whitebox v2.4.2

.gitignore

@@ -16,6 +16,7 @@ whiteboxR.Rproj
 *.shx
 *.prj
 *.dbf
+*.cpg
 *.tif
 settings.json
 __MACOSX

DESCRIPTION

@@ -1,16 +1,16 @@
 Package: whitebox
 Type: Package
 Title: 'WhiteboxTools' R Frontend
-Version: 2.4.1
+Version: 2.4.2
 Description: An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.
 Authors@R: c(person("Qiusheng", "Wu", email = "giswqs@gmail.com", role = c("aut")),
-             person("Andrew", "Brown", email = "brown.andrewg@gmail.com", role = c("ctb", "cre")))
+             person("Andrew", "Brown", email = "brown.andrewg@gmail.com", role = c("aut", "cre"), comment=c(ORCID="0000-0002-4565-533X")))
 Maintainer: Andrew Brown <brown.andrewg@gmail.com>
 License: MIT + file LICENSE
 SystemRequirements: WhiteboxTools (https://github.com/jblindsay/whitebox-tools/releases/latest)
 Encoding: UTF-8
 Language: en-US
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)
 URL: https://whiteboxr.gishub.org/, https://github.com/opengeos/whiteboxR
 BugReports: https://github.com/opengeos/whiteboxR/issues

NEWS.md

@@ -1,3 +1,17 @@
+# whitebox 2.4.2
+
+ * `wbt_source()`: now accepts `tmpdir` argument which defaults to `tempdir()` (not `getwd()` or `wbt_wd()`) that is used for storing the intermediate shapefiles needed for WhiteboxTools
+
+   * Also, the pattern for temporary file names is now customizable via `pattern` argument
+
+ * Bug fixes for `wbt_source()`:
+
+   * No longer writes temporary intermediate shapefiles to the working directory when passed a non-shapefile vector data source. 
+
+      * The temporary directory is used by default, unless new `tmpdir` argument is specified. This could be a breaking change if you were relying on the temporary files to be present in the WhiteboxTools working directory. Specify `tmpdir` in call to `wbt_source()` to make old behavior explicit.
+
+   * Properly uses `layer` argument for data sources (e.g. GPKG) that may contain multiple vector layers of interest (thanks to @mps9506 for reporting; #132)
+
 # whitebox 2.4.1
 
  * Rebuilt `wbttools` and `wbttoolparameters` with WhiteboxTools v2.4.0

R/wbt_source.R

@@ -1,52 +1,116 @@
 #' Initialize an R object containing spatial data for use by WhiteboxTools
 #'
-#' @param x A terra SpatVector or sf object, or a path to a file that can be read as a SpatVectorProxy
+#' @param x A terra SpatVector or sf object (in memory) or a path to a file that
+#'   can be read as a SpatVectorProxy. Or a memory or file-based SpatRaster.
+#'   SpatRaster object. When `x` has multiple layers/bands, the first layer is
+#'   used by default; use the \code{layer} argument to select a specific
+#'   layer/band.
 #' @param dsn Data source path / file name
-#' @param layer Data layer
-#' @param force Force write of vector data to file? Default: FALSE (only write if file does not exist)
-#' @param ... Additional arguments passed to `terra::writeVector()` or `sf::st_write()`
+#' @param layer Data layer. For vectors, `layer` is interpreted as a layer
+#'   name (character); for rasters, `layer` is interpreted as a band index or
+#'   name (integer OR character)
+#' @param tmpdir Directory to write temporary ESRI Shapefiles for vector input
+#'   in memory or otherwise not already in shapefile. Default: `tempdir()`
+#' @param pattern Character vector giving the initial part of the temporary file
+#'   name
+#' @param force Force write of vector data to file? Default: FALSE (only write
+#'   if file does not exist and new file is needed)
 #' @param verbose Print information about data source and contents?
-#' @return An R object with attributes `wbt_dsn` and `wbt_layer` set as needed to support reading and writing R objects from file by WhiteboxTools.
+#' @param ... Additional arguments passed to `terra::writeVector()` or
+#'   `sf::st_write()`, or `terra::writeRaster` (for rasters).
+#' @return An R object (SpatRaster, SpatVector, SpatVectorProxy, sf) with
+#'   attributes `wbt_dsn` and `wbt_layer` set as needed to support reading and
+#'   writing R objects from file by WhiteboxTools.
 #' @keywords General
 #' @export
 wbt_source <- function(x,
                        dsn = NULL,
                        layer = NULL,
                        force = FALSE,
+                       tmpdir = tempdir(),
+                       pattern = "wbt",
                        verbose = wbt_verbose(),
                        ...) {
 
-  if (!requireNamespace("terra")) {
-    stop("package `terra` is required to convert vector sources to `wbt()`-compatible SpatVectorProxy", call. = FALSE)
+  if (length(layer) > 1) {
+    stop("argument `layer` must have length 1 or 0 (NULL)", call. = FALSE)
+  }
+
+  .check_pkg_ns <- function(pkg) {
+    if (!requireNamespace(pkg)) {
+      stop("package `", pkg, "` is required to convert to `wbt()`-compatible data sources", call. = FALSE)
+    }
   }
 
   if (is.character(x)) {
     if (file.exists(x)) {
-      # convert to shapefile if needed
-      if (!grepl("\\.shp$", x)) {
-        xp <- paste0(basename(x), "_", basename(tempfile()), ".shp")
-        fp <- file.path(tempdir(), xp)
+      .check_pkg_ns("terra")
 
-        if (!requireNamespace("terra")) {
-          stop("package `terra` is required to convert non-Shapefile vector sources to Shapefile")
-        }
+      # convert to shapefile if needed
+      x2 <- try(terra::vect(x, layer = ifelse(is.null(layer), "", layer), proxy = TRUE), silent = TRUE)
+      fp <- file.path(tmpdir, paste0(basename(x), "_", basename(tempfile(pattern = pattern))))
+      if (!inherits(x2, 'try-error') && !grepl("\\.shp$", x, ignore.case = TRUE)) {
+        fp <- paste0(fp, ".shp")
 
-        x2 <- terra::vect(x, layer = ifelse(is.null(layer), "", layer))
-        if (terra::writeVector(x2, fp)) {
+        if (terra::writeVector(terra::query(x2), fp)) {
           x <- fp
         } else {
           stop("Failed to convert `x` (", x, ") to Shapefile.")
         }
+      } else if (inherits(x2, 'try-error')) {
+        if (!grepl("\\.tiff?$", x, ignore.case = TRUE) || length(layer) > 0) {
+          # try reading a raster file and writing to geotiff
+          fp <- paste0(fp, ".tif")
+          if (length(layer) > 0) {
+            x2 <- terra::rast(x, lyrs = layer[1])
+          } else {
+            x2 <- terra::rast(x)
+          }
+          if (terra::writeRaster(x2, fp)) {
+            x <- fp
+          } else {
+            stop("Failed to convert `x` (", x, ") to GeoTIFF")
+          }
+        }
+        x <- terra::rast(x)
+      }
+
+      if (!inherits(x, 'SpatRaster')) {
+        # a SpatVectorProxy allows us to get some basic info without loading the whole file
+        x <- terra::vect(x, proxy = TRUE)
+      }
+
+      if (is.character(x) && !file.exists(x)) {
+        stop("File (", x, ") does not exist")
+      }
+
+      if (!inherits(x, c("SpatRaster", "SpatVectorProxy"))) {
+        stop("Unhandled input object type")
       }
 
-      # a SpatVectorProxy allows us to get some basic info without loading the whole file
-      x <- terra::vect(x, proxy = TRUE)
       attr(x, 'wbt_dsn') <- terra::sources(x)
       attr(x, 'wbt_layer') <- layer
       return(x)
     }
   }
 
+  ext <- ".shp"
+  if (inherits(x, c('SpatRaster', 'RasterLayer',
+                    'RasterStack', 'RasterBrick'))) {
+    .check_pkg_ns("terra")
+    if (!inherits(x, 'SpatRaster')) {
+      x <- terra::rast(x)
+    }
+    ext <- ".tif"
+    src <- terra::sources(x)
+    if (length(src) > 0 && any(nzchar(src))) {
+      if (length(src) > 1) {
+        message("Object 'x' has multiple source files; using first non-empty source path")
+      }
+      dsn <- src[which(nzchar(src))[1]]
+    }
+  }
+
   # NULL dsn (TODO: GDAL-supported dsn not supported by WBT)
   if (is.null(dsn)) {
     # if (gpkg) {
@@ -57,35 +121,49 @@ wbt_source <- function(x,
     # only supported vector format is the ESRI Shapefile.
     # TODO: dbf limitations? use alternate wbt/gdal common format?
     if (!is.null(layer)) {
-      bn <- layer
-    } else bn <- "file"
-    wd <- wbt_wd()
-    if (wd == "")
-      wd <- getwd()
-    ext <- ".shp"
-    if (inherits(x, 'SpatRaster') ||
-        inherits(x, 'RasterLayer') ||
-        inherits(x, 'RasterStack') ||
-        inherits(x, 'RasterBrick')) {
-      ext <- ".tif"
+      bn <- paste0(pattern, "_", layer)
+    } else {
+      bn <- pattern
     }
-    dsn <- tempfile(pattern = bn, tmpdir = wd, fileext = ext)
+    dsn <- tempfile(pattern = bn, tmpdir = tmpdir, fileext = ext)
     # }
   }
 
   if (!file.exists(dsn) || force) {
-    # convert less common types to core types
-    if (inherits(x, 'sfc') || inherits(x, 'Spatial')) {
-      x <- sf::st_as_sf(x)
-    }
 
-    # write to file/db
-    if (inherits(x, 'SpatVector')) {
-      terra::writeVector(x, filename = dsn, layer = layer, ...)
-    } else if (inherits(x, 'sf')) {
-      sf::st_write(x, dsn = dsn, layer = layer, quiet = !verbose, ...)
-    } else if (inherits(x, 'SpatRaster')) {
-      terra::writeRaster(x, filename = dsn)
+      # write to file/db
+    if (inherits(x, c('SpatVector', 'SpatVectorProxy', 'SpatRaster'))) {
+      .check_pkg_ns("terra")
+      if (inherits(x, 'SpatVectorProxy')) {
+        x <- terra::query(x)
+      }
+      if (inherits(x, 'SpatVector')) {
+        terra::writeVector(x,
+                           filename = dsn,
+                           layer = layer,
+                           overwrite = force,
+                           ...)
+      } else if (inherits(x, 'SpatRaster')) {
+        terra::writeRaster(x, filename = dsn, overwrite = force, ...)
+      }
+    } else {
+      .check_pkg_ns("sf")
+
+      # convert less common types to core types
+      if (inherits(x, 'sfc') || inherits(x, 'Spatial')) {
+        x <- sf::st_as_sf(x)
+      }
+
+      if (inherits(x, 'sf')) {
+        sf::st_write(
+          x,
+          dsn = dsn,
+          layer = layer,
+          quiet = !verbose,
+          delete_dsn = force,
+          ...
+        )
+      }
     }
   }
 

inst/CITATION

@@ -4,10 +4,10 @@ bibentry(
   bibtype = "Manual",
   title = "'whitebox': 'WhiteboxTools' R Frontend",
   author = "Qiusheng Wu, Andrew Brown",
-  note = "R package version 2.2.0",
+  note = "R package version 2.4.2",
   url = "https://CRAN.R-project.org/package=whitebox",
-  year = "2022",
-  textVersion = "Wu, Q., Brown, A. (2022). whitebox: 'WhiteboxTools' R Frontend. R package version 2.2.0. <https://CRAN.R-project.org/package=whitebox>"
+  year = "2025",
+  textVersion = "Wu, Q., Brown, A. (2025). whitebox: 'WhiteboxTools' R Frontend. R package version 2.4.2. <https://CRAN.R-project.org/package=whitebox>"
 )
 
 bibentry(

inst/WORDLIST

@@ -8,11 +8,9 @@ BACKTRACE
 BreachDepressions
 Breakline
 CMD
-CRS
 CamelCase
 Ceil
 Centre
-Centroid
 Christoph
 ClassificationError
 Colour
@@ -52,6 +50,7 @@ François
 Frontend
 GAT
 GDAL
+GPKG
 GeoKey
 GeoPackage
 GeoTIFF
@@ -77,7 +76,6 @@ InPlaceAdd
 InPlaceSubtract
 InverseMultiQuadric
 Isobasins
-JSON
 JandR
 Jens
 Jenson
@@ -108,6 +106,7 @@ NDI
 NoData
 Northness
 Num
+ORCID
 OSAVI
 OptionList
 POLYLINE
@@ -136,7 +135,6 @@ Rasterizes
 Reclass
 Reinitializes
 RemoveSpurs
-Rescale
 Rgb
 Robinne
 Rosenfeld
@@ -206,7 +204,6 @@ cageo
 centerlines
 centred
 centres
-centroid
 cls
 codecov
 colour
@@ -219,7 +216,6 @@ darboux
 decorrelation
 depressionless
 dev
-differencing
 dinf
 directionality
 doi
@@ -282,7 +278,6 @@ lengthed
 lidar
 liu
 lq
-macOS
 magrittr
 medoid
 meso
@@ -303,12 +298,10 @@ neighbouring
 neighbours
 nn
 nodata
-normals
 num
 nw
 olympic
 parallelepiped
-parallelize
 parsable
 pearson
 planchon
@@ -318,21 +311,17 @@ pre
 pts
 quant
 quartic
-quartile
 ransac
 raster's
-rasters
 rbf
 reclass
-repo
 rgb
 rgdal
 sca
 scattergram
 se
 shapetype
 sibson
-sigmoid
 sigmoidal
 silverman
 sinh
@@ -358,7 +347,6 @@ vals
 viewshed
 viewsheds
 viridi
-viridis
 wang
 watershedding
 wb