Merge pull request #15 from giswqs/develop

Prep for v1.1.0

Author: giswqs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: whitebox
 Type: Package
 Title: 'WhiteboxTools' R Frontend
-Version: 1.0.2
+Version: 1.1.0
 Description: An R frontend of 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: person("Qiusheng", "Wu", email = "giswqs@gmail.com", role = c("aut", "cre"))
 Maintainer: Qiusheng Wu <giswqs@gmail.com>

NAMESPACE

@@ -29,6 +29,7 @@ export(wbt_block_maximum_gridding)
 export(wbt_block_minimum_gridding)
 export(wbt_boundary_shape_complexity)
 export(wbt_breach_depressions)
+export(wbt_breach_depressions_least_cost)
 export(wbt_breach_single_cell_pits)
 export(wbt_buffer_raster)
 export(wbt_burn_streams_at_roads)
@@ -37,6 +38,7 @@ export(wbt_centroid)
 export(wbt_centroid_vector)
 export(wbt_change_vector_analysis)
 export(wbt_circular_variance_of_aspect)
+export(wbt_classify_buildings_in_lidar)
 export(wbt_classify_overlap_points)
 export(wbt_clean_vector)
 export(wbt_clip)
@@ -121,6 +123,7 @@ export(wbt_feature_preserving_smoothing)
 export(wbt_fetch_analysis)
 export(wbt_fill_burn)
 export(wbt_fill_depressions)
+export(wbt_fill_depressions_wang_and_lui)
 export(wbt_fill_missing_data)
 export(wbt_fill_single_cell_pits)
 export(wbt_filter_lidar_classes)
@@ -161,6 +164,7 @@ export(wbt_idw_interpolation)
 export(wbt_ihs_to_rgb)
 export(wbt_image_autocorrelation)
 export(wbt_image_correlation)
+export(wbt_image_correlation_neighbourhood_analysis)
 export(wbt_image_regression)
 export(wbt_image_stack_profile)
 export(wbt_impoundment_size_index)
@@ -211,6 +215,7 @@ export(wbt_lidar_point_stats)
 export(wbt_lidar_ransac_planes)
 export(wbt_lidar_remove_duplicates)
 export(wbt_lidar_remove_outliers)
+export(wbt_lidar_rfb_interpolation)
 export(wbt_lidar_segmentation)
 export(wbt_lidar_segmentation_based_filter)
 export(wbt_lidar_thin)
@@ -275,6 +280,7 @@ export(wbt_multiscale_std_dev_normals)
 export(wbt_multiscale_std_dev_normals_signature)
 export(wbt_multiscale_topographic_position_image)
 export(wbt_narrowness_index)
+export(wbt_natural_neighbour_interpolation)
 export(wbt_nearest_neighbour_gridding)
 export(wbt_negate)
 export(wbt_new_raster_from_base)
@@ -411,6 +417,7 @@ export(wbt_two_sample_ks_test)
 export(wbt_union)
 export(wbt_unnest_basins)
 export(wbt_unsharp_masking)
+export(wbt_upslope_depression_storage)
 export(wbt_user_defined_weights_filter)
 export(wbt_vector_hex_binning)
 export(wbt_vector_lines_to_raster)

PY2R/scripts/gis_analysis.R

@@ -174,11 +174,12 @@ wbt_clump <- function(input, output, diag=TRUE, zero_back=FALSE, verbose_mode=FA
 #' @param field Input field name in attribute table.
 #' @param use_z Use the 'z' dimension of the Shapefile's geometry instead of an attribute field?.
 #' @param output Output vector polygon file.
+#' @param max_triangle_edge_length Optional maximum triangle edge length; triangles larger than this size will not be gridded.
 #' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
 #'
 #' @return Returns the tool text outputs.
 #' @export
-wbt_construct_vector_tin <- function(input, output, field=NULL, use_z=FALSE, verbose_mode=FALSE) {
+wbt_construct_vector_tin <- function(input, output, field=NULL, use_z=FALSE, max_triangle_edge_length=NULL, verbose_mode=FALSE) {
   wbt_init()
   args <- ""
   args <- paste(args, paste0("--input=", input))
@@ -189,6 +190,9 @@ wbt_construct_vector_tin <- function(input, output, field=NULL, use_z=FALSE, ver
   if (use_z) {
     args <- paste(args, "--use_z")
   }
+  if (!is.null(max_triangle_edge_length)) {
+    args <- paste(args, paste0("--max_triangle_edge_length=", max_triangle_edge_length))
+  }
   tool_name <- as.character(match.call()[[1]])
   wbt_run_tool(tool_name, args, verbose_mode)
 }
@@ -614,6 +618,46 @@ wbt_minimum_convex_hull <- function(input, output, features=TRUE, verbose_mode=F
 }
 
 
+#' Natural neighbour interpolation
+#'
+#' Creates a raster grid based on Sibson's natural neighbour method.
+#'
+#' @param input Input vector points file.
+#' @param field Input field name in attribute table.
+#' @param use_z Use the 'z' dimension of the Shapefile's geometry instead of an attribute field?.
+#' @param output Output raster file.
+#' @param cell_size Optionally specified cell size of output raster. Not used when base raster is specified.
+#' @param base Optionally specified input base raster file. Not used when a cell size is specified.
+#' @param clip Clip the data to the convex hull of the points?.
+#' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
+#'
+#' @return Returns the tool text outputs.
+#' @export
+wbt_natural_neighbour_interpolation <- function(input, output, field=NULL, use_z=FALSE, cell_size=NULL, base=NULL, clip=TRUE, verbose_mode=FALSE) {
+  wbt_init()
+  args <- ""
+  args <- paste(args, paste0("--input=", input))
+  args <- paste(args, paste0("--output=", output))
+  if (!is.null(field)) {
+    args <- paste(args, paste0("--field=", field))
+  }
+  if (use_z) {
+    args <- paste(args, "--use_z")
+  }
+  if (!is.null(cell_size)) {
+    args <- paste(args, paste0("--cell_size=", cell_size))
+  }
+  if (!is.null(base)) {
+    args <- paste(args, paste0("--base=", base))
+  }
+  if (clip) {
+    args <- paste(args, "--clip")
+  }
+  tool_name <- as.character(match.call()[[1]])
+  wbt_run_tool(tool_name, args, verbose_mode)
+}
+
+
 #' Nearest neighbour gridding
 #'
 #' Creates a raster grid based on a set of vector points and assigns grid values using the nearest neighbour.
@@ -899,22 +943,32 @@ wbt_smooth_vectors <- function(input, output, filter=3, verbose_mode=FALSE) {
 #' @param use_z Use the 'z' dimension of the Shapefile's geometry instead of an attribute field?.
 #' @param output Output raster file.
 #' @param resolution Output raster's grid resolution.
+#' @param base Optionally specified input base raster file. Not used when a cell size is specified.
+#' @param max_triangle_edge_length Optional maximum triangle edge length; triangles larger than this size will not be gridded.
 #' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
 #'
 #' @return Returns the tool text outputs.
 #' @export
-wbt_tin_gridding <- function(input, output, resolution, field=NULL, use_z=FALSE, verbose_mode=FALSE) {
+wbt_tin_gridding <- function(input, output, field=NULL, use_z=FALSE, resolution=NULL, base=NULL, max_triangle_edge_length=NULL, verbose_mode=FALSE) {
   wbt_init()
   args <- ""
   args <- paste(args, paste0("--input=", input))
   args <- paste(args, paste0("--output=", output))
-  args <- paste(args, paste0("--resolution=", resolution))
   if (!is.null(field)) {
     args <- paste(args, paste0("--field=", field))
   }
   if (use_z) {
     args <- paste(args, "--use_z")
   }
+  if (!is.null(resolution)) {
+    args <- paste(args, paste0("--resolution=", resolution))
+  }
+  if (!is.null(base)) {
+    args <- paste(args, paste0("--base=", base))
+  }
+  if (!is.null(max_triangle_edge_length)) {
+    args <- paste(args, paste0("--max_triangle_edge_length=", max_triangle_edge_length))
+  }
   tool_name <- as.character(match.call()[[1]])
   wbt_run_tool(tool_name, args, verbose_mode)
 }

PY2R/scripts/hydro_analysis.R

@@ -98,6 +98,44 @@ wbt_breach_depressions <- function(dem, output, max_depth=NULL, max_length=NULL,
 }
 
 
+#' Breach depressions least cost
+#'
+#' Breaches the depressions in a DEM using a least-cost pathway method.
+#'
+#' @param dem Input raster DEM file.
+#' @param output Output raster file.
+#' @param radius .
+#' @param max_cost Optional maximum breach cost (default is Inf).
+#' @param min_dist Optional flag indicating whether to minimize breach distances.
+#' @param flat_increment Optional elevation increment applied to flat areas.
+#' @param fill Optional flag indicating whether to fill any remaining unbreached depressions.
+#' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
+#'
+#' @return Returns the tool text outputs.
+#' @export
+wbt_breach_depressions_least_cost <- function(dem, output, radius, max_cost=NULL, min_dist=TRUE, flat_increment=NULL, fill=TRUE, verbose_mode=FALSE) {
+  wbt_init()
+  args <- ""
+  args <- paste(args, paste0("--dem=", dem))
+  args <- paste(args, paste0("--output=", output))
+  args <- paste(args, paste0("--radius=", radius))
+  if (!is.null(max_cost)) {
+    args <- paste(args, paste0("--max_cost=", max_cost))
+  }
+  if (min_dist) {
+    args <- paste(args, "--min_dist")
+  }
+  if (!is.null(flat_increment)) {
+    args <- paste(args, paste0("--flat_increment=", flat_increment))
+  }
+  if (fill) {
+    args <- paste(args, "--fill")
+  }
+  tool_name <- as.character(match.call()[[1]])
+  wbt_run_tool(tool_name, args, verbose_mode)
+}
+
+
 #' Breach single cell pits
 #'
 #' Removes single-cell pits from an input DEM by breaching.
@@ -118,6 +156,34 @@ wbt_breach_single_cell_pits <- function(dem, output, verbose_mode=FALSE) {
 }
 
 
+#' Burn streams at roads
+#'
+#' Burns-in streams at the sites of road embankments.
+#'
+#' @param dem Input raster digital elevation model (DEM) file.
+#' @param streams Input vector streams file.
+#' @param roads Input vector roads file.
+#' @param output Output raster file.
+#' @param width Maximum road embankment width, in map units.
+#' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
+#'
+#' @return Returns the tool text outputs.
+#' @export
+wbt_burn_streams_at_roads <- function(dem, streams, roads, output, width=NULL, verbose_mode=FALSE) {
+  wbt_init()
+  args <- ""
+  args <- paste(args, paste0("--dem=", dem))
+  args <- paste(args, paste0("--streams=", streams))
+  args <- paste(args, paste0("--roads=", roads))
+  args <- paste(args, paste0("--output=", output))
+  if (!is.null(width)) {
+    args <- paste(args, paste0("--width=", width))
+  }
+  tool_name <- as.character(match.call()[[1]])
+  wbt_run_tool(tool_name, args, verbose_mode)
+}
+
+
 #' D8 flow accumulation
 #'
 #' Calculates a D8 flow accumulation raster from an input DEM.
@@ -494,11 +560,43 @@ wbt_fill_burn <- function(dem, streams, output, verbose_mode=FALSE) {
 #' @param output Output raster file.
 #' @param fix_flats Optional flag indicating whether flat areas should have a small gradient applied.
 #' @param flat_increment Optional elevation increment applied to flat areas.
+#' @param max_depth Optional maximum depression depth to fill.
+#' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
+#'
+#' @return Returns the tool text outputs.
+#' @export
+wbt_fill_depressions <- function(dem, output, fix_flats=TRUE, flat_increment=NULL, max_depth=NULL, verbose_mode=FALSE) {
+  wbt_init()
+  args <- ""
+  args <- paste(args, paste0("--dem=", dem))
+  args <- paste(args, paste0("--output=", output))
+  if (fix_flats) {
+    args <- paste(args, "--fix_flats")
+  }
+  if (!is.null(flat_increment)) {
+    args <- paste(args, paste0("--flat_increment=", flat_increment))
+  }
+  if (!is.null(max_depth)) {
+    args <- paste(args, paste0("--max_depth=", max_depth))
+  }
+  tool_name <- as.character(match.call()[[1]])
+  wbt_run_tool(tool_name, args, verbose_mode)
+}
+
+
+#' Fill depressions wang and lui
+#'
+#' Fills all of the depressions in a DEM. Depression breaching should be preferred in most cases.
+#'
+#' @param dem Input raster DEM file.
+#' @param output Output raster file.
+#' @param fix_flats Optional flag indicating whether flat areas should have a small gradient applied.
+#' @param flat_increment Optional elevation increment applied to flat areas.
 #' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
 #'
 #' @return Returns the tool text outputs.
 #' @export
-wbt_fill_depressions <- function(dem, output, fix_flats=TRUE, flat_increment=NULL, verbose_mode=FALSE) {
+wbt_fill_depressions_wang_and_lui <- function(dem, output, fix_flats=TRUE, flat_increment=NULL, verbose_mode=FALSE) {
   wbt_init()
   args <- ""
   args <- paste(args, paste0("--dem=", dem))
@@ -900,17 +998,17 @@ wbt_rho8_pointer <- function(dem, output, esri_pntr=FALSE, verbose_mode=FALSE) {
 #'
 #' Identifies the depressions in a DEM, giving each feature a unique identifier.
 #'
-#' @param dem Input raster DEM file.
+#' @param input Input raster DEM file.
 #' @param output Output raster file.
 #' @param zero_background Flag indicating whether a background value of zero should be used.
 #' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
 #'
 #' @return Returns the tool text outputs.
 #' @export
-wbt_sink <- function(dem, output, zero_background=FALSE, verbose_mode=FALSE) {
+wbt_sink <- function(input, output, zero_background=FALSE, verbose_mode=FALSE) {
   wbt_init()
   args <- ""
-  args <- paste(args, paste0("--dem=", dem))
+  args <- paste(args, paste0("--input=", input))
   args <- paste(args, paste0("--output=", output))
   if (zero_background) {
     args <- paste(args, "--zero_background")
@@ -1080,6 +1178,26 @@ wbt_unnest_basins <- function(d8_pntr, pour_pts, output, esri_pntr=FALSE, verbos
 }
 
 
+#' Upslope depression storage
+#'
+#' Estimates the average upslope depression storage depth.
+#'
+#' @param dem Input raster DEM file.
+#' @param output Output raster file.
+#' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
+#'
+#' @return Returns the tool text outputs.
+#' @export
+wbt_upslope_depression_storage <- function(dem, output, verbose_mode=FALSE) {
+  wbt_init()
+  args <- ""
+  args <- paste(args, paste0("--dem=", dem))
+  args <- paste(args, paste0("--output=", output))
+  tool_name <- as.character(match.call()[[1]])
+  wbt_run_tool(tool_name, args, verbose_mode)
+}
+
+
 #' Watershed
 #'
 #' Identifies the watershed, or drainage basin, draining to a set of target cells.