From blowekamp at mail.nih.gov Wed May 3 09:32:42 2017 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 3 May 2017 13:32:42 +0000 Subject: [ITK-dev] [ANN] SimpleITK 1.0.0 Release In-Reply-To: <6CCDD8FC6578314C902BBF87D511D9D8F2A28B06@exchmbx01> References: <3A9B6734-7719-4069-8E7B-E0F1B35A0A5F@mail.nih.gov> <6CCDD8FC6578314C902BBF87D511D9D8F2A28B06@exchmbx01> Message-ID: Hello, I presume you are have a win64 Python 2.7 version of Anaconda? We are unfortunetly missing conda binaries for win64 with python 2.7 due to linker limitations for Visual Studio 2008. We have not yet found a configuration/flag that gets this configuration to produce the binary. Your options are as follows: 1) Make the jump to Python 3! 2) Try using the wheel binary from PyPI: `pip install simpleitk`. 3) Take a step back to 32-bit Python 2.7. Yes, the `many` term was a intentionally vague because of the large number of platform and version options available. The list of packages can easily be seen here: https://anaconda.org/SimpleITK/SimpleITK/files For completeness here is a list of 1.0.0 packages currently on anaconda.org: linux-32/simpleitk-1.0.0-py27_0.tar.bz2 linux-32/simpleitk-1.0.0-py34_0.tar.bz2 linux-32/simpleitk-1.0.0-py35_0.tar.bz2 linux-32/simpleitk-1.0.0-py36_0.tar.bz2 linux-64/simpleitk-1.0.0-py27_0.tar.bz2 linux-64/simpleitk-1.0.0-py34_0.tar.bz2 linux-64/simpleitk-1.0.0-py35_0.tar.bz2 linux-64/simpleitk-1.0.0-py36_0.tar.bz2 osx-64/simpleitk-1.0.0-py27_0.tar.bz2 osx-64/simpleitk-1.0.0-py34_0.tar.bz2 osx-64/simpleitk-1.0.0-py35_0.tar.bz2 osx-64/simpleitk-1.0.0-py36_0.tar.bz2 win-32/simpleitk-1.0.0-py27_0.tar.bz2 win-32/simpleitk-1.0.0-py34_0.tar.bz2 win-32/simpleitk-1.0.0-py35_0.tar.bz2 win-32/simpleitk-1.0.0-py36_0.tar.bz2 win-64/simpleitk-1.0.0-py34_0.tar.bz2 win-64/simpleitk-1.0.0-py35_0.tar.bz2 win-64/simpleitk-1.0.0-py36_0.tar.bz2 list of 1.0.0 packages available on sourceforge.net/projects/simpleitk/: CSharp/SimpleITK-1.0.0-CSharp-win32-x86.zip CSharp/SimpleITK-1.0.0-CSharp-win64-x64.zip Java/SimpleITK-1.0.0-Java-win32.zip Java/SimpleITK-1.0.0-Java-win64.zip Python/SimpleITK-1.0.0-1.tar.gz Python/SimpleITK-1.0.0-cp27-cp27m-macosx_10_6_intel.whl Python/SimpleITK-1.0.0-cp27-cp27m-macosx_10_6_x86_64.whl Python/SimpleITK-1.0.0-cp27-cp27m-manylinux1_i686.whl Python/SimpleITK-1.0.0-cp27-cp27m-manylinux1_x86_64.whl Python/SimpleITK-1.0.0-cp27-cp27mu-manylinux1_i686.whl Python/SimpleITK-1.0.0-cp27-cp27mu-manylinux1_x86_64.whl Python/SimpleITK-1.0.0-cp27-cp27m-win32.whl Python/SimpleITK-1.0.0-cp27-cp27m-win_amd64.whl Python/SimpleITK-1.0.0-cp33-cp33m-manylinux1_i686.whl Python/SimpleITK-1.0.0-cp33-cp33m-manylinux1_x86_64.whl Python/SimpleITK-1.0.0-cp34-cp34m-macosx_10_6_x86_64.whl Python/SimpleITK-1.0.0-cp34-cp34m-manylinux1_i686.whl Python/SimpleITK-1.0.0-cp34-cp34m-manylinux1_x86_64.whl Python/SimpleITK-1.0.0-cp34-cp34m-win32.whl Python/SimpleITK-1.0.0-cp34-cp34m-win_amd64.whl Python/SimpleITK-1.0.0-cp35-cp35m-macosx_10_6_x86_64.whl Python/SimpleITK-1.0.0-cp35-cp35m-manylinux1_i686.whl Python/SimpleITK-1.0.0-cp35-cp35m-manylinux1_x86_64.whl Python/SimpleITK-1.0.0-cp35-cp35m-win32.whl Python/SimpleITK-1.0.0-cp35-cp35m-win_amd64.whl Python/SimpleITK-1.0.0-cp36-cp36m-macosx_10_6_x86_64.whl Python/SimpleITK-1.0.0-cp36-cp36m-manylinux1_i686.whl Python/SimpleITK-1.0.0-cp36-cp36m-manylinux1_x86_64.whl Python/SimpleITK-1.0.0-cp36-cp36m-win32.whl Python/SimpleITK-1.0.0-cp36-cp36m-win_amd64.whl Python/SimpleITK-1.0.0.zip Python/SimpleITKPythonPackage-1.0.0.tar.gz Source/SimpleITK-1.0.0.tar.gz Source/SimpleITK-1.0.0.tar.xz Source/SimpleITK-1.0.0.zip Source/SimpleITKData-1.0.0.tar.gz Source/SimpleITKData-1.0.0.tar.xz Source/SimpleITKData-1.0.0.zip PyPI is also hosting the above wheels for interoperability with the `pip` package manager, and does not have the SimpleITKPythonPackage source. Hope that clarifies the situations. Brad On May 3, 2017, at 7:10 AM, Robert.Atwood at diamond.ac.uk wrote: Hi, Regarding the 1.0.0 release announcement .. ``` - Many Conda package have been upload to Anaconda Cloud on the `SimpleITK`. These can be installed with: ``` conda install -c simpleitk simpleitk ``` If I do this, I get the version 0.9.1 Is this expected? If so the release announcement should clarify that the ?many? packages uploaded don?t yet include the actual release that is announced ? (C:\Users\kny48981\AppData\Local\Continuum\Anaconda2) C:\Users\kny48981>conda in stall -c simpleitk simpleitk Fetching package metadata ............. Solving package specifications: . Package plan for installation in environment C:\Users\kny48981\AppData\Local\Con tinuum\Anaconda2: The following NEW packages will be INSTALLED: simpleitk: 0.9.1-py27_0 simpleitk Proceed ([y]/n)? y From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Lowekamp, Bradley (NIH/NLM/LHC) [C] Sent: Friday, April 14, 2017 4:56 PM To: itk; ITK; Insight-users Subject: [ITK-users] [ANN] SimpleITK 1.0.0 Release The SimpleITK Development Team and the Insight Software Consortium are proud to announce the first major release of SimpleITK. SimpleITK is a simplified multi-language interface to the National Library of Medicine?s Insight Segmentation and Registration Toolkit (ITK). Providing an easy to use interface to ITK. SimpleITK is intended to broaden the use of ITK to researchers and domain scientist who are novice software developers, enabling them to benefit from the image-analysis power of ITK. For experienced software developers, the toolkit enables rapid prototyping of image segmentation and registration frameworks and facilitates evaluation of the effects algorithmic parameter settings have on results with minimal programming effort. In the educational setting SimpleITK's concise interface allows students to experiment with well known algorithms, enhancing their understanding of algorithm performance without the need for advanced software engineering skills. The toolkit development process follows best software engineering practices including code reviews and continuous integration testing, with results displayed online allowing everyone to gauge the status of the current code and any code that is under consideration for incorporation into the toolkit. User support is available through a dedicated mailing list and the project?s Wiki. SimpleITK is available for the following programing languages: Python, R, Java, C#, C++, Lua, Ruby, and TCL. Binary versions of the toolkit are available for the GNU Linux, Apple OS X, and Microsoft Windows operating systems. All of the source code is freely available on github under an Apache-2.0 license. Downloading SimpleITK Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK Wiki (https://itk.org/Wiki/SimpleITK/GettingStarted). - Python Binary Downloads - Python binary wheels are available for download. It is important to have the latest version of pip to ensure correct wheel compatibility and installation. To install the latest SimpleITK package form PyPI: ``` pip install --upgrade pip pip install SimpleITK ``` - Many Conda package have been upload to Anaconda Cloud on the `SimpleITK`. These can be installed with: ``` conda install -c simpleitk simpleitk ``` - A complete available set of compiled binaries, including select CSharp and Java distributions, along with source and data tar-balls are available on Source Forge (https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/). Release Notes - Key Improvements: - Improved Python data bridge - New Python method `GetArrayViewFromImage` provides copy free read-only access - Updated Python data structures to use `memory view` objects - New language specific building SimpleITK front-ends - R devtools based installer (https://github.com/SimpleITK/SimpleITKRInstaller). - Python: scripts for building wheels (https://github.com/SimpleITK/SimpleITKPythonPackage) and a Conda recipe (https://github.com/SimpleITK/SimpleITKCondaRecipe). - Improved writing DICOM tags when writing a slice, and disabled writing a DICOM series with the ImageSeriesWriter - Support use of virtual image domain in the `ImageRegistrationMethod` - OnePlusOneOptimizer added to registration framework - Improved support for R: propogating C++ exceptions into R, additional R tests - Additional tests for Java - Python and R notebooks repository illustrating the basics and more advanced functionality of SimpleITK (https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks) - Added continous integration via CircleCI - Updated version and improved integration of Google Test - Updated ITK version to 4.11.0+ - Updated minimal required CMake version to 3.0, and numerous CMake changes to support various build configurations - Fix, "pip install" works for Apple Mac OS X. - Updated to usage of SWIG 3.0.11 ( using the latest SIWG is strongly recommended for R ) - Reorganized examples directory into example based sub-directories with multiple languages - Improvements to documentation transmogrification scripts - Many bug fixes and improvement to the build system! - Additional Improvements: - Added multi-hash ExternalData support for sha512 - Added R Documentation files - Update Python and Java documentation strings files - Fix allowing undefined symbols when building standalone language wrapping - Reorganized examples directory - Reorganized filter libraries to match ITK modules - Improved compilation with more specific ITK module usage - Now using modern CMake 3 style properties for exported libraries - API Changes - Replaced return Self with void for wrapped languages, to address memory and segmentation fault issue. - Depricated CMake variables with "SITK" prefix, now consistenly using the "SimpleITK" prefix for configurable CMake variables - Removed `ImageSeriesReader::GetGDCMSeriesFileNames` parameter `loadPrivateTags` parameter. This removes an overloaded version of the class method. - Added `sitkWallClock` enum for a sentinel value for random number seed to indicate initialization from the clock - New method `Image::GetNumberOfPixels` - New method `LabelMapContourOverlayImageFilter::SetColormap` - New method `LabelMapToRGBImageFilter::SetColormap` - New method `ImageRegistrationMethod::SetVirtualDomain` - New method `ImageRegistrationMethod::SetVirtualDomainFromImage` - New seed parameter to `ImageRegistrationMethod::AddMetricSamplingSeed` method - `CastImageFilter::SetOutputPixelType` method no longer accepts the pixel ID by value, uses only enumerated type Enjoy! Bradley Lowekamp -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Wed May 3 10:10:33 2017 From: francois.budin at kitware.com (Francois Budin) Date: Wed, 3 May 2017 10:10:33 -0400 Subject: [ITK-dev] Patches for the 4.11.1 release Message-ID: Hi folks, We would like to publish a 4.11.1 bugfix release on Friday. Here is the current set of patches on the release branch since 4.11.0: Bradley Lowekamp (6): BUG: Correct variable name used to check CXX version COMP: Enable hidden visibility property with NIFTI static libraries COMP: Enable hidden visibility property with GIFTI static libraries BUG: Initialize ConvergenceValue in constructor BUG: Use CMAKE_DL_LIBS instead of explict "dl" library BUG: Apply changes from MetaIO upstream to remove static variables Floris Berendsen (1): COMP: Added missing png_get_uint_31 name mangling Francois Budin (17): BUG: Addresses 'ordered comparison between pointer and zero' error (clang-4) BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: Missing ITK_OVERRIDE BUG: 3523 Even padding most value representations with space instead of '\0' BUG: KWSys symbols should not be exported with WINDOWS_EXPORT_ALL_SYMBOLS BUG: 3519 KernelTransform WMatrix initialization BUG: Wrapping of itkHessianToObjectnessMeasureImageFilter moved out of Review BUG: Wrap EllipseSpatialObject std::list in Python ENH: Improving usability in IPython BUG: Attribute names cannot start with a digit BUG: Test if 'issubclass' only if 'isclass' is True BUG: 3475 AccumulateImageFilter not setting direction cosines of output image BUG: Do not export GDCM and Expat symbols with WINDOWS_EXPORT_ALL_SYMBOLS BUG: Do not export all symbols from third party libraries on Windows BUG: Certain third party libraries need to export their symbols on Windows BUG: ProjectionImageFilter did not copy direction cosine information to output Jon Haitz Legarreta (1): COMP: Fix signed/unsigned mismatch warning. Matthew McCormick (16): COMP: Add missing headers in OpenCVImageBridge COMP: Use double for gradient calculations in MinMaxCurvatureFlow BUG: Address tab completion with IPython >= 5.0.0 BUG: Do not use terminal_progress with the Jupyter Notebook COMP: Do not require numeric_traits::has_infinity BUG: Fix passing _NO_TR1 definition with VS9 and Python BUG: Always wrap basic type RGBUC COMP: Do not add Visual Studio numeric_traits workarounds with MinGWPy COMP: Increase gold linker requirement to GCC 4.9.0 COMP: Detect Windows with _WIN32 in socket++/fork.cpp COMP: Address Python 2.7 Windows _hypot build errors COMP: Undefine Py_hash_t when wrapping VtkGlue BUG: Improve itkTemplate New compatibility with Python 3 BUG: Correct size specification in ImportImageFilter::SetImportPointer BUG: Improve large file support in MetaIO BUG: LevelSetNeighborhoodExtractor uses spacing Taylor Braun-Jones (1): COMP: Only include the headers for required OpenCV modules (fixup) Are there any patches that are missing? These should be patches that fixes critical issues, regressions, documentation, and compiler support. Thank you, Francois -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Wed May 3 10:59:04 2017 From: francois.budin at kitware.com (Francois Budin) Date: Wed, 3 May 2017 10:59:04 -0400 Subject: [ITK-dev] Patches for the ITK 4.12 Release Candidate 1 Message-ID: Hello fellow ITK developers, We are planning to tag ITK 4.12 Release Candidate 1 on Friday, May 5th. If there is any enhancement that you would like to see included in ITK 4.12.0, please submit your patch as soon as possible as they need to be reviewed and merged prior. As a reminder, this means feature freeze for ?master? and, therefore, enhancements should not be merged until after the release candidate period. Thank you, Francois -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Mon May 8 13:52:21 2017 From: francois.budin at kitware.com (Francois Budin) Date: Mon, 8 May 2017 13:52:21 -0400 Subject: [ITK-dev] [ANN] ITK 4.11.1 has been released! Message-ID: On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.11.1 has been released! Download links can be found at: https://itk.org/ITK/resources/software.html This is a patch release that fixes critical issues, regressions, documentation, and compiler support. Of the numerous issues addressed in this release, most notable build support additions include Microsoft Visual C++ Compiler for Python 2.7, recent Clang in FreeBSD, updates for the RHEL / CentOS toolchain, and improved support for Visual Studio 2017. Other fixes include enabling hidden visibility for NIFTI and GIFTI static libraries, MetaIO updates for improved large image support, and better compatibility of the OpenCVImageBridge. The next feature release, 4.12.0, is scheduled for May 24th. Changes from v4.11.0 to v4.11.1 ------------------------------------------------ Bradley Lowekamp (6): BUG: Correct variable name used to check CXX version COMP: Enable hidden visibility property with NIFTI static libraries COMP: Enable hidden visibility property with GIFTI static libraries BUG: Initialize ConvergenceValue in constructor BUG: Use CMAKE_DL_LIBS instead of explict "dl" library BUG: Apply changes from MetaIO upstream to remove static variables Floris Berendsen (1): COMP: Added missing png_get_uint_31 name mangling Francois Budin (17): BUG: Addresses 'ordered comparison between pointer and zero' error (clang-4) BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: Missing ITK_OVERRIDE BUG: 3523 Even padding most value representations with space instead of '\0' BUG: KWSys symbols should not be exported with WINDOWS_EXPORT_ALL_SYMBOLS BUG: 3519 KernelTransform WMatrix initialization BUG: Wrapping of itkHessianToObjectnessMeasureImageFilter moved out of Review BUG: Wrap EllipseSpatialObject std::list in Python ENH: Improving usability in IPython BUG: Attribute names cannot start with a digit BUG: Test if 'issubclass' only if 'isclass' is True BUG: 3475 AccumulateImageFilter not setting direction cosines of output image BUG: Do not export GDCM and Expat symbols with WINDOWS_EXPORT_ALL_SYMBOLS BUG: Do not export all symbols from third party libraries on Windows BUG: Certain third party libraries need to export their symbols on Windows BUG: ProjectionImageFilter did not copy direction cosine information to output Jon Haitz Legarreta (1): COMP: Fix signed/unsigned mismatch warning. Matthew McCormick (16): COMP: Add missing headers in OpenCVImageBridge COMP: Use double for gradient calculations in MinMaxCurvatureFlow BUG: Address tab completion with IPython >= 5.0.0 BUG: Do not use terminal_progress with the Jupyter Notebook COMP: Do not require numeric_traits::has_infinity BUG: Fix passing _NO_TR1 definition with VS9 and Python BUG: Always wrap basic type RGBUC COMP: Do not add Visual Studio numeric_traits workarounds with MinGWPy COMP: Increase gold linker requirement to GCC 4.9.0 COMP: Detect Windows with _WIN32 in socket++/fork.cpp COMP: Address Python 2.7 Windows _hypot build errors COMP: Undefine Py_hash_t when wrapping VtkGlue BUG: Improve itkTemplate New compatibility with Python 3 BUG: Correct size specification in ImportImageFilter::SetImportPointer BUG: Improve large file support in MetaIO BUG: LevelSetNeighborhoodExtractor uses spacing Taylor Braun-Jones (1): COMP: Only include the headers for required OpenCV modules (fixup) -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Tue May 9 10:45:04 2017 From: francois.budin at kitware.com (Francois Budin) Date: Tue, 9 May 2017 10:45:04 -0400 Subject: [ITK-dev] [ITK-users] [ANN] ITK 4.12 Release Candidate 1 is ready for testing! Message-ID: On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.12 release candidate 1 has been tagged and is available for testing! Please take this opportunity to test the new features in the release candidate. To obtain the source code, use the links: https://github.com/Kitware/ITK/archive/v4.12rc01.zip https://github.com/Kitware/ITK/archive/v4.12rc01.tar.gz A few selected highlights for this release: - Strain remote module added to ITK. Strain quantifies local deformation of a solid body. In medical imaging, it can be used to quantify growth or atrophy of tissue. The module contains filters to computes a strain tensor image from a displacement field image or a general spatial transform. In both cases, infinitesimal, Green-Lagrangian, or Eulerian-Almansi strain can be generated. - Many improvements in ITK Python wrapping: convenient functions to read and write images, better integration in Jupyter Notebook, new filters wrapped, build support for Microsoft Visual C++ Compiler for Python 2.7 - Better compilation support for Microsoft Visual Studio 2017, Clang 4, GCC7 - Filters moved out of Review modules: Morphological Watersheds, and itkHessianToObjectnessMeasureImageFilter - Improvement of palette image support for PNG TIFF and BMP: The user can now choose or not to expand the palette image to true color. - Performance improvements for some ITK filters: itkHistogram (increase speed), itkImagePCAShapeModelEstimator (decrease memory usage). Please test the release candidate and share your experiences on the mailing list, issue tracker, and Gerrit Code Review. An Experimental build, which demonstrates how the test suite performs on your local build system, can be submitted to the dashboard [2] with: mkdir ../ITK-build cd ../ITK-build cmake ../ITK ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit Visual Studio builds must also add ?-C Release? to the ctest command. Notify the mailing list if there are any unexpected failures. Testing your own applications against the RC is also appreciated. Congratulations to the 23 contributors to this release. We would especially like to recognize the new contributors: Sam Horvath, Shusil Dangi, Ben Boeckel, Yann Le Poul, Jean-Baptiste Vimort, and Samuel Gerber. The 4.12.0 final release is scheduled for May 24th. [1] http://www.itk.org/Wiki/ITK/Git [2] http://open.cdash.org/index.php?project=Insight New Features -------------------- * Wrapping Improvements - Enable BridgeNumPy by default with Python wrapping - Build support for Microsoft Visual C++ Compiler for Python 2.7 - BridgeNumpy integrates new pairs of functions. GetArrayViewFromImage() and GetImageViewFromArray() return views on the source object given as a parameter to the function. Memory is shared among input and output objects and the source object still manages pixel buffer memory. The existing functions GetArrayFromImage() and GetImageFromArray() perform a deep copy of the source object. - Similar NumPy bridge functions have been created for VNL matrices and VNL vectors. - Convenience functions imread() and imwrite() have been added to the Python itk namespace. These functions facilitate respectively reading and writing images using ITK without having to specify the input or output image component type. The naming of these functions follows the convention used in several other Python project such as scikit-learn and scipy. - Better integration in Jupyter Notebook: addressed tab completion bug for IPython >= 5.0.0, replaced underscore with ?x? to name attributes that start with a digit to show attributes when trying to autocomplete in IPython. - Wrap itkN4BiasFieldCorrectionImageFilter, NormalVariateGenerator, and PathToImageFilter. - Allows calling ImageFileWriter in Python with an ITK filter as input image argument. - Build Python wrapping with hidden visibility * New Remote Modules - Strain - Filters to estimate a strain tensor field from a displacement field or a spatial transformation - http://hdl.handle.net/10380/3573 * Core Improvements - Enable hidden visibility property with NIFTI and GIFTI static libraries - Fix clearing build tree error - Add examples and doc build flag support for external modules - Support for recent Clang in FreeBSD - Improved support for Visual Studio 2017 - Prefer std::atomic over compiler specific implementation * Filtering Improvements - Add OrientedBoudingBox attributes to ShapeLabelMap - Prefer std::atomic over compiler specific implementation - Skip generating export headers if module does not contain a target - Introduce ITK_WRAP_PYTHON_LEGACY to exclude older Python package layout - Move morphological watersheds out of ITKReview - Add SetReferenceImage to GenerateImageSource - Reduce memory usage of itkImagePCAShapeModelEstimator - Improvement of itkHistogram in order to make it faster - Better compatibility with OpenCVImageBridge * IO Improvements - Improvement of palette image support for PNG, TIFF and BMP * Documentation Improvements - Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples * Remote Module Updates - BridgeNumPy updated to latest upstream (04.28.2017) * Third Party Library Updates - Update SWIG version to 3.0.12 - Update PCRE version to 8.40 - MetaIO updated to latest upstream (04.08.2017) - KWSys updated to latest upstream (04.20.2017) - KWIML updated to latest upstream (02.27.2017) - VNL updated to latest upstream (02.01.2017) * Improved Code Coverage -- we are at 85.7% - Jon Haitz-Legarreta's extensive code coverage improvements * *Lots* of important bug fixes * And much more! See details in the log below. Changes from v4.11.0 to v4.12rc01 ------------------------------------------------ Ben Boeckel (1): ENH: Add a script to help update third-party sources Brad King (5): ENH: Update KWIML import script for new upstream URL ENH: Teach update-third-party.bash to add a Change-Id ENH: Port KWSys update script to update-third-party.bash ENH: KWSys: Filter out unused attributes during import ENH: KWSys: Apply attribute changes made upstream Bradley Lowekamp (19): COMP: Enable hidden visibility property with NIFTI static libraries COMP: Enable hidden visibility property with GIFTI static libraries BUG: Correct variable name used to check CXX version BUG: Correct variable name used to check CXX version COMP: Enable hidden visibility property with NIFTI static libraries COMP: Enable hidden visibility property with GIFTI static libraries BUG: Initialize ConvergenceValue in constructor BUG: Initialize ConvergenceValue in constructor ENH: Update CircleCi script to download latest binary tar-ball BUG: Use CMAKE_DL_LIBS instead of explict "dl" library COMP: Fix CircleCI ITK data download file name ENH: Update CircleCI yaml file BUG: Apply changes from MetaIO upstream to remove static variables ENH: Update SWIG version to 3.0.12 ENH: Update PCRE version to 8.40 ENH: Add OrientedBoudingBox attributes to ShapeLabelMap COMP: Use std::abs over vnl_math_abs BUG: Initialize image data to 0 ENH: Fix clearing build tree error David T. Chen (1): BUG: Fixed quote style D?enan Zuki? (3): STYLE: Simplify code by using TestingMacros BUG: fixing wrong check for argument count ENH: Add Strain as a remote module Floris Berendsen (2): COMP: Added missing png_get_uint_31 name mangling COMP: Added missing png_get_uint_31 name mangling Francois Budin (57): STYLE: Typo corrections in itk*TopHatImageFilter.h ENH: Prefer std::atomic over compiler specific implementation BUG: Addresses 'ordered comparison between pointer and zero' error (clang-4) BUG: Addresses InDoxygenGroup Test with Python 3.6 failures BUG: BSplineScatteredDataPointSetToImageFilter output image is not generated BUG: itk::RGBPixel needs to be wrapped for itkTIFFImageIO BUG: Usage of std::atomic was incorrectly used in itk::Detail::AtomicOps ENH: Exposing functions to set real and imaginary part of complex numbers BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: 'typename' cannot be used outside of template declaration BUG: Missing ITK_OVERRIDE BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: ITK_OVERRIDE keyword for non-overriden funtion BUG: Missing ITK_OVERRIDE ENH: Improving usability in IPython ENH: Update BridgeNumPy to most recent version (2017.02.24) BUG: 3523 Even padding most value representations with space instead of '\0' BUG: Remove extra space in chronometer command DOC: Make it more explicit that 'push' authorization is not for everybody BUG: 3523 Even padding most value representations with space instead of '\0' BUG: 3519 KernelTransform WMatrix initialization BUG: KWSys symbols should not be exported with WINDOWS_EXPORT_ALL_SYMBOLS COMP: Do not expose functions to set real and img part of complex numbers BUG: KWSys symbols should not be exported with WINDOWS_EXPORT_ALL_SYMBOLS BUG: 3519 KernelTransform WMatrix initialization DOC: Typo in itkNumberToString.h BUG: Attribute names cannot start with a digit BUG: Do not define deprecated function if ITK_LEGACY_REMOVE is selected BUG: Wrap EllipseSpatialObject std::list in Python ENH: Wrap itkN4BiasFieldCorrectionImageFilter in Python BUG: itkStatisticsAlgorithmTest throwing exception on VS2015Update3 and VS2017 ENH: Skip generating export headers if module does not contain a target BUG: Wrapping of itkHessianToObjectnessMeasureImageFilter moved out of Review ENH: Update BridgeNumPy to most recent version (2017.03.27) BUG: Wrapping of itkHessianToObjectnessMeasureImageFilter moved out of Review BUG: Wrap EllipseSpatialObject std::list in Python ENH: Improving usability in IPython BUG: Attribute names cannot start with a digit BUG: Do not export GDCM and Expat symbols with WINDOWS_EXPORT_ALL_SYMBOLS BUG: Do not export all symbols from third party libraries on Windows ENH: Allows to call ImageFileWriter in Python with Input=Filter BUG: Certain third party libraries need to export their symbols on Windows BUG: Test if 'issubclass' only if 'isclass' is True ENH: Add Python convenience function to read images BUG: 3475 AccumulateImageFilter not setting direction cosines of output image DOC: Removing typos in itkExtractImageFilter comments BUG: ProjectionImageFilter did not copy direction cosine information to output BUG: Test if 'issubclass' only if 'isclass' is True BUG: 3475 AccumulateImageFilter not setting direction cosines of output image BUG: Do not export GDCM and Expat symbols with WINDOWS_EXPORT_ALL_SYMBOLS BUG: Do not export all symbols from third party libraries on Windows BUG: Certain third party libraries need to export their symbols on Windows BUG: ProjectionImageFilter did not copy direction cosine information to output ENH: Update BridgeNumPy (2016.04.28) and update itkExtras.py accordingly BUG: Template type based input function parameter needs to be deterministic ENH: Bump CMakeLists.txt version to 4.11.1 Jean-Baptiste VIMORT (1): PERF: Improvement of the itkHistogram class in order to make it faster Jean-Christophe Fillion-Robin (2): ENH: Introduce ITK_WRAP_PYTHON_LEGACY to exclude older Python package layout BUG: ITKPython: Do not install *.mdx files required only at generation time Johan Andruejol (1): ENH: Add wrapping for PathToImageFilter Jon Haitz Legarreta (133): ENH: Improve the itkFileListVideoIO coverage. STYLE: Improve the BSplineScatteredDataPointSetToImageFilter style, ENH: Improve the itkBSplineScatteredDataPointSetToImageFilter coverage. ENH: Add missing ivars in function PrintSelf. STYLE: Improve ImageNoise filters' style. STYLE: Improve the ImageNoise filters tests' style. STYLE: Improve ITKImageSources module filters' style. STYLE: Improve the itkLinearInterpolateImageFunction style. ENH: Improve the itkLabelOverlapMeasuresImageFilter coverage. STYLE: Improve itkAdaptiveHistogramEqualizationImageFilter style. ENH: Improve itkAdaptiveHistogramEqualizationImageFilter coverage. STYLE: Improve itkKappaStatisticImageToImageMetric style. ENH: Improve the itkKappaStatisticImageToImageMetric coverage. STYLE: Improve itkBinaryGrindPeakImageFilter style. STYLE: Improve the itkCannyEdgeDetectionImageFilter style. ENH: Improve itkCannyEdgeDetectionImageFilter coverage. ENH: Improve itkBarrier class coverage. STYLE: Improve itkFlipImageFilterStyle. STYLE: Improve itkSpatialObjectToPointSetFilter style. STYLE: Improve itkStretchIntensityImageFilter style. ENH: Print all ivars for itkStretchIntensityImageFilter. ENH: Improve itkPhysicalPointImageSource class coverage. ENH: Add missing ivars to LabelMapMaskImageFilter PrintSelf. ENH: Improve itkRealTimeClock coverage. STYLE: Improve the itkRealTimeClock style. ENH: Improve itkBsplineDecompositionImageFilter coverage. ENH: Improve itkTestingStretchIntensityImageFilter coverage. STYLE: Improve itkPathToChainCodePathFilter style. ENH: Add a Get method for itkPathToChainCodePathFilter ivar. ENH: Add specific testing macro for boolean members. STYLE: Improve itkLabelMapMaskImageFilter style. STYLE: Improve BSplineDecompositionImageFilter style. ENH: Finish itkAdaptiveHistogramEqualizationImageFilter PrintSelf. COMP: Fix ImageGrid tests compiler warnings. ENH: Finish BSplineDecompositionImageFilter PrintSelf. BUG: Fix Uninitialized Memory errors reported by Valgrind. ENH: Improve itkLabelMapMaskImageFilter coverage. ENH: Improve itkBinaryGrindPeakImageFilter coverage. ENH: Improve itkPathToChainCodePathFilter coverage. ENH: Move LabelMap module test baselines. ENH: Move BinaryMathMorphology test baselines out of review. ENH: Move ImageFusion test baselines out of review. ENH: Improve itkAutoCropLabelMapFilter tests. ENH: Improve itkSpatialObjectToPointSetFilter coverage. ENH: Move ImageLabel test baselines out of Review. ENH: Move ImageGrid test baselines out of review. STYLE: Improve itkGaussianSpatialFunction class' style. ENH: Improve the ITKPath module classes coverage. BUG: Fix BSplineDecompositionImageFilter Valgrind defects. STYLE: Improve itkColorTable style. ENH: Improve itkHoughTransform2DLinesImageFilter coverage. ENH: Improve itkHoughTransform2DCirclesImageFilter coverage. BUG: Address uninitialized variable defects. STYLE: Improve itk::HistogramThresholdImageFilter style. DOC: Fix a typo in the term "threshold". STYLE: Imporve itkContourSpatialObjectPoint style. ENH: Print all HoughTransform2DLinesImageFilter ivars. STYLE: Fix type in Optimizersv4 and Metricsv4 modules. ENH: Add PhiLattice regression baseline. ENH: Print all itkVoronoiDiagram2DGenerator ivars. ENH: Improve itkColorTable coverage. ENH: Improve the itk::GradientDescentOptimizerv4 style. ENH: Improve the itkImageSources module's filters' coverage. ENH: Add PhiLattice regression baseline. ENH: Add a new test for itk::ContourSpatialObjectPoint. BUG: Fix bug in itkContourSpatialObjectPointTest test. STYLE: Improve the itkGaussianSpatialFunctionTest style. ENH: Improve itkVotingBinaryHoleFillingImageFilter coverage. BUG: Fix precision issues in itkGaborKernelFunctionTest. BUG: Relax tolerance in itkGaborKernelFunctionTest. DOC: Fix minor typo in itkHistogramThresholdImageFilter doc. ENH: Print all ivars in GradientDescentOptimizer base classes. STYLE: Improve TIFFImageIO tests. ENH: Add Get methods for itk::BSplineDecompositionImageFilter ivars. BUG: Fix TimeProbes name in itkLargeTIFFImageWriteReadTest. BUG: Fix memory leaks in BMP and PNG tests. COMP: Fix signed/unsigned mismatch warning. COMP: Fix signed/unsigned mismatch warning. BUG: Fix Superclass for ITKThresholding calculators. BUG: Make the number of filters be an integer. ENH: Honor the itkBooleanMacro for boolean class members. ENH: Improve the Watershed module code coverage. COMP: Fix double to unsigned int cast warning. ENH: Improve coverage for MorphologicalWatersheds filters. STYLE: Improve the Denoising module style. BUG: Fix the itkPatchBasedDenoisingImageFilter RTTI Superclass name. COMP: Fix unsigned char from double conversion warning. ENH: Improve itkWatershedMiniPipelineProgressCommand coverage. ENH: Improve the itkRegionalMin/Max filters member print types. ENH: Improve the itkMorphologicalWatershedFromMarkers coverage. ENH: Improve the itkIsolatedWatershedImageFilter coverage. STYLE: Improve the Denoisinig module style. STYLE: Improve the FEMRegistration module files style. DOC: Fix itkOrientImageFilter UseImageDirection method doc typo. STYLE: Improve the ITKThresholding module classes style. BUG: Fix itkIsolatedWatershedImageFilterTest valgrind errors. STYLE: Improve the itkApproximateSignedDistanceMapImageFilter style. ENH: Improve Denoising module filters' coverage. ENH: Improve the FEMRegistration module coverage. STYLE: Improve the itkDisplacementFieldTransform class style. STYLE: Limit itkFlipImageFilter methods' loops variables' scope. ENH: Improve itkFlipImageFilter coverage. COMP: Fix itkPhysicsBasedNonRigidRegistrationMethodTest cast warning. STYLE: Improve the HessianToObjectnessMeasureImageFilter style. ENH: Improve coverage for HessianToObjectnessMeasureImageFilter. ENH: Improve DiscreteGaussianImage operators review classes' coverage. ENH: Add test for itk::ConicShellInteriorExteriorSpatialFunction. ENH: Print all itkHoughTransform2DCirclesImageFilter ivars. ENH: Improve coverage for itk::DisplacementFieldTransform. STYLE: Make itkPatchBasedDenoisingBaseImageFilter ivars private. STYLE: Improve the itkRobustAutomaticThreshold classes style. COMP: Fix itkDisplacementFieldTransformTest compiler warning. STYLE: Improve the itkGridForwardWarpImageFilter style. ENH: Improve coverage for itkGridForwardWarpImageFilter. ENH: Improve coverage for itkRobustAutomaticThreshold classes. ENH: Remove duplicate test files in Review. DOC: Fix itkDivideByConstantImageFilter doc error. STYLE: Improve exception message. STYLE: Improve ImageIntensity module image arithm op tests' style. STYLE: Improve HConc/Conv HMaxima/HMinima image filters' style. ENH: Improve the HConc/HConv HMaxima/HMinima filters' coverage. ENH: Improve DiscreteGaussianImage operators review classes' coverage. ENH: Change the URL for the PCA remote module repo. STYLE: Make flow control variables have a local scope. ENH: Add examples and doc build flag support for external modules. DOC: Remove wrong group tag for itk::QuadEdgeMeshExtendedTraits. BUG: Fix itk::FastMarchingImageFilter RTTI superclass name. STYLE: Improve the itk::NodePair class style. STYLE: Use the ITK_MANUAL_INSTANTIATION macro consistently. STYLE: Delete FastMarching module classes methods consistently. DOC: Fix typo in the "implementation" word across the code. STYLE: Improve itkWarpHarmonicEnergyCalculator style. DOC: Add a notice to let users know about related implementations. KWIML Upstream (1): KWIML 2017-02-27 (aa3a7733) KWSys Upstream (3): KWSys 2016-11-21 (cb55cf5a) KWSys 2017-03-28 (34999b6a) KWSys 2017-04-20 (8785f84f) Matthew McCormick (40): COMP: Add missing headers in OpenCVImageBridge COMP: Use double for gradient calculations in MinMaxCurvatureFlow ENH: Bump ITK version to 4.12.0. COMP: Add VCL support for GCC 7 COMP: Define ITK_FALLTHROUGH for GCC 7 COMP: Add missing ITK_FALLTHROUGH in TiffImageIO COMP: Avoid -Warray-bounds in FixedArray with GCC 7 COMP: Add ProcessObject include in itkLevelSetBase.hxx ENH: Exclude Kitware Robot from third party update commit messages BUG: Address tab completion with IPython >= 5.0.0 BUG: Do not use terminal_progress with the Jupyter Notebook ENH: Enable BridgeNumPy with Python wrapping COMP: Do not require numeric_traits::has_infinity BUG: Fix passing _NO_TR1 definition with VS9 and Python BUG: Do not tests that require NumPy when it is not available ENH: Build Python wrapping with hidden visibility ENH: Move morphological watersheds out of ITKReview BUG: Do not upload top level folder in ArchiveTestingDataOnGirder.py BUG: Remove unused content links from PNG test additions ENH: Add .sha512 content links for IO pallette test data BUG: Add missing export macros for SpatialObject forward declarations BUG: Always wrap basic type RGBUC COMP: Do not add Visual Studio numeric_traits workarounds with MinGWPy COMP: Increase gold linker requirement to GCC 4.9.0 COMP: Detect Windows with _WIN32 in socket++/fork.cpp BUG: Revert "BUG: Include installed modules in ITK_MODULES_ENABLED" BUG: Set ${itk-module}_ENABLE_SHARED in ITKModuleExternal BUG: PolyLineParametricPath must be loaded before PathToImageFilter COMP: Address Python 2.7 Windows _hypot build errors COMP: Undefine Py_hash_t when wrapping VtkGlue ENH: Update BridgeNumPy to most recent version (2017.03.05) BUG: Improve itkTemplate New compatibility with Python 3 ENH: Bump CastXML to 2017-04-18 STYLE: Remove empty or erroreous comments in ImageToImageFilter ENH: Use itk.imread and itk.imwrite as standard function names BUG: Correct size specification in ImportImageFilter::SetImportPointer BUG: Improve large file support in MetaIO ENH: Wrap itk::IdentifierType for ScalarToRGBColormapImageFilter BUG: LevelSetNeighborhoodExtractor uses spacing BUG: Fix PCRE 8.40 download URL MetaIO Maintainers (1): MetaIO 2017-04-08 (dead6687) Olivier Commowick (1): BUG: Correct ITK eigen system (was producing NaN or different values than VNL) Pablo Hernandez-Cerdan (4): ENH: Add SetReferenceImage to GenerateImageSource. ENH: Change the metadata of all outputs in GenerateImageSource. BUG: Fix Normalization kernel step of ConvolutionImageFilter. BUG: Remove call to Superclass::GenerateOutputInformation. Richard Beare (1): DOC: PrincipleComponent flag incorrectly reported by PrintSelf Sam Horvath (1): PERF: reduce memory usage of itkImagePCAShapeModelEstimator Samuel Gerber (2): DOC: Added description to itkLBFGSOptimizerv4.h DOC: LBFGSOptimizer doc update Shusil Dangi (2): ENH: Ignores MacOS .DS_Store file ENH: Wrap NormalVariateGenerator in the Statistics Module Simon Rit (2): BUG: memory leak in ITK_USE_THREADPOOL BUG: Join threads when using thread pool (ITK_USE_THREADPOOL) Taylor Braun-Jones (1): COMP: Only include the headers for required OpenCV modules (fixup) VXL Maintainers (2): VNL 2017-02-01 (ae6eff5e) VNL 2017-02-08 (ae8eef13) Yann Le Poul (4): ENH: improvement of palette image support for PNG TIFF and BMP. STYLE: Misleading IsReadAsScalarPlusPalette Printing string STYLE: ReadAsScalarPlusPalette info already printed in itkImageIOBase BUG: ExpandRGBPalette used instead of IsReadAsScalarPlusPalette ----------------------------------------------------- Errors or omissions? Please fix them here: https://docs.google.com/document/d/1bEujAWZ9Vh-lSt82mO4X7N1kyibOFX3Wh1xQZUkO-s4/edit -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Mon May 15 12:07:52 2017 From: francois.budin at kitware.com (Francois Budin) Date: Mon, 15 May 2017 12:07:52 -0400 Subject: [ITK-dev] [ITK-users] [ANN] ITK 4.12 Release Candidate 2 is ready for testing! Message-ID: On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.12 release candidate 2 has been tagged and is available for testing! Please take this opportunity to test the new features in the release candidate. For more information on the new features in this release, see our blog entry on the first release candidate . To obtain the source code, use the links: https://github.com/Kitware/ITK/archive/v4.12rc02.zip https://github.com/Kitware/ITK/archive/v4.12rc02.tar.gz Or, to checkout the tag with Git: git clone https://itk.org/ITK.git cd ITK git checkout -q --detach v4.12rc02 Please test the release candidate and share your experiences on the mailing list , issue tracker , and Gerrit Code Review . An Experimental build, which demonstrates how the test suite performs on your local build system, can be submitted to the dashboard [1] with: mkdir ../ITK-build cd ../ITK-build cmake ../ITK ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit Visual Studio builds must also add ?-C Release? to the ctest command. Notify the mailing list if there are any unexpected failures. Testing your own applications against the RC is also appreciated. [1] http://open.cdash.org/index.php?project=Insight Changes from v4.12rc01 to v4.12rc02 ------------------------------------------------ Christina Rossmanith (1): BUG: calculate levelSetValue for IsoContourFilter with float precision David T. Chen (1): DOC: Fix Pysical Typo Francois Budin (3): BUG: Remove doxygen warnings 'Found unknown command \epsilon' ENH: Remove warning messages in GCC 5.1 due to ITK_TEMPLATE_EXPORT BUG: GCC 5.1 warnings 'type attributes ignored after type is already defined' Jon Haitz Legarreta Gorro?o (1): DOC: Add use note to itkGridForwardWarpImageFilter. Matthew McCormick (1): BUG: Update the Strain remote module to 2017-05-05 Vladimir S. FONOV (3): MINC 2017-04-28 (3d79acf3) MINC 2017-05-01 (4caf8f4c) MINC 2017-05-05 (cc682b52) ----------------------------------------------------- Errors or omissions? Please fix them here: https://docs.google.com/document/d/1HWutEtAQt5uMXA-f0ZP_mvEucpmT6P-yUhlZTAzYVg0/edit -------------- next part -------------- An HTML attachment was scrubbed... URL: From alb.net at gmail.com Fri May 19 09:24:33 2017 From: alb.net at gmail.com (Dorian P.) Date: Fri, 19 May 2017 09:24:33 -0400 Subject: [ITK-dev] Cannot write files ending '.img.nii.gz' Message-ID: I sent this in ITK users list, just forwarding it to developers as well. I use ANTs(R) which relies on ITK. When I try to save images ending in '.img.nii.gz' I end up getting files with a different extension '.hdr.gz'. These files are then unusuable, they cannot open anymore with ITK software (ANTsR, ITKsnap). Can you have a look if this is a bug that can be fixed in the near future? -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Fri May 19 13:28:52 2017 From: francois.budin at kitware.com (Francois Budin) Date: Fri, 19 May 2017 13:28:52 -0400 Subject: [ITK-dev] Cannot write files ending '.img.nii.gz' In-Reply-To: References: Message-ID: Hello Dorian, ITK support a large number of file extensions including .hdr, .nii, .nii.gz. .hdr files are saved with a .img file (.hdr is the header and .img is the data. ITK decides which file format to save your data as based on the extension in the filename you provide. Since image format extensions can contain multiple "." (such as .nii.gz), it relies on finding the first "." and finds the extension name from there, thus the problem you are having. You may want to change the file name you save your file as, and either chose .img or .nii.gz, but not both. Hope this helps, Francois On Fri, May 19, 2017 at 9:24 AM, Dorian P. wrote: > I sent this in ITK users list, just forwarding it to developers as well. > > I use ANTs(R) which relies on ITK. When I try to save images ending in > '.img.nii.gz' I end up getting files with a different extension '.hdr.gz'. > These files are then unusuable, they cannot open anymore with ITK software > (ANTsR, ITKsnap). > > Can you have a look if this is a bug that can be fixed in the near future? > > _______________________________________________ > 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 jonathan.lefman at intel.com Mon May 22 15:26:13 2017 From: jonathan.lefman at intel.com (Lefman, Jonathan) Date: Mon, 22 May 2017 19:26:13 +0000 Subject: [ITK-dev] Unsupported protocol error from ExternalData.cmake Message-ID: Hi all, I am building ITK with the cmake arg "-DModule_PerformanceBenchmarking:BOOL=ON". During the make process, I run into a new issue: CMake Error at /home/bw2user1/ITK/CMake/ExternalData.cmake:1113 (message): Object MD5=d72eb9ebf4a60f6cfeaf60717d1926be not found at: https://insightsoftwareconsortium.github.io/ITKTestingData/MD5/d72eb9ebf4a60f6cfeaf60717d1926be ("Unsupported protocol") https://data.kitware.com:443/api/v1/file/hashsum/MD5/d72eb9ebf4a60f6cfeaf60717d1926be/download ("Unsupported protocol") https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d72eb9ebf4a60f6cfeaf60717d1926be&algorithm=MD5 ("Unsupported protocol") https://itk.org/files/ExternalData/MD5/d72eb9ebf4a60f6cfeaf60717d1926be ("Unsupported protocol") https://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=d72eb9ebf4a60f6cfeaf60717d1926be&algorithm=MD5 ("Unsupported protocol") make[2]: *** [ExternalData/Testing/Data/Baseline/BasicFilters/HeadMRVolumeMaximumProjection0.mha-hash-stamp] Error 1 make[1]: *** [CMakeFiles/ITKData.dir/all] Error 2 make: *** [all] Error 2 Any idea what is happening? Thanks, Jon From matt.mccormick at kitware.com Mon May 22 15:41:53 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 22 May 2017 15:41:53 -0400 Subject: [ITK-dev] Unsupported protocol error from ExternalData.cmake In-Reply-To: References: Message-ID: Hi Jon, This may be related to using a cmake without https support. Binary downloads from cmake.org: https://cmake.org/download/ have this support enabled. Hope this helps, Matt On Mon, May 22, 2017 at 3:26 PM, Lefman, Jonathan wrote: > Hi all, > > I am building ITK with the cmake arg "-DModule_PerformanceBenchmarking:BOOL=ON". During the make process, I run into a new issue: > > CMake Error at /home/bw2user1/ITK/CMake/ExternalData.cmake:1113 (message): > > > Object MD5=d72eb9ebf4a60f6cfeaf60717d1926be not found at: > > https://insightsoftwareconsortium.github.io/ITKTestingData/MD5/d72eb9ebf4a60f6cfeaf60717d1926be ("Unsupported protocol") > https://data.kitware.com:443/api/v1/file/hashsum/MD5/d72eb9ebf4a60f6cfeaf60717d1926be/download ("Unsupported protocol") > https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d72eb9ebf4a60f6cfeaf60717d1926be&algorithm=MD5 ("Unsupported protocol") > https://itk.org/files/ExternalData/MD5/d72eb9ebf4a60f6cfeaf60717d1926be ("Unsupported protocol") > https://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=d72eb9ebf4a60f6cfeaf60717d1926be&algorithm=MD5 ("Unsupported protocol") > > > make[2]: *** [ExternalData/Testing/Data/Baseline/BasicFilters/HeadMRVolumeMaximumProjection0.mha-hash-stamp] Error 1 > make[1]: *** [CMakeFiles/ITKData.dir/all] Error 2 > make: *** [all] Error 2 > > Any idea what is happening? > > Thanks, > > Jon > _______________________________________________ > 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 jonathan.lefman at intel.com Mon May 22 15:43:14 2017 From: jonathan.lefman at intel.com (Lefman, Jonathan) Date: Mon, 22 May 2017 19:43:14 +0000 Subject: [ITK-dev] Unsupported protocol error from ExternalData.cmake In-Reply-To: References: Message-ID: Thank you for the quick response. I built from source on a brand new machine which may not have the SSL development headers installed. I will utilize the binaries. -Jon -----Original Message----- From: Matt McCormick [mailto:matt.mccormick at kitware.com] Sent: Monday, May 22, 2017 3:42 PM To: Lefman, Jonathan Cc: insight-developers at itk.org Subject: Re: [ITK-dev] Unsupported protocol error from ExternalData.cmake Hi Jon, This may be related to using a cmake without https support. Binary downloads from cmake.org: https://cmake.org/download/ have this support enabled. Hope this helps, Matt On Mon, May 22, 2017 at 3:26 PM, Lefman, Jonathan wrote: > Hi all, > > I am building ITK with the cmake arg "-DModule_PerformanceBenchmarking:BOOL=ON". During the make process, I run into a new issue: > > CMake Error at /home/bw2user1/ITK/CMake/ExternalData.cmake:1113 (message): > > > Object MD5=d72eb9ebf4a60f6cfeaf60717d1926be not found at: > > https://insightsoftwareconsortium.github.io/ITKTestingData/MD5/d72eb9ebf4a60f6cfeaf60717d1926be ("Unsupported protocol") > https://data.kitware.com:443/api/v1/file/hashsum/MD5/d72eb9ebf4a60f6cfeaf60717d1926be/download ("Unsupported protocol") > https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d72eb9ebf4a60f6cfeaf60717d1926be&algorithm=MD5 ("Unsupported protocol") > https://itk.org/files/ExternalData/MD5/d72eb9ebf4a60f6cfeaf60717d1926be ("Unsupported protocol") > > https://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.down > load&checksum=d72eb9ebf4a60f6cfeaf60717d1926be&algorithm=MD5 > ("Unsupported protocol") > > > make[2]: *** > [ExternalData/Testing/Data/Baseline/BasicFilters/HeadMRVolumeMaximumPr > ojection0.mha-hash-stamp] Error 1 > make[1]: *** [CMakeFiles/ITKData.dir/all] Error 2 > make: *** [all] Error 2 > > Any idea what is happening? > > Thanks, > > Jon > _______________________________________________ > 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 jchris.fillionr at kitware.com Mon May 22 15:48:40 2017 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Mon, 22 May 2017 15:48:40 -0400 Subject: [ITK-dev] Unsupported protocol error from ExternalData.cmake In-Reply-To: References: Message-ID: Hi Jonathan, I built from source on a brand new machine which may not have the SSL > development headers installed. This was probably the issue. With recent CMake, SSL headers should be detected even when bootstrapping it. For example, see https://github.com/dockcross/dockcross/blob/f689116b3f4fd7d106e7bc3abbefb96254ce79bd/imagefiles/install-cmake.sh#L57-L91 The link above also provide a short test allowing to check if CMake support https. Jc -- +1 919 869 8849 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.lefman at intel.com Mon May 22 16:55:25 2017 From: jonathan.lefman at intel.com (Lefman, Jonathan) Date: Mon, 22 May 2017 20:55:25 +0000 Subject: [ITK-dev] How to override optimization compile flag? Message-ID: Hi all, I am trying to override the -O3 flag using ITK_CXX_DISABLE_OPTIMIZATION_FLAG in ITKSetStandardCompilerFlags.cmake. It is not obvious how this is supposed to work. When I set ITK_CXX_DISABLE_OPTIMIZATION_FLAG in the cmake command or in CMAKE_CXX_FLAGS='-O0', the flag is overridden: icpc: command line remark #10120: overriding '-O0' with '-O3' Example: # CMAKE generated file: DO NOT EDIT! # Generated by "Unix Makefiles" Generator, CMake Version 3.8 # compile CXX with /opt/intel/compilers_and_libraries_2017.1.132/linux/bin/intel64/icpc CXX_FLAGS = -O0 -w2 -wd1268 -wd981 -wd383 -wd1418 -wd1419 -wd2259 -wd1572 -wd424 -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -O3 -DNDEBUG -fPIE I do see another variable "CXX_HAS_DISABLE_OPTIMIZATION_FLAG" but it is reported as unused by cmake. Please let me know the right way to remove the -O3 flag. Thanks very much. -Jon -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon May 22 17:00:32 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 22 May 2017 17:00:32 -0400 Subject: [ITK-dev] How to override optimization compile flag? In-Reply-To: References: Message-ID: Hi Jon, This can be disabled by setting CMAKE_BUILD_TYPE to an empty string. The default is "Release", which adds the -O3 flag. HTH, Matt On Mon, May 22, 2017 at 4:55 PM, Lefman, Jonathan wrote: > Hi all, > > > > I am trying to override the -O3 flag using ITK_CXX_DISABLE_OPTIMIZATION_FLAG > in ITKSetStandardCompilerFlags.cmake. It is not obvious how this is supposed > to work. When I set ITK_CXX_DISABLE_OPTIMIZATION_FLAG in the cmake command > or in CMAKE_CXX_FLAGS=?-O0?, the flag is overridden: > > > > icpc: command line remark #10120: overriding '-O0' with '-O3' > > > > Example: > > > > # CMAKE generated file: DO NOT EDIT! > > # Generated by "Unix Makefiles" Generator, CMake Version 3.8 > > > > # compile CXX with > /opt/intel/compilers_and_libraries_2017.1.132/linux/bin/intel64/icpc > > CXX_FLAGS = -O0 -w2 -wd1268 -wd981 -wd383 -wd1418 -wd1419 -wd2259 -wd1572 > -wd424 -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch > -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -Wno-deprecated > -Wno-invalid-offsetof -Woverloaded-virtual -O3 -DNDEBUG ?fPIE > > > > I do see another variable ?CXX_HAS_DISABLE_OPTIMIZATION_FLAG? but it is > reported as unused by cmake. Please let me know the right way to remove the > -O3 flag. Thanks very much. > > > > -Jon > > > > > _______________________________________________ > 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 jonathan.lefman at intel.com Mon May 22 17:16:15 2017 From: jonathan.lefman at intel.com (Lefman, Jonathan) Date: Mon, 22 May 2017 21:16:15 +0000 Subject: [ITK-dev] How to override optimization compile flag? In-Reply-To: References: Message-ID: Thank you -Jon -----Original Message----- From: Matt McCormick [mailto:matt.mccormick at kitware.com] Sent: Monday, May 22, 2017 5:01 PM To: Lefman, Jonathan Cc: insight-developers at itk.org Subject: Re: [ITK-dev] How to override optimization compile flag? Hi Jon, This can be disabled by setting CMAKE_BUILD_TYPE to an empty string. The default is "Release", which adds the -O3 flag. HTH, Matt On Mon, May 22, 2017 at 4:55 PM, Lefman, Jonathan wrote: > Hi all, > > > > I am trying to override the -O3 flag using > ITK_CXX_DISABLE_OPTIMIZATION_FLAG in > ITKSetStandardCompilerFlags.cmake. It is not obvious how this is > supposed to work. When I set ITK_CXX_DISABLE_OPTIMIZATION_FLAG in the cmake command or in CMAKE_CXX_FLAGS=?-O0?, the flag is overridden: > > > > icpc: command line remark #10120: overriding '-O0' with '-O3' > > > > Example: > > > > # CMAKE generated file: DO NOT EDIT! > > # Generated by "Unix Makefiles" Generator, CMake Version 3.8 > > > > # compile CXX with > /opt/intel/compilers_and_libraries_2017.1.132/linux/bin/intel64/icpc > > CXX_FLAGS = -O0 -w2 -wd1268 -wd981 -wd383 -wd1418 -wd1419 -wd2259 > -wd1572 > -wd424 -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch > -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -Wno-deprecated > -Wno-invalid-offsetof -Woverloaded-virtual -O3 -DNDEBUG ?fPIE > > > > I do see another variable ?CXX_HAS_DISABLE_OPTIMIZATION_FLAG? but it > is reported as unused by cmake. Please let me know the right way to > remove the > -O3 flag. Thanks very much. > > > > -Jon > > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > From pablo.hernandez.cerdan at outlook.com Tue May 23 02:37:15 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Tue, 23 May 2017 06:37:15 +0000 Subject: [ITK-dev] Generate Doxygen documentation on only one module Message-ID: Hi all, is it possible to generate Doxygen documentation of only one external/remote module? I want to validate that the documentation is ok in the module, but not eager to build it all. I haven't found any about this in: https://itk.org/Wiki/ITK/Doxygen_Documentation Thanks, Pablo -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Tue May 23 06:53:48 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Tue, 23 May 2017 10:53:48 +0000 Subject: [ITK-dev] Generate Doxygen documentation on only one module In-Reply-To: References: Message-ID: I think I have found it using the doxygen configuration that is generated in the itk build folder. Edit `$ITK_BUILD_DIR/single-doxygen.config`, modify the variable `INPUT` with the path of the module, or the path to the file that you want to check. Then run doxygen: `doxygen $ITK_BUILD_DIR/single-doxygen.config` On Tue, May 23, 2017 at 6:37 PM, Pablo Hern?ndez > wrote: Hi all, is it possible to generate Doxygen documentation of only one external/remote module? I want to validate that the documentation is ok in the module, but not eager to build it all. I haven't found any about this in: https://itk.org/Wiki/ITK/Doxygen_Documentation Thanks, Pablo -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Thu May 25 01:22:39 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 25 May 2017 05:22:39 +0000 Subject: [ITK-dev] Code coverage: using gcov in an itk external module Message-ID: Hi there, I have written a blog post at the same time I was learning how to use gcov for code coverage in an external module. Nothing fancy, but somebody might find it useful: https://phcerdan.github.io/code-coverage/. It works, a bit too much red there though! Cheers, Pablo PS: Thanks to Jon Haitz Legarreta for encourage me to use gcov in the module. -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.budin at kitware.com Thu May 25 08:57:18 2017 From: francois.budin at kitware.com (Francois Budin) Date: Thu, 25 May 2017 08:57:18 -0400 Subject: [ITK-dev] Code coverage: using gcov in an itk external module In-Reply-To: References: Message-ID: That's great! Thanks for sharing! Francois On Thu, May 25, 2017 at 1:22 AM, Pablo Hern?ndez < pablo.hernandez.cerdan at outlook.com> wrote: > Hi there, > I have written a blog post at the same time I was learning how to use gcov > for code coverage in an external module. Nothing fancy, but somebody might > find it useful: https://phcerdan.github.io/code-coverage/. > > > It works, a bit too much red there though! > > Cheers, > Pablo > > PS: Thanks to Jon Haitz Legarreta for encourage me to use gcov in the > module. > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu May 25 10:59:00 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 25 May 2017 10:59:00 -0400 Subject: [ITK-dev] Code coverage: using gcov in an itk external module In-Reply-To: References: Message-ID: On Thu, May 25, 2017 at 8:57 AM, Francois Budin wrote: > That's great! Thanks for sharing! > +1! 90%+ is not too shabby at all :-). Jon and I have investigated CodeCov [1] for ITK [2], but ITK's test suite seems to overwhelm their system. However, tests for a single external module could work? Here are the scripts that we used: https://gist.github.com/thewtex/1f410c90e8b9e9826989c0e04e97738b https://gist.github.com/thewtex/e3f59fdfba4f30ad2580dbb4db7a22e9 https://gist.github.com/thewtex/cc7ade395c7aa309f38b137b8934e075 These work together with the itk_common.cmake CTest script in ITK's Git repository dashboard branch. Cheers, Matt [1] https://codecov.io/ [2] https://codecov.io/gh/InsightSoftwareConsortium/ITK -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Thu May 25 19:56:38 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 25 May 2017 23:56:38 +0000 Subject: [ITK-dev] Code coverage: using gcov in an itk external module In-Reply-To: References: Message-ID: Hi Matt, thanks! yeah, it works for single modules (external or core) modifying the flags in `test/CMakeLists.txt` for the specific ${itk_module}TestDriver. Not sure if CodeCov is overwhelmed by running the tests, generating the `.gcda` files , or by the later stage of generating the lcov report with those files. If the first case, it is hard to selectively modify flags of child targets from parent CMakeLists.txt, right? So other option would be to modify the CreateTestDriver macro to add coverage flags to some modules, depending on additional cmake variables, but I guess is not too elegant? If the later, we can modify the lcov script to generate reports only in selected Modules. And maybe have a CodeCov report per module? In my case, the .gcda files are generated in subfolders, so it is easy to only generate the reports for that module. export GCOV_PREFIX="$HOME/Software/ITK/build/Modules/Remote/IsotropicWavelets/test/CMakeFiles/IsotropicWaveletsTestDriver.dir lcov --directory $GCOV_PREFIX --capture --output-file $GCOV_PREFIX/app.info It would be great to automatize this indeed! Cheers, Pablo On Fri, May 26, 2017 at 2:59 AM, matt.mccormick at kitware.com > wrote: On Thu, May 25, 2017 at 8:57 AM, Francois Budin > wrote: That's great! Thanks for sharing! +1! 90%+ is not too shabby at all :-). Jon and I have investigated CodeCov [1] for ITK [2], but ITK's test suite seems to overwhelm their system. However, tests for a single external module could work? Here are the scripts that we used: https://gist.github.com/thewtex/1f410c90e8b9e9826989c0e04e97738b https://gist.github.com/thewtex/e3f59fdfba4f30ad2580dbb4db7a22e9 https://gist.github.com/thewtex/cc7ade395c7aa309f38b137b8934e075 These work together with the itk_common.cmake CTest script in ITK's Git repository dashboard branch. Cheers, Matt [1] https://codecov.io/ [2] https://codecov.io/gh/InsightSoftwareConsortium/ITK -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Thu May 25 19:56:39 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 25 May 2017 23:56:39 +0000 Subject: [ITK-dev] Code coverage: using gcov in an itk external module In-Reply-To: References: Message-ID: Hi Matt, thanks! yeah, it works for single modules (external or core) modifying the flags in `test/CMakeLists.txt` for the specific ${itk_module}TestDriver. Not sure if CodeCov is overwhelmed by running the tests, generating the `.gcda` files , or by the later stage of generating the lcov report with those files. If the first case, it is hard to selectively modify flags of child targets from parent CMakeLists.txt, right? So other option would be to modify the CreateTestDriver macro to add coverage flags to some modules, depending on additional cmake variables, but I guess is not too elegant? If the later, we can modify the lcov script to generate reports only in selected Modules. And maybe have a CodeCov report per module? In my case, the .gcda files are generated in subfolders, so it is easy to only generate the reports for that module. export GCOV_PREFIX="$HOME/Software/ITK/build/Modules/Remote/IsotropicWavelets/test/CMakeFiles/IsotropicWaveletsTestDriver.dir lcov --directory $GCOV_PREFIX --capture --output-file $GCOV_PREFIX/app.info It would be great to automatize this indeed! Cheers, Pablo On Fri, May 26, 2017 at 2:59 AM, matt.mccormick at kitware.com > wrote: On Thu, May 25, 2017 at 8:57 AM, Francois Budin > wrote: That's great! Thanks for sharing! +1! 90%+ is not too shabby at all :-). Jon and I have investigated CodeCov [1] for ITK [2], but ITK's test suite seems to overwhelm their system. However, tests for a single external module could work? Here are the scripts that we used: https://gist.github.com/thewtex/1f410c90e8b9e9826989c0e04e97738b https://gist.github.com/thewtex/e3f59fdfba4f30ad2580dbb4db7a22e9 https://gist.github.com/thewtex/cc7ade395c7aa309f38b137b8934e075 These work together with the itk_common.cmake CTest script in ITK's Git repository dashboard branch. Cheers, Matt [1] https://codecov.io/ [2] https://codecov.io/gh/InsightSoftwareConsortium/ITK -------------- next part -------------- An HTML attachment was scrubbed... URL: From pablo.hernandez.cerdan at outlook.com Thu May 25 19:56:43 2017 From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=) Date: Thu, 25 May 2017 23:56:43 +0000 Subject: [ITK-dev] Code coverage: using gcov in an itk external module In-Reply-To: References: Message-ID: Hi Matt, thanks! yeah, it works for single modules (external or core) modifying the flags in `test/CMakeLists.txt` for the specific ${itk_module}TestDriver. Not sure if CodeCov is overwhelmed by running the tests, generating the `.gcda` files , or by the later stage of generating the lcov report with those files. If the first case, it is hard to selectively modify flags of child targets from parent CMakeLists.txt, right? So other option would be to modify the CreateTestDriver macro to add coverage flags to some modules, depending on additional cmake variables, but I guess is not too elegant? If the later, we can modify the lcov script to generate reports only in selected Modules. And maybe have a CodeCov report per module? In my case, the .gcda files are generated in subfolders, so it is easy to only generate the reports for that module. export GCOV_PREFIX="$HOME/Software/ITK/build/Modules/Remote/IsotropicWavelets/test/CMakeFiles/IsotropicWaveletsTestDriver.dir lcov --directory $GCOV_PREFIX --capture --output-file $GCOV_PREFIX/app.info It would be great to automatize this indeed! Cheers, Pablo On Fri, May 26, 2017 at 2:59 AM, matt.mccormick at kitware.com > wrote: On Thu, May 25, 2017 at 8:57 AM, Francois Budin > wrote: That's great! Thanks for sharing! +1! 90%+ is not too shabby at all :-). Jon and I have investigated CodeCov [1] for ITK [2], but ITK's test suite seems to overwhelm their system. However, tests for a single external module could work? Here are the scripts that we used: https://gist.github.com/thewtex/1f410c90e8b9e9826989c0e04e97738b https://gist.github.com/thewtex/e3f59fdfba4f30ad2580dbb4db7a22e9 https://gist.github.com/thewtex/cc7ade395c7aa309f38b137b8934e075 These work together with the itk_common.cmake CTest script in ITK's Git repository dashboard branch. Cheers, Matt [1] https://codecov.io/ [2] https://codecov.io/gh/InsightSoftwareConsortium/ITK -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri May 26 17:43:09 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 26 May 2017 17:43:09 -0400 Subject: [ITK-dev] [ANN] ITK 4.12 Release Candidate 3 is ready for testing! Message-ID: On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.12 release candidate 3 has been tagged and is available for testing! Please take this opportunity to test the new features in the release candidate. For more information on the new features in this release, see our blog entry on the first release candidate. To obtain the source code, use the links: https://github.com/Kitware/ITK/archive/v4.12rc03.zip https://github.com/Kitware/ITK/archive/v4.12rc03.tar.gz Or, to checkout the tag with Git: git clone https://itk.org/ITK.git cd ITK git checkout -q --detach v4.12rc03 Please test the release candidate and share your experiences on the mailing list, issue tracker, and Gerrit Code Review. An Experimental build, which demonstrates how the test suite performs on your local build system, can be submitted to the dashboard [1] with: mkdir ../ITK-build cd ../ITK-build cmake ../ITK ctest -j 4 -M Experimental -T Configure -T Build -T Test -T Submit Visual Studio builds must also add ?-C Release? to the ctest command. Notify the mailing list if there are any unexpected failures. Testing your own applications against the RC is also appreciated. The 4.12.0 release is scheduled for next week. [1] http://open.cdash.org/index.php?project=Insight Changes from v4.12rc02 to v4.12rc03 ------------------------------------------------ Bradley Lowekamp (4): BUG: include HDF5 config in ITK config BUG: Add fixed seed to registration tests ENH: Use scikit-ci-addons for CiricleCI CMake installation and junit BUG: Initialized the sampling seed for v3 registration test Francois Budin (1): ENH: Remove 'weak symbol' warning on MacOS Matthew McCormick (5): BUG: itk.ctype does not understand ints without signed BUG: Rename WrapITKBuildOptionsPython.py to itkBuildOptions.py DOC: Remove Doxygen note about GDCM version BUG: Bump Bridge NumPy to address Windows long sizes COMP: Suppress macOS std::string linker visibility warnings Vladimir S. FONOV (1): MINC 2017-05-19 (f6853a70) From sean at rogue-research.com Tue May 30 17:20:01 2017 From: sean at rogue-research.com (Sean McBride) Date: Tue, 30 May 2017 17:20:01 -0400 Subject: [ITK-dev] [ANN] ITK 4.12 Release Candidate 3 is ready for testing! In-Reply-To: References: Message-ID: <20170530212001.1630717323@mail.rogue-research.com> On Fri, 26 May 2017 17:43:09 -0400, Matt McCormick said: >On behalf of the Insight Toolkit community, we are proud to announce >that ITK 4.12 release candidate 3 has been tagged and is available for >testing! Please take this opportunity to test the new features in the >release candidate. Matt, Vlad, I didn't actually try 4.12rc3, but I've just tried git master and found a problem. The install directory doesn't contain "minc_common_defs.h" anywhere, and yet this file is needed by other minc headers (ex by minc2_defs.h, which ITK's install directory _does_ contain). The result being that my app can't compile. The file seems to be new vs 4.11's install directory. Also, it would be nice if minc2_defs.h used #include "" instead of #include <>, but I think maybe that has to happen upstream... Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From matt.mccormick at kitware.com Tue May 30 17:43:29 2017 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 30 May 2017 17:43:29 -0400 Subject: [ITK-dev] [ANN] ITK 4.12 Release Candidate 3 is ready for testing! In-Reply-To: <20170530212001.1630717323@mail.rogue-research.com> References: <20170530212001.1630717323@mail.rogue-research.com> Message-ID: On Tue, May 30, 2017 at 5:20 PM, Sean McBride wrote: > On Fri, 26 May 2017 17:43:09 -0400, Matt McCormick said: > > >On behalf of the Insight Toolkit community, we are proud to announce > >that ITK 4.12 release candidate 3 has been tagged and is available for > >testing! Please take this opportunity to test the new features in the > >release candidate. > > Matt, Vlad, > > I didn't actually try 4.12rc3, but I've just tried git master and found a > problem. > > The install directory doesn't contain "minc_common_defs.h" anywhere, and > yet this file is needed by other minc headers (ex by minc2_defs.h, which > ITK's install directory _does_ contain). The result being that my app > can't compile. The file seems to be new vs 4.11's install directory. > > Also, it would be nice if minc2_defs.h used #include "" instead of > #include <>, but I think maybe that has to happen upstream... > Thanks for the report, Sean. Could you please test this topic: http://review.source.kitware.com/#/q/topic:minc-update which includes this fix: https://github.com/BIC-MNI/libminc/commit/002d510ca7c01f2537070bc8684e80d6f5b95213 ? Thanks, Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: