[Insight-users] Stop flooding pools when "water sheds" would be introduced or use "fill holes" for that

[Gaëtan Lehmann]

Hi,

A possible way to achieve that is to use the Component Tree  
representation.

In a component tree, all the connected component at all the grey level  
are stored in a tree. In your illustration, everything labeled with 1,  
2 or 3 is a branch of the tree with no ramification and terminated by  
a leaf.

    __ ________  ___
..             .333...
   .11.22222222. .3.
    .. .2222...   .
        .22.
         ..

With the component tree representation, it should be easy to tag the  
node in the tree with the required characteristics with a label, as in  
your illustration, and the others with a specific label - for example 0.

I've made a contribution a few years ago on the insight journal on the  
component trees. The article is of very poor quality if I remember  
correctly, but the code to generate and manipulate the component tree  
is there.

Gaëtan



Le 18 févr. 10 à 22:50, Richard Beare a écrit :

> Hi,
> I think I understand what you're getting at. I think that what you
> want to do is find the first grey level at which a basin meets a
> neighbour and designate members of the basin that are less than that
> as members of your ourput label. It has to be strictly less than,
> otherwise plateaus between basins will be included. I don't recognise
> this offhand as a standard operation or as equivalent to any standard
> combination. I'll have to think about that further. Note that while it
> looks like a useful thing in 1D there is a fair chance that it will
> prove a lot less useful in 2Dor 3D, but it is worth checking out.
>
> I can think of a couple of ways of tackling this, but both require
> modified filters. The nice way, I think, is to extend the watershed
> filter. The changes involve recording the grey level at which each
> label first meets a neighbour and then do a post processing step which
> sets each label pixel with a corresponding grey level greater than or
> equal to this to zero. I think the watershed needs to run to
> completion before this step because detecting the collisions is needed
> to find the overflow value.
>
> The alternative sounds like more of a hack, but probably just as fast,
> and nicely isolated from the other filters. Basically you would check
> the grey values at the border of each labelled region to find the
> minimum and then perform the same post processing step. This could be
> done in a single filter that you apply as a post processing step to
> the watershed.
>
> On Thu, Feb 18, 2010 at 6:34 PM,  <lynx.abraxas at freenet.de> wrote:
>> On 17/02/10 21:49:09, Kishore Mosaliganti wrote:
>>> Hi Lynx,
>>>
>>> From your description, I understand that you don't want flat regions
>>> in the image to be covered by the watershed labels. In other words,
>>> you want the labels to exactly cover pixels that lead to a mimina.  
>>> Is
>>> that right?
>>
>> Hello Kishore, Richard and Luis,
>>
>>
>> Yes  that's  pretty  much what I want but with the addition that I  
>> only want a
>> label-mask where every pixel is definitly only leading to one  
>> definit minimum.
>>
>> Here's a simple 1D illustration (for momospaced fonts):
>>
>>    __ ________  ___
>>  ..             .333...
>>   .11.22222222. .3.
>>    .. .2222...   .
>>        .22.
>>         ..
>>
>> The  dots  plot  graph  represents  the greyvalue in y-direction  
>> and the pixel
>> position in x-direction. The numbers represent the labels and   
>> their  seize  I
>> neeed.  They  are  like  a  pool filled only up to a local maxima,  
>> in 2D those
>> points would be saddle points but I don't know what they'd be in 3D.
>>
>> The white interrupted line above is the mask I would need to mask   
>> the  result
>> from  the  itk morphological watershed to achieve what I want. (I  
>> tried to get
>> this mask from the fill holes filter but something is wrong).
>>
>> So I'm either looking for a filter (chain) that could create me  
>> this mask,
>> Or if it would be possible to stop the watershed filter from   
>> filling  up  the
>> basins at the corresponding heights (in 2D a saddle point).
>>
>> I'll paint a drawing to post as well.
>>
>>
>> I hope this helps understanding my problem. If not let me know.
>>
>> Many thanks for looking into this and trying to understand my  
>> problem.
>>
>> Thanks,
>> Lynx
>>
>>
>>
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-- 
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  http://www.itk.org
http://www.mandriva.org  http://www.bepo.fr

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