Warp non-VRT output files (#15)

* Warp non-VRT output files

Fixes #13

* Add test, fix condition

R/stack_rasters.R

@@ -1,18 +1,22 @@
-#' Create and save a multi-band VRT by combining input rasters
+#' Create and save a multi-band output raster by combining input rasters
 #'
-#' This function creates a VRT that "stacks" all the bands of its input rasters,
-#' as though they were loaded one after another into a GIS. The VRT is fast
-#' to create and does not require much space, but does require the input rasters
-#' not be moved or altered. Run
-#' `sf::gdal_utils("warp", output_filename, "some_path.tif")` to turn the output
-#' VRT into a standalone TIFF file.
+#' This function creates an output raster that "stacks" all the bands of its
+#' input rasters, as though they were loaded one after another into a GIS. It
+#' does this by first constructing a GDAL virtual raster, or "VRT", and then
+#' optionally uses GDAL's warper to convert this VRT into a standalone file.
+#' The VRT is fast to create and does not require much space, but does require
+#' the input rasters not be moved or altered. Creating a standalone raster from
+#' this file may take a long time and a large amount of disk space.
 #'
-#' @param rasters A list or character vector of file paths to rasters to combine
-#' into a single multi-band raster. Files will be read by [terra::rast()].
-#' Rasters will be "stacked" upon one another, preserving values.
-#' They must share a CRS.
-#' @param output_filename The location to save the final "stacked" raster. Must be
-#' a VRT file.
+#' @param rasters A list of rasters to combine into a single multi-band raster,
+#' either as SpatRaster objects from [terra::rast()] or character file paths
+#' to files that can be read by [terra::rast()]. Rasters will be "stacked" upon
+#' one another, preserving values. They must share CRS.
+#' @param output_filename The location to save the final "stacked" raster. If
+#' this filename has a "vrt" extension as determined by `tools::file_ext()`,
+#' then this function exits after creating a VRT; otherwise, this function will
+#' create a VRT and then use `sf::gdal_utils("warp")` to convert the VRT into
+#' another format.
 #' @inheritParams rlang::args_dots_empty
 #' @param resolution Numeric of length 2, representing the target X and Y
 #' resolution of the output raster. If only a single value is provided, it will
@@ -29,6 +33,12 @@
 #' @param band_names Either a character vector of band names, or a function that
 #' when given a character vector of band names, returns a character vector of
 #' the same length containing new band names.
+#' @param gdalwarp_options Options passed to `gdalwarp` through the `options`
+#' argument of [sf::gdal_utils()]. This argument is ignored (with a warning)
+#' if `output_filename` is a VRT.
+#' @param gdal_config_options Options passed to `gdalwarp` through the
+#' `config_options` argument of [sf::gdal_utils()].  This argument is ignored
+#' (with a warning) if `output_filename` is a VRT.
 #'
 #' @returns `output_filename`, unchanged.
 #'
@@ -49,7 +59,26 @@ stack_rasters <- function(rasters,
                           extent,
                           reference_raster = 1,
                           resampling_method = "bilinear",
-                          band_names) {
+                          band_names,
+                          gdalwarp_options = c(
+                            "-r", "bilinear",
+                            "-multi",
+                            "-overwrite",
+                            "-co", "COMPRESS=DEFLATE",
+                            "-co", "PREDICTOR=2",
+                            "-co", "NUM_THREADS=ALL_CPUS"
+                          ),
+                          gdal_config_options = c(
+                            VSI_CACHE = "TRUE",
+                            GDAL_CACHEMAX = "30%",
+                            VSI_CACHE_SIZE = "10000000",
+                            GDAL_HTTP_MULTIPLEX = "YES",
+                            GDAL_INGESTED_BYTES_AT_OPEN = "32000",
+                            GDAL_DISABLE_READDIR_ON_OPEN = "EMPTY_DIR",
+                            GDAL_HTTP_VERSION = "2",
+                            GDAL_HTTP_MERGE_CONSECUTIVE_RANGES = "YES",
+                            GDAL_NUM_THREADS = "ALL_CPUS"
+                          )) {
   rlang::check_dots_empty()
 
   check_type_and_length(
@@ -67,6 +96,15 @@ stack_rasters <- function(rasters,
 
   out_dir <- dirname(output_filename)
 
+  use_warper <- tolower(tools::file_ext(output_filename)) != "vrt"
+
+  if (!use_warper && (!missing(gdal_config_options) || !missing(gdalwarp_options))) {
+    rlang::warn(
+      "`gdal_config_options` and `gdalwarp_options` are both ignored when `output_filename` ends in 'vrt'.",
+      class = "rsi_gdal_options_ignored"
+    )
+  }
+
   if (!(reference_raster %in% seq_along(rasters) ||
     reference_raster %in% names(rasters))) {
     if (is.numeric(reference_raster)) {
@@ -212,14 +250,31 @@ stack_rasters <- function(rasters,
     band_no <- band_no + 1
   }
 
+  vrt_destination <- ifelse(
+    use_warper,
+    tempfile(fileext = ".vrt"),
+    output_filename
+  )
+
   band_def <- grep("VRTRasterBand", vrt_container)
   writeLines(
     c(
       vrt_container[1:(band_def[[1]] - 1)],
       unlist(vrt_bands),
       vrt_container[(band_def[[2]] + 1):length(vrt_container)]
     ),
-    output_filename
+    vrt_destination
   )
+
+  if (use_warper) {
+    sf::gdal_utils(
+      "warp",
+      source = vrt_destination,
+      destination = output_filename,
+      options = gdalwarp_options,
+      config_options = gdal_config_options
+    )
+  }
+
   output_filename
 }

tests/testthat/test-stack_rasters.R

@@ -14,6 +14,29 @@ test_that("stack_rasters works", {
   )
 })
 
+test_that("stack_rasters works with non-VRT outputs", {
+  expect_no_error(
+    out_tif <- stack_rasters(
+      list(
+        system.file("rasters/example_sentinel1.tif", package = "rsi")
+      ),
+      tempfile(fileext = ".tif")
+    )
+  )
+
+  # the re-compression means we don't expect this to necessarily be the same size
+  # but it should still be a decent sized file, not just a text file
+  expect_true(
+    file.info(out_tif)$size >
+      (file.info(system.file("rasters/example_sentinel1.tif", package = "rsi"))$size / 2)
+  )
+
+  expect_equal(
+    terra::values(terra::rast(out_tif, drivers = "GTiff")),
+    terra::values(terra::rast(system.file("rasters/example_sentinel1.tif", package = "rsi")))
+  )
+})
+
 test_that("stack_rasters fails when reference_raster isn't in the vector", {
   expect_error(
     stack_rasters(
@@ -96,6 +119,19 @@ test_that("stack_rasters fails when rasters are not character vectors", {
   )
 })
 
+test_that("stack_rasters warns when arguments are being ignored", {
+  expect_warning(
+    stack_rasters(
+      list(
+        system.file("rasters/example_sentinel1.tif", package = "rsi")
+      ),
+      tempfile(fileext = ".vrt"),
+      gdalwarp_options = c("THIS IS IGNORED")
+    ),
+    class = "rsi_gdal_options_ignored"
+  )
+})
+
 test_that("type_and_length checks", {
   expect_snapshot(
     stack_rasters("a", c("a", "b")),

vignettes/rsi.Rmd

@@ -87,8 +87,7 @@ filter_platforms(platforms = "Landsat-OLI") |>
 There's an equivalent function to filter indices based upon the bands that require. For instance, we can filter the list to only indices that use the red and blue band of images:
 
 ```{r}
-filter_bands(bands = c("R", "B")) |> 
-  head()
+filter_bands(bands = c("R", "B"))
 ```
 
 Arguments to these functions let you control whether you're looking for indices that match _all_ platforms and bands you've specified, or _any_ of them.