search

imagej / imagej-itk

ITK integration for ImageJ
Other
8 stars 3 forks source link

Improve SimpleITK Image buffer to Java conversion #2

Open thewtex opened 9 years ago

thewtex commented 9 years ago

More in the SimpleITK issue tracker: https://issues.itk.org/jira/browse/SIMPLEITK-40

bnorthan commented 9 years ago

@ctrueden

bogovicj commented 4 years ago

@thewtex , @bnorthan , @ctrueden , @tischi

Not sure what improvements you all had in mind, and that link is broken (no judgement, its been 4 years, I know).

I wasn't crazy about the fact that the repo as it is copies data, so started work on an in-memory imglib2 wrapper of itk images (accessible by SimpleITK).

Still early, but feedback most welcome.

bnorthan commented 4 years ago

Hi @bogovicj

This looks great. Thank you for picking up this project. One quick question have you done any performance testing on accessing and/or looping and modifying the wrapped ItkImageImg vs a copied Img?? Is there any overhead with the wrappers??

bogovicj commented 4 years ago

have you done any performance testing on accessing and/or looping and modifying the wrapped ItkImageImg vs a copied Img

Not yet

Is there any overhead with the wrappers??

Probably. Though there are improvements possible if we could get access to a lower level of storage. e.g. if it's the case that itk stores the image as a flat array, then working with that directly ( see imglib2-unsafe) would be better than the current state of affairs.

tischi commented 4 years ago

Yes, but I think the higher level API, even if slow, is really nice because it should work for many cases. So I would keep that for sure and implement something faster as an independent version, so the user could choose between safe or fast.

bnorthan commented 4 years ago

I feel like working with a flat native array directly would be ideal, then you could use it for both ITK, and other native code. However I don't know what guarantees ITK makes about the memory layout of the native array.

thewtex commented 4 years ago

@bogovicj thanks for working on this!

. if it's the case that itk stores the image as a flat array

This is true.

Rocsg commented 6 months ago

Hi all, We are Fijiyama developers (registration plugin for Fij). The plugin involves a lot of conversion between ImageJ and Itk Image, and we found out that the old version of Simple ITK libs does not release the accessibility capacity to the Itk Image array of data. Thus we work on a circumvent of this, but that require a more recent version of simple itk, like the last ones (2..), see

https://github.com/SimpleITK/SimpleITK/issues/2110

However if we start working on this, that means that we should ship Fijiyama plugin on an installation including a recent version of simple itk. And we guess that there could be other plugin that rely on simple itk, and that changing the version of simple itk can have side-effect.

Could we discuss a bit this point ? Can you share a vision about this ?

See you !

Romain & Loai