version 1.5.0

Author: gilbertocamara

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sits
 Type: Package
-Version: 1.4.2-3
+Version: 1.5.0
 Title: Satellite Image Time Series Analysis for Earth Observation Data Cubes
 Authors@R: c(person('Rolf', 'Simoes', role = c('aut'), email = '[email protected]'),
              person('Gilberto', 'Camara', role = c('aut', 'cre'), email = '[email protected]'),

R/api_apply.R

@@ -47,11 +47,13 @@
 #' @param  out_band        Output band
 #' @param  in_bands        Input bands
 #' @param  overlap         Overlap between tiles (if required)
+#' @param  normalized      Produce normalized band?
 #' @param  output_dir      Directory where image will be save
 #'
 #' @return                 A feature compose by a combination of tile and band.
 .apply_feature <- function(feature, block, window_size, expr,
-                           out_band, in_bands, overlap, output_dir) {
+                           out_band, in_bands, overlap,
+                           normalized, output_dir) {
     # Output file
     out_file <- .file_eo_name(
         tile = feature, band = out_band,
@@ -76,6 +78,14 @@
     chunks <- .tile_chunks_create(
         tile = feature, overlap = overlap, block = block
     )
+    # Get band configuration
+    band_conf <- .tile_band_conf(tile = feature, band = out_band)
+    if (!.has(band_conf)) {
+        if (normalized)
+            band_conf <- .conf("default_values", "INT2S")
+        else
+            band_conf <- .conf("default_values", "FLT4S")
+    }
     # Process jobs sequentially
     block_files <- .jobs_map_sequential(chunks, function(chunk) {
         # Get job block
@@ -109,7 +119,6 @@
             )
         )
         # Prepare fractions to be saved
-        band_conf <- .tile_band_conf(tile = feature, band = out_band)
         offset <- .offset(band_conf)
         if (.has(offset) && offset != 0) {
             values <- values - offset
@@ -136,6 +145,7 @@
     band_tile <- .tile_eo_merge_blocks(
         files = out_file,
         bands = out_band,
+        band_conf = band_conf,
         base_tile = feature,
         block_files = block_files,
         multicores = 1,

R/api_conf.R

@@ -939,10 +939,7 @@ NULL
     band <- .band_eo(band)
     # Return a default value if band does not exists in config
     if (!.conf_eo_band_exists(source, collection, band)) {
-        if (band %in% .conf_names("default_values", "eo_cube")) {
-            return(.conf("default_values", "eo_cube", band))
-        }
-        return(.conf("default_values", "eo_cube", "default"))
+        return(NULL)
     }
     # Get band config value and return it
     .conf("sources", source, "collections", collection, "bands", band)

R/api_mixture_model.R

@@ -58,6 +58,8 @@
     }
     # Remove remaining incomplete fractions files
     unlink(out_files)
+    # Get band configuration
+    band_conf <- .conf("default_values", "INT2S")
     # Create chunks as jobs
     chunks <- .tile_chunks_create(tile = feature, overlap = 0, block = block)
     # Process jobs sequentially
@@ -79,7 +81,6 @@
         # Apply the non-negative least squares solver
         values <- mixture_fn(values = as.matrix(values))
         # Prepare fractions to be saved
-        band_conf <- .tile_band_conf(tile = feature, band = out_fracs)
         offset <- .offset(band_conf)
         if (!is.null(offset) && offset != 0) {
             values <- values - offset
@@ -105,8 +106,13 @@
     })
     # Merge blocks into a new eo_cube tile feature
     fracs_feature <- .tile_eo_merge_blocks(
-        files = out_files, bands = out_fracs, base_tile = feature,
-        block_files = block_files, multicores = 1, update_bbox = FALSE
+        files = out_files,
+        bands = out_fracs,
+        band_conf = band_conf,
+        base_tile = feature,
+        block_files = block_files,
+        multicores = 1,
+        update_bbox = FALSE
     )
     # Return a eo_cube tile feature
     fracs_feature

R/api_reduce.R

@@ -36,6 +36,8 @@
         in_bands <- c(in_bands, .band_cloud())
     }
     tile <- .tile_filter_bands(tile, in_bands)
+    # Get band configuration
+    band_conf <- .conf("default_values", "INT2S")
     # Process jobs in parallel
     block_files <- .jobs_map_parallel_chr(chunks, function(chunk) {
         # Get job block
@@ -69,7 +71,6 @@
             enclos = .temp_functions()
         )
         # Prepare fractions to be saved
-        band_conf <- .tile_band_conf(tile = tile, band = out_band)
         offset <- .offset(band_conf)
         if (.has(offset) && offset != 0) {
             values <- values - offset
@@ -97,6 +98,7 @@
     band_tile <- .tile_eo_merge_blocks(
         files = out_file,
         bands = out_band,
+        band_conf = band_conf,
         base_tile = tile,
         block_files = block_files,
         multicores = 1,

R/api_smooth.R

@@ -1,5 +1,5 @@
 #' @title Smooth a tile
-#' @name .apply_feature
+#' @name .smooth_tile
 #' @keywords internal
 #' @noRd
 #' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}

R/api_tile.R

@@ -535,10 +535,21 @@ NULL
 }
 #' @export
 .tile_band_conf.eo_cube <- function(tile, band) {
-    .conf_eo_band(
+    band_conf <- .conf_eo_band(
         source = .tile_source(tile), collection = .tile_collection(tile),
         band = band[[1]]
     )
+    if (.has(band_conf))
+        return(band_conf)
+
+    if (band %in% .tile_bands(tile)) {
+        band_path <- .tile_path(tile, band)
+        rast <- terra::rast(band_path)
+        data_type <- terra::datatype(rast)
+        band_conf <- .conf("default_values", data_type)
+        return(band_conf)
+    }
+    return(NULL)
 }
 #' @export
 .tile_band_conf.derived_cube <- function(tile, band) {
@@ -1050,18 +1061,18 @@ NULL
 #' @name .tile_eo_merge_blocks
 #' @keywords internal
 #' @noRd
-#' @param files files to be merged
-#' @param bands bands to be used in the files
-#' @param base_tile  reference tile used in the operation
-#' @param block_files files associated with the the blocks
-#' @param multicores  multicores for processing
-#' @param update_bbox  should bbox be updated?
+#' @param files         Files to be merged
+#' @param bands         Bands to be merged
+#' @param band_conf     Band confuguration
+#' @param base_tile     Reference tile used in the operation
+#' @param block_files   Files associated with the the blocks
+#' @param multicores    Multicores for processing
+#' @param update_bbox   Should bbox be updated?
 #' @return an EO tile with merged blocks
-.tile_eo_merge_blocks <- function(files, bands, base_tile, block_files,
+.tile_eo_merge_blocks <- function(files, bands, band_conf,
+                                  base_tile, block_files,
                                   multicores, update_bbox) {
     base_tile <- .tile(base_tile)
-    # Get conf band
-    band_conf <- .tile_band_conf(tile = base_tile, band = bands)
     # Create a template raster based on the first image of the tile
     .raster_merge_blocks(
         out_files = files,

R/sits_apply.R

@@ -20,6 +20,7 @@
 #' @param memsize       Memory available for classification (in GB).
 #' @param multicores    Number of cores to be used for classification.
 #' @param output_dir    Directory where files will be saved.
+#' @param normalized    Produce normalized band?
 #' @param progress      Show progress bar?
 #' @param ...           Named expressions to be evaluated (see details).
 #'
@@ -116,6 +117,7 @@ sits_apply.raster_cube <- function(data, ...,
                                    window_size = 3L,
                                    memsize = 4L,
                                    multicores = 2L,
+                                   normalized = TRUE,
                                    output_dir,
                                    progress = FALSE) {
     # Check cube
@@ -182,6 +184,7 @@ sits_apply.raster_cube <- function(data, ...,
             out_band = out_band,
             in_bands = in_bands,
             overlap = overlap,
+            normalized = normalized,
             output_dir = output_dir
         )
         return(output_feature)

inst/extdata/config_internals.yml

@@ -126,20 +126,6 @@ default_values       :
         offset_value : 0
         scale_factor : 1
 
-    NDVI             :
-                   <<: *conf_default_int2s
-
-    EVI              :
-                   <<: *conf_default_int2s
-
-    eo_cube          :
-        data_type    : "INT2S"
-        missing_value: -32768
-        minimum_value: -10000
-        maximum_value: 10000
-        offset_value : 0
-        scale_factor : 0.0001
-
 # Derived cube definitions
 derived_cube         :
     probs_cube       :

man/sits_apply.Rd

@@ -44,7 +44,7 @@ test_that("EVI generation", {
 
     gc_cube_new <- sits_apply(gc_cube,
         EVI2 = 2.5 * (B8A - B05) / (B8A + 2.4 * B05 + 1),
-        multicores = 2,
+        multicores = 1,
         output_dir = dir_images
     )
 
@@ -100,7 +100,8 @@ test_that("EVI generation", {
     csv_file <- paste0(tempdir(), "/csv_gc_cube.csv")
     write.csv(csv_tb, file = csv_file)
 
-    evi_tibble <- sits_get_data(gc_cube_new, csv_file, progress = FALSE)
+    evi_tibble <- sits_get_data(gc_cube_new, csv_file, multicores = 1,
+                                progress = FALSE)
     evi_tibble_2 <- sits_apply(
         evi_tibble,
         EVI2_NEW = 2.5 * (B8A - B05) / (B8A + 2.4 * B05 + 1)