[Insight-developers] Re: [Insight-users] concept checking in AccumulateImageFilter

Alberto Bert bert at isi.it
Thu Mar 16 14:27:46 EST 2006 

On Mar 16, 2006 at 10:22:09AM +0100, Gaetan Lehmann wrote:
> 
> Hi,
> 
> The code is modified - are perhaps I should say rewritten at this point -  
> and now accept both N and N-1 dimensions for output image.
> Please, look at  
> http://insight-journal.org/view_reviews.php?back=publications.php%3Fjournalid%3D4%26order%3D%26revision_display%3D&pubid=71  
> .

I watched at the article, but there's something I don't understand,
probably cause I don't know how the information is organized.

I downloaded a .pdf file of the 5th revision (the last one) explaining
all the details of the new filter, which is called
ProjectionImageFilter. But if I try to see the doxygen documetation,
it's not there. Is there a time delay for the doxygen updating, or I'm
missing something.

BTW, I'm using a tar-ball distribution of itk right now, when the new
filter will be included in a new tar-ball? Should I switch to the cvs?
I didn't do it yet since the itk site suggests to use tar-ball dists...
How much will I need to care about stability of the code, if I turn into
cvs?

> It would also be nice if you can test the code, and post a review.

I'll certainly do it.

bye
Alb

> 
> Regards,
> 
> Gaetan
> 
> 
> On Thu, 16 Mar 2006 03:02:36 +0100, Alberto Bert <bert at isi.it> wrote:
> 
> >Hi,
> >
> >I'm one of the people that is using that filter and as Luis poited
> >out, it would be resonable to have a N-1 output image dimension.
> >Right now, I'm just casting the output to reduce the dimension.
> >
> >Are you gus planning to change the code or not?
> >
> >Cheers
> >Alberto
> >
> >On Mar 02, 2006 at 11:22:01AM +0100, Gaetan Lehmann wrote:
> >>
> >>Hi,
> >>
> >>I have checked the AccumulateImageFilter code, and reduce a dimension  
> >>will
> >>work properly only if the dimension is the last one.
> >>
> >>The wanted behavior is, I think, the following one: the dimension which  
> >>is
> >>removed must take the place of the projection dimension.
> >>
> >>For example, for 3D -> 2D:
> >>. projection dim=0
> >> 1->1
> >> 2->0
> >>. projection dim=1
> >> 0->0
> >> 2->1
> >>. projection dim=2
> >> 0->0
> >> 1->1
> >> in that case, there is nothing special: the projected dimension is the
> >>removed one
> >>
> >>AccumulateImageFilter do not take care of that, and so, for 3D to 2D,  
> >>only
> >>the projection on the dimension 2 will work properly.
> >>
> >>Gaetan
> >>
> >>
> >>
> >>On Thu, 02 Mar 2006 01:46:37 +0100, Casey Goodlett <gcasey at gmail.com>
> >>wrote:
> >>
> >>>Hello,
> >>>
> >>>I was the person who initially reported this difficulty to Amy.  I have
> >>>existing code that uses the AccumulateImageFilter to find the mean of
> >>>several volumes stacked into a 4D dataset from the TileImageFilter.  I
> >>>have
> >>>several 3D vector image volumes which I stack into a 4D volume using
> >>>TileImageFilter, and then I use the accumulate filter to find the mean  
> >>3D
> >>>volume.  Requiring the mean image to remain in 4D requires the headache
> >>>of
> >>>further processing to reduce it to a 3D volume.  The AccumulateFilter
> >>>already works for me in going from ND to (N-1)D so there are no code
> >>>changes
> >>>required.
> >>>
> >>>Can the concept check allow either the same dimension or one less,
> >>>because
> >>>people may already be using either of these conventions?  I dont think
> >>>enforcing either one exclusively is a good idea in terms of backwards
> >>>compatibility.
> >>>
> >>>I can provide sample code if necessary, but I'd need to extract it  
> >>from a
> >>>larger project.
> >>>
> >>>Casey Goodlett
> >>>
> >>>On 3/1/06, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> >>>>
> >>>>
> >>>>Hi Gaetan,
> >>>>
> >>>>We agree with you that according to the Doxygen documentation
> >>>>of the filter, the dimensions of the input image and the output
> >>>>image should be the same.
> >>>>
> >>>>
> >>>>However, what is a stake here is the conceptual correctness
> >>>>of the filter. (we can fix the Doxygen documentation accordingly).
> >>>>
> >>>>
> >>>>
> >>>>Since the filter is integrating an image across one dimension,
> >>>>it is equivalent to computing the integral of a function of
> >>>>N-variables along a range of one of those N variables.
> >>>>
> >>>>
> >>>>Something like:
> >>>>
> >>>>
> >>>>          Sum{ F(x,y,z) }    from Z=-inf to Z=inf
> >>>>
> >>>>
> >>>>which we would expect to become a function of the remaining
> >>>>variables,
> >>>>
> >>>>
> >>>>something like
> >>>>
> >>>>
> >>>>          G(x,y).
> >>>>
> >>>>
> >>>>If you take a CT scan and integrate the values along the Z
> >>>>direction, conceptually this is close to generating a DRR
> >>>>(an X-Ray) of that 3D CT image, and therefore it seems
> >>>>reasonable to expect that output image to be a 2D image.
> >>>>
> >>>>
> >>>>Expecting the integral of a 3D function to be a 3D degenerate
> >>>>function (a 3D image of 1 slice) is a dangerous approach, because
> >>>>then filters that are applied to the accumulated image will
> >>>>assume that is a 3D image. For example a gradient will not work
> >>>>properly on the accumulated image.
> >>>>
> >>>>
> >>>>
> >>>>I don't see any difficulty on writing the code for a (N) to (N-1)
> >>>>dimensional image. We only need a linear iterator, and a while loop.
> >>>>The GenerateData method shouldn't require more than 50 lines of code.
> >>>>
> >>>>
> >>>>
> >>>>Have you used this filter ?
> >>>>
> >>>>
> >>>>Could you post some of the cases for which you use this filter ?
> >>>>
> >>>>
> >>>>
> >>>>That could help us to understand if the output should be a
> >>>>N-dimensional or an (N-1)-dimensional image.
> >>>>
> >>>>
> >>>>
> >>>>    Please let us know,
> >>>>
> >>>>
> >>>>
> >>>>        Thanks
> >>>>
> >>>>
> >>>>
> >>>>           Luis
> >>>>
> >>>>
> >>>>
> >>>>--------------------
> >>>>Gaetan Lehmann wrote:
> >>>>> Hi,
> >>>>>
> >>>>> The check is correct. The output is an image of the same dimension  
> >>to
> >>>>keep the
> >>>>> info of the output image on the same dimension (the docstring is
> >>>>surely
> >>>>a lot
> >>>>> more clear than me).
> >>>>> I don't think it will work if you try to build it with a dim=3 in
> >>>>input
> >>>>and
> >>>>> dim=2 in output.
> >>>>> It would be nice to be able to set the dim=3 or dim=2 in output, but
> >>>>the
> >>>>code
> >>>>> will surely be difficult to write.
> >>>>>
> >>>>> Gaetan
> >>>>>
> >>>>>
> >>>>> On Wednesday 01 March 2006 21:04, Amy Squillacote wrote:
> >>>>>
> >>>>>>Hi all,
> >>>>>>
> >>>>>>There is currently a check in the header file of the
> >>>>>>AccumulateImageFilter (in Code/BasicFilters) for whether the input
> >>>>>>and output images have the same dimension.  Another ITK developer
> >>>>>>pointed out to me a couple days ago that this concept check is
> >>>>>>probably wrong.  He suggested that the dimension of the output  
> >>should
> >>>>>>actually be one less than that of the input.  Luis and I discussed
> >>>>>>this earlier today, and we believe that the output's dimension  
> >>should
> >>>>>>be one less than that of the input.  However, if we make this  
> >>change,
> >>>>>>anyone's code depending on the input and output to have the same
> >>>>>>dimensionality would break.
> >>>>>>
> >>>>>>What has been the experience of other people using this filter?   
> >>What
> >>>>>>is your opinion about the dimensionality of the input and output of
> >>>>>>this filter?
> >>>>>>
> >>>>>>- Amy
> >>>>>>
> >>>>>>_______________________________________________
> >>>>>>Insight-users mailing list
> >>>>>>Insight-users at itk.org
> >>>>>>http://www.itk.org/mailman/listinfo/insight-users
> >>>>>>
> >>>>>>
> >>>>>>------------------------------------------------------------------------
> >>>>>>
> >>>>>>_______________________________________________
> >>>>>>Insight-users mailing list
> >>>>>>Insight-users at itk.org
> >>>>>>http://www.itk.org/mailman/listinfo/insight-users
> >>>>
> >>>>_______________________________________________
> >>>>Insight-developers mailing list
> >>>>Insight-developers at itk.org
> >>>>http://www.itk.org/mailman/listinfo/insight-developers
> >>>>
> >>
> >>
> >>
> >>--
> >>Gaëtan Lehmann
> >>Biologie du Développement et de la Reproduction
> >>INRA de Jouy-en-Josas (France)
> >>tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
> >>http://voxel.jouy.inra.fr
> >>_______________________________________________
> >>Insight-users mailing list
> >>Insight-users at itk.org
> >>http://www.itk.org/mailman/listinfo/insight-users
> >_______________________________________________
> >Insight-users mailing list
> >Insight-users at itk.org
> >http://www.itk.org/mailman/listinfo/insight-users
> 
> 
> 
> -- 
> Gaëtan Lehmann
> Biologie du Développement et de la Reproduction
> INRA de Jouy-en-Josas (France)
> tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
> http://voxel.jouy.inra.fr
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