[Insight-developers] Modifying MaskImageFilter to work on VectorImage

Fri Apr 22 12:26:34 EDT 2011

Ok, pushed: http://review.source.kitware.com/#change,1475

On Fri, Apr 22, 2011 at 12:15 PM, Cory Quammen <cquammen at cs.unc.edu> wrote:
> Brad,
>
> Before you start, I have a patch ready for gerrit, but it depends on
> this patch: http://review.source.kitware.com/#change,1381
>
> I'll push the patch to gerrit and add you all as reviewers.
>
> Cory
>
> 2011/4/22 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>:
>>
>> Le 22 avr. 11 à 14:37, Bradley Lowekamp a écrit :
>>
>>> I very much would like to get this filter working with VectorImages.
>>>
>>> I don't want this to get forgotten. I think I will be able to take a stab
>>> at it based on some of Cory's work in github.
>>>
>>> The same technique should be applied to the NotMaskImageFilter as well,
>>> are there other similar masking filters?
>>
>> There is a masking filter for the LabelMap.
>>
>> Gaëtan
>>
>>
>>
>>>
>>> Brad
>>>
>>>
>>> On Apr 12, 2011, at 4:12 AM, Gaëtan Lehmann wrote:
>>>
>>>>
>>>> Le 12 avr. 11 à 07:33, Cory Quammen a écrit :
>>>>
>>>>> Hi Gaëtan,
>>>>>
>>>>> Thank you for your thoughtful comments.
>>>>>
>>>>> 2011/4/11 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>:
>>>>>>
>>>>>> Hi Cory,
>>>>>>
>>>>>> I think this code would fail if the mask filter is run a second
>>>>>> time with a
>>>>>> vector image with a different number of components.
>>>>>> There should be a check for the number of components in
>>>>>> BeforeThreadedGenerateData().
>>>>>
>>>>> Yes, it would be good to check that the number of components in the
>>>>> OutsideValue matches the number in the image, throwing an exception if
>>>>> the number of components doesn't match.
>>>>>
>>>>>> The initialization of the default value of OutsideValue is quite
>>>>>> problematic, as it can be done only when the number of components
>>>>>> is known.
>>>>>
>>>>> Agreed!
>>>>>
>>>>>> A better option would be to have a way to say "I want to use the
>>>>>> default
>>>>>> value" - in that case the value can be generated in
>>>>>> BeforeThreadedGenerateData() and would fit the vector the filter is
>>>>>> currently working on - or "I want to use that value" and then it is
>>>>>> the
>>>>>> responsibility of the user to provide the right number of components.
>>>>>>
>>>>>> One way to implement that is to use a 3rd input for the filter
>>>>>> which would
>>>>>> be of type
>>>>>>
>>>>>> SimpleDataObjectDecorator< PixelType >
>>>>>>
>>>>>> and to not provide a default value by default - just keep the 3rd
>>>>>> input as
>>>>>> NULL. If there is no 3rd input, then the default value of
>>>>>> OutsideValue can
>>>>>> be generated in BeforeThreadedGenerateData(). If there is a 3rd
>>>>>> input, then
>>>>>> just use the value provided.
>>>>>
>>>>> While your suggestion sounds reasonable, the same behavior can also be
>>>>> achieved using the current ITK norm of setting filter constants via a
>>>>> method. All it would take would be to examine the OutsideValue to see
>>>>> if it is zero length or if it consists of all zeros, and if so, infer
>>>>> that the user wants to use the default value with the correct number
>>>>> of components. To get back to the "default" value, all the user would
>>>>> have to do is set the OutsideValue to some vector of zeros or a
>>>>> zero-length vector. Does that seem reasonable?
>>>>>
>>>>>> An additional benefit of that approach: the OutsideValue can be
>>>>>> provided
>>>>>> through the pipeline, which is not the case currently.
>>>>>
>>>>> I think that your notion of treating filter constants as inputs to the
>>>>> pipeline is very interesting and has merit, but I'll defer to more
>>>>> experienced developers to determine if that is where ITK should be
>>>>> heading.
>>>>>
>>>>
>>>> Hi Cory,
>>>>
>>>> You're right, this is not the purpose of this change.
>>>> Your proposition to use the default value for a zero length vector
>>>> seems quite good to me.
>>>>
>>>> Gaëtan
>>>>
>>>>
>>>>> Thanks,
>>>>> Cory
>>>>>
>>>>>>
>>>>>>
>>>>>> Le 11 avr. 11 à 07:30, Cory Quammen a écrit :
>>>>>>
>>>>>>> David and Luis,
>>>>>>>
>>>>>>> I have posted a potential solution on github.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> https://github.com/cquammen/ITK/commit/a92bcc79f267d79f48abb7358881c4b2323ae01d
>>>>>>>
>>>>>>> I will post it to gerrit if you don't see any showstoppers.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Cory
>>>>>>>
>>>>>>> On Sun, Apr 10, 2011 at 5:50 PM, Luis Ibanez <luis.ibanez at kitware.com
>>>>>>>>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Hi David,
>>>>>>>>
>>>>>>>> We have been discussing this problem with Julien Malik from the
>>>>>>>> Orfeo Toolbox team.
>>>>>>>>
>>>>>>>> In summary, there is a function in the NumericTraits that is
>>>>>>>> intended
>>>>>>>> to deal with management of size in containers of variable size
>>>>>>>> such as the VariableLengthVector and the std::vector.
>>>>>>>>
>>>>>>>> Regarding your questions, please see below.
>>>>>>>>
>>>>>>>> On Thu, Apr 7, 2011 at 7:50 PM, David Doria
>>>>>>>> <daviddoria at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>> We have been having some discussion on the best way to allow
>>>>>>>>> MaskImageFilter
>>>>>>>>> to work on VectorImage (with pixels of type
>>>>>>>>> VariableLengthVector) . The
>>>>>>>>> problem is that the length of a VariableLengthVector is not
>>>>>>>>> defined at
>>>>>>>>> compile time. This means that in the MaskInput functor, the
>>>>>>>>> member m_OutsideValue cannot be initialized.
>>>>>>>>>
>>>>>>>>> Brad has identified two problems,
>>>>>>>>>
>>>>>>>>> 1) How do we initialized the member variable in the functor?
>>>>>>>>>
>>>>>>>>
>>>>>>>> We usually add "Set" methods to the functor,
>>>>>>>> the add "Set" methods to the Filter itself,
>>>>>>>> and they simply call the "Set" methods of the functor.
>>>>>>>>
>>>>>>>>> This seems to be the main issue I'm not sure how to address.
>>>>>>>>>
>>>>>>>>> 2) When do we detect the size of the vector image, and use
>>>>>>>>> reasonable
>>>>>>>>> defaults?
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> At run time,
>>>>>>>> by asking them for their "GetNumberOfComponents()
>>>>>>>> from the vector image.
>>>>>>>>
>>>>>>>> Reasonable default (otherwise) is "1".
>>>>>>>>
>>>>>>>>> We think this could be done in BeforeThreadedGenerateData.
>>>>>>>>>
>>>>>>>>
>>>>>>>> Yes, that's a good place.
>>>>>>>>
>>>>>>>> The GenerateInputInformation() or
>>>>>>>> GenerateOutputInformation() may
>>>>>>>> be good places as well.
>>>>>>>>
>>>>>>>>
>>>>>>>>> The complete conversation is here:
>>>>>>>>>
>>>>>>>>> http://review.source.kitware.com/#change,1338
>>>>>>>>> Any thoughts are welcome!
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> David
>>>
>>> ========================================================
>>> Bradley Lowekamp
>>> Lockheed Martin Contractor for
>>> Office of High Performance Computing and Communications
>>> National Library of Medicine
>>> blowekamp at mail.nih.gov
>>>
>>>
>>
>> --
>> 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
>>
>>
>
>
>
> --
> Cory Quammen
> Computer Integrated Systems for Microscopy and Manipulation (CISMM)
> Department of Computer Science
> University of North Carolina at Chapel Hill
> http://www.cs.unc.edu/~cquammen
>


-- 
Cory Quammen
Computer Integrated Systems for Microscopy and Manipulation (CISMM)
Department of Computer Science
University of North Carolina at Chapel Hill
http://www.cs.unc.edu/~cquammen