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

Thu Jan 27 12:39:24 EST 2011

I should have read better, one of my questions was already answered in
your next mail. I'm truly sorry.
Best,
       Juan

On Thu, Jan 27, 2011 at 3:38 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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>>>>>>>
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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:
>>>>>> 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.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
>>>>
>>>> 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:
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>>
>