[Insight-users] Granulometry filter in ITK?

Mon Nov 16 09:46:22 EST 2009

Hi,

There is no filter ready to use for this task in ITK at this time.  
However, I believe that most of the tools needed are there.

If I get it right, you want to do the local texture analysis used page  
322 of Soille's book to segment the two kind of forest. As I  
understand it, with a statistics which is the size of the kernel for  
the maximum value of the derivative, it can be computed that way:

Input: I (the input image), KL (the kernel list), N (the neighbourhood  
where the statistics is computed)
D = domain(I)
M = localMean(I)
O = newImage(D, 0)
for k in KL
   I = opening(I, k)
   M2 = localMean(I, N)
   for i in D
     if M2[i] > M[i]:
       O[i] = size(k)
   M = M2
return O

If the neighbourhood used to compute the mean is a box, it can be  
efficiently computed with http://www.itk.org/Doxygen/html/classitk_1_1BoxMeanImageFilter.html
Richard and I have also contributed some efficient filters for  
morphological opening - http://hdl.handle.net/1926/555 , already in  
ITK Review.

The last missing thing is the implementation of the main algorithm  
above, and the contribution to the insight journal ;-)

Gaëtan

Le 15 nov. 09 à 22:11, Richard Beare a écrit :

> The other easy option to get a histogram of sizes (which doesn't rely
> on segmenting the image into independent blobs, as the label map
> approach does) is to look at regional maxima in the distance transform
> of your mask. This gives basically the same information as a series of
> openings/area measures used to produe the traditional granulometry.
>
> On Mon, Nov 16, 2009 at 2:30 AM, Luis Ibanez  
> <luis.ibanez at kitware.com> wrote:
>> Hi Lynx,
>>
>> Is it your final goal to produce a Histogram of grain sizes ?
>>
>>
>> If so,
>> You may find useful the LabelMap classes that were recently added
>> to the Code/Review directory.
>>
>> They are described in the following Insight Journal paper:
>>
>> "Label object representation and manipulation with ITK"
>> Lehmann G.
>> INRA
>> http://www.insight-journal.org/browse/publication/176
>> http://hdl.handle.net/1926/584
>>
>> In particular, you may want to use the filter:
>>
>>     itkShapeLabelMapFilter
>>
>> to compute the volumes of granules present in the image,
>> and the use the itk::Histogram for building a summarized
>> representation of these population.
>>
>> You may also find useful this other Insight Journal paper:
>>
>> "A Label Geometry Image Filter for Multiple Object Measurement"
>> Padfield D., Miller J.
>> GE Global Research
>> http://www.insight-journal.org/browse/publication/301
>> http://hdl.handle.net/1926/1493
>>
>>
>>       Regards,
>>
>>
>>             Luis
>>
>>
>> --------------------------
>> On Sun, Nov 15, 2009 at 4:22 AM,  <lynx.abraxas at freenet.de> wrote:
>>> Hello again!
>>>
>>>
>>> I've  to  specify  me  need:  I'm  looking  for a segmentation  
>>> filter based on
>>> granulometry like the forrest classification example in Pierre  
>>> Soille book.  I
>>> found   an   IJ   plugin   (sadly   onl   for   2D  granulometry   
>>> evaluation):
>>> http://rsbweb.nih.gov/ij/plugins/download/Granulometry_.java
>>>
>>> Regrads,
>>> Lynx
>>>
>>> On 15/11/09 09:45:24, lynx.abraxas at freenet.de wrote:
>>>> Hello everybody!
>>>>
>>>>
>>>> I read about Granulometry in Pierre Soille book and now I'm  
>>>> wondering if there
>>>> is some kind of Granulometry filter in ITK or some other package?
>>>>
>>>> If not what would be the best way in ITK to extract subvolumes to  
>>>> create  such
>>>> a filter?
>>>>
>>>> Thanks for any hints or help.
>>>> Lynx
>>>>
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>
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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.itk.org
http://www.mandriva.org  http://www.bepo.fr

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