[Insight-users] Re: long time delay during implementation of MathematicalMorphologyBinaryFilters

Sun Apr 22 08:17:38 EDT 2007

Hi,

Just some comments and corrections:

  - you must build your project in release mode to get all the  
efficiency of ITK. According to your logs, your project is built in  
debug mode.

  - 15 is not really huge. I was frequently running some binary  
closing/opening with structuring element of radius 30x30x15 some  
months ago

  - the binary filters are not using the brute force algorithm.  
However, the algorithm used in very sensible to the content of the  
image, especially the number of pixels on the border of the object,  
so depending of the contente of the image, the filter of the  
consolidatedMorphology contribution may give better results. If a box  
structuring element is used the consolidatedMorphology will most of  
the time give better results.

  - most of the time we are doing a opening with such a big  
structuring element to remove the objects in the image to small to be  
an object of interest. This method is really inefficient when the  
objects are big, and a opening by size should be prefered. A (not  
officialy published yet) contribution would let you do that  
efficiently: http://voxel.jouy.inra.fr/darcsweb/darcsweb.cgi? 
r=binaryAttributeMorphology;a=summary . To give an example, an image  
of 512x512x70 is filtered in less than 2 second on a recent computer,  
without dependency on the size of the object to remove.

Gaëtan

Le 22 avr. 07 à 11:04, Richard Beare a écrit :

> Hi,
>
> This is definitely a problem with the default morphology operators -
> they use a direct implementation of max and min over a neighborhood.
> Gaetan and I have been working on faster versions that can give
> implementation times that are independent of SE size, depending on the
> shape of the SE. There are also versions that handle arbitary shape
> and knock one dimension off the complexity - i.e a  x by y by z SE
> will have comlexity x by y instead of x by y by z. The former uses the
> vanHerk, Gil, Werman decomposition while the latter uses the
> Talbot/vanDrogenBroek method.
>
> Anyway, a preliminary version of this was posted to insight journal
> while the current version we use is available in Gaetan's darcs
> repository:
>
> http://voxel.jouy.inra.fr/darcsweb/darcsweb.cgi
>
> The one you are after is consolidatedMorphology.
>
> ITK is missing quite a few of these efficient implementations of quite
> important filters and we are working on them. In many cases this will
> give filters that are similar to the current gaussian smoothing
> filters in terms of complexity because they use recursive techniques
> and decomposition.
>
> On 4/22/07, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>
>> Hi Alireza,
>>
>> A an structural element of radius 15 is Hughe !!.
>>
>> That easily explains that your processing is taking so long.
>>
>>
>> Are you sure that you need such a large structuring element ?
>>
>>
>> What is the size (in pixels) of the image features that you
>> are trying to eliminate ?
>>
>>
>> What is the size (in pixels) of your image. ?
>>
>>
>> Please let us know,
>>
>>
>>     Thanks
>>
>>
>>        Luis
>>
>>
>> ------------------------
>> Alireza Salamy wrote:
>> > hi luis,
>> > I have try to implement
>> > MathematicalMorphologyBinaryFilters.cxx on my 3D.dicom volume  
>> image ,but
>> > it is now around 1 hour that I have debuded it,but it hasn't  
>> finished
>> > yet.the only change that I made to the code:1-I changed the  
>> Dimension
>> > from 2 to 3
>> > 2-set the radius equal to 15
>> > and bellow is mu command line:
>> > C:\>"C:\Documents and Settings\Alireza\Desktop\Segmentation of  
>> Tumors in
>> > MRI\Ins
>> > ightToolkit-3.2.0\ITKb\bin\debug 
>> \MathematicalMorphologyBinaryFilters.exe"
>> > "C:\Do
>> > cuments and Settings\Alireza\Desktop\Segmentation of Tumors in
>> > MRI\InsightToolki
>> > t-3.2.0\ITKb\bin\debug\test.dcm" "C:\Documents and
>> > Settings\Alireza\Desktop\Segm
>> > entation of Tumors in MRI\InsightToolkit-3.2.0\ITKb\bin\debug 
>> \ero1.dcm"
>> > "C:\Docu
>> > ments and Settings\Alireza\Desktop\Segmentation of Tumors in
>> > MRI\InsightToolkit-
>> > 3.2.0\ITKb\bin\debug\dil1.dcm" 300  1750
>> > so what's wrong with that?
>> > it is too important for me to check out what's wrong with  
>> that!!!!!???
>> > Thanks for your help
>> > Alireza
>> >
>> >  
>> --------------------------------------------------------------------- 
>> ---
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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

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