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add exclusion mask for sits_smooth #1241

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merged 3 commits into from
Nov 19, 2024
Merged

add exclusion mask for sits_smooth #1241

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6db9048
add exclusion mask for sits_smooth
M3nin0 Nov 19, 2024
a7a63c6
merge with dev branch
M3nin0 Nov 19, 2024
5d0a302
update sits_smooth docs
M3nin0 Nov 19, 2024
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25 changes: 25 additions & 0 deletions R/api_smooth.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
band,
block,
overlap,
exclusion_mask,
smooth_fn,
output_dir,
version) {
Expand All @@ -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
Expand Down Expand Up @@ -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
}
Expand Down Expand Up @@ -124,6 +147,7 @@
window_size,
neigh_fraction,
smoothness,
exclusion_mask,
multicores,
memsize,
output_dir,
Expand All @@ -146,6 +170,7 @@
band = "bayes",
block = block,
overlap = overlap,
exclusion_mask = exclusion_mask,
smooth_fn = smooth_fn,
output_dir = output_dir,
version = version
Expand Down
10 changes: 10 additions & 0 deletions R/sits_smooth.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand All @@ -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,
Expand All @@ -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,
Expand All @@ -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,
Expand All @@ -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,
Expand Down
9 changes: 9 additions & 0 deletions man/sits_smooth.Rd
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