v0.18.1: Upgrade elastix to 2023-09-18, converts external initial transforms

[N-Dekker]

Supports passing a transform retrieved by GetCombinationTransform() or GetNthTransform(n) to ConvertToItkTransform, when an external initial transform was specified before running the registration.

Also including various performance improvements.

Including:

pull request SuperElastix/elastix#946
commit SuperElastix/elastix@7bcb2b3
ENH: Write external initial transforms to ITK transform file

pull request SuperElastix/elastix#949
commit SuperElastix/elastix@601f465
ENH: ConvertToItkTransform should support external initial transform

pull request SuperElastix/elastix#950
commit SuperElastix/elastix@7e883bf
ENH: Add GetInitialTransform() and GetExternalInitialTransform()

pull request SuperElastix/elastix#959
commit SuperElastix/elastix@3979978
PERF: Speed up ComputeJacobianTerms access to vnl_sparse_matrix

pull request SuperElastix/elastix#960
commit SuperElastix/elastix@4d028f7
PERF: Speed up full, grid, sparse mask samplers by a local sampleVector

[dzenanz]

Could you also bump version number in setup.py? That way we can tag/release immediately after merging this.

[N-Dekker]

That way we can tag/release immediately after merging this.

Wouldn't it be sufficient to you to just locally use one of the wheels produced by the CI?

[dzenanz]

I want other people to be able to reproduce my work 😄 And having pip-installable package is super-useful for that.

There is a compile error: _deps/elx-src/Core/Main/itkElastixRegistrationMethod.hxx:43:10: fatal error: 'itkTransformFileWriter.h' file not found.

[N-Dekker]

There is a compile error: _deps/elx-src/Core/Main/itkElastixRegistrationMethod.hxx:43:10: fatal error: 'itkTransformFileWriter.h' file not found.

Thanks @dzenanz I'm busy preparing a fix now.

---

Update -- here it is:

• COMP: Replace include <itkTransformFileWriter.h> with "elxTransformIO.h" SuperElastix/elastix#963

[thewtex]

@N-Dekker what is meant by "external" here?

[N-Dekker]

what is meant by "external" here?

Thanks for asking, Matt, it's the topic of the following issue:

• Document difference between SetExternalInitialTransform and SetInitialTransform SuperElastix/elastix#961