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ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
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setting ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS from within R #336

Open leonardocerliani opened 3 years ago

leonardocerliani commented 3 years ago

setting ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS appears not to be possible from within R

dear guys,

I am using ANTsR within RStudio (system info at the bottom).

I saw a previous thread where stnava was advising to set the ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS in .Renviron. So I did and it works.

I was wondering however why the same cannot be done from within R. My .Renviron reads: ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=5.

Now inside R I do:

Sys.setenv("ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS" = 10)
Sys.getenv("ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS")
> 10

However when I run an ANTsR registration, I see that I am still using 5 threads. It would be really useful to set the number of threads from within the R script/markdown, so that all the information to re-run the registration (e.g. by a colleague) would be the same.

Can you help me with this? Thank you in advance,

leonardo

sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] misc3d_0.9-0 pixmap_0.4-11 neurobase_1.29.0 ANTsR_0.5.7.5 reticulate_1.18 [6] glue_1.4.2 oro.nifti_0.11.0 ANTsRCore_0.7.4.9 loaded via a namespace (and not attached): [1] Rcpp_1.0.5 rstudioapi_0.11 knitr_1.30 magrittr_1.5 [5] splines_3.6.3 rappdirs_0.3.1 lattice_0.20-41 rlang_0.4.8 [9] stringr_1.4.0 tcltk_3.6.3 tools_3.6.3 grid_3.6.3 [13] xfun_0.19 R.oo_1.24.0 htmltools_0.5.0 matrixStats_0.57.0 [17] yaml_2.2.1 digest_0.6.27 abind_1.4-5 crayon_1.3.4 [21] RcppEigen_0.3.3.7.0 Matrix_1.2-18 R.utils_2.10.1 bitops_1.0-6 [25] evaluate_0.14 rmarkdown_2.5 stringi_1.5.3 RNifti_1.3.0 [29] compiler_3.6.3 ITKR_0.5.3.3.0 R.methodsS3_1.8.1 jsonlite_1.7.1