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No option to set number of threads for Transformix #163

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Svdvoort opened this issue Aug 19, 2022 · 13 comments
Open

No option to set number of threads for Transformix #163

Svdvoort opened this issue Aug 19, 2022 · 13 comments

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@Svdvoort
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The itk.ElastixRegistrationMethod method has the SetNumberOfThreads and GetNumberOfThreads functions to set and get the number of threads respectively.

However, itk.TransformixFilter does not have such functions. Should the number of threads be set in a different way, or can a SetNumberOfThreads function be added?
@thewtex
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thewtex commented Aug 24, 2022

@N-Dekker

@N-Dekker
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@Svdvoort Hi Sebastian, thank you for your suggestion! Do you have a particular use case that would significantly benefit from running itk.TransformixFilter multi-threaded? Would you then expect a large speed-up of the transformation process?

I'm asking, because it may not be entirely trivial to implement this option for TransformixFilter in a thread-safe way. We would have to have a closer look.

@stefanklein
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stefanklein commented Aug 25, 2022 via email

@Svdvoort
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Indeed, as Stefan points out I would just like to set the maximum number of threads transformix uses.
I don't expect a speed-up due to using multiple cores with transformix directly.
However, I do have a lot of cores available and would like to run multiple instances of transformix in parallel.
But because I can't set the (maximum) number of threads at the moment, I'm afraid that a single instance of transformix might use all cores, therefore I would like to be able to set the (maximum) number of threads.

N-Dekker added a commit to SuperElastix/elastix that referenced this issue Aug 25, 2022
@N-Dekker
ENH: Add NumberOfThreads property to itk::TransformixFilter
e5c60f5 
Addressed issue InsightSoftwareConsortium/ITKElastix#163 "No option to set number of threads for Transformix", submitted by Sebastian van der Voort.
@N-Dekker
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N-Dekker commented Aug 25, 2022 •
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@Svdvoort @stefanklein OK, thank you for your clarification. 👍 Please check: SuperElastix/elastix#714 Of course, once it is merged into SuperElastix/elastix (develop branch), it still needs to be included with the ITKElastix Python wrapping as well.

N-Dekker added a commit to SuperElastix/elastix that referenced this issue Aug 25, 2022
@N-Dekker
ENH: Add NumberOfThreads property to itk::TransformixFilter
ae3dbd0 
Addressed issue InsightSoftwareConsortium/ITKElastix#163 "No option to set number of threads for Transformix", submitted by Sebastian van der Voort.
N-Dekker added a commit to SuperElastix/elastix that referenced this issue Aug 26, 2022
@N-Dekker
ENH: Add NumberOfThreads property to itk::TransformixFilter
86623bf 
Addressed issue InsightSoftwareConsortium/ITKElastix#163 "No option to set number of threads for Transformix", submitted by Sebastian van der Voort.
@N-Dekker N-Dekker mentioned this issue Aug 26, 2022
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N-Dekker added a commit to SuperElastix/elastix that referenced this issue Aug 26, 2022
@N-Dekker
ENH: Add NumberOfThreads property to itk::TransformixFilter
ffab4b9 
Addressed issue InsightSoftwareConsortium/ITKElastix#163 "No option to set number of threads for Transformix", submitted by Sebastian van der Voort.
N-Dekker added a commit to SuperElastix/elastix that referenced this issue Aug 26, 2022
@N-Dekker
ENH: Add NumberOfThreads property to itk::TransformixFilter
c3dd02c 
Addressed issue InsightSoftwareConsortium/ITKElastix#163 "No option to set number of threads for Transformix", submitted by Sebastian van der Voort.
@N-Dekker
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N-Dekker commented Aug 26, 2022 •
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@Svdvoort @thewtex Technically, the TransformixFilter option is there in C++ now, with SuperElastix/elastix#714 (Still to be merged, and wrapped by ITKElastix.) Internally it adds the "-threads" option with the specified number of threads, which triggers calling itk::MultiThreaderBase::SetGlobalMaximumNumberOfThreads, just like the transformix executable does. (As was implemented by @stefanklein SuperElastix/elastix@1cf92cb in 2007).

For the transformix executable, "-threads" is certainly a useful option. However, when using ITKElastix with the itk Python wrapping, doesn't itk support calling itk::MultiThreaderBase::SetGlobalMaximumNumberOfThreads directly in Python?

@dzenanz
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dzenanz commented Aug 26, 2022

itk support calling itk::MultiThreaderBase::SetGlobalMaximumNumberOfThreads directly in Python

I guess that would work, but it would affect other filters too (probably not a big deal). I guess it is more intuitive, and easier to find, if the thread limitation exists in the filter.

@N-Dekker
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N-Dekker commented Aug 29, 2022 •
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@Svdvoort As a workaround, does it work for you to just call itk.MultiThreaderBase.SetGlobalMaximumNumberOfThreads yourself (in the Python/ITKElastix environment)?

We are looking into how to add a function like transformixFilter.SetNumberOfThreads(numberOfThreads), which would set the number of threads only for that specific transformixFilter instance, but it takes a little bit more time.

N-Dekker added a commit to SuperElastix/elastix that referenced this issue Sep 3, 2022
@N-Dekker
ENH: Add NumberOfThreads property to itk::TransformixFilter
96df5ee 
Addressed issue InsightSoftwareConsortium/ITKElastix#163 "No option to set number of threads for Transformix", submitted by Sebastian van der Voort.
@N-Dekker N-Dekker mentioned this issue Sep 4, 2022
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@thewtex
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thewtex commented Oct 17, 2022

For the transformix executable, "-threads" is certainly a useful option. However, when using ITKElastix with the itk Python wrapping, doesn't itk support calling itk::MultiThreaderBase::SetGlobalMaximumNumberOfThreads directly in Python?

@N-Dekker in the big picture, moving forward with Elastix output for itk.Transform will allow us to use itk.ResampleImageFilter. This has interfaces for setting the number of threads, etc. We can also take advantage of other GPU-optimized itk.ResampleImageFilter implementations in the works.

@stefanklein
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stefanklein commented Oct 17, 2022 via email

@thewtex
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thewtex commented Oct 17, 2022

Hi @stefanklein ,

Yes, I agree, the flexibility of Elastix helps its adoption. To be clear, I am not suggesting that we do not add the ability to set the number of threads to the Transformix interface. We should continue to increase the flexibility of Elastix so all GPU acceleration versions of resampling, including e.g. Python / CUDA implementations, are available to Elastix users. This is possible by providing an in-memory itk.Transform output that can be used with itk.resample_image_filter.

@thewtex
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thewtex commented Oct 17, 2022

Please see the discussion at SuperElastix/elastix#714 on how to provide this functionality on the Transformix interface.

@stefanklein
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stefanklein commented Oct 17, 2022 via email

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@thewtex @stefanklein @dzenanz @Svdvoort @N-Dekker