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Merge pull request #1036 from OldLipe/feat/temp_seg
Re-introduces `sits_clean` function to SITS API
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,165 @@ | ||
| #' @title Cleans a classified map using a local window | ||
| #' | ||
| #' @name sits_clean | ||
| #' | ||
| #' @author Felipe Carvalho, \email{felipe.carvalho@@inpe.br} | ||
| #' | ||
| #' @description | ||
| #' Applies a modal function to clean up possible noisy pixels keeping | ||
| #' the most frequently values within the neighborhood. | ||
| #' In a tie, the first value of the vector is considered. | ||
| #' | ||
| #' @param cube Classified data cube (tibble of class "class_cube"). | ||
| #' @param window_size An odd integer representing the size of the | ||
| #' sliding window of the modal function (min = 1, max = 15). | ||
| #' @param memsize Memory available for classification in GB | ||
| #' (integer, min = 1, max = 16384). | ||
| #' @param multicores Number of cores to be used for classification | ||
| #' (integer, min = 1, max = 2048). | ||
| #' @param output_dir Valid directory for output file. | ||
| #' (character vector of length 1). | ||
| #' @param version Version of the output file | ||
| #' (character vector of length 1) | ||
| #' @param progress Logical: Show progress bar? | ||
| #' | ||
| #' @return A tibble with an classified map (class = "class_cube"). | ||
| #' | ||
| #' @examples | ||
| #' if (sits_run_examples()) { | ||
| #' rf_model <- sits_train(samples_modis_ndvi, ml_method = sits_rfor) | ||
| #' # create a data cube from local files | ||
| #' data_dir <- system.file("extdata/raster/mod13q1", package = "sits") | ||
| #' cube <- sits_cube( | ||
| #' source = "BDC", | ||
| #' collection = "MOD13Q1-6", | ||
| #' data_dir = data_dir | ||
| #' ) | ||
| #' # classify a data cube | ||
| #' probs_cube <- sits_classify( | ||
| #' data = cube, | ||
| #' ml_model = rf_model, | ||
| #' output_dir = tempdir() | ||
| #' ) | ||
| #' # label the probability cube | ||
| #' label_cube <- sits_label_classification( | ||
| #' probs_cube, | ||
| #' output_dir = tempdir() | ||
| #' ) | ||
| #' # apply a mode function in the labelled cube | ||
| #' clean_cube <- sits_clean( | ||
| #' cube = label_cube, | ||
| #' window_size = 5, | ||
| #' output_dir = tempdir(), | ||
| #' multicores = 1 | ||
| #' ) | ||
| #' } | ||
| #' | ||
| #' @export | ||
| sits_clean <- function(cube, window_size = 5L, memsize = 4L, | ||
| multicores = 2L, output_dir, version = "v1-clean", | ||
| progress = TRUE) { | ||
| # Precondition | ||
| # Check the cube is valid | ||
| .check_valid(cube) | ||
| UseMethod("sits_clean", cube) | ||
| } | ||
| #' @rdname sits_clean | ||
| #' @export | ||
| sits_clean.class_cube <- function(cube, window_size = 5L, memsize = 4L, | ||
| multicores = 2L, output_dir, | ||
| version = "v1-clean", progress = TRUE) { | ||
| # Preconditions | ||
| # Check cube has files | ||
| .check_cube_files(cube) | ||
| # Check window size | ||
| .check_window_size(window_size, min = 1, max = 15) | ||
| # Check memsize | ||
| .check_memsize(memsize, min = 1, max = 16384) | ||
| # Check multicores | ||
| .check_multicores(multicores, min = 1, max = 2048) | ||
| # Check output_dir | ||
| .check_output_dir(output_dir) | ||
| # Check version | ||
| .check_version(version) | ||
| # version is case-insensitive in sits | ||
| version <- tolower(version) | ||
| # Check progress | ||
| .check_progress(progress) | ||
|
|
||
| # Get input band | ||
| band <- .cube_bands(cube) | ||
| # image size | ||
| image_size <- .raster_size(.raster_open_rast(.tile_path(cube))) | ||
| # Overlapping pixels | ||
| overlap <- ceiling(window_size / 2) - 1 | ||
| # Check minimum memory needed to process one block | ||
| job_memsize <- .jobs_memsize( | ||
| job_size = .block_size(block = image_size, overlap = overlap), | ||
| npaths = 1, nbytes = 8, | ||
| proc_bloat = .conf("processing_bloat") | ||
| ) | ||
| # Update multicores parameter | ||
| multicores <- .jobs_max_multicores( | ||
| job_memsize = job_memsize, memsize = memsize, multicores = multicores | ||
| ) | ||
| # Prepare parallelization | ||
| .parallel_start(workers = multicores) | ||
| on.exit(.parallel_stop(), add = TRUE) | ||
|
|
||
| # Process each tile sequentially | ||
| clean_cube <- .cube_foreach_tile(cube, function(tile) { | ||
| # Process the data | ||
| clean_tile <- .clean_tile( | ||
| tile = tile, | ||
| block = image_size, | ||
| band = band, | ||
| window_size = window_size, | ||
| overlap = overlap, | ||
| output_dir = output_dir, | ||
| version = version | ||
| ) | ||
| return(clean_tile) | ||
| }) | ||
| # Update cube class | ||
| class(clean_cube) <- c("class_cube", class(clean_cube)) | ||
| # Return cleaned cube | ||
| return(clean_cube) | ||
| } | ||
|
|
||
| #' @rdname sits_clean | ||
| #' @export | ||
| sits_clean.raster_cube <- function(cube, window_size = 5L, memsize = 4L, | ||
| multicores = 2L, output_dir, | ||
| version = "v1-clean", progress = TRUE) { | ||
| stop("Input should be a classified cube") | ||
| return(cube) | ||
| } | ||
| #' @rdname sits_clean | ||
| #' @export | ||
| sits_clean.derived_cube <- function(cube, window_size = 5L, memsize = 4L, | ||
| multicores = 2L, output_dir, | ||
| version = "v1-clean", progress = TRUE) { | ||
| stop("Input should be a classified cube") | ||
| return(cube) | ||
| } | ||
| #' @rdname sits_clean | ||
| #' @export | ||
| sits_clean.tbl_df <- function(cube, window_size = 5L, memsize = 4L, | ||
| multicores = 2L, output_dir, | ||
| version = "v1-clean", progress = TRUE) { | ||
| cube <- tibble::as_tibble(cube) | ||
| if (all(.conf("sits_cube_cols") %in% colnames(cube))) { | ||
| cube <- .cube_find_class(cube) | ||
| } else | ||
| stop("Input should be a classified cube") | ||
| clean_cube <- sits_clean(cube, window_size, memsize, multicores, | ||
| output_dir, version, progress) | ||
| return(clean_cube) | ||
| } | ||
| #' @rdname sits_clean | ||
| #' @export | ||
| sits_clean.default <- function(cube, window_size = 5L, memsize = 4L, | ||
| multicores = 2L, output_dir, | ||
| version = "v1-clean", progress = TRUE) { | ||
| stop("Input should be a classified cube") | ||
| } |
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