tests/testthat/test-transformation.r

In natverse/nat.flybrains: Additional data for use with the NeuroAnatomy Toolbox (nat)

context("Transformation")

points <- matrix(c(30, 30, 30, 110, 110, 110), ncol=3, byrow=T)
colnames(points) <- c("X", "Y", "Z")

if(is.null(cmtk.bindir())){
  message("skipping transformation tests since CMTK is not installed")
} else {

  test_that("can mirror FCWB", {
  points.mirror <- mirror_brain(points, FCWB)

  points.mirrorexp <- matrix(c(533.852385, NA, 29.7033156, NA, 29.9916627, NA), ncol=3)
  colnames(points.mirrorexp) <- c("X", "Y", "Z")

  expect_equal(points.mirror, points.mirrorexp)
})

test_that("can mirror JFRC2", {
  points.mirror <- mirror_brain(points, JFRC2)

  points.mirrorexp <- matrix(c(601.542797, 522.999806, 12.090383, 97.4817247, 17.7922986, 103.485149), ncol=3)
  colnames(points.mirrorexp) <- c("X", "Y", "Z")

  expect_equal(points.mirror, points.mirrorexp)
})

test_that("can mirror IS2", {
  points.mirror <- mirror_brain(points, IS2)

  points.mirrorexp <- matrix(c(284.682251, 204.314929, 30.2698099, 110.658494, 30.1569345, 110.068235), ncol=3)
  colnames(points.mirrorexp) <- c("X", "Y", "Z")

  expect_equal(points.mirror, points.mirrorexp)
})

test_that("can bridge JFRC2 to FCWB", {
  points.bridge <- xform_brain(points, sample=JFRC2, reference=FCWB)

  points.bridgeexp <- matrix(c(23.1763202, 92.8401558, 35.5010956, 115.450817, 29.7029072, 85.9619354), ncol=3)
  colnames(points.bridgeexp) <- c("X", "Y", "Z")
  expect_equal(points.bridge, points.bridgeexp)

  # test known point left tip of protocerebral bridge in 3 brainsQ
  expect_equal(xform_brain(cbind(198, 134, 150), sample=IS2, reference=JFRC2),
               cbind(365, 113, 112), tolerance=10)
  expect_equal(xform_brain(cbind(365, 113, 112), sample=JFRC2, reference=FCWB),
               cbind(325, 126, 85), tolerance=10)
})

test_that("can bridge JFRC2 to IS2 using inverse registration", {
  points.bridge <- xform_brain(points, sample=JFRC2, reference=IS2)

  points.bridgeexp <- matrix(c(-76.9174206, -14.0714713, 44.4391667, 121.076295, 37.566708, 150.794994), ncol=3)
  colnames(points.bridgeexp) <- c("X", "Y", "Z")

  expect_equal(points.bridge, points.bridgeexp)
})

test_that("can use a via registration", {
  points.bridge1 <- xform_brain(points, sample=IS2, reference=JFRC2)
  points.bridge2 <- xform_brain(points.bridge1, sample=JFRC2, reference=FCWB)

  points.via <- xform_brain(points, sample=IS2, reference=FCWB, via=JFRC2)

  expect_equal(points.bridge2, points.via)

  # test a via registration back and forth to same sample
  expect_equal(xform_brain(points, ref=IS2, sample=IS2, via=JFRC2), points)
  # I think there should be a warning due to a failure to transform points
  # but I'm not seeing one with current CMTK (v3.1.0) streamxform
  # expect_warning(xform_brain(cbind(1,1,1), ref=IS2, sample=IS2, via=JFRC2))

  # test defined points
  expect_equal(xform_brain(cbind(365,113,112), sample=JFRC2, ref=FCWB, via=IS2),
               cbind(325, 126, 85), tolerance=10)
})

}