[Insight-users] Visual programming tool for ITK

Thu Nov 25 20:43:21 EST 2010

You can also consider V3D ( http://penglab.janelia.org/proj/v3d ), a
high-performance 3D+ image visualization and analysis platform, to test your
ITK filters. It is not "visual-programming" yet but it is quite convenient
for you to test individual filters as well as developing new ones. There are
about 100 existing ITK filter examples there developed by Luis Ibaniz and
others (some may not work but the ideas are well demonstrated).

Best,
-hanchuan

> ------------------------------
>
> Message: 4
> Date: Thu, 25 Nov 2010 14:14:26 +0100
> From: Michael Xanadu <xanadu.michael at googlemail.com>
> Subject: [Insight-users] Visual programming tool for ITK
> To: insight-users at itk.org
> Message-ID:
>         <AANLkTimCwAhgfB78YhK68dZUwv6=9UfSUfKanLMQ4gEx at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I'm looking for a tool which provides a graphic user interface and which I
> can use to create image filter pipelines through a visual programming
> environment. I think that such a tool would simplify the process of testing
> filters & pipelines without programming even one line of code. The only
> project I found in the internet was http://itkflowrun.sourceforge.net/ but
> it's not supported anymore and there are no resources available.
> Do you know any other tools like this?
>
> Regards,
> Michael
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> ------------------------------
>
> Message: 5
> Date: Thu, 25 Nov 2010 08:21:37 -0500
> From: John Drescher <drescherjm at gmail.com>
> Subject: Re: [Insight-users] Visual programming tool for ITK
> To: Michael Xanadu <xanadu.michael at googlemail.com>
> Cc: insight-users at itk.org
> Message-ID:
>         <AANLkTikUC-vLF=Z+zQ9iGneJeLR_K57fLQTiAtb6oenX at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Thu, Nov 25, 2010 at 8:14 AM, Michael Xanadu
> <xanadu.michael at googlemail.com> wrote:
>> Hi,
>>
>> I'm looking for a tool which provides a graphic user interface and which I
>> can use to create image filter pipelines through a visual programming
>> environment. I think that such a tool would simplify the process of testing
>> filters & pipelines without programming even one line of code. The only
>> project I found in the internet was http://itkflowrun.sourceforge.net/ but
>> it's not supported anymore and there are no resources available.
>> Do you know any other tools like this?
>>
>
> paraview?
>
> John
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 25 Nov 2010 08:24:12 -0500
> From: John Drescher <drescherjm at gmail.com>
> Subject: Re: [Insight-users] Visual programming tool for ITK
> To: Michael Xanadu <xanadu.michael at googlemail.com>
> Cc: insight-users at itk.org
> Message-ID:
>         <AANLkTi=-vuYRKZLqzk6JLEcGqETNEeBa-EbNuLvApOhL at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Thu, Nov 25, 2010 at 8:21 AM, John Drescher <drescherjm at gmail.com> wrote:
>> On Thu, Nov 25, 2010 at 8:14 AM, Michael Xanadu
>> <xanadu.michael at googlemail.com> wrote:
>>> Hi,
>>>
>>> I'm looking for a tool which provides a graphic user interface and which I
>>> can use to create image filter pipelines through a visual programming
>>> environment. I think that such a tool would simplify the process of testing
>>> filters & pipelines without programming even one line of code. The only
>>> project I found in the internet was http://itkflowrun.sourceforge.net/ but
>>> it's not supported anymore and there are no resources available.
>>> Do you know any other tools like this?
>>>
>>
>> paraview?
>>
>
> I think I was thinking more of volview but that is not free. It does
> have a free trial.
>
> http://www.kitware.com/products/volview.html
>
> John
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 25 Nov 2010 14:35:14 +0100
> From: Sergio Vera <sergio.vera at alma3d.com>
> Subject: Re: [Insight-users] Visual programming tool for ITK
> To: John Drescher <drescherjm at gmail.com>
> Cc: insight-users at itk.org
> Message-ID:
>         <AANLkTikXYnwJEuWkK-Q8peb7O5cV3+E1YhpGDW+bKSEn at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello all,
>
> Mevislab (http://www.mevislab.de) may be what you are looking for.
> It allows you to build pipelines graphically with itk filters, vtk filters
> as well as custom filters. However, not all the filters/classes from vtk and
> itk are implemented in the program
>
> You can integrate itk pipelines with custom / vtk ones as long as the inputs
> are compatible... All in all a very useful tool to try some pipelines before
> writing code. I strongly recommend it.
>
> regards
>
> On Thu, Nov 25, 2010 at 2:24 PM, John Drescher <drescherjm at gmail.com> wrote:
>
>> On Thu, Nov 25, 2010 at 8:21 AM, John Drescher <drescherjm at gmail.com>
>> wrote:
>>> On Thu, Nov 25, 2010 at 8:14 AM, Michael Xanadu
>>> <xanadu.michael at googlemail.com> wrote:
>>>> Hi,
>>>>
>>>> I'm looking for a tool which provides a graphic user interface and which
>> I
>>>> can use to create image filter pipelines through a visual programming
>>>> environment. I think that such a tool would simplify the process of
>> testing
>>>> filters & pipelines without programming even one line of code. The only
>>>> project I found in the internet was http://itkflowrun.sourceforge.net/but
>>>> it's not supported anymore and there are no resources available.
>>>> Do you know any other tools like this?
>>>>
>>>
>>> paraview?
>>>
>>
>> I think I was thinking more of volview but that is not free. It does
>> have a free trial.
>>
>> http://www.kitware.com/products/volview.html
>>
>> John
>> _____________________________________
>> 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.html
>>
>> 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
>>
>
>
>
> --
> Sergio Vera
>
>  Alma IT Systems
>  C/ Vilana, 4B, 4? 1?
>  08022 Barcelona
>  T. (+34) 932 380 592
>  www.alma3d.com
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> ------------------------------
>
> Message: 8
> Date: Thu, 25 Nov 2010 14:38:59 +0100
> From: Dan Mueller <dan.muel at gmail.com>
> Subject: Re: [Insight-users] Visual programming tool for ITK
> To: Michael Xanadu <xanadu.michael at googlemail.com>
> Cc: insight-users at itk.org
> Message-ID:
>         <AANLkTinmBX9AZ5eQiWGWFk7CgCdHE7dHWZcWgvu8Lajb at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Michael,
>
> You may also be interested in the following Insight Journal article,
> which uses Simulink (Matlab) for visual programming of ITK and VTK
> pipelines (though I have not tried it myself):
>     http://www.insight-journal.org/browse/publication/620
>
> HTH
>
> Cheers, Dan
>
> On 25 November 2010 14:35, Sergio Vera <sergio.vera at alma3d.com> wrote:
>> Hello all,
>> Mevislab (http://www.mevislab.de) may be what you are looking for.
>> It allows you to build pipelines graphically with itk filters, vtk filters
>> as well as custom filters. However, not all the filters/classes from vtk and
>> itk are implemented in the program
>> You can integrate itk pipelines with custom / vtk ones as long as the inputs
>> are compatible... All in all a very useful tool to try some pipelines before
>> writing code. I strongly recommend it.
>> regards
>> On Thu, Nov 25, 2010 at 2:24 PM, John Drescher <drescherjm at gmail.com> wrote:
>>>
>>> On Thu, Nov 25, 2010 at 8:21 AM, John Drescher <drescherjm at gmail.com>
>>> wrote:
>>>> On Thu, Nov 25, 2010 at 8:14 AM, Michael Xanadu
>>>> <xanadu.michael at googlemail.com> wrote:
>>>>> Hi,
>>>>>
>>>>> I'm looking for a tool which provides a graphic user interface and
>>>>> which I
>>>>> can use to create image filter pipelines through a visual programming
>>>>> environment. I think that such a tool would simplify the process of
>>>>> testing
>>>>> filters & pipelines without programming even one line of code. The only
>>>>> project I found in the internet was http://itkflowrun.sourceforge.net/
>>>>> but
>>>>> it's not supported anymore and there are no resources available.
>>>>> Do you know any other tools like this?
>>>>>
>>>>
>>>> paraview?
>>>>
>>>
>>> I think I was thinking more of volview but that is not free. It does
>>> have a free trial.
>>>
>>> http://www.kitware.com/products/volview.html
>>>
>>> John
>>
>>
>>
>> --
>> Sergio Vera
>>
>> ?Alma IT Systems
>> ?C/ Vilana, 4B, 4? 1?
>> ?08022 Barcelona
>> ?T. (+34) 932 380 592
>> ?www.alma3d.com
>
>
> ------------------------------
>
> Message: 9
> Date: Thu, 25 Nov 2010 08:55:29 -0500
> From: John Drescher <drescherjm at gmail.com>
> Subject: Re: [Insight-users] Visual programming tool for ITK
> To: Sergio Vera <sergio.vera at alma3d.com>
> Cc: insight-users at itk.org
> Message-ID:
>         <AANLkTin48WLe9siW6iwVYsbnZORAekiHSKKCbEZu3EOH at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Thu, Nov 25, 2010 at 8:35 AM, Sergio Vera <sergio.vera at alma3d.com> wrote:
>> Hello all,
>> Mevislab (http://www.mevislab.de) may be what you are looking for.
>> It allows you to build pipelines graphically with itk filters, vtk filters
>> as well as custom filters. However, not all the filters/classes from vtk and
>> itk are implemented in the program
>> You can integrate itk pipelines with custom / vtk ones as long as the inputs
>> are compatible... All in all a very useful tool to try some pipelines before
>> writing code. I strongly recommend it.
>> regards
>
> Thanks for the suggestion. That looks good. Even though I was not the
> original poster I am always interested in either developing a better
> visualization tool for my work or finding a better tool with source
> code (so I can add my own changes) that does not break the medical
> imaging research budget..
>
> John
>
>
> ------------------------------
>
> Message: 10
> Date: Thu, 25 Nov 2010 10:40:16 -0500
> From: Cory Quammen <cquammen at cs.unc.edu>
> Subject: Re: [Insight-users] Visual programming tool for ITK
> To: Insight Users <insight-users at itk.org>
> Message-ID:
>         <AANLkTi=OV-W=s9ShW-d3sFcAPwHPhR4uoeqrms-Ph5SJ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> You may also want to check out VisTrails (http://www.vistrails.org/).
> I believe you can use it to string together ITK filters as you
> described.
>
> Cory
>
> On Thu, Nov 25, 2010 at 8:55 AM, John Drescher <drescherjm at gmail.com> wrote:
>> On Thu, Nov 25, 2010 at 8:35 AM, Sergio Vera <sergio.vera at alma3d.com> wrote:
>>> Hello all,
>>> Mevislab (http://www.mevislab.de) may be what you are looking for.
>>> It allows you to build pipelines graphically with itk filters, vtk filters
>>> as well as custom filters. However, not all the filters/classes from vtk and
>>> itk are implemented in the program
>>> You can integrate itk pipelines with custom / vtk ones as long as the inputs
>>> are compatible... All in all a very useful tool to try some pipelines before
>>> writing code. I strongly recommend it.
>>> regards
>>
>> Thanks for the suggestion. That looks good. Even though I was not the
>> original poster I am always interested in either developing a better
>> visualization tool for my work or finding a better tool with source
>> code (so I can add my own changes) that does not break the medical
>> imaging research budget..
>>
>> John
>> _____________________________________
>> 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.html
>>
>> 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
>>
>
>
>
> --
> Cory Quammen
> Computer Integrated Systems for Microscopy and Manipulation (CISMM)
> Department of Computer Science
> University of North Carolina at Chapel Hill
> http://www.cs.unc.edu/~cquammen
>
>
> ------------------------------
>
> Message: 11
> Date: Thu, 25 Nov 2010 10:53:31 -0500
> From: Nicholas Tustison <ntustison at gmail.com>
> Subject: Re: [Insight-users] Problem Using the
>         itkBSplineScatteredDataPointSetToImageFilter on Win32
> To: Otmane Lahlou <otmane.lahlou at c-s.fr>
> Cc: ITK Users <insight-users at itk.org>
> Message-ID: <328C0D18-6703-4DA5-BE3E-AC2022902C36 at gmail.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Yeah, that could certainly do it.  The algorithm uses a coarse-to-fine
> approach to fitting the data which is governed by the initial grid of control
> points and the number of fitting levels.  Suppose, for example, you have a 2-D
> domain defined over  the domain [0,512] x [0,512] and you want to fit a cubic
> B-spline object over that domain.  You, as the user, would presumably specify
> an initial coarse grid with a low number of mesh elements, the number of mesh
> elements related to the number of control points by the formula
>
> number of mesh elements = number of control points - spline order
>
> So, getting back to your example, if you wanted to start with a mesh of size
> 2x2 over your domain, you would specify a control point grid of 5x5 with
> actual code looking something like:
>
> BSplineFilterType::ArrayType numberOfControlPoints;
> numberOfControlPoints.Fill( 5 );
> bsplineFilter->SetNumberOfControlPoints( numberOfControlPoints );
>
> As regards number of levels---for each level you specify, the mesh size
> doubles.  So, suppose you specify 5 levels, the algorithm will first fit to
> the data using a mesh size of 2x2.  The solution at the previous level is
> propagated to the next level where additional fitting occurs with a mesh size
> of 4x4, followed by an 8x8 mesh, which continues to a final mesh of 32x32 at
> the 5th level.  You can imagine that with 10 levels, the resulting mesh size
> would be 1024x1024 over the domain which would probably be overkill for image
> data of size 512x512.
>
> As far as advice goes---it's really hard to say as both the initial mesh size
> and the number of levels go into determining the type of fitting you want
> which is really application specific.  For example, I use the BSpline filter
> as the fitting routine in itkN4MRIBiasFieldCorrectionImageFilter.  For that
> application, you typically want to start with a low number of mesh elements
> and perform fitting for only 3-4 (at the most) fitting levels.  However, I
> also use it for B-spline based image registration where, at each level, I
> typically use a relatively larger number of mesh elements and only 1 level.
>
> Nick
>
> On Nov 25, 2010, at 6:50 AM, Otmane Lahlou wrote:
>
>> Hi Nick,
>>
>> Thanks you for your feedbacks,
>>
>> Can those precision values issues be related to the parameter
>> m_NumberOfLevels ?
>> In the test i sent  m_NumberOfLevels  is equal to 10,  and for this value the
>> exception is thrown.
>>
>> In general, the exception is thrown also for  m_NumberOfLevels values  > 5.
>> But it runs well for m_NumberOfLevels <=5.
>>
>> Can you give me a brief explication about that, and the way to choose the
>> right NumberOfLevels  value ?
>>
>> Thank you
>>
>> Otmane
>>
>>
>> Nicholas Tustison a ?crit :
>>> Hi Otmane,
>>>
>>> The problem is that a B-spline object has an open boundary in it's
>>> parametric domain, specifically your domain is defined over [0,512).  You're
>>> querying a point right on that open boundary.  Although I tried to
>>> accommodate calls on the open boundary, due to precision differences, you're
>>> getting that error on Win32 vs your Linus distribution.  What you want to do
>>> is ensure your query of the B-spline object value is inside the B-spline
>>> domain, e.g. 511.9999 instead of 512.
>>>
>>> Nick
>>>
>>> On Nov 24, 2010, at 1:08 PM, Otmane Lahlou wrote:
>>>
>>>
>>>> Hi List;
>>>>
>>>> I have a problem when i use the
>>>> itkBSplineScatteredDataPointSetToImageFilter filter on Win32.
>>>> Actually, On _Linux distributions it runs well_, but on Win32, the
>>>> following exception is thrown:
>>>> Line 1012
>>>> "Description: itk::ERROR: PointSetToImageFilter(01716750): The collapse
>>>> point
>>>> component 512 is outside the corresponding parametric domain of [0, 512]. "
>>>>
>>>> I used ITK 3.20, compiled using a Visual C++ 2008 Express.
>>>> in release mode.
>>>>
>>>> You can find a cmake configurable project attached to this mail that shows
>>>> the problem.
>>>> If someone can have a look and give me a feedback to confirm the problem
>>>> or to explain what i missed,  it will be really helpfull.
>>>>
>>>> Thanks for help.
>>>>
>>>> Otmane
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> <testITKSpline.tar>_____________________________________
>>>> 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.html
>>>>
>>>> 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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