From matt.mccormick at kitware.com  Mon Sep  1 15:09:38 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 1 Sep 2014 15:09:38 -0400
Subject: [ITK-dev] [ITK-users] How to fusion the MR volume to the CT
	volume
In-Reply-To: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com>
References: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com>
Message-ID: <CALzTN-QUVzNgj7rMKbQ7-HNmHmPiePVBfah5ZX=O7heA4H1yew@mail.gmail.com>

Hi Yeutian,

Try a registration algorithm using a mutual information based metric.
See also the Slicer Registration Case Library [1], which uses ITK
under the hood, for examples.

HTH,
Matt

[1] http://www.na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory

On Mon, Sep 1, 2014 at 2:32 AM, Yuetian Liu <yuetian926 at 163.com> wrote:
>
> Hi itkusers,
>
> Recently I want to fuse the MR volume to the CT volume, but I search the itk
> mailist.
> I haven;t known how to realise it. And there isn't example in the
> InsightSoftwareGuide-4.5.0.pdf
> and InsightSphinxExamplesPDF-4.5.0.pdf.
> So I want to ask how to fuse the MR volume to the CT volume by itk.
>
> Thank you for helping me!
>
> Best
> Yuetian
>
>
>
>
>
> _____________________________________
> 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://www.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-users
>

From blowekamp at mail.nih.gov  Tue Sep  2 09:18:47 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 2 Sep 2014 09:18:47 -0400
Subject: [ITK-dev] issues.itk.org maintenance
In-Reply-To: <D024E0AE.B1FF%hans-johnson@uiowa.edu>
References: <D024E0AE.B1FF%hans-johnson@uiowa.edu>
Message-ID: <A50FE510-1E93-4A5A-ADDD-CD0984C1D8DD@mail.nih.gov>

Thanks again for running the server!

Brad
On Aug 28, 2014, at 2:37 PM, Johnson, Hans J <hans-johnson at uiowa.edu> wrote:

> The ITK bug tracker will be down for approximately 30 minutes at 4:30CST today for routine maintenance.
> 
> Hans
> 
> 
> 
> 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.

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From norman-k-williams at uiowa.edu  Wed Sep  3 12:10:02 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Wed, 3 Sep 2014 16:10:02 +0000
Subject: [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent
	topics OK now?
Message-ID: <D02CA788.ACB3%norman-k-williams@uiowa.edu>

I?ve been trying to help out with changes related to the HDF5ImageIO, and there?s a string of 4 different patches:

http://review.source.kitware.com/#/c/16579<http://review.source.kitware.com/#/c/16579/>
http://review.source.kitware.com/#/c/16578
http://review.source.kitware.com/#/c/16577
http://review.source.kitware.com/#/c/16576

Incredibly, 16578 and 16579 seem to be circularly dependent.

I?ve just pushed a new version of 16576 which addresses the comments Matt made.  Should those others be abandoned and one free-standing patch be made of the actually substantive changes?



________________________________
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.
________________________________
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From matt.mccormick at kitware.com  Wed Sep  3 12:26:23 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 3 Sep 2014 12:26:23 -0400
Subject: [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent
 topics OK now?
In-Reply-To: <D02CA788.ACB3%norman-k-williams@uiowa.edu>
References: <D02CA788.ACB3%norman-k-williams@uiowa.edu>
Message-ID: <CALzTN-RjwBj6ASZ6npyUrb+hGV7EnOfnxmxM_OpT+Hq5==F-aw@mail.gmail.com>

Hi Kent,

Thanks for taking a look at these.

We had a good discussion about them this morning at the Google Hangout
[1].  New versions are likely coming soon.

Thanks,
Matt


[1] https://plus.google.com/events/c04l669q5omm7oo5p2ov1dp7kb4?authkey=CIH2womZ7I_9Fw

On Wed, Sep 3, 2014 at 12:10 PM, Williams, Norman K
<norman-k-williams at uiowa.edu> wrote:
> I?ve been trying to help out with changes related to the HDF5ImageIO, and
> there?s a string of 4 different patches:
>
> http://review.source.kitware.com/#/c/16579
> http://review.source.kitware.com/#/c/16578
> http://review.source.kitware.com/#/c/16577
> http://review.source.kitware.com/#/c/16576
>
> Incredibly, 16578 and 16579 seem to be circularly dependent.
>
> I?ve just pushed a new version of 16576 which addresses the comments Matt
> made.  Should those others be abandoned and one free-standing patch be made
> of the actually substantive changes?
>
>
>
> ________________________________
> 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 norman-k-williams at uiowa.edu  Wed Sep  3 12:38:26 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Wed, 3 Sep 2014 16:38:26 +0000
Subject: [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent
 topics OK now?
In-Reply-To: <CALzTN-RjwBj6ASZ6npyUrb+hGV7EnOfnxmxM_OpT+Hq5==F-aw@mail.gmail.com>
References: <D02CA788.ACB3%norman-k-williams@uiowa.edu>
 <CALzTN-RjwBj6ASZ6npyUrb+hGV7EnOfnxmxM_OpT+Hq5==F-aw@mail.gmail.com>
Message-ID: <D02CAE1F.ACB9%norman-k-williams@uiowa.edu>

Watch out for my new version of 16576 ;-)

On 9/3/14, 11:26 AM, "Matt McCormick" <matt.mccormick at kitware.com> wrote:

>Hi Kent,
>
>Thanks for taking a look at these.
>
>We had a good discussion about them this morning at the Google Hangout
>[1].  New versions are likely coming soon.
>
>Thanks,
>Matt
>
>
>[1]
>https://plus.google.com/events/c04l669q5omm7oo5p2ov1dp7kb4?authkey=CIH2wom
>Z7I_9Fw
>
>On Wed, Sep 3, 2014 at 12:10 PM, Williams, Norman K
><norman-k-williams at uiowa.edu> wrote:
>> I?ve been trying to help out with changes related to the HDF5ImageIO,
>>and
>> there?s a string of 4 different patches:
>>
>> http://review.source.kitware.com/#/c/16579
>> http://review.source.kitware.com/#/c/16578
>> http://review.source.kitware.com/#/c/16577
>> http://review.source.kitware.com/#/c/16576
>>
>> Incredibly, 16578 and 16579 seem to be circularly dependent.
>>
>> I?ve just pushed a new version of 16576 which addresses the comments
>>Matt
>> made.  Should those others be abandoned and one free-standing patch be
>>made
>> of the actually substantive changes?
>>
>>
>>
>> ________________________________
>> 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
>>



________________________________
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.
________________________________

From dlrdave at aol.com  Wed Sep  3 12:39:49 2014
From: dlrdave at aol.com (David Cole)
Date: Wed, 3 Sep 2014 12:39:49 -0400
Subject: [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent
 topics OK now?
Message-ID: <8D195ACD03190B6-15CC-C133@webmail-m269.sysops.aol.com>

> http://review.source.kitware.com/#/c/16579
> http://review.source.kitware.com/#/c/16578
> Incredibly, 16578 and 16579 seem to be circularly dependent.


Why do you say they're circularly dependent? It looks to me like 79 is
based on 78... I'm not seeing the circularity.

D



From blowekamp at mail.nih.gov  Wed Sep  3 14:38:29 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 3 Sep 2014 14:38:29 -0400
Subject: [ITK-dev] CMake test macro for standard streaming behavior
Message-ID: <93785A4D-3086-433F-96C3-5E4214BE9EF7@mail.nih.gov>

Hello,

In ITK 3.20 there was a macro to test  the expected behavior of ImageIOs when streaming. It was defined here:
https://github.com/InsightSoftwareConsortium/ITK/blob/v3.20.1/Testing/Code/IO/CMakeLists.txt#L406-L470

The intention of this code block was to reuse this sequence for tests for different file formats. ( I thought it was working for VTK and MRC file formats too, but I think that didn't happen when integrating from the IJ ). 

I wish to create a new and improved version of this macro ( or function ) to help test the HDF5 streaming contributions to ensure it's behavior matches that of the other ImageIOs.  The issues are:

1) Where can "common" cmake testing code go so that other modules can use it?
2) Dependencies with modules and test drivers. It appears that I can call the ImageIOBaseTestDriver from other modules i.e. mha and HDF5. Any problem with this?
3) ImageIO registration - Currently I can just add additional dependencies to the TestingKernel to ensure that the HDF5 imageIO is registered everywhere. Is there any other better alternative?

Thanks,
Brad

p.s.
Alternatively, the test could be refactored to include the different states internally, as opposed to defined in cmake code. But I don't think it should be hard to get the cmake stuff working...

From matt.mccormick at kitware.com  Wed Sep  3 15:01:16 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 3 Sep 2014 15:01:16 -0400
Subject: [ITK-dev] CMake test macro for standard streaming behavior
In-Reply-To: <93785A4D-3086-433F-96C3-5E4214BE9EF7@mail.nih.gov>
References: <93785A4D-3086-433F-96C3-5E4214BE9EF7@mail.nih.gov>
Message-ID: <CALzTN-TtwXhM7MY8i88jhFw04uhT_ytLsJumQncr_+LJ3oN9Fg@mail.gmail.com>

Hi Brad,

> 1) Where can "common" cmake testing code go so that other modules can use it?

This can be added in the CMakeLists.txt for module that other modules
will depend on.  See "include(CreateTestDriver.cmake)" in
Modules/Core/TestKernal/CMakeLists.txt.

> 2) Dependencies with modules and test drivers. It appears that I can call the ImageIOBaseTestDriver from other modules i.e. mha and HDF5. Any problem with this?

I don't think so, as long as all the other modules TEST_DEPEND ITKImageIOBase.

> 3) ImageIO registration - Currently I can just add additional dependencies to the TestingKernel to ensure that the HDF5 imageIO is registered everywhere. Is there any other better alternative?

 Hopefully this can be avoided -- cross-compiling HDF5 is a pain.

Thanks,
Matt

From indianzeppelin at gmail.com  Thu Sep  4 11:29:42 2014
From: indianzeppelin at gmail.com (Girish Mallya Udupi)
Date: Thu, 4 Sep 2014 16:29:42 +0100
Subject: [ITK-dev] New to the Gerrit review process
Message-ID: <CAA+VR6hxO4x2ZBd6cKiHHVHfOr21uTzJ9POAid-PdjYmYuvoGQ@mail.gmail.com>

Hello,

I have a couple of questions about the Gerrit review process -

1) Is the creator of a topic automatically added as a reviewer on
subsequent patches in the topic?

2) As a reviewer, if I am unable to understand the changes made to the code
(simply because I am not an advanced programmer), should I leave the patch
unscored?
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From matt.mccormick at kitware.com  Thu Sep  4 11:34:47 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 4 Sep 2014 11:34:47 -0400
Subject: [ITK-dev] New to the Gerrit review process
In-Reply-To: <CAA+VR6hxO4x2ZBd6cKiHHVHfOr21uTzJ9POAid-PdjYmYuvoGQ@mail.gmail.com>
References: <CAA+VR6hxO4x2ZBd6cKiHHVHfOr21uTzJ9POAid-PdjYmYuvoGQ@mail.gmail.com>
Message-ID: <CALzTN-Rrc_1G9yREFbdZE0Fqaw2BeF1Nafo_zfjcwQVpt5cyDw@mail.gmail.com>

Hi Girish,

Thanks for participating on Gerrit.

> 1) Is the creator of a topic automatically added as a reviewer on subsequent
> patches in the topic?

No, they have to be manually added at the moment.

> 2) As a reviewer, if I am unable to understand the changes made to the code
> (simply because I am not an advanced programmer), should I leave the patch
> unscored?

An feedback is welcome.  If you do not feel very knowledgeable about a
patch, give it a "+1" as opposed to a "+2".  Some more information can
be found here [1].

Thanks,
Matt

[1] https://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/PerformAGerritReview/index.html

From blowekamp at mail.nih.gov  Thu Sep  4 11:43:14 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 4 Sep 2014 11:43:14 -0400
Subject: [ITK-dev] New to the Gerrit review process
In-Reply-To: <CAA+VR6hxO4x2ZBd6cKiHHVHfOr21uTzJ9POAid-PdjYmYuvoGQ@mail.gmail.com>
References: <CAA+VR6hxO4x2ZBd6cKiHHVHfOr21uTzJ9POAid-PdjYmYuvoGQ@mail.gmail.com>
Message-ID: <A4452E5E-7F22-415C-8410-D92A1D98A3EA@mail.nih.gov>

Hello Girish,

I assume you are talking about this patch:
http://review.source.kitware.com/#/c/16868/

Thanks again for contributing the patch which demonstrated the bug you encountered.

For this particular case I would encourage you to download, checkout, and compile the patch and verify that is resolves the issue you initially encountered. Then report back if it fixes the problem.

Brad

On Sep 4, 2014, at 11:29 AM, Girish Mallya Udupi <indianzeppelin at gmail.com> wrote:

> Hello,
> 
> I have a couple of questions about the Gerrit review process - 
> 
> 1) Is the creator of a topic automatically added as a reviewer on subsequent patches in the topic? 
> 
> 2) As a reviewer, if I am unable to understand the changes made to the code (simply because I am not an advanced programmer), should I leave the patch unscored?
> 
> _______________________________________________
> 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  Thu Sep  4 11:50:13 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 4 Sep 2014 11:50:13 -0400
Subject: [ITK-dev] Opportunity to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-QZdjwJeQ=tsxxjTo9+45AEHdR3kVDW-326JkwHEq8gTQ@mail.gmail.com>

There is an opportunity to share, discuss, design, and learn with your
fellow ITK community members.


On Friday, 11 AM Eastern USA time, join us as we discuss ITK
development.  We will use the Hangout link for the Event.

  https://plus.google.com/events/c4np6cgd8oosd5je818d9r1n3j8


For those that cannot join via Hangout, telephone call-in is also
possible.  Dial:

  +1-585-632-6296

Enter pin:

  31423?


All are welcome.  Hope to talk to you then!

From indianzeppelin at gmail.com  Thu Sep  4 11:58:19 2014
From: indianzeppelin at gmail.com (Girish Mallya Udupi)
Date: Thu, 4 Sep 2014 16:58:19 +0100
Subject: [ITK-dev] New to the Gerrit review process
In-Reply-To: <A4452E5E-7F22-415C-8410-D92A1D98A3EA@mail.nih.gov>
References: <CAA+VR6hxO4x2ZBd6cKiHHVHfOr21uTzJ9POAid-PdjYmYuvoGQ@mail.gmail.com>
 <A4452E5E-7F22-415C-8410-D92A1D98A3EA@mail.nih.gov>
Message-ID: <CAA+VR6jj+PGw-Ctg_BcaWLJVW=5Q5WAnOa_PxJfPsOD0-nxDdQ@mail.gmail.com>

Hi Brad,

Yes, that one (and its parent).

I did in fact pull the patch and compile it without any issues. I ran the
related tests too, which passed. But it seemed to me that I couldn't give a
"Verify" score alone and had to give a "Code Review" score as well. Matt's
reply has made it clearer now. Thanks!


On Thu, Sep 4, 2014 at 4:43 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello Girish,
>
> I assume you are talking about this patch:
> http://review.source.kitware.com/#/c/16868/
>
> Thanks again for contributing the patch which demonstrated the bug you
> encountered.
>
> For this particular case I would encourage you to download, checkout, and
> compile the patch and verify that is resolves the issue you initially
> encountered. Then report back if it fixes the problem.
>
> Brad
>
> On Sep 4, 2014, at 11:29 AM, Girish Mallya Udupi <indianzeppelin at gmail.com>
> wrote:
>
> > Hello,
> >
> > I have a couple of questions about the Gerrit review process -
> >
> > 1) Is the creator of a topic automatically added as a reviewer on
> subsequent patches in the topic?
> >
> > 2) As a reviewer, if I am unable to understand the changes made to the
> code (simply because I am not an advanced programmer), should I leave the
> patch unscored?
> >
> > _______________________________________________
> > 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
>
>


-- 
Regards,
Girish
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From marcus.hanwell at kitware.com  Fri Sep  5 11:31:30 2014
From: marcus.hanwell at kitware.com (Marcus D. Hanwell)
Date: Fri, 5 Sep 2014 11:31:30 -0400
Subject: [ITK-dev] Review.Source.Kitware.Com -- are strings of dependent
 topics OK now?
In-Reply-To: <8D195ACD03190B6-15CC-C133@webmail-m269.sysops.aol.com>
References: <8D195ACD03190B6-15CC-C133@webmail-m269.sysops.aol.com>
Message-ID: <CAMkPkZWES-QSwakPkTECK5E0+41nuoxqYgYemCbuXDznjZcUKg@mail.gmail.com>

On Wed, Sep 3, 2014 at 12:39 PM, David Cole via Insight-developers
<insight-developers at itk.org> wrote:
>> http://review.source.kitware.com/#/c/16579
>> http://review.source.kitware.com/#/c/16578
>> Incredibly, 16578 and 16579 seem to be circularly dependent.
>
>
> Why do you say they're circularly dependent? It looks to me like 79 is
> based on 78... I'm not seeing the circularity.
>
If you managed a circular dependency I would love to see it - is that
even possible in git?

From blowekamp at mail.nih.gov  Fri Sep  5 13:23:22 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 5 Sep 2014 13:23:22 -0400
Subject: [ITK-dev] Using ITK with optional components
Message-ID: <1C470533-952F-4836-81C1-1DA697FA8213@mail.nih.gov>

Hello,

I was wondering if anyone had looked into adding support for CMake's find_package OPTIONAL_COMPONENTS option?

This would be quite convenient in some situations.

Brad

From arnaudgelas at gmail.com  Mon Sep 15 06:05:02 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Mon, 15 Sep 2014 12:05:02 +0200
Subject: [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData
Message-ID: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com>

Hi guys,

I have been looking at GDCMImageIO this morning and I thought it would be great if it was possible to iterate directly on the Dictionary and do not use ExposeMetaData cause internally there are 2 finds (HasKeys and [] ) per iterator (in which we already know both keys and values).

https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L700
https://github.com/Kitware/ITK/blob/master/Modules/Core/Common/include/itkMetaDataObject.h#L171-L189

I have tried to create a new function which would take an iterator as parameter, I have compilation error or a failing dynamic_cast? I guess I am missing something obvious?

I have been testing something like that:

http://review.source.kitware.com/#/c/17026/

Any idea on how to fix the code ( both compilation & dynamic_cast ), please?

Thanks,
Arnaud
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From norman-k-williams at uiowa.edu  Tue Sep 16 10:46:05 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Tue, 16 Sep 2014 14:46:05 +0000
Subject: [ITK-dev] Coverity 'Uncaught Exception' errors
Message-ID: <D03DB75B.B0DC%norman-k-williams@uiowa.edu>

Hans asked me to look at a couple of ITK Coverity defects, as they were in code written in our lab.

A couple of them are understandable but problematic.  Basically there?s an exception thrown at itkObjectFactoryBase.cxx at line 533:

531   if ( ObjectFactoryBase::m_StrictVersionChecking )
532      {
    1. exception_thrown: An exception of type "itk::ExceptionObject" is thrown.
533      itkGenericExceptionMacro(<< "Incompatible factory version load attempt:"
534                            << "\nRunning itk version :\n" << Version::GetITKSourceVersion()
535                            << "\nAttempted loading factory version:\n" << factory->GetITKSourceVersion()
536                            << "\nAttempted factory:\n" << factory->m_LibraryPath << "\n");
537      }
538    else
539      {
540      itkGenericOutputMacro(<< "Possible incompatible factory load:"
541                            << "\nRunning itk version :\n" << Version::GetITKSourceVersion()
542                            << "\nLoaded factory version:\n" << factory->GetITKSourceVersion()
543                            << "\nLoading factory:\n" << factory->m_LibraryPath << "\n");
544      }
545    }

There are 4 Coverity defects reported that all point to this code.  Given where the exceptions are thrown, it looks like every call to itk::<className>::New() should be bracketed by a try/catch pair.

But in fact Coverity only reports 4 instances of this being a problem.

I can fix the reported defects for completeness? sake, but I find it mysterious that more defects caused by this occur.


________________________________
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From bill.lorensen at gmail.com  Tue Sep 16 10:53:10 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 16 Sep 2014 10:53:10 -0400
Subject: [ITK-dev] [ITK]  Coverity 'Uncaught Exception' errors
In-Reply-To: <D03DB75B.B0DC%norman-k-williams@uiowa.edu>
References: <D03DB75B.B0DC%norman-k-williams@uiowa.edu>
Message-ID: <CADZJ4hNk4y_jdTohVRfEgUZ5kSSb+Kd26J46YtMEcBrzO=4N9A@mail.gmail.com>

I think we ignored a number of those.


On Tue, Sep 16, 2014 at 10:46 AM, Williams, Norman K
<norman-k-williams at uiowa.edu> wrote:
> Hans asked me to look at a couple of ITK Coverity defects, as they were in
> code written in our lab.
>
> A couple of them are understandable but problematic.  Basically there?s an
> exception thrown at itkObjectFactoryBase.cxx at line 533:
>
> 531   if ( ObjectFactoryBase::m_StrictVersionChecking )
> 532      {
>     1. exception_thrown: An exception of type "itk::ExceptionObject" is
> thrown.
> 533      itkGenericExceptionMacro(<< "Incompatible factory version load
> attempt:"
> 534                            << "\nRunning itk version :\n" <<
> Version::GetITKSourceVersion()
> 535                            << "\nAttempted loading factory version:\n"
> << factory->GetITKSourceVersion()
> 536                            << "\nAttempted factory:\n" <<
> factory->m_LibraryPath << "\n");
> 537      }
> 538    else
> 539      {
> 540      itkGenericOutputMacro(<< "Possible incompatible factory load:"
> 541                            << "\nRunning itk version :\n" <<
> Version::GetITKSourceVersion()
> 542                            << "\nLoaded factory version:\n" <<
> factory->GetITKSourceVersion()
> 543                            << "\nLoading factory:\n" <<
> factory->m_LibraryPath << "\n");
> 544      }
> 545    }
>
> There are 4 Coverity defects reported that all point to this code.  Given
> where the exceptions are thrown, it looks like every call to
> itk::<className>::New() should be bracketed by a try/catch pair.
>
> But in fact Coverity only reports 4 instances of this being a problem.
>
> I can fix the reported defects for completeness? sake, but I find it
> mysterious that more defects caused by this occur.
>
>
> ________________________________
> 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
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>



-- 
Unpaid intern in BillsBasement at noware dot com

From norman-k-williams at uiowa.edu  Tue Sep 16 12:25:02 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Tue, 16 Sep 2014 16:25:02 +0000
Subject: [ITK-dev] [ITK]  Coverity 'Uncaught Exception' errors
In-Reply-To: <CADZJ4hNk4y_jdTohVRfEgUZ5kSSb+Kd26J46YtMEcBrzO=4N9A@mail.gmail.com>
References: <D03DB75B.B0DC%norman-k-williams@uiowa.edu>
 <CADZJ4hNk4y_jdTohVRfEgUZ5kSSb+Kd26J46YtMEcBrzO=4N9A@mail.gmail.com>
Message-ID: <D03DCE4B.B0ED%norman-k-williams@uiowa.edu>

You mean we told Coverity to ignore them?

I guess that makes sense.

On 9/16/14, 9:53 AM, "Bill Lorensen" <bill.lorensen at gmail.com> wrote:

>I think we ignored a number of those.
>
>
>On Tue, Sep 16, 2014 at 10:46 AM, Williams, Norman K
><norman-k-williams at uiowa.edu> wrote:
>> Hans asked me to look at a couple of ITK Coverity defects, as they were
>>in
>> code written in our lab.
>>
>> A couple of them are understandable but problematic.  Basically there?s
>>an
>> exception thrown at itkObjectFactoryBase.cxx at line 533:
>>
>> 531   if ( ObjectFactoryBase::m_StrictVersionChecking )
>> 532      {
>>     1. exception_thrown: An exception of type "itk::ExceptionObject" is
>> thrown.
>> 533      itkGenericExceptionMacro(<< "Incompatible factory version load
>> attempt:"
>> 534                            << "\nRunning itk version :\n" <<
>> Version::GetITKSourceVersion()
>> 535                            << "\nAttempted loading factory
>>version:\n"
>> << factory->GetITKSourceVersion()
>> 536                            << "\nAttempted factory:\n" <<
>> factory->m_LibraryPath << "\n");
>> 537      }
>> 538    else
>> 539      {
>> 540      itkGenericOutputMacro(<< "Possible incompatible factory load:"
>> 541                            << "\nRunning itk version :\n" <<
>> Version::GetITKSourceVersion()
>> 542                            << "\nLoaded factory version:\n" <<
>> factory->GetITKSourceVersion()
>> 543                            << "\nLoading factory:\n" <<
>> factory->m_LibraryPath << "\n");
>> 544      }
>> 545    }
>>
>> There are 4 Coverity defects reported that all point to this code.
>>Given
>> where the exceptions are thrown, it looks like every call to
>> itk::<className>::New() should be bracketed by a try/catch pair.
>>
>> But in fact Coverity only reports 4 instances of this being a problem.
>>
>> I can fix the reported defects for completeness? sake, but I find it
>> mysterious that more defects caused by this occur.
>>
>>
>> ________________________________
>> 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
>>
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>>
>
>
>
>--
>Unpaid intern in BillsBasement at noware dot com



________________________________
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.
________________________________

From norman-k-williams at uiowa.edu  Tue Sep 16 12:50:39 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Tue, 16 Sep 2014 16:50:39 +0000
Subject: [ITK-dev] Review.source.kitware.com down?
Message-ID: <D03DD48D.B0F7%norman-k-williams@uiowa.edu>

Is it just me or is ITK Gerrit inaccessible?




________________________________
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.
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From matt.mccormick at kitware.com  Tue Sep 16 13:02:06 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 16 Sep 2014 13:02:06 -0400
Subject: [ITK-dev] Review.source.kitware.com down?
In-Reply-To: <D03DD48D.B0F7%norman-k-williams@uiowa.edu>
References: <D03DD48D.B0F7%norman-k-williams@uiowa.edu>
Message-ID: <CALzTN-SNJ2BG6ntgQL9OiUunyGYvoeuy5mij59rfia=hj0HZ3A@mail.gmail.com>

It's not just you.  I will find the status.

Thanks,
Matt

On Tue, Sep 16, 2014 at 12:50 PM, Williams, Norman K
<norman-k-williams at uiowa.edu> wrote:
> Is it just me or is ITK Gerrit inaccessible?
>
>
>
>
> ________________________________
> 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 norman-k-williams at uiowa.edu  Tue Sep 16 13:15:48 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Tue, 16 Sep 2014 17:15:48 +0000
Subject: [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData
In-Reply-To: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com>
References: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com>
Message-ID: <D03DD936.B0FD%norman-k-williams@uiowa.edu>

I?ll have a look when review.source.kitware.com comes back up.

It would be OK to replaces the [] operator with using the iterator directly.  The only reason I can think of not to is that even with a DICOM file, the time spent in writing and reading the MetaDataDictionary is not going to have a significant computational cost, since it only happens when you read or write a DICOM file.  It?s not something done in the inner loop of a big computation.


From: Arnaud Gelas <arnaudgelas at gmail.com<mailto:arnaudgelas at gmail.com>>
Date: Monday, September 15, 2014 at 5:05 AM
To: ITK <insight-developers at itk.org<mailto:insight-developers at itk.org>>
Subject: [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData

Hi guys,

I have been looking at GDCMImageIO this morning and I thought it would be great if it was possible to iterate directly on the Dictionary and do not use ExposeMetaData cause internally there are 2 finds (HasKeys and [] ) per iterator (in which we already know both keys and values).

https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L700
https://github.com/Kitware/ITK/blob/master/Modules/Core/Common/include/itkMetaDataObject.h#L171-L189

I have tried to create a new function which would take an iterator as parameter, I have compilation error or a failing dynamic_cast? I guess I am missing something obvious?

I have been testing something like that:

http://review.source.kitware.com/#/c/17026/

Any idea on how to fix the code ( both compilation & dynamic_cast ), please?

Thanks,
Arnaud


________________________________
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.
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From matt.mccormick at kitware.com  Tue Sep 16 13:29:31 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 16 Sep 2014 13:29:31 -0400
Subject: [ITK-dev] Review.source.kitware.com down?
In-Reply-To: <CALzTN-SNJ2BG6ntgQL9OiUunyGYvoeuy5mij59rfia=hj0HZ3A@mail.gmail.com>
References: <D03DD48D.B0F7%norman-k-williams@uiowa.edu>
 <CALzTN-SNJ2BG6ntgQL9OiUunyGYvoeuy5mij59rfia=hj0HZ3A@mail.gmail.com>
Message-ID: <CALzTN-REqkBeOZzrX=n2Tq--p-PjahJ2GwDykcuB6Mn9A4zdKg@mail.gmail.com>

And we're back :-)

On Tue, Sep 16, 2014 at 1:02 PM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> It's not just you.  I will find the status.
>
> Thanks,
> Matt
>
> On Tue, Sep 16, 2014 at 12:50 PM, Williams, Norman K
> <norman-k-williams at uiowa.edu> wrote:
>> Is it just me or is ITK Gerrit inaccessible?
>>
>>
>>
>>
>> ________________________________
>> 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 blowekamp at mail.nih.gov  Tue Sep 16 13:28:20 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 16 Sep 2014 13:28:20 -0400
Subject: [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData
In-Reply-To: <D03DD936.B0FD%norman-k-williams@uiowa.edu>
References: <29C49AEB-2810-45D4-8F6A-66B0C11C61A1@gmail.com>
 <D03DD936.B0FD%norman-k-williams@uiowa.edu>
Message-ID: <6367ECBA-9742-4DCD-A0F7-387C11195CF7@mail.nih.gov>

Kent,

A long time ago, when I was working on IO streaming, I had modified the ImageSeries reader to populate the metadata dictionary on the GenerateOutputInformation phase of the pipeline. This ended up getting called 2 or 3 times, and it caused a significant performance penalty with the GDCM meta-data that the Slicer folks loudly complained and it was fixed [ likely here 1].

I have doubts about your assumption that there are not significant computation expenses with metadata IO. However I am not quite certain if my experience is relavent to this issue. 

just an FYI,
Brad


[1] https://github.com/InsightSoftwareConsortium/ITK/commit/e92d78ee3b26069d3aeb6aa9f6460a46f20ec2de

On Sep 16, 2014, at 1:15 PM, Williams, Norman K <norman-k-williams at uiowa.edu> wrote:

>  the time spent in writing and reading the MetaDataDictionary is not going to have a significant computational cost, since it only happens when you read or write a DICOM file.  It?s not something done in the inner loop of a big computation.

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From bill.lorensen at gmail.com  Tue Sep 16 18:59:59 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 16 Sep 2014 18:59:59 -0400
Subject: [ITK-dev] [ITK]  Coverity 'Uncaught Exception' errors
In-Reply-To: <D03DCE4B.B0ED%norman-k-williams@uiowa.edu>
References: <D03DB75B.B0DC%norman-k-williams@uiowa.edu>
 <CADZJ4hNk4y_jdTohVRfEgUZ5kSSb+Kd26J46YtMEcBrzO=4N9A@mail.gmail.com>
 <D03DCE4B.B0ED%norman-k-williams@uiowa.edu>
Message-ID: <CADZJ4hNKzTbbCJcr68A20dj2zLvtrX-m6g8xkwuQQ6PYUxNnUw@mail.gmail.com>

Yes
On Sep 16, 2014 12:25 PM, "Williams, Norman K" <norman-k-williams at uiowa.edu>
wrote:

> You mean we told Coverity to ignore them?
>
> I guess that makes sense.
>
> On 9/16/14, 9:53 AM, "Bill Lorensen" <bill.lorensen at gmail.com> wrote:
>
> >I think we ignored a number of those.
> >
> >
> >On Tue, Sep 16, 2014 at 10:46 AM, Williams, Norman K
> ><norman-k-williams at uiowa.edu> wrote:
> >> Hans asked me to look at a couple of ITK Coverity defects, as they were
> >>in
> >> code written in our lab.
> >>
> >> A couple of them are understandable but problematic.  Basically there?s
> >>an
> >> exception thrown at itkObjectFactoryBase.cxx at line 533:
> >>
> >> 531   if ( ObjectFactoryBase::m_StrictVersionChecking )
> >> 532      {
> >>     1. exception_thrown: An exception of type "itk::ExceptionObject" is
> >> thrown.
> >> 533      itkGenericExceptionMacro(<< "Incompatible factory version load
> >> attempt:"
> >> 534                            << "\nRunning itk version :\n" <<
> >> Version::GetITKSourceVersion()
> >> 535                            << "\nAttempted loading factory
> >>version:\n"
> >> << factory->GetITKSourceVersion()
> >> 536                            << "\nAttempted factory:\n" <<
> >> factory->m_LibraryPath << "\n");
> >> 537      }
> >> 538    else
> >> 539      {
> >> 540      itkGenericOutputMacro(<< "Possible incompatible factory load:"
> >> 541                            << "\nRunning itk version :\n" <<
> >> Version::GetITKSourceVersion()
> >> 542                            << "\nLoaded factory version:\n" <<
> >> factory->GetITKSourceVersion()
> >> 543                            << "\nLoading factory:\n" <<
> >> factory->m_LibraryPath << "\n");
> >> 544      }
> >> 545    }
> >>
> >> There are 4 Coverity defects reported that all point to this code.
> >>Given
> >> where the exceptions are thrown, it looks like every call to
> >> itk::<className>::New() should be bracketed by a try/catch pair.
> >>
> >> But in fact Coverity only reports 4 instances of this being a problem.
> >>
> >> I can fix the reported defects for completeness? sake, but I find it
> >> mysterious that more defects caused by this occur.
> >>
> >>
> >> ________________________________
> >> 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
> >>
> >> _______________________________________________
> >> Community mailing list
> >> Community at itk.org
> >> http://public.kitware.com/mailman/listinfo/community
> >>
> >
> >
> >
> >--
> >Unpaid intern in BillsBasement at noware dot com
>
>
>
> ________________________________
> 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.
> ________________________________
>
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From arnaudgelas at gmail.com  Wed Sep 17 10:39:59 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 17 Sep 2014 16:39:59 +0200
Subject: [ITK-dev] help itk::GDCMImageIO / itk::ExposeMetaData
In-Reply-To: <7723535C-1110-4A62-BF59-EA02980C2E86@mail.nih.gov>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <7723535C-1110-4A62-BF59-EA02980C2E86@mail.nih.gov>
Message-ID: <4B7CF7FB-4669-403C-A892-98DD219EBDB5@gmail.com>

Brad,

I guess the email was more related to this topic than the ResampleDICOM's one?

Your last commit on itkMetaDataObject.h seems of interest, I'll keep on investigating!

Thanks
Arnaud

On Sep 17, 2014, at 3:13 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:

> Arnaud,
> 
> If using shared libraries causes the dynamic cast to fail, than this may be a side effect of some recent changes [1].
> 
> Brad
> 
> [1] https://github.com/InsightSoftwareConsortium/ITK/commits/master/Modules/Core/Common/include/itkMetaDataObject.h
> 
> 

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From matt.mccormick at kitware.com  Wed Sep 17 11:13:20 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 17 Sep 2014 11:13:20 -0400
Subject: [ITK-dev] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-QF3BM63OzPf7xXM=URec3HDTyix85A757rEG1QWnCdfg@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.


On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/events/cg0n52cqd08ulpr6o9jgku32gj0?authkey=CJ-S7tP5s5_xAw


On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/events/ctabd8pd4oasc3p5ejat27jgko4?authkey=COjR69z2toGlIQ


For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423


All are welcome.  Hope to talk to you then!

From matt.mccormick at kitware.com  Wed Sep 17 16:16:27 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 17 Sep 2014 16:16:27 -0400
Subject: [ITK-dev] Opportunities to share, discuss, design,
 and learn with other ITK community members
In-Reply-To: <CALzTN-QF3BM63OzPf7xXM=URec3HDTyix85A757rEG1QWnCdfg@mail.gmail.com>
References: <CALzTN-QF3BM63OzPf7xXM=URec3HDTyix85A757rEG1QWnCdfg@mail.gmail.com>
Message-ID: <CALzTN-TQKgGsCQU3tenFxSSYLMuT2d-UtTjXzYfo5Z7c9eywdw@mail.gmail.com>

On Wed, Sep 17, 2014 at 11:13 AM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> There are a couple of upcoming opportunities to share, discuss, design, and
> learn with your fellow ITK community members.
>
>
> On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a
> Google+ Hangout
> where we will be doing code reviews:
>
>   https://plus.google.com/events/cg0n52cqd08ulpr6o9jgku32gj0?authkey=CJ-S7tP5s5_xAw
>

Due to a conflict, this had to be changed to 1:00 PM Eastern USA time.
Sorry for schedule variation.

Matt

From blowekamp at mail.nih.gov  Fri Sep 19 09:37:40 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 19 Sep 2014 09:37:40 -0400
Subject: [ITK-dev] ITK Gerrit Primer
Message-ID: <E065495C-3A6D-4462-8458-BA2C8FFBF4F7@mail.nih.gov>

I just stumbled on this wiki web page ( it actually was a paraview url initially ):
http://www.itk.org/Wiki/ITK/Gerrit/ReviewPrimer

I don't recall seeing it before, it looks like it has some good detailed information in it about how to use gerrit and do reviews. 

Brad

From norman-k-williams at uiowa.edu  Fri Sep 19 10:14:01 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Fri, 19 Sep 2014 14:14:01 +0000
Subject: [ITK-dev] The fix for patch in which I torpedoed the Release build
	nightlies
Message-ID: <D041A456.B29D%norman-k-williams@uiowa.edu>

Je suis plus d?sol?e!

I typed ?/ *? instead of ?/*? and if NDEBUG is set, it?s a compiler error every time vml_vector_fixed_ref.h is included, compilers get mad.

http://review.source.kitware.com/#/c/17126/


________________________________
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.
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From hiner at wisc.edu  Fri Sep 19 11:09:13 2014
From: hiner at wisc.edu (Mark Hiner)
Date: Fri, 19 Sep 2014 10:09:13 -0500
Subject: [ITK-dev] SCIFIO nightly build e-mail
Message-ID: <CA+B=mGp6aXvoYcwJ-Q+RgLu6nteNUyN6KYi8wXgE5whn_O3J2A@mail.gmail.com>

Hello ITK developers,

 Would it be possible to add imagej-builds at imagej.net to get build failure
notifications for the SCIFIO nightly build
<http://open.cdash.org/buildSummary.php?buildid=3495012>? I didn't realize
that I had broken the build a couple days ago.

Much appreciated!

Regards,
Mark
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From matt.mccormick at kitware.com  Wed Sep 24 17:53:03 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 24 Sep 2014 17:53:03 -0400
Subject: [ITK-dev] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-SoV8MnMMye+KYSt3UL+YWgG=hdNvAdTv+02ryfRy7dNA@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.


On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk


On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4

For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423


All are welcome.  Hope to talk to you then!

From arnaudgelas at gmail.com  Thu Sep 25 09:09:26 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 25 Sep 2014 15:09:26 +0200
Subject: [ITK-dev] minor release?
Message-ID: <CAK3qF+-16wF7+nnVsqr9iomWuYJY2=+0cSNBYz=CX0Gfb0VffA@mail.gmail.com>

Hi all,

I just wanted to know if there were any plan to release v4.6.1 from the
release branch?
If so, when could it happen?

Thanks,
Arnaud
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From arnaudgelas at gmail.com  Thu Sep 25 09:51:12 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 25 Sep 2014 15:51:12 +0200
Subject: [ITK-dev] packaging ITK with system HDF5?
Message-ID: <CAK3qF+8hv-g91wFaU8n21ragCVVZ7_2P4WZrny5eMd1B2ALyPw@mail.gmail.com>

Hi all,

When installing ITK with system HDF5, I get in the file
${CMAKE_INSTALL_PREFIX}/lib64/cmake/InsightToolkit/Modules/ITKHDF5.cmake

set( ITKHDF5_INCLUDE_DIRS
"${ITK_INSTALL_PREFIX}/include/InsightToolkit;/home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src;/usr/include"
)

Of course it works fine, if you do not delete
/home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src
and if you use the same user...

I could not find anything related to this issue...

It seems to me that the problem comes from:
https://github.com/Kitware/ITK/blob/master/Modules/ThirdParty/HDF5/CMakeLists.txt#L10

I guess this path should not be added there??

Any idea?

Thank you very much
Arnaud
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From blowekamp at mail.nih.gov  Thu Sep 25 10:00:55 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 25 Sep 2014 10:00:55 -0400
Subject: [ITK-dev] [ITK]  packaging ITK with system HDF5?
In-Reply-To: <CAK3qF+8hv-g91wFaU8n21ragCVVZ7_2P4WZrny5eMd1B2ALyPw@mail.gmail.com>
References: <CAK3qF+8hv-g91wFaU8n21ragCVVZ7_2P4WZrny5eMd1B2ALyPw@mail.gmail.com>
Message-ID: <9750EDA2-6F14-41FB-8E4E-4330207C0F17@mail.nih.gov>

Arnaud,

For comparison you can look at libtiff:

https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/TIFF/CMakeLists.txt#L9-L14

There the include are split between ITKTIFF_INCLUDE_DIRS and ITKTIFF_SYSTEM_INCLUDE_DIRS. Likely the SYSTEM variable doesn't get modified when installed.

What to git a shot at making HDF5 follow this TIFF include pattern?

Brad

On Sep 25, 2014, at 9:51 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Hi all,
> 
> When installing ITK with system HDF5, I get in the file ${CMAKE_INSTALL_PREFIX}/lib64/cmake/InsightToolkit/Modules/ITKHDF5.cmake
> 
> set( ITKHDF5_INCLUDE_DIRS "${ITK_INSTALL_PREFIX}/include/InsightToolkit;/home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src;/usr/include" )
> 
> Of course it works fine, if you do not delete /home/builder/rpmbuild/BUILD/InsightToolkit-4.6.0/x86_64-redhat-linux-gnu/Modules/ThirdParty/HDF5/src and if you use the same user...
> 
> I could not find anything related to this issue...
> 
> It seems to me that the problem comes from:
> https://github.com/Kitware/ITK/blob/master/Modules/ThirdParty/HDF5/CMakeLists.txt#L10
> 
> I guess this path should not be added there??
> 
> Any idea?
> 
> Thank you very much
> Arnaud
> _______________________________________________
> 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
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community

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From matt.mccormick at kitware.com  Thu Sep 25 10:25:46 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 25 Sep 2014 10:25:46 -0400
Subject: [ITK-dev] [ITK]  minor release?
In-Reply-To: <CAK3qF+-16wF7+nnVsqr9iomWuYJY2=+0cSNBYz=CX0Gfb0VffA@mail.gmail.com>
References: <CAK3qF+-16wF7+nnVsqr9iomWuYJY2=+0cSNBYz=CX0Gfb0VffA@mail.gmail.com>
Message-ID: <CALzTN-QEzCq63Q-X5hxgY_9rCBfqzqSf0si2Ymf5UtWzBWY+pA@mail.gmail.com>

Hi Arnaud,

Yes, good point.  There are many great bug fixes on the release
branch.  I think we can release 4.6.1 next week.

Thanks,
Matt

On Thu, Sep 25, 2014 at 9:09 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Hi all,
>
> I just wanted to know if there were any plan to release v4.6.1 from the
> release branch?
> If so, when could it happen?
>
> Thanks,
> Arnaud
>
> _______________________________________________
> 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
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From matt.mccormick at kitware.com  Thu Sep 25 10:29:22 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 25 Sep 2014 10:29:22 -0400
Subject: [ITK-dev] Patches for v4.6.1
Message-ID: <CALzTN-R=0e2LmXUUAfFcYYynsbK29Qa8kn=DMH8MacAtM8keJA@mail.gmail.com>

Hi,

We currently have the patches below on the "release" branch for the
v4.6.1 release.  Are there any patches missing?

Thanks,
Matt


Arnaud Gelas (3):
      BUG: fix gdcm version in GDCMImageIO.
      COMP: missing cast when calling gdcm::DataElement::SetByteValue
      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false

Brad King (1):
      COMP: Fix vxl_config_macros usage of CMake check macros

Bradley Lowekamp (7):
      ENH: Adding License file from upstream MetaIO
      ENH: Adding script to update MetaIO from upstream
      ENH: Remove ITK MetaIO to prepare for upstream import
      COMP: Fix variable type for Set/Get macros
      BUG: Use METER of sCAL scale unit
      BUG: Use PNG_SCALE_METER for PNG sCAL unit
      BUG: Fix overflows computing size of read tiff image

Christopher Mullins (1):
      COMP: Allows latex to compile for ITKSoftwareGuide

David T. Chen (1):
      DOC: Fixed HistogramThresholdImageFitler

Gert Wollny (1):
      COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease)

Girish Mallya (1):
      BUG: Tests added for BinaryImageToLabelMapFilter for single-row images.

Hans Johnson (12):
      COMP: Add tolerance for comparing floating point
      PERF: Remove non-threadable algorithm components
      PERF: Remove large foot print of PDF derivatives.
      PERF: Revert Remove large foot print of PDF derivatives.
      STYLE: Test against almost equal for floating point values
      STYLE: Non-exact floating point testing
      PERF: Distribute initialization per thread buffers
      ENH: Remove unnecessary mutable qualifier.
      STYLE: Remove comment with no meaning.
      ENH: Moved accumlator logic to main MI class
      ENH: Allow staggering of accumulations per thread.
      PERF: Zero reset thread buffers during finalize

KWSys Robot (2):
      KWSys 2014-07-18 (65b36ede)
      KWSys 2014-08-04 (e787837a)

Matthew McCormick (30):
      BUG: ArchiveTestingData.py future imports must occur at the beginning.
      DOC: Remove Image2.cxx reference from Book 2.
      DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx.
      DOC: Remove references to Book 1 sections from Book 2.
      DOC: Make BinaryThresholdImageFilter not floating.
      DOC: Fix Software Guide figure caption for FlipImageFilter.
      DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx.
      DOC: Remove duplicate figure in
LaplacianRecursiveGaussianImageFilter2.cxx.
      DOC: ImageRandomConstIteratorWithIndex table reference.
      BUG: Bump GCCXML to 2014-08-06.
      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
      BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().
      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
      BUG: Fix alpha assignment for RGBA TIFF.
      BUG: Fix Nifti IO read with large images.
      BUG: Improve thread-safety and performance of
PCAShapeSignedDistanceFunction.
      DOC: itk::statistics -> itk::Statistics.
      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
      BUG: TransformFileReader does not clear its TransformList.
      BUG: Prevent dangling pointer in HDF5TransformIO.
      COMP: Fix missing prefix in ITKv3ImageRegistration20Test.
      BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform
      STYLE: Improve style in BinaryImageToLabelMapFilter.
      BUG: Fix BinaryImageToLabelMapFilter on 1D image.
      ENH: Improve precision of the joint PDF sum
      BUG: Fix BinShrinkImageFilter for different input/output image types.
      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
      COMP: Add missing wrapping for TransformIOBaseTemplate.
      BUG: gdcm::StringFilter recognizes backslash delimiter.

MetaIO Maintainers (1):
      MetaIO (reduced)

Michka Popoff (4):
      BUG: Improve SWIG version check
      BUG: Add VTK_VERSION for older VTK versions
      BUG: Update VTK minimum version (for release)
      BUG: Fix memory leak in MetaImageIO after exception

From arnaudgelas at gmail.com  Thu Sep 25 10:31:22 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 25 Sep 2014 16:31:22 +0200
Subject: [ITK-dev] Patches for v4.6.1
In-Reply-To: <CALzTN-R=0e2LmXUUAfFcYYynsbK29Qa8kn=DMH8MacAtM8keJA@mail.gmail.com>
References: <CALzTN-R=0e2LmXUUAfFcYYynsbK29Qa8kn=DMH8MacAtM8keJA@mail.gmail.com>
Message-ID: <CAK3qF+-jmYzvWDpLypXO4c_=hCizOOkWww-cPSETZPh4DH46GQ@mail.gmail.com>

Matt,

Following Brad's email, I am testing the following patch right now

http://review.source.kitware.com/#/c/17232/1

If it fixes the issue, I would really like it to be part of 4.6.1

Best
Arnaud


On Thu, Sep 25, 2014 at 4:29 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi,
>
> We currently have the patches below on the "release" branch for the
> v4.6.1 release.  Are there any patches missing?
>
> Thanks,
> Matt
>
>
> Arnaud Gelas (3):
>       BUG: fix gdcm version in GDCMImageIO.
>       COMP: missing cast when calling gdcm::DataElement::SetByteValue
>       BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is
> false
>
> Brad King (1):
>       COMP: Fix vxl_config_macros usage of CMake check macros
>
> Bradley Lowekamp (7):
>       ENH: Adding License file from upstream MetaIO
>       ENH: Adding script to update MetaIO from upstream
>       ENH: Remove ITK MetaIO to prepare for upstream import
>       COMP: Fix variable type for Set/Get macros
>       BUG: Use METER of sCAL scale unit
>       BUG: Use PNG_SCALE_METER for PNG sCAL unit
>       BUG: Fix overflows computing size of read tiff image
>
> Christopher Mullins (1):
>       COMP: Allows latex to compile for ITKSoftwareGuide
>
> David T. Chen (1):
>       DOC: Fixed HistogramThresholdImageFitler
>
> Gert Wollny (1):
>       COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease)
>
> Girish Mallya (1):
>       BUG: Tests added for BinaryImageToLabelMapFilter for single-row
> images.
>
> Hans Johnson (12):
>       COMP: Add tolerance for comparing floating point
>       PERF: Remove non-threadable algorithm components
>       PERF: Remove large foot print of PDF derivatives.
>       PERF: Revert Remove large foot print of PDF derivatives.
>       STYLE: Test against almost equal for floating point values
>       STYLE: Non-exact floating point testing
>       PERF: Distribute initialization per thread buffers
>       ENH: Remove unnecessary mutable qualifier.
>       STYLE: Remove comment with no meaning.
>       ENH: Moved accumlator logic to main MI class
>       ENH: Allow staggering of accumulations per thread.
>       PERF: Zero reset thread buffers during finalize
>
> KWSys Robot (2):
>       KWSys 2014-07-18 (65b36ede)
>       KWSys 2014-08-04 (e787837a)
>
> Matthew McCormick (30):
>       BUG: ArchiveTestingData.py future imports must occur at the
> beginning.
>       DOC: Remove Image2.cxx reference from Book 2.
>       DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx.
>       DOC: Remove references to Book 1 sections from Book 2.
>       DOC: Make BinaryThresholdImageFilter not floating.
>       DOC: Fix Software Guide figure caption for FlipImageFilter.
>       DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx.
>       DOC: Remove duplicate figure in
> LaplacianRecursiveGaussianImageFilter2.cxx.
>       DOC: ImageRandomConstIteratorWithIndex table reference.
>       BUG: Bump GCCXML to 2014-08-06.
>       BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>       BUG: Call clear instead of empty on PatchBasedDenoising
> EmptyCaches().
>       BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
>       BUG: Fix alpha assignment for RGBA TIFF.
>       BUG: Fix Nifti IO read with large images.
>       BUG: Improve thread-safety and performance of
> PCAShapeSignedDistanceFunction.
>       DOC: itk::statistics -> itk::Statistics.
>       DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
>       DOC: Fix Software Guide page overruns in
> IterativeClosestPoint{1,2}.cxx.
>       BUG: TransformFileReader does not clear its TransformList.
>       BUG: Prevent dangling pointer in HDF5TransformIO.
>       COMP: Fix missing prefix in ITKv3ImageRegistration20Test.
>       BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform
>       STYLE: Improve style in BinaryImageToLabelMapFilter.
>       BUG: Fix BinaryImageToLabelMapFilter on 1D image.
>       ENH: Improve precision of the joint PDF sum
>       BUG: Fix BinShrinkImageFilter for different input/output image types.
>       COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
>       COMP: Add missing wrapping for TransformIOBaseTemplate.
>       BUG: gdcm::StringFilter recognizes backslash delimiter.
>
> MetaIO Maintainers (1):
>       MetaIO (reduced)
>
> Michka Popoff (4):
>       BUG: Improve SWIG version check
>       BUG: Add VTK_VERSION for older VTK versions
>       BUG: Update VTK minimum version (for release)
>       BUG: Fix memory leak in MetaImageIO after exception
> _______________________________________________
> 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 blowekamp at mail.nih.gov  Thu Sep 25 10:37:32 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 25 Sep 2014 10:37:32 -0400
Subject: [ITK-dev] Patches for v4.6.1
In-Reply-To: <CALzTN-R=0e2LmXUUAfFcYYynsbK29Qa8kn=DMH8MacAtM8keJA@mail.gmail.com>
References: <CALzTN-R=0e2LmXUUAfFcYYynsbK29Qa8kn=DMH8MacAtM8keJA@mail.gmail.com>
Message-ID: <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov>

This minor one too, fixes something that was merged into release last week:

http://review.source.kitware.com/#/c/17202/

On Sep 25, 2014, at 10:29 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:

> Hi,
> 
> We currently have the patches below on the "release" branch for the
> v4.6.1 release.  Are there any patches missing?
> 
> Thanks,
> Matt
> 
> 
> Arnaud Gelas (3):
>      BUG: fix gdcm version in GDCMImageIO.
>      COMP: missing cast when calling gdcm::DataElement::SetByteValue
>      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false
> 
> Brad King (1):
>      COMP: Fix vxl_config_macros usage of CMake check macros
> 
> Bradley Lowekamp (7):
>      ENH: Adding License file from upstream MetaIO
>      ENH: Adding script to update MetaIO from upstream
>      ENH: Remove ITK MetaIO to prepare for upstream import
>      COMP: Fix variable type for Set/Get macros
>      BUG: Use METER of sCAL scale unit
>      BUG: Use PNG_SCALE_METER for PNG sCAL unit
>      BUG: Fix overflows computing size of read tiff image
> 
> Christopher Mullins (1):
>      COMP: Allows latex to compile for ITKSoftwareGuide
> 
> David T. Chen (1):
>      DOC: Fixed HistogramThresholdImageFitler
> 
> Gert Wollny (1):
>      COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease)
> 
> Girish Mallya (1):
>      BUG: Tests added for BinaryImageToLabelMapFilter for single-row images.
> 
> Hans Johnson (12):
>      COMP: Add tolerance for comparing floating point
>      PERF: Remove non-threadable algorithm components
>      PERF: Remove large foot print of PDF derivatives.
>      PERF: Revert Remove large foot print of PDF derivatives.
>      STYLE: Test against almost equal for floating point values
>      STYLE: Non-exact floating point testing
>      PERF: Distribute initialization per thread buffers
>      ENH: Remove unnecessary mutable qualifier.
>      STYLE: Remove comment with no meaning.
>      ENH: Moved accumlator logic to main MI class
>      ENH: Allow staggering of accumulations per thread.
>      PERF: Zero reset thread buffers during finalize
> 
> KWSys Robot (2):
>      KWSys 2014-07-18 (65b36ede)
>      KWSys 2014-08-04 (e787837a)
> 
> Matthew McCormick (30):
>      BUG: ArchiveTestingData.py future imports must occur at the beginning.
>      DOC: Remove Image2.cxx reference from Book 2.
>      DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx.
>      DOC: Remove references to Book 1 sections from Book 2.
>      DOC: Make BinaryThresholdImageFilter not floating.
>      DOC: Fix Software Guide figure caption for FlipImageFilter.
>      DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx.
>      DOC: Remove duplicate figure in
> LaplacianRecursiveGaussianImageFilter2.cxx.
>      DOC: ImageRandomConstIteratorWithIndex table reference.
>      BUG: Bump GCCXML to 2014-08-06.
>      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>      BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().
>      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
>      BUG: Fix alpha assignment for RGBA TIFF.
>      BUG: Fix Nifti IO read with large images.
>      BUG: Improve thread-safety and performance of
> PCAShapeSignedDistanceFunction.
>      DOC: itk::statistics -> itk::Statistics.
>      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
>      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
>      BUG: TransformFileReader does not clear its TransformList.
>      BUG: Prevent dangling pointer in HDF5TransformIO.
>      COMP: Fix missing prefix in ITKv3ImageRegistration20Test.
>      BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform
>      STYLE: Improve style in BinaryImageToLabelMapFilter.
>      BUG: Fix BinaryImageToLabelMapFilter on 1D image.
>      ENH: Improve precision of the joint PDF sum
>      BUG: Fix BinShrinkImageFilter for different input/output image types.
>      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
>      COMP: Add missing wrapping for TransformIOBaseTemplate.
>      BUG: gdcm::StringFilter recognizes backslash delimiter.
> 
> MetaIO Maintainers (1):
>      MetaIO (reduced)
> 
> Michka Popoff (4):
>      BUG: Improve SWIG version check
>      BUG: Add VTK_VERSION for older VTK versions
>      BUG: Update VTK minimum version (for release)
>      BUG: Fix memory leak in MetaImageIO after exception
> _______________________________________________
> 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 at mmmccormick.com  Thu Sep 25 10:38:56 2014
From: matt at mmmccormick.com (Matthew McCormick (thewtex))
Date: Thu, 25 Sep 2014 10:38:56 -0400
Subject: [ITK-dev] Patches for v4.6.1
In-Reply-To: <CAK3qF+-jmYzvWDpLypXO4c_=hCizOOkWww-cPSETZPh4DH46GQ@mail.gmail.com>
References: <CALzTN-R=0e2LmXUUAfFcYYynsbK29Qa8kn=DMH8MacAtM8keJA@mail.gmail.com>
 <CAK3qF+-jmYzvWDpLypXO4c_=hCizOOkWww-cPSETZPh4DH46GQ@mail.gmail.com>
Message-ID: <CA+XjkaAD0BRnkYWH9OcWs2G_WMwemVZ_7Hf0xf-vc5O4-tcAsA@mail.gmail.com>

Cool!  Please make a note in the commit if it has been verified that
the fix works for you.

On Thu, Sep 25, 2014 at 10:31 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Matt,
>
> Following Brad's email, I am testing the following patch right now
>
> http://review.source.kitware.com/#/c/17232/1
>
> If it fixes the issue, I would really like it to be part of 4.6.1
>
> Best
> Arnaud
>
>
> On Thu, Sep 25, 2014 at 4:29 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Hi,
>>
>> We currently have the patches below on the "release" branch for the
>> v4.6.1 release.  Are there any patches missing?
>>
>> Thanks,
>> Matt
>>
>>
>> Arnaud Gelas (3):
>>       BUG: fix gdcm version in GDCMImageIO.
>>       COMP: missing cast when calling gdcm::DataElement::SetByteValue
>>       BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is
>> false
>>
>> Brad King (1):
>>       COMP: Fix vxl_config_macros usage of CMake check macros
>>
>> Bradley Lowekamp (7):
>>       ENH: Adding License file from upstream MetaIO
>>       ENH: Adding script to update MetaIO from upstream
>>       ENH: Remove ITK MetaIO to prepare for upstream import
>>       COMP: Fix variable type for Set/Get macros
>>       BUG: Use METER of sCAL scale unit
>>       BUG: Use PNG_SCALE_METER for PNG sCAL unit
>>       BUG: Fix overflows computing size of read tiff image
>>
>> Christopher Mullins (1):
>>       COMP: Allows latex to compile for ITKSoftwareGuide
>>
>> David T. Chen (1):
>>       DOC: Fixed HistogramThresholdImageFitler
>>
>> Gert Wollny (1):
>>       COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease)
>>
>> Girish Mallya (1):
>>       BUG: Tests added for BinaryImageToLabelMapFilter for single-row
>> images.
>>
>> Hans Johnson (12):
>>       COMP: Add tolerance for comparing floating point
>>       PERF: Remove non-threadable algorithm components
>>       PERF: Remove large foot print of PDF derivatives.
>>       PERF: Revert Remove large foot print of PDF derivatives.
>>       STYLE: Test against almost equal for floating point values
>>       STYLE: Non-exact floating point testing
>>       PERF: Distribute initialization per thread buffers
>>       ENH: Remove unnecessary mutable qualifier.
>>       STYLE: Remove comment with no meaning.
>>       ENH: Moved accumlator logic to main MI class
>>       ENH: Allow staggering of accumulations per thread.
>>       PERF: Zero reset thread buffers during finalize
>>
>> KWSys Robot (2):
>>       KWSys 2014-07-18 (65b36ede)
>>       KWSys 2014-08-04 (e787837a)
>>
>> Matthew McCormick (30):
>>       BUG: ArchiveTestingData.py future imports must occur at the
>> beginning.
>>       DOC: Remove Image2.cxx reference from Book 2.
>>       DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx.
>>       DOC: Remove references to Book 1 sections from Book 2.
>>       DOC: Make BinaryThresholdImageFilter not floating.
>>       DOC: Fix Software Guide figure caption for FlipImageFilter.
>>       DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx.
>>       DOC: Remove duplicate figure in
>> LaplacianRecursiveGaussianImageFilter2.cxx.
>>       DOC: ImageRandomConstIteratorWithIndex table reference.
>>       BUG: Bump GCCXML to 2014-08-06.
>>       BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>>       BUG: Call clear instead of empty on PatchBasedDenoising
>> EmptyCaches().
>>       BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
>>       BUG: Fix alpha assignment for RGBA TIFF.
>>       BUG: Fix Nifti IO read with large images.
>>       BUG: Improve thread-safety and performance of
>> PCAShapeSignedDistanceFunction.
>>       DOC: itk::statistics -> itk::Statistics.
>>       DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
>>       DOC: Fix Software Guide page overruns in
>> IterativeClosestPoint{1,2}.cxx.
>>       BUG: TransformFileReader does not clear its TransformList.
>>       BUG: Prevent dangling pointer in HDF5TransformIO.
>>       COMP: Fix missing prefix in ITKv3ImageRegistration20Test.
>>       BUG: Do not return SmartPointers in
>> TimeVaryingVelocityFieldTransform
>>       STYLE: Improve style in BinaryImageToLabelMapFilter.
>>       BUG: Fix BinaryImageToLabelMapFilter on 1D image.
>>       ENH: Improve precision of the joint PDF sum
>>       BUG: Fix BinShrinkImageFilter for different input/output image
>> types.
>>       COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
>>       COMP: Add missing wrapping for TransformIOBaseTemplate.
>>       BUG: gdcm::StringFilter recognizes backslash delimiter.
>>
>> MetaIO Maintainers (1):
>>       MetaIO (reduced)
>>
>> Michka Popoff (4):
>>       BUG: Improve SWIG version check
>>       BUG: Add VTK_VERSION for older VTK versions
>>       BUG: Update VTK minimum version (for release)
>>       BUG: Fix memory leak in MetaImageIO after exception
>> _______________________________________________
>> 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
>
>
>
> _______________________________________________
> 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 at mmmccormick.com  Thu Sep 25 10:41:53 2014
From: matt at mmmccormick.com (Matthew McCormick (thewtex))
Date: Thu, 25 Sep 2014 10:41:53 -0400
Subject: [ITK-dev] Patches for v4.6.1
In-Reply-To: <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov>
References: <CALzTN-R=0e2LmXUUAfFcYYynsbK29Qa8kn=DMH8MacAtM8keJA@mail.gmail.com>
 <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov>
Message-ID: <CA+XjkaBDfVdhjTC_RyG5_R7d6FYwxx_gguH70F0g58xyVWrs7g@mail.gmail.com>

Great, thanks!  Merged to master.  Will merge to release tomorrow
after hitting the dashboards.

On Thu, Sep 25, 2014 at 10:37 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> This minor one too, fixes something that was merged into release last week:
>
> http://review.source.kitware.com/#/c/17202/
>
> On Sep 25, 2014, at 10:29 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>
>> Hi,
>>
>> We currently have the patches below on the "release" branch for the
>> v4.6.1 release.  Are there any patches missing?
>>
>> Thanks,
>> Matt
>>
>>
>> Arnaud Gelas (3):
>>      BUG: fix gdcm version in GDCMImageIO.
>>      COMP: missing cast when calling gdcm::DataElement::SetByteValue
>>      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false
>>
>> Brad King (1):
>>      COMP: Fix vxl_config_macros usage of CMake check macros
>>
>> Bradley Lowekamp (7):
>>      ENH: Adding License file from upstream MetaIO
>>      ENH: Adding script to update MetaIO from upstream
>>      ENH: Remove ITK MetaIO to prepare for upstream import
>>      COMP: Fix variable type for Set/Get macros
>>      BUG: Use METER of sCAL scale unit
>>      BUG: Use PNG_SCALE_METER for PNG sCAL unit
>>      BUG: Fix overflows computing size of read tiff image
>>
>> Christopher Mullins (1):
>>      COMP: Allows latex to compile for ITKSoftwareGuide
>>
>> David T. Chen (1):
>>      DOC: Fixed HistogramThresholdImageFitler
>>
>> Gert Wollny (1):
>>      COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease)
>>
>> Girish Mallya (1):
>>      BUG: Tests added for BinaryImageToLabelMapFilter for single-row images.
>>
>> Hans Johnson (12):
>>      COMP: Add tolerance for comparing floating point
>>      PERF: Remove non-threadable algorithm components
>>      PERF: Remove large foot print of PDF derivatives.
>>      PERF: Revert Remove large foot print of PDF derivatives.
>>      STYLE: Test against almost equal for floating point values
>>      STYLE: Non-exact floating point testing
>>      PERF: Distribute initialization per thread buffers
>>      ENH: Remove unnecessary mutable qualifier.
>>      STYLE: Remove comment with no meaning.
>>      ENH: Moved accumlator logic to main MI class
>>      ENH: Allow staggering of accumulations per thread.
>>      PERF: Zero reset thread buffers during finalize
>>
>> KWSys Robot (2):
>>      KWSys 2014-07-18 (65b36ede)
>>      KWSys 2014-08-04 (e787837a)
>>
>> Matthew McCormick (30):
>>      BUG: ArchiveTestingData.py future imports must occur at the beginning.
>>      DOC: Remove Image2.cxx reference from Book 2.
>>      DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx.
>>      DOC: Remove references to Book 1 sections from Book 2.
>>      DOC: Make BinaryThresholdImageFilter not floating.
>>      DOC: Fix Software Guide figure caption for FlipImageFilter.
>>      DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx.
>>      DOC: Remove duplicate figure in
>> LaplacianRecursiveGaussianImageFilter2.cxx.
>>      DOC: ImageRandomConstIteratorWithIndex table reference.
>>      BUG: Bump GCCXML to 2014-08-06.
>>      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>>      BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().
>>      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
>>      BUG: Fix alpha assignment for RGBA TIFF.
>>      BUG: Fix Nifti IO read with large images.
>>      BUG: Improve thread-safety and performance of
>> PCAShapeSignedDistanceFunction.
>>      DOC: itk::statistics -> itk::Statistics.
>>      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
>>      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
>>      BUG: TransformFileReader does not clear its TransformList.
>>      BUG: Prevent dangling pointer in HDF5TransformIO.
>>      COMP: Fix missing prefix in ITKv3ImageRegistration20Test.
>>      BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform
>>      STYLE: Improve style in BinaryImageToLabelMapFilter.
>>      BUG: Fix BinaryImageToLabelMapFilter on 1D image.
>>      ENH: Improve precision of the joint PDF sum
>>      BUG: Fix BinShrinkImageFilter for different input/output image types.
>>      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
>>      COMP: Add missing wrapping for TransformIOBaseTemplate.
>>      BUG: gdcm::StringFilter recognizes backslash delimiter.
>>
>> MetaIO Maintainers (1):
>>      MetaIO (reduced)
>>
>> Michka Popoff (4):
>>      BUG: Improve SWIG version check
>>      BUG: Add VTK_VERSION for older VTK versions
>>      BUG: Update VTK minimum version (for release)
>>      BUG: Fix memory leak in MetaImageIO after exception
>> _______________________________________________
>> 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
>
> _______________________________________________
> 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 blowekamp at mail.nih.gov  Thu Sep 25 10:43:51 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 25 Sep 2014 10:43:51 -0400
Subject: [ITK-dev] [ITK-users] Opportunities to share, discuss, design,
	and learn with other ITK community members
In-Reply-To: <CALzTN-SoV8MnMMye+KYSt3UL+YWgG=hdNvAdTv+02ryfRy7dNA@mail.gmail.com>
References: <CALzTN-SoV8MnMMye+KYSt3UL+YWgG=hdNvAdTv+02ryfRy7dNA@mail.gmail.com>
Message-ID: <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov>

Matt,

The URL for the Confab is from last week, I think this is the URL for the one tomorrow:

https://plus.google.com/u/0/events/c5snoqnkhtkcv1tebfo1cl9quo4

On Sep 24, 2014, at 5:53 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:

> There are a couple of upcoming opportunities to share, discuss, design, and
> learn with your fellow ITK community members.
> 
> 
> On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a
> Google+ Hangout
> where we will be doing code reviews:
> 
>  https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk
> 
> 
> On Friday, 11:00 AM Eastern USA time, an ITK development conference,
> 
>  https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4
> 
> For those that cannot join via Hangout, telephone call-in is also possible.
> Dial:
> 
>  585-632-6296
> 
> Enter pin:
> 
>  31423
> 
> 
> All are welcome.  Hope to talk to you then!
> _____________________________________
> 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://www.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-users


From matt.mccormick at kitware.com  Thu Sep 25 10:45:45 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 25 Sep 2014 10:45:45 -0400
Subject: [ITK-dev] [ITK-users] Opportunities to share, discuss, design,
 and learn with other ITK community members
In-Reply-To: <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov>
References: <CALzTN-SoV8MnMMye+KYSt3UL+YWgG=hdNvAdTv+02ryfRy7dNA@mail.gmail.com>
 <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov>
Message-ID: <CALzTN-S-mFMrX-q54y9xvk2ANqbrZ3v==RnxmCVwJCpNmsLFqA@mail.gmail.com>

Thanks for the correction!

On Thu, Sep 25, 2014 at 10:43 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Matt,
>
> The URL for the Confab is from last week, I think this is the URL for the one tomorrow:
>
> https://plus.google.com/u/0/events/c5snoqnkhtkcv1tebfo1cl9quo4
>
> On Sep 24, 2014, at 5:53 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>
>> There are a couple of upcoming opportunities to share, discuss, design, and
>> learn with your fellow ITK community members.
>>
>>
>> On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a
>> Google+ Hangout
>> where we will be doing code reviews:
>>
>>  https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk
>>
>>
>> On Friday, 11:00 AM Eastern USA time, an ITK development conference,
>>
>>  https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4
>>
>> For those that cannot join via Hangout, telephone call-in is also possible.
>> Dial:
>>
>>  585-632-6296
>>
>> Enter pin:
>>
>>  31423
>>
>>
>> All are welcome.  Hope to talk to you then!
>> _____________________________________
>> 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://www.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-users
>

From arnaudgelas at gmail.com  Thu Sep 25 11:30:25 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 25 Sep 2014 17:30:25 +0200
Subject: [ITK-dev] Patches for v4.6.1
In-Reply-To: <CA+XjkaBDfVdhjTC_RyG5_R7d6FYwxx_gguH70F0g58xyVWrs7g@mail.gmail.com>
References: <CALzTN-R=0e2LmXUUAfFcYYynsbK29Qa8kn=DMH8MacAtM8keJA@mail.gmail.com>
 <0742D6D2-0084-4182-8A0E-964D69839747@mail.nih.gov>
 <CA+XjkaBDfVdhjTC_RyG5_R7d6FYwxx_gguH70F0g58xyVWrs7g@mail.gmail.com>
Message-ID: <CAK3qF+9+WVuTapX=BtmLUewUbu9B0mGjtqkDCtN=Lqi4MXAdJQ@mail.gmail.com>

With system HDF5, the patch works great (thanks to Brad)!

I have also submitted one patch that could go in ITK 4.6.1 with system GDCM:

http://review.source.kitware.com/#/c/17234/

On Thu, Sep 25, 2014 at 4:41 PM, Matthew McCormick (thewtex) <
matt at mmmccormick.com> wrote:

> Great, thanks!  Merged to master.  Will merge to release tomorrow
> after hitting the dashboards.
>
> On Thu, Sep 25, 2014 at 10:37 AM, Bradley Lowekamp
> <blowekamp at mail.nih.gov> wrote:
> > This minor one too, fixes something that was merged into release last
> week:
> >
> > http://review.source.kitware.com/#/c/17202/
> >
> > On Sep 25, 2014, at 10:29 AM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
> >
> >> Hi,
> >>
> >> We currently have the patches below on the "release" branch for the
> >> v4.6.1 release.  Are there any patches missing?
> >>
> >> Thanks,
> >> Matt
> >>
> >>
> >> Arnaud Gelas (3):
> >>      BUG: fix gdcm version in GDCMImageIO.
> >>      COMP: missing cast when calling gdcm::DataElement::SetByteValue
> >>      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID
> is false
> >>
> >> Brad King (1):
> >>      COMP: Fix vxl_config_macros usage of CMake check macros
> >>
> >> Bradley Lowekamp (7):
> >>      ENH: Adding License file from upstream MetaIO
> >>      ENH: Adding script to update MetaIO from upstream
> >>      ENH: Remove ITK MetaIO to prepare for upstream import
> >>      COMP: Fix variable type for Set/Get macros
> >>      BUG: Use METER of sCAL scale unit
> >>      BUG: Use PNG_SCALE_METER for PNG sCAL unit
> >>      BUG: Fix overflows computing size of read tiff image
> >>
> >> Christopher Mullins (1):
> >>      COMP: Allows latex to compile for ITKSoftwareGuide
> >>
> >> David T. Chen (1):
> >>      DOC: Fixed HistogramThresholdImageFitler
> >>
> >> Gert Wollny (1):
> >>      COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease)
> >>
> >> Girish Mallya (1):
> >>      BUG: Tests added for BinaryImageToLabelMapFilter for single-row
> images.
> >>
> >> Hans Johnson (12):
> >>      COMP: Add tolerance for comparing floating point
> >>      PERF: Remove non-threadable algorithm components
> >>      PERF: Remove large foot print of PDF derivatives.
> >>      PERF: Revert Remove large foot print of PDF derivatives.
> >>      STYLE: Test against almost equal for floating point values
> >>      STYLE: Non-exact floating point testing
> >>      PERF: Distribute initialization per thread buffers
> >>      ENH: Remove unnecessary mutable qualifier.
> >>      STYLE: Remove comment with no meaning.
> >>      ENH: Moved accumlator logic to main MI class
> >>      ENH: Allow staggering of accumulations per thread.
> >>      PERF: Zero reset thread buffers during finalize
> >>
> >> KWSys Robot (2):
> >>      KWSys 2014-07-18 (65b36ede)
> >>      KWSys 2014-08-04 (e787837a)
> >>
> >> Matthew McCormick (30):
> >>      BUG: ArchiveTestingData.py future imports must occur at the
> beginning.
> >>      DOC: Remove Image2.cxx reference from Book 2.
> >>      DOC: Fix Software Guide page overruns in
> IterativeClosestPoint3.cxx.
> >>      DOC: Remove references to Book 1 sections from Book 2.
> >>      DOC: Make BinaryThresholdImageFilter not floating.
> >>      DOC: Fix Software Guide figure caption for FlipImageFilter.
> >>      DOC: Avoid duplicate figure description in
> ResampleImageFilter2.cxx.
> >>      DOC: Remove duplicate figure in
> >> LaplacianRecursiveGaussianImageFilter2.cxx.
> >>      DOC: ImageRandomConstIteratorWithIndex table reference.
> >>      BUG: Bump GCCXML to 2014-08-06.
> >>      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
> >>      BUG: Call clear instead of empty on PatchBasedDenoising
> EmptyCaches().
> >>      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
> >>      BUG: Fix alpha assignment for RGBA TIFF.
> >>      BUG: Fix Nifti IO read with large images.
> >>      BUG: Improve thread-safety and performance of
> >> PCAShapeSignedDistanceFunction.
> >>      DOC: itk::statistics -> itk::Statistics.
> >>      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
> >>      DOC: Fix Software Guide page overruns in
> IterativeClosestPoint{1,2}.cxx.
> >>      BUG: TransformFileReader does not clear its TransformList.
> >>      BUG: Prevent dangling pointer in HDF5TransformIO.
> >>      COMP: Fix missing prefix in ITKv3ImageRegistration20Test.
> >>      BUG: Do not return SmartPointers in
> TimeVaryingVelocityFieldTransform
> >>      STYLE: Improve style in BinaryImageToLabelMapFilter.
> >>      BUG: Fix BinaryImageToLabelMapFilter on 1D image.
> >>      ENH: Improve precision of the joint PDF sum
> >>      BUG: Fix BinShrinkImageFilter for different input/output image
> types.
> >>      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
> >>      COMP: Add missing wrapping for TransformIOBaseTemplate.
> >>      BUG: gdcm::StringFilter recognizes backslash delimiter.
> >>
> >> MetaIO Maintainers (1):
> >>      MetaIO (reduced)
> >>
> >> Michka Popoff (4):
> >>      BUG: Improve SWIG version check
> >>      BUG: Add VTK_VERSION for older VTK versions
> >>      BUG: Update VTK minimum version (for release)
> >>      BUG: Fix memory leak in MetaImageIO after exception
> >> _______________________________________________
> >> 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
> >
> > _______________________________________________
> > 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
> _______________________________________________
> 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 blowekamp at mail.nih.gov  Mon Sep 29 08:06:59 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 29 Sep 2014 08:06:59 -0400
Subject: [ITK-dev] Linux CDash@home build missing
Message-ID: <F4B0FD60-7F8C-4766-89AD-DA7BC0A1469B@mail.nih.gov>

Matt,

 I haven't seen the Linux CDash at Home robot for a while now.

Does it need to be persuaded to resume building and testing our gerrit patches?

Thanks,
Brad

From matt.mccormick at kitware.com  Mon Sep 29 10:57:21 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 29 Sep 2014 10:57:21 -0400
Subject: [ITK-dev] Linux CDash@home build missing
In-Reply-To: <F4B0FD60-7F8C-4766-89AD-DA7BC0A1469B@mail.nih.gov>
References: <F4B0FD60-7F8C-4766-89AD-DA7BC0A1469B@mail.nih.gov>
Message-ID: <CALzTN-TBaZMW1WgH9e+8Ry6Uh8QJNt9snOz6+J=qM4tk1sqtZA@mail.gmail.com>

Hi Brad,

Thanks for the note.

My persuasion skills have been applied :-).

Thanks,
Matt

On Mon, Sep 29, 2014 at 8:06 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Matt,
>
>  I haven't seen the Linux CDash at Home robot for a while now.
>
> Does it need to be persuaded to resume building and testing our gerrit patches?
>
> Thanks,
> Brad

From norman-k-williams at uiowa.edu  Tue Sep 30 10:14:15 2014
From: norman-k-williams at uiowa.edu (Williams, Norman K)
Date: Tue, 30 Sep 2014 14:14:15 +0000
Subject: [ITK-dev] find_package issues with ITK and VTK (and SlicerExecution
	Model)
Message-ID: <D05024E5.B649%norman-k-williams@uiowa.edu>

This is a problem that has been cropping up in our projects that use ITK, VTK and SlicerExecutionModel.

You won?t see it UNLESS you turn on the ITKVTK/ITKVtkGlue modules.

The problem is this: if you find packages in this order:

find_package(VTK REQUIRED)
find_package(ITK REQUIRED)

You can?t real compile anything that needs VTK, because down in the ITK deployment stuff, it calls find_package(VTK) like this:
find_package(VTK COMPONENTS
  vtkCommonCore
  vtkRenderingCore
  vtkRenderingOpenGL
  vtkRenderingFreeType
  vtkInteractionStyle
  vtkIOImage
  vtkImagingSources
  REQUIRED)

Which blows away the larger list of include directories and libraries that the first find_package(VTK REQUIRED) built.

Even better ? or worse ? Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt also include find_package(VTK) ? so ITK tries to import VTK twice, with different module lists.

It doesn?t even help to reverse the order:
find_package(ITK REQUIRED)
find_package(VTK REQUIRED)

because apparently there?s some hangover from the find_package(VTK) inside the ITK CMake deployment files.  The only thing that works is to use COMPONENTS, i.e.

find_package(ITK REQUIRED)
find_package(VTK COMPONENTS vtkCommonCore vtkRenderingAnnotation ? REQUIRED)

Which seems to trigger a proper re-scan and build of the library/include lists.

It gets even worse if you use find_package(SlicerExecutionModel) after find_package(ITK), for the same reason ? SlicerExecutionModel depends on ITK, so it clobbers the include/library lists from the first find_package(ITK).




________________________________
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.
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From bill.lorensen at gmail.com  Tue Sep 30 10:23:36 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Tue, 30 Sep 2014 10:23:36 -0400
Subject: [ITK-dev] find_package issues with ITK and VTK (and
 SlicerExecution Model)
In-Reply-To: <D05024E5.B649%norman-k-williams@uiowa.edu>
References: <D05024E5.B649%norman-k-williams@uiowa.edu>
Message-ID: <CADZJ4hNa4t5jRP=V7cos8U=gV5h-Dt4HB3MnK2s+HeohR-znww@mail.gmail.com>

Here is what I do for the WikiExamples remote module:
find_package(VTK REQUIRED)
  include(${VTK_USE_FILE})
  set(VTK_COMPONENTS ${VTK_LIBRARIES})

  find_package(ITK REQUIRED)
  include(${ITK_USE_FILE})
  set(ITK_LIBRARIES ${ITK_LIBRARIES} ${VTK_COMPONENTS})


On Tue, Sep 30, 2014 at 10:14 AM, Williams, Norman K
<norman-k-williams at uiowa.edu> wrote:
> This is a problem that has been cropping up in our projects that use ITK,
> VTK and SlicerExecutionModel.
>
> You won?t see it UNLESS you turn on the ITKVTK/ITKVtkGlue modules.
>
> The problem is this: if you find packages in this order:
>
> find_package(VTK REQUIRED)
> find_package(ITK REQUIRED)
>
> You can?t real compile anything that needs VTK, because down in the ITK
> deployment stuff, it calls find_package(VTK) like this:
> find_package(VTK COMPONENTS
>   vtkCommonCore
>   vtkRenderingCore
>   vtkRenderingOpenGL
>   vtkRenderingFreeType
>   vtkInteractionStyle
>   vtkIOImage
>   vtkImagingSources
>   REQUIRED)
>
> Which blows away the larger list of include directories and libraries that
> the first find_package(VTK REQUIRED) built.
>
> Even better ? or worse ?
> Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt also include
> find_package(VTK) ? so ITK tries to import VTK twice, with different module
> lists.
>
> It doesn?t even help to reverse the order:
> find_package(ITK REQUIRED)
> find_package(VTK REQUIRED)
>
> because apparently there?s some hangover from the find_package(VTK) inside
> the ITK CMake deployment files.  The only thing that works is to use
> COMPONENTS, i.e.
>
> find_package(ITK REQUIRED)
> find_package(VTK COMPONENTS vtkCommonCore vtkRenderingAnnotation ? REQUIRED)
>
> Which seems to trigger a proper re-scan and build of the library/include
> lists.
>
> It gets even worse if you use find_package(SlicerExecutionModel) after
> find_package(ITK), for the same reason ? SlicerExecutionModel depends on
> ITK, so it clobbers the include/library lists from the first
> find_package(ITK).
>
>
>
>
> ________________________________
> 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
>



-- 
Unpaid intern in BillsBasement at noware dot com

From brad.king at kitware.com  Tue Sep 30 10:48:47 2014
From: brad.king at kitware.com (Brad King)
Date: Tue, 30 Sep 2014 10:48:47 -0400
Subject: [ITK-dev] find_package issues with ITK and VTK (and
 SlicerExecution Model)
In-Reply-To: <D05024E5.B649%norman-k-williams@uiowa.edu>
References: <D05024E5.B649%norman-k-williams@uiowa.edu>
Message-ID: <542AC2CF.7030008@kitware.com>

On 09/30/2014 10:14 AM, Williams, Norman K wrote:
> find_package(VTK REQUIRED)
> find_package(ITK REQUIRED)
> 
> You can?t real compile anything that needs VTK, because down in
> the ITK deployment stuff, it calls find_package(VTK) like this:
[snip]
> Which blows away the larger list of include directories and libraries

One may use the itk_module_config and vtk_module_config macros
from the *ModuleAPI.cmake modules that come with the respective
packages to compute the list of libraries and include dirs for
a given list of components.  All ITKConfig and VTKConfig do with
the list of components is:

 itk_module_config(ITK ${ITK_MODULES_REQUESTED})
 # sets ITK_LIBRARIES, ITK_INCLUDE_DIRS, etc.

and

 vtk_module_config(VTK ${VTK_MODULES_REQUESTED})
 # sets VTK_LIBRARIES, VTK_INCLUDE_DIRS, etc.

One can invoke these directly:

 itk_module_config(ITK ${MY_LIST_OF_ITK_COMPONENTS})
 vtk_module_config(VTK ${MY_LIST_OF_VTK_COMPONENTS})

at any time after the find_package calls.  One could even use
a different prefix:

 itk_module_config(MyITK ${MY_LIST_OF_ITK_COMPONENTS})
 # sets MyITK_LIBRARIES, MyITK_INCLUDE_DIRS, etc.

In the long run the plan is to stop recommending use of component
lists at find_package time and instead use imported targets and
usage requirements:

 http://www.cmake.org/cmake/help/v3.0/manual/cmake-buildsystem.7.html#build-specification-and-usage-requirements

but that will have to wait until we can require CMake 3.0.

-Brad


From blowekamp at mail.nih.gov  Tue Sep 30 11:13:22 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 30 Sep 2014 11:13:22 -0400
Subject: [ITK-dev] find_package issues with ITK and VTK (and
	SlicerExecution Model)
In-Reply-To: <542AC2CF.7030008@kitware.com>
References: <D05024E5.B649%norman-k-williams@uiowa.edu>
 <542AC2CF.7030008@kitware.com>
Message-ID: <F9A14ABD-4073-4628-B143-C0A829F7F9C6@mail.nih.gov>

Brad,

Do you have a suggestion on how to conditionally include a module if it's available? e.g. Use ITKDeprecated if ITK was configure with it?

Thanks,
Brad

On Sep 30, 2014, at 10:48 AM, Brad King <brad.king at kitware.com> wrote:

> On 09/30/2014 10:14 AM, Williams, Norman K wrote:
>> find_package(VTK REQUIRED)
>> find_package(ITK REQUIRED)
>> 
>> You can?t real compile anything that needs VTK, because down in
>> the ITK deployment stuff, it calls find_package(VTK) like this:
> [snip]
>> Which blows away the larger list of include directories and libraries
> 
> One may use the itk_module_config and vtk_module_config macros
> from the *ModuleAPI.cmake modules that come with the respective
> packages to compute the list of libraries and include dirs for
> a given list of components.  All ITKConfig and VTKConfig do with
> the list of components is:
> 
> itk_module_config(ITK ${ITK_MODULES_REQUESTED})
> # sets ITK_LIBRARIES, ITK_INCLUDE_DIRS, etc.
> 
> and
> 
> vtk_module_config(VTK ${VTK_MODULES_REQUESTED})
> # sets VTK_LIBRARIES, VTK_INCLUDE_DIRS, etc.
> 
> One can invoke these directly:
> 
> itk_module_config(ITK ${MY_LIST_OF_ITK_COMPONENTS})
> vtk_module_config(VTK ${MY_LIST_OF_VTK_COMPONENTS})
> 
> at any time after the find_package calls.  One could even use
> a different prefix:
> 
> itk_module_config(MyITK ${MY_LIST_OF_ITK_COMPONENTS})
> # sets MyITK_LIBRARIES, MyITK_INCLUDE_DIRS, etc.
> 
> In the long run the plan is to stop recommending use of component
> lists at find_package time and instead use imported targets and
> usage requirements:
> 
> http://www.cmake.org/cmake/help/v3.0/manual/cmake-buildsystem.7.html#build-specification-and-usage-requirements
> 
> but that will have to wait until we can require CMake 3.0.
> 
> -Brad
> 
> _______________________________________________
> 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 brad.king at kitware.com  Tue Sep 30 11:22:57 2014
From: brad.king at kitware.com (Brad King)
Date: Tue, 30 Sep 2014 11:22:57 -0400
Subject: [ITK-dev] find_package issues with ITK and VTK (and
 SlicerExecution Model)
In-Reply-To: <F9A14ABD-4073-4628-B143-C0A829F7F9C6@mail.nih.gov>
References: <D05024E5.B649%norman-k-williams@uiowa.edu>
 <542AC2CF.7030008@kitware.com>
 <F9A14ABD-4073-4628-B143-C0A829F7F9C6@mail.nih.gov>
Message-ID: <542ACAD1.2040805@kitware.com>

On 09/30/2014 11:13 AM, Bradley Lowekamp wrote:
> Do you have a suggestion on how to conditionally include a
> module if it's available? e.g. Use ITKDeprecated if ITK was
> configure with it?

 find_package(ITK REQUIRED)
 set(MY_ITK_COMPONENTS ...) # list required mods here
 if(";${ITK_MODULES_ENABLED};" MATCHES ";ITKDeprecated;")
   list(APPEND MY_ITK_COMPONENTS ITKDeprecated)
 endif()
 itk_module_config(ITK ${MY_ITK_COMPONENTS})

I think the if() line could also be written

 if(TARGET ITKDeprecated)

but I don't remember off the top of my head whether the
library names and module names always match exactly.

-Brad


From matt.mccormick at kitware.com  Tue Sep 30 12:59:39 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 30 Sep 2014 12:59:39 -0400
Subject: [ITK-dev] find_package issues with ITK and VTK (and
 SlicerExecution Model)
In-Reply-To: <D05024E5.B649%norman-k-williams@uiowa.edu>
References: <D05024E5.B649%norman-k-williams@uiowa.edu>
Message-ID: <CALzTN-Qs6o1YXdzm+4R+g3LXKObKhFpMBrS1a3vb57VxO5scgQ@mail.gmail.com>

Hi Kent,

On Tue, Sep 30, 2014 at 10:14 AM, Williams, Norman K
<norman-k-williams at uiowa.edu> wrote:
> This is a problem that has been cropping up in our projects that use ITK,
> VTK and SlicerExecutionModel.
>
> You won?t see it UNLESS you turn on the ITKVTK/ITKVtkGlue modules.
>
> The problem is this: if you find packages in this order:
>
> find_package(VTK REQUIRED)
> find_package(ITK REQUIRED)
>
> You can?t real compile anything that needs VTK, because down in the ITK
> deployment stuff, it calls find_package(VTK) like this:
> find_package(VTK COMPONENTS
>   vtkCommonCore
>   vtkRenderingCore
>   vtkRenderingOpenGL
>   vtkRenderingFreeType
>   vtkInteractionStyle
>   vtkIOImage
>   vtkImagingSources
>   REQUIRED)
>
> Which blows away the larger list of include directories and libraries that
> the first find_package(VTK REQUIRED) built.
>
> Even better ? or worse ?
> Modules/Segmentation/LevelSetsv4Visualization/CMakeLists.txt also include
> find_package(VTK) ? so ITK tries to import VTK twice, with different module
> lists.
>
> It doesn?t even help to reverse the order:
> find_package(ITK REQUIRED)
> find_package(VTK REQUIRED)
>
> because apparently there?s some hangover from the find_package(VTK) inside
> the ITK CMake deployment files.  The only thing that works is to use
> COMPONENTS, i.e.
>
> find_package(ITK REQUIRED)
> find_package(VTK COMPONENTS vtkCommonCore vtkRenderingAnnotation ? REQUIRED)
>
> Which seems to trigger a proper re-scan and build of the library/include
> lists.

This was discussed in this thread [1].  There does not seem to be
interest at this time to have mixed COMPONENTS / non-COMPONENTS calls
to find_package.  It is also recommended to use the MODULE option to
find_package.  A "newer" version of VTK 6 is also required.

> It gets even worse if you use find_package(SlicerExecutionModel) after
> find_package(ITK), for the same reason ? SlicerExecutionModel depends on
> ITK, so it clobbers the include/library lists from the first
> find_package(ITK).
>

A patch was merged a few days ago that might address this issue [2].
Is this behavior still see with current ITK?

Thanks,
Matt


[1] http://public.kitware.com/pipermail/vtk-developers/2014-September/015376.html

[2] http://review.source.kitware.com/#/c/16963/