No option to set number of threads for Transformix

[Svdvoort]

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]

@N-Dekker

[N-Dekker]

@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]

Transformix (the command line version, and I think also the library version) by default already performs multithreading using the default ITK implementation. I think Sebastian's question is just to have a function to set the maximum number of threads, just like possible on the commandline. Cheers, stefan From: Niels Dekker ***@***.***> Sent: Thursday, August 25, 2022 1:47 PM To: InsightSoftwareConsortium/ITKElastix ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [InsightSoftwareConsortium/ITKElastix] No option to set number of threads for Transformix (Issue #163) Waarschuwing: Deze e-mail is afkomstig van buiten de organisatie. Klik niet op links en open geen bijlagen, tenzij u de afzender herkent en weet dat de inhoud veilig is. Caution: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. @Svdvoort<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSvdvoort&data=05%7C01%7Cs.klein%40erasmusmc.nl%7Ce903426332094da9c70708da868f7509%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637970247945080288%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7w4UOshaKFxeNZcmCAzL4cGn8eUZHcI81i7UwzZ7Pz4%3D&reserved=0> 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. - Reply to this email directly, view it on GitHub<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FInsightSoftwareConsortium%2FITKElastix%2Fissues%2F163%23issuecomment-1227150677&data=05%7C01%7Cs.klein%40erasmusmc.nl%7Ce903426332094da9c70708da868f7509%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637970247945080288%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RnHq4rmZ33OY3H9mqPhRrkPaNlaiNWHcW%2Bk%2By0eYoXA%3D&reserved=0>, or unsubscribe<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAF2LNJY3JF3OK2ZWN4VKV3V25MJPANCNFSM57AUFIAA&data=05%7C01%7Cs.klein%40erasmusmc.nl%7Ce903426332094da9c70708da868f7509%7C526638ba6af34b0fa532a1a511f4ac80%7C0%7C0%7C637970247945080288%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=k7uQbedAWFMWHIzxeyOOpn32cIOm7bjy9OoqeugsNjI%3D&reserved=0>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>>

[Svdvoort]

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]

@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]

@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]

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]

@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.