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));
})