ApplyTransforms with Unsigned Char #120
Description
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