version 1.4.0

cran · Jan 7, 2021 · fa13190 · fa13190
1 parent c48bd83
commit fa13190
Show file tree

Hide file tree

Showing 154 changed files with 1,495 additions and 1,091 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,12 @@
 Package: sen2r
 Type: Package
 Title: Find, Download and Process Sentinel-2 Data
-Version: 1.3.9
+Version: 1.4.0
 Authors@R: c(person("Luigi", "Ranghetti",
                     email = "luigi@ranghetti.info",
                     role = c("aut", "cre"),
                     comment = c(ORCID = "0000-0001-6207-5188")),
              person("Lorenzo", "Busetto",
-                    email = "lbusett@gmail.com",
                     role = c("aut"),
                     comment = c(ORCID = "0000-0001-9634-6038")))
 Description: Functions to download Sentinel-2 optical images
@@ -33,12 +32,12 @@ SystemRequirements: GDAL (>= 2.1.2), PROJ (>= 4.9.1), GEOS (>= 3.4.2),
         Cairo, Curl, NetCDF, jq, Protocol Buffers, V8, OpenSSL,
         Libxml2.
 VignetteBuilder: knitr
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Language: en-GB
 NeedsCompilation: no
-Packaged: 2020-10-13 22:21:42 UTC; lranghetti
+Packaged: 2021-01-06 19:28:00 UTC; lranghetti
 Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>),
   Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
 Maintainer: Luigi Ranghetti <luigi@ranghetti.info>
 Repository: CRAN
-Date/Publication: 2020-10-14 04:20:02 UTC
+Date/Publication: 2021-01-07 18:10:02 UTC
diff --git a/MD5 b/MD5
diff --git a/NAMESPACE b/NAMESPACE
@@ -111,6 +111,7 @@ importFrom(sf,st_as_sfc)
 importFrom(sf,st_as_text)
 importFrom(sf,st_bbox)
 importFrom(sf,st_cast)
+importFrom(sf,st_centroid)
 importFrom(sf,st_collection_extract)
 importFrom(sf,st_combine)
 importFrom(sf,st_convex_hull)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,41 @@
+# Version 1.4.0
+
+## Major changes
+- `gdal_warp()` was partially rewritten: now reshaped rasters conserve square
+    pixels also after warping operations. _This change also affects `sen2r()`
+    products if reshaping features (reprojection or custom resolution)
+    are required._
+    This update was necessary due to changes performed in GDAL since version 
+    3.2.0 (see [OSGeo/gdal&#x266F;3294](https://github.com/OSGeo/gdal/issues/3294)),
+    which did not grant homogeneity between outputs produced with different
+    GDAL versions.
+    Note that, in case the user wants to update an existing sen2r archive
+    produced with `{sen2r}` < 1.4.0, the old existing grid is maintained
+    so that product grids are equal (in order to produce outputs with the new
+    grid, users must create a new archive).
+- Manage images split in two SAFE products, to avoid producing black areas
+    in these [uncommon] cases (see #353 for an explanation).
+    As effects:
+    1. now pixels outside footprints (including nodata outside orbits coverage)
+        are always set to nodata;
+    2. now `s2_download()` is no more able to use existing products equivalent
+        to found ones.
+
+## Minor changes
+- Add templates for GitHub issues.
+- Do not return error in tests in case of SciHub server down (#354).
+
+## Changes in default values
+-  Pixels outside footprints (because of previous point, or - more frequently -
+    because outside orbits coverage) are always set to NA even
+    if no cloud masking is performed.
+- `s2_download()` no more uses existing SAFE products instead than downloading 
+    new equivalent ones (this in order to manage images split in two SAFE archives).
+
+## Documentation
+- Update vignette data (granting using online data) (#360).
+
+
 # Version 1.3.9
 
 ## Bug fixes 

diff --git a/R/abs2rel.R b/R/abs2rel.R
@@ -18,9 +18,8 @@
 #' @author Luigi Ranghetti, phD (2017) \email{luigi.ranghetti@@gmail.com}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
-#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. DOI: 
-#'  \href{https://doi.org/10.1016/j.cageo.2020.104473}{10.1016/j.cageo.2020.104473}, 
-#'  URL: \url{http://sen2r.ranghetti.info/}.
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @export
 #'

diff --git a/R/add_rgb_image.R b/R/add_rgb_image.R
@@ -5,9 +5,8 @@
 #' @author Luigi Ranghetti, phD (2019) \email{luigi@@ranghetti.info}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
-#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. DOI: 
-#'  \href{https://doi.org/10.1016/j.cageo.2020.104473}{10.1016/j.cageo.2020.104473}, 
-#'  URL: \url{http://sen2r.ranghetti.info/}.
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 
 add_rgb_image <- function(s2_bands) {

diff --git a/R/add_tile_suffix.R b/R/add_tile_suffix.R
@@ -0,0 +1,105 @@
+#' @title Add/remove suffixes for split tiles
+#' @description `add_tile_suffix()` adds specific suffixes to tile IDs
+#'  in order to distinguish tiled filenames referring to different original
+#'  SAFE products.
+#' @details In some sporadic cases, a tiled Sentinel-2 image is split in two 
+#'  SAFE products (see e.g. products
+#'  [`S2A_MSIL1C_20200408T101021_N0209_R022_T32TNL_20200408T153254`](https://storage.cloud.google.com/gcp-public-data-sentinel-2/tiles/32/T/NL/S2A_MSIL1C_20200408T101021_N0209_R022_T32TNL_20200408T153254.SAFE/GRANULE/L1C_T32TNL_A025044_20200408T101022/QI_DATA/T32TNL_20200408T101021_PVI.jp2) and
+#'  [`S2A_MSIL1C_20200408T101021_N0209_R022_T32TNL_20200408T171107`](https://storage.cloud.google.com/gcp-public-data-sentinel-2/tiles/32/T/NL/S2A_MSIL1C_20200408T101021_N0209_R022_T32TNL_20200408T171107.SAFE/GRANULE/L1C_T32TNL_A025044_20200408T101923/QI_DATA/T32TNL_20200408T101021_PVI.jp2)).
+#'  This split, probably a consequence of the division of the whole orbit image, 
+#'  creates ambiguity in the association among SAFE images and `sen2r` products,
+#'  since the sen2r naming convention is not sufficient to manage them as separate
+#'  products.
+#'  So, in the definition of the filenames of intermediate tiled products
+#'  (output of `s2_translate()`) it is necessary to add a suffix to be able to
+#'  manage them separately and then merge them in `s2_merge()`.
+#'  A lowercase letter ("a" and "b", but potentially "a" to "z") is used.
+#'  Functions `add_tile_suffix()` and `remove_tile_suffix()` are used in the
+#'  `sen2r()` main code as a workaround.
+#' @param paths Paths of the input tiled products
+#' @param suffix Character (1-length): if provided, the specified suffix is
+#'  appended to the tile ID of each path;
+#'  if not provided (default), a sequential suffix is appended only to the tile 
+#'  ID of the duplicated paths.
+#' @return The input paths with/without the tile suffix.
+#'
+#' @author Luigi Ranghetti, phD (2020) \email{luigi@@ranghetti.info}
+#' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
+#'  "sen2r": An R toolbox for automatically downloading and preprocessing 
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#' @note License: GPL 3.0
+#' @examples
+#' safe_names <- c(
+#'   "S2A_MSIL2A_20200408T101021_N0214_R022_T32TNK_20200408T175711.SAFE",
+#'   "S2A_MSIL2A_20200408T101021_N0214_R022_T32TNL_20200408T175711.SAFE",
+#'   "S2A_MSIL2A_20200408T101021_N0214_R022_T32TNL_20200408T161405.SAFE"
+#' )
+#' prod_names <- safe_shortname(safe_names, ext = ".tif", allow_duplicated = TRUE)
+#' ( prod_names_univoc <- sen2r:::add_tile_suffix(prod_names) )
+#' ( prod_names_custom <- sen2r:::add_tile_suffix(prod_names, "a") )
+#' sen2r:::remove_tile_suffix(prod_names_univoc)
+
+add_tile_suffix <- function(paths, suffix) {
+  if (missing(suffix)) {
+    # Default behaviour: add default suffixes to duplicated paths
+    for (sel_upath in names(table(paths))[table(paths)>1]) {
+      n_paths <- sum(paths==sel_upath)
+      paths[paths==sel_upath] <- sapply(seq_len(n_paths), function(i) {
+        gsub(
+          "(S2[AB][12][AC]\\_[0-9]{8}\\_[0-9]{3})\\_([0-9]{2}[A-Z]{3})\\_([^\\_\\.]+\\_[126]0\\.?[^\\_]*$)",
+          paste0("\\1_\\2",letters[i],"_\\3"),
+          sel_upath
+        )
+      })
+    }
+    paths
+  } else {
+    # Custom behaviour: add specific suffix to all the paths
+    gsub(
+      "(S2[AB][12][AC]\\_[0-9]{8}\\_[0-9]{3})\\_([0-9]{2}[A-Z]{3})\\_([^\\_\\.]+\\_[126]0\\.?[^\\_]*$)",
+      paste0("\\1_\\2",suffix,"_\\3"),
+      paths
+    )
+  }
+}
+
+
+#' @name remove_tile_suffix
+#' @rdname add_tile_suffix
+#' @description `remove_tile_suffix()` removes existing suffixes from tile IDs.
+
+remove_tile_suffix <- function(paths) {
+  accepted_suffixes <- "[a-z]?" # Define here the accepted suffixes
+  sapply(paths, function(p) {
+    gsub(
+      paste0(
+        "(S2[AB][12][AC]\\_[0-9]{8}\\_[0-9]{3})\\_([0-9]{2}[A-Z]{3})",
+        accepted_suffixes,
+        "\\_([^\\_\\.]+\\_[126]0\\.?[^\\_]*$)"
+      ),
+      "\\1_\\2_\\3",
+      p
+    )
+  }, simplify = TRUE, USE.NAMES = FALSE)
+}
+
+
+#' @name extract_tile_suffix
+#' @rdname add_tile_suffix
+#' @description `extract_tile_suffix()` extracts suffixes from input paths.
+
+extract_tile_suffix <- function(paths) {
+  accepted_suffixes <- "[a-z]?" # Define here the accepted suffixes
+  sapply(paths, function(p) {
+    gsub(
+      paste0(
+        "^.*S2[AB][12][AC]\\_[0-9]{8}\\_[0-9]{3}\\_[0-9]{2}[A-Z]{3}",
+        "(",accepted_suffixes,")",
+        "\\_[^\\_\\.]+\\_[126]0\\.?[^\\_]*$"
+      ),
+      "\\1",
+      p
+    )
+  }, simplify = TRUE, USE.NAMES = FALSE)
+}
diff --git a/R/build_example_param_file.R b/R/build_example_param_file.R
@@ -11,9 +11,8 @@
 #' @author Luigi Ranghetti, phD (2019) \email{luigi@@ranghetti.info}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
-#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. DOI: 
-#'  \href{https://doi.org/10.1016/j.cageo.2020.104473}{10.1016/j.cageo.2020.104473}, 
-#'  URL: \url{http://sen2r.ranghetti.info/}.
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @importFrom jsonlite toJSON
 #' @export

diff --git a/R/calcindex.R b/R/calcindex.R
@@ -27,10 +27,9 @@
 #'
 #' @author Luigi Ranghetti, phD (2020) \email{luigi@@ranghetti.info}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
-#'  "sen2r": An R toolbox for automatically downloading and preprocessing
-#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. DOI:
-#'  \href{https://doi.org/10.1016/j.cageo.2020.104473}{10.1016/j.cageo.2020.104473},
-#'  URL: \url{http://sen2r.ranghetti.info/}.
+#'  "sen2r": An R toolbox for automatically downloading and preprocessing 
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 
 calcindex_raster <- function(

diff --git a/R/check_gdal.R b/R/check_gdal.R
@@ -24,9 +24,8 @@
 #' @author Luigi Ranghetti, phD (2019) \email{luigi@@ranghetti.info}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
-#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. DOI: 
-#'  \href{https://doi.org/10.1016/j.cageo.2020.104473}{10.1016/j.cageo.2020.104473}, 
-#'  URL: \url{http://sen2r.ranghetti.info/}.
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @importFrom jsonlite toJSON
 #' @export

diff --git a/R/check_gui_deps.R b/R/check_gui_deps.R
@@ -13,9 +13,8 @@
 #' @author Luigi Ranghetti, phD (2020) \email{luigi@@ranghetti.info}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
-#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. DOI: 
-#'  \href{https://doi.org/10.1016/j.cageo.2020.104473}{10.1016/j.cageo.2020.104473}, 
-#'  URL: \url{http://sen2r.ranghetti.info/}.
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @export
 #' @examples

diff --git a/R/check_param_list.R b/R/check_param_list.R
@@ -22,9 +22,8 @@
 #' @author Luigi Ranghetti, phD (2019) \email{luigi@@ranghetti.info}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
-#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. DOI: 
-#'  \href{https://doi.org/10.1016/j.cageo.2020.104473}{10.1016/j.cageo.2020.104473}, 
-#'  URL: \url{http://sen2r.ranghetti.info/}.
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 
 

diff --git a/R/check_sen2r_deps.R b/R/check_sen2r_deps.R
@@ -14,9 +14,8 @@
 #' @author Luigi Ranghetti, phD (2019) \email{luigi@@ranghetti.info}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
-#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. DOI: 
-#'  \href{https://doi.org/10.1016/j.cageo.2020.104473}{10.1016/j.cageo.2020.104473}, 
-#'  URL: \url{http://sen2r.ranghetti.info/}.
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @importFrom utils capture.output
 #' @importFrom httr RETRY write_disk progress

diff --git a/R/compute_s2_paths.R b/R/compute_s2_paths.R
@@ -46,9 +46,8 @@
 #' @author Luigi Ranghetti, phD (2019) \email{luigi@@ranghetti.info}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
-#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. DOI: 
-#'  \href{https://doi.org/10.1016/j.cageo.2020.104473}{10.1016/j.cageo.2020.104473}, 
-#'  URL: \url{http://sen2r.ranghetti.info/}.
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @import data.table
 
@@ -382,7 +381,7 @@ compute_s2_paths <- function(pm,
   # tiles
   if (steps_todo["tiles"]) {
     exp_paths[["tiles"]] <- sapply(list_prods, function(prod){
-      remove_duplicates(nn(
+      nn(
         unlist(c(
           sapply(
             if (prod %in% l1c_prods) {file.path(pm$path_l1c,names(s2_list_l1c))} else
@@ -414,8 +413,14 @@ compute_s2_paths <- function(pm,
           ),
           exi_paths$tiles[[prod]]
         ))
-      ))
+      )
     }, simplify = FALSE, USE.NAMES = TRUE)
+    # Add suffixes in case of splitted tiles (#353)
+    if (any(duplicated(exp_paths[["tiles"]][[1]]))) {
+      exp_paths[["tiles"]] <- sapply(exp_paths[["tiles"]], function(p) {
+        add_tile_suffix(p)
+      }, simplify = FALSE, USE.NAMES = TRUE)
+    }
   }
 
   # merged
@@ -810,7 +815,7 @@ compute_s2_paths <- function(pm,
             level,"_",
             strftime(sensing_date,"%Y%m%d"),"_",
             id_orbit,"_",
-            "[0-9]{2}[A-Z]{3}_",
+            "[0-9]{2}[A-Z]{3}[a-z]?_",
             prod,"_",
             substr(res,1,2),".",
             out_ext[output_dep["merged"]]
@@ -850,10 +855,25 @@ compute_s2_paths <- function(pm,
         "[126]0\\.",
         out_ext["tiles"]
       )]
+      # add proper suffixes in case of multiple SAFE for the same date-tile (#353)
+      if (any(duplicated(tiles_basenames_av))) {
+        for (sel_basename_av in names(table(tiles_basenames_av))[table(tiles_basenames_av)>1]) {
+          tiles_basenames_av[tiles_basenames_av==sel_basename_av] <- sapply(
+            letters[seq_len(sum(tiles_basenames_av==sel_basename_av))], 
+            function(l) {
+              gsub(
+                "_([0-9]{2}[A-Z]{3})_", 
+                paste0("_\\1",l,"_"), 
+                sel_basename_av
+              )
+            }
+          )
+        }
+      }
       list(
         "L1C" = file.path(
           pm$path_l1c,
-          names(s2_list_l1c)[unlist(
+          basename(names(s2_list_l1c))[unlist(
             lapply(
               tiles_basenames_av[safe_dt_av$level=="1C"],
               function(x){length(grep(x,unlist(new_paths[["tiles"]]))) > 0}
@@ -862,7 +882,7 @@ compute_s2_paths <- function(pm,
         ),
         "L2A" = file.path(
           pm$path_l2a,
-          names(s2_list_l2a)[unlist(
+          basename(names(s2_list_l2a))[unlist(
             lapply(
               tiles_basenames_av[safe_dt_av$level=="2A"],
               function(x){length(grep(x,unlist(new_paths[["tiles"]]))) > 0}

diff --git a/R/comsub.R b/R/comsub.R
@@ -11,9 +11,8 @@
 #' @author Luigi Ranghetti, phD (2019) \email{luigi@@ranghetti.info}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
-#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. DOI: 
-#'  \href{https://doi.org/10.1016/j.cageo.2020.104473}{10.1016/j.cageo.2020.104473}, 
-#'  URL: \url{http://sen2r.ranghetti.info/}.
+#'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
 #' @note Modified from a suggestion taken from
 #'  [stackoverflow](https://stackoverflow.com/questions/28273716/r-implementation-for-finding-the-longest-common-starting-substrings-in-a-set-of).
 #' @export