Merge pull request #392 from e-sensing/dev

Release v0.14.1

.gitignore

@@ -24,6 +24,5 @@ Meta
 *.bkp
 Makevars
 Makevars.*
-*.json
 *.gcda
 *.gcno

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sits
 Type: Package
-Version: 0.14.0-2
+Version: 0.14.1
 Title: Satellite Image Time Series Analysis for Remote Sensing Data Cubes
 Authors@R: c(person('Rolf', 'Simoes', role = c('aut'), email = 'rolf.simoes@inpe.br'),
              person('Gilberto', 'Camara', role = c('aut', 'cre'), email = 'gilberto.camara@inpe.br'),
@@ -156,6 +156,7 @@ Collate:
     'sits_source_api_deafrica.R'
     'sits_source_api_local.R'
     'sits_source_api_probs.R'
+    'sits_source_api_opendata.R'
     'sits_source_api_satveg.R'
     'sits_source_api_stac.R'
     'sits_source_api_usgs.R'

NAMESPACE

@@ -6,6 +6,8 @@ S3method("sits_bands<-",predicted)
 S3method("sits_bands<-",sits)
 S3method("sits_labels<-",pattern)
 S3method("sits_labels<-",sits)
+S3method(.gc_format_col,aws_cube)
+S3method(.gc_format_col,opendata_cube)
 S3method(.raster_check_package,default)
 S3method(.raster_check_package,raster)
 S3method(.raster_check_package,terra)
@@ -74,18 +76,22 @@ S3method(.source_cube,wtss_cube)
 S3method(.source_item_get_bands,aws_cube)
 S3method(.source_item_get_bands,bdc_cube)
 S3method(.source_item_get_bands,deafrica_cube)
+S3method(.source_item_get_bands,opendata_cube)
 S3method(.source_item_get_bands,usgs_cube)
 S3method(.source_item_get_date,aws_cube)
 S3method(.source_item_get_date,bdc_cube)
 S3method(.source_item_get_date,deafrica_cube)
+S3method(.source_item_get_date,opendata_cube)
 S3method(.source_item_get_date,usgs_cube)
 S3method(.source_item_get_hrefs,aws_cube)
 S3method(.source_item_get_hrefs,bdc_cube)
 S3method(.source_item_get_hrefs,deafrica_cube)
+S3method(.source_item_get_hrefs,opendata_cube)
 S3method(.source_item_get_hrefs,usgs_cube)
 S3method(.source_item_get_resolutions,aws_cube)
 S3method(.source_item_get_resolutions,bdc_cube)
 S3method(.source_item_get_resolutions,deafrica_cube)
+S3method(.source_item_get_resolutions,opendata_cube)
 S3method(.source_item_get_resolutions,usgs_cube)
 S3method(.source_items_bands_select,aws_cube)
 S3method(.source_items_bands_select,stac_cube)
@@ -96,27 +102,33 @@ S3method(.source_items_fileinfo,wtss_cube)
 S3method(.source_items_new,aws_cube)
 S3method(.source_items_new,bdc_cube)
 S3method(.source_items_new,deafrica_cube)
+S3method(.source_items_new,opendata_cube)
 S3method(.source_items_new,usgs_cube)
 S3method(.source_items_new,wtss_cube)
 S3method(.source_items_tile_get_bbox,aws_cube)
 S3method(.source_items_tile_get_bbox,bdc_cube)
 S3method(.source_items_tile_get_bbox,deafrica_cube)
+S3method(.source_items_tile_get_bbox,opendata_cube)
 S3method(.source_items_tile_get_bbox,usgs_cube)
 S3method(.source_items_tile_get_crs,aws_cube)
 S3method(.source_items_tile_get_crs,bdc_cube)
 S3method(.source_items_tile_get_crs,deafrica_cube)
+S3method(.source_items_tile_get_crs,opendata_cube)
 S3method(.source_items_tile_get_crs,usgs_cube)
 S3method(.source_items_tile_get_name,aws_cube)
 S3method(.source_items_tile_get_name,bdc_cube)
 S3method(.source_items_tile_get_name,deafrica_cube)
+S3method(.source_items_tile_get_name,opendata_cube)
 S3method(.source_items_tile_get_name,usgs_cube)
 S3method(.source_items_tile_get_size,aws_cube)
 S3method(.source_items_tile_get_size,bdc_cube)
 S3method(.source_items_tile_get_size,deafrica_cube)
+S3method(.source_items_tile_get_size,opendata_cube)
 S3method(.source_items_tile_get_size,usgs_cube)
 S3method(.source_items_tiles_group,aws_cube)
 S3method(.source_items_tiles_group,bdc_cube)
 S3method(.source_items_tiles_group,deafrica_cube)
+S3method(.source_items_tiles_group,opendata_cube)
 S3method(.source_items_tiles_group,usgs_cube)
 S3method(plot,classified_image)
 S3method(plot,keras_model)
@@ -144,6 +156,7 @@ S3method(sits_cube,bdc_cube)
 S3method(sits_cube,deafrica_cube)
 S3method(sits_cube,default)
 S3method(sits_cube,local_cube)
+S3method(sits_cube,opendata_cube)
 S3method(sits_cube,probs_cube)
 S3method(sits_cube,satveg_cube)
 S3method(sits_cube,wtss_cube)
@@ -216,6 +229,7 @@ export(sits_labels)
 export(sits_labels_summary)
 export(sits_lda)
 export(sits_linear_interp)
+export(sits_list_collections)
 export(sits_merge)
 export(sits_metadata_to_csv)
 export(sits_missing_values)

NEWS.md

@@ -3,6 +3,25 @@
 We are preparing to release the package on CRAN and are making relevant changes in the development version.
 
 
+# What's new in SITS version 0.14.1
+
+### New features in SITS version 0.14.1
+
+* Implement new function `sits_list_collections()`
+* Update gdalcubes parameters
+* Implement `.source_bands_resampling()`
+* Remove name from demo file
+* Improve `sits_som_clean_samples()` function
+* Improve `sits_bands<-()` function
+* Improve `sits_select()` function
+* Error in cloud band of CBERS4 data example
+* Include a function to list collections available in cloud services
+* sits_cube_copy() does not include information on the tile
+* Get spatial resolution from config file
+* Fix partial merge configuration file
+* Change bbox to roi in sits
+
+
 # What's new in SITS version 0.14.0
 
 ### New features in SITS version 0.14.0-2

R/sits_bands.R

@@ -35,7 +35,7 @@ sits_bands <- function(x) {
 #'
 sits_bands.sits <- function(x) {
 
-    return(names(sits_time_series(x))[-1])
+    return(setdiff(names(sits_time_series(x)), "Index"))
 }
 
 #' @export

R/sits_bands_set.R

@@ -21,23 +21,38 @@
     # set caller to show in errors
     .check_set_caller("sits_bands")
 
-    # get the time series
-    ts <- sits_time_series(x)
-    .check_that(
-        x = ncol(ts) == length(value) + 1,
-        msg = "invalid number of bands to be replaced")
+    # get the data bands
+    data_bands <- sits_bands(x)
 
-    # change band names for all rows of the tibble
-    rows <- slider::slide(x, function(row) {
-        ts <- sits_time_series(row)
-        names(ts) <- c("Index", value)
-        row$time_series[[1]] <- ts
-        return(row)
-    })
-    x <- dplyr::bind_rows(rows)
+    .check_chr(value, allow_empty = FALSE, len_min = length(data_bands),
+               len_max = length(data_bands),
+               msg = "Invalid bands values to be replaced")
+
+    # create an row_id to use later in nest
+    x[["..row_id"]] <- seq_len(nrow(x))
+
+    # unnest bands
+    x <- tidyr::unnest(x, cols = "time_series")
+
+    # here, you could pass a function to process fast
+    new_bands <- colnames(x)
+    names(new_bands) <- new_bands
+
+    new_bands[data_bands] <- toupper(value)
+    colnames(x) <- unname(new_bands)
+
+    # nest again
+    x <- tidyr::nest(x,  time_series = c("Index", toupper(value)))
+
+    # remove ..row_id
+    x <- dplyr::select(x, -"..row_id")
+
+    # set sits tibble class
+    class(x) <- c("sits", class(x))
 
     return(x)
 }
+
 #' @export
 #'
 `sits_bands<-.cube` <- function(x, value) {

R/sits_classification.R

@@ -54,7 +54,7 @@
 #'    The "roi" parameter defines a region of interest. It can be
 #'    an sf_object, a shapefile, or a bounding box vector with
 #'    named XY values ("xmin", "xmax", "ymin", "ymax") or
-#'    named lat/long values ("lat_min", "lat_max", "lon_min", "lon_max")
+#'    named lat/long values ("lon_min", "lat_min", "lon_max", "lat_max")
 #'
 #'    The "filter_fn" parameter specifies a smoothing filter to be applied to
 #'    time series for reducing noise. Currently, options include

R/sits_config.R

@@ -13,9 +13,13 @@
 #'
 #' \code{sits_config_show()} prints the current sits
 #' configuration options. To show specific configuration options for
-#' a source, a collection, or a palette, user can inform the corresponding
+#' a source, a collection, or a palette, users can inform the corresponding
 #' keys to \code{source}, \code{collection}, and \code{palette} parameters.
 #'
+#' \code{sits_list_collections()} prints the collections available
+#' in each cloud service supported by sits. Users can select to get information
+#' only for a single service by using the \code{source} parameter.
+#'
 #' @param processing_bloat       A \code{numeric} value to estimate
 #' growth size of R memory relative to block size.
 #' @param rstac_pagination_limit A \code{numeric} value indicating number of
@@ -81,6 +85,9 @@ sits_config <- function(processing_bloat = NULL,
         message(paste("Additional configurations found in", user_yml_file))
         config <- yaml::yaml.load_file(input = user_yml_file,
                                        merge.precedence = "override")
+        config <- utils::modifyList(sits_env[["config"]],
+                                    config,
+                                    keep.null = FALSE)
 
         # set options defined by user (via YAML file)
         # modifying existing configuration
@@ -190,6 +197,49 @@ sits_config_show <- function(source = NULL,
     return(invisible(config))
 }
 
+#' @rdname sits_configuration
+#'
+#' @return
+#' \code{sits_list_collections()} prints the collections available in
+#' each cloud service supported by sits.
+#'
+#' @export
+sits_list_collections <- function(source = NULL) {
+
+    # get sources available
+    sources <- .sources(internal = FALSE)
+
+    # if the user has required a source
+    # check that it is valid
+    if (!purrr::is_null(source)) {
+        # check if source exists
+        .check_chr_within(
+            x = source,
+            within = sources,
+            msg = "invalid source value"
+        )
+        sources <- source
+    }
+
+    purrr::map(sources, function(s){
+
+        cat(paste0(s, ":\n"))
+        collections <- .source_collections(source = s)
+        purrr::map(collections, function(c){
+            # get collection information
+
+            cat(paste0("- ", c))
+            cat(paste0(" (", .source_collection_satellite(s, c),
+                       "/", .source_collection_sensor(s, c), ")\n"))
+            cat("- bands: ")
+            cat(.source_bands(s, c))
+            cat("\n")
+            cat("\n")
+        })
+    })
+    return(invisible(NULL))
+}
+
 .config_set_options <- function(processing_bloat = NULL,
                                 rstac_pagination_limit = NULL,
                                 raster_api_package = NULL,