Filter RAT to exclude NA/masked raster cells after clipping; add unit test verifying RAT only contains non-NA values

Author: e-kotov

R/stream_grid_raster.R

@@ -265,6 +265,24 @@ stream_grid_raster_terra <- function(
       rat_df <- data.frame(Value = seq_len(n_cells), GRD_ID = id_long)
     }
 
+    # Filter RAT to exclude entries for NA cells (after clipping)
+    # This ensures the RAT only contains entries for valid raster cells
+    raster_values <- terra::values(r_final)
+    valid_values <- unique(raster_values[!is.na(raster_values)])
+    if (length(valid_values) < n_cells) {
+      rat_df <- rat_df[rat_df$Value %in% valid_values, ]
+      if (!quiet) {
+        message(
+          "  Filtered RAT: ",
+          nrow(rat_df),
+          " entries ",
+          "(removed ",
+          n_cells - nrow(rat_df),
+          " entries for masked cells)"
+        )
+      }
+    }
+
     # Format-specific persistence
     if (ext %in% c("nc", "kea")) {
       # NetCDF/KEA: Native support via levels() + writeRaster

tests/testthat/test-inspire_grid-raster-streaming.R

@@ -188,3 +188,53 @@ test_that("inspire_grid streaming errors for HDF5 with include_rat", {
     "supported"
   )
 })
+
+test_that("RAT is filtered to exclude NA cells after clipping", {
+  skip_if_not_installed("terra")
+  skip_if_not_installed("sf")
+
+  # Create an L-shaped polygon that will force some cells to be masked
+  test_poly <- sf::st_as_sfc(
+    "POLYGON((4000000 2800000, 4040000 2800000, 4040000 2840000, 4020000 2840000, 4020000 2820000, 4000000 2820000, 4000000 2800000))"
+  )
+  test_poly <- sf::st_set_crs(test_poly, 3035)
+
+  tf_clipped <- tempfile(fileext = ".tif")
+
+  # Generate grid with clipping and RAT
+  expect_message(
+    inspire_grid(
+      test_poly,
+      cellsize_m = 10000,
+      output_type = "spatraster",
+      dsn = tf_clipped,
+      include_rat = TRUE,
+      clip_to_input = TRUE,
+      quiet = FALSE
+    ),
+    "Filtered RAT"
+  )
+
+  # Load the raster
+  r <- terra::rast(tf_clipped)
+
+  # Get the RAT
+  rat <- terra::levels(r)[[1]]
+
+  # Get actual non-NA cell values
+  raster_values <- terra::values(r)
+  non_na_values <- unique(raster_values[!is.na(raster_values)])
+
+  # Key assertion: RAT should only contain entries for non-NA cells
+  expect_equal(nrow(rat), length(non_na_values))
+
+  # Verify all RAT entries correspond to actual cell values
+  expect_true(all(rat$Value %in% non_na_values))
+
+  # Verify no orphaned entries (RAT values not in raster)
+  orphaned <- setdiff(rat$Value, non_na_values)
+  expect_equal(length(orphaned), 0)
+
+  # Verify there ARE some NA cells (to confirm clipping worked)
+  expect_true(sum(is.na(raster_values)) > 0)
+})