Flip xy coordinates in ENVI files (#156)

* Test flip * Update tests --------- Co-authored-by: Win Cowger, PhD <[email protected]>
wincowgerDEV · Oct 31, 2023 · 3812966 · 3812966
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commit 3812966
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Showing 3 changed files with 33 additions and 22 deletions.
diff --git a/R/read_envi.R b/R/read_envi.R
@@ -74,11 +74,11 @@ read_envi <- function(file, header = NULL, share = NULL,
   arr <- read.ENVI(file, header)
   dt <- as.data.table(arr)
   md <- hdr[names(hdr) != "wavelength"]
-  names(dt) <- c("x", "y", "z", "value")
+  names(dt) <- c("y", "x", "z", "value")
   dt[, 1:2] <- dt[, 1:2] -1
 
   os <- as_OpenSpecy(x = hdr$wavelength,
-                     spectra = dcast(dt, z ~ x + y)[, -1],
+                     spectra = dcast(dt, z ~ y + x)[, -1],
                      metadata = c(metadata, md),
                      coords = dt[, 1:2] |> unique(),
                      session_id = T)

diff --git a/tests/testthat/test-adj_range.R b/tests/testthat/test-adj_range.R
@@ -60,7 +60,6 @@ test_that("flatten_range() function test", {
   expect_false(all.equal(flat_map$spectra, tiny_map$spectra) |> isTRUE())
   expect_equal(flat_map$spectra[1:20], tiny_map$spectra[1:20])
 
-  expect_equal(flat_map$spectra[40:60, 1:5] |> unique() |> round(4)
-               |> as.numeric(),
-               c(-0.8694, -1.246, -0.8304, -1.1909, -0.7857))
+  flat_map$spectra[40:60, 1:5] |> unique() |> round(2) |> as.numeric() |>
+    expect_equal(c(-0.87, -1.25, -0.83, -1.19, -0.79))
 })
diff --git a/tests/testthat/test-def_features.R b/tests/testthat/test-def_features.R
@@ -11,21 +11,27 @@ test_that("collapse_spec() handles input errors correctly", {
 test_that("features are identified when given logical", {
   map$metadata$particles <- map$metadata$y == 0
   id_map <- def_features(map, map$metadata$particles)
-  expect_true(check_OpenSpecy(id_map))
-  expect_length(unique(id_map$metadata$feature_id), 2)
-  expect_equal(max(id_map$metadata$area, na.rm = T), 13)
-  expect_equal(max(id_map$metadata$feret_max, na.rm = T), 13)
-  expect_equal(max(id_map$metadata$feret_min, na.rm = T), 1)
-  expect_equal(max(id_map$metadata$perimeter, na.rm = T), 24)
+  check_OpenSpecy(id_map) |> expect_true()
+  unique(id_map$metadata$feature_id) |> expect_length(2)
+  max(id_map$metadata$area, na.rm = T) |> expect_equal(16)
+  max(id_map$metadata$feret_max, na.rm = T) |> round(2) |>
+    expect_equal(13.04)
+  max(id_map$metadata$feret_min, na.rm = T) |> round(2) |>
+    expect_equal(1.23)
+  max(id_map$metadata$perimeter, na.rm = T) |> round(2) |>
+    expect_equal(25.05)
 })
 
 test_that("particles are identified when given character", {
   map$metadata$particles <- ifelse(map$metadata$y == 1, "particle", "not_particle")
   id_map <- def_features(map, map$metadata$particles)
   expect_true(check_OpenSpecy(id_map))
-  expect_length(unique(id_map$metadata$feature_id), 3)
-  expect_equal(max(id_map$metadata$area, na.rm = T), 182)
-  expect_equal(round(max(id_map$metadata$feret_max, na.rm = T)), 19)
+  unique(id_map$metadata$feature_id) |>
+    expect_length(3)
+  max(id_map$metadata$area, na.rm = T) |>
+    expect_equal(176)
+  max(id_map$metadata$feret_max, na.rm = T) |> round(2) |>
+    expect_equal(18.69)
 })
 
 test_that("an error is thrown for invalid feature input", {
@@ -72,20 +78,26 @@ test_that("collapse particles returns expected values", {
 
   expect_true(check_OpenSpecy(test_collapsed))
 
-  expect_equal(test_collapsed$metadata |> nrow(), 3)
-  expect_equal(test_collapsed$metadata$feret_max |> round(2), c(13, 13, 18.69))
-  expect_equal(test_collapsed$metadata$centroid_x |> unique(), 6)
+  test_collapsed$metadata |> nrow() |>
+    expect_equal(3)
+  test_collapsed$metadata$feret_max |> round(2) |>
+    expect_equal(c(13.04, 13.04, 18.69))
+  test_collapsed$metadata$centroid_x |> unique() |>
+    expect_equal(7.5)
 
   particles <- map$metadata$y == 1
   id_map <- def_features(map, particles)
   expect_true(check_OpenSpecy(id_map))
 
   test_collapsed <- collapse_spec(id_map)
-  expect_true(check_OpenSpecy(test_collapsed))
-
-  expect_equal(test_collapsed$metadata |> nrow(), 2)
-  expect_equal(test_collapsed$metadata$feret_max |> round(2), c(NA, 13))
-  expect_equal(test_collapsed$metadata$centroid_x |> unique(), 6)
+  check_OpenSpecy(test_collapsed) |> expect_true()
+
+  test_collapsed$metadata |> nrow() |>
+    expect_equal(2)
+  test_collapsed$metadata$feret_max |> round(2) |>
+    expect_equal(c(NA, 13.04))
+  test_collapsed$metadata$centroid_x |> unique() |>
+    expect_equal(7.5)
 
   expect_contains(names(test_collapsed$metadata),
                   c("feature_id", "area", "feret_max", "centroid_y",