fix conflicts

Author: OldLipe

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]'),

NAMESPACE

@@ -16,6 +16,8 @@ S3method(.band_rename,sits)
 S3method(.check_samples,default)
 S3method(.check_samples,sits)
 S3method(.check_samples,tbl_df)
+S3method(.cube_adjust_crs,"mpc_cube_sentinel-1-grd")
+S3method(.cube_adjust_crs,default)
 S3method(.cube_as_sf,default)
 S3method(.cube_as_sf,raster_cube)
 S3method(.cube_bands,default)
@@ -304,6 +306,7 @@ S3method(sits_combine_predictions,average)
 S3method(sits_combine_predictions,default)
 S3method(sits_combine_predictions,uncertainty)
 S3method(sits_cube,"mpc_cube_sentinel-1-grd")
+S3method(sits_cube,"mpc_cube_sentinel-1-rtc")
 S3method(sits_cube,default)
 S3method(sits_cube,local_cube)
 S3method(sits_cube,stac_cube)

R/api_apply.R

@@ -39,20 +39,21 @@
 #' @noRd
 #' @author Rolf Simoes, \email{rolf.simoes@@inpe.br}
 #'
-#' @param  feature      Subset of a data cube containing the input bands
-#'                      used in the expression
-#' @param  block        Individual block that will be processed
-#' @param  window_size  Size of the neighbourhood (if required)
-#' @param  normalized   A logical indicating if band is scaled
-#' @param  expr         Expression to be applied
-#' @param  out_band     Output band
-#' @param  in_bands     Input bands
-#' @param  overlap      Overlap between tiles (if required)
-#' @param  output_dir   Directory where image will be save
+#' @param  feature         Subset of a data cube containing the input bands
+#'                         used in the expression
+#' @param  block           Individual block that will be processed
+#' @param  window_size     Size of the neighbourhood (if required)
+#' @param  expr            Expression to be applied
+#' @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, expr, window_size, normalized,
-                           out_band, in_bands, overlap, output_dir) {
+#' @return                 A feature compose by a combination of tile and band.
+.apply_feature <- function(feature, block, window_size, expr,
+                           out_band, in_bands, overlap,
+                           normalized, output_dir) {
     # Output file
     out_file <- .file_eo_name(
         tile = feature, band = out_band,
@@ -77,6 +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
@@ -110,9 +119,6 @@
             )
         )
         # Prepare fractions to be saved
-        band_conf <- .tile_band_conf(
-            tile = feature, band = out_band, normalized = normalized
-        )
         offset <- .offset(band_conf)
         if (.has(offset) && offset != 0) {
             values <- values - offset
@@ -139,6 +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_cube.R

@@ -277,6 +277,24 @@ NULL
     crs <- .cube_crs(cube)
     return(crs)
 }
+#' @title Adjust crs of a data cube
+#' @keywords internal
+#' @noRd
+#' @name .cube_adjust_crs
+#' @param cube  data cube
+#' @return data cube with adjusted crs
+.cube_adjust_crs <- function(cube) {
+    UseMethod(".cube_adjust_crs", cube)
+}
+#' @export
+`.cube_adjust_crs.mpc_cube_sentinel-1-grd` <- function(cube) {
+    cube$crs <- NA
+    return(cube)
+}
+#' @export
+.cube_adjust_crs.default <- function(cube) {
+    return(cube)
+}
 #' @title Return the S3 class of the cube
 #' @name .cube_s3class
 #' @keywords internal

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
@@ -79,9 +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, normalized = TRUE
-        )
         offset <- .offset(band_conf)
         if (!is.null(offset) && offset != 0) {
             values <- values - offset
@@ -107,9 +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,
-        normalized = TRUE
+        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_plot_raster.R

@@ -51,7 +51,20 @@
         tile = tile,
         tmap_options = tmap_options
     )
-
+    if (!.has(.crs(tile))) {
+        temp <- tempfile(fileext = ".tif")
+        .gdal_warp(
+            file = temp,
+            base_files = bw_file,
+            params = list(
+                "-ts" = list(size[["xsize"]], size[["ysize"]]),
+                "-multi" = TRUE,
+                "-q" = TRUE,
+                "-overwrite" = FALSE
+            ),
+            quiet = TRUE)
+        bw_file <- temp
+    }
     # read file
     stars_obj <- stars::read_stars(
         bw_file,

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_source_mpc.R

@@ -99,7 +99,7 @@
 #' @param stac_query Query that follows the STAC protocol
 #' @param bands      Names of the bands to filter
 #' @param ...        Other parameters to be passed for specific types.
-#' @param orbit      Name of the orbit (e.g. "Ascending" or "Descending")
+#' @param orbit      Name of the orbit (e.g. "ascending" or "descending")
 #' @param tiles      Selected tiles (optional)
 #' @param platform   Satellite platform (optional).
 #' @return An object referring the images of a sits cube.
@@ -108,7 +108,7 @@
         source,
         collection,
         bands, ...,
-        orbit = "Descending",
+        orbit = "descending",
         start_date = NULL,
         end_date = NULL,
         dry_run = TRUE) {
@@ -130,7 +130,7 @@
             "ymin" = -10.1973,
             "xmax" = -50.410,
             "ymax" = -10.1510,
-            "crs"  = "EPSG:4386"
+            "crs"  = "EPSG:4326"
         ),
         start_date = start_date,
         end_date = end_date,
@@ -201,6 +201,26 @@
     }
     return(invisible(NULL))
 }
+
+`.source_collection_access_test.mpc_cube_sentinel-1-rtc` <- function(
+        source,
+        collection,
+        bands, ...,
+        orbit = "descending",
+        start_date = NULL,
+        end_date = NULL,
+        dry_run = TRUE) {
+
+    `.source_collection_access_test.mpc_cube_sentinel-1-grd`(
+        source = source,
+        collection = collection,
+        bands = bands, ...,
+        orbit = orbit,
+        start_date = start_date,
+        end_date = end_date,
+        dry_run = dry_run
+    )
+}
 #' @title Get bbox from file info
 #' @keywords internal
 #' @noRd
@@ -237,6 +257,15 @@
     bbox <- c(xmin = xmin, ymin = ymin, xmax = xmax, ymax = ymax)
     return(bbox)
 }
+`.source_tile_get_bbox.mpc_cube_sentinel-1-rtc` <- function(source,
+                                                            file_info, ...,
+                                                            collection = NULL) {
+    `.source_tile_get_bbox.mpc_cube_sentinel-1-grd`(
+        source = source,
+        file_info = file_info, ...,
+        collection = collection
+    )
+}
 #' @keywords internal
 #' @noRd
 #' @export
@@ -304,7 +333,19 @@
     )
     return(items_info)
 }
-
+`.source_items_new.mpc_cube_sentinel-1-rtc` <- function(source,
+                                                        collection,
+                                                        stac_query, ...,
+                                                        tiles = NULL,
+                                                        orbit = "ascending") {
+    `.source_items_new.mpc_cube_sentinel-1-grd`(
+        source = source,
+        collection = collection,
+        stac_query = stac_query, ...,
+        tiles = tiles,
+        orbit = orbit
+    )
+}
 #' @keywords internal
 #' @noRd
 #' @export
@@ -313,6 +354,15 @@
                                                          collection = NULL) {
     rep("NoTilingSystem", rstac::items_length(items))
 }
+`.source_items_tile.mpc_cube_sentinel-1-rtc` <- function(source,
+                                                         items, ...,
+                                                         collection = NULL) {
+    `.source_items_tile.mpc_cube_sentinel-1-grd`(
+        source = source,
+        items = items, ...,
+        collection = collection
+    )
+}
 
 #' @keywords internal
 #' @noRd

R/api_tile.R

@@ -536,29 +536,22 @@ NULL
     UseMethod(".tile_band_conf", tile)
 }
 #' @export
-.tile_band_conf.eo_cube <- function(tile, band, ..., normalized = FALSE) {
-    conf_band <- .conf_eo_band(
+.tile_band_conf.eo_cube <- function(tile, band) {
+    band_conf <- .conf_eo_band(
         source = .tile_source(tile), collection = .tile_collection(tile),
         band = band[[1]]
     )
-    if (.has(conf_band)) {
-        return(conf_band)
-    }
-    # 1ft attempt => case band is normalized
-    if (normalized) {
-        return(.conf("default_values", "eo_cube", "INT2S"))
-    }
-    # 2nd attempt => verify raster data type
+    if (.has(band_conf))
+        return(band_conf)
+
     if (band %in% .tile_bands(tile)) {
-        # Get the first tile path
         band_path <- .tile_path(tile, band)
-        # Get the raster data type
-        data_type <- .raster_datatype(.raster_open_rast(band_path))
-        return(.conf("default_values", "eo_cube", data_type))
+        rast <- terra::rast(band_path)
+        data_type <- terra::datatype(rast)
+        band_conf <- .conf("default_values", data_type)
+        return(band_conf)
     }
-    # Otherwise write band in FLT4S
-    return(.conf("default_values", "eo_cube", "FLT4S"))
-
+    return(NULL)
 }
 #' @export
 .tile_band_conf.derived_cube <- function(tile, band, ...) {
@@ -1070,21 +1063,18 @@ 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 normalized A logical indicating if band is normalized.
+#' @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,
-                                  multicores, update_bbox, normalized = FALSE) {
+.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, normalized = normalized
-    )
     # Create a template raster based on the first image of the tile
     .raster_merge_blocks(
         out_files = files,