diff 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/preprocess_S2.r	Mon Jan 09 13:36:33 2023 +0000
@@ -0,0 +1,121 @@
+#Rscript
+
+###########################################
+##     Preprocessing Sentinel 2 data     ##
+###########################################
+
+#####Packages : sen2r,
+#    jqr,
+#    protolite,
+#    raster,
+#    sf,
+#    rgeos,
+#    sp,
+#    raster,
+#    stars,
+#    stringr,
+#    progress,
+#    rgdal,
+#    R.utils,
+#    gdalUtils,
+#    fasterize,
+#    XML,
+#    XML2
+
+#####Load arguments
+
+args <- commandArgs(trailingOnly = TRUE)
+
+if (length(args) < 1) {
+    stop("This tool needs at least 1 argument")
+}else {
+    data <- args[1]
+    source(args[2])
+    data_source <- as.character(args[3])
+    sat_type <- as.character(args[4])
+}
+
+##____________________________________________________________________##
+##        Define where data is stored and where to write results      ##
+##--------------------------------------------------------------------##
+
+#Create a directory where to unzip your folder of data
+dir.create("data_dir")
+unzip(data, exdir = "data_dir")
+
+# Result directory
+result_path <- "results"
+dir.create(path = result_path, showWarnings = FALSE, recursive = TRUE)
+
+#Csv file for output useless but needed for linter
+write.csv(data_source, "Mission.csv")
+
+# define raster path
+if (data_source == "SAFE") {
+    path_s2 <- file.path("data_dir", list.files("data_dir", pattern = ".SAFE"))
+    #To define the level and know if a correction is needed (convert not ready yet)
+    level_info <- get_s2_level(path_s2)
+    if (level_info == "L1C") {
+        stop("! This tool works for data of L2A level and NOT for the L1C level which is currently a work in progress !")
+    }
+}else {
+    path_s2 <- file.path("data_dir")
+}
+
+##____________________________________________________________________##
+##                  Extract, resample & stack data                    ##
+##--------------------------------------------------------------------##
+# define resolution
+resolution <- 10
+# define source of data
+s2source <- data_source
+
+s2obj <- extract_from_s2_l2a(path_dir_s2 = path_s2,
+                                        path_vector = NULL,
+                                        s2source = s2source,
+                                        resolution = resolution)
+
+##____________________________________________________________________##
+##                        Write CLOUD MASK                            ##
+##--------------------------------------------------------------------##
+
+# directory for cloud mask
+cloud_path <- file.path(result_path, "CloudMask")
+dir.create(path = cloud_path, showWarnings = FALSE, recursive = TRUE)
+# Filename for cloud mask
+cloudmasks <- save_cloud_s2(s2_stars = s2obj$s2_stack,
+                                       cloud_path = cloud_path,
+                                       s2source = s2source, saveraw = TRUE)
+
+zip_cloud <- file.path("Cloud.zip")
+zip::zip(zip_cloud, cloud_path)
+##____________________________________________________________________##
+##                        Write REFLECTANCE                           ##
+##--------------------------------------------------------------------##
+
+# directory for Reflectance
+refl_dir <- file.path(result_path, "Reflectance")
+dir.create(path = refl_dir, showWarnings = FALSE, recursive = TRUE)
+
+if (data_source == "SAFE") {
+    # filename for Reflectance
+    refl_path <- file.path(refl_dir, paste(basename(s2obj$s2_bands$GRANULE), "_Refl", sep = ""))
+
+    # Save Reflectance file as ENVI image with BIL interleaves
+    tile_s2 <- substring(strsplit(basename(s2obj$s2_bands$GRANULE), "_")[[1]][2], 2)
+    dateacq_s2 <- as.Date(substring(strsplit(basename(s2obj$s2_bands$GRANULE), "_")[[1]][4], 1, 8), format = "%Y%m%d")
+}else {
+    # filename for Reflectance
+    refl_path <- file.path(refl_dir, paste(basename(s2obj$s2_bands$path_tile_s2), "_Refl", sep = ""))
+
+    # Save Reflectance file as ENVI image with BIL interleaves
+    tile_s2 <- substring(strsplit(basename(s2obj$s2_bands$path_tile_s2), "_")[[1]][2], 2)
+    dateacq_s2 <- as.Date(substring(strsplit(basename(s2obj$s2_bands$path_tile_s2), "_")[[1]][4], 1, 8), format = "%Y%m%d")
+}
+
+save_data <- save_reflectance_s2(s2_stars = s2obj$s2_stack, refl_path = refl_path,
+                               s2sat = sat_type, tile_s2 = tile_s2, dateacq_s2 = dateacq_s2,
+                               format = "ENVI", datatype = "Int16", mtd = s2obj$s2_bands$metadata, mtd_msi = s2obj$s2_bands$metadata_MSI)
+
+zip_files <- file.path("Refl.zip")
+zip::zip(zip_files, refl_dir)