# Patches for ITK 4.13.2

**URL:** https://discourse.itk.org/t/patches-for-itk-4-13-2/1582
**Category:** Community
**Created:** [February 7, 2019, 11:19pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582 "2019-02-07T23:19:26Z")
**Posts on this page:** 10
**Page:** 1

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### Author: ![matt.mccormick](https://discourse.itk.org/user_avatar/discourse.itk.org/matt.mccormick/32/7_2.png) [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [February 7, 2019, 11:19pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582/1 "2019-02-07T23:19:26Z")

</div>

Hi folks,

The next patch (bugfix) release, ITK 4.13.2, is [planned for February 19th](https://github.com/InsightSoftwareConsortium/ITK/milestone/3).

Patches currently staged on the Git `release-4.13` branch are:

```auto
Bai Shi (1):
      COMP: To fix compilation error of "cannot dynamic_cast 'x'

Bradley Lowekamp (8):
      BUG: Support ITK transform files with corrected group names
      BUG: Update SCIOFIO to ITKv4.13 branch
      BUG: Handle boundary case with max metric
      BUG: Remove static member function variable
      BUG: Synchronize BSpline MeshDomain parameters from fixed params
      COMP: Address CMake policy warnings in ThirdParty libraries
      ENH: Update AzurePipelines configuration from master
      ENH: Explicitly set the XCode version used in Azure

Dženan Zukić (2):
      STYLE: fixing 'No new line at the end of file'
      ENH: ITKv5_CONST macro for VerifyPreconditions() and VerifyInputInformation()

Isaiah Norton (2):
      BUG: prevent segfault when transform reader fails to load .mat
      BUG: don't quote argument to URL_HASH for FFTW

Matthew McCormick (4):
      BUG: Use manylinux to build CastXML linux executable
      COMP: Address empty _FILE_OFFSET_BITS in tif_config.h with MinGW64
      BUG: Remove duplicate ITK version number
      ENH: Add Azure Pipelines configuration

Niels Dekker (2):
      COMP: Fixed GDCM OpenJPEG name mangling
      PERF: Remove SystemInformation data from ResourceProbe, fix issue #350

```

Are there other patches that are missing? Patches should be critical bugfixes, improved support for compilers, and documentation fixes.

---

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### Author: ![Niels\_Dekker](https://discourse.itk.org/letter_avatar_proxy/v4/letter/n/9d8465/32.png) [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)
#### Post date: [February 8, 2019, 10:25am UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582/2 "2019-02-08T10:25:44Z")

</div>

Thanks, @matt.mccormick! I’m especially happy about [“\_PERF: Remove SystemInformation data from ResourceProbe”](https://github.com/InsightSoftwareConsortium/ITK/commit/b13f6a86cb250328f0c185f509649b370bbe49f4), of course, as it will yield a _huge_ performance improvement for [elastix](https://github.com/SuperElastix/elastix).

You might still consider the following commit, as it involves just two lines of code, and yields quite a large performance improvement for `N4BiasFieldCorrectionImageFilter`:

> <https://github.com/InsightSoftwareConsortium/ITK/commit/a77af2a338a01c04379571be0b77c0a322b17d4f>

The original pull request:

> <https://github.com/InsightSoftwareConsortium/ITK/pull/172>

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### Author: ![blowekamp](https://discourse.itk.org/user_avatar/discourse.itk.org/blowekamp/32/79_2.png) [@blowekamp](https://discourse.itk.org/u/blowekamp)
#### Post date: [February 8, 2019, 2:53pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582/3 "2019-02-08T14:53:22Z")

</div>

There are a couple outstayed compilation issue on the CI for the release-4.13 branch for MacOSX:  
[https://open.cdash.org/buildSummary.php?buildid=5742718](https://open.cdash.org/buildSummary.php?buildid=5742718)

1. There is a CMake Warning:

```auto
CMake Warning (dev):
  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake
  --help-policy CMP0042" for policy details. Use the cmake_policy command to
  set the policy and suppress this warning.

  MACOSX_RPATH is not specified for the following targets:

   gdcmcharls
   gdcmjpeg12
   gdcmjpeg16
   gdcmjpeg8
   gdcmsocketxx
   gdcmuuid

This warning is for project developers. Use -Wno-dev to suppress it.
-- Generating done

```

I recently had some linking issues with one of these libraries with SimpleITK against 4.13.1 on OsX, so there may be a really issue here.

Additionally there are a bunch of compilation warning of the following form:

```auto
Modules/Core/Common/test/itkNumericTraitsTest.cxx:129:108: warning: instantiation of variable 'itk::NumericTraits<itk::CovariantVector<char, 1> >::Zero' required here, but no definition is available [-Wundefined-var-template]

```

This may be related to C++11 I believe the Xcode compiler is defaulting to C++11 in Xcode 9.

Beyond OSX there is the following wrapping CMake warnings:

```auto
CMake Warning (dev) at Wrapping/CMakeLists.txt:30 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details. Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at Modules/Remote/BridgeNumPy/CMakeLists.txt:2 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details. Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
This warning is for project developers. Use -Wno-dev to suppress it.

```

And there is the Windows Python build:  
[https://open.cdash.org/buildSummary.php?buildid=5742715](https://open.cdash.org/buildSummary.php?buildid=5742715)

---

<div class="post-metadata">

### Author: ![blowekamp](https://discourse.itk.org/user_avatar/discourse.itk.org/blowekamp/32/79_2.png) [@blowekamp](https://discourse.itk.org/u/blowekamp)
#### Post date: [February 8, 2019, 2:54pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582/4 "2019-02-08T14:54:28Z")

</div>

I am going to investigate my share libraries on OSX. If anyone has additional information on these warning and how they have been resolved in master please chime in.

---

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### Author: ![seanm](https://discourse.itk.org/letter_avatar_proxy/v4/letter/s/a88e4f/32.png) [@seanm](https://discourse.itk.org/u/seanm)
#### Post date: [February 8, 2019, 5:57pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582/5 "2019-02-08T17:57:50Z")

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It’s not fixed in master yet, but it would be good to have this fixed in 4.x branch too:

[https://github.com/InsightSoftwareConsortium/ITK/issues/424](https://github.com/InsightSoftwareConsortium/ITK/issues/424)

Sean

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### Author: ![Niels\_Dekker](https://discourse.itk.org/letter_avatar_proxy/v4/letter/n/9d8465/32.png) [@Niels\_Dekker](https://discourse.itk.org/u/Niels_Dekker)
#### Post date: [February 11, 2019, 1:47pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582/6 "2019-02-11T13:47:39Z")

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> [@Niels\_Dekker](#):
>
> You might still consider the following commit, as it involves just two lines of code, and yields quite a large performance improvement for `N4BiasFieldCorrectionImageFilter` :
> 
> [github.com/InsightSoftwareConsortium/ITK](https://github.com/InsightSoftwareConsortium/ITK/commit/a77af2a338a01c04379571be0b77c0a322b17d4f)
> 
> [![N-Dekker](https://discourse.itk.org/uploads/default/original/1X/95ae06920f4703c5699c9ff41afe79def2d95ddc.jpg) ](https://github.com/N-Dekker)
> 
> #### [PERF: unsharpenedImage iterator in N4Bias…Filter is now “WithIndex”](https://github.com/InsightSoftwareConsortium/ITK/commit/a77af2a338a01c04379571be0b77c0a322b17d4f)
> 
> Declared the unsharpenedImage iterator within N4BiasFieldCorrectionImageFilter::SharpenImage as ImageRegionConstIteratorWithIndex, instead of ImageRegionConstIterator. Observed a significant performance improvement: 10% to 30% reduction of runtime…
> 
> by [N-Dekker](https://github.com/N-Dekker) on [01:06PM - 13 Nov 18 UTC](https://github.com/InsightSoftwareConsortium/ITK/commit/a77af2a338a01c04379571be0b77c0a322b17d4f)

Does anyone think it would be nice to have this in ITK 4.13? I leave it up to you.

---

<div class="post-metadata">

### Author: ![matt.mccormick](https://discourse.itk.org/user_avatar/discourse.itk.org/matt.mccormick/32/7_2.png) [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [February 11, 2019, 4:09pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582/7 "2019-02-11T16:09:38Z")

</div>

> I’m especially happy about [“\_PERF: Remove SystemInformation data from ResourceProbe”](https://github.com/InsightSoftwareConsortium/ITK/commit/b13f6a86cb250328f0c185f509649b370bbe49f4),

Yes, that fix was quite important! Thanks again!

> You might still consider the following commit, as it involves just two lines of code, and yields quite a large performance improvement for `N4BiasFieldCorrectionImageFilter` :

Our bug-fix releases are limited in scope to bug fixes, and in general we do not add performance related patches to bug-fix releases. This is standard practice for [semantic versioning](https://semver.org/), matching expectations for the release content and avoiding bugs that may come along with the performance improvement. The previously mentioned patch is an exception since it passes into the bug-fix category.

The referenced performance patches (along with many other awesome performance improvements) are available in [ITK 5.0 RC 1](https://discourse.itk.org/t/itk-5-0-release-candidate-1-meshes/1576) – everyone is encourage to try it, if they have not already!

---

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### Author: ![blowekamp](https://discourse.itk.org/user_avatar/discourse.itk.org/blowekamp/32/79_2.png) [@blowekamp](https://discourse.itk.org/u/blowekamp)
#### Post date: [February 11, 2019, 4:21pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582/8 "2019-02-11T16:21:08Z")

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I have one more patch to address the CMP0048 warnings in ITK wrapping and external modules:

> <https://github.com/InsightSoftwareConsortium/ITK/pull/495>

---

<div class="post-metadata">

### Author: ![matt.mccormick](https://discourse.itk.org/user_avatar/discourse.itk.org/matt.mccormick/32/7_2.png) [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [February 11, 2019, 4:23pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582/9 "2019-02-11T16:23:52Z")

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> [@blowekamp](#):
>
> 1. There is a CMake Warning:
> 
> ```auto
> CMake Warning (dev):
> Policy CMP0042 is not set: MACOSX_RPATH is enabled by default
> 
> ```

I created [this issue](https://github.com/InsightSoftwareConsortium/ITK/issues/493) to track this.

> [@blowekamp](#):
>
> Additionally there are a bunch of compilation warning of the following form:
> 
> ```auto
> Modules/Core/Common/test/itkNumericTraitsTest.cxx:129:108: warning: instantiation of variable 'itk::NumericT
> 
> ```

Given that VXL has moved on with a major refactoring and C++11, this is a warning for a maintenance-mode branch, I do not think these are worth fixing.

> [@blowekamp](#):
>
> Beyond OSX there is the following wrapping CMake warnings:
> 
> ```auto
> CMake Warning (dev) at Wrapping/CMakeLists.txt:30 (project):
> Policy CMP0048 is not set: project() command manages VERSION variables.
> Run "cmake --help-policy CMP0048" for policy details. Use the cmake_policy
> command to set the policy and suppress this warning.
> 
> ```

I created [this issue](https://github.com/InsightSoftwareConsortium/ITK/issues/494) to track this.

> [@blowekamp](#):
>
> And there is the Windows Python build:  
> [https://open.cdash.org/buildSummary.php?buildid=5742715](https://open.cdash.org/buildSummary.php?buildid=5742715)

I created [this issue](https://github.com/InsightSoftwareConsortium/ITK/issues/496) to track this.

---

<div class="post-metadata">

### Author: ![matt.mccormick](https://discourse.itk.org/user_avatar/discourse.itk.org/matt.mccormick/32/7_2.png) [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [February 11, 2019, 4:26pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-2/1582/10 "2019-02-11T16:26:17Z")

</div>

> [@seanm](#):
>
> It’s not fixed in master yet, but it would be good to have this fixed in 4.x branch too:
> 
> [https://github.com/InsightSoftwareConsortium/ITK/issues/424](https://github.com/InsightSoftwareConsortium/ITK/issues/424)

Yes, if a patch is ready for this issue in time for 4.13.2, we will certainly include it.
