tests/testthat/test-read_fs_patch.R

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

test_that("A FreeSurfer binary patch file can be read using read.fs.patch", {
  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")
  patch_file <- file.path(subjects_dir, "subject1", "ext", "lh.cortex.patch.3d")
  skip_if_not(file.exists(patch_file), message = "Test data missing.")

  fspatch <- read.fs.patch(patch_file)
  patch_data <- fspatch$vertices

  expect_true(is.matrix(patch_data))
  expect_equal(ncol(patch_data), 7)
  expect_equal(nrow(patch_data), 149297)

  # Test indices:
  expect_equal(min(patch_data[, 1]), 1) # smallest one-based index must be 1
  expect_equal(min(patch_data[, 7]), 0) # smallest zero-based index must be 0

  expect_error(read.fs.patch(patch_file, format = "no such format")) # invalid format
})


test_that("A FreeSurfer ASCII patch file can be read using read.fs.patch", {
  testthat::skip_on_cran() # cannot download testdata on CRAN.
  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")
  patch_file <- file.path(subjects_dir, "subject1", "ext", "lh.cortex.patch.3d.asc")
  skip_if_not(file.exists(patch_file), message = "Test data missing.")

  fspatch <- read.fs.patch(patch_file)
  patch_data <- fspatch$vertices

  expect_true(is.matrix(patch_data))
  expect_equal(ncol(patch_data), 7)
  expect_equal(nrow(patch_data), 149297)

  # Test indices:
  expect_equal(min(patch_data[, 1]), 1) # smallest one-based index must be 1
  expect_equal(min(patch_data[, 7]), 0) # smallest zero-based index must be 0

  expect_error(read.fs.patch(patch_file, format = "no such format")) # invalid format
})