[ITK-users] [ANN] ITK 5.0 Alpha 1: Modern C++
Matt McCormick
matt.mccormick at kitware.com
Tue Apr 17 17:13:32 EDT 2018
*ITK 5.0 Alpha 1 is ready for testing!*
* - Source code (zip)
<https://github.com/InsightSoftwareConsortium/ITK/archive/v5.0a01.zip> -
Source code (tar.gz)
<https://github.com/InsightSoftwareConsortium/ITK/archive/v5.0a01.tar.gz> *
ITK 5.0 brings dramatic improvements to ITK's API and performance. At the
same time, there are minimal changes that break backwards compatibility.
This the first in a series of alpha releases to enable the community to
test and improve these major changes.
In this first alpha release, we highlight ITK's adoption of and requirement
for the *C++11 standard*. Prior to this release, a subset of C++11
functionality was utilized, when available, through backports and macros.
ITKv5 deprecates or removes these macros (e.g. ITK_NULLPTR,
ITK_DELETED_FUNCTION, ITK_NOEXCEPT, ITK_CONSTEXPR) and directly uses C++11
keywords such as delete
<https://github.com/InsightSoftwareConsortium/ITK/commit/02128abbd0bf790deadc86a28c62c4a25e23518b>,
constexpr
<https://github.com/InsightSoftwareConsortium/ITK/commit/b8e41d0d1652a8f6ddb84328faef67b207e77430>,
nullptr
<https://github.com/InsightSoftwareConsortium/ITK/commit/3c6372b80ac2900e2e197899989c4cd151f1695f>,
override
<https://github.com/InsightSoftwareConsortium/ITK/commit/3ceacc0ad4ec699b094d96e23d33f9467c2a63c6>,
noexcept
<https://github.com/InsightSoftwareConsortium/ITK/commit/af4f65519abb32b59cebb2d72f0186a96efe3b4e>.
The keywords auto
<https://github.com/InsightSoftwareConsortium/ITK/commit/de713e7ac52f7815a35754de885795ff0a1c4981>
and using
<https://github.com/InsightSoftwareConsortium/ITK/commit/66e5d6b3bcc28f1a85b702086b6cedc8cab6723b>
as well as range-based loops
<https://github.com/InsightSoftwareConsortium/ITK/commit/48daed0751df99bcb5fd1077e78ceb1b47546ccc>
are also now used heavily throughout ITK.
ITKv5 includes some API changes. Even though we tried to minimize backward
compatibility issues, there will be a few (see below for important
changes). These changes were discussed by the community on the ITK
Discourse forum [1] <https://discourse.itk.org/t/gearing-up-for-itk5/515>[2]
<https://discourse.itk.org/t/gearing-up-for-itk5/515/4>[3]
<https://discourse.itk.org/t/new-build-errors-on-cdash-1-24-18-drop-support-for-vs2013-in-itkv5/619/3>
[4]
<https://discourse.itk.org/t/opinions-on-dropping-support-for-c-03/481/4>.
This ITK alpha release is purposefully created with the goal of helping
developers to test their current software with this new ITK version, update
their code if necessary, and report problems they encountered during this
process.
ITK now requires
<https://github.com/InsightSoftwareConsortium/ITK/commit/3525bf45200bd9845259ea9a88f586684cc522db>
CMake 3.9.5 for configuration and a compiler that supports C++11. This
means that Visual Studio 2015 or later is required for Windows development
with the Microsoft toolchain.
Important changes in style
<https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch13.html#x57-259000C>
have also been integrated in ITK to match the C++11 best practices. This
includes replacing typedef calls with the using keyword, the usage of the
keyword auto when appropriate, and moving the macro
ITK_DISALLOW_COPY_AND_ASSIGN from the private class section to the public
class section. The ITK Software Guide
<https://itk.org/ITKSoftwareGuide/html/> has been updated to match these
changes.
As shown below, toolkit has adopted the application of the using keyword
for type aliases <http://en.cppreference.com/w/cpp/language/type_alias>,
which many developers find easier to read and understand.
template< typename TInputImage, typename TOutputImage >
class ITK_TEMPLATE_EXPORT BoxImageFilter:
public ImageToImageFilter< TInputImage, TOutputImage >
{
public:
ITK_DISALLOW_COPY_AND_ASSIGN(BoxImageFilter);
/⋆⋆ Standard class type alias. ⋆/
using Self = BoxImageFilter;
using Superclass = ImageToImageFilter< TInputImage, TOutputImage >;
[...]
protected:
BoxImageFilter();
~BoxImageFilter() {}
void GenerateInputRequestedRegion() override;
void PrintSelf(std::ostream & os, Indent indent) const override;
private:
RadiusType m_Radius;
};
} // end namespace itk
For more information on style changes, see the Coding Style Guide
<https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch13.html#x57-259000C>
found in the ITK Software Guide.
To test the 5.0 Alpha 1 Python packages, run
python -m pip install --upgrade pip
python -m pip install --upgrade --pre itk
For a full list of the new features and changes in API, please review the
log below. The community has been busy -- there have been *319 commits,
97,794 insertions, 152,791 deletions* since 4.13.0 was released in December!
Please discuss your experiences on Discourse <https://discourse.itk.org/>.
The API is expected to change across alpha releases as we improve the
library based on our experiences.
Changes from v4.13.0 to v5.0 Alpha1
------------------------------------------------
Bradley Lowekamp (49):
ENH: Adding more swap methods
BUG: Respect Visibility Preset for initial template visibility
COMP: Use explicit equality for boolean evaluation of real number
BUG: Keep the SetSeed# methods in IsolatedConnectedImageFilter
ENH: Use direct for loops for implementing image transformations
COMP: Use anonymous namespace for internal linkage
ENH: Mark 2 template parameter ModulusTransform to be removed
COMP: Remove legacy marking on definition of SetSeed methods
STYLE: Use itk::v3 nested namespace for Rigid3DTransform
BUG: Preserve option to use a "label value" mask and boolean mask
ENH: update C+11 headers and try compile for headers
ENH: Remove duplicated CMake module from upstream CMake
COMP: Explicitly include the fixed width integer header before usage
COMP: Update SimpleITKFilters for dependency issues
BUG: The CXX language must be enable to check compiler variables
PERF: Support move semantics for ITK smart pointers
ENH: Remove usage of SmartPointerForward reference
ENH: Remove unneeded internal smart pointer type
COMP: Require MSVC VS14 2015 for C++11 compatibility
ENH: Use C++11 template alias for Image::Rebind
STYLE: Use copy-swap idiom for SmartPointer
ENH: Use std::unique_ptr over itk::AutoPointer
DOC: Document additional MaskValue variable
BUG: remove unused cmake CXX try compile file
BUG: Remove un-configured and unused CMake configure define
BUG: Improve Doxygen extraction with blank line
ENH: Remove TEMPLATED_FRIEND macro and try compile
ENH: Replace optional tr1 type_traits with c++11 standard
ENH: Assume c++11, remove configure defines for optional TR1 features
BUG: Add missing extensions to ImageIO
ENH: Only use std::atomic implementation for AtomicInt class
ENH: Add direct SmartPointer conversions to match raw Pointers
PERF: Use emplace when inserting into map for ProcessObject
ENH: Create virtual interface for the MultiTheader
ENH: Trying out the ThreadPool as a separate MultiThreader
BUG: Fix uninitialized cross structuring element buffer
BUG: Disable ThreadPools by default
COMP: Add forward declaration of ExceptionObject in Macro.h
COMP: Add forward declaration of ExceptionObject in Macro.h
ENH: Use gtest_discover_tests if available
DOC: Watershed filters is not stream-able
COMP: Use nullptr over 0 for null pointer
STYLE: Use SmartPointer direct conversion constructors
Revert "BUG: Disable ThreadPools by default"
BUG: Actually disable ThreadPools by default
COMP: Suppress warning on CircleCI about itkIndex out of bounds
ENH: Update CircleCI external data cache
ENH: Address incorrect types with neighborhood iterator base class
COMP: Make MirrorPadImageFilter::DelayBase a conventional parameter
Bryce A Besler (1):
ENH: Move DiscreteGaussianDerivativeImageFilter from Review to
ITKImageFeature
Dženan Zukić (27):
ENH: updating SphinxExamples and pointing to GitHub
COMP: Get rid of warning about registry key
STYLE: minor fixes
BUG: duplicator crashes if buffered region is smaller than largest region
STYLE: reducing code duplication and cleaning up method documentation
ENH: adding itkReviewPrintTest to tests. It existed but was not invoked.
COMP: turn FEM off by default, as it takes a long time to build
COMP: fixing compiler warnings
ENH: making ITKBioCell and ITKNeuralNetworks remote modules
COMP: fixing configure error
COMP: long paths are not yet supported by all the tools in the build chain
COMP: using ITK_DELETED_FUNCTION, and more consistent override specifier
ENH: simplify code and properly support long long type
COMP: fix compile warning
STYLE: avoid redirect for repository address in DVMeshNoise
ENH: update remote modules to require CMake 3.9.5
BUG: fixing crash in test
ENH: Remove ITKFEMRegistration from default configuration
ENH: Fixing error and improving examples' test
ENH: Use MultiThreaderBase
STYLE: reducing duplication and removing commented code in DistanceMap tests
STYLE: fixing typo
BUG: more reliably detect Windows+DLLs case
ENH: enable thread pool by default
ENH: adding exponential decay option to MirrorPadImageFilter
BUG: Set/GetGlobalDefaultNumberOfThreads was forgotten in legacy #ifdef
BUG: fixing Windows+DLL ThreadPool sporadic destructor hanging
Francois Budin (17):
BUG: Update ITK test files SHA and debug ContentLinkSynchronization.sh
ENH: Bump ITK version to 5.0.0.
ENH: lifting path length limitation on Windows 10 version 1607+
BUG: Remove bad guards stopping inclusion of necessary hxx file
BUG: Remove extern "C" call to include <cstring>
BUG: Initializes CMAKE_DEBUG_POSTFIX to be empty
BUG: Initializes CMAKE_DEBUG_POSTFIX to be empty
DOC: Remove CMake comments mentioning CMake 3.4
DOC: ITK_CONSTEXPR* and ITK_HAS_CXX11_RVREF are deprecated
BUG: DCMTK builds fails with ICU ON on Linux and Mac
BUG: LabelErodeDilate remote module repositories are out of sync
BUG: Projects could not link to DCMTK on Windows and MacOS
DOC: Add missing documentation for `github_compare` option
ENH: Update CMake code to use IN_LIST (CMake >= 3.3)
BUG: Update LabelErodeDilate
ENH: Compile ITK with MKL (FFTW) installed on system
BUG: Update ParabolicMorphology remote module
Gregory C. Sharp (1):
DOC: Fix misspelling of vertices
Hans Johnson (86):
ENH: Update Wiki examples for latest code changes
COMP: Remove override warnings
ENH: Cuberille future compilation deprecations
ENH: Strain future compilation deprecations
COMP: TwoProjectionRegistration Future proof code
COMP: LevelSetsv4 used deprecated api
COMP: N4 remove testing of deprecated SetMaskLabel
BUG: Provide consistent GetOutput behavior
BUG: GetModifiableTransformList needs to always be available
BUG: Restore backwards compatibility
DOC: Remove ITKv3 to ITKv4 migration documentation.
COMP: Provide migration documentation old macros
STYLE: Remove deprecated code directory contents
STYLE: Remove all vestiges of ITKv3 code
STYLE: Remove legacy code for ITKv5 starting
ENH: Revert to include itkv3::Rigid3DTransform
STYLE: Move Future deprecated to deprecated
BUG: Restored testing for long HistorgramMatching
COMP: Remove unnecessary conditional tests
COMP: Force using lower deployment targert for fftw
COMP: Use C++ headers over C headers
COMP: Set ITK_VERSION_MAJOR to 5
STYLE: Fix header guard format
COMP: Remove ITK_USE_STRICT_CONCEPT_CHECKING flag
ENH: Set cmake Minimums to 3.9.5
COMP: Change min cmake version to 3.9.5 for circleci
COMP: Directly use cmake compiler_detection.h
STYLE: Fix typo requireing -> requiring
COMP: Consistently set use of CMake 3.9.5 and options
COMP: Enforce building ITK with C++11
COMP: Modularize cmake config like VTK.
COMP: Use C++ headers over C headers (part 2)
ENH: Scripts used during ITKv5 migration
STYLE: Remove conditional version 201103L code
COMP: Need to match type for different threaders
COMP: Preparing for ITKv5 by adding override
COMP: Use C++11 override directly
STYLE: Use override statements for C++11
COMP: Use C++11 ITK_NULLPTR directly
COMP: Use nullptr instead of 0 or NULL
STYLE: Prefer nullptr for C++11
COMP: Use C++11 nullptr directly
BUG: VXL visibility must match ITK visibility
COMP: Use C++11 = delete directly
COMP: Use C++11 constexpr directly
STYLE: ITK_COMPILER_CXX_CONSTEXPR is always true
BUG: Missing external linkage options for float and double.
COMP: Remove deprecated C++ 11 features
ENH: ReplaceitkGetObjectMacro.sh used during ITKv5 migration
ENH: Update SeveralRemotes to latest version.
COMP: Suppress invalid warning
STYLE: Remove outdated conditional code
STYLE: Remove unnecessary old CMakeCode
ENH: Remote for SmoothingRecursiveYvvGaussianFilter
STYLE: Prefer C++11 type alias over typedef
BUG: Type alias errent typo in name
BUG: ConceptChecking type matching failed.
STYLE: Remove ITK_HAS variables that should not be defined
COMP: Allow using cmake 3.9.5 default for RPATH setting
STYLE: Replace itkStaticConstMacro with static constexpr
BUG: Propagate C++11 requirements to external project
STYLE: Prefer constexpr for const numeric literals
STYLE: Use range-based loops from C++11
PERF: Allow compiler to choose best way to construct a copy
PERF: Replace explicit return calls of constructor
STYLE: Use auto for variable creation
BUG: Restore ITK.kws.xml preferences
ENH: Provide advanced development mode for writing GTests
COMP: Use C++11 noexcept directly
ENH: Use simplified/natural conversion to const pointer
ENH: Use natural ConstPointer conversion
STYLE: Use override statements for C++11
COMP: Use C++11 noexcept directly
ENH: Add google test for itkIndex.h
ENH: Make const operator[] conform to standards
STYLE: Change aggregate classes to mirror std::array
ENH: Update all remote modules with C++11 conformance
BUG: New SmartPointer conversion ambiguity
BUG: Error in ITK_VERSION construction
ENH: Add introspection into the build process
COMP: Silence warning of mismatched signs.
ENH: Bring in C++11 updates for ITKBridgeNumPy
STYLE: Do not use itkGetStaticConstMacro in ITK
COMP: Make member name match kwstyle requirements.
BUG: Add ability to construct SmartPointer with NULL
BUG: Update NULL pointer patch with final fixes
Hastings Greer (1):
ENH: Add wrapping for Labeled PointSet to PointSet registration classes
Jean-Christophe Fillion-Robin (3):
BUG: Prevent gdcm "missing implementation" error on macOS
BUG: Prevent gdcm "missing implementation" error on macOS
STYLE: MeshIO: Introduce ITKIOMeshBase module. See #3393
Jon Haitz Legarreta (8):
STYLE: Fix typo in itk::VariableLengthVector struct name.
ENH: Set the InsightSoftwareConsortium repo as the remote.
STYLE: Improve itkHoughTransform2DLinesImageFilter style.
DOC: Add different GitHub badges to the `README.md` file.
DOC: Change the ITK Git tips wiki page reference for Git scm website.
DOC: Add commands in a `Review` section to the ITK Git cheat sheet.
DOC: Change the `ITKGitCheatSheet.tex` file tittle.
DOC: Make references to ITK issue tracking system consistent.
Jon Haitz Legarreta Gorroño (19):
BUG: Fix bug in class LaTeX documentation Doxygen link.
BUG: Fix unnecessary explicit itk namespace mention in Doxygen link.
DOC: Remove redundant ellipsis after "etc." in LaTeX doc.
DOC: Remove unnecessary EOF comments.
DOC: Make namespace closing bracket comments consistent.
DOC: Fix typo: substract to subtract.
DOC: Remove unnecessary ifdef and class ending comments in FEM.
DOC: Remove non-existing namespace comment.
ENH: Add a code of conduct to the ITK project.
ENH: Bump latest version of the ITKSplitComponents remote module.
DOC: Remove unnecessary Doxygen \ref keyword in module crossrefs.
DOC: Remove crossrefs to non-existing classes.
DOC: Improve the ISSUE_TEMPLATE.md markdown file contents.
DOC: Change the term `mailing list` in README.md.
DOC: Fix syntax mistake in `Sharing Data` section of CoC.
DOC: Fix typos in class doc.
ENH: Add Python wrap file to itk::MultiResolutionPDEDeforableRegistration.
STYLE: Update the wrap files to match current CMake syntax.
DOC: Fix typo.
KWSys Upstream (1):
KWSys 2018-01-08 (f7990fc2)
Marcus D. Hanwell (1):
DOC: Add GitCheatSheet sources
Martino Pilia (2):
BUG: fix itkFormatWarning in Python wrapping
BUG: fix itkFormatWarning in Python wrapping
Matthew McCormick (46):
BUG: Remove ITKTubeTK remote
ENH: Add wrapping for BSplineTransformInitializer
ENH: Add PolarTransform remote module
COMP: Do not use absolute path to TestBigEndian.cmake in GDCM
COMP: Enable pthreads shim with Emscripten
COMP: Do not use absolute path to TestBigEndian.cmake in GDCM
COMP: Enable pthreads shim with Emscripten
BUG: Allow module examples to be enabled when built externally
ENH: Ensure external module examples get added to current build tree
COMP: Specify OutputImageType for boundary conditions in FFTPadImageFilter
COMP: Update DCMTK to 2018.01.16 and support Emscripten
COMP: Fix cross compiling DCMTK
BUG: Do not set DCMTK_WITH_XML to ON in DCMTK configuration
COMP: itk::Math perfect forward return type
BUG: Do not segfault when trying to use PDEDeformableRegistrationFilter
COMP: Ensure CastXML uses C++11 with GCC or Clang
COMP: Remove legacy BackTransform methods from Rigid3DTransform
COMP: Explicitly add NumericTraits::max to the API
COMP: Address SG line length warnings in DataRepresentation, Filtering
DOC: Update README Software Guide link
DOC: Update Discussion link in the README
ENH: Add banner to the README
COMP: Bump KWStyle to 2018-02-22 master
COMP: Add missing wrapping for MultiThreaderBase
COMP: Do not wrap methods with ?unknown? type
COMP: Add missing itkSimpleFastMutexLock headers
ENH: Import the ITKBridgeNumPy module
BUG: GetArrayFromImage calls UpdateLargestPossibleRegion
BUG: Add missing wrapping for PoolMultiThreader
BUG: Exclude MultiThreaderBase from GetNameOfClass test
COMP: Add SimpleFastMutexLock include to ESMDemonsRegistrationFunction
BUG: Cast to correct iterator type in PeriodicBoundaryCondition
BUG: Fix casting in PeriodicBoundaryCondition
COMP: Work around RegionGrow2DTest compiler error on ppc64le
BUG: Bump KWStyle for C++11 brace list initialization support
BUG: Fix MeshFileWriter export specification
BUG: Wrap long long instead of long
ENH: Create ITKIOMeshVTK module
COMP: ExceptionObject declaration must come before usage
ENH: Migrate BYU IO into ITKIOMeshBYU
COMP: Bump ParabolicMorphology for MultiThreaderChanges
COMP: Remove SmartPointer NULL initialization compatibility code
DOC: Use http for issues.itk.org
ENH: Migrate MultiScaleHessianBasedMeasureImageFilter out of ITKReview
ENH: Move ContourExtractor2DImageFilter out of ITKReview
DOC: Avoid Voronoi term when referring to the pixel center
Niels Dekker (18):
PERF: Improved speed of copying and resizing NeighborhoodAllocator
STYLE: Removed 'char(255)' casts from NumericTraits min() and max()
STYLE: Removed assignments from Neighborhood copy constructor
BUG: Fixed semantics NeighborhoodAllocator operator== and operator!=
BUG: GaussianDerivativeImageFunction should use image spacing consistently
PERF: NeighborhoodOperatorImageFunction avoids copy ConstNeighborhoodIterator
COMP: Worked around endless VS2015 Release compilation on Math::Floor
PERF: Removed blurring from GaussianDerivativeImageFunction
ENH: Added GetCenterPoint and SetCenterPoint to EllipseSpatialObject
DOC: Explained calling GetCenterPoint() when using Hough filter->GetCircles()
ENH: IsInside(point) made easier, especially for HoughTransform circles
STYLE: Using C++11 auto in HoughTransform2DCirclesImageFilter
PERF: GaussianDerivativeImageFunction now reuses NeighborhoodIterator objects
PERF: GaussianDerivativeImageFunction constructor, RecomputeGaussianKernel()
COMP: ITK_DISALLOW_COPY_AND_ASSIGN now unconditionally does '= delete'
COMP: Moved ITK_DISALLOW_COPY_AND_ASSIGN calls to public section
COMP: Manually moved ITK_DISALLOW_COPY_AND_ASSIGN calls to public section
COMP: Moved ITK_DISALLOW_COPY_AND_ASSIGN calls in *.cxx to public section
Sean McBride (19):
STYLE: Fixed up confusion between base 2 and base 10 prefixes
STYLE: arranged/alphabetized things to make subsequent changes reviewable
COMP: Fixed some missing name mangling of libTIFF symbols
BUG: fixed crash on macOS under guardmalloc from RunOSCheck()
BUG: don't use double underscore, which is reserved in C++
STYLE: fixed some spelling, spacing, and comments
DOC: Fixed comment about LegacyAnalyze75Mode default value
BUG: Some minor cleanup and improvement after itkNiftiImageIO code review
STYLE: arranged/alphabetized things to make subsequent changes reviewable
COMP: Fixed some missing name mangling of libTIFF symbols
BUG: Analyze 7.5 fixes/improvements
COMP: Mangle HDF5 symbol names
COMP: Fixed clang Wrange-loop-analysis warnings
DOC: fixed minor typo in comment
BUG: fixed crash on macOS under guardmalloc from RunOSCheck()
COMP: Mangle HDF5 symbol names
BUG: Revert part of f38b1dd4, which caused a regression
ENH: Added new DetermineFileType() API to NiftiImageIO
COMP: fixed clang warning about unnecessary copy in for loop
Simon Rit (1):
BUG: fix deadlock in FFTW for windows shared libs
Taylor Braun-Jones (1):
BUG: Handle single-component PLANARCONFIG_SEPARATE TIFF images (#ITK-3518)
VXL Maintainers (3):
VNL 2018-01-25 (ed159d55)
VNL 2018-01-31 (39559d06)
VNL 2018-03-04 (09a097e6)
Ziv Yaniv (1):
ENH: Adding user set min and max values for noise.
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