[Insight-users] Attribute opening in 3D images

Mon Dec 22 08:11:06 EST 2008

Well, i took a look at "Label objetc representation and manipulation with 
ITK".

I guess the output of the AreaOpeningImageFilter is an itk:Image. So I need 
a filter to obtain a Label Image (itk::Image) from the output of the area 
opening filter and then use a LabelImage to LabelMap or LabelCollection 
filter to keep moving with a LabelObject representation of the connected 
components.

David

----- Original Message ----- 
From: "David Pastor" <david.pastor at die.upm.es>
To: <Richard.Beare at ieee.org>; "Gaëtan Lehmann" <gaetan.lehmann at jouy.inra.fr>
Cc: "Dan Mueller" <dan.muel at gmail.com>; <insight-users at itk.org>
Sent: Monday, December 22, 2008 12:49 PM
Subject: Re: [Insight-users] Attribute opening in 3D images

> Yes, very useful both packages. As I only need area opening I'll try with 
> the Richard's implementation that should be faster.
>
> I've seen what u mean with the coding styles, but I expect it won't be a 
> problem.
>
> Just to get it clear to myself, the output is just an image where the 
> peaks are thresholded to the level that satisfy the lamda and the rest 
> image is left as the original. So at the end we obtain a set of flat 
> regions (connected sets) with area = Lambda (with different gray leves) 
> and the background original image.
>
> At this point a I need to get a label objects collection for further 
> processing. I need an alternative filter to 
> "itk::BinaryImageToLabelCollectionImageFilter" for an image with flat 
> regions at different levels. Could it be ConnectedComponentsImageFilter?
>
> On the other hand I've seen some related stuff like 
> itkLabelAttributeOpeningImageFilter and 
> itkShapeAttributeOpeningImageFilter, but I guess they should be used after 
> converting the image into a label collection.
>
> Cheers,
> DAvid
>
>
>
> ----- Original Message ----- 
> From: "Richard Beare" <richard.beare at gmail.com>
> To: "Gaëtan Lehmann" <gaetan.lehmann at jouy.inra.fr>
> Cc: "Dan Mueller" <dan.muel at gmail.com>; "David Pastor" 
> <david.pastor at die.upm.es>; <insight-users at itk.org>
> Sent: Saturday, December 20, 2008 1:05 AM
> Subject: Re: [Insight-users] Attribute opening in 3D images
>
>
> Yes, that's right - the one I wrote only does area/volume attribute
> operations, which are the ones I have used most commonly (in fact I
> suspect exclusively). It uses the algorithm described by Michael
> Wilkinson in PAMI. I think I used some non itk coding styles to allow
> direct translation of the algorithm.
>
> On Sat, Dec 20, 2008 at 12:15 AM, Gaëtan Lehmann
> <gaetan.lehmann at jouy.inra.fr> wrote:
>>
>> Le 19 déc. 08 à 12:35, Dan Mueller a écrit :
>>
>>> Hi David,
>>>
>>> Richard Beare also contributed some attribute morphology classes
>>> (though I'm not sure of the full details/implementation/etc. You'll
>>> have to check the paper yourself:
>>>
>>> http://www.insight-journal.org/browse/publication/203
>>>
>>
>> Err, yes, just forgot to cite this one — I'm using it often though.
>> I think it can't handle as much kind of attributes than what can be done
>> with component trees, but for the size opening, it gives much efficients
>> results.
>>
>>> Make sure you leave a review!
>>>
>>> HTH
>>>
>>> Cheers, Dan
>>>
>>> 2008/12/19 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>:
>>>>
>>>> Le 19 déc. 08 à 11:46, David Pastor a écrit :
>>>>
>>>>> Dear all,
>>>>>
>>>>> First, just say hello to everybody (this is my first go on the mailing
>>>>> list).
>>>>>
>>>>> We are using ITK for some image processing based on morphology and I'm
>>>>> missing some attribute openings (closings) filters on the API. I'd 
>>>>> like
>>>>> to
>>>>> know if there is some ongoing work on that or there is some code that 
>>>>> i
>>>>> can
>>>>> reuse to build up a solution.
>>>>>
>>>>> I've seen there is an implementation of a Priority Queue... but maybe 
>>>>> it
>>>>> would be better to use some other potentially faster implementations
>>>>> like
>>>>> Max trees or Union Sets algorithms.
>>>>>
>>>>
>>>> Hi,
>>>>
>>>> I've contributed some code both for the grayscale and the binary case.
>>>> The
>>>> grayscale version is based on max trees - I've called them component
>>>> trees.
>>>> Both are usable (and used) now, but the one for the grayscale case 
>>>> still
>>>> lacks some doc.
>>>> You can get it from the insight journal or from the main repository to
>>>> get
>>>> the last improvements/fixes.
>>>>
>>>> Binary case:
>>>>
>>>> http://www.insight-journal.org/browse/publication/176
>>>> http://voxel.jouy.inra.fr/darcs/contrib-itk/binaryAttributeMorphology/
>>>>
>>>> Grayscale case:
>>>>
>>>> http://www.insight-journal.org/browse/publication/210
>>>> http://voxel.jouy.inra.fr/darcs/contrib-itk/componentTree/
>>>>
>>>> Any comments or improvements are welcome!
>>>>
>>>> Regards,
>>>>
>>>> Gaëtan
>>>>
>>>>
>>>> --
>>>> 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.mandriva.org
>>>> http://www.itk.org  http://www.clavier-dvorak.org
>>>>
>>>>
>>>> _______________________________________________
>>>> 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  http://www.mandriva.org
>> http://www.itk.org  http://www.clavier-dvorak.org
>>
>>
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>> Insight-users mailing list
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>>
>>
>
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