ApplyTransforms with Unsigned Char

[muschellij2]

Describe the bug
Segfault with unsigned char with applyTransforms.

To Reproduce

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
destfile = file.path(tempdir(), "01.tar.xz")
dl = curl::curl_download(
  "https://archive.data.jhu.edu/api/access/datafile/1311?gbrecs=true",
  destfile = destfile)
res = untar(tarfile = destfile, exdir = tempdir())
image = file.path(tempdir(), "01", "BRAIN_1_Anonymized.nii.gz")
mask = file.path(tempdir(), "01", "BRAIN_1_Anonymized_Mask.nii.gz")

template.file = tempfile(fileext = ".nii.gz")
# template.file = system.file(
#   'scct_unsmooth_SS_0.01_128x128x128.nii.gz',
#   package = 'ichseg')
template_url = paste0("https://github.com/muschellij2/ichseg",
  "/raw/master/inst/",
  "scct_unsmooth_SS_0.01_128x128x128.nii.gz")
curl::curl_download(template_url, template.file)
image = check_ants(image)
mask = check_ants(mask)
ss = maskImage(image, mask)

template.file = check_ants(template.file)

reg = antsRegistration(fixed = template.file,
                       moving = ss,
                       typeofTransform = "Rigid",
                       affSampling = 64,
                       verbose = TRUE)
# works fine
native_template = antsApplyTransforms(
  fixed = ss,
  moving = template.file,
  interpolator = "nearestNeighbor",
  transformlist = reg$invtransforms,
  whichtoinvert = 1)

temp_space = reg$warpedmovout > 50
unique(temp_space)
#> [1] 0 1
temp_space
#> antsImage
#>   Pixel Type          : unsigned char 
#>   Components Per Pixel: 1 
#>   Dimensions          : 128x128x128 
#>   Voxel Spacing       : 1.5x1.5x1.5 
#>   Origin              : 90 125 -71 
#>   Direction           : -1 0 0 0 -1 0 0 0 1

# works fine
temp_space2 = antsImageClone(temp_space, "float")
native_template = antsApplyTransforms(
  fixed = ss,
  moving = temp_space2,
  interpolator = "nearestNeighbor",
  transformlist = reg$invtransforms,
  whichtoinvert = 1)

Failures

# segfaults
temp_space2 = antsImageClone(temp_space, "float")
native_template = antsApplyTransforms(
  fixed = ss,
  moving = temp_space,
  interpolator = "nearestNeighbor",
  transformlist = reg$invtransforms,
  whichtoinvert = 1)

 *** caught segfault ***
 *** caught segfault ***

address 0x1124e2000, cause 'memory not mapped'
address 0x112562000, cause 'memory not mapped'

Traceback:
 1: antsApplyTransforms(fixed = ss, moving = temp_space, interpolator = "nearestNeighbor",     transformlist = reg$invtransforms, whichtoinvert = 1)
Traceback:
 1: antsApplyTransforms(fixed = ss, moving = temp_space, interpolator = "nearestNeighbor", 
 *** caught segfault ***

 *** caught segfault ***    transformlist = reg$invtransforms, whichtoinvert = 1)


address 0x1125e2000, cause 'memory not mapped'
address 0x112462000, cause 'memory not mapped'

^{Created on 2020-07-09 by the reprex package (v0.3.0)}

Session info

devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.0.0 (2020-04-24)
#>  os       macOS Mojave 10.14.6        
#>  system   x86_64, darwin17.0          
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       America/New_York            
#>  date     2020-07-09                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version    date       lib source                                
#>  ANTsRCore   * 0.7.4.6    2020-07-07 [1] Github (muschellij2/ANTsRCore@61c37a1)
#>  assertthat    0.2.1      2019-03-21 [1] CRAN (R 4.0.0)                        
#>  backports     1.1.8      2020-06-17 [1] CRAN (R 4.0.0)                        
#>  callr         3.4.3      2020-03-28 [1] CRAN (R 4.0.0)                        
#>  cli           2.0.2      2020-02-28 [1] CRAN (R 4.0.0)                        
#>  crayon        1.3.4      2017-09-16 [1] CRAN (R 4.0.0)                        
#>  curl          4.3        2019-12-02 [1] CRAN (R 4.0.0)                        
#>  desc          1.2.0      2020-06-01 [1] Github (muschellij2/desc@b0c374f)     
#>  devtools      2.3.0.9000 2020-06-01 [1] Github (hadley/devtools@202ea81)      
#>  digest        0.6.25     2020-02-23 [1] CRAN (R 4.0.0)                        
#>  ellipsis      0.3.1      2020-05-15 [1] CRAN (R 4.0.0)                        
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 4.0.0)                        
#>  fansi         0.4.1      2020-01-08 [1] CRAN (R 4.0.0)                        
#>  fs            1.4.2      2020-06-30 [1] CRAN (R 4.0.0)                        
#>  glue          1.4.1      2020-05-13 [1] CRAN (R 4.0.0)                        
#>  highr         0.8        2019-03-20 [1] CRAN (R 4.0.0)                        
#>  htmltools     0.5.0      2020-06-16 [1] CRAN (R 4.0.0)                        
#>  ITKR          0.5.3.2.0  2020-06-01 [1] Github (stnava/ITKR@9bdd5f8)          
#>  knitr         1.29.1     2020-07-06 [1] Github (muschellij2/knitr@538cd65)    
#>  lattice       0.20-41    2020-04-02 [1] CRAN (R 4.0.0)                        
#>  magrittr      1.5        2014-11-22 [1] CRAN (R 4.0.0)                        
#>  Matrix        1.2-18     2019-11-27 [1] CRAN (R 4.0.0)                        
#>  memoise       1.1.0      2017-04-21 [1] CRAN (R 4.0.0)                        
#>  pkgbuild      1.0.8      2020-05-07 [1] CRAN (R 4.0.0)                        
#>  pkgload       1.1.0      2020-05-29 [1] CRAN (R 4.0.0)                        
#>  prettyunits   1.1.1      2020-01-24 [1] CRAN (R 4.0.0)                        
#>  processx      3.4.3      2020-07-05 [1] CRAN (R 4.0.0)                        
#>  ps            1.3.3      2020-05-08 [1] CRAN (R 4.0.0)                        
#>  R6            2.4.1      2019-11-12 [1] CRAN (R 4.0.0)                        
#>  Rcpp          1.0.5      2020-07-06 [1] CRAN (R 4.0.0)                        
#>  RcppEigen     0.3.3.7.0  2019-11-16 [1] CRAN (R 4.0.0)                        
#>  remotes       2.1.1      2020-02-15 [1] CRAN (R 4.0.0)                        
#>  rlang         0.4.6.9000 2020-07-08 [1] Github (r-lib/rlang@f3cdf54)          
#>  rmarkdown     2.3        2020-06-18 [1] CRAN (R 4.0.0)                        
#>  rprojroot     1.3-2      2018-01-03 [1] CRAN (R 4.0.0)                        
#>  sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 4.0.0)                        
#>  stringi       1.4.6      2020-02-17 [1] CRAN (R 4.0.0)                        
#>  stringr       1.4.0      2019-02-10 [1] CRAN (R 4.0.0)                        
#>  testthat      2.3.2      2020-03-02 [1] CRAN (R 4.0.0)                        
#>  usethis       1.6.1.9000 2020-07-06 [1] Github (r-lib/usethis@c1cb6d9)        
#>  withr         2.2.0      2020-04-20 [1] CRAN (R 4.0.0)                        
#>  xfun          0.15       2020-06-21 [1] CRAN (R 4.0.0)                        
#>  yaml          2.2.1      2020-02-01 [1] CRAN (R 4.0.0)                        
#> 
#> [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

[muschellij2]

Also, this works fine as well:

# works fine
noinvert = antsApplyTransforms(
  fixed = template.file,
  moving = antsImageClone(ss > 0, "float"),
  interpolator = "nearestNeighbor",
  transformlist = reg$fwdtransforms)

but this segfaults (so it's not related to whichtoinvert):

# fails
noinvert = antsApplyTransforms(
  fixed = template.file,
  moving = ss > 0,
  interpolator = "nearestNeighbor",
  transformlist = reg$fwdtransforms)