merge cubes with one cube with a single timeline

Author: gilbertocamara

NAMESPACE

@@ -438,6 +438,7 @@ export(sits_combine_predictions)
 export(sits_confidence_sampling)
 export(sits_config)
 export(sits_config_show)
+export(sits_config_user_file)
 export(sits_cube)
 export(sits_cube_copy)
 export(sits_detect_change)

R/api_conf.R

@@ -145,6 +145,19 @@
     .check_that(file.exists(yml_file))
     return(yml_file)
 }
+#' @title Return the user-relevant configuration file
+#' @name .config_file
+#' @keywords internal
+#' @noRd
+#' @return default user-relevant configuration file
+.config_file <- function() {
+    .check_set_caller(".config_file")
+    # load the default configuration file
+    yml_file <- system.file("extdata", "config.yml", package = "sits")
+    # check that the file name is valid
+    .check_that(file.exists(yml_file))
+    return(yml_file)
+}
 #' @title Return the message configuration files (only for developers)
 #' @name .conf_sources_files
 #' @keywords internal
@@ -282,7 +295,7 @@
     # pre condition - table contains name and hex code
     .check_chr_contains(
         x = colnames(color_tb),
-        contains = .conf("sits_color_table_cols"),
+        contains = .conf("color_table_cols"),
         discriminator = "all_of"
     )
     # replace all duplicates
@@ -450,7 +463,8 @@
                     user_config[["gdalcubes_chunk_size"]],
                 sources = user_config[["sources"]],
                 colors = user_config[["colors"]],
-                tmap   = user_config[["tmap"]]
+                view   = user_config[["view"]],
+                plot   = user_config[["plot"]]
             )
         }
     }
@@ -484,6 +498,86 @@
     )
     return(invisible(bands))
 }
+#' @title List configuration parameters
+#' @name .conf_list_params
+#' @description List the contents of a source
+#'
+#' @keywords internal
+#' @noRd
+#' @param params        parameter list
+#'
+#' @return              Called for side effects.
+.conf_list_params <- function(params) {
+    params <- lapply(params, function(x) {
+        if (is.atomic(x)) {
+            return(x)
+        }
+        list(names(x))
+    })
+    params_txt <- yaml::as.yaml(
+        params,
+        indent = 4,
+        handlers = list(
+            character = function(x) {
+                res <- toString(x)
+                class(res) <- "verbatim"
+                res
+            },
+            integer = function(x) {
+                res <- toString(x)
+                class(res) <- "verbatim"
+                res
+            },
+            numeric = function(x) {
+                res <- toString(x)
+                class(res) <- "verbatim"
+                res
+            }
+        )
+    )
+    cat(params_txt, sep = "\n")
+}
+
+#' @title List contents of a source
+#' @name .conf_list_source
+#' @description List the contents of a source
+#'
+#' @keywords internal
+#' @noRd
+#' @param source        Data source
+#'
+#' @return              Called for side effects.
+.conf_list_source <- function(source){
+    cat(paste0(s, ":\n"))
+    collections <- .source_collections(source = s)
+    purrr::map(collections, function(c) {
+        cat(paste0("- ", c))
+        cat(paste0(
+            " (", .source_collection_satellite(s, c),
+            "/", .source_collection_sensor(s, c), ")\n",
+            "- grid system: ", .source_collection_grid_system(s, c), "\n"
+        ))
+        cat("- bands: ")
+        cat(.source_bands(s, c))
+        cat("\n")
+        if (.source_collection_open_data(source = s, collection = c)) {
+            cat("- opendata collection ")
+            if (.source_collection_open_data(
+                source = s,
+                collection = c,
+                token = TRUE
+            )) {
+                cat("(requires access token)")
+            }
+        } else {
+            cat("- not opendata collection")
+        }
+        cat("\n")
+        cat("\n")
+    })
+}
+
+
 #' @title Get names associated to a configuration key
 #' @name .conf_names
 #' @param key   key combination to access config information

R/api_plot_raster.R

@@ -30,7 +30,7 @@
     # select the file to be plotted
     bw_file <- .tile_path(tile, band, date)
     # size of data to be read
-    max_size <- .conf("view_max_size")
+    max_size <- .conf("view", "max_size")
     sizes <- .tile_overview_size(tile = tile, max_size)
     # scale and offset
     band_conf <- .tile_band_conf(tile, band)
@@ -46,9 +46,11 @@
     # extract the values
     vals <- terra::values(rast)
     # obtain the quantiles
+    fst_quant <- .as.numeric(.conf("plot", "first_quantile"))
+    lst_quant <- .as.numeric(.conf("plot", "last_quantile"))
     quantiles <- stats::quantile(
         vals,
-        probs = c(0, 0.02, 0.98, 1),
+        probs = c(0, fst_quant, lst_quant, 1),
         na.rm = TRUE
     )
     minv <- quantiles[[1]]
@@ -70,11 +72,11 @@
     }
 
     # tmap params
-    labels_size <- as.numeric(.conf("tmap", "graticules_labels_size"))
-    legend_bg_color <- .conf("tmap", "legend_bg_color")
-    legend_bg_alpha <- as.numeric(.conf("tmap", "legend_bg_alpha"))
-    legend_title_size <- as.numeric(.conf("tmap", "legend_title_size"))
-    legend_text_size <- as.numeric(.conf("tmap", "legend_text_size"))
+    labels_size <- as.numeric(.conf("plot", "graticules_labels_size"))
+    legend_bg_color <- .conf("plot", "legend_bg_color")
+    legend_bg_alpha <- as.numeric(.conf("plot", "legend_bg_alpha"))
+    legend_title_size <- as.numeric(.conf("plot", "legend_title_size"))
+    legend_text_size <- as.numeric(.conf("plot", "legend_text_size"))
 
     # generate plot
     p <- tmap::tm_shape(rast, raster.downsample = FALSE) +
@@ -135,7 +137,7 @@
     green_file <- .tile_path(tile, band, dates[[2]])
     blue_file  <- .tile_path(tile, band, dates[[3]])
     # size of data to be read
-    max_size <- .conf("plot_max_size")
+    max_size <- .conf("plot", "max_size")
     sizes <- .tile_overview_size(tile = tile, max_size)
     # get the max values
     band_params <- .tile_band_conf(tile, band)
@@ -197,7 +199,7 @@
     band_params <- .tile_band_conf(tile, red)
     max_value <- .max_value(band_params)
     # size of data to be read
-    max_size <- .conf("plot_max_size")
+    max_size <- .conf("plot", "max_size")
     sizes <- .tile_overview_size(tile = tile, max_size)
     # used for SAR images
     if (tile[["tile"]] == "NoTilingSystem") {
@@ -257,16 +259,18 @@
         ),
         proxy = FALSE
     )
+    fst_quant <- .as.numeric(.conf("plot", "first_quantile"))
+    lst_quant <- .as.numeric(.conf("plot", "last_quantile"))
     # open RGB stars
     rgb_st <- stars::st_rgb(rgb_st[, , , 1:3],
                             dimension = "band",
                             maxColorValue = max_value,
                             use_alpha = FALSE,
-                            probs = c(0.05, 0.95),
+                            probs = c(fst_quant, las_quant),
                             stretch = TRUE
     )
     # tmap params
-    labels_size <- as.numeric(.conf("tmap", "graticules_labels_size"))
+    labels_size <- as.numeric(.conf("plot", "graticules_labels_size"))
 
     p <- tmap::tm_shape(rgb_st, raster.downsample = FALSE) +
         tmap::tm_raster() +
@@ -306,7 +310,7 @@
     # verifies if stars package is installed
     .check_require_packages("stars")
     # verifies if tmap package is installed
-    .check_require_packages("tmap")
+    .check_require_packages("plot")
 
     # deal with color palette
     .check_palette(palette)
@@ -321,7 +325,7 @@
     )
     names(colors) <- names(labels)
     # size of data to be read
-    max_size <- .conf("plot_max_size")
+    max_size <- .conf("plot", "max_size")
     sizes <- .tile_overview_size(tile = tile, max_size)
     # select the image to be plotted
     class_file <- .tile_path(tile)
@@ -340,11 +344,11 @@
     stars_obj <- stats::setNames(stars_obj, "labels")
 
     # tmap params
-    labels_size <- as.numeric(.conf("tmap", "graticules_labels_size"))
-    legend_bg_color <- .conf("tmap", "legend_bg_color")
-    legend_bg_alpha <- as.numeric(.conf("tmap", "legend_bg_alpha"))
-    legend_title_size <- as.numeric(.conf("tmap", "legend_title_size"))
-    legend_text_size <- as.numeric(.conf("tmap", "legend_text_size"))
+    labels_size <- as.numeric(.conf("plot", "graticules_labels_size"))
+    legend_bg_color <- .conf("plot", "legend_bg_color")
+    legend_bg_alpha <- as.numeric(.conf("plot", "legend_bg_alpha"))
+    legend_title_size <- as.numeric(.conf("plot", "legend_title_size"))
+    legend_text_size <- as.numeric(.conf("plot", "legend_text_size"))
 
     # plot using tmap
     p <- suppressMessages(
@@ -390,7 +394,7 @@
     # verifies if stars package is installed
     .check_require_packages("stars")
     # verifies if tmap package is installed
-    .check_require_packages("tmap")
+    .check_require_packages("plot")
     # precondition - check color palette
     .check_palette(palette)
     # revert the palette
@@ -408,7 +412,7 @@
         .check_that(all(labels_plot %in% labels))
     }
     # size of data to be read
-    max_size <- .conf("plot_max_size")
+    max_size <- .conf("plot", "max_size")
     sizes <- .tile_overview_size(tile = tile, max_size)
     # get the path
     probs_path <- .tile_path(tile)
@@ -432,11 +436,11 @@
     # select stars bands to be plotted
     bds <- as.numeric(names(labels[labels %in% labels_plot]))
 
-    labels_size <- as.numeric(.conf("tmap", "graticules_labels_size"))
-    legend_bg_color <- .conf("tmap", "legend_bg_color")
-    legend_bg_alpha <- as.numeric(.conf("tmap", "legend_bg_alpha"))
-    legend_title_size <- as.numeric(.conf("tmap", "legend_title_size"))
-    legend_text_size <- as.numeric(.conf("tmap", "legend_text_size"))
+    labels_size <- as.numeric(.conf("plot", "graticules_labels_size"))
+    legend_bg_color <- .conf("plot", "legend_bg_color")
+    legend_bg_alpha <- as.numeric(.conf("plot", "legend_bg_alpha"))
+    legend_title_size <- as.numeric(.conf("plot", "legend_title_size"))
+    legend_text_size <- as.numeric(.conf("plot", "legend_text_size"))
 
     p <- tmap::tm_shape(probs_st[, , , bds]) +
         tmap::tm_raster(

R/api_plot_vector.R

@@ -48,13 +48,13 @@
             palette = colors
         ) +
         tmap::tm_graticules(
-            labels.size = as.numeric(.conf("tmap", "graticules_labels_size"))
+            labels.size = as.numeric(.conf("plot", "graticules_labels_size"))
         ) +
         tmap::tm_compass() +
         tmap::tm_layout(
             scale = scale,
-            legend.bg.color = .conf("tmap", "legend_bg_color"),
-            legend.bg.alpha = as.numeric(.conf("tmap", "legend_bg_alpha"))
+            legend.bg.color = .conf("plot", "legend_bg_color"),
+            legend.bg.alpha = as.numeric(.conf("plot", "legend_bg_alpha"))
         ) +
         tmap::tm_borders(lwd = 0.2)
     return(p)
@@ -87,7 +87,7 @@
     # verifies if stars package is installed
     .check_require_packages("stars")
     # verifies if tmap package is installed
-    .check_require_packages("tmap")
+    .check_require_packages("plot")
     # precondition - check color palette
     .check_palette(palette)
     # revert the palette
@@ -115,14 +115,14 @@
             midpoint = 0.5,
             title = labels[labels %in% labels_plot]) +
         tmap::tm_graticules(
-            labels.size = as.numeric(.conf("tmap", "graticules_labels_size"))
+            labels.size = as.numeric(.conf("plot", "graticules_labels_size"))
         ) +
         tmap::tm_facets() +
         tmap::tm_compass() +
         tmap::tm_layout(
             scale = scale,
-            legend.bg.color = .conf("tmap", "legend_bg_color"),
-            legend.bg.alpha = as.numeric(.conf("tmap", "legend_bg_alpha"))
+            legend.bg.color = .conf("plot", "legend_bg_color"),
+            legend.bg.alpha = as.numeric(.conf("plot", "legend_bg_alpha"))
         ) +
         tmap::tm_borders(lwd = 0.1)
 
@@ -150,7 +150,7 @@
     # verifies if stars package is installed
     .check_require_packages("stars")
     # verifies if tmap package is installed
-    .check_require_packages("tmap")
+    .check_require_packages("plot")
     # precondition - check color palette
     .check_palette(palette)
     # revert the palette
@@ -167,16 +167,16 @@
                           palette = palette,
                           style = "cont") +
         tmap::tm_graticules(
-            labels.size = as.numeric(.conf("tmap", "graticules_labels_size"))
+            labels.size = as.numeric(.conf("plot", "graticules_labels_size"))
         ) +
         tmap::tm_compass() +
         tmap::tm_layout(
             main.title = main_title,
             main.title.size = 1,
             main.title.position = "center",
             scale = scale,
-            legend.bg.color = .conf("tmap", "legend_bg_color"),
-            legend.bg.alpha = as.numeric(.conf("tmap", "legend_bg_alpha"))
+            legend.bg.color = .conf("plot", "legend_bg_color"),
+            legend.bg.alpha = as.numeric(.conf("plot", "legend_bg_alpha"))
         ) +
         tmap::tm_borders(lwd = 0.2)