From M.Staring at lumc.nl Wed Jun 1 03:45:08 2016 From: M.Staring at lumc.nl (M.Staring at lumc.nl) Date: Wed, 1 Jun 2016 07:45:08 +0000 Subject: [ITK-dev] linear interpolator leaks? Message-ID: <24D8AA23EC0DCB4498C35EC60401E76144003202@MAIL-MB02.lumcnet.prod.intern> Hi all, I noticed that our valgrind build of elastix has reports like this: UMR ==5253== Invalid read of size 2 ==5253== at 0x552241: itk::LinearInterpolateImageFunction, double>::EvaluateOptimized(itk::LinearInterpolateImageFunction, double>::Dispatch<2u> const&, itk::ContinuousIndex const&) const (itkLinearInterpolateImageFunction.h:173) ==5253== by 0x54976C: itk::LinearInterpolateImageFunction, double>::EvaluateAtContinuousIndex(itk::ContinuousIndex const&) const (itkLinearInterpolateImageFunction.h:99) ==5253== by 0x54397B: bool TestInterpolators<2u>() (itkAdvancedLinearInterpolatorTest.cxx:171) ==5253== by 0x53E232: main (itkAdvancedLinearInterpolatorTest.cxx:279) ==5253== Address 0x6822b94 is 52 bytes inside a block of size 83 free'd ==5253== at 0x4C2C2BC: operator delete(void*) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==5253== by 0x5ED884: itk::ObjectFactoryBase::CreateObject(char const*) (in /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) ==5253== by 0x5EF91B: itk::ObjectFactoryBase::CreateInstance(char const*) (in /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) ==5253== by 0x550335: itk::ObjectFactory, double> >::Create() (itkObjectFactory.h:60) ==5253== by 0x548A90: itk::LinearInterpolateImageFunction, double>::New() (in /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) ==5253== by 0x543540: bool TestInterpolators<2u>() (itkAdvancedLinearInterpolatorTest.cxx:114) ==5253== by 0x53E232: main (itkAdvancedLinearInterpolatorTest.cxx:279) ==5253== On inspection these lines in itk LinearInterpolateImageFunction.h seem troublesome: const RealType & val000 = inputImagePtr->GetPixel(basei); Note that a real type is obtained by reference from a function that often does not return a real type. Is this allowed? Best, Marius Marius Staring, PhD Division of Image Processing (LKEB) Department of Radiology Leiden University Medical Center PO Box 9600, 2300 RC Leiden, The Netherlands phone: +31 (0)71 52 62137, fax: +31 (0)71 524 8256 m.staring at lumc.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From luc.hermitte at c-s.fr Wed Jun 1 05:02:07 2016 From: luc.hermitte at c-s.fr (Luc Hermitte) Date: Wed, 1 Jun 2016 11:02:07 +0200 Subject: [ITK-dev] linear interpolator leaks? In-Reply-To: <24D8AA23EC0DCB4498C35EC60401E76144003202@MAIL-MB02.lumcnet.prod.intern> References: <24D8AA23EC0DCB4498C35EC60401E76144003202@MAIL-MB02.lumcnet.prod.intern> Message-ID: Hi, Le 01/06/2016 ? 09:45, M.Staring at lumc.nl a ?crit : > I noticed that our valgrind build of elastix has reports like this: > > *UMR*==5253== Invalid read of size 2 > > ==5253== at 0x552241: > itk::LinearInterpolateImageFunction, > double>::EvaluateOptimized(itk::LinearInterpolateImageFunction 2u>, double>::Dispatch<2u> const&, itk::ContinuousIndex > const&) const (itkLinearInterpolateImageFunction.h:173) > > ==5253== by 0x54976C: > itk::LinearInterpolateImageFunction, > double>::EvaluateAtContinuousIndex(itk::ContinuousIndex > const&) const (itkLinearInterpolateImageFunction.h:99) > > ==5253== by 0x54397B: bool TestInterpolators<2u>() > (itkAdvancedLinearInterpolatorTest.cxx:171) > > ==5253== by 0x53E232: main (itkAdvancedLinearInterpolatorTest.cxx:279) > > ==5253== Address 0x6822b94 is 52 bytes inside a block of size 83 free'd > > ==5253== at 0x4C2C2BC: operator delete(void*) (in > /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) > > ==5253== by 0x5ED884: itk::ObjectFactoryBase::CreateObject(char > const*) (in > /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) > > ==5253== by 0x5EF91B: itk::ObjectFactoryBase::CreateInstance(char > const*) (in > /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) > > ==5253== by 0x550335: > itk::ObjectFactory 2u>, double> >::Create() (itkObjectFactory.h:60) > > ==5253== by 0x548A90: > itk::LinearInterpolateImageFunction, > double>::New() (in > /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) > > ==5253== by 0x543540: bool TestInterpolators<2u>() > (itkAdvancedLinearInterpolatorTest.cxx:114) > > ==5253== by 0x53E232: main (itkAdvancedLinearInterpolatorTest.cxx:279) > > ==5253== > > > > On inspection these lines in itk LinearInterpolateImageFunction.h seem > troublesome: > > > > const RealType & val000 = inputImagePtr->GetPixel(basei); > > > Note that a real type is obtained by reference from a function that > often does not return a real type. Is this allowed? It should be fine. We are authorized to get a const reference to the result of a function that returns by value. Most of the time, it's never done because this is quite odd. As long as the function doesn't return a reference/address to a local variable, there is no problem. Have you checked without the "const&" ? Any way, this won't cause a leak. We could have suspected a dangling reference, but there should be none IIRC this part of the code. See https://herbsutter.com/2008/01/01/gotw-88-a-candidate-for-the-most-important-const/ I'd check whether the index produced in within the boundaries on the internal buffer with a `assert(offset < m_Buffer->Size());` in itk::Image::GetPixel. I'd be curious to see what clang address sanatizer says (it may give more information than valgrind -- like where the free'd address was allocated then free'd) Regards -- Luc Hermitte From jchris.fillionr at kitware.com Fri Jun 3 09:52:10 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Fri, 3 Jun 2016 09:52:10 -0400 Subject: [ITK-dev] [ANN] ITK 4.10.0 has been released! Message-ID: The Insight Segmentation and Registration Toolkit (ITK), is an open-source, cross-platform library for multidimensional image analysis. On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.10.0 has been released! Links to the Sourceforge.net tarballs can be found on the download page: http://www.itk.org/ITK/resources/software.html [image: TwoProjectionRegistrationDiagram.png] Insight Journal article included as a Remote Module: TwoProjectionRegistration . Digitally reconstructed radiographs (DRR) generated as part of the registration are shown above. Outline ---------- 1. Introduction 2. New Features 3. ITK Changelog 4. ITK Sphinx Examples Changelog 5. ITK Software Guide Changelog Introduction ----------------- Developed by an international community, ITK collects best-of-breed algorithms for registering, segmenting, analyzing, and quantifying n-dimensional imaging data. The high-quality library facilitates reproducible research, provides a software resource for teaching image analysis, and offersis a platform for commercial product development. A few selected highlights for the 4.10 release include the following: - New Remote module: TwoProjectionRegistration performs simultaneous registration of two projection images to a 3D image volume, which is useful for external beam radiotherapy and other applications. It uses Powell?s method for optimization and the Siddon-Jacobs fast ray-tracing algorithm. - First update to internal VNL in five years. Many improvements were made to upstream VNL. We now push patches upstream and stay in sync via a Git subtree workflow. - Windows builds now support processing 4GB+ images by default - GDCM updated for better DICOM support Congratulations to the 26 contributors to this release. We would especially like to recognize the new contributors: Andrey Fedorov, Sujin Philip, Francois Budin, and b'Alvaro Sanchez. Improved documentation in this release includes new examples on how to convert between ITK and VTK image data structures . Additionally, a new example demonstrates how to perform vector image registration with a mean-squares matching metric . The ITK Software Guide added documentation on how to add third party dependencies when creating an ITK module. This release also brings exciting rapid prototyping improvements to the ITK Python wrapping. Type specification is no longer necessary during the creation of most filters. The required type is inferred from a primary input passed on filter creation. For example, instead of the explicit type specification: median = itk.MedianImageFilter[ImageType, ImageType].New() median.SetInput(reader.GetOutput()) It is now possible to call: median = itk.MedianImageFilter.New(Input=reader.GetOutput()) Or, the shortened: median = itk.MedianImageFilter.New(reader.GetOutput()) Or: median = itk.MedianImageFliter.New(reader) An itk.ImageFileReader can be created by specifying the FileName during instantiation: reader = itk.ImageFileReader.New(FileName=?inputFile.mha?) Enjoy ITK! New Features --------------------- * Wrapping improvements - ITK_USE_64BITS_IDS supported on Windows - Faster builds (CastXML calls and build targets reduced by half) - Faster runtime loading and smaller binary size due to hidden symbol visibility - Wrapping with BUILD_SHARED_LIBS disabled is supported - Do not link to libpython when possible - Filter types do not need to be specified when ?Input=inputImage? is specified in the constructor - Improved wrapping class coverage - Visual Studio 2015 Update 2 Supported - GCC 6.1 supported * New Remote Module - TwoProjectionRegistration - 2D-3D registration designed for radiotherapy - http://hdl.handle.net/10380/3245 * Core Improvements - Data and build tool downloads now over HTTPS - Extended constexpr usage with ITK_CONSTEXPR and ITKCONSTEXPR_FUNC macros - ITK_USE_64BITS_IDS, required to process 4GB+ images on Windows, now enabled by default - VNL updated and modernized - CMake configuration major modernization - vcl has been removed in favor of the standard libraries - vnl_math_ function avoided in favor of std:: and itk::Math - VNL had suppressed integer data conversion warnings on Visual Studio (C4257); this suppression has been removed and all warnings addressed - Various improvements for building a module externally against an ITK build tree - CMAKE_POSITION_INDEPENDENT_CODE is enabled by default - Improved EXERCISE_BASIC_OBJECT_METHODS testing macro * Filtering Improvements - RGB pixel support added to itk::ImageToVTKImageFilter - itk::Box* filters moved out of the Review module - itk::GaussianDerivativeOperator moved out of the Review module - MaskLabel is deprecated in N4BiasFieldCorrectionFilter in favor any non-zero pixel * Registration Improvements - Fixed and moving masks added to the v4 registration methods * Documentation Improvements - Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples - New examples on to convert between ITK and VTK - New example on how to perform vector image registration - The ITK Software Guide describes how to add a third-party dependency to a module * Third Party Library Updates - pygccxml updated to v1.7.3 - GDCM updated to the release branch latest - VNL updated to latest upstream - MINC updated to the latest upstream - SWIG updated to v3.0.8 - PCRE update to v8.38 * Improved code coverage -- we are at 85.0%! * *Lots* of important bug fixes * And much more! See details in the log below. Changes from v4.10rc02..v4.10.0 ------------------------------------------------ Bradley Lowekamp (3): COMP: Address uninitialized warning of size COMP: Devirtualize private methods to prevent instantiation COMP: Use well defined ZeroValue for unused initial value. Hans Johnson (1): BUG: try_compile needs to have CMAKE_CXX_STANDARD passed Hyun Jae Kang (1): COMP: Fix unexpected data-cast results of itkCastImageFilter Jon Haitz Legarreta (1): BUG: Fix OpenCV-2.4.9 camera empty image issue. Matthew McCormick (13): COMP: Bump CastXML for GCC 6.1 support. STYLE: Improvements to HardConnectedComponentsImageFilter. ENH: Add baseline for itkHardConnectedComponentImageFilterTest. STYLE: Improvements for itkHardConnectedComponentImageFilterTest COMP: HardConnectedComponentImageFilter autological constant out of range DOC: Sphinx examples update to 2016-05-22. DOC: Wiki examples update to 2016-05-22. COMP: MSVC result of 32-bit shift implicitly converted to 64 bits BUG: Disable building the netlib example. ENH: Add FloatAddULP BUG: Decrement index in BSplineTransform by ULPs. BUG: Adjust index decrement in BSplineTransform BUG: Remove VNL README left over from subtree merge. Sumedha Singla (1): ENH: WhatModulesITK was not finding modules on Windows Changes from v4.10rc01..v4.10rc02 ------------------------------------------------ Davis Vigneault (1): BUG: Improve error checking and testing for ConnectedRegionsMesh Hyun Jae Kang (2): BUG: Address the issue of "Missing Delete" within SwapZeroCornerToIRP. COMP: Fixed Mac OSX wrapping configuration warning Matthew McCormick (6): BUG: The ImageFileReader internal pipeline methods should be protected. BUG: Use new VNL include directory variables. COMP: Add missing NeighborhoodAccessor methods to PhasedArray3D image. BUG: Adjust itk.org ExternalData URL. COMP: Do not use target_include_directories with CMake 2.8.11.2. BUG: Address missing shared_ptr for VS9 Changes from v4.9.0..v4.10rc01 ------------------------------------------------ Alvaro Sanchez (1): STYLE: moved itkKappaSigmaThresholdImageFilter/Calculator from Nonunit/Review Andrey Fedorov (2): BUG: Add missing itk_expat_mangle.h install target BUG: fix typo in file name Bill Hoffman (2): COMP: fix shared build on Windows when Review is on. COMP: work around for VS 2015 optimizer bug causing test failures. Bill Lorensen (6): ENH: Bump version for style fixups. ENH: Bump wiki examples version, new remote module process ENH: Bump wiki examples version, new remote module process STYLE: SuperClass should be Superclass COMP: Resolve clang linkage issue BUG: Valgrind detected an invalid read Bradley Lowekamp (21): BUG: Compilation problem with GCC 4.1 and explicit instantiation ENH: Update Insight Journal handle links to https ENH: Adding const qualifier to results BUG: Adding missing const qualifier for GetConfusionMatrix method BUG: Use Set/GetMacros, fix const correctness and PrintSelf. ENH: added inlined Zero and one values for integer NumericTraits ENH: Use constexpr for floating point NumericTraits ENH: Make NumericTraits functions constexpr for intrinsic BUG: Add definition of static constexpr NumericTrait members BUG: Declared static constexpr members need to be defined as constexpr ENH: ITK_CONSTEXPR_FUNC implies inline BUG: Addressing VS10 and VS11 NumericTraits linkage issue BUG: Use LargestPossible region for BSpline domain BUG: Remove errant file COMP: Address warning about this usage in initializer list ENH: Prefer ZeroValue function over variable STYLE: Use consistent path for try_compiles binary directory BUG: Don't use "=" in cmake variable name ENH: Test address of NumericTraits One and Zero constexpr ENH: Use ITK_USE_64BITS_IDS for windows 64 by default ENH: Enable run-time dependency on Python library Davis Vigneault (4): ENH: Update itkFileTools to allow std::string arguments. ENH: Add Floored and Truncated Modulus to VNL ENH: Add Ternary Operator Image Filter STYLE: Prefer static cast D?enan Zuki? (1): ENH: CovariantVector's Normalize returns the norm. Francois Budin (6): PERF: Simplify itkTemplate New() input type identification. ENH: Avoid template type specification for image reader in Python wrapping BUG: Missing IOPixelType strings in ImageIOBase BUG: Wrapping intermediate files were not automatically updated ENH: Reduce number of dependencies for XML files generated for wrapping BUG: GCC is limited when calling overloaded base class functions GCC-XML Upstream (1): ENH: pygccxml v1.7.3 (reduced) GDCM Upstream (1): GDCM 2015-09-02 (1efe9e28) Hans Johnson (27): COMP: Static analysis warning COMP: Incorrect delete found by static analysis PERF: Avoid temporary std:vector copying. COMP: Provide VXL backward compatible includes COMP: ITK requires legacy methods ENH: Need propagate ITK_LIBRARY_PROPERTIES ENH: Added UpdateFromUpstream.sh for VNL ENH: Manual copy from vxl/master STYLE: vnl_math_[min|max] -> std::[min|max] STYLE: Text files should end with a newline COMP: Prefer C++11 constexpr when possible COMP: Prefer C++11 constexpr when possible ENH: Simplify std:: math function definitions COMP: Error in constexpr usage COMP: Add const to previous const variables COMP: SizeValueType can has different definition for itkArray ENH: Added utility for modernizing vcl_ to std:: ENH: Reference vnl_math.h constants directly ENH: Avoid using vnl_math_ functions COMP: Missing symbol for itkStaticConstMacro COMP: Function override missing in BioCell ENH: Convert vcl_ to std:: BUG: Windows vcl_snprintf failures addressed COMP: Disabmiguate function calls to SetData ENH: Provided static code API for external applications COMP: Remove possible type conversion warnings ENH: Merge GDCM release branch Hyun Jae Kang (25): COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 BUG: Fixed the runtime crash of itkTimeProbeTest2 BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's tests on OSX 10.6 BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 COMP: Fixed the data conversion warning messages of itkResourceProbe BUG: Fixed the runtime crash of itkLabelOverlapMeasuresImageFilterTest BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 BUG: Fixed the runtime crash of itkMRIBiasFieldCorrectionFilterTest BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1 BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 BUG: Fixed the runtime crash of vnl_test_numeric_traits BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 BUG: Fixed the failed test case of itkSTLThreadTest on OS X 10.8 COMP: Update KWStyle to utilize the latest boost library COMP: Fixed the compiler error of ITK on Mingw-w64 COMP: Temporarily suppress the warning messages of data-conversion on VS14 COMP: Put back the disappeared option of "BUILD EXAMPLES". BUG: Fix segmentation faults on mingw-W64 x86_64. BUG: Fix the failed test of itkCastImageFilterTest on mingw-w64 compiler. COMP: Fixed the cmake configuration for ITK_WRAP_DOC COMP: Fixed the warning messages on VS14. COMP: Add a missing head file at itkNumericTraitsStdVector.h COMP: Fix the wraning message of data-conversion Jean-Christophe Fillion-Robin (4): COMP: ITKExternalModule: Support building module without test directory. STYLE: Facilitate maintenance of CastXML generator refactoring CMakeLists COMP: Allow use of multiple "ITK external modules" in the same project. STYLE: UseITK: Document static registration of ITK IO factories. See #3393 Jon Haitz Legarreta (7): COMP: Delete unused variable compiler warning. ENH: Refactored itkBioCellTest ENH: Exercise non-tested itk::Math methods. ENH: Improve MersenneTwister class and test. ENH: Improve itkFEMLoadPoint coverage. ENH: Improve itkVersion class code coverage. ENH: Perform class name checks in test macro KWSys Robot (1): KWSys 2016-03-09 (36d8666f) Lucas Gandel (9): ENH: Implement GetNumberOfParameter() in ImageToSpatialObjectMetric COMP: Enable wrapping of multiple "ITK external modules" in the same project COMP: Fix CASTXML_EXECUTABLE value for multiple external module COMP: Fix external module testing COMP: Fix git protocol setup ENH: Conditionally add testing for External Modules BUG: Fix call to std::max() with different variable types Manuel Grizonnet (1): COMP: add ITKCommon_EXPORT to fix link issues with external applications Matthew McCormick (73): ENH: Add TwoProjectionRegistration Remote Module. ENH: Allow ITKVideoBridgeOpenCV to be built externally. COMP: Add export specification for itk::ResourceProbe. ENH: Do not force shared libraries when wrapping. BUG: BUILD_TESTING should be not advanced. ENH: Bump ITK version to 4.10.0. DOC: Correct ITKImageNoise description spelling. ENH: Wrap FFTNormalizedCorrelationImageFilter. BUG: Remove Azure ExternalData resource. BUG: ExternalData downloads from midas3.kitware.com only supports https. BUG: Update ExternalData resource. BUG: slicer.kitware.com/midas3/ ExternalData will not support http. ENH: Add ITK_CUSTOM_LIBRARY_SUFFIX variable. ENH: Wrap PipelineMonitorImageFilter. BUG: Update MIDAS url for https in archive testing data script. ENH: Wrap std::vector< itk::ImageRegion >. BUG: Fix wrapping build with DEFAULT_MODULES OFF. ENH: Add RGB pixel support to ImageToVTKImageFilter. ENH: Add RGB and vector pixel type wrapping for ImageToVTKImageFilter. STYLE: Use PixelType and ImageType in Python tests. ENH: Avoid template type specification in Python wrapping. COMP: Do not use has_key in itkTemplate New. DOC: Emphasize that push access is not required to contribute patches. ENH: Download SWIG and PCRE from midas3.kitware.com. COMP: Ignore build warning from KWStyle's boost. BUG: Remove Azure ExternalData resource. BUG: ExternalData downloads from midas3.kitware.com only supports https. BUG: slicer.kitware.com/midas3/ ExternalData will not support http. ENH: Update the VNL README-ITK.txt subtree commit revision. BUG: Mark VXL internal CMake variables as advanced. BUG: Run itk_module_target on itknetlib. DOC: Direct patches for VXL upstream to the GitHub repository. BUG: Run itk_module_target on itknetlib. COMP: Account for removal of vcl_* from upstream VXL. COMP: Remove itkTypeMacro from BioCellHelper. COMP: Convert itkBioCellTest arguments from double to int. COMP: Turn off BUILD_DOCUMENTATION for VNL. BUG: Install VXL config files to backwards-compatible locations. ENH: Remove vcl_complex from the wrapping. BUG: Install vnl_export.h and vnl_algo_export.h to previous locations. BUG: midas3.kitware.com only supports the https protocol. BUG: ImageIOBase SetDimensions should take SizeValueType. ENH: Add wrapping for ImagePCAShapeModelEstimator. COMP: Do not specify COMPONENTS with find_package(VTK. DOC: Fix FFTW warning grammar. COMP: Build against system HDF5 1.8.16. ENH: Set a default CMAKE_BUILD_TYPE when building a module externally COMP: Make initial HDF5 discovery of 1.8.16 quiet. ENH: Use hidden symbol visibility for the CPython extension modules. ENH: Turn on CMAKE_POSITION_INDEPENDENT_CODE by default. BUG: FEMLoadPoint uninitialized value in the constructor. BUG: Fix wrapping of complex types in VNL. ENH: Bump CMakeLists.txt version 4.9.1. COMP: Address ITKCommon Python submodule order. BUG: Extend ExternalData_TIMEOUT_ABSOLUTE to 900 seconds. BUG: Do not run KWStyle Git config on a release tarball. COMP: Ambiguous RGBPixel access in CustomColormapFunction. BUG: Prevent division by zero in PhasedArray3DSpecialCoordinatesImage. BUG: Initialize azimuth and elevation to pi/2 in PhasedArray3D. BUG: Increase MaskLabel backwards compatibility in N4 bias correction. ENH: Deprecate MaskLabel in N4BiasFieldCorrectionImageFilter. COMP: Update CastXML to support Visual Studio 2015 Update 2. COMP: Do not set wrapping library visibility with static builds. COMP: Update CastXML to support Visual Studio 2015 Update 2. COMP: Broaden the KWStyle warning exception. COMP: Update KWStyle version. BUG: Do not use the same output file in N4BiasField Test 2,3. COMP: Expand EXERCISE_BASIC_OBJECT_METHODS for other GCC versions. ENH: Update Cuberille Remote to 2015-05-01. ENH: Enable registration of the IOOpenSlide module through CMake. ENH: Update itk.org URL's for HTTPS support. BUG: Use CastXML built against LLVM with LLVM_ENABLE_TERMINFO OFF. BUG: Fix Python wrapping on Windows when ITK_USE_64BIT_IDS is ON. Michka Popoff (12): ENH: Use importlib for python 3.4 instead of imp ENH: Update to Swig 3.0.8 ENH: Update PCRE to version 8.38 ENH: Wrap RayCastInterpolateImageFunction ENH: Wrap RayCastInterpolateImageFunction COMP: Remove debug output after vcl_complex removal from wrapping ENH: Consolidate .idx file generation with swig .i generation. ENH: Update UpdatepygccxmlFromUpstream.sh script COMP: Set CastXML path and name for pygccxml 1.7.3 COMP: Fix RayCastInterpolateImageFunction wrapping for image dim 2 ENH: Use argparse instead of optparse in igenerator.py ENH: Use https URL for OS X castxml binary (for consistency) Nick Tustison (2): ENH: Add fixed/moving masking in reg. methods. ENH: Making the mask usage consistent with ITK. Pablo Hernandez-Cerdan (1): COMP: Fix warn in FFTW about delete []. Sean McBride (18): COMP: Made script OS X compatible COMP: mark GDCM GetSeriesHelper() method as deprecated BUG: update script to fetch GDCM from its release-2-4 branch instead of master DOC: Updated comment to reflect new GDCM version COMP: Fixed recently introduced build error with deprecated GDCM method BUG: Fixed invalid memory access found by ASan COMP: Fixed clang warning about macro expansion giving defined COMP: Fixed minor dashboards warnings and typos. COMP: Fixed a bunch of clang -Wunreachable-code-break warnings COMP: fixed some dashboard warnings (dead code, false positive) BUG: Fixed off-by-1 error found by ASan COMP: Fixed clang -Wcomma warning COMP: Introduce ITK_FALLTHROUGH, to suppress switch fall through warnings COMP: Fixed -Wwritable-strings warnings COMP: Fixed remaining -Wcomma warnings ENH: switch gdcm to release branch, not release-2-4 COMP: Hack HDF5 to build under ASan & UBSan COMP: fixed clang -Wdeprecated-writable-strings warning Shawn Waldon (1): STYLE: move itkGaussianDerivativeOperator Sujin Philip (1): STYLE: Move itkBox* Filters Sumedha Singla (3): ENH: Issue: ITK#3363 Replaced assignment in SetParameters function. ENH: Remove unnecessary const_cast BUG: Fixed the test itkHDF5ImageIOTest VXL Maintainers (9): VNL 2015-11-22 (ea1d60fb) VNL 2016-03-02 (cb31149e) VNL 2016-03-13 (ae34f0fc) VNL 2016-03-15 (751698ab) VNL 2016-03-19 (df10fefa) VNL 2016-03-25 (f0040231) VNL 2016-03-30 (88f50849) VNL 2016-04-22 (0ed18124) VNL 2016-04-26 (6b168535) Vladimir S. FONOV (3): MINC 2015-12-17 (dcb93a5f) MINC 2016-01-30 (783bca38) MINC 2016-02-24 (8632513e) Ziv Yaniv (1): BUG: Interpretation of the Euler angles ZYX or ZXY was not exported. ITK Sphinx Examples Changelog --------------------------------------------- D?enan Zuki? (1): ENH: Default is current directory. Avoid usage of the class SeriesHelper. Matt McCormick (19): BUG: Do not depend on the VTK/OpenCV build when system provided. ENH: Add ConvertAnitkImageTovtkImageData example. ENH: Bump VTK's superbuild version to 7.0.0. STYLE: CMake style updates to AddOffsetToIndex/CMakeLists.txt ENH: Updates to CreateNewExample.py.in ENH: Add ConvertvtkImageDataToAnitkImage example. ENH: Update sphinx-bootstrap-theme to v0.4.8 ENH: Add Python version of StreamAPipeline. ENH: Add ConvertAnRGBitkImageTovtkImageData ENH: Add a PACE progress bar. ENH: Add more Python content to CreateNewExample.py. ENH: Add ConvertRGBvtkImageDataToAnitkImage BUG: Disable Create3DVolume Python baseline test. ENH: Add PerformRegistrationOnVectorImages. ENH: Update itk.org URL's for HTTPS support. COMP: Use itk::IndexValueType for subdomain index. COMP: Bump OpenCV to 3.1.0. BUG: Fix superbuild dependencies. ENH: Bump ITK to v4.10.0. ITK Software Guide Changelog --------------------------------------------- Matt McCormick (6): DOC: Correct spelling in the wrapping description. BUG: ExternalData servers now use https. ENH: Update itk.org URL's for HTTPS support. DOC: Adding wrapper .dll's to PATH on Windows is no longer necessary. DOC: Document how to add a third-party dependency to a module. ENH: Bump ITK ExternalProject to v4.10.0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From brad at lowekamp.net Mon Jun 6 11:10:27 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Mon, 6 Jun 2016 11:10:27 -0400 Subject: [ITK-dev] Gerrit robots down? Message-ID: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> I am not seeing any of robots working on gerrit. Can we get these working again? Thanks Brad From jchris.fillionr at kitware.com Mon Jun 6 15:17:06 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Mon, 6 Jun 2016 15:17:06 -0400 Subject: [ITK-dev] Gerrit robots down? In-Reply-To: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> Message-ID: Hi Brad, The missing robots are most likely due to the power failure caused by the remodeling/construction in our North Carolina office. I anticipate they will be back online tomorrow or the day after. Thanks for your patience, Jc On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp wrote: > I am not seeing any of robots working on gerrit. Can we get these working > again? > > Thanks > Brad > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From brad at lowekamp.net Thu Jun 9 14:38:02 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Thu, 9 Jun 2016 14:38:02 -0400 Subject: [ITK-dev] Gerrit robots down? In-Reply-To: References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> Message-ID: <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> Hello, I am still not seeing any robot build in gerrit. Thanks, Brad > On Jun 6, 2016, at 3:17 PM, Jean-Christophe Fillion-Robin wrote: > > Hi Brad, > > The missing robots are most likely due to the power failure caused by the remodeling/construction in our North Carolina office. > > I anticipate they will be back online tomorrow or the day after. > > Thanks for your patience, > Jc > > > On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp > wrote: > I am not seeing any of robots working on gerrit. Can we get these working again? > > Thanks > Brad > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > > > -- > +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jchris.fillionr at kitware.com Thu Jun 9 15:10:56 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Thu, 9 Jun 2016 15:10:56 -0400 Subject: [ITK-dev] Gerrit robots down? In-Reply-To: <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> Message-ID: Hi Brad, Considering our office floor is undergoing some construction/remodelling, the power in the room physically hosting the server was out. This most likely explained the downtime. Now the power is back, I just restarted the machine, it is currently running a "disk check". I will let you know how it goes. Thanks Jc On Thu, Jun 9, 2016 at 2:38 PM, Bradley Lowekamp wrote: > Hello, > > I am still not seeing any robot build in gerrit. > > Thanks, > Brad > > On Jun 6, 2016, at 3:17 PM, Jean-Christophe Fillion-Robin < > jchris.fillionr at kitware.com> wrote: > > Hi Brad, > > The missing robots are most likely due to the power failure caused by the > remodeling/construction in our North Carolina office. > > I anticipate they will be back online tomorrow or the day after. > > Thanks for your patience, > Jc > > > On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp > wrote: > >> I am not seeing any of robots working on gerrit. Can we get these working >> again? >> >> Thanks >> Brad >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> > > > > -- > +1 919 869 8849 > > > -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From brad at lowekamp.net Mon Jun 13 09:39:35 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Mon, 13 Jun 2016 09:39:35 -0400 Subject: [ITK-dev] Gerrit robots down? In-Reply-To: References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> Message-ID: I am still not seeing any sign of the robots on the dashboard? Brad > On Jun 9, 2016, at 3:10 PM, Jean-Christophe Fillion-Robin wrote: > > Hi Brad, > > Considering our office floor is undergoing some construction/remodelling, the power in the room physically hosting the server was out. This most likely explained the downtime. > > Now the power is back, I just restarted the machine, it is currently running a "disk check". I will let you know how it goes. > > Thanks > Jc > > On Thu, Jun 9, 2016 at 2:38 PM, Bradley Lowekamp > wrote: > Hello, > > I am still not seeing any robot build in gerrit. > > Thanks, > Brad > >> On Jun 6, 2016, at 3:17 PM, Jean-Christophe Fillion-Robin > wrote: >> >> Hi Brad, >> >> The missing robots are most likely due to the power failure caused by the remodeling/construction in our North Carolina office. >> >> I anticipate they will be back online tomorrow or the day after. >> >> Thanks for your patience, >> Jc >> >> >> On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp > wrote: >> I am not seeing any of robots working on gerrit. Can we get these working again? >> >> Thanks >> Brad >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> >> >> >> -- >> +1 919 869 8849 > > > > > -- > +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jchris.fillionr at kitware.com Tue Jun 14 09:30:14 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Tue, 14 Jun 2016 09:30:14 -0400 Subject: [ITK-dev] Gerrit robots down? In-Reply-To: References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> Message-ID: Hi Hans, Brad, The issue has been identified. The machine used internally as "Jenkins" server (the one mentioned in my earlier email) does not finalize its bootup sequence. We are working on setting up a replacement server using the backed up configuration. Thanks for your patience, Jc On Mon, Jun 13, 2016 at 9:39 AM, Bradley Lowekamp wrote: > I am still not seeing any sign of the robots on the dashboard? > > Brad > > On Jun 9, 2016, at 3:10 PM, Jean-Christophe Fillion-Robin < > jchris.fillionr at kitware.com> wrote: > > Hi Brad, > > Considering our office floor is undergoing some construction/remodelling, > the power in the room physically hosting the server was out. This most > likely explained the downtime. > > Now the power is back, I just restarted the machine, it is currently > running a "disk check". I will let you know how it goes. > > Thanks > Jc > > On Thu, Jun 9, 2016 at 2:38 PM, Bradley Lowekamp > wrote: > >> Hello, >> >> I am still not seeing any robot build in gerrit. >> >> Thanks, >> Brad >> >> On Jun 6, 2016, at 3:17 PM, Jean-Christophe Fillion-Robin < >> jchris.fillionr at kitware.com> wrote: >> >> Hi Brad, >> >> The missing robots are most likely due to the power failure caused by the >> remodeling/construction in our North Carolina office. >> >> I anticipate they will be back online tomorrow or the day after. >> >> Thanks for your patience, >> Jc >> >> >> On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp >> wrote: >> >>> I am not seeing any of robots working on gerrit. Can we get these >>> working again? >>> >>> Thanks >>> Brad >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-developers >>> >> >> >> >> -- >> +1 919 869 8849 >> >> >> > > > -- > +1 919 869 8849 > > > -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jchris.fillionr at kitware.com Tue Jun 14 14:39:13 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Tue, 14 Jun 2016 14:39:13 -0400 Subject: [ITK-dev] Gerrit robots down? In-Reply-To: References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> Message-ID: Hi Brad, Hans, The Jenkins server is now back online (on our internal network). I will check the status of the build bots. We should then expect the queue of topic to be processed. Thanks for your patience, Jc On Jun 14, 2016 9:30 AM, "Jean-Christophe Fillion-Robin" < jchris.fillionr at kitware.com> wrote: Hi Hans, Brad, The issue has been identified. The machine used internally as "Jenkins" server (the one mentioned in my earlier email) does not finalize its bootup sequence. We are working on setting up a replacement server using the backed up configuration. Thanks for your patience, Jc On Mon, Jun 13, 2016 at 9:39 AM, Bradley Lowekamp wrote: > I am still not seeing any sign of the robots on the dashboard? > > Brad > > On Jun 9, 2016, at 3:10 PM, Jean-Christophe Fillion-Robin < > jchris.fillionr at kitware.com> wrote: > > Hi Brad, > > Considering our office floor is undergoing some construction/remodelling, > the power in the room physically hosting the server was out. This most > likely explained the downtime. > > Now the power is back, I just restarted the machine, it is currently > running a "disk check". I will let you know how it goes. > > Thanks > Jc > > On Thu, Jun 9, 2016 at 2:38 PM, Bradley Lowekamp > wrote: > >> Hello, >> >> I am still not seeing any robot build in gerrit. >> >> Thanks, >> Brad >> >> On Jun 6, 2016, at 3:17 PM, Jean-Christophe Fillion-Robin < >> jchris.fillionr at kitware.com> wrote: >> >> Hi Brad, >> >> The missing robots are most likely due to the power failure caused by the >> remodeling/construction in our North Carolina office. >> >> I anticipate they will be back online tomorrow or the day after. >> >> Thanks for your patience, >> Jc >> >> >> On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp >> wrote: >> >>> I am not seeing any of robots working on gerrit. Can we get these >>> working again? >>> >>> Thanks >>> Brad >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-developers >>> >> >> >> >> -- >> +1 919 869 8849 >> >> >> > > > -- > +1 919 869 8849 > > > -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.barbierdereuille at gmail.com Wed Jun 15 09:36:37 2016 From: pierre.barbierdereuille at gmail.com (Pierre Barbier de Reuille) Date: Wed, 15 Jun 2016 13:36:37 +0000 Subject: [ITK-dev] Error using fftwf_* functions when FFTW is compiled with double Message-ID: Hey, I just compiled the latest version of ITK (4.10.0) with MinGW under windows and I had a problem. I compiled it with FFTW compiled with double precision, but in the file Module/Filtering/FFT/src/itkFFTWGlobalConfiguration.cxx the function fftwf_import_wisdom_from_file is used twice when fftw_import_wisdom_from_file should be used: on lines 632 and 709. Otherwise, everything compiled just fine. Cheers, Pierre -- Dr. Barbier de Reuille, Pierre Institute of Plant Sciences University of Bern Altenbergrain 21, CH-3013 Bern, Switzerland -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Wed Jun 15 14:35:18 2016 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Jun 2016 14:35:18 -0400 Subject: [ITK-dev] Error using fftwf_* functions when FFTW is compiled with double In-Reply-To: References: Message-ID: Hello, Looks like you found a bug! Can you please test the change and submit a patch for review? https://itk.org/Wiki/ITK/Git/Develop Thanks, Brad > On Jun 15, 2016, at 9:36 AM, Pierre Barbier de Reuille wrote: > > Hey, > > I just compiled the latest version of ITK (4.10.0) with MinGW under windows and I had a problem. > > I compiled it with FFTW compiled with double precision, but in the file Module/Filtering/FFT/src/itkFFTWGlobalConfiguration.cxx the function fftwf_import_wisdom_from_file is used twice when fftw_import_wisdom_from_file should be used: on lines 632 and 709. > > Otherwise, everything compiled just fine. > > Cheers, > > Pierre > > -- > Dr. Barbier de Reuille, Pierre > Institute of Plant Sciences > University of Bern > Altenbergrain 21, CH-3013 Bern, Switzerland > > _______________________________________________ > 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 pierre.barbierdereuille at gmail.com Fri Jun 17 05:21:05 2016 From: pierre.barbierdereuille at gmail.com (Pierre Barbier de Reuille) Date: Fri, 17 Jun 2016 09:21:05 +0000 Subject: [ITK-dev] Error using fftwf_* functions when FFTW is compiled with double In-Reply-To: References: Message-ID: Hello, sorry for the delay, but it took a while to test everything correctly. So I created a topic called fix_fftwf_used_with_fftwd and made the modification. I tested it with the FFTW compiled by ITK itself and all FFTW-related tests passed without problem. There are some tests failing, but they are unrelated to the modification. For completeness, here is the list of tests that failed: The following tests FAILED: 79 - vnl_algo_test_convolve (Failed) 824 - itkHDF5ImageIOTest (Failed) 825 - itkHDF5ImageIOStreamingReadWriteTest (Failed) 1177 - itkCastImageFilterTest (Failed) Cheers, Pierre On Wed, 15 Jun 2016 at 20:35 Bradley Lowekamp wrote: > Hello, > > Looks like you found a bug! > > Can you please test the change and submit a patch for review? > https://itk.org/Wiki/ITK/Git/Develop > > Thanks, > Brad > > On Jun 15, 2016, at 9:36 AM, Pierre Barbier de Reuille < > pierre.barbierdereuille at gmail.com> wrote: > > Hey, > > I just compiled the latest version of ITK (4.10.0) with MinGW under > windows and I had a problem. > > I compiled it with FFTW compiled with double precision, but in the file > Module/Filtering/FFT/src/itkFFTWGlobalConfiguration.cxx the function > fftwf_import_wisdom_from_file is used twice when > fftw_import_wisdom_from_file should be used: on lines 632 and 709. > > Otherwise, everything compiled just fine. > > Cheers, > > Pierre > > -- > > Dr. Barbier de Reuille, Pierre > Institute of Plant Sciences > University of Bern > Altenbergrain 21, CH-3013 Bern, Switzerland > > _______________________________________________ > 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 > > > -- Dr. Barbier de Reuille, Pierre Institute of Plant Sciences University of Bern Altenbergrain 21, CH-3013 Bern, Switzerland -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Fri Jun 17 07:54:46 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Fri, 17 Jun 2016 11:54:46 +0000 Subject: [ITK-dev] Error using fftwf_* functions when FFTW is compiled with double In-Reply-To: References: Message-ID: <7743F9E5-6F51-4F7F-B7B9-A8C10A4DD550@mail.nih.gov> Nice! Thank you for your contribution. There is already a patch out for the HDF5 issue here: http://review.source.kitware.com/#/c/21231/ You could checkout that patch out, test it and review it, to ensure it addresses your issue. Thanks, Brad On Jun 17, 2016, at 5:21 AM, Pierre Barbier de Reuille > wrote: Hello, sorry for the delay, but it took a while to test everything correctly. So I created a topic called fix_fftwf_used_with_fftwd and made the modification. I tested it with the FFTW compiled by ITK itself and all FFTW-related tests passed without problem. There are some tests failing, but they are unrelated to the modification. For completeness, here is the list of tests that failed: The following tests FAILED: 79 - vnl_algo_test_convolve (Failed) 824 - itkHDF5ImageIOTest (Failed) 825 - itkHDF5ImageIOStreamingReadWriteTest (Failed) 1177 - itkCastImageFilterTest (Failed) Cheers, Pierre On Wed, 15 Jun 2016 at 20:35 Bradley Lowekamp > wrote: Hello, Looks like you found a bug! Can you please test the change and submit a patch for review? https://itk.org/Wiki/ITK/Git/Develop Thanks, Brad On Jun 15, 2016, at 9:36 AM, Pierre Barbier de Reuille > wrote: Hey, I just compiled the latest version of ITK (4.10.0) with MinGW under windows and I had a problem. I compiled it with FFTW compiled with double precision, but in the file Module/Filtering/FFT/src/itkFFTWGlobalConfiguration.cxx the function fftwf_import_wisdom_from_file is used twice when fftw_import_wisdom_from_file should be used: on lines 632 and 709. Otherwise, everything compiled just fine. Cheers, Pierre -- Dr. Barbier de Reuille, Pierre Institute of Plant Sciences University of Bern Altenbergrain 21, CH-3013 Bern, Switzerland _______________________________________________ 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 -- Dr. Barbier de Reuille, Pierre Institute of Plant Sciences University of Bern Altenbergrain 21, CH-3013 Bern, Switzerland -------------- next part -------------- An HTML attachment was scrubbed... URL: From brad at lowekamp.net Mon Jun 20 10:57:25 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Mon, 20 Jun 2016 10:57:25 -0400 Subject: [ITK-dev] A couple critical patches for the release branch Message-ID: Hello, Can a couple critical patches for SimpleITK be merged into the release branch: commit 679b23d1513732b020fb04b7e28d69e3daaed833 Author: Bradley Lowekamp Date: Fri Jun 10 13:35:51 2016 -0400 COMP: Fix undefined NumericTraits::Zero and One errors with mingw64 This correct the preproces variable checked to be specific for Microsofts compiler. Change-Id: I67d295fef24b31b0ab24a8894565fbc249b39292 commit b177530b5d4ceab8097b3fb47376c433e09bfdc8 Author: Bradley Lowekamp Date: Thu May 26 11:34:50 2016 -0400 COMP: Address VS9 ambiguous std::abs call in Haung calculator When using 64-bit indexes with MS Visual Studio 9, std::abs of __int64 is not implemented. We use the concise tri-nary operator to implement abs. Change-Id: I91bb0878f8289144de7ddc61c01f44a0f58ca962 Thanks! Brad -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Jun 21 08:48:16 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 21 Jun 2016 12:48:16 +0000 Subject: [ITK-dev] [ITK] A couple critical patches for the release branch In-Reply-To: References: Message-ID: Hello, Can these patches pleased be merged into the release branch. Thanks, Brad On Jun 20, 2016, at 10:57 AM, Bradley Lowekamp > wrote: Hello, Can a couple critical patches for SimpleITK be merged into the release branch: commit 679b23d1513732b020fb04b7e28d69e3daaed833 Author: Bradley Lowekamp > Date: Fri Jun 10 13:35:51 2016 -0400 COMP: Fix undefined NumericTraits::Zero and One errors with mingw64 This correct the preproces variable checked to be specific for Microsofts compiler. Change-Id: I67d295fef24b31b0ab24a8894565fbc249b39292 commit b177530b5d4ceab8097b3fb47376c433e09bfdc8 Author: Bradley Lowekamp > Date: Thu May 26 11:34:50 2016 -0400 COMP: Address VS9 ambiguous std::abs call in Haung calculator When using 64-bit indexes with MS Visual Studio 9, std::abs of __int64 is not implemented. We use the concise tri-nary operator to implement abs. Change-Id: I91bb0878f8289144de7ddc61c01f44a0f58ca962 Thanks! Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Thu Jun 23 09:56:34 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 23 Jun 2016 13:56:34 +0000 Subject: [ITK-dev] [ITK] A couple critical patches for the release branch In-Reply-To: References: Message-ID: <854C012C-E5E9-4EB5-8E02-A10811EEC51A@mail.nih.gov> Can someone please help me by merging these patches into the ITK release branch? Thanks! Brad On Jun 21, 2016, at 8:48 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] > wrote: Hello, Can these patches pleased be merged into the release branch. Thanks, Brad On Jun 20, 2016, at 10:57 AM, Bradley Lowekamp > wrote: Hello, Can a couple critical patches for SimpleITK be merged into the release branch: commit 679b23d1513732b020fb04b7e28d69e3daaed833 Author: Bradley Lowekamp > Date: Fri Jun 10 13:35:51 2016 -0400 COMP: Fix undefined NumericTraits::Zero and One errors with mingw64 This correct the preproces variable checked to be specific for Microsofts compiler. Change-Id: I67d295fef24b31b0ab24a8894565fbc249b39292 commit b177530b5d4ceab8097b3fb47376c433e09bfdc8 Author: Bradley Lowekamp > Date: Thu May 26 11:34:50 2016 -0400 COMP: Address VS9 ambiguous std::abs call in Haung calculator When using 64-bit indexes with MS Visual Studio 9, std::abs of __int64 is not implemented. We use the concise tri-nary operator to implement abs. Change-Id: I91bb0878f8289144de7ddc61c01f44a0f58ca962 Thanks! Brad _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _______________________________________________ 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 brad.king at kitware.com Thu Jun 23 10:10:25 2016 From: brad.king at kitware.com (Brad King) Date: Thu, 23 Jun 2016 10:10:25 -0400 Subject: [ITK-dev] [ITK] A couple critical patches for the release branch In-Reply-To: <854C012C-E5E9-4EB5-8E02-A10811EEC51A@mail.nih.gov> References: <854C012C-E5E9-4EB5-8E02-A10811EEC51A@mail.nih.gov> Message-ID: <576BEDD1.3030900@kitware.com> On 06/23/2016 09:56 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Can someone please help me by merging these patches into the ITK release branch? Done. Sorry for the delay. Your previous messages seemed to be about SimpleITK rather than ITK. -Brad K From blowekamp at mail.nih.gov Thu Jun 23 10:13:21 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 23 Jun 2016 14:13:21 +0000 Subject: [ITK-dev] [ITK] A couple critical patches for the release branch In-Reply-To: <576BEDD1.3030900@kitware.com> References: <854C012C-E5E9-4EB5-8E02-A10811EEC51A@mail.nih.gov> <576BEDD1.3030900@kitware.com> Message-ID: Thank you very much! I thought that might have been a source of confusion when I re-read the original message. Brad > On Jun 23, 2016, at 10:10 AM, Brad King wrote: > > On 06/23/2016 09:56 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: >> Can someone please help me by merging these patches into the ITK release branch? > > Done. Sorry for the delay. Your previous messages seemed to be > about SimpleITK rather than ITK. > > -Brad K >