From tom.vercauteren at m4x.org Fri Jul 1 04:45:57 2016 From: tom.vercauteren at m4x.org (Tom Vercauteren) Date: Fri, 1 Jul 2016 09:45:57 +0100 Subject: [ITK-dev] LSQR (and related VNL code) Licensing Issues - fix lost Message-ID: Dear all, Sorry for the cross-posting but this refers to an issue linking both ITK and VNL. In 2010, we identified a licensing issue with some code from vnl and at the time Luis Ibanez fixed it from the ITK side: https://issues.itk.org/jira/browse/HISTITK-1160 Luis notably rewrote the LSQR code: https://github.com/InsightSoftwareConsortium/ITK/tree/release-3.20/Utilities/vxl/v3p/netlib/linalg http://svn.na-mic.org/NAMICSandBox/trunk/SparseLinearSolverConversion/C++/ https://github.com/InsightSoftwareConsortium/ITK/commits/release-3.20/Utilities/vxl/v3p/netlib/linalg It seems that this effort was not backported to VXL and was subsequently lost when moving to ITK 4: https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/ThirdParty/VNL/src/vxl/v3p/netlib/linalg It would be great if someone could look into this (important) licensing issue. For the only purpose of LSQR, I copied the LSQR NAMICSandBox code in a standalone github repo here: https://github.com/tvercaut/LSQR-cpp I have also added a comment in the ITK and VXL bug trackers: https://issues.itk.org/jira/browse/HISTITK-1160 https://github.com/vxl/vxl/issues/332 Best wishes, Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Fri Jul 1 10:23:56 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Fri, 1 Jul 2016 10:23:56 -0400 Subject: [ITK-dev] core/vnl/tests/test_container_interface.cxx appeared today Message-ID: After an update today, the filke core/vnl/tests/test_container_interface.cxx appeared in my top level ITK directory Was this checked in my accident? Bill From matt.mccormick at kitware.com Fri Jul 1 13:56:17 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 1 Jul 2016 13:56:17 -0400 Subject: [ITK-dev] [ITK] core/vnl/tests/test_container_interface.cxx appeared today In-Reply-To: References: Message-ID: Hi Bill, Good catch. Yes, the file was accidentally added in a recent VNL subtree merge. Here is a patch: http://review.source.kitware.com/#/c/21294/ Thanks, Matt On Fri, Jul 1, 2016 at 10:23 AM, Bill Lorensen wrote: > After an update today, the filke > core/vnl/tests/test_container_interface.cxx > appeared in my top level ITK directory > > Was this checked in my accident? > > Bill > _______________________________________________ > 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 From marcus.hanwell at kitware.com Fri Jul 1 14:10:27 2016 From: marcus.hanwell at kitware.com (Marcus D. Hanwell) Date: Fri, 1 Jul 2016 14:10:27 -0400 Subject: [ITK-dev] ITK Python wrapping issue with GCC 6.1.1 Message-ID: I am trying to compile ITK master (73dd6af) with GCC 6.1.1 and am seeing a compile error: Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function ?PyObject* _ wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)?: Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5867:65: error: no matchi ng function for call to ?itk::TriangleHelper >::TriangleH elper()? result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2(); ^ In file included from /home/marcus/src/ITK/Modules/Core/Common/include/itkLightO bject.h:21:0, from /home/marcus/src/ITK/Modules/Core/Common/include/itkObject .h:31, from /home/marcus/src/ITK/Modules/Core/Common/include/itkComman d.h:21, from Wrapping/Typedefs/itkTriangleHelperSwigInterface.h:3, from Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:325 8: /home/marcus/src/ITK/Modules/Core/Common/include/itkTriangleHelper.h:88:32: note : candidate: itk::TriangleHelper::TriangleHelper(const itk::TriangleHelp er&) [with TPoint = itk::Point] ITK_DISALLOW_COPY_AND_ASSIGN(TriangleHelper); Is my GCC too new? It only seems to be happening with the wrapping, this is on Linux. I can post more details if it helps. From matt.mccormick at kitware.com Fri Jul 1 14:54:22 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 1 Jul 2016 14:54:22 -0400 Subject: [ITK-dev] [ITK] ITK Python wrapping issue with GCC 6.1.1 In-Reply-To: References: Message-ID: Hi Marcus, Thanks for reporting the issue. Yes, it looks like GCC 6 / wrapping is having issues. There is now an issue to track this: https://issues.itk.org/jira/browse/ITK-3450 Thanks, Matt On Fri, Jul 1, 2016 at 2:10 PM, Marcus D. Hanwell wrote: > I am trying to compile ITK master (73dd6af) with GCC 6.1.1 and am > seeing a compile error: > > Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function ?PyObject* _ > wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)?: > Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5867:65: error: no matchi > ng function for call to ?itk::TriangleHelper >::TriangleH > elper()? > result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2(); > ^ > In file included from /home/marcus/src/ITK/Modules/Core/Common/include/itkLightO > bject.h:21:0, > from /home/marcus/src/ITK/Modules/Core/Common/include/itkObject > .h:31, > from /home/marcus/src/ITK/Modules/Core/Common/include/itkComman > d.h:21, > from Wrapping/Typedefs/itkTriangleHelperSwigInterface.h:3, > from Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:325 > 8: > /home/marcus/src/ITK/Modules/Core/Common/include/itkTriangleHelper.h:88:32: note > : candidate: itk::TriangleHelper::TriangleHelper(const itk::TriangleHelp > er&) [with TPoint = itk::Point] > ITK_DISALLOW_COPY_AND_ASSIGN(TriangleHelper); > > Is my GCC too new? It only seems to be happening with the wrapping, > this is on Linux. I can post more details if it helps. > _______________________________________________ > 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 From marcus.hanwell at kitware.com Fri Jul 1 15:01:10 2016 From: marcus.hanwell at kitware.com (Marcus D. Hanwell) Date: Fri, 1 Jul 2016 15:01:10 -0400 Subject: [ITK-dev] [ITK] ITK Python wrapping issue with GCC 6.1.1 In-Reply-To: References: Message-ID: Matt, thanks for the confirmation, sorry I didn't spot it in the issue tracker. I will monitor the bug. On Fri, Jul 1, 2016 at 2:54 PM, Matt McCormick wrote: > Hi Marcus, > > Thanks for reporting the issue. Yes, it looks like GCC 6 / wrapping is > having issues. There is now an issue to track this: > > https://issues.itk.org/jira/browse/ITK-3450 > > Thanks, > Matt > > On Fri, Jul 1, 2016 at 2:10 PM, Marcus D. Hanwell > wrote: >> I am trying to compile ITK master (73dd6af) with GCC 6.1.1 and am >> seeing a compile error: >> >> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function ?PyObject* _ >> wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)?: >> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5867:65: error: no matchi >> ng function for call to ?itk::TriangleHelper >::TriangleH >> elper()? >> result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2(); >> ^ >> In file included from /home/marcus/src/ITK/Modules/Core/Common/include/itkLightO >> bject.h:21:0, >> from /home/marcus/src/ITK/Modules/Core/Common/include/itkObject >> .h:31, >> from /home/marcus/src/ITK/Modules/Core/Common/include/itkComman >> d.h:21, >> from Wrapping/Typedefs/itkTriangleHelperSwigInterface.h:3, >> from Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:325 >> 8: >> /home/marcus/src/ITK/Modules/Core/Common/include/itkTriangleHelper.h:88:32: note >> : candidate: itk::TriangleHelper::TriangleHelper(const itk::TriangleHelp >> er&) [with TPoint = itk::Point] >> ITK_DISALLOW_COPY_AND_ASSIGN(TriangleHelper); >> >> Is my GCC too new? It only seems to be happening with the wrapping, >> this is on Linux. I can post more details if it helps. >> _______________________________________________ >> 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 From matt.mccormick at kitware.com Tue Jul 5 14:11:27 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 5 Jul 2016 14:11:27 -0400 Subject: [ITK-dev] Patches for 4.10.1 Message-ID: Hi, Looking to the ITK 4.10.1 bugfix release, the following patches are in the release branch: Bradley Lowekamp (4): COMP: Address VS9 ambiguous std::abs call in Haung calculator COMP: Fix undefined NumericTraits::Zero and One errors with mingw64 BUG: Address itkHDF5ImageIO test failures for mingw64 ENH: Enable CMP0063 New behavior Hans Johnson (1): COMP: Add long long usage for HDF5 Hastings Greer (1): BUG: ITK-3448 Wrap itkQuadEdgeCellTraitsInfo more specifically Matthew McCormick (3): BUG: Fix H5File memory leak in HDF5ImageIO. BUG: Limit WRAP_ITK_MODULES when building externally COMP: Fix wrapping with a space in the Python include path Pierre Barbier de Reuille (1): COMP: Fix function naming error when using FFTWD Simon Rit (1): COMP: remove C++11 compiler warning for CUDA compilations The following patches will be added: BUG: remove lsqr because of license issues ITK 1160 http://review.source.kitware.com/#/c/21296/ BUG: ResampleImageFilter honor isInside output of the transform method http://review.source.kitware.com/#/c/21295/ Are there any others that have been missed? Thanks, Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Jul 7 09:48:48 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 7 Jul 2016 09:48:48 -0400 Subject: [ITK-dev] [ITK] ITK Python wrapping issue with GCC 6.1.1 In-Reply-To: References: Message-ID: Following up, this issue was addressed in this patch: http://review.source.kitware.com/#/c/21311/ which will be included in the 4.10.1 release. On Fri, Jul 1, 2016 at 3:01 PM, Marcus D. Hanwell wrote: > Matt, thanks for the confirmation, sorry I didn't spot it in the issue > tracker. I will monitor the bug. > > On Fri, Jul 1, 2016 at 2:54 PM, Matt McCormick > wrote: >> Hi Marcus, >> >> Thanks for reporting the issue. Yes, it looks like GCC 6 / wrapping is >> having issues. There is now an issue to track this: >> >> https://issues.itk.org/jira/browse/ITK-3450 >> >> Thanks, >> Matt >> >> On Fri, Jul 1, 2016 at 2:10 PM, Marcus D. Hanwell >> wrote: >>> I am trying to compile ITK master (73dd6af) with GCC 6.1.1 and am >>> seeing a compile error: >>> >>> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function ?PyObject* _ >>> wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)?: >>> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5867:65: error: no matchi >>> ng function for call to ?itk::TriangleHelper >::TriangleH >>> elper()? >>> result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2(); >>> ^ >>> In file included from /home/marcus/src/ITK/Modules/Core/Common/include/itkLightO >>> bject.h:21:0, >>> from /home/marcus/src/ITK/Modules/Core/Common/include/itkObject >>> .h:31, >>> from /home/marcus/src/ITK/Modules/Core/Common/include/itkComman >>> d.h:21, >>> from Wrapping/Typedefs/itkTriangleHelperSwigInterface.h:3, >>> from Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:325 >>> 8: >>> /home/marcus/src/ITK/Modules/Core/Common/include/itkTriangleHelper.h:88:32: note >>> : candidate: itk::TriangleHelper::TriangleHelper(const itk::TriangleHelp >>> er&) [with TPoint = itk::Point] >>> ITK_DISALLOW_COPY_AND_ASSIGN(TriangleHelper); >>> >>> Is my GCC too new? It only seems to be happening with the wrapping, >>> this is on Linux. I can post more details if it helps. >>> _______________________________________________ >>> 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 From matt.mccormick at kitware.com Thu Jul 7 09:57:47 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 7 Jul 2016 09:57:47 -0400 Subject: [ITK-dev] LSQR (and related VNL code) Licensing Issues - fix lost In-Reply-To: References: Message-ID: Following up, this issue was addressed in this patch: http://review.source.kitware.com/#/c/21296/ and pushed upstream here: https://github.com/vxl/vxl/pull/337 It will be included in the ITK 4.10.1 release. On Fri, Jul 1, 2016 at 4:45 AM, Tom Vercauteren wrote: > Dear all, > > Sorry for the cross-posting but this refers to an issue linking both ITK and > VNL. > > In 2010, we identified a licensing issue with some code from vnl and at the > time Luis Ibanez fixed it from the ITK side: > https://issues.itk.org/jira/browse/HISTITK-1160 > > Luis notably rewrote the LSQR code: > https://github.com/InsightSoftwareConsortium/ITK/tree/release-3.20/Utilities/vxl/v3p/netlib/linalg > http://svn.na-mic.org/NAMICSandBox/trunk/SparseLinearSolverConversion/C++/ > https://github.com/InsightSoftwareConsortium/ITK/commits/release-3.20/Utilities/vxl/v3p/netlib/linalg > > It seems that this effort was not backported to VXL and was subsequently > lost when moving to ITK 4: > https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/ThirdParty/VNL/src/vxl/v3p/netlib/linalg > > It would be great if someone could look into this (important) licensing > issue. > > For the only purpose of LSQR, I copied the LSQR NAMICSandBox code in a > standalone github repo here: > https://github.com/tvercaut/LSQR-cpp > > I have also added a comment in the ITK and VXL bug trackers: > https://issues.itk.org/jira/browse/HISTITK-1160 > https://github.com/vxl/vxl/issues/332 > > Best wishes, > Tom > > _______________________________________________ > 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 Thu Jul 7 10:01:27 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 7 Jul 2016 14:01:27 +0000 Subject: [ITK-dev] LSQR (and related VNL code) Licensing Issues - fix lost In-Reply-To: References: Message-ID: <09B7458A-8DC2-4616-9038-0068115F14C4@mail.nih.gov> Matt, This patch looks like it is the source of a number of valgrind defects on the ITK dashboard that need to be addressed. https://open.cdash.org/viewDynamicAnalysisFile.php?id=3934294 Brad > On Jul 7, 2016, at 9:57 AM, Matt McCormick wrote: > > Following up, this issue was addressed in this patch: > > http://review.source.kitware.com/#/c/21296/ > > and pushed upstream here: > > https://github.com/vxl/vxl/pull/337 > > It will be included in the ITK 4.10.1 release. > > On Fri, Jul 1, 2016 at 4:45 AM, Tom Vercauteren wrote: >> Dear all, >> >> Sorry for the cross-posting but this refers to an issue linking both ITK and >> VNL. >> >> In 2010, we identified a licensing issue with some code from vnl and at the >> time Luis Ibanez fixed it from the ITK side: >> https://issues.itk.org/jira/browse/HISTITK-1160 >> >> Luis notably rewrote the LSQR code: >> https://github.com/InsightSoftwareConsortium/ITK/tree/release-3.20/Utilities/vxl/v3p/netlib/linalg >> http://svn.na-mic.org/NAMICSandBox/trunk/SparseLinearSolverConversion/C++/ >> https://github.com/InsightSoftwareConsortium/ITK/commits/release-3.20/Utilities/vxl/v3p/netlib/linalg >> >> It seems that this effort was not backported to VXL and was subsequently >> lost when moving to ITK 4: >> https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/ThirdParty/VNL/src/vxl/v3p/netlib/linalg >> >> It would be great if someone could look into this (important) licensing >> issue. >> >> For the only purpose of LSQR, I copied the LSQR NAMICSandBox code in a >> standalone github repo here: >> https://github.com/tvercaut/LSQR-cpp >> >> I have also added a comment in the ITK and VXL bug trackers: >> https://issues.itk.org/jira/browse/HISTITK-1160 >> https://github.com/vxl/vxl/issues/332 >> >> Best wishes, >> Tom >> >> _______________________________________________ >> 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 Jul 7 10:57:16 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 7 Jul 2016 10:57:16 -0400 Subject: [ITK-dev] LSQR (and related VNL code) Licensing Issues - fix lost In-Reply-To: <09B7458A-8DC2-4616-9038-0068115F14C4@mail.nih.gov> References: <09B7458A-8DC2-4616-9038-0068115F14C4@mail.nih.gov> Message-ID: Hi, Yes, these will be fixed in a follow-up patch. Thanks, Matt On Thu, Jul 7, 2016 at 10:01 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Matt, > > This patch looks like it is the source of a number of valgrind defects on the ITK dashboard that need to be addressed. > > https://open.cdash.org/viewDynamicAnalysisFile.php?id=3934294 > > Brad > >> On Jul 7, 2016, at 9:57 AM, Matt McCormick wrote: >> >> Following up, this issue was addressed in this patch: >> >> http://review.source.kitware.com/#/c/21296/ >> >> and pushed upstream here: >> >> https://github.com/vxl/vxl/pull/337 >> >> It will be included in the ITK 4.10.1 release. >> >> On Fri, Jul 1, 2016 at 4:45 AM, Tom Vercauteren wrote: >>> Dear all, >>> >>> Sorry for the cross-posting but this refers to an issue linking both ITK and >>> VNL. >>> >>> In 2010, we identified a licensing issue with some code from vnl and at the >>> time Luis Ibanez fixed it from the ITK side: >>> https://issues.itk.org/jira/browse/HISTITK-1160 >>> >>> Luis notably rewrote the LSQR code: >>> https://github.com/InsightSoftwareConsortium/ITK/tree/release-3.20/Utilities/vxl/v3p/netlib/linalg >>> http://svn.na-mic.org/NAMICSandBox/trunk/SparseLinearSolverConversion/C++/ >>> https://github.com/InsightSoftwareConsortium/ITK/commits/release-3.20/Utilities/vxl/v3p/netlib/linalg >>> >>> It seems that this effort was not backported to VXL and was subsequently >>> lost when moving to ITK 4: >>> https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/ThirdParty/VNL/src/vxl/v3p/netlib/linalg >>> >>> It would be great if someone could look into this (important) licensing >>> issue. >>> >>> For the only purpose of LSQR, I copied the LSQR NAMICSandBox code in a >>> standalone github repo here: >>> https://github.com/tvercaut/LSQR-cpp >>> >>> I have also added a comment in the ITK and VXL bug trackers: >>> https://issues.itk.org/jira/browse/HISTITK-1160 >>> https://github.com/vxl/vxl/issues/332 >>> >>> Best wishes, >>> Tom >>> >>> _______________________________________________ >>> 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 Jul 7 11:50:05 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 7 Jul 2016 11:50:05 -0400 Subject: [ITK-dev] Gerrit robot builds offline Message-ID: Hi, Our Gerrit robot builds will be down for at least one day for infrastructure changes. Matt From blowekamp at mail.nih.gov Fri Jul 8 10:22:53 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Fri, 8 Jul 2016 14:22:53 +0000 Subject: [ITK-dev] lhcp-rh6 turned on shared libraries Message-ID: <6A861DE4-BE9D-41C5-A1B6-E0051E2353A8@mail.nih.gov> Hi, I have gone ahead an turned on BUILC_SHARED_LIBS for the lhcp-rh6 builds. Let us see if the transform dynamic_cast issue occurs any place else. Brad From vladimir.fonov at gmail.com Fri Jul 8 17:58:11 2016 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 8 Jul 2016 17:58:11 -0400 Subject: [ITK-dev] patch to build ITK 3.20.1 with gcc 5.3 Message-ID: <578021F3.3080202@gmail.com> Hello, I recently came across an issue with building old version of itk (3.20.1 ) on Ubuntu 16.04, gcc version 5.3.1 Attached find a patch to fix the error. -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com -------------- next part -------------- A non-text attachment was scrubbed... Name: patch_itkv3_gcc5.patch Type: text/x-patch Size: 1039 bytes Desc: not available URL: From matt.mccormick at kitware.com Sat Jul 9 09:50:43 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sat, 9 Jul 2016 09:50:43 -0400 Subject: [ITK-dev] [ITK] patch to build ITK 3.20.1 with gcc 5.3 In-Reply-To: <578021F3.3080202@gmail.com> References: <578021F3.3080202@gmail.com> Message-ID: Hi Vlad, Thank you! Pushed to the release-3.20 Git branch: https://itk.org/gitweb?p=ITK.git;a=commit;h=529bcc7ddc6f523db52d82e4bb91418da737559b Matt On Fri, Jul 8, 2016 at 5:58 PM, Vladimir S. FONOV wrote: > Hello, > > I recently came across an issue with building old version of itk (3.20.1 ) > on Ubuntu 16.04, gcc version 5.3.1 Attached find a patch to fix the error. > > > -- > Best regards, > > Vladimir S. FONOV ~ vladimir.fonov gmail.com > > _______________________________________________ > 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 > From marcus.hanwell at kitware.com Sun Jul 10 06:38:49 2016 From: marcus.hanwell at kitware.com (Marcus D. Hanwell) Date: Sun, 10 Jul 2016 06:38:49 -0400 Subject: [ITK-dev] [ITK] ITK Python wrapping issue with GCC 6.1.1 In-Reply-To: References: Message-ID: Thanks Matt, everything compiles for me locally, and in my initial testing seems to work well too. On Thu, Jul 7, 2016 at 9:48 AM, Matt McCormick wrote: > Following up, this issue was addressed in this patch: > > http://review.source.kitware.com/#/c/21311/ > > which will be included in the 4.10.1 release. > > On Fri, Jul 1, 2016 at 3:01 PM, Marcus D. Hanwell > wrote: >> Matt, thanks for the confirmation, sorry I didn't spot it in the issue >> tracker. I will monitor the bug. >> >> On Fri, Jul 1, 2016 at 2:54 PM, Matt McCormick >> wrote: >>> Hi Marcus, >>> >>> Thanks for reporting the issue. Yes, it looks like GCC 6 / wrapping is >>> having issues. There is now an issue to track this: >>> >>> https://issues.itk.org/jira/browse/ITK-3450 >>> >>> Thanks, >>> Matt >>> >>> On Fri, Jul 1, 2016 at 2:10 PM, Marcus D. Hanwell >>> wrote: >>>> I am trying to compile ITK master (73dd6af) with GCC 6.1.1 and am >>>> seeing a compile error: >>>> >>>> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function ?PyObject* _ >>>> wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)?: >>>> Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5867:65: error: no matchi >>>> ng function for call to ?itk::TriangleHelper >::TriangleH >>>> elper()? >>>> result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2(); >>>> ^ >>>> In file included from /home/marcus/src/ITK/Modules/Core/Common/include/itkLightO >>>> bject.h:21:0, >>>> from /home/marcus/src/ITK/Modules/Core/Common/include/itkObject >>>> .h:31, >>>> from /home/marcus/src/ITK/Modules/Core/Common/include/itkComman >>>> d.h:21, >>>> from Wrapping/Typedefs/itkTriangleHelperSwigInterface.h:3, >>>> from Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:325 >>>> 8: >>>> /home/marcus/src/ITK/Modules/Core/Common/include/itkTriangleHelper.h:88:32: note >>>> : candidate: itk::TriangleHelper::TriangleHelper(const itk::TriangleHelp >>>> er&) [with TPoint = itk::Point] >>>> ITK_DISALLOW_COPY_AND_ASSIGN(TriangleHelper); >>>> >>>> Is my GCC too new? It only seems to be happening with the wrapping, >>>> this is on Linux. I can post more details if it helps. >>>> _______________________________________________ >>>> 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 From brad at lowekamp.net Wed Jul 13 23:03:40 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Wed, 13 Jul 2016 22:03:40 -0500 Subject: [ITK-dev] SimpleITK 0.10 Release Candidate 1 Message-ID: <3136CBFF-D3A7-456F-80DC-567AE5EA0686@mail.nih.gov> Hello, We are pleased to announce the SimpleITK 0.10 Release Candidate 1 is available! The binaries are available for download from Source Forge: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10rc1/ The latest versions of ?pip? is recommended to install the downloaded binary wheel for Python. Python eggs are not longer being distributed. You are encouraged to checkout SimpleITK?s master branch in the git repository for testing building the source code. Key Improvements: * The R language bindings have received extensive improvements and bug fixes. * Added Image::SetMetaData method * Added LandmarkBasedTransformInitializer * Added MultiLableSTAPLEImageFilter * Default sitk::Show support for Fiji over ImageJ * Moved third-party packages Lua, gtest, virtualenv from source code to Superbuild projects * Added Forbid Download option * Enabled each language wrapping to be an independent project dependent on SimpleITK C++ interface and libraries. * Lua languages bindings now compile as a loadable module * Many CMake build improvements to default configurations * CMake version 3.3 is now required Enjoy! Brad From manuel.grizonnet at cnes.fr Tue Jul 19 06:15:10 2016 From: manuel.grizonnet at cnes.fr (Manuel GRIZONNET) Date: Tue, 19 Jul 2016 12:15:10 +0200 Subject: [ITK-dev] Compilation issue with ITK master branch (related to vcl) Message-ID: <578DFDAE.9060504@cnes.fr> Hi all, I've got a compilation error in the ORFEO ToolBox (which depend on ITK) when I tried to compile the library with ITK master branch. You can see the compilation error ('vcl_config_manual.h' file not found) on OTB dashboard: http://dash.orfeo-toolbox.org/viewBuildError.php?buildid=237391 The compilation failed since around mid-June (ITK master branch is updated once a week on this platform): http://dash.orfeo-toolbox.org/buildSummary.php?buildid=237391 I read that there was ongoing work on vcl but I do not know if the error is related to my configuration of ITK or if recent modifications in VCL changes will imply modifications in OTB. Thanks in advance for your help. Best regards, Manuel -- Manuel GRIZONNET From matt.mccormick at kitware.com Tue Jul 19 13:12:40 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 19 Jul 2016 13:12:40 -0400 Subject: [ITK-dev] [ITK] Compilation issue with ITK master branch (related to vcl) In-Reply-To: <578DFDAE.9060504@cnes.fr> References: <578DFDAE.9060504@cnes.fr> Message-ID: Hi Manuel, Thanks for bringing attention to this. A patch is here: http://review.source.kitware.com/#/c/21345/ and upstream: https://github.com/vxl/vxl/pull/345 HTH, Matt On Tue, Jul 19, 2016 at 6:15 AM, Manuel GRIZONNET wrote: > Hi all, > > I've got a compilation error in the ORFEO ToolBox (which depend on ITK) when > I tried to compile the library with ITK master branch. You can see the > compilation error ('vcl_config_manual.h' file not found) on OTB dashboard: > > http://dash.orfeo-toolbox.org/viewBuildError.php?buildid=237391 > > > The compilation failed since around mid-June (ITK master branch is updated > once a week on this platform): > > http://dash.orfeo-toolbox.org/buildSummary.php?buildid=237391 > > I read that there was ongoing work on vcl but I do not know if the error is > related to my configuration of ITK or if recent modifications in VCL changes > will imply modifications in OTB. > > Thanks in advance for your help. > > Best regards, > > Manuel > > -- > Manuel GRIZONNET > > _______________________________________________ > 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 From blowekamp at mail.nih.gov Wed Jul 20 16:25:09 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 20 Jul 2016 20:25:09 +0000 Subject: [ITK-dev] VCL install issues Message-ID: Hello, I can getting the following missing header error when using and installed ITK from master: [ 37%] Generating src/sitkComplexToPhaseImageFilter.cxx In file included from /tmp/SimpleITK/Code/Explicit/src/sitkExplicitITKImageRegion.cxx:19: In file included from /tmp/SimpleITK/Code/Explicit/include/sitkExplicitITKImageRegion.h:21: In file included from /usr/local/include/ITK-4.11/itkImageRegion.h:31: In file included from /usr/local/include/ITK-4.11/itkRegion.h:31: In file included from /usr/local/include/ITK-4.11/itkObject.h:31: In file included from /usr/local/include/ITK-4.11/itkLightObject.h:25: In file included from /usr/local/include/ITK-4.11/itkAtomicInt.h:38: In file included from /usr/local/include/ITK-4.11/itkConceptChecking.h:32: In file included from /usr/local/include/ITK-4.11/itkNumericTraits.h:51: In file included from /usr/local/include/ITK-4.11/vcl_limits.h:5: /usr/local/include/ITK-4.11/vcl_compiler.h:121:10: fatal error: 'vcl_config_manual.h' file not found #include ^ Here is the DockerFile I was working with: == DockerFile == FROM ubuntu:14.04 RUN \ apt-get update && \ apt-get -y upgrade && \ apt-get install -y build-essential clang git curl swig python-dev RUN \ curl -O https://cmake.org/files/v3.6/cmake-3.6.0-Linux-x86_64.sh && \ umask 022 && echo "y\n" | bash cmake-3.6.0-Linux-x86_64.sh --prefix=/usr/local --exclude-subdir WORKDIR /tmp/ RUN \ git clone https://itk.org/ITK.git && \ cd ITK && \ git checkout master && \ mkdir bld RUN \ cd ITK/bld && \ CC=clang CXX=clang++ cmake \ -DBUILD_SHARED_LIBS:BOOL=ON \ -DUSE_COMPILER_HIDDEN_VISIBILITY:BOOL=OFF \ -DBUILD_TESTING:BOOL=OFF \ -DModule_ITKReview:BOOL=ON \ .. && \ make -j $(nproc) install && \ ldconfig RUN \ git clone https://itk.org/SimpleITK.git && \ cd SimpleITK && \ git checkout master && \ mkdir bld RUN \ cd SimpleITK/bld && \ CC=clang CXX=clang++ cmake \ -DBUILD_SHARED_LIBS:BOOL=ON \ -DWRAP_LUA:BOOL=OFF \ -DWRAP_PYTHON:BOOL=ON \ -DUSE_SYSTEM_SWIG:BOOL=ON \ -DUSE_SYSTEM_ITK:BOOL=ON \ -DBUILD_TESTING:BOOL=OFF \ ../SuperBuild && \ make -j $(nproc) == end == Thanks, Brad -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Jul 21 13:15:04 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 21 Jul 2016 13:15:04 -0400 Subject: [ITK-dev] VCL install issues In-Reply-To: References: Message-ID: Hi Brad, This patch should address those issues. http://review.source.kitware.com/#/c/21345/ HTH, Matt On Wed, Jul 20, 2016 at 4:25 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Hello, > > I can getting the following missing header error when using and installed > ITK from master: > > [ 37%] Generating src/sitkComplexToPhaseImageFilter.cxx > In file included from > /tmp/SimpleITK/Code/Explicit/src/sitkExplicitITKImageRegion.cxx:19: > In file included from > /tmp/SimpleITK/Code/Explicit/include/sitkExplicitITKImageRegion.h:21: > In file included from /usr/local/include/ITK-4.11/itkImageRegion.h:31: > In file included from /usr/local/include/ITK-4.11/itkRegion.h:31: > In file included from /usr/local/include/ITK-4.11/itkObject.h:31: > In file included from /usr/local/include/ITK-4.11/itkLightObject.h:25: > In file included from /usr/local/include/ITK-4.11/itkAtomicInt.h:38: > In file included from /usr/local/include/ITK-4.11/itkConceptChecking.h:32: > In file included from /usr/local/include/ITK-4.11/itkNumericTraits.h:51: > In file included from /usr/local/include/ITK-4.11/vcl_limits.h:5: > /usr/local/include/ITK-4.11/vcl_compiler.h:121:10: fatal error: > 'vcl_config_manual.h' file not found > #include > ^ > > Here is the DockerFile I was working with: > > == DockerFile == > > FROM ubuntu:14.04 > > RUN \ > apt-get update && \ > apt-get -y upgrade && \ > apt-get install -y build-essential clang git curl swig python-dev > > RUN \ > curl -O https://cmake.org/files/v3.6/cmake-3.6.0-Linux-x86_64.sh && \ > umask 022 && echo "y\n" | bash cmake-3.6.0-Linux-x86_64.sh > --prefix=/usr/local --exclude-subdir > > WORKDIR /tmp/ > > RUN \ > git clone https://itk.org/ITK.git && \ > cd ITK && \ > git checkout master && \ > mkdir bld > > RUN \ > cd ITK/bld && \ > CC=clang CXX=clang++ cmake \ > -DBUILD_SHARED_LIBS:BOOL=ON \ > -DUSE_COMPILER_HIDDEN_VISIBILITY:BOOL=OFF \ > -DBUILD_TESTING:BOOL=OFF \ > -DModule_ITKReview:BOOL=ON \ > .. && \ > make -j $(nproc) install && \ > ldconfig > > > > RUN \ > git clone https://itk.org/SimpleITK.git && \ > cd SimpleITK && \ > git checkout master && \ > mkdir bld > > RUN \ > cd SimpleITK/bld && \ > CC=clang CXX=clang++ cmake \ > -DBUILD_SHARED_LIBS:BOOL=ON \ > -DWRAP_LUA:BOOL=OFF \ > -DWRAP_PYTHON:BOOL=ON \ > -DUSE_SYSTEM_SWIG:BOOL=ON \ > -DUSE_SYSTEM_ITK:BOOL=ON \ > -DBUILD_TESTING:BOOL=OFF \ > ../SuperBuild && \ > make -j $(nproc) > > == end == > > Thanks, > Brad > > > _______________________________________________ > 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 dzenanz at gmail.com Fri Jul 22 09:00:42 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 22 Jul 2016 09:00:42 -0400 Subject: [ITK-dev] c:\.git\hooks Message-ID: Hi everybody, occasionally, a folder "C:\.git\hooks" appears on my computer. Since I use TortoiseGit, this is very annoying because right-click context menu of entire C: drive thinks it is under version control. I filed a bug report, but support people think that git hooks in some of my projects (almost all instances of ITK, VTK and Slicer builds) are causing this behavior. Did anyone else encounter this or something similar? Regards, D?enan -------------- next part -------------- An HTML attachment was scrubbed... URL: From brad.king at kitware.com Fri Jul 22 09:14:25 2016 From: brad.king at kitware.com (Brad King) Date: Fri, 22 Jul 2016 09:14:25 -0400 Subject: [ITK-dev] c:\.git\hooks In-Reply-To: References: Message-ID: On 07/22/2016 09:00 AM, D?enan Zuki? wrote: > occasionally, a folder "C:\.git\hooks" appears on my computer. [snip] > but support people think that git hooks in some of my projects > (almost all instances of ITK, VTK and Slicer builds) are causing > this behavior. Did anyone else encounter this or something similar? Dig through our Utilities/SetupForDevelopment.sh scripts (or equivalent in each project) and the scripts it invokes. See if running any of them causes this to happen. Otherwise check whether running CMake on each project causes it in case there is any attempt to install hooks that way. You'll likely have to diligently check for the folder after each step of working with each project until you figure out which one causes it. -Brad From blowekamp at mail.nih.gov Fri Jul 22 09:31:01 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Fri, 22 Jul 2016 13:31:01 +0000 Subject: [ITK-dev] Use Vcvarsall.bat in CTest script Message-ID: <7134C252-2E7D-469E-BAD4-3EDC8EEA33F0@mail.nih.gov> Hello, I am finally wanting to start using ninja with some of my windows builds. It seems the critical thing is to invoke the appropriate Vcvarsall.bat file before the cmake configuration. Currently I am just using a ctest script with ctest_run_script to drive my dashboard nightly dashboard scripts. How can I invoke the bat file and then get a ctest command in a sub-process? Currently I have something like this: foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS ) message( "Starting to execute script: ${NEXT_SCRIPT}..." ) ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} ) endforeach() And I want something like the following so that the NEXT_SCRIPT with have the correct environment: foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS ) message( "Starting to execute script: ${NEXT_SCRIPT}...? ) NEW PROCESS RUN Vcvarsall.bat ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} ) endforeach() My googling skills are not finding a solution that is as simple as I would expect it to be. Thank you for the help with this simple question! Brad From jchris.fillionr at kitware.com Fri Jul 22 14:17:37 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Fri, 22 Jul 2016 14:17:37 -0400 Subject: [ITK-dev] Use Vcvarsall.bat in CTest script In-Reply-To: <7134C252-2E7D-469E-BAD4-3EDC8EEA33F0@mail.nih.gov> References: <7134C252-2E7D-469E-BAD4-3EDC8EEA33F0@mail.nih.gov> Message-ID: Hi Brad, If you create a .bat file like the following, it should work as expected: call "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\bin\vcvarsx86_amd64.bat" call "C:\path\to\ctest.exe -S C:\path\to\script" Hth Jc On Fri, Jul 22, 2016 at 9:31 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov> wrote: > Hello, > > I am finally wanting to start using ninja with some of my windows builds. > It seems the critical thing is to invoke the appropriate Vcvarsall.bat file > before the cmake configuration. > > Currently I am just using a ctest script with ctest_run_script to drive > my dashboard nightly dashboard scripts. How can I invoke the bat file and > then get a ctest command in a sub-process? > > Currently I have something like this: > > foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS ) > message( "Starting to execute script: ${NEXT_SCRIPT}..." ) > ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} ) > endforeach() > > And I want something like the following so that the NEXT_SCRIPT with have > the correct environment: > > foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS ) > message( "Starting to execute script: ${NEXT_SCRIPT}...? ) > NEW PROCESS > RUN Vcvarsall.bat > ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} ) > endforeach() > > > > My googling skills are not finding a solution that is as simple as I would > expect it to be. > > Thank you for the help with this simple question! > Brad > > > _______________________________________________ > 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 > -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Fri Jul 22 15:07:18 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Fri, 22 Jul 2016 19:07:18 +0000 Subject: [ITK-dev] Use Vcvarsall.bat in CTest script In-Reply-To: References: <7134C252-2E7D-469E-BAD4-3EDC8EEA33F0@mail.nih.gov> Message-ID: <31FA8F28-9C6F-47C2-91CC-A257ABA14B4A@mail.nih.gov> Generating that bat file on the fly would not be too bad. I am imagining adding something like the following line to the beginning of the nightly ctest scripts: # BAT: "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\bin\vcvarsx86_amd64.bat" Which tells my script to generate your suggested bat file. Thanks JC! On Jul 22, 2016, at 2:17 PM, Jean-Christophe Fillion-Robin > wrote: Hi Brad, If you create a .bat file like the following, it should work as expected: call "C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\bin\vcvarsx86_amd64.bat" call "C:\path\to\ctest.exe -S C:\path\to\script" Hth Jc On Fri, Jul 22, 2016 at 9:31 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] > wrote: Hello, I am finally wanting to start using ninja with some of my windows builds. It seems the critical thing is to invoke the appropriate Vcvarsall.bat file before the cmake configuration. Currently I am just using a ctest script with ctest_run_script to drive my dashboard nightly dashboard scripts. How can I invoke the bat file and then get a ctest command in a sub-process? Currently I have something like this: foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS ) message( "Starting to execute script: ${NEXT_SCRIPT}..." ) ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} ) endforeach() And I want something like the following so that the NEXT_SCRIPT with have the correct environment: foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS ) message( "Starting to execute script: ${NEXT_SCRIPT}...? ) NEW PROCESS RUN Vcvarsall.bat ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} ) endforeach() My googling skills are not finding a solution that is as simple as I would expect it to be. Thank you for the help with this simple question! Brad _______________________________________________ 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 -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jchris.fillionr at kitware.com Fri Jul 22 16:17:43 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Fri, 22 Jul 2016 16:17:43 -0400 Subject: [ITK-dev] Use Vcvarsall.bat in CTest script In-Reply-To: <31FA8F28-9C6F-47C2-91CC-A257ABA14B4A@mail.nih.gov> References: <7134C252-2E7D-469E-BAD4-3EDC8EEA33F0@mail.nih.gov> <31FA8F28-9C6F-47C2-91CC-A257ABA14B4A@mail.nih.gov> Message-ID: Or you could also have a .bat file that would take two params: * path to vcvars batch file * command invoking ctest You could then invoke cmd.exe using execute_process and give the bat file + arguments Jc On Fri, Jul 22, 2016 at 3:07 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov> wrote: > Generating that bat file on the fly would not be too bad. > > I am imagining adding something like the following line to the beginning > of the nightly ctest scripts: > > # BAT: "C:\Program Files (x86)\Microsoft Visual Studio > 9.0\VC\bin\vcvarsx86_amd64.bat" > > Which tells my script to generate your suggested bat file. > > > Thanks JC! > > > > On Jul 22, 2016, at 2:17 PM, Jean-Christophe Fillion-Robin < > jchris.fillionr at kitware.com> wrote: > > Hi Brad, > > If you create a .bat file like the following, it should work as expected: > > call "C:\Program Files (x86)\Microsoft Visual Studio > 9.0\VC\bin\vcvarsx86_amd64.bat" > > call "C:\path\to\ctest.exe -S C:\path\to\script" > > Hth > Jc > > On Fri, Jul 22, 2016 at 9:31 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] < > blowekamp at mail.nih.gov> wrote: > >> Hello, >> >> I am finally wanting to start using ninja with some of my windows builds. >> It seems the critical thing is to invoke the appropriate Vcvarsall.bat file >> before the cmake configuration. >> >> Currently I am just using a ctest script with ctest_run_script to drive >> my dashboard nightly dashboard scripts. How can I invoke the bat file and >> then get a ctest command in a sub-process? >> >> Currently I have something like this: >> >> foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS ) >> message( "Starting to execute script: ${NEXT_SCRIPT}..." ) >> ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} ) >> endforeach() >> >> And I want something like the following so that the NEXT_SCRIPT with have >> the correct environment: >> >> foreach( NEXT_SCRIPT IN LISTS MORE_CTEST_SCRIPTS ) >> message( "Starting to execute script: ${NEXT_SCRIPT}...? ) >> NEW PROCESS >> RUN Vcvarsall.bat >> ctest_run_script( NEW_PROCESS ${NEXT_SCRIPT} ) >> endforeach() >> >> >> >> My googling skills are not finding a solution that is as simple as I >> would expect it to be. >> >> Thank you for the help with this simple question! >> Brad >> >> >> _______________________________________________ >> 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 >> > > > > -- > +1 919 869 8849 > > > -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Jul 25 11:31:53 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 25 Jul 2016 11:31:53 -0400 Subject: [ITK-dev] c:\.git\hooks In-Reply-To: References: Message-ID: I ran all the SetupForDevelopment scripts in ITK git folder. The C:/.git folder was not created. Thanks for suggestion though. This problem is not annoying enough because it is easy to solve by deleting C:/.git folder. I will not spend more time randomly examining everything git-related. If somebody else comes forward with the same problem then we might be able to determine what we have in common and narrow down the problem to perhaps make it reasonably tractable. So if anyone runs into this, don't be shy! On Fri, Jul 22, 2016 at 9:14 AM, Brad King wrote: > On 07/22/2016 09:00 AM, D?enan Zuki? wrote: > > occasionally, a folder "C:\.git\hooks" appears on my computer. > [snip] > > but support people think that git hooks in some of my projects > > (almost all instances of ITK, VTK and Slicer builds) are causing > > this behavior. Did anyone else encounter this or something similar? > > Dig through our Utilities/SetupForDevelopment.sh scripts (or equivalent > in each project) and the scripts it invokes. See if running any of > them causes this to happen. Otherwise check whether running CMake on > each project causes it in case there is any attempt to install hooks > that way. > > You'll likely have to diligently check for the folder after each step > of working with each project until you figure out which one causes it. > > -Brad > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Jul 26 23:28:36 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 27 Jul 2016 03:28:36 +0000 Subject: [ITK-dev] SimpleITK 0.10 Release Candidate 2 Message-ID: Hi! We are pleased to announce the SimpleITK 0.10 Release Candidate 2 is now available! The release is expected to follow shortly. There have been many improvements to better support wrapping for R. SimpleITK for R needs to be compiled from the source. The Python Java and CSharp binaries are available for download from Source Forge: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10rc2/ The latest versions of ?pip? is recommended to install the downloaded binary wheel for Python. Python eggs are no longer being distributed. You are encouraged to checkout SimpleITK?s master branch in the git repository for testing building from the source code. Also we have packages for the Anaconda Python distributions in the SimpleITK group and under the ?dev" label. These packages can be installed with the following command: $ conda install -c https://conda.anaconda.org/simpleitk/label/dev SimpleITK Since the 0.10rc1, there have been a number of configuration and fixes to support gcc 6.1. Additionally, new examples and updated documentation. Please see the git long for further information Key Improvements since 0.9.1: * The R language bindings have received extensive improvements and bug fixes. * Added Image::SetMetaData method * Added LandmarkBasedTransformInitializer * Added MultiLableSTAPLEImageFilter * Default sitk::Show support for Fiji over ImageJ * Moved third-party packages Lua, gtest, virtualenv from source code to Superbuild projects * Added Forbid Download option * Enabled each language wrapping to be an independent project dependent on SimpleITK C++ interface and libraries. * Lua languages bindings now compile as a loadable module * Many CMake build improvements to default configurations * CMake version 3.3 is now required Enjoy! Brad From blowekamp at mail.nih.gov Fri Jul 29 14:43:59 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Fri, 29 Jul 2016 18:43:59 +0000 Subject: [ITK-dev] [ANNOUNCE] SimpleITK 0.10.0 Release Message-ID: <660C990B-C30F-47FC-928F-B9176B2C9CBD@mail.nih.gov> We are pleased to announce the release of SimpleITK 0.10.0! As with all SimpleITK releases, we have a variety of binaries available. This includes fresh Python Wheels for MS Windows, GNU Linux and Apple OS X, along with Java and CSharp binaries for MS Windows. Additionally, binaries for the Python distribution Anaconda are available. This release features major improvements to the build infrastructure, improved support for R, better downloads with pip and many new features! Information on how to get started and download the binaries: https://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries Binary distributions for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/ Release Doxygen Documentation: https://www.itk.org/SimpleITKDoxygen010/html/index.html Additional Release Notes: http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.10.0_Release Key Improvements * The R language bindings have received extensive improvements and bug fixes. * Added Image::SetMetaData method * Added LandmarkBasedTransformInitializer * Added MultiLableSTAPLEImageFilter * Show now prefers Fiji over the basic ImageJ * Refactored Wrapping directory into separate languages (paths have changed!) * Separated Lua, GTest, and virtualenv into SuperBuild dependencies * Added SITK_FORBID_DOWNLOADS option * Enabled each language wrapping to be an independent project dependent on the SimpleITK C++ interface and libraries. * Many CMake build improvements to default configurations such as visibility, and link library interfaces * Support for gcc 6.1 and compatibility with c++14 * CMake version 3.3 is now required Python * Update your pip version! * Added manylinux1 wheels (PEP 513) * SimpleITK_PYTHON_THREADS enabled by default to better support multi-threading in Python * No egg binary distributions, wheels fully support the standard platforms * Python 2.7 is no longer packaged for 64-bit windows * Avoid linking against libpython.so to improve compatibility and portability Lua * Lua languages bindings now compile as a loadable module * Created Lua rockspec builder (https://github.com/SimpleITK/SimpleITKLuaRock) * Can be used in Lua Torch R * Fix issues with the bracket operator preserving physical location * Created script to generate R man pages * Disabled return Self value from functions * Create simplified R Installer (https://github.com/SimpleITK/SimpleITKRInstaller) Enjoy! Brad