[ITK] [ITK-dev] [SimpleITK] Data Bridge for SimpleITK

Hyun Jae Kang hyunjae.kang at kitware.com
Thu Feb 4 19:08:55 EST 2016 

Hi David,

Thanks for your prompt response! That is great news.
It would be very helpful for us if you could share your interface for the
data conversion between numpy/slicer and ITK with us. So, we do not need to
start from scratch.

Thanks,

Hyun Jae

On Thu, Feb 4, 2016 at 6:03 PM, <community-request at itk.org> wrote:

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> Today's Topics:
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>    1. Re: [ITK-users] Problem building jounal paper->cannot open
>       input     file 'ITKAlgorithms.lib' (D?enan Zuki?)
>    2. [ITK-users] Multi-threader and thread pool (Olivier Commowick)
>    3. [ITK-dev] [SimpleITK] Data Bridge for SimpleITK (Hyun Jae Kang)
>    4. Re: [ITK-users] Multi-threader and thread pool (Matt McCormick)
>    5. Re: [ITK-dev] [SimpleITK] Data Bridge for SimpleITK (David Burns)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 4 Feb 2016 13:41:16 -0500
> From: D?enan Zuki? <dzenanz at gmail.com>
> To: vishal <itkhelpacc at gmail.com>
> Cc: Insight-users <insight-users at itk.org>
> Subject: Re: [ITK] [ITK-users] Problem building jounal paper->cannot
>         open    input   file 'ITKAlgorithms.lib'
> Message-ID:
>         <
> CAPf2UMRevWFVsNmOrfF4AFjjjpmRXJLkjCtXbyqF+nO7eutBeQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Vishal,
>
> the most likely reason is listing libraries by name in CMakeLists.txt file.
> You should replace line
> set(Libraries ITKAlgorithms ITKBasicFilters ITKCommon ITKIO)
> by line:
> set(Libraries ${ITK_LIBRARIES})
>
> If it doesn't work, let us know.
>
> HTH
>
> On Thu, Feb 4, 2016 at 12:08 AM, vishal <itkhelpacc at gmail.com> wrote:
>
> > hi,
> > I came across this paper An ITK-Based Framework for 2D-3D Registration
> with
> > Multiple Fixed Images by Alvaro Bertelsen and Diego Borro... first had to
> > replace  ::itk::OStringStream diffName; by std::ostringstream diffName;
> > which solved some errors and now upon building the project again Im
> getting
> > the error saying *cannot open input file 'ITKAlgorithms.lib'*.. I
> searched
> > for ITKAlgorithms in my ITK 4.8.2 build folder  but i *couldnt* find
> it...
> > i
> > build the project in debug mode.. Please advice
> > Regards
> > vishal
> >
> >
> >
> > --
> > View this message in context:
> >
> http://itk-users.7.n7.nabble.com/Problem-building-jounal-paper-cannot-open-input-file-ITKAlgorithms-lib-tp36734.html
> > Sent from the ITK - Users mailing list archive at Nabble.com.
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> ------------------------------
>
> Message: 2
> Date: Thu, 4 Feb 2016 20:07:27 +0100
> From: Olivier Commowick <olivier.commowick at inria.fr>
> To: Insight-users <insight-users at itk.org>
> Subject: [ITK] [ITK-users] Multi-threader and thread pool
> Message-ID: <919FD08C-D1FF-42B2-8806-CA70DE593E77 at inria.fr>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi everyone,
>
> I have recently discovered the existence of a thread pool class in ITK (
> http://itk.org/Doxygen/html/classitk_1_1ThreadPool.html <
> http://itk.org/Doxygen/html/classitk_1_1ThreadPool.html>), closely linked
> to the multi threader. From the doxygen, I am not really able to understand
> how it can be used and I do not see any example for it.
>
> I have been looking for some time for a multi-threader, working on all
> OSes, that can have more jobs in queue than the number of threads and
> execute them when threads gets free, and this would seem like a good start.
> So I was wondering how this thread pool actually behaves when used by the
> multi-threader, what its goal is in ITK and all this sort of things. If
> anyone had some idea about this or may be an example on how it could be
> used, that would be great.
>
> Thanks
> Olivier
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> ------------------------------
>
> Message: 3
> Date: Thu, 4 Feb 2016 14:36:20 -0500
> From: Hyun Jae Kang <hyunjae.kang at kitware.com>
> To: insight-developers at itk.org,  Patrick Reynolds
>         <patrick.reynolds at kitware.com>
> Subject: [ITK] [ITK-dev] [SimpleITK] Data Bridge for SimpleITK
> Message-ID:
>         <
> CAAsPJLowri4GCUDUnVUu858BVFMNYcsEhiuTxRvQz-9Otb4VHw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
>
> To support data transparency between the functions of SimpleITK and NumPy,
> SimpleITK provides functional integration with NumPy-based script and a
> method of data-conversion between SimpleITK?s image data and the
> N-dimensional array object of NumPy. But, there is a significant
> performance bottleneck in the data-conversion which is based on the
> operation of data copy. The performance bottleneck can be increased with
> the size of handling image data and the number of data-conversion.
>
> The performance bottle can be removed by allowing SimpleITK?s image and the
> arrays of NumPy to share pointers to the same memory symmetrically with
> copy-on-write semantics. That is, reduce data-copy operations in the data
> conversion. This approach can be accomplished by developing and/or
> improving existing data handling methods in ITK and SimpleITK to enable
> copy-on-write sharing of data between SimpleITK?s image data and other
> common data object of Python libraries used for scientific computing and
> image processing.
>
> For more detail information, please check the following website:
> http://www.itk.org/Wiki/SimpleITK/Design_And_Proposals/SIP_002
>
> Any your valuable comments are welcome.
>
> Thanks,
>
> Hyun Jae
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> ------------------------------
>
> Message: 4
> Date: Thu, 4 Feb 2016 15:04:11 -0500
> From: Matt McCormick <matt.mccormick at kitware.com>
> To: Olivier Commowick <olivier.commowick at inria.fr>
> Cc: Insight-users <insight-users at itk.org>
> Subject: Re: [ITK] [ITK-users] Multi-threader and thread pool
> Message-ID:
>         <CALzTN-QX3kpT-B7CugKt6priZAhLg+KbT5y8gA5N-aJA1e=
> BSA at mail.gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Olivier,
>
> The itk::ThreadPool is an experimental thread-pool feature.  It is
> considered experimental, and it maybe majorly modified in its API or
> removed in the future. Our preliminary experiences is that ITK runs
> slower when it is enabled.
>
> To enable it, call
>
>   itk::MultiThreader::SetGlobalDefaultUseThreadPool( true );
>
> In the future, we will be moving towards other thread pool backends by
> adopting interfaces similar to vtkSMPTools and VTK-m.
>
> Thanks,
> Matt
>
> On Thu, Feb 4, 2016 at 2:07 PM, Olivier Commowick
> <olivier.commowick at inria.fr> wrote:
> > Hi everyone,
> >
> > I have recently discovered the existence of a thread pool class in ITK
> > (http://itk.org/Doxygen/html/classitk_1_1ThreadPool.html), closely
> linked to
> > the multi threader. From the doxygen, I am not really able to understand
> how
> > it can be used and I do not see any example for it.
> >
> > I have been looking for some time for a multi-threader, working on all
> OSes,
> > that can have more jobs in queue than the number of threads and execute
> them
> > when threads gets free, and this would seem like a good start. So I was
> > wondering how this thread pool actually behaves when used by the
> > multi-threader, what its goal is in ITK and all this sort of things. If
> > anyone had some idea about this or may be an example on how it could be
> > used, that would be great.
> >
> > Thanks
> > Olivier
> >
> > _____________________________________
> > 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:
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>
> ------------------------------
>
> Message: 5
> Date: Thu, 4 Feb 2016 18:03:08 -0500
> From: David Burns <david.mo.burns at gmail.com>
> To: insight-developers at itk.org
> Subject: Re: [ITK] [ITK-dev] [SimpleITK] Data Bridge for SimpleITK
> Message-ID: <56B3D8AC.9090606 at gmail.com>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> I just finished creating an interface between numpy/slicer and my ITK
> C++ project module using SWIG. I use pointers to avoid copying and it
> works well. Happy to share what I have.
>
> - David
>
> On 02/04/2016 02:36 PM, Hyun Jae Kang wrote:
> > Hi all,
> >
> > To support data transparency between the functions of SimpleITK and
> > NumPy, SimpleITK provides functional integration with NumPy-based
> > script and a method of data-conversion between SimpleITK?s image data
> > and the N-dimensional array object of NumPy. But, there is a
> > significant performance bottleneck in the data-conversion which is
> > based on the operation of data copy. The performance bottleneck can be
> > increased with the size of handling image data and the number of
> > data-conversion.
> >
> > The performance bottle can be removed by allowing SimpleITK?s image
> > and the arrays of NumPy to share pointers to the same memory
> > symmetrically with copy-on-write semantics. That is, reduce data-copy
> > operations in the data conversion. This approach can be accomplished
> > by developing and/or improving existing data handling methods in ITK
> > and SimpleITK to enable copy-on-write sharing of data between
> > SimpleITK?s image data and other common data object of Python
> > libraries used for scientific computing and image processing.
> >
> > For more detail information, please check the following website:
> > http://www.itk.org/Wiki/SimpleITK/Design_And_Proposals/SIP_002
> >
> > Any your valuable comments are welcome.
> >
> > Thanks,
> >
> > Hyun Jae
> >
> >
> >
> > _______________________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-developers
>
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