R/deprecated.R

In albhasan/sits.starfm: Use the StarFM Fusion Model on Landsat 8 Images

# CODE TO BE REMOVED IN A POSTERIOR BUILD.

#' @title Build a tibble of the data required to create bricks.
#' @author Alber Sanchez, \email{alber.ipia@@inpe.br}
#' @description Build a tibble with the data required to create bricks.
#'
#' @param landsat_path  A length-one character. Path to a directory of images.
#' @param modis_path    A length-one character. Path to a directory of images.
#' @param scene_shp     A length-one character. Path to a polygon shapefile of
#' Landsat scene borders.
#' @param tile_shp      A length-one character. Path to a polygon shapefile of
#' MODIS tile borders.
#' @param scenes        A character. Constrain to these scenes (e.g. 233067)
#' @param from          A character. Constrain to this starting date.
#' @param to            A character. Constrain to this ending date.
#' @param add_neighbors A logical. Should neighbor images be considered?
#' @return              A tibble.
build_brick_tibble2 <- function(landsat_path, modis_path, scene_shp, tile_shp,
                                        scenes, from, to, add_neighbors){
    .Deprecated("build_brick_landsat_modis")
    build_brick_landsat_modis(landsat_path = landsat_path,
                              modis_path = modis_path, scene_shp = scene_shp,
                              tile_shp = tile_shp, scenes = scenes, from = from,
                              to = to, add_neighbors = add_neighbors) %>%
    return()
}

#' @title Build a tibble with the data required to create bricks.
#' @author Alber Sanchez, \email{alber.ipia@@inpe.br}
#' @description Build a tibble with the data required to create bricks.
#'
#' @param landsat_path A length-one character. Path to a directory of images.
#' @param modis_path   A length-one character. Path to a directory of images.
#' @param scene_shp    A length-one character. Path to a polygon shapefile of
#' Landsat scene borders.
#' @param tile_shp     A length-one character. Path to a polygon shapefile of
#' MODIS tile borders.
#' @param scenes       A character. Constrain to these scenes (e.g. 233067)
#' @param from         A character. Constrain to this starting date.
#' @param to           A character. Constrain to this ending date.
#' @param max_ts_hole  A length-one numeric. Maximum number of missing
#' consecutive images allowed in a time series
#' @param min_miss_ratio A length-one numeric. Minimum proportion of missing
#' images allowed in a time series.
#' @return             A tibble.
#' @export
build_brick_tibble <- function(landsat_path, modis_path, scene_shp, tile_shp,
                               scenes = NULL, from = NULL, to = NULL,
                               max_ts_hole = 1, min_miss_ratio = 0.95){

    .Deprecated("build_brick_tibble2")

    if (!all(dir.exists(landsat_path), dir.exists(modis_path))) {
        stop("Directory not found!")
    }
    if (!all(file.exists(scene_shp), file.exists(tile_shp))) {
        stop("File not found!")
    }

    # Get files into a tibble & filter
    pattern_landsat <- NULL
    if (!is.null(scenes) && is.vector(scenes) && length(scenes) > 0) {
        scene_neigh <- scenes %>% get_tile_neighbors() %>% c(scenes) %>%
            unique() %>% .[!is.na(.)]
        if (length(scene_neigh) > 1) {
            scene_neigh <- paste0('(', paste(scene_neigh, collapse = '|'), ')')
        }
        pattern_landsat <- stringr::str_c("^LC08_L1[TG][PTS]_", scene_neigh,
                                          ".*(tif|_MTL\\.txt)$")
    }
    l8_img <- landsat_path %>% build_landsat_tibble(pattern = pattern_landsat,
                                                    from = from, to = to)

    # check brick completeness & spot missing images
    l8_img <- l8_img %>% build_ts() %>%
        dplyr::mutate(brick_ratio = n_img/n_expected) %>%
        dplyr::filter(brick_ratio > min_miss_ratio, max_hole <= max_ts_hole) %>%
        dplyr::select(tile, prodes_year, ts) %>% tidyr::unnest(ts) %>%
        ensurer::ensure_that(nrow(.) > 0, err_desc = sprintf(
            "Not enough images to to build a brick for %s from %s to %s",
            scenes, from, to)) %>%
        dplyr::select(sat_image, files, tile, img_date, prodes_year, neigh,
                      cloud_cov)

    # match L8 scenes to MOD tiles (in space)
    l8mod_sp <- match_tiles2scenes(scene_path = scene_shp,
                                   tile_path = tile_shp,
                                   scenes = unique(dplyr::pull(l8_img, tile)))
    l8mod_sp$tile <- lapply(l8mod_sp$tile, function(x) {dplyr::pull(x, tile)})
    l8_img <- l8_img %>% dplyr::rename(scene = tile) %>%
        dplyr::inner_join(l8mod_sp, by = 'scene')

    # match L8 scenes to MOD tiles (in time)
    tiles <- l8_img %>% dplyr::pull(tile) %>% unlist() %>% unique()
    if (length(tiles) == 0) {
        return(NA)
    }else if (length(tiles) > 1) {
        tiles <- paste0('(', paste(tiles, collapse = '|'), ')')
    }
    pattern_mod <- stringr::str_c('^MOD13Q1\\.A201[2-8][0-9]{3}\\.', tiles,
                                  '.*hdf$')
    mod_img <- modis_path %>% build_modis_tibble(pattern = pattern_mod,
                                                 from = from, to = to)
    l8_img$tile <- purrr::map2(l8_img$tile, l8_img$img_date, match_tile_date,
                               img_tb = mod_img, untie = 0.001)
    #mod_imgs <- l8_img %>% dplyr::pull(tile) %>% dplyr::bind_rows() %>%
    #    dplyr::pull(sat_image)
    #if (length(mod_imgs) != length(unique(mod_imgs)))
    #    warning("Duplicated MODIS were related to LANDSAT images")
    return(l8_img)
}

.is_input_file_valid <- function(files){
        #TODO: This function can't handle HDF4 datasets.
        if(!any(grepl("HDF4_EOS", files))){
                        if (any(vapply(files, is.null, logical(1))))
                                        return(FALSE)
        if (any(vapply(files, is.na, logical(1))))
                        return(FALSE)
                if (!all(vapply(files, file.exists, logical(1))))
                                return(FALSE)
                    }else{
                                stop("Cannot handle HDF4 datasets.")
                        }
    return(TRUE)
}

.is_resolution_valid <- function(res){
        if (is.atomic(res))
                    return(is.numeric(res) && length(res) == 2)
    if (is.list(res))
                return(vapply(res, .is_resolution_valid, logical(1)))
        return(FALSE)
}

.is_extent_valid <- function(ext){
        if (is.atomic(ext))
                    return(is.numeric(ext) && length(ext) == 4)
    if (is.list(ext))
                return(vapply(ext, .is_extent_valid, logical(1)))
        return(FALSE)
}




#' @title Build a Virtual Dataset file.
#' @author Alber Sanchez, \email{alber.ipia@@inpe.br}
#' @description R wrapper for gdalbuildvrt
#'
#' @param input_files           A character. Paths to the image files.
#' @param out_filename          A length-one character. The path to the
#' destination file.
#' @param tileindex             A length-one character. A tile index field name.
#' @param resolution            A length-one character.
#' @param target_extent         A length-four numeric.
#' @param target_resolution     A length-two numeric.
#' @param tap                   A length-one logical.
#' @param separate              A length-one logical.
#' @param band                  An integer.
#' @param subdataset            A length-one integer.
#' @param q                     A length-one logical. Disable the progress bar.
#' @param optimise              A length-one character.
#' @param addalpha              A length-one logical.
#' @param hidenodata            A length-one logical.
#' @param srcnodata             A numeric.
#' @param vrtnodata             A numeric.
#' @param a_srs                 A length-one character.
#' @param resampling            A length-one character.
#' @param oo                    A length-one character.
#' @param input_file_list       A length-one character. Path to a text file of file paths.
#' @param overwrite             A length-one logical.
#' @param dry_run               A length-one logical. Do not run, just print the sytem call.
#' @return out_filename         A length-one character.
#' @export
gdal_build_vrt <- function(input_files,
                         out_filename = tempfile(pattern = "gdalbuildvrtout_", fileext = ".vrt"),
                         tileindex = NULL, resolution = NULL,
                         target_extent = NULL, target_resolution = NULL,
                         tap = FALSE, separate = FALSE, band = NULL,
                         subdataset = NULL, q = TRUE, optimise = NULL,
                         addalpha = FALSE, hidenodata = FALSE, srcnodata = NULL,
                         vrtnodata = NULL, a_srs = NULL, resampling = NULL,
                         oo = NULL, input_file_list = NULL, overwrite = FALSE,
                         dry_run = FALSE){

    .Deprecated("gdalcmdline::gdal_build_vrt")

    if (any(is.na(input_files))) {
        warning("NAs found in gdalbuildvrt. Removing them...")
        input_files <- input_files[!is.na(input_files)]
    }
    stopifnot(.is_input_file_valid(input_files))
    params <- character()

    if (!is.null(tileindex))
       params <- append(params, paste0("-tileindex ", tileindex))
    if (!is.null(resolution))
        params <- append(params, paste0("-resolution ", resolution))
    if (!is.null(target_extent))
        params <- append(params, paste("-te", paste(target_extent, collapse = " ")))
    if (!is.null(band))
        params <- append(params, paste("-b", paste(band, sep = " ")))
    if (!is.null(subdataset))
        params <- append(params, paste0("-sd ", subdataset))
    if (!is.null(optimise))
        params <- append(params, paste0("-optim ", optimise))
    if (!is.null(srcnodata))
        params <- append(params, paste0("-srcnodata '", paste(srcnodata, collapse = " "), "'"))
    if (!is.null(vrtnodata))
        params <- append(params, paste0("-vrtnodata '", paste(vrtnodata, collapse = " "), "'"))
    if (!is.null(a_srs))
        params <- append(params, paste0("-a_srs ", a_srs))
    if (!is.null(resampling))
        params <- append(params, paste0("-r ", resampling))
    if (!is.null(oo))
        params <- append(params, paste("-oo", oo))
    if (!is.null(input_file_list))
        params <- append(params, paste("-input_file_list", input_file_list))
    if (tap)
        params <- append(params, "-tap")
    if (separate)
        params <- append(params, "-separate")
    if (q)
        params <- append(params, "-q")
    if (addalpha)
        params <- append(params, "-addalpha")
    if (hidenodata)
        params <- append(params, "-hidenodata")
    if (overwrite)
        params <- append(params, "-overwrite")
    params <- append(params, out_filename)
    params <- append(params, input_files)
    error <- call_os(command = "gdalbuildvrt", args = params, dry_run = dry_run)
    if (error) {
        warning("Failed call to gdalbuildvrt")
        return(NA_character_)
    }
    return(out_filename)
}

#' @title Do calculations on images.
#' @author Alber Sanchez, \email{alber.ipia@@inpe.br}
#' @description R wrapper for gdal_calc.py
#'
#' @param input_files           A character. Paths to the image files.
#' @param out_filename          A length-one character. The path to the
#' destination file.
#' @param expression            A character. The expresion to compute on the
#' images using upper case A-Z letters to represent the images in the same order
#' as input_files.
#' @param band_number           An integer. The band numbers in input_files.
#' @param dstnodata             A length-one integer. Output nodata value.
#' @param data_type             A length-one character. Ouput datatype. It must
#' be one of c('Int32', 'Int16', 'Float64', 'UInt16', 'Byte', 'UInt32',
#' 'Float32').
#' @param out_format            A length-one character. The output format.
#' @param creation_option       A character. Creation options for output file
#' e.g. c('NAME1=VALUE1', 'NAME2=VALUE2')
#' @param all_bands             A character. Process all bands of given raster
#' (A-Z).
#' @param overwrite             A length-one logical. The default is FALSE.
#' @param verbose               A length-one logical. Generate a verbose output.
#' The default is FALSE.
#' @param quiet                 A length-one logical. The default is FALSE.
#' @param dry_run               A length-one logical. Do not run, just print the sytem call.
#' @return out_filename A length-one character.
#' @export
gdal_calc <- function(input_files,
                      out_filename = tempfile(pattern = "gdal_calc_out_", fileext = ".tif"),
                      expression,
                      band_number = NULL, dstnodata = NULL, data_type = NULL,
                      out_format = NULL, creation_option = NULL,
                      all_bands = NULL, overwrite = FALSE, verbose = FALSE,
                      quiet = FALSE, dry_run = FALSE) {

    .Deprecated("gdalcmdline::gdal_calc")

    if (any(is.na(input_files))) {
        warning("NAs found in gdal_calc. Removing them...")
        input_files <- input_files[!is.na(input_files)]
    }
    stopifnot(.is_input_file_valid(input_files))
    params <- paste0("--calc=\"", expression, "\"")
    params <- append(params, paste0("--outfile=", out_filename))
    params <- append(params, paste(paste0("-", LETTERS[1:length(input_files)]),
                                   input_files))
    if (!is.null(band_number)) {
        params <- append(params,
                         paste0(paste0("--", LETTERS[1:length(band_number)],
                                       "_band="), band_number))
    }
    if (!is.null(dstnodata))
        params <- append(params, paste0("--NoDataValue=", dstnodata))
    if (!is.null(data_type))
        params <- append(params, paste0("--type=", data_type))
    if (!is.null(out_format))
        params <- append(params, paste0("--format=", out_format))
    if (!is.null(creation_option))
        params <- append(params, paste0("--co=", creation_option))
    if (!is.null(all_bands))
        params <- append(params, paste0("--allBands=", all_bands))
    if (overwrite)
        params <- append(params, "--overwrite")
    if (verbose)
        params <- append(params, "--debug")
    if (quiet)
        params <- append(params, "--quiet")

    error <- call_os(command = "gdal_calc.py", args = params, dry_run = dry_run)
    if (error) {
        warning(sprintf("Failed call to gdal_calc: %s", paste(args, collapse = " ")))
        return(NA_character_)
    }
    return(out_filename)
}



#' @title Convert raster between formats
#' @author Alber Sanchez, \email{albequietr.ipia@@inpe.br}
#' @description R wrapper for gdal_translate
#'
#' @param input_files  A character. Paths to the image files.
#' @param out_filename A length-one character. The path to the destination file.
#' @param of        A length-one character.
#' @param creation_option A character. Creation options for output file e.g.
#' c('NAME1=VALUE1', 'NAME2=VALUE2').
#' @param ot        A length-one character.
#' @param ps        A length-two numeric.
#' @param tap       A length-one logical. The default is FALSE.
#' @param ul_lr     A length-four numeric.
#' @param v         A length-one logical. The default is FALSE.
#' @param separate  A length-one logical. The default is FALSE.
#' @param pct       A length-one logical. The default is FALSE.
#' @param nodata_value A length-one numeric.
#' @param a_nodata  A length-one numeric.
#' @param init      A numeric.
#' @param createonly A length-one logical. The default is FALSE.
#' @param dry_run   A length-one logical. Do not run, just print the sytem call.
#' @return          A length-one character. out_filename.
#' @export
gdal_merge <- function(input_files,
                       out_filename = tempfile(pattern = "gdal_merge_out_", fileext = ".tif"),
                       of = NULL,
                       creation_option = NULL, ot = NULL, ps = NULL,
                       tap = FALSE, ul_lr = NULL, v = FALSE, separate = FALSE,
                       pct = FALSE, nodata_value = NULL, a_nodata = NULL,
                       init = NULL, createonly = FALSE, dry_run = FALSE){

    .Deprecated("gdalcmdline::gdal_merge")

    if (any(is.na(input_files))) {
        warning("NAs found in gdal_merge. Removing them...")
        input_files <- input_files[!is.na(input_files)]
    }
    stopifnot(.is_input_file_valid(input_files))
    params <- character()

    if (!is.null(of))
        params <- append(params, paste("-of", of))
    if (!is.null(creation_option))
        params <- append(params, paste("-co", creation_option))
    if (!is.null(ot))
        params <- append(params, paste("-ot", ot))
    if (!is.null(ps))
        params <- append(params, paste("-ps", paste(ps)))
    if (tap)
        params <- append(params, "-tap")
    if (!is.null(ul_lr))
        params <- append(params, paste("-ul_lr", paste(ul_lr)))
    if (v)
        params <- append(params, "-v")
    if (separate)
        params <- append(params, "-separate")
    if (pct)
        params <- append(params, "-pct")
    if (!is.null(nodata_value))
        params <- append(params, paste("-nodata_value", nodata_value))
    if (!is.null(a_nodata))
        params <- append(params, paste("-a_nodata", a_nodata))
    if (!is.null(init))
        params <- append(params, paste("-init", paste(init)))
    if (createonly)
        params <- append(params, "-createonly")
    #
    params <- append(params, input_files)
    params <- append(paste("-o", out_filename), params)
    error <- call_os(command = "gdal_merge.py", args = params, dry_run = dry_run)
    if (error) {
        warning("Failed call to gdal_merge")
        return(NA_character_)
    }
    return(out_filename)
}


#' @title Convert raster between formats
#' @author Alber Sanchez, \email{albequietr.ipia@@inpe.br}
#' @description R wrapper for gdal_translate
#'
#' @param input_files  A character. Paths to the image files.
#' @param out_filename A length-one character. The path to the destination file.
#' @param ot        A length-one character.
#' @param strict    A length-one logical. The default is FALSE.
#' @param of        A length-one character.
#' @param b         A character.
#' @param mask      A length-one character.
#' @param expand    A length-one character.
#' @param outsize   A length-two numeric. Output size in pixels.
#' @param tr        A length-two numeric. Target resolution in georeferenced
#' @param r         A length-one logical. The default is FALSE.
#' @param scale     A length two or four numeric.
#' @param exponent  A length-one numeric.
#' @param unscale   A length-one logical. The default is FALSE.
#' @param srcwin    A length-four numeric.
#' @param projwin   A length-four numeric.
#' @param projwin_srs A length-one character.
#' @param epo       A length-one logical. The default is FALSE.
#' @param eco       A length-one logical. The default is FALSE.
#' @param a_srs     A length-one character.
#' @param a_scale   A length-one numeric.
#' @param a_offset  A length-one numeric.
#' @param a_ullr    A length-four numeric.
#' @param a_nodata  A length-one numeric.
#' @param colorinterp_X A character.
#' @param colorinterp A length-one character.
#' @param mo        A character.
#' @param creation_option A character. Creation options for output file e.g.
#' c('NAME1=VALUE1', 'NAME2=VALUE2').
#' @param gcp       A list of length-five numeric.
#' @param q         A length-one logical. The default is FALSE.
#' @param sds       A length-one logical. The default is FALSE.
#' @param stats     A length-one logical. The default is FALSE.
#' @param norat     A length-one logical. The default is FALSE.
#' @param oo     A character. Open options for input files e.g.
#' c('NAME1=VALUE1', 'NAME2=VALUE2').
#' @param dry_run   A length-one logical. Do not run, just print the sytem call.
#' @return          A length-one character. out_filename.
gdal_translate <- function(input_files,
    out_filename = tempfile(pattern = "gdal_translate_out_", fileext = ".tif"),
    ot = NULL, strict = FALSE, of = NULL,
    b = NULL, mask = NULL, expand = NULL, outsize = NULL, tr = NULL, r = NULL,
    scale = NULL, exponent = NULL, unscale = FALSE, srcwin = NULL, projwin = NULL,
    projwin_srs = NULL, epo = FALSE, eco = FALSE, a_srs = NULL, a_scale = NULL,
    a_offset = NULL, a_ullr = NULL, a_nodata = NULL, colorinterp_X = NULL,
    colorinterp = NULL, mo = NULL, creation_option = NULL, gcp = NULL, q = FALSE,
    sds = FALSE, stats = FALSE, norat = FALSE, oo = NULL, dry_run = FALSE){

    .Deprecated("gdalcmdline::gdal_translate")

    if (any(is.na(input_files))) {
        warning("NAs found in gdal_translate. Removing them...")
        input_files <- input_files[!is.na(input_files)]
    }
    stopifnot(.is_input_file_valid(input_files))
    params <- character()

    if (!is.null(ot))
        params <- append(params, paste("-ot", ot))
    if (strict)
        params <- append(params, "-strict")
    if (!is.null(of))
        params <- append(params, paste("-of", of))
    if (!is.null(b))
        params <- append(params, paste("-b", b))
    if (!is.null(mask))
        params <- append(params, paste("-b", mask))
    if (!is.null(expand))
        params <- append(params, paste("-expand", expand))
    if (!is.null(outsize))
        params <- append(params, paste("-outsize", paste(outsize)))
    if (!is.null(tr))
        params <- append(params, paste("-tr", paste(tr)))
    if (!is.null(r))
        params <- append(params, paste("-r", r))
    if (!is.null(scale)) {
        params <- append(params, paste("-scale", paste(scale)))
        if (!is.null(exponent))
            params <- append(params, paste("-exponent", paste(exponent)))
    }
    if (!is.null(unscale))
        params <- append(params, paste("-unscale", unscale))
    if (unscale)
        params <- append(params, "-unscale")
    if (!is.null(srcwin))
        params <- append(params, paste("-srcwin", paste(srcwin)))
    if (!is.null(projwin))
        params <- append(params, paste("-projwin", paste(projwin)))
    if (!is.null(projwin_srs))
        params <- append(params, paste("-projwin_srs", projwin))
    if (epo)
        params <- append(params, "-epo")
    if (eco)
        params <- append(params, "-eco")
    if (!is.null(a_srs))
        params <- append(params, paste("-a_srs", a_srs))
    if (!is.null(a_scale))
        params <- append(params, paste("-a_scale", a_scale))
    if (!is.null(a_offset))
        params <- append(params, paste("-a_offset", a_offset))
    if (!is.null(a_ullr))
        params <- append(params, paste("-a_ullr", paste(a_ullr)))
    if (!is.null(a_nodata))
        params <- append(params, paste("-a_nodata", paste(a_nodata)))
    if (!is.null(colorinterp_X))
        params <- append(params, paste(paste0("-colorinterp_", colorinterp_X, sep = ""), colorinterp_X))
    if (!is.null(colorinterp))
        params <- append(params, paste("-colorinterp", colorinterp))
    if (!is.null(mo))
        params <- append(params, paste("-mo '", mo, "'", sep = ""))
    if (!is.null(creation_option))
        params <- append(params, paste("-co", creation_option))
    if (!is.null(gcp))
        for (l in gcp) {
            params <- append(params, paste("-gcp", paste(l)))
        }
    if (q)
        params <- append(params, "-q")
    if (sds)
        params <- append(params, "-sds")
    if (stats)
        params <- append(params, "-stats")
    if (norat)
        params <- append(params, "-norat")
    if (!is.null(oo))
        params <- append(params, paste("-oo", oo))
    #
    params <- append(params, input_files)
    params <- append(params, out_filename)
    error <- call_os(command = "gdal_translate", args = params, dry_run = dry_run)
    if (error) {
        warning("Failed call to gdal_translate")
        return(NA_character_)
    }
    return(out_filename)
}


#' @title Process images
#' @author Alber Sanchez, \email{albequietr.ipia@@inpe.br}
#' @description R wrapper for gdalwarp
#'
#' @param input_files  A character. Paths to the image files.
#' @param out_filename A length-one character. The path to the destination file.
#' @param s_srs        A length-one character.
#' @param target_srs   A length-one character. The target spatial reference set.
#' @param to           A character. e.g c('NAME1=VALUE1', 'NAME2=VALUE2')
#' @param novshiftgrid A length-one logical. The default is FALSE.
#' @param order        A length-one numeric.
#' @param tps          A length-one logical. The default is FALSE.
#' @param rpc          A length-one logical. The default is FALSE.
#' @param geoloc       A length-one logical. The default is FALSE.
#' @param et           A length-one numeric.
#' @param refine_gcps  A length-one numeric.
#' @param extent_output A length-four numeric. The extents of the output file in
#' target SRS by default, or in the SRS specified with extent_output_srs.
#' @param extent_output_srs       A length-one character. SRS of extent_output
#' (when it is different from input_files' SRS).
#' @param tr           A length-two numeric.
#' @param tap          A length-one logical. The default is FALSE.
#' @param size_ouput   A length-two integer. Set output file size in pixels and
#' lines.
#' @param ovr          A length-one character.
#' @param wo           A character. e.g c('NAME1=VALUE1', 'NAME2=VALUE2')
#' @param ot           A length-one character.
#' @param wt           A length-one character.
#' @param resampling   A length-one character. Resampling method to use.
#' @param srcnodata    A numeric.
#' @param dstnodata    A numeric.
#' @param srcalpha     A length-one logical. The default is FALSE.
#' @param nosrcalpha   A length-one logical. The default is FALSE.
#' @param dstalpha     A length-one logical. The default is FALSE.
#' @param wm           A length-one numeric.
#' @param multi        A length-one logical. The default is FALSE.
#' @param quiet        A length-one logical. The default is FALSE.
#' @param out_format   A length-one character. The output format.
#' @param creation_option A character. Creation options for output file e.g.
#' c('NAME1=VALUE1', 'NAME2=VALUE2')
#' @param cutline      A length-one character.
#' @param cl           A length-one character.
#' @param cwhere       A length-one character.
#' @param csql         A length-one character.
#' @param cblend       A length-one numeric.
#' @param crop_to_cutline A length-one logical. The default is FALSE.
#' @param overwrite    A length-one logical. The default is FALSE.
#' @param nomd         A length-one logical. The default is FALSE.
#' @param cvmd         A length-one character.
#' @param setci        A length-one logical. The default is FALSE.
#' @param oo           A character. e.g. c('NAME1=VALUE1', 'NAME2=VALUE2')
#' @param doo          A character. e.g. c('NAME1=VALUE1', 'NAME2=VALUE2')
#' @param dry_run      A length-one logical. Do not run, just print the sytem call.
#' @return out_filename A length-one character.
#' @export
gdal_warp <- function(input_files,
                      out_filename = tempfile(pattern = "gdal_warp_out_", fileext = ".tif"),
                      s_srs = NULL,
                      target_srs = NULL, to = NULL, novshiftgrid = FALSE,
                      order = NULL, tps = FALSE, rpc = FALSE, geoloc = FALSE,
                      et = NULL, refine_gcps = NULL, extent_output = NULL,
                      extent_output_srs = NULL, tr = NULL, tap = FALSE,
                      size_ouput = NULL, ovr = NULL, wo = NULL, ot = NULL,
                      wt = NULL, resampling = NULL, srcnodata = NULL,
                      dstnodata = NULL, srcalpha = FALSE, nosrcalpha = FALSE,
                      dstalpha = FALSE, wm = NULL, multi = FALSE, quiet = FALSE,
                      out_format = NULL, creation_option = NULL, cutline = NULL,
                      cl = NULL, cwhere = NULL, csql = NULL, cblend = NULL,
                      crop_to_cutline = FALSE, overwrite = FALSE, nomd = FALSE,
                      cvmd = NULL, setci = FALSE, oo = NULL, doo = NULL,
                      dry_run = FALSE) {

    .Deprecated("gdalcmdline::gdal_warp")

    if (any(is.na(input_files))) {
        warning("NAs found in gdal_warp. Removing them...")
        input_files <- input_files[!is.na(input_files)]
    }
    stopifnot(.is_input_file_valid(input_files))
    params <- character()

    if (!is.null(s_srs))
        params <- append(params, paste("-s_srs", s_srs))
    if (!is.null(target_srs))
        params <- append(params, paste("-t_srs", target_srs))
    if (!is.null(to))
        params <- append(params, paste("-to", to))
    if (novshiftgrid)
        params <- append(params, "-novshiftgrid")
    if (!is.null(order))
        params <- append(params, paste("-order", order))
    if (tps)
        params <- append(params, "-tps")
    if (rpc)
        params <- append(params, "-rpc")
    if (geoloc)
        params <- append(params, "-geoloc")
    if (!is.null(et))
        params <- append(params, paste("-et", et))
    if (!is.null(refine_gcps))
        params <- append(params, paste("-refine_gcps", refine_gcps))
    if (!is.null(extent_output))
        params <- append(params, paste("-te", paste(extent_output,
                                                    collapse = " ")))
    if (!is.null(extent_output_srs))
        params <- append(params, paste("-te_srs ", extent_output_srs))
    if (!is.null(tr))
        params <- append(params, paste("-tr ", tr))
    if (tap)
        params <- append(params, "-tap")
    if (!is.null(size_ouput))
        params <- append(params, paste("-ts", paste(size_ouput,
                                                    collapse = " ")))
    if (!is.null(ovr))
        params <- append(params, paste("-ovr ", ovr))
    if (!is.null(wo))
        params <- append(params, paste("-wo", wo))
    if (!is.null(ot))
        params <- append(params, paste("-ot", ot))
    if (!is.null(wt))
        params <- append(params, paste("-ot", wt))
    if (!is.null(resampling))
        params <- append(params, paste("-r", resampling))
    if (!is.null(srcnodata))
        params <- append(params, paste0("-srcnodata '", paste(srcnodata,
                                                              collapse = " "),
                                        "'"))
    if (!is.null(dstnodata))
        params <- append(params, paste0("-dstnodata '", paste(dstnodata,
                                                              collapse = " "),
                                        "'"))
    if (srcalpha)
        params <- append(params, "-srcalpha")
    if (nosrcalpha)
        params <- append(params, "-nosrcalpha")
    if (dstalpha)
        params <- append(params, "-dstalpha")
    if (!is.null(wm))
        params <- append(params, paste("-wm", wm))
    if (multi)
        params <- append(params, "-multi")
    if (quiet)
        params <- append(params, "-q")
    if (!is.null(out_format))
        params <- append(params, paste("-of", out_format))
    if (!is.null(creation_option))
        params <- append(params, paste("-co", creation_option))
    if (!is.null(cutline))
        params <- append(params, paste("-cutline", cutline))
    if (!is.null(cl))
        params <- append(params, paste("-cl", cl))
    if (!is.null(cwhere))
        params <- append(params, paste("-cwhere", cwhere))
    if (!is.null(csql))
        params <- append(params, paste("-csql", csql))
    if (!is.null(cblend))
        params <- append(params, paste("-cblend", cblend))
    if (crop_to_cutline)
        params <- append(params, "-crop_to_cutline")
    if (overwrite)
        params <- append(params, "-overwrite")
    if (nomd)
        params <- append(params, "-nomd")
    if (!is.null(cvmd))
        params <- append(params, paste("-cvmd", cvmd))
    if (setci)
        params <- append(params, "-setci")
    if (!is.null(oo))
        params <- append(params, paste("-oo", oo))
    if (!is.null(doo))
        params <- append(params, paste("-doo", doo))
    #
    params <- append(params, input_files)
    params <- append(params, out_filename)
    error <- call_os(command = "gdalwarp", args = params, dry_run = dry_run)
    if (error) {
        warning("Failed call to gdalwarp")
        return(NA_character_)
    }
    return(out_filename)
}