Use Elastix wrapping of ITK for Python

lassoan / SlicerElastix

This extension makes available Elastix medical image registration toolkit (http://elastix.isi.uu.nl/) available in Slicer.

MIT License

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Use Elastix wrapping of ITK for Python #31

Closed BishopWolf closed 1 year ago

BishopWolf commented 4 years ago

https://github.com/InsightSoftwareConsortium/ITKElastix

This would ease the build of this extension as you no longer need to install elastix executable or do any external call.

This example is very clarifying https://github.com/InsightSoftwareConsortium/ITKElastix/blob/master/examples/2_RegistrationParameters.ipynb

lassoan commented 4 years ago

I don't think this is quite usable for us yet.

Slicer uses SimpleITK for Python wrapping, not ITK's Python wrapping. Please check with SimpleITK developers if there are plans for wrapping Elastix.
Elastix does not use ITK transform file format. We implemented a reader for that in SlicerElastix. It would be nice if we did not need to maintain it, but I don't think an alternative is available yet. Please check with Elastix/ITK/SimpleITK developers how Elastix transforms could be made available in ITK transformation objects.

BishopWolf commented 1 year ago

Seems like we are approaching to functionality here https://github.com/SuperElastix/elastix/releases/tag/5.1.0

elastix 5.1.0 is the first new release after elastix 5.0.1, October 2020. It has added support for ITK transform file formats, HDF5 and TFM. While still supporting the original elastix transform parameter files as well, of course. Furthermore, it has extended the library interface, allowing to pass transform objects in memory (bypasssing file I/O). Which allows SimpleITK (https://simpleitk.org/) and ITKElastix (https://github.com/InsightSoftwareConsortium/ITKElastix) to further extend in that direction, with future releases. And it has significant runtime performance improvements.

lassoan commented 1 year ago

Elastix has now been upgraded to 5.1.0.

ITKElastix Python wrapping could be indeed used in this extension. Pros:

it may be easier to collect progress and intermediate state information and display them in Slicer (e.g., show current registration result by moving the moving image)
no need to build Elastix for building the extension Cons:
registration runs in the main thread, therefore the user cannot do anything while the registration is running (in the current SlicerElastix module we block the GUI, too, but this can be changed easily)
a crash in Elastix crashes the application
ongoing registration cannot be easily aborted
cannot customize build options (cannot enable optional components or specify other non-default build options)

Considering pros/cons do not overwhelmingly point towards switching to the ITKElastix, we remain on using Elastix that is built from source.