Merge pull request #1009 from rolfsimoes/feature/s1

Feature/s1

DESCRIPTION

@@ -147,7 +147,9 @@ Collate:
  'api_raster_sub_image.R'
  'api_raster_terra.R'
  'api_reclassify.R'
+ 'api_regularize.R'
  'api_roi.R'
+ 'api_s2tile.R'
  'api_samples.R'
  'api_segments.R'
  'api_sf.R'

NAMESPACE

@@ -86,6 +86,8 @@ S3method(.cube_token_generator,default)
 S3method(.cube_token_generator,mpc_cube)
 S3method(.data_get_ts,class_cube)
 S3method(.data_get_ts,raster_cube)
+S3method(.gc_arrange_images,"mpc_cube_sentinel-1-grd")
+S3method(.gc_arrange_images,raster_cube)
 S3method(.mosaic_split_band_date,derived_cube)
 S3method(.mosaic_split_band_date,raster_cube)
 S3method(.raster_check_package,terra)
@@ -114,6 +116,7 @@ S3method(.raster_ymax,terra)
 S3method(.raster_ymin,terra)
 S3method(.raster_yres,terra)
 S3method(.slice_dfr,numeric)
+S3method(.source_collection_access_test,"mpc_cube_sentinel-1-grd")
 S3method(.source_collection_access_test,mpc_cube)
 S3method(.source_collection_access_test,stac_cube)
 S3method(.source_collection_access_test,usgs_cube)
@@ -131,6 +134,7 @@ S3method(.source_items_cube,stac_cube)
 S3method(.source_items_fid,stac_cube)
 S3method(.source_items_new,"aws_cube_landsat-c2-l2")
 S3method(.source_items_new,"mpc_cube_landsat-c2-l2")
+S3method(.source_items_new,"mpc_cube_sentinel-1-grd")
 S3method(.source_items_new,"mpc_cube_sentinel-2-l2a")
 S3method(.source_items_new,aws_cube)
 S3method(.source_items_new,bdc_cube)
@@ -140,13 +144,15 @@ S3method(.source_items_new,sdc_cube)
 S3method(.source_items_new,usgs_cube)
 S3method(.source_items_tile,"aws_cube_landsat-c2-l2")
 S3method(.source_items_tile,"mpc_cube_landsat-c2-l2")
+S3method(.source_items_tile,"mpc_cube_sentinel-1-grd")
 S3method(.source_items_tile,"mpc_cube_sentinel-2-l2a")
 S3method(.source_items_tile,aws_cube)
 S3method(.source_items_tile,bdc_cube)
 S3method(.source_items_tile,deafrica_cube)
 S3method(.source_items_tile,hls_cube)
 S3method(.source_items_tile,sdc_cube)
 S3method(.source_items_tile,usgs_cube)
+S3method(.source_tile_get_bbox,"mpc_cube_sentinel-1-grd")
 S3method(.source_tile_get_bbox,stac_cube)
 S3method(.tile,default)
 S3method(.tile,raster_cube)
@@ -317,6 +323,7 @@ S3method(sits_model_export,sits_model)
 S3method(sits_reclassify,class_cube)
 S3method(sits_reclassify,default)
 S3method(sits_reclassify,tbl_df)
+S3method(sits_regularize,"mpc_cube_sentinel-1-grd")
 S3method(sits_regularize,default)
 S3method(sits_regularize,derived_cube)
 S3method(sits_regularize,raster_cube)

R/api_cube.R

@@ -248,10 +248,13 @@ NULL
 }
 #' @export
 .cube_s3class.raster_cube <- function(cube) {
- unique(c(
- .source_s3class(source = .cube_source(cube = cube)),
- class(cube)
- ))
+ s3_class <- .source_s3class(source = .cube_source(cube = cube))
+ col_class <- paste(
+ s3_class[[1]],
+ tolower(.tile_collection(cube)),
+ sep = "_"
+ )
+ unique(c(col_class, s3_class, class(cube)))
 }
 #' @export
 .cube_s3class.default <- function(cube) {

R/api_gdal.R

@@ -167,29 +167,54 @@
 #' @param file Files to be written to (with path)
 #' @param base_files Files to be copied from (with path)
 #' @param multicores Number of cores to be used in parallel
+#' @param roi ROI to crop base_files
 #' @returns Name of file that was written to
-.gdal_merge_into <- function(file, base_files, multicores) {
+.gdal_merge_into <- function(file, base_files, multicores, roi = NULL) {
+ r_obj <- .raster_open_rast(file)
+ roi <- .roi_as_sf(roi, as_crs = .raster_crs(r_obj))
  # Merge src_files
  file <- .try(
  {
- .gdal_warp(
- file = file,
- base_files = base_files,
- params = list(
- "-wo" = paste0("NUM_THREADS=", multicores),
- "-multi" = TRUE,
- "-q" = TRUE,
- "-overwrite" = FALSE
- ),
- quiet = TRUE
- )
+ if (.has(roi)) {
+ # Write roi in a temporary file
+ roi_file <- .roi_write(
+ roi = roi,
+ output_file = tempfile(fileext = ".shp"),
+ quiet = TRUE
+ )
+ .gdal_warp(
+ file = file,
+ base_files = base_files,
+ params = list(
+ "-wo" = paste0("NUM_THREADS=", multicores),
+ "-multi" = TRUE,
+ "-cutline" = roi_file,
+ "-q" = TRUE,
+ "-overwrite" = FALSE
+ ),
+ quiet = TRUE
+ )
+ } else {
+ .gdal_warp(
+ file = file,
+ base_files = base_files,
+ params = list(
+ "-wo" = paste0("NUM_THREADS=", multicores),
+ "-multi" = TRUE,
+ "-q" = TRUE,
+ "-overwrite" = FALSE
+ ),
+ quiet = TRUE
+ )
+ }
  },
  .rollback = {
  unlink(file)
  },
  .finally = {
  # Delete auxiliary files
  unlink(paste0(file, ".aux.xml"))
+ if (.has(roi)) unlink(roi_file)
  }
  )
  # Return file

R/api_gdalcubes.R

@@ -6,11 +6,18 @@
 #' @param cube Data cube.
 #' @param timeline Timeline of regularized cube
 #' @param period Period of interval to aggregate images
-#'
+#' @param roi Optional. Used only for Sentinel-1 cube.
 #' @param ... Additional parameters.
 #'
 #' @return Data cube with the images arranged by cloud.
 .gc_arrange_images <- function(cube, timeline, period, ...) {
+ UseMethod(".gc_arrange_images", cube)
+}
+
+#' @keywords internal
+#' @noRd
+#' @export
+.gc_arrange_images.raster_cube <- function(cube, timeline, period, ...) {
  # include the end of last interval
  timeline <- c(
  timeline,
@@ -44,6 +51,64 @@
  return(cube)
 }
 
+#' @keywords internal
+#' @noRd
+#' @export
+`.gc_arrange_images.mpc_cube_sentinel-1-grd` <- function(cube,
+ timeline,
+ period,
+ roi,
+ ...) {
+ # dummy local variables to avoid warnings from tidyverse syntax
+ .x <- NULL
+
+ # pre-requisites
+ .check_that(nrow(cube) == 1,
+ local_msg = "cube must have one row",
+ msg = "invalid sentinel-1 cube")
+
+ # include the end of last interval
+ timeline <- c(
+ timeline,
+ timeline[[length(timeline)]] %m+% lubridate::period(period)
+ )
+
+ # generate Sentinel-2 tiles and intersects it with doi
+ tiles <- .s2tile_open(roi)
+ tiles <- tiles[.intersects(tiles, .roi_as_sf(roi)), ]
+
+ # prepare a sf object representing the bbox of each image in file_info
+ fi_bbox <- .bbox_as_sf(.bbox(
+ x = cube$file_info[[1]],
+ default_crs = cube$crs,
+ by_feature = TRUE
+ ))
+
+ # create a new cube according to Sentinel-2 MGRS
+ cube_class <- .cube_s3class(cube)
+ cube <- tiles |>
+ dplyr::rowwise() |>
+ dplyr::group_map(~{
+ file_info <- .fi(cube)[.intersects({{fi_bbox}}, .x), ]
+ .cube_create(
+ source = .tile_source(cube),
+ collection = .tile_collection(cube),
+ satellite = .tile_satellite(cube),
+ sensor = .tile_sensor(cube),
+ tile = .x$tile_id,
+ xmin = .x$xmin,
+ xmax = .x$xmax,
+ ymin = .x$ymin,
+ ymax = .x$ymax,
+ crs = paste0("EPSG:", .x$epsg),
+ file_info = file_info
+ )
+ }) |>
+ dplyr::bind_rows()
+
+ .cube_set_class(cube, cube_class)
+}
+
 #' @title Create a cube_view object
 #' @name .gc_create_cube_view
 #' @keywords internal
@@ -171,13 +236,19 @@
  unlink(path_db)
  }
 
+ # use crs from tile if there is no crs in file_info
+ if ("crs" %in% names(.fi(cube))) {
+ file_info <- dplyr::select(cube, "file_info") |>
+ tidyr::unnest(cols = c("file_info"))
+ } else {
+ file_info <- dplyr::select(cube, "file_info", "crs") |>
+ tidyr::unnest(cols = c("file_info"))
+ }
+
  # can be "proj:epsg" or "proj:wkt2"
- crs_type <- .gc_detect_crs_type(.cube_crs(cube))
+ crs_type <- .gc_detect_crs_type(file_info$crs[[1]])
 
- file_info <- dplyr::select(
- cube, "file_info", "crs"
- ) |>
- tidyr::unnest(cols = c("file_info")) |>
+ file_info <- file_info |>
  dplyr::transmute(
  fid = .data[["fid"]],
  xmin = .data[["xmin"]],
@@ -320,9 +391,10 @@
 #' @noRd
 #' @param cube Data cube.
 #' @param period ISO8601 time period.
+#' @param extra_date_step Add an extra date in the end of timeline?
 #'
 #' @return a \code{vector} with all timeline values.
-.gc_get_valid_timeline <- function(cube, period) {
+.gc_get_valid_timeline <- function(cube, period, extra_date_step = FALSE) {
  # set caller to show in errors
  .check_set_caller(".gc_get_valid_timeline")
 
@@ -380,13 +452,10 @@
  tl <- c(tl, date)
  }
 
- # timeline cube
- tiles_tl <- suppressWarnings(sits_timeline(cube))
-
- if (!is.list(tiles_tl)) {
- tiles_tl <- list(tiles_tl)
+ # Add extra time step
+ if (extra_date_step) {
+ tl <- c(tl, tl[[length(tl)]] %m+% lubridate::period(period))
  }
-
  return(tl)
 }
 
@@ -493,7 +562,8 @@
  cube <- .gc_arrange_images(
  cube = cube,
  timeline = timeline,
- period = period
+ period = period,
+ roi = roi
  )
 
  # start processes