Merge pull request #36 from giswqs/develop

Update WBT backend to v1.5.0

Author: giswqs

.gitignore

@@ -12,3 +12,4 @@ vignettes/*.tif
 vignettes/*.log
 *.tif
 .vscode/
+WhiteboxTools_linux_amd64.zip

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: whitebox
 Type: Package
 Title: 'WhiteboxTools' R Frontend
-Version: 1.4.0
+Version: 1.5.0
 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>
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 URL: https://github.com/giswqs/whiteboxR
 BugReports: https://github.com/giswqs/whiteboxR/issues
 Suggests: 

NAMESPACE

@@ -15,6 +15,7 @@ export(wbt_arsinh)
 export(wbt_artanh)
 export(wbt_ascii_to_las)
 export(wbt_aspect)
+export(wbt_assess_route)
 export(wbt_atan2)
 export(wbt_attribute_correlation)
 export(wbt_attribute_correlation_neighbourhood_analysis)
@@ -35,6 +36,7 @@ export(wbt_breach_depressions_least_cost)
 export(wbt_breach_single_cell_pits)
 export(wbt_buffer_raster)
 export(wbt_burn_streams_at_roads)
+export(wbt_canny_edge_detection)
 export(wbt_ceil)
 export(wbt_centroid)
 export(wbt_centroid_vector)
@@ -103,13 +105,15 @@ export(wbt_elevation_above_stream)
 export(wbt_elevation_above_stream_euclidean)
 export(wbt_eliminate_coincident_points)
 export(wbt_elongation_ratio)
+export(wbt_embankment_mapping)
 export(wbt_emboss_filter)
 export(wbt_equal_to)
 export(wbt_erase)
 export(wbt_erase_polygon_from_lidar)
 export(wbt_erase_polygon_from_raster)
 export(wbt_euclidean_allocation)
 export(wbt_euclidean_distance)
+export(wbt_evaluate_training_sites)
 export(wbt_exe_path)
 export(wbt_exp)
 export(wbt_exp2)
@@ -174,6 +178,8 @@ export(wbt_image_autocorrelation)
 export(wbt_image_correlation)
 export(wbt_image_correlation_neighbourhood_analysis)
 export(wbt_image_regression)
+export(wbt_image_segmentation)
+export(wbt_image_slider)
 export(wbt_image_stack_profile)
 export(wbt_impoundment_size_index)
 export(wbt_in_place_add)
@@ -186,6 +192,7 @@ export(wbt_insert_dams)
 export(wbt_integer_division)
 export(wbt_integral_image)
 export(wbt_intersect)
+export(wbt_inverse_principal_component_analysis)
 export(wbt_is_no_data)
 export(wbt_isobasins)
 export(wbt_jenson_snap_pour_points)
@@ -229,6 +236,8 @@ export(wbt_lidar_remove_outliers)
 export(wbt_lidar_rooftop_analysis)
 export(wbt_lidar_segmentation)
 export(wbt_lidar_segmentation_based_filter)
+export(wbt_lidar_sibson_interpolation)
+export(wbt_lidar_sort_by_time)
 export(wbt_lidar_thin)
 export(wbt_lidar_thin_high_density)
 export(wbt_lidar_tile)
@@ -248,6 +257,7 @@ export(wbt_log2)
 export(wbt_long_profile)
 export(wbt_long_profile_from_points)
 export(wbt_longest_flowpath)
+export(wbt_low_points_on_headwater_divides)
 export(wbt_lowest_position)
 export(wbt_majority_filter)
 export(wbt_map_off_terrain_objects)
@@ -272,6 +282,7 @@ export(wbt_merge_table_with_csv)
 export(wbt_merge_vectors)
 export(wbt_min)
 export(wbt_min_absolute_overlay)
+export(wbt_min_dist_classification)
 export(wbt_min_downslope_elev_change)
 export(wbt_min_max_contrast_stretch)
 export(wbt_min_overlay)
@@ -308,9 +319,11 @@ export(wbt_num_inflowing_neighbours)
 export(wbt_num_upslope_neighbours)
 export(wbt_olympic_filter)
 export(wbt_opening)
+export(wbt_openness)
 export(wbt_or)
 export(wbt_paired_sample_t_test)
 export(wbt_panchromatic_sharpening)
+export(wbt_parallelepiped_classification)
 export(wbt_patch_orientation)
 export(wbt_pennock_landform_class)
 export(wbt_percent_elev_range)
@@ -320,6 +333,7 @@ export(wbt_percent_less_than)
 export(wbt_percentage_contrast_stretch)
 export(wbt_percentile_filter)
 export(wbt_perimeter_area_ratio)
+export(wbt_phi_coefficient)
 export(wbt_pick_from_list)
 export(wbt_plan_curvature)
 export(wbt_polygon_area)
@@ -355,6 +369,7 @@ export(wbt_reciprocal)
 export(wbt_reclass)
 export(wbt_reclass_equal_interval)
 export(wbt_reclass_from_file)
+export(wbt_recreate_pass_lines)
 export(wbt_reinitialize_attribute_table)
 export(wbt_related_circumscribing_circle)
 export(wbt_relative_aspect)
@@ -376,6 +391,7 @@ export(wbt_scharr_filter)
 export(wbt_sediment_transport_index)
 export(wbt_select_tiles_by_polygon)
 export(wbt_set_nodata_value)
+export(wbt_shadow_animation)
 export(wbt_shape_complexity_index)
 export(wbt_shape_complexity_index_raster)
 export(wbt_shreve_stream_magnitude)
@@ -387,10 +403,12 @@ export(wbt_sink)
 export(wbt_slope)
 export(wbt_slope_vs_elevation_plot)
 export(wbt_smooth_vectors)
+export(wbt_smooth_vegetation_residual)
 export(wbt_snap_pour_points)
 export(wbt_sobel_filter)
 export(wbt_spherical_std_dev_of_normals)
 export(wbt_split_colour_composite)
+export(wbt_split_vector_lines)
 export(wbt_split_with_lines)
 export(wbt_square)
 export(wbt_square_root)
@@ -423,6 +441,7 @@ export(wbt_tool_help)
 export(wbt_tool_parameters)
 export(wbt_toolbox)
 export(wbt_tophat_transform)
+export(wbt_topographic_position_animation)
 export(wbt_topological_stream_order)
 export(wbt_total_curvature)
 export(wbt_total_filter)
@@ -455,6 +474,8 @@ export(wbt_wetness_index)
 export(wbt_wilcoxon_signed_rank_test)
 export(wbt_write_function_memory_insertion)
 export(wbt_xor)
+export(wbt_yield_filter)
+export(wbt_yield_map)
 export(wbt_z_scores)
 export(wbt_zlidar_to_las)
 export(wbt_zonal_statistics)

PY2R/automation.py

@@ -4,7 +4,7 @@
 # Step 2 - Create a new develop branch: git checkout -b develop
 # Step 3 - Delete the old WhiteboxTools_linux_amd64.tar.xz in the root folder if needed
 # Step 4 - Run automation.py
-# Step 5 - Update version number in DESCRIPTION 
+# Step 5 - Update version number and RoxygenNote in DESCRIPTION 
 # Step 6 - Open whiteboxR.Rproj in RStudio and run build_check.R
 # Step 7 - Commit and push changes
 # Step 8 - Test installation from GitHub: devtools::install_github("giswqs/whiteboxR@develop")
@@ -16,7 +16,7 @@
 
 import os 
 import shutil
-import tarfile
+import zipfile
 import urllib.request
 
 # Extract function header
@@ -211,6 +211,7 @@ def function_example(fun_name):
     "# Image Processing Tools #": "image_analysis.R",
     "# LiDAR Tools #": "lidar_analysis.R",
     "# Math and Stats Tools #": "math_stat_analysis.R",
+    "# Precision Agriculture #": "precision_agriculture.R",
     "# Stream Network Analysis #": "stream_network_analysis.R"
 }
 
@@ -219,11 +220,11 @@ def function_example(fun_name):
 root_dir = os.path.dirname(dir_path)
 WBT_dir = os.path.join(root_dir, 'WBT')
 
-linux_tar = "WhiteboxTools_linux_amd64.tar.xz"
+linux_tar = "WhiteboxTools_linux_amd64.zip"
 tar_path = os.path.join(root_dir, linux_tar)
 if not os.path.exists(tar_path):
     print("Downloading WhiteboxTools binary ...")
-    url = "https://jblindsay.github.io/ghrg/WhiteboxTools/WhiteboxTools_linux_amd64.tar.xz"
+    url = "https://www.whiteboxgeo.com/WBT_Linux/WhiteboxTools_linux_amd64.zip"
     urllib.request.urlretrieve(url, tar_path)   # Download WhiteboxTools
 else:
     print("WhiteboxTools binary already exists.")
@@ -232,7 +233,7 @@ def function_example(fun_name):
     shutil.rmtree(WBT_dir)
 
 print("Decompressing {} ...".format(linux_tar))
-with tarfile.open(tar_path, "r") as tar_ref:
+with zipfile.ZipFile(tar_path, "r") as tar_ref:
     tar_ref.extractall(root_dir)
 
 shutil.copyfile(os.path.join(WBT_dir, "whitebox_tools.py"), wbt_py)

PY2R/scripts/gis_analysis.R

@@ -1352,6 +1352,38 @@ wbt_smooth_vectors <- function(input, output, filter=3, wd=NULL, verbose_mode=FA
 }
 
 
+#' Split vector lines
+#'
+#' This tool can be used to approximate the harvester pass lines from yield points.
+#'
+#' @param input Name of the input lines shapefile.
+#' @param output Name of the output lines shapefile.
+#' @param length Maximum segment length (m).
+#' @param wd Changes the working directory.
+#' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
+#' @param compress_rasters Sets the flag used by WhiteboxTools to determine whether to use compression for output rasters.
+#'
+#' @return Returns the tool text outputs.
+#' @export
+wbt_split_vector_lines <- function(input, output, length=NULL, wd=NULL, verbose_mode=FALSE, compress_rasters=FALSE) {
+  wbt_init()
+  args <- ""
+  args <- paste(args, paste0("--input=", input))
+  args <- paste(args, paste0("--output=", output))
+  if (!is.null(length)) {
+    args <- paste(args, paste0("--length=", length))
+  }
+  if (!is.null(wd)) {
+    args <- paste(args, paste0("--wd=", wd))
+  }
+  if (compress_rasters) {
+    args <- paste(args, "--compress_rasters")
+  }
+  tool_name <- as.character(match.call()[[1]])
+  wbt_run_tool(tool_name, args, verbose_mode)
+}
+
+
 #' Tin gridding
 #'
 #' Creates a raster grid based on a triangular irregular network (TIN) fitted to vector points.

PY2R/scripts/hydro_analysis.R

@@ -503,18 +503,22 @@ wbt_depth_in_sink <- function(dem, output, zero_background=FALSE, wd=NULL, verbo
 #' @param dem Input raster DEM file.
 #' @param streams Input raster streams file.
 #' @param output Output raster file.
+#' @param dinf Use the D-infinity flow algoirthm instead of D8?.
 #' @param wd Changes the working directory.
 #' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
 #' @param compress_rasters Sets the flag used by WhiteboxTools to determine whether to use compression for output rasters.
 #'
 #' @return Returns the tool text outputs.
 #' @export
-wbt_downslope_distance_to_stream <- function(dem, streams, output, wd=NULL, verbose_mode=FALSE, compress_rasters=FALSE) {
+wbt_downslope_distance_to_stream <- function(dem, streams, output, dinf=FALSE, wd=NULL, verbose_mode=FALSE, compress_rasters=FALSE) {
   wbt_init()
   args <- ""
   args <- paste(args, paste0("--dem=", dem))
   args <- paste(args, paste0("--streams=", streams))
   args <- paste(args, paste0("--output=", output))
+  if (dinf) {
+    args <- paste(args, "--dinf")
+  }
   if (!is.null(wd)) {
     args <- paste(args, paste0("--wd=", wd))
   }
@@ -1264,6 +1268,36 @@ wbt_longest_flowpath <- function(dem, basins, output, wd=NULL, verbose_mode=FALS
 }
 
 
+#' Low points on headwater divides
+#'
+#' This tool locates saddle points along ridges within a digital elevation model (DEM).
+#'
+#' @param dem Name of the input DEM raster file.
+#' @param streams Name of the input stream channel raster file.
+#' @param output Name of the output vector file.
+#' @param wd Changes the working directory.
+#' @param verbose_mode Sets verbose mode. If verbose mode is False, tools will not print output messages.
+#' @param compress_rasters Sets the flag used by WhiteboxTools to determine whether to use compression for output rasters.
+#'
+#' @return Returns the tool text outputs.
+#' @export
+wbt_low_points_on_headwater_divides <- function(dem, streams, output, wd=NULL, verbose_mode=FALSE, compress_rasters=FALSE) {
+  wbt_init()
+  args <- ""
+  args <- paste(args, paste0("--dem=", dem))
+  args <- paste(args, paste0("--streams=", streams))
+  args <- paste(args, paste0("--output=", output))
+  if (!is.null(wd)) {
+    args <- paste(args, paste0("--wd=", wd))
+  }
+  if (compress_rasters) {
+    args <- paste(args, "--compress_rasters")
+  }
+  tool_name <- as.character(match.call()[[1]])
+  wbt_run_tool(tool_name, args, verbose_mode)
+}
+
+
 #' Max upslope flowpath length
 #'
 #' Measures the maximum length of all upslope flowpaths draining each grid cell.