tests/testthat/test-Image.R

In ome/rOMERO-gateway: OMERO R Gateway

setup <- read.csv("setup.csv", comment.char = "#", header = TRUE)

host <- as.character(setup[grep("omero.host", setup$Key, ignore.case=T), ]$Value)
port <- strtoi(setup[grep("omero.port", setup$Key, ignore.case=T), ]$Value)
user <- as.character(setup[grep("omero.user", setup$Key, ignore.case=T), ]$Value)
pass <- as.character(setup[grep("omero.pass", setup$Key, ignore.case=T), ]$Value)

imageID <- strtoi(setup[grep("imageid", setup$Key, ignore.case=T), ]$Value)

server <- OMEROServer(host=host, port=port, username=user, password=pass)
server <- connect(server)

test_that("Test Image getThumbnail",{
  img <- loadObject(server, "ImageData", imageID)
  thumb <- getThumbnail(img)
  plot(0:1,0:1,type="n",ann=FALSE,axes=FALSE)
  rasterImage(thumb,0,0,1,1)
  expect_that(dim(thumb), equals(c(96,96,3)))
})


test_that("Test Image getPixelValues",{
  img <- loadObject(server, "ImageData", imageID)

  pixels <- getPixelValues(img, 1, 1, 1)

  # Test 100 random pixels. Ignore first 50 pixels
  # because that's this strange black block in the corner
  # of ".fake" images. The rest is a gradient where
  # the x value %% 256 represents the pixel value.
  for(x in sample(51:512, 10)) {
    for(y in sample(51:512, 10)) {
      got <- as.integer(pixels[x, y])
      exp <- as.integer((x-1) %% 256)
      expect_equal(got, exp)
    }
  }
})

test_that("Test Image add/getROIS",{
  img <- loadObject(server, "ImageData", imageID)
  
  rois <- data.frame(x = c(0), y = c(0), rx = c(0), ry = c(0), w = c(0), h = c(0), theta = c(0), text = c('remove'), stringsAsFactors = FALSE)
  rois <- rbind(rois, c(10, 10, NA, NA, NA, NA, NA, "Point"))
  rois <- rbind(rois, c(10, 10, 10, 20, NA, NA, NA, "Ellipse"))
  rois <- rbind(rois, c(10, 10, NA, NA, 10, 20, NA, "Rectangle"))
  rois <- rbind(rois, c(10, 10, NA, NA, 10, 20, 0.5, "Rotated Rectangle"))
  rois <- rois[-1,]
  rownames(rois) <- c()
  
  addROIs(img, coords = rois)
  
  gotRois <- getROIs(img)
  
  expect_equal(gotRois, rois)
})