#' @title frg_def_files
#' @description Helper function used to define required file names and folders
#' @param opts initial options list created by frg_main
#' @return `opts` list containing all main file names and folders
#' @rdname frg_def_files
#' @export
#' @author Lorenzo Busetto, phD (2017) <lbusett@gmail.com>
#' @importFrom tools file_path_sans_ext
#'
frg_def_files <- function(opts) {
opts[["orig_shapefile"]] <- opts$orig_shapefile
# Set Processing log file
opts[["outfile_conn"]] <- file.path(opts$out_dir,
paste("Process_Summary", ".txt", sep = ""))
# Set Dir for storing intermediate processing results
opts[["intermed_dir"]] <- file.path(opts$out_dir, "Intermed_Proc")
# Set Dir for storing EFFIS summaries results
opts[["summary_dir"]] <- file.path(opts$out_dir, "Summaries_for_EFFIS")
# Define Dir were Scaled Indexes time series will be saved
opts[["scaled_dir"]] <- file.path(opts$out_dir, "Scaled_Indexes")
opts[["out_origpath"]] <- file.path(opts$mod_dir, "Originals")
opts[["roi_file"]] <- file.path(
opts$intermed_dir,
"ENVI_ROI",
paste0(file_path_sans_ext(basename(opts$orig_shapefile)), ".ROI")
)
# Define Mask file name and create Dir for mask storing if needed ----
opts[["firemask_file"]] <- file.path(
opts$intermed_dir, "ENVI_Mask",
paste0(file_path_sans_ext(basename(opts$roi_file)),
"_ENVI_Mask"))
# Define Mask file name and create Dir for mask storing if needed ----
opts[["firemask_file_er"]] <- file.path(
opts$intermed_dir, "ENVI_Mask",
paste0(file_path_sans_ext(basename(opts$roi_file)),
"_ENVI_Mask_Eroded"))
opts[["out_dir_extrsvi"]] <- file.path(opts$out_dir,
"Med_SNDVI/TS_Extraction")
opts[["ts_file_single"]] <- file.path(opts$out_dir_extrsvi,
paste0("Med_SNDVI_ts_single"))
opts[["ts_file_multiple"]] <- file.path(opts$out_dir_extrsvi,
paste0("Med_SNDVI_ts_multiple"))
opts[["out_dir_stats"]] <- file.path(opts$out_dir, "Med_SNDVI/Stat_Analysis")
opts[["ts_filename"]] <- file.path(
opts$scaled_dir, "Med_SNDVI",
paste0("Med_SNDVI", "_", opts$start_year, "_", opts$end_year, "_META")
)
# Set Basename for statistics output file
opts[["stats_file_single"]] <- file.path(opts$out_dir_stats,
"Burned_Once",
basename(opts$ts_file_single))
opts[["stats_file_multiple"]] <- file.path(opts$out_dir_stats,
"Burned_Multiple",
basename(opts$ts_file_multiple))
# browser()
opts[["intermed_shapes_dir"]] <- file.path(opts$intermed_dir, "Shapefiles/")
opts[["shapefile_single"]] = file.path(
opts$intermed_dir, "Shapefiles/",
paste0(basename(tools::file_path_sans_ext(opts$orig_shapefile)),
"_Single_Fires.shp")
)
opts[["shapefile_multiple"]] <- file.path(
opts$intermed_dir, "Shapefiles/",
paste0(basename(tools::file_path_sans_ext(opts$orig_shapefile)),
"_Multiple_Fires.shp")
)
opts[["lut_file_multiple"]] <- file.path(
opts$intermed_dir, "Shapefiles/",
paste0(basename(tools::file_path_sans_ext(opts$orig_shapefile)),
"_Intersect_LUT_csv.csv")
)
opts[["out_shape_dir"]] <- file.path(opts$summary_dir, "Shapefiles")
# Create all required Dirs (if needed) ----
dir.create(opts$scaled_dir, recursive = TRUE, showWarnings = FALSE)
dir.create(opts$intermed_dir, recursive = TRUE, showWarnings = FALSE)
dir.create(opts$summary_dir, recursive = TRUE, showWarnings = FALSE)
dir.create(opts$out_origpath, recursive = TRUE, showWarnings = FALSE)
dir.create(dirname(opts$roi_file), recursive = TRUE, showWarnings = FALSE)
dir.create(dirname(opts$firemask_file), recursive = TRUE, showWarnings = FALSE)
dir.create(dirname(opts$firemask_file_er), recursive = TRUE, showWarnings = FALSE)
dir.create(opts$out_dir_extrsvi, recursive = TRUE, showWarnings = FALSE)
dir.create(opts$out_dir_stats, recursive = TRUE, showWarnings = FALSE)
dir.create(dirname(opts$ts_file_single), recursive = TRUE, showWarnings = FALSE)
dir.create(dirname(opts$ts_file_multiple), recursive = TRUE, showWarnings = FALSE)
dir.create(dirname(opts$intermed_shapes_dir), recursive = TRUE, showWarnings = FALSE)
dir.create(dirname(opts[["stats_file_single"]]), recursive = TRUE, showWarnings = FALSE)
dir.create(dirname(opts[["stats_file_multiple"]]), recursive = TRUE, showWarnings = FALSE)
#Send back the updated `opts` list ----
return(opts)
}
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