tests/testthat/test-AFMimport.R

In thomasgredig/nanoscopeAFM: Load and Analyze Atomic Force Microscopy Data Files

context("Importing AFM file")

# == Asylum Research Igor image

test_that("importing Asylum Research AR AFM sample file", {
  filename = system.file("extdata", "AR_20211011.ibw",package="nanoscopeAFM")
  d = AFM.import(filename)
  expect_true(AFM.isImage(d))
  h = AFMinfo(filename)
  expect_equal(as.numeric(h$scanRate.Hz),2,tolerance = 1e-2)
  expect_equal(h$type,'Cypher')
})

test_that("Asylum Research Igor AFM image size check", {
  filename = system.file("extdata", "AR_20211011.ibw",package="nanoscopeAFM")
  d = AFM.import(filename)
  # image is 4 x 4 um
  df = AFM.raster(d)
  expect_equal(max(df$x),4000)
  expect_equal(max(df$y),4000)
  expect_equal(d@x.pixels,128)
  expect_equal(d@y.pixels,128)
  expect_equal(d@x.nm,4000)
  expect_equal(d@y.nm,4000)
})

test_that("Asylum Research Igor AFM image size check", {
  filename = system.file("extdata", "AR_20211011.ibw",package="nanoscopeAFM")
  d = AFM.import(filename)
  r = summary(d)
  # min height -32.46nm
  # max height 50.79nm
  expect_equal(r$z.min[1],-32.46,tolerance = 1e-2)
  expect_equal(r$z.max[1],50.79,tolerance = 1e-2)

})

# == Park

test_that("importing Park AFM sample file", {
  filename = system.file("extdata", "Park_20210916_034.tiff",package="nanoscopeAFM")
  d = AFM.import(filename)
  expect_true(AFM.isImage(d))
  h = AFMinfo(filename)
  expect_equal(as.numeric(h$scanRate.Hz),1.25,tolerance = 1e-2)
  expect_equal(h$type,'Park')
})

test_that("Park AFM image size check", {
  filename = system.file("extdata", "Park_20210916_034.tiff",package="nanoscopeAFM")
  d = AFM.import(filename)
  # image is 4 x 4 um
  df = AFM.raster(d)
  expect_equal(max(df$x),2500)
  expect_equal(max(df$y),2500)
  expect_equal(d@y.pixels,256)
})

test_that("Park AFM image size check", {
  filename = system.file("extdata", "Park_20210916_034.tiff",package="nanoscopeAFM")
  d = AFM.import(filename)
  r = summary(d)
  # min height -2.71nm
  # max height 9.24nm
  expect_equal(r$z.min[1],-2.71, tolerance=1e-2)
  expect_equal(r$z.max[1],9.24, tolerance=1e-3)
})


# == Veeco

test_that("importing Veeco AFM sample file", {
  filename = system.file("extdata", "Veeco_20160622.003",package="nanoscopeAFM")
  d = AFM.import(filename)
  expect_true(AFM.isImage(d))
  h = AFMinfo(filename)
  expect_equal(as.numeric(h$scanRate.Hz),1,tolerance = 1e-2)
  expect_equal(h$type,'Veeco')
})


test_that("Veeco AFM image size check", {
  filename = system.file("extdata", "Veeco_20160622.003",package="nanoscopeAFM")
  d = AFM.import(filename)
  # image is 1.7 x 1.7 um
  df = AFM.raster(d)
  expect_equal(max(df$x),1769,tolerance = 1e-4)
  expect_equal(max(df$y),1769,tolerance = 1e-4)
  expect_equal(d@y.pixels,512)
})

test_that("Veeco AFM image size check", {
  filename = system.file("extdata", "Veeco_20160622.003",package="nanoscopeAFM")
  d = AFM.import(filename)
  r = summary(d)
  # min height -145.6nm
  # max height 13.9nm
  expect_equal(r$z.min[1],-145.6,tolerance = 1e-2)
  expect_equal(r$z.max[1],13.9,tolerance = 1e-2)
})


# == NanoSurf

test_that("importing NanoSurf AFM sample file", {
  filename = system.file("extdata", "NanoSurf_20160301.nid",package="nanoscopeAFM")
  d = AFM.import(filename)
  expect_true(AFM.isImage(d))
  h = AFMinfo(filename)
  expect_equal(as.numeric(h$scanRate.Hz),1,tolerance = 1e-2)
})

test_that("NanoSurf image size check", {
  filename = system.file("extdata", "NanoSurf_20160301.nid",package="nanoscopeAFM")
  d = AFM.import(filename)
  # image is 10 x 10 um
  expect_equal(d@x.pixels*d@x.conv,10000,tolerance = 1e-2)
  expect_equal(d@y.pixels*d@y.conv,10000,tolerance = 1e-2)
})


test_that("NanoSurf image size check", {
  filename = system.file("extdata", "NanoSurf_20160301.nid",package="nanoscopeAFM")
  d = AFM.import(filename)
  r = summary(d)
  # min height -294.2nm
  # max height -88.5nm
  expect_equal(r$z.min[1],-294.2e-9,tolerance = 1e-2)
  expect_equal(r$z.max[1],-88.5e-9,tolerance = 1e-2)
})

test_that("verify all sample images", {
  file.list = AFM.getSampleImages()
  expect_equal(length(file.list), 6)
  
  x.pixels=c()
  for(filename in file.list) {
    d = AFM.import(filename)
    if (AFM.isImage(d)) {
      x.pixels = c(x.pixels, d@x.pixels)
    }
  }
  expect_equal(x.pixels, c(128,128,256,512))
})