From haratron at gmail.com  Fri Jan  2 13:12:34 2015
From: haratron at gmail.com (haratron)
Date: Fri, 2 Jan 2015 20:12:34 +0200
Subject: [ITK-dev] WarpImageFilter wrong output
Message-ID: <CAOJPiNB68Z=u+fGVOP4=wGEOOwWDdM3DXCr9SuHJG+tzHA+MmQ@mail.gmail.com>

Hello and happy new year,

I'm using the WarpImageFilter from here:
http://www.itk.org/Wiki/ITK/Examples/Registration/WarpImageFilter

I have original.png that I'm using as the movingImage and I'm creating
another one ("empty" image filled with white color, size 1800x1800) that is
the fixedImage.

The problem is that a blank image filled with black is created instead of
the warped image that is expected.

original.png : http://i.imgur.com/QQyXgzg.png
output.png: http://i.imgur.com/LkYnZ6n.png

My full WarpImageFilter.cxx file (includes changes from the original
example code):
http://pastebin.com/WNDb2TgM

What am I doing wrong?

John
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From mohammedrashadkm at gmail.com  Wed Jan  7 08:08:53 2015
From: mohammedrashadkm at gmail.com (Rashad M)
Date: Wed, 7 Jan 2015 14:08:53 +0100
Subject: [ITK-dev] cmake variable for itkvcl libraries when linking with ITK
Message-ID: <CANNqv9eT5mNJ0C-2a=W4xTVAe001rpu57xc4LAXkBc4f9mNS1A@mail.gmail.com>

Hello,

When linking with itkvnl libraries from ITK there is a cmake variable that
hold the proper target (ITKVNL_LIBRARIES). This is the proper way to add
ITK vnl modules as dependency for external targets. All this are after
including UseITK.cmake

But what about itk vcl libraries. Ofcourse I could use ITK_VNL_LIBRARIES as
target itkvcl is a dependency for itkvnl.Is there is something similar to
that of vnl like ITK_VCL_LIBRARIES ?


-- 
Regards,
   Rashad
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From matt.mccormick at kitware.com  Wed Jan  7 10:39:22 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 7 Jan 2015 10:39:22 -0500
Subject: [ITK-dev] cmake variable for itkvcl libraries when linking with
	ITK
In-Reply-To: <CANNqv9eT5mNJ0C-2a=W4xTVAe001rpu57xc4LAXkBc4f9mNS1A@mail.gmail.com>
References: <CANNqv9eT5mNJ0C-2a=W4xTVAe001rpu57xc4LAXkBc4f9mNS1A@mail.gmail.com>
Message-ID: <CALzTN-TwiD202_RFL2ZH9M14N-wVcQS649bwChWL3sdxza=kWw@mail.gmail.com>

Hi Rashad,

The itkvcl library is created [1] as part of the ITKVNL [2] module, so
it wiill be listed in the ITKVNL_LIBRARIES CMake variable as described
here [3].

HTH,
Matt

[1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt;h=bfee21e9d32342f7c3b5bb720991978a58acbddc;hb=HEAD#l362


[2] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/VNL/itk-module.cmake;h=353e0b168543723bf70d1aae57c4e98c65ed8e05;hb=HEAD#l5


[3] http://itk.org/gitweb?p=ITK.git;a=blob;f=CMake/ITKModuleAPI.cmake;h=304d864e957a28bc28df1bb49f7d06ebbd641fdd;hb=HEAD#l41

On Wed, Jan 7, 2015 at 8:08 AM, Rashad M <mohammedrashadkm at gmail.com> wrote:
> Hello,
>
> When linking with itkvnl libraries from ITK there is a cmake variable that
> hold the proper target (ITKVNL_LIBRARIES). This is the proper way to add ITK
> vnl modules as dependency for external targets. All this are after including
> UseITK.cmake
>
> But what about itk vcl libraries. Ofcourse I could use ITK_VNL_LIBRARIES as
> target itkvcl is a dependency for itkvnl.Is there is something similar to
> that of vnl like ITK_VCL_LIBRARIES ?
>
>
> --
> Regards,
>    Rashad
>
> _______________________________________________
> 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 mohammedrashadkm at gmail.com  Wed Jan  7 12:40:17 2015
From: mohammedrashadkm at gmail.com (Rashad M)
Date: Wed, 7 Jan 2015 18:40:17 +0100
Subject: [ITK-dev] cmake variable for itkvcl libraries when linking with
	ITK
In-Reply-To: <CALzTN-TwiD202_RFL2ZH9M14N-wVcQS649bwChWL3sdxza=kWw@mail.gmail.com>
References: <CANNqv9eT5mNJ0C-2a=W4xTVAe001rpu57xc4LAXkBc4f9mNS1A@mail.gmail.com>
 <CALzTN-TwiD202_RFL2ZH9M14N-wVcQS649bwChWL3sdxza=kWw@mail.gmail.com>
Message-ID: <CANNqv9fVZsRJ2Ctu=SpgKeWoR6++nA685tFMzVT7MkOVnfvD1Q@mail.gmail.com>

On Wed, Jan 7, 2015 at 4:39 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Rashad,
>
> The itkvcl library is created [1] as part of the ITKVNL [2] module, so
> it wiill be listed in the ITKVNL_LIBRARIES CMake variable as described
> here [3].
>

Thanks Matt. So itkvcl should be changed to ITKVNL_LIBRARIES in cmake. I
think I got 'cannot find -litkvcl' only when linking with external vxl


> HTH,
> Matt
>
> [1]
> http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/VNL/src/vxl/vcl/CMakeLists.txt;h=bfee21e9d32342f7c3b5bb720991978a58acbddc;hb=HEAD#l362
>
>
> [2]
> http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/ThirdParty/VNL/itk-module.cmake;h=353e0b168543723bf70d1aae57c4e98c65ed8e05;hb=HEAD#l5
>
>
> [3]
> http://itk.org/gitweb?p=ITK.git;a=blob;f=CMake/ITKModuleAPI.cmake;h=304d864e957a28bc28df1bb49f7d06ebbd641fdd;hb=HEAD#l41
>
> On Wed, Jan 7, 2015 at 8:08 AM, Rashad M <mohammedrashadkm at gmail.com>
> wrote:
> > Hello,
> >
> > When linking with itkvnl libraries from ITK there is a cmake variable
> that
> > hold the proper target (ITKVNL_LIBRARIES). This is the proper way to add
> ITK
> > vnl modules as dependency for external targets. All this are after
> including
> > UseITK.cmake
> >
> > But what about itk vcl libraries. Ofcourse I could use ITK_VNL_LIBRARIES
> as
> > target itkvcl is a dependency for itkvnl.Is there is something similar to
> > that of vnl like ITK_VCL_LIBRARIES ?
> >
> >
> > --
> > Regards,
> >    Rashad
> >
> > _______________________________________________
> > 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,
   Rashad
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From matt.mccormick at kitware.com  Wed Jan  7 13:05:30 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 7 Jan 2015 13:05:30 -0500
Subject: [ITK-dev] cmake variable for itkvcl libraries when linking with
	ITK
In-Reply-To: <CANNqv9fVZsRJ2Ctu=SpgKeWoR6++nA685tFMzVT7MkOVnfvD1Q@mail.gmail.com>
References: <CANNqv9eT5mNJ0C-2a=W4xTVAe001rpu57xc4LAXkBc4f9mNS1A@mail.gmail.com>
 <CALzTN-TwiD202_RFL2ZH9M14N-wVcQS649bwChWL3sdxza=kWw@mail.gmail.com>
 <CANNqv9fVZsRJ2Ctu=SpgKeWoR6++nA685tFMzVT7MkOVnfvD1Q@mail.gmail.com>
Message-ID: <CALzTN-TLaHNZJWvn7fSoMorf0HR2R7hNFXjf-sAWbY+P1=M2_Q@mail.gmail.com>

On Wed, Jan 7, 2015 at 12:40 PM, Rashad M <mohammedrashadkm at gmail.com> wrote:
>
>
> On Wed, Jan 7, 2015 at 4:39 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Hi Rashad,
>>
>> The itkvcl library is created [1] as part of the ITKVNL [2] module, so
>> it wiill be listed in the ITKVNL_LIBRARIES CMake variable as described
>> here [3].
>
>
> Thanks Matt. So itkvcl should be changed to ITKVNL_LIBRARIES in cmake. I
> think I got 'cannot find -litkvcl' only when linking with external vxl
>

Yes, that should work.

Matt

From matt.mccormick at kitware.com  Wed Jan  7 14:47:05 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 7 Jan 2015 14:47:05 -0500
Subject: [ITK-dev] Discuss what's new ITK in ITK 4.7.0,
	what is coming in ITK 4.8.0
Message-ID: <CALzTN-S9zHv+Q28DCnh_7CCz015uAtW5oDPHcKQJgjXtJgwwRQ@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.  Following the recent
4.7.0, this is also a great time to discuss what was new in ITK 4.7.0,
and what to work on for ITK 4.8.0.


On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/u/1/events/cmapnnf3gu3adnsdpfjr93a6hr8?authkey=CMbjm5aD2rO68gE


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

  https://plus.google.com/u/1/events/cntel7ikg752bo6lmpen8ade22c?authkey=CM2q5_2Bva6asgE


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

  585-632-6296

Enter pin:

  31423



To get regular invites to these events, join the ITK Bar Camp G+ Community:

  https://plus.google.com/u/0/communities/111375098792764998322



All are welcome.  Hope to talk to you then!

From blowekamp at mail.nih.gov  Tue Jan 13 10:08:44 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 13 Jan 2015 10:08:44 -0500
Subject: [ITK-dev] Versor Transform Only Work with Jacobian Scales Estimator
Message-ID: <5FA06B8D-CA2D-41AB-BC6F-E99B12B3DB1D@mail.nih.gov>

Hello,

After experimentation in SimpleITK, I have come to the realization that only the RegistrationParameterScaleFromJacobian is compatible with the Versor based transforms. This is similar to only using the RegularStepGradientDescentOptimizerv4 only correctly normalizing the step for the non-euclidian space. I believe the Index and Physical space don't correctly account for the non-euclidian versor space to the scale estimates are incorrect.


Where should this be documented?

Brad

From matt.mccormick at kitware.com  Wed Jan 14 10:50:20 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 14 Jan 2015 10:50:20 -0500
Subject: [ITK-dev] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-R+uTMDeyTjZiSf0hb5rruo8gOuybEFVK2nWyzPOSc=Ag@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), 1:00 PM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/events/ctg03o79vsd0irnhpugquuatfoc


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

  https://plus.google.com/events/cidukboj4bn3k2ndetr1rqdk3a0


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

  585-632-6296

Enter pin:

  31423



To get regular invites to these events, join the ITK Bar Camp G+ Community:

  https://plus.google.com/u/0/communities/111375098792764998322



All are welcome.  Hope to talk to you then!

From matt.mccormick at kitware.com  Wed Jan 14 12:02:19 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 14 Jan 2015 12:02:19 -0500
Subject: [ITK-dev] Registering for New Gerrit Accounts
Message-ID: <CALzTN-RkfUr77cHyLqr=fUSRY7VZ9BBDDvbfrzMHFB54VRj73Q@mail.gmail.com>

Google is currently dropping support for OpenID authentication through
Google accounts.
 While currently registered Gerrit users '*can still use their
account'*, new Gerrit account
 registrations with Google currently face the error:

   400. That's an error. OpenID auth request contains an unregistered domain.

See the attached image for a screenshot.

 We are currently upgrading the Gerrit infrastructure, and
GitHub-based authentifications will soon
 be possible. Until that time, it is suggested that ''new'' Gerrit
accounts made with a Yahoo account.

Thanks for your patience and sorry for any inconvenience.

Matt
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From matt.mccormick at kitware.com  Wed Jan 21 15:40:44 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 21 Jan 2015 15:40:44 -0500
Subject: [ITK-dev] [ITK] Files not found
In-Reply-To: <CAFxdfT1VFe_0dsKY+dsXxabr5oHs5p91tvkzyxwKV4H10i9W-A@mail.gmail.com>
References: <CAFxdfT1VFe_0dsKY+dsXxabr5oHs5p91tvkzyxwKV4H10i9W-A@mail.gmail.com>
Message-ID: <CALzTN-S-XpuJUJSXeOKxDibJU50=1mNVoPjQOasURjD0FuJ73A@mail.gmail.com>

Hi Edward,

It looks like you are trying to use a project that had a CMake
configuration for ITKv3.  To update the configuration for ITKv4,
change

target_link_libraries(myexecutable
  ITKAlgorithms
  ITKIO
  )

with

target_link_libraries(myexecutable
  ${ITK_LIBRARIES}
  )

HTH,
Matt

On Wed, Jan 21, 2015 at 3:26 PM, Edward Fl?rez Pacheco
<ted.florez at gmail.com> wrote:
> Hi everyone
>
> I am a new ITK user.
> Currently, I am using a set of algorithms that use ITK.
> I installed the InsightToolkit - version 4.6.1 but I had these troubles:
>
> CMakeFiles/DicomSeriesReadImageWrite2.dir/DicomSeriesReadImageWrite2.cxx.o
> Linking CXX executable DicomSeriesReadImageWrite2
> /usr/bin/ld: cannot find -lITKAlgorithms
> /usr/bin/ld: cannot find -lITKIO
> collect2: ld returned 1 exit status
> make[2]: ** [DicomSeriesReadImageWrite2] Erro 1
> make[1]: ** [CMakeFiles/DicomSeriesReadImageWrite2.dir/all] Erro 2
> make: ** [all] Erro 2
>
> If anyone has some idea about these issues and can give me some help I'll be
> very thankful.
> Thank you in advance.
>
> Best regards.
>
> --
> Edward Fl?rez
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From matt.mccormick at kitware.com  Wed Jan 21 17:25:12 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 21 Jan 2015 17:25:12 -0500
Subject: [ITK-dev] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-S1RznTTo97hT4QbwrVTDJKeM1_F6MBO=u0wDNwm2zTFw@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), 1:00 PM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/events/cjudsaidlnb7v4tpiob79q92n8s


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

  https://plus.google.com/events/c4jvg33epbvaldg25skbm81fag4


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

  585-632-6296

Enter pin:

  31423



To get regular invites to these events, join the ITK Bar Camp G+ Community:

  https://plus.google.com/u/0/communities/111375098792764998322



All are welcome.  Hope to talk to you then!

From matt.mccormick at kitware.com  Thu Jan 29 14:04:30 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 29 Jan 2015 14:04:30 -0500
Subject: [ITK-dev] [ANNOUNCE] ITK Software Guide hardcopies are available on
	Amazon!
Message-ID: <CALzTN-QcHsKttuS87sWhMubMODeGUycs_7HwYyjw4Zs=wwcHWg@mail.gmail.com>

Hardcopies of The ITK Software Guide are available on Amazon!


Book 1: http://www.amazon.com/ITK-Software-Guide-Book-Introduction/dp/1930934270/

Book 2: http://www.amazon.com/ITK-Software-Guide-Book-Functionality/dp/1930934289/


Thanks to everyone who helped make this happen!


New versions of the book will be available with subsequent releases.
If you would like to contribute to the Guide, see

  http://itk.org/gitweb?p=ITKSoftwareGuide.git;a=blob;f=README.md;h=eadf34576971b36c6f1c64c9f9590d7194fa4463;hb=HEAD

From hobbsk at ohio.edu  Thu Jan 29 18:18:10 2015
From: hobbsk at ohio.edu (Kevin H. Hobbs)
Date: Thu, 29 Jan 2015 18:18:10 -0500
Subject: [ITK-dev] Function-style preprocessor definitions
Message-ID: <54CABFB2.8080309@ohio.edu>

I have a very simple test case that is broken on bubbles (a host that
submits a nightly dashboard build)

I'm using nightly ITK and nightly CMake

CMakeLists.txt :

  cmake_minimum_required( VERSION 2.8.7 )
  project( Testi_prog )

  find_package( ITK )
  include( ${ITK_USE_FILE} )

  add_executable( test_prog test_prog.cxx )
  target_link_libraries( test_prog )

test_prog.cxx:

  int main( int argc, char** argv)
  {
    return 0;
  }

The build goes fine with the :

  find_package( ITK )
  include( ${ITK_USE_FILE} )

but as soon as those lines are in I get :

WARNING: Function-style preprocessor definitions may not be passed on
the compiler
 command line because many compilers do not support it.
 CMake is dropping a preprocessor definition: (
 Consider defining the macro in a (configured) header file.


 WARNING: Function-style preprocessor definitions may not be passed on
the compiler
 command line because many compilers do not support it.
 CMake is dropping a preprocessor definition: (
 Consider defining the macro in a (configured) header file.

from ccmake and then :

Scanning dependencies of target test_prog
[100%] Building CXX object CMakeFiles/test_prog.dir/test_prog.cxx.o
/bin/sh: -c: line 0: syntax error near unexpected token `)'
/bin/sh: -c: line 0: `/usr/lib64/ccache/c++   -D)
-DITK_IO_FACTORY_REGISTER_MANAGER....

from make

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From hobbsk at ohio.edu  Thu Jan 29 18:28:06 2015
From: hobbsk at ohio.edu (Kevin H. Hobbs)
Date: Thu, 29 Jan 2015 18:28:06 -0500
Subject: [ITK-dev] Function-style preprocessor definitions
In-Reply-To: <54CABFB2.8080309@ohio.edu>
References: <54CABFB2.8080309@ohio.edu>
Message-ID: <54CAC206.6020105@ohio.edu>

On 01/29/2015 06:18 PM, Kevin H. Hobbs wrote:
> The build goes fine with the :
> 
>   find_package( ITK )
>   include( ${ITK_USE_FILE} )

The build goes fine _without_ these lines.

The build also goes fine on my other machine which submits a dashboard
build but without wrapping turned on.

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From mathieu.malaterre at gmail.com  Fri Jan 30 03:51:25 2015
From: mathieu.malaterre at gmail.com (Mathieu Malaterre)
Date: Fri, 30 Jan 2015 09:51:25 +0100
Subject: [ITK-dev] [ANNOUNCE] ITK Software Guide hardcopies are
 available on Amazon!
In-Reply-To: <CALzTN-QcHsKttuS87sWhMubMODeGUycs_7HwYyjw4Zs=wwcHWg@mail.gmail.com>
References: <CALzTN-QcHsKttuS87sWhMubMODeGUycs_7HwYyjw4Zs=wwcHWg@mail.gmail.com>
Message-ID: <CA+7wUsz1Wkd+wVYy8__9yNKV-j1m9GXmC-dYy09DXAkgCKiW8A@mail.gmail.com>

On Thu, Jan 29, 2015 at 8:04 PM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> Hardcopies of The ITK Software Guide are available on Amazon!
>
>
> Book 1: http://www.amazon.com/ITK-Software-Guide-Book-Introduction/dp/1930934270/
>
> Book 2: http://www.amazon.com/ITK-Software-Guide-Book-Functionality/dp/1930934289/
>
>
> Thanks to everyone who helped make this happen!

If you do so, don't forget to set a charity at smile.amazon.com.

For example some people can pick: Software In The Public Interest Inc
[*] among the possible charities.

https://en.wikipedia.org/wiki/Software_in_the_Public_Interest

2cts

From blowekamp at mail.nih.gov  Fri Jan 30 09:16:33 2015
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Fri, 30 Jan 2015 09:16:33 -0500
Subject: [ITK-dev] Reading BSplineDeformableTransform with out V3
	Compatibility
Message-ID: <4ED50C22-6805-47B5-BAA4-AE924BD18B10@mail.nih.gov>

Hello,

I would like suggest that we still support reading the BSplineDeformableTransform by default even when V3 compatibility is disabled [1], to better support ITK ability to read older transform.

The thought is that may be we should still support reading the older transform.

Here is the related Slicer issue:
https://github.com/Slicer/Slicer/pull/227

The registering of these older transforms needs to be done in Slicer on ITK.


Thought?
Brad



[1] https://github.com/InsightSoftwareConsortium/ITK/blob/f02a176972ad4f4266cf8ae20b498c10c4218cd0/Modules/IO/TransformBase/src/itkTransformFactoryBase.cxx#L98-L101

From hobbsk at ohio.edu  Fri Jan 30 12:54:53 2015
From: hobbsk at ohio.edu (Kevin H. Hobbs)
Date: Fri, 30 Jan 2015 12:54:53 -0500
Subject: [ITK-dev] Function-style preprocessor definitions
In-Reply-To: <54CABFB2.8080309@ohio.edu>
References: <54CABFB2.8080309@ohio.edu>
Message-ID: <54CBC56D.5070200@ohio.edu>


The problem goes away when I disable :

Module_ITKVtkGlue:BOOL=ON

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From hobbsk at ohio.edu  Fri Jan 30 13:08:39 2015
From: hobbsk at ohio.edu (Kevin H. Hobbs)
Date: Fri, 30 Jan 2015 13:08:39 -0500
Subject: [ITK-dev] Function-style preprocessor definitions
In-Reply-To: <54CABFB2.8080309@ohio.edu>
References: <54CABFB2.8080309@ohio.edu>
Message-ID: <54CBC8A7.2030500@ohio.edu>

D?enan,

This seems to be related to vtkGlue.

Could it be related to your recent commit?


On 01/29/2015 06:18 PM, Kevin H. Hobbs wrote:
> I have a very simple test case that is broken on bubbles (a host that
> submits a nightly dashboard build)
> 
> I'm using nightly ITK and nightly CMake
> 
> CMakeLists.txt :
> 
>   cmake_minimum_required( VERSION 2.8.7 )
>   project( Testi_prog )
> 
>   find_package( ITK )
>   include( ${ITK_USE_FILE} )
> 
>   add_executable( test_prog test_prog.cxx )
>   target_link_libraries( test_prog )
> 
> test_prog.cxx:
> 
>   int main( int argc, char** argv)
>   {
>     return 0;
>   }
> 
> The build goes fine with the :
> 
>   find_package( ITK )
>   include( ${ITK_USE_FILE} )
> 
> but as soon as those lines are in I get :
> 
> WARNING: Function-style preprocessor definitions may not be passed on
> the compiler
>  command line because many compilers do not support it.
>  CMake is dropping a preprocessor definition: (
>  Consider defining the macro in a (configured) header file.
> 
> 
>  WARNING: Function-style preprocessor definitions may not be passed on
> the compiler
>  command line because many compilers do not support it.
>  CMake is dropping a preprocessor definition: (
>  Consider defining the macro in a (configured) header file.
> 
> from ccmake and then :
> 
> Scanning dependencies of target test_prog
> [100%] Building CXX object CMakeFiles/test_prog.dir/test_prog.cxx.o
> /bin/sh: -c: line 0: syntax error near unexpected token `)'
> /bin/sh: -c: line 0: `/usr/lib64/ccache/c++   -D)
> -DITK_IO_FACTORY_REGISTER_MANAGER....
> 
> from make
> 


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From hobbsk at ohio.edu  Fri Jan 30 13:50:51 2015
From: hobbsk at ohio.edu (Kevin H. Hobbs)
Date: Fri, 30 Jan 2015 13:50:51 -0500
Subject: [ITK-dev] Function-style preprocessor definitions
In-Reply-To: <CAPmoeGa0-DbKHnpEwCFaqhQZEc6YzOgj+kTGW+N4tiNvT3fLsg@mail.gmail.com>
References: <54CABFB2.8080309@ohio.edu>	<54CBC8A7.2030500@ohio.edu>
 <CAPmoeGa0-DbKHnpEwCFaqhQZEc6YzOgj+kTGW+N4tiNvT3fLsg@mail.gmail.com>
Message-ID: <54CBD28B.8010603@ohio.edu>

On 01/30/2015 01:18 PM, Dzenan Zukic wrote:
> /bin/sh: -c: line 0: syntax error near unexpected token `)'
>> /bin/sh: -c: line 0: `/usr/lib64/ccache/c++   -D)

I think it's the -D) that's causing the problem.

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From hans-johnson at uiowa.edu  Fri Jan 30 14:53:29 2015
From: hans-johnson at uiowa.edu (Johnson, Hans J)
Date: Fri, 30 Jan 2015 19:53:29 +0000
Subject: [ITK-dev] Function-style preprocessor definitions
In-Reply-To: <54CBD28B.8010603@ohio.edu>
References: <54CABFB2.8080309@ohio.edu> <54CBC8A7.2030500@ohio.edu>
 <CAPmoeGa0-DbKHnpEwCFaqhQZEc6YzOgj+kTGW+N4tiNvT3fLsg@mail.gmail.com>
 <54CBD28B.8010603@ohio.edu>
Message-ID: <5F91E259-B96D-42DE-A6EB-9A9B0661001C@uiowa.edu>

I too have been fighting with this problem for several days.  I can not seem to track it down.

in a file called flags.make, there is a line:

CXX_DEFINES = -D) -DITK_IOFACTORY_REGISTERMANGER ?.< other stuff>

This happens when building agains VTK and ITK, but with ITK I have VTKGlue turned off.

It has been very hard to track down.  I don?t understand where the ?CXX_DEFINES? are being set.


Additonally, a related error message shows up during configuration:

WARNING:  Function-style preprocessor definitions may not be passed on the compiler command line because many compilers do not support it.
CMake is dropping a preprocessor definiton: (
Consider defining the macro in a (configured) header file.


I have been trying to figure out what is going on for almost a day now.


========================================================================
Hans J. Johnson, Ph.D.,  Associate Professor
Electrical and Computer Engineering (Primary), Biomedical Engineering, Psychiatry
hans-johnson at uiowa.edu
(319) 621 7185 (cell)
(319) 384 3538  ECE Phone (Primary)
(319) 353 8587 Psychiatry Phone (Secondary)

4613 Seamans Center
Iowa City, IA 52242

> On Jan 30, 2015, at 12:50 PM, Kevin H. Hobbs <hobbsk at ohio.edu> wrote:
>
> On 01/30/2015 01:18 PM, Dzenan Zukic wrote:
>> /bin/sh: -c: line 0: syntax error near unexpected token `)'
>>> /bin/sh: -c: line 0: `/usr/lib64/ccache/c++   -D)
>
> I think it's the -D) that's causing the problem.
>
> _______________________________________________
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>
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>
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>
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>
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________________________________
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 matt.mccormick at kitware.com  Fri Jan 30 15:00:31 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 30 Jan 2015 15:00:31 -0500
Subject: [ITK-dev] [ANNOUNCE] ITK Software Guide hardcopies are
 available on Amazon!
In-Reply-To: <CA+7wUsz1Wkd+wVYy8__9yNKV-j1m9GXmC-dYy09DXAkgCKiW8A@mail.gmail.com>
References: <CALzTN-QcHsKttuS87sWhMubMODeGUycs_7HwYyjw4Zs=wwcHWg@mail.gmail.com>
 <CA+7wUsz1Wkd+wVYy8__9yNKV-j1m9GXmC-dYy09DXAkgCKiW8A@mail.gmail.com>
Message-ID: <CALzTN-SG631RJoJDtCrhbTUxPpOe93XCwp71KkrpUErAqrrTTg@mail.gmail.com>

On Fri, Jan 30, 2015 at 3:51 AM, Mathieu Malaterre
<mathieu.malaterre at gmail.com> wrote:
> On Thu, Jan 29, 2015 at 8:04 PM, Matt McCormick
> <matt.mccormick at kitware.com> wrote:
>> Hardcopies of The ITK Software Guide are available on Amazon!
>>
>>
>> Book 1: http://www.amazon.com/ITK-Software-Guide-Book-Introduction/dp/1930934270/
>>
>> Book 2: http://www.amazon.com/ITK-Software-Guide-Book-Functionality/dp/1930934289/
>>
>>
>> Thanks to everyone who helped make this happen!
>
> If you do so, don't forget to set a charity at smile.amazon.com.
>
> For example some people can pick: Software In The Public Interest Inc
> [*] among the possible charities.
>
> https://en.wikipedia.org/wiki/Software_in_the_Public_Interest

+1!


PS. For community members in Europe, the books are also available on
Amazon's sites for Spain, the United Kingdom, Germany, France, and
Italy. Please see the website for the links:

  http://www.kitware.com/products/books.php

From brad.king at kitware.com  Fri Jan 30 16:06:57 2015
From: brad.king at kitware.com (Brad King)
Date: Fri, 30 Jan 2015 16:06:57 -0500
Subject: [ITK-dev] Function-style preprocessor definitions
In-Reply-To: <5F91E259-B96D-42DE-A6EB-9A9B0661001C@uiowa.edu>
References: <54CABFB2.8080309@ohio.edu> <54CBC8A7.2030500@ohio.edu>
 <CAPmoeGa0-DbKHnpEwCFaqhQZEc6YzOgj+kTGW+N4tiNvT3fLsg@mail.gmail.com>
 <54CBD28B.8010603@ohio.edu> <5F91E259-B96D-42DE-A6EB-9A9B0661001C@uiowa.edu>
Message-ID: <54CBF271.5030707@kitware.com>

On 1/30/2015 2:53 PM, Johnson, Hans J wrote:
> CXX_DEFINES = -D) -DITK_IOFACTORY_REGISTERMANGER ?.< other stuff>
> 
> This happens when building agains VTK and ITK, but with ITK I have
> VTKGlue turned off.

I cannot reproduce this with a basic setup of the case described.

What versions (Git commit sha1s) of ITK and VTK did you build?
What version of CMake are you using?
What configuration options were given to each of ITK and VTK?
Can you reproduce it with a simple CMakeLists.txt for the app code?

Thanks,
-Brad

From matt.mccormick at kitware.com  Fri Jan 30 16:14:20 2015
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 30 Jan 2015 16:14:20 -0500
Subject: [ITK-dev] Function-style preprocessor definitions
In-Reply-To: <54CBF271.5030707@kitware.com>
References: <54CABFB2.8080309@ohio.edu> <54CBC8A7.2030500@ohio.edu>
 <CAPmoeGa0-DbKHnpEwCFaqhQZEc6YzOgj+kTGW+N4tiNvT3fLsg@mail.gmail.com>
 <54CBD28B.8010603@ohio.edu>
 <5F91E259-B96D-42DE-A6EB-9A9B0661001C@uiowa.edu>
 <54CBF271.5030707@kitware.com>
Message-ID: <CALzTN-Qyj7mvLY6yLRvgc2GMhJi7KMszZ2CB0D68O_sCHyS4tw@mail.gmail.com>

On Fri, Jan 30, 2015 at 4:06 PM, Brad King <brad.king at kitware.com> wrote:
> On 1/30/2015 2:53 PM, Johnson, Hans J wrote:
>> CXX_DEFINES = -D) -DITK_IOFACTORY_REGISTERMANGER ?.< other stuff>
>>
>> This happens when building agains VTK and ITK, but with ITK I have
>> VTKGlue turned off.
>
> I cannot reproduce this with a basic setup of the case described.
>
> What versions (Git commit sha1s) of ITK and VTK did you build?
> What version of CMake are you using?
> What configuration options were given to each of ITK and VTK?
> Can you reproduce it with a simple CMakeLists.txt for the app code?

I have been able to reproduce it.  It seems to be related to this change:

  http://review.source.kitware.com/#/c/18944/1

I have ITKVtkGlue ON, ITK_WRAP_PYTHON ON (although I do not know if
they are both required).

It happens with both CMake master and CMake 3.1.0 (although I get two
WARNINGS with CMake master and a single warning with CMake 3.1.0).

Without the above change, errors occur on Windows, when
${ITKVtkGlue_VTK_DEFINITIONS} has content.  On Unix, when it does not
have content, it appears to cause issues with the above change.

What is the best approach here?

Thanks,
Matt

From brad.king at kitware.com  Fri Jan 30 16:43:16 2015
From: brad.king at kitware.com (Brad King)
Date: Fri, 30 Jan 2015 16:43:16 -0500
Subject: [ITK-dev] Function-style preprocessor definitions
In-Reply-To: <CALzTN-Qyj7mvLY6yLRvgc2GMhJi7KMszZ2CB0D68O_sCHyS4tw@mail.gmail.com>
References: <54CABFB2.8080309@ohio.edu>	<54CBC8A7.2030500@ohio.edu>	<CAPmoeGa0-DbKHnpEwCFaqhQZEc6YzOgj+kTGW+N4tiNvT3fLsg@mail.gmail.com>	<54CBD28B.8010603@ohio.edu>	<5F91E259-B96D-42DE-A6EB-9A9B0661001C@uiowa.edu>	<54CBF271.5030707@kitware.com>
 <CALzTN-Qyj7mvLY6yLRvgc2GMhJi7KMszZ2CB0D68O_sCHyS4tw@mail.gmail.com>
Message-ID: <54CBFAF4.400@kitware.com>

On 1/30/2015 4:14 PM, Matt McCormick wrote:
> I have been able to reproduce it.  It seems to be related to this change:
> 
>   http://review.source.kitware.com/#/c/18944/1
> 
> Without the above change, errors occur on Windows, when
> ${ITKVtkGlue_VTK_DEFINITIONS} has content.  On Unix, when it does not
> have content, it appears to cause issues with the above change.

The problem is that the variable should not be evaluated during
generation.  A literal reference to the variable should be generated.
Here is a fix:

 http://review.source.kitware.com/19065

-Brad

From hobbsk at ohio.edu  Fri Jan 30 17:43:54 2015
From: hobbsk at ohio.edu (Kevin H. Hobbs)
Date: Fri, 30 Jan 2015 17:43:54 -0500
Subject: [ITK-dev] Function-style preprocessor definitions
In-Reply-To: <54CBFAF4.400@kitware.com>
References: <54CABFB2.8080309@ohio.edu>	<54CBC8A7.2030500@ohio.edu>	<CAPmoeGa0-DbKHnpEwCFaqhQZEc6YzOgj+kTGW+N4tiNvT3fLsg@mail.gmail.com>	<54CBD28B.8010603@ohio.edu>	<5F91E259-B96D-42DE-A6EB-9A9B0661001C@uiowa.edu>	<54CBF271.5030707@kitware.com>
 <CALzTN-Qyj7mvLY6yLRvgc2GMhJi7KMszZ2CB0D68O_sCHyS4tw@mail.gmail.com>
 <54CBFAF4.400@kitware.com>
Message-ID: <54CC092A.9030001@ohio.edu>

On 01/30/2015 04:43 PM, Brad King wrote:
> Here is a fix:
> 
>  http://review.source.kitware.com/19065
> 

Thank you Brad!

I see this has been merged.

I'll check in the morning if my code builds against nightly ITK.


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From hans-johnson at uiowa.edu  Fri Jan 30 17:46:22 2015
From: hans-johnson at uiowa.edu (Johnson, Hans J)
Date: Fri, 30 Jan 2015 22:46:22 +0000
Subject: [ITK-dev] Function-style preprocessor definitions
In-Reply-To: <54CBFAF4.400@kitware.com>
References: <54CABFB2.8080309@ohio.edu> <54CBC8A7.2030500@ohio.edu>
 <CAPmoeGa0-DbKHnpEwCFaqhQZEc6YzOgj+kTGW+N4tiNvT3fLsg@mail.gmail.com>
 <54CBD28B.8010603@ohio.edu> <5F91E259-B96D-42DE-A6EB-9A9B0661001C@uiowa.edu>
 <54CBF271.5030707@kitware.com>
 <CALzTN-Qyj7mvLY6yLRvgc2GMhJi7KMszZ2CB0D68O_sCHyS4tw@mail.gmail.com>
 <54CBFAF4.400@kitware.com>
Message-ID: <C786494A-551E-402E-86F7-AC720484A862@uiowa.edu>

THANK YOU ALL!

I was looking all over VTK code to try to figure out what was wrong.  It is GREAT that you found the real culprit.

Hans

========================================================================
Hans J. Johnson, Ph.D.,  Associate Professor
Electrical and Computer Engineering (Primary), Biomedical Engineering, Psychiatry
hans-johnson at uiowa.edu
(319) 621 7185 (cell)
(319) 384 3538  ECE Phone (Primary)
(319) 353 8587 Psychiatry Phone (Secondary)

4613 Seamans Center
Iowa City, IA 52242

> On Jan 30, 2015, at 3:43 PM, Brad King <brad.king at kitware.com> wrote:
>
> On 1/30/2015 4:14 PM, Matt McCormick wrote:
>> I have been able to reproduce it.  It seems to be related to this change:
>>
>>  http://review.source.kitware.com/#/c/18944/1
>>
>> Without the above change, errors occur on Windows, when
>> ${ITKVtkGlue_VTK_DEFINITIONS} has content.  On Unix, when it does not
>> have content, it appears to cause issues with the above change.
>
> The problem is that the variable should not be evaluated during
> generation.  A literal reference to the variable should be generated.
> Here is a fix:
>
> http://review.source.kitware.com/19065
>
> -Brad



________________________________
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.
________________________________