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Threading speedup #131

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muschellij2 opened this issue Jan 13, 2021 · 1 comment
Open

Threading speedup #131

muschellij2 opened this issue Jan 13, 2021 · 1 comment

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@muschellij2
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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

 
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

 
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
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Related to ANTsX/ANTs#1017

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