Threading speedup

[muschellij2]

Describe the bug Question 1) Should multi-threading help decrease rigid-body registration? 2) Do you have comparable timings as blow

To Reproduce Steps to reproduce the behavior

library(ANTsRCore)
#> 
#> Attaching package: 'ANTsRCore'
#> The following objects are masked from 'package:stats':
#> 
#>     sd, var
#> The following objects are masked from 'package:base':
#> 
#>     all, any, apply, max, min, prod, range, sum
library(kirby21.t1)
library(kirby21.flair)
kirby21.t1::download_t1_data(id = 113)
#> [1] TRUE
t1 = kirby21.t1::get_t1_filenames(id = 113, visit = 1)
kirby21.flair::download_flair_data(id = 113)
#> [1] TRUE
flair = kirby21.flair::get_flair_filenames(id = 113, visit = 1)
fi <- antsImageRead(t1)
fi
#> antsImage
#>   Pixel Type          : float 
#>   Components Per Pixel: 1 
#>   Dimensions          : 170x256x256 
#>   Voxel Spacing       : 1.20000004768372x1x1 
#>   Origin              : 202.8 0 0 
#>   Direction           : -1 0 0 0 1 0 0 0 1 
#>   Filename           : /Users/johnmuschelli/Library/R/4.0/library/kirby21.t1/visit_1/113/113-01-T1.nii.gz
mi <- antsImageRead(flair)
mi
#> antsImage
#>   Pixel Type          : float 
#>   Components Per Pixel: 1 
#>   Dimensions          : 327x576x576 
#>   Voxel Spacing       : 0.550000011920929x0.416666656732559x0.416666656732559 
#>   Origin              : 179.3 239.5833 0 
#>   Direction           : -1 0 0 0 -1 0 0 0 1 
#>   Filename           : /Users/johnmuschelli/Library/R/4.0/library/kirby21.flair/visit_1/113/113-01-FLAIR.nii.gz
Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 8)
speed2 = system.time({
  rig <- antsRegistration(fixed=fi, moving = mi,
                          typeofTransform = 'Rigid', verbose = TRUE)
})
print(speed2)
#>    user  system elapsed 
#> 108.832   3.215  18.748
Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 1)
speed1 = system.time({
  rig <- antsRegistration(fixed=fi, moving = mi,
                          typeofTransform = 'Rigid', verbose = TRUE)
})
print(speed1)
#>    user  system elapsed 
#> 117.935   1.233  19.433

^{Created on 2021-01-13 by the reprex package (v0.3.0.9001)}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.0.2 (2020-06-22) #> os macOS Catalina 10.15.7 #> system x86_64, darwin17.0 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz America/New_York #> date 2021-01-13 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib #> ANTsRCore * 0.7.4.6 2020-07-07 [2] #> assertthat 0.2.1 2019-03-21 [2] #> backports 1.2.0 2020-11-02 [1] #> cli 2.2.0 2020-11-20 [1] #> crayon 1.3.4 2017-09-16 [2] #> digest 0.6.27 2020-10-24 [1] #> ellipsis 0.3.1 2020-05-15 [2] #> evaluate 0.14 2019-05-28 [2] #> fansi 0.4.1 2020-01-08 [2] #> fs 1.5.0 2020-07-31 [2] #> git2r 0.28.0 2021-01-11 [1] #> glue 1.4.2 2020-08-27 [1] #> highr 0.8 2019-03-20 [2] #> htmltools 0.5.0 2020-06-16 [2] #> ITKR 0.5.3.2.0 2020-06-01 [2] #> kirby21.base 1.7.4 2020-10-01 [1] #> kirby21.flair * 1.7.0 2021-01-13 [1] #> kirby21.t1 * 1.7.3.2 2021-01-09 [1] #> knitr 1.30 2020-09-22 [1] #> lattice 0.20-41 2020-04-02 [2] #> lifecycle 0.2.0 2020-03-06 [2] #> magrittr 2.0.1 2020-11-17 [1] #> Matrix 1.2-18 2019-11-27 [2] #> pillar 1.4.7 2020-11-20 [1] #> pkgconfig 2.0.3 2019-09-22 [2] #> purrr 0.3.4 2020-04-17 [2] #> Rcpp 1.0.5 2020-07-06 [1] #> RcppEigen 0.3.3.7.0 2019-11-16 [2] #> reprex 0.3.0.9001 2020-09-30 [1] #> rlang 0.4.9.9000 2020-12-11 [1] #> rmarkdown 2.5 2020-10-21 [1] #> rstudioapi 0.13 2020-11-12 [1] #> sessioninfo 1.1.1 2018-11-05 [2] #> stringi 1.5.3 2020-09-09 [1] #> stringr 1.4.0 2019-02-10 [2] #> styler 1.3.2 2020-02-23 [2] #> tibble 3.0.4 2020-10-12 [1] #> vctrs 0.3.5 2020-11-17 [1] #> withr 2.3.0 2020-09-22 [1] #> xfun 0.19 2020-10-30 [1] #> yaml 2.2.1 2020-02-01 [2] #> source #> Github (muschellij2/ANTsRCore@61c37a1) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> Github (ropensci/git2r@4e342ca) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> Github (stnava/ITKR@9bdd5f8) #> local #> Github (muschellij2/kirby21.flair@461077a) #> local #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> Github (tidyverse/reprex@d3fc4b8) #> Github (r-lib/rlang@1939a71) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> #> [1] /Users/johnmuschelli/Library/R/4.0/library #> [2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library ```

library(ANTsRCore)
#> 
#> Attaching package: 'ANTsRCore'
#> The following objects are masked from 'package:stats':
#> 
#>     sd, var
#> The following objects are masked from 'package:base':
#> 
#>     all, any, apply, max, min, prod, range, sum
library(kirby21.t1)
library(kirby21.flair)
kirby21.t1::download_t1_data(id = 113)
#> [1] TRUE
t1 = kirby21.t1::get_t1_filenames(id = 113, visit = 1)
kirby21.flair::download_flair_data(id = 113)
#> [1] TRUE
flair = kirby21.flair::get_flair_filenames(id = 113, visit = 1)
fi <- antsImageRead(t1)
fi
#> antsImage
#>   Pixel Type          : float 
#>   Components Per Pixel: 1 
#>   Dimensions          : 170x256x256 
#>   Voxel Spacing       : 1.20000004768372x1x1 
#>   Origin              : 202.8 0 0 
#>   Direction           : -1 0 0 0 1 0 0 0 1 
#>   Filename           : /Users/johnmuschelli/Library/R/4.0/library/kirby21.t1/visit_1/113/113-01-T1.nii.gz
mi <- antsImageRead(flair)
mi
#> antsImage
#>   Pixel Type          : float 
#>   Components Per Pixel: 1 
#>   Dimensions          : 327x576x576 
#>   Voxel Spacing       : 0.550000011920929x0.416666656732559x0.416666656732559 
#>   Origin              : 179.3 239.5833 0 
#>   Direction           : -1 0 0 0 -1 0 0 0 1 
#>   Filename           : /Users/johnmuschelli/Library/R/4.0/library/kirby21.flair/visit_1/113/113-01-FLAIR.nii.gz
Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 8)
speed2 = system.time({
  rig <- antsRegistration(fixed=fi, moving = mi,
                          typeofTransform = 'SyN', verbose = TRUE)
})
print(speed2)
#>    user  system elapsed 
#> 271.658   8.046  56.734
Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 1)
speed1 = system.time({
  rig <- antsRegistration(fixed=fi, moving = mi,
                          typeofTransform = 'SyN', verbose = TRUE)
})
print(speed1)
#>    user  system elapsed 
#> 306.933   3.898  59.187

^{Created on 2021-01-13 by the reprex package (v0.3.0.9001)}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.0.2 (2020-06-22) #> os macOS Catalina 10.15.7 #> system x86_64, darwin17.0 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz America/New_York #> date 2021-01-13 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib #> ANTsRCore * 0.7.4.6 2020-07-07 [2] #> assertthat 0.2.1 2019-03-21 [2] #> backports 1.2.0 2020-11-02 [1] #> cli 2.2.0 2020-11-20 [1] #> crayon 1.3.4 2017-09-16 [2] #> digest 0.6.27 2020-10-24 [1] #> ellipsis 0.3.1 2020-05-15 [2] #> evaluate 0.14 2019-05-28 [2] #> fansi 0.4.1 2020-01-08 [2] #> fs 1.5.0 2020-07-31 [2] #> git2r 0.28.0 2021-01-11 [1] #> glue 1.4.2 2020-08-27 [1] #> highr 0.8 2019-03-20 [2] #> htmltools 0.5.0 2020-06-16 [2] #> ITKR 0.5.3.2.0 2020-06-01 [2] #> kirby21.base 1.7.4 2020-10-01 [1] #> kirby21.flair * 1.7.0 2021-01-13 [1] #> kirby21.t1 * 1.7.3.2 2021-01-09 [1] #> knitr 1.30 2020-09-22 [1] #> lattice 0.20-41 2020-04-02 [2] #> lifecycle 0.2.0 2020-03-06 [2] #> magrittr 2.0.1 2020-11-17 [1] #> Matrix 1.2-18 2019-11-27 [2] #> pillar 1.4.7 2020-11-20 [1] #> pkgconfig 2.0.3 2019-09-22 [2] #> purrr 0.3.4 2020-04-17 [2] #> Rcpp 1.0.5 2020-07-06 [1] #> RcppEigen 0.3.3.7.0 2019-11-16 [2] #> reprex 0.3.0.9001 2020-09-30 [1] #> rlang 0.4.9.9000 2020-12-11 [1] #> rmarkdown 2.5 2020-10-21 [1] #> rstudioapi 0.13 2020-11-12 [1] #> sessioninfo 1.1.1 2018-11-05 [2] #> stringi 1.5.3 2020-09-09 [1] #> stringr 1.4.0 2019-02-10 [2] #> styler 1.3.2 2020-02-23 [2] #> tibble 3.0.4 2020-10-12 [1] #> vctrs 0.3.5 2020-11-17 [1] #> withr 2.3.0 2020-09-22 [1] #> xfun 0.19 2020-10-30 [1] #> yaml 2.2.1 2020-02-01 [2] #> source #> Github (muschellij2/ANTsRCore@61c37a1) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> Github (ropensci/git2r@4e342ca) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> Github (stnava/ITKR@9bdd5f8) #> local #> Github (muschellij2/kirby21.flair@461077a) #> local #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> Github (tidyverse/reprex@d3fc4b8) #> Github (r-lib/rlang@1939a71) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> #> [1] /Users/johnmuschelli/Library/R/4.0/library #> [2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library ```

[muschellij2]

Related to https://github.com/ANTsX/ANTs/issues/1017