[Insight-users] filter to create a subgraph of an image

Thu May 27 05:16:47 EDT 2010

Many thanks Luis for Your answer.

I read in P. Soille's book (p. 67,68) that You can use nonflat 
structuring elements for grey-scale images. If I'm not mistaken this is 
the same as the rolling ball filter of imagej if You have a 2D grey 
image and open or close it with a 3D ball.

Richard Beare has submitted a great suite of parabolic morphology tools 
to the insight journal: 
http://www.insight-journal.org/browse/publication/228
If I got it right these are nonflat structuring elements as well. 
Parabolas can only work nonflat because they are infinite in size.

I would need a rolling hyper sphere/ball to filter a 3D grey image. 
Therefore I tried the GrayscaleMorphologicalClosingImageFilter but it 
does not compile if the Kernel is a 
BinaryBallStructuringElement<InputPixelType, Dimension + 1>
So I guess I need to create this subgraph binary image of Dimension + 1 
to be able to use a closing filter with a ball of Dimension + 1 and 
after that I have to convert it back to a grey image.
Or is there a Opening/Closing filter that can take a SE of img-dim + 1 
already in ITK?

Many thanks for any help or hints.
Roman

Luis Ibanez wrote:
> Hi Roman,
> 
> 
> 1) If you are doing this for visualization purposes, you could look at
>     the VTK class
> 
> http://www.vtk.org/doc/nightly/html/classvtkImageDataGeometryFilter.html
> 
> and the example:
> http://www.vtk.org/Wiki/VTK/Examples/ImageData/ImageDataGeometryFilter
> 
> 
> 
> 2) If you really want to get a 3D volume where the lines along Z
>     are filled up, up to the value of the intensities provided by
>     a 2D image, then you could do this by using ImageIterators.
> 
> 
>    In particular,
> 
>      a) Create the 3D volume from scratch (as shown in the
>          ITK Software Guide)
>          making sure that the X,Y dimensions match those of
>          your input 2D image.
> 
>      b) create a Linear iterator
> http://public.kitware.com/Insight/Doxygen/html/classitk_1_1ImageLinearIteratorWithIndex.html
>           to visit the 3D image, and set the direction to "2" (the Z axis).
> 
>           See the ITK Software Guide chapter on "Image Iterators"
> 
>           at every pass of the line, get the X,Y index coordinates
>           in order to get the pixel value from the 2D image.
> 
> 
> 
>     Regards,
> 
> 
>            Luis
> 
> 
> --------------------------------------------------------------------------------------
> On Tue, May 25, 2010 at 12:07 PM, Roman Grothausmann
> <roman.grothausmann at helmholtz-berlin.de> wrote:
>> Dear mailing list members,
>>
>>
>> Now I figured out that what I want is called a subgraph of an image. (As
>> described on p. 19,20 by P. Soille in Morphological Image Analysis)
>>
>> Is there a filter in itk that creates a subgraph of a grey input image?
>> (The only thing I could find for itk+subgraph is a bug-report:
>> http://www.itk.org/Bug/bug_relationship_graph.php?bug_id=8005&graph=dependency)
>>
>> Any help is very much appreciated
>> Roman
>>
>> Roman Grothausmann wrote:
>>> Dear mailing list members,
>>>
>>>
>>> Is there a filter in ITK that converts a grey image into a profile plot
>>> binary image? Eg a 2D grey image into a 3D binary image where the hight of
>>> each voxel column corresponds to the grey value of the corresponding pixel
>>> in the 2D image?
>>> Or how can I apply a morphological closing/opening on the profile of an
>>> image as described below?
>>>
>>> Any help is very much appreciated
>>> Roman
>>>
>>> Roman Grothausmann wrote:
>>>> Dear Richard,
>>>>
>>>> Richard Beare wrote:
>>>>> I've submitted a suite of parabolic morphology tools to the insight
>>>>> journal :
>>>>>
>>>>> http://hdl.handle.net/1926/1370
>>>> I get redirected to http://ij.itk.org/midas/item/view/2280 and then it
>>>> says:
>>>> You cannot access this item!
>>>>
>>>> But I found it over the Insight Journal search:
>>>> http://www.insight-journal.org/browse/publication/228
>>>>
>>>> It seems to be exactly what I'm looking for but reading Your contribution
>>>> article I started to wonder:
>>>> How do You get from a 1D image (as in figure 1) to a 2D binary image
>>>> (which consists of foreground pixel columns whose heights correspond to the
>>>> intensity values of the 1D image pixels) so that You can perform the (2D)
>>>> parabolic dilation?
>>>>
>>>> Or asked differently:
>>>> For smoothing a 2D image a 3D-ball (or paraboloid) is rolled over the
>>>> intensity profile which is a uneven 2D surface in 3D space. But if I look at
>>>> GrayscaleDilateImageFilter it expects a structuring element in 2D if the
>>>> input is a 2D image. (And I'd say it's not the same result as rolling a
>>>> 3D-ball over the intensity profile.)
>>>> So is there a pre-filter that would crate a 3D binary image (from my 2D
>>>> grey image) on which I could apply the BinaryDilateImageFilter with a ball
>>>> structuring element? (And then a filter to convert this 3D binary image back
>>>> to a 2D grey image?)
>>>>
>>>> Many thanks again.
>>>> Roman
>>>>
>>>>
>>>>
>>>>> be sure to fetch the latest version from the repository referenced in
>>>>> the paper.
>>>>>
>>>>> On 4/22/10, Roman Grothausmann <roman.grothausmann at helmholtz-berlin.de>
>>>>> wrote:
>>>>>> Dear mailing list members,
>>>>>>
>>>>>>
>>>>>> To prevent a gradient decent filter from stopping at an insignificant
>>>>>> local minimum I'd like a ball of some radius to roll over the intensity
>>>>>> profile of an image. The result I'm interested in is the trace of the
>>>>>> ball (or paraboloid) centre while the ball is rolling.
>>>>>> I think this is equivalent to smoothing the image with such a rolling
>>>>>> ball filter as this ImageJ filter:
>>>>>>
>>>>>> http://rsbweb.nih.gov/ij/docs/menus/process.html#background
>>>>>>
>>>>>> And then tracing the gradient decent as is done in the Random access
>>>>>> iteration example in the user guide.
>>>>>>
>>>>>> So I wonder now is there a filter in ITK for image smoothing that works
>>>>>> by simulating a sliding ball or paraboloid like the imageJ filter?
>>>>>>
>>>>>> Any help is very much appreciated
>>>>>> Roman
>>>>>>

-- 
Roman Grothausmann

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