[Rtk-users] Python Wrapping

Fri Mar 18 14:16:50 EDT 2016

Hello,
I am trying to do the wrapping for the 
RegularizedConjugateGradientConeBeamReconstructionFilter, do I need to 
wrap all the filters that it uses ?
Is there any guiding document for the wrapping method?

Regards,
Johnson

On 3/18/2016 9:31 AM, Cyril Mory wrote:
> Hi again,
>
> You got the SART filter right. As for the conjugate gradient, the 
> filter is actually ConjugateGradientConeBeamReconstructionFilter (for 
> the 3D non-regularized reconstruction) and 
> RegularizedConjugateGradientConeBeamReconstructionFilter (its 
> regularized counterpart).
>
> The filter you found, 
> FourDConjugateGradientConeBeamReconstructionFilter, is used for 4D 
> reconstruction (you need a cardiac or respiratory phase signal). Its 
> regularized counterpart is FourDROOSTERConeBeamReconstructionFilter.
>
> In addition to those, RTK also has 
> ADMMTotalVariationConeBeamReconstructionFilter and 
> ADMMWaveletsConeBeamReconstructionFilter, which implement the 
> Alternating Direction Method of Multiplier algorithm.
>
> You can find a description of these algorithms in 
> https://hal.inria.fr/tel-00985728/document
>
> Note that the SART filter has a m_NumberOfProjectionsPerSubset member. 
> Setting it to 1 (default) gives you SART, setting it to n with 1 < n < 
> TotalNumberOfProjections gives you OS-SART, and setting it to 
> n=TotalNumberOfProjections gives you SIRT.
>
> That's pretty much all there is in RTK at the moment.
> Cyril
>
> On 03/18/2016 02:11 PM, Johnson Keiriz wrote:
>> Hello,
>> Can you please confirm that the following classes are the ones used 
>> for the iterative reconstruction:
>> 1 - SART: SARTConeBeamReconstructionFilter
>> 2- Conjugate gradient: FourDConjugateGradientConeBeamReconstructionFilter
>>
>> Is there a 3D conjugate gradient?
>> Are these the only classes for iterative reconstruction?
>>
>> Thanks,
>> Johnson
>>
>> On 3/18/2016 4:12 AM, Cyril Mory wrote:
>>> Hi Johnson,
>>>
>>> Regarding the iterative methods:
>>> - In SART, you can use the CUDA forward and back projectors, but the 
>>> rest of the calculation is performed on CPU. We do not use SART a 
>>> lot, so we have not fully optimized it.
>>> - Conjugate gradient, on the other hand, is entirely performed on 
>>> the GPU. Note that a regularized conjugate gradient reconstruction 
>>> filter is also available (with total variation denoising, wavelets 
>>> denoising, and positivity enforcement)
>>>
>>> I hope you will find what you need,
>>> Regards,
>>> Cyril
>>>
>>> On 03/17/2016 08:54 PM, Johnson Keiriz wrote:
>>>>
>>>> Hello,
>>>>
>>>> I did rebuild and now things are working. I tested reconstruction 
>>>> with and without the filtering and there were differences. Though, 
>>>> I am not sure that filtering have provided a better reconstruction.
>>>>
>>>> I want to experiment the iterative methods. Can you please confirm 
>>>> for me which iterative method are fully implemented in CUDA: is it 
>>>> the conjugate gradient or SART ?
>>>>
>>>> I have noticed that they are not wrapped at all, any guide on how 
>>>> to introduce new filters?
>>>>
>>>> Once I have tested my wrapping, I will submit a github pull-request.
>>>>
>>>> Thanks,
>>>>
>>>> Johnson
>>>>
>>>> *From:*simon.rit at gmail.com [mailto:simon.rit at gmail.com] *On Behalf 
>>>> Of *Simon Rit
>>>> *Sent:* Thursday, March 17, 2016 1:54 PM
>>>> *To:* Johnson Keiriz
>>>> *Cc:* rtk-users at public.kitware.com
>>>> *Subject:* Re: [Rtk-users] Python Wrapping
>>>>
>>>> Hi,
>>>>
>>>> Good! Indeed, many things are not wrapped. There is a trick 
>>>> regarding modifications of the wrappings. You need to either start 
>>>> from scratch the compilation or delete the file 
>>>> SimpleRTK-prefix/src/SimpleRTK-stamp/SimpleRTK-configure. This will 
>>>> trigger a reconfiguration of the SimpleRTK and, hopefully, account 
>>>> for your modifications.
>>>>
>>>> Don't hesitate to submit a github pull-request when you have 
>>>> something working.
>>>>
>>>> Simon
>>>>
>>>> On Thu, Mar 17, 2016 at 4:33 PM, Johnson Keiriz 
>>>> <jkeiriz at theobjects.com <mailto:jkeiriz at theobjects.com>> wrote:
>>>>
>>>> Hello again,
>>>>
>>>> I found out about the json wrapping files. I added the wrapping for 
>>>> all the filters, but I haven’t noticed any effect from setting the 
>>>> filters !!!
>>>>
>>>> Any hints ?
>>>>
>>>> Regards,
>>>>
>>>> Johnson
>>>>
>>>> *From:*Rtk-users [mailto:rtk-users-bounces at public.kitware.com 
>>>> <mailto:rtk-users-bounces at public.kitware.com>] *On Behalf Of 
>>>> *Johnson Keiriz
>>>> *Sent:* Thursday, March 17, 2016 9:23 AM
>>>> *To:* rtk-users at public.kitware.com 
>>>> <mailto:rtk-users at public.kitware.com>; Simon Rit
>>>> *Subject:* [Rtk-users] Python Wrapping
>>>>
>>>> Hello,
>>>>
>>>> I am using the Python wrapped version of RTK. I have a question 
>>>> regarding the wrapping:
>>>>
>>>> It seems that not all functionality is available, for example: for 
>>>> the *CudaFDKConeBeamReconstructionFilter, *I was not able to set 
>>>> the cut frequency of the any of the filters
>>>>
>>>> (RamLaK, Cosine, ShepLogan) except for the Hann . Are the methods 
>>>> not wrapped ?
>>>>
>>>> Thanks,
>>>>
>>>> Johnson
>>>>
>>>> *Description: cid:image002.jpg at 01CB5984.4EABACE0*
>>>>
>>>> 	
>>>>
>>>> *Johnson Keiriz, PhD
>>>> Senior Software Engineer*
>>>>
>>>> 760 St-Paul W, #101
>>>> Montreal, QC
>>>> Canada  H3C 1M4
>>>> tel: (514) 843-3861 <tel:%28514%29%20843-3861>
>>>> ext 217
>>>>
>>>> 	
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>
>> -- 
>>
>> *Johnson Keiriz, PhD
>> Senior Software Engineer*
>>
>> 760 St-Paul W, #101
>> Montreal, QC
>> Canada  H3C 1M4
>> tel: (514) 843-3861
>> ext 217
>>
>

-- 

*Johnson Keiriz, PhD
Senior Software Engineer*

760 St-Paul W, #101
Montreal, QC
Canada  H3C 1M4
tel: (514) 843-3861
ext 217

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