install.packages("whitebox")

if (!require("remotes")) install.packages('remotes')
remotes::install_github("opengeos/whiteboxR", build = FALSE)

wbt_init()

wbt_init(exe_path = 'C:/home/user/path/to/whitebox_tools.exe')

wbt_init(exe_path = 'C:/home/user/path/to/whitebox_tools.exe', verbose = FALSE)

??whitebox

??wbt_

whitebox::install_whitebox()

library(whitebox)

# set up as needed
wbt_init()

# Set input raster DEM file
dem <- sample_dem_data()

## 1. FeaturePreservingSmoothing
wbt_feature_preserving_smoothing(
  dem = dem,
  output = "./smoothed.tif",
  filter = 9
)

## 2. BreachDepressions
wbt_breach_depressions(dem = "./smoothed.tif", output = "./breached.tif")

## 3. DInfFlowAccumulation
wbt_d_inf_flow_accumulation(input = dem, output = "./flow_accum.tif")

if (requireNamespace('terra')) {
  terra::plot(terra::rast("./flow_accum.tif"))
}
#> Loading required namespace: terra

library(whitebox)

# cat() output in non-interactive mode
wbt_verbose(TRUE)

# Prints the whitebox-tools help...a listing of available commands
wbt_help()
#> WhiteboxTools Help
#> 
#> The following commands are recognized:
#> --cd, --wd          Changes the working directory; used in conjunction with --run flag.
#> --compress_rasters  Sets the compress_raster option in the settings.json file; determines if newly created rasters are compressed. e.g. --compress_rasters=true
#> -h, --help          Prints help information.
#> -l, --license       Prints the whitebox-tools license. Tool names may also be used, --license="Slope"
#> --listtools         Lists all available tools. Keywords may also be used, --listtools slope.
#> --max_procs         Sets the maximum number of processors used. -1 = all available processors. e.g. --max_procs=2
#> -r, --run           Runs a tool; used in conjunction with --wd flag; -r="LidarInfo".
#> --toolbox           Prints the toolbox associated with a tool; --toolbox=Slope.
#> --toolhelp          Prints the help associated with a tool; --toolhelp="LidarInfo".
#> --toolparameters    Prints the parameters (in json form) for a specific tool; --toolparameters="LidarInfo".
#> -v                  Verbose mode. Without this flag, tool outputs will not be printed.
#> --viewcode          Opens the source code of a tool in a web browser; --viewcode="LidarInfo".
#> --version           Prints the version information.
#> 
#> Example Usage:
#> >> ./whitebox_tools -r=lidar_info --cd="/path/to/data/" -i=input.las --vlr --geokeys

# Prints the whitebox-tools license
wbt_license()
#> WhiteboxTools License
#> Copyright 2017-2023 John Lindsay
#> 
#> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
#> associated documentation files (the "Software"), to deal in the Software without restriction,
#> including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense,
#> and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so,
#> subject to the following conditions:
#> 
#> The above copyright notice and this permission notice shall be included in all copies or substantial
#> portions of the Software.
#> 
#> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT
#> NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
#> NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES
#> OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
#> CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

# Prints the whitebox-tools version
wbt_version()
#> WhiteboxTools v2.3.0 (c) Dr. John Lindsay 2017-2023
#> 
#> WhiteboxTools is an advanced geospatial data analysis platform developed at
#> the University of Guelph's Geomorphometry and Hydrogeomatics Research 
#> Group (GHRG). See www.whiteboxgeo.com for more details.

# Prints the toolbox for a specific tool.
wbt_toolbox("AsciiToLas")
#> LiDAR Tools

# Lists tools with 'lidar' in tool name or description.
wbt_list_tools("lidar")
#> All 63 Tools containing keywords:
#> AsciiToLas: Converts one or more ASCII files containing LiDAR points into LAS files.
#> ClassifyBuildingsInLidar: Reclassifies a LiDAR points that lie within vector building footprints.
#> ClassifyOverlapPoints: Classifies or filters LAS points in regions of overlapping flight lines.
#> ClipLidarToPolygon: Clips a LiDAR point cloud to a vector polygon or polygons.
#> ErasePolygonFromLidar: Erases (cuts out) a vector polygon or polygons from a LiDAR point cloud.
#> FilterLidarClasses: Removes points in a LAS file with certain specified class values.
#> FilterLidarScanAngles: Removes points in a LAS file with scan angles greater than a threshold.
#> FindFlightlineEdgePoints: Identifies points along a flightline's edge in a LAS file.
#> FlightlineOverlap: Reads a LiDAR (LAS) point file and outputs a raster containing the number of overlapping flight-lines in each grid cell.
#> HeightAboveGround: Normalizes a LiDAR point cloud, providing the height above the nearest ground-classified point.
#> LasToAscii: Converts one or more LAS files into ASCII text files.
#> LasToMultipointShapefile: Converts one or more LAS files into MultipointZ vector Shapefiles. When the input parameter is not specified, the tool grids all LAS files contained within the working directory.
#> LasToShapefile: Converts one or more LAS files into a vector Shapefile of POINT ShapeType.
#> LasToZlidar: Converts one or more LAS files into the zlidar compressed LiDAR data format.
#> LidarBlockMaximum: Creates a block-maximum raster from an input LAS file. When the input/output parameters are not specified, the tool grids all LAS files contained within the working directory.
#> LidarBlockMinimum: Creates a block-minimum raster from an input LAS file. When the input/output parameters are not specified, the tool grids all LAS files contained within the working directory.
#> LidarClassifySubset: Classifies the values in one LiDAR point cloud that correspond with points in a subset cloud.
#> LidarColourize: Adds the red-green-blue colour fields of a LiDAR (LAS) file based on an input image.
#> LidarDigitalSurfaceModel: Creates a top-surface digital surface model (DSM) from a LiDAR point cloud.
#> LidarElevationSlice: Outputs all of the points within a LiDAR (LAS) point file that lie between a specified elevation range.
#> LidarGroundPointFilter: Identifies ground points within LiDAR dataset using a slope-based method.
#> LidarHexBinning: Hex-bins a set of LiDAR points.
#> LidarHillshade: Calculates a hillshade value for points within a LAS file and stores these data in the RGB field.
#> LidarHistogram: Creates a histogram of LiDAR data.
#> LidarIdwInterpolation: Interpolates LAS files using an inverse-distance weighted (IDW) scheme. When the input/output parameters are not specified, the tool interpolates all LAS files contained within the working directory.
#> LidarInfo: Prints information about a LiDAR (LAS) dataset, including header, point return frequency, and classification data and information about the variable length records (VLRs) and geokeys.
#> LidarJoin: Joins multiple LiDAR (LAS) files into a single LAS file.
#> LidarKappaIndex: Performs a kappa index of agreement (KIA) analysis on the classifications of two LAS files.
#> LidarNearestNeighbourGridding: Grids LiDAR files using nearest-neighbour scheme. When the input/output parameters are not specified, the tool grids all LAS files contained within the working directory.
#> LidarPointDensity: Calculates the spatial pattern of point density for a LiDAR data set. When the input/output parameters are not specified, the tool grids all LAS files contained within the working directory.
#> LidarPointStats: Creates several rasters summarizing the distribution of LAS point data. When the input/output parameters are not specified, the tool works on all LAS files contained within the working directory.
#> LidarRansacPlanes: Performs a RANSAC analysis to identify points within a LiDAR point cloud that belong to linear planes.
#> LidarRbfInterpolation: Interpolates LAS files using a radial basis function (RBF) scheme. When the input/output parameters are not specified, the tool interpolates all LAS files contained within the working directory.
#> LidarRemoveDuplicates: Removes duplicate points from a LiDAR data set.
#> LidarRemoveOutliers: Removes outliers (high and low points) in a LiDAR point cloud.
#> LidarRooftopAnalysis: Identifies roof segments in a LiDAR point cloud.
#> LidarSegmentation: Segments a LiDAR point cloud based on differences in the orientation of fitted planar surfaces and point proximity.
#> LidarSegmentationBasedFilter: Identifies ground points within LiDAR point clouds using a segmentation based approach.
#> LidarTINGridding: Creates a raster grid based on a Delaunay triangular irregular network (TIN) fitted to LiDAR points.
#> LidarThin: Thins a LiDAR point cloud, reducing point density.
#> LidarThinHighDensity: Thins points from high density areas within a LiDAR point cloud.
#> LidarTile: Tiles a LiDAR LAS file into multiple LAS files.
#> LidarTileFootprint: Creates a vector polygon of the convex hull of a LiDAR point cloud. When the input/output parameters are not specified, the tool works with all LAS files contained within the working directory.
#> LidarTophatTransform: Performs a white top-hat transform on a Lidar dataset; as an estimate of height above ground, this is useful for modelling the vegetation canopy.
#> NormalVectors: Calculates normal vectors for points within a LAS file and stores these data (XYZ vector components) in the RGB field.
#> SelectTilesByPolygon: Copies LiDAR tiles overlapping with a polygon into an output directory.
#> ZlidarToLas: Converts one or more zlidar files into the LAS data format.
#> NormalizeLidar: Normalizes a LiDAR point cloud.
#> LidarShift: Shifts the x,y,z coordinates of a LiDAR file.
#> SmoothVegetationResidual: This tool can smooth the residual roughness due to vegetation cover in LiDAR DEMs.
#> LidarPointReturnAnalysis: This tool performs a quality control check on the return values of points in a LiDAR file.
#> FilterLidar: Filters points within a LiDAR point cloud based on point properties.
#> ColourizeBasedOnClass: Sets the RGB values of a LiDAR point cloud based on the point classification values.
#> SortLidar: Sorts LiDAR points based on their properties.
#> ColourizeBasedOnPointReturns: Sets the RGB values of a LiDAR point cloud based on the point returns.
#> LidarSibsonInterpolation: This tool interpolates one or more LiDAR tiles using Sibson's natural neighbour method.
#> ClassifyLidar: Classify points within a LiDAR point cloud based on point properties.
#> ModifyLidar: Modify points within a LiDAR point cloud based on point properties.
#> IndividualTreeDetection: Identifies points in a LiDAR point cloud that are associated with the tops of individual trees.
#> LidarEigenvalueFeatures: Calculate eigenvalue-based metrics from a LiDAR point cloud.
#> SplitLidar: Splits LiDAR points up into a series of new files based on their properties.
#> LidarContour: This tool creates a vector contour coverage from an input LiDAR point file.
#> RecoverFlightlineInfo: Associates LiDAR points by their flightlines.

# Prints the help for a specific tool.
wbt_tool_help("lidar_info")
#> LidarInfo
#> Description:
#> Prints information about a LiDAR (LAS) dataset, including header, point return frequency, and classification data and information about the variable length records (VLRs) and geokeys.
#> Toolbox: LiDAR Tools
#> Parameters:
#> 
#> Flag               Description
#> -----------------  -----------
#> -i, --input        Input LiDAR file.
#> -o, --output       Output HTML file for summary report.
#> --density          Flag indicating whether or not to calculate the average point density and nominal point spacing.
#> --vlr              Flag indicating whether or not to print the variable length records (VLRs).
#> --geokeys          Flag indicating whether or not to print the geokeys.
#> 
#> 
#> Example usage:
#> >>./whitebox_tools -r=LidarInfo -v --wd="/path/to/data/" -i=file.las --vlr --geokeys"
#> ./whitebox_tools -r=LidarInfo --wd="/path/to/data/" -i=file.las

# Retrieves the tool parameter descriptions for a specific tool.
wbt_tool_parameters("slope")
#> {"parameters": [{"name":"Input DEM File","flags":["-i","--dem"],"description":"Input raster DEM file.","parameter_type":{"ExistingFile":"Raster"},"default_value":null,"optional":false},{"name":"Output File","flags":["-o","--output"],"description":"Output raster file.","parameter_type":{"NewFile":"Raster"},"default_value":null,"optional":false},{"name":"Z Conversion Factor","flags":["--zfactor"],"description":"Optional multiplier for when the vertical and horizontal units are not the same.","parameter_type":"Float","default_value":null,"optional":true},{"name":"Units","flags":["--units"],"description":"Units of output raster; options include 'degrees', 'radians', 'percent'","parameter_type":{"OptionList":["degrees","radians","percent"]},"default_value":"degrees","optional":true}]}

# View the source code for a specific tool on the source code repository.
wbt_view_code("breach_depressions")
#> https://github.com/jblindsay/whitebox-tools/blob/master/whitebox-tools-app/src/tools/hydro_analysis/breach_depressions.rs