Version 1.4.0 RC (#367)

## 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♯3294](OSGeo/gdal#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).

## Documentation
- Update vignette data (granting using online data) (#360).

DESCRIPTION

@@ -1,13 +1,12 @@
 Package: sen2r
 Type: Package
 Title: Find, Download and Process Sentinel-2 Data
-Version: 1.3.9.9002
+Version: 1.4.0
 Authors@R: c(person("Luigi", "Ranghetti",
                     email = "[email protected]",
                     role = c("aut", "cre"),
                     comment = c(ORCID = "0000-0001-6207-5188")),
              person("Lorenzo", "Busetto",
-                    email = "[email protected]",
                     role = c("aut"),
                     comment = c(ORCID = "0000-0001-9634-6038")))
 Description: Functions to download Sentinel-2 optical images

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♯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 

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
 #'

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) {

R/add_tile_suffix.R

@@ -26,9 +26,8 @@
 #' @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
 #' @examples
 #' safe_names <- c(

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

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(

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

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

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
 
 

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

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
 

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

R/create_indices_db.R

@@ -20,9 +20,8 @@
 #' @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
 #' @importFrom XML htmlTreeParse xmlRoot readHTMLTable xmlAttrs saveXML
@@ -195,11 +194,14 @@ create_indices_db <- function(xslt_path = NA,
 
   }
 
-  # last manual corrections on formulas
+  # last manual corrections on names
   s2_table[,s2_formula:=gsub("par\\_([0-9])", "band_\\1", s2_table$s2_formula)] # some bands were wrongly classified as parameters
   s2_table$name[s2_table$name=="TCI"] <- "TCIdx" # in order not to mess with TCI True Color Image product
   s2_table$name[s2_table$name=="NDSI"] <- "NDSaI" # in order not to mess with Normalized Difference Snow Index
 
+  # last manual corrections on formulas
+  s2_table[name=="ARVI", s2_formula := gsub("band_8a", "band_8", s2_formula)] # revert manual change on IDB
+
   # rename parameters (A, B, ...)
   s2_table[,s2_formula:=gsub("par\\_([aALyY]r?)", "par_a", s2_table$s2_formula)] # first parameters (a, A, ar, y, Y, L) -> "a"
   s2_table[,s2_formula:=gsub("par\\_([bB])", "par_b", s2_table$s2_formula)] # second parameters (b, B) -> "b"

R/create_s2_dop.R

@@ -12,9 +12,8 @@
 #' @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
 #' @importFrom jsonlite toJSON fromJSON

R/expand_path.R

@@ -20,9 +20,8 @@
 #' @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
 
 
@@ -81,9 +80,8 @@ expand_path <- function(path, parent=getwd(), silent=TRUE, normalize=TRUE) {
 #' @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
 
 

R/expect_equal_crs.R

@@ -8,9 +8,8 @@
 #' @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
 
 expect_equal_crs <- function(crs1, crs2) {

R/fix_envi_format.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
 
 fix_envi_format <- function(infiles) {

R/gdalUtil.R

@@ -26,9 +26,8 @@
 #' @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
 #' @examples 
 #' # Define product names
@@ -50,8 +49,8 @@
 #'   options = c("-tr", "2", "2", "-r", "cubicspline", "-co", "COMPRESS=DEFLATE")
 #' )
 #' oldpar <- par(mfrow = c(1,2), mar = rep(0,4))
-#' image(stars::read_stars(examplename), rgb = c(11,8,4))
-#' image(stars::read_stars(outname1), rgb = c(11,8,4))
+#' image(stars::read_stars(examplename), rgb = c(11,8,4), useRaster = TRUE)
+#' image(stars::read_stars(outname1), rgb = c(11,8,4), useRaster = TRUE)
 
 #' 
 #' ## gdalwarp
@@ -62,8 +61,8 @@
 #'   options = c("-t_srs", "EPSG:32633", "-co", "COMPRESS=DEFLATE")
 #' )
 #' oldpar <- par(mfrow = c(1,2), mar = rep(0,4))
-#' image(stars::read_stars(examplename), rgb = c(11,8,4))
-#' image(stars::read_stars(outname2), rgb = c(11,8,4))
+#' image(stars::read_stars(examplename), rgb = c(11,8,4), useRaster = TRUE)
+#' image(stars::read_stars(outname2), rgb = c(11,8,4), useRaster = TRUE)
 #' 
 #' ## gdal_calc
 #' outname3 <- tempfile(fileext = ".tif")
@@ -78,8 +77,8 @@
 #'   options = c("--A_band", "8", "--B_band", "4", "--type", "Int16")
 #' )
 #' oldpar <- par(mfrow = c(1,2), mar = rep(0,4))
-#' image(stars::read_stars(ndvirefname))
-#' image(stars::read_stars(outname3))
+#' image(stars::read_stars(ndvirefname), useRaster = TRUE)
+#' image(stars::read_stars(outname3), useRaster = TRUE)
 #' }
 
 

R/gdal_abs2rel.R

@@ -13,9 +13,8 @@
 #' @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
 #' @export
 #' @name gdal_abs2rel