[Insight-users] itkScalarChanAndVeseSparseLevelSetImageFilter

alex gouaillard alexandre_gouaillard at hms.harvard.edu
Sun Jun 7 23:35:56 EDT 2009 

hi eleni,

you can monitor cvs changes in the review directory using this link :
http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/Review/?root=Insight&sortby=date#dirlist

There should be a lot of changes in the next days, so it might be  
unpractical for us to let you know everytime we commit a change. We  
will try to do it though.

cheers.

alex.



On Jun 7, 2009, at 11:28 PM, Sgouritsa, Eleni wrote:

> Thank you very much.
> Yes, I think too that my problem was coming from the foreground term.
> Is it possible to notify me when you finish with the other changes  
> of the class so I can work directly with the corrected version?
>
> Regards,
> Eleni
>
>
> -----Original Message-----
> From: Arnaud Gelas [mailto:arnaud_gelas at hms.harvard.edu]
> Sent: Sun 6/7/2009 6:48 PM
> To: Sgouritsa, Eleni
> Cc: Kishore Mosaliganti; insight-users at itk.org; Luis Ibanez
> Subject: Re: [Insight-users]  
> itkScalarChanAndVeseSparseLevelSetImageFilter
>
> Dear Eleni,
>
> I have corrected a bug in the formula of the foreground constant
> calculation. This error could really affect the results of your
> segmentation process.
> You can get the new version from the cvs repository.
>
> Note that this code may change a lot in the next couple of days
> (Kishore and I will be fixing various parts of the code).
>
> Arnaud
>
> On Jun 7, 2009, at 6:12 PM, Sgouritsa, Eleni wrote:
>
> > What I understand is that the result should be independent of how we
> > define the distance function (negative inside or outside). And if we
> > initialize the level set totally inside the data , the level set
> > should expand according to equation (7) of the paper where you
> > describe the method, whereas if we initialize outside it should
> > shrink. In insight journal it happens like that but not in the itk
> > release.
> > Thank you very much,
> > Eleni
> >
> >
> > -----Original Message-----
> > From: Sgouritsa, Eleni
> > Sent: Sun 6/7/2009 3:30 PM
> > To: Kishore Mosaliganti
> > Cc: Luis Ibanez; insight-users at itk.org
> > Subject: RE: [Insight-users]
> > itkScalarChanAndVeseSparseLevelSetImageFilter
> >
> > Hello,
> > thank you very much for the help. Unfortunately I work with medical
> > data that I am not supposed to give.
> > Can you explain a little more point 2. You mean that I have to
> > define my level set as inside positive and outside negative to have
> > the opposite propagation direction?
> > I tried it but it did not work. I both cases, if I initialize the LS
> > inside the boundary of my data, it shrinks. I use mu=0, nu=0, l1=1
> > and l2=1. Do I need negative l1?When I initialize almost the whole
> > LS outside my data it seems to work in some cases.Generally, I get
> > different results from the insight journal that I was getting  
> correct.
> >
> > Thank you,
> > Eleni
> >
> >
> > -----Original Message-----
> > From: Kishore Mosaliganti [mailto:kishoreraom at gmail.com]
> > Sent: Fri 6/5/2009 1:02 PM
> > To: Sgouritsa, Eleni
> > Cc: Luis Ibanez; insight-users at itk.org
> > Subject: Re: [Insight-users]
> > itkScalarChanAndVeseSparseLevelSetImageFilter
> >
> > Hi Eleni,
> >
> > Thank you for pointing out these problems. You are right that the
> > Review
> > code is not very stable as yet. We are working on fixing them.
> > During the
> > transfer from the IJ paper to the Review directory, a lot of
> > modifications
> > were made. We might have inadvertently introduced new errors.
> >
> > Regarding your problems:
> >
> > 2. The level-set function is defined by convention as inside is
> > negative and
> > outside is positive. So the negative values become your foreground  
> and
> > positive values become the background. This controls the propagation
> > direction.
> >
> > 3. I am looking at the Halt function. Looks like the boundary case
> > of 0
> > iterations is not coded right.
> >
> > 4.  Regarding the high RMS values, the level-set function is re-
> > initialized
> > to a signed distance function after every few iterations. It so
> > happens that
> > the default setting is 1 iteration. Hence, the RMS change is being
> > calculated after the reinitialization while it needs to be done
> > before. We
> > are also working on correcting this. Thank you for pointing this  
> out.
> >
> >
> > Is it possible for you to post a small sample of your data for us to
> > work on
> > the errors.
> >
> >
> > Kishore
> >
> > On Tue, Jun 2, 2009 at 11:24 AM, Sgouritsa, Eleni
> > <esgourit at central.uh.edu>wrote:
> >
> > >  Hello,
> > > I m sorry if my point was not clear. The problems that I am facing
> > using
> > > this class to segment 3D data are the following:
> > >
> > > 1. My data has negative origin (for example (-100, -100, -60).
> > Unless I do
> > > SetOrigin(0,0,0) (or I guess any origin >=0) my program crashes. I
> > have to
> > > set my negative origin as zero for my program to run. Does the
> > class assumes
> > > positive origin of the input image?
> > >
> > > 2. I initialize my level set inside (so the evolution should be
> > outwards).
> > > In this case I can not make my level set expand (it can just
> > shrink, or not
> > > move). I think I should use something like
> > SetReverseExpansionDirection to
> > > control the propagation direction, but I can not find this option
> > in the
> > > class public members. (This is currently my main problem where I
> > am stuck,
> > > any help would be very useful!)
> > >
> > > 3. The maximum RMS Error serves (along with the number of
> > iterations) as a
> > > stopping criteria inside the Halt function (of
> > > itkMultiphaseFiniteDifferenceImageFilter.txx file).
> > > Lets say I set maximum RMS Error = 0.01.
> > > The Halt function returns the following:
> > > return ( (this->GetElapsedIterations() >= this-
> > >m_NumberOfIterations) ||
> > >       ( this->GetMaximumRMSError() >= m_RMSChange ) );
> > > While the Halt function returns false the evolution continues.
> > > However, in iteration 0, I get m_RMSChange = 0, so the evolution
> > always
> > > stops doing 0 iterations (since the condition this-
> > >GetMaximumRMSError() >=
> > > m_RMSChange becomes true)
> > > If I modify the Halt function to returm the following:
> > > if(this->GetElapsedIterations()==0)
> > >         return false;
> > > else
> > >         return ( (this->GetElapsedIterations() >=
> > > this->m_NumberOfIterations) || ( this->GetMaximumRMSError() >=
> > m_RMSChange )
> > > );
> > > then it works.
> > > The other problem is that RMSChange in the next iterations
> > (1,2,3...) has
> > > very big values (like 5000) even near convergence. So the only way
> > to stop
> > > the evolution is through the iterations number.
> > >
> > > I am still investigating the class and I am not absolutely sure
> > about the
> > > points mentioned but I would like to share with you for more  
> advice.
> > >
> > >
> > > Thank you very much,
> > > Lena
> > >
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: Luis Ibanez [mailto:luis.ibanez at kitware.com<luis.ibanez at kitware.com
> > >
> > > ]
> > > Sent: Mon 6/1/2009 8:39 PM
> > > To: Sgouritsa, Eleni
> > > Cc: alex gouaillard; insight-users at itk.org
> > > Subject: Re: [Insight-users]
> > itkScalarChanAndVeseSparseLevelSetImageFilter
> > >
> > >
> > > Hi Lena,
> > >
> > > Could you please be more specific about your problem report on
> > > item (2) ?
> > >
> > > Is there a chance that you can report this in a form that
> > > we could reproduce ?
> > >
> > >
> > >     Thanks
> > >
> > >
> > >        Luis
> > >
> > >
> > > -----------------------------
> > > Sgouritsa, Eleni wrote:
> > > > Hi,
> > > >
> > > > I have two more questions.
> > > > 1. In the insight journal code there was an option
> > > > SetReverseExpansionDirection to control if the expansion of the
> > level
> > > > set will be inwards or outwards. How can I do it using the
> > > > itkScalarChanAndVeseSparseLevelSetImageFilter of 3.14 release?
> > > >
> > > > 2. I still have a problem when my 3D data have negative origin.
> > > >
> > > > Thanks and regards,
> > > > Lena
> > > >
> > > > -----Original Message-----
> > > > From: Sgouritsa, Eleni
> > > > Sent: Mon 6/1/2009 4:00 AM
> > > > To: alex gouaillard
> > > > Cc: insight-users at itk.org
> > > > Subject: RE: [Insight-users]
> > > itkScalarChanAndVeseSparseLevelSetImageFilter
> > > >
> > > > Hello,
> > > > finally the second issue was my fault (I just had a problem  
> while
> > > > including the header files of the review folder).
> > > > For the first, the inconsistency is just a matter of name. The
> > code runs
> > > > correctly, just the name assignement in the txx is a little
> > misleading.
> > > >
> > > > Thank you very much,
> > > > Lena
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: alex gouaillard
> > [mailto:alexandre_gouaillard at hms.harvard.edu<alexandre_gouaillard at hms.harvard.edu
> > >
> > > ]
> > > > Sent: Sun 5/31/2009 11:34 PM
> > > > To: Sgouritsa, Eleni
> > > > Cc: insight-users at itk.org
> > > > Subject: Re: [Insight-users]
> > > itkScalarChanAndVeseSparseLevelSetImageFilter
> > > >
> > > > hi eleni,
> > > >
> > > > we'll take a look tomorrow.
> > > >
> > > > thanks for the feedback.
> > > >
> > > > alex.
> > > >
> > > > On May 31, 2009, at 11:52 PM, Sgouritsa, Eleni wrote:
> > > >
> > > >  > Hello,
> > > >  > I know that the review folder of the new release (3.14) is  
> not
> > > >  > stable yet but I would just like to give two comments:
> > > >  >
> > > >  > 1. I found an inconsistency between the template arguments of
> > the
> > > >  > itkScalarChanAndVeseSparseLevelSetImageFilter.h and the
> > > >  > itkScalarChanAndVeseSparseLevelSetImageFilter.txx.
> > > >  > Specifically, in the header file, the template is :
> > > >  > template < class TInputImage, class TFeatureImage, class
> > > >  > TOutputImage, class TFunction,
> > > >  >   class TSharedData, typename TIdCell = unsigned int >
> > > >  > whereas in the txx it is:
> > > >  > template < class TInput, class TFeature, class TFunction,
> > > >  > class TOutputPixel, class TSharedData, typename TIdCell >
> > > >  > There is a change in the order of the 3rd and 4th argument.
> > > >  >
> > > >  > 2. I can not find this class
> > > >  > (itkScalarChanAndVeseSparseLevelSetImageFilter)  incuded in  
> the
> > > >  > CMakeLists of the review folder
> > > >  >
> > > >  > Regards,
> > > >  > Lena
> > > >  >
> > > >  > <ATT00001.txt>
> > > >
> > > >
> > > >
> > > >
> > > >
> >  
> ------------------------------------------------------------------------
> > > >
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> > >
> >
> >
> >
> > <ATT00001.txt>
>
>
>
> <ATT00001.txt>

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