 4.1 > > Brad > > > https://github.com/SimpleITK/SimpleITK/compare/next#diff-af3b638bc2a3e6c650974192a53c7291 > > > On Jan 20, 2016, at 4:39 AM, Luc Hermitte wrote: > > Le 20/01/2016 09:57, Luc Hermitte a ?crit : > > Hello, > > Le 19/01/2016 21:19, Bradley Lowekamp a ?crit : > > Hello, > > My release builds for SimpleITK are having significant problems with the > change done here [1] to the itkStaticConstMacro. > > My builds on Redhat 5, with gcc 5.1, are filling my disk with errors > along the following: > [...] > > [...] > > > I?ll look into alternatives... > > > Can you isolate the error on a simple test case that reproduce the issue? > > > I've tried the file attached on https://ideone.com/SGlJ1i but it seems > valid with GCC 5.1. > > However, in C++11, constexpr is required. And my g++ 4.8.2, and clang++ > as well, tell me: > > || g++ -std=c++03 -Werror -Wall -pedantic extern-templ.cpp -o > extern-templ > extern-templ.cpp|19 col 24| error: ISO C++ 1998 forbids the use of > 'extern' on explicit instantiations [-Werror=pedantic] > || extern template struct Bar, Foo >; > > > What differs in SimpleITK source code? > > > --Luc > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > From matt.mccormick at kitware.com Thu Jan 21 14:49:29 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 21 Jan 2016 14:49:29 -0500 Subject: [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: <20160121192854.4986335@mail.rogue-research.com> References: <20160104211744.1213332491@mail.rogue-research.com> <20160121192854.4986335@mail.rogue-research.com> Message-ID: On Thu, Jan 21, 2016 at 2:28 PM, Sean McBride wrote: > On Tue, 5 Jan 2016 14:54:47 -0500, Matt McCormick said: > >>To update GDCM, run the >> >> Modules/ThirdParty/GDCM/UpdateFromUpstream.sh >> >>script. >> >> >>Since GDCM 2.6 has been released, we should switch from GDCM "master" >>to GDCM "release" before doing the update. > > Even more conservatively, I'll start from the "release-2-4" branch. Sounds good. > So now the update script works on OS X, Cool! > I've run it successfully and did: > > git merge -X subtree=Modules/ThirdParty/GDCM/src/gdcm upstream-gdcm > > as it instructs. This leaves one file conflicted: > > Modules/ThirdParty/GDCM/src/gdcm/Utilities/socketxx/socket++/CMakeLists.txt > > Due to the change in git SHA 70306386. It should probably still be kept. If it is still relevant to upstream, it could be submitted. Thanks, Matt From sean at rogue-research.com Thu Jan 21 15:05:33 2016 From: sean at rogue-research.com (Sean McBride) Date: Thu, 21 Jan 2016 15:05:33 -0500 Subject: [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: References: <20160104211744.1213332491@mail.rogue-research.com> <20160121192854.4986335@mail.rogue-research.com> Message-ID: <20160121200533.74631707@mail.rogue-research.com> On Thu, 21 Jan 2016 14:49:29 -0500, Matt McCormick said: >> I've run it successfully and did: >> >> git merge -X subtree=Modules/ThirdParty/GDCM/src/gdcm upstream-gdcm >> >> as it instructs. This leaves one file conflicted: >> >> Modules/ThirdParty/GDCM/src/gdcm/Utilities/socketxx/socket++/CMakeLists.txt >> >> Due to the change in git SHA 70306386. > >It should probably still be kept. If it is still relevant to >upstream, it could be submitted. Sorry, what I mean is: what must I do git-wise? Do I just manually fix the conflict in the same commit as my gdcm update, or do I need to make it a separate commit to indicate it's not part of gdcm proper, or...? Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From matt.mccormick at kitware.com Thu Jan 21 15:09:12 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 21 Jan 2016 15:09:12 -0500 Subject: [ITK-dev] [ANN] ITK 4.9 Release Candidate 3 is ready for testing! In-Reply-To: <20160121200533.74631707@mail.rogue-research.com> References: <20160104211744.1213332491@mail.rogue-research.com> <20160121192854.4986335@mail.rogue-research.com> <20160121200533.74631707@mail.rogue-research.com> Message-ID: On Thu, Jan 21, 2016 at 3:05 PM, Sean McBride wrote: > On Thu, 21 Jan 2016 14:49:29 -0500, Matt McCormick said: > >>> I've run it successfully and did: >>> >>> git merge -X subtree=Modules/ThirdParty/GDCM/src/gdcm upstream-gdcm >>> >>> as it instructs. This leaves one file conflicted: >>> >>> Modules/ThirdParty/GDCM/src/gdcm/Utilities/socketxx/socket++/CMakeLists.txt >>> >>> Due to the change in git SHA 70306386. >> >>It should probably still be kept. If it is still relevant to >>upstream, it could be submitted. > > Sorry, what I mean is: what must I do git-wise? Do I just manually fix the conflict in the same commit as my gdcm update, or do I need to make it a separate commit to indicate it's not part of gdcm proper, or...? It can be included in the update commit. Thanks, Matt From blowekamp at mail.nih.gov Thu Jan 21 15:27:03 2016 From: blowekamp at mail.nih.gov (Bradly Lowekamp) Date: Thu, 21 Jan 2016 15:27:03 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> Message-ID: <5EB827E6-9F6D-400A-950B-E22FD8CEF7EA@mail.nih.gov> It?s certainly would be great if I could rely on using gcc 4.8+ for building the distributions for SimpleITK. But my understanding for several situations 4.1 is still essentially required. So you saying you are dropping support for compilers SimpleITK needs for some distributions? Your blog post solution for static linking in un-accetable as I don?t want to use a GPL license. Along with static linking not being recommended with PEP 513, and lastly it can cause conflicts when used in a loaded module with an older libc version. PEP 513 clearly says: GCC <= 4.2.0 I?ll have to explore the manylinux1 docker image more? We know the macro in ITK which needs to be fixed. I don?t understand the resistance? Brad > On Jan 21, 2016, at 2:41 PM, Matt McCormick wrote: > > Hi, > > PEP 513 proposes using GCC 4.8.2 in a CentOS 5 Docker image. This was > discussed here: > > http://kitware.com/blog/home/post/986 > > Our planned compiler support does not explicitly mention GCC 4.1, but > it says GCC 4.2 should be phased out this year: > > http://www.itk.org/Wiki/ITK_Release_4/Modern_C%2B%2B > > Matt > > On Thu, Jan 21, 2016 at 2:27 PM, Bradly Lowekamp wrote: >> Just to re-iterate the importance of maintain full support for GCC 4.1 with >> the ability is instantiate ITK templates, here is the new Python PEP 513[1], >> which suggests using CentOS with gcc 4.1 >> >> Also note my working around for disabling SimpleITK?s explicit template >> instantiation, did not work [2] yet. >> >> Brad >> >> >> [1] https://www.python.org/dev/peps/pep-0513/ >> [2] https://open.cdash.org/index.php?project=SimpleITK >> >> On Jan 20, 2016, at 10:00 AM, Bradly Lowekamp >> wrote: >> >> Hello Luc, >> >> Thanks for looking into this. >> >> This bug is related to the older GCC 4.1 compiler that is found standard >> with Redhat 5 and Fedora 5 and used for distributions such as Anaconda?s >> Python. I apologize for the incorrect version before. >> >> Here is some ITK code to reproduce the error: >> http://review.source.kitware.com/#/c/20674/ >> >> Thank you for exploring a minimal test case. Your code does compile and run >> OK with GCC 4.1. >> >> As a work around for SimpleITK I have disabled the SimpleITK Explicit >> library for now [1], this is not an optimal solution, and we should try to >> get explicit instantiation working again with GCC 4.1 >> >> Brad >> >> >> https://github.com/SimpleITK/SimpleITK/compare/next#diff-af3b638bc2a3e6c650974192a53c7291 >> >> >> On Jan 20, 2016, at 4:39 AM, Luc Hermitte wrote: >> >> Le 20/01/2016 09:57, Luc Hermitte a ?crit : >> >> Hello, >> >> Le 19/01/2016 21:19, Bradley Lowekamp a ?crit : >> >> Hello, >> >> My release builds for SimpleITK are having significant problems with the >> change done here [1] to the itkStaticConstMacro. >> >> My builds on Redhat 5, with gcc 5.1, are filling my disk with errors >> along the following: >> [...] >> >> [...] >> >> >> I?ll look into alternatives... >> >> >> Can you isolate the error on a simple test case that reproduce the issue? >> >> >> I've tried the file attached on https://ideone.com/SGlJ1i but it seems >> valid with GCC 5.1. >> >> However, in C++11, constexpr is required. And my g++ 4.8.2, and clang++ >> as well, tell me: >> >> || g++ -std=c++03 -Werror -Wall -pedantic extern-templ.cpp -o >> extern-templ >> extern-templ.cpp|19 col 24| error: ISO C++ 1998 forbids the use of >> 'extern' on explicit instantiations [-Werror=pedantic] >> || extern template struct Bar, Foo >; >> >> >> What differs in SimpleITK source code? >> >> >> --Luc >> >> >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> >> >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt at mmmccormick.com Thu Jan 21 15:35:23 2016 From: matt at mmmccormick.com (Matthew McCormick (thewtex)) Date: Thu, 21 Jan 2016 15:35:23 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: <5EB827E6-9F6D-400A-950B-E22FD8CEF7EA@mail.nih.gov> References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> <5EB827E6-9F6D-400A-950B-E22FD8CEF7EA@mail.nih.gov> Message-ID: On Thu, Jan 21, 2016 at 3:27 PM, Bradly Lowekamp wrote: > It?s certainly would be great if I could rely on using gcc 4.8+ for building > the distributions for SimpleITK. But my understanding for several situations > 4.1 is still essentially required. What are the situations? GCC 4.1 is not required by PEP 513. > Your blog post solution for static linking in un-accetable as I don?t want > to use a GPL license. Along with static linking not being recommended with > PEP 513, and lastly it can cause conflicts when used in a loaded module with > an older libc version. My blog post does not say static linking is required or the GPL is required. > PEP 513 clearly says: > > GCC <= 4.2.0 This excludes GCC 4.1. Matt From blowekamp at mail.nih.gov Thu Jan 21 16:07:10 2016 From: blowekamp at mail.nih.gov (Bradly Lowekamp) Date: Thu, 21 Jan 2016 16:07:10 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> <5EB827E6-9F6D-400A-950B-E22FD8CEF7EA@mail.nih.gov> Message-ID: <6FDDE3D9-5EBF-44FF-A702-DA31B0B4B024@mail.nih.gov> Gcc 4.2 runs into the same ITK bug with explicit instantiation too. > On Jan 21, 2016, at 3:35 PM, Matthew McCormick (thewtex) wrote: > > On Thu, Jan 21, 2016 at 3:27 PM, Bradly Lowekamp wrote: >> It?s certainly would be great if I could rely on using gcc 4.8+ for building >> the distributions for SimpleITK. But my understanding for several situations >> 4.1 is still essentially required. > > What are the situations? GCC 4.1 is not required by PEP 513. Anaconda Python 2.7, OSX Python.org distribution and OSX system, need apple?s gcc 4.2 > > >> Your blog post solution for static linking in un-accetable as I don?t want >> to use a GPL license. Along with static linking not being recommended with >> PEP 513, and lastly it can cause conflicts when used in a loaded module with >> an older libc version. > > My blog post does not say static linking is required or the GPL is required. "Statically linking libstdc++ avoids version compatibility issues.? Statically, linking an LGPL library such as libstdc++ is ?messy?. > > >> PEP 513 clearly says: >> >> GCC <= 4.2.0 > > This excludes GCC 4.1. 4.1 <= 4.2, so it?s included. > > > Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Jan 21 16:45:42 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 21 Jan 2016 16:45:42 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: <6FDDE3D9-5EBF-44FF-A702-DA31B0B4B024@mail.nih.gov> References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> <5EB827E6-9F6D-400A-950B-E22FD8CEF7EA@mail.nih.gov> <6FDDE3D9-5EBF-44FF-A702-DA31B0B4B024@mail.nih.gov> Message-ID: On Thu, Jan 21, 2016 at 4:07 PM, Bradly Lowekamp wrote: > Gcc 4.2 runs into the same ITK bug with explicit instantiation too. > > On Jan 21, 2016, at 3:35 PM, Matthew McCormick (thewtex) > wrote: > > On Thu, Jan 21, 2016 at 3:27 PM, Bradly Lowekamp > wrote: > > It?s certainly would be great if I could rely on using gcc 4.8+ for building > the distributions for SimpleITK. But my understanding for several situations > 4.1 is still essentially required. > > > What are the situations? GCC 4.1 is not required by PEP 513. > > > Anaconda Python 2.7, OSX Python.org distribution and OSX system, need > apple?s gcc 4.2 How is this build environment reproduced (OSX and XCode version)? > Your blog post solution for static linking in un-accetable as I don?t want > to use a GPL license. Along with static linking not being recommended with > PEP 513, and lastly it can cause conflicts when used in a loaded module with > an older libc version. > > > My blog post does not say static linking is required or the GPL is required. > > > "Statically linking libstdc++ avoids version compatibility issues.? > > Statically, linking an LGPL library such as libstdc++ is ?messy?. libstdc++ is different from glibc. Statically linking libstdc++ in terms of the license is fine. It is available with the GCC Runtime Library Exception: https://gcc.gnu.org/onlinedocs/libstdc++/manual/license.html > PEP 513 clearly says: > > GCC <= 4.2.0 > > > This excludes GCC 4.1. > > > 4.1 <= 4.2, so it?s included. This excludes GCC 4.1 from being a requirement. GCC 4.2 would work. Matt From brad at lowekamp.net Fri Jan 22 10:05:40 2016 From: brad at lowekamp.net (Bradly Lowekamp) Date: Fri, 22 Jan 2016 10:05:40 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> <5EB827E6-9F6D-400A-950B-E22FD8CEF7EA@mail.nih.gov> <6FDDE3D9-5EBF-44FF-A702-DA31B0B4B024@mail.nih.gov> Message-ID: I have reproduced this error now with GCC 4.1, 4.2, and 4.3. GCC version 4.5 works. Thank you for your help in addressing this problem. I apologize for not having documentation for the systems and justifications for the versions of compilation tools. I certainly should move to docker images to build the distributions for Linux as well. We have had great success with the portability and availability of the binary distributions for SimpleITK. This has involve a lot of testing and modification for the build platforms to get where it has been working. I would had for this to be reduce due to one preference for implementing static constant integers. Brad > On Jan 21, 2016, at 4:45 PM, Matt McCormick > wrote: > > On Thu, Jan 21, 2016 at 4:07 PM, Bradly Lowekamp > wrote: >> Gcc 4.2 runs into the same ITK bug with explicit instantiation too. >> >> On Jan 21, 2016, at 3:35 PM, Matthew McCormick (thewtex) >> > wrote: >> >> On Thu, Jan 21, 2016 at 3:27 PM, Bradly Lowekamp > >> wrote: >> >> It?s certainly would be great if I could rely on using gcc 4.8+ for building >> the distributions for SimpleITK. But my understanding for several situations >> 4.1 is still essentially required. >> >> >> What are the situations? GCC 4.1 is not required by PEP 513. >> >> >> Anaconda Python 2.7, OSX Python.org distribution and OSX system, need >> apple?s gcc 4.2 > > How is this build environment reproduced (OSX and XCode version)? > > >> Your blog post solution for static linking in un-accetable as I don?t want >> to use a GPL license. Along with static linking not being recommended with >> PEP 513, and lastly it can cause conflicts when used in a loaded module with >> an older libc version. >> >> >> My blog post does not say static linking is required or the GPL is required. >> >> >> "Statically linking libstdc++ avoids version compatibility issues.? >> >> Statically, linking an LGPL library such as libstdc++ is ?messy?. > > libstdc++ is different from glibc. > > Statically linking libstdc++ in terms of the license is fine. It is > available with the GCC Runtime Library Exception: > > https://gcc.gnu.org/onlinedocs/libstdc++/manual/license.html > > >> PEP 513 clearly says: >> >> GCC <= 4.2.0 >> >> >> This excludes GCC 4.1. >> >> >> 4.1 <= 4.2, so it?s included. > > This excludes GCC 4.1 from being a requirement. GCC 4.2 would work. > > > Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Fri Jan 22 11:00:27 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Fri, 22 Jan 2016 11:00:27 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> <5EB827E6-9F6D-400A-950B-E22FD8CEF7EA@mail.nih.gov> <6FDDE3D9-5EBF-44FF-A702-DA31B0B4B024@mail.nih.gov> Message-ID: I think I am seeing the same error. I get this error on my Mac running gcc 4.2.1 Building CXX object Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/itkImageRegionExplicitTest.cxx.o /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: In instantiation of ?const unsigned int itk::ImageRegion<1u>::ImageDimension?: /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: instantiated from ?itk::ImageRegion<1u>? /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: instantiated from here /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: error: explicit instantiation of ?itk::ImageRegion<1u>::ImageDimension? but no definition available /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: In instantiation of ?const unsigned int itk::ImageRegion<1u>::SliceDimension?: /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: instantiated from ?itk::ImageRegion<1u>? /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: instantiated from here /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: error: explicit instantiation of ?itk::ImageRegion<1u>::SliceDimension? but no definition available /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: In instantiation of ?const unsigned int itk::ImageRegion<1u>::ImageDimension?: /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: instantiated from ?itk::ImageRegion<1u>? /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: instantiated from here /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: error: explicit instantiation of ?itk::ImageRegion<1u>::ImageDimension? but no definition available /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: In instantiation of ?const unsigned int itk::ImageRegion<1u>::SliceDimension?: /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: instantiated from ?itk::ImageRegion<1u>? /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: instantiated from here /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104/Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: In instantiation of ?const unsigned int itk::ImageRegion<1u>::ImageDimension?: /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: instantiated from ?itk::ImageRegion<1u>? /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: instantiated from here /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: error: explicit instantiation of ?itk::ImageRegion<1u>::ImageDimension? but no definition available /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: In instantiation of ?const unsigned int itk::ImageRegion<1u>::SliceDimension?: /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: instantiated from ?itk::ImageRegion<1u>? /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: instantiated from here /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: error: explicit instantiation of ?itk::ImageRegion<1u>::SliceDimension? but no definition available make[2]: *** [Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/itkImageRegionExplicitTest.cxx.o] Error 1 make[1]: *** [Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/all] Error 2 On Fri, Jan 22, 2016 at 10:05 AM, Bradly Lowekamp wrote: > I have reproduced this error now with GCC 4.1, 4.2, and 4.3. GCC version 4.5 > works. > > Thank you for your help in addressing this problem. > > I apologize for not having documentation for the systems and justifications > for the versions of compilation tools. I certainly should move to docker > images to build the distributions for Linux as well. We have had great > success with the portability and availability of the binary distributions > for SimpleITK. This has involve a lot of testing and modification for the > build platforms to get where it has been working. I would had for this to be > reduce due to one preference for implementing static constant integers. > > Brad > > On Jan 21, 2016, at 4:45 PM, Matt McCormick > wrote: > > On Thu, Jan 21, 2016 at 4:07 PM, Bradly Lowekamp > wrote: > > Gcc 4.2 runs into the same ITK bug with explicit instantiation too. > > On Jan 21, 2016, at 3:35 PM, Matthew McCormick (thewtex) > wrote: > > On Thu, Jan 21, 2016 at 3:27 PM, Bradly Lowekamp > wrote: > > It?s certainly would be great if I could rely on using gcc 4.8+ for building > the distributions for SimpleITK. But my understanding for several situations > 4.1 is still essentially required. > > > What are the situations? GCC 4.1 is not required by PEP 513. > > > Anaconda Python 2.7, OSX Python.org distribution and OSX system, need > apple?s gcc 4.2 > > > How is this build environment reproduced (OSX and XCode version)? > > > Your blog post solution for static linking in un-accetable as I don?t want > to use a GPL license. Along with static linking not being recommended with > PEP 513, and lastly it can cause conflicts when used in a loaded module with > an older libc version. > > > My blog post does not say static linking is required or the GPL is required. > > > "Statically linking libstdc++ avoids version compatibility issues.? > > Statically, linking an LGPL library such as libstdc++ is ?messy?. > > > libstdc++ is different from glibc. > > Statically linking libstdc++ in terms of the license is fine. It is > available with the GCC Runtime Library Exception: > > https://gcc.gnu.org/onlinedocs/libstdc++/manual/license.html > > > PEP 513 clearly says: > > GCC <= 4.2.0 > > > This excludes GCC 4.1. > > > 4.1 <= 4.2, so it?s included. > > > This excludes GCC 4.1 from being a requirement. GCC 4.2 would work. > > > Matt > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -- Unpaid intern in BillsBasement at noware dot com From matt.mccormick at kitware.com Fri Jan 22 22:04:21 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 22 Jan 2016 22:04:21 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> <5EB827E6-9F6D-400A-950B-E22FD8CEF7EA@mail.nih.gov> <6FDDE3D9-5EBF-44FF-A702-DA31B0B4B024@mail.nih.gov> Message-ID: Hi, Please test this patch: http://review.source.kitware.com/#/c/20693/ Thanks, Matt On Fri, Jan 22, 2016 at 11:00 AM, Bill Lorensen wrote: > I think I am seeing the same error. I get this error on my Mac running gcc 4.2.1 > Building CXX object > Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/itkImageRegionExplicitTest.cxx.o > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: > In instantiation of ?const unsigned int > itk::ImageRegion<1u>::ImageDimension?: > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: > instantiated from ?itk::ImageRegion<1u>? > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: > instantiated from here > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: > error: explicit instantiation of > ?itk::ImageRegion<1u>::ImageDimension? but no definition available > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: > In instantiation of ?const unsigned int > itk::ImageRegion<1u>::SliceDimension?: > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: > instantiated from ?itk::ImageRegion<1u>? > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: > instantiated from here > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: > error: explicit instantiation of > ?itk::ImageRegion<1u>::SliceDimension? but no definition available > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: > In instantiation of ?const unsigned int > itk::ImageRegion<1u>::ImageDimension?: > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: > instantiated from ?itk::ImageRegion<1u>? > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: > instantiated from here > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: > error: explicit instantiation of > ?itk::ImageRegion<1u>::ImageDimension? but no definition available > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: > In instantiation of ?const unsigned int > itk::ImageRegion<1u>::SliceDimension?: > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: > instantiated from ?itk::ImageRegion<1u>? > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: > instantiated from here > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104/Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: > In instantiation of ?const unsigned int > itk::ImageRegion<1u>::ImageDimension?: > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: > instantiated from ?itk::ImageRegion<1u>? > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: > instantiated from here > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: > error: explicit instantiation of > ?itk::ImageRegion<1u>::ImageDimension? but no definition available > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: > In instantiation of ?const unsigned int > itk::ImageRegion<1u>::SliceDimension?: > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: > instantiated from ?itk::ImageRegion<1u>? > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: > instantiated from here > /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: > error: explicit instantiation of > ?itk::ImageRegion<1u>::SliceDimension? but no definition available > make[2]: *** [Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/itkImageRegionExplicitTest.cxx.o] > Error 1 > make[1]: *** [Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/all] > Error 2 > > > On Fri, Jan 22, 2016 at 10:05 AM, Bradly Lowekamp wrote: >> I have reproduced this error now with GCC 4.1, 4.2, and 4.3. GCC version 4.5 >> works. >> >> Thank you for your help in addressing this problem. >> >> I apologize for not having documentation for the systems and justifications >> for the versions of compilation tools. I certainly should move to docker >> images to build the distributions for Linux as well. We have had great >> success with the portability and availability of the binary distributions >> for SimpleITK. This has involve a lot of testing and modification for the >> build platforms to get where it has been working. I would had for this to be >> reduce due to one preference for implementing static constant integers. >> >> Brad >> >> On Jan 21, 2016, at 4:45 PM, Matt McCormick >> wrote: >> >> On Thu, Jan 21, 2016 at 4:07 PM, Bradly Lowekamp >> wrote: >> >> Gcc 4.2 runs into the same ITK bug with explicit instantiation too. >> >> On Jan 21, 2016, at 3:35 PM, Matthew McCormick (thewtex) >> wrote: >> >> On Thu, Jan 21, 2016 at 3:27 PM, Bradly Lowekamp >> wrote: >> >> It?s certainly would be great if I could rely on using gcc 4.8+ for building >> the distributions for SimpleITK. But my understanding for several situations >> 4.1 is still essentially required. >> >> >> What are the situations? GCC 4.1 is not required by PEP 513. >> >> >> Anaconda Python 2.7, OSX Python.org distribution and OSX system, need >> apple?s gcc 4.2 >> >> >> How is this build environment reproduced (OSX and XCode version)? >> >> >> Your blog post solution for static linking in un-accetable as I don?t want >> to use a GPL license. Along with static linking not being recommended with >> PEP 513, and lastly it can cause conflicts when used in a loaded module with >> an older libc version. >> >> >> My blog post does not say static linking is required or the GPL is required. >> >> >> "Statically linking libstdc++ avoids version compatibility issues.? >> >> Statically, linking an LGPL library such as libstdc++ is ?messy?. >> >> >> libstdc++ is different from glibc. >> >> Statically linking libstdc++ in terms of the license is fine. It is >> available with the GCC Runtime Library Exception: >> >> https://gcc.gnu.org/onlinedocs/libstdc++/manual/license.html >> >> >> PEP 513 clearly says: >> >> GCC <= 4.2.0 >> >> >> This excludes GCC 4.1. >> >> >> 4.1 <= 4.2, so it?s included. >> >> >> This excludes GCC 4.1 from being a requirement. GCC 4.2 would work. >> >> >> Matt >> >> >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> > > > > -- > Unpaid intern in BillsBasement at noware dot com From brad at lowekamp.net Mon Jan 25 09:31:09 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Mon, 25 Jan 2016 09:31:09 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> <5EB827E6-9F6D-400A-950B-E22FD8CEF7EA@mail.nih.gov> <6FDDE3D9-5EBF-44FF-A702-DA31B0B4B024@mail.nih.gov> Message-ID: <95EEAC87-B6AE-4739-A3F4-CAA76664D875@lowekamp.net> Matt, You latest patch fixes the problems with build SimpleITK on my distribution system. I look forward to it being merged into the release branch! Thank you! Brad > On Jan 22, 2016, at 10:04 PM, Matt McCormick wrote: > > Hi, > > Please test this patch: > > http://review.source.kitware.com/#/c/20693/ > > Thanks, > Matt > > On Fri, Jan 22, 2016 at 11:00 AM, Bill Lorensen wrote: >> I think I am seeing the same error. I get this error on my Mac running gcc 4.2.1 >> Building CXX object >> Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/itkImageRegionExplicitTest.cxx.o >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >> In instantiation of ?const unsigned int >> itk::ImageRegion<1u>::ImageDimension?: >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >> instantiated from ?itk::ImageRegion<1u>? >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >> instantiated from here >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >> error: explicit instantiation of >> ?itk::ImageRegion<1u>::ImageDimension? but no definition available >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >> In instantiation of ?const unsigned int >> itk::ImageRegion<1u>::SliceDimension?: >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: >> instantiated from ?itk::ImageRegion<1u>? >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >> instantiated from here >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: >> error: explicit instantiation of >> ?itk::ImageRegion<1u>::SliceDimension? but no definition available >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >> In instantiation of ?const unsigned int >> itk::ImageRegion<1u>::ImageDimension?: >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >> instantiated from ?itk::ImageRegion<1u>? >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >> instantiated from here >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >> error: explicit instantiation of >> ?itk::ImageRegion<1u>::ImageDimension? but no definition available >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >> In instantiation of ?const unsigned int >> itk::ImageRegion<1u>::SliceDimension?: >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: >> instantiated from ?itk::ImageRegion<1u>? >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >> instantiated from here >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104/Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >> In instantiation of ?const unsigned int >> itk::ImageRegion<1u>::ImageDimension?: >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >> instantiated from ?itk::ImageRegion<1u>? >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >> instantiated from here >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >> error: explicit instantiation of >> ?itk::ImageRegion<1u>::ImageDimension? but no definition available >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >> In instantiation of ?const unsigned int >> itk::ImageRegion<1u>::SliceDimension?: >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: >> instantiated from ?itk::ImageRegion<1u>? >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >> instantiated from here >> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: >> error: explicit instantiation of >> ?itk::ImageRegion<1u>::SliceDimension? but no definition available >> make[2]: *** [Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/itkImageRegionExplicitTest.cxx.o] >> Error 1 >> make[1]: *** [Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/all] >> Error 2 >> >> >> On Fri, Jan 22, 2016 at 10:05 AM, Bradly Lowekamp wrote: >>> I have reproduced this error now with GCC 4.1, 4.2, and 4.3. GCC version 4.5 >>> works. >>> >>> Thank you for your help in addressing this problem. >>> >>> I apologize for not having documentation for the systems and justifications >>> for the versions of compilation tools. I certainly should move to docker >>> images to build the distributions for Linux as well. We have had great >>> success with the portability and availability of the binary distributions >>> for SimpleITK. This has involve a lot of testing and modification for the >>> build platforms to get where it has been working. I would had for this to be >>> reduce due to one preference for implementing static constant integers. >>> >>> Brad >>> >>> On Jan 21, 2016, at 4:45 PM, Matt McCormick >>> wrote: >>> >>> On Thu, Jan 21, 2016 at 4:07 PM, Bradly Lowekamp >>> wrote: >>> >>> Gcc 4.2 runs into the same ITK bug with explicit instantiation too. >>> >>> On Jan 21, 2016, at 3:35 PM, Matthew McCormick (thewtex) >>> wrote: >>> >>> On Thu, Jan 21, 2016 at 3:27 PM, Bradly Lowekamp >>> wrote: >>> >>> It?s certainly would be great if I could rely on using gcc 4.8+ for building >>> the distributions for SimpleITK. But my understanding for several situations >>> 4.1 is still essentially required. >>> >>> >>> What are the situations? GCC 4.1 is not required by PEP 513. >>> >>> >>> Anaconda Python 2.7, OSX Python.org distribution and OSX system, need >>> apple?s gcc 4.2 >>> >>> >>> How is this build environment reproduced (OSX and XCode version)? >>> >>> >>> Your blog post solution for static linking in un-accetable as I don?t want >>> to use a GPL license. Along with static linking not being recommended with >>> PEP 513, and lastly it can cause conflicts when used in a loaded module with >>> an older libc version. >>> >>> >>> My blog post does not say static linking is required or the GPL is required. >>> >>> >>> "Statically linking libstdc++ avoids version compatibility issues.? >>> >>> Statically, linking an LGPL library such as libstdc++ is ?messy?. >>> >>> >>> libstdc++ is different from glibc. >>> >>> Statically linking libstdc++ in terms of the license is fine. It is >>> available with the GCC Runtime Library Exception: >>> >>> https://gcc.gnu.org/onlinedocs/libstdc++/manual/license.html >>> >>> >>> PEP 513 clearly says: >>> >>> GCC <= 4.2.0 >>> >>> >>> This excludes GCC 4.1. >>> >>> >>> 4.1 <= 4.2, so it?s included. >>> >>> >>> This excludes GCC 4.1 from being a requirement. GCC 4.2 would work. >>> >>> >>> Matt >>> >>> >>> >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-developers >>> >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com From matt.mccormick at kitware.com Tue Jan 26 10:00:57 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 26 Jan 2016 10:00:57 -0500 Subject: [ITK-dev] Problems with Change in itkStaticConstMacro In-Reply-To: <95EEAC87-B6AE-4739-A3F4-CAA76664D875@lowekamp.net> References: <1BE7360C-A6DD-462D-96B3-A7F5D7996CA8@mail.nih.gov> <569F4BE4.4030607@c-s.fr> <569F55B9.5090606@c-s.fr> <9152FC35-BE44-49E2-AF60-90018B8A2552@mail.nih.gov> <5EB827E6-9F6D-400A-950B-E22FD8CEF7EA@mail.nih.gov> <6FDDE3D9-5EBF-44FF-A702-DA31B0B4B024@mail.nih.gov> <95EEAC87-B6AE-4739-A3F4-CAA76664D875@lowekamp.net> Message-ID: Hi Brad, Thanks for the feedback and help on this. These patches have been merged to the release branch, and they will be included in the 4.9.0 release. Thanks, Matt On Mon, Jan 25, 2016 at 9:31 AM, Bradley Lowekamp wrote: > Matt, > > You latest patch fixes the problems with build SimpleITK on my distribution system. I look forward to it being merged into the release branch! > Thank you! > Brad > > >> On Jan 22, 2016, at 10:04 PM, Matt McCormick wrote: >> >> Hi, >> >> Please test this patch: >> >> http://review.source.kitware.com/#/c/20693/ >> >> Thanks, >> Matt >> >> On Fri, Jan 22, 2016 at 11:00 AM, Bill Lorensen wrote: >>> I think I am seeing the same error. I get this error on my Mac running gcc 4.2.1 >>> Building CXX object >>> Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/itkImageRegionExplicitTest.cxx.o >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >>> In instantiation of ?const unsigned int >>> itk::ImageRegion<1u>::ImageDimension?: >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >>> instantiated from ?itk::ImageRegion<1u>? >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >>> instantiated from here >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >>> error: explicit instantiation of >>> ?itk::ImageRegion<1u>::ImageDimension? but no definition available >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >>> In instantiation of ?const unsigned int >>> itk::ImageRegion<1u>::SliceDimension?: >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: >>> instantiated from ?itk::ImageRegion<1u>? >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >>> instantiated from here >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: >>> error: explicit instantiation of >>> ?itk::ImageRegion<1u>::SliceDimension? but no definition available >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >>> In instantiation of ?const unsigned int >>> itk::ImageRegion<1u>::ImageDimension?: >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >>> instantiated from ?itk::ImageRegion<1u>? >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >>> instantiated from here >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >>> error: explicit instantiation of >>> ?itk::ImageRegion<1u>::ImageDimension? but no definition available >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >>> In instantiation of ?const unsigned int >>> itk::ImageRegion<1u>::SliceDimension?: >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: >>> instantiated from ?itk::ImageRegion<1u>? >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >>> instantiated from here >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104/Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >>> In instantiation of ?const unsigned int >>> itk::ImageRegion<1u>::ImageDimension?: >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >>> instantiated from ?itk::ImageRegion<1u>? >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >>> instantiated from here >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:92: >>> error: explicit instantiation of >>> ?itk::ImageRegion<1u>::ImageDimension? but no definition available >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h: >>> In instantiation of ?const unsigned int >>> itk::ImageRegion<1u>::SliceDimension?: >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: >>> instantiated from ?itk::ImageRegion<1u>? >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/test/itkImageRegionExplicitTest.cxx:22: >>> instantiated from here >>> /Users/lorensen/ProjectsGIT/ITK/Modules/Core/Common/include/itkImageRegion.h:104: >>> error: explicit instantiation of >>> ?itk::ImageRegion<1u>::SliceDimension? but no definition available >>> make[2]: *** [Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/itkImageRegionExplicitTest.cxx.o] >>> Error 1 >>> make[1]: *** [Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/all] >>> Error 2 >>> >>> >>> On Fri, Jan 22, 2016 at 10:05 AM, Bradly Lowekamp wrote: >>>> I have reproduced this error now with GCC 4.1, 4.2, and 4.3. GCC version 4.5 >>>> works. >>>> >>>> Thank you for your help in addressing this problem. >>>> >>>> I apologize for not having documentation for the systems and justifications >>>> for the versions of compilation tools. I certainly should move to docker >>>> images to build the distributions for Linux as well. We have had great >>>> success with the portability and availability of the binary distributions >>>> for SimpleITK. This has involve a lot of testing and modification for the >>>> build platforms to get where it has been working. I would had for this to be >>>> reduce due to one preference for implementing static constant integers. >>>> >>>> Brad >>>> >>>> On Jan 21, 2016, at 4:45 PM, Matt McCormick >>>> wrote: >>>> >>>> On Thu, Jan 21, 2016 at 4:07 PM, Bradly Lowekamp >>>> wrote: >>>> >>>> Gcc 4.2 runs into the same ITK bug with explicit instantiation too. >>>> >>>> On Jan 21, 2016, at 3:35 PM, Matthew McCormick (thewtex) >>>> wrote: >>>> >>>> On Thu, Jan 21, 2016 at 3:27 PM, Bradly Lowekamp >>>> wrote: >>>> >>>> It?s certainly would be great if I could rely on using gcc 4.8+ for building >>>> the distributions for SimpleITK. But my understanding for several situations >>>> 4.1 is still essentially required. >>>> >>>> >>>> What are the situations? GCC 4.1 is not required by PEP 513. >>>> >>>> >>>> Anaconda Python 2.7, OSX Python.org distribution and OSX system, need >>>> apple?s gcc 4.2 >>>> >>>> >>>> How is this build environment reproduced (OSX and XCode version)? >>>> >>>> >>>> Your blog post solution for static linking in un-accetable as I don?t want >>>> to use a GPL license. Along with static linking not being recommended with >>>> PEP 513, and lastly it can cause conflicts when used in a loaded module with >>>> an older libc version. >>>> >>>> >>>> My blog post does not say static linking is required or the GPL is required. >>>> >>>> >>>> "Statically linking libstdc++ avoids version compatibility issues.? >>>> >>>> Statically, linking an LGPL library such as libstdc++ is ?messy?. >>>> >>>> >>>> libstdc++ is different from glibc. >>>> >>>> Statically linking libstdc++ in terms of the license is fine. It is >>>> available with the GCC Runtime Library Exception: >>>> >>>> https://gcc.gnu.org/onlinedocs/libstdc++/manual/license.html >>>> >>>> >>>> PEP 513 clearly says: >>>> >>>> GCC <= 4.2.0 >>>> >>>> >>>> This excludes GCC 4.1. >>>> >>>> >>>> 4.1 <= 4.2, so it?s included. >>>> >>>> >>>> This excludes GCC 4.1 from being a requirement. GCC 4.2 would work. >>>> >>>> >>>> Matt >>>> >>>> >>>> >>>> _______________________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-developers >>>> >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com > From zivrafael.yaniv at nih.gov Thu Jan 28 15:55:23 2016 From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]) Date: Thu, 28 Jan 2016 20:55:23 +0000 Subject: [ITK-dev] Pill Image Recognition Challenge Message-ID: Dear ITK community, As developers of image analysis algorithms I belive the following NLM sponsored challenge may be of interest to you: Pill Image Recognition Challenge (http://pir.nlm.nih.gov/challenge) In this Challenge, the National Library of Medicine at the U.S. National Institutes of Health invites individuals and teams to submit algorithms and software for pill image recognition. The submissions are to rank images taken from NLM's RxIMAGE database of high-quality prescription pill images by similarity to consumer-quality images of the same pills. NLM plans to use the submissions in creating a future software system and a future Application Programming Interface (API) that can be used in identifying an unknown prescription pill from a photo taken of that pill by a smart phone. Prizes: 1st place: $25,000 2nd place: $15,000 3rd place: $5,000 Honorable mentions (2): $2,500 The submission period for the Challenge is April 4, 2016 to May 31, 2016, with winners to be announced August 1, 2016. Parties wishing to participate in the Challenge are provided with a training data set. The Challenge will be judged by calculating mean average precision (MAP) on a similar judging data set. The eligible submission with the highest MAP score will be recommended as the first place winner, with the second, third, fourth, and fifth best MAPs, respectively being recommended to earn second place, third place, and two honorable mentions. best regards Ziv -------------- next part -------------- An HTML attachment was scrubbed... URL: