tests/testthat/test-mosaic_functions.R

In uFTIR: Process and Analyze Agilent Cary 620 FTIR Microscope Images

test_that("Example is load as expected", {
  x <- mosaic_info(system.file("extdata", "mosaic.dmt", package = "uFTIR"))
  x_temp <- x
  x_temp@path <- mosaic_sam(x, primpke, n_cores = 1, temporal = TRUE)

  y <- mosaic_compose(x_temp@path, primpke@clusterlist)
  y1 <- get_profile_sinfo(y, where = list("info" = x, "dmdfile" = "mosaic_0000_0000.dmd"), 5, FALSE, FALSE)
  y2 <- get_profile_sinfo(y, where = list("info" = x, "dmdfile" = "mosaic_0001_0000.dmd"), 5, FALSE, FALSE)

  expect_true(nrow(y1) == 15 & ncol(y1) == length(x@wavenumbers))
  expect_true(nrow(y2) == 25 & ncol(y2) == length(x@wavenumbers))
  
  ## All recovered spectra are the equal
  expect_true(sum(!colSums(y1) == y1[1,]*nrow(y1)) == 0)
  expect_true(sum(!colSums(y2) == y2[1,]*nrow(y2)) == 0)
})

test_that("Functions return S4 and S3 classes", {
  expect_s4_class(x <- mosaic_info(system.file("extdata", "mosaic.dmt", package = "uFTIR")),
                  "SpectralInfo")
  x@path <- mosaic_sam(x, primpke, n_cores = 1, temporal = TRUE)

  expect_s4_class(y <- mosaic_compose(x@path, primpke@clusterlist), "SAM")
  y <- smooth_sam(y, as.integer(length(primpke@clusternames)), 3, 1)
  expect_s4_class(y, "Smooth")
  clip <- toClip(5, 20, c(10,5))
  expect_s3_class(y <- clipper(y, clip@centre, clip@rad, slice = 1), "clipper")
})

test_that("The program can preprocess within mosaic_sam calls", {
  expect_s4_class(x <- mosaic_info(system.file("extdata", "mosaic.dmt", package = "uFTIR")),
                  "SpectralInfo")
  x@path <- mosaic_sam(x, primpke, FUN = function(x){x}, n_cores = 1, temporal = TRUE)

  expect_s4_class(y <- mosaic_compose(x@path, primpke@clusterlist), "SAM")
})

test_that("Can load only a few slices", {
  x <- mosaic_info(system.file("extdata", "mosaic.dmt", package = "uFTIR"))
  x@path <- mosaic_sam(x, primpke, FUN = function(x){x}, n_cores = 1, temporal = TRUE)

  y <- mosaic_compose(x@path, primpke@clusterlist, nslices = 2, drop_raw = TRUE)
  z <- mosaic_compose(x@path, primpke@clusterlist, nslices = 2, drop_raw = FALSE)
  w <- mosaic_compose(x@path, primpke@clusterlist, nslices = NULL, drop_raw = FALSE)
  
  t_test <- 
    all(
      sum(dim(y@raw_sam)) == 0,
      all(dim(w@raw_sam) == dim(w@substances) & dim(w@clusters) == dim(w@substances)),
      length(primpke@clusterlist) == dim(z@raw_sam)[3],
      all(z@raw_sam == w@raw_sam),
      all(y@substances == w@substances[,,c(1,2)])
    )
  
  expect_true(t_test)
})