tests/testthat/test-read.image.R

In aoles/RBioFormats: R interface to Bio-Formats

context("Check read.image")

MAX_INT = min(.Machine$integer.max, 2147483647)

pixelTypes = within(pixelTypes, {
  n = 256^bytesPerPixel
  x = pmin(n, ifelse(isSigned & !isFloatingPoint, (MAX_INT+1)/2, MAX_INT))
  scaleFactor = ifelse(bytesPerPixel>2, round(n/MAX_INT), 1)
  refMin = ifelse(isSigned & !isFloatingPoint, -n/2, 0)
  refMax = trunc(refMin + n - scaleFactor)
})

for(type in pixelTypes$pixelType) {
  with(pixelTypes[type,], {
    test_that(sprintf('Extreme pixel values correspond to the range defined by pixelType "%s"', type), {
      ## minimal value allowed by pixel type
      mockfile = mockFile(pixelType=pixelType)
      res = as.double(read.image(mockfile, subset = list(x=1, y=16), normalize = FALSE))
      expect_identical(res, refMin)
      ## maximal value allowed by pixel type modulo scaleFactor
      mockfile = mockFile(pixelType=pixelType, sizeX=x, scaleFactor=scaleFactor)
      res = as.double(read.image(mockfile, subset = list(x=x, y=16), normalize = FALSE))
      if (bytesPerPixel<=2)
        expect_identical(res, refMax)
      else
        expect_equal(res, refMax)
    })
  })
}

test_that('Read 5D image stack', {
  img = mockImage(sizeX=16,
                  sizeY=16,
                  sizeC=3,
                  sizeZ=5,
                  sizeT=10,
                  series=1)
  expect_s4_class(img, "AnnotatedImage")
  expect_identical(dim(img), c(16L, 16L, 3L, 5L, 10L))
})

test_that('Read single image plane', {
  img = read.image(mockFile(series=1L))
  expect_s4_class(img, "AnnotatedImage")
  expect_identical(seriesCount(img), 1L)
})

test_that('Read image series', {
  img = read.image(mockFile(series=2L))
  expect_s4_class(img, "AnnotatedImageList")
  expect_identical(seriesCount(img), 2L)
})