From simon.esneault at gmail.com  Mon Dec  1 06:54:43 2014
From: simon.esneault at gmail.com (Simon ESNEAULT)
Date: Mon, 1 Dec 2014 12:54:43 +0100
Subject: [ITK-users] Exception in itk::ResampleImageFilter multithreaded
 part after ITK migration from 3.20.1 to 4.6.1
Message-ID: <CAC9gB0DnSC2j9RMTt6gBTPK4dj4w-BZEczx=67xf-oe8FVD2-g@mail.gmail.com>

Hello ITK community

After the migration from ITK 3.20.1 to ITK 4.6.1, I'm getting a runtime
exception when using itk::ResampleImageFilter in our framework. The output
looks like this :

Problem during Resample filtering:
D:\Dev\DevCpp-Qt5\cmake-externals\ITK\src\Modules\Core\Common\src\itkMultiThreader.cxx:358:
itk::ERROR: MultiThreader(31CAAD18): Exception occurred during
SingleMethodExecute
c:\dev\Dev_qt5\externals\itk-4.6.1\win32\include\itkImageSource.hxx:267:
itk::ERROR: ResampleImageFilter(31AC2E90): Subclass should override this
method!!!
The signature of ThreadedGenerateData() has been changed in ITK v4 to use
the new ThreadIdType.
ResampleImageFilter::ThreadedGenerateData() might need to be updated to
used it.

That is weird, because the itkResampleImageFilter is the one delivered with
ITK 4.6.1, so it must have followed the API changed ...

The context is :
Visual Studio 2013 community, 32 bit build, ITK build in shared library
mode. That's quite a big project, with VTK, Qt, OpenCV, DCMTK, zlib ...
I'm not using cmake in the usual way (ie no find_package(ITK)
include(${ITK_USE_FILE})
) but we list the libraries and includes. I know there are some factories
to register in that case, we're doing this in the main.cpp :
itk::TransformFactoryBase::RegisterDefaultTransforms();
itk::PNGImageIOFactory::RegisterOneFactory();
itk::MetaImageIOFactory::RegisterOneFactory();
itk::NrrdImageIOFactory::RegisterOneFactory();

Am I missing some others factories to register in order to run properly the
resampleImageFilter ?
Anyone else had a similar runtime exception with a native ITK filte, or
know what would raise such an exception ?

Thanks

-- 
------------------------------------------------------------------
Simon Esneault
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From fdrakopo at gmail.com  Mon Dec  1 11:56:47 2014
From: fdrakopo at gmail.com (Fotis Drakopoulos)
Date: Mon, 1 Dec 2014 11:56:47 -0500
Subject: [ITK-users] [ITK-dev]  Problem reading a big nifti volume.
In-Reply-To: <CALzTN-RNFaynep_vAhDu2NwNUsuo696SErYZYGn7bGOpaE3kVQ@mail.gmail.com>
References: <CAG6AjROMWzAEWptqC3XmamwqDmwPc88d2YDup84tkDg20ZJdxw@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E826D4E43@uxcn10-tdc06.UoA.auckland.ac.nz>
 <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov>
 <CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com>
 <CALzTN-RPtGjgVY=NPgQOE0tVj5hvP9EQRWFkwdJzBvo64_vyKA@mail.gmail.com>
 <CAG6AjRP9KTRsNgOgDifr33MKvQN7SuuR-XR1r3pWcnwSW_6rcw@mail.gmail.com>
 <CALzTN-RNFaynep_vAhDu2NwNUsuo696SErYZYGn7bGOpaE3kVQ@mail.gmail.com>
Message-ID: <CAG6AjRPaNEkdCtde30nJhf8mjoH0u8Pa1aceCQ9XVfarYVCRog@mail.gmail.com>

Hi all,

I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The
image cannot loaded correctly when I use the itk::ImageFileReader.
The test image contains non-zero values only at indexes (350,350,i)  where
i=0 to 8300.
The pixelType is short.

Thanks
Fotis

On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Thanks! Added.
>
> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <fdrakopo at gmail.com>
> wrote:
> > Hi,
> > I signed up for the ITK community on midas.
> >
> > Thanks,
> > Fotis Drakopoulos
> >
> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick
> > <matt.mccormick at kitware.com> wrote:
> >>
> >> Hi Fotis,
> >>
> >> Thanks for helping to improve large nifti file support.
> >>
> >> The file can be uploaded on midas3.kitware.com.  Sign up for the ITK
> >> community [1], let the list know the name of your account, and myself
> >> or one of the other administrators will add upload priviledges to the
> >> account.
> >>
> >> The file could then be added to
> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
> >>
> >> Thanks,
> >> Matt
> >>
> >> [1] http://midas3.kitware.com/midas/community/12
> >>
> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos <fdrakopo at gmail.com>
> >> wrote:
> >> > Hi all,
> >> >
> >> > I created a test nifti image that reproduces the problem I mentioned
> >> > before.
> >> > How can I share this image with the ITK community?
> >> >
> >> > Best,
> >> > Fotis Drakopoulos
> >> >
> >> >
> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp
> >> > <blowekamp at mail.nih.gov>
> >> > wrote:
> >> >>
> >> >> Shareable test data greatly helps determine the cause and fix these
> >> >> types
> >> >> of issues.
> >> >>
> >> >> Got data?
> >> >>
> >> >> Brad
> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle <g.bogle at auckland.ac.nz>
> wrote:
> >> >>
> >> >> This is reminiscent of the previous problem with big TIFF images, now
> >> >> fixed.
> >> >>
> >> >> Gib
> >> >> ________________________________
> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of
> Fotis
> >> >> Drakopoulos [fdrakopo at gmail.com]
> >> >> Sent: Monday, 24 November 2014 10:51 a.m.
> >> >> To: insight-users at itk.org; insight-developers at itk.org
> >> >> Subject: [ITK-users] Problem reading a big nifti volume.
> >> >>
> >> >> Hi all,
> >> >>
> >> >> For the last couple of days I have been trying reading
> (unsuccessfully)
> >> >> a
> >> >> big nifti volume labeled image from my disk.
> >> >>
> >> >> The pixel type is unsigned char and the rest specs of the image are:
> >> >> Size : [1001, 1001, 8345]  (in voxels)
> >> >> Spacing : [0.012, 0.012, 0.012]  (in mm)
> >> >> Origin : [0, 0, 0]
> >> >> Direction :
> >> >> 1 0 0
> >> >> 0 1 0
> >> >> 0 0 1
> >> >>
> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an
> idea
> >> >> how it looks like. Indeed the object in the volume looks as it was
> >> >> expected.
> >> >> So far no problems. The specs of the image on Slicer are the same as
> >> >> above
> >> >> (except the direction which has flipped signs for the first two
> >> >> diagonal
> >> >> entries, as we know ).
> >> >>
> >> >> Then I tried to load the image in the memory using the
> >> >> itk::ImageFileReader  from ITK4.6.0 (64 bit-linux) version. After
> >> >> loading
> >> >> the image I noticed that there are pixels with zero values instead of
> >> >> non-zero by comparing the same indexes with the loaded image on
> Slicer.
> >> >>
> >> >> Then I decided to write the loaded image on the disk using the
> >> >> itk::ImageFileWriter.
> >> >>
> >> >> After opening the (written from ITK) image on Slicer I checked the
> >> >> specks
> >> >> and were the same with the original image as above. However I noticed
> >> >> that a
> >> >> big portion of the image is completely empty (black)!
> >> >>
> >> >> My workstation has enough memory to load the image (768 GB 1600MHz
> >> >> DDR3L)
> >> >> and is using Red Hat Enterprise Linux Server 6.5.
> >> >> The size of the original nifti volume is :
> >> >>
> >> >> 25.7 MB (.nii.gz)
> >> >> 8.36 GB (.nii)
> >> >>
> >> >> Has anybody experienced similar difficulties trying to load so big
> >> >> volume
> >> >> data?
> >> >>
> >> >> Best,
> >> >> Fotis Drakopoulos
> >> >> CRTC
> >> >>
> >> >> _____________________________________
> >> >> 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
> >> >>
> >> >>
> >> >> ________________________________
> >> >>
> >> >> Spam
> >> >> Not spam
> >> >> Forget previous vote
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > 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
> >> >
> >>
> >>
> >> --
> >>
> >
>
>
> --
> BEGIN-ANTISPAM-VOTING-LINKS
> ------------------------------------------------------
>
> Teach CanIt if this mail (ID 03NkpHcqT) is spam:
> Spam:
> https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=s
> Not spam:
> https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=n
> Forget vote:
> https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=f
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From blowekamp at mail.nih.gov  Tue Dec  2 10:27:28 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 2 Dec 2014 10:27:28 -0500
Subject: [ITK-users] [ITK-dev]  Problem reading a big nifti volume.
In-Reply-To: <CAG6AjRPaNEkdCtde30nJhf8mjoH0u8Pa1aceCQ9XVfarYVCRog@mail.gmail.com>
References: <CAG6AjROMWzAEWptqC3XmamwqDmwPc88d2YDup84tkDg20ZJdxw@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E826D4E43@uxcn10-tdc06.UoA.auckland.ac.nz>
 <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov>
 <CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com>
 <CALzTN-RPtGjgVY=NPgQOE0tVj5hvP9EQRWFkwdJzBvo64_vyKA@mail.gmail.com>
 <CAG6AjRP9KTRsNgOgDifr33MKvQN7SuuR-XR1r3pWcnwSW_6rcw@mail.gmail.com>
 <CALzTN-RNFaynep_vAhDu2NwNUsuo696SErYZYGn7bGOpaE3kVQ@mail.gmail.com>
 <CAG6AjRPaNEkdCtde30nJhf8mjoH0u8Pa1aceCQ9XVfarYVCRog@mail.gmail.com>
Message-ID: <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov>

Hello,

What software did you use to create and validate that this image is correct?

Thanks,
Brad

On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:

> Hi all,
> 
> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader.
> The test image contains non-zero values only at indexes (350,350,i)  where i=0 to 8300.
> The pixelType is short.
>  
> Thanks
> Fotis  
> 
> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
> Thanks! Added.
> 
> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
> > Hi,
> > I signed up for the ITK community on midas.
> >
> > Thanks,
> > Fotis Drakopoulos
> >
> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick
> > <matt.mccormick at kitware.com> wrote:
> >>
> >> Hi Fotis,
> >>
> >> Thanks for helping to improve large nifti file support.
> >>
> >> The file can be uploaded on midas3.kitware.com.  Sign up for the ITK
> >> community [1], let the list know the name of your account, and myself
> >> or one of the other administrators will add upload priviledges to the
> >> account.
> >>
> >> The file could then be added to
> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
> >>
> >> Thanks,
> >> Matt
> >>
> >> [1] http://midas3.kitware.com/midas/community/12
> >>
> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos <fdrakopo at gmail.com>
> >> wrote:
> >> > Hi all,
> >> >
> >> > I created a test nifti image that reproduces the problem I mentioned
> >> > before.
> >> > How can I share this image with the ITK community?
> >> >
> >> > Best,
> >> > Fotis Drakopoulos
> >> >
> >> >
> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp
> >> > <blowekamp at mail.nih.gov>
> >> > wrote:
> >> >>
> >> >> Shareable test data greatly helps determine the cause and fix these
> >> >> types
> >> >> of issues.
> >> >>
> >> >> Got data?
> >> >>
> >> >> Brad
> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
> >> >>
> >> >> This is reminiscent of the previous problem with big TIFF images, now
> >> >> fixed.
> >> >>
> >> >> Gib
> >> >> ________________________________
> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis
> >> >> Drakopoulos [fdrakopo at gmail.com]
> >> >> Sent: Monday, 24 November 2014 10:51 a.m.
> >> >> To: insight-users at itk.org; insight-developers at itk.org
> >> >> Subject: [ITK-users] Problem reading a big nifti volume.
> >> >>
> >> >> Hi all,
> >> >>
> >> >> For the last couple of days I have been trying reading (unsuccessfully)
> >> >> a
> >> >> big nifti volume labeled image from my disk.
> >> >>
> >> >> The pixel type is unsigned char and the rest specs of the image are:
> >> >> Size : [1001, 1001, 8345]  (in voxels)
> >> >> Spacing : [0.012, 0.012, 0.012]  (in mm)
> >> >> Origin : [0, 0, 0]
> >> >> Direction :
> >> >> 1 0 0
> >> >> 0 1 0
> >> >> 0 0 1
> >> >>
> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea
> >> >> how it looks like. Indeed the object in the volume looks as it was
> >> >> expected.
> >> >> So far no problems. The specs of the image on Slicer are the same as
> >> >> above
> >> >> (except the direction which has flipped signs for the first two
> >> >> diagonal
> >> >> entries, as we know ).
> >> >>
> >> >> Then I tried to load the image in the memory using the
> >> >> itk::ImageFileReader  from ITK4.6.0 (64 bit-linux) version. After
> >> >> loading
> >> >> the image I noticed that there are pixels with zero values instead of
> >> >> non-zero by comparing the same indexes with the loaded image on Slicer.
> >> >>
> >> >> Then I decided to write the loaded image on the disk using the
> >> >> itk::ImageFileWriter.
> >> >>
> >> >> After opening the (written from ITK) image on Slicer I checked the
> >> >> specks
> >> >> and were the same with the original image as above. However I noticed
> >> >> that a
> >> >> big portion of the image is completely empty (black)!
> >> >>
> >> >> My workstation has enough memory to load the image (768 GB 1600MHz
> >> >> DDR3L)
> >> >> and is using Red Hat Enterprise Linux Server 6.5.
> >> >> The size of the original nifti volume is :
> >> >>
> >> >> 25.7 MB (.nii.gz)
> >> >> 8.36 GB (.nii)
> >> >>
> >> >> Has anybody experienced similar difficulties trying to load so big
> >> >> volume
> >> >> data?
> >> >>
> >> >> Best,
> >> >> Fotis Drakopoulos
> >> >> CRTC
> >> >>
> >> >> _____________________________________
> >> >> 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
> >> >>
> >> >>
> >> >> ________________________________
> >> >>
> >> >> Spam
> >> >> Not spam
> >> >> Forget previous vote
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > 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
> >> >
> >>
> >>
> >> --
> >>
> >
> 
> 
> --
> BEGIN-ANTISPAM-VOTING-LINKS
> ------------------------------------------------------
> 
> Teach CanIt if this mail (ID 03NkpHcqT) is spam:
> Spam:        https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=s
> Not spam:    https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=n
> Forget vote: https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=f
> ------------------------------------------------------
> END-ANTISPAM-VOTING-LINKS
> 
> 

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From blowekamp at mail.nih.gov  Tue Dec  2 10:21:54 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 2 Dec 2014 10:21:54 -0500
Subject: [ITK-users] [ITK] Otsu Filter for object/background separation
In-Reply-To: <CAA+VR6isWQDHzOj--n0f2iPiceg+1EbBjBPXc+p7us+ZWStejQ@mail.gmail.com>
References: <CADiSopNLpxu4V+W+fbMz_+Wfet3qv_GvekS+9nK46TLMd8GiAA@mail.gmail.com>
 <CAA+VR6isWQDHzOj--n0f2iPiceg+1EbBjBPXc+p7us+ZWStejQ@mail.gmail.com>
Message-ID: <2A284D8D-9690-433C-9456-949744057644@mail.nih.gov>

Hello,

ITK has a histogram based thresholding framework contributed by Richard Beare through the Insight Journal [1]. At the heart of the frame work is the HistrogramThrsholdImageFilter[2], and the HistogramThresholdCalculator[3]. With this framework you should be able to write a calculator to behave as you want and then pass it to the filter with the HistogramThreshold::SetCalculator method.

Also you may want to run the binary segmentation results through the LabelMap framework to analyze the statistics of the shape of the objects and selecting the one you are looking for or rejecting the results.

Brad



[1] http://hdl.handle.net/10380/3279
[2] http://itk.org/Insight/Doxygen/html/classitk_1_1HistogramThresholdImageFilter.html
[3] http://itk.org/Insight/Doxygen/html/classitk_1_1HistogramThresholdCalculator.html

On Nov 12, 2014, at 8:14 AM, Girish Mallya Udupi <indianzeppelin at gmail.com> wrote:

> Hi Zein,
> 
> As you might know, Otsu's method assumes that the histogram of the image is bi-modal. i.e., there are two classes of pixels forming two peaks separated by a valley. 
> All the method (and the corresponding ITK filter) does is calculate the threshold which maximizes the inter-class variance and apply it on the image.
> 
> 
> On Wed, Nov 12, 2014 at 12:43 PM, Zein Salah <zeinsalah at gmail.com> wrote:
> Hello,
> 
> I have been using the otsu filter for doing object-from-background separation. However, I noticed that the filter always comes out with an separation threshold, even if the image does NOT actually have a "reasonable" background, see the attached image, e.g.. 
> 
> My question is: is it possible to control the filter in such a way that it only generate a threshold if there is really a background? 
> 
> Practically, I could, in a post-processing step,  do a decision weather the separation is feasible or not, e.g. computing the comparing the statistics of the two separated areas (average intensity, variance, etc.). But I thought the otsu filter already does such things internally, right? Is it possible to inquire such data from the filter?
> 
> Any ideas would be welcome!!
> 
> Much thanks,
> 
> Zein
> 
> 
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
> 
> 
> 
> 
> -- 
> Regards,
> Girish
> _____________________________________
> 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

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From blowekamp at mail.nih.gov  Tue Dec  2 10:26:50 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 2 Dec 2014 10:26:50 -0500
Subject: [ITK-users] Future of WrapITK
In-Reply-To: <BB43A6B0CAEAFC439640CD9D13607DC24D6A2A89@mbs2.ad.jyu.fi>
References: <BB43A6B0CAEAFC439640CD9D13607DC24D6A284B@mbs2.ad.jyu.fi>,
 <189A597A-010D-4BEC-8A76-29A5046E32DD@gmail.com>
 <BB43A6B0CAEAFC439640CD9D13607DC24D6A2A89@mbs2.ad.jyu.fi>
Message-ID: <D20F27B1-DA3D-4986-BACF-2815D3813F41@mail.nih.gov>

Hello,
> We are using many image filters as well as the registration framework from the ITK. I think I read that the registration framework is not fully usable in SimpleITK.

The development of the SimpleITK registration interface is wrapping up. The current interface is quite usable, and powerful, although there are some minor issue that still need to be addressed.

I'd encourage you to give it a try. You may be able to solve you problem faster and better with the SimpleITK wrapping of the ITKv4 registration framework. Please let us know if it works for your problem and what you think of the interface [1].

Thanks,
Brad

[1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html

> 
> I'll follow the developments for ITK 4.8 and will test and help in anyways possible. Thank you all for your efforts with ITK wrappings.
> 
> Cheers,
> Lassi
> 
> From: michkapopoff at gmail.com [michkapopoff at gmail.com]
> Sent: Thursday, November 27, 2014 17:39
> To: Paavolainen Lassi
> Cc: insight-users at itk.org; community at itk.org
> Subject: Re: [ITK-users] Future of WrapITK
> 
> Hi
> 
> we have been working on Wrapping so the development is going on. 
> Some small improvements were made for ITK 4.7.
> 
> I ported most of the code to Python3, but we have still an error which we have been working on, but is tricky to tackle.
> I hope to get this done for ITK 4.8, and it will need some testing.
> 
> Fixing the problem for Clang is also under way, I don?t know how much resources we can put in it but I am hoping also for ITK 4.8, though I can not
> promise anything here.
> 
> If you really need ITK wrappings on OS X, you can try my ITK binaries for homebrew: https://github.com/iMichka/homebrew-MacVTKITKPythonBottles
> (Please open a ticket on the github page if you have any trouble with these binaries).
> 
> If you would like to help, there are a lot of things to do on the wrapping code.
> (Writing examples for the ITK examples website is a good way to start with).
> 
> For SimpleITK vs Wrapping, it all depends on what image types you want to analyse, and what filters you want to use.
> 
> Michka
> 
>> On 27 Nov 2014, at 14:08, Paavolainen Lassi <lassi.paavolainen at jyu.fi> wrote:
>> 
>> Hi,
>> 
>> I'm developing software that uses ITK through Python wrapping. After some period of slower development progress we are now moving from ITK 3.20 to ITK 4.x. The software is developed and packages are released for 64-bit Windows, Linux and OS X. The problem is that ITK 4.6.1 with Python wrappings can be built only for Linux. It seems that there is no way around the issues with GCCXML and new Visual Studio in Win or Clang in OS X 10.9.
>> 
>> The issue has been raised before in: http://www.itk.org/pipermail/insight-users/2014-July/050562.html
>> 
>> To follow up that question, has there been any progress related to GCCXML replacement or development of GCCXML to support new Visual Studio and Clang? Are there still plans for this or will wrapITK be deprecated and replaced by SimpleITK? Is there anything I can help with?
>> 
>> I noticed the Wiki page (http://www.itk.org/Wiki/ITK/Wrapping) where it is said that ITK 4.7 will include support for Python 3 but will it also fix the problem with Clang or new Visual Studios?
>> 
>> I have to admit that I haven't tried SimpleITK so I don't know whether it could provide the same flexibility as wrapITK and how much of ITK related code would need to be rewritten.
>> 
>> Cheers,
>> Lassi
>> _____________________________________
>> 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
> 
> _____________________________________
> 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

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From fdrakopo at gmail.com  Tue Dec  2 10:49:06 2014
From: fdrakopo at gmail.com (Fotis Drakopoulos)
Date: Tue, 2 Dec 2014 10:49:06 -0500
Subject: [ITK-users] [ITK-dev]  Problem reading a big nifti volume.
In-Reply-To: <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov>
References: <CAG6AjROMWzAEWptqC3XmamwqDmwPc88d2YDup84tkDg20ZJdxw@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E826D4E43@uxcn10-tdc06.UoA.auckland.ac.nz>
 <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov>
 <CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com>
 <CALzTN-RPtGjgVY=NPgQOE0tVj5hvP9EQRWFkwdJzBvo64_vyKA@mail.gmail.com>
 <CAG6AjRP9KTRsNgOgDifr33MKvQN7SuuR-XR1r3pWcnwSW_6rcw@mail.gmail.com>
 <CALzTN-RNFaynep_vAhDu2NwNUsuo696SErYZYGn7bGOpaE3kVQ@mail.gmail.com>
 <CAG6AjRPaNEkdCtde30nJhf8mjoH0u8Pa1aceCQ9XVfarYVCRog@mail.gmail.com>
 <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov>
Message-ID: <CAG6AjRPdVusAYjgBwSw94eE+PbbO2QYGezucvzKho2TJg2=ahQ@mail.gmail.com>

Hi,

I created and wrote the image on the disk using ITK 4.6.0.
I visualized the image using Slicer 4.4.0.

The properties are:
Size : [1001, 1001, 8345]
Spacing : [1,1,1]
Origin : [0, 0, 0]
Direction :
1 0 0
0 1 0
0 0 1

Fotis

On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> What software did you use to create and validate that this image is
> correct?
>
> Thanks,
> Brad
>
> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
>
> Hi all,
>
> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
> The image cannot loaded correctly when I use the itk::ImageFileReader.
> The test image contains non-zero values only at indexes (350,350,i)  where
> i=0 to 8300.
> The pixelType is short.
>
> Thanks
> Fotis
>
> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick <
> matt.mccormick at kitware.com> wrote:
>
>> Thanks! Added.
>>
>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <fdrakopo at gmail.com>
>> wrote:
>> > Hi,
>> > I signed up for the ITK community on midas.
>> >
>> > Thanks,
>> > Fotis Drakopoulos
>> >
>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick
>> > <matt.mccormick at kitware.com> wrote:
>> >>
>> >> Hi Fotis,
>> >>
>> >> Thanks for helping to improve large nifti file support.
>> >>
>> >> The file can be uploaded on midas3.kitware.com.  Sign up for the ITK
>> >> community [1], let the list know the name of your account, and myself
>> >> or one of the other administrators will add upload priviledges to the
>> >> account.
>> >>
>> >> The file could then be added to
>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
>> >>
>> >> Thanks,
>> >> Matt
>> >>
>> >> [1] http://midas3.kitware.com/midas/community/12
>> >>
>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos <fdrakopo at gmail.com
>> >
>> >> wrote:
>> >> > Hi all,
>> >> >
>> >> > I created a test nifti image that reproduces the problem I mentioned
>> >> > before.
>> >> > How can I share this image with the ITK community?
>> >> >
>> >> > Best,
>> >> > Fotis Drakopoulos
>> >> >
>> >> >
>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp
>> >> > <blowekamp at mail.nih.gov>
>> >> > wrote:
>> >> >>
>> >> >> Shareable test data greatly helps determine the cause and fix these
>> >> >> types
>> >> >> of issues.
>> >> >>
>> >> >> Got data?
>> >> >>
>> >> >> Brad
>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>> wrote:
>> >> >>
>> >> >> This is reminiscent of the previous problem with big TIFF images,
>> now
>> >> >> fixed.
>> >> >>
>> >> >> Gib
>> >> >> ________________________________
>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of
>> Fotis
>> >> >> Drakopoulos [fdrakopo at gmail.com]
>> >> >> Sent: Monday, 24 November 2014 10:51 a.m.
>> >> >> To: insight-users at itk.org; insight-developers at itk.org
>> >> >> Subject: [ITK-users] Problem reading a big nifti volume.
>> >> >>
>> >> >> Hi all,
>> >> >>
>> >> >> For the last couple of days I have been trying reading
>> (unsuccessfully)
>> >> >> a
>> >> >> big nifti volume labeled image from my disk.
>> >> >>
>> >> >> The pixel type is unsigned char and the rest specs of the image are:
>> >> >> Size : [1001, 1001, 8345]  (in voxels)
>> >> >> Spacing : [0.012, 0.012, 0.012]  (in mm)
>> >> >> Origin : [0, 0, 0]
>> >> >> Direction :
>> >> >> 1 0 0
>> >> >> 0 1 0
>> >> >> 0 0 1
>> >> >>
>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an
>> idea
>> >> >> how it looks like. Indeed the object in the volume looks as it was
>> >> >> expected.
>> >> >> So far no problems. The specs of the image on Slicer are the same as
>> >> >> above
>> >> >> (except the direction which has flipped signs for the first two
>> >> >> diagonal
>> >> >> entries, as we know ).
>> >> >>
>> >> >> Then I tried to load the image in the memory using the
>> >> >> itk::ImageFileReader  from ITK4.6.0 (64 bit-linux) version. After
>> >> >> loading
>> >> >> the image I noticed that there are pixels with zero values instead
>> of
>> >> >> non-zero by comparing the same indexes with the loaded image on
>> Slicer.
>> >> >>
>> >> >> Then I decided to write the loaded image on the disk using the
>> >> >> itk::ImageFileWriter.
>> >> >>
>> >> >> After opening the (written from ITK) image on Slicer I checked the
>> >> >> specks
>> >> >> and were the same with the original image as above. However I
>> noticed
>> >> >> that a
>> >> >> big portion of the image is completely empty (black)!
>> >> >>
>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz
>> >> >> DDR3L)
>> >> >> and is using Red Hat Enterprise Linux Server 6.5.
>> >> >> The size of the original nifti volume is :
>> >> >>
>> >> >> 25.7 MB (.nii.gz)
>> >> >> 8.36 GB (.nii)
>> >> >>
>> >> >> Has anybody experienced similar difficulties trying to load so big
>> >> >> volume
>> >> >> data?
>> >> >>
>> >> >> Best,
>> >> >> Fotis Drakopoulos
>> >> >> CRTC
>> >> >>
>> >> >> _____________________________________
>> >> >> 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
>> >> >>
>> >> >>
>> >> >> ________________________________
>> >> >>
>> >> >> Spam
>> >> >> Not spam
>> >> >> Forget previous vote
>> >> >
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > 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
>> >> >
>> >>
>> >>
>> >> --
>> >>
>> >
>>
>>
>> --
>> BEGIN-ANTISPAM-VOTING-LINKS
>> ------------------------------------------------------
>>
>> Teach CanIt if this mail (ID 03NkpHcqT) is spam:
>> Spam:        about:blank
>> Not spam:    about:blank
>> Forget vote: about:blank
>> ------------------------------------------------------
>> END-ANTISPAM-VOTING-LINKS
>>
>>
>
>  ------------------------------
>
> Spam
> <https://www.spamtrap.odu.edu/canit/b.php?i=03NmDyijL&m=0a26c0248a9e&t=20141202&c=s>
> Not spam
> <https://www.spamtrap.odu.edu/canit/b.php?i=03NmDyijL&m=0a26c0248a9e&t=20141202&c=n>
> Forget previous vote
> <https://www.spamtrap.odu.edu/canit/b.php?i=03NmDyijL&m=0a26c0248a9e&t=20141202&c=f>
>
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From lassi.paavolainen at jyu.fi  Tue Dec  2 10:56:02 2014
From: lassi.paavolainen at jyu.fi (Paavolainen Lassi)
Date: Tue, 2 Dec 2014 15:56:02 +0000
Subject: [ITK-users] Future of WrapITK
In-Reply-To: <D20F27B1-DA3D-4986-BACF-2815D3813F41@mail.nih.gov>
References: <BB43A6B0CAEAFC439640CD9D13607DC24D6A284B@mbs2.ad.jyu.fi>,
 <189A597A-010D-4BEC-8A76-29A5046E32DD@gmail.com>
 <BB43A6B0CAEAFC439640CD9D13607DC24D6A2A89@mbs2.ad.jyu.fi>,
 <D20F27B1-DA3D-4986-BACF-2815D3813F41@mail.nih.gov>
Message-ID: <BB43A6B0CAEAFC439640CD9D13607DC24D6A30F6@mbs2.ad.jyu.fi>

Thanks Brad,

I'll give SimpleITK a try and let you know how well its able to replace our current use of WrapITK.

By the way, I found Visual Studio 2008 Pro on one of our development machines, and I was able to build VTK 6.1.0 and ITK 4.6.1 with Python wrappings. So at least we are set for now except the OS X package and library needing C++11.

Cheers,
Lassi

________________________________
From: Bradley Lowekamp [blowekamp at mail.nih.gov]
Sent: Tuesday, December 02, 2014 17:26
To: Paavolainen Lassi
Cc: michkapopoff at gmail.com; insight-users at itk.org
Subject: Re: [ITK-users] Future of WrapITK

Hello,
We are using many image filters as well as the registration framework from the ITK. I think I read that the registration framework is not fully usable in SimpleITK.

The development of the SimpleITK registration interface is wrapping up. The current interface is quite usable, and powerful, although there are some minor issue that still need to be addressed.

I'd encourage you to give it a try. You may be able to solve you problem faster and better with the SimpleITK wrapping of the ITKv4 registration framework. Please let us know if it works for your problem and what you think of the interface [1].

Thanks,
Brad

[1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html


I'll follow the developments for ITK 4.8 and will test and help in anyways possible. Thank you all for your efforts with ITK wrappings.

Cheers,
Lassi

________________________________
From: michkapopoff at gmail.com<mailto:michkapopoff at gmail.com> [michkapopoff at gmail.com<mailto:michkapopoff at gmail.com>]
Sent: Thursday, November 27, 2014 17:39
To: Paavolainen Lassi
Cc: insight-users at itk.org<mailto:insight-users at itk.org>; community at itk.org<mailto:community at itk.org>
Subject: Re: [ITK-users] Future of WrapITK

Hi

we have been working on Wrapping so the development is going on.
Some small improvements were made for ITK 4.7.

I ported most of the code to Python3, but we have still an error which we have been working on, but is tricky to tackle.
I hope to get this done for ITK 4.8, and it will need some testing.

Fixing the problem for Clang is also under way, I don?t know how much resources we can put in it but I am hoping also for ITK 4.8, though I can not
promise anything here.

If you really need ITK wrappings on OS X, you can try my ITK binaries for homebrew: https://github.com/iMichka/homebrew-MacVTKITKPythonBottles
(Please open a ticket on the github page if you have any trouble with these binaries).

If you would like to help, there are a lot of things to do on the wrapping code.
(Writing examples for the ITK examples website is a good way to start with).

For SimpleITK vs Wrapping, it all depends on what image types you want to analyse, and what filters you want to use.

Michka

On 27 Nov 2014, at 14:08, Paavolainen Lassi <lassi.paavolainen at jyu.fi<mailto:lassi.paavolainen at jyu.fi>> wrote:

Hi,

I'm developing software that uses ITK through Python wrapping. After some period of slower development progress we are now moving from ITK 3.20 to ITK 4.x. The software is developed and packages are released for 64-bit Windows, Linux and OS X. The problem is that ITK 4.6.1 with Python wrappings can be built only for Linux. It seems that there is no way around the issues with GCCXML and new Visual Studio in Win or Clang in OS X 10.9.

The issue has been raised before in: http://www.itk.org/pipermail/insight-users/2014-July/050562.html

To follow up that question, has there been any progress related to GCCXML replacement or development of GCCXML to support new Visual Studio and Clang? Are there still plans for this or will wrapITK be deprecated and replaced by SimpleITK? Is there anything I can help with?

I noticed the Wiki page (http://www.itk.org/Wiki/ITK/Wrapping) where it is said that ITK 4.7 will include support for Python 3 but will it also fix the problem with Clang or new Visual Studios?

I have to admit that I haven't tried SimpleITK so I don't know whether it could provide the same flexibility as wrapITK and how much of ITK related code would need to be rewritten.

Cheers,
Lassi
_____________________________________
Powered by www.kitware.com<http://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

_____________________________________
Powered by www.kitware.com<http://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

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From blowekamp at mail.nih.gov  Tue Dec  2 10:58:40 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 2 Dec 2014 10:58:40 -0500
Subject: [ITK-users] [ITK-dev]  Problem reading a big nifti volume.
In-Reply-To: <CAG6AjRPdVusAYjgBwSw94eE+PbbO2QYGezucvzKho2TJg2=ahQ@mail.gmail.com>
References: <CAG6AjROMWzAEWptqC3XmamwqDmwPc88d2YDup84tkDg20ZJdxw@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E826D4E43@uxcn10-tdc06.UoA.auckland.ac.nz>
 <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov>
 <CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com>
 <CALzTN-RPtGjgVY=NPgQOE0tVj5hvP9EQRWFkwdJzBvo64_vyKA@mail.gmail.com>
 <CAG6AjRP9KTRsNgOgDifr33MKvQN7SuuR-XR1r3pWcnwSW_6rcw@mail.gmail.com>
 <CALzTN-RNFaynep_vAhDu2NwNUsuo696SErYZYGn7bGOpaE3kVQ@mail.gmail.com>
 <CAG6AjRPaNEkdCtde30nJhf8mjoH0u8Pa1aceCQ9XVfarYVCRog@mail.gmail.com>
 <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov>
 <CAG6AjRPdVusAYjgBwSw94eE+PbbO2QYGezucvzKho2TJg2=ahQ@mail.gmail.com>
Message-ID: <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov>

So if you wrote and read with ITK ( via Slicer ), how do you know that the file is correct as you expect?

I see the file has a ".nii.gz" extension, meaning that it's compressed. Does the same issue occur when it's not compressed?

Brad


On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:

> Hi,
> 
> I created and wrote the image on the disk using ITK 4.6.0. 
> I visualized the image using Slicer 4.4.0.
> 
> The properties are:
> Size : [1001, 1001, 8345]  
> Spacing : [1,1,1]
> Origin : [0, 0, 0]
> Direction : 
> 1 0 0
> 0 1 0
> 0 0 1
> 
> Fotis
> 
> On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
> 
> What software did you use to create and validate that this image is correct?
> 
> Thanks,
> Brad
> 
> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
> 
>> Hi all,
>> 
>> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader.
>> The test image contains non-zero values only at indexes (350,350,i)  where i=0 to 8300.
>> The pixelType is short.
>>  
>> Thanks
>> Fotis  
>> 
>> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>> Thanks! Added.
>> 
>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
>> > Hi,
>> > I signed up for the ITK community on midas.
>> >
>> > Thanks,
>> > Fotis Drakopoulos
>> >
>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick
>> > <matt.mccormick at kitware.com> wrote:
>> >>
>> >> Hi Fotis,
>> >>
>> >> Thanks for helping to improve large nifti file support.
>> >>
>> >> The file can be uploaded on midas3.kitware.com.  Sign up for the ITK
>> >> community [1], let the list know the name of your account, and myself
>> >> or one of the other administrators will add upload priviledges to the
>> >> account.
>> >>
>> >> The file could then be added to
>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
>> >>
>> >> Thanks,
>> >> Matt
>> >>
>> >> [1] http://midas3.kitware.com/midas/community/12
>> >>
>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos <fdrakopo at gmail.com>
>> >> wrote:
>> >> > Hi all,
>> >> >
>> >> > I created a test nifti image that reproduces the problem I mentioned
>> >> > before.
>> >> > How can I share this image with the ITK community?
>> >> >
>> >> > Best,
>> >> > Fotis Drakopoulos
>> >> >
>> >> >
>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp
>> >> > <blowekamp at mail.nih.gov>
>> >> > wrote:
>> >> >>
>> >> >> Shareable test data greatly helps determine the cause and fix these
>> >> >> types
>> >> >> of issues.
>> >> >>
>> >> >> Got data?
>> >> >>
>> >> >> Brad
>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
>> >> >>
>> >> >> This is reminiscent of the previous problem with big TIFF images, now
>> >> >> fixed.
>> >> >>
>> >> >> Gib
>> >> >> ________________________________
>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis
>> >> >> Drakopoulos [fdrakopo at gmail.com]
>> >> >> Sent: Monday, 24 November 2014 10:51 a.m.
>> >> >> To: insight-users at itk.org; insight-developers at itk.org
>> >> >> Subject: [ITK-users] Problem reading a big nifti volume.
>> >> >>
>> >> >> Hi all,
>> >> >>
>> >> >> For the last couple of days I have been trying reading (unsuccessfully)
>> >> >> a
>> >> >> big nifti volume labeled image from my disk.
>> >> >>
>> >> >> The pixel type is unsigned char and the rest specs of the image are:
>> >> >> Size : [1001, 1001, 8345]  (in voxels)
>> >> >> Spacing : [0.012, 0.012, 0.012]  (in mm)
>> >> >> Origin : [0, 0, 0]
>> >> >> Direction :
>> >> >> 1 0 0
>> >> >> 0 1 0
>> >> >> 0 0 1
>> >> >>
>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea
>> >> >> how it looks like. Indeed the object in the volume looks as it was
>> >> >> expected.
>> >> >> So far no problems. The specs of the image on Slicer are the same as
>> >> >> above
>> >> >> (except the direction which has flipped signs for the first two
>> >> >> diagonal
>> >> >> entries, as we know ).
>> >> >>
>> >> >> Then I tried to load the image in the memory using the
>> >> >> itk::ImageFileReader  from ITK4.6.0 (64 bit-linux) version. After
>> >> >> loading
>> >> >> the image I noticed that there are pixels with zero values instead of
>> >> >> non-zero by comparing the same indexes with the loaded image on Slicer.
>> >> >>
>> >> >> Then I decided to write the loaded image on the disk using the
>> >> >> itk::ImageFileWriter.
>> >> >>
>> >> >> After opening the (written from ITK) image on Slicer I checked the
>> >> >> specks
>> >> >> and were the same with the original image as above. However I noticed
>> >> >> that a
>> >> >> big portion of the image is completely empty (black)!
>> >> >>
>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz
>> >> >> DDR3L)
>> >> >> and is using Red Hat Enterprise Linux Server 6.5.
>> >> >> The size of the original nifti volume is :
>> >> >>
>> >> >> 25.7 MB (.nii.gz)
>> >> >> 8.36 GB (.nii)
>> >> >>
>> >> >> Has anybody experienced similar difficulties trying to load so big
>> >> >> volume
>> >> >> data?
>> >> >>
>> >> >> Best,
>> >> >> Fotis Drakopoulos
>> >> >> CRTC
>> >> >>
>> >> >> _____________________________________
>> >> >> 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
>> >> >>
>> >> >>
>> >> >> ________________________________
>> >> >>
>> >> >> Spam
>> >> >> Not spam
>> >> >> Forget previous vote
>> >> >
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > 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
>> >> >
>> >>
>> >>
>> >> --
>> >>
>> >
>> 
>> 
>> --
>> BEGIN-ANTISPAM-VOTING-LINKS
>> ------------------------------------------------------
>> 
>> Teach CanIt if this mail (ID 03NkpHcqT) is spam:
>> Spam:        about:blank
>> Not spam:    about:blank
>> Forget vote: about:blank
>> ------------------------------------------------------
>> END-ANTISPAM-VOTING-LINKS
>> 
>> 
> 
> 
> Spam
> Not spam
> Forget previous vote
> 

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From blowekamp at mail.nih.gov  Tue Dec  2 11:04:56 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 2 Dec 2014 11:04:56 -0500
Subject: [ITK-users] Future of WrapITK
In-Reply-To: <BB43A6B0CAEAFC439640CD9D13607DC24D6A30F6@mbs2.ad.jyu.fi>
References: <BB43A6B0CAEAFC439640CD9D13607DC24D6A284B@mbs2.ad.jyu.fi>,
 <189A597A-010D-4BEC-8A76-29A5046E32DD@gmail.com>
 <BB43A6B0CAEAFC439640CD9D13607DC24D6A2A89@mbs2.ad.jyu.fi>,
 <D20F27B1-DA3D-4986-BACF-2815D3813F41@mail.nih.gov>
 <BB43A6B0CAEAFC439640CD9D13607DC24D6A30F6@mbs2.ad.jyu.fi>
Message-ID: <2C9D32C3-635E-4597-8829-ABE435259EBD@mail.nih.gov>

Hello,

The complications of OSX's clang 5.0 switching to libc++ from GNU's libstdc++ are complex. If you set CMAKE_OSX_DEPLOYMENT_TARGET < 10.9, then GNU's libstdc++ will still be used and support for tr1 will exists, so the C++11 requirement may be relaxed for some cases.

Currently the SimpleITK's master has a linking issue on Visual Studio when static libraries are created. If you choose to create shared libraries you can get it too link, although the installation of all ITK and SimpleITK shared libraries is more complicated and not automatic.

Brad

On Dec 2, 2014, at 10:56 AM, Paavolainen Lassi <lassi.paavolainen at jyu.fi> wrote:

> So at least we are set for now except the OS X package and library needing C++11.

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From fdrakopo at gmail.com  Tue Dec  2 11:14:46 2014
From: fdrakopo at gmail.com (Fotis Drakopoulos)
Date: Tue, 2 Dec 2014 11:14:46 -0500
Subject: [ITK-users] [ITK-dev]  Problem reading a big nifti volume.
In-Reply-To: <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov>
References: <CAG6AjROMWzAEWptqC3XmamwqDmwPc88d2YDup84tkDg20ZJdxw@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E826D4E43@uxcn10-tdc06.UoA.auckland.ac.nz>
 <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov>
 <CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com>
 <CALzTN-RPtGjgVY=NPgQOE0tVj5hvP9EQRWFkwdJzBvo64_vyKA@mail.gmail.com>
 <CAG6AjRP9KTRsNgOgDifr33MKvQN7SuuR-XR1r3pWcnwSW_6rcw@mail.gmail.com>
 <CALzTN-RNFaynep_vAhDu2NwNUsuo696SErYZYGn7bGOpaE3kVQ@mail.gmail.com>
 <CAG6AjRPaNEkdCtde30nJhf8mjoH0u8Pa1aceCQ9XVfarYVCRog@mail.gmail.com>
 <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov>
 <CAG6AjRPdVusAYjgBwSw94eE+PbbO2QYGezucvzKho2TJg2=ahQ@mail.gmail.com>
 <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov>
Message-ID: <CAG6AjRPsLq+cEAAmsV-Ask0L6Ohb92SQPwDrwGzXeExaBjbdSw@mail.gmail.com>

The image contains a single non-zero voxel on each axial slice.

When I load the image on Slicer the non-zero voxels are preserved as you
traverse the image using the window slider.
When I read the image using a simple main program a big portion of the
the non-zero voxels do not exist.

I had the same issue when the file was .nii (not compressed).

Fotis


On Tue, Dec 2, 2014 at 10:58 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> So if you wrote and read with ITK ( via Slicer ), how do you know that the
> file is correct as you expect?
>
> I see the file has a ".nii.gz" extension, meaning that it's compressed.
> Does the same issue occur when it's not compressed?
>
> Brad
>
>
>
> On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
>
> Hi,
>
> I created and wrote the image on the disk using ITK 4.6.0.
> I visualized the image using Slicer 4.4.0.
>
> The properties are:
> Size : [1001, 1001, 8345]
> Spacing : [1,1,1]
> Origin : [0, 0, 0]
> Direction :
> 1 0 0
> 0 1 0
> 0 0 1
>
> Fotis
>
> On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
>> Hello,
>>
>> What software did you use to create and validate that this image is
>> correct?
>>
>> Thanks,
>> Brad
>>
>> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos <fdrakopo at gmail.com>
>> wrote:
>>
>> Hi all,
>>
>> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
>> The image cannot loaded correctly when I use the itk::ImageFileReader.
>> The test image contains non-zero values only at indexes (350,350,i)
>>  where i=0 to 8300.
>> The pixelType is short.
>>
>> Thanks
>> Fotis
>>
>> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick <
>> matt.mccormick at kitware.com> wrote:
>>
>>> Thanks! Added.
>>>
>>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <fdrakopo at gmail.com>
>>> wrote:
>>> > Hi,
>>> > I signed up for the ITK community on midas.
>>> >
>>> > Thanks,
>>> > Fotis Drakopoulos
>>> >
>>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick
>>> > <matt.mccormick at kitware.com> wrote:
>>> >>
>>> >> Hi Fotis,
>>> >>
>>> >> Thanks for helping to improve large nifti file support.
>>> >>
>>> >> The file can be uploaded on midas3.kitware.com.  Sign up for the ITK
>>> >> community [1], let the list know the name of your account, and myself
>>> >> or one of the other administrators will add upload priviledges to the
>>> >> account.
>>> >>
>>> >> The file could then be added to
>>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
>>> >>
>>> >> Thanks,
>>> >> Matt
>>> >>
>>> >> [1] http://midas3.kitware.com/midas/community/12
>>> >>
>>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos <
>>> fdrakopo at gmail.com>
>>> >> wrote:
>>> >> > Hi all,
>>> >> >
>>> >> > I created a test nifti image that reproduces the problem I mentioned
>>> >> > before.
>>> >> > How can I share this image with the ITK community?
>>> >> >
>>> >> > Best,
>>> >> > Fotis Drakopoulos
>>> >> >
>>> >> >
>>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp
>>> >> > <blowekamp at mail.nih.gov>
>>> >> > wrote:
>>> >> >>
>>> >> >> Shareable test data greatly helps determine the cause and fix these
>>> >> >> types
>>> >> >> of issues.
>>> >> >>
>>> >> >> Got data?
>>> >> >>
>>> >> >> Brad
>>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>> wrote:
>>> >> >>
>>> >> >> This is reminiscent of the previous problem with big TIFF images,
>>> now
>>> >> >> fixed.
>>> >> >>
>>> >> >> Gib
>>> >> >> ________________________________
>>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of
>>> Fotis
>>> >> >> Drakopoulos [fdrakopo at gmail.com]
>>> >> >> Sent: Monday, 24 November 2014 10:51 a.m.
>>> >> >> To: insight-users at itk.org; insight-developers at itk.org
>>> >> >> Subject: [ITK-users] Problem reading a big nifti volume.
>>> >> >>
>>> >> >> Hi all,
>>> >> >>
>>> >> >> For the last couple of days I have been trying reading
>>> (unsuccessfully)
>>> >> >> a
>>> >> >> big nifti volume labeled image from my disk.
>>> >> >>
>>> >> >> The pixel type is unsigned char and the rest specs of the image
>>> are:
>>> >> >> Size : [1001, 1001, 8345]  (in voxels)
>>> >> >> Spacing : [0.012, 0.012, 0.012]  (in mm)
>>> >> >> Origin : [0, 0, 0]
>>> >> >> Direction :
>>> >> >> 1 0 0
>>> >> >> 0 1 0
>>> >> >> 0 0 1
>>> >> >>
>>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an
>>> idea
>>> >> >> how it looks like. Indeed the object in the volume looks as it was
>>> >> >> expected.
>>> >> >> So far no problems. The specs of the image on Slicer are the same
>>> as
>>> >> >> above
>>> >> >> (except the direction which has flipped signs for the first two
>>> >> >> diagonal
>>> >> >> entries, as we know ).
>>> >> >>
>>> >> >> Then I tried to load the image in the memory using the
>>> >> >> itk::ImageFileReader  from ITK4.6.0 (64 bit-linux) version. After
>>> >> >> loading
>>> >> >> the image I noticed that there are pixels with zero values instead
>>> of
>>> >> >> non-zero by comparing the same indexes with the loaded image on
>>> Slicer.
>>> >> >>
>>> >> >> Then I decided to write the loaded image on the disk using the
>>> >> >> itk::ImageFileWriter.
>>> >> >>
>>> >> >> After opening the (written from ITK) image on Slicer I checked the
>>> >> >> specks
>>> >> >> and were the same with the original image as above. However I
>>> noticed
>>> >> >> that a
>>> >> >> big portion of the image is completely empty (black)!
>>> >> >>
>>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz
>>> >> >> DDR3L)
>>> >> >> and is using Red Hat Enterprise Linux Server 6.5.
>>> >> >> The size of the original nifti volume is :
>>> >> >>
>>> >> >> 25.7 MB (.nii.gz)
>>> >> >> 8.36 GB (.nii)
>>> >> >>
>>> >> >> Has anybody experienced similar difficulties trying to load so big
>>> >> >> volume
>>> >> >> data?
>>> >> >>
>>> >> >> Best,
>>> >> >> Fotis Drakopoulos
>>> >> >> CRTC
>>> >> >>
>>> >> >> _____________________________________
>>> >> >> 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
>>> >> >>
>>> >> >>
>>> >> >> ________________________________
>>> >> >>
>>> >> >> Spam
>>> >> >> Not spam
>>> >> >> Forget previous vote
>>> >> >
>>> >> >
>>> >> >
>>> >> > _______________________________________________
>>> >> > 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
>>> >> >
>>> >>
>>> >>
>>> >> --
>>> >>
>>> >
>>>
>>>
>>> --
>>> BEGIN-ANTISPAM-VOTING-LINKS
>>> ------------------------------------------------------
>>>
>>> Teach CanIt if this mail (ID 03NkpHcqT) is spam:
>>> Spam:        about:blank
>>> Not spam:    about:blank
>>> Forget vote: about:blank
>>> ------------------------------------------------------
>>> END-ANTISPAM-VOTING-LINKS
>>>
>>>
>>
>>  ------------------------------
>>
>> Spam
>> Not spam
>> Forget previous vote
>>
>
>
>  ------------------------------
>
> Spam
> <https://www.spamtrap.odu.edu/canit/b.php?i=03NmE09Ru&m=eb19ac9fd119&t=20141202&c=s>
> Not spam
> <https://www.spamtrap.odu.edu/canit/b.php?i=03NmE09Ru&m=eb19ac9fd119&t=20141202&c=n>
> Forget previous vote
> <https://www.spamtrap.odu.edu/canit/b.php?i=03NmE09Ru&m=eb19ac9fd119&t=20141202&c=f>
>
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From blowekamp at mail.nih.gov  Tue Dec  2 11:34:17 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 2 Dec 2014 11:34:17 -0500
Subject: [ITK-users] [ITK-dev]  Problem reading a big nifti volume.
In-Reply-To: <CAG6AjRPsLq+cEAAmsV-Ask0L6Ohb92SQPwDrwGzXeExaBjbdSw@mail.gmail.com>
References: <CAG6AjROMWzAEWptqC3XmamwqDmwPc88d2YDup84tkDg20ZJdxw@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E826D4E43@uxcn10-tdc06.UoA.auckland.ac.nz>
 <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov>
 <CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com>
 <CALzTN-RPtGjgVY=NPgQOE0tVj5hvP9EQRWFkwdJzBvo64_vyKA@mail.gmail.com>
 <CAG6AjRP9KTRsNgOgDifr33MKvQN7SuuR-XR1r3pWcnwSW_6rcw@mail.gmail.com>
 <CALzTN-RNFaynep_vAhDu2NwNUsuo696SErYZYGn7bGOpaE3kVQ@mail.gmail.com>
 <CAG6AjRPaNEkdCtde30nJhf8mjoH0u8Pa1aceCQ9XVfarYVCRog@mail.gmail.com>
 <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov>
 <CAG6AjRPdVusAYjgBwSw94eE+PbbO2QYGezucvzKho2TJg2=ahQ@mail.gmail.com>
 <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov>
 <CAG6AjRPsLq+cEAAmsV-Ask0L6Ohb92SQPwDrwGzXeExaBjbdSw@mail.gmail.com>
Message-ID: <05E3077F-5FD7-4718-8E88-529BCD441F5F@mail.nih.gov>

Hello,

Unfortunately, I don't see the logic with it working with Slicer, but not working in native ITK as it uses the same code.

I have perused the NIFT1 C library that ITK has in the ThirdParty group, which appears up to date with the latest released version: 2.0.0.

There a quite a number of places where the calculation of the size of the image is not done at size_t/64-bits safe fashion, along with other 64-bit safe operations. I am concluding that the nifit file format doesn't readily support image > 4GB. Even if we then through the extensive effort of updating our version of the third party library the resulting images are very likely not going to work with other toosl that work with nifti images.

Brad

On Dec 2, 2014, at 11:14 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:

> The image contains a single non-zero voxel on each axial slice. 
> 
> When I load the image on Slicer the non-zero voxels are preserved as you traverse the image using the window slider.  
> When I read the image using a simple main program a big portion of the the non-zero voxels do not exist.
> 
> I had the same issue when the file was .nii (not compressed).
> 
> Fotis
>   
> 
> On Tue, Dec 2, 2014 at 10:58 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> So if you wrote and read with ITK ( via Slicer ), how do you know that the file is correct as you expect?
> 
> I see the file has a ".nii.gz" extension, meaning that it's compressed. Does the same issue occur when it's not compressed?
> 
> Brad
> 
> 
> 
> On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
> 
>> Hi,
>> 
>> I created and wrote the image on the disk using ITK 4.6.0. 
>> I visualized the image using Slicer 4.4.0.
>> 
>> The properties are:
>> Size : [1001, 1001, 8345]  
>> Spacing : [1,1,1]
>> Origin : [0, 0, 0]
>> Direction : 
>> 1 0 0
>> 0 1 0
>> 0 0 1
>> 
>> Fotis
>> 
>> On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>> Hello,
>> 
>> What software did you use to create and validate that this image is correct?
>> 
>> Thanks,
>> Brad
>> 
>> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
>> 
>>> Hi all,
>>> 
>>> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader.
>>> The test image contains non-zero values only at indexes (350,350,i)  where i=0 to 8300.
>>> The pixelType is short.
>>>  
>>> Thanks
>>> Fotis  
>>> 
>>> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>>> Thanks! Added.
>>> 
>>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
>>> > Hi,
>>> > I signed up for the ITK community on midas.
>>> >
>>> > Thanks,
>>> > Fotis Drakopoulos
>>> >
>>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick
>>> > <matt.mccormick at kitware.com> wrote:
>>> >>
>>> >> Hi Fotis,
>>> >>
>>> >> Thanks for helping to improve large nifti file support.
>>> >>
>>> >> The file can be uploaded on midas3.kitware.com.  Sign up for the ITK
>>> >> community [1], let the list know the name of your account, and myself
>>> >> or one of the other administrators will add upload priviledges to the
>>> >> account.
>>> >>
>>> >> The file could then be added to
>>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
>>> >>
>>> >> Thanks,
>>> >> Matt
>>> >>
>>> >> [1] http://midas3.kitware.com/midas/community/12
>>> >>
>>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos <fdrakopo at gmail.com>
>>> >> wrote:
>>> >> > Hi all,
>>> >> >
>>> >> > I created a test nifti image that reproduces the problem I mentioned
>>> >> > before.
>>> >> > How can I share this image with the ITK community?
>>> >> >
>>> >> > Best,
>>> >> > Fotis Drakopoulos
>>> >> >
>>> >> >
>>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp
>>> >> > <blowekamp at mail.nih.gov>
>>> >> > wrote:
>>> >> >>
>>> >> >> Shareable test data greatly helps determine the cause and fix these
>>> >> >> types
>>> >> >> of issues.
>>> >> >>
>>> >> >> Got data?
>>> >> >>
>>> >> >> Brad
>>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
>>> >> >>
>>> >> >> This is reminiscent of the previous problem with big TIFF images, now
>>> >> >> fixed.
>>> >> >>
>>> >> >> Gib
>>> >> >> ________________________________
>>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis
>>> >> >> Drakopoulos [fdrakopo at gmail.com]
>>> >> >> Sent: Monday, 24 November 2014 10:51 a.m.
>>> >> >> To: insight-users at itk.org; insight-developers at itk.org
>>> >> >> Subject: [ITK-users] Problem reading a big nifti volume.
>>> >> >>
>>> >> >> Hi all,
>>> >> >>
>>> >> >> For the last couple of days I have been trying reading (unsuccessfully)
>>> >> >> a
>>> >> >> big nifti volume labeled image from my disk.
>>> >> >>
>>> >> >> The pixel type is unsigned char and the rest specs of the image are:
>>> >> >> Size : [1001, 1001, 8345]  (in voxels)
>>> >> >> Spacing : [0.012, 0.012, 0.012]  (in mm)
>>> >> >> Origin : [0, 0, 0]
>>> >> >> Direction :
>>> >> >> 1 0 0
>>> >> >> 0 1 0
>>> >> >> 0 0 1
>>> >> >>
>>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea
>>> >> >> how it looks like. Indeed the object in the volume looks as it was
>>> >> >> expected.
>>> >> >> So far no problems. The specs of the image on Slicer are the same as
>>> >> >> above
>>> >> >> (except the direction which has flipped signs for the first two
>>> >> >> diagonal
>>> >> >> entries, as we know ).
>>> >> >>
>>> >> >> Then I tried to load the image in the memory using the
>>> >> >> itk::ImageFileReader  from ITK4.6.0 (64 bit-linux) version. After
>>> >> >> loading
>>> >> >> the image I noticed that there are pixels with zero values instead of
>>> >> >> non-zero by comparing the same indexes with the loaded image on Slicer.
>>> >> >>
>>> >> >> Then I decided to write the loaded image on the disk using the
>>> >> >> itk::ImageFileWriter.
>>> >> >>
>>> >> >> After opening the (written from ITK) image on Slicer I checked the
>>> >> >> specks
>>> >> >> and were the same with the original image as above. However I noticed
>>> >> >> that a
>>> >> >> big portion of the image is completely empty (black)!
>>> >> >>
>>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz
>>> >> >> DDR3L)
>>> >> >> and is using Red Hat Enterprise Linux Server 6.5.
>>> >> >> The size of the original nifti volume is :
>>> >> >>
>>> >> >> 25.7 MB (.nii.gz)
>>> >> >> 8.36 GB (.nii)
>>> >> >>
>>> >> >> Has anybody experienced similar difficulties trying to load so big
>>> >> >> volume
>>> >> >> data?
>>> >> >>
>>> >> >> Best,
>>> >> >> Fotis Drakopoulos
>>> >> >> CRTC
>>> >> >>
>>> >> >> _____________________________________
>>> >> >> 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
>>> >> >>
>>> >> >>
>>> >> >> ________________________________
>>> >> >>
>>> >> >> Spam
>>> >> >> Not spam
>>> >> >> Forget previous vote
>>> >> >
>>> >> >
>>> >> >
>>> >> > _______________________________________________
>>> >> > 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
>>> >> >
>>> >>
>>> >>
>>> >> --
>>> >>
>>> >
>>> 
>>> 
>>> --
>>> BEGIN-ANTISPAM-VOTING-LINKS
>>> ------------------------------------------------------
>>> 
>>> Teach CanIt if this mail (ID 03NkpHcqT) is spam:
>>> Spam:        about:blank
>>> Not spam:    about:blank
>>> Forget vote: about:blank
>>> ------------------------------------------------------
>>> END-ANTISPAM-VOTING-LINKS
>>> 
>>> 
>> 
>> 
>> Spam
>> Not spam
>> Forget previous vote
>> 
> 
> 
> Spam
> Not spam
> Forget previous vote
> 

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From dr.tim.allman at gmail.com  Tue Dec  2 14:35:27 2014
From: dr.tim.allman at gmail.com (Tim Allman)
Date: Tue, 2 Dec 2014 14:35:27 -0500
Subject: [ITK-users] Float dicom images
Message-ID: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com>

I have been having a bit of trouble trying to write Dicom images using itk::GDCMImageIO. The code suggests that this is supported but I know that this is a new feature. Has anyone else had any experience with this?

Thanks,
Tim


From matimontg at gmail.com  Tue Dec  2 14:44:59 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Tue, 2 Dec 2014 16:44:59 -0300
Subject: [ITK-users] Float dicom images
In-Reply-To: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com>
References: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com>
Message-ID: <CAKKNfuJE7b2qAghyt9UR5xze2Zx0N4zJW5sCo9AHJ0ryhQbyCg@mail.gmail.com>

are you trying to write float dicom images?

On Tue, Dec 2, 2014 at 4:35 PM, Tim Allman <dr.tim.allman at gmail.com> wrote:

> I have been having a bit of trouble trying to write Dicom images using
> itk::GDCMImageIO. The code suggests that this is supported but I know that
> this is a new feature. Has anyone else had any experience with this?
>
> Thanks,
> Tim
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://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
>
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From matimontg at gmail.com  Tue Dec  2 15:40:54 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Tue, 2 Dec 2014 17:40:54 -0300
Subject: [ITK-users] Float dicom images
In-Reply-To: <593F2FAE-DB1C-4C93-9AB0-A950AFDEDFCB@gmail.com>
References: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com>
 <CAKKNfuJE7b2qAghyt9UR5xze2Zx0N4zJW5sCo9AHJ0ryhQbyCg@mail.gmail.com>
 <593F2FAE-DB1C-4C93-9AB0-A950AFDEDFCB@gmail.com>
Message-ID: <CAKKNfu+uju1a2Yk37B+8f8GAdi=xp_8GThkoyK0HM7=_ULU3xg@mail.gmail.com>

adding insight users..

I've never dealt with float dicom images, can you send me a sample image? I
can try to write and see what's the problem. isn's saving the image or you
get a wrong saved image, such as WL WC changed etc?

On Tue, Dec 2, 2014 at 4:53 PM, Tim Allman <dr.tim.allman at gmail.com> wrote:

>
> On Dec 2, 2014, at 14:44 , Matias Montroull <matimontg at gmail.com> wrote:
>
> > are you trying to write float dicom images?
>
> Yes. Sorry for noting that only in the subject line. :-(
>
> >
> > On Tue, Dec 2, 2014 at 4:35 PM, Tim Allman <dr.tim.allman at gmail.com>
> wrote:
> > I have been having a bit of trouble trying to write Dicom images using
> itk::GDCMImageIO. The code suggests that this is supported but I know that
> this is a new feature. Has anyone else had any experience with this?
> >
> > Thanks,
> > Tim
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://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
> >
>
>
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From davis.vigneault at gmail.com  Tue Dec  2 15:56:19 2014
From: davis.vigneault at gmail.com (DVigneault)
Date: Tue, 2 Dec 2014 13:56:19 -0700 (MST)
Subject: [ITK-users] Pointing CMake to Updated ITK Library
Message-ID: <1417553779482-7586653.post@n2.nabble.com>

All--

I'm wondering how I need to update my CMakeLists.txt file to point it to a
particular version of ITK.  I'm working on OsX.  I previously had version
4.4.2 installed, and have recently installed 4.6.1.  However, when I run
this code...

itk::Version::Pointer version = itk::Version::New();
std::cout << version->GetITKVersion() << std::endl;

...it outputs 4.4.2.  I've copied my CMakeLists.txt file below.  I have
tried changing this line...

find_package(ITK REQUIRED)

...to...

find_package(ITK 4.6.1 REQUIRED)

...but when I do, I get the following error:

dyld: Library not loaded: /Applications/ITK/build/fftw/lib/libfftw3.3.dylib
  Referenced from: /Volumes/NO
NAME/Chicago/example_for_jack_yao/bin/./dv-simulated_phase
  Reason: image not found
Trace/BPT trap: 5

Thanks in advance for your help!

Best,

--Davis

# This is the root ITK CMakeLists file.
cmake_minimum_required(VERSION 2.4)
if(COMMAND CMAKE_POLICY)
  cmake_policy(SET CMP0003 NEW)
endif()

# This project is designed to be built outside the Insight source tree.
project(dv-simulated_phase)

# Find ITK.
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})

add_executable(dv-simulated_phase dv-simulated_phase.cxx )

target_link_libraries(dv-simulated_phase ${ITK_LIBRARIES})



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Pointing-CMake-to-Updated-ITK-Library-tp7586653.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Tue Dec  2 16:20:21 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 2 Dec 2014 16:20:21 -0500
Subject: [ITK-users] Pointing CMake to Updated ITK Library
In-Reply-To: <1417553779482-7586653.post@n2.nabble.com>
References: <1417553779482-7586653.post@n2.nabble.com>
Message-ID: <CALzTN-RwsP=hgiyfPQTvm+BLtp+6QE-oPQWa=QmiPSoaSHE32Q@mail.gmail.com>

Hi Davis,

The ITK build to use is usually selected in the CMake build
configuration (not in the source file CMakeLists.txt), by setting the
"ITK_DIR" variable.  This should point to the path that has the
desired ITKConfig.cmake file.

HTH,
Matt

On Tue, Dec 2, 2014 at 3:56 PM, DVigneault <davis.vigneault at gmail.com> wrote:
> All--
>
> I'm wondering how I need to update my CMakeLists.txt file to point it to a
> particular version of ITK.  I'm working on OsX.  I previously had version
> 4.4.2 installed, and have recently installed 4.6.1.  However, when I run
> this code...
>
> itk::Version::Pointer version = itk::Version::New();
> std::cout << version->GetITKVersion() << std::endl;
>
> ...it outputs 4.4.2.  I've copied my CMakeLists.txt file below.  I have
> tried changing this line...
>
> find_package(ITK REQUIRED)
>
> ...to...
>
> find_package(ITK 4.6.1 REQUIRED)
>
> ...but when I do, I get the following error:
>
> dyld: Library not loaded: /Applications/ITK/build/fftw/lib/libfftw3.3.dylib
>   Referenced from: /Volumes/NO
> NAME/Chicago/example_for_jack_yao/bin/./dv-simulated_phase
>   Reason: image not found
> Trace/BPT trap: 5
>
> Thanks in advance for your help!
>
> Best,
>
> --Davis
>
> # This is the root ITK CMakeLists file.
> cmake_minimum_required(VERSION 2.4)
> if(COMMAND CMAKE_POLICY)
>   cmake_policy(SET CMP0003 NEW)
> endif()
>
> # This project is designed to be built outside the Insight source tree.
> project(dv-simulated_phase)
>
> # Find ITK.
> find_package(ITK REQUIRED)
> include(${ITK_USE_FILE})
>
> add_executable(dv-simulated_phase dv-simulated_phase.cxx )
>
> target_link_libraries(dv-simulated_phase ${ITK_LIBRARIES})
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Pointing-CMake-to-Updated-ITK-Library-tp7586653.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://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 dclunie at dclunie.com  Tue Dec  2 17:14:29 2014
From: dclunie at dclunie.com (David Clunie)
Date: Tue, 02 Dec 2014 17:14:29 -0500
Subject: [ITK-users] Float dicom images
In-Reply-To: <CAKKNfu+uju1a2Yk37B+8f8GAdi=xp_8GThkoyK0HM7=_ULU3xg@mail.gmail.com>
References: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com>
 <CAKKNfuJE7b2qAghyt9UR5xze2Zx0N4zJW5sCo9AHJ0ryhQbyCg@mail.gmail.com>
 <593F2FAE-DB1C-4C93-9AB0-A950AFDEDFCB@gmail.com>
 <CAKKNfu+uju1a2Yk37B+8f8GAdi=xp_8GThkoyK0HM7=_ULU3xg@mail.gmail.com>
Message-ID: <547E39C5.9040801@dclunie.com>

We (DICOM) have only recently added support for floating point
pixel data in DICOM (Sup 172), so I don't know if any of the
toolkits used by ITK support it yet.

I know dcmtk will, hopefully soon, but I can't speak for GDCM.

I have some samples at:

   https://www.dropbox.com/sh/n4iqdjbhmwljx5e/AABllea-Muk0C2oo576nm_Mua?dl=0

if you want to try them; not perfect yet, but they have the float pixel
data payload.

I am assuming that you actually want to write floating point pixels,
rather than integer quantized pixels with a floating point scaling
factor.

David

On 12/2/14 3:40 PM, Matias Montroull wrote:
> adding insight users..
>
> I've never dealt with float dicom images, can you send me a sample image? I
> can try to write and see what's the problem. isn's saving the image or you
> get a wrong saved image, such as WL WC changed etc?
>
> On Tue, Dec 2, 2014 at 4:53 PM, Tim Allman <dr.tim.allman at gmail.com> wrote:
>
>>
>> On Dec 2, 2014, at 14:44 , Matias Montroull <matimontg at gmail.com> wrote:
>>
>>> are you trying to write float dicom images?
>>
>> Yes. Sorry for noting that only in the subject line. :-(
>>
>>>
>>> On Tue, Dec 2, 2014 at 4:35 PM, Tim Allman <dr.tim.allman at gmail.com>
>> wrote:
>>> I have been having a bit of trouble trying to write Dicom images using
>> itk::GDCMImageIO. The code suggests that this is supported but I know that
>> this is a new feature. Has anyone else had any experience with this?
>>>
>>> Thanks,
>>> Tim

From richard.beare at gmail.com  Wed Dec  3 01:03:06 2014
From: richard.beare at gmail.com (Richard Beare)
Date: Wed, 3 Dec 2014 17:03:06 +1100
Subject: [ITK-users] [ITK-dev] Problem reading a big nifti volume.
In-Reply-To: <05E3077F-5FD7-4718-8E88-529BCD441F5F@mail.nih.gov>
References: <CAG6AjROMWzAEWptqC3XmamwqDmwPc88d2YDup84tkDg20ZJdxw@mail.gmail.com>
 <BD80F91C3E2E394894ED4780703D7F9E826D4E43@uxcn10-tdc06.UoA.auckland.ac.nz>
 <790CBE9F-0722-4C59-9B6B-2FB619068CB9@mail.nih.gov>
 <CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com>
 <CALzTN-RPtGjgVY=NPgQOE0tVj5hvP9EQRWFkwdJzBvo64_vyKA@mail.gmail.com>
 <CAG6AjRP9KTRsNgOgDifr33MKvQN7SuuR-XR1r3pWcnwSW_6rcw@mail.gmail.com>
 <CALzTN-RNFaynep_vAhDu2NwNUsuo696SErYZYGn7bGOpaE3kVQ@mail.gmail.com>
 <CAG6AjRPaNEkdCtde30nJhf8mjoH0u8Pa1aceCQ9XVfarYVCRog@mail.gmail.com>
 <8A1F276D-37D7-48EB-9A95-87529ECA704A@mail.nih.gov>
 <CAG6AjRPdVusAYjgBwSw94eE+PbbO2QYGezucvzKho2TJg2=ahQ@mail.gmail.com>
 <287BA746-6F23-48D9-A7C5-2A87A37BD88E@mail.nih.gov>
 <CAG6AjRPsLq+cEAAmsV-Ask0L6Ohb92SQPwDrwGzXeExaBjbdSw@mail.gmail.com>
 <05E3077F-5FD7-4718-8E88-529BCD441F5F@mail.nih.gov>
Message-ID: <CA+V7QS92mMsKnGuhO44ARCRxNBmt3hncAgfgAwvDWcGCa-i5SQ@mail.gmail.com>

Hi,
I have, coincidentally, run into what I presume is the same issue. I'll add
what I've observed, but note that I haven't gone into investigations very
thoroughly.

I started with a 5.9GB mha volume. I found that an old version of ITK snap
crashed when attempting to view it.

I converted to nifti using the ConvertBetweenFileFormats tool, and found
that fslview crashed, itksnap crashed, mrview  (from mrtrix) was able to
view. I tested a newer version of itksnap and found crashing with nifti.
The new version of itksnap would load the mha but would only display part
of it (probably the first 2GB), the rest was blank.

I also found that imageJ was able to view the nifti.

So, I think writing large nifti files from ITK is OK. Reading appears
broken. I think there may be additional issues with large files with
itksnap.


On Wed, Dec 3, 2014 at 3:34 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> Unfortunately, I don't see the logic with it working with Slicer, but not
> working in native ITK as it uses the same code.
>
> I have perused the NIFT1 C library that ITK has in the ThirdParty group,
> which appears up to date with the latest released version: 2.0.0.
>
> There a quite a number of places where the calculation of the size of the
> image is not done at size_t/64-bits safe fashion, along with other 64-bit
> safe operations. I am concluding that the nifit file format doesn't readily
> support image > 4GB. Even if we then through the extensive effort of
> updating our version of the third party library the resulting images are
> very likely not going to work with other toosl that work with nifti images.
>
> Brad
>
> On Dec 2, 2014, at 11:14 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
>
> The image contains a single non-zero voxel on each axial slice.
>
> When I load the image on Slicer the non-zero voxels are preserved as you
> traverse the image using the window slider.
> When I read the image using a simple main program a big portion of the
> the non-zero voxels do not exist.
>
> I had the same issue when the file was .nii (not compressed).
>
> Fotis
>
>
> On Tue, Dec 2, 2014 at 10:58 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
>> So if you wrote and read with ITK ( via Slicer ), how do you know that
>> the file is correct as you expect?
>>
>> I see the file has a ".nii.gz" extension, meaning that it's compressed.
>> Does the same issue occur when it's not compressed?
>>
>> Brad
>>
>>
>>
>> On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos <fdrakopo at gmail.com>
>> wrote:
>>
>> Hi,
>>
>> I created and wrote the image on the disk using ITK 4.6.0.
>> I visualized the image using Slicer 4.4.0.
>>
>> The properties are:
>> Size : [1001, 1001, 8345]
>> Spacing : [1,1,1]
>> Origin : [0, 0, 0]
>> Direction :
>> 1 0 0
>> 0 1 0
>> 0 0 1
>>
>> Fotis
>>
>> On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp <blowekamp at mail.nih.gov
>> > wrote:
>>
>>> Hello,
>>>
>>> What software did you use to create and validate that this image is
>>> correct?
>>>
>>> Thanks,
>>> Brad
>>>
>>> On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos <fdrakopo at gmail.com>
>>> wrote:
>>>
>>> Hi all,
>>>
>>> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
>>> The image cannot loaded correctly when I use the itk::ImageFileReader.
>>> The test image contains non-zero values only at indexes (350,350,i)
>>>  where i=0 to 8300.
>>> The pixelType is short.
>>>
>>> Thanks
>>> Fotis
>>>
>>> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick <
>>> matt.mccormick at kitware.com> wrote:
>>>
>>>> Thanks! Added.
>>>>
>>>> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <fdrakopo at gmail.com>
>>>> wrote:
>>>> > Hi,
>>>> > I signed up for the ITK community on midas.
>>>> >
>>>> > Thanks,
>>>> > Fotis Drakopoulos
>>>> >
>>>> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick
>>>> > <matt.mccormick at kitware.com> wrote:
>>>> >>
>>>> >> Hi Fotis,
>>>> >>
>>>> >> Thanks for helping to improve large nifti file support.
>>>> >>
>>>> >> The file can be uploaded on midas3.kitware.com.  Sign up for the ITK
>>>> >> community [1], let the list know the name of your account, and myself
>>>> >> or one of the other administrators will add upload priviledges to the
>>>> >> account.
>>>> >>
>>>> >> The file could then be added to
>>>> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
>>>> >>
>>>> >> Thanks,
>>>> >> Matt
>>>> >>
>>>> >> [1] http://midas3.kitware.com/midas/community/12
>>>> >>
>>>> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos <
>>>> fdrakopo at gmail.com>
>>>> >> wrote:
>>>> >> > Hi all,
>>>> >> >
>>>> >> > I created a test nifti image that reproduces the problem I
>>>> mentioned
>>>> >> > before.
>>>> >> > How can I share this image with the ITK community?
>>>> >> >
>>>> >> > Best,
>>>> >> > Fotis Drakopoulos
>>>> >> >
>>>> >> >
>>>> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp
>>>> >> > <blowekamp at mail.nih.gov>
>>>> >> > wrote:
>>>> >> >>
>>>> >> >> Shareable test data greatly helps determine the cause and fix
>>>> these
>>>> >> >> types
>>>> >> >> of issues.
>>>> >> >>
>>>> >> >> Got data?
>>>> >> >>
>>>> >> >> Brad
>>>> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle <g.bogle at auckland.ac.nz>
>>>> wrote:
>>>> >> >>
>>>> >> >> This is reminiscent of the previous problem with big TIFF images,
>>>> now
>>>> >> >> fixed.
>>>> >> >>
>>>> >> >> Gib
>>>> >> >> ________________________________
>>>> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of
>>>> Fotis
>>>> >> >> Drakopoulos [fdrakopo at gmail.com]
>>>> >> >> Sent: Monday, 24 November 2014 10:51 a.m.
>>>> >> >> To: insight-users at itk.org; insight-developers at itk.org
>>>> >> >> Subject: [ITK-users] Problem reading a big nifti volume.
>>>> >> >>
>>>> >> >> Hi all,
>>>> >> >>
>>>> >> >> For the last couple of days I have been trying reading
>>>> (unsuccessfully)
>>>> >> >> a
>>>> >> >> big nifti volume labeled image from my disk.
>>>> >> >>
>>>> >> >> The pixel type is unsigned char and the rest specs of the image
>>>> are:
>>>> >> >> Size : [1001, 1001, 8345]  (in voxels)
>>>> >> >> Spacing : [0.012, 0.012, 0.012]  (in mm)
>>>> >> >> Origin : [0, 0, 0]
>>>> >> >> Direction :
>>>> >> >> 1 0 0
>>>> >> >> 0 1 0
>>>> >> >> 0 0 1
>>>> >> >>
>>>> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get
>>>> an idea
>>>> >> >> how it looks like. Indeed the object in the volume looks as it was
>>>> >> >> expected.
>>>> >> >> So far no problems. The specs of the image on Slicer are the same
>>>> as
>>>> >> >> above
>>>> >> >> (except the direction which has flipped signs for the first two
>>>> >> >> diagonal
>>>> >> >> entries, as we know ).
>>>> >> >>
>>>> >> >> Then I tried to load the image in the memory using the
>>>> >> >> itk::ImageFileReader  from ITK4.6.0 (64 bit-linux) version. After
>>>> >> >> loading
>>>> >> >> the image I noticed that there are pixels with zero values
>>>> instead of
>>>> >> >> non-zero by comparing the same indexes with the loaded image on
>>>> Slicer.
>>>> >> >>
>>>> >> >> Then I decided to write the loaded image on the disk using the
>>>> >> >> itk::ImageFileWriter.
>>>> >> >>
>>>> >> >> After opening the (written from ITK) image on Slicer I checked the
>>>> >> >> specks
>>>> >> >> and were the same with the original image as above. However I
>>>> noticed
>>>> >> >> that a
>>>> >> >> big portion of the image is completely empty (black)!
>>>> >> >>
>>>> >> >> My workstation has enough memory to load the image (768 GB 1600MHz
>>>> >> >> DDR3L)
>>>> >> >> and is using Red Hat Enterprise Linux Server 6.5.
>>>> >> >> The size of the original nifti volume is :
>>>> >> >>
>>>> >> >> 25.7 MB (.nii.gz)
>>>> >> >> 8.36 GB (.nii)
>>>> >> >>
>>>> >> >> Has anybody experienced similar difficulties trying to load so big
>>>> >> >> volume
>>>> >> >> data?
>>>> >> >>
>>>> >> >> Best,
>>>> >> >> Fotis Drakopoulos
>>>> >> >> CRTC
>>>> >> >>
>>>> >> >> _____________________________________
>>>> >> >> 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
>>>> >> >>
>>>> >> >>
>>>> >> >> ________________________________
>>>> >> >>
>>>> >> >> Spam
>>>> >> >> Not spam
>>>> >> >> Forget previous vote
>>>> >> >
>>>> >> >
>>>> >> >
>>>> >> > _______________________________________________
>>>> >> > 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
>>>> >> >
>>>> >>
>>>> >>
>>>> >> --
>>>> >>
>>>> >
>>>>
>>>>
>>>> --
>>>> BEGIN-ANTISPAM-VOTING-LINKS
>>>> ------------------------------------------------------
>>>>
>>>> Teach CanIt if this mail (ID 03NkpHcqT) is spam:
>>>> Spam:        about:blank
>>>> Not spam:    about:blank
>>>> Forget vote: about:blank
>>>> ------------------------------------------------------
>>>> END-ANTISPAM-VOTING-LINKS
>>>>
>>>>
>>>
>>>  ------------------------------
>>>
>>> Spam
>>> Not spam
>>> Forget previous vote
>>>
>>
>>
>>  ------------------------------
>>
>> Spam
>> <https://www.spamtrap.odu.edu/canit/b.php?i=03NmE09Ru&m=eb19ac9fd119&t=20141202&c=s>
>> Not spam
>> <https://www.spamtrap.odu.edu/canit/b.php?i=03NmE09Ru&m=eb19ac9fd119&t=20141202&c=n>
>> Forget previous vote
>> <https://www.spamtrap.odu.edu/canit/b.php?i=03NmE09Ru&m=eb19ac9fd119&t=20141202&c=f>
>>
>
>
>
> _____________________________________
> 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
>
>
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From matimontg at gmail.com  Wed Dec  3 06:30:35 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 3 Dec 2014 08:30:35 -0300
Subject: [ITK-users] CT MR Fusion
Message-ID: <CAKKNfuJMyFn=HmUbFts8xMyGQ8JS+SH6bMbSqpGf1YOB-0ttWg@mail.gmail.com>

Hi,

I have a set of DICOM images (CT) and another set of images from the same
patient (CT) which I need to fuse.

Looking at the examples, I noticed most of them are 2D, is there any
example that would fuse a set of CT/MR images?

I looked at some examples where the input was a single file but I actually
need to input a 2 directories, (the CT image directory and the MR image
directory). (I hope is that easy)

Thanks,

Matias.
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From yxp233 at postech.ac.kr  Wed Dec  3 21:55:01 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Thu, 4 Dec 2014 11:55:01 +0900
Subject: [ITK-users] GPU Manual
In-Reply-To: <1417620036528671.016779.ptmail04@ptmail04>
References: <CAC9gB0A8bOM3WmT1NMsCs6y4aNmxzZ3HF8_fidb2i_2xDwuCQw@mail.gmail.com>
 <CADZJ4hN0pwtPmNTN7KDN3ak-k5vpuCiJRSZbJVy6B1LivrEBwA@mail.gmail.com>
 <CAC9gB0AW=DifXebaFrrHfNXdi5hpbrs4wYsRC+X+qL+JE8iHmA@mail.gmail.com>
 <AFF9994E-9580-451B-B9AA-B73B668E66BC@mail.nih.gov>
 <CAC9gB0AqPe1hsvWvec6t2LbqFMrymrDrnxjY8qOEHwK5w9z+0Q@mail.gmail.com>
 <1417620036528671.016779.ptmail04@ptmail04>
Message-ID: <02aa01d00f6d$b2b199e0$1814cda0$@ac.kr>

Hi,

 

I have tried to build ITK with GPU ON to use GPU filters for a couple of
months but unfortunately I still cannot get it work. I searched with Google
but found little instruction or documentation available for how to compile.
May I ask whether there is any manual for how to compile ITK with GPU ON and
how to setup OpenCL directories? I have been feeling so frustrated with ITK
GPU. If you can share your knowledge about ITK GPU, I would appreciate it
very much. Thank you very much.

 

Best regards,

Yang

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From zeinsalah at gmail.com  Thu Dec  4 04:46:36 2014
From: zeinsalah at gmail.com (Zein Salah)
Date: Thu, 4 Dec 2014 10:46:36 +0100
Subject: [ITK-users] itkShapeLabelObject and
	itkBinaryImageToShapeLabelMapFilter. are missing
Message-ID: <CADiSopNoTOUVqJ79GyYmiWKci9VmSLRtD48AYo2ea6aR0VhiDg@mail.gmail.com>

Hi,

I am trying to do binary image labelling. My program claims that the files
itkShapeLabelObject.h and itkBinaryImageToShapeLabelMapFilter.h
are missing. I am using ITK 3.14.0. Are the filters not included in this
release? Or I am should configure something?

Thanks,
Zein

From waldovalenzuela at yahoo.com  Thu Dec  4 05:04:36 2014
From: waldovalenzuela at yahoo.com (Waldo Valenzuela)
Date: Thu, 4 Dec 2014 11:04:36 +0100
Subject: [ITK-users] About Compile ITK Ubuntu c++11
Message-ID: <EF6CF764-73A1-484E-AB68-6F83942F5BD9@yahoo.com>

Hi Guys,

I have been using ITK on Mac and Windows for a while, but I started to do it on linux and I have some problems enabling c++11 feature.

On my Scientific Linux 7 machine, I didn?t have any problem to compile ITK adding CMAKE_CXX_FLAG= -std=gnu++11, but in a Ubuntu 14.04 machine with gcc 4.8.2, I have the error ?constexpr needed? from the VNL library.

I know that this was a common error in the past with c++11, but I google it to solve it and couldn?t find any answer that really works.

There is a special configuration on CMAKE to solve this in Ubuntu?

Any help or guide is really welcome.

Cheers,

Waldo. 



From blowekamp at mail.nih.gov  Thu Dec  4 08:33:22 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 4 Dec 2014 08:33:22 -0500
Subject: [ITK-users] About Compile ITK Ubuntu c++11
In-Reply-To: <EF6CF764-73A1-484E-AB68-6F83942F5BD9@yahoo.com>
References: <EF6CF764-73A1-484E-AB68-6F83942F5BD9@yahoo.com>
Message-ID: <EE07FBCD-A8BC-4B13-A529-C486F6440A98@mail.nih.gov>

Hello,

When CMake does it's initial configuration it does a bunch of try compiles. The correct compiler and language flags are needed when this initial configuration is done. I suggest starting with a completely empty directory, then do some thing like: cmake -DCMAKE_CXX_FLAGS=-std=c++11 ~/src/ITK This will ensure the flags are there for the initial configuration to correctly detect C++11 features.

Brad

On Dec 4, 2014, at 5:04 AM, Waldo Valenzuela via Insight-users <insight-users at itk.org> wrote:

> Hi Guys,
> 
> I have been using ITK on Mac and Windows for a while, but I started to do it on linux and I have some problems enabling c++11 feature.
> 
> On my Scientific Linux 7 machine, I didn?t have any problem to compile ITK adding CMAKE_CXX_FLAG= -std=gnu++11, but in a Ubuntu 14.04 machine with gcc 4.8.2, I have the error ?constexpr needed? from the VNL library.
> 
> I know that this was a common error in the past with c++11, but I google it to solve it and couldn?t find any answer that really works.
> 
> There is a special configuration on CMAKE to solve this in Ubuntu?
> 
> Any help or guide is really welcome.
> 
> Cheers,
> 
> Waldo. 
> 
> 
> _____________________________________
> 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 zeinsalah at gmail.com  Thu Dec  4 10:35:28 2014
From: zeinsalah at gmail.com (Zein Salah)
Date: Thu, 4 Dec 2014 16:35:28 +0100
Subject: [ITK-users] registration of two point sets
Message-ID: <CADiSopMQTMfaYNgKp8_ynWAYuaEYuN-S8r2SOhF4WeY86Lidsg@mail.gmail.com>

Hi,

as I am not a registration expert, I have the following question.

I have two point sets to be registered with each other, e.g., A and B,
where points in A correspond to a subset of the points in B. The correspondences
are not known. Moreover, I want need to register the points in A to the
best fitting corresponding points in B, in a pair point fashion.

Has someone dealt with such an issue? Does ITK or IGSTK have suitable
mechanisms for such thing?

Much thanks,
Zeno

From matimontg at gmail.com  Thu Dec  4 10:41:49 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Thu, 4 Dec 2014 12:41:49 -0300
Subject: [ITK-users] [ITK] registration of two point sets
In-Reply-To: <CADiSopMQTMfaYNgKp8_ynWAYuaEYuN-S8r2SOhF4WeY86Lidsg@mail.gmail.com>
References: <CADiSopMQTMfaYNgKp8_ynWAYuaEYuN-S8r2SOhF4WeY86Lidsg@mail.gmail.com>
Message-ID: <CAKKNfuJ+2eKvsNJqcggZ69AAcNMVmK+m16-Q=R4hUed9b9XB4A@mail.gmail.com>

I've done that using VTK in C# if it helps

On Thu, Dec 4, 2014 at 12:35 PM, Zein Salah <zeinsalah at gmail.com> wrote:

> Hi,
>
> as I am not a registration expert, I have the following question.
>
> I have two point sets to be registered with each other, e.g., A and B,
> where points in A correspond to a subset of the points in B. The
> correspondences
> are not known. Moreover, I want need to register the points in A to the
> best fitting corresponding points in B, in a pair point fashion.
>
> Has someone dealt with such an issue? Does ITK or IGSTK have suitable
> mechanisms for such thing?
>
> Much thanks,
> Zeno
> _______________________________________________
> 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 Dec  4 13:13:21 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 4 Dec 2014 13:13:21 -0500
Subject: [ITK-users] ITK Development Confab
Message-ID: <CALzTN-TXw5mju_Rhn_zTwhYk4-Dme+RqNas8DaEQO3fvCCdOaw@mail.gmail.com>

Tomorrow we will to share, discuss, design, and learn with your fellow
ITK community members at the ITK Development Confab.  Bring your ITK
related topic of interest.  We will also discuss the 4.7 Software
Guide printing and 4.7 release candidate.


Details:
Friday, 11:00 AM Eastern USA time:

  https://plus.google.com/events/cstc9fe3njoggjqlaiacpiae9a4


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 dr.tim.allman at gmail.com  Thu Dec  4 13:42:11 2014
From: dr.tim.allman at gmail.com (Tim Allman)
Date: Thu, 04 Dec 2014 13:42:11 -0500
Subject: [ITK-users] Float dicom images
In-Reply-To: <547E39C5.9040801@dclunie.com>
References: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com>
 <CAKKNfuJE7b2qAghyt9UR5xze2Zx0N4zJW5sCo9AHJ0ryhQbyCg@mail.gmail.com>
 <593F2FAE-DB1C-4C93-9AB0-A950AFDEDFCB@gmail.com>
 <CAKKNfu+uju1a2Yk37B+8f8GAdi=xp_8GThkoyK0HM7=_ULU3xg@mail.gmail.com>
 <547E39C5.9040801@dclunie.com>
Message-ID: <5480AB03.1080705@gmail.com>

I just read Supplement 172 and it certainly addresses what I want which 
is to create parametric maps and not lose information (sign, dynamic 
range etc.) on storage.

My situation is that I am writing a plugin for Osirix, a DICOM (only) 
viewer which runs on OSX (only). I can create the maps I want internally 
as the viewer uses float as its pixel type internally but it saves 
everything as unsigned 16 bit integers. It will read floating point 
images however so perhaps writing them will come soon.

I single stepped through the writing of a float image and discovered 
that GDCM has some code clearly intended to support I/O of these images 
but it is incomplete. It will indeed write float images but they are 
rescaled to have a range of 0 - MAXFLOAT.

Tim

On 14-12-02 05:14 PM, David Clunie wrote:
> We (DICOM) have only recently added support for floating point
> pixel data in DICOM (Sup 172), so I don't know if any of the
> toolkits used by ITK support it yet.
>
> I know dcmtk will, hopefully soon, but I can't speak for GDCM.
>
> I have some samples at:
>
> https://www.dropbox.com/sh/n4iqdjbhmwljx5e/AABllea-Muk0C2oo576nm_Mua?dl=0
>
> if you want to try them; not perfect yet, but they have the float pixel
> data payload.
>
> I am assuming that you actually want to write floating point pixels,
> rather than integer quantized pixels with a floating point scaling
> factor.
>
> David
>
> On 12/2/14 3:40 PM, Matias Montroull wrote:
>> adding insight users..
>>
>> I've never dealt with float dicom images, can you send me a sample 
>> image? I
>> can try to write and see what's the problem. isn's saving the image 
>> or you
>> get a wrong saved image, such as WL WC changed etc?
>>
>> On Tue, Dec 2, 2014 at 4:53 PM, Tim Allman <dr.tim.allman at gmail.com> 
>> wrote:
>>
>>>
>>> On Dec 2, 2014, at 14:44 , Matias Montroull <matimontg at gmail.com> 
>>> wrote:
>>>
>>>> are you trying to write float dicom images?
>>>
>>> Yes. Sorry for noting that only in the subject line. :-(
>>>
>>>>
>>>> On Tue, Dec 2, 2014 at 4:35 PM, Tim Allman <dr.tim.allman at gmail.com>
>>> wrote:
>>>> I have been having a bit of trouble trying to write Dicom images using
>>> itk::GDCMImageIO. The code suggests that this is supported but I 
>>> know that
>>> this is a new feature. Has anyone else had any experience with this?
>>>>
>>>> Thanks,
>>>> Tim
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://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

-- 
Tim Allman, Ph.D.
35 Margaret Street,
Guelph Ontario N1E 5R6
Canada

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From millerjv at gmail.com  Thu Dec  4 15:41:42 2014
From: millerjv at gmail.com (Jim Miller)
Date: Thu, 4 Dec 2014 15:41:42 -0500
Subject: [ITK-users] GPU Manual
In-Reply-To: <02aa01d00f6d$b2b199e0$1814cda0$@ac.kr>
References: <CAC9gB0A8bOM3WmT1NMsCs6y4aNmxzZ3HF8_fidb2i_2xDwuCQw@mail.gmail.com>
 <CADZJ4hN0pwtPmNTN7KDN3ak-k5vpuCiJRSZbJVy6B1LivrEBwA@mail.gmail.com>
 <CAC9gB0AW=DifXebaFrrHfNXdi5hpbrs4wYsRC+X+qL+JE8iHmA@mail.gmail.com>
 <AFF9994E-9580-451B-B9AA-B73B668E66BC@mail.nih.gov>
 <CAC9gB0AqPe1hsvWvec6t2LbqFMrymrDrnxjY8qOEHwK5w9z+0Q@mail.gmail.com>
 <1417620036528671.016779.ptmail04@ptmail04>
 <02aa01d00f6d$b2b199e0$1814cda0$@ac.kr>
Message-ID: <6738AC11-E741-4152-AFAC-0E79FDD36CF9@gmail.com>

I just did a fresh checkout of ITK and clean build on the Mac. When configuring with CMake, I turned on BUILD_EXAMPLES, BUILD_TESTING, and ITK_USE_GPU. 

All the GPU related tests passed. 

Jim

> On Dec 3, 2014, at 9:55 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi,
>  
> I have tried to build ITK with GPU ON to use GPU filters for a couple of months but unfortunately I still cannot get it work. I searched with Google but found little instruction or documentation available for how to compile. May I ask whether there is any manual for how to compile ITK with GPU ON and how to setup OpenCL directories? I have been feeling so frustrated with ITK GPU. If you can share your knowledge about ITK GPU, I would appreciate it very much. Thank you very much.
>  
> Best regards,
> Yang
> _____________________________________
> 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
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From millerjv at gmail.com  Thu Dec  4 16:25:59 2014
From: millerjv at gmail.com (Jim Miller)
Date: Thu, 4 Dec 2014 16:25:59 -0500
Subject: [ITK-users] GPU Implementation
In-Reply-To: <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
Message-ID: <CAPqm7ahA5tcZZoxboRfd3QO491dqEw7Z9AjTDQfGxH3ry4t7bw@mail.gmail.com>

Xiaopeng,

I changed your target_link_libraries line to be

target_link_libraries(itkGPUDemonsRegistrationFilterTest
ITKGPUPDEDeformable ${ITK_LIBRARIES} )

Without adding ITKGPUPDEDeformable to the target_link_libraries, I would
get an error in linking like you had.

When ITK is built, the kernel functions (OpenCL code) are "compiled into"
the C++ code. Basically, the .cl files are converted into a C++ file where
the OpenCL code is encoded as a C++ string. This C++ code implements the
method GetOpenCLSource() which returns that string containing the OpenCL
code.  The PDE registration OpenCL kernels are compiled into the library
ITKGPUPDEDeformable. If you had used other GPU filters, you would have had
to add the libraries that contain those kernels as well to your
target_link_libraries.

Jim



On Thu, Nov 27, 2014 at 7:34 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

> Hi Jim,
>
> I am sorry but could you please build the code enclosed to check whether
> you
> also have that kind of errors or not?
>
> Thank you very much.
>
> Best,
> Xiaopeng
>
> -----Original Message-----
> From: Xiaopeng Yang [mailto:yxp233 at postech.ac.kr]
> Sent: Wednesday, November 26, 2014 9:34 PM
> To: 'Jim Miller'
> Cc: 'Michael Pinkert'; 'insight-users at itk.org'
> Subject: RE: [ITK-users] GPU Implementation
>
> Hi,
>
> I tried to compile the code from Modules\Registration\GPUPDEDeformable\test
> folder. Enclosed please find the code and CMakeLists file. I am quite new
> to
> GPU, sorry I could not understand your explanation. Could you point out
> what
> I missed please?
>
> Thanks,
> Xiaopeng
>
> -----Original Message-----
> From: Jim Miller [mailto:millerjv at gmail.com]
> Sent: Wednesday, November 26, 2014 9:10 PM
> To: Xiaopeng Yang
> Cc: Michael Pinkert; insight-users at itk.org
> Subject: Re: [ITK-users] GPU Implementation
>
> This doesn't look like any issue with finding OpenCL. The link error is
> saying it cannot find the implementation of an ITK method.
>
> I think  GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void) is
> supposed to return the kernel's implementation (probably as a string
> containing the OpenCL code).
>
> Is there a txx file that is not being included? Does your program contain
> the same headers and test?
>
> (I guess the error could occur if OpenCL was not found if the
> implementation
> of this method in  GPUPDEDeformableRegistrationFilterKernel is within
> #ifdef/#endif on OpenCL.)
>
> Jim
>
> > On Nov 25, 2014, at 10:03 PM, Xiaopeng Yang <yxp233 at postech.ac.kr>
> wrote:
> >
> > Hi Michael,
> >
> > I also had the same errors while building my GPU registration program.
> > Have you solved the problems? I guess the error was caused by improper
> > setting in CMakeLists.txt file, but I could not find any
> > CMakeLists.txt sample regarding GPU implementation in ITK. I doubt
> > whether there are users using this GPU module or not.
> >
> > Best regards,
> > Xiaopeng Yang
> >
> >
> > This is the question you raised:
> >
> > I am trying to implement the GPU demons registration algorithm, but I
> > have been having difficulty getting the program to compile.  I believe
> > the errors are because it cannot find the OpenCL library correctly,
> > but I'm not sure how to fix it.
> >
> > I am using a NVIDIA Quadro FX 570 and am currently using OpenCL
> > through the CUDA Computing Toolkit 4.2.  My cmake file is attached,
> > but I have had to manually enter in the directory locations to CMake
> > because I have not been able to find a FindOpenCL.cmake file that
> > works correctly.  My operating system is Windows 7 x64.
> >
> > I am able to compile ITK after generating it in CMake with manually
> > linked directories and Itk_Use_Gpu checked, but I have not been able
> > to compile my program without getting errors, which are listed at the
> bottom.
> >
> > Does anyone have suggestions as to how to fix this?
> >
> > Best regards,
> > Michael Pinkert
> >
> > 2>registrationFunctions.obj : error LNK2019: unresolved external
> > 2>symbol
> > "public: static char const * __cdecl
> > itk::GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void)"
> > (?GetOpenCLSource at GPUPDEDeformableRegistrationFilterKernel@itk@@SAPEBD
> > XZ) referenced in function "public: static char const * __cdecl
> > itk::GPUPDEDeformableRegistrationFilter<class
> > itk::GPUImage<float,3>,class itk::GPUImage<float,3>,class
> > itk::GPUImage<class itk::Vector<float,3>,3>,class
> > itk::DemonsRegistrationFilter<class
> > itk::GPUImage<float,3>,class itk::GPUImage<float,3>,class
> > itk::GPUImage<class itk::Vector<float,3>,3> > >::GetOpenCLSource(void)"
> > (?GetOpenCLSource@?$GPUPDEDeformableRegistrationFilter at V?$GPUImage at M$0
> > 2 at itk@
> > @V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@V?$DemonsRegistrationFilter
> > @V?$GP
> > UImage at M$02 at itk@@V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@2@@itk@@SA
> > PEBDXZ
> > )
> >
> > 2>registrationFunctions.obj : error LNK2019: unresolved external
> > 2>symbol
> > "public: static char const * __cdecl
> > itk::GPUDemonsRegistrationFunctionKernel::GetOpenCLSource(void)"
> > (?GetOpenCLSource at GPUDemonsRegistrationFunctionKernel@itk@@SAPEBDXZ)
> > referenced in function "public: static char const * __cdecl
> > itk::GPUDemonsRegistrationFunction<class itk::GPUImage<float,3>,class
> > itk::GPUImage<float,3>,classitk::GPUImage<class
> > itk::Vector<float,3>,3>
> >> ::GetOpenCLSource(void)"
> > (?GetOpenCLSource@?$GPUDemonsRegistrationFunction at V?$GPUImage at M$02 at itk
> > @@V12@
> > V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@itk@@SAPEBDXZ)
> >
> >
> >
> >
> > _____________________________________
> > 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
>
>
>
>
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From lloyd at itis.ethz.ch  Thu Dec  4 17:18:11 2014
From: lloyd at itis.ethz.ch (Bryn Lloyd)
Date: Thu, 04 Dec 2014 23:18:11 +0100
Subject: [ITK-users] How to abort execution of ImageRegistrationMethodv4 /
	Optimizer
Message-ID: <5480DDA3.905@itis.ethz.ch>

Hi

I recently started using ITK again and am trying out the ITK 
registration framework v4.


I am trying to gracefully abort/stop the ImageRegistrationMethodv4 
process, however it just continues.

In my Command class, which observes an IterationEvent of the 
ImageRegistrationMethodv4 and Optimizer  I call
1.  registration_method_v4->SetAbortGenerateData( true ); // object of 
type ImageRegistrationMethodv4<...>

2. optimizer->StopOptimization();

However, the process just continues to execute. Is this supposed to 
work? What am I doing wrong?

Thanks and best regards
Bryn



From lloyd at itis.ethz.ch  Thu Dec  4 17:48:09 2014
From: lloyd at itis.ethz.ch (Bryn Lloyd)
Date: Thu, 04 Dec 2014 23:48:09 +0100
Subject: [ITK-users] How to abort execution of ImageRegistrationMethodv4
 / Optimizer
In-Reply-To: <5480DDA3.905@itis.ethz.ch>
References: <5480DDA3.905@itis.ethz.ch>
Message-ID: <5480E4A9.3050304@itis.ethz.ch>

At a first glance it seems that ImageRegistrationMethodv4 does not check 
for the abort flag:

ImageRegistrationMethodv4<TFixedImage, TMovingImage, TTransform, 
TVirtualImage>
::GenerateData()
{
   this->AllocateOutputs();
   for( this->m_CurrentLevel = 0; this->m_CurrentLevel < 
this->m_NumberOfLevels; this->m_CurrentLevel++ )
     {
     this->InitializeRegistrationAtEachLevel( this->m_CurrentLevel );

     this->m_Metric->Initialize();

     this->m_Optimizer->StartOptimization();
     }
}

If I modify this code to check for m_AbortGenerateData, the registration 
terminates as expected.


In addition it seems that the members m_CurrentMetricValue, 
m_CurrentIteration etc. are never updated during optimization.

Best regards
Bryn



On 04.12.2014 23:18, Bryn Lloyd wrote:
> Hi
>
> I recently started using ITK again and am trying out the ITK 
> registration framework v4.
>
>
> I am trying to gracefully abort/stop the ImageRegistrationMethodv4 
> process, however it just continues.
>
> In my Command class, which observes an IterationEvent of the 
> ImageRegistrationMethodv4 and Optimizer  I call
> 1.  registration_method_v4->SetAbortGenerateData( true ); // object of 
> type ImageRegistrationMethodv4<...>
>
> 2. optimizer->StopOptimization();
>
> However, the process just continues to execute. Is this supposed to 
> work? What am I doing wrong?
>
> Thanks and best regards
> Bryn
>
>
> _____________________________________
> 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 yxp233 at postech.ac.kr  Fri Dec  5 00:41:20 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Fri, 5 Dec 2014 14:41:20 +0900
Subject: [ITK-users] GPU Implementation
In-Reply-To: <141772836420039.030290.ptmail04@ptmail04>
References: <1405441657014-7585907.post@n2.nabble.com>	<4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>	<1405533203306221.02118.ptmail04@ptmail04>	<035401d00925$9a422350$cec669f0$@ac.kr>	<1417003820802645.09215.ptmail03@ptmail03>	<042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
Message-ID: <001801d0104e$19711800$4c534800$@ac.kr>

Dear Jim,

 

Thanks for your help. I built the test successfully, but I met an error when
I run the program. Please see the attached image file. 

 

Best,

Xiaopeng

 



 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Friday, December 05, 2014 6:26 AM
To: Xiaopeng Yang
Cc: Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

Xiaopeng, 

 

I changed your target_link_libraries line to be

 

target_link_libraries(itkGPUDemonsRegistrationFilterTest ITKGPUPDEDeformable
${ITK_LIBRARIES} )

 

Without adding ITKGPUPDEDeformable to the target_link_libraries, I would get
an error in linking like you had.    

 

When ITK is built, the kernel functions (OpenCL code) are "compiled into"
the C++ code. Basically, the .cl files are converted into a C++ file where
the OpenCL code is encoded as a C++ string. This C++ code implements the
method GetOpenCLSource() which returns that string containing the OpenCL
code.  The PDE registration OpenCL kernels are compiled into the library
ITKGPUPDEDeformable. If you had used other GPU filters, you would have had
to add the libraries that contain those kernels as well to your
target_link_libraries.

 

Jim

 

 

 

On Thu, Nov 27, 2014 at 7:34 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi Jim,

I am sorry but could you please build the code enclosed to check whether you
also have that kind of errors or not?

Thank you very much.

Best,
Xiaopeng

-----Original Message-----
From: Xiaopeng Yang [mailto:yxp233 at postech.ac.kr]
Sent: Wednesday, November 26, 2014 9:34 PM
To: 'Jim Miller'
Cc: 'Michael Pinkert'; 'insight-users at itk.org'
Subject: RE: [ITK-users] GPU Implementation

Hi,

I tried to compile the code from Modules\Registration\GPUPDEDeformable\test
folder. Enclosed please find the code and CMakeLists file. I am quite new to
GPU, sorry I could not understand your explanation. Could you point out what
I missed please?

Thanks,
Xiaopeng


-----Original Message-----
From: Jim Miller [mailto:millerjv at gmail.com]
Sent: Wednesday, November 26, 2014 9:10 PM
To: Xiaopeng Yang
Cc: Michael Pinkert; insight-users at itk.org
Subject: Re: [ITK-users] GPU Implementation

This doesn't look like any issue with finding OpenCL. The link error is
saying it cannot find the implementation of an ITK method.

I think  GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void) is
supposed to return the kernel's implementation (probably as a string
containing the OpenCL code).

Is there a txx file that is not being included? Does your program contain
the same headers and test?

(I guess the error could occur if OpenCL was not found if the implementation
of this method in  GPUPDEDeformableRegistrationFilterKernel is within
#ifdef/#endif on OpenCL.)

Jim

> On Nov 25, 2014, at 10:03 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
>
> Hi Michael,
>
> I also had the same errors while building my GPU registration program.
> Have you solved the problems? I guess the error was caused by improper
> setting in CMakeLists.txt file, but I could not find any
> CMakeLists.txt sample regarding GPU implementation in ITK. I doubt
> whether there are users using this GPU module or not.
>
> Best regards,
> Xiaopeng Yang
>
>
> This is the question you raised:
>
> I am trying to implement the GPU demons registration algorithm, but I
> have been having difficulty getting the program to compile.  I believe
> the errors are because it cannot find the OpenCL library correctly,
> but I'm not sure how to fix it.
>
> I am using a NVIDIA Quadro FX 570 and am currently using OpenCL
> through the CUDA Computing Toolkit 4.2.  My cmake file is attached,
> but I have had to manually enter in the directory locations to CMake
> because I have not been able to find a FindOpenCL.cmake file that
> works correctly.  My operating system is Windows 7 x64.
>
> I am able to compile ITK after generating it in CMake with manually
> linked directories and Itk_Use_Gpu checked, but I have not been able
> to compile my program without getting errors, which are listed at the
bottom.
>
> Does anyone have suggestions as to how to fix this?
>
> Best regards,
> Michael Pinkert
>
> 2>registrationFunctions.obj : error LNK2019: unresolved external

> 2>symbol
> "public: static char const * __cdecl
> itk::GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void)"
> (?GetOpenCLSource at GPUPDEDeformableRegistrationFilterKernel@itk@@SAPEBD
> XZ) referenced in function "public: static char const * __cdecl
> itk::GPUPDEDeformableRegistrationFilter<class
> itk::GPUImage<float,3>,class itk::GPUImage<float,3>,class
> itk::GPUImage<class itk::Vector<float,3>,3>,class
> itk::DemonsRegistrationFilter<class
> itk::GPUImage<float,3>,class itk::GPUImage<float,3>,class
> itk::GPUImage<class itk::Vector<float,3>,3> > >::GetOpenCLSource(void)"
> (?GetOpenCLSource@?$GPUPDEDeformableRegistrationFilter at V?$GPUImage at M$0
> 2 at itk@
> @V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@V?$DemonsRegistrationFilter
> @V?$GP
> UImage at M$02 at itk@@V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@2@@itk@@SA
> PEBDXZ
> )
>
> 2>registrationFunctions.obj : error LNK2019: unresolved external
> 2>symbol

> "public: static char const * __cdecl
> itk::GPUDemonsRegistrationFunctionKernel::GetOpenCLSource(void)"
> (?GetOpenCLSource at GPUDemonsRegistrationFunctionKernel@itk@@SAPEBDXZ)
> referenced in function "public: static char const * __cdecl
> itk::GPUDemonsRegistrationFunction<class itk::GPUImage<float,3>,class
> itk::GPUImage<float,3>,classitk::GPUImage<class
> itk::Vector<float,3>,3>
>> ::GetOpenCLSource(void)"
> (?GetOpenCLSource@?$GPUDemonsRegistrationFunction at V?$GPUImage at M$02 at itk
> @@V12@
> V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@itk@@SAPEBDXZ)
>
>
>
>
> _____________________________________
> 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




 

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From drescherjm at gmail.com  Fri Dec  5 02:23:52 2014
From: drescherjm at gmail.com (John Drescher)
Date: Fri, 5 Dec 2014 02:23:52 -0500
Subject: [ITK-users] GPU Implementation
In-Reply-To: <001801d0104e$19711800$4c534800$@ac.kr>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
Message-ID: <CAEhu1-5i=Bu-fJrm8W1GF2tp-UiwqVAJOhs9bdfmQkgr+kUoHA@mail.gmail.com>

On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

> Dear Jim,
>
>
>
> Thanks for your help. I built the test successfully, but I met an error
> when I run the program. Please see the attached image file.
>
>
>
> Best,
>
> Xiaopeng
>
>
>
>
>

Is that an error?

John
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From yxp233 at postech.ac.kr  Fri Dec  5 02:43:10 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Fri, 5 Dec 2014 16:43:10 +0900
Subject: [ITK-users] GPU Implementation
In-Reply-To: <141776427270398.129323.ptmail04@ptmail04>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
Message-ID: <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>

Hi John,

 

Sorry I mean the program got crashed after showing #define T float. 

 

Thanks,

Xiaopeng

 

From: John Drescher [mailto:drescherjm at gmail.com] 
Sent: Friday, December 05, 2014 4:24 PM
To: Xiaopeng Yang
Cc: Jim Miller; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

 

 

On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear Jim,

 

Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. 

 

Best,

Xiaopeng

 



 

 

Is that an error? 

John 

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From millerjv at gmail.com  Fri Dec  5 09:14:43 2014
From: millerjv at gmail.com (Jim Miller)
Date: Fri, 5 Dec 2014 09:14:43 -0500
Subject: [ITK-users] GPU Implementation
In-Reply-To: <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
Message-ID: <40B2E025-88FB-4EB1-B23D-64CB2C983C0D@gmail.com>

How large are the images that you are using?

Jim

> On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi John,
>  
> Sorry I mean the program got crashed after showing #define T float.
>  
> Thanks,
> Xiaopeng
>  
> From: John Drescher [mailto:drescherjm at gmail.com] 
> Sent: Friday, December 05, 2014 4:24 PM
> To: Xiaopeng Yang
> Cc: Jim Miller; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
>  
>  
> On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> Dear Jim,
>  
> Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file.
>  
> Best,
> Xiaopeng
>  
> <image001.png>
>  
>  
> Is that an error?
> 
> John
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From millerjv at gmail.com  Fri Dec  5 11:57:17 2014
From: millerjv at gmail.com (Jim Miller)
Date: Fri, 5 Dec 2014 11:57:17 -0500
Subject: [ITK-users] GPU Implementation
In-Reply-To: <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
Message-ID: <5D56294F-D85B-4F45-AAE5-3CE151862C03@gmail.com>

Do the GPU tests run our system?

$ cd ITK-build
$ ctest -V -R GPU


Jim

> On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi John,
>  
> Sorry I mean the program got crashed after showing #define T float.
>  
> Thanks,
> Xiaopeng
>  
> From: John Drescher [mailto:drescherjm at gmail.com] 
> Sent: Friday, December 05, 2014 4:24 PM
> To: Xiaopeng Yang
> Cc: Jim Miller; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
>  
>  
> On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> Dear Jim,
>  
> Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file.
>  
> Best,
> Xiaopeng
>  
> <image001.png>
>  
>  
> Is that an error?
> 
> John
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From llliu at umich.edu  Fri Dec  5 17:19:18 2014
From: llliu at umich.edu (Lianli Liu)
Date: Fri, 5 Dec 2014 17:19:18 -0500
Subject: [ITK-users] compling itkScaleInvariantFeatureImageFilter
Message-ID: <CAGKqDmd+PPiBsr5nomC+dK31QMAiS5kQCN6vne17rW5SD9xUWA@mail.gmail.com>

Hi all,

I want to use the itkScaleInvariantFeatureImageFilter but I am getting
several errors when compiling, such as:
 error: ?FeatureType? was not declared in this scope
 error: ?PointSetType? is not a class or namespace

Does anyone has experience in using this filter?

Also, I am unclear how where to specify input image in the filter.

Thanks!
Lianli
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From yxp233 at postech.ac.kr  Fri Dec  5 18:45:13 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Sat, 6 Dec 2014 08:45:13 +0900
Subject: [ITK-users] GPU Implementation
In-Reply-To: <1417788892216194.03990.ptmail04@ptmail04>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
 <1417788892216194.03990.ptmail04@ptmail04>
Message-ID: <008c01d010e5$84172950$8c457bf0$@ac.kr>

Dear Jim,

 

The images are quite large: 512 * 512 *300. 

 

I did not build test when I compile ITK.

 

Thanks,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Friday, December 05, 2014 11:15 PM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

How large are the images that you are using?

Jim


On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi John,

 

Sorry I mean the program got crashed after showing #define T float. 

 

Thanks,

Xiaopeng

 

From: John Drescher [mailto:drescherjm at gmail.com] 
Sent: Friday, December 05, 2014 4:24 PM
To: Xiaopeng Yang
Cc: Jim Miller; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

 

 

On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear Jim,

 

Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. 

 

Best,

Xiaopeng

 

<image001.png>

 

 

Is that an error? 

John 

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From millerjv at gmail.com  Fri Dec  5 20:11:04 2014
From: millerjv at gmail.com (Jim Miller)
Date: Fri, 5 Dec 2014 20:11:04 -0500
Subject: [ITK-users] GPU Implementation
In-Reply-To: <008c01d010e5$84172950$8c457bf0$@ac.kr>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
 <1417788892216194.03990.ptmail04@ptmail04>
 <008c01d010e5$84172950$8c457bf0$@ac.kr>
Message-ID: <DB1DC723-1C47-45AA-BDCD-6C8E6EC1A852@gmail.com>

I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. 

Jim

> On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Dear Jim,
>  
> The images are quite large: 512 * 512 *300.
>  
> I did not build test when I compile ITK.
>  
> Thanks,
> Xiaopeng
>  
> From: Jim Miller [mailto:millerjv at gmail.com] 
> Sent: Friday, December 05, 2014 11:15 PM
> To: Xiaopeng Yang
> Cc: John Drescher; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
> How large are the images that you are using?
> 
> Jim
> 
> On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi John,
>  
> Sorry I mean the program got crashed after showing #define T float.
>  
> Thanks,
> Xiaopeng
>  
> From: John Drescher [mailto:drescherjm at gmail.com] 
> Sent: Friday, December 05, 2014 4:24 PM
> To: Xiaopeng Yang
> Cc: Jim Miller; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
>  
>  
> On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> Dear Jim,
>  
> Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file.
>  
> Best,
> Xiaopeng
>  
> <image001.png>
>  
>  
> Is that an error?
> 
> John
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From yxp233 at postech.ac.kr  Fri Dec  5 20:39:33 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Sat, 6 Dec 2014 10:39:33 +0900
Subject: [ITK-users] GPU Implementation
In-Reply-To: <1417828271180838.110987.ptmail04@ptmail04>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
 <1417788892216194.03990.ptmail04@ptmail04>
 <008c01d010e5$84172950$8c457bf0$@ac.kr>
 <1417828271180838.110987.ptmail04@ptmail04>
Message-ID: <009a01d010f5$7d4043e0$77c0cba0$@ac.kr>

Hi Jim,

 

So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? 

 

Thanks,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Saturday, December 06, 2014 10:11 AM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. 

Jim


On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear Jim,

 

The images are quite large: 512 * 512 *300. 

 

I did not build test when I compile ITK.

 

Thanks,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Friday, December 05, 2014 11:15 PM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

How large are the images that you are using?

Jim


On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi John,

 

Sorry I mean the program got crashed after showing #define T float. 

 

Thanks,

Xiaopeng

 

From: John Drescher [mailto:drescherjm at gmail.com] 
Sent: Friday, December 05, 2014 4:24 PM
To: Xiaopeng Yang
Cc: Jim Miller; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

 

 

On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear Jim,

 

Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. 

 

Best,

Xiaopeng

 

<image001.png>

 

 

Is that an error? 

John 

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From millerjv at gmail.com  Fri Dec  5 22:50:04 2014
From: millerjv at gmail.com (Jim Miller)
Date: Fri, 5 Dec 2014 22:50:04 -0500
Subject: [ITK-users] GPU Implementation
In-Reply-To: <009a01d010f5$7d4043e0$77c0cba0$@ac.kr>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
 <1417788892216194.03990.ptmail04@ptmail04>
 <008c01d010e5$84172950$8c457bf0$@ac.kr>
 <1417828271180838.110987.ptmail04@ptmail04>
 <009a01d010f5$7d4043e0$77c0cba0$@ac.kr>
Message-ID: <0C9B1AAB-2795-4526-BE27-008DB18EE7F1@gmail.com>

I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. 

Jim

> On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi Jim,
>  
> So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card?
>  
> Thanks,
> Xiaopeng
>  
> From: Jim Miller [mailto:millerjv at gmail.com] 
> Sent: Saturday, December 06, 2014 10:11 AM
> To: Xiaopeng Yang
> Cc: John Drescher; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
> I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. 
> 
> Jim
> 
> On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Dear Jim,
>  
> The images are quite large: 512 * 512 *300.
>  
> I did not build test when I compile ITK.
>  
> Thanks,
> Xiaopeng
>  
> From: Jim Miller [mailto:millerjv at gmail.com] 
> Sent: Friday, December 05, 2014 11:15 PM
> To: Xiaopeng Yang
> Cc: John Drescher; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
> How large are the images that you are using?
> 
> Jim
> 
> On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi John,
>  
> Sorry I mean the program got crashed after showing #define T float.
>  
> Thanks,
> Xiaopeng
>  
> From: John Drescher [mailto:drescherjm at gmail.com] 
> Sent: Friday, December 05, 2014 4:24 PM
> To: Xiaopeng Yang
> Cc: Jim Miller; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
>  
>  
> On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> Dear Jim,
>  
> Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file.
>  
> Best,
> Xiaopeng
>  
> <image001.png>
>  
>  
> Is that an error?
> 
> John
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From matimontg at gmail.com  Sat Dec  6 10:44:25 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Sat, 6 Dec 2014 12:44:25 -0300
Subject: [ITK-users] registration->StartRegistration();
Message-ID: <CAKKNfuKSg8ghHqMQtPubqkxZeRC-L2F2gU_Ypvzf=V2Txpu+_g@mail.gmail.com>

Hi,

I was trying to compile some registration examples and I get this:
    2    IntelliSense: class
"itk::ImageRegistrationMethod<itk::Image<signed short, 3U>,
itk::Image<signed short, 3U>>" has no member "StartRegistration"

Should I use Update(); instead?

I tried but I get an error when running the program.

(I tried both examples registration8 and registration20

Thanks,
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From matimontg at gmail.com  Sat Dec  6 11:19:39 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Sat, 6 Dec 2014 13:19:39 -0300
Subject: [ITK-users] convert mha to stack of dicom images
Message-ID: <CAKKNfuKD-gr8w9c=vEcnLHsKGjacG-EjHbxQBuWsXFpA1etmZA@mail.gmail.com>

HI,

I jave a .mha file which is the result of a fusion between CT and RM and
would like to convert the resulting mha into a DICOM series or stack. How
can I do this?

Thanks,

Matias.
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From dr.tim.allman at gmail.com  Sat Dec  6 14:08:31 2014
From: dr.tim.allman at gmail.com (Tim Allman)
Date: Sat, 6 Dec 2014 14:08:31 -0500
Subject: [ITK-users] convert mha to stack of dicom images
In-Reply-To: <CAKKNfuKD-gr8w9c=vEcnLHsKGjacG-EjHbxQBuWsXFpA1etmZA@mail.gmail.com>
References: <CAKKNfuKD-gr8w9c=vEcnLHsKGjacG-EjHbxQBuWsXFpA1etmZA@mail.gmail.com>
Message-ID: <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com>

I wrote a program for OSX to convert any file format recognized by ITK to DICOM. I wrote it for myself so most of the formats, including mha, haven?t been tested. If you have a Mac then you may even be able to run it. If not, the code should be helpful in showing how to construct a DICOM series.

source and binary: https://github.com/TimAllman/ConvertToDicom/releases/tag/v0.1-beta

I hope you find this helpful. If you have questions about the program feel free to email me.

Tim
 
On Dec 6, 2014, at 11:19 , Matias Montroull <matimontg at gmail.com> wrote:

> HI,
> 
> I jave a .mha file which is the result of a fusion between CT and RM and would like to convert the resulting mha into a DICOM series or stack. How can I do this?
> 
> Thanks,
> 
> Matias.
> _____________________________________
> 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 dclunie at dclunie.com  Sat Dec  6 19:18:06 2014
From: dclunie at dclunie.com (David Clunie)
Date: Sat, 06 Dec 2014 19:18:06 -0500
Subject: [ITK-users] DICOM Floating point output from Osirix,
 was Re:  Float dicom images
In-Reply-To: <5480AB03.1080705@gmail.com>
References: <50584801-A75A-4F6C-8255-C824812DA0D8@gmail.com>
 <CAKKNfuJE7b2qAghyt9UR5xze2Zx0N4zJW5sCo9AHJ0ryhQbyCg@mail.gmail.com>
 <593F2FAE-DB1C-4C93-9AB0-A950AFDEDFCB@gmail.com>
 <CAKKNfu+uju1a2Yk37B+8f8GAdi=xp_8GThkoyK0HM7=_ULU3xg@mail.gmail.com>
 <547E39C5.9040801@dclunie.com> <5480AB03.1080705@gmail.com>
Message-ID: <54839CBE.1090807@dclunie.com>

Hi Tim

Antoine Rosset was going to implement this in Osirix when we finalized
the SOP Class UID and data element tags in DICOM, so you might want to
check with him about how far he has got, before writing any code yourself.

I have cc'd him.

Osirix uses dcmtk (or Papyrus).

David

On 12/4/14 1:42 PM, Tim Allman wrote:
> I just read Supplement 172 and it certainly addresses what I want which
> is to create parametric maps and not lose information (sign, dynamic
> range etc.) on storage.
>
> My situation is that I am writing a plugin for Osirix, a DICOM (only)
> viewer which runs on OSX (only). I can create the maps I want internally
> as the viewer uses float as its pixel type internally but it saves
> everything as unsigned 16 bit integers. It will read floating point
> images however so perhaps writing them will come soon.
>
> I single stepped through the writing of a float image and discovered
> that GDCM has some code clearly intended to support I/O of these images
> but it is incomplete. It will indeed write float images but they are
> rescaled to have a range of 0 - MAXFLOAT.
>
> Tim
>
> On 14-12-02 05:14 PM, David Clunie wrote:
>> We (DICOM) have only recently added support for floating point
>> pixel data in DICOM (Sup 172), so I don't know if any of the
>> toolkits used by ITK support it yet.
>>
>> I know dcmtk will, hopefully soon, but I can't speak for GDCM.
>>
>> I have some samples at:
>>
>> https://www.dropbox.com/sh/n4iqdjbhmwljx5e/AABllea-Muk0C2oo576nm_Mua?dl=0
>>
>> if you want to try them; not perfect yet, but they have the float pixel
>> data payload.
>>
>> I am assuming that you actually want to write floating point pixels,
>> rather than integer quantized pixels with a floating point scaling
>> factor.
>>
>> David
>>
>> On 12/2/14 3:40 PM, Matias Montroull wrote:
>>> adding insight users..
>>>
>>> I've never dealt with float dicom images, can you send me a sample
>>> image? I
>>> can try to write and see what's the problem. isn's saving the image
>>> or you
>>> get a wrong saved image, such as WL WC changed etc?
>>>
>>> On Tue, Dec 2, 2014 at 4:53 PM, Tim Allman <dr.tim.allman at gmail.com>
>>> wrote:
>>>
>>>>
>>>> On Dec 2, 2014, at 14:44 , Matias Montroull <matimontg at gmail.com>
>>>> wrote:
>>>>
>>>>> are you trying to write float dicom images?
>>>>
>>>> Yes. Sorry for noting that only in the subject line. :-(
>>>>
>>>>>
>>>>> On Tue, Dec 2, 2014 at 4:35 PM, Tim Allman <dr.tim.allman at gmail.com>
>>>> wrote:
>>>>> I have been having a bit of trouble trying to write Dicom images using
>>>> itk::GDCMImageIO. The code suggests that this is supported but I
>>>> know that
>>>> this is a new feature. Has anyone else had any experience with this?
>>>>>
>>>>> Thanks,
>>>>> Tim
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://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
>
>
>
> _____________________________________
> 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 dclunie at dclunie.com  Sun Dec  7 17:42:07 2014
From: dclunie at dclunie.com (David Clunie)
Date: Sun, 07 Dec 2014 17:42:07 -0500
Subject: [ITK-users] convert mha to stack of dicom images
In-Reply-To: <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com>
References: <CAKKNfuKD-gr8w9c=vEcnLHsKGjacG-EjHbxQBuWsXFpA1etmZA@mail.gmail.com>
 <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com>
Message-ID: <5484D7BF.4070403@dclunie.com>

Make sure you run dciodvfy and dcentvfy on DICOM files that you
create, to check that they are compliant (within the limits of
what these tools can mechanically check). See:

   http://www.dclunie.com/dicom3tools/dciodvfy.html

David

On 12/6/14 2:08 PM, Tim Allman wrote:
> I wrote a program for OSX to convert any file format recognized by ITK to DICOM. I wrote it for myself so most of the formats, including mha, haven?t been tested. If you have a Mac then you may even be able to run it. If not, the code should be helpful in showing how to construct a DICOM series.
>
> source and binary: https://github.com/TimAllman/ConvertToDicom/releases/tag/v0.1-beta
>
> I hope you find this helpful. If you have questions about the program feel free to email me.
>
> Tim
>
> On Dec 6, 2014, at 11:19 , Matias Montroull <matimontg at gmail.com> wrote:
>
>> HI,
>>
>> I jave a .mha file which is the result of a fusion between CT and RM and would like to convert the resulting mha into a DICOM series or stack. How can I do this?
>>
>> Thanks,
>>
>> Matias.

From zeinsalah at gmail.com  Mon Dec  8 08:20:29 2014
From: zeinsalah at gmail.com (Zein Salah)
Date: Mon, 8 Dec 2014 14:20:29 +0100
Subject: [ITK-users] GetOrigin of an itk image
Message-ID: <CADiSopOadr4Xs=1yhirXyA0bQSCxjyQ4Ys9Nmd4sq_FSyhksUQ@mail.gmail.com>

Hi,

To saome reason I don't know, I fail to get the origin of itk images.
The following simple code prints the spacing. for the origin, it always
prints 0,0,0.

    typedef itk::Image<short, 3>            ImageType;
    ImageType::SpacingType spacing = image->GetSpacing();
    ImageType::PointType origin = image->GetOrigin();
    printf("Spacing: %f %f %f\n", spacing[0], spacing[1], spacing[2]);
    printf("Origin: %f %f %f\n", origin[0], origin[1], origin[2]);

The values of the Offset field in the Header og the input file (mhd)
are definitely not zero.

Was this the right way to read out the origin? o I am missing something?

thanks

zein

From bill.lorensen at gmail.com  Mon Dec  8 08:25:11 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Mon, 8 Dec 2014 08:25:11 -0500
Subject: [ITK-users] [ITK] GetOrigin of an itk image
In-Reply-To: <CADiSopOadr4Xs=1yhirXyA0bQSCxjyQ4Ys9Nmd4sq_FSyhksUQ@mail.gmail.com>
References: <CADiSopOadr4Xs=1yhirXyA0bQSCxjyQ4Ys9Nmd4sq_FSyhksUQ@mail.gmail.com>
Message-ID: <CADZJ4hN1kA4UWqgrw__o0+R9-AmnctpOE+wpvsezjRPh99yqcw@mail.gmail.com>

That is correct. What does the rest of your code look like? Have you
done an Update() on the reader?


On Mon, Dec 8, 2014 at 8:20 AM, Zein Salah <zeinsalah at gmail.com> wrote:
> Hi,
>
> To saome reason I don't know, I fail to get the origin of itk images.
> The following simple code prints the spacing. for the origin, it always
> prints 0,0,0.
>
>     typedef itk::Image<short, 3>            ImageType;
>     ImageType::SpacingType spacing = image->GetSpacing();
>     ImageType::PointType origin = image->GetOrigin();
>     printf("Spacing: %f %f %f\n", spacing[0], spacing[1], spacing[2]);
>     printf("Origin: %f %f %f\n", origin[0], origin[1], origin[2]);
>
> The values of the Offset field in the Header og the input file (mhd)
> are definitely not zero.
>
> Was this the right way to read out the origin? o I am missing something?
>
> thanks
>
> zein
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community



-- 
Unpaid intern in BillsBasement at noware dot com

From dr.tim.allman at gmail.com  Mon Dec  8 09:01:54 2014
From: dr.tim.allman at gmail.com (Tim Allman)
Date: Mon, 8 Dec 2014 09:01:54 -0500
Subject: [ITK-users] convert mha to stack of dicom images
In-Reply-To: <5484D7BF.4070403@dclunie.com>
References: <CAKKNfuKD-gr8w9c=vEcnLHsKGjacG-EjHbxQBuWsXFpA1etmZA@mail.gmail.com>
 <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com>
 <5484D7BF.4070403@dclunie.com>
Message-ID: <B21774CA-A021-4546-8773-0F27337F7805@gmail.com>

Good idea. I have not done that. I was merely happy if Osirix would read the files.

Tim

On Dec 7, 2014, at 17:42 , David Clunie <dclunie at dclunie.com> wrote:

> Make sure you run dciodvfy and dcentvfy on DICOM files that you
> create, to check that they are compliant (within the limits of
> what these tools can mechanically check). See:
> 
>  http://www.dclunie.com/dicom3tools/dciodvfy.html
> 
> David
> 
> On 12/6/14 2:08 PM, Tim Allman wrote:
>> I wrote a program for OSX to convert any file format recognized by ITK to DICOM. I wrote it for myself so most of the formats, including mha, haven?t been tested. If you have a Mac then you may even be able to run it. If not, the code should be helpful in showing how to construct a DICOM series.
>> 
>> source and binary: https://github.com/TimAllman/ConvertToDicom/releases/tag/v0.1-beta
>> 
>> I hope you find this helpful. If you have questions about the program feel free to email me.
>> 
>> Tim
>> 
>> On Dec 6, 2014, at 11:19 , Matias Montroull <matimontg at gmail.com> wrote:
>> 
>>> HI,
>>> 
>>> I jave a .mha file which is the result of a fusion between CT and RM and would like to convert the resulting mha into a DICOM series or stack. How can I do this?
>>> 
>>> Thanks,
>>> 
>>> Matias.
> _____________________________________
> 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  Mon Dec  8 09:58:38 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 8 Dec 2014 09:58:38 -0500
Subject: [ITK-users] compling itkScaleInvariantFeatureImageFilter
In-Reply-To: <CAGKqDmd+PPiBsr5nomC+dK31QMAiS5kQCN6vne17rW5SD9xUWA@mail.gmail.com>
References: <CAGKqDmd+PPiBsr5nomC+dK31QMAiS5kQCN6vne17rW5SD9xUWA@mail.gmail.com>
Message-ID: <CALzTN-TaXhDRXY9FQi6HemoDTCJYB6aLMh3P61U2wHCj6nBdmQ@mail.gmail.com>

Hi Lianli,

I assume you are using the code with this article [1] ?  It looks like
there is example test code in testnD.cxx.

HTH,
Matt

[1] http://hdl.handle.net/1926/1321

On Fri, Dec 5, 2014 at 5:19 PM, Lianli Liu <llliu at umich.edu> wrote:
> Hi all,
>
> I want to use the itkScaleInvariantFeatureImageFilter but I am getting
> several errors when compiling, such as:
>  error: ?FeatureType? was not declared in this scope
>  error: ?PointSetType? is not a class or namespace
>
> Does anyone has experience in using this filter?
>
> Also, I am unclear how where to specify input image in the filter.
>
> Thanks!
> Lianli
>
>
> _____________________________________
> 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 zeinsalah at gmail.com  Mon Dec  8 10:11:06 2014
From: zeinsalah at gmail.com (Zein Salah)
Date: Mon, 8 Dec 2014 16:11:06 +0100
Subject: [ITK-users] BinaryImageToShapeLabelMapFilter problem
Message-ID: <CADiSopOYuqmYQSK+9pj04r4+t82ufqmN5gUBFPN1=CbeVn0bbA@mail.gmail.com>

Hi,

I am using the BinaryImageToShapeLabelMapFilter to label connected
component in a binaty image. I recycled some code as follows:


   typedef unsigned long LabelType;
   typedef itk::ShapeLabelObject< LabelType, 3 > LabelObjectType;
   typedef itk::LabelMap< LabelObjectType > LabelMapType;

   typedef itk::BinaryImageToShapeLabelMapFilter< BinaryImageType,
LabelMapType > ConverterType;
   ConverterType::Pointer converter = ConverterType::New();
   converter->SetInput(m_SegmentedImage);
   converter->SetInputForegroundValue(255);
   converter->Update();

   LabelMapType::Pointer labelMap = converter->GetOutput();


   MarkerPositions detectedMarkers;
   for( unsigned int label=0;
label<labelMap->GetNumberOfLabelObjects(); label++ )
   {
       const LabelObjectType * labelObject = labelMap->GetNthLabelObject(label);
       ImageType::PointType point = labelObject->GetCentroid();
       std::cout << label << "\t" << labelObject->GetPhysicalSize() <<
" at:  " << point[0] << "," << point[1] << "," << point[2] <<
std::endl;
   }

The code actually generates some labels (for the image I used, it
generates 35 labels).
The thing I could not understand is that the centroids of the labeled
object do not correspond
to components in the image. I.e., when I take one centroid and select the point
in the image, in most, if not all, cases it is an empty area. Are elements in
a label map no more related to there position in the image? or I am
missing some point here??
Centroids are computed in the pixels coordinates, not physical locations. Right?

thanks,
Zein

From blowekamp at mail.nih.gov  Mon Dec  8 10:18:28 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 8 Dec 2014 10:18:28 -0500
Subject: [ITK-users] BinaryImageToShapeLabelMapFilter problem
In-Reply-To: <CADiSopOYuqmYQSK+9pj04r4+t82ufqmN5gUBFPN1=CbeVn0bbA@mail.gmail.com>
References: <CADiSopOYuqmYQSK+9pj04r4+t82ufqmN5gUBFPN1=CbeVn0bbA@mail.gmail.com>
Message-ID: <1DC38089-CFCC-43BF-9C6D-8BD148DC8BF5@mail.nih.gov>

Hello,

The  BinaryImageToShapeLabelMapFilter's Centroids are computed in physical space and are represented as a point.

ITK uses strong type which makes this type of issue clear. The type of itk::ShapreLabelObject::CentroidType[1] is an itk::Point. This is used for physical coordinates. While the itk::Index type ( or itk::ContinuousIndex ) is used for indices.

Also the PhysicalSize is going to be in your physical units, and not the number of voxels.

Brad


[1] http://www.itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#a34402f70c483dfe5b7e412d891d5abf6

On Dec 8, 2014, at 10:11 AM, Zein Salah <zeinsalah at gmail.com> wrote:

> Are elements in
> a label map no more related to there position in the image? or I am
> missing some point here??

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From matt.mccormick at kitware.com  Mon Dec  8 10:36:18 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 8 Dec 2014 10:36:18 -0500
Subject: [ITK-users] registration->StartRegistration();
In-Reply-To: <CAKKNfuKSg8ghHqMQtPubqkxZeRC-L2F2gU_Ypvzf=V2Txpu+_g@mail.gmail.com>
References: <CAKKNfuKSg8ghHqMQtPubqkxZeRC-L2F2gU_Ypvzf=V2Txpu+_g@mail.gmail.com>
Message-ID: <CALzTN-QVYLhuSm-B7QmPN0DPsHVXMPyDi0ptYZ_78b8RMxQmcA@mail.gmail.com>

Hi Matias,

->StartRegistration();

has been deprecated in favor of

->Update();

which is more consistent with how the rest of the algorithms are start in ITK.

HTH,
Matt

On Sat, Dec 6, 2014 at 10:44 AM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi,
>
> I was trying to compile some registration examples and I get this:
>     2    IntelliSense: class "itk::ImageRegistrationMethod<itk::Image<signed
> short, 3U>, itk::Image<signed short, 3U>>" has no member "StartRegistration"
>
> Should I use Update(); instead?
>
> I tried but I get an error when running the program.
>
> (I tried both examples registration8 and registration20
>
> Thanks,
>
>
> _____________________________________
> 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 lasso at queensu.ca  Mon Dec  8 12:00:16 2014
From: lasso at queensu.ca (Andras Lasso)
Date: Mon, 8 Dec 2014 17:00:16 +0000
Subject: [ITK-users] [ITK]  convert mha to stack of dicom images
In-Reply-To: <B21774CA-A021-4546-8773-0F27337F7805@gmail.com>
References: <CAKKNfuKD-gr8w9c=vEcnLHsKGjacG-EjHbxQBuWsXFpA1etmZA@mail.gmail.com>
 <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com>
 <5484D7BF.4070403@dclunie.com>
 <B21774CA-A021-4546-8773-0F27337F7805@gmail.com>
Message-ID: <B6FC5543F5C41E479B8B89158B0C58FF31E0CE08@QU-MBX02-PRD.AD.QUEENSU.CA>

You may also use latest nightly version of 3D Slicer to load data in almost any research format (nrrd, mha, stl, ...), process it (apply deformation, filters, etc.) and export it to DICOM (image, structure set, etc).

http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DICOM

Andras

-----Original Message-----
From: Community [mailto:community-bounces at itk.org] On Behalf Of Tim Allman
Sent: Monday, December 8, 2014 09:02
To: insight-users at itk.org Users
Subject: Re: [ITK] [ITK-users] convert mha to stack of dicom images

Good idea. I have not done that. I was merely happy if Osirix would read the files.

Tim

On Dec 7, 2014, at 17:42 , David Clunie <dclunie at dclunie.com> wrote:

> Make sure you run dciodvfy and dcentvfy on DICOM files that you 
> create, to check that they are compliant (within the limits of what 
> these tools can mechanically check). See:
> 
>  http://www.dclunie.com/dicom3tools/dciodvfy.html
> 
> David
> 
> On 12/6/14 2:08 PM, Tim Allman wrote:
>> I wrote a program for OSX to convert any file format recognized by ITK to DICOM. I wrote it for myself so most of the formats, including mha, haven't been tested. If you have a Mac then you may even be able to run it. If not, the code should be helpful in showing how to construct a DICOM series.
>> 
>> source and binary: 
>> https://github.com/TimAllman/ConvertToDicom/releases/tag/v0.1-beta
>> 
>> I hope you find this helpful. If you have questions about the program feel free to email me.
>> 
>> Tim
>> 
>> On Dec 6, 2014, at 11:19 , Matias Montroull <matimontg at gmail.com> wrote:
>> 
>>> HI,
>>> 
>>> I jave a .mha file which is the result of a fusion between CT and RM and would like to convert the resulting mha into a DICOM series or stack. How can I do this?
>>> 
>>> Thanks,
>>> 
>>> Matias.
> _____________________________________
> 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

_____________________________________
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
_______________________________________________
Community mailing list
Community at itk.org
http://public.kitware.com/mailman/listinfo/community

From matt.mccormick at kitware.com  Mon Dec  8 12:37:42 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 8 Dec 2014 12:37:42 -0500
Subject: [ITK-users] How to abort execution of ImageRegistrationMethodv4
	/ Optimizer
In-Reply-To: <5480E4A9.3050304@itis.ethz.ch>
References: <5480DDA3.905@itis.ethz.ch>
	<5480E4A9.3050304@itis.ethz.ch>
Message-ID: <CALzTN-RWhm6AVtKvMpLTmMh=TP-kTcWPwPqfRmXiUbnfrecfvQ@mail.gmail.com>

Hi Bryn,

Thanks for looking into these issues.

Could a patches please be created to address them? [1].  I think a
separate patch could be created for each member.  The check for
AbortGenerateData should use the method:

  this->GetAbortGenerateData()

Thanks,
Matt

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

On Thu, Dec 4, 2014 at 5:48 PM, Bryn Lloyd <lloyd at itis.ethz.ch> wrote:
> At a first glance it seems that ImageRegistrationMethodv4 does not check for
> the abort flag:
>
> ImageRegistrationMethodv4<TFixedImage, TMovingImage, TTransform,
> TVirtualImage>
> ::GenerateData()
> {
>   this->AllocateOutputs();
>   for( this->m_CurrentLevel = 0; this->m_CurrentLevel <
> this->m_NumberOfLevels; this->m_CurrentLevel++ )
>     {
>     this->InitializeRegistrationAtEachLevel( this->m_CurrentLevel );
>
>     this->m_Metric->Initialize();
>
>     this->m_Optimizer->StartOptimization();
>     }
> }
>
> If I modify this code to check for m_AbortGenerateData, the registration
> terminates as expected.
>
>
> In addition it seems that the members m_CurrentMetricValue,
> m_CurrentIteration etc. are never updated during optimization.
>
> Best regards
> Bryn
>
>
>
>
> On 04.12.2014 23:18, Bryn Lloyd wrote:
>>
>> Hi
>>
>> I recently started using ITK again and am trying out the ITK registration
>> framework v4.
>>
>>
>> I am trying to gracefully abort/stop the ImageRegistrationMethodv4
>> process, however it just continues.
>>
>> In my Command class, which observes an IterationEvent of the
>> ImageRegistrationMethodv4 and Optimizer  I call
>> 1.  registration_method_v4->SetAbortGenerateData( true ); // object of
>> type ImageRegistrationMethodv4<...>
>>
>> 2. optimizer->StopOptimization();
>>
>> However, the process just continues to execute. Is this supposed to work?
>> What am I doing wrong?
>>
>> Thanks and best regards
>> Bryn
>>
>>
>> _____________________________________
>> 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
>
>
> _____________________________________
> 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  Mon Dec  8 12:51:42 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 8 Dec 2014 12:51:42 -0500
Subject: [ITK-users] How to abort execution of ImageRegistrationMethodv4
	/ Optimizer
In-Reply-To: <CALzTN-RWhm6AVtKvMpLTmMh=TP-kTcWPwPqfRmXiUbnfrecfvQ@mail.gmail.com>
References: <5480DDA3.905@itis.ethz.ch> <5480E4A9.3050304@itis.ethz.ch>
 <CALzTN-RWhm6AVtKvMpLTmMh=TP-kTcWPwPqfRmXiUbnfrecfvQ@mail.gmail.com>
Message-ID: <3B98C36F-15E5-4D7E-9DB6-4DD056EE5EDE@mail.nih.gov>

Hello,

I think that the optimizer needs to be stopped or told to abort. Perhaps the registration method should forward the request to the optimizer?

Brad

On Dec 8, 2014, at 12:37 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:

> Hi Bryn,
> 
> Thanks for looking into these issues.
> 
> Could a patches please be created to address them? [1].  I think a
> separate patch could be created for each member.  The check for
> AbortGenerateData should use the method:
> 
>  this->GetAbortGenerateData()
> 
> Thanks,
> Matt
> 
> [1] https://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/SubmitAPatchToGerrit/index.html
> 
> On Thu, Dec 4, 2014 at 5:48 PM, Bryn Lloyd <lloyd at itis.ethz.ch> wrote:
>> At a first glance it seems that ImageRegistrationMethodv4 does not check for
>> the abort flag:
>> 
>> ImageRegistrationMethodv4<TFixedImage, TMovingImage, TTransform,
>> TVirtualImage>
>> ::GenerateData()
>> {
>>  this->AllocateOutputs();
>>  for( this->m_CurrentLevel = 0; this->m_CurrentLevel <
>> this->m_NumberOfLevels; this->m_CurrentLevel++ )
>>    {
>>    this->InitializeRegistrationAtEachLevel( this->m_CurrentLevel );
>> 
>>    this->m_Metric->Initialize();
>> 
>>    this->m_Optimizer->StartOptimization();
>>    }
>> }
>> 
>> If I modify this code to check for m_AbortGenerateData, the registration
>> terminates as expected.
>> 
>> 
>> In addition it seems that the members m_CurrentMetricValue,
>> m_CurrentIteration etc. are never updated during optimization.
>> 
>> Best regards
>> Bryn
>> 
>> 
>> 
>> 
>> On 04.12.2014 23:18, Bryn Lloyd wrote:
>>> 
>>> Hi
>>> 
>>> I recently started using ITK again and am trying out the ITK registration
>>> framework v4.
>>> 
>>> 
>>> I am trying to gracefully abort/stop the ImageRegistrationMethodv4
>>> process, however it just continues.
>>> 
>>> In my Command class, which observes an IterationEvent of the
>>> ImageRegistrationMethodv4 and Optimizer  I call
>>> 1.  registration_method_v4->SetAbortGenerateData( true ); // object of
>>> type ImageRegistrationMethodv4<...>
>>> 
>>> 2. optimizer->StopOptimization();
>>> 
>>> However, the process just continues to execute. Is this supposed to work?
>>> What am I doing wrong?
>>> 
>>> Thanks and best regards
>>> Bryn
>>> 
>>> 
>>> _____________________________________
>>> 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
>> 
>> 
>> _____________________________________
>> 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
> _____________________________________
> 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 marina.bendersky at gmail.com  Mon Dec  8 15:39:20 2014
From: marina.bendersky at gmail.com (MB)
Date: Mon, 8 Dec 2014 13:39:20 -0700 (MST)
Subject: [ITK-users] [ITK]  convert mha to stack of dicom images
In-Reply-To: <B6FC5543F5C41E479B8B89158B0C58FF31E0CE08@QU-MBX02-PRD.AD.QUEENSU.CA>
References: <CAKKNfuKD-gr8w9c=vEcnLHsKGjacG-EjHbxQBuWsXFpA1etmZA@mail.gmail.com>
 <8F56FAAC-69A9-4533-B8D7-D0B0DA56A996@gmail.com>
 <5484D7BF.4070403@dclunie.com>
 <B21774CA-A021-4546-8773-0F27337F7805@gmail.com>
 <B6FC5543F5C41E479B8B89158B0C58FF31E0CE08@QU-MBX02-PRD.AD.QUEENSU.CA>
Message-ID: <1418071160353-35033.post@n7.nabble.com>

What about extracting the 2D images from the 3D volume using, for example, 

IO/ImageReadExtractWrite.cxx?

Maybe this is not the most efficient way, but you could call the program in
a loop and extract all of the slices automatically. (I'm a newbie so I tried
this solution using a bash script.).

Thanks





--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-convert-mha-to-stack-of-dicom-images-tp35019p35033.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Mon Dec  8 23:44:31 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 8 Dec 2014 23:44:31 -0500
Subject: [ITK-users] [ANNOUNCE] ITK 4.7 Release Candidate 1 has been tagged!
Message-ID: <CALzTN-T3=pKTmLCsBUR2HoNxZeHeMAL7C+yHiW3rS13jr2_TBA@mail.gmail.com>

On behalf of the Insight Toolkit community, we are proud to announce
that ITK 4.7.0 release candidate 1 has been tagged and is available
for testing!


To obtain the source code,

  git clone http://itk.org/ITK.git
  cd ITK
  git checkout -q --detach v4.7rc01

For more details, please see the Git documentation [1].


Please test the release candidate and share your experiences on the
mailing list, issue tracker, and Gerrit Code Review. Please help
identify issues submitting an Experimental build to the dashboard [2]
with:

  ctest -M Experimental  -T Configure -T Build -T Test -T Submit

and notifying the mailing list.  Testing your own applications against
the RC is also appreciated.


Congratulations and well done to everyone that has contributed to this
release. Release candidates are tagged every week.  The final release
is scheduled for December 18th.


[1] http://www.itk.org/Wiki/ITK/Git

[2] http://open.cdash.org/index.php?project=Insight



New Features
------------------
* Documentation Improvements
  - Update Software Guide registration examples to ITKv4 framework
  - Wiki and Sphinx examples are indexed in Doxygen
  - Clean Software Guide dashboard build

* Filtering Improvements
  - New Laplacian deformation filter?s for QuadEdgeMesh?s
    - IJ article: http://hdl.handle.net/10380/3410
 - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations

* ImageIO improvements
  - PNG sCAL unit support
  - TIFF IO performance greatly improved
  - TIFF tags read into Image MetaDataDictionary
  - MetaIO updated
  - Better support for system GDCM

* Infrastructure improvements
  - New method to erase a MetaDataDictionary entry
  - New global method to set physical space tolerance
  - New, experimental thread pool support
  - NumericTraits::Zero and ::One are deprecated in favor of
::ZeroValue() and ::OneValue()

* New Remote Modules
  - Higher Order Accurate Gradient
    - http://hdl.handle.net/10380/3231
  - IO Transform DCMTK
    - http://hdl.handle.net/10380/3468

* Registration improvements
  - LandmarkBasedTransformInitializer supports BSplineTransform
  - Transverse inverse consistency increased
  - Automatic initialization of the transform center for multi-stage
registrations
  - Sparse point B-spline field estimate

* Performance improvements
  - Faster recursive Gaussian on VectorImage
  - Mutual information faster, lower memory usage

* Wrapping improvements
  - Wrapping now builds without type warnings
  - pygccxml bumped to 1.6.2
  - Latest GCCXML
  - CMake wrapping infrastructure cleanup
  - Build with Ninja CMake generator
  - New GetTypes() and GetTypesAsList() methods
  - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake

* Many style improvements -- ITK gets more stylish with every release!

* Improved code coverage -- we are over 85%!

* *Lots* of important bug fixes

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


List of changes since v4.5.0
--------------------------------------

Alexander Schmidt-Richberg (1):
      ENH: Updated Remote Module VariationalRegistration to new git tag

Ali Ghayoor (10):
      ENH: Make ITKv4 compatible with ITKSoftwareGuide
      ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4
      ENH: Convert three ImageRegistration Examples to ITKv4
      ENH: Add multi-Res and multistage registration Examples to ITKv4
      ENH: Convert DeformableReg examples to ITKv4 reg framework
      BUG: Expand a test to reflect multi-metric registration bug
      BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4
      ENH: Add direct initialization to SyN registration
      ENH: Direct initialization of SyN by restoring the state
      ENH: LandmarkBasedTransformInitializer supports BSplineTransformType

Arnaud Gelas (15):
      COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization
      ENH: Importing Laplacian Deformation for QuadEdgeMesh
      DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage
      ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified()
      ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter
      BUG: fix gdcm version in GDCMImageIO.
      COMP: missing cast when calling gdcm::DataElement::SetByteValue
      COMP: missing cast when calling gdcm::DataElement::SetByteValue
      ENH: increase LaplacianDeformation code coverage
      STYLE: use typedef rather than inheritance
      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false
      BUG: split include directories into appropriate cmake variables HDF5
      BUG: missing gdcm libraries when using system GDCM
      DOC: fix doxygen documentaiton for
itk::LaplacianDeformationQuadEdgeMeshFilter
      ENH: Add one method to erase a tag into MetaDataDictionary

Bill Lorensen (5):
      ENH: Specify required VTK modules
      COMP: Wiki examples require additional vtk modules
      ENH: Modify WikiExamples remote config
      COMP: Bad test signature
      COMP: Update tag for wiki examples

Brad King (6):
      COMP: Fix vxl_config_macros usage of CMake check macros
      ENH: Use if(DEFINED) to simplify conditions
      COMP: Fix vxl_config_macros checks broken by refactoring
      COMP: Fix one more vxl_config_macros check broken by refactoring
      BUG: Fix itk_module_config for repeated calls
      BUG: Fix itk_module_config for repeated calls

Bradley Lowekamp (52):
      ENH: Adding License file from upstream MetaIO
      ENH: Adding script to update MetaIO from upstream
      ENH: Remove ITK MetaIO to prepare for upstream import
      PERF: Remove dynamically allocated temporary in evaluate method
      COMP: Fix variable type for Set/Get macros
      BUG: Implement ITK Style Singleton design pattern
      ENH: Add no throw exception specification for UnRegister methods
      COMP: Must specify order as "noexcept override"
      BUG: Add GetInverse for IdentityTransform
      ENH: Adding SetIdentity method to base DisplacementField class
      BUG: Remove unused redefinition of NULL
      BUG: Don't print to std::cout in PrintSelf
      ENH: Prefer the PrintSelfObjectMacro for printing nested objects
      BUG: Use METER of sCAL scale unit
      BUG: Use PNG_SCALE_METER for PNG sCAL unit
      BUG: Use METER of sCAL scale unit
      BUG: Use PNG_SCALE_METER for PNG sCAL unit
      COMP: Fix signed to unsigned int comparison
      BUG: Fix overflows computing size of read tiff image
      ENH: Extract TiffReaderInternal to separate file
      ENH: Refactor ReadTwoSamplePerPixelImage into template function
      ENH: Refactor GenericReadImage into template function
      BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO )
      ENH: Refactor method to convert RGBA image to output buffer
      ENH: Refactor duplicated code to read a page
      BUG: Fix right oriented tiff images
      BUG: Remove dead separated plannar code, add test
      STYLE: Fix minor kwstyle defects in test and test results
      BUG: Use array delete operator for array new allocations
      ENH: add arbitrary TIFF TAGs to meta-data dictionary
      ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
      BUG: Address Coverity warning about null pointer dereferences
      ENH: Remove support for TIFF tile as 3D and dead code
      ENH: RGBA read images should stay unchanged.
      BUG: Override method to MakeOutput by name
      ENH: Refactor per pixel conversion function to per scan-line method
      PERF: Refactor color table lookup
      BUG: Adding missing parentheses around boolean expression
      ENH: adding TIFFImageIO test for RGB palette images
      PERF: Improve recursive Gaussian perfromance with VectorImages
      ENH: Query libtiff to determine compression support
      BUG: Support TIFF tiled image with TIFFReadRGBAImage
      BUG: Use SizeValueType for length of scanline
      PERF: Store causal results directly in output buffers
      COMP: Add explicit conversion to const char
      COMP: Explicitly add override to GetNameOfClass method
      COMP: Address internal segmentation fault with Intel compiler
      ENH: Adding method to set global physical space tolerance
      COMP: Explicitly add override to GetNameOfClass method
      BUG: Add new TypeMacro for non-overloaded classes
      BUG: Fix obscure race condition on access thread pool initialization
      BUG: Updating FDFImageIO remote module

Christopher Mullins (15):
      COMP: Allows latex to compile for ITKSoftwareGuide
      COMP: Allows latex to compile for ITKSoftwareGuide
      COMP: Wrap MeshBase templates
      COMP: Wrap MeshBase templates
      COMP: Fix warning in BlockMatchingImageFilter
      STYLE: Line lengths in examples should be no longer than 80 chars.
      COMP: Wrap the remaining MeshBase and MeshToMeshFilter types.
      COMP: Fix LaTeX warnings.
      STYLE: Fix formatting/punctuation errors.
      STYLE: Formatting and punctuation fixes.
      DOC: Edits for Book 2 Chapter 1 documentation in the Examples.
      DOC: Edits for book 2 chapter 2.
      DOC: More chapter 2 edits
      DOC: Book 2 Chapter 3 edits (part 1)
      DOC: book 2 chapter 4 Segmentation edits

Danny Perry (2):
      BUG: adding test for vnl_sparse_matrix::mult()
      BUG: size of q buffer should actually be (this->rows())*pcols.

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

Dirk Padfield (1):
      BUG: Corrected processing of last sigma

GCC-XML Upstream (1):
      ENH: pygccxml v1.6.2 (reduced)

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 (24):
      COMP: Add tolerance for comparing floating point
      PERF: Remove non-threadable algorithm components
      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
      BUG: Syntax error in comment
      PERF: Add non-blocking mutex locking.
      ENH: Use TryLock minimize thread stalls
      BUG: ThreadedIndexedContainerPartitioner is inclusive
      STYLE: Remove include_regular_expression from Examples
      BUG: Demonstrate Inv(Inv(T)) != T
      BUG: Ensure Inv(Inv(T)) == T for transforms
      COMP: Valgrind detects uninitialized memory read
      COMP: Missing required base class API component
      ENH: Expand interface for selecting threadpool

Ismael Belghiti (1):
      DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter

Jim Miller (1):
      STYLE: Removing what appears to be a temporary file

Johan Andruejol (1):
      ENH: Fix normalization for null vectors and return the norm

Jon Haitz Legarreta (1):
      ENH: New test for itkLabelShapeOpeningImageFilter

Kent Williams (9):
      COMP: use find_package(VTK COMPONENTS) to specify just needed
VTK Components
      BUG: ImageSources/test/CMakeLists.txt incorrect library var reference
      COMP: Fix coverity defects related to RegistrationV4 examples
      COMP: silence warning of vnl_vector_fixed_ref::assert_size
      COMP: Fix various Coverity warnings
      COMP: Fix a typo in an error message print statement.
      COMP: itk::Command-derived class used pointless dynamic_cast.
      PERF: Don't recompute InternalInverse repeatedly
      COMP: Correct orientation/spacing for Philips MultiFrame

Mark Hiner (2):
      ENH: Update SCIFIO remote module hash
      BUG: Fix duplicate variables in Windows

Matthew McCormick (105):
      DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro.
      ENH: Move FFTComplexToComplexImageFilter out of Review.
      ENH: Add VnlComplexToComplexFFTImageFilter.
      BUG: Use fixed seed for Vnl FFT tests for repeatibility.
      ENH: Bump CMakeLists.txt version to 4.7.0.
      BUG: ArchiveTestingData.py future imports must occur at the beginning.
      BUG: Do not run vnl_test_na with broken libc++.
      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.
      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
      BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter.
      BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest.
      STYLE: Fix style in VoronoiDiagram2D.
      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
      BUG: Bump GCCXML to 2014-08-06.
      BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}.
      BUG: Fix Win MultiThreader check for successful process creation.
      BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor.
      COMP: Fix ImageRegistration8RegisteredSlice.png baseline name.
      DOC: itk::statistics -> itk::Statistics.
      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
      COMP: Improve const correctness of GradientRecursiveGaussianImageFilter.
      BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().
      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
      COMP: ThreadJob NULL not defined.
      BUG: Fix alpha assignment for RGBA TIFF.
      COMP: Remove unused typedefs in LevelSetsv4Visualization.
      COMP: Remove unused typedef's in VtkGlue.
      ENH: Mark BSplineWarping2Test as RUNS_LONG.
      BUG: Fix Nifti IO read with large images.
      COMP: Remove call for non-existent variable in Nifti debugging.
      BUG: Close the file on Read and Write in HDF5TransformIO.
      BUG: Remove InsightLegacy test code from TransformHDF5Test.
      ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}.
      STYLE: Use SeriesUIDContainerType and FileNamesContainerType
      ENH: Allow specification of orthogonality tolerance in rigid transforms.
      BUG: TransformFileReader does not clear its TransformList.
      BUG: Prevent dangling pointer in HDF5TransformIO.
      COMP: Do not use _stat64 with MinGW-32.
      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.
      COMP: Address LaplacianDeformation Doxygen warnings.
      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
      COMP: Do not wrap the FixedArray of Image SmartPointer's.
      COMP: Add missing wrapping for TransformIOBaseTemplate.
      COMP: Mark DeformableRegistration6Test as RUNS_LONG.
      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.
      BUG: Use -py3 when building wrapping for Python 3.
      COMP: Add missing wrapping for TransformIOBaseTemplate.
      DOC: Improve ImageRegistration4 grammar.
      ENH: Add IOTransformDCMTK Remote module.
      BUG: gdcm::StringFilter recognizes backslash delimiter.
      DOC: Add migration guide for GDCM Rescale slope intercept apply on write.
      COMP: Remove unused typedef's in GPU code.
      STYLE: Improve style of HoughTransform2DLinesImageFilter example.
      COMP: Use ConceptChecking for IterativeInverse dimension check.
      COMP: Wrap TransformIOBaseTemplate for const SmartPointer.
      COMP: Add warning exceptions for third party pcre, swig, gccxml.
      ENH: Bump ITK version to 4.6.1.
      BUG: Add missing ITK_OVERRIDE to ITKImageeSources module.
      BUG: Remove GaussianImageSource members shadowing GenerateImageSource.
      STYLE: Style fixes to ITKImageSources module.
      BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType.
      BUG: Do not perform itk_download_attempt_check when not building ITK.
      DOC: Update GDCMImageIO rescale slope intercept doc.
      BUG: Only register requestion IO COMPONENT modules.
      BUG: Fix wrapping .i, .idx CMake dependencies.
      COMP: Add VTK Python module when wrapping ITKVtkGlue.
      STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator.
      STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef.
      COMP: Add missing VTK module dependency for LevelSetsv4Visualization.
      BUG: By default, do not create any fixed parameters.
      STYLE: Remove trivial method comments in itkTransform.hxx.
      BUG: PolylineMask Filter's GenerateData is protected / virtual.
      ENH: Add HigherOrderAccurateGradient Module.
      BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal.
      COMP: Remove extra semi-colon, variable scope in DCMTKFileReader.
      STYLE: Style fixes for Transform classes.
      DOC: Increase Doxygen LOOKUP_CACHE_SIZE.
      BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe.
      DOC: Index Wiki examples with Doxygen.
      COMP: Bump SphinxExamples remote module.
      DOC: Index Sphinx examples in Doxygen.
      COMP: Remove old java examples.
      COMP: Remove duplicate DiffusionTensor3DReconstruction example reference.
      COMP: Address GradientAnisotropicDiffusionImageFilter example settings.
      COMP: Bump Sphinx Examples remote.
      COMP: Bump WikiExamples remote.

MetaIO Maintainers (1):
      MetaIO (reduced)

Michka Popoff (40):
      ENH: Fixes for python 3 support
      BUG: Add VTK_VERSION for older VTK versions
      BUG: Improve SWIG version check
      COMP: Add wrapping for ThreadPool and ThreadJob
      COMP: Remove unimplemented DestroyPool method
      COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping
      COMP: Do not hide pygccxml warnings
      ENH: Update links in readme file
      BUG: Improve SWIG version check
      BUG: Add VTK_VERSION for older VTK versions
      STYLE: Remove trailing whitespaces
      STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP
      BUG: Fix memory leak in MetaImageIO after exception
      ENH: Add script to update pygccxml from upstream
      BUG: Update VTK minimum version (for release)
      BUG: Fix memory leak in MetaImageIO after exception
      ENH: Remove Sun OS compatibility for the wrappings
      COMP: Fix for conversion to non-pointer like type warning
      STYLE: LabelObject style
      DOC: Remove broken link from LabelObject class description
      ENH: Do not setup the python tests if not asked
      ENH: Add new GetTypes() and GetTypesAsList() methods to the template class
      COMP: Fix CMP0054 warnings in wrappings
      STYLE: Remove old cmake < 2.8.4 specific code
      STYLE: Remove old cmake < 2.8.5 specific code
      ENH: Update to PCRE 8.36
      COMP: Refactor Wrapping setup and fix legacy warnings
      ENH: Add wrapping configuration to ITKConfig.cmake
      STYLE: Some minor code cleanup in the wrapping setup
      DOC: Fix typo in RelabelComponentImageFilter
      ENH: Deprecate VectorResampleImageFilter
      DOC: Add migration guide for ::Zero and ::One
      ENH: Deprecate ::Zero and ::One
      ENH: Add option to disable sorting by size in
itkRelabelComponentImageFilter
      ENH: Add Vector and RGB wrapping to linear interpolator
      STYLE: Remove SORT macro in wrappings
      COMP: Fix warning for InterpolateImageFunction wrapping
      COMP: Add a check for Blocks in GPU module
      COMP: Bump SCIFIO to fix test build warnings
      COMP: Fix wrapping of itkImageFunctionBase

Nick Tustison (7):
      BUG:  Need to explicitly specify spline order.
      ENH:  Initializing the transform center.
      BUG:  Need to check the dynamic cast before any calls.
      ENH:  Adding modifications for point set metrics.
      BUG:  Need to specify TInternalComputationValueType for default metric.
      ENH:  Adding sparse points to B-spline field estimate.
      BUG:  Uninitialized variables.

Richard Beare (1):
      ENH: Include TIFF tags in the MetaDataDictionary

Taylor Braun-Jones (1):
      BUG: Fix SliceBySliceImageFilter doesn't propagate information internally

Umang B (1):
      ENH: Use thread pool to dispatch multithreading tasks

Vivien Delmon (2):
      BUG: ExtractImageFilter::CollapseToSubMatrix fix
      ENH: Add a test on extracted directions in CollapseToSubMatrix mode

Vladimir S. FONOV (1):
      BUG: Fixing incorrect MINC style inverse transform



-----------------------------------------------------
Errors or omissions? Please fix them here:

https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing

From zeinsalah at gmail.com  Tue Dec  9 08:25:21 2014
From: zeinsalah at gmail.com (Zein Salah)
Date: Tue, 9 Dec 2014 14:25:21 +0100
Subject: [ITK-users] Computing/Getting the attributes of ShapeLabelObject
Message-ID: <CADiSopPvMNg=S42Fir=es6anaY3=mCBz4=qoChhvfB+jVH3Sxw@mail.gmail.com>

Hi,

I want to compute some shape properties  of segmented objects in a binary image.
S I used the code below to create a labelmap.  BTW, I am using ITK 3.14.

   typedef unsigned long LabelType;
   typedef itk::ShapeLabelObject< LabelType, 3 > LabelObjectType;
   typedef itk::LabelMap< LabelObjectType > LabelMapType;

   typedef itk::BinaryImageToShapeLabelMapFilter< OverlayImageType,
LabelMapType > ConverterType;
   ConverterType::Pointer converter = ConverterType::New();
   converter->SetInput(m_SegmentedImage);
   converter->SetInputForegroundValue(255);
   converter->Update();

   LabelMapType::Pointer labelMap = converter->GetOutput();

   for( unsigned int label=0; label <
labelMap->GetNumberOfLabelObjects(); label++ )
   {
       const LabelObjectType * labelObject = labelMap->GetNthLabelObject(label);
       LabelObjectType::CentroidType centroid = labelObject->GetCentroid();
       std::cout << label << ": " << labelObject->GetCentroid() << "   "
                                  << labelObject->GetPhysicalSize() << "   "
                                  << labelObject->GetRegionElongation() << "   "
                                  << labelObject->GeRoundness()
                                  << std::endl;
   }


Strangely, the output of the Roundness is always 0. Moreover, it seems that
some attrubutes are not implemented, e.g. GetElongation,
GetboundingBox. From the
corresponding IJ paper, I could not really understand if the the
attributes are computed
or need to computed elsewhere.

Any hints how this should work?

Thanks,
Zein

From zeinsalah at gmail.com  Tue Dec  9 09:03:58 2014
From: zeinsalah at gmail.com (Zein Salah)
Date: Tue, 9 Dec 2014 15:03:58 +0100
Subject: [ITK-users] Computing/Getting the attributes of ShapeLabelObject
In-Reply-To: <CADiSopPvMNg=S42Fir=es6anaY3=mCBz4=qoChhvfB+jVH3Sxw@mail.gmail.com>
References: <CADiSopPvMNg=S42Fir=es6anaY3=mCBz4=qoChhvfB+jVH3Sxw@mail.gmail.com>
Message-ID: <CADiSopN7+kQ9cPWNznvVPCm=h5ahMZ1Stc5R1h2prL8BPA0CfA@mail.gmail.com>

And by the way, some attributes, like centroid, physical size,
regionelongation are computed. Others, like roundness are not !


On Tue, Dec 9, 2014 at 2:25 PM, Zein Salah <zeinsalah at gmail.com> wrote:
> Hi,
>
> I want to compute some shape properties  of segmented objects in a binary image.
> S I used the code below to create a labelmap.  BTW, I am using ITK 3.14.
>
>    typedef unsigned long LabelType;
>    typedef itk::ShapeLabelObject< LabelType, 3 > LabelObjectType;
>    typedef itk::LabelMap< LabelObjectType > LabelMapType;
>
>    typedef itk::BinaryImageToShapeLabelMapFilter< OverlayImageType,
> LabelMapType > ConverterType;
>    ConverterType::Pointer converter = ConverterType::New();
>    converter->SetInput(m_SegmentedImage);
>    converter->SetInputForegroundValue(255);
>    converter->Update();
>
>    LabelMapType::Pointer labelMap = converter->GetOutput();
>
>    for( unsigned int label=0; label <
> labelMap->GetNumberOfLabelObjects(); label++ )
>    {
>        const LabelObjectType * labelObject = labelMap->GetNthLabelObject(label);
>        LabelObjectType::CentroidType centroid = labelObject->GetCentroid();
>        std::cout << label << ": " << labelObject->GetCentroid() << "   "
>                                   << labelObject->GetPhysicalSize() << "   "
>                                   << labelObject->GetRegionElongation() << "   "
>                                   << labelObject->GeRoundness()
>                                   << std::endl;
>    }
>
>
> Strangely, the output of the Roundness is always 0. Moreover, it seems that
> some attrubutes are not implemented, e.g. GetElongation,
> GetboundingBox. From the
> corresponding IJ paper, I could not really understand if the the
> attributes are computed
> or need to computed elsewhere.
>
> Any hints how this should work?
>
> Thanks,
> Zein

From blowekamp at mail.nih.gov  Tue Dec  9 09:11:06 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 9 Dec 2014 09:11:06 -0500
Subject: [ITK-users] [ITK] Computing/Getting the attributes of
	ShapeLabelObject
In-Reply-To: <CADiSopPvMNg=S42Fir=es6anaY3=mCBz4=qoChhvfB+jVH3Sxw@mail.gmail.com>
References: <CADiSopPvMNg=S42Fir=es6anaY3=mCBz4=qoChhvfB+jVH3Sxw@mail.gmail.com>
Message-ID: <6235C0ED-0277-40A9-9B97-D46DFF3280A6@mail.nih.gov>

Hello,

ITK 3.14 is over 5 years old, and appears not to even have this IJ paper merged into the Review directory. I _strongly_ recommend upgrading! I don't even know what code you are using.

It looks like the IJ paper says the roundness is related to the ratio of the areas, but currently (4.7rc1) it computation is does as a ratio of the perimeters[1]. The BinaryImageToShapeLabelMapFilter has some optional computation, among those are computing the peremeter, did you try calling BinaryImageToShapeLabelMapFilter::ComputePerimeterOn()?


Brad

[1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/include/itkShapeLabelMapFilter.hxx#L625

On Dec 9, 2014, at 8:25 AM, Zein Salah <zeinsalah at gmail.com> wrote:

> Hi,
> 
> I want to compute some shape properties  of segmented objects in a binary image.
> S I used the code below to create a labelmap.  BTW, I am using ITK 3.14.
> 
>   typedef unsigned long LabelType;
>   typedef itk::ShapeLabelObject< LabelType, 3 > LabelObjectType;
>   typedef itk::LabelMap< LabelObjectType > LabelMapType;
> 
>   typedef itk::BinaryImageToShapeLabelMapFilter< OverlayImageType,
> LabelMapType > ConverterType;
>   ConverterType::Pointer converter = ConverterType::New();
>   converter->SetInput(m_SegmentedImage);
>   converter->SetInputForegroundValue(255);
>   converter->Update();
> 
>   LabelMapType::Pointer labelMap = converter->GetOutput();
> 
>   for( unsigned int label=0; label <
> labelMap->GetNumberOfLabelObjects(); label++ )
>   {
>       const LabelObjectType * labelObject = labelMap->GetNthLabelObject(label);
>       LabelObjectType::CentroidType centroid = labelObject->GetCentroid();
>       std::cout << label << ": " << labelObject->GetCentroid() << "   "
>                                  << labelObject->GetPhysicalSize() << "   "
>                                  << labelObject->GetRegionElongation() << "   "
>                                  << labelObject->GeRoundness()
>                                  << std::endl;
>   }
> 
> 
> Strangely, the output of the Roundness is always 0. Moreover, it seems that
> some attrubutes are not implemented, e.g. GetElongation,
> GetboundingBox. From the
> corresponding IJ paper, I could not really understand if the the
> attributes are computed
> or need to computed elsewhere.
> 
> Any hints how this should work?
> 
> Thanks,
> Zein
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From blowekamp at mail.nih.gov  Tue Dec  9 09:29:17 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 9 Dec 2014 09:29:17 -0500
Subject: [ITK-users] [ITK] [ANNOUNCE] ITK 4.7 Release Candidate 1 has
	been tagged!
In-Reply-To: <CALzTN-T3=pKTmLCsBUR2HoNxZeHeMAL7C+yHiW3rS13jr2_TBA@mail.gmail.com>
References: <CALzTN-T3=pKTmLCsBUR2HoNxZeHeMAL7C+yHiW3rS13jr2_TBA@mail.gmail.com>
Message-ID: <45FEEDBD-1DEF-4D1B-B9D0-46EC83FAE6CC@mail.nih.gov>

Matt,

I don't think you sufficiently highlighted that now all ITK examples from the Software Guide, Wiki Examples, and SphinxExamples are indexed and crossed linked in Doxygen[1]. So now when you go to your favorite filter or other object, say the ResampleImageFilter[2], there is a large selection of examples in the examples sections. This should make it much easier to fine sample code on how to use an ITK class!

Brad

[1] http://itk.org/Insight/Doxygen/html/examples.html
[2] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html

On Dec 8, 2014, at 11:44 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:

> On behalf of the Insight Toolkit community, we are proud to announce
> that ITK 4.7.0 release candidate 1 has been tagged and is available
> for testing!
> 
> 
> To obtain the source code,
> 
>  git clone http://itk.org/ITK.git
>  cd ITK
>  git checkout -q --detach v4.7rc01
> 
> For more details, please see the Git documentation [1].
> 
> 
> Please test the release candidate and share your experiences on the
> mailing list, issue tracker, and Gerrit Code Review. Please help
> identify issues submitting an Experimental build to the dashboard [2]
> with:
> 
>  ctest -M Experimental  -T Configure -T Build -T Test -T Submit
> 
> and notifying the mailing list.  Testing your own applications against
> the RC is also appreciated.
> 
> 
> Congratulations and well done to everyone that has contributed to this
> release. Release candidates are tagged every week.  The final release
> is scheduled for December 18th.
> 
> 
> [1] http://www.itk.org/Wiki/ITK/Git
> 
> [2] http://open.cdash.org/index.php?project=Insight
> 
> 
> 
> New Features
> ------------------
> * Documentation Improvements
>  - Update Software Guide registration examples to ITKv4 framework
>  - Wiki and Sphinx examples are indexed in Doxygen
>  - Clean Software Guide dashboard build
> 
> * Filtering Improvements
>  - New Laplacian deformation filter?s for QuadEdgeMesh?s
>    - IJ article: http://hdl.handle.net/10380/3410
> - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations
> 
> * ImageIO improvements
>  - PNG sCAL unit support
>  - TIFF IO performance greatly improved
>  - TIFF tags read into Image MetaDataDictionary
>  - MetaIO updated
>  - Better support for system GDCM
> 
> * Infrastructure improvements
>  - New method to erase a MetaDataDictionary entry
>  - New global method to set physical space tolerance
>  - New, experimental thread pool support
>  - NumericTraits::Zero and ::One are deprecated in favor of
> ::ZeroValue() and ::OneValue()
> 
> * New Remote Modules
>  - Higher Order Accurate Gradient
>    - http://hdl.handle.net/10380/3231
>  - IO Transform DCMTK
>    - http://hdl.handle.net/10380/3468
> 
> * Registration improvements
>  - LandmarkBasedTransformInitializer supports BSplineTransform
>  - Transverse inverse consistency increased
>  - Automatic initialization of the transform center for multi-stage
> registrations
>  - Sparse point B-spline field estimate
> 
> * Performance improvements
>  - Faster recursive Gaussian on VectorImage
>  - Mutual information faster, lower memory usage
> 
> * Wrapping improvements
>  - Wrapping now builds without type warnings
>  - pygccxml bumped to 1.6.2
>  - Latest GCCXML
>  - CMake wrapping infrastructure cleanup
>  - Build with Ninja CMake generator
>  - New GetTypes() and GetTypesAsList() methods
>  - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake
> 
> * Many style improvements -- ITK gets more stylish with every release!
> 
> * Improved code coverage -- we are over 85%!
> 
> * *Lots* of important bug fixes
> 
> * And much more! See details in the log below.
> 
> 
> List of changes since v4.5.0
> --------------------------------------
> 
> Alexander Schmidt-Richberg (1):
>      ENH: Updated Remote Module VariationalRegistration to new git tag
> 
> Ali Ghayoor (10):
>      ENH: Make ITKv4 compatible with ITKSoftwareGuide
>      ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4
>      ENH: Convert three ImageRegistration Examples to ITKv4
>      ENH: Add multi-Res and multistage registration Examples to ITKv4
>      ENH: Convert DeformableReg examples to ITKv4 reg framework
>      BUG: Expand a test to reflect multi-metric registration bug
>      BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4
>      ENH: Add direct initialization to SyN registration
>      ENH: Direct initialization of SyN by restoring the state
>      ENH: LandmarkBasedTransformInitializer supports BSplineTransformType
> 
> Arnaud Gelas (15):
>      COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization
>      ENH: Importing Laplacian Deformation for QuadEdgeMesh
>      DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage
>      ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified()
>      ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter
>      BUG: fix gdcm version in GDCMImageIO.
>      COMP: missing cast when calling gdcm::DataElement::SetByteValue
>      COMP: missing cast when calling gdcm::DataElement::SetByteValue
>      ENH: increase LaplacianDeformation code coverage
>      STYLE: use typedef rather than inheritance
>      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false
>      BUG: split include directories into appropriate cmake variables HDF5
>      BUG: missing gdcm libraries when using system GDCM
>      DOC: fix doxygen documentaiton for
> itk::LaplacianDeformationQuadEdgeMeshFilter
>      ENH: Add one method to erase a tag into MetaDataDictionary
> 
> Bill Lorensen (5):
>      ENH: Specify required VTK modules
>      COMP: Wiki examples require additional vtk modules
>      ENH: Modify WikiExamples remote config
>      COMP: Bad test signature
>      COMP: Update tag for wiki examples
> 
> Brad King (6):
>      COMP: Fix vxl_config_macros usage of CMake check macros
>      ENH: Use if(DEFINED) to simplify conditions
>      COMP: Fix vxl_config_macros checks broken by refactoring
>      COMP: Fix one more vxl_config_macros check broken by refactoring
>      BUG: Fix itk_module_config for repeated calls
>      BUG: Fix itk_module_config for repeated calls
> 
> Bradley Lowekamp (52):
>      ENH: Adding License file from upstream MetaIO
>      ENH: Adding script to update MetaIO from upstream
>      ENH: Remove ITK MetaIO to prepare for upstream import
>      PERF: Remove dynamically allocated temporary in evaluate method
>      COMP: Fix variable type for Set/Get macros
>      BUG: Implement ITK Style Singleton design pattern
>      ENH: Add no throw exception specification for UnRegister methods
>      COMP: Must specify order as "noexcept override"
>      BUG: Add GetInverse for IdentityTransform
>      ENH: Adding SetIdentity method to base DisplacementField class
>      BUG: Remove unused redefinition of NULL
>      BUG: Don't print to std::cout in PrintSelf
>      ENH: Prefer the PrintSelfObjectMacro for printing nested objects
>      BUG: Use METER of sCAL scale unit
>      BUG: Use PNG_SCALE_METER for PNG sCAL unit
>      BUG: Use METER of sCAL scale unit
>      BUG: Use PNG_SCALE_METER for PNG sCAL unit
>      COMP: Fix signed to unsigned int comparison
>      BUG: Fix overflows computing size of read tiff image
>      ENH: Extract TiffReaderInternal to separate file
>      ENH: Refactor ReadTwoSamplePerPixelImage into template function
>      ENH: Refactor GenericReadImage into template function
>      BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO )
>      ENH: Refactor method to convert RGBA image to output buffer
>      ENH: Refactor duplicated code to read a page
>      BUG: Fix right oriented tiff images
>      BUG: Remove dead separated plannar code, add test
>      STYLE: Fix minor kwstyle defects in test and test results
>      BUG: Use array delete operator for array new allocations
>      ENH: add arbitrary TIFF TAGs to meta-data dictionary
>      ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
>      BUG: Address Coverity warning about null pointer dereferences
>      ENH: Remove support for TIFF tile as 3D and dead code
>      ENH: RGBA read images should stay unchanged.
>      BUG: Override method to MakeOutput by name
>      ENH: Refactor per pixel conversion function to per scan-line method
>      PERF: Refactor color table lookup
>      BUG: Adding missing parentheses around boolean expression
>      ENH: adding TIFFImageIO test for RGB palette images
>      PERF: Improve recursive Gaussian perfromance with VectorImages
>      ENH: Query libtiff to determine compression support
>      BUG: Support TIFF tiled image with TIFFReadRGBAImage
>      BUG: Use SizeValueType for length of scanline
>      PERF: Store causal results directly in output buffers
>      COMP: Add explicit conversion to const char
>      COMP: Explicitly add override to GetNameOfClass method
>      COMP: Address internal segmentation fault with Intel compiler
>      ENH: Adding method to set global physical space tolerance
>      COMP: Explicitly add override to GetNameOfClass method
>      BUG: Add new TypeMacro for non-overloaded classes
>      BUG: Fix obscure race condition on access thread pool initialization
>      BUG: Updating FDFImageIO remote module
> 
> Christopher Mullins (15):
>      COMP: Allows latex to compile for ITKSoftwareGuide
>      COMP: Allows latex to compile for ITKSoftwareGuide
>      COMP: Wrap MeshBase templates
>      COMP: Wrap MeshBase templates
>      COMP: Fix warning in BlockMatchingImageFilter
>      STYLE: Line lengths in examples should be no longer than 80 chars.
>      COMP: Wrap the remaining MeshBase and MeshToMeshFilter types.
>      COMP: Fix LaTeX warnings.
>      STYLE: Fix formatting/punctuation errors.
>      STYLE: Formatting and punctuation fixes.
>      DOC: Edits for Book 2 Chapter 1 documentation in the Examples.
>      DOC: Edits for book 2 chapter 2.
>      DOC: More chapter 2 edits
>      DOC: Book 2 Chapter 3 edits (part 1)
>      DOC: book 2 chapter 4 Segmentation edits
> 
> Danny Perry (2):
>      BUG: adding test for vnl_sparse_matrix::mult()
>      BUG: size of q buffer should actually be (this->rows())*pcols.
> 
> David T. Chen (1):
>      DOC: Fixed HistogramThresholdImageFitler
> 
> Dirk Padfield (1):
>      BUG: Corrected processing of last sigma
> 
> GCC-XML Upstream (1):
>      ENH: pygccxml v1.6.2 (reduced)
> 
> 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 (24):
>      COMP: Add tolerance for comparing floating point
>      PERF: Remove non-threadable algorithm components
>      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
>      BUG: Syntax error in comment
>      PERF: Add non-blocking mutex locking.
>      ENH: Use TryLock minimize thread stalls
>      BUG: ThreadedIndexedContainerPartitioner is inclusive
>      STYLE: Remove include_regular_expression from Examples
>      BUG: Demonstrate Inv(Inv(T)) != T
>      BUG: Ensure Inv(Inv(T)) == T for transforms
>      COMP: Valgrind detects uninitialized memory read
>      COMP: Missing required base class API component
>      ENH: Expand interface for selecting threadpool
> 
> Ismael Belghiti (1):
>      DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter
> 
> Jim Miller (1):
>      STYLE: Removing what appears to be a temporary file
> 
> Johan Andruejol (1):
>      ENH: Fix normalization for null vectors and return the norm
> 
> Jon Haitz Legarreta (1):
>      ENH: New test for itkLabelShapeOpeningImageFilter
> 
> Kent Williams (9):
>      COMP: use find_package(VTK COMPONENTS) to specify just needed
> VTK Components
>      BUG: ImageSources/test/CMakeLists.txt incorrect library var reference
>      COMP: Fix coverity defects related to RegistrationV4 examples
>      COMP: silence warning of vnl_vector_fixed_ref::assert_size
>      COMP: Fix various Coverity warnings
>      COMP: Fix a typo in an error message print statement.
>      COMP: itk::Command-derived class used pointless dynamic_cast.
>      PERF: Don't recompute InternalInverse repeatedly
>      COMP: Correct orientation/spacing for Philips MultiFrame
> 
> Mark Hiner (2):
>      ENH: Update SCIFIO remote module hash
>      BUG: Fix duplicate variables in Windows
> 
> Matthew McCormick (105):
>      DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro.
>      ENH: Move FFTComplexToComplexImageFilter out of Review.
>      ENH: Add VnlComplexToComplexFFTImageFilter.
>      BUG: Use fixed seed for Vnl FFT tests for repeatibility.
>      ENH: Bump CMakeLists.txt version to 4.7.0.
>      BUG: ArchiveTestingData.py future imports must occur at the beginning.
>      BUG: Do not run vnl_test_na with broken libc++.
>      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.
>      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
>      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
>      BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter.
>      BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest.
>      STYLE: Fix style in VoronoiDiagram2D.
>      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>      BUG: Bump GCCXML to 2014-08-06.
>      BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}.
>      BUG: Fix Win MultiThreader check for successful process creation.
>      BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor.
>      COMP: Fix ImageRegistration8RegisteredSlice.png baseline name.
>      DOC: itk::statistics -> itk::Statistics.
>      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
>      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>      COMP: Improve const correctness of GradientRecursiveGaussianImageFilter.
>      BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().
>      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
>      COMP: ThreadJob NULL not defined.
>      BUG: Fix alpha assignment for RGBA TIFF.
>      COMP: Remove unused typedefs in LevelSetsv4Visualization.
>      COMP: Remove unused typedef's in VtkGlue.
>      ENH: Mark BSplineWarping2Test as RUNS_LONG.
>      BUG: Fix Nifti IO read with large images.
>      COMP: Remove call for non-existent variable in Nifti debugging.
>      BUG: Close the file on Read and Write in HDF5TransformIO.
>      BUG: Remove InsightLegacy test code from TransformHDF5Test.
>      ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}.
>      STYLE: Use SeriesUIDContainerType and FileNamesContainerType
>      ENH: Allow specification of orthogonality tolerance in rigid transforms.
>      BUG: TransformFileReader does not clear its TransformList.
>      BUG: Prevent dangling pointer in HDF5TransformIO.
>      COMP: Do not use _stat64 with MinGW-32.
>      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.
>      COMP: Address LaplacianDeformation Doxygen warnings.
>      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
>      COMP: Do not wrap the FixedArray of Image SmartPointer's.
>      COMP: Add missing wrapping for TransformIOBaseTemplate.
>      COMP: Mark DeformableRegistration6Test as RUNS_LONG.
>      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.
>      BUG: Use -py3 when building wrapping for Python 3.
>      COMP: Add missing wrapping for TransformIOBaseTemplate.
>      DOC: Improve ImageRegistration4 grammar.
>      ENH: Add IOTransformDCMTK Remote module.
>      BUG: gdcm::StringFilter recognizes backslash delimiter.
>      DOC: Add migration guide for GDCM Rescale slope intercept apply on write.
>      COMP: Remove unused typedef's in GPU code.
>      STYLE: Improve style of HoughTransform2DLinesImageFilter example.
>      COMP: Use ConceptChecking for IterativeInverse dimension check.
>      COMP: Wrap TransformIOBaseTemplate for const SmartPointer.
>      COMP: Add warning exceptions for third party pcre, swig, gccxml.
>      ENH: Bump ITK version to 4.6.1.
>      BUG: Add missing ITK_OVERRIDE to ITKImageeSources module.
>      BUG: Remove GaussianImageSource members shadowing GenerateImageSource.
>      STYLE: Style fixes to ITKImageSources module.
>      BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType.
>      BUG: Do not perform itk_download_attempt_check when not building ITK.
>      DOC: Update GDCMImageIO rescale slope intercept doc.
>      BUG: Only register requestion IO COMPONENT modules.
>      BUG: Fix wrapping .i, .idx CMake dependencies.
>      COMP: Add VTK Python module when wrapping ITKVtkGlue.
>      STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator.
>      STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef.
>      COMP: Add missing VTK module dependency for LevelSetsv4Visualization.
>      BUG: By default, do not create any fixed parameters.
>      STYLE: Remove trivial method comments in itkTransform.hxx.
>      BUG: PolylineMask Filter's GenerateData is protected / virtual.
>      ENH: Add HigherOrderAccurateGradient Module.
>      BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal.
>      COMP: Remove extra semi-colon, variable scope in DCMTKFileReader.
>      STYLE: Style fixes for Transform classes.
>      DOC: Increase Doxygen LOOKUP_CACHE_SIZE.
>      BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe.
>      DOC: Index Wiki examples with Doxygen.
>      COMP: Bump SphinxExamples remote module.
>      DOC: Index Sphinx examples in Doxygen.
>      COMP: Remove old java examples.
>      COMP: Remove duplicate DiffusionTensor3DReconstruction example reference.
>      COMP: Address GradientAnisotropicDiffusionImageFilter example settings.
>      COMP: Bump Sphinx Examples remote.
>      COMP: Bump WikiExamples remote.
> 
> MetaIO Maintainers (1):
>      MetaIO (reduced)
> 
> Michka Popoff (40):
>      ENH: Fixes for python 3 support
>      BUG: Add VTK_VERSION for older VTK versions
>      BUG: Improve SWIG version check
>      COMP: Add wrapping for ThreadPool and ThreadJob
>      COMP: Remove unimplemented DestroyPool method
>      COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping
>      COMP: Do not hide pygccxml warnings
>      ENH: Update links in readme file
>      BUG: Improve SWIG version check
>      BUG: Add VTK_VERSION for older VTK versions
>      STYLE: Remove trailing whitespaces
>      STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP
>      BUG: Fix memory leak in MetaImageIO after exception
>      ENH: Add script to update pygccxml from upstream
>      BUG: Update VTK minimum version (for release)
>      BUG: Fix memory leak in MetaImageIO after exception
>      ENH: Remove Sun OS compatibility for the wrappings
>      COMP: Fix for conversion to non-pointer like type warning
>      STYLE: LabelObject style
>      DOC: Remove broken link from LabelObject class description
>      ENH: Do not setup the python tests if not asked
>      ENH: Add new GetTypes() and GetTypesAsList() methods to the template class
>      COMP: Fix CMP0054 warnings in wrappings
>      STYLE: Remove old cmake < 2.8.4 specific code
>      STYLE: Remove old cmake < 2.8.5 specific code
>      ENH: Update to PCRE 8.36
>      COMP: Refactor Wrapping setup and fix legacy warnings
>      ENH: Add wrapping configuration to ITKConfig.cmake
>      STYLE: Some minor code cleanup in the wrapping setup
>      DOC: Fix typo in RelabelComponentImageFilter
>      ENH: Deprecate VectorResampleImageFilter
>      DOC: Add migration guide for ::Zero and ::One
>      ENH: Deprecate ::Zero and ::One
>      ENH: Add option to disable sorting by size in
> itkRelabelComponentImageFilter
>      ENH: Add Vector and RGB wrapping to linear interpolator
>      STYLE: Remove SORT macro in wrappings
>      COMP: Fix warning for InterpolateImageFunction wrapping
>      COMP: Add a check for Blocks in GPU module
>      COMP: Bump SCIFIO to fix test build warnings
>      COMP: Fix wrapping of itkImageFunctionBase
> 
> Nick Tustison (7):
>      BUG:  Need to explicitly specify spline order.
>      ENH:  Initializing the transform center.
>      BUG:  Need to check the dynamic cast before any calls.
>      ENH:  Adding modifications for point set metrics.
>      BUG:  Need to specify TInternalComputationValueType for default metric.
>      ENH:  Adding sparse points to B-spline field estimate.
>      BUG:  Uninitialized variables.
> 
> Richard Beare (1):
>      ENH: Include TIFF tags in the MetaDataDictionary
> 
> Taylor Braun-Jones (1):
>      BUG: Fix SliceBySliceImageFilter doesn't propagate information internally
> 
> Umang B (1):
>      ENH: Use thread pool to dispatch multithreading tasks
> 
> Vivien Delmon (2):
>      BUG: ExtractImageFilter::CollapseToSubMatrix fix
>      ENH: Add a test on extracted directions in CollapseToSubMatrix mode
> 
> Vladimir S. FONOV (1):
>      BUG: Fixing incorrect MINC style inverse transform
> 
> 
> 
> -----------------------------------------------------
> Errors or omissions? Please fix them here:
> 
> https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From matt.mccormick at kitware.com  Tue Dec  9 11:22:23 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 9 Dec 2014 11:22:23 -0500
Subject: [ITK-users] [ITK] [ANNOUNCE] ITK 4.7 Release Candidate 1 has
	been tagged!
In-Reply-To: <45FEEDBD-1DEF-4D1B-B9D0-46EC83FAE6CC@mail.nih.gov>
References: <CALzTN-T3=pKTmLCsBUR2HoNxZeHeMAL7C+yHiW3rS13jr2_TBA@mail.gmail.com>
 <45FEEDBD-1DEF-4D1B-B9D0-46EC83FAE6CC@mail.nih.gov>
Message-ID: <CALzTN-SrNj4KBc1Y5aiKvkbKt43Drek2THmGBmHJ4kgxSTQT+Q@mail.gmail.com>

Hi Brad,

Thanks for the feedback.  I've tweaked the release text accordingly.

On a side note, I also created this issue [1], so that we will
remember to allow modules to declare their own examples in the future.

Thanks,
Matt

[1] https://issues.itk.org/jira/browse/ITK-3336

On Tue, Dec 9, 2014 at 9:29 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Matt,
>
> I don't think you sufficiently highlighted that now all ITK examples from the Software Guide, Wiki Examples, and SphinxExamples are indexed and crossed linked in Doxygen[1]. So now when you go to your favorite filter or other object, say the ResampleImageFilter[2], there is a large selection of examples in the examples sections. This should make it much easier to fine sample code on how to use an ITK class!
>
> Brad
>
> [1] http://itk.org/Insight/Doxygen/html/examples.html
> [2] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html
>
> On Dec 8, 2014, at 11:44 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>
>> On behalf of the Insight Toolkit community, we are proud to announce
>> that ITK 4.7.0 release candidate 1 has been tagged and is available
>> for testing!
>>
>>
>> To obtain the source code,
>>
>>  git clone http://itk.org/ITK.git
>>  cd ITK
>>  git checkout -q --detach v4.7rc01
>>
>> For more details, please see the Git documentation [1].
>>
>>
>> Please test the release candidate and share your experiences on the
>> mailing list, issue tracker, and Gerrit Code Review. Please help
>> identify issues submitting an Experimental build to the dashboard [2]
>> with:
>>
>>  ctest -M Experimental  -T Configure -T Build -T Test -T Submit
>>
>> and notifying the mailing list.  Testing your own applications against
>> the RC is also appreciated.
>>
>>
>> Congratulations and well done to everyone that has contributed to this
>> release. Release candidates are tagged every week.  The final release
>> is scheduled for December 18th.
>>
>>
>> [1] http://www.itk.org/Wiki/ITK/Git
>>
>> [2] http://open.cdash.org/index.php?project=Insight
>>
>>
>>
>> New Features
>> ------------------
>> * Documentation Improvements
>>  - Update Software Guide registration examples to ITKv4 framework
>>  - Wiki and Sphinx examples are indexed in Doxygen
>>  - Clean Software Guide dashboard build
>>
>> * Filtering Improvements
>>  - New Laplacian deformation filter?s for QuadEdgeMesh?s
>>    - IJ article: http://hdl.handle.net/10380/3410
>> - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations
>>
>> * ImageIO improvements
>>  - PNG sCAL unit support
>>  - TIFF IO performance greatly improved
>>  - TIFF tags read into Image MetaDataDictionary
>>  - MetaIO updated
>>  - Better support for system GDCM
>>
>> * Infrastructure improvements
>>  - New method to erase a MetaDataDictionary entry
>>  - New global method to set physical space tolerance
>>  - New, experimental thread pool support
>>  - NumericTraits::Zero and ::One are deprecated in favor of
>> ::ZeroValue() and ::OneValue()
>>
>> * New Remote Modules
>>  - Higher Order Accurate Gradient
>>    - http://hdl.handle.net/10380/3231
>>  - IO Transform DCMTK
>>    - http://hdl.handle.net/10380/3468
>>
>> * Registration improvements
>>  - LandmarkBasedTransformInitializer supports BSplineTransform
>>  - Transverse inverse consistency increased
>>  - Automatic initialization of the transform center for multi-stage
>> registrations
>>  - Sparse point B-spline field estimate
>>
>> * Performance improvements
>>  - Faster recursive Gaussian on VectorImage
>>  - Mutual information faster, lower memory usage
>>
>> * Wrapping improvements
>>  - Wrapping now builds without type warnings
>>  - pygccxml bumped to 1.6.2
>>  - Latest GCCXML
>>  - CMake wrapping infrastructure cleanup
>>  - Build with Ninja CMake generator
>>  - New GetTypes() and GetTypesAsList() methods
>>  - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake
>>
>> * Many style improvements -- ITK gets more stylish with every release!
>>
>> * Improved code coverage -- we are over 85%!
>>
>> * *Lots* of important bug fixes
>>
>> * And much more! See details in the log below.
>>
>>
>> List of changes since v4.5.0
>> --------------------------------------
>>
>> Alexander Schmidt-Richberg (1):
>>      ENH: Updated Remote Module VariationalRegistration to new git tag
>>
>> Ali Ghayoor (10):
>>      ENH: Make ITKv4 compatible with ITKSoftwareGuide
>>      ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4
>>      ENH: Convert three ImageRegistration Examples to ITKv4
>>      ENH: Add multi-Res and multistage registration Examples to ITKv4
>>      ENH: Convert DeformableReg examples to ITKv4 reg framework
>>      BUG: Expand a test to reflect multi-metric registration bug
>>      BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4
>>      ENH: Add direct initialization to SyN registration
>>      ENH: Direct initialization of SyN by restoring the state
>>      ENH: LandmarkBasedTransformInitializer supports BSplineTransformType
>>
>> Arnaud Gelas (15):
>>      COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization
>>      ENH: Importing Laplacian Deformation for QuadEdgeMesh
>>      DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage
>>      ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified()
>>      ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter
>>      BUG: fix gdcm version in GDCMImageIO.
>>      COMP: missing cast when calling gdcm::DataElement::SetByteValue
>>      COMP: missing cast when calling gdcm::DataElement::SetByteValue
>>      ENH: increase LaplacianDeformation code coverage
>>      STYLE: use typedef rather than inheritance
>>      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false
>>      BUG: split include directories into appropriate cmake variables HDF5
>>      BUG: missing gdcm libraries when using system GDCM
>>      DOC: fix doxygen documentaiton for
>> itk::LaplacianDeformationQuadEdgeMeshFilter
>>      ENH: Add one method to erase a tag into MetaDataDictionary
>>
>> Bill Lorensen (5):
>>      ENH: Specify required VTK modules
>>      COMP: Wiki examples require additional vtk modules
>>      ENH: Modify WikiExamples remote config
>>      COMP: Bad test signature
>>      COMP: Update tag for wiki examples
>>
>> Brad King (6):
>>      COMP: Fix vxl_config_macros usage of CMake check macros
>>      ENH: Use if(DEFINED) to simplify conditions
>>      COMP: Fix vxl_config_macros checks broken by refactoring
>>      COMP: Fix one more vxl_config_macros check broken by refactoring
>>      BUG: Fix itk_module_config for repeated calls
>>      BUG: Fix itk_module_config for repeated calls
>>
>> Bradley Lowekamp (52):
>>      ENH: Adding License file from upstream MetaIO
>>      ENH: Adding script to update MetaIO from upstream
>>      ENH: Remove ITK MetaIO to prepare for upstream import
>>      PERF: Remove dynamically allocated temporary in evaluate method
>>      COMP: Fix variable type for Set/Get macros
>>      BUG: Implement ITK Style Singleton design pattern
>>      ENH: Add no throw exception specification for UnRegister methods
>>      COMP: Must specify order as "noexcept override"
>>      BUG: Add GetInverse for IdentityTransform
>>      ENH: Adding SetIdentity method to base DisplacementField class
>>      BUG: Remove unused redefinition of NULL
>>      BUG: Don't print to std::cout in PrintSelf
>>      ENH: Prefer the PrintSelfObjectMacro for printing nested objects
>>      BUG: Use METER of sCAL scale unit
>>      BUG: Use PNG_SCALE_METER for PNG sCAL unit
>>      BUG: Use METER of sCAL scale unit
>>      BUG: Use PNG_SCALE_METER for PNG sCAL unit
>>      COMP: Fix signed to unsigned int comparison
>>      BUG: Fix overflows computing size of read tiff image
>>      ENH: Extract TiffReaderInternal to separate file
>>      ENH: Refactor ReadTwoSamplePerPixelImage into template function
>>      ENH: Refactor GenericReadImage into template function
>>      BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO )
>>      ENH: Refactor method to convert RGBA image to output buffer
>>      ENH: Refactor duplicated code to read a page
>>      BUG: Fix right oriented tiff images
>>      BUG: Remove dead separated plannar code, add test
>>      STYLE: Fix minor kwstyle defects in test and test results
>>      BUG: Use array delete operator for array new allocations
>>      ENH: add arbitrary TIFF TAGs to meta-data dictionary
>>      ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
>>      BUG: Address Coverity warning about null pointer dereferences
>>      ENH: Remove support for TIFF tile as 3D and dead code
>>      ENH: RGBA read images should stay unchanged.
>>      BUG: Override method to MakeOutput by name
>>      ENH: Refactor per pixel conversion function to per scan-line method
>>      PERF: Refactor color table lookup
>>      BUG: Adding missing parentheses around boolean expression
>>      ENH: adding TIFFImageIO test for RGB palette images
>>      PERF: Improve recursive Gaussian perfromance with VectorImages
>>      ENH: Query libtiff to determine compression support
>>      BUG: Support TIFF tiled image with TIFFReadRGBAImage
>>      BUG: Use SizeValueType for length of scanline
>>      PERF: Store causal results directly in output buffers
>>      COMP: Add explicit conversion to const char
>>      COMP: Explicitly add override to GetNameOfClass method
>>      COMP: Address internal segmentation fault with Intel compiler
>>      ENH: Adding method to set global physical space tolerance
>>      COMP: Explicitly add override to GetNameOfClass method
>>      BUG: Add new TypeMacro for non-overloaded classes
>>      BUG: Fix obscure race condition on access thread pool initialization
>>      BUG: Updating FDFImageIO remote module
>>
>> Christopher Mullins (15):
>>      COMP: Allows latex to compile for ITKSoftwareGuide
>>      COMP: Allows latex to compile for ITKSoftwareGuide
>>      COMP: Wrap MeshBase templates
>>      COMP: Wrap MeshBase templates
>>      COMP: Fix warning in BlockMatchingImageFilter
>>      STYLE: Line lengths in examples should be no longer than 80 chars.
>>      COMP: Wrap the remaining MeshBase and MeshToMeshFilter types.
>>      COMP: Fix LaTeX warnings.
>>      STYLE: Fix formatting/punctuation errors.
>>      STYLE: Formatting and punctuation fixes.
>>      DOC: Edits for Book 2 Chapter 1 documentation in the Examples.
>>      DOC: Edits for book 2 chapter 2.
>>      DOC: More chapter 2 edits
>>      DOC: Book 2 Chapter 3 edits (part 1)
>>      DOC: book 2 chapter 4 Segmentation edits
>>
>> Danny Perry (2):
>>      BUG: adding test for vnl_sparse_matrix::mult()
>>      BUG: size of q buffer should actually be (this->rows())*pcols.
>>
>> David T. Chen (1):
>>      DOC: Fixed HistogramThresholdImageFitler
>>
>> Dirk Padfield (1):
>>      BUG: Corrected processing of last sigma
>>
>> GCC-XML Upstream (1):
>>      ENH: pygccxml v1.6.2 (reduced)
>>
>> 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 (24):
>>      COMP: Add tolerance for comparing floating point
>>      PERF: Remove non-threadable algorithm components
>>      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
>>      BUG: Syntax error in comment
>>      PERF: Add non-blocking mutex locking.
>>      ENH: Use TryLock minimize thread stalls
>>      BUG: ThreadedIndexedContainerPartitioner is inclusive
>>      STYLE: Remove include_regular_expression from Examples
>>      BUG: Demonstrate Inv(Inv(T)) != T
>>      BUG: Ensure Inv(Inv(T)) == T for transforms
>>      COMP: Valgrind detects uninitialized memory read
>>      COMP: Missing required base class API component
>>      ENH: Expand interface for selecting threadpool
>>
>> Ismael Belghiti (1):
>>      DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter
>>
>> Jim Miller (1):
>>      STYLE: Removing what appears to be a temporary file
>>
>> Johan Andruejol (1):
>>      ENH: Fix normalization for null vectors and return the norm
>>
>> Jon Haitz Legarreta (1):
>>      ENH: New test for itkLabelShapeOpeningImageFilter
>>
>> Kent Williams (9):
>>      COMP: use find_package(VTK COMPONENTS) to specify just needed
>> VTK Components
>>      BUG: ImageSources/test/CMakeLists.txt incorrect library var reference
>>      COMP: Fix coverity defects related to RegistrationV4 examples
>>      COMP: silence warning of vnl_vector_fixed_ref::assert_size
>>      COMP: Fix various Coverity warnings
>>      COMP: Fix a typo in an error message print statement.
>>      COMP: itk::Command-derived class used pointless dynamic_cast.
>>      PERF: Don't recompute InternalInverse repeatedly
>>      COMP: Correct orientation/spacing for Philips MultiFrame
>>
>> Mark Hiner (2):
>>      ENH: Update SCIFIO remote module hash
>>      BUG: Fix duplicate variables in Windows
>>
>> Matthew McCormick (105):
>>      DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro.
>>      ENH: Move FFTComplexToComplexImageFilter out of Review.
>>      ENH: Add VnlComplexToComplexFFTImageFilter.
>>      BUG: Use fixed seed for Vnl FFT tests for repeatibility.
>>      ENH: Bump CMakeLists.txt version to 4.7.0.
>>      BUG: ArchiveTestingData.py future imports must occur at the beginning.
>>      BUG: Do not run vnl_test_na with broken libc++.
>>      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.
>>      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
>>      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
>>      BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter.
>>      BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest.
>>      STYLE: Fix style in VoronoiDiagram2D.
>>      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>>      BUG: Bump GCCXML to 2014-08-06.
>>      BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}.
>>      BUG: Fix Win MultiThreader check for successful process creation.
>>      BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor.
>>      COMP: Fix ImageRegistration8RegisteredSlice.png baseline name.
>>      DOC: itk::statistics -> itk::Statistics.
>>      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
>>      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>>      COMP: Improve const correctness of GradientRecursiveGaussianImageFilter.
>>      BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().
>>      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
>>      COMP: ThreadJob NULL not defined.
>>      BUG: Fix alpha assignment for RGBA TIFF.
>>      COMP: Remove unused typedefs in LevelSetsv4Visualization.
>>      COMP: Remove unused typedef's in VtkGlue.
>>      ENH: Mark BSplineWarping2Test as RUNS_LONG.
>>      BUG: Fix Nifti IO read with large images.
>>      COMP: Remove call for non-existent variable in Nifti debugging.
>>      BUG: Close the file on Read and Write in HDF5TransformIO.
>>      BUG: Remove InsightLegacy test code from TransformHDF5Test.
>>      ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}.
>>      STYLE: Use SeriesUIDContainerType and FileNamesContainerType
>>      ENH: Allow specification of orthogonality tolerance in rigid transforms.
>>      BUG: TransformFileReader does not clear its TransformList.
>>      BUG: Prevent dangling pointer in HDF5TransformIO.
>>      COMP: Do not use _stat64 with MinGW-32.
>>      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.
>>      COMP: Address LaplacianDeformation Doxygen warnings.
>>      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
>>      COMP: Do not wrap the FixedArray of Image SmartPointer's.
>>      COMP: Add missing wrapping for TransformIOBaseTemplate.
>>      COMP: Mark DeformableRegistration6Test as RUNS_LONG.
>>      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.
>>      BUG: Use -py3 when building wrapping for Python 3.
>>      COMP: Add missing wrapping for TransformIOBaseTemplate.
>>      DOC: Improve ImageRegistration4 grammar.
>>      ENH: Add IOTransformDCMTK Remote module.
>>      BUG: gdcm::StringFilter recognizes backslash delimiter.
>>      DOC: Add migration guide for GDCM Rescale slope intercept apply on write.
>>      COMP: Remove unused typedef's in GPU code.
>>      STYLE: Improve style of HoughTransform2DLinesImageFilter example.
>>      COMP: Use ConceptChecking for IterativeInverse dimension check.
>>      COMP: Wrap TransformIOBaseTemplate for const SmartPointer.
>>      COMP: Add warning exceptions for third party pcre, swig, gccxml.
>>      ENH: Bump ITK version to 4.6.1.
>>      BUG: Add missing ITK_OVERRIDE to ITKImageeSources module.
>>      BUG: Remove GaussianImageSource members shadowing GenerateImageSource.
>>      STYLE: Style fixes to ITKImageSources module.
>>      BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType.
>>      BUG: Do not perform itk_download_attempt_check when not building ITK.
>>      DOC: Update GDCMImageIO rescale slope intercept doc.
>>      BUG: Only register requestion IO COMPONENT modules.
>>      BUG: Fix wrapping .i, .idx CMake dependencies.
>>      COMP: Add VTK Python module when wrapping ITKVtkGlue.
>>      STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator.
>>      STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef.
>>      COMP: Add missing VTK module dependency for LevelSetsv4Visualization.
>>      BUG: By default, do not create any fixed parameters.
>>      STYLE: Remove trivial method comments in itkTransform.hxx.
>>      BUG: PolylineMask Filter's GenerateData is protected / virtual.
>>      ENH: Add HigherOrderAccurateGradient Module.
>>      BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal.
>>      COMP: Remove extra semi-colon, variable scope in DCMTKFileReader.
>>      STYLE: Style fixes for Transform classes.
>>      DOC: Increase Doxygen LOOKUP_CACHE_SIZE.
>>      BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe.
>>      DOC: Index Wiki examples with Doxygen.
>>      COMP: Bump SphinxExamples remote module.
>>      DOC: Index Sphinx examples in Doxygen.
>>      COMP: Remove old java examples.
>>      COMP: Remove duplicate DiffusionTensor3DReconstruction example reference.
>>      COMP: Address GradientAnisotropicDiffusionImageFilter example settings.
>>      COMP: Bump Sphinx Examples remote.
>>      COMP: Bump WikiExamples remote.
>>
>> MetaIO Maintainers (1):
>>      MetaIO (reduced)
>>
>> Michka Popoff (40):
>>      ENH: Fixes for python 3 support
>>      BUG: Add VTK_VERSION for older VTK versions
>>      BUG: Improve SWIG version check
>>      COMP: Add wrapping for ThreadPool and ThreadJob
>>      COMP: Remove unimplemented DestroyPool method
>>      COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping
>>      COMP: Do not hide pygccxml warnings
>>      ENH: Update links in readme file
>>      BUG: Improve SWIG version check
>>      BUG: Add VTK_VERSION for older VTK versions
>>      STYLE: Remove trailing whitespaces
>>      STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP
>>      BUG: Fix memory leak in MetaImageIO after exception
>>      ENH: Add script to update pygccxml from upstream
>>      BUG: Update VTK minimum version (for release)
>>      BUG: Fix memory leak in MetaImageIO after exception
>>      ENH: Remove Sun OS compatibility for the wrappings
>>      COMP: Fix for conversion to non-pointer like type warning
>>      STYLE: LabelObject style
>>      DOC: Remove broken link from LabelObject class description
>>      ENH: Do not setup the python tests if not asked
>>      ENH: Add new GetTypes() and GetTypesAsList() methods to the template class
>>      COMP: Fix CMP0054 warnings in wrappings
>>      STYLE: Remove old cmake < 2.8.4 specific code
>>      STYLE: Remove old cmake < 2.8.5 specific code
>>      ENH: Update to PCRE 8.36
>>      COMP: Refactor Wrapping setup and fix legacy warnings
>>      ENH: Add wrapping configuration to ITKConfig.cmake
>>      STYLE: Some minor code cleanup in the wrapping setup
>>      DOC: Fix typo in RelabelComponentImageFilter
>>      ENH: Deprecate VectorResampleImageFilter
>>      DOC: Add migration guide for ::Zero and ::One
>>      ENH: Deprecate ::Zero and ::One
>>      ENH: Add option to disable sorting by size in
>> itkRelabelComponentImageFilter
>>      ENH: Add Vector and RGB wrapping to linear interpolator
>>      STYLE: Remove SORT macro in wrappings
>>      COMP: Fix warning for InterpolateImageFunction wrapping
>>      COMP: Add a check for Blocks in GPU module
>>      COMP: Bump SCIFIO to fix test build warnings
>>      COMP: Fix wrapping of itkImageFunctionBase
>>
>> Nick Tustison (7):
>>      BUG:  Need to explicitly specify spline order.
>>      ENH:  Initializing the transform center.
>>      BUG:  Need to check the dynamic cast before any calls.
>>      ENH:  Adding modifications for point set metrics.
>>      BUG:  Need to specify TInternalComputationValueType for default metric.
>>      ENH:  Adding sparse points to B-spline field estimate.
>>      BUG:  Uninitialized variables.
>>
>> Richard Beare (1):
>>      ENH: Include TIFF tags in the MetaDataDictionary
>>
>> Taylor Braun-Jones (1):
>>      BUG: Fix SliceBySliceImageFilter doesn't propagate information internally
>>
>> Umang B (1):
>>      ENH: Use thread pool to dispatch multithreading tasks
>>
>> Vivien Delmon (2):
>>      BUG: ExtractImageFilter::CollapseToSubMatrix fix
>>      ENH: Add a test on extracted directions in CollapseToSubMatrix mode
>>
>> Vladimir S. FONOV (1):
>>      BUG: Fixing incorrect MINC style inverse transform
>>
>>
>>
>> -----------------------------------------------------
>> Errors or omissions? Please fix them here:
>>
>> https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing
>> _______________________________________________
>> Community mailing list
>> Community at itk.org
>> http://public.kitware.com/mailman/listinfo/community
>

From mpinkert at wisc.edu  Tue Dec  9 14:15:56 2014
From: mpinkert at wisc.edu (Michael Pinkert)
Date: Tue, 09 Dec 2014 13:15:56 -0600
Subject: [ITK-users] GPU Implementation
In-Reply-To: <76f08a62167ec.54874a47@wiscmail.wisc.edu>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <039601d00975$3f03c660$bd0b5320$@ac.kr>
 <76f08a62167ec.54874a47@wiscmail.wisc.edu>
Message-ID: <76a0870a10478.5486f60c@wiscmail.wisc.edu>

Hi Xiaopeng,

Unfortunately, I was not able to fix this problem in my code. Please let us know if Jim's explanation is accurate. 

Best regards,
Michael Pinkert

On 11/26/14, Xiaopeng Yang  wrote:
> Hi,
> 
> I tried to compile the code from Modules\Registration\GPUPDEDeformable\test
> folder. Enclosed please find the code and CMakeLists file. I am quite new to
> GPU, sorry I could not understand your explanation. Could you point out what
> I missed please?
> 
> Thanks,
> Xiaopeng
> 
> -----Original Message-----
> From: Jim Miller [mailto:millerjv at gmail.com](javascript:main.compose() 
> Sent: Wednesday, November 26, 2014 9:10 PM
> To: Xiaopeng Yang
> Cc: Michael Pinkert; insight-users at itk.org
> Subject: Re: [ITK-users] GPU Implementation
> 
> This doesn't look like any issue with finding OpenCL. The link error is
> saying it cannot find the implementation of an ITK method. 
> 
> I think GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void) is
> supposed to return the kernel's implementation (probably as a string
> containing the OpenCL code). 
> 
> Is there a txx file that is not being included? Does your program contain
> the same headers and test?
> 
> (I guess the error could occur if OpenCL was not found if the implementation
> of this method in GPUPDEDeformableRegistrationFilterKernel is within
> #ifdef/#endif on OpenCL.)
> 
> Jim
> 
> > On Nov 25, 2014, at 10:03 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> > 
> > Hi Michael,
> > 
> > I also had the same errors while building my GPU registration program. 
> > Have you solved the problems? I guess the error was caused by improper 
> > setting in CMakeLists.txt file, but I could not find any 
> > CMakeLists.txt sample regarding GPU implementation in ITK. I doubt 
> > whether there are users using this GPU module or not.
> > 
> > Best regards,
> > Xiaopeng Yang
> > 
> > 
> > This is the question you raised:
> > 
> > I am trying to implement the GPU demons registration algorithm, but I 
> > have been having difficulty getting the program to compile. I believe 
> > the errors are because it cannot find the OpenCL library correctly, 
> > but I'm not sure how to fix it.
> > 
> > I am using a NVIDIA Quadro FX 570 and am currently using OpenCL 
> > through the CUDA Computing Toolkit 4.2. My cmake file is attached, 
> > but I have had to manually enter in the directory locations to CMake 
> > because I have not been able to find a FindOpenCL.cmake file that 
> > works correctly. My operating system is Windows 7 x64.
> > 
> > I am able to compile ITK after generating it in CMake with manually 
> > linked directories and Itk_Use_Gpu checked, but I have not been able 
> > to compile my program without getting errors, which are listed at the
> bottom.
> > 
> > Does anyone have suggestions as to how to fix this? 
> > 
> > Best regards,
> > Michael Pinkert
> > 
> > 2>registrationFunctions.obj : error LNK2019: unresolved external 
> > 2>symbol
> > "public: static char const * __cdecl
> > itk::GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void)"
> > (?GetOpenCLSource at GPUPDEDeformableRegistrationFilterKernel@itk@@SAPEBD
> > XZ) referenced in function "public: static char const * __cdecl 
> > itk::GPUPDEDeformableRegistrationFilter<class 
> > itk::GPUImage<float,3>,class itk::GPUImage<float,3>,class 
> > itk::GPUImage<class itk::Vector<float,3>,3>,class 
> > itk::DemonsRegistrationFilter<class
> > itk::GPUImage<float,3>,class itk::GPUImage<float,3>,class 
> > itk::GPUImage<class itk::Vector<float,3>,3> > >::GetOpenCLSource(void)"
> > (?GetOpenCLSource@?$GPUPDEDeformableRegistrationFilter at V?$GPUImage at M$0
> > 2 at itk@ 
> > @V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@V?$DemonsRegistrationFilter
> > @V?$GP 
> > UImage at M$02 at itk@@V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@2@@itk@@SA
> > PEBDXZ
> > )
> > 
> > 2>registrationFunctions.obj : error LNK2019: unresolved external 
> > 2>symbol
> > "public: static char const * __cdecl
> > itk::GPUDemonsRegistrationFunctionKernel::GetOpenCLSource(void)"
> > (?GetOpenCLSource at GPUDemonsRegistrationFunctionKernel@itk@@SAPEBDXZ)
> > referenced in function "public: static char const * __cdecl 
> > itk::GPUDemonsRegistrationFunction<class itk::GPUImage<float,3>,class 
> > itk::GPUImage<float,3>,classitk::GPUImage<class 
> > itk::Vector<float,3>,3>
> >> ::GetOpenCLSource(void)"
> > (?GetOpenCLSource@?$GPUDemonsRegistrationFunction at V?$GPUImage at M$02 at itk
> > @@V12@
> > V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@itk@@SAPEBDXZ)
> > 
> > 
> > 
> > 
> > _____________________________________
> > 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 franciscolopezdelafranca at gmail.com  Wed Dec 10 02:08:35 2014
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Wed, 10 Dec 2014 08:08:35 +0100
Subject: [ITK-users] Description of ShapeLabelObject attributes
Message-ID: <CAJqi3EJ8rcEWsPiXT2g-R3=gOy4AU_bFQ5+n1mRwzzEBJmHQtA@mail.gmail.com>

Hi everybody.
Is there any place with a description of the different attributes contained
in the ShapeLabelObject?

For instance, what elongation, flatness, roundness, etc. are?

Thank you very much.
Best regards.
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From zeinsalah at gmail.com  Wed Dec 10 03:11:24 2014
From: zeinsalah at gmail.com (Zein Salah)
Date: Wed, 10 Dec 2014 09:11:24 +0100
Subject: [ITK-users] Description of ShapeLabelObject attributes
In-Reply-To: <CAJqi3EJ8rcEWsPiXT2g-R3=gOy4AU_bFQ5+n1mRwzzEBJmHQtA@mail.gmail.com>
References: <CAJqi3EJ8rcEWsPiXT2g-R3=gOy4AU_bFQ5+n1mRwzzEBJmHQtA@mail.gmail.com>
Message-ID: <CADiSopMTOvX4ZQJvricjx1vMViO8HYRNMgQ6skU-szmZX-tEcQ@mail.gmail.com>

Probably the related Insight Journal paper.

http://www.insight-journal.org/browse/publication/176


On Wed, Dec 10, 2014 at 8:08 AM, Francisco Lopez de la Franca
<franciscolopezdelafranca at gmail.com> wrote:
> Hi everybody.
> Is there any place with a description of the different attributes contained
> in the ShapeLabelObject?
>
> For instance, what elongation, flatness, roundness, etc. are?
>
> Thank you very much.
> Best regards.
>
> _____________________________________
> 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 franciscolopezdelafranca at gmail.com  Wed Dec 10 04:32:25 2014
From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca)
Date: Wed, 10 Dec 2014 10:32:25 +0100
Subject: [ITK-users] Description of ShapeLabelObject attributes
In-Reply-To: <CADiSopMTOvX4ZQJvricjx1vMViO8HYRNMgQ6skU-szmZX-tEcQ@mail.gmail.com>
References: <CAJqi3EJ8rcEWsPiXT2g-R3=gOy4AU_bFQ5+n1mRwzzEBJmHQtA@mail.gmail.com>
 <CADiSopMTOvX4ZQJvricjx1vMViO8HYRNMgQ6skU-szmZX-tEcQ@mail.gmail.com>
Message-ID: <CAJqi3EKrs9r3z=jYo5mRB4xDYHOCDooAgS56ONec_Q_qBw18+A@mail.gmail.com>

Thanks a lot, but I've read the paper and don?t find the criteria to
segment the objects and label them, I mean, how does the filter know that a
group of pixels/voxels belong to the same blob? Does it use, for example,
some x-connectivity mechanism?
Thanks.


2014-12-10 9:11 GMT+01:00 Zein Salah <zeinsalah at gmail.com>:

> Probably the related Insight Journal paper.
>
> http://www.insight-journal.org/browse/publication/176
>
>
> On Wed, Dec 10, 2014 at 8:08 AM, Francisco Lopez de la Franca
> <franciscolopezdelafranca at gmail.com> wrote:
> > Hi everybody.
> > Is there any place with a description of the different attributes
> contained
> > in the ShapeLabelObject?
> >
> > For instance, what elongation, flatness, roundness, etc. are?
> >
> > Thank you very much.
> > Best regards.
> >
> > _____________________________________
> > 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
> >
>
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From zeinsalah at gmail.com  Wed Dec 10 07:17:13 2014
From: zeinsalah at gmail.com (Zein Salah)
Date: Wed, 10 Dec 2014 13:17:13 +0100
Subject: [ITK-users] Question about ShapeLabelObject attribute
Message-ID: <CADiSopP43KH0GDhnW+XeLEySxQG_G2cdjaw7n=RYsa8PNAtiPg@mail.gmail.com>

Hi,

i need to compute the maximum length of objects in a a LabelMap, i.e.
something like LabelGeometryImageFilter::GetMajorAxisLength.
Does any of the attributes of ShapeLabelObject stores this? Is there a
way to compute this from the existing attribute, preferably without
the need to compute perimeters?

One more question: what do binary principal moments of an object
practically mean?

thanks.
z.

From yxp233 at postech.ac.kr  Wed Dec 10 09:02:06 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Wed, 10 Dec 2014 23:02:06 +0900
Subject: [ITK-users] GPU Implementation
In-Reply-To: <1418152562580616.023858.ptmail04@ptmail04>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <039601d00975$3f03c660$bd0b5320$@ac.kr>
 <76f08a62167ec.54874a47@wiscmail.wisc.edu>
 <1418152562580616.023858.ptmail04@ptmail04>
Message-ID: <02e801d01481$e1d82540$a5886fc0$@ac.kr>

Hi Michael,

I solved the problem according to Jim's explanation. You need to add
ITKGPUPDEDeformable to your target_link_libraries line in CMakeLists:

target_link_libraries(itkGPUDemonsRegistrationFilterTest ITKGPUPDEDeformable
${ITK_LIBRARIES} ).

Best regards,
Xiaopeng

-----Original Message-----
From: Michael Pinkert [mailto:mpinkert at wisc.edu] 
Sent: Wednesday, December 10, 2014 4:16 AM
To: Xiaopeng Yang; 'Jim Miller'
Cc: insight-users at itk.org
Subject: RE: [ITK-users] GPU Implementation

Hi Xiaopeng,

Unfortunately, I was not able to fix this problem in my code. Please let us
know if Jim's explanation is accurate. 

Best regards,
Michael Pinkert

On 11/26/14, Xiaopeng Yang  wrote:
> Hi,
> 
> I tried to compile the code from 
> Modules\Registration\GPUPDEDeformable\test
> folder. Enclosed please find the code and CMakeLists file. I am quite 
> new to GPU, sorry I could not understand your explanation. Could you 
> point out what I missed please?
> 
> Thanks,
> Xiaopeng
> 
> -----Original Message-----
> From: Jim Miller [mailto:millerjv at gmail.com](javascript:main.compose()
> Sent: Wednesday, November 26, 2014 9:10 PM
> To: Xiaopeng Yang
> Cc: Michael Pinkert; insight-users at itk.org
> Subject: Re: [ITK-users] GPU Implementation
> 
> This doesn't look like any issue with finding OpenCL. The link error 
> is saying it cannot find the implementation of an ITK method.
> 
> I think 
> GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void) is 
> supposed to return the kernel's implementation (probably as a string
containing the OpenCL code).
> 
> Is there a txx file that is not being included? Does your program 
> contain the same headers and test?
> 
> (I guess the error could occur if OpenCL was not found if the 
> implementation of this method in 
> GPUPDEDeformableRegistrationFilterKernel is within #ifdef/#endif on 
> OpenCL.)
> 
> Jim
> 
> > On Nov 25, 2014, at 10:03 PM, Xiaopeng Yang <yxp233 at postech.ac.kr>
wrote:
> > 
> > Hi Michael,
> > 
> > I also had the same errors while building my GPU registration program. 
> > Have you solved the problems? I guess the error was caused by 
> > improper setting in CMakeLists.txt file, but I could not find any 
> > CMakeLists.txt sample regarding GPU implementation in ITK. I doubt 
> > whether there are users using this GPU module or not.
> > 
> > Best regards,
> > Xiaopeng Yang
> > 
> > 
> > This is the question you raised:
> > 
> > I am trying to implement the GPU demons registration algorithm, but 
> > I have been having difficulty getting the program to compile. I 
> > believe the errors are because it cannot find the OpenCL library 
> > correctly, but I'm not sure how to fix it.
> > 
> > I am using a NVIDIA Quadro FX 570 and am currently using OpenCL 
> > through the CUDA Computing Toolkit 4.2. My cmake file is attached, 
> > but I have had to manually enter in the directory locations to CMake 
> > because I have not been able to find a FindOpenCL.cmake file that 
> > works correctly. My operating system is Windows 7 x64.
> > 
> > I am able to compile ITK after generating it in CMake with manually 
> > linked directories and Itk_Use_Gpu checked, but I have not been able 
> > to compile my program without getting errors, which are listed at 
> > the
> bottom.
> > 
> > Does anyone have suggestions as to how to fix this? 
> > 
> > Best regards,
> > Michael Pinkert
> > 
> > 2>registrationFunctions.obj : error LNK2019: unresolved external 
> > 2>symbol
> > "public: static char const * __cdecl 
> > itk::GPUPDEDeformableRegistrationFilterKernel::GetOpenCLSource(void)"
> > (?GetOpenCLSource at GPUPDEDeformableRegistrationFilterKernel@itk@@SAPE
> > BD
> > XZ) referenced in function "public: static char const * __cdecl 
> > itk::GPUPDEDeformableRegistrationFilter<class
> > itk::GPUImage<float,3>,class itk::GPUImage<float,3>,class 
> > itk::GPUImage<class itk::Vector<float,3>,3>,class 
> > itk::DemonsRegistrationFilter<class
> > itk::GPUImage<float,3>,class itk::GPUImage<float,3>,class 
> > itk::GPUImage<class itk::Vector<float,3>,3> > >::GetOpenCLSource(void)"
> > (?GetOpenCLSource@?$GPUPDEDeformableRegistrationFilter at V?$GPUImage at M
> > $0
> > 2 at itk@
> > @V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@V?$DemonsRegistrationFilt
> > er
> > @V?$GP
> > UImage at M$02 at itk@@V12 at V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@2@@itk@@
> > SA
> > PEBDXZ
> > )
> > 
> > 2>registrationFunctions.obj : error LNK2019: unresolved external 
> > 2>symbol
> > "public: static char const * __cdecl 
> > itk::GPUDemonsRegistrationFunctionKernel::GetOpenCLSource(void)"
> > (?GetOpenCLSource at GPUDemonsRegistrationFunctionKernel@itk@@SAPEBDXZ)
> > referenced in function "public: static char const * __cdecl 
> > itk::GPUDemonsRegistrationFunction<class 
> > itk::GPUImage<float,3>,class 
> > itk::GPUImage<float,3>,classitk::GPUImage<class
> > itk::Vector<float,3>,3>
> >> ::GetOpenCLSource(void)"
> > (?GetOpenCLSource@?$GPUDemonsRegistrationFunction at V?$GPUImage at M$02 at i
> > tk
> > @@V12@
> > V?$GPUImage at V?$Vector at M$02 at itk@@$02 at 2@@itk@@SAPEBDXZ)
> > 
> > 
> > 
> > 
> > _____________________________________
> > 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 yxp233 at postech.ac.kr  Wed Dec 10 09:04:04 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Wed, 10 Dec 2014 23:04:04 +0900
Subject: [ITK-users] GPU Implementation
In-Reply-To: <1417837813159280.04286.ptmail04@ptmail04>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
 <1417788892216194.03990.ptmail04@ptmail04>
 <008c01d010e5$84172950$8c457bf0$@ac.kr>
 <1417828271180838.110987.ptmail04@ptmail04>
 <009a01d010f5$7d4043e0$77c0cba0$@ac.kr>
 <1417837813159280.04286.ptmail04@ptmail04>
Message-ID: <02e901d01482$28372130$78a56390$@ac.kr>

Hi Jim,

 

Thanks for your suggestion. I tested with a smaller dataset: 512 ? 512 ? 75 and it worked. No crash occurred. 

 

Best regards,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Saturday, December 06, 2014 12:50 PM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. 

Jim


On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi Jim,

 

So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? 

 

Thanks,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Saturday, December 06, 2014 10:11 AM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. 

Jim


On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear Jim,

 

The images are quite large: 512 * 512 *300. 

 

I did not build test when I compile ITK.

 

Thanks,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Friday, December 05, 2014 11:15 PM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

How large are the images that you are using?

Jim


On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi John,

 

Sorry I mean the program got crashed after showing #define T float. 

 

Thanks,

Xiaopeng

 

From: John Drescher [mailto:drescherjm at gmail.com] 
Sent: Friday, December 05, 2014 4:24 PM
To: Xiaopeng Yang
Cc: Jim Miller; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

 

 

On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear Jim,

 

Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. 

 

Best,

Xiaopeng

 

<image001.png>

 

 

Is that an error? 

John 

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From blowekamp at mail.nih.gov  Wed Dec 10 09:43:03 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 10 Dec 2014 09:43:03 -0500
Subject: [ITK-users] [ITK] Question about ShapeLabelObject attribute
In-Reply-To: <CADiSopP43KH0GDhnW+XeLEySxQG_G2cdjaw7n=RYsa8PNAtiPg@mail.gmail.com>
References: <CADiSopP43KH0GDhnW+XeLEySxQG_G2cdjaw7n=RYsa8PNAtiPg@mail.gmail.com>
Message-ID: <64D53F04-F156-4E1C-8D84-EC6A613DB15A@mail.nih.gov>

Hello,

There are many ways to measure the maximum length of an object.

Principal moments of share are an important shape description that is common an I suggest further reading to be done on. You may be able to start on the wikipedia [1]. For some case I prefer to use second principle moments to measure the size of an object over length as it is a more robust statistics. It similar to using the standard deviation as opposed to the range to describe a set of samples. So the second principle moments in the shape label object are similar to the LabelGeometryFilter's axis measurements.

I have an external module which computes an oriented bounding box based on the second principle moments and provide access to this value you are looking for [2]. The computation done there should be much more efficient that what's done in the LabelGeometryImageFilter. If you want a simular interface to the LabelGeometryImageFilter that the LabelShapeStatisticsImageFilter should be the interface you are looking for[3][4]. 

Hope that helps,
Brad



[1] http://en.wikipedia.org/wiki/Second_moment_of_area
[2] https://github.com/blowekamp/itkOBBLabelMap
[3] https://github.com/blowekamp/itkOBBLabelMap/blob/master/include/itkLabelShapeStatisticsImageFilter.h
[4] https://github.com/blowekamp/itkOBBLabelMap/blob/master/test/itkLabelShapeStatisticsImageFilterTest.cxx

On Dec 10, 2014, at 7:17 AM, Zein Salah <zeinsalah at gmail.com> wrote:

> Hi,
> 
> i need to compute the maximum length of objects in a a LabelMap, i.e.
> something like LabelGeometryImageFilter::GetMajorAxisLength.
> Does any of the attributes of ShapeLabelObject stores this? Is there a
> way to compute this from the existing attribute, preferably without
> the need to compute perimeters?
> 
> One more question: what do binary principal moments of an object
> practically mean?
> 
> thanks.
> z.
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From millerjv at gmail.com  Wed Dec 10 10:48:50 2014
From: millerjv at gmail.com (Jim Miller)
Date: Wed, 10 Dec 2014 10:48:50 -0500
Subject: [ITK-users] GPU Implementation
In-Reply-To: <02e901d01482$28372130$78a56390$@ac.kr>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
 <1417788892216194.03990.ptmail04@ptmail04>
 <008c01d010e5$84172950$8c457bf0$@ac.kr>
 <1417828271180838.110987.ptmail04@ptmail04>
 <009a01d010f5$7d4043e0$77c0cba0$@ac.kr>
 <1417837813159280.04286.ptmail04@ptmail04>
 <02e901d01482$28372130$78a56390$@ac.kr>
Message-ID: <58B0CB8C-557C-4F16-A283-F65D69F850A3@gmail.com>

Great. You can experiment further to see how large of a dataset you can handle. Then decide if you need to upgrade your graphic card to one with more memory to support the dataset size you want to process. 

Jim

> On Dec 10, 2014, at 9:04 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi Jim,
>  
> Thanks for your suggestion. I tested with a smaller dataset: 512 ? 512 ? 75 and it worked. No crash occurred.
>  
> Best regards,
> Xiaopeng
>  
> From: Jim Miller [mailto:millerjv at gmail.com] 
> Sent: Saturday, December 06, 2014 12:50 PM
> To: Xiaopeng Yang
> Cc: John Drescher; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
> I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. 
> 
> Jim
> 
> On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi Jim,
>  
> So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card?
>  
> Thanks,
> Xiaopeng
>  
> From: Jim Miller [mailto:millerjv at gmail.com] 
> Sent: Saturday, December 06, 2014 10:11 AM
> To: Xiaopeng Yang
> Cc: John Drescher; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
> I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. 
> 
> Jim
> 
> On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Dear Jim,
>  
> The images are quite large: 512 * 512 *300.
>  
> I did not build test when I compile ITK.
>  
> Thanks,
> Xiaopeng
>  
> From: Jim Miller [mailto:millerjv at gmail.com] 
> Sent: Friday, December 05, 2014 11:15 PM
> To: Xiaopeng Yang
> Cc: John Drescher; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
> How large are the images that you are using?
> 
> Jim
> 
> On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi John,
>  
> Sorry I mean the program got crashed after showing #define T float.
>  
> Thanks,
> Xiaopeng
>  
> From: John Drescher [mailto:drescherjm at gmail.com] 
> Sent: Friday, December 05, 2014 4:24 PM
> To: Xiaopeng Yang
> Cc: Jim Miller; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
>  
>  
> On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> Dear Jim,
>  
> Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file.
>  
> Best,
> Xiaopeng
>  
> <image001.png>
>  
>  
> Is that an error?
> 
> John
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From matimontg at gmail.com  Sat Dec 13 10:09:37 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Sat, 13 Dec 2014 12:09:37 -0300
Subject: [ITK-users] Fusion | Need the resulting image, not the fused image
Message-ID: <CAKKNfuLv6_tReY7_5+EZFitx2nO=D75eMVaen1yfBxQN2oTDeA@mail.gmail.com>

Hi,

I've ran the example ImageRegistration5 to do RM-CT fusion and works pretty
well for 2D images, now, the resulting image is a fused image. How can I
obtain the moving image in the position of the fixed image?
I'm trying to overlap, not fuse.
Thanks,
Matias.
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From matt.mccormick at kitware.com  Sun Dec 14 22:54:45 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 14 Dec 2014 22:54:45 -0500
Subject: [ITK-users] Fusion | Need the resulting image,
	not the fused image
In-Reply-To: <CAKKNfuLv6_tReY7_5+EZFitx2nO=D75eMVaen1yfBxQN2oTDeA@mail.gmail.com>
References: <CAKKNfuLv6_tReY7_5+EZFitx2nO=D75eMVaen1yfBxQN2oTDeA@mail.gmail.com>
Message-ID: <CALzTN-R9qhZyJwRh+30cO05i5NOUUwGC8c-1-TDR9nQARoMwxQ@mail.gmail.com>

Hi Matias,

The moving image in the position of the fixed image is the output of
the ResampleImageFilter in ImageRegistration5.

HTH,
Matt

On Sat, Dec 13, 2014 at 10:09 AM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi,
>
> I've ran the example ImageRegistration5 to do RM-CT fusion and works pretty
> well for 2D images, now, the resulting image is a fused image. How can I
> obtain the moving image in the position of the fixed image?
> I'm trying to overlap, not fuse.
> Thanks,
> Matias.
>
> _____________________________________
> 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 matimontg at gmail.com  Mon Dec 15 07:14:24 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Mon, 15 Dec 2014 09:14:24 -0300
Subject: [ITK-users] Fusion | Need the resulting image,
	not the fused image
In-Reply-To: <CALzTN-R9qhZyJwRh+30cO05i5NOUUwGC8c-1-TDR9nQARoMwxQ@mail.gmail.com>
References: <CAKKNfuLv6_tReY7_5+EZFitx2nO=D75eMVaen1yfBxQN2oTDeA@mail.gmail.com>
 <CALzTN-R9qhZyJwRh+30cO05i5NOUUwGC8c-1-TDR9nQARoMwxQ@mail.gmail.com>
Message-ID: <CAKKNfuJzo4uWE+Y1anQfa0a+SwM+5rYpHirGWymHA+Tfayg58g@mail.gmail.com>

Thanks Matt, I'll give it a try

On Mon, Dec 15, 2014 at 12:54 AM, Matt McCormick <matt.mccormick at kitware.com
> wrote:
>
> Hi Matias,
>
> The moving image in the position of the fixed image is the output of
> the ResampleImageFilter in ImageRegistration5.
>
> HTH,
> Matt
>
> On Sat, Dec 13, 2014 at 10:09 AM, Matias Montroull <matimontg at gmail.com>
> wrote:
> > Hi,
> >
> > I've ran the example ImageRegistration5 to do RM-CT fusion and works
> pretty
> > well for 2D images, now, the resulting image is a fused image. How can I
> > obtain the moving image in the position of the fixed image?
> > I'm trying to overlap, not fuse.
> > Thanks,
> > Matias.
> >
> > _____________________________________
> > 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
> >
>
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From matt.mccormick at kitware.com  Tue Dec 16 02:42:34 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 16 Dec 2014 02:42:34 -0500
Subject: [ITK-users] ITK 4.7 Release Candidate 2 has been tagged!
Message-ID: <CALzTN-SxHg_xxwwGEq5DW3djy_CZoZ-Dq_zN3GczCBCoHsT5sg@mail.gmail.com>

On behalf of the Insight Toolkit community, we are proud to announce that
ITK 4.7.0 release candidate 2 has been tagged and is available for testing!
Please test the release candidate in the coming days for an imminent
release.

To obtain the source code,

 git clone http://itk.org/ITK.git
 cd ITK
 git checkout -q --detach v4.7rc02

For more details, please see the Git documentation
<http://www.itk.org/Wiki/ITK/Git> [1].

A few highlights for this release: all ITK examples from the Software
Guide, Wiki Examples, and SphinxExamples are new indexed and crossed linked
in Doxygen <http://itk.org/Insight/Doxygen/html/examples.html>. So now when
you go to your favorite filter or other object, say the ResampleImageFilter
<http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html>,
there is a large selection of examples in the examples sections. This
should make it much easier to fine sample code on how to use an ITK class!
TIFF IO has undergone a significant cleanup and speed-up, and now TIFF tags
are read into the MetaDataDictionary. Three new Remote Modules are
available, for gradient computation, DICOM IO, and QuadEdgeMesh filtering.
Python wrapping, CMake configuration, and registration continue to improve.
A new, experimental thread pool is available -- to enable set the
ITK_USE_THREADPOOL or call
itk::MultiThreader::SetGlobalDefaultUseThreadPool(true).


Please test the release candidate and share your experiences on the mailing
list, issue tracker, and Gerrit Code Review. Please help identify issues
submitting an Experimental build to the dashboard
<http://open.cdash.org/index.php?project=Insight> [2] with:

 ctest -M Experimental  -T Configure -T Build -T Test -T Submit

and notifying the mailing list.  Testing your own applications against the
RC is also appreciated.


Congratulations and well done to the 29 contributors to this release. We
would especially like to recognize the new contributors, Gert Wollny,
Girish Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry,
Johan Andruejol, and Ismael Belghiti.


The final release is scheduled for December 18th.

[1] http://www.itk.org/Wiki/ITK/Git

[2] http://itk.org/Insight/Doxygen/html/examples.html

[3] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html

[2] http://open.cdash.org/index.php?project=Insight



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

* Documentation Improvements

 - Update Software Guide registration examples to ITKv4 framework

 - Wiki and Sphinx examples are indexed in Doxygen

 - Clean Software Guide dashboard build

* Filtering Improvements

 - New Laplacian deformation filter?s for QuadEdgeMesh?s

   - IJ article: http://hdl.handle.net/10380/3410

- FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations

- Faster recursive Gaussian on VectorImage

* ImageIO improvements

 - PNG sCAL unit support

 - TIFF IO performance greatly improved

 - TIFF tags read into Image MetaDataDictionary

 - MetaIO updated

 - Better support for system GDCM

* Infrastructure improvements

 - New method to erase a MetaDataDictionary entry

 - New global method to set physical space tolerance

 - New, experimental thread pool support

 - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue()
and ::OneValue()

 - VTK bridge modules only request required VTK modules

* New Remote Modules

 - Higher Order Accurate Gradient

   - http://hdl.handle.net/10380/3231

 - IO Transform DCMTK

   - http://hdl.handle.net/10380/3468

 - Subdivision Quad Edge Mesh Filters

   - http://hdl.handle.net/10380/3307

* Registration improvements

 - LandmarkBasedTransformInitializer supports BSplineTransform

 - Transverse inverse consistency increased

 - Automatic initialization of the transform center for multi-stage
registrations

 - Sparse point B-spline field estimate

 - Mutual information faster, lower memory usage

* Wrapping improvements

 - Wrapping now builds without type warnings

 - pygccxml bumped to 1.6.2

 - Latest GCCXML

 - CMake wrapping infrastructure cleanup

 - Build with Ninja CMake generator

 - New GetTypes() and GetTypesAsList() methods

 - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake



* Many style improvements -- ITK gets more stylish with every release!

* Improved code coverage -- we are over 85%!

* *Lots* of important bug fixes

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

List of changes since v4.7-rc01

--------------------------------------

Ali Ghayoor (1):
     DOC: Revise the registration examples of ITKSoftwareGuide

Arnaud Gelas (3):
     ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module
     COMP: address clang -Winconsistent-missing-override in ITKQuadEdgeMesh
     COMP: fix warnings on dashboard for Subdivision remote module

Bradley Lowekamp (5):
     BUG: Fix segfault when setting displacement field as null
     BUG: Don't enable SSE rounding with OSX and gccxml
     BUG: Add portable access to Tiff field name
     BUG: Fix conversion compilation error
     BUG: Rename remote module FDFImageIO -> IOFDF

Christopher Mullins (6):
     STYLE: Fix line length in OpenJPEG license for 80 character.
     DOC: Finish the ImageLinearIteratorWithIndex example.
     DOC: Text and picture problems, book2
     BUG: Fix text in margin issues
     DOC: Edits for the beginning of chapter 5, Statistics
     DOC: Fix empty code block.

Cory Quammen (1):
     COMP: Avoid including VTK_USE_FILE within ITK

Kent Williams (1):
     ENH: Add test to exercise issue with Transform::GetInverse

Matthew McCormick (7):
     BUG: Register AzimuthElevationToCartesianTransform to factories.
     DOC: Update texture feature class references.
     BUG: Fix texture feature correlation computation for constant image.
     STYLE: Put ImageToImageFilterCommon in its own file.
     BUG: Wrap ImageToImageFilterCommon.
     STYLE: Put ImageSourceCommon in its own file.
     COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon.

Michka Popoff (1):
     ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter
wrappings

Ziv Yaniv (1):
     COMP: fixed warnings from gcc4.1.2, made implicit casts explicit


List of changes since v4.6.0

--------------------------------------

Alexander Schmidt-Richberg (1):

     ENH: Updated Remote Module VariationalRegistration to new git tag

Ali Ghayoor (10):

     ENH: Make ITKv4 compatible with ITKSoftwareGuide

     ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4

     ENH: Convert three ImageRegistration Examples to ITKv4

     ENH: Add multi-Res and multistage registration Examples to ITKv4

     ENH: Convert DeformableReg examples to ITKv4 reg framework

     BUG: Expand a test to reflect multi-metric registration bug

     BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4

     ENH: Add direct initialization to SyN registration

     ENH: Direct initialization of SyN by restoring the state

     ENH: LandmarkBasedTransformInitializer supports BSplineTransformType

Arnaud Gelas (15):

     COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization

     ENH: Importing Laplacian Deformation for QuadEdgeMesh

     DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage

     ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified()

     ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter

     BUG: fix gdcm version in GDCMImageIO.

     COMP: missing cast when calling gdcm::DataElement::SetByteValue

     COMP: missing cast when calling gdcm::DataElement::SetByteValue

     ENH: increase LaplacianDeformation code coverage

     STYLE: use typedef rather than inheritance

     BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is
false

     BUG: split include directories into appropriate cmake variables HDF5

     BUG: missing gdcm libraries when using system GDCM

     DOC: fix doxygen documentaiton for
itk::LaplacianDeformationQuadEdgeMeshFilter

     ENH: Add one method to erase a tag into MetaDataDictionary

Bill Lorensen (5):

     ENH: Specify required VTK modules

     COMP: Wiki examples require additional vtk modules

     ENH: Modify WikiExamples remote config

     COMP: Bad test signature

     COMP: Update tag for wiki examples

Brad King (6):

     COMP: Fix vxl_config_macros usage of CMake check macros

     ENH: Use if(DEFINED) to simplify conditions

     COMP: Fix vxl_config_macros checks broken by refactoring

     COMP: Fix one more vxl_config_macros check broken by refactoring

     BUG: Fix itk_module_config for repeated calls

     BUG: Fix itk_module_config for repeated calls

Bradley Lowekamp (52):

     ENH: Adding License file from upstream MetaIO

     ENH: Adding script to update MetaIO from upstream

     ENH: Remove ITK MetaIO to prepare for upstream import

     PERF: Remove dynamically allocated temporary in evaluate method

     COMP: Fix variable type for Set/Get macros

     BUG: Implement ITK Style Singleton design pattern

     ENH: Add no throw exception specification for UnRegister methods

     COMP: Must specify order as "noexcept override"

     BUG: Add GetInverse for IdentityTransform

     ENH: Adding SetIdentity method to base DisplacementField class

     BUG: Remove unused redefinition of NULL

     BUG: Don't print to std::cout in PrintSelf

     ENH: Prefer the PrintSelfObjectMacro for printing nested objects

     BUG: Use METER of sCAL scale unit

     BUG: Use PNG_SCALE_METER for PNG sCAL unit

     BUG: Use METER of sCAL scale unit

     BUG: Use PNG_SCALE_METER for PNG sCAL unit

     COMP: Fix signed to unsigned int comparison

     BUG: Fix overflows computing size of read tiff image

     ENH: Extract TiffReaderInternal to separate file

     ENH: Refactor ReadTwoSamplePerPixelImage into template function

     ENH: Refactor GenericReadImage into template function

     BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and
LSMImageIO )

     ENH: Refactor method to convert RGBA image to output buffer

     ENH: Refactor duplicated code to read a page

     BUG: Fix right oriented tiff images

     BUG: Remove dead separated plannar code, add test

     STYLE: Fix minor kwstyle defects in test and test results

     BUG: Use array delete operator for array new allocations

     ENH: add arbitrary TIFF TAGs to meta-data dictionary

     ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage

     BUG: Address Coverity warning about null pointer dereferences

     ENH: Remove support for TIFF tile as 3D and dead code

     ENH: RGBA read images should stay unchanged.

     BUG: Override method to MakeOutput by name

     ENH: Refactor per pixel conversion function to per scan-line method

     PERF: Refactor color table lookup

     BUG: Adding missing parentheses around boolean expression

     ENH: adding TIFFImageIO test for RGB palette images

     PERF: Improve recursive Gaussian perfromance with VectorImages

     ENH: Query libtiff to determine compression support

     BUG: Support TIFF tiled image with TIFFReadRGBAImage

     BUG: Use SizeValueType for length of scanline

     PERF: Store causal results directly in output buffers

     COMP: Add explicit conversion to const char

     COMP: Explicitly add override to GetNameOfClass method

     COMP: Address internal segmentation fault with Intel compiler

     ENH: Adding method to set global physical space tolerance

     COMP: Explicitly add override to GetNameOfClass method

     BUG: Add new TypeMacro for non-overloaded classes

     BUG: Fix obscure race condition on access thread pool initialization

     BUG: Updating FDFImageIO remote module

Christopher Mullins (15):

     COMP: Allows latex to compile for ITKSoftwareGuide

     COMP: Allows latex to compile for ITKSoftwareGuide

     COMP: Wrap MeshBase templates

     COMP: Wrap MeshBase templates

     COMP: Fix warning in BlockMatchingImageFilter

     STYLE: Line lengths in examples should be no longer than 80 chars.

     COMP: Wrap the remaining MeshBase and MeshToMeshFilter types.

     COMP: Fix LaTeX warnings.

     STYLE: Fix formatting/punctuation errors.

     STYLE: Formatting and punctuation fixes.

     DOC: Edits for Book 2 Chapter 1 documentation in the Examples.

     DOC: Edits for book 2 chapter 2.

     DOC: More chapter 2 edits

     DOC: Book 2 Chapter 3 edits (part 1)

     DOC: book 2 chapter 4 Segmentation edits

Danny Perry (2):

     BUG: adding test for vnl_sparse_matrix::mult()

     BUG: size of q buffer should actually be (this->rows())*pcols.

David T. Chen (1):

     DOC: Fixed HistogramThresholdImageFitler

Dirk Padfield (1):

     BUG: Corrected processing of last sigma

GCC-XML Upstream (1):

     ENH: pygccxml v1.6.2 (reduced)

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 (24):

     COMP: Add tolerance for comparing floating point

     PERF: Remove non-threadable algorithm components

     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

     BUG: Syntax error in comment

     PERF: Add non-blocking mutex locking.

     ENH: Use TryLock minimize thread stalls

     BUG: ThreadedIndexedContainerPartitioner is inclusive

     STYLE: Remove include_regular_expression from Examples

     BUG: Demonstrate Inv(Inv(T)) != T

     BUG: Ensure Inv(Inv(T)) == T for transforms

     COMP: Valgrind detects uninitialized memory read

     COMP: Missing required base class API component

     ENH: Expand interface for selecting threadpool

Ismael Belghiti (1):

     DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter

Jim Miller (1):

     STYLE: Removing what appears to be a temporary file

Johan Andruejol (1):

     ENH: Fix normalization for null vectors and return the norm

Jon Haitz Legarreta (1):

     ENH: New test for itkLabelShapeOpeningImageFilter

Kent Williams (9):

     COMP: use find_package(VTK COMPONENTS) to specify just needed VTK
Components

     BUG: ImageSources/test/CMakeLists.txt incorrect library var reference

     COMP: Fix coverity defects related to RegistrationV4 examples

     COMP: silence warning of vnl_vector_fixed_ref::assert_size

     COMP: Fix various Coverity warnings

     COMP: Fix a typo in an error message print statement.

     COMP: itk::Command-derived class used pointless dynamic_cast.

     PERF: Don't recompute InternalInverse repeatedly

     COMP: Correct orientation/spacing for Philips MultiFrame

Mark Hiner (2):

     ENH: Update SCIFIO remote module hash

     BUG: Fix duplicate variables in Windows

Matthew McCormick (105):

     DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro.

     ENH: Move FFTComplexToComplexImageFilter out of Review.

     ENH: Add VnlComplexToComplexFFTImageFilter.

     BUG: Use fixed seed for Vnl FFT tests for repeatibility.

     ENH: Bump CMakeLists.txt version to 4.7.0.

     BUG: ArchiveTestingData.py future imports must occur at the beginning.

     BUG: Do not run vnl_test_na with broken libc++.

     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.

     DOC: Fix Software Guide page overruns in
IterativeClosestPoint{1,2}.cxx.

     DOC: Remove duplicate text in LaplacianRecursiveGaussian example.

     BUG: Uninitialized m_TransformDirection in
ComplexToComplexFFTImageFilter.

     BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest.

     STYLE: Fix style in VoronoiDiagram2D.

     BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.

     BUG: Bump GCCXML to 2014-08-06.

     BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}.

     BUG: Fix Win MultiThreader check for successful process creation.

     BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor.

     COMP: Fix ImageRegistration8RegisteredSlice.png baseline name.

     DOC: itk::statistics -> itk::Statistics.

     COMP: Fix transform type for ITKv3/IterativeClosestPoint2.

     BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.

     COMP: Improve const correctness of
GradientRecursiveGaussianImageFilter.

     BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().

     BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.

     COMP: ThreadJob NULL not defined.

     BUG: Fix alpha assignment for RGBA TIFF.

     COMP: Remove unused typedefs in LevelSetsv4Visualization.

     COMP: Remove unused typedef's in VtkGlue.

     ENH: Mark BSplineWarping2Test as RUNS_LONG.

     BUG: Fix Nifti IO read with large images.

     COMP: Remove call for non-existent variable in Nifti debugging.

     BUG: Close the file on Read and Write in HDF5TransformIO.

     BUG: Remove InsightLegacy test code from TransformHDF5Test.

     ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}.

     STYLE: Use SeriesUIDContainerType and FileNamesContainerType

     ENH: Allow specification of orthogonality tolerance in rigid
transforms.

     BUG: TransformFileReader does not clear its TransformList.

     BUG: Prevent dangling pointer in HDF5TransformIO.

     COMP: Do not use _stat64 with MinGW-32.

     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.

     COMP: Address LaplacianDeformation Doxygen warnings.

     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

     COMP: Do not wrap the FixedArray of Image SmartPointer's.

     COMP: Add missing wrapping for TransformIOBaseTemplate.

     COMP: Mark DeformableRegistration6Test as RUNS_LONG.

     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.

     BUG: Use -py3 when building wrapping for Python 3.

     COMP: Add missing wrapping for TransformIOBaseTemplate.

     DOC: Improve ImageRegistration4 grammar.

     ENH: Add IOTransformDCMTK Remote module.

     BUG: gdcm::StringFilter recognizes backslash delimiter.

     DOC: Add migration guide for GDCM Rescale slope intercept apply on
write.

     COMP: Remove unused typedef's in GPU code.

     STYLE: Improve style of HoughTransform2DLinesImageFilter example.

     COMP: Use ConceptChecking for IterativeInverse dimension check.

     COMP: Wrap TransformIOBaseTemplate for const SmartPointer.

     COMP: Add warning exceptions for third party pcre, swig, gccxml.

     ENH: Bump ITK version to 4.6.1.

     BUG: Add missing ITK_OVERRIDE to ITKImageeSources module.

     BUG: Remove GaussianImageSource members shadowing GenerateImageSource.

     STYLE: Style fixes to ITKImageSources module.

     BUG: GaussianSpatialFunction and GaborImageSource use
SpacePrecisionType.

     BUG: Do not perform itk_download_attempt_check when not building ITK.

     DOC: Update GDCMImageIO rescale slope intercept doc.

     BUG: Only register requestion IO COMPONENT modules.

     BUG: Fix wrapping .i, .idx CMake dependencies.

     COMP: Add VTK Python module when wrapping ITKVtkGlue.

     STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator.

     STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef.

     COMP: Add missing VTK module dependency for LevelSetsv4Visualization.

     BUG: By default, do not create any fixed parameters.

     STYLE: Remove trivial method comments in itkTransform.hxx.

     BUG: PolylineMask Filter's GenerateData is protected / virtual.

     ENH: Add HigherOrderAccurateGradient Module.

     BUG: Use input RequestedRegion Index in SliceBySliceImageFilter
internal.

     COMP: Remove extra semi-colon, variable scope in DCMTKFileReader.

     STYLE: Style fixes for Transform classes.

     DOC: Increase Doxygen LOOKUP_CACHE_SIZE.

     BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe.

     DOC: Index Wiki examples with Doxygen.

     COMP: Bump SphinxExamples remote module.

     DOC: Index Sphinx examples in Doxygen.

     COMP: Remove old java examples.

     COMP: Remove duplicate DiffusionTensor3DReconstruction example
reference.

     COMP: Address GradientAnisotropicDiffusionImageFilter example settings.

     COMP: Bump Sphinx Examples remote.

     COMP: Bump WikiExamples remote.

MetaIO Maintainers (1):

     MetaIO (reduced)

Michka Popoff (40):

     ENH: Fixes for python 3 support

     BUG: Add VTK_VERSION for older VTK versions

     BUG: Improve SWIG version check

     COMP: Add wrapping for ThreadPool and ThreadJob

     COMP: Remove unimplemented DestroyPool method

     COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping

     COMP: Do not hide pygccxml warnings

     ENH: Update links in readme file

     BUG: Improve SWIG version check

     BUG: Add VTK_VERSION for older VTK versions

     STYLE: Remove trailing whitespaces

     STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP

     BUG: Fix memory leak in MetaImageIO after exception

     ENH: Add script to update pygccxml from upstream

     BUG: Update VTK minimum version (for release)

     BUG: Fix memory leak in MetaImageIO after exception

     ENH: Remove Sun OS compatibility for the wrappings

     COMP: Fix for conversion to non-pointer like type warning

     STYLE: LabelObject style

     DOC: Remove broken link from LabelObject class description

     ENH: Do not setup the python tests if not asked

     ENH: Add new GetTypes() and GetTypesAsList() methods to the template
class

     COMP: Fix CMP0054 warnings in wrappings

     STYLE: Remove old cmake < 2.8.4 specific code

     STYLE: Remove old cmake < 2.8.5 specific code

     ENH: Update to PCRE 8.36

     COMP: Refactor Wrapping setup and fix legacy warnings

     ENH: Add wrapping configuration to ITKConfig.cmake

     STYLE: Some minor code cleanup in the wrapping setup

     DOC: Fix typo in RelabelComponentImageFilter

     ENH: Deprecate VectorResampleImageFilter

     DOC: Add migration guide for ::Zero and ::One

     ENH: Deprecate ::Zero and ::One

     ENH: Add option to disable sorting by size in
itkRelabelComponentImageFilter

     ENH: Add Vector and RGB wrapping to linear interpolator

     STYLE: Remove SORT macro in wrappings

     COMP: Fix warning for InterpolateImageFunction wrapping

     COMP: Add a check for Blocks in GPU module

     COMP: Bump SCIFIO to fix test build warnings

     COMP: Fix wrapping of itkImageFunctionBase

Nick Tustison (7):

     BUG:  Need to explicitly specify spline order.

     ENH:  Initializing the transform center.

     BUG:  Need to check the dynamic cast before any calls.

     ENH:  Adding modifications for point set metrics.

     BUG:  Need to specify TInternalComputationValueType for default metric.

     ENH:  Adding sparse points to B-spline field estimate.

     BUG:  Uninitialized variables.

Richard Beare (1):

     ENH: Include TIFF tags in the MetaDataDictionary

Taylor Braun-Jones (1):

     BUG: Fix SliceBySliceImageFilter doesn't propagate information
internally

Umang B (1):

     ENH: Use thread pool to dispatch multithreading tasks

Vivien Delmon (2):

     BUG: ExtractImageFilter::CollapseToSubMatrix fix

     ENH: Add a test on extracted directions in CollapseToSubMatrix mode

Vladimir S. FONOV (1):

     BUG: Fixing incorrect MINC style inverse transform


-----------------------------------------------------

Errors or omissions? Please fix them here:

https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing
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From DLRdave at aol.com  Wed Dec 17 14:40:08 2014
From: DLRdave at aol.com (David Cole)
Date: Wed, 17 Dec 2014 14:40:08 -0500
Subject: [ITK-users] [ITK-dev] ITK 4.7 Release Candidate 2 has been
	tagged!
In-Reply-To: <CALzTN-SxHg_xxwwGEq5DW3djy_CZoZ-Dq_zN3GczCBCoHsT5sg@mail.gmail.com>
References: <CALzTN-SxHg_xxwwGEq5DW3djy_CZoZ-Dq_zN3GczCBCoHsT5sg@mail.gmail.com>
Message-ID: <CAKME8fFLUo_dJ=i1yJ3WCmtfNu7xf+vZrEpyyonht6assruOkQ@mail.gmail.com>

I did this build with the VS 2013 compiler, and the Ninja cmake
generator, and it basically worked:

https://open.cdash.org/buildSummary.php?buildid=3614855

The 3 test timeouts I guess are expected because it's a Debug build.

I tried to do it by following just the directions in this email to run
the dashboard, and there are some things I would add to future emails
to make it even easier:

- running "ctest" like that works fine for submitting an Experimental
dashboard, but: it assumes you've configured an ITK build tree already
with CMake... perhaps it should be mentioned that you need to run
cmake first

- when running CMake, and using make files or Ninja generator, the
default build type appears to be Debug -- when configuring, use -D
CMAKE_BUILD_TYPE=Release to avoid the long long long test times of a
Debug build on Windows

- when running ctest, use "-j 4" or "-j 8" or however many processors
you can spare to actually run the tests..... My dashboard took over 4
hours because it was a Debug build, and I was running the exact
command line in the email with ctest, and just simply forgot that when
running a dashboard this way, you have to tell ctest how many
processes to test at once...

Bottom line:
4.7rc02 looks good to me, go for it!


Cheers,
David C.



On Tue, Dec 16, 2014 at 2:42 AM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> On behalf of the Insight Toolkit community, we are proud to announce that
> ITK 4.7.0 release candidate 2 has been tagged and is available for testing!
> Please test the release candidate in the coming days for an imminent
> release.
>
>
> To obtain the source code,
>
>  git clone http://itk.org/ITK.git
>  cd ITK
>  git checkout -q --detach v4.7rc02
>
> For more details, please see the Git documentation [1].
>
> A few highlights for this release: all ITK examples from the Software Guide,
> Wiki Examples, and SphinxExamples are new indexed and crossed linked in
> Doxygen. So now when you go to your favorite filter or other object, say the
> ResampleImageFilter, there is a large selection of examples in the examples
> sections. This should make it much easier to fine sample code on how to use
> an ITK class! TIFF IO has undergone a significant cleanup and speed-up, and
> now TIFF tags are read into the MetaDataDictionary. Three new Remote Modules
> are available, for gradient computation, DICOM IO, and QuadEdgeMesh
> filtering. Python wrapping, CMake configuration, and registration continue
> to improve. A new, experimental thread pool is available -- to enable set
> the ITK_USE_THREADPOOL or call
> itk::MultiThreader::SetGlobalDefaultUseThreadPool(true).
>
>
>
> Please test the release candidate and share your experiences on the mailing
> list, issue tracker, and Gerrit Code Review. Please help identify issues
> submitting an Experimental build to the dashboard [2] with:
>
>  ctest -M Experimental  -T Configure -T Build -T Test -T Submit
>
> and notifying the mailing list.  Testing your own applications against the
> RC is also appreciated.
>
>
>
> Congratulations and well done to the 29 contributors to this release. We
> would especially like to recognize the new contributors, Gert Wollny, Girish
> Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, Johan
> Andruejol, and Ismael Belghiti.
>
>
> The final release is scheduled for December 18th.
>
> [1] http://www.itk.org/Wiki/ITK/Git
>
>
> [2] http://itk.org/Insight/Doxygen/html/examples.html
>
>
> [3] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html
>
>
> [2] http://open.cdash.org/index.php?project=Insight
>
>
>
>
> New Features
> ------------------
>
> * Documentation Improvements
>
>  - Update Software Guide registration examples to ITKv4 framework
>
>  - Wiki and Sphinx examples are indexed in Doxygen
>
>  - Clean Software Guide dashboard build
>
>
> * Filtering Improvements
>
>  - New Laplacian deformation filter?s for QuadEdgeMesh?s
>
>    - IJ article: http://hdl.handle.net/10380/3410
>
> - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations
>
> - Faster recursive Gaussian on VectorImage
>
>
> * ImageIO improvements
>
>  - PNG sCAL unit support
>
>  - TIFF IO performance greatly improved
>
>  - TIFF tags read into Image MetaDataDictionary
>
>  - MetaIO updated
>
>  - Better support for system GDCM
>
>
> * Infrastructure improvements
>
>  - New method to erase a MetaDataDictionary entry
>
>  - New global method to set physical space tolerance
>
>  - New, experimental thread pool support
>
>  - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue()
> and ::OneValue()
>
>  - VTK bridge modules only request required VTK modules
>
>
> * New Remote Modules
>
>  - Higher Order Accurate Gradient
>
>    - http://hdl.handle.net/10380/3231
>
>  - IO Transform DCMTK
>
>    - http://hdl.handle.net/10380/3468
>
>  - Subdivision Quad Edge Mesh Filters
>
>    - http://hdl.handle.net/10380/3307
>
>
> * Registration improvements
>
>  - LandmarkBasedTransformInitializer supports BSplineTransform
>
>  - Transverse inverse consistency increased
>
>  - Automatic initialization of the transform center for multi-stage
> registrations
>
>  - Sparse point B-spline field estimate
>
>  - Mutual information faster, lower memory usage
>
>
> * Wrapping improvements
>
>  - Wrapping now builds without type warnings
>
>  - pygccxml bumped to 1.6.2
>
>  - Latest GCCXML
>
>  - CMake wrapping infrastructure cleanup
>
>  - Build with Ninja CMake generator
>
>  - New GetTypes() and GetTypesAsList() methods
>
>  - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake
>
>
>
> * Many style improvements -- ITK gets more stylish with every release!
>
>
> * Improved code coverage -- we are over 85%!
>
>
> * *Lots* of important bug fixes
>
>
> * And much more! See details in the log below.
>
>
> List of changes since v4.7-rc01
>
> --------------------------------------
>
>
> Ali Ghayoor (1):
>      DOC: Revise the registration examples of ITKSoftwareGuide
>
> Arnaud Gelas (3):
>      ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module
>      COMP: address clang -Winconsistent-missing-override in ITKQuadEdgeMesh
>      COMP: fix warnings on dashboard for Subdivision remote module
>
> Bradley Lowekamp (5):
>      BUG: Fix segfault when setting displacement field as null
>      BUG: Don't enable SSE rounding with OSX and gccxml
>      BUG: Add portable access to Tiff field name
>      BUG: Fix conversion compilation error
>      BUG: Rename remote module FDFImageIO -> IOFDF
>
> Christopher Mullins (6):
>      STYLE: Fix line length in OpenJPEG license for 80 character.
>      DOC: Finish the ImageLinearIteratorWithIndex example.
>      DOC: Text and picture problems, book2
>      BUG: Fix text in margin issues
>      DOC: Edits for the beginning of chapter 5, Statistics
>      DOC: Fix empty code block.
>
> Cory Quammen (1):
>      COMP: Avoid including VTK_USE_FILE within ITK
>
> Kent Williams (1):
>      ENH: Add test to exercise issue with Transform::GetInverse
>
> Matthew McCormick (7):
>      BUG: Register AzimuthElevationToCartesianTransform to factories.
>      DOC: Update texture feature class references.
>      BUG: Fix texture feature correlation computation for constant image.
>      STYLE: Put ImageToImageFilterCommon in its own file.
>      BUG: Wrap ImageToImageFilterCommon.
>      STYLE: Put ImageSourceCommon in its own file.
>      COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon.
>
> Michka Popoff (1):
>      ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter
> wrappings
>
> Ziv Yaniv (1):
>      COMP: fixed warnings from gcc4.1.2, made implicit casts explicit
>
>
> List of changes since v4.6.0
>
> --------------------------------------
>
>
> Alexander Schmidt-Richberg (1):
>
>      ENH: Updated Remote Module VariationalRegistration to new git tag
>
>
> Ali Ghayoor (10):
>
>      ENH: Make ITKv4 compatible with ITKSoftwareGuide
>
>      ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4
>
>      ENH: Convert three ImageRegistration Examples to ITKv4
>
>      ENH: Add multi-Res and multistage registration Examples to ITKv4
>
>      ENH: Convert DeformableReg examples to ITKv4 reg framework
>
>      BUG: Expand a test to reflect multi-metric registration bug
>
>      BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4
>
>      ENH: Add direct initialization to SyN registration
>
>      ENH: Direct initialization of SyN by restoring the state
>
>      ENH: LandmarkBasedTransformInitializer supports BSplineTransformType
>
>
> Arnaud Gelas (15):
>
>      COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization
>
>      ENH: Importing Laplacian Deformation for QuadEdgeMesh
>
>      DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage
>
>      ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified()
>
>      ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter
>
>      BUG: fix gdcm version in GDCMImageIO.
>
>      COMP: missing cast when calling gdcm::DataElement::SetByteValue
>
>      COMP: missing cast when calling gdcm::DataElement::SetByteValue
>
>      ENH: increase LaplacianDeformation code coverage
>
>      STYLE: use typedef rather than inheritance
>
>      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is
> false
>
>      BUG: split include directories into appropriate cmake variables HDF5
>
>      BUG: missing gdcm libraries when using system GDCM
>
>      DOC: fix doxygen documentaiton for
> itk::LaplacianDeformationQuadEdgeMeshFilter
>
>      ENH: Add one method to erase a tag into MetaDataDictionary
>
>
> Bill Lorensen (5):
>
>      ENH: Specify required VTK modules
>
>      COMP: Wiki examples require additional vtk modules
>
>      ENH: Modify WikiExamples remote config
>
>      COMP: Bad test signature
>
>      COMP: Update tag for wiki examples
>
>
> Brad King (6):
>
>      COMP: Fix vxl_config_macros usage of CMake check macros
>
>      ENH: Use if(DEFINED) to simplify conditions
>
>      COMP: Fix vxl_config_macros checks broken by refactoring
>
>      COMP: Fix one more vxl_config_macros check broken by refactoring
>
>      BUG: Fix itk_module_config for repeated calls
>
>      BUG: Fix itk_module_config for repeated calls
>
>
> Bradley Lowekamp (52):
>
>      ENH: Adding License file from upstream MetaIO
>
>      ENH: Adding script to update MetaIO from upstream
>
>      ENH: Remove ITK MetaIO to prepare for upstream import
>
>      PERF: Remove dynamically allocated temporary in evaluate method
>
>      COMP: Fix variable type for Set/Get macros
>
>      BUG: Implement ITK Style Singleton design pattern
>
>      ENH: Add no throw exception specification for UnRegister methods
>
>      COMP: Must specify order as "noexcept override"
>
>      BUG: Add GetInverse for IdentityTransform
>
>      ENH: Adding SetIdentity method to base DisplacementField class
>
>      BUG: Remove unused redefinition of NULL
>
>      BUG: Don't print to std::cout in PrintSelf
>
>      ENH: Prefer the PrintSelfObjectMacro for printing nested objects
>
>      BUG: Use METER of sCAL scale unit
>
>      BUG: Use PNG_SCALE_METER for PNG sCAL unit
>
>      BUG: Use METER of sCAL scale unit
>
>      BUG: Use PNG_SCALE_METER for PNG sCAL unit
>
>      COMP: Fix signed to unsigned int comparison
>
>      BUG: Fix overflows computing size of read tiff image
>
>      ENH: Extract TiffReaderInternal to separate file
>
>      ENH: Refactor ReadTwoSamplePerPixelImage into template function
>
>      ENH: Refactor GenericReadImage into template function
>
>      BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and
> LSMImageIO )
>
>      ENH: Refactor method to convert RGBA image to output buffer
>
>      ENH: Refactor duplicated code to read a page
>
>      BUG: Fix right oriented tiff images
>
>      BUG: Remove dead separated plannar code, add test
>
>      STYLE: Fix minor kwstyle defects in test and test results
>
>      BUG: Use array delete operator for array new allocations
>
>      ENH: add arbitrary TIFF TAGs to meta-data dictionary
>
>      ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
>
>      BUG: Address Coverity warning about null pointer dereferences
>
>      ENH: Remove support for TIFF tile as 3D and dead code
>
>      ENH: RGBA read images should stay unchanged.
>
>      BUG: Override method to MakeOutput by name
>
>      ENH: Refactor per pixel conversion function to per scan-line method
>
>      PERF: Refactor color table lookup
>
>      BUG: Adding missing parentheses around boolean expression
>
>      ENH: adding TIFFImageIO test for RGB palette images
>
>      PERF: Improve recursive Gaussian perfromance with VectorImages
>
>      ENH: Query libtiff to determine compression support
>
>      BUG: Support TIFF tiled image with TIFFReadRGBAImage
>
>      BUG: Use SizeValueType for length of scanline
>
>      PERF: Store causal results directly in output buffers
>
>      COMP: Add explicit conversion to const char
>
>      COMP: Explicitly add override to GetNameOfClass method
>
>      COMP: Address internal segmentation fault with Intel compiler
>
>      ENH: Adding method to set global physical space tolerance
>
>      COMP: Explicitly add override to GetNameOfClass method
>
>      BUG: Add new TypeMacro for non-overloaded classes
>
>      BUG: Fix obscure race condition on access thread pool initialization
>
>      BUG: Updating FDFImageIO remote module
>
>
> Christopher Mullins (15):
>
>      COMP: Allows latex to compile for ITKSoftwareGuide
>
>      COMP: Allows latex to compile for ITKSoftwareGuide
>
>      COMP: Wrap MeshBase templates
>
>      COMP: Wrap MeshBase templates
>
>      COMP: Fix warning in BlockMatchingImageFilter
>
>      STYLE: Line lengths in examples should be no longer than 80 chars.
>
>      COMP: Wrap the remaining MeshBase and MeshToMeshFilter types.
>
>      COMP: Fix LaTeX warnings.
>
>      STYLE: Fix formatting/punctuation errors.
>
>      STYLE: Formatting and punctuation fixes.
>
>      DOC: Edits for Book 2 Chapter 1 documentation in the Examples.
>
>      DOC: Edits for book 2 chapter 2.
>
>      DOC: More chapter 2 edits
>
>      DOC: Book 2 Chapter 3 edits (part 1)
>
>      DOC: book 2 chapter 4 Segmentation edits
>
>
> Danny Perry (2):
>
>      BUG: adding test for vnl_sparse_matrix::mult()
>
>      BUG: size of q buffer should actually be (this->rows())*pcols.
>
>
> David T. Chen (1):
>
>      DOC: Fixed HistogramThresholdImageFitler
>
>
> Dirk Padfield (1):
>
>      BUG: Corrected processing of last sigma
>
>
> GCC-XML Upstream (1):
>
>      ENH: pygccxml v1.6.2 (reduced)
>
>
> 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 (24):
>
>      COMP: Add tolerance for comparing floating point
>
>      PERF: Remove non-threadable algorithm components
>
>      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
>
>      BUG: Syntax error in comment
>
>      PERF: Add non-blocking mutex locking.
>
>      ENH: Use TryLock minimize thread stalls
>
>      BUG: ThreadedIndexedContainerPartitioner is inclusive
>
>      STYLE: Remove include_regular_expression from Examples
>
>      BUG: Demonstrate Inv(Inv(T)) != T
>
>      BUG: Ensure Inv(Inv(T)) == T for transforms
>
>      COMP: Valgrind detects uninitialized memory read
>
>      COMP: Missing required base class API component
>
>      ENH: Expand interface for selecting threadpool
>
>
> Ismael Belghiti (1):
>
>      DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter
>
>
> Jim Miller (1):
>
>      STYLE: Removing what appears to be a temporary file
>
>
> Johan Andruejol (1):
>
>      ENH: Fix normalization for null vectors and return the norm
>
>
> Jon Haitz Legarreta (1):
>
>      ENH: New test for itkLabelShapeOpeningImageFilter
>
>
> Kent Williams (9):
>
>      COMP: use find_package(VTK COMPONENTS) to specify just needed VTK
> Components
>
>      BUG: ImageSources/test/CMakeLists.txt incorrect library var reference
>
>      COMP: Fix coverity defects related to RegistrationV4 examples
>
>      COMP: silence warning of vnl_vector_fixed_ref::assert_size
>
>      COMP: Fix various Coverity warnings
>
>      COMP: Fix a typo in an error message print statement.
>
>      COMP: itk::Command-derived class used pointless dynamic_cast.
>
>      PERF: Don't recompute InternalInverse repeatedly
>
>      COMP: Correct orientation/spacing for Philips MultiFrame
>
>
> Mark Hiner (2):
>
>      ENH: Update SCIFIO remote module hash
>
>      BUG: Fix duplicate variables in Windows
>
>
> Matthew McCormick (105):
>
>      DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro.
>
>      ENH: Move FFTComplexToComplexImageFilter out of Review.
>
>      ENH: Add VnlComplexToComplexFFTImageFilter.
>
>      BUG: Use fixed seed for Vnl FFT tests for repeatibility.
>
>      ENH: Bump CMakeLists.txt version to 4.7.0.
>
>      BUG: ArchiveTestingData.py future imports must occur at the beginning.
>
>      BUG: Do not run vnl_test_na with broken libc++.
>
>      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.
>
>      DOC: Fix Software Guide page overruns in
> IterativeClosestPoint{1,2}.cxx.
>
>      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
>
>      BUG: Uninitialized m_TransformDirection in
> ComplexToComplexFFTImageFilter.
>
>      BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest.
>
>      STYLE: Fix style in VoronoiDiagram2D.
>
>      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>
>      BUG: Bump GCCXML to 2014-08-06.
>
>      BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}.
>
>      BUG: Fix Win MultiThreader check for successful process creation.
>
>      BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor.
>
>      COMP: Fix ImageRegistration8RegisteredSlice.png baseline name.
>
>      DOC: itk::statistics -> itk::Statistics.
>
>      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
>
>      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>
>      COMP: Improve const correctness of
> GradientRecursiveGaussianImageFilter.
>
>      BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().
>
>      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
>
>      COMP: ThreadJob NULL not defined.
>
>      BUG: Fix alpha assignment for RGBA TIFF.
>
>      COMP: Remove unused typedefs in LevelSetsv4Visualization.
>
>      COMP: Remove unused typedef's in VtkGlue.
>
>      ENH: Mark BSplineWarping2Test as RUNS_LONG.
>
>      BUG: Fix Nifti IO read with large images.
>
>      COMP: Remove call for non-existent variable in Nifti debugging.
>
>      BUG: Close the file on Read and Write in HDF5TransformIO.
>
>      BUG: Remove InsightLegacy test code from TransformHDF5Test.
>
>      ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}.
>
>      STYLE: Use SeriesUIDContainerType and FileNamesContainerType
>
>      ENH: Allow specification of orthogonality tolerance in rigid
> transforms.
>
>      BUG: TransformFileReader does not clear its TransformList.
>
>      BUG: Prevent dangling pointer in HDF5TransformIO.
>
>      COMP: Do not use _stat64 with MinGW-32.
>
>      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.
>
>      COMP: Address LaplacianDeformation Doxygen warnings.
>
>      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
>
>      COMP: Do not wrap the FixedArray of Image SmartPointer's.
>
>      COMP: Add missing wrapping for TransformIOBaseTemplate.
>
>      COMP: Mark DeformableRegistration6Test as RUNS_LONG.
>
>      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.
>
>      BUG: Use -py3 when building wrapping for Python 3.
>
>      COMP: Add missing wrapping for TransformIOBaseTemplate.
>
>      DOC: Improve ImageRegistration4 grammar.
>
>      ENH: Add IOTransformDCMTK Remote module.
>
>      BUG: gdcm::StringFilter recognizes backslash delimiter.
>
>      DOC: Add migration guide for GDCM Rescale slope intercept apply on
> write.
>
>      COMP: Remove unused typedef's in GPU code.
>
>      STYLE: Improve style of HoughTransform2DLinesImageFilter example.
>
>      COMP: Use ConceptChecking for IterativeInverse dimension check.
>
>      COMP: Wrap TransformIOBaseTemplate for const SmartPointer.
>
>      COMP: Add warning exceptions for third party pcre, swig, gccxml.
>
>      ENH: Bump ITK version to 4.6.1.
>
>      BUG: Add missing ITK_OVERRIDE to ITKImageeSources module.
>
>      BUG: Remove GaussianImageSource members shadowing GenerateImageSource.
>
>      STYLE: Style fixes to ITKImageSources module.
>
>      BUG: GaussianSpatialFunction and GaborImageSource use
> SpacePrecisionType.
>
>      BUG: Do not perform itk_download_attempt_check when not building ITK.
>
>      DOC: Update GDCMImageIO rescale slope intercept doc.
>
>      BUG: Only register requestion IO COMPONENT modules.
>
>      BUG: Fix wrapping .i, .idx CMake dependencies.
>
>      COMP: Add VTK Python module when wrapping ITKVtkGlue.
>
>      STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator.
>
>      STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef.
>
>      COMP: Add missing VTK module dependency for LevelSetsv4Visualization.
>
>      BUG: By default, do not create any fixed parameters.
>
>      STYLE: Remove trivial method comments in itkTransform.hxx.
>
>      BUG: PolylineMask Filter's GenerateData is protected / virtual.
>
>      ENH: Add HigherOrderAccurateGradient Module.
>
>      BUG: Use input RequestedRegion Index in SliceBySliceImageFilter
> internal.
>
>      COMP: Remove extra semi-colon, variable scope in DCMTKFileReader.
>
>      STYLE: Style fixes for Transform classes.
>
>      DOC: Increase Doxygen LOOKUP_CACHE_SIZE.
>
>      BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe.
>
>      DOC: Index Wiki examples with Doxygen.
>
>      COMP: Bump SphinxExamples remote module.
>
>      DOC: Index Sphinx examples in Doxygen.
>
>      COMP: Remove old java examples.
>
>      COMP: Remove duplicate DiffusionTensor3DReconstruction example
> reference.
>
>      COMP: Address GradientAnisotropicDiffusionImageFilter example settings.
>
>      COMP: Bump Sphinx Examples remote.
>
>      COMP: Bump WikiExamples remote.
>
>
> MetaIO Maintainers (1):
>
>      MetaIO (reduced)
>
>
> Michka Popoff (40):
>
>      ENH: Fixes for python 3 support
>
>      BUG: Add VTK_VERSION for older VTK versions
>
>      BUG: Improve SWIG version check
>
>      COMP: Add wrapping for ThreadPool and ThreadJob
>
>      COMP: Remove unimplemented DestroyPool method
>
>      COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping
>
>      COMP: Do not hide pygccxml warnings
>
>      ENH: Update links in readme file
>
>      BUG: Improve SWIG version check
>
>      BUG: Add VTK_VERSION for older VTK versions
>
>      STYLE: Remove trailing whitespaces
>
>      STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP
>
>      BUG: Fix memory leak in MetaImageIO after exception
>
>      ENH: Add script to update pygccxml from upstream
>
>      BUG: Update VTK minimum version (for release)
>
>      BUG: Fix memory leak in MetaImageIO after exception
>
>      ENH: Remove Sun OS compatibility for the wrappings
>
>      COMP: Fix for conversion to non-pointer like type warning
>
>      STYLE: LabelObject style
>
>      DOC: Remove broken link from LabelObject class description
>
>      ENH: Do not setup the python tests if not asked
>
>      ENH: Add new GetTypes() and GetTypesAsList() methods to the template
> class
>
>      COMP: Fix CMP0054 warnings in wrappings
>
>      STYLE: Remove old cmake < 2.8.4 specific code
>
>      STYLE: Remove old cmake < 2.8.5 specific code
>
>      ENH: Update to PCRE 8.36
>
>      COMP: Refactor Wrapping setup and fix legacy warnings
>
>      ENH: Add wrapping configuration to ITKConfig.cmake
>
>      STYLE: Some minor code cleanup in the wrapping setup
>
>      DOC: Fix typo in RelabelComponentImageFilter
>
>      ENH: Deprecate VectorResampleImageFilter
>
>      DOC: Add migration guide for ::Zero and ::One
>
>      ENH: Deprecate ::Zero and ::One
>
>      ENH: Add option to disable sorting by size in
> itkRelabelComponentImageFilter
>
>      ENH: Add Vector and RGB wrapping to linear interpolator
>
>      STYLE: Remove SORT macro in wrappings
>
>      COMP: Fix warning for InterpolateImageFunction wrapping
>
>      COMP: Add a check for Blocks in GPU module
>
>      COMP: Bump SCIFIO to fix test build warnings
>
>      COMP: Fix wrapping of itkImageFunctionBase
>
>
> Nick Tustison (7):
>
>      BUG:  Need to explicitly specify spline order.
>
>      ENH:  Initializing the transform center.
>
>      BUG:  Need to check the dynamic cast before any calls.
>
>      ENH:  Adding modifications for point set metrics.
>
>      BUG:  Need to specify TInternalComputationValueType for default metric.
>
>      ENH:  Adding sparse points to B-spline field estimate.
>
>      BUG:  Uninitialized variables.
>
>
> Richard Beare (1):
>
>      ENH: Include TIFF tags in the MetaDataDictionary
>
>
> Taylor Braun-Jones (1):
>
>      BUG: Fix SliceBySliceImageFilter doesn't propagate information
> internally
>
>
> Umang B (1):
>
>      ENH: Use thread pool to dispatch multithreading tasks
>
>
> Vivien Delmon (2):
>
>      BUG: ExtractImageFilter::CollapseToSubMatrix fix
>
>      ENH: Add a test on extracted directions in CollapseToSubMatrix mode
>
>
> Vladimir S. FONOV (1):
>
>      BUG: Fixing incorrect MINC style inverse transform
>
>
>
> -----------------------------------------------------
>
> Errors or omissions? Please fix them here:
>
>
> https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing
>
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-developers
>

From matt.mccormick at kitware.com  Wed Dec 17 15:34:56 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 17 Dec 2014 15:34:56 -0500
Subject: [ITK-users] [ITK-dev] ITK 4.7 Release Candidate 2 has been
	tagged!
In-Reply-To: <CAKME8fFLUo_dJ=i1yJ3WCmtfNu7xf+vZrEpyyonht6assruOkQ@mail.gmail.com>
References: <CALzTN-SxHg_xxwwGEq5DW3djy_CZoZ-Dq_zN3GczCBCoHsT5sg@mail.gmail.com>
 <CAKME8fFLUo_dJ=i1yJ3WCmtfNu7xf+vZrEpyyonht6assruOkQ@mail.gmail.com>
Message-ID: <CALzTN-R0stjFBOz5cLyTi834J9JYZG24yr-xJvOps0UNkVT5aA@mail.gmail.com>

Hi Dave,

Thanks for the build and feedback!

I've improve the testing instructions based on your suggestions.  There is
now explicit cmake configuration steps, and a -j flag to ctest.  I am
surprised that you got a Debug build by default -- we try to make it
Release for a clean build [1].

Thanks,
Matt

[1]
http://itk.org/gitweb?p=ITK.git;a=blob;f=CMakeLists.txt;h=a913e4e065239edbf8d89b51969a8a51fc67fb8e;hb=HEAD#l95

On Wed, Dec 17, 2014 at 2:40 PM, David Cole <DLRdave at aol.com> wrote:
>
> I did this build with the VS 2013 compiler, and the Ninja cmake
> generator, and it basically worked:
>
> https://open.cdash.org/buildSummary.php?buildid=3614855
>
> The 3 test timeouts I guess are expected because it's a Debug build.
>
> I tried to do it by following just the directions in this email to run
> the dashboard, and there are some things I would add to future emails
> to make it even easier:
>
> - running "ctest" like that works fine for submitting an Experimental
> dashboard, but: it assumes you've configured an ITK build tree already
> with CMake... perhaps it should be mentioned that you need to run
> cmake first
>
> - when running CMake, and using make files or Ninja generator, the
> default build type appears to be Debug -- when configuring, use -D
> CMAKE_BUILD_TYPE=Release to avoid the long long long test times of a
> Debug build on Windows
>
> - when running ctest, use "-j 4" or "-j 8" or however many processors
> you can spare to actually run the tests..... My dashboard took over 4
> hours because it was a Debug build, and I was running the exact
> command line in the email with ctest, and just simply forgot that when
> running a dashboard this way, you have to tell ctest how many
> processes to test at once...
>
> Bottom line:
> 4.7rc02 looks good to me, go for it!
>
>
> Cheers,
> David C.
>
>
>
> On Tue, Dec 16, 2014 at 2:42 AM, Matt McCormick
> <matt.mccormick at kitware.com> wrote:
> > On behalf of the Insight Toolkit community, we are proud to announce that
> > ITK 4.7.0 release candidate 2 has been tagged and is available for
> testing!
> > Please test the release candidate in the coming days for an imminent
> > release.
> >
> >
> > To obtain the source code,
> >
> >  git clone http://itk.org/ITK.git
> >  cd ITK
> >  git checkout -q --detach v4.7rc02
> >
> > For more details, please see the Git documentation [1].
> >
> > A few highlights for this release: all ITK examples from the Software
> Guide,
> > Wiki Examples, and SphinxExamples are new indexed and crossed linked in
> > Doxygen. So now when you go to your favorite filter or other object, say
> the
> > ResampleImageFilter, there is a large selection of examples in the
> examples
> > sections. This should make it much easier to fine sample code on how to
> use
> > an ITK class! TIFF IO has undergone a significant cleanup and speed-up,
> and
> > now TIFF tags are read into the MetaDataDictionary. Three new Remote
> Modules
> > are available, for gradient computation, DICOM IO, and QuadEdgeMesh
> > filtering. Python wrapping, CMake configuration, and registration
> continue
> > to improve. A new, experimental thread pool is available -- to enable set
> > the ITK_USE_THREADPOOL or call
> > itk::MultiThreader::SetGlobalDefaultUseThreadPool(true).
> >
> >
> >
> > Please test the release candidate and share your experiences on the
> mailing
> > list, issue tracker, and Gerrit Code Review. Please help identify issues
> > submitting an Experimental build to the dashboard [2] with:
> >
> >  ctest -M Experimental  -T Configure -T Build -T Test -T Submit
> >
> > and notifying the mailing list.  Testing your own applications against
> the
> > RC is also appreciated.
> >
> >
> >
> > Congratulations and well done to the 29 contributors to this release. We
> > would especially like to recognize the new contributors, Gert Wollny,
> Girish
> > Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, Johan
> > Andruejol, and Ismael Belghiti.
> >
> >
> > The final release is scheduled for December 18th.
> >
> > [1] http://www.itk.org/Wiki/ITK/Git
> >
> >
> > [2] http://itk.org/Insight/Doxygen/html/examples.html
> >
> >
> > [3] http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html
> >
> >
> > [2] http://open.cdash.org/index.php?project=Insight
> >
> >
> >
> >
> > New Features
> > ------------------
> >
> > * Documentation Improvements
> >
> >  - Update Software Guide registration examples to ITKv4 framework
> >
> >  - Wiki and Sphinx examples are indexed in Doxygen
> >
> >  - Clean Software Guide dashboard build
> >
> >
> > * Filtering Improvements
> >
> >  - New Laplacian deformation filter?s for QuadEdgeMesh?s
> >
> >    - IJ article: http://hdl.handle.net/10380/3410
> >
> > - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations
> >
> > - Faster recursive Gaussian on VectorImage
> >
> >
> > * ImageIO improvements
> >
> >  - PNG sCAL unit support
> >
> >  - TIFF IO performance greatly improved
> >
> >  - TIFF tags read into Image MetaDataDictionary
> >
> >  - MetaIO updated
> >
> >  - Better support for system GDCM
> >
> >
> > * Infrastructure improvements
> >
> >  - New method to erase a MetaDataDictionary entry
> >
> >  - New global method to set physical space tolerance
> >
> >  - New, experimental thread pool support
> >
> >  - NumericTraits::Zero and ::One are deprecated in favor of ::ZeroValue()
> > and ::OneValue()
> >
> >  - VTK bridge modules only request required VTK modules
> >
> >
> > * New Remote Modules
> >
> >  - Higher Order Accurate Gradient
> >
> >    - http://hdl.handle.net/10380/3231
> >
> >  - IO Transform DCMTK
> >
> >    - http://hdl.handle.net/10380/3468
> >
> >  - Subdivision Quad Edge Mesh Filters
> >
> >    - http://hdl.handle.net/10380/3307
> >
> >
> > * Registration improvements
> >
> >  - LandmarkBasedTransformInitializer supports BSplineTransform
> >
> >  - Transverse inverse consistency increased
> >
> >  - Automatic initialization of the transform center for multi-stage
> > registrations
> >
> >  - Sparse point B-spline field estimate
> >
> >  - Mutual information faster, lower memory usage
> >
> >
> > * Wrapping improvements
> >
> >  - Wrapping now builds without type warnings
> >
> >  - pygccxml bumped to 1.6.2
> >
> >  - Latest GCCXML
> >
> >  - CMake wrapping infrastructure cleanup
> >
> >  - Build with Ninja CMake generator
> >
> >  - New GetTypes() and GetTypesAsList() methods
> >
> >  - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake
> >
> >
> >
> > * Many style improvements -- ITK gets more stylish with every release!
> >
> >
> > * Improved code coverage -- we are over 85%!
> >
> >
> > * *Lots* of important bug fixes
> >
> >
> > * And much more! See details in the log below.
> >
> >
> > List of changes since v4.7-rc01
> >
> > --------------------------------------
> >
> >
> > Ali Ghayoor (1):
> >      DOC: Revise the registration examples of ITKSoftwareGuide
> >
> > Arnaud Gelas (3):
> >      ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module
> >      COMP: address clang -Winconsistent-missing-override in
> ITKQuadEdgeMesh
> >      COMP: fix warnings on dashboard for Subdivision remote module
> >
> > Bradley Lowekamp (5):
> >      BUG: Fix segfault when setting displacement field as null
> >      BUG: Don't enable SSE rounding with OSX and gccxml
> >      BUG: Add portable access to Tiff field name
> >      BUG: Fix conversion compilation error
> >      BUG: Rename remote module FDFImageIO -> IOFDF
> >
> > Christopher Mullins (6):
> >      STYLE: Fix line length in OpenJPEG license for 80 character.
> >      DOC: Finish the ImageLinearIteratorWithIndex example.
> >      DOC: Text and picture problems, book2
> >      BUG: Fix text in margin issues
> >      DOC: Edits for the beginning of chapter 5, Statistics
> >      DOC: Fix empty code block.
> >
> > Cory Quammen (1):
> >      COMP: Avoid including VTK_USE_FILE within ITK
> >
> > Kent Williams (1):
> >      ENH: Add test to exercise issue with Transform::GetInverse
> >
> > Matthew McCormick (7):
> >      BUG: Register AzimuthElevationToCartesianTransform to factories.
> >      DOC: Update texture feature class references.
> >      BUG: Fix texture feature correlation computation for constant image.
> >      STYLE: Put ImageToImageFilterCommon in its own file.
> >      BUG: Wrap ImageToImageFilterCommon.
> >      STYLE: Put ImageSourceCommon in its own file.
> >      COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon.
> >
> > Michka Popoff (1):
> >      ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter
> > wrappings
> >
> > Ziv Yaniv (1):
> >      COMP: fixed warnings from gcc4.1.2, made implicit casts explicit
> >
> >
> > List of changes since v4.6.0
> >
> > --------------------------------------
> >
> >
> > Alexander Schmidt-Richberg (1):
> >
> >      ENH: Updated Remote Module VariationalRegistration to new git tag
> >
> >
> > Ali Ghayoor (10):
> >
> >      ENH: Make ITKv4 compatible with ITKSoftwareGuide
> >
> >      ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4
> >
> >      ENH: Convert three ImageRegistration Examples to ITKv4
> >
> >      ENH: Add multi-Res and multistage registration Examples to ITKv4
> >
> >      ENH: Convert DeformableReg examples to ITKv4 reg framework
> >
> >      BUG: Expand a test to reflect multi-metric registration bug
> >
> >      BUG: Fix multi metric point sampling bug in
> ImageRegistrationMethodv4
> >
> >      ENH: Add direct initialization to SyN registration
> >
> >      ENH: Direct initialization of SyN by restoring the state
> >
> >      ENH: LandmarkBasedTransformInitializer supports BSplineTransformType
> >
> >
> > Arnaud Gelas (15):
> >
> >      COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization
> >
> >      ENH: Importing Laplacian Deformation for QuadEdgeMesh
> >
> >      DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage
> >
> >      ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls
> Modified()
> >
> >      ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter
> >
> >      BUG: fix gdcm version in GDCMImageIO.
> >
> >      COMP: missing cast when calling gdcm::DataElement::SetByteValue
> >
> >      COMP: missing cast when calling gdcm::DataElement::SetByteValue
> >
> >      ENH: increase LaplacianDeformation code coverage
> >
> >      STYLE: use typedef rather than inheritance
> >
> >      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is
> > false
> >
> >      BUG: split include directories into appropriate cmake variables HDF5
> >
> >      BUG: missing gdcm libraries when using system GDCM
> >
> >      DOC: fix doxygen documentaiton for
> > itk::LaplacianDeformationQuadEdgeMeshFilter
> >
> >      ENH: Add one method to erase a tag into MetaDataDictionary
> >
> >
> > Bill Lorensen (5):
> >
> >      ENH: Specify required VTK modules
> >
> >      COMP: Wiki examples require additional vtk modules
> >
> >      ENH: Modify WikiExamples remote config
> >
> >      COMP: Bad test signature
> >
> >      COMP: Update tag for wiki examples
> >
> >
> > Brad King (6):
> >
> >      COMP: Fix vxl_config_macros usage of CMake check macros
> >
> >      ENH: Use if(DEFINED) to simplify conditions
> >
> >      COMP: Fix vxl_config_macros checks broken by refactoring
> >
> >      COMP: Fix one more vxl_config_macros check broken by refactoring
> >
> >      BUG: Fix itk_module_config for repeated calls
> >
> >      BUG: Fix itk_module_config for repeated calls
> >
> >
> > Bradley Lowekamp (52):
> >
> >      ENH: Adding License file from upstream MetaIO
> >
> >      ENH: Adding script to update MetaIO from upstream
> >
> >      ENH: Remove ITK MetaIO to prepare for upstream import
> >
> >      PERF: Remove dynamically allocated temporary in evaluate method
> >
> >      COMP: Fix variable type for Set/Get macros
> >
> >      BUG: Implement ITK Style Singleton design pattern
> >
> >      ENH: Add no throw exception specification for UnRegister methods
> >
> >      COMP: Must specify order as "noexcept override"
> >
> >      BUG: Add GetInverse for IdentityTransform
> >
> >      ENH: Adding SetIdentity method to base DisplacementField class
> >
> >      BUG: Remove unused redefinition of NULL
> >
> >      BUG: Don't print to std::cout in PrintSelf
> >
> >      ENH: Prefer the PrintSelfObjectMacro for printing nested objects
> >
> >      BUG: Use METER of sCAL scale unit
> >
> >      BUG: Use PNG_SCALE_METER for PNG sCAL unit
> >
> >      BUG: Use METER of sCAL scale unit
> >
> >      BUG: Use PNG_SCALE_METER for PNG sCAL unit
> >
> >      COMP: Fix signed to unsigned int comparison
> >
> >      BUG: Fix overflows computing size of read tiff image
> >
> >      ENH: Extract TiffReaderInternal to separate file
> >
> >      ENH: Refactor ReadTwoSamplePerPixelImage into template function
> >
> >      ENH: Refactor GenericReadImage into template function
> >
> >      BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and
> > LSMImageIO )
> >
> >      ENH: Refactor method to convert RGBA image to output buffer
> >
> >      ENH: Refactor duplicated code to read a page
> >
> >      BUG: Fix right oriented tiff images
> >
> >      BUG: Remove dead separated plannar code, add test
> >
> >      STYLE: Fix minor kwstyle defects in test and test results
> >
> >      BUG: Use array delete operator for array new allocations
> >
> >      ENH: add arbitrary TIFF TAGs to meta-data dictionary
> >
> >      ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
> >
> >      BUG: Address Coverity warning about null pointer dereferences
> >
> >      ENH: Remove support for TIFF tile as 3D and dead code
> >
> >      ENH: RGBA read images should stay unchanged.
> >
> >      BUG: Override method to MakeOutput by name
> >
> >      ENH: Refactor per pixel conversion function to per scan-line method
> >
> >      PERF: Refactor color table lookup
> >
> >      BUG: Adding missing parentheses around boolean expression
> >
> >      ENH: adding TIFFImageIO test for RGB palette images
> >
> >      PERF: Improve recursive Gaussian perfromance with VectorImages
> >
> >      ENH: Query libtiff to determine compression support
> >
> >      BUG: Support TIFF tiled image with TIFFReadRGBAImage
> >
> >      BUG: Use SizeValueType for length of scanline
> >
> >      PERF: Store causal results directly in output buffers
> >
> >      COMP: Add explicit conversion to const char
> >
> >      COMP: Explicitly add override to GetNameOfClass method
> >
> >      COMP: Address internal segmentation fault with Intel compiler
> >
> >      ENH: Adding method to set global physical space tolerance
> >
> >      COMP: Explicitly add override to GetNameOfClass method
> >
> >      BUG: Add new TypeMacro for non-overloaded classes
> >
> >      BUG: Fix obscure race condition on access thread pool initialization
> >
> >      BUG: Updating FDFImageIO remote module
> >
> >
> > Christopher Mullins (15):
> >
> >      COMP: Allows latex to compile for ITKSoftwareGuide
> >
> >      COMP: Allows latex to compile for ITKSoftwareGuide
> >
> >      COMP: Wrap MeshBase templates
> >
> >      COMP: Wrap MeshBase templates
> >
> >      COMP: Fix warning in BlockMatchingImageFilter
> >
> >      STYLE: Line lengths in examples should be no longer than 80 chars.
> >
> >      COMP: Wrap the remaining MeshBase and MeshToMeshFilter types.
> >
> >      COMP: Fix LaTeX warnings.
> >
> >      STYLE: Fix formatting/punctuation errors.
> >
> >      STYLE: Formatting and punctuation fixes.
> >
> >      DOC: Edits for Book 2 Chapter 1 documentation in the Examples.
> >
> >      DOC: Edits for book 2 chapter 2.
> >
> >      DOC: More chapter 2 edits
> >
> >      DOC: Book 2 Chapter 3 edits (part 1)
> >
> >      DOC: book 2 chapter 4 Segmentation edits
> >
> >
> > Danny Perry (2):
> >
> >      BUG: adding test for vnl_sparse_matrix::mult()
> >
> >      BUG: size of q buffer should actually be (this->rows())*pcols.
> >
> >
> > David T. Chen (1):
> >
> >      DOC: Fixed HistogramThresholdImageFitler
> >
> >
> > Dirk Padfield (1):
> >
> >      BUG: Corrected processing of last sigma
> >
> >
> > GCC-XML Upstream (1):
> >
> >      ENH: pygccxml v1.6.2 (reduced)
> >
> >
> > 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 (24):
> >
> >      COMP: Add tolerance for comparing floating point
> >
> >      PERF: Remove non-threadable algorithm components
> >
> >      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
> >
> >      BUG: Syntax error in comment
> >
> >      PERF: Add non-blocking mutex locking.
> >
> >      ENH: Use TryLock minimize thread stalls
> >
> >      BUG: ThreadedIndexedContainerPartitioner is inclusive
> >
> >      STYLE: Remove include_regular_expression from Examples
> >
> >      BUG: Demonstrate Inv(Inv(T)) != T
> >
> >      BUG: Ensure Inv(Inv(T)) == T for transforms
> >
> >      COMP: Valgrind detects uninitialized memory read
> >
> >      COMP: Missing required base class API component
> >
> >      ENH: Expand interface for selecting threadpool
> >
> >
> > Ismael Belghiti (1):
> >
> >      DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter
> >
> >
> > Jim Miller (1):
> >
> >      STYLE: Removing what appears to be a temporary file
> >
> >
> > Johan Andruejol (1):
> >
> >      ENH: Fix normalization for null vectors and return the norm
> >
> >
> > Jon Haitz Legarreta (1):
> >
> >      ENH: New test for itkLabelShapeOpeningImageFilter
> >
> >
> > Kent Williams (9):
> >
> >      COMP: use find_package(VTK COMPONENTS) to specify just needed VTK
> > Components
> >
> >      BUG: ImageSources/test/CMakeLists.txt incorrect library var
> reference
> >
> >      COMP: Fix coverity defects related to RegistrationV4 examples
> >
> >      COMP: silence warning of vnl_vector_fixed_ref::assert_size
> >
> >      COMP: Fix various Coverity warnings
> >
> >      COMP: Fix a typo in an error message print statement.
> >
> >      COMP: itk::Command-derived class used pointless dynamic_cast.
> >
> >      PERF: Don't recompute InternalInverse repeatedly
> >
> >      COMP: Correct orientation/spacing for Philips MultiFrame
> >
> >
> > Mark Hiner (2):
> >
> >      ENH: Update SCIFIO remote module hash
> >
> >      BUG: Fix duplicate variables in Windows
> >
> >
> > Matthew McCormick (105):
> >
> >      DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro.
> >
> >      ENH: Move FFTComplexToComplexImageFilter out of Review.
> >
> >      ENH: Add VnlComplexToComplexFFTImageFilter.
> >
> >      BUG: Use fixed seed for Vnl FFT tests for repeatibility.
> >
> >      ENH: Bump CMakeLists.txt version to 4.7.0.
> >
> >      BUG: ArchiveTestingData.py future imports must occur at the
> beginning.
> >
> >      BUG: Do not run vnl_test_na with broken libc++.
> >
> >      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.
> >
> >      DOC: Fix Software Guide page overruns in
> > IterativeClosestPoint{1,2}.cxx.
> >
> >      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
> >
> >      BUG: Uninitialized m_TransformDirection in
> > ComplexToComplexFFTImageFilter.
> >
> >      BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest.
> >
> >      STYLE: Fix style in VoronoiDiagram2D.
> >
> >      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
> >
> >      BUG: Bump GCCXML to 2014-08-06.
> >
> >      BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}.
> >
> >      BUG: Fix Win MultiThreader check for successful process creation.
> >
> >      BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor.
> >
> >      COMP: Fix ImageRegistration8RegisteredSlice.png baseline name.
> >
> >      DOC: itk::statistics -> itk::Statistics.
> >
> >      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
> >
> >      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
> >
> >      COMP: Improve const correctness of
> > GradientRecursiveGaussianImageFilter.
> >
> >      BUG: Call clear instead of empty on PatchBasedDenoising
> EmptyCaches().
> >
> >      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
> >
> >      COMP: ThreadJob NULL not defined.
> >
> >      BUG: Fix alpha assignment for RGBA TIFF.
> >
> >      COMP: Remove unused typedefs in LevelSetsv4Visualization.
> >
> >      COMP: Remove unused typedef's in VtkGlue.
> >
> >      ENH: Mark BSplineWarping2Test as RUNS_LONG.
> >
> >      BUG: Fix Nifti IO read with large images.
> >
> >      COMP: Remove call for non-existent variable in Nifti debugging.
> >
> >      BUG: Close the file on Read and Write in HDF5TransformIO.
> >
> >      BUG: Remove InsightLegacy test code from TransformHDF5Test.
> >
> >      ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}.
> >
> >      STYLE: Use SeriesUIDContainerType and FileNamesContainerType
> >
> >      ENH: Allow specification of orthogonality tolerance in rigid
> > transforms.
> >
> >      BUG: TransformFileReader does not clear its TransformList.
> >
> >      BUG: Prevent dangling pointer in HDF5TransformIO.
> >
> >      COMP: Do not use _stat64 with MinGW-32.
> >
> >      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.
> >
> >      COMP: Address LaplacianDeformation Doxygen warnings.
> >
> >      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
> >
> >      COMP: Do not wrap the FixedArray of Image SmartPointer's.
> >
> >      COMP: Add missing wrapping for TransformIOBaseTemplate.
> >
> >      COMP: Mark DeformableRegistration6Test as RUNS_LONG.
> >
> >      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.
> >
> >      BUG: Use -py3 when building wrapping for Python 3.
> >
> >      COMP: Add missing wrapping for TransformIOBaseTemplate.
> >
> >      DOC: Improve ImageRegistration4 grammar.
> >
> >      ENH: Add IOTransformDCMTK Remote module.
> >
> >      BUG: gdcm::StringFilter recognizes backslash delimiter.
> >
> >      DOC: Add migration guide for GDCM Rescale slope intercept apply on
> > write.
> >
> >      COMP: Remove unused typedef's in GPU code.
> >
> >      STYLE: Improve style of HoughTransform2DLinesImageFilter example.
> >
> >      COMP: Use ConceptChecking for IterativeInverse dimension check.
> >
> >      COMP: Wrap TransformIOBaseTemplate for const SmartPointer.
> >
> >      COMP: Add warning exceptions for third party pcre, swig, gccxml.
> >
> >      ENH: Bump ITK version to 4.6.1.
> >
> >      BUG: Add missing ITK_OVERRIDE to ITKImageeSources module.
> >
> >      BUG: Remove GaussianImageSource members shadowing
> GenerateImageSource.
> >
> >      STYLE: Style fixes to ITKImageSources module.
> >
> >      BUG: GaussianSpatialFunction and GaborImageSource use
> > SpacePrecisionType.
> >
> >      BUG: Do not perform itk_download_attempt_check when not building
> ITK.
> >
> >      DOC: Update GDCMImageIO rescale slope intercept doc.
> >
> >      BUG: Only register requestion IO COMPONENT modules.
> >
> >      BUG: Fix wrapping .i, .idx CMake dependencies.
> >
> >      COMP: Add VTK Python module when wrapping ITKVtkGlue.
> >
> >      STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator.
> >
> >      STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType
> typedef.
> >
> >      COMP: Add missing VTK module dependency for
> LevelSetsv4Visualization.
> >
> >      BUG: By default, do not create any fixed parameters.
> >
> >      STYLE: Remove trivial method comments in itkTransform.hxx.
> >
> >      BUG: PolylineMask Filter's GenerateData is protected / virtual.
> >
> >      ENH: Add HigherOrderAccurateGradient Module.
> >
> >      BUG: Use input RequestedRegion Index in SliceBySliceImageFilter
> > internal.
> >
> >      COMP: Remove extra semi-colon, variable scope in DCMTKFileReader.
> >
> >      STYLE: Style fixes for Transform classes.
> >
> >      DOC: Increase Doxygen LOOKUP_CACHE_SIZE.
> >
> >      BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe.
> >
> >      DOC: Index Wiki examples with Doxygen.
> >
> >      COMP: Bump SphinxExamples remote module.
> >
> >      DOC: Index Sphinx examples in Doxygen.
> >
> >      COMP: Remove old java examples.
> >
> >      COMP: Remove duplicate DiffusionTensor3DReconstruction example
> > reference.
> >
> >      COMP: Address GradientAnisotropicDiffusionImageFilter example
> settings.
> >
> >      COMP: Bump Sphinx Examples remote.
> >
> >      COMP: Bump WikiExamples remote.
> >
> >
> > MetaIO Maintainers (1):
> >
> >      MetaIO (reduced)
> >
> >
> > Michka Popoff (40):
> >
> >      ENH: Fixes for python 3 support
> >
> >      BUG: Add VTK_VERSION for older VTK versions
> >
> >      BUG: Improve SWIG version check
> >
> >      COMP: Add wrapping for ThreadPool and ThreadJob
> >
> >      COMP: Remove unimplemented DestroyPool method
> >
> >      COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping
> >
> >      COMP: Do not hide pygccxml warnings
> >
> >      ENH: Update links in readme file
> >
> >      BUG: Improve SWIG version check
> >
> >      BUG: Add VTK_VERSION for older VTK versions
> >
> >      STYLE: Remove trailing whitespaces
> >
> >      STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP
> >
> >      BUG: Fix memory leak in MetaImageIO after exception
> >
> >      ENH: Add script to update pygccxml from upstream
> >
> >      BUG: Update VTK minimum version (for release)
> >
> >      BUG: Fix memory leak in MetaImageIO after exception
> >
> >      ENH: Remove Sun OS compatibility for the wrappings
> >
> >      COMP: Fix for conversion to non-pointer like type warning
> >
> >      STYLE: LabelObject style
> >
> >      DOC: Remove broken link from LabelObject class description
> >
> >      ENH: Do not setup the python tests if not asked
> >
> >      ENH: Add new GetTypes() and GetTypesAsList() methods to the template
> > class
> >
> >      COMP: Fix CMP0054 warnings in wrappings
> >
> >      STYLE: Remove old cmake < 2.8.4 specific code
> >
> >      STYLE: Remove old cmake < 2.8.5 specific code
> >
> >      ENH: Update to PCRE 8.36
> >
> >      COMP: Refactor Wrapping setup and fix legacy warnings
> >
> >      ENH: Add wrapping configuration to ITKConfig.cmake
> >
> >      STYLE: Some minor code cleanup in the wrapping setup
> >
> >      DOC: Fix typo in RelabelComponentImageFilter
> >
> >      ENH: Deprecate VectorResampleImageFilter
> >
> >      DOC: Add migration guide for ::Zero and ::One
> >
> >      ENH: Deprecate ::Zero and ::One
> >
> >      ENH: Add option to disable sorting by size in
> > itkRelabelComponentImageFilter
> >
> >      ENH: Add Vector and RGB wrapping to linear interpolator
> >
> >      STYLE: Remove SORT macro in wrappings
> >
> >      COMP: Fix warning for InterpolateImageFunction wrapping
> >
> >      COMP: Add a check for Blocks in GPU module
> >
> >      COMP: Bump SCIFIO to fix test build warnings
> >
> >      COMP: Fix wrapping of itkImageFunctionBase
> >
> >
> > Nick Tustison (7):
> >
> >      BUG:  Need to explicitly specify spline order.
> >
> >      ENH:  Initializing the transform center.
> >
> >      BUG:  Need to check the dynamic cast before any calls.
> >
> >      ENH:  Adding modifications for point set metrics.
> >
> >      BUG:  Need to specify TInternalComputationValueType for default
> metric.
> >
> >      ENH:  Adding sparse points to B-spline field estimate.
> >
> >      BUG:  Uninitialized variables.
> >
> >
> > Richard Beare (1):
> >
> >      ENH: Include TIFF tags in the MetaDataDictionary
> >
> >
> > Taylor Braun-Jones (1):
> >
> >      BUG: Fix SliceBySliceImageFilter doesn't propagate information
> > internally
> >
> >
> > Umang B (1):
> >
> >      ENH: Use thread pool to dispatch multithreading tasks
> >
> >
> > Vivien Delmon (2):
> >
> >      BUG: ExtractImageFilter::CollapseToSubMatrix fix
> >
> >      ENH: Add a test on extracted directions in CollapseToSubMatrix mode
> >
> >
> > Vladimir S. FONOV (1):
> >
> >      BUG: Fixing incorrect MINC style inverse transform
> >
> >
> >
> > -----------------------------------------------------
> >
> > Errors or omissions? Please fix them here:
> >
> >
> >
> https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing
> >
> >
> >
> >
> > _______________________________________________
> > 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 DLRdave at aol.com  Wed Dec 17 20:46:39 2014
From: DLRdave at aol.com (David Cole)
Date: Wed, 17 Dec 2014 20:46:39 -0500
Subject: [ITK-users] [ITK-dev] ITK 4.7 Release Candidate 2 has been
	tagged!
In-Reply-To: <CALzTN-R0stjFBOz5cLyTi834J9JYZG24yr-xJvOps0UNkVT5aA@mail.gmail.com>
References: <CALzTN-SxHg_xxwwGEq5DW3djy_CZoZ-Dq_zN3GczCBCoHsT5sg@mail.gmail.com>
 <CAKME8fFLUo_dJ=i1yJ3WCmtfNu7xf+vZrEpyyonht6assruOkQ@mail.gmail.com>
 <CALzTN-R0stjFBOz5cLyTi834J9JYZG24yr-xJvOps0UNkVT5aA@mail.gmail.com>
Message-ID: <CAKME8fGTQPFzAjAnuXCd1TtExKbzPJM6OSnHNeU1Yb3yoNK+gg@mail.gmail.com>

I'm surprised too, after seeing the code you pointed to.... But there it is
right in the CMakeCache.txt as seen in this test result:

https://open.cdash.org/testDetails.php?test=300879476&build=3614855

I'm pretty sure I didn't ask for Debug... If I still have that prompt open
on that machine next time I get to it, I'll double check the command
history. Probably not till Friday.


D


On Wednesday, December 17, 2014, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Dave,
>
> Thanks for the build and feedback!
>
> I've improve the testing instructions based on your suggestions.  There is
> now explicit cmake configuration steps, and a -j flag to ctest.  I am
> surprised that you got a Debug build by default -- we try to make it
> Release for a clean build [1].
>
> Thanks,
> Matt
>
> [1]
> http://itk.org/gitweb?p=ITK.git;a=blob;f=CMakeLists.txt;h=a913e4e065239edbf8d89b51969a8a51fc67fb8e;hb=HEAD#l95
>
> On Wed, Dec 17, 2014 at 2:40 PM, David Cole <DLRdave at aol.com
> <javascript:_e(%7B%7D,'cvml','DLRdave at aol.com');>> wrote:
>>
>> I did this build with the VS 2013 compiler, and the Ninja cmake
>> generator, and it basically worked:
>>
>> https://open.cdash.org/buildSummary.php?buildid=3614855
>>
>> The 3 test timeouts I guess are expected because it's a Debug build.
>>
>> I tried to do it by following just the directions in this email to run
>> the dashboard, and there are some things I would add to future emails
>> to make it even easier:
>>
>> - running "ctest" like that works fine for submitting an Experimental
>> dashboard, but: it assumes you've configured an ITK build tree already
>> with CMake... perhaps it should be mentioned that you need to run
>> cmake first
>>
>> - when running CMake, and using make files or Ninja generator, the
>> default build type appears to be Debug -- when configuring, use -D
>> CMAKE_BUILD_TYPE=Release to avoid the long long long test times of a
>> Debug build on Windows
>>
>> - when running ctest, use "-j 4" or "-j 8" or however many processors
>> you can spare to actually run the tests..... My dashboard took over 4
>> hours because it was a Debug build, and I was running the exact
>> command line in the email with ctest, and just simply forgot that when
>> running a dashboard this way, you have to tell ctest how many
>> processes to test at once...
>>
>> Bottom line:
>> 4.7rc02 looks good to me, go for it!
>>
>>
>> Cheers,
>> David C.
>>
>>
>>
>> On Tue, Dec 16, 2014 at 2:42 AM, Matt McCormick
>> <matt.mccormick at kitware.com
>> <javascript:_e(%7B%7D,'cvml','matt.mccormick at kitware.com');>> wrote:
>> > On behalf of the Insight Toolkit community, we are proud to announce
>> that
>> > ITK 4.7.0 release candidate 2 has been tagged and is available for
>> testing!
>> > Please test the release candidate in the coming days for an imminent
>> > release.
>> >
>> >
>> > To obtain the source code,
>> >
>> >  git clone http://itk.org/ITK.git
>> >  cd ITK
>> >  git checkout -q --detach v4.7rc02
>> >
>> > For more details, please see the Git documentation [1].
>> >
>> > A few highlights for this release: all ITK examples from the Software
>> Guide,
>> > Wiki Examples, and SphinxExamples are new indexed and crossed linked in
>> > Doxygen. So now when you go to your favorite filter or other object,
>> say the
>> > ResampleImageFilter, there is a large selection of examples in the
>> examples
>> > sections. This should make it much easier to fine sample code on how to
>> use
>> > an ITK class! TIFF IO has undergone a significant cleanup and speed-up,
>> and
>> > now TIFF tags are read into the MetaDataDictionary. Three new Remote
>> Modules
>> > are available, for gradient computation, DICOM IO, and QuadEdgeMesh
>> > filtering. Python wrapping, CMake configuration, and registration
>> continue
>> > to improve. A new, experimental thread pool is available -- to enable
>> set
>> > the ITK_USE_THREADPOOL or call
>> > itk::MultiThreader::SetGlobalDefaultUseThreadPool(true).
>> >
>> >
>> >
>> > Please test the release candidate and share your experiences on the
>> mailing
>> > list, issue tracker, and Gerrit Code Review. Please help identify issues
>> > submitting an Experimental build to the dashboard [2] with:
>> >
>> >  ctest -M Experimental  -T Configure -T Build -T Test -T Submit
>> >
>> > and notifying the mailing list.  Testing your own applications against
>> the
>> > RC is also appreciated.
>> >
>> >
>> >
>> > Congratulations and well done to the 29 contributors to this release. We
>> > would especially like to recognize the new contributors, Gert Wollny,
>> Girish
>> > Mallya, Christopher Mullins, Umang B, David T. Chen, Danny Perry, Johan
>> > Andruejol, and Ismael Belghiti.
>> >
>> >
>> > The final release is scheduled for December 18th.
>> >
>> > [1] http://www.itk.org/Wiki/ITK/Git
>> >
>> >
>> > [2] http://itk.org/Insight/Doxygen/html/examples.html
>> >
>> >
>> > [3]
>> http://www.itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html
>> >
>> >
>> > [2] http://open.cdash.org/index.php?project=Insight
>> >
>> >
>> >
>> >
>> > New Features
>> > ------------------
>> >
>> > * Documentation Improvements
>> >
>> >  - Update Software Guide registration examples to ITKv4 framework
>> >
>> >  - Wiki and Sphinx examples are indexed in Doxygen
>> >
>> >  - Clean Software Guide dashboard build
>> >
>> >
>> > * Filtering Improvements
>> >
>> >  - New Laplacian deformation filter?s for QuadEdgeMesh?s
>> >
>> >    - IJ article: http://hdl.handle.net/10380/3410
>> >
>> > - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW
>> implementations
>> >
>> > - Faster recursive Gaussian on VectorImage
>> >
>> >
>> > * ImageIO improvements
>> >
>> >  - PNG sCAL unit support
>> >
>> >  - TIFF IO performance greatly improved
>> >
>> >  - TIFF tags read into Image MetaDataDictionary
>> >
>> >  - MetaIO updated
>> >
>> >  - Better support for system GDCM
>> >
>> >
>> > * Infrastructure improvements
>> >
>> >  - New method to erase a MetaDataDictionary entry
>> >
>> >  - New global method to set physical space tolerance
>> >
>> >  - New, experimental thread pool support
>> >
>> >  - NumericTraits::Zero and ::One are deprecated in favor of
>> ::ZeroValue()
>> > and ::OneValue()
>> >
>> >  - VTK bridge modules only request required VTK modules
>> >
>> >
>> > * New Remote Modules
>> >
>> >  - Higher Order Accurate Gradient
>> >
>> >    - http://hdl.handle.net/10380/3231
>> >
>> >  - IO Transform DCMTK
>> >
>> >    - http://hdl.handle.net/10380/3468
>> >
>> >  - Subdivision Quad Edge Mesh Filters
>> >
>> >    - http://hdl.handle.net/10380/3307
>> >
>> >
>> > * Registration improvements
>> >
>> >  - LandmarkBasedTransformInitializer supports BSplineTransform
>> >
>> >  - Transverse inverse consistency increased
>> >
>> >  - Automatic initialization of the transform center for multi-stage
>> > registrations
>> >
>> >  - Sparse point B-spline field estimate
>> >
>> >  - Mutual information faster, lower memory usage
>> >
>> >
>> > * Wrapping improvements
>> >
>> >  - Wrapping now builds without type warnings
>> >
>> >  - pygccxml bumped to 1.6.2
>> >
>> >  - Latest GCCXML
>> >
>> >  - CMake wrapping infrastructure cleanup
>> >
>> >  - Build with Ninja CMake generator
>> >
>> >  - New GetTypes() and GetTypesAsList() methods
>> >
>> >  - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake
>> >
>> >
>> >
>> > * Many style improvements -- ITK gets more stylish with every release!
>> >
>> >
>> > * Improved code coverage -- we are over 85%!
>> >
>> >
>> > * *Lots* of important bug fixes
>> >
>> >
>> > * And much more! See details in the log below.
>> >
>> >
>> > List of changes since v4.7-rc01
>> >
>> > --------------------------------------
>> >
>> >
>> > Ali Ghayoor (1):
>> >      DOC: Revise the registration examples of ITKSoftwareGuide
>> >
>> > Arnaud Gelas (3):
>> >      ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module
>> >      COMP: address clang -Winconsistent-missing-override in
>> ITKQuadEdgeMesh
>> >      COMP: fix warnings on dashboard for Subdivision remote module
>> >
>> > Bradley Lowekamp (5):
>> >      BUG: Fix segfault when setting displacement field as null
>> >      BUG: Don't enable SSE rounding with OSX and gccxml
>> >      BUG: Add portable access to Tiff field name
>> >      BUG: Fix conversion compilation error
>> >      BUG: Rename remote module FDFImageIO -> IOFDF
>> >
>> > Christopher Mullins (6):
>> >      STYLE: Fix line length in OpenJPEG license for 80 character.
>> >      DOC: Finish the ImageLinearIteratorWithIndex example.
>> >      DOC: Text and picture problems, book2
>> >      BUG: Fix text in margin issues
>> >      DOC: Edits for the beginning of chapter 5, Statistics
>> >      DOC: Fix empty code block.
>> >
>> > Cory Quammen (1):
>> >      COMP: Avoid including VTK_USE_FILE within ITK
>> >
>> > Kent Williams (1):
>> >      ENH: Add test to exercise issue with Transform::GetInverse
>> >
>> > Matthew McCormick (7):
>> >      BUG: Register AzimuthElevationToCartesianTransform to factories.
>> >      DOC: Update texture feature class references.
>> >      BUG: Fix texture feature correlation computation for constant
>> image.
>> >      STYLE: Put ImageToImageFilterCommon in its own file.
>> >      BUG: Wrap ImageToImageFilterCommon.
>> >      STYLE: Put ImageSourceCommon in its own file.
>> >      COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon.
>> >
>> > Michka Popoff (1):
>> >      ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter
>> > wrappings
>> >
>> > Ziv Yaniv (1):
>> >      COMP: fixed warnings from gcc4.1.2, made implicit casts explicit
>> >
>> >
>> > List of changes since v4.6.0
>> >
>> > --------------------------------------
>> >
>> >
>> > Alexander Schmidt-Richberg (1):
>> >
>> >      ENH: Updated Remote Module VariationalRegistration to new git tag
>> >
>> >
>> > Ali Ghayoor (10):
>> >
>> >      ENH: Make ITKv4 compatible with ITKSoftwareGuide
>> >
>> >      ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4
>> >
>> >      ENH: Convert three ImageRegistration Examples to ITKv4
>> >
>> >      ENH: Add multi-Res and multistage registration Examples to ITKv4
>> >
>> >      ENH: Convert DeformableReg examples to ITKv4 reg framework
>> >
>> >      BUG: Expand a test to reflect multi-metric registration bug
>> >
>> >      BUG: Fix multi metric point sampling bug in
>> ImageRegistrationMethodv4
>> >
>> >      ENH: Add direct initialization to SyN registration
>> >
>> >      ENH: Direct initialization of SyN by restoring the state
>> >
>> >      ENH: LandmarkBasedTransformInitializer supports
>> BSplineTransformType
>> >
>> >
>> > Arnaud Gelas (15):
>> >
>> >      COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization
>> >
>> >      ENH: Importing Laplacian Deformation for QuadEdgeMesh
>> >
>> >      DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage
>> >
>> >      ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls
>> Modified()
>> >
>> >      ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter
>> >
>> >      BUG: fix gdcm version in GDCMImageIO.
>> >
>> >      COMP: missing cast when calling gdcm::DataElement::SetByteValue
>> >
>> >      COMP: missing cast when calling gdcm::DataElement::SetByteValue
>> >
>> >      ENH: increase LaplacianDeformation code coverage
>> >
>> >      STYLE: use typedef rather than inheritance
>> >
>> >      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is
>> > false
>> >
>> >      BUG: split include directories into appropriate cmake variables
>> HDF5
>> >
>> >      BUG: missing gdcm libraries when using system GDCM
>> >
>> >      DOC: fix doxygen documentaiton for
>> > itk::LaplacianDeformationQuadEdgeMeshFilter
>> >
>> >      ENH: Add one method to erase a tag into MetaDataDictionary
>> >
>> >
>> > Bill Lorensen (5):
>> >
>> >      ENH: Specify required VTK modules
>> >
>> >      COMP: Wiki examples require additional vtk modules
>> >
>> >      ENH: Modify WikiExamples remote config
>> >
>> >      COMP: Bad test signature
>> >
>> >      COMP: Update tag for wiki examples
>> >
>> >
>> > Brad King (6):
>> >
>> >      COMP: Fix vxl_config_macros usage of CMake check macros
>> >
>> >      ENH: Use if(DEFINED) to simplify conditions
>> >
>> >      COMP: Fix vxl_config_macros checks broken by refactoring
>> >
>> >      COMP: Fix one more vxl_config_macros check broken by refactoring
>> >
>> >      BUG: Fix itk_module_config for repeated calls
>> >
>> >      BUG: Fix itk_module_config for repeated calls
>> >
>> >
>> > Bradley Lowekamp (52):
>> >
>> >      ENH: Adding License file from upstream MetaIO
>> >
>> >      ENH: Adding script to update MetaIO from upstream
>> >
>> >      ENH: Remove ITK MetaIO to prepare for upstream import
>> >
>> >      PERF: Remove dynamically allocated temporary in evaluate method
>> >
>> >      COMP: Fix variable type for Set/Get macros
>> >
>> >      BUG: Implement ITK Style Singleton design pattern
>> >
>> >      ENH: Add no throw exception specification for UnRegister methods
>> >
>> >      COMP: Must specify order as "noexcept override"
>> >
>> >      BUG: Add GetInverse for IdentityTransform
>> >
>> >      ENH: Adding SetIdentity method to base DisplacementField class
>> >
>> >      BUG: Remove unused redefinition of NULL
>> >
>> >      BUG: Don't print to std::cout in PrintSelf
>> >
>> >      ENH: Prefer the PrintSelfObjectMacro for printing nested objects
>> >
>> >      BUG: Use METER of sCAL scale unit
>> >
>> >      BUG: Use PNG_SCALE_METER for PNG sCAL unit
>> >
>> >      BUG: Use METER of sCAL scale unit
>> >
>> >      BUG: Use PNG_SCALE_METER for PNG sCAL unit
>> >
>> >      COMP: Fix signed to unsigned int comparison
>> >
>> >      BUG: Fix overflows computing size of read tiff image
>> >
>> >      ENH: Extract TiffReaderInternal to separate file
>> >
>> >      ENH: Refactor ReadTwoSamplePerPixelImage into template function
>> >
>> >      ENH: Refactor GenericReadImage into template function
>> >
>> >      BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and
>> > LSMImageIO )
>> >
>> >      ENH: Refactor method to convert RGBA image to output buffer
>> >
>> >      ENH: Refactor duplicated code to read a page
>> >
>> >      BUG: Fix right oriented tiff images
>> >
>> >      BUG: Remove dead separated plannar code, add test
>> >
>> >      STYLE: Fix minor kwstyle defects in test and test results
>> >
>> >      BUG: Use array delete operator for array new allocations
>> >
>> >      ENH: add arbitrary TIFF TAGs to meta-data dictionary
>> >
>> >      ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
>> >
>> >      BUG: Address Coverity warning about null pointer dereferences
>> >
>> >      ENH: Remove support for TIFF tile as 3D and dead code
>> >
>> >      ENH: RGBA read images should stay unchanged.
>> >
>> >      BUG: Override method to MakeOutput by name
>> >
>> >      ENH: Refactor per pixel conversion function to per scan-line method
>> >
>> >      PERF: Refactor color table lookup
>> >
>> >      BUG: Adding missing parentheses around boolean expression
>> >
>> >      ENH: adding TIFFImageIO test for RGB palette images
>> >
>> >      PERF: Improve recursive Gaussian perfromance with VectorImages
>> >
>> >      ENH: Query libtiff to determine compression support
>> >
>> >      BUG: Support TIFF tiled image with TIFFReadRGBAImage
>> >
>> >      BUG: Use SizeValueType for length of scanline
>> >
>> >      PERF: Store causal results directly in output buffers
>> >
>> >      COMP: Add explicit conversion to const char
>> >
>> >      COMP: Explicitly add override to GetNameOfClass method
>> >
>> >      COMP: Address internal segmentation fault with Intel compiler
>> >
>> >      ENH: Adding method to set global physical space tolerance
>> >
>> >      COMP: Explicitly add override to GetNameOfClass method
>> >
>> >      BUG: Add new TypeMacro for non-overloaded classes
>> >
>> >      BUG: Fix obscure race condition on access thread pool
>> initialization
>> >
>> >      BUG: Updating FDFImageIO remote module
>> >
>> >
>> > Christopher Mullins (15):
>> >
>> >      COMP: Allows latex to compile for ITKSoftwareGuide
>> >
>> >      COMP: Allows latex to compile for ITKSoftwareGuide
>> >
>> >      COMP: Wrap MeshBase templates
>> >
>> >      COMP: Wrap MeshBase templates
>> >
>> >      COMP: Fix warning in BlockMatchingImageFilter
>> >
>> >      STYLE: Line lengths in examples should be no longer than 80 chars.
>> >
>> >      COMP: Wrap the remaining MeshBase and MeshToMeshFilter types.
>> >
>> >      COMP: Fix LaTeX warnings.
>> >
>> >      STYLE: Fix formatting/punctuation errors.
>> >
>> >      STYLE: Formatting and punctuation fixes.
>> >
>> >      DOC: Edits for Book 2 Chapter 1 documentation in the Examples.
>> >
>> >      DOC: Edits for book 2 chapter 2.
>> >
>> >      DOC: More chapter 2 edits
>> >
>> >      DOC: Book 2 Chapter 3 edits (part 1)
>> >
>> >      DOC: book 2 chapter 4 Segmentation edits
>> >
>> >
>> > Danny Perry (2):
>> >
>> >      BUG: adding test for vnl_sparse_matrix::mult()
>> >
>> >      BUG: size of q buffer should actually be (this->rows())*pcols.
>> >
>> >
>> > David T. Chen (1):
>> >
>> >      DOC: Fixed HistogramThresholdImageFitler
>> >
>> >
>> > Dirk Padfield (1):
>> >
>> >      BUG: Corrected processing of last sigma
>> >
>> >
>> > GCC-XML Upstream (1):
>> >
>> >      ENH: pygccxml v1.6.2 (reduced)
>> >
>> >
>> > 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 (24):
>> >
>> >      COMP: Add tolerance for comparing floating point
>> >
>> >      PERF: Remove non-threadable algorithm components
>> >
>> >      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
>> >
>> >      BUG: Syntax error in comment
>> >
>> >      PERF: Add non-blocking mutex locking.
>> >
>> >      ENH: Use TryLock minimize thread stalls
>> >
>> >      BUG: ThreadedIndexedContainerPartitioner is inclusive
>> >
>> >      STYLE: Remove include_regular_expression from Examples
>> >
>> >      BUG: Demonstrate Inv(Inv(T)) != T
>> >
>> >      BUG: Ensure Inv(Inv(T)) == T for transforms
>> >
>> >      COMP: Valgrind detects uninitialized memory read
>> >
>> >      COMP: Missing required base class API component
>> >
>> >      ENH: Expand interface for selecting threadpool
>> >
>> >
>> > Ismael Belghiti (1):
>> >
>> >      DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter
>> >
>> >
>> > Jim Miller (1):
>> >
>> >      STYLE: Removing what appears to be a temporary file
>> >
>> >
>> > Johan Andruejol (1):
>> >
>> >      ENH: Fix normalization for null vectors and return the norm
>> >
>> >
>> > Jon Haitz Legarreta (1):
>> >
>> >      ENH: New test for itkLabelShapeOpeningImageFilter
>> >
>> >
>> > Kent Williams (9):
>> >
>> >      COMP: use find_package(VTK COMPONENTS) to specify just needed VTK
>> > Components
>> >
>> >      BUG: ImageSources/test/CMakeLists.txt incorrect library var
>> reference
>> >
>> >      COMP: Fix coverity defects related to RegistrationV4 examples
>> >
>> >      COMP: silence warning of vnl_vector_fixed_ref::assert_size
>> >
>> >      COMP: Fix various Coverity warnings
>> >
>> >      COMP: Fix a typo in an error message print statement.
>> >
>> >      COMP: itk::Command-derived class used pointless dynamic_cast.
>> >
>> >      PERF: Don't recompute InternalInverse repeatedly
>> >
>> >      COMP: Correct orientation/spacing for Philips MultiFrame
>> >
>> >
>> > Mark Hiner (2):
>> >
>> >      ENH: Update SCIFIO remote module hash
>> >
>> >      BUG: Fix duplicate variables in Windows
>> >
>> >
>> > Matthew McCormick (105):
>> >
>> >      DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro.
>> >
>> >      ENH: Move FFTComplexToComplexImageFilter out of Review.
>> >
>> >      ENH: Add VnlComplexToComplexFFTImageFilter.
>> >
>> >      BUG: Use fixed seed for Vnl FFT tests for repeatibility.
>> >
>> >      ENH: Bump CMakeLists.txt version to 4.7.0.
>> >
>> >      BUG: ArchiveTestingData.py future imports must occur at the
>> beginning.
>> >
>> >      BUG: Do not run vnl_test_na with broken libc++.
>> >
>> >      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.
>> >
>> >      DOC: Fix Software Guide page overruns in
>> > IterativeClosestPoint{1,2}.cxx.
>> >
>> >      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
>> >
>> >      BUG: Uninitialized m_TransformDirection in
>> > ComplexToComplexFFTImageFilter.
>> >
>> >      BUG: Fix offset[2] in
>> PointSetToSpatialObjectDemonsRegistrationTest.
>> >
>> >      STYLE: Fix style in VoronoiDiagram2D.
>> >
>> >      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>> >
>> >      BUG: Bump GCCXML to 2014-08-06.
>> >
>> >      BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}.
>> >
>> >      BUG: Fix Win MultiThreader check for successful process creation.
>> >
>> >      BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor.
>> >
>> >      COMP: Fix ImageRegistration8RegisteredSlice.png baseline name.
>> >
>> >      DOC: itk::statistics -> itk::Statistics.
>> >
>> >      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
>> >
>> >      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
>> >
>> >      COMP: Improve const correctness of
>> > GradientRecursiveGaussianImageFilter.
>> >
>> >      BUG: Call clear instead of empty on PatchBasedDenoising
>> EmptyCaches().
>> >
>> >      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
>> >
>> >      COMP: ThreadJob NULL not defined.
>> >
>> >      BUG: Fix alpha assignment for RGBA TIFF.
>> >
>> >      COMP: Remove unused typedefs in LevelSetsv4Visualization.
>> >
>> >      COMP: Remove unused typedef's in VtkGlue.
>> >
>> >      ENH: Mark BSplineWarping2Test as RUNS_LONG.
>> >
>> >      BUG: Fix Nifti IO read with large images.
>> >
>> >      COMP: Remove call for non-existent variable in Nifti debugging.
>> >
>> >      BUG: Close the file on Read and Write in HDF5TransformIO.
>> >
>> >      BUG: Remove InsightLegacy test code from TransformHDF5Test.
>> >
>> >      ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}.
>> >
>> >      STYLE: Use SeriesUIDContainerType and FileNamesContainerType
>> >
>> >      ENH: Allow specification of orthogonality tolerance in rigid
>> > transforms.
>> >
>> >      BUG: TransformFileReader does not clear its TransformList.
>> >
>> >      BUG: Prevent dangling pointer in HDF5TransformIO.
>> >
>> >      COMP: Do not use _stat64 with MinGW-32.
>> >
>> >      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.
>> >
>> >      COMP: Address LaplacianDeformation Doxygen warnings.
>> >
>> >      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
>> >
>> >      COMP: Do not wrap the FixedArray of Image SmartPointer's.
>> >
>> >      COMP: Add missing wrapping for TransformIOBaseTemplate.
>> >
>> >      COMP: Mark DeformableRegistration6Test as RUNS_LONG.
>> >
>> >      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.
>> >
>> >      BUG: Use -py3 when building wrapping for Python 3.
>> >
>> >      COMP: Add missing wrapping for TransformIOBaseTemplate.
>> >
>> >      DOC: Improve ImageRegistration4 grammar.
>> >
>> >      ENH: Add IOTransformDCMTK Remote module.
>> >
>> >      BUG: gdcm::StringFilter recognizes backslash delimiter.
>> >
>> >      DOC: Add migration guide for GDCM Rescale slope intercept apply on
>> > write.
>> >
>> >      COMP: Remove unused typedef's in GPU code.
>> >
>> >      STYLE: Improve style of HoughTransform2DLinesImageFilter example.
>> >
>> >      COMP: Use ConceptChecking for IterativeInverse dimension check.
>> >
>> >      COMP: Wrap TransformIOBaseTemplate for const SmartPointer.
>> >
>> >      COMP: Add warning exceptions for third party pcre, swig, gccxml.
>> >
>> >      ENH: Bump ITK version to 4.6.1.
>> >
>> >      BUG: Add missing ITK_OVERRIDE to ITKImageeSources module.
>> >
>> >      BUG: Remove GaussianImageSource members shadowing
>> GenerateImageSource.
>> >
>> >      STYLE: Style fixes to ITKImageSources module.
>> >
>> >      BUG: GaussianSpatialFunction and GaborImageSource use
>> > SpacePrecisionType.
>> >
>> >      BUG: Do not perform itk_download_attempt_check when not building
>> ITK.
>> >
>> >      DOC: Update GDCMImageIO rescale slope intercept doc.
>> >
>> >      BUG: Only register requestion IO COMPONENT modules.
>> >
>> >      BUG: Fix wrapping .i, .idx CMake dependencies.
>> >
>> >      COMP: Add VTK Python module when wrapping ITKVtkGlue.
>> >
>> >      STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator.
>> >
>> >      STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType
>> typedef.
>> >
>> >      COMP: Add missing VTK module dependency for
>> LevelSetsv4Visualization.
>> >
>> >      BUG: By default, do not create any fixed parameters.
>> >
>> >      STYLE: Remove trivial method comments in itkTransform.hxx.
>> >
>> >      BUG: PolylineMask Filter's GenerateData is protected / virtual.
>> >
>> >      ENH: Add HigherOrderAccurateGradient Module.
>> >
>> >      BUG: Use input RequestedRegion Index in SliceBySliceImageFilter
>> > internal.
>> >
>> >      COMP: Remove extra semi-colon, variable scope in DCMTKFileReader.
>> >
>> >      STYLE: Style fixes for Transform classes.
>> >
>> >      DOC: Increase Doxygen LOOKUP_CACHE_SIZE.
>> >
>> >      BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe.
>> >
>> >      DOC: Index Wiki examples with Doxygen.
>> >
>> >      COMP: Bump SphinxExamples remote module.
>> >
>> >      DOC: Index Sphinx examples in Doxygen.
>> >
>> >      COMP: Remove old java examples.
>> >
>> >      COMP: Remove duplicate DiffusionTensor3DReconstruction example
>> > reference.
>> >
>> >      COMP: Address GradientAnisotropicDiffusionImageFilter example
>> settings.
>> >
>> >      COMP: Bump Sphinx Examples remote.
>> >
>> >      COMP: Bump WikiExamples remote.
>> >
>> >
>> > MetaIO Maintainers (1):
>> >
>> >      MetaIO (reduced)
>> >
>> >
>> > Michka Popoff (40):
>> >
>> >      ENH: Fixes for python 3 support
>> >
>> >      BUG: Add VTK_VERSION for older VTK versions
>> >
>> >      BUG: Improve SWIG version check
>> >
>> >      COMP: Add wrapping for ThreadPool and ThreadJob
>> >
>> >      COMP: Remove unimplemented DestroyPool method
>> >
>> >      COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping
>> >
>> >      COMP: Do not hide pygccxml warnings
>> >
>> >      ENH: Update links in readme file
>> >
>> >      BUG: Improve SWIG version check
>> >
>> >      BUG: Add VTK_VERSION for older VTK versions
>> >
>> >      STYLE: Remove trailing whitespaces
>> >
>> >      STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP
>> >
>> >      BUG: Fix memory leak in MetaImageIO after exception
>> >
>> >      ENH: Add script to update pygccxml from upstream
>> >
>> >      BUG: Update VTK minimum version (for release)
>> >
>> >      BUG: Fix memory leak in MetaImageIO after exception
>> >
>> >      ENH: Remove Sun OS compatibility for the wrappings
>> >
>> >      COMP: Fix for conversion to non-pointer like type warning
>> >
>> >      STYLE: LabelObject style
>> >
>> >      DOC: Remove broken link from LabelObject class description
>> >
>> >      ENH: Do not setup the python tests if not asked
>> >
>> >      ENH: Add new GetTypes() and GetTypesAsList() methods to the
>> template
>> > class
>> >
>> >      COMP: Fix CMP0054 warnings in wrappings
>> >
>> >      STYLE: Remove old cmake < 2.8.4 specific code
>> >
>> >      STYLE: Remove old cmake < 2.8.5 specific code
>> >
>> >      ENH: Update to PCRE 8.36
>> >
>> >      COMP: Refactor Wrapping setup and fix legacy warnings
>> >
>> >      ENH: Add wrapping configuration to ITKConfig.cmake
>> >
>> >      STYLE: Some minor code cleanup in the wrapping setup
>> >
>> >      DOC: Fix typo in RelabelComponentImageFilter
>> >
>> >      ENH: Deprecate VectorResampleImageFilter
>> >
>> >      DOC: Add migration guide for ::Zero and ::One
>> >
>> >      ENH: Deprecate ::Zero and ::One
>> >
>> >      ENH: Add option to disable sorting by size in
>> > itkRelabelComponentImageFilter
>> >
>> >      ENH: Add Vector and RGB wrapping to linear interpolator
>> >
>> >      STYLE: Remove SORT macro in wrappings
>> >
>> >      COMP: Fix warning for InterpolateImageFunction wrapping
>> >
>> >      COMP: Add a check for Blocks in GPU module
>> >
>> >      COMP: Bump SCIFIO to fix test build warnings
>> >
>> >      COMP: Fix wrapping of itkImageFunctionBase
>> >
>> >
>> > Nick Tustison (7):
>> >
>> >      BUG:  Need to explicitly specify spline order.
>> >
>> >      ENH:  Initializing the transform center.
>> >
>> >      BUG:  Need to check the dynamic cast before any calls.
>> >
>> >      ENH:  Adding modifications for point set metrics.
>> >
>> >      BUG:  Need to specify TInternalComputationValueType for default
>> metric.
>> >
>> >      ENH:  Adding sparse points to B-spline field estimate.
>> >
>> >      BUG:  Uninitialized variables.
>> >
>> >
>> > Richard Beare (1):
>> >
>> >      ENH: Include TIFF tags in the MetaDataDictionary
>> >
>> >
>> > Taylor Braun-Jones (1):
>> >
>> >      BUG: Fix SliceBySliceImageFilter doesn't propagate information
>> > internally
>> >
>> >
>> > Umang B (1):
>> >
>> >      ENH: Use thread pool to dispatch multithreading tasks
>> >
>> >
>> > Vivien Delmon (2):
>> >
>> >      BUG: ExtractImageFilter::CollapseToSubMatrix fix
>> >
>> >      ENH: Add a test on extracted directions in CollapseToSubMatrix mode
>> >
>> >
>> > Vladimir S. FONOV (1):
>> >
>> >      BUG: Fixing incorrect MINC style inverse transform
>> >
>> >
>> >
>> > -----------------------------------------------------
>> >
>> > Errors or omissions? Please fix them here:
>> >
>> >
>> >
>> https://docs.google.com/document/d/1V0zNgFrm_GyF1jOC00fMq-7VBXk4hHmHL62qByfeKP4/edit?usp=sharing
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > 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 matimontg at gmail.com  Fri Dec 19 08:16:13 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Fri, 19 Dec 2014 10:16:13 -0300
Subject: [ITK-users] ITK Apps | MRIRegistration not included in compilation
Message-ID: <CAKKNfuKXSDsBwKVTYbJvwG-=fzz1k0osbgoXJ3__ziy1XYeUOw@mail.gmail.com>

Hi,

I downloaded ITK Apps from GIT and generated the .sln in Visual Studio
(2012) with Cmake.

Now, this particular example: MRIRegistration is not included in the build
directory, any reason why this is happening?

Thank you,

Matias.
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From bill.lorensen at gmail.com  Fri Dec 19 08:34:32 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 19 Dec 2014 08:34:32 -0500
Subject: [ITK-users] ITK Apps | MRIRegistration not included in
	compilation
In-Reply-To: <CAKKNfuKXSDsBwKVTYbJvwG-=fzz1k0osbgoXJ3__ziy1XYeUOw@mail.gmail.com>
References: <CAKKNfuKXSDsBwKVTYbJvwG-=fzz1k0osbgoXJ3__ziy1XYeUOw@mail.gmail.com>
Message-ID: <CADZJ4hOcHVgEBfVmJFdWwPBb5=W3oLBpoCrazH-F1EDdxj6VXw@mail.gmail.com>

Are you using the superbuild to build itk and vtk or are you pointing
to your own itk and vtk?


On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi,
>
> I downloaded ITK Apps from GIT and generated the .sln in Visual Studio
> (2012) with Cmake.
>
> Now, this particular example: MRIRegistration is not included in the build
> directory, any reason why this is happening?
>
> Thank you,
>
> Matias.
>
> _____________________________________
> 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
>



-- 
Unpaid intern in BillsBasement at noware dot com

From matimontg at gmail.com  Fri Dec 19 09:20:19 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Fri, 19 Dec 2014 11:20:19 -0300
Subject: [ITK-users] ITK Apps | MRIRegistration not included in
	compilation
In-Reply-To: <CADZJ4hOcHVgEBfVmJFdWwPBb5=W3oLBpoCrazH-F1EDdxj6VXw@mail.gmail.com>
References: <CAKKNfuKXSDsBwKVTYbJvwG-=fzz1k0osbgoXJ3__ziy1XYeUOw@mail.gmail.com>
 <CADZJ4hOcHVgEBfVmJFdWwPBb5=W3oLBpoCrazH-F1EDdxj6VXw@mail.gmail.com>
Message-ID: <CAKKNfu+Axd2XO06CXoY5Ejj2B2tHavKe8mSJvTSYRy1QZzUGDw@mail.gmail.com>

Hi Bill,

I've downloaded and compiled ITK in a directory and FLTK as well

Regards,

Matias.

On Fri, Dec 19, 2014 at 10:34 AM, Bill Lorensen <bill.lorensen at gmail.com>
wrote:
>
> Are you using the superbuild to build itk and vtk or are you pointing
> to your own itk and vtk?
>
>
> On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull <matimontg at gmail.com>
> wrote:
> > Hi,
> >
> > I downloaded ITK Apps from GIT and generated the .sln in Visual Studio
> > (2012) with Cmake.
> >
> > Now, this particular example: MRIRegistration is not included in the
> build
> > directory, any reason why this is happening?
> >
> > Thank you,
> >
> > Matias.
> >
> > _____________________________________
> > 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
> >
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
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From matimontg at gmail.com  Fri Dec 19 09:23:09 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Fri, 19 Dec 2014 11:23:09 -0300
Subject: [ITK-users] ITK Apps | MRIRegistration not included in
	compilation
In-Reply-To: <CAKKNfu+Axd2XO06CXoY5Ejj2B2tHavKe8mSJvTSYRy1QZzUGDw@mail.gmail.com>
References: <CAKKNfuKXSDsBwKVTYbJvwG-=fzz1k0osbgoXJ3__ziy1XYeUOw@mail.gmail.com>
 <CADZJ4hOcHVgEBfVmJFdWwPBb5=W3oLBpoCrazH-F1EDdxj6VXw@mail.gmail.com>
 <CAKKNfu+Axd2XO06CXoY5Ejj2B2tHavKe8mSJvTSYRy1QZzUGDw@mail.gmail.com>
Message-ID: <CAKKNfuLK0f4FRtLtE8UjV+LkLBEvL5z_oTQAFgs3v8qfw1H3kQ@mail.gmail.com>

I've seen in the Cmake.txt list these lines:
so how do I specidy these optional apps need to be included in the binaries
build?
IF(FLTK_FOUND)
  IF(WIN32)
    ADD_DEFINITIONS(-DWIN32)
  ENDIF(WIN32)
*  OPTIONAL_APP(MultiResMIRegistration)*
  OPTIONAL_APP(DigitalArchive)
  OPTIONAL_APP(DistanceMapFilter)
  OPTIONAL_APP(DicomImageViewer)
......

On Fri, Dec 19, 2014 at 11:20 AM, Matias Montroull <matimontg at gmail.com>
wrote:
>
> Hi Bill,
>
> I've downloaded and compiled ITK in a directory and FLTK as well
>
> Regards,
>
> Matias.
>
> On Fri, Dec 19, 2014 at 10:34 AM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>>
>> Are you using the superbuild to build itk and vtk or are you pointing
>> to your own itk and vtk?
>>
>>
>> On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull <matimontg at gmail.com>
>> wrote:
>> > Hi,
>> >
>> > I downloaded ITK Apps from GIT and generated the .sln in Visual Studio
>> > (2012) with Cmake.
>> >
>> > Now, this particular example: MRIRegistration is not included in the
>> build
>> > directory, any reason why this is happening?
>> >
>> > Thank you,
>> >
>> > Matias.
>> >
>> > _____________________________________
>> > 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
>> >
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>>
>
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From bill.lorensen at gmail.com  Fri Dec 19 10:32:39 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 19 Dec 2014 10:32:39 -0500
Subject: [ITK-users] ITK Apps | MRIRegistration not included in
	compilation
In-Reply-To: <CAKKNfuLK0f4FRtLtE8UjV+LkLBEvL5z_oTQAFgs3v8qfw1H3kQ@mail.gmail.com>
References: <CAKKNfuKXSDsBwKVTYbJvwG-=fzz1k0osbgoXJ3__ziy1XYeUOw@mail.gmail.com>
 <CADZJ4hOcHVgEBfVmJFdWwPBb5=W3oLBpoCrazH-F1EDdxj6VXw@mail.gmail.com>
 <CAKKNfu+Axd2XO06CXoY5Ejj2B2tHavKe8mSJvTSYRy1QZzUGDw@mail.gmail.com>
 <CAKKNfuLK0f4FRtLtE8UjV+LkLBEvL5z_oTQAFgs3v8qfw1H3kQ@mail.gmail.com>
Message-ID: <CADZJ4hNOVgG2Vb59qomea6nzcXe3eVGTcjh_E9GBLfTRSxu1tg@mail.gmail.com>

You really should use the Superbuild for ITKApps. Configuration can be
very tricky.


On Fri, Dec 19, 2014 at 9:23 AM, Matias Montroull <matimontg at gmail.com> wrote:
> I've seen in the Cmake.txt list these lines:
> so how do I specidy these optional apps need to be included in the binaries
> build?
> IF(FLTK_FOUND)
>   IF(WIN32)
>     ADD_DEFINITIONS(-DWIN32)
>   ENDIF(WIN32)
>   OPTIONAL_APP(MultiResMIRegistration)
>   OPTIONAL_APP(DigitalArchive)
>   OPTIONAL_APP(DistanceMapFilter)
>   OPTIONAL_APP(DicomImageViewer)
> ......
>
> On Fri, Dec 19, 2014 at 11:20 AM, Matias Montroull <matimontg at gmail.com>
> wrote:
>>
>> Hi Bill,
>>
>> I've downloaded and compiled ITK in a directory and FLTK as well
>>
>> Regards,
>>
>> Matias.
>>
>> On Fri, Dec 19, 2014 at 10:34 AM, Bill Lorensen <bill.lorensen at gmail.com>
>> wrote:
>>>
>>> Are you using the superbuild to build itk and vtk or are you pointing
>>> to your own itk and vtk?
>>>
>>>
>>> On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull <matimontg at gmail.com>
>>> wrote:
>>> > Hi,
>>> >
>>> > I downloaded ITK Apps from GIT and generated the .sln in Visual Studio
>>> > (2012) with Cmake.
>>> >
>>> > Now, this particular example: MRIRegistration is not included in the
>>> > build
>>> > directory, any reason why this is happening?
>>> >
>>> > Thank you,
>>> >
>>> > Matias.
>>> >
>>> > _____________________________________
>>> > 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
>>> >
>>>
>>>
>>>
>>> --
>>> Unpaid intern in BillsBasement at noware dot com



-- 
Unpaid intern in BillsBasement at noware dot com

From dzenanz at gmail.com  Fri Dec 19 13:34:52 2014
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 19 Dec 2014 13:34:52 -0500
Subject: [ITK-users] [Insight-users] [ITK-USER]Compile ITK3.20.1 with
	VS2012
In-Reply-To: <DFB2170F-8DD6-4B6E-8891-EB202F651BF1@mail.nih.gov>
References: <CAA4xxgbWyEj0BTUtVJtQo8NZt9Wp8V_mDExzP87AzhyUP+Pifg@mail.gmail.com>
 <DFB2170F-8DD6-4B6E-8891-EB202F651BF1@mail.nih.gov>
Message-ID: <CAPf2UMSOHWdGv-0gb+tzuDg15LG7W8HL7MOPtOdnC4084n3Atg@mail.gmail.com>

Probably too late for JX, but I found a solution. When configuring ITK with
CMake, in the field CMAKE_CXX_FLAGS add the
following: /D_ALLOW_KEYWORD_MACROS
Article which helped me:
http://mostlybuggy.wordpress.com/2012/12/18/getting-around-vs2012-c1189c4005-keyword-re-defined-in-macros/


On Wed, May 29, 2013 at 9:33 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:
>
> Hi,
>
> Why no upgrade to ITK v4?
>
> ITK v3.20 was released in 2010, well before Visual Studio 2012. So it
> should be no surprise it does not work with it. I believe VS 2010 should
> work with it, and VS9, and VS8, and VS7....
>
>
> Brad
>
>
>
> On May 28, 2013, at 10:41 PM, JX NIE <njx937 at gmail.com> wrote:
>
> > Hi Everyone,
> >     I have tried to compile ITK(version 3.20.1 ) with VS2012, but failed.
> >     It has ended up with a lot of  Redifine errors as follow.
> >    Could you please tell me how to solve this compile problem.
> >    Regards,
> >
> > NIE JUNXIAO
> >
> >
> > >C:\Program Files (x86)\Microsoft Visual Studio
> 11.0\VC\include\xkeycheck.h(242): fatal error C1189: #error :  The C++
> Standard Library forbids macroizing keywords. Enable warning C4005 to find
> the forbidden macro.
> >
> >       1       IntelliSense: #error directive: The C++ Standard Library
> forbids macroizing keywords. Enable warning C4005 to find the forbidden
> macro. c:\Program Files (x86)\Microsoft Visual Studio
> 11.0\VC\include\xkeycheck.h      242
> >       2       IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\sal.h    2367
> >       3       IntelliSense: expected a declaration    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\vadefs.h 139
> >       4       IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        437
> >       5       IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        446
> >       6       IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        464
> >       7       IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        475
> >       8       IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        476
> >       9       IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        497
> >       10      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        501
> >       11      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        506
> >       12      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        514
> >       13      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        571
> >       14      IntelliSense: attribute "noreturn" does not apply here
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h
>     572
> >       15      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        572
> >       16      IntelliSense: attribute "noreturn" does not apply here
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h
>     575
> >       17      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        576
> >       18      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1979
> >       19      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1980
> >       20      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1981
> >       21      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1982
> >       22      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1983
> >       23      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1985
> >       24      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1992
> >       25      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1999
> >       26      IntelliSense: expected a declaration    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        2023
> >       27      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  510
> >       28      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  528
> >       29      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  529
> >       30      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  542
> >       31      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  576
> >       32      IntelliSense: invalid destructor declaration    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  577
> >       33      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  583
> >       34      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  585
> >       35      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  586
> >       36      IntelliSense: explicit type is missing ('int' assumed)
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  588
> >       37      IntelliSense: identifier "EMIT" is undefined    c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  588
> >       38      IntelliSense: function "_Lockit" is not a type name
>  c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  589
> >       39      IntelliSense: reference variable "EMIT" requires an
> initializer c:\Program Files (x86)\Microsoft Visual Studio
> 11.0\VC\include\yvals.h  589
> >       40      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  591
> >       41      IntelliSense: expected a declaration    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  606
> >       42      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  693
> >       43      IntelliSense: expected a declaration    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  726
> >       44      IntelliSense: expected a declaration    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  729
> >       45      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  740
> >       46      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  741
> >       47      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 23
> >       48      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 47
> >       49      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 48
> >       50      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 49
> >       51      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 50
> >       52      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 54
> >       53      IntelliSense: identifier "errno_t" is undefined c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 56
> >       54      IntelliSense: variable "memcpy_s" may not be initialized
>       c:\Program Files (x86)\Microsoft Visual Studio
> 11.0\VC\include\string.h 56
> >       55      IntelliSense: expected a ')'    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 56
> >       56      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 93
> >       57      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 97
> >       58      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 98
> >       59      IntelliSense: identifier "errno_t" is undefined c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 103
> >       60      IntelliSense: variable "_strset_s" may not be initialized
>      c:\Program Files (x86)\Microsoft Visual Studio
> 11.0\VC\include\string.h 103
> >       61      IntelliSense: expected a ')'    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 103
> >       62      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 104
> >       63      IntelliSense: identifier "errno_t" is undefined c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 107
> >       64      IntelliSense: variable "strcpy_s" may not be initialized
>       c:\Program Files (x86)\Microsoft Visual Studio
> 11.0\VC\include\string.h 107
> >       65      IntelliSense: expected a ')'    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 107
> >       66      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 109
> >       67      IntelliSense: identifier "errno_t" is undefined c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 112
> >       68      IntelliSense: variable "strcat_s" may not be initialized
>       c:\Program Files (x86)\Microsoft Visual Studio
> 11.0\VC\include\string.h 112
> >       69      IntelliSense: expected a ')'    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 112
> >       70      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 114
> >       71      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 116
> >       72      IntelliSense: expected a ')'    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 117
> >       73      IntelliSense: variable "strnlen" may not be initialized
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 121
> >       74      IntelliSense: expected a ')'    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 121
> >       75      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 123
> >       76      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 135
> >       77      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 142
> >       78      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 148
> >       79      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 149
> >       80      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 150
> >       81      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 151
> >       82      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 152
> >       83      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 153
> >       84      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 154
> >       85      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 155
> >       86      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 156
> >       87      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 157
> >       88      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 158
> >       89      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 159
> >       90      IntelliSense: variable "strcspn" may not be initialized
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 160
> >       91      IntelliSense: expected a ')'    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 160
> >       92      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 161
> >       93      IntelliSense: identifier "errno_t" is undefined c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 162
> >       94      IntelliSense: variable "_strerror_s" may not be
> initialized     c:\Program Files (x86)\Microsoft Visual Studio
> 11.0\VC\include\string.h 162
> >       95      IntelliSense: expected a ')'    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 162
> >       96      IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 163
> >       97      IntelliSense: identifier "errno_t" is undefined c:\Program
> Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 166
> >       98      IntelliSense: variable "strerror_s" may not be
> initialized      c:\Program Files (x86)\Microsoft Visual Studio
> 11.0\VC\include\string.h 166
> >       99      IntelliSense: expected a ')'    c:\Program Files
> (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 166
> >       100     IntelliSense: variable "EMIT" is not a type name
> c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 168
> >
> > <CMakeCache.txt>_____________________________________
> > 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://www.itk.org/mailman/listinfo/insight-users
>
> _____________________________________
> 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://www.itk.org/mailman/listinfo/insight-users
>
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From matimontg at gmail.com  Fri Dec 19 15:16:37 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Fri, 19 Dec 2014 17:16:37 -0300
Subject: [ITK-users] ITK Apps | MRIRegistration not included in
	compilation
In-Reply-To: <CADZJ4hNOVgG2Vb59qomea6nzcXe3eVGTcjh_E9GBLfTRSxu1tg@mail.gmail.com>
References: <CAKKNfuKXSDsBwKVTYbJvwG-=fzz1k0osbgoXJ3__ziy1XYeUOw@mail.gmail.com>
 <CADZJ4hOcHVgEBfVmJFdWwPBb5=W3oLBpoCrazH-F1EDdxj6VXw@mail.gmail.com>
 <CAKKNfu+Axd2XO06CXoY5Ejj2B2tHavKe8mSJvTSYRy1QZzUGDw@mail.gmail.com>
 <CAKKNfuLK0f4FRtLtE8UjV+LkLBEvL5z_oTQAFgs3v8qfw1H3kQ@mail.gmail.com>
 <CADZJ4hNOVgG2Vb59qomea6nzcXe3eVGTcjh_E9GBLfTRSxu1tg@mail.gmail.com>
Message-ID: <CAKKNfuKXBr5JD8x1v8=eqkE4AuKJP4abRsXJ2psu1XH3oDgmWg@mail.gmail.com>

Hi Bill, I was able to make it work, I had to enable use of FLTK in Cmake
when building ITKApps binaries

On Fri, Dec 19, 2014 at 12:32 PM, Bill Lorensen <bill.lorensen at gmail.com>
wrote:
>
> You really should use the Superbuild for ITKApps. Configuration can be
> very tricky.
>
>
> On Fri, Dec 19, 2014 at 9:23 AM, Matias Montroull <matimontg at gmail.com>
> wrote:
> > I've seen in the Cmake.txt list these lines:
> > so how do I specidy these optional apps need to be included in the
> binaries
> > build?
> > IF(FLTK_FOUND)
> >   IF(WIN32)
> >     ADD_DEFINITIONS(-DWIN32)
> >   ENDIF(WIN32)
> >   OPTIONAL_APP(MultiResMIRegistration)
> >   OPTIONAL_APP(DigitalArchive)
> >   OPTIONAL_APP(DistanceMapFilter)
> >   OPTIONAL_APP(DicomImageViewer)
> > ......
> >
> > On Fri, Dec 19, 2014 at 11:20 AM, Matias Montroull <matimontg at gmail.com>
> > wrote:
> >>
> >> Hi Bill,
> >>
> >> I've downloaded and compiled ITK in a directory and FLTK as well
> >>
> >> Regards,
> >>
> >> Matias.
> >>
> >> On Fri, Dec 19, 2014 at 10:34 AM, Bill Lorensen <
> bill.lorensen at gmail.com>
> >> wrote:
> >>>
> >>> Are you using the superbuild to build itk and vtk or are you pointing
> >>> to your own itk and vtk?
> >>>
> >>>
> >>> On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull <matimontg at gmail.com
> >
> >>> wrote:
> >>> > Hi,
> >>> >
> >>> > I downloaded ITK Apps from GIT and generated the .sln in Visual
> Studio
> >>> > (2012) with Cmake.
> >>> >
> >>> > Now, this particular example: MRIRegistration is not included in the
> >>> > build
> >>> > directory, any reason why this is happening?
> >>> >
> >>> > Thank you,
> >>> >
> >>> > Matias.
> >>> >
> >>> > _____________________________________
> >>> > 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
> >>> >
> >>>
> >>>
> >>>
> >>> --
> >>> Unpaid intern in BillsBasement at noware dot com
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
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From bill.lorensen at gmail.com  Fri Dec 19 15:31:52 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Fri, 19 Dec 2014 15:31:52 -0500
Subject: [ITK-users] ITK Apps | MRIRegistration not included in
	compilation
In-Reply-To: <CAKKNfuKXBr5JD8x1v8=eqkE4AuKJP4abRsXJ2psu1XH3oDgmWg@mail.gmail.com>
References: <CAKKNfuKXSDsBwKVTYbJvwG-=fzz1k0osbgoXJ3__ziy1XYeUOw@mail.gmail.com>
 <CADZJ4hOcHVgEBfVmJFdWwPBb5=W3oLBpoCrazH-F1EDdxj6VXw@mail.gmail.com>
 <CAKKNfu+Axd2XO06CXoY5Ejj2B2tHavKe8mSJvTSYRy1QZzUGDw@mail.gmail.com>
 <CAKKNfuLK0f4FRtLtE8UjV+LkLBEvL5z_oTQAFgs3v8qfw1H3kQ@mail.gmail.com>
 <CADZJ4hNOVgG2Vb59qomea6nzcXe3eVGTcjh_E9GBLfTRSxu1tg@mail.gmail.com>
 <CAKKNfuKXBr5JD8x1v8=eqkE4AuKJP4abRsXJ2psu1XH3oDgmWg@mail.gmail.com>
Message-ID: <CADZJ4hMXVwUhk96mYtHaVJQsh+-WEoDJyHWdyzugvFAqSBBtDQ@mail.gmail.com>

Excellent!


On Fri, Dec 19, 2014 at 3:16 PM, Matias Montroull <matimontg at gmail.com> wrote:
> Hi Bill, I was able to make it work, I had to enable use of FLTK in Cmake
> when building ITKApps binaries
>
> On Fri, Dec 19, 2014 at 12:32 PM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>>
>> You really should use the Superbuild for ITKApps. Configuration can be
>> very tricky.
>>
>>
>> On Fri, Dec 19, 2014 at 9:23 AM, Matias Montroull <matimontg at gmail.com>
>> wrote:
>> > I've seen in the Cmake.txt list these lines:
>> > so how do I specidy these optional apps need to be included in the
>> > binaries
>> > build?
>> > IF(FLTK_FOUND)
>> >   IF(WIN32)
>> >     ADD_DEFINITIONS(-DWIN32)
>> >   ENDIF(WIN32)
>> >   OPTIONAL_APP(MultiResMIRegistration)
>> >   OPTIONAL_APP(DigitalArchive)
>> >   OPTIONAL_APP(DistanceMapFilter)
>> >   OPTIONAL_APP(DicomImageViewer)
>> > ......
>> >
>> > On Fri, Dec 19, 2014 at 11:20 AM, Matias Montroull <matimontg at gmail.com>
>> > wrote:
>> >>
>> >> Hi Bill,
>> >>
>> >> I've downloaded and compiled ITK in a directory and FLTK as well
>> >>
>> >> Regards,
>> >>
>> >> Matias.
>> >>
>> >> On Fri, Dec 19, 2014 at 10:34 AM, Bill Lorensen
>> >> <bill.lorensen at gmail.com>
>> >> wrote:
>> >>>
>> >>> Are you using the superbuild to build itk and vtk or are you pointing
>> >>> to your own itk and vtk?
>> >>>
>> >>>
>> >>> On Fri, Dec 19, 2014 at 8:16 AM, Matias Montroull
>> >>> <matimontg at gmail.com>
>> >>> wrote:
>> >>> > Hi,
>> >>> >
>> >>> > I downloaded ITK Apps from GIT and generated the .sln in Visual
>> >>> > Studio
>> >>> > (2012) with Cmake.
>> >>> >
>> >>> > Now, this particular example: MRIRegistration is not included in the
>> >>> > build
>> >>> > directory, any reason why this is happening?
>> >>> >
>> >>> > Thank you,
>> >>> >
>> >>> > Matias.
>> >>> >
>> >>> > _____________________________________
>> >>> > 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
>> >>> >
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> Unpaid intern in BillsBasement at noware dot com
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com



-- 
Unpaid intern in BillsBasement at noware dot com

From matt.mccormick at kitware.com  Fri Dec 19 17:59:20 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 19 Dec 2014 17:59:20 -0500
Subject: [ITK-users] [ANNOUNCE] ITK 4.7.0 has been released!
Message-ID: <CALzTN-Q_pjUi86hX8THZp70oi4e5qqt0HtTmCG3EP+gARq+NOQ@mail.gmail.com>

On behalf of the Insight Toolkit community, we are proud to announce
that ITK 4.7.0 has been released!

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

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

Outline
----------

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

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

The 4.7 release is a major milestone that marks the hard work of many
outstanding community members. Congratulations and well done to the 29
contributors to this release. We would especially like to recognize
the new contributors, Gert Wollny, Girish Mallya, Christopher Mullins,
Umang B, David T. Chen, Danny Perry, Johan Andruejol, and Ismael
Belghiti.

Among the major contributions in this release: all ITK examples from
the Software Guide, Wiki Examples, and SphinxExamples are new indexed
and crossed linked in Doxygen -- when you visit the Doxygen page for
your favorite filter or other object, say the ResampleImageFilter,
there is a large selection of examples in the Examples section. TIFF
IO has undergone a significant cleanup and speed-up, and TIFF tags are
now read into the Image?s MetaDataDictionary. Three new Remote Modules
are available, for gradient computation, DICOM IO, and QuadEdgeMesh
filtering. Python wrapping, CMake configuration, and registration
continue to improve. A new, experimental thread pool is available --
to enable set the ITK_USE_THREADPOOL or call
itk::MultiThreader::SetGlobalDefaultUseThreadPool(true).

Thanks to everyone for their hard work!

Enjoy ITK!


New Features
------------------
* Documentation Improvements
  - Update Software Guide registration examples to ITKv4 framework
  - Wiki and Sphinx examples are indexed in Doxygen
  - Clean Software Guide dashboard build

* Filtering Improvements
  - New Laplacian deformation filter?s for QuadEdgeMesh?s
    - IJ article: http://hdl.handle.net/10380/3410
 - FFTComplexToComplexImageFilter out of Review, Vnl, FFTW implementations
 - Faster recursive Gaussian on VectorImage

* ImageIO improvements
  - PNG sCAL unit support
  - TIFF IO performance greatly improved
  - TIFF tags read into Image MetaDataDictionary
  - MetaIO updated
  - Better support for system GDCM

* Infrastructure improvements
  - New method to erase a MetaDataDictionary entry
  - New global method to set physical space tolerance
  - New, experimental thread pool support
  - NumericTraits::Zero and ::One are deprecated in favor of
::ZeroValue() and ::OneValue()
  - VTK bridge modules only request required VTK modules

* New Remote Modules
  - Higher Order Accurate Gradient
    - http://hdl.handle.net/10380/3231
  - IO Transform DCMTK
    - http://hdl.handle.net/10380/3468
  - Subdivision Quad Edge Mesh Filters
    - http://hdl.handle.net/10380/3307

* Registration improvements
  - LandmarkBasedTransformInitializer supports BSplineTransform
  - Transverse inverse consistency increased
  - Automatic initialization of the transform center for multi-stage
registrations
  - Sparse point B-spline field estimate
  - Mutual information faster, lower memory usage

* Wrapping improvements
  - Wrapping now builds without type warnings
  - pygccxml bumped to 1.6.2
  - Latest GCCXML
  - CMake wrapping infrastructure cleanup
  - Build with Ninja CMake generator
  - New GetTypes() and GetTypesAsList() methods
  - ITK_WRAP_PYTHON is exposed in ITKConfig.cmake

* Many style improvements -- ITK gets more stylish with every release!

* Improved code coverage -- we are over 85%!

* *Lots* of important bug fixes

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


List of changes since v4.7-rc02
-----------------------------------------

Bradley Lowekamp (1):
      BUG: IOFDF remote module should stay with InsightConsortium repo

Christopher Mullins (3):
      DOC: Fix code overlapping figure
      STYLE: Keep the text in the margins
      STYLE: Put newline before long doxygen reference

Cory Quammen (1):
      BUG: Fix segfaults in ITKExamples

Matthew McCormick (8):
      BUG: Reset ITK_MODULES_REQUESTED to all modules with multiple calls.
      BUG: Configure against VTK 5.
      COMP: Add ITK_SOURCE_DIR to doxygen EXAMPLE_PATH.
      COMP: Increase DOT_GRAPH_MAX_NODES.
      DOC: Add Doxygen macros for itkSetGetDecoratedObjectMacro.
      ENH: Warning when reading a PNG with UNKNOWN unit and non-unit spacing.
      BUG: Fix VTK5 module export code.
      BUG: Fix LevelSetsv4Visualization VTK variable names.

Michka Popoff (1):
      DOC: Improvements for Book1, Chap4


List of changes since v4.7-rc01
-----------------------------------------

Ali Ghayoor (1):
      DOC: Revise the registration examples of ITKSoftwareGuide

Arnaud Gelas (3):
      ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module
      COMP: address clang -Winconsistent-missing-override in ITKQuadEdgeMesh
      COMP: fix warnings on dashboard for Subdivision remote module

Bradley Lowekamp (5):
      BUG: Fix segfault when setting displacement field as null
      BUG: Don't enable SSE rounding with OSX and gccxml
      BUG: Add portable access to Tiff field name
      BUG: Fix conversion compilation error
      BUG: Rename remote module FDFImageIO -> IOFDF

Christopher Mullins (6):
      STYLE: Fix line length in OpenJPEG license for 80 character.
      DOC: Finish the ImageLinearIteratorWithIndex example.
      DOC: Text and picture problems, book2
      BUG: Fix text in margin issues
      DOC: Edits for the beginning of chapter 5, Statistics
      DOC: Fix empty code block.

Cory Quammen (1):
      COMP: Avoid including VTK_USE_FILE within ITK

Kent Williams (1):
      ENH: Add test to exercise issue with Transform::GetInverse

Matthew McCormick (7):
      BUG: Register AzimuthElevationToCartesianTransform to factories.
      DOC: Update texture feature class references.
      BUG: Fix texture feature correlation computation for constant image.
      STYLE: Put ImageToImageFilterCommon in its own file.
      BUG: Wrap ImageToImageFilterCommon.
      STYLE: Put ImageSourceCommon in its own file.
      COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon.

Michka Popoff (1):
      ENH: Add CVD and CVF types to
VectorIndexSelectionCastImageFilter wrappings

Ziv Yaniv (1):
      COMP: fixed warnings from gcc4.1.2, made implicit casts explicit



List of changes since v4.6.0
--------------------------------------

Alexander Schmidt-Richberg (1):
      ENH: Updated Remote Module VariationalRegistration to new git tag

Ali Ghayoor (10):
      ENH: Make ITKv4 compatible with ITKSoftwareGuide
      ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4
      ENH: Convert three ImageRegistration Examples to ITKv4
      ENH: Add multi-Res and multistage registration Examples to ITKv4
      ENH: Convert DeformableReg examples to ITKv4 reg framework
      BUG: Expand a test to reflect multi-metric registration bug
      BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4
      ENH: Add direct initialization to SyN registration
      ENH: Direct initialization of SyN by restoring the state
      ENH: LandmarkBasedTransformInitializer supports BSplineTransformType

Arnaud Gelas (15):
      COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization
      ENH: Importing Laplacian Deformation for QuadEdgeMesh
      DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage
      ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified()
      ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter
      BUG: fix gdcm version in GDCMImageIO.
      COMP: missing cast when calling gdcm::DataElement::SetByteValue
      COMP: missing cast when calling gdcm::DataElement::SetByteValue
      ENH: increase LaplacianDeformation code coverage
      STYLE: use typedef rather than inheritance
      BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false
      BUG: split include directories into appropriate cmake variables HDF5
      BUG: missing gdcm libraries when using system GDCM
      DOC: fix doxygen documentaiton for
itk::LaplacianDeformationQuadEdgeMeshFilter
      ENH: Add one method to erase a tag into MetaDataDictionary

Bill Lorensen (5):
      ENH: Specify required VTK modules
      COMP: Wiki examples require additional vtk modules
      ENH: Modify WikiExamples remote config
      COMP: Bad test signature
      COMP: Update tag for wiki examples

Brad King (6):
      COMP: Fix vxl_config_macros usage of CMake check macros
      ENH: Use if(DEFINED) to simplify conditions
      COMP: Fix vxl_config_macros checks broken by refactoring
      COMP: Fix one more vxl_config_macros check broken by refactoring
      BUG: Fix itk_module_config for repeated calls
      BUG: Fix itk_module_config for repeated calls

Bradley Lowekamp (52):
      ENH: Adding License file from upstream MetaIO
      ENH: Adding script to update MetaIO from upstream
      ENH: Remove ITK MetaIO to prepare for upstream import
      PERF: Remove dynamically allocated temporary in evaluate method
      COMP: Fix variable type for Set/Get macros
      BUG: Implement ITK Style Singleton design pattern
      ENH: Add no throw exception specification for UnRegister methods
      COMP: Must specify order as "noexcept override"
      BUG: Add GetInverse for IdentityTransform
      ENH: Adding SetIdentity method to base DisplacementField class
      BUG: Remove unused redefinition of NULL
      BUG: Don't print to std::cout in PrintSelf
      ENH: Prefer the PrintSelfObjectMacro for printing nested objects
      BUG: Use METER of sCAL scale unit
      BUG: Use PNG_SCALE_METER for PNG sCAL unit
      BUG: Use METER of sCAL scale unit
      BUG: Use PNG_SCALE_METER for PNG sCAL unit
      COMP: Fix signed to unsigned int comparison
      BUG: Fix overflows computing size of read tiff image
      ENH: Extract TiffReaderInternal to separate file
      ENH: Refactor ReadTwoSamplePerPixelImage into template function
      ENH: Refactor GenericReadImage into template function
      BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO )
      ENH: Refactor method to convert RGBA image to output buffer
      ENH: Refactor duplicated code to read a page
      BUG: Fix right oriented tiff images
      BUG: Remove dead separated plannar code, add test
      STYLE: Fix minor kwstyle defects in test and test results
      BUG: Use array delete operator for array new allocations
      ENH: add arbitrary TIFF TAGs to meta-data dictionary
      ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
      BUG: Address Coverity warning about null pointer dereferences
      ENH: Remove support for TIFF tile as 3D and dead code
      ENH: RGBA read images should stay unchanged.
      BUG: Override method to MakeOutput by name
      ENH: Refactor per pixel conversion function to per scan-line method
      PERF: Refactor color table lookup
      BUG: Adding missing parentheses around boolean expression
      ENH: adding TIFFImageIO test for RGB palette images
      PERF: Improve recursive Gaussian perfromance with VectorImages
      ENH: Query libtiff to determine compression support
      BUG: Support TIFF tiled image with TIFFReadRGBAImage
      BUG: Use SizeValueType for length of scanline
      PERF: Store causal results directly in output buffers
      COMP: Add explicit conversion to const char
      COMP: Explicitly add override to GetNameOfClass method
      COMP: Address internal segmentation fault with Intel compiler
      ENH: Adding method to set global physical space tolerance
      COMP: Explicitly add override to GetNameOfClass method
      BUG: Add new TypeMacro for non-overloaded classes
      BUG: Fix obscure race condition on access thread pool initialization
      BUG: Updating FDFImageIO remote module

Christopher Mullins (15):
      COMP: Allows latex to compile for ITKSoftwareGuide
      COMP: Allows latex to compile for ITKSoftwareGuide
      COMP: Wrap MeshBase templates
      COMP: Wrap MeshBase templates
      COMP: Fix warning in BlockMatchingImageFilter
      STYLE: Line lengths in examples should be no longer than 80 chars.
      COMP: Wrap the remaining MeshBase and MeshToMeshFilter types.
      COMP: Fix LaTeX warnings.
      STYLE: Fix formatting/punctuation errors.
      STYLE: Formatting and punctuation fixes.
      DOC: Edits for Book 2 Chapter 1 documentation in the Examples.
      DOC: Edits for book 2 chapter 2.
      DOC: More chapter 2 edits
      DOC: Book 2 Chapter 3 edits (part 1)
      DOC: book 2 chapter 4 Segmentation edits

Danny Perry (2):
      BUG: adding test for vnl_sparse_matrix::mult()
      BUG: size of q buffer should actually be (this->rows())*pcols.

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

Dirk Padfield (1):
      BUG: Corrected processing of last sigma

GCC-XML Upstream (1):
      ENH: pygccxml v1.6.2 (reduced)

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 (24):
      COMP: Add tolerance for comparing floating point
      PERF: Remove non-threadable algorithm components
      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
      BUG: Syntax error in comment
      PERF: Add non-blocking mutex locking.
      ENH: Use TryLock minimize thread stalls
      BUG: ThreadedIndexedContainerPartitioner is inclusive
      STYLE: Remove include_regular_expression from Examples
      BUG: Demonstrate Inv(Inv(T)) != T
      BUG: Ensure Inv(Inv(T)) == T for transforms
      COMP: Valgrind detects uninitialized memory read
      COMP: Missing required base class API component
      ENH: Expand interface for selecting threadpool

Ismael Belghiti (1):
      DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter

Jim Miller (1):
      STYLE: Removing what appears to be a temporary file

Johan Andruejol (1):
      ENH: Fix normalization for null vectors and return the norm

Jon Haitz Legarreta (1):
      ENH: New test for itkLabelShapeOpeningImageFilter

Kent Williams (9):
      COMP: use find_package(VTK COMPONENTS) to specify just needed
VTK Components
      BUG: ImageSources/test/CMakeLists.txt incorrect library var reference
      COMP: Fix coverity defects related to RegistrationV4 examples
      COMP: silence warning of vnl_vector_fixed_ref::assert_size
      COMP: Fix various Coverity warnings
      COMP: Fix a typo in an error message print statement.
      COMP: itk::Command-derived class used pointless dynamic_cast.
      PERF: Don't recompute InternalInverse repeatedly
      COMP: Correct orientation/spacing for Philips MultiFrame

Mark Hiner (2):
      ENH: Update SCIFIO remote module hash
      BUG: Fix duplicate variables in Windows

Matthew McCormick (105):
      DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro.
      ENH: Move FFTComplexToComplexImageFilter out of Review.
      ENH: Add VnlComplexToComplexFFTImageFilter.
      BUG: Use fixed seed for Vnl FFT tests for repeatibility.
      ENH: Bump CMakeLists.txt version to 4.7.0.
      BUG: ArchiveTestingData.py future imports must occur at the beginning.
      BUG: Do not run vnl_test_na with broken libc++.
      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.
      DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx.
      DOC: Remove duplicate text in LaplacianRecursiveGaussian example.
      BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter.
      BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest.
      STYLE: Fix style in VoronoiDiagram2D.
      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
      BUG: Bump GCCXML to 2014-08-06.
      BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}.
      BUG: Fix Win MultiThreader check for successful process creation.
      BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor.
      COMP: Fix ImageRegistration8RegisteredSlice.png baseline name.
      DOC: itk::statistics -> itk::Statistics.
      COMP: Fix transform type for ITKv3/IterativeClosestPoint2.
      BUG: Fix invalid assignment of second VoronoiBoundaryOrigin.
      COMP: Improve const correctness of GradientRecursiveGaussianImageFilter.
      BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches().
      BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's.
      COMP: ThreadJob NULL not defined.
      BUG: Fix alpha assignment for RGBA TIFF.
      COMP: Remove unused typedefs in LevelSetsv4Visualization.
      COMP: Remove unused typedef's in VtkGlue.
      ENH: Mark BSplineWarping2Test as RUNS_LONG.
      BUG: Fix Nifti IO read with large images.
      COMP: Remove call for non-existent variable in Nifti debugging.
      BUG: Close the file on Read and Write in HDF5TransformIO.
      BUG: Remove InsightLegacy test code from TransformHDF5Test.
      ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}.
      STYLE: Use SeriesUIDContainerType and FileNamesContainerType
      ENH: Allow specification of orthogonality tolerance in rigid transforms.
      BUG: TransformFileReader does not clear its TransformList.
      BUG: Prevent dangling pointer in HDF5TransformIO.
      COMP: Do not use _stat64 with MinGW-32.
      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.
      COMP: Address LaplacianDeformation Doxygen warnings.
      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
      COMP: Do not wrap the FixedArray of Image SmartPointer's.
      COMP: Add missing wrapping for TransformIOBaseTemplate.
      COMP: Mark DeformableRegistration6Test as RUNS_LONG.
      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.
      BUG: Use -py3 when building wrapping for Python 3.
      COMP: Add missing wrapping for TransformIOBaseTemplate.
      DOC: Improve ImageRegistration4 grammar.
      ENH: Add IOTransformDCMTK Remote module.
      BUG: gdcm::StringFilter recognizes backslash delimiter.
      DOC: Add migration guide for GDCM Rescale slope intercept apply on write.
      COMP: Remove unused typedef's in GPU code.
      STYLE: Improve style of HoughTransform2DLinesImageFilter example.
      COMP: Use ConceptChecking for IterativeInverse dimension check.
      COMP: Wrap TransformIOBaseTemplate for const SmartPointer.
      COMP: Add warning exceptions for third party pcre, swig, gccxml.
      ENH: Bump ITK version to 4.6.1.
      BUG: Add missing ITK_OVERRIDE to ITKImageeSources module.
      BUG: Remove GaussianImageSource members shadowing GenerateImageSource.
      STYLE: Style fixes to ITKImageSources module.
      BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType.
      BUG: Do not perform itk_download_attempt_check when not building ITK.
      DOC: Update GDCMImageIO rescale slope intercept doc.
      BUG: Only register requestion IO COMPONENT modules.
      BUG: Fix wrapping .i, .idx CMake dependencies.
      COMP: Add VTK Python module when wrapping ITKVtkGlue.
      STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator.
      STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef.
      COMP: Add missing VTK module dependency for LevelSetsv4Visualization.
      BUG: By default, do not create any fixed parameters.
      STYLE: Remove trivial method comments in itkTransform.hxx.
      BUG: PolylineMask Filter's GenerateData is protected / virtual.
      ENH: Add HigherOrderAccurateGradient Module.
      BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal.
      COMP: Remove extra semi-colon, variable scope in DCMTKFileReader.
      STYLE: Style fixes for Transform classes.
      DOC: Increase Doxygen LOOKUP_CACHE_SIZE.
      BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe.
      DOC: Index Wiki examples with Doxygen.
      COMP: Bump SphinxExamples remote module.
      DOC: Index Sphinx examples in Doxygen.
      COMP: Remove old java examples.
      COMP: Remove duplicate DiffusionTensor3DReconstruction example reference.
      COMP: Address GradientAnisotropicDiffusionImageFilter example settings.
      COMP: Bump Sphinx Examples remote.
      COMP: Bump WikiExamples remote.

MetaIO Maintainers (1):
      MetaIO (reduced)

Michka Popoff (40):
      ENH: Fixes for python 3 support
      BUG: Add VTK_VERSION for older VTK versions
      BUG: Improve SWIG version check
      COMP: Add wrapping for ThreadPool and ThreadJob
      COMP: Remove unimplemented DestroyPool method
      COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping
      COMP: Do not hide pygccxml warnings
      ENH: Update links in readme file
      BUG: Improve SWIG version check
      BUG: Add VTK_VERSION for older VTK versions
      STYLE: Remove trailing whitespaces
      STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP
      BUG: Fix memory leak in MetaImageIO after exception
      ENH: Add script to update pygccxml from upstream
      BUG: Update VTK minimum version (for release)
      BUG: Fix memory leak in MetaImageIO after exception
      ENH: Remove Sun OS compatibility for the wrappings
      COMP: Fix for conversion to non-pointer like type warning
      STYLE: LabelObject style
      DOC: Remove broken link from LabelObject class description
      ENH: Do not setup the python tests if not asked
      ENH: Add new GetTypes() and GetTypesAsList() methods to the template class
      COMP: Fix CMP0054 warnings in wrappings
      STYLE: Remove old cmake < 2.8.4 specific code
      STYLE: Remove old cmake < 2.8.5 specific code
      ENH: Update to PCRE 8.36
      COMP: Refactor Wrapping setup and fix legacy warnings
      ENH: Add wrapping configuration to ITKConfig.cmake
      STYLE: Some minor code cleanup in the wrapping setup
      DOC: Fix typo in RelabelComponentImageFilter
      ENH: Deprecate VectorResampleImageFilter
      DOC: Add migration guide for ::Zero and ::One
      ENH: Deprecate ::Zero and ::One
      ENH: Add option to disable sorting by size in
itkRelabelComponentImageFilter
      ENH: Add Vector and RGB wrapping to linear interpolator
      STYLE: Remove SORT macro in wrappings
      COMP: Fix warning for InterpolateImageFunction wrapping
      COMP: Add a check for Blocks in GPU module
      COMP: Bump SCIFIO to fix test build warnings
      COMP: Fix wrapping of itkImageFunctionBase

Nick Tustison (7):
      BUG:  Need to explicitly specify spline order.
      ENH:  Initializing the transform center.
      BUG:  Need to check the dynamic cast before any calls.
      ENH:  Adding modifications for point set metrics.
      BUG:  Need to specify TInternalComputationValueType for default metric.
      ENH:  Adding sparse points to B-spline field estimate.
      BUG:  Uninitialized variables.

Richard Beare (1):
      ENH: Include TIFF tags in the MetaDataDictionary

Taylor Braun-Jones (1):
      BUG: Fix SliceBySliceImageFilter doesn't propagate information internally

Umang B (1):
      ENH: Use thread pool to dispatch multithreading tasks

Vivien Delmon (2):
      BUG: ExtractImageFilter::CollapseToSubMatrix fix
      ENH: Add a test on extracted directions in CollapseToSubMatrix mode

Vladimir S. FONOV (1):
      BUG: Fixing incorrect MINC style inverse transform


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

Arnaud Gelas (12):
      add one example to translate one itk::Image
      add PasteImageFilter example
      fix path in ArchiveBinaryData.py.in
      BUG: error when TEST_IMAGE_PREFIX was used
      fix broken links as detected by linkcheck
      add example for PermuteAxesImageFilter
      Add one example to apply an affine transform given homogeneous matrix
      Add one example to multiply 2 images
      use ITK 4.6.1 for superbuild
      update breathe to 3.1.0
      Add one example to generate slices from volume
      Add one example about RegionOfInterestImageFilter

Brad King (1):
      setup-hooks: Create .git hooks directory if necessary

Matt McCormick (15):
      ENH: Bump ITK Superbuild tag to 4.6.0.
      BUG: Fix ConvertAnITKGrayScaleImageToCVMat compare_to_baseline.
      COMP: Remove breathe link to ConstantPadImageFilter.
      BUG: Fix figure path for Iterative Hole Filling.
      BUG: Evolution.gif needs to be ..only:: html
      COMP: Content not permitted in image:: directive.
      BUG: Require CMake 2.8.6 in CreateNewExample template.
      BUG: Update CreateNewExample.py for new compare_to_baseline syntax.
      COMP: Fix ITKMathematicalMorphology COMPONENT dependency.
      COMP: Fix build as a Remote module.
      COMP: Fix fresh configuration as an ITK module.
      COMP: Fix configuration ITK_WRAP_PYTHON is not defined.
      BUG: Annotate ReadUnknownImageType component type correctly.
      ENH: Bump Superbuild VTK version to 6.1.0.
      ENH: Bump Superbuild ITK version to 4.7.0.

Michka Popoff (15):
      COMP: Fix failing setup of SegmentBloodVessels example
      STYLE: Update title for Apply Affine Transform example
      ENH: Add GeodesicActiveContourLevelSetImageFilter example
      COMP: Fix failing MultiplyTwoImagesTestBaselineComparison test
      COMP: Add images to the MultiplyTwoImages documentation
      COMP: Fix and improve ForwardFFTExample
      COMP: Fix Multiply two images output
      COMP: Update all cmake versions to 2.8.6
      COMP: Fix MultiplyTwoImagesTestBaselineComparison
      ENH: Add infrastructure for Python tests
      ENH: Add example on how to resample a RGB image
      BUG: Add missing images to ResampleAVectorImage documentation
      COMP: Fix path for favicon
      COMP: Fix for CleanQuadEdgeMesh documentation
      BUG: Add missing semicolon to example


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

Ali Ghayoor (4):
      ENH: Part one of converting Registration chapter to ITKv4
      ENH: Part two of converting Registration chapter to ITKv4
      ENH: Part three of converting Registration chapter to ITKv4
      DOC: Revise the registration chapter

Christopher Mullins (16):
      COMP: Use RegistrationITKv3 examples with ITKv3_COMPATIBILITY
      STYLE: Use minted to highlight code syntax
      DOC: Add instructions for using ITK from python
      COMP: Sort and run the examples topologically.
      COMP: add_custom_command no longer takes SOURCE parameter
      STYLE: Fix python indentation
      COMP: BuildTexFiles target should depend on SoftwareGuideExamples
      COMP: Update the .eps generation command to use the OUTPUT signature.
      STYLE: Fix quotes.
      DOC: Language edits mostly from Book 2
      ENH: Only flip the images we want to flip
      BUG: Figure overlaps text in 4.3.
      DOC: More language fixes, use minted instead of code tags.
      STYLE: Put a new line before code blocks
      STYLE: Fix margin problems with filenames and floating figure overlaps
      STYLE: Change margins using the geometry package.

Hans Johnson (1):
      ENH: Bring ITK code closer to the 4.7 release code

Matt McCormick (25):
      ENH: Pass PDF_QUALITY_LEVEL in superbuild.
      BUG: Remove unused RunExamples.py imports.
      ENH: Reduce verbosity of RunExamples.py.
      BUG: Do not include RegistrationITKv4 example sources in the build.
      BUG: Fix caption on Confidence Connectened on BrainWeb figures.
      BUG: Bump the ITK superbuild for LaTeX fixes.
      ENH: Add new ISBN numbers.
      DOC: CDash has replaced Dart.
      DOC: itk::statistics -> itk::Statistics.
      ENH: Update ITK logo.
      STYLE: Remove box around CC logo.
      DOC: Document instructions for building from the Docker image.
      DOC: Docker build instruction improvements.
      ENH: New path for starting the docker environment.
      ENH: Change paper size.
      COMP: Improve arguments for GradientAnisotropicDiffusionImageFilter.
      ENH: Bump ITK Superbuild version to 2014-12-03.
      BUG: Add flags for PDF_QUALITY_LEVEL STREQUAL ""
      ENH: Add contributors for print release.
      ENH: Upsample when building with PDF_QUALITY_LEVEL "Printer".
      BUG: Specify cc-by logo size explicitly.
      BUG: Use original ITK configuration images.
      ENH: Use file(COPY to copy over .eps images.
      ENH: Margin tightening.
      ENH: Bump ITK ExternalProject to v4.7.0.

Michka Popoff (5):
      ENH: Use the new licence file for MetaIO
      DOC: Fixes for the ITK 4.7 book
      DOC: Fixes for book1, part1, chapter 2
      DOC: Fixes and improvements for Book 1, chapter 3
      DOC: Minor fixes for Book 1, Chapter 4

Sandy McKenzie (1):
      STYLE: Add new line before code block


ITKApps Changelog
---------------------------

Bill Lorensen (1):
      COMP: Update CTEST_DROP_SITE

Matt McCormick (4):
      COMP: Use ::ZeroValue() instead of ::Zero.
      COMP: Patch FLTK for build against newer freetype.
      COMP: Address %d type for VolviewPlugins.
      ENH: Bump ITK Superbuild version to v4.7.0.

From matt.mccormick at kitware.com  Fri Dec 19 19:47:39 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 19 Dec 2014 19:47:39 -0500
Subject: [ITK-users] [Insight-users] [ITK-USER]Compile ITK3.20.1 with
	VS2012
In-Reply-To: <CAPf2UMSOHWdGv-0gb+tzuDg15LG7W8HL7MOPtOdnC4084n3Atg@mail.gmail.com>
References: <CAA4xxgbWyEj0BTUtVJtQo8NZt9Wp8V_mDExzP87AzhyUP+Pifg@mail.gmail.com>
 <DFB2170F-8DD6-4B6E-8891-EB202F651BF1@mail.nih.gov>
 <CAPf2UMSOHWdGv-0gb+tzuDg15LG7W8HL7MOPtOdnC4084n3Atg@mail.gmail.com>
Message-ID: <CALzTN-QcQYviH92LF66Nv_hRJr1cK2wQhFeX4CQ=39D3XXKQ+w@mail.gmail.com>

Hi,

Dzenan sent a patch for building ITKv3 with Visual Studio 2013.  It
has been pushed to Git "release-3.20" branch.

For more information on ITK's Git, see [1].

Thanks,
Matt

[1] http://www.itk.org/Wiki/ITK/Git

On Fri, Dec 19, 2014 at 1:34 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
> Probably too late for JX, but I found a solution. When configuring ITK with
> CMake, in the field CMAKE_CXX_FLAGS add the following:
> /D_ALLOW_KEYWORD_MACROS
> Article which helped me:
> http://mostlybuggy.wordpress.com/2012/12/18/getting-around-vs2012-c1189c4005-keyword-re-defined-in-macros/
>
>
> On Wed, May 29, 2013 at 9:33 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>>
>> Hi,
>>
>> Why no upgrade to ITK v4?
>>
>> ITK v3.20 was released in 2010, well before Visual Studio 2012. So it
>> should be no surprise it does not work with it. I believe VS 2010 should
>> work with it, and VS9, and VS8, and VS7....
>>
>>
>> Brad
>>
>>
>>
>> On May 28, 2013, at 10:41 PM, JX NIE <njx937 at gmail.com> wrote:
>>
>> > Hi Everyone,
>> >     I have tried to compile ITK(version 3.20.1 ) with VS2012, but
>> > failed.
>> >     It has ended up with a lot of  Redifine errors as follow.
>> >    Could you please tell me how to solve this compile problem.
>> >    Regards,
>> >
>> > NIE JUNXIAO
>> >
>> >
>> > >C:\Program Files (x86)\Microsoft Visual Studio
>> > > 11.0\VC\include\xkeycheck.h(242): fatal error C1189: #error :  The C++
>> > > Standard Library forbids macroizing keywords. Enable warning C4005 to find
>> > > the forbidden macro.
>> >
>> >       1       IntelliSense: #error directive: The C++ Standard Library
>> > forbids macroizing keywords. Enable warning C4005 to find the forbidden
>> > macro. c:\Program Files (x86)\Microsoft Visual Studio
>> > 11.0\VC\include\xkeycheck.h      242
>> >       2       IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\sal.h    2367
>> >       3       IntelliSense: expected a declaration    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\vadefs.h 139
>> >       4       IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        437
>> >       5       IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        446
>> >       6       IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        464
>> >       7       IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        475
>> >       8       IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        476
>> >       9       IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        497
>> >       10      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        501
>> >       11      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        506
>> >       12      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        514
>> >       13      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        571
>> >       14      IntelliSense: attribute "noreturn" does not apply here
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h
>> > 572
>> >       15      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        572
>> >       16      IntelliSense: attribute "noreturn" does not apply here
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h
>> > 575
>> >       17      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        576
>> >       18      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1979
>> >       19      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1980
>> >       20      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1981
>> >       21      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1982
>> >       22      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1983
>> >       23      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1985
>> >       24      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1992
>> >       25      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        1999
>> >       26      IntelliSense: expected a declaration    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\crtdefs.h        2023
>> >       27      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  510
>> >       28      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  528
>> >       29      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  529
>> >       30      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  542
>> >       31      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  576
>> >       32      IntelliSense: invalid destructor declaration    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  577
>> >       33      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  583
>> >       34      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  585
>> >       35      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  586
>> >       36      IntelliSense: explicit type is missing ('int' assumed)
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  588
>> >       37      IntelliSense: identifier "EMIT" is undefined    c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  588
>> >       38      IntelliSense: function "_Lockit" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  589
>> >       39      IntelliSense: reference variable "EMIT" requires an
>> > initializer c:\Program Files (x86)\Microsoft Visual Studio
>> > 11.0\VC\include\yvals.h  589
>> >       40      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  591
>> >       41      IntelliSense: expected a declaration    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  606
>> >       42      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  693
>> >       43      IntelliSense: expected a declaration    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  726
>> >       44      IntelliSense: expected a declaration    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  729
>> >       45      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  740
>> >       46      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\yvals.h  741
>> >       47      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 23
>> >       48      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 47
>> >       49      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 48
>> >       50      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 49
>> >       51      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 50
>> >       52      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 54
>> >       53      IntelliSense: identifier "errno_t" is undefined c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 56
>> >       54      IntelliSense: variable "memcpy_s" may not be initialized
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 56
>> >       55      IntelliSense: expected a ')'    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 56
>> >       56      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 93
>> >       57      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 97
>> >       58      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 98
>> >       59      IntelliSense: identifier "errno_t" is undefined c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 103
>> >       60      IntelliSense: variable "_strset_s" may not be initialized
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 103
>> >       61      IntelliSense: expected a ')'    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 103
>> >       62      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 104
>> >       63      IntelliSense: identifier "errno_t" is undefined c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 107
>> >       64      IntelliSense: variable "strcpy_s" may not be initialized
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 107
>> >       65      IntelliSense: expected a ')'    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 107
>> >       66      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 109
>> >       67      IntelliSense: identifier "errno_t" is undefined c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 112
>> >       68      IntelliSense: variable "strcat_s" may not be initialized
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 112
>> >       69      IntelliSense: expected a ')'    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 112
>> >       70      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 114
>> >       71      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 116
>> >       72      IntelliSense: expected a ')'    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 117
>> >       73      IntelliSense: variable "strnlen" may not be initialized
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 121
>> >       74      IntelliSense: expected a ')'    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 121
>> >       75      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 123
>> >       76      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 135
>> >       77      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 142
>> >       78      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 148
>> >       79      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 149
>> >       80      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 150
>> >       81      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 151
>> >       82      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 152
>> >       83      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 153
>> >       84      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 154
>> >       85      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 155
>> >       86      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 156
>> >       87      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 157
>> >       88      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 158
>> >       89      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 159
>> >       90      IntelliSense: variable "strcspn" may not be initialized
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 160
>> >       91      IntelliSense: expected a ')'    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 160
>> >       92      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 161
>> >       93      IntelliSense: identifier "errno_t" is undefined c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 162
>> >       94      IntelliSense: variable "_strerror_s" may not be
>> > initialized     c:\Program Files (x86)\Microsoft Visual Studio
>> > 11.0\VC\include\string.h 162
>> >       95      IntelliSense: expected a ')'    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 162
>> >       96      IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 163
>> >       97      IntelliSense: identifier "errno_t" is undefined c:\Program
>> > Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 166
>> >       98      IntelliSense: variable "strerror_s" may not be initialized
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 166
>> >       99      IntelliSense: expected a ')'    c:\Program Files
>> > (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 166
>> >       100     IntelliSense: variable "EMIT" is not a type name
>> > c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\include\string.h 168
>> >
>> > <CMakeCache.txt>_____________________________________
>> > 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://www.itk.org/mailman/listinfo/insight-users
>>
>> _____________________________________
>> 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://www.itk.org/mailman/listinfo/insight-users
>
>
> _____________________________________
> 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
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From kevin.keraudren10 at imperial.ac.uk  Sat Dec 20 05:24:58 2014
From: kevin.keraudren10 at imperial.ac.uk (Kevin Keraudren)
Date: Sat, 20 Dec 2014 10:24:58 +0000
Subject: [ITK-users] Medical Image Analysis IPython Notebooks
Message-ID: <54954E7A.3050503@imperial.ac.uk>

Hi,

The IPython notebooks used for the tutorials in the Medical Image 
Analysis course at Imperial College London are now on github:
https://github.com/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials

These might be of interest to the mailing list as they rely on SimpleITK 
and could be useful either as teaching material or example applications.

They can be browsed directly in nbviewer:
http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/tree/master/

The following blog post is a quick presentation of the github repository:
http://kevin-keraudren.blogspot.co.uk/2014/12/medical-image-analysis-ipython-tutorials.html

Please do not hesitate to let us  know if you have questions or comments 
regarding these tutorials.

Kind regards,

Kevin Keraudren,
PhD student, Imperial College London
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From blowekamp at mail.nih.gov  Mon Dec 22 09:26:11 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 22 Dec 2014 09:26:11 -0500
Subject: [ITK-users] Medical Image Analysis IPython Notebooks
In-Reply-To: <54954E7A.3050503@imperial.ac.uk>
References: <54954E7A.3050503@imperial.ac.uk>
Message-ID: <B97C13C1-82C0-473B-B4A4-85D5E59B1913@mail.nih.gov>

Hello Kevin,

These notebooks look outstanding. Thank you very much for sharing.

I very much like what you did here:
http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/blob/master/tutorial_2/basics_reg.ipynb
to illustrate the different metrics' values, and the impact of apply Gaussian smoothing to the images.

Also please note that you were using the an experimental version of the ImageRegistrationMethod in SimpleITK which was based on ITKv3 registration frameworks. Since then the development has evolved to be based on the ITKv4 registration framework and many, many features have been added.

This includes a couple transform initializers which estimate some basic transform parameters and very importantly set the fixed parameter for the center of the transform. Additionally the interface to the transforms is much improved.

Brad

On Dec 20, 2014, at 5:24 AM, Kevin Keraudren <kevin.keraudren10 at imperial.ac.uk> wrote:

> Hi,
> 
> The IPython notebooks used for the tutorials in the Medical Image Analysis course at Imperial College London are now on github:
> https://github.com/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials
> 
> These might be of interest to the mailing list as they rely on SimpleITK and could be useful either as teaching material or example applications.
> 
> They can be browsed directly in nbviewer:
> http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/tree/master/
> 
> The following blog post is a quick presentation of the github repository:
> http://kevin-keraudren.blogspot.co.uk/2014/12/medical-image-analysis-ipython-tutorials.html
> 
> Please do not hesitate to let us  know if you have questions or comments regarding these tutorials.
> 
> Kind regards,
> 
> Kevin Keraudren,
> PhD student, Imperial College London
> _____________________________________
> 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

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From noreply at insightsoftwareconsortium.org  Mon Dec 22 10:37:56 2014
From: noreply at insightsoftwareconsortium.org (Insight Journal)
Date: Mon, 22 Dec 2014 10:37:56 -0500 (EST)
Subject: [ITK-users] New Submission: A generic interpolator for multi-label
	images
Message-ID: <20141222153756.61A7F3D6C186@insightsoftwareconsortium.org>

Hello,

A new submission has been added to the Insight Journal.

Title: A generic interpolator for multi-label images
Authors: Schaerer J., Roche F., Belaroussi B.
Abstract: We present a generic interpolator for label images. The basic idea is to interpolate each label with an ordinary image interpolator, and return the label with the highest value. This is the idea used by the itk::LabelImageGaussianInterpolateImageFunction interpolator. Unfortunately, this class is currently limited to Gaussian interpolation. Using generic programming, our proposed interpolator extends this idea to any image interpolator. Combined with linear interpolation, this results in similar or better accuracy and much improved computation speeds on a test image.

Download and review this publication at: http://hdl.handle.net/10380/3506

Generated by the Insight Journal

You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://www.insight-journal.org/ .

From kevin.keraudren10 at imperial.ac.uk  Mon Dec 22 13:04:23 2014
From: kevin.keraudren10 at imperial.ac.uk (Keraudren, Kevin)
Date: Mon, 22 Dec 2014 18:04:23 +0000
Subject: [ITK-users] Medical Image Analysis IPython Notebooks
In-Reply-To: <B97C13C1-82C0-473B-B4A4-85D5E59B1913@mail.nih.gov>
References: <54954E7A.3050503@imperial.ac.uk>,
 <B97C13C1-82C0-473B-B4A4-85D5E59B1913@mail.nih.gov>
Message-ID: <BA8E286B8B701E4DB61241EE91B96BF51457EC8A@icexch-m2.ic.ac.uk>

Hi Brad,

I am glad the notebooks are appreciated, all the credit goes to Ozan (in copy) who is the main author!

If I understand correctly you are mentioning in your email the ImageRegistrationMethod which will be in the next release of SimpleITK (0.9.0):
  http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html
  https://github.com/SimpleITK/SimpleITK/tree/next

This will definitely be something to look at for the next iteration of these tutorials.

Kind regards,

Kevin

________________________________
From: Bradley Lowekamp [blowekamp at mail.nih.gov]
Sent: Monday, December 22, 2014 2:26 PM
To: Keraudren, Kevin
Cc: insight-users at itk.org Users; Oktay, Ozan
Subject: Re: [ITK-users] Medical Image Analysis IPython Notebooks

Hello Kevin,

These notebooks look outstanding. Thank you very much for sharing.

I very much like what you did here:
http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/blob/master/tutorial_2/basics_reg.ipynb
to illustrate the different metrics' values, and the impact of apply Gaussian smoothing to the images.

Also please note that you were using the an experimental version of the ImageRegistrationMethod in SimpleITK which was based on ITKv3 registration frameworks. Since then the development has evolved to be based on the ITKv4 registration framework and many, many features have been added.

This includes a couple transform initializers which estimate some basic transform parameters and very importantly set the fixed parameter for the center of the transform. Additionally the interface to the transforms is much improved.

Brad

On Dec 20, 2014, at 5:24 AM, Kevin Keraudren <kevin.keraudren10 at imperial.ac.uk<mailto:kevin.keraudren10 at imperial.ac.uk>> wrote:

Hi,

The IPython notebooks used for the tutorials in the Medical Image Analysis course at Imperial College London are now on github:
https://github.com/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials

These might be of interest to the mailing list as they rely on SimpleITK and could be useful either as teaching material or example applications.

They can be browsed directly in nbviewer:
http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/tree/master/

The following blog post is a quick presentation of the github repository:
http://kevin-keraudren.blogspot.co.uk/2014/12/medical-image-analysis-ipython-tutorials.html

Please do not hesitate to let us  know if you have questions or comments regarding these tutorials.

Kind regards,

Kevin Keraudren,
PhD student, Imperial College London
_____________________________________
Powered by www.kitware.com<http://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

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From matimontg at gmail.com  Mon Dec 22 13:14:32 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Mon, 22 Dec 2014 15:14:32 -0300
Subject: [ITK-users] SimpleITK | Read non dicom file and write it as series
	of slices
Message-ID: <CAKKNfuKXT-7y5OUjtZ=9jA97J+DDwLj3nDEc6a68eFt6r98miw@mail.gmail.com>

Hi,

is there an example out there similar to this but in C#:

http://www.itk.org/Doxygen/html/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html

Thank you,
Matias.
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From millerjv at gmail.com  Mon Dec 22 15:32:59 2014
From: millerjv at gmail.com (Jim Miller)
Date: Mon, 22 Dec 2014 15:32:59 -0500
Subject: [ITK-users] Medical Image Analysis IPython Notebooks
In-Reply-To: <BA8E286B8B701E4DB61241EE91B96BF51457EC8A@icexch-m2.ic.ac.uk>
References: <54954E7A.3050503@imperial.ac.uk>
 <B97C13C1-82C0-473B-B4A4-85D5E59B1913@mail.nih.gov>
 <BA8E286B8B701E4DB61241EE91B96BF51457EC8A@icexch-m2.ic.ac.uk>
Message-ID: <6CDB3AF3-447E-4A51-822B-2C9187B52A67@gmail.com>

How about we add a link to these off the ITK Wiki.  Perhaps off the page

http://itk.org/Wiki/ITK/Course_Ware


Jim

> On Dec 22, 2014, at 1:04 PM, Keraudren, Kevin <kevin.keraudren10 at imperial.ac.uk> wrote:
> 
> Hi Brad,
> 
> I am glad the notebooks are appreciated, all the credit goes to Ozan (in copy) who is the main author! 
> 
> If I understand correctly you are mentioning in your email the ImageRegistrationMethod which will be in the next release of SimpleITK (0.9.0):
>   http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html 
>   https://github.com/SimpleITK/SimpleITK/tree/next
> 
> This will definitely be something to look at for the next iteration of these tutorials.
> 
> Kind regards,
> 
> Kevin
> 
> From: Bradley Lowekamp [blowekamp at mail.nih.gov]
> Sent: Monday, December 22, 2014 2:26 PM
> To: Keraudren, Kevin
> Cc: insight-users at itk.org Users; Oktay, Ozan
> Subject: Re: [ITK-users] Medical Image Analysis IPython Notebooks
> 
> Hello Kevin,
> 
> These notebooks look outstanding. Thank you very much for sharing.
> 
> I very much like what you did here:
> http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/blob/master/tutorial_2/basics_reg.ipynb
> to illustrate the different metrics' values, and the impact of apply Gaussian smoothing to the images.
> 
> Also please note that you were using the an experimental version of the ImageRegistrationMethod in SimpleITK which was based on ITKv3 registration frameworks. Since then the development has evolved to be based on the ITKv4 registration framework and many, many features have been added.
> 
> This includes a couple transform initializers which estimate some basic transform parameters and very importantly set the fixed parameter for the center of the transform. Additionally the interface to the transforms is much improved.
> 
> Brad
> 
>> On Dec 20, 2014, at 5:24 AM, Kevin Keraudren <kevin.keraudren10 at imperial.ac.uk> wrote:
>> 
>> Hi,
>> 
>> The IPython notebooks used for the tutorials in the Medical Image Analysis course at Imperial College London are now on github:
>> https://github.com/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials
>> 
>> These might be of interest to the mailing list as they rely on SimpleITK and could be useful either as teaching material or example applications.
>> 
>> They can be browsed directly in nbviewer:
>> http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/tree/master/
>> 
>> The following blog post is a quick presentation of the github repository:
>> http://kevin-keraudren.blogspot.co.uk/2014/12/medical-image-analysis-ipython-tutorials.html
>> 
>> Please do not hesitate to let us  know if you have questions or comments regarding these tutorials.
>> 
>> Kind regards,
>> 
>> Kevin Keraudren,
>> PhD student, Imperial College London
>> _____________________________________
>> 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
> 
> _____________________________________
> 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
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From matt.mccormick at kitware.com  Tue Dec 23 00:55:18 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 23 Dec 2014 00:55:18 -0500
Subject: [ITK-users] [ITK]  Medical Image Analysis IPython Notebooks
In-Reply-To: <6CDB3AF3-447E-4A51-822B-2C9187B52A67@gmail.com>
References: <54954E7A.3050503@imperial.ac.uk>
 <B97C13C1-82C0-473B-B4A4-85D5E59B1913@mail.nih.gov>
 <BA8E286B8B701E4DB61241EE91B96BF51457EC8A@icexch-m2.ic.ac.uk>
 <6CDB3AF3-447E-4A51-822B-2C9187B52A67@gmail.com>
Message-ID: <CALzTN-QSkC6xqjigWw59BReo2dBj45HDCMxbWAzammTNhN2bNw@mail.gmail.com>

I was unaware of this wiki page (thanks!).  I added a link to that
page and a link to the course here:

  http://www.itk.org/Wiki/ITK/Documentation#Courses

This page is linked from the main ITK web page and from the
http://www.itk.org/ITK/help/documentation.html page.

Thanks again for sharing this wonderful resource! Well done!

Matt

On Mon, Dec 22, 2014 at 3:32 PM, Jim Miller <millerjv at gmail.com> wrote:
> How about we add a link to these off the ITK Wiki.  Perhaps off the page
>
> http://itk.org/Wiki/ITK/Course_Ware
>
>
> Jim
>
> On Dec 22, 2014, at 1:04 PM, Keraudren, Kevin
> <kevin.keraudren10 at imperial.ac.uk> wrote:
>
> Hi Brad,
>
> I am glad the notebooks are appreciated, all the credit goes to Ozan (in
> copy) who is the main author!
>
> If I understand correctly you are mentioning in your email the
> ImageRegistrationMethod which will be in the next release of SimpleITK
> (0.9.0):
>
> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html
>   https://github.com/SimpleITK/SimpleITK/tree/next
>
> This will definitely be something to look at for the next iteration of these
> tutorials.
>
> Kind regards,
>
> Kevin
>
> ________________________________
> From: Bradley Lowekamp [blowekamp at mail.nih.gov]
> Sent: Monday, December 22, 2014 2:26 PM
> To: Keraudren, Kevin
> Cc: insight-users at itk.org Users; Oktay, Ozan
> Subject: Re: [ITK-users] Medical Image Analysis IPython Notebooks
>
> Hello Kevin,
>
> These notebooks look outstanding. Thank you very much for sharing.
>
> I very much like what you did here:
> http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/blob/master/tutorial_2/basics_reg.ipynb
> to illustrate the different metrics' values, and the impact of apply
> Gaussian smoothing to the images.
>
> Also please note that you were using the an experimental version of the
> ImageRegistrationMethod in SimpleITK which was based on ITKv3 registration
> frameworks. Since then the development has evolved to be based on the ITKv4
> registration framework and many, many features have been added.
>
> This includes a couple transform initializers which estimate some basic
> transform parameters and very importantly set the fixed parameter for the
> center of the transform. Additionally the interface to the transforms is
> much improved.
>
> Brad
>
> On Dec 20, 2014, at 5:24 AM, Kevin Keraudren
> <kevin.keraudren10 at imperial.ac.uk> wrote:
>
> Hi,
>
> The IPython notebooks used for the tutorials in the Medical Image Analysis
> course at Imperial College London are now on github:
> https://github.com/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials
>
> These might be of interest to the mailing list as they rely on SimpleITK and
> could be useful either as teaching material or example applications.
>
> They can be browsed directly in nbviewer:
> http://nbviewer.ipython.org/github/ozan-oktay/Medical-Image-Analysis-IPython-Tutorials/tree/master/
>
> The following blog post is a quick presentation of the github repository:
> http://kevin-keraudren.blogspot.co.uk/2014/12/medical-image-analysis-ipython-tutorials.html
>
> Please do not hesitate to let us  know if you have questions or comments
> regarding these tutorials.
>
> Kind regards,
>
> Kevin Keraudren,
> PhD student, Imperial College London
> _____________________________________
> 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
>
>
> _____________________________________
> 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
>
>
> _____________________________________
> 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
>
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>

From blowekamp at mail.nih.gov  Tue Dec 23 11:34:35 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Tue, 23 Dec 2014 11:34:35 -0500
Subject: [ITK-users] [ANNOUNCE] SimpleITK 0.8.1 Release
Message-ID: <96262E2C-0CF1-4C15-B17C-5D063F830B45@mail.nih.gov>

We are pleased to announce the SimpleITK 0.8.1 Release.

SimpleITK is a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education and interpreted languages. SimpleITK provides binaries for several wrapped languages to enable users to rapidly get started using ITK.

Information on how to get started and download the binaries: http://www.itk.org/Wiki/SimpleITK/GettingStarted#Binaries


This patch release updates the ITK version to the newly released 4.7.0. Additionally, this patch contains improved support for CMake 3.0, fixes for compilation issues, the addition of the LabelOverlapMeasures filter, and a fix for the ClampCast filter.


Also, we are now compiling for Python 3.4, and have stopped compiling for Python 3.2.  Lastly, we are providing some binaries for the Anaconda Python distribution on Binstar.


Binary distributions for many platforms and languages are available for downloading: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.8.1/

Release Doxygen Documentation: http://www.itk.org/SimpleITKDoxygen08/html/index.html

Additional Release Notes: http://www.itk.org/Wiki/SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.8.1_Release

Enjoy,
Brad

From m.mashdi at gmail.com  Sun Dec 28 08:36:10 2014
From: m.mashdi at gmail.com (imashti)
Date: Sun, 28 Dec 2014 06:36:10 -0700 (MST)
Subject: [ITK-users] Create java VM failure SimpleITK, Python, Windows
In-Reply-To: <1419771563210-35074.post@n7.nabble.com>
References: <1379456385734-32371.post@n7.nabble.com>
 <CALzTN-SKpQ1yUK-KBtH4cikY5qKU6tKMfyUKbHYArX8-kX8Lfg@mail.gmail.com>
 <1379463383239-32376.post@n7.nabble.com>
 <1403721309106-34160.post@n7.nabble.com>
 <1419771563210-35074.post@n7.nabble.com>
Message-ID: <1419773770742-35075.post@n7.nabble.com>

Hi jmerkow,

I have got the same error in Windows but I do not know how to change the
mentioned environment variable. Could you please tell me how these variables
could be changed in Windows OS?

Regards 


jmerkow wrote
> Hello,
> 
> I solved this recently on my windows machine.
> For some reason, on windows the -o was not working properly with the
> ImageJ 64 (with jre) and ImageJ 32 (with jre).  Even if you change your
> cfg to use your system jre this option was not recognized.
> 
> I followed Matt's suggestion and changed my SITK_SHOW_COMMAND  environment
> variable to %a %f
> 
> This worked.  Also, note that you can increase the memory in the
> ImageJ.cfg file, and you do not need to set _JAVA_OPTIONS variable to
> increase memory allocation.
> 
> Hope this helps anyone else that runs into this problem!
> 
> -Jameson





--
View this message in context: http://itk-users.7.n7.nabble.com/Create-java-VM-failure-SimpleITK-Python-Windows-tp32371p35075.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From matimontg at gmail.com  Mon Dec 29 11:09:41 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Mon, 29 Dec 2014 13:09:41 -0300
Subject: [ITK-users] VersorRigid3DTransformOptimizer question
Message-ID: <CAKKNfu+DKtUr5KgkmV1UcEHqipXJBH_4rLZ-HhTr02QW_uLMYQ@mail.gmail.com>

Hi,

What are the components or what each element represents (0 to 5) in
the VersorRigid3DTransformOptimizer?

 typedef OptimizerType::ScalesType       OptimizerScalesType;
  OptimizerScalesType optimizerScales( transform->GetNumberOfParameters() );
  const double translationScale = 1.0 / 1000.0;

  optimizerScales[0] = 1.0;
  optimizerScales[1] = 1.0;
  optimizerScales[2] = 1.0;
  optimizerScales[3] = translationScale;
  optimizerScales[4] = translationScale;
  optimizerScales[5] = translationScale;

Thanks!
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From christopher.mullins at kitware.com  Mon Dec 29 12:12:46 2014
From: christopher.mullins at kitware.com (Christopher Mullins)
Date: Mon, 29 Dec 2014 12:12:46 -0500
Subject: [ITK-users] VersorRigid3DTransformOptimizer question
In-Reply-To: <CAKKNfu+DKtUr5KgkmV1UcEHqipXJBH_4rLZ-HhTr02QW_uLMYQ@mail.gmail.com>
References: <CAKKNfu+DKtUr5KgkmV1UcEHqipXJBH_4rLZ-HhTr02QW_uLMYQ@mail.gmail.com>
Message-ID: <CABVTP-Kn6yw8uSctUfh24QX-CNxWDTXf2F6pLakXSJO4QjHihg@mail.gmail.com>

>From Examples/RegistrationITKv4/MultiResImageRegistration2.cxx [1]:

*The set of parameters in the AffineTransform have different dynamic
ranges. Typically the parameters associated with the matrix have values
around [-1:1], although they are not restricted to this interval.
Parameters associated with translations, on the other hand, tend to have
much higher values, typically in the order of 10.0 to 100.0. This
difference in dynamic range negatively affects the performance of gradient
descent optimizers. ITK provides a mechanism to compensate for such
differences in values among the parameters when they are passed to the
optimizer. The mechanism consists of providing an array of scale factors to
the optimizer. These factors re-normalize the gradient components before
they are used to compute the step of the optimizer at the current
iteration. In our particular case, a common choice for the scale parameters
is to set to 1.0 all those associated with the matrix coefficients, that
is, the first N x N factors. Then, we set the remaining scale factors to a
small value. The following code sets up the scale coefficients.*

>From the ImageRegistration7 example [5]:

*Keeping in mind that the scale of units in scaling, rotation
and translation are quite different, we take advantage of the
scaling functionality provided by the optimizers. We know that the first
element of the parameters array corresponds to the scale factor, the
second corresponds to the angle, third and fourth are the center of
rotation and fifth and sixth are the remaining translation. We use
henceforth small factors in the scales associated with translations and the
rotation center.*

>From the ScalesType doxygen [2]:

*Scale type. This array defines scale to be applied to parameters before
being evaluated in the cost function. This allows to map to a more
convenient space. In particular this is used to normalize parameter spaces
in which some parameters have a different dynamic range.*

[5] is the most specific I can find.  Looking at how it's used in [1] might
also be useful, as the example you mentioned doesn't provide much
explanation (perhaps I or someone else should address that soon).

>From [3] (warning, outdated (2002!)):

*e.g. for an 3D AffineTransform, you get 12 parameters: the first 9 are the
coefficients of the matrix (representing rotation, scale and shearing) the
last 3 are the components of a translation vector. You want then to provide
an array of 12 values with the first 9 being =1.0 and the last three being
on the range of 1.0 / the image size (in millimeters).*

Here is another useful thread which is only half a decade old [4].

Perhaps an explanation for this is deserving of better accommodations,
maybe on the wiki.

In the meantime, hope this helps!

[1]
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/MultiResImageRegistration2.cxx#L291-322

[2]
http://www.itk.org/Doxygen/html/classitk_1_1Optimizer.html#a4c2e8eb9d9390e0e2988e78ea094492a

[3]
http://public.kitware.com/pipermail/insight-users/2002-October/001400.html

[4]
http://itk-insight-users.2283740.n2.nabble.com/Confused-abour-Optimizer-Scales-td4010857.html

[5]
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/ImageRegistration7.cxx


On Mon, Dec 29, 2014 at 11:09 AM, Matias Montroull <matimontg at gmail.com>
wrote:

> Hi,
>
> What are the components or what each element represents (0 to 5) in
> the VersorRigid3DTransformOptimizer?
>
>  typedef OptimizerType::ScalesType       OptimizerScalesType;
>   OptimizerScalesType optimizerScales( transform->GetNumberOfParameters()
> );
>   const double translationScale = 1.0 / 1000.0;
>
>   optimizerScales[0] = 1.0;
>   optimizerScales[1] = 1.0;
>   optimizerScales[2] = 1.0;
>   optimizerScales[3] = translationScale;
>   optimizerScales[4] = translationScale;
>   optimizerScales[5] = translationScale;
>
> Thanks!
>
> _____________________________________
> 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
>
>


-- 
Christopher Mullins
R&D Engineer
Kitware Inc.,
919.869.8871
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From matimontg at gmail.com  Mon Dec 29 14:48:03 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Mon, 29 Dec 2014 16:48:03 -0300
Subject: [ITK-users] SimpleITK | read a 3D image from a non DICOM file and
 write it as a series of DICOM slices
Message-ID: <CAKKNfuLN-pq7D097_CAq5vwe6yJBuSh=yeiOAgUbYNJu28Go-A@mail.gmail.com>

Hi,

Is there an example for SimpleITK to read a 3D image from a non Dicom file
such as mhd and then write it as a series of DICOM Slices?

I can do this with C++ but I haven't been able to figure out how to do it
using simpleITK.

Thanks,

Matias.
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From matimontg at gmail.com  Mon Dec 29 14:48:32 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Mon, 29 Dec 2014 16:48:32 -0300
Subject: [ITK-users] VersorRigid3DTransformOptimizer question
In-Reply-To: <CABVTP-Kn6yw8uSctUfh24QX-CNxWDTXf2F6pLakXSJO4QjHihg@mail.gmail.com>
References: <CAKKNfu+DKtUr5KgkmV1UcEHqipXJBH_4rLZ-HhTr02QW_uLMYQ@mail.gmail.com>
 <CABVTP-Kn6yw8uSctUfh24QX-CNxWDTXf2F6pLakXSJO4QjHihg@mail.gmail.com>
Message-ID: <CAKKNfuKThGM57Yvtq7+6OcvBFYVL4nGvtBJAL+fpLLhW6saQPg@mail.gmail.com>

Thanks Chris! very useful articles.

On Mon, Dec 29, 2014 at 2:12 PM, Christopher Mullins <
christopher.mullins at kitware.com> wrote:

> From Examples/RegistrationITKv4/MultiResImageRegistration2.cxx [1]:
>
> *The set of parameters in the AffineTransform have different dynamic
> ranges. Typically the parameters associated with the matrix have values
> around [-1:1], although they are not restricted to this interval.
> Parameters associated with translations, on the other hand, tend to have
> much higher values, typically in the order of 10.0 to 100.0. This
> difference in dynamic range negatively affects the performance of gradient
> descent optimizers. ITK provides a mechanism to compensate for such
> differences in values among the parameters when they are passed to the
> optimizer. The mechanism consists of providing an array of scale factors to
> the optimizer. These factors re-normalize the gradient components before
> they are used to compute the step of the optimizer at the current
> iteration. In our particular case, a common choice for the scale parameters
> is to set to 1.0 all those associated with the matrix coefficients, that
> is, the first N x N factors. Then, we set the remaining scale factors to a
> small value. The following code sets up the scale coefficients.*
>
> From the ImageRegistration7 example [5]:
>
> *Keeping in mind that the scale of units in scaling, rotation
> and translation are quite different, we take advantage of the
> scaling functionality provided by the optimizers. We know that the first
> element of the parameters array corresponds to the scale factor, the
> second corresponds to the angle, third and fourth are the center of
> rotation and fifth and sixth are the remaining translation. We use
> henceforth small factors in the scales associated with translations and the
> rotation center.*
>
> From the ScalesType doxygen [2]:
>
> *Scale type. This array defines scale to be applied to parameters before
> being evaluated in the cost function. This allows to map to a more
> convenient space. In particular this is used to normalize parameter spaces
> in which some parameters have a different dynamic range.*
>
> [5] is the most specific I can find.  Looking at how it's used in [1]
> might also be useful, as the example you mentioned doesn't provide much
> explanation (perhaps I or someone else should address that soon).
>
> From [3] (warning, outdated (2002!)):
>
> *e.g. for an 3D AffineTransform, you get 12 parameters: the first 9 are
> the coefficients of the matrix (representing rotation, scale and shearing)
> the last 3 are the components of a translation vector. You want then to
> provide an array of 12 values with the first 9 being =1.0 and the last
> three being on the range of 1.0 / the image size (in millimeters).*
>
> Here is another useful thread which is only half a decade old [4].
>
> Perhaps an explanation for this is deserving of better accommodations,
> maybe on the wiki.
>
> In the meantime, hope this helps!
>
> [1]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/MultiResImageRegistration2.cxx#L291-322
>
> [2]
> http://www.itk.org/Doxygen/html/classitk_1_1Optimizer.html#a4c2e8eb9d9390e0e2988e78ea094492a
>
> [3]
> http://public.kitware.com/pipermail/insight-users/2002-October/001400.html
>
> [4]
> http://itk-insight-users.2283740.n2.nabble.com/Confused-abour-Optimizer-Scales-td4010857.html
>
> [5]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/ImageRegistration7.cxx
>
>
> On Mon, Dec 29, 2014 at 11:09 AM, Matias Montroull <matimontg at gmail.com>
> wrote:
>
>> Hi,
>>
>> What are the components or what each element represents (0 to 5) in
>> the VersorRigid3DTransformOptimizer?
>>
>>  typedef OptimizerType::ScalesType       OptimizerScalesType;
>>   OptimizerScalesType optimizerScales( transform->GetNumberOfParameters()
>> );
>>   const double translationScale = 1.0 / 1000.0;
>>
>>   optimizerScales[0] = 1.0;
>>   optimizerScales[1] = 1.0;
>>   optimizerScales[2] = 1.0;
>>   optimizerScales[3] = translationScale;
>>   optimizerScales[4] = translationScale;
>>   optimizerScales[5] = translationScale;
>>
>> Thanks!
>>
>> _____________________________________
>> 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
>>
>>
>
>
> --
> Christopher Mullins
> R&D Engineer
> Kitware Inc.,
> 919.869.8871
>
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From yxp233 at postech.ac.kr  Tue Dec 30 07:57:27 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Tue, 30 Dec 2014 21:57:27 +0900
Subject: [ITK-users] GPU Implementation
In-Reply-To: <1418226543917722.015107.ptmail04@ptmail04>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
 <1417788892216194.03990.ptmail04@ptmail04>
 <008c01d010e5$84172950$8c457bf0$@ac.kr>
 <1417828271180838.110987.ptmail04@ptmail04>
 <009a01d010f5$7d4043e0$77c0cba0$@ac.kr>
 <1417837813159280.04286.ptmail04@ptmail04>
 <02e901d01482$28372130$78a56390$@ac.kr>
 <1418226543917722.015107.ptmail04@ptmail04>
Message-ID: <005001d02430$2a385770$7ea90650$@ac.kr>

Hi Jim,

 

How are you doing?

 

I have a new question about dataset size. I did an experiment to see how large of a dataset I can handle and the result was 512 ? 512 ? 140 (140 CT slices). Then I upgraded my graphic card which has 12 GB memory (previous card has 4 GB memory) and did the same experiment. However, only up to 218 slices, the new graphic card worked properly.  In my case, sometimes I need to process more than 350 slices, what would be a solution for processing this large dataset? I know there are 16 GB and 24 GB graphic cards, but I am not sure whether they can handle up to 350 slices or not and they are very expensive as you know. Maybe there should be any solution by coding? Thank you.

 

Best regards,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Thursday, December 11, 2014 12:49 AM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

Great. You can experiment further to see how large of a dataset you can handle. Then decide if you need to upgrade your graphic card to one with more memory to support the dataset size you want to process. 

Jim


On Dec 10, 2014, at 9:04 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi Jim,

 

Thanks for your suggestion. I tested with a smaller dataset: 512 ? 512 ? 75 and it worked. No crash occurred. 

 

Best regards,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Saturday, December 06, 2014 12:50 PM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. 

Jim


On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi Jim,

 

So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? 

 

Thanks,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Saturday, December 06, 2014 10:11 AM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. 

Jim


On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear Jim,

 

The images are quite large: 512 * 512 *300. 

 

I did not build test when I compile ITK.

 

Thanks,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Friday, December 05, 2014 11:15 PM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

How large are the images that you are using?

Jim


On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi John,

 

Sorry I mean the program got crashed after showing #define T float. 

 

Thanks,

Xiaopeng

 

From: John Drescher [mailto:drescherjm at gmail.com] 
Sent: Friday, December 05, 2014 4:24 PM
To: Xiaopeng Yang
Cc: Jim Miller; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

 

 

On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear Jim,

 

Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. 

 

Best,

Xiaopeng

 

<image001.png>

 

 

Is that an error? 

John 

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From millerjv at gmail.com  Tue Dec 30 09:15:34 2014
From: millerjv at gmail.com (Jim Miller)
Date: Tue, 30 Dec 2014 09:15:34 -0500
Subject: [ITK-users] GPU Implementation
In-Reply-To: <005001d02430$2a385770$7ea90650$@ac.kr>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
 <1417788892216194.03990.ptmail04@ptmail04>
 <008c01d010e5$84172950$8c457bf0$@ac.kr>
 <1417828271180838.110987.ptmail04@ptmail04>
 <009a01d010f5$7d4043e0$77c0cba0$@ac.kr>
 <1417837813159280.04286.ptmail04@ptmail04>
 <02e901d01482$28372130$78a56390$@ac.kr>
 <1418226543917722.015107.ptmail04@ptmail04>
 <005001d02430$2a385770$7ea90650$@ac.kr>
Message-ID: <B9BA6678-DE3A-456F-9137-C3C8CC90763F@gmail.com>

A simple solution is to downsample the images. Instead of 512x512x350 images, downsample to 256x256x175 images. 

With the regularization in the registration algorithm, the results will be very similar on the two datasets. 

If you wanted, after running the registration on the downsampled versions, you can upsample the deformation field and run a few iterations of the algorithm on the cpu at full resolution. 

Jim

> On Dec 30, 2014, at 7:57 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi Jim,
>  
> How are you doing?
>  
> I have a new question about dataset size. I did an experiment to see how large of a dataset I can handle and the result was 512 ? 512 ? 140 (140 CT slices). Then I upgraded my graphic card which has 12 GB memory (previous card has 4 GB memory) and did the same experiment. However, only up to 218 slices, the new graphic card worked properly.  In my case, sometimes I need to process more than 350 slices, what would be a solution for processing this large dataset? I know there are 16 GB and 24 GB graphic cards, but I am not sure whether they can handle up to 350 slices or not and they are very expensive as you know. Maybe there should be any solution by coding? Thank you.
>  
> Best regards,
> Xiaopeng
>  
> From: Jim Miller [mailto:millerjv at gmail.com] 
> Sent: Thursday, December 11, 2014 12:49 AM
> To: Xiaopeng Yang
> Cc: John Drescher; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
> Great. You can experiment further to see how large of a dataset you can handle. Then decide if you need to upgrade your graphic card to one with more memory to support the dataset size you want to process. 
> 
> Jim
> 
> On Dec 10, 2014, at 9:04 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi Jim,
>  
> Thanks for your suggestion. I tested with a smaller dataset: 512 ? 512 ? 75 and it worked. No crash occurred.
>  
> Best regards,
> Xiaopeng
>  
> From: Jim Miller [mailto:millerjv at gmail.com] 
> Sent: Saturday, December 06, 2014 12:50 PM
> To: Xiaopeng Yang
> Cc: John Drescher; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
> I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. 
> 
> Jim
> 
> On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi Jim,
>  
> So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card?
>  
> Thanks,
> Xiaopeng
>  
> From: Jim Miller [mailto:millerjv at gmail.com] 
> Sent: Saturday, December 06, 2014 10:11 AM
> To: Xiaopeng Yang
> Cc: John Drescher; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
> I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. 
> 
> Jim
> 
> On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Dear Jim,
>  
> The images are quite large: 512 * 512 *300.
>  
> I did not build test when I compile ITK.
>  
> Thanks,
> Xiaopeng
>  
> From: Jim Miller [mailto:millerjv at gmail.com] 
> Sent: Friday, December 05, 2014 11:15 PM
> To: Xiaopeng Yang
> Cc: John Drescher; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
> How large are the images that you are using?
> 
> Jim
> 
> On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> 
> Hi John,
>  
> Sorry I mean the program got crashed after showing #define T float.
>  
> Thanks,
> Xiaopeng
>  
> From: John Drescher [mailto:drescherjm at gmail.com] 
> Sent: Friday, December 05, 2014 4:24 PM
> To: Xiaopeng Yang
> Cc: Jim Miller; Insight-Users at Itk. Org
> Subject: Re: [ITK-users] GPU Implementation
>  
>  
>  
> On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:
> Dear Jim,
>  
> Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file.
>  
> Best,
> Xiaopeng
>  
> <image001.png>
>  
>  
> Is that an error?
> 
> John
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From yxp233 at postech.ac.kr  Tue Dec 30 18:41:57 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Wed, 31 Dec 2014 08:41:57 +0900
Subject: [ITK-users] GPU Implementation
In-Reply-To: <1419948940352555.011699.ptmail03@ptmail03>
References: <1405441657014-7585907.post@n2.nabble.com>
 <4C3F118B-E049-4168-9542-FC8D288FC38E@mail.nih.gov>
 <1405533203306221.02118.ptmail04@ptmail04>
 <035401d00925$9a422350$cec669f0$@ac.kr>
 <1417003820802645.09215.ptmail03@ptmail03>
 <042401d00a3e$7bea7f00$73bf7d00$@ac.kr>
 <141772836420039.030290.ptmail04@ptmail04>
 <001801d0104e$19711800$4c534800$@ac.kr>
 <141776427270398.129323.ptmail04@ptmail04>
 <003901d0105f$1e6a39c0$5b3ead40$@ac.kr>
 <1417788892216194.03990.ptmail04@ptmail04>
 <008c01d010e5$84172950$8c457bf0$@ac.kr>
 <1417828271180838.110987.ptmail04@ptmail04>
 <009a01d010f5$7d4043e0$77c0cba0$@ac.kr>
 <1417837813159280.04286.ptmail04@ptmail04>
 <02e901d01482$28372130$78a56390$@ac.kr>
 <1418226543917722.015107.ptmail04@ptmail04>
 <005001d02430$2a385770$7ea90650$@ac.kr>
 <1419948940352555.011699.ptmail03@ptmail03>
Message-ID: <007301d0248a$333962b0$99ac2810$@ac.kr>

Hi Jim,

 

I also thought about sampling the images, but I was worried about losing accuracy after sampling. If they are very similar, this can be a very simple solution. I will try it first. Thank you very much.

 

Best regards,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Tuesday, December 30, 2014 11:16 PM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

A simple solution is to downsample the images. Instead of 512x512x350 images, downsample to 256x256x175 images. 

 

With the regularization in the registration algorithm, the results will be very similar on the two datasets. 

 

If you wanted, after running the registration on the downsampled versions, you can upsample the deformation field and run a few iterations of the algorithm on the cpu at full resolution. 

Jim


On Dec 30, 2014, at 7:57 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi Jim,

 

How are you doing?

 

I have a new question about dataset size. I did an experiment to see how large of a dataset I can handle and the result was 512 ? 512 ? 140 (140 CT slices). Then I upgraded my graphic card which has 12 GB memory (previous card has 4 GB memory) and did the same experiment. However, only up to 218 slices, the new graphic card worked properly.  In my case, sometimes I need to process more than 350 slices, what would be a solution for processing this large dataset? I know there are 16 GB and 24 GB graphic cards, but I am not sure whether they can handle up to 350 slices or not and they are very expensive as you know. Maybe there should be any solution by coding? Thank you.

 

Best regards,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Thursday, December 11, 2014 12:49 AM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

Great. You can experiment further to see how large of a dataset you can handle. Then decide if you need to upgrade your graphic card to one with more memory to support the dataset size you want to process. 

Jim


On Dec 10, 2014, at 9:04 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi Jim,

 

Thanks for your suggestion. I tested with a smaller dataset: 512 ? 512 ? 75 and it worked. No crash occurred. 

 

Best regards,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Saturday, December 06, 2014 12:50 PM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

I'd start by using a smaller dataset. Perhaps downsample your dataset to 256x256x150 to see if that works on your card. 

Jim


On Dec 5, 2014, at 8:39 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi Jim,

 

So you mean I need to change graphics card or set some parameters? How to allocate the memory of graphics card? 

 

Thanks,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Saturday, December 06, 2014 10:11 AM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

I estimate that you would need over 2GB on your graphics card to run the demons algorithm on that size of a dataset. 

Jim


On Dec 5, 2014, at 6:45 PM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear Jim,

 

The images are quite large: 512 * 512 *300. 

 

I did not build test when I compile ITK.

 

Thanks,

Xiaopeng

 

From: Jim Miller [mailto:millerjv at gmail.com] 
Sent: Friday, December 05, 2014 11:15 PM
To: Xiaopeng Yang
Cc: John Drescher; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

How large are the images that you are using?

Jim


On Dec 5, 2014, at 2:43 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Hi John,

 

Sorry I mean the program got crashed after showing #define T float. 

 

Thanks,

Xiaopeng

 

From: John Drescher [mailto:drescherjm at gmail.com] 
Sent: Friday, December 05, 2014 4:24 PM
To: Xiaopeng Yang
Cc: Jim Miller; Insight-Users at Itk. Org
Subject: Re: [ITK-users] GPU Implementation

 

 

 

On Fri, Dec 5, 2014 at 12:41 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

Dear Jim,

 

Thanks for your help. I built the test successfully, but I met an error when I run the program. Please see the attached image file. 

 

Best,

Xiaopeng

 

<image001.png>

 

 

Is that an error? 

John 

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From fabian.trobles at gmail.com  Wed Dec 31 03:14:07 2014
From: fabian.trobles at gmail.com (Fabian Torres)
Date: Wed, 31 Dec 2014 16:14:07 +0800
Subject: [ITK-users] create a mesh
Message-ID: <CALD_EpLB1UgxOkX4SZQ08t=p116M_2kdZU0Y13H=KYfZ3n5ajQ@mail.gmail.com>

Hi every one

I have a segmented image (object in white, background in black) and I want
to obtain a mesh for the segmented object.
I am using tetgen software to use obtain a Delaunay tetrahedralization to
obtain the mesh. With this software I obtain a list of nodes, a list of
tethraedrons and a list of convexhull faces.

Is there a way to use the information obtained with tetgen with ITK and/or
VTK to create a mesh that I can use in MeshLab or  Comsol (.py or .stl)?

Thanks

-- 
Fabi?n Torres Robles
Maestria en Ciencias en Ingenier?a Electr?nica
Ingenier?a en Sistemas Electr?nicos
tel. 58081280, 0445534661338
e-mail fabian.trobles at gmail.com, dae.wong at gmail.com
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From fabian.trobles at gmail.com  Wed Dec 31 05:18:42 2014
From: fabian.trobles at gmail.com (Fabian Torres)
Date: Wed, 31 Dec 2014 18:18:42 +0800
Subject: [ITK-users] Mesh to stl or ply
Message-ID: <CALD_Ep+_AS6YnURFv+ofKG04QvTgpPz1NUZZNy4=q0y2Qsqf1w@mail.gmail.com>

Hi every one

I have a segmented image (object in white, background in black) and I want
to obtain a mesh for the segmented object.
I am using tetgen software to use obtain a Delaunay tetrahedralization to
obtain the mesh. With this software I obtain a list of nodes, a list of
tethraedrons and a list of triangle faces.

Is there a way to use the information obtained with tetgen with ITK and/or
VTK to create a mesh that I can use in MeshLab or  Comsol (.py or .stl)?

Thanks

-- 
Fabi?n Torres Robles
Maestria en Ciencias en Ingenier?a Electr?nica
Ingenier?a en Sistemas Electr?nicos
tel. 58081280, 0445534661338
e-mail fabian.trobles at gmail.com, dae.wong at gmail.com
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From dae.wong at gmail.com  Wed Dec 31 06:22:22 2014
From: dae.wong at gmail.com (Fabian Torres)
Date: Wed, 31 Dec 2014 19:22:22 +0800
Subject: [ITK-users] Itk mesh to stl
Message-ID: <CALD_Ep+xmoXLzzCoW4O3YkiU70OMFuL9UDUHsoy0p4RmcUMxdA@mail.gmail.com>

Hi every one

I have a segmented image (object in white, background in black) and I want
to obtain a mesh for the segmented object.
I am using tetgen software to use obtain a Delaunay tetrahedralization to
obtain the mesh. With this software I obtain a list of nodes, a list of
tethraedrons and a list of triangle faces.

Is there a way to use the information obtained with tetgen with ITK and/or
VTK to create a mesh that I can use in MeshLab or  Comsol (.ply or .stl)?

Thanks


-- 
Fabi?n Torres Robles
Maestria en Ciencias en Ingenier?a Electr?nica
Ingenier?a en Sistemas Electr?nicos
tel. 58081280, 0445534661338
e-mail fabian.trobles at gmail.com, dae.wong at gmail.com
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From blowekamp at mail.nih.gov  Wed Dec 31 10:46:45 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 31 Dec 2014 10:46:45 -0500
Subject: [ITK-users] SimpleITK | read a 3D image from a non DICOM file
	and write it as a series of DICOM slices
In-Reply-To: <CAKKNfuLN-pq7D097_CAq5vwe6yJBuSh=yeiOAgUbYNJu28Go-A@mail.gmail.com>
References: <CAKKNfuLN-pq7D097_CAq5vwe6yJBuSh=yeiOAgUbYNJu28Go-A@mail.gmail.com>
Message-ID: <FC4D270F-46B6-4935-8919-C38AFCF408C8@mail.nih.gov>

Hello,

Sorry for the slow reply. Earlier you linked to this nice example for reference:
http://www.itk.org/Doxygen/html/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html

With SimpleITK I have done the following when I needed to write a series in Python:

for i in range(img.GetSize()[2]):
    sitk.WriteImage(img[:,:,i],"test_{0:04}.tif".format(i))


However it is not quite this simple for a DICOM series. The metadata tags need to be correct too. SimpleITK is not designed to be a full fledge interface to DICOM files. Other tools may be better for that. But this seems like a reasonable thing to do but it's not currently readily available in the SimpleITK interface. Perhaps after some discussion on the best way to do it it and be added.


There are 3 main components to this example:

1) MetaDataDictionary

In SimpleITK the MetaDataDictionary interface is only part of the Image class. Currently it provides a read only interface, with the GetMetaDataKeys(), and GetMetaData(key) methods[1]. This get method only returns the type of data in the dictionary converted to a string.

The required method would be Image::SetMetaData(key,value). The issue would be what types of value need to be supported. For this example only std::string is needed, perhaps others should be overloaded?

2) NumericSeriesFileNameGenerator

This class only produces a "list" of file names. I think that many of the languages may have a more convenient way to do this. For example in Python:

[ "test_{0:04}.png".format(i) for i in range(img.GetSize()[2]) ]

So I don't think this is so important.

3) SeriesWriter

What we just used above is different then the SeriesWriter, as special metadata is passed from the ImageSeriesWriter to the ImageIO [2]. Here is the JIRA issue for this task [3].


So after these get done something like the following would do what you ask:

import SimpleITK as sitk

img = stik.ReadImage(argv[1])
img.SetMetaData("008|0060", "MR") // Modality
img.SetMetaData("008|0008", "DERIVED\\SECONDARY") // Image Type
img.SetMetaData("008|0064", "DV") // Conversion Type
sitk.WriteImage(img, [ "test_{0:04}.dcm".format(i) for i in range(img.GetSize()[2]) ])

Does that look like what you are looking for?

Brad

[1] http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1Image.html#a3d6cb12a211352ee38da5405b9c75928
[2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/ImageBase/include/itkImageSeriesWriter.hxx#L327-L368
[3] https://issues.itk.org/jira/browse/SIMPLEITK-122

On Dec 29, 2014, at 2:48 PM, Matias Montroull <matimontg at gmail.com> wrote:

> Hi,
> 
> Is there an example for SimpleITK to read a 3D image from a non Dicom file such as mhd and then write it as a series of DICOM Slices?
> 
> I can do this with C++ but I haven't been able to figure out how to do it using simpleITK.
> 
> Thanks,
> 
> Matias.
> _____________________________________
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> 
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> 
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> 
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