Threading speedup #131
Description
Describe the bug
Question
- Should multi-threading help decrease rigid-body registration?
- 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 19.433Created on 2021-01-13 by the reprex package (v0.3.0.9001)
Session info
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/librarylibrary(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 59.187Created on 2021-01-13 by the reprex package (v0.3.0.9001)
Session info
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