[ITK-dev] [ANN] ITK 4.9.0 has been released!

Matt McCormick matt.mccormick at kitware.com
Wed Feb 3 10:04:29 EST 2016


The Insight Segmentation and Registration Toolkit (ITK), is an
open-source, cross-platform library for multidimensional image
analysis. On behalf of the Insight Toolkit community, we are proud to
announce that ITK 4.9.0 has been released!


Links to the Sourceforge.net tarballs can be found on the download page:

 http://www.itk.org/ITK/resources/software.html


Outline
-------

1. Introduction
2. New Features
3. ITK Changelog
4. ITK Sphinx Examples Changelog
5. ITK Software Guide Changelog


Introduction
-----------------

Developed by an international community, ITK collects best-of-breed algorithms
for registering, segmenting, analyzing, and quantifying n-dimensional imaging
data. The high-quality library facilitates reproducible research, provides a
software resource for teaching image analysis, and is a platform for
commercial product development.

A few selected highlights for the 4.9 release include the following:

* new remote modules, such as the Cuberille module for smooth
generation of meshes from binary segmentation images, and
enhancements, such as advanced edge-preserving smoothing for the
AnisotropicDiffusionLBR module;
* the ability to build Python wrapping, including Python 3, faster
with a more standard installation;
* improved performance of itk::Image::GetPixel and operations on
itk::VariableLengthVector;
* the ability to generate a FlatStructuringElement from an image
* the ability to perform point-set registration with time-varying B-splines
* the ability to specify module dependencies as public / private /
compile / test


Congratulations and well done to the 48 contributors to this release. We would
especially like to recognize new contributors: Mikhail Isakov, Sreekanth
Arikatla, Tobias Wood, Ricardo Ortiz, Junjie Bai, Alexander Leinoff, Eugene
Prilepin, Seun Odutola, Martin Michlmayr, Betsy McPhail, Luc Hermitte,
Abhishek Tiwari, Sumedha Singla, Lucas Gandel, Alexis Girault, Max Smolens,
Shawn Waldon, Hyun Jae Kang, Adam Snyder, Isaiah Norton, Pablo
Hernandez-Cerdan, Zach Williamson, Laurentiu Nicola, and Floris Berendsen.


New in the ITK Software Guide is a chapter on how to create an ITK module.
Since a module can now be configured as a separate CMake project outside of
the ITK build tree, external module development is faster and amenable to
continuous integration testing. With an external module, Python wrapping can
easily be added to algorithms implemented in C++. For example External
modules, see the InsightSoftwareConsortium GitHub organization.

Since the Insight Applications (ITKApps) are no longer actively being
developed, and they are a considerable maintenance burden, ITKApps will no
longer be released. There are a number of other projects that provide this
functionality, like 3D Slicer and ITK-SNAP. Archived versions of some ITKApps
executables will be made available in Docker images in the future.

This release also brings support, including Python wrapping support, to the
latest compilers including Visual Studio 2015 and the soon-to-be released GCC
6.


New Features
------------

Wrapping improvements
^^^^^^^^^^^^^^^^^^^^^

* Python 3 supported
* Visual Studio 2015 supported
* C++14 standard supported
* GCC 6 supported
* Wrapping builds much faster due to CastXML binaries
* LandmarkBasedTransformInitializer now wrapped
* NumPy bridge with VisualStudio
* Wrapping for the MinimalPathExtraction module
* Wrapping is now installed into Python’s site-packages directory in
the “itk” package
* Wrapping package size is decreased
* Better package portability on Mac OSX

New Remote Modules
^^^^^^^^^^^^^^^^^^

* Cuberille
   * Insight Journal Article: http://hdl.handle.net/10380/3186
* AnisotropicDiffusionLBR
   * Insight Journal Article: http://hdl.handle.net/10380/3505
   * Web browser reproducibility: http://www.kitware.com/blog/home/post/942

Core Improvements
^^^^^^^^^^^^^^^^^

* External Modules can now be developed outside of the ITK source tree
and on GitHub
   * Details: http://www.kitware.com/blog/home/post/997
* New utilities in itk::Math:
   * AlmostEquals
   * NotAlmostEquals
   * ExactlyEquals
   * NotExactlyEquals
* New itk::NumericTraits
   * IsInteger
   * IsSigned
* Improved C++11 support
   * New ITK_DELETE_FUNCTION macro for “=delete”
   * New ITK_NOEXCEPT macro for the “noexcept” keyword
* Improved capabilities of itk::ResourceProbe and
itk::ResourceProbesCollectorBase
* Improve numerical stability in VNL eigen system estimation
* itksys_ios:: and itksys_stl:: have been remove (use std::)
* ImageIO and TransformIO classes only get registered once in the object factory
   * The use of dynamic_cast with itk::TransformTemplate pointers
should be avoided. It can fail on Mac OSX and older Linux systems.

Filtering Improvements
^^^^^^^^^^^^^^^^^^^^^^

* Generate a FlatStructuringElement from an image
* WarpImageFilter support VectorImage’s
* ConvertLabelMap supports different LabelMap types
* ImageToPathFilter moved from the ITKReview to the ITKPath module
* itk::MovingHistogramImageFilter moved to the ITKImageFilterBase module

Registration Improvements
^^^^^^^^^^^^^^^^^^^^^^^^^

* Point-set registration with time-varying B-splines

Build Improvements
^^^^^^^^^^^^^^^^^^

* Module dependencies can now be specified as public / private / compile / test
* BUILD_EXAMPLES CMake option is now OFF by default
* Option to export all library symbols on Windows:
   * Details: http://www.kitware.com/blog/home/post/939
* Expat third party library is now name mangled
* Many more modules can be built as shared libraries
* KWStyle is automatically built and configured when tests are built

Performance Improvements
^^^^^^^^^^^^^^^^^^^^^^^^

* New MetaProgrammingLibrary namespace (itk::mpl) holds members for
metaprogramming for compile-time determination of optimal code paths
   * itk::mpl::{TrueType,FalseType}
   * itk::mpl::{If,Not,And,Or,Xor}
   * itk::mpl::EnableIf
   * itk::mpl::IsBaseOf
   * itk::mpl::IsConvertible
   * itk::mpl::IsNumber
   * itk::mpl::IsSame
   * itk::mpl::PromoteType
* Image::GetPixel performance improvements
* Many itk::VariableLengthVector performance improvements
* AdaptiveHistogramEqualization uses a moving histogram
* WarpImageFilter performance improvements

Documentation Improvements
^^^^^^^^^^^^^^^^^^^^^^^^^^

* Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples
* ITK Software Guide improvements
   * How to use Python wrapping
   * How to create an ITK module
   * Improvements to segmentation examples
   * Expanded Canny edge detection example
   * Expanded tree container example
* ITK Sphinx Examples improvements
   * Python wrapping in the ITK superbuild
   * Bootstrap-based HTML rendering
   * Python versions of examples
   * New examples

Third Party Library Updates
^^^^^^^^^^^^^^^^^^^^^^^^^^^

* FFTW updated to latest upstream
* Build with recent OpenCV 2 and 3
* Build with the latest VTK
* PNG update to the latest upstream
* KWSys updated to the latest upstream
* MINC updated to the latest upstream
* SWIG updated to the latest upstream
* Third party PNG and MINC are now Git subtrees

Style improvements -- ITK gets more stylish with every release!
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Private copy constructors and operator= use ITK_DELETE_FUNCTION

* Improved code coverage -- we are at 84.9%!

*Lots* of important bug fixes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  * Histogram-related outputs may change due to a fix to Histogram
interval computation (Change-Id:
I2063912edee79422d88125ffd5f7513c31a9e98c)

* And much more! See details in the log below.



Changes from v4.9rc03..v4.9.0
-----------------------------

Bill Hoffman (3):
      COMP: fix 64 bit build warnings with windows auto-export on.
      COMP: work around for VS 2015 optimizer bug causing test failures.
      COMP: work around for VS 2015 optimizer bug causing test failures.


Bradley Lowekamp (1):
      BUG: Fix precision with accumulation and scaling in AdaptiveHistogram


Davis Vigneault (1):
      COMP: Include itkMacro.h in itkTestingMacros.h


Dzenan Zukic (1):
      COMP: fix itkStaticAssert warnings with clang++


Hans Johnson (6):
      COMP: BSD command lines do not have --version
      COMP: Respect CMAKE_CXX_STANDARD during config
      COMP: Clang Override warnings removed
      BUG: Download URL was wrong for macosx
      COMP: The ComputeUpdate function is needed
      COMP: Incomplete solution for operators corrected


Hyun Jae Kang (12):
      COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6
      BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6
      BUG: Fixed the runtime crash of itkTimeProbeTest2
      BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6
      BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6
      BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's
tests on OSX 10.6
      COMP: Fixed the data conversion warning messages of itkResourceProbe
      BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6
      BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1
      BUG: Fixed the runtime crash of test_pow_log on OSX 10.6
      BUG: Fixed the runtime crash of vnl_test_numeric_traits
      BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6


Isaiah Norton (1):
      COMP: fix build with -std=c++11 when ITK/VXL initially configured without


Jon Haitz Legarreta (1):
      BUG: Fix OpenCVBridge bug for two-byte images.


Lucas Gandel (2):
      BUG: Change CMAKE_SOURCE_DIR to CMAKE_CURRENT_SOURCE_DIR
      BUG: Fix multiple external modules wrapping


Martin Michlmayr (1):
      COMP: fixed error "Dunno about this gcc" for gcc 6


Matthew McCormick (22):
      BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper.
      COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5.
      DOC: Update the location of the GNUPlot Software Guide scripts.
      DOC: Update the Software Guide repo location in Examples/README.txt.
      COMP: Add export specification for itk::ResourceProbe.
      COMP: Require NO_MODULE with DCMTK find_package.
      COMP: Update CastXML revision for C++14 VS 2015.
      BUG: Fix PythonTransformCoverage test for Python 3.4.
      BUG: Fix PythonExtras test with Python 3.
      BUG: Fix PythonTypemaps tests with Python 3.
      ENH: Do not force shared libraries when wrapping.
      DOC: Update WikiExamples to 2016-10-20
      BUG: BUILD_TESTING should be not advanced.
      COMP: Use enum in itkStaticConstMacro for old GCC.
      BUG: Correct FlatStructuringElement wrapping location.
      BUG: Correct itkStaticConstMacro GCC version comparison operator.
      BUG: Improve GCC detection in itkStaticAssert.h preprocessor macro.
      BUG: Fix OpenCV version check.
      DOC: Update the SphinxExamples Remote Module.
      COMP: Wrap FlatStructuringElement before other classes.
      COMP: Workaround inconsistent OpenCV pre-processor variables.
      COMP: Update CastXML to support wrapping with GCC 6.


Michka Popoff (3):
      ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7
      COMP: Re-enable review module for python 3 and older VTK's
      ENH: Use importlib for python 3.4 instead of imp


Nick Tustison (1):
      ENH:  Accommodate epsilon error on left side.


Sean McBride (1):
      DOC: Update some woefully out-of-date GDCM comments, and typos


Seun Odutola (1):
      BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions


Sumedha Singla (3):
      ENH: Fixed the numeric traits for datatypes
      DOC: Added a comment to support the changes in numeric traits datatypes.
      BUG: Invalid memory access of itk::NotAlmostEquals Bug#ITK-3403



Changes from v4.9rc02..v4.9rc03
------------------------------------------------


Alexis Girault (1):
      BUG: Implement SetAutoMinimumMaximum in itkScalarImageToHistogramGenerator


Bill Lorensen (1):
      BUG: nifti_read_subregion_image was leaking file pointers


Brad King (7):
      ENH: Teach ITK module macros to support independent header-only modules
      ENH: Add script to import KWIML library source code
      ENH: Add `ITKKWIML` module to provide external KWIML library
      ENH: Port TIFF integer types from KWSys to KWIML
      ENH: Port LSM integer types from KWSys to KWIML
      ENH: Port itkIntTypes.h from KWSys to KWIML
      ENH: Drop KWSys FundamentalType component


Bradley Lowekamp (1):
      ENH: Add option to choose scheme for git download


Davis Vigneault (1):
      STYLE: Use cstdlib return macros in ITK examples


Dženan Zukić (3):
      BUG: do not pass 0,0,0 to Versor.Set()
      STYLE: Removing the unused NeighborhoodRadius property
      ENH: Write out transform in DeformableRegistration15


Gert Wollny (1):
      BUG: Remove double-conversion from public interface, use system.


Hyun Jae Kang (8):
      ENH: Create a test for the SpawnThread function ( ITK-3317)
      STYLE: Remove an unnecessary file (-w) from source code
      BUG: Fixed the failed case of itkStdStreamStateSaveTest on OS X 10.8
      BUG: Fixed the failed test case of itkThreadPoolTest on OS X 10.8
      BUG: Fixed a failed test of ITKDistanceMapTestDriver
      BUG: Fixed the failed test VideoSourceTest
      PERF: Improve the performance of a test of
ITKRegistrationMethodsv4TestDriver
      COMP: Fixed the compiler error of
itkDisplacementFieldToBSplineImageFilterTest


Jean-Christophe Fillion-Robin (25):
      BUG: Build ITKIOTransformHDF5 as shared library. See #3393
      BUG: Build ITKIOTransformMINC as shared library. See #3393
      BUG: Build ITKIOTransformMatlab as shared library. See #3393
      BUG: Build ITKIOTransformInsightLegacy as shared library. See #3393
      STYLE: TransformIOFactory: Remove obsolete declaration. See #3393
      COMP: TransformIOFactory: Add missing ctor/dtor from hxx file. See #3393
      COMP: TransformFileWriter: Remove method "OpenStream()" without definition
      COMP: TransformFileReaderTemplate: Remove undefined method
"CreateTransform()"
      ENH: Update ITKIOPhilipsREC to allow static initialization. See #3393
      ENH: Update ITKIOTransformMINC to allow static initialization. See #3393
      COMP: MINC: Fix VS2008 "unknown round" build error. See #3393
      COMP: MINC: Fix VS2008 "unknown arpa/inet.h" build error. See #3393
      COMP: Configure ENABLE_SHARED into <ModuleName>.cmake file. See #3393
      COMP: Fix configuration of IOFactory header. See #3393
      STYLE: UseITK: Removed redundant code setting ImageIO factory
name. See #3393
      STYLE: UseITK: Re-factor introducing _configure_IOFactoryRegisterManager
      STYLE: UseITK: Set TransformIO factory and module name using convention.
      BUG: Ensure Image IO factories are registered once. See #3393
      BUG: Ensure Transform IO factories are registered once.
      COMP: ITKIOXML: Fix VS11 "already defined std::string" link
error. See #3393
      BUG: TransformIO: Implement explicit template instantiation
using "extern".
      COMP: TransformIO: Fix VS build errors removing extra EXPORT
      COMP: TransformIO: Handle compiler not supporting "pragma diagnostic".
      COMP: TransformIO: TransformFile(Reader|Writer) still need to be exported.
      COMP: TransformIO: Fix explicit instantiation approach


Johan Andruejol (1):
      ENH: Add ITK_RUNTIME_LIBRARY_DIRS for external projects


KWIML Upstream (1):
      KWIML 2015-12-09 (43f9f8d0)


Lucas Gandel (1):
      BUG: PhysicsBasedNonRigidRegistrationMethod test failure on Debian 32bit


Matthew McCormick (16):
      COMP: Fix PointDimension reference in AzimuthElevationToCartesian test.
      STYLE: Improve scoping in AzimuthElevationToCartesian test.
      STYLE: Explicitly mark the ProcessObject methods virtual in SignedMaurer.
      BUG: Do not try to install targets that do not exist when
building externally.
      BUG: ITKIOMeta needs a public dependency on ITKMetaIO.
      COMP: Update LesionSizingToolkit for external build and style
test failures.
      BUG: Add CMake OpenCV export code to ITKVideoBridgeOpenCV.
      COMP: Improve compatibility with OpenCV 3.
      DOC: Fix class references in StatisticsLabelMapFilter.
      STYLE: Improved readability of itkStatisticsUniqueLabelMapFilterTest1.
      DOC: Correct ReverseOrdering description in ShapeUniqueLabelMapFilter.
      STYLE: Add own copy of GenerateExportHeader
      COMP: Create _TEMPLATE_EXPORT macros.
      COMP: TransformIOBaseTemplate must be explicitly instantiated.
      BUG: Do not use dynamic_cast for DisplacementFieldType in HDF5 test.
      COMP: Do not use string(MAKE_C_IDENTIFIER with CMake < 2.8.12


Max Smolens (1):
      BUG: VoronoiSegmentationRGBImageFilter: add pixel dimension check


Mikhail Isakov (1):
      DOC: correction in DiffusionTensor3D Reconstruction


Ricardo Ortiz (1):
      BUG: Set itkBinaryImageTo*LabelMapFilter foreground/background values


Seun Odutola (1):
      BUG: absolute value of tolerance taken to cater for negative spacing


Shawn Waldon (1):
      COMP: OSX set deployment target when building fftw


Simon Alexander (4):
      STYLE: Change to make git bash on windows happy with the function name
      COMP: fixes for visual studio 2015update1 x86 in release mode
      COMP: fixes for visual studio 2015update1 x86 in release mode
      COMP: fixes for visual studio 2015update1 x86 in release mode


Sreekanth Arikatla (2):
      BUG: Resolved const correctness in itkMatrix.h
      ENH: Fixes the symmetry of AzimuthElevationToCartesianTransform
and adds tests

Changes from v4.9rc01..v4.9rc02
------------------------------------------------


Bill Lorensen (1):
      BUG: Valgrind detected an invalid read


Davis Vigneault (1):
      STYLE: Address some warnings when running cppcheck


Hyun Jae Kang (2):
      COMP: Fixed a warning message of data-conversion on VS14
      COMP: Update KWStyle to remove format-string warning message


Matthew McCormick (3):
      DOC: Remove invalid wrapping example.
      BUG: Wrap AdaptiveEqualizationHistogram.
      COMP: Ignore Doxygen endcond warning in itkIsConvertible.h.


Seun Odutola (1):
      COMP: Corrected minc2.h path installation from libsrc2/minc2.h to minc2.h


Ziv Yaniv (2):
      BUG: Affine transformation was estimated without sufficient
number of points.
      BUG: fixed BSpline initializer crash when reference image not set.



Changes from v4.8.0..v4.9rc01
--------------------------------------------


Abhishek Tiwari (1):
     BUG: "tmpImageIndex" not initialized to 0.

Adam Snyder (1):
     PERF: Reworked MMI Threading using a per-thread buffer

Alexander Leinoff (6):
     ENH: Adds IsInteger and IsSigned to NumericTraits.
     COMP: Doxygen itkMath.h 'OneValue()' could not be resolved.
     ENH: Adds ExactlyEquals and NotExactlyEquals functions to itkMath.h
     COMP: Removes floating-point equality checks
     ENH: COMP: Adds support for complex values to Math::AlmostEquals
     ENH: Updates fftw dependency

Arnaud Gelas (5):
     COMP: fix warning (unused local typedef)
     COMP: simplify ITKVideoBridgeOpenCV dependency
     DOC: add doxgen documentation for BinaryImageToLevelSetImageAdaptor
     ENH: add tests to exercise itk::ThreadedIteratorRangePartitioner
     COMP: fix compilation error with OpenCV2 and OpenCV3

Betsy McPhail (1):
     BUG: Improve buffer alignment in OctreeNode .

Bill Hoffman (2):
     ENH: Use new CMake Windows export symbol dll feature.
     COMP: Put vnl_export.h in the list of sources so it gets installed.

Bill Lorensen (4):
     COMP: VTkGlue linker errors
     BUG: Inappropriate use of AlmostEquals
     ENH: Bump tag for wiki examples
     ENH: Better layout strategy

Brad King (3):
     ENH: Remove use of include <itksys/ios/*> and itksys_ios::*
     ENH: Remove use of include <itksys/stl/*> and itksys_stl::*
     ENH: Update CMake Policy settings in Testing/TestExternal project

Bradley Lowekamp (31):
     BUG: Avoid null deference in PrintSelf with default construction
     ENH: Enable base classes for templates of landmark initializer
     STYLE: Use "Swap" for ITK member name
     BUG: Demonstrate Eigen analysis failure
     BUG: Fix computation of Eigen analysis
     ENH: Update DiscreteHessianGaussian Test baseline
     ENH: Correctly demonstrate float point Eigen failure
     ENH: compile vnl_math_hypot, and use at least double
     ENH: Adding initial update script from used libpng version.
     ENH: removing non-subtree files for itkpng
     ENH: Ported ITK changes for building to subtree merged code
     ENH: Update libpng update script for v1.6.9
     BUG: Use ParameterValueType for computation of landmark affine
     ENH: Wrap LandmarkBasedTransformInitializer
     BUG: Avoid potential exception in itk::Object::UnRegister
     ENH: Update itkpng zlib, configuration, and rename
     ENH: Update itkpng name mangling
     BUG: Use const pointer in Set method for constant ReferenceImage ivar
     BUG: Increase tolerance for PhysicsBasedNonRigidRegistrationMethod
     BUG: Demonstrate side effect on registration due to BSplineScatter change
     ENH: Move MovingHistogramImageFilter base classes to ImageFilterBase
     BUG: Avoid potential exception in itk::Object::UnRegister
     BUG: Avoid null deference in PrintSelf with default construction
     BUG: Use const pointer in Set method for constant ReferenceImage ivar
     ENH: Optimize AdaptiveHistogramEqualization with MovingHistogram base
     COMP: address sign unsigned comparison warning
     COMP: Address signed unsigned comparison warning
     COMP: Address unused member variable and methods in anonymous ns
     BUG: Fix segfault when with empty IsolatedWatershed Threshold range
     BUG: Adjust intensity tolerance for PhysicsBasedNonRigid test
     BUG: Reduce number of targets with MSVC

Davis Vigneault (7):
     DOC: Minor improvements to segmentation examples.
     DOC: Expanded Canny Edge Detection Example
     DOC: Expanded TreeContainer Example
     COMP: Warnings in itkVTKImageExport when compiling with c++11
     COMP: Warnings in FFTW Classes when compiling with c++11
     COMP: Update Git Tag for Subdivision Module
     COMP: Warnings in FFTW Classes when compiling with c++11

Dženan Zukić (1):
     STYLE: better formatting of the "usage" message

Eugene Prilepin (1):
     BUG: Fix a template name formation in python wrappings

Floris Berendsen (1):
     STYLE: Improve naming conventions in comments.

Hans Johnson (29):
     STYLE: Instrument for FixedParameters typedef
     BUG: Demonstrate DisplacementTransformFailure
     BUG: FixedParameters should be double precision
     STYLE: Minor code style issues for MGHIO
     COMP: Update to version for WikiExamples
     ENH: Update Sphinx for ITK 4.8.0
     ENH: Update MGHIO to be shared lib
     ENH: Provide consistent floating point comparisons
     BUG: Fix MGHIO to fix write failures
     PERF: Remove floating point as sentinal value
     COMP: Const correctness needs to be maintained
     BUG: Preserve backwards compatibility
     DOC: Provide consistent naming in comments
     ENH: Conversion between transform type tolerance
     STYLE: Prefer initialization to assignment
     ENH: Missing ITK_OVERRIDE
     COMP: Need to propagate ITKGDCM
     COMP: Need to propagate ITKGDCM
     COMP: Add missing ITK_OVERRIDE
     STYLE: Minor code style issues for MGHIO
     COMP: Update to version for WikiExamples
     ENH: Update Sphinx for ITK 4.8.0
     ENH: Update MGHIO to be shared lib
     BUG: Fix MGHIO to fix write failures
     ENH: C++11 allows for rigorous =delete
     COMP: Remove unnecessary failing assert test
     ENH: Ignore internal files for the Clion editor
     COMP: Fix VNL compilation for wider C++11 support
     BUG: In configuration test need to mirror code

Hyun Jae Kang (27):
     BUG: Remove std::cout calls from class
     BUG: Avoid an unexpected output of static_cast
     BUG: Update python example codes for ImageRegistration
     BUG: Retrieve the missed wrap file
     BUG: itkVTKImageIO class does not handle blank lines in VTK file header.
     BUG: Fix HDF5 CMake configuration with VS2015
     BUG: Fix a compilation issue on ITK4 with FFTW and shared libraries
     BUG: Fixed older XCode linking error
     ENH: Use CastXML binaries when building with x86_64 Mac OS X
     BUG: Remove std::cout calls from class
     BUG: itkVTKImageIO class does not handle blank lines in VTK file header.
     BUG: Fixed older XCode linking error
     ENH: Add automatic KWStyle build and configuration setup
     COMP: KWStyle shadow, format-nonliteral and autological-compare warning.
     COMP: Fixed the warning messages from itkGPU Module
     COMP: Fixed a warning message of unused-private-field
     COMP: Apply latest version of KWStyle
     COMP: Update KWStyle to fix its additional warning messages
     COMP: Update KWStyle to fix its additional warning messages
     COMP: Fix data-conversion warning messages on Windows
     ENH: Update itkResourceProbe to calculate statistical data
     COMP: Fix data-conversion warning messages on VS14
     COMP: Fixed 'std::sqrt' : ambiguous call to overloaded function
     ENH: Update the Report() function of itkResourceProbesCollectorBase
     COMP: Fix data-conversion warning message on itkResourceProbe
     COMP: Fix additional warning messages of KWStyle
     COMP: Fix data-conversion warning messages

Jon Haitz Legarreta (6):
     ENH: Add test for itkStatisticsUniqueLabelMapFilter
     BUG: Fix compilation issues for StatisticsUniqueLabelMapFilterTest
     BUG: Fix comparison issues for itkStatisticsUniqueLabelMapFilter
     BUG: Test for StatisticsUniqueLabelMapFilter stability
     ENH: Add test for itkParametricStpaceToImageSpaceFilter
     ENH: Improve code coverage for itkParametricSpaceToImageSpaceMeshFilter

Julien Michel (1):
     ENH: Support of VectorImage as template parameters for WarpImageFilter

Junjie Bai (2):
     BUG: ConvertLabelMap with different LabelMapTypes
     BUG: LabelObject CopyAttribute support different LabelObject type

KWSys Robot (4):
     KWSys 2015-07-10 (c9336bcf)
     KWSys 2015-07-30 (f63febb7)
     KWSys 2015-08-24 (cdaf522c)
     KWSys 2015-08-28 (dc3fdd7f)

LIBPNG Upstream (2):
     PNG 2009-04-06 (e68f5a36)
     PNG 2014-02-05 (3e753eb8)

Laurentiu Nicola (2):
     PERF: Avoid temporary smartptr in ProcessObject::GetInput
     PERF: Optimize WarpImageFilter by avoiding refcount bouncing

Luc Hermitte (8):
     PERF: itk::Image::GetPixel() performance improvment.
     PERF: Performance enhancements on VariableLengthVectors 1/...
     ENH: Dependencies on itkVariableLengthVector.h reduced
     BUG: Error in VariableLengthVector Unit Tests
     PERF: Performance enhancements on VLV 2/...
     PERF: Performances enhancements on VLV 3/...
     COMP: Fix signed/unsigned warnings
     BUG: std::copy/fill on empty VLV

Lucas Gandel (4):
     ENH: Move ImageToPathFilter from ITKReview to ITKPath module.
     BUG: Fixing ImageToPathFilter wrapping call from Review Module
     STYLE: Fix KWStyle dashboard errors
     BUG: Fix external module BUILD_SHARED_LIBS status

Mathieu Malaterre (1):
     BUG: Name mangle the included expat third party library.

Matthew McCormick (94):
     ENH: Change itkSystemInformationTest to itkCMakeConfigurationTest.
     ENH: Add AnisotropicDiffusionLBR Remote Module.
     ENH: Bump ITK version to 4.9.0.
     BUG: Remove std::cout calls from classes.
     COMP: Remove unused argument in ConditionVariableNoThreads.
     BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter.
     COMP: Add link interface specification for wrapping target_link_libraries.
     STYLE: Fix indentation in itkMINCTransformIOFactory.cxx.
     COMP: Fix MINCTransformIO factory registration.
     COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with Emscripten-1.
     COMP: Remove unknown doxygen command in AnisotropicDiffusionLBR.
     BUG: Initialize mutex for 32 bit AtomicInt.
     ENH: Use CastXML binaries when building with x86_64 Linux.
     STYLE: Rename gccxml -> castxml in {idx,igenerator}.py.
     COMP: Disable the gold linker for static builds on Ubuntu 14.04.
     ENH: Use Windows binaries for CastXML.
     ENH: Add better scoping in igenerator.py.
     BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + MSVC.
     BUG: LevelSetsv4 used signed char instead of char.
     ENH: Add better scoping to idx.py.
     COMP: Define newSize and oldSize in VariableLengthVector.
     STYLE: Use prefix increment operator in ImageBase.
     DOC: Correct spelling of Continuous.
     ENH: Add more progress information to IterativeClosestPoint2.
     BUG: Build BridgeNumPy with Visual Studio.
     ENH: Add ITKModuleExternal.cmake
     COMP: Wrap Image< bool, D > for FlatStructuringElement.
     BUG: Use CastXML binary built in Release.
     BUG: ContinuousIndex should not be templated over TCoordRep.
     COMP: Set CMP0054 to new.
     COMP: Address line length too long for Software Guide.
     COMP: Fix CannyEdgeDetectionImageFilter.cxx types.
     BUG: Support Python 3 wrapping module initialization.
     BUG: Update itkTemplate.py for Python 3.
     BUG: Update itkExtras.py for Python 3.
     BUG: Prevent Python callback addition recursion.
     BUG: Fix test scripts for Python 3.
     BUG: Replace __GCCXML__ with CABLE_CONFIGURATION.
     ENH: Allow projects to build against an external module.
     ENH: Replace CABLE_CONFIGURATION with ITK_WRAPPING_PARSER.
     ENH: Rename _cable_ to _wrappers_.
     BUG: Replace __GCCXML__ with CABLE_CONFIGURATION.
     BUG: Define ITK_WRAPPING_PARSER when wrapping.
     COMP: Do not use C++11 alignas in itkAlignedTypedef.
     ENH: Bump CMakeLists.txt version to 4.8.1.
     BUG: Pass the CMAKE_CXX_FLAGS to castxml.
     ENH: Bump CastXML version to 2015-30-29.
     ENH: Bump LLVM / Clang to 3.7.0.
     COMP: Avoid itklibminc linking with ITK_USE_SYSTEM_HDF5.
     COMP: Add missing ITKIOImageBase dependency for ITKTransformMINC.
     COMP: Use itkSimpleNewMacro in ThreadedIteratorRangePartitionerTest.
     ENH: Add wrapping support for building modules externally.
     BUG: Fix KWStyle test paths when building a module externally.
     ENH: Add Cuberille Remote module.
     COMP: Remove carriage returns from Cuberille remote.
     COMP: Remove unused argument in ConditionVariableNoThreads.
     DOC: Correct spelling of Continuous.
     ENH: Bump the MinimalPathExtraction Remote to 2015-10-20.
     COMP: Fix KernelTransform SetFixedParameters argument type.
     STYLE: Use prefix increment operator in ImageBase.
     COMP: Use ITK's pygccxml by correctly setting up the sys.path
     Revert "COMP: Put vnl_export.h in the list of sources so it gets
installed."
     BUG: Revert "BUG: ConvertLabelMap with different LabelMapTypes"
     ENH: Marking wrapping CMake configuration variables as advanced.
     STYLE: Rename CASTXML to CASTXML_EXECUTABLE.
     COMP: Non-virtual copy attribute members in LabelMap cannot have override.
     COMP: Add wrapping for AdaptiveHistogramEqualizationImageFilter.
     COMP: Add itkMacro.h to itkPromoteType.h for ITK_EXCEPT.
     ENH: Remove CMake version check in ITKModuleHeaderTest.cmake
     BUG: Improve KWStyle ExternalProject utilization.
     ENH: Remove old KWStyle build script.
     COMP: Address VariableLengthVector Doxygen rhs @param not found.
     ENH: Rename WRAPPING_LIBRARY_GROUPS to WRAPPING_SUBMODULE_ORDER.
     ENH: Install Python bindings into site-packages.
     ENH: Improve readability of Python site-packages path detection.
     COMP: DiscreteGaussianDerivativeImageFilter unsigned expression warning.
     BUG: ITKCommon publically depends on ITKDoubleConversion.
     COMP: Improve scoping in CovariantVectorGeometryTest.
     ENH: Improves names and export of module dependencies.
     STYLE: Improve namespace bracket style in itkIsConvertible.
     COMP: Set CMP0054 to new.
     BUG: Remove unused wrapping files.
     BUG: Do install install wrapping development files.
     ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER.
     BUG: Remove duplicate inclusion of wrapping submodules.
     COMP: Do not use C++ style comments for Doxygen cond.
     BUG: Fix detection of the gold linker.
     BUG: Update Python package installation locations.
     ENH: Bump CMakeLists.txt version to 4.8.2.
     ENH: Change BUILD_EXAMPLES default to OFF.
     BUG: Use 'from itk import ITKCommon' in module2module test.
     COMP: Link to VTK Python when built with Kits support.
     BUG: Install itk_minc2.h header.
     COMP: ITKIOMINC has a public dependency on ITKIOImageBase.

Michka Popoff (9):
     ENH: Update to swig 3.0.7
     ENH: Do not link against specific Python library on OS X
     COMP: Fix wrapping warnings when building with ITK_WRAP_IMAGE_DIMS=2
     COMP: Add missing wrapping for TransformBase
     COMP: Use ITK's pygccxml by correctly setting up the sys.path
     COMP: Disable incompatible modules when using Python 3 wrapping
     COMP: Move MovingHistogramImageFilterBase wrapping to
ImageFilterBase module
     COMP: Disable incompatible modules when using Python 3 wrapping
     ENH: Allow operations on Indexes and Offsets in Python

Mikhail Isakov (1):
     BUG: DiffusionTensor3DReconstruction segfault if no baseline image

Nick Tustison (5):
     BUG:  Set a default b-spline epsilon.
     ENH: Adding testing for closed loop.
     BUG:  Updating B-spline classes with the same epsilon strategy.
     PERF:  Switch vnl_vectors for fixed arrays.
     ENH:  Point-set registration with time-varying B-spline.

Olivier Commowick (3):
     BUG: Correct discrepancy in tridiagonal reduction wrt VNL eigen system
     BUG: Correct under/overflows in vnl_math_hypot (taken from pythag from V3P)
     BUG: Switch eigenvalues computation to double

Pablo Hernandez-Cerdan (2):
     ENH: Help class for itkFlatStructuringElement with constructor from images.
     COMP: Fix test errors and warnings in FlatStructuringElement.

Seun Odutola (1):
     COMP: Fixed name clash with Apple header (check Macro), renamed
check to Check

Shawn Waldon (1):
     COMP: Set target OS X version in environment for tools using compiler

Simon Alexander (1):
     BUG: incorrect closest point computation

Tobias Wood (2):
     BUG: LBFGSB was printing messages even with debug switched off.
     BUG: Removed an unguarded print statement.

Vladimir S. FONOV (9):
     BUG: Missing ITKIOMINC_EXPORT on __Private()
     COMP: Changing the order of HDF5 library components
     COMP: Splitting up IOMINC module into two parts: MINC and Transform
     STYLE: updated comments to properly reference LIBMINC
     ENH: Add script to merge upstream MINC as a subtree
     MINC 2015-07-23 (c033d431)
     COMP: Update MINC CMake code
     MINC 2015-08-18 (6d7e3ba8)
     MINC 2015-09-13 (95cd5374)

Xiaoxiao Liu (1):
     DOC: update email address for xiaoxiao.

Zach Williamson (10):
     BUG: Use correct libraries for ImageFusion tests
     ENH: Consolidate Library Dependencies
     COMP: Add a missing link to Review module
     COMP: Use correct linking macro in DCMTK
     BUG: Use correct libraries for TestKernel tests
     COMP: Fix inconsistant naming of GPUPDEDeformableRegistration
     ENH: Use new linking system macros
     PERF: Avoid searching private dependencies for include directories
     COMP: Recover missing dependencies
     ENH: use new linking macros in Filtering module


ITK Sphinx Examples Changelog
---------------------------------------------

Brad King (1):
      ENH: Remove use of itksys_ios::*


Dženan Zukić (1):
      ENH: Avoid warning window when the directory does not contain
any DICOM series


Hans Johnson (1):
      BUG: FixedParameters different from Parameters


Matt McCormick (38):
      ENH: Bump ITK ExternalProject to v4.8.0.
      COMP: Do not try to add html files twice to the tarballs.
      BUG: Turn off ITK modules when superbuild options are disabled.
      DOC: Consistently refer to source directory in length warning.
      BUG: Use os.path.sep for CreateNewExample.py on both Unix and Windows.
      ENH: Use a StringIO for the headers content in CreateNewExample.
      ENH: Make CreateNewExample compatible with Python 3.
      ENH: Enable BridgeNumPy in the Superbuild when NumPy available.
      ENH: Silence gitstats execution.
      ENH: Add sphinx-bootstrap-theme submodule.
      ENH: Update ITK ExternalProject to 4.9rc02.
      COMP: Support OpenCV 3.0.0.
      BUG: Pass the Sphinx output components in the superbuild.
      BUG: Work around epub output filename irregularity.
      ENH: Use side-by-side images in Binary Mathematical Morphology.
      ENH: Use all caps in Binary Mathematical Morphology examples.
      ENH: Move the Download button location.
      BUG: Rename CreateAnApplyCustomColormap -> CreateACustomColorMap.
      ENH: Use note directive in CreateACustomColorMap.
      ENH: Move ITkExampleMacros.cmake into the CMake/ directory.
      STYLE: Use more standard spacing in ITKExamplesMacros.cmake.
      DOC: Improve TryCatchException result rendering and synopsis.
      DOC: Update the Download page image for the bootstrap layout.
      ENH: Use presence of Code.py to create Python baseline comparison tests.
      DOC: Fix ComputeTimeBetweenPoints output rendering.
      ENH: Add Python version of ComputeTimeBetweenPoints.
      ENH: Demonstrate Report() in ComputeTimeBetweenPoints.
      ENH: Add Python superbuild.
      COMP: Fix type of Sphinx output variables.
      BUG: Ensure that the JavaScript files get copied to HTML output.
      COMP: Fix ConceptCheckingIsFloatingPoint index entry.
      BUG: Avoid system installation without superbuild Python.
      COMP: Find ITKExamplesMacros.cmake when build as a Remote Module.
      COMP: Support OpenCV 3 in ConvertAnITKGrayScaleImageToCVMat.
      COMP: Support double typed FixedParameters in ITK 4.9.0
      BUG: Do not run Python comparison tests without ITK_WRAP_PYTHON.
      BUG: Correct CreateACustomColorMapTestPython test name.
      ENH: Bump ITK ExternalProject to 4.9.0.


Michka Popoff (4):
      ENH: Add ImageRegistration1 example
      COMP: Fix images in 2D Translation Registration
      ENH: Add AddOffsetToIndex Python example
      ENH: Add missing licence headers and hide headers in doc



ITK Software Guide Changelog
---------------------------------------------

Matt McCormick (9):
      COMP: Address missing bracket and backslash escapes.
      BUG: Fix backslash specification in Windows PATH.
      DOC: Recommend the Release build configuration when wrapping.
      DOC: Document .GetTypes and Python type conversion.
      DOC: Add chapter on how to create a module.
      COMP: Do not set PYTHONCXXPARSER with find_program.
      ENH: Update ITK ExternalProject to v4.9rc01.
      DOC: Corrections to formatting of wrapping content.
      ENH: Bump ITK ExternalProject version to v4.9.0.


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