tests/testthat/test-read_nifti1.R

In freesurferformats: Read and Write 'FreeSurfer' Neuroimaging File Formats

test_that("NIFTI v1 files with FreeSurfer hack can be read.", {
  testthat::skip_on_cran() # cannot download testdata on CRAN.
  skip_if(rversion.less.than(vmajor = 3, vminor = 5), message = "Skipping under R < 3.5.")
  skip_if(tests_running_on_cran_under_macos(), message = "Skipping on CRAN under MacOS, required test data cannot be downloaded.")
  freesurferformats::download_opt_data()
  subjects_dir <- freesurferformats::get_opt_data_filepath("subjects_dir")

  morph_file_curv <- file.path(subjects_dir, "subject1", "surf", "lh.thickness")
  morph_file_nii <- file.path(subjects_dir, "subject1", "surf", "lh.thickness.nii.gz")

  morph_data_curv <- read.fs.morph(morph_file_curv)
  morph_data_nii <- read.nifti1.data(morph_file_nii)

  testthat::expect_equal(morph_data_curv, morph_data_nii)
})


test_that("NIFTI v1 files with FreeSurfer hack can be read using read.fs.morph.", {
  skip_if(rversion.less.than(vmajor = 3, vminor = 5), message = "Skipping under R < 3.5.")
  skip_if(tests_running_on_cran_under_macos(), message = "Skipping on CRAN under MacOS, required test data cannot be downloaded.")
  testthat::skip_on_cran() # cannot download testdata on CRAN.
  freesurferformats::download_opt_data()
  subjects_dir <- freesurferformats::get_opt_data_filepath("subjects_dir")

  morph_file_curv <- file.path(subjects_dir, "subject1", "surf", "lh.thickness")
  morph_file_nii <- file.path(subjects_dir, "subject1", "surf", "lh.thickness.nii.gz")

  morph_data_curv <- read.fs.morph(morph_file_curv)
  morph_data_nii <- read.fs.morph(morph_file_nii)

  testthat::expect_equal(morph_data_curv, morph_data_nii)
  testthat::expect_true(nifti.file.uses.fshack(morph_file_nii))
})


test_that("NIFTI v1 file headers with FreeSurfer hack can be read.", {
  skip_if(rversion.less.than(vmajor = 3, vminor = 5), message = "Skipping under R < 3.5.")
  skip_if(tests_running_on_cran_under_macos(), message = "Skipping on CRAN under MacOS, required test data cannot be downloaded.")
  testthat::skip_on_cran() # cannot download testdata on CRAN.
  freesurferformats::download_opt_data()
  subjects_dir <- freesurferformats::get_opt_data_filepath("subjects_dir")

  morph_file_nii <- file.path(subjects_dir, "subject1", "surf", "lh.thickness.nii.gz")

  nh <- read.nifti1.header(morph_file_nii)
  testthat::expect_equal(nh$endian, "little")
  testthat::expect_equal(nh$glmin, 149244L)
  testthat::expect_equal(nh$vox_offset, 352L)
  testthat::expect_equal(nh$dim_raw, c(3, -1, 1, 1, 1, 1, 1, 1))
  testthat::expect_equal(nh$dim, c(3, 149244, 1, 1, 1, 1, 1, 1))
})


test_that("The NIFTI version can be determined for a file.", {
  skip_if(rversion.less.than(vmajor = 3, vminor = 5), message = "Skipping under R < 3.5.")
  skip_if(tests_running_on_cran_under_macos(), message = "Skipping on CRAN under MacOS, required test data cannot be downloaded.")
  testthat::skip_on_cran() # cannot download testdata on CRAN.
  freesurferformats::download_opt_data()
  subjects_dir <- freesurferformats::get_opt_data_filepath("subjects_dir")

  nii1_file <- file.path(subjects_dir, "subject1", "surf", "lh.thickness.nii.gz")

  data_dir <- freesurferformats::get_opt_data_filepath("nifti2")
  nii2_file <- file.path(data_dir, "avg152T1_LR_nifti2.nii.gz")

  testthat::expect_equal(nifti.file.version(nii1_file), 1L)
  testthat::expect_equal(nifti.file.version(nii2_file), 2L)

  not_a_nifti_file <- system.file("extdata", "cube.off", package = "freesurferformats", mustWork = TRUE)
  testthat::expect_true(is.null(nifti.file.version(not_a_nifti_file)))
})


test_that("It can be determined whether a NIFTI file uses the FreeSurfer hack.", {
  skip_if(rversion.less.than(vmajor = 3, vminor = 5), message = "Skipping under R < 3.5.")
  skip_if(tests_running_on_cran_under_macos(), message = "Skipping on CRAN under MacOS, required test data cannot be downloaded.")
  testthat::skip_on_cran() # cannot download testdata on CRAN.
  freesurferformats::download_opt_data()
  subjects_dir <- freesurferformats::get_opt_data_filepath("subjects_dir")

  nii1_file_with_hack <- file.path(subjects_dir, "subject1", "surf", "lh.thickness.nii.gz")
  nii1_file_without_hack <- system.file("extdata", "vol27int.nii.gz", package = "freesurferformats", mustWork = TRUE)
  data_dir <- freesurferformats::get_opt_data_filepath("nifti2")
  nii2_file <- file.path(data_dir, "avg152T1_LR_nifti2.nii.gz")

  testthat::expect_true(nifti.file.uses.fshack(nii1_file_with_hack))
  testthat::expect_false(nifti.file.uses.fshack(nii1_file_without_hack))
  testthat::expect_false(nifti.file.uses.fshack(nii2_file))

  not_a_nifti_file <- system.file("extdata", "cube.off", package = "freesurferformats", mustWork = TRUE)
  testthat::expect_error(nifti.file.uses.fshack(not_a_nifti_file))
})