[Insight-users] Issue with BinaryErodeImageFilter

Wed Sep 12 17:00:46 EDT 2007

Le 12 sept. 07 à 22:42, Robert Tamburo a écrit :

> Hi Dan,
>
>> To perform erosion in a slice-by-slice manner,
>> you simply set one of the sizes in your structuring element to zero,
>> eg. Size=[1,1,0].
> Worked like a charm!

so there is no bug in the filter - great :-)

>
>> Alternatively, if eventually you want to apply other
>> filters on a slice-by-slice basis, you could employ the
>> SliceBySliceImageFilter which Gaetan submitted to the Insight  
>> Journal:
>>    http://insight-journal.org/dspace/handle/1926/368
> Nice filter. I had just finished writing a sizeable chunk of code  
> to do that. Oops.
>

If you think it can be useful, please submit a (small) review!
Several people said they were interested, but nobody has posted a  
review until now...

Thanks,

Gaëtan

> Thanks again,
> Robert
>
> On Sep 12, 2007, at 3:11 PM, Dan Mueller wrote:
>
>> Hi Robert,
>>
>> I had a look at your data, it seems to be highly anisotropic (the
>> out-of-plane resolution is much bigger than the in-plane resolution,
>> Spacing=[1.87500, 1.87500, 7.00000]). In this case perhaps 3-D  
>> erosion
>> is not really suitable. To perform erosion in a slice-by-slice  
>> manner,
>> you simply set one of the sizes in your structuring element to zero,
>> eg. Size=[1,1,0]. Alternatively, if eventually you want to apply  
>> other
>> filters on a slice-by-slice basis, you could employ the
>> SliceBySliceImageFilter which Gaetan submitted to the Insight  
>> Journal:
>>    http://insight-journal.org/dspace/handle/1926/368
>>
>> In terms of boundary conditions, the BinaryErodeImageFilter uses a
>> ConstantBoundaryCondition with pixels outside set to zero:
>>    see Code/BasicFilters/itkBinaryMorphologyImageFilter.txx, line  
>> 201-204
>>
>> Welcome to the world of open-source, where you can peer directly into
>> the guts of the code to see how the algorithm is implemented!
>>
>> HTH
>>
>> Cheers, Dan
>>
>> On 13/09/2007, Robert Tamburo <robert.tamburo at gmail.com> wrote:
>>> Hi Gaëtan and Dan,
>>>
>>> Thanks for the replies.  I've uploaded the code and data to http://
>>> www.tamburo.us/temp/erosion_files/erosion.zip
>>>
>>> Dan, that does make some sense. I forgot that the structure element
>>> was a sphere and not a disc. I suppose that I was expecting a slice
>>> by slice erosion in the volume. Is there currently a way to do this?
>>> I tried using a 2D structure element, but received an awful error.
>>>
>>> How are boundary conditions handled? In the case that I removed the
>>> blank slices, what is being used as the "previous slice"? What
>>> accounts for the seemingly repeated first slice in the output image?
>>>
>>> Thanks again,
>>> Robert
>>>
>>>
>>> On Sep 11, 2007, at 6:29 PM, Dan Mueller wrote:
>>>
>>>> Hi Robert,
>>>>
>>>> From your description, it appears the erode filter is working
>>>> correctly. If slice 0 and 18 are blank in your input image, after
>>>> eroding with a structuring element [1,1,1] I would expect slice  
>>>> 1 and
>>>> 17 to also be blank in the output. Remember, the erode filter takes
>>>> the minimum value of all those under the element; for slices 1  
>>>> and 17
>>>> the element will include pixels from slice 0 (and 2) and slice  
>>>> 18 (and
>>>> 16), which are blank (ie. the minimum). I don't think the
>>>> corresponding slice index is being moved, but simply the erosion  
>>>> has
>>>> been applied changing the shape for all given slices.
>>>>
>>>> As Gaetan said, providing the source code would be very helpful.  
>>>> Also,
>>>> perhaps you could upload your original 3-D dataset to the URL so we
>>>> can confirm nothing funny is happening.
>>>>
>>>> Anyway, hope this helps.
>>>>
>>>> Cheers, Dan
>>>>
>>>> On 12/09/2007, Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
>>>>>
>>>>> Hi Robert,
>>>>>
>>>>> Le 11 sept. 07 à 23:48, Robert Tamburo a écrit :
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I'm trying to use the erosion filter on a 3D binary image. I'm
>>>>>> using the itkBinaryErodeImageFilter with an
>>>>>> itkBinaryBallStructuringElement in the same way that is
>>>>>> demonstrated in the SoftwareGuide. The input image has a total of
>>>>>> 19 slices with the first and last slices being blank (black,
>>>>>> background). In the output image the first 2 and last 2 slices  
>>>>>> end
>>>>>> up being blank... two slices of data are missing.  Moreover, an
>>>>>> obviously corresponding slice no longer has the same index.
>>>>>>
>>>>>> I tried a couple of things to try and understand what was
>>>>>> happening. First, I tried padding the image with additional blank
>>>>>> slices. I added 1, 2, and 3 additional slices and got the same
>>>>>> results.  Then I tried removing the blank slices. No blank slices
>>>>>> were introduced. However, the index problem is still an issue.
>>>>>> I've created a temp web page with some screen captures to better
>>>>>> illustrate the problem. The URL is: http://www.tamburo.us/temp/
>>>>>> erosion.htm
>>>>>>
>>>>>> The results are confusing to me and not what I expected. Any
>>>>>> clarification on these issues would be greatly appreciated.  
>>>>>> Source
>>>>>> code and images can be made available if needed.
>>>>>
>>>>> The source code would be really useful. If you can send it,  
>>>>> I'll look
>>>>> at that problem tomorrow.
>>>>> In the mean time, here are some possible cause of the problem:
>>>>>   - be sure to call the CreateStructuringElement() method on the
>>>>> BinaryBallStructuringElement
>>>>>   - try with ITK cvs - it include a fix for a bug in ITK 3.2 which
>>>>> highly slow down the filter. The speed may not the only effect of
>>>>> that bug...
>>>>>
>>>>>>
>>>>>> Regards,
>>>>>> Robert
>>>>>>
>>>>>> P. S. I'm using a MacBook Pro with ITK version 3.2.0 and gcc  
>>>>>> 4.0.1.
>>>>>
>>>>> I'm doing the same - works great for me :-)
>>>>>
>>>>>> P. P. S. The documentation in the header for the erosion  
>>>>>> filter is
>>>>>> incorrect in that it describes dilation.
>>>>>
>>>>> I'll fix that (I must be the one who made that mistake). Thanks  
>>>>> for
>>>>> the report!
>>>>>
>>>>> Regards,
>>>>>
>>>>> Gaëtan
>
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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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