tests/testthat/test-read_nifti2.R

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

test_that("The header of NIFTI v2 files can be read using nifti2.header.", {
  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();
  data_dir = freesurferformats::get_opt_data_filepath("nifti2");
  nii_v2_file = file.path(data_dir, 'avg152T1_LR_nifti2.nii.gz');

  hdr = read.nifti2.header(nii_v2_file);

  testthat::expect_true(is.list(hdr));
  testthat::expect_equal(hdr$descrip, 'FSL3.2beta');
  testthat::expect_equal(hdr$cal_max, 255); # max color display value (display range definition)
  testthat::expect_equal(hdr$cal_min, 0);   # min color display value
  testthat::expect_equal(hdr$vox_offset, 544L);   # start of data (offset in bytes)
  testthat::expect_equal(hdr$dim, c(3L, 91L, 109L, 91L, 1L, 1L, 1L, 1L));   # dimensions. first entry is number of used dimensions (num_dim). then follow dim sizes. the ones after num_dim + 1 should be ignored.
  testthat::expect_equal(hdr$bitpix, 32L);   # number of bytes per value (in the data part of the file)
  testthat::expect_equal(hdr$datatype, 16L);   # the NIFTI data type (defines whether this is integer, float, etc). See NIFTI2 spec.
})


test_that("Data from NIFTI v2 files 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();
  data_dir = freesurferformats::get_opt_data_filepath("nifti2");
  nii_v2_file = file.path(data_dir, 'avg152T1_LR_nifti2.nii.gz');

  hdr = read.nifti2.header(nii_v2_file);
  niidata = read.nifti2.data(nii_v2_file);
  niidata2 = read.nifti2.data(nii_v2_file, drop_empty_dims = FALSE);

  testthat::expect_equal(dim(niidata), c(91, 109, 91));
})


test_that("Trying to read NIFTI v1 files with NIFTI v2 function leads to errors.", {
  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");


  nii_v1_file = file.path(subjects_dir, "subject1", "surf", "lh.thickness.nii.gz");
  not_nii_file = file.path(subjects_dir, "subject1", "surf", "lh.thickness");

  testthat::expect_error(read.nifti2.header(nii_v2_file));
  testthat::expect_error(read.nifti2.header(not_nii_file));
})


test_that("NIFTI header dim field can be converted to dim_raw and back", {

  dim_raw = c(3, 256, 256, 256, 1, 1, 1, 1);
  datadim  = nifti.datadim.from.dimfield(dim_raw);
  testthat::expect_equal(datadim, c(256, 256, 256));

  # now test other way around
  dim_raw_recomputed = nifti.datadim.to.dimfield(datadim);
  testthat::expect_equal(dim_raw, dim_raw_recomputed);


  # error handling
  testthat::expect_error(nifti.datadim.from.dimfield(c(1, 2, 3, 4, 5)));  # field length 5 invalid, must be 8.
  testthat::expect_error(nifti.datadim.to.dimfield(c(1, 2, 3, 4, 5, 6, 7, 8)));  # data array dimension length 8 invalid, must be <= 7.
})