Mercurial > repos > ecology > srs_pca
view preprocess_S2.r @ 1:21e21363a8b4 draft default tip
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit 0f331043178bbfbe5cda0e31d887971464b3071c
author | ecology |
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date | Fri, 07 Apr 2023 14:38:58 +0000 |
parents | 0931c98270c9 |
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#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)