R/install_sen2cor.R

In pobsteta/theia2r: An R toolbox to find, download and preprocess Sentinel-2 data

#' @title Download and install sen2cor.
#' @description This function download and install standalone version of
#'  [sen2cor 2.5.5](http://step.esa.int/main/third-party-plugins-2/sen2cor).
#' @param sen2cor_dir (optional) Path where sen2cor will be installed
#'  (default: a subdirectory of the package path).
#' @param force (optional) Logical: if TRUE, install even if it is already 
#'  installed (default is FALSE).
#' @return NULL
#'
#' @author Luigi Ranghetti, phD (2017) \email{ranghetti.l@@irea.cnr.it}
#' @note License: GPL 3.0
#' @importFrom jsonlite toJSON fromJSON
#' @importFrom utils download.file unzip
#' @importFrom magrittr '%>%'
#' @importFrom stringr str_pad
#' @export
#' @examples \dontrun{
#' install_sen2cor()
#' }

install_sen2cor <- function(sen2cor_dir = NA, force = FALSE) {
    .install_sen2cor(sen2cor_dir = sen2cor_dir, force = force, interactive = TRUE)
}

.install_sen2cor <- function(sen2cor_dir = NA, force = FALSE, interactive = TRUE) {
    
    # sen2cor version
    sen2cor_version <- package_version("2.5.5")
    
    # check if it is already installed
    binpaths <- load_binpaths()
    if (force != TRUE & !is.null(binpaths$sen2cor)) {
        sen2cor_bin <- binpaths$sen2cor
        if (file.exists(sen2cor_bin)) {
            print_message(type = "message", "sen2cor is already installed; to overwrite, set force = TRUE.")
            return(invisible(NULL))
        }
    }
    
    # define sen2cor_dir (where to install or update)
    if (is.na(sen2cor_dir)) {
        sen2cor_dir <- file.path(system.file(package = "theia2r"), "sen2cor")
    }
    if (!file.exists(sen2cor_dir)) {
        dir.create(sen2cor_dir, recursive = FALSE, showWarnings = FALSE)
    } else if (!file.info(sen2cor_dir)$isdir) {
        print_message(type = "error", sen2cor_dir, " already exists and it is a file; please provide a different value (or leave blank).")
    }
    if (length(list.files(sen2cor_dir)) > 0) {
        if (interactive & interactive()) {
            print_message(type = "waiting", sen2cor_dir, " already exists and will be erased: ENTER to proceed or ESC to cancel...")
        } else {
            print_message(type = "warning", sen2cor_dir, " already exists and will be erased.")
        }
        unlink(sen2cor_dir, recursive = TRUE)
        dir.create(sen2cor_dir)
    }
    
    # Set path
    if (Sys.info()["sysname"] == "Linux") {
        sen2cor_url <- paste0("http://step.esa.int/thirdparties/sen2cor/", sen2cor_version, "/Sen2Cor-", str_pad(sen2cor_version[, 1], 2, "left", "0"), ".", str_pad(sen2cor_version[, 
            2], 2, "left", "0"), ".", str_pad(sen2cor_version[, 3], 2, "left", "0"), "-Linux64.run")
    } else if (Sys.info()["sysname"] == "Windows") {
        sen2cor_url <- paste0("http://step.esa.int/thirdparties/sen2cor/", sen2cor_version, "/Sen2Cor-", str_pad(sen2cor_version[, 1], 2, "left", "0"), ".", str_pad(sen2cor_version[, 
            2], 2, "left", "0"), ".", str_pad(sen2cor_version[, 3], 2, "left", "0"), "-win64.zip")
    } else {
        print_message(type = "error", "Installing sen2cor on ", Sys.info()["sysname"], " was not yet implemented.")
    }
    sen2cor_installer <- file.path(sen2cor_dir, basename(sen2cor_url))
    
    # download, extract and delete archive
    download.file(sen2cor_url, destfile = sen2cor_installer)
    if (Sys.info()["sysname"] == "Linux") {
        curr_dir <- getwd()
        setwd(sen2cor_dir)
        # os.chmod(sen2cor_installer, 0755)
        system(paste0("/bin/bash ./", basename(sen2cor_url), " --quiet --nox11 --target ./"), intern = FALSE)
        unlink(sen2cor_installer)
        setwd(curr_dir)
        sen2cor_bin <- file.path(sen2cor_dir, "bin", "L2A_Process")
    } else if (Sys.info()["sysname"] == "Windows") {
        suppressWarnings(unzip(zipfile = sen2cor_installer, exdir = sen2cor_dir, unzip = "internal"))
        unlink(sen2cor_installer)
        sen2cor_bin <- system.file("sen2cor", gsub("\\.zip$", "", basename(sen2cor_installer)), "L2A_Process.bat", package = "theia2r")
    }
    
    # fix bug #71
    script_tofix_path <- file.path(if (Sys.info()["sysname"] == "Windows") {
        dirname(sen2cor_bin)
    } else {
        dirname(dirname(sen2cor_bin))
    }, "lib/python2.7/site-packages/sen2cor/L2A_Tables.py")
    if (file.exists(script_tofix_path)) {
        script_tofix <- readLines(script_tofix_path)
        linenumber_tofix <- grep("t2a_split[2] + '_' + t2a_split[1] + '_' + t1c_split[10]", script_tofix, fixed = TRUE)
        if (length(linenumber_tofix) > 0) {
            script_tofix[linenumber_tofix] <- gsub("t1c_split[10]", "t1c_split[-1]", script_tofix[linenumber_tofix], fixed = TRUE)
            writeLines(script_tofix, script_tofix_path)
        }
    }
    
    # Save a text file with the L2A_Process path, including also paths of GDAL apps
    binpaths$sen2cor <- normalize_path(sen2cor_bin)
    writeLines(jsonlite::toJSON(binpaths, pretty = TRUE), attr(binpaths, "path"))
    
}