R Wrapping: node stack overflow about simpleelastix HOT 9 CLOSED

New R bindings have now been merged into SimpleElastix.

from simpleelastix.

Hi zarquon,

To set the inputs on the SimpleElastix objects in R, you need to use the following (admittedly, awkard) syntax:

elastix <- elastix$SetFixedImage(fixedImage)

This is because of the way SWIG wraps C++ code into R code. If you find this syntax annoying, you can use the procedural notation:

resultImage <- Elastix(fixedImage, movingImage, parameterMap)

Use Elastix(fixedImage, movingImage, parameterMap, TRUE) to print progress to console. This is the full example:

library(SimpleITK)

fixedImage <- ReadImage("target_trans.nii.gz")
movingImage <- ReadImage("moving_trans.nii.gz")
elastix <- SimpleElastix()
elastix <- elastix$SetFixedImage(fixedImage)
elastix <- elastix$SetMovingImage(movingImage)
parameterMap <- GetDefaultParameterMap("nonrigid")
elastix <- elastix$SetParameterMap(parameterMap)
elastix <- elastix$LogToConsoleOn()
elastix <- elastix$Execute()

Good luck! I hope you find it useful for your work.

from simpleelastix.

Awesome, thanks a lot.

from simpleelastix.

I still have a question: do you know why/how the generic SimpleITK R-wrapping provides this functionality (calling a member function using $)?
And: calling elastix$GetResultImage() fails (all Get functions - is there also a workaround?)

from simpleelastix.

I don't know why they use the $-notation. Perhaps you can ask at https://github.com/SimpleITK/SimpleITK/issues?

Can you provide a log of your R-commands, elastix output (i.e. run with LogToConsoleOn()) and full error message caused by GetResultImage()?

from simpleelastix.

Sorry, my last post was a bit confusing. I am OK with the $-notation. What I meant was why $DoSomething() does not work for elastix related functions but the core functions of SimpleITK. See the example with the CastImageFilter below. I guess this might be related to the issue of not being able to call the $Get* functions.

require(SimpleITK)
image1 <- ReadImage("./target_trans.nii-subvolume-scale_1.nii.gz")
image2 <- ReadImage("templateResampled.nii.gz")

ci <- CastImageFilter()
ci$SetOutputPixelType("sitkFloat32")
image1 <- ci$Execute(targetname)
image2 <- ci$Execute(movingimage)

elastix <- SimpleElastix()
elastix <- elastix$SetFixedImage(image2)
elastix <- elastix$SetMovingImage(image1)
pm <- GetDefaultParameterMap("affine")
elastix <- elastix$SetParameterMap(pm)
elastix <- elastix$LogToConsoleOn()
elastix <- elastix$Execute()
outimage <- Elastix(image1,image2,pm)
image <- elastix$GetResultImage()

Error in .getClassFromCache(Class, where, package = package, resolve.msg = resolve.msg) : 
  node stack overflow

I get the same error for all Get functions.
As you can see, the CastImageFilter from SimpleITK does not need the workaround but is pretty much identical to the code in python (with the "$" instead of the ".")

from simpleelastix.

You are right, I can reproduce the errors you see and will have to look into it before I can give a solution. Does the Elastix(image1,image2,pm) notation work for you?

from simpleelastix.

There is a bit of working going on in SimpleITK to fix some issues with the R wrapping. This is mostly done by @richardbeare

Please stay tuned to the SimpleITK repository for some changes.

Specifically you may be interested in this change in review:

http://review.source.kitware.com/#/c/20435/2/Examples/SimpleGaussian.R

from simpleelastix.

Thank you for the info Bradley, will do.

from simpleelastix.