Merge pull request #1241 from M3nin0/sits-dev

add exclusion mask for sits_smooth

R/api_smooth.R

@@ -16,6 +16,7 @@
                          band,
                          block,
                          overlap,
+                         exclusion_mask,
                          smooth_fn,
                          output_dir,
                          version) {
@@ -39,6 +40,19 @@
     }
     # Create chunks as jobs
     chunks <- .tile_chunks_create(tile = tile, overlap = overlap, block = block)
+    # Calculate exclusion mask
+    if (.has(exclusion_mask)) {
+        # Remove chunks within the exclusion mask
+        chunks <- .chunks_filter_mask(
+            chunks = chunks,
+            mask = exclusion_mask
+        )
+
+        exclusion_mask <- .chunks_crop_mask(
+            chunks = chunks,
+            mask = exclusion_mask
+        )
+    }
     # Process jobs in parallel
     block_files <- .jobs_map_parallel_chr(chunks, function(chunk) {
         # Job block
@@ -96,6 +110,15 @@
         multicores = .jobs_multicores(),
         update_bbox = FALSE
     )
+    # Exclude masked areas
+    probs_tile <- .crop(
+        cube = probs_tile,
+        roi = exclusion_mask,
+        output_dir = output_dir,
+        multicores = 1,
+        overwrite = TRUE,
+        progress = FALSE
+    )
     # Return probs tile
     probs_tile
 }
@@ -124,6 +147,7 @@
                     window_size,
                     neigh_fraction,
                     smoothness,
+                    exclusion_mask,
                     multicores,
                     memsize,
                     output_dir,
@@ -146,6 +170,7 @@
             band = "bayes",
             block = block,
             overlap = overlap,
+            exclusion_mask = exclusion_mask,
             smooth_fn = smooth_fn,
             output_dir = output_dir,
             version = version

R/sits_smooth.R

@@ -18,6 +18,9 @@
 #' @param  smoothness        Estimated variance of logit of class probabilities
 #'                           (Bayesian smoothing parameter)
 #'                           (integer vector or scalar, min = 1, max = 200).
+#' @param  exclusion_mask    Areas to be excluded from the classification
+#'                           process. It can be defined as a sf object or a
+#'                           shapefile.
 #' @param  memsize           Memory available for classification in GB
 #'                           (integer, min = 1, max = 16384).
 #' @param  multicores        Number of cores to be used for classification
@@ -63,6 +66,7 @@ sits_smooth <- function(cube,
                         window_size = 9L,
                         neigh_fraction = 0.5,
                         smoothness = 20L,
+                        exclusion_mask = NULL,
                         memsize = 4L,
                         multicores = 2L,
                         output_dir,
@@ -100,6 +104,7 @@ sits_smooth.probs_cube <- function(cube,
                                    window_size = 9L,
                                    neigh_fraction = 0.5,
                                    smoothness = 20L,
+                                   exclusion_mask = NULL,
                                    memsize = 4L,
                                    multicores = 2L,
                                    output_dir,
@@ -147,6 +152,7 @@ sits_smooth.probs_cube <- function(cube,
         window_size = window_size,
         neigh_fraction = neigh_fraction,
         smoothness = smoothness,
+        exclusion_mask = exclusion_mask,
         multicores = multicores,
         memsize = memsize,
         output_dir = output_dir,
@@ -159,6 +165,7 @@ sits_smooth.raster_cube <- function(cube,
                                     window_size = 7L,
                                     neigh_fraction = 0.5,
                                     smoothness = 10L,
+                                    exclusion_mask = NULL,
                                     memsize = 4L,
                                     multicores = 2L,
                                     output_dir,
@@ -170,6 +177,7 @@ sits_smooth.raster_cube <- function(cube,
 sits_smooth.derived_cube <- function(cube, window_size = 7L,
                                      neigh_fraction = 0.5,
                                      smoothness = 10L,
+                                     exclusion_mask = NULL,
                                      memsize = 4L,
                                      multicores = 2L,
                                      output_dir,
@@ -182,6 +190,7 @@ sits_smooth.default <- function(cube,
                                 window_size = 7L,
                                 neigh_fraction = 0.5,
                                 smoothness = 10L,
+                                exclusion_mask = NULL,
                                 memsize = 4L,
                                 multicores = 2L,
                                 output_dir,
@@ -196,6 +205,7 @@ sits_smooth.default <- function(cube,
                         window_size = 7L,
                         neigh_fraction = 0.5,
                         smoothness = 10L,
+                        exclusion_mask = NULL,
                         memsize = 4L,
                         multicores = 2L,
                         output_dir,