Cannot restart after error about simpleelastix HOT 19 CLOSED

Ah, found out that the RandomSparseMask ImageSampler should only be used with a fixed image mask.

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Hi Jorrit!

xout is indeed problematic and I am afraid that it is tied to the implementation of elastix itself. xout lives as as a global object outside the elastix namespace and thus is not tied to lifetime of the elastix class. Instead, any open xout buffers have to be closed manually after elastix as run. This wasn't a problem when elastix was an executable because the OS would close these buffers regardless of how the process would exit (as long as it exits). SimpleElastix has to manage these connections manually (read: I have to hack elastix) which is also why we don't use the vanilla elastix version.

It boils down the fact that xout is not closed if SimpleElastix crashes before finishing because that part of the code isn't reached, and instead xout dangles for as long as the host executable is running, e.g. your python session. The error you see is because xout tries to open the same buffers twice.

Perhaps it is possible to call the xout close code during error handling. Can you weigh in on this @mstaring? Would this be a feasible approach?

Not being able to assign parameters inside a parameter map list is known issue that is possibly tied to SWIG generated code. I don't know what to do about that :/

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Hi!

Thanks for your fast response! Is it possible to expose the xoutClose, so I can call it when I know there is an error? Or wouldn't that work?

And indeed, not being able to assign parameters inside a parameter map list was my problem, but just getting them and modifying works, so not a real problem 😊

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What about this issue? Does fix work?

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I am currently in the middle of rewriting some code 😋, but I'll test it soon!

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👍

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I'm still receiving the error using transformix (haven't tested elastix), is that right?

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Can you send a minimum viable example (a few lines of code and example data) to [email protected] so I can test locally?

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Yes, will have to be this weekend or next week. Have to work on another project next couple days :(

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Np!

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I've tried it up to 9574263, and it still fails. But I see you already have a newer version, so it's compiling! 😋

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I'm running it from iPython right now and it crashes after every registration. I'll try to gather some debug info.

Edit:
Hmm, it stops with a Segmentation fault: 11

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If you send me a minimum viable example that reproduces the problem I will take a look!

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Sorry for the delay, but this example fails for me with commit c98a803:

import SimpleITK as sitk

def register(fixed, moving):
    selx = sitk.SimpleElastix()
    selx.LogToConsoleOn()

    affine = sitk.GetDefaultParameterMap('affine')
    affine['RequiredRatioOfValidSamples'] = ("0.99",) # Make it fail :P

    plist = sitk.ParameterMapList()
    plist.append(affine)

    selx.SetParameterMap(plist)
    selx.SetFixedImage(fixed)
    selx.SetMovingImage(moving)

    selx.Execute()

fixed = sitk.ReadImage('fixed.nii.gz')
moving = sitk.ReadImage('moving.nii.gz')

try:
    register(fixed, moving)
except Exception as e:
    print e

# This time will fail with xout
try:
    register(fixed, moving)
except Exception as e:
    print e

If you want, I can send you the images also?

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Yes, please do!

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https://www.dropbox.com/s/bgq4mv9mmisgxl6/fixed.nii.gz?dl=0
https://www.dropbox.com/s/sn9fah3hkmrsfo6/moving.nii.gz?dl=0

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Hi Jorrit

I have tested your script with your data and the problem seems to be solved with the new tip of the SimpleElastix branch (dde6134). Let me know if the problem persists.

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Ran it using 43167de (at the moment, latest develop) and the bug is resolved!

Sorry for the long wait!

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No problem, glad the issue has been resolved!

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