tests/testthat/test-test_scrubbing.R

In fMRIscrub: Scrubbing and Other Data Cleaning Routines for fMRI

test_that("pscrub works", {
  psx <- testthat::expect_warning(fMRIscrub:::pscrub_multi(
    Dat1,
    projection = c("ICA", "ICA_kurt"),
    ICA_method="R" # "all"
  ))
  fMRIscrub:::plot.scrub_projection_multi(psx) # expect_warning w/ fusedPCA?

  # fusedPCA
  psx <- testthat::expect_warning(fMRIscrub:::pscrub_multi(
    Dat2,
    projection = c(
      #"fusedPCA",
      "ICA_kurt"
    ),
    kurt_quantile = .90,
    cutoff = 5,
    ICA_method="R",
    verbose = TRUE
  ))
  fMRIscrub:::plot.scrub_projection_multi(psx, title = "My Plot")

  psx <- testthat::expect_warning(scrub(Dat1, ICA_method="R"))
  print(psx)

  psx <- pscrub(
    Dat2[,Dat2[1,]!=0], "PCA", 1, center=FALSE, PESEL=FALSE, kurt_quantile=.8,
    full_PCA = TRUE, cutoff=5, ICA_method="R", verbose=TRUE
  )
  plot(psx)

  psx <- testthat::expect_warning(pscrub(Dat1, ICA_method="R"))

  psx <- testthat::expect_warning(pscrub(
    Dat1, nuisance=fMRItools::dct_bases(nrow(Dat1), 3),
    ICA_method="R"
  ))

  # psx <- testthat::expect_warning(pscrub(
  #   Dat2, projection="fusedPCA", nuisance=cbind(1, fMRItools::dct_bases(nrow(Dat2), 12)),
  #   comps_mean_dt=2, comps_var_dt=2, get_dirs=TRUE, get_outliers=FALSE
  # ))
  # plot(psx)
})

test_that("DVARS works", {
  dv <- DVARS(Dat1)
  plot(dv)

  dv <- DVARS(scale(Dat2[,Dat2[1,]!=0]), normalize=FALSE, cutoff_DPD=3, verbose=TRUE)
  plot(dv)
  testthat::expect_true(TRUE)
})

# test_that("ciftiTools-related functions work", {
#   if (is.null(ciftiTools.getOption("wb_path"))) {
#     skip("Connectome Workbench is not available.")
#   }
#
#   cii_fname <- "../../Data/MSC/MSC.6k.dtseries.nii"
#   if (!file.exists(cii_fname)) {
#     skip("Could not find the CIFTI file.")
#   }
#
#   psx <- pscrub(ciftiTools::read_xifti(cii_fname, brainstructures="left"), ICA_method="R")
#   plot(psx)
#   psx2 <- pscrub(t(as.matrix(
#     ciftiTools::read_xifti(cii_fname, brainstructures="left")
#   )), ICA_method="R")
#   testthat::expect_equal(psx$measure, psx2$measure)
#
#   dv <- DVARS(ciftiTools::read_xifti(cii_fname, brainstructures="right"))
#   plot(dv)
#   dv <- scrub_xifti(cii_fname, "DVARS", c("left", "right"))
#   print(dv)
# })

test_that("Miscellaneous functions work", {
  testthat::expect_warning(summary(pscrub(fMRItools::fsl_bptf(Dat2), ICA_method="R")))
})