Merge pull request #88 from giswqs/v220

whitebox v2.2.0

Author: brownag

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: whitebox
 Type: Package
 Title: 'WhiteboxTools' R Frontend
-Version: 2.1.5.9000
+Version: 2.2.0
 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")))

NAMESPACE

@@ -39,6 +39,7 @@ export(wbt_boundary_shape_complexity)
 export(wbt_breach_depressions)
 export(wbt_breach_depressions_least_cost)
 export(wbt_breach_single_cell_pits)
+export(wbt_breakline_mapping)
 export(wbt_buffer_raster)
 export(wbt_burn_streams_at_roads)
 export(wbt_canny_edge_detection)
@@ -48,16 +49,20 @@ export(wbt_centroid_vector)
 export(wbt_change_vector_analysis)
 export(wbt_circular_variance_of_aspect)
 export(wbt_classify_buildings_in_lidar)
+export(wbt_classify_lidar)
 export(wbt_classify_overlap_points)
 export(wbt_clean_vector)
 export(wbt_clip)
 export(wbt_clip_lidar_to_polygon)
 export(wbt_clip_raster_to_polygon)
 export(wbt_closing)
 export(wbt_clump)
+export(wbt_colourize_based_on_class)
+export(wbt_colourize_based_on_point_returns)
 export(wbt_compactness_ratio)
 export(wbt_compress_rasters)
 export(wbt_conditional_evaluation)
+export(wbt_conditioned_latin_hypercube)
 export(wbt_conservative_smoothing_filter)
 export(wbt_construct_vector_tin)
 export(wbt_contours_from_points)
@@ -91,6 +96,7 @@ export(wbt_dbscan)
 export(wbt_decrement)
 export(wbt_default_path)
 export(wbt_depth_in_sink)
+export(wbt_depth_to_water)
 export(wbt_dev_from_mean_elev)
 export(wbt_diff_from_mean_elev)
 export(wbt_diff_of_gaussian_filter)
@@ -148,6 +154,7 @@ export(wbt_fill_depressions_planchon_and_darboux)
 export(wbt_fill_depressions_wang_and_liu)
 export(wbt_fill_missing_data)
 export(wbt_fill_single_cell_pits)
+export(wbt_filter_lidar)
 export(wbt_filter_lidar_classes)
 export(wbt_filter_lidar_scan_angles)
 export(wbt_filter_raster_features_by_area)
@@ -177,8 +184,10 @@ export(wbt_generating_function)
 export(wbt_geomorphons)
 export(wbt_greater_than)
 export(wbt_hack_stream_order)
+export(wbt_heat_map)
 export(wbt_height_above_ground)
 export(wbt_help)
+export(wbt_high_pass_bilateral_filter)
 export(wbt_high_pass_filter)
 export(wbt_high_pass_median_filter)
 export(wbt_highest_position)
@@ -246,6 +255,7 @@ export(wbt_lidar_classify_subset)
 export(wbt_lidar_colourize)
 export(wbt_lidar_contour)
 export(wbt_lidar_digital_surface_model)
+export(wbt_lidar_eigenvalue_features)
 export(wbt_lidar_elevation_slice)
 export(wbt_lidar_ground_point_filter)
 export(wbt_lidar_hex_binning)
@@ -308,6 +318,7 @@ export(wbt_max_overlay)
 export(wbt_max_procs)
 export(wbt_max_upslope_elev_change)
 export(wbt_max_upslope_flowpath_length)
+export(wbt_max_upslope_value)
 export(wbt_maximal_curvature)
 export(wbt_maximum_filter)
 export(wbt_md_inf_flow_accumulation)
@@ -331,13 +342,15 @@ export(wbt_minimum_bounding_envelope)
 export(wbt_minimum_convex_hull)
 export(wbt_minimum_filter)
 export(wbt_modified_k_means_clustering)
+export(wbt_modify_lidar)
 export(wbt_modify_no_data_value)
 export(wbt_modulo)
 export(wbt_mosaic)
 export(wbt_mosaic_with_feathering)
 export(wbt_multi_part_to_single_part)
 export(wbt_multidirectional_hillshade)
 export(wbt_multiply)
+export(wbt_multiply_overlay)
 export(wbt_multiscale_elevation_percentile)
 export(wbt_multiscale_roughness)
 export(wbt_multiscale_roughness_signature)
@@ -375,6 +388,7 @@ export(wbt_percentile_filter)
 export(wbt_perimeter_area_ratio)
 export(wbt_phi_coefficient)
 export(wbt_pick_from_list)
+export(wbt_piecewise_contrast_stretch)
 export(wbt_plan_curvature)
 export(wbt_polygon_area)
 export(wbt_polygon_long_axis)
@@ -415,6 +429,7 @@ export(wbt_reclass)
 export(wbt_reclass_equal_interval)
 export(wbt_reclass_from_file)
 export(wbt_reconcile_multiple_headers)
+export(wbt_recover_flightline_info)
 export(wbt_recreate_pass_lines)
 export(wbt_reinitialize_attribute_table)
 export(wbt_related_circumscribing_circle)
@@ -461,8 +476,10 @@ export(wbt_smooth_vectors)
 export(wbt_smooth_vegetation_residual)
 export(wbt_snap_pour_points)
 export(wbt_sobel_filter)
+export(wbt_sort_lidar)
 export(wbt_spherical_std_dev_of_normals)
 export(wbt_split_colour_composite)
+export(wbt_split_lidar)
 export(wbt_split_vector_lines)
 export(wbt_split_with_lines)
 export(wbt_square)
@@ -503,6 +520,7 @@ export(wbt_topological_stream_order)
 export(wbt_total_curvature)
 export(wbt_total_filter)
 export(wbt_trace_downslope_flowpaths)
+export(wbt_travelling_salesman_problem)
 export(wbt_trend_surface)
 export(wbt_trend_surface_vector_points)
 export(wbt_tributary_identifier)

PY2R/automation.py

@@ -32,6 +32,7 @@ def function_header(line):
         line = line.replace(
             "callback=None", "wd=NULL, verbose_mode=FALSE, compress_rasters=False"
         )
+        line = line.replace('function=""', 'FUN=""')
         line = line.replace("False", "FALSE")
         line = line.replace("True", "TRUE")
         line = line.replace("None", "NULL")
@@ -110,7 +111,7 @@ def function_block(line, ff):
                   + "\n"
               )
               ff.write("  }" + "\n")
-            elif "inputs" in para or "variant" in para:
+            elif "output" in para or "inputs" in para or "variant" in para or "streams" in para or "lakes" in para:
               ff.write("  if (!is.null(" + para + ")) {" + "\n")
               ff.write(
                   '    args <- paste(args, paste0("--'
@@ -248,9 +249,15 @@ def function_example(fun_name):
 toolboxes = {
     "# Data Tools #": "data_tools.R",
     "# GIS Analysis #": "gis_analysis.R",
+    "# GIS Analysis/Distance Tools #": "gis_analysis_distance.R",
+    "# GIS Analysis/Overlay Tools #": "gis_analysis_overlay.R",
+    "# GIS Analysis/Patch Shape Tools #": "gis_analysis_patch_shape.R",
     "# Geomorphometric Analysis #": "terrain_analysis.R",
     "# Hydrological Analysis #": "hydro_analysis.R",
     "# Image Processing Tools #": "image_analysis.R",
+    "# Image Processing Tools/Classification #": "image_analysis_classification.R",
+    "# Image Processing Tools/Filters #": "image_analysis_filters.R",
+    "# Image Processing Tools/Image Enhancement #": "image_analysis_enhancement.R",
     "# LiDAR Tools #": "lidar_analysis.R",
     "# Machine Learning #": "machine_learning.R",
     "# Math and Stats Tools #": "math_stat_analysis.R",
@@ -290,7 +297,7 @@ def function_example(fun_name):
     lines = f.readlines()
 
     for index, line in enumerate(lines):
-        if index > 566:
+        if index > 700:
             line = line.strip()
 
             # Create an R script for each toolbox
@@ -325,6 +332,12 @@ def function_example(fun_name):
                     elif ("--" in doc_line) and (
                         doc_line.startswith("callback") == False
                     ):
+                        # fix expected cross-reference (use code block)
+                        doc_line = doc_line.replace("[0,1]", "`[0,1]`")
+                        # fix reserved keywords used as argument names
+                        if doc_line.startswith("function"):
+                            doc_line = doc_line.replace("function ", "")
+                            doc_line = "FUN " + doc_line
                         if doc_line.startswith("i --"):
                             doc_line = doc_line.replace("i --", "input --")
                         doc_line = doc_line.replace("-- ", "")

PY2R/scripts/data_tools.R

@@ -235,14 +235,16 @@ wbt_fix_dangling_arcs <- function(input, output, dist="", wd=NULL, verbose_mode=
 #'
 #' @return Returns the tool text outputs.
 #' @export
-wbt_join_tables <- function(input1, pkey, input2, fkey, import_field, wd=NULL, verbose_mode=FALSE, compress_rasters=FALSE, command_only=FALSE) {
+wbt_join_tables <- function(input1, pkey, input2, fkey, import_field=NULL, wd=NULL, verbose_mode=FALSE, compress_rasters=FALSE, command_only=FALSE) {
   wbt_init()
   args <- ""
   args <- paste(args, paste0("--input1=", wbt_file_path(input1)))
   args <- paste(args, paste0("--pkey=", wbt_file_path(pkey)))
   args <- paste(args, paste0("--input2=", wbt_file_path(input2)))
   args <- paste(args, paste0("--fkey=", wbt_file_path(fkey)))
-  args <- paste(args, paste0("--import_field=", wbt_file_path(import_field)))
+  if (!is.null(import_field)) {
+    args <- paste(args, paste0("--import_field=", import_field))
+  }
   if (!missing(wd)) {
     args <- paste(args, paste0("--wd=", wbt_file_path(wd)))
   }
@@ -771,7 +773,7 @@ wbt_vector_lines_to_raster <- function(input, output, field="FID", nodata=TRUE,
 #' @param input Input vector Points file.
 #' @param field Input field name in attribute table.
 #' @param output Output raster file.
-#' @param assign Assignment operation, where multiple points are in the same grid cell; options include 'first', 'last' (default), 'min', 'max', 'sum'.
+#' @param assign Assignment operation, where multiple points are in the same grid cell; options include 'first', 'last' (default), 'min', 'max', 'sum', 'number'.
 #' @param nodata Background value to set to NoData. Without this flag, it will be set to 0.0.
 #' @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.