[Insight-users] Granulometry filter in ITK?

Gaëtan Lehmann gaetan.lehmann at jouy.inra.fr
Mon Nov 16 09:58:31 EST 2009 

Le 16 nov. 09 à 15:46, Gaëtan Lehmann a écrit :

>
> 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]:

Sorry, obviously, this is not the right check. The difference between  
M2[i] and M[I] must be compared to the highest derivative seen before  
- I should re-read my mails before sending them.

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)
H = newImage(D, 0)
for k in KL
   I = opening(I, k)
   M2 = localMean(I, N)
   for i in D
     d = M[i] - M2[i]
     if d > H[i]:
       O[i] = size(k)
       H[i] = d
   M = M2
return O

>      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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>
> -- 
> 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
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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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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