ITK 5.0 Alpha 1: Modern C++

c-plus-plus-11
release
itk-releases

(Matt McCormick) #1

ITK 5.0 Alpha 1 is ready for testing!

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, constexpr, nullptr, override, noexcept. The keywords auto and using as well as range-based loops 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][2][3][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 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 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 has been updated to match these changes.

As shown below, toolkit has adopted the application of the using keyword for type aliases, 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 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. 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.

ITK 5.0 Alpha 2: Performance
ITK 5.0 Beta 1: Pythonic Interface
(Niels Dekker) #2

Thank you for the update, Matt!

Would it still be feasible to get my latest patch “ENH: Added NeighborhoodRange for efficient modern C++ style iteration” into ITK 5.0.0? Do you think it’s worth it?

See also itk::NeighborhoodRange: a new class for efficient modern C++ style iteration


(Matt McCormick) #3

Definitely!

It would be great to make it available for testing and feedback in ITK 5.0 Alpha 2. Could you please follow-up with the remaining issues on the patch? Also, it would be very helpful to have some documentation for the class in the Iterators section of the ITK Software Guide.


(Andras Lasso) #4

This is great! Do you have some numbers on performance improvement? Which parts of ITK got faster and by how much?


(Matt McCormick) #5

More information on this should be available in ITKv5 Alpha 2 :slight_smile:


(Niels Dekker) #6

It appears that the current ITK master branch is in some cases > 40 x faster (yes, more than forty times!) than 4.13. :star_struck: At least, that’s what I observed, doing HoughTransform2DCirclesImageFilter::Update(), compiled with MSVC 2015 64-bit Release. The source of my little test is at item 4 of the topic Removal of `virtual` keywords from ConstNeighborhoodIterator

The specific filter->Update() call in that test takes me more than 10 minutes when using ITK 4.13, and less than 15 seconds when using the ITK master branch!!! As I observed with commit https://github.com/Kitware/ITK/commit/fa68b5365071b3e07f3861c836d3fd93935471d5.

This performance gain was achieved by a number of independent improvements, including:

  • A rigorous code cleanup of GaussianDerivativeImageFunction, especially
  • Reducing the number of memory allocation during neighborhood operations, for example:
  • Removing virtual function calls during neighborhood iteration:
  • Introduction of a new ShapedImageNeighborhoodRange class

Hope that helps, Niels


(Andras Lasso) #7

Awesome! Thanks to all ITK developers for their hard work.

It is very useful to know that performance improvement is so significant, as it bumps up priority of ITK update in 3D Slicer.


ITK 5.0 Beta 1: Pythonic Interface