[Insight-users] problem with Chan and Vese method of segmentation

Kishore Mosaliganti kishoreraom at gmail.com
Thu Jan 27 15:47:42 EST 2011 

Hi Juan,

Thank you for the email.

1. This is a process issue with the Insight Journal. Hopefully, it
will improve through the ITKv4 efforts (via the GIT repository).

2. One of the problems with the PDF update is that the person who
submitted the article is only allowed to modify it. Outside users
cannot add or modify the content. So, this process needs to be changed
as well. This article can be copied to a wiki page that will allow
users to update it.

3. We are now refactoring the level-set code in ITK for the v4
release. You will see many changes soon. We will also improve
documentation and provide many examples for users. If you would like
to contribute in the code development or on the documentation aspect,
that will be great.

4. The multiphase examples were placed in InsightoClopedia wiki page.

HTH,
Kishore

On Thu, Jan 27, 2011 at 12:38 PM, Juan Cardelino
<juan.cardelino at gmail.com> wrote:
> Hey Kishore,
>
> Thank you very much for your answer,
>
> I've learned everything you tell me in this mail, the day after my
> quests,  after long hours of digging around the  ITK source code. I
> was able to run the examples successfully, but the Insight Journal
> submission really misdirected me, and I didn't find that mistake until
> I found a previous post from you on the list.
>
> That makes me wonder two things:
> 1) why is that code still kept in the IJ site? It is not being
> compiled against new versions of ITK so now it is kinda broken, and
> somehow shadows the classes on the review code.
> 2) Would it make sense to update the PDF on IJ to reflect this? I'm
> not only asking, I could volunteer to do it. I mean, the names of the
> examples and the parameter list doesn't match the ones on the IJ
> submission, and that's an additional rock on the path of people trying
> to learn about this filters.
>
> I think many good features of ITK (those not on the Software Guide)
> suffer from visibility problems and lack of a clear starting point
> from a newcomer. Which in turn reflects in many repetitive questions
> being posted in the list. That triggers the 3rd question to me:
>
> 3) Is it possible, and of interest of the community, to add this kind
> of documentation (like the PDF in the IJ) to the Software Guide?
>
> I had this same problem when trying to learn about the Geodesic Active
> Contours with Shape Guidance, there were many obscure parts out there
> that I had to fill in, and I would like to contribute.
>
>
> Back to the Chan-Vese code, I have a few questions left:
> 4) is there any examples of the multiphase version of the code? It is
> not on the review examples folder for sure.
>
> I'm very interested on this because In my group we have our own level
> set toolbox and I intend to port the interesting things to ITK. i.e.
> one region based algorithm that I've made in my master's thesis, which
> will add some features to the current chan-vese framework.
>
> Anyway, thanks for the answer and for your great contribution to our community.
> Best regards,
>                  Juan
>
> On Wed, Jan 19, 2011 at 4:26 PM, Kishore Mosaliganti
> <kishoreraom at gmail.com> wrote:
>> Hi all,
>>
>> There is *NO* need for borrowing the Insight Journal classes. Please
>> make sure that you compile ITK with the Review option turned on.
>>
>> The level set filters were renamed and moved to the ITK/Code/Review folders.
>>
>> Two examples of using the dense and sparse field filters are located
>> at ITK/Examples/Review/itkScalarSinglePhaseDense2DTest.cxx and
>> ITK/Examples/Review/itkScalarSinglePhaseSparse2DTest.cxx.
>>
>> There are also numerous examples of its usage at
>> ITK/Testing/Code/Review/. You can grep the relevant files in that
>> folder.
>>
>> I am able to compile and use these filters with ITK4.0. If you face
>> any further difficulties, please send me the error message.
>>
>> Kishore
>>
>> On Tue, Jan 18, 2011 at 6:57 AM, Juan Cardelino
>> <juan.cardelino at gmail.com> wrote:
>>> Hello Julien,
>>> Where you been able to do solve this? I've been struggling with the
>>> same issue without luck. I'm using ITK 3.19, and I get the following
>>> results:
>>> * If I remove everything but the main, the includes are not found.
>>> * If I add them, it seems that they conflict somehow with the
>>> installed ITK classes.
>>> If someone is interested, I could upload the error I got.
>>>
>>> For the original authors,
>>> I gave it a try with ITK 4.0 from GIT but there were some classes that
>>> have been refactored (itkEuclideanDistance).  So I fell back to 3.19.
>>> Are you planning to update this? or have you already done it?
>>> In addition, would it be possible to enumerate explicitly which
>>> classes are required and which not? It is really hard to tell at the
>>> begining.
>>>
>>> Thanks in advance and great work.
>>> Best regards,
>>>                   Juan
>>>
>>>
>>> On Wed, Jun 23, 2010 at 4:26 AM, julien_s <surchenjohn at gmail.com> wrote:
>>>>
>>>> I did a folder just with my .cxx et a CMakeList.txt but I have errors because
>>>> my file .cxx include ".h" which were present in the Insight Journal Folders
>>>> but not in the Review folder.
>>>>
>>>> For example : "itkSparseMultiphaseLevelSetImageFilter.h"
>>>>
>>>>
>>>> (Maybe I also make some errros in the next CMakelist:
>>>>
>>>> # This is the root ITK CMakeLists file.
>>>> CMAKE_MINIMUM_REQUIRED(VERSION 2.4)
>>>> IF(COMMAND CMAKE_POLICY)
>>>>  CMAKE_POLICY(SET CMP0003 NEW)
>>>> ENDIF(COMMAND CMAKE_POLICY)
>>>>
>>>>
>>>> # This project is designed to be built outside the Insight sourcetree.
>>>> PROJECT(ScalarMultiPhase2DTest)
>>>>
>>>> # Find ITK.
>>>> FIND_PACKAGE(ITK REQUIRED)
>>>> INCLUDE(${ITK_USE_FILE})
>>>>
>>>> ADD_EXECUTABLE(ScalarMultiPhase2DTest ScalarMultiPhase2DTest.cxx )
>>>>
>>>> TARGET_LINK_LIBRARIES(ScalarMultiPhase2DTest ITKCommon)
>>>> TARGET_LINK_LIBRARIES(ScalarMultiPhase2DTest ITKNumerics ITKIO)
>>>> TARGET_LINK_LIBRARIES(ScalarMultiPhase2DTest ITKReview)
>>>>
>>>>
>>>>
>>>>
>>>> Kishore Mosaliganti wrote:
>>>>>
>>>>> Hi Surcin,
>>>>>
>>>>> You don't have to make any changes in the ITK source folder. After
>>>>> downloading ITK, use cmake and build it.
>>>>>
>>>>> In your project folder, you just need the main.cxx file with a
>>>>> CMakeLists.txt and build it.
>>>>>
>>>>> You don't need the Insight Journal classes at all.
>>>>>
>>>>> Kishore
>>>>>
>>>>> On Tue, Jun 22, 2010 at 7:23 AM, julien_s <surchenjohn at gmail.com> wrote:
>>>>>>
>>>>>> First, thank you for your help
>>>>>>
>>>>>> Now,I compiled ITK with ITK_USE_REVIEW turned on.
>>>>>>
>>>>>> About the Review folder, if I understand, I have to replace the classes
>>>>>> downloaded from the Insight Journal by the classes available in the
>>>>>> Review
>>>>>> Folder?
>>>>>> I tried to do that but I have a lot of errors so I think I didn't
>>>>>> understand.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Kishore Mosaliganti wrote:
>>>>>>>
>>>>>>> Hi Surcin,
>>>>>>>
>>>>>>> These set of filters were moved to the ITK Review folder and
>>>>>>> subsequent changes were made to the filters directly in the Review
>>>>>>> folders.
>>>>>>>
>>>>>>> Therefore, in your project, you should compile ITK with the
>>>>>>> ITK_USE_REVIEW turned on in the cmake configuration. You can eliminate
>>>>>>> the classes that you downloaded from the Insight Journal.
>>>>>>>
>>>>>>> Can you then repeat your example and let us know how it goes.
>>>>>>>
>>>>>>> Kishore
>>>>>>>
>>>>>>> On Mon, Jun 21, 2010 at 1:03 PM, Surcin Julien <juliensurcin at gmail.com>
>>>>>>> wrote:
>>>>>>>> Dear ITK users,
>>>>>>>>
>>>>>>>> I'm working on the Chan and Vese method of segmentation.
>>>>>>>> Consequently I tried to use the example of the next publication:
>>>>>>>>
>>>>>>>> http://www.insight-journal.org/browse/publication/322
>>>>>>>>
>>>>>>>> I have no errors during the compilation but I have execution errors.
>>>>>>>>
>>>>>>>> "Debug Assertion Failed!
>>>>>>>>
>>>>>>>> Program:
>>>>>>>> ..eContoursWhithoutEdges\
>>>>>>>> Debug\ScalarSinglePhaseSparse2DTest.exe
>>>>>>>> File:C:\Program Files\Microsoft Visual Studio 9.0\include\vector
>>>>>>>> Line:779
>>>>>>>>
>>>>>>>> Expression:vector subscript out of range"
>>>>>>>>
>>>>>>>>
>>>>>>>> In fact, it is the same error that in the next post :
>>>>>>>> http://www.itk.org/pipermail/insight-users/2009-May/030324.html
>>>>>>>>
>>>>>>>> (I use Visual Studio 2008 on Windows Vista)
>>>>>>>>
>>>>>>>> I'm searching a solution for one week but I don't find a solution.
>>>>>>>>
>>>>>>>> Thanks in advance,
>>>>>>>>
>>>>>>>> Julien Surcin
>>>>>>>>
>>>>>>>> Student in 4th year at Polytech'Orleans, School of Engineering, FRANCE
>>>>>>>>
>>>>>>>> _____________________________________
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>>>>>>>>
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>>>>>>
>>>>>> --
>>>>>> View this message in context:
>>>>>> http://old.nabble.com/problem-with-Chan-and-Vese-method-of-segmentation-tp28951053p28958913.html
>>>>>> Sent from the ITK - 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.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:
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>>>>>>
>>>>> _____________________________________
>>>>> 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
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>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>
>>>> --
>>>> View this message in context: http://old.nabble.com/problem-with-Chan-and-Vese-method-of-segmentation-tp28951053p28968627.html
>>>> Sent from the ITK - 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.html
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
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>>> _____________________________________
>>> 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:
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>>
>

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