From matt.mccormick at kitware.com  Mon Feb  1 17:01:34 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 1 Feb 2016 17:01:34 -0500
Subject: [ITK-dev] [Paraview] Retire expected builds
In-Reply-To: <568BE9A6.4020303@ohio.edu>
References: <568BE9A6.4020303@ohio.edu>
Message-ID: <CALzTN-QxRSGPV_Lxgk=bxPdE_ESvL3bGCtniMvO65puZwm3itQ@mail.gmail.com>

Hi Kevin,

Sorry to hear this, but thank you for your many helpful years of submissions!

Best wishes as you begin your new job!

Matt

On Tue, Jan 5, 2016 at 11:04 AM, Kevin H. Hobbs <hobbsk at ohio.edu> wrote:
> I'm moving to a new job, and will no longer be able to maintain my
> nightly builds (even in their neglected state.)
>
> Please expect the expected builds from bubbles, murron, and k450e to
> dissapear.
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
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From matt.mccormick at kitware.com  Mon Feb  1 17:07:09 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 1 Feb 2016 17:07:09 -0500
Subject: [ITK-dev] Future of ITKApps
In-Reply-To: <CALzTN-QkarPWryaJgfcZ9vbVSy1Q-ASOCiy1RT+C7h099SmAJw@mail.gmail.com>
References: <CADZJ4hNG8R5P11O9goBXFOu37i437tv9UPYjwmb6S6-w6PrenQ@mail.gmail.com>
 <9DB0559B-F7FD-4FEB-8423-C7398659CBD4@uiowa.edu>
 <CALzTN-QkarPWryaJgfcZ9vbVSy1Q-ASOCiy1RT+C7h099SmAJw@mail.gmail.com>
Message-ID: <CALzTN-SVpZq97=xkMmWy8RhHFh41avP3RnndJ05y40xTTgySqw@mail.gmail.com>

Follow-up: the Docker image has come along well, but a little more
work is required.

We ran into a CMake issue that means we will not release ITKApps with 4.9.0 [1].

I will plan on releasing Docker versions of some of the ITKApps
executables in the future.


Matt


[1] http://review.source.kitware.com/#/c/20730/

On Fri, Nov 20, 2015 at 11:53 AM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> +1.
>
> I patched most of the apps for VTK 6, which is what we have in the
> Superbuild, so I would like to get that merged.
>
> FLTK makes these building these quite finicky and hard to maintain.
> There are many other better tools and demonstrations out there on how
> to develop an app based on ITK. Yet, these apps still provide value
> both in the functionality they provide and in the minimal,
> self-contained demonstration of how to use ITK + VTK.
>
> There was a discussion recently on GitHub on how to use one of the
> Apps on Windows [1]. Following that thread, I created a Docker image
> to run the apps [2]. This runs on OSX / Linux / Windows, and can be
> interacted with on all platforms, including tablets, phones. People
> will be able to use the apps in perpetuity without requiring further
> maintenance.
>
> I propose we create the create the Docker apps, then freeze
> development.  ITKApps released with ITK 4.9 would be the final
> release.
>
> Thanks,
> Matt
>
>
> [1] https://github.com/InsightSoftwareConsortium/ITKDevelopmentEnvironment/issues/1
>
> [2] https://github.com/thewtex/docker-opengl
>
> On Fri, Nov 20, 2015 at 10:49 AM, Johnson, Hans J
> <hans-johnson at uiowa.edu> wrote:
>> +10  ? That is not a typo.  Really +10.
>>
>> The slicer extensions framework is one of many improved solutions over fltk apps.
>> Heck? many of the demo apps could be easily re-written in SimpleITK with ipython notebook widgets.
>>
>> Hans
>>
>>
>> On 11/20/15, 9:29 AM, "Insight-developers on behalf of Bill Lorensen" <insight-developers-bounces at itk.org on behalf of bill.lorensen at gmail.com> wrote:
>>
>>>Folks,
>>>
>>>ITKApps contains applications written a long time ago. We as a group
>>>have been patching the apps, fixing compile errors as ITK and VTK
>>>api's change.
>>>
>>>Also, many of the apps use an old version of FLTK as a gui.
>>>
>>>I think the maintenance cost is too much for these old applications.
>>>
>>>We should consider freezing it at VTK5.10 and the last ITK version
>>>that works with it.
>>>
>>>As Matt has mentioned there are several modern apps like slicer and
>>>SNAP that can provide users with a better experience.
>>>
>>>Thoughts?
>>>
>>>Bill
>>>
>>>--
>>>Unpaid intern in BillsBasement at noware dot com
>>>_______________________________________________
>>>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
>>
>>
>> ________________________________
>> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
>> ________________________________
>> _______________________________________________
>> 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 matt.mccormick at kitware.com  Wed Feb  3 10:04:29 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 3 Feb 2016 10:04:29 -0500
Subject: [ITK-dev] =?utf-8?b?77u/W0FOTl0gSVRLIDQuOS4wIGhhcyBiZWVuIHJlbGVh?=
	=?utf-8?q?sed!?=
Message-ID: <CALzTN-Rr1VATnDe5sqsaE02aoJrrOA23xY2k5Z9x8h9EkpDm3Q@mail.gmail.com>

?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


D?enan Zuki? (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

D?enan Zuki? (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::*


D?enan Zuki? (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.

From hyunjae.kang at kitware.com  Thu Feb  4 14:36:20 2016
From: hyunjae.kang at kitware.com (Hyun Jae Kang)
Date: Thu, 4 Feb 2016 14:36:20 -0500
Subject: [ITK-dev] [SimpleITK] Data Bridge for SimpleITK
Message-ID: <CAAsPJLowri4GCUDUnVUu858BVFMNYcsEhiuTxRvQz-9Otb4VHw@mail.gmail.com>

Hi all,

To support data transparency between the functions of SimpleITK and NumPy,
SimpleITK provides functional integration with NumPy-based script and a
method of data-conversion between SimpleITK?s image data and the
N-dimensional array object of NumPy. But, there is a significant
performance bottleneck in the data-conversion which is based on the
operation of data copy. The performance bottleneck can be increased with
the size of handling image data and the number of data-conversion.

The performance bottle can be removed by allowing SimpleITK?s image and the
arrays of NumPy to share pointers to the same memory symmetrically with
copy-on-write semantics. That is, reduce data-copy operations in the data
conversion. This approach can be accomplished by developing and/or
improving existing data handling methods in ITK and SimpleITK to enable
copy-on-write sharing of data between SimpleITK?s image data and other
common data object of Python libraries used for scientific computing and
image processing.

For more detail information, please check the following website:
http://www.itk.org/Wiki/SimpleITK/Design_And_Proposals/SIP_002

Any your valuable comments are welcome.

Thanks,

Hyun Jae
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From david.mo.burns at gmail.com  Thu Feb  4 18:03:08 2016
From: david.mo.burns at gmail.com (David Burns)
Date: Thu, 4 Feb 2016 18:03:08 -0500
Subject: [ITK-dev] [SimpleITK] Data Bridge for SimpleITK
In-Reply-To: <CAAsPJLowri4GCUDUnVUu858BVFMNYcsEhiuTxRvQz-9Otb4VHw@mail.gmail.com>
References: <CAAsPJLowri4GCUDUnVUu858BVFMNYcsEhiuTxRvQz-9Otb4VHw@mail.gmail.com>
Message-ID: <56B3D8AC.9090606@gmail.com>

I just finished creating an interface between numpy/slicer and my ITK 
C++ project module using SWIG. I use pointers to avoid copying and it 
works well. Happy to share what I have.

- David

On 02/04/2016 02:36 PM, Hyun Jae Kang wrote:
> Hi all,
>
> To support data transparency between the functions of SimpleITK and 
> NumPy, SimpleITK provides functional integration with NumPy-based 
> script and a method of data-conversion between SimpleITK?s image data 
> and the N-dimensional array object of NumPy. But, there is a 
> significant performance bottleneck in the data-conversion which is 
> based on the operation of data copy. The performance bottleneck can be 
> increased with the size of handling image data and the number of 
> data-conversion.
>
> The performance bottle can be removed by allowing SimpleITK?s image 
> and the arrays of NumPy to share pointers to the same memory 
> symmetrically with copy-on-write semantics. That is, reduce data-copy 
> operations in the data conversion. This approach can be accomplished 
> by developing and/or improving existing data handling methods in ITK 
> and SimpleITK to enable copy-on-write sharing of data between 
> SimpleITK?s image data and other common data object of Python 
> libraries used for scientific computing and image processing.
>
> For more detail information, please check the following website:
> http://www.itk.org/Wiki/SimpleITK/Design_And_Proposals/SIP_002
>
> Any your valuable comments are welcome.
>
> Thanks,
>
> Hyun Jae
>
>
>
> _______________________________________________
> 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:
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From steve at sumost.ca  Fri Feb  5 08:49:37 2016
From: steve at sumost.ca (Steve M. Robbins)
Date: Fri, 05 Feb 2016 07:49:37 -0600
Subject: [ITK-dev] Nightly dashboard name changes
Message-ID: <1700402.5GriD2y9rb@riemann>

Hi,

Last weekend, I realized that my nightly dashboard submissions were misnamed 
-- they had "gcc4" in the name, dating from the time that Debian's default gcc 
was switching to 4.  In reality, the configuration uses the Debian default gcc 
which is now 5.x.

So, please change the expected builds from:
	Debian-sid-gcc4-64bit
	Debian-sid-gcc4-32bit

to:
	Debian-sid-default-64bit
	Debian-sid-default-32bit

I also took the opportunity to update the configuration -- in terms of modules 
and external libs -- to match the current Debian package configuration.   And 
now the 32-bit build is showing segfaults with FFTW.  I believe we have seen 
this for a while; e.g. Debian's ITK 4.9 packages disabled FFTW on 32-bit for 
this reason.

Thanks!
-Steve
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From sean at rogue-research.com  Fri Feb  5 15:12:10 2016
From: sean at rogue-research.com (Sean McBride)
Date: Fri, 5 Feb 2016 15:12:10 -0500
Subject: [ITK-dev] Possible to build ITK libs without version number in
	filename?
Message-ID: <20160205201210.521704264@mail.rogue-research.com>

Hi all,

Is it possible to build ITK such that the resulting library names do not have version numbers in them?  ie instead of "libITKCommon-4.9.a" could it be just "libITKCommon.a"?

VTK has a build option VTK_CUSTOM_LIBRARY_SUFFIX that you can set to an empty string to get this.  Does ITK have something analogous?

(The version numbers are annoying for me because my Xcode projects reference the ITK libs by filename, and every time the version is bumped it's a pain to switch back and forth.)

Thanks,

-- 
____________________________________________________________
Sean McBride, B. Eng                 sean at rogue-research.com
Rogue Research                        www.rogue-research.com 
Mac Software Developer              Montr?al, Qu?bec, Canada



From marcus.hanwell at kitware.com  Fri Feb  5 18:44:13 2016
From: marcus.hanwell at kitware.com (Marcus D. Hanwell)
Date: Fri, 5 Feb 2016 18:44:13 -0500
Subject: [ITK-dev] Possible to build ITK libs without version number in
	filename?
In-Reply-To: <20160205201210.521704264@mail.rogue-research.com>
References: <20160205201210.521704264@mail.rogue-research.com>
Message-ID: <CAMkPkZV9aTVNBDvnp-dVDnmBbiqagU493_pSeWVhAB7hF6KVig@mail.gmail.com>

On Fri, Feb 5, 2016 at 3:12 PM, Sean McBride <sean at rogue-research.com> wrote:
> Hi all,
>
> Is it possible to build ITK such that the resulting library names do not have version numbers in them?  ie instead of "libITKCommon-4.9.a" could it be just "libITKCommon.a"?
>
> VTK has a build option VTK_CUSTOM_LIBRARY_SUFFIX that you can set to an empty string to get this.  Does ITK have something analogous?
>
> (The version numbers are annoying for me because my Xcode projects reference the ITK libs by filename, and every time the version is bumped it's a pain to switch back and forth.)
>
This is something I would love to see, and I have been looking at this
for VTK/ParaView too. You can set variables as you point out there to
remove the version numbers, but there is not currently a simple option
to turn it off. When creating binary packages the version numbers add
to path lengths (can be an issue on Windows), and offer another point
of failure.

I can see why they are useful, but it would be good to make it simpler
to turn them off in projects offering versioned install
libraries/directories.

Best,

Marcus

From matt.mccormick at kitware.com  Fri Feb  5 23:17:03 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 5 Feb 2016 23:17:03 -0500
Subject: [ITK-dev] Nightly dashboard name changes
In-Reply-To: <1700402.5GriD2y9rb@riemann>
References: <1700402.5GriD2y9rb@riemann>
Message-ID: <CALzTN-TXeYxpM2dMsr-Ry=wjJy=9L2EF16tr4uXCfVgSk0XrHg@mail.gmail.com>

Hi Steve,

Thanks for the updates! The builds have been move out / in of the
Expected Nightly section on the dashboard.

Thanks,
Matt

On Fri, Feb 5, 2016 at 8:49 AM, Steve M. Robbins <steve at sumost.ca> wrote:
> Hi,
>
> Last weekend, I realized that my nightly dashboard submissions were misnamed
> -- they had "gcc4" in the name, dating from the time that Debian's default gcc
> was switching to 4.  In reality, the configuration uses the Debian default gcc
> which is now 5.x.
>
> So, please change the expected builds from:
>         Debian-sid-gcc4-64bit
>         Debian-sid-gcc4-32bit
>
> to:
>         Debian-sid-default-64bit
>         Debian-sid-default-32bit
>
> I also took the opportunity to update the configuration -- in terms of modules
> and external libs -- to match the current Debian package configuration.   And
> now the 32-bit build is showing segfaults with FFTW.  I believe we have seen
> this for a while; e.g. Debian's ITK 4.9 packages disabled FFTW on 32-bit for
> this reason.
>
> Thanks!
> -Steve
>
> _______________________________________________
> 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 dzenanz at gmail.com  Sat Feb  6 12:51:58 2016
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 6 Feb 2016 12:51:58 -0500
Subject: [ITK-dev] Possible to build ITK libs without version number in
	filename?
In-Reply-To: <20160205201210.521704264@mail.rogue-research.com>
References: <20160205201210.521704264@mail.rogue-research.com>
Message-ID: <CAPf2UMS0ARFX+T1ZiDwpFm_1CzQW7haoPqPqdgc+HHpRobsuPA@mail.gmail.com>

Hi Sean,

version numbers shouldn't be an issue if you configure your project using
CMake (which automatically takes care of all library paths). I forgot how
much of a pain in the ass it is to set those paths without CMake -
something one project reminded me of this week.

HTH,
D?enan

On Fri, Feb 5, 2016 at 3:12 PM, Sean McBride <sean at rogue-research.com>
wrote:

> Hi all,
>
> Is it possible to build ITK such that the resulting library names do not
> have version numbers in them?  ie instead of "libITKCommon-4.9.a" could it
> be just "libITKCommon.a"?
>
> VTK has a build option VTK_CUSTOM_LIBRARY_SUFFIX that you can set to an
> empty string to get this.  Does ITK have something analogous?
>
> (The version numbers are annoying for me because my Xcode projects
> reference the ITK libs by filename, and every time the version is bumped
> it's a pain to switch back and forth.)
>
> Thanks,
>
> --
> ____________________________________________________________
> Sean McBride, B. Eng                 sean at rogue-research.com
> Rogue Research                        www.rogue-research.com
> Mac Software Developer              Montr?al, Qu?bec, Canada
>
>
> _______________________________________________
> 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
>
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From sean at rogue-research.com  Sat Feb  6 13:55:57 2016
From: sean at rogue-research.com (Sean McBride)
Date: Sat, 6 Feb 2016 13:55:57 -0500
Subject: [ITK-dev] Possible to build ITK libs without version number in
 filename?
In-Reply-To: <CAPf2UMS0ARFX+T1ZiDwpFm_1CzQW7haoPqPqdgc+HHpRobsuPA@mail.gmail.com>
References: <20160205201210.521704264@mail.rogue-research.com>
 <CAPf2UMS0ARFX+T1ZiDwpFm_1CzQW7haoPqPqdgc+HHpRobsuPA@mail.gmail.com>
Message-ID: <20160206185557.1429073654@mail.rogue-research.com>

On Sat, 6 Feb 2016 12:51:58 -0500, D?enan Zuki? said:

>version numbers shouldn't be an issue if you configure your project using
>CMake (which automatically takes care of all library paths).

I know, but as I said in my post, I don't use CMake.  I use CMake to build ITK of course, but my main app, which links to ITK, uses Xcode, and that can't/won't change.  ITK is a library, it's common to link to libraries in a variety of ways.  Do you know how your libc was built?  Do you care?

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  Sat Feb  6 16:03:21 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sat, 6 Feb 2016 16:03:21 -0500
Subject: [ITK-dev] Possible to build ITK libs without version number in
	filename?
In-Reply-To: <20160206185557.1429073654@mail.rogue-research.com>
References: <20160205201210.521704264@mail.rogue-research.com>
 <CAPf2UMS0ARFX+T1ZiDwpFm_1CzQW7haoPqPqdgc+HHpRobsuPA@mail.gmail.com>
 <20160206185557.1429073654@mail.rogue-research.com>
Message-ID: <CALzTN-SNq+6ddCFS5LeF6CKXG0H50RJhoE4Pbvb1ZJphxb8HQQ@mail.gmail.com>

Hi,

Please review this patch, which adds an ITK_CUSTOM_LIBRARY_SUFFIX
variable similar to VTK.

HTH,
Matt

On Sat, Feb 6, 2016 at 1:55 PM, Sean McBride <sean at rogue-research.com> wrote:
> On Sat, 6 Feb 2016 12:51:58 -0500, D?enan Zuki? said:
>
>>version numbers shouldn't be an issue if you configure your project using
>>CMake (which automatically takes care of all library paths).
>
> I know, but as I said in my post, I don't use CMake.  I use CMake to build ITK of course, but my main app, which links to ITK, uses Xcode, and that can't/won't change.  ITK is a library, it's common to link to libraries in a variety of ways.  Do you know how your libc was built?  Do you care?
>
> Cheers,
>
> --
> ____________________________________________________________
> Sean McBride, B. Eng                 sean at rogue-research.com
> Rogue Research                        www.rogue-research.com
> Mac Software Developer              Montr?al, Qu?bec, Canada
> _______________________________________________
> 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 tj.jackson1226 at gmail.com  Thu Feb 18 13:06:55 2016
From: tj.jackson1226 at gmail.com (Tim Jackson)
Date: Thu, 18 Feb 2016 13:06:55 -0500
Subject: [ITK-dev] method of concatenating 2D images into a 5D image
Message-ID: <CAE-Q1HemOfRiQu7Cxs-obhWWUrJ-AdTbzQmef6XZAS2u1Zqfuw@mail.gmail.com>

Hi everyone,

I've recently started working with a very large .nd2 format time lapse
image, that was taken on a Nikon confocal microscope.  These image
sequences are 5D (x,y,z,time,channel).  Because these images are so large,
trying to work on the entire image at once will cause a memory allocation
error.  Therefore I set the reader up in ITK, use a series of
ExtractImageFilters to break down the giant file into 2D images (I iterate
over the time sequence in a for loop, obtaining a 2D x, y image for each
time frame for each channel).

This all works fine, and I'm able to complete the necessary image
filtering/corrections on these 2D images within the for loop.  My problem
arises when I'm trying to write the output file.  Ideally, I would like to
be able to compose all of these images back into one large 5D .nd2 file,
but if I do this outright, I'm guessing the writer will have a memory
allocation error.  Is there a way to write the file one frame at a time,
adding the next frame onto the file as the filtering occurs?  Or is there
some other way to handle the writing of very large image files to skirt
around memory allocation problems?  I know I could write each frame as an
individual file in an image sequence, but then I would have to use a
third-party program like ImageJ to make them into a stack, merge channels,
etc, which is not a simple task with the volume of image files I will be
analyzing.

Thanks for your help!
Tim
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From matt.mccormick at kitware.com  Thu Feb 18 13:45:37 2016
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 18 Feb 2016 13:45:37 -0500
Subject: [ITK-dev] method of concatenating 2D images into a 5D image
In-Reply-To: <CAE-Q1HemOfRiQu7Cxs-obhWWUrJ-AdTbzQmef6XZAS2u1Zqfuw@mail.gmail.com>
References: <CAE-Q1HemOfRiQu7Cxs-obhWWUrJ-AdTbzQmef6XZAS2u1Zqfuw@mail.gmail.com>
Message-ID: <CALzTN-QjmowB6+VYWwfyt6U8+POQaCHJr4E0s4a4Po0AMnXQiA@mail.gmail.com>

Hi Tim,

It is possible to stream-write an image if the output format supports
streamed writing.  MetaImage (.mha) has good support for this. See
this example on how to stream the writer:

  http://www.itk.org/Doxygen/html/Examples_2IO_2VisibleHumanStreamReadWrite_8cxx-example.html#_a7

To generate the image, use an itk::PasteImageFilter.  To keep track of
the higher order indices, itk::RegionOfInterestImageFilter is
suggested instead of itk::ExtractImageFilter.

HTH,
Matt



On Thu, Feb 18, 2016 at 1:06 PM, Tim Jackson <tj.jackson1226 at gmail.com> wrote:
> Hi everyone,
>
> I've recently started working with a very large .nd2 format time lapse
> image, that was taken on a Nikon confocal microscope.  These image sequences
> are 5D (x,y,z,time,channel).  Because these images are so large, trying to
> work on the entire image at once will cause a memory allocation error.
> Therefore I set the reader up in ITK, use a series of ExtractImageFilters to
> break down the giant file into 2D images (I iterate over the time sequence
> in a for loop, obtaining a 2D x, y image for each time frame for each
> channel).
>
> This all works fine, and I'm able to complete the necessary image
> filtering/corrections on these 2D images within the for loop.  My problem
> arises when I'm trying to write the output file.  Ideally, I would like to
> be able to compose all of these images back into one large 5D .nd2 file, but
> if I do this outright, I'm guessing the writer will have a memory allocation
> error.  Is there a way to write the file one frame at a time, adding the
> next frame onto the file as the filtering occurs?  Or is there some other
> way to handle the writing of very large image files to skirt around memory
> allocation problems?  I know I could write each frame as an individual file
> in an image sequence, but then I would have to use a third-party program
> like ImageJ to make them into a stack, merge channels, etc, which is not a
> simple task with the volume of image files I will be analyzing.
>
> Thanks for your help!
> Tim
>
> _______________________________________________
> 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 simon.warfield at childrens.harvard.edu  Fri Feb 19 12:14:30 2016
From: simon.warfield at childrens.harvard.edu (Simon Warfield)
Date: Fri, 19 Feb 2016 12:14:30 -0500
Subject: [ITK-dev] include file header double underscore
In-Reply-To: <mailman.21.1455901211.30506.insight-developers@itk.org>
References: <mailman.21.1455901211.30506.insight-developers@itk.org>
Message-ID: <56C74D76.2090505@childrens.harvard.edu>


Did itk include file ifndef lines lose their double underscore at some 
point?
Was there a reason for that ?  It has an impact on backwards compatibility.

http://www.itk.org/Doxygen47/html/itkAbsImageFilter_8h_source.html
line 18 :
#ifndef __itkAbsImageFilter_h

http://www.itk.org/Doxygen48/html/itkAbsImageFilter_8h_source.html
line 18 :
#ifndef itkAbsImageFilter_h


--Simon


From bill.lorensen at gmail.com  Fri Feb 19 13:07:18 2016
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 19 Feb 2016 13:07:18 -0500
Subject: [ITK-dev] include file header double underscore
In-Reply-To: <56C74D76.2090505@childrens.harvard.edu>
References: <mailman.21.1455901211.30506.insight-developers@itk.org>
 <56C74D76.2090505@childrens.harvard.edu>
Message-ID: <CADZJ4hNRtNOB8_sktfadZzY17zg8x=YbEJTz0nO4tvk_DSHMCA@mail.gmail.com>

Simon,

Apparently the use of _ and __ is reserved and newer c++'s warn about
it. These changes were made back in December 2014...
http://itk.org/gitweb?p=ITK.git;a=commit;h=4d8c82c5bfdf340a4201e91d7d35694852328199

http://stackoverflow.com/questions/228783/what-are-the-rules-about-using-an-underscore-in-a-c-identifier

What backward compatibility issues do you see?

Bill

On Fri, Feb 19, 2016 at 12:14 PM, Simon Warfield
<simon.warfield at childrens.harvard.edu> wrote:
>
> Did itk include file ifndef lines lose their double underscore at some
> point?
> Was there a reason for that ?  It has an impact on backwards compatibility.
>
> http://www.itk.org/Doxygen47/html/itkAbsImageFilter_8h_source.html
> line 18 :
> #ifndef __itkAbsImageFilter_h
>
> http://www.itk.org/Doxygen48/html/itkAbsImageFilter_8h_source.html
> line 18 :
> #ifndef itkAbsImageFilter_h
>
>
> --Simon
>
> _______________________________________________
> 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



-- 
Unpaid intern in BillsBasement at noware dot com

From andinet.enqu at kitware.com  Thu Feb 25 07:50:19 2016
From: andinet.enqu at kitware.com (Andinet Enquobahrie)
Date: Thu, 25 Feb 2016 07:50:19 -0500
Subject: [ITK-dev] ANN: Medical Computing Group at Kitware is hiring R&D
 engineers and technical leads in image analysis and visualization
Message-ID: <CANrU59_ENjQMu-0KR4tKvjif4VsxCp64Q71-oEVvb7sZ5tRgLw@mail.gmail.com>

Apologies for duplicate postings.

===================

Hi folks,

We are looking to hire talented individuals for image guided
intervention and image analysis and visualization application
development in our Medical Computing group. We have four job
opportunities

Technical Lead in Biomedical Image Analysis and Visualization
http://tinyurl.com/jx3cgnc

Image-Guided Intervention Applications Research and Development Engineer
http://tinyurl.com/zxlpyyj

Biomechanical Modeling and Surgical Simulation Research and Development Engineer
http://tinyurl.com/jtsnf2y

Research and Development Involving Machine Learning and Medical Image Analysis
http://tinyurl.com/hy58kq8

For other job openings at Kitware, please check
http://jobs.kitware.com/opportunities.html





-- 
Andinet Enquobahrie, Ph.D., MBA
Assistant Director of Medical Computing
Kitware, Inc.

http://www.kitware.com
(919) 969-6990 x311