Don't include qa band in output (#36)

* Don't include qa band in output * Fix test * Don't expect T * Redocument
Permian-Global-Research · Jan 23, 2024 · 25e2dd2 · 25e2dd2
1 parent fc2b981
commit 25e2dd2
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diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,9 @@
 # rsi (development version)
 
+* `get_stac_data()` no longer includes `mask_band` in its outputs when 
+  `composite_function = NULL`. Add this band to `asset_names` to include it in 
+  the download.
+
 # rsi 0.1.1
 
 * `get_stac_data()` now removes colons (`:`) from the file names generated when

diff --git a/R/get_stac_data.R b/R/get_stac_data.R
@@ -745,26 +745,70 @@ complex_download <- function(items,
 
   if (!is.null(mask_band)) apply_masks(mask_band, mask_function, download_locations, p)
 
+  out <- make_composite_bands(
+    download_locations[, names(download_locations) %in% names(asset_names), drop = FALSE],
+    composite_function,
+    p
+  )
+
+  if (rescale_bands) lapply(out$final_bands, rescale_band, scale_strings, p)
+  out
+}
+
+
+make_composite_bands <- function(downloaded_bands, composite_function, p) {
+
   if (is.null(composite_function)) {
-    out_vrt <- replicate(nrow(download_locations), tempfile(fileext = ".tif"))
-    final_bands <- apply(download_locations, 1, identity, simplify = FALSE)
-  } else {
-    out_vrt <- tempfile(fileext = ".vrt")
-    final_bands <- list(
-      make_composite_bands(
-        download_locations[, names(download_locations) %in% names(asset_names), drop = FALSE],
-        composite_function,
-        p
+    return(
+      list(
+        out_vrt = replicate(nrow(downloaded_bands), tempfile(fileext = ".tif")),
+        final_bands = apply(downloaded_bands, 1, identity, simplify = FALSE)
       )
     )
   }
-  if (rescale_bands) lapply(final_bands, rescale_band, scale_strings, p)
+
+  download_dir <- file.path(tempdir(), "composite_dir")
+  if (!dir.exists(download_dir)) dir.create(download_dir)
+
+  out <- vapply(
+    names(downloaded_bands),
+    function(band_name) {
+      p(glue::glue("Compositing {band_name}"))
+      out_file <- file.path(download_dir, paste0(toupper(band_name), ".tif"))
+
+      if (length(downloaded_bands[[band_name]]) == 1) {
+        file.copy(downloaded_bands[[band_name]], out_file)
+      } else if (composite_function == "merge") {
+        do.call(
+          terra::merge,
+          list(
+            x = terra::sprc(lapply(downloaded_bands[[band_name]], terra::rast)),
+            filename = out_file,
+            overwrite = TRUE
+          )
+        )
+      } else {
+        do.call(
+          terra::mosaic,
+          list(
+            x = terra::sprc(lapply(downloaded_bands[[band_name]], terra::rast)),
+            fun = composite_function,
+            filename = out_file,
+            overwrite = TRUE
+          )
+        )
+      }
+
+      out_file
+    },
+    character(1)
+  )
+
   list(
-    final_bands = final_bands,
-    out_vrt = out_vrt
+    out_vrt = tempfile(fileext = ".vrt"),
+    final_bands = list(out)
   )
 }
-
 calc_scale_strings <- function(download_locations, items) {
   # Assign scale, offset attributes if they exist
   scales <- vapply(
@@ -889,45 +933,6 @@ extract_urls <- function(asset_names, items) {
   items_urls
 }
 
-make_composite_bands <- function(downloaded_bands, composite_function, p) {
-  download_dir <- file.path(tempdir(), "composite_dir")
-  if (!dir.exists(download_dir)) dir.create(download_dir)
-
-  vapply(
-    names(downloaded_bands),
-    function(band_name) {
-      p(glue::glue("Compositing {band_name}"))
-      out_file <- file.path(download_dir, paste0(toupper(band_name), ".tif"))
-
-      if (length(downloaded_bands[[band_name]]) == 1) {
-        file.copy(downloaded_bands[[band_name]], out_file)
-      } else if (composite_function == "merge") {
-        do.call(
-          terra::merge,
-          list(
-            x = terra::sprc(lapply(downloaded_bands[[band_name]], terra::rast)),
-            filename = out_file,
-            overwrite = TRUE
-          )
-        )
-      } else {
-        do.call(
-          terra::mosaic,
-          list(
-            x = terra::sprc(lapply(downloaded_bands[[band_name]], terra::rast)),
-            fun = composite_function,
-            filename = out_file,
-            overwrite = TRUE
-          )
-        )
-      }
-
-      out_file
-    },
-    character(1)
-  )
-}
-
 maybe_sign_items <- function(items, sign_function) {
   if (!is.null(sign_function)) {
     items <- sign_function(items)

diff --git a/tests/testthat/test-get_stac_data.R b/tests/testthat/test-get_stac_data.R
@@ -2,7 +2,7 @@ test_that("get_landsat_imagery() is stable", {
   skip_on_cran()
   aoi <- sf::st_point(c(-74.912131, 44.080410))
   aoi <- sf::st_set_crs(sf::st_sfc(aoi), 4326)
-  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 1000)
+  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 100)
 
   expect_no_error(
     out <- get_landsat_imagery(
@@ -25,7 +25,7 @@ test_that("get_sentinel1_imagery() is stable", {
   skip_on_cran()
   aoi <- sf::st_point(c(-74.912131, 44.080410))
   aoi <- sf::st_set_crs(sf::st_sfc(aoi), 4326)
-  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 1000)
+  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 100)
 
   expect_no_error(
     out <- get_sentinel1_imagery(
@@ -48,7 +48,7 @@ test_that("get_sentinel2_imagery() is stable", {
   skip_on_cran()
   aoi <- sf::st_point(c(-74.912131, 44.080410))
   aoi <- sf::st_set_crs(sf::st_sfc(aoi), 4326)
-  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 1000)
+  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 100)
 
   expect_no_error(
     out <- get_sentinel2_imagery(
@@ -72,7 +72,7 @@ test_that("get_dem() is stable", {
   skip_on_cran()
   aoi <- sf::st_point(c(-74.912131, 44.080410))
   aoi <- sf::st_set_crs(sf::st_sfc(aoi), 4326)
-  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 1000)
+  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 100)
 
   expect_no_error(
     out <- get_dem(
@@ -93,7 +93,7 @@ test_that("non-default mappings work", {
   skip_on_cran()
   aoi <- sf::st_point(c(-74.912131, 44.080410))
   aoi <- sf::st_set_crs(sf::st_sfc(aoi), 4326)
-  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 1000)
+  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 100)
 
   expect_no_error(
     out <- get_sentinel2_imagery(
@@ -118,7 +118,7 @@ test_that("can download RTC products", {
   skip_on_cran()
   aoi <- sf::st_point(c(-74.912131, 44.080410))
   aoi <- sf::st_set_crs(sf::st_sfc(aoi), 4326)
-  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 1000)
+  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 100)
 
   expect_no_error(
     out <- get_sentinel1_imagery(
@@ -142,7 +142,7 @@ test_that("hidden arguments work", {
   skip_on_cran()
   aoi <- sf::st_point(c(-74.912131, 44.080410))
   aoi <- sf::st_set_crs(sf::st_sfc(aoi), 4326)
-  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 1000)
+  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 100)
 
   expect_no_error(
     out <- get_landsat_imagery(
@@ -167,7 +167,7 @@ test_that("simple merge method works", {
   skip_on_cran()
   aoi <- sf::st_point(c(-74.912131, 44.080410))
   aoi <- sf::st_set_crs(sf::st_sfc(aoi), 4326)
-  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 1000)
+  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 100)
 
   expect_no_error(
     out <- get_stac_data(
@@ -189,7 +189,7 @@ test_that("warning (but not error) fires if `mask_band` is not NULL with NULL `m
   skip_on_cran()
   aoi <- sf::st_point(c(-74.912131, 44.080410))
   aoi <- sf::st_set_crs(sf::st_sfc(aoi), 4326)
-  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 1000)
+  aoi <- sf::st_buffer(sf::st_transform(aoi, 3857), 100)
 
   expect_snapshot(
     x <- get_landsat_imagery(
@@ -207,7 +207,7 @@ test_that("get_*_data works with mapply() (#17)", {
   skip_on_cran()
   san_antonio = sf::st_point(c(-98.491142, 29.424349))
   san_antonio = sf::st_sfc(san_antonio, crs = "EPSG:4326")
-  san_antonio = sf::st_buffer(sf::st_transform(san_antonio, "EPSG:3081"), 1000)
+  san_antonio = sf::st_buffer(sf::st_transform(san_antonio, "EPSG:3081"), 100)
 
   expect_no_error(
     mapply(
@@ -226,12 +226,12 @@ test_that("proper error if no items are found", {
 
   aoi <- sf::st_point(c(-74.912131, 44.080410))
   aoi <- sf::st_set_crs(sf::st_sfc(aoi), 4326)
-  aoi <- sf::st_buffer(sf::st_transform(aoi, 5070), 1000)
+  aoi <- sf::st_buffer(sf::st_transform(aoi, 5070), 100)
 
   expect_error(
     get_stac_data(
       aoi,
-      start_date = "1970-01-01",
+      start_date = "1970-01-01", # pre-LCMAP dates
       end_date = "1970-12-31",
       asset_names = "lcpri",
       stac_source = "https://planetarycomputer.microsoft.com/api/stac/v1/",
@@ -253,7 +253,7 @@ test_that("no-composite paths work on Windows #29, #32", {
       sf::st_sfc(sf::st_point(c(-74.912131, 44.080410)), crs = 4326),
       3857
     ),
-    1000
+    100
   )
 
   expect_no_error(
@@ -264,5 +264,31 @@ test_that("no-composite paths work on Windows #29, #32", {
       composite_function = NULL
     )
   )
+})
+
+test_that("no-composites return the same data", {
+  skip_if_offline()
+  skip_on_cran()
 
+  aoi <- sf::st_buffer(
+    sf::st_transform(
+      sf::st_sfc(sf::st_point(c(-74.912131, 44.080410)), crs = 4326),
+      3857
+    ),
+    100
+  )
+
+  expect_contains(
+    names(
+      terra::rast(
+        get_landsat_imagery(
+          aoi = aoi,
+          start_date = "2022-07-01",
+          end_date = "2022-07-05",
+          composite_function = NULL
+        )
+      )
+    ),
+    setdiff(rsi::landsat_band_mapping$planetary_computer_v1, "T")
+  )
 })