From matt.mccormick at kitware.com Fri Jul 3 12:37:31 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 3 Jul 2015 12:37:31 -0400 Subject: [ITK-dev] ITK repository feature freeze lifted Message-ID: Hi, The ITK repository has been tagged with v4.8.0, and we are on our way to 4.9! :-) Merge on! Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From wumengda at gmail.com Sun Jul 5 21:24:45 2015 From: wumengda at gmail.com (Wei Xiong) Date: Mon, 6 Jul 2015 03:24:45 +0200 Subject: [ITK-dev] from: Wei Xiong Message-ID: <6FA0C931-4595-4D4C-B842-0A7974916CDE@pcbox.it> Sup insight http://yourleads.info/presence.php?rule=r8z6hywyw1hu7s Wei Xiong Sent from my iPhone From bill.lorensen at gmail.com Mon Jul 6 07:52:20 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 6 Jul 2015 07:52:20 -0400 Subject: [ITK-dev] Compile errors in wiki and sphinx examples after recent changes Message-ID: Folks, Something in this commit https://open.cdash.org/viewChanges.php?project=Insight&date=2015-07-04 is causing these errors: https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887517 and https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887806 Bill -- Unpaid intern in BillsBasement at noware dot com From hans-johnson at uiowa.edu Mon Jul 6 08:46:33 2015 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Mon, 6 Jul 2015 12:46:33 +0000 Subject: [ITK-dev] Compile errors in wiki and sphinx examples after recent changes In-Reply-To: References: Message-ID: Bill, The problem is almost certainly that the variable ?parameters? is of type ?ParametersType? rather than ?FixedParametersType?. // The ITK_FIXED_PARAMETERS_ARE_DOUBLE is intended // to facilitate transition of ITK for those very // rare cases where multiple versions of ITK // may need to be supported simultaneously. #if defined( ITK_LEGACY_REMOVE ) #undef ITK_FIXED_PARAMETERS_ARE_DOUBLE #else #define ITK_FIXED_PARAMETERS_ARE_DOUBLE // #if !defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // typedef ParametersValueType FixedParametersValueType; // #endif #endif Hans On Jul 6, 2015, at 6:52 AM, Bill Lorensen > wrote: Folks, Something in this commit https://open.cdash.org/viewChanges.php?project=Insight&date=2015-07-04 is causing these errors: https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887517 and https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887806 Bill -- Unpaid intern in BillsBasement at noware dot 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 ________________________________ 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 bill.lorensen at gmail.com Mon Jul 6 16:23:50 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 6 Jul 2015 16:23:50 -0400 Subject: [ITK-dev] Compile errors in wiki and sphinx examples after recent changes In-Reply-To: References: Message-ID: Hans, That was the problem. Just a surprise for me. Bill On Mon, Jul 6, 2015 at 8:46 AM, Johnson, Hans J wrote: > Bill, > > The problem is almost certainly that the variable ?parameters? is of type > ?ParametersType? rather than ?FixedParametersType?. > > // The ITK_FIXED_PARAMETERS_ARE_DOUBLE is intended > // to facilitate transition of ITK for those very > // rare cases where multiple versions of ITK > // may need to be supported simultaneously. > #if defined( ITK_LEGACY_REMOVE ) > #undef ITK_FIXED_PARAMETERS_ARE_DOUBLE > #else > #define ITK_FIXED_PARAMETERS_ARE_DOUBLE > // #if !defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) > // typedef ParametersValueType FixedParametersValueType; > // #endif > #endif > > > Hans > > > > On Jul 6, 2015, at 6:52 AM, Bill Lorensen wrote: > > Folks, > > Something in this commit > > https://open.cdash.org/viewChanges.php?project=Insight&date=2015-07-04 > > is causing these errors: > > https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887517 > > and > > https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887806 > > Bill > -- > Unpaid intern in BillsBasement at noware dot 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 > > > > > ________________________________ > 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. > ________________________________ -- Unpaid intern in BillsBasement at noware dot com From bill.lorensen at gmail.com Tue Jul 7 08:48:35 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 7 Jul 2015 08:48:35 -0400 Subject: [ITK-dev] Compile errors in wiki and sphinx examples after recent changes In-Reply-To: References: Message-ID: Hans, There is a problem with the change. My code will no longer build with older versions of ITK. I get: ITKWikiExamplesNightly/Utilities/FileOutputWindow.cxx:23: error: 'FixedParametersType' is not a member of 'main(int, char**)::TransformType' This is not good, unless I'm noising something... On Mon, Jul 6, 2015 at 4:23 PM, Bill Lorensen wrote: > Hans, > > That was the problem. Just a surprise for me. > > Bill > > > On Mon, Jul 6, 2015 at 8:46 AM, Johnson, Hans J wrote: >> Bill, >> >> The problem is almost certainly that the variable ?parameters? is of type >> ?ParametersType? rather than ?FixedParametersType?. >> >> // The ITK_FIXED_PARAMETERS_ARE_DOUBLE is intended >> // to facilitate transition of ITK for those very >> // rare cases where multiple versions of ITK >> // may need to be supported simultaneously. >> #if defined( ITK_LEGACY_REMOVE ) >> #undef ITK_FIXED_PARAMETERS_ARE_DOUBLE >> #else >> #define ITK_FIXED_PARAMETERS_ARE_DOUBLE >> // #if !defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) >> // typedef ParametersValueType FixedParametersValueType; >> // #endif >> #endif >> >> >> Hans >> >> >> >> On Jul 6, 2015, at 6:52 AM, Bill Lorensen wrote: >> >> Folks, >> >> Something in this commit >> >> https://open.cdash.org/viewChanges.php?project=Insight&date=2015-07-04 >> >> is causing these errors: >> >> https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887517 >> >> and >> >> https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887806 >> >> Bill >> -- >> Unpaid intern in BillsBasement at noware dot 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 >> >> >> >> >> ________________________________ >> 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. >> ________________________________ > > > > -- > Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com From hans-johnson at uiowa.edu Tue Jul 7 09:34:09 2015 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Tue, 7 Jul 2015 13:34:09 +0000 Subject: [ITK-dev] Compile errors in wiki and sphinx examples after recent changes In-Reply-To: References: Message-ID: Bill, After several T-Con discussions and e-mails, it was determined that there was no way to preserve backwards and forwards compatibility for fixing this bug. Here is the solution that is inplace for ANTs and Slicer (NOTE BRAINSTools, DTIPrep, DTIProcess, DTIReg, UKFTractography, SimpleITK, and many other tools needed no modifications). #if defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // After 4.8.1 typename BSplineTransformType::FixedParametersValueType transformFixedParamsItk; #else //Pre 4.8.1 typename BSplineTransformType::ParametersType transformFixedParamsItk; #endif Hans ======================================================================== Hans J. Johnson, Ph.D., Associate Professor Electrical and Computer Engineering (Primary), Biomedical Engineering, Psychiatry hans-johnson at uiowa.edu (319) 621 7185 (cell) (319) 384 3538 ECE Phone (Primary) (319) 353 8587 Psychiatry Phone (Secondary) 4316 Seamans Center Iowa City, IA 52242 On Jul 7, 2015, at 7:48 AM, Bill Lorensen > wrote: Hans, There is a problem with the change. My code will no longer build with older versions of ITK. I get: ITKWikiExamplesNightly/Utilities/FileOutputWindow.cxx:23: error: 'FixedParametersType' is not a member of 'main(int, char**)::TransformType' This is not good, unless I'm noising something... On Mon, Jul 6, 2015 at 4:23 PM, Bill Lorensen > wrote: Hans, That was the problem. Just a surprise for me. Bill On Mon, Jul 6, 2015 at 8:46 AM, Johnson, Hans J > wrote: Bill, The problem is almost certainly that the variable ?parameters? is of type ?ParametersType? rather than ?FixedParametersType?. // The ITK_FIXED_PARAMETERS_ARE_DOUBLE is intended // to facilitate transition of ITK for those very // rare cases where multiple versions of ITK // may need to be supported simultaneously. #if defined( ITK_LEGACY_REMOVE ) #undef ITK_FIXED_PARAMETERS_ARE_DOUBLE #else #define ITK_FIXED_PARAMETERS_ARE_DOUBLE // #if !defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // typedef ParametersValueType FixedParametersValueType; // #endif #endif Hans On Jul 6, 2015, at 6:52 AM, Bill Lorensen > wrote: Folks, Something in this commit https://open.cdash.org/viewChanges.php?project=Insight&date=2015-07-04 is causing these errors: https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887517 and https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887806 Bill -- Unpaid intern in BillsBasement at noware dot 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 ________________________________ 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. ________________________________ -- Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com ________________________________ 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 bill.lorensen at gmail.com Tue Jul 7 10:17:14 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 7 Jul 2015 10:17:14 -0400 Subject: [ITK-dev] Compile errors in wiki and sphinx examples after recent changes In-Reply-To: References: Message-ID: Thanks. Works for me. Is this documented in the migration guide or somewhere else? Bill On Tue, Jul 7, 2015 at 9:34 AM, Johnson, Hans J wrote: > Bill, > > After several T-Con discussions and e-mails, it was determined that there > was no way to preserve backwards and forwards compatibility for fixing this > bug. > > Here is the solution that is inplace for ANTs and Slicer (NOTE BRAINSTools, > DTIPrep, DTIProcess, DTIReg, UKFTractography, SimpleITK, and many other > tools needed no modifications). > > #if defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // After 4.8.1 > typename BSplineTransformType::FixedParametersValueType > transformFixedParamsItk; > #else //Pre 4.8.1 > typename BSplineTransformType::ParametersType transformFixedParamsItk; > #endif > > Hans > > ======================================================================== > Hans J. Johnson, Ph.D., Associate Professor > Electrical and Computer Engineering (Primary), Biomedical Engineering, > Psychiatry > hans-johnson at uiowa.edu > (319) 621 7185 (cell) > (319) 384 3538 ECE Phone (Primary) > (319) 353 8587 Psychiatry Phone (Secondary) > > 4316 Seamans Center > Iowa City, IA 52242 > > On Jul 7, 2015, at 7:48 AM, Bill Lorensen wrote: > > Hans, > > There is a problem with the change. My code will no longer build with > older versions of ITK. > I get: > > ITKWikiExamplesNightly/Utilities/FileOutputWindow.cxx:23: error: > 'FixedParametersType' is not a member of 'main(int, > char**)::TransformType' > > This is not good, unless I'm noising something... > > On Mon, Jul 6, 2015 at 4:23 PM, Bill Lorensen > wrote: > > Hans, > > That was the problem. Just a surprise for me. > > Bill > > > On Mon, Jul 6, 2015 at 8:46 AM, Johnson, Hans J > wrote: > > Bill, > > The problem is almost certainly that the variable ?parameters? is of type > ?ParametersType? rather than ?FixedParametersType?. > > // The ITK_FIXED_PARAMETERS_ARE_DOUBLE is intended > // to facilitate transition of ITK for those very > // rare cases where multiple versions of ITK > // may need to be supported simultaneously. > #if defined( ITK_LEGACY_REMOVE ) > #undef ITK_FIXED_PARAMETERS_ARE_DOUBLE > #else > #define ITK_FIXED_PARAMETERS_ARE_DOUBLE > // #if !defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) > // typedef ParametersValueType FixedParametersValueType; > // #endif > #endif > > > Hans > > > > On Jul 6, 2015, at 6:52 AM, Bill Lorensen wrote: > > Folks, > > Something in this commit > > https://open.cdash.org/viewChanges.php?project=Insight&date=2015-07-04 > > is causing these errors: > > https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887517 > > and > > https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887806 > > Bill > -- > Unpaid intern in BillsBasement at noware dot 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 > > > > > ________________________________ > 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. > ________________________________ > > > > > -- > Unpaid intern in BillsBasement at noware dot com > > > > > -- > Unpaid intern in BillsBasement at noware dot com > > > > > ________________________________ > 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. > ________________________________ -- Unpaid intern in BillsBasement at noware dot com From matt.mccormick at kitware.com Tue Jul 7 10:20:14 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Jul 2015 10:20:14 -0400 Subject: [ITK-dev] [ANNOUNCE] ITK 4.8.0 has been released! Message-ID: On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.8.0 has been released! Links to the Sourceforge.net tarballs can be found on the download page: http://www.itk.org/ITK/resources/software.html Outline ---------- 1. Introduction 2. New Features 3. ITK Changelog 4. ITK Sphinx Examples Changelog 5. ITK Software Guide Changelog 6. ITK Apps Changelog Introduction ----------------- The 4.8 release offers substantial benefits to the medical and scientific imaging community by making the toolkit more accessible to non-C++ programmers and by providing greater availability on mobile, high-performance computing (HPC), and web-browser platforms. A few selected highlights for this release are: - New remote modules: BridgeNumPy, LabelErodeDilate, ParabolicMorphology, MinimalPathExtraction - itk::FFTPadImageFilter to automatically pad images for the FFT implementation?s supported greatest prime factor - Additional point set registration capabilities. - More modules can be built as shared libraries. - GDCM, MetaIO, KWSys,and MINC have been updated to their latest upstream versions. - Python wrapping is in excellent shape and works with the latest GCC, Clang, and MSVC. - Experimental cross-compilation support for Windows (MinGW-w64), ARMv6 (Raspberry Pi), ARMv7 (Android), ppc64le (POWER8), and JavaScript (Emscripten). This release is a major milestone that marks the hard work of many outstanding community members. Congratulations and well done to the 31 contributors to this release. We would especially like to recognize the new contributors, David Froger, Cyril Mory, Dzenan Zukic, Ivan Setiawan, Jan Bergmeier, Rolf Eike Beer, Davis Vigneault, Gary Jia, and Alexander Hewer. Testing data is available separately from the release archives starting with this release. Unpack the ?InsightData? archive in the same directory that the ?InsightToolkit? archive was unpacked to make the archive testing data available to a build. When archive testing data is not present, the BUILD_TESTING CMake configuration option will be off by default. Turn on BUILD_TESTING without the testing data archive to fetch the data via the network automatically. This release introduces CastXML [1], a C-family abstract syntax tree XML output tool based on Clang. This is a more maintainable replacement for GCC-XML that works with the latest Microsoft Visual C++ (MSVC), Clang, and GNU Compiler Collection (GCC) compilers. CastXML generates XML output that is backwards-compatible with GCC-XML output, which is parsed by pygccxml [2] in the wrapping process. Enjoy ITK! [1] https://github.com/CastXML/CastXML [2] https://github.com/gccxml/pygccxml New Features --------------------- * Wrapping improvements - Wrapping now uses CastXML instead of GCCXML - The latest GCC, Clang, and MSVC are fully supported - Details: http://kitware.com/blog/home/post/888 - Cross-compilation and packaging support - Details: http://kitware.com/blog/home/post/904 - ITK_WRAP_VECTOR_COMPONENTS option to specify number of wrapped vector components - More classes wrapped * Compiler Support - GCC 5.1 - Clang 3.6.0 - Better cross-compilation support (requires CMake 3.3) - Experimental support for Emscripten (JavaScript) - Details: http://kitware.com/blog/home/post/912 - Experimental support for the Raspberry Pi - Details: http://kitware.com/blog/home/post/887 - Experimental support for Android - Details: http://kitware.com/blog/home/post/893 - Experimental support for MXE/MinGW-w64 - Details: http://kitware.com/blog/home/post/883 - Experimental support for the POWER8 - Details: http://kitware.com/blog/home/post/891 * New Remote Modules - MinimalPathExtraction - Insight Journal Article: http://hdl.handle.net/1926/1332 - BridgeNumPy - Convert itk.Image to NumPy array?s and back - LabelErodeDilate - Insight Journal Article: http://hdl.handle.net/10380/3399 - ParabolicMorphology - Insight Journal Article: http://hdl.handle.net/1926/1370 * Infrastructure Improvements - An UpdateThirdPartyFromUpstream.sh script for 3rd party updates with Git subtree - Details: http://kitware.com/blog/home/post/899 - Minimum required CMake version is now 2.8.9 - Many more modules can be built as shared libraries - ITK_USE_SYSTEM_LIBRARIES variable during initial configuration to turn on use of common system third party libraries by default - Release testing data tarball split from source tarball - Gold linker used by default on Linux * Filtering Improvements - itk::FFTPadImageFilter to automatically pad images for the FFT implementation?s supported greatest prime factor - itk::AtomicInt class for parallel computation - Various performance enhancements * Registration Improvements - Point set SyN registration - Point set BSpline SyN registration * Documentation Improvements - The ITK Software Guide is now available in HTML - Details: http://kitware.com/blog/home/post/890 - Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples * Third Party Library Updates - GDCM updated to latest upstream - KWSys updated to the latest upstream - MetaIO updated to the latest upstream - MINC updated to the latest upstream * Style improvements -- ITK gets more stylish with every release! * Improved code coverage -- we are at 85.4%! * *Lots* of important bug fixes * And much more! See details in the log below. Changes from v4.8rc03..v4.8.0 ----------------------------------------------- Davis Vigneault (1): COMP: C++11 Warnings in thirdparty PNG module. Matthew McCormick (9): COMP: Fix unused parameter warnings in itkMultiThreaderNoThreads. BUG: Do not output CMake log files in itkSystemInformationTest. COMP: Work around segfaults with VS12 in RegionOfInterestImageFilter. DOC: Update Wiki Examples Remote to June 26, 2015. COMP: Update ParabolicMorphology to address doxygen warning. COMP: Add missing exports in the ITKFEM module. BUG: Use CMAKE_LIBRARY_OUTPUT_DIRECTORY for build tree WrapITK.pth. DOC: Document grafting the input image in composite filters. DOC: Bump SphinxExample remote module version to 2015-07-02. Changes from v4.8rc02..v4.8rc03 ------------------------------------------------ Bradley Lowekamp (3): BUG: Remove reliance on exceptions in StringTools::ToData methods BUG: Fix WriteCellsAsBinary and valgrind defects COMP: Explicitly export SingleValuedNonLinearVnlOptimizerv4 Matthew McCormick (4): COMP: Address may be used uninitialized in IdentityTransformTest. COMP: Address array subscript above bounds in VTKPolyDataReader. COMP: Work around GDCM test segfault with Clang 3.5+. BUG: Do not use pthreads with Emscripten. Michka Popoff (1): ENH: Update PyInit for Python 3 Changes from v4.8rc01..v4.8rc02 ------------------------------------------------ Arnaud Gelas (2): BUG: memory leaks when calling itk::Mesh::Graft BUG: fix memory leaks in BorderQuadEdgeMeshFilter using itk::AutoPointer Bradley Lowekamp (1): Revert selection "ENH: Add shared libraries for ITK libraries" Davis Vigneault (1): STYLE: Minor typographical changes in ParameterizationQuadEdgeMeshFilter D?enan Zuki? (1): DOC: Improve docs for ConnectedComponentImageFilter Hans Johnson (1): STYLE: Use consistent names in template parameters Sean McBride (2): COMP: Update MINC to upstream 85145dca36 BUG: updated MINC to a77da29 Changes from v4.7.0..v4.8rc01 -------------------------------------------- Alexander Hewer (1): COMP: fixed error "Dunno about this gcc" for gcc 5.1 Arnaud Gelas (14): ENH: add MinimalPathExtraction as a remote module ENH: fix KWStyle errors for SubdivisionQuadEdgeMesh COMP: fix warning with non default template parameter for OutputImage COMP: missing ';' in itkSetClampMacro STYLE: no need to expose internal type COMP: fix warning with non default template parameter for OutputImage COMP: fix warning with non default template parameter for OutputImage BUG: fix BinaryImageToLabelMapFilter with negative OutputBackgroundValue DOC: add explanations about input and out filters COMP: missing include in IterativeTriangleCellSubdivision DOC: Improve documentation for ParameterizationQuadEdgeMeshFilter BUG: not all combinations were actually test ENH: add an exception in BorderQuadEdgeMeshFilter if no boundaries COMP: fix CMake warning in ITKModuleHeaderTest Bill Lorensen (7): ENH: Update to KWStyle conformant version ENH: Add interpolate capability ENH: WikiExamples QuickView Update COMP: VTK AUTOINIT redefinition warnings COMP: Only require the minimal VTK modules COMP: Compiler hidden visibility on Mac compiler COMP: EventMacro backward compatibility Brad King (25): COMP: Fix variable reference in ITKVtkGlue module files ENH: ExternalData: Allow local stores without any URL templates ENH: ExternalData: Warn on missing file instead of failing ENH: ExternalData: Add support for custom download scripts ENH: ExternalData: Add support for custom algorithm-to-URL mapping DOC: ExternalData: Update documentation to match CMake copy ENH: Teach UpdateThirdPartyFromUpstream to support spaces in path ENH: Improve UpdateThirdPartyFromUpstream for initial imports ENH: Require CMake 2.8.9 or greater ENH: Do not produce ITKGDCM library when using system GDCM ENH: Drop gdcm source subtree to prepare for fresh import ENH: Add script to update GDCM from upstream STYLE: Tell Git not to check whitespace in GDCM STYLE: Tell Git about larger files in GDCM COMP: Configure GDCM to build inside ITK COMP: Fix GDCM to handle older expat library COMP: Cleanup CMP0022 warnings in GDCM module COMP: Add missing include in GDCM source COMP: Teach GDCM to honor ITK_DYNAMIC_LOADING option ENH: KWSys: Tell Git not to export .gitattributes COMP: Remove cmake_minimum_required calls from GDCM COMP: Remove extra CMake policy settings in GDCM COMP: Use more standard SSE intrinsics in GDCM copy of OpenJPEG COMP: Fix GDCM std::accumulate initial value type ENH: Update version of CastXML built for wrapper generation Bradley Lowekamp (48): PERF: Use ImageAlgorithm::Copy in ImageSeriesWriter BUG: Enable setting all zeroes for fixed parameters for displacement ENH: Refactor versor to matrix transform code DOC: Clarify that Scale Skew Versor does addition COMP: Fix unsafe usage of sprintf BUG: Correct Simularity3D Jacobian BUG: Ensure OptimizerParameters doesn't leak its helper BUG: Fix incorrectly ordering of template parameters COMP: check for search.h in libtiff BUG: restore the center point fixed parameters for scale transforms PERF: Remove frequent dynamic allocations used with std::vector COMP: Use _timezone for Visual Studio BUG: Restore IO support for BSplineDeformableTransform BUG: Enable VectorImage to work with the ImageSeriesWriter BUG: Replace std::cout message Warning marco BUG: Correct ExtractImageFilters Type macro DOC: Separately document IsNull and IsNotNull ENH: Modularize KWStyleTests BUG: Remove ExhaustiveOptimizer ivar which was unused STYLE: Update IOFDF to address KWStyle issues BUG: Fix undefined signed integer shift BUG: Fix IOFDFInDoxygenGroup test BUG: Update MGHImageIO for header guarder style BUG: Fix itkFDFImageIOTest link error on windows STYLE: Update SCIFIO for KWStyke failures BUG: Move LBFGSB callback helper to parent BUG: Use base's NumberOfIterations for stopping condition BUG: Update AmoebaOptimizer NumberOfIterations BUG: Use base's NumberOfIterations for stopping condition PERF: Report progress for linear transform only at scanline completion BUG: Correct convergence string check BUG: Avoid underflow in gradient range calculation ENH: Use return by value for ImageAlgorithm::EnlargeRegionOverBox BUG: No exception for 0 parameter transforms COMP: Address conversion compilation warning ENH: Use PrinSelfObjectMacro BUG: Use module's libraries for linking header test. ENH: Add export specifications to FFT library COMP: Address conversion compilation warning COMP: This patch address linking errors with WrapITK DOC: Improving documentation for the names inputs of the ProcessObject BUG: Isolate CannyEdgeDetection's internal filter from external PERF: Refactor ExpandImageFilter loop ENH: Add AtmoicInt class, use TimeStamp & LightObject COMP: Address signed to unsigned comparison warning in AtomicInt Test ENH: Move IsPrime and GreatestPrimeFactor to compiled cxx file COMP: Add export missing export specifications BUG: Fix reading HDF5 images into different dimension. Brian Helba (2): ENH: Add scripts for automated updating of ThirdParty libraries ENH: Make Vector construction from scalar value explicit Christopher Mullins (12): STYLE: Keep codesnippet lines under 80 characters. STYLE: Fix Latex blocks in documentation to include newlines. COMP: Fix clang warnings DOC: Fix Latex underscore for SoftwareGuide BUG: Return a correct voronoi partition in Danielsson filter example. STYLE: Fix Latex blocks in documentation to include newlines. DOC: Use the dilated version of the FivePoints image COMP: Use c++11 noexcept declarator. COMP: Fix override warnings on clang with GPU module and MINC COMP: Fix clang override warnings for Review module. COMP: Fix more clang warnings in review module COMP: Fix more clang override warnings in Review module. Cyril Mory (3): BUG: Fixed itkWarpImageFilter wrong result in some cases ENH: Method to compute InputRequestedRegion in itkWarpImageFilter ENH: Moved some of itkWarpFilter from private to protected David Froger (2): ENH: Check regions in HDF5 streaming test BUG: Fix HDF5 write streaming test. Davis Vigneault (4): STYLE: Minor style and documentation changes to ITK examples. DOC: Minor changes and clarifications to the registration chapter of Book 2. STYLE: Minor wording and formatting changes to Software Guide Mesh examples. COMP: Build failure using EuclideanDistancePointMetric with mismatched meshes. D?enan Zuki? (4): COMP: VS 2012+ compile fixes and CMake warnings COMP: fixing quote matching in vtkGlue-related .cmake file ENH: adding reverse iteration test ENH: using scanline iterator instead of linear iterator GDCM Upstream (1): GDCM 2015-04-29 (81e551fc) Gary JIA (1): BUG: Fix memory leak at GPUCommon Ga?tan Lehmann (21): BUG: fix extra carriage return in python callbacks ENH: use castxml in wrapping COMP: almost fix java build ENH: use modern cmake list operations in wrapping COMP: hide compiler warnings when building pcre and swig COMP: fix the IOFDF module name used in wrapping COMP: fix last python runtime warnings about unknown types COMP: fix undefined __float128 type with gcc BUG: reactivate PythonGetNameOfClass and fix the FDFImageIOFactory name COMP: fix warnings due to double MultipleValuedCostFunction wrapper BUG: fix ipython custom completion BUG: fix runtime information for cross correlation filters ENH: let the user choose the tradeoff between size and speed in fft operations ENH: update progress in ImageFileReader ENH: initialize the progress in ImageFileWriter BUG: fix extra line return in terminal progress display BUG: fix missing space before "done" in progress display ENH: pass ActualXDimensionIsOdd through the pipeline COMP: fixes for SizeGreatestPrimeFactor ENH: Add itkFFTPadImageFilter ENH: factorize shared code in itk::PadImageFilterBase Gert Wollny (1): COMP: defining ITK_USE_FLOAT_SPACE_PRECISION Hans Johnson (39): COMP: Add c++11 override designation COMP: Identify null pointer assignments STYLE: rm explicit void for parameterless function STYLE: Use ITK_NULLPTR to utilize c++11 features BUG: Incorrect addition of ITK_OVERRIDE COMP: Use STREQUAL instead of MATCH BUG: return type defaults to zero. BUG: ImageType, CofficientImageArray types missing DOC: Invalid doxygen return for void function. COMP: _Pragma suppress fltpnt equality warnings COMP: Allow exact floatpnt equality checks. COMP: Avoid floatpnt equality check COMP: Floatpnt equality for divisor COMP: Avoid unnecessary float pnt equality checks. PERF: Improve perf of ANTSNeighborhoodCorrelation BUG: Test depending on itkMesh.h in Common COMP: Make DCMTK header functions const Revert "COMP: VTK AUTOINIT redefinition warnings" COMP: VTK and ITK H5 build program collision COMP: Create out-of-line virtual method defintions COMP: Create out-of-line virtual method macros DOC: Clarify strange syntax for itk::MetaEvent COMP: Fix ENABLE_SHARED variable name STYLE: Remove outdated cmake version support STYLE: Move SymmetricEigenAnalysis to Deprecated COMP: Prefer modern CMake visibility settings STYLE: Use ITK_NOEXCEPTION macro ENH: Continue to deprecate ::Zero and ::One ENH: Avoid need for const_cast, ensure consistency BUG: Incorrect function signature COMP: Intel compiler warning suppression ENH: Add shared libraries for ITK libraries ENH: Remove unnecessary const_cast STYLE: Move utility TransformIOHelper to cxx file BUG: Missing ITKIOMINC_EXPORT on __Private() STYLE: Fixed AnalyzeObjectMap header guard style. COMP: Missing exports for templates ENH: Update MGHIO for consistency with ITK. BUG: Remove shared specifications from TransformIO Ivan Setiawan (2): BUG: Fix initial ImageTrueMax to the most negative value. BUG: Test case to verify fix of ImageTrueMax in MattesMI. Jan Bergmeier (1): DOC: Changed indices for steps in ExhaustiveOptimizer. Jon Haitz Legarreta (10): ENH: New test for the BinaryStatisticsKeepNObjectsImageFilter ENH: New test for the itkLabelShapeKeepNObjectsImageFilter ENH: Add test for itkShapeRelabelImageFilter ENH: Add test for the itkLabelStatisticsKeepNObjectsImageFilter ENH: Add test for itkBinaryShapeKeepNObjectsImageFilter ENH: Add test for itkLabelStatisticsOpeningImageFilter DOC: Correct documentation typo. ENH: Increase code coverage for itkCustomColormapFunction ENH: Increase code coverage for itkCustomColormapFunction ENH: New test for the itkMetaGaussianConverter Julien Jomier (1): BUG: Output pointer origin is not set causing a memory access error. KWSys Robot (3): KWSys 2015-04-19 (4f39791b) KWSys 2015-05-12 (b1d560a0) KWSys 2015-05-18 (9a6b7c3f) Kevin H. Hobbs (1): COMP: new baseline for building against VTK master Marius Staring (2): BUG: workaround for 64bit VS2013 Release segfaults COMP: workaround for 64bit VS2013 Release ICE Matthew McCormick (160): ENH: Add BridgeNumPy Remote Module. COMP: Bump AnalyzeObjectMapIO to fix doxygen warning. STYLE: Style changes for itkGaussianDerivativeImageFunctionTest. ENH: Test GaussianDerivativeImageFunction with unsigned short. ENH: Bump CMakeLists.txt version to 4.8.0. DOC: Add C++11 macros to doxygen configuration. ENH: Remove FindNUMARRAY.cmake. STYLE: Too many spaces before semi-colon in PCAShapeSignedDistanceFunction. COMP: Bump Wiki Examples revision to fix Doxygen warnings. COMP: Fix ITK_OVERRIDE update DebugMacro build errors. DOC: Updates to GettingStarted.txt. BUG: Remove Testing/Temporary/CTestCostData.txt. ENH: Update doxygen.config for Doxygen 1.8.9.1. ENH: Bump release branch version to 4.7.1. ENH: Bump CMakeLists.txt version to 4.8.0. BUG: Clear TransformIO's list of transforms in TransformFileReader. DOC: Rename duplicate doxygen section. Revert Doxygen version 1.8.9.1 to 1.8.5 config to clean up dashboard DOC: Fix Doxygen override, nullptr, noexcept definitions. DOC: Note that push access is not required to get patches merged. COMP: Fix wrapping runtime warning on unknown itk::Matrix. COMP: Add missing types for MeshTraits wrapping. COMP: Do not wrap the Container types for CellInterface * types. COMP: Add wrapping for CellTraitsInfo. COMP: Wrap missing Mesh templates. DOC: Clean up some wrapping comments. ENH: Add wrapping for ITKImageNoise module. STYLE: Clean up inter-definition space for Image,ImageBase,ProcessObject. ENH: Fetch source tarball external data from midas3.kitware.com. BUG: Fix BridgeNumPy signed / unsigned short correspondance. DOC: Improve ImageScanlineIterator documentation. ENH: Add missing {Set,Get}Element methods to Array2D. BUG: Fix linking SmoothingRecursiveYvvGaussianFilter with install tree. BUG: Add CMake export code for ITK_USE_SYSTEM_GDCM. ENH: Pass CMAKE_GENERATOR to ExternalProject's. ENH: Update LLVM/Clang ExternalProject to 3.6.0. ENH: Update MetaIO License from Upstream. ENH: Bump MetaIO to latest upstream. BUG: Export ITK_FFTW_INCLUDE_PATH as CMake path. COMP: Do not include tests/ directory in clang tarball. ENH: Add Azure Storage as ExternalData source. STYLE: Update SplitComponents module for KWStyle fixes. COMP: Fix LevelSetsv4 tests with libc++. STYLE: Style fixes for LevelSetsv4 and related classes. BUG: Move MagnitudeAndPhaseToComplex filter wrapping to ITKImageIntensity. ENH: Document testModules.sh and move to Utilities/Maintenance BUG: Fix Python tests on Windows with Ninja generator. STYLE: Update IOSTL module for KWStyle test. BUG: Set ITK_BUILD_SHARED in ITKConfig.cmake on Windows. BUG: Suppress wrapping type conversions warnings with MSVC. COMP: Address quoted MSVC variable in GDCM. BUG: WrapITK.pth should contain the lib/ directory with VS. COMP: Suppress swig build configure warning. ENH: Use CMAKE_CROSSCOMPILING_EMULATOR to run HDF5 detection. BUG: Do not use EXECUTABLE_OUTPUT_PATH for vcl tests. BUG: Do not enable floating point exceptions in tests with MinGW. DOC: Update KWStyle location. BUG: Add QuickViewTest baseline for Mac. ENH: MetaIO use UpdateThirdPartyFromUpstream.sh ENH: Arrange MetaIO sources for UpdateThirdPartyFromUpstream.sh. ENH: Add root snapshot commit support to UpdateThirdPartyFromUpstream.sh COMP: Do not try to generate tiff_fax3sm.c when cross compiling. COMP: Android does not currently have posix_memalign. COMP: The Android pwd.h passwd struct does not have a pw_gecos entry. COMP: Android does not have pthread_setcancelstate. COMP: Do not do __errno_location workaround on Android. COMP: Removed unused parameters in itkThreadPoolTest. BUG: Address detection of TransformReadWriteTest as executable. ENH: Set CMP0056 to NEW. COMP: Work around test file too big with x64_64-w64-mingw32. COMP: Increase itkMattesMutualInformationImageToIMageMetricv4Test tolerance. COMP: Address NumericTraits warning related to POWER8 char. BUG: Add new ResampleImageFilter9Test baseline for MinGW. BUG: Add MinGW baseline for VoronoiPartitioningImageFilterTest1. COMP: Fix vnl_sample.cxx for srand48 but no drand48. ENH: Add ITK_DYNAMIC_LOADING CMake option. COMP: Support S_IRUSR and S_IWUSR. COMP: Do not log swig configure output. BUG: NumericTraits< char > does not have Self typedef. ENH: Do not use TestBigEndian from CMAKE_ROOT. COMP: Use sizeof(void *) instead of sizeof(size_t) for address model. COMP: Do not use GCC demangling with emscripten. ENH: Use try_run to determine if double correction required. COMP: Address quoted MSVC variable in GDCM. COMP: Suppress Swig configure output. COMP: Remove duplicate InternalLabelType typedef. COMP: Set CMP0058 to NEW. COMP: Add missing InternalLabelType. BUG: Specify absolute path to double-conversion-configure.h for install. DOC: Clarify the UpdateThirdPartyFromUpstream.sh commit message. BUG: Link to VTK 6 rendering backend modules. COMP: Pass --quiet to swig's configure script. STYLE: Update HigherOrderAccurateGradient module for style fixes. ENH: Mark ITK_DYNAMIC_LOADING as an advanced CMake variable. COMP: Ignore swig-prefix warnings. BUG: GDCM set default ultrasound spacing when not found. COMP: Initialize arrays in itkCurvatureFlowFunction. BUG: Add VTK modules for annotation rendering. BUG: Link vtkRenderingFreeType in the VTK modules. COMP: Add itkIntTypes.h header for SizeValueType in itkVnlFFTCommon.h STYLE: Style fixes for RayCastHelper::CalcRayIntercepts COMP: Run the SWIG configure step in a CMake script. ENH: Bump release branch version to 4.7.2. STYLE: Bump IOFDF module for style and cleanup. BUG: Fix DoxygenInGroup test from .zip release files. COMP: Do not wrap exotic QuadEdgeMesh CellInterface types. COMP: Remove FFTWGlobalConfiguration param doxygen keyword. COMP: Do not reference ::MetaEvent in itkMetaEvent.h docs. DOC: itkSymmetricEigenSystem is now in the ITKDeprecated module. BUG: Fix TestDriver executable for itkSymmetricEigenSystemTest. BUG: Use consistent SizeGreatestPrimeFactor in deconvolution tests. COMP: Use signed char in ImageToImageMetricv4 test. COMP: Do not include itkDynamicLoader in header tests. COMP: Include byteswap.h for Android in GDCM. COMP: Use signal.h instead of sys/signal.h in GDCM. COMP: Not all versions of Android have posix_memalign. COMP: Initialize variable in PointSetToListSampleAdaptorTest. COMP: Suppress getpwnam warning with static executables. COMP: Tighten LandmarkWarping2 lines for Software Guide. ENH: Allow skip of FloatPointExceptions implementation for absent fenv.h. COMP: Define feenableexcept for Emscripten. BUG: HDF5 do not force CMake CheckTypeSize on include. STYLE: Style fixes to itkVideoStream.e COMP: Ignore build warnings for libs unfound by emscripten. BUG: Run HDF5 H5detect in working directory with the executable. BUG: HDF5 use CMAKE_EXECUTABLE_SUFFIX. COMP: Work around Emscripten internal compiler crash in VideoStream. COMP: Use byteswap.h with GDCM with Emscripten. COMP: Recognize Emscripten in socket++. BUG: Remove HDF5's own internal CheckTypeSize.cmake. ENH: Enable cross-compiling of the wrapping. COMP: Missing semi-colon in FFT Hermitian filters. ENH: Add ExternalData_NO_SYMLINKS option. ENH: Mount local filesystem in the test driver for Emscripten. BUG: Do not install wrapping with CMAKE_PREFIX_PATH. ENH: Define CPACK_PACKAGE_CONTACT. ENH: Add post-commit hook for third party library patches. ENH: Pass the CastXML flags directly. STYLE: Rename GCC-XML references to CastXML. ENH: Send an error when CMAKE_CXX_COMPILER_TARGET is not set. ENH: Bump CastXML version for cross-compiling target fix. BUG: Use STRING type for PY_SITE_PACKAGES_PATH. BUG: Continue when IPython.get_ipython throws an AttributeError. ENH: Add ITK_USE_SYSTEM_LIBRARIES STYLE: Fix indentation in ITKSetStandardCompilerFlags.cmake. COMP: Do not enable ITK_HAVE_SYNC_BUILTINS with Emscripten. COMP: Fix MinGW ITK_HAVE_SYNC_BUILTINS detection. ENH: Split testing data tarball form source tarball. COMP: Do not use ITK_NULLPTR as sentinel. ENH: Use gold linker on Linux with GCC. COMP: Add try_compile check for gold linker. COMP: Do not build dsrc2c.c with -fvisibility-inlines-hidden. BUG: Remove shared specifications from IOTransformBase. BUG: Required GCC version for gold linker is 4.8.3. BUG: Fix ITKIOMINCExport.h capitalization. BUG: Add missing include directory required after MINC update. BUG: Bring in IOFDF license updates. COMP: Add missing HDF5 include for MINC. COMP: Add missing HDF5 include directory for ITKIOMINC. COMP: Fix itkVTKImageExport.h header name in VtkGlue.i. MetaIO Maintainers (2): MetaIO 2015-04-12 (b7969294) MetaIO 2015-04-21 (dc4f7d16) Michka Popoff (20): COMP: Use c++ style comments in pyBase.i ENH: Update to swig 3.0.3 STYLE: Cleanup up cmake files (if, endif, foreach, endforeach). ENH: Update to SWIG 3.0.5 COMP: Fix PythonReadDicomTagTest on OS X ENH: Improve wrapping for Vector image types ENH: Cleanup itkComposeImageFilter wrapping ENH: Setup correct wrapping of GradientRecursiveGaussianImageFilter ENH: Add Get/SetSigmaArray to GradientRecursiveGaussianImageFilter ENH: Add checks for base types when wrapping more complex types COMP: Fix DiffeomorphicDemonsRegistration Wrapping STYLE: Rename ITK_WRAP_DIMS to ITK_WRAP_IMAGE_DIMS ENH: Add ITK_WRAP_VECTOR_COMPONENTS option STYLE: Replace GCCXML by CASTXML BUG: Wrap FixedArray sizes also for vector components ENH: Wrap MersenneTwisterRandomVariateGenerator ENH: Wrap CustomColormapFunction ENH: Update to PCRE 8.37 ENH: Enable wrapping of 4 dimensional vectors ENH: Remove inline namespace fix for Wrapping Nick Tustison (10): ENH: Adding point set reg. capabilities for SyN. PERF: Tolerance for testing needs to be increased. BUG: Coverity divide by zero complaint. BUG: Metric evaluation had an incorrect sign. ENH: Making the point set type visible. BUG: Need to check if maxNorm == 0. BUG: Pixel type shouldn't be initialized with scalar. ENH: Cleaning up point set reg. in BSplineSyN ENH: Adding tangent space calculation for SyN methods. BUG: Added sampling only within the specified mask. Niels Dekker (2): BUG: workaround for 64bit VS2013 Release segfault COMP: Fixed MSVC warnings, "warning D9025: overriding '/W1' with '/w'" Richard Beare (3): ENH: LabelErodeDilate as a remote module ENH: remote.cmake for parabolic morphology ENH: Use SHA for LabelErodeDilate module. Rolf Eike Beer (2): STYLE: ExternalData: Replace MATCHES with STREQUAL where possible STYLE: ExternalData: Clean up duplicate regex matches with CMAKE_MATCH_ Sean McBride (12): COMP: Changed KWStyle check for header include guard names COMP: Remove double underscore in header guards (.h & __itk*_h form) COMP: Remove double underscore in header guards (.hxx & __itk*_h form) COMP: Remove double underscore in header guards (.in & __itk*_h form) COMP: Remove remaining double underscore in header guards (__itk form) COMP: Remove unnecessary header guards in .cxx files COMP: Manually search for "__itk" and clean up double underscore usage COMP: fixed clang -Wkeyword-macro warning by removing invalid #undef COMP: Suppress clang -Wdocumentation-unknown-command false positive COMP: properly escape @ char in doxygen comments COMP: Escaped @ character in doxygen comments BUG: updated libminc SHA to newest Ziv Yaniv (1): BUG: Versor initialized with null axis (0,0,0) did not throw exception. ITK Sphinx Examples Changelog ------------------------------------------------- Arnaud Gelas (9): DOC: recommend to use CreateNewExample.py ENH: Add one example for BinaryFillholeImageFilter add one example to illustrate the usage of LabelSelectionLabelMapFilter Apply BinaryMorphologicalClosingFilter on all LabelObjects of given LabelMap Add one example to apply morphological closing on specific LabelObject fix rst formatting Add one example to overlay one label map on top of one image Minor fixes in page title COMP: Fix sphinx warning (missing '.' for one title) Bradley Lowekamp (1): BUG: Fix ITK_WRAP_PYTHON check D?enan Zuki? (1): Adding DicomSeriesReadImageWrite3 Matt McCormick (11): ENH: Add option to build Python wrapping in the superbuild. COMP: Remove "ImageFilter" from ApplyGradientRecursiveGaussian. COMP: Set CMP0054 to NEW. BUG: Fix links to Midas community. ENH: Send an error when the source/build path is too long on Windows. BUG: Extend the superbuild path limit. BUG: Add ITKMetaIO to ComputePeronaMalikAnisotropicDiffusion to create output. ENH: Update VTK version to 6.2.0. COMP: Do not log ExternalProject steps that generate false positives. COMP: Remove unused variables and types. ENH: Bump ITK ExternalProject to v4.8.0. Michka Popoff (19): ENH: Add GradientRecursiveGaussianImageFilter example COMP: Fix failing ApplyGradientRecursiveGaussianImageFilter tests DOC: Fix GradientRecursiveGaussianImageFilter documentation COMP: Fix missing images in ApplyGradientRecursiveGaussianFilter ENH: Add new example with GradientRecursiveGaussianImageFilter BUG: Correctly detect and set python_file ENH: Add Python code to RemoveHolesNotConnectedToImageBoundaries STYLE: Remove example_name and folder variables STYLE: Pep8 cleanup for CreateNewExample.py.in ENH: Improve CreateNewExample script ENH: ADD ComputePeronaMalikAnisotropicDiffusion Python Example ENH: Add Anti Alias Python Example ENH: Add tests for Python examples in AnisotropicSmoothing BUG: Fix PeronaMalik python example ENH: Add ApplyColorMap Python example ENH: Simplify CMakeLists Python setup ENH: Add custom colormap Python example ENH: Improve Python SuperBuild ENH: Replace double with float in python examples ITK Software Guide Changelog --------------------------------------------- * Note that improvements in the Examples/ directory of the ITK repository also contribute to the improvements in the Software Guide. Davis Vigneault (1): DOC: Fix typo's in SystemOverview and DataRepresentation. Matt McCormick (9): ENH: Update the MetaIO license file location. ENH: Add option to build HTML output with tex4ht. ENH: Remove the 000- and 001- prefixes to the main .tex files. ENH: Add CMake option to turn off the draft watermark. ENH: Add some styling to the HTML index. DOC: Update Python wrapping information. BUG: Fixes to How To Write A Filter. ENH: Bump ITK ExternalProject to July 01, 2015. COMP: Address missing bracket and backslash escapes. ITK Apps Changelog ------------------------------ Matt McCormick (2): COMP: Fix @only capitalization in External-FLTK.cmake. ENH: Bump ITK Superbuild version to 4.8.0. From matt.mccormick at kitware.com Tue Jul 7 11:45:53 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Jul 2015 11:45:53 -0400 Subject: [ITK-dev] [ITK] Compile errors in wiki and sphinx examples after recent changes In-Reply-To: References: Message-ID: The examples and apps highlight that this will be a headache for pre-existing code. We could ensure a smooth transition by overloading the SetFixedParameters methods with a backwards compatible versions that accept ParametersType. This would prevent build errors. These overloaded methods could also emit a warning that points to a migration guide entry on why and how to upgrade the code. 2 cents, Matt On Tue, Jul 7, 2015 at 10:17 AM, Bill Lorensen wrote: > Thanks. Works for me. > > Is this documented in the migration guide or somewhere else? > > Bill > > > On Tue, Jul 7, 2015 at 9:34 AM, Johnson, Hans J wrote: >> Bill, >> >> After several T-Con discussions and e-mails, it was determined that there >> was no way to preserve backwards and forwards compatibility for fixing this >> bug. >> >> Here is the solution that is inplace for ANTs and Slicer (NOTE BRAINSTools, >> DTIPrep, DTIProcess, DTIReg, UKFTractography, SimpleITK, and many other >> tools needed no modifications). >> >> #if defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // After 4.8.1 >> typename BSplineTransformType::FixedParametersValueType >> transformFixedParamsItk; >> #else //Pre 4.8.1 >> typename BSplineTransformType::ParametersType transformFixedParamsItk; >> #endif >> >> Hans >> >> ======================================================================== >> Hans J. Johnson, Ph.D., Associate Professor >> Electrical and Computer Engineering (Primary), Biomedical Engineering, >> Psychiatry >> hans-johnson at uiowa.edu >> (319) 621 7185 (cell) >> (319) 384 3538 ECE Phone (Primary) >> (319) 353 8587 Psychiatry Phone (Secondary) >> >> 4316 Seamans Center >> Iowa City, IA 52242 >> >> On Jul 7, 2015, at 7:48 AM, Bill Lorensen wrote: >> >> Hans, >> >> There is a problem with the change. My code will no longer build with >> older versions of ITK. >> I get: >> >> ITKWikiExamplesNightly/Utilities/FileOutputWindow.cxx:23: error: >> 'FixedParametersType' is not a member of 'main(int, >> char**)::TransformType' >> >> This is not good, unless I'm noising something... >> >> On Mon, Jul 6, 2015 at 4:23 PM, Bill Lorensen >> wrote: >> >> Hans, >> >> That was the problem. Just a surprise for me. >> >> Bill >> >> >> On Mon, Jul 6, 2015 at 8:46 AM, Johnson, Hans J >> wrote: >> >> Bill, >> >> The problem is almost certainly that the variable ?parameters? is of type >> ?ParametersType? rather than ?FixedParametersType?. >> >> // The ITK_FIXED_PARAMETERS_ARE_DOUBLE is intended >> // to facilitate transition of ITK for those very >> // rare cases where multiple versions of ITK >> // may need to be supported simultaneously. >> #if defined( ITK_LEGACY_REMOVE ) >> #undef ITK_FIXED_PARAMETERS_ARE_DOUBLE >> #else >> #define ITK_FIXED_PARAMETERS_ARE_DOUBLE >> // #if !defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) >> // typedef ParametersValueType FixedParametersValueType; >> // #endif >> #endif >> >> >> Hans >> >> >> >> On Jul 6, 2015, at 6:52 AM, Bill Lorensen wrote: >> >> Folks, >> >> Something in this commit >> >> https://open.cdash.org/viewChanges.php?project=Insight&date=2015-07-04 >> >> is causing these errors: >> >> https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887517 >> >> and >> >> https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887806 >> >> Bill >> -- >> Unpaid intern in BillsBasement at noware dot 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 >> >> >> >> >> ________________________________ >> 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. >> ________________________________ >> >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> >> >> >> >> ________________________________ >> 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. >> ________________________________ > > > > -- > Unpaid intern in BillsBasement at noware dot 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 bill.lorensen at gmail.com Tue Jul 7 12:08:15 2015 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 7 Jul 2015 12:08:15 -0400 Subject: [ITK-dev] [ITK] Compile errors in wiki and sphinx examples after recent changes In-Reply-To: References: Message-ID: I agree with Matt... We need to avoid these suprises. Bill On Tue, Jul 7, 2015 at 11:45 AM, Matt McCormick wrote: > The examples and apps highlight that this will be a headache for > pre-existing code. We could ensure a smooth transition by overloading > the SetFixedParameters methods with a backwards compatible versions > that accept ParametersType. This would prevent build errors. These > overloaded methods could also emit a warning that points to a > migration guide entry on why and how to upgrade the code. > > 2 cents, > Matt > > On Tue, Jul 7, 2015 at 10:17 AM, Bill Lorensen wrote: >> Thanks. Works for me. >> >> Is this documented in the migration guide or somewhere else? >> >> Bill >> >> >> On Tue, Jul 7, 2015 at 9:34 AM, Johnson, Hans J wrote: >>> Bill, >>> >>> After several T-Con discussions and e-mails, it was determined that there >>> was no way to preserve backwards and forwards compatibility for fixing this >>> bug. >>> >>> Here is the solution that is inplace for ANTs and Slicer (NOTE BRAINSTools, >>> DTIPrep, DTIProcess, DTIReg, UKFTractography, SimpleITK, and many other >>> tools needed no modifications). >>> >>> #if defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // After 4.8.1 >>> typename BSplineTransformType::FixedParametersValueType >>> transformFixedParamsItk; >>> #else //Pre 4.8.1 >>> typename BSplineTransformType::ParametersType transformFixedParamsItk; >>> #endif >>> >>> Hans >>> >>> ======================================================================== >>> Hans J. Johnson, Ph.D., Associate Professor >>> Electrical and Computer Engineering (Primary), Biomedical Engineering, >>> Psychiatry >>> hans-johnson at uiowa.edu >>> (319) 621 7185 (cell) >>> (319) 384 3538 ECE Phone (Primary) >>> (319) 353 8587 Psychiatry Phone (Secondary) >>> >>> 4316 Seamans Center >>> Iowa City, IA 52242 >>> >>> On Jul 7, 2015, at 7:48 AM, Bill Lorensen wrote: >>> >>> Hans, >>> >>> There is a problem with the change. My code will no longer build with >>> older versions of ITK. >>> I get: >>> >>> ITKWikiExamplesNightly/Utilities/FileOutputWindow.cxx:23: error: >>> 'FixedParametersType' is not a member of 'main(int, >>> char**)::TransformType' >>> >>> This is not good, unless I'm noising something... >>> >>> On Mon, Jul 6, 2015 at 4:23 PM, Bill Lorensen >>> wrote: >>> >>> Hans, >>> >>> That was the problem. Just a surprise for me. >>> >>> Bill >>> >>> >>> On Mon, Jul 6, 2015 at 8:46 AM, Johnson, Hans J >>> wrote: >>> >>> Bill, >>> >>> The problem is almost certainly that the variable ?parameters? is of type >>> ?ParametersType? rather than ?FixedParametersType?. >>> >>> // The ITK_FIXED_PARAMETERS_ARE_DOUBLE is intended >>> // to facilitate transition of ITK for those very >>> // rare cases where multiple versions of ITK >>> // may need to be supported simultaneously. >>> #if defined( ITK_LEGACY_REMOVE ) >>> #undef ITK_FIXED_PARAMETERS_ARE_DOUBLE >>> #else >>> #define ITK_FIXED_PARAMETERS_ARE_DOUBLE >>> // #if !defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) >>> // typedef ParametersValueType FixedParametersValueType; >>> // #endif >>> #endif >>> >>> >>> Hans >>> >>> >>> >>> On Jul 6, 2015, at 6:52 AM, Bill Lorensen wrote: >>> >>> Folks, >>> >>> Something in this commit >>> >>> https://open.cdash.org/viewChanges.php?project=Insight&date=2015-07-04 >>> >>> is causing these errors: >>> >>> https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887517 >>> >>> and >>> >>> https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887806 >>> >>> Bill >>> -- >>> Unpaid intern in BillsBasement at noware dot 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 >>> >>> >>> >>> >>> ________________________________ >>> 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. >>> ________________________________ >>> >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> >>> ________________________________ >>> 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. >>> ________________________________ >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot 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 -- Unpaid intern in BillsBasement at noware dot com From hans-johnson at uiowa.edu Thu Jul 9 08:46:24 2015 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Thu, 9 Jul 2015 12:46:24 +0000 Subject: [ITK-dev] [ITK] Compile errors in wiki and sphinx examples after recent changes In-Reply-To: References: Message-ID: <2D10BF4D-6896-40E2-B427-5D626A505977@uiowa.edu> Bill, Thank you for fixing the WikiExamples. I would recommend copying the ?.gitignore? file from the ITK repository to the ITKWikiExamples repository, and then remove the *.pyc files from the master branch. Hans ======================================================================== Hans J. Johnson, Ph.D., Associate Professor Electrical and Computer Engineering (Primary), Biomedical Engineering, Psychiatry hans-johnson at uiowa.edu (319) 621 7185 (cell) (319) 384 3538 ECE Phone (Primary) (319) 353 8587 Psychiatry Phone (Secondary) 4316 Seamans Center Iowa City, IA 52242 On Jul 7, 2015, at 11:08 AM, Bill Lorensen > wrote: I agree with Matt... We need to avoid these suprises. Bill On Tue, Jul 7, 2015 at 11:45 AM, Matt McCormick > wrote: The examples and apps highlight that this will be a headache for pre-existing code. We could ensure a smooth transition by overloading the SetFixedParameters methods with a backwards compatible versions that accept ParametersType. This would prevent build errors. These overloaded methods could also emit a warning that points to a migration guide entry on why and how to upgrade the code. 2 cents, Matt On Tue, Jul 7, 2015 at 10:17 AM, Bill Lorensen > wrote: Thanks. Works for me. Is this documented in the migration guide or somewhere else? Bill On Tue, Jul 7, 2015 at 9:34 AM, Johnson, Hans J > wrote: Bill, After several T-Con discussions and e-mails, it was determined that there was no way to preserve backwards and forwards compatibility for fixing this bug. Here is the solution that is inplace for ANTs and Slicer (NOTE BRAINSTools, DTIPrep, DTIProcess, DTIReg, UKFTractography, SimpleITK, and many other tools needed no modifications). #if defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // After 4.8.1 typename BSplineTransformType::FixedParametersValueType transformFixedParamsItk; #else //Pre 4.8.1 typename BSplineTransformType::ParametersType transformFixedParamsItk; #endif Hans ======================================================================== Hans J. Johnson, Ph.D., Associate Professor Electrical and Computer Engineering (Primary), Biomedical Engineering, Psychiatry hans-johnson at uiowa.edu (319) 621 7185 (cell) (319) 384 3538 ECE Phone (Primary) (319) 353 8587 Psychiatry Phone (Secondary) 4316 Seamans Center Iowa City, IA 52242 On Jul 7, 2015, at 7:48 AM, Bill Lorensen wrote: Hans, There is a problem with the change. My code will no longer build with older versions of ITK. I get: ITKWikiExamplesNightly/Utilities/FileOutputWindow.cxx:23: error: 'FixedParametersType' is not a member of 'main(int, char**)::TransformType' This is not good, unless I'm noising something... On Mon, Jul 6, 2015 at 4:23 PM, Bill Lorensen wrote: Hans, That was the problem. Just a surprise for me. Bill On Mon, Jul 6, 2015 at 8:46 AM, Johnson, Hans J wrote: Bill, The problem is almost certainly that the variable ?parameters? is of type ?ParametersType? rather than ?FixedParametersType?. // The ITK_FIXED_PARAMETERS_ARE_DOUBLE is intended // to facilitate transition of ITK for those very // rare cases where multiple versions of ITK // may need to be supported simultaneously. #if defined( ITK_LEGACY_REMOVE ) #undef ITK_FIXED_PARAMETERS_ARE_DOUBLE #else #define ITK_FIXED_PARAMETERS_ARE_DOUBLE // #if !defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // typedef ParametersValueType FixedParametersValueType; // #endif #endif Hans On Jul 6, 2015, at 6:52 AM, Bill Lorensen wrote: Folks, Something in this commit https://open.cdash.org/viewChanges.php?project=Insight&date=2015-07-04 is causing these errors: https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887517 and https://open.cdash.org/viewBuildError.php?onlydeltap&buildid=3887806 Bill -- Unpaid intern in BillsBasement at noware dot 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 ________________________________ 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. ________________________________ -- Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com ________________________________ 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. ________________________________ -- Unpaid intern in BillsBasement at noware dot 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 -- Unpaid intern in BillsBasement at noware dot com ________________________________ 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 Tue Jul 14 18:50:30 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 14 Jul 2015 18:50:30 -0400 Subject: [ITK-dev] ITK Cube Mementos for 4.8.0 Message-ID: Hi folks, As a memento of their contributions to the 4.8.0 release, a 3D printed ITK cube (see attached), was sent to community members. The cube was derived [1] from a set of code created by community members Bill Lorensen and Jim Miller written in 1998 that generates a VTK cube. The model emulates an image on the cover page of the book G?del, Escher, Bach: An Eternal Golden Braid (GEB) by Douglas Hofstadter. GEB is a favorite tome of many in the community. As summarized by Wikipedia, it explores ?common themes in the lives and works of logician Kurt G?del, artist M. C. Escher and composer Johann Sebastian Bach. GEB expounds concepts fundamental to mathematics, symmetry, and intelligence. Through illustration and analysis, the book discusses how self-reference and formal rules allow systems to acquire meaning despite being made of ?meaningless? elements. It also discusses what it means to communicate, how knowledge can be represented and stored, the methods and limitations of symbolic representation, and even the fundamental notion of ?meaning? itself.? This model seemed appropriate for those furthering ?Insight into Images? with the Insight Toolkit. The physical object is a fitting realization in appreciation of efforts which often are hard to recognize in the form of ethereal transmissions of patches and electronic communication. ITK cubes were sent to authors in the Git logs from v4.7.0..v4.8.0 of ITK, the ITK Software Guide, ITK Apps, or the ITK Sphinx Examples repositories [2]. This release?s cube color was blue. To contribute for the next release, see the contribution instructions in the ITK Software Guide [3]. There are many ways to be an active member of the community. Davis Vigneault, for example, improved our Software Guide documentation. Or, like Jon Haitz Legarreta, improve testing code coverage. Or, improve the Python interface like Michka Popoff. Or, add new features, like Nick Tustison. Or, improve compatibility with compilers and libraries, like Sean McBride. Or, improve the doxygen and examples like Arnaud Gelas. We could also use help addressing our Coverity issues [4]. If there are questions or issues with the contribution process, please do not hesitate to discuss on the lists. Thanks to everyone who contributed to ITK 4.8.0, whether it was through patches, messages on the mailing lists, code reviews, or other means. 4.9.0 will be an exciting release! [1] https://github.com/InsightSoftwareConsortium/ITKGEB [2] http://www.itk.org/Wiki/ITK/Release_4.8_Changed_From_Previous [3] http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1.html [4] https://scan.coverity.com/projects/783 -------------- next part -------------- A non-text attachment was scrubbed... Name: 2015.07.07-ITKCubes.jpg Type: image/jpeg Size: 67677 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2015.07.07-ITKCubesPackaged.jpg Type: image/jpeg Size: 110254 bytes Desc: not available URL: From blowekamp at mail.nih.gov Wed Jul 15 09:10:24 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Jul 2015 09:10:24 -0400 Subject: [ITK-dev] Todays dashboard needs a little TLC Message-ID: Looks like there is some type of library linking issue on the dashboard today. Any one on it yet? Brad From hans-johnson at uiowa.edu Wed Jul 15 09:26:08 2015 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Wed, 15 Jul 2015 13:26:08 +0000 Subject: [ITK-dev] Todays dashboard needs a little TLC In-Reply-To: References: Message-ID: <9D3A4608-E3E8-4318-BC32-140EB70F9443@healthcare.uiowa.edu> I?ve asked Zach to look into this. I verified local build failures when Module_ITKReview:BOOL=ON I know that Zach will not be able to work on this fix until this afternoon, and he is fairly new to ITK, so it might take him a little longer. Any assistance, suggestions would be greatly appreciated. Hans On Jul 15, 2015, at 8:10 AM, Bradley Lowekamp > wrote: Looks like there is some type of library linking issue on the dashboard today. Any one on it yet? Brad ________________________________ 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 mcherel at newtone.fr Fri Jul 17 10:12:26 2015 From: mcherel at newtone.fr (Marie Cherel) Date: Fri, 17 Jul 2015 16:12:26 +0200 Subject: [ITK-dev] Setting minimum and maximum values for parameters in Amodea optimizer Message-ID: <006801d0c09a$9c782340$d56869c0$@newtone.fr> Hi all, I am using the AmoebaOptimizer with a customized SingleValueCostFunction to resolve an optimization problem. I am pretty happy with it, the only thing is that the parameters I want to optimize are percent and I do not want a percent to be lower than 0 or greater than 100. I looked into the documentation for a way of setting minimum and maximum values for the parameters to optimize, but I did not find anything. Does anybody have an idea of how to do this ? Many thanks for your help, Marie -------------- next part -------------- An HTML attachment was scrubbed... URL: From zivrafael.yaniv at nih.gov Fri Jul 17 11:52:49 2015 From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]) Date: Fri, 17 Jul 2015 15:52:49 +0000 Subject: [ITK-dev] [ITK] Setting minimum and maximum values for parameters in Amodea optimizer In-Reply-To: References: <006801d0c09a$9c782340$d56869c0$@newtone.fr> Message-ID: Hello Marie, The Amoeba (downhill simplex) method is an unconstrained optimization method and therefore will allow for any real value. An artificial way that may work is that your similarity measure return itk::NumericTraits::max() when one of the parameters is outside the valid range. I am assuming here you are minimizing the function and using float. This is breaking the heuristic underlying the downhill simplex method, but it may get you what you want. If you are using the ITK3.2 registration framework (still part of the 4.x releases) there are two optimizers that accommodate simple bound constraints: http://www.itk.org/Doxygen/html/classitk_1_1LBFGSBOptimizer.html http://www.itk.org/Doxygen/html/classitk_1_1ParticleSwarmOptimizer.html If using the ITK4 registration framework there is: http://www.itk.org/Doxygen/html/classitk_1_1LBFGSBOptimizerv4.html Please take care to read the correct documentation when selecting an optimizer. Those that are part of the v4 registration framework have ?v4? appended to their name (see the LBFGSB optimizers above). hope this helps Ziv -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.hoffman at kitware.com Fri Jul 24 17:01:46 2015 From: bill.hoffman at kitware.com (Bill Hoffman) Date: Fri, 24 Jul 2015 17:01:46 -0400 Subject: [ITK-dev] New CMake feature creates dll's on Windows without declspec Message-ID: <55B2A7BA.30602@kitware.com> I have created a new feature in CMake that can auto-export symbols in shared libraries on Windows like what happens with Linx/Unix compilers. I have a gerrit patch in review with this applied to ITK. I also wrote a blog post that can be found here: http://www.kitware.com/blog/home/post/939 Initial results with ITK are good. The disk usage is 14G for the dll build tree. A static build is 33G, and the current ITK limited dll build is 23G. The compile times are faster as well. http://review.source.kitware.com/#/c/20020 -Bill From DLRdave at aol.com Fri Jul 24 18:13:30 2015 From: DLRdave at aol.com (David Cole) Date: Fri, 24 Jul 2015 18:13:30 -0400 Subject: [ITK-dev] New CMake feature creates dll's on Windows without declspec In-Reply-To: <55B2A7BA.30602@kitware.com> References: <55B2A7BA.30602@kitware.com> Message-ID: Whoa. Cool. On Friday, July 24, 2015, Bill Hoffman wrote: > I have created a new feature in CMake that can auto-export symbols in > shared libraries on Windows like what happens with Linx/Unix compilers. I > have a gerrit patch in review with this applied to ITK. I also wrote a > blog post that can be found here: > > http://www.kitware.com/blog/home/post/939 > > Initial results with ITK are good. > > The disk usage is 14G for the dll build tree. A static build is 33G, and > the current ITK limited dll build is 23G. The compile times are faster as > well. > > http://review.source.kitware.com/#/c/20020 > > -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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.dev.open at gmail.com Mon Jul 27 07:49:15 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Mon, 27 Jul 2015 16:19:15 +0430 Subject: [ITK-dev] itk::ImportImageFilter buffer Message-ID: Hi dears, How can I pass the string as unsigned char to importimagefilter I casted but Just for one character const bool importImageFilterWillOwnTheBuffer = true; importFilter->SetImportPointer( localBuffer, numberOfPixels, importImageFilterWillOwnTheBuffer ); thanks in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Jul 27 10:05:22 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 27 Jul 2015 10:05:22 -0400 Subject: [ITK-dev] itk::ImportImageFilter buffer In-Reply-To: References: Message-ID: Hi Marco, Is numberOfPixels correct? Matt On Mon, Jul 27, 2015 at 7:49 AM, Marco Dev wrote: > Hi dears, > How can I pass the string as unsigned char to importimagefilter I casted but > Just for one character > > const bool importImageFilterWillOwnTheBuffer = true; > > importFilter->SetImportPointer( localBuffer, numberOfPixels, > > importImageFilterWillOwnTheBuffer ); > > > thanks in advance > > > _______________________________________________ > 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 Mon Jul 27 10:48:56 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 27 Jul 2015 10:48:56 -0400 Subject: [ITK-dev] itk::ImportImageFilter buffer In-Reply-To: References: Message-ID: Hi Marco, std::vector is usually contiguous in memory, so you can pass the buffer directly. However, you will want to set importImageFilterWillOwnTheBuffer = false; since the std::vector will de-allocate the memory when it goes out of scope. HTH, Matt PS. Please reply-to-all so the message goes on the mailing lists. On Mon, Jul 27, 2015 at 10:28 AM, Marco Dev wrote: > I have a question about numberofpixel I have a 113mb pixel so how can I > allocate the a standard c array ? > I parsed this file on IO then hold the content of file in std::vector > and I have to chunk the space and pass to localBuffer > Is my idea is correct ? > I want to add a big source file as a buffer into a Itk image > Thanks in advance > > On Mon, Jul 27, 2015 at 6:35 PM, Matt McCormick > wrote: >> >> Hi Marco, >> >> Is numberOfPixels correct? >> >> Matt >> >> On Mon, Jul 27, 2015 at 7:49 AM, Marco Dev >> wrote: >> > Hi dears, >> > How can I pass the string as unsigned char to importimagefilter I casted >> > but >> > Just for one character >> > >> > const bool importImageFilterWillOwnTheBuffer = true; >> > >> > importFilter->SetImportPointer( localBuffer, numberOfPixels, >> > >> > importImageFilterWillOwnTheBuffer ); >> > >> > >> > thanks in advance >> > >> > >> > _______________________________________________ >> > 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 marco.dev.open at gmail.com Mon Jul 27 10:59:45 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Mon, 27 Jul 2015 19:29:45 +0430 Subject: [ITK-dev] making a localbuffer from a big file Message-ID: Hi dears, How can to make a Local Buffer from a big file and pass it to importimagefilter const char * buffer typedef ImageType::PixelType PixelType; PixelType* pixelData = static_cast< PixelType*>( buffer ); const unsigned int totalNumberOfPixels= nx * ny; import->SetImportPointer(pixelData,totalNumberOfPixels,importFilterWillDeleteTheInputBuffer ); importer->Update(); return importer->GetOutput(); How can I generate Buffer when I have a big file for example 300MB and when I cast to pixel Data Just brings one char Thanks in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: From marco.dev.open at gmail.com Tue Jul 28 02:48:25 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Tue, 28 Jul 2015 11:18:25 +0430 Subject: [ITK-dev] Import volume into ITK image Message-ID: Hi dears, Is possible import volume image source as dumped memory file into an itk image The volume file size is 130 MB and using with importimagefilter .... Is any way for importing this kind of memory dump to itk image Thanks in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: From millerjv at ge.com Tue Jul 28 07:03:31 2015 From: millerjv at ge.com (Miller, James V (GE Global Research)) Date: Tue, 28 Jul 2015 11:03:31 +0000 Subject: [ITK-dev] Import volume into ITK image In-Reply-To: References: Message-ID: <18F9F8C1-42B1-42FA-8F2D-AD08095474B8@ge.com> Not quite sure what you are referring to as a "dumped memory file". ImportImageFilter facilitates the creation of an ITK image wrapped around a block of memory that was allocated outside of ITK. This is useful when integrating ITK with image sources (scanners and cameras) or when integrating ITK with other imaging codebases. If you just have a file on disk which is just the pixel data, you can read that into ITK by first creating a small ascii header file that describes the data and then references that file. The MetaIO format is great for doing this. For a file on disk named foo, create a header file called foo.mhd to describe the meta data. There are example mhd files in ITK and documentation on the web. Jim Principal Scientist Clinical Systems and Signal Processing GE Research GE imagination at work > On Jul 28, 2015, at 2:48 AM, Marco Dev wrote: > > Hi dears, > Is possible import volume image source as dumped memory file into an itk image > The volume file size is 130 MB and using with importimagefilter .... > Is any way for importing this kind of memory dump to itk image > Thanks in advance. > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.kitware.com_opensource_opensource.html&d=AwICAg&c=IV_clAzoPDE253xZdHuilRgztyh_RiV3wUrLrDQYWSI&r=3zoP8244p5-bYip1v4EUgQ&m=To9FTW6P8ITyCui_w5nMxILgLJQ0_2LrUvLjvHXVRc4&s=l6YOedDIO4dTY-c4AwoqdJ8OlDuGl2-GDVIXmfSk5XI&e= > > Kitware offers ITK Training Courses, for more information visit: > https://urldefense.proofpoint.com/v2/url?u=http-3A__kitware.com_products_protraining.php&d=AwICAg&c=IV_clAzoPDE253xZdHuilRgztyh_RiV3wUrLrDQYWSI&r=3zoP8244p5-bYip1v4EUgQ&m=To9FTW6P8ITyCui_w5nMxILgLJQ0_2LrUvLjvHXVRc4&s=D8bQUVrOcAEbRbQGhbR2xioB--WhJlds61jsqeMkaj4&e= > > Please keep messages on-topic and check the ITK FAQ at: > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.itk.org_Wiki_ITK-5FFAQ&d=AwICAg&c=IV_clAzoPDE253xZdHuilRgztyh_RiV3wUrLrDQYWSI&r=3zoP8244p5-bYip1v4EUgQ&m=To9FTW6P8ITyCui_w5nMxILgLJQ0_2LrUvLjvHXVRc4&s=2JXafvR5G9MevCaQykedXfbkwAG3CCs9eDA4bPiP1kM&e= > > Follow this link to subscribe/unsubscribe: > https://urldefense.proofpoint.com/v2/url?u=http-3A__public.kitware.com_mailman_listinfo_insight-2Ddevelopers&d=AwICAg&c=IV_clAzoPDE253xZdHuilRgztyh_RiV3wUrLrDQYWSI&r=3zoP8244p5-bYip1v4EUgQ&m=To9FTW6P8ITyCui_w5nMxILgLJQ0_2LrUvLjvHXVRc4&s=XEHgH_iN2zxfHXxm_gLqwv0w_wwkz6OUkSF3gca8P8c&e= From marco.dev.open at gmail.com Thu Jul 30 04:42:11 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Thu, 30 Jul 2015 13:12:11 +0430 Subject: [ITK-dev] Different 3D View Message-ID: Hi dears, why we have different 3D view from reading .mhd file or reading dicom files through FixedPointVolumeRayCastMapperCT for example : dicom reader --> vtkDICOMImageReader *dicomReader = vtkDICOMImageReader:: New(); dicomReader->SetDirectoryName(dirname); dicomReader->Update(); input=dicomReader->GetOutput(); reader=dicomReader; . . .. colorFun->AddRGBPoint( -3024, 0, 0, 0, 0.5, 0.0 ); colorFun->AddRGBPoint( -1000, .62, .36, .18, 0.5, 0.0 ); colorFun->AddRGBPoint( -500, .88, .60, .29, 0.33, 0.45 ); colorFun->AddRGBPoint( 3071, .83, .66, 1, 0.5, 0.0 ); opacityFun->AddPoint(-3024, 0, 0.5, 0.0 ); opacityFun->AddPoint(-1000, 0, 0.5, 0.0 ); opacityFun->AddPoint(-500, 1.0, 0.33, 0.45 ); opacityFun->AddPoint(3071, 1.0, 0.5, 0.0); mapper->SetBlendModeToComposite(); property->ShadeOn(); property->SetAmbient(0.1); property->SetDiffuse(0.9); property->SetSpecular(0.2); property->SetSpecularPower(10.0); property->SetScalarOpacityUnitDistance(0.8919); =========================================================== mhd reader -- > vtkMetaImageReader *metaReader = vtkMetaImageReader::New(); metaReader->SetFileName(fileName); metaReader->Update(); input=metaReader->GetOutput(); reader=metaReader; . . . . . colorFun->AddRGBPoint( -3024, 0, 0, 0, 0.5, 0.0 ); colorFun->AddRGBPoint( -1000, .62, .36, .18, 0.5, 0.0 ); colorFun->AddRGBPoint( -500, .88, .60, .29, 0.33, 0.45 ); colorFun->AddRGBPoint( 3071, .83, .66, 1, 0.5, 0.0 ); opacityFun->AddPoint(-3024, 0, 0.5, 0.0 ); opacityFun->AddPoint(-1000, 0, 0.5, 0.0 ); opacityFun->AddPoint(-500, 1.0, 0.33, 0.45 ); opacityFun->AddPoint(3071, 1.0, 0.5, 0.0); mapper->SetBlendModeToComposite(); property->ShadeOn(); property->SetAmbient(0.1); property->SetDiffuse(0.9); property->SetSpecular(0.2); property->SetSpecularPower(10.0); property->SetScalarOpacityUnitDistance(0.8919); -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Fri Jul 31 10:55:47 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 31 Jul 2015 10:55:47 -0400 Subject: [ITK-dev] ITK Static Initialization Issue with pthreads and atomic ints Message-ID: <2EAEBEA2-877F-4455-9854-62D55F66A13B@mail.nih.gov> Greeting, I am investigating the test failures: https://open.cdash.org/viewTest.php?onlyfailed&buildid=3931664 Which began occurring with upgrade to ITK 4.8. Doing a git bisect I narrowed the problem down to the change to the atomic integer class done here: https://github.com/InsightSoftwareConsortium/ITK/commit/33bcbd822f761e407db851d218b1e3204e6194d9 Then I was able to get a stack trace for a failing ITK test: (gdb) #0 0x00a77d2d in pthread_mutex_lock () from /lib/libpthread.so.0 #1 0x086cede3 in itk::SimpleFastMutexLock::Lock (this=0x0) at /home/blowekamp/src/ITK/Modules/Core/Common/src/itkSimpleFastMutexLockPThreads.cxx:50 #2 0x0869976c in itk::MutexLockHolder::MutexLockHolder (this=0xbfffe6fc, mutex=..., noblock=false) at /home/blowekamp/src/ITK/Modules/Core/Common/include/itkMutexLockHolder.h:56 #3 0x086d4308 in itk::Detail::AtomicOps<4u>::PreIncrement (ref=0x8982c78) at /home/blowekamp/src/ITK/Modules/Core/Common/src/itkAtomicInt.cxx:214 #4 0x086c7e45 in itk::AtomicInt::operator++ (this=0x8982c78) at /home/blowekamp/src/ITK/Modules/Core/Common/include/itkAtomicInt.h:93 #5 0x086c7dd6 in itk::TimeStamp::Modified (this=0x8c81980) at /home/blowekamp/src/ITK/Modules/Core/Common/src/itkTimeStamp.cxx:63 #6 0x086a11fb in itk::Object::Modified (this=0x8c81970) at /home/blowekamp/src/ITK/Modules/Core/Common/src/itkObject.cxx:389 #7 0x086a1346 in itk::Object::Object (this=0x8c81970) at /home/blowekamp/src/ITK/Modules/Core/Common/src/itkObject.cxx:593 #8 0x086c9be6 in itk::ObjectFactoryBase::ObjectFactoryBase (this=0x8c81970) at /home/blowekamp/src/ITK/Modules/Core/Common/src/itkObjectFactoryBase.cxx:476 #9 0x08379b12 in itk::MetaImageIOFactory::MetaImageIOFactory (this=0x8c81970) at /home/blowekamp/src/ITK/Modules/IO/Meta/src/itkMetaImageIOFactory.cxx:24 #10 0x08296048 in itk::MetaImageIOFactory::New () at /home/blowekamp/src/ITK/Modules/IO/Meta/include/itkMetaImageIOFactory.h:46 #11 0x08224ae0 in RegisterRequiredFactories () at /home/blowekamp/src/ITK/Modules/Core/TestKernel/include/itkTestDriverIncludeRequiredIOFactories.h:41 #12 0x08229720 in ProcessArgumentsAndRegisterRequiredFactories (ac=0xbfffeaf0, av=0xbfffeaf4) at /home/blowekamp/src/ITK/Modules/Core/TestKernel/include/itkTestDriverIncludeRequiredIOFactories.h:58 #13 0x082297f7 in main (ac=1, av=0xbfffeb74) at /scratch/blowekamp/build/Modules/Video/Core/test/ITKVideoCoreTestDriver.cxx:102 So, this stack trace shows that there is a problem using pthreads during static initialization for the Object's reference counting. As the implementation is basically that of VTK, I and wondering if anyone else knows about this problem or work arounds. Thanks, Brad -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Fri Jul 31 13:03:59 2015 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 31 Jul 2015 13:03:59 -0400 Subject: [ITK-dev] Ubuntu 14 Test failure bisect results Message-ID: <17F6093C-A7C6-4D7F-B579-3152D75A898F@mail.nih.gov> Matt, I was digging into these test failures: https://open.cdash.org/viewTest.php?onlyfailed&buildid=3932451 Here are the results of the git bisect: 674acdb2dd5546b7045f7253c84e4f9f237405e8 is the first bad commit commit 674acdb2dd5546b7045f7253c84e4f9f237405e8 Author: Matt McCormick Date: Sun May 31 21:00:55 2015 -0400 ENH: Use gold linker on Linux with GCC. The gold linker is approximately three times as fast as the default linker. Enable it with GCC 4.8 and newer where it was tested. The gold linker only works with ELF executables, so it is only enabled for Linux. Timing tests: Static libs link time: ld: 452 sec ld-gold: 179 sec Shared libs link time, wrapping enabled: ld: 164 sec ld-gold: 48 sec Change-Id: Ic8d9b5132ad6b71e5f100b5436615d6a8fac3e5c Disabling ld-gold seems to fix the problem. Versions: blowekamp at lhcp-vm-ubu14:~/ITK$ gcc --version gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. blowekamp at lhcp-vm-ubu14:~/ITK$ ld --version GNU ld (GNU Binutils for Ubuntu) 2.24 Copyright 2013 Free Software Foundation, Inc. This program is free software; you may redistribute it under the terms of the GNU General Public License version 3 or (at your option) a later version. This program has absolutely no warranty. blowekamp at lhcp-vm-ubu14:~/ITK$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 14.04.2 LTS Release: 14.04 Codename: trusty Currently we have a check for using gold with > 4.8.3: https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKSetStandardCompilerFlags.cmake#L206 But looking at this change: https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e We should have know about these related test failures: https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e So what do you recall about what versions of GCC ld-gold works on? Thanks, Brad -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Jul 31 15:20:08 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 31 Jul 2015 15:20:08 -0400 Subject: [ITK-dev] ITK Static Initialization Issue with pthreads and atomic ints In-Reply-To: <2EAEBEA2-877F-4455-9854-62D55F66A13B@mail.nih.gov> References: <2EAEBEA2-877F-4455-9854-62D55F66A13B@mail.nih.gov> Message-ID: Hi Brad, Sujin took a look, and he spotted a missing initialization of the mutex lock for the 32 bit case. I put the change in a patch here: http://review.source.kitware.com/#/c/20039/ Please test on the 32 bit system. Thanks, Matt On Fri, Jul 31, 2015 at 10:55 AM, Bradley Lowekamp wrote: > Greeting, > > I am investigating the test failures: > > https://open.cdash.org/viewTest.php?onlyfailed&buildid=3931664 > > Which began occurring with upgrade to ITK 4.8. > > Doing a git bisect I narrowed the problem down to the change to the atomic > integer class done here: > > https://github.com/InsightSoftwareConsortium/ITK/commit/33bcbd822f761e407db851d218b1e3204e6194d9 > > Then I was able to get a stack trace for a failing ITK test: > > (gdb) > #0 0x00a77d2d in pthread_mutex_lock () from /lib/libpthread.so.0 > #1 0x086cede3 in itk::SimpleFastMutexLock::Lock (this=0x0) at > /home/blowekamp/src/ITK/Modules/Core/Common/src/itkSimpleFastMutexLockPThreads.cxx:50 > #2 0x0869976c in > itk::MutexLockHolder::MutexLockHolder > (this=0xbfffe6fc, mutex=..., noblock=false) > at > /home/blowekamp/src/ITK/Modules/Core/Common/include/itkMutexLockHolder.h:56 > #3 0x086d4308 in itk::Detail::AtomicOps<4u>::PreIncrement (ref=0x8982c78) > at /home/blowekamp/src/ITK/Modules/Core/Common/src/itkAtomicInt.cxx:214 > #4 0x086c7e45 in itk::AtomicInt::operator++ (this=0x8982c78) > at /home/blowekamp/src/ITK/Modules/Core/Common/include/itkAtomicInt.h:93 > #5 0x086c7dd6 in itk::TimeStamp::Modified (this=0x8c81980) at > /home/blowekamp/src/ITK/Modules/Core/Common/src/itkTimeStamp.cxx:63 > #6 0x086a11fb in itk::Object::Modified (this=0x8c81970) at > /home/blowekamp/src/ITK/Modules/Core/Common/src/itkObject.cxx:389 > #7 0x086a1346 in itk::Object::Object (this=0x8c81970) at > /home/blowekamp/src/ITK/Modules/Core/Common/src/itkObject.cxx:593 > #8 0x086c9be6 in itk::ObjectFactoryBase::ObjectFactoryBase (this=0x8c81970) > at > /home/blowekamp/src/ITK/Modules/Core/Common/src/itkObjectFactoryBase.cxx:476 > #9 0x08379b12 in itk::MetaImageIOFactory::MetaImageIOFactory > (this=0x8c81970) > at > /home/blowekamp/src/ITK/Modules/IO/Meta/src/itkMetaImageIOFactory.cxx:24 > #10 0x08296048 in itk::MetaImageIOFactory::New () at > /home/blowekamp/src/ITK/Modules/IO/Meta/include/itkMetaImageIOFactory.h:46 > #11 0x08224ae0 in RegisterRequiredFactories () > at > /home/blowekamp/src/ITK/Modules/Core/TestKernel/include/itkTestDriverIncludeRequiredIOFactories.h:41 > #12 0x08229720 in ProcessArgumentsAndRegisterRequiredFactories > (ac=0xbfffeaf0, av=0xbfffeaf4) > at > /home/blowekamp/src/ITK/Modules/Core/TestKernel/include/itkTestDriverIncludeRequiredIOFactories.h:58 > #13 0x082297f7 in main (ac=1, av=0xbfffeb74) at > /scratch/blowekamp/build/Modules/Video/Core/test/ITKVideoCoreTestDriver.cxx:102 > > So, this stack trace shows that there is a problem using pthreads during > static initialization for the Object's reference counting. > > As the implementation is basically that of VTK, I and wondering if anyone > else knows about this problem or work arounds. > > Thanks, > Brad From matt.mccormick at kitware.com Fri Jul 31 15:29:27 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 31 Jul 2015 15:29:27 -0400 Subject: [ITK-dev] Ubuntu 14 Test failure bisect results In-Reply-To: <17F6093C-A7C6-4D7F-B579-3152D75A898F@mail.nih.gov> References: <17F6093C-A7C6-4D7F-B579-3152D75A898F@mail.nih.gov> Message-ID: Hi Brad, Thanks for investigating and getting great information out of git bisect. I developed the patch on Gentoo with GCC 4.8.4 / binutils 2.24, and I have not seen any issues. The eldorado builds on the dashboard are all Ubuntu 14.04.2, too. I will start an Experimental build with BUILD_SHARED_LIBS set on eldorado to be sure it can be reproduced. Thanks, Matt On Fri, Jul 31, 2015 at 1:03 PM, Bradley Lowekamp wrote: > Matt, > > I was digging into these test failures: > > https://open.cdash.org/viewTest.php?onlyfailed&buildid=3932451 > > Here are the results of the git bisect: > > 674acdb2dd5546b7045f7253c84e4f9f237405e8 is the first bad commit > commit 674acdb2dd5546b7045f7253c84e4f9f237405e8 > Author: Matt McCormick > Date: Sun May 31 21:00:55 2015 -0400 > > ENH: Use gold linker on Linux with GCC. > > > > The gold linker is approximately three times as fast as the default > linker. > Enable it with GCC 4.8 and newer where it was tested. The gold linker > only > works with ELF executables, so it is only enabled for Linux. > > > > Timing tests: > > > > Static libs link time: > > > > ld: 452 sec > ld-gold: 179 sec > > > > Shared libs link time, wrapping enabled: > > > > ld: 164 sec > ld-gold: 48 sec > > > > Change-Id: Ic8d9b5132ad6b71e5f100b5436615d6a8fac3e5c > > Disabling ld-gold seems to fix the problem. > > Versions: > > blowekamp at lhcp-vm-ubu14:~/ITK$ gcc --version > gcc (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4 > Copyright (C) 2013 Free Software Foundation, Inc. > This is free software; see the source for copying conditions. There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > > blowekamp at lhcp-vm-ubu14:~/ITK$ ld --version > GNU ld (GNU Binutils for Ubuntu) 2.24 > Copyright 2013 Free Software Foundation, Inc. > This program is free software; you may redistribute it under the terms of > the GNU General Public License version 3 or (at your option) a later > version. > This program has absolutely no warranty. > > blowekamp at lhcp-vm-ubu14:~/ITK$ lsb_release -a > No LSB modules are available. > Distributor ID: Ubuntu > Description: Ubuntu 14.04.2 LTS > Release: 14.04 > Codename: trusty > > > Currently we have a check for using gold with > 4.8.3: > https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKSetStandardCompilerFlags.cmake#L206 > > But looking at this change: > https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e > > We should have know about these related test failures: > https://github.com/InsightSoftwareConsortium/ITK/commit/102c79bd3bb50cc649f2733c472bdfaa138c453e > > So what do you recall about what versions of GCC ld-gold works on? > > Thanks, > Brad > > > > > > > > > > > From matt.mccormick at kitware.com Tue Jul 14 18:43:27 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 14 Jul 2015 22:43:27 -0000 Subject: [ITK-dev] ITK Cube Mementos for 4.8.0 Message-ID: Hi folks, As a memento of their contributions to the 4.8.0 release, a 3D printed ITK cube (see attached), was sent to community members. The cube was derived [1] from a set of code created by community members Bill Lorensen and Jim Miller written in 1998 that generates a VTK cube. The model emulates an image on the cover page of the book G?del, Escher, Bach: An Eternal Golden Braid (GEB) by Douglas Hofstadter. GEB is a favorite tome of many in the community. As summarized by Wikipedia, it explores ?common themes in the lives and works of logician Kurt G?del, artist M. C. Escher and composer Johann Sebastian Bach. GEB expounds concepts fundamental to mathematics, symmetry, and intelligence. Through illustration and analysis, the book discusses how self-reference and formal rules allow systems to acquire meaning despite being made of ?meaningless? elements. It also discusses what it means to communicate, how knowledge can be represented and stored, the methods and limitations of symbolic representation, and even the fundamental notion of ?meaning? itself.? This model seemed appropriate for those furthering ?Insight into Images? with the Insight Toolkit. The physical object is a fitting realization in appreciation of efforts which often are hard to recognize in the form of ethereal transmissions of patches and electronic communication. ITK cubes were sent to authors in the Git logs from v4.7.0..v4.8.0 of ITK, the ITK Software Guide, ITK Apps, or the ITK Sphinx Examples repositories [2]. This release?s cube color was blue. To contribute for the next release, see the contribution instructions in the ITK Software Guide [3]. There are many ways to be an active member of the community. Davis Vigneault, for example, improved our Software Guide documentation. Or, like Jon Haitz Legarreta, improve testing code coverage. Or, improve the Python interface like Michka Popoff. Or, add new features, like Nick Tustison. Or, improve compatibility with compilers and libraries, like Sean McBride. Or, improve the doxygen and examples like Arnaud Gelas. We could also use help addressing our Coverity issues [4]. If there are questions or issues with the contribution process, please do not hesitate to discuss on the lists. Thanks to everyone who contributed to ITK 4.8.0, whether it was through patches, messages on the mailing lists, code reviews, or other means. 4.9.0 will be an exciting release! [1] https://github.com/InsightSoftwareConsortium/ITKGEB [2] http://www.itk.org/Wiki/ITK/Release_4.8_Changed_From_Previous [3] http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1.html [4] https://scan.coverity.com/projects/783 -------------- next part -------------- A non-text attachment was scrubbed... Name: 2015.07.07-ITKCubes.jpg Type: image/jpeg Size: 290968 bytes Desc: not available URL: From matt.mccormick at kitware.com Tue Jul 14 18:48:38 2015 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 14 Jul 2015 22:48:38 -0000 Subject: [ITK-dev] ITK Cube Mementos for 4.8.0 Message-ID: Hi folks, As a memento of their contributions to the 4.8.0 release, a 3D printed ITK cube (see attached), was sent to community members. The cube was derived [1] from a set of code created by community members Bill Lorensen and Jim Miller written in 1998 that generates a VTK cube. The model emulates an image on the cover page of the book G?del, Escher, Bach: An Eternal Golden Braid (GEB) by Douglas Hofstadter. GEB is a favorite tome of many in the community. As summarized by Wikipedia, it explores ?common themes in the lives and works of logician Kurt G?del, artist M. C. Escher and composer Johann Sebastian Bach. GEB expounds concepts fundamental to mathematics, symmetry, and intelligence. Through illustration and analysis, the book discusses how self-reference and formal rules allow systems to acquire meaning despite being made of ?meaningless? elements. It also discusses what it means to communicate, how knowledge can be represented and stored, the methods and limitations of symbolic representation, and even the fundamental notion of ?meaning? itself.? This model seemed appropriate for those furthering ?Insight into Images? with the Insight Toolkit. The physical object is a fitting realization in appreciation of efforts which often are hard to recognize in the form of ethereal transmissions of patches and electronic communication. ITK cubes were sent to authors in the Git logs from v4.7.0..v4.8.0 of ITK, the ITK Software Guide, ITK Apps, or the ITK Sphinx Examples repositories [2]. This release?s cube color was blue. To contribute for the next release, see the contribution instructions in the ITK Software Guide [3]. There are many ways to be an active member of the community. Davis Vigneault, for example, improved our Software Guide documentation. Or, like Jon Haitz Legarreta, improve testing code coverage. Or, improve the Python interface like Michka Popoff. Or, add new features, like Nick Tustison. Or, improve compatibility with compilers and libraries, like Sean McBride. Or, improve the doxygen and examples like Arnaud Gelas. We could also use help addressing our Coverity issues [4]. If there are questions or issues with the contribution process, please do not hesitate to discuss on the lists. Thanks to everyone who contributed to ITK 4.8.0, whether it was through patches, messages on the mailing lists, code reviews, or other means. 4.9.0 will be an exciting release! [1] https://github.com/InsightSoftwareConsortium/ITKGEB [2] http://www.itk.org/Wiki/ITK/Release_4.8_Changed_From_Previous [3] http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1.html [4] https://scan.coverity.com/projects/783 -------------- next part -------------- A non-text attachment was scrubbed... Name: 2015.07.07-ITKCubes.jpg Type: image/jpeg Size: 130057 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2015.07.07-ITKCubesPackaged.jpg Type: image/jpeg Size: 110254 bytes Desc: not available URL: From marco.dev.open at gmail.com Thu Jul 30 04:18:43 2015 From: marco.dev.open at gmail.com (Marco Dev) Date: Thu, 30 Jul 2015 08:18:43 -0000 Subject: [ITK-dev] Different 3D view for reading Message-ID: Hi dears, why we have different 3D view from reading .mhd file or reading dicom files through FixedPointVolumeRayCastMapperCT for example : dicom reader --> vtkDICOMImageReader *dicomReader = vtkDICOMImageReader:: New(); dicomReader->SetDirectoryName(dirname); dicomReader->Update(); input=dicomReader->GetOutput(); reader=dicomReader; . . .. colorFun->AddRGBPoint( -3024, 0, 0, 0, 0.5, 0.0 ); colorFun->AddRGBPoint( -1000, .62, .36, .18, 0.5, 0.0 ); colorFun->AddRGBPoint( -500, .88, .60, .29, 0.33, 0.45 ); colorFun->AddRGBPoint( 3071, .83, .66, 1, 0.5, 0.0 ); opacityFun->AddPoint(-3024, 0, 0.5, 0.0 ); opacityFun->AddPoint(-1000, 0, 0.5, 0.0 ); opacityFun->AddPoint(-500, 1.0, 0.33, 0.45 ); opacityFun->AddPoint(3071, 1.0, 0.5, 0.0); mapper->SetBlendModeToComposite(); property->ShadeOn(); property->SetAmbient(0.1); property->SetDiffuse(0.9); property->SetSpecular(0.2); property->SetSpecularPower(10.0); property->SetScalarOpacityUnitDistance(0.8919); =========================================================== mhd reader -- > vtkMetaImageReader *metaReader = vtkMetaImageReader::New(); metaReader->SetFileName(fileName); metaReader->Update(); input=metaReader->GetOutput(); reader=metaReader; . . . . . colorFun->AddRGBPoint( -3024, 0, 0, 0, 0.5, 0.0 ); colorFun->AddRGBPoint( -1000, .62, .36, .18, 0.5, 0.0 ); colorFun->AddRGBPoint( -500, .88, .60, .29, 0.33, 0.45 ); colorFun->AddRGBPoint( 3071, .83, .66, 1, 0.5, 0.0 ); opacityFun->AddPoint(-3024, 0, 0.5, 0.0 ); opacityFun->AddPoint(-1000, 0, 0.5, 0.0 ); opacityFun->AddPoint(-500, 1.0, 0.33, 0.45 ); opacityFun->AddPoint(3071, 1.0, 0.5, 0.0); mapper->SetBlendModeToComposite(); property->ShadeOn(); property->SetAmbient(0.1); property->SetDiffuse(0.9); property->SetSpecular(0.2); property->SetSpecularPower(10.0); property->SetScalarOpacityUnitDistance(0.8919); -------------- next part -------------- An HTML attachment was scrubbed... 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