diff Lib_preprocess_S2.r @ 0:5cae678042ec draft default tip

planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Lib_preprocess_S2.r	Mon Jan 09 13:36:33 2023 +0000
@@ -0,0 +1,1335 @@
+# == == == == == == == == == == == == == == == == == == == == == == == == == == ==
+# preprocS2
+# Lib_preprocess_S2.R
+# == == == == == == == == == == == == == == == == == == == == == == == == == == ==
+# PROGRAMMERS:
+# Jean-Baptiste FERET <[e-mail]>
+# Copyright 2021/08 Jean-Baptiste FERET
+# == == == == == == == == == == == == == == == == == == == == == == == == == == ==
+# This Library contains functions to preprocess Sentinel-2 images downloaded from
+# different data hubs, such as THEIA, PEPS or SCIHUB
+# == == == == == == == == == == == == == == == == == == == == == == == == == == ==
+
+#" This function adjusts information from ENVI header
+#"
+#" @param dsn character. path where to store the stack
+#" @param bands list. should include "bandname", and if possible "wavelength"
+#" @param sensor character. Name of the sensor used to acquire the image
+#" @param stretch boolean. Set TRUE to get 10% stretching at display for reflectance, mentioned in hdr only
+#"
+#" @return None
+#" @importFrom utils read.table
+#" @importFrom raster hdr raster
+#" @export
+adjust_envi_hdr <- function(dsn, bands, sensor = "Unknown", stretch = FALSE) {
+
+  # Edit hdr file to add metadata
+  hdr <- read_envi_header(get_hdr_name(dsn))
+  hdr$`band names` <- bands$bandname
+  if (length(bands$wavelength) == length(bands$bandname)) {
+    hdr$wavelength <- bands$wavelength
+  }else {
+    hdr$wavelength <- NULL
+  }
+  if (stretch == TRUE) {
+    hdr$`default stretch` <- "0.000000 1000.000000 linear"
+  }
+  hdr$`z plot range` <- NULL
+  hdr$`data ignore value` <- "-Inf"
+  hdr$`sensor type` <- sensor
+  write_envi_header(hdr = hdr, hdrpath = get_hdr_name(dsn))
+
+  # remove unnecessary files
+  file2remove <- paste(dsn, ".aux.xml", sep = "")
+  if (file.exists(file2remove)) file.remove(file2remove)
+  file2remove <- paste(dsn, ".prj", sep = "")
+  if (file.exists(file2remove)) file.remove(file2remove)
+  file2remove <- paste(dsn, ".stx", sep = "")
+  if (file.exists(file2remove)) file.remove(file2remove)
+  return(invisible())
+}
+
+#" This function saves reflectance files
+#"
+#" @param s2sat character. Sentinel-2 mission ("2A" or "2B")
+#" @param tile_s2 character. S2 tile name (2 numbers + 3 letters)
+#" @param dateacq_s2 double. date of acquisition
+#"
+#" @return s2mission character. name of the S2 mission (2A or 2B)
+#" @importFrom sen2r safe_getMetadata check_scihub_connection s2_list
+#" @export
+check_s2mission <- function(s2sat, tile_s2, dateacq_s2) {
+
+  # is mission already defined by user?
+  if (!is.null(s2sat)) {
+    if (s2sat == "2A") {
+      s2mission <- "2A"
+    }else if (s2sat == "2B") {
+      s2mission <- "2B"
+    }else {
+      message("Could not identify if image from Sentinel-2A or -2B")
+      message("Defining central wavelength of spectral bands based on S2A")
+      s2mission <- "2A"
+    }
+  }else {
+    message("Could not identify if image from Sentinel-2A or -2B")
+    message("Defining central wavelength of spectral bands based on S2A")
+    s2mission <- "2A"
+  }
+  return(s2mission)
+}
+
+#" this function aims at computing directory size
+#" @param path character. path for directory
+#" @param recursive boolean . set T if recursive
+#"
+#" @return size_files numeric. size in bytes
+#" - image stack
+#" - path for individual band files corresponding to the stack
+#" - path for vector (reprojected if needed)
+#"
+#" @importFrom raster raster
+#" @importFrom tools file_path_sans_ext file_ext
+#" @export
+dir_size <- function(path, recursive = TRUE) {
+  stopifnot(is.character(path))
+  files <- list.files(path, full.names = TRUE, recursive = recursive)
+  vect_size <- sapply(files, function(x) file.size(x))
+  size_files <- sum(vect_size)
+  return(size_files)
+}
+
+#" This function reads S2 data from L2A directories downloaded from
+#" various data hubs including THEIA, PEPS & SCIHUB (SAFE format & LaSRC)
+#" @param path_dir_s2 character. path for S2 directory
+#" @param path_vector character. path for vector file
+#" @param s2source character. type of directory format (depends on atmospheric correction: SAFE produced from Sen2Cor)
+#" @param resolution numeric. buffer applied to vector file (in meters)
+#" @param interpolation character. method for resampling. default = "bilinear"
+#" @param fre_sre character. SRE or FRE products from THEIA
+#"
+#" @return listout list.
+#" - image stack
+#" - path for individual band files corresponding to the stack
+#" - path for vector (reprojected if needed)
+#"
+#" @importFrom raster raster
+#" @importFrom tools file_path_sans_ext file_ext
+#" @export
+extract_from_s2_l2a <- function(path_dir_s2, path_vector = NULL, s2source = "SAFE",
+                                resolution = 10, interpolation = "bilinear", fre_sre = "FRE") {
+  # Get list of paths corresponding to S2 bands and depending on S2 directory
+  s2_bands <- get_s2_bands(path_dir_s2 = path_dir_s2,
+                           s2source = s2source,
+                           resolution = resolution,
+                           fre_sre = fre_sre)
+
+  if (length(s2_bands$s2bands_10m) > 0) {
+    rastmp <- raster::raster(s2_bands$s2bands_10m[[1]])
+  } else if (length(s2_bands$s2bands_20m) > 0) {
+    rastmp <- raster::raster(s2_bands$s2bands_20m[[1]])
+  }
+  # check if vector and raster share the same projection. if not, re-project vector
+  if (!is.null(path_vector)) {
+    raster_proj <- raster::projection(rastmp)
+    path_vector_reproj <- paste(tools::file_path_sans_ext(path_vector), "_reprojected.shp", sep = "")
+    path_vector <- reproject_shp(path_vector_init = path_vector,
+                                 newprojection = raster_proj,
+                                 path_vector_reproj = path_vector_reproj)
+  }
+  # Extract data corresponding to the vector footprint (if provided) & resample data if needed
+  if (length(s2_bands$s2bands_10m) > 0) {
+    stack_10m <- read_s2bands(s2_bands = s2_bands$s2bands_10m, path_vector = path_vector,
+                              resampling = 1, interpolation = interpolation)
+  }
+  if (length(s2_bands$s2bands_20m) > 0) {
+    if (resolution == 10 && s2source != "LaSRC") {
+      resampling <- 2
+    }else {
+      resampling <- 1
+    }
+    stack_20m <- read_s2bands(s2_bands = s2_bands$s2bands_20m, path_vector = path_vector,
+                              resampling = resampling, interpolation = interpolation)
+  }
+  # get full stack including 10m and 20m spatial resolution
+  if (length(s2_bands$s2bands_10m) > 0 && length(s2_bands$s2bands_20m) > 0) {
+    diffxstart <- attributes(stack_10m)$dimensions[[1]]$from - attributes(stack_20m)$dimensions[[1]]$from
+    diffxstop <- attributes(stack_10m)$dimensions[[1]]$to - attributes(stack_20m)$dimensions[[1]]$to
+    diffystart <- attributes(stack_10m)$dimensions[[2]]$from - attributes(stack_20m)$dimensions[[2]]$from
+    diffystop <- attributes(stack_10m)$dimensions[[2]]$to - attributes(stack_20m)$dimensions[[2]]$to
+    if (!diffxstop == 0) {
+      # size of 20m > size of 10m --> reduce 20m
+      # size of 10m > size of 20m --> reduce 10m
+      if (diffxstop > 0) {
+        stack_10m <- stack_10m[, 1:(dim(stack_10m)[1] - diffxstop), , ]
+      }else if (diffxstop < 0) {
+        stack_20m <- stack_20m[, 1:(dim(stack_20m)[1] + diffxstop), , ]
+      }
+    }
+    if (!diffystop == 0) {
+      if (diffystop > 0) {
+        stack_10m <- stack_10m[, , 1:(dim(stack_10m)[2] - diffystop), ]
+      }else if (diffystop < 0) {
+        stack_20m <- stack_20m[, , 1:(dim(stack_20m)[2] + diffystop), ]
+      }
+    }
+    if (!diffxstart == 0) {
+      if (diffxstart > 0) {
+        stack_20m <- stack_20m[, (1 + diffxstart):dim(stack_20m)[1], , ]
+      }else if (diffxstart < 0) {
+        stack_10m <- stack_10m[, (1 - diffxstart):dim(stack_10m)[1], , ]
+      }
+    }
+    if (!diffystart == 0) {
+      if (diffystart > 0) {
+        stack_20m <- stack_20m[, , (1 + diffystart):dim(stack_20m)[2], ]
+      }else if (diffystart < 0) {
+        stack_10m <- stack_10m[, , (1 - diffystart):dim(stack_10m)[2], ]
+      }
+    }
+    # reorder bands with increasing wavelength
+    s2bands <- c("B02", "B03", "B04", "B05", "B06", "B07", "B08", "B8A", "B11", "B12", "Cloud")
+    namebands <- c(names(s2_bands$s2bands_10m), names(s2_bands$s2bands_20m))
+    reorder_bands <- match(s2bands, namebands)
+    namebands <- namebands[reorder_bands]
+    listfiles <- c(stack_10m$attr, stack_20m$attr)[reorder_bands]
+
+    # adjust size to initial vector footprint without buffer
+    # --> buffer is needed in order to ensure that extraction following
+    # footprint of vector matches for images of different spatial resolution
+    # get bounding box corresponding to footprint of image or image subset
+    bb_xycoords <- get_bb(path_raster = listfiles[1],
+                          path_vector = path_vector, buffer = 0)
+
+    # prepare reading data for extent defined by bounding box
+    nxoff <- bb_xycoords$UL$col
+    nyoff <- bb_xycoords$UL$row
+    nxsize <- bb_xycoords$UR$col - bb_xycoords$UL$col + 1
+    nysize <- bb_xycoords$LR$row - bb_xycoords$UR$row + 1
+    nbufxsize <- nxsize
+    nbufysize <- nysize
+    s2_stack <- stars::read_stars(listfiles, along = "band",
+                                  RasterIO = list(nXOff = nxoff, nYOff = nyoff,
+                                                  nXSize = nxsize, nYSize = nysize,
+                                                  nBufXSize = nbufxsize, nBufYSize = nbufysize,
+                                                  resample = "nearest_neighbour"), proxy = TRUE)
+
+
+    names(s2_stack$attr) <- namebands
+  }else if (length(s2_bands$s2bands_10m) > 0) {
+    s2_stack <- stack_10m
+    namebands <- names(s2_bands$s2bands_10m)
+    names(s2_stack$attr) <- namebands
+  }else if (length(s2_bands$s2bands_20m) > 0) {
+    s2_stack <- stack_20m
+    namebands <- names(s2_bands$s2bands_20m)
+    names(s2_stack$attr) <- namebands
+  }
+
+  listout <- list("s2_stack" = s2_stack, "s2_bands" = s2_bands, "path_vector" = path_vector,
+                  "namebands" = namebands)
+  return(listout)
+}
+
+#" This function gets coordinates of a bounding box defined by a vector (optional) and a raster
+#"
+#" @param path_raster character. path for raster file
+#" @param path_vector character. path for vector file
+#" @param buffer numeric. buffer applied to vector file (in meters)
+#"
+#" @return bb_xycoords list. Coordinates (in pixels) of the upper/lower right/left corners of bounding box
+#" @export
+get_bb <- function(path_raster, path_vector = NULL, buffer = 0) {
+
+  if (!is.null(path_vector)) {
+    # get bounding box with a 50m buffer in order to allow for interpolation
+    bb_xycoords <- get_bb_from_vector(path_raster = path_raster,
+                                      path_vector = path_vector,
+                                      buffer = buffer)
+  }else if (is.null(path_vector)) {
+    bb_xycoords <- get_bb_from_fullimage(path_raster)
+  }
+  return(bb_xycoords)
+}
+
+#" This function gets extreme coordinates of a bounding box corresponding to a full image
+#"
+#" @param path_raster character. path for raster file
+#"
+#" @return bb_xycoords list. Coordinates (in pixels) of the upper/lower right/left corners of bounding box
+#" @importFrom raster raster
+#" @export
+get_bb_from_fullimage <- function(path_raster) {
+  # get raster coordinates corresponding to Full image
+  rasterobj <- raster::raster(path_raster)
+  bb_xycoords <- list()
+  bb_xycoords[["UL"]] <- data.frame("row" = 1, "col" = 1)
+  bb_xycoords[["UR"]] <- data.frame("row" = 1, "col" = dim(rasterobj)[2])
+  bb_xycoords[["LL"]] <- data.frame("row" = dim(rasterobj)[1], "col" = 1)
+  bb_xycoords[["LR"]] <- data.frame("row" = dim(rasterobj)[1], "col" = dim(rasterobj)[2])
+  return(bb_xycoords)
+}
+
+#" This gets bounding box corresponding to a vector from a raster (UL, UR, LL, LR corners)
+#"
+#" @param path_raster character. path for raster file
+#" @param path_vector character. path for vector file
+#" @param buffer numeric. buffer applied to vector file (in meters)
+#"
+#" @return bb_xycoords list. Coordinates (in pixels) of the upper/lower right/left corners of bounding box
+#" @importFrom sf st_read st_bbox st_crop
+#" @importFrom rgeos gbuffer bbox2SP
+#" @importFrom sp SpatialPoints bbox
+#" @importFrom raster projection extract extent raster
+#" @importFrom methods as
+#" @export
+get_bb_from_vector <- function(path_raster, path_vector, buffer = 0) {
+
+  data_raster <- raster::raster(path_raster)
+  # extract BB coordinates from vector
+  bb_vector <- rgeos::gbuffer(spgeom = as(sf::st_read(dsn = path_vector, quiet = TRUE), "Spatial"),
+                              width = buffer, byid = TRUE)
+  # extract BB coordinates from raster
+  bb_raster <- rgeos::bbox2SP(bbox = bbox(data_raster))
+  # compute intersection
+  intersect <- rgeos::gIntersection(bb_vector, bb_raster)
+  bbext <- raster::extent(intersect)
+  xmin <- bbext[1]
+  xmax <- bbext[2]
+  ymin <- bbext[3]
+  ymax <- bbext[4]
+  # get coordinates of bounding box corresponding to vector
+  corners <- list()
+  corners[["UR"]] <- sp::SpatialPoints(coords = cbind(xmax, ymax))
+  corners[["LR"]] <- sp::SpatialPoints(coords = cbind(xmax, ymin))
+  corners[["UL"]] <- sp::SpatialPoints(coords = cbind(xmin, ymax))
+  corners[["LL"]] <- sp::SpatialPoints(coords = cbind(xmin, ymin))
+  raster::projection(corners[["UL"]]) <- raster::projection(corners[["UR"]]) <-
+    raster::projection(corners[["LL"]]) <- raster::projection(corners[["LR"]]) <-
+    raster::projection(sf::st_read(dsn = path_vector, quiet = TRUE))
+  # get coordinates for corners of bounding box
+  bb_xycoords <- list()
+  for (corner in names(corners)) {
+    ex_df <- as.data.frame(raster::extract(data_raster, corners[[corner]], cellnumbers = TRUE))
+    colrow <- ind2sub(data_raster, ex_df$cell)
+    bb_xycoords[[corner]] <- data.frame("row" = colrow$row, "col" = colrow$col)
+  }
+  return(bb_xycoords)
+}
+
+#" get hdr name from image file name, assuming it is BIL format
+#"
+#" @param impath path of the image
+#"
+#" @return corresponding hdr
+#" @import tools
+#" @export
+get_hdr_name <- function(impath) {
+  if (tools::file_ext(impath) == "") {
+    impathhdr <- paste(impath, ".hdr", sep = "")
+  }else if (tools::file_ext(impath) == "bil") {
+    impathhdr <- gsub(".bil", ".hdr", impath)
+  }else if (tools::file_ext(impath) == "zip") {
+    impathhdr <- gsub(".zip", ".hdr", impath)
+  }else {
+    impathhdr <- paste(tools::file_path_sans_ext(impath), ".hdr", sep = "")
+  }
+
+  if (!file.exists(impathhdr)) {
+    message("WARNING : COULD NOT FIND hdr FILE")
+    print(impathhdr)
+    message("Process may stop")
+  }
+  return(impathhdr)
+}
+
+#" This function returns path for the spectral bands to be used
+#"
+#" @param path_dir_s2 character. Path for the directory containing S2 data. either L2A .SAFE S2 file or THEIA directory
+#" @param s2source character. defines if data comes from SciHub as SAFE directory, from THEIA or from LaSRC
+#" @param resolution numeric. spatial resolution of the final image: 10m or 20m
+#" @param fre_sre character. SRE or FRE products from THEIA
+#"
+#" @return listbands list. contains path for spectral bands corresponding to 10m and 20m resolution
+#" @export
+get_s2_bands <- function(path_dir_s2, s2source = "SAFE", resolution = 10, fre_sre = "FRE") {
+
+  if (s2source == "SAFE" || s2source == "Sen2Cor") {
+    listbands <- get_s2_bands_from_sen2cor(path_dir_s2 = path_dir_s2, resolution = resolution)
+  }else if (s2source == "THEIA") {
+    listbands <- get_s2_bands_from_theia(path_dir_s2 = path_dir_s2, resolution = resolution,
+                                         fre_sre = fre_sre)
+  }else if (s2source == "LaSRC") {
+    listbands <- get_s2_bands_from_lasrc(path_dir_s2 = path_dir_s2, resolution = resolution)
+  }else {
+    message("The data source (Atmospheric correction) for Sentinel-2 image is unknown")
+    message("Please provide S2 images from one of the following data sources:")
+    message("- LaSRC (atmospheric correction: LaSRC)")
+    message("- THEIA (atmospheric correction: MAJA)")
+    message("- SAFE (atmospheric correction: Sen2Cor)")
+    s2bands_10m <- s2bands_20m <- granule <- mtdfile <- metadata_msi <- metadata_lasrc <- NULL
+    listbands <- list("s2bands_10m" = s2bands_10m, "s2bands_20m" = s2bands_20m, "GRANULE" = granule,
+                      "metadata" = mtdfile, "metadata_MSI" = metadata_msi,
+                      "metadata_lasrc" = metadata_lasrc)
+  }
+  return(listbands)
+}
+
+#" This function returns path for the spectral bands in SAFE / sen2Cor directory
+#"
+#" @param path_dir_s2 character. Path for the SAFE directory containing S2 data
+#" @param resolution numeric. spatial resolution of the final image: 10m or 20m
+#"
+#" @return listbands list. contains path for spectral bands corresponding to 10m and 20m resolution, as well name of as granule
+#" @export
+get_s2_bands_from_sen2cor <- function(path_dir_s2, resolution = 10) {
+  # build path for all bands
+  if (resolution == 10) {
+    b10m <- c("B02", "B03", "B04", "B08")
+    b20m <- c("B05", "B06", "B07", "B8A", "B11", "B12")
+  }else {
+    b10m <- c()
+    b20m <- c("B02", "B03", "B04", "B05", "B06", "B07", "B08", "B8A", "B11", "B12")
+  }
+  # get granule directory & path for corresponding metadata XML file
+  granule <- list.dirs(list.dirs(path_dir_s2, recursive = FALSE)[grep(pattern = "GRANULE",
+                                                                     x = list.dirs(path_dir_s2, recursive = FALSE))], recursive = FALSE)
+  mtdfile <- file.path(granule, "MTD_TL.xml")
+  if (file.exists(file.path(path_dir_s2, "MTD_MSIL2A.xml"))) {
+    mtd_msi_file <- file.path(path_dir_s2, "MTD_MSIL2A.xml")
+  } else {
+    mtd_msi_file <- NULL
+  }
+
+  # Define path for bands
+  s2bands_20m_dir <- file.path(granule, "IMG_DATA", "R20m")
+  s2bands_10m_dir <- file.path(granule, "IMG_DATA", "R10m")
+  s2bands_10m <- s2bands_20m <- list()
+  for (band in b20m) {
+    s2bands_20m[[band]] <- file.path(s2bands_20m_dir, list.files(s2bands_20m_dir, pattern = band))
+  }
+  for (band in b10m) {
+    s2bands_10m[[band]] <- file.path(s2bands_10m_dir, list.files(s2bands_10m_dir, pattern = band))
+  }
+  # get cloud mask
+  cloud <- "MSK_CLDPRB_20m"
+  cloud_20m_dir <- file.path(granule, "QI_DATA")
+  s2bands_20m[["Cloud"]] <- file.path(cloud_20m_dir, list.files(cloud_20m_dir, pattern = cloud))
+  listbands <- list("s2bands_10m" = s2bands_10m,
+                    "s2bands_20m" = s2bands_20m,
+                    "GRANULE" = granule,
+                    "metadata" = mtdfile,
+                    "metadata_MSI" = mtd_msi_file,
+                    "metadata_lasrc" = NULL)
+  return(listbands)
+}
+
+#" This function returns path for the spectral bands in LaSRC directory
+#"
+#" @param path_dir_s2 character. Path for the SAFE directory containing S2 data
+#" @param resolution numeric. spatial resolution of the final image: 10m or 20m
+#"
+#" @return listbands list. contains path for spectral bands corresponding to 10m and 20m resolution, as well name of as granule
+#" @importFrom stringr str_subset
+#" @export
+get_s2_bands_from_lasrc <- function(path_dir_s2, resolution = 10) {
+
+  # get granule directory & path for corresponding metadata XML file
+  granule <- path_dir_s2
+  mtdfile <- file.path(granule, "MTD_TL.xml")
+  if (file.exists(file.path(path_dir_s2, "MTD_MSIL1C.xml"))) {
+    mtd_msi_file <- file.path(path_dir_s2, "MTD_MSIL1C.xml")
+  } else {
+    mtd_msi_file <- NULL
+  }
+
+  # build path for all bands
+  b10m <- c("band2", "band3", "band4", "band5", "band6", "band7", "band8", "band8a", "band11", "band12")
+  b10m_standard <- c("B02", "B03", "B04", "B05", "B06", "B07", "B08", "B8A", "B11", "B12")
+  # Define path for bands
+  s2bands_10m <- s2bands_20m <- list()
+  for (i in 1:seq_along(b10m)) {
+    s2bands_10m[[b10m_standard[i]]] <- file.path(path_dir_s2,
+                                                 list.files(path_dir_s2,
+                                                            pattern = paste(b10m[i], ".tif", sep = "")))
+  }
+
+  # get metadata file containing offset
+  mtd_lasrc <- str_subset(list.files(path_dir_s2, pattern = "S2"), ".xml$")
+  if (file.exists(file.path(path_dir_s2, mtd_lasrc))) {
+    metadata_lasrc <- file.path(path_dir_s2, mtd_lasrc)
+  } else {
+    metadata_lasrc <- NULL
+  }
+  # get cloud mask
+  cloud <- "CLM"
+  s2bands_10m[["Cloud"]] <- file.path(path_dir_s2, list.files(path_dir_s2, pattern = cloud))
+  listbands <- list("s2bands_10m" = s2bands_10m,
+                    "s2bands_20m" = s2bands_20m,
+                    "GRANULE" = granule,
+                    "metadata" = mtdfile,
+                    "metadata_MSI" = mtd_msi_file,
+                    "metadata_lasrc" = metadata_lasrc)
+  return(listbands)
+}
+
+#" This function returns path for the spectral bands in THEIA directory
+#"
+#" @param path_dir_s2 character. Path for the SAFE directory containing S2 data
+#" @param resolution numeric. spatial resolution of the final image: 10m or 20m
+#" @param fre_sre character. SRE or FRE products from THEIA
+#"
+#" @return listbands list. contains path for spectral bands corresponding to 10m and 20m resolution, as well name of as granule
+#" @export
+get_s2_bands_from_theia <- function(path_dir_s2, resolution = 10, fre_sre = "FRE") {
+
+  # build path for all bands
+  if (resolution == 10) {
+    b10m <- c("B02", "B03", "B04", "B08")
+    b20m <- c("B05", "B06", "B07", "B8A", "B11", "B12")
+  } else {
+    b10m <- c()
+    b20m <- c("B02", "B03", "B04", "B05", "B06", "B07", "B08", "B8A", "B11", "B12")
+  }
+
+  # get path_tile_s2 directory & path for corresponding metadata XML file
+  path_tile_s2 <- list.dirs(path_dir_s2, recursive = FALSE)
+  files_tile_s2 <- list.files(path_tile_s2, recursive = FALSE)
+  mtdfile <- file.path(path_tile_s2, files_tile_s2[grep(pattern = "MTD_ALL.xml", x = files_tile_s2)])
+
+  # Define path for bands
+  s2bands_10m_dir <- s2bands_20m_dir <- path_tile_s2
+  s2bands_10m <- s2bands_20m <- list()
+  for (band in b20m) {
+    band_20m_pattern <- paste0(gsub("0", "", band), ".tif") # for THEAI band 2 is "B2" ("B02" for SAFE)
+    list_files_20m <- list.files(s2bands_20m_dir, pattern = band_20m_pattern)
+    s2bands_20m[[band]] <- file.path(s2bands_20m_dir, list_files_20m)[grep(pattern = fre_sre,
+                                                                           x = file.path(s2bands_20m_dir, list_files_20m))]
+  }
+  for (band in b10m) {
+    band_10m_pattern <- paste0(gsub("0", "", band), ".tif") # for THEAI band 2 is "B2" ("B02" for SAFE)
+    list_files_10m <- list.files(s2bands_10m_dir, pattern = band_10m_pattern)
+    s2bands_10m[[band]] <- file.path(s2bands_10m_dir, list_files_10m)[grep(pattern = fre_sre,
+                                                                           x = file.path(s2bands_10m_dir, list_files_10m))]
+  }
+
+  # get cloud mask 10m
+  cloud_10m <- "CLM_R1"
+  cloud_10m_dir <- file.path(path_tile_s2, "MASKS")
+  s2bands_10m[["Cloud"]] <- file.path(cloud_10m_dir, list.files(cloud_10m_dir, pattern = cloud_10m))
+
+  # get cloud mask 20m
+  cloud_20m <- "CLM_R2"
+  cloud_20m_dir <- file.path(path_tile_s2, "MASKS")
+  s2bands_20m[["Cloud"]] <- file.path(cloud_20m_dir, list.files(cloud_20m_dir, pattern = cloud_20m))
+
+  # return list bands
+  listbands <- list("s2bands_10m" = s2bands_10m,
+                    "s2bands_20m" = s2bands_20m,
+                    "path_tile_s2" = path_tile_s2,
+                    "metadata" = mtdfile)
+  return(listbands)
+}
+
+#" This function check S2 data level:
+#" - L2A: already atmospherically corrected
+#" - L1C: requires atmospheric corrections with sen2cor
+#"
+#" @param prodname character. original name for the S2 image
+#"
+#" @return s2level character. S2 level: L1C or L2A
+#" @export
+get_s2_level <- function(prodname) {
+  prodname <- basename(prodname)
+  if (length(grep(pattern = "L1C_", x = prodname)) == 1) {
+    s2level <- "L1C"
+  } else if (length(grep(pattern = "L2A_", x = prodname)) == 1) {
+    s2level <- "L2A"
+  }
+  return(s2level)
+}
+
+#" This function gets tile from S2 image
+#"
+#" @param prodname character. original name for the S2 image
+#"
+#" @return tilename character
+#" @importFrom tools file_path_sans_ext
+#" @export
+get_tile <- function(prodname) {
+  prodname <- basename(prodname)
+  tilename <- tools::file_path_sans_ext(gsub("_.*", "", gsub(".*_T", "", prodname)))
+  return(tilename)
+}
+
+#" This function gets acquisition date from S2 image
+#"
+#" @param prodname character. original name for the S2 image
+#"
+#" @return dateacq character
+#" @export
+get_date <- function(prodname) {
+  prodname <- basename(prodname)
+  dateacq <- as.Date(gsub("T.*", "", gsub(".*_20", "20", prodname)), format = "%Y%m%d")
+  return(dateacq)
+}
+
+#" download S2 L1C data from Copernicus hub or Google cloud
+#"
+#" @param list_safe safe object. produced with sen2r::s2_list
+#" @param l1c_path character. path for storage of L1C image
+#" @param path_vector path for a vector file
+#" @param time_interval dates. time interval for S2 query
+#" @param googlecloud boolean. set to TRUE if google cloud SDK is installed and
+#" @param forcegoogle boolean. set to TRUE if only google requested
+#" sen2r configured as an alternative hub for S2 download
+#"
+#" @return prodname character. S2 Product name
+#" @importFrom sen2r safe_is_online s2_list s2_download s2_order check_gcloud
+#" @export
+get_s2_l1c_image <- function(list_safe, l1c_path, path_vector, time_interval,
+                             googlecloud = FALSE, forcegoogle = FALSE) {
+  # Check if available from Copernicus hub first
+  copernicus_avail <- sen2r::safe_is_online(list_safe)
+  # if available: download
+  prodname <- attr(list_safe, which = "name")
+  if (file.exists(file.path(l1c_path, prodname))) {
+    message("L1C file already downloaded")
+    message(file.path(l1c_path, prodname))
+  } else {
+    if (copernicus_avail == TRUE && forcegoogle == FALSE) {
+      sen2r::s2_download(list_safe, outdir = l1c_path)
+    } else if (copernicus_avail == FALSE || forcegoogle == TRUE) {
+      # if not available and googlecloud==TRUE
+      if (googlecloud == TRUE) {
+        # check if google cloud SDK available from this computer
+        ggc <- sen2r::check_gcloud()
+        if (ggc == TRUE) {
+          message("downloading from Google cloud")
+          list_safe_ggc <- sen2r::s2_list(spatial_extent = sf::st_read(dsn = path_vector),
+                                          time_interval = time_interval,
+                                          server = "gcloud")
+          prodname <- attr(list_safe_ggc, which = "name")
+          if (file.exists(file.path(l1c_path, prodname))) {
+            message("L1C file already downloaded")
+            message(file.path(l1c_path, prodname))
+          } else {
+            sen2r::s2_download(list_safe_ggc, outdir = l1c_path)
+            # check if QI_DATA exists in DATASTRIP, and create it if not the case
+            datastrip_path <- file.path(l1c_path, prodname, "DATASTRIP")
+            dsdir <- list.dirs(datastrip_path, recursive = FALSE)
+            if (length(match(list.dirs(dsdir, recursive = FALSE, full.names = FALSE), "QI_DATA")) == 0) {
+              dir.create(file.path(dsdir, "QI_DATA"))
+            }
+          }
+        } else if (ggc == FALSE) {
+          message("googlecloud set to TRUE but missing")
+          message("Please install Google cloud SDK")
+          message("https://cloud.google.com/sdk/docs/install")
+          message("and/or set configuration of sen2r following instructions")
+          message("https://www.r-bloggers.com/2021/06/downloading-sentinel-2-archives-from-google-cloud-with-sen2r/")
+        }
+      }
+    }
+    if (copernicus_avail == FALSE && googlecloud == FALSE) {
+      message("S2 image in Long Term Archive (LTA)")
+      message("Ordering image from  LTA")
+      message("This may take 1 day, please run your script later")
+      orders2 <- sen2r::s2_order(list_safe)
+      message("An alternative is possible with Google cloud SDK")
+      message("https://cloud.google.com/sdk/docs/install")
+      message("and/or set configuration of sen2r following instructions")
+      message("https://www.r-bloggers.com/2021/06/downloading-sentinel-2-archives-from-google-cloud-with-sen2r/")
+    }
+  }
+  return(prodname)
+}
+
+#" download S2 L2A data from Copernicus hub or convert L1C to L2A
+#"
+#" @param l2a_path character. path for storage of L2A image
+#" @param spatial_extent path for a vector file
+#" @param dateacq character. date of acquisition
+#" @param deletel1c Boolean. set TRUE to delete L1C images
+#" @param Sen2Cor Boolean. set TRUE to automatically perform atmospheric corrections using sen2Cor
+#" @param googlecloud boolean. set to TRUE if google cloud SDK is installed and
+#" sen2r configured as an alternative hub for S2 download
+#"
+#" @return pathl2a character. Path for L2A image
+#" @importFrom sen2r s2_list s2_download
+#" @importFrom R.utils getAbsolutePath
+
+#" @export
+get_s2_l2a_image <- function(l2a_path, spatial_extent, dateacq,
+                             deletel1c = FALSE, sen2cor = TRUE,
+                             googlecloud = FALSE) {
+
+  # Needs to be updated: define path for L1c data
+  l1c_path <- l2a_path
+  # define time interval
+  time_interval <- as.Date(c(dateacq, dateacq))
+  # get list S2 products corresponding to study area and date of interest using sen2r package
+  if (googlecloud == TRUE) {
+    server <- c("scihub", "gcloud")
+  } else if (googlecloud == FALSE) {
+    server <- "scihub"
+  }
+  list_safe <- sen2r::s2_list(spatial_extent = sf::st_read(dsn = spatial_extent),
+                              time_interval = time_interval,
+                              server = server, availability = "check")
+  # download products
+  sen2r::s2_download(list_safe, outdir = l2a_path)
+  # name all products
+  prodname <- attr(list_safe, which = "name")
+  prodfullpath <- file.path(l2a_path, prodname)
+  if (sen2cor == TRUE) {
+    for (imgname in prodname) {
+      s2level <- get_s2_level(imgname)
+      if (s2level == "L1C") {
+        datepattern <- gsub(pattern = "-", replacement = "", x = dateacq)
+        pathl2a <- s2_from_l1c_to_l2a(prodname = imgname, l1c_path = l2a_path, l2a_path = l2a_path,
+                                      datepattern = datepattern, tmp_path = NULL)
+        if (deletel1c == TRUE) {
+          unlink(x = R.utils::getAbsolutePath(file.path(l1c_path, prodname)),
+                 recursive = TRUE, force = TRUE)
+          # delete from full path and add atmospherically corrected
+          whichimg <- grep(x = prodfullpath, pattern = imgname)
+          dateacq <- get_date(imgname)
+          tilename <- get_tile(imgname)
+          pathl2a <- list.files(path = l2a_path, pattern = tilename, full.names = TRUE)
+          pathl2a <- pathl2a[grep(x = pathl2a, pattern = dateacq)]
+          pathl2a <- pathl2a[grep(x = basename(pathl2a), pattern = "L2A")]
+          prodfullpath[whichimg] <- pathl2a
+        }
+      }
+    }
+  }
+
+  return(prodfullpath)
+}
+
+#" convert image coordinates from index to X-Y
+#"
+#" @param Raster image raster object
+#" @param image_index coordinates corresponding to the raster
+ind2sub <- function(data_raster, image_index) {
+  c <- ((image_index - 1) %% data_raster@ncols) + 1
+  r <- floor((image_index - 1) / data_raster@ncols) + 1
+  my_list <- list("col" = c, "row" = r)
+  return(my_list)
+}
+
+#" mosaicing a set of rasters
+#"
+#" @param list_rasters character. list of paths corresponding to rasters to mosaic
+#" @param dst_mosaic character. path and name of mosaic produced
+#" @param stretch boolean. Set TRUE to get 10% stretching at display for reflectance, mentioned in hdr only
+#"
+#" @return None
+#" @importFrom gdalUtils mosaic_rasters
+#" @importFrom raster hdr raster
+#" @export
+mosaic_rasters <- function(list_rasters, dst_mosaic, stretch = FALSE) {
+
+  # produce mosaic
+  gdalUtils::mosaic_rasters(gdalfile = list_rasters, dst_dataset = dst_mosaic,
+                            separate = FALSE, of = "Ehdr", verbose = TRUE)
+
+  # convert hdr to ENVI format
+  raster::hdr(raster(dst_mosaic), format = "ENVI")
+  # add info to hdr based on initial rasters
+  hdr_init <- read_envi_header(get_hdr_name(list_rasters[1]))
+  hdr <- read_envi_header(get_hdr_name(dst_mosaic))
+  hdr$`band names` <- hdr_init$`band names`
+  hdr$wavelength <- hdr_init$wavelength
+  if (stretch == TRUE) {
+    hdr$`default stretch` <- "0.000000 1000.000000 linear"
+  }
+  hdr$`z plot range` <- NULL
+  hdr$`data ignore value` <- "-Inf"
+  hdr$`sensor type` <- hdr_init$`sensor type`
+  hdr$`coordinate system string` <- read.table(paste(file_path_sans_ext(dst_mosaic), ".prj", sep = ""))
+  write_envi_header(hdr = hdr, hdrpath = get_hdr_name(dst_mosaic))
+  return(invisible())
+}
+
+#" Reads ENVI hdr file
+#"
+#" @param hdrpath Path of the hdr file
+#"
+#" @return list of the content of the hdr file
+#" @export
+read_envi_header <- function(hdrpath) {
+  if (!grepl(".hdr$", hdrpath)) {
+    stop("File extension should be .hdr")
+  }
+  hdr <- readLines(hdrpath)
+  ## check ENVI at beginning of file
+  if (!grepl("ENVI", hdr[1])) {
+    stop("Not an ENVI header (ENVI keyword missing)")
+  } else {
+    hdr <- hdr [-1]
+  }
+  ## remove curly braces and put multi-line key-value-pairs into one line
+  hdr <- gsub("\\{([^}]*)\\}", "\\1", hdr)
+  l <- grep("\\{", hdr)
+  r <- grep("\\}", hdr)
+
+  if (length(l) != length(r)) {
+    stop("Error matching curly braces in header (differing numbers).")
+  }
+
+  if (any(r <= l)) {
+    stop("Mismatch of curly braces in header.")
+  }
+
+  hdr[l] <- sub("\\{", "", hdr[l])
+  hdr[r] <- sub("\\}", "", hdr[r])
+
+  for (i in rev(seq_along(l))) {
+    hdr <- c(
+      hdr [seq_len(l [i] - 1)],
+      paste(hdr [l [i]:r [i]], collapse = "\n"),
+      hdr [-seq_len(r [i])]
+    )
+  }
+
+  ## split key = value constructs into list with keys as names
+  hdr <- sapply(hdr, split_line, "=", USE.NAMES = FALSE)
+  names(hdr) <- tolower(names(hdr))
+
+  ## process numeric values
+  tmp <- names(hdr) %in% c(
+    "samples", "lines", "bands", "header offset", "data type",
+    "byte order", "default bands", "data ignore value",
+    "wavelength", "fwhm", "data gain values"
+  )
+  hdr [tmp] <- lapply(hdr [tmp], function(x) {
+    as.numeric(unlist(strsplit(x, ", ")))
+  })
+
+  return(hdr)
+}
+
+#" This function reads a list of files corresponding to S2 bands
+#" S2 bands are expected to have uniform spatial resolution and footprint
+#" @param s2_bands list. list of S2 bands obtained from get_s2_bands
+#" @param path_vector path for a vector file
+#" @param resampling numeric. resampling factor (default = 1, set to resampling = 2 to convert 20m into 10m resolution)
+#" @param interpolation character. method for resampling. default = "bilinear"
+#"
+#" @return stack_s2 list. contains stack of S2 bands
+#"
+#" @importFrom stars read_stars
+#" @importFrom sf st_bbox st_read st_crop
+#" @export
+
+read_s2bands <- function(s2_bands, path_vector = NULL,
+                         resampling = 1, interpolation = "bilinear") {
+  # get bounding box corresponding to footprint of image or image subset
+  bb_xycoords <- get_bb(path_raster = s2_bands[[1]],
+                        path_vector = path_vector, buffer = 50)
+
+  # prepare reading data for extent defined by bounding box
+  nxoff <- bb_xycoords$UL$col
+  nyoff <- bb_xycoords$UL$row
+  nxsize <- bb_xycoords$UR$col - bb_xycoords$UL$col + 1
+  nysize <- bb_xycoords$LR$row - bb_xycoords$UR$row + 1
+  nbufxsize <- resampling * nxsize
+  nbufysize <- resampling * nysize
+  if (resampling == 1) {
+    interpolation <- "nearest_neighbour"
+  }
+  # write interpolated individual bands in temp directory
+  tmpdir <- tempdir()
+  tmpfile <- list()
+  for (band in names(s2_bands)) {
+    stack_s2_tmp <- stars::read_stars(s2_bands[[band]], along = "band",
+                                      RasterIO = list(nXOff = nxoff, nYOff = nyoff,
+                                                      nXSize = nxsize, nYSize = nysize,
+                                                      nBufXSize = nbufxsize, nBufYSize = nbufysize,
+                                                      resample = interpolation), proxy = FALSE)
+    if (!is.null(path_vector)) {
+      stack_s2_tmp <- sf::st_crop(x = stack_s2_tmp, y = st_bbox(st_read(dsn = path_vector, quiet = TRUE)))
+    }
+    tmpfile[[band]] <- file.path(tmpdir, tools::file_path_sans_ext(basename(s2_bands[[band]])))
+    if (band == "Cloud") {
+      stars::write_stars(obj = stack_s2_tmp, dsn = tmpfile[[band]],
+                         driver =  "ENVI", type = "Byte", overwrite = TRUE)
+    } else {
+      stars::write_stars(obj = stack_s2_tmp, dsn = tmpfile[[band]],
+                         driver =  "ENVI", type = "Int16", overwrite = TRUE)
+    }
+    gc()
+  }
+
+  stack_s2 <- stars::read_stars(tmpfile, along = "band", proxy = TRUE)
+  return(stack_s2)
+}
+
+#" This function reads a raster stack, and gets footprint as pixel coordinates or vector file as input
+#" @param path_raster character. path for raster file
+#" @param path_vector character. path for vector file
+#" @param bbpix list. coordinates of pixels corresponding to a bounding box
+#"
+#" @return starsobj stars object corresponding to raster or raster subset
+#"
+#" @importFrom stars read_stars
+#" @importFrom sf st_bbox st_read st_crop
+#" @export
+read_raster <- function(path_raster, path_vector = NULL, bbpix = NULL) {
+  # get bounding box corresponding to footprint of image or image subset
+  if (is.null(bbpix)) {
+    bb_xycoords <- get_bb(path_raster = path_raster,
+                          path_vector = path_vector, buffer = 0)
+  } else {
+    bb_xycoords <- bbpix
+  }
+  # prepare reading data for extent defined by bounding box
+  nxoff <- bb_xycoords$UL$col
+  nyoff <- bb_xycoords$UL$row
+  nxsize <- bb_xycoords$UR$col - bb_xycoords$UL$col + 1
+  nysize <- bb_xycoords$LR$row - bb_xycoords$UR$row + 1
+  nbufxsize <- nxsize
+  nbufysize <- nysize
+  starsobj <- stars::read_stars(path_raster, along = "band",
+                                RasterIO = list(nXOff = nxoff, nYOff = nyoff,
+                                                  nXSize = nxsize, nYSize = nysize,
+                                                  nBufXSize = nbufxsize, nBufYSize = nbufysize),
+                                proxy = FALSE)
+  return(starsobj)
+}
+
+#" This function reprojects a shapefile and saves reprojected shapefile
+#"
+#" @param path_vector_init character. path for a shapefile to be reprojected
+#" @param newprojection character. projection to be applied to path_vector_init
+#" @param path_vector_reproj character. path for the reprojected shapefile
+#"
+#" @return path_vector character. path of the shapefile
+#" - path_vector_init if the vector did not need reprojection
+#" - path_vector_reproj if the vector needed reprojection
+#"
+#" @importFrom rgdal readOGR writeOGR
+#" @importFrom sp spTransform
+#" @importFrom raster projection
+#" @export
+reproject_shp <- function(path_vector_init, newprojection, path_vector_reproj) {
+
+  dir_vector_init <- dirname(path_vector_init)
+  # shapefile extension
+  fileext <- file_ext(basename(path_vector_init))
+  if (fileext == "shp") {
+    name_vector_init <- file_path_sans_ext(basename(path_vector_init))
+    vector_init_ogr <- rgdal::readOGR(dir_vector_init, name_vector_init, verbose = FALSE)
+  } else if (fileext == "kml") {
+    vector_init_ogr <- rgdal::readOGR(path_vector_init, verbose = FALSE)
+  }
+  vector_init_proj <- raster::projection(vector_init_ogr)
+
+  if (!vector_init_proj == newprojection) {
+    dir_vector_reproj <- dirname(path_vector_reproj)
+    name_vector_reproj <- file_path_sans_ext(basename(path_vector_reproj))
+    vector_reproj <- sp::spTransform(vector_init_ogr, newprojection)
+    rgdal::writeOGR(obj = vector_reproj, dsn = dir_vector_reproj, layer = name_vector_reproj,
+                    driver = "ESRI Shapefile", overwrite_layer = TRUE)
+    path_vector <- path_vector_reproj
+  } else {
+    path_vector <- path_vector_init
+  }
+  return(path_vector)
+}
+
+
+#" perform atmospheric corrections to convert L1C to L2A data with Sen2cor
+#"
+#" @param prodname character. produced with sen2r::s2_list
+#" @param l1c_path character. path of directory where L1C image is stored
+#" @param l2a_path character. path of directory where L2A image is stored
+#" @param datepattern character. pattern corresponding to date of acquisition to identify L2A directory
+#" @param tmp_path character. path of temporary directory where L2A image is stored
+#" sen2r configured as an alternative hub for S2 download
+#"
+#" @return pathl2a character. S2 Product name
+#" @importFrom sen2r safe_is_online s2_list s2_download s2_order
+#" @importFrom R.utils getAbsolutePath
+#"
+#" @export
+s2_from_l1c_to_l2a <- function(prodname, l1c_path, l2a_path, datepattern, tmp_path = NULL) {
+
+  # define path for tmp directory
+  if (is.null(tmp_path)) {
+    tmp_path <- tempdir(check = TRUE)
+  }
+  tmp_prodlist <- prodname
+  # perform Sen2Cor atmospheric corrections
+  binpath <- sen2r::load_binpaths()
+  # 2- open a command prompt and directly run sen2cor with following command line
+  cmd <- paste(binpath$sen2cor,
+               "--output_dir", R.utils::getAbsolutePath(l2a_path),
+               R.utils::getAbsolutePath(file.path(l1c_path, prodname)), sep = " ")
+  system(cmd)
+  pathl2a <- list.files(path = l2a_path, pattern = datepattern, full.names = TRUE)
+
+  return(pathl2a)
+}
+
+#" This function saves cloud masks.
+#" "cloudMask_Binary" is default binary mask with 0 where clouds are detected and 1 for clean pixels
+#" "cloudMask_RAW" is the original cloud layer produced by atmospheric correction algorithm
+#" --> may be useful to refine cloud mask
+#"
+#" @param s2_stars list. stars object containing raster data. Can be produced with function extract_from_s2_l2a
+#" @param cloud_path character.
+#" @param s2source character.
+#" @param footprint character. path for vector file defining footprint of interest in the image
+#" @param saveraw boolean. should the original cloud mask layer be saved?
+#" @param maxchunk numeric. Size of individual chunks to be written (in Mb)
+#"
+#" @return list of cloudmasks (binary mask, and raw mask if required)
+#" @importFrom sf st_read
+#" @importFrom stars write_stars
+#" @importFrom raster raster
+#" @export
+save_cloud_s2 <- function(s2_stars, cloud_path, s2source = "SAFE",
+                          footprint = NULL, saveraw = FALSE, maxchunk = 256) {
+
+  whichcloud <- which(names(s2_stars$attr) == "Cloud")
+  # Save cloud mask
+  if (saveraw == TRUE) {
+    cloudraw <- file.path(cloud_path, "CloudMask_RAW")
+    obj <- stars::read_stars(s2_stars$attr[whichcloud], proxy = TRUE)
+    sizeobj <- dim(obj)[1] * dim(obj)[2] / (1024**2)
+    nbchunks <- ceiling(sizeobj / maxchunk)
+    stars::write_stars(obj,
+                       dsn = cloudraw,
+                       driver =  "ENVI",
+                       type = "Byte",
+                       chunk_size = c(dim(obj)[1], dim(obj)[2] / nbchunks),
+                       progress = TRUE)
+  } else {
+    cloudraw <- NULL
+  }
+  # Save cloud mask as in biodivMapR (0 = clouds, 1 = pixel ok)
+  cloudmask <- stars::read_stars(s2_stars$attr[whichcloud], proxy = FALSE)
+  if (s2source == "SAFE" || s2source == "THEIA") {
+    cloudy <- which(cloudmask[[1]] > 0)
+    sunny <- which(cloudmask[[1]] == 0)
+  } else if (s2source == "LaSRC") {
+    cloudy <- which(is.na(cloudmask[[1]]))
+    sunny <- which(cloudmask[[1]] == 1)
+  }
+
+  cloudmask[[1]][cloudy] <- 0
+  cloudmask[[1]][sunny] <- 1
+  cloudbin <- file.path(cloud_path, "CloudMask_Binary")
+  stars::write_stars(cloudmask, dsn = cloudbin, driver =  "ENVI", type = "Byte", overwrite = TRUE)
+  cloudmasks <- list("BinaryMask" = cloudbin, "RawMask" = cloudraw)
+  # delete temporary file
+  file.remove(s2_stars$attr[whichcloud])
+  if (file.exists(paste(s2_stars$attr[whichcloud], ".hdr", sep = ""))) file.remove(paste(s2_stars$attr[whichcloud], ".hdr", sep = ""))
+  gc()
+  return(cloudmasks)
+}
+
+#" This function saves reflectance files
+#"
+#" @param s2_stars list. stars object containing raster data. Can be produced with function extract_from_s2_l2a
+#" @param refl_path character. path for reflectance file to be stored
+#" @param format character. file format for reflectance data
+#" @param datatype character. data type (integer, float, 16bits, 32bits...)
+#" @param s2sat character. Sentinel-2 mission ("2A" or "2B")
+#" @param tile_s2 character. S2 tile name (2 numbers + 3 letters)
+#" @param dateacq_s2 double. date of acquisition
+#" @param MTD character. path for metadata file
+#" @param MTD_MSI character. path for metadata MSI file
+#" @param mtd_lasrc character. path for metadata LaSRC file
+#" @param maxchunk numeric. Size of individual chunks to be written (in Mb)
+#"
+#" @return None
+#" @importFrom stars write_stars st_apply
+#" @importFrom XML xml
+#" @export
+save_reflectance_s2 <- function(s2_stars, refl_path, format = "ENVI", datatype = "Int16",
+                                s2sat = NULL, tile_s2 = NULL, dateacq_s2 = NULL,
+                                mtd = NULL, mtd_msi = NULL, mtd_lasrc = NULL,
+                                maxchunk = 256) {
+  # identify if S2A or S2B, if possible
+  s2mission <- check_s2mission(s2sat = s2sat, tile_s2 = tile_s2, dateacq_s2 = dateacq_s2)
+
+  # define central wavelength corresponding to each spectral band
+  if (s2mission == "2A") {
+    wl_s2 <- list("B02" = 496.6, "B03" = 560.0, "B04" = 664.5,
+                  "B05" = 703.9, "B06" = 740.2, "B07" = 782.5, "B08" = 835.1,
+                  "B8A" = 864.8, "B11" = 1613.7, "B12" = 2202.4)
+  } else if (s2mission == "2B") {
+    wl_s2 <- list("B02" = 492.1, "B03" = 559.0, "B04" = 665.0,
+                  "B05" = 703.8, "B06" = 739.1, "B07" = 779.7, "B08" = 833.0,
+                  "B8A" = 864.0, "B11" = 1610.4, "B12" = 2185.7)
+  }
+  if (s2mission == "2A") {
+    sensor <- "Sentinel_2A"
+  } else if (s2mission == "2B") {
+    sensor <- "Sentinel_2B"
+  }
+
+  # apply offset when necessary
+  listbands_bis <- c("B2", "B3", "B4", "B5", "B6", "B7", "B8", "B8A", "B11", "B12")
+  if (!is.null(mtd_msi) && is.null(mtd_lasrc)) {
+    # read XML file containing info about geometry of acquisition
+    s2xml <- XML::xmlToList(mtd_msi)
+    xml_offset <- s2xml$General_Info$Product_Image_Characteristics$BOA_ADD_offset_VALUES_LIST
+    bands <- lapply(s2xml$General_Info$Product_Image_Characteristics$Spectral_Information_List, "[[", 4)
+    if (!is.null(xml_offset) && !is.null(bands)) {
+      bandid  <- lapply(bands, "[[", 1)
+      bandname  <- lapply(bands, "[[", 2)
+      offset <- data.frame("bandname" = unlist(bandname),
+                           "bandid" = unlist(bandid),
+                           "offset" = unlist(lapply(xml_offset, "[[", 1)))
+      selbands <- match(listbands_bis, offset$bandname)
+      offset <- offset[selbands, ]
+      boa_quantval <- as.numeric(s2xml$General_Info$Product_Image_Characteristics$QUANTIFICATION_VALUES_LIST$BOA_QUANTIFICATION_VALUE[1])
+    } else {
+      offset <- data.frame("bandname" = listbands_bis,
+                           "bandid" = c(1, 2, 3, 4, 5, 6, 7, 8, 11, 12),
+                           "offset" = 0)
+      boa_quantval <- 10000
+    }
+  } else if (!is.null(mtd_lasrc)) {
+    # read XML file containing info about geometry of acquisition
+    s2xml <- XML::xmlToList(mtd_lasrc)
+    attributes_lasrc <- s2xml$bands[[14]]$.attrs
+    attributes_lasrc_df <- data.frame(attributes_lasrc)
+    if (match("add_offset", rownames(attributes_lasrc_df)) > 0 && match("scale_factor", rownames(attributes_lasrc_df)) > 0) {
+      xml_offset <- as.numeric(attributes_lasrc[["add_offset"]])
+      boa_quantval <- 1 / as.numeric(attributes_lasrc[["scale_factor"]])
+      offset <- data.frame("bandname" = listbands_bis,
+                           "bandid" = c(1, 2, 3, 4, 5, 6, 7, 8, 11, 12),
+                           "offset" = xml_offset)
+    } else {
+      offset <- data.frame("bandname" = listbands_bis,
+                           "bandid" = c(1, 2, 3, 4, 5, 6, 7, 8, 11, 12),
+                           "offset" = 0)
+      boa_quantval <- 10000
+    }
+  } else {
+    offset <- data.frame("bandname" = listbands_bis,
+                         "bandid" = c(1, 2, 3, 4, 5, 6, 7, 8, 11, 12),
+                         "offset" = 0)
+    boa_quantval <- 10000
+  }
+
+  # identify where spectral bands are in the stars object
+  stars_spectral <- list()
+  starsnames <- names(s2_stars$attr)
+  stars_spectral$bandname <- starsnames[which(!starsnames == "Cloud")]
+  stars_spectral$wavelength <- wl_s2[stars_spectral$bandname]
+
+  sortedwl <- names(wl_s2)
+  reorder <- match(sortedwl, stars_spectral$bandname)
+  elim <- which(is.na(reorder))
+  if (length(elim) > 0) {
+    reorder <- reorder[-elim]
+  }
+  pathr <- s2_stars$attr[reorder]
+
+  names(pathr) <- NULL
+  s2_stars2 <- stars::read_stars(pathr, along = "band", proxy = TRUE)
+  stars_spectral$bandname <- stars_spectral$bandname[reorder]
+  stars_spectral$wavelength <- stars_spectral$wavelength[reorder]
+
+  uniqueoffset <- as.numeric(unique(offset$offset))
+  if (length(uniqueoffset) > 1) {
+    message("Warning: BOA offset differs between bands.")
+    message("offset will not be applied to the final S2 reflectance raster")
+    message("check metadata file to identify the offset applied on each band")
+    print(mtd_msi)
+  } else {
+    message("applying offset to reflectance data")
+    if (is.null(mtd_lasrc) || uniqueoffset == 0) {
+      offsets2 <- function(x) (round(x + uniqueoffset) * (10000 / boa_quantval))
+      s2_stars2 <- stars::st_apply(X = s2_stars2, MARGIN = "band", FUN = offsets2)
+    } else {
+      offsets2 <- function(x) (round(10000 * ((x + uniqueoffset * boa_quantval) / boa_quantval)))
+      s2_stars2 <- stars::st_apply(X = s2_stars2, MARGIN = "band", FUN = offsets2)
+    }
+  }
+  write_stack_s2(stars_s2 = s2_stars2, stars_spectral = stars_spectral, refl_path = refl_path,
+                 format = format, datatype = datatype, sensor = sensor, maxchunk = maxchunk)
+  # save metadata file as well if available
+  if (!is.null(mtd)) {
+    if (file.exists(mtd)) {
+      file.copy(from = mtd, to = file.path(dirname(refl_path), basename(mtd)), overwrite = TRUE)
+    }
+  }
+  # save metadata file as well if available
+  if (!is.null(mtd_msi)) {
+    if (file.exists(mtd_msi)) {
+      file.copy(from = mtd_msi, to = file.path(dirname(refl_path), basename(mtd_msi)), overwrite = TRUE)
+    }
+  }
+  # save LaSRC metadata file as well if available
+  if (!is.null(mtd_lasrc)) {
+    if (file.exists(mtd_lasrc)) {
+      file.copy(from = mtd_lasrc, to = file.path(dirname(refl_path), basename(mtd_lasrc)), overwrite = TRUE)
+    }
+  }
+  # delete temporary file
+  for (pathtemp in pathr) {
+    file.remove(pathtemp)
+    if (file.exists(paste(pathtemp, ".hdr", sep = ""))) file.remove(paste(pathtemp, ".hdr", sep = ""))
+  }
+  gc()
+  return(invisible())
+}
+
+#" ENVI functions
+#"
+#" based on https://github.com/cran/hyperSpec/blob/master/R/read.ENVI.R
+#" added wavelength, fwhm, ... to header reading
+#" Title
+#"
+#" @param x character.
+#" @param separator character
+#" @param trim_blank boolean.
+#"
+#" @return list.
+#" @export
+split_line <- function(x, separator, trim_blank = TRUE) {
+  tmp <- regexpr(separator, x)
+  key <- substr(x, 1, tmp - 1)
+  value <- substr(x, tmp + 1, nchar(x))
+  if (trim_blank) {
+    blank_pattern <- "^[[:blank:]]*([^[:blank:]]+.*[^[:blank:]]+)[[:blank:]]*$"
+    key <- sub(blank_pattern, "\\1", key)
+    value <- sub(blank_pattern, "\\1", value)
+  }
+  value <- as.list(value)
+  names(value) <- key
+  return(value)
+}
+
+#" save raster footprint as vector file
+#"
+#" @param path_raster character. path for a raster file
+#" @param path_vector character. path for a vector file
+#" @param driver character. driver for vector
+#"
+#" @return None
+#" @importFrom raster raster extent projection
+#" @importFrom sf st_as_sf st_write
+#" @export
+vectorize_raster_extent <- function(path_raster, path_vector, driver = "ESRI Shapefile") {
+  rast <- raster(path_raster)
+  e <- extent(rast)
+  # coerce to a SpatialPolygons object
+  p <- as(e, "SpatialPolygons")
+  projection(p) <- projection(rast)
+  p <- sf::st_as_sf(p)
+  sf::st_write(obj = p, path_vector, driver = driver)  # create to a shapefile
+  return(invisible())
+}
+
+#" writes ENVI hdr file
+#"
+#" @param hdr content to be written
+#" @param hdrpath Path of the hdr file
+#"
+#" @return None
+#" @importFrom stringr str_count
+#" @export
+write_envi_header <- function(hdr, hdrpath) {
+  h <- lapply(hdr, function(x) {
+    if (length(x) > 1 || (is.character(x) && stringr::str_count(x, "\\w+") > 1)) {
+      x <- paste0("{", paste(x, collapse = ", "), "}")
+    }
+    # convert last numerics
+    x <- as.character(x)
+  })
+  writeLines(c("ENVI", paste(names(hdr), h, sep = " = ")), con = hdrpath)
+  return(invisible())
+}
+
+#" This function writes a raster Stack object into a ENVI raster file
+#"
+#" @param stackobj list. raster stack
+#" @param stackpath character. path where to store the stack
+#" @param bands list. should include "bandname", and if possible "wavelength"
+#" @param datatype character. should be INT2S or FLT4S for example
+#" @param sensor character. Name of the sensor used to acquire the image
+#" @param stretch boolean. Set TRUE to get 10% stretching at display for reflectance, mentioned in hdr only
+#"
+#" @return None
+#" @importFrom utils read.table
+#" @export
+write_rasterstack_envi <- function(stackobj, stackpath, bands, datatype = "INT2S",
+                                   sensor = "Unknown", stretch = FALSE) {
+
+  r <- raster::writeRaster(x = stackobj, filename = stackpath, format = "Ehdr", overwrite = TRUE, datatype = datatype)
+  raster::hdr(r, format = "ENVI")
+  # Edit hdr file to add metadata
+  hdr <- read_envi_header(get_hdr_name(stackpath))
+  hdr$`band names` <- bands$bandname
+  if (length(bands$wavelength) == length(bands$bandname)) {
+    hdr$wavelength <- bands$wavelength
+  } else {
+    hdr$wavelength <- NULL
+  }
+  if (stretch == TRUE) {
+    hdr$`default stretch` <- "0.000000 1000.000000 linear"
+  }
+  hdr$`z plot range` <- NULL
+  hdr$`data ignore value` <- "-Inf"
+  hdr$`coordinate system string` <- read.table(paste(stackpath, ".prj", sep = ""))
+  proj <- strsplit(x = strsplit(x = projection(stackobj), split = " ")[[1]][1], split = "=")[[1]][2]
+  zone <- strsplit(x = strsplit(x = projection(stackobj), split = " ")[[1]][2], split = "=")[[1]][2]
+  datum <- strsplit(x = strsplit(x = projection(stackobj), split = " ")[[1]][3], split = "=")[[1]][2]
+  oldproj <- hdr$`map info`
+  newproj <- gsub(pattern = "projection", replacement = proj, x = oldproj)
+  newproj <- paste(newproj, zone, datum, sep = ", ")
+  hdr$`map info` <- newproj
+  hdr$`sensor type` <- sensor
+  write_envi_header(hdr = hdr, hdrpath = get_hdr_name(stackpath))
+
+  # remove unnecessary files
+  file2remove <- paste(stackpath, ".aux.xml", sep = "")
+  file.remove(file2remove)
+  file2remove <- paste(stackpath, ".prj", sep = "")
+  file.remove(file2remove)
+  file2remove <- paste(stackpath, ".stx", sep = "")
+  file.remove(file2remove)
+  return(invisible())
+}
+
+
+#" This function writes a stars object into a raster file
+#"
+#" @param stars_s2 list. stars object containing raster data. Can be produced with function Crop_n_resample_S2
+#" @param stars_spectral list. band name to be saved in the stack and spectral bands corresponding to the image
+#" @param refl_path character. path where to store the image
+#" @param format character. default = ENVI BSQ. otherwise use gdal drivers
+#" @param datatype character. should be Int16 or Float64 for example
+#" @param sensor character. Name of the sensor used to acquire the image
+#" @param maxchunk numeric. Size of individual chunks to be written (in Mb)
+#"
+#" @return None
+#" @export
+write_stack_s2 <- function(stars_s2, stars_spectral, refl_path, format = "ENVI",
+                           datatype = "Int16", sensor = "Unknown", maxchunk = 256) {
+
+  # write raster file from proxy using chunks
+  sizeobj <- 2 * dim(stars_s2)[1] * dim(stars_s2)[2] * dim(stars_s2)[3] / (1024**2)
+  nbchunks <- ceiling(sizeobj / maxchunk)
+  stars::write_stars(obj = stars_s2,
+                     dsn = refl_path,
+                     driver =  format,
+                     type = datatype,
+                     chunk_size = c(dim(stars_s2)[1], ceiling(dim(stars_s2)[2] / nbchunks)),
+                     progress = TRUE)
+
+  if (format == "ENVI") {
+    adjust_envi_hdr(dsn = refl_path, bands = stars_spectral,
+                    sensor = sensor, stretch = TRUE)
+  }
+  return(invisible())
+}