tests/testthat/test-write.image.R

In aoles/RBioFormats: R interface to Bio-Formats

context("Check write.image")

for(type in pixelTypes$pixelType) {
  with(pixelTypes[type,], {
    test_that(sprintf('Image writer for pixel type "%s"', type), {
      img = testImage(type)
      ref = as.vector(img)
      res = as.vector(read.image(write.image(img, tempimg(), pixelType=type), normalize=FALSE))
      if (!isFloatingPoint)
        expect_identical(res, ref)
      else
        expect_equal(res, ref)
    })
  })
}

test_that('Write 5D image stack', {
  img = mockImage(sizeX=16, sizeY=16, sizeC=3, sizeZ=5, sizeT=10)
  img = read.image(write.image(img, tempimg()))
  expect_s4_class(img, "AnnotatedImage")
  expect_identical(dim(img), c(16L, 16L, 3L, 5L, 10L))
})

test_that('Write single image plane', {
  img = read.image(write.image(mockImage(series=1L), tempimg()))
  expect_s4_class(img, "AnnotatedImage")
  expect_identical(seriesCount(img), 1L)
})

test_that('Write image series', {
  img = read.image(write.image(mockImage(series=2L), tempimg()))
  expect_s4_class(img, "AnnotatedImageList")
  expect_identical(seriesCount(img), 2L)
})

test_that('Write single image plane', {
  img = read.image(write.image(mockImage(series=1L), tempimg()))
  expect_s4_class(img, "AnnotatedImage")
  expect_identical(seriesCount(img), 1L)
})

test_that('Write global metadata', {
  ref = list(integer = 1L, numeric = 2.0, string = "3")
  img = mockImage()
  globalMetadata(img) = ref
  img = read.image(write.image(img, tempimg()))
  res = globalMetadata(img)
  nres = names(res)
  nref = names(ref)
  expect_identical(nres[match(nres, nref)], nref)
})