Merge pull request #1067 from rolfsimoes/dev2

Fix MPC S1 cube, added orbit parameter to `sits_cube()`, Fix ROI XY bug in `sits_regularize()`

Author: rolfsimoes

DESCRIPTION

@@ -106,7 +106,7 @@ Config/testthat/start-first: cube, raster, regularize, data, ml
 LinkingTo:
     Rcpp,
     RcppArmadillo
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Collate: 
     'api_accessors.R'
     'api_accuracy.R'

NAMESPACE

@@ -303,6 +303,7 @@ S3method(sits_cluster_dendro,tbl_df)
 S3method(sits_combine_predictions,average)
 S3method(sits_combine_predictions,default)
 S3method(sits_combine_predictions,uncertainty)
+S3method(sits_cube,"mpc_cube_sentinel-1-grd")
 S3method(sits_cube,default)
 S3method(sits_cube,local_cube)
 S3method(sits_cube,stac_cube)

R/api_source_mpc.R

@@ -97,7 +97,9 @@
 #' @param source     Name of the STAC provider.
 #' @param collection Collection to be searched in the data source.
 #' @param stac_query Query that follows the STAC protocol
+#' @param bands      Names of the bands to filter
 #' @param ...        Other parameters to be passed for specific types.
+#' @param orbit      Name of the orbit (e.g. "Ascending" or "Descending")
 #' @param tiles      Selected tiles (optional)
 #' @param platform   Satellite platform (optional).
 #' @return An object referring the images of a sits cube.
@@ -106,33 +108,39 @@
         source,
         collection,
         bands, ...,
+        orbit = "Descending",
         start_date = NULL,
         end_date = NULL,
         dry_run = TRUE) {
 
     # require package
     .check_require_packages("rstac")
+    orbits <- .conf("sources", source, "collections", collection, "orbits")
+    .check_chr_within(
+        x = orbit,
+        within = orbits,
+        msg = "Invalid `orbit` parameter"
+    )
 
     stac_query <- .stac_create_items_query(
         source = source,
         collection = collection,
         roi = list(
-            "xmin" = -50.379,
-            "ymin" = -10.1573,
+            "xmin" = -50.479,
+            "ymin" = -10.1973,
             "xmax" = -50.410,
-            "ymax" = -10.1910,
+            "ymax" = -10.1510,
             "crs"  = "EPSG:4386"
         ),
         start_date = start_date,
         end_date = end_date,
         limit = 1
     )
-
     stac_query <- rstac::ext_filter(
         stac_query,
         `sar:frequency_band` == "C" &&
             `sar:instrument_mode` == "IW" &&
-            `sat:orbit_state` == "descending"
+            `sat:orbit_state` == {{orbit}}
     )
 
     # assert that service is online
@@ -235,15 +243,23 @@
 `.source_items_new.mpc_cube_sentinel-1-grd` <- function(source,
                                                         collection,
                                                         stac_query, ...,
-                                                        tiles = NULL) {
+                                                        tiles = NULL,
+                                                        orbit = "ascending") {
 
     # set caller to show in errors
     .check_set_caller(".source_items_new.mpc_cube_sentinel-1-grd")
+    orbits <- .conf("sources", source, "collections", collection, "orbits")
+    .check_chr_within(
+        x = orbit,
+        within = orbits,
+        msg = "Invalid `orbit` parameter"
+    )
 
     stac_query <- rstac::ext_filter(
         stac_query,
         `sar:frequency_band` == "C" &&
-        `sar:instrument_mode` == "IW"
+            `sar:instrument_mode` == "IW" &&
+            `sat:orbit_state` == {{orbit}}
     )
 
     # mpc does not support %in% operator, so we have to

R/sits_cube.R

@@ -33,6 +33,7 @@
 #'                     in the cube (optional - character vector).
 #'                     Use \code{\link{sits_list_collections}()} to find out
 #'                     the bands available for each collection.
+#' @param orbit        Orbit name ("ascending", "descending") for SAR cubes.
 #' @param vector_band  Band for vector cube ("segments", "probs", "class")
 #' @param start_date,end_date Initial and final dates to include
 #'                     images from the collection in the cube (optional).
@@ -253,6 +254,7 @@
 #'        source = "MPC",
 #'        collection = "SENTINEL-1-GRD",
 #'        bands = c("VV", "VH"),
+#'        orbit = "ascending",
 #'        roi = roi_sar,
 #'        start_date = "2020-06-01",
 #'        end_date = "2020-09-28"
@@ -281,6 +283,33 @@ sits_cube <- function(source, collection, ...) {
     # Dispatch
     UseMethod("sits_cube", source)
 }
+#' @rdname sits_cube
+#'
+#' @export
+`sits_cube.mpc_cube_sentinel-1-grd` <- function(source,
+                                                collection, ...,
+                                                orbit = "ascending",
+                                                bands = NULL,
+                                                tiles = NULL,
+                                                roi = NULL,
+                                                start_date = NULL,
+                                                end_date = NULL,
+                                                platform = NULL,
+                                                progress = TRUE) {
+    sits_cube.stac_cube(
+        source = source,
+        collection = collection,
+        bands = bands,
+        tiles = tiles,
+        roi = roi,
+        start_date = start_date,
+        end_date = end_date,
+        platform = platform,
+        progress = progress,
+        orbit = orbit
+    )
+}
+
 #' @rdname sits_cube
 #'
 #' @export

R/sits_regularize.R

@@ -132,7 +132,18 @@ sits_regularize.raster_cube <- function(cube,
         }
     }
     if (.has(roi)) {
-        roi <- .roi_as_sf(roi)
+        crs <- NULL
+        if (.roi_type(roi) == "bbox" && !.has(roi[["crs"]])) {
+            crs <- .crs(cube)
+            if (length(crs) > 1 && .check_warnings()) {
+                warning("Multiple CRS found in provided cube.",
+                        "Using the CRS of the first tile to create ROI.",
+                        call. = FALSE,
+                        immediate. = TRUE
+                )
+            }
+        }
+        roi <- .roi_as_sf(roi, default_crs = crs[[1]])
     }
     # Display warning message in case STAC cube
     if (!.cube_is_local(cube)) {

inst/extdata/config.yml

@@ -1250,6 +1250,7 @@ sources:
                         band_name     : "vh"
                 satellite   : "SENTINEL-1"
                 sensor      : "GRD"
+                orbits      : ["ascending", "descending"]
                 platforms   :
                     SENTINEL-1A: "Sentinel-1A"
                     SENTINEL-1B: "Sentinel-1B"

inst/extdata/config_internals.yml

@@ -112,7 +112,7 @@ default_values       :
 
     INT4S            : &conf_default_int4s
         data_type    : "INT4S"
-        missing_value: -2147483648
+        missing_value: -2147483647
         minimum_value: -2147483647
         maximum_value:  2147483647
         offset_value : 0