[Insight-users] bug in Morphology with parabolic structuring elements?

Fri Sep 17 10:06:49 EDT 2010

Hi Richard,

Since it did not work with my "specific" images, I am using the "simplest"
images to localize the problem.
By saying that I mean the following.

1) I use only gray-scale images with no multi-channels (RGB, CMYK, alpha,
etc...).
2) Voxel size is in a header and equals 1.
3) Intensity range is similar to that in your images.

4) To make it even more simple, I have not modified your programs 
so I keep all parameters the same as you suggested (SE, Borders, Scales,
etc..).

5) Images do not have any natural borders except "end of rows and columns".

6) I do not see any reasons why the closing  produces 
streak artifacts whereas the opening does not.
Do not forget that both were applied to the same image with the same
parameters.

BTW, in addition to the scale can I control the size of SE?
Did you commit changes to INRA or Isight-Journal?

Thanks,

Alex

Richard Beare wrote:
> 
> Hi,
> 
> The bright edge was definitely a bug - I forgot to change the way the
> "SafeBorder" was implemented for a closing. I think that is fixed now.
> Note that if your image already has a natural boundary then you can
> turn this off with the SetSafeBorder
> 
> The streaks that you're seeing that aren't related to the border are
> correct, I think. That sort of thing happens if the image structure
> matches the scale of the structuring element.
> 
> The blank image problem is less obvious, but I can think of a couple
> of things to check.
> 
> Does the input image have voxel spacing information? If so, does the
> scale of the structuring element seem appropriate. If the scale was
> very large then the bug with the edge safety would lead to an image
> with every voxel set to the maximum.
> 
> Anyway, the changes are committed, so we can test it out.
> 
> PS dilateBinary had been moved to dilateBinary3D
> 
> On Fri, Sep 17, 2010 at 1:48 AM, Oleksandr Dzyubak <adzyubak at gmail.com>
> wrote:
>>
>> Hi Richard,
>>
>> Many thanks for you prompt response.
>> I successfully downloaded the latest version from the link you provided.
>> I see that you greatly updated your package. Now you have 47 files vs 31
>> in
>> the submission!
>> In your Cmake file there was a typo giving me the error below.
>>
>>  CMake Error in CMakeLists.txt:
>>   Cannot find source file "dilateBinary.cxx".  Tried extensions .c .C
>> .c++
>>   .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp .hxx .in .txx
>>
>> So to get rolling, I just commented out the "dilateBinary.cxx" file from
>> my
>> building list.
>>
>> Yes, you are right. Now testClose works but in a way I did not expect it
>> to
>> (see uploaded result).
>>
>> Closed cthead1 Image.
>> http://old.nabble.com/file/p29729933/close_cthead1_x1_y05.png
>> close_cthead1_x1_y05.png
>>
>> I observe couple "artifacts" there (which do not appear in testOpen! ):
>> "White Border" and "Severe Streaks".
>>
>> However real Mystery starts later when I try to apply your Open-Close
>> algorithms to my images.
>> To demonstrate the problem, I also uploaded the input, opened, and closed
>> images.
>>
>> Input Image.
>> http://old.nabble.com/file/p29729933/SheppLogan_Proj_720.jpg
>> SheppLogan_Proj_720.jpg
>>
>> Opened Image.
>> http://old.nabble.com/file/p29729933/open_SheppLogan_Proj_720.jpg
>> open_SheppLogan_Proj_720.jpg
>>
>> Closed Image.
>> http://old.nabble.com/file/p29729933/close_SheppLogan_Proj_720.jpg
>> close_SheppLogan_Proj_720.jpg
>>
>> As you can see, testOpen still works but testClose does not.
>> Is that what you also observe in your tests or it is just me?
>>
>> Regards,
>>
>> Alex
>>
>>
>> Richard Beare wrote:
>>>
>>> Hi,
>>> There have been a few updates that aren't in the IJ version. You can
>>> get the latest version using
>>>
>>> darcs get
>>> http://voxel.jouy.inra.fr/darcs/contrib-itk/parabolicMorphology
>>>
>>> The biggest changes are classes for fast circular and spherical
>>> erosions and dilations on binary images.
>>>
>>>
>>> I've added testClose, in the way that you described, and it seems to
>>> run sensibly on the cthead test image. It is possible that there is a
>>> bug in the IJ version that I've fixed since.
>>>
>>>
>>> On Thu, Sep 16, 2010 at 6:06 AM, Oleksandr Dzyubak <adzyubak at gmail.com>
>>> wrote:
>>>>
>>>> Dear ITK users,
>>>>
>>>> Recently I tried classes "Morphology with parabolic structuring
>>>> elements"
>>>> by
>>>> Richard Beare.
>>>> Since it is not available in the ITK lib yet,
>>>> I downloaded the submission version from the link below.
>>>>
>>>> http://www.insight-journal.org/browse/publication/228
>>>>
>>>> BTW, on the submission page there is a recommendation which basically
>>>> does
>>>> not work.
>>>> *************
>>>> Please use this identifier to cite or link to this publication:
>>>> http://hdl.handle.net/1926/1370
>>>> *******
>>>> If I click on the provided link,
>>>> it gives (me at least) the error message "You cannot access this item!"
>>>>
>>>> In submission everything compiles well and provided examples work.
>>>> I am, in particular, interested in "Open-Close" morphological
>>>> operations.
>>>> Richard provided an example testOpen.cxx which works
>>>> and produces reasonable results.
>>>> Thus, I took it as basis to build testClose.cxx.
>>>>
>>>> To make my life easier, I included
>>>> #include "itkParabolicCloseImageFilter.h"
>>>>
>>>> and substituted
>>>> typedef itk::ParabolicOpenImageFilter< IType,IType > FilterType;
>>>> with
>>>>  typedef itk::ParabolicCloseImageFilter< IType,IType > FilterType;
>>>>
>>>> After those manipulations, I was able to succesfully compile my code
>>>> testClose.cxx.
>>>> However, as opposed to testOpen.cxx code,
>>>> in the output image all the pixels have the same value 3.4E38.
>>>>
>>>> Is this a bug or I am doing something terribly wrong?
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Alex
>>>>
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>>
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> _____________________________________
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> http://www.kitware.com/products/protraining.html
> 
> Please keep messages on-topic and check the ITK FAQ at:
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