merge cubes with one cube with a single timeline

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)