[Insight-users] Attribute opening in 3D images

Gaëtan Lehmann gaetan.lehmann at jouy.inra.fr
Mon Dec 22 14:21:17 EST 2008 

Le 22 déc. 08 à 14:11, David Pastor a écrit :

> Well, i took a look at "Label objetc representation and manipulation  
> with ITK".
>
> I guess the output of the AreaOpeningImageFilter is an itk:Image.

that's it

> So I need a filter to obtain a Label Image (itk::Image)

A label image or a binary image, as you prefer:  
BinaryImageToLabelMapFilter will search the connected component for  
you in case of a binary 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.

If you want to get the flat regions extracted by the  
AreaOpeningImageFilter, you can use itk::RegionalMaximaImageFilter to  
have them as a binary image.
Then convert to a LabelMap with BinaryImageToLabelMapFilter.

Gaëtan


PS: LabelMap is the new name of the LabelCollectionImage —  
LabelCollectionImage was too long to type and the word Image is  
already used in several ways in ITK (LabelImage, BinaryImage, …) so  
LabelCollectionImage can be seen as a new special content of an Image.  
Be sure to read the last version of the article!
Also, the last version of the sources is here: http://voxel.jouy.inra.fr/darcs/contrib-itk/binaryAttributeMorphology/binaryAttributeMorphology.tar.gz

>
>
> 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
>>>
>>>
>>> _______________________________________________
>>> Insight-users mailing list
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>>>
>>
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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.mandriva.org
http://www.itk.org  http://www.clavier-dvorak.org

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