[Insight-developers] RGB colormapping IJ contribution, Gaetan's comments

Tue Jan 6 15:28:52 EST 2009

Hi Gaetan,

Thanks for the response and the files.  All the changes including the  
OverUnder colormap have been incorporated into a new revision of the  
submission and unless you insist otherwise, I'll keep you as a co- 
author since I'm intrinsically lazy and that is easier than specifying  
the contributions you made.  ;-)

I just tried to upload a new revision but was denied by the IJ gods.   
Not only that but I can no longer access previous revisions or other  
related information about the submission.  It's quite bizarre perhaps  
requiring Julien's attention.  Anyway, I'll try resubmitting later.

Thanks again,
Nick

On Jan 6, 2009, at 2:23 PM, Gaëtan Lehmann wrote:

>
> Le 6 janv. 09 à 18:25, Nicholas Tustison a écrit :
>
>> Hi Gaetan,
>>
>
> Hi Nick,
>
>> I hope you don't mind but the IJ commenting mechanism doesn't seem  
>> to have the back-and-forth niceties of regular email and instead of  
>> simply contacting you directly I thought the developer's list would  
>> be more appropriate.  First off, thank you for the suggestions-- 
>> they were great.  In fact, I included you as a co-author on the  
>> revision because of the resulting substantive changes.
>>
>
> Thank you, but I don't think I should be in the authors: I've only  
> made a small reviewing work, nothing more - you made the hard job!
>
>> As you can see below, I've made all the changes you suggested and  
>> am currently revising the document accordingly.  However, I had a  
>> couple of questions regarding a couple of your comments/suggestions.
>>
>> 1.  You ask why I didn't derive the filter from the  
>> UnaryFunctorImageFilter class.  Actually, this was my original  
>> implementation idea but it seems that swapping the colormap  
>> functors is not possible within that framework since the  
>> UnaryFunctorImageFilter class is templated over the specific  
>> functor.  There is the SetFunctor() function but as its description  
>> says "This allows the user to specify a functor that has ivars set  
>> differently than the default functor."  Is there something that I'm  
>> missing such that swapping of the different colormap functors would  
>> be possible?
>
> No, you're right. It would have be possible if the functor was  
> managed with a pointer in UnaryFunctorImageFilter, but that's not  
> the case.
>
>>
>> 2. I'm afraid I'm not quite understanding your concern about the  
>> rgb channels and the rgb property not being respected by the custom  
>> colormap functor.  Could you please elaborate a little more?
>>
>
> My mistake: I thought that it was a shared feature of all the  
> colormaps, but I realize it's only in  
> ScalarToRGBCustomColormapFunctor.
> Please just forget about that.
>
>> 3.  Unfortunately, I cannot access the attachment you give in your  
>> review which is unfortunate because I would like to include your  
>> colormap.  When I download it, all I get is a text file with a  
>> single zero in it which doesn't seem to be a very interesting  
>> colormap. :-)
>>
>
> It is attached to this mail.
>
> Regards,
>
> Gaëtan
>
>> Thanks,
>> Nick
>>
>>
>>
>>
>>
>>
>> Reproducing the examples has required a bit more work, because the  
>> test program simply doesn't write the output result to the disk. I  
>> would suggest writing the output to the disk (see attached file)  
>> and make the tests check the produced image. This can be acheived  
>> easily with itkTestDriver with the following lines:
>>
>> FIND_PROGRAM(ITK_TEST_DRIVER itkTestDriver)
>> SET(TEST_COMMAND ${ITK_TEST_DRIVER} --add-before-env PATH $ 
>> {CMAKE_BINARY_DIR})
>>
>> ADD_TEST( RGBColormapTestSpring ${TEST_COMMAND} ${CurrentExe}
>>          ${CMAKE_SOURCE_DIR}/images/grey.png spring.png spring
>>          --compare spring.png ${CMAKE_SOURCE_DIR}/images/spring.png
>> )
>>
>> ** done **
>>
>>
>> IMO, color map functor should have the whole pixel type as template  
>> parameter, to be able to use the RGBA pixels the same way
>>
>> ** done **
>>
>> are you sure that the Get/SetRed/Green/BlueChannel() method should  
>> be there? I think they are quite strange, because itk::RGBPixel  
>> clearly use the first channel as red, the second as green and the  
>> last one as blue, so changing that in the functor means that this  
>> property is not respected by the functor
>>
>> ** ?? **
>>
>> maybe m_MinimumRGBComponentValue and m_MaximumRGBComponentValue  
>> default values should be min() and max() rather than Zero and One?
>>
>> ** done **
>>
>> is there a reason to not have implemented  
>> ScalarToRGBColormapImageFilter as a subclass of  
>> UnaryFunctorImageFilter? It is said in the paper that that filter  
>> has large parts of code from UnaryFunctorImageFilter - maybe  
>> subclassing it would be a better way to reuse the code without  
>> duplication
>>
>> ** ?? **
>>
>> would you agree to add an option to compute the min and max values  
>> to be used in the functor automatically? That way, the filter would  
>> fit better in the pipeline architecture
>>
>> ** done **
>>
>> to make the usage of the predefined colormaps easier, I would  
>> suggest the addition of a new method to  
>> ScalarToRGBColormapImageFilter which would allow to use one of  
>> those colormap in a single line. For example rgbfilter- 
>> >SetColormap( RGBFilterType::HSV ) or rgbfilter->SetColormap( "hsv" )
>>
>> ** done **
>>
>> I would also suggest to drop the ScalarToRGB part in the colormap  
>> names, and maybe also the Functor suffix -  
>> ScalarToRGBJetColormapFunctor would become JetColormapFunctor, or  
>> even JetColormap, which is a lot easier to read and write
>>
>> ** done **
>>
>> finally, I have contributed another colormap used quive often by  
>> microscopists to see the saturation in the images - feel free to  
>> use it :-)
>>
>> _______________________________________________
>> Insight-developers mailing list
>> Insight-developers at itk.org
>> http://www.itk.org/mailman/listinfo/insight-developers
>
> <files.tgz>
> -- 
> 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.mandriva.org
> http://www.itk.org  http://www.clavier-dvorak.org
>