R version issues
Closed this issue · 3 comments
I recently moved to R 4.3.1 from 4.1.2. This line of code for two step registrations seems to work fine in 4.1.2, with a warning about transform orders (which I always got).
fi <- antsImageRead(getANTsRData("r16") )
mi <- antsImageRead(getANTsRData("r64") )
mytx2 <- antsRegistration(fixed=fi, moving=mi, typeofTransform = 'SyN')
mytx3 <- antsRegistration(fixed=fi, moving=mi, typeofTransform = 'SyNCC', initialTransform=mytx2$fwdtransforms)but same code fails with this error in 4.3.1
Error in if (is.na(initx)) { : the condition has length > 1
Here is the session info for both R versions. As far as I can tell both have the same ANTs versions. Not sure where the error is coming from.
R4.1.2
> antsVersions
Dependency GitTag
1 ANTs d30526f9cb5159bc0a3e9011f7ae5f409b3634c8
2 ANTsRCore 8e234fd1363c0d618f9dc21c9566f3d5464655a2
3 ANTsURL https://github.com/ANTsX/ANTs.git
4 ITK v5.3rc04
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ANTsR_0.5.7.5 ANTsRCore_0.7.5
loaded via a namespace (and not attached):
[1] compiler_4.1.2 RcppEigen_0.3.3.9.3 magrittr_2.0.3
[4] Matrix_1.4-0 tools_4.1.2 ITKR_0.6.0.0.2
[7] Rcpp_1.0.9 grid_4.1.2 lattice_0.20-45
R 4.3.1:
Dependency GitTag
1 ANTs d30526f9cb5159bc0a3e9011f7ae5f409b3634c8
2 ANTsRCore 8e234fd1363c0d618f9dc21c9566f3d5464655a2
3 ANTsURL https://github.com/ANTsX/ANTs.git
4 ITK v5.3rc04
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
time zone: America/Vancouver
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ANTsR_0.5.7.5 ANTsRCore_0.7.5
loaded via a namespace (and not attached):
[1] compiler_4.3.1 RcppEigen_0.3.3.9.3 magrittr_2.0.3
[4] Matrix_1.4-0 tools_4.3.1 ITKR_0.6.0.0.2
[7] Rcpp_1.0.9 grid_4.3.1 lattice_0.20-45
I think the problem (for R >=4.2) is here over in ANTsRCore:
The breaking change in R 4.2.0 is documented in R news as follows:
Calling if() or while() with a condition of length greater than one gives an error rather than a warning. Consequently, environment variable R_CHECK_LENGTH_1_CONDITION no longer has any effect.
I guess you can do something like
if (all(is.na(initx))) {
initx = paste("[", f, ",", m, ",1]", sep = "")
}
to ensure that the result is a logical of length 1 or check for whatever else distinguishes between the signalling value of NA vs when initx contains a transform.
Fix works fine, thank you.
I wonder if this needs to be committed to the repo? Because this is going to fail for anyone who has more than items in the transform. if this is a frowned upon thing (i.e., the goal of transformList is only to pass a single transform, like a prior affine), than perhaps documentation needs to be updated.
In the current implementation, multiple transform files should be allowed, but multiple linear antsTransform objects are not. There's some manipulation of the antsTransform objects that I don't understand, so I've left it alone. But it should support using a vector of file names like my_registration$fwdtransforms. Fixed and documented in #397